Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013136.1 Kokia drynarioides strain JFW-HI SEQ_128155, 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: 5168
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:4105 original size:926 final size:876
Alignment explanation
Indices: 2314--4116 Score: 2759
Period size: 926 Copynumber: 2.0 Consensus size: 876
2304 GCCATTTTTT
2314 AACACCTCTTTCTCAGCATCACTATTTTCTTTTTTTCAAATTGATAAAAAATTATAAACATTTCC
1 AACACCTCTTTCTCAGCATCACTATTTTCTTTTTTTCAAATTGATAAAAAATTATAAACATTTCC
2379 AACATTTTATGCATTTATTACTGTCCAAAAATGACACAATTTTTTTCTTAAAAAATACTTGATGT
66 AACATTTTATGCATTTATTACTGTCCAAAAATGACACAATTTTTTTCTTAAAAAATACTTGATGT
2444 AAGGGTAACTTAAAAATTACACAAATATTTTTTTTCTCAAATTCTTAAATATTCTTCTTTGCTCG
131 AAGGGTAACTTAAAAATTACACAAATATTTTTTTTCTCAAATTCTTAAATATTCTTCTTTGCTCG
2509 ATTGTCTGAAATTTGGAAAAAAGAAAAGAAAACGATTGGAGCAAGTTGTTTGAAAATTTCTTGCT
196 ATTGTCTGAAATTTGGAAAAAAGAAAAGAAAACGATTGGAGCAAGTTGTTTGAAAATTTCTTGCT
2574 CACCATTTTGGACACCATCGTAATTCTAGTTTTATGATCACTACCCATTTTTCTCTATTACAAAA
261 CACCATTTTGGACACCATCGTAATTCTAGTTTTATGATCACTACCCATTTTTCTCTATTACAAAA
* *
2639 AAGGTTAAATATAATATTGATACTTATATATATATTTTTATCTCATATTAGCATTTGAATATTTT
326 AAGGTTAAATATAAAATTGATAATTATATATATATTTTTATCTCATATTAGCATTTGAATATTTT
*
2704 TTTTCGTCCATTATATTGTTATTCGAGCCTAACGTCGTTATTTTTTTGCTGACATGGCAGCCTGA
391 TTTTCGTCCATTATATTGTTATTCGAGCCTAACGTCGTTATTTTTTTGCAGACATGGCAGCCTGA
2769 CCATTCACACGCCACCACATATTATCCTATTTGACAATAGAAACTCTCCAATTTCTTTCTCTCAC
456 CCATTCACACGCCACCACATATTATCCTATTTGACAATAGAAACTCTCCAATTTCTTTCTCTCAC
*
2834 GTTTTTTCCCCTGTTTTCTAATCTTTTCCACGTGTCATCAAGAAGGAAGAGACGAGAGAACAGGG
521 GTTTTTTCCCCTGTTTTCTAATCTTTTCCACGTGTAATCAAGAAGGAAGAGACGAGAGAACAGGG
*
2899 GAAAGAAATGTGAAAGAGAAAGAAATTGGAGAGTTTCTATTGCTAAATAGGATGACACGTGGCAG
586 GAAAGAAATGTGAAAGAGAAAGAAATTGGAGAGTTTCTATTGCCAAATAGGATGACACGTGGCAG
2964 CGCACAAATGGCCAATGCTGCCACATGAAAAAAAAGTAACAACGTTAAGTTGGGTACCAATATAG
651 CGCACAAATGGCCAATGCTGCCACATGAAAAAAAAGTAACAACGTTAAGTTGGGTACCAATATAG
3029 TAAACGAAAAAAGTTCGAGTACCAATCTGAGATAAAAAAACTATAAGTATCAATTTGTGAGAAGT
716 TAAACGAAAAAAGTTCGAGTACCAATCTGAGATAAAAAAACTATAAGTATCAATTTGTGAGAAGT
3094 GAACAAATTAAGATACCAATTTTATATTTAACCCTACAAAAAATTGTGAAACTCGTATATTTCTT
781 GAACAAATTAAGATACCAATTTTATATTTAACCCTACAAAAAATTGTGAAACTCGTATATTTCTT
3159 AATTCTTTGTAATTTTTTGTTTTCTTTGAAA
846 AATTCTTTGTAATTTTTTGTTTTCTTTGAAA
***************** * *
3190 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACACCTCTTTCTCA
1 ---------------------------------AACACCTCTTTCTCAGCATCA-CTATTT-T--
* ** ***
3255 GCATCACTATTTTC---TTTTTTTCAAATTGATAAAAAATTATAAACATTTCCAACATTTTATGC
29 -C-T---TTTTTTCAAATTGATAAAAAATT-AT--A--------AACATTTCCAACATTTTATGC
3317 ATTTATTACTGTCCAAAAATGACACAATTTTTTTCTTAAAAAATACTTGATGTAAGGGTAACTTA
78 ATTTATTACTGTCCAAAAATGACACAATTTTTTTCTTAAAAAATACTTGATGTAAGGGTAACTTA
3382 AAAATTACACAAATATTTTTTTTCTCAAATTCTTAAATATTCTTCTTTGCTCGATTGTCTGAAAT
143 AAAATTACACAAATATTTTTTTTCTCAAATTCTTAAATATTCTTCTTTGCTCGATTGTCTGAAAT
3447 TTGGAAAAAAGAAAAGAAAACGATTGGAGCAAGTTGTTTGAAAATTTCTTGCTCACCATTTTGGA
208 TTGGAAAAAAGAAAAGAAAACGATTGGAGCAAGTTGTTTGAAAATTTCTTGCTCACCATTTTGGA
