Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010194.1 Corchorus olitorius cultivar O-4 contig10226, 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: 10895
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1005 original size:30 final size:31
Alignment explanation
Indices: 941--1021 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 31
931 TTTTAGTTCT
*
941 AAACTTCTAATAGTTCTGCTGTCAAAAAAAAAAAA
1 AAACTTCTAATAGTTCTGATGTC----AAAAAAAA
976 AAACTTCTAATAGTTCTGATGTC-AAAAAAA
1 AAACTTCTAATAGTTCTGATGTCAAAAAAAA
**
1006 AGGCTTCTAATAGTTC
1 AAACTTCTAATAGTTC
1022 CTACCAAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 21 0.49
35 22 0.51
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (31 bp):
AAACTTCTAATAGTTCTGATGTCAAAAAAAA
Found at i:4922 original size:170 final size:170
Alignment explanation
Indices: 4635--4977 Score: 677
Period size: 170 Copynumber: 2.0 Consensus size: 170
4625 CCGATTAATG
4635 ATCCAGGAGTTTTGGGATCCATTTGTCATGGAACACACGAACAGTTCGGCCATCACCAATACGCC
1 ATCCAGGAGTTTTGGGATCCATTTGTCATGGAACACACGAACAGTTCGGCCATCACCAATACGCC
4700 ATTGCAGACCATGCCTTAAGAGCTCTCTTCCCTTAATTATACTACACCAAGTAAATGATGGTAGC
66 ATTGCAGACCATGCCTTAAGAGCTCTCTTCCCTTAATTATACTACACCAAGTAAATGATGGTAGC
4765 CAACCTGTTTTAGCTTCCAAGAAAGTGCCTCGGGGATAGT
131 CAACCTGTTTTAGCTTCCAAGAAAGTGCCTCGGGGATAGT
*
4805 ATCCGGGAGTTTTGGGATCCATTTGTCATGGAACACACGAACAGTTCGGCCATCACCAATACGCC
1 ATCCAGGAGTTTTGGGATCCATTTGTCATGGAACACACGAACAGTTCGGCCATCACCAATACGCC
4870 ATTGCAGACCATGCCTTAAGAGCTCTCTTCCCTTAATTATACTACACCAAGTAAATGATGGTAGC
66 ATTGCAGACCATGCCTTAAGAGCTCTCTTCCCTTAATTATACTACACCAAGTAAATGATGGTAGC
4935 CAACCTGTTTTAGCTTCCAAGAAAGTGCCTCGGGGATAGT
131 CAACCTGTTTTAGCTTCCAAGAAAGTGCCTCGGGGATAGT
4975 ATC
1 ATC
4978 TTGCTTTTAG
Statistics
Matches: 172, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 172 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (170 bp):
ATCCAGGAGTTTTGGGATCCATTTGTCATGGAACACACGAACAGTTCGGCCATCACCAATACGCC
ATTGCAGACCATGCCTTAAGAGCTCTCTTCCCTTAATTATACTACACCAAGTAAATGATGGTAGC
CAACCTGTTTTAGCTTCCAAGAAAGTGCCTCGGGGATAGT
Found at i:8503 original size:124 final size:125
Alignment explanation
Indices: 8199--8517 Score: 491
Period size: 126 Copynumber: 2.6 Consensus size: 125
8189 CCCCATGCAA
* *
8199 ATGGAACTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACACACTACATATTT
1 ATGGAACTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCATATTT
8264 ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATACATAGCATCTCACTCTATAT
66 ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATA-ATAGCATCTCACTCTATAT
** * *
8325 ATGGGGCTAGTGTTTGTCGAAACTTTTGCTAACATATGTCGTTATAGACGACATACTGCATATTT
1 ATGGAACTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCATATTT
8390 ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCAT-A-A-CATCTCACTCTGTATAT
66 ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATAATAGCATCTCACTC--TATAT
* * * * *
8449 ATGGAACTCGTGTTTGTTGAAACTTTTCCTAACACATGTCGTTATAAACAACATATTGCATATTT
1 ATGGAACTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCATATTT
8514 ATCT
66 ATCT
8518 AACACTTACT
Statistics
Matches: 176, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
122 10 0.06
123 1 0.01
124 66 0.38
126 99 0.56
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (125 bp):
ATGGAACTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCATATTT
ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATAATAGCATCTCACTCTATAT
Found at i:10268 original size:6 final size:6
Alignment explanation
Indices: 10254--10314 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
10244 GAAAGGAAGC
* * * * * *
10254 AGGATA AGGAGA AGGAGA AGGAAA AGGAGA AGGAGA ATGAAA AGGAAA
1 AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA
10302 AGGAAA AGGAAA A
1 AGGAAA AGGAAA A
10315 TTCTTTTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (6 bp):
AGGAAA
Found at i:10280 original size:18 final size:18
Alignment explanation
Indices: 10254--10314 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
10244 GAAAGGAAGC
*
10254 AGGATAAGGAGAAGGAGA
1 AGGAAAAGGAGAAGGAGA
10272 AGGAAAAGGAGAAGGAGA
1 AGGAAAAGGAGAAGGAGA
* * *
10290 ATGAAAAGGAAAAGGAAA
1 AGGAAAAGGAGAAGGAGA
10308 AGGAAAA
1 AGGAAAA
10315 TTCTTTTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (18 bp):
AGGAAAAGGAGAAGGAGA
Done.