Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011418.1 Kokia drynarioides strain JFW-HI SEQ_126402, 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: 25388
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Warning! 132 characters in sequence are not A, C, G, or T
Found at i:3507 original size:96 final size:95
Alignment explanation
Indices: 3336--3521 Score: 225
Period size: 96 Copynumber: 1.9 Consensus size: 95
3326 GGGAAAATGA
* ** * * *
3336 TATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATCTCAGAATC
1 TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAATATCTCAAAATC
*
3401 GAAGATAAAGAAACATTGCCTCGATTAAGGG
66 GAAGATAAAG-AACATTACCTCGATTAAGGG
* *
3432 TATTCGATTATTTCAATTTGAAGAAAAATTGCACC-AGTAAGTTAAGACACAA-ATTTTCAAAAC
1 TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAATA-TCTCAAAA-
*
3495 TCGAA-ATAAAAGAATATTACCTCGATT
64 TCGAAGAT-AAAGAACATTACCTCGATT
3522 TTAAAGCCTT
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
94 1 0.01
95 36 0.47
96 40 0.52
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (95 bp):
TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAATATCTCAAAATC
GAAGATAAAGAACATTACCTCGATTAAGGG
Found at i:3856 original size:59 final size:57
Alignment explanation
Indices: 3785--4154 Score: 297
Period size: 59 Copynumber: 6.3 Consensus size: 57
3775 ATTTAAGGTT
*
3785 TAAAAATAGAATTTTTAGACA-TTCGAGGG-T-AAAAGGGTATTTTT-GAGAGTTTTAGGGG
1 TAAAAATGGAATTTTTAGA-AGTTCG-GGGTTAAAAAGGG-ATTTTTAGA-AG-TTTAGGGG
*
3843 TAAAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAAAGGGATTTTTAGAAGTTTAGGGG
1 T-AAAAATGGAATTTTTAGAAG-TTCGGGGTT-AAAAAGGGATTTTTAGAAGTTTAGGGG
* * * * *
3903 TAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAG-TTCGAGGG
1 TAAAAATGGAATTTTTAGAAG-TTCGGGGTTAAAAA-GGGATTTTTAGAAGTTTAG-GGG
* * * * *
3962 TAAAAATGGATTTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAG-TTCGAGGG
1 TAAAAATGGAATTTTTAGAAG-TTCGGGGTTAAAAA-GGGATTTTTAGAAGTTTAG-GGG
* * * * *
4021 TAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG-TTCGATGG
1 TAAAAATGGAATTTTTAGAAG-TTCGGGGTTAAAAA-GGGATTTTTAGAAGTTTAG-GGG
* * * * * *
4080 TAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAG-TTCGAGGG
1 TAAAAATGGAATTTTTAGAAG-TTCGGGGTTAAAAA-GGGATTTTTAGAAGTTTAG-GGG
4139 TAAAAATGGAATTTTT
1 TAAAAATGGAATTTTT
4155 GAAAGTTTAG
Statistics
Matches: 286, Mismatches: 17, Indels: 17
0.89 0.05 0.05
Matches are distributed among these distances:
58 10 0.03
59 246 0.86
60 13 0.05
61 8 0.03
62 9 0.03
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (57 bp):
TAAAAATGGAATTTTTAGAAGTTCGGGGTTAAAAAGGGATTTTTAGAAGTTTAGGGG
Found at i:3879 original size:30 final size:30
Alignment explanation
Indices: 3839--4162 Score: 362
Period size: 30 Copynumber: 11.0 Consensus size: 30
3829 GAGAGTTTTA
* * *
3839 GGGGTAAAAAATGGAATTTTTAGAAGTTTT
1 GGGGTTAAAAATGGAATTTTTGGAAGTTTC
* * * *
3869 GGGGTTAAAAAAGGGATTTTTAGAAGTTTA
1 GGGGTTAAAAATGGAATTTTTGGAAGTTTC
*
3899 GGGG-TAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTTAAAAATGGAATTTTTGGAAGTTTC
* *
3928 GAGGTTAAAAATGGGATTTTTGGAAG-TTC
1 GGGGTTAAAAATGGAATTTTTGGAAGTTTC
