Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000517.1 Kokia drynarioides strain JFW-HI SEQ_111402, 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: 3465
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Found at i:1147 original size:348 final size:341
Alignment explanation
Indices: 14--1167 Score: 1325
Period size: 348 Copynumber: 3.3 Consensus size: 341
4 ATCAAATTAT
*
14 GATTATCATTTAAATATAATTTATCTAAAGTCAAGCCTAAAAAAATTTAATTCAAAATAATTCAA
1 GATTATCATTTAAATATAATTTATCTAAAGTCAAGCCT-AAAAAATTTAATTCAAAATAAATCAA
* * *
79 TTTGAATCGAATTACTATTCTAATAATAATAACAACAATTAATTAGGCTATAAACATTTAAAATA
65 TTTGAATCGAATTACTATTCTAATAATAAT------AGTTAATCA-ACTATAAACATTTAAAATA
* * * * * * *
144 ATAACAAGACTTTTCAATTACCCA-TGAAGTCATATAAGTAGTTTGTATAGAATATGGTTCCTTT
123 ATAGCAAG-CTTTTCAATTA-CCATTGAAGTCATATAA-AAG-TTGCATAGAATCTGATTCATTC
* * * *
208 GTTGAAGTTCCTCTTGAAGTCATTAGTTGCAAAAAAACATGGTATAATTAATTTTTTTAATT-TA
184 CTTGAAGTTCCTC-TGAAGTCATTAGTTGCATAAAAGCATGG-ATAATTAA-TTTTTTAATTAAA
* * *
272 AGAAGAACATAACTAATTAAATAATATCAATGGACAAGAAACTTTTTTAGGATACACTTGAAAAT
246 AAAAG-ACATAACTAAATAAATAATATCAATGGACAAGAAACTTATTTAGGATACACTTGAAAAT
*
337 CAAATTATATTACTATATTAGAATTGAAAAAAC
310 CAAATTATATTACTATATTAG-ATTGAAAAAAA
*
370 GATTATCATTTAAATATAATTTATCTAAAGTCGAGCCTAAAAGAATTTAATTCAAAAT-AATCCA
1 GATTATCATTTAAATATAATTTATCTAAAGTCAAGCCTAAAA-AATTTAATTCAAAATAAAT-CA
* *
434 ATTTGAATCGAATTACTATTCTAATAATAAAAATAATAGTTAACCGACTATAAACATTTAAAATA
64 ATTTGAATCGAATTACTATTC---TAAT---AATAATAGTTAATCAACTATAAACATTTAAAATA
* ** *
499 ACAGCAAAATTTTTCAATTA-CACTAGAAGTCATATAAATAGTTGACATAGAATCTGATTCATTC
123 ATAGC-AAGCTTTTCAATTACCA-TTGAAGTCATATAAA-AGTTG-CATAGAATCTGATTCATTC
* * * * * *
563 CTTAGAAGTTACTCCTGAAGCCATTAGTTGCATAAAAGAAAGGGATACTTATTTTTTTAATTTAA
184 CTT-GAAGTTCCT-CTGAAGTCATTAGTTGCATAAAAG-CATGGATAATTAATTTTTTAA-TTAA
* * *
628 TAAGAAAAACATAACTAAGTAAATAATATCAATGGACAAGAAACTTATTTAGGATACACTCGAAA
245 -AA-AAAGACATAACTAAATAAATAATATCAATGGACAAGAAACTTATTTAGGATACACTTGAAA
* *
693 ATCAAATTATATTACTTTATTAAAATTGAAAAAAA
308 ATCAAATTATATTACTATATT-AGATTGAAAAAAA
* * * **
728 GATTATCTTTTAAATATAATTCATTTAAAGTCAAGCCTAAAAAA--TAATTCACGATAAATCAAT
1 GATTATCATTTAAATATAATTTATCTAAAGTCAAGCCTAAAAAATTTAATTCAAAATAAATCAAT
*
791 TT-AATCGAATTACTATTCTAATAATAATAGTTAATCAACTATAAACATTGAAAATAATAGCAAT
66 TTGAATCGAATTACTATTCTAATAATAATAGTTAATCAACTATAAACATTTAAAATAATAGCAA-
* * * * * *
855 GCTTTTAAATTACCATTGGAGCCATCTCTAAAAGTTGCATAGAATCTAATTCATTCCTTGGAAGC
130 GCTTTTCAATTACCATTGAAGTCA--TATAAAAGTTGCATAGAATCTGATTCATTCCTT-GAAGT
*
