Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008551.1 Hibiscus syriacus cultivar Beakdansim tig00111446_pilon, 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: 121184
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2111 original size:31 final size:30
Alignment explanation
Indices: 2062--2122 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
2052 ACACCATTCT
*
2062 AAATTTCCAGCAAACTAATTCATTCTCTTTC
1 AAATTTCCAACAAACTAATTCATTCT-TTTC
* * *
2093 AAATTTCTAACAACCTAATTCCTTCTTTTC
1 AAATTTCCAACAAACTAATTCATTCTTTTC
2123 TTCATCCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.31, C:0.26, G:0.02, T:0.41
Consensus pattern (30 bp):
AAATTTCCAACAAACTAATTCATTCTTTTC
Found at i:9720 original size:5 final size:5
Alignment explanation
Indices: 9710--9766 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
9700 TTCTTTTTGG
*
9710 CTTTT CTTTT CTTTT CTTTT -TTTGAAT -TTTT CTTCTT TTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTT---T CTTTT CTT-TT CTTTT CTTTT
9757 CTTTT CTTTT
1 CTTTT CTTTT
9767 TTGTACTCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 33 0.73
6 4 0.09
7 4 0.09
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (5 bp):
CTTTT
Found at i:9728 original size:27 final size:26
Alignment explanation
Indices: 9698--9756 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
9688 CCTTGGCTTG
** *
9698 CTTTCTTTTTGGCTTTTCTTTTCTTTT
1 CTTTCTTTTTGAATTTT-TCTTCTTTT
9725 C-TT-TTTTTGAATTTTTCTTCTTTT
1 CTTTCTTTTTGAATTTTTCTTCTTTT
9749 -TTTCTTTT
1 CTTTCTTTT
9757 CTTTTCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
24 10 0.37
25 14 0.52
26 2 0.07
27 1 0.04
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.76
Consensus pattern (26 bp):
CTTTCTTTTTGAATTTTTCTTCTTTT
Found at i:11314 original size:47 final size:45
Alignment explanation
Indices: 11242--11367 Score: 166
Period size: 47 Copynumber: 2.8 Consensus size: 45
11232 TATAAAATCT
11242 CTTACCATTTA-TCCTATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
11287 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
11334 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
11368 GCATGGTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 35 0.48
48 3 0.04
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:15488 original size:44 final size:46
Alignment explanation
Indices: 15368--15493 Score: 159
Period size: 47 Copynumber: 2.8 Consensus size: 46
15358 TATAAAATCT
* *
15368 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTAGTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
15413 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
15460 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
15494 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:20020 original size:15 final size:14
Alignment explanation
Indices: 19999--20040 Score: 68
Period size: 13 Copynumber: 3.0 Consensus size: 14
19989 AATTTTATCC
19999 CTTTCATTTCTTAT
1 CTTTCATTTCTTAT
20013 CATTTCATTTCTT-T
1 C-TTTCATTTCTTAT
20027 CTTTCATTTCTTAT
1 CTTTCATTTCTTAT
20041 TTCATTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
CTTTCATTTCTTAT
Found at i:20036 original size:9 final size:9
Alignment explanation
Indices: 19999--20038 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
19989 AATTTTATCC
19999 CTTTCATTT
1 CTTTCATTT
20008 CTTATCATTT
1 CTT-TCATTT
20018 CATTTC-TTT
1 C-TTTCATTT
20027 CTTTCATTT
1 CTTTCATTT
20036 CTT
1 CTT
20039 ATTTCATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.14
9 13 0.46
10 9 0.32
11 2 0.07
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (9 bp):
CTTTCATTT
Found at i:24961 original size:11 final size:11
Alignment explanation
Indices: 24937--24970 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
24927 TTGGTACTGG
24937 AAACAAGATAA
1 AAACAAGATAA
* *
24948 AAATAAGATTA
1 AAACAAGATAA
24959 AAACAAGATAA
1 AAACAAGATAA
24970 A
1 A
24971 GAAAATATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.15
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:29178 original size:15 final size:15
Alignment explanation
Indices: 29158--29197 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 15
29148 TTGACTTTTT
29158 TTTTGTTTTTTTGCC
1 TTTTGTTTTTTTGCC
29173 TTTTG--TTTTTGCC
1 TTTTGTTTTTTTGCC
29186 TTTT-TTTTTTTG
1 TTTTGTTTTTTTG
29198 AAAAACAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.52
14 6 0.26
15 5 0.22
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (15 bp):
TTTTGTTTTTTTGCC
Found at i:29542 original size:11 final size:11
Alignment explanation
Indices: 29526--29570 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
29516 TTGGTGCTGG
29526 AAACAAGATAA
1 AAACAAGATAA
*
29537 AAACAAGATTA
1 AAACAAGATAA
*
29548 AAACAAAATAA
1 AAACAAGATAA
29559 AGAA-AAGATAA
1 A-AACAAGATAA
29570 A
1 A
