Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012461.1 Corchorus olitorius cultivar O-4 contig12494, 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: 49526
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1436 original size:49 final size:47
Alignment explanation
Indices: 1359--1499 Score: 151
Period size: 49 Copynumber: 2.9 Consensus size: 47
1349 CAAGCAATCC
* *
1359 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTAAACT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTAAACT
* * * *
1407 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTAAACT
* *
1456 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTAA
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTAA
1500 TTGGCACGCT
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
47 14 0.18
48 22 0.29
49 34 0.44
50 7 0.09
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.50
Consensus pattern (47 bp):
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTAAACT
Found at i:10890 original size:27 final size:27
Alignment explanation
Indices: 10852--10908 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
10842 CGTTGGTGTG
10852 TCTGCGATCCCTTGGAGAAGGGCTACC
1 TCTGCGATCCCTTGGAGAAGGGCTACC
*
10879 TCTGCGTTCCCTTGGAGAAGGGCTACC
1 TCTGCGATCCCTTGGAGAAGGGCTACC
10906 TCT
1 TCT
10909 CTCTCGTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (27 bp):
TCTGCGATCCCTTGGAGAAGGGCTACC
Found at i:23988 original size:20 final size:20
Alignment explanation
Indices: 23963--24009 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
23953 AATAACATTA
*
23963 ATATATATTAT-AATATATAT
1 ATATATATGATCAATA-ATAT
23983 ATATATATGATCAATAATAT
1 ATATATATGATCAATAATAT
24003 ATATATA
1 ATATATA
24010 ATCAAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATATATGATCAATAATAT
Found at i:24013 original size:18 final size:18
Alignment explanation
Indices: 23961--24014 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
23951 AAAATAACAT
23961 TAATATATATTATAAT--A
1 TAATATATA-TATAATCAA
*
23978 TATATATATATATGATCAA
1 TA-ATATATATATAATCAA
23997 TAATATATATATAATCAA
1 TAATATATATATAATCAA
24015 ATTCATGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 7 0.22
18 22 0.69
19 3 0.09
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATATATATATAATCAA
Found at i:28454 original size:28 final size:28
Alignment explanation
Indices: 28418--28472 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
28408 AAAAGTCCTA
28418 TATTGACTCTTTTTTCAAAGTCCTAAGG
1 TATTGACTCTTTTTTCAAAGTCCTAAGG
28446 TATTGACTCTTTTTTCAAAGTCCTAAG
1 TATTGACTCTTTTTTCAAAGTCCTAAG
28473 TTATAGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (28 bp):
