Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001882.1 Kokia drynarioides strain JFW-HI SEQ_113654, 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: 3894
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Found at i:216 original size:3 final size:3
Alignment explanation
Indices: 208--243 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
198 TCGAATTACT
208 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
244 CTTTCCTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:763 original size:89 final size:89
Alignment explanation
Indices: 601--868 Score: 414
Period size: 89 Copynumber: 3.0 Consensus size: 89
591 ATAGTTGAAG
* * * *
601 TTAGTTGCATAAAAA-CATAGGATAATTAATTTTTTAATTTAAG-AAGAAAACATAACTATGTAA
1 TTAGTTGCA-AAAAAGCATGGGATAAATAATTTTTTAATTTAAGAAATAAAACATAACTAAGTAA
664 ATAATATCAATGTACAAGAAACTTA
65 ATAATATCAATGTACAAGAAACTTA
* *
689 TTAGTTGCAAAAAAGCATGGGATAAATAGTTTGTTAATTTAAGAAATAAAACATAACTAAGTAAA
1 TTAGTTGCAAAAAAGCATGGGATAAATAATTTTTTAATTTAAGAAATAAAACATAACTAAGTAAA
*
754 TAATATCAATGTACAAGAAACTTT
66 TAATATCAATGTACAAGAAACTTA
* *
778 TTAGTTGCAAAAAAGCATGGGATAAGTAATTTTTTAATTTAAGAAGTAAAACATAACTAAGTAAA
1 TTAGTTGCAAAAAAGCATGGGATAAATAATTTTTTAATTTAAGAAATAAAACATAACTAAGTAAA
* *
843 TAATATCAATGTACAATAATCTTA
66 TAATATCAATGTACAAGAAACTTA
867 TT
1 TT
869 TAGGATACAC
Statistics
Matches: 164, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
87 5 0.03
88 33 0.20
89 126 0.77
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (89 bp):
TTAGTTGCAAAAAAGCATGGGATAAATAATTTTTTAATTTAAGAAATAAAACATAACTAAGTAAA
TAATATCAATGTACAAGAAACTTA
Found at i:1547 original size:24 final size:24
Alignment explanation
Indices: 1515--1564 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1505 AAAAATAACT
*
1515 AAGTAAATAGTATCAATGTACAAA
1 AAGTAAATAGTATCAACGTACAAA
1539 AAGTAAATAGTATCAACGTACAAA
1 AAGTAAATAGTATCAACGTACAAA
1563 AA
1 AA
1565 AATTATTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAGTAAATAGTATCAACGTACAAA
Found at i:3252 original size:354 final size:353
Alignment explanation
Indices: 2599--3759 Score: 1509
Period size: 356 Copynumber: 3.3 Consensus size: 353
2589 TCAAATTATG
* * *
2599 ATTATCATTTAAATATAATTTATCTAAAGTCAAACCTAAAAAAATTTAATTCAAAATAATTCAAT
1 ATTATCATTTAAATATAATTTATCTAAAGTCGAGCCTAAAAAAATTTAATTCAAAATAAATCAAT
* *
2664 TTGAATCGAATTACTATTC---TAATAATAATAGTTAATCAACTATAAACATTGAAAATAATAGC
66 TTGAATCGAATTACTATTCTAATAATAATAATAGTTAATCGACTATAAACATTTAAAATAATAGC
* * * ** *
2726 AATG-CTTTTAAATTACCATTGAAGC-CATCTCATACAT-TT-GCATAGAATCTAATTCATTCCT
131 AA-GACTTTTCAATTACCCTTGAA-CTCATAT-A-AGTTGTTGGCATAGAAT-TTATTCATTCCT
* *
2787 TAGAAGCTCC-ATTGAAGTCATTAGTTGCATAAAAGCATGAGATAATTAATTTTTTAATTTAAAA
191 TAGAAGTTCCTATTGAAGTCATTAGTTGCATAAAAGCATGGGATAATTAATTTTTTAATTT--AA
* * * *
