Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012860.1 Kokia drynarioides strain JFW-HI SEQ_127874, 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: 42342
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6206 original size:36 final size:36
Alignment explanation
Indices: 6166--6238 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
6156 TACTCAAAGG
6166 TAATCTATTGATTCTTCTAATTAATTTAATATTTGT
1 TAATCTATTGATTCTTCTAATTAATTTAATATTTGT
6202 TAATCTATTGATTCTTCTAATTAATTTAATATTTGT
1 TAATCTATTGATTCTTCTAATTAATTTAATATTTGT
6238 T
1 T
6239 TTCACTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.56
Consensus pattern (36 bp):
TAATCTATTGATTCTTCTAATTAATTTAATATTTGT
Found at i:9605 original size:21 final size:20
Alignment explanation
Indices: 9565--9603 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
9555 AAGACAACAC
9565 AAAACCAAAATAAATAAAAT
1 AAAACCAAAATAAATAAAAT
9585 AAAATCCAAAA-AAATAAAA
1 AAAA-CCAAAATAAATAAAA
9604 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAACCAAAATAAATAAAAT
Found at i:9657 original size:18 final size:18
Alignment explanation
Indices: 9636--9682 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
9626 TTACAAAAAT
9636 ACCCATTTACACAAA-TTA
1 ACCCATTTAC-CAAACTTA
***
9654 ACCCAAAAACCAAACTTA
1 ACCCATTTACCAAACTTA
9672 ACCCATTTACC
1 ACCCATTTACC
9683 CTCACTAGCC
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (18 bp):
ACCCATTTACCAAACTTA
Found at i:10913 original size:14 final size:14
Alignment explanation
Indices: 10894--10923 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10884 AATCCTTCCC
*
10894 TTTTTATTTTTCTT
1 TTTTTATTTTTATT
10908 TTTTTATTTTTATT
1 TTTTTATTTTTATT
10922 TT
1 TT
10924 GCCCATACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:15062 original size:8 final size:8
Alignment explanation
Indices: 15049--15087 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
15039 CTTGAAACCC
15049 AAGAAAAA
1 AAGAAAAA
*
15057 AAGAAAGA
1 AAGAAAAA
15065 AAGAAAAAA
1 AAG-AAAAA
*
15074 AAGAAAAG
1 AAGAAAAA
15082 AAGAAA
1 AAGAAA
15088 GAGTCAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:15800 original size:10 final size:9
Alignment explanation
Indices: 15772--15873 Score: 75
Period size: 9 Copynumber: 11.4 Consensus size: 9
15762 AATTTCACCC
15772 AAAAAAAGA
1 AAAAAAAGA
*
15781 AAGAAAA-A
1 AAAAAAAGA
*
15789 AAATAAAGA
1 AAAAAAAGA
**
15798 AAAGGAAGA
1 AAAAAAAGA
15807 AAAAAGAAGA
1 AAAAA-AAGA
15817 AAGAAAAA-A
1 AA-AAAAAGA
*
15826 GAAAAAAGA
1 AAAAAAAGA
*
15835 AAAAGAA-A
1 AAAAAAAGA
* *
15843 AGAAAAAGG
1 AAAAAAAGA
*
15852 AAAAAAGGA
1 AAAAAAAGA
*
15861 AAAAAGAGA
1 AAAAAAAGA
15870 AAAA
1 AAAA
15874 GATGAAGTCG
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
8 17 0.24
9 42 0.60
10 8 0.11
11 3 0.04
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:15819 original size:7 final size:7
Alignment explanation
Indices: 15780--15875 Score: 101
Period size: 7 Copynumber: 13.7 Consensus size: 7
15770 CCAAAAAAAG
15780 AAAGAAA
1 AAAGAAA
*
15787 AAA-AAT
1 AAAGAAA
15793 AAAGAAA
1 AAAGAAA
15800 AGGAAGAAA
1 A--AAGAAA
*
15809 AAAGAAG
