Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009997.1 Kokia drynarioides strain JFW-HI SEQ_124752, 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: 55179
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 289 characters in sequence are not A, C, G, or T
Found at i:2147 original size:2 final size:2
Alignment explanation
Indices: 2136--2169 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2126 AGTCTCGTCT
2136 TA TA -A 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 TA TA T
2170 TAATGTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3192 original size:43 final size:43
Alignment explanation
Indices: 3114--3457 Score: 465
Period size: 43 Copynumber: 8.0 Consensus size: 43
3104 GTGCGTAGAT
* * *
3114 CTCGGATGTGCAGGTGCCTCTAACACCGTCGGCACCTTGGTGC
1 CTCGGATGTGCGGGAGCCTCGAACACCGTCGGCACCTTGGTGC
* * * *
3157 CTCGAATGTACGGGAGCCTCGGACACCGTCAGCACCTTGGTGC
1 CTCGGATGTGCGGGAGCCTCGAACACCGTCGGCACCTTGGTGC
* * * *
3200 CCCGAATGTGCGGGAGCCTCGAACACCATTGGCACCTTGGTGC
1 CTCGGATGTGCGGGAGCCTCGAACACCGTCGGCACCTTGGTGC
* * * * *
3243 CCCGGATGTGCGGGAGCATCGGACACCCTCGACACCTTGGTGC
1 CTCGGATGTGCGGGAGCCTCGAACACCGTCGGCACCTTGGTGC
* *
3286 CTCGGATGTGCGGGAGCCTCGGACACTGTCGGCACCTTGGTGC
1 CTCGGATGTGCGGGAGCCTCGAACACCGTCGGCACCTTGGTGC
*
3329 CTCGGATGTGCGGGAGCCTCGAACACCGTCAGCACCTTGGTGC
1 CTCGGATGTGCGGGAGCCTCGAACACCGTCGGCACCTTGGTGC
*
3372 CAT-GGATGTGCGGGTGCCTCGAACACCGTCGGCACCTTGGTGC
1 C-TCGGATGTGCGGGAGCCTCGAACACCGTCGGCACCTTGGTGC
* * *
3415 CTCGGATGTGCGGGTGCCTTGAACATCGTCGGCACCTTGGTGC
1 CTCGGATGTGCGGGAGCCTCGAACACCGTCGGCACCTTGGTGC
3458 ATCATCGACA
Statistics
Matches: 268, Mismatches: 31, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
42 1 0.00
43 266 0.99
44 1 0.00
ACGTcount: A:0.15, C:0.32, G:0.33, T:0.20
Consensus pattern (43 bp):
CTCGGATGTGCGGGAGCCTCGAACACCGTCGGCACCTTGGTGC
Found at i:5850 original size:17 final size:18
Alignment explanation
Indices: 5825--5858 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5815 TTGTTGTCAT
5825 TGCATTTTTATTTGTTAA
1 TGCATTTTTATTTGTTAA
5843 TGCA-TTTTATTTGTTA
1 TGCATTTTTATTTGTTA
5859 GCTTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.62
Consensus pattern (18 bp):
TGCATTTTTATTTGTTAA
Found at i:18689 original size:16 final size:15
Alignment explanation
Indices: 18662--18694 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
18652 ATGAATTTAA
18662 AATTAAATTAATTCT
1 AATTAAATTAATTCT
18677 AATTAAATATAATTCT
1 AATTAAAT-TAATTCT
18693 AA
1 AA
18695 CTCATCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAAATTAATTCT
Found at i:19916 original size:21 final size:21
Alignment explanation
Indices: 19899--19949 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
19889 GACTTCTATT
19899 GATACAAGTGACAATTCTACC
1 GATACAAGTGACAATTCTACC
**
19920 GATACAAGTGACTCTTCTACC
1 GATACAAGTGACAATTCTACC
*
19941 GAAACAAGT
1 GATACAAGT
19950 CTTACTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24
Consensus pattern (21 bp):
GATACAAGTGACAATTCTACC
Found at i:20687 original size:52 final size:52
Alignment explanation
Indices: 20605--20791 Score: 259
Period size: 52 Copynumber: 3.6 Consensus size: 52
20595 ATTTCATTTA
* * * * **
20605 ATACTCACGATGACACATAGTTAACAGACCTCTTAATCCGTAAAGGAAACAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
20657 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
20709 ATACTCATC-ATGACACATAGTCATCGGACCTCATAATCCATAAACGATTCAT
1 ATACTCA-CGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
20761 ATGCTCACGATGACACATAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
20792 TTTTCATTTA
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
51 1 0.01
52 119 0.98
