Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014478.1 Kokia drynarioides strain JFW-HI SEQ_129517, 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: 45297
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 58 characters in sequence are not A, C, G, or T
Found at i:611 original size:14 final size:14
Alignment explanation
Indices: 586--619 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
576 TTCGATTTTT
*
586 TTCGAA-TTTCGAG
1 TTCGAATTTTCGAA
599 TTCGAATTTTCGAA
1 TTCGAATTTTCGAA
613 TTCGAAT
1 TTCGAAT
620 AAACTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (14 bp):
TTCGAATTTTCGAA
Found at i:4880 original size:29 final size:28
Alignment explanation
Indices: 4834--4900 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
4824 AAATATATAA
*
4834 TATAAAAAATTAAGAAAATATCCTAAAAT
1 TATAAAAAATTAAAAAAATATCC-AAAAT
*
4863 TATAAAAAA-TAATAAAAATTTCCAAAAT
1 TATAAAAAATTAA-AAAAATATCCAAAAT
*
4891 TTTGAAAAAA
1 TAT-AAAAAA
4901 AAAAAACATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 10 0.30
29 23 0.70
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.28
Consensus pattern (28 bp):
TATAAAAAATTAAAAAAATATCCAAAAT
Found at i:5956 original size:12 final size:11
Alignment explanation
Indices: 5941--5993 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
5931 TAAACATCAA
5941 ATTAAATTTAAT
1 ATTAAA-TTAAT
5953 ATTAAATTAAT
1 ATTAAATTAAT
5964 A--AAA-TAAT
1 ATTAAATTAAT
5972 ATTAAGA-TAATT
1 ATTAA-ATTAA-T
5984 ATTAAATTAA
1 ATTAAATTAA
5994 AATTTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 5 0.14
9 3 0.08
10 2 0.06
11 11 0.31
12 15 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
ATTAAATTAAT
Found at i:6180 original size:14 final size:14
Alignment explanation
Indices: 6161--6188 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6151 GCGAGGTCTT
6161 GTGAAACCTGCCCC
1 GTGAAACCTGCCCC
6175 GTGAAACCTGCCCC
1 GTGAAACCTGCCCC
6189 ACTGACATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.14
Consensus pattern (14 bp):
GTGAAACCTGCCCC
Found at i:13016 original size:19 final size:19
Alignment explanation
Indices: 12992--13029 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12982 TTATAAGCCC
12992 ATTAAAGGGGTAAATGCTG
1 ATTAAAGGGGTAAATGCTG
13011 ATTAAAGGGGTAAATGCTG
1 ATTAAAGGGGTAAATGCTG
13030 GTTACGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (19 bp):
ATTAAAGGGGTAAATGCTG
Found at i:16155 original size:32 final size:32
Alignment explanation
Indices: 16110--16194 Score: 143
Period size: 32 Copynumber: 2.7 Consensus size: 32
16100 TTTTGAACTT
* *
16110 TTAAAGTATAGGGATTACAATCTCATATTCTA
1 TTAAAGTAAAGGGATAACAATCTCATATTCTA
16142 TTAAAGTAAAGGGATAACAATCTCATATTCTA
1 TTAAAGTAAAGGGATAACAATCTCATATTCTA
*
16174 TAAAAGTAAAGGGATAACAAT
1 TTAAAGTAAAGGGATAACAAT
16195 ATATTTTAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.31
Consensus pattern (32 bp):
TTAAAGTAAAGGGATAACAATCTCATATTCTA
Found at i:22868 original size:15 final size:15
Alignment explanation
Indices: 22832--22866 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
22822 AAATTTTGTC
*
22832 ATATTTCTTTTTCTA
1 ATATTTATTTTTCTA
22847 ATATTTATTTTT-TA
1 ATATTTATTTTTCTA
22861 ATATTT
1 ATATTT
22867 TACTATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATTTATTTTTCTA
