Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012311.1 Corchorus capsularis cultivar CVL-1 contig12332, 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: 9692
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:2775 original size:16 final size:16
Alignment explanation
Indices: 2729--2819 Score: 73
Period size: 16 Copynumber: 5.8 Consensus size: 16
2719 GTTTTTTCGA
*
2729 GTCATTCGGGTCTCGG
1 GTCATTCTGGTCTCGG
2745 GTCA-TCTGG-CTTCGG
1 GTCATTCTGGTC-TCGG
*
2760 GTTATTCTGGTCTCGG
1 GTCATTCTGGTCTCGG
* * *
2776 GTCATAC-GGTTTCCAG
1 GTCATTCTGGTCT-CGG
2792 GTCATTC-GGCTCTCGG
1 GTCATTCTGG-TCTCGG
*
2808 GTCATTCAGGTC
1 GTCATTCTGGTC
2820 CCAGATCATT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
14 1 0.02
15 15 0.25
16 39 0.65
17 5 0.08
ACGTcount: A:0.10, C:0.25, G:0.31, T:0.34
Consensus pattern (16 bp):
GTCATTCTGGTCTCGG
Found at i:2829 original size:32 final size:32
Alignment explanation
Indices: 2770--2831 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2760 GTTATTCTGG
* *
2770 TCTCGGGTCATACGGTTTCCAGGTCATTCGGC
1 TCTCGGGTCATACGGTTCCCAGATCATTCGGC
*
2802 TCTCGGGTCATTCAGG-TCCCAGATCATTCG
1 TCTCGGGTCATAC-GGTTCCCAGATCATTCG
2832 AGTCTCAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.15, C:0.29, G:0.26, T:0.31
Consensus pattern (32 bp):
TCTCGGGTCATACGGTTCCCAGATCATTCGGC
Found at i:3712 original size:16 final size:15
Alignment explanation
Indices: 3678--3750 Score: 78
Period size: 16 Copynumber: 4.7 Consensus size: 15
3668 TTTCGGATTA
3678 TACGGGTC-TTGGGT
1 TACGGGTCATTGGGT
*
3692 CACGGGTCATCTGGGT
1 TACGGGTCAT-TGGGT
3708 TACGGGTCATTCGGGT
1 TACGGGTCATT-GGGT
3724 CT-CGGGTCATCTGGGT
1 -TACGGGTCAT-TGGGT
*
3740 TGCGGGTCATT
1 TACGGGTCATT
3751 TGGTCACGCG
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 7 0.14
15 4 0.08
16 38 0.75
17 2 0.04
ACGTcount: A:0.10, C:0.21, G:0.38, T:0.32
Consensus pattern (15 bp):
TACGGGTCATTGGGT
Found at i:3730 original size:32 final size:31
Alignment explanation
Indices: 3678--3758 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 31
3668 TTTCGGATTA
3678 TACGGGTC-TTGGGTCACGGGTCATCTGGGT
1 TACGGGTCATTGGGTCACGGGTCATCTGGGT
*
3708 TACGGGTCATTCGGGTCTCGGGTCATCTGGGT
1 TACGGGTCATT-GGGTCACGGGTCATCTGGGT
* *
3740 TGCGGGTCATTTGGTCACG
1 TACGGGTCATTGGGTCACG
3759 CGTTCGCCGG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
30 8 0.18
31 8 0.18
32 29 0.64
ACGTcount: A:0.10, C:0.21, G:0.38, T:0.31
Consensus pattern (31 bp):
TACGGGTCATTGGGTCACGGGTCATCTGGGT
Found at i:4983 original size:25 final size:25
Alignment explanation
Indices: 4955--5002 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
4945 GTAATTGTCT
* *
4955 ACTAGTATTCTCATGTTTAGTTAAA
1 ACTAGCATTCTCATATTTAGTTAAA
4980 ACTAGCATTCTCATATTTAGTTA
1 ACTAGCATTCTCATATTTAGTTA
5003 TTTTAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (25 bp):
ACTAGCATTCTCATATTTAGTTAAA
