Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019051.1 Corchorus olitorius cultivar O-4 contig19084, 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: 44679
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4603 original size:27 final size:27
Alignment explanation
Indices: 4549--4620 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
4539 AGTGAACCTA
*
4549 AAATGAGCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
* **
4576 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGAACATGC
* *
4603 AAATAACTAAAATGCCCC
1 AAATGACCAAAATGCCCC
4621 CTAGGTGACC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:5576 original size:17 final size:16
Alignment explanation
Indices: 5551--5622 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 16
5541 ATTATTGAGC
*
5551 TAATGATAATTATTTCA
1 TAATTATAATTA-TTCA
5568 TAATTATAATTATTC-
1 TAATTATAATTATTCA
*
5583 -AATGATAATTACTTCA
1 TAATTATAATTA-TTCA
*
5599 TAATTATTATTATTCAA
1 TAATTATAATTATTC-A
5616 TAATTAT
1 TAATTAT
5623 TCCTTAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
14 10 0.21
15 3 0.06
16 6 0.13
17 28 0.60
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.49
Consensus pattern (16 bp):
TAATTATAATTATTCA
Found at i:5588 original size:31 final size:31
Alignment explanation
Indices: 5552--5616 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
5542 TTATTGAGCT
*
5552 AATGATAATTATTTCATAATTATAATTATTC
1 AATGATAATTACTTCATAATTATAATTATTC
*
5583 AATGATAATTACTTCATAATTATTATTATTC
1 AATGATAATTACTTCATAATTATAATTATTC
5614 AAT
1 AAT
5617 AATTATTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.48
Consensus pattern (31 bp):
AATGATAATTACTTCATAATTATAATTATTC
Found at i:5592 original size:14 final size:15
Alignment explanation
Indices: 5552--5598 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
5542 TTATTGAGCT
*
5552 AATGATAATTATTTC
1 AATGATAATTACTTC
*
5567 ATAATTATAATTA-TTC
1 --AATGATAATTACTTC
5583 AATGATAATTACTTC
1 AATGATAATTACTTC
5598 A
1 A
5599 TAATTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 10 0.37
15 4 0.15
16 3 0.11
17 10 0.37
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (15 bp):
AATGATAATTACTTC
Found at i:9202 original size:2 final size:2
Alignment explanation
Indices: 9195--9223 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9185 AATGATTTTA
9195 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9224 GAAAGGGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9857 original size:11 final size:12
Alignment explanation
Indices: 9841--9873 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
9831 TGTAATTTGT
9841 ATTTTT-TGTTA
1 ATTTTTATGTTA
9852 ATTTTTAT-TTA
1 ATTTTTATGTTA
9863 ATTTTTATGTT
1 ATTTTTATGTT
9874 GTAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (12 bp):
ATTTTTATGTTA
Found at i:9914 original size:18 final size:18
Alignment explanation
Indices: 9887--9921 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9877 AAAAAAATAG
* *
9887 TTCAATTCCAATTCCAAT
1 TTCAAATCCAAATCCAAT
9905 TTCAAATCCAAATCCAA
1 TTCAAATCCAAATCCAA
9922 ATATTAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (18 bp):
TTCAAATCCAAATCCAAT
Found at i:11854 original size:29 final size:29
Alignment explanation
Indices: 11817--11886 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
11807 ACTTGTATGG
* * *
11817 TTTGAATGTTTTGTCCCCTAAA-TCTTAAT
1 TTTGGATGTTTTG-CACCTAAACTCTCAAT
11846 TTTGGATGTTTTGCACCTAAACTCTCAAT
1 TTTGGATGTTTTGCACCTAAACTCTCAAT
*
11875 TTTGGACGTTTT
1 TTTGGATGTTTT
11887 AATCCCTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 7 0.19
29 29 0.81
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTGGATGTTTTGCACCTAAACTCTCAAT
Found at i:12214 original size:26 final size:26
Alignment explanation
Indices: 12185--12265 Score: 144
Period size: 26 Copynumber: 3.1 Consensus size: 26
12175 TTCATAATTT
* *
12185 TATTTAATTAAATAATGATATAAAAA
1 TATTAAATTAAATAATAATATAAAAA
12211 TATTAAATTAAATAATAATATAAAAA
1 TATTAAATTAAATAATAATATAAAAA
12237 TATTAAATTAAATAATAATATAAAAA
1 TATTAAATTAAATAATAATATAAAAA
12263 TAT
1 TAT
12266 AGAAAAATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (26 bp):
TATTAAATTAAATAATAATATAAAAA
Found at i:12230 original size:18 final size:19
Alignment explanation
Indices: 12208--12276 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 19
12198 AATGATATAA
*
12208 AAATATTAA-ATTAAATAAT
1 AAATAATAATATTAAAT-AT
*
12227 AATATAAAAATATTAAAT-T
1 AA-ATAATAATATTAAATAT
*
12246 AAATAATAATATAAAAATAT
1 AAATAATAATAT-TAAATAT
*
12266 AGAAAAATAAT
1 A-AATAATAAT
12277 TTTTTTTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 9 0.22
