Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015485.1 Corchorus olitorius cultivar O-4 contig15518, 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: 14295
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:3415 original size:38 final size:38
Alignment explanation
Indices: 3340--3549 Score: 245
Period size: 38 Copynumber: 5.7 Consensus size: 38
3330 TAAACACCCG
*
3340 AAGCGAATAATGAAATTGA----TT-GGTCTTG-GCCC
1 AAGCGAATAATGAAATTGATCGCTTAGGTCTTGATCCC
3372 TAAGCGAATAATGAAATTGATCGCTTAGGTCTTGATCCC
1 -AAGCGAATAATGAAATTGATCGCTTAGGTCTTGATCCC
* * * *
3411 AAGCGAATGATGAAATTGATCGCTTGGGTCTTGGTCCT
1 AAGCGAATAATGAAATTGATCGCTTAGGTCTTGATCCC
* *
3449 AAGCGAATGATGAAATTGATCGCTTAGGTCTTAATCCC
1 AAGCGAATAATGAAATTGATCGCTTAGGTCTTGATCCC
* * **
3487 AAGCGAATAAAGAAATTGATCGCTTGGGTCTTGATCAA
1 AAGCGAATAATGAAATTGATCGCTTAGGTCTTGATCCC
*
3525 AAGCGAATAAT-AAATTTGGTCGCTT
1 AAGCGAATAATGAAA-TTGATCGCTT
3550 TGTCGCAAGT
Statistics
Matches: 153, Mismatches: 17, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
33 19 0.12
37 5 0.03
38 126 0.82
39 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (38 bp):
AAGCGAATAATGAAATTGATCGCTTAGGTCTTGATCCC
Found at i:3462 original size:76 final size:76
Alignment explanation
Indices: 3361--3519 Score: 273
Period size: 76 Copynumber: 2.1 Consensus size: 76
3351 GAAATTGATT
* * *
3361 GGTCTTGGCCCTAAGCGAATAATGAAATTGATCGCTTAGGTCTTGATCCCAAGCGAATGATGAAA
1 GGTCTTGGCCCTAAGCGAATAATGAAATTGATCGCTTAGGTCTTAATCCCAAGCGAATAAAGAAA
3426 TTGATCGCTTG
66 TTGATCGCTTG
* *
3437 GGTCTTGGTCCTAAGCGAATGATGAAATTGATCGCTTAGGTCTTAATCCCAAGCGAATAAAGAAA
1 GGTCTTGGCCCTAAGCGAATAATGAAATTGATCGCTTAGGTCTTAATCCCAAGCGAATAAAGAAA
3502 TTGATCGCTTG
66 TTGATCGCTTG
3513 GGTCTTG
1 GGTCTTG
3520 ATCAAAAGCG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (76 bp):
GGTCTTGGCCCTAAGCGAATAATGAAATTGATCGCTTAGGTCTTAATCCCAAGCGAATAAAGAAA
TTGATCGCTTG
Found at i:4154 original size:81 final size:81
Alignment explanation
Indices: 4019--4184 Score: 305
Period size: 81 Copynumber: 2.0 Consensus size: 81
4009 ACCTTACTGC
*
4019 TCAAATTTTTAATGGCTCAAATCAAGTTAGTGGGTGAATGTATGTACATGTGTCGATCTTCATGG
1 TCAAATTTTTAATGGCTCAAATCAAGTTAGTGGGTGAATGTATGTACATGTGTCGATCTTCATGA
4084 ATGGCAAGAAGAAAAA
66 ATGGCAAGAAGAAAAA
*
4100 TCAAATTTTTAATGTCTCAAATCAAGTTAGTGGGTGAATGTATGTACATGTGTCGATCTTCATGA
1 TCAAATTTTTAATGGCTCAAATCAAGTTAGTGGGTGAATGTATGTACATGTGTCGATCTTCATGA
*
4165 ATGGCAAGGAGAAAAA
66 ATGGCAAGAAGAAAAA
4181 TCAA
1 TCAA
4185 CAAAACAAAG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (81 bp):
TCAAATTTTTAATGGCTCAAATCAAGTTAGTGGGTGAATGTATGTACATGTGTCGATCTTCATGA
ATGGCAAGAAGAAAAA
Found at i:5100 original size:16 final size:16
Alignment explanation
Indices: 5081--5112 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5071 ACTCTACAAG
*
5081 GCAGAAAAGCTCTAAA
1 GCAGAAAAGCCCTAAA
5097 GCAGAAAAGCCCTAAA
1 GCAGAAAAGCCCTAAA
5113 AAATCAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.22, G:0.19, T:0.09
Consensus pattern (16 bp):
GCAGAAAAGCCCTAAA
Found at i:5997 original size:11 final size:11
Alignment explanation
Indices: 5981--6005 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5971 ATTTCTCCCA
5981 AAAAAAAAATG
1 AAAAAAAAATG
5992 AAAAAAAAATG
1 AAAAAAAAATG
6003 AAA
1 AAA
6006 CAAGAACAAC
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:9743 original size:22 final size:23
Alignment explanation
Indices: 9715--9771 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
