Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012080.1 Kokia drynarioides strain JFW-HI SEQ_127079, 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: 2169
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Found at i:300 original size:59 final size:59
Alignment explanation
Indices: 201--605 Score: 543
Period size: 59 Copynumber: 6.9 Consensus size: 59
191 GGAGGTCCCT
*
201 AAACTATCCAAAAATTCCATTTTTATCCC-CGAACTTCCAAAAATTCCATTTTCGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * * * *
261 AAACTCCCAAAAATTCCATTTTTACCCTCAAAC-TCCCAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* *
319 AAACTTCCAAAAATTCCATTTTTACCC-CTGAACTTCTAAAAATTCC-TTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTGACCTCG
* *
377 AAAC-TCCTAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCTATTTTTGACCTCG
1 AAACTTCC-AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * *
436 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTCCCAAAAATTCCATTTTTTACATCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * * * *
495 AAACTTTCAAAAATTCCATTTTTACCCTCGAACTCCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* *
554 AAACTTTCAAAAATTCCATTTTTACCCTCGAA-TGTCTAAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTT
606 TAAACCCTAA
Statistics
Matches: 308, Mismatches: 29, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
57 4 0.01
58 101 0.33
59 195 0.63
60 8 0.03
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:606 original size:30 final size:29
Alignment explanation
Indices: 202--605 Score: 427
Period size: 29 Copynumber: 13.8 Consensus size: 29
192 GAGGTCCCTA
202 AACTATCCAAAAATTCCATTTTTATCCC-CG
1 AACT-TCCAAAAATTCCATTTTTA-CCCTCG
*
232 AACTTCCAAAAATTCCATTTTCGA-CCTCG
1 AACTTCCAAAAATTCCATTTT-TACCCTCG
* *
261 AAACTCCCAAAAATTCCATTTTTACCCTCA
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* *
291 AAC-TCCCAAAATTCCATTTTTGACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
320 AACTTCCAAAAATTCCATTTTTACCC-CTG
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
* *
349 AACTTCTAAAAATTCC-TTTTCGA-CCTCG
1 AACTTCCAAAAATTCCATTTT-TACCCTCG
*
377 AAAC-TCCTAAAAATTCCATTTTTACCCTTG
1 -AACTTCC-AAAAATTCCATTTTTACCCTCG
*
407 AACTTCCAAAAATTCTATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
436 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* *
466 AACTCCCAAAAATTCCATTTTTTA-CATCG
1 AACTTCCAAAAATTCCA-TTTTTACCCTCG
*
495 AAACTTTCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* *
525 AACTCCCAAAAATTCCATTTTTAACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
*
555 AACTTTCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
584 AA-TGTCTAAAAATTCCATTTTT
1 AACT-TCCAAAAATTCCATTTTT
606 TAAACCCTAA
Statistics
Matches: 320, Mismatches: 30, Indels: 49
0.80 0.08 0.12
Matches are distributed among these distances:
28 29 0.09
29 157 0.49
30 134 0.42
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:680 original size:29 final size:29
Alignment explanation
Indices: 206--674 Score: 115
Period size: 29 Copynumber: 15.9 Consensus size: 29
196 TCCCTAAACT
* *
206 ATCCAAAAATT-CCATTTTTATCCCCGAAC
1 ATCCAAAAATTACCA-TTTTACCCCCGAAA
* *
235 TTCCAAAAATT-CCATTTT-CGACCTCGAAA
1 ATCCAAAAATTACCATTTTAC--CCCCGAAA
* *
264 CTCCCAAAAATT-CCATTTTTACCCTC-AAA
1 AT-CCAAAAATTACCA-TTTTACCCCCGAAA
* *
293 CTCCCAAAATT-CCATTTTTGA-CCCC-AAA
1 ATCCAAAAATTACCA-TTTT-ACCCCCGAAA
* *
321 ACTTCCAAAAATT-CCATTTTTACCCCTGAAC
1 A--TCCAAAAATTACCA-TTTTACCCCCGAAA
* * *
352 TTCTAAAAATT-CC-TTTT-CGACCTCGAAA
1 ATCCAAAAATTACCATTTTAC--CCCCGAAA
* ** *
380 CTCCTAAAAATT-CCATTTTTACCCTTGAAC
1 ATCC-AAAAATTACCA-TTTTACCCCCGAAA
* * *
410 TTCCAAAAATT-CTATTTTTGA-CCTCGAAA
1 ATCCAAAAATTACCA-TTTT-ACCCCCGAAA
* *
439 CTTCCAAAAATT-CCATTTTTACCCTCG-AA
1 -ATCCAAAAATTACCA-TTTTACCCCCGAAA
* **
468 CTCCCAAAAATT-CCATTTTTTA-CATCGAAA
1 AT-CCAAAAATTACCA--TTTTACCCCCGAAA
* * *
498 CTTTCAAAAATT-CCATTTTTACCCTCG-AA
1 -ATCCAAAAATTACCA-TTTTACCCCCGAAA
* *
527 CTCCCAAAAATT-CCATTTTTAACCCC-AAA
1 AT-CCAAAAATTACCA-TTTTACCCCCGAAA
* * *
556 ACTTTCAAAAATT-CCATTTTTACCCTCGAAT
1 A--TCCAAAAATTACCA-TTTTACCCCCGAAA
* * ** *
587 GTCTAAAAATT-CCATTTTTTAAACCCTAAA
1 ATCCAAAAATTACCA--TTTTACCCCCGAAA
* *
617 ATTTCCCAAAATTACCATTTTGCCCCCGAAA
1 A--TCCAAAAATTACCATTTTACCCCCGAAA
648 ATCCAAAAATTACCATTTTACCCCCGA
1 ATCCAAAAATTACCATTTTACCCCCGA
675 GTATCCGGAA
Statistics
Matches: 351, Mismatches: 56, Indels: 66
0.74 0.12 0.14
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 35 0.10
29 151 0.43
30 122 0.35
31 25 0.07
32 10 0.03
33 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
ATCCAAAAATTACCATTTTACCCCCGAAA
Done.