Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007174.1 Kokia drynarioides strain JFW-HI SEQ_121786, 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: 67468
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 116 characters in sequence are not A, C, G, or T
Found at i:242 original size:21 final size:21
Alignment explanation
Indices: 218--282 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 21
208 TATTTTATTT
218 TATTTAATATTAATATAATTA
1 TATTTAATATTAATATAATTA
*
239 TATTT-GT-TTAATAT-ATTA
1 TATTTAATATTAATATAATTA
*
257 -ATATAAATATTAA-ATATATTA
1 TAT-TTAATATTAATATA-ATTA
278 TATTT
1 TATTT
283 TTTTAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
17 2 0.06
18 5 0.15
19 10 0.29
20 5 0.15
21 10 0.29
22 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTAATATTAATATAATTA
Found at i:288 original size:19 final size:19
Alignment explanation
Indices: 229--307 Score: 63
Period size: 19 Copynumber: 4.1 Consensus size: 19
219 ATTTAATATT
229 AATATAATTATAT-TTGTTT-
1 AATAT-ATTATATATT-TTTA
* *
248 AATATATTAATATAAATATTA
1 AATATATT-ATAT-ATTTTTA
*
269 AATATATTATATTTTTTTA
1 AATATATTATATATTTTTA
* *
288 AAAATATTATGTATTTTTA
1 AATATATTATATATTTTTA
307 A
1 A
308 TATTTCTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
18 3 0.06
19 30 0.62
20 6 0.12
21 9 0.19
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
AATATATTATATATTTTTA
Found at i:1507 original size:26 final size:26
Alignment explanation
Indices: 1464--1514 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1454 TATACAAAAT
*
1464 ATAAAAATACTCCCATAATACTATTG
1 ATAAAAATACTCCCATAATAATATTG
**
1490 ATAAAAATACTCTTATAATAATATT
1 ATAAAAATACTCCCATAATAATATT
1515 TTTTACTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (26 bp):
ATAAAAATACTCCCATAATAATATTG
Found at i:1979 original size:2 final size:2
Alignment explanation
Indices: 1972--2010 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1962 ACTGTCTCAA
1972 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2011 TTTGCTCAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31186 original size:27 final size:27
Alignment explanation
Indices: 31124--31187 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
31114 ATTTTGGCTT
*
31124 TTTATAAAAATAATATAAAAATAATTA
1 TTTACAAAAATAATATAAAAATAATTA
* *
31151 ATTACAAAAATAAATTTGAAAAA-AATTA
1 TTTACAAAAAT-AATAT-AAAAATAATTA
31179 TTTA-AAAAA
1 TTTACAAAAA
31188 CAAAGTGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 14 0.45
28 12 0.39
29 5 0.16
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (27 bp):
TTTACAAAAATAATATAAAAATAATTA
Found at i:32032 original size:17 final size:18
Alignment explanation
Indices: 31988--32035 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
31978 CATTTTTGTT
*
31988 GCTATTTTTTTAATATGA
1 GCTAATTTTTTAATATGA
*
32006 GTTAATTTTTTAATA-GAA
1 GCTAATTTTTTAATATG-A
32024 GCTAATTTTTTA
1 GCTAATTTTTTA
32036 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54
Consensus pattern (18 bp):
GCTAATTTTTTAATATGA
Found at i:32064 original size:40 final size:42
Alignment explanation
Indices: 32013--32093 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
32003 TGAGTTAATT
32013 TTTTAATAGAAGCT-A-ATTTTTTATTTTTAATTTATTTTAC
1 TTTTAATAGAAGCTAATATTTTTTATTTTTAATTTATTTTAC
*
32053 TTTTAATAGAAGCTAATATTTTTTATTTTTTATTTATTTTA
1 TTTTAATAGAAGCTAATATTTTTTATTTTTAATTTATTTTA
32094 TAGATTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 14 0.37
41 1 0.03
42 23 0.61
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.62
Consensus pattern (42 bp):
TTTTAATAGAAGCTAATATTTTTTATTTTTAATTTATTTTAC
Found at i:32097 original size:35 final size:39
Alignment explanation
Indices: 32013--32087 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
32003 TGAGTTAATT
*
32013 TTTTAATAGAAGCTAATTTTTTATTTTTAATTTATTTTAC
1 TTTTAATAGAAGCTAATTTTTTATATTT-ATTTATTTTAC
32053 TTTTAATAGAAGCTAATATTTTT-TATTT-TTTATTT
1 TTTTAATAGAAGCTAAT-TTTTTATATTTATTTATTT
32088 ATTTTATAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
38 7 0.21
40 21 0.64
41 5 0.15
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.61
Consensus pattern (39 bp):
TTTTAATAGAAGCTAATTTTTTATATTTATTTATTTTAC
Found at i:43038 original size:7 final size:7
Alignment explanation
Indices: 42994--43025 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
42984 CTTGGAAAAA
42994 GTCAATG
1 GTCAATG
43001 GTCAATG
1 GTCAATG
43008 GTCAATG
1 GTCAATG
43015 GTCAATAG
1 GTCAAT-G
43023 GTC
1 GTC
43026 GGGTCAACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (7 bp):
GTCAATG
Found at i:43049 original size:24 final size:24
Alignment explanation
Indices: 43015--43086 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
43005 ATGGTCAATG
*
43015 GTCAATAGGTCGGGTCAACGGTCA