TATTGACTCTTTTTTCAAAGTCCTAAGG
Found at i:29433 original size:27 final size:27
Alignment explanation
Indices: 29391--29524 Score: 145
Period size: 27 Copynumber: 5.2 Consensus size: 27
29381 GAAACATGGA
* *
29391 ACTCCAAGTTTCCAAAACCAGCATCCT
1 ACTCCAAGTTTTCAAAATCAGCATCCT
* *
29418 ACTCCAAGTTTTCAAAATCAGTATCCA
1 ACTCCAAGTTTTCAAAATCAGCATCCT
* * **
29445 ACTCCTACTCCTCAAAATCAGCATCCT
1 ACTCCAAGTTTTCAAAATCAGCATCCT
29472 ACTCC------TCAAAATCAGCATCCT
1 ACTCCAAGTTTTCAAAATCAGCATCCT
*
29493 ACTCCAAGTTTCCAAAATCAGCATCCT
1 ACTCCAAGTTTTCAAAATCAGCATCCT
29520 ACTCC
1 ACTCC
29525 GGTACAGCCA
Statistics
Matches: 90, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
21 21 0.23
27 69 0.77
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.25
Consensus pattern (27 bp):
ACTCCAAGTTTTCAAAATCAGCATCCT
Found at i:29473 original size:21 final size:21
Alignment explanation
Indices: 29447--29524 Score: 102
Period size: 21 Copynumber: 3.4 Consensus size: 21
29437 AGTATCCAAC
29447 TCCTACTCCTCAAAATCAGCA
1 TCCTACTCCTCAAAATCAGCA
29468 TCCTACTCCTCAAAATCAGCA
1 TCCTACTCCTCAAAATCAGCA
29489 TCCTACTCCAAGTTTCCAAAATCAGCA
1 TCCTACTCC-----T-CAAAATCAGCA
29516 TCCTACTCC
1 TCCTACTCC
29525 GGTACAGCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
21 30 0.59
26 1 0.02
27 20 0.39
ACGTcount: A:0.31, C:0.38, G:0.05, T:0.26
Consensus pattern (21 bp):
TCCTACTCCTCAAAATCAGCA
Found at i:29485 original size:48 final size:48
Alignment explanation
Indices: 29429--29524 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
29419 CTCCAAGTTT
* *
29429 TCAAAATCAGTATCCAACTCCTACTC-CTCAAAATCAGCATCCTACTCC
1 TCAAAATCAGCATCCAACTCCAACTCTC-CAAAATCAGCATCCTACTCC
* * *
29477 TCAAAATCAGCATCCTACTCCAAGTTTCCAAAATCAGCATCCTACTCC
1 TCAAAATCAGCATCCAACTCCAACTCTCCAAAATCAGCATCCTACTCC
29525 GGTACAGCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 41 0.98
49 1 0.02
ACGTcount: A:0.33, C:0.36, G:0.05, T:0.25
Consensus pattern (48 bp):
TCAAAATCAGCATCCAACTCCAACTCTCCAAAATCAGCATCCTACTCC
Found at i:37133 original size:45 final size:45
Alignment explanation
Indices: 37069--37171 Score: 197
Period size: 45 Copynumber: 2.3 Consensus size: 45
37059 TAATCAGCAG
*
37069 CAGCAGCAGCAGCCTCCCACTGAGAAAAAGAGTCCCAACCAATTT
1 CAGCAGCAGCAGCCTCCCACTGAGAAAAAGAGTCCCAACCAATCT
37114 CAGCAGCAGCAGCCTCCCACTGAGAAAAAGAGTCCCAACCAATCT
1 CAGCAGCAGCAGCCTCCCACTGAGAAAAAGAGTCCCAACCAATCT
37159 CAGCAGCAGCAGC
1 CAGCAGCAGCAGC
37172 AGCCCTCAGC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.11
Consensus pattern (45 bp):
CAGCAGCAGCAGCCTCCCACTGAGAAAAAGAGTCCCAACCAATCT
Found at i:38910 original size:14 final size:14
