BLASTN 2.2.26+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. Database: minirefseq_mrna 23 sequences; 67,750 total letters Query= random_s00 Length=128 ***** No hits found ***** Lambda K H 1.33 0.621 1.12 Gapped Lambda K H 1.28 0.460 0.850 Effective search space used: 7616765 Query= gi|356995852:1-490 Mus musculus POU domain, class 5, transcription factor 1 (Pou5f1), transcript variant 1, mRNA Length=490 Score E Sequences producing significant alignments: (Bits) Value gi|356995852|ref|NM_013633.3| Mus musculus POU domain, class 5,... 905 0.0 gi|377833530|ref|XR_141831.1| PREDICTED: Mus musculus predicted... 900 0.0 gi|260269517|ref|NM_001009178.2| Rattus norvegicus POU class 5 ... 734 0.0 gi|295390144|ref|NR_033594.1| Mus musculus predicted gene 5712 ... 446 2e-127 gi|354487499|ref|XM_003505863.1| PREDICTED: Cricetulus griseus ... 433 1e-123 > gi|356995852|ref|NM_013633.3| Mus musculus POU domain, class 5, transcription factor 1 (Pou5f1), transcript variant 1, mRNA Length=1353 Score = 905 bits (490), Expect = 0.0 Identities = 490/490 (100%), Gaps = 0/490 (0%) Strand=Plus/Plus Query 1 GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCA 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1 GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCA 60 Query 61 CCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGG 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 61 CCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGG 120 Query 121 GTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCC 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 121 GTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCC 180 Query 181 AAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCAT 240 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 181 AAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCAT 240 Query 241 GTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGG 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 241 GTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGG 300 Query 301 GCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAG 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 301 GCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAG 360 Query 361 TGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGA 420 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 361 TGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGA 420 Query 421 AGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGG 480 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 421 AGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGG 480 Query 481 AGCTAGAACA 490 |||||||||| Sbjct 481 AGCTAGAACA 490 > gi|377833530|ref|XR_141831.1| PREDICTED: Mus musculus predicted gene, 19553 (Gm19553), miscRNA Length=570 Score = 900 bits (487), Expect = 0.0 Identities = 489/490 (99%), Gaps = 0/490 (0%) Strand=Plus/Minus Query 1 GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCA 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 570 GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCA 511 Query 61 CCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGG 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 510 CCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGG 451 Query 121 GTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCC 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 450 GTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCC 391 Query 181 AAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCAT 240 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 390 AAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCAT 331 Query 241 GTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGG 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 330 GTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGG 271 Query 301 GCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAG 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 270 GCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAG 211 Query 361 TGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGA 420 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 210 TGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGA 151 Query 421 AGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGG 480 ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| Sbjct 150 AGTTGGAGAAGGTGGAACCAACTCCAGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGG 91 Query 481 AGCTAGAACA 490 |||||||||| Sbjct 90 AGCTAGAACA 81 > gi|260269517|ref|NM_001009178.2| Rattus norvegicus POU class 5 