Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010052.1 Corchorus capsularis cultivar CVL-1 contig10073, 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: 8839
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Found at i:6661 original size:22 final size:22
Alignment explanation
Indices: 6636--6713 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
6626 AATTTATATT
*
6636 AAATTTTGATAATTACACCATA
1 AAATTTTGATAATCACACCATA
* *
6658 AAA-TTT--TAATGACGTCCATA
1 AAATTTTGATAATCAC-ACCATA
* *
6678 TGAAATTTTGATAATCACACTATG
1 --AAATTTTGATAATCACACCATA
6702 AAATTTTGATAA
1 AAATTTTGATAA
6714 CGATATCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
19 6 0.14
20 5 0.11
21 3 0.07
22 18 0.41
23 3 0.07
24 3 0.07
25 6 0.14
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAATCACACCATA
Found at i:6882 original size:21 final size:21
Alignment explanation
Indices: 6856--6912 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
6846 CAAAACTATG
*
6856 AAAATTTAATAAGCTATTTAT
1 AAAATTTAATAAGCTACTTAT
* * *
6877 AAAATTTTGATAACCTCCTTAT
1 AAAA-TTTAATAAGCTACTTAT
*
6899 GAAATTTAATAAGC
1 AAAATTTAATAAGC
6913 ACAAAATGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (21 bp):
AAAATTTAATAAGCTACTTAT
Found at i:6992 original size:44 final size:44
Alignment explanation
Indices: 6944--7042 Score: 180
Period size: 44 Copynumber: 2.2 Consensus size: 44
6934 CTCCATGTGG
*
6944 AATGTTGGTAAGCACATTACAAAATTTTGATCACCTTCCTATAA
1 AATGTTGGTAAGCACACTACAAAATTTTGATCACCTTCCTATAA
*
6988 AATGTTGGTAAGCACACTACAAAATTTTGATCACTTTCCTATAA
1 AATGTTGGTAAGCACACTACAAAATTTTGATCACCTTCCTATAA
7032 AATGTTGGTAA
1 AATGTTGGTAA
7043 TCACTATCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (44 bp):
AATGTTGGTAAGCACACTACAAAATTTTGATCACCTTCCTATAA
Found at i:7011 original size:22 final size:22
Alignment explanation
Indices: 6944--7012 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
6934 CTCCATGTGG
*
6944 AATGTTGGTAAGCACATTACAA
1 AATGTTGGTAAGCACACTACAA
* * * * * *
6966 AATTTTGATCACCTTC-CTATAA
1 AATGTTGGTAAGC-ACACTACAA
6988 AATGTTGGTAAGCACACTACAA
1 AATGTTGGTAAGCACACTACAA
7010 AAT
1 AAT
7013 TTTGATCACT
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (22 bp):
AATGTTGGTAAGCACACTACAA
Found at i:7033 original size:22 final size:21
Alignment explanation
Indices: 6964--7034 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 21
6954 AGCACATTAC
6964 AAAATTTTGATCACCTTCCTAT
1 AAAATTTTGATCA-CTTCCTAT
* * * * *
6986 AAAATGTTGGTAAGC-ACACTAC
1 AAAATTTTGATCA-CTTC-CTAT
7008 AAAATTTTGATCACTTTCCTAT
1 AAAATTTTGATCAC-TTCCTAT
7030 AAAAT
1 AAAAT
7035 GTTGGTAATC
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 2 0.06
22 32 0.91
23 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (21 bp):
AAAATTTTGATCACTTCCTAT
Found at i:7046 original size:25 final size:25
Alignment explanation
Indices: 6973--7047 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 25
6963 CAAAATTTTG
*
6973 ATCACCTTCCTATAAAATGTTGGTA
1 ATCACTTTCCTATAAAATGTTGGTA
* * * *
6998 AGCAC---ACTACAAAAT-TT--TG
1 ATCACTTTCCTATAAAATGTTGGTA
7017 ATCACTTTCCTATAAAATGTTGGTA
1 ATCACTTTCCTATAAAATGTTGGTA
7042 ATCACT
1 ATCACT
7048 ATCAAATTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
19 5 0.14
21 2 0.06
22 16 0.44
23 2 0.06
25 11 0.31
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (25 bp):
ATCACTTTCCTATAAAATGTTGGTA
Found at i:7086 original size:23 final size:22
Alignment explanation
Indices: 7059--7169 Score: 86
Period size: 22 Copynumber: 5.1 Consensus size: 22
7049 TCAAATTGTG
*
7059 AAACCTCATAATAAAATTTTGAT
1 AAACCTC-TTATAAAATTTTGAT
*
7082 AAACCTCTTTGTAAAATTTTGAT
1 AAACCTC-TTATAAAATTTTGAT
* * *
7105 AACCCTCTTTTGAAATTTTGAT
1 AAACCTCTTATAAAATTTTGAT
* *
7127 -AA--TCTCATGAAATTTTGAT
1 AAACCTCTTATAAAATTTTGAT
* *
7146 -AACCATCTCATGAAATTTTGAT
1 AAACC-TCTTATAAAATTTTGAT
7168 AA
1 AA
7170 CTACGCTATC
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
19 17 0.23
21 1 0.01
22 30 0.40
23 27 0.36
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (22 bp):
AAACCTCTTATAAAATTTTGAT
Found at i:7120 original size:22 final size:22
Alignment explanation
Indices: 7072--7170 Score: 107
Period size: 22 Copynumber: 4.6 Consensus size: 22
7062 CCTCATAATA
* *
