Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002278.1 Hibiscus syriacus cultivar Beakdansim tig00004634_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: 191382
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2699 original size:34 final size:34
Alignment explanation
Indices: 2650--2715 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
2640 GGCAACCAAC
*
2650 TTGAAAATAGTTTTCAAAGTTTGGTAAATGTTTCT
1 TTGAAAATAGTTTTCAAAATTTGGTAAA-GTTTCT
*
2685 TTGAAAA-GGTTTTCAAAATTTGGTAAAGTTT
1 TTGAAAATAGTTTTCAAAATTTGGTAAAGTTT
2716 GGTAGATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 4 0.14
34 18 0.62
35 7 0.24
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (34 bp):
TTGAAAATAGTTTTCAAAATTTGGTAAAGTTTCT
Found at i:4465 original size:22 final size:25
Alignment explanation
Indices: 4437--4489 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
4427 AAGTCAAAAT
4437 TTTTAA-ATTTTAAAA-A-TAATTA
1 TTTTAATATTTTAAAAGATTAATTA
*
4459 TTTTAAATATTTTAAAAGATTAATTT
1 TTTT-AATATTTTAAAAGATTAATTA
4485 TTTTA
1 TTTTA
4490 TAAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 4 0.15
23 2 0.08
24 9 0.35
25 2 0.08
26 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTAATATTTTAAAAGATTAATTA
Found at i:4575 original size:17 final size:18
Alignment explanation
Indices: 4545--4584 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
4535 TATTTTTTAT
4545 ATTTTTATCAAATAATAA
1 ATTTTTATCAAATAATAA
4563 ATTTTTATC-AATAATAA
1 ATTTTTATCAAATAATAA
4580 ATTTT
1 ATTTT
4585 AAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTTATCAAATAATAA
Found at i:4589 original size:14 final size:15
Alignment explanation
Indices: 4554--4593 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
4544 TATTTTTATC
4554 AAATAATAAATTTTT
1 AAATAATAAATTTTT
4569 ATCAATAATAAA-TTTT
1 A--AATAATAAATTTTT
4585 AAATAATAA
1 AAATAATAA
4594 TTAGTCGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 1 0.04
16 5 0.22
17 9 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAATAAATTTTT
Found at i:8932 original size:31 final size:31
Alignment explanation
Indices: 8897--8971 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
8887 AAAAAAATAA
8897 TAAGATATGGTCACTTTCATTTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
* **
8928 TAAGATATGGTCGCTTTTGTTTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
*
8959 TAAGATGTGGTCA
1 TAAGATATGGTCA
8972 TCATGGGTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCATTTTTATTTAAT
Found at i:9142 original size:25 final size:23
Alignment explanation
Indices: 9110--9179 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 23
9100 ATTTTTAAAT
*
9110 TAAGTTAATAATAAACTATATTTAA
1 TAAGTTAATAATAAA-AATATTT-A
*
9135 TAAGTTAAT-ATAAAAATATTTT
1 TAAGTTAATAATAAAAATATTTA
9157 TAAGTTAATATATATAAAATATT
1 TAAGTTAATA-ATA-AAAATATT
9180 ATGAATTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.22
23 6 0.15
24 8 0.20
25 17 0.43
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAGTTAATAATAAAAATATTTA
Found at i:10112 original size:21 final size:21
Alignment explanation
Indices: 10086--10126 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10076 CCATAACATG
* *
10086 GGGTATCGGTACCCCTTCATA
1 GGGTATCGATACACCTTCATA
10107 GGGTATCGATACACCTTCAT
1 GGGTATCGATACACCTTCAT
10127 TAAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACACCTTCATA
Found at i:10191 original size:20 final size:19
Alignment explanation
Indices: 10166--10231 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
10156 CCGTTGCAGC
10166 CAGGGTGTATGGATACACT
1 CAGGGTGTATGGATACACT
10185 ACAGGGTGTATCGG-TACAC-
1 -CAGGGTGTAT-GGATACACT
10204 CA--GTGTATGGATACACT
1 CAGGGTGTATGGATACACT
10221 GCAGGGTGTAT
1 -CAGGGTGTAT
10232 TGGTTCACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.05
16 11 0.28
18 4 0.10
20 21 0.52
21 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
CAGGGTGTATGGATACACT
Found at i:10340 original size:36 final size:37
Alignment explanation
Indices: 10271--10340 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
10261 CAGTCATAGG
* *
10271 TGTATGGATACACCTGCAGGGGGTATCGGTACACCAA
1 TGTATGGATACACCTGCAAGGGGTATCGATACACCAA
10308 TGTATGGATACA-CT-CATAGGGGTATCGATACAC
1 TGTATGGATACACCTGCA-AGGGGTATCGATACAC
10341 ATTTGCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 2 0.07
36 16 0.53
37 12 0.40
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (37 bp):
TGTATGGATACACCTGCAAGGGGTATCGATACACCAA
Found at i:10571 original size:21 final size:21
Alignment explanation
Indices: 10553--10591 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10543 ATGTTTAATG
*
10553 AAAA-GATATCAATTGTTAAC
1 AAAAGGATACCAATTGTTAAC
10573 AAAAGGATACCAATTGTTA
1 AAAAGGATACCAATTGTTA
10592 CCAATTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (21 bp):
AAAAGGATACCAATTGTTAAC
Found at i:13703 original size:20 final size:20
Alignment explanation
Indices: 13677--13741 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
13667 CCGTTGCAGC
13677 CAGGGTGTATGGATACACTG
1 CAGGGTGTATGGATACACTG
* *
13697 TAGGGTGTATGG-TAAAC--
1 CAGGGTGTATGGATACACTG
13714 CA--GTGTATGGATACACTG
1 CAGGGTGTATGGATACACTG
13732 CAGGGTGTAT
1 CAGGGTGTAT
13742 CAGTACACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
15 8 0.22
16 4 0.11
17 1 0.03
18 2 0.06
19 4 0.11
20 17 0.47
ACGTcount: A:0.26, C:0.12, G:0.34, T:0.28
Consensus pattern (20 bp):
CAGGGTGTATGGATACACTG
Found at i:15049 original size:29 final size:29
Alignment explanation
Indices: 15007--15063 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
14997 AAAATTATCG
*
15007 CTTTGGTCCCTAAACTTCCAAACTTTATA
1 CTTTGGTCCCTAAACTTCCAAAATTTATA
*
15036 CTTTGG-CCACTAAACTTTCAAAATTTAT
1 CTTTGGTCC-CTAAACTTCCAAAATTTAT
15064 GTTTTAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (29 bp):
CTTTGGTCCCTAAACTTCCAAAATTTATA
Found at i:20867 original size:8 final size:8
Alignment explanation
Indices: 20854--20894 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
20844 CTCATTTTCA
20854 GAGAATTT
1 GAGAATTT
20862 GAGAATTT
1 GAGAATTT
*
20870 -AGAGTTT
1 GAGAATTT
*
20877 GGGAATTT
1 GAGAATTT
20885 GAGAATTT
1 GAGAATTT
20893 GA
1 GA
20895 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:21194 original size:128 final size:128
Alignment explanation
Indices: 20967--21720 Score: 1350
Period size: 128 Copynumber: 5.9 Consensus size: 128
20957 ATCGGAGTAT
20967 TATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
21031 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
21094 TATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTGTCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
21159 TTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
**
21222 TATTCACATGAAGGCGCGTTCCCAAGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
21287 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
21350 TATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCTTTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
21415 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
21478 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
* *
21543 TTGCCCTATTATGTCACTCATGTCCCTCGGAGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * *
21606 -AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
*
21670 ATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTA
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
