Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015201.1 Corchorus olitorius cultivar O-4 contig15234, 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: 96149
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2019 original size:45 final size:42
Alignment explanation
Indices: 1920--2066 Score: 213
Period size: 42 Copynumber: 3.4 Consensus size: 42
1910 TTTGCACATA
* * *
1920 TGAAAAGCCAAGCGGAGGAGCTGCCATCGAACGACGTTCCAT
1 TGAAAGGCCAAGCGGAGGAGCTGCCATCAAACGACGTTGCAT
*
1962 TGAAAAGCCAAGCGGAGGAGCTGCCAATATCAAACGACGTTGCAT
1 TGAAAGGCCAAGCGGAGGAGCTGCC---ATCAAACGACGTTGCAT
*
2007 TGAAAGGACAAGCGGAGGAGCTGCCATCAAACGACGTTGCAT
1 TGAAAGGCCAAGCGGAGGAGCTGCCATCAAACGACGTTGCAT
*
2049 TGAAAGGCCAAGCCGAGG
1 TGAAAGGCCAAGCGGAGG
2067 GAGGCTTTTT
Statistics
Matches: 96, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
42 58 0.60
45 38 0.40
ACGTcount: A:0.33, C:0.23, G:0.30, T:0.14
Consensus pattern (42 bp):
TGAAAGGCCAAGCGGAGGAGCTGCCATCAAACGACGTTGCAT
Found at i:2432 original size:33 final size:33
Alignment explanation
Indices: 2395--2491 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 33
2385 AAATTAAAAT
2395 AATAATTGAAATTAATTACTATAAATCAAAAGA
1 AATAATTGAAATTAATTACTATAAATCAAAAGA
* * *
2428 AATAATTG-CA-T-GTTA--AT---T-AAAA-T
1 AATAATTGAAATTAATTACTATAAATCAAAAGA
*
2451 AATAATTGAAATTAATTACTATAAATCAAAGGA
1 AATAATTGAAATTAATTACTATAAATCAAAAGA
2484 AATAATTG
1 AATAATTG
2492 CATGTTACTT
Statistics
Matches: 47, Mismatches: 7, Indels: 20
0.64 0.09 0.27
Matches are distributed among these distances:
23 8 0.17
24 5 0.11
25 2 0.04
26 3 0.06
28 4 0.09
30 3 0.06
31 2 0.04
32 4 0.09
33 16 0.34
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (33 bp):
AATAATTGAAATTAATTACTATAAATCAAAAGA
Found at i:2447 original size:56 final size:56
Alignment explanation
Indices: 2386--2498 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
2376 AATTAAAAAA
2386 AATTAAAATAATAATTGAAATTAATTACTATAAATCAAAAGAAATAATTGCATGTT
1 AATTAAAATAATAATTGAAATTAATTACTATAAATCAAAAGAAATAATTGCATGTT
*
2442 AATTAAAATAATAATTGAAATTAATTACTATAAATCAAAGGAAATAATTGCATGTT
1 AATTAAAATAATAATTGAAATTAATTACTATAAATCAAAAGAAATAATTGCATGTT
2498 A
1 A
2499 CTTTTCTTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (56 bp):
AATTAAAATAATAATTGAAATTAATTACTATAAATCAAAAGAAATAATTGCATGTT
Found at i:11419 original size:28 final size:28
Alignment explanation
Indices: 11381--11434 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
11371 ATATAATTGA
*
11381 CTTGTTCAATTCTAGCAAT-TTGGAATTT
1 CTTGTTAAATTCTAGC-ATCTTGGAATTT
11409 CTTGTTAAATTCTAGCATCTTGGAAT
1 CTTGTTAAATTCTAGCATCTTGGAAT
11435 CAATATCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (28 bp):
CTTGTTAAATTCTAGCATCTTGGAATTT
Found at i:14517 original size:33 final size:34
Alignment explanation
Indices: 14475--14545 Score: 108
