Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013591.1 Kokia drynarioides strain JFW-HI SEQ_128618, 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: 39153
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:15721 original size:33 final size:34
Alignment explanation
Indices: 15621--15699 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
15611 ACAACTCACT
* * *
15621 TTGTAAGTTTTGAAGCTCAAGAAATCAATATGTA
1 TTGTAAGTTTTAAAACTCAAGAAATTAATATGTA
15655 TTGTAAGTTTTAAAACTCAAGAAATTAATATGTA
1 TTGTAAGTTTTAAAACTCAAGAAATTAATATGTA
*
15689 TTTTAAGTTTT
1 TTGTAAGTTTT
15700 CCAACTGAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (34 bp):
TTGTAAGTTTTAAAACTCAAGAAATTAATATGTA
Found at i:18469 original size:19 final size:20
Alignment explanation
Indices: 18423--18509 Score: 81
Period size: 20 Copynumber: 4.3 Consensus size: 20
18413 TATTCTTTAC
* *
18423 AATTTTTTAAAATAAATTTTG
1 AATTTTTAAAAAT-TATTTTG
*
18444 AAATTTTTATAAA-TATTTTG
1 -AATTTTTAAAAATTATTTTG
*
18464 AA-TTTTAAAAATTATTTTT
1 AATTTTTAAAAATTATTTTG
*
18483 AATTTTTGAAAATTTATTTT-
1 AATTTTT-AAAAATTATTTTG
18503 AATTTTT
1 AATTTTT
18510 TTTGTGAGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
18 8 0.14
19 10 0.18
20 17 0.30
21 11 0.20
22 10 0.18
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:24793 original size:18 final size:17
Alignment explanation
Indices: 24747--24817 Score: 92
Period size: 17 Copynumber: 4.2 Consensus size: 17
24737 CATTTTTTTA
*
24747 AAATTTATTTAAAATTTT
1 AAATTTATTTTAAA-TTT
24765 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
24782 AAATTTATTTTTAATTT
1 AAATTTATTTTAAATTT
24799 AAA--TATTTTCAAATTT
1 AAATTTATTTT-AAATTT
24815 AAA
1 AAA
24818 ATTGCTAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
15 6 0.12
16 8 0.16
17 22 0.45
18 13 0.27
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:25544 original size:16 final size:18
Alignment explanation
Indices: 25523--25559 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
25513 AGTGATAAGT
25523 ATTAAT-AG-TAATATTA
1 ATTAATCAGATAATATTA
25539 ATTAATCAGAATAATATTA
1 ATTAATCAG-ATAATATTA
25558 AT
1 AT
25560 AATGGACGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
19 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTAATCAGATAATATTA
Found at i:26812 original size:30 final size:28
Alignment explanation
Indices: 26759--27169 Score: 249
Period size: 30 Copynumber: 14.1 Consensus size: 28
26749 AAAATTACCA
26759 TTTTACCCCCGAA-CTTCCAAAAATCCTAT
1 TTTTA-CCCCGAACCTTCCAAAAATCC-AT
* *
26788 TTTTGACCTCGAACCTTTCAAAAATTACCA-
1 TTTT-ACCCCGAACCTTCCAAAAA-T-CCAT
26818 TTTTACCCCCGAA-CTTCCAAAAATCCCAT
1 TTTTA-CCCCGAACCTTCCAAAAAT-CCAT
* *
26847 TTTTGACCTCGAACCTTTCAAAAATTACCA-
1 TTTT-ACCCCGAACCTTCCAAAAA-T-CCAT
*
26877 TTTTATCCTCGAA-CTTCCAAAAATCCCAT
1 TTTTA-CCCCGAACCTTCCAAAAAT-CCAT
** *
26906 TTTTGGCCCG-AGC-T--AAAAATTACCA-
1 TTTTACCCCGAACCTTCCAAAAA-T-CCAT
* *
26931 TTTTACCCCCAAACTTCCAAAAATCCTAT
1 TTTTACCCCGAACCTTCCAAAAATCC-AT
*
26960 TTTTAACCCCGAACCTTCTAAAAATTTCCA-
1 TTTT-ACCCCGAACCTTCCAAAAA--TCCAT
*
26990 TTTTACCCTC-AAACTTCCAAAAATCCCAT
1 TTTTACCC-CGAACCTTCCAAAAAT-CCAT
* *
27019 TTTTGACCCCGAACCTTTCAAAAAT-TACT
1 TTTT-ACCCCGAACCTTCCAAAAATCCA-T
* *
27048 ATTTTACCCCTAAACTTCCAAAAATCCCAT
1 -TTTTACCCCGAACCTTCCAAAAAT-CCAT
*
27078 TTTTGACCCCGAACCTTTCAAAAATTACCA-
1 TTTT-ACCCCGAACCTTCCAAAAA-T-CCAT
*
27108 TTTTACCCCCGGA-CTTCCAAAAATCCCAT
1 TTTTA-CCCCGAACCTTCCAAAAAT-CCAT
* * *
27137 TTTTGACTCCGAACCCTCCAAAACTACCAT
1 TTTT-ACCCCGAACCTTCCAAAAAT-CCAT
27167 TTT
1 TTT
27170 GCCCCCGTGC
Statistics
