Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004927.1 Corchorus capsularis cultivar CVL-1 contig04945, 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: 14342
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:233 original size:19 final size:21
Alignment explanation
Indices: 197--238 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
187 TTTCTTCTAT
197 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
217 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
237 TT
1 TT
239 CATATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:1665 original size:48 final size:48
Alignment explanation
Indices: 1604--1858 Score: 288
Period size: 48 Copynumber: 5.3 Consensus size: 48
1594 AAATACTAAT
* *
1604 TTCTGTTTTTGTTTGCTGCATTTTACTGCATTTATATTATACTCAAAG
1 TTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATATTATACTCAAAA
*
1652 TTCTGTTTTTGTTTGCTGCATTTTACTGCATTTATATTATACTCAAAA
1 TTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATATTATACTCAAAA
* *
1700 TTCTGTTTTTGTTTGGTGCATTTTATTGCATTT-TAGTTAAATACT--AAT
1 TTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATA-TT--ATACTCAAAA
* *
1748 TTCTGTTTTTTGTTTACTGCATTTTATTGCATCATT-T-TTATACTTAAAA
1 TTCTG-TTTTTGTTTGCTGCATTTTATTGCAT--TTATATTATACTCAAAA
* * * * *
1797 TTCTATTTTTGTTTGTTGCATTTTATTGCGTTTATATTATGCTCATTAA
1 TTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATATTATACTCA-AAA
*
1846 TTTTG-TTTTGTTT
1 TTCTGTTTTTGTTT
1859 TCTAATATGC
Statistics
Matches: 180, Mismatches: 16, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
46 2 0.01
47 8 0.04
48 125 0.69
49 37 0.21
50 5 0.03
51 3 0.02
ACGTcount: A:0.20, C:0.11, G:0.12, T:0.57
Consensus pattern (48 bp):
TTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATATTATACTCAAAA
Found at i:1806 original size:97 final size:95
Alignment explanation
Indices: 1604--1836 Score: 294
Period size: 97 Copynumber: 2.4 Consensus size: 95
1594 AAATACTAAT
* *
1604 TTCTGTTTTTGTTTGCTGCATTTTACTGCATTTATATTATACTCAAAGTTCTGTTTTTGTTTGCT
1 TTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATATTATACT-AAAGTTCTGTTTTTGTTTACT
1669 GCATTTTACTGCATTTATATTATACTCAAAA
65 GCATTTTACTGCATTTATATTATACTCAAAA
* *
1700 TTCTGTTTTTGTTTGGTGCATTTTATTGCATTT-TAGTTAAATACT-AATTTCTGTTTTTTGTTT
1 TTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATA-TT--ATACTAAAGTTCTG-TTTTTGTTT
* *
1763 ACTGCATTTTATTGCATCATT-T-TTATACTTAAAA
62 ACTGCATTTTACTGCAT--TTATATTATACTCAAAA
* * *
1797 TTCTATTTTTGTTTGTTGCATTTTATTGCGTTTATATTAT
1 TTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATATTAT
1837 GCTCATTAAT
Statistics
Matches: 121, Mismatches: 9, Indels: 15
0.83 0.06 0.10
Matches are distributed among these distances:
95 4 0.03
96 40 0.33
97 67 0.55
98 8 0.07
99 2 0.02
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.56
Consensus pattern (95 bp):
TTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATATTATACTAAAGTTCTGTTTTTGTTTACTG
CATTTTACTGCATTTATATTATACTCAAAA
