Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013438.1 Corchorus capsularis cultivar CVL-1 contig13459, 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: 51601
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Found at i:2931 original size:15 final size:16
Alignment explanation
Indices: 2911--2940 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2901 GAATAGCGAG
2911 GAAAG-AACAAAAATA
1 GAAAGAAACAAAAATA
2926 GAAAGAAACAAAAAT
1 GAAAGAAACAAAAAT
2941 CAAGAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.07, G:0.13, T:0.07
Consensus pattern (16 bp):
GAAAGAAACAAAAATA
Found at i:5282 original size:25 final size:25
Alignment explanation
Indices: 5254--5304 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5244 TGAATTCTTG
5254 AAACATATGGTCTCATTATGAACCA
1 AAACATATGGTCTCATTATGAACCA
5279 AAACATATGGTCTCATTATGAACCA
1 AAACATATGGTCTCATTATGAACCA
5304 A
1 A
5305 TTCAACATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (25 bp):
AAACATATGGTCTCATTATGAACCA
Found at i:7010 original size:116 final size:116
Alignment explanation
Indices: 6810--7228 Score: 626
Period size: 116 Copynumber: 3.6 Consensus size: 116
6800 ATATCGATCG
* * * ** *
6810 AGCATCCCTCGGTCGCACGACCAAGTGGGCATCCCCCACTCATGTAATAAGACGATCGAGCATCT
1 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAATCGAGCATCC
* *
6875 CTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCG
66 CTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCA
* *
6926 AGCATCCCTCGGTCATACGGCCCAGTGGGCATCCCCCACTCATGCAATAAGAAAATCGAGCATCC
1 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAATCGAGCATCC
6991 CTCGGTCACACGGCCAAGTGGGCAT-CCCCACTCATGTAATAAATAAATCA
66 CTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCA
* * *
7041 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCTACTCACGCAATAAGAAAACCGAGCATCC
1 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAATCGAGCATCC
*
7106 CTCGGTCACAAGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCA
66 CTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCA
* * * * * *
7157 AGCATCCCTCGGTCACATGGCCCAA-TGGGCATCCCCCACACGTGCAAGAAGAAAAACAAGCATC
1 AGCATCCCTCGGTCACACGG-CCAAGTGGGCATCCCCCACTCATGCAATAAGAAAATCGAGCATC
*
7221 CCTTGGTC
65 CCTCGGTC
7229 GCACAACCTA
Statistics
Matches: 276, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
115 108 0.39
116 164 0.59
117 4 0.01
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.17
Consensus pattern (116 bp):
AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAATCGAGCATCC
CTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCA
Found at i:7103 original size:173 final size:173
Alignment explanation
Indices: 6806--7228 Score: 557
Period size: 173 Copynumber: 2.4 Consensus size: 173
6796 AGCAATATCG
* * ** *
6806 ATCGAGCATCCCTCGGTCGCACGACCAAGTGGGCATCCCCCACTCATGTAATAAGACGATCGAGC
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCAT-CCCCACTCATGTAATAAGAAAATCAAGC
* * * * *
6871 ATCTCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCGAGCATCCCTC
65 ATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCACGCAATAAATAAACCGAGCATCCCTC
* * *
6936 GGTCATACGGCCCAGTGGGCATCCCCCACTCATGCAATAAGA-AA
130 GGTCACAAGGCCAAGTGGGCATCCCCCACTCATGCAATAA-ATAA
6980 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCACTCATGTAATAA-ATAAATCAAGC
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCACTCATGTAATAAGA-AAATCAAGC
*
7044 ATCCCTCGGTCACACGGCCAAGTGGGCATCCCCTACTCACGCAATAAGA-AAACCGAGCATCCCT
65 ATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCACGCAATAA-ATAAACCGAGCATCCCT
*
