Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009406.1 Corchorus capsularis cultivar CVL-1 contig09427, 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: 134111
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6108 original size:27 final size:29
Alignment explanation
Indices: 6048--6110 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
6038 ACTTTAAGGA
* *
6048 GCAAAGTTGGATAAAAAAAAAAGATTGTGGG
1 GCAAAGTTGGAT--AAAAAAAAGATTATGAG
6079 GCAAAGTTGGAT-AAAAAAA-ATTATGAG
1 GCAAAGTTGGATAAAAAAAAGATTATGAG
6106 GCAAA
1 GCAAA
6111 ATGTCCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 11 0.37
28 7 0.23
31 12 0.40
ACGTcount: A:0.51, C:0.05, G:0.25, T:0.19
Consensus pattern (29 bp):
GCAAAGTTGGATAAAAAAAAGATTATGAG
Found at i:12893 original size:2 final size:2
Alignment explanation
Indices: 12855--12880 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12845 TCAAGATCCC
12855 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
12881 CCACCTTATA
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:13438 original size:29 final size:28
Alignment explanation
Indices: 13404--13458 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
13394 GCAAAACCTC
*
13404 CCAAAATTGAAGTTCAAGGGACAAAATAT
1 CCAAAATTGAAGCTCAAGGG-CAAAATAT
*
13433 CCAAAATTGAAGCTCATGGGCAAAAT
1 CCAAAATTGAAGCTCAAGGGCAAAAT
13459 TGTAGTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (28 bp):
CCAAAATTGAAGCTCAAGGGCAAAATAT
Found at i:17250 original size:48 final size:48
Alignment explanation
Indices: 17179--17277 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 48
17169 TATAACATTA
* * * *
17179 ATTCTTTGCTAAGATGGGGGAGGCTTCAAATTCCAAATCAGGAGATAT
1 ATTCTTTGCTAAAATGGGAGAGGCTTCAAATTCCAAATCAAGAAATAT
17227 ATTCTTTGCTAAAATGGGAGAGGCTTCAAATTCCAAATCAAGAAATAT
1 ATTCTTTGCTAAAATGGGAGAGGCTTCAAATTCCAAATCAAGAAATAT
17275 ATT
1 ATT
17278 ATTAAGCTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (48 bp):
ATTCTTTGCTAAAATGGGAGAGGCTTCAAATTCCAAATCAAGAAATAT
Found at i:21089 original size:21 final size:20
Alignment explanation
Indices: 21051--21090 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21041 TTTTATTTTT
*
21051 CTCTTCCTTCAACGTCTTCC
1 CTCTTCCTTCAACCTCTTCC
*
21071 CTCTTCTCTTCTACCTCTTC
1 CTCTTC-CTTCAACCTCTTC
21091 TCGACACCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.07, C:0.45, G:0.03, T:0.45
Consensus pattern (20 bp):
CTCTTCCTTCAACCTCTTCC
Found at i:22682 original size:19 final size:17
Alignment explanation
Indices: 22658--22700 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
22648 TATTGACTAT
22658 GAGAGAGTAAGTGGGAGG
1 GAGAGAGTAAGT-GGAGG
* *
22676 AGAGAGACTTAGTGGAGG
1 -GAGAGAGTAAGTGGAGG
22694 GAGAGAG
1 GAGAGAG
22701 AAAAGGGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 5 0.24
19 10 0.48
ACGTcount: A:0.35, C:0.02, G:0.51, T:0.12
Consensus pattern (17 bp):
GAGAGAGTAAGTGGAGG
Found at i:25145 original size:93 final size:93
Alignment explanation
Indices: 24986--25167 Score: 240
Period size: 93 Copynumber: 2.0 Consensus size: 93
24976 GATTTAAAGA
* *
