Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014217.1 Kokia drynarioides strain JFW-HI SEQ_129250, 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: 41527
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:705 original size:2 final size:2
Alignment explanation
Indices: 698--739 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
688 TTCCAACTTC
698 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
740 TAAATTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7492 original size:29 final size:29
Alignment explanation
Indices: 7450--7516 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
7440 GATGAAACAG
*
7450 CAAGGGTTTCTCTTACCTTAACCCATGGT
1 CAAGGGTTCCTCTTACCTTAACCCATGGT
7479 CAAGGGTTCCTCTTACCTTAACCCATGGT
1 CAAGGGTTCCTCTTACCTTAACCCATGGT
7508 CAAGGGTTC
1 CAAGGGTTC
7517 GATCTTTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.31
Consensus pattern (29 bp):
CAAGGGTTCCTCTTACCTTAACCCATGGT
Found at i:9388 original size:6 final size:6
Alignment explanation
Indices: 9377--9405 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9367 AAGGAGGAAT
9377 CTATGA CTATGA CTATGA CTATGA CTATG
1 CTATGA CTATGA CTATGA CTATGA CTATG
9406 GCTTTATCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (6 bp):
CTATGA
Found at i:18165 original size:21 final size:21
Alignment explanation
Indices: 18135--18187 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
18125 CTTATTAAAG
18135 TTAT-AAAATTATAAAAAATT
1 TTATAAAAATTATAAAAAATT
* * *
18155 TTATAAAAATTCTAATAAGTT
1 TTATAAAAATTATAAAAAATT
18176 TTA-AAAAATTAT
1 TTATAAAAATTAT
18188 TAAATTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTATAAAAATTATAAAAAATT
Found at i:18815 original size:18 final size:19
Alignment explanation
Indices: 18775--18820 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
18765 ATTCTATTAT
* * *
18775 TTTTATAATATTTTAATTT
1 TTTTATAATAATTTAAATA
18794 TTTTATAA-AATTTAAATA
1 TTTTATAATAATTTAAATA
18812 TTTTA-AATA
1 TTTTATAATA
18821 TGTTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 2 0.09
18 13 0.57
19 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATAATAATTTAAATA
Found at i:18815 original size:19 final size:19
Alignment explanation
Indices: 18772--18815 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
18762 ATAATTCTAT
* *
18772 TATTTTTATAATATTTTAA
1 TATTTTTATAAAATTTAAA
*
18791 TTTTTTTATAAAATTTAAA
1 TATTTTTATAAAATTTAAA
18810 TATTTT
1 TATTTT
18816 AAATATGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTTTATAAAATTTAAA
Found at i:37390 original size:17 final size:16
Alignment explanation
Indices: 37356--37393 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
37346 GATTCACATG
37356 TTAAAAAATTTTATTA
1 TTAAAAAATTTTATTA
37372 TTAAAAATATTATTA-TA
1 TTAAAAA-ATT-TTATTA
37389 TTAAA
1 TTAAA
37394 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 10 0.50
18 3 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAAAATTTTATTA
Done.