Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024200.1 Corchorus olitorius cultivar O-4 contig24233, 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: 9569
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:408 original size:20 final size:20
Alignment explanation
Indices: 385--431 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
375 AATAAAAAAC
*
385 AAAAAAAAAGAAGAAAA-GA
1 AAAAAAAAAAAAGAAAATGA
*
404 AAAAAATGAAAAAGAAAATGA
1 AAAAAA-AAAAAAGAAAATGA
425 AAAAAAA
1 AAAAAAA
432 GCACTTGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.26
20 9 0.39
21 8 0.35
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAAAAAAAAAAGAAAATGA
Found at i:838 original size:5 final size:5
Alignment explanation
Indices: 824--856 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
814 TCAAAAGGTT
*
824 AAAA- AAAAC AAAAC AAAAC AAAAC AAATC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
857 AAATTGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (5 bp):
AAAAC
Found at i:1573 original size:50 final size:50
Alignment explanation
Indices: 1494--1643 Score: 228
Period size: 50 Copynumber: 3.0 Consensus size: 50
1484 AGTTTTACAA
* *
1494 TAAAATTGCTTTCCACTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCAATTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
* *
1544 TAAAATTGCTTTCCAATTGTAAGTCCAAGATCAAAATTCGCTTTTCAAGG
1 TAAAATTGCTTTCCAATTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
** * *
1594 TAGGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCAATTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1644 GACATTGAAG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (50 bp):
TAAAATTGCTTTCCAATTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
Found at i:2377 original size:50 final size:50
Alignment explanation
Indices: 2302--2670 Score: 616
Period size: 50 Copynumber: 7.4 Consensus size: 50
2292 CCGAATGCAC
*
2302 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACGT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
* *
2352 AGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
2402 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
2452 AGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
2502 AGGC-TTTCTCACAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACAT
1 AGGCTTTTC-CACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
2552 AGGC-TTTCTCACAAGCCAAACTCGTTTCCATACGGGTCAATTATCAACAT
1 AGGCTTTTC-CACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
* * *
2602 GGGCTTTTCCACAAGCCAAACTCGCTTCCATACGAGTCAATTATCAACAG
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
2652 AGGCTTTTCCATAAGCCAA
1 AGGCTTTTCCACAAGCCAA
2671 GTTTAATGAA
Statistics
Matches: 301, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
49 4 0.01
50 293 0.97
51 4 0.01
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (50 bp):
AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
Found at i:3106 original size:27 final size:27
Alignment explanation
Indices: 3068--3168 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
3058 AGGGTCATCT
* * *
3068 AGGGGCATTTTAGTCTTTTTAATATTC
1 AGGGGCATTTTAGTCATTTGAATATCC
*
3095 AGGGGCATTTTAGTCATTTGAATGTCC
1 AGGGGCATTTTAGTCATTTGAATATCC
* * * *
3122 AGGGGCATTTTGGTCATTTGCACACTCA
1 AGGGGCATTTTAGTCATTTGAATA-TCC
* *
3150 AGGGGCATTGTGGTCATTT
1 AGGGGCATTTTAGTCATTT
3169 TAAGTTCACA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 43 0.68
28 20 0.32
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.39
Consensus pattern (27 bp):
AGGGGCATTTTAGTCATTTGAATATCC
Found at i:5283 original size:4 final size:4
Alignment explanation
Indices: 5274--5329 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
5264 ACCATTTAAA
* * * * *
5274 AGAG AGAG AGAG AGAC AGAC AGAC AGAC AGAC AGAG AGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
*
5322 AGAA AGAG
1 AGAG AGAG
5330 GGGAAAGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.52, C:0.09, G:0.39, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:5482 original size:18 final size:18
Alignment explanation
Indices: 5459--5501 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5449 CCTGGCCAAG
* * *
5459 AAGGAAGAAGTAAAGGAA
1 AAGGAAAAAGAAAAGAAA
5477 AAGGAAAAAGAAAAGAAA
1 AAGGAAAAAGAAAAGAAA
5495 AAGGAAA
1 AAGGAAA
5502 TAAAGAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (18 bp):
AAGGAAAAAGAAAAGAAA
Found at i:5501 original size:12 final size:13
Alignment explanation
Indices: 5470--5501 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5460 AGGAAGAAGT
5470 AAAGGAAAAGGAA
1 AAAGGAAAAGGAA
5483 AAA-GAAAA-GAA
1 AAAGGAAAAGGAA
5494 AAAGGAAA
1 AAAGGAAA
5502 TAAAGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 9 0.50
13 3 0.17
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AAAGGAAAAGGAA
Done.