Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009832.1 Corchorus capsularis cultivar CVL-1 contig09853, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13677
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:734 original size:323 final size:321
Alignment explanation
Indices: 1--4672 Score: 6067
Period size: 323 Copynumber: 14.5 Consensus size: 321
* *
1 ATTAAATTGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* * *
66 TGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATAATGCAAAATTGAGCCGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* *
131 GC-TCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGATTAAAAACTGA
131 GCTTC-GGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTGA
195 CCCGAAAATTTTTTTCAT-AATGTTTTT-CCACAATACTTACA-AAAAAATATATAATTCAATGC
195 CCCGAAAATTTTTTTC-TCAAT-TTTTTGCCACAATAC--ACAGAAAAAATATATAATTCAATGC
* *
257 CAAAAATATTGACAGG-CTTTTCACGTTTCTCATATCGTTTTTCCATTTTTTCTGAATTAATTTC
256 CAAAAATATTGAC-GGACTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTC
321 TA
320 TA
* * *
323 ATTAAATCGAAACAAGATTTAGATGCTCGAAAAAACAAATCATTTTATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* ** *
388 TGGTTAGATGAATATAGATATTTCGGGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGTCGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* * *
453 ACTTCGGAACACGTTTTTAGCCAAAAAAATCGTGATGGTAAGTACACAATTTCGACTAAAAACTG
131 GCTTCGGAACGCGTTTTTAGCC--AAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTG
* * *
518 ATCCGAAAATTTTTTTATCAATTTTTTGCCACAATACACAGATAAAATATATAATTCAATGCCAA
194 ACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAA
* *
583 AAATATTGACGGACTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCCGAATTAATTTCTA
259 AAATATTGACGGACTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
* * * * * * *
646 ATTAAATCGAGACAAGATTGAAATGCTTGAAAAAAGAAATCCTTATATCTAATTTTGCTAAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* * * * * **
711 TTGTTCGATTAATATATATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTAAATCGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* * * *
776 GCTCCGGAATGCGTTTTTAGCCAAAAACCGTGATGCTTAGTACACAATTTCGACTAAAAACTGAC
131 GCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTGAC
* * *
841 CCAAAATATATTTTTTCTCAA-TTTTTGTCACAATACACCGAAAAAAAATATATAATTCAATGCC
196 CCGAAA-AT-TTTTTTCTCAATTTTTTGCCACAATACA-C-AGAAAAAATATATAATTCAATGCC
* * * * **
905 AAAAATATTGAC--A--ATCCACGTTTGTAATATTGTTTTTCCATTTTTTTCAAAATTAATTTCT
257 AAAAATATTGACGGACTTTTCACGTTTCTAATATCGTTTTTCCA-TTTTTTCCGAATTAATTTCT
966 A
321 A
* ** * *
967 ATTAAATGGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTCGATCGAATATTACTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* * * *
1032 TGGTCCGATGAATATAGATATTTCAGGGAGTCTTTGTGCAAAAAATCATGCATAATTGAGCCGAG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* * * * * * * *
1097 GCTTCGGAACGTGTTTTTAGCCAAAAAAACCATAATGATAAGTATAAAATTTCGACTAAAACCTT
131 GCTTCGGAACGCGTTTTTAGCC--AAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTG
* * * *
1162 ATCCGAAAATTTTTTTTCTCAATTTTTTGACACAATACACAGTAAAAAATATATAATTTAATACC
194 ACCCGAAAA-TTTTTTTCTCAATTTTTTGCCACAATACACAG-AAAAAATATATAATTCAATGCC
* *
1227 AAAAATATTGACGGACTTTTCACGCTTCTAATATCATTTTTCCCATTTTTTTCCGAATTAATTTC
257 AAAAATATTGACGGACTTTTCACGTTTCTAATATCGTTTTT-CCA-TTTTTTCCGAATTAATTTC
1292 TA
320 TA
*
1294 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* *
1359 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAATAAATCATGCAAAATTCAACCG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGC-AAA-AAATCATGCAAAATTGAGCCG
* * * *
1424 GTGCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTAAAAACTG
129 GGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTG
* * *
1489 ACCCGAAAAATTTTTTTTCACAATTTTATGCCACAATACATAGAAAAAATATATAATTCAATGCC
194 ACCCG-AAAA-TTTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCC
* *
1554 AAAAATATTGACGGGCTTTTCACGTTTCTAATATCCGTTTTT-CTTTTTTTCCGAATTAATTTCT
257 AAAAATATTGACGGACTTTTCACGTTTCTAATAT-CGTTTTTCCATTTTTTCCGAATTAATTTCT
1618 A
321 A
* *
1619 ATTAAATCGAAATAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* * *
1684 TGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCTGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* * * * * *
1749 GCTCCAGAACGCGTTTTTAGCCAAAAACAGTGATGTTTAA-TACACAATTTCGATTAAAAAGTGA
131 GCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATG-GTAAGTACACAATTTCGACTAAAAACTGA
* * * *
1813 CTCGAAAAATTTTTTTCCCAATTTTTTGCCACAATACATAGAAAAAGTATATAATTCAATGCCAA
195 CCCG-AAAATTTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAA
**
1878 AAATATTGACAGG-CTTTTCACGTTTCGCATATCGTTTTTCCA-TTTTTCCGAATTAATTTCTA
259 AAATATTGAC-GGACTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
* * * *
1940 ATTAAATCGAAACAAGATTTAGATGCTCGAAGAAACTAATCCTTTTATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* * * * * *
2005 TGGTTAGATGAATATAGATATTTC-GGAGAGACTCTGTGCAAAAAATCATGCATAATTGAGCCGA
66 TGGTTCGATGAATATAGATATTTCAAG-GAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGG
* * * * * *
2069 GTCTTCGGAACGCATTTTTAGCCAAAAAACAGTGATGGTAAGTATAAAATTTCGACTAAAAACTT
130 GGCTTCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTG
* * *
2134 ATCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACACAGTAAAAAATATATAATTTAATGCCA
194 ACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACACAG-AAAAAATATATAATTCAATGCCA
* *
2199 AAAATATTGACGGACTTTTCACACACGCTTCTAATATCATTTTTCCATTTTTTCCGAATTAATTT
258 AAAATATTGACGGACTTTT----CACGTTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTT
