Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009540.1 Corchorus capsularis cultivar CVL-1 contig09561, 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: 25501
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:3554 original size:16 final size:17
Alignment explanation
Indices: 3522--3555 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3512 AAAGAACAAC
3522 ATTTAAAAGTTTATAATA
1 ATTTAAAAG-TTATAATA
3540 ATTTAAAAG-TATAATA
1 ATTTAAAAGTTATAATA
3556 GATTGGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTTAAAAGTTATAATA
Found at i:11737 original size:13 final size:13
Alignment explanation
Indices: 11715--11745 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11705 TTCATTATTC
11715 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
11728 AAAAAGAAAAAAG
1 AAAAAAAAAAAAG
11741 AAAAA
1 AAAAA
11746 TCATCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:17882 original size:26 final size:25
Alignment explanation
Indices: 17849--17900 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
17839 TAGTAGTTTA
17849 TTTTTGCATGGAGTTTCAGTATAGT
1 TTTTTGCATGGAGTTTCAGTATAGT
* *
17874 TTTTCTGCATTGAGTTTCAGTGTAGT
1 TTTT-TGCATGGAGTTTCAGTATAGT
17900 T
1 T
17901 GATTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.17, C:0.10, G:0.23, T:0.50
Consensus pattern (25 bp):
TTTTTGCATGGAGTTTCAGTATAGT
Found at i:21299 original size:332 final size:329
Alignment explanation
Indices: 20545--21490 Score: 1252
Period size: 332 Copynumber: 2.9 Consensus size: 329
20535 ATTTAAGTCG
* * * * **
20545 AAAAATTATAAAATTTAATGCCGAAAAGATATAAGGGTTTTTCACTG-TTCTAGCATCGATTTTC
1 AAAAAATATATAATTTAATGCCCAAAAGATTTAAGGGTTTTTCAC-GCTTCTAATATCGATTTTC
* ** *
20609 CTATTTTTT-TAATCAATTTCT-AATGAAATTTAAAACGGTTATCTGATGCTTGTAAAAACAAAT
65 CTATTTTTTCTAATTAATTTCTAAAT-AAATCGAAAACGGTT-TCTGATGCTCGTAAAAACAAAT
** * * * ** * * *
20672 TATTAAATTCAATATGGCTGATTTTTGCTTACATGAATATAGATATTTCAAAGAGTTTCGGCACA
128 CCTTATATCCAATATGGTTGAGATTTGATTACATGAATATAGATATTTCAAGGAGTCTCGGCACA
* *
20737 AAAAATCATCCAAAATTGAGCCGGGGTCCCGGAACACGTTTTTAGGCAAAAACC-G-T-GA-A--
193 AAAAATCATCCAAAACTGAG-CGGGGTCTCGGAACACGTTTTTAGGCAAAAACCGGATGGATAGT
**
20796 ACATAATTTCAGCTAAAATTTTACAAAAAATGACCCGAAATAGTTTTCCTCAATTTTTAGCCGAA
257 ACACGATTTCAGCTAAAATTTTACAAAAAATGACCCGAAATAGTTTTCCTCAATTTTTAGCCGAA
20861 ATACTCAT
322 ATACTCAT
* * *
20869 AAAAAATATATAATTCAATGCCCAAAAAATTTAAGGGCTTTTCACGCTTCTAATATCGATTTTCC
1 AAAAAATATATAATTTAATGCCCAAAAGATTTAAGGGTTTTTCACGCTTCTAATATCGATTTTCC
20934 TATTTTTTCTTAATTAATTTCTAAATAAATCGAAAACGGTTTCTGATGCTCGTAAAAACAAATCC
66 TATTTTTTC-TAATTAATTTCTAAATAAATCGAAAACGGTTTCTGATGCTCGTAAAAACAAATCC
*
20999 TTATATCCAATATGGTTGAGATTTGATAACATGAATATAGATATTTCAAGGAGTCTCGGCACAAA
130 TTATATCCAATATGGTTGAGATTTGATTACATGAATATAGATATTTCAAGGAGTCTCGGCACAAA
*
21064 AAATCATCCAAAACTCG-GTCGGGGTCTCGGAACGCGTTTTTAGGCAAAAACCGTGATGGATAGT
195 AAATCATCCAAAACT-GAG-CGGGGTCTCGGAACACGTTTTTAGGCAAAAACCG-GATGGATAGT
* * *
21128 ACACGATTTCAGCTAAAATTTTGCAAAAAATGACCCGAAATA-TTTTCCCTCAATTTTTGGCTGA
257 ACACGATTTCAGCTAAAATTTTACAAAAAATGACCCGAAATAGTTTT-CCTCAATTTTTAGCCGA
21192 AATACTCAT
321 AATACTCAT
* *
21201 AAAAAAATATATAATTTAATTCCCAAAAGATTTAAGGGTTTTTCACGCTTTTAATATCGA-TTTC
1 -AAAAAATATATAATTTAATGCCCAAAAGATTTAAGGGTTTTTCACGCTTCTAATATCGATTTTC
