Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014752.1 Corchorus olitorius cultivar O-4 contig14785, 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: 50502
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:5471 original size:30 final size:30
Alignment explanation
Indices: 5437--5497 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
5427 TACAAGTTGT
* *
5437 AATTTTTCAATTAAGGTCATGGGATGCTAA
1 AATTTTTCAACTAAGGTCATGGGATACTAA
5467 AATTTTTCAACTAAGGTCATGGGATACTAA
1 AATTTTTCAACTAAGGTCATGGGATACTAA
5497 A
1 A
5498 TAAAACCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (30 bp):
AATTTTTCAACTAAGGTCATGGGATACTAA
Found at i:6822 original size:13 final size:13
Alignment explanation
Indices: 6804--6829 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6794 CTTGGCATGA
6804 GTGATGATTTTTG
1 GTGATGATTTTTG
6817 GTGATGATTTTTG
1 GTGATGATTTTTG
6830 TTGCTACCTT
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:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:11039 original size:48 final size:49
Alignment explanation
Indices: 10968--11062 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 49
10958 GGGCCCTGGA
* * *
10968 TGGGCCTAGGTTTGATGATAATAGTATTAATGTTTACCCAAG-CCGGAT
1 TGGGCCTAGGCTTGATAAAAATAGTATTAATGTTTACCCAAGTCCGGAT
*
11016 TGGGCCTAGGCTTGATAAAAATAGTATTAATGTTTGCCCAAGTCCGG
1 TGGGCCTAGGCTTGATAAAAATAGTATTAATGTTTACCCAAGTCCGG
11063 CCTGGTCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 38 0.90
49 4 0.10
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (49 bp):
TGGGCCTAGGCTTGATAAAAATAGTATTAATGTTTACCCAAGTCCGGAT
Found at i:12269 original size:117 final size:120
Alignment explanation
Indices: 12081--12324 Score: 370
Period size: 117 Copynumber: 2.0 Consensus size: 120
12071 CATTGTTTAA
* * *
12081 ACTTTTATAGTTTTAGTCAACTAAAAACTTTATTTTTATTTAATTAAATCTAATATCCTTGTAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
*
12146 TATTTTATTTTTATCATTTTACT-A-TT-TTAATTAAAAAACTTTA-ATATATTAT
66 TATTTTATTTTTACCATTTTACTAATTTATTAATTAAAAAA-TTTATATATATTAT
* *
12198 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTATATCTAATATCCTTATACC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
*
12263 TTTTTTATTTTTACCATTTTACTAATTTAATTAATTAAAAAATTTATATATATTAT
66 TATTTTATTTTTACCATTTTACTAATTT-ATTAATTAAAAAATTTATATATATTAT
*
12319 AATTTT
1 ACTTTT
12325 TAAAATATAT
Statistics
Matches: 114, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
117 81 0.71
118 1 0.01
119 2 0.02
120 4 0.04
121 26 0.23
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (120 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTTATTTTTACCATTTTACTAATTTATTAATTAAAAAATTTATATATATTAT
Found at i:21351 original size:14 final size:13
Alignment explanation
Indices: 21306--21364 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
21296 CATGCACCTA
*
21306 AAAAAAATTTAAT
1 AAAAACATTTAAT
21319 AAAAATCATTT-AT
1 AAAAA-CATTTAAT
21332 -AAAACACTTTAAT
1 AAAAACA-TTTAAT
*
21345 AAAAACA-ATAAT
1 AAAAACATTTAAT
21357 GAAAAACA
1 -AAAAACA
21365 ATTTCCTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 2 0.05
12 11 0.28
13 16 0.41
14 10 0.26
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.25
Consensus pattern (13 bp):
AAAAACATTTAAT
Found at i:24404 original size:54 final size:54
Alignment explanation
Indices: 24212--24861 Score: 745
Period size: 54 Copynumber: 12.0 Consensus size: 54
24202 TGATCCTTGG
* * * *
24212 AAACTTCT-TGAAATGACCACACCGGATCATC-TTA-A-AAACCTTAGATTTCTGA
1 AAACTTCTATGAAA-GACCACACTGGGTCATCTTTAGATCAA-CTTAGATCTCTGA
* * * * *
24264 AAACTTTTATGAAAGACCGCACTGGATCATCTTGAGATCAACTTAGATCTC-AA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
* * *
24317 AAAGTTCTATGAAAGACCACACT-GGTCATCTTGAGATCAACTTAAATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
* * *
24370 AAA-ATCTTATGAAAGACCACACTGGGTCATCTTGAAATCAACTT--A-----GA
1 AAACTTC-TATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
*
24417 AAACTTCTATGAAAGACCACACT-GGTTATCTTTAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
24470 AAACTTCTATGAAAGACCGCACTGGGACCGCACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGA---C-C----A---CACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
* * *
24535 AAACTTCTATGAAAGACCGCACTGGGTCATCTTTAGATCAACTTAAATCTCTAA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
* * * *
24589 AAACTTCTATGAAAGGCCACACTAGGTCATCCTGAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
* * *
24643 AAACTTCTATGAAAGGCCGCACTGGGTCATATTTAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
* * *
24697 AAACTTTTATGAAAGACCGCACTGGGTCATCTTTAGATCAACTTAGATCTCTAA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
* * * *
24751 AAACTTCTATGAAAGGCCACACTAGGTCATCCTGAGATCAACTTAGATCTCTGAA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTG-A
* *
24806 AAACTTCTATGAAGGACCACACTGGGTAATCTTTAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
24860 AA
1 AA
24862 GATTCCATAC
Statistics
Matches: 518, Mismatches: 52, Indels: 54
0.83 0.08 0.09
Matches are distributed among these distances:
46 17 0.03
47 21 0.04
48 3 0.01
52 50 0.10
53 66 0.13
54 257 0.50
55 50 0.10
56 1 0.00
57 1 0.00
61 2 0.00
62 1 0.00
64 4 0.01
65 45 0.09
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (54 bp):
AAACTTCTATGAAAGACCACACTGGGTCATCTTTAGATCAACTTAGATCTCTGA
Found at i:27128 original size:21 final size:24
Alignment explanation
Indices: 27078--27123 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
27068 TTTACTATCT
27078 TAAAT-ATAATATATATTATTAAA
1 TAAATAATAATATATATTATTAAA
27101 TAAATAATAA-ATATATT-TTAAA
1 TAAATAATAATATATATTATTAAA
27123 T
1 T
27124 GATAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 12 0.55
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAATAATAATATATATTATTAAA
Found at i:49350 original size:26 final size:26
Alignment explanation
Indices: 49269--49350 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
49259 GTCACCCAGG
* * * *
49269 GGGCGTTTTGATCATTCGCATGTTCA
1 GGGCATTTTGGTCATTTGCATATTCA
* ** * * *
49295 GGGTCATTTTGGTTATTTTTACAATAA
1 GGG-CATTTTGGTCATTTGCATATTCA
49322 GGGCATTTTGGTCATTTGCATATTCA
1 GGGCATTTTGGTCATTTGCATATTCA
49348 GGG
1 GGG
49351 GCACGCGGGT
Statistics
Matches: 39, Mismatches: 16, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
26 23 0.59
27 16 0.41
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTGCATATTCA
Done.