Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007799.1 Corchorus capsularis cultivar CVL-1 contig07820, 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: 36294
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:2161 original size:15 final size:14
Alignment explanation
Indices: 2122--2166 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 14
2112 ATTTAGCACT
* *
2122 AAAACGAAAAATAA
1 AAAATGAAAAAGAA
2136 AAAAT-AAAAAGAA
1 AAAATGAAAAAGAA
2149 AATAATGAAAAAGAA
1 AA-AATGAAAAAGAA
2164 AAA
1 AAA
2167 GATAAGGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 9 0.33
14 8 0.30
15 10 0.37
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAATGAAAAAGAA
Found at i:6652 original size:25 final size:26
Alignment explanation
Indices: 6624--6674 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
6614 GGCATTAGTG
*
6624 TCACA-TAAGGGCATTTTGGTCATTT
1 TCACACTAAGGGCATTCTGGTCATTT
6649 TCACACTAAGGGCATTCTGGTCATTT
1 TCACACTAAGGGCATTCTGGTCATTT
6675 GCTAATTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (26 bp):
TCACACTAAGGGCATTCTGGTCATTT
Found at i:6861 original size:15 final size:14
Alignment explanation
Indices: 6826--6863 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
6816 AATTAGTAGA
6826 TTAG-CATTAGCAC
1 TTAGTCATTAGCAC
6839 TTAGGTCATTAGCAC
1 TTA-GTCATTAGCAC
6854 TTTAGTCATT
1 -TTAGTCATT
6864 CTATCTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.14
14 1 0.05
15 15 0.68
16 3 0.14
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (14 bp):
TTAGTCATTAGCAC
Found at i:9987 original size:48 final size:48
Alignment explanation
Indices: 9916--10442 Score: 709
Period size: 48 Copynumber: 11.0 Consensus size: 48
9906 GGGTCAGCAA
* *
9916 TGTCTATTTCCAATCTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
*
9964 TGTCTATTTCCAGTTTTACCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * *
10012 TGTCTATTTCCTGTTTCGCCCTTCCCGGTCGGAAGCTGCTGTTTTCAA
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* *
10060 TGTCTATTTCCAGTTTTGCCATTCCCGGTCGGAAGGTGCTATTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * *
10108 TGTTTGTTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAA
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * *
10156 TGTCTATTTCCTA-TTTCGCCCTTCCAGGTCGGAAGGTGCTGTCTTCAG
1 TGTCTATTTCC-AGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* *
10204 TGTCTATTTCCAGTTTTGCCATTCCCGGTCGGAAGGTGCTATTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
** *
10252 TGTCTCCTT-CAGTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* *
10299 TGTCTATTT-TAGTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * * * * * *
10346 TGTTTATTTCCTGTTTCGCGCTTCCCGGTCGGAAGGTACTATTTCCAT
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * ** *
10394 TGTCTATTTCAAATTTTGCCCTAGCTGGTCGGAAGGTGCTGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
10442 T
1 T
10443 CTCTTTCGGA
Statistics
Matches: 419, Mismatches: 57, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