Found at i:4207 original size:50 final size:50
Alignment explanation
Indices: 4149--4280 Score: 264
Period size: 50 Copynumber: 2.6 Consensus size: 50
4139 AGAATATGTG
4149 ATCTTTGCTTGATGGCTGAATTGGATGTTGAATTCTGATTGCTTTCCCAT
1 ATCTTTGCTTGATGGCTGAATTGGATGTTGAATTCTGATTGCTTTCCCAT
4199 ATCTTTGCTTGATGGCTGAATTGGATGTTGAATTCTGATTGCTTTCCCAT
1 ATCTTTGCTTGATGGCTGAATTGGATGTTGAATTCTGATTGCTTTCCCAT
4249 ATCTTTGCTTGATGGCTGAATTGGATGTTGAA
1 ATCTTTGCTTGATGGCTGAATTGGATGTTGAA
4281 ACAATGTGTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.43
Consensus pattern (50 bp):
ATCTTTGCTTGATGGCTGAATTGGATGTTGAATTCTGATTGCTTTCCCAT
Found at i:6164 original size:23 final size:25
Alignment explanation
Indices: 6120--6168 Score: 84
Period size: 23 Copynumber: 2.0 Consensus size: 25
6110 ATATCTACAT
6120 ACTCATCTATCTTACTATTCATTTA
1 ACTCATCTATCTTACTATTCATTTA
6145 ACTCATCTATC-T-CTATTCATTTA
1 ACTCATCTATCTTACTATTCATTTA
6168 A
1 A
6169 GTATAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 12 0.50
24 1 0.04
25 11 0.46
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (25 bp):
ACTCATCTATCTTACTATTCATTTA
Found at i:7906 original size:19 final size:19
Alignment explanation
Indices: 7882--7920 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
7872 TTGATGAATT
7882 TAAATCATACTTTGCAGAC
1 TAAATCATACTTTGCAGAC
7901 TAAATCATACTTTGCAGAC
1 TAAATCATACTTTGCAGAC
7920 T
1 T
7921 GATTCACTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (19 bp):
TAAATCATACTTTGCAGAC
Found at i:8356 original size:24 final size:24
Alignment explanation
Indices: 8324--8371 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
8314 GTGGTTCTCA
*
8324 TGGCGGCGGCCAAGGAGGAGGAAG
1 TGGCGGCGGCAAAGGAGGAGGAAG
*
8348 TGGCGGCGGTAAAGGAGGAGGAAG
1 TGGCGGCGGCAAAGGAGGAGGAAG
8372 CAGTGGCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.54, T:0.06
Consensus pattern (24 bp):
TGGCGGCGGCAAAGGAGGAGGAAG
Found at i:8386 original size:24 final size:24
Alignment explanation
Indices: 8335--8392 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
8325 GGCGGCGGCC
** *
8335 AAGGAGGAGGAAGTGGCGGCGGTA
1 AAGGAGGAGGAAGCAGCGGCAGTA
* *
8359 AAGGAGGAGGAAGCAGTGGCAGTG
1 AAGGAGGAGGAAGCAGCGGCAGTA
8383 AAGGAGGAGG
1 AAGGAGGAGG
8393 TGGCTCTGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.53, T:0.07
Consensus pattern (24 bp):
AAGGAGGAGGAAGCAGCGGCAGTA
Found at i:8565 original size:18 final size:18
Alignment explanation
Indices: 8544--8578 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8534 AGGTTATGGC
8544 GGCGGAGGGGGACGTGGT
1 GGCGGAGGGGGACGTGGT
*
8562 GGCGGAGGGGGCCGTGG
1 GGCGGAGGGGGACGTGG
8579 CGGAGGTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.14, G:0.69, T:0.09
Consensus pattern (18 bp):
GGCGGAGGGGGACGTGGT
Found at i:11400 original size:40 final size:40
Alignment explanation
Indices: 11345--11426 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
11335 AGCGGGGGAC
11345 TTAGAGCCCCTAGGATCGATACGCCCACCAAGAGACCCTT
