Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012825.1 Kokia drynarioides strain JFW-HI SEQ_127838, 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, 925
Length: 1543
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Found at i:675 original size:58 final size:58
Alignment explanation
Indices: 587--764 Score: 288
Period size: 59 Copynumber: 3.1 Consensus size: 58
577 AAACCTTTCA
*
587 AAAATTACTA-TTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCC
1 AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCC
**
644 AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTCAACCCCGAATCTTCC
1 AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCC
*
702 AAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCCCC-AAACTTCC
1 -AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCCGAATCTTCC
761 AAAA
1 AAAA
765 ATCCCATTTT
Statistics
Matches: 112, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
57 10 0.09
58 48 0.43
59 50 0.45
60 4 0.04
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (58 bp):
AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCC
Found at i:795 original size:59 final size:58
Alignment explanation
Indices: 597--1008 Score: 331
Period size: 58 Copynumber: 7.1 Consensus size: 58
587 AAAATTACTA
* * * *
597 TTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCCAAAATTACTA-T
1 TTTACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCGAAACTTCCAAAAATCCCATT
* * * **
655 TTTACCCCCGAACTTCCAAAAATCCCATTTTCAACCCCGAATCTTCCAAAAATTAC-TAT
1 TTTACCCCCAAACTTCCAAAAATCCCATTTT-TACCCCGAAACTTCCAAAAATCCCAT-T
*
714 TTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCCCC-AAACTTCCAAAAATCCCATT
1 TTTACCCCCAAACTTCCAAAAATCCCATTTTT-A-CCCCGAAACTTCCAAAAATCCCATT
* * * *
773 TTTGATCCCCAAACTTCCAAAATTACTA-TTTTACCCCTG-AACTTCCAAAAATCCCATT
1 TTT-ACCCCCAAACTTCCAAAAATCCCATTTTTACCCC-GAAACTTCCAAAAATCCCATT
* * * ** * *
831 TTTAACCCCAAACCTTCTTAAAATTATCA-TTTTACCCCCAAACTTCCAACAATCCCATT
1 TTTACCCCCAAA-CTTC-CAAAAATCCCATTTTTACCCCGAAACTTCCAAAAATCCCATT
*** * * * * *
890 TTTGACCTTGAATCTTCCAAAAATTACTATTTTT-CCTCG-AATTTCCAAAAATCCCATT
1 TTT-ACCCCCAAACTTCCAAAAA-TCCCATTTTTACCCCGAAACTTCCAAAAATCCCATT
* * * * *
948 TTTACCCCGAATCTTCCAAAAATTACCA-CTTTACCCTCG-AACTTCCAAAAATCCTATT
1 TTTACCCCCAAACTTCCAAAAA-TCCCATTTTTACCC-CGAAACTTCCAAAAATCCCATT
1006 TTT
1 TTT
1009 GATTTCGAAC
Statistics
Matches: 296, Mismatches: 41, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
56 3 0.01
57 36 0.12
58 122 0.41
59 103 0.35
60 32 0.11
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.33
Consensus pattern (58 bp):
TTTACCCCCAAACTTCCAAAAATCCCATTTTTACCCCGAAACTTCCAAAAATCCCATT
Found at i:822 original size:58 final size:58
Alignment explanation
Indices: 602--1010 Score: 281
Period size: 59 Copynumber: 7.0 Consensus size: 58
592 TACTATTTAC
* * * * *
602 CCCCAAACTTCCAAAAA-TCCCATTTTTGACCCC-GAATCTTCCAAAATTACTA-TTTT-A
1 CCCCAAACTTCCAAAAATTACTA-TTTT-ACCCCTGAA-CTTCCAAAAATCCCATTTTTGA
* * * **
659 CCCCCGAACTTCCAAAAA-TCCCATTTTCAACCCC-GAATCTTCCAAAAATTAC-TATTTT-A
1 -CCCCAAACTTCCAAAAATTACTATTTT--ACCCCTGAA-CTTCCAAAAATCCCAT-TTTTGA
* * * *
718 CCCCCGAACTTCCAAAAA-TCCCATTTTTGATCCCC-AAACTTCCAAAAATCCCATTTTTGA
1 -CCCCAAACTTCCAAAAATTACTA-TTTT-A-CCCCTGAACTTCCAAAAATCCCATTTTTGA
*
778 TCCCCAAACTTCC-AAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTAA
1 -CCCCAAACTTCCAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
** ** *
836 CCCCAAACCTTCTTAAAATTA-TCATTTTACCCCCAAACTTCCAACAATCCCATTTTTGA
1 CCCCAAA-CTTCCAAAAATTACT-ATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
** * * * *
895 CCTTGAATCTTCCAAAAATTACTATTTTTCCTC-GAATTTCCAAAAATCCCATTTTT-A
1 CC-CCAAACTTCCAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
* * * *
952 CCCCGAATCTTCCAAAAATTACCACTTTA-CCCTCGAACTTCCAAAAATCCTATTTTTGA
1 CCCC-AAACTTCCAAAAATTACTATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGA
1011 TTTCGAACAT
Statistics
Matches: 294, Mismatches: 39, Indels: 35
0.80 0.11 0.10
Matches are distributed among these distances:
56 2 0.01
57 39 0.13
58 110 0.37
59 114 0.39
60 29 0.10
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (58 bp):
CCCCAAACTTCCAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
Found at i:913 original size:147 final size:147
Alignment explanation
Indices: 602--894 Score: 473
Period size: 147 Copynumber: 2.0 Consensus size: 147
592 TACTATTTAC
*
602 CCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCCAAAATTACTATTTTACCCCCGAA
1 CCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAATTACTATTTTACCCCCGAA
* * *
667 CTTCCAAAAATCCCATTTTCAACCCCGAATCTTCCAAAAATTACTATTTTACCCCCGAACTTCCA
66 CTTCCAAAAATCCCATTTTCAACCCCAAACCTTCCAAAAATTACTATTTTACCCCCAAACTTCCA
732 AAAATCCCATTTTTGAT
131 AAAATCCCATTTTTGAT
*
749 CCCCAAACTTCCAAAAATCCCATTTTTGATCCCC-AAACTTCCAAAATTACTATTTTACCCCTGA
1 CCCCAAACTTCCAAAAATCCCATTTTTGA-CCCCGAAACTTCCAAAATTACTATTTTACCCCCGA
* **
813 ACTTCCAAAAATCCCATTTTTAACCCCAAACCTTCTTAAAATTA-TCATTTTACCCCCAAACTTC
65 ACTTCCAAAAATCCCATTTTCAACCCCAAACCTTCCAAAAATTACT-ATTTTACCCCCAAACTTC
*
877 CAACAATCCCATTTTTGA
129 CAAAAATCCCATTTTTGA
895 CCTTGAATCT
Statistics
Matches: 135, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
146 1 0.01
147 130 0.96
148 4 0.03
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (147 bp):
CCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAATTACTATTTTACCCCCGAA
CTTCCAAAAATCCCATTTTCAACCCCAAACCTTCCAAAAATTACTATTTTACCCCCAAACTTCCA
AAAATCCCATTTTTGAT
Done.