2264 CTA
319 CTA
* * *
2267 AATAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTACTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
*
2332 TGGTTCGATGAATATATATATTTCAAGGAGTCTTTGTGCAAAAAAAAAATCATGCAAAATTGAGC
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGC----AAAAAATCATGCAAAATTGAGC
* *
2397 CGGGGCTCCGGAAAGCG--TTT------------T--T--T--GT-CACAATTTCGACTAAAAAC
127 CGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAAC
* * *
2441 TGACTCGAAAATTTTTTTCTGAATTTTTTGCCACAATACATAGAAAAAATATATAATTCAATGCC
192 TGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCC
*
2506 AAAAATATTGAC-GAGCTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTCCGAATTAATTTCT
257 AAAAATATTGACGGA-CTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCT
2570 A
321 A
* *
2571 ATTAAATTGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* * * **
2636 TGATTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGATTCGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* * * *
2701 GCTCCGGAACGCGTTTTTAGCCAAAACCCGTGATGGTTAGTACACAATTTCGATTAAAAACTGAC
131 GCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTGAC
*** * *
2766 CCGAAAAAGAATTTTCTCAATTTTTTGCCACAATACATAGAAAAAAATATATAATTTAATGCCAA
196 CCG-AAAATTTTTTTCTCAATTTTTTGCCACAATACACAG-AAAAAATATATAATTCAATGCCAA
** *
2831 AAATATTGACAGG-CTTTTCACACTTCTCATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
259 AAATATTGAC-GGACTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
* * * * *
2894 ATTAAATCGAAACAAGATTTAGATGCTCGAAAAGACTAATTCTTTTATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* * * * * **
2959 TGGTTAGATGAATATAGATATTTC-GGAGAGACTCTGTGCAAAAAATCATGCATAATTGAGCCAA
66 TGGTTCGATGAATATAGATATTTCAAG-GAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGG
* * * *
3023 GTCTTCGGAACGCGTTTTTAGCCAAAAAATCAGTGATGGTAAGTATAAAATTTCGACTAAAAACT
130 GGCTTCGGAACGCGTTTTTAGCC-AAAAA-CCGTGATGGTAAGTACACAATTTCGACTAAAAACT
*
3088 GACCCG-AAATTATTTTTCTCAATTTTTTGCCACAATACACAGTAAAAATATATAATTCAATGCC
193 GACCCGAAAATT-TTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCC
* * * *
3152 AAAAATATTGACGAACTTTTCACGCTTCTAATATCATTTTTTCATTTTTTTTCCCGAATTAATTT
257 AAAAATATTGACGGACTTTTCACGTTTCTAATATCGTTTTTCCA--TTTTTT-CCGAATTAATTT
3217 CTA
319 CTA
* *
3220 ATTAAATCGAGACAAGATTGAGATGCTCGAAAAAAGCAAATCCTTACATCCAATATTGCTGAGAT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAA-CAAATCCTTATATCCAATATTGCTGAGAT
* * * * * *
3285 TTGGTTCGATGAATATATATATTTCATGGAGCCTTTGTGCAAAAAATCGTGCAAATTTGAGCCGA
65 TTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGG
* * * *
3350 GGCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTACAAACTGA
130 GGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTGA
*
3415 CCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAA-A-ATAATTCAATGCCAA
195 CCCGAAAA-TTTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAA
* *
3478 ACATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCC--TTTTTCCGAATTAATTTCTA
259 AAATATTGACGGACTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
* *
3539 ATTAAATC-AAACCAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGATAT
1 ATTAAATCGAAA-CAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGAT
* *
3603 TTGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGG
65 TTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGG
* * *** * * *
3668 GGCTTCAGAACGTGTTTTTAATAAAAAAACCGTGATGTTTAGTACACAATTTCGATTAAAAACTG
130 GGCTTCGGAACGCGTTTTT-AGCCAAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTG
* **** * *
3733 ACTCGAAAAAAAAAATTTCTCATTTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAATGC
194 ACCCG--AAAATTTTTTTCTCAATTTTTTGCCACAATACACAG-AAAAAATATATAATTCAATGC
* * *
3798 CAAAAATTTTGTCAGG-CTTTTCACGTTTCTCATATCGTTTTTCCATTTTTTTCCGAATTAATTT
256 CAAAAATATTGAC-GGACTTTTCACGTTTCTAATATCGTTTTTCCA-TTTTTTCCGAATTAATTT
3862 CTA
319 CTA
* *
3865 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAAACAAATTCTTACATCCAATATTGCTGAGAT
1 ATTAAATCGAAACAAGATTGAGATGCTCG-AAAAAACAAATCCTTATATCCAATATTGCTGAGAT
* * * *
3930 TTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGAGTCGG
65 TTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGG
* * * * * *
3995 GGCTCCGCAATGCGTTTTTAGCTAAAAACCCTG-T--T--GTACACAATTTC-AGCTAAAAATTG
130 GGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGA-CTAAAAACTG
* *
4054 ACCC-AAATATTTTTTTCTCAA-TTTTTGCCACAATACACAGAGAAAATATATATTTCAATGCCA
194 ACCCGAAA-ATTTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCA
** * * * *
4117 AAAATATTGACAAACTTTTCACGCTTCTGATATCATTTTTCCATTTTTTTCGAATTAATTTCTA
258 AAAATATTGACGGACTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
4181 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* *
4246 TGGTTCGATGATTATAGATATTTCAAGGAGTCTTTGTGCAAAAAAATCATGAAAAATTGAGCCGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGC-AAAAAATCATGCAAAATTGAGCCGG
*
4311 GGCTTCGGAACGCGTTTTTAGGCAAAAACCGTGAT-GTAAAGTACACAATTTCGACTAAAAACTG
130 GGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGT-AAGTACACAATTTCGACTAAAAACTG
* * * * *
4375 AACTGAAAAATATTTTTCTCAATTTTTTACCACAATACACAG-AAAAATA-ATATATTCATTGCC
194 ACCCG-AAAATTTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATA-ATTCAATGCC
* *
4438 AAAAATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTTCTGAATTAATTT
257 AAAAATATTGACGGACTTTTCACGTTTCTAATATCGTTTTTCCA---TTTTTTCCGAATTAATTT
4503 CTA
319 CTA
* * * *
4506 ATTAAATCGAAACGAGATTGAGATGCTCGAAAAAACAAATCTTTTTATCCAATATTGTTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* * *
