Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009649.1 Corchorus capsularis cultivar CVL-1 contig09670, 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: 25312
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:994 original size:16 final size:16
Alignment explanation
Indices: 975--1027 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
965 TTTTTCATTC
975 ATTTTATTCTTTCAAA
1 ATTTTATTCTTTCAAA
*
991 ATTTTAAT-TTT-AAA
1 ATTTTATTCTTTCAAA
1005 CATTTTATTCTTTCAAA
1 -ATTTTATTCTTTCAAA
1022 ATTTTA
1 ATTTTA
1028 AGTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 3 0.09
15 10 0.31
16 16 0.50
17 3 0.09
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTATTCTTTCAAA
Found at i:1009 original size:31 final size:32
Alignment explanation
Indices: 974--1033 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
964 TTTTTTCATT
974 CATTTTATTCTTTCAAAATTTTAA-TTTTAAA
1 CATTTTATTCTTTCAAAATTTTAAGTTTTAAA
1005 CATTTTATTCTTTCAAAATTTTAAGTTTT
1 CATTTTATTCTTTCAAAATTTTAAGTTTT
1034 TTTTTCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.57
Consensus pattern (32 bp):
CATTTTATTCTTTCAAAATTTTAAGTTTTAAA
Found at i:2576 original size:1 final size:1
Alignment explanation
Indices: 2570--2602 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
2560 GTTCTAAGGG
2570 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2603 GCAGAAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19258 original size:50 final size:50
Alignment explanation
Indices: 19186--19634 Score: 724
Period size: 50 Copynumber: 9.2 Consensus size: 50
19176 GTTTAAAAAT
*
19186 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCGCGAACATCTAAAAGA
1 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
* * *
19236 TTTAGTAATTAGGAGACTGATGGGAGCTGACTCCCCGAACATTTAAAACA
1 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
19286 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
1 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
*
19336 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATGTAAAAGA
1 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
19386 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
1 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
*
19436 TTTAGTAATTAGGAGA-C--------C--A-TCCCCGAACATCTAAAAAA
1 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
*
19474 TTTAGTAATTAGGAGACTGATGGGAGCTGACTCCCCGAACATCTAAAAGA
1 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
*
19524 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAAA
1 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
* *
19574 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCTAACATCTAAAAAA
1 TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
19624 TTTAGTAATTA
1 TTTAGTAATTA
19635 AGACTGATGG
Statistics
Matches: 372, Mismatches: 15, Indels: 24
0.91 0.04 0.06
Matches are distributed among these distances:
38 34 0.09
39 1 0.00
41 1 0.00
47 1 0.00
49 2 0.01
50 333 0.90
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (50 bp):
TTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGA
Found at i:19468 original size:38 final size:38
Alignment explanation
Indices: 19417--19490 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
19407 GGGAGCTGAC
*
19417 TCCCCGAACATCTAAAAGATTTAGTAATTAGGAGACCA
1 TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCA
19455 TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGAC
1 TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGAC
19491 TGATGGGAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (38 bp):
TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCA
Found at i:19516 original size:88 final size:92
Alignment explanation
Indices: 19364--19634 Score: 397
Period size: 88 Copynumber: 2.9 Consensus size: 92
19354 GATGGGAGCT
* *
19364 GACTCCCCGAACATGTAAAAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATC
1 GACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATC
19429 TAAAAGATTTAGTAATTAGGAGA-C-C
66 TAAAAGATTTAGTAATTAGGAGACCGC
*
19454 -A-TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACTGATGGGAGCTGACTCCCCGAACATC
1 GACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATC
19517 TAAAAGATTTAGTAATTAGGAGACCGATGGGAGC
66 TAAAAGATTTAGTAATTAGGAGACC-------GC
*
19551 TGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCTAACAT
1 -GACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACAT
*
19616 CTAAAAAATTTAGTAATTA
65 CTAAAAGATTTAGTAATTA
19635 AGACTGATGG
Statistics
Matches: 163, Mismatches: 6, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
88 82 0.50
89 2 0.01
97 1 0.01
99 1 0.01
100 77 0.47
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (92 bp):
GACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATC
TAAAAGATTTAGTAATTAGGAGACCGC
Found at i:19565 original size:138 final size:138
Alignment explanation
Indices: 19317--19591 Score: 514
Period size: 138 Copynumber: 2.0 Consensus size: 138
19307 GGGAGCTGAC
* *
19317 TCCCCGAACATCTAAAAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATGTAA
1 TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAA
*
19382 AAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGATTTAGTAATTA
66 AAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTA
19447 GGAGACCA
131 GGAGACCA
*
19455 TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACTGATGGGAGCTGACTCCCCGAACATCTAA
1 TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAA
19520 AAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTA
66 AAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTA
19585 GGAGACC
131 GGAGACC
19592 GATGGGAGCT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 133 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (138 bp):
TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAA
AAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTA
GGAGACCA
Found at i:19584 original size:188 final size:191
Alignment explanation
Indices: 19179--19634 Score: 729
Period size: 188 Copynumber: 2.4 Consensus size: 191
