Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010635.1 Corchorus capsularis cultivar CVL-1 contig10656, 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: 42098
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:5708 original size:13 final size:13
Alignment explanation
Indices: 5690--5716 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5680 ACATTTGAAT
5690 TTCAAACTTAAGA
1 TTCAAACTTAAGA
5703 TTCAAACTTAAGA
1 TTCAAACTTAAGA
5716 T
1 T
5717 AAGTAAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TTCAAACTTAAGA
Found at i:7855 original size:67 final size:67
Alignment explanation
Indices: 7747--7883 Score: 256
Period size: 67 Copynumber: 2.0 Consensus size: 67
7737 TGCTAACCTT
*
7747 AAGAAGTGCACCTTTTGCACAAACAAGCTTGTTTTTCTTGGTTTTGTGGTGTCATCGCAAGGTAT
1 AAGAAGTGCACATTTTGCACAAACAAGCTTGTTTTTCTTGGTTTTGTGGTGTCATCGCAAGGTAT
7812 AG
66 AG
*
7814 AAGAAGTGCACATTTTGCACAAACAAGCTTGTTTTTCTTGGTTTTGTGGTGTCATCGGAAGGTAT
1 AAGAAGTGCACATTTTGCACAAACAAGCTTGTTTTTCTTGGTTTTGTGGTGTCATCGCAAGGTAT
7879 AG
66 AG
7881 AAG
1 AAG
7884 TTGATGAGGA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (67 bp):
AAGAAGTGCACATTTTGCACAAACAAGCTTGTTTTTCTTGGTTTTGTGGTGTCATCGCAAGGTAT
AG
Found at i:10043 original size:30 final size:30
Alignment explanation
Indices: 10009--10067 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
9999 CGCATGTGCC
10009 ATCGCATGAGGCCA-CCG-GCCACAACCGGCT
1 ATCGCATG-GGCCATCCGCG-CACAACCGGCT
*
10039 ATCGCATGGGGCATCCGCGCACAACCGGC
1 ATCGCATGGGCCATCCGCGCACAACCGGC
10068 CAATGGATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 21 0.81
31 1 0.04
ACGTcount: A:0.22, C:0.39, G:0.29, T:0.10
Consensus pattern (30 bp):
ATCGCATGGGCCATCCGCGCACAACCGGCT
Found at i:13747 original size:13 final size:13
Alignment explanation
Indices: 13729--13755 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13719 AAGTTTGAAT
13729 TTCAAACTTAAGA
1 TTCAAACTTAAGA
13742 TTCAAACTTAAGA
1 TTCAAACTTAAGA
13755 T
1 T
13756 AAGTAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TTCAAACTTAAGA
Found at i:15270 original size:17 final size:16
Alignment explanation
Indices: 15230--15272 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
15220 CATGTAATCT
*
15230 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
15246 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
15263 TTAGATCACT
1 TT-GATCACT
15273 AGTAATCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:15280 original size:17 final size:16
Alignment explanation
Indices: 15223--15280 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
15213 ATAAACCCAT
*
15223 GTAATCTTTGATCACCG
1 GTAATC-TTGATCACTG
*
15240 GTGATCTTGCATCACTG
1 GTAATCTTG-ATCACTG
* *
15257 GTGATCTTAGATCACTA
1 GTAATCTT-GATCACTG
15274 GTAATCT
1 GTAATCT
15281 GGGGGGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.09
17 31 0.89
18 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (16 bp):
GTAATCTTGATCACTG
Found at i:15360 original size:16 final size:17
Alignment explanation
Indices: 15341--15378 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
15331 TGCAATATGC
*
15341 AAAATTA-ATTATTAAA
1 AAAATTATAATATTAAA
*
15357 AAAATTATAATATTCAA
1 AAAATTATAATATTAAA
15374 AAAAT
1 AAAAT
15379 ATGCAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAATATTAAA
Found at i:16072 original size:18 final size:18
Alignment explanation
Indices: 16051--16097 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
16041 ACTAGACTCG
16051 AAACTGACTCAATAAAAC
1 AAACTGACTCAATAAAAC
16069 AAACTGACTCAATAAAAC
1 AAACTGACTCAATAAAAC
16087 AAACTGACTCA
1 AAACTGACTCA
16098 GAACAACTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.53, C:0.23, G:0.06, T:0.17
Consensus pattern (18 bp):
AAACTGACTCAATAAAAC
Found at i:18655 original size:6 final size:6
Alignment explanation
Indices: 18636--18668 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
18626 TATATCTTCA
*
18636 TATCTT TATTTT TATCTT TATCTT TATCTT TAT
1 TATCTT TATCTT TATCTT TATCTT TATCTT TAT
18669 ATAAGTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (6 bp):
TATCTT
Found at i:18794 original size:32 final size:33
Alignment explanation
Indices: 18758--18829 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 33
18748 AAGGATAAAC
18758 ATGTATTTTTATTTAATTTAGATTAA-TTAATT
1 ATGTATTTTTATTTAATTTAGATTAATTTAATT
** *
18790 ATGTAAATTTATTTCATTTAGATTAATTTAATT
1 ATGTATTTTTATTTAATTTAGATTAATTTAATT
18823 ATGTATT
1 ATGTATT
18830 ATGTTTTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 23 0.68
33 11 0.32
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (33 bp):
ATGTATTTTTATTTAATTTAGATTAATTTAATT
Found at i:23347 original size:27 final size:28
Alignment explanation
Indices: 23285--23349 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
