Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012006.1 Corchorus olitorius cultivar O-4 contig12039, 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: 23867
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--47 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 TAG
4 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
46 TA
1 TA
48 CTAGATAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3943 original size:13 final size:13
Alignment explanation
Indices: 3925--3949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3915 AAAAAATTAT
3925 TATACTATATATC
1 TATACTATATATC
3938 TATACTATATAT
1 TATACTATATAT
3950 AAAAGCACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TATACTATATATC
Found at i:5215 original size:19 final size:18
Alignment explanation
Indices: 5179--5222 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5169 GAAATTTATC
5179 AATTATTTATTAAATAAT
1 AATTATTTATTAAATAAT
5197 AATTATTT-TTCAGAATAAT
1 AATTATTTATT-A-AATAAT
*
5216 TATTATT
1 AATTATT
5223 AATATTCCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 9 0.39
19 12 0.52
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
AATTATTTATTAAATAAT
Found at i:7044 original size:26 final size:26
Alignment explanation
Indices: 6969--7045 Score: 127
Period size: 26 Copynumber: 3.0 Consensus size: 26
6959 ATTATTAAAA
* * *
6969 TATTTTATTAAGAAAAATTCAGTATT
1 TATTTTATTTAGAAAAATTCAATTTT
6995 TATTTTATTTAGAAAAATTCAATTTT
1 TATTTTATTTAGAAAAATTCAATTTT
7021 TATTTTATTTAGAAAAATTCAATTT
1 TATTTTATTTAGAAAAATTCAATTT
7046 CTAAAGTACC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (26 bp):
TATTTTATTTAGAAAAATTCAATTTT
Found at i:8031 original size:18 final size:19
Alignment explanation
Indices: 8008--8047 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
7998 ATATATAATA
8008 ATAGTAA-ATCAAA-ATAAG
1 ATAGTAAGAT-AAACATAAG
8026 ATAGTAAGATAAACATAAG
1 ATAGTAAGATAAACATAAG
8045 ATA
1 ATA
8048 AGTATAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.23
Consensus pattern (19 bp):
ATAGTAAGATAAACATAAG
Found at i:21588 original size:6 final size:6
Alignment explanation
Indices: 21577--21612 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
21567 AGATTCTCTA
*
21577 TATATC TATATC TATATC TATATC TGTATAC TATAT
1 TATATC TATATC TATATC TATATC TATAT-C TATAT
21613 AAGTCTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:21879 original size:39 final size:40
Alignment explanation
Indices: 21823--21903 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
21813 TTTAATTCCT
21823 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA
* * *
21863 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA
21902 AT
1 AT
21904 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA
Found at i:21930 original size:25 final size:24
Alignment explanation
Indices: 21894--21940 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
21884 AATACTTACA
*
21894 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTAAGGTATTTTT
21918 TTAATTCAAATTCTAAGGTATTT
1 TTAATT-AAATTCTAAGGTATTT
21941 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (24 bp):
TTAATTAAATTCTAAGGTATTTTT
Found at i:22254 original size:205 final size:193
Alignment explanation
Indices: 22015--22411 Score: 632
Period size: 205 Copynumber: 2.0 Consensus size: 193
22005 TTAATAATAA
22015 ATAAATCGGATCTTTATATCTTTTATAATTTTGAAATTTTGTTTGACATTGACCTAATTTAATTT
1 ATAAATCGGATCTTTATATCTTTTATAATTTTGAAATTTTGTTTGACATTGACCTAATTTAATTT
* *
22080 AATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATATAATAGTAAT
66 AATAAATCAACCACTAATGTTCAACT-ACTTTTTTTTGGTATAGTT-T-TATATATAATAATAAT
22145 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
128 GTGTTGTATCTTATTCACT---A-----TTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
*
22210 CATTGATAT
185 CATCGATAT
*
22219 ATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
1 ATAAATCGGATCTTT-ATATCTTTTATAATTTTGAAATTTTGTTTGACATTGACCTAATTTAATT
*
22284 TAATAAATCAACCATTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAATAATGT
65 TAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAATAATGT
*
22349 GTTGTATCTTATTCACTATTAGTAATCTTAGACTTAAAAAATTAATAACATTCATCATCGATA
130 GTTGTATCTTATTCACTATTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATCGATA
22412 AAGTTATTAA
Statistics
Matches: 186, Mismatches: 6, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
194 43 0.23
199 1 0.01
202 34 0.18
203 1 0.01
204 33 0.18
205 74 0.40
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (193 bp):
ATAAATCGGATCTTTATATCTTTTATAATTTTGAAATTTTGTTTGACATTGACCTAATTTAATTT
AATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAATAATGTG
TTGTATCTTATTCACTATTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATCGATAT
Done.