Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005124.1 Corchorus capsularis cultivar CVL-1 contig05142, 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: 3990
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Found at i:762 original size:55 final size:55
Alignment explanation
Indices: 704--1221 Score: 602
Period size: 55 Copynumber: 9.3 Consensus size: 55
694 AAAAGGGGGC
* *
704 AATCAGTAATTAAGTAAAAAGAGATTAATAAGAGTTAAAGTAATAGTAATCAGTCAATCAATA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAG--------TA
* *
767 AATCAGTAATTAAGTAAAAAGAGATTAATTAGAGTTAAAGTAATAGTAATCAGTCAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAG-T----CAA-AGTAAT-AGT-AATCAGTA
*
830 AATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* * *
885 AATC--------AGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGAAATTAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
932 AATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* * * *
987 AATTATTAATTAAGTGAAAAGAAATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* * * * *
1042 AATCAATAGTTAAGTAAAAAGAGGTAAATCAGAGTCAAAGTAACAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* * * *
1097 AATCAGTAATTAAGTGAAAAGAGATTAATCAAAGGCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* *
1152 AATCAGTAATTAAGTAAAAAAGAAATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGT-AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
1208 AATCAATAATTAAG
1 AATCAGTAATTAAG
1222 AGTTAAAATG
Statistics
Matches: 401, Mismatches: 37, Indels: 41
0.84 0.08 0.09
Matches are distributed among these distances:
47 43 0.11
55 211 0.53
56 52 0.13
57 6 0.01
58 2 0.00
62 1 0.00
63 67 0.17
64 1 0.00
68 3 0.01
69 6 0.01
70 3 0.01
71 6 0.01
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.26
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
Found at i:777 original size:63 final size:63
Alignment explanation
Indices: 704--894 Score: 328
Period size: 63 Copynumber: 3.0 Consensus size: 63
694 AAAAGGGGGC
*
704 AATCAGTAATTAAGTAAAAAGAGATTAATAAGAGTTAAAGTAATAGTAATCAGTCAATCAATA
1 AATCAGTAATTAAGTAAAAAGAGATTAATAAGAGTTAAAGTAATAGTAATCAGTCAATCAGTA
*
767 AATCAGTAATTAAGTAAAAAGAGATTAATTAGAGTTAAAGTAATAGTAATCAGTCAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATAAGAGTTAAAGTAATAGTAATCAGTCAATCAGTA
* * * *
830 AATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATAAGAGTTAAAGTAATAGTAATCAGTCAATCAGTA
893 AA
1 AA
895 AAGAGATTAA
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 122 1.00
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.27
Consensus pattern (63 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATAAGAGTTAAAGTAATAGTAATCAGTCAATCAGTA
Found at i:1111 original size:29 final size:28
Alignment explanation
Indices: 1024--1111 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 28
1014 ATCAGAGTCA
*
1024 AAGTAATAGTAATCAGTAAATCAATAGTT
1 AAGTAA-AGTAATCAGTAAATCAGTAGTT
* *
1053 AAGTAAA--AA-GAGGTAAATCAG-AGTCA
1 AAGTAAAGTAATCA-GTAAATCAGTAGT-T
*
1079 AAGTAACAGTAATCAGTAAATCAGTAATT
1 AAGTAA-AGTAATCAGTAAATCAGTAGTT
1108 AAGT
1 AAGT
1112 GAAAAGAGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
25 4 0.09
26 16 0.35
27 1 0.02
28 1 0.02
29 21 0.46
30 3 0.07
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (28 bp):
AAGTAAAGTAATCAGTAAATCAGTAGTT
Found at i:1526 original size:22 final size:21
Alignment explanation
Indices: 1452--1685 Score: 147
Period size: 22 Copynumber: 10.8 Consensus size: 21
1442 AATGGTAATT
*
1452 AGTAATCAGTAAAAAGCAAGAA
1 AGTAATCAGTAAAAAGTAA-AA
* *
1474 GGTAATCA--ACAAGAGTAACATA
1 AGTAATCAGTA-AAAAGTAA-A-A
*
1496 A-TAAGCAGTAAAAAGTAAAA
1 AGTAATCAGTAAAAAGTAAAA
*
1516 TAGTAATCAGT-AAGAGTAAAAAA
1 -AGTAATCAGTAAAAAGT--AAAA
* *
1539 AGTAATAAGTAAGAAGTAAAA
