Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014455.1 Kokia drynarioides strain JFW-HI SEQ_129494, 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: 326107
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 41 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:307040 original size:21 final size:20
Alignment explanation
Indices: 307008--307047 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
306998 AATTTAAATA
*
307008 TCATCACCAATTATTTCAAC
1 TCATCACCAATTATCTCAAC
*
307028 TCATCACATAATTATCTCAA
1 TCATCAC-CAATTATCTCAA
307048 ATAATTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.35
Consensus pattern (20 bp):
TCATCACCAATTATCTCAAC
Found at i:307585 original size:21 final size:20
Alignment explanation
Indices: 307547--307585 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
307537 TTTCATAGCT
* *
307547 TCAAAATCTAACATTTTCTA
1 TCAAAATCAAACAATTTCTA
307567 TCAAAACTCAAACAATTTC
1 TCAAAA-TCAAACAATTTC
307586 ACTCTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
TCAAAATCAAACAATTTCTA
Found at i:313782 original size:440 final size:439
Alignment explanation
Indices: 312723--313927 Score: 1676
Period size: 441 Copynumber: 2.7 Consensus size: 439
312713 ATCATAGGGT
* *** *
312723 AAAAGTAAATATGAAAGATTTTATTTTATTTTATTTAAATTAGTGGCATCATTTGATCCCTTGAT
1 AAAAGTAGATATGAAA-A--TTATTTTATTTTATTTAAATTAGTGGCATCATTTGATGTGTTAAT
* * * * * *
312788 TGTCGGAGAATTTTCACATCCAATACATCTAATATAAATATTTATTTTTCTTAGTATTATAATTA
63 TGTTGGTGAATTTTCACAGCCAATACATCAAATATAAATTTTTATTTTTCTTAATATTATAATTA
* * * * * *
312853 TTTATTTTCTATTTATTTTTTACTGT-TTAAAGCAAGTAGTTGACGCTTAAAAGTAATACGATTA
128 CTTATTTTCTTTTTATTTTTTACT-TCCTAAAGCAAGTAGTTGATGCTTAAAAGTAATGCAATTA
* ** * * * * *
312917 -TTATTTTTAAACAAGACCCTGTTAATTTAAGGAAAATTTACAA--TCCACATTG-TAGAAATTT
192 TTTTTTTTTGTACAGGACCTTGTTAATTTAAGGAAAA-TTA-AAGTTTCAAATTGCAAG-AATTT
*
312978 AAAGG-AGATACATAATCTTTCAAGAGCAATCAACCTTGAATTACTTGATTGCTCTAACTGTGAA
254 -AAGGAAGATACATAATCTTTCAAGAGCCATCAACCTTGAATTACTTGATTGCTCTAACTGTGAA
*
313042 AGTTCGGTTGAACTTTGGAATGAAGATGATCATAGGGTATGTGTTTCCATACTTTCTTTGAAAAA
318 AGTTCAGTTGAACTTTGGAATGAAGATGATCATAGGGTATGTGTTTCCATACTTTCTTTGAAAAA
* * *
313107 GATTTATAATTTTATGTATCAAATATTTATATTATGACATCTTATTTAAAGTTTTTA
383 GATTTATAATTTTATGTATCAAATATTCATATGATGACATCTTATTTAAAGTGTTTA
313164 AAAAGTAGATATGAAAAAATTTATTTTATTTTATTTAAATTAGTGGCATCATTTGATGTGTTAAT
1 AAAAGTAGATATG--AAAA-TTATTTTATTTTATTTAAATTAGTGGCATCATTTGATGTGTTAAT
*
313229 TGTTGGTGAATTTTCACAGCCAAAACATCAAATATAAATTTTTATTTTTCTTAATATTATAATTA
63 TGTTGGTGAATTTTCACAGCCAATACATCAAATATAAATTTTTATTTTTCTTAATATTATAATTA
* * * *
313294 CTTATTTCCTTTTTGTTTTTTACTGCCTAAAGCAAGTAGTTAATGCTTAAAAGTAATGCAATTAT