1 GTCAATAGGTCGGGTGAACGGTCA
* * *
43039 GTCAATGGGTCGAGTGAACGATCA
1 GTCAATAGGTCGGGTGAACGGTCA
*
43063 GTCAATAGGTCAGGTGAACGGTCA
1 GTCAATAGGTCGGGTGAACGGTCA
43087 ATTAACGGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (24 bp):
GTCAATAGGTCGGGTGAACGGTCA
Found at i:53710 original size:39 final size:40
Alignment explanation
Indices: 53656--53735 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
53646 TATGCACTCA
53656 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
* *
53695 ATGGACACCTTTTGAAGAGTCACATCCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
53735 A
1 A
53736 CATACCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:53752 original size:39 final size:38
Alignment explanation
Indices: 53660--53748 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 38
53650 CACTCAATGG
*
53660 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGG
1 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGA-GC
* *
53699 ACACCTTTTGAAGAGTCACATCCCTTTTCATATTGGA-C
1 ACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGGAGC
* *
53737 ATACCTCTTGAA
1 ACACCTTTTGAA
53749 AGAGACTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
38 10 0.23
39 23 0.52
40 11 0.25
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (38 bp):
ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:55789 original size:18 final size:18
Alignment explanation
Indices: 55766--55801 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55756 GAAGATCAAC
*
55766 TAGAATTCAAGTATTATT
1 TAGAATCCAAGTATTATT
55784 TAGAATCCAAGTATTATT
1 TAGAATCCAAGTATTATT
55802 GGACAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (18 bp):
TAGAATCCAAGTATTATT
Found at i:58646 original size:39 final size:40
Alignment explanation
Indices: 58592--58671 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
58582 TATGCACTCA
58592 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
** *
58631 ATGGACACCTTTTGAAGAGTCACGTCCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
58671 A
1 A
58672 CATACCTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 26 0.70
40 11 0.30
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:64302 original size:120 final size:119
Alignment explanation
Indices: 64089--64440 Score: 461
Period size: 120 Copynumber: 2.9 Consensus size: 119
64079 ACAGATATCC
* * * *
64089 TATCGATGGCTGAGGTACTGCATATGTTGCGAGTCCTTAACAGCTCGTGTGAGCAGCATCATATA
1 TATCGATGGTTG-GGTACCGCATATGTTGCGAGTCCTTGACAGCTCGTGTGAGCAGCATCGTATA
* * *
64154 CTGGTAATAGAGTTGATACTGACATGAGAATGAAATTCTGGATTATAACATACTG
65 CTGGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGATTATAACATACCG
* * * *
64209 TATCGATGGTTGGGATACCGCATATGTTGCGAGTCCTTGATAACTCATGTGAGCTGCATCGTATA
1 TATCGATGGTTGGG-TACCGCATATGTTGCGAGTCCTTGACAGCTCGTGTGAGCAGCATCGTATA
* * *
64274 CTAGTAACAGAGTTGATACGGACATGAGAATGAAATTCTGGATTATAGCATACCG
65 CTGGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGATTATAACATACCG
* * * *
64329 TATCGATGGTTGGGGTATCACAAATGTTTCGAGTCCTTGACAGCTCGTGTGAGCAGCATCGTATA
1 TATCGATGGTT-GGGTACCGCATATGTTGCGAGTCCTTGACAGCTCGTGTGAGCAGCATCGTATA
* * * * * *
64394 CTGGTAACAGAGTTAATAAAAACATGAGGACGAAATTTTGGATTATA
65 CTGGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGATTATA
64441 GCTTGTGGAA
Statistics
Matches: 201, Mismatches: 29, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
119 2 0.01
120 196 0.98
121 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (119 bp):
TATCGATGGTTGGGTACCGCATATGTTGCGAGTCCTTGACAGCTCGTGTGAGCAGCATCGTATAC
TGGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGATTATAACATACCG
Found at i:66224 original size:17 final size:17
Alignment explanation
Indices: 66202--66280 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
66192 TTTAAATTGG
66202 TTTAAATTTTTTTTAAA
1 TTTAAATTTTTTTTAAA
* **
66219 TTTAAATTTTTCTTATG
1 TTTAAATTTTTTTTAAA
66236 TTTAAATTTATCTTTTAAA
1 TTTAAATTT-T-TTTTAAA
**
66255 TTTAAATTTGCTTTAAA
1 TTTAAATTTTTTTTAAA
66272 TTT-AATTTT
1 TTTAAATTTT
66281 AATCAAATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
16 5 0.10
17 32 0.63
18 1 0.02
19 13 0.25
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTAAATTTTTTTTAAA
Found at i:66276 original size:36 final size:35
Alignment explanation
Indices: 66202--66281 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
66192 TTTAAATTGG
* **
66202 TTTAAATTT-TTTTTAAATTTAAATTTTTCTTATG
1 TTTAAATTTATTTTTAAATTTAAATTTCTCTTAAA
66236 TTTAAATTTATCTTTTAAATTTAAATTTGCT-TTAAA
1 TTTAAATTTAT-TTTTAAATTTAAATTT-CTCTTAAA
*
66272 TTTAATTTTA
1 TTTAAATTTA
66282 ATCAAATTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 9 0.23
35 1 0.03
36 28 0.72
37 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (35 bp):
TTTAAATTTATTTTTAAATTTAAATTTCTCTTAAA
Done.