7108 CGGTCACAAGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
129 CGGTCACAAGGCCAAGTGGGCATCCCCCACTCATGCAATAAATAA
* * * * * * *
7153 ATCAAGCATCCCTCGGTCACATGGCCCAA-TGGGCATCCCCCACACGTGCAAGAAGAAAAACAAG
1 ATCGAGCATCCCTCGGTCACACGG-CCAAGTGGGCAT-CCCCACTCATGTAATAAGAAAATCAAG
*
7217 CATCCCTTGGTC
64 CATCCCTCGGTC
7229 GCACAACCTA
Statistics
Matches: 220, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
172 2 0.01
173 147 0.67
174 70 0.32
175 1 0.00
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.17
Consensus pattern (173 bp):
ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCACTCATGTAATAAGAAAATCAAGCA
TCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCACGCAATAAATAAACCGAGCATCCCTCG
GTCACAAGGCCAAGTGGGCATCCCCCACTCATGCAATAAATAA
Found at i:7217 original size:58 final size:58
Alignment explanation
Indices: 6806--7228 Score: 559
Period size: 58 Copynumber: 7.3 Consensus size: 58
6796 AGCAATATCG
* * **
6806 ATCGAGCATCCCTCGGTCGCACGACCAAGTGGGCATCCCCCACTCATGTAATAAGACG
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAA
* *
6864 ATCGAGCATCTCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAA-ATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGA-AA
* * *
6922 ATCGAGCATCCCTCGGTCATACGGCCCAGTGGGCATCCCCCACTCATGCAATAAGAAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAA
6980 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCAT-CCCCACTCATGTAATAA-ATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGA-AA
* * * *
7037 ATCAAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCTACTCACGCAATAAGAAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAA
* *
7095 ACCGAGCATCCCTCGGTCACAAGGCCAAGTGGGCATCCCCCACTCATGTAATAA-ATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGA-AA
* * * * * *
7153 ATCAAGCATCCCTCGGTCACATGGCCCAA-TGGGCATCCCCCACACGTGCAAGAAGAAA
1 ATCGAGCATCCCTCGGTCACACGG-CCAAGTGGGCATCCCCCACTCATGTAATAAGAAA
* * *
7211 AACAAGCATCCCTTGGTC
1 ATCGAGCATCCCTCGGTC
7229 GCACAACCTA
Statistics
Matches: 326, Mismatches: 31, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
56 1 0.00
57 55 0.17
58 263 0.81
59 7 0.02
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.17
Consensus pattern (58 bp):
ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAA
Found at i:7221 original size:231 final size:231
Alignment explanation
Indices: 6810--7228 Score: 649
Period size: 231 Copynumber: 1.8 Consensus size: 231
6800 ATATCGATCG
* * * ** * *
6810 AGCATCCCTCGGTCGCACGACCAAGTGGGCATCCCCCACTCATGTAATAAGACGATCGAGCATCT
1 AGCATCCCTCGGTCACACGACCAAGTGGGCATCCCCCACTCACGCAATAAGAAAACCGAGCATCC
* * *
6875 CTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCGAGCATCCCTCGGTC
66 CTCGGTCACAAGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCGGTC
* * * * * *
6940 ATACGGCCCAGTGGGCATCCCCCACTCATGCAATAAGAAAATCGAGCATCCCTCGGTCACACGGC
131 ACACGGCCCAATGGGCATCCCCCACACATGCAAGAAGAAAAACAAGCATCCCTCGGTCACACGGC
7005 CAAGTGGGCATCCCCACTCATGTAATAAATAAATCA
196 CAAGTGGGCATCCCCACTCATGTAATAAATAAATCA
* *
7041 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCTACTCACGCAATAAGAAAACCGAGCATCC
1 AGCATCCCTCGGTCACACGACCAAGTGGGCATCCCCCACTCACGCAATAAGAAAACCGAGCATCC
7106 CTCGGTCACAAGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCGGTC
66 CTCGGTCACAAGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCGGTC
* * *
7171 ACATGGCCCAATGGGCATCCCCCACACGTGCAAGAAGAAAAACAAGCATCCCTTGGTC
131 ACACGGCCCAATGGGCATCCCCCACACATGCAAGAAGAAAAACAAGCATCCCTCGGTC
7229 GCACAACCTA
Statistics
Matches: 167, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
231 167 1.00
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.17
