Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008225.1 Kokia drynarioides strain JFW-HI SEQ_122889, 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: 7444
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:1831 original size:57 final size:56
Alignment explanation
Indices: 1717--1956 Score: 200
Period size: 57 Copynumber: 4.3 Consensus size: 56
1707 AGGGAAAAAT
* *** * * *
1717 AAAGATAGTGTAGGTCATTGGATGGCAATCAC-AAAAAAATATTTTTAAATCTAAA
1 AAAGATGGTGTAGGTCATTACTTGCCAAACACAAAAAAAATATTTTTAAATCTGAA
*
1772 AAAGATGGCGTAGGTCATTACTTGCCAAACATCAAAAAAAATATTTTTAAATCTGAA
1 AAAGATGGTGTAGGTCATTACTTGCCAAACA-CAAAAAAAATATTTTTAAATCTGAA
* *** * * ** **
1829 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAAA-A-AATT-AATCTGGG
1 AAAGATGGTGTAGGTCATTACTTGCCAAACACAAAAAAAATATTTTTAAATCTGAA
*** * * *
1882 AAAGATGGTGTACACCATTACTTGCCAAACACCAAAAAAATATTTTTAAATTTGGA
1 AAAGATGGTGTAGGTCATTACTTGCCAAACACAAAAAAAATATTTTTAAATCTGAA
* * *
1938 AAAGGTGATGTAGATCATT
1 AAAGATGGTGTAGGTCATT
1957 GAGTGGCAAA
Statistics
Matches: 143, Mismatches: 37, Indels: 9
0.76 0.20 0.05
Matches are distributed among these distances:
53 36 0.25
54 3 0.02
55 27 0.19
56 31 0.22
57 46 0.32
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.28
Consensus pattern (56 bp):
AAAGATGGTGTAGGTCATTACTTGCCAAACACAAAAAAAATATTTTTAAATCTGAA
Found at i:1921 original size:112 final size:111
Alignment explanation
Indices: 1717--1941 Score: 310
Period size: 112 Copynumber: 2.0 Consensus size: 111
1707 AGGGAAAAAT
***
1717 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAATATTTTTAAATCTAAAAAAGATGGCG
1 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAATAAAATTAAATCTAAAAAAGATGGCG
*** *
1782 TAGGTCATTACTTGCCAAACATCAAAAAAAATATTTTTAAATCTGAA
66 TACACCATTACTTGCCAAACA-CCAAAAAAATATTTTTAAATCTGAA
*** *
1829 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAA-AAAATT-AATCTGGGAAAGATGGTG
1 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAATAAAATTAAATCTAAAAAAGATGGCG
* *
1892 TACACCATTACTTGCCAAACACCAAAAAAATATTTTTAAATTTGGA
66 TACACCATTACTTGCCAAACACCAAAAAAATATTTTTAAATCTGAA
1938 AAAG
1 AAAG
1942 GTGATGTAGA
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
109 26 0.26
110 32 0.32
111 3 0.03
112 39 0.39
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (111 bp):
AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAATAAAATTAAATCTAAAAAAGATGGCG
TACACCATTACTTGCCAAACACCAAAAAAATATTTTTAAATCTGAA
Found at i:2075 original size:53 final size:53
Alignment explanation
Indices: 2018--2132 Score: 140
Period size: 55 Copynumber: 2.1 Consensus size: 53
2008 CATTGCTTGT
2018 CAAACATAAAAAAAAAATTAAATTTGAAAAAAATGGTGCAAGTCATTGGGTGG
1 CAAACATAAAAAAAAAATTAAATTTGAAAAAAATGGTGCAAGTCATTGGGTGG
* *** * * * *
2071 CAAACACCCAAAAAAATTTTTTAATTTGATAAAAGTGGTGTAAGTCATTGGGTGG
1 CAAACA--TAAAAAAAAAATTAAATTTGAAAAAAATGGTGCAAGTCATTGGGTGG
2126 CAAACAT
1 CAAACAT
2133 CCAAAAATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
53 6 0.12
55 45 0.88
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.26
Consensus pattern (53 bp):
CAAACATAAAAAAAAAATTAAATTTGAAAAAAATGGTGCAAGTCATTGGGTGG
Found at i:2110 original size:55 final size:56
Alignment explanation
Indices: 2038--2148 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 56
2028 AAAAAAATTA
2038 AATTTGAAAAAAATGGTGCAAGTCATTGGGTGGCAAACACCCAAAAA-AATTTTTT
1 AATTTGAAAAAAATGGTGCAAGTCATTGGGTGGCAAACACCCAAAAATAATTTTTT
* * * * *
2093 AATTTGATAAAAGTGGTGTAAGTCATTGGGTGGCAAACATCCAAAAATTATTTTTT
1 AATTTGAAAAAAATGGTGCAAGTCATTGGGTGGCAAACACCCAAAAATAATTTTTT
2149 TTTATTCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 43 0.86
56 7 0.14
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (56 bp):
AATTTGAAAAAAATGGTGCAAGTCATTGGGTGGCAAACACCCAAAAATAATTTTTT
Found at i:2406 original size:13 final size:13
Alignment explanation
Indices: 2388--2412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2378 TATAAGTATG
2388 GAAAACTTAAAAA
1 GAAAACTTAAAAA
2401 GAAAACTTAAAA
1 GAAAACTTAAAA
2413 TTTTTCATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (13 bp):
GAAAACTTAAAAA
Found at i:2623 original size:23 final size:23
Alignment explanation
Indices: 2584--2629 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2574 GTACATTCTA
*
2584 AAATTTTCTTTAAAAAAAGTTAG
1 AAATTTTCTTAAAAAAAAGTTAG
*
2607 AAATTTT-TTAAACAAAAATTTAG
1 AAATTTTCTTAAA-AAAAAGTTAG
2630 GTTGGGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (23 bp):
AAATTTTCTTAAAAAAAAGTTAG
Done.