Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012239.1 Kokia drynarioides strain JFW-HI SEQ_127240, 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: 12679
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:8029 original size:17 final size:17
Alignment explanation
Indices: 8009--8068 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
7999 TCCTTGACTT
8009 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
*
8026 TTAACC-TCC-CCTTGACC
1 TTAACCTTCCATCTT--CC
8043 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
*
8061 TCAACCTT
1 TTAACCTT
8069 TCATATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
15 3 0.09
16 3 0.09
17 15 0.43
18 8 0.23
19 3 0.09
20 3 0.09
ACGTcount: A:0.18, C:0.42, G:0.02, T:0.38
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:8047 original size:35 final size:35
Alignment explanation
Indices: 8000--8067 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
7990 CTTTCATCTT
* *
8000 CCTTGACTTTTAACCTTCCATCTTCCTTAACCTCC
1 CCTTGACCTTTAACCTTCCATCTTCCTCAACCTCC
8035 CCTTGACCTTTAACCTTCCATCTTCCTCAACCT
1 CCTTGACCTTTAACCTTCCATCTTCCTCAACCT
8068 TTCATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.18, C:0.41, G:0.03, T:0.38
Consensus pattern (35 bp):
CCTTGACCTTTAACCTTCCATCTTCCTCAACCTCC
Found at i:9268 original size:24 final size:24
Alignment explanation
Indices: 9222--9267 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
9212 ATAAAAACAT
9222 AAAAATAAAAAAAATATTTTTTTA
1 AAAAATAAAAAAAATATTTTTTTA
*
9246 AAAAAT-ACAAAAATATTTTTTT
1 AAAAATAAAAAAAATATTTTTTT
9268 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAAATAAAAAAAATATTTTTTTA
Found at i:9274 original size:23 final size:22
Alignment explanation
Indices: 9221--9281 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
9211 AATAAAAACA
*
9221 TAAAAATAAAAAAAATATTTTTT
1 TAAAAA-ATAAAAAATATTTTTT
9244 TAAAAAATACAAAAATATTTTTT
1 TAAAAAATA-AAAAATATTTTTT
***
9267 TTTTAAATAAAAAAT
1 TAAAAAATAAAAAAT
9282 TATAATTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 8 0.24
23 25 0.76
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAAAAATAAAAAATATTTTTT
Found at i:9882 original size:14 final size:14
Alignment explanation
Indices: 9865--9912 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
9855 TCATAAATAA
9865 AAAATTAAAAAATT
1 AAAATTAAAAAATT
9879 AAAATTAAAAAAATAT
1 AAAATT-AAAAAAT-T
*
9895 AAAA--AAAAAATC
1 AAAATTAAAAAATT
9907 AAAATT
1 AAAATT
9913 TAATGTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
12 4 0.14
13 7 0.24
14 6 0.21
15 7 0.24
16 5 0.17
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATTAAAAAATT
Found at i:9904 original size:22 final size:22
Alignment explanation
Indices: 9863--9910 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
9853 ATTCATAAAT
*
9863 AAAAAATTAAAAAATTAAAATTA
1 AAAAAATTAAAAAA-TAAAATCA
9886 AAAAAATATAAAAAA-AAAATCA
1 AAAAAAT-TAAAAAATAAAATCA
9908 AAA
1 AAA
9911 TTTAATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
23 7 0.30
24 7 0.30
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAAAATTAAAAAATAAAATCA
Found at i:12616 original size:27 final size:27
Alignment explanation
Indices: 12586--12657 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
12576 ACCTGTGAGC
12586 AAAGAGAGAGGAGAGAGAAAG-GAGGAA-
1 AAAGAGAGAGGAGAGAGAAAGTGA--AAG
* * *
12613 AAAGA-ACTATGACAGAGAAAGTGAAAG
1 AAAGAGA-GAGGAGAGAGAAAGTGAAAG
12640 AAAGAGAGAGGAGAGAGA
1 AAAGAGAGAGGAGAGAGA
12658 GAAAAGAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
26 3 0.09
27 29 0.83
28 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.38, T:0.04
Consensus pattern (27 bp):
AAAGAGAGAGGAGAGAGAAAGTGAAAG
Done.