Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018334.1 Corchorus olitorius cultivar O-4 contig18367, 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: 107975
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:13222 original size:29 final size:29
Alignment explanation
Indices: 13178--13234 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
13168 ACACCCTTGC
13178 TTAACCTCTAACTCTTGAGCAAATAAAAT
1 TTAACCTCTAACTCTTGAGCAAATAAAAT
*
13207 TTAACCTCTAATTCTTGAGCAAATAAAA
1 TTAACCTCTAACTCTTGAGCAAATAAAA
13235 ACTGGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (29 bp):
TTAACCTCTAACTCTTGAGCAAATAAAAT
Found at i:19100 original size:4 final size:4
Alignment explanation
Indices: 19091--19117 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19081 ATAGGAAACT
19091 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
19118 GTAGACTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:19916 original size:2 final size:2
Alignment explanation
Indices: 19909--19943 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19899 CTAATTCTAT
19909 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19944 GGAAAAGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20674 original size:35 final size:35
Alignment explanation
Indices: 20608--20675 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
20598 TTCTAGACTT
* **
20608 GAAGATTTAATTTTTTCTTCATTCAAAAAAAAAAA
1 GAAGATTTAATTCTTTCTTCACCCAAAAAAAAAAA
* *
20643 GAAGATTTAATTCTTTCTTTACCCAAGAAAAAA
1 GAAGATTTAATTCTTTCTTCACCCAAAAAAAAA
20676 GATACCATCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (35 bp):
GAAGATTTAATTCTTTCTTCACCCAAAAAAAAAAA
Found at i:31873 original size:3 final size:3
Alignment explanation
Indices: 31856--31894 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
31846 CCTAATGAAT
*
31856 GAA GAT GAA -AA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
31895 CTAGCTTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:32037 original size:15 final size:14
Alignment explanation
Indices: 32013--32042 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
32003 TAGGTTTTTC
32013 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
32027 TTTTCTCTTTTCTTT
1 TTTT-TCTTTTCTTT
32042 T
1 T
32043 AACAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTTTTCTTT
Found at i:34248 original size:21 final size:21
Alignment explanation
Indices: 34198--34291 Score: 100
Period size: 22 Copynumber: 4.3 Consensus size: 21
34188 CTCCAATGTA
*
34198 GAAATATTGATAACCACACTGT
1 GAAAT-TTGATAACCACACTAT
* *
34220 GAAAATTTGATAACCTCATTAT
1 G-AAATTTGATAACCACACTAT
* *
34242 GAAATTTCAATAACCTC-CTAT
1 GAAATTT-GATAACCACACTAT
34263 GAAAATTTGATAACCACACTAT
1 G-AAATTTGATAACCACACTAT
34285 GAAATTT
1 GAAATTT
34292 CGACTTATTG
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
21 23 0.38
22 34 0.56
23 4 0.07
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (21 bp):
GAAATTTGATAACCACACTAT
Found at i:34347 original size:22 final size:22
Alignment explanation
Indices: 34304--34404 Score: 82
Period size: 22 Copynumber: 4.6 Consensus size: 22
34294 ACTTATTGTG
* *
34304 AAATTTTGATAATCTCTA-TATA
1 AAATTTTGATAACCAC-ACTATA
*
34326 AAATTTTGATAATCACACTATA
1 AAATTTTGATAACCACACTATA
* * *
34348 TAA--TTGGTAACCGCACTATGA
1 AAATTTTGATAACCACACTAT-A
* *
34369 AAATTTTAATAACCACACCATA
1 AAATTTTGATAACCACACTATA
*
34391 AAAATTTGATAACC
1 AAATTTTGATAACC
34405 TCCCAATGAG
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
20 13 0.21
21 4 0.06
22 34 0.54
23 12 0.19
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:34583 original size:22 final size:22
Alignment explanation
Indices: 34545--34763 Score: 115
