Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019003.1 Corchorus olitorius cultivar O-4 contig19036, 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: 12908
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:2707 original size:24 final size:21
Alignment explanation
Indices: 2660--2699 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2650 CCACTAATAA
*
2660 TAATTATTATAATATTAAGTT
1 TAATAATTATAATATTAAGTT
2681 TAATAATTATAATATTAAG
1 TAATAATTATAATATTAAG
2700 ATGTTTAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
TAATAATTATAATATTAAGTT
Found at i:5413 original size:374 final size:379
Alignment explanation
Indices: 4984--5743 Score: 1171
Period size: 374 Copynumber: 2.0 Consensus size: 379
4974 TAAAAAAATG
4984 TTTTACTTTATATTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGATTAACCAAAATGTGACA
1 TTTTACTTTATATTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGATTAACCAAAATGTGACA
* * *
5049 AATAAATAGGAACAGAGGAAGTATCAATTGAAGGTTATTAAAACAATTATGATACTATGAATAAA
66 AATAAATAGGAACAAAGGAAGTATCAATTAAAGGTTATTAAAACAATTATGATACTATGAACAAA
* *
5114 TTCAATAACCTTACATTCTTATTAACTTTAGTAAACTTTCATTAAT-GTACCAAAAAGATTACCA
131 TTCAATAACCTTACATTCTTATTAACTTTAGTAAAATTTCATTAATGGT-----AAAGATCACCA
5178 ATTTTCCATCTAA-TTTTTATGAAGATTACCAATTTTCTA-TC-T-ATTTTGTTT-AAAAA-AA-
191 ATTTTCCATCTAATTTTTTATGAAGATTACCAATTTTCTATTCTTCATTTTGTTTGAAAAAGAAC
*
5236 C-ATAATGATTA-CAAAAAATGTATAGTACTATCAACTAATCTAATAACCTTACATTCTCAATAT
256 CTATAATGATTATAAAAAAATGTATAGTACTATCAACTAATCTAATAACCTTACATTCTCAATAT
** *
5299 TTTTGGTTATCAAGTTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
321 TTTTAATTATCAAATTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
*
5358 TTTTACTTTATATTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGGTTAACCAAAATGTGACA
1 TTTTACTTTATATTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGATTAACCAAAATGTGACA
* *
5423 AATAAATAGGAACAAAGGGAGTATCAATTAAATGTTATTAAAACAATTATGATACTATGAACAAA
66 AATAAATAGGAACAAAGGAAGTATCAATTAAAGGTTATTAAAACAATTATGATACTATGAACAAA
* * *
5488 TTCAATAACCTTACATTCTTATTAACTTTAGTAAAATTTCATTGATGGTGAAGATCATCAATTTT
131 TTCAATAACCTTACATTCTTATTAACTTTAGTAAAATTTCATTAATGGTAAAGATCACCAATTTT
* * * *
5553 CTATCTAATTTTTTGTGAAGATTACCAATTTTCTATCTTCTTCTTCTTTTTTTTTGAAAAAGAAT
196 CCATCTAATTTTTTATGAAGATTACCAATTTTCTA-----TTCTTCATTTTGTTTGAAAAAGAA-
*
5618 CCTATAATGATTATAAAAAAATGTATAGTACTATCAACTAATCTAATAACTTTACATTCTCAATA
255 CCTATAATGATTATAAAAAAATGTATAGTACTATCAACTAATCTAATAACCTTACATTCTCAATA
5683 TTTTTAATTATCAAATTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
320 TTTTTAATTATCAAATTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
5743 T
1 T
5744 ACCAAAATTT
Statistics
Matches: 350, Mismatches: 20, Indels: 21
0.90 0.05 0.05
Matches are distributed among these distances:
370 20 0.06
371 25 0.07
374 168 0.48
375 2 0.01
377 2 0.01
378 1 0.00
379 7 0.02
380 5 0.01
381 2 0.01
383 1 0.00
384 10 0.03
385 107 0.31
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (379 bp):
TTTTACTTTATATTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGATTAACCAAAATGTGACA
AATAAATAGGAACAAAGGAAGTATCAATTAAAGGTTATTAAAACAATTATGATACTATGAACAAA
TTCAATAACCTTACATTCTTATTAACTTTAGTAAAATTTCATTAATGGTAAAGATCACCAATTTT
