Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024755.1 Corchorus olitorius cultivar O-4 contig24788, 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: 51829
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:10178 original size:12 final size:11
Alignment explanation
Indices: 10160--10188 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
10150 GGTGAAGAAG
10160 ATTTTTTTTTT
1 ATTTTTTTTTT
10171 ATTTTTTTTTT
1 ATTTTTTTTTT
10182 ATTTTTT
1 ATTTTTT
10189 GCCAAAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (11 bp):
ATTTTTTTTTT
Found at i:17375 original size:5 final size:5
Alignment explanation
Indices: 17365--17390 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17355 GCATGGGGGC
17365 GTTTT GTTTT GTTTT GTTTT GTTTT G
1 GTTTT GTTTT GTTTT GTTTT GTTTT G
17391 ATGTTAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (5 bp):
GTTTT
Found at i:19632 original size:13 final size:13
Alignment explanation
Indices: 19616--19643 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19606 ATAAGTTCTA
19616 AGTTTTAGTTTTT
1 AGTTTTAGTTTTT
19629 AGTTTTAGTTTTT
1 AGTTTTAGTTTTT
19642 AG
1 AG
19644 GGAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (13 bp):
AGTTTTAGTTTTT
Found at i:23532 original size:21 final size:21
Alignment explanation
Indices: 23508--23556 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
23498 ATAGTTTAGA
* *
23508 TTTAATTTACTTTGC-TTTGTT
1 TTTAATTTA-ATTGCTTTTCTT
*
23529 TTTAGTTTAATTGCTTTTCTT
1 TTTAATTTAATTGCTTTTCTT
23550 TTTAATT
1 TTTAATT
23557 GCTATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTAATTTAATTGCTTTTCTT
Found at i:27505 original size:40 final size:41
Alignment explanation
Indices: 27409--27508 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 41
27399 TTTCCGTTTA
* * *
27409 CAATTTAGTCCCTGATTTAGGTTTATATTTGTTAATTGATT
1 CAATTTAGTCCCTGATTTAGGTTAATATTTATTAATTGATG
* *
27450 CAATTTTGTCCCTGATTTAGAG-TAATATTTATTTATTG-TG
1 CAATTTAGTCCCTGATTTAG-GTTAATATTTATTAATTGATG
* *
27490 CAATTTCGCCCCTGATTTA
1 CAATTTAGTCCCTGATTTA
27509 AGATTTTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 18 0.35
41 32 0.63
42 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (41 bp):
CAATTTAGTCCCTGATTTAGGTTAATATTTATTAATTGATG
Found at i:34969 original size:31 final size:32
Alignment explanation
Indices: 34933--34997 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
34923 ATTACTATTG
* *
34933 ATATTTAATTAA-TAAGTAGGGTTAAATGCAT
1 ATATTTAATAAATTAAGTAGGGTCAAATGCAT
* * *
34964 ATATTTCATAAATTCAGTGGGGTCAAATGCAT
1 ATATTTAATAAATTAAGTAGGGTCAAATGCAT
34996 AT
1 AT
34998 TTCACAACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (32 bp):
ATATTTAATAAATTAAGTAGGGTCAAATGCAT
Found at i:37947 original size:101 final size:102
Alignment explanation
Indices: 37770--37978 Score: 366
Period size: 101 Copynumber: 2.0 Consensus size: 102
37760 CCAATTTTCT
*
37770 AATATGTGAATAGCACTAATTAGTTTTATATATATACAAGTACTATTGTCTTACTAATTACTCCC
1 AATATGTGAATAACACTAATTAG-TTTATATATATACAAGTACTATTGTCTTACTAATTACTCCC
*
37835 TCCGTCCCATATTATCTGTCCATTTTAATCATATCACA
65 TCCGTCCCATATTATCTGTCCATTTTAACCATATCACA
37873 AATATGTGAATAACACTAATTAG-TTATATATATACAAGTACTATTGTCTTACTAATTACTCCCT
1 AATATGTGAATAACACTAATTAGTTTATATATATACAAGTACTATTGTCTTACTAATTACTCCCT
* *
37937 CCGTCCCATATTATTTGTCCATTTTGACCATATCACA
66 CCGTCCCATATTATCTGTCCATTTTAACCATATCACA
37974 AATAT
1 AATAT
37979 TAAGAAAGTT
Statistics
Matches: 102, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
101 80 0.78
103 22 0.22
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (102 bp):
AATATGTGAATAACACTAATTAGTTTATATATATACAAGTACTATTGTCTTACTAATTACTCCCT
CCGTCCCATATTATCTGTCCATTTTAACCATATCACA
Found at i:45629 original size:22 final size:22
Alignment explanation
Indices: 45604--45656 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