*
3957 GAGGG-TAAAAATGGATTTTTTGGAAGTTTC
1 G-GGGTTAAAAATGGAATTTTTGGAAGTTTC
* *
3987 GAGGTTAAAAATGGGATTTTTGGAAG-TTC
1 GGGGTTAAAAATGGAATTTTTGGAAGTTTC
*
4016 GAGGG-TAAAAATGGAATTTTTGGAAGTTTT
1 G-GGGTTAAAAATGGAATTTTTGGAAGTTTC
*
4046 GGGGTTAAAAATGGGATTTTTGGAAG-TTC
1 GGGGTTAAAAATGGAATTTTTGGAAGTTTC
*
4075 GATGG-TAAAAATGGAATTTTTGGAAGTTTC
1 G-GGGTTAAAAATGGAATTTTTGGAAGTTTC
* *
4105 GAGGTCAAAAATAGG-ATTTTTGGAAG-TTC
1 GGGGTTAAAAAT-GGAATTTTTGGAAGTTTC
*
4134 GAGGG-TAAAAATGGAATTTTTGAAAGTTT
1 G-GGGTTAAAAATGGAATTTTTGGAAGTTT
4163 AGGGACCTCT
Statistics
Matches: 251, Mismatches: 29, Indels: 28
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.01
29 120 0.48
30 127 0.51
31 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (30 bp):
GGGGTTAAAAATGGAATTTTTGGAAGTTTC
Found at i:4155 original size:29 final size:29
Alignment explanation
Indices: 3785--4161 Score: 374
Period size: 29 Copynumber: 12.8 Consensus size: 29
3775 ATTTAAGGTT
* *
3785 TAAAAATAGAATTTTTAGACA-TTCGAGGG
1 TAAAAATGGAATTTTTGGA-AGTTCGAGGG
* * **
3814 T-AAAAGGGTATTTTT-GAGAGTTTTAGGGG
1 TAAAAATGGAATTTTTGGA-AGTTCGA-GGG
* *
3843 TAAAAAATGGAATTTTTAGAAGTTTTG-GGG
1 T-AAAAATGGAATTTTTGGAAG-TTCGAGGG
* * * *
3873 TTAAAAAAGGGATTTTTAGAAGTT-TAGGGG
1 -TAAAAATGGAATTTTTGGAAGTTCGA-GGG
* *
3903 TAAAAATGGAATTTTTGGAAGTTTTGAGGT
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
*
3933 TAAAAATGGGATTTTTGGAAGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTCGAGGG
* *
3962 TAAAAATGGATTTTTTGGAAGTTTCGAGGT
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
*
3992 TAAAAATGGGATTTTTGGAAGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTCGAGGG
*
4021 TAAAAATGGAATTTTTGGAAGTTTTG-GGG
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
* *
4050 TTAAAAATGGGATTTTTGGAAGTTCGATGG
1 -TAAAAATGGAATTTTTGGAAGTTCGAGGG
4080 TAAAAATGGAATTTTTGGAAGTTTCGA-GG
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
4109 TCAAAAATAGG-ATTTTTGGAAGTTCGAGGG
1 T-AAAAAT-GGAATTTTTGGAAGTTCGAGGG
*
4139 TAAAAATGGAATTTTTGAAAGTT
1 TAAAAATGGAATTTTTGGAAGTT
4162 TAGGGACCTC
Statistics
Matches: 295, Mismatches: 33, Indels: 40
0.80 0.09 0.11
Matches are distributed among these distances:
27 3 0.01
28 16 0.05
29 129 0.44
30 124 0.42
31 18 0.06
32 5 0.02
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTCGAGGG
Found at i:4155 original size:59 final size:59
Alignment explanation
Indices: 3840--4162 Score: 504
Period size: 59 Copynumber: 5.5 Consensus size: 59
3830 AGAGTTTTAG
* * * * *
3840 GGGTAAAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAAAGGGATTTTTAGAAGTT-TA
1 GGGT-AAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGA
3899 GGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGA
1 -GGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGA
* *
3959 GGGTAAAAATGGATTTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGA
*
4018 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGA
* * * *
4077 TGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGA
*
4136 GGGTAAAAATGGAATTTTTGAAAGTTT
1 GGGTAAAAATGGAATTTTTGGAAGTTT
4163 AGGGACCTCT
Statistics
