Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016552.1 Corchorus olitorius cultivar O-4 contig16585, 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: 43848
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:211 original size:111 final size:111
Alignment explanation
Indices: 17--231 Score: 421
Period size: 111 Copynumber: 1.9 Consensus size: 111
7 CGCATAGAGA
17 ATGGTGAAGTAAAGCATGTCCCTACGTCTTAACCCATGTCCCTCCTAAAACATAGTCCAACCATC
1 ATGGTGAAGTAAAGCATGTCCCTACGTCTTAACCCATGTCCCTCCTAAAACATAGTCCAACCATC
82 ACATATCTCAATGCGGCCGTCTTTCATGTGTAGCGTTGCCTCAAAC
66 ACATATCTCAATGCGGCCGTCTTTCATGTGTAGCGTTGCCTCAAAC
*
128 ATGGTGAAGTAAAGCATGTCCCTACGTCTTAACCCATGTCCCTCGTAAAACATAGTCCAACCATC
1 ATGGTGAAGTAAAGCATGTCCCTACGTCTTAACCCATGTCCCTCCTAAAACATAGTCCAACCATC
193 ACATATCTCAATGCGGCCGTCTTTCATGTGTAGCGTTGC
66 ACATATCTCAATGCGGCCGTCTTTCATGTGTAGCGTTGC
232 TTGAGTTGTT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (111 bp):
ATGGTGAAGTAAAGCATGTCCCTACGTCTTAACCCATGTCCCTCCTAAAACATAGTCCAACCATC
ACATATCTCAATGCGGCCGTCTTTCATGTGTAGCGTTGCCTCAAAC
Found at i:17941 original size:6 final size:6
Alignment explanation
Indices: 17930--17958 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17920 TCTTACTGTG
17930 TGAAAA TGAAAA TGAAAA TGAAAA TGAAA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGAAA
17959 TACTCCCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
TGAAAA
Found at i:29309 original size:445 final size:447
Alignment explanation
Indices: 28468--29324 Score: 1169
Period size: 445 Copynumber: 1.9 Consensus size: 447
28458 CAACTTTATT
* * * **
28468 TTTTTAAAATTTTTTGTTCTATTTGTCCGATTAAGGTAATTCAGGTGTCTATTAAAATTTAATTT
1 TTTTTAAAATTTTTTGTTCTATTTGTCCCATTAAAGTAATTCAAGTGTCTATTAAAAGGTAATTT
* *
28533 CATGATCTACAACTTTCATGAAAGACTCAAAGGCCAATTTTTATGTTTCAAATAAAAAAATGCTT
66 CATGATCTACAACTTTCATGAAAGACTCAAAAGCCAATTTTGATGTTTCAAATAAAAAAATGCTT
* * * * * **
28598 CTGAAATTTGGTGGTTTCAATTGTCATTCTATTTAATAATTAATATCATGCAATTTTTGATCCAC
131 CCGAAATTTGGTCGTTTCAATTGACAGTCTATTTAATAATT-ACATCAT-CAATTTTCAATCCAC
** *
28663 ATGTCCGATTAAAGTTATTCAACTTTCGATTAAAAGGTTATTGAATGATCTACGACTTTCATGAA
194 ATGTCCGATTAAAGTTATTCAACAGTCGATTAAAAGATTATTGAATGATCTACGACTTTCATGAA
* * *
28728 GGCTCCAAAAGCTCAATTTGATCTACGAGTTTCATGAACGACTCAAAATGAAATTTTTATGTTTT
259 GACTCCAAAAGCTAAATTTGATCTACGAGTTTCATGAACGACTCAAAATGAAATTTTTATGTTTA
* ** * *
28793 AGAATCTCCATCAACAAATATTTTCTTATTTGGATTATTTTTCGAATGATCCTCATTTTTTTCTA
324 AGAATCTCCATCAACAAACATTTTCTTATTTGGATTATTCATCAAATGATCCTCATATTTTTCTA
28858 CTTTATACTATTTAGTCCTTTACTACTTTTATCTTTATCGATTTAATGCTTCAGCTTTA
389 CTTTATACTATTTAGTCCTTTACTACTTTTATCTTTATCGATTTAATGCTTCAGCTTTA
* *
28917 TTTTT-AAATTTTTTTTTCTATTTGTCCCATTAAAGTGATTCAAGTGTCTATTAAAAGGTAATTT
1 TTTTTAAAATTTTTTGTTCTATTTGTCCCATTAAAGTAATTCAAGTGTCTATTAAAAGGTAATTT
* * * * *
28981 CATGATCTACAACTTTCATGAAGGATTCAAAAGCCAATTTTGATGTTTCAATTCTAAAAAATGTT
66 CATGATCTACAACTTTCATGAAAGACTCAAAAGCCAATTTTGATGTTTCAAAT-AAAAAAATGCT
*
29046 TCCGAAATTTGGTCGTTTCAATTGACGGTCTATTTAAT-A-T-CAT-AT-AATTTTCAATCCACA
130 TCCGAAATTTGGTCGTTTCAATTGACAGTCTATTTAATAATTACATCATCAATTTTCAATCCACA
* *
29106 TGTCCGATTAAAGTTATTCAA-AGTCGGTTAAAAGATTATTGTATGATCTACGACTTTCATGAAA
195 TGTCCGATTAAAGTTATTCAACAGTCGATTAAAAGATTATTGAATGATCTACGACTTTCATG-AA
** * * *
29170 GAC-CTGAAAGCTAAATTTTATCTACGTACGAGTTTCATGAATGGCTCAAAA-GAAAATTTTTAT
259 GACTCCAAAAGCTAAATTTGA--T-C-TACGAGTTTCATGAACGACTCAAAATG-AAATTTTTAT
*
29233 GTTTCAAG-ATCTCCATCAACAAACATTTTCTTATTTGGGTTATTCATCAAATGA-CTCTCATAT
