Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019698.1 Corchorus olitorius cultivar O-4 contig19731, 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: 42314
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2015 original size:981 final size:980
Alignment explanation
Indices: 7--2414 Score: 2582
Period size: 981 Copynumber: 2.4 Consensus size: 980
1 ATTGAG
* * * * *
7 AAGCTCGTAAAAACAAATTCTCAAATCCATTGTGGTTGAAATTTTGTTAGATGAATATAGATATT
1 AAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAAATTTGGTTCGATGAATATAGATATT
* * * * * * * *
72 TCAAGGAGTCTTTCTGCTAAAAATCATATAAAACTGAGTCGGGATCCGAAATGCGTTTTTTAGCC
66 TCAAGGAGTCTTTGTGCCAAAAATCATGTAAAATTGAG-CCGGCTCCGGAACGCG-TTTTTAGCC
* * * * *
137 AAAAA-TCGTAATGGTTAGTACATGATTTCCGCT---A----AAAACTAACCCGAAAAGTTGTTC
129 AAAAACT-GTGATGGTTAGTACACGATTTCGGCTAAAATTTGAAAACTGACCCGAAAAGTTTTTC
* * * *
194 TCAATTTTTTG-CAAAATATTCAGAGAAAATATATAATTCAACGTCAAAAAGATTGACA-GACTT
193 TCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACG-CAAAAAAATTGA-AGGGCTT
* ** * *
257 TTCGCTTTTCTAATATCGTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAAAT
256 TTCACACTTCTAATATCG--TT---TTTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAGAT
* * * ** *
322 TCAGATGCTCGTAAAAACAAATCCTTATATACAATGTGGCTGAGATTTGCTTCGATGAATATAGA
316 TCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGA
* * * * *
387 TATTTCAAGGAATCTTTACGCAAAAAATCATGCAAAATTGAATCGGGACTCCGAAATGTGTTTTT
381 TATTTCAAGGAATCTTTACGCAAAAAATCATGCAAAACTGAACCGGGACCCCGAAACGCGTTTTT
* ** * *
452 TGCCAAAAAACCGTGTTAGTACATGATTTCGTTGGCAAAAAAAAAGTATACGATTTCGGCTAAAA
446 AGCCAAAAAACAATGTTAG-A-ATGATTACG-TGGC-----------A-ACGATTTCAGCTAAAA
* * *
517 TTGTGCAAAAACTGACCCGAAAAGTTTTTCCTTAATTTTTTTCCACAATACTCAGAAAAAATATA
496 TTGTGCAAAAACTGACACGAAAAATTTTTCCTCAATTTTTTTCCACAATACTCAGAAAAAATATA
* * * * *
582 TAATTTAACACCAAAAAAATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTTTC
561 TAACTGAACA-CAAAAAAATTGAAGGATTTTTCACGTTTCTAATATCATTTTTCCTTTTTTTTCC
* * *
647 TGAATTTATTTCTAATTAAATCGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCC
625 TGAATTTATTTCTAATTAAATCGAAACAAAGATTGAGACGCTCGTAAAAACAAATCCGTAAATCC
* * * * **
712 ATTGTGGCTAAAATTTTGTTAGAAGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAATCATTT
690 AATGTAGCTAAAATTTGGTTAGAAGAATATAGATATTTCAAGGAGTCTTTCTCCCAAAATCATGC
* ** * * * **
777 AAAACTGAGTCGGGATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACATGATTTCG
755 AAAACTAAACCGGGACCCGAAACGCGTTTTCAGCCAAAAACCGTGAACGTTA-TACATGATTTCG
*** * * * * * **
842 GCTAAAAAGTGATACGAAAATTTTTTTTCTAATTTTTTTACGAAATATTTTGAAAAAATATATAA
819 GCTAAAAACAAACACGAAAATTTCTTTTCTAATCTTATTACCAAATATCATGAAAAAATATATAA
* **
907 TTCAATGCCGAAAAAATTGACAGGCTTTTCACCCATCTAATATCGTTTTTCCATTTGTTTTTGAA
884 TTCAATGCCGAAAAAATTGACAGGCTTTTCACCCATCTAATATCGGTTTTCCATTTGTTTTCAAA
* * ** *
972 TTAATTTCTAATTAAATTAAAATACGATCGAG
949 TTAATTTCTAATTAAATCAAAACAAAATCGAA
* ** * *
1004 ATGCTAATAAAAACAAATCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATT
1 AAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAAATTTGGTTCGATGAATATAGATATT
* *
1069 TCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGCTCTCTGGAACGCGTTTTTAGCC
66 TCAAGGAGTCTTTGTGCCAAAAATCATGTAAAATTGAGCCGGCTC-C-GGAACGCGTTTTTAGCC
*
1134 AAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGCCAAAATTGACCCGAAAAGTTTT
129 AAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTT-G--AAAACTGACCCGAAAAGTTTT
** *
1199 TCCTCAATTTTTTGCCTGAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGT
191 T-CTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACG-CAAAAAAATTGAAGGGC
*
1264 TTTTCACGCTTCTAATATCGTTTTTTTTTCCCAAATTTATTTCTAATTAAATCGAAACAAGATTC
254 TTTTCACACTTCTAATATCGTTTTTTTTT-CCAAATTTATTTCTAATTAAATCGAAACAAGATTC
* *
1329 AGATGTTTGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATA
318 AGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATA
* * ** *
1394 TTTCATGGAGTCTTT-CTGCCTAAAATCATGCAAAACTGAGCCGGGACCCCGAAACGCGTTTTTA
383 TTTCAAGGAATCTTTAC-GCAAAAAATCATGCAAAACTGAACCGGGACCCCGAAACGCGTTTTTA
* * *
1458 G-CAAAAAACAAATG-T-G-ATGGTTAC-T-GC-ACGATTTTAGTTAAAATT-T-CGAAAAACTG
447 GCCAAAAAAC-AATGTTAGAATGATTACGTGGCAACGATTTCAGCTAAAATTGTGC-AAAAACTG
1514 ACACGAAAAATTTTTCCTCAATTTTTTTACCACAATACTCAGAAAAAATATATAACTGAACGA-A
510 ACACGAAAAATTTTTCCTCAATTTTTTT-CCACAATACTCAGAAAAAATATATAACTGAAC-ACA
1578 AAAAAATTGAAGGATTTTTCACGCTTT-TAATATCATTTTTCCATTTTTTTTCCT-AATTTATTT
573 AAAAAATTGAAGGATTTTTCACG-TTTCTAATATCATTTTTCC-TTTTTTTTCCTGAATTTATTT
* * * * *
1641 CTAATTAAATCTAAAC-AAGATTTAGACGCTCGTAAAAACAAATCCGTGAATCTAATGTAGCTGA
636 CTAATTAAATCGAAACAAAGATTGAGACGCTCGTAAAAACAAATCCGTAAATCCAATGTAGCTAA
* * *
1705 GATTTGGTTAGATGAATATAGATATTTCAAGGATTCTTTCTCCCAAAAATCATGCAAAACTAAAC
701 AATTTGGTTAGAAGAATATAGATATTTCAAGGAGTCTTTCTCCC-AAAATCATGCAAAACTAAAC
*
1770 CGGGGCCGCGAAACGCGTTTTCAGCCAAAAACCGT-AACGTT-TACATGATTTCGGCTAAAAACA
765 CGGGACC-CGAAACGCGTTTTCAGCCAAAAACCGTGAACGTTATACATGATTTCGGCTAAAAACA
* * *
1833 AACCCG-AAATTTCTTTTCTCAA-CTTATTGCCACAATACTCAT-AAAAATTATATAATTCAATG
829 AACACGAAAATTTCTTTTCT-AATCTTATTACCA-AATA-TCATGAAAAAATATATAATTCAATG
* * *** *
1895 CC-AAAAGGATTGACGGGCTTTTCGGGCTTCTAATATCGGTTTTCCATTT-TTTTCCAAATTAAT
891 CCGAAAA-AATTGACAGGCTTTTCACCCATCTAATATCGGTTTTCCATTTGTTTT-CAAATTAAT
* **
1958 TTCTAATTAAATCGAAACAAAATTTAA
954 TTCTAATTAAATCAAAACAAAATCGAA
* * *
1985 AAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATTAATATAGATATT
1 AAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAAATTTGGTTCGATGAATATAGATATT
*
2050 TCAAGGAGTCTTTGCGCCAAAAATCATGTAAAATTGAGCCGTGACTCCGGAACGCGTTTTTAGCC
66 TCAAGGAGTCTTTGTGCCAAAAATCATGTAAAATTGAGCCG-G-CTCCGGAACGCGTTTTTAGCC
* * *
2115 AAAAACTGTGTTAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAGAACTGACCTGAAAAGTT
129 AAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA-TTTG---AA-AACTGACCCGAAAAG--
* * * * **
2180 TTTTTTTCAATTTTTTGCCACAATACTTAGAATAAATATATAATTCAACGCTGAAAAATTGAAGG
187 TTTTTCTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCAAAAAAATTGAAGG
* * * ** * *
2245 GGTTTTCACACTTTTAATATC-ATTTTTTTTCTGAATTTATTTCTAATAAAATCAAAACAAGATT
252 GCTTTTCACACTTCTAATATCGTTTTTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAGATT
* ** * * *
2309 CAGATGCTCATAAAAAACAAA-TCTTTAAATCCAATGTGGCTGAGATTTGGTTACATGAGTCTAG
317 CAGATGCTCGT-AAAAACAAATTC-TTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAG
* * * *
2373 ATATTT-AAAGAATTTTGTATGTC-AAAAACCATGCAAAACTGA
380 ATATTTCAAGGAATCTT-TACG-CAAAAAATCATGCAAAACTGA
2415 GTGGAGGCCT
Statistics
Matches: 1193, Mismatches: 175, Indels: 101
0.81 0.12 0.07
Matches are distributed among these distances:
980 26 0.02
981 306 0.26
982 165 0.14
983 167 0.14