1 AAAGAAA
15816 AAAGAAA
1 AAAGAAA
15823 AAAGAAA
1 AAAGAAA
15830 AAAG-AA
1 AAAGAAA
15836 AAAG--A
1 AAAGAAA
15841 AAAGAAA
1 AAAGAAA
*
15848 AAGGAAA
1 AAAGAAA
15855 AAAGGAAA
1 AAA-GAAA
15863 AAAGAGAA
1 AAAGA-AA
15871 AAAGA
1 AAAGA
15876 TGAAGTCGAG
Statistics
Matches: 76, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
5 5 0.07
6 11 0.14
7 39 0.51
8 14 0.18
9 7 0.09
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (7 bp):
AAAGAAA
Found at i:15825 original size:47 final size:47
Alignment explanation
Indices: 15773--15875 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 47
15763 ATTTCACCCA
* *
15773 AAAAAAGAAAGAAA-AAAAA-TAAAG-AAAAGGAAGAAAAAAGAAGAAAG
1 AAAAAAGAAA-AAAGAAAAAGAAAAGAAAAAGG-A-AAAAAAGAAAAAAG
*
15820 AAAAAAGAAAAAAGAAAAAGAAAAGAAAAAGGAAAAAAGGAAAAAAG
1 AAAAAAGAAAAAAGAAAAAGAAAAGAAAAAGGAAAAAAAGAAAAAAG
15867 AGAAAAAGA
1 A-AAAAAGA
15876 TGAAGTCGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
46 3 0.06
47 28 0.57
48 12 0.24
49 6 0.12
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (47 bp):
AAAAAAGAAAAAAGAAAAAGAAAAGAAAAAGGAAAAAAAGAAAAAAG
Found at i:15855 original size:32 final size:32
Alignment explanation
Indices: 15772--15872 Score: 91
Period size: 36 Copynumber: 3.0 Consensus size: 32
15762 AATTTCACCC
*
15772 AAAAA-AAGAAAGAAAAAA-AATAAAGAAAAGGAAG
1 AAAAAGAA-AAAGAAAAAAGAAAAAAG-AAA--AAG
15806 AAAAAAGAAGAAAGAAAAAAGAAAAAAGAAAAAG
1 -AAAAAGAA-AAAGAAAAAAGAAAAAAGAAAAAG
15840 -AAAAGAAAAAGGAAAAAAGGAAAAAAGAGAAAA
1 AAAAAGAAAAA-GAAAAAA-GAAAAAAGA-AAAA
15873 AGATGAAGTC
Statistics
Matches: 60, Mismatches: 1, Indels: 11
0.83 0.01 0.15
Matches are distributed among these distances:
31 3 0.05
32 14 0.23
33 9 0.15
34 7 0.12
35 5 0.08
36 16 0.27
37 6 0.10
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (32 bp):
AAAAAGAAAAAGAAAAAAGAAAAAAGAAAAAG
Found at i:16939 original size:49 final size:49
Alignment explanation
Indices: 16886--17139 Score: 161
Period size: 49 Copynumber: 5.1 Consensus size: 49
16876 GAACAAGAAT
* * *
16886 GGGAAATATTGAAGCCACAACGACGAATCTAGTACCATGAAAATATAAA
1 GGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCATGAAAATATAAA
* * * * * * * * *
16935 GGGAAAGGTTGAGGTCGCAACGGCGAACCTTGTACCTTAAAAGATGTAAT
1 GGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCATGAAA-ATATAAA
* * * * *
16985 GAGAAGGATTGAGGCCGCAACGACGAATCCAATACCATGAAGATATAAA
1 GGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCATGAAAATATAAA
* * * * * * * ***
17034 GGGAAAGGTTGAGGTCGCAACGGCAAATCCT-GTACCTTAGAAGATGTGTT
1 GGGAAAGATTGAGGCCGCAACGACGAAT-CTAGTACCAT-GAAAATATAAA
* * * ** *
17084 GGTAAGGATTGAGGCCTCAACGGTGAATCT-GATACCATGAAAATATGAA
1 GGGAAAGATTGAGGCCGCAACGACGAATCTAG-TACCATGAAAATATAAA
17133 GGGAAAG
1 GGGAAAG
17140 GTTAAGGTAG
Statistics
Matches: 148, Mismatches: 53, Indels: 8
0.71 0.25 0.04
Matches are distributed among these distances:
49 79 0.53
50 69 0.47
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (49 bp):
GGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCATGAAAATATAAA
Found at i:17041 original size:99 final size:99
Alignment explanation
