Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021438.1 Corchorus olitorius cultivar O-4 contig21471, 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: 10043
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:347 original size:26 final size:26
Alignment explanation
Indices: 306--359 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
296 AAGCTAGTAA
*
306 TGAAGTACGAAAGACCAAAGTGCCCC
1 TGAAGTACGAAAGACCAAAATGCCCC
332 TGAAGTAC-AAATGACCAAAATGCCCC
1 TGAAGTACGAAA-GACCAAAATGCCCC
358 TG
1 TG
360 GACTTTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (26 bp):
TGAAGTACGAAAGACCAAAATGCCCC
Found at i:942 original size:30 final size:30
Alignment explanation
Indices: 902--1453 Score: 740
Period size: 30 Copynumber: 18.3 Consensus size: 30
892 CTAACTGATG
*
902 AAGCAATGATCCT-AAACCAGGATTAAAACA
1 AAGCAATGATCCTCAAA-CAGGATTAAAATA
* *
932 AAGTAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* *
962 AAGCAAAT-ATCCTCAACCAGGATAAAAATA
1 AAGC-AATGATCCTCAAACAGGATTAAAATA
992 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* *
1022 GAGCAAAT-ATCCTCAACCAGGATTAAAATA
1 AAGC-AATGATCCTCAAACAGGATTAAAATA
1052 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* * *
1082 GAGTAAAT-ATCCTCAACCAGGATTAAAATA
1 AAG-CAATGATCCTCAAACAGGATTAAAATA
*
1112 AAGCAATGATCCTCAAACAGGATTAAAACA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
1142 AAGCAATGATCCTCAAACAGGATTAAGATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
1172 AAGCAATGATCCTCAAACAGGATTAAGATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
1202 AAGCAAAT-ATCCTCAACCAGGATTAAAATA
1 AAGC-AATGATCCTCAAACAGGATTAAAATA
1232 AAGCAATGATCCTCAAACAGGATTAACAATA
1 AAGCAATGATCCTCAAACAGGATTAA-AATA
*
1263 AAGCAATGATCCTCAAACAGGATTAAAACA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* * *
1293 AAGCAATGATCCTCAAATAGGATTAAGATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
1323 AAGCAATGATCCTCAAACAGGATTAAAAATG
1 AAGCAATGATCCTCAAACAGGATT-AAAATA
* *
1354 AAGCAAAT-ATCCTCAACCAGGATAAAAATA
1 AAGC-AATGATCCTCAAACAGGATTAAAATA
*
1384 AAGCAATGATCCTCAAACAGGATAAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* ** *
1414 AAGCAATGATCC-GAAACCAGGATCGAAATG
1 AAGCAATGATCCTCAAA-CAGGATTAAAATA
1444 AAGCAATGAT
1 AAGCAATGAT
1454 GCCATGATCC
Statistics
Matches: 470, Mismatches: 38, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
29 18 0.04
30 382 0.81
31 67 0.14
32 3 0.01
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (30 bp):
AAGCAATGATCCTCAAACAGGATTAAAATA
Found at i:3752 original size:20 final size:18
Alignment explanation
Indices: 3715--3779 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 18
3705 CAATCAATTC
*
3715 TTTTTCGATTTTGATTTTGA
1 TTTTTTGATTTT--TTTTGA
3735 TTTTGATTGATTTTTTTTGA
1 TTTT--TTGATTTTTTTTGA
3755 TTTTTTGATTTTTTGATTGA
1 TTTTTTGATTTTTT--TTGA
3775 TTTTT
1 TTTTT
3780 ATTTTTTGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 10 0.25
20 23 0.57
22 7 0.17
ACGTcount: A:0.14, C:0.02, G:0.14, T:0.71
Consensus pattern (18 bp):
TTTTTTGATTTTTTTTGA
Found at i:3756 original size:26 final size:28
Alignment explanation
Indices: 3723--3779 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
3713 TCTTTTTCGA
3723 TTTTGA-TTTTGA-TTTTGATTGATTTT
1 TTTTGATTTTTGATTTTTGATTGATTTT
3749 TTTTGATTTTTTGATTTTTTGATTGATTTT
1 TTTTGA-TTTTTGA-TTTTTGATTGATTTT
3779 T
1 T
3780 ATTTTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 6 0.22
28 6 0.22
30 15 0.56
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (28 bp):
TTTTGATTTTTGATTTTTGATTGATTTT
Found at i:3760 original size:8 final size:8
Alignment explanation
Indices: 3747--3787 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
3737 TTGATTGATT
3747 TTTTTTGA
1 TTTTTTGA
3755 TTTTTTGA
1 TTTTTTGA
3763 TTTTTTGA
1 TTTTTTGA
*
3771 TTGATTTTTA
1 TT--TTTTGA
3781 TTTTTTG
1 TTTTTTG
3788 GTTGAATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 22 0.76
10 7 0.24
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (8 bp):
TTTTTTGA
Found at i:3778 original size:18 final size:18
Alignment explanation
Indices: 3725--3792 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 18
3715 TTTTTCGATT
3725 TTGATTTTGA--TTTTGA
1 TTGATTTTGATTTTTTGA
3741 TTGA--TT--TTTTTTGA
1 TTGATTTTGATTTTTTGA
3755 TT--TTTTGATTTTTTGA
1 TTGATTTTGATTTTTTGA
* *
3771 TTGATTTTTATTTTTTGG
1 TTGATTTTGATTTTTTGA
3789 TTGA
1 TTGA
3793 ATTTCTTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
14 12 0.29
16 14 0.33
18 16 0.38
ACGTcount: A:0.15, C:0.00, G:0.16, T:0.69
Consensus pattern (18 bp):
TTGATTTTGATTTTTTGA
Found at i:6966 original size:16 final size:16
Alignment explanation
Indices: 6941--6971 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6931 CAGATACTTA
6941 TGATGATTTGCATGAC
1 TGATGATTTGCATGAC
*
6957 TGATGCTTTGCATGA
1 TGATGATTTGCATGA
6972 ATGCATTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (16 bp):
TGATGATTTGCATGAC
Done.