Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017213.1 Corchorus olitorius cultivar O-4 contig17246, 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: 60441
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4266 original size:16 final size:14
Alignment explanation
Indices: 4245--4286 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 14
4235 TGTTTTTTTT
4245 TGTGTGTGCAAGAGAG
1 TGTGTGTG--AGAGAG
4261 TGTGTGTGAGAGA-
1 TGTGTGTGAGAGAG
4274 T-TGTGTGAGAGAG
1 TGTGTGTGAGAGAG
4287 AAAAAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.44
13 1 0.04
14 5 0.20
16 8 0.32
ACGTcount: A:0.24, C:0.02, G:0.45, T:0.29
Consensus pattern (14 bp):
TGTGTGTGAGAGAG
Found at i:4285 original size:14 final size:14
Alignment explanation
Indices: 4246--4287 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
4236 GTTTTTTTTT
4246 GTGTGTGCA-AGAGA
1 GTGTGTG-AGAGAGA
*
4260 GTGTGTGTGAGAGA
1 GTGTGTGAGAGAGA
*
4274 TTGTGTGAGAGAGA
1 GTGTGTGAGAGAGA
4288 AAAAACTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.45, T:0.26
Consensus pattern (14 bp):
GTGTGTGAGAGAGA
Found at i:10237 original size:36 final size:36
Alignment explanation
Indices: 10190--10259 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
10180 TTCAATAACC
* *
10190 TTACATCTTTTGTGATTTTGTTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
10226 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
10260 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.61
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:11149 original size:201 final size:202
Alignment explanation
Indices: 10773--11180 Score: 732
Period size: 201 Copynumber: 2.0 Consensus size: 202
10763 GCTTAATAAC
10773 TTTATCAATGGTGAATGTTATTAAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
* * *
10838 AGATATAACACATTATTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
66 AGATACAACACATTACTATTATATATAGAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
10903 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGGAT
131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAA-GAT
10968 CCGATTTA
195 CCGATTTA
10976 TTTATCAATGGTGAATGTTATT-AATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
* *
11040 AGATACAACACATTACTA-T-TATATAGAACTATACCAAAAAAAAATTAGTTGAATATTAGTGGT
66 AGATACAACACATTACTATTATATATAGAACTATACC-AAAAAAAAGTAGTTGAACATTAGTGGT
11103 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
130 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
11168 CCGATTTA
195 CCGATTTA
11176 TTTAT
1 TTTAT
11181 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
200 31 0.16
201 88 0.44
202 58 0.29
203 22 0.11
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
AGATACAACACATTACTATTATATATAGAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
CGATTTA
Found at i:11346 original size:39 final size:38
Alignment explanation
Indices: 11292--11367 Score: 134
Period size: 39 Copynumber: 2.0 Consensus size: 38
11282 ATACCTAAAA
11292 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATA-TATTAC
*
11331 ATTTAATTAATGTAAGTATTTTAGTTATTATATATTA
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATTA
11368 TTACATAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 5 0.14
39 31 0.86
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (38 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATTAC
Found at i:11601 original size:2 final size:2
Alignment explanation
Indices: 11589--11636 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
11579 AGTTTAGACT
* *
11589 TA TA TA GTA TA TA GA TA TA GA 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 TA TA TA TA TA TA TA TA
11632 TA TA T
1 TA TA T
11637 TACTATAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:12205 original size:31 final size:31
Alignment explanation
Indices: 12148--12206 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