*
21265 CTATTTTTTCTGAATTAATTTCTAAATAAATCGAAAACGGTTTCTGATGCTCGTAAAAGCAAATC
65 CTATTTTTTCT-AATTAATTTCTAAATAAATCGAAAACGGTTTCTGATGCTCGTAAAAACAAATC
* * * *
21330 CTTATATCCAATGTGGTTGAGATTTGGTTACATGATTATAGATATTTCAAGGAGTCTCGACACAA
129 CTTATATCCAATATGGTTGAGATTTGATTACATGAATATAGATATTTCAAGGAGTCTCGGCACAA
* * * * * * * * *
21395 AAAATAATCAAAAACTGAGCCGGGCCTCTG-ACCCGTTATTAGGCAAAAATCGAGATGGTTAGTA
194 AAAATCATCCAAAACTGAGCGGGGTCTCGGAACACGTTTTTAGGCAAAAACCG-GATGGATAGTA
*
21459 TACGATTTCAGCTAAAATTTTACAAAAAATGA
258 CACGATTTCAGCTAAAATTTTACAAAAAATGA
21491 ATCCTTAAAT
Statistics
Matches: 550, Mismatches: 56, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
323 1 0.00
324 62 0.11
325 123 0.22
326 25 0.05
327 4 0.01
328 1 0.00
329 2 0.00
330 60 0.11
331 14 0.03
332 204 0.37
333 54 0.10
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (329 bp):
AAAAAATATATAATTTAATGCCCAAAAGATTTAAGGGTTTTTCACGCTTCTAATATCGATTTTCC
TATTTTTTCTAATTAATTTCTAAATAAATCGAAAACGGTTTCTGATGCTCGTAAAAACAAATCCT
TATATCCAATATGGTTGAGATTTGATTACATGAATATAGATATTTCAAGGAGTCTCGGCACAAAA
AATCATCCAAAACTGAGCGGGGTCTCGGAACACGTTTTTAGGCAAAAACCGGATGGATAGTACAC
GATTTCAGCTAAAATTTTACAAAAAATGACCCGAAATAGTTTTCCTCAATTTTTAGCCGAAATAC
TCAT
Found at i:22108 original size:331 final size:331
Alignment explanation
Indices: 21536--22721 Score: 1779
Period size: 331 Copynumber: 3.6 Consensus size: 331
21526 TCCTCACATA
* * *
21536 AATATAGATATTTCAAGGAGTCTAGGCACTAAAAATCATCCAAAACTGAGCCGGGGCCCCGTAAC
1 AATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATCCAAAACTGAGCCGGGGCCCCGGAAC
*
21601 GCGTTTTTAGGGAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGAC
66 GCGTTTTTAGGCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGAC
* *
21666 CCGAAATATTTTCCCTCAATTTTTGGCCGAAATAGTCATAAAAAATATATAATTCAATGCCCAAA
131 CCGAAATATTTTCCCTAAATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAATGCCCAAA
* *
21731 AGATTTAAGGGCTTTTCACACTTTTAATATCGATTTTCCTATTTTTTCTGAATCAATTTCAAATG
196 AGATTTAAGGGCTTTTCACGCTTTTAATATCGATTTTCCAATTTTTTCTGAATCAATTTCAAATG
*
21796 AAATTGAATACGGTTTCTGATGCTCGTAAAAACATATCCTTAAATCCAATATAGCTGAGATTTGC
261 AAATTGAATACGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATAT-GCTGAGATTTGC
*
21861 TTATTTG
325 TTATATG
* *
21868 AATATAGATATTTCAAGGAGTTTCGGCACAAAAAATCATCCAAAACTGAGCCGGGG-CCAGGAAC
1 AATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATCCAAAACTGAGCCGGGGCCCCGGAAC
* * *
21932 GCGTTTTTAGGCATAAACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAAATAAC
66 GCGTTTTTAGGCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGAC
* * *
21997 CCGAAATATTTTCCCTAATTTTTTGGCCGAAATACTCATAAAATACATATAATTCAATGCCCAAA
131 CCGAAATATTTTCCCTAAATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAATGCCCAAA
* * * *
22062 AGATTTAAGGGCTTTTTACGCTTTTAATATCGATATTCCAATTTTTTCTGAATTAATTTAAAATG
196 AGATTTAAGGGCTTTTCACGCTTTTAATATCGATTTTCCAATTTTTTCTGAATCAATTTCAAATG
*
22127 AAATTGAATACGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGACTAAGATTTGC
261 AAATTGAATACGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATG-CTGAGATTTGC
22192 TT-TCATG
325 TTAT-ATG
* * * * * *
22199 AATATAGATATTTCAAGAAGTTTCGGTACCAAAAACCATCCAAAACTGAGCCGGGGCCCCGGAAT