Found at i:5026 original size:35 final size:35
Alignment explanation
Indices: 4980--5052 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
4970 TTTAGTTAAA
4980 ACTAGCATTCTCATATTTAGTTATTTTAATTGTAT
1 ACTAGCATTCTCATATTTAGTTATTTTAATTGTAT
* * * *
5015 ACTAGTATTCTCATGTTTAGTTGTTTTAATTGTGT
1 ACTAGCATTCTCATATTTAGTTATTTTAATTGTAT
5050 ACT
1 ACT
5053 TCTCTTCCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (35 bp):
ACTAGCATTCTCATATTTAGTTATTTTAATTGTAT
Found at i:5369 original size:28 final size:28
Alignment explanation
Indices: 5317--5370 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5307 TAGTTGTTTT
* *
5317 TGTAATTTATTTTCTTTTTAATCTATGG
1 TGTAATTTATTTTCATTTCAATCTATGG
5345 TGTAATTTATTTT-ATTTCAACTCTAT
1 TGTAATTTATTTTCATTTCAA-TCTAT
5371 TTAAGTTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.59
Consensus pattern (28 bp):
TGTAATTTATTTTCATTTCAATCTATGG
Found at i:5385 original size:33 final size:30
Alignment explanation
Indices: 5348--5424 Score: 75
Period size: 33 Copynumber: 2.4 Consensus size: 30
5338 TCTATGGTGT
*
5348 AATTTATTTTATTTCAACTCTATTTAAGTTGTA
1 AATTTATTTTATTT-AACTCAATTTAA-TT-TA
* *
5381 AATTTATCTTAATTTAAGTCAATTTAATTTA
1 AATTTAT-TTTATTTAACTCAATTTAATTTA
5412 AACTTT-TTTTATT
1 AA-TTTATTTTATT
5425 AAATTGTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 5 0.13
31 5 0.13
32 5 0.13
33 17 0.45
34 6 0.16
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (30 bp):
AATTTATTTTATTTAACTCAATTTAATTTA
Found at i:5552 original size:18 final size:19
Alignment explanation
Indices: 5525--5560 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5515 AGGTCTCAAT
5525 TAATTCTTT-CTAATGATA
1 TAATTCTTTCCTAATGATA
*
5543 TAATTTTTTCCTAATGAT
1 TAATTCTTTCCTAATGAT
5561 TTAAAGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.53
Consensus pattern (19 bp):
TAATTCTTTCCTAATGATA
Found at i:6617 original size:2 final size:2
Alignment explanation
Indices: 6610--6640 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6600 TATTTATACG
6610 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
6641 AACACACATG
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:7016 original size:76 final size:76
Alignment explanation
Indices: 6890--7042 Score: 261
Period size: 76 Copynumber: 2.0 Consensus size: 76
6880 TCTTGATTGG
* * * *
6890 CCTCTCTGAACACATGCTGAATTTTGAAATGAGACACTTTCTTCCTTAACAAAATAATATGAGTA
1 CCTCTCTGAACACATGCTAAATTTTGAAATCAGACACCTTCTTCCTTAACAAAATAATATGAGCA
6955 GCCCACTTCCT
66 GCCCACTTCCT
6966 CCTCTCTGAACACATGCTAAATTTTGAAATCAGACACCTTCTTCCTTAACAAAATAATATGAGCA
1 CCTCTCTGAACACATGCTAAATTTTGAAATCAGACACCTTCTTCCTTAACAAAATAATATGAGCA
*
7031 GTCCACTTCCT
66 GCCCACTTCCT
7042 C
1 C
7043 ATACGCCATG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.31
Consensus pattern (76 bp):
CCTCTCTGAACACATGCTAAATTTTGAAATCAGACACCTTCTTCCTTAACAAAATAATATGAGCA
GCCCACTTCCT
Done.