Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016412.1 Corchorus olitorius cultivar O-4 contig16445, 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: 9062
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2810 original size:11 final size:10
Alignment explanation
Indices: 2794--2840 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
2784 AAGTTCGTGT
2794 TTGAAGACTCA
1 TTGAAGA-TCA
*
2805 TTGAAGATAA
1 TTGAAGATCA
2815 TTTGAAGAT--
1 -TTGAAGATCA
2824 TTGAAGATCA
1 TTGAAGATCA
2834 TTGAAGA
1 TTGAAGA
2841 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:2829 original size:19 final size:18
Alignment explanation
Indices: 2805--2840 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2795 TGAAGACTCA
2805 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
2824 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
2841 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:8528 original size:25 final size:25
Alignment explanation
Indices: 8500--8553 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
8490 GTTTTAAAAT
*
8500 TAAAAATGGTAAATTAAAATATTTA
1 TAAAAATAGTAAATTAAAATATTTA
* * *
8525 TAAAAATATTAAATTTAATTATTTA
1 TAAAAATAGTAAATTAAAATATTTA
8550 -AAAA
1 TAAAA
8554 TAGAGTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
TAAAAATAGTAAATTAAAATATTTA
Found at i:8659 original size:387 final size:385
Alignment explanation
Indices: 7943--8725 Score: 1372
Period size: 387 Copynumber: 2.0 Consensus size: 385
7933 ATAATTAAAT
7943 TTTAAATAAATTTTTAACTTAATTATTTTAAAAATGATGAATAATTAATGATTAGGTAAATTATT
1 TTTAAATAAATTTTTAACTTAATTATTTTAAAAATGATGAATAATTAATGATTAGGTAAATTATT
8008 TTAACTTTTAAACTTGATAATAAGATTTTTGTTAGTTTATATTATAATTTTTTTTGTTCAAATTA
66 TTAACTTTTAAACTTGATAATAAGATTTTTGTTAGTTTATATTATAATTTTTTTTGTTCAAATTA
*
8073 GTTTATATTATAATTGAAAAAAGTCTCCAATTTTTTAAAATTAAAATGGTAAATTAAAATATTTA
131 GTTTATATTATAATTGAAAAAAGTCTCCAATGTTTTAAAATTAAAATGGTAAATTAAAATATTTA
* * * * *
8138 TAACAATATTGAATTTAATTAAATAAAAATATAGTTTTTAGTAGCATAATTATTAAAGTTTATTT
196 TAAAAATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAATTATAAAAGTTTATTT
* *
8203 CTTAAAAAAGCTGTAAAATTTAAACAATGTCATTTAAGAAATATATTTCAAAAATTCTAATATAT
261 CTTAAAAAAACTGTAAAATTTAAACAATGTCATTTAAGAAATATATTTCAAAAATTCTAATACAT
*
8268 CTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATTA-AATAGGTATAAGGATATTAGA
326 CTAAGTTTTTTAATTAAATTAGTAAATTGAT-AAAAGTAGAATAGGTATAAGGATATTAGA
8328 TTTAAATAAATTTTTAACTTAATTATTTTAAAAAATGATGAATAATTAATGATTAGGTAAATTAT
1 TTTAAATAAATTTTTAACTTAATTATTTT-AAAAATGATGAATAATTAATGATTAGGTAAATTAT
8393 TTTAACTTTTAAACTTGATAATAAGATTTTTGTTAGTTTATATTATAA-TTTTTTTGTTCAAATT
65 TTTAACTTTTAAACTTGATAATAAGATTTTTGTTAGTTTATATTATAATTTTTTTTGTTCAAATT
*
8457 AGTTTATATTATAATTGGAAAAAAGTCTCCGATGTTTTAAAATTAAAAATGGTAAATTAAAATAT
130 AGTTTATATTATAATT-GAAAAAAGTCTCCAATGTTTTAAAATT-AAAATGGTAAATTAAAATAT
** *
8522 TTATAAAAATATTAAATTTAATTATTTAAAAATAGAGTTTTTAGTAGAATAATTGTAAAAGTTTA
193 TTATAAAAATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAATTATAAAAGTTTA
*
8587 TTTCTTAAAAAAACTGTAAAATTTAAACAATGTCATTTAAGAAATATATTTTAAAAATTCTAATA
258 TTTCTTAAAAAAACTGTAAAATTTAAACAATGTCATTTAAGAAATATATTTCAAAAATTCTAATA
*
8652 CATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAGTAGAATAGGTATAAGGATATTATA
323 CATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAGTAGAATAGGTATAAGGATATTAGA
*
8715 TTTAATTAAAT
1 TTTAAATAAAT
8726 AAAAATAGTG
Statistics
Matches: 378, Mismatches: 16, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
385 61 0.16
386 114 0.30
387 203 0.54
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (385 bp):
TTTAAATAAATTTTTAACTTAATTATTTTAAAAATGATGAATAATTAATGATTAGGTAAATTATT
TTAACTTTTAAACTTGATAATAAGATTTTTGTTAGTTTATATTATAATTTTTTTTGTTCAAATTA
GTTTATATTATAATTGAAAAAAGTCTCCAATGTTTTAAAATTAAAATGGTAAATTAAAATATTTA
TAAAAATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAATTATAAAAGTTTATTT
CTTAAAAAAACTGTAAAATTTAAACAATGTCATTTAAGAAATATATTTCAAAAATTCTAATACAT
CTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAGTAGAATAGGTATAAGGATATTAGA
Found at i:9024 original size:6 final size:6
Alignment explanation
Indices: 9008--9055 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
8998 TACATTTTTA
*
9008 ATATA- ATATAG ATATAG ATATAG ATAT-- ATATAT ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
9053 ATA
1 ATA
9056 AAGGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
4 4 0.10
5 5 0.13
6 30 0.77
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (6 bp):
ATATAG
Found at i:9039 original size:22 final size:23
Alignment explanation
Indices: 9008--9055 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
8998 TACATTTTTA
9008 ATATAATATAGATATAGATATAG
1 ATATAATATAGATATAGATATAG
*
9031 ATAT-ATATATATATAGATATAG
1 ATATAATATAGATATAGATATAG
9053 ATA
1 ATA
9056 AAGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (23 bp):
ATATAATATAGATATAGATATAG
Found at i:9044 original size:16 final size:16
Alignment explanation
Indices: 9008--9055 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
8998 TACATTTTTA
9008 ATATA-ATATAGATAT
1 ATATAGATATAGATAT
*
9023 AGATATAGATATATATAT
1 --ATATAGATATAGATAT
9041 ATATAGATATAGATA
1 ATATAGATATAGATA
9056 AAGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 14 0.50
17 5 0.18
18 9 0.32
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (16 bp):
ATATAGATATAGATAT
Done.