Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016236.1 Corchorus olitorius cultivar O-4 contig16269, 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: 26224
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1926 original size:63 final size:64
Alignment explanation
Indices: 1848--1980 Score: 243
Period size: 63 Copynumber: 2.1 Consensus size: 64
1838 ACTCCCTATT
*
1848 AAACT-CAACACACAAAACTACCCTTCCTGGAGAGCCCAGTTTAACTCTCTTTTGCTTGGTCAC
1 AAACTCCAACACACAAAACTACCCTTCCTGGAGAGCCCAGATTAACTCTCTTTTGCTTGGTCAC
1911 AAACTCCAA-ACACAAAACTACCCTTCCTGGAGAGCCCAGATTAACTCTCTTTTGCTTGGTCAC
1 AAACTCCAACACACAAAACTACCCTTCCTGGAGAGCCCAGATTAACTCTCTTTTGCTTGGTCAC
1974 AAACTCC
1 AAACTCC
1981 TTGGATTTGT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
63 65 0.96
64 3 0.04
ACGTcount: A:0.30, C:0.32, G:0.12, T:0.26
Consensus pattern (64 bp):
AAACTCCAACACACAAAACTACCCTTCCTGGAGAGCCCAGATTAACTCTCTTTTGCTTGGTCAC
Found at i:9141 original size:19 final size:20
Alignment explanation
Indices: 9117--9177 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 20
9107 TACTGTGCTT
9117 TGTTTTGCTGTGTCTGTT-A
1 TGTTTTGCTGTGTCTGTTGA
* *
9136 TGTTTTGCTTGCGTCTGTTGT
1 TGTTTTGC-TGTGTCTGTTGA
9157 TGCGTTTTGCTGTGTCTGTTG
1 T--GTTTTGCTGTGTCTGTTG
9178 TTAGGTGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 8 0.23
20 9 0.26
21 1 0.03
22 10 0.29
23 7 0.20
ACGTcount: A:0.02, C:0.13, G:0.30, T:0.56
Consensus pattern (20 bp):
TGTTTTGCTGTGTCTGTTGA
Found at i:9153 original size:20 final size:19
Alignment explanation
Indices: 9117--9154 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
9107 TACTGTGCTT
*
9117 TGTTTTGCTGTGTCTGTTA
1 TGTTTTGCTGCGTCTGTTA
9136 TGTTTTGCTTGCGTCTGTT
1 TGTTTTGC-TGCGTCTGTT
9155 GTTGCGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (19 bp):
TGTTTTGCTGCGTCTGTTA
Found at i:9811 original size:27 final size:27
Alignment explanation
Indices: 9754--9811 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
9744 TTATCCATCT
**
9754 AAAAAGGAAAATTGTTACATAAAATGT
1 AAAAAGGAAAATTGTTACATAAAATCA
9781 AAAAAGGAAAATTGTTACATAAGAA-CA
1 AAAAAGGAAAATTGTTACATAA-AATCA
9808 AAAA
1 AAAA
9812 CAACTTACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (27 bp):
AAAAAGGAAAATTGTTACATAAAATCA
Found at i:10093 original size:2 final size:2
Alignment explanation
Indices: 10086--10117 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10076 TCGATCTTAA
10086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10118 TCATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12290 original size:117 final size:126
Alignment explanation
Indices: 12124--12369 Score: 357
Period size: 117 Copynumber: 2.0 Consensus size: 126
12114 ATTGTTTAAA
* *
12124 CTTTTATAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAAT-ATC-T-TTA-T
1 CTTTTACAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATTACT
12185 A-A-TTTTACCATTTTACTA-TTTAATT-AAAACTTATATATATTAGAATTTTTAAATATG
66 ATATTTTTACCATTTTACTATTTTAATTAAAAACTTATATATATTAGAATTTTTAAATATG
*
