Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010391.1 Corchorus capsularis cultivar CVL-1 contig10412, 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: 3571
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Found at i:937 original size:45 final size:45
Alignment explanation
Indices: 865--951 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
855 GGATAGTTTG
*
865 AGCACTCGGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAA
1 AGCACTCGGCAATCATGGAGCCAAAGCTCTCCTTGATCTCCTTAA
* * * *
910 AGCATTCGGCAATCATGGATCCTAAGCTTTCCTTGATCTCCT
1 AGCACTCGGCAATCATGGAGCCAAAGCTCTCCTTGATCTCCT
952 GCACATTGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (45 bp):
AGCACTCGGCAATCATGGAGCCAAAGCTCTCCTTGATCTCCTTAA
Found at i:1490 original size:29 final size:29
Alignment explanation
Indices: 1453--1534 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
1443 GGAGTACCAC
*
1453 TGTGCCTTCTCGTGTACCTTTGTGTGTGT
1 TGTGCCTTCTCGTGTACCTTCGTGTGTGT
* *
1482 TGTGTCTTCTTGTGTACCTTC--GTGTG-
1 TGTGCCTTCTCGTGTACCTTCGTGTGTGT
*
1508 TGT--CTTCTCGTGTAGCTTCGTGTGTGT
1 TGTGCCTTCTCGTGTACCTTCGTGTGTGT
1535 CTTCTCGTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
24 14 0.31
26 8 0.18
27 5 0.11
29 18 0.40
ACGTcount: A:0.04, C:0.20, G:0.28, T:0.49
Consensus pattern (29 bp):
TGTGCCTTCTCGTGTACCTTCGTGTGTGT
Found at i:1507 original size:12 final size:12
Alignment explanation
Indices: 1487--1554 Score: 54
Period size: 12 Copynumber: 5.7 Consensus size: 12
1477 TGTGTTGTGT
* *
1487 CTTCTTGTGTAC
1 CTTCGTGTGTAG
1499 CTTCGTGTGT-G
1 CTTCGTGTGTAG
1510 TCTTC-TCGTGTAG
1 -CTTCGT-GTGTAG
1523 CTTCGTGTGT-G
1 CTTCGTGTGTAG
1534 TCTTC-TCGTGTAG
1 -CTTCGT-GTGTAG
1547 CTTCGTGT
1 CTTCGTGT
1555 CTGCTGGCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
11 3 0.07
12 39 0.85
13 4 0.09
ACGTcount: A:0.04, C:0.22, G:0.26, T:0.47
Consensus pattern (12 bp):
CTTCGTGTGTAG
Found at i:1511 original size:24 final size:24
Alignment explanation
Indices: 1482--1554 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
1472 TTGTGTGTGT
* *
1482 TGTGTCTTCTTGTGTACCTTCGTG
1 TGTGTCTTCTCGTGTAGCTTCGTG
1506 TGTGTCTTCTCGTGTAGCTTCGTG
1 TGTGTCTTCTCGTGTAGCTTCGTG
1530 TGTGTCTTCTCGTGTAGCTTCGTG
1 TGTGTCTTCTCGTGTAGCTTCGTG
1554 T
1 T
1555 CTGCTGGCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.04, C:0.21, G:0.27, T:0.48
Consensus pattern (24 bp):
TGTGTCTTCTCGTGTAGCTTCGTG
Found at i:1518 original size:14 final size:14
Alignment explanation
Indices: 1501--1544 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1491 TTGTGTACCT
1501 TCGTGTGTGTCTTC
1 TCGTGTGTGTCTTC
*
1515 TCGTGT-AG-C-T-
1 TCGTGTGTGTCTTC
1525 TCGTGTGTGTCTTC
1 TCGTGTGTGTCTTC
1539 TCGTGT
1 TCGTGT
1545 AGCTTCGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 6 0.25
