Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011783.1 Corchorus capsularis cultivar CVL-1 contig11804, 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: 42586
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:731 original size:4 final size:4
Alignment explanation
Indices: 722--753 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
712 CCCCTAAATT
*
722 TACA TACA TACA TACA TACA TATA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA
754 CAGGGGCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:1178 original size:34 final size:34
Alignment explanation
Indices: 1135--1237 Score: 206
Period size: 34 Copynumber: 3.0 Consensus size: 34
1125 TTTCTGACTC
1135 CACCACTGTACATACATGAAGCAATTGATGATAT
1 CACCACTGTACATACATGAAGCAATTGATGATAT
1169 CACCACTGTACATACATGAAGCAATTGATGATAT
1 CACCACTGTACATACATGAAGCAATTGATGATAT
1203 CACCACTGTACATACATGAAGCAATTGATGATAT
1 CACCACTGTACATACATGAAGCAATTGATGATAT
1237 C
1 C
1238 GGGGTTAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (34 bp):
CACCACTGTACATACATGAAGCAATTGATGATAT
Found at i:2473 original size:2 final size:2
Alignment explanation
Indices: 2466--2496 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2456 CTCCAAATCA
2466 AT 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 AT A
2497 GACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 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):
AT
Found at i:4189 original size:16 final size:15
Alignment explanation
Indices: 4163--4194 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
4153 TAATTGAAAG
4163 AATACATCTTTAATT
1 AATACATCTTTAATT
4178 AATACTATCTTTAATT
1 AATAC-ATCTTTAATT
4194 A
1 A
4195 CTTTTAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (15 bp):
AATACATCTTTAATT
Found at i:5545 original size:40 final size:40
Alignment explanation
Indices: 5487--5567 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
5477 TTTATAACTA
* *
5487 GGGGCTAAACCTGAATTTAAATTCTTACCTTAATTATTAG
1 GGGGCTAAACATGAATTTAAATTATTACCTTAATTATTAG
* * *
5527 GGGGCTAAACATGGATTTAATTTATTTCCTTAATTATTAG
1 GGGGCTAAACATGAATTTAAATTATTACCTTAATTATTAG
5567 G
1 G
5568 AGGGACAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (40 bp):
GGGGCTAAACATGAATTTAAATTATTACCTTAATTATTAG
Found at i:8790 original size:2 final size:2
Alignment explanation
Indices: 8783--8815 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8773 TTAAAACTAG
8783 TA TA TA TA TA TA TA TA 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
8816 GTTGACGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11869 original size:37 final size:37
Alignment explanation
Indices: 11819--11891 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
11809 ACATAGGGTA
*
11819 CTTAGTTCCTATTTTAATTAGGAGAACTAGTCCATAC
1 CTTAGTTCCTATTTTAACTAGGAGAACTAGTCCATAC
* *
11856 CTTAGTTTCTATTTTGACTAGGAGAACTAGTCCATA
1 CTTAGTTCCTATTTTAACTAGGAGAACTAGTCCATA
11892 TCCCCGCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (37 bp):
CTTAGTTCCTATTTTAACTAGGAGAACTAGTCCATAC
Found at i:12039 original size:37 final size:37
Alignment explanation
Indices: 11989--12063 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
11979 ACATAGGGTA
11989 CTTAGTTCCTATTTTAACTA-AGAGAACTAGTCCATAC
1 CTTAGTTCCTATTTTAACTAGA-AGAACTAGTCCATAC
* * * *
12026 CTTAGTTTCTATTTTGAGTAGAAGAATTAGTCCATAC
1 CTTAGTTCCTATTTTAACTAGAAGAACTAGTCCATAC
12063 C
1 C
12064 CCTGCATCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 32 0.97
38 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (37 bp):
CTTAGTTCCTATTTTAACTAGAAGAACTAGTCCATAC
Found at i:12077 original size:170 final size:170
Alignment explanation
Indices: 11788--12123 Score: 575
Period size: 170 Copynumber: 2.0 Consensus size: 170
11778 TTAAGAATAC
* * *
11788 AAGAGATGATCTCTTATATAAACATAGGGTACTTAGTTCCTATTTTAATTAGGAGAACTAGTCCA
1 AAGAGATGACCTCTTATATAAACATAGGGTACTTAGTTCCTATTTTAACTAAGAGAACTAGTCCA
*
11853 TACCTTAGTTTCTATTTTGACTAGGAGAACTAGTCCATATCCCCGCAACCCTACGCCTATTCTGC
66 TACCTTAGTTTCTATTTTGACTAGAAGAACTAGTCCATATCCCCGCAACCCTACGCCTATTCTGC
11918 GTCTTCCCACATGAACAGTCTAGAATAGGATTTCTTATAT
131 GTCTTCCCACATGAACAGTCTAGAATAGGATTTCTTATAT
11958 AAGAGATGACCTCTTATATAAACATAGGGTACTTAGTTCCTATTTTAACTAAGAGAACTAGTCCA
1 AAGAGATGACCTCTTATATAAACATAGGGTACTTAGTTCCTATTTTAACTAAGAGAACTAGTCCA
* * *
12023 TACCTTAGTTTCTATTTTGAGTAGAAGAATTAGTCCATA-CCCCTGCATCCCTACGCCTATTCTG
66 TACCTTAGTTTCTATTTTGACTAGAAGAACTAGTCCATATCCCC-GCAACCCTACGCCTATTCTG
* *
