Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010947.1 Kokia drynarioides strain JFW-HI SEQ_125915, 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: 4447
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:312 original size:48 final size:47
Alignment explanation
Indices: 204--619 Score: 338
Period size: 48 Copynumber: 8.8 Consensus size: 47
194 TACATCACTA
* * * *
204 AATCTTATACCCTAAATCTAGAGGGGCAGATTGAA---ACCAAATCC
1 AATCTTATACCTTAAATCCAAAGGGGCAGATTGAAGCCACCACATCC
* * * *
248 AATCTTATACCTTTAAATCCAAAGGGGCAAATTAAAGCTACCACATCA
1 AATCTTATACC-TTAAATCCAAAGGGGCAGATTGAAGCCACCACATCC
* * * * * * *
296 AATTTTATACACTTAAATCTAGAGTGGCATATTAAAGCCACCATATCC
1 AATCTTATAC-CTTAAATCCAAAGGGGCAGATTGAAGCCACCACATCC
* * *
344 AATCTTATACTCCTAAATCC-AAGGGGCAGATTGAAGCTACCATATCC
1 AATCTTATAC-CTTAAATCCAAAGGGGCAGATTGAAGCCACCACATCC
* * **
391 AATCTTATACCCCTAAATCCAAAGGGGTAGATTGAAGCCACTGCATCC
1 AATCTTATA-CCTTAAATCCAAAGGGGCAGATTGAAGCCACCACATCC
* * * * * *
439 AATATTATACGCCTAAATCTAAAGGGACAGATTGAAGCCACCATATCT
1 AATCTTATAC-CTTAAATCCAAAGGGGCAGATTGAAGCCACCACATCC
* * **
487 AATCTTATACCTATAAATCCAGAGGGGTAGATTGAAGCTGCCACATCC
1 AATCTTATACCT-TAAATCCAAAGGGGCAGATTGAAGCCACCACATCC
* * ** * * * *
535 TATCTTATTCCCTTAAATATAAAAGGGCAAATTGAAGCCACCAAATCA
1 AATCTTA-TACCTTAAATCCAAAGGGGCAGATTGAAGCCACCACATCC
* *
583 AATCTTATATCAC-TAAATCCAAAGAGGTAGATTGAAG
1 AATCTTATA-C-CTTAAATCCAAAGGGGCAGATTGAAG
620 TTGCAAAACC
Statistics
Matches: 293, Mismatches: 67, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
44 11 0.04
45 19 0.06
47 43 0.15
48 214 0.73
49 6 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (47 bp):
AATCTTATACCTTAAATCCAAAGGGGCAGATTGAAGCCACCACATCC
Found at i:410 original size:143 final size:142
Alignment explanation
Indices: 204--606 Score: 456
Period size: 143 Copynumber: 2.8 Consensus size: 142
194 TACATCACTA
* *
204 AATCTTATACCCTAAATCTAGAGGGGCAGATTGAA---ACCAAATCCAATCTTATACCTTTAAAT
1 AATCTTATACCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATACCCTTAAAT
* * * * *
266 CCAAAGGGGCAAATTAAAGCTACCACATCAAATTTTATACACTTAAATCTAGAGTGG-CATATTA
66 CCAAAGGGGCAAATTGAAGCCACCACATCAAATATTATACAC-TAAATCTAAAG-GGACAGATTA
330 AAGCCACCATATCC
129 AAGCCACCATATCC
* *
344 AATCTTATACTCCTAAATCCA-AGGGGCAGATTGAAGCTACCATATCCAATCTTATACCCCTAAA
1 AATCTTATAC-CCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATACCCTTAAA
* * ** * * *
408 TCCAAAGGGGTAGATTGAAGCCACTGCATCCAATATTATACGCCTAAATCTAAAGGGACAGATTG
65 TCCAAAGGGGCAAATTGAAGCCACCACATCAAATATTATAC-ACTAAATCTAAAGGGACAGATTA
*
473 AAGCCACCATATCT
129 AAGCCACCATATCC
* * * * * *
487 AATCTTATACCTATAAATCCAGAGGGGTAGATTGAAGCTGCCACATCCTATCTTATTCCCTTAAA
1 AATCTTATACC-CTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATACCCTTAAA
** * * * *
552 TATAAAAGGGCAAATTGAAGCCACCAAATCAAATCTTATATCACTAAATCCAAAG
65 TCCAAAGGGGCAAATTGAAGCCACCACATCAAATATTATA-CACTAAATCTAAAG
607 AGGTAGATTG
Statistics
Matches: 218, Mismatches: 36, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
140 24 0.11
141 9 0.04
142 3 0.01
143 102 0.47
144 79 0.36
145 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (142 bp):
AATCTTATACCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATACCCTTAAAT
CCAAAGGGGCAAATTGAAGCCACCACATCAAATATTATACACTAAATCTAAAGGGACAGATTAAA
GCCACCATATCC
Found at i:855 original size:14 final size:14
Alignment explanation
Indices: 836--865 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
826 ATAACAAAAT
836 TTATCTCTTTGAAG
1 TTATCTCTTTGAAG
850 TTATCTCTTTGAAG
1 TTATCTCTTTGAAG
864 TT
1 TT
866 TTCATGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (14 bp):
TTATCTCTTTGAAG
Found at i:1131 original size:16 final size:15
Alignment explanation
Indices: 1110--1139 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1100 AGTTCGACCC
1110 AAAATAAAAGAAAAAA
1 AAAATAAAA-AAAAAA
1126 AAAATAAAAAAAAA
1 AAAATAAAAAAAAA
1140 TATAAAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.90, C:0.00, G:0.03, T:0.07
Consensus pattern (15 bp):
AAAATAAAAAAAAAA
Found at i:2804 original size:21 final size:20
Alignment explanation
Indices: 2763--2805 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2753 TTAATGTGTA
**
2763 TTTATTATTTTTATGTTATT
1 TTTATTATTTTTATGACATT
*
2783 TTTATTCATTTTTTTGACATT
1 TTTATT-ATTTTTATGACATT
2804 TT
1 TT
2806 AATTTTTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTATTATTTTTATGACATT
Found at i:2827 original size:19 final size:18
Alignment explanation
Indices: 2803--2842 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2793 TTTTTGACAT
2803 TTTAATT-TTTGTCATTTTA
1 TTTAATTATTTGT-A-TTTA
2822 TTTAATTATTTGTATTTA
1 TTTAATTATTTGTATTTA
2840 TTT
1 TTT
2843 CACCTCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 8 0.40
20 5 0.25
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTAATTATTTGTATTTA
Done.