Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013453.1 Corchorus olitorius cultivar O-4 contig13486, 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: 36553
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2147 original size:27 final size:27
Alignment explanation
Indices: 2112--2228 Score: 126
Period size: 28 Copynumber: 4.3 Consensus size: 27
2102 GGTATTTTGG
** * *
2112 GTCATTTGCATGTTCAGGGGCATTTTT
1 GTCATTTGCACATCCAGGGGCATTTTA
*
2139 GTCATTTGCACGTCCAGGGGCATTTTA
1 GTCATTTGCACATCCAGGGGCATTTTA
2166 GTCATTTTGCACATCCAGGGGCATTTTA
1 GTCA-TTTGCACATCCAGGGGCATTTTA
* * * **
2194 GTCATTTTGCATATTCAAGGGCATTTCG
1 GTCA-TTTGCACATCCAGGGGCATTTTA
2222 GTCATTT
1 GTCATTT
2229 TGAGCTCATT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 31 0.39
28 49 0.61
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (27 bp):
GTCATTTGCACATCCAGGGGCATTTTA
Found at i:2183 original size:28 final size:28
Alignment explanation
Indices: 2126--2230 Score: 140
Period size: 28 Copynumber: 3.8 Consensus size: 28
2116 TTTGCATGTT
* *
2126 CAGGGGCATTTTTGTCA-TTTGCACGTC
1 CAGGGGCATTTTAGTCATTTTGCACATC
2153 CAGGGGCATTTTAGTCATTTTGCACATC
1 CAGGGGCATTTTAGTCATTTTGCACATC
* *
2181 CAGGGGCATTTTAGTCATTTTGCATATT
1 CAGGGGCATTTTAGTCATTTTGCACATC
* **
2209 CAAGGGCATTTCGGTCATTTTG
1 CAGGGGCATTTTAGTCATTTTG
2231 AGCTCATTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
27 16 0.23
28 54 0.77
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (28 bp):
CAGGGGCATTTTAGTCATTTTGCACATC
Found at i:10907 original size:14 final size:14
Alignment explanation
Indices: 10888--10918 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10878 ACAACAATTA
10888 CAAACATCCAAGTT
1 CAAACATCCAAGTT
*
10902 CAAACATTCAAGTT
1 CAAACATCCAAGTT
10916 CAA
1 CAA
10919 CAAAGCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (14 bp):
CAAACATCCAAGTT
Found at i:11946 original size:25 final size:25
Alignment explanation
Indices: 11912--11960 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
11902 GGTTAGGGTT
*
11912 AGGGGGAAAGAAGAATAGAAGATGA
1 AGGGGGAAAGAAGAATAAAAGATGA
11937 AGGGGGAAAGAAGAATAAAAGATG
1 AGGGGGAAAGAAGAATAAAAGATG
11961 GGGGGCGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.39, T:0.08
Consensus pattern (25 bp):
AGGGGGAAAGAAGAATAAAAGATGA
Found at i:13498 original size:19 final size:19
Alignment explanation
Indices: 13451--13487 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13441 TATTTAATAA
*
13451 AATTGAATATAACGTTAAC
1 AATTAAATATAACGTTAAC
13470 AATTAAATATAACGTTAA
1 AATTAAATATAACGTTAA
13488 TATTCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTAAATATAACGTTAAC
Found at i:15476 original size:19 final size:19
Alignment explanation
Indices: 15449--15485 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15439 TATTTAATAA
* *
15449 AATTGAATATAATGTTAAC
1 AATTAAATATAACGTTAAC
15468 AATTAAATATAACGTTAA
1 AATTAAATATAACGTTAA
15486 TATTCATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (19 bp):
AATTAAATATAACGTTAAC
Found at i:18245 original size:22 final size:22
Alignment explanation
Indices: 18220--18261 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18210 GAAATACAGG
*
18220 ACAAGACCTGGGCAGGAGTTAC
1 ACAAGACCTGGCCAGGAGTTAC
* *
18242 ACAAGTCCTGTCCAGGAGTT
1 ACAAGACCTGGCCAGGAGTT
18262 GTTGCGGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.19
Consensus pattern (22 bp):
ACAAGACCTGGCCAGGAGTTAC
Found at i:34333 original size:23 final size:23
Alignment explanation
Indices: 34274--34362 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
34264 CAGCATTTAA
* *
34274 TCAAATTGTTGTTGTTTTTTCTGT
1 TCAAAATGTTGCTG-TTTTTCTGT
* * *
34298 TGAAAATGATGCTGTTTTTCTTT
1 TCAAAATGTTGCTGTTTTTCTGT
* **
34321 TCAAGATGTTGCTGTTTTGATGT
1 TCAAAATGTTGCTGTTTTTCTGT
*
34344 TCAAAATGTTGCTTTTTTT
1 TCAAAATGTTGCTGTTTTT
34363 TTCTTTTTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 41 0.80
24 10 0.20
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (23 bp):
TCAAAATGTTGCTGTTTTTCTGT
Done.