Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007093.1 Corchorus capsularis cultivar CVL-1 contig07114, 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: 18720
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:2521 original size:33 final size:32
Alignment explanation
Indices: 2478--2582 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 32
2468 TTGGAAATCT
*
2478 GGCCACGCGACTTGGAGATGCCCGCGCAACACC
1 GGCCACGCGACATGGAGATGCCCG-GCAACACC
* *
2511 GGCCATGCGACATGGAGATGCCCGGCCATCACC
1 GGCCACGCGACATGGAGATGCCCGG-CAACACC
** *
2544 GGCCACGCGACATGGCCATGCCCGGCCACACCC
1 GGCCACGCGACATGGAGATGCCCGGCAACA-CC
2577 GGCCAC
1 GGCCAC
2583 ATGACTCGGT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 4 0.06
33 58 0.94
ACGTcount: A:0.20, C:0.42, G:0.30, T:0.09
Consensus pattern (32 bp):
GGCCACGCGACATGGAGATGCCCGGCAACACC
Found at i:2597 original size:33 final size:32
Alignment explanation
Indices: 2495--2619 Score: 108
Period size: 33 Copynumber: 3.8 Consensus size: 32
2485 CGACTTGGAG
* *** **
2495 ATGCCCGCGCAACACCGGCCATGCGACATGGAG
1 ATGCCCG-GCCACACCGGCCACATGACATGGCC
**
2528 ATGCCCGGCCATCACCGGCCACGCGACATGGCC
1 ATGCCCGGCCA-CACCGGCCACATGACATGGCC
*
2561 ATGCCCGGCCACACCCGGCCACATGAC-TCGGTC
1 ATGCCCGGCCACA-CCGGCCACATGACAT-GGCC
*
2594 ATGCCCGGCCACAACCGGCCATATGA
1 ATGCCCGGCCAC-ACCGGCCACATGA
2620 TCCTTTAGCT
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
32 6 0.08
33 73 0.91
34 1 0.01
ACGTcount: A:0.22, C:0.42, G:0.26, T:0.10
Consensus pattern (32 bp):
ATGCCCGGCCACACCGGCCACATGACATGGCC
Found at i:8858 original size:75 final size:75
Alignment explanation
Indices: 8735--8887 Score: 297
Period size: 75 Copynumber: 2.0 Consensus size: 75
8725 TTTTTACGTA
*
8735 GAATATTACTAATAAAATAAAAATATATTATACCTATCAAGGCCCCATTGCTATAGTCTTGGACA
1 GAATATTACTAATAAAATAAAAATATATTATACCTATCAAGGCCCCATTGCTATAGTCTTGAACA
8800 TCTTCCAATT
66 TCTTCCAATT
8810 GAATATTACTAATAAAATAAAAATATATTATACCTATCAAGGCCCCATTGCTATAGTCTTGAACA
1 GAATATTACTAATAAAATAAAAATATATTATACCTATCAAGGCCCCATTGCTATAGTCTTGAACA
8875 TCTTCCAATT
66 TCTTCCAATT
8885 GAA
1 GAA
8888 CAAACTGATG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (75 bp):
GAATATTACTAATAAAATAAAAATATATTATACCTATCAAGGCCCCATTGCTATAGTCTTGAACA
TCTTCCAATT
Found at i:10467 original size:21 final size:21
Alignment explanation
Indices: 10443--10509 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
10433 ACGTTTTGAG
10443 CAAGAATATTCCAATCGATTC
1 CAAGAATATTCCAATCGATTC
*
10464 CAAG-CT-TCTCACAATCGATTC
1 CAAGAATAT-TC-CAATCGATTC
* * *
10485 TAGGAATATTTCAATCGATTC
1 CAAGAATATTCCAATCGATTC
10506 CAAG
1 CAAG
10510 TTTTGCACTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.03
20 3 0.09
21 28 0.80
22 2 0.06
23 1 0.03
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (21 bp):
CAAGAATATTCCAATCGATTC
Found at i:11680 original size:20 final size:20
Alignment explanation
Indices: 11655--11692 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11645 TTCAGGCCCT
11655 ATTGGATTCAAGTGGTACAA
1 ATTGGATTCAAGTGGTACAA
*
11675 ATTGGATTTAAGTGGTAC
1 ATTGGATTCAAGTGGTAC
11693 TAGGGTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (20 bp):
ATTGGATTCAAGTGGTACAA
Found at i:12722 original size:21 final size:21
Alignment explanation
Indices: 12684--12724 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12674 CCTTGGCTTA
*
12684 TGATCTTCAATACTCTTCAAT
1 TGATCTTCAATACACTTCAAT
**
12705 TGATCTTCAATGGACTTCAA
1 TGATCTTCAATACACTTCAA
12725 GCCTTCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
TGATCTTCAATACACTTCAAT
Found at i:17410 original size:21 final size:21
Alignment explanation
Indices: 17371--17420 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
17361 TCAATGCTTT
**
17371 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
17393 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
*
17414 AGAAAGC
1 AGGAAGC
17421 TACAATTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.42, C:0.16, G:0.28, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.