Matches: 245, Mismatches: 17, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
59 240 0.98
60 5 0.02
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.35
Consensus pattern (59 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGA
Found at i:5258 original size:12 final size:10
Alignment explanation
Indices: 5239--5280 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
5229 TTCCTTTTTT
5239 ATTATTATTA
1 ATTATTATTA
5249 ATGCTATTATTA
1 AT--TATTATTA
5261 ATTATTATT-
1 ATTATTATTA
5270 ATTATTATTA
1 ATTATTATTA
5280 A
1 A
5281 AACATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.31
10 10 0.34
12 10 0.34
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
ATTATTATTA
Found at i:5275 original size:19 final size:21
Alignment explanation
Indices: 5239--5280 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 21
5229 TTCCTTTTTT
5239 ATTATTATTAATGCTATTATTA
1 ATTATTATTAAT-CTATTATTA
5261 ATTATTATT-AT-TATTATTA
1 ATTATTATTAATCTATTATTA
5280 A
1 A
5281 AACATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTATTATTAATCTATTATTA
Found at i:5291 original size:3 final size:3
Alignment explanation
Indices: 5237--5279 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
5227 TTTTCCTTTT
* * *
5237 TTA TTA TTA TTA ATG CTA TTA TTAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
5280 AAACATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:6068 original size:18 final size:17
Alignment explanation
Indices: 6035--6073 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
6025 TTTTAAATCC
6035 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
6052 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
6070 ATTT
1 ATTT
6074 GAATCAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:6843 original size:205 final size:206
Alignment explanation
Indices: 6541--7030 Score: 655
Period size: 206 Copynumber: 2.4 Consensus size: 206
6531 GTATCAGGAC
** * * * *
6541 GCTAATCCATTTTATTATTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAA-AG
1 GCTAA-CCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTTGAAGA-
* * * * *
6605 TTTGCCCACACCGAGCGTGGGCTTGACTTGGTCTTCTTCTCGGTATCTCATCAGGAAGAT-ACTG
64 TTTGCTCACATCGAGCATGGGCTTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCG
* * ** * * *
6669 CGTCGTTTGTTTCAATTTGCTTCTTTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTGAGT
129 CATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGATTCACTTCTCAGT
* *
6734 ATCTCATTAGGAA
194 ATCTCATCAAGAA
* *
6747 GCTAACCGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCGTCAGGAAGCTGGGATTTGAAGATT
1 GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTTGAAGATT
* *
6812 TGCTCACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCA
66 TGCTCACATCGAGCATGGGCTTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCA
*
6877 TTGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTAT
131 TCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTAT
6942 CTCATCAAGAA
196 CTCATCAAGAA
* * *
6953 GCTAACTATTTTATTGCTTCGACCTGCTTCTCATTATCTCATCAGGAAG-T-TGATGTTCGAAGA
1 GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGAT-TT-GAAGA
*
7016 TTTGCTCGCATCGAG
