Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005007.1 Kokia drynarioides strain JFW-HI SEQ_118766, 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: 80319
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:2410 original size:14 final size:14
Alignment explanation
Indices: 2391--2417 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2381 CGTCAACTGC
2391 TTTCTTTATATATT
1 TTTCTTTATATATT
2405 TTTCTTTATATAT
1 TTTCTTTATATAT
2418 AAGATGAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTCTTTATATATT
Found at i:7939 original size:23 final size:23
Alignment explanation
Indices: 7913--7982 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
7903 TTCATTTAAC
7913 TTAATCGAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* * * *
7936 TTAAACTAACATGTTCATGAATA
1 TTAATCGAACATGTTCACGAACA
* *
7959 TATAATTGAAAATGTTCACGAACA
1 T-TAATCGAACATGTTCACGAACA
7983 ATTTTAATGA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 20 0.56
24 16 0.44
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:25627 original size:16 final size:16
Alignment explanation
Indices: 25606--25636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25596 TGTTGAAGTC
25606 AAATCTCAAATTTTTG
1 AAATCTCAAATTTTTG
*
25622 AAATCTCTAATTTTT
1 AAATCTCAAATTTTT
25637 AATTTATGTA
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:0.35, C:0.13, G:0.03, T:0.48
Consensus pattern (16 bp):
AAATCTCAAATTTTTG
Found at i:27016 original size:69 final size:69
Alignment explanation
Indices: 26905--27043 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
26895 AAACAATGTA
26905 AAACATTGATTAAAGATGATTATACGATTGAGAGTAATTAACATGCAGCAATATTGAGAAAGGTA
1 AAACATTGATTAAAGATGATTATACGATTGAGAGTAATTAACATGCAGCAATATTGAGAAAGGTA
26970 CCAT
66 CCAT
26974 AAACATTGATTAAAGATGATTATACGATTGAGAGTAATTAACATGCAGCAATATTGAGAAAGGTA
1 AAACATTGATTAAAGATGATTATACGATTGAGAGTAATTAACATGCAGCAATATTGAGAAAGGTA
27039 CCAT
66 CCAT
27043 A
1 A
27044 TCATCACTGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (69 bp):
AAACATTGATTAAAGATGATTATACGATTGAGAGTAATTAACATGCAGCAATATTGAGAAAGGTA
CCAT
Found at i:29512 original size:6 final size:6
Alignment explanation
Indices: 29501--29542 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
29491 GTTTCACATA
* *
29501 TGAGAG TGAGAG TGAGAG TGAGAG -AAGAG TGAGAG AGAGAG T
1 TGAGAG TGAGAG TGAGAG TGAGAG TGAGAG TGAGAG TGAGAG T
29543 AGGTACAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.38, C:0.00, G:0.48, T:0.14
Consensus pattern (6 bp):
TGAGAG
Found at i:29531 original size:17 final size:17
Alignment explanation
Indices: 29509--29541 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29499 TATGAGAGTG
*
29509 AGAGTGAGAGTGAGAGA
1 AGAGTGAGAGAGAGAGA
29526 AGAGTGAGAGAGAGAG
1 AGAGTGAGAGAGAGAG
29542 TAGGTACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.48, T:0.09
Consensus pattern (17 bp):
AGAGTGAGAGAGAGAGA
Found at i:29679 original size:6 final size:6
Alignment explanation
Indices: 29668--29700 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
29658 GTTGAGGGAG
29668 GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA GGA
1 GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA GGA
29701 GGGCTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
GGAAAA
Found at i:34214 original size:40 final size:40
Alignment explanation