920 TCCATCAGAAGTCATTAGTTGCATAAAAGCATGAGATAATTAATTTTTTAATTAAAAAAAGACAT
192 TCC-TCTGAAGTCATTAGTTGCATAAAAGCATG-GATAATTAATTTTTTAATTAAAAAAAGACAT
* * *
985 AACTAAATAAACAATATCAATAGG-TAACAAACTTATTTAGGATACACTTGAAAATCAAATTATA
255 AACTAAATAAATAATATCAAT-GGACAAGAAACTTATTTAGGATACACTTGAAAATCAAATTATA
*
1049 TTACTATATTAGATTTAAAAAAA
319 TTACTATATTAGATTGAAAAAAA
* * *
1072 AATTATCATTTAAATATAATTTATTTAAAGTCAAGCCTAATAAAATTTAATTCAAGATAAATCAA
1 GATTATCATTTAAATATAATTTATCTAAAGTCAAGCCTAA-AAAATTTAATTCAAAATAAATCAA
**
1137 TTTGAATCGAATTACTATAATAATAATAATA
65 TTTGAATCGAATTACTATTCTAATAATAATA
1168 ATAAAAAAAA
Statistics
Matches: 687, Mismatches: 78, Indels: 74
0.82 0.09 0.09
Matches are distributed among these distances:
344 48 0.07
345 76 0.11
346 4 0.01
347 28 0.04
348 139 0.20
349 8 0.01
350 5 0.01
351 4 0.01
353 2 0.00
354 19 0.03
355 90 0.13
356 121 0.18
357 6 0.01
358 124 0.18
359 7 0.01
362 6 0.01
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (341 bp):
GATTATCATTTAAATATAATTTATCTAAAGTCAAGCCTAAAAAATTTAATTCAAAATAAATCAAT
TTGAATCGAATTACTATTCTAATAATAATAGTTAATCAACTATAAACATTTAAAATAATAGCAAG
CTTTTCAATTACCATTGAAGTCATATAAAAGTTGCATAGAATCTGATTCATTCCTTGAAGTTCCT
CTGAAGTCATTAGTTGCATAAAAGCATGGATAATTAATTTTTTAATTAAAAAAAGACATAACTAA
ATAAATAATATCAATGGACAAGAAACTTATTTAGGATACACTTGAAAATCAAATTATATTACTAT
ATTAGATTGAAAAAAA
Found at i:1327 original size:78 final size:77
Alignment explanation
Indices: 1171--1327 Score: 178
Period size: 77 Copynumber: 2.0 Consensus size: 77
1161 AATAATAATA
* *
1171 AAAAAAAATAACTTTCCTAAAGTCATTAGTTGTAAAAAGCATGGATAAGTAATTTTTTAAATTCT
1 AAAAAAAATAACTTTCCTAAAGTCATTAGTTGAAAAAAACATGGATAAGTAATTTTTTAAATTCT
** *
1236 AAAGTCAAGCAT
66 AAAGAAAAACAT
* *
1248 AAAAAAAATAACATTT-TTGAAGTCATTAGTTGCAAAAAAACATGGGATAAGTAA-TTTTT-AAT
1 AAAAAAAATAAC-TTTCCTAAAGTCATTAGTTG-AAAAAAACAT-GGATAAGTAATTTTTTAAAT
1310 T-TAAGAAGAAAAACAT
63 TCT-A-AAGAAAAACAT
1326 AA
1 AA
1328 GTAAATATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
76 1 0.01
77 31 0.46
78 26 0.38
79 10 0.15
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (77 bp):
AAAAAAAATAACTTTCCTAAAGTCATTAGTTGAAAAAAACATGGATAAGTAATTTTTTAAATTCT
AAAGAAAAACAT
Found at i:1631 original size:43 final size:43
Alignment explanation
Indices: 1583--1668 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
1573 TTAAGAAAAA
* *
1583 AAACATAACTATGTAAATAATATCAATGTACAATAAACTTATT
1 AAACATAAATAAGTAAATAATATCAATGTACAATAAACTTATT
* *
1626 AAACATAAATAAGTAAATTATATCAATGTACAATAATCTTATT
1 AAACATAAATAAGTAAATAATATCAATGTACAATAAACTTATT
1669 TAGGATACAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (43 bp):
