Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015554.1 Corchorus capsularis cultivar CVL-1 contig15575, 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: 4039
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Found at i:740 original size:31 final size:31
Alignment explanation
Indices: 704--763 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
694 TAAAAAGGGC
* *
704 AATCAGTAATTAAGTTCAATAAGGAAAAAGT
1 AATCAGTAACTAAGTTCAATAAGAAAAAAGT
* *
735 AATCAGTGACTGAGTTCAATAAGAAAAAA
1 AATCAGTAACTAAGTTCAATAAGAAAAAA
764 AGCAAACAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (31 bp):
AATCAGTAACTAAGTTCAATAAGAAAAAAGT
Found at i:830 original size:19 final size:20
Alignment explanation
Indices: 796--845 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
786 AAGTAAAATG
*
796 GTAATTAGTAAAGAGTAATA
1 GTAATTAGTAAAGAGTAACA
*
816 GTAATTAG-CAAGAGTAACA
1 GTAATTAGTAAAGAGTAACA
*
835 GTAATCAGTAA
1 GTAATTAGTAA
846 TCAGTAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (20 bp):
GTAATTAGTAAAGAGTAACA
Found at i:869 original size:14 final size:14
Alignment explanation
Indices: 825--923 Score: 69
Period size: 14 Copynumber: 7.3 Consensus size: 14
815 AGTAATTAGC
825 AAGAGTAA-CAGTA
1 AAGAGTAATCAGTA
**
838 ATCAGTAATCAGTA
1 AAGAGTAATCAGTA
*
852 AAGAGTAATCAGTG
1 AAGAGTAATCAGTA
** *
866 AAGAAAAAT-GGTA
1 AAGAGTAATCAGTA
* *
879 AAGAGTAATCAATG
1 AAGAGTAATCAGTA
** *
893 AAGAAAAAT-GGTA
1 AAGAGTAATCAGTA
*
906 AAGAGTAATCAGTG
1 AAGAGTAATCAGTA
920 AAGA
1 AAGA
924 AAAATGGAAA
Statistics
Matches: 60, Mismatches: 23, Indels: 5
0.68 0.26 0.06
Matches are distributed among these distances:
13 23 0.38
14 37 0.62
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (14 bp):
AAGAGTAATCAGTA
Found at i:879 original size:27 final size:27
Alignment explanation
Indices: 849--940 Score: 166
Period size: 27 Copynumber: 3.4 Consensus size: 27
839 TCAGTAATCA
849 GTAAAGAGTAATCAGTGAAGAAAAATG
1 GTAAAGAGTAATCAGTGAAGAAAAATG
*
876 GTAAAGAGTAATCAATGAAGAAAAATG
1 GTAAAGAGTAATCAGTGAAGAAAAATG
903 GTAAAGAGTAATCAGTGAAGAAAAATG
1 GTAAAGAGTAATCAGTGAAGAAAAATG
*
930 GAAAAGAGTAA
1 GTAAAGAGTAA
941 AAAGTAATCA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.54, C:0.03, G:0.25, T:0.17
Consensus pattern (27 bp):
GTAAAGAGTAATCAGTGAAGAAAAATG
Found at i:883 original size:54 final size:53
Alignment explanation
Indices: 825--954 Score: 154
Period size: 54 Copynumber: 2.4 Consensus size: 53
815 AGTAATTAGC
*
825 AAGAGTAACAGTAATCAGTAATCAGTAAAGAGTAATCAGTGAAGAAAAATGGTA
1 AAGAGTAACAGTAATCAGTAAT-AGTAAAGAGTAATCAGTGAAGAAAAATGGAA
* * ** *
879 AAGAGTAATCAATGAA-GAAAAATGGTAAAGAGTAATCAGTGAAGAAAAATGGAA
1 AAGAGTAA-CAGT-AATCAGTAATAGTAAAGAGTAATCAGTGAAGAAAAATGGAA
*
933 AAGAGTAAAAAGTAATCAGTAA
1 AAGAGT-AACAGTAATCAGTAA
955 AGAAAAACAA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
53 2 0.03
54 48 0.79
55 9 0.15
56 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.18
Consensus pattern (53 bp):
AAGAGTAACAGTAATCAGTAATAGTAAAGAGTAATCAGTGAAGAAAAATGGAA
Found at i:971 original size:34 final size:33
Alignment explanation
Indices: 903--974 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 33
893 AAGAAAAATG
* * *
903 GTAAAGAGTAATCAGTGAAGAAAAATGGAAAAGA
1 GTAAAAAGTAATCAGTAAAGAAAAA-GCAAAAGA
937 GTAAAAAGTAATCAGTAAAGAAAAA-CAATGAAGA
1 GTAAAAAGTAATCAGTAAAGAAAAAGCAA--AAGA
971 GTAA
1 GTAA
