Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000888.1 Kokia drynarioides strain JFW-HI SEQ_112011, 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: 8040
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:214 original size:16 final size:15
Alignment explanation
Indices: 159--218 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
149 CACTTTATAA
*
159 TTGGACCATTTGTAT
1 TTGGGCCATTTGTAT
* *
174 TTGGGCCATCTGTAA
1 TTGGGCCATTTGTAT
* *
189 CTGGGTCATTTGTTAT
1 TTGGGCCATTTG-TAT
205 TTGGGCCATTTGTA
1 TTGGGCCATTTGTA
219 ATTGAGACTT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 23 0.66
16 12 0.34
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43
Consensus pattern (15 bp):
TTGGGCCATTTGTAT
Found at i:232 original size:31 final size:31
Alignment explanation
Indices: 165--233 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
155 ATAATTGGAC
* *
165 CATTTG-TATTTGGGCCATCTGTAACTGGGT
1 CATTTGTTATTTGGGCCATCTGTAACTGAGA
* *
195 CATTTGTTATTTGGGCCATTTGTAATTGAGA
1 CATTTGTTATTTGGGCCATCTGTAACTGAGA
*
226 CTTTTGTT
1 CATTTGTT
234 TTGGATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.17, C:0.13, G:0.23, T:0.46
Consensus pattern (31 bp):
CATTTGTTATTTGGGCCATCTGTAACTGAGA
Found at i:325 original size:17 final size:17
Alignment explanation
Indices: 265--327 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
255 TGGACTTTTC
* *
265 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
*
282 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
299 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
316 TAAACTTAAATT
1 TAAATTTAAATT
328 CAATTTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:2180 original size:20 final size:20
Alignment explanation
Indices: 2155--2192 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2145 CTTCAGTGAG
* *
2155 ACTTCTATCGATAGAACTTC
1 ACTTCTACCGATACAACTTC
2175 ACTTCTACCGATACAACT
1 ACTTCTACCGATACAACT
2193 ACAGTTCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.32
Consensus pattern (20 bp):
ACTTCTACCGATACAACTTC
Found at i:2431 original size:20 final size:20
Alignment explanation
Indices: 2408--2449 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2398 CTACCAGTAA
2408 AACTTCACTTCTACTGATAC
1 AACTTCACTTCTACTGATAC
*
2428 AACTTCAGTTCTACTGATAC
1 AACTTCACTTCTACTGATAC
2448 AA
1 AA
2450 GTATGCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (20 bp):
AACTTCACTTCTACTGATAC
Found at i:4701 original size:24 final size:24
Alignment explanation
Indices: 4674--4720 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4664 AGTTTTTAGA
*
4674 ATATTTAATATTTATTAAAATAAT
1 ATATTTAACATTTATTAAAATAAT
* *
4698 ATATTTGACATTTATTAGAATAA
1 ATATTTAACATTTATTAAAATAA
4721 AATCTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
ATATTTAACATTTATTAAAATAAT
Found at i:4757 original size:17 final size:18
Alignment explanation
Indices: 4723--4769 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
4713 TAGAATAAAA
*
4723 TCTT-TTATTAATTCTTT
1 TCTTATTATAAATTCTTT
* *
4740 TTTTATT-TAAATTTTTT
1 TCTTATTATAAATTCTTT
4757 TCTTATTATAAAT
1 TCTTATTATAAAT
4770 ATCTATGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (18 bp):
TCTTATTATAAATTCTTT
Found at i:5107 original size:43 final size:43
Alignment explanation
Indices: 5032--5114 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
5022 ACCACTAAAT
* * * *
5032 AACATGGTCTTTAACGGCGCTTTTCTCACAAACGCCGCTACAA
1 AACATGATCTTTAACGACGCTTTCCCCACAAACGCCGCTACAA
* * *
5075 AACATGATCTTTAACGATGCTTTCCCCGCAAACGTCGCTA
1 AACATGATCTTTAACGACGCTTTCCCCACAAACGCCGCTA
5115 AAATTAACAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (43 bp):
AACATGATCTTTAACGACGCTTTCCCCACAAACGCCGCTACAA
Found at i:7219 original size:33 final size:34
Alignment explanation
Indices: 7182--7248 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
7172 AAATAATTAA
7182 TTAAATATTTGGATTG-TTTTAATAATTAAATAT
1 TTAAATATTTGGATTGTTTTTAATAATTAAATAT
*
7215 TTAAATATTTGGATTGTTTTTAATTATTAAATAT
1 TTAAATATTTGGATTGTTTTTAATAATTAAATAT
7249 AATTAACTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (34 bp):
TTAAATATTTGGATTGTTTTTAATAATTAAATAT
Done.