Found at i:29468 original size:11 final size:10
Alignment explanation
Indices: 29442--29481 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
29432 TTGTTATATA
29442 TATAA-TTTT
1 TATAATTTTT
*
29451 TAGAATTTTT
1 TATAATTTTT
29461 TAATAATTTTT
1 T-ATAATTTTT
29472 TATAATTTTT
1 TATAATTTTT
29482 ACAGCTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 4 0.15
10 14 0.52
11 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (10 bp):
TATAATTTTT
Found at i:29468 original size:20 final size:21
Alignment explanation
Indices: 29443--29481 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29433 TGTTATATAT
29443 ATAA-TTTTTAGAATTTTTTA
1 ATAATTTTTTAGAATTTTTTA
*
29463 ATAATTTTTTATAATTTTT
1 ATAATTTTTTAGAATTTTT
29482 ACAGCTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
ATAATTTTTTAGAATTTTTTA
Found at i:32151 original size:13 final size:15
Alignment explanation
Indices: 32127--32159 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
32117 ATATCTGTGT
32127 AATTATTTGCTT-CA
1 AATTATTTGCTTGCA
32141 AATTA-TTGCTTGCA
1 AATTATTTGCTTGCA
32155 AATTA
1 AATTA
32160 CCGTACGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (15 bp):
AATTATTTGCTTGCA
Found at i:36971 original size:17 final size:19
Alignment explanation
Indices: 36940--36978 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
36930 TGAAAAATAT
*
36940 AAAGAAGGATTAAAT-TGA
1 AAAGAAGGATAAAATCTGA
36958 AAAGAA-GATAAAATCTGA
1 AAAGAAGGATAAAATCTGA
36976 AAA
1 AAA
36979 AAATATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.62, C:0.03, G:0.18, T:0.18
Consensus pattern (19 bp):
AAAGAAGGATAAAATCTGA
Found at i:38749 original size:41 final size:41
Alignment explanation
Indices: 38680--38895 Score: 240
Period size: 41 Copynumber: 5.2 Consensus size: 41
38670 ACTTGATGTA
38680 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* * * *
38722 TAAAGGAAGACTCGTGACTCAAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* * *
38763 TAAAGGAAGACTCATGTCTCGGGGTGAGCATGAAATTATAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* * * *
38804 TGAAGGAAGACTCGTGTCTTGGGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATA-T
* * * *
38846 TAAAGGAAGACTTATGACTCG-G-TAGAGCATAAGATTGT-T
1 TAAAGGAAGACTCATGTCTCGAGAT-GAGCATGAGATTATAT
38885 TAAAAGGAAGA
1 T-AAAGGAAGA
38896 TCTACGACTC
Statistics
Matches: 148, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
39 2 0.01
40 10 0.07
41 115 0.78
42 21 0.14
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.27
Consensus pattern (41 bp):
TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
Found at i:41270 original size:24 final size:24
Alignment explanation
Indices: 41242--41312 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
41232 TTATGGTTCG
41242 TTTGTTAA-CTAATTTATAAGCTCA
1 TTTG-TAAGCTAATTTATAAGCTCA
* *
41266 TTTGTAAGCTCATTTATAAGGTCA
1 TTTGTAAGCTAATTTATAAGCTCA
** **
41290 TTTAAAAGCTCGTTTATAAGCTC
1 TTTGTAAGCTAATTTATAAGCTC
41313 GATTATAAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 3 0.08
24 37 0.93
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (24 bp):
TTTGTAAGCTAATTTATAAGCTCA
Found at i:41325 original size:12 final size:12
Alignment explanation
Indices: 41253--41324 Score: 92
Period size: 12 Copynumber: 6.0 Consensus size: 12
41243 TTGTTAACTA
41253 ATTTATAAGCTC