29571 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.73, C:0.07, G:0.09, T:0.11
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:37988 original size:16 final size:16
Alignment explanation
Indices: 37958--38005 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
37948 AAGTAATGAA
37958 AATAAGAAAAGATGAAAG
1 AATAAG-AAA-ATGAAAG
*
37976 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
*
37992 AGTAAGAAAATGAA
1 AATAAGAAAATGAA
38006 GATAACTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 19 0.68
17 3 0.11
18 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:43665 original size:24 final size:24
Alignment explanation
Indices: 43638--43688 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
43628 TGTAGATCAC
* *
43638 CAAAAGTCATGTCTATTGATTCTT
1 CAAAAGACATGTCTATTGAATCTT
* *
43662 CAAAAGACATGTTTCTTGAATCTT
1 CAAAAGACATGTCTATTGAATCTT
43686 CAA
1 CAA
43689 CTTGAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGACATGTCTATTGAATCTT
Found at i:48241 original size:31 final size:31
Alignment explanation
Indices: 48206--48267 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
48196 AATGTAAGAT
* *
48206 AGAAAAGGTTAAAAGA-TAAGGTAATGAAATA
1 AGAAAA-GATAAAAGATTAAGGAAATGAAATA
*
48237 AGAAAAGATGAAAGATTAAGGAAATGAAATA
1 AGAAAAGATAAAAGATTAAGGAAATGAAATA
48268 GTAAGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.18
Consensus pattern (31 bp):
AGAAAAGATAAAAGATTAAGGAAATGAAATA
Found at i:48715 original size:25 final size:25
Alignment explanation
Indices: 48691--48745 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 25
48681 GAAAATATGA
48691 AATAAGAAATGG-AA-GAAAGAAATG
1 AATAAGAAA-GGAAAGGAAAGAAATG
48715 -ATAAGAAAGGAAATGGAAAGAAATG
1 AATAAGAAAGGAAA-GGAAAGAAATG
48740 ATATAA
1 A-ATAA
48746 AAGTAGGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 2 0.08
23 10 0.38
25 10 0.38
27 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (25 bp):
AATAAGAAAGGAAAGGAAAGAAATG
Found at i:48735 original size:15 final size:14
Alignment explanation
Indices: 48694--48737 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
48684 AATATGAAAT
48694 AAGAAATGG-AAGA
1 AAGAAATGGAAAGA
48707 AAGAAAT-GATAAGA
1 AAGAAATGGA-AAGA
48721 AAGGAAATGGAAAGA
1 AA-GAAATGGAAAGA
48736 AA
1 AA
48738 TGATATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 7 0.26
14 6 0.22
15 11 0.41
16 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (14 bp):
AAGAAATGGAAAGA
Found at i:52472 original size:21 final size:21
Alignment explanation
Indices: 52433--52472 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52423 ATGCATTCAT
* * *
52433 ATTAGCTCATAGACTTTATTA
1 ATTAGCTCACACACATTATTA
52454 ATTAGCTCACACACATTAT
1 ATTAGCTCACACACATTAT
52473 GAGATGATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
ATTAGCTCACACACATTATTA
Found at i:53828 original size:12 final size:12
Alignment explanation
Indices: 53808--53844 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
53798 TACCAAAAAG
53808 AAGTGCAAGTGA
1 AAGTGCAAGTGA
*
53820 AAGTACAAGTG-
1 AAGTGCAAGTGA
53831 -AGTGCAAGTGA
1 AAGTGCAAGTGA
53842 AAG
1 AAG
53845 AAAAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.43, C:0.08, G:0.32, T:0.16
Consensus pattern (12 bp):
AAGTGCAAGTGA
Found at i:62944 original size:22 final size:22
Alignment explanation
Indices: 62916--62975 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
62906 CTATTTTTAA
*
62916 AAAAAAAACAAG-AACAAAAGGC
1 AAAAAAAA-AAGCAAAAAAAGGC
*
62938 AAAAAAAAAGGCAAAAAAAGGC
1 AAAAAAAAAAGCAAAAAAAGGC
*
62960 -AAAACAAAAG-AAAAAA
1 AAAAAAAAAAGCAAAAAA
62976 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.18
21 10 0.30
22 17 0.52
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAGCAAAAAAAGGC
Found at i:62946 original size:12 final size:12
Alignment explanation
Indices: 62931--62969 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
62921 AAACAAGAAC
62931 AAAAGGCAAAAA
1 AAAAGGCAAAAA
62943 AAAAGGC--AAA
1 AAAAGGCAAAAA
*
62953 AAAAGGCAAAAC
1 AAAAGGCAAAAA
62965 AAAAG
1 AAAAG
62970 AAAAAAGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.72, C:0.10, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAGGCAAAAA
Found at i:69595 original size:18 final size:17
Alignment explanation
Indices: 69572--69610 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 17
69562 TTTTTTTCAA
69572 AAAAAAACAAAAAAAGGC
1 AAAAAAAC-AAAAAAGGC
69590 AAAAAAACAAAAAAGGC
1 AAAAAAACAAAAAAGGC
69607 AAAA
1 AAAA
69611 TTTCAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAAAAGGC
Found at i:71932 original size:21 final size:21
Alignment explanation
Indices: 71893--71932 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
71883 AAGGAAGATT
*
71893 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
71914 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