45594 ATTACATTAT
*
45604 TTTTGATGA-CTTTCTTATGAAA
1 TTTTGATAACCTTTC-TATGAAA
45626 TTTTGATAACCTTTCTATGAAA
1 TTTTGATAACCTTTCTATGAAA
*
45648 TTTTAATAA
1 TTTTGATAA
45657 TGATACTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTTGATAACCTTTCTATGAAA
Found at i:45710 original size:22 final size:22
Alignment explanation
Indices: 45684--45725 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45674 GAGAACTTTT
* *
45684 TTATAAATTTTTTTTAACCTTC
1 TTATAAAATTTTGTTAACCTTC
45706 TTATAAAATTTTGTTAACCT
1 TTATAAAATTTTGTTAACCT
45726 CCCTAAGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATAAAATTTTGTTAACCTTC
Found at i:45994 original size:22 final size:22
Alignment explanation
Indices: 45711--46134 Score: 224
Period size: 22 Copynumber: 19.4 Consensus size: 22
45701 CCTTCTTATA
* *
45711 AAATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACCTCCCTATG
*
45733 GAATTTTGA-AGACCTCACC-ATG
1 AAATTTTGATA-ACCTC-CCTATG
* * ** *
45755 AAATTTTGTTTATTTCCCAATG
1 AAATTTTGATAACCTCCCTATG
* *
45777 AAATTTTGATAACCAACACTATG
1 AAATTTTGATAACC-TCCCTATG
* * *
45800 AAATGTTGATAACTTCCATATG
1 AAATTTTGATAACCTCCCTATG
* * * **
45822 ATATATTGATAACCACGTTATG
1 AAATTTTGATAACCTCCCTATG
* * * * *
45844 AAAATTTAAAAATCTCCATATG
1 AAATTTTGATAACCTCCCTATG
* * * *
45866 -AATTGTT-AGTAATCACACTCTG
1 AAATT-TTGA-TAACCTCCCTATG
* * *
45888 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCTCCCTATG
* * *
45910 AAATTGTAATAACCTCGCTATG
1 AAATTTTGATAACCTCCCTATG
* *
45932 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGAT-AACCTCCCTATG
*
45955 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCCCTATG
*
45978 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCCCTATG
** *
46000 AAACCTTGATAA-----CTA-C
1 AAATTTTGATAACCTCCCTATG
46016 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
46038 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
* * *
46060 AAATTTTGTTAATCTCCTTATG
1 AAATTTTGATAACCTCCCTATG
* * *
46082 AAATTTTGATCTA-CACGCTATG
1 AAATTTTGAT-AACCTCCCTATG
*
46104 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CCTATG
46126 AAATTTTGA
1 AAATTTTGA
46135 AAACTAAACT
Statistics
Matches: 304, Mismatches: 79, Indels: 38
0.72 0.19 0.09
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
21 12 0.04
22 214 0.70
23 66 0.22
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:46374 original size:66 final size:65
Alignment explanation
Indices: 46263--46416 Score: 173
Period size: 66 Copynumber: 2.3 Consensus size: 65
46253 CCCTAGAAAT
* * * * *
46263 AACACTATGAAATTTTGGTAAATCACATTTTGAAAATTTGATAACCTCTCTATAAAATTTTGTTA
1 AACACTATGAAATTTTGAT-AATAACATTCTGAAAATTTGATAACCTCGCTATAAAA-TTTGATA
46328 AC
64 AC
** * * * * *
46330 CCCTCTATGAAATTTTGATAATAACATTCTGTAATTTTGATAACCTCGCTTTGAAATTTGATAAC
1 AACACTATGAAATTTTGATAATAACATTCTGAAAATTTGATAACCTCGCTATAAAATTTGATAAC
*
46395 AACAGTATGAAATTTTGATAAT
1 AACACTATGAAATTTTGATAAT
46417 CTTCCGATAA
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
65 26 0.37
66 30 0.42
67 15 0.21
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (65 bp):
AACACTATGAAATTTTGATAATAACATTCTGAAAATTTGATAACCTCGCTATAAAATTTGATAAC
Found at i:46409 original size:43 final size:44
Alignment explanation
Indices: 46317--46415 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 44
46307 CCTCTCTATA
* * * * *
46317 AAATTTTGTTAACCCCTCTATGAAATTTTGATAATAACATTCTG
1 AAATTTTGATAACCCCGCTATGAAATTTTGATAACAACAGTATG
* * *
46361 TAATTTTGATAACCTCGCTTTGAAA-TTTGATAACAACAGTATG
1 AAATTTTGATAACCCCGCTATGAAATTTTGATAACAACAGTATG
46404 AAATTTTGATAA
1 AAATTTTGATAA
46416 TCTTCCGATA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 26 0.57
44 20 0.43
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (44 bp):
AAATTTTGATAACCCCGCTATGAAATTTTGATAACAACAGTATG
Found at i:46596 original size:22 final size:22
