Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016228.1 Corchorus olitorius cultivar O-4 contig16261, 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: 41644
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:72 original size:22 final size:23
Alignment explanation
Indices: 30--74 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
20 TTTTGTTTTA
*
30 TAGTTTAGACAAAGATTAGTTAT
1 TAGTTTAGACAAAGATAAGTTAT
53 TAGTTTAGTA-AAAGA-AAGTTAT
1 TAGTTTAG-ACAAAGATAAGTTAT
75 GGGCCGTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 13 0.65
24 1 0.05
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (23 bp):
TAGTTTAGACAAAGATAAGTTAT
Found at i:2416 original size:10 final size:10
Alignment explanation
Indices: 2401--2456 Score: 85
Period size: 10 Copynumber: 5.6 Consensus size: 10
2391 AATTTAATAT
2401 GGATATTTAC
1 GGATATTTAC
2411 GGATATTTAC
1 GGATATTTAC
*
2421 AGATATTTAC
1 GGATATTTAC
*
2431 AGATATTTAC
1 GGATATTTAC
*
2441 GAATATTTAC
1 GGATATTTAC
2451 GGATAT
1 GGATAT
2457 ATCGAGGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (10 bp):
GGATATTTAC
Found at i:3835 original size:35 final size:36
Alignment explanation
Indices: 3788--3857 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 36
3778 AAACATTAAT
* *
3788 AATTGGACAAAAAGAAAAAAAAGTTGAAGCATCAAC
1 AATTGGACAAAAAGAAAAAAAAGATAAAGCATCAAC
*
3824 AATTGG-CAAAAAGAAAAAGAAGATAAAGCATCAA
1 AATTGGACAAAAAGAAAAAAAAGATAAAGCATCAA
3858 TAGTCAATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.13
Consensus pattern (36 bp):
AATTGGACAAAAAGAAAAAAAAGATAAAGCATCAAC
Found at i:4771 original size:2 final size:2
Alignment explanation
Indices: 4766--4798 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4756 TTCGTGTGTG
4766 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4799 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4803 original size:2 final size:2
Alignment explanation
Indices: 4798--4822 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4788 TCTCTCTCTC
4798 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4823 CTCCTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6664 original size:13 final size:13
Alignment explanation
Indices: 6643--6672 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6633 CTTCTCTATA
6643 TCTTCTTCTTTTT
1 TCTTCTTCTTTTT
*
6656 TCTTTTTCTTTTT
1 TCTTCTTCTTTTT
6669 TCTT
1 TCTT
6673 GTCAATTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TCTTCTTCTTTTT
Found at i:7304 original size:16 final size:16
Alignment explanation
Indices: 7283--7313 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7273 CGAAATTTCC
*
7283 TTTGGACATTGAGAAT
1 TTTGGACATTAAGAAT
7299 TTTGGACATTAAGAA
1 TTTGGACATTAAGAA
7314 CTAGGGTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (16 bp):
TTTGGACATTAAGAAT
Found at i:7773 original size:51 final size:52
Alignment explanation
Indices: 7697--7795 Score: 182
Period size: 51 Copynumber: 1.9 Consensus size: 52
7687 AACCCTAGGC
*
7697 CAATAAATAATAATAATAATTATATAATTACCATAATTAGAAGTATAAAGGT
1 CAATAAATAATAATAATAATGATATAATTACCATAATTAGAAGTATAAAGGT
7749 CAAT-AATAATAATAATAATGATATAATTACCATAATTAGAAGTATAA
1 CAATAAATAATAATAATAATGATATAATTACCATAATTAGAAGTATAA
7796 TAGATTAACA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 42 0.91
52 4 0.09
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.32
Consensus pattern (52 bp):
CAATAAATAATAATAATAATGATATAATTACCATAATTAGAAGTATAAAGGT
Found at i:8401 original size:4 final size:4
Alignment explanation
Indices: 8384--8417 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
8374 TAGTTCTCTT
* *
8384 TTTC TTTT TTTC TTTC TTTC TATC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
8418 CTATGTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:13261 original size:27 final size:27
Alignment explanation
Indices: 13224--13277 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
13214 GATCAGTTTA
13224 AAAAATGGCAGCAGGCTCATTTGGGGT
1 AAAAATGGCAGCAGGCTCATTTGGGGT
13251 AAAAATGGCAGCAGGCTCATTTGGGGT
1 AAAAATGGCAGCAGGCTCATTTGGGGT
13278 TTTAGCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (27 bp):
AAAAATGGCAGCAGGCTCATTTGGGGT
Found at i:18473 original size:17 final size:18
Alignment explanation
Indices: 18436--18482 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
18426 AGTGAGGCAT
*
18436 TAAAAAAAAAG-AGAGAA
1 TAAAGAAAAAGAAGAGAA
18453 -AAAGAAAAAGAAGA-AA
1 TAAAGAAAAAGAAGAGAA
*
