Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003654.1 Hibiscus syriacus cultivar Beakdansim tig00007770_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: 74427
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3019 original size:18 final size:20
Alignment explanation
Indices: 2992--3032 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
2982 ATTTCACCAC
2992 ATGCAACTATATG-T-CTAA
1 ATGCAACTATATGATCCTAA
*
3010 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
3030 ATG
1 ATG
3033 GGCTCTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 1 0.05
20 7 0.35
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3545 original size:11 final size:12
Alignment explanation
Indices: 3529--3557 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3519 GAATTCAAGA
3529 GAACAACTG-TT
1 GAACAACTGTTT
3540 GAACAACTGTTT
1 GAACAACTGTTT
3552 GAACAA
1 GAACAA
3558 ACGATGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (12 bp):
GAACAACTGTTT
Found at i:8056 original size:42 final size:42
Alignment explanation
Indices: 7987--8105 Score: 168
Period size: 42 Copynumber: 2.8 Consensus size: 42
7977 CATATTATCA
*
7987 AATAAGTCTCAATAAGTCTAAATTAAATAACATCATAACACC
1 AATAAGTCTCAATAAGTCTAAAATAAATAACATCATAACACC
* * * *
8029 ATTAATTCTCAATAAGTCTAAAATAAATAACACCATAACACT
1 AATAAGTCTCAATAAGTCTAAAATAAATAACATCATAACACC
*
8071 AATAAGTCTCAATAAGTCT-AAATAAAATCACATCA
1 AATAAGTCTCAATAAGTCTAAAAT-AAATAACATCA
8106 ATATATTCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
41 4 0.06
42 63 0.94
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.27
Consensus pattern (42 bp):
AATAAGTCTCAATAAGTCTAAAATAAATAACATCATAACACC
Found at i:10855 original size:4 final size:4
Alignment explanation
Indices: 10848--10925 Score: 74
Period size: 4 Copynumber: 19.5 Consensus size: 4
10838 AATGAATTGA
*
10848 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAT GAAA- GAAT -AAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT
*
10893 AAATT GAAACT AAAT AAAT ACAT AAAT AAAT AA
1 AAA-T -AAA-T AAAT AAAT AAAT AAAT AAAT AA
10926 TGCAAGAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
3 11 0.17
4 43 0.68
5 5 0.08
6 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:10856 original size:19 final size:18
Alignment explanation
Indices: 10832--10912 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 18
10822 TCTAACAAAG
10832 TAAATAAATGAATTGAAAA
1 TAAATAAAT-AATTGAAAA
*
10851 TAAATAAATAAAT--AAA
1 TAAATAAATAATTGAAAA
10867 TAAATAAATAA-TGAAAGA
1 TAAATAAATAATTGAAA-A
* *
10885 -ATAATAAAAAATTGAAAC
1 TA-AATAAATAATTGAAAA
10903 TAAATAAATA
1 TAAATAAATA
10913 CATAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.02
16 14 0.27
17 3 0.06
18 19 0.37
19 15 0.29
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (18 bp):
TAAATAAATAATTGAAAA
Found at i:10926 original size:48 final size:48
Alignment explanation
Indices: 10855--10949 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
10845 TGAAAATAAA
10855 TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAAC
1 TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAAC
* * *
10903 TAAATAAATACATAAATAAATAATGCAAGAATAATAAAATATTGAAA
1 TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAA
10950 ATAATTGTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.24
Consensus pattern (48 bp):
TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAAC
Found at i:18112 original size:20 final size:20
Alignment explanation
Indices: 18083--18125 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18073 ATTTCACCAC
*
18083 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
18103 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
18123 ATG
1 ATG
18126 GGCTCTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:18649 original size:11 final size:11
Alignment explanation
Indices: 18633--18660 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
18623 GAATTCAAGA
18633 GAACAACTGTT
1 GAACAACTGTT
18644 GAACAACTGTT
1 GAACAACTGTT
18655 GAACAA
1 GAACAA
18661 ACGATGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (11 bp):
GAACAACTGTT
Found at i:23181 original size:42 final size:42
Alignment explanation
Indices: 23112--23231 Score: 170
Period size: 42 Copynumber: 2.8 Consensus size: 42
23102 CATATTATCA
*
23112 AATAAGTCTCAATAAGTCTAAATTAAATAACATCATAACACC
1 AATAAGTCTCAATAAGTCTAAAATAAATAACATCATAACACC
* * * *
23154 ATTAATTCTCAATAAGTCTAAAATAAATAACACCATAACACT
