Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006132.1 Kokia drynarioides strain JFW-HI SEQ_120659, 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: 50644
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:13841 original size:3 final size:3
Alignment explanation
Indices: 13835--13862 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13825 AAGCAGCAGG
13835 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
13863 GATGGTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:26363 original size:20 final size:22
Alignment explanation
Indices: 26317--26356 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
26307 AAATTTTATG
*
26317 AATTTGTTATAATTTTTAAGTT
1 AATTTGTTATAATTTTTAAATT
26339 AATTT-TTAT-ATTTTTAAA
1 AATTTGTTATAATTTTTAAA
26357 ATTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
AATTTGTTATAATTTTTAAATT
Found at i:27479 original size:25 final size:24
Alignment explanation
Indices: 27447--27496 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
27437 AAAAATTAAT
*
27447 AATTAAATATAACTAAGAATA-ATAA
1 AATTAAAT-TAA-TAAAAATATATAA
27472 AATTAAATTAATAAAAATATATAA
1 AATTAAATTAATAAAAATATATAA
27496 A
1 A
27497 CATATAGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 8 0.35
25 8 0.35
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATTAAATTAATAAAAATATATAA
Found at i:33232 original size:162 final size:162
Alignment explanation
Indices: 32965--33276 Score: 425
Period size: 162 Copynumber: 1.9 Consensus size: 162
32955 ATTTTCTTTT
*
32965 GAATTTGTATAAGTTCCTCATGTATTATTCTTTGCTTCTAATGCAGAGAGGTCCAACACGGCAAT
1 GAATTTGTATAAGTTCCTCATGTATTATTCTTTGCTTCTAATGCAGAGAGGTCCAACAAGGCAAT
* * * *
33030 CCCGTACTCAGTCTTCAGTGTGGACTTCTCAGAATTCTTCAAATAGGAGAGGAGTATGGGCTCGT
66 CCCGTACCCAGTCTCCAGTGCGGACTTCTCAGAATTCTTCAAATAGGAGAGGAGTACGGGCTCGT
* *
33095 TCTTGTACTTCTGCTGGAGTCCCTTTCCTTAA
131 TCTTCTACTTCTGCTAGAGTCCCTTTCCTTAA
* *
33127 GAATTTGTGTAAGTTCCTCCTGTAACATTATTCTTTGC-T-T-ATGCAGAGAGGGT-CAACAAGG
1 GAATTTGTATAAGTTCCTCATGT---ATTATTCTTTGCTTCTAATGCAGAGA-GGTCCAACAAGG
* * * *
33188 CAGTCTCGTACCCGGTCTCCATTGCGGACTTCTCAGAATTCTTCAAATAGGAGAGGAGTACGGGC
62 CAATCCCGTACCCAGTCTCCAGTGCGGACTTCTCAGAATTCTTCAAATAGGAGAGGAGTACGGGC
* *
33253 TCGTTTTTCTAGTTCTGCTAGAGT
127 TCGTTCTTCTACTTCTGCTAGAGT
33277 GCCACGGTTG
Statistics
Matches: 131, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
162 114 0.87
163 4 0.03
164 1 0.01
165 12 0.09
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (162 bp):
GAATTTGTATAAGTTCCTCATGTATTATTCTTTGCTTCTAATGCAGAGAGGTCCAACAAGGCAAT
CCCGTACCCAGTCTCCAGTGCGGACTTCTCAGAATTCTTCAAATAGGAGAGGAGTACGGGCTCGT
TCTTCTACTTCTGCTAGAGTCCCTTTCCTTAA
Found at i:43309 original size:6 final size:6
Alignment explanation
Indices: 43300--43325 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43290 ATAGAGATTC
43300 GTGCTG GTGCTG GTGCTG GTGCTG GT
1 GTGCTG GTGCTG GTGCTG GTGCTG GT
43326 TTTACTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
GTGCTG
Found at i:47309 original size:6 final size:7
Alignment explanation
Indices: 47291--47315 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47281 GAAAGGGGAA
47291 ATTTTTT
1 ATTTTTT
47298 ATTTTTT
1 ATTTTTT
47305 ATTTTTT
1 ATTTTTT
47312 ATTT
1 ATTT
47316 AAAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
ATTTTTT
Found at i:47481 original size:27 final size:27
Alignment explanation
Indices: 47443--47497 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
47433 GTAAATCTGC
47443 TTGTCAGCTCTGAATCTCCCACTTTGG
1 TTGTCAGCTCTGAATCTCCCACTTTGG
47470 TTGTCAGCTCTGAATCTCCCACTTTGG
1 TTGTCAGCTCTGAATCTCCCACTTTGG
47497 T
1 T
47498 CGTTGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (27 bp):
TTGTCAGCTCTGAATCTCCCACTTTGG
Done.