Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009573.1 Corchorus olitorius cultivar O-4 contig09605, 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: 10306
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:8473 original size:17 final size:19
Alignment explanation
Indices: 8431--8473 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
8421 TTTTGAAGAT
8431 AGAAGAATGAAGAAGGAAA
1 AGAAGAATGAAGAAGGAAA
8450 A-AGAGAAT-AA-AAGGAAA
1 AGA-AGAATGAAGAAGGAAA
8467 AGAAGAA
1 AGAAGAA
8474 AAGAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 12 0.55
18 4 0.18
19 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (19 bp):
AGAAGAATGAAGAAGGAAA
Found at i:8475 original size:24 final size:24
Alignment explanation
Indices: 8447--8499 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
8437 ATGAAGAAGG
* *
8447 AAAAAGAGAATAAAAGGAAAAGAA
1 AAAAAGAAAAGAAAAGGAAAAGAA
* *
8471 GAAAAGAAAAGAAAAGGAAGAGAA
1 AAAAAGAAAAGAAAAGGAAAAGAA
8495 AAAAA
1 AAAAA
8500 AAGAGTGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (24 bp):
AAAAAGAAAAGAAAAGGAAAAGAA
Found at i:8499 original size:19 final size:18
Alignment explanation
Indices: 8450--8499 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
8440 AAGAAGGAAA
*
8450 AAGAGAATAAAAGGAAAAG
1 AAGAGAA-AAAAAGAAAAG
8469 AAGA-AAAGAAAAGAAAAGG
1 AAGAGAAA-AAAAGAAAA-G
8488 AAGAGAAAAAAA
1 AAGAGAAAAAAA
8500 AAGAGTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.04
18 10 0.37
19 13 0.48
20 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (18 bp):
AAGAGAAAAAAAGAAAAG
Found at i:8878 original size:13 final size:13
Alignment explanation
Indices: 8862--8898 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
8852 GATAATTCTT
8862 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
8875 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
8888 CTTGACCCTCC
1 TTTGACCCTCC
8899 TAATAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:8960 original size:41 final size:41
Alignment explanation
Indices: 8897--8978 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
8887 ACTTGACCCT
* * *
8897 CCTAATAATTATGGAAATAAATTAAATCCAGGTTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCCC
**
8938 CCTAATAATTAAGGTGAGAAATTAAATCCAGATTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCCC
8979 TAGTTATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (41 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCCC
Found at i:9713 original size:29 final size:29
Alignment explanation
Indices: 9671--9744 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
9661 GGCTTTGGAA
9671 AGCAAATTAAATCCTAAATCACTTGAACT
1 AGCAAATTAAATCCTAAATCACTTGAACT
9700 AGCAAATTAAATCCTAAATCACTTGAACT
1 AGCAAATTAAATCCTAAATCACTTGAACT
9729 AGCAAATTAAATCCTA
1 AGCAAATTAAATCCTA
9745 GAAGAGACCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (29 bp):
AGCAAATTAAATCCTAAATCACTTGAACT
Done.