Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013804.1 Corchorus capsularis cultivar CVL-1 contig13825, 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: 94981
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:75 original size:14 final size:15
Alignment explanation
Indices: 52--80 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42 ATATTTTTTC
52 AAATT-TTTTTGAAA
1 AAATTATTTTTGAAA
66 AAATTATTTTTGAAA
1 AAATTATTTTTGAAA
81 TAAAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AAATTATTTTTGAAA
Found at i:2201 original size:30 final size:28
Alignment explanation
Indices: 2165--2233 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
2155 TTTACCGAAA
* *
2165 TATAATATCTTGAAAACTTATTTCCCATTC
1 TATAATAT-TT-AAAACTTAATTCCCAATC
*
2195 TATAATAGTTTTAAACTTAATTCCCAATC
1 TATAATA-TTTAAAACTTAATTCCCAATC
2224 TATAATATTT
1 TATAATATTT
2234 TTTGCCACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.09
29 22 0.63
30 9 0.26
31 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (28 bp):
TATAATATTTAAAACTTAATTCCCAATC
Found at i:2213 original size:29 final size:29
Alignment explanation
Indices: 2178--2235 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2168 AATATCTTGA
* *
2178 AAACTTATTTCCCATTCTATAATAGTTTT
1 AAACTTAATTCCCAATCTATAATAGTTTT
*
2207 AAACTTAATTCCCAATCTATAATATTTTT
1 AAACTTAATTCCCAATCTATAATAGTTTT
2236 TGCCACATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (29 bp):
AAACTTAATTCCCAATCTATAATAGTTTT
Found at i:7026 original size:25 final size:24
Alignment explanation
Indices: 6996--7046 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
6986 TGCTTTTTGC
*
6996 TTTCCCCTGCTATATCCTCTGTTTT
1 TTTCCCCTCCT-TATCCTCTGTTTT
* *
7021 TTTCCCCTCCTTGTGCTCTGTTTT
1 TTTCCCCTCCTTATCCTCTGTTTT
7045 TT
1 TT
7047 ACGTCTTCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.04, C:0.31, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCCCCTCCTTATCCTCTGTTTT
Found at i:10147 original size:2 final size:2
Alignment explanation
Indices: 10140--10170 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
10130 AACTAAAACC
*
10140 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10171 TGATGGAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11111 original size:12 final size:12
Alignment explanation
Indices: 11094--11119 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11084 TTGATTTACC
11094 ACTACCATTGAG
1 ACTACCATTGAG
11106 ACTACCATTGAG
1 ACTACCATTGAG
11118 AC
1 AC
11120 CAACAAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (12 bp):
ACTACCATTGAG
Found at i:16555 original size:16 final size:16
Alignment explanation
Indices: 16536--16615 Score: 72
Period size: 16 Copynumber: 5.0 Consensus size: 16
16526 AATCTGTTTG
16536 AATCTGAATCCGAAAA
1 AATCTGAATCCGAAAA
*
16552 AATCTGAATCTGAAAA
1 AATCTGAATCCGAAAA
* * * *
16568 AGTTTAAACCCGAAAA
1 AATCTGAATCCGAAAA
* *
16584 AA-CTCAAACCCGAAAA
1 AATCT-GAATCCGAAAA
*
16600 AATCCGAATCCGAAAA
1 AATCTGAATCCGAAAA
16616 TTTATGAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
15 1 0.02