Period size: 36 Copynumber: 2.1 Consensus size: 34
14465 ATCCGTAAGC
14475 TGAATATCCTTCATAT-CCGCAATAACGACCTTG
1 TGAATATCCTTCATATCCCGCAATAACGACCTTG
*
14508 TGAATATCCTTCATATCCGCCGCACTAACGACCTTG
1 TGAATATCCTTCATAT-C-CCGCAATAACGACCTTG
14544 TG
1 TG
14546 TTCAGTTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 16 0.47
36 18 0.53
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.30
Consensus pattern (34 bp):
TGAATATCCTTCATATCCCGCAATAACGACCTTG
Found at i:14559 original size:15 final size:15
Alignment explanation
Indices: 14539--14569 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
14529 GCACTAACGA
14539 CCTTGTGTTCAGTTT
1 CCTTGTGTTCAGTTT
14554 CCTTGTGTTCAGTTT
1 CCTTGTGTTCAGTTT
14569 C
1 C
14570 GGACAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.23, G:0.19, T:0.52
Consensus pattern (15 bp):
CCTTGTGTTCAGTTT
Found at i:20809 original size:29 final size:29
Alignment explanation
Indices: 20745--20843 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
20735 CTTAATACCC
* **
20745 TTTTCCCCCTTAAACTTGTAGCGTTTGGACG
1 TTTTGCCCCTTAAACTT-TA-ATTTTGGACG
*
20776 TTTTGCCCCTTAAACTTTAATTTTGGACA
1 TTTTGCCCCTTAAACTTTAATTTTGGACG
* *
20805 TTTTGCCTCC-TGAACTTCAATTTTAGGACG
1 TTTTGCC-CCTTAAACTTTAATTTT-GGACG
20835 TTTTGCCCC
1 TTTTGCCCC
20844 CTAAGGCTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 28 0.47
30 15 0.25
31 16 0.27
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.41
Consensus pattern (29 bp):
TTTTGCCCCTTAAACTTTAATTTTGGACG
Found at i:23404 original size:29 final size:29
Alignment explanation
Indices: 23372--23428 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
23362 ATGCTATATA
* *
23372 TTTTAAGATATACCCCAAAATTGTAATTG
1 TTTTAAGACAAACCCCAAAATTGTAATTG
** *
23401 TTTTTGGCCAAACCCCAAAATTGTAATT
1 TTTTAAGACAAACCCCAAAATTGTAATT
23429 ATTTCCTCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (29 bp):
TTTTAAGACAAACCCCAAAATTGTAATTG
Found at i:38464 original size:16 final size:16
Alignment explanation
Indices: 38443--38475 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38433 ATGTTCCCAT
38443 GGATTCGTGATTTGAC
1 GGATTCGTGATTTGAC
38459 GGATTCGTGATTTGAC
1 GGATTCGTGATTTGAC
38475 G
1 G
38476 AGTGATGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.33, T:0.36
Consensus pattern (16 bp):
GGATTCGTGATTTGAC
Found at i:38515 original size:24 final size:24
Alignment explanation
Indices: 38488--38535 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
38478 TGATGATCAA
38488 ATGGATTCGATTCTATTCTAATTT
1 ATGGATTCGATTCTATTCTAATTT
* *
38512 ATGGATTCGATTGTATTCTGATTT
1 ATGGATTCGATTCTATTCTAATTT
38536 TTAGTCCGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (24 bp):
ATGGATTCGATTCTATTCTAATTT
Found at i:38601 original size:82 final size:82
Alignment explanation
Indices: 38504--38669 Score: 305
