Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018397.1 Corchorus olitorius cultivar O-4 contig18430, 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: 9264
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Found at i:1612 original size:31 final size:31
Alignment explanation
Indices: 1585--1669 Score: 138
Period size: 30 Copynumber: 2.8 Consensus size: 31
1575 GTAATTTGTT
1585 GAACTTTTTCTTGGGTTATTTTAAATTTATG
1 GAACTTTTTCTTGGGTTATTTTAAATTTATG
1616 GAACTTTTTCTTGGG-TATTTTAAATTTATG
1 GAACTTTTTCTTGGGTTATTTTAAATTTATG
*
1646 GAA-TTGTTTCTTGGGTTGTTTTAA
1 GAACTT-TTTCTTGGGTTATTTTAA
1670 TTTCTAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
29 2 0.04
30 27 0.53
31 22 0.43
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.54
Consensus pattern (31 bp):
GAACTTTTTCTTGGGTTATTTTAAATTTATG
Found at i:1672 original size:30 final size:29
Alignment explanation
Indices: 1576--1672 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 29
1566 GGTTACAATG
* *
1576 TAATTTGTTGAACTTTTTCTTGGGTTATTT
1 TAATTTATGGAACTTTTTCTTGGGTT-TTT
1606 TAAATTTATGGAACTTTTTCTTGGGTATTTT
1 T-AATTTATGGAACTTTTTCTTGGGT-TTTT
*
1637 AAATTTATGGAA-TTGTTTCTTGGGTTGTTT
1 TAATTTATGGAACTT-TTTCTTGGGTT-TTT
1667 TAATTT
1 TAATTT
1673 CTAAAAAAGG
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.05
30 30 0.51
31 25 0.42
32 1 0.02
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.57
Consensus pattern (29 bp):
TAATTTATGGAACTTTTTCTTGGGTTTTT
Found at i:1818 original size:21 final size:21
Alignment explanation
Indices: 1780--1819 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1770 TATAATTTAT
*
1780 ATTCATTTTCATTCCATATTC
1 ATTCATTTTCATTACATATTC
1801 ATTCATTTT-ATTTACATAT
1 ATTCATTTTCA-TTACATAT
1820 ATATATTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTCATTTTCATTACATATTC
Found at i:5321 original size:26 final size:26
Alignment explanation
Indices: 5292--5370 Score: 61
Period size: 26 Copynumber: 3.1 Consensus size: 26
5282 GAAAAATAAA
*
5292 GGTTTGAGTTGAAAACCTGAAAGGGC
1 GGTTTGAGTTGAAAACCAGAAAGGGC
** ** * ** *
5318 GGTTCAAACTAAAAAAAAAAAAGGG-
1 GGTTTGAGTTGAAAACCAGAAAGGGC
*
5343 GGTTTGAGTTGAAAACCCGAAAGGGC
1 GGTTTGAGTTGAAAACCAGAAAGGGC
5369 GG
1 GG
5371 CTCAAACTAC
Statistics
Matches: 34, Mismatches: 18, Indels: 2
0.63 0.33 0.04
Matches are distributed among these distances:
25 16 0.47
26 18 0.53
ACGTcount: A:0.39, C:0.11, G:0.32, T:0.18
Consensus pattern (26 bp):
GGTTTGAGTTGAAAACCAGAAAGGGC
Found at i:5411 original size:54 final size:54
Alignment explanation
Indices: 5291--5498 Score: 323
Period size: 54 Copynumber: 3.9 Consensus size: 54
5281 GGAAAAATAA
* * *
5291 AGGTTTGAGTTGAAAACCTGAAAGGGCGGTTCAAACTA--AAAAAAAAAAAG-G
1 AGGTTTGAGTTGAAAACCCGAAAGGGCGGCTCAAACTACCAAAAAAAAAGAGAG
* *
5342 GGGTTTGAGTTGAAAACCCGAAAGGGCGGCTCAAACTACCCAAAAAAAAGAGAG
1 AGGTTTGAGTTGAAAACCCGAAAGGGCGGCTCAAACTACCAAAAAAAAAGAGAG
*
5396 AGGTTTGAGTTGAAAACCCGAAAGAGCGGCTCAAACTACCAAAAAAAAAGAGAG
1 AGGTTTGAGTTGAAAACCCGAAAGGGCGGCTCAAACTACCAAAAAAAAAGAGAG
**
5450 AGGTTTGAGTTGAAAACCCGAAAGGGCGGCTCAAACTAAAAAAAAAAAA
1 AGGTTTGAGTTGAAAACCCGAAAGGGCGGCTCAAACTACCAAAAAAAAA
5499 AGAAAGGGTG
Statistics
Matches: 143, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
51 35 0.24
53 10 0.07
54 98 0.69
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.14
Consensus pattern (54 bp):
AGGTTTGAGTTGAAAACCCGAAAGGGCGGCTCAAACTACCAAAAAAAAAGAGAG
Found at i:6085 original size:13 final size:13
Alignment explanation
Indices: 6067--6093 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6057 AACTATTCAT
6067 TGAAGTGGGGCAA
1 TGAAGTGGGGCAA
6080 TGAAGTGGGGCAA
1 TGAAGTGGGGCAA
6093 T
1 T
6094 CATGGATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.44, T:0.19
Consensus pattern (13 bp):
TGAAGTGGGGCAA
Found at i:6666 original size:17 final size:17
Alignment explanation
Indices: 6644--6683 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6634 AAGGGTTATA
6644 AGGGTTCATTAA-ATTTC
1 AGGGTTCATTAAGA-TTC
*
6661 AGGGTTCTTTAAGATTC
1 AGGGTTCATTAAGATTC
6678 AGGGTT
1 AGGGTT
6684 ATCTGGGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (17 bp):
AGGGTTCATTAAGATTC
Found at i:6749 original size:23 final size:24
Alignment explanation
Indices: 6720--6765 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6710 GGGTTATAAT
6720 GGTTCTTT-A-ATTTCTGGGTTATG
1 GGTTCTTTAAGATTT-TGGGTTATG
6743 GGTTCTTTAAGATTTTGGGTTAT
1 GGTTCTTTAAGATTTTGGGTTAT
6766 TTGGGTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 9 0.43
25 4 0.19
ACGTcount: A:0.15, C:0.07, G:0.26, T:0.52
Consensus pattern (24 bp):
GGTTCTTTAAGATTTTGGGTTATG
Done.