Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010529.1 Kokia drynarioides strain JFW-HI SEQ_125446, 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: 48478
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:12774 original size:32 final size:33
Alignment explanation
Indices: 12729--12796 Score: 129
Period size: 32 Copynumber: 2.1 Consensus size: 33
12719 ATGTTAGTGA
12729 TTGTGCTTGCTTGTATTTGTTCTTTAGGTGTGC
1 TTGTGCTTGCTTGTATTTGTTCTTTAGGTGTGC
12762 TTGTGC-TGCTTGTATTTGTTCTTTAGGTGTGC
1 TTGTGCTTGCTTGTATTTGTTCTTTAGGTGTGC
12794 TTG
1 TTG
12797 AATGTTCTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 29 0.83
33 6 0.17
ACGTcount: A:0.06, C:0.12, G:0.28, T:0.54
Consensus pattern (33 bp):
TTGTGCTTGCTTGTATTTGTTCTTTAGGTGTGC
Found at i:28591 original size:30 final size:31
Alignment explanation
Indices: 28557--28628 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
28547 GTTACATTTA
*
28557 ACAAAACAGTCAATCAACTT-T-GAAAATGTG
1 ACAAAACAGTCAATAAACTTATCGAAAA-GTG
* * *
28587 ACAAAACAATCACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCAATAAACTTATCGAAAAGTG
28618 ACAAAACAGTC
1 ACAAAACAGTC
28629 CTCTACTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 16 0.46
31 14 0.40
32 5 0.14
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (31 bp):
ACAAAACAGTCAATAAACTTATCGAAAAGTG
Found at i:29479 original size:30 final size:31
Alignment explanation
Indices: 29418--29485 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
29408 CCAAGAGGAT
* * *
29418 TGTTTTGTCACTTTTTGATAACTTTAGTGAC
1 TGTTTTGTCACATTTTCATAACTTGAGTGAC
*
29449 TGTTTTGTCACATTTTCA-AAGTTGAGTGAC
1 TGTTTTGTCACATTTTCATAACTTGAGTGAC
29479 TGTTTTG
1 TGTTTTG
29486 CTAAATGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (31 bp):
TGTTTTGTCACATTTTCATAACTTGAGTGAC
Found at i:36744 original size:96 final size:96
Alignment explanation
Indices: 36566--36746 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 96
36556 AGGATGTTCG
** ** *
36566 ATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGTGCAAATTTTTAGAATCGAAGAT
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAAATTTTGAGAATCGAAGAT
* *
36631 AAGGAAACATTGTCTCGATTAAGGGTATTCA
66 AAAGAAACATTGCCTCGATTAAGGGTATTCA
*
36662 ATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAAATTTTCGA-AACTCGAA-
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAAATTTT-GAGAA-TCGAAG
*
36725 ATAAA-AGAATATTGCCTCGATT
64 ATAAAGA-AACATTGCCTCGATT
36747 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 66 0.90
97 6 0.08
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAAATTTTGAGAATCGAAGAT
AAAGAAACATTGCCTCGATTAAGGGTATTCA
Found at i:37102 original size:29 final size:29
Alignment explanation
Indices: 37072--37351 Score: 221
Period size: 29 Copynumber: 9.5 Consensus size: 29
37062 ATTCAGGGGT
*
37072 AAAATGGTAATTTTTGAAAGTTTCGAGGTA
1 AAAAT-GTAATTTTTGGAAGTTTCGAGGTA
* * * *
37102 AAAATGGAGTTTTCGGACA--TTCAAGGGTA
1 AAAATGTAATTTTTGGA-AGTTTCGA-GGTA
* *
37131 AAAATGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGTAATTTTTGGAAGTTTCGAGGT-A
* * *
37161 AAAATGAAATTTTCGGAAGTTT-TAGGGTCA
1 AAAATGTAATTTTTGGAAGTTTCGA-GGT-A
* *
37191 AAAATGAAAATTTTT-GAAGTTTTG-GAGTA
1 AAAATG-TAATTTTTGGAAGTTTCGAG-GTA
* *
37220 AAAATGTATTTTTTTGAAGTTTCGAGGTCA
1 AAAATGTAATTTTTGGAAGTTTCGAGGT-A
* * * *
37250 AAAATGAAATTTTTGGAAGTTTGGGGGTT
1 AAAATGTAATTTTTGGAAGTTTCGAGGTA
*
37279 AAAATGTAATTTTTGGAAGTTTC-ATGGTC
1 AAAATGTAATTTTTGGAAGTTTCGA-GGTA
* * * *
37308 AAAATGGAATTTTTGGAAGTTTAGGGGTT
1 AAAATGTAATTTTTGGAAGTTTCGAGGTA
37337 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
37352 AACATTTTAG
Statistics
Matches: 201, Mismatches: 35, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
28 11 0.05
29 109 0.54
30 74 0.37
31 7 0.03
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTCGAGGTA
Found at i:37121 original size:58 final size:59
Alignment explanation
Indices: 37044--37212 Score: 168
Period size: 58 Copynumber: 2.9 Consensus size: 59
37034 ATTTAGGGTT
* * *
37044 AAAAAAGAAATTTT-AGACATTCAGGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGT-