19 9 0.22
20 7 0.17
21 15 0.38
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (19 bp):
AAATAATAATATTAAATAT
Found at i:15451 original size:14 final size:15
Alignment explanation
Indices: 15422--15459 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
15412 TTTTTGGCTA
15422 AAAAATGAAGAGCAT
1 AAAAATGAAGAGCAT
*
15437 AAAAATGAATA-CAT
1 AAAAATGAAGAGCAT
15451 AACAAATGA
1 AA-AAATGA
15460 CAATAGCCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.63, C:0.08, G:0.13, T:0.16
Consensus pattern (15 bp):
AAAAATGAAGAGCAT
Found at i:16859 original size:2 final size:2
Alignment explanation
Indices: 16852--16884 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16842 ATCTAAAGTT
*
16852 TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16885 TCTTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28300 original size:12 final size:11
Alignment explanation
Indices: 28275--28299 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28265 TGCTAATAAA
28275 TTTAAAATTTT
1 TTTAAAATTTT
28286 TTTAAAATTTT
1 TTTAAAATTTT
28297 TTT
1 TTT
28300 TTTATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTAAAATTTT
Found at i:31562 original size:31 final size:32
Alignment explanation
Indices: 31527--31606 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
31517 TTGCGTCAAG
31527 GACATTTTGCCCCCTGAA-TTTCAAAATT-TAA
1 GACATTTTGCCCCCTGAACTTTCAAAATTCT-A
* * *
31558 GACATTTTGCCCCCTAAACTTTCCAAATTCTG
1 GACATTTTGCCCCCTGAACTTTCAAAATTCTA
*
31590 GACATTTTACCCCCTGA
1 GACATTTTGCCCCCTGA
31607 CGTAGGGGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 17 0.40
32 24 0.57
33 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.34
Consensus pattern (32 bp):
GACATTTTGCCCCCTGAACTTTCAAAATTCTA
Found at i:31647 original size:32 final size:28
Alignment explanation
Indices: 31610--31688 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 28
31600 CCCCTGACGT
*
31610 AGGGGGCAAATTGTCCTTAATTTGAAAAGTTC
1 AGGGGGCAAAATGTCCTTAATTT----AGTTC
*
31642 AGGGGGCAAAATGT-CTTGAATTTAGTTT
1 AGGGGGCAAAATGTCCTT-AATTTAGTTC
*
31670 AGGGGGCAAAGTGTCCTTA
1 AGGGGGCAAAATGTCCTTA
31689 GCCCCATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 18 0.43
29 3 0.07
31 3 0.07
32 18 0.43
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.30
Consensus pattern (28 bp):
AGGGGGCAAAATGTCCTTAATTTAGTTC
Found at i:36639 original size:90 final size:87
Alignment explanation
Indices: 36489--36667 Score: 304
Period size: 90 Copynumber: 2.0 Consensus size: 87
36479 TTTCAGTAGG
*
36489 TAGTCATCATGTATACAAACAAAAGCTTGGAGTGTGGATTGCCTTCGCAGCTTCCTCAGCTAGAG
1 TAGTCATCATATATACAAACAAAAGCTTGGAGTGTGGATTGCCTTCGCAGCTTCCTCAGCTAGAG
*
36554 TATAACAGCACTTGAACCTTGA
66 TATAACAGCACTTCAACCTTGA
*
36576 TAGTCATCATATATACAAACAAAAGCTTGGAAGAGTGTGGATTGCCTTCGCAGCTTTCTCAGCTA
1 TAGTCATCATATATACAAACAAAAGCTT-G--GAGTGTGGATTGCCTTCGCAGCTTCCTCAGCTA
36641 GAGTATAACAGCACTTCAACCTTGA
63 GAGTATAACAGCACTTCAACCTTGA
36666 TA
1 TA
36668 AAGTGTTGAC
Statistics
Matches: 86, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
87 27 0.31
88 1 0.01
90 58 0.67
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (87 bp):
TAGTCATCATATATACAAACAAAAGCTTGGAGTGTGGATTGCCTTCGCAGCTTCCTCAGCTAGAG
TATAACAGCACTTCAACCTTGA
Found at i:37248 original size:17 final size:17
Alignment explanation
Indices: 37214--37250 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
37204 AATAAACCTT
37214 AACAGATAAAAGGGAAA
1 AACAGATAAAAGGGAAA
37231 AACA-ATAAAAGGGAAA
1 AACAGATAAAAGGGAAA
37247 AACA
1 AACA
37251 TGAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.68, C:0.08, G:0.19, T:0.05
Consensus pattern (17 bp):
AACAGATAAAAGGGAAA
Found at i:42039 original size:21 final size:22
Alignment explanation
Indices: 42015--42058 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
42005 TGTTTGCTAT
*
42015 CTTCCTCTTCC-TCGACTCAAA
1 CTTCCTCTTCCTTCCACTCAAA
*
42036 CTTCTTCTTCCTTCCACTCAAA
1 CTTCCTCTTCCTTCCACTCAAA
42058 C
1 C
42059 CCTAGATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.18, C:0.43, G:0.02, T:0.36
Consensus pattern (22 bp):
CTTCCTCTTCCTTCCACTCAAA
Found at i:44635 original size:29 final size:29
Alignment explanation
Indices: 44595--44674 Score: 124
Period size: 29 Copynumber: 2.8 Consensus size: 29
44585 ACCCAGAGTA
*
44595 TGCAAAAATGACCAAAATGCCCCTAGATG
1 TGCAAAAATGACCAAAATGCCCCTAGACG
* *
44624 TGCAAAAGTGACCAAAATGCCCCTGGACG
1 TGCAAAAATGACCAAAATGCCCCTAGACG
*
44653 TGAAAAAATGACCAAAATGCCC
1 TGCAAAAATGACCAAAATGCCC
44675 ATTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCCCTAGACG
Done.