Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016095.1 Corchorus olitorius cultivar O-4 contig16128, 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: 24766
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:854 original size:6 final size:6
Alignment explanation
Indices: 828--881 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
818 AAAAGCATCT
* * * *
828 AAAAGA ATATGA AAAATA AAAAGA AAAAAA AAAAG- AAAAG- AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
874 AAAAGA AA
1 AAAAGA AA
882 GTCTTATTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (6 bp):
AAAAGA
Found at i:4132 original size:16 final size:17
Alignment explanation
Indices: 4101--4136 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
4091 AGTCGATCAT
4101 AAACACACTAATATTGG
1 AAACACACTAATATTGG
*
4118 AAACA-ACTCATATTGG
1 AAACACACTAATATTGG
4134 AAA
1 AAA
4137 ATATAATCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (17 bp):
AAACACACTAATATTGG
Found at i:5056 original size:13 final size:13
Alignment explanation
Indices: 5038--5071 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
5028 TTTGTTGAGT
5038 TTGGGTTTGAGAA
1 TTGGGTTTGAGAA
5051 TTGGGTTTGAGAA
1 TTGGGTTTGAGAA
5064 TTGGGTTT
1 TTGGGTTT
5072 TCAAAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.38, T:0.44
Consensus pattern (13 bp):
TTGGGTTTGAGAA
Found at i:10652 original size:2 final size:2
Alignment explanation
Indices: 10645--10670 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10635 TTGCTTATTT
10645 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
10671 ACAATGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12537 original size:21 final size:20
Alignment explanation
Indices: 12507--12547 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
12497 GTGTTTTAGA
12507 TATTTTGTTGGATAATTGTT
1 TATTTTGTTGGATAATTGTT
12527 TATTTCTGTTGGATAATTGTT
1 TATTT-TGTTGGATAATTGTT
12548 CAATTATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.59
Consensus pattern (20 bp):
TATTTTGTTGGATAATTGTT
Found at i:20965 original size:5 final size:5
Alignment explanation
Indices: 20955--21002 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
20945 AAAAAATAAT
*
20955 TATTA TATTA TATTA TATTA TATATA TATATA TATCTA TACTA TATTA
1 TATTA TATTA TATTA TATTA TAT-TA TAT-TA TAT-TA TATTA TATTA
21003 AAAAGTATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
5 24 0.62
6 15 0.38
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (5 bp):
TATTA
Found at i:21234 original size:123 final size:128
Alignment explanation
Indices: 21096--21341 Score: 394
Period size: 123 Copynumber: 1.9 Consensus size: 128
21086 ACTTTTATAA
*
21096 TTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-TA-ATTTTTAC
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTATATTTTTAC
21157 CATTTTACTATTTAAATT-AAAAAACTTATATATATTAGAATTTTTTAAATATACAGTTACAG
66 CATTTTACTATTTAAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATACAGTTACAG
*
21219 TTTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAC-TA---TATTT
*
21284 TTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATA
62 TTACCATTTTACTATTTAAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATA
21342 TTTCTTAAAT
Statistics
Matches: 111, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
123 44 0.40
124 3 0.03
125 2 0.02
127 2 0.02
131 25 0.23
132 35 0.32
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.50
Consensus pattern (128 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTATATTTTTAC
CATTTTACTATTTAAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATACAGTTACAG
Found at i:23396 original size:21 final size:22
Alignment explanation
Indices: 23372--23413 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
23362 GTTTATAATA
*
23372 TTCTTGGGTCA-TCAGGTTATC
1 TTCTCGGGTCATTCAGGTTATC
*
23393 TTCTCGGGTTATTCAGGTTAT
1 TTCTCGGGTCATTCAGGTTAT
23414 GAGTTTGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (22 bp):
TTCTCGGGTCATTCAGGTTATC
Found at i:23893 original size:124 final size:127
Alignment explanation
Indices: 23692--23947 Score: 353
Period size: 124 Copynumber: 2.0 Consensus size: 127
23682 CATTGTTTAA
* *
23692 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTCTATTTAATTAAATCTAATATCTTTATGAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTCTATTTAATTAAATCTAATATCCTTATGAT
*
23757 TTTTACCATTTTACTATTTT-A-A-TTAA-AAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTA-CATTTTACCATTTTAATATTTAATAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
23816 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-AC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTCTATTTAATTAAATCTAATATCCTTATGA-
*
23880 CTATTTTA-TTTTTACCATTTTAATATTTTAATTTAAAAACTTATATATATTAGAATTTTTTAAA
65 -T-TTTTACATTTTACCATTTTAATA-TTTAA--TAAAAACTTATATATATTAGAATTTTTTAAA
23944 TAT
125 TAT
23947 A
1 A
23948 TTTCTTAAAT
Statistics
Matches: 116, Mismatches: 6, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
123 1 0.01
124 69 0.59
125 2 0.02
126 6 0.05
128 4 0.03
131 34 0.29
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTCTATTTAATTAAATCTAATATCCTTATGAT
TTTTACATTTTACCATTTTAATATTTAATAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:23969 original size:14 final size:13
Alignment explanation
Indices: 23933--23971 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
23923 TATATATTAG
23933 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
23946 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
23960 AATTTTTTAAAT
1 AATTTTTTAAAT
23972 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Done.