Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013339.1 Corchorus olitorius cultivar O-4 contig13372, 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: 39858
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:2132 original size:14 final size:14
Alignment explanation
Indices: 2113--2161 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
2103 AATGAAAAAT
2113 AATAAAATGGTAAA
1 AATAAAATGGTAAA
* * *
2127 AATAAACT-TTTAA
1 AATAAAATGGTAAA
*
2140 ATTAAAATGGTAAA
1 AATAAAATGGTAAA
2154 AATAAAAT
1 AATAAAAT
2162 AATTATAAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (14 bp):
AATAAAATGGTAAA
Found at i:2139 original size:151 final size:150
Alignment explanation
Indices: 1976--2255 Score: 470
Period size: 151 Copynumber: 1.9 Consensus size: 150
1966 GATCAATCAC
* * * *
1976 AATAACCTTTTAAATTGAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTCATTTAATA
1 AATAAACTTTTAAATTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATA
* * *
2041 AAAATAGATTTTTTAGTAGAATAAAACTGTATATTAAAATTTTTTAATATATCCAAGTTTTTAAT
66 AAAATAGAATTTTTAGTAGAATAAAAATGTATATTAAAA-ATTTTAATATATCCAAGTTTTTAAT
2106 GAAAAATAATAAAATGGTAAA
130 GAAAAATAATAAAATGGTAAA
* *
2127 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATA
2192 AAAATAGAATTTTTAGTAGAATAAAAATGTATATTAAAAATTTTAATATATCCAAGTTTTTAAT
66 AAAATAGAATTTTTAGTAGAATAAAAATGTATATTAAAAATTTTAATATATCCAAGTTTTTAAT
2256 AGAGTTTTTA
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
150 24 0.20
151 96 0.80
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (150 bp):
AATAAACTTTTAAATTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATA
AAAATAGAATTTTTAGTAGAATAAAAATGTATATTAAAAATTTTAATATATCCAAGTTTTTAATG
AAAAATAATAAAATGGTAAA
Found at i:4197 original size:28 final size:29
Alignment explanation
Indices: 4143--4220 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
4133 TACTCTTCAC
* * ** *
4143 AATAATTCCCCCTCTTTTTTGGGT-AAAT
1 AATAATCCCCCCTCTTTATTGCCTAAAAA
4171 AATAATCCCCCCTCTTTATTGCCTAAAAAA
1 AATAATCCCCCCTCTTTATTGCCT-AAAAA
*
4201 AAAAATCCCCCCTCTTTATT
1 AATAATCCCCCCTCTTTATT
4221 AAGGCCAATG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 20 0.48
30 22 0.52
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (29 bp):
AATAATCCCCCCTCTTTATTGCCTAAAAA
Found at i:9904 original size:328 final size:329
Alignment explanation
Indices: 9293--9944 Score: 1288
Period size: 328 Copynumber: 2.0 Consensus size: 329
9283 TTCACAAAAT
9293 ATTTTTAATTTAATTTTTTTTCGTAGAAAGCTTCCGGGGATGTTTTCAATTCAAATTAATTGTTT
1 ATTTTTAATTTAATTTTTTTTCGTAGAAAGCTTCCGGGGATGTTTTCAATTCAAATTAATTGTTT
9358 GTTAGAATATTCAATATATGCAGTACTATTCTTTTGCTTGTAAAAACTCGAATGTGACGAATGTC
66 GTTAGAATATTCAATATATGCAGTACTATTCTTTTGCTTGTAAAAACTCGAATGTGACGAATGTC
9423 GATGTTTCTCAAAGTTGGCACAGATCAATGTGCAAAGTTGAAATTGTATGTTTTAGGAGCCCAAA
131 GATGTTTCTCAAAGTTGGCACAGATCAATGTGCAAAGTTGAAATTGTATGTTTTAGGAGCCCAAA
*
9488 ACCAGCCAACCAAAGAAATTGACCAACTTTCCTAAAAAAAGAAAAAAGCAATTGACCAATTGGCC
196 ACCAGCCAACCAAAGAAATTGACCAACTTTCCTAAAAAAAGAAAAAAGCAATTGACCAACTGGCC
9553 CAAGAGCTATAAGTCCAAGCAACTAGCCCATATGGTTTATAGCTAATCAATAATTATTTAAGTGA
261 CAAGAGCTATAAGTCCAAGCAACTAGCCCATATGGTTTATAGCTAATCAATAATTATTTAAGTGA
9618 TACC
326 TACC
9622 ATTTTTAATTTAA-TTTTTTTCGTAGAAAGCTTCCGGGGATGTTTTCAATTCAAATTAATTGTTT
1 ATTTTTAATTTAATTTTTTTTCGTAGAAAGCTTCCGGGGATGTTTTCAATTCAAATTAATTGTTT