24986 TATTTTGACAAGTTAATCAATTGAGGGTGAACATCTACGACCAAATAAGGGTGAACACCATGTAA
1 TATTTTCACAAGTTAATCAATTGAGGGTGAACATCTAAGACCAAATAAGGGTGAACACCATGTAA
25051 AATTACATACAAAATATTAAGAAATGGG
66 AATTACATACAAAATATTAAGAAATGGG
* * * ** * **
25079 TATTTTCACGAGTTAATTACTTGAGGGTGGGCATCTAAGACCATGA-AAGGGTGGGCACCATGTA
1 TATTTTCACAAGTTAATCAATTGAGGGTGAACATCTAAGACCA-AATAAGGGTGAACACCATGTA
* *
25143 AAATTACATAGAAAATGTTAAGAAA
65 AAATTACATACAAAATATTAAGAAA
25168 GTTGAACGTT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
93 75 0.99
94 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (93 bp):
TATTTTCACAAGTTAATCAATTGAGGGTGAACATCTAAGACCAAATAAGGGTGAACACCATGTAA
AATTACATACAAAATATTAAGAAATGGG
Found at i:30451 original size:25 final size:25
Alignment explanation
Indices: 30396--30451 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
30386 TAAAATAAAA
*
30396 AAATTATAAAATACTGAATTTTTTG
1 AAATGATAAAATACTGAATTTTTTG
* *
30421 AGATGATAAAATATTGAATTTATTT-
1 AAATGATAAAATACTGAATTT-TTTG
30446 AAATGA
1 AAATGA
30452 AAATAGTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (25 bp):
AAATGATAAAATACTGAATTTTTTG
Found at i:31532 original size:2 final size:2
Alignment explanation
Indices: 31525--31561 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
31515 TATTTTATTT
31525 TA TA TA TA T- TA TA T- TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31562 ATAATAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:31534 original size:16 final size:16
Alignment explanation
Indices: 31513--31561 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
31503 AGAAGAAACT
* *
31513 TATATTTTATTTTATA
1 TATATTATATTATATA
31529 TATATTATATTATATA
1 TATATTATATTATATA
31545 TATATATATATTATATA
1 TATAT-TATATTATATA
31562 ATAATAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 19 0.63
17 11 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTATATTATATA
Found at i:31537 original size:5 final size:5
Alignment explanation
Indices: 31512--31560 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
31502 AAGAAGAAAC
* *
31512 TTATA TTTTA TTTTA TATATA TTATA TTATA TATATA TATATA TTATA
1 TTATA TTATA TTATA T-TATA TTATA TTATA T-TATA T-TATA TTATA
31560 T
1 T
31561 AATAATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 25 0.62
6 15 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:32970 original size:27 final size:30
Alignment explanation
Indices: 32937--33000 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
32927 GTATGCAATT
32937 TTCTTTCCTTGTAAA-TATGAACCTTGATG
1 TTCTTTCCTTGTAAAGTATGAACCTTGATG
32966 TTTTCTTTCCTTGTAAATGTATGAACCTTGATG
1 --TTCTTTCCTTGTAAA-GTATGAACCTTGATG
32999 TT
1 TT
33001 TTTTTTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 17 0.55
33 14 0.45
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (30 bp):
TTCTTTCCTTGTAAAGTATGAACCTTGATG
Found at i:32973 original size:31 final size:32
Alignment explanation
Indices: 32935--33002 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
32925 AGGTATGCAA
32935 TTTTCTTTCCTTGTAAA-TATGAACCTTGATG
1 TTTTCTTTCCTTGTAAAGTATGAACCTTGATG
32966 TTTTCTTTCCTTGTAAATGTATGAACCTTGATG
