Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014075.1 Corchorus capsularis cultivar CVL-1 contig14096, 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: 67242
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:163 original size:23 final size:23
Alignment explanation
Indices: 98--165 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
88 TTTTCATAAC
* *
98 GTGGTTATCAATATATCATA-TG
1 GTGGTTATCAAAATTTCATAGTG
* *
120 GAGGTTATCAACATCTT-ATAGTG
1 GTGGTTATCAAAAT-TTCATAGTG
*
143 TTGGTTATCAAAATTTCATAGTG
1 GTGGTTATCAAAATTTCATAGTG
166 AGATCTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (23 bp):
GTGGTTATCAAAATTTCATAGTG
Found at i:342 original size:22 final size:22
Alignment explanation
Indices: 317--413 Score: 69
Period size: 22 Copynumber: 4.6 Consensus size: 22
307 AATAGTGTAA
317 TTATCATAATTTCATAGGAAGG
1 TTATCATAATTTCATAGGAAGG
* *
339 TTATCAAAATTTCATAAGG-ACG
1 TTATCATAATTTCAT-AGGAAGG
* * * * * *
361 TCATAAAAAATAC-T-GTAA--
1 TTATCATAATTTCATAGGAAGG
*
379 TTATCATAATTTAATAGGAAGG
1 TTATCATAATTTCATAGGAAGG
401 TTATCATAATTTC
1 TTATCATAATTTC
414 GTATCAATAT
Statistics
Matches: 54, Mismatches: 15, Indels: 12
0.67 0.19 0.15
Matches are distributed among these distances:
18 7 0.13
19 2 0.04
20 4 0.07
21 1 0.02
22 37 0.69
23 3 0.06
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
TTATCATAATTTCATAGGAAGG
Found at i:355 original size:62 final size:62
Alignment explanation
Indices: 259--413 Score: 256
Period size: 62 Copynumber: 2.5 Consensus size: 62
249 ATCGTTATTA
*
259 AATTTCATGAGGAAGGATTATCAAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
1 AATTTCAT-AGGAAGG-TTATC-AAAATTTCATAAGGACGTCATAAAAAATACTGTAATTATCAT
324 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATACTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATACTGTAATTATCAT
* *
386 AATTTAATAGGAAGGTTATCATAATTTC
1 AATTTCATAGGAAGGTTATCAAAATTTC
414 GTATCAATAT
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
62 67 0.77
63 5 0.06
64 7 0.08
65 8 0.09
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATACTGTAATTATCAT
Found at i:5565 original size:30 final size:31
Alignment explanation
Indices: 5531--5592 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
5521 AATGAGTTCT
5531 TGAAG-TGAACTTAA-CGAGCAATTGAGTCCC
1 TGAAGTTG-ACTTAATCGAGCAATTGAGTCCC
* * *
5561 TGAAGTTGAGTTAATTGAGCAATTGGGTCCC
1 TGAAGTTGACTTAATCGAGCAATTGAGTCCC
5592 T
1 T
5593 CACCTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (31 bp):
TGAAGTTGACTTAATCGAGCAATTGAGTCCC
Found at i:14268 original size:30 final size:32
Alignment explanation
Indices: 14198--14268 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
14188 CTGAGAGGGT
*
14198 ATAAAATGTCTTGAATTTGAGAAATTCAGGAG
1 ATAAAATGTCTGGAATTTGAGAAATTCAGGAG
* * *
14230 ACAAAATGTC-GGAATTTG-GAAGTTCATGAG
1 ATAAAATGTCTGGAATTTGAGAAATTCAGGAG
*
14260 GTAAAATGT
1 ATAAAATGT
14269 TCTTGATGCA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 17 0.52
31 7 0.21
32 9 0.27
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (32 bp):
ATAAAATGTCTGGAATTTGAGAAATTCAGGAG
Found at i:15003 original size:16 final size:16
Alignment explanation
Indices: 14982--15093 Score: 129
