Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023836.1 Corchorus olitorius cultivar O-4 contig23869, 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: 10604
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:1075 original size:321 final size:319
Alignment explanation
Indices: 420--1818 Score: 1402
Period size: 334 Copynumber: 4.2 Consensus size: 319
410 GCATCATGCC
* *
420 TTTTTAGCCATAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAGTTGACC
1 TTTTTAG-CA-AAAAATGTGATGGTTAGTACACGATTTCGGC----A---TG-AAAAA-CTGACC
* * *
485 C-ACAAAATTTTCCTCAATTTTTTTGCCACACA-ACTCAGAAAAAATATATAATTC-TCTGCCAA
55 CGA-AAATTTTTCCTCAA-TTTTTTG-CA-AAATACTCAGAAAAAATATATAATTCAAC-GCCAA
** * *
547 AAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTATTTTCCGAATTAATTTCTA
115 AAAGATTAAAGGTTTTTTCACGCTTCTAATA-TCGTTTTCCCACT-TTTTCTGAATTAATTTCTA
* *
612 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAACCAAATCCTTAAATCCAATGTGGCTGAAATT
178 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* ** * * *
677 TGGTAAGATGAATATAGATATTTCAAGGAGTCCGTGCATCCAAAATCATGTAAAATTGAGCCGGG
243 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATGCAAAATTGAGTCGGG
742 CTCCGAAACGCG
308 CTCCGAAACGCG
*
754 TTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTCGGC-T-AAAAACTGACGCGGAAAATTT
1 TTTTTAGCAAAAAA-TGTGATGGTTAGTACACGATTTCGGCATGAAAAACTGAC-CCGAAAATTT
* * * **
817 TTTCTCAATTTTTTGAAACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACCGT
64 TTCCTCAATTTTTTGCAA-AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGT
* *
882 ATTTTT-ACGCTTCTAAATATCGTTTTCCCA-TTTCTTCTGAATTAATTTCTAAATAAATCAAAA
128 -TTTTTCACGCTTCT-AATATCGTTTTCCCACTTT-TTCTGAATTAATTTCTAATTAAATCGAAA
* * * * * *
945 TAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCGAATGTGGCTGACATTTGGTTAGATGAA
190 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAA
* ** *
1010 TATAGATATTTCAAGGAGTCTTTGCATCCAAAATCATTTAAAATTGAGTCGGGCTCCGGAACGCG
255 TATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATGCAAAATTGAGTCGGGCTCCGAAACGCG
* * *
1075 TTTTTAGCCAAAAACTGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
1 TTTTTAG-CAAAAAATGTGATGGTTAGTACACGATTTCGGC----A---TG-AAAAACTGACCCG
* * *
1140 AAAAATTTTCCTCAAATTTTTTGCCATACTACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
57 AAAATTTTTCCTC-AATTTTTTG-CAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
** * * * *
1205 TTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCATTTTTTTTTCGAATTAATTTCCAATTAA
120 TTAAAGGTTTTTTCACGCTTCTAATATCGTTTTCCCA-CTTTTTCT-GAATTAATTTCTAATTAA
* * * *
1270 ATCGAAATAAAATTCAGATGCTTGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTT
183 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT
* * * * * * * * *
1335 CGATTAATATAGATATTTCAATGAGACTTTGCGCCCAAAATCATTCAAAACTGA-TCCGGACTAC
248 AGATGAATATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATGCAAAATTGAGT-CGGGCTCC
*
1399 GAAATGCG
312 GAAACGCG
* * * * *
1407 TTTTTATCCGAAAAAAAGTAATTGTTAGTACACGATTTCGGCTAAAATTTTGAAAAAATTGACCC
1 TTTTTA-GC-AAAAAATGTGATGGTTAGTACACGATTTCGGC----A---TG-AAAAACTGACCC
* * *
1472 GAAAAGTTTTTCCTCAACTTTTTTGCCAAAATACTTAGAAAAAATATATAATTTAACGCCAGAAA
56 GAAAA-TTTTTCCTCAA-TTTTTTG-CAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAA
* * *
1537 GATTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAACCTTTTTCCT-AATTAATTTATAAT
118 GATTAAAGGTTTTTTCACGCTTCTAATATCG-TTTTCCCA-CTTTTT-CTGAATTAATTTCTAAT
*
1601 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTG
180 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
* *
1666 GTTAGATGAATATAGATATTACAAGG-GATCTTTGCGCCCAAAATCATGCAAAATAATGGAG-CG
245 GTTAGATGAATATAGATATTTCAAGGAG-TCTTTGCACCCAAAATCATGCAAAAT--T-GAGTCG
*
1729 GGCTTCGAAACGCG
306 GGCTCCGAAACGCG
* * * * * * **
1743 TTTTTAGCCAAAAATCGTGATGGTTAATACACCATTCCAGC-T-AAAAACTTATCCAAAAAATTT
1 TTTTTAGCAAAAAAT-GTGATGGTTAGTACACGATTTCGGCATGAAAAACTGA-CCCGAAAATTT
*
1806 TTACTCAATTTTT
64 TTCCTCAATTTTT
1819 ACCATAACGT
Statistics
Matches: 906, Mismatches: 119, Indels: 90
0.81 0.11 0.08
Matches are distributed among these distances:
320 3 0.00
321 178 0.20
322 70 0.08
323 28 0.03
324 6 0.01
325 18 0.02
326 6 0.01
327 1 0.00
329 1 0.00