4571 TGGTTCAATGAATATAGATATTTTAAGGAGTATTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* *
4636 AC-TCAAGAACGCGTTTTTAGCCAAAAACCGTGATGGT
131 GCTTC-GGAACGCGTTTTTAGCCAAAAACCGTGATGGT
4673 TAGATTTTTT
Statistics
Matches: 3796, Mismatches: 440, Indels: 225
0.85 0.10 0.05
Matches are distributed among these distances:
300 36 0.01
302 3 0.00
304 137 0.04
307 2 0.00
308 38 0.01
309 54 0.01
310 2 0.00
312 1 0.00
314 2 0.00
315 70 0.02
316 100 0.03
317 57 0.02
318 125 0.03
319 95 0.03
320 56 0.01
321 470 0.12
322 455 0.12
323 706 0.19
324 242 0.06
325 318 0.08
326 181 0.05
327 528 0.14
328 44 0.01
329 41 0.01
331 33 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (321 bp):
ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
GCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGACTAAAAACTGAC
CCGAAAATTTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAA
ATATTGACGGACTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
Found at i:1934 original size:973 final size:968
Alignment explanation
Indices: 1--4675 Score: 6450
Period size: 973 Copynumber: 4.8 Consensus size: 968
* * *
1 ATTAAATTGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTCTATCCAATATTGCTGAGATT
* * * * * *
66 TGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATAATGCAAAATTGAGCCGGG
66 TGGTTCGATGAATATAGATATTTCAGGGAGTCTTTGTGCAAAAAATCATGCATAATTGAGCCGAG
* * * * * *
131 GC-TCTGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACAATTTCGATTAAAAACTG
131 GCTTC-GGAACGCGTTTTTAGCCAAAAAACCATGATGGTAAGTATAAAATTTCGACTAAAAACTT
* *
194 ACCCGAAAATTTTTTTCAT-AATGTTTTT-CCACAATACTTACA--AAAAAATATATAATTCAAT
195 ACCCGAAATTTTTTTTC-TCAAT-TTTTTGCCACAATAC--ACAGTAAAAAATATATAATTTAAT
* * * *
255 GCCAAAAATATTGACAGG-CTTTTCACGTTTCTCATATCGTTTTTCCA-TTTTTTCTGAATTAAT
256 GCCAAAAATATTGAC-GGACTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAAT
* * **
318 TTCTAATTAAATCGAAACAAGATTTAGATGCTCGAAAAAACAAATCATTTTATCCAATATTGCTG
320 TTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTG
* **
383 AGATTTGGTTAGATGAATATAGATATTTCGGGGAGTCTTTGTGC-AAAAAATCATGCAAAATTGA
385 AGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAAATCATGCAAAATTGA
* * * *
447 GTCGGGACTTCGGAACACGTTTTTAGCCAAAAAAAT-CGTGATGGTAAGTACACAATTTCGACTA
450 GCCGGG-CTCCGGAACGCGTTTTTAGCC---AAAATCCGTGATGGTTAGTACACAATTTCGACTA
* * * *
511 AAAACTGATCCGAAAATTTTTTTATCAATTTTTTGCCACAATACACAGATAAAATATATAATTCA
511 AAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAATATATAATTCA
* * * *
576 ATGCCAAAAATATTGACGGACTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCCGAATTAAT
576 ATGCCAAAAATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTCCGAATTAAT
* * * * * * *
641 TTCTAATTAAATCGAGACAAGATTGAAATGCTTGAAAAAAGAAATCCTTATATCTAATTTTGCTA
641 TTCTAATTAAATCGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTG
* * * * * * *
706 AGATTTTGTTCGATTAATATATATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAATT-AA
706 AGATTTGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAG
* * * * *
770 ATCGGGGCTCCGGAATGCGTTTTTAGCCAAAAACCGTGATGCTTAGTACACAATTTCGACTAAAA
771 CT-GGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGTTTAGTACACAATTTCGATTAAAA
* * * **
835 ACTGAC-CCAAAATATATTTTTTCTCAA-TTTTTGTCACAATACACCGAAAAAAAATATATAATT
835 ACTGACTCGAAAA-ATA-ATTTTCTCAATTTTTTGCCACAATACATAG-AAAAAAATATATAATT
* * * * **
898 CAATGCCAAAAATATTGACA----ATCCACGTTT-GTAATATTGTTTTTCCATTTTTTTCAAAAT
897 CAATGCCAAAAATATTGACAGGCTTTTCACGTTTCG-CATATCGTTTTTCCA-TTTTTTCCGAAT
958 TAATTTCTA
960 TAATTTCTA
* * * *
967 ATTAAATGGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTCGATCGAATATTACTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTCTATCCAATATTGCTGAGATT
*
1032 TGGTCCGATGAATATAGATATTTCAGGGAGTCTTTGTGCAAAAAATCATGCATAATTGAGCCGAG
66 TGGTTCGATGAATATAGATATTTCAGGGAGTCTTTGTGCAAAAAATCATGCATAATTGAGCCGAG
* * * *
1097 GCTTCGGAACGTGTTTTTAGCCAAAAAAACCATAATGATAAGTATAAAATTTCGACTAAAACCTT
131 GCTTCGGAACGCGTTTTTAGCC-AAAAAACCATGATGGTAAGTATAAAATTTCGACTAAAAACTT
* * *
1162 ATCCGAAAATTTTTTTTCTCAATTTTTTGACACAATACACAGTAAAAAATATATAATTTAATACC
195 ACCCG-AAATTTTTTTTCTCAATTTTTTGCCACAATACACAGTAAAAAATATATAATTTAATGCC
1227 AAAAATATTGACGGACTTTTCACGCTTCTAATATCATTTTTCCCATTTTTTTCCGAATTAATTTC
259 AAAAATATTGACGGACTTTTCACGCTTCTAATATCATTTTT-CCATTTTTTTCCGAATTAATTTC
1292 TAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGA
323 TAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGA
* *
1357 TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAATAAATCATGCAAAATTCAAC
388 TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAA-AAATCATGCAAAATTGAGC
1422 CGGTGCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTAAAAAC
452 CGG-GCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTAAAAAC
* *
1487 TGACCCGAAAAATTTTTTTTCACAATTTTATGCCACAATACATAGAAAAAATATATAATTCAATG
516 TGACCCG-AAAA-TTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAATATATAATTCAATG
1552 CCAAAAATATTGACGGGCTTTTCACGTTTCTAATATCCGTTTTT-CTTTTTTTCCGAATTAATTT
579 CCAAAAATATTGACGGGCTTTTCACGTTTCTAATAT-CGTTTTTCCTTTTTTTCCGAATTAATTT
*
1616 CTAATTAAATCGAAATAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAG
643 CTAATTAAATCGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAG
1681 ATTTGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCT
708 ATTTGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCT
* * *
1746 GGGGCTCCAGAACGCGTTTTTAGCCAAAAACAGTGATGTTTAATACACAATTTCGATTAAAAAGT
773 GGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGTTTAGTACACAATTTCGATTAAAAACT
** * *
1811 GACTCGAAAAATTTTTTTCCCAATTTTTTGCCACAATACATAG-AAAAAGTATATAATTCAATGC