CCATCTAATTTTTTATGAAGATTACCAATTTTCTATTCTTCATTTTGTTTGAAAAAGAACCTATA
ATGATTATAAAAAAATGTATAGTACTATCAACTAATCTAATAACCTTACATTCTCAATATTTTTA
ATTATCAAATTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
Found at i:6386 original size:134 final size:134
Alignment explanation
Indices: 6121--6386 Score: 279
Period size: 134 Copynumber: 2.0 Consensus size: 134
6111 TTGTTTAAAG
* *
6121 TTTTATAGTTTTACTAAACTAAAAACTCTATTTTTTATTTAATTAAGTCTAATATCCTTATAACT
1 TTTTATAGTTTTACTAAACTAAAAACTCTATTTTTTATATAATTAAATCTAATATCCTTATAACT
* * * * * ** **
6186 ATTTTATTTTTAGCAGTTTACTATTTTATTTTAATTAAAAAACCTAAATATTAGAATTTTTTAAA
66 ATTTTATTTTTACCAGTTTACTAATTTATATTAA-TAAAAAACATAAATATTAAAATAATAAAAA
6251 TATAT
130 TATAT
* * ** *
6256 TTTTATAGTTTTACTCAATTAAAAACTCTA-TTTTTATCAT-ATTAAATCTAATATTTTTATACC
1 TTTTATAGTTTTACTAAACTAAAAACTCTATTTTTTAT-ATAATTAAATCTAATATCCTTATAAC
* ** *
6319 TATTTTATTTTTACCATTTTACTAATTTA-ATTAA-AAAAATTATAAAGTTTTTAAAAATAATAA
65 TATTTTATTTTTACCAGTTTACTAATTTATATTAATAAAAAACATAAA--TATT-AAAATAATAA
6382 AAATA
127 AAATA
6387 GTAACATGCA
Statistics
Matches: 107, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
131 9 0.08
133 7 0.07
134 62 0.58
135 29 0.27
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (134 bp):
TTTTATAGTTTTACTAAACTAAAAACTCTATTTTTTATATAATTAAATCTAATATCCTTATAACT
ATTTTATTTTTACCAGTTTACTAATTTATATTAATAAAAAACATAAATATTAAAATAATAAAAAT
ATAT
Found at i:10789 original size:60 final size:60
Alignment explanation
Indices: 10708--10873 Score: 289
Period size: 60 Copynumber: 2.8 Consensus size: 60
10698 GCTAATTGCT
*
10708 CAAATAAGGGCTTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
* *
10768 CAAAGAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGGG-CTCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCT-GATCTTTTAATTTGGC
10828 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGA
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGA
10874 CATAGAAAAT
Statistics
Matches: 99, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
59 2 0.02
60 95 0.96
61 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:10870 original size:31 final size:31
Alignment explanation
Indices: 10704--10871 Score: 136
Period size: 31 Copynumber: 5.5 Consensus size: 31
10694 TTAGGCTAAT
*
10704 TGCTCAAATAAGGGCTTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * **
10735 TGCTCAAATAAGGGCCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAAAA
*
10764 TGGC-CAAAGAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * * **
10795 TACTCAAATAAGGGCTCGATC-TTT--TAATT
1 TGCTCAAATAAGGGC-CTAACGTTTGCCAAAA
10824 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
10855 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
10872 GACATAGAAA
Statistics
Matches: 102, Mismatches: 23, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
28 5 0.05
29 35 0.34
30 6 0.06
31 51 0.50
32 5 0.05
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:10949 original size:31 final size:31
Alignment explanation
Indices: 10910--11044 Score: 125
Period size: 31 Copynumber: 4.4 Consensus size: 31
10900 AACTGATTTC
* *
10910 AGGCCCTTATTTGAGCATTTTTGATAACGTT
1 AGGCCCTTATTTGAGAATTTTCGATAACGTT
* *
10941 AGGTCCTTATTTGAGAATTTTCGGTAACGTT
1 AGGCCCTTATTTGAGAATTTTCGATAACGTT
* *** *