12138 TGTCTATAAA
*
12148 CATATGAACAACAAGTAGATAAGATTGACGT
1 CATATGAACAACAAGTAAATAAGATTGACGT
* *
12179 CATATGAAGAA-AATGTAAATAGGATTGA
1 CATATGAACAACAA-GTAAATAAGATTGA
12207 TTTTATGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.24
Consensus pattern (31 bp):
CATATGAACAACAAGTAAATAAGATTGACGT
Found at i:18301 original size:2 final size:2
Alignment explanation
Indices: 18289--18323 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
18279 AAACTACTAA
* *
18289 AT AT TT AT AT AT AT TT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18324 ACTTAAAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:18304 original size:10 final size:10
Alignment explanation
Indices: 18289--18322 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
18279 AAACTACTAA
18289 ATATTTATAT
1 ATATTTATAT
18299 ATATTTATAT
1 ATATTTATAT
*
18309 ATATATATAT
1 ATATTTATAT
18319 ATAT
1 ATAT
18323 AACTTAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATTTATAT
Found at i:18621 original size:31 final size:31
Alignment explanation
Indices: 18550--18621 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
18540 GTCTATCAGC
*
18550 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
* *
18581 TAATT-ATTTGTTTAATTTAATGC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAGGCTTTAATTT
18611 GTTTTAATTTG
1 -TTTTAATTTG
18622 CAATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.24
31 24 0.71
32 2 0.06
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTTAATTT
Found at i:18929 original size:13 final size:12
Alignment explanation
Indices: 18872--18939 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 12
18862 TATTCAATCT
18872 TTATATATATAATA
1 TTATAT-TAT-ATA
*
18886 ATATATATATATA
1 TTATAT-TATATA
*
18899 TTGATA--ATCATG
1 TT-ATATTAT-ATA
18911 TTATATTATATTA
1 TTATATTATA-TA
18924 TTATATTATATA
1 TTATATTATATA
18936 TTAT
1 TTAT
18940 CAATAAACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
11 5 0.11
12 11 0.24
13 17 0.38
14 12 0.27
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (12 bp):
TTATATTATATA
Found at i:19164 original size:16 final size:16
Alignment explanation
Indices: 19143--19193 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
19133 ATATGATATA
19143 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
19159 ACCCGAACCCGAATGA-
1 ACCCGAACCCGAA-AAT
*
19175 ACCTGAACCCG-AAAT
1 ACCCGAACCCGAAAAT
19190 ACCC
1 ACCC
19194 AAACTCGCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 1 0.03
15 4 0.14
16 23 0.79
17 1 0.03
ACGTcount: A:0.39, C:0.39, G:0.14, T:0.08
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:20452 original size:16 final size:16
Alignment explanation
Indices: 20428--20467 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20418 CAAGGATTAA
20428 AGCCCAAACTAGAAGT
1 AGCCCAAACTAGAAGT
* *
20444 AGCCTAAACTAGCAGT
1 AGCCCAAACTAGAAGT
*
20460 AACCCAAA
1 AGCCCAAA
20468 TATTAAGAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.12
Consensus pattern (16 bp):
AGCCCAAACTAGAAGT
Found at i:21269 original size:17 final size:17
Alignment explanation
Indices: 21243--21276 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21233 AAGAAATTAG
21243 GAAAAGAAAAAAGAAAA
1 GAAAAGAAAAAAGAAAA
* *
21260 GAAAATAAAATAGAAAA
1 GAAAAGAAAAAAGAAAA
21277 AAAGGTTAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAAAGAAAAAAGAAAA
Found at i:25635 original size:28 final size:28
Alignment explanation
Indices: 25601--25685 Score: 170
Period size: 28 Copynumber: 3.0 Consensus size: 28
25591 TGTGGTAGTT
25601 TAGTTTCATAGGTAGCTTCTTGAGTTAA
1 TAGTTTCATAGGTAGCTTCTTGAGTTAA
25629 TAGTTTCATAGGTAGCTTCTTGAGTTAA
1 TAGTTTCATAGGTAGCTTCTTGAGTTAA
25657 TAGTTTCATAGGTAGCTTCTTGAGTTAA
1 TAGTTTCATAGGTAGCTTCTTGAGTTAA
25685 T
1 T
25686 GAAAGTGACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.44