Consensus pattern (231 bp):
AGCATCCCTCGGTCACACGACCAAGTGGGCATCCCCCACTCACGCAATAAGAAAACCGAGCATCC
CTCGGTCACAAGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCGGTC
ACACGGCCCAATGGGCATCCCCCACACATGCAAGAAGAAAAACAAGCATCCCTCGGTCACACGGC
CAAGTGGGCATCCCCACTCATGTAATAAATAAATCA
Found at i:7745 original size:29 final size:29
Alignment explanation
Indices: 7682--7835 Score: 238
Period size: 29 Copynumber: 5.3 Consensus size: 29
7672 AAAAAAAAAG
* * *
7682 GTGGTAGTACGCCCT-CAAGGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGTTCACGAA
7710 GTGGTAGTACTCCCTCCAAAGTTCACGAA
1 GTGGTAGTACTCCCTCCAAAGTTCACGAA
*
7739 GTGGTAGTACTCCCTCCAAAGTTCCCGAA
1 GTGGTAGTACTCCCTCCAAAGTTCACGAA
*
7768 GTGGTAGTACTCCCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGTTCACGAA
*
7797 GTAGTAGTACTCCCTCCAAAGTTCACGAA
1 GTGGTAGTACTCCCTCCAAAGTTCACGAA
*
7826 GTGATAGTAC
1 GTGGTAGTAC
7836 ACCCCCTAGA
Statistics
Matches: 115, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
28 14 0.12
29 101 0.88
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (29 bp):
GTGGTAGTACTCCCTCCAAAGTTCACGAA
Found at i:8029 original size:27 final size:27
Alignment explanation
Indices: 7966--8307 Score: 447
Period size: 27 Copynumber: 12.6 Consensus size: 27
7956 CAAAAGAGAA
7966 AGCGCCGTACA---ACCATCTTGGACGAG
1 AGCGCCGTACATCCACCATCTTGGAC--G
** *
7992 AGCGTTGTACATCCACCATTTTGGACG
1 AGCGCCGTACATCCACCATCTTGGACG
* * *
8019 AGCGCTGTACATCCACTATTTTGGACG
1 AGCGCCGTACATCCACCATCTTGGACG
* * *
8046 AGCGTCGTACATCCACTATTTTGGACG
1 AGCGCCGTACATCCACCATCTTGGACG
* * * *
8073 AGCACTGTACAGCCACCATTTTGGACG
1 AGCGCCGTACATCCACCATCTTGGACG
*
8100 AGCGTCGTACATCCACCATCTTGGACG
1 AGCGCCGTACATCCACCATCTTGGACG
8127 AGCGCCGTACATCCACCATCTTGGACG
1 AGCGCCGTACATCCACCATCTTGGACG
8154 AGCGCCGTACATCCACCATCTTGGACG
1 AGCGCCGTACATCCACCATCTTGGACG
8181 AGCGCCGTACATCCACCATCTTGGACG
1 AGCGCCGTACATCCACCATCTTGGACG
*
8208 AGCGCCGTGCATCCACCATCTTGGACG
1 AGCGCCGTACATCCACCATCTTGGACG
* *
8235 AGCGCCGTGCATCCACCATCTTGGAAGAG
1 AGCGCCGTACATCCACCATCTTGG-A-CG
*
8264 AGCGCCGTACATCCACCATCTTGGATGAG
1 AGCGCCGTACATCCACCATCTTGGA--CG
8293 AGCGCCGTACATCCA
1 AGCGCCGTACATCCA
8308 TATTGGAAAA
Statistics
Matches: 289, Mismatches: 21, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
26 9 0.03
27 225 0.78
28 2 0.01
29 53 0.18
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.21
Consensus pattern (27 bp):
AGCGCCGTACATCCACCATCTTGGACG
Found at i:8370 original size:27 final size:27
Alignment explanation
Indices: 8320--8387 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
8310 TTGGAAAAGG
*
8320 GCGCCGCATGCCCACCATAACAAGAAA
1 GCGCCGCACGCCCACCATAACAAGAAA
* ** **
8347 GCGCCGCGCGCCCACCATCGCAAGAGG
1 GCGCCGCACGCCCACCATAACAAGAAA
*
8374 GCGCCGTACGCCCA
1 GCGCCGCACGCCCA
8388 TTGTCAGGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.25, C:0.43, G:0.26, T:0.06
Consensus pattern (27 bp):
GCGCCGCACGCCCACCATAACAAGAAA
Found at i:8426 original size:27 final size:27
Alignment explanation
Indices: 8348--8427 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
8338 AACAAGAAAG
* *
8348 CGCCGCGCGCCCACCATCGCAAGAGGG
1 CGCCGCGCGCCCACCATCGGAAGAGGA
** ***
8375 CGCCGTACGCCCATTGTCAGG-AGAGGA
1 CGCCGCGCGCCCACCATC-GGAAGAGGA
8402 CGCCGCGCGCCCACCATCGGAAGAGG
1 CGCCGCGCGCCCACCATCGGAAGAGG
8428 GAGTGCGCCC
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
26 2 0.05
27 36 0.92
28 1 0.03
ACGTcount: A:0.20, C:0.39, G:0.34, T:0.07
Consensus pattern (27 bp):
CGCCGCGCGCCCACCATCGGAAGAGGA
Found at i:9462 original size:34 final size:35
Alignment explanation
