Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000834.1 Kokia drynarioides strain JFW-HI SEQ_111929, 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: 5122
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Found at i:1419 original size:15 final size:15
Alignment explanation
Indices: 1399--1438 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
1389 TTTAATGTAT
1399 GTTGCAACCACTAAA
1 GTTGCAACCACTAAA
1414 GTTGCAACCACTAAA
1 GTTGCAACCACTAAA
1429 GTTGCAACCA
1 GTTGCAACCA
1439 GAGTAGAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.20
Consensus pattern (15 bp):
GTTGCAACCACTAAA
Found at i:4334 original size:78 final size:78
Alignment explanation
Indices: 4240--4770 Score: 534
Period size: 78 Copynumber: 6.8 Consensus size: 78
4230 CAGCCATTCG
* * * * * * *
4240 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAACCATCCAATCTTTTACCCTGAGCCTGGGGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTACCCTGAGCTTGGGGCAGA
*
4305 TTACCATCAGCCA
66 TCACCATCAGCCA
* * * * * * * ** *
4318 ATCTCTTAACCTGAGCCTGAGGCAGATTGCAACCGTCCGATCTTTTACCCCGAGCTTAAGGCATA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTACCCTGAGCTTGGGGCAGA
* *
4383 TCACTATAAGCCA
66 TCACCATCAGCCA
* * * * ** *
4396 ATCTCTTACCCCGAGCTTGAGGCAGATTGTAGCCA-TCTGATCTTTTA-CCTCGAGCCTAAGGTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTC-GATCTTTTACCCT-GAGCTTGGGGCA
* *
4459 GATCACCATTAACCA
64 GATCACCATCAGCCA
*
4474 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTACCCTGAGCTTGGGGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTACCCTGAGCTTGGGGCAGA
*
4539 TCACCATCACCCA
66 TCACCATCAGCCA
** * * * * * * *
4552 ATCTCTTACCTTGAGCTTGGGGTATATTGTAGCCATTCGATC--TTACCCCGAGCTTGAGGCAAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTACCCTGAGCTTGGGGCAGA
*
4615 TCACCATCA-ACA
66 TCACCATCAGCCA
* * * * * *
4627 ATCTCTTACCCCAAGCCTGGGGCAGATTGTAGCCATTCAATTTTTTA-CCTCAAGCATGGGGCAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTACCCT-GAGCTTGGGGCAG
4691 ATCACCATCAGCCA
65 ATCACCATCAGCCA
* * * *
4705 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTCACCCCGAGCTTGGGACAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTACCCTGAGCTTGGGGCAGA
4770 T
66 T
4771 TGTAGCCATT
Statistics
Matches: 371, Mismatches: 73, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
75 36 0.10
76 28 0.08
77 25 0.07
78 275 0.74
79 7 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTACCCTGAGCTTGGGGCAGA
TCACCATCAGCCA
Found at i:4862 original size:39 final size:39
Alignment explanation
Indices: 4198--4870 Score: 302
Period size: 39 Copynumber: 17.3 Consensus size: 39
4188 TCACCATTAA
* * * * *
4198 CCAATCTCTTTCCCCAAGCTTAGGGCAGATTGCAGCCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * *
4237 TCGATCTTTTACCCCGAGCCTGGGGTAGATTGCAACCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * * * * *
4276 CCAATCTTTTACCCTGAGCCTGGGGTAGATTACCATCAG
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * *
4315 CCAATCTCTTAACCTGAGCCTGAGGCAGATTGCAACCGT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * ** * ** * ** *
4354 CCGATCTTTTACCCCGAGCTTAAGGCATATCACTATAAG
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * *
4393 CCAATCTCTTACCCCGAGCTTGAGGCAGATTGTAGCCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
** * * ** *
4432 CTGATCTTTTACCTCGAGCCTAAGGTAGA-T-C-ACCATT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCA-T
*
4469 AACCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT
1 --CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * * * * ** * * *
4510 TCGATCTTTTACCCTGAGCTTGGGGTAGATCACCATCAC
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
** * * * * *
4549 CCAATCTCTTACCTTGAGCTTGGGGTATATTGTAGCCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * * *
4588 TCGA--TCTTACCCCGAGCTTGAGGCA-AAT-C-ACCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * *
4622 CAACAATCTCTTACCCCAAGCCTGGGGCAGATTGTAGCCAT
1 C--CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * * * * ** * * *
4663 TCAATTTTTTACCTCAAGCATGGGGCAGATCACCATCAG
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* *
4702 CCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * * * *
4741 TCGATCT-TTCACCCCGAGCTTGGGACAGATTGTAGCCAT
1 CCAATCTCTT-ACCCCGAGCCTGGGGCAGATTGCAACCAT
* * * * * * ** * * *
4780 TCGATCTTTTACCCTGAGCATGAGGCAGATCACCATCAA
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
* *
4819 CCAATCTCTTACCCCGAGCCAGGGGCAGATTACAACCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
*
4858 CCAATATCTTACC
1 CCAATCTCTTACC
4871 TAAAAAAAAT
Statistics
Matches: 459, Mismatches: 160, Indels: 30
0.71 0.25 0.05
Matches are distributed among these distances:
34 4 0.01
36 7 0.02
37 18 0.04
38 21 0.05
39 397 0.86
40 3 0.01
41 6 0.01
42 3 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (39 bp):
CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCAT
Done.