Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014530.1 Kokia drynarioides strain JFW-HI SEQ_129569, 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: 73236
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 163 characters in sequence are not A, C, G, or T
Found at i:235 original size:2 final size:2
Alignment explanation
Indices: 230--260 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
220 AATATGTAAT
230 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
261 GGTTCAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:309 original size:3 final size:3
Alignment explanation
Indices: 301--339 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
291 CACATTACAT
301 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
340 TGTTATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20900 original size:16 final size:16
Alignment explanation
Indices: 20853--20902 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
20843 TATAATAAAT
20853 TATATTATAAAACTTTA
1 TATATTATAAAA-TTTA
**
20870 T-T-TTATAAAGGTTA
1 TATATTATAAAATTTA
20884 TATATTATAAAATTTA
1 TATATTATAAAATTTA
20900 TAT
1 TAT
20903 TGCTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 14 0.52
17 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (16 bp):
TATATTATAAAATTTA
Found at i:20901 original size:14 final size:14
Alignment explanation
Indices: 20852--20903 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
20842 ATATAATAAA
20852 TTATATTATAAAACT
1 TTATATTATAAAA-T
* *
20867 TTATTTTATAAAGGT
1 TTATATTATAAA-AT
20882 TATATATTATAAAAT
1 T-TATATTATAAAAT
20897 TTATATT
1 TTATATT
20904 GCTTTTATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (14 bp):
TTATATTATAAAAT
Found at i:24366 original size:17 final size:18
Alignment explanation
Indices: 24335--24368 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
24325 ATTTTTAAAT
24335 ATATATATTTAATATTTA
1 ATATATATTTAATATTTA
*
24353 ATATA-ATTTTATATTT
1 ATATATATTTAATATTT
24369 TTTATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATATATTTAATATTTA
Found at i:24387 original size:24 final size:24
Alignment explanation
Indices: 24319--24389 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
24309 CCCGTATTTT
* * *
24319 TTTAAAATTT-TTAAATATATATA
1 TTTAATATTTATTAAAAATTTATA
* * *
24342 TTTAATATTTAATATAATTTTATA
1 TTTAATATTTATTAAAAATTTATA
**
24366 TTTTTTATTTATTAAAAATTTATA
1 TTTAATATTTATTAAAAATTTATA
24390 CATAATCTTA
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
23 9 0.25
24 27 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTAATATTTATTAAAAATTTATA
Found at i:26964 original size:4 final size:4
Alignment explanation
Indices: 26950--26979 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
26940 CAAATACAAG
*
26950 TTGT GTGT TTGT TTGT TTGT TTGT TTGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TT
26980 TCAACGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.27, T:0.73
Consensus pattern (4 bp):
TTGT
Found at i:31026 original size:17 final size:17
Alignment explanation
Indices: 31004--31036 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30994 GCAAAACAAA
31004 AATTCA-TATATGAAAAT
1 AATTCATTA-ATGAAAAT
31021 AATTCATTAATGAAAA
1 AATTCATTAATGAAAA
31037 GATCTGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (17 bp):
AATTCATTAATGAAAAT
Found at i:32709 original size:148 final size:148
Alignment explanation
Indices: 32441--32721 Score: 456
Period size: 148 Copynumber: 1.9 Consensus size: 148
32431 ACAATAGCAA
* * *
32441 ATAGGATTCGTCAATCACCATCCAGTATCATTATTAGACATGTTTCATTCTACCCAATGAAAAAA
1 ATAGGATTCATCAATCACCATCCAGTATCACTATTAGACATGTTTCATTCCACCCAATGAAAAAA
*