Period size: 16 Copynumber: 7.1 Consensus size: 16
14972 CATGTAGTTT
14982 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
14998 TTTCGGGTCA-TCTGGG
1 TTTCGGGTCATTC-GGG
* * *
15014 -TTCGGATTATTCGAG
1 TTTCGGGTCATTCGGG
* *
15029 TCTCGGGTCGTTCGGG
1 TTTCGGGTCATTCGGG
* *
15045 TCTCGGGTCATACGGG
1 TTTCGGGTCATTCGGG
15061 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
15077 TTCCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
15093 T
1 T
15094 CCCGGGTCTA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
15 11 0.14
16 69 0.86
ACGTcount: A:0.08, C:0.21, G:0.37, T:0.35
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:15588 original size:21 final size:21
Alignment explanation
Indices: 15563--15610 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
15553 TAGCCAATTT
15563 ATAATAGGTAAAATCATAACA
1 ATAATAGGTAAAATCATAACA
* *
15584 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATCATAACA
15605 ATAATA
1 ATAATA
15611 TAAATTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (21 bp):
ATAATAGGTAAAATCATAACA
Found at i:15763 original size:16 final size:16
Alignment explanation
Indices: 15715--15769 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
15705 TCGGGTTAAT
* *
15715 GTCTCAGGTTATTCGG
1 GTCTCGGGTCATTCGG
* **
15731 GTTTCGGGTCAAACGG
1 GTCTCGGGTCATTCGG
15747 GTCTCGGGTCATTCGG
1 GTCTCGGGTCATTCGG
*
15763 GTTTCGG
1 GTCTCGG
15770 ATTATCTGGG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.11, C:0.20, G:0.36, T:0.33
Consensus pattern (16 bp):
GTCTCGGGTCATTCGG
Found at i:15812 original size:16 final size:16
Alignment explanation
Indices: 15725--15835 Score: 75
Period size: 16 Copynumber: 6.9 Consensus size: 16
15715 GTCTCAGGTT
15725 ATTCGGGTTTCGGGTC
1 ATTCGGGTTTCGGGTC
** *
15741 AAACGGGTCTCGGGTC
1 ATTCGGGTTTCGGGTC
* *
15757 ATTCGGGTTTCGGATT
1 ATTCGGGTTTCGGGTC
* *
15773 A-TCTGGGTTACGGATC
1 ATTC-GGGTTTCGGGTC
*
15789 A-TCTGGGTTGCGGGTC
1 ATTC-GGGTTTCGGGTC
**
15805 ATTCGGGTCACGGGTTC
1 ATTCGGGTTTCGGG-TC
*
15822 -GTCGGGTTTCGGGT
1 ATTCGGGTTTCGGGT
15836 TGGGCGGGTT
Statistics
Matches: 75, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
15 3 0.04
16 68 0.91
17 4 0.05
ACGTcount: A:0.11, C:0.19, G:0.38, T:0.32
Consensus pattern (16 bp):
ATTCGGGTTTCGGGTC
Found at i:15835 original size:32 final size:30
Alignment explanation
Indices: 15727--15835 Score: 92
Period size: 32 Copynumber: 3.4 Consensus size: 30
15717 CTCAGGTTAT
* *
15727 TCGGGTTTCGGGTCAAACGGGTCTCGGGTCA
1 TCGGGTTTCGGGTC-ATCGGGTCACGGGTCA
* * * *
15758 TTCGGGTTTCGGATTATCTGGGTTACGGATCA
1 -TCGGGTTTCGGGTCATC-GGGTCACGGGTCA
* *
15790 TCTGGGTTGCGGGTCATTCGGGTCACGGGTTCG
1 TC-GGGTTTCGGGTCA-TCGGGTCACGGG-TCA
15823 TCGGGTTTCGGGT
1 TCGGGTTTCGGGT
15836 TGGGCGGGTT
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
31 4 0.07
32 50 0.83
33 6 0.10
ACGTcount: A:0.10, C:0.19, G:0.39, T:0.32
Consensus pattern (30 bp):
TCGGGTTTCGGGTCATCGGGTCACGGGTCA
Found at i:15917 original size:18 final size:18
Alignment explanation
Indices: 15872--15917 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
15862 TTCTAGTCAA
15872 ATCGGGTT-GGGCGGGTT
1 ATCGGGTTCGGGCGGGTT
* *
15889 A-CAGATTCGGGCGGGTT
1 ATCGGGTTCGGGCGGGTT
