Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023043.1 Corchorus olitorius cultivar O-4 contig23076, 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: 31334
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:48 original size:30 final size:30
Alignment explanation
Indices: 13--276 Score: 420
Period size: 30 Copynumber: 8.8 Consensus size: 30
3 ATTGAATAAA
* *
13 ATCATGACATCTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
43 ATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
73 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
103 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
133 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
163 ATTATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
193 AGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
223 ATTATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
253 ACCATGACAACTTCTCGTGTCAAT
1 ATCATGACAACTTCTGGTGTCAAT
277 ATATATTAGC
Statistics
Matches: 220, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 220 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:1514 original size:2 final size:2
Alignment explanation
Indices: 1507--1545 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1497 ATTCCATAAC
1507 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1546 GCTTCATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1527 original size:17 final size:17
Alignment explanation
Indices: 1502--1538 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1492 CCATAATTCC
1502 ATAACATATATATATAT
1 ATAACATATATATATAT
*
1519 ATAATATATATATATAT
1 ATAACATATATATATAT
1536 ATA
1 ATA
1539 TATTATAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAACATATATATATAT
Found at i:1531 original size:19 final size:19
Alignment explanation
Indices: 1507--1545 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1497 ATTCCATAAC
1507 ATATATATATATATAATAT
1 ATATATATATATATAATAT
*
1526 ATATATATATATATATTAT
1 ATATATATATATATAATAT
1545 A
1 A
1546 GCTTCATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATATATATAATAT
Found at i:5239 original size:2 final size:2
Alignment explanation
Indices: 5229--5267 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
5219 TATCATTTCC
*
5229 AT AT GT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5268 GAGAAGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:19690 original size:21 final size:21
Alignment explanation
Indices: 19660--19699 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19650 TGAAATCGAT
* *
19660 TTGCTTAAGTCGATTTCTCCC
1 TTGCTCAAGTCGACTTCTCCC
19681 TTGCTCAAGTCGACTTCTC
1 TTGCTCAAGTCGACTTCTC
19700 TCTTAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.40
Consensus pattern (21 bp):
TTGCTCAAGTCGACTTCTCCC
Found at i:20236 original size:22 final size:22
Alignment explanation
Indices: 20218--20274 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
20208 GGCATGGTCG
*
20218 AGTCATGACCGGGCTATGGCCT
1 AGTCATGTCCGGGCTATGGCCT
*
20240 AGTCATGTTCGGGCTATGGCCT
1 AGTCATGTCCGGGCTATGGCCT
20262 AGTCATGTCCGGG
1 AGTCATGTCCGGG
20275 TGCCACCGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.16, C:0.25, G:0.33, T:0.26
Consensus pattern (22 bp):
AGTCATGTCCGGGCTATGGCCT
Done.