1 TTAGAGCCCCTAGGATCGATACGCCCACCAAGAGACCCTT
11385 TTAGAGCCCCTAGGATCGATACGCCCACCAAGAGACCCTT
1 TTAGAGCCCCTAGGATCGATACGCCCACCAAGAGACCCTT
11425 TT
1 TT
11427 TTCTACTGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.20
Consensus pattern (40 bp):
TTAGAGCCCCTAGGATCGATACGCCCACCAAGAGACCCTT
Found at i:11721 original size:30 final size:30
Alignment explanation
Indices: 11687--11752 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
11677 GTGGCGGATA
* *
11687 TGGTGGAGGACGTGGAC-GTGGTGGTTATGG
1 TGGTGGAGGACATGG-CGGTGGTGGCTATGG
11717 TGGTGGAGGACATGGCGGTGGTGGCTATGG
1 TGGTGGAGGACATGGCGGTGGTGGCTATGG
11747 TGGTGG
1 TGGTGG
11753 TGGTCACGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.12, C:0.08, G:0.55, T:0.26
Consensus pattern (30 bp):
TGGTGGAGGACATGGCGGTGGTGGCTATGG
Found at i:11722 original size:15 final size:15
Alignment explanation
Indices: 11704--11756 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
11694 GGACGTGGAC
11704 GTGGTGGTTATGGTG
1 GTGGTGGTTATGGTG
* ** *
11719 GTGGAGGACATGGCG
1 GTGGTGGTTATGGTG
*
11734 GTGGTGGCTATGGTG
1 GTGGTGGTTATGGTG
11749 GTGGTGGT
1 GTGGTGGT
11757 CACGGAGGAG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.09, C:0.06, G:0.55, T:0.30
Consensus pattern (15 bp):
GTGGTGGTTATGGTG
Found at i:11812 original size:36 final size:36
Alignment explanation
Indices: 11735--11813 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
11725 GACATGGCGG
* * *
11735 TGGTGGCTATGGTGGTGGTGGTCACGGAGGAGGAAA
1 TGGTGGTTATGGTGGTGGCGGGCACGGAGGAGGAAA
* * **
11771 GGGTGGTTATGGTGGTGGCGGGCATGGAGGAGGTTA
1 TGGTGGTTATGGTGGTGGCGGGCACGGAGGAGGAAA
11807 TGGTGGT
1 TGGTGGT
11814 GGAGGTGGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.15, C:0.06, G:0.53, T:0.25
Consensus pattern (36 bp):
TGGTGGTTATGGTGGTGGCGGGCACGGAGGAGGAAA
Found at i:11818 original size:18 final size:18
Alignment explanation
Indices: 11795--11857 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
11785 GTGGCGGGCA
11795 TGGAGGAGGTTATGGTGG
1 TGGAGGAGGTTATGGTGG
* **
11813 TGGAGGTGGACATGGTGG
1 TGGAGGAGGTTATGGTGG
* *
11831 CGGAAGAGGTGGATATGGTGG
1 TGGAGGAGGT---TATGGTGG
11852 TGGAGG
1 TGGAGG
11858 GGGACGTGGC
Statistics
Matches: 32, Mismatches: 10, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
18 21 0.66
21 11 0.34
ACGTcount: A:0.19, C:0.03, G:0.56, T:0.22
Consensus pattern (18 bp):
TGGAGGAGGTTATGGTGG
Found at i:11841 original size:21 final size:21
Alignment explanation
Indices: 11815--11902 Score: 65
Period size: 21 Copynumber: 4.2 Consensus size: 21
11805 TATGGTGGTG
11815 GAGGTGGACATGGTGGCGGAA
1 GAGGTGGACATGGTGGCGGAA
* *
11836 GAGGTGGATATGGTGGTGG-A
1 GAGGTGGACATGGTGGCGGAA
* *
11856 G-GG-GGACGTGGCGGTGGCGGCA
1 GAGGTGGACAT---GGTGGCGGAA
* * *
11878 GAGGTGGATATGGTGGTGGAG
1 GAGGTGGACATGGTGGCGGAA
11899 GAGG
1 GAGG
11903 ACGTGGTGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
18 4 0.08
19 2 0.04
20 2 0.04
21 35 0.69
22 2 0.04
23 2 0.04
