Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007155.1 Corchorus capsularis cultivar CVL-1 contig07176, 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: 24720
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Found at i:1621 original size:27 final size:27
Alignment explanation
Indices: 1584--1750 Score: 271
Period size: 27 Copynumber: 6.2 Consensus size: 27
1574 GTCTTCTCTC
* *
1584 CCCACTTCGACCCCAGAAGTGGATCAT
1 CCCACTTCGACCCCAGCAGTGGATCCT
*
1611 CCCACTTCGACCCCAGCATTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
* *
1638 CCTACTTCGACCCCTGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
1665 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
*
1692 CCTACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
*
1719 CCCACTTCGATCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
1746 CCCAC
1 CCCAC
1751 CTCGCCTATG
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 129 1.00
ACGTcount: A:0.19, C:0.43, G:0.17, T:0.21
Consensus pattern (27 bp):
CCCACTTCGACCCCAGCAGTGGATCCT
Found at i:2580 original size:17 final size:17
Alignment explanation
Indices: 2558--2592 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2548 GAAAAAGTGG
2558 ATTCTTGGTGGCACATT
1 ATTCTTGGTGGCACATT
* *
2575 ATTCTTGTTGGCATATT
1 ATTCTTGGTGGCACATT
2592 A
1 A
2593 ACATTATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (17 bp):
ATTCTTGGTGGCACATT
Found at i:4279 original size:24 final size:24
Alignment explanation
Indices: 4252--4320 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
4242 CCTAAATGGT
*
4252 GGCGTCTAGACGCCACTATTT-CG
1 GGCGTCTAGACGCCACTATTTAAG
* *
4275 CGGCGTCTCGACGCCACCATTTAAG
1 -GGCGTCTAGACGCCACTATTTAAG
* *
4300 GGCGTCTGGACGCCGCTATTT
1 GGCGTCTAGACGCCACTATTT
4321 GCAATTGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 37 0.97
25 1 0.03
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.25
Consensus pattern (24 bp):
GGCGTCTAGACGCCACTATTTAAG
Found at i:6197 original size:19 final size:20
Alignment explanation
Indices: 6173--6215 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
6163 GAGAAGGAAA
* *
6173 AAGAAAATAAAAGGAAAA-G
1 AAGAAAAGAAAAAGAAAAGG
6192 AAGAAAAGAAAAAGAAAAGG
1 AAGAAAAGAAAAAGAAAAGG
6212 AAGA
1 AAGA
6216 GGAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (20 bp):
AAGAAAAGAAAAAGAAAAGG
Found at i:6223 original size:25 final size:23
Alignment explanation
Indices: 6160--6223 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 23
6150 AAGAACGAAG
* * *
6160 AAGGAGAAGGAAAAAGAAAATAA
1 AAGGAAAAGAAAAAAGAAAAGAA
6183 AAGGAAAAGAAGAAAAGAAAAAGAA
1 AAGGAAAAGAA-AAAAG-AAAAGAA
*
6208 AAGGAAGAGGAAAAAA
1 AAGGAA-AAGAAAAAA
6224 ATAATTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 9 0.26
24 5 0.15
25 16 0.47
26 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.02
Consensus pattern (23 bp):
AAGGAAAAGAAAAAAGAAAAGAA
Found at i:8934 original size:24 final size:24
Alignment explanation
Indices: 8911--9013 Score: 145
Period size: 24 Copynumber: 4.2 Consensus size: 24
8901 TGACACGTGG
* *
8911 CATGCCACGTGTACCAAAAGGTGG
1 CATGTCACGTGTACCAAAAGGTGA
8935 CACT-TCACGTGTACCAAAAGGTGA
1 CA-TGTCACGTGTACCAAAAGGTGA
8959 CATGTGGCACGTGTACCAAAAGGTGA
1 CATGT--CACGTGTACCAAAAGGTGA
*
8985 CACGTCACGTGTACCAAAAGGTGA
1 CATGTCACGTGTACCAAAAGGTGA
9009 CATGT
1 CATGT
9014 GGCACGTCAC
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
23 1 0.01
24 46 0.65
25 1 0.01
26 23 0.32
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.19
Consensus pattern (24 bp):
CATGTCACGTGTACCAAAAGGTGA
Found at i:8981 original size:50 final size:50
Alignment explanation
Indices: 8916--9020 Score: 192
Period size: 50 Copynumber: 2.1 Consensus size: 50
8906 CGTGGCATGC
* *
8916 CACGTGTACCAAAAGGTGGCACTTCACGTGTACCAAAAGGTGACATGTGG
1 CACGTGTACCAAAAGGTGACACGTCACGTGTACCAAAAGGTGACATGTGG
8966 CACGTGTACCAAAAGGTGACACGTCACGTGTACCAAAAGGTGACATGTGG