Indices: 34158--34234 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
34148 GCCGAGTTGG
*
34158 GCAAGATGATAAGTAGGTTCCTCAACAACTGATCTTTCGA
1 GCAAGATGATAAGTAGGTTCCTCAACAACCGATCTTTCGA
*
34198 GCAAGATGATAGGTAGGTTCCTCAACAACCGATCTTT
1 GCAAGATGATAAGTAGGTTCCTCAACAACCGATCTTT
34235 GGAGATCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (40 bp):
GCAAGATGATAAGTAGGTTCCTCAACAACCGATCTTTCGA
Found at i:35194 original size:13 final size:13
Alignment explanation
Indices: 35157--35194 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
35147 AAGCTGTCCT
*
35157 TTTC-TTGTCTCA
1 TTTCTTTGTCTCC
*
35169 TTTATTTGTCTCC
1 TTTCTTTGTCTCC
35182 TTTCTTTGTCTCC
1 TTTCTTTGTCTCC
35195 ACAAATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.05, C:0.26, G:0.08, T:0.61
Consensus pattern (13 bp):
TTTCTTTGTCTCC
Found at i:37593 original size:27 final size:27
Alignment explanation
Indices: 37563--37631 Score: 115
Period size: 25 Copynumber: 2.6 Consensus size: 27
37553 TGGCCATGGA
37563 CATTCCTTTTAGAGTGTGCCACAAAGG
1 CATTCCTTTTAGAGTGTGCCACAAAGG
37590 CATTCCTTTTAGA--GTGCCACAAAGG
1 CATTCCTTTTAGAGTGTGCCACAAAGG
*
37615 CATTCCTTTCAGAGTGT
1 CATTCCTTTTAGAGTGT
37632 CTTATCAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 24 0.62
27 15 0.38
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (27 bp):
CATTCCTTTTAGAGTGTGCCACAAAGG
Found at i:42182 original size:31 final size:31
Alignment explanation
Indices: 42141--42209 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
42131 TTCACAACTC
* *
42141 AATAATTTAAATAAAAAATTTTCAATAGTCT
1 AATAAATTAAATAAAAAATTTTCAATAATCT
* * * *
42172 AATAAATTAAATGAAAATTTTTGAATAATTT
1 AATAAATTAAATAAAAAATTTTCAATAATCT
42203 AATAAAT
1 AATAAAT
42210 ACATTATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (31 bp):
AATAAATTAAATAAAAAATTTTCAATAATCT
Found at i:50895 original size:16 final size:17
Alignment explanation
Indices: 50861--50902 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
50851 TGTAAACAAT
50861 AATTTAAAATTATAAAA
1 AATTTAAAATTATAAAA
50878 AATTTAAAATTA-AAAA
1 AATTTAAAATTATAAAA
*
50894 AATATAAAA
1 AATTTAAAA
50903 AGTTCATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTTAAAATTATAAAA
Found at i:50903 original size:17 final size:17
Alignment explanation
Indices: 50861--50919 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
50851 TGTAAACAAT
*
50861 AATTTAAAATTATAAAA
1 AATTAAAAATTATAAAA
*
50878 AATTTAAAATTA-AAAA
1 AATTAAAAATTATAAAA
50894 AATATAAAAAGTTCAT-AAA
1 AAT-TAAAAA-TT-ATAAAA
50913 AATTAAA
1 AATTAAA
50920 GGCATAATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 7 0.19
17 17 0.46
18 6 0.16
19 7 0.19
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
AATTAAAAATTATAAAA
Found at i:51047 original size:21 final size:21
Alignment explanation
Indices: 51023--51065 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
51013 AAATCACCTC
*
51023 AAAATTAATTTTAAAAATTTT
1 AAAAATAATTTTAAAAATTTT
* * *
51044 AAAAATATTTTTATAATTTTT
1 AAAAATAATTTTAAAAATTTT
51065 A
1 A
51066 TACTTATTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAAATAATTTTAAAAATTTT
Found at i:51104 original size:29 final size:29
Alignment explanation
Indices: 51031--51106 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
51021 TCAAAATTAA
*
51031 TTTTAAAAATTTTAAAAATATTTTTATAAT
1 TTTTATAAATTTT-AAAATATTTTTATAAT
* *
51061 TTTTAT-ACTTATTAAAATATTTTTTTAAT
