Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011706.1 Corchorus capsularis cultivar CVL-1 contig11727, 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: 31581
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:449 original size:16 final size:17
Alignment explanation
Indices: 428--459 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
418 ATTTCAACCT
428 AACTAAATAAA-AAAAA
1 AACTAAATAAATAAAAA
444 AACTAAATAAATAAAA
1 AACTAAATAAATAAAA
460 CACCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (17 bp):
AACTAAATAAATAAAAA
Found at i:2242 original size:18 final size:18
Alignment explanation
Indices: 2219--2255 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2209 TATTATTTAA
*
2219 TTTTCATTAAACTTACCT
1 TTTTCATTAAACCTACCT
2237 TTTTCATTAAACCTACCT
1 TTTTCATTAAACCTACCT
2255 T
1 T
2256 CGTCATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTCATTAAACCTACCT
Found at i:2261 original size:18 final size:18
Alignment explanation
Indices: 2222--2262 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2212 TATTTAATTT
* **
2222 TCATTAAACTTACCTTTT
1 TCATTAAACCTACCTTCG
2240 TCATTAAACCTACCTTCG
1 TCATTAAACCTACCTTCG
2258 TCATT
1 TCATT
2263 CTTCTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (18 bp):
TCATTAAACCTACCTTCG
Found at i:2988 original size:145 final size:146
Alignment explanation
Indices: 2723--3014 Score: 507
Period size: 145 Copynumber: 2.0 Consensus size: 146
2713 ATATATATGA
*
2723 TTATAACAAGGGTCCAGTTAACTGGTGCACCCATGCACCAATTAGGCACAAAACCCAAGAGAATA
1 TTATAACAAGGGTCCAGCTAACTGGTGCACCCATGCACCAATTAGGCACAAAACCCAAGAGAATA
2788 ATGTATTAGAAAAGTCTAATAATTGCATAAAAAGTGGGTATAGAACT-AAATAATAATTGTTCAT
66 ATGTATTAGAAAAGTCTAATAATTGCATAAAAAGTGGGTATAGAACTAAAATAATAATTGTTCAT
2852 AAAAAGAGAATTTGCC
131 AAAAAGAGAATTTGCC
*
2868 TTATAACAAGGGTCCAGCTAACTGGTGCACCCATGCACCAATTAGGCACAAAACCTAAGAGAATA
1 TTATAACAAGGGTCCAGCTAACTGGTGCACCCATGCACCAATTAGGCACAAAACCCAAGAGAATA
*
2933 ATGTATTAGAAAAGTCTAATGATTGCATAAAAAGTGGGTATAGAATTGCT-AAATAATAATTGTT
66 ATGTATTAGAAAAGTCTAATAATTGCATAAAAAGTGGGTATAGAA---CTAAAATAATAATTGTT
*
2997 CATGAAAAGAGAATTTGC
128 CATAAAAAGAGAATTTGC
3015 ATGTTAAAAC
Statistics
Matches: 140, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
145 107 0.76
148 33 0.24
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (146 bp):
TTATAACAAGGGTCCAGCTAACTGGTGCACCCATGCACCAATTAGGCACAAAACCCAAGAGAATA
ATGTATTAGAAAAGTCTAATAATTGCATAAAAAGTGGGTATAGAACTAAAATAATAATTGTTCAT
AAAAAGAGAATTTGCC
Found at i:6703 original size:162 final size:162
Alignment explanation
Indices: 6436--6761 Score: 634
Period size: 162 Copynumber: 2.0 Consensus size: 162
6426 CTAAGGTCCC
6436 AAGAACTAGAATTCCAATTAATAACATCACTAAGTTTAAGATTCTGAAGATATGAAGGGATATGA
1 AAGAACTAGAATTCCAATTAATAACATCACTAAGTTTAAGATTCTGAAGATATGAAGGGATATGA
6501 GATGTTATTAATTGATCAATTGCTAAATTATTAAACCATTTGTCAGTCCAAAAATTAATAGTGTT
66 GATGTTATTAATTGATCAATTGCTAAATTATTAAACCATTTGTCAGTCCAAAAATTAATAGTGTT
6566 CCCATTTCCAATAATCAGCTTAAATTGTCTTT
131 CCCATTTCCAATAATCAGCTTAAATTGTCTTT
* *
6598 AAGAACTAGAATTCCAGTTAATAACATCACTAAGTTTAAGATTCTGAAGATATGAATGGATATGA
1 AAGAACTAGAATTCCAATTAATAACATCACTAAGTTTAAGATTCTGAAGATATGAAGGGATATGA
6663 GATGTTATTAATTGATCAATTGCTAAATTATTAAACCATTTGTCAGTCCAAAAATTAATAGTGTT
66 GATGTTATTAATTGATCAATTGCTAAATTATTAAACCATTTGTCAGTCCAAAAATTAATAGTGTT
6728 CCCATTTCCAATAATCAGCTTAAATTGTCTTT
131 CCCATTTCCAATAATCAGCTTAAATTGTCTTT
6760 AA
1 AA