1 AGTAATCAGTAAAAAGTAAAA
* * **
1560 GGAAATCAGT-AAGTGTAAAA
1 AGTAATCAGTAAAAAGTAAAA
* *
1580 AGGTGATCAGTAAAGAGTAAAA
1 A-GTAATCAGTAAAAAGTAAAA
*
1602 AGCTAATCAGCAAGAAA-TAAAA
1 AG-TAATCAGTAA-AAAGTAAAA
*
1624 AGGTAATCAGTAAAAAGCAAAA
1 A-GTAATCAGTAAAAAGTAAAA
* *
1646 GGCAATCAGTAAAAAAGTAAAAA
1 AGTAATCAGT-AAAAAGT-AAAA
1669 GAGTAATCAGTAAAAAG
1 -AGTAATCAGTAAAAAG
1686 AGAGAGAGAG
Statistics
Matches: 162, Mismatches: 32, Indels: 35
0.71 0.14 0.15
Matches are distributed among these distances:
20 9 0.06
21 49 0.30
22 74 0.46
23 22 0.14
24 8 0.05
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (21 bp):
AGTAATCAGTAAAAAGTAAAA
Found at i:1535 original size:21 final size:20
Alignment explanation
Indices: 1509--1873 Score: 115
Period size: 21 Copynumber: 17.3 Consensus size: 20
1499 AGCAGTAAAA
1509 AGTAAAATAGTAATCAGTAAG
1 AGTAAAA-AGTAATCAGTAAG
*
1530 AGTAAAAAAAGTAATAAGTAAG
1 AGT--AAAAAGTAATCAGTAAG
* *
1552 AAGTAAAAGGAAATCAGTAAG
1 -AGTAAAAAGTAATCAGTAAG
* *
1573 TGTAAAAAGGTGATCAGTAAAG
1 AGTAAAAA-GTAATCAGT-AAG
*
1595 AGTAAAAAGCTAATCAGCAAG
1 AGTAAAAAG-TAATCAGTAAG
* *
1616 AAATAAAAAGGTAATCAGTAAAA
1 -AGTAAAAA-GTAATCAGT-AAG
* * * *
1639 AGCAAAAGGCAATCAGTAAAAA
1 AGTAAAAAGTAATCAGT--AAG
1661 AGTAAAAAGAGTAATCAGT-A-
1 AGT-AAAA-AGTAATCAGTAAG
* *
1681 A--AAAGAG-AGA-GAG-AGAG
1 AGTAAAAAGTA-ATCAGTA-AG
1698 CAG-AAAATAGTAATCAGTAAAAG
1 -AGTAAAA-AGTAATCAGT--AAG
* * *
1721 AGTAAAATGGTAATTAGTAAA
1 AGTAAAA-AGTAATCAGTAAG
*
1742 AGTAAGAAGGTAATCAGTAAAG
1 AGTAA-AAAGTAATCAGT-AAG
* *
1764 AGTAAAATCCGTAA--AG-AATC
1 AGTAAAA--AGTAATCAGTAA-G
*
1784 AGT-AAAAGATAATCATTAAG
1 AGTAAAAAG-TAATCAGTAAG
* *
1804 AGTAAAACAGTAACCAATAAG
1 AGTAAAA-AGTAATCAGTAAG
* ** *
1825 AGCAAAGTGATAATTAGTAAG
1 AGTAAAAAG-TAATCAGTAAG
*
1846 AGTCAAATAGTAATCAGTAAAG
1 AGT-AAAAAGTAATCAGT-AAG
1868 AGTAAA
1 AGTAAA
1874 GGGTGATCAG
Statistics
Matches: 258, Mismatches: 47, Indels: 78
0.67 0.12 0.20
Matches are distributed among these distances:
15 3 0.01
16 4 0.02
17 4 0.02
18 4 0.02
19 8 0.03
20 18 0.07
21 99 0.38
22 76 0.29
23 33 0.13
24 9 0.03
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.18
Consensus pattern (20 bp):
AGTAAAAAGTAATCAGTAAG
Found at i:1695 original size:24 final size:22
Alignment explanation
Indices: 1622--1693 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
1612 CAAGAAATAA
1622 AAAG-GTAATCAGTAAAAAGCA-
1 AAAGAGTAATCAGTAAAAAG-AG
* *
1643 AAAG-GCAATCAGTAAAAAAGTAA
1 AAAGAGTAATCAGT-AAAAAG-AG
1666 AAAGAGTAATCAGTAAAAAGAG
1 AAAGAGTAATCAGTAAAAAGAG
*
1688 AGAGAG
1 AAAGAG
1694 AGAGCAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 12 0.28
22 13 0.30
23 10 0.23
24 8 0.19
ACGTcount: A:0.58, C:0.07, G:0.22, T:0.12
Consensus pattern (22 bp):
AAAGAGTAATCAGTAAAAAGAG
Found at i:1963 original size:29 final size:28
Alignment explanation
Indices: 1937--1999 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
1927 GTAAAAAGTG
1937 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
*** *
1965 GTAATTGGTAAAA-AGAGTAAGAAAAAA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
1992 GTAA-AAAT
1 GTAATAAAT
2000 GATAAAAGTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 1 0.04
27 17 0.61
28 10 0.36
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:2005 original size:29 final size:28
Alignment explanation
Indices: 1944--2007 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
1934 GTGGTAATAA
* *
1944 ATAAAAGAGAGTAAGAAAAGAGTAATTG
1 ATAAAAGAGAGTAAGAAAAAAGTAAATG
*
1972 GTAAAA-AGAGTAAGAAAAAAGTAAAAATG
1 ATAAAAGAGAGTAAGAAAAAAGT--AAATG
2001 ATAAAAG
1 ATAAAAG
2008 TAGCAAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 15 0.52
28 5 0.17
29 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (28 bp):
ATAAAAGAGAGTAAGAAAAAAGTAAATG
Done.