330 30 0.03
331 72 0.08
332 148 0.16
333 84 0.09
334 207 0.23
335 31 0.03
336 21 0.02
337 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (319 bp):
TTTTTAGCAAAAAATGTGATGGTTAGTACACGATTTCGGCATGAAAAACTGACCCGAAAATTTTT
CCTCAATTTTTTGCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGTTTT
TTCACGCTTCTAATATCGTTTTCCCACTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGAT
TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
TATTTCAAGGAGTCTTTGCACCCAAAATCATGCAAAATTGAGTCGGGCTCCGAAACGCG
Found at i:2891 original size:239 final size:239
Alignment explanation
Indices: 2456--2902 Score: 671
Period size: 239 Copynumber: 1.9 Consensus size: 239
2446 ACTACTTAGA
* *
2456 AAAAATATATAATTCAACGCCAAAAAGATTAAAGGTTTTTTCACCCTACTAATATTATTTTTCCA
1 AAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCACCCTACTAATATCATTTTTCCA
* * *
2521 ATTTTTTTACGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCC
66 ACTTTTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCC
* * * *
2586 TTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAATGAAACTTTGTACCCA
131 TTAAATCCAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAAACTTTGCACCCA
*
2651 AAATCATTCAAAACTGATCCGAACTACGAAATGCCAGAAAGATT
196 AAATCATGCAAAACTGATCCGAACTACGAAATGCCAGAAAGATT
* * * *
2695 AAAAATATATAATTCAACGCCAGAAAGATTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA
1 AAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCACCCTACTAATATCATTTTTCCA
* * * * * *
2760 ACTTTTTTCCTAATTTATTTCTAATTAAATCGATACAAGATTTAGATGA-TCATAAAAACAAATT
66 ACTTTTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT-ACTCATAAAAACAAATC
* * *
2824 CTTAAATCCAATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTGCACCC
130 CTTAAATCCAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAAACTTTGCACCC
2889 AAAATCATGCAAAA
195 AAAATCATGCAAAA
2903 TGGAGCCGGG
Statistics
Matches: 184, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
239 183 0.99
240 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (239 bp):
AAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCACCCTACTAATATCATTTTTCCA
ACTTTTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCC
TTAAATCCAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAAACTTTGCACCCA
AAATCATGCAAAACTGATCCGAACTACGAAATGCCAGAAAGATT
Found at i:3055 original size:17 final size:17
Alignment explanation
Indices: 3033--3066 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3023 GGTTGAGGCG
3033 AGGCGGTTCATTCGGTT
1 AGGCGGTTCATTCGGTT
3050 AGGCGGTTCATTCGGTT
1 AGGCGGTTCATTCGGTT
3067 GCAAGGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.35, T:0.35
Consensus pattern (17 bp):
AGGCGGTTCATTCGGTT
Found at i:6091 original size:306 final size:314
Alignment explanation
Indices: 5522--6794 Score: 1176
Period size: 337 Copynumber: 4.0 Consensus size: 314
5512 AAAATTTTGT
* * * * *
5522 AAAAATTGAACCGAAAAATTTTCCACAAATTTTTTGCCACACTACTCAGAAAAAATATATTATTC
1 AAAAACTGACCCG-AAAATTTTTCATAAATTTTTTGCCACACTACTCAGAAAAAATATATAATTC
*
5587 AACGCCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCAAATT
65 AACACCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCAAATT
* * *
5652 AATTTATAATTAAATCGAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
130 AATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * *
5717 CTGAGATTTGGTAAGATAAATATAAATATTTCAAGGAGACCTTGTGTCA---AAAATAATGTAAA
195 CTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGA-CTT-T-TCACCCAAAATCATGTAAA
*
5779 ATTGAGCCGGACTCCGAAACGCGTTTTTAGCCAAAAAC-TG-T-G-ATG-T-GGC-T-
257 ATTGAGCCGGACTCCGAAATGCGTTTTTAGCCAAAAACGTGATAGAATGTTCGGCATC
* ** *
5829 AAAAACTGACCCGACAAATTTTTTC-TCAATTTTTTGAGACAATACTCAGAAAAAATATATAATT
1 AAAAACTGACCCGA-AAA-TTTTTCATAAATTTTTTGCCACACTACTCAGAAAAAATATATAATT
* * *** * * *
5893 CAACCCCAAGAAGATTGTCCGG-ATTTTCACGCTTCTAA-ATATCTTTTTCCCA-TTTTTTCCAA
64 CAACACCAAAAAGATT-AAAGGTTTTTTCACGCTTCTAATAT-TATTTTTCCAACTTTTTTCCAA
* * * *
5955 ATTAATTTCTAATTAAATCGAAATAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCGAATG
127 ATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * *
6020 TGGCTGAGATTTGGTTAGTTAAATATAGATATTTCACGGAGTCTTTTCACCCAAAATCATGTAAA
192 TGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGACTTTTCACCCAAAATCATGTAAA