12242 CTTTTACAGTTTTACTCAACT-AAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATTACC
1 CTTTTACAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATTA-C
*
12306 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAACTTATATATATTAGAATTTTTAAATAT
65 TA---TATTTTTACCATTTTACTATTTTAATTAAAAACTTATATATATTAGAATTTTTAAATAT
12370 ATTTCTTAAA
Statistics
Matches: 112, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
117 31 0.28
118 21 0.19
119 1 0.01
120 3 0.03
122 2 0.02
126 1 0.01
127 16 0.14
128 6 0.05
129 31 0.28
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (126 bp):
CTTTTACAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATTACT
ATATTTTTACCATTTTACTATTTTAATTAAAAACTTATATATATTAGAATTTTTAAATATG
Found at i:12552 original size:82 final size:83
Alignment explanation
Indices: 12408--12572 Score: 280
Period size: 82 Copynumber: 2.0 Consensus size: 83
12398 CAATTTTTTA
* *
12408 GAAATAAACTTTTACAGTTATTCTACTAAAAAATCTATTTTTATTTAATTAAATTCAATATTATT
1 GAAATAAACTTTTACAATTATTCTACTAAAAAATATATTTTTATTTAATTAAATTCAATATTATT
12473 ATAAATATTTTATTTTACC
66 ATAAATA-TTTATTTTACC
12492 GAAATAAACTTTTACAATTATTCTACT-AAAAATATA-TTTTATTTAATTAAATTCAATATTATT
1 GAAATAAACTTTTACAATTATTCTACTAAAAAATATATTTTTATTTAATTAAATTCAATATTATT
*
12555 ATAACTATTTATTTTACC
66 ATAAATATTTATTTTACC
12573 ATTTTAATTT
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
81 11 0.14
82 33 0.42
83 8 0.10
84 26 0.33
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (83 bp):
GAAATAAACTTTTACAATTATTCTACTAAAAAATATATTTTTATTTAATTAAATTCAATATTATT
ATAAATATTTATTTTACC
Found at i:15022 original size:10 final size:10
Alignment explanation
Indices: 15004--15069 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
14994 TAGTTCAATT
*
15004 GGGGAGGGGA
1 GGGGTGGGGA
*
15014 GGGGTGGGGT
1 GGGGTGGGGA
15024 GGGGTGGGGA
1 GGGGTGGGGA
* *
15034 TGGGTGGGGT
1 GGGGTGGGGA
15044 GGGGT-GGGA
1 GGGGTGGGGA
*
15053 TGGGGAGGGGTA
1 -GGGGTGGGG-A
15065 GGGGT
1 GGGGT
15070 AGGGTTTGGG
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
9 3 0.07
10 33 0.75
11 7 0.16
12 1 0.02
ACGTcount: A:0.09, C:0.00, G:0.76, T:0.15
Consensus pattern (10 bp):
GGGGTGGGGA
Found at i:15032 original size:20 final size:20
Alignment explanation
Indices: 15003--15069 Score: 82
Period size: 20 Copynumber: 3.3 Consensus size: 20
14993 TTAGTTCAAT
*
15003 TGGGGAGGGGAGGGGTGGGG
1 TGGGGTGGGGAGGGGTGGGG
*
15023 TGGGGTGGGGATGGGTGGGG
1 TGGGGTGGGGAGGGGTGGGG
*
15043 TGGGGT-GGGATGGGGAGGGG
1 TGGGGTGGGGA-GGGGTGGGG
15063 TAGGGGT
1 T-GGGGT
15070 AGGGTTTGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
19 4 0.10
20 32 0.78
21 5 0.12
ACGTcount: A:0.09, C:0.00, G:0.75, T:0.16
Consensus pattern (20 bp):
TGGGGTGGGGAGGGGTGGGG
Found at i:25886 original size:17 final size:17
Alignment explanation
Indices: 25854--25888 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25844 ATAATTATAT
* *
25854 TATTAATAATTTAGAAA
1 TATTAATAAATCAGAAA
25871 TATTAATAAATCAGAAA
1 TATTAATAAATCAGAAA
25888 T
1 T
25889 TATAAAAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (17 bp):
TATTAATAAATCAGAAA
Done.