Indices: 16828--17749 Score: 771
Period size: 99 Copynumber: 9.3 Consensus size: 99
16818 GGAAACATAG
** * * * * * *
16828 AGATATAAAGGGAAAGGTTGAGGTCGCAATAGTAAACCTTGTACCTTAGAACAAG-AATGGGAAA
1 AGATATAAAGGGAAAGGTTGAGGTCGCAACGGCAAACCTTGTACCTTAAAAGATGTGATGGGAAG
* * * ** * *
16892 TATTGAAGCCACAACGACGAATCTAGTACCATGA
66 GATTGAGGCCGCAACGGTGAATCCAATACCATGA
* * * *
16926 AAATATAAAGGGAAAGGTTGAGGTCGCAACGGCGAACCTTGTACCTTAAAAGATGTAATGAGAAG
1 AGATATAAAGGGAAAGGTTGAGGTCGCAACGGCAAACCTTGTACCTTAAAAGATGTGATGGGAAG
**
16991 GATTGAGGCCGCAACGACGAATCCAATACCATGA
66 GATTGAGGCCGCAACGGTGAATCCAATACCATGA
* * *
17025 AGATATAAAGGGAAAGGTTGAGGTCGCAACGGCAAATCC-TGTACCTTAGAAGATGTGTTGGTAA
1 AGATATAAAGGGAAAGGTTGAGGTCGCAACGGCAAA-CCTTGTACCTTAAAAGATGTGATGGGAA
* **
17089 GGATTGAGGCCTCAACGGTGAATCTGATACCATGA
65 GGATTGAGGCCGCAACGGTGAATCCAATACCATGA
* * * * * *
17124 AAATATGAAGGGAAAGGTTAAGGTAGTAACGG-AGAACCCTGTACCTTAAAAGATGTGATGGGAA
1 AGATATAAAGGGAAAGGTTGAGGTCGCAACGGCA-AACCTTGTACCTTAAAAGATGTGATGGGAA
* * *
17188 GGATTGAGGCTGTAACGGTGAATCCGATACCATGA
65 GGATTGAGGCCGCAACGGTGAATCCAATACCATGA
* * * * * **
17223 ATATATGAAA-AGAAAGGTTGAGGCCGCAATGACAAA-CTCTGTACCTTAAAAGATGTGATTTGA
1 AGATAT-AAAGGGAAAGGTTGAGGTCGCAACGGCAAACCT-TGTACCTTAAAAGATGTGATGGGA
* * * * *
17286 AAGAATAAGGCCTCAACGGTGAATCCGATACCATGA
64 AGGATTGAGGCCGCAACGGTGAATCCAATACCATGA
* *
17322 AGATATGAAA-GGAAAAGTTGAGG-CTGCAACGGTAAACCCTT-TACCTTAAAAGATGTGATGGG
1 AGATAT-AAAGGGAAAGGTTGAGGTC-GCAACGGCAAA-CCTTGTACCTTAAAAGATGTGATGGG
*
17384 AAGGATTGAGGCCGCAACGGTGAATCCAGTACCATGA
63 AAGGATTGAGGCCGCAACGGTGAATCCAATACCATGA
* *** * * *
17421 AGATATAAAGGGAAATGTTGAGG-CTGCAACGGTGTACCCTGTGCCTTAAAAGATGTGATAGGAA
1 AGATATAAAGGGAAAGGTTGAGGTC-GCAACGGCAAACCTTGTACCTTAAAAGATGTGATGGGAA
**
17485 GGATTGAGGCCGCAACGGTGAATCCGGTACCATGA
65 GGATTGAGGCCGCAACGGTGAATCCAATACCATGA
* * ** * * * * *
17520 AGATATGAAGGGAAATGTTGAGACCGCAATGGCGAACC-TGATACCTT-AGAGACGTGATGGAAA
1 AGATATAAAGGGAAAGGTTGAGGTCGCAACGGCAAACCTTG-TACCTTAAAAGATGTGATGGGAA
* ** * * * * *
17583 AGATCAAGGCCGCAACAGCGGATCTAGTACCATGCA
65 GGATTGAGGCCGCAACGGTGAATCCAATACCATG-A
* * * *
17619 A-ATATAAAACGGAAAGGTTGAGGCCGTAACGGTAAACCTTGTA-CTCTAAAAGCATGT--TGGG
1 AGATAT-AAAGGGAAAGGTTGAGGTCGCAACGGCAAACCTTGTACCT-TAAAAG-ATGTGATGGG
* * * * **
17680 AAAGATTGAGCCCGTAATGGTGAATCTGGA-ACCATGA
63 AAGGATTGAGGCCGCAACGGTGAATC-CAATACCATGA
* * * *
17717 AGAT-TTAAGGAGAAAGATTGAGGTTGTAACGGC
1 AGATATAAAGG-GAAAGGTTGAGGTCGCAACGGC
17750 GAATCTGGAA
Statistics
Matches: 677, Mismatches: 124, Indels: 46
0.80 0.15 0.05
Matches are distributed among these distances:
97 3 0.00
98 125 0.18
99 532 0.79
100 12 0.02
101 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.21
Consensus pattern (99 bp):
AGATATAAAGGGAAAGGTTGAGGTCGCAACGGCAAACCTTGTACCTTAAAAGATGTGATGGGAAG
GATTGAGGCCGCAACGGTGAATCCAATACCATGA
Found at i:17547 original size:49 final size:49
Alignment explanation
Indices: 16917--17548 Score: 310
Period size: 50 Copynumber: 12.8 Consensus size: 49
16907 GACGAATCTA
* * * * *
16917 GTACCATGAAAATATAAAGGGAAAGGTTGAGGTCGCAACGGCGAA-CCTT
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCC-G