838 GACTCGAAAAATAATTTTCTCAATTTTTTGCCACAATACATAGAAAAAAATATATAATTCAATGC
1875 CAAAAATATTGACAGGCTTTTCACGTTTCGCATATCGTTTTTCCA-TTTTTCCGAATTAATTTCT
903 CAAAAATATTGACAGGCTTTTCACGTTTCGCATATCGTTTTTCCATTTTTTCCGAATTAATTTCT
1939 A
968 A
* * * *
1940 ATTAAATCGAAACAAGATTTAGATGCTCGAAGAAACTAATCCTTTTATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTCTATCCAATATTGCTGAGATT
* * *
2005 TGGTTAGATGAATATAGATATTTC-GGAGAGACTCTGTGCAAAAAATCATGCATAATTGAGCCGA
66 TGGTTCGATGAATATAGATATTTCAGG-GAGTCTTTGTGCAAAAAATCATGCATAATTGAGCCGA
* *
2069 GTCTTCGGAACGCATTTTTAGCCAAAAAA-CAGTGATGGTAAGTATAAAATTTCGACTAAAAACT
130 GGCTTCGGAACGCGTTTTTAGCCAAAAAACCA-TGATGGTAAGTATAAAATTTCGACTAAAAACT
*
2133 TATCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACACAGTAAAAAATATATAATTTAATGCC
194 TACCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACACAGTAAAAAATATATAATTTAATGCC
2198 AAAAATATTGACGGACTTTTCACACACGCTTCTAATATCATTTTTCCA-TTTTTTCCGAATTAAT
259 AAAAATATTGACGGACTTTT----CACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAAT
* *
2262 TTCTAAATAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTACTG
320 TTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTG
*
2327 AGATTTGGTTCGATGAATATATATATTTCAAGGAGTCTTTGTGCAAAAAAAAAATCATGCAAAAT
385 AGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGC---AAAAAAATCATGCAAAAT
*
2392 TGAGCCGGGGCTCCGGAAAGCG----T--------T---T--T--TT-GT-CACAATTTCGACTA
447 TGAGCC-GGGCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTA
* *
2436 AAAACTGACTCGAAAATTTTTTTCTGAATTTTTTGCCACAATACATAGAAAAAATATATAATTCA
511 AAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAATATATAATTCA
*
2501 ATGCCAAAAATATTGACGAGCTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTCCGAATTAAT
576 ATGCCAAAAATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTCCGAATTAAT
*
2566 TTCTAATTAAATTGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTG
641 TTCTAATTAAATCGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTG
*
2631 AGATTTGATTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGA-
706 AGATTTGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAG
* * * *
2695 TTCGGGGCTCCGGAACGCGTTTTTAGCCAAAACCCGTGATGGTTAGTACACAATTTCGATTAAAA
771 CT-GGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGTTTAGTACACAATTTCGATTAAAA
* * *
2760 ACTGACCCGAAAAAGAATTTTCTCAATTTTTTGCCACAATACATAGAAAAAAATATATAATTTAA
835 ACTGACTCGAAAAATAATTTTCTCAATTTTTTGCCACAATACATAGAAAAAAATATATAATTCAA
** *
2825 TGCCAAAAATATTGACAGGCTTTTCACACTTCTCATATCGTTTTTCCATTTTTTCCGAATTAATT
900 TGCCAAAAATATTGACAGGCTTTTCACGTTTCGCATATCGTTTTTCCATTTTTTCCGAATTAATT
2890 TCTA
965 TCTA
* * * * *
2894 ATTAAATCGAAACAAGATTTAGATGCTCGAAAAGACTAATTCTTTTATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTCTATCCAATATTGCTGAGATT
* * * *
2959 TGGTTAGATGAATATAGATATTTC-GGAGAGACTCTGTGCAAAAAATCATGCATAATTGAGCCAA
66 TGGTTCGATGAATATAGATATTTCAGG-GAGTCTTTGTGCAAAAAATCATGCATAATTGAGCCGA
* *
3023 GTCTTCGGAACGCGTTTTTAGCCAAAAAATCAGTGATGGTAAGTATAAAATTTCGACTAAAAACT
130 GGCTTCGGAACGCGTTTTTAGCCAAAAAACCA-TGATGGTAAGTATAAAATTTCGACTAAAAACT
* * *
3088 GACCCGAAATTATTTTTCTCAATTTTTTGCCACAATACACAGT-AAAAATATATAATTCAATGCC
194 TACCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACACAGTAAAAAATATATAATTTAATGCC
* *
3152 AAAAATATTGACGAACTTTTCACGCTTCTAATATCATTTTTTCATTTTTTTTCCCGAATTAATTT
259 AAAAATATTGACGGACTTTTCACGCTTCTAATATCATTTTTCCA-TTTTTTT-CCGAATTAATTT
*
3217 CTAATTAAATCGAGACAAGATTGAGATGCTCGAAAAAAGCAAATCCTTACATCCAATATTGCTGA
322 CTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAA-CAAATCCTTACATCCAATATTGCTGA
* * * * *
3282 GATTTGGTTCGATGAATATATATATTTCATGGAGCCTTTGTGC-AAAAAATCGTGCAAATTTGAG
386 GATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAAATCATGCAAAATTGAG
*
3346 CCGAGGCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTACAAA
451 CCG-GGCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTAAAAA
3411 CTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAA-A-ATAATTCAATG
515 CTGACCCGAAAA-TTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAATATATAATTCAATG
*
3474 CCAAACATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCC--TTTTTCCGAATTAATTTC
579 CCAAAAATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTCCGAATTAATTTC
*
3537 TAATTAAATC-AAACCAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAT
644 TAATTAAATCGAAA-CAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAG
*
3601 ATTTGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCC
708 ATTTGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCT
* * ***
3666 GGGGCTTCAGAACGTGTTTTTAATAAAAAAACCGTGATGTTTAGTACACAATTTCGATTAAAAAC
773 GGGGCTCCAGAACGCGTTTTT-AGCCAAAAACCGTGATGTTTAGTACACAATTTCGATTAAAAAC
* * * *
3731 TGACTCGAAAAAAAAAATTTCTCATTTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAAT
837 TGACTCG-AAAAATAATTTTCTCAATTTTTTGCCACAATACATAGAAAAAAATATATAATTCAAT
* * *
3796 GCCAAAAATTTTGTCAGGCTTTTCACGTTTCTCATATCGTTTTTCCATTTTTTTCCGAATTAATT
901 GCCAAAAATATTGACAGGCTTTTCACGTTTCGCATATCGTTTTTCCA-TTTTTTCCGAATTAATT
3861 TCTA
965 TCTA
*
3865 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAAACAAATTCTTAC-ATCCAATATTGCTGAGA
1 ATTAAATCGAAACAAGATTGAGATGCTCG-AAAAAACAAATCCTT-CTATCCAATATTGCTGAGA
* * * * * *
3929 TTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGAGTCG
64 TTTGGTTCGATGAATATAGATATTTCAGGGAGTCTTTGTGCAAAAAATCATGCATAATTGAGCCG
* * * * * * * *
3994 GGGCTCCGCAATGCGTTTTTAG-CTAAAAACCCTG-T--T--GTACACAATTTC-AGCTAAAAA-
129 AGGCTTCGGAACGCGTTTTTAGCCAAAAAACCATGATGGTAAGTATAAAATTTCGA-CTAAAAAC
*
4051 TTGACCC-AAATATTTTTTTCTCAA-TTTTTGCCACAATACACAG-AGAAAATATAT-ATTTCAA
