Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007953.1 Corchorus capsularis cultivar CVL-1 contig07974, 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: 55623
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3085 original size:21 final size:21
Alignment explanation
Indices: 3040--3088 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3030 CAGTTGGGGG
* * *
3040 CCCATGTGGTATGCTTGGTGC
1 CCCATGTGGTATGCTTCGCGA
*
3061 CCCATGTGGTTTGCTTCGCGA
1 CCCATGTGGTATGCTTCGCGA
3082 CCCATGT
1 CCCATGT
3089 CCTCCAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.29, G:0.29, T:0.33
Consensus pattern (21 bp):
CCCATGTGGTATGCTTCGCGA
Found at i:3955 original size:1 final size:1
Alignment explanation
Indices: 3949--3978 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3939 CTTCTTTTAT
3949 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3979 CTTTAATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14207 original size:12 final size:12
Alignment explanation
Indices: 14190--14214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14180 TTTTTAACCC
14190 GTTTAACCCGCA
1 GTTTAACCCGCA
14202 GTTTAACCCGCA
1 GTTTAACCCGCA
14214 G
1 G
14215 CGAAGCGCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (12 bp):
GTTTAACCCGCA
Found at i:15657 original size:44 final size:44
Alignment explanation
Indices: 15565--15657 Score: 98
Period size: 44 Copynumber: 2.1 Consensus size: 44
15555 AAAATGCAAG
* * * * * *
15565 ATTTTAAATTCAATAATTTGAAATTCTTTCTTTGGGTATTAGTA
1 ATTTGAAATTCAATAATTTCAAATTCATTCTTTGGATACTAATA
* *
15609 ATTTGAAATTCTATAATTTCAAATTCATTGTTTGGATGACTAAT-
1 ATTTGAAATTCAATAATTTCAAATTCATTCTTTGGAT-ACTAATA
15653 ATTTG
1 ATTTG
15658 GATTTGGAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 36 0.90
45 4 0.10
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (44 bp):
ATTTGAAATTCAATAATTTCAAATTCATTCTTTGGATACTAATA
Found at i:18158 original size:14 final size:14
Alignment explanation
Indices: 18135--18164 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18125 GGCATCGATC
*
18135 TTCTGGGTTTTGAT
1 TTCTGAGTTTTGAT
18149 TTCTGAGTTTTGAT
1 TTCTGAGTTTTGAT
18163 TT
1 TT
18165 TGGGGAGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.07, G:0.23, T:0.60
Consensus pattern (14 bp):
TTCTGAGTTTTGAT
Found at i:20279 original size:19 final size:20
Alignment explanation
Indices: 20244--20286 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
20234 ACCAAAAAAA
*
20244 TTAATTTCAATTTATT-AAT
1 TTAATTTCAATTAATTAAAT
20263 TTAATCTTC-ATTAATTAAAT
1 TTAAT-TTCAATTAATTAAAT
20283 TTAA
1 TTAA