Period size: 22 Copynumber: 10.0 Consensus size: 22
34535 ATTCCCTCCC
34545 TATGAAATTTT-ATTAACCTTCT
1 TATGAAATTTTGA-TAACCTTCT
**
34567 TATGAAATTTTGATAACCAAAC-
1 TATGAAATTTTGATAACC-TTCT
* * * ** *
34589 TATAAAATGTCGATAATTTTCG
1 TATGAAATTTTGATAACCTTCT
* * *
34611 TATAAAATTTTGTTAACCTTCC
1 TATGAAATTTTGATAACCTTCT
* * * *
34633 TAGGAAATTTTAATAATCTTTT
1 TATGAAATTTTGATAACCTTCT
* *
34655 TATGAAAATTTGGTAACCTT-T
1 TATGAAATTTTGATAACCTTCT
* *
34676 GTATGAAATTTTGATAA-CTACAC
1 -TATGAAATTTTGATAACCTTC-T
* * ** *
34699 AATGAAGTTTTGATAATTTTCA
1 TATGAAATTTTGATAACCTTCT
* * *
34721 TATGAAATTTTGGTGACCATAC-
1 TATGAAATTTTGATAACC-TTCT
34743 TATGAAATTTTGATAACCTTC
1 TATGAAATTTTGATAACCTTC
34764 CCATGTAATT
Statistics
Matches: 143, Mismatches: 46, Indels: 17
0.69 0.22 0.08
Matches are distributed among these distances:
21 6 0.04
22 131 0.92
23 6 0.04
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCT
Found at i:34685 original size:66 final size:66
Alignment explanation
Indices: 34610--34764 Score: 161
Period size: 66 Copynumber: 2.3 Consensus size: 66
34600 GATAATTTTC
* * * * *
34610 GTATAAAATTTTGTTAACCTTCCTAGGAAATTTTAATAATCTTT-TTATGAAAATTTGGTAACCT
1 GTATGAAATTTTGATAACCTTCCAAGGAAATTTTAATAAT-TTTCATATGAAAATTTGGTAACCA
*
34674 TT
65 TA
* * * * * *
34676 GTATGAAATTTTGATAA-CTACACAATGAAGTTTTGATAATTTTCATATGAAATTTTGGTGACCA
1 GTATGAAATTTTGATAACCTTC-CAAGGAAATTTTAATAATTTTCATATGAAAATTTGGTAACCA
34740 TA
65 TA
*
34742 CTATGAAATTTTGATAACCTTCC
1 GTATGAAATTTTGATAACCTTCC
34765 CATGTAATTT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
65 6 0.08
66 63 0.88
67 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (66 bp):
GTATGAAATTTTGATAACCTTCCAAGGAAATTTTAATAATTTTCATATGAAAATTTGGTAACCAT
A
Found at i:35318 original size:70 final size:70
Alignment explanation
Indices: 35193--35329 Score: 229
Period size: 70 Copynumber: 2.0 Consensus size: 70
35183 TATTTTTATG
* * *
35193 AAATTTTTCCTTTTGCTTATGTGGAATTTTTAGTCACGTGTCGCGATGGTATGACACTGTTTGAT
1 AAATTTTTCCTTTTGCTTACGTGGAATTTTTAGCCACGTGTCGCGATGATATGACACTGTTTGAT
35258 GACGT
66 GACGT
* *
35263 AAATTTTTCCTTTTGCTTACGTGGAATTTTTAGCCACGTGTCGTGATGATGTGACACTGTTTGAT
1 AAATTTTTCCTTTTGCTTACGTGGAATTTTTAGCCACGTGTCGCGATGATATGACACTGTTTGAT
35328 GA
66 GA
35330 TGTCATTAGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (70 bp):
AAATTTTTCCTTTTGCTTACGTGGAATTTTTAGCCACGTGTCGCGATGATATGACACTGTTTGAT
GACGT
Found at i:57328 original size:48 final size:48
Alignment explanation
Indices: 57257--57354 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
57247 TTTTTTTTGA
*
57257 GAAATAAACTTTTTGATTAATGAGATTGAGATTACAAATGCACATGAT
1 GAAATAAACTTTTTGATTAATGAGATTGAGATTACAAATGCACAGGAT
*
57305 GAAATAAACTTTTTGATTAATGAGATTGGGATTACAAATGCACAGGAT
1 GAAATAAACTTTTTGATTAATGAGATTGAGATTACAAATGCACAGGAT
57353 GA
1 GA
57355 CCCGTAACCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (48 bp):
GAAATAAACTTTTTGATTAATGAGATTGAGATTACAAATGCACAGGAT
Found at i:61123 original size:12 final size:13
Alignment explanation
Indices: 61100--61128 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
61090 TTAGACGCAA
61100 AAAAAACAAAAAC
1 AAAAAACAAAAAC
61113 AAAAAAC-AAAAC
1 AAAAAACAAAAAC
61125 AAAA
1 AAAA
61129 CACACACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:63629 original size:17 final size:17
Alignment explanation
Indices: 63607--63640 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
63597 AGAAAATAGT
63607 TGAATTAACTAGAGACG
1 TGAATTAACTAGAGACG
63624 TGAATTAACTAGAGACG
1 TGAATTAACTAGAGACG
63641 ACAGGCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
TGAATTAACTAGAGACG
Found at i:66558 original size:14 final size:13
Alignment explanation
Indices: 66539--66577 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