Alignment explanation
Indices: 38891--38925 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
38881 GGAAATCCCC
38891 TGCCTCAAGTTTTG
1 TGCCTCAAGTTTTG
*
38905 TGCCTCGAGTTTTG
1 TGCCTCAAGTTTTG
*
38919 TGTCTCA
1 TGCCTCA
38926 CTCATGCCCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
TGCCTCAAGTTTTG
Found at i:40045 original size:129 final size:126
Alignment explanation
Indices: 39815--40090 Score: 336
Period size: 129 Copynumber: 2.2 Consensus size: 126
39805 CAGTTGAAGT
** * *
39815 AGCAAAATCTCCTCAAAAGAAGCAGAACCACCGTCAGCAAGAGCCGCAGCCACCAGTTTCGGCAG
1 AGCAAAATCTCCTCACCAGAAGCAGAACCACCATCAGCAAGAGCAGCAGCCACCAGTTTCGGCAG
* * * * * *
39880 CGAAATCTCCTCAAAATAAGCAGAGCCACCACCAGCAGGAGTCGCAGCCACCTGTTTCAGC
66 CAAAACCTCCTCAAAAGAAGCAGAACCACCACCAGCAGGAGCCGCAGCCACCAGTTTCAGC
*
39941 AGCAAAATCTCCTCTCCAGAAGCAGAACCACCATCAGCAGCAGGAGCAGCAGCCACCAGTTTCGG
1 AGCAAAATCTCCTCACCAGAAGCAGAACCACCATCAGCA--A-GAGCAGCAGCCACCAGTTTCGG
* *** * * **
40006 CGGCAAAACCTCCTCTCCAGAAGCAGAACCACCATCAGCAGGAGCCGCGGCCACCAGTTTTGGC
63 CAGCAAAACCTCCTCAAAAGAAGCAGAACCACCACCAGCAGGAGCCGCAGCCACCAGTTTCAGC
* *
40070 GGCAAAACCTCCTCACCAGAA
1 AGCAAAATCTCCTCACCAGAA
40091 TCAGCCGGAG
Statistics
Matches: 125, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
126 35 0.28
128 1 0.01
129 89 0.71
ACGTcount: A:0.32, C:0.35, G:0.21, T:0.12
Consensus pattern (126 bp):
AGCAAAATCTCCTCACCAGAAGCAGAACCACCATCAGCAAGAGCAGCAGCCACCAGTTTCGGCAG
CAAAACCTCCTCAAAAGAAGCAGAACCACCACCAGCAGGAGCCGCAGCCACCAGTTTCAGC
Found at i:40089 original size:63 final size:63
Alignment explanation
Indices: 39815--40090 Score: 327
Period size: 63 Copynumber: 4.3 Consensus size: 63
39805 CAGTTGAAGT
** * *
39815 AGCAAAATCTCCTCAAAAGAAGCAGAACCACCGTCAGCAAGAGCCGCAGCCACCAGTTTCGGC
1 AGCAAAATCTCCTCACCAGAAGCAGAACCACCATCAGCAGGAGCCGCAGCCACCAGTTTCGGC
* ** * * * * * *
39878 AGCGAAATCTCCTCAAAATAAGCAGAGCCACCACCAGCAGGAGTCGCAGCCACCTGTTTCAGC
1 AGCAAAATCTCCTCACCAGAAGCAGAACCACCATCAGCAGGAGCCGCAGCCACCAGTTTCGGC
* *
39941 AGCAAAATCTCCTCTCCAGAAGCAGAACCACCATCAGCAGCAGGAGCAGCAGCCACCAGTTTCGG
1 AGCAAAATCTCCTCACCAGAAGCAGAACCACCAT---CAGCAGGAGCCGCAGCCACCAGTTTCGG
40006 C
63 C
* * * * *
40007 GGCAAAACCTCCTCTCCAGAAGCAGAACCACCATCAGCAGGAGCCGCGGCCACCAGTTTTGGC
1 AGCAAAATCTCCTCACCAGAAGCAGAACCACCATCAGCAGGAGCCGCAGCCACCAGTTTCGGC
* *
40070 GGCAAAACCTCCTCACCAGAA
1 AGCAAAATCTCCTCACCAGAA
40091 TCAGCCGGAG
Statistics
Matches: 184, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
63 127 0.69
66 57 0.31
ACGTcount: A:0.32, C:0.35, G:0.21, T:0.12
Consensus pattern (63 bp):
AGCAAAATCTCCTCACCAGAAGCAGAACCACCATCAGCAGGAGCCGCAGCCACCAGTTTCGGC
Found at i:43306 original size:669 final size:669
