Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012134.1 Corchorus capsularis cultivar CVL-1 contig12155, 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: 119739
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:7366 original size:61 final size:58
Alignment explanation
Indices: 7261--7381 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 58
7251 TTAAGTAAAA
* * *
7261 CTATAACAAATAAATAGAGCAAACTGATGTAGGATGGATTGGAGATTACAACTTGCAG
1 CTATAAAAAATAAATAGAGCAAACTGATGTAGGATGGATAGGAGATTACAACTTGAAG
*
7319 CTATAAAAAATAAATAGAGCGACCAACTGATGTAGGATGGCTAGGAGATTACAACTTGAAG
1 CTATAAAAAATAAATAGAGC-A--AACTGATGTAGGATGGATAGGAGATTACAACTTGAAG
7380 CT
1 CT
7382 GTATAAATCT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
58 19 0.34
59 1 0.02
61 36 0.64
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.23
Consensus pattern (58 bp):
CTATAAAAAATAAATAGAGCAAACTGATGTAGGATGGATAGGAGATTACAACTTGAAG
Found at i:13725 original size:29 final size:29
Alignment explanation
Indices: 13689--13748 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
13679 GACTCAAATC
13689 AATGTTTACTAAAGATAATGAAGAAATGG
1 AATGTTTACTAAAGATAATGAAGAAATGG
13718 AATGTTTACTAAAGATAATGAAGAAATGG
1 AATGTTTACTAAAGATAATGAAGAAATGG
13747 AA
1 AA
13749 GAGAGGAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.27
Consensus pattern (29 bp):
AATGTTTACTAAAGATAATGAAGAAATGG
Found at i:26420 original size:77 final size:77
Alignment explanation
Indices: 26320--26465 Score: 204
Period size: 77 Copynumber: 1.9 Consensus size: 77
26310 TTTTTTCAAC
* ** * * *
26320 CCAAACAAGATTTGCTCATCTAATAACAAAACTTGTAGCATCTTGTCTACCCTCTTTGAAACTAT
1 CCAAACAAGATTTGCTCACCTAATAACAAAACTCATAGAATATTGTATACCCTCTTTGAAACTAT
26385 TAACAACTCAGA
66 TAACAACTCAGA
* *
26397 CCAAACAA-ATTTGGCTCACCTAATAACAAAACTCATAGAATATTTTATACCCTCTTTGCAACTA
1 CCAAACAAGATTT-GCTCACCTAATAACAAAACTCATAGAATATTGTATACCCTCTTTGAAACTA
26461 TTAAC
65 TTAAC
26466 CGTAAGGATC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 4 0.07
77 56 0.93
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.30
Consensus pattern (77 bp):
CCAAACAAGATTTGCTCACCTAATAACAAAACTCATAGAATATTGTATACCCTCTTTGAAACTAT
TAACAACTCAGA
Found at i:34977 original size:17 final size:18
Alignment explanation
Indices: 34957--34997 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
34947 ATGCAGCATC
34957 AATATATATATCAATA-T
1 AATATATATATCAATAGT
*
34974 AATATATATATCCATAGT
1 AATATATATATCAATAGT
34992 AATATA
1 AATATA
34998 CTCACCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (18 bp):
AATATATATATCAATAGT
Found at i:35478 original size:31 final size:31
Alignment explanation
Indices: 35407--35491 Score: 73
Period size: 31 Copynumber: 2.7 Consensus size: 31
35397 TGGTATGATC
* *
35407 TTGTCACGTGGTATTTTGGTCCAACGTAGCA
1 TTGTCATGTGATATTTTGGTCCAACGTAGCA
* * ** * *
35438 TAGTTATGTGATATTTTGGTCTGATGTGGCA
1 TTGTCATGTGATATTTTGGTCCAACGTAGCA
35469 TTGTCATGTGGA-ATTTTTGGTCC
1 TTGTCATGT-GATA-TTTTGGTCC
35492 CACATAGTAT
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
31 31 0.76
32 10 0.24
ACGTcount: A:0.18, C:0.13, G:0.27, T:0.42
Consensus pattern (31 bp):
TTGTCATGTGATATTTTGGTCCAACGTAGCA
Found at i:52206 original size:17 final size:17
Alignment explanation
Indices: 52184--52225 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
52174 GCACTATCAA
52184 ATCAATCAATTACAATC
1 ATCAATCAATTACAATC
52201 ATCAATCAATTACAATC
1 ATCAATCAATTACAATC
*
52218 ACCAATCA
1 ATCAATCA
52226 TAACAATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (17 bp):
ATCAATCAATTACAATC
Found at i:56305 original size:6 final size:6
Alignment explanation
Indices: 56294--56319 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56284 GACGGAACAT