1 TTTTCTTTCCTTGTAAA-GTATGAACCTTGATG
32999 TTTT
1 TTTT
33003 TTTTTTGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 17 0.49
33 18 0.51
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (32 bp):
TTTTCTTTCCTTGTAAAGTATGAACCTTGATG
Found at i:42145 original size:2 final size:2
Alignment explanation
Indices: 42093--42126 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42083 AACATTTACC
42093 AT AT AT AT 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 AT AT AT AT
42127 GCATTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50186 original size:18 final size:18
Alignment explanation
Indices: 50163--50220 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
50153 GATTCTGCCC
50163 TTTAAGAAAAGTCTCGAG
1 TTTAAGAAAAGTCTCGAG
* ** **
50181 TTTAAGTATTGT-TC-CC
1 TTTAAGAAAAGTCTCGAG
50197 TTTAAGAAAAGTCTCGAG
1 TTTAAGAAAAGTCTCGAG
50215 TTTAAG
1 TTTAAG
50221 TATTGTGAAT
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
16 9 0.32
17 4 0.14
18 15 0.54
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (18 bp):
TTTAAGAAAAGTCTCGAG
Found at i:50203 original size:34 final size:34
Alignment explanation
Indices: 50160--50226 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
50150 AGTGATTCTG
50160 CCCTTTAAGAAAAGTCTCGAGTTTAAGTATTGTT
1 CCCTTTAAGAAAAGTCTCGAGTTTAAGTATTGTT
50194 CCCTTTAAGAAAAGTCTCGAGTTTAAGTATTGT
1 CCCTTTAAGAAAAGTCTCGAGTTTAAGTATTGT
50227 GAATGAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (34 bp):
CCCTTTAAGAAAAGTCTCGAGTTTAAGTATTGTT
Found at i:55525 original size:40 final size:40
Alignment explanation
Indices: 55470--55548 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
55460 ACTTCCAAGC
55470 TCCATTGAAATCCCATTTACACACAGATTTAAGCTTTAAA
1 TCCATTGAAATCCCATTTACACACAGATTTAAGCTTTAAA
55510 TCCATTGAAATCCCATTTACACACAGATTTAAGCTTTAA
1 TCCATTGAAATCCCATTTACACACAGATTTAAGCTTTAA
55549 CACTAGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.33
Consensus pattern (40 bp):
TCCATTGAAATCCCATTTACACACAGATTTAAGCTTTAAA
Found at i:55935 original size:14 final size:14
Alignment explanation
Indices: 55918--55950 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
55908 TTTGGTTTTT
55918 TAAACAATTTTTAA
1 TAAACAATTTTTAA
55932 TAAACAATTTTTAA
1 TAAACAATTTTTAA
55946 TAAAC
1 TAAAC
55951 CTTAATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAACAATTTTTAA
Found at i:58043 original size:33 final size:33
Alignment explanation
Indices: 57991--58053 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
57981 GATCTTTTTT
**
57991 TTTTAGTCGGTTTGCCTAACTATACCTTGATGC
1 TTTTAGTCGGTTTAACTAACTATACCTTGATGC
* *
58024 TTTTAGTCTGTTTAACTAACTTTACCTTGA
1 TTTTAGTCGGTTTAACTAACTATACCTTGA
58054 CAGCTACTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (33 bp):
TTTTAGTCGGTTTAACTAACTATACCTTGATGC
Found at i:61246 original size:20 final size:20
Alignment explanation
Indices: 61201--61531 Score: 274
Period size: 20 Copynumber: 16.5 Consensus size: 20
61191 CATTGAGGGC
*
61201 CAATGTGAATTAAGGCAAGTT
1 CAATGTGAATT-AGGAAAGTT
*
61222 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
