Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013650.1 Kokia drynarioides strain JFW-HI SEQ_128678, 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: 13879
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Warning! 205 characters in sequence are not A, C, G, or T
Found at i:221 original size:23 final size:24
Alignment explanation
Indices: 182--233 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
172 TAATAGGGAT
182 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCATTATCAC
* *
205 TTTCAA-TTCCAATTTCATTTTCAC
1 TTTCAATTTACAA-TTCATTATCAC
229 TTTCA
1 TTTCA
234 TTTTCACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 10 0.40
24 10 0.40
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTCAATTTACAATTCATTATCAC
Found at i:226 original size:6 final size:6
Alignment explanation
Indices: 201--251 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
191 ACAATTCATA
* * * * *
201 TCACTT TCAATT CCAATT TCATTT TCACTT TCATTT TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
249 TCA
1 TCA
252 ATTTTGATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (6 bp):
TCACTT
Found at i:232 original size:12 final size:12
Alignment explanation
Indices: 201--251 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
191 ACAATTCATA
*
201 TCACTTTCAATT
1 TCACTTTCATTT
* *
213 CCAATTTCATTT
1 TCACTTTCATTT
225 TCACTTTCATTT
1 TCACTTTCATTT
*
237 TCACTTTCACTT
1 TCACTTTCATTT
249 TCA
1 TCA
252 ATTTTGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (12 bp):
TCACTTTCATTT
Found at i:238 original size:18 final size:19
Alignment explanation
Indices: 201--256 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 19
191 ACAATTCATA
* *
201 TCACTTTCAATTCCAA-TT
1 TCACTTTCACTTTCAATTT
*
219 TCATTTTCACTTTC-ATTT
1 TCACTTTCACTTTCAATTT
237 TCACTTTCACTTTCAATTT
1 TCACTTTCACTTTCAATTT
256 T
1 T
257 GATCACAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 1 0.03
18 26 0.81
19 5 0.16
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (19 bp):
TCACTTTCACTTTCAATTT
Found at i:2557 original size:11 final size:11
Alignment explanation
Indices: 2541--2571 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
2531 TTCTGACTTT
2541 GAAAAATTATA
1 GAAAAATTATA
2552 GAAAAA-TATA
1 GAAAAATTATA
2562 GAAAAATTAT
1 GAAAAATTAT
2572 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:3119 original size:6 final size:6
Alignment explanation
Indices: 3108--3158 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
3098 TGATCAAAAT
* * * * *
3108 TGAAAG TGAAAG TGAAAA TGAAAG TGAAAA TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
3156 TGA
1 TGA
3159 TATGAATTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:3129 original size:12 final size:12
Alignment explanation
Indices: 3108--3158 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
3098 TGATCAAAAT
*
3108 TGAAAGTGAAAG
1 TGAAAATGAAAG
3120 TGAAAATGAAAG
1 TGAAAATGAAAG
*
3132 TGAAAATGAAAT
1 TGAAAATGAAAG
* *
3144 TGGAATTGAAAG
1 TGAAAATGAAAG
3156 TGA
1 TGA
3159 TATGAATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (12 bp):
TGAAAATGAAAG
Found at i:3131 original size:18 final size:18
Alignment explanation
Indices: 3103--3158 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
3093 ATTTGTGATC
3103 AAAATTGAAAGTGAAAGTG
1 AAAA-TGAAAGTGAAAGTG
*
3122 AAAATGAAAGTGAAAATG
1 AAAATGAAAGTGAAAGTG
* * *
3140 AAATTGGAATTGAAAGTG
1 AAAATGAAAGTGAAAGTG
3158 A
1 A
3159 TATGAATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (18 bp):
AAAATGAAAGTGAAAGTG
Found at i:4036 original size:92 final size:92
Alignment explanation
Indices: 3879--4062 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
3869 GGTAATTTAC
3879 TTTGAAGAAAAATCACATGTACAAATGGTATACTTAGGTGTACCTAATGAATAGATTATCAATAT
1 TTTGAAGAAAAATCACATGTACAAATGGTATACTTAGGTGTACCTAATGAATAGATTATCAATAT
3944 TGTTTTGAAAATTTACATGAATTGAAA
66 TGTTTTGAAAATTTACATGAATTGAAA
3971 TTTGAAGAAAAATCACATGTACAAATGGTATACTTAGGTGTACCTAATGAATAGATTATCAATAT
1 TTTGAAGAAAAATCACATGTACAAATGGTATACTTAGGTGTACCTAATGAATAGATTATCAATAT
4036 TGTTTTGAAAATTTACATGAATTGAAA
66 TGTTTTGAAAATTTACATGAATTGAAA
4063 GAAAAAATTT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (92 bp):
TTTGAAGAAAAATCACATGTACAAATGGTATACTTAGGTGTACCTAATGAATAGATTATCAATAT
TGTTTTGAAAATTTACATGAATTGAAA
Found at i:11871 original size:21 final size:21
Alignment explanation
Indices: 11847--11886 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11837 CTGTAAAGTT
*
11847 AATTTAAAAGTTACAAACAAA
1 AATTTAAAAGATACAAACAAA
* *
11868 AATTTTATAGATACAAACA
1 AATTTAAAAGATACAAACA
11887 CACATATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (21 bp):
AATTTAAAAGATACAAACAAA
Done.