Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006735.1 Corchorus capsularis cultivar CVL-1 contig06756, 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: 68880
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5311 original size:32 final size:33
Alignment explanation
Indices: 5275--5342 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
5265 CGCCACCATT
** *
5275 TAGCGGCGCCTA-ACGAAGAAAACGCTGCTATA
1 TAGCGGCGCCTACAAAAAGAAAACGCCGCTATA
* *
5307 TAGCGGCGTCTACAAAAAGCAAACGCCGCTATA
1 TAGCGGCGCCTACAAAAAGAAAACGCCGCTATA
5340 TAG
1 TAG
5343 TGGAGTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 11 0.37
33 19 0.63
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (33 bp):
TAGCGGCGCCTACAAAAAGAAAACGCCGCTATA
Found at i:5338 original size:33 final size:32
Alignment explanation
Indices: 5242--5342 Score: 103
Period size: 32 Copynumber: 3.1 Consensus size: 32
5232 TTGCAGCAGA
* * * *
5242 ATAGCGGCGTCTAATGAATCAAACGCCACCAT
1 ATAGCGGCGTCTAAAGAAGCAAACGCCGCTAT
* * * * *
5274 TTAGCGGCGCCTAACGAAGAAAACGCTGCTAT
1 ATAGCGGCGTCTAAAGAAGCAAACGCCGCTAT
*
5306 ATAGCGGCGTCTACAAAAAGCAAACGCCGCTAT
1 ATAGCGGCGTCTA-AAGAAGCAAACGCCGCTAT
5339 ATAG
1 ATAG
5343 TGGAGTCAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
32 35 0.65
33 19 0.35
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.18
Consensus pattern (32 bp):
ATAGCGGCGTCTAAAGAAGCAAACGCCGCTAT
Found at i:5917 original size:23 final size:23
Alignment explanation
Indices: 5889--5932 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
5879 AAAATTGTCG
5889 ATTCGCAGCGCCCTTTTCGCATC
1 ATTCGCAGCGCCCTTTTCGCATC
5912 ATTCGCAGCGCCCTTTTCGCA
1 ATTCGCAGCGCCCTTTTCGCA
5933 GGTCTCTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.14, C:0.39, G:0.18, T:0.30
Consensus pattern (23 bp):
ATTCGCAGCGCCCTTTTCGCATC
Found at i:5996 original size:13 final size:13
Alignment explanation
Indices: 5978--6014 Score: 60
Period size: 11 Copynumber: 3.0 Consensus size: 13
5968 AAAAAATGGG
5978 TTCTCCTTTCCTT
1 TTCTCCTTTCCTT
5991 TTCTCCTTTCC--
1 TTCTCCTTTCCTT
6002 TTCTCCTTTCCTT
1 TTCTCCTTTCCTT
6015 CCGTTCGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (13 bp):
TTCTCCTTTCCTT
Found at i:8722 original size:2 final size:2
Alignment explanation
Indices: 8715--8740 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8705 AATAATTTTC
8715 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8741 GCTACTTTGA
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):
AT
Found at i:8972 original size:32 final size:32
Alignment explanation
Indices: 8926--8988 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
8916 GGGTATACCT
*
8926 TTATATAGCGGCGTCTGAAGAACAAAACGCCC
1 TTATATAGCGGCGTCTAAAGAACAAAACGCCC
* *
8958 TTATCTAGCGGCGTCTAAAGAACAAGACGCC
1 TTATATAGCGGCGTCTAAAGAACAAAACGCC
8989 ACTATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.19
Consensus pattern (32 bp):
TTATATAGCGGCGTCTAAAGAACAAAACGCCC
Found at i:12482 original size:21 final size:20
Alignment explanation
Indices: 12456--12495 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
12446 GCAAAGTCAA
12456 CTCTCTCTCTAACATGAGAGT
1 CTCTCTCTCTAAC-TGAGAGT
*
12477 CTCTCTCTCTATCTGAGAG
1 CTCTCTCTCTAACTGAGAG
12496 CTTCTCCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (20 bp):
CTCTCTCTCTAACTGAGAGT
Found at i:15040 original size:61 final size:61
Alignment explanation
Indices: 14944--15066 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 61
