Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009017.1 Corchorus capsularis cultivar CVL-1 contig09038, 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: 18879
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36 GTGTTTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1211 original size:2 final size:2
Alignment explanation
Indices: 1204--1232 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1194 AGATCTGTAT
1204 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1233 GCTAATTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4760 original size:13 final size:13
Alignment explanation
Indices: 4739--4772 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
4729 TGTGATGCAT
*
4739 CTTTCTTCTTTTC
1 CTTTTTTCTTTTC
4752 CTTTTTTCTTTTC
1 CTTTTTTCTTTTC
4765 CTTTTTTC
1 CTTTTTTC
4773 AGGTTGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTTTTCTTTTC
Found at i:11509 original size:14 final size:14
Alignment explanation
Indices: 11490--11540 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
11480 TGTCATTAAT
11490 AATTAGCACAAAAC
1 AATTAGCACAAAAC
* *
11504 AATTAGCTCCATTAAC
1 AATTAGC-ACA-AAAC
11520 AATTAGCACAAAAC
1 AATTAGCACAAAAC
11534 AATTAGC
1 AATTAGC
11541 TATACAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 17 0.55
15 4 0.13
16 10 0.32
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.22
Consensus pattern (14 bp):
AATTAGCACAAAAC
Found at i:11524 original size:30 final size:30
Alignment explanation
Indices: 11483--11541 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
11473 GTTGGAATGT
*
11483 CATTAATAATTAGCACAAAACAATTAGCTC
1 CATTAACAATTAGCACAAAACAATTAGCTC
11513 CATTAACAATTAGCACAAAACAATTAGCT
1 CATTAACAATTAGCACAAAACAATTAGCT
11542 ATACAACAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (30 bp):
CATTAACAATTAGCACAAAACAATTAGCTC
Found at i:15130 original size:33 final size:33
Alignment explanation
Indices: 15078--15428 Score: 414
Period size: 33 Copynumber: 10.5 Consensus size: 33
15068 AAGCTGCTGG
*
15078 TAGCGGTTGGAGCCATAGTCTGGAAGATTCCGA
1 TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
* *
15111 TAGCTGTTGGACCCGTAGTCTGGAAGATTCCGA
1 TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
* *
15144 TAGCGGTTGGAGCTGTGGTCTGGAAGATTCCGA
1 TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
* * *
15177 TAGCTGTTGGATCCGTGGTCTGGAAGATTCCGA
1 TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
* * * *
15210 TAGCGGTTCGAGCTGTAGTTTGGAAGATTCCGG
1 TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
* * * *
15243 TAGCTGTTCGAGCCGTACCCGTAATCCGGAATATTCCGA
1 TAGCGGTTGGAGCCGTA---G---TCTGGAAGATTCCGA
*
15282 TAGCGGTTGGAGCCGTAGTCCGGAAGATTCCGA
1 TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
* *
15315 TAGCGGTTGGAGCCGTAGTCCGGAATATTCCGA
1 TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
* ** * *
15348 TAGCGGTTGCAATCGTAGTCCGGAATATTCCGA
1 TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
* *
15381 TAGCGGTTGAAGCTGTAGTCTGGAAGATTCCGA
1 TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
15414 TAGCGGTTGGAGCCG
1 TAGCGGTTGGAGCCG
15429 AGAATGGGAA
Statistics
Matches: 274, Mismatches: 38, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
33 246 0.90
36 2 0.01
39 26 0.09
