Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001357.1 Kokia drynarioides strain JFW-HI SEQ_112808, 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: 32001
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:8658 original size:6 final size:6
Alignment explanation
Indices: 8643--8683 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
8633 TGAGACAGCG
* *
8643 AGAGAT AGAGAA AGAGAA AGAGAA AGGGAA AGAGAA AGAGA
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGA
8684 GCAACGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (6 bp):
AGAGAA
Found at i:18553 original size:21 final size:21
Alignment explanation
Indices: 18532--18571 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
18522 TTAAATTTTA
18532 AAATATGAAAAA-TAAAAATT
1 AAATATGAAAAAGTAAAAATT
* *
18552 AAATTTTAAAAAGTAAAAAT
1 AAATATGAAAAAGTAAAAAT
18572 ATAAGGACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
AAATATGAAAAAGTAAAAATT
Found at i:28402 original size:20 final size:20
Alignment explanation
Indices: 28377--28416 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28367 AATGATTTCT
*
28377 GAAAAA-TAATTTATTTTTTA
1 GAAAAATTAATAT-TTTTTTA
28397 GAAAAATTAATATTTTTTTA
1 GAAAAATTAATATTTTTTTA
28417 TTATTTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
GAAAAATTAATATTTTTTTA
Found at i:28494 original size:15 final size:15
Alignment explanation
Indices: 28468--28500 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
28458 TAGATTTCTT
28468 AAAATTTTTTC-ATA
1 AAAATTTTTTCAATA
28482 AAAATTGTTTTCAATA
1 AAAATT-TTTTCAATA
28498 AAA
1 AAA
28501 CAAACATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 5 0.29
16 6 0.35
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
AAAATTTTTTCAATA
Found at i:28872 original size:15 final size:15
Alignment explanation
Indices: 28852--28903 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
28842 ACTACAAAAC
28852 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
28867 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
28886 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
28901 ATT
1 ATT
28904 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:28889 original size:19 final size:19
Alignment explanation
Indices: 28865--28901 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28855 TATTATTAAT
*
28865 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
28884 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
28902 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:29336 original size:90 final size:89
Alignment explanation
Indices: 29142--29336 Score: 241
Period size: 90 Copynumber: 2.2 Consensus size: 89
29132 TTAAGGGTGT
* * * *
29142 AAAAAGCCCTCAAACTTTTTCAAAAGAAGCAATTAAGCCATTGCTTTTAGTTTGCACTCACTTGG
1 AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCACTGCTTTTAGTTTACACTCAATTGG
*
29207 ATACTTAAACTTCCAAAATACATC
66 ATACTTAAACTTCCAAAATACATA
* * *
29231 AAAAAGACTCACAAACTTTTTCAAAAAAAGCAATTAAGACC-CTGCTTTTATTTTACACTCAATT
1 AAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATTAAG-CCACTGCTTTTAGTTTACACTCAATT
* * *
29295 AGG-TACTTAAACTTTCAAAGTGCATAA
64 -GGATACTTAAACTTCCAAAATACAT-A
29322 AAAAAGCCCTCAAAC
1 AAAAAGCCCTCAAAC
29337 ATAAAAAAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
89 6 0.07
90 73 0.82
91 10 0.11
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.29
Consensus pattern (89 bp):
AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCACTGCTTTTAGTTTACACTCAATTGG
ATACTTAAACTTCCAAAATACATA
Found at i:29522 original size:8 final size:9
Alignment explanation
Indices: 29499--29523 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29489 ATTTTTTTTT
29499 AATTTTTAA
1 AATTTTTAA
29508 AATTTTTAA
1 AATTTTTAA
29517 AATTTTT
1 AATTTTT
29524 TATTAACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
AATTTTTAA
Found at i:29868 original size:35 final size:35
Alignment explanation
Indices: 29828--29896 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
29818 CCAGTATAGA
*
29828 AAAAAAAACCAAGTTATGTAAGAATTTTTTTTTTTC
1 AAAAAAAA-CAAGTCATGTAAGAATTTTTTTTTTTC
**
29864 AAAAAAAAGGAGTCATGTAAGAATTTTTTTTTT
1 AAAAAAAACAAGTCATGTAAGAATTTTTTTTTT
29897 CATCAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 22 0.73
36 8 0.27
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.41
Consensus pattern (35 bp):
AAAAAAAACAAGTCATGTAAGAATTTTTTTTTTTC
Found at i:30691 original size:23 final size:22
Alignment explanation
Indices: 30665--30763 Score: 90
Period size: 23 Copynumber: 4.4 Consensus size: 22
30655 TGTTGGGAAA
*
30665 CAGTAAGCACATACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
*
30687 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* * * *
30710 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGC-AAT
* * *
30733 CAGTAGGCACACAAAGTGCGAAA
1 CAGTAAGCACACACAGTGC-AAT
30756 CAGTAAGC
1 CAGTAAGC
30764 GCGCTAGCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.25
23 48 0.75
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.13
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:30864 original size:24 final size:26
Alignment explanation
Indices: 30826--30873 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
30816 TCTACATGGA
30826 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
30852 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
30874 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
Done.