984 123 0.10
985 6 0.01
996 5 0.00
997 127 0.11
998 8 0.01
1000 7 0.01
1003 1 0.00
1004 17 0.01
1005 144 0.12
1007 21 0.02
1008 13 0.01
1009 57 0.05
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (980 bp):
AAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAAATTTGGTTCGATGAATATAGATATT
TCAAGGAGTCTTTGTGCCAAAAATCATGTAAAATTGAGCCGGCTCCGGAACGCGTTTTTAGCCAA
AAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTGAAAACTGACCCGAAAAGTTTTTCTCA
ATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCAAAAAAATTGAAGGGCTTTTCAC
ACTTCTAATATCGTTTTTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
GTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTCAAGG
AATCTTTACGCAAAAAATCATGCAAAACTGAACCGGGACCCCGAAACGCGTTTTTAGCCAAAAAA
CAATGTTAGAATGATTACGTGGCAACGATTTCAGCTAAAATTGTGCAAAAACTGACACGAAAAAT
TTTTCCTCAATTTTTTTCCACAATACTCAGAAAAAATATATAACTGAACACAAAAAAATTGAAGG
ATTTTTCACGTTTCTAATATCATTTTTCCTTTTTTTTCCTGAATTTATTTCTAATTAAATCGAAA
CAAAGATTGAGACGCTCGTAAAAACAAATCCGTAAATCCAATGTAGCTAAAATTTGGTTAGAAGA
ATATAGATATTTCAAGGAGTCTTTCTCCCAAAATCATGCAAAACTAAACCGGGACCCGAAACGCG
TTTTCAGCCAAAAACCGTGAACGTTATACATGATTTCGGCTAAAAACAAACACGAAAATTTCTTT
TCTAATCTTATTACCAAATATCATGAAAAAATATATAATTCAATGCCGAAAAAATTGACAGGCTT
TTCACCCATCTAATATCGGTTTTCCATTTGTTTTCAAATTAATTTCTAATTAAATCAAAACAAAA
TCGAA
Found at i:2110 original size:654 final size:648
Alignment explanation
Indices: 531--2626 Score: 2043
Period size: 654 Copynumber: 3.2 Consensus size: 648
521 GCAAAAACTG
* * * * * *
531 ACCCGAAAAGTTTTTCCTTAATTTTTTTCCACAATACTCAGAAAAAATATATAATTTAACACCAA
1 ACCCG-AAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAA
* * * ** *
596 AAAAATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTTTCTGAATTTATTTCTA
65 AAAAATTGAAGGGTTTTTCACGCTTCTAATATCGGTTTTCC-ATTTTTTTCCAAATTAATTTCTA
* * * *
661 ATTAAATCGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTAAAAT
129 ATTAAATCGAAACAAA-ATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGAT
* * * *
726 TTTGTTAGAAGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAATCATTTAAAACTGAGTCGGG
193 TTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAATCATGTAAAACTGAGCCGGG
* * * *
791 A-TCCGAAACGCGTTTTTAGC--CAA-AAATCGTGATGGTTAGTACATGA-TTTCG-------GC
258 ACTCCGAAACGCGTTTTTAGCAAAAACAAAT-GTGATGGTTAGTACACGATTTTAGTAAAATTTC
* * * * * *
844 TAAAAAGTGATACG-AAAATTTTTTTTCTAATTTTTTTACGA-AATATTTTGAAAAAATATATAA
322 GAAAAACTGACACGAAAAATTTTTTTTC-AATTTTTTTACCACAATACTTAGAAAAAATATATAA
* * * * * * *
907 TTCAATGCCGAAAAAATTGACAGGCTTTTCACCCATCTAATATCGTTTTTCCATTTGTTTTT-GA
386 TTCAACG-CAAAAAAATTGA-AGGCTTTTCACACTTTTAATATCATTTTTCCATTT-TTTTTCTA
* * *
971 ATTAATTTCTAATTAAAT-TAAA-ATACGA-TCGAGATGCTAATAAAAACAAATCCTTATATCCA
448 ATTTATTTCTAATTAAATCTAAACA-A-GATTC-AGATGCTCATAAAAACAAATCC-TAAATCCA
* * * * * *
1033 ATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGC
509 ATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGATTCTTTATGCCAAAAATCATGC
* * *
1098 AAAATTGAGCC--GGCTCTCTGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATT
574 AAAACT-AACCGGGGC-CTC-GGAACGCGTTTTTAGCCAAAAACAGTGATGGTTA-TACACGATT
*
1161 TCGGCTAAAATTTGGCCAAAA
635 TCGGCTAAAA-------ACAA
* * **
1182 TTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCTGAATACTCAGAAAAAATATATAATTCAACGC
1 ---ACCCG-AAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC
* *
1247 CAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATC-G-TTT---TTTTTTCCCAAATTTATTTC
62 CAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGGTTTTCCATTTTTTTCCAAATTAATTTC
* * *
1307 TAATTAAATCGAAACAAGATTCAGATGTTTGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGA
127 TAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGA
* * *
1372 TTTAATTAGATGAATATAGATATTTCATGGAGTCTTTCTGCCTAAAATCATGCAAAACTGAGCCG
192 TTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCC-AAAATCATGTAAAACTGAGCCG
* * *
1437 GGACCCCGAAACGCGTTTTTAGCAAAAAACAAATGTGATGGTTACTGCACGATTTTAGTTAAAAT
256 GGACTCCGAAACGCGTTTTTAGC-AAAAACAAATGTGATGGTTAGTACACGATTTTAG-TAAAAT
** *
1502 TTCGAAAAACTGACACGAAAAATTTTTCCTCAATTTTTTTACCACAATACTCAGAAAAAATATAT
319 TTCGAAAAACTGACACGAAAAATTTTTTTTCAATTTTTTTACCACAATACTTAGAAAAAATATAT
* * * * *
1567 AACTGAACGAAAAAAAATTGAAGGATTTTTCACGCTTTTAATATCATTTTTCCATTTTTTTTCCT
384 AATTCAACGCAAAAAAATTGAAGG-CTTTTCACACTTTTAATATCATTTTTCCATTTTTTTT-CT
* * * * *
1632 AATTTATTTCTAATTAAATCTAAACAAGATTTAGACGCTCGTAAAAACAAATCCGTGAATCTAAT
447 AATTTATTTCTAATTAAATCTAAACAAGATTCAGATGCTCATAAAAACAAATCC-TAAATCCAAT
* * *
1697 GTAGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGATTCTTTCTCCCAAAAATCATGCAA
511 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGATTCTTTATGCCAAAAATCATGCAA
* * * * ** *
1762 AACTAAACCGGGGCCGCGAAACGCGTTTTCAGCCAAAAACCGT-AACGTT-TACATGATTTCGGC
576 AACT-AACCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTATACACGATTTCGGC
1825 TAAAAACAA
640 TAAAAACAA
* * * * *
1834 ACCCGAAATTTCTTTTCTCAACTTATTGCCACAATACTCATAAAAATTATATAATTCAATGCCAA
1 ACCCGAAATTT-TTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAA
** * * **
1899 AAGGATTGACGGGCTTTTCGGGCTTCTAATATCGGTTTTCCATTTTTTTCCAAATTAATTTCTAA
65 AAAAATTGAAGGGTTTTTCACGCTTCTAATATCGGTTTTCCATTTTTTTCCAAATTAATTTCTAA
* * * *
1964 TTAAATCGAAACAAAATTTAAAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
130 TTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTT
* * * * *
2029 GGTTCGATTAATATAGATATTTCAAGGAGTCTTTGC-GCCAAAAATCATGTAAAATTGAGCCGTG
195 AGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCC-AAAATCATGTAAAACTGAGCCGGG
* * * **
2093 ACTCCGGAACGCGTTTTTAGCCAAAAAC---TGTGTTAGTTAGTACACGATTTCGGCTAAAATTT
258 ACTCCGAAACGCGTTTTTAG-CAAAAACAAATGTGATGGTTAGTACACGATTTTAG-TAAAATTT
* * * *
2155 TGTAAAAGAACTGAC-CTGAAAAGTTTTTTTTTCAA-TTTTTTGCCACAATACTTAGAATAAATA
321 CG--AAA-AACTGACAC-GAAAA-ATTTTTTTTCAATTTTTTTACCACAATACTTAGAAAAAATA
** *
2218 TATAATTCAACGCTGAAAAATTGAAGGGGTTTTCACACTTTT-A-AT-A----T-CATTTTTTTT
381 TATAATTCAACGCAAAAAAATTGAA-GGCTTTTCACACTTTTAATATCATTTTTCCATTTTTTTT
* * *
2275 CTGAATTTATTTCTAATAAAATCAAAACAAGATTCAGATGCTCATAAAAAACAAATCTTTAAATC
445 CT-AATTTATTTCTAATTAAATCTAAACAAGATTCAGATGCTCAT-AAAAACAAATC-CTAAATC
* * * * * * *
2340 CAATGTGGCTGAGATTTGGTTACATGAGTCTAGATATTTAAAGAATT-TTGTATGTCAAAAACCA
507 CAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGATTCTT-TATGCCAAAAATCA
* ** * * *
2404 TGCAAAACTGAGTGGAGGCCTCGGAACACGTTTTTAGCTAAAAATAGTGATGGTTAATACACGAT
571 TGCAAAACTAACCGG-GGCCTCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTT-ATACACGAT
**
2469 TTCGGCTAAAAACTG
634 TTCGGCTAAAAACAA
** * * * *
2484 ACACAAAATTATTTTTTTTTCAATTTTTTGGCACAATAAT-A-AAAAAA-AAATAATTCAACGCC
1 AC-CCGAA--ATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC
* * **
2546 AAAAATATTGAAGGG-TTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCTGAATTAATTTC
63 AAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGGTTTTCCATTT-TTTTCCAAATTAATTTC
2610 TAATTAAATCGAAACAA
127 TAATTAAATCGAAACAA
2627 CACGATTTCG
Statistics
Matches: 1204, Mismatches: 187, Indels: 107
0.80 0.12 0.07
Matches are distributed among these distances:
645 2 0.00
646 52 0.04
647 180 0.15
648 93 0.08
649 152 0.13
650 28 0.02
651 36 0.03
652 46 0.04
653 17 0.01
654 316 0.26
655 13 0.01
659 18 0.01
660 8 0.01
661 65 0.05
662 166 0.14
663 8 0.01
664 4 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (648 bp):
ACCCGAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAA
AAAATTGAAGGGTTTTTCACGCTTCTAATATCGGTTTTCCATTTTTTTCCAAATTAATTTCTAAT
TAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTA
GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAATCATGTAAAACTGAGCCGGGACT
CCGAAACGCGTTTTTAGCAAAAACAAATGTGATGGTTAGTACACGATTTTAGTAAAATTTCGAAA
AACTGACACGAAAAATTTTTTTTCAATTTTTTTACCACAATACTTAGAAAAAATATATAATTCAA
CGCAAAAAAATTGAAGGCTTTTCACACTTTTAATATCATTTTTCCATTTTTTTTCTAATTTATTT
CTAATTAAATCTAAACAAGATTCAGATGCTCATAAAAACAAATCCTAAATCCAATGTGGCTGAGA
TTTGGTTAGATGAATATAGATATTTCAAGGATTCTTTATGCCAAAAATCATGCAAAACTAACCGG
GGCCTCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTATACACGATTTCGGCTAAAAACAA
Found at i:4701 original size:341 final size:342
Alignment explanation
Indices: 4073--4753 Score: 1134
Period size: 341 Copynumber: 2.0 Consensus size: 342
4063 TATTCACCTA
* * *
4073 TTGTTTACTCATCAATTCCTAAAACATGAAGTGAGACCAGGAAAAACTAATCAAACAACAGTAAA
1 TTGTTTACACAACAATTCCTAAAACATGAAGTGAAACCAGGAAAAACTAATCAAACAACAGTAAA
* *
4138 TACTAAATTGAAAACTATATCTCACTTTTCATTGATTGTTGTATAAATTGCAGATAAATTATCGG
66 TACTAAATTGAAAACTACATCTCACTTTTCATTGATTGTTGCATAAATTGCAGATAAATTATCGG
*
4203 TTGCTGCCTTTATAAGCAAAAGCAACCGATGTACATAACTCTAGGCTTCATTCTTCATAGAGTGA
131 TTGCAGCC-TTAT-A--AAAAGCAACCGATGTACATAACTCTAGGCTTCATTCTTCATAGAGTGA
*
4268 AGGCTTACCTGAAGTCCATGTTGAGGCTTAAGCATAAGAAAAGGATTTGGGGCGTGGATGTAGGT
192 AGGATTACCTGAAGTCCATGTTGAGGCTTAAGCATAAGAAAAGGATTTGGGGCGTGGATGTAGGT
* *
4333 TGGGAAGAGGGAAATGATGTAGCGTTGTAGAATCATTGAGAGGGCAATCTTTATTTGTGTCAATA
257 TGGGAAGAGGGAAATGATGTAGCGTTGTAGAATCATTGAGAGGGCAATCTTCATTTCTGTCAATA
4398 CAAAGCTCATTCCTAAATTTG
322 CAAAGCTCATTCCTAAATTTG
4419 TTGTTTACACAACAAATT-CTAAAACATGAAGTGAAACCAGGAAAAACTAATCAAAACAACAGTA
1 TTGTTTACACAAC-AATTCCTAAAACATGAAGTGAAACCAGGAAAAACTAATC-AAACAACAGTA
* *
4483 AATACTAAATTGAAAAGTACATCTCACTTTTCATTGATTGTTGCATAAATTGCAGATAAATTATT
64 AATACTAAATTGAAAACTACATCTCACTTTTCATTGATTGTTGCATAAATTGCAGATAAATTATC
* * *
4548 GGTTGCAGCC-TAT-ATAAGCAACTGATGTACGTAACTCTAGGCTTCATTCTTCATAGAGTGAAG
129 GGTTGCAGCCTTATAAAAAGCAACCGATGTACATAACTCTAGGCTTCATTCTTCATAGAGTGAAG
*
4611 GATTACCTGAAGTCCATGTTGAGGCTTAAGCATAAGAGAAGGATTTGGGGCGTGGATGTAGGTTG
194 GATTACCTGAAGTCCATGTTGAGGCTTAAGCATAAGAAAAGGATTTGGGGCGTGGATGTAGGTTG
* *
4676 GGGAGAGGGAAATGGTGTAGCGTTGTAGAATCATTGAGAGGGCAATCTTCATTTCTGTCAATACA
259 GGAAGAGGGAAATGATGTAGCGTTGTAGAATCATTGAGAGGGCAATCTTCATTTCTGTCAATACA
4741 AAGCTCATTCCTA
324 AAGCTCATTCCTA
4754 CACAAGATCG
Statistics
Matches: 316, Mismatches: 17, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
341 184 0.58
345 3 0.01
346 44 0.14
347 85 0.27
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (342 bp):
TTGTTTACACAACAATTCCTAAAACATGAAGTGAAACCAGGAAAAACTAATCAAACAACAGTAAA
TACTAAATTGAAAACTACATCTCACTTTTCATTGATTGTTGCATAAATTGCAGATAAATTATCGG
TTGCAGCCTTATAAAAAGCAACCGATGTACATAACTCTAGGCTTCATTCTTCATAGAGTGAAGGA
TTACCTGAAGTCCATGTTGAGGCTTAAGCATAAGAAAAGGATTTGGGGCGTGGATGTAGGTTGGG
AAGAGGGAAATGATGTAGCGTTGTAGAATCATTGAGAGGGCAATCTTCATTTCTGTCAATACAAA
GCTCATTCCTAAATTTG
Found at i:7291 original size:31 final size:31
Alignment explanation
Indices: 7251--7382 Score: 183
Period size: 31 Copynumber: 4.3 Consensus size: 31
7241 GCACGAGGCA
7251 TGCCACATGTCACTTTTTGGTACACATGGCG
1 TGCCACATGTCACTTTTTGGTACACATGGCG
** *
7282 TGATACATGTCACTTTTTGGTACACGTGGCG
1 TGCCACATGTCACTTTTTGGTACACATGGCG
* * * *
7313 TGCCACGTGTCGCTTTTTGGTACACGTGGCT
1 TGCCACATGTCACTTTTTGGTACACATGGCG
* *
7344 TGCCACATGTCGCTTTTTGGTACACATGGCA
1 TGCCACATGTCACTTTTTGGTACACATGGCG
7375 TGCCACAT
1 TGCCACAT
7383 CAGACACCGT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (31 bp):
TGCCACATGTCACTTTTTGGTACACATGGCG
Found at i:9542 original size:44 final size:44
Alignment explanation
Indices: 9479--9573 Score: 172
Period size: 44 Copynumber: 2.2 Consensus size: 44
9469 ACAGAGCCAA
9479 ATCTAATAAACTCTACAATCATATTATGGAATTCACATAATGAC
1 ATCTAATAAACTCTACAATCATATTATGGAATTCACATAATGAC
*
9523 ATCTAATAAATTCTACAATCATATTATGGAATTCACATAATGAC
1 ATCTAATAAACTCTACAATCATATTATGGAATTCACATAATGAC
*
9567 ATGTAAT
1 ATCTAAT
9574 TCAAGCACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (44 bp):
ATCTAATAAACTCTACAATCATATTATGGAATTCACATAATGAC
Found at i:11643 original size:8 final size:8
Alignment explanation
Indices: 11630--11672 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
11620 ATCACGAACG
11630 CAAAAATT
1 CAAAAATT
11638 CAAAAATT
1 CAAAAATT
**
11646 C-AAAACG
1 CAAAAATT
11653 CAAAAATT
1 CAAAAATT
11661 CAAAAATT
1 CAAAAATT
11669 CAAA
1 CAAA
11673 TTGAGAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 5 0.17
8 25 0.83
ACGTcount: A:0.63, C:0.16, G:0.02, T:0.19
Consensus pattern (8 bp):
CAAAAATT
Found at i:11650 original size:15 final size:16
Alignment explanation
Indices: 11630--11672 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
11620 ATCACGAACG
11630 CAAAAATTCAAAAATT
1 CAAAAATTCAAAAATT
**
11646 C-AAAACGCAAAAATT
1 CAAAAATTCAAAAATT
11661 CAAAAATTCAAA
1 CAAAAATTCAAA
11673 TTGAGAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.63, C:0.16, G:0.02, T:0.19
Consensus pattern (16 bp):
CAAAAATTCAAAAATT
Found at i:11652 original size:23 final size:23
Alignment explanation
Indices: 11626--11672 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
11616 TAAAATCACG
11626 AACGCAAAAATTCAAAAATTCAA
1 AACGCAAAAATTCAAAAATTCAA
11649 AACGCAAAAATTCAAAAATTCAA
1 AACGCAAAAATTCAAAAATTCAA
11672 A
1 A
11673 TTGAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.62, C:0.17, G:0.04, T:0.17
Consensus pattern (23 bp):
AACGCAAAAATTCAAAAATTCAA
Found at i:12935 original size:336 final size:327
Alignment explanation
Indices: 12184--15381 Score: 2870
Period size: 336 Copynumber: 9.6 Consensus size: 327
12174 ATACTTTACA
* * * * *
12184 TCATCTAACCAAATCTCAGCAACATTGGATTTAAGAATTTGCTTTTACGAGCATATGAATCTTGT
1 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
* * * * * * *
12249 TTCGATTTAATTAAAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGAGTAAAAAGCCC
65 TTCGATTTAATTAGAAATTAA-TTCGGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG-CC
12314 TCCAATCTTTTTGGCGTTGAA-T-TATATATTTTTATGAGTATTTTAGCCAAAAATTGA--AAAA
128 -CCAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * * * *
12375 TTATCTTTCAGGTTAATTTTTACAAAATTTT-GCCGAAATCGTGTAATATAACCATCACAGTTTT
192 --A-CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-A-CTAACCATCACGGTTTT
** * * *
12439 TGGCTAAAAAAACG-TTCTAGGGCCCCGGCTCAGGTTTGCATGATTTTTGACGCCAAGACTCCTT
252 TGGCTAAAAACGCGTTTC-AGGGCCCCAGCTCAGTTTTGCATGATTTTTG-CGCCGAGACTCCTT
*
12503 -AAGATATCCATAT
315 GAA-ATATCTATAT
* **
12516 TCATCGAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
*
12581 TTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTCCC
65 TTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG-CCC
* *
12646 CAAATCTTTTTGGCGTTAAATTATATATATATTTTATGAGTATTTTATCCAAAAATTG-GGAAAA
129 C-AATCTTTTTGGCGTTGAATTATATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * * * * *
12710 AATTT-AGGTTATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCCATCACACGATTTTTT
192 ACTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CCAT--CACG----GTT
** ** * *
12774 TTTGGCTAAAAACATGTTTCAGGGCCCCAGCTCAGTTTTGCATGGCTTTTGCACCGACACTCCTT
250 TTTGGCTAAAAACGCGTTTCAGGGCCCCAGCTCAGTTTTGCATGATTTTTGCGCCGAGACTCCTT
12839 GAAATATCTATAT
315 GAAATATCTATAT
* * * * * * * *
12852 TCATATAACAAAATCTTAGCCACATTGCATTTAAGGGTATGTTTTTACGAGCATGTAAATCTTGT
1 TCATCTAAC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
* * * * *
12917 TTCAATTTAATTAGAAATTAATTTAGAAAAAATATGAAAATCGATATTAAAAACGTGAAAAGCAC
65 TTCGATTTAATTAGAAATTAA-TTCGGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGC-C
* * * * * *
12982 TTCAATCTTTTTGGCATTGAAATATATAT-TTTTTATGAGTATTATGGCTAAAAATTGAGGAAAT
128 -CCAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-
* * * * *
13046 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATTAGGGTTTTTGGC
191 AACTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC
* * *** * ** * *
13111 TAAAAACGCG-TTCCGGGACTTGGTTCAACTTTGAATGATTTTTGACGACGAGACTCCTTGAAAT
256 TAAAAACGCGTTTCAGGGCCCCAGCTCAGTTTTGCATGATTTTTG-CGCCGAGACTCCTTGAAAT
13175 ATCTATAT
320 ATCTATAT
* * *
13183 TCATCTAACCAAATCCCAG-C-C-------------A-TTGTTTTTACAAACATCTGAATCATGT
1 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
* * * * * *
13232 TTCGTTTTAATTAGAACTTAATTCGGAAAAAGTAGGGAAAACAATATTAGAAGCGTGAAAAGTCC
65 TTCGATTTAATTAGAAATTAATTCGGAAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAG-CC
* * * * **
13297 TTCAATCTTTTTAGTGTTGAATTATATAT-TTTTTATGAGTATTGT-GTTTAAAAATTGAGGAAT
128 -CCAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTTAG-CCAAAAATTGAGGAA-
** ** ** * *
13360 AATTTTTTTGGTCTTTTTTTTTTTGCAAAATTTTAGCTGAAATCATGTACTAACCATCACGGTTT
190 AAACTTTCGGGTC----AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG---
* * * *
13425 TTTGTTGTTGCTAAAAACGCGTTTCGGGGCCCCAGCTCAATTTTGCATGATTTTTGGCGTCGAAA
248 TTT-TTG--GCTAAAAACGCGTTTCAGGGCCCCAGCTCAGTTTTGCATGATTTTT-GCGCCGAGA
*
13490 CTCCTTGTAATATCTATAT
309 CTCCTTGAAATATCTATAT
* * * * *
13509 TCATCTAATGAAGTCTCAGCCATATTGCATTTAAGGATTTTTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
* * * *
13574 TTCGATTTAATTAGAAATTAATTCAGAAAGATATGAAAAACGATATTAAAAGCGTAAAAAGTACT
65 TTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG--CC
* * * * * *
13639 CAAATCTTTTTTGAGTTGAATTATATATA-TTTTATAAGTATTTTAGACAAAATTTGA-GAAAAA
128 CCAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
* * * * * *
13702 TATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACGTTAGTCGAAATCACGGTCTT
193 -CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TA-AC--CATCACGGTTTT
* * * * * *
13767 TGGCTAAAAAGGCG-TTCATGGG-CCCAGGTTCAATGTGGCATGATTTTTTGCGCCTAGACTCCT
252 TGGCTAAAAACGCGTTTCA-GGGCCCCA-GCTCAGTTTTGCATGA-TTTTTGCGCCGAGACTCCT
13830 TGAAATATCTATAT
314 TGAAATATCTATAT
* * * *** *
13844 TCATCTAACCAAATTTCAGTCAAATTGGATTTAAGGATTTG-TAAAACAAGCATCTGAATCATGT
1 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
** * * *
13908 TTCGATTTAATTAGAAATTAATTCAATAAATAATAGGAAAAACGATATTAGAAGCATGAAAAGCC
65 TTCGATTTAATTAGAAATTAATTC-GGAAA-AATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* * * *
13973 CTTCAGTCTTTTTGGCGTTGAATTATATA-ATTTTTATGAGTATTGTGGCTAAAAATTGAGGAAA
128 C--CAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * * * * *
14037 TAACTTTCGAGTCGATTTTTGAAAAATTCTAGCCGATCGAAATCGTGTAATAATCATCACGGTTT
191 -AACTTTCGGGTCAATTTTTGCAAAATTTTAG-C---CGAAATCGTGTACTAACCATCACGG-TT
* * * * * *
14102 TTTGGCTAAAAATGCG-TTCTGGGCCCCGGCTAAGTTTTGCATGATTTTTGACGTC-A-ATTCTC
250 TTTGGCTAAAAACGCGTTTCAGGGCCCCAGCTCAGTTTTGCATGATTTTTG-CGCCGAGACTC-C
* *
14164 TTCGAGATATCCATAT
313 TT-GAAATATCTATAT
* ** * *
14180 TCATTTAATCAAATCTCAGTTAAATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
* *
14245 TTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCT
65 TTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCC-
* * *
14310 CCATTTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTTTAGTCAAAAATTGACGGAATAA
129 CAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGA-GGAA-AA
** * * *
14374 TTTTTCGGGTCATTTTTTGCAAAA-TTTAACCGAAATCGTGTACTAACCATCACGGTTTTCGGCT
192 ACTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCT
* * * *
14438 AAAAACGCGTTTCGGGGCCCCATCTTAGTTTTACATGATTTTTGGCGCCGAGACTCCTTGAAATA
257 AAAAACGCGTTTCAGGGCCCCAGCTCAGTTTTGCATGATTTTT-GCGCCGAGACTCCTTGAAATA
*
14503 TTTATAT
321 TCTATAT
** * * *
14510 TCATCTAATCAAATCTCAGCCACAACGAATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGT
1 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
* ** *
14575 TTCGATTTAGTTAGAAATTAATTCACAAAAA-ATGAAAAACGATACTAAAAGCGTGAAAAAGGCT
65 TTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAAAAGCGTG-AAAA-GC-
** * * * * ** * *
14639 TTCAATTTTTTTGGCATTGAATTATA-GT-TTTTTATGAGTATTTTCGTTATAAATCGAGGAAAA
127 CCCAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* *** *
14702 ATCTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTGTTCATCACGGTTTTCGGC
192 A-CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC
* * * * * * *
14767 TAAAAATGCGTTAT-GGGGCCCGA-CTCAGTTTTGCATGATTTATGATG--TA-A-TCCATGAAA
256 TAAAAACGCGTT-TCAGGGCCCCAGCTCAGTTTTGCATGATTTTTG-CGCCGAGACTCCTTGAAA
14826 TATCTATAT
319 TATCTATAT
* * * * * * *
14835 TCATCTAACCAAATCTCAGACACATTAGATTTAACGATTTATTTTTACGAGCATTTGAATCATGT
1 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
* * * * *
14900 TTCGATTTAATTAGAAATTAATTTGGAAAAAAATTGGAAAAACAATATTAGAAGCGTTAAAAGCC
65 TTCGATTTAATTAGAAATTAATTCGGAAAAATA-T-GAAAAACGATATTAAAAGCGTGAAAAGCC
* *
14965 CTTCAATCTTTTTGGTGTCGAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
128 C--CAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * *
15030 TATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACAGTTTTTGG
191 -AACTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
* * * * * *
15095 CTAAAAACGCGCTCCAGGACCACAACTCTA-TTTTGCATGATTTTTGGCGTCGAGACTCCTTGAA
255 CTAAAAACGCGTTTCAGGGCCCCAGCTC-AGTTTTGCATGATTTTT-GCGCCGAGACTCCTTGAA
* *
15159 ATATATTTAT
318 ATATCTATAT
* *** *
15169 TCATCTAATCAAATCTCATG-CACATTGGATTTAAGAATTTGTTTTTATGTGCATCTGAAAACTT
1 TCATCTAA-CAAATCTCA-GCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTG-AATCTT
* * *
15233 TTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT
63 GTTTCGATTTAATTAGAAATTAA-TTCGGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG-
* * *
15298 CCTCCAATCCTTTTGGTGTTGAATTATATATA--TTTATGAGTAGTTTT-GCCAAAAAAATGAGG
126 CC-CCAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTA-TTTTAGCC-AAAAATTGAGG
*
15360 AAAAATCTTTCGGATC-ATTTTT
188 AAAAA-CTTTCGGGTCAATTTTT
15382 ACCATCATGG
Statistics
Matches: 2349, Mismatches: 392, Indels: 250
0.79 0.13 0.08
Matches are distributed among these distances:
314 9 0.00
315 127 0.05
316 2 0.00
319 37 0.02
322 3 0.00
323 3 0.00
325 109 0.05
326 68 0.03
327 28 0.01
328 22 0.01
329 184 0.08
330 278 0.12
331 163 0.07
332 119 0.05
333 39 0.02
334 244 0.10
335 215 0.09
336 289 0.12
337 204 0.09
338 47 0.02
339 5 0.00
340 11 0.00
341 90 0.04
342 53 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (327 bp):
TCATCTAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTT
TCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCCA
ATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAACTT
TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
ACGCGTTTCAGGGCCCCAGCTCAGTTTTGCATGATTTTTGCGCCGAGACTCCTTGAAATATCTAT
AT
Found at i:14512 original size:330 final size:329
Alignment explanation
Indices: 13205--15381 Score: 2170
Period size: 330 Copynumber: 6.5 Consensus size: 329
13195 ATCCCAGCCA
* * * * * * *
13205 TTGTTTTTACAAACATCTGAATCATGTTTCGTTTTAATTAGAACTTAATTCGGAAAAAGTAGGGA
1 TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAA-TATGAA
* * * * * *
13270 AAACAATATTAGAAGCGTGAAAAGTCCTTCAATCTTTTTAGTGTTGAATTATATATTTTTTATGA
65 AAACGATATTAAAAGCGTGAAAAG-CCCTCAATCTTTTTGGCGTTGAATTATATATATTTTATGA
* * * * ** ** *
13335 GTATTGTGTTTAAAAATTGAGGAATAATTTTTTTGGTCTTTTTTTTTTTGCAAAATTTTAGCTGA
129 GTATTTTG-TCAAAAATTGAGGAAAAATCTTTCGGGTC----AATTTTTGCAAAATTTTAGCCGA
* * *
13400 AATCATGTACTAACCATCACGGTTTTTTGTTGTTGCTAAAAACGCGTTTCGGGGCCCCAGCTCAA
189 AATCGTGTACTAACCATCACGG---TTT-TTG--GCTAAAAACGCGTTTCGGGGCCCCAGCTTAG
* * * * *
13465 TTTTGCATGATTTTTGGCGTCGAAACTCCTTGTAATATCTATATTCATCTAATGAAGTCTCAGCC
248 TTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGTC
* *
13530 ATATTGCATTTAAGGAT
313 AAATTGGATTTAAGGAT
* *
13547 TTTTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAGATATGAAA
1 TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
* ** * * *
13612 AACGATATTAAAAGCGTAAAAAGTACTCAAATCTTTTTTGAGTTGAATTATATATATTTTATAAG
66 AACGATATTAAAAGCGTGAAAAGCCCTC-AATCTTTTTGGCGTTGAATTATATATATTTTATGAG
* * * * *
13677 TATTTTAGACAAAATTTGA-GAAAAATATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAATCG
130 TATTTT-GTCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
* * * * * * * * *
13741 TGTACGTTAGTCGAAATCACGGTCTTTGGCTAAAAAGGCG-TTCATGGG-CCCAGGTTCAATGTG
194 TGTAC--TA-AC--CATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGGCCCCAGCTT-AGTTTT
* * * * *
13804 GCATGATTTTTTGCGCCTAGACTCCTTGAAATATCTATATTCATCTAACCAAATTTCAGTCAAAT
252 GCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGTCAAAT
13869 TGGATTTAAGGAT
317 TGGATTTAAGGAT
*** * * *
13882 TTG-TAAAACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAATAAATAATAGGA
1 TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAA-AATATGA
* * *
13946 AAAACGATATTAGAAGCATGAAAAGCCCTTCAGTCTTTTTGGCGTTGAATTATATA-ATTTTTAT
64 AAAACGATATTAAAAGCGTGAAAAGCCC-TCAATCTTTTTGGCGTTGAATTATATATA-TTTTAT
* * * * * *
14010 GAGTATTGTGGCTAAAAATTGAGGAAATAA-CTTTCGAGTCGATTTTTGAAAAATTCTAGCCGAT
127 GAGTATTTTGTC-AAAAATTGAGGAAA-AATCTTTCGGGTCAATTTTTGCAAAATTTTAG-C---
* * * * * *
14074 CGAAATCGTGTAATAATCATCACGGTTTTTTGGCTAAAAATGCG-TTCTGGGCCCCGGCTAAGTT
186 CGAAATCGTGTACTAACCATCACGG-TTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCTTAGTT
* * * * * *
14138 TTGCATGATTTTTGACGTC-A-ATTCTCTTCGAGATATCCATATTCATTTAATCAAATCTCAGTT
250 TTGCATGATTTTTGGCGTCGAGACTC-CTT-GAAATATCTATATTCATCTAATCAAATCTCAGTC
*
14201 AAATTGGATTTAAGAAT
313 AAATTGGATTTAAGGAT
*
14218 TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAA
1 TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
* *
14283 AACGATATTAAAAGCGTGAAAAGCCCTCCATTTTTTTGGCGTTGAATTATATATATTTTATGAGT
66 AACGATATTAAAAGCGTGAAAAGCCCTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGT
* * * *
14348 ATTTTAGTCAAAAATTGACGGAATAATTTTTCGGGTCATTTTTTGCAAAA-TTTAACCGAAATCG
131 ATTTT-GTCAAAAATTGA-GGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
* * *
14412 TGTACTAACCATCACGGTTTTCGGCTAAAAACGCGTTTCGGGGCCCCATCTTAGTTTTACATGAT
194 TGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGAT
* * * * *
14477 TTTTGGCGCCGAGACTCCTTGAAATATTTATATTCATCTAATCAAATCTCAGCCACAA-CGAATT
259 TTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGTCA-AATTGGATT
14541 TAAGGAT
323 TAAGGAT
* * * *
14548 TTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAGTTAGAAATTAATTCACAAAAA-ATGAAA
1 TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
* ** * *
14612 AACGATACTAAAAGCGTGAAAAAGGCTTTCAATTTTTTTGGCATTGAATTATAGT-T-TTTTATG
66 AACGATATTAAAAGCGTG-AAAA-GCCCTCAATCTTTTTGGCGTTGAATTATA-TATATTTTATG
* * * *
14675 AGTATTTTCGTTATAAATCGAGGAAAAATCTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAAT
128 AGTATTTT-GTCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
*** * * * *
14740 CGTGTACTGTTCATCACGGTTTTCGGCTAAAAATGCGTTAT-GGGGCCCGA-CTCAGTTTTGCAT
192 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTT-TCGGGGCCCCAGCTTAGTTTTGCAT
* ** * * * * *
14803 GATTTATGATGT--A-A-TCCATGAAATATCTATATTCATCTAACCAAATCTCAGACACATTAGA
256 GATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGTCAAATTGGA
*
14864 TTTAACGAT
321 TTTAAGGAT
* * * * ** *
14873 TTATTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATTGGA
1 TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATA-T-GA
* * * * *
14938 AAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGGTGTCGAATTATATATATTTTTAT
64 AAAACGATATTAAAAGCGTGAAAAGCCC-TCAATCTTTTTGGCGTTGAATTATATATA-TTTTAT
* *
15003 GAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA
127 GAGTATTTT-GTCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA
* * * * * * * *
