Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004894.1 Kokia drynarioides strain JFW-HI SEQ_118582, 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: 12736
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:409 original size:29 final size:30
Alignment explanation
Indices: 326--420 Score: 129
Period size: 30 Copynumber: 3.2 Consensus size: 30
316 TCTGTTTACT
* * * *
326 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
356 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
* *
386 TTTTAAATTT-TTTTCTATTTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
415 TTTTAA
1 TTTTAA
421 TTATTATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 23 0.39
30 36 0.61
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTGTATA
Found at i:875 original size:60 final size:61
Alignment explanation
Indices: 800--967 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 61
790 TGCCGAGAAC
* **
800 AGGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTG-AATTTTTTTATCTGAAAA
1 AGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGAAATTTTTTTATCACAAAA
* * *
860 AGGGGGTGTCGGCCA-TGCAATGACCAACACC-CAAAAA--TGCAATTTTTTTTTCACAAAA
1 AGGGGGTGTCGGCCATTGC-ATGACCAACACCAAAAAAATTTGAAATTTTTTTATCACAAAA
* * *
918 A--GGGTGTCGACCATTGTATGATCAACA-CAAAAAAATTTTGAAATTTTTTT
1 AGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAA-TTTGAAATTTTTTT
968 CTCAAAGGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
55 1 0.01
56 25 0.27
57 4 0.04
58 16 0.18
59 19 0.21
60 26 0.29
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (61 bp):
AGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGAAATTTTTTTATCACAAAA
Found at i:952 original size:56 final size:56
Alignment explanation
Indices: 802--953 Score: 146
Period size: 56 Copynumber: 2.6 Consensus size: 56
792 CCGAGAACAG
* * **
802 GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAATTTTTTTATCTGAAAAA
1 GGGGTGTCGGCCATTGAATGACCAACA-CAAAAAAA--TGAATTTTTTTATCACAAAAA
** *
861 GGGGGTGTCGGCCA-TGCAATGACCAACACCCAAAAATGCAATTTTTTTTTCACAAAAA
1 -GGGGTGTCGGCCATTG-AATGACCAACACAAAAAAATG-AATTTTTTTATCACAAAAA
* * *
919 -GGGTGTCGACCATTGTATGATCAACACAAAAAAAT
1 GGGGTGTCGGCCATTGAATGACCAACACAAAAAAAT
954 TTTGAAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
56 27 0.35
57 4 0.05
58 16 0.21
59 8 0.10
60 22 0.29
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (56 bp):
GGGGTGTCGGCCATTGAATGACCAACACAAAAAAATGAATTTTTTTATCACAAAAA
Found at i:1044 original size:96 final size:93
Alignment explanation
Indices: 883--1063 Score: 272
Period size: 96 Copynumber: 1.9 Consensus size: 93
873 CATGCAATGA
* *
883 CCAACACCCAAAAATGCAATTTTTTTTTCACAAAAAGGGTGTCGACCATTGTATGATCAACACAA
1 CCAACACCCAAAAATGCAATTTTTTTTTCACAAAAAGGGTGTCGACCATTGCATGACCAACACAA
*
948 AAAAATTTTGAAATTTTTTTCTCAAAGG
66 AAAAAATTTGAAATTTTTTTCTCAAAGG
* * * *
976 CCAACACCCAAAAAATGTAATTTTTTTTTCTCAAAAAGGGAGTGTCGATCATTGCATGGCCAACA
1 CCAACACCC-AAAAATGCAATTTTTTTTTCACAAAAA-GG-GTGTCGACCATTGCATGACCAACA
1041 CAAAAAAAATTTGAAATTTTTTT
63 CAAAAAAAATTTGAAATTTTTTT
1064 TCTGAAAAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
93 9 0.12
94 25 0.32
95 2 0.03
96 42 0.54
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (93 bp):
CCAACACCCAAAAATGCAATTTTTTTTTCACAAAAAGGGTGTCGACCATTGCATGACCAACACAA
AAAAAATTTGAAATTTTTTTCTCAAAGG
Found at i:2601 original size:12 final size:12
Alignment explanation
Indices: 2586--2611 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2576 ATACACTTAA
2586 AAATATTAAAAC
1 AAATATTAAAAC
2598 AAATATTAAAAC
1 AAATATTAAAAC
2610 AA
1 AA
2612 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:2649 original size:41 final size:40
Alignment explanation
Indices: 2584--2667 Score: 114
Period size: 41 Copynumber: 2.1 Consensus size: 40
2574 AAATACACTT
*
2584 AAAAATATTAAAACAAATATTAAAACAACAAACAAATTAA
1 AAAAATATTAAAACAAATAGTAAAACAACAAACAAATTAA
* * * *
2624 AAAAGATATTAAAACAATTCGTAAAATAACAAACAAATTGA
1 AAAA-ATATTAAAACAAATAGTAAAACAACAAACAAATTAA
2665 AAA
1 AAA
2668 TACAATAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.67, C:0.10, G:0.04, T:0.20
Consensus pattern (40 bp):
AAAAATATTAAAACAAATAGTAAAACAACAAACAAATTAA
Found at i:2873 original size:23 final size:23
Alignment explanation
Indices: 2847--2908 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
2837 AAAACATCCA
* * *
2847 AAAACAGCACTAAAAATAGTACT
1 AAAACAGCACCAAAAACAGTACC
**
2870 AAAACAAAACCAAAAACAGTACC
1 AAAACAGCACCAAAAACAGTACC
*
2893 AAAACTGCACCAAAAA
1 AAAACAGCACCAAAAA
2909 ACATCAAATC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.61, C:0.23, G:0.06, T:0.10
Consensus pattern (23 bp):
AAAACAGCACCAAAAACAGTACC
Found at i:12431 original size:3 final size:3
Alignment explanation
Indices: 12423--12470 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
12413 CCTAAACTAC
12423 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12471 GGACATGCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.