Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010730.1 Corchorus capsularis cultivar CVL-1 contig10751, 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: 27318
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1245 original size:45 final size:45
Alignment explanation
Indices: 1194--1279 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
1184 TAATAGAGTA
*
1194 GTGGAATTACTAAAAGATCTCTAC-CCTGAATTAATGATGAGTTGG
1 GTGGAATTACTAAAAGATCCCTACGCC-GAATTAATGATGAGTTGG
*
1239 GTGGAATTACTAAAAGATCCCTACGCCGGATTAATGATGAG
1 GTGGAATTACTAAAAGATCCCTACGCCGAATTAATGATGAG
1280 CTGGAGAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
45 36 0.95
46 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACGCCGAATTAATGATGAGTTGG
Found at i:1721 original size:12 final size:11
Alignment explanation
Indices: 1704--1736 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1694 AAGAATTAGT
1704 TTATATATATAA
1 TTATATATAT-A
1716 TTATATATAT-
1 TTATATATATA
1726 TTATATATATA
1 TTATATATATA
1737 CTACGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATATATATA
Found at i:1748 original size:22 final size:21
Alignment explanation
Indices: 1698--1749 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
1688 TAAATAAAGA
*
1698 ATTAGTTTATATATATAATTAT
1 ATTA-TTTATATATATAACTAT
1720 ATATATTTATATATAT-ACTACGT
1 AT-TATTTATATATATAACTA--T
1743 ATTATTT
1 ATTATTT
1750 GAATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.12
22 18 0.69
23 5 0.19
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTATTTATATATATAACTAT
Found at i:2039 original size:168 final size:165
Alignment explanation
Indices: 1813--2244 Score: 482
Period size: 168 Copynumber: 2.6 Consensus size: 165
1803 AGAGAACTAA
* * *
1813 TTTTTTTTTTCGTCTTTTACC-ACTTGACAGATTACTTAAATAT-CTCAGCTTTTGATTCTTGAG
1 TTTTTTTTTTCGTCTTTT-CCTACTTGGCAGATTACTTAAATGTCCT-AACTTTTGATTCTTGAG
* * *
1876 GGGATTAAATAACTAGACTTTTTGGTCATTTCTCAATTGACTTTAACAGAGTAGTGGAATTACTA
64 GGGATTAAATAACTA-ACTTTTTGGTCATTTCTCAATTGACTTGAACAGAGTAGTGAAATTAATA
* * * * ** *
1941 AAAGATCTCTACCAAGGCTTGCTTTTGGAGTTAGAAAAC
128 AAAGATCCCCACCAAGGATTGATGAT-GAGCTAGAAAAC
* *
1980 TTTTTTTTTTGTGTCTTTTCCTATTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGG
1 TTTTTTTTTT-CGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGG
* * * * *
2045 GGATTAAATAAGTAATCATTTTGGTCATTTCTCAATGGACTTGAATAGAGTGGTGAAATTAATAA
65 GGATTAAATAACTAA-CTTTTTGGTCATTTCTCAATTGACTTGAACAGAGTAGTGAAATTAATAA
* *
2110 AAGATCCCCATCAAGGATTGATGATGAGCTAGAGAAC
129 AAGATCCCCACCAAGGATTGATGATGAGCTAGAAAAC
** * * * **
2147 TAATCTTTTTCGTCTTTACCTACTTGGTAGAAAACTTAAATGTCCTAA-----GATTCTTGAGGG
1 TTTTTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGG
*
2207 GATTAAATAACTAAACTTTTTAGTCATTTCTCAATTGA
66 GATTAAATAACT-AACTTTTTGGTCATTTCTCAATTGA
2245 TAAATGACTC
Statistics
Matches: 225, Mismatches: 35, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
161 43 0.19
162 2 0.01
166 32 0.14
167 30 0.13
168 116 0.52
169 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (165 bp):
TTTTTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGG
GATTAAATAACTAACTTTTTGGTCATTTCTCAATTGACTTGAACAGAGTAGTGAAATTAATAAAA
GATCCCCACCAAGGATTGATGATGAGCTAGAAAAC
Found at i:17927 original size:30 final size:30
Alignment explanation
Indices: 17891--17956 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
17881 AAAGGATCGA
* *
17891 ATGGCCGGTTATGG-TGCGATGGCCCGTGCG
1 ATGGCCGGTTATGGCCG-GATGGCCCGCGCG
* *
17921 ATGGCCGGTTCTGGCCGGATGGCTCGCGCG
1 ATGGCCGGTTATGGCCGGATGGCCCGCGCG
17951 ATGGCC
1 ATGGCC
17957 CGTGCGGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.09, C:0.27, G:0.42, T:0.21
Consensus pattern (30 bp):
ATGGCCGGTTATGGCCGGATGGCCCGCGCG
Found at i:23522 original size:28 final size:28
Alignment explanation
Indices: 23490--23544 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
23480 TTTGCATCCA
*
23490 GGGGCATTTTGGTCATTTTTAAGTTCAG
1 GGGGCATTTTAGTCATTTTTAAGTTCAG
23518 GGGGCATTTTAGTCATTTTTAAGTTCA
1 GGGGCATTTTAGTCATTTTTAAGTTCA
23545 CCTTCAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.25, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTAGTCATTTTTAAGTTCAG
Done.