Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009844.1 Corchorus capsularis cultivar CVL-1 contig09865, 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: 43341
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:3735 original size:36 final size:36
Alignment explanation
Indices: 3688--3757 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
3678 AATCCTCAAC
3688 AGAATCACCCGTGATGATGCCAGAACTTGTTCATAT
1 AGAATCACCCGTGATGATGCCAGAACTTGTTCATAT
3724 AGAATCACCCGTGATGATGCCAGAACTTGTTCAT
1 AGAATCACCCGTGATGATGCCAGAACTTGTTCAT
3758 GGAGATCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (36 bp):
AGAATCACCCGTGATGATGCCAGAACTTGTTCATAT
Found at i:6261 original size:83 final size:80
Alignment explanation
Indices: 6113--6265 Score: 270
Period size: 80 Copynumber: 1.9 Consensus size: 80
6103 TCTAACATCT
6113 TAAAGCTATATAAAAACTTAGATAATAATAATAATATAAAAACTAAATTGGAAGCTTCAATCCTT
1 TAAAGCTATATAAAAACTTAGATAATAATAATAATATAAAAACTAAATTGGAAGCTTCAATCCTT
6178 CCCATACATCTTAGA
66 CCCATACATCTTAGA
*
6193 TAAAGCTATATAAAAACTTAGATAATAATAATAATATAATCAAAACTAAATTTGAAGCTTCAATC
1 TAAAGCTATATAAAAACTTAGATAATAATAATAATAT-A--AAAACTAAATTGGAAGCTTCAATC
6258 CTTCCCAT
63 CTTCCCAT
6266 TTCCATTGCT
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
80 37 0.54
81 1 0.01
83 31 0.45
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.31
Consensus pattern (80 bp):
TAAAGCTATATAAAAACTTAGATAATAATAATAATATAAAAACTAAATTGGAAGCTTCAATCCTT
CCCATACATCTTAGA
Found at i:9917 original size:14 final size:14
Alignment explanation
Indices: 9882--9918 Score: 53
Period size: 11 Copynumber: 2.9 Consensus size: 14
9872 AATAATTCAT
9882 TTGCCTTTGAAGTA
1 TTGCCTTTGAAGTA
9896 TTG-C--TGAAGTA
1 TTGCCTTTGAAGTA
9907 TTGCCTTTGAAG
1 TTGCCTTTGAAG
9919 CATGTAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
11 10 0.50
12 1 0.05
13 1 0.05
14 8 0.40
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.41
Consensus pattern (14 bp):
TTGCCTTTGAAGTA
Found at i:10186 original size:81 final size:80
Alignment explanation
Indices: 10043--10203 Score: 254
Period size: 81 Copynumber: 2.0 Consensus size: 80
10033 TAACCCTCTA
* *
10043 ACATCTTAGATAAAGCTATATAAAAACTTAGATATTAATTAATAATATAAAAACTATATTGGAAG
1 ACATCTTAGATAAAGCTATATAAAAACTTAGATAATAATTAATAATATAAAAACTAAATTGG-AG
10108 CTTCAATCCTTCCCAT
65 CTTCAATCCTTCCCAT
*
10124 ACATCTTAGATAAAGCTATATAAAAACTTAGATAATAA-TAAT-ATAATTAAAACTAAATTTGGA
1 ACATCTTAGATAAAGCTATATAAAAACTTAGATAATAATTAATAAT-ATAAAAACTAAA-TTGGA
10187 GCTTCAATCCTTCCCAT
64 GCTTCAATCCTTCCCAT
10204 TTCCATTGCT
Statistics
Matches: 75, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
79 2 0.03
80 32 0.43
81 41 0.55
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (80 bp):
ACATCTTAGATAAAGCTATATAAAAACTTAGATAATAATTAATAATATAAAAACTAAATTGGAGC
TTCAATCCTTCCCAT
Found at i:16537 original size:13 final size:13
Alignment explanation
Indices: 16519--16543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16509 AGTGTTTCTC
16519 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
16532 TTCTTTTTTTTT
1 TTCTTTTTTTTT
16544 AAACAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:30437 original size:14 final size:15
Alignment explanation
Indices: 30409--30443 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
30399 AAATTAATGG
*
30409 AGAAGAAAAGGAAAA
1 AGAAGAAAAGAAAAA
30424 AGAA-AAAAGAAAAA
1 AGAAGAAAAGAAAAA
30438 AGAAGA
1 AGAAGA
30444 GTCTCTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAAGAAAAGAAAAA
Found at i:31142 original size:4 final size:4
Alignment explanation
Indices: 31133--31166 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
31123 GAAGAGGAAG
*
31133 TAAA TAAA TAAA TAAA TAACA TAAA TAAA AAAA T
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA T
31167 TACTACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:31158 original size:13 final size:12
Alignment explanation
Indices: 31133--31166 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
31123 GAAGAGGAAG
31133 TAAATAAATAAA
1 TAAATAAATAAA
31145 TAAATAACATAAA
1 TAAATAA-ATAAA
*
31158 TAAAAAAAT
1 TAAATAAAT
31167 TACTACATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAATAAATAAA
Found at i:32012 original size:27 final size:27
Alignment explanation
Indices: 31982--32088 Score: 187
Period size: 27 Copynumber: 4.0 Consensus size: 27
31972 GGAAGAAATA
31982 AAGGCGGAAGAGAAGAAACCACCTGCC
1 AAGGCGGAAGAGAAGAAACCACCTGCC
32009 AAGGCGGAAGAGAAGAAACCACCTGCC
1 AAGGCGGAAGAGAAGAAACCACCTGCC
* *
32036 AAGGAGGAAGACAAGAAACCACCTGCC
1 AAGGCGGAAGAGAAGAAACCACCTGCC
*
32063 AAGGTGGAAGAGAAGAAACCACCTGC
1 AAGGCGGAAGAGAAGAAACCACCTGC
32089 TGCCGCCGCC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 76 1.00
ACGTcount: A:0.42, C:0.24, G:0.29, T:0.05
Consensus pattern (27 bp):
AAGGCGGAAGAGAAGAAACCACCTGCC
Found at i:40069 original size:2 final size:2
Alignment explanation
Indices: 40062--40098 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
40052 GAAAATATTA
40062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40099 CACTTCTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:42870 original size:2 final size:2
Alignment explanation
Indices: 42863--42899 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
42853 CGAGAAAATC
42863 AT AT AT AT CAT 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
42900 TAAAACTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43213 original size:81 final size:81
Alignment explanation
Indices: 43078--43240 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
43068 TAGATCCAAA
*
43078 ATTTTCTCCTTAATTGTTGTGTTAAACCTAATTGTACATCTCATTTTAGATCCAAAATTAACTCC
1 ATTTTCTCCCTAATTGTTGTGTTAAACCTAATTGTACATCTCATTTTAGATCCAAAATTAACTCC
43143 AAAATTGTAGTTTCAT
66 AAAATTGTAGTTTCAT
43159 ATTTTCTCCCTAATTGTTGTGTTAAACCTAATTGTACATCTCATTTTAGATCCAAAATTAACTCC
1 ATTTTCTCCCTAATTGTTGTGTTAAACCTAATTGTACATCTCATTTTAGATCCAAAATTAACTCC
43224 AAAATTGTAGTTTCAT
66 AAAATTGTAGTTTCAT
43240 A
1 A
43241 ATAAATACTA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (81 bp):
ATTTTCTCCCTAATTGTTGTGTTAAACCTAATTGTACATCTCATTTTAGATCCAAAATTAACTCC
AAAATTGTAGTTTCAT
Done.