56294 GCCGAC GCCGAC GCCGAC GCCGAC GC
1 GCCGAC GCCGAC GCCGAC GCCGAC GC
56320 ACCAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.35, T:0.00
Consensus pattern (6 bp):
GCCGAC
Found at i:67601 original size:9 final size:9
Alignment explanation
Indices: 67587--67626 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
67577 TTAATTTCTT
*
67587 TTAATTTAA
1 TTAATTAAA
67596 TTAATTAAA
1 TTAATTAAA
**
67605 TTAAAGAAA
1 TTAATTAAA
67614 TTAATTAAA
1 TTAATTAAA
67623 TTAA
1 TTAA
67627 GTTGAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (9 bp):
TTAATTAAA
Found at i:75963 original size:16 final size:17
Alignment explanation
Indices: 75933--75967 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
75923 ATGACGTGTC
*
75933 TTCTCTTTTCTTTCTTT
1 TTCTCTTTTCATTCTTT
75950 TTCT-TTTTCATTCTTT
1 TTCTCTTTTCATTCTTT
75966 TT
1 TT
75968 AGTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTCTTTTCATTCTTT
Found at i:76179 original size:107 final size:107
Alignment explanation
Indices: 76008--76339 Score: 361
Period size: 107 Copynumber: 3.1 Consensus size: 107
75998 GAAATTTAAT
* * * * * * *
76008 TTTTAAGAGTAAATTATGAAAATAAAGATTTTA-TATTATAGAGTTTTAGAAGTAAAATATAAAA
1 TTTTAAGGGTAAATT-TCAAAATTAATAATTTATTGTTATAGAGTTTTAGAAATAAAATATAAAA
*
76072 CTAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTA
65 CTAATTTCACTAAGTTTAGACCCAAATTAAAATTTTATTTTTA
* *
76115 TTTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGCGTTTTAGAAATAAAATACAAAAC
1 TTTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGAGTTTTAGAAATAAAATATAAAAC
*
76180 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTTA
66 TAATTTCACTAAGTTTAGACCCAAATT-AAA----A-TTTTATTTTTA
* * * * * *
76228 TTTTAAGGGTAAA-TCCATAATTAATAA--TATTGTTGTAGGGTTTTAGAAATAAAATATATAAT
1 TTTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGAGTTTTAGAAATAAAATATAAAAC
* ** * *
76290 TAA-TTCACTAAGTTTA-AACCAAATTAAAATTAAAATTTTG
66 TAATTTCACTAAGTTTAGACCCAAATTAAAATTTTATTTTTA
76330 TTTTAAGGGT
1 TTTTAAGGGT
76340 TAGAAAAATT
Statistics
Matches: 195, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
102 17 0.09
103 1 0.01
106 13 0.07
107 71 0.36
108 10 0.05
109 13 0.07
110 33 0.17
112 13 0.07
113 24 0.12
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (107 bp):
TTTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGAGTTTTAGAAATAAAATATAAAAC
TAATTTCACTAAGTTTAGACCCAAATTAAAATTTTATTTTTA
Found at i:76470 original size:2 final size:2
Alignment explanation
Indices: 76463--76511 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
76453 ACATTGTAGA
*
76463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76504 ACT AT AT A
1 A-T AT AT A
76512 GGAAAGCACG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:77332 original size:2 final size:2
Alignment explanation
Indices: 77325--77360 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
77315 CAATTTAGAA
*
77325 AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
77361 AAAGTATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:79971 original size:119 final size:118
Alignment explanation
Indices: 79777--80014 Score: 377
Period size: 119 Copynumber: 2.0 Consensus size: 118
79767 CTAATATTGG
**
79777 AGTATATCTACCACAACATGTTTTCTCCCATGCACAACTATATGTCGCACTCTCTCGGGAATTTC
1 AGTATATCTACCACAACATGTTTTCTCCCACACACAACTATATGTCGCACTCTCTCGGGAATTTC
*
79842 AATGACTTCAATGAAAATTTTGGTCAAGTTAGAAAACACAATGAATCAAAATGA
66 AATGACTTCAACGAAAATTTTGGTCAAGTTAGAAAACAC-ATGAATCAAAATGA
* * * *
79896 AGTATATCTGCCACAATATGTTTTCTCCCACACACAAGTATATGTTGCACTCTCTCGGGAATTTC
1 AGTATATCTACCACAACATGTTTTCTCCCACACACAACTATATGTCGCACTCTCTCGGGAATTTC
* **
79961 AATGCCTTCAACGAAAATTTTGGTCAAGTTAGAAAATTCATGAATCAAAATGA
66 AATGACTTCAACGAAAATTTTGGTCAAGTTAGAAAACACATGAATCAAAATGA