20287 ACGCGATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATTTCAATTAATTAAAT
Found at i:38809 original size:15 final size:16
Alignment explanation
Indices: 38777--38810 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38767 AAAGAAGAAT
*
38777 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
38793 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
38808 TAA
1 TAA
38811 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:40128 original size:19 final size:18
Alignment explanation
Indices: 40095--40130 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40085 TTGAAATAAT
40095 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
40113 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
40131 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:45571 original size:57 final size:54
Alignment explanation
Indices: 45458--45937 Score: 373
Period size: 57 Copynumber: 8.9 Consensus size: 54
45448 AGTCAAAAGC
* * * ** * *
45458 TTAATTCGGAGT-AATTAAGCT-AAAGAGTAAAAGATGCCAGTCAGTAGTTAGC
1 TTAATTCAGAGTAAATTAAGTTAAAAGAGTAAAAAATGGTAATCAGTAGTTAGT
**
45510 TTAATTCAGAGTAATTAGTTAAGTTAAAAGAGTAAAAAATGGTAATCAACAGTTAGT
1 TTAATTCAGAGTAA--A-TTAAGTTAAAAGAGTAAAAAATGGTAATCAGTAGTTAGT
* * * *
45567 TTAATTCAGAGT-AATTAAGCT-AAA-AGTAAAAGA-GAGTAATCAGTAGATTGGC
1 TTAATTCAGAGTAAATTAAGTTAAAAGAGTAAAAAATG-GTAATCAGTAG-TTAGT
*
45619 TTAATTCAGAGT-AATTAAGTTAAAAAGAGTAAAAAAAATGATAATCAGTAGTTAGT
1 TTAATTCAGAGTAAATTAAGTT-AAAAGAGT--AAAAAATGGTAATCAGTAGTTAGT
* * * * *
45675 TTAATTAAGAG-AAATTAAGCTAAAA-AGTAAAAAGATGGCAAACAGTAGTTAGC
1 TTAATTCAGAGTAAATTAAGTTAAAAGAGTAAAAA-ATGGTAATCAGTAGTTAGT
**
45728 TTAATTCAGAGT-AATTAAGTTAAAAAGAGTAAAAAATGGTAATCACCAGTTAGT
1 TTAATTCAGAGTAAATTAAGTT-AAAAGAGTAAAAAATGGTAATCAGTAGTTAGT
* * * *
45782 TTAATTTAGAG-AAATTAAACTAAAAAGAGTAAGAGAAA-GAGTAAGCAGTAGATTAGT
1 TTAATTCAGAGTAAATT-AAGTTAAAAGAGTAA-A-AAATG-GTAATCAGTAG-TTAGT
** * * * *
45839 TTAATTCAGAGT-AATTAAACTAAAA-AGAATAAAAACGGTAATCAGTAATT-GAC
1 TTAATTCAGAGTAAATTAAGTTAAAAGAGTA-AAAAATGGTAATCAGTAGTTAG-T
* * * *
45892 TTGATTCAGAGT-AATTAAATTAAAA-AGTAAAAAATTGTAATAAGTA
1 TTAATTCAGAGTAAATTAAGTTAAAAGAGTAAAAAATGGTAATCAGTA
45938 AAATTGGCTT
Statistics
Matches: 347, Mismatches: 53, Indels: 56
0.76 0.12 0.12
Matches are distributed among these distances:
50 1 0.00
51 17 0.05
52 57 0.16
53 68 0.20
54 61 0.18
55 26 0.07
56 46 0.13
57 70 0.20
58 1 0.00
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (54 bp):
TTAATTCAGAGTAAATTAAGTTAAAAGAGTAAAAAATGGTAATCAGTAGTTAGT
Found at i:45680 original size:108 final size:107
Alignment explanation
Indices: 45458--45882 Score: 461
Period size: 109 Copynumber: 3.9 Consensus size: 107