47 90 0.21
48 328 0.78
49 1 0.00
ACGTcount: A:0.13, C:0.24, G:0.23, T:0.40
Consensus pattern (48 bp):
TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
Found at i:10451 original size:26 final size:26
Alignment explanation
Indices: 10422--10474 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
10412 CCCTAGCTGG
10422 TCGGAAGGTGCTGTTTTCAGTCTCTT
1 TCGGAAGGTGCTGTTTTCAGTCTCTT
*
10448 TCGGAAGGTGTTGTTTTCAGTCTCTT
1 TCGGAAGGTGCTGTTTTCAGTCTCTT
10474 T
1 T
10475 TCTGTTTCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.45
Consensus pattern (26 bp):
TCGGAAGGTGCTGTTTTCAGTCTCTT
Found at i:10544 original size:120 final size:122
Alignment explanation
Indices: 10326--10548 Score: 279
Period size: 120 Copynumber: 1.8 Consensus size: 122
10316 CCCTTCCCGG
* * *
10326 TCGGAAGGTGCTATTTTCAGTGTTTATTTCCTGTTTCGCGCTTCCCGGTCGGAAGGTACTATTTC
1 TCGGAAGGTGCTATTTTCAGTCTCTATTTCCTGTTTCGCCCTTCCCGGTCGGAAGGTACTATTTC
* * * * *
10391 CATTGTCTATTTCAAATTTTGCCCTAGCTGGTCGGAAGGTGCTGTTTTCAGTCTCTT
66 CAATGTCTACTTCAAATGTTGCCCTACCCGGTCGGAAGGTGCTGTTTTCAGTCTCTT
* * * * *
10448 TCGGAAGGTGTTGTTTTCAGTCTCT-TTT-CTGTTTCGCCCTTCCCGGTTGGAAGGTGCTATTTT
1 TCGGAAGGTGCTATTTTCAGTCTCTATTTCCTGTTTCGCCCTTCCCGGTCGGAAGGTACTATTTC
*** *
10511 CAATGTCTACTTCCTGTGTTGCCCTTCCCGGTCGGAAG
66 CAATGTCTACTTCAAATGTTGCCCTACCCGGTCGGAAG
10549 CTACAGTCTT
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
120 60 0.71
121 3 0.04
122 21 0.25
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.40
Consensus pattern (122 bp):
TCGGAAGGTGCTATTTTCAGTCTCTATTTCCTGTTTCGCCCTTCCCGGTCGGAAGGTACTATTTC
CAATGTCTACTTCAAATGTTGCCCTACCCGGTCGGAAGGTGCTGTTTTCAGTCTCTT
Found at i:10548 original size:48 final size:48
Alignment explanation
Indices: 10467--10650 Score: 237
Period size: 48 Copynumber: 3.8 Consensus size: 48
10457 GTTGTTTTCA
* * * * *
10467 GTCTCTTTTCTGTTTCGCCCTTCCCGGTTGGAAGGTGCTATTTTCAAT
1 GTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGT
* * *
10515 GTCTAC-TTCCTGTGTTGCCCTTCCCGGTCGGAAGCTAC-AGTCTTCAGT
1 GTCT-CTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTA-TCTTCAGT
* *
10563 GTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGTTGCAATCTTCAGT
1 GTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGT
*
10611 GTCTCTTTCCTGTTTTGCCCTTCCCGGTCGAAAGGTGCTA
1 GTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTA
10651 GATTTGTCTT
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
47 2 0.02
48 114 0.97
49 2 0.02
ACGTcount: A:0.11, C:0.29, G:0.22, T:0.39
Consensus pattern (48 bp):
GTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGT
Found at i:10594 original size:168 final size:169
Alignment explanation
Indices: 10279--10596 Score: 403
Period size: 168 Copynumber: 1.9 Consensus size: 169
10269 CCCTTCCCGG
* *
10279 TCGGAAGGTGCTATTTTCAGTGTCTATTTTAGTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTC
1 TCGGAAGGTGCTATTTTCAGTCTCTATTTTAGTTTCGCCCTTCCCGGTCGGAAGGTGCTATTTTC
