Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001531.1 Kokia drynarioides strain JFW-HI SEQ_113098, 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: 15381
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:96 original size:30 final size:30
Alignment explanation
Indices: 39--180 Score: 187
Period size: 30 Copynumber: 4.8 Consensus size: 30
29 GAGGGTCCCG
* * * *
39 AAACTTCCAAAAATCTCGTTTTT-ACCCCC
1 AAACTTCTAAAAATCCCATTTTTGACCCCA
* *
68 GAACTTTTAAAAATCCCATTTTTGACCCCA
1 AAACTTCTAAAAATCCCATTTTTGACCCCA
98 AAACTTCTAAAAATCCCATTTTTGACCCCA
1 AAACTTCTAAAAATCCCATTTTTGACCCCA
* **
128 AAACTTCCAAAAATATCATTTTTGACCCCA
1 AAACTTCTAAAAATCCCATTTTTGACCCCA
*
158 AAACTTCTAAAAATTCCATTTTT
1 AAACTTCTAAAAATCCCATTTTT
181 AGCCCCGAAC
Statistics
Matches: 98, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
29 18 0.18
30 80 0.82
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
AAACTTCTAAAAATCCCATTTTTGACCCCA
Found at i:148 original size:60 final size:59
Alignment explanation
Indices: 39--244 Score: 193
Period size: 60 Copynumber: 3.5 Consensus size: 59
29 GAGGGTCCCG
* * * ** ** *
39 AAACTTCCAAAAATCTCGTTTTTACCCCCGAACTTTTAAAAATCCCATTTTTGACCCCA
1 AAACTTCTAAAAATCCCATTTTTACCCCAAAACTTCCAAAAATACCATTTTTGACCCCA
*
98 AAACTTCTAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATATCATTTTTGACCCCA
1 AAACTTCTAAAAATCCCATTTTT-ACCCCAAAACTTCCAAAAATACCATTTTTGACCCCA
* * * * * * *
158 AAACTTCTAAAAATTCCATTTTTAGCCCC-GAACTTCCCAAAATTCCAATTTT-ATCTCCG
1 AAACTTCTAAAAATCCCATTTTTA-CCCCAAAACTTCCAAAAATACCATTTTTGA-CCCCA
* *
217 AAACTTCCTAAAATTACCA-TTTTACCCC
1 AAACTT-CTAAAAATCCCATTTTTACCCC
245 CGTATGTCCA
Statistics
Matches: 124, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
58 5 0.04
59 53 0.43
60 66 0.53
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
AAACTTCTAAAAATCCCATTTTTACCCCAAAACTTCCAAAAATACCATTTTTGACCCCA
Found at i:191 original size:29 final size:29
Alignment explanation
Indices: 64--239 Score: 144
Period size: 30 Copynumber: 5.9 Consensus size: 29
54 TCGTTTTTAC
* *
64 CCCCGAACTTTTAAAAATCCCATTTTTGA
1 CCCCGAACTTCTAAAAATTCCATTTTTGA
* *
93 CCCCAAAACTTCTAAAAATCCCATTTTTGA
1 CCCC-GAACTTCTAAAAATTCCATTTTTGA
* *
123 CCCCAAAACTTCCAAAAATAT-CATTTTTGA
1 CCCC-GAACTTCTAAAAAT-TCCATTTTTGA
*
153 CCCCAAAACTTCTAAAAATTCCATTTTT-A
1 CCCC-GAACTTCTAAAAATTCCATTTTTGA
** *
182 GCCCCGAACTTCCCAAAATTCCAATTTT-A
1 -CCCCGAACTTCTAAAAATTCCATTTTTGA
*
211 TCTCCGAAACTTCCT-AAAATTACCATTTT
1 -CCCCG-AACTT-CTAAAAATT-CCATTTT
240 ACCCCCGTAT
Statistics
Matches: 127, Mismatches: 13, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
29 30 0.24
30 90 0.71
31 7 0.06
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
CCCCGAACTTCTAAAAATTCCATTTTTGA
Found at i:209 original size:30 final size:30
Alignment explanation
Indices: 35--239 Score: 127
Period size: 30 Copynumber: 6.9 Consensus size: 30
25 CCCCGAGGGT
* * *
35 CCCGAAACTT-CCAAAAATCTCGTTTTTACC
1 CCCGAAACTTCCCAAAATTC-CATTTTTAGC
*** *
65 CCCG-AACTTTTAAAAATCCCATTTTT-GAC
1 CCCGAAACTTCCCAAAATTCCATTTTTAG-C
* ** *
94 CCCAAAACTTCTAAAAATCCCATTTTT-GAC
1 CCCGAAACTTCCCAAAATTCCATTTTTAG-C
* *
124 CCCAAAACTTCCAAAAATAT-CATTTTT-GAC
1 CCCGAAACTTCCCAAAAT-TCCATTTTTAG-C
* **
154 CCCAAAACTTCTAAAAATTCCATTTTTAGC
1 CCCGAAACTTCCCAAAATTCCATTTTTAGC
* *
184 CCCG-AACTTCCCAAAATTCCAATTTTATC
1 CCCGAAACTTCCCAAAATTCCATTTTTAGC
* *
213 TCCGAAACTTCCTAAAATTACCATTTT
1 CCCGAAACTTCCCAAAATT-CCATTTT
240 ACCCCCGTAT
Statistics
Matches: 148, Mismatches: 19, Indels: 15
0.81 0.10 0.08
Matches are distributed among these distances:
29 40 0.27
30 101 0.68
31 7 0.05
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (30 bp):
CCCGAAACTTCCCAAAATTCCATTTTTAGC
Found at i:11231 original size:21 final size:21
Alignment explanation
Indices: 11205--11270 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
11195 CAAACATTAT
11205 TAAAATTAAGTATCATAATAA
1 TAAAATTAAGTATCATAATAA
* * *
11226 TAAAATCACA--AACAT--TAT
1 TAAAATTA-AGTATCATAATAA
11244 TAAAATTAAGTATCATAATAA
1 TAAAATTAAGTATCATAATAA
11265 TAAAAT
1 TAAAAT
11271 ACGTATTGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
17 1 0.03
18 9 0.26
19 4 0.12
20 4 0.12
21 15 0.44
22 1 0.03
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (21 bp):
TAAAATTAAGTATCATAATAA
Found at i:11240 original size:39 final size:39
Alignment explanation
Indices: 11187--11270 Score: 159
Period size: 39 Copynumber: 2.1 Consensus size: 39
11177 GATTAATTTA
11187 AAAATTCACAAACATTATTAAAATTAAGTATCATAATAAT
1 AAAA-TCACAAACATTATTAAAATTAAGTATCATAATAAT
11227 AAAATCACAAACATTATTAAAATTAAGTATCATAATAAT
1 AAAATCACAAACATTATTAAAATTAAGTATCATAATAAT
11266 AAAAT
1 AAAAT
11271 ACGTATTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 40 0.91
40 4 0.09
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (39 bp):
AAAATCACAAACATTATTAAAATTAAGTATCATAATAAT
Done.