64 TTTGCTCACATCGAG
7031 TCCTGAGTTG
Statistics
Matches: 249, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
204 3 0.01
205 105 0.42
206 141 0.57
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (206 bp):
GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTTGAAGATT
TGCTCACATCGAGCATGGGCTTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCA
TCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTAT
CTCATCAAGAA
Found at i:18780 original size:29 final size:28
Alignment explanation
Indices: 18748--18809 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
18738 AAAATGAGAC
*
18748 TTTTCGGATGCTCAGGG-ATAAAATGGTAA
1 TTTT-GGATGATCAGGGCA-AAAATGGTAA
* *
18777 TTTTGGATTATCGGGGCAAAAATGGTAA
1 TTTTGGATGATCAGGGCAAAAATGGTAA
18805 TTTTG
1 TTTTG
18810 TGAAAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (28 bp):
TTTTGGATGATCAGGGCAAAAATGGTAA
Found at i:18918 original size:30 final size:30
Alignment explanation
Indices: 18872--19112 Score: 226
Period size: 30 Copynumber: 8.2 Consensus size: 30
18862 TAATTTTGAG
*
18872 AGTTTCGGGG-TAAAAATAGAATTTTTGGA
1 AGTTTCGGGGTTAAAAATGGAATTTTTGGA
*
18901 AGTTTCGGGGTTAAAAATGTG-ATTTTTGAA
1 AGTTTCGGGGTTAAAAATG-GAATTTTTGGA
* *
18931 AGTTT-GAGGG-TAAAAATGGGATTTTTGAA
1 AGTTTCG-GGGTTAAAAATGGAATTTTTGGA
** * * * *
18960 AGTTTTAGGATCAAAAATGGGATTTTTGAA
1 AGTTTCGGGGTTAAAAATGGAATTTTTGGA
** * * *
18990 AGTTTTAGGATCAAAAATGGGATTTTTGGA
1 AGTTTCGGGGTTAAAAATGGAATTTTTGGA
*
19020 AGTTT-GAGGTTAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTTAAAAATGGAATTTTTGGA
* * *
19049 AGTTTTGAGGTCAAAAAT-GAGATTTTTGGA
1 AGTTTCGGGGTTAAAAATGGA-ATTTTTGGA
*
19079 AG-TTCGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTTAAAAATGGAATTTTTGGA
19108 AGTTT
1 AGTTT
19113 AGGGACCTCC
Statistics
Matches: 186, Mismatches: 16, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
28 1 0.01
29 83 0.45
30 101 0.54
31 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (30 bp):
AGTTTCGGGGTTAAAAATGGAATTTTTGGA
Found at i:18943 original size:59 final size:60
Alignment explanation
Indices: 18865--19116 Score: 261
Period size: 59 Copynumber: 4.3 Consensus size: 60
18855 AAAAGGGTAA
* *
18865 TTTTGAGAGTTTCG-GGGT-AAAAATAGAATTTTTGGAAGTTTCGGGGTTAAAAATGTG-AT
1 TTTTGAAAGTTT-GAGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATG-GAAT
* * ** * * *
18924 TTTTGAAAGTTTGAGGGT-AAAAATGGGATTTTTGAAAGTTTTAGGATCAAAAATGGGAT
1 TTTTGAAAGTTTGAGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAAT
* * * *
18983 TTTTGAAAGTTTTAGGATCAAAAATGGGATTTTTGGAAGTTT-GAGGTTAAAAATGGAAT
1 TTTTGAAAGTTTGAGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAAT
* *
19042 TTTTGGAAGTTTTGA-GGTCAAAAAT-GAGATTTTTGGAAG-TTCGGGGGTAAAAATGGAAT
1 TTTTGAAAG-TTTGAGGGTCAAAAATGGA-ATTTTTGGAAGTTTCGGGGTTAAAAATGGAAT
*
19101 TTTTGGAAGTTT-AGGG
1 TTTTGAAAGTTTGAGGG
19117 ACCTCCAGGG
Statistics
Matches: 164, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 10 0.06
59 127 0.77
60 26 0.16
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.37
Consensus pattern (60 bp):
TTTTGAAAGTTTGAGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAAT
Done.