* * * * ** *
16966 GTACC-TTAAAAGATGTAA-TGAGAAGGATTGAGGCCGCAACGACGAATCCA
1 GTACCATGAAGATATG-AAGGGA-AAGG-TTGAGGCCGCAACGGTGAATCCG
* * * ** *
17016 ATACCATGAAGATATAAAGGGAAAGGTTGAGGTCGCAACGGCAAATCCT
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCCG
* * ** * * *
17065 GTACCTTAGAAGATGTG-TTGGTAAGGATTGAGGCCTCAACGGTGAATCTG
1 GTACCAT-GAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGGTGAATCCG
* * * ** * * * *
17115 ATACCATGAAAATATGAAGGGAAAGGTTAAGGTAGTAACGGAGAACCCT
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCCG
* * * * * *
17164 GTACCTTAAAAGATGTGATGGG-AAGGATTGAGGCTGTAACGGTGAATCCG
1 GTACCAT-GAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGGTGAATCCG
* * ** * ** * *
17214 ATACCATGAATATATGAAAAGAAAGGTTGAGGCCGCAA-TGACAAACTCT
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATC-CG
* * * *** ** * *
17263 GTACCTTAAAAGATGTGATTTGAAAGAATAAGGCCTCAACGGTGAATCCG
1 GTACCAT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCCG
* * * * * * *
17313 ATACCATGAAGATATGAAAGGAAAAGTTGAGGCTGCAACGGTAAACCCT
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCCG
* * * * * *
17362 TTACCTTAAAAGATGTGATGGG-AAGGATTGAGGCCGCAACGGTGAATCCA
1 GTACCAT-GAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGGTGAATCCG
* * * * * *
17412 GTACCATGAAGATATAAAGGGAAATGTTGAGGCTGCAACGGTGTACCCT
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCCG
* * * *
17461 GTGCCTTAAAAGATGTGATA-GG-AAGGATTGAGGCCGCAACGGTGAATCCG
1 GTACCAT-GAAGATATGA-AGGGAAAGG-TTGAGGCCGCAACGGTGAATCCG
* *
17511 GTACCATGAAGATATGAAGGGAAATGTTGAGACCGCAA
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAA
17549 TGGCGAACCT
Statistics
Matches: 416, Mismatches: 144, Indels: 46
0.69 0.24 0.08
Matches are distributed among these distances:
48 14 0.03
49 189 0.45
50 198 0.48
51 15 0.04
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (49 bp):
GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCCG
Found at i:17847 original size:47 final size:49
Alignment explanation
Indices: 17796--17907 Score: 122
Period size: 51 Copynumber: 2.3 Consensus size: 49
17786 GGTCGCAGAA
* * *
17796 GCAAACCTTATATCTTGAAAAATAT-GA-GAAAGA-TTGAGGCCGTAATG
1 GCAAACCTTATACCATG-AAAATATGGAGGAAAGAGTTGAAGCCGTAATG
* *
17843 GCAAATCTTATACCATGAAGATATGGAGGGAAAGAGGTTGAAGCCGTAATG
1 GCAAACCTTATACCATGAAAATATGGA-GGAAAGA-GTTGAAGCCGTAATG
*
17894 GCAAACCTTGTACC
1 GCAAACCTTATACC
17908 CTAAAAATGA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
46 6 0.11
47 16 0.30
49 6 0.11
51 25 0.47
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (49 bp):
GCAAACCTTATACCATGAAAATATGGAGGAAAGAGTTGAAGCCGTAATG
Found at i:18233 original size:114 final size:113
Alignment explanation
Indices: 18046--18349 Score: 387
Period size: 114 Copynumber: 2.7 Consensus size: 113
18036 CGAAGTAGAT
* * * * * * *
18046 CTCAACGTCCCCAATGATACAATGAAGTGAAGTGAAAATTCAAATCCCATCTTCCTGGTGAGATA
1 CTCAACGTCCCTAAGGATACAGTGAAGTG-AGTGAGACTTCAAATCCCATCTTTCTGGTGAGGTA
*
18111 CAAAGAAGTGGGTGC-AAACAGTATGTTGAATCAAAACAACGAAGCCGAG
65 CAGAGAAGTGGGT-CAAAACAGTATGTTGAATCAAAACAACGAAGCCGAG
* *
