Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023452.1 Corchorus olitorius cultivar O-4 contig23485, 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: 18638
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:1388 original size:12 final size:12
Alignment explanation
Indices: 1371--1409 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
1361 TTATGCACCC
1371 AAAACATTTATT
1 AAAACATTTATT
1383 AAAACATTTA-T
1 AAAACATTTATT
*
1394 AAAGCATTTATAT
1 AAAACATTTAT-T
1407 AAA
1 AAA
1410 GCAGTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 10 0.42
12 10 0.42
13 4 0.17
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (12 bp):
AAAACATTTATT
Found at i:1426 original size:24 final size:23
Alignment explanation
Indices: 1371--1426 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
1361 TTATGCACCC
*
1371 AAAACATTTATTAAAACATTTAT
1 AAAACATTTATTAAAACAGTTAT
* *
1394 AAAGCATTTATATAAAGCAGTTAT
1 AAAACATTTAT-TAAAACAGTTAT
*
1418 AAAATATTT
1 AAAACATTT
1427 CCTCAACGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (23 bp):
AAAACATTTATTAAAACAGTTAT
Found at i:2486 original size:27 final size:27
Alignment explanation
Indices: 2447--2510 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 27
2437 TCTAAATTCT
2447 TATTATTTTAATAATAGAATAAT-TA-AAA
1 TATT-TTTTAATAAT--AATAATATAGAAA
2475 TATTTTTTAATAATAATAATATAGAAA
1 TATTTTTTAATAATAATAATATAGAAA
2502 TATATTTTT
1 TAT-TTTTT
2511 TTAAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.18
26 2 0.06
27 16 0.48
28 9 0.27
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (27 bp):
TATTTTTTAATAATAATAATATAGAAA
Found at i:6648 original size:21 final size:23
Alignment explanation
Indices: 6622--6679 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 23
6612 TCTAAACTTC
*
6622 ATTATATGAATATGAAC-AAT-A
1 ATTATATGAATAAGAACGAATCA
*
6643 ATTATATGAATAAGTACTGAATCA
1 ATTATATGAATAAGAAC-GAATCA
6667 ATTATATGAATAA
1 ATTATATGAATAA
6680 TTTATGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 15 0.47
23 3 0.09
24 14 0.44
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.34
Consensus pattern (23 bp):
ATTATATGAATAAGAACGAATCA
Found at i:7329 original size:9 final size:9
Alignment explanation
Indices: 7315--7341 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
7305 CCGATCCTGA
7315 AACCCGTCC
1 AACCCGTCC
7324 AACCCGTCC
1 AACCCGTCC
7333 AACCCGTCC
1 AACCCGTCC
7342 GATTGACTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.56, G:0.11, T:0.11
Consensus pattern (9 bp):
AACCCGTCC
Found at i:7492 original size:71 final size:71
Alignment explanation
Indices: 7376--7519 Score: 209
Period size: 71 Copynumber: 2.0 Consensus size: 71
7366 TCAAAGGAAA
*
7376 TAATTGAATGTTATTAATCTTTTTAGATTTAACAACTTTAAATTCTTGTCAAAAACTCCAATACA
1 TAATTGAATGTTACTAATCTTTTTAGATTTAACAACTTTAAATTCTTGTCAAAAACTCCAATACA
7441 TTAAAC
66 TTAAAC
** * * * *
7447 TAATTGAATGTTACTCTTCTTTTTA-TTTCTAATAACTTTAAATTCTTGTCATACACTCCAATAC
1 TAATTGAATGTTACTAATCTTTTTAGATT-TAACAACTTTAAATTCTTGTCAAAAACTCCAATAC
7511 ATTAAAC
65 ATTAAAC
7518 TA
1 TA
7520 CCAATACACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 2 0.03
71 63 0.97
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (71 bp):
TAATTGAATGTTACTAATCTTTTTAGATTTAACAACTTTAAATTCTTGTCAAAAACTCCAATACA
TTAAAC
Found at i:16471 original size:6 final size:6
Alignment explanation
Indices: 16440--16483 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
16430 CGTATTTTTA
* *
16440 ATATAG CATATAT AGATAG A-ATAG ATATAG ATATAG ATATAG AT
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT
16484 TTTAGTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
5 5 0.15
6 23 0.70
7 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (6 bp):
ATATAG
Found at i:17071 original size:21 final size:24
Alignment explanation
Indices: 17042--17092 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
17032 TTTTGAACTC
17042 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
17065 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
17088 ATTAT
1 ATTAT
17093 ATCTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:17087 original size:25 final size:25
Alignment explanation
Indices: 17042--17090 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17032 TTTTGAACTC
*
17042 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
17067 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
17091 ATATCTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:17740 original size:9 final size:9
Alignment explanation
Indices: 17726--17772 Score: 78
Period size: 9 Copynumber: 5.3 Consensus size: 9
17716 CCCAAATTAC
17726 TTATGGAAA
1 TTATGGAAA
17735 TTATGGAAA
1 TTATGGAAA
*
17744 TTAAGGAAA
1 TTATGGAAA
17753 TTATGGAAA
1 TTATGGAAA
17762 TTAT-GAAA
1 TTATGGAAA
17770 TTA
1 TTA
17773 AATGAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
8 7 0.19
9 29 0.81
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Done.