Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021981.1 Corchorus olitorius cultivar O-4 contig22014, 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: 7017
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Found at i:1463 original size:15 final size:15
Alignment explanation
Indices: 1443--1479 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1433 CAAGGGACGT
**
1443 TTTTCAAGAAAATTG
1 TTTTCAAGAAAAAGG
1458 TTTTCAAGAAAAAGG
1 TTTTCAAGAAAAAGG
1473 TTTTCAA
1 TTTTCAA
1480 AAATGAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (15 bp):
TTTTCAAGAAAAAGG
Found at i:3851 original size:50 final size:49
Alignment explanation
Indices: 3747--4066 Score: 514
Period size: 50 Copynumber: 6.5 Consensus size: 49
3737 GGAAAGTAAT
3747 ATTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACA
1 ATTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACA
*
3796 ATTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACA
1 ATTCAAAGGATAAGCGGAAGACGGTCC-TTTAAGATAGAATTGGAAGACA
* *
3846 GTTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGAGA
1 ATTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACA
* *
3895 ATTCAAAGGATAAGCGAAAGACGGTCCTTTAAGATAGAATTGGCAGACA
1 ATTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACA
*
3944 ATTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACA
1 ATTCAAAGGATAAGCGGAAGACGGTCC-TTTAAGATAGAATTGGAAGACA
* * * *
3994 GTTCAAAGGATAAGCGGAAGGCGGTCCTTTTGAGATTGAATTGGAAGACA
1 ATTCAAAGGATAAGCGGAAGACGGTCC-TTTAAGATAGAATTGGAAGACA
*
4044 GTTCAAAGGATAAGCGGAAGACG
1 ATTCAAAGGATAAGCGGAAGACG
4067 ACTCTTTAAT
Statistics
Matches: 254, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
49 118 0.46
50 136 0.54
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (49 bp):
ATTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACA
Found at i:4019 original size:148 final size:149
Alignment explanation
Indices: 3747--4066 Score: 570
Period size: 148 Copynumber: 2.2 Consensus size: 149
3737 GGAAAGTAAT
3747 ATTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACAATTCAAAGGATAAGCG
1 ATTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACAATTCAAAGGATAAGCG
3812 GAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTT
66 GAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
*
3876 AAGATAGAATTGGAAGAGA
131 AAGATAGAATTGGAAGACA
* *
3895 ATTCAAAGGATAAGCGAAAGACGGTCCTTTAAGATAGAATTGGCAGACAATTCAAAGGATAAGCG
1 ATTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACAATTCAAAGGATAAGCG
*
3960 GAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGGCGGTCCTTTT
66 GAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* *
4025 GAGATTGAATTGGAAGACA
131 AAGATAGAATTGGAAGACA
*
4044 GTTCAAAGGATAAGCGGAAGACG
1 ATTCAAAGGATAAGCGGAAGACG
4067 ACTCTTTAAT
Statistics
Matches: 163, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
148 123 0.75
149 40 0.25
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (149 bp):
ATTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACAATTCAAAGGATAAGCG
GAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
AAGATAGAATTGGAAGACA
Found at i:4098 original size:99 final size:99
Alignment explanation
Indices: 3748--4066 Score: 541
Period size: 99 Copynumber: 3.2 Consensus size: 99
3738 GAAAGTAATA
3748 TTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACAATTCAAAGGATAAGCGG
1 TTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACAATTCAAAGGATAAGCGG
3813 AAGACGGTCCTTTTAAGATTGAATTGGAAGACAG
66 AAGACGGTCCTTTTAAGATTGAATTGGAAGACAG
* *
3847 TTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGAGAATTCAAAGGATAAGCGA
1 TTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACAATTCAAAGGATAAGCGG
* * *
3912 AAGACGGTCC-TTTAAGATAGAATTGGCAGACAA
66 AAGACGGTCCTTTTAAGATTGAATTGGAAGACAG
* *
3945 TTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCG
1 TTCAAAGGATAAGCGGAAGACGGTCC-TTTAAGATAGAATTGGAAGACAATTCAAAGGATAAGCG
* *
4010 GAAGGCGGTCCTTTTGAGATTGAATTGGAAGACAG
65 GAAGACGGTCCTTTTAAGATTGAATTGGAAGACAG
4045 TTCAAAGGATAAGCGGAAGACG
1 TTCAAAGGATAAGCGGAAGACG
4067 ACTCTTTAAT
Statistics
Matches: 204, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
98 46 0.23
99 117 0.57
100 41 0.20
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (99 bp):
TTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATAGAATTGGAAGACAATTCAAAGGATAAGCGG
AAGACGGTCCTTTTAAGATTGAATTGGAAGACAG
Found at i:4407 original size:27 final size:27
Alignment explanation
Indices: 4342--4415 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 27
4332 AGGGTTATCC
* * *
4342 AGGGGCATTTTGGTCATTTGCACGTCT
1 AGGGGTATTTTGGTCATTTTCACATCT
* *
4369 -GGGGTATTTTGGTCATTTTTACATTT
1 AGGGGTATTTTGGTCATTTTCACATCT
*
4395 AGGGGTATTTTGGTCCTTTTC
1 AGGGGTATTTTGGTCATTTTC
4416 GTAGTTGATA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.14, C:0.14, G:0.27, T:0.46
Consensus pattern (27 bp):
AGGGGTATTTTGGTCATTTTCACATCT
Found at i:6955 original size:17 final size:17
Alignment explanation
Indices: 6908--6951 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
6898 GGGTTAGGGG
6908 AGAAGAGAAAATG-A-GA
1 AGAAGAGAAAA-GAAGGA
6924 AGAAGAGAAAAGAAGGA
1 AGAAGAGAAAAGAAGGA
6941 AGAAGA-AAAAG
1 AGAAGAGAAAAG
6952 GAAGATGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.04
16 17 0.65
17 8 0.31
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (17 bp):
AGAAGAGAAAAGAAGGA
Done.