Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006723.1 Corchorus capsularis cultivar CVL-1 contig06744, 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: 23316
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1361 original size:22 final size:22
Alignment explanation
Indices: 1336--1567 Score: 110
Period size: 22 Copynumber: 10.7 Consensus size: 22
1326 AGAAATATTA
* *
1336 ATAACCACACTGTGAAAATTTG
1 ATAACCTCACTATGAAAATTTG
* *
1358 ATAACCTCATTATG-GAATTTCG
1 ATAACCTCACTATGAAAATTT-G
**
1380 ATAACCTCTTTATGAAAATTTG
1 ATAACCTCACTATGAAAATTTG
**
1402 ATAACGACACTAT-AAAATTTTG
1 ATAACCTCACTATGAAAA-TTTG
* * * *
1424 ATAACCTTAGTGTGAAATTTTG
1 ATAACCTCACTATGAAAATTTG
* *
1446 ATAATCTC-CGTAT-AGAATTTTG
1 ATAACCTCAC-TATGA-AAATTTG
*
1468 ATAA--TCACAAT-AAAA-TTG
1 ATAACCTCACTATGAAAATTTG
* * *
1486 GTAACCGT-ATTATGAAACTTTTG
1 ATAACC-TCACTATGAAA-ATTTG
1509 ATAACCTC-CTCAT-AAAATTTTG
1 ATAACCTCACT-ATGAAAA-TTTG
* *
1531 ATAACCACACCATG-AAATTTCG
1 ATAACCTCACTATGAAAATTT-G
*
1553 ATAACCTCCCTATGA
1 ATAACCTCACTATGA
1568 GAATGAAACT
Statistics
Matches: 156, Mismatches: 34, Indels: 39
0.68 0.15 0.17
Matches are distributed among these distances:
18 6 0.04
19 2 0.01
20 8 0.05
21 18 0.12
22 103 0.66
23 19 0.12
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (22 bp):
ATAACCTCACTATGAAAATTTG
Found at i:1443 original size:66 final size:64
Alignment explanation
Indices: 1336--1559 Score: 211
Period size: 66 Copynumber: 3.4 Consensus size: 64
1326 AGAAATATTA
* * * * *
1336 ATAACCACACTGTGAAAATTTGATAACCTCATTATGGAATTTCGATAACCTCTTTATGAAAATTT
1 ATAACCACACTAT-AAAATTTGATAACCTTATTATGAAATTTTGATAACCTCCTTAT-AAAATTT
1401 G
64 G
* * * * * *
1402 ATAACGACACTATAAAATTTTGATAACCTTAGTGTGAAATTTTGATAATCTCCGTATAGAATTTT
1 ATAACCACACTATAAAA-TTTGATAACCTTATTATGAAATTTTGATAACCTCCTTATA-AAATTT
1467 G
64 G
* * * *
1468 ATAATCACA--ATAAAA-TTGGTAACCGTATTATGAAACTTTTGATAACCTCCTCATAAAATTTT
1 ATAACCACACTATAAAATTTGATAACCTTATTATGAAA-TTTTGATAACCTCCTTATAAAA-TTT
1530 G
64 G
* *
1531 ATAACCACACCATGAAATTTCGATAACCT
1 ATAACCACACTATAAAATTT-GATAACCT
1560 CCCTATGAGA
Statistics
Matches: 125, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
62 18 0.14
63 28 0.22
64 6 0.05
65 10 0.08
66 57 0.46
67 6 0.05
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (64 bp):
ATAACCACACTATAAAATTTGATAACCTTATTATGAAATTTTGATAACCTCCTTATAAAATTTG
Found at i:3741 original size:16 final size:16
Alignment explanation
Indices: 3722--3771 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
3712 CGCAACCCAG
3722 ATGACCCGAGACCCGA
1 ATGACCCGAGACCCGA
* *
3738 ATGA--TGAAACCCGA
1 ATGACCCGAGACCCGA
*
3752 ATGACCCGAGACCCGT
1 ATGACCCGAGACCCGA
3768 ATGA
1 ATGA
3772 ATCCGAGACA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 12 0.44
16 15 0.56
ACGTcount: A:0.34, C:0.30, G:0.24, T:0.12
Consensus pattern (16 bp):
ATGACCCGAGACCCGA
Found at i:3911 original size:21 final size:21
Alignment explanation
Indices: 3886--3932 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3876 TACAATTTAT
3886 ATTATTGTTATAATTTTACCA
1 ATTATTGTTATAATTTTACCA