18160 CTCAACATCCCTAAGGATACAGTGAAGTAGAGTGAGACTTCAAATCCCATCTTTCTAGTGAGGTA
1 CTCAACGTCCCTAAGGATACAGTGAAGT-GAGTGAGACTTCAAATCCCATCTTTCTGGTGAGGTA
* * * * *
18225 CAGAGAAGTGGGTCAAAATAGTGTGTTGAATCAAAATAATGAAGCTGAG
65 CAGAGAAGTGGGTCAAAACAGTATGTTGAATCAAAACAACGAAGCCGAG
* * *
18274 CTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATC-TTCTTGGTGAGGT
1 CTCAACGTCCCTAAGGATACAGTGAAGT-GAGTGAGACTTCAAATCCCATCTTTC-TGGTGAGGT
18338 ACAGAGAAGTGG
64 ACAGAGAAGTGG
18350 TTAAAAATAA
Statistics
Matches: 166, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
113 4 0.02
114 161 0.97
115 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (113 bp):
CTCAACGTCCCTAAGGATACAGTGAAGTGAGTGAGACTTCAAATCCCATCTTTCTGGTGAGGTAC
AGAGAAGTGGGTCAAAACAGTATGTTGAATCAAAACAACGAAGCCGAG
Found at i:18421 original size:96 final size:95
Alignment explanation
Indices: 18255--18549 Score: 468
Period size: 96 Copynumber: 3.1 Consensus size: 95
18245 GTGTGTTGAA
*
18255 TCAAAATAATGAAGCT-GAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAAT
1 TCAAAATAATGAAG-TAGAGCTCAACGTCCCTGAGGATACAGTGGAGTGGAGTGAGACTTCAAAT
*
18319 CCCATCTTCTTGGTGAGGTACAGAGAAGTGG
65 CCCATCTTCCTGGTGAGGTACAGAGAAGTGG
* * * *
18350 TTAAAAATAATAAAGTAGAGCTCAACGTCCCTGTGGATACAGTGGAGTGGAGTGAGACTGCAAAT
1 -TCAAAATAATGAAGTAGAGCTCAACGTCCCTGAGGATACAGTGGAGTGGAGTGAGACTTCAAAT
18415 CCCATCTTCCTGGTGAGGTACAGAGAAGTGAG
65 CCCATCTTCCTGGTGAGGTACAGAGAAGTG-G
*
18447 TCAAAATAATGAAG-AGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATC
1 TCAAAATAATGAAGTAGAGCTCAACGTCCCTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATC
*
18511 CCATCTTCCTAGTGAGGTACAGAGAAGTGGG
66 CCATCTTCCTGGTGAGGTACAGAGAAGT-GG
18542 TCAAAATA
1 TCAAAATA
18550 GTGTGTTGAA
Statistics
Matches: 184, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
95 84 0.46
96 99 0.54
97 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (95 bp):
TCAAAATAATGAAGTAGAGCTCAACGTCCCTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATC
CCATCTTCCTGGTGAGGTACAGAGAAGTGG
Found at i:18603 original size:114 final size:113
Alignment explanation
Indices: 18447--18663 Score: 353
Period size: 114 Copynumber: 1.9 Consensus size: 113
18437 GAGAAGTGAG
* *
18447 TCAAAATAATGAAGAGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCC
1 TCAAAATAATGAAGAGAGCTCAACGTCCTTGAAGATACAGTGGAGTGGAGTGAGACTACAAATCC
18512 CATCTTCCTAGTGAGGTACAGAGAAGTGGGTCAAAATAGTGTGTTGAA
66 CATCTTCCTAGTGAGGTACAGAGAAGTGGGTCAAAATAGTGTGTTGAA
* *
18560 TCAAAATAATGAAGCCGAGCTCAACGTCCTTGAAGTTACAGTGGAGTGGAGTGAGACTACAAATC
1 TCAAAATAATGAAG-AGAGCTCAACGTCCTTGAAGATACAGTGGAGTGGAGTGAGACTACAAATC
* * * *
18625 TCATCTTTCTAGTGCGGTATAGAGAAGTGGGTCAAAATA
65 CCATCTTCCTAGTGAGGTACAGAGAAGTGGGTCAAAATA
18664 ATGAAGCAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
113 14 0.15
114 81 0.85
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (113 bp):
TCAAAATAATGAAGAGAGCTCAACGTCCTTGAAGATACAGTGGAGTGGAGTGAGACTACAAATCC
CATCTTCCTAGTGAGGTACAGAGAAGTGGGTCAAAATAGTGTGTTGAA
Found at i:18651 original size:209 final size:212
Alignment explanation
Indices: 18353--18868 Score: 630
Period size: 215 Copynumber: 2.4 Consensus size: 212