* * *
6085 ATTGAGCCGGGCTCCGGAATGCGTTTTTGGCCAAAAACTGTGATTAGTACATGATTTCGGCTAAA
257 ATTGAGCCGGACTCCGAAATGCGTTTTTAGCCAAAAAC-GTGA-TAG-A-ATG--TTCGGC----
6150 ATTTTGC
312 A---T-C
* *
6157 AAAAATTGACCCGAAAATTTTTCATTAAATTTTTTGCCACACTACTCTGAAAAAATATATAATTC
1 AAAAACTGACCCGAAAATTTTTCA-TAAATTTTTTGCCACACTACTCAGAAAAAATATATAATTC
* **
6222 AACACCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGCATT
65 AACACCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCAAATT
*
6287 AATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
130 AATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * ** * * *
6352 CTAAGACTTGGTTCGATGAATATAGATATTTCAATAAGACTTTGCGCCCAAAATCAT-TCAAAAC
195 CTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGACTTTTCACCCAAAATCATGT-AAAAT
* * * * * *
6416 TGATCCGGACTACGAAATGCGTTTTTATCCGAAAAAAAAGTATTTGTTAGTACACGATTTCGGCT
259 TGAGCCGGACTCCGAAATGCGTTTTTAGCC---AAAAACG----TGATAG-A-ATG--TTCGGC-
*
6481 AAAATTTTGT
312 ---A---T-C
* ** * * ** * * * *
6491 AAAAATTGACTCAAAAAATTTTCCCTCCATTTTTTGTTGCCAAAATACTTAGCAAAAATATATAA
1 AAAAACTGAC-CCGAAAATTTTTCAT--AAATTTT-TTGCCACACTACTCAGAAAAAATATATAA
* * * ** * *
6556 TTCAACGCCAAAAAGATTAAAGGGTTTTTCAAGCTTCTAATATCGTTTTTCCAACTTTCTTCCTA
62 TTCAACACCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCAA
* * * * *
6621 ATTAATTTCTAATTAAATCGAAACAAGATTTAGATGATCATAAAAACAAATTCTTAAATCCAATG
127 ATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * * *
6686 TGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA-ATCTTTGCGCCCAAAATCATGCAA
192 TGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGA-CTTTTCACCCAAAATCATGTAA
* * * * *
6750 AATGGAGCCGGGCTTCGGAACGCGTTTTTAGCCAAAAATCGTGAT
256 AATTGAGCCGGACTCCGAAATGCGTTTTTAGCCAAAAA-CGTGAT
6795 GATTAGTACA
Statistics
Matches: 798, Mismatches: 119, Indels: 74
0.81 0.12 0.07
Matches are distributed among these distances:
303 3 0.00
304 1 0.00
305 3 0.00
306 154 0.19
307 85 0.11
308 9 0.01
310 1 0.00
311 1 0.00
314 3 0.00
317 1 0.00
318 3 0.00
326 7 0.01
327 5 0.01
328 86 0.11
329 147 0.18
331 4 0.01
332 5 0.01
334 42 0.05
335 13 0.02
336 6 0.01
337 219 0.27
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (314 bp):
AAAAACTGACCCGAAAATTTTTCATAAATTTTTTGCCACACTACTCAGAAAAAATATATAATTCA
ACACCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCAAATTA
ATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
TGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGACTTTTCACCCAAAATCATGTAAAATTG
AGCCGGACTCCGAAATGCGTTTTTAGCCAAAAACGTGATAGAATGTTCGGCATC
Found at i:6268 original size:635 final size:648
Alignment explanation
Indices: 5468--6819 Score: 1631
Period size: 635 Copynumber: 2.1 Consensus size: 648
5458 GCATCATGCT
* * *
5468 TTTTTAGCCAAAAAAAGCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGAAC
1 TTTTTAGCC--AAAAATCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAAC
* *
5533 CGAAAAATTTTCCACAAATTTTTTGCCACACTACTCAGAAAAAATATATTATTCAACGCCAAAAA
64 CGAAAAATTTTCCACAAATTTTTTGCCACACTACTCAGAAAAAATATATAATTCAACACCAAAAA
5598 GATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCAAATTAATTTATAATT
129 GATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCAAATTAATTTATAATT
* * * *
5663 AAATCGAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG
194 AAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGACTTGG
* * * *
5728 TAAGATAAATATAAATATTTCAAGGAGACCTTGTGTCAAAAATAATGT-AAAATTGAGCCGGACT
259 TAAGATAAATATAAATATTTCAAGAAGACCTTGCGCCAAAAATAAT-TCAAAACTGAGCCGGACT
* * *
5792 CCGAAACGCGTTTTTAGCC-AAAA-A-CT-GT-GATGT-GGC-TAAAAACTGACCCGACAAATTT
323 ACGAAACGCGTTTTTAGCCAAAAAGATCTAGTAGATGTCGGCTTAAAAACTGACCCAAAAAATTT
** * * ***
5850 TTTCTCAATTTTTTG-AG-ACAATACTCAGAAAAAATATATAATTCAACCCCAAGAAGATTGTCC
388 TCCCTCAATTTTTTGTAGCAAAATACTCAGAAAAAATATATAATTCAACCCCAAAAAGATTAAAC
* * *
5913 GGATTTTCACGCTTCTAAATATC-TTTTTCCCA-TTTTTTCCAAATTAATTTCTAATTAAATCGA
453 GGATTTTCAAGCTTCT-AATATCGTTTTTCCAACTTTCTTCCAAATTAATTTCTAATTAAATCGA
* * * * * *
5976 AATAAGATTCAG-TTACTCGTAAAAACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGTT
517 AACAAGATTCAGATGA-TCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
* * * * * *
