Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015710.1 Corchorus olitorius cultivar O-4 contig15743, 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: 26636
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1670 original size:2 final size:2
Alignment explanation
Indices: 1663--1698 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1653 CTTTAACTAG
1663 TA TA 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 TA TA
1699 GTCAAATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4769 original size:83 final size:81
Alignment explanation
Indices: 4657--4834 Score: 210
Period size: 83 Copynumber: 2.3 Consensus size: 81
4647 TTTTTTTAAG
* * * *
4657 ATCTATGAATCTTTAATAATCTAGTTTATAT-T-A-T-T--ATAAATCGCTTTTTTT-TAA-AAA
1 ATCTATAAATCTCTAATAATCTGGTTTATATATCATTATAAATAAATCGCTTTTTTTAAAATAAA
* *
4714 AATAAAAATAAATTAG
66 AATAAAAATAAAATAA
*
4730 ATCTATAAATCTCTAATAATCTGGTTTATATATCATTATAAATAAATCTCTTTTTTTAAAAAATA
1 ATCTATAAATCTCTAATAATCTGGTTTATATATCATTATAAATAAATCGCTTTTTTT--AAAATA
4795 AAAATAAAAATAAAATAA
64 AAAATAAAAATAAAATAA
*
4813 ATCTATGAATCTCTAATAATCT
1 ATCTATAAATCTCTAATAATCT
4835 TTTTTTTTTA
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
73 28 0.32
74 1 0.01
75 1 0.01
76 1 0.01
77 1 0.01
79 15 0.17
82 2 0.02
83 38 0.44
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (81 bp):
ATCTATAAATCTCTAATAATCTGGTTTATATATCATTATAAATAAATCGCTTTTTTTAAAATAAA
AATAAAAATAAAATAA
Found at i:4816 original size:75 final size:72
Alignment explanation
Indices: 4664--4816 Score: 168
Period size: 73 Copynumber: 2.1 Consensus size: 72
4654 AAGATCTATG
* *
4664 AATCTTTAATAATCTAGTTTATATTATTATAAATCGCTTTTTTTTAAAAAAATAAAAATAAATTA
1 AATCTCTAATAATCTAGTTTATATTATTATAAATAGCTTTTTTTTAAAAAAATAAAAATAAA-TA
**
4729 GATCTATA
65 GATAAATA
* *
4737 AATCTCTAATAATCTGGTTTATATATCATTATAAATAAATCTCTTTTTTT-AAAAAATAAAAATA
1 AATCTCTAATAATCTAGTTTATAT-T-ATTATAAAT--AGCT-TTTTTTTAAAAAAATAAAAATA
4801 AA-A-ATAAAATA
61 AATAGAT-AAATA
4812 AATCT
1 AATCT
4817 ATGAATCTCT
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
73 22 0.32
74 3 0.04
75 18 0.26
77 18 0.26
78 7 0.10
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (72 bp):
AATCTCTAATAATCTAGTTTATATTATTATAAATAGCTTTTTTTTAAAAAAATAAAAATAAATAG
ATAAATA
Found at i:12888 original size:38 final size:38
Alignment explanation
Indices: 12837--12921 Score: 161
Period size: 38 Copynumber: 2.2 Consensus size: 38
12827 ATACAACTAA
12837 ATTATTATATTTAGACTTGTCCAAATAGCACTTACATGT
1 ATTATT-TATTTAGACTTGTCCAAATAGCACTTACATGT
12876 ATTATTTATTTAGACTTGTCCAAATAGCACTTACATGT
1 ATTATTTATTTAGACTTGTCCAAATAGCACTTACATGT
12914 ATTATTTA
1 ATTATTTA
12922 AATTATTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 40 0.87
39 6 0.13
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (38 bp):
ATTATTTATTTAGACTTGTCCAAATAGCACTTACATGT
Found at i:13314 original size:19 final size:19
Alignment explanation
Indices: 13290--13326 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13280 CTTATCTGTA
13290 ATCGTTTCATCATCGTTTG
1 ATCGTTTCATCATCGTTTG
*
13309 ATCGTTTTATCATCGTTT
1 ATCGTTTCATCATCGTTT
13327 TGGGACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.14, T:0.51
Consensus pattern (19 bp):
ATCGTTTCATCATCGTTTG
Found at i:19329 original size:20 final size:21
Alignment explanation
Indices: 19304--19346 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
19294 TGACTTCAAT
19304 AAATAGATG-ATAAATAATAG
1 AAATAGATGAATAAATAATAG
19324 AAATAGATGAATAAATAATAG
1 AAATAGATGAATAAATAATAG
19345 AA
1 AA
19347 TTAAGGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (21 bp):
AAATAGATGAATAAATAATAG
Found at i:19790 original size:25 final size:25
Alignment explanation
Indices: 19749--19877 Score: 188
Period size: 25 Copynumber: 5.2 Consensus size: 25
19739 TCACCAATGT
* * *
19749 GTTGCCACGTAGGTGTGGACTTTGTA
1 GTTGCCACATAGATGTGGGCTTTG-A
19775 -TTGCCACATAGATGTGGGCTTTGA
1 GTTGCCACATAGATGTGGGCTTTGA
19799 GTTGCCACATAGATGTGGGCTTTGA
1 GTTGCCACATAGATGTGGGCTTTGA
*
19824 GTTGCCACATAGGTGTGGGCTTTGA
1 GTTGCCACATAGATGTGGGCTTTGA
* *
19849 GTTGCCACATATATGTGGGCTTTGT
1 GTTGCCACATAGATGTGGGCTTTGA
19874 GTTG
1 GTTG
19878 AACCATGAGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
24 1 0.01
25 94 0.99
ACGTcount: A:0.17, C:0.16, G:0.33, T:0.35
Consensus pattern (25 bp):
GTTGCCACATAGATGTGGGCTTTGA
Found at i:20468 original size:18 final size:19
Alignment explanation
Indices: 20445--20483 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
20435 TGGGTTTTTT
20445 GTGTTTG-ATTTGGGCTAA
1 GTGTTTGAATTTGGGCTAA
20463 GTGTTTGTAATTTGGGCTAA
1 GTGTTTG-AATTTGGGCTAA
20483 G
1 G
20484 AGAAGTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.18, C:0.05, G:0.33, T:0.44
Consensus pattern (19 bp):
GTGTTTGAATTTGGGCTAA
Found at i:22203 original size:13 final size:13
Alignment explanation
Indices: 22185--22209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22175 GAAATTCTAT
22185 ATAATACATAAAA
1 ATAATACATAAAA
22198 ATAATACATAAA
1 ATAATACATAAA
22210 TAAAAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAATACATAAAA
Found at i:22484 original size:2 final size:2
Alignment explanation
Indices: 22479--22505 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22469 TTAGTTTGAC
22479 AT 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 AT A
22506 CTAGGATCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24431 original size:22 final size:20
Alignment explanation
Indices: 24395--24435 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
24385 ATGTGAGTTG
24395 CAAAGTTTTTCTCTTGCTTGT
1 CAAAGTTTTTCTCTT-CTTGT
*
24416 CAAAGTTTTTTTTCTTCTTG
1 CAAAG-TTTTTCTCTTCTTG
24436 CTTGTGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (20 bp):
CAAAGTTTTTCTCTTCTTGT
Done.