Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017163.1 Corchorus olitorius cultivar O-4 contig17196, 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: 19919
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:7343 original size:19 final size:20
Alignment explanation
Indices: 7319--7374 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
7309 GTTTGGCAAC
7319 TGTACAGATGAGATTA-CAT
1 TGTACAGATGAGATTAGCAT
* * *
7338 TGTACATATTAGATTAGGTAT
1 TGTACAGATGAGATTA-GCAT
*
7359 TGTATAGATGAGATTA
1 TGTACAGATGAGATTA
7375 TTAGAGTAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 14 0.48
21 15 0.52
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (20 bp):
TGTACAGATGAGATTAGCAT
Found at i:16743 original size:3 final size:3
Alignment explanation
Indices: 16729--16769 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
16719 AGGTTGAGTT
* *
16729 AAG AAT AAG AAG AAG AATT AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG A
16770 GGCATCGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.27, T:0.07
Consensus pattern (3 bp):
AAG
Found at i:16751 original size:19 final size:19
Alignment explanation
Indices: 16727--16764 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16717 TAAGGTTGAG
*
16727 TTAAGAATAAGAAGAAGAA
1 TTAAGAAGAAGAAGAAGAA
16746 TTAAGAAGAAGAAGAAGAA
1 TTAAGAAGAAGAAGAAGAA
16765 GAAGAGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (19 bp):
TTAAGAAGAAGAAGAAGAA
Found at i:17187 original size:21 final size:20
Alignment explanation
Indices: 17161--17224 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
17151 GTTGTTCTAA
17161 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACAGT-TC
* * *
17182 TAATCTAATTTGTACAG-TG
1 TAATCTCATCTGTACAGTTC
17201 TAATCTCATCTGTACAGTTGC
1 TAATCTCATCTGTACAGTT-C
17222 TAA
1 TAA
17225 ATAGTGTCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.46
20 1 0.03
21 18 0.51
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTTC
Found at i:17206 original size:19 final size:19
Alignment explanation
Indices: 17161--17218 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
17151 GTTGTTCTAA
* *
17161 TAATCTCATCTGTACAGTATC
1 TAATCTAATCTGTACAG--TG
*
17182 TAATCTAATTTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
17201 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
17219 TGCTAAATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:18881 original size:32 final size:31
Alignment explanation
Indices: 18787--18882 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 31
18777 AAGGGACTAA
* * *
18787 TTTGTCCAAAAAAAAAAACATAAGGGGTTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
18818 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
* * * *
18849 TTTGTCCCAAACGAAAAATATTATGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
18880 TTT
1 TTT
18883 AGTATTTAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:19182 original size:126 final size:124
Alignment explanation
Indices: 19035--19273 Score: 345
Period size: 126 Copynumber: 1.9 Consensus size: 124
19025 ATTCCCTAAA
* *
19035 AAAATGGTAAAGATAAAATAGTTATAAAAATATT-GAATTTAATTAAATAAAAATAGAATTTTTG
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTAG-ATTTAATTAAATAAAAATAGAATTTTTA
* *
19099 GTAAAATAAAACTGTAAAAGTTTAAATAATGTCATTTAAGAAATATATTTAATTAAAATAGT
65 ATAAAATAAAACTGTAAAAGTTTAAA-AATGGCATTTAA-AAATATATTTAATTAAAATAGT
* * *
19161 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTGATTAAATAAAAATAGAGTTTTTAA
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTAA
** * *
19226 TTGAGTAAAATTGTAAAAGTTTAAAAATGGCATTTAAAAATATATTTA
66 TAAAATAAAACTGTAAAAGTTTAAAAATGGCATTTAAAAATATATTTA
19274 GAAAAATAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
124 11 0.11
125 11 0.11
126 78 0.77
127 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.36
Consensus pattern (124 bp):
AAAATGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTAA
TAAAATAAAACTGTAAAAGTTTAAAAATGGCATTTAAAAATATATTTAATTAAAATAGT
Done.