Consensus pattern (28 bp):
TAGTTTCATAGGTAGCTTCTTGAGTTAA
Found at i:29607 original size:14 final size:14
Alignment explanation
Indices: 29588--29639 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
29578 TATGCCAAAA
29588 CAATGATATATTTC
1 CAATGATATATTTC
29602 CAATGATATCATGTTGC
1 CAATGATAT-AT-TT-C
*
29619 CAATTGATAT-TTGC
1 CAA-TGATATATTTC
29633 CAATGAT
1 CAATGAT
29640 TTCAATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
13 4 0.12
14 13 0.39
15 3 0.09
16 3 0.09
17 4 0.12
18 6 0.18
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (14 bp):
CAATGATATATTTC
Found at i:30587 original size:67 final size:65
Alignment explanation
Indices: 30477--30606 Score: 199
Period size: 67 Copynumber: 2.0 Consensus size: 65
30467 TATATGAACA
** *
30477 TAAATTAAAAATACATATGAGGTAATATATATGAAGATTACTATATTGCTAATGAAGTACCATAA
1 TAAATTAAAAATACATATGAGCAAATATATATGAAGATAAC--TATTGCTAATGAAGTACCATAA
30542 CG
64 CG
30544 TAAATTAAAAATACATATGAGCAAATATATATGAATG-TAACTATTGCTAATGAAGTACCATAA
1 TAAATTAAAAATACATATGAGCAAATATATATGAA-GATAACTATTGCTAATGAAGTACCATAA
30607 AAGGGTCTCG
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
65 22 0.37
67 36 0.61
68 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (65 bp):
TAAATTAAAAATACATATGAGCAAATATATATGAAGATAACTATTGCTAATGAAGTACCATAACG
Found at i:32943 original size:56 final size:56
Alignment explanation
Indices: 32857--32968 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
32847 TAGCTTATAG
*
32857 CTACTTCTGAGCTAAACAGCCAATGTTTTTAAGAACCAAAATTCTAAGAACACAAA
1 CTACTTCTGAGCTAAACAGCAAATGTTTTTAAGAACCAAAATTCTAAGAACACAAA
*
32913 CTACTTCTGAGCTAAACAGCAAATGTTTTTAAGTACCAAAATTCTAAGAACACAAA
1 CTACTTCTGAGCTAAACAGCAAATGTTTTTAAGAACCAAAATTCTAAGAACACAAA
32969 ACTAAAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.26
Consensus pattern (56 bp):
CTACTTCTGAGCTAAACAGCAAATGTTTTTAAGAACCAAAATTCTAAGAACACAAA
Found at i:33776 original size:50 final size:50
Alignment explanation
Indices: 33717--33812 Score: 192
Period size: 50 Copynumber: 1.9 Consensus size: 50
33707 CTAATCAATC
33717 AAACCCTTCATACAAAAGCAGTCCCCCGGGCTTGATTTATTACAGCGGTT
1 AAACCCTTCATACAAAAGCAGTCCCCCGGGCTTGATTTATTACAGCGGTT
33767 AAACCCTTCATACAAAAGCAGTCCCCCGGGCTTGATTTATTACAGC
1 AAACCCTTCATACAAAAGCAGTCCCCCGGGCTTGATTTATTACAGC
33813 TGTCCCAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (50 bp):
AAACCCTTCATACAAAAGCAGTCCCCCGGGCTTGATTTATTACAGCGGTT
Found at i:36926 original size:32 final size:34
Alignment explanation
Indices: 36865--36932 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 34
36855 TTTCATTTAA
36865 TGGAGTCATGAGTCATCTATGTAATGTATGATAGAAG
1 TGGAGTCATGAGTCATC--T-TAATGTATGATAGAAG
36902 TGGAGTCATGAGTCATC-T-ATGTATGATAGAA
1 TGGAGTCATGAGTCATCTTAATGTATGATAGAA
36933 ATTCTATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 13 0.42
33 1 0.03
37 17 0.55
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (34 bp):
TGGAGTCATGAGTCATCTTAATGTATGATAGAAG
Found at i:37620 original size:27 final size:27
Alignment explanation
Indices: 37588--37641 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
37578 TGGAAATGCC
37588 TTCTCCAGGTGCAGGTGTGAAATGAAA
1 TTCTCCAGGTGCAGGTGTGAAATGAAA
37615 TTCTCCAGGTGCAGGTGTGAAATGAAA
1 TTCTCCAGGTGCAGGTGTGAAATGAAA
37642 GAACCAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (27 bp):
TTCTCCAGGTGCAGGTGTGAAATGAAA
Found at i:39600 original size:22 final size:23
Alignment explanation
Indices: 39572--39621 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
39562 AGTAAATCTC
39572 ATCTGGTG-AAATTTGGGGCTAA
1 ATCTGGTGCAAATTTGGGGCTAA
* *
39594 ATCTGGTGCTAAATTTGTGTCTAA
1 ATCTGGTGC-AAATTTGGGGCTAA
39618 ATCT
1 ATCT
39622 ATATTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
24 16 0.67
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (23 bp):
ATCTGGTGCAAATTTGGGGCTAA
Found at i:39813 original size:93 final size:94
