Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022510.1 Corchorus olitorius cultivar O-4 contig22543, 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: 28567
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:420 original size:98 final size:98
Alignment explanation
Indices: 272--470 Score: 389
Period size: 98 Copynumber: 2.0 Consensus size: 98
262 ATTATGAATG
*
272 TTATTAATCTTGTAATCTAAAATTACTAAAAAAATTTATAAAAGGTATTAAAATAGCTATAATGC
1 TTATTAATCTTGTAATCTAAAATTACTAAAAAAAATTATAAAAGGTATTAAAATAGCTATAATGC
337 TCTCTACAAACCTAATTGCCCTCTTGGATGATT
66 TCTCTACAAACCTAATTGCCCTCTTGGATGATT
370 TTATTAATCTTGTAATCTAAAATTACTAAAAAAAATTATAAAAGGTATTAAAATAGCTATAATGC
1 TTATTAATCTTGTAATCTAAAATTACTAAAAAAAATTATAAAAGGTATTAAAATAGCTATAATGC
435 TCTCTACAAACCTAATTGCCCTCTTGGATGATT
66 TCTCTACAAACCTAATTGCCCTCTTGGATGATT
468 TTA
1 TTA
471 GTAACTTTTT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (98 bp):
TTATTAATCTTGTAATCTAAAATTACTAAAAAAAATTATAAAAGGTATTAAAATAGCTATAATGC
TCTCTACAAACCTAATTGCCCTCTTGGATGATT
Found at i:2971 original size:36 final size:36
Alignment explanation
Indices: 2924--2993 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2914 TTCAATAACC
* *
2924 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
2960 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
2994 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3887 original size:203 final size:200
Alignment explanation
Indices: 3504--3911 Score: 726
Period size: 203 Copynumber: 2.0 Consensus size: 200
3494 GCTTAATAAC
* *
3504 TTTATCTATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAATCTAAGATTACTAACAAAGTTGTAGTGAATAAG
*
3569 ATACAACATATTACTATTATATATAAAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTGAT
66 ATACAACACATTACTATTATATATAAAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTGAT
*
3634 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGACCCG
131 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAACCCG
3699 ATTTA
196 ATTTA
*
3704 TTTATCAATGGTGAATGTTATTATTTTTTAAATCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAATCTAAGATTACTAACAAAGTTGTAGTGAATAAG
3769 ATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTT
66 ATACAACACATTACTATTATATATA-A-AACTATACC-AAAAAAATTAGTTGAACATTAGTGGTT
* *
3834 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCCAAATTATAAAAGATATTAAAAAT
128 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAAC
3899 CCGATTTA
193 CCGATTTA
3907 TTTAT
1 TTTAT
3912 TATTAAGGAA
Statistics
Matches: 198, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
200 86 0.43
201 1 0.01
202 9 0.05
203 102 0.52
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (200 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAATCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATATATAAAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTGAT
TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAACCCG
ATTTA
Found at i:19946 original size:60 final size:59
Alignment explanation
Indices: 19871--20038 Score: 171
Period size: 59 Copynumber: 2.8 Consensus size: 59
19861 TTTTTAAGGG
* * * * *
19871 TTAA-TTGCTCAAATAAGGATCTAA-AGTTTGCCAAAATGTTTAAATAAGG-TCCTGATCTT
1 TTAATTTGATCAAATAAGGACCTAACA-TAT-CCAAAATGCTCAAATAAGGATCC-GATCTT
* *
19930 TTAATTTGATCAAATAAGGGCCTAACATATCGAAAATGCTCAAATAAGGATCCGATCTT
1 TTAATTTGATCAAATAAGGACCTAACATATCCAAAATGCTCAAATAAGGATCCGATCTT
** * * *
19989 TTAATTTGGCCAAATAAGGGCTTAACATTATCGAAAATGCTCAAATAAGG
1 TTAATTTGATCAAATAAGGACCTAACA-TATCCAAAATGCTCAAATAAGG
20039 GCCTGACATC
Statistics
Matches: 95, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
59 50 0.53
60 44 0.46
61 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (59 bp):
TTAATTTGATCAAATAAGGACCTAACATATCCAAAATGCTCAAATAAGGATCCGATCTT
Found at i:19966 original size:59 final size:60
Alignment explanation
Indices: 19903--20044 Score: 207
Period size: 59 Copynumber: 2.4 Consensus size: 60
19893 AAAGTTTGCC
* * *
19903 AAAATGTTTAAATAAGGTCCTGATCTTTTAATTTGATCAAATAAGGGCCTAACA-TATCG
1 AAAATGCTCAAATAAGGTCCTGATCTTTTAATTTGACCAAATAAGGGCCTAACATTATCG
* *
19962 AAAATGCTCAAATAAGGATCC-GATCTTTTAATTTGGCCAAATAAGGGCTTAACATTATCG
1 AAAATGCTCAAATAAGG-TCCTGATCTTTTAATTTGACCAAATAAGGGCCTAACATTATCG
*
20022 AAAATGCTCAAATAAGGGCCTGA
1 AAAATGCTCAAATAAGGTCCTGA
20045 CATCAGTTTG
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
59 47 0.64
60 27 0.36
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGTCCTGATCTTTTAATTTGACCAAATAAGGGCCTAACATTATCG
Found at i:22533 original size:17 final size:17
Alignment explanation
Indices: 22479--22526 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
22469 ATCACCCCCC
* **
22479 AGATCACTAGTGATTTA
1 AGATCACCAGTGATGCA
22496 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
*
22513 AGATCACCGGTGAT
1 AGATCACCAGTGAT
22527 CAAAGATTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:23479 original size:14 final size:14
Alignment explanation
Indices: 23457--23498 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
23447 CTTCAAAGTA
23457 TAAAATAAGAAAAC
1 TAAAATAAGAAAAC
*
23471 TAAAGTAAGAAAA-
1 TAAAATAAGAAAAC
* *
23484 GAAAATTAGAAAAC
1 TAAAATAAGAAAAC
23498 T
1 T
23499 TGCATATAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.17
Consensus pattern (14 bp):
TAAAATAAGAAAAC
Found at i:24814 original size:15 final size:16
Alignment explanation
Indices: 24794--24823 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24784 CATATTACAC
24794 AAAAGGAAAA-AAAAA
1 AAAAGGAAAAGAAAAA
24809 AAAAGGAAAAGAAAA
1 AAAAGGAAAAGAAAA
24824 GGGTAATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGGAAAAGAAAAA
Found at i:25790 original size:6 final size:6
Alignment explanation
Indices: 25779--25805 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25769 AAGGGTGATT
25779 TTGGTG TTGGTG TTGGTG TTGGTG TTG
1 TTGGTG TTGGTG TTGGTG TTGGTG TTG
25806 ATGAGGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TTGGTG
Found at i:25917 original size:16 final size:16
Alignment explanation
Indices: 25894--25937 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
25884 GGAGGGGTGG
*
25894 AATTTTTTTTT-GCTC
1 AATTTTTTTTTCTCTC
25909 AATTTTTTTTTCTCTC
1 AATTTTTTTTTCTCTC
25925 AATTTTTTTTTCT
1 AATTTTTTTTTCT
25938 ATTTTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (16 bp):
AATTTTTTTTTCTCTC
Done.