Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024490.1 Corchorus olitorius cultivar O-4 contig24523, 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: 11032
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1859 original size:6 final size:6
Alignment explanation
Indices: 1809--1840 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1799 ATTAGTGTAT
*
1809 AAATTA AAAATA AAATTA AAATTA AAATTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AA
1841 TGTGCAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATTA
Found at i:5597 original size:106 final size:106
Alignment explanation
Indices: 5456--5769 Score: 417
Period size: 106 Copynumber: 3.0 Consensus size: 106
5446 TAAATATTTT
* * * *
5456 TTATTATAGGATTTTAGAAATAAAATATAAAACTAATTTCACTAGGTTTAGCTCCAAATTAACAT
1 TTATTATAGGGTTTCAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAA-AT
5521 TTTAATTTTATTTTAAGGGTAAATTCCAAAATTAATAACTTA
65 TTTAATTTTATTTTAAGGGTAAATTCCAAAATTAATAACTTA
* *
5563 TTGTTATAGGG-TTCAGAAATAAAATATAAAACTAATTTTACTAAGTTTAGCCCCAAA-T---TT
1 TTATTATAGGGTTTCAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAATT
* * *
5623 TTAATTTTATGTTAAGGGCAAATTCCAAAATTAATAACTAA
66 TTAATTTTATTTTAAGGGTAAATTCCAAAATTAATAACTTA
* * * *
5664 TTATTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACCAAGATTAGCCCCAAATTAAAAT
1 TTATTATAGGGTTTCAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATT-AAAT
* *
5728 TTTAATTTTATTTTAAGAGTAAATGT-TAAAATTAATAACTTA
65 TTTAATTTTATTTTAAGGGTAAAT-TCCAAAATTAATAACTTA
5770 GACAAATTAA
Statistics
Matches: 180, Mismatches: 20, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
101 68 0.38
102 23 0.13
105 1 0.01
106 78 0.43
107 10 0.06
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.39
Consensus pattern (106 bp):
TTATTATAGGGTTTCAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAATT
TTAATTTTATTTTAAGGGTAAATTCCAAAATTAATAACTTA
Found at i:5655 original size:101 final size:102
Alignment explanation
Indices: 5456--5722 Score: 358
Period size: 101 Copynumber: 2.6 Consensus size: 102
5446 TAAATATTTT
* * * *
5456 TTATTATAGGATTTTAGAAATAAAATATAAAACTAATTTCACTAGGTTTAGCTCCAAATTAACAT
1 TTATTATAGGGTTTCAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAA-T----T
* * *
5521 TTTAATTTTATTTTAAGGGTAAATTCCAAAATTAATAACTTA
61 TTTAATTTTATGTTAAGGGCAAATTCCAAAATTAATAACTAA
* *
5563 TTGTTATAGGG-TTCAGAAATAAAATATAAAACTAATTTTACTAAGTTTAGCCCCAAATTTTTAA
1 TTATTATAGGGTTTCAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTTTTAA
5627 TTTTATGTTAAGGGCAAATTCCAAAATTAATAACTAA
66 TTTTATGTTAAGGGCAAATTCCAAAATTAATAACTAA
* * * *
5664 TTATTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACCAAGATTAGCCCCAAATT
1 TTATTATAGGGTTTCAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATT
5723 AAAATTTTAA
Statistics
Matches: 144, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
101 70 0.49
102 22 0.15
105 1 0.01
106 42 0.29
107 9 0.06
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (102 bp):
TTATTATAGGGTTTCAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTTTTAA
TTTTATGTTAAGGGCAAATTCCAAAATTAATAACTAA
Found at i:8766 original size:17 final size:17
Alignment explanation