11 2 0.08
12 2 0.08
13 2 0.08
14 12 0.50
ACGTcount: A:0.02, C:0.20, G:0.30, T:0.48
Consensus pattern (14 bp):
TCGTGTGTGTCTTC
Found at i:1598 original size:53 final size:53
Alignment explanation
Indices: 1532--2074 Score: 809
Period size: 53 Copynumber: 10.2 Consensus size: 53
1522 GCTTCGTGTG
* *
1532 TGTCTTCTCGTGTAGCTTCGTGTCTGCTGGCCTCGCCTCACTCCGGAGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* *
1585 TGTCTTCTTGTGTAGCTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * * * *
1638 -GTTTTCTCGTGTAGCTTTGTGTCTGCTGGCCGCGCCTCACTCCGGAGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * *
1690 TGTGTTCTCGTGCAGATTCGTGTCTGCTGGCCTCGCCTCACTCCGGAGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * *
1743 TGTCTTCTTGTGCAGATTCGTGTCTGCTGGCCTCGCCTCACGGCGGAGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* *
1796 TGTCTTCTCGTGCAGATTCGGGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * *
1849 TGTCTTCTCGTGCAGATTCGGGTCTGCTGGCCTCGCTTCACTGCGGAGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * *
1902 TATCTTCTCGTGCAGATTTGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
*
1955 TGTCTTCTCGTGTAGCTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * * *
2008 TGTCTTCCCCTGTAGTTTCGTGTCTGCTGGCCTCGCCTCACTGCAGAGGGCCTC
1 TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGA-GGCCTC
*
2062 TCTCTTCTCGTGT
1 TGTCTTCTCGTGT
2075 GCCTTTGTGT
Statistics
Matches: 453, Mismatches: 35, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
52 47 0.10
53 390 0.86
54 16 0.04
ACGTcount: A:0.07, C:0.33, G:0.28, T:0.32
Consensus pattern (53 bp):
TGTCTTCTCGTGTAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
Found at i:1899 original size:159 final size:159
Alignment explanation
Indices: 1532--2194 Score: 864
Period size: 159 Copynumber: 4.1 Consensus size: 159
1522 GCTTCGTGTG
* *
1532 TGTCTTCTCGTGTAGCTTCGTGTCTGCTGGCCTCGCCTCACTCCGGAGGCCTCTGTCTTCTTGTG
1 TGTCTTCTCGTGCAGATTCGTGTCTGCTGGCCTCGCCTCACTCCGGAGGCCTCTGTCTTCTTGTG
* * * *
1597 TAGCTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC-GTTTTCTCGTGTAGCTTTGTGTC
66 CAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGTAGCTTCGTGTC
* *
1661 TGCTGGCCGCGCCTCACTCCGGAGGCCTC
131 TGCTGGCCTCGCCTCACTGCGGAGGCCTC
*
1690 TGTGTTCTCGTGCAGATTCGTGTCTGCTGGCCTCGCCTCACTCCGGAGGCCTCTGTCTTCTTGTG
1 TGTCTTCTCGTGCAGATTCGTGTCTGCTGGCCTCGCCTCACTCCGGAGGCCTCTGTCTTCTTGTG
* * * *
1755 CAGATTCGTGTCTGCTGGCCTCGCCTCACGGCGGAGGCCTCTGTCTTCTCGTGCAGATTCGGGTC
66 CAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGTAGCTTCGTGTC
1820 TGCTGGCCTCGCCTCACTGCGGAGGCCTC
131 TGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * * * *
1849 TGTCTTCTCGTGCAGATTCGGGTCTGCTGGCCTCGCTTCACTGCGGAGGCCTCTATCTTCTCGTG