1 ATTTATAAGCTC
*
41265 ATTTGTAAGCTC
1 ATTTATAAGCTC
*
41277 ATTTATAAGGTC
1 ATTTATAAGCTC
*
41289 ATTTAAAAGCTC
1 ATTTATAAGCTC
*
41301 GTTTATAAGCTC
1 ATTTATAAGCTC
41313 GA-TTATAAGCTC
1 -ATTTATAAGCTC
41325 GTTTGTTATA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (12 bp):
ATTTATAAGCTC
Found at i:42612 original size:12 final size:12
Alignment explanation
Indices: 42595--42620 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42585 CAATTTCAGG
42595 TTATTGAATATA
1 TTATTGAATATA
42607 TTATTGAATATA
1 TTATTGAATATA
42619 TT
1 TT
42621 GTTATTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (12 bp):
TTATTGAATATA
Found at i:42958 original size:24 final size:24
Alignment explanation
Indices: 42931--43139 Score: 219
Period size: 24 Copynumber: 8.9 Consensus size: 24
42921 TTTAGTTAAC
* *
42931 ATAAACGAACATGTTCATGAACGT
1 ATAAACGAACATGTTCGTGAACAT
**
42955 ATAAACGAACATGTTCGTGAATGT
1 ATAAACGAACATGTTCGTGAACAT
* * *
42979 -TAGACGAACATGTTTGCGAACAT
1 ATAAACGAACATGTTCGTGAACAT
* * **
43002 AAAAACGAACATGTTTGTGAATGT
1 ATAAACGAACATGTTCGTGAACAT
* *
43026 -TAGACGAACATGTTCGCGAACAT
1 ATAAACGAACATGTTCGTGAACAT
*
43049 ATAAACGAACATGTTCGCGAACAT
1 ATAAACGAACATGTTCGTGAACAT
* *
43073 -TAAACGAACATGTTCATAAACAT
1 ATAAACGAACATGTTCGTGAACAT
* * *
43096 ATAAACGAACATGTTTGTTAACGT
1 ATAAACGAACATGTTCGTGAACAT
43120 -TAAACGAACATGTTCGTGAA
1 ATAAACGAACATGTTCGTGAA
43140 TGATAAATGA
Statistics
Matches: 154, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
23 73 0.47
24 81 0.53
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (24 bp):
ATAAACGAACATGTTCGTGAACAT
Found at i:43000 original size:12 final size:12
Alignment explanation
Indices: 42975--43086 Score: 59
Period size: 12 Copynumber: 9.4 Consensus size: 12
42965 ATGTTCGTGA
42975 ATGTTAGACGAAC
1 ATGTTAG-CGAAC
*
42988 ATGTTTGCGAAC
1 ATGTTAGCGAAC
*** *
43000 ATAAAAACGAAC
1 ATGTTAGCGAAC
* *
43012 ATGTTTGTG-A-
1 ATGTTAGCGAAC
43022 ATGTTAGACGAAC
1 ATGTTAG-CGAAC
*
43035 ATGTTCGCGAAC
1 ATGTTAGCGAAC
* * *
43047 ATATAAACGAAC
1 ATGTTAGCGAAC
*
43059 ATGTTCGCGAAC
1 ATGTTAGCGAAC
* *
43071 AT-TAAACGAAC
1 ATGTTAGCGAAC
43082 ATGTT
1 ATGTT
43087 CATAAACATA
Statistics
Matches: 68, Mismatches: 27, Indels: 9
0.65 0.26 0.09
Matches are distributed among these distances:
10 6 0.09
11 10 0.15
12 40 0.59
13 12 0.18
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (12 bp):
ATGTTAGCGAAC
Found at i:43008 original size:47 final size:47
Alignment explanation
Indices: 42932--43135 Score: 255
Period size: 47 Copynumber: 4.3 Consensus size: 47
42922 TTAGTTAACA
** * *
42932 TAAACGAACATGTTCATGAACGTATAAACGAACATGTTCGTGAATGT
1 TAAACGAACATGTTCGCGAACATATAAACGAACATGTTCGTGAACGT
* * * * *
42979 TAGACGAACATGTTTGCGAACATAAAAACGAACATGTTTGTGAATGT
1 TAAACGAACATGTTCGCGAACATATAAACGAACATGTTCGTGAACGT
* * *
43026 TAGACGAACATGTTCGCGAACATATAAACGAACATGTTCGCGAACAT
1 TAAACGAACATGTTCGCGAACATATAAACGAACATGTTCGTGAACGT
*** * *
43073 TAAACGAACATGTTCATAAACATATAAACGAACATGTTTGTTAACGT
1 TAAACGAACATGTTCGCGAACATATAAACGAACATGTTCGTGAACGT
43120 TAAACGAACATGTTCG
1 TAAACGAACATGTTCG
43136 TGAATGATAA
Statistics
Matches: 135, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 135 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (47 bp):
TAAACGAACATGTTCGCGAACATATAAACGAACATGTTCGTGAACGT
Done.