Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008970.1 Corchorus capsularis cultivar CVL-1 contig08991, 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: 33036
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:6829 original size:2 final size:2
Alignment explanation
Indices: 6822--6853 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6812 TATTCTTTAT
6822 TA TA 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 TA TA
6854 ATAGTTTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7668 original size:2 final size:2
Alignment explanation
Indices: 7661--7685 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7651 CTGGTACGTA
7661 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
7686 GTAATTAAAA
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:9420 original size:110 final size:109
Alignment explanation
Indices: 9181--9456 Score: 439
Period size: 110 Copynumber: 2.5 Consensus size: 109
9171 ATTATTATAG
* *
9181 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
9246 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
9295 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
9360 TTACCAAAAAATTTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAA-TTTGGATATACTAAAATTTTTTCTAATATACAA
*
9405 TTTTATTCTACTAAAAACTCTAATTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
9457 TAATTTTTTT
Statistics
Matches: 156, Mismatches: 4, Indels: 9
0.92 0.02 0.05
Matches are distributed among these distances:
109 55 0.35
110 78 0.50
111 2 0.01
114 21 0.13
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:14164 original size:14 final size:13
Alignment explanation
Indices: 14142--14171 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
14132 TATTATTATT
14142 AAAAAAAATTAAA
1 AAAAAAAATTAAA
14155 AAAAATAAATTAAA
1 AAAAA-AAATTAAA
14169 AAA
1 AAA
14172 TTTGGGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTAAA
Found at i:22226 original size:18 final size:17
Alignment explanation
Indices: 22203--22240 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
22193 ACTTCATTTG
22203 AAACACAAACACAAACCC
1 AAACACAAACAC-AACCC
*
22221 AAACACAAACTCAACCC
1 AAACACAAACACAACCC
22238 AAA
1 AAA
22241 GGCCTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.61, C:0.37, G:0.00, T:0.03
Consensus pattern (17 bp):
AAACACAAACACAACCC
Found at i:28722 original size:19 final size:20
Alignment explanation
Indices: 28698--28735 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28688 GCTTTACAAA
*
28698 TGTTCAATATC-ATGTTTGT
1 TGTTCAAAATCTATGTTTGT
28717 TGTTCAAAATCTATGTTTG
1 TGTTCAAAATCTATGTTTG
28736 CCAACAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (20 bp):
TGTTCAAAATCTATGTTTGT
Found at i:29259 original size:26 final size:24
Alignment explanation
Indices: 29230--29304 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 24
29220 AAATGAATAT
*
29230 AATAAATGACATATTTTTTTATCGAA
1 AATAAATGAAATATTTTTTTAT--AA
** *
29256 AATAAATGGTATATTATTTTATAA
1 AATAAATGAAATATTTTTTTATAA
*
29280 TATAATATGAAAT-TTTTTTTATAA
1 AATAA-ATGAAATATTTTTTTATAA
29304 A
1 A
29305 TCATATATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 16 0.40
25 5 0.12
26 19 0.47
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (24 bp):
AATAAATGAAATATTTTTTTATAA
Found at i:32066 original size:29 final size:29
Alignment explanation
Indices: 32006--32077 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
31996 CCGTGTATTT
32006 ACAAAGGCAGAG-A--ATTGTTGGTGAAA
1 ACAAAGGCAGAGAATTATTGTTGGTGAAA
* *
32032 ATAAAGGCAGAGAATTATTTTTGGTGAAA
1 ACAAAGGCAGAGAATTATTGTTGGTGAAA
* *
32061 GCAAAGGTAGAGAATTA
1 ACAAAGGCAGAGAATTA
32078 GAGTGAGGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 11 0.29
27 1 0.03
29 26 0.68
ACGTcount: A:0.43, C:0.06, G:0.28, T:0.24
Consensus pattern (29 bp):
ACAAAGGCAGAGAATTATTGTTGGTGAAA
Done.