Alignment explanation
Indices: 41830--43588 Score: 3245
Period size: 668 Copynumber: 2.6 Consensus size: 669
41820 TTCATGAAAG
*
41830 TTGTAGATAATGAAATCACATTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAACAAA
1 TTGTAGATAATGAAATCACATTTTAAT----A-TTGAATCACCTAAATCGGACAAATAGAACAAA
* * *
41895 AAATACAAAAATAAAAGTTGAAGCGTTAAATCGCCCAACCCATAATTGTAAAAGATTAAATAGCA
61 AAATACAAAAGTAAAAGCTGAAGCGTTAAATCGTCCAACCCATAATTGTAAAAGATTAAATAGCA
41960 TAAAACATAAAAGTATGAGGATCATTTGATAAATAATCCAGACAAAAAAATTTGTTTATGGAGAC
126 TAAAACATAAAAGTATGAGGATCATTTGATAAATAATCCA-ACAAAAAAATTTGTTTATGGAGAC
*
42025 CAAACATAAAAATTCCCTCTTAAACCTTCCACGAAACTCATTAATCAAATTCAGGTTTCAAGCCC
190 CAAACATAAAAATTCCCTCTTAAACCTTCCACGAAACTCATTAATCAAATTCAGGTTTCAGGCCC
42090 TTGACGAAAGTTGTAGATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAA
255 TTGACGAAAGTTGTAGATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAA
*
42155 ATGGACCGAAAATTATGCAATATTAGATAGACCGGCAATAGAGACCACAAATCTTCAGAAGCATT
320 GTGGACCGAAAATTATGCAATATTAGATAGACCGGCAATAGAGACCACAAATCTTCAGAAGCATT
42220 TTTTTAAAATCAAAACATTAAAATTGGCTTTTGAGTACTTCATGAAAGTTGTAGATCATTAAATT
385 TTTTTAAAATCAAAACATTAAAATTGGCTTTTGAGTACTTCATGAAAGTTGTAGATCATTAAATT
42285 ACCTTAAAATAGACACTTGAATCACCTTGATCGGACAGACATAACGAAAAATAAAAGAATTAAAG
450 ACCTTAAAATAGACACTTGAATCACCTTGATCGGACAGACATAACGAAAAATAAAAGAATTAAAG
42350 CCGAAATGTTAAATCGTACAACCCAGAATTTGTGAGAGATTAAATAACATAAACCATAAAAGTAT
515 CCGAAATGTTAAATCGTACAACCCAGAATTTGTGAGAGATTAAATAACATAAACCATAAAAGTAT
42415 AGGGATCATTTGCTATATATTCCAGCAAAAAAAATAGTTTATTGAGAGTGGGATCCACTAATAGT
580 AGGGATCATTTGCTATATATTCCAGCAAAAAAAATAGTTTATTGAGAGTGGGATCCACTAATAGT
42480 AACTTTTAATCAAAGTTCCCAAAAC
645 AACTTTTAATCAAAGTTCCCAAAAC
42505 TTGTAGATAATGAAATCACATTTTAATATTGAATCACCTAAATCGGACAAATAGAACAAAAAATA
1 TTGTAGATAATGAAATCACATTTTAATATTGAATCACCTAAATCGGACAAATAGAACAAAAAATA
*
42570 CAAAAGTAAAAGCCGAAGCGTTAAATCGTCCAACCCATAATTGTAAAAGATTAAATAGCAT-AAA
66 CAAAAGTAAAAGCTGAAGCGTTAAATCGTCCAACCCATAATTGTAAAAGATTAAATAGCATAAAA
*
42634 CATAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAAGAATTTGTTTATGAAGACCAAAC
131 CATAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAA-AATTTGTTTATGGAGACCAAAC
42699 ATAAAAATTCCCTCTTAAACCTTCCACGAAACTCATTAATCAAATTCAGGTTTCAGGCCCTTGAC
195 ATAAAAATTCCCTCTTAAACCTTCCACGAAACTCATTAATCAAATTCAGGTTTCAGGCCCTTGAC
42764 GAAAGTTGTAGATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGA
260 GAAAGTTGTAGATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGA
42829 CCGAAAATTATGCAATATTAGATAGACCGGCAATAGAGACCACAAATCTTCAGAAGCA-TTTTTT
325 CCGAAAATTATGCAATATTAGATAGACCGGCAATAGAGACCACAAATCTTCAGAAGCATTTTTTT