1 AATAAGTCTCAATAAGTCTAAAATAAATAACATCATAACACC
23196 AATAAGTCTCAATAAGTCT-AAATAAAATCAACATCA
1 AATAAGTCTCAATAAGTCTAAAAT-AAAT-AACATCA
23232 ATAATATTCA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (42 bp):
AATAAGTCTCAATAAGTCTAAAATAAATAACATCATAACACC
Found at i:25681 original size:22 final size:21
Alignment explanation
Indices: 25655--25697 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
25645 TTAACTAATT
25655 ATTTATAAAAAATATTATTATA
1 ATTTATAAAAAATATT-TTATA
**
25677 ATTTATAAGTAATATTTTATA
1 ATTTATAAAAAATATTTTATA
25698 GTATTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTATAAAAAATATTTTATA
Found at i:25696 original size:36 final size:36
Alignment explanation
Indices: 25618--25697 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
25608 GTTATATTGC
* * * * *
25618 ATTTTATCAACAATATTATTTTATTTTTTAACTAAT
1 ATTTTATAAAAAATATTATTATAATTTATAACTAAT
*
25654 -TATTTATAAAAAATATTATTATAATTTATAAGTAAT
1 AT-TTTATAAAAAATATTATTATAATTTATAACTAAT
25690 ATTTTATA
1 ATTTTATA
25698 GTATTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
35 1 0.03
36 34 0.94
37 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (36 bp):
ATTTTATAAAAAATATTATTATAATTTATAACTAAT
Found at i:25998 original size:4 final size:4
Alignment explanation
Indices: 25991--26068 Score: 74
Period size: 4 Copynumber: 19.5 Consensus size: 4
25981 AATGAATTGA
*
25991 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAT GAAA- GAAT -AAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT
*
26036 AAATT GAAACT AAAT AAAT ACAT AAAT AAAT AA
1 AAA-T -AAA-T AAAT AAAT AAAT AAAT AAAT AA
26069 TGCAAGAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
3 11 0.17
4 43 0.68
5 5 0.08
6 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:25999 original size:19 final size:18
Alignment explanation
Indices: 25975--26055 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 18
25965 TCTAACAAAG
25975 TAAATAAATGAATTGAAAA
1 TAAATAAAT-AATTGAAAA
*
25994 TAAATAAATAAAT--AAA
1 TAAATAAATAATTGAAAA
26010 TAAATAAATAA-TGAAAGA
1 TAAATAAATAATTGAAA-A
* *
26028 -ATAATAAAAAATTGAAAC
1 TA-AATAAATAATTGAAAA
26046 TAAATAAATA
1 TAAATAAATA
26056 CATAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.02
16 14 0.27
17 3 0.06
18 19 0.37
19 15 0.29
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (18 bp):
TAAATAAATAATTGAAAA
Found at i:26069 original size:48 final size:48
Alignment explanation
Indices: 25998--26092 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
25988 TGAAAATAAA
25998 TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAAC
1 TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAAC
* * *
26046 TAAATAAATACATAAATAAATAATGCAAGAATAATAAAATATTGAAA
1 TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAA
26093 ATAATTGTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.24
Consensus pattern (48 bp):
TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAAC
Found at i:27967 original size:21 final size:20
Alignment explanation
Indices: 27939--27981 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
27929 GTAAATTTTC
*
27939 ACAAAGGTTTCAAAACCTCT
1 ACAAAGGTTTCAAAACCCCT
*
27959 ACAATAGGTTTCGAAACCCCT
1 ACAA-AGGTTTCAAAACCCCT
27980 AC
1 AC
27982 TAGACCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (20 bp):
ACAAAGGTTTCAAAACCCCT
Found at i:35254 original size:20 final size:20
Alignment explanation
Indices: 35225--35267 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
35215 ATTTCACCAC
*
35225 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
35245 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
35265 ATG
1 ATG
35268 GGCTCTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:35790 original size:11 final size:11
Alignment explanation
Indices: 35774--35801 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
35764 GAATTCAAGA
35774 GAACAACTGTT
1 GAACAACTGTT
35785 GAACAACTGTT
1 GAACAACTGTT
35796 GAACAA
1 GAACAA
35802 ACGATGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (11 bp):
GAACAACTGTT
Found at i:40315 original size:42 final size:42
Alignment explanation
Indices: 40246--40365 Score: 170
Period size: 42 Copynumber: 2.8 Consensus size: 42
40236 CATATTATCA
*
40246 AATAAGTCTCAATAAGTCTAAATTAAATAACATCATAACACC
1 AATAAGTCTCAATAAGTCTAAAATAAATAACATCATAACACC
* * * *
40288 ATTAATTCTCAATAAGTCTAAAATAAATAACACCATAACACT
1 AATAAGTCTCAATAAGTCTAAAATAAATAACATCATAACACC
