Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018013.1 Corchorus olitorius cultivar O-4 contig18046, 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: 66400
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:3280 original size:4 final size:4
Alignment explanation
Indices: 3273--3298 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3263 TTTCATTCAC
3273 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
3299 TCCTTTGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:7761 original size:54 final size:54
Alignment explanation
Indices: 7675--7783 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
7665 GAAACAGGTG
* *
7675 TTCAGATGATCCAGTGCGGTCATTCCAGGAAGTTTTCAATGGTCAGAGTTGATC
1 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
*
7729 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
7783 T
1 T
7784 CGTTTCAAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (54 bp):
TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
Found at i:7800 original size:35 final size:35
Alignment explanation
Indices: 7748--8137 Score: 455
Period size: 35 Copynumber: 11.1 Consensus size: 35
7738 TCCAGTGCGG
*
7748 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * *
7783 TCGTTTCAAGGAGTTTTCGTTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
**
7818 TCATTTCAAGAAGTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTCGATGATCAGAGTTGATC
*
7854 TTATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
7889 TCGTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * **
7924 TCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
7959 TCATTTTCAA-AATGCTTAT--ATGGTCAGAGTTGATC
1 TCA-TTTCAAGAA-G-TTTTCGATGATCAGAGTTGATC
*
7994 TCATTTCAAGAAGTTTTCGATGATCAAAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * * *
8029 TTATTTCAA-AGGGTTTTTGTTGATCAGAGTTGATC
1 TCATTTCAAGA-AGTTTTCGATGATCAGAGTTGATC
* **
8064 TCCTTTCAAGAAGTTTTAATTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTT--CGATGATCAGAGTTGATC
* * *
8101 TTATTCCTAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
8136 TC
1 TC
8138 CAATTTGATT
Statistics
Matches: 302, Mismatches: 42, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
33 3 0.01
34 8 0.03
35 221 0.73
36 38 0.13
37 32 0.11
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
Found at i:9712 original size:13 final size:13
Alignment explanation
Indices: 9694--9719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9684 ATAAATCTGA
9694 TAACTTGTGTTAT
1 TAACTTGTGTTAT
9707 TAACTTGTGTTAT
1 TAACTTGTGTTAT
9720 ATAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TAACTTGTGTTAT
Found at i:11801 original size:26 final size:26
Alignment explanation
Indices: 11763--11813 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
11753 GCTACTATAG
* *
11763 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTGAAATTTTCTAAAAAAAATAA
11789 AAATTGAAATTTTCTAAAAAAAATA
1 AAATTGAAATTTTCTAAAAAAAATA
11814 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (26 bp):
AAATTGAAATTTTCTAAAAAAAATAA
Found at i:22171 original size:21 final size:21
Alignment explanation
Indices: 22141--22181 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
22131 TCCTGGTATA
22141 GGCCGCGCCTTGGCAAGGTTG
1 GGCCGCGCCTTGGCAAGGTTG
*
22162 GGCCGTGCCTTGGCAAGGTT
1 GGCCGCGCCTTGGCAAGGTT
22182 TTCTAGCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.22
Consensus pattern (21 bp):
GGCCGCGCCTTGGCAAGGTTG
Found at i:22374 original size:21 final size:21
Alignment explanation
Indices: 22350--22394 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
22340 TCCAATCAAC
22350 CAAGAACCCTAATTTTGAACT
1 CAAGAACCCTAATTTTGAACT
*
22371 CAAGAACCCTAATTTTGAATT
1 CAAGAACCCTAATTTTGAACT
22392 CAA
1 CAA
22395 TAAGCTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (21 bp):
CAAGAACCCTAATTTTGAACT
Found at i:22720 original size:10 final size:10
