Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013446.1 Corchorus capsularis cultivar CVL-1 contig13467, 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: 48111
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2350 original size:67 final size:67
Alignment explanation
Indices: 2242--2377 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
2232 ACAATTGCGA
*
2242 TGAGAAATCGTCGAGCTCAACTTAAATGATTTAGGATTATGTAATAATCATTTTTCTTTAATTAT
1 TGAGAAATCGTCGAGCTCAACTTAAATGATTTAGGATTATGTAACAATCATTTTTCTTTAATTAT
2307 AT
66 AT
2309 TGAGAAATCGTCGAGCTCAACTTAAATGATTTAGGATTATGTAACAATCATTTTTCTTTAATTAT
1 TGAGAAATCGTCGAGCTCAACTTAAATGATTTAGGATTATGTAACAATCATTTTTCTTTAATTAT
2374 AT
66 AT
2376 TG
1 TG
2378 TTATTTAGCG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (67 bp):
TGAGAAATCGTCGAGCTCAACTTAAATGATTTAGGATTATGTAACAATCATTTTTCTTTAATTAT
AT
Found at i:2911 original size:16 final size:16
Alignment explanation
Indices: 2890--2948 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
2880 GTCTGAACTT
2890 GAACCCGAAAAAACCC
1 GAACCCGAAAAAACCC
* *
2906 GAACCCGAAAAAGCTC
1 GAACCCGAAAAAACCC
* *
2922 AAACCCGAAATAACCC
1 GAACCCGAAAAAACCC
*
2938 GAATCCGAAAA
1 GAACCCGAAAA
2949 TTTATGAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.49, C:0.32, G:0.14, T:0.05
Consensus pattern (16 bp):
GAACCCGAAAAAACCC
Found at i:3126 original size:15 final size:15
Alignment explanation
Indices: 3103--3219 Score: 94
Period size: 15 Copynumber: 7.5 Consensus size: 15
3093 CAGAACATGA
*
3103 ACCCGAATTAACCTG
1 ACCCAAATTAACCTG
3118 ACCCAAATTAATCC-G
1 ACCCAAATTAA-CCTG
* *
3133 AACCCGAATTAACCTA
1 -ACCCAAATTAACCTG
* *
3149 ACCCAAATCCAACCCG
1 ACCCAAAT-TAACCTG
*
3165 AACCCGAATTAACCTG
1 -ACCCAAATTAACCTG
3181 ACCCAAATTAATCC-G
1 ACCCAAATTAA-CCTG
* *
3196 AACCCGAATTAACCTA
1 -ACCCAAATTAACCTG
3212 ACCCAAAT
1 ACCCAAAT
3220 CCAACCCGAA
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
15 40 0.50
16 33 0.41
17 7 0.09
ACGTcount: A:0.40, C:0.35, G:0.08, T:0.17
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:3138 original size:31 final size:32
Alignment explanation
Indices: 3101--3234 Score: 200
Period size: 31 Copynumber: 4.2 Consensus size: 32
3091 AACAGAACAT
* * *
3101 GAACCCGAATTAACCTGACCCAAAT-TAATCC
1 GAACCCGAATTAACCTAACCCAAATCCAACCC
3132 GAACCCGAATTAACCTAACCCAAATCCAACCC
1 GAACCCGAATTAACCTAACCCAAATCCAACCC
* * *
3164 GAACCCGAATTAACCTGACCCAAAT-TAATCC
1 GAACCCGAATTAACCTAACCCAAATCCAACCC
3195 GAACCCGAATTAACCTAACCCAAATCCAACCC
1 GAACCCGAATTAACCTAACCCAAATCCAACCC
3227 GAACCCGA
1 GAACCCGA
3235 CTCAAATCCG
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 52 0.57
32 40 0.43
ACGTcount: A:0.40, C:0.37, G:0.09, T:0.15
Consensus pattern (32 bp):
GAACCCGAATTAACCTAACCCAAATCCAACCC
Found at i:3184 original size:63 final size:63
Alignment explanation
Indices: 3101--3234 Score: 268
Period size: 63 Copynumber: 2.1 Consensus size: 63
3091 AACAGAACAT
3101 GAACCCGAATTAACCTGACCCAAATTAATCCGAACCCGAATTAACCTAACCCAAATCCAACCC
1 GAACCCGAATTAACCTGACCCAAATTAATCCGAACCCGAATTAACCTAACCCAAATCCAACCC
3164 GAACCCGAATTAACCTGACCCAAATTAATCCGAACCCGAATTAACCTAACCCAAATCCAACCC
1 GAACCCGAATTAACCTGACCCAAATTAATCCGAACCCGAATTAACCTAACCCAAATCCAACCC
3227 GAACCCGA
1 GAACCCGA
3235 CTCAAATCCG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.40, C:0.37, G:0.09, T:0.15
Consensus pattern (63 bp):
GAACCCGAATTAACCTGACCCAAATTAATCCGAACCCGAATTAACCTAACCCAAATCCAACCC
Found at i:3922 original size:26 final size:26
Alignment explanation
Indices: 3902--3955 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3892 CAAACTATAT
3902 AACAATTCACCAAAAAAAAACAGTAA
1 AACAATTCACCAAAAAAAAACAGTAA
3928 AACAATTCACCAAAAAAAAACAGTAA
1 AACAATTCACCAAAAAAAAACAGTAA
3954 AA
1 AA
3956 TTAGTCTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.67, C:0.19, G:0.04, T:0.11
Consensus pattern (26 bp):
AACAATTCACCAAAAAAAAACAGTAA
Found at i:5032 original size:2 final size:2
Alignment explanation
Indices: 5025--5054 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5015 CATGGTAAGA
