Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000733.1 Kokia drynarioides strain JFW-HI SEQ_111762, 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: 2211
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Found at i:458 original size:185 final size:185
Alignment explanation
Indices: 121--489 Score: 490
Period size: 185 Copynumber: 2.0 Consensus size: 185
111 ATCAAATTCG
* * ** * *
121 TCTTCCTTATGAGATATAGAGAAGTGAATTTAAACAATGAAGGGGTCATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAATGAAGCGGTCATCTTCCTGATGAGATAC
* * *** * * *
186 AGAGAAGTAGACCAATTCAATGAAGCGAAGCTCAATGTGAGTGAAATTTCCAAACCCCATCTTTC
66 AAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACAAATGAAACTTCCAAACCCCATCTTCC
* *
251 TTATGAGATACAAAGAAGTGGGTCAAACCGATAAAGAGGTCATCTTCCTAATGAC
131 TGATGAGATACAAAGAAGTGGGTCAAACCAATAAAGAGGTCATCTTCCTAATGAC
*
306 TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAAGTGATA-CGGTTATCTTCCTGATGAGAT
1 TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAA-TGA-AGCGGTCATCTTCCTGATGAGAT
* *
370 ACAAAGAAGTAGACCAAATCAATGAAGCGAAGCTTAATACAAATGAGACTT-CAAACCCCATCTT
64 ACAAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACAAATGAAACTTCCAAACCCCATCTT
* * * * *
434 CCTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCCTGATGA
129 CCTGATGAGATACAAAGAAGTGGGTCAAACCAATAAAGAGGTCATCTTCCTAATGA
490 GATGCAGAGA
Statistics
Matches: 158, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
185 93 0.59
186 64 0.41
187 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (185 bp):
TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAATGAAGCGGTCATCTTCCTGATGAGATAC
AAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACAAATGAAACTTCCAAACCCCATCTTCC
TGATGAGATACAAAGAAGTGGGTCAAACCAATAAAGAGGTCATCTTCCTAATGAC
Found at i:573 original size:85 final size:85
Alignment explanation
Indices: 430--594 Score: 240
Period size: 85 Copynumber: 1.9 Consensus size: 85
420 TCAAACCCCA
* * * * * *
430 TCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCCTGATGAGATGC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCATATTCCTGATGAGATAC
495 AGAGAAGTAAACCAAATCAG
66 AGAGAAGTAAACCAAATCAG
* * *
515 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATATTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCATATTCCTGATGAGATAC
*
580 AGAGAAGTAGACCAA
66 AGAGAAGTAAACCAA
595 TTCAACGAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCATATTCCTGATGAGATAC
AGAGAAGTAAACCAAATCAG
Found at i:665 original size:208 final size:209
Alignment explanation
Indices: 306--979 Score: 762
Period size: 208 Copynumber: 3.3 Consensus size: 209
296 TCCTAATGAC
** * * *
306 TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAAGTGATA-CGGTTATCTTCCTGATGAGAT
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAA-TGA-AGCGGTCATCTTCCTGATGAGAT
* * * * * * *
370 ACAAAGAAGTAGACCAAATCAATGAAGCGAAGCTTAATACAAATGAGACTT-CAAACCCCATCTT
64 ACAGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGCGAGTGAAACTTCCAAACCCCATCTT
* *** * *
434 CCTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCCTGATGAGATGCAGAG
129 CTTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGAAATCATCTTCCTGATGAGATACAAAG
499 AAGTAAACCAAAT-CA
194 AAGTAAACCAAATCCA
*
514 GTCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATATTCCTGATGAGATA
1 -TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATCTTCCTGATGAGATA
*
579 CAGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGTGAGTGAAACTTCCAAA-CCCATCTTC
65 CAGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGCGAGTGAAACTTCCAAACCCCATCTTC
* * * *
643 TTGATGAGATACAAAGAAGTGGGTCAAAGTAATAAAGAAATCATCTTCCTGATGAGATATAAAGA
130 TTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGAAATCATCTTCCTGATGAGATACAAAGA
