Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012281.1 Kokia drynarioides strain JFW-HI SEQ_127282, 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: 3158
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.26
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:2611 original size:98 final size:96
Alignment explanation
Indices: 2326--2619 Score: 311
Period size: 96 Copynumber: 3.0 Consensus size: 96
2316 GACTAGTGAA
* *
2326 ACACCAAATCCTATCTTCCTGAAGTTGTAGTGAAGCAGATTAAAACAAGTAGCAGATCTCAATCT
1 ACACCAAATCCTATCTTCTTGAAGTTGTAATGAAGCAGATTAAAACAAGTAGCAGATCTCAATCT
* * * *
2391 CTACTGAAGTTGCAGTGGAATGGAGTGACGCC
66 C-CCTGAAGTTGCAGTGGAATAGAGTGAAGCT
* * * * * * * * * *
2423 ACCCCAAATCCTATATCCTTGAAGTTGCAA-GGATCAGAGTAAAACGAGTAGCATATATCAATCT
1 ACACCAAATCCTATCTTCTTGAAGTTGTAATGAAGCAGATTAAAACAAGTAGCAGATCTCAATCT
* *
2487 CCACTGAAGTTGTAGTGGAACAGAGTGAAGCT
66 CC-CTGAAGTTGCAGTGGAATAGAGTGAAGCT
* * * * * *
2519 ACACCAAATCCTACCTTCTTGAAGTAGTAATGAAGCGGATTAAAACTACAGTAACGGGTCTCAAT
1 ACACCAAATCCTATCTTCTTGAAGTTGTAATGAAGCAGATTAAAAC-A-AGTAGCAGATCTCAAT
* *
2584 CTCCCTGAAATTGCAGTGGAATAGAGTGAAGTT
64 CTCCCTGAAGTTGCAGTGGAATAGAGTGAAGCT
2617 ACA
1 ACA
2620 TCACTAAATC
Statistics
Matches: 155, Mismatches: 38, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
96 77 0.50
97 35 0.23
98 28 0.18
99 15 0.10
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (96 bp):
ACACCAAATCCTATCTTCTTGAAGTTGTAATGAAGCAGATTAAAACAAGTAGCAGATCTCAATCT
CCCTGAAGTTGCAGTGGAATAGAGTGAAGCT
Found at i:2700 original size:48 final size:48
Alignment explanation
Indices: 2629--3044 Score: 366
Period size: 48 Copynumber: 8.7 Consensus size: 48
2619 ATCACTAAAT
* * *
2629 CTTATACC-CTAAATCTAGAGGGGCAGATTGAAGCTACCAAATCCAAA
1 CTTATACCACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCCAAA
*
2676 CTTATACCACTAAATCCAAAGGGGCAGATTAAAGCTACCACAT-CAAA
1 CTTATACCACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCCAAA
* * * * *
2723 TCTTATA-CACTTAAATCCAAAGTGGCATATTAAAGCCACCACATCCAAT
1 -CTTATACCAC-TAAATCCAAAGGGGCAGATTGAAGCTACCACATCCAAA
* * *
2772 CTTATACCCCTAAATCC-AAGGGGCAGATTGAAGCTACCATATCCAAT
1 CTTATACCACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCCAAA
* * *
2819 CTTATACCCCTAAATCCAAAGGGGTAGATTGAAG-TCACTACATCCAATA
1 CTTATACCACTAAATCCAAAGGGGCAGATTGAAGCT-ACCACATCCAA-A
** * * * * * * *
2868 -TTATACGC-CTAAATATAAAAGGACAGATTGAAGCCACTATATCTAAT
1 CTTATAC-CACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCCAAA
* * * *
2915 CTTATACCTA-TAAATCCAGAGGGGTAGATTGAAGCTACCACATCCTAT
1 CTTATACC-ACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCCAAA
* * * * * *
2963 CTTATTCC-CTTAAATCTAAAAGGGCAAATTGAAGCCACCAAAT-CAAA
1 CTTATACCAC-TAAATCCAAAGGGGCAGATTGAAGCTACCACATCCAAA
* *
3010 TCTTATACCACTAAATCCAAAGAGGTAGATTGAAG
1 -CTTATACCACTAAATCCAAAGGGGCAGATTGAAG
3045 TTGCAAAACC
Statistics
Matches: 298, Mismatches: 54, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
47 61 0.20
48 230 0.77
49 7 0.02
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (48 bp):
CTTATACCACTAAATCCAAAGGGGCAGATTGAAGCTACCACATCCAAA
