Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015494.1 Corchorus olitorius cultivar O-4 contig15527, 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: 44115
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:1392 original size:29 final size:29
Alignment explanation
Indices: 1350--1414 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1340 AAGAGTGACT
*
1350 AAAACGTCCAAAATTGAAATTTAAAGGAC
1 AAAACGTCCAAAATTGAAACTTAAAGGAC
* *
1379 AAAACGTCCAAAATTGAAGCTTAGAGGAC
1 AAAACGTCCAAAATTGAAACTTAAAGGAC
*
1408 ACAACGT
1 AAAACGT
1415 TAAAACCCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (29 bp):
AAAACGTCCAAAATTGAAACTTAAAGGAC
Found at i:4950 original size:31 final size:31
Alignment explanation
Indices: 4915--5113 Score: 222
Period size: 31 Copynumber: 6.3 Consensus size: 31
4905 CACAATGAGG
* *
4915 ACTAAACTGACCCAATCTTGTGAGTACAGTA
1 ACTAAATTGACCCAATCTTGTGAGTACAGGA
* * *
4946 ACTAAATTGTCCCAATTTTGTGAGTATAGGA
1 ACTAAATTGACCCAATCTTGTGAGTACAGGA
* *
4977 ACTAAATTGACCCAATCTTGTCAGTACAGGG
1 ACTAAATTGACCCAATCTTGTGAGTACAGGA
* *
5008 ACTCAATTGACCCAATCTTATGAGTACAGGA
1 ACTAAATTGACCCAATCTTGTGAGTACAGGA
*
5039 ACTAAACATTGACCCAATCTTGTGAGAACATGGA
1 ACT-AA-ATTGACCCAATCTTGTGAGTACA-GGA
* *
5073 A-TAAAATTG-CCCAAATCTTGTGAGTGCAGGG
1 ACT-AAATTGACCC-AATCTTGTGAGTACAGGA
*
5104 ATTAAATTGA
1 ACTAAATTGA
5114 TCGCGTTTTG
Statistics
Matches: 142, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
31 94 0.66
32 19 0.13
33 25 0.18
34 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (31 bp):
ACTAAATTGACCCAATCTTGTGAGTACAGGA
Found at i:8429 original size:26 final size:24
Alignment explanation
Indices: 8379--8442 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 24
8369 GTTAACAAAT
*
8379 ATGTACTATATA-ATATATTAATA
1 ATGTAATATATATATATATTAATA
8402 ATGTAATATATATATATATATAATTA
1 ATGTAATATATATATATAT-TAA-TA
*
8428 AT-TGAATATAAATAT
1 ATGT-AATATATATAT
8443 CTAAAATCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 11 0.31
24 6 0.17
25 4 0.11
26 14 0.40
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (24 bp):
ATGTAATATATATATATATTAATA
Found at i:15684 original size:16 final size:15
Alignment explanation
Indices: 15643--15687 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
15633 GGGAGGGAAT
15643 GGGAAGGAAAGAAGAG
1 GGGAAGGAAAGAA-AG
*
15659 GGG-CGGAAAGAAATG
1 GGGAAGGAAAGAAA-G
15674 GGGAAGGAAAGAAA
1 GGGAAGGAAAGAAA
15688 AGCTTTCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 12 0.48
16 12 0.48
ACGTcount: A:0.49, C:0.02, G:0.47, T:0.02
Consensus pattern (15 bp):
GGGAAGGAAAGAAAG
Found at i:16222 original size:9 final size:11
Alignment explanation
Indices: 16193--16220 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
16183 TAACGTTCTG
16193 TAATATATTTA
1 TAATATATTTA
16204 TAATATATTTA
1 TAATATATTTA
16215 TAATAT
1 TAATAT
16221 TTTGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TAATATATTTA
Found at i:16535 original size:16 final size:16
Alignment explanation
Indices: 16510--16569 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
16500 TATGACTTCC
*
16510 TTTCCCTTCCTCCCTA
1 TTTCCTTTCCTCCCTA
***
16526 TTTCCTTTCCCTTGTTA
1 TTTCCTTT-CCTCCCTA
*
16543 TTTCCTTTCCTTCCTA
1 TTTCCTTTCCTCCCTA
16559 TTT-CTTTCCTC
1 TTTCCTTTCCTC
16570 TCAACCAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 7 0.19
16 16 0.44
17 13 0.36
ACGTcount: A:0.05, C:0.38, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTCCTTTCCTCCCTA
Found at i:17815 original size:21 final size:21
Alignment explanation
Indices: 17780--17821 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17770 TATGTGTGTG
*
17780 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
17802 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
17822 GACCGAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:18687 original size:21 final size:21
Alignment explanation
Indices: 18652--18693 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18642 TGGGTGTGTG
*
18652 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
18674 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
18694 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:34479 original size:15 final size:15
Alignment explanation
Indices: 34459--34489 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34449 GATTAACCTG
34459 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
34474 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
34489 T
1 T
34490 AATGTATTGT
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:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:35818 original size:2 final size:2
Alignment explanation
Indices: 35760--35803 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
35750 TAAGGTCATA
*
35760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
35803 A
1 A
