Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001280.1 Kokia drynarioides strain JFW-HI SEQ_112667, 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: 4519
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Found at i:183 original size:29 final size:29
Alignment explanation
Indices: 146--932 Score: 558
Period size: 29 Copynumber: 27.0 Consensus size: 29
136 AAGGTCCCTA
146 AACTATCCAAAAATTACCATTTTACCCTCG
1 AACT-TCCAAAAATTACCATTTTACCCTCG
* * *
176 AACTTCCAAAAA-TCCCATTTTAGACCTCA
1 AACTTCCAAAAATTACCATTTTA-CCCTCG
* *
205 AACCTTCC-AAAATTACCATTTTACCCCCA
1 AA-CTTCCAAAAATTACCATTTTACCCTCG
*
234 AACTTCCAAAAA-TCCCATTTTGA-CCTCG
1 AACTTCCAAAAATTACCATTTT-ACCCTCG
*
262 AACCTTCCCAAAATTACCATTTTA-CCTCG
1 AA-CTTCCAAAAATTACCATTTTACCCTCG
* *
291 AACTTCCAAAAA-TCCCATTTTTAACCTCG
1 AACTTCCAAAAATTACCA-TTTTACCCTCG
*
320 AACCTTCCAAAAAATACCATTTTACCC-CTG
1 AA-CTTCCAAAAATTACCATTTTACCCTC-G
*
350 AACTTCC-AAAATT-CCATTTTGGTCCCT--
1 AACTTCCAAAAATTACCATTTT--ACCCTCG
*
377 AACCTTCCAAAAATTACCATTTTACCCTTG
1 AA-CTTCCAAAAATTACCATTTTACCCTCG
** * * *
407 GGCTTCCAAAAA-TCCCATTTTTAACCTCA
1 AACTTCCAAAAATTACCA-TTTTACCCTCG
* *
436 AACCTTCCAAAAATTACTATTTTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTACCCTCG
*
466 AACTTCCAAAAA-TATCATTTTTGA-CCTCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCTCG
* *
495 AACCTTCC-AAAATTACCATTTTACCCCCA
1 AA-CTTCCAAAAATTACCATTTTACCCTCG
*
524 AACTTCTAAAAATCTA--ATTTTTAACCCT-G
1 AACTTCCAAAAAT-TACCA-TTTT-ACCCTCG
* *
553 AACTTTCCCAAAATTACCATTTT-CCCCCG
1 AAC-TTCCAAAAATTACCATTTTACCCTCG
*
582 AACTTCCAAAAA-TCCCATTTTCACCC-CG
1 AACTTCCAAAAATTACCATTTT-ACCCTCG
*
610 AACCTTCCCAAAAA-TACCATTTTACCAC-CA
1 AA-CTT-CCAAAAATTACCATTTTACC-CTCG
* * *
640 AACTACCAAAAA-TCCCATTTTAACCTCG
1 AACTTCCAAAAATTACCATTTTACCCTCG
668 AACCTTCCAAAAATTACCATTTTACCCTCG
1 AA-CTTCCAAAAATTACCATTTTACCCTCG
* **
698 AACTTCCAAAAA-TCCCATTTTTGGCCTCG
1 AACTTCCAAAAATTACCA-TTTTACCCTCG
*
727 AACCTTCCAAAAATTACCATTTTACACTCG
1 AA-CTTCCAAAAATTACCATTTTACCCTCG
** * * *
757 GGCTTCCAAAAA-TCCCATTTTTCACCTTG
1 AACTTCCAAAAATTACCATTTTAC-CCTCG
* *
786 AACCTTCCAAAAATTGCCATTTTACCC-CA
1 AA-CTTCCAAAAATTACCATTTTACCCTCG
* *
815 AGACTTCCAACAA-TCCCATTTTGA-CCTCG
1 A-ACTTCCAAAAATTACCATTTT-ACCCTCG
** * *
844 AACCTTTTAGAAATTACCATTTTACCC-CC
1 AA-CTTCCAAAAATTACCATTTTACCCTCG
* *
873 AGACTTCCTAAAA-TCCCATTTTTTA-CCTCG
1 A-ACTTCCAAAAATTACCA--TTTTACCCTCG
* * *
903 AGACATCCAAAAATTACTATTTTACTCTCG
1 A-ACTTCCAAAAATTACCATTTTACCCTCG
933 GATGTCCAAA
Statistics
Matches: 602, Mismatches: 93, Indels: 124
0.74 0.11 0.15
Matches are distributed among these distances:
27 22 0.04
28 131 0.22
29 226 0.38
30 199 0.33
31 24 0.04
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (29 bp):
AACTTCCAAAAATTACCATTTTACCCTCG
Found at i:458 original size:59 final size:59
Alignment explanation
Indices: 151--927 Score: 911
Period size: 58 Copynumber: 13.3 Consensus size: 59
141 CCCTAAACTA
* *
151 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTAGACCTCAAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTA-ACCTCGAACCT
* *
210 TCC-AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTGACCTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
* *
267 TCCCAAAATTACCATTTTA-CCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
* * * *** *
325 TCCAAAAAATACCATTTTACCCCTGAACTTCC-AAAATTCCATTTTGGTCC-CTAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
** ** *
382 TCCAAAAATTACCATTTTACCCTTGGGCTTCCAAAAATCCCATTTTTAACCTCAAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
* ** *
441 TCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATATCATTTTTGACCTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
* * ** *
500 TCC-AAAATTACCATTTTACCCCCAAACTTCTAAAAATCTAATTTTTAACC-CTGAACTT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTC-GAACCT
* * *
558 TCCCAAAATTACCATTTT-CCCCCGAACTTCCAAAAATCCCA-TTTTCACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
* * *
615 TCCCAAAAA-TACCATTTTACCACCAAACTACCAAAAATCCCA-TTTTAACCTCGAACCT
1 T-CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
* **
673 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
* * ** * *
732 TCCAAAAATTACCATTTTACACTCGGGCTTCCAAAAATCCCATTTTTCACCTTGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
* * * *
791 TCCAAAAATTGCCATTTTA-CCCCAAGACTTCCAACAATCCCA-TTTTGACCTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGA-ACTTCCAAAAATCCCATTTTTAACCTCGAACCT
** * * * *
849 TTTAGAAATTACCATTTTACCCCC-AGACTTCCTAAAATCCCATTTTTTACCTCGAGA-CA
1 TCCAAAAATTACCATTTTACCCCCGA-ACTTCCAAAAATCCCATTTTTAACCTCGA-ACCT
*
908 TCCAAAAATTACTATTTTAC
1 TCCAAAAATTACCATTTTAC
928 TCTCGGATGT
Statistics
Matches: 616, Mismatches: 86, Indels: 32
0.84 0.12 0.04
Matches are distributed among these distances:
57 97 0.16
58 301 0.49
59 217 0.35
60 1 0.00
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.31
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCT
Done.