3512 CACCATCGTAATTCTAGTTTTATGATCACTACCCATTTTTCTCTATTACAAAAAAGGTTAAATAT
273 CACCATCGTAATTCTAGTTTTATGATCACTACCCATTTTTCTCTATTACAAAAAAGGTTAAATAT
*
3577 AAAATTGATAATTATATATATTTTTTTATCTCATATTAGCATTTGAATATTTTTTTTCGTCCATT
338 AAAATTGATAATTATATATATATTTTTATCTCATATTAGCATTTGAATATTTTTTTTCGTCCATT
*
3642 ATATTGTTATTCGAGCCTAACGTCGTTATTTTTTTGCAGATATGGCAGCCTGACCATTCACACGC
403 ATATTGTTATTCGAGCCTAACGTCGTTATTTTTTTGCAGACATGGCAGCCTGACCATTCACACGC
*
3707 CACCACATATTATCTTATTTGACAATAGAAACTCTCCAATTTCTTTCTCTCACGTTTTTTCCCCT
468 CACCACATATTATCCTATTTGACAATAGAAACTCTCCAATTTCTTTCTCTCACGTTTTTTCCCCT
3772 GTTTTCTAATCTTTTCCACGTGTAATCAAGAAGGAAGAGACGAGAGAACAGGGGAAAGAAATGTG
533 GTTTTCTAATCTTTTCCACGTGTAATCAAGAAGGAAGAGACGAGAGAACAGGGGAAAGAAATGTG
3837 AAAGAGAAAGAAATTGGAGAGTTTCTATTGCCAAATAGGATGACACGTGGCAGCGCACAAATGGC
598 AAAGAGAAAGAAATTGGAGAGTTTCTATTGCCAAATAGGATGACACGTGGCAGCGCACAAATGGC
*
3902 CAATGCTGCCACGTG-AAAAAAAGTAACAACGTTAAGTTGGGTACCAATATAGTAAACGAAAAAA
663 CAATGCTGCCACATGAAAAAAAAGTAACAACGTTAAGTTGGGTACCAATATAGTAAACGAAAAAA
* *
3966 GTTCGGGTACCAATCTGAGATAAAAAAAACTATAAGTATCAATTTGTGAGAAGTGAACAAATTCA
728 GTTCGAGTACCAATCTGAGAT-AAAAAAACTATAAGTATCAATTTGTGAGAAGTGAACAAATTAA
*
4031 TATACCAATTTTATATTTAACCCTACAAAAAATTGTGAAACTCGTATATTTCTTAATTCTTTGTA
792 GATACCAATTTTATATTTAACCCTACAAAAAATTGTGAAACTCGTATATTTCTTAATTCTTTGTA
4096 ATTTTTTGTTTTCTTTGAAA
857 ATTTTTTGTTTTCTTTGAAA
4116 A
1 A
4117 TATTTAAAAA
Statistics
Matches: 835, Mismatches: 38, Indels: 58
0.90 0.04 0.06
Matches are distributed among these distances:
909 3 0.00
910 5 0.01
911 1 0.00
914 1 0.00
915 9 0.01
916 2 0.00
918 7 0.01
925 69 0.08
926 738 0.88
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.35
Consensus pattern (876 bp):
AACACCTCTTTCTCAGCATCACTATTTTCTTTTTTTCAAATTGATAAAAAATTATAAACATTTCC
AACATTTTATGCATTTATTACTGTCCAAAAATGACACAATTTTTTTCTTAAAAAATACTTGATGT
AAGGGTAACTTAAAAATTACACAAATATTTTTTTTCTCAAATTCTTAAATATTCTTCTTTGCTCG
ATTGTCTGAAATTTGGAAAAAAGAAAAGAAAACGATTGGAGCAAGTTGTTTGAAAATTTCTTGCT
CACCATTTTGGACACCATCGTAATTCTAGTTTTATGATCACTACCCATTTTTCTCTATTACAAAA
AAGGTTAAATATAAAATTGATAATTATATATATATTTTTATCTCATATTAGCATTTGAATATTTT
TTTTCGTCCATTATATTGTTATTCGAGCCTAACGTCGTTATTTTTTTGCAGACATGGCAGCCTGA
CCATTCACACGCCACCACATATTATCCTATTTGACAATAGAAACTCTCCAATTTCTTTCTCTCAC
GTTTTTTCCCCTGTTTTCTAATCTTTTCCACGTGTAATCAAGAAGGAAGAGACGAGAGAACAGGG
GAAAGAAATGTGAAAGAGAAAGAAATTGGAGAGTTTCTATTGCCAAATAGGATGACACGTGGCAG
CGCACAAATGGCCAATGCTGCCACATGAAAAAAAAGTAACAACGTTAAGTTGGGTACCAATATAG
TAAACGAAAAAAGTTCGAGTACCAATCTGAGATAAAAAAACTATAAGTATCAATTTGTGAGAAGT
GAACAAATTAAGATACCAATTTTATATTTAACCCTACAAAAAATTGTGAAACTCGTATATTTCTT
AATTCTTTGTAATTTTTTGTTTTCTTTGAAA
Found at i:5102 original size:28 final size:30
Alignment explanation
Indices: 5071--5128 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
5061 TTCATAATTG
*
5071 AGTGA-CAAAAAA-TATTTACTAATAGTTA
1 AGTGACCAAAAAAGAATTTACTAATAGTTA
5099 AGTGACCAAAAAAGGAATTTACTAATAGTT
1 AGTGACCAAAAAA-GAATTTACTAATAGTT
5129 GGGTGACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 7 0.27
31 14 0.54
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (30 bp):
AGTGACCAAAAAAGAATTTACTAATAGTTA
Done.