40330 AATAAGTCTCAATAAGTCT-AAATAAAATCAACATCA
1 AATAAGTCTCAATAAGTCTAAAAT-AAAT-AACATCA
40366 ATAATATTCA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (42 bp):
AATAAGTCTCAATAAGTCTAAAATAAATAACATCATAACACC
Found at i:43129 original size:4 final size:4
Alignment explanation
Indices: 43122--43199 Score: 74
Period size: 4 Copynumber: 19.5 Consensus size: 4
43112 AATGAATTGA
*
43122 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAT GAAA- GAAT -AAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT
*
43167 AAATT GAAACT AAAT AAAT ACAT AAAT AAAT AA
1 AAA-T -AAA-T AAAT AAAT AAAT AAAT AAAT AA
43200 TGCAAGAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
3 11 0.17
4 43 0.68
5 5 0.08
6 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:43130 original size:19 final size:18
Alignment explanation
Indices: 43106--43186 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 18
43096 TCTAACAAAG
43106 TAAATAAATGAATTGAAAA
1 TAAATAAAT-AATTGAAAA
*
43125 TAAATAAATAAAT--AAA
1 TAAATAAATAATTGAAAA
43141 TAAATAAATAA-TGAAAGA
1 TAAATAAATAATTGAAA-A
* *
43159 -ATAATAAAAAATTGAAAC
1 TA-AATAAATAATTGAAAA
43177 TAAATAAATA
1 TAAATAAATA
43187 CATAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.02
16 14 0.27
17 3 0.06
18 19 0.37
19 15 0.29
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (18 bp):
TAAATAAATAATTGAAAA
Found at i:43200 original size:48 final size:48
Alignment explanation
Indices: 43129--43223 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
43119 TGAAAATAAA
43129 TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAAC
1 TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAAC
* * *
43177 TAAATAAATACATAAATAAATAATGCAAGAATAATAAAATATTGAAA
1 TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAA
43224 ATAATTGTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.24
Consensus pattern (48 bp):
TAAATAAATAAATAAATAAATAATGAAAGAATAATAAAAAATTGAAAC
Found at i:50349 original size:34 final size:37
Alignment explanation
Indices: 50302--50403 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
50292 TTTCGTCCTA
50302 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGATATTTT
*
50337 -TAGGATTTAAACTCCTAAAAATAGGATA-ATATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGATATTTT
50372 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
50404 GTTATACTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.47
35 3 0.05
37 27 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGATATTTT
Found at i:50427 original size:37 final size:35
Alignment explanation
Indices: 50302--50437 Score: 150
Period size: 37 Copynumber: 3.8 Consensus size: 35
50292 TTTCGTCCTA
*
50302 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTTAAACTCCTAAAAATAGGATAGAATTT
50337 -TAGGATTTAAACTCCTAAAAATAGGATA-ATATTTT
1 CTAGGATTTAAACTCCTAAAAATAGGATAGA-A-TTT
* *
50372 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTAT
1 -CTAGGATTTAAACTCCTAAAAATAGGATAGAATT-T
** * *
50409 ACTATTATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTTAAACTCCTAAAAATAGGAT
50438 CCACAAGCAC
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
33 1 0.01
34 28 0.33
35 3 0.03
36 2 0.02
37 51 0.59
38 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (35 bp):
CTAGGATTTAAACTCCTAAAAATAGGATAGAATTT
Found at i:50902 original size:2 final size:2
Alignment explanation
Indices: 50895--50941 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
50885 TTATTATTAT
50895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50937 TA TA T
1 TA TA T
50942 TTCTTTAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51354 original size:38 final size:40
Alignment explanation
Indices: 51303--51382 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
51293 AGTGAGAGGG
*
51303 TAGCTTTTCTATTTT-TAAATA-TTTGGTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
51341 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
51381 TA
1 TA
51383 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:51378 original size:2 final size:2
Alignment explanation
Indices: 51371--51405 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
51361 TACTTTGATG
51371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51406 TTTCCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55872 original size:15 final size:13
Alignment explanation
Indices: 55848--55912 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
55838 TAAAAAGGGC