6040 AAATATAGATATTTCACGGAGTCTTTTCACCCAAAATCATGTAAAATTGAGCCGGGCTCCGGAAT
581 AAATATAGATATTTCAAGGAATCTTTGCACCCAAAATCATGCAAAATGGAGCCGGGCTCCGGAAC
6105 GCG
646 GCG
* * *
6108 TTTTTGGCCAAAAA-C-TG-TGATTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
1 TTTTTAGCCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACCG
* * *
6170 -AAAATTTTTCATTAAATTTTTTGCCACACTACTCTGAAAAAATATATAATTCAACACCAAAAAG
66 AAAAATTTTCCA-CAAATTTTTTGCCACACTACTCAGAAAAAATATATAATTCAACACCAAAAAG
* ** *
6234 ATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGCATTAATTTCTAATTA
130 ATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCAAATTAATTTATAATTA
*
6299 AATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGACTTGGT
195 AATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGACTTGGT
** * * * * * * *
6364 TCGATGAATATAGATATTTCAATAAGACTTTGCGCCCAAAATCATTCAAAACTGATCCGGACTAC
260 AAGATAAATATAAATATTTCAAGAAGACCTTGCGCCAAAAATAATTCAAAACTGAGCCGGACTAC
* * * *
6429 GAAATGCGTTTTTATCCGAAAAAAAAGTATTTGTTAGTACACGATTTCGGCTAAAATTTTGTAAA
325 GAAACGCGTTTTTAGCC----AAAAAG-A--T-CTAGT--A-GATGTCGGC--------T-TAAA
* * * * * *
6494 AATTGACTCAAAAAATTTTCCCTCCATTTTTTGTTGCCAAAATACTTAGCAAAAATATATAATTC
370 AACTGACCCAAAAAATTTTCCCTCAATTTTTTGTAG-CAAAATACTCAGAAAAAATATATAATTC
* * * *
6559 AACGCCAAAAAGATTAAAGGGTTTTTCAAGCTTCTAATATCGTTTTTCCAACTTTCTTCCTAATT
434 AACCCCAAAAAGATTAAACGGATTTTCAAGCTTCTAATATCGTTTTTCCAACTTTCTTCCAAATT
* *
6624 AATTTCTAATTAAATCGAAACAAGATTTAGATGATCATAAAAACAAATTCTTAAATCCAATGTGG
499 AATTTCTAATTAAATCGAAACAAGATTCAGATGATCATAAAAACAAATCCTTAAATCCAATGTGG
* * *
6689 GTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTGCGCCCAAAATCATGCAAAATG
564 CTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAATCTTTGCACCCAAAATCATGCAAAATG
*
6754 GAGCCGGGCTTCGGAACGCG
629 GAGCCGGGCTCCGGAACGCG
*
6774 TTTTTAGCCAAAAATCGTGATGATTAGTACACGATTTCGGCAAAAA
1 TTTTTAGCCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAA
6820 ACTGACCCAA
Statistics
Matches: 594, Mismatches: 80, Indels: 47
0.82 0.11 0.07
Matches are distributed among these distances:
634 11 0.02
635 274 0.46
636 2 0.00
637 1 0.00
638 5 0.01
640 12 0.02
642 1 0.00
646 1 0.00
647 2 0.00
651 4 0.01
652 3 0.01
662 30 0.05
663 1 0.00
664 6 0.01
665 59 0.10
666 153 0.26
667 3 0.01
668 2 0.00
669 24 0.04
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (648 bp):
TTTTTAGCCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACCG
AAAAATTTTCCACAAATTTTTTGCCACACTACTCAGAAAAAATATATAATTCAACACCAAAAAGA
TTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCAAATTAATTTATAATTAA
ATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGACTTGGTA
AGATAAATATAAATATTTCAAGAAGACCTTGCGCCAAAAATAATTCAAAACTGAGCCGGACTACG
AAACGCGTTTTTAGCCAAAAAGATCTAGTAGATGTCGGCTTAAAAACTGACCCAAAAAATTTTCC
CTCAATTTTTTGTAGCAAAATACTCAGAAAAAATATATAATTCAACCCCAAAAAGATTAAACGGA
TTTTCAAGCTTCTAATATCGTTTTTCCAACTTTCTTCCAAATTAATTTCTAATTAAATCGAAACA
AGATTCAGATGATCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATAAATA
TAGATATTTCAAGGAATCTTTGCACCCAAAATCATGCAAAATGGAGCCGGGCTCCGGAACGCG
Found at i:6437 original size:329 final size:326
Alignment explanation
Indices: 5829--8427 Score: 1117
Period size: 337 Copynumber: 8.0 Consensus size: 326
5819 TGATGTGGCT
* * ** *
5829 AAAAACTGACCCGACAAATTTTT-TCTCAATTTTTTGAGACAATACTCAGAAAAAATATATAATT
1 AAAAATTGACCCGA-AAATTTTTCTCTAAATTTTTTGCCACAATACTCTGAAAAAATATATAATT
* * *** * * *
5893 CAACCCCAAGAAGATTGTCCGGATTTTCACGCTTCTAA-ATATCTTTTTCCCATTTTTTCCAAAT
65 CAACACCAAAAAGATT-AAAGGTTTTTCACGCTTCTAATAT-TATTTTTCCAATTTTTTCCAAAT
* * * * *
5957 TAATTTCTAATTAAATCGAAATAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCGAATGTG
128 TAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * *
6022 GCTGAGATTTGGTTAGTTAAATATAGATATTTCACGGAGTCTTTTCACCCAAAATCATGT-AAAA
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTGCGCCCAAAATCAT-TCAAAA
* * *
6086 TTGAGCCGGGCTCCGGAATGCGTTTTTGGCCAAAAACTGTGATTAGTACATGATTTCGGCTAAAA
257 -TGAGCCGGGCTACGGAATGCGTTTTTAGCCAAAAACTGTGATTAGTACACGATTTCGGCTAAAA
6151 TTTTGC
321 TTTTGC
*
6157 AAAAATTGACCCGAAAATTTTTCAT-TAAATTTTTTGCCACACTACTCTGAAAAAATATATAATT
1 AAAAATTGACCCGAAAATTTTTC-TCTAAATTTTTTGCCACAATACTCTGAAAAAATATATAATT