66529 AAATTATAAA
66539 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
66552 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
66566 ATTTAAAAAATT
1 ATTTAAAAAATT
66578 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:66805 original size:122 final size:128
Alignment explanation
Indices: 66563--66816 Score: 394
Period size: 122 Copynumber: 2.0 Consensus size: 128
66553 ATTTAAGAAA
66563 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGT---AATAAAA
* *
66628 TAGATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TACATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
66693 G
128 G
* *
66694 TATATTT-TAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-C
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC
*
66755 ATA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66816 T
1 T
66817 TTAAACAATG
Statistics
Matches: 118, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
122 55 0.47
123 2 0.02
124 3 0.03
125 5 0.04
126 1 0.01
130 45 0.38
131 7 0.06
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (128 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC
ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:72592 original size:3 final size:3
Alignment explanation
Indices: 72584--72635 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
72574 TATAAGGTTA
72584 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
72632 TAT T
1 TAT T
72636 GCAATAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:74615 original size:18 final size:18
Alignment explanation
Indices: 74576--74618 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
74566 TTCAAAGATC
*
74576 AGAAACAACCCATTGATGA
1 AGAAA-AACCCATTGAAGA
74595 AGAAAAACCC-TTGAAGCA
1 AGAAAAACCCATTGAAG-A
74613 AGAAAA
1 AGAAAA
74619 TGGGAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 12 0.55
19 5 0.23
ACGTcount: A:0.53, C:0.19, G:0.16, T:0.12
Consensus pattern (18 bp):
AGAAAAACCCATTGAAGA
Found at i:76645 original size:13 final size:13
Alignment explanation
Indices: 76627--76653 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
76617 TTCTTGTAAT
76627 ATAACAAATATCA
1 ATAACAAATATCA
76640 ATAACAAATATCA
1 ATAACAAATATCA
76653 A
1 A
76654 GTTTCTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAACAAATATCA
Found at i:77706 original size:20 final size:20
Alignment explanation
Indices: 77670--77707 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
77660 GATTCGAAAA
*
77670 AAATTCGAGTTCGGCTCGGG
1 AAATTCGAGTCCGGCTCGGG
77690 AAATTCGAG-CCGAGCTCG
1 AAATTCGAGTCCG-GCTCG
77708 AGCTATGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (20 bp):
AAATTCGAGTCCGGCTCGGG
Found at i:81688 original size:6 final size:6
Alignment explanation
Indices: 81670--81757 Score: 95
Period size: 6 Copynumber: 14.5 Consensus size: 6
81660 GAGCAAGGAG
* * * *
81670 AGGGAC AGGGAA AGAGAA AGAGAA AGGGAA AGGGAA AGGGAA AGGGAT
1 AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA
* * * *
81718 AGGGAC AGAGAA AGGGAT AGGGAT AGGGAA AGGGCAA AGG
1 AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGGG-AA AGG
81758 TCCGGGATCG
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
6 66 0.93
7 5 0.07
ACGTcount: A:0.47, C:0.03, G:0.47, T:0.03
Consensus pattern (6 bp):
AGGGAA
Found at i:84118 original size:11 final size:11
Alignment explanation
Indices: 84102--84132 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
84092 TCTCTCTTCC
84102 TTTCTTTTTTT
1 TTTCTTTTTTT
84113 TTTCTTTTTTT
1 TTTCTTTTTTT
*
84124 ATTCTTTTT
1 TTTCTTTTT
84133 ATTAAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:84344 original size:101 final size:105
Alignment explanation