55848 AAAAAG-AAAAATA
1 AAAAAGCAAAAA-A
*
55861 AAGAAGCAAAAAA
1 AAAAAGCAAAAAA
*
55874 CAAAAGC-AAAAA
1 AAAAAGCAAAAAA
*
55886 AAGAA-CAAAAAGA
1 AAAAAGCAAAAA-A
55899 AAAAAG-AAAAAA
1 AAAAAGCAAAAAA
55911 AA
1 AA
55913 GAAAAAGGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
11 1 0.02
12 15 0.36
13 21 0.50
14 5 0.12
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAGCAAAAAA
Found at i:55896 original size:25 final size:25
Alignment explanation
Indices: 55848--55915 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
55838 TAAAAAGGGC
55848 AAAAAGAAAAATAAAGAAGCAAAA-A
1 AAAAAGAAAAA-AAAGAAGCAAAAGA
*
55873 ACAAAAGCAAAAAAAGAA-CAAAAAGA
1 A-AAAAGAAAAAAAAGAAGC-AAAAGA
55899 AAAAAGAAAAAAAAGAA
1 AAAAAGAAAAAAAAGAA
55916 AAAGGGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 1 0.03
25 26 0.68
26 11 0.29
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (25 bp):
AAAAAGAAAAAAAAGAAGCAAAAGA
Found at i:55929 original size:16 final size:16
Alignment explanation
Indices: 55848--55918 Score: 72
Period size: 16 Copynumber: 4.2 Consensus size: 16
55838 TAAAAAGGGC
55848 AAAAAGAAAAATAAAGA
1 AAAAAGAAAAA-AAAGA
* *
55865 AGCAAA-AAACAAAAGCAA
1 A-AAAAGAAAAAAAAG--A
*
55883 AAAAAGAACAAAAAGA
1 AAAAAGAAAAAAAAGA
55899 AAAAAGAAAAAAAAGA
1 AAAAAGAAAAAAAAGA
55915 AAAA
1 AAAA
55919 GGGATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 24 0.55
17 8 0.18
18 12 0.27
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.01
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGA
Found at i:56553 original size:22 final size:22
Alignment explanation
Indices: 56517--56560 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
56507 AGCTACCCCA
56517 TCAAACATTTGAGCATCAAATG
1 TCAAACATTTGAGCATCAAATG
56539 TCAAACCATTT-AGCATCAAATG
1 TCAAA-CATTTGAGCATCAAATG
56561 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACATTTGAGCATCAAATG
Found at i:56566 original size:23 final size:22
Alignment explanation
Indices: 56518--56566 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
56508 GCTACCCCAT
*
56518 CAAACATTTGAGCATCAAATGT
1 CAAACATTTGAGCATCAAATGA
56540 CAAACCATTT-AGCATCAAATGAA
1 CAAA-CATTTGAGCATCAAATG-A
56563 CAAA
1 CAAA
56567 AATGCCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.22
Consensus pattern (22 bp):
CAAACATTTGAGCATCAAATGA
Found at i:57019 original size:18 final size:18
Alignment explanation
Indices: 56996--57031 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
56986 TTAACATCAA
*
56996 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
57014 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
57032 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:57693 original size:36 final size:36
Alignment explanation
Indices: 57595--57752 Score: 280
Period size: 36 Copynumber: 4.3 Consensus size: 36
57585 ATTGAAAACA
*
57595 TTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAG
*
57632 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACAG
57669 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
57705 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
57741 TTTCCCTTGAAA
1 TTTCCCTTGAAA
57753 CAAAATATTT
Statistics
Matches: 117, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
36 71 0.61
37 39 0.33
38 7 0.06
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
Found at i:57700 original size:173 final size:172
Alignment explanation
Indices: 57512--57893 Score: 509
Period size: 173 Copynumber: 2.2 Consensus size: 172
57502 ACTAGAAGAG
* *
57512 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTGTCTCCCTTGAGATAGTTTCTCTTGA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTGTCTCCCTTGAGACAGTTTCCCTTGA
* * *
57576 AACATAAACA-TTGAAAACATTTCC-CTTGAAATAAATTTTCGTCTCTCTTGAGATAGTTTCCCT
66 AACA-AAACATTTGAAAACATTTCCTC-TGAAACAAA-TTTCGTC-CCCTTGAGACAGTTTCCCT
*
57639 TGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
127 TGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
57685 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTTGTCTCCCTTGAGACAGTTTCCCTTG
* * ** * ** *
57750 AAACAAAATATTTGAATATGTTTTCTCTGAAACAAATTTCGTCCCCTTGAGACAGTTTCTTTTGG
65 AAACAAAACATTTGAAAACATTTCCTCTGAAACAAATTTCGTCCCCTTGAGACAGTTTCCCTTGA
* * *
57815 AACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
130 AACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
57858 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
57894 ATCTTTGAAT