1 AATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATCCAAAACTGAGCCGGGGCCCCGGAAC
* *
22264 GCGTTTTTAGGCAAAAACCGTGATGATTAGTACATGATTTCAGCTAAAATTTTGCAAAAAATGAC
66 GCGTTTTTAGGCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGAC
* *
22329 CCGAAATATTTTCCC-ACAATTTTTGGCCAAAATACTCATAAAAAATATATAATTCAATGCACAA
131 CCGAAATATTTTCCCTA-AATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAATGCCCAA
* * *
22393 AAGATTTAAGGGCTTTTCACGCTTTTAATATTGATTTTCCTATTTTTTTTTGAATCAATTTCAAA
195 AAGATTTAAGGGCTTTTCACGCTTTTAATATCGATTTTCC-AATTTTTTCTGAATCAATTTCAAA
* * * * * * *
22458 TTAAATTGAATAAGGTTTCTAATGCTCGTAAAAAAAAAAAAATCCTTATATCCAGTATGGTTGAG
259 TGAAATTGAATACGGTTTCTGATGCTCGT----AAAAACAAATCCTTAAATCCAATAT-GCTGAG
* *
22523 ATTTGGTTACATG
319 ATTTGCTTATATG
* * *
22536 AATATAGATATTTCAAGGAATCTCGGCAAAAAAAATTATCCAAAACTGAGCCGGGGCCCCGGAAC
1 AATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATCCAAAACTGAGCCGGGGCCCCGGAAC
* *
22601 ACGTTTTTAGGCAAAAACCGTGACGGTTAGTACACGATTTCAGCTAAAATTTTGC-AAAAATGAC
66 GCGTTTTTAGGCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGAC
* *
22665 CC-AAATGTTTTCCCTAAATTTTTGGCCGAAATACTCATAAAAAATTTATAATTCAAT
131 CCGAAATATTTTCCCTAAATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAAT
22722 CCTATTTTTT
Statistics
Matches: 772, Mismatches: 70, Indels: 21
0.89 0.08 0.02
Matches are distributed among these distances:
330 2 0.00
331 304 0.39
332 215 0.28
333 46 0.06
335 50 0.06
336 12 0.02
337 142 0.18
338 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (331 bp):
AATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATCCAAAACTGAGCCGGGGCCCCGGAAC
GCGTTTTTAGGCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGAC
CCGAAATATTTTCCCTAAATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAATGCCCAAA
AGATTTAAGGGCTTTTCACGCTTTTAATATCGATTTTCCAATTTTTTCTGAATCAATTTCAAATG
AAATTGAATACGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGCTGAGATTTGCT
TATATG
Found at i:23794 original size:333 final size:333
Alignment explanation
Indices: 22783--24962 Score: 3127
Period size: 333 Copynumber: 6.6 Consensus size: 333
22773 TTGTAAAAAA
* * * * * * * *
22783 AAATCCTTAAATCCAATATGGCTGAGATGTTCG-TACATGAATATAGATTTTTCAATTAGTCATG
1 AAATCCTTAAATCCATTGTGGCTGAGAT-TTGGTTAGATGAATATAGGTATTTCAATGAGTCTTG
* *
22847 GCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACACATTTTCAGCCAAAAACCGTGATG
65 GCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATG
* * * * *
22912 GTTAGTATACGATTTGGGCTAAAATATTCCAAAAATTGATCCGAAAAATTTTTCCTCAAATTTTG
130 GTTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTG
* * **
22977 GCCAGAATACTCAT-AAAAATATATAATTCAATGCCAAACATTTTGATGGGCTTTTCACGCTTCT
195 GCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCT
* ** * * *
23041 AATATCGATTTTCCTACATTTTAACGAATTAATTTCTCATTAAATCGACACAAGATTTTGATGCT
260 AATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCT
23106 CGTCAAATC
325 CGTCAAATC
* * * * * **
23115 AAATCCCTAAATCCATTGTGCCTAAGATTTGGTTAGTTGATTATAGAAATTTCAATGAGTCTTGG
1 AAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGGTATTTCAATGAGTCTTGG
* * * * *
23180 CGCAAAAAATCATGCAAAACTGATCCGTAGCACCGGAACACATTTTTAGCAAAAAACCGTGATAG
66 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGG
* * * * *