14934 AATAAATTAA
* * *
14944 TATGGTTCTCTTTAAGATGCTGAGGAGATATTTTCTTTTCTGTTCTCTTCTCTTAAACATT
1 TATGGTTCTCTTTAAAATGCTAAGGAGATAGTTTCTTTTCTGTTCTCTTCTCTTAAACATT
* *
15005 TATGGTTCTTTTTAAAATGCTAAGGAGATAGTTTCTTTTTTGTTCTCTTCTCTTAAACATT
1 TATGGTTCTCTTTAAAATGCTAAGGAGATAGTTTCTTTTCTGTTCTCTTCTCTTAAACATT
15066 T
1 T
15067 CTTTTGTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.21, C:0.15, G:0.14, T:0.50
Consensus pattern (61 bp):
TATGGTTCTCTTTAAAATGCTAAGGAGATAGTTTCTTTTCTGTTCTCTTCTCTTAAACATT
Found at i:16198 original size:3 final size:3
Alignment explanation
Indices: 16190--16219 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
16180 CATGTCTAGA
*
16190 TTC TTC TTC CTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
16220 CCTCATAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:16337 original size:22 final size:22
Alignment explanation
Indices: 16312--16367 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
16302 ATTTATGTCT
*
16312 ATTTCTTTTCTTTTTTCTCCCC
1 ATTTCTTTTCTTTTGTCTCCCC
*
16334 ATTT-TTCTTCTTTTGTCTTCCC
1 ATTTCTT-TTCTTTTGTCTCCCC
* *
16356 ATGTCTCTTCTT
1 ATTTCTTTTCTT
16368 CTTCTTCTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 25 0.89
23 1 0.04
ACGTcount: A:0.05, C:0.29, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTCTTTTCTTTTGTCTCCCC
Found at i:17034 original size:19 final size:18
Alignment explanation
Indices: 17010--17045 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17000 TGAAGATTTC
17010 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
17029 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
17046 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:22296 original size:11 final size:10
Alignment explanation
Indices: 22278--22311 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
22268 GAAGTTCGTG
22278 TTTTGAAGAT
1 TTTTGAAGAT
22288 TTCTTGAAGAT
1 TT-TTGAAGAT
22299 ATTTTGAAGAT
1 -TTTTGAAGAT
22310 TT
1 TT
22312 GAAGACTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:24098 original size:34 final size:35
Alignment explanation
Indices: 24033--24099 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
24023 ATTTGCGATG
* * *
24033 TAAAAAAAATTTCTTTTCCGTTTTTCCTTTTAAAA
1 TAAAAAAAATTTATTTTCCATTTTGCCTTTTAAAA
* *
24068 TAAAAAAAA-TTATTTTCTATTTTGCTTTTTAA
1 TAAAAAAAATTTATTTTCCATTTTGCCTTTTAA
24100 TTTTTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 18 0.67
35 9 0.33
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (35 bp):
TAAAAAAAATTTATTTTCCATTTTGCCTTTTAAAA
Found at i:29112 original size:11 final size:10
Alignment explanation
Indices: 29094--29127 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
29084 GAAGTTCGTG
29094 TTTTGAAGAT
1 TTTTGAAGAT
29104 TTCTTGAAGAT
1 TT-TTGAAGAT
29115 ATTTTGAAGAT
1 -TTTTGAAGAT
29126 TT
1 TT
29128 GAAGACTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:35014 original size:75 final size:75
Alignment explanation
Indices: 34891--35284 Score: 531
Period size: 75 Copynumber: 5.2 Consensus size: 75
34881 TCCAACTCTA
*
34891 AGCGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCCAGCAGACGCCACCCG
1 AGCGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCCACCCG
34956 CAGACGGCTG
66 CAGACGGCTG
* * *
34966 AGCGCCTAGACTAGCACCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCCAGCAGACGCCACCCC
1 AGCGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCCA-CCC
*
35031 GTAGACGGCTG
65 GCAGACGGCTG
* * *