9705 ATCTGCCTAA
* *
9715 GAAATTTTGATAAACTTTTG-AT
1 GAAATTTTGATAAACTTCTGTAC
*
9737 GAAATTTTGGT-AACTTCTGTAC
1 GAAATTTTGATAAACTTCTGTAC
9759 GAAATTTTGATAA
1 GAAATTTTGATAA
9772 TTATACTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.24
22 21 0.72
23 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (23 bp):
GAAATTTTGATAAACTTCTGTAC
Found at i:9783 original size:44 final size:44
Alignment explanation
Indices: 9735--9837 Score: 102
Period size: 44 Copynumber: 2.3 Consensus size: 44
9725 TAAACTTTTG
* * ** *
9735 ATGAAATTTTGGTAA-CTTC-TGTACGAAATTTTGATAATTATACT
1 ATGAAATTTTGATAAGCTTCATATA--AAATTTTGATAACCACACT
* *
9779 ATGAAGTTTTGATAAGCTTCATATAAAATTTTGGTAACCACACT
1 ATGAAATTTTGATAAGCTTCATATAAAATTTTGATAACCACACT
*
9823 ATGAAATTTTAATAA
1 ATGAAATTTTGATAA
9838 AATTTCTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
44 41 0.85
45 4 0.08
46 3 0.06
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.40
Consensus pattern (44 bp):
ATGAAATTTTGATAAGCTTCATATAAAATTTTGATAACCACACT
Found at i:10673 original size:13 final size:13
Alignment explanation
Indices: 10655--10683 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10645 TTAATGAGTA
10655 ATTAAACTTTGAG
1 ATTAAACTTTGAG
10668 ATTAAACTTTGAG
1 ATTAAACTTTGAG
10681 ATT
1 ATT
10684 GAATGAGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (13 bp):
ATTAAACTTTGAG
Found at i:12790 original size:22 final size:22
Alignment explanation
Indices: 12681--12845 Score: 133
Period size: 22 Copynumber: 7.6 Consensus size: 22
12671 CTCCAATGTA
*
12681 GAAATATTGATAACCACACTGA-
1 GAAATTTTGATAACCACACT-AT
12703 GAAATTTTGATAACCACACTAT
1 GAAATTTTGATAACCACACTAT
* * *
12725 GAAATTTTGATAACCTCAGTGT
1 GAAATTTTGATAACCACACTAT
* * *
12747 GAAATTTTGATAATCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* *
12769 GAAATTTTGATAATCAAACTAT
1 GAAATTTTGATAACCACACTAT
** * *
12791 -AAA-ACTG-TAACCGCGCTAT
1 GAAATTTTGATAACCACACTAT
*
12810 GAAAATTTTGATAAACACAAC-AT
1 G-AAATTTTGATAACCAC-ACTAT
*
12833 GAAATTTCGATAA
1 GAAATTTTGATAA
12846 TGTCTCTATG
Statistics
Matches: 114, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
19 8 0.07
20 2 0.02
21 7 0.06
22 88 0.77
23 8 0.07
24 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:12900 original size:22 final size:22
Alignment explanation
Indices: 12870--12966 Score: 99
Period size: 22 Copynumber: 4.5 Consensus size: 22
12860 TGAAATTGTG
* * *
12870 AATTGTGATATCCTCTCTATGT
1 AATTTTGATAACCTCTCTATGA
* *
12892 AATTTTGATAACTTCTCCATGA
1 AATTTTGATAACCTCTCTATGA
* *
12914 AATTTTCATAACCTCCCTATGA
1 AATTTTGATAACCTCTCTATGA
* *
12936 AATTTTGTTAACCTC-C-AGGA
1 AATTTTGATAACCTCTCTATGA
12956 AATTTTGATAA
1 AATTTTGATAA
12967 GCACGAATAT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 13 0.21
21 1 0.02
22 48 0.77
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (22 bp):
AATTTTGATAACCTCTCTATGA
Found at i:12960 original size:42 final size:43
Alignment explanation
Indices: 12881--12966 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
12871 ATTGTGATAT
* * *
12881 CCTCTCTATGTAATTTTGATAACTTCTCCATGAAATTTTCATAA
1 CCTCCCTATGAAATTTTGATAAC-TCTCCAGGAAATTTTCATAA
* *
12925 CCTCCCTATGAAATTTTGTTAAC-CTCCAGGAAATTTTGATAA
1 CCTCCCTATGAAATTTTGATAACTCTCCAGGAAATTTTCATAA
12967 GCACGAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 17 0.46
44 20 0.54
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (43 bp):
CCTCCCTATGAAATTTTGATAACTCTCCAGGAAATTTTCATAA
Done.