15906 ATCGGGTTCGGG
1 ATCGGGTTCGGG
15918 TCAGATTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (18 bp):
ATCGGGTTCGGGCGGGTT
Found at i:16107 original size:107 final size:107
Alignment explanation
Indices: 15937--16236 Score: 541
Period size: 107 Copynumber: 2.8 Consensus size: 107
15927 GACAGCTGTA
* *
15937 TCTAAAACCCTATAACAAT--ATTATTAATTATGGAATTTACCCTTAAAATAAAAATAAAATTTT
1 TCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTT
16000 AATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATT
66 AATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATT
16042 TCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTT
1 TCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTT
*
16107 AATTTGGGACTAAACTTAGTGAAATTAGTTTTGTATTTTATT
66 AATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATT
* *
16149 TCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTAGCCGTAAAATAAAAATAAAATTTT
1 TCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTT
16214 AATTTGGGGCTAAACTTAGTGAA
66 AATTTGGGGCTAAACTTAGTGAA
16237 GTTAAGGCTA
Statistics
Matches: 187, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
105 19 0.10
107 168 0.90
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (107 bp):
TCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTT
AATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATT
Found at i:23755 original size:423 final size:429
Alignment explanation
Indices: 23158--23979 Score: 1070
Period size: 423 Copynumber: 1.9 Consensus size: 429
23148 TCAAATAAGA
** * *
23158 TAGAATTTGTAAACGGGTAAGTAGCATAAAATAGAAAAGTATGAGGGTCATTTGATAACTAATTC
1 TAGAATTTGTAAACGGCAAAGTAGCATAAAATAGAAAAATATGAGGGTCATTTGATAACTAATCC
* *
23223 AAATAAGCAAAATTTTCTTAAAGGATATCTTGAAACATAAAAATTCCCTTTTGAACCTTTCATGA
66 AAATAAGCAAAATTTTCTTAAAGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGA
* * * *
23288 AACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAGATCATACAGTAACCTTTTA
131 AACCCGTAGATCAAATTAACTTTCGGGCTCTTCATGAAAGTCGTAAATCATACAATAACCTTTTA
* *** * * *
23353 ACCGACA-C-T-ATCGGACATGTGGATCGAAAATTATATGGTATTAAATAGACCAACAATTGAAA
196 ACCAACATCATAATCGGACATGTGGAAAAAAAATTATACGATATTAAATAGACCAACAATTAAAA
* * * *
23415 CGACCAAA-TTCAGGAAGCATTTTTTTA-AATTAAAACA-TAAAATTTGCTTTTGAGTCCTTCAT
261 CGACAAAATTTC-GGAAGCATTTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAATCCTTCAT
*
23477 GAAAGTTGTAGATCATGAAACTAACTTTTAATAGACA-GAATCAACTTAATCGAACAAATAGAAC
325 GAAAATTGTAGATCATGAAACTAACTTTTAATAGACACGAATCAACTTAATCGAACAAATAGAAC
23541 AAAGAATAAAAAAATAACTCTTAAACGTTAGATTAAAATC
390 AAAGAATAAAAAAATAACTCTTAAACGTTAGATTAAAATC
* *
23581 TAGAATTTGTAAA-GGACAAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTTGATAA-TAATC
1 TAGAATTTGTAAACGG-CAAAGTAGCATAAAATAGAAAAATATGAGGGTCATTTGATAACTAATC
* * *
23644 CAAATAAG-AAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAATTCCCTTTTGAACCCTTCAT
65 CAAATAAGCAAAAT-TTTCTTAAAGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCAT
* *
23708 GAAACCCGTAGATCAAATTTAGCTTTCGGGCTCTTCATGAAAGTCGTAAATCATGCAATAACCTT
129 GAAACCCGTAGATCAAA-TTAACTTTCGGGCTCTTCATGAAAGTCGTAAATCATACAATAACCTT
* *
23773 TTAACTAACACTTCAATAAATTCAATCGGACATGTGGAAAAAAAATTATACGATATTAAATTGAC