9686 GTTAGAATATTCAATATATGCAGTACTATTCTTTTGCTTGTAAAAACTCGAATGTGACGAATGTC
66 GTTAGAATATTCAATATATGCAGTACTATTCTTTTGCTTGTAAAAACTCGAATGTGACGAATGTC
9751 GATGTTTCTCAAAGTTGGCACAGATCAATGTGCAAAGTTGAAATTGTATGTTTTAGGAGCCCAAA
131 GATGTTTCTCAAAGTTGGCACAGATCAATGTGCAAAGTTGAAATTGTATGTTTTAGGAGCCCAAA
9816 ACCAGCCAACCAAAGAAATTGACCAACTTTCCTAAAAAAAGAAAAAAGCAATTGACCAACTGGCC
196 ACCAGCCAACCAAAGAAATTGACCAACTTTCCTAAAAAAAGAAAAAAGCAATTGACCAACTGGCC
9881 CAAGAGCTATAAGTCCAAGCAACTAGCCCATATGGTTTATAGCTAATCAATAATTATTTAAGTG
261 CAAGAGCTATAAGTCCAAGCAACTAGCCCATATGGTTTATAGCTAATCAATAATTATTTAAGTG
9945 CTTTCTTAAC
Statistics
Matches: 322, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
328 309 0.96
329 13 0.04
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (329 bp):
ATTTTTAATTTAATTTTTTTTCGTAGAAAGCTTCCGGGGATGTTTTCAATTCAAATTAATTGTTT
GTTAGAATATTCAATATATGCAGTACTATTCTTTTGCTTGTAAAAACTCGAATGTGACGAATGTC
GATGTTTCTCAAAGTTGGCACAGATCAATGTGCAAAGTTGAAATTGTATGTTTTAGGAGCCCAAA
ACCAGCCAACCAAAGAAATTGACCAACTTTCCTAAAAAAAGAAAAAAGCAATTGACCAACTGGCC
CAAGAGCTATAAGTCCAAGCAACTAGCCCATATGGTTTATAGCTAATCAATAATTATTTAAGTGA
TACC
Found at i:11859 original size:30 final size:31
Alignment explanation
Indices: 11823--11884 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 31
11813 CACTCAGTTA
11823 TCTGATA-CTATTTCATTGACAGGTGGCCCT
1 TCTGATACCTATTTCATTGACAGGTGGCCCT
*
11853 TCTGATACTCCTTTTTCATTGACAGGTGGCCC
1 TCTGATA--CCTATTTCATTGACAGGTGGCCC
11885 CTTATTAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.25
33 21 0.75
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (31 bp):
TCTGATACCTATTTCATTGACAGGTGGCCCT
Found at i:20921 original size:18 final size:19
Alignment explanation
Indices: 20893--20929 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
20883 CTTCATCTAT
20893 TTTTCTCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
20912 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
20930 ACTAGGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:24492 original size:17 final size:18
Alignment explanation
Indices: 24457--24492 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24447 CTACTCTATC
*
24457 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
24475 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
24492 A
1 A
24493 ATTACCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:35617 original size:72 final size:72
Alignment explanation
Indices: 35500--35637 Score: 231
Period size: 72 Copynumber: 1.9 Consensus size: 72
35490 CATCCTGCAG
* *
35500 GATATCCAATGATCTCATAGCACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCGCACCTT
1 GATATCCAATGATCTCATAACACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCTT
35565 GCAGCAT
66 GCAGCAT
* * *
35572 GATATCCAATGATCTCATAACATTGATCTTTCGTGTGCCCCATCTTTTGACAATGTTCACACCTT
1 GATATCCAATGATCTCATAACACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCTT
35637 G
66 G
35638 GCTTGTCTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (72 bp):
GATATCCAATGATCTCATAACACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCTT
GCAGCAT
Found at i:36860 original size:2 final size:2
Alignment explanation
Indices: 36853--36881 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36843 ATTCACATGC
36853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36882 AGGAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.