Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009364.1 Kokia drynarioides strain JFW-HI SEQ_124071, 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: 35503
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6900 original size:52 final size:51
Alignment explanation
Indices: 6835--7015 Score: 197
Period size: 52 Copynumber: 3.5 Consensus size: 51
6825 TGATGAGTAA
* *
6835 GTGTCATCGTGAGTAAATGAATCCTTTACTGATTACGAGGTCCGATAACTTT
1 GTGTCATCGTGAGTATATGAATCCTTTACTGATTA-GAGGTCCGATGACTTT
* * *
6887 GTGTCATCATGAGTATATGAAATCCTTTA-TGGATTTAAAGGTCCGATGA-TTAA
1 GTGTCATCGTGAGTATATG-AATCCTTTACT-GA-TTAGAGGTCCGATGACTT-T
* * *
6940 GTGTCATCGTGAGTATATGGATCCTTTAC-GAATTAAGAGGTTCGATGACTCT
1 GTGTCATCGTGAGTATATGAATCCTTTACTG-ATT-AGAGGTCCGATGACTTT
*
6992 GTGTCATCGTGAGTATACGAATCC
1 GTGTCATCGTGAGTATATGAATCC
7016 CTCGTGGATT
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
51 3 0.03
52 62 0.57
53 40 0.37
54 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (51 bp):
GTGTCATCGTGAGTATATGAATCCTTTACTGATTAGAGGTCCGATGACTTT
Found at i:7005 original size:105 final size:105
Alignment explanation
Indices: 6818--7008 Score: 285
Period size: 105 Copynumber: 1.8 Consensus size: 105
6808 TAAATGAAAA
* *
6818 AAAGGTCTGATGAGTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTACGAGGTCCGATAA
1 AAAGGTCCGATGAGTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTAAGAGGTCCGATAA
*
6883 CTTTGTGTCATCATGAGTATATGAAATCCTTTATGGATTT
66 CTCTGTGTCATCATGAGTATATGAAATCCTTTATGGATTT
* * * * *
6923 AAAGGTCCGATGATTAAGTGTCATCGTGAGTATATGGATCCTTTAC-GAATTAAGAGGTTCGATG
1 AAAGGTCCGATGAGTAAGTGTCATCGTGAGTAAATGAATCCTTTACTG-ATTAAGAGGTCCGATA
*
6987 ACTCTGTGTCATCGTGAGTATA
65 ACTCTGTGTCATCATGAGTATA
7009 CGAATCCCTC
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
104 1 0.01
105 75 0.99
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (105 bp):
AAAGGTCCGATGAGTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTAAGAGGTCCGATAA
CTCTGTGTCATCATGAGTATATGAAATCCTTTATGGATTT
Found at i:12929 original size:53 final size:51
Alignment explanation
Indices: 12837--13073 Score: 208
Period size: 52 Copynumber: 4.5 Consensus size: 51
12827 GAGTCTAATA
* * *
12837 ACTAAGTGTCATCGTGAGTAAATGAATCTTTTTACGGATTATGAGGTCCAATG
1 ACTATGTGTCATCGTGAGTATATGAATC--TTTACGGATTATGAGGTCCGATG
* * * * *
12890 ACTCTGTGTCATTGTGAGTATATGAAATGCTTTATGGATT-TAAAGGTCTGATG
1 ACTATGTGTCATCGTGAGTATATG-AAT-CTTTACGGATTAT-GAGGTCCGATG
* * * *
12943 ATTAAGTGTCATCGTGAGTATATGGATCCTTTACGGATTAAGAGGTCCGATG
1 ACTATGTGTCATCGTGAGTATATGAAT-CTTTACGGATTATGAGGTCCGATG
* * ** * *
12995 ACTTTGTGTCATCGTGAGTATACGAATCCCT-CGTGGATTATAAGGTCCGCTG
1 ACTATGTGTCATCGTGAGTATATGAATCTTTAC--GGATTATGAGGTCCGATG
* *
13047 GCTATGTGTCATCGTGTGTATATGAAT
1 ACTATGTGTCATCGTGAGTATATGAAT
13074 GAAGTGAAAT
Statistics
Matches: 146, Mismatches: 32, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
50 1 0.01
51 2 0.01
52 82 0.56
53 57 0.39
54 3 0.02
55 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (51 bp):
ACTATGTGTCATCGTGAGTATATGAATCTTTACGGATTATGAGGTCCGATG
Found at i:29615 original size:34 final size:34
Alignment explanation
Indices: 29576--29642 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
29566 TTTCATCTCT
*
29576 CTTGACTTTTAAT-TTTTCATCTTCTTTAACTTTC
1 CTTGACTTTTAATCTTTT-ATCTTCCTTAACTTTC
29610 CTTGACTTTTAATCTTTTATCTTCCTTAACTTT
1 CTTGACTTTTAATCTTTTATCTTCCTTAACTTT
29643 TCATATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.58
Consensus pattern (34 bp):
CTTGACTTTTAATCTTTTATCTTCCTTAACTTTC
Found at i:29625 original size:24 final size:24
Alignment explanation
Indices: 29598--29643 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
29588 TTTTTCATCT
*
29598 TCTTTAA-CTTTCCTTGACTTTTAA
1 TCTTTAATC-TTCCTTAACTTTTAA
*
29622 TCTTTTATCTTCCTTAACTTTT
1 TCTTTAATCTTCCTTAACTTTT
29644 CATATTCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.17, C:0.22, G:0.02, T:0.59
Consensus pattern (24 bp):
TCTTTAATCTTCCTTAACTTTTAA
Found at i:34551 original size:6 final size:6
Alignment explanation
Indices: 34517--34578 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
34507 TAATAGGGAT
* * * *
34517 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*
34564 TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTT
34579 TGATCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 40 0.85
7 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Done.