Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000413.1 Kokia drynarioides strain JFW-HI SEQ_111233, 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: 23390
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:860 original size:18 final size:17
Alignment explanation
Indices: 818--856 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
808 TCTCCCTTTA
*
818 TCTTTAACCTTCCATCT
1 TCTTTAACCTTCCATAT
*
835 TCTTTAACCTTTCATAT
1 TCTTTAACCTTCCATAT
852 TCTTT
1 TCTTT
857 TAACTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.28, G:0.00, T:0.54
Consensus pattern (17 bp):
TCTTTAACCTTCCATAT
Found at i:8477 original size:21 final size:22
Alignment explanation
Indices: 8438--8478 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
8428 GGTTTTTAAA
* *
8438 GGGTTTGGGTTTAATTGGTTTG
1 GGGTTTGAGTTTAAATGGTTTG
8460 GGGTTTGAG-TTAAATGGTT
1 GGGTTTGAGTTTAAATGGTT
8479 AATAAGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.15, C:0.00, G:0.39, T:0.46
Consensus pattern (22 bp):
GGGTTTGAGTTTAAATGGTTTG
Found at i:14221 original size:23 final size:23
Alignment explanation
Indices: 14195--14240 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
14185 TTTTGGAAGT
14195 CATCCTTTATATTCAATTAATGA
1 CATCCTTTATATTCAATTAATGA
*
14218 CATCCTTTATATTTAATTAATGA
1 CATCCTTTATATTCAATTAATGA
14241 TACCAACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (23 bp):
CATCCTTTATATTCAATTAATGA
Found at i:18295 original size:87 final size:87
Alignment explanation
Indices: 18131--18322 Score: 266
Period size: 89 Copynumber: 2.2 Consensus size: 87
18121 TCAAAAAAAA
* * * *
18131 AAAAAAAACAATTAAG-TCTTATTTTTTTCACTCAATTGAGTACTTGAACTTTCAAAATACATAA
1 AAAAAAAGCAATTAAGCCCTTATTTTTTTCACTCAATTAAGTACTTAAACTTTCAAAATACATAA
18195 AAAAAAGTCCCTC-AAATTTCTTC
66 AAAAAAG-CCCTCAAAATTT-TTC
** *
18218 AAAAAAAGCAATTAAGCCCTTATTTTTTTCCACTCAATTAAGTACTTAAACTTTCAAAATGTATC
1 AAAAAAAGCAATTAAGCCCTTATTTTTTT-CACTCAATTAAGTACTTAAACTTTCAAAATACATA
18283 AAAAAAA-CCCTCAAAATTTTTC
65 AAAAAAAGCCCTCAAAATTTTTC
18305 -AAAAAAGCAATTAAGCCC
1 AAAAAAAGCAATTAAGCCC
18323 ATGCTCTTGT
Statistics
Matches: 95, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
86 18 0.19
87 23 0.24
88 17 0.18
89 37 0.39
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.32
Consensus pattern (87 bp):
AAAAAAAGCAATTAAGCCCTTATTTTTTTCACTCAATTAAGTACTTAAACTTTCAAAATACATAA
AAAAAAGCCCTCAAAATTTTTC
Found at i:18709 original size:28 final size:28
Alignment explanation
Indices: 18678--18772 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 28
18668 CTTTATAAAA
18678 TTTATAATTTTTTTATATTTTATATTTT
1 TTTATAATTTTTTTATATTTTATATTTT
** * * *
18706 TTTACGATTTTTATATATTTTCTAATTT
1 TTTATAATTTTTTTATATTTTATATTTT
* * * * * *
18734 TTAATAAATTTGTAATATTTGAATTTTTT
1 TTTATAATTTTTTTATATTT-TATATTTT
18763 TTTATAATTT
1 TTTATAATTT
18773 AATAATATTT
Statistics
Matches: 48, Mismatches: 18, Indels: 1
0.72 0.27 0.01
Matches are distributed among these distances:
28 36 0.75
29 12 0.25
