Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009115.1 Corchorus capsularis cultivar CVL-1 contig09136, 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: 40359
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:9405 original size:18 final size:18
Alignment explanation
Indices: 9382--9417 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
9372 AAAATGTTTT
*
9382 TTTTGAAGATTTTTTGGA
1 TTTTGAAAATTTTTTGGA
9400 TTTTGAAAATTTTTTGGA
1 TTTTGAAAATTTTTTGGA
9418 ATTTCATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (18 bp):
TTTTGAAAATTTTTTGGA
Found at i:12855 original size:16 final size:15
Alignment explanation
Indices: 12834--12863 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12824 AGCCGGCTTG
12834 AGCCGAGCCGCGTTCC
1 AGCCGAGCCG-GTTCC
12850 AGCCGAGCCGGTTC
1 AGCCGAGCCGGTTC
12864 AAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.40, G:0.33, T:0.13
Consensus pattern (15 bp):
AGCCGAGCCGGTTCC
Found at i:13387 original size:14 final size:12
Alignment explanation
Indices: 13331--13387 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
13321 GAGGGACTTA
* *
13331 TTTTTATTACTG
1 TTTTTATAAATG
13343 TTTTTAATAAATTG
1 TTTTT-ATAAA-TG
13357 TTTTTATAAATG
1 TTTTTATAAATG
13369 ATTTTTATTAAGATG
1 -TTTTTA-TAA-ATG
13384 TTTT
1 TTTT
13388 GGGTGCATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 7 0.18
13 14 0.37
14 14 0.37
15 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (12 bp):
TTTTTATAAATG
Found at i:26218 original size:2 final size:2
Alignment explanation
Indices: 26213--26239 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26203 ATATATGGAC
26213 TA 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 TA T
26240 CAAATGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26941 original size:2 final size:2
Alignment explanation
Indices: 26934--26964 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
26924 ATTTTTGAAT
26934 TA TA TA 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 TA TA TA T
26965 CTTATCTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29889 original size:22 final size:22
Alignment explanation
Indices: 29798--29880 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
29788 ATCATTGTGT
* *
29798 GGTTATCAAAATTCCATAAT-AA
1 GGTTATCAAAATTTCAT-ATGGA
* * *
29820 GATTATCAAAATTTCAAAAGGA
1 GGTTATCAAAATTTCATATGGA
* *
29842 TGTCATCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATATGGA
*
29864 GGTTATCAAATTTTCAT
1 GGTTATCAAAATTTCAT
29881 TGTATGGTTT
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
21 1 0.02
22 46 0.98
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATATGGA
Found at i:30085 original size:6 final size:6
Alignment explanation
Indices: 30074--30104 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
30064 AAAGTCAAGG
30074 AATACA AATACA AATACA AATACA AATACA A
1 AATACA AATACA AATACA AATACA AATACA A
30105 TAAAGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AATACA
Found at i:34494 original size:2 final size:2
Alignment explanation
Indices: 34487--34515 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34477 AACCAAATGG
34487 TA TA 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 TA TA T
34516 GTAATTTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35194 original size:22 final size:22
Alignment explanation
Indices: 34896--35202 Score: 134
Period size: 22 Copynumber: 14.1 Consensus size: 22
34886 ACAATCAAAC
* * *
34896 CAAAATTACATAGAAAGATTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
34918 C-AAATTTCATAGTGTA-GTTAC
1 CAAAATTTCATAGAG-AGGTTAT
* * * *
34939 CAAACTTTCATATAGAAGTCAT
1 CAAAATTTCATAGAGAGGTTAT
* **
34961 CAAAACTTCATATTGTA-GTTAT
1 CAAAATTTCATAGAG-AGGTTAT
* *
34983 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGAGAGGTTAT
* * * *
35005 CAAAATTTTATAAAAAGGTTAC
1 CAAAATTTCATAGAGAGGTTAT
* * *
35027 CAAAATTTCTTAGGGATGTTAAT
1 CAAAATTTCATAGAGAGGTT-AT
* *
35050 -AAAATTTCATACGA-AAGTTAA
1 CAAAATTTCATA-GAGAGGTTAT
*
35071 CAAAATTTCATAGAGAGAGAGGTTAC
1 CAAAATTTCAT----AGAGAGGTTAT
* *
35097 CAAAA-TT--T---GTGCTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
35113 CAAAATTTCCTATG-GAGGTTAA
1 CAAAATTTCATA-GAGAGGTTAT
* *
35135 CAAAATTTTATAGGGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
35157 GAAAATTTTATGGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
35179 CAAAATTACATAGAGAGGATAT
1 CAAAATTTCATAGAGAGGTTAT
35201 CA
1 CA
35203 TAGTTTTATT
Statistics
Matches: 214, Mismatches: 51, Indels: 40
0.70 0.17 0.13
Matches are distributed among these distances:
16 10 0.05
17 2 0.01
19 1 0.00
21 18 0.08
22 164 0.77
23 4 0.02
25 4 0.02
26 11 0.05
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTTAT
Found at i:35659 original size:2 final size:2
Alignment explanation
Indices: 35652--35682 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35642 CTAGCTAGTG
35652 TA TA TA 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 TA TA TA T
35683 GTCTGTAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.