7072 AAATTTTGATAAACCTCT-TTG
1 AAATTTTGATAACCCTCTCATG
**
7093 TAAAATTTTGATAACCCTCTTTTG
1 --AAATTTTGATAACCCTCTCATG
7117 AAATTTTGATAA---TCTCATG
1 AAATTTTGATAACCCTCTCATG
*
7136 AAATTTTGATAACCATCTCATG
1 AAATTTTGATAACCCTCTCATG
7158 AAATTTTGATAAC
1 AAATTTTGATAAC
7171 TACGCTATCA
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
19 17 0.25
22 32 0.46
23 17 0.25
24 3 0.04
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCCTCTCATG
Found at i:7183 original size:22 final size:22
Alignment explanation
Indices: 7117--7193 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
7107 CCCTCTTTTG
*
7117 AAATTTTGATAA-T--CTCATG
1 AAATTTTGATAACTAGCTCATC
* * *
7136 AAATTTTGATAACCATCTCATG
1 AAATTTTGATAACTAGCTCATC
7158 AAATTTTGATAACTACGCT-ATC
1 AAATTTTGATAACTA-GCTCATC
*
7180 AAATTTTCATAACT
1 AAATTTTGATAACT
7194 TGTCTCTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.24
22 35 0.71
23 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACTAGCTCATC
Found at i:7288 original size:22 final size:22
Alignment explanation
Indices: 7270--7325 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
7260 CATACTATTA
7270 AATTTTGATAACTCCACTATGT
1 AATTTTGATAACTCCACTATGT
**
7292 AATTACGATAACCTCCA-TATGT
1 AATTTTGATAA-CTCCACTATGT
7314 AATTTTGATAAC
1 AATTTTGATAAC
7326 AAAACTATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 23 0.79
23 5 0.17
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACTCCACTATGT
Found at i:8112 original size:14 final size:14
Alignment explanation
Indices: 8093--8121 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8083 TTTCGTATAG
8093 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
8107 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
8121 T
1 T
8122 ATATAATCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.41, T:0.52
Consensus pattern (14 bp):
TGTGTGTGTGTGTA
Found at i:8231 original size:19 final size:21
Alignment explanation
Indices: 8183--8233 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
8173 ATAATCCGAT
**
8183 TTAAATTGAAAAATTTTATAA
1 TTAAATTTTAAAATTTTATAA
*
8204 TTAATTTTTAAAATTTT-T-A
1 TTAAATTTTAAAATTTTATAA
8223 TTAAATTTTAA
1 TTAAATTTTAA
8234 TAATGGCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 11 0.42
20 1 0.04
21 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAAATTTTAAAATTTTATAA
Found at i:8231 original size:20 final size:21
Alignment explanation
Indices: 8192--8233 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
8182 TTTAAATTGA
8192 AAAATTTTATAATTAATTTTT
1 AAAATTTTATAATTAATTTTT
*
8213 AAAATTTT-T-ATTAAATTTT
1 AAAATTTTATAATTAATTTTT
8232 AA
1 AA
8234 TAATGGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAAATTTTATAATTAATTTTT
Found at i:8377 original size:32 final size:32
Alignment explanation
Indices: 8341--8407 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
8331 TTAATAATGT
* *
8341 CAATTTAGAAATTTATATGAAACTAAAGGGTA
1 CAATTTAGAAATATATATGAAAATAAAGGGTA
*
8373 CAA-TTGGAAATATATATGAAAATAAAGGGTA
1 CAATTTAGAAATATATATGAAAATAAAGGGTA
8404 CAAT
1 CAAT
8408 CGGAAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.28
Consensus pattern (32 bp):
CAATTTAGAAATATATATGAAAATAAAGGGTA
Found at i:8383 original size:31 final size:31
Alignment explanation
Indices: 8348--8413 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
8338 TGTCAATTTA
* * *
8348 GAAATTTATATGAAACTAAAGGGTACAATTG
1 GAAATATATATGAAAATAAAGGGTACAATCG
8379 GAAATATATATGAAAATAAAGGGTACAATCG
1 GAAATATATATGAAAATAAAGGGTACAATCG
8410 GAAA
1 GAAA
8414 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.20, T:0.24
Consensus pattern (31 bp):
GAAATATATATGAAAATAAAGGGTACAATCG
Found at i:8467 original size:2 final size:2
Alignment explanation
Indices: 8462--8489 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8452 ATATATATAG
8462 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
8490 CTTATACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:8663 original size:13 final size:13
Alignment explanation
Indices: 8641--8670 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
8631 TATATTTAGA
8641 ATTT-TAAATAAT
1 ATTTATAAATAAT
8653 ATTTATAAATAAT
1 ATTTATAAATAAT
8666 ATTTA
1 ATTTA
8671 CAACATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTATAAATAAT
Done.