Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010943.1 Corchorus capsularis cultivar CVL-1 contig10964, 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: 22820
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--40 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
*
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41 ACACTTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:949 original size:74 final size:73
Alignment explanation
Indices: 871--1019 Score: 228
Period size: 74 Copynumber: 2.0 Consensus size: 73
861 GTCTTTTCAT
* *
871 ACTTTTCGGATGACTAAAAAGC-CCTTCTATAAGCTTCCCCCATTCCTTTTCCTTCTATCCTTTT
1 ACTTTTCGGACGACTAAAAAGCACC-TCTATAAGCTTCCCCCATTCC-TTTCCTTCTACCCTTTT
935 TCGTAATTAC
64 TCGTAATTAC
** *
945 ACTTTTCGGACGACTAAAAAGCACCTCTATGGGTTTCCCCCATTCCTTTCCTTCTACCCTTTTTC
1 ACTTTTCGGACGACTAAAAAGCACCTCTATAAGCTTCCCCCATTCCTTTCCTTCTACCCTTTTTC
1010 GTAATTAC
66 GTAATTAC
1018 AC
1 AC
1020 ATTCCCCTTC
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
73 28 0.41
74 39 0.57
75 2 0.03
ACGTcount: A:0.21, C:0.31, G:0.09, T:0.38
Consensus pattern (73 bp):
ACTTTTCGGACGACTAAAAAGCACCTCTATAAGCTTCCCCCATTCCTTTCCTTCTACCCTTTTTC
GTAATTAC
Found at i:2588 original size:2 final size:2
Alignment explanation
Indices: 2581--2605 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2571 TTATGATAGC
2581 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
2606 TGCAAACCAA
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
Found at i:11362 original size:2 final size:2
Alignment explanation
Indices: 11355--11387 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11345 TTCGTTTGTT
*
11355 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11388 TAGCTTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14284 original size:67 final size:67
Alignment explanation
Indices: 14176--14307 Score: 255
Period size: 67 Copynumber: 2.0 Consensus size: 67
14166 CACTCTGCTA
14176 GGAAAAGAAAGAAGTGATTAATTAAATTAAGCCACGGCAAGTGTGCCAGTCCGCACAGTTTTATT
1 GGAAAAGAAAGAAGTGATTAATTAAATTAAGCCACGGCAAGTGTGCCAGTCCGCACAGTTTTATT
14241 TG
66 TG
*
14243 GGAAAAGCAAGAAGTGATTAATTAAATTAAGCCACGGCAAGTGTGCCAGTCCGCACAGTTTTATT
1 GGAAAAGAAAGAAGTGATTAATTAAATTAAGCCACGGCAAGTGTGCCAGTCCGCACAGTTTTATT
14308 GGCTGAAATC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (67 bp):
GGAAAAGAAAGAAGTGATTAATTAAATTAAGCCACGGCAAGTGTGCCAGTCCGCACAGTTTTATT
TG
Found at i:18571 original size:7 final size:7
Alignment explanation
Indices: 18561--18585 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18551 TTACTTTTTG
18561 TTTTGTT
1 TTTTGTT
18568 TTTTGTT
1 TTTTGTT
18575 TTTTGTT
1 TTTTGTT
18582 TTTT
1 TTTT
18586 TCTTCCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:18571 original size:19 final size:19
Alignment explanation
Indices: 18547--18583 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18537 ATGTTTCCAT
18547 TTTTTTACTTTTTGTTTTG
1 TTTTTTACTTTTTGTTTTG
**
18566 TTTTTTGTTTTTTGTTTT
1 TTTTTTACTTTTTGTTTT
18584 TTTCTTCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.03, G:0.11, T:0.84
Consensus pattern (19 bp):
TTTTTTACTTTTTGTTTTG
Found at i:19105 original size:7 final size:7
Alignment explanation
Indices: 19095--19126 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
19085 ATATTATTTA
19095 TTTATTC
1 TTTATTC
19102 TTTATTC
1 TTTATTC
19109 TTTATTC
1 TTTATTC
19116 -TT-TTC
1 TTTATTC
19121 TTTATT
1 TTTATT
19127 AAATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 3 0.13
6 4 0.17
7 16 0.70
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTATTC
Found at i:21380 original size:25 final size:25
Alignment explanation
Indices: 21331--21381 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
21321 TTAGTAGAAT
*
21331 AATTGTAAAAATTTATTTCTAAAAA
1 AATTGTAAAAATATATTTCTAAAAA
21356 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGT-AAA-AATATATTTCTAAAAA
21382 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 9 0.39
27 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAATATATTTCTAAAAA
Found at i:22498 original size:20 final size:21
Alignment explanation
Indices: 22470--22508 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
22460 TACTGATTAT
22470 TAAACACCGC-CCCCTTTTAC
1 TAAACACCGCACCCCTTTTAC
*
22490 TAAATACCGCACCCCTTTT
1 TAAACACCGCACCCCTTTT
22509 TACACTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.26, C:0.41, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAACACCGCACCCCTTTTAC
Found at i:22681 original size:11 final size:11
Alignment explanation
Indices: 22667--22741 Score: 69
Period size: 11 Copynumber: 6.1 Consensus size: 11
22657 TTAATCATAA
22667 ACTAATTAAAT
1 ACTAATTAAAT
22678 ACTAATTAATCAT
1 ACTAATTAA--AT
22691 AAACTAATTAAAT
1 --ACTAATTAAAT
*
22704 ACTAATAAAACAT
1 ACTAAT-TAA-AT
22717 AAACTAATTAAAT
1 --ACTAATTAAAT
22730 ACTAATTAAAT
1 ACTAATTAAAT
22741 A
1 A
22742 TAAACTAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
11 27 0.50
12 2 0.04
13 8 0.15
14 2 0.04
15 15 0.28
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:22686 original size:26 final size:26
Alignment explanation
Indices: 22657--22750 Score: 154
Period size: 26 Copynumber: 3.6 Consensus size: 26
22647 TTCCTTCATT
22657 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
22683 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
22709 TAAAACATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
22735 TTAAAT-ATAAACTAAT
1 TT-AATCATAAACTAAT
22751 AAACTAAGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 61 0.97
27 2 0.03
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:22687 original size:15 final size:15
Alignment explanation
Indices: 22657--22750 Score: 70
Period size: 15 Copynumber: 7.1 Consensus size: 15
22647 TTCCTTCATT
22657 TTAATCATAAACTAA
1 TTAATCATAAACTAA
22672 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
22683 TTAATCATAAACTAA
1 TTAATCATAAACTAA
22698 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
* *
22709 TAAAACATAAACTAA
1 TTAATCATAAACTAA
22724 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
22735 TTAAAT-ATAAACTAA
1 TT-AATCATAAACTAA
22750 T
1 T
22751 AAACTAAGTA
Statistics
Matches: 65, Mismatches: 2, Indels: 24
0.71 0.02 0.26
Matches are distributed among these distances:
11 24 0.37
12 2 0.03
13 12 0.18
15 27 0.42
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAATCATAAACTAA
Done.