Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005821.1 Corchorus capsularis cultivar CVL-1 contig05839, 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: 9463
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Found at i:3074 original size:15 final size:16
Alignment explanation
Indices: 3054--3090 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3044 CGTTATCGAG
3054 TACGACAAAAGT-GAA
1 TACGACAAAAGTGGAA
*
3069 TACGACATAAGTGGAA
1 TACGACAAAAGTGGAA
3085 -ACGACA
1 TACGACA
3091 CAGGCACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.14
Consensus pattern (16 bp):
TACGACAAAAGTGGAA
Found at i:4602 original size:19 final size:19
Alignment explanation
Indices: 4578--4615 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4568 ACACCCCCAA
4578 AGTCAATCCACTGTGAGCC
1 AGTCAATCCACTGTGAGCC
4597 AGTCAATCCACTGTGAGCC
1 AGTCAATCCACTGTGAGCC
4616 TAGCCGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (19 bp):
AGTCAATCCACTGTGAGCC
Found at i:6442 original size:22 final size:22
Alignment explanation
Indices: 6394--6501 Score: 85
Period size: 22 Copynumber: 4.9 Consensus size: 22
6384 TGGTATTACA
**
6394 TTATGAAATTTTGATAA-GTTCC
1 TTATGAAATTTTGATAACCAT-C
* *
6416 ATATGAAATTTTGATAACCATG
1 TTATGAAATTTTGATAACCATC
*
6438 TTATGGAATTTTGATAACC-TCC
1 TTATGAAATTTTGATAACCAT-C
* * * * *
6460 TCATGAAATTATAATAATCATT
1 TTATGAAATTTTGATAACCATC
*
6482 TTATGAAATTTTGAAAACCA
1 TTATGAAATTTTGATAACCA
6502 CATAGATACA
Statistics
Matches: 65, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
21 1 0.02
22 62 0.95
23 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCATC
Found at i:6466 original size:44 final size:44
Alignment explanation
Indices: 6394--6500 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
6384 TGGTATTACA
** * *
6394 TTATGAAATTTTGATAAGTTCCATATGAAATTTTGATAACCATG
1 TTATGAAATTTTGATAACCTCCATATGAAATTATAATAACCATG
* * *
6438 TTATGGAATTTTGATAACCTCC-TCATGAAATTATAATAATCATT
1 TTATGAAATTTTGATAACCTCCAT-ATGAAATTATAATAACCATG
*
6482 TTATGAAATTTTGAAAACC
1 TTATGAAATTTTGATAACC
6501 ACATAGATAC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.02
44 52 0.98
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (44 bp):
TTATGAAATTTTGATAACCTCCATATGAAATTATAATAACCATG
Found at i:6698 original size:19 final size:20
Alignment explanation
Indices: 6667--6704 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6657 TATTGACATT
6667 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
6686 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
6705 ACTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:6915 original size:32 final size:32
Alignment explanation
Indices: 6879--6945 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
6869 TTAGTAATGG
* *
6879 CAATTTAGAAATATGTTTTTAAAAA-AGGGGTA
1 CAATTTAGAAATAT-ATTTTAAAAATAAGGGTA
*
6911 CAA-TTGGAAATATATTTTAAAAATAAGGGTA
1 CAATTTAGAAATATATTTTAAAAATAAGGGTA
6942 CAAT
1 CAAT
6946 CGGAAAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 9 0.30
31 18 0.60
32 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.33
Consensus pattern (32 bp):
CAATTTAGAAATATATTTTAAAAATAAGGGTA
Found at i:6931 original size:30 final size:32
Alignment explanation
Indices: 6886--6951 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
6876 TGGCAATTTA
* * *
6886 GAAATATGTTTTTAAAAA-AGGGGTACAATTG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
6917 GAAATAT-ATTTTAAAAATAAGGGTACAATCG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
6948 GAAA
1 GAAA
6952 ACATAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.29
Consensus pattern (32 bp):
GAAATATGATTTTAAAAATAAGGGTACAATCG
Found at i:9035 original size:18 final size:19
Alignment explanation
Indices: 9009--9044 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
8999 GACATAGACA
9009 GAAACACAGATA-GAGAGG
1 GAAACACAGATAGGAGAGG
*
9027 GAAAGACAGATAGGAGAG
1 GAAACACAGATAGGAGAG
9045 ACAAAGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.08, G:0.36, T:0.06
Consensus pattern (19 bp):
GAAACACAGATAGGAGAGG
Found at i:9050 original size:19 final size:18
Alignment explanation
Indices: 9014--9056 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
9004 AGACAGAAAC
**
9014 ACAGATAGAGAGGGAAAG
1 ACAGATAGAGAGACAAAG
9032 ACAGATAGGAGAGACAAAG
1 ACAGATA-GAGAGACAAAG
*
9051 ATAGAT
1 ACAGAT
9057 GAATACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.51, C:0.07, G:0.33, T:0.09
Consensus pattern (18 bp):
ACAGATAGAGAGACAAAG
Done.