12087 CGTCTTCCCGCATGAACAGTCTAGTATAGGATTTCTT
130 CGTCTTCCCACATGAACAGTCTAGAATAGGATTTCTT
12124 GGCAACGGCG
Statistics
Matches: 156, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
169 4 0.03
170 152 0.97
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (170 bp):
AAGAGATGACCTCTTATATAAACATAGGGTACTTAGTTCCTATTTTAACTAAGAGAACTAGTCCA
TACCTTAGTTTCTATTTTGACTAGAAGAACTAGTCCATATCCCCGCAACCCTACGCCTATTCTGC
GTCTTCCCACATGAACAGTCTAGAATAGGATTTCTTATAT
Found at i:12764 original size:12 final size:12
Alignment explanation
Indices: 12747--12771 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12737 TTTGATAAGA
12747 AGAGGCAGAAGC
1 AGAGGCAGAAGC
12759 AGAGGCAGAAGC
1 AGAGGCAGAAGC
12771 A
1 A
12772 AAAGCAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.40, T:0.00
Consensus pattern (12 bp):
AGAGGCAGAAGC
Found at i:15080 original size:2 final size:2
Alignment explanation
Indices: 15073--15114 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
15063 AGTTGATTAA
15073 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
15115 CAATGGCACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:17158 original size:18 final size:18
Alignment explanation
Indices: 17049--17149 Score: 157
Period size: 18 Copynumber: 5.6 Consensus size: 18
17039 CCCTTCGAGG
* *
17049 ACCACGTTCAGTACGAGG
1 ACCACGTTCAGTATGAGT
*
17067 ACCACGTTCAGTACGAGT
1 ACCACGTTCAGTATGAGT
*
17085 ACCACATTCAGTATGAGT
1 ACCACGTTCAGTATGAGT
*
17103 ACCACGTTCAGTATAAGT
1 ACCACGTTCAGTATGAGT
17121 ACCACGTTCAGTATGAGT
1 ACCACGTTCAGTATGAGT
17139 ACCACGTTCAG
1 ACCACGTTCAG
17150 CATATGTACG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 77 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (18 bp):
ACCACGTTCAGTATGAGT
Found at i:19419 original size:12 final size:12
Alignment explanation
Indices: 19402--19426 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19392 TTGTTGACTT
19402 AAATTAGTAGTA
1 AAATTAGTAGTA
19414 AAATTAGTAGTA
1 AAATTAGTAGTA
19426 A
1 A
19427 TTGATTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
AAATTAGTAGTA
Found at i:20397 original size:16 final size:16
Alignment explanation
Indices: 20378--20410 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20368 AACATGGGGC
20378 AAAAAGAAAAAGAAGA
1 AAAAAGAAAAAGAAGA
*
20394 AAAAAGAAGAAGAAGA
1 AAAAAGAAAAAGAAGA
20410 A
1 A
20411 GAAGATCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAGAAGA
Found at i:27326 original size:21 final size:20
Alignment explanation
Indices: 27289--27327 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27279 TTTAGAAGCA
*
27289 ATTAATTAAAAGCATTAAAC
1 ATTAATTAAAAACATTAAAC
27309 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAAC-ATTAA
27328 GGAAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAAACATTAAAC
Found at i:27436 original size:73 final size:73
Alignment explanation
Indices: 27334--27488 Score: 224
Period size: 73 Copynumber: 2.1 Consensus size: 73
27324 TTAAGGAAGA
* * *
27334 GAAATGTGTAATTATGAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAAAGGAG-CTTTT
1 GAAAAGTGTAATTACGAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGAGTCTTTT
27398 AGTCATCC-
66 AGTCA-CCT
* * *
27406 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGTTTTT
1 GAAAAGTGTAATTACG-AAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGAGTCTTT
27471 TAGTCACCT
65 TAGTCACCT
27480 GAAAAGTGT
1 GAAAAGTGT
27489 GAAAAGATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
72 14 0.19
73 42 0.57
74 18 0.24
ACGTcount: A:0.41, C:0.08, G:0.30, T:0.22
Consensus pattern (73 bp):
GAAAAGTGTAATTACGAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGAGTCTTTT
AGTCACCT
Found at i:30676 original size:25 final size:27
Alignment explanation
Indices: 30639--30691 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
30629 ATGACCCATT
30639 ATTATATACTAATA-TATGAAGGAAAAA
1 ATTATATACTAATATTA-GAAGGAAAAA
*
30666 ATTAT-TA-TAATATTAGAAGTAAAAA
1 ATTATATACTAATATTAGAAGGAAAAA
30691 A
1 A
30692 AAAAAGTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 15 0.62
26 4 0.17
27 5 0.21
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (27 bp):
ATTATATACTAATATTAGAAGGAAAAA
Found at i:31104 original size:2 final size:2
Alignment explanation
Indices: 31097--31132 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31087 TGGAAGAAGA
31097 AT AT AT 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 AT AT AT
31133 GTATGATAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.