16 49 0.96
17 1 0.02
ACGTcount: A:0.51, C:0.21, G:0.11, T:0.16
Consensus pattern (16 bp):
AATCTGAATCCGAAAA
Found at i:19586 original size:37 final size:37
Alignment explanation
Indices: 19542--19612 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
19532 CTTGATCAAC
* * *
19542 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAAACATAACTTTATGATCA
19579 ATACATGTCTTTCCAAATAAACATAACTTTATGA
1 ATACATGTCTTTCCAAATAAACATAACTTTATGA
19613 ACATTCATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAAACATAACTTTATGATCA
Found at i:29078 original size:200 final size:200
Alignment explanation
Indices: 28736--29122 Score: 614
Period size: 200 Copynumber: 1.9 Consensus size: 200
28726 CTAAAATGCG
** * *
28736 ATACACCGTCAGTGGAGTTTAGCAGTCTACACATGCGGGGTCTAAGGTTGATATGTGTCCTTTAG
1 ATACACCGTCAGTGGAGTTTAGCAAACTACACATGCGAGGTCTAAGGTTGACATGTGTCCTTTAG
* * * * *
28801 GGAATAATTTTGAATTTTGAAAACAAAATTAATTTTGAAATGTGTATGTGTCAACTTCTCACCCC
66 AGAATAATTTGGAATTTTAAAAACAAAATTAATTCTGAAATGTGTATGTGTCAACTCCTCACCCC
*
28866 GCTTGTGGAGTCCAAATTTTACACTATTAGTGTATCAAA-AATTATCCTTATTTTATGGAAAATT
131 GCTTGTGGAGTCCAAATTTTACACTATTAGTGTATCAAATAATTATCCTTATATTATGGAAAATT
28930 ATACA
196 ATACA
* * * *
28935 ATACACCTTTAGTGGAGTTTAGCAAACTACACATGCGAGGTTTAAGAGTTTACATGTGTCCTTTA
1 ATACACCGTCAGTGGAGTTTAGCAAACTACACATGCGAGGTCTAAG-GTTGACATGTGTCCTTTA
*
29000 GAGAATAATTTGGAATTTTAAAAACAAAATTAATTCTGAAATGTGTATGTGTCAACTCCTCACCT
65 GAGAATAATTTGGAATTTTAAAAACAAAATTAATTCTGAAATGTGTATGTGTCAACTCCTCACCC
*
29065 CGCTTGTGGAGTCCAAATTTTACACTATTAGTGTATCAAATAGTTATCCTTATATTAT
130 CGCTTGTGGAGTCCAAATTTTACACTATTAGTGTATCAAATAATTATCCTTATATTAT
29123 TTGACTTATA
Statistics
Matches: 170, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
199 40 0.24
200 115 0.68
201 15 0.09
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (200 bp):
ATACACCGTCAGTGGAGTTTAGCAAACTACACATGCGAGGTCTAAGGTTGACATGTGTCCTTTAG
AGAATAATTTGGAATTTTAAAAACAAAATTAATTCTGAAATGTGTATGTGTCAACTCCTCACCCC
GCTTGTGGAGTCCAAATTTTACACTATTAGTGTATCAAATAATTATCCTTATATTATGGAAAATT
ATACA
Found at i:33729 original size:5 final size:5
Alignment explanation
Indices: 33719--33743 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
33709 GTTTTTATGA
33719 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
33744 ATGATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:33751 original size:15 final size:15
Alignment explanation
Indices: 33713--33755 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
33703 TCATTTGTTT
33713 TTATGA-TAATTTAA
1 TTATGATTAATTTAA
*
33727 TT-TAATTTAATTTAA
1 TTATGA-TTAATTTAA
33742 TTATGATTAATTTA
1 TTATGATTAATTTA
33756 TTAATTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 2 0.08
14 2 0.08
15 18 0.75
16 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (15 bp):
TTATGATTAATTTAA
Found at i:34283 original size:25 final size:25
Alignment explanation
Indices: 34255--34305 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
34245 ATAAATATAA
34255 TTTAATTAAAGTGCATACA-AAATTG
1 TTTAATTAAAGTGCATA-AGAAATTG
*
34280 TTTAATTCAAGTGCATAAGAAATTG