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (33 bp):
TAGCGGTTGGAGCCGTAGTCTGGAAGATTCCGA
Found at i:15366 original size:138 final size:138
Alignment explanation
Indices: 15093--15428 Score: 367
Period size: 138 Copynumber: 2.5 Consensus size: 138
15083 GTTGGAGCCA
* * *
15093 TAGTCTGGAAGATTCCGATAGCTGTT---G--G-ACCCGTAGTCTGGAAGATTCCGATAGCGGTT
1 TAGTCCGGAAGATTCCGATAGCTGTTCGAGCCGTACCCGTAATCCGGAAGATTCCGATAGCGGTT
* * * * * * *
15152 GGAGCTGTGGTCTGGAAGATTCCGATAGCTGTTGGATCCGTGGTCTGGAAGATTCCGATAGCGGT
66 GGAGCCGTAGTCCGGAAGATTCCGATAGCGGTTGGAGCCGTAGTCCGGAAGATTCCGATAGCGGT
*
15217 TCGAGCTG
131 TCAAGCTG
** * *
15225 TAGTTTGGAAGATTCCGGTAGCTGTTCGAGCCGTACCCGTAATCCGGAATATTCCGATAGCGGTT
1 TAGTCCGGAAGATTCCGATAGCTGTTCGAGCCGTACCCGTAATCCGGAAGATTCCGATAGCGGTT
*
15290 GGAGCCGTAGTCCGGAAGATTCCGATAGCGGTTGGAGCCGTAGTCCGGAATATTCCGATAGCGGT
66 GGAGCCGTAGTCCGGAAGATTCCGATAGCGGTTGGAGCCGTAGTCCGGAAGATTCCGATAGCGGT
*
15355 TGCAATC-G
131 T-CAAGCTG
* * * *
15363 TAGTCCGGAATATTCCGATAGCGGTT-GAAG-C-T----GTAGTCTGGAAGATTCCGATAGCGGT
1 TAGTCCGGAAGATTCCGATAGCTGTTCG-AGCCGTACCCGTAATCCGGAAGATTCCGATAGCGGT
15421 TGGAGCCG
65 TGGAGCCG
15429 AGAATGGGAA
Statistics
Matches: 173, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
132 55 0.32
135 1 0.01
136 1 0.01
137 3 0.02
138 110 0.64
139 3 0.02
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (138 bp):
TAGTCCGGAAGATTCCGATAGCTGTTCGAGCCGTACCCGTAATCCGGAAGATTCCGATAGCGGTT
GGAGCCGTAGTCCGGAAGATTCCGATAGCGGTTGGAGCCGTAGTCCGGAAGATTCCGATAGCGGT
TCAAGCTG
Found at i:15397 original size:171 final size:171
Alignment explanation
Indices: 15099--15428 Score: 475
Period size: 171 Copynumber: 1.9 Consensus size: 171
15089 GCCATAGTCT
* * * *
15099 GGAAGATTCCGATAGCTGTTGGACCCGTAGTCTGGAAGATTCCGATAGCGGTTGGAGCTGTGGTC
1 GGAAGATTCCGATAGCGGTTGGACCCGTAGTCCGGAAGATTCCGATAGCGGTTGGAGCCGTAGTC
* * * * *
15164 TGGAAGATTCCGATAGCTGTTGGATCCGTGGTCTGGAAGATTCCGATAGCGGTTCGAGCTGTAGT
66 CGGAAGATTCCGATAGCGGTTGAATCCGTAGTCCGGAAGATTCCGATAGCGGTTCGAGCTGTAGT
* * *
15229 TTGGAAGATTCCGGTAGCTGTTCGAGCCGTACCCGTAATCC
131 CTGGAAGATTCCGATAGCGGTTCGAGCCGTACCCGTAATCC
* *
15270 GGAATATTCCGATAGCGGTTGGAGCCGTAGTCCGGAAGATTCCGATAGCGGTTGGAGCCGTAGTC
1 GGAAGATTCCGATAGCGGTTGGACCCGTAGTCCGGAAGATTCCGATAGCGGTTGGAGCCGTAGTC
* *
15335 CGGAATATTCCGATAGCGGTTGCAAT-CGTAGTCCGGAATATTCCGATAGCGGTT-GAAGCTGTA
66 CGGAAGATTCCGATAGCGGTTG-AATCCGTAGTCCGGAAGATTCCGATAGCGGTTCG-AGCTGTA
*
15398 GTCTGGAAGATTCCGATAGCGGTTGGAGCCG
129 GTCTGGAAGATTCCGATAGCGGTTCGAGCCG
15429 AGAATGGGAA
Statistics
Matches: 140, Mismatches: 17, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
170 1 0.01
171 137 0.98
172 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (171 bp):
GGAAGATTCCGATAGCGGTTGGACCCGTAGTCCGGAAGATTCCGATAGCGGTTGGAGCCGTAGTC
CGGAAGATTCCGATAGCGGTTGAATCCGTAGTCCGGAAGATTCCGATAGCGGTTCGAGCTGTAGT
CTGGAAGATTCCGATAGCGGTTCGAGCCGTACCCGTAATCC
Found at i:15468 original size:18 final size:18
Alignment explanation
Indices: 15445--15479 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
15435 GGAACTCCTT
15445 TGTAACGAAGAAAATCGA
1 TGTAACGAAGAAAATCGA
15463 TGTAACGAAGAAAATCG
1 TGTAACGAAGAAAATCG
15480 GTTCGAGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTAACGAAGAAAATCGA
Found at i:15549 original size:18 final size:18
Alignment explanation