975 TTGGTAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 2 0.06
34 31 0.94
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.15
Consensus pattern (33 bp):
GTAAAAAGTAATCAGTAAAGAAAAAGCAAAAGA
Found at i:1126 original size:22 final size:22
Alignment explanation
Indices: 1049--1154 Score: 124
Period size: 22 Copynumber: 4.8 Consensus size: 22
1039 GGTGAAGAGT
* *
1049 AAAGAGTTAATCAATAAGAAGTA
1 AAAGAG-TAATCAGTAAAAAGTA
*
1072 AAAG-GTAATCAGTAAAAAGCA
1 AAAGAGTAATCAGTAAAAAGTA
* *
1093 ACAAGGGCAATCAGTAAAAAGTA
1 A-AAGAGTAATCAGTAAAAAGTA
*
1116 AAAGAGTAATCAGTAAAGAGTA
1 AAAGAGTAATCAGTAAAAAGTA
*
1138 AAATAGTAATCAGTAAA
1 AAAGAGTAATCAGTAAA
1155 TCAGTAATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
21 14 0.19
22 38 0.53
23 20 0.28
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.18
Consensus pattern (22 bp):
AAAGAGTAATCAGTAAAAAGTA
Found at i:1252 original size:54 final size:55
Alignment explanation
Indices: 1139--1399 Score: 349
Period size: 54 Copynumber: 4.8 Consensus size: 55
1129 TAAAGAGTAA
* * *
1139 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAGGA
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGT
* *
1194 AATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGTTTAATTAGAGACAAGGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGT
** *
1248 AATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAG--TAATCAG-TA-AAGAGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAG-GT
1300 AAAATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATCAGAGACAAGGT
1 --AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGT
**
1356 AATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAG--TAATCAG
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAG
1400 TAAAGAGTAA
Statistics
Matches: 183, Mismatches: 14, Indels: 20
0.84 0.06 0.09
Matches are distributed among these distances:
51 3 0.02
52 3 0.02
53 20 0.11
54 101 0.55
55 50 0.27
56 3 0.02
57 3 0.02
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.24
Consensus pattern (55 bp):
AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGT
Found at i:1322 original size:108 final size:108
Alignment explanation
Indices: 1139--1409 Score: 431
Period size: 108 Copynumber: 2.5 Consensus size: 108
1129 TAAAGAGTAA
** * *
1139 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAG-G--AAATAGTA
1 AATAGTAATCAGTAAATCAACAATTAAGTAAAAAG--AGTAATC--AGTAAAGAGTAAAATAGTA
* *
1201 ATCAGTAAATCAGTAATTAAGTAAAAGAGTTTAATTAGAGACAAGGT
62 ATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGAGACAAGGT
1248 AATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGTAATCAGTAAAGAGTAAAATAGTAATCA
1 AATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGTAATCAGTAAAGAGTAAAATAGTAATCA
1313 GTAAATCAGTAATTAAGTAAAAGAGATTAATCAGAGACAAGGT
66 GTAAATCAGTAATTAAGTAAAAGAGATTAATCAGAGACAAGGT
1356 AATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGTAATCAGTAAAGAGTAA
1 AATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGTAATCAGTAAAGAGTAA
1410 TCAGTAAAGA
Statistics
Matches: 153, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
105 6 0.04
106 1 0.01
107 6 0.04
108 107 0.70
109 33 0.22
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (108 bp):
AATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGTAATCAGTAAAGAGTAAAATAGTAATCA
GTAAATCAGTAATTAAGTAAAAGAGATTAATCAGAGACAAGGT