53 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:26107 original size:14 final size:13
Alignment explanation
Indices: 26079--26104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26069 TTTACACTAG
26079 AATTTTTTAATTT
1 AATTTTTTAATTT
26092 AATTTTTTAATTT
1 AATTTTTTAATTT
26105 TAAAATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTTTTAATTT
Found at i:26164 original size:19 final size:19
Alignment explanation
Indices: 26098--26165 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 19
26088 ATTTAATTTT
26098 TTAATTTTAAAATATAATTTAA
1 TTAATTTT--AATA-AATTTAA
* *
26120 TCAAATTTCAAT-AATTTAAA
1 T-TAATTTTAATAAATTT-AA
26140 TT-ATTTTAATAAATTTAA
1 TTAATTTTAATAAATTTAA
26158 TTAATTTT
1 TTAATTTT
26166 TTATTAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
18 11 0.29
19 15 0.39
20 3 0.08
21 3 0.08
22 1 0.03
23 5 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAATTTTAATAAATTTAA
Found at i:28230 original size:23 final size:23
Alignment explanation
Indices: 28200--28324 Score: 105
Period size: 23 Copynumber: 5.3 Consensus size: 23
28190 TGTTGGATAA
28200 CAGAGGGCACACAAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
*
28223 CAGAGGGCACACGAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
* * *
28246 AACAAAGGGTACACACAGTGCTGAA-
1 --CAGAGGGCACACAAAGTGCT-AAT
* *
28271 CAGAGGGCACGA-AACGTGCTAAA
1 CAGAGGGCAC-ACAAAGTGCTAAT
*
28294 CAGAGGGCACGA-AACGTGCTAAAT
1 CAGAGGGCAC-ACAAAGTGCT-AAT
28318 -AGAGGGC
1 CAGAGGGC
28325 GAGCTAGTGT
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
22 2 0.02
23 63 0.73
24 3 0.03
25 16 0.19
26 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.30, T:0.11
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTGCTAAT
Found at i:28248 original size:48 final size:49
Alignment explanation
Indices: 28196--28324 Score: 130
Period size: 48 Copynumber: 2.7 Consensus size: 49
28186 TAAGTGTTGG
28196 ATAACAGAGGGCACACAAAGTGCT-AATCAGAGGGCACACG-AA-GTGCT
1 ATAACAGAGGGCACACAAAGTGCTAAATCAGAGGGC-CACGAAACGTGCT
* * * *
28243 AATAACAAAGGGTACACACAGTGCTGAA-CAGAGGG-CACGAAACGTGCT
1 -ATAACAGAGGGCACACAAAGTGCTAAATCAGAGGGCCACGAAACGTGCT
*
28291 A-AACAGAGGGCACGA-AACGTGCTAAAT-AGAGGGC
1 ATAACAGAGGGCAC-ACAAAGTGCTAAATCAGAGGGC
28325 GAGCTAGTGT
Statistics
Matches: 67, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
46 28 0.42
47 4 0.06
48 33 0.49
49 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.29, T:0.12
Consensus pattern (49 bp):
ATAACAGAGGGCACACAAAGTGCTAAATCAGAGGGCCACGAAACGTGCT
Found at i:28265 original size:25 final size:24
Alignment explanation
Indices: 28172--28303 Score: 98
Period size: 23 Copynumber: 5.5 Consensus size: 24
28162 CCGAAGTACT
* * * *
28172 TAACAGAGGACACATAAGTGTTGGA
1 TAACAGAGGGCACACAAGTGCT-AA
28197 TAACAGAGGGCACACAAAGTGCTAA
1 TAACAGAGGGCACAC-AAGTGCTAA
28222 T--CAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACAC-AAGTGCTAA
* *
28245 TAACAAAGGGTACACACAGTGCT--
1 TAACAGAGGGCACACA-AGTGCTAA
*
28268 GAACAGAGGGCACGA-AACGTGCT-A
1 TAACAGAGGGCAC-ACAA-GTGCTAA
28292 -AACAGAGGGCAC
1 TAACAGAGGGCAC
28304 GAAACGTGCT
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
22 1 0.01
23 50 0.56
24 2 0.02
25 31 0.34
26 6 0.07
ACGTcount: A:0.39, C:0.20, G:0.28, T:0.13
Consensus pattern (24 bp):
TAACAGAGGGCACACAAGTGCTAA
Found at i:35391 original size:23 final size:23
Alignment explanation
Indices: 35355--35438 Score: 91
Period size: 23 Copynumber: 3.6 Consensus size: 23
35345 AAGTGCTGGG
35355 TAAT-AGAGGGCACACAAAGTGC
1 TAATCAGAGGGCACACAAAGTGC
* *
35377 TAATCAAAGGGCACACGAAGTGC
1 TAATCAGAGGGCACACAAAGTGC
*
35400 TAATAACAGAGGGCACGA-AACGTGC
1 TAAT--CAGAGGGCAC-ACAAAGTGC
*
35425 TAAACAGAGGGCAC
1 TAATCAGAGGGCAC
