Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010006.1 Corchorus capsularis cultivar CVL-1 contig10027, 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: 73457
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1404 original size:11 final size:11
Alignment explanation
Indices: 1388--1418 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1378 AAATGTTCGA
1388 CTCTGTTTTTC
1 CTCTGTTTTTC
*
1399 CTCTGTTTTTG
1 CTCTGTTTTTC
1410 CTCTGTTTT
1 CTCTGTTTT
1419 CCTTCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.13, T:0.65
Consensus pattern (11 bp):
CTCTGTTTTTC
Found at i:5730 original size:27 final size:27
Alignment explanation
Indices: 5700--5755 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5690 ATTGCTTTTG
5700 TACTTTCTTTTTATTCAAAGATTCTTT
1 TACTTTCTTTTTATTCAAAGATTCTTT
5727 TACTTTCTTTTTATTCAAAGATTCTTT
1 TACTTTCTTTTTATTCAAAGATTCTTT
5754 TA
1 TA
5756 AATGATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.14, G:0.04, T:0.59
Consensus pattern (27 bp):
TACTTTCTTTTTATTCAAAGATTCTTT
Found at i:7328 original size:23 final size:23
Alignment explanation
Indices: 7298--7343 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
7288 GTTAGTTTGT
7298 TAGAGACCGAGCGAGAGTGCTCA
1 TAGAGACCGAGCGAGAGTGCTCA
7321 TAGAGACCGAGCGAGAGTGCTCA
1 TAGAGACCGAGCGAGAGTGCTCA
7344 AGATTGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.35, T:0.13
Consensus pattern (23 bp):
TAGAGACCGAGCGAGAGTGCTCA
Found at i:8258 original size:2 final size:2
Alignment explanation
Indices: 8253--8279 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8243 TATATATATA
8253 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
8280 CCAAAGCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:8929 original size:41 final size:41
Alignment explanation
Indices: 8884--8964 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
8874 ACTTGACCCT
*
8884 CCTAATAATTAAAGAAATAAATTAAATCCAAGTTTAGCCCC
1 CCTAATAATTAAAGAAAGAAATTAAATCCAAGTTTAGCCCC
* *
8925 CCTAATAATTAACGTAAGAAATTAAATCCAAGTTTAGCCC
1 CCTAATAATTAAAGAAAGAAATTAAATCCAAGTTTAGCCC
8965 ATAGCTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (41 bp):
CCTAATAATTAAAGAAAGAAATTAAATCCAAGTTTAGCCCC
Found at i:12062 original size:28 final size:28
Alignment explanation
Indices: 12016--12072 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
12006 TCTACGAAAT
12016 TAATCAATCTTACTCCTCCTCTCTAACC
1 TAATCAATCTTACTCCTCCTCTCTAACC
* * *
12044 TAATCAATCTTTCTTCTCCTCTCTGACC
1 TAATCAATCTTACTCCTCCTCTCTAACC
12072 T
1 T
12073 GAGTTTTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.37, G:0.02, T:0.40
Consensus pattern (28 bp):
TAATCAATCTTACTCCTCCTCTCTAACC
Found at i:20939 original size:17 final size:19
Alignment explanation
Indices: 20902--20940 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
20892 TGAGGATAAT
*
20902 TTCCTTGTTTATGACTGTA
1 TTCCTTATTTATGACTGTA
20921 TTCCTTATTT-TGA-TGTA
1 TTCCTTATTTATGACTGTA
20938 TTC
1 TTC
20941 ATAGATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 9 0.47
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.56
Consensus pattern (19 bp):
TTCCTTATTTATGACTGTA
Found at i:28387 original size:41 final size:42
Alignment explanation
Indices: 28324--28404 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
28314 TGGGAGGAGA
28324 GGATTTTAACAATTTATGCACCCAATATAAAAG-GATTAGTC
1 GGATTTTAACAATTTATGCACCCAATATAAAAGAGATTAGTC
*
28365 GGATTTTAACAATTTACT-CACCCAATATGAAAGAGATTAG
1 GGATTTTAACAATTTA-TGCACCCAATATAAAAGAGATTAG
28405 GGATTAGTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 30 0.81
42 7 0.19
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (42 bp):
GGATTTTAACAATTTATGCACCCAATATAAAAGAGATTAGTC
Found at i:28758 original size:13 final size:13
Alignment explanation
Indices: 28740--28770 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28730 ACTCACAAAA
28740 GTCAAAGTCAACG
1 GTCAAAGTCAACG
*
28753 GTCAAAGTCAACT
1 GTCAAAGTCAACG
28766 GTCAA
1 GTCAA
28771 CTTCAATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (13 bp):
GTCAAAGTCAACG
Found at i:32712 original size:25 final size:24
Alignment explanation
Indices: 32684--32750 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
32674 TCACAACTTT
32684 CCTTTCTTCTTCTTCTCTCTCTAAC
1 CCTTTCTTC-TCTTCTCTCTCTAAC
* *
32709 CCTTCCCTTCATC-TCTCTCTCTATC
1 CCTT-TCTTC-TCTTCTCTCTCTAAC
*
32734 CCTCTTCATCTCTTCTC
1 CCT-TTCTTCTCTTCTC
32751 CAATTCCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
24 2 0.06
25 25 0.74
26 7 0.21
ACGTcount: A:0.07, C:0.45, G:0.00, T:0.48
Consensus pattern (24 bp):
CCTTTCTTCTCTTCTCTCTCTAAC
Found at i:46286 original size:17 final size:18
Alignment explanation
Indices: 46264--46303 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
46254 TTTTTTGTTT
46264 TAAAATCTTAAATTCTA-
1 TAAAATCTTAAATTCTAG
46281 TAAAATCTTAAATTCTAG
1 TAAAATCTTAAATTCTAG
46299 TAAAA
1 TAAAA
46304 CATACCACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAATCTTAAATTCTAG
Found at i:58870 original size:23 final size:24
Alignment explanation
Indices: 58843--58890 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
58833 GAGGTACATT
58843 TGTC-AAGATTTATCATATTATTC
1 TGTCAAAGATTTATCATATTATTC
58866 TGTCAATAAGATTTATCATATTATT
1 TGTC-A-AAGATTTATCATATTATT
58891 GAACATGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
26 18 0.82
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (24 bp):
TGTCAAAGATTTATCATATTATTC
Found at i:61460 original size:2 final size:2
Alignment explanation
Indices: 61453--61477 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61443 TATAAAGTAC
61453 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 T
61478 TCGTATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.