Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008208.1 Corchorus capsularis cultivar CVL-1 contig08229, 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: 2229
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Found at i:1516 original size:31 final size:31
Alignment explanation
Indices: 1480--1547 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1470 AAAAAGGGGC
1480 AATCAGCAATTAAAGTTCAATAAGAAA-AAGT
1 AATCAGCAATT-AAGTTCAATAAGAAAGAAGT
** *
1511 AATCAGTGATTAAGTTCAATAAGAAAGATGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
1542 AATCAG
1 AATCAG
1548 TAAAAGGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (31 bp):
AATCAGCAATTAAGTTCAATAAGAAAGAAGT
Found at i:1567 original size:22 final size:23
Alignment explanation
Indices: 1542--1601 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
1532 AGAAAGATGT
*
1542 AATCAGTAAAAG-GTAAAGCGGC
1 AATCAGTAAAAGAGTAAAGCGAC
* *
1564 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAGCGAC
1586 AATCAGT-AAAGAGTAA
1 AATCAGTAAAAGAGTAA
1602 TAAAAATCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.18
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAGCGAC
Found at i:1720 original size:54 final size:54
Alignment explanation
Indices: 1585--1891 Score: 386
Period size: 54 Copynumber: 5.8 Consensus size: 54
1575 AGTAAAGTGA
* *
1585 TAATC-AGTAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGT--AA-AAAT
1 TAATCAAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
*
1635 TAATCAAAGTCAAG-GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
1 TAATC-AAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAAT
* *
1690 TAATC-AGTAAAGAGTAATAGAAATCAGTAAATTAGTAATTAAGT--AA-AAAT
1 TAATCAAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
*
1740 TAATCAGAGTCAAG-GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
1 TAATCA-AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAAT
* *
1795 TAATC-AGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAGAGAT
1 TAATCAAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
* * *
1848 TAATCAGAGTCAA-AGTAATAGTAATCAATAAATCAATAATTAAG
1 TAATCA-AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAG
1892 AGTTAAAATG
Statistics
Matches: 225, Mismatches: 16, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
50 14 0.06
51 60 0.27
52 12 0.05
53 25 0.11
54 91 0.40
55 23 0.10
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (54 bp):
TAATCAAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
Found at i:1909 original size:105 final size:105
Alignment explanation
Indices: 1585--1891 Score: 533
Period size: 105 Copynumber: 2.9 Consensus size: 105
1575 AGTAAAGTGA
* *
1585 TAATCAGTAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGTAAAAATTAATCAAAGTCAAGG
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAATTAATCAGAGTCAAGG
1650 TAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
66 TAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
*
1690 TAATCAGTAAAGAGTAATAGAAATCAGTAAATTAGTAATTAAGTAAAAATTAATCAGAGTCAAGG
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAATTAATCAGAGTCAAGG
1755 TAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
66 TAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
1795 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCA
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGT-AAA-A-ATTAATCAGAGTCA
* * *
1860 AAGTAATAGTAATCAATAAATCAATAATTAAG
63 AGGTAATAGAAATCAGTAAATCAATAATTAAG
1892 AGTTAAAATG
Statistics
Matches: 192, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
105 145 0.76
106 3 0.02
107 1 0.01
108 43 0.22
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (105 bp):
TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAATTAATCAGAGTCAAGG
TAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
Found at i:2162 original size:66 final size:63
Alignment explanation
Indices: 2082--2228 Score: 165
Period size: 66 Copynumber: 2.3 Consensus size: 63
2072 AATAGCAGGC
* * *
2082 AATCAGTAAAAAGTAAAAAGGT-ACCTGA-AAGGGTAAAAAGAGTAATCAGTAAAAGAGTAAAAT
1 AATCAGTAAAAAGTAAAAAGGTAATC-AACAAGAGT-AAAAGAGTAATCAGT-AAA-AGT-AAAT
2145 AGT
61 AGT
* * *
2148 AATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAGTAAATAGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAAGAGTAATCAGTAAAAGTAAATAGT
*
2211 AATCAGT-AAGAGTAAAAA
1 AATCAGTAAAAAGTAAAAA
2229 A
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
62 9 0.13
63 14 0.20
64 3 0.04
65 3 0.04
66 35 0.49
67 7 0.10
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (63 bp):
AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAAGAGTAATCAGTAAAAGTAAATAGT
Found at i:2184 original size:43 final size:41
Alignment explanation
Indices: 2134--2227 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 41
2124 TAATCAGTAA
2134 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGA-AGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGT-AAAAGTAA-ATA-GTAATCAAC
* **
2177 AAGAGTAAAATAGTAGTCAGTAAAAGTAAATAGTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAGTAAATAGTAATCAAC
2218 AAGAGTAAAA
1 AAGAGTAAAA
2228 AA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 18 0.38
42 9 0.19
43 20 0.43
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.20
Consensus pattern (41 bp):
AAGAGTAAAATAGTAATCAGTAAAAGTAAATAGTAATCAAC
Found at i:2209 original size:20 final size:20
Alignment explanation
Indices: 2122--2226 Score: 95
Period size: 20 Copynumber: 5.0 Consensus size: 20
2112 GGGTAAAAAG
2122 AGTAATCAGTAAAAGAGTAAAAT
1 AGTAATCAGT-AAA-AGT-AAAT
2145 AGTAATCAGTAAAAAGTAAGA-
1 AGTAATCAGT-AAAAGTAA-AT
** *
2166 AGGTAATCAACAAGAGTAAAAT
1 A-GTAATCAGTAAAAGT-AAAT
*
2188 AGTAGTCAGTAAAAGTAAAT
1 AGTAATCAGTAAAAGTAAAT
*
2208 AGTAATCAGTAAGAGTAAA
1 AGTAATCAGTAAAAGTAAA
2227 AAA
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
20 21 0.30
21 20 0.29
22 14 0.20
23 14 0.20
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (20 bp):
AGTAATCAGTAAAAGTAAAT
Done.