Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012203.1 Corchorus capsularis cultivar CVL-1 contig12224, 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: 76092
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1534 original size:6 final size:6
Alignment explanation
Indices: 1523--1558 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
1513 TTTCCTTTAG
1523 TTTTGT TTTTGT TTTTGGT ATTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTT
1559 CATTTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 20 0.71
7 4 0.14
8 4 0.14
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.81
Consensus pattern (6 bp):
TTTTGT
Found at i:6158 original size:1 final size:1
Alignment explanation
Indices: 6152--6180 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
6142 AATCAGTAGG
6152 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6181 GAGATCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10485 original size:50 final size:49
Alignment explanation
Indices: 10413--10510 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 49
10403 TCCCTCAACT
10413 TTCCAAATTCAGGAGCAAATTGTCCTGATTTGAAGTTCAAGGGGCAAAAC
1 TTCCAAATTCAGGAGCAAATTGTCCTGATTTGAAGTTC-AGGGGCAAAAC
*
10463 TTCCAAATTCGGGAGCAAATTGTCCTGATTTGAAGTTCAGGGGCAAAA
1 TTCCAAATTCAGGAGCAAATTGTCCTGATTTGAAGTTCAGGGGCAAAA
10511 AGACTATAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 10 0.21
50 37 0.79
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (49 bp):
TTCCAAATTCAGGAGCAAATTGTCCTGATTTGAAGTTCAGGGGCAAAAC
Found at i:23995 original size:31 final size:31
Alignment explanation
Indices: 23960--24036 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
23950 GTAAAATTAC
23960 CAATTTGAACCTAAACATTTCAAAAGTTGCT
1 CAATTTGAACCTAAACATTTCAAAAGTTGCT
* *
23991 CAATTT-AAGTCTAAACATTTCAAAATTTGCT
1 CAATTTGAA-CCTAAACATTTCAAAAGTTGCT
* *
24022 CAATTCGAGCCTAAA
1 CAATTTGAACCTAAA
24037 GACAAAAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 2 0.05
31 36 0.92
32 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (31 bp):
CAATTTGAACCTAAACATTTCAAAAGTTGCT
Found at i:28740 original size:13 final size:13
Alignment explanation
Indices: 28722--28747 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28712 ACCAGTTCAA
28722 CTCCAAAGTGTAT
1 CTCCAAAGTGTAT
28735 CTCCAAAGTGTAT
1 CTCCAAAGTGTAT
28748 AGAGTTCCTC
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
CTCCAAAGTGTAT
Found at i:31332 original size:108 final size:105
Alignment explanation
Indices: 31118--31399 Score: 326
Period size: 103 Copynumber: 2.7 Consensus size: 105
31108 AATTTTTCTA
* ** *
31118 ACCCTTAAAATAAAATTTTAATTTTAATTT-AGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTT-TTTATTTTA
* * * *
31181 TTTCT-AAAATCCTATAACAATATTATTAATTATGGAATTT
65 TTTTTAAAAACCCTATAACAATATTACTAATTATGAAATTT
** *
31221 ACCCTTAAAATAAAAATAAAATTTTAATTTGAACCTAAACTTAGTGAAATTATAGTTTTGTTTTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAA-T-TAGTTTT-TATTT
* *
31286 TATTTTTAAAAACCCTATAATTAA-ATTACTAATTTTGAAATTT
63 TATTTTTAAAAACCCTATAA-CAATATTACTAATTATGAAATTT
* *
31329 ACCCTTAAAATTAAAAA-AAAA--TTAATTTGAGGCTAAACTTAATGAAATTAGTTTTAATTTTA
1 ACCCTTAAAA-TAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTTTTATTTTA
31391 TTTTTAAAA
65 TTTTTAAAA