18343 GAAGTGGTTA
* ** *
18353 AAAATAATAAAGTAGAGCTCAACGTCCCTGTGGATACAGTGGAGTGGAGTGAGACTGCAAATCCC
1 AAAATAATAAAGCAGAGCTCAACGTCCCTGAAGATACAGTGGAGTGGAGTGAGACTACAAATCCC
* *
18418 ATCTTCCTGGTGAGGTACAGAGAAGTGAGTCAAAATAATGAAG-AGAGCTCAACGTCCTTGAGGA
66 ATCTTCCTAGTGAGGTACAGAGAAGTGAGTCAAAATAATGAAGCAAAGCTCAACGTCCTTGAGGA
* *
18482 TACAGTGGAGT-G-GAGTGAGACTTCAAATCCCATCTTCCTAG-TGAGGTACAGAGAAGTGGGTC
131 TACAGTGGAGTGGAGAGTGAGACTTCAAATCCCAACTTCCT-GTTGAGGTACAAAGAAGTGGGTC
18544 AAAATAGTGTGTTGAATC
195 AAAATAGTGTGTTGAATC
* * * * *
18562 AAAATAATGAAGCCGAGCTCAACGTCCTTGAAGTTACAGTGGAGTGGAGTGAGACTACAAATCTC
1 AAAATAATAAAGCAGAGCTCAACGTCCCTGAAGATACAGTGGAGTGGAGTGAGACTACAAATCCC
* * * *
18627 ATCTTTCTAGTGCGGTATAGAGAAGTGGGTCAAAATAATGAAGCAAAGCTCAACGTCCTTGAGGA
66 ATCTTCCTAGTGAGGTACAGAGAAGTGAGTCAAAATAATGAAGCAAAGCTCAACGTCCTTGAGGA
*
18692 TACAGTGGAGTGGAGTAGAGTGAGACTTCAAATCCCAACTTCCTGTTTAGGTACAAAGAAGTGGG
131 TACAGTGGAGT-G-G-AGAGTGAGACTTCAAATCCCAACTTCCTGTTGAGGTACAAAGAAGTGGG
*
18757 TCAAAATAGTGTGTTGAATT
193 TCAAAATAGTGTGTTGAATC
* ** * * * * * * *
18777 GAAACGACAAAGTAGAGCTCAATGTTCCT-AAGGATAC-GTTGGAGTGGACTGAGATTTCAAATC
1 AAAATAATAAAGCAGAGCTCAACGTCCCTGAA-GATACAG-TGGAGTGGAGTGAGACTACAAATC
* ** * *
18840 CCATATTATTGGTGAGGTACAAAGAAGTG
64 CCATCTTCCTAGTGAGGTACAGAGAAGTG
18869 GGTTTAAACA
Statistics
Matches: 257, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
209 94 0.37
210 31 0.12
213 1 0.00
214 4 0.02
215 127 0.49
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.24
Consensus pattern (212 bp):
AAAATAATAAAGCAGAGCTCAACGTCCCTGAAGATACAGTGGAGTGGAGTGAGACTACAAATCCC
ATCTTCCTAGTGAGGTACAGAGAAGTGAGTCAAAATAATGAAGCAAAGCTCAACGTCCTTGAGGA
TACAGTGGAGTGGAGAGTGAGACTTCAAATCCCAACTTCCTGTTGAGGTACAAAGAAGTGGGTCA
AAATAGTGTGTTGAATC
Found at i:19721 original size:15 final size:15
Alignment explanation
Indices: 19701--19735 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
19691 TATACACATA
* *
19701 TATTTTTTTATTTTT
1 TATTTTATTATTTAT
19716 TATTTTATTATTTAT
1 TATTTTATTATTTAT
19731 TATTT
1 TATTT
19736 AAGTTTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TATTTTATTATTTAT
Found at i:20663 original size:25 final size:25
Alignment explanation
Indices: 20606--20666 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
20596 CATTTTGTTT
*
20606 TTTGTTTTAAATTAAATCCTTTTTA
1 TTTGTTTTAAATTAAATCCTTATTA
* *
20631 TTTATTTTTAATTAAATCC-TATTA
1 TTTGTTTTAAATTAAATCCTTATTA
20655 TTCTGTTTTAAA
1 TT-TGTTTTAAA
20667 AATTAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 6 0.20
25 24 0.80
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (25 bp):
TTTGTTTTAAATTAAATCCTTATTA
Found at i:24712 original size:38 final size:38
Alignment explanation
Indices: 24661--24737 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
24651 AACTAATTCT
* *
24661 TGCGCAACCGATGAGAGGTTGATTTGGTTTTCTTTATC
1 TGCGCAACCGATGAAAGGCTGATTTGGTTTTCTTTATC
*
24699 TGCGCAATCGATGAAAGGCTGATTTGGTTTTCTTTATC
1 TGCGCAACCGATGAAAGGCTGATTTGGTTTTCTTTATC
24737 T
1 T
24738 TCTTCCTTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (38 bp):
TGCGCAACCGATGAAAGGCTGATTTGGTTTTCTTTATC