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
173 124 0.68
174 11 0.06
175 47 0.26
176 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (172 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTGTCTCCCTTGAGACAGTTTCCCTTGA
AACAAAACATTTGAAAACATTTCCTCTGAAACAAATTTCGTCCCCTTGAGACAGTTTCCCTTGAA
ACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:57787 original size:137 final size:137
Alignment explanation
Indices: 57632--57954 Score: 459
Period size: 137 Copynumber: 2.4 Consensus size: 137
57622 CTTGAGATAG
* * *
57632 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCT
1 TTTCCCCTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATAAATTTTGTCTCTCT
* * *
57697 TGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATT
65 TGAGACAGTTTCCCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATT
*
57762 TGAATATG
130 TGAATATA
* * * * * *
57770 TTTTCTCTGAAACAAATTTCGTC-CCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCCTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT-GAAATAAATTTTGTCTCTCT
* *
57834 TGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTT
65 TGAGACAGTTTCCCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATT
*
57899 TGAATTTA
130 TGAATATA
* *
57907 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAA
1 TTTCCCCTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
57955 CACAAAATCT
Statistics
Matches: 160, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
136 17 0.11
137 115 0.72
138 28 0.17
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (137 bp):
TTTCCCCTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:57851 original size:101 final size:101
Alignment explanation
Indices: 57676--57857 Score: 276
Period size: 101 Copynumber: 1.8 Consensus size: 101
57666 CAGTTTCCCT
* * *
57676 TGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
57741 TTTCCCTTGAAACAAAATATTTGAATATGTTTTCTC
66 TTTCCCTTGAAACAAAATATTTGAATATGTTTTCTC
** * *
57777 TGAAACAAATTTCGTC-CCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 TGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGACA
*
57841 GTTTCTCTTGAAACAAA
65 GTTTCCCTTGAAACAAA
57858 TTTCGTCTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 17 0.24
101 55 0.76
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (101 bp):
TGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
TTTCCCTTGAAACAAAATATTTGAATATGTTTTCTC
Found at i:57878 original size:36 final size:36
Alignment explanation
Indices: 57771--57893 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
57761 TTGAATATGT
*
57771 TTTCTC-TGAAACAAATTTCGTC-CCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * *
57805 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
*
57842 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
57878 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
57894 ATCTTTGAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
34 5 0.07
35 5 0.07
36 43 0.57
37 22 0.29
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:57955 original size:65 final size:65
Alignment explanation
Indices: 57851--58025 Score: 233
Period size: 67 Copynumber: 2.6 Consensus size: 65
57841 GTTTCTCTTG
* ** * *
57851 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTTAAATTTATTTCCCCTA
* *
57916 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTTAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTTAAATTTATTTCCCC
57981 TA
64 TA
* * *
57983 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
58026 CAGATATCTT
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
65 31 0.32
66 6 0.06
67 32 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTTAAATTTATTTCCCCTA
Found at i:58860 original size:105 final size:105
Alignment explanation
Indices: 58629--59289 Score: 911
Period size: 105 Copynumber: 6.3 Consensus size: 105
58619 GCCATCCGCG
* * * * * *
58629 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
58694 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
58738 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
58803 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
58843 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
58908 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
58948 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
59013 ACCGCTTCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
59053 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* ***