193 TT-ACCCGAAAT-TTTTTTTCTCAATTTTTTGCCACAATACACAGTAAAAAATATATAATTT-AA
** *
4112 TGCCAAAAATATTGACAAACTTTTCACGCTTCTGATATCATTTTTCCATTTTTTT-CGAATTAAT
255 TGCCAAAAATATTGACGGACTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAAT
*
4176 TTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTG
320 TTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTG
* *
4241 AGATTTGGTTCGATGATTATAGATATTTCAAGGAGTCTTTGTGCAAAAAAATCATGAAAAATTGA
385 AGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAAATCATGCAAAATTGA
* * * *
4306 GCCGGGGCTTCGGAACGCGTTTTTAGGCAAAAACCGTGAT-GTAAAGTACACAATTTCGACTAAA
450 GCC-GGGCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGT-TAGTACACAATTTCGACTAAA
* * * * *
4370 AACTGAACTGAAAAATATTTTTCTCAATTTTTTACCACAATACACAG-AAAAATA-ATATATTCA
513 AACTGACCCG-AAAATTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAATATATA-ATTCA
* *
4433 TTGCCAAAAATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTTCTGAATT
576 ATGCCAAAAATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCC---TTTTTTTCCGAATT
* * * *
4498 AATTTCTAATTAAATCGAAACGAGATTGAGATGCTCGAAAAAACAAATCTTTTTATCCAATATTG
638 AATTTCTAATTAAATCGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTG
* * * * * *
4563 TTGAGATTTGGTTCAATGAATATAGATATTTTAAGGAGTATTTGTGCAAAAAATCATGCAAAATT
703 CTGAGATTTGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATT
* * * *
4628 GAGCCGGGACTCAAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
768 GAGCTGGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGTTTAG
4676 ATTTTTTCTG
Statistics
Matches: 3355, Mismatches: 261, Indels: 186
0.88 0.07 0.05
Matches are distributed among these distances:
949 1 0.00
950 57 0.02
951 8 0.00
952 331 0.10
953 113 0.03
954 304 0.09
955 77 0.02
956 2 0.00
958 1 0.00
960 72 0.02
961 160 0.05
962 57 0.02
963 11 0.00
964 81 0.02
965 33 0.01
966 153 0.05
967 158 0.05
968 202 0.06
969 124 0.04
970 161 0.05
971 354 0.11
972 196 0.06
973 603 0.18
974 17 0.01
975 72 0.02
976 7 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (968 bp):
ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTCTATCCAATATTGCTGAGATT
TGGTTCGATGAATATAGATATTTCAGGGAGTCTTTGTGCAAAAAATCATGCATAATTGAGCCGAG
GCTTCGGAACGCGTTTTTAGCCAAAAAACCATGATGGTAAGTATAAAATTTCGACTAAAAACTTA
CCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACACAGTAAAAAATATATAATTTAATGCCAA
AAATATTGACGGACTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAA
TTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATTT
GGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAAATCATGCAAAATTGAGCCGGG
CTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTAAAAACTGACC
CGAAAATTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAATATATAATTCAATGCCAAAAA
TATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTCCGAATTAATTTCTAATTAA
ATCGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATTTGGTT
CGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCTGGGGCTCC
AGAACGCGTTTTTAGCCAAAAACCGTGATGTTTAGTACACAATTTCGATTAAAAACTGACTCGAA
AAATAATTTTCTCAATTTTTTGCCACAATACATAGAAAAAAATATATAATTCAATGCCAAAAATA
TTGACAGGCTTTTCACGTTTCGCATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
Found at i:3889 original size:645 final size:643
Alignment explanation
Indices: 1--4675 Score: 5967
Period size: 645 Copynumber: 7.3 Consensus size: 643
* * *
1 ATTAAATTGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATT
* * *
66 TGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATAATGCAAAATTGAGCCGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* *
131 GCTCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGATTAAAAACTGAC
131 GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGACTAAAAACTGAC
* *
196 CCGAAAA-TTTTTTTCAT-AATGTTTTT-CCACAATACTTACAAAAAAATATATAATTCAATGCC
196 CCGAAAATTTTTTTTC-TCAAT-TTTTTGCCACAATACATA-GAAAAAA-A-ATAATTCAATGCC
* * *
258 AAAAATATTGACAGGCTTTTCACGTTTCTCATATCGTTTTTCCATTTTTTCTGAATTAATTTCTA
256 AAAAATATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTCCGAATTAATTTCTA
* * *
323 ATTAAATCGAAACAAGATTTAGATGCTCGAAAAAACAAATCATTTTATCCAATATTGCTGAGATT
320 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* * ** *
388 TGGTTAGATGAATATAGATATTTCGGGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGTCGGG
385 TGGTTCGATGATTATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* * * * *
453 ACTTCGGAACACGTTTTTAGCCAAAAAAATCGTGATGGTAAGTACACAATTTCGACTAAAAACTG
450 GCTTCGGAACGCGTTTTTA-ACAAAAAAACCGTGATGTTAAGTACACAATTTCGACTAAAAACTG
* * *
518 A-TCCGAAAATTTTTTTATCAATTTTTTGCCACAATACACAGATAAAATATATAATTCAATGCCA
514 ACT-CGAAAATATTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCA
* *
582 AAAATATTGACG-GACTTTTCACGCTTCTAATATCATTTTTCCA--TTTTTTCCGAATTAATTTC
578 AAAATATTGACGAG-CTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTC
644 TA
642 TA
* * * * * * * *
646 ATTAAATCGAGACAAGATTGAAATGCTTGAAAAAAGAAATCCTTATATCTAATTTTGCTAAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATT
* * * * * **
711 TTGTTCGATTAATATATATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTAAATCGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* *
776 GCTCCGGAATGCGTTTTTAGCCAAAAACCGTGATGCTTAGTACACAATTTCGACTAAAAACTGAC
131 GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGACTAAAAACTGAC
* * *
841 CC-AAAATATATTTTTTCTCAA-TTTTTGTCACAATACACCGAAAAAAAATATATAATTCAATGC
196 CCGAAAAT-T-TTTTTTCTCAATTTTTTGCCACAATACA--TAGAAAAAA-A-ATAATTCAATGC
* * * * * **
904 CAAAAATATTGACA----ATCCACGTTTGTAATATTGTTTTTCCATTTTTTTCAAAATTAATTTC