19169 TTAAAATGTT
* *
19179 TAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGACTCCGCGAACATCTAAAAGATTTAGTAA
1 TAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGATTTAGTAA
* *
19244 TTAGGAGACTGATGGGAGCTGACTCCCCGAACATTTAAAACATTTAGTAATTAGGAGACCGATGG
66 TTAGGAGAC--------GC-GACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGG
19309 GAGCTGACTCCCCGAACATCTAAAAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGA
122 GAGCTGACTCCCCGAACATCTAAAAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGA
*
19374 ACATG
187 ACATC
*
19379 TAAAAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGATTTAGTAA
1 TAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGATTTAGTAA
*
19444 TTAGGAGAC-C-A-TCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACTGATGGGAGCTGACT
66 TTAGGAGACGCGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACT
19506 CCCCGAACATCTAAAAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATC
131 CCCCGAACATCTAAAAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATC
* *
19567 TAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCTAACATCTAAAAAATTTAGTAA
1 TAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGATTTAGTAA
19632 TTA
66 TTA
19635 AGACTGATGG
Statistics
Matches: 246, Mismatches: 10, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
188 173 0.70
189 1 0.00
191 1 0.00
200 71 0.29
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (191 bp):
TAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATCTAAAAGATTTAGTAA
TTAGGAGACGCGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTGACT
CCCCGAACATCTAAAAGATTTAGTAATTAGGAGACCGATGGGAGCTGACTCCCCGAACATC
Found at i:20087 original size:228 final size:221
Alignment explanation
Indices: 19696--20105 Score: 631
Period size: 228 Copynumber: 1.8 Consensus size: 221
19686 AAGATACAAG
*
19696 GCAGACATGGAGGGTACTTTGACAACATAGACAACAATCATAGTGATAGACGCGGAAGATACAGT
1 GCAGACATGGAGGGTACTTTGACAACATAGACAACAATCATAGTGACAGACGCGGAAGATACAGT
* * * **
19761 AAATGGTCAGCAGCTGCAAGTGAAGTAAGTTTATCATATTCTCAAATTTCCCTTCTTTATGATAA
66 AAATGGCCAGCAGCTGCAAATGAAGTAAGTTTATCATATTCTCAAATTTCCATTCTTTACAATAA
* * * *
19826 AATGTTTTATTTGTGAATATTCCATTGCATGTGGCTGATAAAATTTTTTCTTTGTTTTTTTTTTC
131 AATGTTTTATTTGTGAATATCCCACTGCATGTGGCTAATAAAA-TCTTTCTTTGTTTTTTTTTTC
19891 CCAGGTAGTTCTTGTGGCTGATAGAAA
195 CCAGGTAGTTCTTGTGGCTGATAGAAA
*
19918 GCAGACATGGAGGGTACTTTGACAACATAGACAACAATCGTAGTGACAGACACGGAAGCGGAAGA
1 GCAGACATGGAGGGTACTTTGACAACATAGACAACAATCATAGTGACAG--AC----GCGGAAGA
* * *
19983 TACAGTAAATGGCCATCAGCTGCAAATGAAGTAAGTTTATCATATTCTTAAATTTCCATTCTTTG
60 TACAGTAAATGGCCAGCAGCTGCAAATGAAGTAAGTTTATCATATTCTCAAATTTCCATTCTTTA
20048 CAATAAAATGTTTTATTTGTGAATATCCCACTGCATGTGGCTAATAAAATCTTTCTTT
125 CAATAAAATGTTTTATTTGTGAATATCCCACTGCATGTGGCTAATAAAATCTTTCTTT
20106 TTCCCAGATA
Statistics
Matches: 168, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
222 47 0.28
224 2 0.01
227 8 0.05
228 111 0.66
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (221 bp):