15068 TCGTGTACTAATCATCACAGTTTTTGGCTAAAAACGCGCTCCAGGACCACAACTCTA-TTTTGCA
191 TCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCT-TAGTTTTGCA
* * *
15132 TGATTTTTGGCGTCGAGACTCCTTGAAATATATTTATTCATCTAATCAAATCTCA-TGCACATTG
255 TGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGT-CAAATTG
*
15196 GATTTAAGAAT
319 GATTTAAGGAT
*** * * *
15207 TTGTTTTTATGTGCATCTGAAAACTTTTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGA
1 TTGTTTTTACAAGCATCTG-AATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGA
* * *
15272 AAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGGTGTTGAATTATATATA-TTTATG
64 AAAACGATATTAAAAGCGTGAAAAGCCCT-CAATCTTTTTGGCGTTGAATTATATATATTTTATG
* * *
15336 AGTAGTTTTGCCAAAAAAATGAGGAAAAATCTTTCGGATC-ATTTTT
128 AGTA-TTTTGTC-AAAAATTGAGGAAAAATCTTTCGGGTCAATTTTT
15382 ACCATCATGG
Statistics
Matches: 1526, Mismatches: 250, Indels: 128
0.80 0.13 0.07
Matches are distributed among these distances:
324 1 0.00
325 95 0.06
326 5 0.00
327 28 0.02
328 18 0.01
329 188 0.12
330 248 0.16
331 34 0.02
332 24 0.02
333 31 0.02
334 221 0.14
335 185 0.12
336 184 0.12
337 97 0.06
338 7 0.00
339 3 0.00
340 16 0.01
341 89 0.06
342 52 0.03
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (329 bp):
TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
AACGATATTAAAAGCGTGAAAAGCCCTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGT
ATTTTGTCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
TACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTT
TTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGTCAAATTGGATTTAA
GGAT
Found at i:20453 original size:16 final size:16
Alignment explanation
Indices: 20432--20462 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20422 TGACATGTCA
*
20432 ACAAAGCTAGGTGCTC
1 ACAAAGCAAGGTGCTC
20448 ACAAAGCAAGGTGCT
1 ACAAAGCAAGGTGCT
20463 TGCTTTACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (16 bp):
ACAAAGCAAGGTGCTC
Found at i:22055 original size:669 final size:672
Alignment explanation
Indices: 20813--22082 Score: 1558
Period size: 669 Copynumber: 1.9 Consensus size: 672
20803 TATTTCAAGG
**
20813 AGTCTCAGCGCCAAAAATCATGCAAAACTAAGTTGGAGCCACGAAACACGTTTTTAGCCAAAAAC
1 AGTCTCAGCGCCAAAAATCATGCAAAACTAAGCCGGAGCCACGAAACACGTTTTTAGCCAAAAAC
* *
20878 CGTGATGATTAATACACGATTTTGGCTAAAATCCCGCAAAAAATGACCAAATAAATTTTACCTTA
66 CGTGATGATTAATACACGATTTCGGCTAAAATCCCGCAAAAAATGACCAAAT-AATTTTACCTCA
* * * * * * *
20943 ATTTTTGGCTAAAATACTTTTAAAATATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCA
130 ATTTTTAGCCAAAATACTTATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTCTCA
* * * * * *
21008 TGTTTTTAATATCGTTTTTCATATTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
195 CGCTTCTAATATCGTTTTTCATATTTTTATAAATTAATTTATAATTAAATCGAAACAAGATTCAA
* *
21073 ATGCTTGTAAAAAATAATTCTTAAATTCAATGTGGCTGAGATTTGATCAGAAGGATATAAATATT
260 ATGCTTCT-----ATAA----TAAA-TCAA-GTGGCTGAGATTTGATCAGAAGAATATAAATATT
** * *
21138 TCAAGGAGTCTCGGCGTCAAAAATCATGCAAAACTAAACCGGGACCCCGAAACGCGTTTTTAGCC
314 TCAAGGAGTCTCGGCACCAAAAATCATGCAAAACTAAACCGGGACCACGAAACGCGCTTTTAGCC
*
21203 AAAAACCGTGATAGTTAATACACGATTTCGGCAAAAATTTTGCAAAAAAGACCCAAAAAATTTTC
379 AAAAACCATGATAGTTAATACACGATTTCGGCAAAAATTTTGCAAAAAAGACCCAAAAAATTTTC
* * * * * * * ** *
21268 CTCAATTTTTATCTAAAATATTCATAAAATATATATAATTTAACGTCAAAAATTTTGGAGAACTT
444 CACAATATTTAGCCAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGAACTT
*
21333 GTCACGCTTTTAATATCGTTTTTCATATTTTCTAAATTAATTTCTAATTAAATCGAAACAAAATT
509 GTCACGCTTTTAATATCGTTTTCCATATTTTCTAAATTAATTTCTAATTAAATCGAAACAAAATT
*
21398 CAGATACTCGTAAAAAAAAAAAATCTTAAATCCAATGTAGCTGAGATTTGATTAAATGAATATGG
574 CAGATACTCATAAAAAAAAAAAATCTTAAATCCAATGTAGCTGAGATTTGATTAAATGAATATGG
21463 ATTTTCAAAAATCATGCAAAAGCCCTTCAAAAAT
639 ATTTTCAAAAATCATGCAAAAGCCCTTCAAAAAT
* * * **
21497 AGTCTCGGCGCCAAAAATCATGCAAAACTTAGCCGG-G-CACCGGAACGTGTTTTTAGCCAAAAA
1 AGTCTCAGCGCCAAAAATCATGCAAAACTAAGCCGGAGCCA-CGAAACACGTTTTTAGCCAAAAA
** *** * * *
21560 CCGTGATGATTTCT-CACGATTTCGGCTAAAATTTTGTAAAAATTGACGCGAAAT-ATTTT-TCT
65 CCGTGATGATTAATACACGATTTCGGCTAAAATCCCGCAAAAAATGAC-C-AAATAATTTTACCT
* * *
21622 CAATTTTTAGCCACAATACTTATAAAAAATATATAATTCAGCGCCAAAAAGATTGAAGGGCTTCT
128 CAATTTTTAGCCAAAATACTTATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTCT
* * *
21687 CACGCTTCTAATATCGTTTTTCCTATTTTTTTTAAAATTAATTTATAATTAAATCGAAACATGAT
193 CACGCTTCTAATATCGTTTTTCATA-TTTTTAT-AAATTAATTTATAATTAAATCGAAACAAGAT
* * * * * * *
21752 TCAAATGC-TCT-TAA-AAA-CAA-TGGTTGTGATTTGGTTAGATGAATATAGATATTTCTAGGA
256 TCAAATGCTTCTATAATAAATCAAGTGGCTGAGATTTGATCAGAAGAATATAAATATTTCAAGGA
* * *
21812 GTCTCGGTACCAAAAATCATGTAAAACTAAACCGGG-CCACGGAACGCGCTTTTAGCCAAAAACC
321 GTCTCGGCACCAAAAATCATGCAAAACTAAACCGGGACCACGAAACGCGCTTTTAGCCAAAAACC
* * * *
21876 ATGAT-GATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTT-CAC
386 ATGATAG-TTAATACACGATTTCGGCAAAAATTTTGCAAAAA-AGACCC-AAA-AAATTTTCCAC
* * ** *
21939 AATATTTAGCCAAAATACTCATAAATATATATATTATTCAATGCCAAAAAGATTGAAGGGCTTTT
447 AATATTTAGCCAAAATACTCATAAA-ATATATATAATTCAACGCCAAAAAGATTGAAGAACTTGT
* *
22004 CACGCTTTTAATATCGTTTTCCATATTTTCTCAATTAATTTCTAATTAAATCGAAACAAGATTCA
511 CACGCTTTTAATATCGTTTTCCATATTTTCTAAATTAATTTCTAATTAAATCGAAACAAAATTCA
*
22069 GATGCTCATAAAAA
576 GATACTCATAAAAA
22083 CGAATCTTTA
Statistics
Matches: 499, Mismatches: 77, Indels: 35
0.82 0.13 0.06
Matches are distributed among these distances:
665 1 0.00
666 61 0.12
667 69 0.14
668 26 0.05
669 112 0.22
671 3 0.01
676 3 0.01
681 77 0.15
682 42 0.08
683 69 0.14
684 36 0.07
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (672 bp):
AGTCTCAGCGCCAAAAATCATGCAAAACTAAGCCGGAGCCACGAAACACGTTTTTAGCCAAAAAC
CGTGATGATTAATACACGATTTCGGCTAAAATCCCGCAAAAAATGACCAAATAATTTTACCTCAA
TTTTTAGCCAAAATACTTATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTCTCAC
GCTTCTAATATCGTTTTTCATATTTTTATAAATTAATTTATAATTAAATCGAAACAAGATTCAAA
TGCTTCTATAATAAATCAAGTGGCTGAGATTTGATCAGAAGAATATAAATATTTCAAGGAGTCTC
GGCACCAAAAATCATGCAAAACTAAACCGGGACCACGAAACGCGCTTTTAGCCAAAAACCATGAT
AGTTAATACACGATTTCGGCAAAAATTTTGCAAAAAAGACCCAAAAAATTTTCCACAATATTTAG
CCAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGAACTTGTCACGCTTTTA
ATATCGTTTTCCATATTTTCTAAATTAATTTCTAATTAAATCGAAACAAAATTCAGATACTCATA
AAAAAAAAAAATCTTAAATCCAATGTAGCTGAGATTTGATTAAATGAATATGGATTTTCAAAAAT
CATGCAAAAGCCCTTCAAAAAT
Found at i:22499 original size:329 final size:327
Alignment explanation
Indices: 20668--22654 Score: 1265
Period size: 329 Copynumber: 6.0 Consensus size: 327
20658 TCCCGTGTCA
* * * * *
20668 ACTTTTCATGTTTTTAATATCGTTTTTCATATTTTCTGAATTAATTTTTAATTAAATCGAAACAA
1 ACTTTTCACGCTTTTAATATCGTTTTCCATATTTTCTCAATTAATTTCTAATTAAATCGAAACAA
* * * * * * * * * *
