Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016049.1 Corchorus capsularis cultivar CVL-1 contig16070, 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: 34152
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:50 original size:2 final size:2
Alignment explanation
Indices: 43--67 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33 AGTTGTTATC
43 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 A
68 CTTTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10443 original size:13 final size:13
Alignment explanation
Indices: 10425--10450 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10415 CATGGAAAAA
10425 CTTGAAGAAGAAG
1 CTTGAAGAAGAAG
10438 CTTGAAGAAGAAG
1 CTTGAAGAAGAAG
10451 GAGGAATCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (13 bp):
CTTGAAGAAGAAG
Found at i:10655 original size:21 final size:21
Alignment explanation
Indices: 10629--10670 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10619 ATCTTGAAGG
*
10629 ATTGAAGTCCATTGAAGATCA
1 ATTGAAGACCATTGAAGATCA
**
10650 ATTGAAGAGTATTGAAGATCA
1 ATTGAAGACCATTGAAGATCA
10671 TAAGCCAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (21 bp):
ATTGAAGACCATTGAAGATCA
Found at i:13309 original size:16 final size:16
Alignment explanation
Indices: 13290--13396 Score: 97
Period size: 16 Copynumber: 6.6 Consensus size: 16
13280 CCTGAACCTG
13290 AACCCGAAAAAACCCA
1 AACCCGAAAAAACCCA
* *
13306 AACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCA
** *
13322 AACCCGAAAAAAATACG
1 AACCCG-AAAAAACCCA
* *
13339 AACCCGGAAAAACTCA
1 AACCCGAAAAAACCCA
* *
13355 AACTCGAAAAAACCCG
1 AACCCGAAAAAACCCA
* *
13371 AATCCGAAAAAACCCG
1 AACCCGAAAAAACCCA
*
13387 AATCCGAAAA
1 AACCCGAAAA
13397 TTTATGAAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
16 62 0.84
17 12 0.16
ACGTcount: A:0.53, C:0.30, G:0.11, T:0.06
Consensus pattern (16 bp):
AACCCGAAAAAACCCA
Found at i:13378 original size:49 final size:49
Alignment explanation
Indices: 13289--13382 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
13279 ACCTGAACCT
* *
13289 GAACCCGAAAAAACCCAAACCCGAAAAAGCTCAAACCCGAAAAAAATAC
1 GAACCCGAAAAAACCCAAACCCGAAAAAACCCAAACCCGAAAAAAATAC
* * * * *
13338 GAACCCGGAAAAACTCAAACTCGAAAAAACCCGAATCCGAAAAAA
1 GAACCCGAAAAAACCCAAACCCGAAAAAACCCAAACCCGAAAAAA
13383 CCCGAATCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.54, C:0.29, G:0.12, T:0.05
Consensus pattern (49 bp):
GAACCCGAAAAAACCCAAACCCGAAAAAACCCAAACCCGAAAAAAATAC
Found at i:13565 original size:16 final size:16
Alignment explanation
Indices: 13544--13597 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
13534 ACCCAAACAG
*
13544 AACCTGAATCCGGATT
1 AACCTGAATCCGAATT
*
13560 AACCTG-ATCCAAATT
1 AACCTGAATCCGAATT
*
13575 AA-CTCGAACCCGAATT
1 AACCT-GAATCCGAATT
13591 AACCTGA
1 AACCTGA
13598 CCCAAATCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 2 0.06
15 10 0.32
16 17 0.55
17 2 0.06
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (16 bp):
AACCTGAATCCGAATT
Found at i:13575 original size:15 final size:15
Alignment explanation
Indices: 13557--13604 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
13547 CTGAATCCGG
*
13557 ATTAACCTGATCCAA
1 ATTAACCTGACCCAA
*
13572 ATTAA-CTCGAACCCGA
1 ATTAACCT-G-ACCCAA
13588 ATTAACCTGACCCAA
1 ATTAACCTGACCCAA
13603 AT
1 AT
13605 CCAACCCGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.07
15 13 0.48
16 10 0.37
17 2 0.07
ACGTcount: A:0.40, C:0.29, G:0.08, T:0.23
Consensus pattern (15 bp):
ATTAACCTGACCCAA
Found at i:14373 original size:2 final size:2
Alignment explanation
Indices: 14366--14400 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14356 ATTTATTAAC
14366 AT AT 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 AT AT A
14401 GAAAGTGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16587 original size:89 final size:90
Alignment explanation
Indices: 16490--16658 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 90
16480 TTCAATATAC
* * *
16490 ATATATACATCATGAATAGAAGC-TATATGAATGATTGAAGAGATATGAACCTTCGTCTGGAAAA
1 ATATATACAACATGAACAGAAGCATATATGAATGATTGAAGAGAAATGAACCTTCGTCTGGAAAA
16554 TAAACTATACACGTACGTGCCACAT
66 TAAACTATACACGTACGTGCCACAT
* *
16579 ATATATACAACATGAACAGAAGCTATATATGAATGATTGAAGAGAAATGAACTTTCGTGTGGAAA
1 ATATATACAACATGAACAGAAGC-ATATATGAATGATTGAAGAGAAATGAACCTTCGTCTGGAAA
16644 ATAAACTATACACGT
65 ATAAACTATACACGT
16659 GCCACATATC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
89 21 0.29
91 52 0.71
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (90 bp):
ATATATACAACATGAACAGAAGCATATATGAATGATTGAAGAGAAATGAACCTTCGTCTGGAAAA
TAAACTATACACGTACGTGCCACAT
Found at i:16751 original size:19 final size:17
Alignment explanation
Indices: 16715--16766 Score: 77
Period size: 19 Copynumber: 2.9 Consensus size: 17
16705 ATTTTCTGTG
16715 GCGTAAGGTGACCATAA
1 GCGTAAGGTGACCATAA
16732 GCGTAAGGTGACCACATAA
1 GCGTAAGGTGA-C-CATAA
*
16751 GCGTAAGGTGAACATA
1 GCGTAAGGTGACCATA
16767 TCCAATTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
19 16 0.50
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (17 bp):
GCGTAAGGTGACCATAA
Found at i:17359 original size:6 final size:6
Alignment explanation
Indices: 17348--17373 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17338 AAATTGGGTC
17348 GAAATG GAAATG GAAATG GAAATG GA
1 GAAATG GAAATG GAAATG GAAATG GA
17374 TGTAATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAATG
Found at i:24758 original size:2 final size:2
Alignment explanation
Indices: 24751--24778 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24741 ATGTTGAAAC
24751 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
24779 TTTACTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.