Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015975.1 Corchorus capsularis cultivar CVL-1 contig15996, 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: 29552
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:215 original size:2 final size:2
Alignment explanation
Indices: 210--240 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
200 ATAAACATTA
*
210 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
241 CCATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1177 original size:22 final size:22
Alignment explanation
Indices: 1149--1192 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1139 AGTTTTTGGA
*
1149 GAAACTCAATCTTACTGCAATT
1 GAAACTCAATATTACTGCAATT
1171 GAAACTCAATATTACTGCAATT
1 GAAACTCAATATTACTGCAATT
1193 TTTCTTCGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
GAAACTCAATATTACTGCAATT
Found at i:2953 original size:11 final size:10
Alignment explanation
Indices: 2935--2968 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
2925 AATTGTCTTC
2935 AAATCTTCAA
1 AAATCTTCAA
2945 AATATCTTCAA
1 AA-ATCTTCAA
2956 GAAATCTTCAA
1 -AAATCTTCAA
2967 AA
1 AA
2969 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:9662 original size:11 final size:10
Alignment explanation
Indices: 9644--9677 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
9634 AATTGTCTTC
9644 AAATCTTCAA
1 AAATCTTCAA
9654 AATATCTTCAA
1 AA-ATCTTCAA
9665 GAAATCTTCAA
1 -AAATCTTCAA
9676 AA
1 AA
9678 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:16265 original size:24 final size:24
Alignment explanation
Indices: 16225--16350 Score: 101
Period size: 24 Copynumber: 5.2 Consensus size: 24
16215 ACTGCTTCTG
* *
16225 AATCTGAACAGCCATCTCGACAGC
1 AATCTGAACAGCAATCTGGACAGC
* *
16249 AATCTGAAGAGCAATCTGGACTGC
1 AATCTGAACAGCAATCTGGACAGC
* * *
16273 AATTTGAACAGCCATCTGGACAAC
1 AATCTGAACAGCAATCTGGACAGC
* * *
16297 AGTCTGGACAGCAATCTGGTCAG-
1 AATCTGAACAGCAATCTGGACAGC
* * ** *
16320 AATTCTGGACAGCGATAAGGACAAC
1 AA-TCTGAACAGCAATCTGGACAGC
16345 AATCTG
1 AATCTG
16351 TGGCTGTAGA
Statistics
Matches: 79, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
23 1 0.01
24 76 0.96
25 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (24 bp):
AATCTGAACAGCAATCTGGACAGC
Found at i:16274 original size:12 final size:12
Alignment explanation
Indices: 16225--16332 Score: 92
Period size: 12 Copynumber: 9.0 Consensus size: 12
16215 ACTGCTTCTG
*
16225 AATCTGAACAGC
1 AATCTGGACAGC
* *
16237 CATCTCGACAGC
1 AATCTGGACAGC
* *
16249 AATCTGAAGAGC
1 AATCTGGACAGC
*
16261 AATCTGGACTGC
1 AATCTGGACAGC
* *
16273 AATTTGAACAGC
1 AATCTGGACAGC
* *
16285 CATCTGGACAAC
1 AATCTGGACAGC
*
16297 AGTCTGGACAGC
1 AATCTGGACAGC
*
16309 AATCTGGTCAG-
1 AATCTGGACAGC
16320 AATTCTGGACAGC
1 AA-TCTGGACAGC
16333 GATAAGGACA
Statistics
Matches: 71, Mismatches: 23, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
11 2 0.03
12 69 0.97
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.20
Consensus pattern (12 bp):
AATCTGGACAGC
Found at i:21813 original size:23 final size:24
Alignment explanation
Indices: 21779--21823 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
21769 GATTTTTTCA
*
21779 TTTTTTTATTTTTCTTTTCTTCTC
1 TTTTTTTATTTTCCTTTTCTTCTC
21803 TTTTTTT-TTTTCCTTTTCTTC
1 TTTTTTTATTTTCCTTTTCTTC
21824 AAATTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTTATTTTCCTTTTCTTCTC
Found at i:21830 original size:23 final size:24
Alignment explanation
Indices: 21780--21830 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
21770 ATTTTTTCAT
* **
21780 TTTTTTATTTTTCTTTTCTTC-TC
1 TTTTTTATTTTCCTTTTCTTCAAA
*
21803 TTTTTTTTTTTCCTTTTCTTCAAA
1 TTTTTTATTTTCCTTTTCTTCAAA
21827 TTTT
1 TTTT
21831 GATCTAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTTATTTTCCTTTTCTTCAAA
Found at i:29361 original size:2 final size:2
Alignment explanation
Indices: 29354--29381 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29344 CAATTAAAAC
29354 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
29382 AAAGACAACC
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
Done.