31400 CTCTATGATA
Statistics
Matches: 153, Mismatches: 18, Indels: 16
0.82 0.10 0.09
Matches are distributed among these distances:
103 41 0.27
104 20 0.13
105 3 0.02
106 25 0.16
107 15 0.10
108 41 0.27
109 8 0.05
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTTTTATTTTAT
TTTTAAAAACCCTATAACAATATTACTAATTATGAAATTT
Found at i:32156 original size:26 final size:27
Alignment explanation
Indices: 32108--32159 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
32098 TAGATGAGTA
** *
32108 AAATCCAAAAATCATTTATAAAGATCC
1 AAATCCAAAAAGAATATATAAAGATCC
32135 AAATCCAAAAAGAATATA-AAAGATC
1 AAATCCAAAAAGAATATATAAAGATC
32160 AATAATGTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (27 bp):
AAATCCAAAAAGAATATATAAAGATCC
Found at i:36876 original size:3 final size:3
Alignment explanation
Indices: 36868--36893 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36858 TGACTCTTCA
36868 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
36894 AGACTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:41918 original size:2 final size:2
Alignment explanation
Indices: 41911--41938 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41901 TTTTATATCA
41911 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
41939 GCTAAGCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42512 original size:207 final size:207
Alignment explanation
Indices: 42144--42516 Score: 491
Period size: 207 Copynumber: 1.8 Consensus size: 207
42134 AAACCCTCTA
* *
42144 CTTCAGATCGCATTGTAAAAGTTTGTTTCGGCATCTGAGTTGGTAGAACTTCTGTCATCATGCCT
1 CTTCAGATCGCATTGTAAAAGTTTGTTTAGGCATCTGAGCTGGTAGAACTTCTGTCATCATGCCT
* * * **
42209 GTCAACTTACTTCGTCCATCATCAAAACGCAAATGGTCACTCTTTAAATATTGTTCTGATATCCC
66 GTCAACTTAATCCGTCCATCATCAAAACGCAAACGGTCACTCTTTAAATATTGTTCCAATATCCC
*
42274 CATTTGCATGCTAGAACTAGCACCTTGAGACATTCTCTTAGGCGCTGCATTGCTCGATATCCTAA
131 CATTTGCATGCTAGAACTAGCACCCTGAGACATTCTCTTAGGCGCTGCATTGCTCGATATCCTAA
42339 CATGGCCATTCT
196 CATGGCCATTCT
* * * **
42351 CTTCAGATTGGATTGTAAAAGTTTGTTTAGGCATCTGAGCTGGTATAACTTCTGTTGTCATGCCT
1 CTTCAGATCGCATTGTAAAAGTTTGTTTAGGCATCTGAGCTGGTAGAACTTCTGTCATCATGCCT
** * * * * *
42416 GTCAACTTAATCCGTCCATCATCAAAGTGTAACCGGTCA-TTTTGTACATGTTGTTCCAATA-CA
66 GTCAACTTAATCCGTCCATCATCAAAACGCAAACGGTCACTCTT-TAAATATTGTTCCAATATC-
* * *
42479 CCTATTTGCATGCTAGAAGT-GCCCCCCTGAGACATTCT
129 CCCATTTGCATGCTAGAACTAG-CACCCTGAGACATTCT
42517 ATGAGCTGAT
Statistics
Matches: 140, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
206 5 0.04
207 135 0.96
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (207 bp):
CTTCAGATCGCATTGTAAAAGTTTGTTTAGGCATCTGAGCTGGTAGAACTTCTGTCATCATGCCT
GTCAACTTAATCCGTCCATCATCAAAACGCAAACGGTCACTCTTTAAATATTGTTCCAATATCCC
CATTTGCATGCTAGAACTAGCACCCTGAGACATTCTCTTAGGCGCTGCATTGCTCGATATCCTAA
CATGGCCATTCT
Found at i:45594 original size:26 final size:26
Alignment explanation
Indices: 45565--45614 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
45555 TATAAATAAC
45565 TTTTGAATCAATGGGTTTATACTTTT
1 TTTTGAATCAATGGGTTTATACTTTT
45591 TTTTGAATCAATGGGTTTATACTT
1 TTTTGAATCAATGGGTTTATACTT
45615 GGCCCAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (26 bp):
TTTTGAATCAATGGGTTTATACTTTT
Found at i:48371 original size:29 final size:29
Alignment explanation