21721 AATCAGGTAA
Statistics
Matches: 602, Mismatches: 23, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
127 28 0.05
128 574 0.95
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:22133 original size:33 final size:34
Alignment explanation
Indices: 22072--22171 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
22062 AAATTTAATG
*
22072 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
22106 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
22139 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
22172 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:22741 original size:21 final size:21
Alignment explanation
Indices: 22690--22783 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
22680 TATGGTATAA
* *
22690 AACCCTACGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
22711 AA-CATGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
22732 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
22753 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
22774 AACCCTGCGG
1 AACCCTGCGG
22784 AGATGGCATA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 2 0.03
21 62 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:22813 original size:21 final size:21
Alignment explanation
Indices: 22787--22834 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
22777 CCTGCGGAGA
*
22787 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
22808 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
22829 GGGCAT
1 TGGCAT
22835 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:24604 original size:17 final size:19
Alignment explanation
Indices: 24582--24625 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
24572 ATAAATATAT
24582 AAATATTAT-TTTA-ATAA
1 AAATATTATATTTACATAA
*
24599 AAATATAATATTTACATAA
1 AAATATTATATTTACATAA
*
24618 ATATATTA
1 AAATATTA
24626 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTATATTTACATAA
Found at i:24608 original size:34 final size:32
Alignment explanation
Indices: 24562--24650 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 32
24552 TTAATAATTC
24562 TAAATAAATAATAAATATATAAATATTATTTTAATA
1 TAAA-AAATAATAAATATATAAATA-TA--TTAATA
* ** *
24598 -AAAATATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAAATATATAAATATATTAATA
* *
24629 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAAATATATAAA
24651 AAAATACTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
31 6 0.14
32 16 0.37
33 2 0.05
34 16 0.37
35 3 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATAAATATATAAATATATTAATA
Found at i:24666 original size:34 final size:34
Alignment explanation
Indices: 24597--24668 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
24587 TTATTTTAAT
* * *
24597 AAAAATATAATATTTACATAAATATATTAATATA
1 AAAAATATAATATTTACATAAAAATACTAACATA
24631 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAAT-ATAA-TATTTACATAAAAATACTAACATA
24665 AAAA
1 AAAA
24669 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 22 0.67
35 5 0.15
36 6 0.18
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAAATATAATATTTACATAAAAATACTAACATA
Found at i:28892 original size:21 final size:22
Alignment explanation
Indices: 28859--28903 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28849 TAAGAATTTT
*
28859 TATTTTTATATT-ATTAAAATA
1 TATTTTTATATTAATAAAAATA
28880 TATTATTTA-ATTAATAAAAATA
1 TATT-TTTATATTAATAAAAATA
28902 TA
1 TA
28904 AAATATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTTTATATTAATAAAAATA
Found at i:31095 original size:16 final size:15
Alignment explanation
Indices: 31070--31127 Score: 80
Period size: 16 Copynumber: 3.7 Consensus size: 15
31060 TGAAAAATTA
31070 GCAAAGTTGAAAGTT
1 GCAAAGTTGAAAGTT
*
31085 GACAAAATTGAAAGTTT
1 G-CAAAGTTGAAAG-TT
31102 GCAAAGTTGAAAGTT
1 GCAAAGTTGAAAGTT
31117 GGCAAAGTTGA
1 -GCAAAGTTGA
31128 CACCTTTGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
15 3 0.08
16 32 0.84
17 3 0.08
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.26
Consensus pattern (15 bp):
GCAAAGTTGAAAGTT
Found at i:31126 original size:9 final size:8
Alignment explanation
Indices: 31070--31126 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 8
31060 TGAAAAATTA
31070 GCAAAGTT
1 GCAAAGTT
31078 G-AAAGTT
1 GCAAAGTT
*
31085 GACAAAATT
1 G-CAAAGTT
31094 G-AAAGTTT
1 GCAAAG-TT
31102 GCAAAGTT
1 GCAAAGTT
31110 G-AAAGTT
1 GCAAAGTT
31117 GGCAAAGTT
1 -GCAAAGTT
31126 G
1 G
31127 ACACCTTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 16 0.39
8 9 0.22
9 16 0.39
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.26
Consensus pattern (8 bp):
GCAAAGTT
Found at i:35830 original size:7 final size:7
Alignment explanation
Indices: 35818--35880 Score: 54
Period size: 7 Copynumber: 8.1 Consensus size: 7
35808 AAAAATTAGC
35818 AAAGTTG
1 AAAGTTG
35825 AAAGTTG
1 AAAGTTG
*
35832 ACAAAATTG
1 --AAAGTTG
35841 AAAGTTGG
1 AAAGTT-G
35849 CAAAGTTG
1 -AAAGTTG
35857 AAAGTTGG
1 AAAGTT-G
*
35865 CAAAATTG
1 -AAAGTTG
35873 AAAGTTG
1 AAAGTTG
35880 A
1 A
35881 CAAAGTTGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
7 25 0.54
8 4 0.09
9 17 0.37
ACGTcount: A:0.44, C:0.05, G:0.25, T:0.25
Consensus pattern (7 bp):
AAAGTTG
Found at i:35841 original size:16 final size:16
Alignment explanation
Indices: 35817--35889 Score: 110
Period size: 16 Copynumber: 4.6 Consensus size: 16
35807 GAAAAATTAG
35817 CAAAGTTGAAAGTTGA
1 CAAAGTTGAAAGTTGA
* *
35833 CAAAATTGAAAGTTGG
1 CAAAGTTGAAAGTTGA
*
35849 CAAAGTTGAAAGTTGG
1 CAAAGTTGAAAGTTGA
*
35865 CAAAATTGAAAGTTGA
1 CAAAGTTGAAAGTTGA
35881 CAAAGTTGA
1 CAAAGTTGA
35890 CATCTTTGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.44, C:0.07, G:0.25, T:0.25
Consensus pattern (16 bp):
CAAAGTTGAAAGTTGA
Found at i:35853 original size:32 final size:32
Alignment explanation
Indices: 35816--35889 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
35806 TGAAAAATTA
35816 GCAAAGTTGAAAGTTGACAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTGACAAAATTGAAAGTTG
*
35848 GCAAAGTTGAAAGTTGGCAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTGACAAAATTGAAAGTTG
*
35880 ACAAAGTTGA
1 GCAAAGTTGA
35890 CATCTTTGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (32 bp):
GCAAAGTTGAAAGTTGACAAAATTGAAAGTTG
Found at i:37056 original size:38 final size:38
Alignment explanation
Indices: 37013--37155 Score: 144
Period size: 38 Copynumber: 3.6 Consensus size: 38
37003 TAGGATAGAA
37013 ATTTTAATTAGATGGAGAGATTTTAGATAAAAGATAAG
1 ATTTTAATTAGATGGAGAGATTTTAGATAAAAGATAAG
* *
37051 ATTTTAATTAGATGGAG-GATTTTTGAATGAAAGATATCGGGAGAG
1 ATTTTAATTAGATGGAGAGATTTTAG-AT-AAA-AGAT----A-AG
* * *
37096 ATTTTAATTAGATGGAGAGATCTTGGATGAAAGATAAG
1 ATTTTAATTAGATGGAGAGATTTTAGATAAAAGATAAG
* *
37134 ATTTTAATTAAATGGAGGGATT
1 ATTTTAATTAGATGGAGAGATT
37156 GCTGAATGAA
Statistics
Matches: 87, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
37 7 0.08
38 40 0.46
39 4 0.05
40 3 0.03
43 3 0.03
44 3 0.03
45 21 0.24
46 6 0.07
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.34
Consensus pattern (38 bp):
ATTTTAATTAGATGGAGAGATTTTAGATAAAAGATAAG
Found at i:37073 original size:18 final size:18
Alignment explanation
Indices: 37013--37073 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
37003 TAGGATAGAA
37013 ATTTTAATTAGATGGAGAG
1 ATTTTAATTAGATGGAG-G
* *
37032 ATTTTAGATAAAAGAT--AAG
1 ATTTTA-AT--TAGATGGAGG
37051 ATTTTAATTAGATGGAGG