1 AAAAATGAAATTTTCGGACATTCAAGGGTAAAAAT-GTAATTTTTGAAAGTTTCGAGGTC
* * * * *
37101 AAAAATGGAGTTTTCGGACATTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGAAATTTTCGGACATTCAAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGTC
** *
37160 AAAAATGAAATTTTCGGA-AGTTTTAGGGTCAAAAATGAAAATTTTTG-AAGTTT
1 AAAAATGAAATTTTCGGACA-TTCAAGGGT-AAAAATG-TAATTTTTGAAAGTTT
37213 TGGAGTAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
57 11 0.12
58 33 0.35
59 28 0.30
60 13 0.14
61 8 0.09
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (59 bp):
AAAAATGAAATTTTCGGACATTCAAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGTC
Found at i:37175 original size:59 final size:58
Alignment explanation
Indices: 37063--37349 Score: 251
Period size: 59 Copynumber: 4.9 Consensus size: 58
37053 ATTTTAGACA
* * * * * * *
37063 TTCAGGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTAAAAATGGAGTTTTCGGACA-
1 TTCAAGGGTAAAAAT-GAAATTTTTGGAAGTTTTGGGGTAAAAATGTAATTTTCGGA-AG
* *
37121 TTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAAATTTTCGGAAG
1 TTCAAGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGT-AAAAATGTAATTTTCGGAAG
** * * **
37180 TTTTAGGGTCAAAAATGAAAATTTTT-GAAGTTTTGGAGTAAAAATGTATTTTTTTGAAG
1 TTCAAGGGT-AAAAATG-AAATTTTTGGAAGTTTTGGGGTAAAAATGTAATTTTCGGAAG
* * * *
37239 TTTCGA-GGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTTAAAATGTAATTTTTGGAAG
1 -TTCAAGGGT-AAAAATGAAATTTTTGGAAGTTTTGGGGTAAAAATGTAATTTTCGGAAG
* * * * *
37298 TTTC-ATGGTCAAAATGGAATTTTTGGAAGTTTAGGGGTTAAAATGTAATTTT
1 -TTCAAGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGTAAAAATGTAATTTT
37350 TGAACATTTT
Statistics
Matches: 197, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
58 78 0.40
59 90 0.46
60 22 0.11
61 7 0.04
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (58 bp):
TTCAAGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGTAAAAATGTAATTTTCGGAAG
Found at i:38859 original size:23 final size:23
Alignment explanation
Indices: 38819--38884 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
38809 CTGGACTTTT
*
38819 AATTA-ATTTAAATTTTAAATTCA
1 AATTATATTTAAA-CTTAAATTCA
*
38842 AATTATATTTAAACTT-AATTTA
1 AATTATATTTAAACTTAAATTCA
* *
38864 AATTTTAACTTAAAC-TAAATT
1 AATTAT-ATTTAAACTTAAATT
38885 TAAACCCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 11 0.31
23 18 0.50
24 7 0.19
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTATATTTAAACTTAAATTCA
Found at i:38868 original size:17 final size:17
Alignment explanation
Indices: 38821--38889 Score: 68
Period size: 17 Copynumber: 4.0 Consensus size: 17
38811 GGACTTTTAA
*
38821 TTAATTTAAATTTTAAA-
1 TTAAATTAAA-TTTAAAC
*
38838 TTCAAATTATATTTAAAC
1 TT-AAATTAAATTTAAAC
* *
38856 TTAATTTAAATTTTAAC
1 TTAAATTAAATTTAAAC
*
38873 TTAAACTAAATTTAAAC
1 TTAAATTAAATTTAAAC
38890 CCAAAATGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
17 34 0.81
18 8 0.19
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATTAAATTTAAAC
Found at i:38876 original size:12 final size:12
Alignment explanation
Indices: 38821--38877 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
38811 GGACTTTTAA
38821 TTAATTTAAATT
1 TTAATTTAAATT
*
38833 TTAAATTCAAATT
1 TT-AATTTAAATT
* *
38846 AT-ATTTAAA-C
1 TTAATTTAAATT
38856 TTAATTTAAATT
1 TTAATTTAAATT
*
38868 TTAACTTAAA
1 TTAATTTAAA
38878 CTAAATTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.03
11 13 0.37
12 11 0.31
13 10 0.29
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (12 bp):
TTAATTTAAATT
Found at i:39779 original size:201 final size:201
Alignment explanation
Indices: 39277--39907 Score: 743
Period size: 201 Copynumber: 3.1 Consensus size: 201
39267 ACTTAGCCTT
* ** * * * * *
39277 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTATCTGTGTTTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCTCAT
* * * * *
39342 TAGGAAGAC--GGTTTGG-CTCACTTCTCCA-TATCTTATCAGGAAGCTAACAACTTTATTGCTT
66 CAGGAAGACAAAG-TTGGTC-CACTTCT-CAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* * * * *
39403 CGACCTGCTTCTCAGTATCTCATTAGGAAGCTGAGGTTCGAAGGTTTGCTCACATCGAG-CATGA
128 CGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGA
* *
