Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012976.1 Corchorus capsularis cultivar CVL-1 contig12997, 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: 18003
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:656 original size:40 final size:42
Alignment explanation
Indices: 553--656 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 42
543 ATGCATTAAC
* * * *
553 GAAGAAATCAGTGAAATCAGTAATTAGAGAGTCAAAGTAAAA
1 GAAGTAATCAGTAAAATCGGTAATTAGAGAGTAAAAGTAAAA
595 GAAGTAATCAGTAAAAT-GGTAATTA-AGAGTAAAAGTAAAA
1 GAAGTAATCAGTAAAATCGGTAATTAGAGAGTAAAAGTAAAA
*
635 GAAGTGATCAGT-AAATCGGTAA
1 GAAGTAATCAGTAAAATCGGTAA
657 AGAATAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 4 0.07
40 30 0.54
41 7 0.12
42 15 0.27
ACGTcount: A:0.51, C:0.06, G:0.22, T:0.21
Consensus pattern (42 bp):
GAAGTAATCAGTAAAATCGGTAATTAGAGAGTAAAAGTAAAA
Found at i:769 original size:26 final size:26
Alignment explanation
Indices: 740--793 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
730 TCAAATGGTG
*
740 ATTAAGTTCAA-AGAGTGAAAATAGTA
1 ATTAAATTCAAGAGA-TGAAAATAGTA
*
766 ATTAAATTCAAGAGATTAAAATAGTA
1 ATTAAATTCAAGAGATGAAAATAGTA
792 AT
1 AT
794 CAATAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.30
Consensus pattern (26 bp):
ATTAAATTCAAGAGATGAAAATAGTA
Found at i:868 original size:30 final size:31
Alignment explanation
Indices: 788--874 Score: 86
Period size: 36 Copynumber: 2.6 Consensus size: 31
778 AGATTAAAAT
788 AGTAATCAATAAAATGGTAAAAAAATAAAGAG
1 AGTAATCAATAAAATGGT-AAAAAATAAAGAG
* * *
820 AGATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGA-
1 AG-T-AAT-CA-A-TAAAATGGTAAAAAATAAAGAG
855 AGTAATCAATAAAATGGTAA
1 AGTAATCAATAAAATGGTAA
875 TTAAATTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
30 11 0.24
31 1 0.02
32 3 0.07
33 3 0.07
34 3 0.07
35 3 0.07
36 12 0.27
37 9 0.20
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.20
Consensus pattern (31 bp):
AGTAATCAATAAAATGGTAAAAAATAAAGAG
Found at i:962 original size:56 final size:56
Alignment explanation
Indices: 887--1025 Score: 163
Period size: 56 Copynumber: 2.5 Consensus size: 56
877 AAATTCAAAA
* * ** *
887 AGTAAAATGGTAAAAAGTAATGGTAATCAGAAAAAATAAGAA-GGTAATCAGTAAAG
1 AGTAAAATAGTAATAAGTAAAAGTAATCAGAAAAAACAA-AATGGTAATCAGTAAAG
* * *
943 AGTAAAATAGTAATTAGTAAAAGTAATCAGTAAGAACAAAATGGTAATCAGTAAAG
1 AGTAAAATAGTAATAAGTAAAAGTAATCAGAAAAAACAAAATGGTAATCAGTAAAG
* *
999 AGTAAAATATTAATCAGTAAAAAGTAA
1 AGTAAAATAGTAATAAGT-AAAAGTAA
1026 GAAGGTAATC
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
55 2 0.03
56 61 0.86
57 8 0.11
ACGTcount: A:0.55, C:0.04, G:0.18, T:0.22
Consensus pattern (56 bp):
AGTAAAATAGTAATAAGTAAAAGTAATCAGAAAAAACAAAATGGTAATCAGTAAAG
Found at i:1005 original size:22 final size:22
Alignment explanation
Indices: 958--1063 Score: 121
Period size: 22 Copynumber: 5.0 Consensus size: 22
948 AATAGTAATT
958 AGTAAAA--GTAATCAGT-AAG
1 AGTAAAATGGTAATCAGTAAAG
**
977 AACAAAATGGTAATCAGTAAAG
1 AGTAAAATGGTAATCAGTAAAG
** *
999 AGTAAAATATTAATCAGTAAAA
1 AGTAAAATGGTAATCAGTAAAG
1021 AGTAAGAA-GGTAATCAGTAAAG
1 AGTAA-AATGGTAATCAGTAAAG
*
1043 AGTAAAATGATAATCAGTAAA
1 AGTAAAATGGTAATCAGTAAA
1064 TGGTAATCAG
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
19 5 0.07
21 11 0.15
22 53 0.75
23 2 0.03
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.22
Consensus pattern (22 bp):
AGTAAAATGGTAATCAGTAAAG
Found at i:1063 original size:15 final size:15
Alignment explanation
Indices: 1043--1077 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1033 ATCAGTAAAG
1043 AGTAAAATGATAATC
1 AGTAAAATGATAATC
*
1058 AGT-AAATGGTAATC
1 AGTAAAATGATAATC
1072 AGTAAA
1 AGTAAA
1078 GAGTAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (15 bp):
AGTAAAATGATAATC
Found at i:1180 original size:36 final size:34
Alignment explanation
Indices: 1101--1180 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
1091 TCAGTGATTC
* * *
1101 AAAGAGTAAAATGGTAGTCAATATAAGAAAAAGA
1 AAAGAGAAAAATGGTAATCAATAAAAGAAAAAGA
* * *
1135 AGAGTGAAAAATGGTAATCAATAAAAGAGAGTAAGA
1 AAAGAGAAAAATGGTAATCAATAAAAGA-A-AAAGA
1171 AAAGAGAAAA
1 AAAGAGAAAA
1181 TATAAAAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
34 23 0.64
35 1 0.03
36 12 0.33
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (34 bp):
AAAGAGAAAAATGGTAATCAATAAAAGAAAAAGA
Found at i:1200 original size:26 final size:29
Alignment explanation
Indices: 1155--1217 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 29
1145 ATGGTAATCA
1155 ATAAAAGAGAGTAAGAAAAGAG-AAAAT-
1 ATAAAAGAGAGTAAGAAAAGAGAAAAATG
* *
1182 ATAAAA-AGAGTGAGGAAAGAGTAAAAATG
1 ATAAAAGAGAGTAAGAAAAGAG-AAAAATG
1211 ATAAAAG
1 ATAAAAG
1218 TAGCATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 13 0.43
27 6 0.20
28 5 0.17
29 6 0.20
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (29 bp):
ATAAAAGAGAGTAAGAAAAGAGAAAAATG
Found at i:7130 original size:30 final size:30
Alignment explanation
Indices: 7094--7152 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
7084 CAAGGGGGAG
7094 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
*
7124 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
7153 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:9081 original size:21 final size:19
Alignment explanation
Indices: 9049--9087 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
9039 CAATCAAGCA
9049 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
9068 AATCATAGCATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
9088 ATGAGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
AATCAAGATTCAAAGCATC
Found at i:12142 original size:21 final size:20
Alignment explanation
Indices: 12103--12147 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12093 ACAGATTAAT
* *
12103 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
12123 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
12144 TAAA
1 TAAA
12148 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Done.