Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014324.1 Kokia drynarioides strain JFW-HI SEQ_129361, 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: 7547
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:4931 original size:9 final size:9
Alignment explanation
Indices: 4917--4965 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
4907 AAATTTCAAA
4917 AAAAAAGAG
1 AAAAAAGAG
*
4926 AAAAAATTA-
1 AAAAAA-GAG
4935 AAAAAA-ATG
1 AAAAAAGA-G
4944 AAAAAAGAG
1 AAAAAAGAG
4953 -AAAAAGAG
1 AAAAAAGAG
4961 AAAAA
1 AAAAA
4966 GAAAAGGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
7 1 0.03
8 8 0.24
9 23 0.68
10 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:4964 original size:27 final size:28
Alignment explanation
Indices: 4917--4983 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
4907 AAATTTCAAA
* *
4917 AAAAAAGAGAAAAAATTAAAAA-AAATG
1 AAAAAAGAGAAAAAATGAAAAAGAAAAG
4944 AAAAAAGAGAAAAAGA-GAAAAAGAAAAG
1 AAAAAAGAGAAAAA-ATGAAAAAGAAAAG
*
4972 GAAAAAGA-AAAA
1 AAAAAAGAGAAAA
4984 GAGGAGGTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 23 0.66
28 12 0.34
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (28 bp):
AAAAAAGAGAAAAAATGAAAAAGAAAAG
Found at i:4975 original size:20 final size:20
Alignment explanation
Indices: 4946--4983 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4936 AAAAAATGAA
4946 AAAAGAGAAAAAGAGAAAAAG
1 AAAAGAGAAAAAGA-AAAAAG
4967 AAAAG-GAAAAAGAAAAA
1 AAAAGAGAAAAAGAAAAA
4984 GAGGAGGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAGAGAAAAAGAAAAAAG
Found at i:4977 original size:12 final size:13
Alignment explanation
Indices: 4954--4982 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4944 AAAAAAGAGA
4954 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
4967 AAAAG-GAAAAAG
1 AAAAGAGAAAAAG
4979 AAAA
1 AAAA
4983 AGAGGAGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:6069 original size:50 final size:50
Alignment explanation
Indices: 5893--6068 Score: 217
Period size: 50 Copynumber: 3.5 Consensus size: 50
5883 TCTTTTACCT
* * *
5893 CTAAAGCTGTGGAGGTGAAAATTGAAACTGTAATGGAAAATCTCATACAC
1 CTAAAGCTGTAGAGGTGAAGATTGAAACTGTAATGGCAAATCTCATACAC
* * *
5943 CTAAAGCTGTGGAGGTGCAGATTGAAACCGTAATGGCAAATCTCATACAC
1 CTAAAGCTGTAGAGGTGAAGATTGAAACTGTAATGGCAAATCTCATACAC
* * * * * * * *
5993 CAAAAGCTTTAGAGGGGCAGAATGAAGCTGCAATGGCAAATCTCATTCAC
1 CTAAAGCTGTAGAGGTGAAGATTGAAACTGTAATGGCAAATCTCATACAC
*
6043 CTAAAGCTGTAGAGGAGAAGATTGAA
1 CTAAAGCTGTAGAGGTGAAGATTGAA
6069 GTCACAAGGA
Statistics
Matches: 108, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (50 bp):
CTAAAGCTGTAGAGGTGAAGATTGAAACTGTAATGGCAAATCTCATACAC
Found at i:6263 original size:80 final size:80
Alignment explanation
Indices: 6126--6935 Score: 958
Period size: 80 Copynumber: 10.2 Consensus size: 80
6116 TACAACCTCC
* * *
6126 AATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATATTTTACCTCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
6191 AGATTGAAGAAATCT
66 AGATTGAAGAAATCT
** * *
6206 AATCTTTTACCCTAATTAGAGGGCAACATTGAAGACTATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
6271 AGATTGAAAAAATCT
66 AGATTGAAGAAATCT
* * *
6286 AATCTTTTACCCTAACCAGAGGGCAACATTGAAGACCATCTGATCTTTTACCCCGATCATGGGAC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
6351 AAATTGAAGAAAT-T
66 AGATTGAAGAAATCT
* * *
6365 CAATCTTTTACCCTAACCAAAGGGCAAGATTAAAGACCATTCGATCTTTTACCCCGATCATGGGG
1 -AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGG
6430 CAGATTGAAGAAATCT
65 CAGATTGAAGAAATCT
* * * * * * *
6446 AATATTTTACCTTAATCAAAGGGAAAGATTGAAGACCATCCGATCTTTTACCCCAATCATGGGTC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
* *
6511 AAATTGAAGATAT-T
66 AGATTGAAGAAATCT
* * *
6525 CAATCTTTTATCCTAACCAGAGGACAAGATTGAAGACTATCCGATCTTTTACCCCGATCATGGGG
1 -AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGG
* *
6590 TAGATTGAAGAAATCC
65 CAGATTGAAGAAATCT
* * * * *
6606 AATCTTTTACCCTAACCAAAGGTCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGAGGT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
6671 AGATTGAAGAAATCC
66 AGATTGAAGAAATCT
* * * * * *
6686 AATCTTTTACCCTAACTAAAGGACAAGATTGAATACCATCCAATCTTTTACCCCAATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
6751 AGATTGAAGAAATCC
66 AGATTGAAGAAATCT
* * * * * * * *
6766 AATCTTTTACCAC-GACTATG-GGG-TAGATTGAAG-CAATTCAATCTTTTA-CCCTAAC-TAGA
1 AATCTTTTACC-CTAACCA-GAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCAT-G-
* * *
6825 GGACAGATTGAAGCAATCC
62 GGGCAGATTGAAGAAATCT
* * * *
6844 AATCTTTTACCCTAACTAGAGGGC-AGATTGAAGACCATCAGATCTCTTACCCCGACCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
6908 AGATTGAA-ATAAT-T
66 AGATTGAAGA-AATCT
6922 CAATCTTTTACCCT
1 -AATCTTTTACCCT
6936 TAAAACTATA
Statistics
Matches: 632, Mismatches: 82, Indels: 33
0.85 0.11 0.04
Matches are distributed among these distances:
76 1 0.00
77 8 0.01
78 57 0.09
79 47 0.07
80 516 0.82
81 3 0.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (80 bp):
AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
AGATTGAAGAAATCT
Done.