Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000428.1 Kokia drynarioides strain JFW-HI SEQ_111260, 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, 832
Length: 1388
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Found at i:334 original size:95 final size:97
Alignment explanation
Indices: 26--389 Score: 327
Period size: 96 Copynumber: 3.7 Consensus size: 97
16 TATGTATTTT
* * * **
26 TTTGTTTATTATCTATTCT-TTTTAT--AATTTTAAAT-T-TA-TTTCTTTTTGATGGAGTCATT
1 TTTGTTTTTTAT-TATT-TATTTTATAAAATTTTAAATGTATATTTTATTTTTGGTGGAACCATT
* * *
85 TTAAATGAA-GTCACCAATACAC-TTTTACTATTA
64 CTAAAT-AACGTCACCAGTTCACTTTTTACTATTA
* *
118 TTTGTTTTTTATTATTTATTTTATAATATTTTAAATGTATATTTTATTTTTGGTGGAGCCATTCT
1 TTTGTTTTTTATTATTTATTTTATAAAATTTTAAATGTATATTTTATTTTTGGTGGAACCATTCT
** * * *
183 AAATGGCGCCACCAGTTCTCAATGTATGTTTTAATTTATGTA
66 AAATAACGTCACCAG-T-TC-A---CT-TTTT-A-CTAT-TA
* * *
225 TTTTTTTGTTTATTATTTATTTTTTAAAATTTTAAAT-T-TA-TTTATTTTTGGTGGAACAATTC
1 TTTGTTT-TTTATTATTTATTTTATAAAATTTTAAATGTATATTTTATTTTTGGTGGAACCATTC
287 TAAATAACGTCACCAGTTCACTTTTTACTATTA
65 TAAATAACGTCACCAGTTCACTTTTTACTATTA
* * *
320 TTTGTCTTTTTATTATTTGTTTTACAATATTTTAAATGTATATTTTATTTTTGGTGGAACCATTC
1 TTTGT-TTTTTATTATTTATTTTATAAAATTTTAAATGTATATTTTATTTTTGGTGGAACCATTC
385 TAAAT
65 TAAAT
390 GGCGCCACCA
Statistics
Matches: 220, Mismatches: 29, Indels: 40
0.76 0.10 0.14
Matches are distributed among these distances:
90 1 0.00
91 10 0.05
92 11 0.05
93 9 0.04
94 1 0.00
95 33 0.15
96 35 0.16
97 4 0.02
98 31 0.14
99 2 0.01
102 1 0.00
103 2 0.01
104 5 0.02
105 34 0.15
106 5 0.02
107 9 0.04
108 27 0.12
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.54
Consensus pattern (97 bp):
TTTGTTTTTTATTATTTATTTTATAAAATTTTAAATGTATATTTTATTTTTGGTGGAACCATTCT
AAATAACGTCACCAGTTCACTTTTTACTATTA
Found at i:351 original size:203 final size:203
Alignment explanation
Indices: 1--399 Score: 626
Period size: 203 Copynumber: 2.0 Consensus size: 203
*
1 ATGTATGCTTTAATTTATGTATTTTTTTGTTTATTATCTATTCTTTTTATAATTTTAAATTTATT
1 ATGTATGCTTTAATTTATGTATTTTTTTGTTTATTATCTATTCTTTTTAAAATTTTAAATTTATT
* * *
66 TCTTTTTGATGGAGTCATTTTAAATGAAGTCACCAATACACTTTTACTATTATTTGTTTTTTATT
66 TATTTTTGATGGAGACATTCTAAATGAAGTCACCAATACACTTTTACTATTATTTGTTTTTTATT
* *
131 ATTTATTTTATAATATTTTAAATGTATATTTTATTTTTGGTGGAGCCATTCTAAATGGCGCCACC
131 ATTTATTTTACAATATTTTAAATGTATATTTTATTTTTGGTGGAACCATTCTAAATGGCGCCACC
196 AGTTCTCA
196 AGTTCTCA
* *
204 ATGTATGTTTTAATTTATGTATTTTTTTGTTTATTATTTA-T-TTTTTAAAATTTTAAATTTATT
1 ATGTATGCTTTAATTTATGTATTTTTTTGTTTATTATCTATTCTTTTTAAAATTTTAAATTTATT
* * *
267 TATTTTTGGTGGA-ACAATTCTAAAT-AACGTCACCAGTTCACTTTTTACTATTATTTGTCTTTT
66 TATTTTTGATGGAGAC-ATTCTAAATGAA-GTCACCAATACAC-TTTTACTATTATTTGT-TTTT
*
330 TATTATTTGTTTTACAATATTTTAAATGTATATTTTATTTTTGGTGGAACCATTCTAAATGGCGC
127 TATTATTTATTTTACAATATTTTAAATGTATATTTTATTTTTGGTGGAACCATTCTAAATGGCGC
395 CACCA
192 CACCA
400 TCCTTGGTGT
Statistics
Matches: 180, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
200 3 0.02
201 51 0.28
202 17 0.09
203 109 0.61
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (203 bp):
ATGTATGCTTTAATTTATGTATTTTTTTGTTTATTATCTATTCTTTTTAAAATTTTAAATTTATT
TATTTTTGATGGAGACATTCTAAATGAAGTCACCAATACACTTTTACTATTATTTGTTTTTTATT
ATTTATTTTACAATATTTTAAATGTATATTTTATTTTTGGTGGAACCATTCTAAATGGCGCCACC
AGTTCTCA
Found at i:399 original size:98 final size:102
Alignment explanation
Indices: 107--399 Score: 359
Period size: 98 Copynumber: 2.9 Consensus size: 102
97 ACCAATACAC
107 TTTTACTATTATTTGTTTTTTATTATTTATTTTATAATATTTTAAATGTATATTTTATTTTTGGT
1 TTTTACTATTATTTGTTTTTTATTATTTATTTTATAATATTTTAAATGTATATTTTATTTTTGGT
*
172 GGAGCCATTCTAAATGGCGCCACCAGTTCTCAATGTATG
66 GGAACCATTCTAAATGGCGCCACCAGTTCTCAA--TATG
* * * *
211 TTTTAATTTATGTATTTTTTTGTTTATTATTTATTTTTTAAAATTTTAAAT-T-TA-TTTATTTT
1 TTTT-A-CTAT-TATTTGTTT-TTTATTATTTATTTTATAATATTTTAAATGTATATTTTATTTT
* ** * *
273 TGGTGGAACAATTCTAAATAACGTCACCAG-T-TC-A-CT-
62 TGGTGGAACCATTCTAAATGGCGCCACCAGTTCTCAATATG
* *
309 TTTTACTATTATTTGTCTTTTTATTATTTGTTTTACAATATTTTAAATGTATATTTTATTTTTGG
1 TTTTACTATTATTTGT-TTTTTATTATTTATTTTATAATATTTTAAATGTATATTTTATTTTTGG
374 TGGAACCATTCTAAATGGCGCCACCA
65 TGGAACCATTCTAAATGGCGCCACCA
400 TCCTTGGTGT
Statistics
Matches: 161, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
95 31 0.19
96 6 0.04
97 3 0.02
98 37 0.23
99 1 0.01
102 1 0.01
103 2 0.01
104 5 0.03
105 34 0.21
106 5 0.03
107 9 0.06
108 27 0.17
ACGTcount: A:0.26, C:0.10, G:0.11, T:0.53
Consensus pattern (102 bp):
TTTTACTATTATTTGTTTTTTATTATTTATTTTATAATATTTTAAATGTATATTTTATTTTTGGT
GGAACCATTCTAAATGGCGCCACCAGTTCTCAATATG
Done.