Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009996.1 Kokia drynarioides strain JFW-HI SEQ_124751, 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: 2656
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Found at i:409 original size:30 final size:28
Alignment explanation
Indices: 329--467 Score: 93
Period size: 29 Copynumber: 4.7 Consensus size: 28
319 TAAATAGTCA
* * *
329 AAAAATTACATTTTAGCCCTCGAACTTTCC
1 AAAAATTCCATTTTA-CCC-CTAATTTTCC
359 -AAAATTCCATTATTGA-CCCTAATTTTTCC
1 AAAAATTCCATT-TT-ACCCCTAA-TTTTCC
**
388 AAAAATTACCATTTTACCCCTAAACTTCC
1 AAAAATT-CCATTTTACCCCTAATTTTCC
* * * *
417 AAAAATTCCATTTTTGACCTCGATTTTTTC
1 AAAAATTCCA-TTTT-ACCCCTAATTTTCC
*
447 AAAAATGGCCATTTTACCCCT
1 AAAAAT-TCCATTTTACCCCT
468 GAACTTCAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
28 6 0.07
29 37 0.43
30 34 0.40
31 9 0.10
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (28 bp):
AAAAATTCCATTTTACCCCTAATTTTCC
Found at i:422 original size:59 final size:59
Alignment explanation
Indices: 329--583 Score: 250
Period size: 59 Copynumber: 4.3 Consensus size: 59
319 TAAATAGTCA
* *
329 AAAAATTA-CATTTTAGCCCTCGAACTTTCC-AAAATTCCATTATTGACCCTAATTTTTCC
1 AAAAATTACCATTTTACCCCT-GAAC-TTCCAAAAATTCCATTTTTGACCCTAATTTTTCC
* * *
388 AAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGA-CCTCGATTTTTTC
1 AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCT-AATTTTTCC
** * ** *
447 AAAAATGGCCATTTTACCCCTGAACTT-CAAAAAATCCTATTTTTGACCCCGATTCTTCC
1 AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCC-ATTTTTGACCCTAATTTTTCC
** * * * * * *
506 AAAAGGTATCATTTTACCCCCGAACGTCTAAAAATTCCGTTTTTGACCCCTAA-CTTTCC
1 AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGA-CCCTAATTTTTCC
*
565 CAAAATTACCATTTTACCC
1 AAAAATTACCATTTTACCC
584 TCGAGTGACC
Statistics
Matches: 159, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
58 16 0.10
59 118 0.74
60 25 0.16
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCTAATTTTTCC
Found at i:539 original size:118 final size:119
Alignment explanation
Indices: 337--553 Score: 276
Period size: 118 Copynumber: 1.8 Consensus size: 119
327 CAAAAAATTA
* * * * * *
337 CATTTTAGCCCTCGAACTTTCCAAAATTCCATTATTGACCCTAATTTTTCCAAAAATTACCATTT
1 CATTTTACCCCTCGAACTTTCAAAAAATCCATTATTGACCCCAATTCTTCCAAAAAGTACCATTT
* *
402 TACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTTCAAAAATGGC
66 TACCCCCAAACGTCCAAAAATTCCATTTTTGACCTCGATTTTTTCAAAAATGGC
* * * *
456 CATTTTACCCCT-GAAC-TTCAAAAAATCCTATTTTTGACCCCGATTCTTCCAAAAGGTATCATT
1 CATTTTACCCCTCGAACTTTCAAAAAATCC-ATTATTGACCCCAATTCTTCCAAAAAGTACCATT
* * *
519 TTACCCCCGAACGTCTAAAAATTCCGTTTTTGACC
65 TTACCCCCAAACGTCCAAAAATTCCATTTTTGACC
554 CCTAACTTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
117 10 0.12
118 61 0.74
119 11 0.13
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.35
Consensus pattern (119 bp):
CATTTTACCCCTCGAACTTTCAAAAAATCCATTATTGACCCCAATTCTTCCAAAAAGTACCATTT
TACCCCCAAACGTCCAAAAATTCCATTTTTGACCTCGATTTTTTCAAAAATGGC
Found at i:626 original size:28 final size:28
Alignment explanation
Indices: 564--624 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
554 CCTAACTTTC
564 CCAAAATTACCATTTTACCCTCGAGTGA
1 CCAAAATTACCATTTTACCCTCGAGTGA
*
592 CCAAAATTACCATTTTGCCC-CGAGT-A
1 CCAAAATTACCATTTTACCCTCGAGTGA
618 TCCAAAA
1 -CCAAAA
625 ATCACATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 11 0.35
28 19 0.61
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCTCGAGTGA
Found at i:971 original size:97 final size:97
Alignment explanation
Indices: 832--1025 Score: 239
Period size: 97 Copynumber: 2.0 Consensus size: 97
822 GAAAACTTTA
* * * ** * *
832 AAATCGAGGCAATATTATTTTATTTCGAGTTTTGAAAATTTGTGTCTTAACTTACTAGGCACGAT
1 AAATCGAGGCAATATTATTTTATCTCGAATTCTGAAAATTTGTACCTAAACTTACTAGGCACGAC
* *
897 TTTTCTTCAAAT-AGGAATAATCGAATATCCTT
66 TTTTCTTCAAATCAAG-ATAATCGAACATCCTT
* * **
929 AAATCGAGGCAATGTT-TCTTTATCTCTAATTCTGAAAATTTGTACCTAAACTTACTAGGTGCGA
1 AAATCGAGGCAATATTAT-TTTATCTCGAATTCTGAAAATTTGTACCTAAACTTACTAGGCACGA
993 CTTTTCTTCAAATCAAGATAATCGAACATCCTT
65 CTTTTCTTCAAATCAAGATAATCGAACATCCTT
1026 TTCCAAAGTT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
96 1 0.01
97 79 0.96
98 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (97 bp):
AAATCGAGGCAATATTATTTTATCTCGAATTCTGAAAATTTGTACCTAAACTTACTAGGCACGAC
TTTTCTTCAAATCAAGATAATCGAACATCCTT
Done.