Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001076.1 Kokia drynarioides strain JFW-HI SEQ_112332, 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: 3463
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Found at i:656 original size:59 final size:59
Alignment explanation
Indices: 583--916 Score: 270
Period size: 59 Copynumber: 5.5 Consensus size: 59
573 AAATTGTTCG
* * * *
583 AAAATTATCATTTTACCCTCGAACATCTAAAAATCCCATTTTTGACACCAAAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACACCAAAACTTCCA
* * *
642 AAAATTACCATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTGACCCCAAAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACACCAAAACTTCCA
** * **
701 AAAATTACCATTTTACCCCCGAACTTCCAAAAAATATCA-TTTT-ACCCCTCGAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCC-AAAAATCCCATTTTTGACACC-AAAACTTCCA
* ** * * ** **
760 AAAA-TCCCATTTTTGACCCCAAAACTTACAAAACTTACA-TTTT-AC-CCTCGAACTTCCA
1 AAAATTACCA-TTTT-ACCCCCGAACTTCCAAAAATCCCATTTTTGACACC-AAAACTTCCA
* *
818 AAAATTACCATTTTACCCCCGAA-TTCCCAAAAATCTCATTTTTGAC-CCTGAAACTTCCAAATT
1 AAAATTACCATTTTACCCCCGAACTT-CCAAAAATCCCATTTTTGACACC---AA-----AACTT
881 CCA
57 CCA
884 AAAATTACCATTTTACCCCCGACACTTCCAAAA
1 AAAATTACCATTTTACCCCCGA-ACTTCCAAAA
917 TTTACCATTT
Statistics
Matches: 227, Mismatches: 31, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
56 2 0.01
57 15 0.07
58 34 0.15
59 120 0.53
60 18 0.08
66 29 0.13
67 7 0.03
68 2 0.01
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.29
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACACCAAAACTTCCA
Found at i:664 original size:30 final size:29
Alignment explanation
Indices: 583--929 Score: 242
Period size: 29 Copynumber: 11.6 Consensus size: 29
573 AAATTGTTCG
* * * * *
583 AAAATTATCATTTTACCCTCGAACATCTA
1 AAAATTACCATTTTACCCCCAAACTTCCA
* * *
612 AAAA-TCCCATTTTTGACACCAAAACTTCCA
1 AAAATTACCA-TTTT-ACCCCCAAACTTCCA
642 AAAATTACCATTTTACCCCCAAACTTCC-
1 AAAATTACCATTTTACCCCCAAACTTCCA
* * *
670 AAAAGTCCCATTTTTGACCCCAAAACTTCCA
1 AAAATTACCA-TTTT-ACCCCCAAACTTCCA
*
701 AAAATTACCATTTTACCCCCGAACTTCCA
1 AAAATTACCATTTTACCCCCAAACTTCCA
* * *
730 AAAAATATCATTTTACCCCTCGAACTTCCA
1 AAAATTACCATTTTACCCC-CAAACTTCCA
* * *
760 AAAA-TCCCATTTTTGACCCCAAAACTTACA
1 AAAATTACCA-TTTT-ACCCCCAAACTTCCA
* * *
790 AAACTTA-CATTTTACCCTCGAACTTCCA
1 AAAATTACCATTTTACCCCCAAACTTCCA
*
818 AAAATTACCATTTTACCCCCGAA-TTCCCA
1 AAAATTACCATTTTACCCCCAAACTT-CCA
847 AAAA-T-CTCATTTTTGACCCTGAAACTTCCAAA-TTCCA
1 AAAATTAC-CA-TTTT-A-CC-----C--CCAAACTTCCA
*
884 AAAATTACCATTTTACCCCCGACACTTCCA
1 AAAATTACCATTTTACCCCC-AAACTTCCA
*
914 AAATTTACCATTTTAC
1 AAAATTACCATTTTAC
930 TCCCGAATGT
Statistics
Matches: 255, Mismatches: 36, Indels: 53
0.74 0.10 0.15
Matches are distributed among these distances:
27 1 0.00
28 35 0.14
29 88 0.35
30 86 0.34
31 20 0.08
35 2 0.01
36 2 0.01
37 11 0.04
38 9 0.04
39 1 0.00
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAACTTCCA
Found at i:840 original size:29 final size:29
Alignment explanation
Indices: 583--936 Score: 263
Period size: 30 Copynumber: 11.8 Consensus size: 29
573 AAATTGTTCG
* * * *
583 AAAATTATCATTTTACCCTCGAACATCTA
1 AAAATTACCATTTTACCCCCGAACTTCCA
* * **
612 AAAA-TCCCATTTTTGACACCAAAACTTCCA
1 AAAATTACCA-TTTT-ACCCCCGAACTTCCA
*
642 AAAATTACCATTTTACCCCCAAACTTCC-
1 AAAATTACCATTTTACCCCCGAACTTCCA
* * **
670 AAAAGTCCCATTTTTGACCCCAAAACTTCCA
1 AAAATTACCA-TTTT-ACCCCCGAACTTCCA
701 AAAATTACCATTTTACCCCCGAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCA
* *
730 AAAAATATCATTTTACCCCTCGAACTTCCA
1 AAAATTACCATTTTACCCC-CGAACTTCCA
* ** *
760 AAAA-TCCCATTTTTGACCCCAAAACTTACA
1 AAAATTACCA-TTTT-ACCCCCGAACTTCCA
* *
790 AAACTTA-CATTTTACCCTCGAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCA
818 AAAATTACCATTTTACCCCCGAA-TTCCCA
1 AAAATTACCATTTTACCCCCGAACTT-CCA
* *
847 AAAA-T-CTCATTTTTGACCCTGAAACTTCCAAATTCCA
1 AAAATTAC-CA-TTTT-ACCC-----C--CGAACTTCCA
884 AAAATTACCATTTTACCCCCGACACTTCCA
1 AAAATTACCATTTTACCCCCGA-ACTTCCA
* *
914 AAATTTACCATTTTACTCCCGAA
1 AAAATTACCATTTTACCCCCGAA
937 TGTCTGAAGG
Statistics
Matches: 261, Mismatches: 38, Indels: 52
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.00
28 33 0.13
29 89 0.34
30 94 0.36
31 19 0.07
35 1 0.00
36 4 0.02
37 14 0.05
38 5 0.02
39 1 0.00
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAACTTCCA
Found at i:3427 original size:17 final size:17
Alignment explanation
Indices: 3400--3439 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
3390 ATAAATTCTA
*
3400 AATAGACTAAATATAAAT
1 AATA-ACTAAATAAAAAT
3418 AATAACTAAATAAAAAT
1 AATAACTAAATAAAAAT
3435 AATAA
1 AATAA
3440 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (17 bp):
AATAACTAAATAAAAAT
Done.