Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022187.1 Corchorus olitorius cultivar O-4 contig22220, 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: 32813
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2980 original size:11 final size:11
Alignment explanation
Indices: 2964--2989 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2954 CTAGCCCTAA
2964 AAAACTAGAAG
1 AAAACTAGAAG
2975 AAAACTAGAAG
1 AAAACTAGAAG
2986 AAAA
1 AAAA
2990 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:7729 original size:120 final size:120
Alignment explanation
Indices: 7511--7744 Score: 441
Period size: 120 Copynumber: 1.9 Consensus size: 120
7501 CAAGAACCAG
7511 TTCTACCATCTTCAAGCCCAAAAATGCCGTTGAAGTCACTGCACGAATTCAGCAAAAATTCAGGA
1 TTCTACCATCTTCAAGCCCAAAAATGCCGTTGAAGTCACTGCACGAATTCAGCAAAAATTCAGGA
*
7576 TCCTATTTTAACTTGGATTCTACTCTAGGATGACTTTTAATCCAACTTGACCCAA
66 TCCTATTTTAACTTGGACTCTACTCTAGGATGACTTTTAATCCAACTTGACCCAA
* *
7631 TTCTGCCATCTTCAAGCCCAAAAATGCCGTTGAAGTCACTGCACGAGTTCAGCAAAAATTCAGGA
1 TTCTACCATCTTCAAGCCCAAAAATGCCGTTGAAGTCACTGCACGAATTCAGCAAAAATTCAGGA
7696 TCCTATTTTAACTTGGACTCTACTCTAGGATGACTTTTAATCCAACTTG
66 TCCTATTTTAACTTGGACTCTACTCTAGGATGACTTTTAATCCAACTTG
7745 GAGTCCAAGT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 111 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (120 bp):
TTCTACCATCTTCAAGCCCAAAAATGCCGTTGAAGTCACTGCACGAATTCAGCAAAAATTCAGGA
TCCTATTTTAACTTGGACTCTACTCTAGGATGACTTTTAATCCAACTTGACCCAA
Found at i:16052 original size:4 final size:4
Alignment explanation
Indices: 16043--16092 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
16033 TTTATTTTTT
* * *
16043 TAAA TAAA TAAA TTAA TATA TATAA TACTA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TA-AA TA-AA TAAA TAAA TAAA TAAA TAAA
16093 AATTAAAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
4 32 0.84
5 6 0.16
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (4 bp):
TAAA
Found at i:17341 original size:19 final size:19
Alignment explanation
Indices: 17317--17353 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17307 TGCAAGGTTG
17317 AATGTTCTTAGTGATCATA
1 AATGTTCTTAGTGATCATA
*
17336 AATGTTCTTAGTGTTCAT
1 AATGTTCTTAGTGATCAT
17354 GGTGAGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (19 bp):
AATGTTCTTAGTGATCATA
Found at i:18329 original size:20 final size:21
Alignment explanation
Indices: 18304--18344 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
18294 AAAATTAAAA
18304 GGGAAAG-AAATCTTTATTGC
1 GGGAAAGAAAATCTTTATTGC
18324 GGGAAAGAAAATCTTTATTGC
1 GGGAAAGAAAATCTTTATTGC
18345 TAGGTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
GGGAAAGAAAATCTTTATTGC
Found at i:18728 original size:30 final size:30
Alignment explanation
Indices: 18694--18760 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
18684 AATAACACAT
18694 ATAATCATATATTCATTCTAAAACCTTGTC
1 ATAATCATATATTCATTCTAAAACCTTGTC
*
18724 ATAATCATATATTCATTCTAAAATCTTGTC
1 ATAATCATATATTCATTCTAAAACCTTGTC
18754 ATAATCA
1 ATAATCA
18761 ATGCTTAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (30 bp):
ATAATCATATATTCATTCTAAAACCTTGTC
Found at i:21272 original size:19 final size:19
Alignment explanation
Indices: 21222--21272 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
21212 TGTGGGATTT
21222 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
21240 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
21259 TTAATAATTAATTA
1 TTAATAATTAATTA
21273 ATGTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:21649 original size:13 final size:13
Alignment explanation
Indices: 21631--21656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21621 AAGGTAACAA
21631 CAAAAATCATCAC
1 CAAAAATCATCAC
21644 CAAAAATCATCAC
1 CAAAAATCATCAC
21657 TCATTCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:22265 original size:12 final size:12
Alignment explanation
Indices: 22248--22275 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
22238 GGACTAGGAA
22248 ATTACAAATCCT
1 ATTACAAATCCT
22260 ATTACAAATCCT
1 ATTACAAATCCT
22272 ATTA
1 ATTA
22276 AACCCTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (12 bp):
ATTACAAATCCT
Found at i:31371 original size:31 final size:31
Alignment explanation
Indices: 31336--31394 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
31326 TTGGACGAAA
* *
31336 TAAAAGGTTTCGTACTAAGTTGAGATTTTCT
1 TAAAAGGTTTCGTACCAAATTGAGATTTTCT
*
31367 TAAAAGGTTTGGTACCAAATTGAGATTT
1 TAAAAGGTTTCGTACCAAATTGAGATTT
31395 CAGCCGTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (31 bp):
TAAAAGGTTTCGTACCAAATTGAGATTTTCT
Done.