Indices: 9383--9463 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 35
9373 TGATGGTGAC
9383 ACGTTCTGAAGGCTTTGTATCACTTGTTGACCATG
1 ACGTTCTGAAGGCTTTGTATCACTTGTTGACCATG
* * *
9418 A-GTTCCGAAGGTTTTAG-ATCACTTGTTG-CTGAT-
1 ACGTTCTGAAGGCTTT-GTATCACTTGTTGAC-CATG
9451 ACGTTCTGAAGGC
1 ACGTTCTGAAGGC
9464 ACGTTCTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
33 2 0.05
34 34 0.89
35 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (35 bp):
ACGTTCTGAAGGCTTTGTATCACTTGTTGACCATG
Found at i:9469 original size:13 final size:13
Alignment explanation
Indices: 9451--9476 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9441 TGTTGCTGAT
9451 ACGTTCTGAAGGC
1 ACGTTCTGAAGGC
9464 ACGTTCTGAAGGC
1 ACGTTCTGAAGGC
9477 TTTGTATCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (13 bp):
ACGTTCTGAAGGC
Found at i:21755 original size:25 final size:25
Alignment explanation
Indices: 21721--21770 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
21711 ATTGCTGTCT
21721 AAATTACTAAGCTAAGGTTTGAAAA
1 AAATTACTAAGCTAAGGTTTGAAAA
21746 AAATTACTAAGCTAAGGTTTGAAAA
1 AAATTACTAAGCTAAGGTTTGAAAA
21771 CTCACAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (25 bp):
AAATTACTAAGCTAAGGTTTGAAAA
Found at i:25303 original size:107 final size:107
Alignment explanation
Indices: 25100--25366 Score: 396
Period size: 107 Copynumber: 2.5 Consensus size: 107
25090 AAATTTTCTA
**
25100 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAA-TAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATTATATATTTTA
* *
25163 TTTCTAAAACCCTATAACAATATTATTATTAATTATGGAATTT
65 TTTCTAAAACCCTATAACAATATAATTATTAATTATGAAATTT
* * * *
25206 ACCCTTAAAATGAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAAT-AAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATTATATATTTTA
* *
25271 TTTCTAAAACCCTATAATAATA-AATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAATATAATTATTAATTATGAAATTT
25313 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAAT
1 ACCCTTAAAAT-AAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAAT
25367 GCTAAACTTA
Statistics
Matches: 145, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
106 23 0.16
107 86 0.59
108 36 0.25
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (107 bp):
ACCCTTAAAATAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATTATATATTTTAT
TTCTAAAACCCTATAACAATATAATTATTAATTATGAAATTT
Found at i:36047 original size:39 final size:39
Alignment explanation
Indices: 36003--36083 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
35993 ATGCCCGTTA
36003 ACACTTATTTATATATTATTATAAATGATTATATAATAC
1 ACACTTATTTATATATTATTATAAATGATTATATAATAC
*
36042 ACACTTATTTATATATTATTATGAATGATTATATAATAC
1 ACACTTATTTATATATTATTATAAATGATTATATAATAC
36081 ACA
1 ACA
36084 GTATAAAGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (39 bp):
ACACTTATTTATATATTATTATAAATGATTATATAATAC
Found at i:38161 original size:69 final size:69
Alignment explanation
Indices: 38050--38193 Score: 279
Period size: 69 Copynumber: 2.1 Consensus size: 69
38040 ATAACCTCTC
38050 TATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAGTTTTCCTAT
1 TATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAGTTTTCCTAT
38115 GAAA
66 GAAA
38119 TATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAGTTTTCCTAT
1 TATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAGTTTTCCTAT
38184 GAAA
66 GAAA
*
38188 TTTTAA
1 TATTAA
38194 TAATGATGGA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (69 bp):
TATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAGTTTTCCTAT
GAAA
Found at i:38542 original size:22 final size:23
