Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003867.1 Corchorus capsularis cultivar CVL-1 contig03875, 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: 29175
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3082 original size:30 final size:30
Alignment explanation
Indices: 3045--3114 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
3035 ACAATTTTTA
** *
3045 ACACGTGGCACACCATGTGTCATTTTTTGT
1 ACACGTGGCACACCACATGTCATTTTTGGT
* **
3075 GCACGTGGCATGCCACATGTCATTTTTGGT
1 ACACGTGGCACACCACATGTCATTTTTGGT
3105 ACACGTGGCA
1 ACACGTGGCA
3115 TGTAACGTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (30 bp):
ACACGTGGCACACCACATGTCATTTTTGGT
Found at i:3136 original size:31 final size:30
Alignment explanation
Indices: 3061--3147 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 30
3051 GGCACACCAT
* * *
3061 GTGTCATTTTTTGTGCACGTGGCATGCCAC
1 GTGTCATTTTTGGTACACGTGGCATGCAAC
* *
3091 ATGTCATTTTTGGTACACGTGGCATGTAAC
1 GTGTCATTTTTGGTACACGTGGCATGCAAC
*
3121 GTGTCATCTTTTGGTACACATGGCATG
1 GTGTCAT-TTTTGGTACACGTGGCATG
3148 AAACCGTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 31 0.63
31 18 0.37
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (30 bp):
GTGTCATTTTTGGTACACGTGGCATGCAAC
Found at i:4661 original size:18 final size:18
Alignment explanation
Indices: 4638--4673 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4628 TGTTATTAAA
4638 CATATTTGCATATATAAT
1 CATATTTGCATATATAAT
4656 CATATTTGCATATATAAT
1 CATATTTGCATATATAAT
4674 GAACATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
CATATTTGCATATATAAT
Found at i:7355 original size:15 final size:16
Alignment explanation
Indices: 7328--7362 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
7318 TATTATAGCC
*
7328 TAGTTGAAAATTATTA
1 TAGTTGAAAATTACTA
7344 TAGTTG-AAATTACTA
1 TAGTTGAAAATTACTA
7359 TAGT
1 TAGT
7363 GGATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (16 bp):
TAGTTGAAAATTACTA
Found at i:8570 original size:19 final size:21
Alignment explanation
Indices: 8523--8570 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
8513 TGTGGCACGC
*
8523 CACATGTACCAAAAAGTCGTG
1 CACATGTACCAAAAAGTCGTA
8544 CTACATGTACCAAAAAGT-G-A
1 C-ACATGTACCAAAAAGTCGTA
8564 CACATGT
1 CACATGT
8571 CACGCCACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
21 2 0.08
22 16 0.64
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (21 bp):
CACATGTACCAAAAAGTCGTA
Found at i:8633 original size:31 final size:31
Alignment explanation
Indices: 8546--8640 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 31
8536 AAGTCGTGCT
* * * * *
8546 ACATGTACCAAAAAGTGACACATGTCACGCC
1 ACATGTATCAAAAAATGACACGTGGCATGCC
*
8577 ACATGTATCAAAAAGTGACACGTGGCATGCC
1 ACATGTATCAAAAAATGACACGTGGCATGCC
* * *
8608 ACATGTTTCAAAAAATGGCATGTGGCATGCC
1 ACATGTATCAAAAAATGACACGTGGCATGCC
8639 AC
1 AC
8641 GTGCACAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (31 bp):
ACATGTATCAAAAAATGACACGTGGCATGCC
Found at i:12662 original size:4 final size:4
Alignment explanation
Indices: 12655--12698 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
12645 TATATATATA
12655 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12699 AACAAAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:20324 original size:42 final size:42
Alignment explanation
Indices: 20277--20490 Score: 248
Period size: 42 Copynumber: 5.0 Consensus size: 42
20267 CGAGGAGCTG
* **
20277 CCATCAAATGTTGCATTGGAAAGCCTGGCCGAGGCAGGCTTC
1 CCATCAAACGTTGCATTGGAAAGCCAAGCCGAGGCAGGCTTC
* **
20319 CCATCAAACGTTGCATTGGAAAGCCATGTTGAGGCAGGCTTC