Indices: 84152--84353 Score: 297
Period size: 103 Copynumber: 1.9 Consensus size: 105
84142 ACTTTAGCCT
* * * *
84152 TAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATT-AAATTTTATTTTTATTTAAAAGGTAAATTCCAAAATT
84217 AATAATTTATTGTTATATGGTTTTAGAAATAAAATACAAAAC
65 AATAA-TTATTGTTATATGGTTTTAGAAATAAAATACAAAAC
*
84259 TAATTTCACTAAGTTTAGCCCCAAATT-AA-TTT-TTTTTATTTAAAAGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCCAAATTAAATTTTATTTTTATTTAAAAGGTAAATTCCAAAATTA
84321 ATAA-TATTGTTATA-GAGTTTTAGAAATAAAATA
66 ATAATTATTGTTATATG-GTTTTAGAAATAAAATA
84354 TATACAATGT
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
100 1 0.01
101 27 0.30
103 30 0.34
104 3 0.03
105 2 0.02
107 26 0.29
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAATTTTATTTTTATTTAAAAGGTAAATTCCAAAATTA
ATAATTATTGTTATATGGTTTTAGAAATAAAATACAAAAC
Found at i:86483 original size:23 final size:23
Alignment explanation
Indices: 86457--86503 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
86447 TTAAGGTTAT
86457 TGTTTTTACTGTTATACATGAGA
1 TGTTTTTACTGTTATACATGAGA
86480 TGTTTTTACTGTTATACATGAGA
1 TGTTTTTACTGTTATACATGAGA
86503 T
1 T
86504 ATAAGGTATC
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:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (23 bp):
TGTTTTTACTGTTATACATGAGA
Found at i:105967 original size:31 final size:31
Alignment explanation
Indices: 105929--106050 Score: 128
Period size: 31 Copynumber: 4.0 Consensus size: 31
105919 CGATACCAGA
*
105929 CCCTTATTTTAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
105960 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
* ** * *
105991 -TCTTCATTTG-GCCAAATT--A-AAAGATATGG
1 CCCTT-ATTTGAG-CATTTTCGATAACGTTA-GG
106020 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
106051 TCAGGGCCCT
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
28 5 0.07
29 12 0.17
30 8 0.11
31 42 0.58
32 5 0.07
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGG
Found at i:106092 original size:31 final size:31
Alignment explanation
Indices: 106057--106159 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 31
106047 TAGGTCAGGG
106057 CCCTTATTTGAGCATTTTTGCAAACATTAGA
1 CCCTTATTTGAGCATTTTTGCAAACATTAGA
** * * *
106088 CCCTTATTTG-GTCA-AATT-AAAAGATCAGA
1 CCCTTATTTGAG-CATTTTTGCAAACATTAGA
* * *
106117 CCCTTATTTAAGCATTTTGGCAAACATTAGG
1 CCCTTATTTGAGCATTTTTGCAAACATTAGA
106148 CCCTTATTTGAG
1 CCCTTATTTGAG
106160 TAATTAGCCA
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
29 19 0.35
30 5 0.09
31 30 0.56
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTTGCAAACATTAGA
Found at i:106104 original size:97 final size:91
Alignment explanation
Indices: 105925--106159 Score: 262
Period size: 97 Copynumber: 2.5 Consensus size: 91
105915 GTTTCGATAC
* *
105925 CAGACCCTTATTTTAGCATTTTCGATAACGTTAGGCCCTTATTTGAGCATTTTCGATAACGTTAG
1 CAGACCCTTATTTAAGCATTTTCGATAACGTTAGGCCCTTATTTGAGCATTTTCGATAACATTAG
**
105990 GTCTTCATTTGGCCAAATTAAAAGAT
66 CCCTTCATTTGGCCAAATTAAAAGAT
* * *
106016 -ATGGCCCTTATTTGAGCATTTTCGATAACGTTAGGTCAGGGCCCTTATTTGAGCATTTTTGCA-
1 CA-GACCCTTATTTAAGCATTTTCGATAACG-T---T-A-GGCCCTTATTTGAGCATTTTCG-AT
*
106079 AACATTAGACCCTT-ATTTGGTCAAATTAAAAGAT
58 AACATTAG-CCCTTCATTTGGCCAAATTAAAAGAT
* *
106113 CAGACCCTTATTTAAGCATTTTGGCA-AACATTAGGCCCTTATTTGAG
1 CAGACCCTTATTTAAGCATTTTCG-ATAACGTTAGGCCCTTATTTGAG
106160 TAATTAGCCA
Statistics
Matches: 122, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
90 1 0.01
91 40 0.33
92 2 0.02
93 1 0.01
95 1 0.01
96 2 0.02
97 69 0.57
98 6 0.05
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (91 bp):
CAGACCCTTATTTAAGCATTTTCGATAACGTTAGGCCCTTATTTGAGCATTTTCGATAACATTAG
CCCTTCATTTGGCCAAATTAAAAGAT
Done.