45448 AGTCAAAAGC
* * * *
45458 TTAATTCGGAGTAATTAAGCT-AAAGAGTAAAAGATG-CCAGTCAGTAGTTAGCTTAATTCAGAG
1 TTAATTCAGAGAAATTAAGCTAAAAGAGTAAAAGA-GAGCAATCAGTAGTTAGCTTAATTCAGAG
45521 TAATT-AGTTAAGTTAAAAGAGTAAAAAATGGTAATCAACAGTTAGT
65 TAATTAAGTT-A---AAAAGAGTAAAAAATGGTAATCAACAGTTAGT
* * *
45567 TTAATTCAGAGTAATTAAGCT-AAA-AGTAAAAGAGAGTAATCAGTAGATTGGCTTAATTCAGAG
1 TTAATTCAGAGAAATTAAGCTAAAAGAGTAAAAGAGAGCAATCAGTAG-TTAGCTTAATTCAGAG
* **
45630 TAATTAAGTTAAAAAGAGTAAAAAAAATGATAATCAGTAGTTAGT
65 TAATTAAGTTAAAAAGAGT--AAAAAATGGTAATCAACAGTTAGT
* *
45675 TTAATTAAGAGAAATTAAGCTAAAA-AGTAAAA-AGATGGCAAACAGTAGTTAGCTTAATTCAGA
1 TTAATTCAGAGAAATTAAGCTAAAAGAGTAAAAGAGA--GCAATCAGTAGTTAGCTTAATTCAGA
*
45738 GTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCACCAGTTAGT
64 GTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCAACAGTTAGT
* * * * * *
45782 TTAATTTAGAGAAATTAAACTAAAAAGAGTAAGAGAAAGAGTAAGCAGTAGATTAGTTTAATTCA
1 TTAATTCAGAGAAATTAAGCT-AAAAGAGTAA-A-AGAGAGCAATCAGTAG-TTAGCTTAATTCA
** * *
45847 GAGTAATTAAACTAAAAAGAAT-AAAAACGGTAATCA
62 GAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCA
45883 GTAATTGACT
Statistics
Matches: 277, Mismatches: 25, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
106 8 0.03
107 41 0.15
108 64 0.23
109 93 0.34
110 36 0.13
111 32 0.12
112 3 0.01
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (107 bp):
TTAATTCAGAGAAATTAAGCTAAAAGAGTAAAAGAGAGCAATCAGTAGTTAGCTTAATTCAGAGT
AATTAAGTTAAAAAGAGTAAAAAATGGTAATCAACAGTTAGT
Found at i:45840 original size:164 final size:161
Alignment explanation
Indices: 45499--45932 Score: 446
Period size: 164 Copynumber: 2.6 Consensus size: 161
45489 AGATGCCAGT
* * * **
45499 CAGTAGTTAGCTTAATTCAGAGTAATTAGTTAAGTTAAAAGAGTAAAAAATGGTAATCAACAGTT
1 CAGTAGTTAGTTTAATTAAGAG-AA--A-TTAAGCTAAAA-AGTAAAAAATGGTAATCAGTAGTT
* * * ** *
45564 AGTTTAATTCAGAGTAATTAAGCT-AAAAGTAAAAGA-GAGTAATCAGTAGATTGGCTTAATTCA
61 AGCTTAATTCAGAGTAATTAAGTTAAAAAGTAAAAAATG-GTAATCACCAGATTAGCTTAATTCA
* ** *
45627 GAGTAATTAAGTTAAAAAGAGTAAAAAAAATGATAAT
125 GAGAAATTAAACTAAAAAGAGTAAAAAAAATGATAAG
* *
45664 CAGTAGTTAGTTTAATTAAGAGAAATTAAGCTAAAAAGTAAAAAGATGGCAAACAGTAGTTAGCT
1 CAGTAGTTAGTTTAATTAAGAGAAATTAAGCTAAAAAGTAAAAA-ATGGTAATCAGTAGTTAGCT
* *
45729 TAATTCAGAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCACCAG-TTAGTTTAATTTAGAG
65 TAATTCAGAGTAATTAAGTT-AAAA-AGTAAAAAATGGTAATCACCAGATTAGCTTAATTCAGAG
* *
45793 AAATTAAACTAAAAAGAGTAAGAGAAA-GAGTAAG
128 AAATTAAACTAAAAAGAGTAAAAAAAATGA-TAAG
* * * * * *
45827 CAGTAGATTAGTTTAATTCAGAGTAATTAAACTAAAAAGAATAAAAACGGTAATCAGTAATT-GA
1 CAGTAG-TTAGTTTAATTAAGAGAAATTAAGCTAAAAAGTA-AAAAATGGTAATCAGTAGTTAG-