35804 CTATTTGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37251 original size:111 final size:112
Alignment explanation
Indices: 37052--37269 Score: 402
Period size: 111 Copynumber: 2.0 Consensus size: 112
37042 GATCCACTTG
37052 TTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACA
1 TTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACA
*
37117 AAATGCAATGAACTATTGGATTTAAAG-AAAATACAAGCACCTATTA
66 AAATGCAATGAACTATTGAATTTAAAGAAAAATACAAGCACCTATTA
*
37163 TTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACA
1 TTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACA
*
37228 AAGTGCAATGAACTATTGAATTTAAAGAAAAATACAAGCACC
66 AAATGCAATGAACTATTGAATTTAAAGAAAAATACAAGCACC
37270 AAAATGATTA
Statistics
Matches: 103, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
111 89 0.86
112 14 0.14
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (112 bp):
TTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACA
AAATGCAATGAACTATTGAATTTAAAGAAAAATACAAGCACCTATTA
Found at i:38475 original size:107 final size:105
Alignment explanation
Indices: 38338--38538 Score: 285
Period size: 107 Copynumber: 1.9 Consensus size: 105
38328 AAGAATTGAT
* * * * *
38338 TTATAGGGTTAGTATTAAAATTTAAAATTTATTATTATAGGGTTTTAGTTCGAATATATTTAATC
1 TTATAGGGTAAGTATTAAAATATAAAATTTATAATTATAGGCTTTTAGTTCG-A-ATATTTAACC
*
38403 ATAATAATTTCATAGAGTAAAGCCCCAAATTTAAAAAGAAAA
64 ATAATAATTTCATAAAGTAAAGCCCCAAATTTAAAAAGAAAA
* * *
38445 TTATAGGGTAAGTATTAAAATATAAGATTTATAATTATAGGCTTTTAGTTTGAATATTTAGCCAT
1 TTATAGGGTAAGTATTAAAATATAAAATTTATAATTATAGGCTTTTAGTTCGAATATTTAACCAT
* *
38510 AATAATTTCATAAAGTTAAGCTCCAAATT
66 AATAATTTCATAAAGTAAAGCCCCAAATT
38539 AAGAAAAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
105 36 0.43
106 1 0.01
107 46 0.55
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (105 bp):
TTATAGGGTAAGTATTAAAATATAAAATTTATAATTATAGGCTTTTAGTTCGAATATTTAACCAT
AATAATTTCATAAAGTAAAGCCCCAAATTTAAAAAGAAAA
Found at i:38576 original size:105 final size:106
Alignment explanation
Indices: 38342--38577 Score: 248
Period size: 105 Copynumber: 2.2 Consensus size: 106
38332 ATTGATTTAT
* * * * * *
38342 AGGGTTAGTATTAAAATTTAAAATTTATTATTATAGGGTTTTAGTTCGAATATATTTAATCATAA
1 AGGGTAAGCATTAAAATTTAAGATTTATAATTATAGGCTTTTAGTTCGAATATATTTAACCATAA
* *
38407 TAATTTCATAGAGTAAAGCCCCAAATTTAAAAAGAAAATTAT
66 TAATTTCATAAAGTAAAGCCCCAAATTTAAAAAGAAAA-TAA
* * * *
38449 AGGGTAAGTATTAAAATATAAGATTTATAATTATAGGCTTTTAGTTTG-A-ATATTTAGCCATAA
1 AGGGTAAGCATTAAAATTTAAGATTTATAATTATAGGCTTTTAGTTCGAATATATTTAACCATAA
* *
38512 TAATTTCATAAAGTTAAGCTCCAAA-TTAAGAAA-AAAA-AA
66 TAATTTCATAAAGTAAAGCCCCAAATTTAA-AAAGAAAATAA
* *
38551 AGGGGCTAAAGCCTTATAATTTAAGAT
1 A-GGG-T-AAGCATTAAAATTTAAGAT
38578 ATACTACTAT
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
102 2 0.02
103 3 0.03
104 9 0.08
105 52 0.48
106 1 0.01
107 42 0.39
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (106 bp):
AGGGTAAGCATTAAAATTTAAGATTTATAATTATAGGCTTTTAGTTCGAATATATTTAACCATAA
TAATTTCATAAAGTAAAGCCCCAAATTTAAAAAGAAAATAA
Found at i:42164 original size:122 final size:124
Alignment explanation
Indices: 42027--42273 Score: 426
Period size: 122 Copynumber: 2.0 Consensus size: 124
42017 CATTGTTTAA
* *
42027 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTA-TGA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATTGA
*
42091 TTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAA-TTTTTAAATAT
66 TTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAAAATTTTTTAAATAT
* *
42149 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATTTA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATTGA
*
42214 TTTTTACCATTTTACTATTTTATTTAAAAAACTTATATATATTAAAATTTTTTAAATAT
66 TTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAAAATTTTTTAAATAT
42273 A
1 A
42274 TTTCTTAAAT
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
122 58 0.50
123 47 0.40
124 12 0.10
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (124 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATTGA
TTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAAAATTTTTTAAATAT
Found at i:42295 original size:14 final size:13
Alignment explanation
Indices: 42258--42297 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
42248 ATATATATTA
42258 AAATTTTTTAAAT
1 AAATTTTTTAAAT
* *
42271 ATATTTCTTAAAT
1 AAATTTTTTAAAT
42284 GAAATTTTTTAAAT
1 -AAATTTTTTAAAT
42298 TTTACAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (13 bp):
AAATTTTTTAAAT
Found at i:43172 original size:16 final size:16
Alignment explanation
Indices: 43151--43187 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
43141 ATTAGGTTTA
43151 TGTAATTTGCCAAAAT
1 TGTAATTTGCCAAAAT
*
43167 TGTAATTTGGCAAAAT
1 TGTAATTTGCCAAAAT
*
43183 CGTAA
1 TGTAA
43188 AAGGCAGCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (16 bp):
TGTAATTTGCCAAAAT
Done.