193 TTAACCAACA--TC-----A-T-AATCGGACATGTGGAAAAAAAATTATACGATATTAAATAGAC
** *
23838 TGACAATTAAAACTACAAAATTTCGGAAGCATTTTTTTAGAATCAAAACATTAAAATTGGCTTTT
249 CAACAATTAAAACGACAAAATTTCGGAAGCATTTTTTTAGAATCAAAACATTAAAATTGGCTTTT
* * * * *
23903 GAATTCTTCATGAAAATTGTAGGTCATGAAATTACCTTTTAATAGACACCTGAATCATCTTAATC
314 GAATCCTTCATGAAAATTGTAGATCATGAAACTAACTTTTAATAGACA-C-GAATCAACTTAATC
* *
23968 GGACGAATAGAA
377 GAACAAATAGAA
23980 AAAAAAATTT
Statistics
Matches: 337, Mismatches: 41, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
421 5 0.01
422 75 0.22
423 100 0.30
426 1 0.00
433 1 0.00
435 65 0.19
436 12 0.04
437 55 0.16
440 23 0.07
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (429 bp):
TAGAATTTGTAAACGGCAAAGTAGCATAAAATAGAAAAATATGAGGGTCATTTGATAACTAATCC
AAATAAGCAAAATTTTCTTAAAGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGA
AACCCGTAGATCAAATTAACTTTCGGGCTCTTCATGAAAGTCGTAAATCATACAATAACCTTTTA
ACCAACATCATAATCGGACATGTGGAAAAAAAATTATACGATATTAAATAGACCAACAATTAAAA
CGACAAAATTTCGGAAGCATTTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAATCCTTCATG
AAAATTGTAGATCATGAAACTAACTTTTAATAGACACGAATCAACTTAATCGAACAAATAGAACA
AAGAATAAAAAAATAACTCTTAAACGTTAGATTAAAATC
Found at i:28209 original size:108 final size:105
Alignment explanation
Indices: 28065--28299 Score: 335
Period size: 108 Copynumber: 2.2 Consensus size: 105
28055 AATTTTTATC
* * **
28065 ATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCCAAATTAAAATTGTAT
1 ATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAACCCCAAATTAAAATTGTAT
*
28130 TTTTATTTTAAAGGTAAATTTTCAAAATTAATAATTTATTGTT
66 TTTTATTTTAAAGGTAAA-TTCCAAAATTAATAA--TATTGTT
* *
28173 ATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAATTTTAACCCCAAATTAAAATTTTAT
1 ATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAACCCCAAATTAAAATTGTAT
* *
28238 TTTTATTTTAAGGGTAAATTCCATAATTAATAATATTGTT
66 TTTTATTTTAAAGGTAAATTCCAAAATTAATAATATTGTT
* **
28278 AGAGGGTTTTAGATTTAAAATA
1 ATAGGGTTTTAGAAATAAAATA
28300 TACACATTCT
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
105 26 0.23
107 13 0.11
108 76 0.66
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.41
Consensus pattern (105 bp):
ATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAACCCCAAATTAAAATTGTAT
TTTTATTTTAAAGGTAAATTCCAAAATTAATAATATTGTT
Found at i:30207 original size:32 final size:32
Alignment explanation
Indices: 30141--30213 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
30131 AATGAGGACA
* * * *
30141 TTTAGTCCCATGAACTTCGAAATTCAGGACAT
1 TTTAGCCCCATGAACTTCCAAATTCAAGAAAT
30173 TTTA-CCCCATGAACTTCCCAAATTCAAGAAAT
1 TTTAGCCCCATGAACTT-CCAAATTCAAGAAAT
30205 TTTAGCCCC
1 TTTAGCCCC
30214 TGGCGAAGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 11 0.31
32 20 0.57
33 4 0.11
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (32 bp):
TTTAGCCCCATGAACTTCCAAATTCAAGAAAT
Found at i:39728 original size:22 final size:21
Alignment explanation
Indices: 39675--39729 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
39665 ACCATTTCTC
39675 TTTT-TTTA-TTTTCTTTCAA
1 TTTTATTTATTTTTCTTTCAA
* *
39694 TTTAATCTT-TTTTTTTTTCTAA
1 TTTTAT-TTATTTTTCTTTC-AA
39716 TTTTATTTATTTTT
1 TTTTATTTATTTTT