1 ATTTTAATTAGATGGAGG
37069 ATTTT
1 ATTTT
37074 TGAATGAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
16 4 0.12
18 9 0.27
19 13 0.39
20 3 0.09
22 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (18 bp):
ATTTTAATTAGATGGAGG
Found at i:37101 original size:45 final size:43
Alignment explanation
Indices: 37049--37198 Score: 143
Period size: 45 Copynumber: 3.4 Consensus size: 43
37039 ATAAAAGATA
*
37049 AGATTTTAATTAGATGGAGGATTTTTGAATGAAAGATATCGGGAG
1 AGATTTTAATTAGATGGAGGATTCTTGAATGAAAGATAT--GGAG
*
37094 AGATTTTAATTAGATGGAGAGA-TCTTGGATGAAAG--AT--A-
1 AGATTTTAATTAGATGGAG-GATTCTTGAATGAAAGATATGGAG
*
37132 AGATTTTAATTAAATGGAGGGATTGC-TGAATGAAAGATATATGAAGAG
1 AGATTTTAATTAGATGGA-GGATT-CTTGAATGAAAG--ATATG--GAG
37180 AGATTTTAATTAGATGGAG
1 AGATTTTAATTAGATGGAG
37199 ATATTTTAGG
Statistics
Matches: 87, Mismatches: 5, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
38 19 0.22
39 12 0.14
40 1 0.01
43 4 0.05
45 30 0.34
46 2 0.02
47 2 0.02
48 17 0.20
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (43 bp):
AGATTTTAATTAGATGGAGGATTCTTGAATGAAAGATATGGAG
Found at i:37226 original size:84 final size:82
Alignment explanation
Indices: 37013--37211 Score: 249
Period size: 83 Copynumber: 2.4 Consensus size: 82
37003 TAGGATAGAA
* **
37013 ATTTTAATTAGATGGAGAGATTTTA-GATAAAAGATAAGATTTTAATTAGATGGAGGATTTTTGA
1 ATTTTAATTAGATGGAGAGATTTTAGGATAAAAGAT--GATTTTAATTAAATGGAGGATTGCTGA
*
37077 ATGAAAGATATCGGGAGAG
64 ATGAAAGATATCGAGAGAG
* *
37096 ATTTTAATTAGATGGAGAGATCTT-GGATGAAAGATAAGATTTTAATTAAATGGAGGGATTGCTG
1 ATTTTAATTAGATGGAGAGATTTTAGGATAAAAGAT--GATTTTAATTAAATGGA-GGATTGCTG
*
37160 AATGAAAGATATATGAAGAGAG
63 AATGAAAGATAT-CG-AGAGAG
*
37182 ATTTTAATTAGATGGAGATATTTTAGGATA
1 ATTTTAATTAGATGGAGAGATTTTAGGATA
37212 CAAAATCATT
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
83 50 0.50
84 19 0.19
85 1 0.01
86 27 0.27
87 4 0.04
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.34
Consensus pattern (82 bp):
ATTTTAATTAGATGGAGAGATTTTAGGATAAAAGATGATTTTAATTAAATGGAGGATTGCTGAAT
GAAAGATATCGAGAGAG
Found at i:40412 original size:3 final size:3
Alignment explanation
Indices: 40392--40472 Score: 87
Period size: 3 Copynumber: 27.7 Consensus size: 3
40382 TTTTCATTTT
* *
40392 TTA TT- TTA TT- TATA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
40436 TTA TAA TTA TAA TTA TTA TTA TTA TTA ATA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40473 TAATATTACA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
2 5 0.08
3 59 0.91
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:40889 original size:20 final size:20
Alignment explanation
Indices: 40860--40908 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
40850 CATCTGCGAG
40860 CAAA-AAAAAGAGACAGAGA
1 CAAAGAAAAAGAGACAGAGA
*
40879 CAGAGAAAAAGAGACAGAGA
1 CAAAGAAAAAGAGACAGAGA
40899 CAAAGAAAAA
1 CAAAGAAAAA
40909 AAGAGGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.67, C:0.10, G:0.22, T:0.00
Consensus pattern (20 bp):
CAAAGAAAAAGAGACAGAGA
Found at i:40893 original size:14 final size:14
Alignment explanation
Indices: 40874--40904 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40864 AAAAAGAGAC
40874 AGAGACAGAGAAAA
1 AGAGACAGAGAAAA
*
40888 AGAGACAGAGACAA
1 AGAGACAGAGAAAA
40902 AGA
1 AGA
40905 AAAAAAGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.10, G:0.29, T:0.00
Consensus pattern (14 bp):
AGAGACAGAGAAAA
Found at i:41613 original size:30 final size:28
Alignment explanation
Indices: 41579--41634 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
41569 TATATTTAGG
41579 ATAAATAACAGATTTAATCCCTTAATTTTA
1 ATAAATAACA-ATTTAATCCC-TAATTTTA
* *
41609 ATAAATAATATTTTAATCCCTAATTT
1 ATAAATAACAATTTAATCCCTAATTT
41635 ATATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 9 0.38
30 9 0.38
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (28 bp):
ATAAATAACAATTTAATCCCTAATTTTA
Found at i:42612 original size:18 final size:18
Alignment explanation
Indices: 42571--42613 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
42561 AATTTTTATA
42571 TTTATTTATTATTTTCAT
1 TTTATTTATTATTTTCAT
**
42589 AATATTTA-TATGTTTCAT
1 TTTATTTATTAT-TTTCAT
42607 TTTATTT
1 TTTATTT
42614 TATTTGCAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTATTATTTTCAT
Found at i:42628 original size:15 final size:13
Alignment explanation
Indices: 42608--42645 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
42598 ATGTTTCATT
42608 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
42623 TTATTTTATTTCA
1 TTATTTTATTTCA
42636 TTA-TTTATTT
1 TTATTTTATTT
42646 TTCTGTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:53622 original size:16 final size:16
Alignment explanation
Indices: 53596--53640 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
53586 TTTGAATACA
*
53596 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
53613 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
53628 ATTCAATTTATTT
1 ATTCAATTTATTT
53641 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:54528 original size:83 final size:83
Alignment explanation
Indices: 54389--55148 Score: 1394
Period size: 83 Copynumber: 9.2 Consensus size: 83
54379 GAATAAGTGC
54389 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
54454 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
*
54472 AATTTCCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
*
54537 CATTGAATTTAGAAGATG
66 CATTGAATTTGGAAGATG
* * *
54555 AATTTGCTAATAGCATCTTCTGGAAGTGTTTTTTGAGTTATCTGATCCGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
54620 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
54638 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
*
54703 CATTGAATTTAGAAGATG
66 CATTGAATTTGGAAGATG
*
54721 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
54786 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
54804 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
*
54869 CATTGAATTTAGAAGATG
66 CATTGAATTTGGAAGATG
*
54887 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
54952 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* *
54970 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAC
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
*
55035 CATTGAATTTGAAAGATG
66 CATTGAATTTGGAAGATG
* *
55053 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
55118 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
55136 AATTTGCTCATAG
1 AATTTGCTCATAG
55149 TAGAAATAAG
Statistics
Matches: 652, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 652 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.37
Consensus pattern (83 bp):
AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
CATTGAATTTGGAAGATG
Found at i:56261 original size:112 final size:112
Alignment explanation
Indices: 55933--56737 Score: 1152
Period size: 112 Copynumber: 7.1 Consensus size: 112
55923 TAGCAAAGAT
* * * * *
55933 TCAAATCCATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
55998 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * * *
56045 TTGAAT-TCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCA
1 TCAAATCT-ATCACTTGATGGAGCAGCTTTTCCAGAG-A-AGTTCATAATGAGAAGAA--C-TCA
*
56108 TCTGAAGAAGCAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
60 TCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
56161 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