61242 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
61262 CAATGTGAATTAGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
61282 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
*
61302 CAATGTGAATT-GGAAAGCT
1 CAATGTGAATTAGGAAAGTT
* * *
61321 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
61341 CAATGTGAATT-GGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
61360 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGAAAGTT
* * * * *
61381 CAATGTCATTTGGGAAACTA
1 CAATGTGAATTAGGAAAGTT
* * *
61401 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
* *
61421 CAATGTGAATTGGGAATGTT
1 CAATGTGAATTAGGAAAGTT
* * *
61441 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
*
61461 CAATGTAAATT-GGAAATGTT
1 CAATGTGAATTAGGAAA-GTT
* * *
61481 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGAAAGTT
* *
61502 CAATGTCAATT-GGAAAATTT
1 CAATGTGAATTAGG-AAAGTT
*
61522 GAATGTGAAT
1 CAATGTGAAT
61532 ACGCCGCGTA
Statistics
Matches: 236, Mismatches: 67, Indels: 15
0.74 0.21 0.05
Matches are distributed among these distances:
19 37 0.16
20 159 0.67
21 36 0.15
22 4 0.02
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (20 bp):
CAATGTGAATTAGGAAAGTT
Found at i:61259 original size:40 final size:40
Alignment explanation
Indices: 61202--61532 Score: 506
Period size: 40 Copynumber: 8.2 Consensus size: 40
61192 ATTGAGGGCC
61202 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
*
61243 AATGTGAATAAGGCAAGTTCAATGTGAATTAGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
*
61283 AATGTGAATAAGGCAAGTTCAATGTGAATT-GGAAAGCTG
1 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
61322 AATGTGAATAAGGCAAGTTCAATGTGAATT-GGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
* * * *
61361 AATGTGAATCAAGGCAAGTTCAATGTCATTTGGGAAACTAG
1 AATGTGAAT-AAGGCAAGTTCAATGTGAATTGGGAAAGTTG
*
61402 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAATGTTG
1 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
*
61442 AATGTGAATAAGGCAAGTTCAATGTAAATT-GGAAATGTTG
1 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAA-GTTG
* * *
61482 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGAAAATTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTGAATTGGGAAAGTTG
61523 AATGTGAATA
1 AATGTGAATA
61533 CGCCGCGTAA
Statistics
Matches: 268, Mismatches: 17, Indels: 11
0.91 0.06 0.04
Matches are distributed among these distances:
39 59 0.22
40 149 0.56
41 56 0.21
42 4 0.01
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (40 bp):
AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
Found at i:61551 original size:159 final size:159
Alignment explanation
Indices: 61231--61531 Score: 467
Period size: 159 Copynumber: 1.9 Consensus size: 159
61221 TCAATGTGAA
* *
61231 TTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTGAATTAGGAAAGTTGAATGTGAATAAGG
1 TTGGGAAACTAGAATGTGAATAAGGCAAGTTCAATGTGAATTAGGAAAGTTGAATGTGAATAAGG
* *
61296 CAAGTTCAATGTGAATTGGAAAGCTGAATGTGAATAAGGCAAGTTCAATGTGAATTGGAAAGTTG
66 CAAGTTCAATGTAAATTGGAAAGCTGAATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAGTTG
* ***
61361 AATGTGAATCAAGGCAAGTTCAATGTCAT
131 AATGTGAATCAAGCCAAGTTCAACCCCAT
* *
61390 TTGGGAAACTAGAATGTGAATAAGGCAAGTTCAATGTGAATTGGGAATGTTGAATGTGAATAAGG
1 TTGGGAAACTAGAATGTGAATAAGGCAAGTTCAATGTGAATTAGGAAAGTTGAATGTGAATAAGG
* *
61455 CAAGTTCAATGTAAATTGGAAATGTTGAATGTGAATCAAGGCAAGTTCAATGTCAATTGGAAAAT
66 CAAGTTCAATGTAAATTGGAAA-GCTGAATGTGAAT-AAGGCAAGTTCAATGTCAATTGG-AAAG
61520 TTGAATGTGAAT
128 TTGAATGTGAAT
61532 ACGCCGCGTA
Statistics
Matches: 131, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
159 82 0.63
160 12 0.09
161 22 0.17
162 15 0.11
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (159 bp):
TTGGGAAACTAGAATGTGAATAAGGCAAGTTCAATGTGAATTAGGAAAGTTGAATGTGAATAAGG
CAAGTTCAATGTAAATTGGAAAGCTGAATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAGTTG
AATGTGAATCAAGCCAAGTTCAACCCCAT
Found at i:63103 original size:6 final size:6
Alignment explanation
Indices: 63092--63133 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
63082 GTTTGACATC
* * *
63092 GTTTTT GTTTTT GTTTTT G-TTTC GTTTTC GTTTTT TTTTTT G
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT G
63134 CGTTGTCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.79
Consensus pattern (6 bp):
GTTTTT
Found at i:63116 original size:23 final size:23
Alignment explanation
Indices: 63090--63133 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
63080 CCGTTTGACA
*
63090 TCGTTTTTGTTTTTGTTTTTGTT
1 TCGTTTTCGTTTTTGTTTTTGTT
*
63113 TCGTTTTCGTTTTTTTTTTTG
1 TCGTTTTCGTTTTTGTTTTTG
63134 CGTTGTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.00, C:0.07, G:0.16, T:0.77
Consensus pattern (23 bp):
TCGTTTTCGTTTTTGTTTTTGTT
Found at i:63380 original size:43 final size:43
Alignment explanation
Indices: 63333--63421 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
63323 ACTGATTTTG
*
63333 TTTCCAAAATTTTTGAAAACAGCAACAGCCTACCAAACATGTT
1 TTTCCAAAATTTTTGAAAACAACAACAGCCTACCAAACATGTT
*
63376 TTTCCAAAATTTTTGAAAACAACAACAGCCTATCAAACATGTT
1 TTTCCAAAATTTTTGAAAACAACAACAGCCTACCAAACATGTT
63419 TTT
1 TTT
63422 ACTATTTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (43 bp):
TTTCCAAAATTTTTGAAAACAACAACAGCCTACCAAACATGTT
Found at i:65436 original size:49 final size:49
Alignment explanation
Indices: 65341--65510 Score: 290
Period size: 49 Copynumber: 3.5 Consensus size: 49
65331 CAACACGCAA
* *
65341 AGACACGAAGATATACGAGAAGAC--AGCCTCCGCAGTGAGGCGAGGCC
1 AGACACAAAGATACACGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCC
65388 AGACACAAAGATACACGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCC
1 AGACACAAAGATACACGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCC
65437 AGACACAAAGATACACGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCC
1 AGACACAAAGATACACGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCC
* *
65486 AGACACGAAGGTACACGAGAAGACA
1 AGACACAAAGATACACGAGAAGACA
65511 CACACGAAGG
Statistics
Matches: 117, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
47 22 0.19
49 95 0.81
ACGTcount: A:0.38, C:0.25, G:0.29, T:0.08
Consensus pattern (49 bp):
AGACACAAAGATACACGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCC
Found at i:65519 original size:24 final size:24
Alignment explanation
Indices: 65488--65535 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
65478 GCGAGGCCAG
65488 ACACGAAGGTACACGAGAAGACAC
1 ACACGAAGGTACACGAGAAGACAC
65512 ACACGAAGGTACACGAGAAGACAC
1 ACACGAAGGTACACGAGAAGACAC
65536 GGTGGTGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.25, G:0.25, T:0.04
Consensus pattern (24 bp):
ACACGAAGGTACACGAGAAGACAC
Found at i:67496 original size:239 final size:240
Alignment explanation
Indices: 67076--67540 Score: 833
Period size: 239 Copynumber: 1.9 Consensus size: 240
67066 CTGAGAGTCA
*
67076 AAATCTGTTTCTCCCATCTTCCGCTACACACTCTCGTTGCTTTTGAATTTTTTTTCGACGCAACC
1 AAATCTGTTTCTCCCATCTTCCGCTACACACTCTCGTTGCTTTTGAATTTTTTTTCAACGCAACC
* *
67141 CTGAATAGGAAGGGAAAGAACATGAGTTAAAATCCAGAATGATGATTTACACTAAAATTTATAAG
66 CTGAATAGGAAGAGAAAGAACATGAGTTAAAATCCAGAATGATGATTTACACTAAAATATATAAG
67206 GCATCTCGGCAGATGACTTTTCAGGCATAAGGAGGATCTACTGTAATAAAATAAATTTACCTGTA
131 GCATCTCGGCAGATGACTTTTCAGGCATAAGGAGGATCTACTGTAATAAAATAAATTTACCTGTA
*
67271 TGATTTTCTCAATCCCTGTTGCGGTGAAATCCAGAATAGTAAAAT
196 TGATTTTATCAATCCCTGTTGCGGTGAAATCCAGAATAGTAAAAT
*
67316 AAATCTGTTTCTCCCATCTTCCGCTACACACTCTCGTTGCTTTTGAA-TTTTTTTCAACGTAACC
1 AAATCTGTTTCTCCCATCTTCCGCTACACACTCTCGTTGCTTTTGAATTTTTTTTCAACGCAACC
* * *
67380 CTGAATAGGAAGAGAAAGAACATGAGTTCAAATCCAGAATGTTGATTTTCACTAAAATATATAAG
66 CTGAATAGGAAGAGAAAGAACATGAGTTAAAATCCAGAATGATGATTTACACTAAAATATATAAG
* *
67445 GCATCTTGGTAGATGACTTTTCAGGCATAAGGAGGATCTACTGTAATAAAATAAATTTACCTGTA
131 GCATCTCGGCAGATGACTTTTCAGGCATAAGGAGGATCTACTGTAATAAAATAAATTTACCTGTA
67510 TGATTTTATCAATCCCTGTTGCGGTGAAATC
196 TGATTTTATCAATCCCTGTTGCGGTGAAATC
67541 AGTAAGCTGA
Statistics
Matches: 215, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
239 168 0.78
240 47 0.22
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (240 bp):
AAATCTGTTTCTCCCATCTTCCGCTACACACTCTCGTTGCTTTTGAATTTTTTTTCAACGCAACC
CTGAATAGGAAGAGAAAGAACATGAGTTAAAATCCAGAATGATGATTTACACTAAAATATATAAG
GCATCTCGGCAGATGACTTTTCAGGCATAAGGAGGATCTACTGTAATAAAATAAATTTACCTGTA
TGATTTTATCAATCCCTGTTGCGGTGAAATCCAGAATAGTAAAAT
Found at i:71788 original size:24 final size:23
Alignment explanation
Indices: 71738--71781 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
71728 CCTTATTTGA
71738 CCGAGACTAATCCGTCTTCTGAGT
1 CCGAGACTAATCCG-CTTCTGAGT
71762 CCGAGACTAATCC-CTTCTGA
1 CCGAGACTAATCCGCTTCTGA
71782 CATTCCGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (23 bp):
CCGAGACTAATCCGCTTCTGAGT
Found at i:71864 original size:79 final size:78
Alignment explanation
Indices: 71730--71888 Score: 246
Period size: 79 Copynumber: 2.0 Consensus size: 78
71720 CATATATACC
* * * *
71730 TTATTTGACCGAGACTAATCCGTCTTCTGAGTCCGAGACTAATCCCTTCTGACATTCCGGATTGA
1 TTATTTGACCGAGACTAATCCGCCTTATGAGTCCGAGAATAATCCCTTCTAACATTCCGGATTGA
71795 AAGATTTTACGAG
66 AAGATTTTACGAG
* *
71808 TTATTTGTCCGAGACTAATCCCGCCTTATGAGTTCGAGAATAATCCCTTCTAACATTCCGGATTG
1 TTATTTGACCGAGACTAAT-CCGCCTTATGAGTCCGAGAATAATCCCTTCTAACATTCCGGATTG
