Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009086.1 Corchorus capsularis cultivar CVL-1 contig09107, 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: 15314
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:2794 original size:27 final size:27
Alignment explanation
Indices: 2727--2805 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
2717 AAAAGAACTT
* *
2727 AAAATGACAAAAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGCA
*
2754 AAAATGACCAAAATGCCCCTGGATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
* *
2781 AAAAT-AGCCTAAATGCCCCCGAATG
1 AAAATGA-CCAAAATGCCCCTGAATG
2806 ACCCTAATGC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.02
27 44 0.98
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:3522 original size:40 final size:41
Alignment explanation
Indices: 3467--3549 Score: 141
Period size: 40 Copynumber: 2.0 Consensus size: 41
3457 AACTCTGGTT
*
3467 TTGAAGACCTTCTGCTAGAAGTGCAGCTA-ATACAGATGAA
1 TTGAAAACCTTCTGCTAGAAGTGCAGCTACATACAGATGAA
*
3507 TTGAAAACCTTCTGCTAGAAGTGCAGCTACCTACAGATGAA
1 TTGAAAACCTTCTGCTAGAAGTGCAGCTACATACAGATGAA
3548 TT
1 TT
3550 AACTGATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 28 0.70
41 12 0.30
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (41 bp):
TTGAAAACCTTCTGCTAGAAGTGCAGCTACATACAGATGAA
Found at i:5008 original size:15 final size:16
Alignment explanation
Indices: 4981--5010 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4971 TGGCAAAGTG
4981 AATCCGATCCGAAAAA
1 AATCCGATCCGAAAAA
4997 AATCCG-TCCGAAAA
1 AATCCGATCCGAAAA
5011 CCTGAATCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.27, G:0.13, T:0.13
Consensus pattern (16 bp):
AATCCGATCCGAAAAA
Found at i:5283 original size:32 final size:32
Alignment explanation
Indices: 5236--5323 Score: 131
Period size: 32 Copynumber: 2.8 Consensus size: 32
5226 ATCTGGTCAA
* *
5236 AACCCAAACTGAACCCGAACCCGAATTAACCT
1 AACCCAAATTCAACCCGAACCCGAATTAACCT
* *
5268 GACCCAAATTCAACCCGAATCCGAATTAACCT
1 AACCCAAATTCAACCCGAACCCGAATTAACCT
*
5300 AACCCAAATTCAATCCGAACCCGA
1 AACCCAAATTCAACCCGAACCCGA
5324 TTCAAGTCCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.40, C:0.36, G:0.09, T:0.15
Consensus pattern (32 bp):
AACCCAAATTCAACCCGAACCCGAATTAACCT
Found at i:5328 original size:16 final size:17
Alignment explanation
Indices: 5307--5340 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5297 CCTAACCCAA
5307 ATTCAA-TCCGAACCCG
1 ATTCAAGTCCGAACCCG
5323 ATTCAAGTCCGAACCCG
1 ATTCAAGTCCGAACCCG
5340 A
1 A
5341 AAATGGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.32, C:0.35, G:0.15, T:0.18
Consensus pattern (17 bp):
ATTCAAGTCCGAACCCG
Found at i:6076 original size:15 final size:14
Alignment explanation
Indices: 6053--6082 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
6043 ATAAAAATTA
6053 AATATTTTTATTTT
1 AATATTTTTATTTT
6067 AATATATTTTATTTT
1 AATAT-TTTTATTTT
6082 A
1 A
6083 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:6871 original size:15 final size:15
Alignment explanation
Indices: 6851--6880 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6841 GCTCCCAAAA
*
6851 CAACTGAAAGCACCG
1 CAACTGAAAGAACCG
6866 CAACTGAAAGAACCG
1 CAACTGAAAGAACCG
6881 GATCCATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.30, G:0.20, T:0.07
Consensus pattern (15 bp):
CAACTGAAAGAACCG
Found at i:7183 original size:13 final size:13
Alignment explanation
Indices: 7165--7189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7155 TTGCTCTCTG
7165 CCATTCTGTTATA
1 CCATTCTGTTATA
7178 CCATTCTGTTAT
1 CCATTCTGTTAT
7190 TCCTTGTACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (13 bp):
CCATTCTGTTATA
Found at i:12011 original size:13 final size:13
Alignment explanation
Indices: 11993--12017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11983 TTGCTCTCTG
11993 CCATTCTGTTATA
1 CCATTCTGTTATA
12006 CCATTCTGTTAT
1 CCATTCTGTTAT
12018 TCCTTGTACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (13 bp):
CCATTCTGTTATA
Found at i:12217 original size:14 final size:14
Alignment explanation
Indices: 12198--12224 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12188 ATCAGTTCTC
12198 AATACATAATGCAG
1 AATACATAATGCAG
12212 AATACATAATGCA
1 AATACATAATGCA
12225 AGAAGTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
AATACATAATGCAG
Found at i:12448 original size:15 final size:15
Alignment explanation
Indices: 12402--12445 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
12392 TTATTTTTCA
* * *
12402 AAAATAAATTTTAAT
1 AAAATAAAATATATT
12417 AAAATAAAATATATT
1 AAAATAAAATATATT
12432 AAAATAAAA-ATATT
1 AAAATAAAATATATT
12446 TAATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATAAAATATATT
Found at i:13417 original size:20 final size:20
Alignment explanation
Indices: 13392--13433 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13382 AGTATAATAA
13392 CTTTTATTTTTATTT-GTTTT
1 CTTTTA-TTTTATTTAGTTTT
13412 CTTTTATTTTATTTAGTTTT
1 CTTTTATTTTATTTAGTTTT
13432 CT
1 CT
13434 ATATTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (20 bp):
CTTTTATTTTATTTAGTTTT
Found at i:13438 original size:19 final size:19
Alignment explanation
Indices: 13395--13440 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
13385 ATAATAACTT
13395 TTAT-TTTTATTTGTTTTC
1 TTATATTTTATTTGTTTTC
*
13413 TTTTATTTTATTTAGTTTTC
1 TTATATTTTATTT-GTTTTC
13433 -TATATTTT
1 TTATATTTT
13441 CTCTCTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 15 0.62
20 6 0.25
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (19 bp):
TTATATTTTATTTGTTTTC
Found at i:14353 original size:27 final size:27
Alignment explanation
Indices: 14315--14366 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
14305 CCTCATTTGC
14315 GTTAATATATTACTTATATGATGATGT
1 GTTAATATATTACTTATATGATGATGT
14342 GTTAATATATTACTTATATGATGAT
1 GTTAATATATTACTTATATGATGAT
14367 TTGGCCTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (27 bp):
GTTAATATATTACTTATATGATGATGT
Found at i:14676 original size:75 final size:75
Alignment explanation
Indices: 14592--14860 Score: 466
Period size: 75 Copynumber: 3.6 Consensus size: 75
14582 AAAATAATAA
*
14592 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTATGAGATATTTTAAGAAATAAAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
14657 ATAATAAAGT
66 ATAATAAAGT
14667 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
14732 ATAATAAAGT
66 ATAATAAAGT
*
14742 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAAAA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
* *
14807 ATTATAAAGAA
66 ATAATAAAG-T
* *
14818 TAAGAATATTTCTCTAAATCTTGCCAGATTGTGGGAGATTTAG
1 TGAGAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAG
14861 AAAATATCAA
Statistics
Matches: 186, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
75 146 0.78
76 10 0.05
77 30 0.16
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (75 bp):
TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
ATAATAAAGT
Done.