* * *
45891 CTTGATTCAGAGTAATTAAATTAAAAAGTAAAAAATTGTAAT
63 CTTAATTCAGAGTAATTAAGTTAAAAAGTAAAAAATGGTAAT
45933 AAGTAAAATT
Statistics
Matches: 228, Mismatches: 32, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
160 8 0.04
161 44 0.19
162 18 0.08
163 52 0.23
164 81 0.36
165 25 0.11
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (161 bp):
CAGTAGTTAGTTTAATTAAGAGAAATTAAGCTAAAAAGTAAAAAATGGTAATCAGTAGTTAGCTT
AATTCAGAGTAATTAAGTTAAAAAGTAAAAAATGGTAATCACCAGATTAGCTTAATTCAGAGAAA
TTAAACTAAAAAGAGTAAAAAAAATGATAAG
Found at i:45908 original size:53 final size:53
Alignment explanation
Indices: 45455--45938 Score: 322
Period size: 53 Copynumber: 9.0 Consensus size: 53
45445 ACTAGTCAAA
* * ** * *
45455 AGCTTAATTCGGAGTAATTAAGCT--AAAGAGTAAAAGATGCCAGTCAGTAGTT
1 AGCTTAATTCAGAGTAATTAAGCTAAAAAGAATAAAA-ATGGTAATCAGTAATT
* * ** *
45507 AGCTTAATTCAGAGTAATTAGTTAAG-TTAAAAGAGTAAAAAATGGTAATCAACAGTT
1 AGCTTAATTCAGAGT-A--A-TTAAGCTAAAAAGAAT-AAAAATGGTAATCAGTAATT
*
45564 AGTTTAATTCAGAGTAATTAAGCT-AAAAG--TAAAAGA-GAGTAATCAGTAGATT
1 AGCTTAATTCAGAGTAATTAAGCTAAAAAGAATAAAA-ATG-GTAATCAGTA-ATT
* * * * *
45616 GGCTTAATTCAGAGTAATTAAGTTAAAAAGAGTAAAAAAAATGATAATCAGTAGTT
1 AGCTTAATTCAGAGTAATTAAGCT-AAAA-AG-AATAAAAATGGTAATCAGTAATT
* * * * * * *
45672 AGTTTAATTAAGAGAAATTAAGCTAAAAAGTAA-AAAGATGGCAAACAGTAGTT
1 AGCTTAATTCAGAGTAATTAAGCTAAAAAG-AATAAAAATGGTAATCAGTAATT
* * ** *
45725 AGCTTAATTCAGAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCACCAGTT
1 AGCTTAATTCAGAGTAATTAAGCTAAAAAGAAT-AAAAATGGTAATCAGTAATT
* * * * * * *
45779 AGTTTAATTTAGAGAAATTAAACTAAAAAGAGTAAGAGAAAGAGTAAGCAGTAGATT
1 AGCTTAATTCAGAGTAATTAAGCTAAAAAGAATAA-A-AATG-GTAATCAGTA-ATT
* * *
45836 AGTTTAATTCAGAGTAATTAAACTAAAAAGAATAAAAACGGTAATCAGTAATT
1 AGCTTAATTCAGAGTAATTAAGCTAAAAAGAATAAAAATGGTAATCAGTAATT
* ** * * *
45889 -GACTTGATTCAGAGTAATTAAATTAAAAAGTA-AAAAATTGTAATAAGTAA
1 AG-CTTAATTCAGAGTAATTAAGCTAAAAAGAATAAAAATGGTAATCAGTAA
45939 AATTGGCTTA
Statistics
Matches: 350, Mismatches: 57, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
50 5 0.01
51 10 0.03
52 54 0.15
53 84 0.24
54 63 0.18
55 14 0.04
56 35 0.10
57 76 0.22
58 9 0.03
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.28
Consensus pattern (53 bp):
AGCTTAATTCAGAGTAATTAAGCTAAAAAGAATAAAAATGGTAATCAGTAATT
Found at i:51503 original size:2 final size:2
Alignment explanation
Indices: 51496--51527 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
51486 ATGAATTTAC
*
51496 AT AT AT AT AC 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
51528 TAAATTTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.