*
71873 AAAGGTTTTACGAG
65 AAAGATTTTACGAG
71887 TT
1 TT
71889 TGAGACTCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 18 0.25
79 55 0.75
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (78 bp):
TTATTTGACCGAGACTAATCCGCCTTATGAGTCCGAGAATAATCCCTTCTAACATTCCGGATTGA
AAGATTTTACGAG
Found at i:75013 original size:230 final size:229
Alignment explanation
Indices: 74601--75034 Score: 816
Period size: 230 Copynumber: 1.9 Consensus size: 229
74591 AGATCTACTA
74601 AAGGAATTTTTGCTCGTTAAGCTTAGCTTCTAAACTCAAATTTCACTTGCTAAATAAAGCAATAT
1 AAGGAATTTTTGCTCGTTAAGCTTAGCTTCTAAACTCAAATTTCACTTGCTAAATAAAGCAATAT
74666 AATTTGTCGGTTTAAGGAGACACATGGAGGGCAGGGAACAAGAAGGTTAAACATAGGGTAATGAA
66 AATTTGTCGGTTTAAGGAGACACATGGAGGGCAGGGAACAAGAAGGTTAAACATAGGGTAATGAA
* *
74731 AATAAAGAAAGAAACATAAACGAGGATAAGGCAATAAAAACCAGTTTGACACGTAATGAATGCTA
131 AATAAAGAAAGAAACATAAACGAAGATAAGGCAATAAAAACCAGTCTGACACGTAATGAATGCTA
74796 AAACTGCATTGGTTCAGATCTACTAATGACACGT
196 AAACTGCATTGGTTCAGATCTACTAATGACACGT
74830 AAGGAA-TTTTGCTCGTTAAGCTTAGCTTCTAAACTCAAATTTCACTTGCTAAATAAAGCAATAT
1 AAGGAATTTTTGCTCGTTAAGCTTAGCTTCTAAACTCAAATTTCACTTGCTAAATAAAGCAATAT
*
74894 AATTTATGTCGGTTTAAGGAGACACGTGGAGGGCAGGGAACAAGAAGGTTAAACATAGGGTAATG
66 AA-TT-TGTCGGTTTAAGGAGACACATGGAGGGCAGGGAACAAGAAGGTTAAACATAGGGTAATG
74959 AAAATAAAGAAAGAAACATAAACGAAGATAAGGCAATAAAAACCAGTCTGACACGTAATGAATGC
129 AAAATAAAGAAAGAAACATAAACGAAGATAAGGCAATAAAAACCAGTCTGACACGTAATGAATGC
75024 TAAAACTGCAT
194 TAAAACTGCAT
75035 ATAAACAAAT
Statistics
Matches: 200, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
228 60 0.30
229 8 0.04
230 132 0.66
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (229 bp):
AAGGAATTTTTGCTCGTTAAGCTTAGCTTCTAAACTCAAATTTCACTTGCTAAATAAAGCAATAT
AATTTGTCGGTTTAAGGAGACACATGGAGGGCAGGGAACAAGAAGGTTAAACATAGGGTAATGAA
AATAAAGAAAGAAACATAAACGAAGATAAGGCAATAAAAACCAGTCTGACACGTAATGAATGCTA
AAACTGCATTGGTTCAGATCTACTAATGACACGT
Found at i:84255 original size:8 final size:8
Alignment explanation
Indices: 84238--84266 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
84228 GAATTGCTGG
84238 TTTTTT-T
1 TTTTTTGT
84245 TTTTTTGT
1 TTTTTTGT
84253 TTTTTTGT
1 TTTTTTGT
84261 TTTTTT
1 TTTTTT
84267 AATGAACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (8 bp):
TTTTTTGT
Found at i:102622 original size:28 final size:28
Alignment explanation
Indices: 102591--102664 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
102581 GTTGTAGCGT
*
102591 TTGGATGTTTTGCCCCTGAACTTCAATC
1 TTGGACGTTTTGCCCCTGAACTTCAATC
* ** * *
102619 TTGGACATTTTGTCCATTGAATTTCAATT
1 TTGGACGTTTTG-CCCCTGAACTTCAATC
102648 TTGAGACGTTTTGCCCC
1 TTG-GACGTTTTGCCCC
102665 CTCAACCTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
28 10 0.29
29 17 0.49
30 8 0.23
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.42
Consensus pattern (28 bp):
TTGGACGTTTTGCCCCTGAACTTCAATC
Found at i:103921 original size:19 final size:19
Alignment explanation
Indices: 103897--103935 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
103887 GGATTCGGGC
103897 TTGTCTGATGGTTAACTGT
1 TTGTCTGATGGTTAACTGT