GCAGACATGGAGGGTACTTTGACAACATAGACAACAATCATAGTGACAGACGCGGAAGATACAGT
AAATGGCCAGCAGCTGCAAATGAAGTAAGTTTATCATATTCTCAAATTTCCATTCTTTACAATAA
AATGTTTTATTTGTGAATATCCCACTGCATGTGGCTAATAAAATCTTTCTTTGTTTTTTTTTTCC
CAGGTAGTTCTTGTGGCTGATAGAAA
Found at i:22444 original size:48 final size:48
Alignment explanation
Indices: 22392--22489 Score: 110
Period size: 48 Copynumber: 2.0 Consensus size: 48
22382 TAACCGTCTC
*
22392 GACTTTAAGAGA-CAGAAAATGA-CTGAAAGTCTAAAGGCTAACTATCAT
1 GACTTTAAGAGATC-GAAAATGACCAG-AAGTCTAAAGGCTAACTATCAT
** * * *
22440 GACTTTTCGGGATCGAAATTGGCCAGAAGTCTAAAGGCTAACTATCAT
1 GACTTTAAGAGATCGAAAATGACCAGAAGTCTAAAGGCTAACTATCAT
22488 GA
1 GA
22490 TTTTTCGGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
48 39 0.93
49 3 0.07
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (48 bp):
GACTTTAAGAGATCGAAAATGACCAGAAGTCTAAAGGCTAACTATCAT
Found at i:22495 original size:48 final size:48
Alignment explanation
Indices: 22418--22528 Score: 177
Period size: 48 Copynumber: 2.3 Consensus size: 48
22408 AAATGACTGA
*
22418 AAGTCTAAAGGCTAACTATCATGACTTTTCGGGATCGAAATTGGCCAG
1 AAGTCTAAAGGCTAACTATCATGACTTTTCGGGACCGAAATTGGCCAG
* *
22466 AAGTCTAAAGGCTAACTATCATGATTTTTCGGGACCGAAATTGGCTAG
1 AAGTCTAAAGGCTAACTATCATGACTTTTCGGGACCGAAATTGGCCAG
* *
22514 AAGTCCAAATGCTAA
1 AAGTCTAAAGGCTAA
22529 TCATCACCAC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (48 bp):
AAGTCTAAAGGCTAACTATCATGACTTTTCGGGACCGAAATTGGCCAG
Found at i:24689 original size:333 final size:332
Alignment explanation
Indices: 23729--25300 Score: 1679
Period size: 333 Copynumber: 4.7 Consensus size: 332
23719 TGCTTGCAAA
* * * * * * * * * *
23729 AAATCCAATGTAGCAGAGATTTGGTTAAATGATTGTAGATATTACAAGGAATCTTGGCACAAAAA
1 AAATCCAATGTGGAAGAGAATTGGTTAGATGAATATAGATATTTCAAAGAGTCTTGGCACCAAAA
* * * * *
23794 ATCATGCAAAATTGAGTCGGGGAC-CTCGG-A-GCATGTTTTTATCAAAAAAATTTGATTGTTAG
66 ATCATGCAAAATTGAGTCGGGG-CTCTCGGAACGCA--TTTTTAGCCAAAAACTGTGATGGTTAG
* ** * *
23856 TACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGTAACAATTTTTCCTC-ATTTCTTAGTC
128 TACACGATTTTGGCTAAAATTTTGCAAAAATTGACCCGTAA-GATTTTTCCTCAATTT-TTAGCC
* * * *
23920 ACAATACTCATAAAAAAAATTACAATTTAACACCAAAAAGATTGAAGGGCTTTTCATGCTTTTAA
191 ACAATACTCAT-AAAAATA-TATAATTTAACGCCAAAAAGATTGAAGGACTTTTCATGCTTTTAA
* * * * * * * *
23985 TATCGTTTTTCATTTTTTTTCCGAATTAATTTTTAATTAAATTGAAACATGATTTAGATGCTCAT
254 TATCATTTTTCCTTTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
*
24050 AAAAACAAATACTT
319 AAAAACAAATCCTT
* * * ** * * ** *
24064 TAATGCAAAGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAAGAGTCTTGGTGCCAAAG
1 AAATCCAATGTGGAAGAGAATTGGTTAGATGAATATAGATATTTCAAAGAGTCTTGGCACCAAAA
* * * ** * **
24129 ATCATGCAAAATTGAGCCAGAGCTC-CTAAACGCGTTTTTAG-CAAAAACTGTGAAAGTTAGTAC
66 ATCATGCAAAATTGAGTCGGGGCTCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTAC
* * * *
24192 ACGATTTCGGCTAAAATTTTGTAAAAATTGACCC-AATAGATTTTTCCACAATTTTTAGCCACAA
131 ACGATTTTGGCTAAAATTTTGCAAAAATTGACCCGTA-AGATTTTTCCTCAATTTTTAGCCACAA
* * * *