2851 AAAAAAAAGACATAACTAAGTAAATAATATTAATGGACAAGAAACTTATTTAGGATACAATTGAA
254 AAAGAAAA-ACATAACTAAATAAATAATATCAATGGACAAGAAACTTATTTAGGATACACTTGAA
2916 AATCAAATTATATTACTTTATTAAAATTGAAAATAAT
318 AATCAAATTATATTACTTTATTAAAATTGAAAA-AAT
* * ** *
2953 ATTATCATTTAAATATAATTTATCTAAAATCGAGTCTAAAAATTTTTAATTCAAGATAAATCAAT
1 ATTATCATTTAAATATAATTTATCTAAAGTCGAGCCTAAAAAAATTTAATTCAAAATAAATCAAT
* * * * *
3018 TTAAATCGAATTACTATTCTAATAATAATAATAATTAAGCGACTATAAACATTTAAAATAACAGT
66 TTGAATCGAATTACTATTCTAATAATAATAATAGTTAATCGACTATAAACATTTAAAATAATAGC
*
3083 AAGACTTTTCAATT-CCCTTGAACTCATATAAGTTGTTGGCATATAATTTATTTCATTCCTTAGA
131 AAGACTTTTCAATTACCCTTGAACTCATATAAGTTGTTGGCATAGAATTTA-TTCATTCCTTAGA
* * * ** *
3147 ATTTCCTATTGAAGTCATTAATTGAATAAAAGTGTGGGATAATTAATTTTTTAATTTAAGAAGAA
195 AGTTCCTATTGAAGTCATTAGTTGCATAAAAGCATGGGATAATTAATTTTTTAATTTAAAAAGAA
* *
3212 AAACATAACTAAATAAATAATATCAATGGACAAAAAACTTATTTTGGATACACTTGAAAATCAAA
260 AAACATAACTAAATAAATAATATCAATGGACAAGAAACTTATTTAGGATACACTTGAAAATCAAA
*
3277 TTATA-TACTTTATTAGAATTG-AAAAAT
325 TTATATTACTTTATTAAAATTGAAAAAAT
* * *
3304 GATTATCATTTAAATATAATTTATCTAAAGTCGAGCCTAGAAGAATTTAATTCAAAATAACTCAA
1 -ATTATCATTTAAATATAATTTATCTAAAGTCGAGCCTAAAAAAATTTAATTCAAAATAAATCAA
* *
3369 TTTGAATCTAATTACTATTATAATAATAAAAATAATAGTTAATCGACTATAAACATTTAAAATAA
65 TTTGAATCGAATTACTATTCTAATAAT---AATAATAGTTAATCGACTATAAACATTTAAAATAA
* * * * * * * *
3434 TAGCAAAACTTTTCAGTTACACTAGAAGTCATATAAGTAGCTGGCATAGAATATGATTCATTCCT
127 TAGCAAGACTTTTCAATTACCCTTGAACTCATATAAGTTGTTGGCATAGAAT-TTATTCATTCCT
* ** * *
3499 TAAAAGTTCCTCCTGAAGCCATTAGTTGCGTAAAAGCATGGGATAATTAATTTTTTAATTTAAAA
191 TAGAAGTTCCTATTGAAGTCATTAGTTGCATAAAAGCATGGGATAATTAATTTTTTAATTTAAAA
* *
3564 AGAAAAATATAACTAAATAAATAATATCAATGTACAAGAAACTTATTTAGGATACACTTGAAAAT
256 AGAAAAACATAACTAAATAAATAATATCAATGGACAAGAAACTTATTTAGGATACACTTGAAAAT
* *
3629 CGAATTATATTACTTTATTAAAATTTTAAAAAA-
321 CAAATTATATTACTTTATTAAAA-TTGAAAAAAT
* *
3662 ATTTATCATTTAAATATAATTTATTTAAAGTCGAGCCTAAAAGAAATTTAATTCAAAATAAATTA
1 A-TTATCATTTAAATATAATTTATCTAAAGTCGAGCCTAAAA-AAATTTAATTCAAAATAAATCA
* *
3727 ATTTGAATCAAATTACTATTTTAATAATAATAA
64 ATTTGAATCGAATTACTATTCTAATAATAATAA
3760 CAATAATAAT
Statistics
Matches: 701, Mismatches: 86, Indels: 38
0.85 0.10 0.05
Matches are distributed among these distances:
351 3 0.00
352 83 0.12
353 15 0.02
354 140 0.20
355 61 0.09
356 201 0.29
357 108 0.15
358 40 0.06
359 50 0.07
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (353 bp):
ATTATCATTTAAATATAATTTATCTAAAGTCGAGCCTAAAAAAATTTAATTCAAAATAAATCAAT
TTGAATCGAATTACTATTCTAATAATAATAATAGTTAATCGACTATAAACATTTAAAATAATAGC
AAGACTTTTCAATTACCCTTGAACTCATATAAGTTGTTGGCATAGAATTTATTCATTCCTTAGAA
GTTCCTATTGAAGTCATTAGTTGCATAAAAGCATGGGATAATTAATTTTTTAATTTAAAAAGAAA
AACATAACTAAATAAATAATATCAATGGACAAGAAACTTATTTAGGATACACTTGAAAATCAAAT
TATATTACTTTATTAAAATTGAAAAAAT
Done.