Alignment explanation
Indices: 38461--38545 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
38451 GATAACCTCG
*
38461 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
*
38484 CTATAAAATTTTGATAAATCTCC
1 CTATAAAATTTTGATAAATCTTC
38507 CTATAAAATTTTGATAAAT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
38529 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
38546 CTAGAAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
22 16 0.29
23 40 0.71
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:38600 original size:22 final size:22
Alignment explanation
Indices: 38241--38734 Score: 211
Period size: 22 Copynumber: 22.6 Consensus size: 22
38231 TTAACATTCT
* *
38241 TATGAAATTTTGTTAACCTCTC
1 TATGAAATTTTGATAACCTCAC
* * * *
38263 TAAGGAATTTTGA-AGACATCAA
1 TATGAAATTTTGATA-ACCTCAC
* *
38285 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* **
38307 AATGAAATTTTGATAATCAACAC
1 TATGAAATTTTGATAA-CCTCAC
* *
38330 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
38351 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* *
38374 TATGAAA-ATTGAAAAACCTC-C
1 TATGAAATTTTG-ATAACCTCAC
* *
38395 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * * *
38418 TCTGAACTTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* *
38440 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
*
38462 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* * *
38485 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* ** *
38508 TATAAAATTTTGATAAATTTC-T
1 TATGAAATTTTGAT-AACCTCAC
*
38530 TATGAAATCTTGAT-A----AC
1 TATGAAATTTTGATAACCTCAC
* *
38547 TA-GAAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
38568 TAT-AATTTTTTGATAACCTCAT
1 TATGAA-ATTTTGATAACCTCAC
* * *
38590 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
38612 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
* *
38634 TATGAAATTTTTATAAACACTC-T
1 TATGAAATTTTGAT-AAC-CTCAC
* *
38657 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
*
38679 TATGAAATTTTGTTAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
38701 TATGAAATTTTGATATCCT-AC
1 TATGAAATTTTGATAACCTCAC
*
38722 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
38735 TACTGCATAA
Statistics
Matches: 358, Mismatches: 81, Indels: 68
0.71 0.16 0.13
Matches are distributed among these distances:
16 10 0.03
17 3 0.01
20 16 0.04
21 17 0.05
22 223 0.62
23 85 0.24
24 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:39157 original size:22 final size:22
Alignment explanation
Indices: 38840--39231 Score: 151
Period size: 22 Copynumber: 17.6 Consensus size: 22
38830 AATCACATTT
* **
38840 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCACTA
**
38862 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCACTA
** * * * * *
38884 CAAAATGTTGTTGACCACTCTA
1 TGAAATTTTGATAACCTCACTA
* * * * *
38906 TGAAATTCTGATAATCACATTG
1 TGAAATTTTGATAACCTCACTA
* * *
38928 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCACTA
* ** *
38950 TGAAATTTTGATATCAACATTA
1 TGAAATTTTGATAACCTCACTA
* *
38972 TGAAATTTTTATAATCTTCA-TA
1 TGAAATTTTGATAA-CCTCACTA
*
38994 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCACTA
* * * *
39018 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCACTA
* *
39040 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCACTA
*
39060 TCAAATTTTGAT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCAC-TA
*
39080 TGAAATTGAGACTTTTATAACCTTCA-TA
1 TGAAA-T-----TTTGATAACC-TCACTA
* *
39108 AGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCACTA
* * *
39130 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCACTA
* *
39152 TGAAA-TATAAGTAACCTC-CTAA
1 TGAAATTTTGA-TAACCTCACT-A
*
39174 TGAAATTTTGTTAACCAT-ACTA
1 TGAAATTTTGATAACC-TCACTA
*
39196 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCACTA
*
39218 TGACATTTTGATAA
1 TGAAATTTTGATAA
39232 TCTCTTTGAT
Statistics
Matches: 275, Mismatches: 68, Indels: 54
0.69 0.17 0.14
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 37 0.13
22 178 0.65
23 12 0.04
24 4 0.01
25 11 0.04
26 5 0.02
27 2 0.01
28 7 0.03
29 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCACTA
Found at i:39328 original size:24 final size:22
Alignment explanation
Indices: 39267--39423 Score: 92
Period size: 22 Copynumber: 7.3 Consensus size: 22
39257 TTGTAATAAT
* * *
39267 TAACCACCCCATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
39289 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
39311 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
* **
39335 TAATC-ACACTATGAAATTTTTG
1 TAACCAAC-CTATGAAATTTTAA
* *
39357 TAACC-A-CTATGGAATTTTGA
1 TAACCAACCTATGAAATTTTAA
* *
39377 TAA-C--CTTATGAAATTATAA
1 TAACCAACCTATGAAATTTTAA
* * *
39396 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
39418 TAACCA
1 TAACCA
39424 CACATAGACA
Statistics
Matches: 107, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
19 14 0.13
20 15 0.14
21 1 0.01
22 60 0.56
24 17 0.16
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:39349 original size:22 final size:20
Alignment explanation
Indices: 39321--39424 Score: 93
Period size: 22 Copynumber: 5.0 Consensus size: 20
39311 TAACCTGATC
39321 CTATGAAATTTTGGTAATCACA
1 CTATGAAATTTTGGTAA-C-CA
*
39343 CTATGAAATTTTTGTAACCA
1 CTATGAAATTTTGGTAACCA
* *
39363 CTATGGAATTTTGATAACC-
1 CTATGAAATTTTGGTAACCA
* * **
39382 TTATGAAATTATAATAACCA
1 CTATGAAATTTTGGTAACCA
*
39402 TCTTATGAAATTTTGATAACCA
1 -C-TATGAAATTTTGGTAACCA
39424 C
1 C
39425 ACATAGACAA
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
19 15 0.22
20 18 0.26
21 2 0.03
22 33 0.49
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (20 bp):
CTATGAAATTTTGGTAACCA
Found at i:39386 original size:19 final size:19
Alignment explanation
Indices: 39344--39422 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 19
39334 GTAATCACAC
*
39344 TATGAAATTTTTG-TAACCAC
1 TATGAAA-TTTTGATAACC-T
*
39364 TATGGAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
* *
39383 TATGAAATTATAATAACCATCT
1 TATGAAATTTTGATAA-C--CT
39405 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
39423 ACACATAGAC
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 19 0.40
20 12 0.25
21 1 0.02
22 16 0.33
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (19 bp):
TATGAAATTTTGATAACCT
Found at i:40445 original size:19 final size:18
Alignment explanation
Indices: 40424--40458 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40414 TAAACAGACT
* *
40424 TTTTTTTGAAAGACAAGA
1 TTTTATTGAAAAACAAGA
40442 TTTTATTGAAAAACAAG
1 TTTTATTGAAAAACAAG
40459 GGGAACAAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (18 bp):
TTTTATTGAAAAACAAGA
Found at i:41574 original size:71 final size:71
Alignment explanation
Indices: 41329--41578 Score: 321
Period size: 71 Copynumber: 3.6 Consensus size: 71
41319 CTAAAGATGA
*
41329 TAATCAATCCATGCATGTTATT-TCTA--TC-TT-ATTAATCAATCAATCAATCAACGTATCATC
1 TAATCAATCCATGCATGTTATTAT-TATCTCATTAATCAATCAATCAATCAATCAACGTATCATC
*
41389 AACCATC
65 AACTATC
* * ** * * * *
41396 TAATCAATCCATGCATGTTAATATTATCTTATTAATTTATCAACCAATCAATAAACATATAATCA
1 TAATCAATCCATGCATGTTATTATTATCTCATTAATCAATCAATCAATCAATCAACGTATCATCA
41461 ACTATC
66 ACTATC
* ** * *