23275 TTGCGGGCTC
* * *
23285 TTGCAATTCTGGTTAGTTGCGGAAAATT
1 TTGCAATTTTGGGTACTTGCGGAAAATT
* *
23313 TTGGAATTTTGGGTACTTGCGG-TAATT
1 TTGCAATTTTGGGTACTTGCGGAAAATT
23340 TTGCAATTTT
1 TTGCAATTTT
23350 TTGGTTGCTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.45
Consensus pattern (28 bp):
TTGCAATTTTGGGTACTTGCGGAAAATT
Found at i:23735 original size:15 final size:15
Alignment explanation
Indices: 23700--23740 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
23690 GCTTGTTCCC
*
23700 TCTTTTCTTTTCTTT
1 TCTTTTCTTTTATTT
23715 TCTTTTCTTTTATTAT
1 TCTTTTCTTTTATT-T
23731 T-TTTT-TTTTA
1 TCTTTTCTTTTA
23741 AAAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 17 0.71
16 2 0.08
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTTCTTTTATTT
Found at i:23739 original size:5 final size:5
Alignment explanation
Indices: 23700--23725 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
23690 GCTTGTTCCC
23700 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
23726 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:27235 original size:107 final size:104
Alignment explanation
Indices: 27068--27324 Score: 373
Period size: 105 Copynumber: 2.5 Consensus size: 104
27058 AGTTTAGCCT
27068 TAATTTCACTAAGTTTAGCCCCAAATT--AA-TTT-TTTTATTTTAAGGGTAAATTTCAAAATTA
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTATTTTAAGGGTAAATTTCAAAATTA
27129 ATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 ATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
27170 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTCATTTTAAGGGTAAATTTCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTT-ATTTTAAGGGTAAATTTCAAAATT
* * * *
27235 AATAATGTTGTTATAGGGTTTTAGAAATAAAATATATAAT
65 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
**
27275 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATT-TTATTTTATTTTAAGGGT
27325 TAGAAAAATT
Statistics
Matches: 142, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
102 27 0.19
103 25 0.18
104 21 0.15
105 37 0.26
106 4 0.03
107 28 0.20
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTATTTTAAGGGTAAATTTCAAAATTA
ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:40497 original size:24 final size:25
Alignment explanation
Indices: 40465--40532 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 25
40455 CTTTGGTTTT
40465 ATCTTCTCTAATTTTTTTTT-CCAG
1 ATCTTCTCTAATTTTTTTTTGCCAG
40489 ATCTTCTCTAAATTTCTTTTTTTGGCCAG
1 ATCTTCTCT-AA-TT-TTTTTTT-GCCAG
*
40518 AACTTCTCTAATTTT
1 ATCTTCTCTAATTTT
40533 ATTAGGTTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 9 0.24
25 2 0.05
26 4 0.11
27 9 0.24
28 2 0.05
29 12 0.32
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (25 bp):
ATCTTCTCTAATTTTTTTTTGCCAG
Found at i:40898 original size:20 final size:20
Alignment explanation
Indices: 40848--40920 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 20
40838 GGTGGTTTAT
* * *
40848 GGTAGTTTTCTTTTAAAAAG
1 GGTAGTTTTTTTTTTAAATG
*
40868 GGTAG---TTTTTTTAATTG
1 GGTAGTTTTTTTTTTAAATG
*
40885 GGT-GCTTTTTTTTTCAAATG
1 GGTAG-TTTTTTTTTTAAATG
40905 GGTAGTTTTTATTTTT
1 GGTAGTTTTT-TTTTT
40921 GGTTTTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.28
20 23 0.57
21 5 0.12
ACGTcount: A:0.19, C:0.04, G:0.21, T:0.56
Consensus pattern (20 bp):
GGTAGTTTTTTTTTTAAATG
Found at i:41158 original size:20 final size:20
Alignment explanation
Indices: 41139--41175 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41129 AATTAATTAT
41139 TTTA-ATATTAAATTTTTTA
1 TTTATATATTAAATTTTTTA
*
41158 TTTATATATTATATTTTT
1 TTTATATATTAAATTTTT
41176 ACTTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATATATTAAATTTTTTA
Found at i:41580 original size:22 final size:22
Alignment explanation
Indices: 41555--41597 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
41545 ATAATTGGTA
41555 TAGATTTATATGATTGCGAATT
1 TAGATTTATATGATTGCGAATT
41577 TAGATTTATATGATTGCGAAT
1 TAGATTTATATGATTGCGAAT
41598 GAAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.44
Consensus pattern (22 bp):
TAGATTTATATGATTGCGAATT
Found at i:41605 original size:22 final size:22
Alignment explanation
Indices: 41558--41605 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
41548 ATTGGTATAG
** *
41558 ATTTATATGATTGCGAATTTAG
1 ATTTATATGATTGCGAATGAAA
41580 ATTTATATGATTGCGAATGAAA
1 ATTTATATGATTGCGAATGAAA
41602 ATTT
1 ATTT
41606 TTAATCCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (22 bp):
ATTTATATGATTGCGAATGAAA
Found at i:41969 original size:2 final size:2
Alignment explanation
Indices: 41962--41992 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41952 AGTGAGGGAG
41962 TA 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 TA T
41993 TGTAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.