Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017076.1 Corchorus olitorius cultivar O-4 contig17109, 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: 8062
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:4967 original size:7 final size:8
Alignment explanation
Indices: 4943--4967 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4933 AAAAAAGATG
4943 AAATGAAA
1 AAATGAAA
4951 AAATGAAA
1 AAATGAAA
4959 AAATGAAA
1 AAATGAAA
4967 A
1 A
4968 TAAAGGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:5391 original size:13 final size:13
Alignment explanation
Indices: 5375--5445 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 13
5365 AAAAGGAAAG
5375 AAAAAATCAAATC
1 AAAAAATCAAATC
5388 AAAAAATCAAATC
1 AAAAAATCAAATC
5401 AAGGTCAAAATCAATAGT-
1 AA----AAAATCAA-A-TC
*
5419 AAAAAA-AAAATC
1 AAAAAATCAAATC
5431 -AAAAATCAAATC
1 AAAAAATCAAATC
5443 AAA
1 AAA
5446 TCAAAATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
11 6 0.13
12 6 0.13
13 19 0.40
14 4 0.09
17 8 0.17
18 3 0.06
19 1 0.02
ACGTcount: A:0.68, C:0.13, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAAATCAAATC
Found at i:6179 original size:50 final size:50
Alignment explanation
Indices: 6085--6210 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 50
6075 ATTTGTGAGC
* *
6085 CCAAGATTAAAATTCGCTTTTCAAAGTAAAATTGCTTCCCATTTGCAAGT
1 CCAAGATCAAAATTCGCTTTTCAAAGTAAAATGGCTTCCCATTTGCAAGT
* ** * **
6135 TCAAGATCAAAATTCGCTTTTCAAAGTAGGATGGCATT-CTATTTGTGAGT
1 CCAAGATCAAAATTCGCTTTTCAAAGTAAAATGGC-TTCCCATTTGCAAGT
*
6185 CCAAGATCAAAATTCGCATTTCAAAG
1 CCAAGATCAAAATTCGCTTTTCAAAG
6211 GACAGTGAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 63 0.97
51 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (50 bp):
CCAAGATCAAAATTCGCTTTTCAAAGTAAAATGGCTTCCCATTTGCAAGT
Found at i:6924 original size:50 final size:50
Alignment explanation
Indices: 6867--7155 Score: 416
Period size: 50 Copynumber: 5.8 Consensus size: 50
6857 CGAATGCTTT
* * * * **
6867 GGCTTTTCCATAAGTCGAACTCGTTTGCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
*
6917 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
* * *
6967 GGCTTTTCCACAAGTCGAACTCGTTTCCATACGAGTCAATTGTCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
*
7017 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTGTCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
* *
7067 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTACCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
* * * * *
7117 GGCTTTTCCATAAGTCAAACCCGCTTCCATATGAGTCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAA
7156 GCCTTACTTT
Statistics
Matches: 220, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 220 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
Found at i:7517 original size:27 final size:28
Alignment explanation
Indices: 7480--7560 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
7470 CAAAATCCAA
7480 GGGCATTTTGGTCATTTTTACA-TTCAG
1 GGGCATTTTGGTCATTTTTACAGTTCAG
* *
7507 GGGCATTTTGGTCA-TTTTGCATGTTCGG
1 GGGCATTTTGGTCATTTTTACA-GTTCAG
7535 GGAGCATTTTGGTCA-TTTTA-AGTTCA
1 GG-GCATTTTGGTCATTTTTACAGTTCA
7561 CTGTTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.13
27 18 0.38
28 7 0.15
29 16 0.34
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTTACAGTTCAG
Found at i:7551 original size:29 final size:26
Alignment explanation
Indices: 7480--7554 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 26
7470 CAAAATCCAA
7480 GGGCATTTTGGTCATTTTTACATTCAG
1 GGGCATTTTGGTCA-TTTTACATTCAG
* *
7507 GGGCATTTTGGTCATTTTGCATGTTCGG
1 GGGCATTTTGGTCATTTTACA--TTCAG
7535 GGAGCATTTTGGTCATTTTA
1 GG-GCATTTTGGTCATTTTA
7555 AGTTCACTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 6 0.14
27 14 0.33
28 6 0.14
29 16 0.38
ACGTcount: A:0.16, C:0.13, G:0.27, T:0.44
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTTACATTCAG
Done.