* * * * * *
10344 AGTGTTTATTTCCTGTTTCGCGCTTCCCGGTCGGAAGGTACTATTTCCATTGTCTATTTCAAATT
66 AATGTCTACTTCCTGTTTCGCCCTTCCCGGTCGGAAGCTACTATTTCCAGTGTCTATTTCAAATT
* *
10409 TTGCCCTAGCTGGTCGGAAGGTGCTGTTTTCAGTCTCTT
131 TTGCCCTACCCGGTCGGAAGGTGCTGTTTTCAGTCTCTT
* * *
10448 TCGGAAGGTGTTGTTTTCAGTCTCT-TTTCT-GTTTCGCCCTTCCCGGTTGGAAGGTGCTATTTT
1 TCGGAAGGTGCTATTTTCAGTCTCTATTT-TAGTTTCGCCCTTCCCGGTCGGAAGGTGCTATTTT
* *
10511 CAATGTCTACTTCCTGTGTT-GCCCTTCCCGGTCGGAAGCTAC-AGTCTT-CAGTGTCTCTTTCC
65 CAATGTCTACTTCCTGT-TTCGCCCTTCCCGGTCGGAAGCTACTA-T-TTCCAGTGTCTATTTCA
** *
10573 TGTTTTGCCCTTCCCGGTCGGAAG
127 AATTTTGCCCTACCCGGTCGGAAG
10597 TTGCAATCTT
Statistics
Matches: 127, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
167 1 0.01
168 99 0.78
169 27 0.21
ACGTcount: A:0.13, C:0.24, G:0.23, T:0.40
Consensus pattern (169 bp):
TCGGAAGGTGCTATTTTCAGTCTCTATTTTAGTTTCGCCCTTCCCGGTCGGAAGGTGCTATTTTC
AATGTCTACTTCCTGTTTCGCCCTTCCCGGTCGGAAGCTACTATTTCCAGTGTCTATTTCAAATT
TTGCCCTACCCGGTCGGAAGGTGCTGTTTTCAGTCTCTT
Found at i:10629 original size:216 final size:216
Alignment explanation
Indices: 10232--10649 Score: 511
Period size: 216 Copynumber: 1.9 Consensus size: 216
10222 CCATTCCCGG
* *
10232 TCGGAAGGTGCTATTTTCAGTGTCTCCTTCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTC
1 TCGGAAGGTGCTATTTTCAGTCTCTCCTTCAGTTTCGCCCTTCCCGGTCGGAAGGTGCTATTTTC
* * * * * * *
10297 AGTGTCTATTTTAGTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTTTATTTCCTGTTT
66 AATGTCTATTCTAGTGTTGCCCTTCCCGGTCGGAAGCTACTATCTTCAGTGTCTATTTCCTGTTT
* * * * * *
10362 CGCGCTTCCCGGTCGGAAGGTACTATTTCCATTGTCTATTTCAAATTTTGCCCTAGCTGGTCGGA
131 CGCCCTTCCCGGTCGGAAGGTACAATTTCCAGTGTCTATTTCAAATTTTGCCCTACCCGGTCGAA
10427 AGGTGCTGTTTTCAGTCTCTT
196 AGGTGCTGTTTTCAGTCTCTT
* * * * *
10448 TCGGAAGGTGTTGTTTTCAGTCTCT-TTTCTGTTTCGCCCTTCCCGGTTGGAAGGTGCTATTTTC
1 TCGGAAGGTGCTATTTTCAGTCTCTCCTTCAGTTTCGCCCTTCCCGGTCGGAAGGTGCTATTTTC
*
10512 AATGTCTACTTCCT-GTGTTGCCCTTCCCGGTCGGAAGCTAC-AGTCTTCAGTGTCTCTTTCCTG
66 AATGTCTA-TT-CTAGTGTTGCCCTTCCCGGTCGGAAGCTACTA-TCTTCAGTGTCTATTTCCTG
* * * * *** *
10575 TTTTGCCCTTCCCGGTCGGAAGTTGCAATCTT-CAGTGTCTCTTTCCTGTTTTGCCCTTCCCGGT
128 TTTCGCCCTTCCCGGTCGGAAGGTACAAT-TTCCAGTGTCTATTTCAAATTTTGCCCTACCCGGT
10639 CGAAAGGTGCT
192 CGAAAGGTGCT
10650 AGATTTGTCT
Statistics
Matches: 169, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
215 43 0.25
216 123 0.73
217 3 0.02
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (216 bp):
TCGGAAGGTGCTATTTTCAGTCTCTCCTTCAGTTTCGCCCTTCCCGGTCGGAAGGTGCTATTTTC
AATGTCTATTCTAGTGTTGCCCTTCCCGGTCGGAAGCTACTATCTTCAGTGTCTATTTCCTGTTT
CGCCCTTCCCGGTCGGAAGGTACAATTTCCAGTGTCTATTTCAAATTTTGCCCTACCCGGTCGAA
AGGTGCTGTTTTCAGTCTCTT
Found at i:13284 original size:14 final size:14
Alignment explanation
Indices: 13251--13300 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
13241 CAAAAAACGT
*
13251 TTTTCAAGAAAATTG
1 TTTTCAAGAAAA-AG
13266 TTTTCAAGAAAAAG
1 TTTTCAAGAAAAAG
*