24 4 0.08
ACGTcount: A:0.18, C:0.07, G:0.58, T:0.17
Consensus pattern (21 bp):
GAGGTGGACATGGTGGCGGAA
Found at i:11895 original size:24 final size:23
Alignment explanation
Indices: 11825--11901 Score: 65
Period size: 24 Copynumber: 3.5 Consensus size: 23
11815 GAGGTGGACA
11825 TGGTGGCGGAAGAGGTGGATATGG
1 TGGTGGCGG-AGAGGTGGATATGG
**
11849 TGGT---GGAG-GG-GGACGTGG
1 TGGTGGCGGAGAGGTGGATATGG
*
11867 CGGTGGCGGCAGAGGTGGATATGG
1 TGGTGGCGG-AGAGGTGGATATGG
*
11891 TGGTGGAGGAG
1 TGGTGGCGGAG
11902 GACGTGGTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 13
0.67 0.12 0.22
Matches are distributed among these distances:
18 9 0.22
19 2 0.05
20 2 0.05
21 4 0.10
22 2 0.05
23 4 0.10
24 17 0.43
ACGTcount: A:0.17, C:0.06, G:0.58, T:0.18
Consensus pattern (23 bp):
TGGTGGCGGAGAGGTGGATATGG
Found at i:11899 original size:18 final size:18
Alignment explanation
Indices: 11878--11920 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
11868 GGTGGCGGCA
*
11878 GAGGTGGATATGGTGGTG
1 GAGGTGGACATGGTGGTG
* *
11896 GAGGAGGACGTGGTGGTG
1 GAGGTGGACATGGTGGTG
*
11914 GCGGTGG
1 GAGGTGG
11921 CGGATATGAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.14, C:0.05, G:0.60, T:0.21
Consensus pattern (18 bp):
GAGGTGGACATGGTGGTG
Found at i:11905 original size:42 final size:41
Alignment explanation
Indices: 11805--11917 Score: 158
Period size: 42 Copynumber: 2.8 Consensus size: 41
11795 TGGAGGAGGT
* *
11805 TATGGTGGTGGAGGTGGACAT--GGTGGCGGAAGAGGTGGA
1 TATGGTGGTGGAGGAGGACGTGGGGTGGCGGAAGAGGTGGA
* *
11844 TATGGTGGTGGAGGGGGACGTGGCGGTGGCGGCAGAGGTGGA
1 TATGGTGGTGGAGGAGGACGTGG-GGTGGCGGAAGAGGTGGA
11886 TATGGTGGTGGAGGAGGACGTGGTGGTGGCGG
1 TATGGTGGTGGAGGAGGACGTGG-GGTGGCGG
11918 TGGCGGATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
39 19 0.29
42 47 0.71
ACGTcount: A:0.16, C:0.07, G:0.58, T:0.19
Consensus pattern (41 bp):
TATGGTGGTGGAGGAGGACGTGGGGTGGCGGAAGAGGTGGA
Found at i:11926 original size:39 final size:39
Alignment explanation
Indices: 11796--11935 Score: 145
Period size: 39 Copynumber: 3.5 Consensus size: 39
11786 TGGCGGGCAT
* * * * * *
11796 GGAGGAGGTTATGGTGGTGGAGGTGGACATGGTGGCGGA
1 GGAGGTGGATATGGTGGTGGAGGAGGACGTGGTGGTGGC
* * *
11835 AGAGGTGGATATGGTGGTGGAGGGGGACGTGGCGGTGGC
1 GGAGGTGGATATGGTGGTGGAGGAGGACGTGGTGGTGGC
11874 GGCAGAGGTGGATATGGTGGTGGAGGAGGACGTGGTGGTGGC
1 -G--GAGGTGGATATGGTGGTGGAGGAGGACGTGGTGGTGGC
* * *
11916 GGTGGCGGATATGATGGTGG
1 GGAGGTGGATATGGTGGTGG
11936 TGAAGCCAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 47 0.56
41 1 0.01
42 36 0.43
ACGTcount: A:0.16, C:0.06, G:0.57, T:0.20
Consensus pattern (39 bp):
GGAGGTGGATATGGTGGTGGAGGAGGACGTGGTGGTGGC
Found at i:13003 original size:2 final size:2
Alignment explanation
Indices: 12996--13024 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12986 CCACAATCAA
12996 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
13025 GTCTATTTTT
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
Done.