1 TTTAATTAAAGTGCATAAGAAATTG
34305 T
1 T
34306 ATAGTAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (25 bp):
TTTAATTAAAGTGCATAAGAAATTG
Found at i:46583 original size:26 final size:26
Alignment explanation
Indices: 46533--46583 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
46523 AAAGCTGACT
*
46533 CGAACCCGATTAACCGTCCAACTCGCC
1 CGAACCCGA-TAACCGCCCAACTCGCC
46560 CGAACCCG-TAACCCGCCCAACTCG
1 CGAACCCGATAA-CCGCCCAACTCG
46584 ATTGGACTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 11 0.50
27 8 0.36
ACGTcount: A:0.25, C:0.47, G:0.16, T:0.12
Consensus pattern (26 bp):
CGAACCCGATAACCGCCCAACTCGCC
Found at i:46640 original size:16 final size:15
Alignment explanation
Indices: 46621--46712 Score: 51
Period size: 16 Copynumber: 5.8 Consensus size: 15
46611 AACCCGCCCG
46621 ACCCGAAACCCGACTA
1 ACCCGAAACCCGA-TA
** *
46637 ACCCGTGACCCAAATA
1 ACCCGAAACCC-GATA
* *
46653 ACCCGAGAGCCGTATA
1 ACCCGAAACCCG-ATA
* *
46669 ACCCAAAACCCGTATG
1 ACCCGAAACCCG-ATA
*
46685 ACTCGAAACCCG-TGAA
1 ACCCGAAACCCGAT--A
46701 ACCCGAAACCCG
1 ACCCGAAACCCG
46713 TGAGACTCGA
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
14 1 0.02
16 56 0.97
17 1 0.02
ACGTcount: A:0.36, C:0.38, G:0.16, T:0.10
Consensus pattern (15 bp):
ACCCGAAACCCGATA
Found at i:46901 original size:13 final size:14
Alignment explanation
Indices: 46883--46919 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
46873 AATTTAAATT
46883 ATAGAATAAAG-AA
1 ATAGAATAAAGAAA
*
46896 ATAGAATATAGAAA
1 ATAGAATAAAGAAA
46910 ATAGAATAAA
1 ATAGAATAAA
46920 CTTGTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (14 bp):
ATAGAATAAAGAAA
Found at i:47500 original size:16 final size:16
Alignment explanation
Indices: 47481--47623 Score: 109
Period size: 16 Copynumber: 9.2 Consensus size: 16
47471 CTGACCCATT
47481 TGACCCGAGACCCGAA
1 TGACCCGAGACCCGAA
** *
47497 TGACCCGA-AGTCTAA
1 TGACCCGAGACCCGAA
47512 --ACCCGA-ACCCGAA
1 TGACCCGAGACCCGAA
* *
47525 TAACCCGAGAACCGAA
1 TGACCCGAGACCCGAA
*
47541 TGACCCGAGACCC-AGT
1 TGACCCGAGACCCGA-A
* *
47557 TAACCCGAGACCCGAT
1 TGACCCGAGACCCGAA
* * *
47573 TGACCTGAAACCCGAT
1 TGACCCGAGACCCGAA
* *
47589 TAACCCGA-ACCCAAA
1 TGACCCGAGACCCGAA
*
47604 TGACCCGAAACCCGAA
1 TGACCCGAGACCCGAA
47620 TGAC
1 TGAC
47624 TCAAAAAAAC
Statistics
Matches: 101, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
13 10 0.10
15 23 0.23
16 67 0.66
17 1 0.01
ACGTcount: A:0.35, C:0.36, G:0.19, T:0.10
Consensus pattern (16 bp):
TGACCCGAGACCCGAA
Found at i:47562 original size:32 final size:32
Alignment explanation
Indices: 47512--47618 Score: 130
Period size: 32 Copynumber: 3.4 Consensus size: 32
47502 CGAAGTCTAA
* *
47512 ACCCG-AACCCGAATAACCCGAGAACCGAATG
1 ACCCGAAACCCGATTAACCCGAGACCCGAATG
* *
47543 ACCCGAGACCC-AGTTAACCCGAGACCCGATTG
1 ACCCGAAACCCGA-TTAACCCGAGACCCGAATG
* *
47575 ACCTGAAACCCGATTAACCCGA-ACCCAAATG
1 ACCCGAAACCCGATTAACCCGAGACCCGAATG
47606 ACCCGAAACCCGA
1 ACCCGAAACCCGA
47619 ATGACTCAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 25 0.39
32 38 0.59
33 1 0.02