319 GTTT-AAGAATCTCCATCAACAAACATTTTCTTATTTGGATTATTCATCAAATGATC-CTCATAT
29296 TTTTCTACTTTATACTATTTAGTCCTTTA
382 TTTTCTACTTTATACTATTTAGTCCTTTA
29325 TTATTGTTAA
Statistics
Matches: 358, Mismatches: 41, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
441 48 0.13
442 38 0.11
443 1 0.00
444 5 0.01
445 115 0.32
446 2 0.01
447 1 0.00
448 101 0.28
449 47 0.13
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (447 bp):
TTTTTAAAATTTTTTGTTCTATTTGTCCCATTAAAGTAATTCAAGTGTCTATTAAAAGGTAATTT
CATGATCTACAACTTTCATGAAAGACTCAAAAGCCAATTTTGATGTTTCAAATAAAAAAATGCTT
CCGAAATTTGGTCGTTTCAATTGACAGTCTATTTAATAATTACATCATCAATTTTCAATCCACAT
GTCCGATTAAAGTTATTCAACAGTCGATTAAAAGATTATTGAATGATCTACGACTTTCATGAAGA
CTCCAAAAGCTAAATTTGATCTACGAGTTTCATGAACGACTCAAAATGAAATTTTTATGTTTAAG
AATCTCCATCAACAAACATTTTCTTATTTGGATTATTCATCAAATGATCCTCATATTTTTCTACT
TTATACTATTTAGTCCTTTACTACTTTTATCTTTATCGATTTAATGCTTCAGCTTTA
Found at i:29440 original size:25 final size:25
Alignment explanation
Indices: 29412--29460 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
29402 AGTGAAGAAT
* *
29412 TAGTTTTTTAAATGTTTGATATATA
1 TAGTGTTTTAAATGTATGATATATA
* *
29437 TAGTGTTTTCAATGTATGTTATAT
1 TAGTGTTTTAAATGTATGATATAT
29461 TGTTTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (25 bp):
TAGTGTTTTAAATGTATGATATATA
Found at i:32998 original size:42 final size:42
Alignment explanation
Indices: 32895--33005 Score: 204
Period size: 42 Copynumber: 2.6 Consensus size: 42
32885 TAGATGCCTT
**
32895 TGTGTTATATATGTGCTTGAAGACTTTTGAGAGAGTTGCCCC
1 TGTGTTATATATGTGCTTGGGGACTTTTGAGAGAGTTGCCCC
32937 TGTGTTATATATGTGCTTGGGGACTTTTGAGAGAGTTGCCCC
1 TGTGTTATATATGTGCTTGGGGACTTTTGAGAGAGTTGCCCC
32979 TGTGTTATATATGTGCTTGGGGACTTT
1 TGTGTTATATATGTGCTTGGGGACTTT
33006 GGCTATTGGG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.41
Consensus pattern (42 bp):
TGTGTTATATATGTGCTTGGGGACTTTTGAGAGAGTTGCCCC
Found at i:33242 original size:14 final size:15
Alignment explanation
Indices: 33206--33242 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
33196 GGTTTCTTTT
33206 TTCTGTTTTTCATTGA
1 TTCT-TTTTTCATTGA
33222 TTCTTTTTT-ATT-A
1 TTCTTTTTTCATTGA
33235 TTCTTTTT
1 TTCTTTTT
33243 GCTTTAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.43
14 3 0.14
15 5 0.24
16 4 0.19
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.73
Consensus pattern (15 bp):
TTCTTTTTTCATTGA
Found at i:37898 original size:150 final size:150
Alignment explanation
Indices: 37627--37926 Score: 494
Period size: 150 Copynumber: 2.0 Consensus size: 150
37617 GAAGCCCGTA
*
37627 CCAAAAAATAAATTGAGAAGTAAATTTGTAATTTGAAACAATATTTAAGGGCATGGCAGTCTTTT
1 CCAAAAAATAAATTGAGAAGTAAACTTGTAATTTGAAACAATATTTAAGGGCATGGCAGTCTTTT
* * * *
37692 CAAGATACTGAAGCAGTGGCTTCTTTCTTTCTCTACCATTTCCGCCCAACTTTGGGCGGAAGTAA
66 CAAGATACTAAAGCAGTGGCTTCCTTCTTTCCCCACCATTTCCGCCCAACTTTGGGCGGAAGTAA
*
37757 ATTATGCAGAAATGGCTTGT
131 ATTATACAGAAATGGCTTGT
*
37777 CCAAAAAATAAATTGAGAAGTAAACTTGTAATTTGAAACAATTTTTAAGGGCATGGCAGTCTTTT
1 CCAAAAAATAAATTGAGAAGTAAACTTGTAATTTGAAACAATATTTAAGGGCATGGCAGTCTTTT
*
37842 CAAGATACTAAAGCAGTGGGCTTCCTTC-TTCCCCATCATTTCCGCCCAACTTTGGGCGGAAGTA
66 CAAGATACTAAAGCAGT-GGCTTCCTTCTTTCCCCACCATTTCCGCCCAACTTTGGGCGGAAGTA
* *
37906 AGTTCTACAGAAATGGCTTGT
130 AATTATACAGAAATGGCTTGT
37927 ACATTTCTCT
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
150 130 0.94
151 9 0.06
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (150 bp):
CCAAAAAATAAATTGAGAAGTAAACTTGTAATTTGAAACAATATTTAAGGGCATGGCAGTCTTTT