1 TTTTATAAATT-TTAAAATATTTTTATAAT
*
51090 TTTTTTAAATTTTAAAA
1 TTTTATAAATTTTAAAA
51107 AAATTAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 29 0.74
30 10 0.26
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTATAAATTTTAAAATATTTTTATAAT
Found at i:55031 original size:10 final size:10
Alignment explanation
Indices: 55016--55040 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55006 GGTAAGAACC
55016 AAAAAAATAA
1 AAAAAAATAA
55026 AAAAAAATAA
1 AAAAAAATAA
55036 AAAAA
1 AAAAA
55041 GAAAGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:66463 original size:23 final size:23
Alignment explanation
Indices: 66429--66568 Score: 208
Period size: 23 Copynumber: 6.1 Consensus size: 23
66419 ACGCTAGCGC
* *
66429 GCTTACTATTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* *
66452 GCTTATTGTTTCACACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
66475 GCTTACTGTTTCGCACTTCATGT
1 GCTTACTGTTTCGCACTTCGTGT
*
66498 GCTTACTGTTTCGCACTTCGCGT
1 GCTTACTGTTTCGCACTTCGTGT
*
66521 GCTTACTGTTTCGCACTTCGCGT
1 GCTTACTGTTTCGCACTTCGTGT
*
66544 GCTTACTGTTTCGCACCTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
66567 GC
1 GC
66569 CTATTGATTT
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 106 1.00
ACGTcount: A:0.11, C:0.27, G:0.20, T:0.42
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:66627 original size:23 final size:23
Alignment explanation
Indices: 66585--66665 Score: 146
Period size: 23 Copynumber: 3.6 Consensus size: 23
66575 ATTTGTGCTA
66585 TGTGTGCCTACT-GATTGCACTG
1 TGTGTGCCTACTGGATTGCACTG
66607 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACTGGATTGCACTG
66630 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACTGGATTGCACTG
*
66653 TGTGTGCTTACTG
1 TGTGTGCCTACTG
66666 TTTCCCTAGC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 12 0.21
23 45 0.79
ACGTcount: A:0.12, C:0.21, G:0.30, T:0.37
Consensus pattern (23 bp):
TGTGTGCCTACTGGATTGCACTG
Found at i:68005 original size:17 final size:17
Alignment explanation
Indices: 67980--68015 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
67970 GGTATTGTAT
*
67980 ATGTCATATCGGGTCAA
1 ATGTAATATCGGGTCAA
67997 ATGTAATATCGGGTCAA
1 ATGTAATATCGGGTCAA
68014 AT
1 AT
68016 TACATAGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (17 bp):
ATGTAATATCGGGTCAA
Found at i:68785 original size:6 final size:6
Alignment explanation
Indices: 68720--68787 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
68710 TTCTGGCTCA
* * * *
68720 TCATCA TCATCT TCAT-T TCCATCT CCATCT TGATCT TCATCT TAATCT
1 TCATCT TCATCT TCATCT T-CATCT TCATCT TCATCT TCATCT TCATCT
* *
68768 CCAACGT T-ATCT TCATCT TC
1 TCATC-T TCATCT TCATCT TC
68788 CGTGCTAGAC
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
5 4 0.09
6 41 0.87
7 2 0.04
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:79363 original size:28 final size:25
Alignment explanation
Indices: 79332--79392 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 25
79322 ATTTTAAAAA
79332 TATATATTTATATTATATTTAATAATTT
1 TATATATTTATATT-TA-TTAA-AATTT
*
79360 TATATAATTTTTATTTATTAAAATTT
1 TATAT-ATTTATATTTATTAAAATTT
79386 TATATAT
1 TATATAT
79393 GATCACCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 2 0.06
26 10 0.32
27 4 0.13
28 7 0.23
29 8 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATATTTATATTTATTAAAATTT
Done.