Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000361.1 Kokia drynarioides strain JFW-HI SEQ_111146, 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, 967
Length: 1613
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:549 original size:30 final size:31
Alignment explanation
Indices: 514--787 Score: 195
Period size: 30 Copynumber: 9.2 Consensus size: 31
504 CCAAAAATCT
514 CATTTTTGACCCCGAAACTTTC-AAAATTAC
1 CATTTTTGACCCCGAAACTTTCAAAAATTAC
* *
544 AATTTTT-ACCCTCG-AA-TTTCCAAAAA-TCC
1 CATTTTTGACCC-CGAAACTTT-CAAAAATTAC
* * *
573 CATTTTTGACCCCAAAACTTTC-AAAGTTCC
1 CATTTTTGACCCCGAAACTTTCAAAAATTAC
* * *
603 CATTTTTTACCCCTAAACTTCCAAAAA-T-C
1 CATTTTTGACCCCGAAACTTTCAAAAATTAC
* * *
632 TCATTTTTAACCCTGAACCTTTCAAAAATTAC
1 -CATTTTTGACCCCGAAACTTTCAAAAATTAC
* *
664 CA-TTTT-ACCCCCG-AACTTCCAAAAATT-T
1 CATTTTTGA-CCCCGAAACTTTCAAAAATTAC
*
692 CATTTTTGACCCCGAACCTTTCAAAAATTAC
1 CATTTTTGACCCCGAAACTTTCAAAAATTAC
** *
723 CA-TTTT-ACCCTCG-AACTGCCAAAAA-TCC
1 CATTTTTGACCC-CGAAACTTTCAAAAATTAC
* * * *
751 CATTTTTGACTCCG-AACCTTCCAAAACTAC
1 CATTTTTGACCCCGAAACTTTCAAAAATTAC
781 CATTTTT
1 CATTTTT
788 CCCTCGTGCA
Statistics
Matches: 193, Mismatches: 31, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
28 9 0.05
29 69 0.36
30 103 0.53
31 11 0.06
32 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.34
Consensus pattern (31 bp):
CATTTTTGACCCCGAAACTTTCAAAAATTAC
Found at i:577 original size:59 final size:59
Alignment explanation
Indices: 503--793 Score: 356
Period size: 59 Copynumber: 4.9 Consensus size: 59
493 CCCTAGATTG
* * *
503 TCCAAAAATCTCATTTTTGACCCCGAAACTTTCAAAATTACAATTTTTACCCTCGAATT
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTTCAAAATTACCATTTTTACCCTCGAACT
* * * * * *
562 TCCAAAAATCCCATTTTTGACCCCAAAACTTTCAAAGTTCCCATTTTTTACCC-CTAAACT
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTTCAAAATTACCA-TTTTTACCCTC-GAACT
* * *
622 TCCAAAAATCTCATTTTTAACCCTGAACCTTTCAAAAATTACCA-TTTTACCCCCGAACT
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTTC-AAAATTACCATTTTTACCCTCGAACT
*
681 TCCAAAAATTTCATTTTTGACCCCGAACCTTTCAAAAATTACCA-TTTTACCCTCGAACT
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTTC-AAAATTACCATTTTTACCCTCGAACT
* * * * *
740 GCCAAAAATCCCATTTTTGACTCCGAACCTTCCAAAACTACCATTTTT-CCCTCG
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTTCAAAATTACCATTTTTACCCTCG
794 TGCATCCGAA
Statistics
Matches: 202, Mismatches: 25, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
58 15 0.07
59 138 0.68
60 41 0.20
61 8 0.04
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (59 bp):
TCCAAAAATCTCATTTTTGACCCCGAACCTTTCAAAATTACCATTTTTACCCTCGAACT
Found at i:785 original size:89 final size:89
Alignment explanation
Indices: 503--787 Score: 280
Period size: 89 Copynumber: 3.2 Consensus size: 89
493 CCCTAGATTG
* *
503 TCCAAAAAT-CTCATTTTTGACCCCGAAACTTTC-AAAATTACAATTTTTACCCTCGAATTTCCA
1 TCCAAAAATAC-CATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTTACCCTCGAACTTCCA
*
566 AAAATCCCATTTTTGACCCCAAAACT
65 AAAATCCCATTTTTGACCCC-GAACT
* ** * * * * *
592 TTCAAAGTTCCCATTTTTTACCCCTAAACTTCCAAAAA-T-CTCATTTTTAACCCT-GAACCTTT
1 TCCAAAAATACCATTTTTGACCCCGAAACTTTCAAAAATTAC-CATTTTT-ACCCTCGAA-CTTC
*
654 CAAAAATTACCA-TTTT-ACCCCCGAACT
63 CAAAAA-TCCCATTTTTGA-CCCCGAACT
** * *
681 TCCAAAAATTTCATTTTTGACCCCGAACCTTTCAAAAATTACCA-TTTTACCCTCGAACTGCCAA
1 TCCAAAAATACCATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTTACCCTCGAACTTCCAA
*
745 AAATCCCATTTTTGACTCCGAACCT
66 AAATCCCATTTTTGACCCCGAA-CT
*
770 TCCAAAACTACCATTTTT
1 TCCAAAAATACCATTTTT
788 CCCTCGTGCA
Statistics
Matches: 156, Mismatches: 27, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
87 4 0.03
88 24 0.15
89 94 0.60
90 29 0.19
91 5 0.03
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (89 bp):
TCCAAAAATACCATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTTACCCTCGAACTTCCAA
AAATCCCATTTTTGACCCCGAACT
Done.