Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013499.1 Corchorus olitorius cultivar O-4 contig13532, 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: 67762
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--37 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
*
1 TTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38 ATTAGAAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:18 original size:13 final size:13
Alignment explanation
Indices: 1--40 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
1 TTTTTTTTTTTTA
1 TTTTTTTTTTTTA
14 TTTTTTTTTTTT-
1 TTTTTTTTTTTTA
26 TTTTTTTTTTTTA
1 TTTTTTTTTTTTA
39 TT
1 TT
41 AGAAAGCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.05, C:0.00, G:0.00, T:0.95
Consensus pattern (13 bp):
TTTTTTTTTTTTA
Found at i:2124 original size:11 final size:11
Alignment explanation
Indices: 2108--2135 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2098 CATTGTCATT
2108 AAAGTAGATCA
1 AAAGTAGATCA
2119 AAAGTAGATCA
1 AAAGTAGATCA
2130 AAAGTA
1 AAAGTA
2136 CTACTACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (11 bp):
AAAGTAGATCA
Found at i:6829 original size:2 final size:2
Alignment explanation
Indices: 6822--6859 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6812 TGATTATTAC
6822 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6860 ACCAATTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7875 original size:21 final size:21
Alignment explanation
Indices: 7837--7888 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
7827 GCAATTATAT
*
7837 AGATGAGATTA--CACTGTAC
1 AGATGAGATTATGTACTGTAC
*
7856 AGATTAGATTATGTACTGTAC
1 AGATGAGATTATGTACTGTAC
7877 AGATGAGATTAT
1 AGATGAGATTAT
7889 TAGAGCAGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
21 18 0.64
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (21 bp):
AGATGAGATTATGTACTGTAC
Found at i:18834 original size:64 final size:64
Alignment explanation
Indices: 18677--18853 Score: 187
Period size: 64 Copynumber: 2.7 Consensus size: 64
18667 AGTTTTACAT
* * ** ** *
18677 CCATTC-CTAAAACTCAAACTCGAGACGTTATTTTAGGGAAATAAGTGACACGTTACTTGAACCA
1 CCATTCAC-AAAACTCGAACTCGAGACCTTATTTTAGGG-AATAAGTGACACGCCAAATCAACCA
18741 A
64 A
* * * *
18742 CCATTCACAAAATTTGAACTCGAAACCTTATTTTAAGGGAATAAGTGACAC-CCAAATCAACCAT
1 CCATTCACAAAACTCGAACTCGAGACCTTATTTT-AGGGAATAAGTGACACGCCAAATCAACCAA
* *
18806 TCATTCACAAAACTCGAACTCGAGACCTTGTTTTAGGAGAATAAGTGA
1 CCATTCACAAAACTCGAACTCGAGACCTTATTTTAGG-GAATAAGTGA
18854 GAGACCACTT
Statistics
Matches: 93, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
63 3 0.03
64 46 0.49
65 39 0.42
66 5 0.05
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (64 bp):
CCATTCACAAAACTCGAACTCGAGACCTTATTTTAGGGAATAAGTGACACGCCAAATCAACCAA
Found at i:37381 original size:49 final size:49
Alignment explanation
Indices: 37328--37429 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
37318 TTGGGAATAT
*
37328 ATTTATTTATATATGACTTTGTAAATTACTAAACTTAAGATAAATGTAA
1 ATTTATTTATATATGACTTTATAAATTACTAAACTTAAGATAAATGTAA
37377 ATTTATTTATATATGACTTTATAAATTACTAAACTTAAGATAAATGTAA
1 ATTTATTTATATATGACTTTATAAATTACTAAACTTAAGATAAATGTAA
37426 ATTT
1 ATTT
37430 TGACTTTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (49 bp):
ATTTATTTATATATGACTTTATAAATTACTAAACTTAAGATAAATGTAA
Found at i:38155 original size:23 final size:25
Alignment explanation
Indices: 38129--38175 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
38119 AAAATAGGTG
38129 AAAAAATAT-ATATAAA-TAAATAT
1 AAAAAATATAATATAAAGTAAATAT
* *
38152 AAAAGATATAATTTAAAGTAAATA
1 AAAAAATATAATATAAAGTAAATA
38176 AAAGCAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (25 bp):
AAAAAATATAATATAAAGTAAATAT
Found at i:48053 original size:3 final size:3
Alignment explanation
Indices: 48045--48114 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
48035 CCTAATATAT
48045 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48093 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
48115 GAAGGTAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48507 original size:120 final size:121
Alignment explanation
Indices: 48285--48522 Score: 345
Period size: 120 Copynumber: 2.0 Consensus size: 121
48275 AAAACAAGGT
* ** * * *
48285 AAATTATACAATACATCGTTAGTGGAGTTTAGCAGATTATACAAAACGGATTCTGAAAGGTGACA
1 AAATTATACAATACACCGGCAGTGGAGTTTAGCAGACTACACAAAACGGATTCTGAAAGGTAACA
*
48350 TGTGTCCTTTAGAGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAGAC
66 TGTGTCCTTAAGAGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAGAC
* * * * *
48406 AAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACAC-AAGCGGGTTTTGAAGGGTAACA
1 AAATTATACAATACACCGGCAGTGGAGTTTAGCAGACTACACAAAACGGATTCTGAAAGGTAACA
48470 TGTGTCCTCTAAG-GACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAA
66 TGTGTCCT-TAAGAGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAA
48523 TGGACATGTG
Statistics
Matches: 104, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
120 65 0.62
121 39 0.38
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (121 bp):
AAATTATACAATACACCGGCAGTGGAGTTTAGCAGACTACACAAAACGGATTCTGAAAGGTAACA
TGTGTCCTTAAGAGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAGAC
Found at i:48646 original size:82 final size:82
Alignment explanation
Indices: 48514--48682 Score: 230
Period size: 82 Copynumber: 2.1 Consensus size: 82
48504 ACTTAATTAA
* * * * *
48514 TTAAAAAAATGGACATGTGTCAACTCAACAACCCGCTTGTGGAGTCCAAAATTTACTCCGCCGGT
1 TTAAAAAAATGGACATATATAAACTCAACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGAT
*
48579 GTATCAAATAATTACCC
66 ATATCAAATAATTACCC
* * * * * *
48596 TTAAAAAAATGGATATATATAAATTCCACAACTCGCTTGTGGAGTTCAAAATTTACACCGCTGAT
1 TTAAAAAAATGGACATATATAAACTCAACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGAT
48661 ATATCAAATAATTACCC
66 ATATCAAATAATTACCC
48678 TTAAA
1 TTAAA
48683 TTAAAGGAAG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (82 bp):
TTAAAAAAATGGACATATATAAACTCAACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGAT
ATATCAAATAATTACCC
Found at i:65605 original size:14 final size:14
Alignment explanation
Indices: 65588--65614 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65578 ATCATGCACT
65588 AATATACAAAACAA
1 AATATACAAAACAA
65602 AATATACAAAACA
1 AATATACAAAACA
65615 GTCTAATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (14 bp):
AATATACAAAACAA
Done.