56226 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * * *
56273 TTGAAT-TCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCA
1 TCAAATCT-ATCACTTGATGGAGCAGCTTTTCCAGAG-A-AGTTCATAATGAGAAGAA--C-TCA
56336 TCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
60 TCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
56389 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
56454 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
56501 TCAAATCTATCACTTGATGGAGCAGCTTTTTCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
56566 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
56613 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
56678 GAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
66 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
56725 AT-AATTCTATCAC
1 -TCAAATCTATCAC
56738 AGAAGGAGAT
Statistics
Matches: 630, Mismatches: 46, Indels: 34
0.89 0.06 0.05
Matches are distributed among these distances:
111 3 0.00
112 391 0.62
113 39 0.06
115 38 0.06
116 155 0.25
117 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (112 bp):
TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:56330 original size:228 final size:228
Alignment explanation
Indices: 55933--56723 Score: 1351
Period size: 228 Copynumber: 3.5 Consensus size: 228
55923 TAGCAAAGAT
* * * * *
55933 TCAAATCCATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
55998 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGAT
*
56063 GGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGCAAGAAGAAA
131 GGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAA
56128 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
196 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
56161 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
56226 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGAT
56291 GGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAA
131 GGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAA
56356 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
196 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
56389 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
* * * * * * *
56454 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTCAAATCTATCACTTGA
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC-ATCATTTGA
* * * **
56518 TGGAGCAGCTTTTTCA-G-AGAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGA
130 TGGATCAACATTGCCAGGTAG-AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGA
56578 AATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
194 AATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
56613 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
*
56678 GAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTG
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
56724 CATAATTCTA
Statistics
Matches: 539, Mismatches: 22, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
224 163 0.30
225 1 0.00
226 2 0.00
227 24 0.04
228 349 0.65
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (228 bp):
TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGAT
GGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAA
TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:56566 original size:340 final size:337
Alignment explanation
Indices: 55933--56737 Score: 1217
Period size: 340 Copynumber: 2.4 Consensus size: 337
55923 TAGCAAAGAT
55933 TCAAATCCATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAAT-CATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
55998 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAAT-TCATCATTTGA
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-CTAAATCT-ATCACTTGA
*
56062 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGCAAGAAGAA
128 TGGAGCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGCAAGAAGAA
56127 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGAGCAGCTTTTC
192 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGAGCAGCTTTTC
*
56192 CAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
257 CAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAC
* *
56257 TTGTTCAACTTTTTGTT
322 TTGTTCAACCTTTTG-C
* * *
56274 TGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATC
1 TCAAATCATCACTTGATGGATCAACATTGCCAGAG-A-AGTTCATAATGAGAAGAA--C-TCATC
* * *
56338 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACT
61 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCT-AAATCTATCACT
* * * *
56403 TGATGGAGCAGCTTTTCCA-G-AGAAGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAA
125 TGATGGAGCAACATTGCCAGGTAG-AGTTCATAATGAGAAGAACCGTCATCTGAAGAAGCAAGAA
56464 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGAGCAGCTT
189 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGAGCAGCTT
*
56529 TTTCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
254 TTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
*
56594 AATTTGTTCAACCTTTTGC
319 AACTTGTTCAACCTTTTGC
* * * *
56613 TCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATC-ATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
* *
56678 GAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCAC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC-TAAATCTATCAC
56738 AGAAGGAGAT
Statistics
Matches: 422, Mismatches: 31, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
336 62 0.15
337 2 0.00
339 24 0.06
340 211 0.50
341 24 0.06
342 2 0.00
343 21 0.05
344 75 0.18
345 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (337 bp):
TCAAATCATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTAAATCTATCACTTGATGG
AGCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGCAAGAAGAAATTC
ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGAGCAGCTTTTCCAGA
GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGT
TCAACCTTTTGC
Found at i:57034 original size:15 final size:15
Alignment explanation
Indices: 57011--57091 Score: 94
Period size: 15 Copynumber: 5.3 Consensus size: 15
57001 TTTTCATTTT
57011 TTATT-TTATT-TATA
1 TTATTATTATTATA-A
57025 TTATTATTATTATAA
1 TTATTATTATTATAA
*
57040 TTATAATTATTATAA
1 TTATTATTATTATAA
* *
57055 TTATAATTATAATAA
1 TTATTATTATTATAA
57070 TTATTATTATTAATATA
1 TTATTATTATT-ATA-A
57087 TTATT
1 TTATT
57092 TAATATTACA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
14 5 0.08
15 43 0.73
16 5 0.08
17 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATTATTATAA
Found at i:57042 original size:6 final size:6
Alignment explanation
Indices: 57027--57081 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
57017 TATTTATATT
* * *
57027 ATTATT ATTATA ATTATA A-T-T- ATTATA ATTATA ATTATA ATAATT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA
*
57072 ATTATT ATTA
1 ATTATA ATTA
57082 ATATATTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
3 1 0.02
4 2 0.05
5 2 0.05
6 37 0.88
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
ATTATA
Found at i:57498 original size:6 final size:6
Alignment explanation
Indices: 57487--57539 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
57477 AGCAAAAAAA
* *
57487 AGAGAC AGAGAC AGAGAAAA AGAGAC AGAGAC AGAGAAAA AGAGAC AGAGAC
1 AGAGAC AGAGAC AGAG--AC AGAGAC AGAGAC AGAG--AC AGAGAC AGAGAC
57539 A
1 A
57540 AAGAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 29 0.74
8 10 0.26
ACGTcount: A:0.58, C:0.11, G:0.30, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:57508 original size:20 final size:20
