Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000992.1 Kokia drynarioides strain JFW-HI SEQ_112189, 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: 2812
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Found at i:180 original size:17 final size:17
Alignment explanation
Indices: 150--197 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
140 TGGGCCCAAC
*
150 AAAATTTAAATTTATTTT
1 AAAA-TTAAATTTATTTG
*
168 AAAATTAAGTTTATTTG
1 AAAATTAAATTTATTTG
*
185 AAATTTAAATTTA
1 AAAATTAAATTTA
198 AATTTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
AAAATTAAATTTATTTG
Found at i:191 original size:23 final size:22
Alignment explanation
Indices: 165--210 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
155 TTAAATTTAT
*
165 TTTAAAATTAAGTTTATTTGAAA
1 TTTAAAATTAAATTTATTT-AAA
*
188 TTTAAATTTAAATTTATTTAAA
1 TTTAAAATTAAATTTATTTAAA
210 T
1 T
211 AATGTCCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTAAAATTAAATTTATTTAAA
Found at i:2124 original size:30 final size:30
Alignment explanation
Indices: 2063--2424 Score: 313
Period size: 30 Copynumber: 12.2 Consensus size: 30
2053 TAAGAGGTCC
*
2063 CGAAACTTCCAAAAA-TCACATTTTTTTACCT
1 CGAAACTTCCAAAAATTC-CA-TTTTTGACCT
*
2094 CGAAACTTCTAAAAATTCCATTTTTGACCT
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
2124 CG-AACTTCCAAAAATTCCATTTTT-ACCCT
1 CGAAACTTCCAAAAATTCCATTTTTGA-CCT
* * *
2153 CTG-AACTTCCAAAAATCCCATTTTTAACCC
1 C-GAAACTTCCAAAAATTCCATTTTTGACCT
*
2183 CAAAACTTCCAAAAATTCCATTTTTGACC-
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
* * *
2212 CTAAAACTTCTAAAAATCCCATTTTTGACCT
1 C-GAAACTTCCAAAAATTCCATTTTTGACCT
*
2243 CAAAACTTCCAAAAATTCCATTTTT-ACCCT
1 CGAAACTTCCAAAAATTCCATTTTTGA-CCT
* *
2273 CG-AACTT-CAAAAATTTCATTTTT-ACCC
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
* * * * *
2300 CTAAAACTTCAAAAAATTCTAATTTT-ACCC
1 C-GAAACTTCCAAAAATTCCATTTTTGACCT
* *
2330 CTG-AACTTCTAAAAACTCCATTTTTGACC-
1 C-GAAACTTCCAAAAATTCCATTTTTGACCT
* *
2359 CTAAACTTCCAAAAATTACCA-TTTTGCCCT
1 CGAAACTTCCAAAAATT-CCATTTTTGACCT
* * *
2389 TG-AA-TGTCCAAAAACTCCATTTTCGACCT
1 CGAAACT-TCCAAAAATTCCATTTTTGACCT
2418 CGAAACT
1 CGAAACT
2425 CTTAAAATTA
Statistics
Matches: 277, Mismatches: 35, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
27 3 0.01
28 21 0.08
29 94 0.34
30 138 0.50
31 19 0.07
32 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (30 bp):
CGAAACTTCCAAAAATTCCATTTTTGACCT
Found at i:2190 original size:60 final size:60
Alignment explanation
Indices: 2065--2416 Score: 347
Period size: 58 Copynumber: 6.0 Consensus size: 60
2055 AGAGGTCCCG
* * *
2065 AAACTTCCAAAAA-TCACATTTTTTTA-CCTC-GAAACTTCTAAAAATTCCATTTTTGACCTC-
1 AAACTTCCAAAAATTC-CA--TTTTTACCCTCTG-AACTTCCAAAAATCCCATTTTTGACCCCA
* *
2125 GAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATCCCATTTTTGACCCCA
** * *
2185 AAACTTCCAAAAATTCCATTTTTGACCCT-AAAACTTCTAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCTGAACTTCCAAAAATCCCATTTTTGACCCCA
**
2245 AAACTTCCAAAAATTCCATTTTTACCCTC-GAACTT-CAAAAATTTCATTTTT-ACCCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATCCCATTTTTGACCCC-A
* * * * *
2303 AAACTTCAAAAAATTCTAATTTTACCC-CTGAACTTCTAAAAA-CTCCATTTTTGA-CCCT
1 AAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATC-CCATTTTTGACCCCA
* *
2361 AAACTTCCAAAAATTACCA-TTTTGCCCT-TGAA-TGTCCAAAAA-CTCCATTTTCGACC
1 AAACTTCCAAAAATT-CCATTTTTACCCTCTGAACT-TCCAAAAATC-CCATTTTTGACC
2417 TCGAAACTCT
Statistics
Matches: 249, Mismatches: 28, Indels: 31
0.81 0.09 0.10
Matches are distributed among these distances:
57 6 0.02
58 93 0.37
59 56 0.22
60 87 0.35
61 7 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.34
Consensus pattern (60 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:2452 original size:58 final size:58
Alignment explanation
Indices: 2061--2504 Score: 206
Period size: 58 Copynumber: 7.5 Consensus size: 58
2051 TCTAAGAGGT
* * * *
2061 CCCGAAACTTCCAAAAATCA-CATTTTTTTA-CCTCGAAACT-TCTAAAAATTCCATTTTTGA
1 CCCGAAACTTCCAAAAATTACCA---TTTTACCCTCG-AA-TGTCCAAAAACTCCATTTTCGA
**
2121 CCTCG-AACTTCCAAAAATT-CCATTTTTACCCTCTGAACT-TCCAAAAA-TCCCATTTTTAA
1 CC-CGAAACTTCCAAAAATTACCA-TTTTACCCTC-GAA-TGTCCAAAAACT-CCATTTTCGA
* ** * *
2180 CCCCAAAACTTCCAAAAATT-CCATTTTTGACCCTAAAACT-TCTAAAAA-TCCCATTTTTGA
1 -CCCGAAACTTCCAAAAATTACCA-TTTT-ACCCTCGAA-TGTCCAAAAACT-CCATTTTCGA
* * * *
2240 CCTCAAAACTTCCAAAAATT-CCATTTTTACCCTCGAACT-T-CAAAAATTTCATTTT-TA
1 CC-CGAAACTTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCCAAAAACTCCATTTTCGA
* * * * *
2297 CCCCTAAAACTTCAAAAAATT-CTAATTTTACCC-CTGAACT-TCTAAAAACTCCATTTTTGA
1 -CCC-GAAACTTCCAAAAATTAC-CATTTTACCCTC-GAA-TGTCCAAAAACTCCATTTTCGA
* * *
2357 CCCTAAACTTCCAAAAATTACCATTTTGCCCTTGAATGTCCAAAAACTCCATTTTCGA
1 CCCGAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCCATTTTCGA
** * * * * **
2415 CCTCGAAAC-TCTTAAAATTACCCTTTTA-CCTCCGAATGTCTAAAAATTCCTTTTTTAA
1 CC-CGAAACTTCCAAAAATTACCATTTTACCCT-CGAATGTCCAAAAACTCCATTTTCGA
** * *
2473 CTCCGAATTTTCCCAAAATTACCATTTCACCC
1 C-CCGAAACTTCCAAAAATTACCATTTTACCC
2505 CCAAGAATCC
Statistics
Matches: 317, Mismatches: 43, Indels: 48
0.78 0.11 0.12
Matches are distributed among these distances:
57 7 0.02
58 135 0.43
59 76 0.24
60 92 0.29
61 7 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
CCCGAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCCATTTTCGA
Done.