Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000663.1 Kokia drynarioides strain JFW-HI SEQ_111645, 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, 935
Length: 1559
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Found at i:277 original size:48 final size:49
Alignment explanation
Indices: 203--644 Score: 394
Period size: 48 Copynumber: 9.2 Consensus size: 49
193 TTACATCACT
* * *
203 AAATCTTATACC-CTAAATCTAGAGGGGCAGATTGAAGCTACCAAATCC
1 AAATCTTATACCACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCC
*
251 AAAT-TTATACCACTAAATCCAAAGGGGCAGATTAAAGCTACCACAT-C
1 AAATCTTATACCACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCC
* * * *
298 AAATCTTATA-CACTTAAATCCAAAGTGGCATATTAAAGCCACCACATCC
1 AAATCTTATACCAC-TAAATCCAAAGGGGCAGATTGAAGCTACCACATCC
* *
347 -AATCTTATACCCCTAAATCC-AAGGGGCAGATTGAAGCTACCATATCC
1 AAATCTTATACCACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCC
* * *
394 -AATCTTATACCCCTAAATCCAAAGGGGTAGATTGAAG-TCACTACATCC
1 AAATCTTATACCACTAAATCCAAAGGGGCAGATTGAAGCT-ACCACATCC
* ** * * * * *
442 -AATATTATACGC-CTAAATATAAAAGGACAGATTGAAGCCACTATAT-C
1 AAATCTTATAC-CACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCC
* * *
489 TAATCTTATACCTA-TAAATCCAGAGGGGTAGATTGAAGCTACCACATCC
1 AAATCTTATACC-ACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCC
* * * * * * *
538 -TATCTTATTCC-CTTAAATCTAAAAGGGCAAATTGAAGCCACCAAAT-C
1 AAATCTTATACCAC-TAAATCCAAAGGGGCAGATTGAAGCTACCACATCC
* * ** * *
585 AAATCTTATACCACTAAATCCAAAGAGGTAGATTGAAG-TTGCAAAACC
1 AAATCTTATACCACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCC
633 AAATCTTATACC
1 AAATCTTATACC
645 CCTGAAGTTG
Statistics
Matches: 322, Mismatches: 54, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
47 65 0.20
48 251 0.78
49 6 0.02
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (49 bp):
AAATCTTATACCACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCC
Found at i:372 original size:143 final size:141
Alignment explanation
Indices: 204--609 Score: 451
Period size: 143 Copynumber: 2.8 Consensus size: 141
194 TACATCACTA
*
204 AATCTTATA-CCCTAAATCTAGAGGGGCAGATTGAAGCTACCAAATCCAAAT-TTATACCACTAA
1 AATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCC-AATCTTATACC-CTAA
* * *
267 ATCCAAAGGGGCAGATTAAAGCTACCACATCAAATCTTATACACTTAAATCCAAAGTGGCATATT
64 ATCCAAAGGGGCAGATTGAAGCTACCACATCAAATCTTATACAC-TAAATCCAAAG-GACAGATT
332 AAAGCCACCACATCC
127 AAAGCCACCACATCC
*
347 AATCTTATACCCCTAAATCCA-AGGGGCAGATTGAAGCTACCATATCCAATCTTATACCCCTAAA
1 AATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATA-CCCTAAA
* * * * * **
411 TCCAAAGGGGTAGATTGAAG-TCACTACATCCAATATTATACGCCTAAATATAAAAGGACAGATT
65 TCCAAAGGGGCAGATTGAAGCT-ACCACATCAAATCTTATAC-ACTAAAT-CCAAAGGACAGATT
* * * *
475 GAAGCCACTATATCT
127 AAAGCCACCACATCC
** * * * *
490 AATCTTATACCTATAAATCCAGAGGGGTAGATTGAAGCTACCACATCCTATCTTATTCCCTTAAA
1 AATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATACCC-TAAA
* * * * *
555 TCTAAAAGGGCAAATTGAAGCCACCAAATCAAATCTTATACCACTAAATCCAAAG
65 TCCAAAGGGGCAGATTGAAGCTACCACATCAAATCTTATA-CACTAAATCCAAAG
610 AGGTAGATTG
Statistics
Matches: 219, Mismatches: 34, Indels: 20
0.80 0.12 0.07
Matches are distributed among these distances:
142 4 0.02
143 126 0.58
144 88 0.40
145 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (141 bp):
AATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATACCCTAAAT
CCAAAGGGGCAGATTGAAGCTACCACATCAAATCTTATACACTAAATCCAAAGGACAGATTAAAG
CCACCACATCC
Found at i:641 original size:96 final size:95
Alignment explanation
Indices: 203--622 Score: 447
Period size: 96 Copynumber: 4.4 Consensus size: 95
193 TTACATCACT
* * * *
203 AAATCTTATACC-CTAAATCTAGAGGGGCAGATTGAAGCTACCAAATCCAAAT-TTATACCACTA
1 AAATCTTATACCACTAAATCCAAAGGGGTAGATTGAAGCTACCACATCC-AATCTTATACC-CTA
* * * * *
266 AATCCAAAGGGGCAGATTAAAGCTACCACATC
64 AATCTAAAAGGGCAGATTGAAGCCACCATATC
* * * * *
298 AAATCTTATA-CACTTAAATCCAAAGTGGCATATTAAAGCCACCACATCCAATCTTATACCCCTA
1 AAATCTTATACCAC-TAAATCCAAAGGGGTAGATTGAAGCTACCACATCCAATCTTATA-CCCTA
* * *
362 AATC-CAAGGGGCAGATTGAAGCTACCATATC
64 AATCTAAAAGGGCAGATTGAAGCCACCATATC
* * * *
393 CAATCTTATACCCCTAAATCCAAAGGGGTAGATTGAAG-TCACTACATCCAATATTATACGCCTA
1 AAATCTTATACCACTAAATCCAAAGGGGTAGATTGAAGCT-ACCACATCCAATCTTATAC-CCTA
* * *
457 AATATAAAAGGACAGATTGAAGCCACTATATC
64 AATCTAAAAGGGCAGATTGAAGCCACCATATC
* * * *
489 TAATCTTATACCTA-TAAATCCAGAGGGGTAGATTGAAGCTACCACATCCTATCTTATTCCCTTA
1 AAATCTTATACC-ACTAAATCCAAAGGGGTAGATTGAAGCTACCACATCCAATCTTATACCC-TA
* *
553 AATCTAAAAGGGCAAATTGAAGCCACCAAATC
64 AATCTAAAAGGGCAGATTGAAGCCACCATATC
*
585 AAATCTTATACCACTAAATCCAAAGAGGTAGATTGAAG
1 AAATCTTATACCACTAAATCCAAAGGGGTAGATTGAAG
623 TTGCAAAACC
Statistics
Matches: 273, Mismatches: 40, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
94 2 0.01
95 93 0.34
96 175 0.64
97 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (95 bp):
AAATCTTATACCACTAAATCCAAAGGGGTAGATTGAAGCTACCACATCCAATCTTATACCCTAAA
TCTAAAAGGGCAGATTGAAGCCACCATATC
Found at i:856 original size:14 final size:14
Alignment explanation
Indices: 833--862 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
823 ACAACAAAAT
833 TTATCCCTTTGAAG
1 TTATCCCTTTGAAG
*
847 TTATCTCTTTGAAG
1 TTATCCCTTTGAAG
861 TT
1 TT
863 TTCATGAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (14 bp):
TTATCCCTTTGAAG
Done.