Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002129.1 Kokia drynarioides strain JFW-HI SEQ_114063, 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: 24764
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 94 characters in sequence are not A, C, G, or T
Found at i:312 original size:24 final size:25
Alignment explanation
Indices: 282--348 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
272 TGTGTAGTAT
282 AAAATTATAAAATTAAATATTG-TA
1 AAAATTATAAAATTAAATATTGATA
*
306 AAAATTATAAAA--AATTATTGATA
1 AAAATTATAAAATTAAATATTGATA
*
329 ATAA-TATAAAATTAAATATT
1 AAAATTATAAAATTAAATATT
349 CTATTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 14 0.38
23 5 0.14
24 18 0.49
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (25 bp):
AAAATTATAAAATTAAATATTGATA
Found at i:1151 original size:22 final size:22
Alignment explanation
Indices: 1101--1152 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1091 GTTTTATTGT
*
1101 AACAATATTTTAATTTGACATG
1 AACAATTTTTTAATTTGACATG
*** *
1123 TTTAATTTTTTAATTTGACTTG
1 AACAATTTTTTAATTTGACATG
1145 AACAATTT
1 AACAATTT
1153 CATTCGACTT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (22 bp):
AACAATTTTTTAATTTGACATG
Found at i:1568 original size:31 final size:31
Alignment explanation
Indices: 1506--1568 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
1496 TTTATCCCTC
*
1506 ATTTCTATTAATTTTATAAATATGATTTATAT
1 ATTTATATTAATTTTATAAATA-GATTTATAT
1538 ATTTATATTGAATTTTATAAATA-ATTTATAT
1 ATTTATATT-AATTTTATAAATAGATTTATAT
1569 TAATTGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 8 0.28
32 8 0.28
33 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (31 bp):
ATTTATATTAATTTTATAAATAGATTTATAT
Found at i:9553 original size:2 final size:2
Alignment explanation
Indices: 9546--9570 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9536 GTATACCTTG
9546 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9571 ATAAATCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14222 original size:15 final size:14
Alignment explanation
Indices: 14202--14258 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
14192 TGACTTGTAT
*
14202 ATAAAACTATGATAA
1 ATAAAAATAT-ATAA
14217 ATAAAAATATATAA
1 ATAAAAATATATAA
*
14231 ATTTATTAAATAT-TAA
1 A--TA-AAAATATATAA
14247 ATAAAAATATAT
1 ATAAAAATATAT
14259 TTTTAATGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
13 6 0.17
14 8 0.23
15 9 0.26
16 6 0.17
17 6 0.17
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAAAAATATATAA
Found at i:22260 original size:35 final size:35
Alignment explanation
Indices: 22195--22281 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 35
22185 GTGACGGATC
* ** *
22195 CACATTGCGAGCTCAATTCTTCTGCAAGCTCTCCA
1 CACATTGCGAGCTCAACTCACCTACAAGCTCTCCA
*
22230 CACATTGCGAGCTCAACTCACCTACGAGCTCTCCA
1 CACATTGCGAGCTCAACTCACCTACAAGCTCTCCA
* * *
22265 CATAGTGCGACCTCAAC
1 CACATTGCGAGCTCAAC
22282 AAATCTGTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.25, C:0.37, G:0.15, T:0.23
Consensus pattern (35 bp):
CACATTGCGAGCTCAACTCACCTACAAGCTCTCCA
Done.