**
6221 CAACACCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGCAT
65 CAACACCAAAAAGATTAAAGG-TTTTTCACGCTTCTAATATTATTTTTCCAA-TTTTTTCCAAAT
6286 TAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
128 TAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * *
6351 GCTAAGACTTGGTTCGATGAATATAGATATTTCAATAAGACTTTGCGCCCAAAATCATTCAAAAC
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTGCGCCCAAAATCATTCAAAA-
* * * * **
6416 TGATCCGGACTACGAAATGCGTTTTTATCCGAAAAAAAAGT-ATTTGTTAGTACACGATTTCGGC
257 TGAGCCGGGCTACGGAATGCGTTTTTAGCC--AAAAACTGTGA----TTAGTACACGATTTCGGC
*
6480 TAAAATTTTGT
316 TAAAATTTTGC
** * * ** * *
6491 AAAAATTGACTCAAAAAATTTTCCCTCCATTTTTTGTTGCCAAAATACT-TAGCAAAAATATATA
1 AAAAATTGAC-CCGAAAATTTT-TCTCTAAATTTT-TTGCCACAATACTCT-GAAAAAATATATA
* * ** * *
6555 ATTCAACGCCAAAAAGATTAAAGGGTTTTTCAAGCTTCTAATATCGTTTTTCCAACTTTCTTCCT
62 ATTCAACACCAAAAAGATTAAA-GGTTTTTCACGCTTCTAATATTATTTTTCCAA-TTTTTTCCA
* * * * *
6620 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGATCATAAAAACAAATTCTTAAATCCAAT
125 AATTAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* *
6685 GTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAA-TCTTTGCGCCCAAAATCATGCA
190 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA-GAAGTCTTTGCGCCCAAAATCATTCA
* *
6749 AAATGGAGCCGGGCTTCGGAACGCGTTTTTAGCCAAAAATCGTGATGATTAGTACACGATTTCGG
254 AAAT-GAGCCGGGCTACGGAATGCGTTTTTAGCCAAAAA-C-TG-TGATTAGTACACGATTTCGG
***
6814 C-AAAAAACTGACCC
315 CTAAAATTTTG---C
* * ** * * **
6828 AAAAATATTTACTC---AATTTTTAC-C-ACAATGTATTCGGTTCA-AATCAGTCTCCGGAAAGG
1 -AAAA-ATTGACCCGAAAATTTTT-CTCTA-AAT-T-TTTTG-CCACAAT-A--CT-CTGAAAAA
* * * ** * * * ** * * **
6887 TTTTATAATAGCCAA-ACCGATTTACGATTTGAAA--ATTATGGC-CTT-T--T-TAAGTTAACC
55 ATATATAAT--TCAACACC-A-AAAAGA-TT-AAAGGTTTTTCACGCTTCTAATATTATTTTTCC
* ** * * * *** * * * * * *** *
6944 CA---CCTGCAGA--AACTTC-AGGCCCGAAATCGAAA-ACG-TT-ACACGCCCTTTCGAACGGA
114 AATTTTTTCCAAATTAATTTCTA---ATTAAATCGAAATAAGATTAAGATGCTCGTAAAAAC-AA
* * * * * * * * * * ** * * *** ** * *
7000 TTTCTGAGGATCCATACGAT--C-CATATAT-GATATATCTATCT-CAT-CCGCATCATGCCTTT
175 ATCCTTA-AATCCA-ATG-TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTC-TT
** **** * * *
7059 TTAG--CAAAA--A---AAAACTGATGGTTAG-TACACGATTTCGGCTAAAATTTT-G-CAAAAA
236 TGCGCCCAAAATCATTCAAAA-TGA-GCCGGGCTAC-GGAATGC-G-T----TTTTAGCCAAAAA
** * **
7114 -T-TGACCCA--A-A-AATTTTC--CTCAATTTTTTTGC
292 CTGTGA-TTAGTACACGA-TTTCGGCT-AA-AATTTTGC
* * * * *** * * * * * * * *
7145 -CACACT-ACTCAGAAAA-AAATATAT-AATTCTCTGCCA-AAAAGAT-T--AAAGAT-T-T-TT
1 AAAAATTGAC-CCGAAAATTTTTCTCTAAATTTTTTGCCACAATA-CTCTGAAAAAATATATAAT
* **** * * * **
7199 TC-ACGCTTCTAATATT--A--TTTTT-ACAACTT-T--T-TTCTAAATT--AA-----------
64 TCAACACCAAAAAGATTAAAGGTTTTTCAC-GCTTCTAATATTAT-TTTTCCAATTTTTTCCAAA
* * *
7241 ----TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATACTTAAATCCAATGT
127 TTAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *
7301 GGCTGAGATTTGGTAAGAAGAATATAGATATTTCAAGAAGTCCTTGCGTCCAAAATCATGT-AAA
192 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTGCGCCCAAAATCAT-TCAAA
* * * *
7365 ATTGAGCCAGGCTCCGAAATGAGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGC-
256 A-TGAGCCGGGCTACGGAATGCGTTTTTAGCCAAAAACTGTGA---TTAGTACACGATTTCGGCT
7429 -------T--
317 AAAATTTTGC
* * ** *
7430 AAAAACTGACCCGAAAAATTTTT-TCTCAATTTTTTGAAACAATACTCAGAAAAAATATATAATT
1 AAAAATTGACCCG-AAAATTTTTCTCTAAATTTTTTGCCACAATACTCTGAAAAAATATATAATT
** * * *** ** *
7494 CAATGCAAAAAAGATTGACCATATTTTCACGCTTCTAAATATCGTTTTTCCATTTTTTTCCAAAT
65 CAACACCAAAAAGATTAAAGGT-TTTTCACGCTTCT-AATATTATTTTTCCAATTTTTTCCAAAT
* * * * *
7559 TAATTTCTAATTAAATCGAAATAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCAAATGTG
128 TAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* *
7624 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATGT-ATAA
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTGCGCCCAAAATCAT-TCA-AA
* * * * *
7688 TTGAGTCGGGCTCCGGAACGCGTTTTTTAGCCAAAAACTGTGATGGATAGTACACAATTTCGGCT
256 ATGAGCCGGGCTACGGAATGCG-TTTTTAGCCAAAAACTGTGAT---TAGTACACGATTTCGGCT
7753 AAAATTTTGC
317 AAAATTTTGC
* * *
7763 AAAAATTGACCCGAAAAATTTTC-CTCAAATTTTTTGCCACACTACTCAGAAAAAATATATAATT