ACGTcount: A:0.36, C:0.37, G:0.18, T:0.09
Consensus pattern (32 bp):
ACCCGAAACCCGATTAACCCGAGACCCGAATG
Found at i:50043 original size:2 final size:2
Alignment explanation
Indices: 50036--50064 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
50026 TCCTTGACCC
50036 AT AT AT AT AT 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 A
50065 AGAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57331 original size:6 final size:6
Alignment explanation
Indices: 57322--57352 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
57312 CATTTATTAT
57322 TATTTA TATTTA TATTTA TATTTA TATTTA T
1 TATTTA TATTTA TATTTA TATTTA TATTTA T
57353 GGAATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:57720 original size:2 final size:2
Alignment explanation
Indices: 57713--57749 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
57703 ATTAAACCAG
57713 AT AT AT AT AT AT AT AT AT 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 AT A
57750 GCCAGTCCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58896 original size:21 final size:21
Alignment explanation
Indices: 58853--58896 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
58843 TCAATGGGGC
*
58853 TTGCTAAATACCGCCCTAATT
1 TTGCTAAATACCGCCCCAATT
*
58874 TTGCTAAATACCGCCCCACTT
1 TTGCTAAATACCGCCCCAATT
58895 TT
1 TT
58897 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.32, G:0.09, T:0.34
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCAATT
Found at i:59158 original size:34 final size:33
Alignment explanation
Indices: 59069--59204 Score: 159
Period size: 34 Copynumber: 4.2 Consensus size: 33
59059 CCCCACCGGT
* * **
59069 GCGGCCTG-CCGTGGCGAAGCCGCCCCGGTGGG
1 GCGGCCTGCCCATGGTGAAGCCGCCCTAGTGGG
*** *
59101 GCGGCCTATTCATAGTGAAGCCGCCCTAGTGGG
1 GCGGCCTGCCCATGGTGAAGCCGCCCTAGTGGG
59134 GCGGCCTGCCCAATGGTGAAGCCGCCCTAGTGGG
1 GCGGCCTGCCC-ATGGTGAAGCCGCCCTAGTGGG
**
59168 GCGGCCTGCCCATGGT-AAGCCGCCCTCTTGGG
1 GCGGCCTGCCCATGGTGAAGCCGCCCTAGTGGG
59200 GCGGC
1 GCGGC
59205 ACGGGTCATC
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
32 26 0.29
33 31 0.35
34 32 0.36
ACGTcount: A:0.12, C:0.34, G:0.39, T:0.15
Consensus pattern (33 bp):
GCGGCCTGCCCATGGTGAAGCCGCCCTAGTGGG
Found at i:61223 original size:23 final size:23
Alignment explanation
Indices: 61197--61243 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
61187 ATAACAGGTC
61197 GTGTATTGGCAATATCATTTCCT
1 GTGTATTGGCAATATCATTTCCT
61220 GTGTATTGGCAATATCATTTCCT
1 GTGTATTGGCAATATCATTTCCT
61243 G
1 G
61244 ATGAACGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (23 bp):
GTGTATTGGCAATATCATTTCCT
Found at i:67387 original size:34 final size:34
Alignment explanation
Indices: 67344--67412 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
67334 TGCACAATTA
67344 CAATTATTATCCAACATCAACTTAAAATCTCAAG
1 CAATTATTATCCAACATCAACTTAAAATCTCAAG
*
67378 CAATTATTATCCAACATCGACTTAAAATCTCAAG
1 CAATTATTATCCAACATCAACTTAAAATCTCAAG
67412 C
1 C
67413 CCGCGGCGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (34 bp):
CAATTATTATCCAACATCAACTTAAAATCTCAAG
