Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013874.1 Corchorus capsularis cultivar CVL-1 contig13895, 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: 4011
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Found at i:60 original size:17 final size:18
Alignment explanation
Indices: 37--84 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
27 GGGGATAAGT
37 GGAAAAAATGAAAAA-AAA
1 GGAAAAAA-GAAAAAGAAA
*
55 TGAAAAAAGAAAAAGAAA
1 GGAAAAAAGAAAAAGAAA
*
73 GGAAAAGAGAAA
1 GGAAAAAAGAAA
85 GAGTAACGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (18 bp):
GGAAAAAAGAAAAAGAAA
Found at i:168 original size:44 final size:44
Alignment explanation
Indices: 93--241 Score: 190
Period size: 45 Copynumber: 3.3 Consensus size: 44
83 AAGAGTAACG
* *
93 ATGGTTTTCAAAAAATAGTCATGGCTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTC-AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
*
138 ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
* * * *
182 ATGTTTTTTCAAGAAGAATCATGGTTTTCAAGAGGGTTTTGATAAA
1 ATG-GTTTTCAAAAAGAGTCATGGTTTTCAA-AAGGTTTTGATAAA
* *
228 AGGGTTTTCCAAAA
1 ATGGTTTTCAAAAA
242 TTGCATTTTC
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
44 35 0.39
45 40 0.44
46 15 0.17
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (44 bp):
ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
Found at i:606 original size:14 final size:15
Alignment explanation
Indices: 582--611 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
572 AAGGAAATAA
582 AAAAGAAAGAAAAAG
1 AAAAGAAAGAAAAAG
597 AAAA-AAAGAAAAAG
1 AAAAGAAAGAAAAAG
611 A
1 A
612 GGAGGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAAG
Found at i:1015 original size:16 final size:17
Alignment explanation
Indices: 979--1015 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
969 CATGTAAAAA
979 AAAAACAAAAAGACAAG
1 AAAAACAAAAAGACAAG
*
996 -AAAACAAAAAG-GAAG
1 AAAAACAAAAAGACAAG
1011 AAAAA
1 AAAAA
1016 TGATGAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAGACAAG
Found at i:1028 original size:24 final size:24
Alignment explanation
Indices: 1001--1077 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
991 ACAAGAAAAC
1001 AAAAAGGAAGAAAAATGATGAAAG
1 AAAAAGGAAGAAAAATGATGAAAG
* * *
1025 -AAAAGAAAAGAAAAATGAAAGAAGG
1 AAAAAG-GAAGAAAAATG-ATGAAAG
*
1050 AAAAAAGAA-AAATGAATGATG-AAG
1 AAAAAGGAAGAAA--AATGATGAAAG
1074 AAAA
1 AAAA
1078 GGAGCTCTAG
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
23 5 0.12
24 19 0.46
25 9 0.22
26 8 0.20
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.08
Consensus pattern (24 bp):
AAAAAGGAAGAAAAATGATGAAAG
Found at i:1077 original size:22 final size:23
Alignment explanation
Indices: 1018--1078 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
1008 AAGAAAAATG
1018 ATGAAAGAA--AAGAAAAGAAAA
1 ATGAAAGAAGGAAGAAAAGAAAA
1039 ATGAAAGAAGGAA-AAAAGAAAA
1 ATGAAAGAAGGAAGAAAAGAAAA
* *
1061 ATGAATG-ATGAAGAAAAG
1 ATGAAAGAAGGAAGAAAAG
1079 GAGCTCTAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 13 0.37
22 20 0.57
23 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (23 bp):
ATGAAAGAAGGAAGAAAAGAAAA
Found at i:2276 original size:49 final size:49
Alignment explanation
Indices: 2212--2307 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
2202 AGTTTATCCA
* * * *
2212 AGTTTATGTTAGAATGATTGATTCAGTTGACCCAGGGTGGTTTTTCTCC
1 AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTCC
2261 AGTTTAT-TTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCT
1 AGTTTATGTT-AGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCT
2308 TTAGTAGCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 2 0.05
49 40 0.95
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (49 bp):
AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTCC
Found at i:2413 original size:36 final size:36
Alignment explanation
Indices: 2364--2471 Score: 103
Period size: 36 Copynumber: 3.0 Consensus size: 36