13280 TTTTCAA-AAATGAG
1 TTTTCAAGAAA-AAG
13294 TTTTCAA
1 TTTTCAA
13301 AAGGTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 3 0.09
14 17 0.53
15 12 0.38
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (14 bp):
TTTTCAAGAAAAAG
Found at i:13301 original size:14 final size:13
Alignment explanation
Indices: 13241--13302 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 13
13231 ACCATCAAAA
*
13241 CAAAAAACGTTTTT
1 CAAAAAAAG-TTTT
*
13255 CAAGAAAATTGTTTT
1 CAA-AAAA-AGTTTT
13270 CAAGAAAAAGTTTT
1 CAA-AAAAAGTTTT
*
13284 CAAAAATGAGTTTT
1 CAAAAA-AAGTTTT
13298 CAAAA
1 CAAAA
13303 GGTTTTTAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.07
14 22 0.52
15 16 0.38
16 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (13 bp):
CAAAAAAAGTTTT
Found at i:13985 original size:11 final size:11
Alignment explanation
Indices: 13969--14009 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
13959 TCAACACAAA
13969 AAAAAAAGAAG
1 AAAAAAAGAAG
13980 AAAAAAAG-AG
1 AAAAAAAGAAG
13990 AAAGAAAAGAAGG
1 AAA-AAAAGAA-G
14003 AAAAAAA
1 AAAAAAA
14010 ACTTGGCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.19
11 13 0.48
12 5 0.19
13 4 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:14271 original size:17 final size:18
Alignment explanation
Indices: 14249--14291 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
14239 AGAAAGAAGT
*
14249 AAGAAGGAAAAGTGA-AA
1 AAGAAGGAAAAGGGAGAA
14266 AAGAA-GAAAAGGGAGAA
1 AAGAAGGAAAAGGGAGAA
*
14283 AAGATGGAA
1 AAGAAGGAA
14292 TAAAGAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
17 11 0.50
18 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.05
Consensus pattern (18 bp):
AAGAAGGAAAAGGGAGAA
Found at i:15853 original size:35 final size:35
Alignment explanation
Indices: 15739--16198 Score: 595
Period size: 35 Copynumber: 13.0 Consensus size: 35
15729 GTTTAGTAAA
*
15739 TCAGATGACTCGGTGTAGCATCTTCAAAAATTGGAT
1 TCAGATGACTCGGTGTAGCATCTTC-AAAGTTGGAT
*
15775 TCAGATGACTCGGTGTAGCATCTTTCAAAGTTGGTT
1 TCAGATGACTCGGTGTAGCATC-TTCAAAGTTGGAT
15811 TCAGATGACTCGGTGTAGCATCTTCAAAAG-TGGAT
1 TCAGATGACTCGGTGTAGCATCTTC-AAAGTTGGAT
* *
15846 TCGGATGACTCGGTGCAGCATCTTCAAAGTTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
15881 TCAGATGACTCGGTGTAGCATCTTCGAAA-TTGGAT
1 TCAGATGACTCGGTGTAGCATCTTC-AAAGTTGGAT
** * *
15916 TC-GAAAAACTCGGTGCAGCATCTTAAAAGTTGGAT
1 TCAG-ATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* *
15951 TCAGATCACTCGATGTAGCATCTTTCAAAGTTGG-T
1 TCAGATGACTCGGTGTAGCATC-TTCAAAGTTGGAT
* * *
15986 TCCAGGTGACTCGGTGTAGCAACTTTCAAAGTTGGTT
1 T-CAGATGACTCGGTGTAGCATC-TTCAAAGTTGGAT
*
16023 TCAGATGACTCGGTGTAGCATCTTCAAAATTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* *
16058 TCAGATGACTCGGTGCAGCATCTTCAAAGTTGGGT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
*
16093 TCAGATGACTCGGTGTAGCGTCTTCAAAGTTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* * * *
16128 TTAGATGACGCGGTGCAGCATCTTCAAAATTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* * * *
