Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009806.1 Kokia drynarioides strain JFW-HI SEQ_124527, 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, 788
Length: 1314
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.38
Found at i:352 original size:30 final size:30
Alignment explanation
Indices: 290--551 Score: 255
Period size: 30 Copynumber: 8.8 Consensus size: 30
280 AGAGGTCCCT
*
290 AAACTATCCGAAAATTCCATTTTT-ACCCCA
1 AAACT-TCCAAAAATTCCATTTTTGACCCCA
* *
320 AAACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
* *
350 AAACTTCCAAAAATTCCAATTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
** * *
380 AAACTTTTAAAAATTCAATTTTT-ACCCCT
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
* * * *
409 GAACTTCTAAAAATTCAATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
* * *
439 AAACTTCCAAAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
469 AAACTTCCAAAAATTCCATTTTT-ACCCTC-
1 AAACTTCCAAAAATTCCATTTTTGACCC-CA
* * * * *
498 GAA-TATCCAAAATTTCCATTTTTAACACCG
1 AAACT-TCCAAAAATTCCATTTTTGACCCCA
*
528 AAACTTTCAAAAATTACCATTTTT
1 AAACTTCCAAAAATT-CCATTTTT
552 TGCCCCCGGA
Statistics
Matches: 196, Mismatches: 28, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 64 0.33
30 122 0.62
31 9 0.05
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCA
Found at i:443 original size:89 final size:90
Alignment explanation
Indices: 290--551 Score: 289
Period size: 89 Copynumber: 2.9 Consensus size: 90
280 AGAGGTCCCT
* ** * * *
290 AAACTATCCGAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTGACCTCAAAACT
1 AAACT-TCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
*
355 TCCAAAAATTCCAATTTTGACCCT-A
65 TCCAAAAATTCCAATTTTGAACCTCA
** * * *
380 AAACTTTTAAAAATTCAATTTTTACCCCTGAACTTCTAAAAATTCAATTTTTGACCCCGAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTT
* *
445 CCAAAAATTCC-ATTTTTAACCTCG
66 CCAAAAATTCCAATTTTGAACCTCA
* * *
469 AAACTTCCAAAAATTCCATTTTTA-CCCTCGAA-TATCCAAAATTTCCATTTTTAACACCGAAAC
1 AAACTTCCAAAAATTCCATTTTTACCCCT-GAACT-TCCAAAAATTCCATTTTTGACCCCGAAAC
* *
532 TTTCAAAAATTACCATTTTT
64 TTCCAAAAATT-CCAATTTT
552 TGCCCCCGGA
Statistics
Matches: 143, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
88 14 0.10
89 118 0.83
90 7 0.05
91 4 0.03
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (90 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTT
CCAAAAATTCCAATTTTGAACCTCA
Found at i:616 original size:29 final size:28
Alignment explanation
Indices: 584--692 Score: 71
Period size: 29 Copynumber: 3.8 Consensus size: 28
574 CCATTTTCAA
*
584 CCTCGAAACCCTCAAAATTACCTTTTTAC
1 CCTCGAAAACC-CAAAATTACCTTTTTAC
** **
613 CCTCGAATGTCTAAAAATT-CCATTTTTAAC
1 CCTCGAA-AACCCAAAATTACC-TTTTT-AC
*
643 CCT--AAAATTTCCCAAAATTACCATTTTAC
1 CCTCGAAAA---CCCAAAATTACCTTTTTAC
*
672 CCTCGAAAATCCAAAATTACC
1 CCTCGAAAACCCAAAATTACC
693 AATTTACCTC
Statistics