2354 CAGTTGACCC
2364 AGGGTGGTTTTTCTTCAGTTTATGTTGGAATGATCG
1 AGGGTGGTTTTTCTTCAGTTTATGTTGGAATGATCG
* ** * * *
2400 AGGGTGGTCTTTCTTTGGTTTAT-TTCGG-TTGACCC
1 AGGGTGGTTTTTCTTCAGTTTATGTT-GGAATGATCG
* * **
2435 AGAGCGGTTTTTCTTCAGTTTATGTCAGAATGATCG
1 AGGGTGGTTTTTCTTCAGTTTATGTTGGAATGATCG
2471 A
1 A
2472 TTCAGTCGAC
Statistics
Matches: 53, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
35 25 0.47
36 28 0.53
ACGTcount: A:0.17, C:0.13, G:0.28, T:0.43
Consensus pattern (36 bp):
AGGGTGGTTTTTCTTCAGTTTATGTTGGAATGATCG
Found at i:2456 original size:35 final size:35
Alignment explanation
Indices: 2356--2459 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 35
2346 TATCGATTCA
2356 GTTGACCCAGGGTGGTTTTTCTTCAGTTTATGTTG
1 GTTGACCCAGGGTGGTTTTTCTTCAGTTTATGTTG
* * * * **
2391 GAATGATCGAGGGTGGTCTTTCTTTGGTTTAT-TTCG
1 G-TTGACCCAGGGTGGTTTTTCTTCAGTTTATGTT-G
* *
2427 GTTGACCCAGAGCGGTTTTTCTTCAGTTTATGT
1 GTTGACCCAGGGTGGTTTTTCTTCAGTTTATGT
2460 CAGAATGATC
Statistics
Matches: 52, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
35 25 0.48
36 27 0.52
ACGTcount: A:0.13, C:0.14, G:0.28, T:0.44
Consensus pattern (35 bp):
GTTGACCCAGGGTGGTTTTTCTTCAGTTTATGTTG
Found at i:2642 original size:70 final size:70
Alignment explanation
Indices: 2451--2871 Score: 603
Period size: 70 Copynumber: 6.0 Consensus size: 70
2441 GTTTTTCTTC
*
2451 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
2516 ATTCGA
66 A-TCCA
*
2522 AGTTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAATT
1 AG-TTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
2587 TATCCA
65 TATCCA
* * * * * *
2593 AGTTTGTGTCAGAATGATTGATTCGGTCGACCTAGGGTGGTCTTTCTTCAGTAGTTTCCATA-TT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCA-AGTT
2657 TATCCA
65 TATCCA
2663 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
2728 ATCCA
66 ATCCA
* * * * * *
2733 AGTTTGTGTCAAAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
2798 ATCAA
66 ATCCA
* * * * * *
2803 AGTTTATGTTAGAGTGATCGATTCAGTTGACCCAGGGCGGTTTTTCATCAGTTGTTTCC-AGTTG
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
2867 ATCCA
66 ATCCA
2872 GGGTGGTCTA
Statistics
Matches: 312, Mismatches: 35, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
69 8 0.03
70 234 0.75
71 8 0.03
72 62 0.20
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATCCA
Found at i:2991 original size:40 final size:40
Alignment explanation
Indices: 2921--2996 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
2911 GTCTTCGTCA
*
2921 AAGATTTATTACTTTATCAGTTAATTTCAGAATCCTGTTC
1 AAGATTTATTACTTTATCAGTTAATCTCAGAATCCTGTTC
*
2961 AAGATTGT-TTACTTTATCAG-TAGGTCTCAGAATCCT
1 AAGATT-TATTACTTTATCAGTTA-ATCTCAGAATCCT
2997 ATTTGAGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.06
40 29 0.91
41 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (40 bp):
AAGATTTATTACTTTATCAGTTAATCTCAGAATCCTGTTC
Found at i:3223 original size:58 final size:57
Alignment explanation
Indices: 3085--3305 Score: 253
Period size: 58 Copynumber: 3.7 Consensus size: 57
3075 CTGTTGGAGA
* *
3085 GTTTCATTTCAAATCCTGTTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATATT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAG-----T-TTTCAATT-CAAAATCTT
* * * * *
3149 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTATCAATTCTAAGTCCT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAATTCAAAATCTT
* * * **
3206 GTTTCATTTTCAAATCCTACTCGAGGTCTCTAATCGAGAGTTTTCAACCCAAAATCTT
1 GTTTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAATTCAAAATCTT
*
3264 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGCCGAGAGTTT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT
3306 CTGTTTCAAT
Statistics
Matches: 135, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
57 43 0.32
58 54 0.40
59 1 0.01
64 37 0.27
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (57 bp):
GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAATTCAAAATCTT
Done.