32506 AAAATTATTATAGATTCATTCGGTATAATTCTCTTCCAAATAATTTTAGCGTACATGTTATCGCA
66 AAAATTATCATAGATTCATTCGGTATAATTCTCTTCCAAATAATTTTAGCGTACATGTTATCGCA
32571 CATTATACATATATATAT
131 CATTATACATATATATAT
** * *
32589 ATAGGATTCATCAATCACCATTTA-TGATCACTATTAGACATGTTTCATTCCACCTAATGAGAAA
1 ATAGGATTCATCAATCACCATCCAGT-ATCACTATTAGACATGTTTCATTCCACCCAATGAAAAA
* *
32653 AAAAGTTATCATAGATTCATTCGGTATAATTCTCTTCCAAATAATTTTGGCGTACATGTTATCGC
65 AAAAATTATCATAGATTCATTCGGTATAATTCTCTTCCAAATAATTTTAGCGTACATGTTATCGC
32718 ACAT
130 ACAT
32722 ATATGACTTA
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
147 1 0.01
148 121 0.99
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (148 bp):
ATAGGATTCATCAATCACCATCCAGTATCACTATTAGACATGTTTCATTCCACCCAATGAAAAAA
AAAATTATCATAGATTCATTCGGTATAATTCTCTTCCAAATAATTTTAGCGTACATGTTATCGCA
CATTATACATATATATAT
Found at i:33923 original size:12 final size:12
Alignment explanation
Indices: 33893--33926 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
33883 TTAGATTTAA
33893 GTATAATTATTT
1 GTATAATTATTT
33905 G--TAATTATTT
1 GTATAATTATTT
33915 GTATAATTATTT
1 GTATAATTATTT
33927 TAATTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (12 bp):
GTATAATTATTT
Found at i:43228 original size:2 final size:2
Alignment explanation
Indices: 43221--43250 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43211 TTTATTCAAC
43221 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
43251 TCAAAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:54877 original size:16 final size:16
Alignment explanation
Indices: 54858--54888 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54848 AAAAAAACAC
*
54858 TAAAACAGTAAAAAAT
1 TAAAACAGCAAAAAAT
54874 TAAAACAGCAAAAAA
1 TAAAACAGCAAAAAA
54889 AACAACTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (16 bp):
TAAAACAGCAAAAAAT
Found at i:57946 original size:22 final size:22
Alignment explanation
Indices: 57902--57946 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
57892 AAAACCTTTA
* *
57902 AAAAATTTTATATTTACTTTTT
1 AAAAATTTTATACTTACTATTT
57924 AAAAATTTTATAACTTA-TATTT
1 AAAAATTTTAT-ACTTACTATTT
57946 A
1 A
57947 CTTTCTCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
AAAAATTTTATACTTACTATTT
Found at i:58601 original size:2 final size:2
Alignment explanation
Indices: 58594--58624 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
58584 CATAAAAACA
58594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58625 ACATATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65953 original size:24 final size:24
Alignment explanation
Indices: 65907--65953 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
65897 TATGGATCGT
**
65907 AAAATAGATATAAAAAGGTAGATA
1 AAAATAGATATAAAAAAATAGATA
65931 AAAAT-GATATAAAAAAATGAGAT
1 AAAATAGATATAAAAAAAT-AGAT
65954 GGAATATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (24 bp):
AAAATAGATATAAAAAAATAGATA
Found at i:69810 original size:16 final size:17
Alignment explanation
Indices: 69782--69818 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
69772 CTTTTTGCAT
69782 GCCATGCCATGCAGCAC
1 GCCATGCCATGCAGCAC
69799 GCCATG-CATGCAGCAC
1 GCCATGCCATGCAGCAC
69815 GCCA
1 GCCA
69819 ATCCATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.24, C:0.41, G:0.24, T:0.11
Consensus pattern (17 bp):
GCCATGCCATGCAGCAC
Found at i:73186 original size:21 final size:20
Alignment explanation
Indices: 73162--73204 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
73152 ACCCTGTGAC
*
73162 CTTGGAAGCTCCTGAGAATCT
1 CTTGGAAGCCCCTGAGAA-CT
* *
73183 CTTGTAAGCCCCTGTGAACT
1 CTTGGAAGCCCCTGAGAACT
73203 CT
1 CT
73205 GATCAGAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (20 bp):
CTTGGAAGCCCCTGAGAACT
Done.