Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012433.1 Corchorus olitorius cultivar O-4 contig12466, 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: 23853
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5921 original size:15 final size:15
Alignment explanation
Indices: 5892--5940 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
5882 TGGTATGAAG
*
5892 GAAACGGGAAGGAAA
1 GAAAGGGGAAGGAAA
5907 GAAGAGGGG-AGGAAA
1 GAA-AGGGGAAGGAAA
*
5922 GAAAGGGGAAGGAAG
1 GAAAGGGGAAGGAAA
5937 GAAA
1 GAAA
5941 AGGGTTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.17
15 21 0.70
16 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.47, T:0.00
Consensus pattern (15 bp):
GAAAGGGGAAGGAAA
Found at i:8393 original size:11 final size:11
Alignment explanation
Indices: 8369--8403 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
8359 TTGACAGCGC
8369 AACAAAAACAA
1 AACAAAAACAA
* *
8380 AACGAAAACGA
1 AACAAAAACAA
8391 AACAAAAACAA
1 AACAAAAACAA
8402 AA
1 AA
8404 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:8395 original size:16 final size:16
Alignment explanation
Indices: 8374--8432 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
8364 AGCGCAACAA
8374 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
8390 AAACAAAAACAAAAAAC-
1 AAAC-AAAAC-GAAAACG
*
8407 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
* *
8422 ATACCAAACGA
1 AAACAAAACGA
8433 CCCCTAAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 10 0.29
17 7 0.21
18 5 0.15
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:10020 original size:27 final size:27
Alignment explanation
Indices: 9980--10044 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
9970 AGAAAGCTAC
** *
9980 TTGATTTATTTTGGTTATATTTTGTAA
1 TTGATTTAGATTGGTCATATTTTGTAA
10007 TTGATTTAGATTGGTCATATTTTGTAA
1 TTGATTTAGATTGGTCATATTTTGTAA
*
10034 TTGTTTTAGAT
1 TTGATTTAGAT
10045 GACATTTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.23, C:0.02, G:0.17, T:0.58
Consensus pattern (27 bp):
TTGATTTAGATTGGTCATATTTTGTAA
Found at i:12591 original size:12 final size:12
Alignment explanation
Indices: 12574--12598 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12564 TCCTGTAAAA
12574 GAGGTAAGACAG
1 GAGGTAAGACAG
12586 GAGGTAAGACAG
1 GAGGTAAGACAG
12598 G
1 G
12599 CTCTACTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGGTAAGACAG
Found at i:16534 original size:123 final size:128
Alignment explanation
Indices: 16398--16650 Score: 374
Period size: 131 Copynumber: 2.0 Consensus size: 128
16388 ATTGTTTAAA
*
16398 TTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA-T
1 TTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTATT
16458 GATTTTTACCATTTTACTATTTTA-ATTAAAAGACTTATATATATTAGAATTTTTTAAATATAC
66 GATTTTTACCATTTTACTATTTTATATTAAAA-ACTTATATATATTAGAATTTTTTAAATATAC
* *
16521 TTTTACAGTTTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATCTAATATCCTTATACCTA
1 TTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--CTA
* * *
16586 TTTTATTTTTACCGTTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATATA
64 -TTGATTTTTACCATTTTACTATTTTATATTAAAAACTTATATATATTAGAATTTTTTAAATATA
16651 TTTCTTAAAT
Statistics
Matches: 115, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
123 51 0.44
124 1 0.01
125 1 0.01
126 1 0.01
129 2 0.02
131 53 0.46
132 6 0.05
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.51
Consensus pattern (128 bp):
TTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTATT
GATTTTTACCATTTTACTATTTTATATTAAAAACTTATATATATTAGAATTTTTTAAATATAC
Found at i:16672 original size:14 final size:13
Alignment explanation
Indices: 16636--16674 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
16626 TATATATTAG
16636 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
16649 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
16663 AATTTTTTAAAT
1 AATTTTTTAAAT
16675 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:20279 original size:54 final size:50
Alignment explanation
Indices: 20187--20336 Score: 160
Period size: 50 Copynumber: 2.9 Consensus size: 50
20177 CTCTGATGTG
* *
20187 GAAATCTCTTTCCATGAGTAAAGCAAAATCCAGAGAAAAAAAAAGGAAGAAGAA
1 GAAATCTCCTTCGATGAGTAAAGCAAAATCCAGAG-AAAAAAAA-G-A-AAGAA
* * *
20241 GAAATCTCCTTCGATGAGTAAAGCAGAA-CCAGGGGAAAAAGAAGAAAGAA
1 GAAATCTCCTTCGATGAGTAAAGCAAAATCCA-GAGAAAAAAAAGAAAGAA
* * * *
20291 AAAATCTTCTTCGATGAGTGAAGCAAAAT-CAGAAAAAAAAAAGAAA
1 GAAATCTCCTTCGATGAGTAAAGCAAAATCCAGAGAAAAAAAAGAAA
20337 AAAGGAAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
49 12 0.15
50 31 0.38
51 1 0.01
52 1 0.01
53 10 0.12
54 27 0.33
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.15
Consensus pattern (50 bp):
GAAATCTCCTTCGATGAGTAAAGCAAAATCCAGAGAAAAAAAAGAAAGAA
Found at i:22140 original size:22 final size:24
Alignment explanation
Indices: 22105--22163 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
22095 ATAAATGTTG
* *
22105 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
22127 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
22150 CTTGATAATATCTT
1 C-TGATAAT-TCTT
22164 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Done.