Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023592.1 Corchorus olitorius cultivar O-4 contig23625, 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: 16911
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Found at i:5070 original size:43 final size:43
Alignment explanation
Indices: 5022--5259 Score: 326
Period size: 43 Copynumber: 5.6 Consensus size: 43
5012 CAATAACCAG
5022 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACA
* *
5065 AAGTCCTCAAACACATATATAACACAGAGGC-A-TCTA-TATCA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTA-CA
5106 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACA
* ** * *
5149 AAGTCCTCAAACACATATATAACACATAGAC-A-TTTA-TATCA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTA-CA
*
5190 AAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACA
* *
5233 AAGTCCTCAAATACATATATAACACAG
1 AAGTCCCCAAACACATATATAACACAG
5260 AGACATTTCT
Statistics
Matches: 170, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
40 4 0.02
41 67 0.39
42 3 0.02
43 92 0.54
44 4 0.02
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (43 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACA
Found at i:5266 original size:84 final size:84
Alignment explanation
Indices: 5022--5267 Score: 447
Period size: 84 Copynumber: 2.9 Consensus size: 84
5012 CAATAACCAG
5022 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
* *
5087 CACAGAGGCATCTATATCA
66 CACAGAGACATTTATATCA
5106 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
*
5171 CACATAGACATTTATATCA
66 CACAGAGACATTTATATCA
* *
5190 AAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAATACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
5255 CACAGAGACATTT
66 CACAGAGACATTT
5268 CTCCTTATGG
Statistics
Matches: 156, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 156 1.00
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.22
Consensus pattern (84 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
CACAGAGACATTTATATCA
Found at i:5381 original size:2 final size:2
Alignment explanation
Indices: 5374--5404 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5364 ACCAAATTCC
*
5374 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5405 GTAACAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7913 original size:2 final size:2
Alignment explanation
Indices: 7901--7939 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
7891 TTTGAAAGCC
7901 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7940 TAAAACTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8163 original size:55 final size:55
Alignment explanation
Indices: 8102--8241 Score: 226
Period size: 55 Copynumber: 2.5 Consensus size: 55
8092 ATATGTAATC
* *
8102 TTTCATTTTAGATCCAAAATTTTTTCCTAATTATTAAGCTATACTTAAATGTAAA
1 TTTCATTTTAGATCCAAAATTTTCTCCTAATTATTAAGCTATACTTAAATGCAAA
*
8157 TTTCATTTTAGATCCAAAATTTTCTCCTAATTATTAAGCTATACTTGAATGCAAA
1 TTTCATTTTAGATCCAAAATTTTCTCCTAATTATTAAGCTATACTTAAATGCAAA
* **
8212 TTTCATTTTAAATCCAAAATTAACTCCTAA
1 TTTCATTTTAGATCCAAAATTTTCTCCTAA
8242 ATTGTGGAAC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 79 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (55 bp):
TTTCATTTTAGATCCAAAATTTTCTCCTAATTATTAAGCTATACTTAAATGCAAA
Found at i:11525 original size:13 final size:13
Alignment explanation
Indices: 11507--11536 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
11497 TCCCGAATGT
11507 GGTGTTAAAGGGG
1 GGTGTTAAAGGGG
11520 GGTGTTAAAGGGG
1 GGTGTTAAAGGGG
11533 GGTG
1 GGTG
11537 AATAACCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.57, T:0.23
Consensus pattern (13 bp):
GGTGTTAAAGGGG
Found at i:13006 original size:16 final size:16
Alignment explanation
Indices: 12985--13016 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12975 CACATTCCCA
12985 CTTGATACCCTGAACC
1 CTTGATACCCTGAACC
13001 CTTGATACCCTGAACC
1 CTTGATACCCTGAACC
13017 AAACACCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.25
Consensus pattern (16 bp):
CTTGATACCCTGAACC
Found at i:14575 original size:73 final size:73
Alignment explanation
Indices: 14447--14588 Score: 221
Period size: 73 Copynumber: 1.9 Consensus size: 73
14437 AGTTTGACAA
* * *
14447 GTTAGGAACATTAATGTAAACTAGTCCCAAGACCCGCGCTCCGCGCTGAGATTGTGAAGGGACGG
1 GTTAGGAACATTAATGTAAACTAGTCCCAACACCAGCGCTCCGCGCCGAGATTGTGAAGGGACGG
14512 AACAGTTT
66 AACAGTTT
* * * *
14520 GTTATGAATATTAATGTAAACTAGTCCCAACACCAGCGCTCCGCGCCGGGATTGTGAAGGGAGGG
1 GTTAGGAACATTAATGTAAACTAGTCCCAACACCAGCGCTCCGCGCCGAGATTGTGAAGGGACGG
14585 AACA
66 AACA
14589 TGTCACGCCC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (73 bp):
GTTAGGAACATTAATGTAAACTAGTCCCAACACCAGCGCTCCGCGCCGAGATTGTGAAGGGACGG
AACAGTTT
Done.