Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010901.1 Corchorus olitorius cultivar O-4 contig10933, 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: 45241
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6983 original size:19 final size:19
Alignment explanation
Indices: 6956--6998 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
6946 AATTTTTCAT
* **
6956 ATTTAAAATATTCTCTTTA
1 ATTTTAAATATTAACTTTA
6975 ATTTTAAATATTAACTTTA
1 ATTTTAAATATTAACTTTA
6994 ATTTT
1 ATTTT
6999 TATTTTGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTAAATATTAACTTTA
Found at i:7273 original size:2 final size:2
Alignment explanation
Indices: 7266--7294 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7256 ATAATTGTCC
7266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7295 AATCAGAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9157 original size:24 final size:23
Alignment explanation
Indices: 9130--9182 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
9120 CTGGTTAGAT
*
9130 ATTATCAAGTA-ATAAATGGAGAAA
1 ATTATCAAG-AGATAAA-AGAGAAA
9154 ATTATC-AGAGATAAAAGAGAAA
1 ATTATCAAGAGATAAAAGAGAAA
9176 ATTATCA
1 ATTATCA
9183 GCAACATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 13 0.50
23 7 0.27
24 6 0.23
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.25
Consensus pattern (23 bp):
ATTATCAAGAGATAAAAGAGAAA
Found at i:10275 original size:30 final size:30
Alignment explanation
Indices: 10243--10607 Score: 516
Period size: 30 Copynumber: 12.0 Consensus size: 30
10233 AATCTCCAAA
* *
10243 TGACACCAGAAGTTGTCATGATCTTGCAAA
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
10273 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* * * *
10303 TAACACCATAAGTTCTCATGGTATTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
10333 TGACACCAGAAGTTGTCAATGATCTTGCAAT
1 TGACACCAGAAGTTGTC-ATGGTCTTGCAAT
* *
10364 TGGCACCAGAAAGTTGTCAATGATCTTGCAAT
1 TGACACCAG-AAGTTGTC-ATGGTCTTGCAAT
*
10396 TGACACCAGAAGTTGTCATGGTCTTCCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* **
10426 TGACACTAGAAGTTGTCGGGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
10456 TGACACCAAAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
10486 TGACACTAGAAGTTGTCATGGAT-TTGCAAT
1 TGACACCAGAAGTTGTCATGG-TCTTGCAAT
10516 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
10546 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* * *
10576 TGACACCAGAATTTGTCAATGATCTCGCAAT
1 TGACACCAGAAGTTGTC-ATGGTCTTGCAAT
10607 T
1 T
10608 TACCTGGTGT
Statistics
Matches: 301, Mismatches: 29, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
29 1 0.00
30 230 0.76
31 40 0.13
32 30 0.10
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGGTCTTGCAAT
Found at i:14373 original size:12 final size:13
Alignment explanation
Indices: 14356--14384 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
14346 TCGTTACTTT
14356 ATTTTTA-TTTTC
1 ATTTTTATTTTTC
14368 ATTTTTATTTTTC
1 ATTTTTATTTTTC
14381 ATTT
1 ATTT
14385 AAGTGCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTATTTTTC
Found at i:14744 original size:28 final size:28
Alignment explanation
Indices: 14704--14828 Score: 160
Period size: 28 Copynumber: 4.5 Consensus size: 28
14694 TTTACTCCTT
*
14704 ATTTTGGTCATTTTTCGTGTCCAGGGGC
1 ATTTTGGTCATTTTTCGTATCCAGGGGC
14732 ATTTTGGTCATTTTTCGTATCCAGGGGC
1 ATTTTGGTCATTTTTCGTATCCAGGGGC