255 CAAAAATATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCA--TTTTTCCGAATTAATTTC
* ** * *
965 TAATTAAATGGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTCGATCGAATATTACTGAGA
318 TAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGA
* * * *
1030 TTTGGTCCGATGAATATAGATATTTCAGGGAGTCTTTGTGCAAAAAATCATGCATAATTGAGCCG
383 TTTGGTTCGATGATTATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCG
* * * * * * * * *
1095 AGGCTTCGGAACGTGTTTTTAGCCAAAAAAACCATAATGATAAGTATAAAATTTCGACTAAAACC
448 GGGCTTCGGAACGCGTTTTTA-ACAAAAAAACCGTGATGTTAAGTACACAATTTCGACTAAAAAC
* * * *
1160 TTA-TCCGAAAATTTTTTTTCTCAATTTTTTGACACAATACACAGTAAAAAATATATAATTTAAT
512 TGACT-CGAAAA-TATTTTTCTCAATTTTTTGCCACAATACACAG-AAAAAATATATAATTCAAT
* * *
1224 ACCAAAAATATTGACG-GACTTTTCACGCTTCTAATATCATTTTTCCCA-TTTTTTTCCGAATTA
574 GCCAAAAATATTGACGAG-CTTTTCACGTTTCTAATATCGTTTTT-CCATTTTTTTTCCGAATTA
1287 ATTTCTA
637 ATTTCTA
1294 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATT
* *
1359 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAATAAATCATGCAAAATTCAACCG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGC-AAA-AAATCATGCAAAATTGAGCCG
* *
1424 GTGCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTAAAAACTG
129 GGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGACTAAAAACTG
* *
1489 ACCCGAAAAATTTTTTTTCACAATTTTATGCCACAATACATAGAAAAAATATATAATTCAATGCC
194 ACCCG-AAAATTTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAA-A-ATAATTCAATGCC
* * **
1554 AAAAATATTGACGGGCTTTTCACGTTTCTAATATCCGTTTTTCTTTTTTTCCGAATTAATTTCTA
256 AAAAATATTGACAGGCTTTTCACGCTTCTAATAT-CGTTTTTCCATTTTTCCGAATTAATTTCTA
* *
1619 ATTAAATCGAAATAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
320 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
* *
1684 TGGTTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCTGGG
385 TGGTTCGATGATTATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* * * * * * *
1749 GCTCCAGAACGCGTTTTTAGC-CAAAAACAGTGATGTTTAA-TACACAATTTCGATTAAAAAGTG
450 GCTTCGGAACGCGTTTTTAACAAAAAAACCGTGATG-TTAAGTACACAATTTCGACTAAAAACTG
* * * *
1812 ACTCGAAAAATTTTTTTCCCAATTTTTTGCCACAATACATAGAAAAAGTATATAATTCAATGCCA
514 ACTCG-AAAATATTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCA
**
1877 AAAATATTGAC-AGGCTTTTCACGTTTCGCATATCGTTTTTCCA---TTTTTCCGAATTAATTTC
578 AAAATATTGACGA-GCTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTC
1938 TA
642 TA
* * * **
1940 ATTAAATCGAAACAAGATTTAGATGCTCGAAGAAACTAATCCTTTTATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATT
* * * * * *
2005 TGGTTAGATGAATATAGATATTTC-GGAGAGACTCTGTGCAAAAAATCATGCATAATTGAGCCGA
66 TGGTTCGATGAATATAGATATTTCAAG-GAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGG
* * * * * * * *
2069 GTCTTCGGAACGCATTTTTAGCCAAAAAACAGTGATGGTAAGTATAAAATTTCGACTAAAAACTT
130 GGCTCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACAATTTCGACTAAAAACTG
* * *
2134 ATCCG-AAATTTTTTTTCTCAATTTTTTGCCACAATACACAGTAAAAAATATATAATTTAATGCC
194 ACCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACATAG-AAAAAA-A-ATAATTCAATGCC
*
2198 AAAAATATTGAC-GGACTTTTCACACACGCTTCTAATATCATTTTTCCATTTTTTCCGAATTAAT
256 AAAAATATTGACAGG-CTTTT----CACGCTTCTAATATCGTTTTTCCA-TTTTTCCGAATTAAT
* * *
2262 TTCTAAATAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTACTG
315 TTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTG
* *
2327 AGATTTGGTTCGATGAATATATATATTTCAAGGAGTCTTTGTGCAAAAAAAAAATCATGCAAAAT
380 AGATTTGGTTCGATGATTATAGATATTTCAAGGAGTCTTTGTGC----AAAAAATCATGCAAAAT
* *
2392 TGAGCCGGGGCTCCGGAAAGCG---TT-------------T--T-TT--GT-CACAATTTCGACT
441 TGAGCCGGGGCTTCGGAACGCGTTTTTAACAAAAAAACCGTGATGTTAAGTACACAATTTCGACT
* * *
2435 AAAAACTGACTCGAAAATTTTTTTCTGAATTTTTTGCCACAATACATAGAAAAAATATATAATTC
506 AAAAACTGACTCGAAAATATTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTC
2500 AATGCCAAAAATATTGACGAGCTTTTCACGTTTCTAATATCGTTTTTCC--TTTTTTTCCGAATT
571 AATGCCAAAAATATTGACGAGCTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTCCGAATT
2563 AATTTCTA
636 AATTTCTA
* * *
2571 ATTAAATTGAAACAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATT
* * * **
2636 TGATTCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGATTCGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* *
2701 GCTCCGGAACGCGTTTTTAGCCAAAACCCGTGATGGTTAGTACACAATTTCGATTAAAAACTGAC
131 GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGACTAAAAACTGAC
**** *
2766 CCGAAAAAGAATTTTCTCAATTTTTTGCCACAATACATAGAAAAAAATATATAATTTAATGCCAA
196 CCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACATAG-AAAAAA-A-ATAATTCAATGCCAA
* *
2831 AAATATTGACAGGCTTTTCACACTTCTCATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAAT
258 AAATATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTCCGAATTAATTTCTAAT
* * * * *
2896 TAAATCGAAACAAGATTTAGATGCTCGAAAAGACTAATTCTTTTATCCAATATTGCTGAGATTTG
322 TAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATTTG
* * * * * * ** *
2961 GTTAGATGAATATAGATATTTC-GGAGAGACTCTGTGCAAAAAATCATGCATAATTGAGCCAAGT
387 GTTCGATGATTATAGATATTTCAAG-GAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGGG
* * * * * *
3025 CTTCGGAACGCGTTTTTAGCCAAAAAATCAGTGATGGTAAGTATAAAATTTCGACTAAAAACTGA
451 CTTCGGAACGCGTTTTTA-ACAAAAAAACCGTGATGTTAAGTACACAATTTCGACTAAAAACTGA
* * *
3090 CCCGAAATTATTTTTCTCAATTTTTTGCCACAATACACAGTAAAAATATATAATTCAATGCCAAA
515 CTCGAAAATATTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAA
* * * *
3155 AATATTGACGAACTTTTCACGCTTCTAATATCATTTTTTCATTTTTTTTCCCGAATTAATTTCTA
580 AATATTGACGAGCTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTT-CCGAATTAATTTCTA
*
