Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007068.1 Hibiscus syriacus cultivar Beakdansim tig00018390_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: 617230
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:3611 original size:13 final size:13
Alignment explanation
Indices: 3590--3620 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3580 TATTGAGTGA
3590 TGTTGAACATACT
1 TGTTGAACATACT
*
3603 TGTTTAACATACT
1 TGTTGAACATACT
3616 TGTTG
1 TGTTG
3621 CATCCCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (13 bp):
TGTTGAACATACT
Found at i:5117 original size:35 final size:35
Alignment explanation
Indices: 5078--5164 Score: 156
Period size: 35 Copynumber: 2.5 Consensus size: 35
5068 CCCGAACCCG
*
5078 AAAATATTTTATATATAATTAATATAAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAAATAT
*
5113 AAAATATTATATATATAATTAATATAAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAAATAT
5148 AAAATATTATATATATA
1 AAAATATTATATATATA
5165 TATATATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (35 bp):
AAAATATTATATATATAATTAATATAAAAAAATAT
Found at i:5125 original size:2 final size:2
Alignment explanation
Indices: 5116--5180 Score: 61
Period size: 2 Copynumber: 35.5 Consensus size: 2
5106 AAAATATAAA
* * *
5116 AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5153 AT -T 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 AT A
5181 ATCGGGGCGG
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
1 6 0.11
2 48 0.89
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:8030 original size:141 final size:141
Alignment explanation
Indices: 7816--8366 Score: 800
Period size: 141 Copynumber: 3.9 Consensus size: 141
7806 TAAGGAATGC
7816 GGAAGACTCTTGATAGGATTGAAGGAAAGATCAAGAATCTTGAGTTCATTCGTATCATCGAAGAA
1 GGAAGACTCTTGATAGGATTGAAGGAAAGATCAAGAATCTTGAGTTCATTCGTATCATCGAAGAA
* *
7881 GCTTTCTGGAATACTTTCTATAAGACAACCAGACAACAACAATGTTGTGAGCCCGGGACACTTCG
66 GCTTTCTGGAATACTTTCTATACGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTTCG
7946 ACAAGGAAATT
131 ACAAGGAAATT
* * * *
7957 GGAAGACTCTTGATAGGGTTGGAGGAAAGATCAAGAGTCTTGAGTTCATTCGTAACATCGAAGAA
1 GGAAGACTCTTGATAGGATTGAAGGAAAGATCAAGAATCTTGAGTTCATTCGTATCATCGAAGAA
* * *
8022 GCTTTCTGGAATACTTTCTATACGACAATGACACAACAACAATGTCGTGAGCCCGGGACACTTCG
66 GCTTTCTGGAATACTTTCTATACGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTTCG
8087 ACAAGGAAATT
131 ACAAGGAAATT
* *
8098 GGAAGACACTTGATAGGATTGAAGGAAAGATCAAGAATCTTGAGTTCATTCGTATCATCAAAGAA
1 GGAAGACTCTTGATAGGATTGAAGGAAAGATCAAGAATCTTGAGTTCATTCGTATCATCGAAGAA
* *
8163 GCTTTCTGGAATACTTTCTATACGACAATCAGACAACAACAATGTTGTGAGGCTGGGACACTTCG
66 GCTTTCTGGAATACTTTCTATACGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTTCG
8228 ACAAGGAAATT
131 ACAAGGAAATT
** * * * * * * *
8239 GGAAGACTCTTGATAGGATTCCAGGAAAGATCAAGAACCTTAAGTGCATCCATATGC-TTGAAAA
1 GGAAGACTCTTGATAGGATTGAAGGAAAGATCAAGAATCTTGAGTTCATTCGTAT-CATCGAAGA
* * ** ** * *
8303 ATCCTTCTGGAATACTCGCTATTTTG-CAATGAGACAACAACAATGTTGTGAGCCTGGGACACTT
65 AGCTTTCTGGAATACTTTCTA-TACGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTT
8367 TGGGGGTGAC
Statistics
Matches: 369, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
141 366 0.99
142 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (141 bp):
GGAAGACTCTTGATAGGATTGAAGGAAAGATCAAGAATCTTGAGTTCATTCGTATCATCGAAGAA
GCTTTCTGGAATACTTTCTATACGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTTCG
ACAAGGAAATT
Found at i:11774 original size:17 final size:17
Alignment explanation
Indices: 11752--11786 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11742 TTTACTTTGT
11752 TTAAAAATATAA-AAATA
1 TTAAAAATA-AATAAATA
11769 TTAAAAATAAATAAATA
1 TTAAAAATAAATAAATA
11786 T
1 T
11787 GTAACACCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAAATAAATAAATA
Found at i:13478 original size:64 final size:64
Alignment explanation
Indices: 13410--13629 Score: 218
Period size: 64 Copynumber: 3.5 Consensus size: 64
13400 TTGAAGGTGT
* ** * *
13410 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATTAGTG
13473 C
64 C
* * *
13474 ATCGATGCATAAGTAGTGCATCAATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
* * * * *
13538 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAA-ACAACATCGAATACATTTTA-TG
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-ATTAGTG
*
13600 T
64 C
*
13601 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
13630 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
62 2 0.02
63 37 0.28
64 84 0.64
65 8 0.06
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
Found at i:14533 original size:103 final size:103
Alignment explanation
