Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001236.1 Kokia drynarioides strain JFW-HI SEQ_112598, 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, 693
Length: 1155
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Found at i:359 original size:29 final size:29
Alignment explanation
Indices: 294--529 Score: 188
Period size: 29 Copynumber: 8.0 Consensus size: 29
284 GGAGATCCCT
* * *
294 AAACTATCCAAAAATTCTATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCC
325 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * * * *
354 ACACTTTCAATAATCCCATTTTTTTACCTCA
1 AAACTTCCAAAAATTCCA--TTTTTACCCCC
* *
385 AAACTTTCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
414 GAACTCCCAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
**
444 AAACTTCCAAAAATTCTGTTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * * * *
473 GAGCTT-CTAAAATCCCATTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCC
*
501 AAACATCCAAAAATTACCA-TTTTACCCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCCC
530 GAATGTTCGA
Statistics
Matches: 158, Mismatches: 42, Indels: 12
0.75 0.20 0.06
Matches are distributed among these distances:
28 19 0.12
29 68 0.43
30 42 0.27
31 29 0.18
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:404 original size:60 final size:57
Alignment explanation
Indices: 312--529 Score: 226
Period size: 60 Copynumber: 3.7 Consensus size: 57
302 CAAAAATTCT
* *
312 ATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCACACTTTCAATAATCCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCA-ACTTTCAA-AATCCC
* * * * **
371 ATTTTTTTACCTCAAAACTTTCAAAAATTCCATTTTTACCCTCGAACTCCCAAAAATCCC
1 A-TTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCC-CCAACTTTC-AAAATCCC
* ** *
431 ATTTTTGACCCCGAAACTTCCAAAAATTCTGTTTTTACCCCCGAGC-TTCTAAAATCCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC-AACTTTC-AAAATCCC
*
489 A-TTTTGACCCCAAAACATCCAAAAATTACCA-TTTTACCCCC
1 ATTTTTGACCCCAAAACTTCCAAAAATT-CCATTTTTACCCCC
530 GAATGTTCGA
Statistics
Matches: 133, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
57 34 0.26
58 12 0.09
59 36 0.27
60 47 0.35
61 4 0.03
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.33
Consensus pattern (57 bp):
ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAACTTTCAAAATCCC
Found at i:789 original size:17 final size:17
Alignment explanation
Indices: 767--853 Score: 95
Period size: 17 Copynumber: 5.1 Consensus size: 17
757 CATACTCCCT
767 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
784 TTAAATTT-GTTTAAAA
1 TTAAATTTATTTTAAAA
*
800 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
* **
818 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAA
* *
835 TTAAAATTATTTTCAAA
1 TTAAATTTATTTTAAAA
852 TT
1 TT
854 TAAAATAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
16 7 0.12
17 45 0.78
18 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:804 original size:34 final size:34
Alignment explanation
Indices: 766--853 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
756 CCATACTCCC
*
766 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTAAAATTAAATTTAATTT-AAA
* *
800 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAAATTAAATTTAATTTAAA
* *
834 TTTAAAATTATTTTCAAATT
1 TTTAAATTTATTTTAAAATT
854 TAAAATAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 44 0.94
35 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAAATTAAATTTAATTTAAA
Found at i:814 original size:11 final size:11
Alignment explanation
Indices: 800--855 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
790 TTGTTTAAAA
800 TTTAAATTTAT
1 TTTAAATTTAT
*
811 TTTAAATTTAAA
1 TTTAAATTT-AT
*
823 TTT-AATTTAAG
1 TTTAAATTT-AT
*
834 TTTAAAATTAT
1 TTTAAATTTAT
845 TTTCAAATTTA
1 TTT-AAATTTA
856 AAATAAAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 23 0.62
12 14 0.38
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:819 original size:7 final size:6
Alignment explanation
Indices: 766--857 Score: 61
Period size: 6 Copynumber: 16.0 Consensus size: 6
756 CCATACTCCC
* * * *
766 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * *
811 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA ATT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
858 ATAAAACCTA
Statistics
Matches: 64, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
4 3 0.05
5 16 0.25
6 38 0.59
7 7 0.11
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Done.