Alignment explanation
Indices: 46264--46683 Score: 157
Period size: 22 Copynumber: 18.9 Consensus size: 22
46254 CCTAGAAATA
* *
46264 ACACTATGAAATTTTGGTAAATC
1 ACACTATGAAATTTTGAT-AACC
* * *
46287 ACATTTTGAAAATTTGATAACC
1 ACACTATGAAATTTTGATAACC
* * * *
46309 TCTCTATAAAATTTTGTTAACC
1 ACACTATGAAATTTTGATAACC
* * **
46331 CCTCTATGAAATTTTGATAATA
1 ACACTATGAAATTTTGATAACC
* * *
46353 ACATTCTGTAATTTTGATAACC
1 ACACTATGAAATTTTGATAACC
* * * *
46375 TCGCTTTGAAA-TTTGATAACA
1 ACACTATGAAATTTTGATAACC
* *
46396 ACAGTATGAAATTTTGATAATCT
1 ACACTATGAAATTTTGATAA-CC
* *
46419 TC-CGAT-AAATTTTGATAATCC
1 ACACTATGAAATTTTGATAA-CC
* * *
46440 TATCTCTATGAAATTTCGATAATC
1 -A-CACTATGAAATTTTGATAACC
* * *
46464 ACTCTATGATATTTT-ACAACC
1 ACACTATGAAATTTTGATAACC
** * *
46485 -TTCTATCAAATTTTGGT-ACTC
1 ACACTATGAAATTTTGATAAC-C
* *
46506 -C-TTATGAAATTGAGACTTTTATAACC
1 ACACTATGAAA-T-----TTTGATAACC
*
46532 TTCA-TATGAAATTTTGATAACC
1 -ACACTATGAAATTTTGATAACC
*
46554 ACACTA-AAAACTTTTGATAACC
1 ACACTATGAAA-TTTTGATAACC
46576 ACACTATGAAATTTTGATAACC
1 ACACTATGAAATTTTGATAACC
* * * *
46598 TCCCCATGAAATATT-AGTAACC
1 ACACTATGAAATTTTGA-TAACC
* * *
46620 TC-CTTATGAAATTTTGTTGACC
1 ACAC-TATGAAATTTTGATAACC
46642 ACACTATGAAATTCTT-ATAACC
1 ACACTATGAAATT-TTGATAACC
* *
46664 TCGCTATGACAA-TTTGATAA
1 ACACTATGA-AATTTTGATAA
46684 TCTCTTTGAT
Statistics
Matches: 295, Mismatches: 74, Indels: 57
0.69 0.17 0.13
Matches are distributed among these distances:
20 19 0.06
21 45 0.15
22 174 0.59
23 26 0.09
24 4 0.01
25 11 0.04
26 5 0.02
27 3 0.01
28 8 0.03
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
ACACTATGAAATTTTGATAACC
Found at i:46776 original size:24 final size:22
Alignment explanation
Indices: 46692--46823 Score: 90
Period size: 22 Copynumber: 5.9 Consensus size: 22
46682 AATCTCTTTG
* * * *
46692 ATAACCTTTCTATAAAATTGTG
1 ATAACCTTCCTATGAAATTTTA
* *
46714 ATAACC-ACGCTATGAAATTTCA
1 ATAACCTTC-CTATGAAATTTTA
*
46736 ATAACCTTCCTAAGAAATTTTA
1 ATAACCTTCCTATGAAATTTTA
*
46758 ATAACCTTATCCTATGAAATTTTG
1 ATAACC-T-TCCTATGAAATTTTA
* * *
46782 GTAACC-ACACTATGAAATTTTG
1 ATAACCTTC-CTATGAAATTTTA
*
46804 ATAA-CTTCCATATAAAATTT
1 ATAACCTTCC-TATGAAATTT
46824 CGGTAACCAC
Statistics
Matches: 87, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
21 3 0.03
22 64 0.74
23 2 0.02
24 18 0.21
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (22 bp):
ATAACCTTCCTATGAAATTTTA
Found at i:46844 original size:22 final size:22
Alignment explanation
Indices: 46769--46853 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
46759 TAACCTTATC
46769 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
46791 CTATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGGTAAC--CACA
* *
46814 -TATAAAATTTCGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
46835 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
46854 TCCTCATGGA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 45 0.88
23 2 0.04
24 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:50454 original size:13 final size:13
Alignment explanation
Indices: 50421--50473 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
50411 GCACCCAAAA
*
50421 CATTTAT-TAAAA
1 CATTTATATAAAG
50433 CATTT-TATAAAG
1 CATTTATATAAAG
50445 CATTTATATAAAG
1 CATTTATATAAAG
*
50458 CAGTTATA-AAA-
1 CATTTATATAAAG
50469 CATTT
1 CATTT
50474 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:50687 original size:19 final size:19
Alignment explanation
Indices: 50646--50687 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
50636 TAGATCATAG
* *
50646 CAAAACCAAGATAATCAAT
1 CAAAACCAAGATAATAAAC
*
50665 CAAAACCGAGATAATAAAC
1 CAAAACCAAGATAATAAAC
50684 CAAA
1 CAAA
50688 TCAATCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.21, G:0.07, T:0.12
Consensus pattern (19 bp):
CAAAACCAAGATAATAAAC
Done.