Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010520.1 Kokia drynarioides strain JFW-HI SEQ_125432, 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: 31377
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3445 original size:6 final size:6
Alignment explanation
Indices: 3434--3467 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
3424 AGCACACACA
3434 TAAAAT TAAAAT TAAAAT TAAAA- TAAAAT ATAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT -TAAA
3468 CTAAAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 17 0.65
7 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
TAAAAT
Found at i:3451 original size:12 final size:11
Alignment explanation
Indices: 3433--3473 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
3423 AAGCACACAC
3433 ATAAAATTAAA
1 ATAAAATTAAA
3444 ATTAAAATTAAA
1 A-TAAAATTAAA
3456 ATAAAATATAAA
1 ATAAAAT-TAAA
*
3468 CTAAAA
1 ATAAAA
3474 ATTCACATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.26
12 20 0.74
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAAATTAAA
Found at i:3474 original size:18 final size:17
Alignment explanation
Indices: 3433--3475 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3423 AAGCACACAC
*
3433 ATAAAATTAAAATTAAA
1 ATAAAAATAAAATTAAA
*
3450 ATTAAAATAAAATATAAA
1 ATAAAAATAAAAT-TAAA
*
3468 CTAAAAAT
1 ATAAAAAT
3476 TCACATATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATAAAATTAAA
Found at i:9891 original size:22 final size:22
Alignment explanation
Indices: 9847--9894 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
9837 TTTTGAATAG
*
9847 TTTAATTTTTTTTTTTATGTTCT
1 TTTAATTTTTTTTTTCA-GTTCT
9870 TTTAACTTTTTTTTTTCA-TTCT
1 TTTAA-TTTTTTTTTTCAGTTCT
9892 TTT
1 TTT
9895 TTATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 5 0.22
24 11 0.48
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTAATTTTTTTTTTCAGTTCT
Found at i:12006 original size:83 final size:83
Alignment explanation
Indices: 11730--11980 Score: 502
Period size: 83 Copynumber: 3.0 Consensus size: 83
11720 TTTACTATCA
11730 ACTTAGATAATTTTAATGATTATTGAAAGTGGAGGAAAATGGGATAGAAGAAGGGTGGTTGGACG
1 ACTTAGATAATTTTAATGATTATTGAAAGTGGAGGAAAATGGGATAGAAGAAGGGTGGTTGGACG
11795 GTAATAACAAGGTTTCGG
66 GTAATAACAAGGTTTCGG
11813 ACTTAGATAATTTTAATGATTATTGAAAGTGGAGGAAAATGGGATAGAAGAAGGGTGGTTGGACG
1 ACTTAGATAATTTTAATGATTATTGAAAGTGGAGGAAAATGGGATAGAAGAAGGGTGGTTGGACG
11878 GTAATAACAAGGTTTCGG
66 GTAATAACAAGGTTTCGG
11896 ACTTAGATAATTTTAATGATTATTGAAAGTGGAGGAAAATGGGATAGAAGAAGGGTGGTTGGACG
1 ACTTAGATAATTTTAATGATTATTGAAAGTGGAGGAAAATGGGATAGAAGAAGGGTGGTTGGACG
11961 GTAATAACAAGGTTTCGG
66 GTAATAACAAGGTTTCGG
11979 AC
1 AC
11981 AATGATGTTA
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 168 1.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.27
Consensus pattern (83 bp):
ACTTAGATAATTTTAATGATTATTGAAAGTGGAGGAAAATGGGATAGAAGAAGGGTGGTTGGACG
GTAATAACAAGGTTTCGG
Found at i:13886 original size:35 final size:35
Alignment explanation
Indices: 13840--13910 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
13830 AATTATGATA
13840 TAAATTGGATTATTCTTTGTATAAGCCAAGTTGGT
1 TAAATTGGATTATTCTTTGTATAAGCCAAGTTGGT
13875 TAAATTGGATTATTCTTTGTATAAGCCAAGTTGGT
1 TAAATTGGATTATTCTTTGTATAAGCCAAGTTGGT
13910 T
1 T
13911 TTATGATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (35 bp):
TAAATTGGATTATTCTTTGTATAAGCCAAGTTGGT
Found at i:24336 original size:25 final size:25
Alignment explanation
Indices: 24303--24355 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
24293 TTTTTAAAAG
*
24303 TTTAAAAA-TATATTTTTTATACTT
1 TTTAAAAATTATATTTTTAATACTT
* *
24327 TTTAATAAATTTTATTTTTAATAGTT
1 TTTAA-AAATTATATTTTTAATACTT
24353 TTT
1 TTT
24356 TAAATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
25 3 0.12
26 16 0.67
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTAAAAATTATATTTTTAATACTT
Found at i:24354 original size:26 final size:24
Alignment explanation
Indices: 24313--24362 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
24303 TTTAAAAATA
*
24313 TATTTTTTATACTTTTTAATAAATTT
1 TATTTTTAATACTTTTT--TAAATTT
*
24339 TATTTTTAATAGTTTTTTAAATTT
1 TATTTTTAATACTTTTTTAAATTT
24363 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
26 15 0.68
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTTTTAATACTTTTTTAAATTT
Found at i:26412 original size:2 final size:2
Alignment explanation
Indices: 26405--26429 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26395 TTATTCCTTG
26405 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
26430 TTTTGCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30176 original size:114 final size:114
Alignment explanation
Indices: 29976--30201 Score: 407
Period size: 114 Copynumber: 2.0 Consensus size: 114
29966 GTATTACTAT
* *
29976 AATTCAAATTATAAATAGCCAAATAAATTTCACATAATCAATCATATAATAAATGAACACATATT
1 AATTCAAATTATAAATAACCAAATAAATTTCACATAATCAACCATATAATAAATGAACACATATT
30041 ATCTTAATTTATACACCACTTTCATTCCATATCAATATAAAATCAATAG
66 ATCTTAATTTATACACCACTTTCATTCCATATCAATATAAAATCAATAG
*
30090 AATTCAAATTATAAATAACCAAATAAATTTCACATAATCAACCATATAATACATGAACACATATT
1 AATTCAAATTATAAATAACCAAATAAATTTCACATAATCAACCATATAATAAATGAACACATATT
* *
30155 ATCTTAATTTATACACCACTTTCATTCTATATCAATATCAAATCAAT
66 ATCTTAATTTATACACCACTTTCATTCCATATCAATATAAAATCAAT
30202 TTAACCATTT
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (114 bp):
AATTCAAATTATAAATAACCAAATAAATTTCACATAATCAACCATATAATAAATGAACACATATT
ATCTTAATTTATACACCACTTTCATTCCATATCAATATAAAATCAATAG
Found at i:30864 original size:17 final size:18
Alignment explanation
Indices: 30832--30865 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30822 AATTTCTATC
30832 CAATTTATACCCTAATTT
1 CAATTTATACCCTAATTT
*
30850 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
30866 AACTTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
CAATTTATACCCTAATTT
Done.