6762 TTAATGGTAT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 162 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (162 bp):
AAGAACTAGAATTCCAATTAATAACATCACTAAGTTTAAGATTCTGAAGATATGAAGGGATATGA
GATGTTATTAATTGATCAATTGCTAAATTATTAAACCATTTGTCAGTCCAAAAATTAATAGTGTT
CCCATTTCCAATAATCAGCTTAAATTGTCTTT
Found at i:15525 original size:32 final size:32
Alignment explanation
Indices: 15489--15549 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
15479 ATTGGGCGGG
15489 TTCAGGTTCGGGTATTTTCGGGTTCGGGTATT
1 TTCAGGTTCGGGTATTTTCGGGTTCGGGTATT
*
15521 TTCAGGTTCGGGTTTTTTCGGGTTCGGGT
1 TTCAGGTTCGGGTATTTTCGGGTTCGGGT
15550 TCGGGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.07, C:0.13, G:0.36, T:0.44
Consensus pattern (32 bp):
TTCAGGTTCGGGTATTTTCGGGTTCGGGTATT
Found at i:15546 original size:6 final size:6
Alignment explanation
Indices: 15537--15613 Score: 50
Period size: 6 Copynumber: 12.5 Consensus size: 6
15527 TTCGGGTTTT
* * *
15537 TTCGGG TTCGGG TTCGGG TATTTTCGGG TTCGGG CTCGGA TT-GGG TTTGGG
1 TTCGGG TTCGGG TTCGGG ----TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
* **
15588 TTCGAG CCCGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTC
15614 ACTTTCGATA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
5 8 0.15
6 41 0.75
10 6 0.11
ACGTcount: A:0.04, C:0.18, G:0.44, T:0.34
Consensus pattern (6 bp):
TTCGGG
Found at i:15555 original size:22 final size:22
Alignment explanation
Indices: 15525--15575 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
15515 GGTATTTTCA
*
15525 GGTTCGGGTTTTTTCGGGTTCG
1 GGTTCGGGTATTTTCGGGTTCG
15547 GGTTCGGGTATTTTCGGGTTCG
1 GGTTCGGGTATTTTCGGGTTCG
*
15569 GGCTCGG
1 GGTTCGG
15576 ATTGGGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.02, C:0.16, G:0.43, T:0.39
Consensus pattern (22 bp):
GGTTCGGGTATTTTCGGGTTCG
Found at i:15570 original size:16 final size:16
Alignment explanation
Indices: 15493--15549 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
15483 GGCGGGTTCA
15493 GGTTCGGGTATTTTCG
1 GGTTCGGGTATTTTCG
*
15509 GGTTCGGGTATTTTCA
1 GGTTCGGGTATTTTCG
*
15525 GGTTCGGGTTTTTTCG
1 GGTTCGGGTATTTTCG
15541 GGTTCGGGT
1 GGTTCGGGT
15550 TCGGGTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.05, C:0.12, G:0.39, T:0.44
Consensus pattern (16 bp):
GGTTCGGGTATTTTCG
Found at i:16389 original size:16 final size:15
Alignment explanation
Indices: 16368--16428 Score: 77
Period size: 16 Copynumber: 3.9 Consensus size: 15
16358 CGGGCTCGGG
*
16368 TCGGGTTCGGGTTGTC
1 TCGGGTTCGGGTT-TT
16384 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGT-TTT
*
16400 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGT-TTT
16416 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
16429 CGGGCGGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
16 40 0.98
17 1 0.02
ACGTcount: A:0.05, C:0.15, G:0.41, T:0.39
Consensus pattern (15 bp):
TCGGGTTCGGGTTTT
Found at i:16437 original size:32 final size:32
Alignment explanation
Indices: 16357--16442 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
16347 TATTTTGATC
* **
16357 TCGGGCTCGGGTCGGGTTCGGGTTGTCTCGGGT
1 TCGGGTTCGGG-CGGGTTCGGGTAATCTCGGGT
*** *
16390 TCGGGTAT-TTTCGGGTTCGGGTAATTTCGGGT
1 TCGGGT-TCGGGCGGGTTCGGGTAATCTCGGGT
16422 TCGGGTTCGGGCGGGTTCGGG
1 TCGGGTTCGGGCGGGTTCGGG
16443 ACGTTGACTT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
31 1 0.02
32 34 0.83
33 5 0.12
34 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.47, T:0.33
Consensus pattern (32 bp):
TCGGGTTCGGGCGGGTTCGGGTAATCTCGGGT
Done.