Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015518.1 Corchorus olitorius cultivar O-4 contig15551, 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: 17455
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1485 original size:99 final size:100
Alignment explanation
Indices: 1289--1518 Score: 291
Period size: 100 Copynumber: 2.3 Consensus size: 100
1279 ATTTAATATG
* * * * * ** *
1289 TTTTCTAAAATCCTAGGGAACAAACACTTTAAGTTTAGGTTATACCCTTAAATTAATTTTTTTAA
1 TTTTCTAAAACCCTA-GAAATAAATATTTTAAGTTTAGGACATACCCTTAAAATAATTTTTTTAA
* * *
1354 TTTAGGGGTAAACCTTATTAATTTGGGGCTATTTTT
65 TTTAGGGGTAAACCTTATTAACTTAGGACTATTTTT
*
1390 TTTTCTAAAACCCTAGAAATAAATATTTTAAGTTTAGGACATACCCTTAAAATCA-TTTTTTAAT
1 TTTTCTAAAACCCTAGAAATAAATATTTTAAGTTTAGGACATACCCTTAAAATAATTTTTTTAAT
* *
1454 TTATGGTTAAACCTTATTAACTTAGGACTATTTTT
66 TTAGGGGTAAACCTTATTAACTTAGGACTATTTTT
* *
1489 TTTATCTAAAACTCTATAAATAAATATTTT
1 TTT-TCTAAAACCCTAGAAATAAATATTTT
1519 CACTCTAAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
99 42 0.38
100 56 0.50
101 14 0.12
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (100 bp):
TTTTCTAAAACCCTAGAAATAAATATTTTAAGTTTAGGACATACCCTTAAAATAATTTTTTTAAT
TTAGGGGTAAACCTTATTAACTTAGGACTATTTTT
Found at i:4199 original size:12 final size:12
Alignment explanation
Indices: 4182--4231 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 12
4172 TGTAGAAAAA
4182 ATATTTTTGTTG
1 ATATTTTTGTTG
4194 ATATTTTTGTATG
1 ATATTTTTGT-TG
*
4207 AAAATATTTTTATTG
1 ---ATATTTTTGTTG
4222 ATATTTTTGT
1 ATATTTTTGT
4232 ATGAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 19 0.59
13 2 0.06
15 2 0.06
16 9 0.28
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (12 bp):
ATATTTTTGTTG
Found at i:4245 original size:27 final size:28
Alignment explanation
Indices: 4179--4244 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
4169 AAATGTAGAA
*
4179 AAAATATTTTTGTTGATATTTTTGTATG
1 AAAATATTTTTATTGATATTTTTGTATG
4207 AAAATATTTTTATTGATATTTTTGTATG
1 AAAATATTTTTATTGATATTTTTGTATG
4235 AAAATATTTT
1 AAAATATTTT
4245 AAAAAATACG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (28 bp):
AAAATATTTTTATTGATATTTTTGTATG
Found at i:5192 original size:20 final size:22
Alignment explanation
Indices: 5144--5192 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
5134 GAGGTAAACA
* *
5144 AAATTTCATAAGGAGATTATAAG
1 AAATTT-ACAAGGAGATTATAAC
5167 AAATTTACAAGGAGA-T-TAAC
1 AAATTTACAAGGAGATTATAAC
5187 AAATTT
1 AAATTT
5193 TCATAAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 1 0.04
22 8 0.33
23 6 0.25
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (22 bp):
AAATTTACAAGGAGATTATAAC
Found at i:5200 original size:22 final size:22
Alignment explanation
Indices: 5120--5202 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 22
5110 GGGTTATGAT
* * *
5120 CAAAATTTCGTAAGGAGGTAAA
1 CAAAATTTCATAAGGAGATTAA
5142 CAAAATTTCATAAGGAGATTATA
1 CAAAATTTCATAAGGAGATTA-A
*
5165 -AGAAATTT-ACAAGGAGATTAA
1 CA-AAATTTCATAAGGAGATTAA
*
5186 CAAATTTTCATAAGGAG
1 CAAAATTTCATAAGGAG
5203 GTTATCACAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
21 6 0.12
22 38 0.75
23 7 0.14
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (22 bp):
CAAAATTTCATAAGGAGATTAA
Found at i:8581 original size:19 final size:18
Alignment explanation
Indices: 8553--8594 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
8543 AATTAATTGT
8553 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
8571 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
8590 CTTAA
1 TTTAA
8595 AAGTTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:10453 original size:16 final size:17
Alignment explanation
Indices: 10421--10453 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10411 CGGGATTAGT
10421 TAGGCTAATTAAGCCTA
1 TAGGCTAATTAAGCCTA
*
10438 TAGGTTAATT-AGCCTA
1 TAGGCTAATTAAGCCTA
10454 ACTAAGCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (17 bp):
TAGGCTAATTAAGCCTA
Found at i:11674 original size:20 final size:20
Alignment explanation
Indices: 11651--11692 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
11641 GCCAATTTAA
11651 TCTTTACAATGTGTTCCCTT
1 TCTTTACAATGTGTTCCCTT
11671 TCTTTACAATGTGTTCCCTT
1 TCTTTACAATGTGTTCCCTT
11691 TC
1 TC
11693 CACTTTCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.10, T:0.50
Consensus pattern (20 bp):
TCTTTACAATGTGTTCCCTT
Found at i:14499 original size:16 final size:15
Alignment explanation
Indices: 14458--14499 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
14448 AACTAATCAG
14458 ATCATGACTCCACTA
1 ATCATGACTCCACTA
14473 A-CAAT-ACTCCACTAA
1 ATC-ATGACTCCACT-A
14488 ATCATGACTCCA
1 ATCATGACTCCA
14500 ATATCAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.39
15 7 0.30
16 7 0.30
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.24
Consensus pattern (15 bp):
ATCATGACTCCACTA
Done.