Alignment explanation
Indices: 57483--57547 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
57473 TGCGAGCAAA
57483 AAAAAGAGACAGAGACAGAG
1 AAAAAGAGACAGAGACAGAG
57503 AAAAAGAGACAGAGACAGAG
1 AAAAAGAGACAGAGACAGAG
*
57523 AAAAAGAGACAGAGACAAAG
1 AAAAAGAGACAGAGACAGAG
57543 AAAAA
1 AAAAA
57548 AAGAGGAAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.65, C:0.09, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAAGAGACAGAGACAGAG
Found at i:57512 original size:14 final size:14
Alignment explanation
Indices: 57483--57543 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
57473 TGCGAGCAAA
57483 AAAAAGAGACAGAG
1 AAAAAGAGACAGAG
* * *
57497 --ACAGAGAAAAAG
1 AAAAAGAGACAGAG
* *
57509 AGACAGAGACAGAG
1 AAAAAGAGACAGAG
57523 AAAAAGAGACAGAG
1 AAAAAGAGACAGAG
*
57537 ACAAAGA
1 AAAAAGA
57544 AAAAAAGAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
12 9 0.24
14 28 0.76
ACGTcount: A:0.62, C:0.10, G:0.28, T:0.00
Consensus pattern (14 bp):
AAAAAGAGACAGAG
Found at i:58253 original size:30 final size:28
Alignment explanation
Indices: 58219--58274 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
58209 TATATTTAGG
58219 ATAAATAACAGATTTAATCCCTTAATTTTA
1 ATAAATAACA-ATTTAATCCC-TAATTTTA
* *
58249 ATAAATAATATTTTAATCCCTAATTT
1 ATAAATAACAATTTAATCCCTAATTT
58275 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 9 0.38
30 9 0.38
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (28 bp):
ATAAATAACAATTTAATCCCTAATTTTA
Found at i:62829 original size:32 final size:32
Alignment explanation
Indices: 62793--62888 Score: 93
Period size: 32 Copynumber: 3.0 Consensus size: 32
62783 AATTCGCAGT
62793 AGAGTCAATATTACATTTAGATAATGCACAAC
1 AGAGTCAATATTACATTTAGATAATGCACAAC
* *** * * * **
62825 AGAGTTAGCGTTGCATTCAGATAGTGCACATG
1 AGAGTCAATATTACATTTAGATAATGCACAAC
* *
62857 AGAGTCAATATCATATTTAGATAATGCACAAC
1 AGAGTCAATATTACATTTAGATAATGCACAAC
62889 TTATACCCCT
Statistics
Matches: 44, Mismatches: 20, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (32 bp):
AGAGTCAATATTACATTTAGATAATGCACAAC
Found at i:64783 original size:21 final size:23
Alignment explanation
Indices: 64752--64794 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
64742 ATATTTTTTT
64752 TATATTTTTAATAAT-TAAATAA
1 TATATTTTTAATAATATAAATAA
64774 TATA-TTTTAATAATATAAATA
1 TATATTTTTAATAATATAAATA
64795 TAAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATTTTTAATAATATAAATAA
Found at i:69021 original size:20 final size:20
Alignment explanation
Indices: 68996--69047 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
68986 CAAAAGTTAG
*
68996 TAGTATCGATACCTAGAGGT
1 TAGTATCGATACCCAGAGGT
*
69016 TAGTATCGATACCCAGATGT
1 TAGTATCGATACCCAGAGGT
* *
69036 TAATACCGATAC
1 TAGTATCGATAC
69048 TGAAGGGTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (20 bp):
TAGTATCGATACCCAGAGGT
Found at i:85391 original size:2 final size:2
Alignment explanation
Indices: 85384--85410 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
85374 CTACACAATC
85384 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
85411 CTATCAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85535 original size:24 final size:20
Alignment explanation
Indices: 85486--85543 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
85476 TTCCCATTGA
*
85486 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
85506 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
85529 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
85544 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:92377 original size:19 final size:20
Alignment explanation
Indices: 92338--92381 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
92328 TCCCAGTTAG
* *
92338 GTTCAGCTCCTTTTCAGCTA
1 GTTCAGCTCCTTTCCAACTA
92358 GTTCAGCT-CTTTCCAACTA
1 GTTCAGCTCCTTTCCAACTA
92377 GTTCA
1 GTTCA
92382 AATACCTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.39
Consensus pattern (20 bp):
GTTCAGCTCCTTTCCAACTA
Found at i:96457 original size:37 final size:37
Alignment explanation
Indices: 96416--96494 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
96406 CATGAAGAAA
*
96416 GTTGGTGCTGATTAGGATCATATCATCCCTTCTTATT
1 GTTGGTGCTGATTAGGATCATATCATCCCTCCTTATT
96453 GTTGGTGCTGATTAGGATCATATCATCCCTCCTTATT
1 GTTGGTGCTGATTAGGATCATATCATCCCTCCTTATT
*
96490 ATTGG
1 GTTGG
96495 CAATTTTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (37 bp):
GTTGGTGCTGATTAGGATCATATCATCCCTCCTTATT
Found at i:99384 original size:21 final size:19
Alignment explanation
Indices: 99350--99389 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
99340 GAAAATACAT
99350 GTTTTTAATGAAGTTTCATG
1 GTTTTTAATGAAG-TTCATG
*
99370 GTTTTTACTGAAAGTTCATG
1 GTTTTTAATG-AAGTTCATG
99390 CTCTTGGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (19 bp):
GTTTTTAATGAAGTTCATG
Found at i:101139 original size:28 final size:28
Alignment explanation
Indices: 101099--101156 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
101089 GAAGAAAGAA
*
101099 AAAAATTAGATGGTTTTGGTTCAAAACT
1 AAAAATTAGATGGTTTTGGTTAAAAACT
101127 AAAAATTAGATGGTTTTGGTTAAAAACT
1 AAAAATTAGATGGTTTTGGTTAAAAACT
101155 AA
1 AA
101157 CACTGAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.34
Consensus pattern (28 bp):
AAAAATTAGATGGTTTTGGTTAAAAACT
Found at i:103911 original size:14 final size:14
Alignment explanation
Indices: 103892--103934 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 14
103882 TCATGTTCAG
103892 ATTTTAAAAAATAT
1 ATTTTAAAAAATAT
*
103906 ATTTTAAATAATAATTT
1 ATTTT-AA-AA-AATAT
103923 ATTTTAAAAAAT
1 ATTTTAAAAAAT
103935 TTTGACACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 8 0.32
15 4 0.16
16 4 0.16
17 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTTAAAAAATAT
Found at i:103935 original size:14 final size:14
Alignment explanation
Indices: 103892--103936 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
103882 TCATGTTCAG
*
103892 ATTTTAAAAAATAT
1 ATTTTAAAAAATTT
103906 ATTTTAAATAATAATTT
1 ATTTT-AA-AA-AATTT
103923 ATTTTAAAAAATTT
1 ATTTTAAAAAATTT
103937 TGACACGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 10 0.37
15 4 0.15
16 4 0.15
17 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTTAAAAAATTT
Found at i:104605 original size:7 final size:7
Alignment explanation
Indices: 104593--104623 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
104583 AAAATTATTT
104593 AAATATA
1 AAATATA
104600 AAATATA
1 AAATATA
104607 AAATATA
1 AAATATA
104614 AAATATA
1 AAATATA
104621 AAA
1 AAA
104624 AATTATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATATA
Found at i:105715 original size:19 final size:21
Alignment explanation
Indices: 105677--105715 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
105667 TTAGCATTTT
*
105677 AAAGAAAAATAAGTAAAAACA
1 AAAGAAAAATAAGGAAAAACA
105698 AAAG-AAAA-AAGGAAAAAC
1 AAAGAAAAATAAGGAAAAAC
105716 TTTTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.77, C:0.05, G:0.13, T:0.05
Consensus pattern (21 bp):
AAAGAAAAATAAGGAAAAACA
Found at i:106249 original size:20 final size:19
Alignment explanation
Indices: 106202--106261 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
106192 TTTATATAAA
*
106202 AATTAAATATTTTATAATT
1 AATTAAATAATTTATAATT
** *
106221 CAAAAAAATAGTTTATAATT
1 -AATTAAATAATTTATAATT
*
106241 AATTTAAATAATATATAATT
1 AA-TTAAATAATTTATAATT
106261 A