39730 AGTGCTATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 3 0.11
20 1 0.04
21 12 0.43
22 12 0.43
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTATTTATTTTTCTTTCAA
Found at i:42462 original size:44 final size:43
Alignment explanation
Indices: 42395--42517 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 43
42385 TCTCTGTGTG
** *
42395 GTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGA-GGAA
1 GTTATCAAAATTTCAT-AGATGGTTACCAAAATTTCAT-ATGGAA
*
42439 GTTATCAAAATTCCATAGCATGGTTACCAAAATTTCATATGGAA
1 GTTATCAAAATTTCATAG-ATGGTTACCAAAATTTCATATGGAA
* *
42483 GTTATCAAAATTTCATAGTGTGGTTACTAAAATTT
1 GTTATCAAAATTTCATAG-ATGGTTACCAAAATTT
42518 AATAGTATCA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 3 0.04
44 66 0.96
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (43 bp):
GTTATCAAAATTTCATAGATGGTTACCAAAATTTCATATGGAA
Found at i:42508 original size:22 final size:22
Alignment explanation
Indices: 42390--42590 Score: 110
Period size: 22 Copynumber: 9.0 Consensus size: 22
42380 TCTTGTCTCT
42390 GTGTGGTTATCAAAATTTCATAA
1 GTGTGGTTATCAAAATTTCAT-A
* * *
42413 G-ATGGTTATTATAATTTCATGA
1 GTGTGGTTATCAAAATTTCAT-A
** *
42435 G-GAAGTTATCAAAATTCCATA
1 GTGTGGTTATCAAAATTTCATA
** *
42456 GCATGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
42478 -TG-GAAGTTATCAAAATTTCATA
1 GTGTG--GTTATCAAAATTTCATA
*
42500 GTGTGGTTA-CTAAAATTTAATA
1 GTGTGGTTATC-AAAATTTCATA
* *
42522 GTATCAGGTTATTAAAATTTC-TCA
1 GTGT--GGTTATCAAAATTTCAT-A
* ** *
42546 G-GAAGGTTATTGAAATTTCGTA
1 GTG-TGGTTATCAAAATTTCATA
* *
42568 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
42590 G
1 G
42591 AAAGGTTATT
Statistics
Matches: 134, Mismatches: 31, Indels: 27
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.01
21 3 0.02
22 109 0.81
23 6 0.04
24 15 0.11
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:42537 original size:24 final size:22
Alignment explanation
Indices: 42483--42603 Score: 64
Period size: 22 Copynumber: 5.4 Consensus size: 22
42473 TCATATGGAA
* * *
42483 GTTATCAAAATTTCATAGTGTG
1 GTTATTAAAATTTAATAGTATG
*
42505 GTTACTAAAATTTAATAGTATCAG
1 GTTATTAAAATTTAATAGTAT--G
* * *
42529 GTTATTAAAATTT-CTCAGGAAG
1 GTTATTAAAATTTAAT-AGTATG
* ** *
42551 GTTATTGAAATTTCGTAGTGTG
1 GTTATTAAAATTTAATAGTATG
* * * * *
42573 GTTATCACAATTTTATAGAAAG
1 GTTATTAAAATTTAATAGTATG
42595 GTTATTAAA
1 GTTATTAAA
42604 GAGATTATCA
Statistics
Matches: 72, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
22 54 0.75
23 2 0.03
24 16 0.22
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (22 bp):
GTTATTAAAATTTAATAGTATG
Found at i:42707 original size:22 final size:22
Alignment explanation
Indices: 42694--42930 Score: 117
Period size: 22 Copynumber: 10.5 Consensus size: 22
42684 TTCATGGGGA
42694 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
42716 GATTATCAAAATTAT-TTAGTGT
1 GGTTATCAAAATT-TCATAGTGT
*
42738 GGTTATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGTG-T
**
42760 GGTTAT-AAAAGTTTCAATTTCA-TAA
1 GGTTATCAAAA-TTTC-A--T-AGTGT
* * * **
42785 GGAGTACCAAAATTTGATAG-AA
1 GG-TTATCAAAATTTCATAGTGT
* * *
42807 AGTTATC-AAATCTCATAGAGT
1 GGTTATCAAAATTTCATAGTGT
* * * * *
42828 GATCATCGAAATTTAATAGAGAT
1 GGTTATCAAAATTTCATAGTG-T