3220 ATTAAATCGAGACAAGATTGAGATGCTCGAAAAAAGCAAATCCTTACATCCAATATTGCTGAGAT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAA-CAAATCCTTACATCCAATATTGCTGAGAT
* * * * * *
3285 TTGGTTCGATGAATATATATATTTCATGGAGCCTTTGTGCAAAAAATCGTGCAAATTTGAGCCGA
65 TTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGG
* *
3350 GGCTCCGGAACGCGTTTTTAGCCAAAATCCGTGATGGTTAGTACACAATTTCGACTACAAACTGA
130 GGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGACTAAAAACTGA
*
3415 CCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAAAATAATTCAATGCCAAAC
195 CCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAAAATAATTCAATGCCAAAA
* *
3480 ATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCC-TTTTTCCGAATTAATTTCTAATTAA
260 ATATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTCCGAATTAATTTCTAATTAA
* *
3544 ATC-AAACCAAGATTGATATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGATATTTGGT
325 ATCGAAA-CAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATTTGGT
*
3608 TCGATGATTATAGATATATCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGGGCTT
389 TCGATGATTATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGGGCTT
* * * * *
3673 CAGAACGTGTTTTTAATAAAAAAACCGTGATGTTTAGTACACAATTTCGATTAAAAACTGACTCG
454 CGGAACGCGTTTTTAACAAAAAAACCGTGATGTTAAGTACACAATTTCGACTAAAAACTGACTCG
* ** * *
3738 AAAAAAAAAATTTCTCATTTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAATGCCAAAA
519 --AAAATATTTTTCTCAATTTTTTGCCACAATACACAG-AAAAAATATATAATTCAATGCCAAAA
* * *
3803 ATTTTGTC-AGGCTTTTCACGTTTCTCATATCGTTTTTCCA-TTTTTTTCCGAATTAATTTCTA
581 ATATTGACGA-GCTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTA
*
3865 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAAACAAATTCTTACATCCAATATTGCTGAGAT
1 ATTAAATCGAAACAAGATTGAGATGCTCG-AAAAAACAAATCCTTACATCCAATATTGCTGAGAT
* * * *
3930 TTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGAGTCGG
65 TTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGG
* * * * *
3995 GGCTCCGCAATGCGTTTTTAGCTAAAAACC---CT-GTT-GTACACAATTTC-AGCTAAAAATTG
130 GGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGA-CTAAAAACTG
* * *
4054 ACCC--AAATATTTTTTTCTCAA-TTTTTGCCACAATACACAGAGAAAATATATATTTCAATGCC
194 ACCCGAAAAT-TTTTTTTCTCAATTTTTTGCCACAATACATAGA-AAAA-AAATAATTCAATGCC
** * * *
4116 AAAAATATTGACAAACTTTTCACGCTTCTGATATCATTTTTCCATTTTTTTCGAATTAATTTCTA
256 AAAAATATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTCCGAATTAATTTCTA
4181 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
320 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATT
*
4246 TGGTTCGATGATTATAGATATTTCAAGGAGTCTTTGTGCAAAAAAATCATGAAAAATTGAGCCGG
385 TGGTTCGATGATTATAGATATTTCAAGGAGTCTTTGTGC-AAAAAATCATGCAAAATTGAGCCGG
* *
4311 GGCTTCGGAACGCGTTTTTAGGC--AAAAACCGTGATGTAAAGTACACAATTTCGACTAAAAACT
449 GGCTTCGGAACGCGTTTTTA-ACAAAAAAACCGTGATGTTAAGTACACAATTTCGACTAAAAACT
* *
4374 GAACT-GAAAAATATTTTTCTCAATTTTTTACCACAATACACAG-AAAAATA-ATATATTCATTG
513 G-ACTCG-AAAATATTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATA-ATTCAATG
* *
4436 CCAAAAATATTGACGGGCTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTTCTGAATTAAT
575 CCAAAAATATTGACGAGCTTTTCACGTTTCTAATATCGTTTTTCCA-TTTTTTTTCCGAATTAAT
4501 TTCTA
639 TTCTA
* * ** *
4506 ATTAAATCGAAACGAGATTGAGATGCTCGAAAAAACAAATCTTTTTATCCAATATTGTTGAGATT
1 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATT
* * *
4571 TGGTTCAATGAATATAGATATTTTAAGGAGTATTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
66 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
* **
4636 ACTCAAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
131 GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
4676 ATTTTTTCTG
Statistics
Matches: 3535, Mismatches: 394, Indels: 202
0.86 0.10 0.05
Matches are distributed among these distances:
623 33 0.01
626 3 0.00
627 131 0.04
630 132 0.04
631 245 0.07
632 4 0.00
633 2 0.00
635 1 0.00
637 1 0.00
638 26 0.01
639 72 0.02
640 187 0.05
641 83 0.02
642 157 0.04
643 107 0.03
644 324 0.09
645 552 0.16
646 343 0.10
647 161 0.05
648 254 0.07
649 146 0.04
650 335 0.09
651 24 0.01
652 191 0.05
653 14 0.00
654 7 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (643 bp):
ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTACATCCAATATTGCTGAGATT
TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGG
GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGACTAAAAACTGAC
CCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACATAGAAAAAAAATAATTCAATGCCAAAAA
TATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTCCGAATTAATTTCTAATTAAA
TCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATTTGGTTC
GATGATTATAGATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAATTGAGCCGGGGCTTCG
GAACGCGTTTTTAACAAAAAAACCGTGATGTTAAGTACACAATTTCGACTAAAAACTGACTCGAA
AATATTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAATATT
GACGAGCTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTA
Found at i:5110 original size:78 final size:78
Alignment explanation
Indices: 5020--5266 Score: 356
Period size: 78 Copynumber: 3.2 Consensus size: 78
5010 TTGTTTAGAT
* *
5020 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTA-ATTAATTAAATATAATATCTTTATAAC
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATA-TAATTAAATCTAATATCCTTATAAC
*
5083 TATTTTATTTTACCA
64 TATTATATTTTACCA
*
5098 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAAGTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
5163 TTATATTTTACCA
66 TTATATTTTACCA
* * * *
5176 TTTTACTATTTTATTCAACTAAAAACTCTATTTTTATATAATTACATCTATTAACCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