41467 TAATCTATCCATGCATGTTATTGCTGTCTTATTAATCAATCAATCAATCAATCAACGTATCATCA
1 TAATCAATCCATGCATGTTATTATTATCTCATTAATCAATCAATCAATCAATCAACGTATCATCA
41532 ACTATC
66 ACTATC
41538 TAATCAATCCATGCATGTTATTATTATCTCATTAATCAATC
1 TAATCAATCCATGCATGTTATTATTATCTCATTAATCAATC
41579 GATATAAATA
Statistics
Matches: 154, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
67 23 0.15
68 1 0.01
69 1 0.01
70 2 0.01
71 127 0.82
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (71 bp):
TAATCAATCCATGCATGTTATTATTATCTCATTAATCAATCAATCAATCAATCAACGTATCATCA
ACTATC
Found at i:41637 original size:96 final size:96
Alignment explanation
Indices: 41527--41706 Score: 333
Period size: 96 Copynumber: 1.9 Consensus size: 96
41517 ATCAACGTAT
*
41527 CATCAACTATCTAATCAATCCATGCATGTTATTATTATCTCATTAATCAATCGATATAAATATCT
1 CATCAACTATCTAATCAATCCATGCATATTATTATTATCTCATTAATCAATCGATATAAATATCT
41592 CATCAACTATCTTATTAATAAATAAACATAC
66 CATCAACTATCTTATTAATAAATAAACATAC
* *
41623 CATCAACTATCTAATCAATCCATGCATATTATTATTATCTTATTAATCAATCGATATAAATGTCT
1 CATCAACTATCTAATCAATCCATGCATATTATTATTATCTCATTAATCAATCGATATAAATATCT
41688 CATCAACTATCTTATTAAT
66 CATCAACTATCTTATTAAT
41707 CTATGCATGT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.38
Consensus pattern (96 bp):
CATCAACTATCTAATCAATCCATGCATATTATTATTATCTCATTAATCAATCGATATAAATATCT
CATCAACTATCTTATTAATAAATAAACATAC
Found at i:41667 original size:59 final size:63
Alignment explanation
Indices: 41599--41732 Score: 152
Period size: 65 Copynumber: 2.2 Consensus size: 63
41589 TCTCATCAAC
*
41599 TATCTTATTAAT-AA-ATA-AACAT-AC-CATCAACTATCTAATCAATCCATGCATATTATTAT
1 TATCTTATTAATCAACATATAA-ATGACTCATCAACTATCTAATCAATCCATGCATATTATTAG
* * * * *
41658 TATCTTATTAATCAATCGATATAAATGTCTCATCAACTATCTTATTAATCTATGCATGTTATTAG
1 TATCTTATTAATCAA-C-ATATAAATGACTCATCAACTATCTAATCAATCCATGCATATTATTAG
41723 TATCTTATTA
1 TATCTTATTA
41733 TTAATTAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
59 12 0.19
60 2 0.03
63 5 0.08
64 3 0.05
65 40 0.65
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.42
Consensus pattern (63 bp):
TATCTTATTAATCAACATATAAATGACTCATCAACTATCTAATCAATCCATGCATATTATTAG
Found at i:46960 original size:18 final size:19
Alignment explanation
Indices: 46934--46971 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
46924 GATTTATTTT
46934 ATCTATCTGTTGAATTTGA
1 ATCTATCTGTTGAATTTGA
*
46953 ATCT-TCTGTTGGATTTGA
1 ATCTATCTGTTGAATTTGA
46971 A
1 A
46972 ATTCTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (19 bp):
ATCTATCTGTTGAATTTGA
Found at i:48414 original size:1 final size:1
Alignment explanation
Indices: 48408--48435 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
48398 TATAAGAAGG
48408 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
48436 AATAAATGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:50640 original size:20 final size:22
Alignment explanation
Indices: 50609--50653 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
50599 TAATAATTAT
50609 AATAAGAATTATATTTTGA-AA
1 AATAAGAATTATATTTTGAGAA
50630 AATAA-AATTATATTTTGAGAA
1 AATAAGAATTATATTTTGAGAA
50651 AAT
1 AAT
50654 TTAAATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (22 bp):
AATAAGAATTATATTTTGAGAA
Found at i:51532 original size:22 final size:22
Alignment explanation
Indices: 51507--51551 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
51497 GTGGTGTTTC
* *
51507 TGTATTGCTTACTTAATTCTTA
1 TGTAATGCTTACTTAACTCTTA
51529 TGTAATGCTTACTTAACTCTTA
1 TGTAATGCTTACTTAACTCTTA
51551 T
1 T
51552 ATAACTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (22 bp):
TGTAATGCTTACTTAACTCTTA
Done.