Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014791.1 Corchorus olitorius cultivar O-4 contig14824, 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: 25266
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:612 original size:17 final size:17
Alignment explanation
Indices: 592--636 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
582 GATATCTTTT
*
592 TATTTCTTATATATTTA
1 TATTTCTTATAGATTTA
*
609 TATTTCTTACAGATTTA
1 TATTTCTTATAGATTTA
*
626 TATATCTTATA
1 TATTTCTTATA
637 ACGTTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTCTTATAGATTTA
Found at i:6265 original size:17 final size:17
Alignment explanation
Indices: 6245--6288 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
6235 ATATCTTTTG
*
6245 ATTTCTTATATATTTAT
1 ATTTCTTATAGATTTAT
*
6262 ATTTCTTACAGATTTAT
1 ATTTCTTATAGATTTAT
*
6279 ATATCTTATA
1 ATTTCTTATA
6289 ACGTTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTCTTATAGATTTAT
Found at i:6351 original size:2 final size:2
Alignment explanation
Indices: 6344--6372 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6334 CTTATAATGT
6344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6373 TTGACTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12248 original size:22 final size:25
Alignment explanation
Indices: 12222--12270 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
12212 ATGTTGTCCT
*
12222 TAATG-AATAAA-ATCA-AATATAA
1 TAATGAAATAAATATAATAATATAA
12244 TAATGAAATAAATATAATAATATAA
1 TAATGAAATAAATATAATAATATAA
12269 TA
1 TA
12271 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 6 0.26
24 3 0.13
25 9 0.39
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (25 bp):
TAATGAAATAAATATAATAATATAA
Found at i:12258 original size:17 final size:18
Alignment explanation
Indices: 12231--12264 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12221 TTAATGAATA
12231 AAATCAAATATAATAATG
1 AAATCAAATATAATAATG
12249 AAAT-AAATATAATAAT
1 AAATCAAATATAATAAT
12265 ATAATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATCAAATATAATAATG
Found at i:12270 original size:17 final size:16
Alignment explanation
Indices: 12231--12270 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 16
12221 TTAATGAATA
12231 AAATCAAATATAATAAT
1 AAAT-AAATATAATAAT
12248 GAAATAAATATAATAAT
1 -AAATAAATATAATAAT
12265 ATAATA
1 A-AATA
12271 TAATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.76
18 4 0.19
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (16 bp):
AAATAAATATAATAAT
Found at i:12358 original size:17 final size:17
Alignment explanation
Indices: 12336--12368 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12326 AGGAATATAT
*
12336 AATAATTTATTTTTTAA
1 AATAATTTATATTTTAA
12353 AATAATTTATATTTTA
1 AATAATTTATATTTTA
12369 TTTCTTTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATAATTTATATTTTAA
Found at i:15986 original size:79 final size:79
Alignment explanation
Indices: 15857--16008 Score: 241
Period size: 79 Copynumber: 1.9 Consensus size: 79
15847 AACTTTTATA
* * *
15857 ATTTTAGTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATGTCCTTATAACTATTTCATT
1 ATTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTACAACTATTTCATT
15922 TTTATCATTTTACT
66 TTTATCATTTTACT
* * *
15936 ATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTACACCTATTTTATT
1 ATTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTACAACTATTTCATT
*
16001 TTTGTCAT
66 TTTATCAT
16009 ATTATTAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (79 bp):
ATTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTACAACTATTTCATT
TTTATCATTTTACT
Found at i:16098 original size:31 final size:31
Alignment explanation
Indices: 16060--16121 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
16050 AGTTTTGTAA
*
16060 AACTTTTGAAACGCCTATTGTACCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
* *
16091 AACTTTTGAAACGTCTATTATATCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
16122 GTCTAACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (31 bp):
AACTTTTGAAACGCCTATTATACCCTTATTT
Found at i:16598 original size:119 final size:122
Alignment explanation
Indices: 16417--16657 Score: 382
Period size: 119 Copynumber: 2.0 Consensus size: 122
16407 CATTGTTTAA
*
16417 ACTTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATTCTTATAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATTCTTATAAC
*
16482 -TA-TTTTATTTTTACCATTTTACTATTTTAATTAA-AAAAAACTTAAATATATTAT