Found at i:38318 original size:63 final size:59
Alignment explanation
Indices: 38251--38402 Score: 171
Period size: 60 Copynumber: 2.5 Consensus size: 59
38241 AATATTATAT
* *
38251 TATATTTTTATTTTTATTAATTCATATTTTAATAATAAATATA-TTACGAATGTTATTAAATTA
1 TATATTTTTATTTTTATTAATT-ACA-TTTAATAATAAATATATTTA-AAATG--ATTAAATTA
* *
38314 TATATTTTTATTTGTATTAAATTACATTTAATAATAATTATATTTAAAATGATTAAATTA
1 TATATTTTTATTTTTATT-AATTACATTTAATAATAAATATATTTAAAATGATTAAATTA
* * *
38374 TTTATTATTATTATTATTAAATTACATTT
1 TATATTTTTATTTTTATT-AATTACATTT
38403 GTCGAAATCA
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
60 34 0.43
62 19 0.24
63 22 0.28
64 4 0.05
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (59 bp):
TATATTTTTATTTTTATTAATTACATTTAATAATAAATATATTTAAAATGATTAAATTA
Found at i:39047 original size:96 final size:96
Alignment explanation
Indices: 38863--39054 Score: 228
Period size: 96 Copynumber: 2.0 Consensus size: 96
38853 TCTTTGCAAA
* * *
38863 AAGGATATTTGATTATCTCGATTTGAAGAGAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
** *
38928 AAATTGAAGATAAGGAAACATTGCCTCGATT
66 AAACCGAAGATAAAGAAACATTGCCTCGATT
* * * * *
38959 AAGGGTATTCGATTATTTTGATTTGGAGAAAAGTTGCACCTAGTGAGTTAAGGCGCAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAATA-TTTC
*
39023 GAAACCCGAA-ATGAAAG-AATATTGCCTCGATT
65 GAAA-CCGAAGAT-AAAGAAACATTGCCTCGATT
39055 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 1 0.01
96 74 0.91
97 6 0.07
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
AAACCGAAGATAAAGAAACATTGCCTCGATT
Found at i:39303 original size:30 final size:29
Alignment explanation
Indices: 39267--39328 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
39257 ATCGAAGTTT
*
39267 AAAATGAGACTTTTCGGATTCCCAGGGGTG
1 AAAATGAGAATTTT-GGATTCCCAGGGGTG
* * *
39297 AAAATGATAATTTTGGATTCTCGGGGGTG
1 AAAATGAGAATTTTGGATTCCCAGGGGTG
39326 AAA
1 AAA
39329 CGATAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (29 bp):
AAAATGAGAATTTTGGATTCCCAGGGGTG
Found at i:39323 original size:29 final size:29
Alignment explanation
Indices: 39267--39340 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
39257 ATCGAAGTTT
* *
39267 AAAATGAGACTTTTCGGATTCCCAGGGGTG
1 AAAATGATAATTTT-GGATTCCCAGGGGTG
* *
39297 AAAATGATAATTTTGGATTCTCGGGGGTG
1 AAAATGATAATTTTGGATTCCCAGGGGTG
*
39326 -AAACGATAATTTTGG
1 AAAATGATAATTTTGG
39341 GAAAATTCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.36
29 13 0.33
30 12 0.31
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (29 bp):
AAAATGATAATTTTGGATTCCCAGGGGTG
Found at i:39368 original size:30 final size:30
Alignment explanation
Indices: 39334--39524 Score: 173
Period size: 29 Copynumber: 6.5 Consensus size: 30
39324 TGAAACGATA
* *
39334 ATTTTGGGAAAATTCGGGGTCAAAAATGGG
1 ATTTTTGGAAAGTTCGGGGTCAAAAATGGG
*
39364 ATTTTT-GAAAGTTCGAGGG-AAAAAATGGG
1 ATTTTTGGAAAGTTCG-GGGTCAAAAATGGG
** *
39393 ATTTTTGG-AAGTTTTAGGGTCAAAAATGAG
1 ATTTTTGGAAAG-TTCGGGGTCAAAAATGGG
* *
39423 ATTTTTGG-AAGTTCAAGGGT-AAAAATGGA
1 ATTTTTGGAAAGTTC-GGGGTCAAAAATGGG
39452 ATTTTTGG-AAGTTTCGGGGTCAAAAATGGG
1 ATTTTTGGAAAG-TTCGGGGTCAAAAATGGG