homeobox 1 (Pou5f1), mRNA Length=1388 Score = 734 bits (397), Expect = 0.0 Identities = 459/489 (94%), Gaps = 3/489 (1%) Strand=Plus/Plus Query 1 GAGGTG-AAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCC 59 |||||| |||| ||||||||||||| |||| |||||||||||||||||||||||| |||| Sbjct 12 GAGGTGCAAACAGTCCCTAGGTGAGTCGTCCTTCCACCAGGCCCCCGGCTCGGGGAGCCC 71 Query 60 ACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGG 119 ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| Sbjct 72 ACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCTGGTGGG 131 Query 120 GGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTC 179 |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| Sbjct 132 GGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGACCCTCGAACCTGGCTAAGCTTC 191 Query 180 CAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCA 239 || ||||||||| |||||||||||||||||||||| |||||||| ||||||||||||| Sbjct 192 CAGGGGCCTCCAAGTGGGCCTGGAATCGGACCAGGTTCAGAGGTGCTGGGGATCTCCCCG 251 Query 240 TGTCCGCCC-GCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACT 298 ||||| ||| |||||||||||||| ||||||||||||||||||||||||||||||||||| Sbjct 252 TGTCC-CCCAGCATACGAGTTCTGTGGAGGGATGGCATACTGTGGACCTCAGGTTGGACT 310 Query 299 GGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACG 358 ||||||||||||||||||||||||||||||| ||||||| |||||||||||||||||||| Sbjct 311 GGGCCTAGTCCCCCAAGTTGGCGTGGAGACTCTGCAGCCCGAGGGCCAGGCAGGAGCACG 370 Query 359 AGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGT 418 |||||| |||||||| |||||| ||||||||| ||||||| | | |||||||| ||||| Sbjct 371 AGTGGAGAGCAACTCGGAGGGAGCCTCCTCTGGGCCCTGTACTGCCCGCCCCAGCGCCGT 430 Query 419 GAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAA 478 ||||||||||||||||||||| | |||||||||||||||||| ||||||||||||||||| Sbjct 431 GAAGTTGGAGAAGGTGGAACCTAGTCCCGAGGAGTCCCAGGATATGAAAGCCCTGCAGAA 490 Query 479 GGAGCTAGA 487 ||||||||| Sbjct 491 GGAGCTAGA 499 > gi|295390144|ref|NR_033594.1| Mus musculus predicted gene 5712 (Gm5712), non-coding RNA Length=1040 Score = 446 bits (241), Expect = 2e-127 Identities = 367/422 (87%), Gaps = 32/422 (8%) Strand=Plus/Plus Query 69 ATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGG 128 |||||||||||||||||||||||||||||||||||||||| |||||||||||| |||||| Sbjct 1 ATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCC-ACCAGGTGGGGGCGATGGG 59 Query 129 TCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCT 188 ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| Sbjct 60 TCAGCAGGGCTGGAGCCGGGCTGGGTGGACCCTCGAACCTGGCTAAGCTTCCAAGGGCCT 119 Query 189 CCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCC 248 | |||||||||||||| |||||||||| |||||||||||| |||||||||||||| || Sbjct 120 CTGGGTGGGCCTGGAATAGGACCAGGCTTAGAGGTATTGGG-ATCTCCCCATGTCCACCG 178 Query 249 GCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTC 308 | ||| ||||||||||||||||||||||||||||||||||||| |||| | || Sbjct 179 GTATATGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGG-----CTGG-C---GT- 228 Query 309 CCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGC 368 | | ||||||||||||||||| |||||||| ||||| | ||||| ||| Sbjct 229 ------G--G------AGACTTTGCAGCCTGAGAGCCAGGCAAGAGCAGGTGTGGAGAGC 274 Query 369 AACTCAGAGGGAA-CCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGA 427 |||||||||| || ||| ||||| ||| |||||||||| ||||| ||||||||||||||| Sbjct 275 AACTCAGAGG-AAGCCTTCTCTGGGCCTTGTGCCGACCACCCCAGTGCCGTGAAGTTGGA 333 Query 428 GAAG-GTGGAACCAAC-TCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTA 485 || | | ||||||| | |||||||| ||||||||||||||||| |||||||||||||||| Sbjct 334 GATGAG-GGAACCA-CGTCCCGAGGGGTCCCAGGACATGAAAGTCCTGCAGAAGGAGCTA 391 Query 486 GA 487 || Sbjct 392 GA 393 > gi|354487499|ref|XM_003505863.1| PREDICTED: Cricetulus griseus POU domain, class 5, transcription factor 1-like (LOC100754998), mRNA Length=1077 Score = 433 bits (234), Expect = 1e-123 Identities = 377/442 (85%), Gaps = 25/442 (6%) Strand=Plus/Plus Query 69 ATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGG 128 |||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||||||| Sbjct 1 ATGGCTGGACACCTGGCTTCAGACTTTGCCTTCTCACCTCCACCTGGTGGGGGTGATGGG 60 Query 129 TCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCT 188 |||| |||||||||||| ||||||||||| ||||| ||||||||||||||||||||||| Sbjct 61 TCAGGAGGGCTGGAGCCTGGCTGGGTGGACCCTCGGACCTGGCTAAGCTTCCAAGGGCCA 120 Query 189 CCAGGTGGGCCTGGAAT-----C-------GGACCAGGCTCAGAGGTATTGGGGATCTCC 236 ||||||||||||||||| | |||||||||||||| || ||||||| ||| Sbjct 121 CCAGGTGGGCCTGGAATCGGGCCAGGGGTTGGACCAGGCTCAGAAGTGCTGGGGATTTCC 180 Query 237 CCATGTCCGCCC-GCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGG 295 || ||||| ||| ||||||||||||| |||||| ||||||||||||||||||||||||| Sbjct 181 CCTTGTCC-CCCACCATACGAGTTCTGTGGAGGGGTGGCATACTGTGGACCTCAGGTTGG 239 Query 296 ACTGGGCCTAGTCCC-CCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAG 354 |||||| ||||| || ||| |||||| ||||||||| ||||||||||||||| |||||| Sbjct 240 ACTGGGTCTAGTGCCGCCA-GTTGGCCTGGAGACTTCACAGCCTGAGGGCCAGTCAGGAG 298 Query 355 CACGAGTGGA-AAGCAACTCAGAGG-GAACCTCCTCTGAGCCCTGTGCCGACC-GCCCCA 411 || ||||||| || | |||| |||| | ||||| ||| ||||||| | | || | |||| Sbjct 299 CAGGAGTGGAGAA-CGACTCGGAGGAGT-CCTCCCCTGGGCCCTGTACTG-CCAGGCCCA 355 Query 412 ATG-CC--GTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAG 468 || || ||||||||||||||||||||||| | |||||||||||||||||| |||| | Sbjct 356 TTGTCCCCGTGAAGTTGGAGAAGGTGGAACCGAGTCCCGAGGAGTCCCAGGATGTGAAGG 415 Query 469 CCCTGCAGAAGGAGCTAGAACA 490 || |||||||||| || ||||| Sbjct 416 CCTTGCAGAAGGAACTGGAACA 437 Lambda K H 1.33 0.621 1.12 Gapped Lambda K H 1.28 0.460 0.850 Effective search space used: 31860807 Query= hg19_dna range=chr1:1207307-1207372 5'pad=0 3'pad=0 strand=+ repeatMasking=none Length=66 Score E Sequences producing significant alignments: (Bits) Value gi|94721341|ref|NM_001040441.1| Homo sapiens zinc finger and BT... 115 6e-29 gi|332237160|ref|XM_003267724.1| PREDICTED: Nomascus leucogenys... 115 6e-29 gi|332254616|ref|XM_003276378.1| PREDICTED: Nomascus leucogenys... 111 7e-28 gi|332865370|ref|XM_527768.3| PREDICTED: Pan troglodytes zinc f... 111 7e-28 gi|332865372|ref|XM_003318468.1| PREDICTED: Pan troglodytes zin... 111 7e-28 > gi|94721341|ref|NM_001040441.1| Homo sapiens zinc finger and BTB domain containing 8A (ZBTB8A), mRNA Length=7333 Score = 115 bits (62), Expect = 6e-29 Identities = 62/62 (100%), Gaps = 0/62 (0%) Strand=Plus/Plus Query 5 GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaaaaaa 64 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 3677 GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAA 3736 Query 65 aa 66 || Sbjct 3737 AA 3738 Score = 99.0 bits (53), Expect = 6e-24 Identities = 53/53 (100%), Gaps = 0/53 (0%) Strand=Plus/Plus Query 6 CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaa 58 ||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2824 CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA 2876 > gi|332237160|ref|XM_003267724.1| PREDICTED: Nomascus leucogenys ATG14 autophagy related 14 homolog (S. cerevisiae) (ATG14), mRNA Length=4771 Score = 115 bits (62), Expect = 6e-29 Identities = 62/62 (100%), Gaps = 0/62 (0%) Strand=Plus/Plus Query 5 GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaaaaaa 64 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2865 GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAA 2924 Query 65 aa 66 || Sbjct 2925 AA 2926 > gi|332254616|ref|XM_003276378.1| PREDICTED: Nomascus leucogenys S100P binding protein, transcript variant 2 (S100PBP), mRNA Length=4345 Score = 111 bits (60), Expect = 7e-28 Identities = 64/66 (97%), Gaps = 0/66 (0%) Strand=Plus/Minus Query 1 TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaa 60 ||| |||| ||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2857 TCATGCCACTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAA 2798 Query 61 aaaaaa 66 |||||| Sbjct 2797 AAAAAA 2792 > gi|332865370|ref|XM_527768.3| PREDICTED: Pan troglodytes zinc finger protein 273, transcript variant 2 (ZNF273), mRNA Length=4335 Score = 111 bits (60), Expect = 7e-28 Identities = 64/66 (97%), Gaps = 0/66 (0%) Strand=Plus/Minus Query 1 TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaa 60 ||| |||||||||||||||||||||||||||||| ||||||||||||||||||||||||| Sbjct 2705 TCACGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCGTCTCAAAAAAAAAAAA 2646 Query 61 aaaaaa 66 |||||| Sbjct 2645 AAAAAA 2640 > gi|332865372|ref|XM_003318468.1| PREDICTED: Pan troglodytes zinc finger protein 273, transcript variant 1 (ZNF273), mRNA Length=4430 Score = 111 bits (60), Expect = 7e-28 Identities = 64/66 (97%), Gaps = 0/66 (0%) Strand=Plus/Minus Query 1 TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaa 60 ||| |||||||||||||||||||||||||||||| ||||||||||||||||||||||||| Sbjct 2800 TCACGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCGTCTCAAAAAAAAAAAA 2741 Query 61 aaaaaa 66 |||||| Sbjct 2740 AAAAAA 2735 Lambda K H 1.33 0.621 1.12 Gapped Lambda K H 1.28 0.460 0.850 Effective search space used: 3506256 Database: minirefseq_mrna Posted date: Jun 9, 2012 2:05 PM Number of letters in database: 67,750 Number of sequences in database: 23 Matrix: blastn matrix 1 -2 Gap Penalties: Existence: 0, Extension: 2.5