24256 TACTCATAAAAATATATAATTCAACGCC-AAAAGATTAAAGGGCTTTTCATGCTTTTAATGTCAT
195 TACTCATAAAAATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCATGCTTTTAATATCAT
* *
24320 TTTCCCGTTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
260 TTTTCCTTTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
24385 AAATCCTT
325 AAATCCTT
* * * * *
24393 AAATCCAATGCGGAAGAGAATTGGTTAGATGAATATAGATATTTTAAAAAGTTTTGGCACCACAA
1 AAATCCAATGTGGAAGAGAATTGGTTAGATGAATATAGATATTTCAAAGAGTCTTGGCACCAAAA
* *
24458 ATCATGTAAAATTGAGTCGGGGCTC-CGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTAT
66 ATCATGCAAAATTGAGTCGGGGCTCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTAC
* * * * * * * * *
24522 ATGATTTTGGCTAAAATTATGCAAAAAATGATCTGATATA-ATTTTTTCTCAGTTTTAAGCCAGA
131 ACGATTTTGGCTAAAATTTTGCAAAAATTGACCCG-TA-AGATTTTTCCTCAATTTTTAGCCACA
* * * *
24586 ATACTCATAGAAAATATATAATTTATCGCCAAAAAGATTGATGGATTTTTCATGGTTTTAATATC
194 ATACTCATA-AAAATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCATGCTTTTAATATC
* * *
24651 ATTTTTCCTTTATTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGAAT-CACGTAAA
258 ATTTTTCCTTTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAG-ATGCTCGTAAA
* *
24715 ATCATATCCTT
322 AACAAATCCTT
** * ** * *
24726 AAATGTAATGTGGCAA-AGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACAAAA
1 AAATCCAATGTGG-AAGAGAATTGGTTAGATGAATATAGATATTTCAAAGAGTCTTGGCACCAAA
* *
24790 AATCATGCAAAATTGAAT-GGGGGTCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTA
65 AATCATGCAAAATTGAGTCGGGGCTCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTA
* * * *
24854 CACAATTTCT-GCTAAAATTTTGCAAAATTTGACCCGTAAGGTTTTATTCTCAATTTTTAGCCAC
130 CACGATTT-TGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTT-TCCTCAATTTTTAGCCAC
* * * * * *
24918 AATACACATAAAAAATATATAATTTAACCCCAAAAGGTTTGAAGGACTTCTCAT-TTTTCTAATA
193 AATACTCAT-AAAAATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCATGCTTT-TAATA
* * * * * *
24982 TCGTTTTACCTTTATTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATACTCGTTA
256 TCATTTTTCCTTTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
25047 AAA-AAATCCTT
321 AAACAAATCCTT
* *
25058 AAATCCGATGTGGAAGAGAA-TCGTTAGATGAATATAGATATTT-AAAGGAGTCTTGGCACCAAA
1 AAATCCAATGTGGAAGAGAATTGGTTAGATGAATATAGATATTTCAAA-GAGTCTTGGCACCAAA
* * * *
25121 AATCATGCAAAATTGAGTCAGGAC-CTCGGAACGCGTTTTTAGCAAAAAACTGTGATGGTTAGTA
65 AATCATGCAAAATTGAGTCGGGGCTCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTA
* ** * * * *
25185 CACAATTTTTACTAAAATTTTGCAAAAATTGACCTGTAAGATTTTTCCTTATTTTTTAGACACAA
130 CACGATTTTGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAA
* * * * *
25250 TAATCATAAGGAATATATAATTCAACGCCAAAAAGATTAAATGACTTTTCA
195 TACTCATAA-AAATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCA
25301 CTCTTCTAAT
Statistics
Matches: 1029, Mismatches: 184, Indels: 53
0.81 0.15 0.04
Matches are distributed among these distances:
329 182 0.18
330 114 0.11
331 167 0.16
332 86 0.08
333 395 0.38
334 14 0.01
335 69 0.07