20733 AATTCAAATGCTCACAAAAAAAAAGATCCTTAAATTCAATGTAGCTGAGATTTGTTTTGATGAAT
66 GATTCAGATGCTCA-TAAAAACAA-ATCTTTAAATCCAATGTGGCTCAGATTTGATTAGATGAAT
* * * * * ** *
20798 ATAGATATTTCAAGGAGTCTC-AGCGCCAAAAATCATGCAAAACTAAGTTGGAGCCACGAAACAC
129 ATAGATATTTCAATGAGTCTCGA-CACAAAAAATCATGTAAAACTGAGCCGG-GCCACG-AACGC
* * * *** *
20862 GTTTTTAGCCAAAAACCGTGATGATTAATACACGATTTTGGCTAAAATCCCGCAAAAAATGA-CC
191 GTTTTTA-CCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
* * * * ** * * *
20926 -AAATAAATTTTACCTTAATTTTTGGCTAAAATACTTTTAAAATATATATAATTTAACGCCAAAA
255 GAAAGATATTTT--CTCAATTTTTAGCTAAAATACTCATAATATATATATAATTCAATGCCAAAA
*
20990 AGATTGGAGG
318 AGATTGAAGG
* * * * *
21000 ACTTTTCATGTTTTTAATATCGTTTTTCATATTTTTATGAATTAATTTCTAATTAAATCGAAACA
1 ACTTTTCACGCTTTTAATATCGTTTTCCATA-TTTTCTCAATTAATTTCTAATTAAATCGAAACA
** * * * * *
21065 AGATTCAGATGCTTGTAAAAA-ATAAT-TCTTAAATTCAATGTGGCTGAGATTTGATCAGAAGGA
65 AGATTCAGATGCTCATAAAAACA-AATCT-TTAAATCCAATGTGGCTCAGATTTGATTAGATGAA
* * * * * * * *
21128 TATAAATATTTCAAGGAGTCTCGGCGTC-AAAAATCATGCAAAACTAAACCGGGACCCCGAAACG
128 TATAGATATTTCAATGAGTCTCGAC-ACAAAAAATCATGTAAAACTGAGCCGGG-CCACG-AACG
* * * *
21192 CGTTTTTAGCCAAAAACCGTGAT-AGTTAATACACGATTTCGGCAAAAATTTTGCAAAAA-AGAC
190 CGTTTTTA-CCAAAAATCGTGATGA-TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * * * * *
21255 CC-AAA-AAATTTTCCTCAATTTTTATCTAAAATATTCATAAAATATATATAATTTAACGTCAAA
253 CCGAAAGATATTTT-CTCAATTTTTAGCTAAAATACTCATAATATATATATAATTCAATGCCAAA
** * *
21318 AATTTTGGAGA
317 AAGATTGAAGG
* * *
21329 ACTTGTCACGCTTTTAATATCGTTTTTCATATTTTCTAAATTAATTTCTAATTAAATCGAAACAA
1 ACTTTTCACGCTTTTAATATCGTTTTCCATATTTTCTCAATTAATTTCTAATTAAATCGAAACAA
* * * * * * *
21394 AATTCAGATACTCGTAAAAAAAAAAAATC-TTAAATCCAATGTAGCTGAGATTTGATTAAATGAA
66 GATTCAGATGCTC---ATAAAAACAAATCTTTAAATCCAATGTGGCTCAGATTTGATTAGATGAA
* * * ** * * **
21458 TATGGAT-TTTCAA-AAATCAT-G---C-AAAAGCCCT-TCAAAAAT-AGTCTCGGCGCCAAAAA
128 TATAGATATTTCAATGAGTC-TCGACACAAAAAATCATGT-AAAACTGAG-C-CGG-GCCACGAA
**** ** ** * *
21514 TCATGCAAAACTTAGCCGGGCACCGGAA-CGTG-TTTTTAGCCAAAAACCGTGATGATTTCTCAC
188 -C--GC-GTTTTTA--C---CA--AAAATCGTGATGATTAG-----TA-C---ACGA-TT-T--C
* *** ** * * * * *
21577 GATTTCGGCTAAAATTTTGTAAAAATTGACGCGAAATAT-TTTTCTCAATTTTTAGCCACAATAC
229 G---GC-TAAAATT--TTGCAAAAATTGACCCGAAAGATATTTTCTCAATTTTTAGCTAAAATAC
* * * **
21641 TTATAAAAAATATATAATTCAGCGCCAAAAAGATTGAAGG
288 TCATAATATATATATAATTCAATGCCAAAAAGATTGAAGG
* * * * * * *
21681 GCTTCTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTAAAATTAATTTATAATTAAATCGAAA
1 ACTTTTCACGCTTTTAATATCG-TTTTCC-ATATTTTCT-CAATTAATTTCTAATTAAATCGAAA
* * * * * *
21746 CATGATTCAAATGCTC-T--TAA-AAA-C----AAT----GGTTG-T--GATTTGGTTAGATGAA
63 CAAGATTCAGATGCTCATAAAAACAAATCTTTAAATCCAATGTGGCTCAGATTTGATTAGATGAA
* * ** * * *
21795 TATAGATATTTCTAGGAGTCTCGGTACCAAAAATCATGTAAAACTAAACCGGGCCACGGAACGCG
128 TATAGATATTTCAATGAGTCTCGACACAAAAAATCATGTAAAACTGAGCCGGGCCAC-GAACGCG
* * * *
21860 CTTTTAGCCAAAAACCATGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
192 TTTTTA-CCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
* * * *
21925 AAAGATATTTTCACAATATTTAGCCAAAATACTCATAAATATATATATTATTCAATGCCAAAAAG
256 AAAGATATTTTCTCAATTTTTAGCTAAAATACTCAT-AATATATATATAATTCAATGCCAAAAAG
21990 ATTGAAGG
320 ATTGAAGG
*
21998 GCTTTTCACGCTTTTAATATCGTTTTCCATATTTTCTCAATTAATTTCTAATTAAATCGAAACAA
1 ACTTTTCACGCTTTTAATATCGTTTTCCATATTTTCTCAATTAATTTCTAATTAAATCGAAACAA
* * * *
22063 GATTCAGATGCTCATAAAAACGAATCTTTAAATGCAATTTGGCTCAGATTTTATTAGATGAATAT
66 GATTCAGATGCTCATAAAAACAAATCTTTAAATCCAATGTGGCTCAGATTTGATTAGATGAATAT
* * * **
22128 AGATGTTTCAATGAGTCTCGACGCAAAAAATCATGCAAAACTGAGCCGGGCCTTGAAACGCGTTT
131 AGATATTTCAATGAGTCTCGACACAAAAAATCATGTAAAACTGAGCCGGGCCACG-AACGCGTTT
* * * *
22193 TTGACCAAAAATCGTGATGATTAGTAAATGATTTTGGCTAAAATTTTGCAAAAAATGACCCGAAA
195 TT-ACCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
* * * *
22258 -ATTTTTTCCTCAATTTTTGGATAAAATACTCATAATATATATATAATTTAA-GACCAAAAAGAT
259 GATATTTT-CTCAATTTTTAGCTAAAATACTCATAATATATATATAATTCAATG-CCAAAAAGAT
*
22321 TGGAGG
322 TGAAGG
** * * *
22327 ACTTTTCAC-CTTTTTAATATCGTTTTTTATATTTTTTGTGAATT-ATTTTTAATTAAATCGAAA
1 ACTTTTCACGC-TTTTAATATCGTTTTCCATA--TTTTCTCAATTAATTTCTAATTAAATCGAAA
* * ** * *
22390 CAAGATTCAGATTCTCGT-AGTACAAATTTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
63 CAAGATTCAGATGCTCATAAAAACAAATCTTTAAATCCAATGTGGCTCAGATTTGATTAGATGAA
* * * ** * * *
22454 TATTGATATCTCAATGAGTCTTGACACAAAAAATCATGTAAAACTGAGTTGGCGCCCCGAGCGCT
128 TATAGATATTTCAATGAGTCTCGACACAAAAAATCATGTAAAACTGAGCCGG-GCCACGAACGCG
* * * * *
22519 TTTTTAACAAAAAATTGTGATGGTT-GTTACACGATTTCGGCTAAAAGTTTGTAAAAATTGACCC
192 TTTTT-ACCAAAAATCGTGATGATTAG-TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
* * *
22583 GAAAGATATTTTCTCAATTTTTTGCTAAAATACTCATAAAAAATTATATAATTCAATGCCAAAAA
255 GAAAGATATTTTCTCAATTTTTAGCTAAAATACTCATAATATA-TATATAATTCAATGCCAAAAA
22648 GATTGAA
319 GATTGAA
22655 TAGCTTTTGT
Statistics
Matches: 1310, Mismatches: 249, Indels: 194
0.75 0.14 0.11
Matches are distributed among these distances:
314 37 0.03
315 28 0.02
316 31 0.02
317 55 0.04
318 3 0.00
319 1 0.00
321 2 0.00
323 5 0.00
324 17 0.01
325 9 0.01
326 1 0.00
327 4 0.00
328 54 0.04
329 322 0.25
330 256 0.20
331 159 0.12
332 47 0.04
333 49 0.04
334 8 0.01
337 22 0.02
338 10 0.01
339 7 0.01
340 3 0.00
341 8 0.01
342 8 0.01
343 13 0.01
344 5 0.00
345 2 0.00
347 1 0.00
348 4 0.00
349 4 0.00
351 8 0.01
352 71 0.05
353 12 0.01
354 8 0.01
355 36 0.03
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (327 bp):
ACTTTTCACGCTTTTAATATCGTTTTCCATATTTTCTCAATTAATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCATAAAAACAAATCTTTAAATCCAATGTGGCTCAGATTTGATTAGATGAATAT
AGATATTTCAATGAGTCTCGACACAAAAAATCATGTAAAACTGAGCCGGGCCACGAACGCGTTTT
TACCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA
TATTTTCTCAATTTTTAGCTAAAATACTCATAATATATATATAATTCAATGCCAAAAAGATTGAA
GG
Found at i:27643 original size:78 final size:79
Alignment explanation
Indices: 27543--27703 Score: 288
Period size: 79 Copynumber: 2.1 Consensus size: 79
27533 AATTATATAA
*
27543 AATGGTTAATCCTAAATATTAACATATTCC-CTTAGAATTTTAGAATAAAAATATGTAATTTAAT
1 AATGGTTAATCCTAAATATTAACATATTCCTCATAGAATTTTAGAATAAAAATATGTAATTTAAT
27607 TTAACCAGGCAAAC
66 TTAACCAGGCAAAC
* *
27621 AATGGTTAATCCTAAATATTAACATATTCCTCATAGAGTTTTAGAATGAAAATATGTAATTTAAT
1 AATGGTTAATCCTAAATATTAACATATTCCTCATAGAATTTTAGAATAAAAATATGTAATTTAAT
27686 TTAACCAGGCAAAC
66 TTAACCAGGCAAAC
27700 AATG
1 AATG
27704 ACCAACATTA
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 30 0.38
79 49 0.62
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (79 bp):
AATGGTTAATCCTAAATATTAACATATTCCTCATAGAATTTTAGAATAAAAATATGTAATTTAAT