80014 A
1 A
80015 ACATATAAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
118 15 0.14
119 94 0.86
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (118 bp):
AGTATATCTACCACAACATGTTTTCTCCCACACACAACTATATGTCGCACTCTCTCGGGAATTTC
AATGACTTCAACGAAAATTTTGGTCAAGTTAGAAAACACATGAATCAAAATGA
Found at i:81375 original size:22 final size:23
Alignment explanation
Indices: 81336--81406 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
81326 ACTGATTAGT
*
81336 ATTTTACTC--TTGTTGATTACC
1 ATTTTACTCTTTTATTGATTACC
81357 -TTCTTACT-TTTTATTGATTACC
1 ATT-TTACTCTTTTATTGATTACC
* *
81379 ATTTTACTCTTTTACTGATTACT
1 ATTTTACTCTTTTATTGATTACC
81402 ATTTT
1 ATTTT
81407 CTGCTCCTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.05
21 5 0.12
22 16 0.38
23 19 0.45
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.58
Consensus pattern (23 bp):
ATTTTACTCTTTTATTGATTACC
Found at i:81400 original size:15 final size:15
Alignment explanation
Indices: 81382--81437 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
81372 GATTACCATT
81382 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
81397 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
81410 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
81425 TTACTCTTTTACT
1 TTACTCTTTTACT
81438 TCTTACTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 19 0.59
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:81464 original size:21 final size:21
Alignment explanation
Indices: 81418--81533 Score: 133
Period size: 21 Copynumber: 5.4 Consensus size: 21
81408 TGCTCCTTTT
*
81418 TTACTGATTACTCTTTTACTTC
1 TTACTGATTACTATTTTAC-TC
*
81440 TTACTGATTACTATTTGACTC
1 TTACTGATTACTATTTTACTC
* * * *
81461 TTACTAATTACCACTTTGCTC
1 TTACTGATTACTATTTTACTC
* * *
81482 TCACTGGTTACTGTTTTACTC
1 TTACTGATTACTATTTTACTC
81503 TTACTGATTACTATTTTACTC
1 TTACTGATTACTATTTTACTC
81524 TTTACTGATT
1 -TTACTGATT
81534 GTCATTATTT
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
21 50 0.66
22 26 0.34
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.50
Consensus pattern (21 bp):
TTACTGATTACTATTTTACTC
Found at i:81613 original size:22 final size:21
Alignment explanation
Indices: 81572--81621 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
81562 ACTATTTCAT
* *
81572 TCTTTACTGATTATCTTTTTAC
1 TCTTTACTGATTACCCTTTT-C
*
81594 TTTTTACTGATTACCCTTTTC
1 TCTTTACTGATTACCCTTTTC
81615 TCTTTAC
1 TCTTTAC
81622 CATTCTTCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.58
Consensus pattern (21 bp):
TCTTTACTGATTACCCTTTTC
Found at i:81637 original size:35 final size:35
Alignment explanation
Indices: 81596--81722 Score: 148
Period size: 35 Copynumber: 3.6 Consensus size: 35
81586 CTTTTTACTT
* *
81596 TTTACTGATTACCCTTTTCTCTTTACCATTCTTCC
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
* *
81631 TTTACTGATTACTCTTTACTTTTTACCATTCTTCT
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
* *
81666 TTTACTGATTACTCTTTACTTTTTTATCATT-TTACTC
1 TTTACTGATTACTCTTTAC-TCTTTACCATTCTT-C-C
* *
81703 TTTACTAATTACTCCTTACT
1 TTTACTGATTACTCTTTACT
81723 GATTATTCTT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
35 52 0.64
36 12 0.15
37 17 0.21
ACGTcount: A:0.18, C:0.24, G:0.02, T:0.55
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
Found at i:83318 original size:15 final size:15
Alignment explanation
Indices: 83295--83329 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
83285 TTTTTTTCTA
* *
83295 TTTTCTGTATGTATT
1 TTTTTTGTATCTATT
83310 TTTTTTGTATCTATT
1 TTTTTTGTATCTATT
83325 TTTTT
1 TTTTT
83330 GAGTTTCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.11, C:0.06, G:0.09, T:0.74
Consensus pattern (15 bp):
TTTTTTGTATCTATT
Found at i:86624 original size:31 final size:31