Found at i:78025 original size:18 final size:18
Alignment explanation
Indices: 78002--78036 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
77992 GATCACCAGC
*
78002 TTAATCAAAATACTTTAA
1 TTAATCAAAATAATTTAA
78020 TTAATCAAAATAATTTA
1 TTAATCAAAATAATTTA
78037 GAGTAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAATCAAAATAATTTAA
Found at i:80283 original size:93 final size:93
Alignment explanation
Indices: 80107--80283 Score: 273
Period size: 93 Copynumber: 1.9 Consensus size: 93
80097 GTTTAAATTA
* * *
80107 TTATAATTTTAGTCAACTAAAAACTCTATTTTTAATTAATTAAATCTAATATCTTTGTAACTATT
1 TTATAATTTTACTCAACTAAAAACTCTATTTTTAATTAATTAAATCTAATATCCTTATAACTATT
* *
80172 TTATTTATACCATTTTACTTTTTTACTT
66 TTATTTATAACATATTACTTTTTTACTT
* * *
80200 TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATT
1 TTATAATTTTACTCAACTAAAAACTCTATTTTTAATTAATTAAATCTAATATCCTTATAACTATT
*
80265 TTATTTTTAACATATTACT
66 TTATTTATAACATATTACT
80284 AATTTAATTA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (93 bp):
TTATAATTTTACTCAACTAAAAACTCTATTTTTAATTAATTAAATCTAATATCCTTATAACTATT
TTATTTATAACATATTACTTTTTTACTT
Found at i:86738 original size:20 final size:20
Alignment explanation
Indices: 86701--86739 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
86691 AGAGAATCAT
***
86701 TTTTTTTTCAATTTAAATAC
1 TTTTTTTTCAAAAAAAATAC
86721 TTTTTTTTCAAAAAAAATA
1 TTTTTTTTCAAAAAAAATA
86740 TCGAAAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTTTTCAAAAAAAATAC
Found at i:89715 original size:2 final size:2
Alignment explanation
Indices: 89703--89735 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
89693 ATTCCTCAAT
*
89703 TA TA CA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89736 CAATCCGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:91859 original size:30 final size:30
Alignment explanation
Indices: 91820--91896 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
91810 GAGTATGAAG
*
91820 AGGAGGAAGATTCTGATCTCTTTGTTTGTGA
1 AGGA-GAAGATTCTGATCTCTTTGTTGGTGA
91851 AGGAGAAGATTCTGATCTCTTTGTTGGTGA
1 AGGAGAAGATTCTGATCTCTTTGTTGGTGA
* *
91881 AGGAGAACAATCTGAT
1 AGGAGAAGATTCTGAT
91897 TTTGTTCTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 39 0.91
31 4 0.09
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (30 bp):
AGGAGAAGATTCTGATCTCTTTGTTGGTGA
Found at i:94854 original size:23 final size:23
Alignment explanation
Indices: 94828--94873 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
94818 TTACCATTAC
94828 ACCAATGTCAACAGTAACCAAAT
1 ACCAATGTCAACAGTAACCAAAT
94851 ACCAATGTCAACAGTAACCAAAT
1 ACCAATGTCAACAGTAACCAAAT
94874 CAATAAGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.09, T:0.17
Consensus pattern (23 bp):
ACCAATGTCAACAGTAACCAAAT
Found at i:94946 original size:2 final size:2
Alignment explanation
Indices: 94937--94981 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
94927 TATTGTTTTT
94937 TA TA -A TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
94978 TA TA
1 TA TA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.