Found at i:2794 original size:143 final size:141
Alignment explanation
Indices: 2626--3031 Score: 458
Period size: 143 Copynumber: 2.8 Consensus size: 141
2616 TACATCACTA
* *
2626 AATCTTATA-CCCTAAATCTAGAGGGGCAGATTGAAGCTACCAAATCCAAACTTATACCACTAAA
1 AATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATACC-CTAAA
* * *
2690 TCCAAAGGGGCAGATTAAAGCTACCACATCAAATCTTATACACTTAAATCCAAAGTGGCATATTA
65 TCCAAAGGGGCAGATTGAAGCTACCACATCAAATCTTATACAC-TAAATCCAAAG-GACAGATTA
2755 AAGCCACCACATCC
128 AAGCCACCACATCC
*
2769 AATCTTATACCCCTAAATCCA-AGGGGCAGATTGAAGCTACCATATCCAATCTTATACCCCTAAA
1 AATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATA-CCCTAAA
* * * * * **
2833 TCCAAAGGGGTAGATTGAAG-TCACTACATCCAATATTATACGCCTAAATATAAAAGGACAGATT
65 TCCAAAGGGGCAGATTGAAGCT-ACCACATCAAATCTTATAC-ACTAAAT-CCAAAGGACAGATT
* * * *
2897 GAAGCCACTATATCT
127 AAAGCCACCACATCC
** * * * *
2912 AATCTTATACCTATAAATCCAGAGGGGTAGATTGAAGCTACCACATCCTATCTTATTCCCTTAAA
1 AATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATACCC-TAAA
* * * * *
2977 TCTAAAAGGGCAAATTGAAGCCACCAAATCAAATCTTATACCACTAAATCCAAAG
65 TCCAAAGGGGCAGATTGAAGCTACCACATCAAATCTTATA-CACTAAATCCAAAG
3032 AGGTAGATTG
Statistics
Matches: 219, Mismatches: 35, Indels: 18
0.81 0.13 0.07
Matches are distributed among these distances:
142 1 0.00
143 129 0.59
144 88 0.40
145 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (141 bp):
AATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGCTACCAAATCCAATCTTATACCCTAAAT
CCAAAGGGGCAGATTGAAGCTACCACATCAAATCTTATACACTAAATCCAAAGGACAGATTAAAG
CCACCACATCC
Found at i:3063 original size:96 final size:95
Alignment explanation
Indices: 2625--3044 Score: 454
Period size: 96 Copynumber: 4.4 Consensus size: 95
2615 TTACATCACT
* * * * *
2625 AAATCTTATACC-CTAAATCTAGAGGGGCAGATTGAAGCTACCAAATCCAAACTTATACCACTAA
1 AAATCTTATACCACTAAATCCAAAGGGGTAGATTGAAGCTACCACATCCAATCTTATACC-CTAA
* * * * *
2689 ATCCAAAGGGGCAGATTAAAGCTACCACATC
65 ATCTAAAAGGGCAGATTGAAGCCACCATATC
* * * * *
2720 AAATCTTATA-CACTTAAATCCAAAGTGGCATATTAAAGCCACCACATCCAATCTTATACCCCTA
1 AAATCTTATACCAC-TAAATCCAAAGGGGTAGATTGAAGCTACCACATCCAATCTTATA-CCCTA
* * *
2784 AATC-CAAGGGGCAGATTGAAGCTACCATATC
64 AATCTAAAAGGGCAGATTGAAGCCACCATATC
* * * *
2815 CAATCTTATACCCCTAAATCCAAAGGGGTAGATTGAAG-TCACTACATCCAATATTATACGCCTA
1 AAATCTTATACCACTAAATCCAAAGGGGTAGATTGAAGCT-ACCACATCCAATCTTATAC-CCTA
* * *
2879 AATATAAAAGGACAGATTGAAGCCACTATATC
64 AATCTAAAAGGGCAGATTGAAGCCACCATATC
* * * *
2911 TAATCTTATACCTA-TAAATCCAGAGGGGTAGATTGAAGCTACCACATCCTATCTTATTCCCTTA
1 AAATCTTATACC-ACTAAATCCAAAGGGGTAGATTGAAGCTACCACATCCAATCTTATACCC-TA
* *
2975 AATCTAAAAGGGCAAATTGAAGCCACCAAATC
64 AATCTAAAAGGGCAGATTGAAGCCACCATATC
*
3007 AAATCTTATACCACTAAATCCAAAGAGGTAGATTGAAG
1 AAATCTTATACCACTAAATCCAAAGGGGTAGATTGAAG
3045 TTGCAAAACC
Statistics
Matches: 273, Mismatches: 41, Indels: 21
0.81 0.12 0.06
Matches are distributed among these distances:
94 2 0.01
95 90 0.33
96 178 0.65
97 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (95 bp):
AAATCTTATACCACTAAATCCAAAGGGGTAGATTGAAGCTACCACATCCAATCTTATACCCTAAA
TCTAAAAGGGCAGATTGAAGCCACCATATC
Done.