35439 GCTAGTGTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
22 4 0.08
23 30 0.58
25 17 0.33
26 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.12
Consensus pattern (23 bp):
TAATCAGAGGGCACACAAAGTGC
Found at i:38401 original size:38 final size:38
Alignment explanation
Indices: 38350--38425 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
38340 GGCCTTAGCA
38350 CATAGTTTACACAATTTATTCAAAAGATAAAAACTAAG
1 CATAGTTTACACAATTTATTCAAAAGATAAAAACTAAG
38388 CATAGTTTACACAATTTATTCAAAAGATAAAAACTAAG
1 CATAGTTTACACAATTTATTCAAAAGATAAAAACTAAG
38426 TTAAATCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (38 bp):
CATAGTTTACACAATTTATTCAAAAGATAAAAACTAAG
Found at i:44756 original size:19 final size:19
Alignment explanation
Indices: 44734--44778 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
44724 TTATATTACG
44734 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
*
44753 ATTTAATATTTAAATTTGT
1 ATTTAATATTTAAATATGT
44772 ATTTAAT
1 ATTTAAT
44779 TTATGTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:49347 original size:103 final size:103
Alignment explanation
Indices: 49221--49414 Score: 293
Period size: 103 Copynumber: 1.9 Consensus size: 103
49211 ATGTATTAGA
* * *
49221 CTGAGTAACCGGGATGGAGTGCTTGGTTGTCATTTCACTTCGCGTCAAAAGGGCTAACGCATTC-
1 CTGAGTAACCGGGATGGACTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAACGCATTCT
49285 TACAA-AAAAAAAAGAAGAAAAAATTGAGAGCATGTTGGG
66 TA-AAGAAAAAAAAG-AGAAAAAATTGAGAGCATGTTGGG
* * * *
49324 CTGAGTAACCGGGATGGACTGCTTGGGTGTCATTTCATTTCGCGTCAAAAGGTCCAATGTATTCT
1 CTGAGTAACCGGGATGGACTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAACGCATTCT
49389 TAAAGAAAAAAAAGAGAAAAAATTGA
66 TAAAGAAAAAAAAGAGAAAAAATTGA
49415 CAAAATAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
103 71 0.87
104 11 0.13
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.25
Consensus pattern (103 bp):
CTGAGTAACCGGGATGGACTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAACGCATTCT
TAAAGAAAAAAAAGAGAAAAAATTGAGAGCATGTTGGG
Found at i:49997 original size:19 final size:19
Alignment explanation
Indices: 49975--50019 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
49965 TTATATTAGG
49975 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
49994 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
50013 ATTTAAT
1 ATTTAAT
50020 TTATGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:50045 original size:14 final size:14
Alignment explanation
Indices: 50008--50049 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
49998 ATTATTTAAA
*
50008 TTTGTATTTA-ATT
1 TTTGTATTTATCTT
*
50021 TATGT-TTTATCTT
1 TTTGTATTTATCTT
50034 TTTGTATTTATCTT
1 TTTGTATTTATCTT
50048 TT
1 TT
50050 AGAGTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.17
13 10 0.42
14 10 0.42
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.71
Consensus pattern (14 bp):
TTTGTATTTATCTT
Found at i:50844 original size:22 final size:22
Alignment explanation
Indices: 50817--50862 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
50807 TTCGACTTCC
*
50817 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTAT-TTTACTTTTAATT
*
50839 CTATTTTATTTTATTTTTAATT
1 CTATTTTATTTTACTTTTAATT
50861 CT
1 CT
50863 GTTTCTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (22 bp):
CTATTTTATTTTACTTTTAATT
Found at i:50877 original size:22 final size:22
Alignment explanation
Indices: 50831--50877 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
50821 TTTCTATTTC
*
50831 TTTTAATTCTATTTTATTTTAT
1 TTTTAATTCTAGTTTATTTTAT
*
50853 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTATTTTAT
50874 TTTT
1 TTTT
50878 CCTTAGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTATTTTAT
Done.