Period size: 82 Copynumber: 2.0 Consensus size: 82
38494 TCGATTCTAT
*
38504 TCTAATTTATGGATTCGATTGTATTCTGATTTTTAGTCCGGTTATGGAACTCAGTGATGATCCCA
1 TCTAATTTATGGATTCGATTGTATTCTGATTTATAGTCCGGTTATGGAACTCAGTGATGATCCCA
* *
38569 TGGGCTCGGTTTTGATC
66 TAGACTCGGTTTTGATC
38586 TCTAATTTATGGATTCGATTGTATTCTGATTTATAGTCCGGTTATGGAACTCAGTGATGATCCCA
1 TCTAATTTATGGATTCGATTGTATTCTGATTTATAGTCCGGTTATGGAACTCAGTGATGATCCCA
38651 TAGACTCGGTTTTGATC
66 TAGACTCGGTTTTGATC
38668 TC
1 TC
38670 GGACCTCTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (82 bp):
TCTAATTTATGGATTCGATTGTATTCTGATTTATAGTCCGGTTATGGAACTCAGTGATGATCCCA
TAGACTCGGTTTTGATC
Found at i:41917 original size:19 final size:19
Alignment explanation
Indices: 41893--41929 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41883 GTAAAGTACC
41893 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
41912 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
41930 TGTTAAATAG
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:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:56942 original size:24 final size:24
Alignment explanation
Indices: 56910--56957 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
56900 TCATTGTACC
56910 TGGTTCTACACATCCAATCAGTTA
1 TGGTTCTACACATCCAATCAGTTA
* *
56934 TGGTTCTACATATTCAATCAGTTA
1 TGGTTCTACACATCCAATCAGTTA
56958 GGTGCATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (24 bp):
TGGTTCTACACATCCAATCAGTTA
Found at i:75234 original size:180 final size:180
Alignment explanation
Indices: 74910--75264 Score: 577
Period size: 180 Copynumber: 2.0 Consensus size: 180
74900 GGCAGGTTTG
74910 AGACTTAATAATTATTCATTTTGATAGATTTTCTCTTAACTTTTGCTTTAGGGTGAAAAGAAGTT
1 AGACTTAATAATTATTCATTTTGATAGATTTTCTCTTAACTTTTGCTTTAGGGTGAAAAGAAGTT
* *
74975 AATAATGCCTTTCTTGAAGGGTTTAGACCAGGAATTCATTAGGTTTGTTTTGATTCATAGCGGTT
66 AATAATGCCTGTCTTGAAGGGTTTAGACCAGAAATTCATTAGGTTTGTTTTGATTCATAGCGGTT
* * *
75040 TTGCTGTTGATGGCCTGCATACTTGTTTTATAGTAATTATATACACATTA
131 TTGCTGTAGATGGCCTGCATACTTGCTTTATAGCAATTATATACACATTA
* * * * *
75090 AGACTTGATAATTATTCATTTTGATAGATTTTC-CATTCATTTTTGCTTTAGGGTGAAATGATGT
1 AGACTTAATAATTATTCATTTTGATAGATTTTCTC-TTAACTTTTGCTTTAGGGTGAAAAGAAGT
* *
75154 TAATAATGTCTGTCTTGAAGGGTTTAGACCAGAAATTCATTAGGTTTGTTTTGATTCATAGCGTT
65 TAATAATGCCTGTCTTGAAGGGTTTAGACCAGAAATTCATTAGGTTTGTTTTGATTCATAGCGGT
*
75219 TTTTCTGTAGATGGCCTGCATACTTGCTTTATAGCAATTATATACA
130 TTTGCTGTAGATGGCCTGCATACTTGCTTTATAGCAATTATATACA
75265 TTGAAAAAGT
Statistics
Matches: 161, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
179 1 0.01
180 160 0.99
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (180 bp):
AGACTTAATAATTATTCATTTTGATAGATTTTCTCTTAACTTTTGCTTTAGGGTGAAAAGAAGTT
AATAATGCCTGTCTTGAAGGGTTTAGACCAGAAATTCATTAGGTTTGTTTTGATTCATAGCGGTT
TTGCTGTAGATGGCCTGCATACTTGCTTTATAGCAATTATATACACATTA
Done.