1 CACGTGTACCAAAAGGTGACACGTCACGTGTACCAAAAGGTGACATGTGG
9016 CACGT
1 CACGT
9021 CACGTGTACC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (50 bp):
CACGTGTACCAAAAGGTGACACGTCACGTGTACCAAAAGGTGACATGTGG
Found at i:9023 original size:31 final size:31
Alignment explanation
Indices: 8985--9140 Score: 185
Period size: 31 Copynumber: 5.2 Consensus size: 31
8975 CAAAAGGTGA
8985 CACGTCACGTGTACCAAAAGGTGACATGTGG
1 CACGTCACGTGTACCAAAAGGTGACATGTGG
9016 CACGTCACGTGTACCAAAAGGTGACATGTGG
1 CACGTCACGTGTACCAAAAGGTGACATGTGG
* * *
9047 CACGTCATGTGTTCCAAAAGGTGACATGTGT
1 CACGTCACGTGTACCAAAAGGTGACATGTGG
* * * *
9078 CACGCCACATGTACCAAAA-GTGACACGTGA
1 CACGTCACGTGTACCAAAAGGTGACATGTGG
* * * *
9108 CATGCCACGTGCA-CAAAA-G-GACATGTGT
1 CACGTCACGTGTACCAAAAGGTGACATGTGG
9136 CACGT
1 CACGT
9141 GTCATTTTTT
Statistics
Matches: 109, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
28 10 0.09
29 6 0.06
30 19 0.17
31 74 0.68
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (31 bp):
CACGTCACGTGTACCAAAAGGTGACATGTGG
Found at i:9091 original size:62 final size:61
Alignment explanation
Indices: 8931--9102 Score: 195
Period size: 62 Copynumber: 3.0 Consensus size: 61
8921 GTACCAAAAG
*
8931 GTGGCACTTCACGTGTACCAAAAGGTGACATGTGGCACG-----TGTACCAAAA--G----
1 GTGGCACGTCACGTGTACCAAAAGGTGACATGTGGCACGCCACATGTACCAAAAGTGACAT
* * *
8981 GTGACACGTCACGTGTACCAAAAGGTGACATGTGGCACGTCACGTGTACCAAAAGGTGACAT
1 GTGGCACGTCACGTGTACCAAAAGGTGACATGTGGCACGCCACATGTACCAAAA-GTGACAT
* * *
9043 GTGGCACGTCATGTGTTCCAAAAGGTGACATGTGTCACGCCACATGTACCAAAAGTGACA
1 GTGGCACGTCACGTGTACCAAAAGGTGACATGTGGCACGCCACATGTACCAAAAGTGACA
9103 CGTGACATGC
Statistics
Matches: 102, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
50 37 0.36
55 10 0.10
58 1 0.01
61 6 0.06
62 48 0.47
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (61 bp):
GTGGCACGTCACGTGTACCAAAAGGTGACATGTGGCACGCCACATGTACCAAAAGTGACAT
Found at i:9661 original size:2 final size:2
Alignment explanation
Indices: 9656--9709 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
9646 AATAACACAC
* *
9656 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9698 AT AT AT -T AT AT A
1 AT AT AT AT AT AT A
9710 GATAAGTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10077 original size:22 final size:21
Alignment explanation
Indices: 10044--10101 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
10034 TCTCTATGTG
*
10044 GTTATCAAAATTTTATAGTG-C
1 GTTAACAAAATTTTA-AGTGTC
*
10065 GATTAACAAAATTTCAAGTGTC
1 G-TTAACAAAATTTTAAGTGTC
*
10087 GTTACCAAAATTTTA
1 GTTAACAAAATTTTA
10102 CAGGTAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (21 bp):
GTTAACAAAATTTTAAGTGTC
Found at i:10272 original size:22 final size:22
Alignment explanation
Indices: 10232--10291 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
10222 TTTTAGAGGG
* *
10232 AGGTTATCAAACTTGCATAGTGT
1 AGGTTATCAAAATTTCATAG-GT
10255 -GGTTA-CAAAAATTTCATAGGT
1 AGGTTATC-AAAATTTCATAGGT
10276 AGGTTATCAAAATTTC
1 AGGTTATCAAAATTTC
10292 GTAGAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 3 0.09
22 28 0.88
23 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGT
Found at i:11403 original size:22 final size:22
Alignment explanation
Indices: 11375--11421 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
11365 GTCATGTGAT
11375 TATATAGTATACCATGAAACTA
1 TATATAGTATACCATGAAACTA
* *
11397 TATATAGTATACCATGGAATTA
1 TATATAGTATACCATGAAACTA
11419 TAT
1 TAT
11422 GGTGTACGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (22 bp):
TATATAGTATACCATGAAACTA
Found at i:22453 original size:26 final size:27
Alignment explanation
Indices: 22408--22459 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
22398 TTTTTCAAAT
22408 ATATTTCTAAATTGTCATTATTAAAAA
1 ATATTTCTAAATTGTCATTATTAAAAA
* *
22435 ATATTT-TAATTTTTCATTATTAAAA
1 ATATTTCTAAATTGTCATTATTAAAA
22460 TAATGGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (27 bp):
ATATTTCTAAATTGTCATTATTAAAAA
Done.