59118 ACCGCTGATTGTCAACAA-AA-TT-TC-A-TTCAGATTTA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* ** * *
59153 ATTTCAACTTCACAATGAAGGATATTGGACTTGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * * ** *
59218 ACGGCTGGTTATCAATAAACAATTTC-CTGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAACTTCTC-AATTTCAGAGCCA
* *
59259 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
59290 TGGAACAATG
Statistics
Matches: 504, Mismatches: 41, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
100 77 0.15
101 3 0.01
102 3 0.01
103 5 0.01
104 2 0.00
105 307 0.61
106 82 0.16
107 3 0.01
109 22 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:59881 original size:34 final size:36
Alignment explanation
Indices: 59837--59938 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
59827 TTTTGTCCTA
59837 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
59872 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
59907 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
59939 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:60366 original size:3 final size:3
Alignment explanation
Indices: 60342--60433 Score: 52
Period size: 3 Copynumber: 31.3 Consensus size: 3
60332 TTTTATTCAT
* *
60342 TTA TTT TTA TTA TTCA -TG TTA TTA TTA TTA TTA TTA TATA TATA TATA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA
* * * *
60390 TT- TTA -TA TTA TTC TCA TTC TT- TTA CTA -TA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
60433 T
1 T
60434 ATATATATAT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
2 10 0.14
3 49 0.69
4 12 0.17
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:60369 original size:18 final size:17
Alignment explanation
Indices: 60330--60373 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
60320 ATTATATGGA
60330 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
60346 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
60364 TATTATTATT
1 TATTATTATT
60374 ATTATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 13 0.54
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:60438 original size:2 final size:2
Alignment explanation
Indices: 60431--60459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60421 TTATTATTAT
60431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60460 TTCTTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60572 original size:2 final size:2
Alignment explanation
Indices: 60567--60591 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60557 TACCTATTAT
60567 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
60592 TCTTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60871 original size:38 final size:40
Alignment explanation
Indices: 60820--60899 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
60810 AGTGAGAGTG
*
60820 TAGCTTTTCTATTTT-TAAATA-TTTGGTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
60858 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
60898 TA
1 TA
60900 TATATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:72213 original size:31 final size:32
Alignment explanation
Indices: 72175--72250 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
72165 TTGTATATTC
* *
72175 TCTAAATGTGACACTGACA-CTATTGTG-ATTA
1 TCTAAATGTAACACT-AAATCTATTGTGCATTA
* *
72206 TCTAAATGTAATACTAAATCTGTTGTGCATTA
1 TCTAAATGTAACACTAAATCTATTGTGCATTA
*
72238 TCTAAATGCAACA
1 TCTAAATGTAACA
72251 TTGACTCTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.05
31 20 0.54
32 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (32 bp):
TCTAAATGTAACACTAAATCTATTGTGCATTA
Found at i:73464 original size:20 final size:20
Alignment explanation
Indices: 73441--73485 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
73431 TTAGAGGCAA
*
73441 TATCGATACTCTCCCAGCAT
1 TATCAATACTCTCCCAGCAT
*
73461 TATCAATACTCTCCTAGCAT
1 TATCAATACTCTCCCAGCAT
73481 TATCA
1 TATCA
73486 TAATCCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (20 bp):
TATCAATACTCTCCCAGCAT
Found at i:74273 original size:36 final size:36
Alignment explanation
Indices: 74226--74297 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
74216 ATAACTAACG
74226 TGGAAGATGGTAATTTGGATCTCTCATAATCGTCAT
1 TGGAAGATGGTAATTTGGATCTCTCATAATCGTCAT
74262 TGGAAGATGGTAATTTGGATCTCTCATAATCGTCAT
1 TGGAAGATGGTAATTTGGATCTCTCATAATCGTCAT
74298 ACTTTTTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (36 bp):
TGGAAGATGGTAATTTGGATCTCTCATAATCGTCAT
Done.