1 A
106262 TAAAATAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTAAATAATTTATAATT
Found at i:106521 original size:186 final size:186
Alignment explanation
Indices: 106207--106585 Score: 641
Period size: 186 Copynumber: 2.0 Consensus size: 186
106197 ATAAAAATTA
* *
106207 AATATTTTATAATTCAAAAAAATAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAA
1 AATATTTTATAATTCAAAAAAATAATTTAAAATTAATTTAAATAATATATAATTATAAAATAAAA
106272 ATTTTATATAAAGTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATT
66 ATTTTATATAAAGTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATT
* *
106337 ATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATAT
131 ATTAATTGGGTATTAAATGGTTTGGGCTGAACCCATATGTTATATATAATATATAT
* *
106393 AATATTTTTTAATTCAGAAAAATAATTTAAAATTAATTTAAATAATATATAATTATAAAATAAAA
1 AATATTTTATAATTCAAAAAAATAATTTAAAATTAATTTAAATAATATATAATTATAAAATAAAA
** * * *
106458 ATTTTATATAATTTTTTTAATTATTTAATATTTATTTAGGTTTAAAAGTTATTGGATCTTAAATT
66 ATTTTATATAAAGTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATT
*
106523 ATTAATTGGGTATTAAATGGTTTGGGCTGAACCCATATGTTATATATAATATATTT
131 ATTAATTGGGTATTAAATGGTTTGGGCTGAACCCATATGTTATATATAATATATAT
*
106579 AAAATTT
1 AATATTT
106586 AAAATTTTAT
Statistics
Matches: 180, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
186 180 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (186 bp):
AATATTTTATAATTCAAAAAAATAATTTAAAATTAATTTAAATAATATATAATTATAAAATAAAA
ATTTTATATAAAGTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATT
ATTAATTGGGTATTAAATGGTTTGGGCTGAACCCATATGTTATATATAATATATAT
Found at i:112283 original size:2 final size:2
Alignment explanation
Indices: 112276--112351 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
112266 TCAAAGTTAG
112276 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
112318 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
112352 GTTAAAAAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:112530 original size:15 final size:15
Alignment explanation
Indices: 112512--112549 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
112502 TATTATAAAC
112512 AAATAAAAAATAA-TT
1 AAATAAAAAA-AAGTT
112527 AAATTAAAAAAAAGTT
1 AAA-TAAAAAAAAGTT
112543 AAATAAA
1 AAATAAA
112550 TGAAGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAATAAAAAAAAGTT
Found at i:114996 original size:20 final size:20
Alignment explanation
Indices: 114973--115010 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
114963 AAAAAATATT
*
114973 ATTTTATTCAAAAAATAAGA
1 ATTTAATTCAAAAAATAAGA
*
114993 ATTTAATTGAAAAAATAA
1 ATTTAATTCAAAAAATAA
115011 TATATAGAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (20 bp):
ATTTAATTCAAAAAATAAGA
Found at i:118272 original size:27 final size:27
Alignment explanation
Indices: 118239--118299 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
118229 ACAAGTTCTG
118239 AGTTGTTACATAACATGGGGGATGAGA
1 AGTTGTTACATAACATGGGGGATGAGA
*
118266 AGTTGTTACATAACGTGGGGGATGAGA
1 AGTTGTTACATAACATGGGGGATGAGA
118293 AGTTGTT
1 AGTTGTT
118300 TTGTCAACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.30, C:0.07, G:0.34, T:0.30
Consensus pattern (27 bp):
AGTTGTTACATAACATGGGGGATGAGA
Found at i:119277 original size:21 final size:19
Alignment explanation
Indices: 119239--119277 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
119229 TTTTATATTC
*
119239 TCTCATTTTCTTTTCTTCA
1 TCTCATTTTCTTTACTTCA
119258 TCTCATTTTCCATTTACTTC
1 TCTCATTTT-C-TTTACTTC
119278 TTCTTCCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (19 bp):
TCTCATTTTCTTTACTTCA
Found at i:121935 original size:122 final size:122
Alignment explanation
Indices: 121718--121967 Score: 349
Period size: 122 Copynumber: 2.0 Consensus size: 122
121708 GGTCTATTCT
* * * *
121718 TATGATATAAACAGTGATCAAAGTGGTATAGGATAAGAAAAGCTTTTAATGACCATTGTGTTCTG
1 TATGATATAAACAGCGATCAAAGTAGTATAGGATAAGAAAAGCTTTTAATGACCATTGAGTGCTG
** * * *
121783 AAGTGAACTGAGCAACATAAGTCACTTATGTGATAGTGAAGTGGGGTCACTTCAACC
66 AAGTGAACCAAGCAACATAAGTCACTTATGTGAGAGTGAAATGAGGTCACTTCAACC
* **
121840 TATGATATAAACAGCGATCAAAGTAGTATAGGCTAATCAAAGCTTTTAATGACCATTGAGTGCTG
1 TATGATATAAACAGCGATCAAAGTAGTATAGGATAAGAAAAGCTTTTAATGACCATTGAGTGCTG
** *
121905 TGGTGAACCAAGCAACATTAA-TGACTTATGTGAGAGTGAAATGAGGTCACTTCAACC
66 AAGTGAACCAAGCAACA-TAAGTCACTTATGTGAGAGTGAAATGAGGTCACTTCAACC
121962 TATGAT
1 TATGAT
121968 TATTGGGCAT
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
122 109 0.97
123 3 0.03
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (122 bp):
TATGATATAAACAGCGATCAAAGTAGTATAGGATAAGAAAAGCTTTTAATGACCATTGAGTGCTG
AAGTGAACCAAGCAACATAAGTCACTTATGTGAGAGTGAAATGAGGTCACTTCAACC
Found at i:123466 original size:2 final size:2
Alignment explanation
Indices: 123459--123503 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
123449 ATACTAACCA
* *
123459 AC AC AC AC AC AC AC AC AT AC AC AC AT AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
123501 AC A
1 AC A
123504 TACATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.44, G:0.00, T:0.04
Consensus pattern (2 bp):
AC
Found at i:132375 original size:31 final size:32
Alignment explanation
Indices: 132331--132399 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
132321 GTTTCAAAAA
* * *
132331 TAAC-AAATCGGTCATAAATATTATCGATTTG
1 TAACAAAATCGGTCACAAACATTACCGATTTG
*
132362 TAACAAAAT-GGTCACCAACATTACCGATTTG
1 TAACAAAATCGGTCACAAACATTACCGATTTG
132393 TAACAAA
1 TAACAAA
132400 GTAGTCACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (32 bp):
TAACAAAATCGGTCACAAACATTACCGATTTG
Found at i:134049 original size:19 final size:19
Alignment explanation
Indices: 134027--134067 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
134017 TCTCTATTGT
134027 TATTTTATT-ATAATATTTA
1 TATTTTATTGATAA-ATTTA
*
134046 TATTTTTTTGATAAATTTA
1 TATTTTATTGATAAATTTA
134065 TAT
1 TAT
134068 ACACCTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTTATTGATAAATTTA
Found at i:138631 original size:11 final size:11
Alignment explanation
Indices: 138615--138664 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
138605 AAACTGGTTT
138615 AACCGGTTTTC
1 AACCGGTTTTC
138626 AACCGGTTTTC
1 AACCGGTTTTC
138637 AACCGGTTTT-
1 AACCGGTTTTC
*
138647 GACCGG-TTTC
1 AACCGGTTTTC
138657 AACCGGTT
1 AACCGGTT
138665 CGAACCGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 3 0.09
10 10 0.29
11 22 0.63
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (11 bp):
AACCGGTTTTC
Found at i:138653 original size:10 final size:10
Alignment explanation
Indices: 138616--138701 Score: 54
Period size: 10 Copynumber: 8.6 Consensus size: 10
138606 AACTGGTTTA
*
138616 ACCGGTTTTCA
1 ACCGGTTTT-G
*
138627 ACCGGTTTTCA
1 ACCGGTTTT-G
138638 ACCGGTTTTG
1 ACCGGTTTTG
**
138648 ACCGGTTTCA
1 ACCGGTTTTG
*
138658 ACCGG-TTCG
1 ACCGGTTTTG
138667 AACCGG-TTTG
1 -ACCGGTTTTG
*
138677 ACCGG-TCTG
1 ACCGGTTTTG
138686 AACCGG-TTTG
1 -ACCGGTTTTG
138696 ACCGGT
1 ACCGGT
138702 CTGACCCGAC
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
9 16 0.25
10 29 0.45
11 20 0.31
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:138658 original size:20 final size:21
Alignment explanation
Indices: 138610--138664 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
138600 GCTGGAAACT
138610 GGTTT-AACCGGTTTTCAACC
1 GGTTTCAACCGGTTTTCAACC
*
138630 GGTTTTCAACCGGTTTT-GACC
1 GG-TTTCAACCGGTTTTCAACC
138651 GGTTTCAACCGGTT
1 GGTTTCAACCGGTT