16163 TTAGATGACTCGATGAAGCATTTTCAAAGTTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
16198 T
1 T
16199 AGGTAAATCA
Statistics
Matches: 374, Mismatches: 40, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
34 8 0.02
35 243 0.65
36 118 0.32
37 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
Found at i:16128 original size:212 final size:212
Alignment explanation
Indices: 15739--16198 Score: 698
Period size: 212 Copynumber: 2.2 Consensus size: 212
15729 GTTTAGTAAA
* * *
15739 TCAGATGACTCGGTGTAGCATC-TTCAAAAATTGGATTCAGATGACTCGGTGTAGCATCTTTCAA
1 TCAGATGACTCGATGTAGCATCTTTC-AAAGTTGGATTCAGATGACTCGGTGTAGCAACTTTCAA
*
15803 AGTTGGTTTCAGATGACTCGGTGTAGCATCTTCAAAAGTGGATTCGGATGACTCGGTGCAGCATC
65 AGTTGGTTTCAGATGACTCGGTGTAGCATCTTCAAAAGTGGATTCAGATGACTCGGTGCAGCATC
*
15868 TTCAAAGTTGGATTCAGATGACTCGGTGTAGCATCTTCGAAATTGGATTCGA-AAAACTCGGTGC
130 TTCAAAGTTGGATTCAGATGACTCGGTGTAGCATCTTCGAAATTGGATT-GAGAAAACGCGGTGC
15932 AGCATCTT-AAAAGTTGGAT
194 AGCATCTTCAAAA-TTGGAT
* *
15951 TCAGATCACTCGATGTAGCATCTTTCAAAGTTGG-TTCCAGGTGACTCGGTGTAGCAACTTTCAA
1 TCAGATGACTCGATGTAGCATCTTTCAAAGTTGGATT-CAGATGACTCGGTGTAGCAACTTTCAA
*
16015 AGTTGGTTTCAGATGACTCGGTGTAGCATCTTCAAAATTGGATTCAGATGACTCGGTGCAGCATC
65 AGTTGGTTTCAGATGACTCGGTGTAGCATCTTCAAAAGTGGATTCAGATGACTCGGTGCAGCATC
* * * **
16080 TTCAAAGTTGGGTTCAGATGACTCGGTGTAGCGTCTTC-AAAGTTGGATTTAGATGACGCGGTGC
130 TTCAAAGTTGGATTCAGATGACTCGGTGTAGCATCTTCGAAA-TTGGATTGAGAAAACGCGGTGC
16144 AGCATCTTCAAAATTGGAT
194 AGCATCTTCAAAATTGGAT
* *
16163 TTAGATGACTCGATGAAGCAT-TTTCAAAGTTGGATT
1 TCAGATGACTCGATGTAGCATCTTTCAAAGTTGGATT
16199 AGGTAAATCA
Statistics
Matches: 226, Mismatches: 16, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
211 18 0.08
212 201 0.89
213 7 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (212 bp):
TCAGATGACTCGATGTAGCATCTTTCAAAGTTGGATTCAGATGACTCGGTGTAGCAACTTTCAAA
GTTGGTTTCAGATGACTCGGTGTAGCATCTTCAAAAGTGGATTCAGATGACTCGGTGCAGCATCT
TCAAAGTTGGATTCAGATGACTCGGTGTAGCATCTTCGAAATTGGATTGAGAAAACGCGGTGCAG
CATCTTCAAAATTGGAT
Found at i:16380 original size:89 final size:88
Alignment explanation
Indices: 16229--16892 Score: 759
Period size: 89 Copynumber: 7.4 Consensus size: 88
16219 TACAGTATCT
* * *
16229 TCATGGTGATTCGGTGAATTAGGTTAATGCGGTGCATTTCCTTAAAGATTGGAATTCTGTGAGCT
1 TCATGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTT-CTTAAAGATTGGAATTCGGTGAGCT
* *
16294 CGGTGCAACACGTTTTCAAATAGA
65 CGGTGCAGCACATTTTCAAATAGA
* *
16318 TCATGGTGATTCGGTGAATCAGGTTAATGCGGTGCATTTCCTTAAAGATTGGAATTCAGTGAGCT
1 TCATGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTT-CTTAAAGATTGGAATTCGGTGAGCT
16383 CGGTGCAGCACATTTTCAAATAGA
65 CGGTGCAGCACATTTTCAAATAGA
* * *
16407 TTATGGTGATTCGATGAATCAAGTTAATGCGGTGCATTTCTTCAAAGGTTGGAATTCGGTGAGCT
1 TCATGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTTCTT-AAAGATTGGAATTCGGTGAGCT
*
16472 CGGTGCAGTACATTTTCAAATAGA
65 CGGTGCAGCACATTTTCAAATAGA
* *