1 AAAAATTGACCCGAAAATTTTTCTCT-AAATTTTTTGCCACAATACTCTGAAAAAATATATAATT
* ** *
7827 CAACACGAAAAAGATTAAAGGTTTTTTCACATTTCTAATATTATTTTTCCAACTTTTTTCCGAAT
65 CAACACCAAAAAGATTAAAGG-TTTTTCACGCTTCTAATATTATTTTTCCAA-TTTTTTCCAAAT
* * *
7892 TGATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTG
128 TAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* *
7957 GCTGAGATTTGGTTTGATGAATATAGATATTTCAATG-AGACTTTGCGCCCAAAATCATTCAAAA
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAA-GAAGTCTTTGCGCCCAAAATCATTCAAAA
* * * *** ** * *
8021 CT--TCTCGGGACTACGAAATGCATTTTTCTCTGAAAAAAAAAAAGTAATTTTTAGTACACGACT
257 -TGAGC-CGGG-CTACGGAATGC--GTTT-T-T-AGCCAAAAACTGTGA---TTAGTACACGATT
*
8084 TCGGCTAAAATTTTGT
311 TCGGCTAAAATTTTGC
* ** * * *
8100 AAAAAATGACCCGAAAAGTTTTTC-C-ACCTTTTTTTTGTCAAAATACTCAGAAAAAAATATATA
1 AAAAATTGACCCGAAAA-TTTTTCTCTA--AATTTTTTGCCACAATACTCTG-AAAAAATATATA
* * ** * *
8163 ATTCAAC-GCAAGAAAGATTAAAGGGTTTTTCATGCTTCTAATATCGTTTTTCTAACTTTCTTCC
62 ATTCAACACCAA-AAAGATTAAA-GGTTTTTCACGCTTCTAATATTATTTTTCCAA-TTTTTTCC
* * * *
8227 TAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCCAA
124 AAATTAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * *
8292 TGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAA-TCTTTGCGCTCAAAATCATGC
189 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA-GAAGTCTTTGCGCCCAAAATCATTC
* * * *
8356 AAAATGGAGCCGGGCTTCGAAACGCGTTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTCG
253 AAAAT-GAGCCGGGCTACGGAATGCGTTTTTAGCCAAAAA-C-TG-TGATTAGTACACGATTTCG
8421 GCTAAAA
314 GCTAAAA
8428 ACTGACCCAA
Statistics
Matches: 1681, Mismatches: 395, Indels: 384
0.68 0.16 0.16
Matches are distributed among these distances:
281 1 0.00
282 2 0.00
283 15 0.01
284 11 0.01
285 11 0.01
286 24 0.01
287 15 0.01
288 21 0.01
289 4 0.00
290 5 0.00
291 6 0.00
292 6 0.00
293 10 0.01
294 5 0.00
295 18 0.01
296 7 0.00
297 1 0.00
298 2 0.00
299 4 0.00
300 8 0.00
301 5 0.00
303 1 0.00
304 4 0.00
305 3 0.00
306 5 0.00
310 1 0.00
311 1 0.00
312 4 0.00
313 5 0.00
314 3 0.00
315 4 0.00
316 1 0.00
317 4 0.00
318 1 0.00
319 7 0.00
320 4 0.00
321 49 0.03
322 95 0.06
323 40 0.02
324 2 0.00
326 12 0.01
327 14 0.01
328 96 0.06
329 165 0.10
330 18 0.01
331 15 0.01
332 45 0.03
333 208 0.12
334 78 0.05
335 47 0.03
336 23 0.01
337 273 0.16
338 37 0.02
339 206 0.12
340 13 0.01
341 8 0.00
342 3 0.00
343 2 0.00
344 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (326 bp):
AAAAATTGACCCGAAAATTTTTCTCTAAATTTTTTGCCACAATACTCTGAAAAAATATATAATTC
AACACCAAAAAGATTAAAGGTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTCCAAATTAA
TTTCTAATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTGCGCCCAAAATCATTCAAAATGAG
CCGGGCTACGGAATGCGTTTTTAGCCAAAAACTGTGATTAGTACACGATTTCGGCTAAAATTTTG
C
Found at i:7842 original size:333 final size:331
Alignment explanation
Indices: 7074--8427 Score: 1589
Period size: 333 Copynumber: 4.1 Consensus size: 331
7064 AAAAAAAAAC
*
7074 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC-AAAAATTTTCCTCAATT
1 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTCCTCAAAT
* *
7138 TTTTTGCCACACTACTCAGAAAAAAATATATAATTC-TCTGCCAAAAAGATTAAAGATTTTTTCA
66 TTTTTGCCACAATACTCAGAAAAAAATATATAATTCAAC-G-CAAAAAGATTAAAGATTTTTTCA
* *
7202 CGCTTCTAATATTATTTTTACAACTTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTC
129 CGCTTCTAATATCATTTTT-CAACTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTC
* * *
7267 AGATGCTCGTAAAAA-AAATACTTAAATCCAATGTGGCTGAGATTTGGTAAGAAGAATATAGATA
193 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * * * *
7331 TTTCAAGAAGTCCTTGCGTCCAAAATCATGTAAAATTGAGCCAGGCTCCGAAATGAGTTTTTAGC
258 TTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCTCCGAAACGCGTTTTTAGC
7396 CAAAAACTG
323 CAAAAACTG
* *
7405 TGATGGTTAGTACACGATTTCGGC--------T--AAAAACTGACCCGAAAAATTTTTTCTC-AA
1 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAA-TTTTCCTCAAA
** * * ** *
7459 TTTTTTGAAACAATACTCAG-AAAAAATATATAATTCAATGCAAAAAAGATTGACCATATTTTCA
65 TTTTTTGCCACAATACTCAGAAAAAAATATATAATTCAACGC-AAAAAGATTAAAGATTTTTTCA
* * * *
7523 CGCTTCTAAATATCGTTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAATAAGATTC
129 CGCTTCT-AATATCATTTTTCAACTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTC
