Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013557.1 Kokia drynarioides strain JFW-HI SEQ_128583, 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: 8959
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:490 original size:39 final size:39
Alignment explanation
Indices: 447--547 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
437 GATGGCTGTA
* * *
447 ATCTGCCCCATGATCGGGGTAAGAGATTTGCTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAATGATG
*
486 ATCTGCCCCAGGCTCGGGGTATGAGATTTGCTAATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAATGATG
525 ATCTGCCCCAGGCTCGGGGTAAG
1 ATCTGCCCCAGGCTCGGGGTAAG
548 GGATCGGATG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.26
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAATGATG
Found at i:738 original size:39 final size:39
Alignment explanation
Indices: 684--768 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
674 GATGTAACTT
* * * *
684 GGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCG
1 GGGTAAGAGATTTGCTAAAGATGATCTGCCCCAAGCTCA
*
723 GGGTAAGAGATTTGCTAAAGATGATCTGCCTCAAGCTCA
1 GGGTAAGAGATTTGCTAAAGATGATCTGCCCCAAGCTCA
762 GGGTAAG
1 GGGTAAG
769 GGATCGGATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (39 bp):
GGGTAAGAGATTTGCTAAAGATGATCTGCCCCAAGCTCA
Found at i:846 original size:221 final size:221
Alignment explanation
Indices: 463--905 Score: 796
Period size: 221 Copynumber: 2.0 Consensus size: 221
453 CCCATGATCG
* *
463 GGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTATGAGATTTGCTAATGATGATC
1 GGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAAAGATGATC
* *
528 TGCCCCAGGCTCGGGGTAAGGGATCGGATGGCCACAATTTGCCCCAGGCTCGGGGTAAAAAATTG
66 TGCCCCAAGCTCAGGGTAAGGGATCGGATGGCCACAATTTGCCCCAGGCTCGGGGTAAAAAATTG
* * *
593 GCTGATGGTGATCTGCCTCAGGCTTGGGGTAAAAGATTGGATCTTCGATCTGCCTTTCTTGATTA
131 GCTGATGGTGATCTACCTCAGGCTCGGGGTAAAAGATCGGATCTTCGATCTGCCTTTCTTGATTA
658 AGGGTATATATGAAATGATGTAACTT
196 AGGGTATATATGAAATGATGTAACTT
684 GGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAAAGATGATC
1 GGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAAAGATGATC
* * *
749 TGCCTCAAGCTCAGGGTAAGGGATCGGATGGCCACAATTTGCCTCAGGCTTGGGGTAAAAAATTG
66 TGCCCCAAGCTCAGGGTAAGGGATCGGATGGCCACAATTTGCCCCAGGCTCGGGGTAAAAAATTG
814 GCTGATGGTGATCTACCTCAGGCTCGGGGTAAAAGATCGGATCTTCGATCTGCCTTTCTTGATTA
131 GCTGATGGTGATCTACCTCAGGCTCGGGGTAAAAGATCGGATCTTCGATCTGCCTTTCTTGATTA
879 AGGGTATATATGAAATGATGTAACTT
196 AGGGTATATATGAAATGATGTAACTT
905 G
1 G
906 AATCCAACTC
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
221 212 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (221 bp):
GGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAAAGATGATC
TGCCCCAAGCTCAGGGTAAGGGATCGGATGGCCACAATTTGCCCCAGGCTCGGGGTAAAAAATTG
GCTGATGGTGATCTACCTCAGGCTCGGGGTAAAAGATCGGATCTTCGATCTGCCTTTCTTGATTA
AGGGTATATATGAAATGATGTAACTT
Found at i:7294 original size:22 final size:22
Alignment explanation
Indices: 7268--7377 Score: 132
Period size: 22 Copynumber: 4.9 Consensus size: 22
7258 GCAACAGTAG
* *
7268 GCACACAAAGTGTTAAACAGAA
1 GCACACACAGTGCTAAACAGAA
7290 GCACACACAGTGCTAAACAGAA
1 GCACACACAGTGCTAAACAGAA
*
7312 GCACACACAGTGCTGAACAGAAA
1 GCACACACAGTGCTAAACAG-AA
* *
7335 GCACACACAGTGCTGAACAGAGG
1 GCACACACAGTGCTAAACAGA-A
*
7358 GCACA-AGACGTGCTAAACAG
1 GCACACACA-GTGCTAAACAG
7378 TAGGCGCGCT
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
22 42 0.53
23 37 0.47
ACGTcount: A:0.43, C:0.25, G:0.23, T:0.10
Consensus pattern (22 bp):
GCACACACAGTGCTAAACAGAA
Found at i:7339 original size:45 final size:44
Alignment explanation
Indices: 7268--7377 Score: 132
Period size: 45 Copynumber: 2.5 Consensus size: 44
7258 GCAACAGTAG
*
7268 GCACACAAAGTGTTAAACAGAAGCACACACAGTGCTAAACAGAA
1 GCACACAAAGTGCTAAACAGAAGCACACACAGTGCTAAACAGAA
* * * *
7312 GCACACACAGTGCTGAACAGAAAGCACACACAGTGCTGAACAGAGG
1 GCACACAAAGTGCTAAACAG-AAGCACACACAGTGCTAAACAGA-A
*
7358 GCACA-AGACGTGCTAAACAG
1 GCACACA-AAGTGCTAAACAG
7378 TAGGCGCGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
44 17 0.31
45 23 0.42
46 15 0.27
ACGTcount: A:0.43, C:0.25, G:0.23, T:0.10
Consensus pattern (44 bp):
GCACACAAAGTGCTAAACAGAAGCACACACAGTGCTAAACAGAA
Found at i:7483 original size:24 final size:26
Alignment explanation
Indices: 7445--7492 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
7435 TCTACATGGG
7445 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
7471 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
7493 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:8787 original size:40 final size:40
Alignment explanation
Indices: 8743--8823 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
8733 AACTCTTGTA
8743 GTACTTACAACACTTGTAGGTAATTTCTTCTCACTCCATG
1 GTACTTACAACACTTGTAGGTAATTTCTTCTCACTCCATG
8783 GTACTTACAACACTTGTAGGTAATTTCTTCTCACTCCATG
1 GTACTTACAACACTTGTAGGTAATTTCTTCTCACTCCATG
8823 G
1 G
8824 CTTTCTCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (40 bp):
GTACTTACAACACTTGTAGGTAATTTCTTCTCACTCCATG
Done.