Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014645.1 Corchorus capsularis cultivar CVL-1 contig14666, 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: 7306
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:1069 original size:22 final size:22
Alignment explanation
Indices: 1000--1082 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 22
990 TCATAGGAAG
* * **
1000 GTTATCAGAATTTTATAGCGAA
1 GTTATCAAAATTTCATAAAGAA
* * **
1022 CTTATCAAAATTTCATAATGTG
1 GTTATCAAAATTTCATAAAGAA
*
1044 GTTATCAAAATTTCTTAAAGAA
1 GTTATCAAAATTTCATAAAGAA
*
1066 GTTA-CGGAAATTTCATA
1 GTTATC-AAAATTTCATA
1083 GCTCATCGAT
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
21 1 0.02
22 45 0.98
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAAGAA
Found at i:1227 original size:22 final size:22
Alignment explanation
Indices: 1202--1250 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1192 AATAAAACGA
* *
1202 TTATCAAAATTGCATAGAGAGG
1 TTATCAAAATTACAAAGAGAGG
*
1224 TTATCAAAATTACAAAGTGAGG
1 TTATCAAAATTACAAAGAGAGG
1246 TTATC
1 TTATC
1251 GAATTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (22 bp):
TTATCAAAATTACAAAGAGAGG
Found at i:1673 original size:22 final size:22
Alignment explanation
Indices: 1658--1721 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
1648 CAAATTTTTT
1658 TAGTGTGGTTATCAAAATTTCA
1 TAGTGTGGTTATCAAAATTTCA
*
1680 TAGTGAGGTTATCAAAATTTCA
1 TAGTGTGGTTATCAAAATTTCA
*
1702 TAGAGTGGTTATCAAAATTT
1 TAGTGTGGTTATCAAAATTT
1722 TAATATGGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (22 bp):
TAGTGTGGTTATCAAAATTTCA
Found at i:1959 original size:22 final size:22
Alignment explanation
Indices: 1934--1977 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1924 TTTTTTTTTT
1934 TTTTCATCTCAAAATTTCATAG
1 TTTTCATCTCAAAATTTCATAG
** * *
1956 TTTTGTTTTCAAGATTTCATAG
1 TTTTCATCTCAAAATTTCATAG
1978 GGGGTTATCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (22 bp):
TTTTCATCTCAAAATTTCATAG
Found at i:1993 original size:21 final size:21
Alignment explanation
Indices: 1964--2039 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
1954 AGTTTTGTTT
*
1964 TCAAGATTTCATAGGGGGTTA
1 TCAAAATTTCATAGGGGGTTA
*
1985 TCAAAATTTCATAGTGTGG-T-
1 TCAAAATTTCATAG-GGGGTTA
* * *
2005 TCAAAAATTAATAGGGAGATTA
1 TCAAAATTTCATAGGG-GGTTA
*
2027 ACAAAATTTCATA
1 TCAAAATTTCATA
2040 ATGAGATTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
19 1 0.02
20 13 0.31
21 15 0.36
22 13 0.31
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (21 bp):
TCAAAATTTCATAGGGGGTTA
Found at i:2204 original size:31 final size:29
Alignment explanation
Indices: 2169--2252 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
2159 TACATTTTAC
* *
2169 AAGTTCATGGGGCAAAATTTCCTGAATTTGG
1 AAGTTCATGGGGTAAAATGTCCTG-ATTT-G
* *
2200 AAGTTTAGGGGGGTAAAATGTCCTGATTTG
1 AAGTTCA-TGGGGTAAAATGTCCTGATTTG
*
2230 AAGTTCATGGGGTAAAACGTCCT
1 AAGTTCATGGGGTAAAATGTCCT
2253 TTGCGTAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
29 14 0.31
30 7 0.16
31 10 0.22
32 14 0.31
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (29 bp):
AAGTTCATGGGGTAAAATGTCCTGATTTG
Found at i:2562 original size:22 final size:22
Alignment explanation
Indices: 2513--2578 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
2503 GGGAGATTAA
* * * *
2513 TTCATAGAGAGTTTATCGAGAT
1 TTCATAGAAAGGTTATCAAAAT
*
2535 TCCATAGAAAGGTTATCAAAAT
1 TTCATAGAAAGGTTATCAAAAT
2557 TTCATAGAAAGGTTATCAAAAT
1 TTCATAGAAAGGTTATCAAAAT
2579 CTTAATAGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (22 bp):
TTCATAGAAAGGTTATCAAAAT
Found at i:3299 original size:3 final size:3
Alignment explanation
Indices: 3281--3314 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
3271 AGGCTGCAGG
* *
3281 TAA TAA TAG TAT TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3315 CCTTTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3379 original size:2 final size:2
Alignment explanation
Indices: 3372--3412 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3362 CTCCCCATAC
3372 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3413 GTGTGTGTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4975 original size:17 final size:17
Alignment explanation
Indices: 4953--4986 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4943 AAAATATAAA
4953 CAAATTAAGTCTCTCAT
1 CAAATTAAGTCTCTCAT
4970 CAAATTAAGTCTCTCAT
1 CAAATTAAGTCTCTCAT
4987 GTATTAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (17 bp):
CAAATTAAGTCTCTCAT
Found at i:5931 original size:116 final size:114
Alignment explanation
Indices: 5741--5952 Score: 300
Period size: 116 Copynumber: 1.8 Consensus size: 114
5731 ATAAAATCTT
*
5741 AATTTTAATTTGGGATAAACTTAATGAATTAGTTATATATTTTATTTCTAAAACCCTATATGACA
1 AATTTTAATTTGGGATAAACTTAATGAATTAGTTATATATTTAATTTCTAAAACCCTATA-GACA
*
5806 ATAAGTTATTAATCATGAAATATTACCCTTAATAAATAAAAATAACACCAA
65 ATAAATTATTAATCATGAAAT-TTACCCTTAATAAATAAAAATAACACCAA
* * * * *
5857 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTAATTTCTAAAATCCTATA-AC
1 AATTTTAATTT-GGGATAAACTTAATG-AATTAGTTATATATTTAATTTCTAAAACCCTATAGAC
**
5921 AATAAATTATTAATTTTGAAATTTACCCTTAA
64 AATAAATTATTAATCATGAAATTTACCCTTAA
5953 AATAAGAATA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
115 10 0.12
116 32 0.38
117 13 0.15
118 30 0.35
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (114 bp):
AATTTTAATTTGGGATAAACTTAATGAATTAGTTATATATTTAATTTCTAAAACCCTATAGACAA
TAAATTATTAATCATGAAATTTACCCTTAATAAATAAAAATAACACCAA
Done.