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTATAATTTTTTTATATTTTATATTTT
Found at i:18715 original size:18 final size:18
Alignment explanation
Indices: 18678--18736 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
18668 CTTTATAAAA
*
18678 TTTATAATTTTTTTATA-T
1 TTTAT-ATTTTTTTAGATT
18696 TTTATATTTTTTTACGATT
1 TTTATATTTTTTTA-GATT
*
18715 TTTATATATTTTCTA-ATT
1 TTTATAT-TTTTTTAGATT
18733 TTTA
1 TTTA
18737 ATAAATTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 9 0.25
18 13 0.36
19 8 0.22
20 6 0.17
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTATATTTTTTTAGATT
Found at i:23266 original size:122 final size:121
Alignment explanation
Indices: 23105--23390 Score: 468
Period size: 121 Copynumber: 2.4 Consensus size: 121
23095 GAACATTAAA
* *
23105 TAAATTTATTTCTTT-TTTCATTTTTT-TATATCATATATTTTAACTTTTTAATTTTAAATAAAT
1 TAAA-TTATTTCTTTCTTT-ATTTTTTCCATATCATATATTTTAACTTTTTAACTTTAAATAAAT
* *
23168 ATTTCTTTTTTTATTTTTTTTTTCATATCATATATTTTAACTTTAAATATTTATATAAT
64 ATTTCCTTTTTTA-TTTATTTTTCATATCATATATTTTAACTTTAAATATTTATATAAT
* *
23227 TAAATTATTCCTTTCTTTATTTTTTCCATATAATATATTTTAACTTTTTAACTTTAAATAAATAT
1 TAAATTATTTCTTTCTTTATTTTTTCCATATCATATATTTTAACTTTTTAACTTTAAATAAATAT
23292 TTCCTTTTTTATTTATTTTTCATATCATATATTTTAACTTTAAATATTTATATAAT
66 TTCCTTTTTTATTTATTTTTCATATCATATATTTTAACTTTAAATATTTATATAAT
*
23348 AAAATTATTTCTTTCTTTATTTTTTCCATATCATATATTTTAA
1 TAAATTATTTCTTTCTTTATTTTTTCCATATCATATATTTTAA
Statistics
Matches: 153, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
121 100 0.65
122 53 0.35
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (121 bp):
TAAATTATTTCTTTCTTTATTTTTTCCATATCATATATTTTAACTTTTTAACTTTAAATAAATAT
TTCCTTTTTTATTTATTTTTCATATCATATATTTTAACTTTAAATATTTATATAAT
Found at i:23271 original size:62 final size:57
Alignment explanation
Indices: 23100--23390 Score: 300
Period size: 62 Copynumber: 4.8 Consensus size: 57
23090 ACTTTGAACA
* **
23100 TTAAATAAATTTATTTCTTTTTTCATTTTTT-TATATCATATATTTTAACTTTTTAATT
1 TTAAATAAA-TTATTTCTTTTTT-ATTTTTTCCATATCATATATTTTAACTTTAAAATT
*
23158 TTAAATAAA-TATTTCTTTTTTTATTTTTTTTTTCATATCATATATTTTAACTTTAAATATT
1 TTAAATAAATTATTTC-TTTTTTA---TTTTTTCCATATCATATATTTTAACTTTAAA-ATT
* * ** *
23219 TATATAATTAAATTATTCCTTTCTTTATTTTTTCCATATAATATATTTTAACTTTTTAACT
1 T-TA-AA-TAAATTATTTCTTT-TTTATTTTTTCCATATCATATATTTTAACTTTAAAATT
*
23280 TTAAATAAA-TATTTCCTTTTTTATTTATTTTTCATATCATATATTTTAACTTTAAATATT
1 TTAAATAAATTATTT-CTTTTTTA-TT-TTTTCCATATCATATATTTTAACTTTAAA-ATT
23340 TATATAATAAAATTATTTCTTTCTTTATTTTTTCCATATCATATATTTTAA
1 T-TA-AAT-AAATTATTTCTTT-TTTATTTTTTCCATATCATATATTTTAA
Statistics
Matches: 197, Mismatches: 16, Indels: 36
0.79 0.06 0.14
Matches are distributed among these distances:
56 7 0.04
57 14 0.07
58 19 0.10
59 33 0.17
60 26 0.13
61 9 0.05
62 53 0.27
63 11 0.06
64 16 0.08
65 9 0.05
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.60
Consensus pattern (57 bp):
TTAAATAAATTATTTCTTTTTTATTTTTTCCATATCATATATTTTAACTTTAAAATT
Done.