* **
39482 ATTTTT-GAAAGTTCGAGGG-AAAAAATGAA
1 ATTTTTGGAAAGTTCG-GGGTCAAAAATGGG
*
39511 ATTTTTGGACAGTT
1 ATTTTTGGAAAGTT
39525 TAGGGACCTT
Statistics
Matches: 135, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
29 71 0.53
30 64 0.47
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.32
Consensus pattern (30 bp):
ATTTTTGGAAAGTTCGGGGTCAAAAATGGG
Found at i:39397 original size:59 final size:59
Alignment explanation
Indices: 39346--39525 Score: 279
Period size: 59 Copynumber: 3.0 Consensus size: 59
39336 TTTGGGAAAA
*
39346 TTCGGGGTCAAAAATGGGATTTTTGAAAGTTCGAGGGAAAAAATGGGATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGAAAGTTCGAGGGAAAAAATGGAATTTTTGGAAGT
** * * * *
39405 TTTAGGGTCAAAAATGAGATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGAAAGTTCGAGGGAAAAAATGGAATTTTTGGAAGT
*
39464 TTCGGGGTCAAAAATGGGATTTTTGAAAGTTCGAGGGAAAAAATGAAATTTTTGGACAGT
1 TTCGGGGTCAAAAATGGGATTTTTGAAAGTTCGAGGGAAAAAATGGAATTTTTGGA-AGT
39524 TT
1 TT
39526 AGGGACCTTC
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
59 101 0.95
60 5 0.05
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (59 bp):
TTCGGGGTCAAAAATGGGATTTTTGAAAGTTCGAGGGAAAAAATGGAATTTTTGGAAGT
Found at i:39505 original size:29 final size:29
Alignment explanation
Indices: 39355--39524 Score: 189
Period size: 29 Copynumber: 5.8 Consensus size: 29
39345 ATTCGGGGTC
*
39355 AAAAATGGGATTTTTGAAAGTTCGAGGGA
1 AAAAATGGGATTTTTGGAAGTTCGAGGGA
** *
39384 AAAAATGGGATTTTTGGAAGTTTTAGGGTC
1 AAAAATGGGATTTTTGGAAGTTCGAGGG-A
* * *
39414 AAAAATGAGATTTTTGGAAGTTCAAGGGT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGA
* *
39443 AAAAATGGAATTTTTGGAAGTTTCG-GGGTC
1 AAAAATGGGATTTTTGGAAG-TTCGAGGG-A
*
39473 AAAAATGGGATTTTTGAAAGTTCGAGGGA
1 AAAAATGGGATTTTTGGAAGTTCGAGGGA
**
39502 AAAAATGAAATTTTTGGACAGTT
1 AAAAATGGGATTTTTGGA-AGTT
39525 TAGGGACCTT
Statistics
Matches: 118, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
29 65 0.55
30 53 0.45
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGA
Found at i:41468 original size:6 final size:6
Alignment explanation
Indices: 41454--41517 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
41444 ATTTGGAAAA
* *
41454 TAAATT TAAACT TAAA-T TAAATT TAAATT CGAAA-- TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT TAAATT
*
41500 T-AATA TAAATT TAAATT T
1 TAAATT TAAATT TAAATT T
41518 CTACACAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 33 0.69
7 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:41517 original size:17 final size:16
Alignment explanation
Indices: 41422--41517 Score: 95
Period size: 17 Copynumber: 5.6 Consensus size: 16
41412 CTTTATTTAT
41422 TTTAAATTTATAAT-AA
1 TTTAAATTTA-AATAAA
41438 TCTTAAATTTGGAAAATAAA
1 T-TTAAATTT---AAATAAA
*
41458 TTTAAACTTAAATTAAA
1 TTTAAATTTAAA-TAAA
*
41475 TTTAAATTCGAAATAAA
1 TTTAAATT-TAAATAAA
41492 TTTAAATTTAATATAAA
1 TTTAAATTTAA-ATAAA
41509 TTTAAATTT
1 TTTAAATTT
41518 CTACACAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
16 6 0.09
17 45 0.66
18 3 0.04
19 10 0.15
20 4 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Done.