Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016151.1 Corchorus olitorius cultivar O-4 contig16184, 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: 6926
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:3560 original size:8 final size:8
Alignment explanation
Indices: 3521--3551 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
3511 TCCCAATAAT
3521 AAAAAATTG
1 AAAAAA-TG
3530 AAAAAATG
1 AAAAAATG
3538 AAAAAATG
1 AAAAAATG
3546 AAAAAA
1 AAAAAA
3552 AAAGGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (8 bp):
AAAAAATG
Found at i:3955 original size:21 final size:20
Alignment explanation
Indices: 3929--3969 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
3919 TCCACTCCAT
3929 AAAGAAATTCAAAAGAAAAAA
1 AAAGAAATTCAAAA-AAAAAA
3950 AAAGAAATTCAAAAAAAAAA
1 AAAGAAATTCAAAAAAAAAA
3970 TCAAATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAGAAATTCAAAAAAAAAA
Found at i:3989 original size:26 final size:26
Alignment explanation
Indices: 3961--4010 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3951 AAGAAATTCA
*
3961 AAAAAAAAATC-AAATCAAAGTCAAT
1 AAAAAAAAATCAAAATCAAAATCAAT
3986 AAAAAAAAATCAAAATCAAAATCAA
1 AAAAAAAAATCAAAATCAAAATCAA
4011 AAGAGAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.72, C:0.12, G:0.02, T:0.14
Consensus pattern (26 bp):
AAAAAAAAATCAAAATCAAAATCAAT
Found at i:4784 original size:50 final size:50
Alignment explanation
Indices: 4587--4773 Score: 268
Period size: 50 Copynumber: 3.7 Consensus size: 50
4577 GAAGATTTAC
* *
4587 AATAAGATTGCATTCTATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* * * *
4637 AGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
*
4687 AACGAA-ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
1 AA-TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* * *
4737 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAA
4774 GGTCGATTTT
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 2 0.02
50 117 0.97
51 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
Found at i:5434 original size:50 final size:50
Alignment explanation
Indices: 5375--6118 Score: 1213
Period size: 50 Copynumber: 14.8 Consensus size: 50
5365 CGAATGCTTT
* * *
5375 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
5425 GGCTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
5475 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
5525 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
5575 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC-CTA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC-A
5625 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
5675 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
5725 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
5775 GGCTTTTCCACAAGCCAAACTCTTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* *
5825 GGTTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
5875 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAAC-CTA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC-A
* *
5925 GGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* * * *
5975 GGCTTTTCCACAAGCCAAACTCGCTTCCATACGAGTCGATTATGAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* * *
6025 GGCTTTTCCACAAGCCAAACTCGTTTCCGTACGAGTCAACTATCCAAGCCATATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAT-CAA--C--ACA
* * * * *
6080 GACTTTTCCATAAGTCAAACACGTTTCCATATGAGTCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAA
6119 GCCTTACGTC
Statistics
Matches: 657, Mismatches: 28, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
49 2 0.00
50 615 0.94
51 3 0.00
53 1 0.00
55 36 0.05
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
Found at i:6487 original size:29 final size:28
Alignment explanation
Indices: 6443--6635 Score: 219
Period size: 29 Copynumber: 6.8 Consensus size: 28
6433 AAAAAAAAAC
6443 CAGGGGCATTTTGGTCATTTTTCACATT
1 CAGGGGCATTTTGGTCATTTTTCACATT
*
6471 CAGGGGGCATTTTGGTCATTTCTGCACATT
1 CA-GGGGCATTTTGGTCATTT-TTCACATT
* * *
6501 CAGTGGCATTTTGGTCATTTCTGCACACT
1 CAGGGGCATTTTGGTCATTT-TTCACATT
* * *
6530 CAGGGACATTGTGGTCA-TTTTCGTATATT
1 CAGGGGCATTTTGGTCATTTTTC--ACATT
* * *
6559 CAAGGGCATTTTGGTCATTTTTTTACATG
1 CAGGGGCATTTTGGTCA-TTTTTCACATT
*
6588 CAGGGGCATTTTGGTCAGTTTT-ACATT
1 CAGGGGCATTTTGGTCATTTTTCACATT
6615 CAGGGGCATTTTGGTCATTTT
1 CAGGGGCATTTTGGTCATTTT
6636 AAGTTCACAT
Statistics
Matches: 140, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
27 26 0.19
28 8 0.06
29 93 0.66
30 9 0.06
31 4 0.03
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (28 bp):
CAGGGGCATTTTGGTCATTTTTCACATT
Done.