10972 AGGCCCTTATTTG-GCCAAATTAAAATATCG--
1 AGGCCCTTATTTGAG--AATTTTCGATAACGTT
*
11002 -GGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGAATTTTCGATAACGTT
*
11032 AGACCCTTATTTG
1 AGGCCCTTATTTG
11045 GCTAAATTAA
Statistics
Matches: 80, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
28 8 0.10
29 12 0.15
30 2 0.03
31 50 0.62
32 8 0.10
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (31 bp):
AGGCCCTTATTTGAGAATTTTCGATAACGTT
Found at i:11021 original size:60 final size:60
Alignment explanation
Indices: 10945--11103 Score: 230
Period size: 60 Copynumber: 2.6 Consensus size: 60
10935 AACGTTAGGT
* * * *
10945 CCTTATTTGAGAATTTTCGGTAACGTTAGGCCCTTATTTGGCCAAATTAAAATATCGGGC
1 CCTTATTTGAGCATTTTCGGTAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGAC
* *
11005 CCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCTAAATTAAAAGATCGGAC
1 CCTTATTTGAGCATTTTCGGTAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGAC
* *
11065 CCTTATTTGAGCATTTT-GGCAAACGTTAGATCCTTATTT
1 CCTTATTTGAGCATTTTCGG-TAACGTTAGACCCTTATTT
11104 TAACAATTAG
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 1 0.01
60 88 0.99
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTCGGTAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGAC
Found at i:12499 original size:48 final size:48
Alignment explanation
Indices: 12382--12849 Score: 665
Period size: 48 Copynumber: 9.8 Consensus size: 48
12372 TTGATAACAA
* * * *
12382 AATAAAATATTGAGAACAACACCTTTCGACCGGGAAGGGCAAAA-GGG
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
* * *
12429 AATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCGAAACTGG
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
* * * *
12477 AATAGAACATTGAAAACGACACCTTCCGACTGGGAAGGGC-AAACTGGG
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAC-AGG
* *
12525 GATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGG
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
* * *
12573 AATAAAATATTGAAGACAACACCTCCCGACC-GGAAGGGCAAAAC-GAG
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAG-G
* * *
12620 AATAAAATATTGAAAACAACACCTTCCGATCGGGAAGGGCAAAATAGG
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
* * *
12668 AATAAAATATTGAAAACAAAACCTTCCGACCGGGAAGGGCAAAAGAGG
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
*
12716 AATAACACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
12764 AATGAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
1 AAT-AAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
12813 AATGAAAACATTGAAAACAACACCTTCCGACCGGGAA
1 AAT-AAAACATTGAAAACAACACCTTCCGACCGGGAA
12850 TGGGTATTTT
Statistics
Matches: 385, Mismatches: 29, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.00
47 87 0.23
48 211 0.55
49 86 0.22
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (48 bp):
AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
Found at i:12563 original size:143 final size:142
Alignment explanation
Indices: 12382--12849 Score: 681
Period size: 143 Copynumber: 3.3 Consensus size: 142
12372 TTGATAACAA
* * *
12382 AATAAAATATTGAGAACAACACCTTTCGACCGGGAAGGGCAAAAGGGAATAAAATATTGAAAACA
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAGGGAATAAAATATTGAAAACA
* * *