Indices: 48318--48395 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
48308 ACTTGTAGCG
*
48318 TTTGGACGTTTTG-TCCCATGCACTTCAAT
1 TTTGGACGTTTTGCTCCC-TGAACTTCAAT
*
48347 TTTGGACATTTTGCTCCCTGAACTTCAAT
1 TTTGGACGTTTTGCTCCCTGAACTTCAAT
*
48376 TTTGAGACGTTTTGCCCCCT
1 TTTG-GACGTTTTGCTCCCT
48396 CAACCTAACG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 26 0.60
30 17 0.40
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.41
Consensus pattern (29 bp):
TTTGGACGTTTTGCTCCCTGAACTTCAAT
Found at i:48638 original size:29 final size:29
Alignment explanation
Indices: 48557--48640 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
48547 CGGAGCTGTT
* *
48557 AAGTTGAGAGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGT-CCAAAATTG
* * *
48587 AAGTTCAGGAGGTAAAATGTCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCAAAATTG
*
48616 AAGTTCAGGGGGCAAAACATCCAAA
1 AAGTTCAGGGGGCAAAACGTCCAAA
48641 CGCTACAAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 30 0.67
30 15 0.33
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (29 bp):
AAGTTCAGGGGGCAAAACGTCCAAAATTG
Found at i:60310 original size:21 final size:21
Alignment explanation
Indices: 60270--60324 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 21
60260 GAACCTGACT
60270 TATCATTATTA-TTC--AGAG
1 TATCATTATTATTTCTAAGAG
*
60288 TATCATTATTATTTCTAATAG
1 TATCATTATTATTTCTAAGAG
* *
60309 TAACA-TAATATTTCTA
1 TATCATTATTATTTCTA
60325 TAATCCATCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 11 0.35
19 3 0.10
20 10 0.32
21 7 0.23
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.47
Consensus pattern (21 bp):
TATCATTATTATTTCTAAGAG
Found at i:67656 original size:38 final size:38
Alignment explanation
Indices: 67588--67668 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
67578 TTGATTAGGA
67588 CAAAACATTTCAAAACCAGTTCAATTTGGGGCAATCCGTT
1 CAAAACATTTCAAAA-CAGTTCAATTTGGGGCAATCCG-T
* *
67628 CAAAACGTTTCAAAA-AGTTCAATTTGGGGCAATTCGT
1 CAAAACATTTCAAAACAGTTCAATTTGGGGCAATCCGT
67665 CAAA
1 CAAA
67669 TAGGGGCACA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
37 5 0.13
38 20 0.51
40 14 0.36
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (38 bp):
CAAAACATTTCAAAACAGTTCAATTTGGGGCAATCCGT
Found at i:70086 original size:25 final size:25
Alignment explanation
Indices: 70052--70101 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
70042 CTTATATACC
70052 AAGAGATAAACCCAATCCATGTCAA
1 AAGAGATAAACCCAATCCATGTCAA
*
70077 AAGAGATAAAGCCAATCCATGTCAA
1 AAGAGATAAACCCAATCCATGTCAA
70102 TCCATGAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.22, G:0.14, T:0.16
Consensus pattern (25 bp):
AAGAGATAAACCCAATCCATGTCAA
Found at i:74641 original size:30 final size:30
Alignment explanation
Indices: 74586--74668 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 30
74576 GGCATCCAAC
*
74586 GTGGCATGCCACGTGTACTCAAAAAA-TACCAT
1 GTGGCATGCCACGTGTA--CAAAAAAGGA-CAT
74618 GTGGCATGCCACGTGTACAAAAAAGGACAT
1 GTGGCATGCCACGTGTACAAAAAAGGACAT
*
74648 GTGGCACGCCACGTGT-CAAAA
1 GTGGCATGCCACGTGTACAAAA
74669 TGTCATGTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 5 0.10
30 25 0.52
31 1 0.02
32 17 0.35
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (30 bp):
GTGGCATGCCACGTGTACAAAAAAGGACAT
Done.