Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009839.1 Corchorus olitorius cultivar O-4 contig09871, 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: 8779
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:5755 original size:13 final size:13
Alignment explanation
Indices: 5737--5776 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 13
5727 AAGAGAATAA
5737 AAAAAAATCAATC
1 AAAAAAATCAATC
5750 AAAAAAATCAAATC
1 AAAAAAATC-AATC
5764 AAATCAAAATCAA
1 AAA--AAAATCAA
5777 AAGAGAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.38
14 7 0.29
15 2 0.08
16 6 0.25
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAAATCAATC
Found at i:6400 original size:48 final size:48
Alignment explanation
Indices: 6339--6492 Score: 209
Period size: 48 Copynumber: 3.1 Consensus size: 48
6329 GAACAAGAAG
* *
6339 TTTTACAATAAAATTGCTTTCCATTTATGAGTTCAAGGTCAAAATTCGC
1 TTTT-CAATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
* * *
6388 TTTTCAATAAAATTGCTTTCCATTCGTGAGTTCAATATCAAAATTTGC
1 TTTTCAATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
* * *
6436 TTTTCAAAGTAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
1 TTTTC-AA-TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
6486 TTTTCAA
1 TTTTCAA
6493 AGGACATTGA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
48 44 0.48
49 8 0.09
50 40 0.43
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (48 bp):
TTTTCAATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
Found at i:6478 original size:50 final size:50
Alignment explanation
Indices: 6347--6494 Score: 210
Period size: 50 Copynumber: 3.0 Consensus size: 50
6337 AGTTTTACAA
* *
6347 TAAAATTGCTTTCCATTTATGAGTTCAAGGTCAAAATTCGCTTTTC-AA-
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * *
6395 TAAAATTGCTTTCCATTCGTGAGTTCAATATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * *
6445 TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
6495 GACATTGAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
48 41 0.47
49 2 0.02
50 44 0.51
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:7078 original size:91 final size:91
Alignment explanation
Indices: 6918--7121 Score: 327
Period size: 91 Copynumber: 2.2 Consensus size: 91
6908 TCATAACGTT
* *
6918 AGACTCAGAGTTATTTTTCAAGTTGTTTGTCAAGTTGACTGCAAATTGGTCCTCTTTCATCATCG
1 AGACTCAGAGTTATTTTTCAAGTTGTTTGTCAAGTTGACCGCAAATTGGTCCTCTTTCATCATCA
6983 ATCAAGAAGTTTTCAGTTACAACATC
66 ATCAAGAAGTTTTCAGTTACAACATC
* * *
7009 AGACTCAGAGTTATTTTTCAAGTTGTTTTTCAAGTTGACCGCACATTGGTCCTTTTTCATCATCA
1 AGACTCAGAGTTATTTTTCAAGTTGTTTGTCAAGTTGACCGCAAATTGGTCCTCTTTCATCATCA
7074 ATCAAGAAGTTTTCAGTTACAACATC
66 ATCAAGAAGTTTTCAGTTACAACATC
* * * *
7100 ATATTCAGAATTATTTTCCAAG
1 AGACTCAGAGTTATTTTTCAAG
7122 GTATTTTCTT
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 104 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (91 bp):
AGACTCAGAGTTATTTTTCAAGTTGTTTGTCAAGTTGACCGCAAATTGGTCCTCTTTCATCATCA
ATCAAGAAGTTTTCAGTTACAACATC
Found at i:7275 original size:50 final size:50
Alignment explanation
Indices: 7200--7385 Score: 302
Period size: 50 Copynumber: 3.7 Consensus size: 50
7190 CGAATGCTTT
* * * *
7200 GGCTTTTCCATAAGCCGAACTCGTTTCCATACGAGTCAATTCTCACCACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
7250 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
7300 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA-A
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* *
7349 GGGCTTTTCCACAAGCCGAACTCGTTTCCATGCGAGT
1 -GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGT
7386 TATTTCAAAC
Statistics
Matches: 129, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
49 1 0.01
50 128 0.99
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
Found at i:7620 original size:100 final size:100
Alignment explanation
Indices: 7447--7677 Score: 365
Period size: 100 Copynumber: 2.3 Consensus size: 100
7437 TACCTTTTTT
* **
7447 TTTTAAGATTAGATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAGATTGAATT
1 TTTTAAGATTAGATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTCAAGATTGAATT
7512 GGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
66 GGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
7547 TTTTAAGATT-GAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTCAAGATTGAAT
1 TTTTAAGATTAG-ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTCAAGATTGAAT
**
7611 TGGTAGACAGTTCAAAGGATAAGCGGAAGATGGTCC
65 TGGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
* * * *
7647 TTTTAATATTAGTTTGGAAGACAATTCAAAG
1 TTTTAAGATTAGATTGGTAGACAGTTCAAAG
7678 AAGTTGAATC
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
99 1 0.01
100 118 0.98
101 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (100 bp):
TTTTAAGATTAGATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTCAAGATTGAATT
GGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
Found at i:7677 original size:50 final size:50
Alignment explanation
Indices: 7447--7652 Score: 351
Period size: 50 Copynumber: 4.1 Consensus size: 50
7437 TACCTTTTTT
7447 TTTTAAGATT-AGATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGA-ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
7497 TTTTTAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
7547 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
7597 TTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGATGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
7647 TTTTAA
1 TTTTAA
7653 TATTAGTTTG
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
50 145 0.99
51 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:7997 original size:27 final size:27
Alignment explanation
Indices: 7952--8095 Score: 132
Period size: 27 Copynumber: 5.3 Consensus size: 27
7942 AATGTTTTGG
* *
7952 GGTCATTTGCACGTCCAGGGGCATTTT
1 GGTCATTTACACATCCAGGGGCATTTT
* * *
7979 AGTCATTTACACATTCAGGGGCATCTT
1 GGTCATTTACACATCCAGGGGCATTTT
*
8006 GGTCATTCTTACAC-T--AAGGGCATTTT
1 GGTCA-T-TTACACATCCAGGGGCATTTT
* *
8032 GGTCATTTGCATATCCAGGGGCATTTT
1 GGTCATTTACACATCCAGGGGCATTTT
* * *
8059 GGTCATTTTAAAAAATCCAGGGGCATTTC
1 GGTCA-TTT-ACACATCCAGGGGCATTTT
8088 GGTCATTT
1 GGTCATTT
8096 TAAGTTCACT
Statistics
Matches: 95, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
24 4 0.04
25 2 0.02
26 14 0.15
27 41 0.43
28 8 0.08
29 26 0.27
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (27 bp):
GGTCATTTACACATCCAGGGGCATTTT
Found at i:8086 original size:29 final size:29
Alignment explanation
Indices: 8023--8098 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
8013 CTTACACTAA
** *
8023 GGGCATTTTGGTCA-TTT-GCATATCCAG
1 GGGCATTTTGGTCATTTTAAAAAATCCAG
8050 GGGCATTTTGGTCATTTTAAAAAATCCAG
1 GGGCATTTTGGTCATTTTAAAAAATCCAG
*
8079 GGGCATTTCGGTCATTTTAA
1 GGGCATTTTGGTCATTTTAA
8099 GTTCACTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.33
28 3 0.07
29 26 0.60
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTAAAAAATCCAG
Done.