*
708 AGTAGACCAAATCCA
195 AGTAAACCAAATCCA
* * * *
723 TCTTCCTTATGAGATACAGAGAAGTAGATT-AAATCAACGAAGCGGTCATCTTCCTGGTGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAAT-AATGAAGCGGTCATCTTCCTGATGAGATA
* * * * *
787 CAGAGAAATAGACCAATTCAACAAAGTGAAGCTCAATGCGAGTGAAACTTCCAAACCCCATCTTT
65 CAGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGCGAGTGAAACTTCCAAACCCCATCTTC
* * * *
852 TTTATGAGATACAGAGAAGTGGGT--------T---G--A--A-GTTCCTGACGAGATGCAAAGA
130 TTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGAAATCATCTTCCTGATGAGATACAAAGA
*
901 AGTGAACCAAATCCA
195 AGTAAACCAAATCCA
* * * *
916 TCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGATCATCTTCCT-ATTGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATCTTCCTGA-TGAGATA
980 TAAAGAATTA
Statistics
Matches: 406, Mismatches: 52, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
193 81 0.20
194 4 0.01
196 1 0.00
198 1 0.00
201 1 0.00
207 5 0.01
208 244 0.60
209 69 0.17
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (209 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATCTTCCTGATGAGATAC
AGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGCGAGTGAAACTTCCAAACCCCATCTTCT
TGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGAAATCATCTTCCTGATGAGATACAAAGAA
GTAAACCAAATCCA
Found at i:757 original size:37 final size:37
Alignment explanation
Indices: 680--750 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
670 AGTAATAAAG
*
680 AAAT-CATCTTCCTGATGAGATATAAAGAAGTAGACC
1 AAATCCATCTTCCTGATGAGATACAAAGAAGTAGACC
* *
716 AAATCCATCTTCCTTATGAGATACAGAGAAGTAGA
1 AAATCCATCTTCCTGATGAGATACAAAGAAGTAGA
751 TTAAATCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 4 0.13
37 27 0.87
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (37 bp):
AAATCCATCTTCCTGATGAGATACAAAGAAGTAGACC
Found at i:1870 original size:10 final size:10
Alignment explanation
Indices: 1857--1904 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
1847 CAAAGCGTTT
1857 TTAATATATA
1 TTAATATATA
1867 TTAATATAT-
1 TTAATATATA
*
1876 TTAATATTTA
1 TTAATATATA
*
1886 TTTATTATATA
1 -TTAATATATA
1897 TTAATATA
1 TTAATATA
1905 CTTATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATATATA
Found at i:1878 original size:19 final size:20
Alignment explanation
Indices: 1856--1904 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1846 TCAAAGCGTT
1856 TTTAATATATA-TTAATATA
1 TTTAATATATATTTAATATA
* *
1875 TTTAATATTTATTTATTATA
1 TTTAATATATATTTAATATA
1895 TATTAATATA
1 T-TTAATATA
1905 CTTATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.40
20 8 0.32
21 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAATATATATTTAATATA
Found at i:1911 original size:19 final size:19
Alignment explanation
Indices: 1856--1911 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
1846 TCAAAGCGTT
1856 TTTAATATA-TATTAATATA
1 TTTAATATATTATT-ATATA
1875 TTTAATAT-TTATTTATTATA
1 TTTAATATATTA-TTA-TATA
1895 TATTAATATACTTATTA
1 T-TTAATATA-TTATTA
1912 ATTGCTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
19 11 0.35
20 7 0.23
21 7 0.23
22 3 0.10
23 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATATATTATTATATA
Found at i:1921 original size:33 final size:30
Alignment explanation
Indices: 1856--1926 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
1846 TCAAAGCGTT
* *
1856 TTTAATATATATTAATATATTTAATATTTA
1 TTTATTATATATTAATATACTTAATATTTA
*
1886 TTTATTATATATTAATATACTTATTAATTGCTA
1 TTTATTATATATTAATATACTTAAT-ATT--TA
1919 TTTATTAT
1 TTTATTAT
1927 TACCTACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 22 0.63
31 3 0.09
33 10 0.29
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTATTATATATTAATATACTTAATATTTA
Done.