Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014317.1 Kokia drynarioides strain JFW-HI SEQ_129354, 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: 8851
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.32
Warning! 529 characters in sequence are not A, C, G, or T
Found at i:1387 original size:67 final size:63
Alignment explanation
Indices: 1253--1483 Score: 353
Period size: 63 Copynumber: 3.6 Consensus size: 63
1243 TTATTTATTT
* *
1253 ATTTATTTATCTATATTCATAAAATAATAAATAAATAATATAACAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATACAATAATAAATAAATAATATAACAAAATTAATATTATTTTAC
1316 ATTTATTTATTTATATTCATACAATAATAAATAAATAATATAACAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATACAATAATAAATAAATAATATAACAAAATTAATATTATTTTAC
1379 ATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAACAAAATTAATATTATTTT
1 ATTTATTTATTTATATTCATACAATAATAAATAAAT-AAT-AT--AACAAAATTAATATTATTTT
1444 --
62 AC
*
1444 A--TATTTATTTATATTCATAAAAATAATAAATAAATGAATA
1 ATTTATTTATTTATATTCAT-ACAATAATAAATAAAT-AATA
1484 AAAATAATAA
Statistics
Matches: 159, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
63 115 0.72
64 21 0.13
65 3 0.02
67 20 0.13
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (63 bp):
ATTTATTTATTTATATTCATACAATAATAAATAAATAATATAACAAAATTAATATTATTTTAC
Found at i:2415 original size:40 final size:40
Alignment explanation
Indices: 2371--2663 Score: 251
Period size: 40 Copynumber: 7.4 Consensus size: 40
2361 CCCATAGTCG
* *
2371 GGGTAAGAGATCGAATGGTCTTCAATCTGACCTCTGGTTA
1 GGGTAAGAGATTGGATGGTCTTCAATCTGACCTCTGGTTA
* * * **
2411 GGGTAAAAGATTGGATTGT-TTCAATCT-ACCCCATGGTCG
1 GGGTAAGAGATTGGATGGTCTTCAATCTGACCTC-TGGTTA
* * *
2450 GGGTAAGAGATCGAATGGTCTTCAATCT-ACCCTTTGGTTA
1 GGGTAAGAGATTGGATGGTCTTCAATCTGA-CCTCTGGTTA
* * * **
2490 GGGTAAAAGATTGGATTGT-TTCAATCTG-CCCCATGGTCG
1 GGGTAAGAGATTGGATGGTCTTCAATCTGACCTC-TGGTTA
** *
2529 GGGTAAGAGATCAGATGGTCTTCAATCT-ACCCTCTAGTTA
1 GGGTAAGAGATTGGATGGTCTTCAATCTGA-CCTCTGGTTA
* * * **
2569 GGGTAAAAGATTGGATTG-CTTCAATCTG-CCCCATGGTCG
1 GGGTAAGAGATTGGATGGTCTTCAATCTGACCTC-TGGTTA
*
2608 GGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
1 GGGTAAGAGATTGGATGGTCTTCAATCTGACCTCTGGTTA
* *
2648 GGGTAAAATATTGGAT
1 GGGTAAGAGATTGGAT
2664 TACTTCATTT
Statistics
Matches: 195, Mismatches: 46, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
38 9 0.05
39 82 0.42
40 96 0.49
41 8 0.04
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (40 bp):
GGGTAAGAGATTGGATGGTCTTCAATCTGACCTCTGGTTA
Found at i:2423 original size:79 final size:79
Alignment explanation
Indices: 2332--2737 Score: 577
Period size: 79 Copynumber: 5.1 Consensus size: 79
2322 ATAGATTTAG
* *
2332 GGGTAAAAGATTGGATTGTTTTAATCTGCCCCATAGTCGGGGTAAGAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
2397 CTGACCTCTGGTTA
66 CTGACCTCTGGTTA
*
2411 GGGTAAAAGATTGGATTGTTTCAATCTACCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
*
2476 CT-ACCCTTTGGTTA
66 CTGA-CCTCTGGTTA
2490 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATC-AGATGGTCTTCAA
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGA-ATGGTCTTCAA
*
2554 TCT-ACCCTCTAGTTA
65 TCTGA-CCTCTGGTTA
* * *
2569 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
*
2634 CTGCCCTCTGGTTA
66 CTGACCTCTGGTTA
* ** * * * *
2648 GGGTAAAATATTGGATTACTTCATTTTGCCCCACGGTCGGGGTAAGAGATCGAATGATCTTCAAT
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
* **
2713 CTG-CTCTCTGATCG
66 CTGAC-CTCTGGTTA
2727 GGGTAAAAGAT
1 GGGTAAAAGAT
2738 CGGAGGGTCT
Statistics
Matches: 298, Mismatches: 24, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
78 3 0.01
79 295 0.99
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
CTGACCTCTGGTTA
Found at i:7846 original size:31 final size:31
Alignment explanation
Indices: 7795--7874 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
7785 CATCTTTCTC
7795 AAACTTT-T-AATGCATGAAAATGCGATGCA
1 AAACTTTATGAATGCATGAAAATGCGATGCA
* *
7824 AAACTTTATGAATGCATTAAAATGCGATGCG
1 AAACTTTATGAATGCATGAAAATGCGATGCA
*
7855 AAATTTTATGAATGCATGAA
1 AAACTTTATGAATGCATGAA
7875 TGCATATGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 7 0.16
30 1 0.02
31 37 0.82
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (31 bp):
AAACTTTATGAATGCATGAAAATGCGATGCA
Done.