Alignment explanation
Indices: 22679--22720 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
22669 TCTGGTCAAA
22679 ATTTTTTT-T
1 ATTTTTTTAT
*
22688 ATTTTTTTGT
1 ATTTTTTTAT
*
22698 TTTTTTTTAAT
1 ATTTTTTT-AT
22709 ATTTTTTTAT
1 ATTTTTTTAT
22719 AT
1 AT
22721 AGCCTTGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 8 0.29
10 12 0.43
11 8 0.29
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:23760 original size:10 final size:10
Alignment explanation
Indices: 23736--23784 Score: 73
Period size: 10 Copynumber: 5.0 Consensus size: 10
23726 GCTCAACGAT
*
23736 ATCTCCATG-
1 ATCTTCATGC
23745 ATCTTCATGC
1 ATCTTCATGC
23755 ATCTTCATGC
1 ATCTTCATGC
23765 ATCTTCATGC
1 ATCTTCATGC
*
23775 ATCTCCATGC
1 ATCTTCATGC
23785 TTCCTTACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
9 8 0.22
10 29 0.78
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (10 bp):
ATCTTCATGC
Found at i:23770 original size:20 final size:20
Alignment explanation
Indices: 23736--23784 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
23726 GCTCAACGAT
23736 ATCTCCATG-ATCTTCATGC
1 ATCTCCATGCATCTTCATGC
*
23755 ATCTTCATGCATCTTCATGC
1 ATCTCCATGCATCTTCATGC
23775 ATCTCCATGC
1 ATCTCCATGC
23785 TTCCTTACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (20 bp):
ATCTCCATGCATCTTCATGC
Found at i:36663 original size:18 final size:18
Alignment explanation
Indices: 36618--36663 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
36608 GATCCTATTT
*
36618 TAACTTGGA-TTCTACTC
1 TAACTTGGACTTCTAATC
*
36635 TAACATT-GACTTTTAATC
1 TAAC-TTGGACTTCTAATC
36653 TAACTTGGACT
1 TAACTTGGACT
36664 CCAAGTTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (18 bp):
TAACTTGGACTTCTAATC
Found at i:39071 original size:30 final size:31
Alignment explanation
Indices: 39035--39102 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
39025 TTTTTAAACC
*
39035 GGCTCAAATAGGTACT-AACATTTTAAAATT
1 GGCTCAAATAGGTACTAAACATTTCAAAATT
*
39065 GGCTCAAATAGGTACTAAACGTTTCAAAATT
1 GGCTCAAATAGGTACTAAACATTTCAAAATT
*
39096 GGATCAA
1 GGCTCAA
39103 TTAAGATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (31 bp):
GGCTCAAATAGGTACTAAACATTTCAAAATT
Found at i:42271 original size:16 final size:19
Alignment explanation
Indices: 42236--42271 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 19
42226 TACTCACAGA
42236 AAAACAACATTCGTAACCC
1 AAAACAACATTCGTAACCC
42255 AAAA-AACA-TCG-AACCC
1 AAAACAACATTCGTAACCC
42271 A
1 A
42272 TTCCATCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 4 0.24
19 4 0.24
ACGTcount: A:0.53, C:0.31, G:0.06, T:0.11
Consensus pattern (19 bp):
AAAACAACATTCGTAACCC
Found at i:52486 original size:22 final size:23
Alignment explanation
Indices: 52444--52488 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
52434 TGAAATAAGA
52444 CAAACGCTCTCACAAAGGAGTCC
1 CAAACGCTCTCACAAAGGAGTCC
*
52467 CAAATGCTCTCAC-AAGGAGTCC
1 CAAACGCTCTCACAAAGGAGTCC
52489 TGGTTATGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.16
Consensus pattern (23 bp):
CAAACGCTCTCACAAAGGAGTCC
Found at i:53543 original size:2 final size:2
Alignment explanation
Indices: 53536--53564 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53526 ATTGGCTAAA
53536 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 T
53565 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:65044 original size:28 final size:29
Alignment explanation
Indices: 64981--65049 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
64971 TTAAACTGAT
* *
64981 CAAAATGCCCCTTAATATGCAGAAATGAC
1 CAAAATGCCCCTGAATATGCAAAAATGAC
*
65010 CATAATGCCCCTGAATATG-AAAAATGAC
1 CAAAATGCCCCTGAATATGCAAAAATGAC
65038 CAAAATGCCCCT
1 CAAAATGCCCCT
65050 AGGTGATCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 19 0.53
29 17 0.47
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAAATGCCCCTGAATATGCAAAAATGAC
Done.