TTAACCAGGCAAAC
Found at i:28310 original size:56 final size:56
Alignment explanation
Indices: 28193--28354 Score: 272
Period size: 56 Copynumber: 2.9 Consensus size: 56
28183 GTGAGAAAAG
*
28193 ACAATAAATGTTATAATAAATCCTAT-CCCCTATTTCTACTTAATTATTCTTTCAC
1 ACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATTCTTTCAC
* * *
28248 ACAATAAATGTTATAATAAATCTTATCCCCCTATCTCTACTGAATTATTCTTTCAC
1 ACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATTCTTTCAC
*
28304 ATAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATTCT
1 ACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATTCT
28355 ACAAAATAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
55 25 0.25
56 74 0.75
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.41
Consensus pattern (56 bp):
ACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATTCTTTCAC
Found at i:28545 original size:118 final size:118
Alignment explanation
Indices: 28337--28578 Score: 457
Period size: 118 Copynumber: 2.1 Consensus size: 118
28327 TATCCCCCTA
*
28337 TTTCTACTTAATTATTCTACAAAATAAATAATATTTTCTTTTAAGTTAGAACAAAGTTGTTAGAT
1 TTTCTACTTAATTATTCTACAAAATAAATAATATTTTCTTTTAAGTTAGAACAAAGTTGTTAGAG
28402 AAGATAGCTAAGGATTAGGATTTGAGTTGAGTATTTCTTAATTTACAAAGAAT
66 AAGATAGCTAAGGATTAGGATTTGAGTTGAGTATTTCTTAATTTACAAAGAAT
28455 TTTCTACTTAATTATTCTACAAAATAAATAATATTTTCTTTTAAGTTAGAACAAAGTTGTTAGAG
1 TTTCTACTTAATTATTCTACAAAATAAATAATATTTTCTTTTAAGTTAGAACAAAGTTGTTAGAG
* *
28520 AAGATAGCTAAGGATTAGGATTTGAGTTGAGTGTTTCTTATTTTACAAAGAAT
66 AAGATAGCTAAGGATTAGGATTTGAGTTGAGTATTTCTTAATTTACAAAGAAT
28573 TTTCTA
1 TTTCTA
28579 TGATTTGTGT
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 121 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (118 bp):
TTTCTACTTAATTATTCTACAAAATAAATAATATTTTCTTTTAAGTTAGAACAAAGTTGTTAGAG
AAGATAGCTAAGGATTAGGATTTGAGTTGAGTATTTCTTAATTTACAAAGAAT
Found at i:28599 original size:42 final size:42
Alignment explanation
Indices: 28538--28618 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
28528 TAAGGATTAG
* *
28538 GATTTGAGTTGAGTGTTTCTTATTTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
* *
28580 GATTTGTGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
28619 AAGACTTAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.49
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:31605 original size:14 final size:14
Alignment explanation
Indices: 31586--31629 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
31576 CAAGTTCAGG
31586 TAGTATATTATATA
1 TAGTATATTATATA
*
31600 TAGTATATAATATTA
1 TAGTATATTATA-TA
31615 TATGTAGTATTATAT
1 TA-GTA-TATTATAT
31630 TATATTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 11 0.44
15 4 0.16
16 4 0.16
17 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (14 bp):
TAGTATATTATATA
Found at i:31629 original size:17 final size:18
Alignment explanation
Indices: 31589--31634 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
31579 GTTCAGGTAG
31589 TATATTATATATAGTATA
1 TATATTATATATAGTATA
*
31607 TAATATTATATGTAGTAT-
1 T-ATATTATATATAGTATA
31625 TATATTATAT
1 TATATTATAT
31635 TATCCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 2 0.08
19 15 0.58
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATATTATATATAGTATA
Found at i:31630 original size:5 final size:5
Alignment explanation
Indices: 31589--31637 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
31579 GTTCAGGTAG
* *
31589 TATAT TATA- TATAG TATAT AATAT TATAT GTAGTAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TA-TAT TATAT TATAT TAT
31638 CCTAAATCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
4 4 0.11
5 27 0.71
6 4 0.11
7 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (5 bp):
TATAT
Found at i:32618 original size:4 final size:4
Alignment explanation
Indices: 32609--32633 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
32599 CTATTAGTTT
32609 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
32634 AGTTGATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:35222 original size:220 final size:221
Alignment explanation
Indices: 34833--35278 Score: 668
Period size: 220 Copynumber: 2.0 Consensus size: 221
34823 ATTTTATCTT
* *
34833 AGCAATCAAGTTAAATGGAAGGAAATATTGTAAGAATTATAATGTCTATTCATATAATTATCTAT
1 AGCAATCAAGCTAAATGAAAGGAAATATTGTAAGAATTATAATGTCTATTCA-ATAATTA--TAT
*
34898 TGTTAACAAAAAAATAATCATCTATTGGAAAAAAGAAATGGAGTTTTACTTTAATTATAATTCAA
63 TATTAACAAAAAAATAATCATCTATTGGAAAAAAGAAATGGAGTTTTACTTTAATTATAATTCAA
*
34963 TGTTGTAAAATATTATTTGAAATTCTAAATATATAATAATATTATATCTTAGTTTTCTTTCAACT
128 TGTTGTAAAATATTATTTGAAATTCTAAATATATAATAATA-TATA--TTAGTTTTCTTTCAACC
**
35028 AATCAACTTTGGACAAATGTCAGTATGAGAAG
190 AATCAACTTTGGACAAATGTCAACATGAGAAG
*
35060 AGCAATCAAGCTAAATGAAAGGAAATATTGTTAGAATTATAATGTCTATTC-A-AA-TA-ATTAT
1 AGCAATCAAGCTAAATGAAAGGAAATATTGTAAGAATTATAATGTCTATTCAATAATTATATTAT
* * * ** *
35121 TAACAAAAAAA-AAGTTATCTATTGGAGAAAAGAGATGGAGTTTTACTTTGCTTATATTTCAATG
66 TAACAAAAAAATAA-TCATCTATTGGAAAAAAGAAATGGAGTTTTACTTTAATTATAATTCAATG
*
35185 TTGTAAAATATTATTTGAAATTCTAAATATATAATAATATATATTGGTTTTCTTTCAACCAATCA
130 TTGTAAAATATTATTTGAAATTCTAAATATATAATAATATATATTAGTTTTCTTTCAACCAATCA
35250 ACTTTGGACAAATGTCAACATGAGAAG
195 ACTTTGGACAAATGTCAACATGAGAAG
35277 AG
1 AG
35279 GCAAATATAC
Statistics
Matches: 204, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
217 47 0.23
219 6 0.03
220 98 0.48
223 2 0.01
224 2 0.01
225 1 0.00
227 48 0.24
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (221 bp):
AGCAATCAAGCTAAATGAAAGGAAATATTGTAAGAATTATAATGTCTATTCAATAATTATATTAT
TAACAAAAAAATAATCATCTATTGGAAAAAAGAAATGGAGTTTTACTTTAATTATAATTCAATGT
TGTAAAATATTATTTGAAATTCTAAATATATAATAATATATATTAGTTTTCTTTCAACCAATCAA
CTTTGGACAAATGTCAACATGAGAAG
Found at i:38476 original size:2 final size:2
Alignment explanation
Indices: 38469--38498 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38459 GCTTAAAATT
*
38469 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38499 CTAGTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:39298 original size:2 final size:2
Alignment explanation
Indices: 39293--39332 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
39283 TATAGTAGTA
39293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39333 TAGTTAAACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41580 original size:36 final size:36
Alignment explanation
Indices: 41533--41602 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
41523 TTCAATAACC
* *
41533 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
41569 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
41603 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.