336 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (332 bp):
AAATCCAATGTGGAAGAGAATTGGTTAGATGAATATAGATATTTCAAAGAGTCTTGGCACCAAAA
ATCATGCAAAATTGAGTCGGGGCTCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTAC
ACGATTTTGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAAT
ACTCATAAAAATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCATGCTTTTAATATCATT
TTTCCTTTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
AATCCTT
Found at i:24763 original size:662 final size:659
Alignment explanation
Indices: 23564--25300 Score: 1920
Period size: 663 Copynumber: 2.6 Consensus size: 659
23554 CTAAAAGTTT
* * *
23564 ACCCATAAGATTTTTCCTCAATTTATAGCCGCAATACTCATAAAAAATATATAATTTAACGCAAA
1 ACCCATAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTTAACGC--C
* * * * **
23629 AAAAAATTTAGAGGGTTTTTCATGCTTCTAATATCATTTTTCCCTTTATTTTATGAATTAATTTC
64 AAAAGA-TTAAAGGGCTTTTCATGCTTTTAATATCA-TTTTCCCTTTATTTTCCGAATTAATTTC
* * * * *
23694 TAATTAAATCGAAACAAGATTCAAATGCT--T---GCAAA-----AAATCCAATGTAGCAGAGAT
127 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCAATGTGGAAGAGAA
* * * ** * *
23749 TTGGTTAAATGATTGTAGATATTACAAGGAA-TCTTGGCACAAAAAATCATGCAAAATTGAGTCG
192 TTGGTTAGATGAATATAGATATTTTAA-AAAGTCTTGGCACCAAAAATCATGCAAAATTGAGTCG
* * * * *
23813 GGGACCTCGG-A-GCATGTTTTTATCAAAAAAATTTGATTGTTAGTACATGATTTCAGCTAAAAT
256 GGG-CCTCGGAACGCA--TTTTTAGCAAAAAACTGTGATGGTTAGTACATGATTTTAGCTAAAAT
* * *
23876 TTTGCAAAAATTGACCCGTAACAATTTTTCCTCATTTCTTAGTCACAATACTCATAAAAAAAATT
318 TTTGCAAAAATTGACCTGT-A-AATTTTTCCTCATTT-TTAGACACAATACTCAT-AAAAATA-T
* * * * *
23941 ACAATTTAACACCAAAAAGATTGAAGGGCTTTTCATGCTTTTAATATCGTTTTTCATTTTTTTTC
378 ATAATTTAACGCCAAAAAGATTGAAGGACTTTTCATGCTTTTAATATCATTTTTCATTTATTTTC
* * * * *
24006 CGAATTAATTTTTAATTAAATTGAAACATGATTTAGATGCTCATAAAAACAAATACTTTAATGCA
443 CGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCACATAAAAACAAATACTTAAATGCA
*** ** * ** * *
24071 AAGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAAGAGTCTTGGTGCCAAAGATCATGC
508 AAGTGGCAAAGATTTAATTAGATGAATATAGATATTTCAAAGAGTCTTGGCACAAAAAATCATGC
* * * *
24136 AAAATTGAGCCAGAGCTC-CTAAACGCGTTTTTAG-CAAAAACTGTGAAAGTTAGTACACGATTT
573 AAAATTGA-ACAGAGCTCTCGAAACGCATTTTTAGCCAAAAACTGTGAAAGTTAGTACACAATTT
*
24199 CGGCTAAAATTTTGTAAAAATTG
637 CGGCTAAAATTTTGCAAAAATTG
* *
24222 ACCCA-ATAGATTTTTCCACAATTTTTAGCCACAATACTCAT-AAAAATATATAATTCAACGCCA
1 ACCCATA-AGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTTAACGCCA
* *
24285 AAAGATTAAAGGGCTTTTCATGCTTTTAATGTCATTTTCCCGTTATTTTCCGAATTAATTTCTAA
65 AAAGATTAAAGGGCTTTTCATGCTTTTAATATCATTTTCCCTTTATTTTCCGAATTAATTTCTAA
*
24350 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGCGGAAGAGAATT
130 TTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATCCAATGTGGAAGAGAATT
* * *
24415 GGTTAGATGAATATAGATATTTTAAAAAGTTTTGGCACCACAAATCATGTAAAATTGAGTCGGGG
194 GGTTAGATGAATATAGATATTTTAAAAAGTCTTGGCACCAAAAATCATGCAAAATTGAGTCGGGG
* * * *
24480 -CTCCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTATATGATTTTGGCTAAAATTATGC
259 CCT-CGGAACGCATTTTTAGCAAAAAACTGTGATGGTTAGTACATGATTTTAGCTAAAATTTTGC
* * * * * *
24544 AAAAAATGATCTGATATAATTTTTTCTCAGTTTTAAGCCAGAATACTCATAGAAAATATATAATT
323 AAAAATTGACCTG-TA-AATTTTTCCTCA-TTTTTAGACACAATACTCATA-AAAATATATAATT
* * * * * *
24609 TATCGCCAAAAAGATTGATGGATTTTTCATGGTTTTAATATCATTTTTCCTTTATTTTCTGAATT
384 TAACGCCAAAAAGATTGAAGGACTTTTCATGCTTTTAATATCATTTTTCATTTATTTTCCGAATT
* * * * * *
24674 AATTTCTAATTAAATCGAAACAAGATTTAGAAT-CACGTAAAATCATATCCTTAAATGTAATGTG
449 AATTTCTAATTAAATCGAAACAAGATTTAG-ATGCACATAAAAACAAATACTTAAATGCAAAGTG
*
24738 GCAAAGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACAAAAAATCATGCAAAAT
513 GCAAAGATTTAATTAGATGAATATAGATATTTCAAAGAGTCTTGGCACAAAAAATCATGCAAAAT
** * * * ** *
24803 TGAATGGGGGTCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACAATTTCTGCTA
578 TGAACAGAGCTCTCGAAACGCATTTTTAGCCAAAAACTGTGAAAGTTAGTACACAATTTCGGCTA
*
24868 AAATTTTGCAAAATTTG
643 AAATTTTGCAAAAATTG
* * * * *
24885 ACCCGTAAGGTTTTATTCTCAATTTTTAGCCACAATACACATAAAAAATATATAATTTAACCCCA
1 ACCCATAAGATTTT-TCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTTAACGCCA
* * * * * * * *
24950 AAAGGTTTGAAGGACTTCTCAT-TTTTCTAATATCGTTTTACCTTTATTTTCCAAATTAATTTCT
65 AAA-GATTAAAGGGCTTTTCATGCTTT-TAATATCATTTTCCCTTTATTTTCCGAATTAATTTCT
* * *
25014 AATTAAATCGAAACATGATTCAGATACTCGTTAAAA-AAATCCTTAAATCCGATGTGGAAGAGAA
128 AATTAAATCGAAACAAGATTCAGATGCTCG-TAAAACAAATCCTTAAATCCAATGTGGAAGAGAA
* * *
25078 -TCGTTAGATGAATATAGATA-TTTAAAGGAGTCTTGGCACCAAAAATCATGCAAAATTGAGTCA
192 TTGGTTAGATGAATATAGATATTTTAAA-AAGTCTTGGCACCAAAAATCATGCAAAATTGAGTCG
* * **
25141 GGACCTCGGAACGCGTTTTTAGCAAAAAACTGTGATGGTTAGTACACAATTTTTA-CTAAAATTT
256 GGGCCTCGGAACGCATTTTTAGCAAAAAACTGTGATGGTTAGTACATGA-TTTTAGCTAAAATTT
* * *
25205 TGCAAAAATTGACCTGTAAGATTTTTCCTTATTTTTTAGACACAATAATCATAAGGAATATATAA
320 TGCAAAAATTGACCTGTAA-ATTTTTCCTCA-TTTTTAGACACAATACTCATAA-AAATATATAA
* * *
25270 TTCAACGCCAAAAAGATTAAATGACTTTTCA
382 TTTAACGCCAAAAAGATTGAAGGACTTTTCA
25301 CTCTTCTAAT
Statistics
Matches: 901, Mismatches: 145, Indels: 61
0.81 0.13 0.06
Matches are distributed among these distances:
653 53 0.06
654 25 0.03
655 6 0.01
657 20 0.02
658 36 0.04
659 4 0.00
661 4 0.00
662 186 0.21
663 215 0.24
664 212 0.24
665 61 0.07
666 78 0.09
667 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (659 bp):
ACCCATAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTTAACGCCAA
AAGATTAAAGGGCTTTTCATGCTTTTAATATCATTTTCCCTTTATTTTCCGAATTAATTTCTAAT
TAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCAATGTGGAAGAGAATTGG
TTAGATGAATATAGATATTTTAAAAAGTCTTGGCACCAAAAATCATGCAAAATTGAGTCGGGGCC
TCGGAACGCATTTTTAGCAAAAAACTGTGATGGTTAGTACATGATTTTAGCTAAAATTTTGCAAA
AATTGACCTGTAAATTTTTCCTCATTTTTAGACACAATACTCATAAAAATATATAATTTAACGCC
AAAAAGATTGAAGGACTTTTCATGCTTTTAATATCATTTTTCATTTATTTTCCGAATTAATTTCT
AATTAAATCGAAACAAGATTTAGATGCACATAAAAACAAATACTTAAATGCAAAGTGGCAAAGAT
TTAATTAGATGAATATAGATATTTCAAAGAGTCTTGGCACAAAAAATCATGCAAAATTGAACAGA
GCTCTCGAAACGCATTTTTAGCCAAAAACTGTGAAAGTTAGTACACAATTTCGGCTAAAATTTTG
CAAAAATTG
Done.