Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010608.1 Corchorus capsularis cultivar CVL-1 contig10629, 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: 12688
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:511 original size:122 final size:121
Alignment explanation
Indices: 224--643 Score: 605
Period size: 124 Copynumber: 3.4 Consensus size: 121
214 TGCGTCAATA
*
224 AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATACATTAAAAAT
1 AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAA-
* *
289 TTTTAATATATCTAAGTTTTTAACGAAAAATAGTGAAATGGTAAAAATAAAATAATTAT
65 TTTTAATATATCCAAGTTTTTAA-TAAAAATAGT-AAATGGTAAAAATAAAATAATTAT
*
348 AAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTGAAAAA
1 AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATT-AAAAA
413 TTTTAATATATCCAAGTTTTTAATAAAAAATAGT-AATGGTAAAAATAAAATAATTAT
65 TTTTAATATATCCAAGTTTTTAAT-AAAAATAGTAAATGGTAAAAATAAAATAATTAT
* *
470 AAAAATATTGAATTTAGTTAAATGAAAATAGAGTTTTTAGTAGAATCAAAATATATATTAAAAA-
1 AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAT
* * * *
534 TTTAATATATCCAAATTTTTAATAAAAATAGTAAAATTGTAAAAATAAAGTCATTA-
66 TTTAATATATCCAAGTTTTTAATAAAAATAGT-AAATGGTAAAAATAAAATAATTAT
* * * * *
590 AAAAGATATT-AGATTTAACTAAATAAAAATAGAGTTTTAAGTATAATAAAACTA
1 AAAA-ATATTGA-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTA
644 CAATAGTTTA
Statistics
Matches: 272, Mismatches: 18, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
119 9 0.03
120 27 0.10
121 64 0.24
122 79 0.29
124 88 0.32
125 5 0.02
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (121 bp):
AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAT
TTTAATATATCCAAGTTTTTAATAAAAATAGTAAATGGTAAAAATAAAATAATTAT
Found at i:2192 original size:24 final size:25
Alignment explanation
Indices: 2158--2216 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
2148 AAATGATGGA
*
2158 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
2181 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
*
2206 AAATAAAGTTT
1 AAATGAAGTTT
2217 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 7 0.22
25 18 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:2315 original size:20 final size:21
Alignment explanation
Indices: 2286--2329 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2276 GCAAAAGTGT
*
2286 AAAAAAGGGGCGGTATTTAGC
1 AAAAGAGGGGCGGTATTTAGC
* *
2307 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGAGGGGCGGTATTTAGC
2328 AA
1 AA
2330 TCCAGTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.39, T:0.18
Consensus pattern (21 bp):
AAAAGAGGGGCGGTATTTAGC
Found at i:2786 original size:27 final size:31
Alignment explanation
Indices: 2743--2798 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 31
2733 AAGAACTGAG
2743 ACTAGACTCAAAACTGACT-AAAA-AAACAA
1 ACTAGACTCAAAACTGACTCAAAACAAACAA
2772 ACTA-ACTC-AAACTGACTCAAAACAAAC
1 ACTAGACTCAAAACTGACTCAAAACAAAC
2799 TCAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
28 8 0.32
29 8 0.32
ACGTcount: A:0.55, C:0.25, G:0.05, T:0.14
Consensus pattern (31 bp):
ACTAGACTCAAAACTGACTCAAAACAAACAA
Found at i:2974 original size:16 final size:14
Alignment explanation
Indices: 2943--2981 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
2933 AATGAGAACT
2943 AGAGAGGGAGAAGG
1 AGAGAGGGAGAAGG
2957 AGAGAGGGAGAAGG
1 AGAGAGGGAGAAGG
*
2971 GGAGAGAGGAG
1 AGAGAG-GGAG
2982 CGGCTAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (14 bp):
AGAGAGGGAGAAGG
Found at i:4720 original size:59 final size:59
Alignment explanation
Indices: 4649--4767 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
4639 CTTAGAGCAG
4649 AGCAGAGTTTGGGTATTATTAACAAGGGTTTAGGGCTTTCTTTGATCTTTCCGGAAACA
1 AGCAGAGTTTGGGTATTATTAACAAGGGTTTAGGGCTTTCTTTGATCTTTCCGGAAACA
* *
4708 AGCAGAGTTTGGGTATTGTTCACAAGGGTTTAGGGCTTTCTTTGATCTTTCCGGAAACA
1 AGCAGAGTTTGGGTATTATTAACAAGGGTTTAGGGCTTTCTTTGATCTTTCCGGAAACA
4767 A
1 A
4768 AAAATCCTAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.35
Consensus pattern (59 bp):
AGCAGAGTTTGGGTATTATTAACAAGGGTTTAGGGCTTTCTTTGATCTTTCCGGAAACA
Found at i:5682 original size:29 final size:29
Alignment explanation
Indices: 5609--5705 Score: 90
Period size: 31 Copynumber: 3.3 Consensus size: 29
5599 AAAAATGACA
*
5609 CATGACACGTGGCA-TTTTC-ACACGTGG
1 CATGCCACGTGGCATTTTTCTACACGTGG
* * * * *
5636 CGTGTCATGTGTCCTTTTTCTACACGTGG
1 CATGCCACGTGGCATTTTTCTACACGTGG
* *
5665 CATGCCACGTGGCATTTTTGTGTACACATGG
1 CATGCCACGTGGCA-TTTT-TCTACACGTGG
5696 CATGCCACGT
1 CATGCCACGT
5706 CGGATGCCTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
27 9 0.17
28 5 0.09
29 17 0.31
30 4 0.07
31 19 0.35
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.32
Consensus pattern (29 bp):
CATGCCACGTGGCATTTTTCTACACGTGG
Done.