103916 TTGTCTGATGGTTAACTGT
1 TTGTCTGATGGTTAACTGT
103935 T
1 T
103936 AAACTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (19 bp):
TTGTCTGATGGTTAACTGT
Found at i:112829 original size:24 final size:25
Alignment explanation
Indices: 112797--112853 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
112787 CCCCTCTCTT
*
112797 TTTTTTTTTCTTG-TTCTT-CTTTAA
1 TTTTTTTTT-TAGATTCTTCCTTTAA
*
112821 TTTTTTTTTTAGATTTTTCCTTTAA
1 TTTTTTTTTTAGATTCTTCCTTTAA
112846 TTTTTTTT
1 TTTTTTTT
112854 ATCCTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 13 0.45
25 14 0.48
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTTTTTTTTAGATTCTTCCTTTAA
Found at i:119034 original size:50 final size:50
Alignment explanation
Indices: 118952--119102 Score: 223
Period size: 50 Copynumber: 3.0 Consensus size: 50
118942 TGCTTAGAGC
* * *
118952 TTGAGATTTTTTAT-AAGAGTTTTCGAATTCTAAGCCCGATAAGGGTAAAA
1 TTGAGATTTTATATGAAG-GATTTCGAATTCTAATCCCGATAAGGGTAAAA
* * *
119002 TTGAGATTTTCTATGAAGGATTTCAAACTCTAATCCCGATAAGGGTAAAA
1 TTGAGATTTTATATGAAGGATTTCGAATTCTAATCCCGATAAGGGTAAAA
*
119052 TTGATATTTTATATGAAGGATTTCGAATTCTAATCCCGATAAGGGTAAAA
1 TTGAGATTTTATATGAAGGATTTCGAATTCTAATCCCGATAAGGGTAAAA
119102 T
1 T
119103 GGGGTCTACG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
50 88 0.97
51 3 0.03
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (50 bp):
TTGAGATTTTATATGAAGGATTTCGAATTCTAATCCCGATAAGGGTAAAA
Found at i:119387 original size:45 final size:47
Alignment explanation
Indices: 119331--119444 Score: 124
Period size: 52 Copynumber: 2.4 Consensus size: 47
119321 TCCTCTATGG
*
119331 TTAGAGCTTGAGATTTTT-T-ACGAGGGATTTCAATTTCTCCATAGT
1 TTAGAGTTTGAGATTTTTGTGACGAGGGATTTCAATTTCTCCATAGT
* * *
119376 TTAGAGTTTGAGATTTTTTGTGAGGGATGAGGGGTTTCGATTTCTCCATAGT
1 TTAGAGTTTGAGA-TTTTTGT----GACGAGGGATTTCAATTTCTCCATAGT
*
119428 TAAGAGTTTGAGATTTT
1 TTAGAGTTTGAGATTTT
119445 ATATGAGGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
45 12 0.21
46 5 0.09
47 1 0.02
51 4 0.07
52 35 0.61
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (47 bp):
TTAGAGTTTGAGATTTTTGTGACGAGGGATTTCAATTTCTCCATAGT
Found at i:119452 original size:52 final size:52
Alignment explanation
Indices: 119352--119452 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
119342 GATTTTTTAC
* * *
119352 GAGGGATTTCAATTTCTCCATAGTTTAGAGTTTGAGATTTTTTGTGAGGGAT
1 GAGGGATTTCAATTTCTCCATAGTTAAGAGTTTGAGATTTTATATGAGGGAT
* *
119404 GAGGGGTTTCGATTTCTCCATAGTTAAGAGTTTGAGATTTTATATGAGG
1 GAGGGATTTCAATTTCTCCATAGTTAAGAGTTTGAGATTTTATATGAGG
119453 AATTTTGAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (52 bp):
GAGGGATTTCAATTTCTCCATAGTTAAGAGTTTGAGATTTTATATGAGGGAT
Found at i:119645 original size:24 final size:24
Alignment explanation
Indices: 119617--119664 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
119607 TTATGGTTTA
119617 TTCACTTATTTGCTCCAAGTATTG
1 TTCACTTATTTGCTCCAAGTATTG
119641 TTCACTTATTTGCTCCAAGTATTG
1 TTCACTTATTTGCTCCAAGTATTG
119665 ACTCTAGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (24 bp):
TTCACTTATTTGCTCCAAGTATTG
Done.