Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013764.1 Kokia drynarioides strain JFW-HI SEQ_128792, 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: 7092
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:467 original size:29 final size:29
Alignment explanation
Indices: 417--822 Score: 396
Period size: 29 Copynumber: 13.8 Consensus size: 29
407 GAGGTCACTA
* *
417 AACTGTCCAAAAATTCCGTTTTTACCTTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
* *
447 AACTTCCAAAAATTCAATTTTTACCCTCT
1 AACTTCCAAAAATTCCATTTTTACCCTCG
476 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
505 AACTTCCAAAAATTCCATTTTTGACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
*
535 AACTTCCAAAAAATTCCATTTTTACCCCCG
1 AACTTCC-AAAAATTCCATTTTTACCCTCG
* * ** **
565 AACTTCTAAGAACCCCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
**
595 AACTTCCAAAAATTCCATTTACACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * **
624 AACTTCTAAAAATTCCAATTTTAACCCCTAA
1 AACTTCCAAAAATTCC-ATTTTTA-CCCTCG
*
655 AACTTCCAAAAATTCCATTTTTACCTTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
684 AACTTCCAAAAATTCCATTTTTGACCCT-G
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* * *
713 TAAC-TCCAAAAATTCCAGTTTTGCCC-CT
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * * *
741 AGA-TATCTAAAAACTCTATTTTCGA-CCTCG
1 A-ACT-TCCAAAAATTCCATTTT-TACCCTCG
771 AAAC-TCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
800 AA-TGTCCAAAAATTCCATTTTTA
1 AACT-TCCAAAAATTCCATTTTTA
823 ACATCTAATT
Statistics
Matches: 308, Mismatches: 48, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.00
28 7 0.02
29 199 0.65
30 65 0.21
31 36 0.12
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:567 original size:60 final size:59
Alignment explanation
Indices: 416--821 Score: 448
Period size: 58 Copynumber: 6.9 Consensus size: 59
406 GGAGGTCACT
* * *
416 AAACTGTCCAAAAATTCCGTTTTTACCTTCGAACTTCCAAAAATTCAATTTTT-ACCCTC-
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCC-CA
*
475 TAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
* * * ** *
534 AAACTTCCAAAAAATTCCATTTTTACCCCCGAACTTCTAAGAACCCCATTTTTGACCCTA
1 AAACTTCC-AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
** * * *
594 AAACTTCCAAAAATTCCATTTACACCCTCGAACTTCTAAAAATTCCAATTTTAACCCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCC-A
* **
654 AAACTTCCAAAAATTCCATTTTTACCTTCGAACTTCCAAAAATTCCATTTTTGACCCTG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
* * * * * * * * * *
713 TAAC-TCCAAAAATTCCAGTTTTGCCC-CTAGA-TATCTAAAAACTCTATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGA-ACT-TCCAAAAATTCCATTTTTGACCCCA
771 AAAC-TCCAAAAATTCCATTTTTACCCTCGAA-TGTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTT
822 AACATCTAAT
Statistics
Matches: 292, Mismatches: 48, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
57 3 0.01
58 123 0.42
59 61 0.21
60 105 0.36
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
Found at i:627 original size:119 final size:118
Alignment explanation
Indices: 416--821 Score: 484
Period size: 119 Copynumber: 3.4 Consensus size: 118
406 GGAGGTCACT
* * * *
416 AAACTGTCCAAAAATTCCGTTTTTACCTTCGAACTTCCAAAAATTCAATTTTT-ACCCTCTAACT
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTATAACT
** *
480 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
65 TCCAAAAATTCCATTTACACCCTCGAACTTCTAAAAATTCCATTTTTGACCCCA
* * * ** *
534 AAACTTCCAAAAAATTCCATTTTTACCCCCGAACTTCTAAGAACCCCATTTTTGACCCTAAAACT
1 AAACTTCC-AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTATAACT
* *
599 TCCAAAAATTCCATTTACACCCTCGAACTTCTAAAAATTCCAATTTTAACCCCTA
65 TCCAAAAATTCCATTTACACCCTCGAACTTCTAAAAATTCCATTTTTGACCCC-A
* *
654 AAACTTCCAAAAATTCCATTTTTACCTTCGAACTTCCAAAAATTCCATTTTTGACCCTGTAAC-T
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTATAACTT
* * * * * * *
718 CCAAAAATTCCAGTTTTGC-CCCTAG-A-TATCTAAAAACTCTATTTTCGACCTCG
66 CCAAAAATTCCA--TTTACACCCTCGAACT-TCTAAAAATTCCATTTTTGACCCCA
771 AAAC-TCCAAAAATTCCATTTTTACCCTCGAA-TGTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTT
822 AACATCTAAT
Statistics
Matches: 248, Mismatches: 33, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
115 1 0.00
116 44 0.18
117 8 0.03
118 73 0.29
119 109 0.44
120 13 0.05
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (118 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTATAACTT
CCAAAAATTCCATTTACACCCTCGAACTTCTAAAAATTCCATTTTTGACCCCA
Done.