1 TGTCTTCTCGTGCAGATTCGTGTCTGCTGGCCTCGCCTCACTCCGGAGGCCTCTGTCTTCTTGTG
*
1914 CAGATTTGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGTAGCTTCGTGTC
66 CAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGTAGCTTCGTGTC
1979 TGCTGGCCTCGCCTCACTGCGGAGGCCTC
131 TGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * * * * * *
2008 TGTCTTCCCCTGTAGTTTCGTGTCTGCTGGCCTCGCCTCACTGCAGAGGGCCTCTCTCTTCTCGT
1 TGTCTTCTCGTGCAGATTCGTGTCTGCTGGCCTCGCCTCACTCCGGA-GG---C-CTC-TGTC-T
* *
2073 GTGCCTTTGTGTCTTCGCGTGTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTC
59 -T--C-TTGTG----C-AG-ATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTC
* * *
2138 CCGTGTAGCTTTGTGTCTGCTGGCCTCGCCTCACTGCAGAGGGCCTC
114 TCGTGTAGCTTCGTGTCTGCTGGCCTCGCCTCACTGCGGA-GGCCTC
2185 --TCTTCTCGTG
1 TGTCTTCTCGTG
2195 TACCTTCATG
Statistics
Matches: 445, Mismatches: 41, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
158 100 0.22
159 233 0.52
160 2 0.00
163 1 0.00
164 3 0.01
165 3 0.01
166 1 0.00
167 1 0.00
169 1 0.00
170 4 0.01
174 1 0.00
175 9 0.02
176 80 0.18
177 6 0.01
ACGTcount: A:0.06, C:0.33, G:0.28, T:0.32
Consensus pattern (159 bp):
TGTCTTCTCGTGCAGATTCGTGTCTGCTGGCCTCGCCTCACTCCGGAGGCCTCTGTCTTCTTGTG
CAGATTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGTAGCTTCGTGTC
TGCTGGCCTCGCCTCACTGCGGAGGCCTC
Found at i:2104 original size:70 final size:69
Alignment explanation
Indices: 2024--2155 Score: 212
Period size: 70 Copynumber: 1.9 Consensus size: 69
2014 CCCCTGTAGT
*
2024 TTCGTGTCTGCTGGCCTCGCCTCACTGCAGAGGGCCTCTCTCTTCTCGTGT-GCCTTTGTGTCTT
1 TTCGTGTCTGCTGGCCTCGCCTCACTGCAGA-GGCCTCTCTCTTCCCGTGTAG-CTTTGTGTCTT
2088 CGCGTG
64 CGCGTG
* *
2094 TTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCCCGTGTAGCTTTGTGTCT
1 TTCGTGTCTGCTGGCCTCGCCTCACTGCAGAGGCCTCTCTCTTCCCGTGTAGCTTTGTGTCT
2156 GCTGGCCTCG
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
69 27 0.47
70 31 0.53
ACGTcount: A:0.05, C:0.33, G:0.27, T:0.36
Consensus pattern (69 bp):
TTCGTGTCTGCTGGCCTCGCCTCACTGCAGAGGCCTCTCTCTTCCCGTGTAGCTTTGTGTCTTCG
CGTG
Found at i:2136 original size:49 final size:53
Alignment explanation
Indices: 2082--2185 Score: 144
Period size: 53 Copynumber: 2.0 Consensus size: 53
2072 TGTGCCTTTG
*
2082 TGTCTT-CGCGT-G-TTCGTGTCTGCTGGCCTCGCCTCACTGCGGA-GGCCTC
1 TGTCTTCCGCGTAGCTTCGTGTCTGCTGGCCTCGCCTCACTGCAGAGGGCCTC
* *
2131 TGTCTTCCCGTGTAGCTTTGTGTCTGCTGGCCTCGCCTCACTGCAGAGGGCCTC
1 TGTCTT-CCGCGTAGCTTCGTGTCTGCTGGCCTCGCCTCACTGCAGAGGGCCTC
2185 T
1 T
2186 CTTCTCGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
49 6 0.13
51 4 0.09
52 1 0.02
53 29 0.62
54 7 0.15
ACGTcount: A:0.06, C:0.34, G:0.29, T:0.32
Consensus pattern (53 bp):
TGTCTTCCGCGTAGCTTCGTGTCTGCTGGCCTCGCCTCACTGCAGAGGGCCTC
Done.