* *
3907 ATTATTGTTATGATTTTACCT
1 ATTATTGTTATAATTTTACCA
3928 ATTAT
1 ATTAT
3933 AAATTGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTGTTATAATTTTACCA
Found at i:4419 original size:16 final size:16
Alignment explanation
Indices: 4392--4517 Score: 127
Period size: 16 Copynumber: 8.1 Consensus size: 16
4382 GAGACTCGGT
4392 AGACCCG-A-GACCCG
1 AGACCCGAATGACCCG
*
4406 -GAACCCAAATGACCCG
1 AG-ACCCGAATGACCCG
*
4422 AGACCCGTATGACCCG
1 AGACCCGAATGACCCG
*
4438 AGACTCGAATGACCCG
1 AGACCCGAATGACCCG
*
4454 AGACCCGAACGACCCG
1 AGACCCGAATGACCCG
* *
4470 AGACACGAATAACCCG
1 AGACCCGAATGACCCG
*
4486 A-ACCC-AGATGATCCG
1 AGACCCGA-ATGACCCG
*
4501 AAACCCGAATGACCCG
1 AGACCCGAATGACCCG
4517 A
1 A
4518 AAAAACTGCA
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
13 1 0.01
14 5 0.05
15 11 0.12
16 72 0.79
17 2 0.02
ACGTcount: A:0.34, C:0.37, G:0.22, T:0.07
Consensus pattern (16 bp):
AGACCCGAATGACCCG
Found at i:4435 original size:9 final size:8
Alignment explanation
Indices: 4414--4517 Score: 51
Period size: 9 Copynumber: 13.1 Consensus size: 8
4404 CGGAACCCAA
4414 ATGACCCG
1 ATGACCCG
4422 A-GACCCG
1 ATGACCCG
4429 TATGACCCG
1 -ATGACCCG
*
4438 A-GACTCG
1 ATGACCCG
4445 AATGACCCG
1 -ATGACCCG
4454 A-GACCCG
1 ATGACCCG
*
4461 AACGACCCG
1 -ATGACCCG
*
4470 A-GACACG
1 ATGACCCG
*
4477 AATAACCCG
1 -ATGACCCG
4486 A--ACCCAG
1 ATGACCC-G
*
4493 ATGATCCG
1 ATGACCCG
*
4501 A-AACCCG
1 ATGACCCG
4508 AATGACCCG
1 -ATGACCCG
4517 A
1 A
4518 AAAAACTGCA
Statistics
Matches: 74, Mismatches: 9, Indels: 26
0.68 0.08 0.24
Matches are distributed among these distances:
6 4 0.05
7 28 0.38
8 13 0.18
9 29 0.39
ACGTcount: A:0.34, C:0.36, G:0.22, T:0.09
Consensus pattern (8 bp):
ATGACCCG
Found at i:12091 original size:31 final size:30
Alignment explanation
Indices: 12056--12170 Score: 106
Period size: 31 Copynumber: 3.7 Consensus size: 30
12046 GGCGGATTCG
* * *
12056 GGTTCGGGTACTTCGGGTTTGAGTATTTTC
1 GGTTCGGATATTTCGGGTTCGAGTATTTTC
* * *
12086 AGGTTCGGAATTTTTCGGGTTCGGGTTTTTTC
1 -GGTTCGG-ATATTTCGGGTTCGAGTATTTTC
*
12118 GGATTCGGATATTTTGGGTTCGAGTA-TTTC
1 GG-TTCGGATATTTCGGGTTCGAGTATTTTC
*
12148 GGGTTCGGGTATTTTCGGGTTCG
1 -GGTTCGGATA-TTTCGGGTTCG
12171 GATTCGGTTC
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
30 11 0.16
31 35 0.51
32 22 0.32
ACGTcount: A:0.10, C:0.12, G:0.34, T:0.43
Consensus pattern (30 bp):
GGTTCGGATATTTCGGGTTCGAGTATTTTC
Found at i:12165 original size:16 final size:16
Alignment explanation
Indices: 12052--12171 Score: 122
Period size: 16 Copynumber: 7.7 Consensus size: 16
12042 TTTGGGCGGA
*
12052 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
* *
12067 TTCGGGTTTGAGTATT
1 TTCGGGTTCGGGTATT
* *
12083 TTCAGGTTC-GGAATTT
1 TTCGGGTTCGGGTA-TT
*
12099 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTATT
* *
12115 TTCGGATTCGGATATT
1 TTCGGGTTCGGGTATT
*
12131 TT-GGGTTCGAGTA-T
1 TTCGGGTTCGGGTATT
12145 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
12161 TTCGGGTTCGG
1 TTCGGGTTCGG
12172 ATTCGGTTCG
Statistics
Matches: 83, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