18469 TAAAGAAAGAGAAG
1 TAAAGAAAAAGAAG
18483 CCGCGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (18 bp):
TAAAGAAAAAGAAGAGAA
Found at i:20730 original size:75 final size:75
Alignment explanation
Indices: 20607--20756 Score: 246
Period size: 75 Copynumber: 2.0 Consensus size: 75
20597 AGACCTACAT
* *
20607 GCACATAATCAAGTTCATGATAAAGTATAGGATAGAACCTGAACTAATACCATGTATCTCAGCCA
1 GCACACAACCAAGTTCATGATAAAGTATAGGATAGAACCTGAACTAATACCATGTATCTCAGCCA
20672 CCTACAATTA
66 CCTACAATTA
* * * *
20682 GCACACAACCAAGTTCATGATAAAGTATATGATAGAACCTGAACTAATACCATGTATTTCGGCTA
1 GCACACAACCAAGTTCATGATAAAGTATAGGATAGAACCTGAACTAATACCATGTATCTCAGCCA
20747 CCTACAATTA
66 CCTACAATTA
20757 ATCGACAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (75 bp):
GCACACAACCAAGTTCATGATAAAGTATAGGATAGAACCTGAACTAATACCATGTATCTCAGCCA
CCTACAATTA
Found at i:29688 original size:17 final size:19
Alignment explanation
Indices: 29666--29704 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
29656 AATTTCCCCT
*
29666 AAAAAA-TTCCTC-AAAAA
1 AAAAAATTTCCCCTAAAAA
29683 AAAAAATTTCCCCTAAAAA
1 AAAAAATTTCCCCTAAAAA
29702 AAA
1 AAA
29705 GAAAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 5 0.26
19 8 0.42
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAAATTTCCCCTAAAAA
Found at i:38217 original size:31 final size:31
Alignment explanation
Indices: 38195--38280 Score: 154
Period size: 31 Copynumber: 2.8 Consensus size: 31
38185 GCATACCGCG
*
38195 TGTACCAAAAAGCGACAAGTGGCACGCCACA
1 TGTACCAAAAAGCGACACGTGGCACGCCACA
38226 TGTACCAAAAAGCGACACGTGGCACGCCACA
1 TGTACCAAAAAGCGACACGTGGCACGCCACA
*
38257 TGTACCAAAAAGTGACACGTGGCA
1 TGTACCAAAAAGCGACACGTGGCA
38281 TGCCTCGTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.37, C:0.28, G:0.23, T:0.12
Consensus pattern (31 bp):
TGTACCAAAAAGCGACACGTGGCACGCCACA
Found at i:38726 original size:18 final size:18
Alignment explanation
Indices: 38703--38740 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
38693 TAGTATTGTA
38703 ATATATATA-TATTATATT
1 ATATATATACTA-TATATT
38721 ATATATATACTATATATT
1 ATATATATACTATATATT
38739 AT
1 AT
38741 TTTTAGTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATATATACTATATATT
Found at i:40300 original size:293 final size:293
Alignment explanation
Indices: 39867--40454 Score: 1000
Period size: 293 Copynumber: 2.0 Consensus size: 293
39857 ATTTTTAGTG
*
39867 GCTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCTTTTTTTGG
1 GCTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTACCTCCTTTTGGCTTTTTTTGG
* *
39932 TCTTTTCTCACTTTTCAGGTGACTAAAAAGGCCCTTGATGAATTTCCTCCCTTACTTTTCCTGCT
66 TCTTTTCTCACTTTTCAGGTGACTAAAAAGACCCTCGATGAATTTCCTCCCTTACTTTTCCTGCT
*
39997 GCCCTTTTTTGTAATTTACTATTTTTGTATTTATGATTAAGTGTGTTTT-AATGACATATTAATT
131 GCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAAAT-ACATATTAATT
* * * **
40061 GTGTGTGGATATTAGGATTTACTGGTTCAACTCCTCTGCCGGAATTCCAAATGATTGGTGCTATA
195 GTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCAGAATTCCAAAGGATTAATGCTATA
40126 AATGTATCTACCCGAATTCATTAATTTAACAATT
260 AATGTATCTACCCGAATTCATTAATTTAACAATT
*
40160 GCTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTACCTCCTTTTGGCTTTTGTTTT
1 GCTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTACCTCCTTTTGGCTTTT-TTTG
* * *
40225 GTCTTTTCTCACTTTTCGGGTGACTAAAAATACCCTCGATGAATTTCCTCCCTTACTTTTTCTGC
65 GTCTTTTCTCACTTTTCAGGTGACTAAAAAGACCCTCGATGAATTTCCTCCCTTACTTTTCCTGC
*
40290 TG-CTTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAAATACATATTAATT
130 TGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAAATACATATTAATT
40354 GTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCAGAATTCCAAAGGATTAATGCTATA
195 GTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCAGAATTCCAAAGGATTAATGCTATA
* *
40419 AATGTGTCTACCCGAGTTCATTAATTTAACAATT
260 AATGTATCTACCCGAATTCATTAATTTAACAATT
40453 GC
1 GC
40455 AATCAAGATT
Statistics
Matches: 277, Mismatches: 16, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
293 209 0.75
294 68 0.25
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (293 bp):
GCTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTACCTCCTTTTGGCTTTTTTTGG
TCTTTTCTCACTTTTCAGGTGACTAAAAAGACCCTCGATGAATTTCCTCCCTTACTTTTCCTGCT
GCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAAATACATATTAATTG
TGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCAGAATTCCAAAGGATTAATGCTATAA
ATGTATCTACCCGAATTCATTAATTTAACAATT
Done.