Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012159.1 Corchorus capsularis cultivar CVL-1 contig12180, 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: 47118
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:15 original size:3 final size:3
Alignment explanation
Indices: 8--44 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1 ATTATTG
8 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45 TAAGCTTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6224 original size:14 final size:14
Alignment explanation
Indices: 6205--6231 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6195 CTGCAAAAAA
6205 TTATAGGCTCACTG
1 TTATAGGCTCACTG
6219 TTATAGGCTCACT
1 TTATAGGCTCACT
6232 TTTGCTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATAGGCTCACTG
Found at i:16020 original size:37 final size:37
Alignment explanation
Indices: 15962--16032 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
15952 GACTGTAGCT
* *
15962 AAATCAAATCTGTCCTAATATTATGATAGTCGTTGCA
1 AAATCAAATCTGTACTAATATTATGATAGCCGTTGCA
* * *
15999 AAATCAAATTTGTACTGATATTATGCTAGCCGTT
1 AAATCAAATCTGTACTAATATTATGATAGCCGTT
16033 TTACATATGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (37 bp):
AAATCAAATCTGTACTAATATTATGATAGCCGTTGCA
Found at i:16376 original size:14 final size:15
Alignment explanation
Indices: 16357--16385 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16347 CGGTTGCCGG
16357 AGGAA-GAAAAAAAA
1 AGGAAGGAAAAAAAA
16371 AGGAAGGAAAAAAAA
1 AGGAAGGAAAAAAAA
16386 CAATAAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGGAAGGAAAAAAAA
Found at i:16611 original size:29 final size:29
Alignment explanation
Indices: 16545--16617 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
16535 AATTTGAAAG
16545 GGGAAATTG-AAAA-AAAATAAAAATAAAA
1 GGGAAA-TGAAAAAGAAAATAAAAATAAAA
* *
16573 GGG-AAGGAAAAAGAAAATAATTAAT-AAA
1 GGGAAATGAAAAAGAAAATAA-AAATAAAA
*
16601 GGGAAATGAAAGAGAAA
1 GGGAAATGAAAAAGAAA
16618 TTTTGGAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.03
27 6 0.16
28 16 0.43
29 14 0.38
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (29 bp):
GGGAAATGAAAAAGAAAATAAAAATAAAA
Found at i:18555 original size:37 final size:38
Alignment explanation
Indices: 18514--18591 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 38
18504 AGTTGCCTTC
18514 TATTTTCATTTATTTTACCTTATGCACTTCTTTGTT-T
1 TATTTTCATTTATTTTACCTTATGCACTTCTTTGTTGT
*
18551 TATTTTCATTTATTTTACCTTATGCTCTTCTTTGTTGT
1 TATTTTCATTTATTTTACCTTATGCACTTCTTTGTTGT
18589 TAT
1 TAT
18592 ATTCTGTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 35 0.90
38 4 0.10
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.63
Consensus pattern (38 bp):
TATTTTCATTTATTTTACCTTATGCACTTCTTTGTTGT
Found at i:21005 original size:2 final size:2
Alignment explanation
Indices: 20998--21027 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20988 ACTGAATTCC
20998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21028 TAGTATCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23104 original size:73 final size:73
Alignment explanation
Indices: 22970--23115 Score: 199
Period size: 74 Copynumber: 2.0 Consensus size: 73
22960 TCAATCTATT
*
22970 TAACTACAAATCACATTGTAAATTGTATGATTTTCTTACCTTATTAATGATTTCACGTTCAATA-
1 TAACTACAAATCACATTGTAAATTGTATGATTTTCTTACCTTATTAATGATTTCACATTCAATAT
*
23034 ATTTTTTC
66 AATTTTTC
* * *
23042 TAACTACAAATCACACATTGTAAATTGTATGGTTTT-TTATCTTATTAA-GAATTTCATATTCAA
1 TAACTACAAAT--CACATTGTAAATTGTATGATTTTCTTACCTTATTAATG-ATTTCACATTCAA
23105 TATAATTTTTC
63 TATAATTTTTC
23116 CAGCATTATA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
72 12 0.18
73 24 0.37
74 29 0.45
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.46
Consensus pattern (73 bp):
TAACTACAAATCACATTGTAAATTGTATGATTTTCTTACCTTATTAATGATTTCACATTCAATAT
AATTTTTC
Found at i:38303 original size:2 final size:2
Alignment explanation
Indices: 38296--38326 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
38286 TTCCAATACT
38296 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38327 ATGACAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38472 original size:44 final size:45
Alignment explanation
Indices: 38371--38487 Score: 173
Period size: 44 Copynumber: 2.6 Consensus size: 45
38361 CCTCAACGTC
* * * *
38371 ACAACTTCTAGTGTCAAAAATAATTTACAGTATATATTTATTTTG
1 ACAACTTCTGGTGTCAAAAATAATTTAAACTATATATTTATTATG
*
38416 ACAACTTTTGGTGTCAAAAATAATTTAAACTA-ATATTTATTATG
1 ACAACTTCTGGTGTCAAAAATAATTTAAACTATATATTTATTATG
*
38460 ACAACATCTGGTGTCAAAAATAATTTAA
1 ACAACTTCTGGTGTCAAAAATAATTTAA
38488 TGTGGTAATT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 37 0.57
45 28 0.43
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.38
Consensus pattern (45 bp):
ACAACTTCTGGTGTCAAAAATAATTTAAACTATATATTTATTATG
Done.