Indices: 8744--8892 Score: 190
Period size: 17 Copynumber: 8.4 Consensus size: 17
8734 CTTTGTTTTT
8744 TTTTTTTGTATGAACTG
1 TTTTTTTGTATGAACTG
* *
8761 TTTTTTGGTATGAAATG
1 TTTTTTTGTATGAACTG
*
8778 TTTTTTGGTATGAACTG
1 TTTTTTTGTATGAACTG
*
8795 CTTTTTTTGGGTATGAATTG
1 -TTTTTTT--GTATGAACTG
8815 TTTTTTTGTATGAACTG
1 TTTTTTTGTATGAACTG
*
8832 TTTTTTGGTATGAACTG
1 TTTTTTTGTATGAACTG
*
8849 CTTTTTTGGTATGAACTG
1 -TTTTTTTGTATGAACTG
8867 TTTTTTTTTGTATGAACTG
1 --TTTTTTTGTATGAACTG
8886 TTTTTTT
1 TTTTTTT
8893 TTTTTGTATC
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
17 63 0.53
18 23 0.19
19 23 0.19
20 9 0.08
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.58
Consensus pattern (17 bp):
TTTTTTTGTATGAACTG
Found at i:8809 original size:54 final size:53
Alignment explanation
Indices: 8743--8891 Score: 228
Period size: 54 Copynumber: 2.8 Consensus size: 53
8733 ACTTTGTTTT
* * *
8743 TTTTTTTTGTATGAACTGTTTTTTGGTATGAAATGTTTTTTGGTATGAACTGC
1 TTTTTTTGGTATGAACTGTTTTTTTGTATGAACTGTTTTTTGGTATGAACTGC
*
8796 TTTTTTTGGGTATGAATTGTTTTTTTGTATGAACTGTTTTTTGGTATGAACTGC
1 TTTTTTT-GGTATGAACTGTTTTTTTGTATGAACTGTTTTTTGGTATGAACTGC
8850 -TTTTTTGGTATGAACTGTTTTTTTTTGTATGAACTGTTTTTT
1 TTTTTTTGGTATGAACTG--TTTTTTTGTATGAACTGTTTTTT
8892 TTTTTTGTAT
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
52 10 0.11
53 13 0.15
54 65 0.74
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.58
Consensus pattern (53 bp):
TTTTTTTGGTATGAACTGTTTTTTTGTATGAACTGTTTTTTGGTATGAACTGC
Found at i:8829 original size:71 final size:71
Alignment explanation
Indices: 8744--8892 Score: 246
Period size: 71 Copynumber: 2.1 Consensus size: 71
8734 CTTTGTTTTT
8744 TTTTTTTGTATGAACTGTTTTTTGGTATGAAATG-TTTTTTGGTATGAACTGCTTTTTTTGGGTA
1 TTTTTTTGTATGAACTGTTTTTTGGTATGAAATGCTTTTTTGGTATGAACTG-TTTTTTTGGGTA
*
8808 TGAATTG
65 TGAACTG
* **
8815 TTTTTTTGTATGAACTGTTTTTTGGTATGAACTGCTTTTTTGGTATGAACTGTTTTTTTTTGTAT
1 TTTTTTTGTATGAACTGTTTTTTGGTATGAAATGCTTTTTTGGTATGAACTGTTTTTTTGGGTAT
8880 GAACTG
66 GAACTG
8886 TTTTTTT
1 TTTTTTT
8893 TTTTTGTATC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 56 0.77
72 17 0.23
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.58
Consensus pattern (71 bp):
TTTTTTTGTATGAACTGTTTTTTGGTATGAAATGCTTTTTTGGTATGAACTGTTTTTTTGGGTAT
GAACTG
Found at i:9649 original size:36 final size:36
Alignment explanation
Indices: 9609--9682 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
9599 TATAGAGAAT
* *
9609 AAACTATGATTATGATTAGGAATTTAGGAAATTTAA
1 AAACTAAGATTATGACTAGGAATTTAGGAAATTTAA
*
9645 AAACTAAGGTTATGACTAGGAATTTAGGAAATTTAA
1 AAACTAAGATTATGACTAGGAATTTAGGAAATTTAA
9681 AA
1 AA
9683 GAAACGTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (36 bp):
AAACTAAGATTATGACTAGGAATTTAGGAAATTTAA
Found at i:9721 original size:21 final size:21
Alignment explanation
Indices: 9697--9737 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9687 CGTAAGTAAC
9697 GAAATGA-AACAAGTAACTCAT
1 GAAATGAGAA-AAGTAACTCAT
9718 GAAATGAGAAAAGTAACTCA
1 GAAATGAGAAAAGTAACTCA
9738 AACATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.12, G:0.17, T:0.17
Consensus pattern (21 bp):
GAAATGAGAAAAGTAACTCAT
Done.