Found at i:1415 original size:122 final size:123
Alignment explanation
Indices: 1279--1523 Score: 465
Period size: 122 Copynumber: 2.0 Consensus size: 123
1269 AATTAAGTAA
1279 AAAGAGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAAT
1 AAAGAGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAAT
1344 CAGAGACAAGGTAATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAG-TAATCAGT
66 CAGAGACAAGGTAATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGATAATCAGT
*
1401 AAAGAGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAATCAGTAATTGAGTAAAAGAGATTAAT
1 AAAGAGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAAT
1466 CAGAGACAAGGTAATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGATTAATCAG
66 CAGAGACAAGGTAATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGA-TAATCAG
1524 AGTCAAGGTA
Statistics
Matches: 120, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
122 113 0.94
124 7 0.06
ACGTcount: A:0.52, C:0.07, G:0.18, T:0.23
Consensus pattern (123 bp):
AAAGAGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAAT
CAGAGACAAGGTAATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGATAATCAGT
Found at i:1440 original size:14 final size:14
Alignment explanation
Indices: 1387--1423 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1377 AATTAAGTAA
1387 AAAGAGTAATCAGT
1 AAAGAGTAATCAGT
1401 AAAGAGTAATCAGT
1 AAAGAGTAATCAGT
1415 AAAGAGTAA
1 AAAGAGTAA
1424 AATAGTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (14 bp):
AAAGAGTAATCAGT
Found at i:1489 original size:54 final size:55
Alignment explanation
Indices: 1424--1578 Score: 231
Period size: 55 Copynumber: 2.8 Consensus size: 55
1414 TAAAGAGTAA
*
1424 AATAGTAATCAGTAAATCAGTAATTGAGT-AAAAGAGATTAATCAGAGACAAGGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGT
** *
1478 AATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGT
* * * *
1533 AATAGTAATCAGTAAATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAG
1579 TAAATTGATT
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
54 26 0.29
55 64 0.71
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.24
Consensus pattern (55 bp):
AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGT
Found at i:1496 original size:29 final size:29
Alignment explanation
Indices: 1463--1552 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
1453 AAAAGAGATT
1463 AATCAGAGACAAGGTAATAGTAATCAGTA
1 AATCAGAGACAAGGTAATAGTAATCAGTA
* * ** *
1492 AATC--A-ACAA-TTAAGTA-AAAAGAGATT
1 AATCAGAGACAAGGTAA-TAGTAATCAG-TA
*
1518 AATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGAGACAAGGTAATAGTAATCAGTA
1547 AATCAG
1 AATCAG
1553 TAATCAGGTA
Statistics
Matches: 43, Mismatches: 11, Indels: 14
0.63 0.16 0.21
Matches are distributed among these distances:
25 7 0.16
26 11 0.26
27 1 0.02
28 1 0.02
29 16 0.37
30 7 0.16
ACGTcount: A:0.50, C:0.10, G:0.18, T:0.22
Consensus pattern (29 bp):
AATCAGAGACAAGGTAATAGTAATCAGTA
Found at i:1952 original size:23 final size:23
Alignment explanation
Indices: 1914--1961 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1904 AAGGGAGCAG
**
1914 AAAATAGTAATCAGTAA-AAGAGT
1 AAAATAGTAAAAAGTAAGAAG-GT
1937 AAAATAGTAAAAAGTAAGAAGGT
1 AAAATAGTAAAAAGTAAGAAGGT
1960 AA
1 AA
1962 TCAACAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (23 bp):
AAAATAGTAAAAAGTAAGAAGGT
Done.