66 TTATTTTTATTTTTACCATTTTACTAATTTAATTAATAAAAAACTTAAATATATTAT
* * *
16536 ACTTTTATAGTTTTACTCCACTAAAAACTCTATTTTTATTTAATTAAATCTAATA-TCTTTATAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATTC-TTATAA
*
16600 CTTATTTTTATTTTTACCATTTTACTAATTTAATTAATTAAAAAACTTAGATATATTA
65 CTTATTTTTATTTTTACCATTTTACTAATTTAATTAA-TAAAAAACTTAAATATATTA
16658 GAATTTTTAA
Statistics
Matches: 111, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
118 2 0.02
119 58 0.52
120 2 0.02
121 31 0.28
123 18 0.16
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (122 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATTCTTATAAC
TTATTTTTATTTTTACCATTTTACTAATTTAATTAATAAAAAACTTAAATATATTAT
Found at i:17380 original size:17 final size:16
Alignment explanation
Indices: 17347--17384 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
17337 AATTTTTTAA
17347 TATTTAATTCTTAAATT
1 TATTTAATTCTTAAA-T
17364 TATTTAATATCTT-AAT
1 TATTTAAT-TCTTAAAT
17380 TATTT
1 TATTT
17385 GATTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTAATTCTTAAAT
Found at i:17389 original size:25 final size:24
Alignment explanation
Indices: 17337--17392 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
17327 GCCAGCCTTG
*
17337 AATTT-TTTAATATTTAATTCTTA
1 AATTTATTTAATATTTAATTATTA
*
17360 AATTTATTTAATATCTTAATTATTT
1 AATTTATTTAATAT-TTAATTATTA
*
17385 GATTTATT
1 AATTTATT
17393 ATTTTACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.18
24 8 0.29
25 15 0.54
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
AATTTATTTAATATTTAATTATTA
Found at i:17960 original size:22 final size:23
Alignment explanation
Indices: 17930--17976 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
17920 TTTTAGTTTA
**
17930 TAATATTCTTGGGTCATTCAGGT
1 TAATATTCTCAGGTCATTCAGGT
*
17953 TAAT-TTCTCAGGTCATTCATGT
1 TAATATTCTCAGGTCATTCAGGT
17975 TA
1 TA
17977 CAAGTTTGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (23 bp):
TAATATTCTCAGGTCATTCAGGT
Found at i:20402 original size:18 final size:18
Alignment explanation
Indices: 20355--20405 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 18
20345 GGGTATGTGG
20355 AAGAATTTGGCTTCTGAT
1 AAGAATTTGGCTTCTGAT
20373 AAGGAA---GGCTTCTGAT
1 AA-GAATTTGGCTTCTGAT
20389 AAGAATTTGGCTTCTGA
1 AAGAATTTGGCTTCTGA
20406 AAGTGGAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 3 0.10
16 12 0.41
18 11 0.38
19 3 0.10
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.33
Consensus pattern (18 bp):
AAGAATTTGGCTTCTGAT
Found at i:21961 original size:26 final size:26
Alignment explanation
Indices: 21914--21976 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
21904 CACGTGCGAT
* *
21914 GTCACATGTGGAGGTGTCCG-TTGGAG
1 GTCACGTGT-GAGGTGTACGTTTGGAG
21940 GTCACGTGTGAGGTCGTACGTTTGGAG
1 GTCACGTGTGAGGT-GTACGTTTGGAG
21967 GTCACGTGTG
1 GTCACGTGTG
21977 GGATGCCAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 5 0.15
26 12 0.36
27 16 0.48
ACGTcount: A:0.14, C:0.16, G:0.41, T:0.29
Consensus pattern (26 bp):
GTCACGTGTGAGGTGTACGTTTGGAG
Found at i:24663 original size:29 final size:30
Alignment explanation
Indices: 24609--24682 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
24599 TACCCAGAAA
*
24609 AATCCCTTATGTTTTGCTTTTGGGACAAAAT
1 AATCCCTTATGTTTT-CTTTCGGGACAAAAT
*
24640 AATCCCTTATGTTTT-TTTCGGGACAAATT
1 AATCCCTTATGTTTTCTTTCGGGACAAAAT
*
24669 AATCCCTTACGTTT
1 AATCCCTTATGTTT
24683 CAAAAATGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 25 0.62
31 15 0.38
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (30 bp):
AATCCCTTATGTTTTCTTTCGGGACAAAAT
Found at i:24949 original size:15 final size:16
Alignment explanation
Indices: 24929--24971 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
24919 AAAAATTGAT
24929 TTTTTTCCTTTTTT-C
1 TTTTTTCCTTTTTTCC
24944 TTTTTT-CTTTTTTCC
1 TTTTTTCCTTTTTTCC
*
24959 TTCTTCTCCTTTT
1 TT-TTTTCCTTTT
24972 CAAAAACTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.29
15 9 0.38
16 3 0.12
17 5 0.21
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTCCTTTTTTCC
Found at i:24971 original size:22 final size:22
Alignment explanation
Indices: 24929--24972 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
24919 AAAAATTGAT
* *
24929 TTTTTTCCTTTTTTCTTTTTTC
1 TTTTTTCCTTTTCTCTCTTTTC
24951 TTTTTTCCTTCTTCTC-CTTTTC
1 TTTTTTCCTT-TTCTCTCTTTTC
24973 AAAAACTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTTCCTTTTCTCTCTTTTC
Done.