Matches: 303, Mismatches: 42, Indels: 73
0.72 0.10 0.17
Matches are distributed among these distances:
25 12 0.04
26 6 0.02
27 6 0.02
28 22 0.07
29 114 0.38
30 126 0.42
31 12 0.04
32 5 0.02
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (28 bp):
TTTTACCCCGAACCTTCCAAAAATCCAT
Found at i:26840 original size:59 final size:59
Alignment explanation
Indices: 26742--27176 Score: 605
Period size: 59 Copynumber: 7.5 Consensus size: 59
26732 GGTCCCTAAA
* *
26742 CTTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGACCTCGAAC
1 CTTTC-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
*
26802 CTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAC
1 CTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * * *
26861 CTTTCAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCATTTTTG-GCCCG-AG
1 CTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * *
26918 C--T-AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCTATTTTTAACCCCGAAC
1 CTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * *
26974 C-TTCTAAAAATTTCCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAAC
1 CTTTC-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* **
27033 CTTTCAAAAATTACTATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAC
1 CTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* *
27092 CTTTCAAAAATTACCATTTTACCCCCGGACTTCCAAAAATCCCATTTTTGACTCCGAAC
1 CTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * * *
27151 C-CTCCAAAACTACCATTTTGCCCCCG
1 CTTTCAAAAATTACCATTTTACCCCCG
27177 TGCATTAGAA
Statistics
Matches: 339, Mismatches: 30, Indels: 14
0.89 0.08 0.04
Matches are distributed among these distances:
54 40 0.12
55 5 0.01
56 2 0.01
57 3 0.01
58 24 0.07
59 257 0.76
60 8 0.02
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (59 bp):
CTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
Found at i:27034 original size:172 final size:174
Alignment explanation
Indices: 26746--27175 Score: 609
Period size: 172 Copynumber: 2.5 Consensus size: 174
26736 CCTAAACTTT
*
26746 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGACCTCGAACCTTTCAAAA
1 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGACCCCGAACCTTTCAAAA
* *
26811 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTTCAAAAATTACC
66 ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACC
* * * *
26876 ATTTTA-TCCTCGAACTTCCAAAAATCCCATTTTTG-GCCCG-AG
131 ATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* *
26918 CTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCTATTTTTAACCCCGAACC-TTCTAAA
1 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGACCCCGAACCTTTC-AAA
* *
26982 AATTTCCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTAC
65 AATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTAC
*
27047 TATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAC
130 CATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * * * *
27092 CTTTCAAAAATTACCATTTTACCCCCGGACTTCCAAAAATCCCATTTTTGACTCCGAACC-CTCC
1 C--T-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGACCCCGAACCTTTCA
* *
27156 AAAACTACCATTTTGCCCCC
63 AAAATTACCATTTTACCCCC
27176 GTGCATTAGA
Statistics
Matches: 228, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
171 3 0.01
172 147 0.64
173 7 0.03
174 2 0.01
176 17 0.07
177 52 0.23
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (174 bp):
CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGACCCCGAACCTTTCAAAA
ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACC
ATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAC
Done.