14 3 0.04
15 32 0.39
16 46 0.55
17 2 0.02
ACGTcount: A:0.10, C:0.12, G:0.34, T:0.43
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:12170 original size:6 final size:6
Alignment explanation
Indices: 12161--12203 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
12151 TTCGGGTATT
* *
12161 TTCGGG TTCGGA TTC-GG TTCGGG TCCGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC
12204 ACTTTCGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 8 0.26
6 23 0.74
ACGTcount: A:0.02, C:0.21, G:0.44, T:0.33
Consensus pattern (6 bp):
TTCGGG
Found at i:12183 original size:17 final size:17
Alignment explanation
Indices: 12161--12203 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
12151 TTCGGGTATT
*
12161 TTCGGGTTCGGATTC-GG
1 TTCGGGTTCGG-GTCGGG
*
12178 TTCGGGTCCGGGTCGGG
1 TTCGGGTTCGGGTCGGG
12195 TTCGGGTTC
1 TTCGGGTTC
12204 ACTTTCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.02, C:0.21, G:0.44, T:0.33
Consensus pattern (17 bp):
TTCGGGTTCGGGTCGGG
Found at i:12962 original size:16 final size:16
Alignment explanation
Indices: 12941--12980 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
12931 GTCGGGTTCG
12941 GGTTCGGGT-ATTTTCA
1 GGTTCGGGTAATTTT-A
*
12957 GGTTCGGGTAATTTTG
1 GGTTCGGGTAATTTTA
12973 GGTTCGGG
1 GGTTCGGG
12981 ATGTTGACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.10, C:0.10, G:0.40, T:0.40
Consensus pattern (16 bp):
GGTTCGGGTAATTTTA
Found at i:18980 original size:21 final size:21
Alignment explanation
Indices: 18930--18972 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18920 TTTAAATCAT
*
18930 ACAATGCATCATACATGTAAA
1 ACAATTCATCATACATGTAAA
18951 ACAATTCATCATACATGTAAA
1 ACAATTCATCATACATGTAAA
18972 A
1 A
18973 ACTATCATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.26
Consensus pattern (21 bp):
ACAATTCATCATACATGTAAA
Found at i:20406 original size:6 final size:6
Alignment explanation
Indices: 20390--20422 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
20380 TAAAGCAAAG
20390 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAA
20423 GCAGAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATC
Found at i:20434 original size:18 final size:18
Alignment explanation
Indices: 20369--20434 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 18
20359 AGAAAACAAT
* *
20369 TAAA-CTAAAAATAAAGC
1 TAAAGCTAAATATAAATC
20386 -AAAG-TAAAT-TAAATC
1 TAAAGCTAAATATAAATC
* *
20401 TAAATCTAAATCTAAATC
1 TAAAGCTAAATATAAATC
20419 TAAAGC-AGAATATAAA
1 TAAAGCTA-AATATAAA
20435 GCAAACAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.13
16 10 0.26
17 6 0.15
18 18 0.46
ACGTcount: A:0.59, C:0.11, G:0.06, T:0.24
Consensus pattern (18 bp):
TAAAGCTAAATATAAATC
Found at i:23233 original size:2 final size:2
Alignment explanation
Indices: 23226--23280 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
23216 ATTAGTAAAA
23226 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23268 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
23281 AATCAAAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.