CAAGATACTAAAGCAGTGGCTTCCTTCTTTCCCCACCATTTCCGCCCAACTTTGGGCGGAAGTAA
ATTATACAGAAATGGCTTGT
Found at i:38180 original size:29 final size:31
Alignment explanation
Indices: 38143--38212 Score: 92
Period size: 29 Copynumber: 2.3 Consensus size: 31
38133 GGACTGCCAT
*
38143 TTTGCACCC-AACTTTTTTA-TTTTGAT-CAC
1 TTTGCACCCTAA-TGTTTTATTTTTGATCCAC
*
38172 TTTGCACCCTAATGTTTTATTTTTGTTCCAC
1 TTTGCACCCTAATGTTTTATTTTTGATCCAC
38203 TTTGCACCCT
1 TTTGCACCCT
38213 CCGTTATCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 15 0.42
30 8 0.22
31 13 0.36
ACGTcount: A:0.17, C:0.26, G:0.09, T:0.49
Consensus pattern (31 bp):
TTTGCACCCTAATGTTTTATTTTTGATCCAC
Found at i:42681 original size:2 final size:2
Alignment explanation
Indices: 42674--42716 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
42664 ATTAAATTCT
42674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
42717 AGTCTAAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:42907 original size:111 final size:111
Alignment explanation
Indices: 42713--42936 Score: 412
Period size: 111 Copynumber: 2.0 Consensus size: 111
42703 ATATATACTA
* *
42713 TATAAGTCTAAACTTTAAAACCATTGACCTGTAATATCTAAAATAACCTTTTTAATTTCAAAAGT
1 TATAAGTCTAAACTTCAAAACCATTGACCTGTAATATCTAAAATAACCTCTTTAATTTCAAAAGT
*
42778 TTAGTATCATTTAAAGGGTAAACATGTATTTATTAAATTAAACTTT
66 TTAGTATCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTT
*
42824 TATAAGTCTAAACTTCAAAACCATTGACCTGTAATATCTAAAATAACCTCTTTAATTTTAAAAGT
1 TATAAGTCTAAACTTCAAAACCATTGACCTGTAATATCTAAAATAACCTCTTTAATTTCAAAAGT
42889 TTAGTATCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTT
66 TTAGTATCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTT
42935 TA
1 TA
42937 AGGTTCAATA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (111 bp):
TATAAGTCTAAACTTCAAAACCATTGACCTGTAATATCTAAAATAACCTCTTTAATTTCAAAAGT
TTAGTATCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTT
Found at i:43476 original size:205 final size:204
Alignment explanation
Indices: 43231--43646 Score: 708
Period size: 205 Copynumber: 2.0 Consensus size: 204
43221 ATTTCCTTGA
*
43231 TAATAAATAAATCGGGTCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
1 TAATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
*
43296 TAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATACTTCTATATAT-ATAA
66 TAATTTAATAAATCAACCACTAATGTTCAACT-ACTTTTTTTTGGTATACTTCTATATATAATAA
*
43360 TAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAA
130 TAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAA
*
43425 CATTTACCAT
195 CATTCACCAT
*
43435 TAATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATTTAAT
1 TAATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAAT
* *
43500 TTAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAA
65 TTAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATACTTCTATATATAATAA
* * *
43565 TAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTATTTTTAGACTTAAAAAGTTAATAA
130 TAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAA
43630 CATTCACCAT
195 CATTCACCAT
*
43640 TGATAAA
1 TAATAAA
43647 GTTATTAAGC
Statistics
Matches: 199, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
204 41 0.21
205 158 0.79
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (204 bp):
TAATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
TAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATACTTCTATATATAATAAT
AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
ATTCACCAT
Done.