5241 TTATATTTTGA-TA
66 TTATATTTT-ACCA
*
5254 TTTTACGATTTTA
1 TTTTACTATTTTA
5267 ATAAAAAAAC
Statistics
Matches: 155, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
78 151 0.97
79 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.50
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACCA
Found at i:5354 original size:23 final size:23
Alignment explanation
Indices: 5325--5368 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5315 AAACTTTTGC
*
5325 AATTGAAAACACTATTTTTATTT
1 AATTGAAAACAATATTTTTATTT
**
5348 AATTGAATTCAATATTTTTAT
1 AATTGAAAACAATATTTTTAT
5369 AATTATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (23 bp):
AATTGAAAACAATATTTTTATTT
Found at i:6172 original size:53 final size:53
Alignment explanation
Indices: 6092--6198 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
6082 TTGTTATCAT
*
6092 TTCACAACAAAATTTCATTTCTTAACTGAATTTTCTTAAGAGAATTTATAAAA
1 TTCACAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
* *
6145 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAATAATTTATAAAA
1 TTCACAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
6198 T
1 T
6199 AAAACAGCCG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (53 bp):
TTCACAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
Found at i:8961 original size:491 final size:495
Alignment explanation
Indices: 8108--9107 Score: 1828
Period size: 491 Copynumber: 2.0 Consensus size: 495
8098 CAGCTTCCGC
* *
8108 CTTTACCTGATGGAATTCCTTTCTGCGTCTCGCTGTGCATTCTCTGCTTCAACTCATAGCTGTTG
1 CTTTGCCTGATGGAATTCCTCTCTGCGTCTCGCTGTGCATTCTCTGCTTCAACTCATAGCTGTTG
* *
8173 GAGTGTCAAAATCATTTTTTCACAGGCACCTCTTGTTTTGGATTCCTCTGCAAGGAAAGCTTCCA
66 GAGTGTCAAAATCATTTCTTCACAGGCACCTCTCGTTTTGGATTCCTCTGCAAGGAAAGCTTCCA
8238 GTTCAGATTCTGACGTGCAGATTCCCAGCAATGGACTCTGTTGCTGCTTCCTTCTCCTTCAGTTC
131 GTTCAGATTCTGACGTGCAGATTCCCAGCAA--GA-----TTGCTGCTTCCTTCTCCTTCAGTTC
8303 AGAATGGTCTTTCTTCAGTCTTCACATACTCTAGCTCACAACTAACTGGCCTCAGACTCCAGAAT
189 AGAATGGTCTTTCTTCAGTCTTCACATACTCTAGCTCACAACTAACTGGCCTCAGACTCCAGAAT
8368 GGTAACTGAAATTTCCCTAGAGAGCTCCCCAACCTTCTCCAAGTTAACCTTCACAGGAGGTTCAG
254 GGTAACTGAAATTTCCCTAGAGAGCTCCCCAACCTTCTCCAAGTTAACCTTCACAGGAGGTTCAG
*
8433 ATCCTTCTGTTTGGTTCAAGGCGCCATTTTTGCTTTCTGATGAACCTTCCTCAACTCTTGTTTTG
319 ATCCTTCTGTTTGGTTCAAGGCGCCACTTTTGCTTTCTGATGAACCTTCCTCAACTCTTGTTTTG
*
8498 CAGCATCAAGTTCAGAGATCATAGTCATGTATTGTTCCCTTGCAATTTCCAAGTCCTGAATTCTG
384 CAGCATCAAGTTCAGAGATCATAGTCATGTATTGTTCCCTTGCAATTTCCAAGTCCTGAATTCTA
8563 GCACCATCAGGTCCAGGGAGAGTACCAGAATTTGCTTCTTCAATCTG
449 GCACCATCAGGTCCAGGGAGAGTACCAGAATTTGCTTCTTCAATCTG
8610 CTTTGCCTGATGGAATTCCTCTCTGCGTCTCGCTGTGCATTCTCTGCTTCAACTCATAGCTGTTG
1 CTTTGCCTGATGGAATTCCTCTCTGCGTCTCGCTGTGCATTCTCTGCTTCAACTCATAGCTGTTG
*
8675 GAGTGTCGAAATCATTTCTTCACAGGCACCTCTCGTTTTGGATTCCTCTGCAAGGAAAGCTTCCA
66 GAGTGTCAAAATCATTTCTTCACAGGCACCTCTCGTTTTGGATTCCTCTGCAAGGAAAGCTTCCA
* *
8740 GTTCAGATTTTGACGTGCAGATTCCCAGC-A-A-T-CTGCTTCCTTCTCCTTTAGTTCAGAATGG
131 GTTCAGATTCTGACGTGCAGATTCCCAGCAAGATTGCTGCTTCCTTCTCCTTCAGTTCAGAATGG
8801 TCTTTCTTCAGTCTTCACATACTCTAGCTCACAACTAACTGGCCTCAGACTCCAGAATGGTAACT
196 TCTTTCTTCAGTCTTCACATACTCTAGCTCACAACTAACTGGCCTCAGACTCCAGAATGGTAACT
8866 GAAATTTCCCTAGAGAGCTCCCCAACCTTCTCCAAGTTAACCTTCACAGGAGGTTCAGATCCTTC
261 GAAATTTCCCTAGAGAGCTCCCCAACCTTCTCCAAGTTAACCTTCACAGGAGGTTCAGATCCTTC
8931 TGTTTGGTTCAAGGCGCCACTTTTGCTTTCTGATGAACCTTCCTCAACTCTTGTTTTGCAGCATC
326 TGTTTGGTTCAAGGCGCCACTTTTGCTTTCTGATGAACCTTCCTCAACTCTTGTTTTGCAGCATC
8996 AAGTTCAGAGATCATAGTCATGTATTGTTCCCTTGCAATTTCCAAGTCCTGAATTCTAGCACCAT
391 AAGTTCAGAGATCATAGTCATGTATTGTTCCCTTGCAATTTCCAAGTCCTGAATTCTAGCACCAT
9061 CAGGTCCAGGGAGAGTACCAGAATTTGCTTCTTCAATCTG
456 CAGGTCCAGGGAGAGTACCAGAATTTGCTTCTTCAATCTG
9101 CTTTGCC
1 CTTTGCC
9108 CGATTCTTGG
Statistics
Matches: 489, Mismatches: 9, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
491 333 0.68
492 1 0.00
498 1 0.00
501 1 0.00
502 153 0.31
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.34
Consensus pattern (495 bp):
CTTTGCCTGATGGAATTCCTCTCTGCGTCTCGCTGTGCATTCTCTGCTTCAACTCATAGCTGTTG
GAGTGTCAAAATCATTTCTTCACAGGCACCTCTCGTTTTGGATTCCTCTGCAAGGAAAGCTTCCA
GTTCAGATTCTGACGTGCAGATTCCCAGCAAGATTGCTGCTTCCTTCTCCTTCAGTTCAGAATGG
TCTTTCTTCAGTCTTCACATACTCTAGCTCACAACTAACTGGCCTCAGACTCCAGAATGGTAACT
GAAATTTCCCTAGAGAGCTCCCCAACCTTCTCCAAGTTAACCTTCACAGGAGGTTCAGATCCTTC
TGTTTGGTTCAAGGCGCCACTTTTGCTTTCTGATGAACCTTCCTCAACTCTTGTTTTGCAGCATC
AAGTTCAGAGATCATAGTCATGTATTGTTCCCTTGCAATTTCCAAGTCCTGAATTCTAGCACCAT
CAGGTCCAGGGAGAGTACCAGAATTTGCTTCTTCAATCTG
Found at i:12099 original size:4 final size:4
Alignment explanation
Indices: 12090--12115 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12080 TATATTCTTG
12090 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
12116 TAACAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:12637 original size:22 final size:21
Alignment explanation
Indices: 12612--12658 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12602 GCAAATTTCC
12612 TCTTATGTCGTCAACCT-TTTTT
1 TCTT-TGT-GTCAACCTCTTTTT
*
12634 TCTTTGTGTGAACCTCTTTTT
1 TCTTTGTGTCAACCTCTTTTT
12655 TCTT
1 TCTT
12659 GTTACAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.11, C:0.21, G:0.11, T:0.57
Consensus pattern (21 bp):
TCTTTGTGTCAACCTCTTTTT
Found at i:13630 original size:2 final size:2
Alignment explanation
Indices: 13619--13677 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
13609 AATCAAACTA
13619 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13660 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Done.