Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004135.1 Kokia drynarioides strain JFW-HI SEQ_117330, 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: 24651
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:6227 original size:7 final size:8
Alignment explanation
Indices: 6203--6247 Score: 74
Period size: 8 Copynumber: 5.6 Consensus size: 8
6193 AGTCATATAT
6203 ATAAAAATA
1 ATAAAAA-A
6212 ATAAAAAA
1 ATAAAAAA
6220 ATAAAAAA
1 ATAAAAAA
6228 AT-AAAAA
1 ATAAAAAA
6235 ATAAAAAA
1 ATAAAAAA
6243 ATAAA
1 ATAAA
6248 TTGAAAAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.20
8 21 0.60
9 7 0.20
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
ATAAAAAA
Found at i:6235 original size:15 final size:15
Alignment explanation
Indices: 6203--6247 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
6193 AGTCATATAT
6203 ATAAAAATAATAAAAAA
1 ATAAAAA-AAT-AAAAA
6220 ATAAAAAAATAAAAA
1 ATAAAAAAATAAAAA
6235 ATAAAAAAATAAA
1 ATAAAAAAATAAA
6248 TTGAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 18 0.64
16 3 0.11
17 7 0.25
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
ATAAAAAAATAAAAA
Found at i:10694 original size:53 final size:52
Alignment explanation
Indices: 10629--10917 Score: 307
Period size: 53 Copynumber: 5.5 Consensus size: 52
10619 GAAAATGTCC
* *
10629 GATGACTTTGTGTCATCGTGAGTTATATGAATCCTATCACGAATTAAAGGTCT
1 GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCA-GAATTAAAGGTCT
* *
10682 GATGACTCTGTGTCATCATGAGTTATATGAATCTTATCACGGATTAAAGGT-T
1 GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCA-GAATTAAAGGTCT
* * *
10734 AGATGACTCAGTGTCATCGTGAGTTATATGAATCCTATCATAGATTAAAGGTCT
1 -GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCAGA-ATTAAAGGTCT
* * * * *
10788 GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATTAGAAATTAAGGGTCC
1 GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCAG-AATTAAAGGTCT
* * * * * *
10841 GATGA--CTGTGTCCTCATGAGTTACA-GAAATCTTATCATGGATTAAAGCTCC
1 GATGACTCTGTGTCATCATGAGTTATATG-AATCCTATCA-GAATTAAAGGTCT
* *
10892 GATGACTTTGTGTCGTCATGAGTTAT
1 GATGACTCTGTGTCATCATGAGTTAT
10918 CACATGTGAA
Statistics
Matches: 203, Mismatches: 25, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
50 1 0.00
51 38 0.19
52 2 0.01
53 160 0.79
54 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (52 bp):
GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCAGAATTAAAGGTCT
Found at i:10764 original size:25 final size:25
Alignment explanation
Indices: 10731--10817 Score: 59
Period size: 25 Copynumber: 3.4 Consensus size: 25
10721 CGGATTAAAG
*
10731 GTTAGATGACTCAGTGTCATCGTGA
1 GTTATATGACTCAGTGTCATCGTGA
* * * * *
10756 GTTATATGAATC-CTATCATAGATTAAA
1 GTTATATGACTCAGTGTCATCG--T-GA
* *
10783 GGTCTGATGACTCAGTGTCATCGTGA
1 GTTAT-ATGACTCAGTGTCATCGTGA
10809 GTTATATGA
1 GTTATATGA
10818 ATCCTATTAG
Statistics
Matches: 42, Mismatches: 15, Indels: 10
0.63 0.22 0.15
Matches are distributed among these distances:
24 6 0.14
25 14 0.33
26 5 0.12
27 5 0.12
28 6 0.14
29 6 0.14
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (25 bp):
GTTATATGACTCAGTGTCATCGTGA
Found at i:10898 original size:157 final size:158
Alignment explanation
Indices: 10629--10917 Score: 395
Period size: 157 Copynumber: 1.8 Consensus size: 158
10619 GAAAATGTCC
** *
10629 GATGACTTTGTGTCATCGTGAGTTATATGAATCCTATCACGAATTAAAGGTCTGATGACTCTGTG
1 GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATCACGAATTAAAGGTCCGATGAC-CTGTG
* * * *
10694 TCATCATGAGTTATATGAATCTTATCACGGATTAAAGGTTAGATGACTCAGTGTCATCGTGAGTT
65 TCATCATGAGTTACATGAATCTTATCACGGATTAAAGCTCAGATGACTCAGTGTCATCATGAGTT
10759 ATATGAATCCTATCATAGATTAAAGGTCT
130 ATATGAATCCTATCATAGATTAAAGGTCT
* *
10788 GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATTA-GAAATTAAGGGTCCGATGA-CTGTG
1 GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATCACG-AATTAAAGGTCCGATGACCTGTG
* * * ** *
10851 TCCTCATGAGTTACA-GAAATCTTATCATGGATTAAAGCTCCGATGACTTTGTGTCGTCATGAGT
65 TCATCATGAGTTACATG-AATCTTATCACGGATTAAAGCTCAGATGACTCAGTGTCATCATGAGT
10915 TAT
129 TAT
10918 CACATGTGAA
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
156 1 0.01
157 60 0.53
158 1 0.01
159 51 0.45
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (158 bp):
GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATCACGAATTAAAGGTCCGATGACCTGTGT
CATCATGAGTTACATGAATCTTATCACGGATTAAAGCTCAGATGACTCAGTGTCATCATGAGTTA
TATGAATCCTATCATAGATTAAAGGTCT
Found at i:11478 original size:24 final size:25
Alignment explanation
Indices: 11451--11498 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
11441 GTTGATTAGT
*
11451 AAGTATCGGTAG-TTCTGTACTTGA
1 AAGTATCGATAGATTCTGTACTTGA
*
11475 AAGTATCGATAGATTTTGTACTTG
1 AAGTATCGATAGATTCTGTACTTG
11499 TATCGGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (25 bp):
AAGTATCGATAGATTCTGTACTTGA
Found at i:13487 original size:18 final size:17
Alignment explanation
Indices: 13464--13497 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13454 AAAATGAGTG
13464 CAGTGAAAATATAAAATC
1 CAGTGAAAATA-AAAATC
*
13482 CAGTGACAATAAAAAT
1 CAGTGAAAATAAAAAT
13498 GCAAAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (17 bp):
CAGTGAAAATAAAAATC
Done.