5025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5055 TTCTATTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8177 original size:16 final size:17
Alignment explanation
Indices: 8158--8190 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
8148 TCGAAAGAAT
8158 AAAGGAGAGAG-ATGAG
1 AAAGGAGAGAGAATGAG
8174 AAAGGAGAGAGAATGAG
1 AAAGGAGAGAGAATGAG
8191 TGGAAGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.42, T:0.06
Consensus pattern (17 bp):
AAAGGAGAGAGAATGAG
Found at i:8633 original size:21 final size:21
Alignment explanation
Indices: 8609--8666 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
8599 ACAGAAGCAA
8609 GTAGAACAGAGCAGACAAAAC
1 GTAGAACAGAGCAGACAAAAC
8630 GTAGAACAGAGCAGACAAAAC
1 GTAGAACAGAGCAGACAAAAC
*
8651 TTAGAACAGAGCAGAC
1 GTAGAACAGAGCAGAC
8667 CAAGACAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.50, C:0.19, G:0.24, T:0.07
Consensus pattern (21 bp):
GTAGAACAGAGCAGACAAAAC
Found at i:13956 original size:153 final size:162
Alignment explanation
Indices: 13612--13980 Score: 440
Period size: 167 Copynumber: 2.3 Consensus size: 162
13602 CTTTTTTTTA
* * *
13612 AATCTAATATCTTTATTACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTAGATA
1 AATCTAATATCTTTATAAATATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTAAGATA
* * **
13677 TATTAGAATTTTTTTAATATATTTCTTAAATGATATTGTTTAAACTTTTACAGTTTAATTTATTC
66 TATTAGAATTTTTTAAATATATTTCTTAAATGAAATTGTTTAAACCGTTACAG-TT-ATTTATTC
*
13742 TACTACAAACTCCATATTTGTTTAATTTTTATTTAATT
129 TACTACAAACT-CATA-TTGTTTAA-TTTTATATAA-T
* * * *
13780 AATCTAATATCTTTATAACTATTTTACTTTTATCATTTTACTATTTTAATT-AAAAACTAAGGTA
1 AATCTAATATCTTTATAAATATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTAAGATA
*
13844 TATTAGAATTTTTTAAATATATTTCTTAAATGAAATTGTTTAAACCGTTATAG-T-TTTATTCTA
66 TATTAGAATTTTTTAAATATATTTCTTAAATGAAATTGTTTAAACCGTTACAGTTATTTATTCTA
13907 CTA-AAAGCT-ATA-TGTTT-A-TTTA-ATAA-
131 CTACAAA-CTCATATTGTTTAATTTTATATAAT
*
13933 AAT-TCAATAAT-TTTATAAATATTTTATTTTTACCATTTTAAT-TTTTAA
1 AATCT-AAT-ATCTTTATAAATATTTTATTTTTACCATTTTACTATTTTAA
13981 AAATTGGAGG
Statistics
Matches: 183, Mismatches: 15, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
152 7 0.04
153 33 0.18
154 2 0.01
155 3 0.02
156 4 0.02
158 1 0.01
159 5 0.03
161 3 0.02
162 3 0.02
163 14 0.08
165 1 0.01
167 59 0.32
168 48 0.26
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (162 bp):
AATCTAATATCTTTATAAATATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTAAGATA
TATTAGAATTTTTTAAATATATTTCTTAAATGAAATTGTTTAAACCGTTACAGTTATTTATTCTA
CTACAAACTCATATTGTTTAATTTTATATAAT
Found at i:14191 original size:31 final size:31
Alignment explanation
Indices: 14153--14211 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
14143 TTTGTAAAAC
*
14153 TTTTGAAACGCCTATTGTACCCTTATTTAAT
1 TTTTGAAACGCCTATTATACCCTTATTTAAT
* * *
14184 TTTTGAAATGTCTATTATATCCTTATTT
1 TTTTGAAACGCCTATTATACCCTTATTT
14212 GTCTAACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.51
Consensus pattern (31 bp):
TTTTGAAACGCCTATTATACCCTTATTTAAT
Found at i:15680 original size:21 final size:21
Alignment explanation
Indices: 15656--15698 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15646 ATAAACTGGA
15656 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
15677 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
15698 T
1 T
15699 GACGCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:18846 original size:6 final size:6
Alignment explanation
Indices: 18835--18864 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
18825 AACAAGTCCC
18835 CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT
1 CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT
18865 GGATTGGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.17, T:0.50
Consensus pattern (6 bp):
CTGCTT
Found at i:20695 original size:13 final size:13
Alignment explanation
Indices: 20677--20714 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
20667 GATTGCTTTG
