Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010477.1 Corchorus capsularis cultivar CVL-1 contig10498, 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: 37206
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:4290 original size:10 final size:12
Alignment explanation
Indices: 4255--4296 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
4245 ATTATGCATG
4255 TTTTTATAGCTA
1 TTTTTATAGCTA
4267 TTTTTATAGCTA
1 TTTTTATAGCTA
4279 TTTTT-T-GCTA
1 TTTTTATAGCTA
4289 TTTTTATA
1 TTTTTATA
4297 TGTGTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.32
11 2 0.07
12 17 0.61
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (12 bp):
TTTTTATAGCTA
Found at i:4304 original size:22 final size:24
Alignment explanation
Indices: 4253--4306 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
4243 AAATTATGCA
4253 TGTTTTTATAGCTATTTTTATAGC
1 TGTTTTTATAGCTATTTTTATAGC
*
4277 TATTTTT-T-GCTATTTTTATATG-
1 TGTTTTTATAGCTATTTTTATA-GC
4299 TGTTTTTA
1 TGTTTTTA
4307 CCCTATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 18 0.69
23 2 0.08
24 6 0.23
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.65
Consensus pattern (24 bp):
TGTTTTTATAGCTATTTTTATAGC
Found at i:5841 original size:13 final size:14
Alignment explanation
Indices: 5823--5852 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5813 ATAATTATTG
5823 TTTGCTTTATTA-A
1 TTTGCTTTATTAGA
5836 TTTGCTTTATTAGA
1 TTTGCTTTATTAGA
5850 TTT
1 TTT
5853 AGATTTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (14 bp):
TTTGCTTTATTAGA
Found at i:13829 original size:19 final size:19
Alignment explanation
Indices: 13794--13831 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
13784 GGCTAACCGA
*
13794 TTTGATTGTGTTATTTGTG
1 TTTGATTGAGTTATTTGTG
13813 TTTGAATTGAGTT-TTTGTG
1 TTTG-ATTGAGTTATTTGTG
13832 CAGCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (19 bp):
TTTGATTGAGTTATTTGTG
Found at i:21484 original size:17 final size:17
Alignment explanation
Indices: 21462--21495 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21452 AGAGTCATGA
*
21462 TTTTCAAAACTGTTTTT
1 TTTTCAAAAATGTTTTT
21479 TTTTCAAAAATGTTTTT
1 TTTTCAAAAATGTTTTT
21496 CAAAAATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTCAAAAATGTTTTT
Found at i:21494 original size:14 final size:13
Alignment explanation
Indices: 21478--21509 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
21468 AAACTGTTTT
21478 TTTTTCAAAAATG
1 TTTTTCAAAAATG
21491 TTTTTCAAAAATG
1 TTTTTCAAAAATG
*
21504 GTTTTC
1 TTTTTC
21510 GAAACTCGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.50
Consensus pattern (13 bp):
TTTTTCAAAAATG
Found at i:21841 original size:10 final size:10
Alignment explanation
Indices: 21826--21870 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
21816 ATGAAGAAGT
21826 GAAAAAAAAA
1 GAAAAAAAAA
*
21836 GAAAAAAGAA
1 GAAAAAAAAA
*
21846 G-AAAAAAGA
1 GAAAAAAAAA
21855 GAAAAAAAGAA
1 GAAAAAAA-AA
21866 GAAAA
1 GAAAA
21871 TGAAAGGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 7 0.24
10 16 0.55
11 6 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:21849 original size:20 final size:21
Alignment explanation
Indices: 21826--21870 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
21816 ATGAAGAAGT
21826 GAAAAAAAAAG-AAAAAAGAA
1 GAAAAAAAAAGAAAAAAAGAA
*
21846 G-AAAAAAGAGAAAAAAAGAA
1 GAAAAAAAAAGAAAAAAAGAA
21866 GAAAA
1 GAAAA
21871 TGAAAGGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 11 0.50
21 3 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
GAAAAAAAAAGAAAAAAAGAA
Found at i:21852 original size:17 final size:16
Alignment explanation
Indices: 21830--21875 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 16
21820 AGAAGTGAAA
21830 AAAAAAGAAAAAAGAAG
1 AAAAAAGAAAAAA-AAG
21847 AAAAAAGAGAAAAAAAG
1 AAAAAAGA-AAAAAAAG
21864 AAGAAAATGAAA
1 AA-AAAA-GAAA
21876 GGGGAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 13 0.50
18 11 0.42
19 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:30189 original size:37 final size:36
Alignment explanation
Indices: 30124--30201 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 36
30114 CCCTAATTTT
*
30124 AAAAACGGAAAAATATTTTTTTTTAG-AAAAATCGG
1 AAAAACGGAAAAATATTTTTTTTTAGAAAAAAACGG
*
30159 AAAAACGGAAAAAACTTTTTTTTTTTAGAAAAAAACGG
1 AAAAACGG-AAAAA-TATTTTTTTTTAGAAAAAAACGG
30197 AAAAA
1 AAAAA
30202 ACAAAAACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 8 0.21
36 5 0.13
37 12 0.32
38 13 0.34
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (36 bp):
AAAAACGGAAAAATATTTTTTTTTAGAAAAAAACGG
Found at i:30859 original size:19 final size:18
Alignment explanation
Indices: 30835--30870 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30825 TGAAGATTTC
30835 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
30854 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
30871 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.