* * * *
7588 AGTTACTCGTAAAAACAAATCCTTATATCAAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
193 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * *
7653 TTTCAAGGAGTCTTTGCACCCAAAATCATGTATAATTGAGTCGGGCTCCGGAACGCGTTTTTTAG
258 TTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCTCCGAAACGCG-TTTTTAG
7718 CCAAAAACTG
322 CCAAAAACTG
* *
7728 TGATGGATAGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTCCTCAAAT
1 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTCCTCAAAT
* * *
7793 TTTTTGCCACACTACTCAG-AAAAAATATATAATTCAACACGAAAAAGATTAAAGGTTTTTTCAC
66 TTTTTGCCACAATACTCAGAAAAAAATATATAATTCAACGC-AAAAAGATTAAAGATTTTTTCAC
** * * * *
7857 ATTTCTAATATTATTTTTCCAACTTTTTTCCGAATTGATTTCTAATTAAATCGAAATAAGATTCA
130 GCTTCTAATATCATTTTT-CAACTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCA
* *
7922 GATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTTGATGAATATAGATAT
194 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATAT
* * * * *
7987 TTCAATGAGACTTTGCGCCCAAAATCAT-TCAAAACTT---CTCGGGACTACGAAATGCATTTTT
259 TTCAAGGAGTCTTTGCGCCCAAAATCATGT-AAAA-TTGAGC-CGGG-CTCCGAAACGC--GTTT
*** **
8048 CTCTGAAAAAAAAAAAG
318 -T-T-AGCCAAAAACTG
* ** * * * * * ***
8065 TAATTTTTAGTACACGACTTCGGCTAAAATTTTGTAAAAAATGACCCGAAAAGTTTTTCCACCTT
1 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAA-ATTTTCCTCAAA
* * **
8130 TTTTTTGTCAAAATACTCAGAAAAAAATATATAATTCAACGCAAGAAAGATTAAAGGGTTTTTCA
65 TTTTTTGCCACAATACTCAGAAAAAAATATATAATTCAACGCAA-AAAGATTAAAGATTTTTTCA
* * * * *
8195 TGCTTCTAATATCGTTTTTCTAACTTTCTTCCTAATTAATTTCTAATTAAATCGAAACAAGATTT
129 CGCTTCTAATATCATTTTTC-AACTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTC
* *
8260 AGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATA
193 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * * *
8325 TTTCAAGGAATCTTTGCGCTCAAAATCATGCAAAATGGAGCCGGGCTTCGAAACGCGTTTTTAGC
258 TTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCTCCGAAACGCGTTTTTAGC
*
8390 CAAAAA-TCA
323 CAAAAACT-G
8399 TGATGGTTAGTACACGATTTCGGCTAAAA
1 TGATGGTTAGTACACGATTTCGGCTAAAA
8428 ACTGACCCAA
Statistics
Matches: 860, Mismatches: 126, Indels: 71
0.81 0.12 0.07
Matches are distributed among these distances:
320 1 0.00
321 107 0.12
322 124 0.14
323 47 0.05
331 25 0.03
332 22 0.03
333 216 0.25
334 36 0.04
335 2 0.00
336 2 0.00
337 54 0.06
338 28 0.03
339 191 0.22
340 4 0.00
341 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (331 bp):
TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTCCTCAAAT
TTTTTGCCACAATACTCAGAAAAAAATATATAATTCAACGCAAAAAGATTAAAGATTTTTTCACG
CTTCTAATATCATTTTTCAACTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTT
CAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCTCCGAAACGCGTTTTTAGCCAA
AAACTG
Found at i:9298 original size:340 final size:337
Alignment explanation
Indices: 8681--9300 Score: 945
Period size: 340 Copynumber: 1.8 Consensus size: 337
8671 AACGTGATGG
8681 TTAGTACACGATTTAGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTCCTCAAATTTTTTG
1 TTAGTACACGATTTAGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTCCTCAAATTTTTTG
* * *
8746 CCATACTACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGTTTTTTCACGCTTCTA
66 CCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCACGCTTCTA
* * * ** *
8811 ATATTATTTTTCCAATTTTTTCCGAATTAATTTCCAATTAAATTGAAATAAGATTCAGATGCTCG
131 ATATCATTTTTCCAATTTTTTCCGAATTAATTTACAATAAAATCAAAACAAGATTCAGATGCTCG
* * * *
8876 TAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAATGA
196 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTACAAGGA
*
8941 GACTTTGCGCCCAAAATCATTCAAAACTGATCCGGACTACGAAATGCGTTTTTATCCGAAAAAAA
261 GACTTTACGCCCAAAATCATTCAAAACTGATCCGGACTACGAAATGCGTTTTTATCCGAAAAAAA
9006 AAAGAGTAATTA
326 AAAGAGTAATTA
* * * * * *
9018 TTAGTACCCGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAAGTTTTTCCTCCATTTTTTT
1 TTAGTACACGATTTAGGCTAAAATTTTGCAAAAATTGACCCGAAAA-ATTTTCCTCAAATTTTTT
* *
9083 GCCAAAATACTTAGAAAAAATATATAAATTCAACGCCATAAAGATTAAAGGGTTTTTCACGCTTC
65 GCCAAAATACTCAGAAAAAATATAT-AATTCAACGCCAAAAAGATTAAAGGGTTTTTCACGCTTC
* * * *
9148 TAATATCGTTTTTCCAACTTTTTTCCTAATTAATTTATAATAAAATCAAAACAAGATTTAGATGC
