Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011411.1 Corchorus olitorius cultivar O-4 contig11444, 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: 16840
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:137 original size:9 final size:9
Alignment explanation
Indices: 120--153 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
110 CTCGTACTTT
*
120 TATATATAG
1 TATAGATAG
129 TATAGATAG
1 TATAGATAG
138 -ATAGATAG
1 TATAGATAG
146 TATAGATA
1 TATAGATA
154 AGTCTCCTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (9 bp):
TATAGATAG
Found at i:6924 original size:29 final size:30
Alignment explanation
Indices: 6891--6948 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
6881 TTTTGCTCCA
6891 TGAACT-TCAATTTTGGATATTTTACCCCC
1 TGAACTCTCAATTTTGGATATTTTACCCCC
*
6920 TGAACTCTCAATTTTGGATTTTTTACCCC
1 TGAACTCTCAATTTTGGATATTTTACCCC
6949 TTCAAGCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.43
Consensus pattern (30 bp):
TGAACTCTCAATTTTGGATATTTTACCCCC
Found at i:7054 original size:42 final size:42
Alignment explanation
Indices: 6995--7078 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
6985 GACGTGGCAA
6995 TGCCACGTGACGCAAAAATCCGACATGGCAATGCCACGTCAT
1 TGCCACGTGACGCAAAAATCCGACATGGCAATGCCACGTCAT
7037 TGCCACGTGACGCAAAAATCCGACATGGCAATGCCACGTCAT
1 TGCCACGTGACGCAAAAATCCGACATGGCAATGCCACGTCAT
7079 CGGGTTGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (42 bp):
TGCCACGTGACGCAAAAATCCGACATGGCAATGCCACGTCAT
Found at i:13449 original size:12 final size:12
Alignment explanation
Indices: 13434--13458 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13424 TTACAACCTC
13434 TCTTTTTTTTTT
1 TCTTTTTTTTTT
13446 TCTTTTTTTTTT
1 TCTTTTTTTTTT
13458 T
1 T
13459 AATTTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:14047 original size:349 final size:352
Alignment explanation
Indices: 13544--14200 Score: 1025
Period size: 349 Copynumber: 1.9 Consensus size: 352
13534 CAGTTAGTGG
* * ** *
13544 AGTTTAGCAGACTTCATGTGCGGGTCTAGAAGGGTGACATGTGTCTTCTTAGGGATTAGATTGAA
1 AGTTTAGCAGACTGCATGTGCGGGTCTAGAAAGGTGACATGTGTCCCCTTAGGGACTAGATTGAA
13609 ATATTAAAAATCTAATTAATTCTGAAAAATGAGGAACTTGTCAATCTTTGAACCCGCTTGTGGAG
66 ATATTAAAAATCTAATTAATTCTGAAAAATGAGGAACTTGTCAATCTTTGAACCCGCTTGTGGAG
* * ** * *
13674 TCCCAAAACTATACTGACGGTGTATCAAATAATAACTTATAGTTTATTTAGCTCTACTATTAGTA
131 TCCAAAAACTACACTGACGGTGTATCAAATAATAACCCATAGCTTATTTAGCTCTACTATTAGCA
** * * *
13739 GAGGTAGCAAAATGAACTTGATCAGATTGTCCGAAGCCAAAATTGTCGGAATTCCGAATTTGGAA
196 GAAATAGCAAAATGAACTTGATCAAATTGTCCGAAGCCAAAATCGTCGGAACTCCGAATTTGGAA
13804 GAAAAAATGAGAGAGTTGATAACCAAAAATTTTACTATTAAAGTTATTGATAAAATTATTATCTA
261 GAAAAAATGAGAGAGTTGATAACCAAAAATTTTACTATTAAAGTTATTGATAAAATTATTATCTA
13869 AAACATATTAGCCAAAATCGTCAGTAA
326 AAACATATTAGCCAAAATCGTCAGTAA
* *
13896 AGTTTAGTAGACTGCACT-TGCGGGTCTAGAAAGGTGACATGTGTCCCCTTA-GGACTAGATTGG
1 AGTTTAGCAGACTGCA-TGTGCGGGTCTAGAAAGGTGACATGTGTCCCCTTAGGGACTAGATTGA
* * * *
13959 AATATTAAAATTTTAATTAATTCTGAAATA-G-GGTACTTGTCAATCTTTGAACCCGCTTGTGGA
65 AATATTAAAAATCTAATTAATTCTGAAAAATGAGGAACTTGTCAATCTTTGAACCCGCTTGTGGA
* * * *
14022 GTCGAAAAATTGCACTGATGGTGTATCAAATAATAACCCATAGCTTATTTAGCTCTACTATTAGC
130 GTCCAAAAACTACACTGACGGTGTATCAAATAATAACCCATAGCTTATTTAGCTCTACTATTAGC
*
14087 AGAAATAGCAAAATGAACTTGATCAAATTGTCCGAAGCCAAAATCGTCGGAACTCGGAATTTGGA
195 AGAAATAGCAAAATGAACTTGATCAAATTGTCCGAAGCCAAAATCGTCGGAACTCCGAATTTGGA
*
14152 AGAAAAATTGAGAGAGTTGATAACCAAAAATTTTACTATTAAAGTTATT
260 AGAAAAAATGAGAGAGTTGATAACCAAAAATTTTACTATTAAAGTTATT
14201 ATTTATAAAA
Statistics
Matches: 276, Mismatches: 28, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
349 193 0.70
350 1 0.00
351 37 0.13
352 44 0.16
353 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (352 bp):
AGTTTAGCAGACTGCATGTGCGGGTCTAGAAAGGTGACATGTGTCCCCTTAGGGACTAGATTGAA
ATATTAAAAATCTAATTAATTCTGAAAAATGAGGAACTTGTCAATCTTTGAACCCGCTTGTGGAG
TCCAAAAACTACACTGACGGTGTATCAAATAATAACCCATAGCTTATTTAGCTCTACTATTAGCA
GAAATAGCAAAATGAACTTGATCAAATTGTCCGAAGCCAAAATCGTCGGAACTCCGAATTTGGAA
GAAAAAATGAGAGAGTTGATAACCAAAAATTTTACTATTAAAGTTATTGATAAAATTATTATCTA
AAACATATTAGCCAAAATCGTCAGTAA
Found at i:14215 original size:20 final size:20
Alignment explanation
Indices: 14192--14230 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
14182 TTTTACTATT
*
14192 AAAGTTATTATTTATAAAAA
1 AAAGTTATTATTGATAAAAA
14212 AAAGTTATTATTGATAAAA
1 AAAGTTATTATTGATAAAA
14231 TTATTTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
AAAGTTATTATTGATAAAAA
Found at i:15979 original size:15 final size:15
Alignment explanation
Indices: 15959--15989 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15949 TTTTTTGCTT
15959 AAGAAAAAAAAATTA
1 AAGAAAAAAAAATTA
*
15974 AAGAAAAGAAAATTA
1 AAGAAAAAAAAATTA
15989 A
1 A
15990 TCACCTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AAGAAAAAAAAATTA
Done.