Alignment explanation
Indices: 39716--39901 Score: 275
Period size: 94 Copynumber: 2.0 Consensus size: 94
39706 TTGTTTTAAT
* *
39716 TTTTATAGTTTTAGTCAACTAAAAACT-CTATTTTTATTTAATTAAATTTAATATCCTTATAACT
1 TTTTATAGTTTTACTCAACTAAAAACTCCTATTTTTATTTAATTAAATCTAATATCCTTATAACT
* * *
39780 TTTTTATTTTTACCATTTTACTATTTTAC
66 ATTTTATTTTTACCATATTACTAATTTAC
* ** *
39809 TTTTATAGTTTTACTCAACTAAAAACTCCTCTTTTTATTTAATTAAATCTAATATTTTTATACCT
1 TTTTATAGTTTTACTCAACTAAAAACTCCTATTTTTATTTAATTAAATCTAATATCCTTATAACT
*
39874 ATTTTATTTTTACGATATTACTAATTTA
66 ATTTTATTTTTACCATATTACTAATTTA
39902 ATTAAAAAGC
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
93 26 0.32
94 56 0.68
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (94 bp):
TTTTATAGTTTTACTCAACTAAAAACTCCTATTTTTATTTAATTAAATCTAATATCCTTATAACT
ATTTTATTTTTACCATATTACTAATTTAC
Found at i:40556 original size:16 final size:16
Alignment explanation
Indices: 40531--40565 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40521 TTTGGCCTCA
*
40531 GGTCACTCGGGTTTTG
1 GGTCACTCGGGATTTG
*
40547 GGTCATTCGGGATTTG
1 GGTCACTCGGGATTTG
40563 GGT
1 GGT
40566 TTTTCATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.14, G:0.40, T:0.37
Consensus pattern (16 bp):
GGTCACTCGGGATTTG
Found at i:41466 original size:37 final size:37
Alignment explanation
Indices: 41370--41518 Score: 190
Period size: 37 Copynumber: 3.9 Consensus size: 37
41360 AACCAAAACC
* * *
41370 TGATGGGAACTTTCCCAATTTGAAAACTTTTTAAAAAAACT
1 TGATGGGAACTTTCCCAATTTGAAAAC--TAT-GAAGAA-T
*
41411 TGATGGGAACTTTTCCAATTTGAAAACTATGAAGAAT
1 TGATGGGAACTTTCCCAATTTGAAAACTATGAAGAAT
* * *
41448 TCATGGGAATTTTCCCAATTTGAAAACTATGAAGACT
1 TGATGGGAACTTTCCCAATTTGAAAACTATGAAGAAT
*
41485 TGATGGGAACTTTCCCAATTTGAAAACTTTGAAG
1 TGATGGGAACTTTCCCAATTTGAAAACTATGAAG
41519 GAAATGTTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
37 65 0.67
38 4 0.04
39 2 0.02
41 26 0.27
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (37 bp):
TGATGGGAACTTTCCCAATTTGAAAACTATGAAGAAT
Found at i:42488 original size:15 final size:15
Alignment explanation
Indices: 42459--42503 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
42449 TACATCAGAT
*
42459 TTAAGCAAA-GGAAA
1 TTAAGGAAATGGAAA
*
42473 TTAAGGAGATGGAAA
1 TTAAGGAAATGGAAA
42488 TTAAGGAAATGGAAA
1 TTAAGGAAATGGAAA
42503 T
1 T
42504 CGTGAGCGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.51, C:0.02, G:0.27, T:0.20
Consensus pattern (15 bp):
TTAAGGAAATGGAAA
Found at i:47315 original size:15 final size:15
Alignment explanation
Indices: 47286--47330 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
47276 TACATCACAT
*
47286 TTAAGCAAA-GGAAA
1 TTAAGAAAATGGAAA
47300 TTAAGAAAATGGAAA
1 TTAAGAAAATGGAAA
* *
47315 TTAAGGAAATGTAAA
1 TTAAGAAAATGGAAA
47330 T
1 T
47331 CGTGAGCGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (15 bp):
TTAAGAAAATGGAAA
Found at i:54948 original size:31 final size:31
Alignment explanation
Indices: 54901--54972 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
54891 CTACCCAAGA
* *
54901 CCGAACCCGACATAACCCGAG-TCGAAAATAC
1 CCGAACCCGACATAACCCAAGCCCGAAAA-AC
* *
54932 CCGAACCTGACTTAACCCAAGCCCGAAAAAC
1 CCGAACCCGACATAACCCAAGCCCGAAAAAC
54963 CCGAACCCGA
1 CCGAACCCGA
54973 AGTACCCGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 29 0.83
32 6 0.17
ACGTcount: A:0.38, C:0.39, G:0.15, T:0.08
Consensus pattern (31 bp):
CCGAACCCGACATAACCCAAGCCCGAAAAAC
Found at i:58357 original size:30 final size:30
Alignment explanation
Indices: 58321--58378 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
58311 AGTTAGTTTT
58321 AAAAGGCATAACTAACCATTCATACAATCC
1 AAAAGGCATAACTAACCATTCATACAATCC
58351 AAAAGGCATAACTAACCATTCATACAAT
1 AAAAGGCATAACTAACCATTCATACAAT
58379 TCTAACTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.21
Consensus pattern (30 bp):
AAAAGGCATAACTAACCATTCATACAATCC
Done.