Alignment explanation
Indices: 86589--86650 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
86579 AAACTGAACT
86589 AACTCAAACATCCAAGATCTAAAGATCTGGA
1 AACTCAAACATCCAAGATCTAAAGATCTGGA
86620 AACTCAAACATCCAAGATCTAAAGATCTGGA
1 AACTCAAACATCCAAGATCTAAAGATCTGGA
86651 GACTGATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (31 bp):
AACTCAAACATCCAAGATCTAAAGATCTGGA
Found at i:90749 original size:1 final size:1
Alignment explanation
Indices: 90745--90773 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
90735 CTTTTTTTTT
90745 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
90774 CTGCCAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:92202 original size:5 final size:5
Alignment explanation
Indices: 92154--92189 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
92144 ACAATTGAAA
92154 AGAAC AG-AC AG-AC AGAAC AGAAC AGAAC AGAAC AGA
1 AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGA
92190 GTAAAACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.58, C:0.19, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAC
Found at i:94085 original size:16 final size:16
Alignment explanation
Indices: 94064--94097 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
94054 TTGAGTTTAC
94064 TTGAGTTGGTAAGACG
1 TTGAGTTGGTAAGACG
*
94080 TTGAGTTGGTCAGACG
1 TTGAGTTGGTAAGACG
94096 TT
1 TT
94098 TTAGCTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.35, T:0.35
Consensus pattern (16 bp):
TTGAGTTGGTAAGACG
Found at i:96501 original size:70 final size:70
Alignment explanation
Indices: 96425--96649 Score: 297
Period size: 70 Copynumber: 3.1 Consensus size: 70
96415 TAACTAAAAT
*
96425 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
96490 AGTTG
66 AGTTG
* *
96495 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGAATATTAGATTTCATTATATAAAAATA
1 AGT-AAA-A-T----T-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
96560 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
* * * * * *
96573 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
96638 AGTTG
66 AGTTG
96643 AGTAAAA
1 AGTAAAA
96650 CTATAAGAAG
Statistics
Matches: 136, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
70 64 0.47
71 3 0.02
72 1 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 4 0.03
78 61 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (70 bp):
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:96502 original size:78 final size:77
Alignment explanation
Indices: 96419--96649 Score: 341
Period size: 78 Copynumber: 3.1 Consensus size: 77
96409 TTTTTTTAAC
*
96419 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
96484 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* *
96497 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGAATATTAGATTTCATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
96562 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
96575 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
96633 TTTTTAGTTGAG
66 TTTTTAGTTGAG
96645 TAAAA
1 TAAAA
96650 CTATAAGAAG
Statistics
Matches: 144, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
70 49 0.34
71 1 0.01
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 86 0.60
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:96762 original size:6 final size:6
Alignment explanation
Indices: 96745--96790 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
96735 GTACTTTTTA
*
96745 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG ATATAA ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
96791 TATTTGCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:97271 original size:54 final size:54
Alignment explanation