42893 AAAATCAAAACATTAAAATTGGCTTTTGAGTACTTCATGAAAGTTGTAGATCATTAAATTACCTT
390 AAAATCAAAACATTAAAATTGGCTTTTGAGTACTTCATGAAAGTTGTAGATCATTAAATTACCTT
42958 AAAATAGACACTTGAATCACCTTGATCGGACAGACATAACG-AAAATAAAAGAATTAAAGCCGAA
455 AAAATAGACACTTGAATCACCTTGATCGGACAGACATAACGAAAAATAAAAGAATTAAAGCCGAA
43022 ATGTTAAATCGTACAACCCAGAATTTGTGAGAGATTAAATAACATAAACCATAAAAGTATAGGGA
520 ATGTTAAATCGTACAACCCAGAATTTGTGAGAGATTAAATAACATAAACCATAAAAGTATAGGGA
43087 TCATTTGCTATATATTCCAGCAAAAAAAAATAGTTTATTGAGAGTGGGATCCACTAATAGTAACT
585 TCATTTGCTATATATTCCAGC-AAAAAAAATAGTTTATTGAGAGTGGGATCCACTAATAGTAACT
43152 TTTAATCAAAGTTCCCAAAAC
649 TTTAATCAAAGTTCCCAAAAC
* * *
43173 TTGTAGATCATGTAATCACATTTTAATATTGAATCACCTAAATCAGACAAATAGAACAAAAAATA
1 TTGTAGATAATGAAATCACATTTTAATATTGAATCACCTAAATCGGACAAATAGAACAAAAAATA
43238 CAAAAGTAAAAGCTGAAGCGTTAAATCGTCCAACCCATAATTGTAAAAGATTAAATAGCATAAAA
66 CAAAAGTAAAAGCTGAAGCGTTAAATCGTCCAACCCATAATTGTAAAAGATTAAATAGCATAAAA
*
43303 CATAAAAGTATGAGGATTATTTGATAAATAATCCAACAAAAAAATTTGTTTATGGAGACCAAACA
131 CATAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAAAATTTGTTTATGGAGACCAAACA
*
43368 TAAAAATTCCCTCTTAAACCCTCCACGAAACTCATTAATCAAATTCAGGTTTCAGGCCCTTGACG
196 TAAAAATTCCCTCTTAAACCTTCCACGAAACTCATTAATCAAATTCAGGTTTCAGGCCCTTGACG
* *
43433 AAAGTTGTAGATCACACAATAACCTTTTAACCGACAGTTGAACAACTTCAATCGGACAAGTGGAC
261 AAAGTTGTAGATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGAC
* * * *
43498 TGAAAATTATACAATATTAGATAGACCGACAATCGAGACCACAAATCTTCAGAAGCATTTTTTTA
326 CGAAAATTATGCAATATTAGATAGACCGGCAATAGAGACCACAAATCTTCAGAAGCATTTTTTTA
*
43563 AAATCAAAACATTAAAATTGACTTTT
391 AAATCAAAACATTAAAATTGGCTTTT
43589 TGCTTTTGAT
Statistics
Matches: 1058, Mismatches: 22, Indels: 14
0.97 0.02 0.01
Matches are distributed among these distances:
667 109 0.10
668 507 0.48
669 321 0.30
670 93 0.09
671 1 0.00
675 27 0.03
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (669 bp):
TTGTAGATAATGAAATCACATTTTAATATTGAATCACCTAAATCGGACAAATAGAACAAAAAATA
CAAAAGTAAAAGCTGAAGCGTTAAATCGTCCAACCCATAATTGTAAAAGATTAAATAGCATAAAA
CATAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAAAATTTGTTTATGGAGACCAAACA
TAAAAATTCCCTCTTAAACCTTCCACGAAACTCATTAATCAAATTCAGGTTTCAGGCCCTTGACG
AAAGTTGTAGATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGAC
CGAAAATTATGCAATATTAGATAGACCGGCAATAGAGACCACAAATCTTCAGAAGCATTTTTTTA
AAATCAAAACATTAAAATTGGCTTTTGAGTACTTCATGAAAGTTGTAGATCATTAAATTACCTTA
AAATAGACACTTGAATCACCTTGATCGGACAGACATAACGAAAAATAAAAGAATTAAAGCCGAAA
TGTTAAATCGTACAACCCAGAATTTGTGAGAGATTAAATAACATAAACCATAAAAGTATAGGGAT
CATTTGCTATATATTCCAGCAAAAAAAATAGTTTATTGAGAGTGGGATCCACTAATAGTAACTTT
TAATCAAAGTTCCCAAAAC
Done.