16496 TCATGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTTCTTCAAAGGTTTGAATTCGGTGAGCT
1 TCATGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTTCTT-AAAGATTGGAATTCGGTGAGCT
* *
16561 TGGTGCAGTACATTTTCAAATAGA
65 CGGTGCAGCACATTTTCAAATAGA
16585 TCATGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGATTGG-ATTCGGTGA
1 TCATGGTGATTCGGTGAATCAAGTTAATGCGGTGC---ATTTCTT-AAAGATTGGAATTCGGTGA
* *
16649 GCTCGGTGCAGCACA-TTTCAAAACAGT
62 GCTCGGTGCAGCACATTTTC-AAATAGA
* * * * * * *
16676 TCA-GGACGTTTCAGTGAGTCAAGTTGAGGCGGTGCCTTATTTCTTCAA-ATTCGG-ATTCGGTG
1 TCATGG-TGATTCGGTGAATCAAGTTAATGCGGTG-C--ATTTCTTAAAGATT-GGAATTCGGTG
* * * *
16738 AGCTCGGTGCAGCAGATTTTCAGACAGT
61 AGCTCGGTGCAGCACATTTTCAAATAGA
* * * *
16766 TCA-GGATAATTCGGTGAATCAAGATTGAGGCGGTGCCTTATTTCTTCAAGATTGG-ATTCGGTG
1 TCATGG-TGATTCGGTGAATCAAG-TTAATGCGGTG-C--ATTTCTTAAAGATTGGAATTCGGTG
* *
16829 CGCTCGGTGCAGCACATTTTCAAATAGT
61 AGCTCGGTGCAGCACATTTTCAAATAGA
* * *
16857 TTA-GGATGATTCGGTGGATCAAGTTACTGCGGTGCA
1 TCATGG-TGATTCGGTGAATCAAGTTAATGCGGTGCA
16893 GTATGTCTTC
Statistics
Matches: 520, Mismatches: 44, Indels: 24
0.88 0.07 0.04
Matches are distributed among these distances:
87 1 0.00
88 3 0.01
89 288 0.55
90 65 0.12
91 144 0.28
92 19 0.04
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (88 bp):
TCATGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTTCTTAAAGATTGGAATTCGGTGAGCTC
GGTGCAGCACATTTTCAAATAGA
Found at i:19318 original size:22 final size:20
Alignment explanation
Indices: 19289--19353 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 20
19279 AAAATAAATC
19289 TTTGTAAAAAGTTAGGTCCT
1 TTTGTAAAAAGTTAGGTCCT
* *
19309 TTTGGCTAAAAAAGTAAGCTTTCC-
1 TTT-G-T-AAAAAGTTAG--GTCCT
19333 TTTGTAAAAAGTTAGGTCCT
1 TTTGTAAAAAGTTAGGTCCT
19353 T
1 T
19354 AACCTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
19 3 0.09
20 4 0.11
21 10 0.29
22 2 0.06
23 10 0.29
24 3 0.09
25 3 0.09
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTGTAAAAAGTTAGGTCCT
Found at i:20485 original size:48 final size:48
Alignment explanation
Indices: 20412--21169 Score: 892
Period size: 48 Copynumber: 15.8 Consensus size: 48
20402 GGGTCAGCAA
*** *
20412 TGTCTATTTCCAACCTTGCCATTCCCGGTCGGAAGGTGCTGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * *
20460 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGCGCTGTTTTTAA
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * *
20508 TGTCTATTTCCTGTTTCGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAA
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* *
20556 TGTCTACTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * *
20604 TGTTTGTTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAA
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * *
20652 TGTCTATTTCCTA-ATTCGCCCTTCCAGGTCGGAAGGTGCTGTCTTCAG
1 TGTCTATTTCC-AGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
** *
20700 TGTCTATTTCCAGTTTTGCCCTTCCTAGTCGGAAGGTGATGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * *
20748 TGTCTATTT-CAGTTTAGCCCTTCTCGGTCGGAAGGTGCTATTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* *
20795 TGTCTATTT-TAGGTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * * * * * *
20842 CGTTTATTACCTGTTTCGCCCTTCCCGATCGGAAGGTACTGTTTTCAT
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * *
20890 TGTCTATTTCCAATTTTGCCCTTCCTGGTCGGAAGGTGGTGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* *
20938 TGTCTATTTCCAATTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * * * * * *
20986 TGTCTCTTTTCTGCTTCGCCCTTCCCGGTTGGAAGGTGCTATTTTCAA
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * * * *
21034 TGTCTACTTCCTGTGTTGCCCTTCCCGGTCGGAAGCTGCAGTCTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
** ** * ** *
21082 TGTCCCTTTCCTTTTTTGCCCTTCCCGGTCGGAAGCTGCAATCTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * *
21130 TGTCTCTTTTCTGTTTTGACCTTCCCGGTCGGAAGGTGCT
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCT
21170 AAATTTGTCT
Statistics
Matches: 606, Mismatches: 101, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
47 81 0.13
48 524 0.86
49 1 0.00
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.39
Consensus pattern (48 bp):
TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
Found at i:24183 original size:33 final size:33
Alignment explanation
Indices: 24105--24209 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
24095 TTGTAAAGAG
* * * *
24105 TGTTTTAGATGTCGTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
* * *
24138 TGATTT-GAGTGTTGTTTGCAATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC
* *
24171 TGTTTTAGGTGTTCTTTGTGATGAAACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
24204 TGTTTT
1 TGTTTT
24210 GGATGCTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 1 0.02
33 57 0.97
34 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
Found at i:24223 original size:33 final size:32
Alignment explanation
Indices: 24158--24245 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 32
24148 GTTGTTTGCA
* * **
24158 ATGACACTAAATCTGTTTTAGGTGTTCTTTGTG
1 ATGAAACTAAATCTGTTTT-GGTGCTAATTGTG
24191 ATGAAACTAAATCTGTTTTGGATGCTAATTGTG
1 ATGAAACTAAATCTGTTTTGG-TGCTAATTGTG
24224 ATGAAAAC-AAATCTGTTTTGGT
1 ATG-AAACTAAATCTGTTTTGGT
24246 TGATCATAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
32 3 0.06
33 42 0.86
34 4 0.08
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (32 bp):
ATGAAACTAAATCTGTTTTGGTGCTAATTGTG
Found at i:24276 original size:33 final size:33
Alignment explanation
Indices: 24225--24343 Score: 166
Period size: 33 Copynumber: 3.6 Consensus size: 33
24215 CTAATTGTGA
* *
24225 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
* *
24258 TGCAAATAATTCTATTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
**
24291 TGAAAATAATTCTGTTTTGGTTGATCATAATAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
* *
24324 TGGAAATAATTTTGTTTTGG