35042 AGTGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCATCCAAGCAGACGCCACCTG
1 AGCGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCCACCCG
35107 CAGACGGCTG
66 CAGACGGCTG
* * * * *
35117 AGCGCCTAGACTGGCGCCCCCGTATAACCCTAAGCGAGGTCGAGCATCCGAGCTGACGCCACTCG
1 AGCGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCCACCCG
*
35182 CAGA-GGGTCG
66 CAGACGGCT-G
* * * * * *
35192 AACGCCTAGACTGGCGTCCCCGTATAACTCTCAGCAAGGTCGTGCGTCCAAGC-GAACGTCACCC
1 AGCGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAG-ACGCCACCC
* * *
35256 GCGGACAGCAG
65 GCAGACGGCTG
*
35267 AGAGCCTAGACTGGCGCC
1 AGCGCCTAGACTGGCGCC
35285 ATGTCAAACC
Statistics
Matches: 281, Mismatches: 34, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
74 4 0.01
75 207 0.74
76 70 0.25
ACGTcount: A:0.23, C:0.35, G:0.28, T:0.13
Consensus pattern (75 bp):
AGCGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCCACCCG
CAGACGGCTG
Found at i:35175 original size:151 final size:150
Alignment explanation
Indices: 34893--35284 Score: 536
Period size: 151 Copynumber: 2.6 Consensus size: 150
34883 CAACTCTAAG
*
34893 CGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCCAGCAGACGCCACCCGCA
1 CGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCCACCCGCA
* * * *
34958 GACGGCTGAGCGCCTAGACTAGCACCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCCAGCAGAC
66 GACGGCTGAGCGCCTAGACTGGCGCCCCCGTATAACCCTAAGCGAGGTCGAGCATCCCAGCAGAC
* *
35023 GCCACCCCGTAGACGGCT-GAG
131 GCCA-CCCGCAGA-GGCTCGAA
* * *
35044 TGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCATCCAAGCAGACGCCACCTGCA
1 CGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCCACCCGCA
* *
35109 GACGGCTGAGCGCCTAGACTGGCGCCCCCGTATAACCCTAAGCGAGGTCGAGCATCCGAGCTGAC
66 GACGGCTGAGCGCCTAGACTGGCGCCCCCGTATAACCCTAAGCGAGGTCGAGCATCCCAGCAGAC
* *
35174 GCCACTCGCAGAGGGTCGAA
131 GCCACCCGCAGAGGCTCGAA
* * * * *
35194 CGCCTAGACTGGCGTCCCCGTATAACTCTCAGCAAGGTCGTGCGTCCAAGC-GAACGTCACCCGC
1 CGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAG-ACGCCACCCGC
* * * *
35258 GGACAGCAGAGAGCCTAGACTGGCGCC
65 AGACGGCTGAGCGCCTAGACTGGCGCC
35285 ATGTCAAACC
Statistics
Matches: 213, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
149 4 0.02
150 85 0.40
151 124 0.58
ACGTcount: A:0.23, C:0.35, G:0.28, T:0.14
Consensus pattern (150 bp):
CGCCTAGACTGGCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCCACCCGCA
GACGGCTGAGCGCCTAGACTGGCGCCCCCGTATAACCCTAAGCGAGGTCGAGCATCCCAGCAGAC
GCCACCCGCAGAGGCTCGAA
Found at i:43574 original size:9 final size:9
Alignment explanation
Indices: 43560--43590 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
43550 CATGGGTCTC
43560 AAATTCATG
1 AAATTCATG
43569 AAATTCATG
1 AAATTCATG
43578 AAATTCATG
1 AAATTCATG
43587 AAAT
1 AAAT
43591 CCCACTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (9 bp):
AAATTCATG
Found at i:45622 original size:33 final size:31
Alignment explanation
Indices: 45585--45645 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
45575 TGGCAGACCA
*
45585 TGGTTTTCATATGATTGAACTGGTTTTATTACT
1 TGGTTTTCATAT-ACT-AACTGGTTTTATTACT
* *
45618 TGGTTTTGATATACTATCTGGTTTTATT
1 TGGTTTTCATATACTAACTGGTTTTATT
45646 GATAAACTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.48
32 2 0.08
33 11 0.44
ACGTcount: A:0.20, C:0.08, G:0.18, T:0.54
Consensus pattern (31 bp):
TGGTTTTCATATACTAACTGGTTTTATTACT
Found at i:52639 original size:11 final size:11
Alignment explanation
Indices: 52623--52652 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