AAACATAAATAAGTAAATAATATCAATGTACAATAAACTTATT
Found at i:1678 original size:310 final size:312
Alignment explanation
Indices: 1324--1949 Score: 882
Period size: 309 Copynumber: 2.0 Consensus size: 312
1314 GAAGAAAAAC
*
1324 ATAAGTAAATATTATCAATGTACAAGAAACTTATTTAGGATACACTTGAAAGTTAAATATAATTT
1 ATAAGTAAATATTATCAATGTACAAGAAACTTATTTAGGATACACTTAAAAGTTAAATATAATTT
*
1389 ATCTAAAGTCGAGCCTAAAAAAAAATTAATTCAAAATAATTCAATTTGAATCAAATTACTATTTT
66 ATCTAAAGTCGAGCCT-AAAAAAAATTAATTCAAAATAATTCAATTTGAATCAAATTACTATTCT
* * * * *
1454 AGTAATAATAATGCAAGACTTTTCAATTACCCTTGAAGTCATATAAGTAGTTGGCATAGAACTTT
130 AATAATAATAATGCAAGACTTTACAATTACCCTTGAAGTCATATAAATAGTTGACATAGAACTTC
* * **
1519 GTTCTGGTAGTTGAAG-TT-AG-TTGCAAAAAAACATAGGATAATTAATTTTTTAATTTAAGAAA
195 GTTCCGGTAGTTGAAGTTTAAGATTGCAAAAAAACATAGGATAAGTAAAATTTTAATTTAAGAAA
* *
1581 AAAAACATAACTATGTAAATAATATCAATGTACAATAAACTTATTAAACATAA
260 AAAAACATAACTAAGTAAATAATATCAATGTACAAAAAACTTATTAAACATAA
* *
1634 ATAAGTAAAT-TATATCAATGTACAATAATCTTATTTAGGATACACTTAAAAGTTAAATATAATT
1 ATAAGTAAATAT-TATCAATGTACAAGAAACTTATTTAGGATACACTTAAAAGTTAAATATAATT
* * ** *
1698 TATCTAAAGTCTATCCTAAAAAAGTTTAATTCAAAATAATTCAATTTGAATCGAATTACTATTCT
65 TATCTAAAGTCGAGCCTAAAAAAAATTAATTCAAAATAATTCAATTTGAATCAAATTACTATTCT
*
1763 AATAATAATAATGCAAGACTTTACAATTACTCTTGAAGTCATATAAATAGTTGACATAGAACTTC
130 AATAATAATAATGCAAGACTTTACAATTACCCTTGAAGTCATATAAATAGTTGACATAGAACTTC
*
1828 GTTCCGGTAGTTGAAGTTTCTCTTAAAGTCATTAATTGCAAAAAAGCATAGGATAAGTAAAATTT
195 GTTCCGGTAGTTGAAG----T-TT-AAG------ATTGCAAAAAAACATAGGATAAGTAAAATTT
* *
1893 TAATTTAAGAAGAAAAACATAACTAAGTAAATAATATCAATGTATAAAAAACTTATT
248 TAATTTAAGAAAAAAAACATAACTAAGTAAATAATATCAATGTACAAAAAACTTATT
1950 TAGGATACAC
Statistics
Matches: 276, Mismatches: 24, Indels: 18
0.87 0.08 0.06
Matches are distributed among these distances:
309 119 0.43
310 74 0.27
315 2 0.01
317 2 0.01
324 79 0.29
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (312 bp):
ATAAGTAAATATTATCAATGTACAAGAAACTTATTTAGGATACACTTAAAAGTTAAATATAATTT
ATCTAAAGTCGAGCCTAAAAAAAATTAATTCAAAATAATTCAATTTGAATCAAATTACTATTCTA
ATAATAATAATGCAAGACTTTACAATTACCCTTGAAGTCATATAAATAGTTGACATAGAACTTCG
TTCCGGTAGTTGAAGTTTAAGATTGCAAAAAAACATAGGATAAGTAAAATTTTAATTTAAGAAAA
AAAACATAACTAAGTAAATAATATCAATGTACAAAAAACTTATTAAACATAA
Found at i:2616 original size:3 final size:3
Alignment explanation
Indices: 2608--2642 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2598 TCGAATTACT
2608 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2643 TAATCGACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.