39467 GTTTGATTTGGTCTT
193 ----G--TTGGTATA
* ** *
39482 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCTCAT
* * *
39547 CAGGAAGGCAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACAAAGTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * *
39612 CTTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTTGAAGATTTGCTCACATCGAGCCCCGAGTT
131 CCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTT
39677 GGTATA
196 GGTATA
* * ** * *
39683 CTTGTCTGTGTCTCATCAGGAAGATGATTGCCTCACTTGTTTCCATCCGCTTCTCTATATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCTCAT
** *
39748 CAGGAAGATGAAGTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGA
66 CAGGAAGACAAAGTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * *
39813 CCTGCTTCTTAGTATCTTATCAGGAAGCT-GGATTCGAATATTTGCTCACATCGAGCCCTGAGTT
131 CCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTT
*
39877 TGTATA
196 GGTATA
*
39883 TTTCTCTGTATCTCATCAGGAAGAT
1 CTTCTCTGTATCTCATCAGGAAGAT
39908 AACCATTTTA
Statistics
Matches: 369, Mismatches: 52, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
200 58 0.16
201 147 0.40
203 1 0.00
205 66 0.18
206 93 0.25
207 4 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (201 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCTCAT
CAGGAAGACAAAGTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTT
GGTATA
Found at i:40026 original size:115 final size:115
Alignment explanation
Indices: 39759--40204 Score: 644
Period size: 115 Copynumber: 3.9 Consensus size: 115
39749 AGGAAGATGA
** * *
39759 AGTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTTA
1 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCA
* * *
39824 GTATCTTATCAGGAAGCT-GGATTCGAATATTTGCTCACATCGAGCCCTG
66 ATATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCCCTG
* * * * *
39873 AGTTTGTATATTTCTCTGTATCTCATCAGGAAGATAACCATTTTATTACTTCGACCTGCTTTTTA
1 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCA
* *
39938 ATATCTCATCAGGAAGCTGAGATTCGAAGATTTGCTAACATCGAGCCCTG
66 ATATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCCCTG
* *
39988 AGTTGGTATACTTCTCTGTATCTCATCAAGAAGCTAACCATTTTATCACTTCGACCTGCTTCTCA
1 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCA
* * * * *
40053 GTATCTCATCAGGAAGTTGGGGTTTGAAGATTTACTCACATCGAG-CCTCG
66 ATATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCCCT-G
* * *
40103 AGTTGGTATACTTCTCTATATCTAATCAGGAAGCTAACCATTTTATTAATTCGACCTGCTTCTCA
1 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCA
*
40168 ATATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
66 ATATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTC
40205 GCTTTGAGCC
Statistics
Matches: 295, Mismatches: 35, Indels: 3
0.89 0.11 0.01
Matches are distributed among these distances:
114 77 0.26
115 218 0.74
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (115 bp):
AGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCA
ATATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCCCTG
Found at i:41107 original size:42 final size:42
Alignment explanation
Indices: 40989--41108 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
40979 GGATCTGAAT
* * ** *
40989 CGCCTTTTGCGGGTTTTCAACTCAAAATTTCTTTGGTTCCAGGA
1 CGCCCTTTGCGGGTTTTCAACTC--AATTTTTTTTTTTCCAAGA
* * **
41033 CGCCCTTTGCGGGTTTTCAGCTTGAACCTTTTTTTTT-CAAGA
1 CGCCCTTTGCGGGTTTTCAAC-TCAATTTTTTTTTTTCCAAGA
*
41075 CGCCCTTTGCGGGTTTTCATCTCAATTTTTTTTT
1 CGCCCTTTGCGGGTTTTCAACTCAATTTTTTTTT
41109 AGGCGAAGTA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
41 10 0.16
42 24 0.39
43 8 0.13
44 19 0.31
45 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.44
Consensus pattern (42 bp):
CGCCCTTTGCGGGTTTTCAACTCAATTTTTTTTTTTCCAAGA
Found at i:47804 original size:21 final size:22
Alignment explanation
Indices: 47775--47815 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
47765 AATTTCCTAC
47775 ATCGCATTG-ATTTTCTCCTCTA
1 ATCGCATTGTATTTT-TCCTCTA
47797 ATCG-ATTGTATTTTTCCTC
1 ATCGCATTGTATTTTTCCTC
47816 CATTTGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.17, C:0.24, G:0.10, T:0.49
Consensus pattern (22 bp):
ATCGCATTGTATTTTTCCTCTA
Done.