Indices: 97186--97295 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
97176 AATTCTTTAT
* * * * *
97186 GTGAAAATTGAATCCAAAATTTCATGGTTCAGGCACGATGCACCTATTAGTCGA
1 GTGAAAATTGAATCCAAAACTTCATGATTCAGGCACGATACACCTACTAATCGA
*
97240 GTGAAAATTGAATCCAGAACTTCATGATTCAGGCACGATACACCTACTAATCGA
1 GTGAAAATTGAATCCAAAACTTCATGATTCAGGCACGATACACCTACTAATCGA
97294 GT
1 GT
97296 TAATAACACA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (54 bp):
GTGAAAATTGAATCCAAAACTTCATGATTCAGGCACGATACACCTACTAATCGA
Found at i:97655 original size:78 final size:80
Alignment explanation
Indices: 97566--97726 Score: 299
Period size: 78 Copynumber: 2.0 Consensus size: 80
97556 ACTACACTAT
*
97566 ATAATTCTCTTTTATTTTTAAGAAAATGAAAAAGAAAGTTGTTTACTGT-AAAAAAGGAAAATTT
1 ATAATTCTCTTTTATTTTTAAGAAAATGAAAAAGAAAGTTGTTTACTATAAAAAAAGGAAAATTT
97630 GTAAAAT-ATGGGCC
66 GTAAAATAATGGGCC
97644 ATAATTCTCTTTTATTTTTAAGAAAATGAAAAAGAAAGTTGTTTACTATAAAAAAAGGAAAATTT
1 ATAATTCTCTTTTATTTTTAAGAAAATGAAAAAGAAAGTTGTTTACTATAAAAAAAGGAAAATTT
97709 GTAAAATAATGGGCC
66 GTAAAATAATGGGCC
97724 ATA
1 ATA
97727 CATAAACATG
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
78 48 0.60
79 22 0.28
80 10 0.12
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.34
Consensus pattern (80 bp):
ATAATTCTCTTTTATTTTTAAGAAAATGAAAAAGAAAGTTGTTTACTATAAAAAAAGGAAAATTT
GTAAAATAATGGGCC
Found at i:101034 original size:31 final size:31
Alignment explanation
Indices: 100973--101040 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
100963 CAAAAAATGT
* * *
100973 TCAATTTCATCTTTATACTTACAATGTTTGG
1 TCAATTTAATCCTTATACTCACAATGTTTGG
*
101004 TCAATTTAATCCTTGTACTCACAA-GATTTGG
1 TCAATTTAATCCTTATACTCACAATG-TTTGG
*
101035 TTAATT
1 TCAATT
101041 GAGTCTAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (31 bp):
TCAATTTAATCCTTATACTCACAATGTTTGG
Found at i:102320 original size:15 final size:15
Alignment explanation
Indices: 102291--102337 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
102281 AAATTAAAAC
*
102291 TAAAAATATTAATATT
1 TAAAAATATT-ATATA
* *
102307 TAGATATATTATATA
1 TAAAAATATTATATA
102322 TAAAAATATTATATA
1 TAAAAATATTATATA
102337 T
1 T
102338 TTTATTGGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TAAAAATATTATATA
Found at i:114226 original size:13 final size:13
Alignment explanation
Indices: 114197--114229 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
114187 TGGGGTACAC
114197 AAATAAT-ATATA
1 AAATAATAATATA
*
114209 TAATAATAATATA
1 AAATAATAATATA
114222 AAATAATA
1 AAATAATA
114230 TAATAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATAATAATATA
Found at i:114228 original size:10 final size:11
Alignment explanation
Indices: 114198--114235 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
114188 GGGGTACACA
114198 AATAATATATAT
1 AATAATA-ATAT
114210 AATAATAATAT
1 AATAATAATAT
114221 AA-AATAATAT
1 AATAATAATAT
114231 AATAA
1 AATAA
114236 ATCAAAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.40
11 8 0.32
12 7 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAATAATAT
Found at i:117072 original size:2 final size:2
Alignment explanation
Indices: 117067--117092 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
117057 TGTGTGTGTG
117067 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
117093 AAATATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119642 original size:29 final size:29
Alignment explanation
Indices: 119600--119655 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
119590 GCTTCAAAGC
*
119600 GACTGAATTTCAACCCATCTAAAATGAGT
1 GACTGAATTTCAACCCATCGAAAATGAGT
119629 GACTGAATTTCAACCCATCGAAAATGA
1 GACTGAATTTCAACCCATCGAAAATGA
119656 CTGAATCAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (29 bp):
GACTGAATTTCAACCCATCGAAAATGAGT
Done.