Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014272.1 Corchorus olitorius cultivar O-4 contig14305, 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: 80601
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5737 original size:84 final size:84
Alignment explanation
Indices: 5597--5814 Score: 357
Period size: 84 Copynumber: 2.6 Consensus size: 84
5587 AAGAATTCTT
* *
5597 ACCAACCTTTATTC-GATGCACCATTATACCTTGAAGTATAATAGGAATGCCATCCCTTTCACTG
1 ACCAACTTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCCCTTTCACTG
* *
5661 CAAAATAGAAATTTCTGTC
66 CAAAACAGAAATTCCTGTC
*
5680 ACCAACTTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCCCTTTTACTG
1 ACCAACTTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCCCTTTCACTG
*
5745 CAGAACAGAAATTCCTGTC
66 CAAAACAGAAATTCCTGTC
* *
5764 ACCAAATTTTATTCAGAAGCACCATTATACCTTGATGTATAATAGGAATGC
1 ACCAACTTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGC
5815 TACTGTTGTG
Statistics
Matches: 126, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
83 13 0.10
84 113 0.90
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (84 bp):
ACCAACTTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCCCTTTCACTG
CAAAACAGAAATTCCTGTC
Found at i:12802 original size:24 final size:24
Alignment explanation
Indices: 12750--12802 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
12740 GATACTACTA
**
12750 AAAAGAAAATTTCTTATTTACTGT
1 AAAAGAAAATTTCTTATTTAAAGT
*
12774 CAAAGAAAATTTCTTATTGTAAAG-
1 AAAAGAAAATTTCTTATT-TAAAGT
12798 AAAAG
1 AAAAG
12803 TAGAAGTGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (24 bp):
AAAAGAAAATTTCTTATTTAAAGT
Found at i:21269 original size:22 final size:22
Alignment explanation
Indices: 21221--21269 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
21211 TTGCCCTTTT
*
21221 TCTCT-CTCCCCCCACTAACTC
1 TCTCTCCTCCCCCCACTAACTA
* * *
21242 TTTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCCCCCCACTAACTA
21264 TCTCTC
1 TCTCTC
21270 TTCATAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.35
Consensus pattern (22 bp):
TCTCTCCTCCCCCCACTAACTA
Found at i:36658 original size:12 final size:12
Alignment explanation
Indices: 36641--36680 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
36631 GGGAGGTTGC
36641 AGAGAGGAAAAG
1 AGAGAGGAAAAG
*
36653 AGAGAGGAAGAG
1 AGAGAGGAAAAG
*
36665 AAAGAGGAAGAAG
1 AGAGAGGAA-AAG
36678 AGA
1 AGA
36681 AAACGCGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
AGAGAGGAAAAG
Found at i:36679 original size:15 final size:16
Alignment explanation
Indices: 36649--36682 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
36639 GCAGAGAGGA
*
36649 AAAGAGAGAGGAAGAG
1 AAAGAGAGAAGAAGAG
36665 AAAGAG-GAAGAAGAG
1 AAAGAGAGAAGAAGAG
36680 AAA
1 AAA
36683 ACGCGAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AAAGAGAGAAGAAGAG
Found at i:37219 original size:2 final size:2
Alignment explanation
Indices: 37212--37241 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
37202 TAATAAGAAC
37212 AT AT AT AT AT AT 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
37242 TGATGGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61648 original size:28 final size:28
Alignment explanation
Indices: 61609--61664 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
61599 ACAGAGTCTG
61609 ACACAACTCGATTCCGGACTAATCGAGC
1 ACACAACTCGATTCCGGACTAATCGAGC
61637 ACACAACTCGATTCCGGACTAATCGAGC
1 ACACAACTCGATTCCGGACTAATCGAGC
61665 CCTAATGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (28 bp):
ACACAACTCGATTCCGGACTAATCGAGC
Found at i:71571 original size:31 final size:32
Alignment explanation
Indices: 71535--71605 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
71525 AATATTTATT
*
71535 TAAAAATACAAATTTT-TT-ACTAAAAAAATAA
1 TAAAAATAC-AATTTTGTTAACTAAAAAAAAAA
*
71566 TAAAAATACAATTTTGTTAAGTAAAAAAAAAA
1 TAAAAATACAATTTTGTTAACTAAAAAAAAAA
*
71598 TCAAAATA
1 TAAAAATA
71606 TGTTGCTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 6 0.17
31 11 0.31
32 18 0.51
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.30
Consensus pattern (32 bp):
TAAAAATACAATTTTGTTAACTAAAAAAAAAA
Found at i:76540 original size:17 final size:17
Alignment explanation
Indices: 76518--76551 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
76508 ACCATATCAA
76518 CAAAGACTATACCATAT
1 CAAAGACTATACCATAT
* *
76535 CAAAGATTATACTATAT
1 CAAAGACTATACCATAT
76552 GGATAAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (17 bp):
CAAAGACTATACCATAT
Found at i:78309 original size:3 final size:3
Alignment explanation
Indices: 78301--78370 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
78291 GATGAGTTAA
* * * * *
78301 AAG AAG AAG AAG AGG AAG AGG AGG AAG AAG AAG ACG AAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
78349 AAG AAG -AG AAAG AAG AAG AAG A
1 AAG AAG AAG -AAG AAG AAG AAG A
78371 GGAGGAGAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 53 0.93
4 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:78378 original size:21 final size:20
Alignment explanation
Indices: 78300--78379 Score: 87
Period size: 18 Copynumber: 4.1 Consensus size: 20
78290 TGATGAGTTA
78300 AAAGAAGAAGAAGAGGAAGAG
1 AAAGAAGAAGAAGAGG-AGAG
* * *
78321 GAGGAAGAAGAAGACGA-AG
1 AAAGAAGAAGAAGAGGAGAG
78340 AAA-AAGAAGAAGA--AGAG
1 AAAGAAGAAGAAGAGGAGAG
78357 AAAGAAGAAGAAGAGGAGGAG
1 AAAGAAGAAGAAGAGGA-GAG
78378 AA
1 AA
78380 GGCTGAAGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
16 1 0.02
17 5 0.10
18 20 0.41
19 3 0.06
20 2 0.04
21 18 0.37
ACGTcount: A:0.61, C:0.01, G:0.38, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGAAGAGGAGAG
Found at i:78793 original size:16 final size:16
Alignment explanation
Indices: 78772--78806 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
78762 AGATTATTTG
* *
78772 CTTGAAGTCGTTTATT
1 CTTGAAGTCCTCTATT
78788 CTTGAAGTCCTCTATT
1 CTTGAAGTCCTCTATT
78804 CTT
1 CTT
78807 TATACAGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (16 bp):
CTTGAAGTCCTCTATT
Done.