1 TGAAAATAATTCTGTTTTGG
24344 GTGAAAAGAA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:27079 original size:12 final size:12
Alignment explanation
Indices: 27062--27090 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27052 AGTTTTTAAT
27062 TTTTATAAGAAC
1 TTTTATAAGAAC
27074 TTTTATAAGAAC
1 TTTTATAAGAAC
27086 TTTTA
1 TTTTA
27091 CAGCTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTTATAAGAAC
Found at i:29869 original size:21 final size:21
Alignment explanation
Indices: 29838--29933 Score: 67
Period size: 21 Copynumber: 4.5 Consensus size: 21
29828 CATTGCCTGG
29838 CTATGGCCCGGCCATCCGCGCA
1 CTAT-GCCCGGCCATCCGCGCA
* *
29860 CTATGCCCGGCTAGGACCG-GC-
1 CTATGCCCGGCCA--TCCGCGCA
**
29881 CTCAT-CCGCATCCATCCGCGCCA
1 CT-ATGCC-CGGCCATCCGCG-CA
29904 CTA--CCCGGCCATCCGCGCA
1 CTATGCCCGGCCATCCGCGCA
29923 CTATGCCCGGC
1 CTATGCCCGGC
29934 TAGGACCGGC
Statistics
Matches: 57, Mismatches: 8, Indels: 19
0.68 0.10 0.23
Matches are distributed among these distances:
19 5 0.09
20 13 0.23
21 21 0.37
22 13 0.23
23 5 0.09
ACGTcount: A:0.15, C:0.47, G:0.24, T:0.15
Consensus pattern (21 bp):
CTATGCCCGGCCATCCGCGCA
Found at i:29943 original size:63 final size:63
Alignment explanation
Indices: 29844--29977 Score: 268
Period size: 63 Copynumber: 2.1 Consensus size: 63
29834 CTGGCTATGG
29844 CCCGGCCATCCGCGCACTATGCCCGGCTAGGACCGGCCTCATCCGCATCCATCCGCGCCACTA
1 CCCGGCCATCCGCGCACTATGCCCGGCTAGGACCGGCCTCATCCGCATCCATCCGCGCCACTA
29907 CCCGGCCATCCGCGCACTATGCCCGGCTAGGACCGGCCTCATCCGCATCCATCCGCGCCACTA
1 CCCGGCCATCCGCGCACTATGCCCGGCTAGGACCGGCCTCATCCGCATCCATCCGCGCCACTA
29970 CCCGGCCA
1 CCCGGCCA
29978 GGATCGGCCA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13
Consensus pattern (63 bp):
CCCGGCCATCCGCGCACTATGCCCGGCTAGGACCGGCCTCATCCGCATCCATCCGCGCCACTA
Found at i:31650 original size:21 final size:22
Alignment explanation
Indices: 31607--31650 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
31597 AACAAATACT
*
31607 AAGTGAGAAAACAACAGTCAAG
1 AAGTGAGAAAACAACAATCAAG
* *
31629 AAGTGAG-AATCAACAATGAAG
1 AAGTGAGAAAACAACAATCAAG
31650 A
1 A
31651 GAAAGATAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.55, C:0.11, G:0.23, T:0.11
Consensus pattern (22 bp):
AAGTGAGAAAACAACAATCAAG
Found at i:32426 original size:13 final size:13
Alignment explanation
Indices: 32385--32430 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
32375 TCATGCACCC
*
32385 AAAACAATTTATT
1 AAAACAATTTAAT
* *
32398 AAAACCACTTATAT
1 AAAACAATTTA-AT
32412 AAAACAATTTAAT
1 AAAACAATTTAAT
32425 AAAACA
1 AAAACA
32431 GTAATAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:34441 original size:13 final size:14
Alignment explanation
Indices: 34423--34451 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34413 ATAATTGGAC
34423 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
34436 TTTGCATTCATGCA
1 TTTGCATTCATGCA
34450 TT
1 TT
34452 GAGTAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Done.