1 CCATCAAACGTTGCATTGGAAAGCCAAGCCGAGGCAGGCTTC
* * *
20361 CCATCAAACGTAGCATTGAAAAGCCAAGCAGAGGCAGGCTTC
1 CCATCAAACGTTGCATTGGAAAGCCAAGCCGAGGCAGGCTTC
* * *
20403 CCATCAAATGTTGAATTGGAAAGACAAGCCGAGGCTGCAGGCTTC
1 CCATCAAACGTTGCATTGGAAAGCCAAGCCGA-G--GCAGGCTTC
* *
20448 CCATCAAACAACGTAGCATTGAAAAGCCAAGCCGAGGCAGGCT
1 CCATC--A-AACGTTGCATTGGAAAGCCAAGCCGAGGCAGGCT
20491 ACAATGTGGT
Statistics
Matches: 145, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
42 100 0.69
43 1 0.01
45 21 0.14
47 2 0.01
48 21 0.14
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (42 bp):
CCATCAAACGTTGCATTGGAAAGCCAAGCCGAGGCAGGCTTC
Found at i:21099 original size:69 final size:63
Alignment explanation
Indices: 20968--21165 Score: 200
Period size: 63 Copynumber: 3.0 Consensus size: 63
20958 CAGAGGTTCG
** * * * *
20968 ACAATGTGGTCATCGAGGAGCTGCCATCAGACCTT-GATTTGATCAAAAGCCAAGCCGAGGCAGG
1 ACAATGTGGTCATTAAGGAGCGGCCATCAAACGTTGGA-TTG---AAAAGCCAAGCAGAGGCAGG
21032 CT
62 CT
* * * *
21034 ACAATGTGGTCATGGAGATGGAGGAGCTGCCATCAAACGTTGGATTGAATAGCCAAGCGGAGGCA
1 ACAATGTGGTCAT-----T-AAGGAGCGGCCATCAAACGTTGGATTGAAAAGCCAAGCAGAGGCA
21099 GGCT
60 GGCT
*
21103 ACGATGTGGTCATTAAGGAGCGGCCATCAAACGTTGGATTGAAAAGCCAAGCAGAGGCAGGCT
1 ACAATGTGGTCATTAAGGAGCGGCCATCAAACGTTGGATTGAAAAGCCAAGCAGAGGCAGGCT
21166 TTTTAGTGGG
Statistics
Matches: 115, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
63 45 0.39
64 1 0.01
66 13 0.11
69 32 0.28
72 22 0.19
73 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.19
Consensus pattern (63 bp):
ACAATGTGGTCATTAAGGAGCGGCCATCAAACGTTGGATTGAAAAGCCAAGCAGAGGCAGGCT
Found at i:21154 original size:63 final size:65
Alignment explanation
Indices: 21012--21165 Score: 204
Period size: 63 Copynumber: 2.3 Consensus size: 65
21002 TGATTTGATC
* * *
21012 AAAAGCCAAGCCGAGGCAGGCTACAATGTGGTCATGGAGATGGAGGAGCTGCCATCAAACGTTGG
1 AAAAGCCAAGCAGAGGCAGGCTACAATGTGGTCAT---G-TGAAGGAGCGGCCATCAAACGTTGG
21077 ATTG
62 ATTG
* * *
21081 AATAGCCAAGCGGAGGCAGGCTACGATGTGGTCAT-T-AAGGAGCGGCCATCAAACGTTGGATTG
1 AAAAGCCAAGCAGAGGCAGGCTACAATGTGGTCATGTGAAGGAGCGGCCATCAAACGTTGGATTG
21144 AAAAGCCAAGCAGAGGCAGGCT
1 AAAAGCCAAGCAGAGGCAGGCT
21166 TTTTAGTGGG
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
63 45 0.58
64 1 0.01
69 32 0.41
ACGTcount: A:0.31, C:0.19, G:0.33, T:0.16
Consensus pattern (65 bp):
AAAAGCCAAGCAGAGGCAGGCTACAATGTGGTCATGTGAAGGAGCGGCCATCAAACGTTGGATTG
Found at i:23834 original size:21 final size:21
Alignment explanation
Indices: 23816--23862 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
23806 TGCTTTTTTG
*
23816 GTTTGTTGGATTTGATTTTAT
1 GTTTATTGGATTTGATTTTAT
23837 GTTTATTGGATTT-AGTTTTACT
1 GTTTATTGGATTTGA-TTTTA-T
23859 GTTT
1 GTTT
23863 GGGATCTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.15, C:0.02, G:0.21, T:0.62
Consensus pattern (21 bp):
GTTTATTGGATTTGATTTTAT
Found at i:27268 original size:23 final size:23
Alignment explanation
Indices: 27239--27285 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
27229 TAATAGAGCA
27239 ATTGTGTCATAACCAGGTAAGCG
1 ATTGTGTCATAACCAGGTAAGCG
27262 ATTGTGTCATAACCAGGTAAGCG
1 ATTGTGTCATAACCAGGTAAGCG
27285 A
1 A
27286 CGTAGGTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (23 bp):
ATTGTGTCATAACCAGGTAAGCG
Found at i:29024 original size:12 final size:10
Alignment explanation
Indices: 28996--29024 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
28986 CAAAATTTTC
28996 AATTCTCTCA
1 AATTCTCTCA
29006 AATTCTCTCA
1 AATTCTCTCA
29016 AATTCTCTC
1 AATTCTCTC
29025 GACCTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (10 bp):
AATTCTCTCA
Done.