Indices: 15528--15572 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
15518 GATTACTTGA
15528 TTGGGATTGGCTGCTCAT
1 TTGGGATTGGCTGCTCAT
15546 TTGGGATTGGCTGCTCAT
1 TTGGGATTGGCTGCTCAT
15564 TTGGGATTG
1 TTGGGATTG
15573 TGACAACCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.13, G:0.36, T:0.40
Consensus pattern (18 bp):
TTGGGATTGGCTGCTCAT
Found at i:17490 original size:33 final size:33
Alignment explanation
Indices: 17448--17511 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
17438 TCTGTCAAAC
17448 GTTAAATTGGTTGAAAGAAAACCAATATATAAT
1 GTTAAATTGGTTGAAAGAAAACCAATATATAAT
17481 GTTAAATTGGTTGAAAGAAAACCAATATATA
1 GTTAAATTGGTTGAAAGAAAACCAATATATA
17512 TTATTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (33 bp):
GTTAAATTGGTTGAAAGAAAACCAATATATAAT
Found at i:18705 original size:24 final size:23
Alignment explanation
Indices: 18649--18727 Score: 122
Period size: 23 Copynumber: 3.3 Consensus size: 23
18639 AACCCTAAAC
* *
18649 TTCATTTCTAACAACTTCTTCAAA
1 TTCATTTTTAACAA-ATCTTCAAA
18673 CTTCATTTTTAACAAATCTTCAAA
1 -TTCATTTTTAACAAATCTTCAAA
18697 TTCATTTTTAACAAATCTTCAAA
1 TTCATTTTTAACAAATCTTCAAA
18720 TTCATTTT
1 TTCATTTT
18728 CCTTCATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 31 0.60
24 8 0.15
25 13 0.25
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (23 bp):
TTCATTTTTAACAAATCTTCAAA
Found at i:18760 original size:11 final size:11
Alignment explanation
Indices: 18746--18790 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
18736 TTAATCATAA
18746 ACTAATTAAAT
1 ACTAATTAAAT
18757 ACTAATT-AAT
1 ACTAATTAAAT
*
18767 AACTAATTATAT
1 -ACTAATTAAAT
18779 ACTAATTAAAT
1 ACTAATTAAAT
18790 A
1 A
18791 TAAACTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 3 0.10
11 25 0.83
12 2 0.07
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:18762 original size:22 final size:22
Alignment explanation
Indices: 18737--18784 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18727 TCCTTCATTT
18737 TAATC-ATAAACTAATTAAATAC
1 TAATCAAT-AACTAATTAAATAC
* *
18759 TAATTAATAACTAATTATATAC
1 TAATCAATAACTAATTAAATAC
18781 TAAT
1 TAAT
18785 TAAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATCAATAACTAATTAAATAC
Found at i:18785 original size:22 final size:22
Alignment explanation
Indices: 18745--18787 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
18735 TTTAATCATA
18745 AACTAATTAAATACTAATTAAT
1 AACTAATTAAATACTAATTAAT
*
18767 AACTAATTATATACTAATTAA
1 AACTAATTAAATACTAATTAA
18788 ATATAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
AACTAATTAAATACTAATTAAT
Found at i:18788 original size:33 final size:33
Alignment explanation
Indices: 18737--18849 Score: 105
Period size: 33 Copynumber: 3.5 Consensus size: 33
18727 TCCTTCATTT
18737 TAATCATAAACTAATTAAATACTAATTAATAAC
1 TAATCATAAACTAATTAAATACTAATTAATAAC
* * *
18770 TAATTATATACTAATTAAATA-TAAACTAATAAAC
1 TAATCATAAACTAATTAAATACT-AATTAAT-AAC
* *
18804 TAA--AT-AA-T-TTTAATTAACTAATTAA-AAC
1 TAATCATAAACTAATTAAAT-ACTAATTAATAAC
18832 TAATCATAAACTAATTAA
1 TAATCATAAACTAATTAA
18850 TATTAAAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
28 6 0.10
29 5 0.08
30 9 0.14
31 4 0.06
32 4 0.06
33 29 0.46
34 6 0.10
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (33 bp):
TAATCATAAACTAATTAAATACTAATTAATAAC
Done.