23245 TTAGTATACGATTTGAGCTAAAACTTTCCAAAAATTGACCCGAAAAAATTTTTCATCAATTTTTG
131 TTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCG-AAAAATTTTTCCTCAATTTTTG
* * *
23310 GCCATAATACTCATAGAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCAAGCTTCT
195 GCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCT
* * * * * * *
23375 AATATCCATTTTCCTATATTTTTCTGAATTGATTTCTCATTAAGTCGACGCAAGATTCTGATGCT
260 AATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCT
*
23440 TGTCAAATC
325 CGTCAAATC
* * *
23449 AAATCCTTAAATCCATAGTGCCTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTTGG
1 AAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGGTATTTCAATGAGTCTTGG
* *
23514 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCAGAATGCATTTTTAGCCAAAAACCGTGATGG
66 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGG
* * *
23579 TTAGTATACGATTTAGGCTAAAATTTTGCAAAAATTGACTCGAAAAATTTTTCCTCAATTTTTGG
131 TTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGG
* * * *
23644 CCAGAATACTTATAAAAAATATATAATTCAATGCCAAAAAAATTGATGGGCTTATCACGCTTCTA
196 CCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTA
23709 ATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTC
261 ATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTC
23774 GTCAAATC
326 GTCAAATC
* * *
23782 AAATCCTTAAATCCATTGTGGCTGTGATTTTGG-TAGATGTATATAGGTACTTCAATGAGTCTTG
1 AAATCCTTAAATCCATTGTGGCTGAGA-TTTGGTTAGATGAATATAGGTATTTCAATGAGTCTTG
23846 GCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCA----T---------CCGTGATG
65 GCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATG
*
23898 GTTAGTACACGATTTGGGATAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTG
130 GTTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTG
* *
23963 GCCAGAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGATGGGCTTATCACGCTTCT
195 GCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCT
*
24028 AATATTGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCT
260 AATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCT
24093 CGTCAAATC
325 CGTCAAATC
* * *
24102 AAATCCTTAAATCCATTGTGGCTGTGATTTTGG-TAGATGTATATAGGTACTTCAATGAGTCTTG
1 AAATCCTTAAATCCATTGTGGCTGAGA-TTTGGTTAGATGAATATAGGTATTTCAATGAGTCTTG
*
24166 GCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCAATTTTAGCCAAAAACCGTGATG
65 GCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATG
* * *
24231 GCTAGTACACAATTTGGGCTAAATTTTTGCAAAAATTGACCCG-AAAATTTCTTCCTCAATTTTT
130 GTTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT-TTCCTCAATTTTT
* * *
24295 GGCCAGAATACTCATAAAAATTATATAATTCAACGCCAAAAAGATTGATGGGTTTTTCAGGCTTC
194 GGCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTC
* *
24360 TAATATCGATTTTCCTATATTTTTCCGAATCAATTTCTCTTTAAATCGACACATGATTCTCATGC
259 TAATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGC
24425 TCGTCAAATC
324 TCGTCAAATC
* *
24435 AAATCCTTAAATCCATTGTGGTTGAGATTTTGTTAGATGAATATAGGTACTTT-AATGAGTCTTG
1 AAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGGTA-TTTCAATGAGTCTTG
* * * *
24499 GCGCAAAAAGTCATGCAAAACTGAACCGGAGCACTGGAA-GCATATTTAGCCAAAAATCGTGA--
65 GCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATG
* * *
24561 --T-GTACACGATTTGGGCTAAAATTTTGAAAAAACTGACCCGAAAATTTTTTCCTCAATTTTTG