42851 CGGATTATCAAAATTTCATAGTGT
1 -GG-TTATCAAAATTTCATAGTGT
* * *
42875 TGTTATCAAAATTTCAAAGTGA
1 GGTTATCAAAATTTCATAGTGT
* *
42897 GGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCATAGTGT
*
42919 GATTATCAAAAT
1 GGTTATCAAAAT
42931 ATCGAATCTC
Statistics
Matches: 164, Mismatches: 35, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
20 9 0.05
21 14 0.09
22 103 0.63
23 5 0.03
24 2 0.01
25 20 0.12
26 7 0.04
27 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:43164 original size:22 final size:22
Alignment explanation
Indices: 43137--43192 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
43127 CTTGGGTCAA
* *
43137 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTTACAAAGAGGTTAT
*
43159 CAAAATTTCACAAAGAGGTTAT
1 CAAAATTTTACAAAGAGGTTAT
43181 C-AAATTTT-CAAA
1 CAAAATTTTACAAA
43193 ATGTGATTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (22 bp):
CAAAATTTTACAAAGAGGTTAT
Found at i:43363 original size:22 final size:22
Alignment explanation
Indices: 43335--43588 Score: 88
Period size: 22 Copynumber: 11.7 Consensus size: 22
43325 TTTATATGAA
43335 GGTTATCAAAATTTCATAAGAG
1 GGTTATCAAAATTTCATAAGAG
*
43357 GGTTATCAAAATTTC-TTAGTA-
1 GGTTATCAAAATTTCATAAG-AG
* *
43378 TGTAAATCAAAATTTCAT-AG-G
1 GGT-TATCAAAATTTCATAAGAG
* * *
43399 GAAATCAACAAAATTTCATAATGA-
1 G--GTTATCAAAATTTCATAA-GAG
** *
43423 GGTTATCAAAAAATCAT-AGTG
1 GGTTATCAAAATTTCATAAGAG
** *
43444 AACTTATCAAAATTT-GT---A-
1 -GGTTATCAAAATTTCATAAGAG
*
43462 -GTTATCAAGATTTCATAAG-G
1 GGTTATCAAAATTTCATAAGAG
* *
43482 AGGTTATCAAAATTTTATAGGGAG
1 -GGTTATCAAAATTTCATA-AGAG
* * **
43506 GTTTATCAAAATTTTATCGGAAG
1 GGTTATCAAAATTTCATAAG-AG
*
43529 GTTTATCAAAATTTCATAACGA-
1 GGTTATCAAAATTTCATAA-GAG
* * *
43551 GATTATCACAATTTCAT-AGTG
1 GGTTATCAAAATTTCATAAGAG
*
43572 TGATTATCAAAATTTCA
1 -GGTTATCAAAATTTCA
43589 AAGTGTGATT
Statistics
Matches: 174, Mismatches: 34, Indels: 48
0.68 0.13 0.19
Matches are distributed among these distances:
16 11 0.06
17 1 0.01
20 2 0.01
21 8 0.05
22 109 0.63
23 39 0.22
24 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAG
Found at i:43515 original size:23 final size:23
Alignment explanation
Indices: 43463--43542 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
43453 AAATTTGTAG
* * *
43463 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
43485 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
43508 TTATCAAAATTTTATCGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
43531 TTATCAAAATTT
1 TTATCAAAATTT
43543 CATAACGAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
22 19 0.37
23 33 0.63
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:43593 original size:22 final size:22
Alignment explanation
Indices: 43531--43599 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
43521 ATCGGAAGGT
* *
43531 TTATCAAAATTTCATAA-CGAGA
1 TTATCAAAATTTCA-AAGTGTGA
* *
43553 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
43575 TTATCAAAATTTCAAAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
43597 TTA
1 TTA
43600 CTAACAATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 1 0.03
22 39 0.98
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCAAAGTGTGA
Found at i:43610 original size:22 final size:23
Alignment explanation
Indices: 43551--43608 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
43541 TTCATAACGA
*
43551 GATTATC-ACAATTTCATAGTGT
1 GATTATCAACAATTTCAAAGTGT
43573 GATTATCAA-AATTTCAAAGTGT
1 GATTATCAACAATTTCAAAGTGT
43595 GATTA-CTAACAATT
1 GATTATC-AACAATT
43609 CATATGGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 1 0.03
22 26 0.81
23 5 0.16
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (23 bp):
GATTATCAACAATTTCAAAGTGT
Found at i:43869 original size:22 final size:22
Alignment explanation
Indices: 43691--43862 Score: 84
Period size: 22 Copynumber: 7.8 Consensus size: 22
43681 TCATAGTGTT
*
43691 GGTTATCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCA-TAGGAA
43714 -GTTATCAAAATTTCATAGCG-A
1 GGTTATCAAAATTTCATAG-GAA
* * * *
43735 GGTCT-TAAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAGGAA
* *
43757 GGTTAACAAAATTAT-ATAAGAA
1 GGTTATCAAAATT-TCATAGGAA
** **
43779 GGTTAAAAAAAATTT-ATAAAAA
1 GGTT-ATCAAAATTTCATAGGAA
** * * ** *
43801 GGTTCCCGAAATTCCATAATAT
1 GGTTATCAAAATTTCATAGGAA
* *
43823 CGTTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAGGAA
43845 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
43863 ATGAGGTCAT
Statistics
Matches: 111, Mismatches: 30, Indels: 17
0.70 0.19 0.11
Matches are distributed among these distances:
21 10 0.09
22 92 0.83
23 9 0.08
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGAA
Found at i:43874 original size:22 final size:22
Alignment explanation
Indices: 43830--43877 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43820 TATCGTTATT
*
43830 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGGAAGGTCATC
*
43852 AAAATTTCATAATG-AGGTCATC
1 AAAATTTCAT-AGGAAGGTCATC
43874 AAAA
1 AAAA
43878 ATAGTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATC
Found at i:49012 original size:25 final size:26
Alignment explanation
Indices: 48984--49033 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
48974 ATTATAAAAA
*
48984 TATTTTATTTAG-AAAATTCAATTTT
1 TATTTTATTTAGAAAAAATCAATTTT
49009 TATTTTATTTAGAAAAAATCAATTT
1 TATTTTATTTAGAAAAAATCAATTT
49034 CTAGAATACC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (26 bp):
TATTTTATTTAGAAAAAATCAATTTT
Found at i:61966 original size:17 final size:17
Alignment explanation
Indices: 61928--61960 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
61918 CTCATAGTAC
*
61928 CTAGGTGGTATGAGGTA
1 CTAGGTAGTATGAGGTA
61945 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
61961 GATAGGCTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.39, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:63548 original size:21 final size:20
Alignment explanation
Indices: 63518--63579 Score: 81
Period size: 21 Copynumber: 3.1 Consensus size: 20
63508 ACTTTTAACC
*
63518 CATC-ATATATTTATATTTT
1 CATCAATATATCTATATTTT
*
63537 CATCAAATATATCTATATTCT
1 CATC-AATATATCTATATTTT
*
63558 CATCCATATATCTATATTTT
1 CATCAATATATCTATATTTT
63578 CA
1 CA
63580 CTTTTAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 4 0.11
20 16 0.43
21 17 0.46
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (20 bp):
CATCAATATATCTATATTTT
Done.