* **
14760 ATTTTGGTCATTTTGCAAATCCAGGGGC
1 ATTTTGGTCATTTTTCGTATCCAGGGGC
* * ** *
14788 ATTTTGGTCATTATGCACATCCAGGGGT
1 ATTTTGGTCATTTTTCGTATCCAGGGGC
*
14816 ATTTTGATCATTT
1 ATTTTGGTCATTT
14829 CAAGGGCACT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 88 1.00
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (28 bp):
ATTTTGGTCATTTTTCGTATCCAGGGGC
Found at i:20652 original size:33 final size:33
Alignment explanation
Indices: 20610--20681 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
20600 ATTTAAAACA
*
20610 ACCATTTATCAATCTCTTTTGCCTTTAATTATC
1 ACCAATTATCAATCTCTTTTGCCTTTAATTATC
*
20643 ACCAATTATCAGTCTCTTTTGCCTTTAATTATC
1 ACCAATTATCAATCTCTTTTGCCTTTAATTATC
20676 ACCAAT
1 ACCAAT
20682 AGAGACACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.44
Consensus pattern (33 bp):
ACCAATTATCAATCTCTTTTGCCTTTAATTATC
Found at i:42093 original size:8 final size:9
Alignment explanation
Indices: 42067--42095 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42057 CCCAAATTAC
42067 TTATGGAAA
1 TTATGGAAA
42076 TTATGGAAA
1 TTATGGAAA
42085 TTA-GGAAA
1 TTATGGAAA
42093 TTA
1 TTA
42096 AATGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Found at i:42976 original size:12 final size:12
Alignment explanation
Indices: 42959--43011 Score: 88
Period size: 12 Copynumber: 4.4 Consensus size: 12
42949 AAAGCAGCAG
*
42959 TCTCCAACAACC
1 TCTCCAAAAACC
42971 TCTCCAAAAACC
1 TCTCCAAAAACC
*
42983 TCTCCAACAACC
1 TCTCCAAAAACC
42995 TCTCCAAAAACC
1 TCTCCAAAAACC
43007 TCTCC
1 TCTCC
43012 TCAGAGTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (12 bp):
TCTCCAAAAACC
Found at i:42991 original size:24 final size:24
Alignment explanation
Indices: 42959--43011 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
42949 AAAGCAGCAG
42959 TCTCCAACAACCTCTCCAAAAACC
1 TCTCCAACAACCTCTCCAAAAACC
42983 TCTCCAACAACCTCTCCAAAAACC
1 TCTCCAACAACCTCTCCAAAAACC
43007 TCTCC
1 TCTCC
43012 TCAGAGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (24 bp):
TCTCCAACAACCTCTCCAAAAACC
Found at i:43453 original size:49 final size:46
Alignment explanation
Indices: 43381--43521 Score: 151
Period size: 49 Copynumber: 2.9 Consensus size: 46
43371 AAAGCAATCA
43381 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTGCTACAAAATTGAACT
1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTT--TACAAAATTGAACT
* *
43429 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTATTTTTACTTGCA-CTTTTTCTCAATTTTT--TACAAAATTGAACT
* * *
43478 TTTAATTTT-CATCGCACTTTTTATCAATTTTTTGACAAAATTGA
1 TTTATTTTTAC-TTGCACTTTTTCTCAATTTTTT-ACAAAATTGA
43522 TTGGCACGCT
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 17 0.21
48 24 0.30
49 40 0.49
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (46 bp):
TTTATTTTTACTTGCACTTTTTCTCAATTTTTTACAAAATTGAACT
Found at i:44078 original size:18 final size:18
Alignment explanation
Indices: 44055--44142 Score: 131
Period size: 18 Copynumber: 4.9 Consensus size: 18
44045 CAACAACAAA
**
44055 TCGCACCGCACCAAGTAT
1 TCGCACCGCACCAAGTGG
*
44073 TCGCACCGCACCAAATGG
1 TCGCACCGCACCAAGTGG
*
44091 TCGCACCACACCAAGTGG
1 TCGCACCGCACCAAGTGG
*
44109 TCGCACCGCACCCAGTGG
1 TCGCACCGCACCAAGTGG
44127 TCGCACCGCACCAAGT
1 TCGCACCGCACCAAGT
44143 TGCCACACTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.25, C:0.41, G:0.22, T:0.12
Consensus pattern (18 bp):
TCGCACCGCACCAAGTGG
Done.