138665 CGAACCGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 14 0.44
21 8 0.25
22 10 0.31
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (21 bp):
GGTTTCAACCGGTTTTCAACC
Found at i:138682 original size:9 final size:9
Alignment explanation
Indices: 138638--138707 Score: 68
Period size: 10 Copynumber: 7.3 Consensus size: 9
138628 CCGGTTTTCA
138638 ACCGGTTTTG
1 ACCGG-TTTG
*
138648 ACCGGTTTCA
1 ACCGGTTT-G
*
138658 ACCGGTTCG
1 ACCGGTTTG
138667 AACCGGTTTG
1 -ACCGGTTTG
*
138677 ACCGGTCTG
1 ACCGGTTTG
138686 AACCGGTTTG
1 -ACCGGTTTG
*
138696 ACCGGTCTG
1 ACCGGTTTG
138705 ACC
1 ACC
138708 CGACCCGACC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 22 0.44
10 28 0.56
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:138682 original size:19 final size:20
Alignment explanation
Indices: 138610--138705 Score: 83
Period size: 19 Copynumber: 4.8 Consensus size: 20
138600 GCTGGAAACT
* * *
138610 GGTTTAACCGGTTTTCAACC
1 GGTTTGACCGGTTCTGAACC
* *
138630 GGTTTTCAACCGGTTTTG-ACC
1 GG-TTT-GACCGGTTCTGAACC
*
138651 GGTTTCAACCGGTTC-GAACC
1 GGTTT-GACCGGTTCTGAACC
138671 GGTTTGACCGG-TCTGAACC
1 GGTTTGACCGGTTCTGAACC
138690 GGTTTGACCGG-TCTGA
1 GGTTTGACCGGTTCTGA
138706 CCCGACCCGA
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.03
19 27 0.39
20 22 0.32
21 8 0.12
22 10 0.14
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31
Consensus pattern (20 bp):
GGTTTGACCGGTTCTGAACC
Found at i:138725 original size:17 final size:17
Alignment explanation
Indices: 138703--138741 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
138693 TTGACCGGTC
138703 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
138720 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
138737 TGACC
1 TGACC
138742 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:138741 original size:7 final size:7
Alignment explanation
Indices: 138731--138761 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
138721 GACCCGACCC
138731 GACCGTT
1 GACCGTT
138738 GACCGTT
1 GACCGTT
138745 GACCGTT
1 GACCGTT
138752 GACCGTT
1 GACCGTT
138759 GAC
1 GAC
138762 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:145936 original size:9 final size:9
Alignment explanation
Indices: 145922--145965 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
145912 GGCTGCTGGA
145922 AACCGGTTT
1 AACCGGTTT
145931 AACCGGTTT
1 AACCGGTTT
* *
145940 GACCGGTCTG
1 AACCGGT-TT
145950 AACCGGTTT
1 AACCGGTTT
*
145959 GACCGGT
1 AACCGGT
145966 CTGACCCGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (9 bp):
AACCGGTTT
Found at i:145955 original size:19 final size:19
Alignment explanation
Indices: 145931--145969 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
145921 AAACCGGTTT
145931 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
145950 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
145969 A
1 A
145970 CCCGACCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.26
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:145970 original size:9 final size:9
Alignment explanation
Indices: 145932--145971 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
145922 AACCGGTTTA
*
145932 ACCGGTTTG
1 ACCGGTCTG
145941 ACCGGTCTG
1 ACCGGTCTG
*
145950 AACCGGTTTG
1 -ACCGGTCTG
145960 ACCGGTCTG
1 ACCGGTCTG
145969 ACC
1 ACC
145972 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:145994 original size:22 final size:22
Alignment explanation
Indices: 145968--146010 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
145958 TGACCGGTCT
145968 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
145990 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
146011 GTTGACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:149755 original size:27 final size:26
Alignment explanation
Indices: 149724--149791 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
149714 CATAAATGTT
149724 TAAAC-TCAAGATCTCAAAGAATAATAA
1 TAAACTTCAA-AT-TCAAAGAATAATAA
*
149751 TAAACCTTTAAATTCAAAGAATAATAA
1 TAAA-CTTCAAATTCAAAGAATAATAA
*
149778 TAAACCTTTAAATT
1 TAAA-CTTCAAATT
149792 GAGGTGGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
27 32 0.84
28 3 0.08
29 3 0.08
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (26 bp):
TAAACTTCAAATTCAAAGAATAATAA
Found at i:150602 original size:38 final size:38
Alignment explanation
Indices: 150551--150626 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
150541 TGCAGAACAC
150551 CTATGCATATTTAATTTCTCTTTTTAATAATATTTTTT
1 CTATGCATATTTAATTTCTCTTTTTAATAATATTTTTT
*
150589 CTATGCATCTTTAATTTCTCTTTTTAATAATATTTTTT
1 CTATGCATATTTAATTTCTCTTTTTAATAATATTTTTT
150627 TTAATTTCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.61
Consensus pattern (38 bp):
CTATGCATATTTAATTTCTCTTTTTAATAATATTTTTT
Found at i:175213 original size:24 final size:24
Alignment explanation
Indices: 175181--175236 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
175171 AACTGCACCA
*
175181 AATGTCTTTGATGCCTACACCATT
1 AATGGCTTTGATGCCTACACCATT
175205 AATGGCTTTGATGCCTACACCATT
1 AATGGCTTTGATGCCTACACCATT
175229 AATGGCTT
1 AATGGCTT
175237 ACCAGGTCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (24 bp):
AATGGCTTTGATGCCTACACCATT
Found at i:176529 original size:81 final size:81
Alignment explanation
Indices: 176438--176587 Score: 196
Period size: 81 Copynumber: 1.8 Consensus size: 81
176428 TTTCTTCGAC
* * * * *
176438 AAACGTCGCAACAGAGT-AGTACTTTAGCGGCGTTTCTATAAAATAT-CGCAGTAGGTTAATCTA
1 AAACGCCGCAAAAGA-TCAGTACGTTAGCGGCGTTTCTAT-AAATATCCGCAATAGGTGAATCTA
176501 TAGTGGCATTATTTCAAT
64 TAGTGGCATTATTTCAAT
* *
176519 AAACGCCGCAAAAGATCAGTACGTTAGCGGCGTTTGTATAAATATGCCGCAATAGGTGCATCTAT
1 AAACGCCGCAAAAGATCAGTACGTTAGCGGCGTTTCTATAAATAT-CCGCAATAGGTGAATCTAT
176584 AGTG
65 AGTG
176588 ACGTTTTTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
80 7 0.12
81 33 0.56
82 19 0.32
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (81 bp):
AAACGCCGCAAAAGATCAGTACGTTAGCGGCGTTTCTATAAATATCCGCAATAGGTGAATCTATA
GTGGCATTATTTCAAT
Found at i:180000 original size:21 final size:21
Alignment explanation
Indices: 179967--180010 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
179957 ATTTACTATA
* *
179967 ATGGATTTTAAGTTGGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
*
179988 ATGGAATTAAAGTTTGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
180009 AT
1 AT
180011 ATATGTCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (21 bp):
ATGGAATTAAAGTTGGTTGTT
Found at i:180250 original size:39 final size:40
Alignment explanation
Indices: 180201--180326 Score: 107
Period size: 39 Copynumber: 3.1 Consensus size: 40
180191 CGTTTATACA
*
180201 AAAAATGCCACTATAATTGTCAATAGC-GCGTTTTATTAT
1 AAAAACGCCACTATAATTGTCAATAGCGGCGTTTTATTAT
* * *
180240 AAAAACGCCACTA-AAGTGTTAGATAATTTGCGGCG-TTTATGACT
1 AAAAACGCCACTATAATTGTCA-AT-A---GCGGCGTTTTATTA-T
* * *
180284 -AAAACTCCACTATATTTGTCAATAGCGGCGTTTTAATAT
1 AAAAACGCCACTATAATTGTCAATAGCGGCGTTTTATTAT
180323 AAAA
1 AAAA
180327 GCCGCTATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
38 6 0.09
39 21 0.31
40 9 0.13
42 1 0.01
43 21 0.31
44 9 0.13
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (40 bp):
AAAAACGCCACTATAATTGTCAATAGCGGCGTTTTATTAT
Found at i:180251 original size:79 final size:81
Alignment explanation
Indices: 180142--180326 Score: 227
Period size: 82 Copynumber: 2.3 Consensus size: 81
180132 AAATACATAA
* * * *