71933 AGGATTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:76274 original size:90 final size:89
Alignment explanation
Indices: 76122--76294 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
76112 ACACACTCTT
*
76122 TTATAGCCAAGTTATCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
76187 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
*
76211 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
76276 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
76295 TTCGGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:77407 original size:21 final size:21
Alignment explanation
Indices: 77368--77407 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
77358 AAGGAAGATT
*
77368 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
77389 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
77408 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:78604 original size:26 final size:25
Alignment explanation
Indices: 78570--78618 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
78560 AGAATTAAGT
*
78570 TAAGTATATGAATTATTATAAAGTAA
1 TAAGGATATGAA-TATTATAAAGTAA
*
78596 TAAGGATATGCATATTATAAAGT
1 TAAGGATATGAATATTATAAAGT
78619 TGTGAACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (25 bp):
TAAGGATATGAATATTATAAAGTAA
Found at i:89967 original size:20 final size:20
Alignment explanation
Indices: 89944--89983 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
89934 CACTTTCCTA
*
89944 CCTTTGATAACATTTCTTTC
1 CCTTTCATAACATTTCTTTC
**
89964 CCTTTCATTTCATTTCTTTC
1 CCTTTCATAACATTTCTTTC
89984 ATTCACTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.03, T:0.55
Consensus pattern (20 bp):
CCTTTCATAACATTTCTTTC
Found at i:90214 original size:17 final size:16
Alignment explanation
Indices: 90180--90224 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
90170 GTGTTGCAAT
90180 AAAAACAAAAAGAAAG
1 AAAAACAAAAAGAAAG
*
90196 AAAAACAAACA-AAAG
1 AAAAACAAAAAGAAAG
*
90211 AGAAAAGAAAAAGA
1 A-AAAACAAAAAGA
90225 CTCCTACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.21
16 18 0.75
17 1 0.04
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAGAAAG
Found at i:106911 original size:18 final size:16
Alignment explanation
Indices: 106866--106924 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
106856 TCATGTTATA
106866 TCATTTAAGCATG-AGT
1 TCATTTAAGCATGCA-T
106882 TCATTTAAGCATGCAT
1 TCATTTAAGCATGCAT
106898 TGCATTTAAAGCAT-CTATT
1 T-CATTT-AAGCATGC-A-T
106917 TCATTTAA
1 TCATTTAA
106925 TAAAGTTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 15 0.39
17 9 0.24
18 12 0.32
19 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (16 bp):
TCATTTAAGCATGCAT
Found at i:106951 original size:17 final size:17
Alignment explanation
Indices: 106931--106983 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
106921 TTAATAAAGT
106931 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
106948 TAGTTC-TTAAATCAAAC
1 TAGTTCATT-AATTAAAC
*
106965 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
106982 TA
1 TA
106984 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 2 0.06
17 27 0.87
18 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:111635 original size:18 final size:18
Alignment explanation
Indices: 111612--111646 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
111602 TTGGTTTGCT
111612 TTTCTTTACCCTTGCTAC
1 TTTCTTTACCCTTGCTAC
111630 TTTCTTTACCCTTGCTA
1 TTTCTTTACCCTTGCTA
111647 GATTCGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.31, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTCTTTACCCTTGCTAC
Found at i:113853 original size:12 final size:12
Alignment explanation
Indices: 113821--113860 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
113811 TCATCATCAA
*
113821 CATCATCAACATC
1 CATCATCAAGA-C
*
113834 CTTCATCAAGAC
1 CATCATCAAGAC
113846 CATCATCAAGAC
1 CATCATCAAGAC
113858 CAT
1 CAT
113861 AATTCCGCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.23
Consensus pattern (12 bp):
CATCATCAAGAC
Found at i:114207 original size:5 final size:5
Alignment explanation
Indices: 114177--114223 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
114167 TTGGAGTGCA
*
114177 AAAAG -AAAG AAAAA AAAAG AAGAAG AAAAG --AAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAA
114224 AGAATTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 3 0.08
4 4 0.11
5 24 0.67
6 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:114210 original size:24 final size:25
Alignment explanation
Indices: 114177--114227 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
114167 TTGGAGTGCA
*
114177 AAAAGAAAGAAAAAAAAAGAAGAAG
1 AAAAGAAAGAAAAAAAAAGAAAAAG
*
114202 AAAAG-AAGAAAAGAAAAGAAAAAG
1 AAAAGAAAGAAAAAAAAAGAAAAAG
114226 AA
1 AA
114228 TTCAAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (25 bp):
AAAAGAAAGAAAAAAAAAGAAAAAG
Done.