130 GTTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTG
*
24623 GCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCGCGCTTCT
195 GCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCT
* *
24688 AATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATGAAATCGACACCTGATTCTCATGCT
260 AATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCT
**
24753 CGTGGAATC
325 CGTCAAATC
** *
24762 AAATCCTTAAATCCATTGTGGCTGAGAATTT-GTTAGATGAATATAAATATTTCTATGAGTCTTG
1 AAATCCTTAAATCCATTGTGGCTGAG-ATTTGGTTAGATGAATATAGGTATTTCAATGAGTCTTG
* *
24826 GCGCAAAAAGTCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTCAGCCAAAAACCGTGATG
65 GCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATG
* * * * *
24891 GTTAGTAGACGATTTGCGCTAGAATTTTGCAAAAATTGACCAGAAAAATTGTTT-CTCCATTTTT
130 GTTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT-TTTCCTCAATTTTT
24955 GGCCAGAA
194 GGCCAGAA
24963 ATTGAGGGAT
Statistics
Matches: 1673, Mismatches: 145, Indels: 59
0.89 0.08 0.03
Matches are distributed among these distances:
320 310 0.19
324 1 0.00
326 3 0.00
327 267 0.16
328 31 0.02
329 1 0.00
331 3 0.00
332 178 0.11
333 607 0.36
334 272 0.16
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (333 bp):
AAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGGTATTTCAATGAGTCTTGG
CGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGG
TTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGG
CCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTA
ATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTC
GTCAAATC
Found at i:24186 original size:653 final size:653
Alignment explanation
Indices: 22783--25496 Score: 3511
Period size: 653 Copynumber: 4.2 Consensus size: 653
22773 TTGTAAAAAA
* * * * * * *
22783 AAATCCTTAAATCCAATATGGCTGAGATGTTCGTACATGAATATAGATTTTTCAATTAGTCATGG
1 AAATCCTTAAATCCATTGTGGCTGAGAT-TTGGTAGATGAATATAGATATTTCAATGAGTCTTGG
*
22848 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACACATTTTCAGCCAAAAACCGTGATGG
65 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTCAGCCAAAAACCGTGATGG
* * *
22913 TTAGTATACGATTTGGGCTAAAATATTCCAAAAATTGA-TCCGAAAAATTTTTCCTCAAATTTTG
130 TTAGTATACGATTTGGGCTAAAATTTTGCAAAAATTGACT-CGAAAAATTTTTCCTCAATTTTTG
**
22977 GCCAGAATACTCATAAAAATATATAATTCAATGCCAAACATTTTGATGGGCTTTTCACGCTTCTA
194 GCCAGAATACTCATAAAAATATATAATTCAATGCCAAA-AAATTGATGGGCTTTTCACGCTTCTA
* ** * * * *
23042 ATATCGATTTTCCTACATTTTAACGAATTAATTTCTCATTAAATCGACACAAGATTTTGATGCTC
258 ATATCGATTTTCCTATATTTTTCCGAATCAATTTCTCATTAAATCGACACATGATTCTCATGCTC
* * * * * ** *
23107 GTCAAATCAAATCCCTAAATCCATTGTGCCTAAGA-TTTGGTTAGTTGATTATAGAAATTTCAAT
323 GTCAAATCAAATCCTTAAATCCATTGTGGCTGAGATTTTGG-TAGATGAATATAGGTACTTCAAT
* * **
23171 GAGTCTTGGCGCAAAAAATCATGCAAAACTGATCCGTAGCACCGGAACACATTTTTAGCAAAAAA
387 GAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGG-A-AC-------GC-AATTA
* * * * *
23236 CCGTGATAGTTAGTATACGATTTGAGCTAAAACTTTCCAAAAATTGACCCGAAAAAATTTTTCAT
442 CCGTGATAGTTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCG-AAAAATTTTTCCT
* * *
23301 CAATTTTTGGCCATAATACTCATAGAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTT
506 CAATTTTTGGCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTAT
* * * * * * *
