Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014033.1 Corchorus olitorius cultivar O-4 contig14066, 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: 41527
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2652 original size:76 final size:76
Alignment explanation
Indices: 2502--2645 Score: 168
Period size: 76 Copynumber: 1.9 Consensus size: 76
2492 ACAAGGACCC
* * * *
2502 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACTCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
2567 GGGCAGTGTCA
66 GGGCAGTGTCA
* * **
2578 CGACTCCAGCTGGGCGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
2640 GATGGG
63 GATGGG
2646 TTGTGTCTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
75 4 0.07
76 47 0.82
77 6 0.11
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:13460 original size:11 final size:11
Alignment explanation
Indices: 13426--13473 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
13416 TTGAAATAAT
13426 TCTTC-AATAG
1 TCTTCAAATAG
13436 TCTTC--A-AG
1 TCTTCAAATAG
13444 TCTTCAAATTA-
1 TCTTCAAA-TAG
13455 TCTTCAAATAG
1 TCTTCAAATAG
13466 TCTTCAAA
1 TCTTCAAA
13474 CACGAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 8 0.24
11 16 0.48
12 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAG
Found at i:14822 original size:17 final size:18
Alignment explanation
Indices: 14787--14822 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
14777 CTCCTCTTGC
*
14787 ATGAAAACACTTGTTTTT
1 ATGAAAACAATTGTTTTT
14805 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTGTTTTT
14822 A
1 A
14823 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTGTTTTT
Found at i:22450 original size:11 final size:11
Alignment explanation
Indices: 22416--22463 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
22406 TTGAAATAAT
22416 TCTTC-AATAG
1 TCTTCAAATAG
22426 TCTTC--A-AG
1 TCTTCAAATAG
22434 TCTTCAAATTA-
1 TCTTCAAA-TAG
22445 TCTTCAAATAG
1 TCTTCAAATAG
22456 TCTTCAAA
1 TCTTCAAA
22464 CACGAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 8 0.24
11 16 0.48
12 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAG
Found at i:25852 original size:21 final size:21
Alignment explanation
Indices: 25826--25868 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
25816 AAGCACCAAA
25826 AAGATGCC-ATTTGATCCATTG
1 AAGATGCCTA-TTGATCCATTG
*
25847 AAGATGCCTATTGGTCCATTG
1 AAGATGCCTATTGATCCATTG
25868 A
1 A
25869 CAAGAGCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
AAGATGCCTATTGATCCATTG
Found at i:26870 original size:5 final size:5
Alignment explanation
Indices: 26860--26884 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
26850 AAATATCAAA
26860 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
26885 TTCGACCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:32113 original size:33 final size:33
Alignment explanation
Indices: 32054--32138 Score: 145
Period size: 33 Copynumber: 2.6 Consensus size: 33
32044 TTTGTAATGC
*
32054 ATAAAGGAAGAATTTAG-TTTTTTTTTAACACA
1 ATAAAGGAAGAAATTAGTTTTTTTTTTAACACA
32086 ATAAAGGAAGAAATTAGTTTTTTTTTTAACACA
1 ATAAAGGAAGAAATTAGTTTTTTTTTTAACACA
*
32119 AAAAAGGAAGAAATTAGTTT
1 ATAAAGGAAGAAATTAGTTT
32139 AAAATGCTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 16 0.32
33 34 0.68
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (33 bp):
ATAAAGGAAGAAATTAGTTTTTTTTTTAACACA
Found at i:32518 original size:38 final size:38
Alignment explanation
Indices: 32462--32539 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
32452 AAATCCAAGC
*
32462 ATGATTAAAAAGAATATTAATTACAAATTAAT-TT-ATAA
1 ATGACTAAAAAGAATATTAATT--AAATTAATATTCATAA
*
32500 ATGACTAAAAATAATATTAATTAAATTAATATTCATAA
1 ATGACTAAAAAGAATATTAATTAAATTAATATTCATAA
32538 AT
1 AT
32540 TAATTCTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 8 0.22
37 2 0.06
38 26 0.72
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (38 bp):
ATGACTAAAAAGAATATTAATTAAATTAATATTCATAA
Found at i:32538 original size:14 final size:15
Alignment explanation
Indices: 32511--32543 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
32501 TGACTAAAAA
32511 TAATATTAATTAAAT
1 TAATATTAATTAAAT
*
32526 TAATATTCA-TAAAT
1 TAATATTAATTAAAT
32540 TAAT
1 TAAT
32544 TCTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATTAATTAAAT
Found at i:32552 original size:42 final size:38
Alignment explanation
Indices: 32466--32553 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 38
32456 CCAAGCATGA
* *
32466 TTAAAAAGAATATTAATTACAAATTAATTTATAAATGAC
1 TTAAAAATAATATTAATTA-AAATTAATTTATAAATAAC
32505 -TAAAAATAATATTAATT-AAATTAATATTCATAAATTAATTC
1 TTAAAAATAATATTAATTAAAATTAAT-TT-ATAAA-TAA--C
32546 TTAAAAAT
1 TTAAAAAT
32554 TAAAGTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
36 8 0.20
37 2 0.05
38 21 0.51
39 2 0.05
41 1 0.02
42 7 0.17
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (38 bp):
TTAAAAATAATATTAATTAAAATTAATTTATAAATAAC
Found at i:33320 original size:5 final size:5
Alignment explanation
Indices: 33310--33336 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
33300 GTTCGTACTC
33310 TAAGA TAAGA TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TA
33337 GTAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:39177 original size:22 final size:22
Alignment explanation
Indices: 39152--39198 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
39142 TTTTTAGTTG
*
39152 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
39174 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
39196 AGT
1 AGT
39199 TATAAGTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Done.