Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009989.1 Kokia drynarioides strain JFW-HI SEQ_124744, 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: 7370
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Found at i:4895 original size:205 final size:205
Alignment explanation
Indices: 4537--5309 Score: 1289
Period size: 205 Copynumber: 3.8 Consensus size: 205
4527 GTGATTATCC
* *
4537 ACAAAAGACGCGGTCATCTTCCTGATGGGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGA
* * * *
4602 TGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAAACACTGAGAAGCATGTCGAAGCAATAGAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* * *
4667 GGTTAGCTTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGGGATACAAAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAA
4732 GCGAATTGAA
196 GCGAATTGAA
*
4742 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGA
*
4807 TGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* *
4872 GGTTAGCCTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAA
4937 GCGAATTGAA
196 GCGAATTGAA
4947 ACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGA
* * * *
5012 TGTGAGCAGATCTTCAAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAACAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* *
5077 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGTCCAAATTCGTCTTCTTGATGAGATACAGAA-A
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA-AAGA
*
5141 AACGAATTGAA
195 AGCGAATTGAA
* * *
5152 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGTAGAAGACCAAACCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGA
* * *
5217 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATAAGACACTGAGAAGTAGGTCGAAGCAAT-AGA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
5281 GGTTAGCTTCCTGATGAGATACTGAGAAG
131 GGTTAGCTTCCTGATGAGATACTGAGAAG
5310 AAGACTAAAT
Statistics
Matches: 533, Mismatches: 34, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
204 31 0.06
205 501 0.94
206 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (205 bp):
ACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGA
TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAA
GCGAATTGAA
Found at i:5453 original size:119 final size:119
Alignment explanation
Indices: 5169--5548 Score: 555
Period size: 119 Copynumber: 3.2 Consensus size: 119
5159 ACGCGGTCAT
* *
5169 CTTCCTGATGAGATACTGAGTAGAAGACCAAACCAAACCCACGCTCGATGTGAGCAAATCTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
* * *
5234 ACCCCAGCTTCCTGATAAGACACTGAGAAGTAGGTCGAAGCAAT-AGAGGTTAG
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* *
5287 CTTCCTGATGAGATACTGAGAAGAAGACTAAATCAAACCCACGCTCGATGTGAGCAAATCTTTGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
* * * * * *
5352 ACACTAGTTTCCTGATGAGACACTGAGAAACAGGTTGAAGCGATAAAAGGTTAG
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
5406 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
* * * * *
5471 ACCCCAACTTCTTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAATGGTTAG
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA-GGTTAG
* * *
5526 CTTCCCGATGAAATACTGGGAAG
1 CTTCCTGATGAGATACTGAGAAG
5549 TGAACCAAAA
Statistics
Matches: 231, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
118 97 0.42
119 108 0.47
120 26 0.11
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (119 bp):
CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
Found at i:6011 original size:6 final size:6
Alignment explanation
Indices: 5991--6064 Score: 55
Period size: 6 Copynumber: 12.7 Consensus size: 6
5981 ATTTTGAATA
* ** *
5991 TAAATT T-ATTT TAAATT TAAATT T-GTTT TAAAATT TAAATT T-AATA
1 TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT
* * *
6037 AAAATT TAGATT TATATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAA
6065 ACTTATTATA
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
5 10 0.20
6 38 0.75
7 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:6026 original size:18 final size:17
Alignment explanation
Indices: 5975--6064 Score: 99
Period size: 17 Copynumber: 5.2 Consensus size: 17
5965 ACTCATTCTA
* *
5975 AAATTTATTTTGAATAT
1 AAATTTATTTTAAATTT
5992 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
6009 AAATTTGTTTTAAAATTT
1 AAATTTATTTT-AAATTT
* **
6027 AAATTTAATAAAAATTT
1 AAATTTATTTTAAATTT
*
6044 AGATTTATATTTAAATTT
1 AAATTTAT-TTTAAATTT
6062 AAA
1 AAA
6065 ACTTATTATA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
17 37 0.63
18 22 0.37
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:6031 original size:35 final size:35
Alignment explanation
Indices: 5975--6064 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
5965 ACTCATTCTA
* * * **
5975 AAATTTAT-TTTGAATATAAATTTATTTTAAATTT
1 AAATTTATATTTAAATTTAAATTTAATAAAAATTT
*
6009 AAATTTGT-TTTAAAATTTAAATTTAATAAAAATTT
1 AAATTTATATTT-AAATTTAAATTTAATAAAAATTT
*
6044 AGATTTATATTTAAATTTAAA
1 AAATTTATATTTAAATTTAAA
6065 ACTTATTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
34 10 0.22
35 33 0.72
36 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (35 bp):
AAATTTATATTTAAATTTAAATTTAATAAAAATTT
Found at i:6805 original size:3 final size:3
Alignment explanation
Indices: 6791--6829 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
6781 GATCGTAAGT
*
6791 ATA ATA ATTA ATA ATA ATTA ATA ATA ATA TTA ATA ATA A
1 ATA ATA A-TA ATA ATA A-TA ATA ATA ATA ATA ATA ATA A
6830 AGTATTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:6806 original size:10 final size:10
Alignment explanation
Indices: 6791--6829 Score: 60
Period size: 10 Copynumber: 3.7 Consensus size: 10
6781 GATCGTAAGT
6791 ATAATAATTA
1 ATAATAATTA
6801 ATAATAATTA
1 ATAATAATTA
6811 ATAATAATATTA
1 ATAAT-A-ATTA
6823 ATAATAA
1 ATAATAA
6830 AGTATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 16 0.59
11 2 0.07
12 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATAATTA
Found at i:6837 original size:14 final size:14
Alignment explanation
Indices: 6807--6845 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
6797 ATTAATAATA
6807 ATTAATAAT-AA-T
1 ATTAATAATAAAGT
6819 ATTAATAATAAAGT
1 ATTAATAATAAAGT
*
6833 ATTAATAAAAAAG
1 ATTAATAATAAAG
6846 GAAAATTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.38
13 2 0.08
14 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (14 bp):
ATTAATAATAAAGT
Done.