23366 CAAGCTTCTAATATCCATTTTCCTATATTTTTCTGAATTGATTTCTCATTAAGTCGACGCAAGAT
571 CACGCTTCTAATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGAT
* *
23431 TCTGATGCTTGTCAAATC
636 TCTCATGCTCGTCAAATC
* *
23449 AAATCCTTAAATCCATAGTGCCTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTTGG
1 AAATCCTTAAATCCATTGTGGCTGAGATTTGG-TAGATGAATATAGATATTTCAATGAGTCTTGG
* * *
23514 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCAGAATGCATTTTTAGCCAAAAACCGTGATGG
65 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTCAGCCAAAAACCGTGATGG
*
23579 TTAGTATACGATTTAGGCTAAAATTTTGCAAAAATTGACTCGAAAAATTTTTCCTCAATTTTTGG
130 TTAGTATACGATTTGGGCTAAAATTTTGCAAAAATTGACTCGAAAAATTTTTCCTCAATTTTTGG
* *
23644 CCAGAATACTTATAAAAAATATATAATTCAATGCCAAAAAAATTGATGGGCTTATCACGCTTCTA
195 CCAGAATACTCAT-AAAAATATATAATTCAATGCC-AAAAAATTGATGGGCTTTTCACGCTTCTA
*
23709 ATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTC
258 ATATCGATTTTCCTATATTTTTCCGAATCAATTTCTCATTAAATCGACACATGATTCTCATGCTC
* *
23774 GTCAAATCAAATCCTTAAATCCATTGTGGCTGTGATTTTGGTAGATGTATATAGGTACTTCAATG
323 GTCAAATCAAATCCTTAAATCCATTGTGGCTGAGATTTTGGTAGATGAATATAGGTACTTCAATG
*
23839 AGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGC-A-T-CCGTGATGGTT
388 AGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCAATTACCGTGATAGTT
*
23901 AGTACACGATTTGGGATAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCC
453 AGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCC
*
23966 AGAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGATGGGCTTATCACGCTTCTAAT
518 AGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAAT
*
24031 ATTGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGT
583 ATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGT
24096 CAAATC
648 CAAATC
* * * *
24102 AAATCCTTAAATCCATTGTGGCTGTGATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGG
1 AAATCCTTAAATCCATTGTGGCTGAGA-TTTGGTAGATGAATATAGATATTTCAATGAGTCTTGG
24167 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCAATTTT-AGCCAAAAACCGTGATG
65 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGC-ATTTTCAGCCAAAAACCGTGATG
* * * * *
24231 GCTAGTACACAATTTGGGCTAAATTTTTGCAAAAATTGACCCG-AAAATTTCTTCCTCAATTTTT
129 GTTAGTATACGATTTGGGCTAAAATTTTGCAAAAATTGACTCGAAAAATTT-TTCCTCAATTTTT
* * *
24295 GGCCAGAATACTCATAAAAATTATATAATTCAACGCCAAAAAGATTGATGGGTTTTTCAGGCTTC
193 GGCCAGAATACTCATAAAAA-TATATAATTCAATGCCAAAAA-ATTGATGGGCTTTTCACGCTTC
*
24360 TAATATCGATTTTCCTATATTTTTCCGAATCAATTTCTCTTTAAATCGACACATGATTCTCATGC
256 TAATATCGATTTTCCTATATTTTTCCGAATCAATTTCTCATTAAATCGACACATGATTCTCATGC
* * *
24425 TCGTCAAATCAAATCCTTAAATCCATTGTGGTTGAGATTTTGTTAGATGAATATAGGTACTTTAA
321 TCGTCAAATCAAATCCTTAAATCCATTGTGGCTGAGATTTTGGTAGATGAATATAGGTACTTCAA
* * ***
24490 TGAGTCTTGGCGCAAAAAGTCATGCAAAACTGAACCGGAGCACTGGAA-GCATATTTAGCCAAAA
386 TGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCA-A-TTA-CC-GTG
* * * * *
24554 ATCGTGATGTACACGATTTGGGCTAAAATTTTGAAAAAACTGACCCGAAAATTTTTTCCTCAATT
447 ATAGTTA-GTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATT
* *
24619 TTTGGCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCGCGC
511 TTTGGCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTATCACGC
* *
24684 TTCTAATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATGAAATCGACACCTGATTCTCA
576 TTCTAATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCA
**
24749 TGCTCGTGGAATC
641 TGCTCGTCAAATC
* * *
24762 AAATCCTTAAATCCATTGTGGCTGAGAATTTGTTAGATGAATATAAATATTTCTATGAGTCTTGG
1 AAATCCTTAAATCCATTGTGGCTGAG-ATTTGGTAGATGAATATAGATATTTCAATGAGTCTTGG
*
24827 CGCAAAAAGTCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTCAGCCAAAAACCGTGATGG
65 CGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTCAGCCAAAAACCGTGATGG
* * * *
24892 TTAGTAGACGATTTGCGCTAGAATTTTGCAAAAATTGAC-CAGAAAAATTGTTT-CTCCATTTTT
130 TTAGTATACGATTTGGGCTAAAATTTTGCAAAAATTGACTC-GAAAAATT-TTTCCTCAATTTTT
**
24955 GGCCAG-----------------A-AA-T---TG-------A--G--GGATTTTTCACGCTTCTA
193 GGCCAGAATACTCATAAAAATATATAATTCAATGCCAAAAAATTGATGGGCTTTTCACGCTTCTA
* * * *
24987 ATATCGATTTTCCTATATTTTTCCGAATCAATTTCTTATTAAAACAACAGATGATTCTCATGCTC
258 ATATCGATTTTCCTATATTTTTCCGAATCAATTTCTCATTAAATCGACACATGATTCTCATGCTC
* * *
25052 GTCAAATCAAATCCTTAAATCCATTGTGGTTGAGATTTTGTTAGATGAATATAGGTACTTTAATG
323 GTCAAATCAAATCCTTAAATCCATTGTGGCTGAGATTTTGGTAGATGAATATAGGTACTTCAATG
* * * * * *
25117 AGTCTTGGTGCAAAAAATCATTCAAAATTGAACCGGTGCACTGGAACGCATTTTTAGCCAAAAAC
388 AGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCA--ATT--------AC
* * *
25182 CGTGATAGTTAGTACACGATATAGGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTCCTCA
443 CGTGATAGTTAGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCA
* * *
25247 ATTTTTTTGCCAGAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGATGGACTTATC
508 A-TTTTTGGCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTATC
* * *
25312 ACGCTTCTAATATTGATTTTCCTATATTTTTCCGAATTAATTTCTCTTTAAATCGACACATAATT
572 ACGCTTCTAATATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATT
25377 CTCATGCTCGTCAAATC
637 CTCATGCTCGTCAAATC
* * * * *
25394 AAATCCTTAAATCCATAGTGGCTGTGATTTAGTAGATGTATATAGGTACTTT-AATGAGTCTTGG
1 AAATCCTTAAATCCATTGTGGCTGAGATTTGGTAGATGAATATAGATA-TTTCAATGAGTCTTGG
*
25458 CGACAAAAAA-CATTCAAAACTGAACCGGAGCACCGGAAC
65 CG-CAAAAAATCATGCAAAACTGAACCGGAGCACCGGAAC
25497 ACAAT
Statistics
Matches: 1845, Mismatches: 167, Indels: 107
0.87 0.08 0.05
Matches are distributed among these distances:
625 182 0.10
626 5 0.00
627 2 0.00
629 1 0.00
631 108 0.06
632 171 0.09
633 2 0.00
634 1 0.00
637 1 0.00
640 1 0.00
641 2 0.00
642 1 0.00
652 19 0.01
653 522 0.28
654 56 0.03
656 2 0.00
658 4 0.00
659 11 0.01
660 351 0.19
661 9 0.00
662 1 0.00
665 5 0.00
666 185 0.10
667 195 0.11
668 8 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (653 bp):
AAATCCTTAAATCCATTGTGGCTGAGATTTGGTAGATGAATATAGATATTTCAATGAGTCTTGGC
GCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTCAGCCAAAAACCGTGATGGT
TAGTATACGATTTGGGCTAAAATTTTGCAAAAATTGACTCGAAAAATTTTTCCTCAATTTTTGGC
CAGAATACTCATAAAAATATATAATTCAATGCCAAAAAATTGATGGGCTTTTCACGCTTCTAATA
TCGATTTTCCTATATTTTTCCGAATCAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTC
AAATCAAATCCTTAAATCCATTGTGGCTGAGATTTTGGTAGATGAATATAGGTACTTCAATGAGT
CTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCAATTACCGTGATAGTTAGT
ACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCCAGA
ATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAATATC
GATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAA
ATC
Done.