20677 ATTCTTTCTTAGA
1 ATTCTTTCTTAGA
20690 ATTCTTTCTTAGA
1 ATTCTTTCTTAGA
20703 ATTCTTTCTTAG
1 ATTCTTTCTTAG
20715 GATACAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (13 bp):
ATTCTTTCTTAGA
Found at i:21189 original size:30 final size:30
Alignment explanation
Indices: 21153--21217 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
21143 TATTTTTATC
* *
21153 GATTGATATAGAAAAAGTCATGGAATTTCT
1 GATTGATATAGAAAAAGGCATAGAATTTCT
*
21183 GATTGATATAGAAAAAGGCCTAGAATTTCT
1 GATTGATATAGAAAAAGGCATAGAATTTCT
21213 GATTG
1 GATTG
21218 GAAGGAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (30 bp):
GATTGATATAGAAAAAGGCATAGAATTTCT
Found at i:24496 original size:11 final size:11
Alignment explanation
Indices: 24480--24511 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
24470 TTGATAATTG
24480 GCTACGGACAT
1 GCTACGGACAT
24491 GCTACGGACAT
1 GCTACGGACAT
*
24502 GCTACAGACA
1 GCTACGGACA
24512 AAATAGACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (11 bp):
GCTACGGACAT
Found at i:24993 original size:4 final size:4
Alignment explanation
Indices: 24984--25014 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
24974 TATAAATCTA
24984 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
25015 ATCTATATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:25023 original size:8 final size:8
Alignment explanation
Indices: 24982--25031 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
24972 AATATAAATC
24982 TATATCTA
1 TATATCTA
*
24990 TCTATCTA
1 TATATCTA
*
24998 TCTATCTA
1 TATATCTA
*
25006 TCTATC--
1 TATATCTA
25012 TATATCTA
1 TATATCTA
25020 TATA-CTA
1 TATATCTA
25027 TATAT
1 TATAT
25032 AAAAGTACGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 5 0.14
7 7 0.19
8 25 0.68
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATCTA
Found at i:25172 original size:26 final size:25
Alignment explanation
Indices: 25143--25198 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
25133 CTAAAAACTC
25143 TATTTTTATTCAATTA-TTAAATCTAA
1 TATTTTTA-T-AATTACTTAAATCTAA
25169 TATTTTTATAATTACTTTAAATCTAA
1 TATTTTTATAATTAC-TTAAATCTAA
25195 TATT
1 TATT
25199 ACCTCTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.18
25 1 0.04
26 22 0.79
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTTTTATAATTACTTAAATCTAA
Found at i:25612 original size:15 final size:16
Alignment explanation
Indices: 25563--25617 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
25553 TTGGAACCAT
25563 ATGACCCAAAACCGAAAA
1 ATGACCC-AAACC-AAAA
*
25581 A-CACCCAAACCAAAA
1 ATGACCCAAACCAAAA
*
25596 ATGACCCAAACC-CAA
1 ATGACCCAAACCAAAA
25611 ATGACCC
1 ATGACCC
25618 GACATTTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 14 0.42
16 14 0.42
17 4 0.12
18 1 0.03
ACGTcount: A:0.51, C:0.36, G:0.07, T:0.05
Consensus pattern (16 bp):
ATGACCCAAACCAAAA
Found at i:27551 original size:18 final size:18
Alignment explanation
Indices: 27528--27563 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27518 CGCATGTCAA
*
27528 CTGTTACTCATTTGAGTT
1 CTGTTACTCACTTGAGTT
27546 CTGTTACTCACTTGAGTT
1 CTGTTACTCACTTGAGTT
27564 GACTTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (18 bp):
CTGTTACTCACTTGAGTT
Found at i:42914 original size:21 final size:20
Alignment explanation
Indices: 42866--42918 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 20
42856 AGCAAAAGAG
42866 GCAAAAG-AGAAAGAGGAAA
1 GCAAAAGAAGAAAGAGGAAA
42885 -CTAAAAAGAAGAAAGAGGAAA
1 GC--AAAAGAAGAAAGAGGAAA
42906 GC--AAGAAGAAAGA
1 GCAAAAGAAGAAAGA
42919 TGAACAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
18 12 0.40
20 5 0.17
21 12 0.40
22 1 0.03
ACGTcount: A:0.64, C:0.06, G:0.28, T:0.02
Consensus pattern (20 bp):
GCAAAAGAAGAAAGAGGAAA
Found at i:43055 original size:6 final size:6
Alignment explanation
Indices: 43046--43070 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43036 TTAGTTGCCG
43046 CCTTAC CCTTAC CCTTAC CCTTAC C
1 CCTTAC CCTTAC CCTTAC CCTTAC C
43071 AAGTTGTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTTAC
Done.