12447 ACACCTTCCGACCGGGAAGGGCGAAACTGGAATAGAACATTGAAAACGACACCTTCCGACTGGGA
66 ACACCTTCCGACCGGGAAGGGCAAAAC-GGAATAAAACATTGAAAACAACACCTTCCGACTGGGA
*
12512 AGGGCAAACTGGG
130 AGGGCAAACTAGG
* *
12525 GATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAATATTGAAGAC
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAA-GGGAATAAAATATTGAAAAC
* *
12590 AACACCTCCCGACC-GGAAGGGCAAAACGAGAATAAAATATTGAAAACAACACCTTCCGA-TCGG
65 AACACCTTCCGACCGGGAAGGGCAAAACG-GAATAAAACATTGAAAACAACACCTTCCGACT-GG
*
12653 GAAGGGCAAAATAGG
128 GAAGGGCAAACTAGG
* * * *
12668 AATAAAATATTGAAAACAAAACCTTCCGACCGGGAAGGGCAAAAGAGGAATAACACATTGAAAAC
1 AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAG-GGAATAAAATATTGAAAAC
*
12733 AACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAAACATTGAAAACAACACCTTCCGACCGG
65 AACACCTTCCGACCGGGAAGGGCAAAAC-GGAAT-AAAACATTGAAAACAACACCTTCCGACTGG
12798 GAAGGGCAAAAC-AGG
128 GAAGGGC-AAACTAGG
12813 AATGAAAACATTGAAAACAACACCTTCCGACCGGGAA
1 AAT-AAAACATTGAAAACAACACCTTCCGACCGGGAA
12850 TGGGTATTTT
Statistics
Matches: 291, Mismatches: 24, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
142 3 0.01
143 164 0.56
144 49 0.17
145 41 0.14
146 34 0.12
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (142 bp):
AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAGGGAATAAAATATTGAAAACA
ACACCTTCCGACCGGGAAGGGCAAAACGGAATAAAACATTGAAAACAACACCTTCCGACTGGGAA
GGGCAAACTAGG
Found at i:12706 original size:191 final size:192
Alignment explanation
Indices: 12382--12849 Score: 687
Period size: 191 Copynumber: 2.4 Consensus size: 192
12372 TTGATAACAA
* *
12382 AATAAAATATTG-AGAACAACACCTTTCGACCGGGAAGGGCAAAA-GGGAATAAAATATTGAAAA
1 AATAAAATATTGAAG-ACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATAAAATATTGAAAA
* * * * *
12445 CAACACCTTCCGACCGGGAAGGGCGAAACTGGAATAGAACATTGAAAACGACACCTTCCGACTGG
65 CAACACCTTCCGACCGGGAAGGGCGAAAATGGAATAAAACATTGAAAACAAAACCTTCCGACCGG
* * *
12510 GAAGGGCAAACTG-GGGATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGG
130 GAAGGGCAAA-AGAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
*
12573 AATAAAATATTGAAGACAACACCTCCCGACC-GGAAGGGCAAAACGAGAATAAAATATTGAAAAC
1 AATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATAAAATATTGAAAAC
* *
12637 AACACCTTCCGATCGGGAAGGGC-AAAATAGGAATAAAATATTGAAAACAAAACCTTCCGACCGG
66 AACACCTTCCGACCGGGAAGGGCGAAAAT-GGAATAAAACATTGAAAACAAAACCTTCCGACCGG
*
12701 GAAGGGCAAAAGAGGAATAACACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
130 GAAGGGCAAAAGAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
* * *
12764 AATGAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAC-AGGAATGAAAACATTGAA
1 AAT-AAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGA-GAAT-AAAATATTGAA
12828 AACAACACCTTCCGACCGGGAA
63 AACAACACCTTCCGACCGGGAA
12850 TGGGTATTTT
Statistics
Matches: 250, Mismatches: 19, Indels: 13
0.89 0.07 0.05
Matches are distributed among these distances:
190 17 0.07
191 157 0.63
192 28 0.11
193 17 0.07
194 31 0.12
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (192 bp):
AATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATAAAATATTGAAAAC
AACACCTTCCGACCGGGAAGGGCGAAAATGGAATAAAACATTGAAAACAAAACCTTCCGACCGGG
AAGGGCAAAAGAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGG
Done.