Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013792.1 Corchorus olitorius cultivar O-4 contig13825, 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: 21943
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2653 original size:107 final size:105
Alignment explanation
Indices: 2434--2707 Score: 417
Period size: 107 Copynumber: 2.6 Consensus size: 105
2424 ATATGCTTTT
* *
2434 AATTTTAATTT-GGGCTAAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAATCCTATAAC
1 AATTTTAATTTGGGGCT-AAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAC
*
2497 AATATTATTAATTATGGAATTTACCCTTAAAATAAAAATAA
65 AATATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
* *
2538 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTGTAAAACCCTATAACA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
*
2603 ATAGATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAA
66 AT--ATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
* * * *
2645 AATTTTAATTTGGGACTAAGCTTAGTGAAATTAGTTTTATGTTTTATTTCTAAAACTCTATAA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA
2708 TAAAAAACCT
Statistics
Matches: 154, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
104 21 0.14
105 40 0.26
107 93 0.60
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (105 bp):
AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
ATATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
Found at i:6189 original size:7 final size:7
Alignment explanation
Indices: 6177--6210 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
6167 ACAAAGTGAT
6177 TTTTTTA
1 TTTTTTA
6184 TTTTTTA
1 TTTTTTA
**
6191 TTTTTCC
1 TTTTTTA
6198 TTTTTTA
1 TTTTTTA
6205 TTTTTT
1 TTTTTT
6211 TGAATTTTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:16111 original size:2 final size:2
Alignment explanation
Indices: 16104--16131 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16094 GTTAATTAAC
16104 TA TA TA 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
16132 GTAGTTGGCC
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):
TA
Found at i:18634 original size:12 final size:12
Alignment explanation
Indices: 18609--18659 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
18599 CTTCAAACTA
* *
18609 TTATTGTTTTTT
1 TTATTATTTATT
18621 TTATTATTTATT
1 TTATTATTTATT
18633 TTATTATTT-TT
1 TTATTATTTATT
*
18644 ATTATTTTATTATT
1 -TTATTAT-TTATT
18658 TT
1 TT
18660 TATGAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 2 0.06
12 25 0.76
13 4 0.12
14 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TTATTATTTATT
Found at i:18641 original size:8 final size:8
Alignment explanation
Indices: 18628--18659 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
18618 TTTTTATTAT
18628 TTATTTTA
1 TTATTTTA
18636 TTATTTTTA
1 TTA-TTTTA
18645 TTATTTTA
1 TTATTTTA
18653 TTATTTT
1 TTATTTT
18660 TATGAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTATTTTA
Found at i:18643 original size:9 final size:9
Alignment explanation
Indices: 18631--18662 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
18621 TTATTATTTA
18631 TTTTATTAT
1 TTTTATTAT
18640 TTTTATTA-
1 TTTTATTAT
18648 TTTTATTAT
1 TTTTATTAT
18657 TTTTAT
1 TTTTAT
18663 GAATAATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTAT
Found at i:18650 original size:17 final size:17
Alignment explanation
Indices: 18628--18662 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18618 TTTTTATTAT
18628 TTATTTTATTATTTTTA
1 TTATTTTATTATTTTTA
18645 TTATTTTATTATTTTTA
1 TTATTTTATTATTTTTA
18662 T
1 T
18663 GAATAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTATTATTTTTA
Done.