129 TAATATCATTTTTCCAA-TTTTTTCCGAATTAATTTACAATAAAATCAAAACAAGATTCAGATGC
*
9213 TCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTACAA
193 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTACAA
*
9278 GGA-ATCTTTACGCTCAAAATCAT
258 GGAGA-CTTTACGCCCAAAATCAT
9301 GTAAATTGGA
Statistics
Matches: 251, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
337 43 0.17
338 37 0.15
339 53 0.21
340 118 0.47
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (337 bp):
TTAGTACACGATTTAGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTCCTCAAATTTTTTG
CCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCACGCTTCTA
ATATCATTTTTCCAATTTTTTCCGAATTAATTTACAATAAAATCAAAACAAGATTCAGATGCTCG
TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTACAAGGA
GACTTTACGCCCAAAATCATTCAAAACTGATCCGGACTACGAAATGCGTTTTTATCCGAAAAAAA
AAAGAGTAATTA
Found at i:10515 original size:329 final size:330
Alignment explanation
Indices: 9611--10572 Score: 1405
Period size: 329 Copynumber: 2.9 Consensus size: 330
9601 TGCATCATGA
** *
9611 GTTTTTAGCCAAAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
1 GTTTTTAGCCAAAAACTA--TGATGG-AAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * *
9676 CCGAAAAATTTTGCTCAATTTTTTTGCCACACTACTCAGAAAAAACATAAAATTCAACGCCAAAA
63 CCGAAAAATTTTCCTCAAATTTTTTGCCACACTACTCAGAAAAAAAATATAATTCAACGCCAAAA
* *
9741 AGATTAAAGGTTTTTTCACGCTTCTAATATTA-TTTTCCAACTTTTTTCCGAATTGATGTCTAAT
128 AGATTAAAGGTTTTTTCACG-TTCTAATATTATTTTTCCAACTTTTTTTCGAATTGATTTCTAAT
* * * *
9805 TAAATCGAAATAAGATTCAGTTACTCGT---AA-AAA--C-TATATCTAATGTGCCTGTGGTTTG
192 TAAATCGAAATAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTG
* * * *
9863 GTTGGATAAATATAGATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGATCCGGGCT
257 GTTAGATGAATATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATGTAAAATTGAGCCGGGCT
9928 CCGGAACAC
322 CCGGAACAC
9937 GTTTTTAGCCAAAAACTATGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
1 GTTTTTAGCCAAAAACTATGATGGA-AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
* *
10002 GAAAAGTTTTCCTC-AATTTTTCTGCCACACTACTCAGAAAAAAAAAATATAATTCAACGTCAAA
65 GAAAAATTTTCCTCAAATTTTT-TGCCACACTACTCAG--AAAAAAAATATAATTCAACGCCAAA
*
10066 AAGATTTTAAAGGTTTTTTCAC-TTCTAATATTATTTTTCCAA-TTTTTTTACGAATTAATTTCT
127 AAGA--TTAAAGGTTTTTTCACGTTCTAATATTATTTTTCCAACTTTTTTT-CGAATTGATTTCT
* * *
10129 AATTAAATCGAAACAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCGAATGTGGTTGAGAT
189 AATTAAATCGAAATAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGAT
10194 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATGTAAAATTGAGCCGG
254 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATGTAAAATTGAGCCGG
*
10259 GCTCCGGAACGC
319 GCTCCGGAACAC
* *
10271 GTTTTTAGCCAAAAACTGTGAT-G-AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCG
1 GTTTTTAGCCAAAAACTATGATGGAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
*
10334 AAAAATTTTCCTCAAATTTTTTGCCACACTACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
66 AAAAATTTTCCTCAAATTTTTTGCCACACTACTCAGAAAAAAAATATAATTCAACGCCAAAAAGA
10399 TTAAAGG-TTTTTCACGTTTCTAATATTATTTTTCCAACTTTTTTTCTGAATTGATTTCTAATTA
131 TTAAAGGTTTTTTCACG-TTCTAATATTATTTTTCCAACTTTTTTTC-GAATTGATTTCTAATTA
* *
10463 AATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGT
194 AATCGAAATAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGT
* * *
10528 TCGATGAATATAGATATTTCAATGA-TACTTTGCCCCCAAAATCAT
259 TAGATGAATATAGATATTTCAAGGAGT-CTTTGCACCCAAAATCAT
10573 TCAAAACTTC
Statistics
Matches: 578, Mismatches: 37, Indels: 39
0.88 0.06 0.06
Matches are distributed among these distances:
323 6 0.01
324 72 0.12
326 67 0.12
327 56 0.10
328 38 0.07
329 150 0.26
330 2 0.00
331 69 0.12
332 7 0.01
333 2 0.00
334 109 0.19
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (330 bp):
GTTTTTAGCCAAAAACTATGATGGAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
AAAAATTTTCCTCAAATTTTTTGCCACACTACTCAGAAAAAAAATATAATTCAACGCCAAAAAGA
TTAAAGGTTTTTTCACGTTCTAATATTATTTTTCCAACTTTTTTTCGAATTGATTTCTAATTAAA
TCGAAATAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTA
GATGAATATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATGTAAAATTGAGCCGGGCTCCGG
AACAC
Done.