Matches: 61, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
28 15 0.25
29 23 0.38
30 17 0.28
31 6 0.10
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (28 bp):
CCTCGAAAACCCAAAATTACCTTTTTAC
Found at i:672 original size:59 final size:60
Alignment explanation
Indices: 300--687 Score: 243
Period size: 59 Copynumber: 6.5 Consensus size: 60
290 AAACTATCCG
* * * *
300 AAAATT-CCATTTTTACCC-CAAAACT-TCCAAAAATCCCATTTTTGACCTCAAAACTTCCA
1 AAAATTACCATTTTTACCCTC-GAA-TGTCCAAAAATTCCATTTTTAACCTCAAAATTTCCA
* ** ** * * ** * *
359 AAAATT-CCAATTTTGACCCTAAAACT-TTTAAAAATTCAATTTTT-ACCCCTGAACTTCTA
1 AAAATTACC-ATTTTTACCCTCGAA-TGTCCAAAAATTCCATTTTTAACCTCAAAATTTCCA
* * *
418 AAAATT-CAATTTTTGACCC-CGAAACT-TCCAAAAATTCCATTTTTAACCTCGAAACTTCCA
1 AAAATTACCATTTTT-ACCCTCG-AA-TGTCCAAAAATTCCATTTTTAACCTCAAAATTTCCA
* * *
478 AAAATT-CCATTTTTACCCTCGAATATCCAAAATTTCCATTTTTAACAC-CGAAACTTT-CA
1 AAAATTACCATTTTTACCCTCGAATGTCCAAAAATTCCATTTTTAAC-CTC-AAAATTTCCA
* * * ** * * * *
537 AAAATTACCATTTTTTGCCCCCGGATGTCCAAAAACACCATTTTCAACCTCGAAA--CCCTC
1 AAAATTACCA-TTTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCTCAAAATTTCC-A
* *
597 AAAATTACC-TTTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACC-CTAAAATTTCCC
1 AAAATTACCATTTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCTC-AAAATTTCCA
**
656 AAAATTACCA-TTTTACCCTCGAAAATCCAAAA
1 AAAATTACCATTTTTACCCTCGAATGTCCAAAA
688 TTACCAATTT
Statistics
Matches: 261, Mismatches: 50, Indels: 36
0.75 0.14 0.10
Matches are distributed among these distances:
57 1 0.00
58 40 0.15
59 114 0.44
60 76 0.29
61 30 0.11
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.32
Consensus pattern (60 bp):
AAAATTACCATTTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCTCAAAATTTCCA
Found at i:697 original size:29 final size:29
Alignment explanation
Indices: 418--693 Score: 140
Period size: 30 Copynumber: 9.3 Consensus size: 29
408 TGAACTTCTA
* *
418 AAAATT-CAATTTTTGACCC-CGAAACTTCC
1 AAAATTACCATTTTT-ACCCTCGAAA-ATCC
* *
447 AAAAATT-CCATTTTTAACCTCGAAACTTCC
1 -AAAATTACCATTTTTACCCTCGAAA-ATCC
*
477 AAAAATT-CCATTTTTACCCTCGAATATCC
1 -AAAATTACCATTTTTACCCTCGAAAATCC
* * * *
506 AAAATTTCCATTTTTAACAC-CGAAACTTTCA
1 AAAATTACCATTTTT-ACCCTCGAAA--ATCC
* * * **
537 AAAATTACCATTTTTTGCCCCCGGATGTCC
1 AAAATTACCA-TTTTTACCCTCGAAAATCC
** * * **
567 AAAAACACCATTTTCAACCTCGAAACCCTC
1 AAAATTACCATTTTTACCCTCGAAAATC-C
** *
597 AAAATTACC-TTTTTACCCTCGAATGTCTA
1 AAAATTACCATTTTTACCCTCGAAAATC-C
626 AAAATT-CCATTTTTAACCCT--AAAATTTCCC
1 AAAATTACCATTTTT-ACCCTCGAAAA--T-CC
656 AAAATTACCA-TTTTACCCTCGAAAATCC
1 AAAATTACCATTTTTACCCTCGAAAATCC
684 AAAATTACCA
1 AAAATTACCA
694 ATTTACCTCC
Statistics
Matches: 193, Mismatches: 37, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
28 22 0.11
29 59 0.31
30 83 0.43
31 21 0.11
32 8 0.04
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTTACCCTCGAAAATCC
Done.