128 CTTATTTTCTTTTTATTTTTTACTTCCTAAAGCAAGTAGTTGATGCTTAAAAGTAATGCAATTAT
* * *
313359 TTCTTTTTTGTATAGGACCTTGTTAATTTATGGAAAATTAAGGTTTCAAATTGCAAGAATTTAAG
193 TT-TTTTTTGTACAGGACCTTGTTAATTTAAGGAAAATTAAAGTTTCAAATTGCAAGAATTTAAG
* *
313424 GAAGATACCTAATCTTTCAAGAGCCATCAACCTTGAATCT-CTTGATTGTTCTAACTGTGAAAGC
257 GAAGATACATAATCTTTCAAGAGCCATCAACCTTGAAT-TACTTGATTGCTCTAACTGTGAAAG-
* *
313488 TT-AGTTGAACTTTGGAATGAAGATGATCATAGGGTATGTGTTTTCGTACTTTCTTTGGAAAAAA
320 TTCAGTTGAACTTTGGAATGAAGATGATCATAGGGTATGTGTTTCCATACTTTCTTT-G-AAAAA
*
313552 GATTTATAATTTTATGTATCAAATATTCATATGGTGACATCTTATTTAAAGTGTTTA
383 GATTTATAATTTTATGTATCAAATATTCATATGATGACATCTTATTTAAAGTGTTTA
* * *
313609 GAAAA-TATATATG-AAA-TATTTTATTTTATTTAAATTGGTGGCATCATTTAATGTGTTAATTG
1 -AAAAGTAGATATGAAAATTATTTTATTTTATTTAAATTAGTGGCATCATTTGATGTGTTAATTG
* *
313671 TTGGTGAATTTTCATAGCCAATACATCAAAAATAAATTTTTATTTTTCTTAATATTATAATTACT
65 TTGGTGAATTTTCACAGCCAATACATCAAATATAAATTTTTATTTTTCTTAATATTATAATTACT
* * *
313736 TATTTTCTTTTTATTTTTTACTTCCTAAAACAAGTAGTTGATGCTTAAAAGTAATGCAGTTTTTT
130 TATTTTCTTTTTATTTTTTACTTCCTAAAGCAAGTAGTTGATGCTTAAAAGTAATGCAATTATTT
* * * *
313801 TTTTTTGTACAGGATCTTATTAATTTAAGGATAATTAAAGTTTCAAATTGCAAGAATTTAAAGAA
195 TTTTTTGTACAGGACCTTGTTAATTTAAGGAAAATTAAAGTTTCAAATTGCAAGAATTTAAGGAA
*
313866 GATACTTAATCTTTCAAGAGCCATCAACCTTGAATTACTTGATTGCTCTAACTGTGAAAGTT
260 GATACATAATCTTTCAAGAGCCATCAACCTTGAATTACTTGATTGCTCTAACTGTGAAAGTT
313928 TTGTCGAACT
Statistics
Matches: 684, Mismatches: 65, Indels: 33
0.87 0.08 0.04
Matches are distributed among these distances:
438 3 0.00
439 114 0.17
440 164 0.24
441 166 0.24
442 13 0.02
443 149 0.22
444 6 0.01
445 65 0.10
446 4 0.01
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (439 bp):
AAAAGTAGATATGAAAATTATTTTATTTTATTTAAATTAGTGGCATCATTTGATGTGTTAATTGT
TGGTGAATTTTCACAGCCAATACATCAAATATAAATTTTTATTTTTCTTAATATTATAATTACTT
ATTTTCTTTTTATTTTTTACTTCCTAAAGCAAGTAGTTGATGCTTAAAAGTAATGCAATTATTTT
TTTTTGTACAGGACCTTGTTAATTTAAGGAAAATTAAAGTTTCAAATTGCAAGAATTTAAGGAAG
ATACATAATCTTTCAAGAGCCATCAACCTTGAATTACTTGATTGCTCTAACTGTGAAAGTTCAGT
TGAACTTTGGAATGAAGATGATCATAGGGTATGTGTTTCCATACTTTCTTTGAAAAAGATTTATA
ATTTTATGTATCAAATATTCATATGATGACATCTTATTTAAAGTGTTTA
Found at i:325605 original size:40 final size:40
Alignment explanation
Indices: 325550--325626 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
325540 AAGACTGTTT
** *
325550 ATGTGTGAGATTGGTTTTTGTTGTAATCTGTGATTTTCTC
1 ATGTGTGAGATTGGTTCGTGTTATAATCTGTGATTTTCTC
*
325590 ATGTGTGAGATTGGTTCGTGTTATAATCTGTGGTTTT
1 ATGTGTGAGATTGGTTCGTGTTATAATCTGTGATTTT
325627 ATCTTGAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.16, C:0.06, G:0.27, T:0.51
Consensus pattern (40 bp):
ATGTGTGAGATTGGTTCGTGTTATAATCTGTGATTTTCTC
Done.