Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008380.1 Corchorus capsularis cultivar CVL-1 contig08401, 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: 20872
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:192 original size:19 final size:21
Alignment explanation
Indices: 150--192 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
140 ATTTGTAATT
150 TTTTATCAAATATGAATTAGA
1 TTTTATCAAATATGAATTAGA
* *
171 TTTTAT-AAGTATG-ATTATA
1 TTTTATCAAATATGAATTAGA
190 TTT
1 TTT
193 ATGTAGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTTATCAAATATGAATTAGA
Found at i:6468 original size:3 final size:3
Alignment explanation
Indices: 6460--6487 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6450 AGCTGCAATT
6460 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
6488 GCTTGGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:8283 original size:15 final size:15
Alignment explanation
Indices: 8260--8326 Score: 80
Period size: 15 Copynumber: 4.5 Consensus size: 15
8250 TTTCTTCCAA
8260 TTTGATGCAGCTTGG
1 TTTGATGCAGCTTGG
*
8275 TTGGATGCAGCTTGG
1 TTTGATGCAGCTTGG
* **
8290 GTTGATGTTGCTTGG
1 TTTGATGCAGCTTGG
* *
8305 TTTGAGGTAGCTTGG
1 TTTGATGCAGCTTGG
8320 TTTGATG
1 TTTGATG
8327 TTGATGCAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.12, C:0.09, G:0.37, T:0.42
Consensus pattern (15 bp):
TTTGATGCAGCTTGG
Found at i:10773 original size:18 final size:20
Alignment explanation
Indices: 10750--10797 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 20
10740 TTATTGTCAG
10750 CATTCTCT-G-CTTGCTCAC
1 CATTCTCTCGCCTTGCTCAC
10768 CATTCTCACCTCGCCTTGCTCAC
1 CATTCT---CTCGCCTTGCTCAC
10791 CATTCTC
1 CATTCTC
10798 ACCATCATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 6 0.24
20 1 0.04
21 2 0.08
22 1 0.04
23 15 0.60
ACGTcount: A:0.12, C:0.44, G:0.08, T:0.35
Consensus pattern (20 bp):
CATTCTCTCGCCTTGCTCAC
Found at i:13484 original size:23 final size:23
Alignment explanation
Indices: 13431--13484 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
13421 AGGGAATAAA
13431 TTCTTATAAATCTGTTTTTCACTT
1 TTCTT-TAAATCTGTTTTTCACTT
13455 TTCCTTTAAATTCT-TTTTATCA-TT
1 TT-CTTTAAA-TCTGTTTT-TCACTT
13479 TTCTTT
1 TTCTTT
13485 TTTATTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
23 4 0.15
24 14 0.52
25 9 0.33
ACGTcount: A:0.19, C:0.17, G:0.02, T:0.63
Consensus pattern (23 bp):
TTCTTTAAATCTGTTTTTCACTT
Found at i:18374 original size:187 final size:186
Alignment explanation
Indices: 18053--18417 Score: 685
Period size: 187 Copynumber: 2.0 Consensus size: 186
18043 TTGCCGTGCC
*
18053 TGTTATACCTACCGTTTTTTTAATTAACATACATATTACTTATTTTGGATCGGATGGAGTATTTC
1 TGTTATACCTACCGTTTTTTTAATTAACATACAGATTACTTATTTTGGATCGGATGGAGTATTTC
*
18118 ATTGGATTGAACTCCATGAACAAAGATAGGAAGCGATCTGATTCCAATATTAAATTCAAATTCAT
66 ATTGGATTGAACTCCATGAACAAAGATAGGAAGCGATCTAATTCCAATATTAAATTCAAATTCAT
18183 TATCAAGGGAAGAATCTAATTAATTGTTTAAAATTGATGAAGGTATTATTAGATTT
131 TATCAAGGGAAGAATCTAATTAATTGTTTAAAATTGATGAAGGTATTATTAGATTT
*
18239 TGTTATACCTACCATTTTTTTTAATTAACATACAGATTACTTATTTTGGATCGGATGGAGTATTT
1 TGTTATACCTACC-GTTTTTTTAATTAACATACAGATTACTTATTTTGGATCGGATGGAGTATTT
*
18304 CATTGGATTGAACTCCATGAACAAAGATAGGAAGCGATCTAATTCCAATATTAAATTCAAATTTA
65 CATTGGATTGAACTCCATGAACAAAGATAGGAAGCGATCTAATTCCAATATTAAATTCAAATTCA
18369 TTATCAAGGGAAGAATCTAATTAATTGTTTAAAATTGATGAAGGTATTA
130 TTATCAAGGGAAGAATCTAATTAATTGTTTAAAATTGATGAAGGTATTA
18418 GATTTTAGTT
Statistics
Matches: 174, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
186 13 0.07
187 161 0.93
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (186 bp):
TGTTATACCTACCGTTTTTTTAATTAACATACAGATTACTTATTTTGGATCGGATGGAGTATTTC
ATTGGATTGAACTCCATGAACAAAGATAGGAAGCGATCTAATTCCAATATTAAATTCAAATTCAT
TATCAAGGGAAGAATCTAATTAATTGTTTAAAATTGATGAAGGTATTATTAGATTT
Found at i:18604 original size:2 final size:2
Alignment explanation
Indices: 18566--18591 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18556 AAAGATAAAG
18566 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
18592 GNGAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18792 original size:2 final size:2
Alignment explanation
Indices: 18785--18809 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18775 ATAATTACCC
18785 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18810 GAAAATACTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.