180142 TCAATACCGGCGTTTT-ACA-AAAAAAGCCACTAAAGTTTTAGATTATTT-GCGTTTAT-ACAAA
1 TCAATAGCGGCGTTTTAATATAAAAAAGCCACTAAAGTGTTAGATAATTTGGCGTTTATGACAAA
180203 AAATGCCACTATAATTG
66 AAAT-CCACTATAATTG
* * *
180220 TCAATAGC-GCGTTTTATTATAAAAACGCCACTAAAGTGTTAGATAATTTGCGGCGTTTATGACT
1 TCAATAGCGGCGTTTTAATATAAAAAAGCCACTAAAGTGTTAGATAATTT--GGCGTTTATGACA
* *
180284 AAAACTCCACTATATTTG
64 AAAAATCCACTATAATTG
180302 TCAATAGCGGCGTTTTAATATAAAA
1 TCAATAGCGGCGTTTTAATATAAAA
180327 GCCGCTATAT
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
77 7 0.08
78 8 0.09
79 26 0.29
82 27 0.30
83 22 0.24
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (81 bp):
TCAATAGCGGCGTTTTAATATAAAAAAGCCACTAAAGTGTTAGATAATTTGGCGTTTATGACAAA
AAATCCACTATAATTG
Found at i:181261 original size:22 final size:22
Alignment explanation
Indices: 181176--181261 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
181166 CCATCAGATA
*
181176 ACTAAAATGCCTTAGCACT-AGT
1 ACTAAAGTGCCTTAGCACTGA-T
* *
181198 ACTAAAGTGACTCAGCACTGAT
1 ACTAAAGTGCCTTAGCACTGAT
* * *
181220 AC-AGAAGTGCATTTGGACTGAT
1 ACTA-AAGTGCCTTAGCACTGAT
181242 ACTAAAGTGCCTTAGCACTG
1 ACTAAAGTGCCTTAGCACTG
181262 CTGAGAATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
21 1 0.02
22 47 0.94
23 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (22 bp):
ACTAAAGTGCCTTAGCACTGAT
Found at i:186713 original size:27 final size:30
Alignment explanation
Indices: 186644--186715 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 30
186634 TCTTTCTATT
186644 TAAGTATCTAAAGTTATCTTTGTTGTCAAAA
1 TAAGTATCTAAAG-TATCTTTGTTGTCAAAA
186675 TAAGTA-CTTAAAGT-T-TTT-TTGTCAAAA
1 TAAGTATC-TAAAGTATCTTTGTTGTCAAAA
*
186702 TATGTATCTAAAGT
1 TAAGTATCTAAAGT
186716 GTTCAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 20 0.53
28 4 0.11
29 1 0.03
30 2 0.05
31 11 0.29
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.43
Consensus pattern (30 bp):
TAAGTATCTAAAGTATCTTTGTTGTCAAAA
Found at i:188718 original size:6 final size:6
Alignment explanation
Indices: 188707--188733 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
188697 CGAAAATTTG
188707 AAATTA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAA
188734 AGTCCTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:190710 original size:76 final size:78
Alignment explanation
Indices: 190601--191379 Score: 628
Period size: 76 Copynumber: 9.9 Consensus size: 78
190591 CTTAGTGTAA
* * * *
190601 TCGAACTCTAAGGTCTTTG-TGACAGATAGCCCTTCTCG-CTTA-AGCTATAAATGATGTGCCTT
1 TCGAACTCGAAGGTCTTTGTTG-CAGATAACCCTTCTAGCCTTATAGCTACAAATGATGTGCCTT
190663 GGAGCTGAGCGTAG
65 GGAGCTGAGCGTAG
* ** *
190677 TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTGAGTTA-TTGTAAATGATATGCC
1 TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTT-A--TAGCTACAAATGATGTGCC
190741 TTGGAGCTGAGCGTAG
63 TTGGAGCTGAGCGTAG
* * * * *
190757 TCGAACTCGAAGGTCTTTGTTGCA-AGAGCCCTTATA-ACTTAGTTGCTACAAATGATGTGCCTT
1 TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTA-TAGCTACAAATGATGTGCCTT
*
190820 GGAG-T-AGCATAG
65 GGAGCTGAGCGTAG
* * * *
190832 T--AA--CGAAGGTCTTTGGTTGAAGAT-AGCCTTCTCAGCCTTAGTTATGCTGCAAATAATGTG
1 TCGAACTCGAAGGTCTTT-GTTGCAGATAACCCTTCT-AGCCTTA--TA-GCTACAAATGATGTG
*
190892 CCTTGGAGTTGAGCGTAG
61 CCTTGGAGCTGAGCGTAG
* * * * *
190910 TCGAACTC-AAGGTTTTTGTTGGAAGATAACCCTT-TAGCCTTGAGTTGCTGCAAATGATATGCC
1 TCGAACTCGAAGGTCTTTGTT-GCAGATAACCCTTCTAGCCTT-A-TAGCTACAAATGATGTGCC
*
190973 TTGG-G-TGAACGTAG
63 TTGGAGCTGAGCGTAG
* * *
190987 TAGAAATCGAAGGTCTTTTGTTG-AAATAA-CCTTCTAGCCTTATATGCTACAAATGATGTGCCT
1 TCGAACTCGAAGGTC-TTTGTTGCAGATAACCCTTCTAGCCTTATA-GCTACAAATGATGTGCCT
*
191050 T--AGATGAGCGTAG
64 TGGAGCTGAGCGTAG
* * * * *
191063 TAGAACTCGAAGGTCTTTGGTTGACAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTT-GTTG-CAGATAACCCTTCTAGCCTT-A--TA-GCTACAAATGATGT
*
191128 GCCTTAGAGCTGAGCGTAG
60 GCCTTGGAGCTGAGCGTAG
* * *
191147 TTGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG-CTTA-AGCTATGTGTAAATAATGT
1 TCGAACTCGAAGGTC-TTTGTT-GCAGATAACCCTTCTAGCCTTATAGCTA----CAAATGATGT
*
191210 GCCTT-G-GCTAAG-GTAG
60 GCCTTGGAGCTGAGCGTAG
*
191226 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTAGCTATGCTACAAAT-ATGTG
1 TCGAACTCGAAGGTC-TTTGTTG-CAGATAACCCTTCTAGCCTTA--TA-GCTACAAATGATGTG
191290 CCTTGGAGCTGAGCGTAG
61 CCTTGGAGCTGAGCGTAG
* * *
191308 TCGAACTCGAAGGTCTTTTGGTTGGTAGATAGCCCTTCTAGCCTT-GAGCTATGC-AATGATGTG
1 TCGAACTCGAAGGTC-TTT-GTT-GCAGATAACCCTTCTAGCCTTATAGCTA--CAAATGATGTG
191371 CCTT-GAGCT
61 CCTTGGAGCT
191380 AAG
Statistics
Matches: 581, Mismatches: 65, Indels: 110
0.77 0.09 0.15
Matches are distributed among these distances:
71 11 0.02
72 10 0.02
73 4 0.01
74 4 0.01
75 13 0.02
76 103 0.18
77 51 0.09
78 26 0.04
79 98 0.17
80 89 0.15
81 33 0.06
82 64 0.11
83 24 0.04
84 47 0.08
85 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (78 bp):
TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTATAGCTACAAATGATGTGCCTTG
GAGCTGAGCGTAG
Found at i:190974 original size:79 final size:82
Alignment explanation
Indices: 190649--191379 Score: 750
Period size: 79 Copynumber: 9.2 Consensus size: 82
190639 CTTAAGCTAT
*
190649 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGCAGATAACCCTTCT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGAAGATAACCCTTCT
* *
190713 AGCCTTGAGTTAT--TGT
66 AGCCTT-AGCTATGCTGC
* * *
190729 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGCAAG--AGCCCTTA
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTG-AAGATAACCCTTC
* *
190791 TA-ACTTAG-T-TGCTAC
65 TAGCCTTAGCTATGCTGC
* * *
190806 AAATGATGTGCCTTGGAG-T-AGCATAGT--AA--CGAAGGTCTTTGGTTGAAGAT-AGCCTTCT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGAAGATAACCCTTCT
*
190864 CAGCCTTAGTTATGCTGC
66 -AGCCTTAGCTATGCTGC
* *
190882 AAATAATGTGCCTTGGAGTTGAGCGTAGTCGAACTC-AAGGT-TTTTGTTGGAAGATAACCCTT-
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTT-GAAGATAACCCTTC
190944 TAGCCTTGAG-T-TGCTGC
65 TAGCCTT-AGCTATGCTGC
* * * *
190961 AAATGATATGCCTTGG-G-TGAACGTAGTAGAAATCGAAGGTCTTTTGTTGAA-ATAA-CCTTCT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGAAGATAACCCTTCT
*
191022 AGCCTTA--TATGCTAC
66 AGCCTTAGCTATGCTGC
* * * *
191037 AAATGATGTGCCTT--AGATGAGCGTAGTAGAACTCGAAGGTCTTTGGTTGACAGATAGCCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGA-AGATAACCCTTC
* *
191100 TCGACTTAAGCTATGCTGC
65 TAGCCTT-AGCTATGCTGC
* * *
191119 AAATGATGTGCCTTAGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTT-GAAGATAACCCTTC
*
191184 TAG-CTTAAGCTATG-TGT
65 TAGCCTT-AGCTATGCTGC
* * *
191201 AAATAATGTGCCTT-G-GCTAAG-GTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGA-AGATAACCCTTC
*
191263 TAGCCTTAGCTATGCTAC
65 TAGCCTTAGCTATGCTGC
* *
191281 AAAT-ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTTGGTAGATAGCCCTT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT-GTT-GAAGATAACCCTT
191345 CTAGCCTTGAGCTA---TGC
64 CTAGCCTT-AGCTATGCTGC
191362 -AATGATGTGCCTT-GAGCT
1 AAATGATGTGCCTTGGAGCT
191380 AAG
Statistics
Matches: 555, Mismatches: 52, Indels: 88
0.80 0.07 0.13
Matches are distributed among these distances:
71 11 0.02
72 11 0.02
73 3 0.01
74 5 0.01
75 11 0.02
76 77 0.14
77 47 0.08
78 23 0.04
79 100 0.18
80 87 0.16
81 33 0.06
82 65 0.12
83 31 0.06
84 50 0.09
85 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (82 bp):
AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGAAGATAACCCTTCT
AGCCTTAGCTATGCTGC
Done.