52613 GGTCTTCAAT
*
52623 TCTTCAAATTA
1 TCTTCAAATAA
52634 TCTTCAAATAA
1 TCTTCAAATAA
52645 TCTTCAAA
1 TCTTCAAA
52653 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:53960 original size:16 final size:15
Alignment explanation
Indices: 53931--53959 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53921 ATAGGCTTTT
53931 CCCTTCTCCTCTCTC
1 CCCTTCTCCTCTCTC
53946 CCCTTCTCC-CTCTC
1 CCCTTCTCCTCTCTC
53960 TAGTTCTCTT
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:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (15 bp):
CCCTTCTCCTCTCTC
Found at i:55085 original size:20 final size:21
Alignment explanation
Indices: 55062--55104 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
55052 CAAATCAAGG
* *
55062 AATAGGCAATC-AATCAAAAC
1 AATAAGCAATCAAAGCAAAAC
*
55082 AATAATCAATCAAAGCAAAAC
1 AATAAGCAATCAAAGCAAAAC
55103 AA
1 AA
55105 GGCGAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.60, C:0.19, G:0.07, T:0.14
Consensus pattern (21 bp):
AATAAGCAATCAAAGCAAAAC
Found at i:57243 original size:22 final size:23
Alignment explanation
Indices: 57200--57243 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
57190 CAAACCCTAA
*
57200 TTTTTTTTAGAAAAAAAGGCAAT
1 TTTTTTTTAGAAAAAAACGCAAT
57223 TTTTTTTTAG-AAAAAACGCAA
1 TTTTTTTTAGAAAAAAACGCAA
57244 CAAGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (23 bp):
TTTTTTTTAGAAAAAAACGCAAT
Found at i:58906 original size:11 final size:11
Alignment explanation
Indices: 58890--58919 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
58880 GGTCTTCAAT
*
58890 TCTTCAAATTA
1 TCTTCAAATAA
58901 TCTTCAAATAA
1 TCTTCAAATAA
58912 TCTTCAAA
1 TCTTCAAA
58920 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:60194 original size:24 final size:24
Alignment explanation
Indices: 60167--60221 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
60157 GTTATTACCG
60167 TGCCACCACCGGCCATCCATGCGC
1 TGCCACCACCGGCCATCCATGCGC
*
60191 TGCCACCACCGGCCATCCATGCGT
1 TGCCACCACCGGCCATCCATGCGC
60215 TGCCACC
1 TGCCACC
60222 TCTACATACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.49, G:0.20, T:0.15
Consensus pattern (24 bp):
TGCCACCACCGGCCATCCATGCGC
Found at i:63526 original size:19 final size:18
Alignment explanation
Indices: 63502--63541 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
63492 TTGAAAATTT
*
63502 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
63521 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
63539 ATT
1 ATT
63542 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:68393 original size:12 final size:12
Alignment explanation
Indices: 68376--68400 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68366 GGAAATTACA
68376 AGCAAGGCAGAG
1 AGCAAGGCAGAG
68388 AGCAAGGCAGAG
1 AGCAAGGCAGAG
68400 A
1 A
68401 ATAAGGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.40, T:0.00
Consensus pattern (12 bp):
AGCAAGGCAGAG
Found at i:68435 original size:39 final size:39
Alignment explanation
Indices: 68354--68435 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
68344 AGCACCCCAT
* * *
68354 GGCAGAGAATAAGGAAATTACAAGCAAGGCAGAGAGCAA
1 GGCAGAGAATAAGGAAATTACAAGCAAAGCAAAGAACAA
* *
68393 GGCAGAGAATAAGGCAATTACAAGCAAAGTAAAGTAAC-A
1 GGCAGAGAATAAGGAAATTACAAGCAAAGCAAAG-AACAA
68432 GGCA
1 GGCA
68436 ATCGTGAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.49, C:0.13, G:0.28, T:0.10
Consensus pattern (39 bp):
GGCAGAGAATAAGGAAATTACAAGCAAAGCAAAGAACAA
Done.