Indices: 14350--14670 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
14340 GTCGAGGGTC
14350 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
14415 TTGATCCTTGTCATATGTATATGATTCTTAATGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
14453 TATGTGGTCCTTCGGGACATATATGTATTTTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
14518 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
14556 TATGTAGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
14621 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
14659 TATGTGGTCCTT
1 TATGTGGTCCTT
14671 ATGGACAGTA
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:14753 original size:23 final size:23
Alignment explanation
Indices: 14689--14754 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
14679 TATTATATGA
* * *
14689 CACTACGGTGCAATTCTACGCGG
1 CACTCCGGTGCAATTATATGCGG
*
14712 CACTCCGGTGCAATTATATGTGG
1 CACTCCGGTGCAATTATATGCGG
**
14735 CACTTTGGTGCAATTATATG
1 CACTCCGGTGCAATTATATG
14755 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (23 bp):
CACTCCGGTGCAATTATATGCGG
Found at i:16884 original size:18 final size:18
Alignment explanation
Indices: 16858--16898 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
16848 TCGAAAGGAC
* *
16858 TGAAGTAAATGATAAGAT
1 TGAATTAAATAATAAGAT
16876 TGAATTAAATAATAAGAT
1 TGAATTAAATAATAAGAT
*
16894 CGAAT
1 TGAAT
16899 GGCAGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAATTAAATAATAAGAT
Found at i:18093 original size:24 final size:24
Alignment explanation
Indices: 18059--18130 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
18049 GATACATTAC
* *
18059 CTGAATTCTGTTCTGATTTATGAT
1 CTGAATACTGTTCTGATTTCTGAT
* *
18083 CTGGATACTGTTCTGATATCTGAT
1 CTGAATACTGTTCTGATTTCTGAT
* *
18107 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATACTGTTCTGATTTCTGAT
18131 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (24 bp):
CTGAATACTGTTCTGATTTCTGAT
Found at i:21232 original size:14 final size:14
Alignment explanation
Indices: 21213--21242 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21203 ATCATTTCCT
21213 TTTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
*
21227 TTTCTTTTTTTTTC
1 TTTCTTTTTCTTTC
21241 TT
1 TT
21243 GTCTCACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTCTTTTTCTTTC
Found at i:22020 original size:30 final size:30
Alignment explanation
Indices: 21986--22071 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 30
21976 AATGAACAAT
*
21986 AACACTTTTAAAAATAAGTAAACGAACATA
1 AACACTTTTAAAAATAAATAAACGAACATA
* * * *
22016 AACACGATATTAAAAAT--TTAAACAAACATG
1 AACAC--TTTTAAAAATAAATAAACGAACATA
* *
22046 AACATTTTTAAAATTAAATAAACGAA
1 AACACTTTTAAAAATAAATAAACGAA
22072 GGAAACCGTC
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
28 8 0.19
30 26 0.60
32 9 0.21
ACGTcount: A:0.57, C:0.12, G:0.06, T:0.26
Consensus pattern (30 bp):
AACACTTTTAAAAATAAATAAACGAACATA
Found at i:25011 original size:55 final size:55
Alignment explanation
Indices: 24936--25291 Score: 406
Period size: 55 Copynumber: 6.6 Consensus size: 55
24926 ATGGCGGGTT
* * * *
24936 CGCTCCCTATTCCTTTAGGGAGTATAAGACTCAAACAATCTTCAGCAAACGTGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* ** *
24991 TGCTCCCTATTTGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTG-C
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * * * * *
25045 CTACTCCCTATTCGTTCGGGGAGTATAAGACTCGAATAATCTTCAATAAACGGGTC
1 C-GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
*
25101 CGCTCCCTATTCCTTCAGAGAGTATAGGACTCG----ATCTTCAACAAACGTGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * * *
25152 CACTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAATGTGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* *
25207 CGCTCCCTATTCTTTCAGAGAGTATAAGAC-C---CGATCTTCAACAAACGTGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * *
25258 CGCTCCCTATTCTTTTAGAGAGTATAGGACTCGA
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGA
25292 TCCTCATAAA
Statistics
Matches: 259, Mismatches: 33, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
51 92 0.36
52 1 0.00
54 1 0.00
55 163 0.63
56 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (55 bp):
CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
Found at i:25195 original size:106 final size:106
Alignment explanation
Indices: 24938--25291 Score: 431
Period size: 106 Copynumber: 3.3 Consensus size: 106
24928 GGCGGGTTCG
* * * ** * *
24938 CTCCCTATTCCTTTAGGGAGTATAAGACTCAAACAATCTTCAGCAAACGTGTCTGCTCCCTATTT
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAAAAACGTGTCCGCTCCCTATTC
* *
25003 GTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTG-CCTA
66 CTTCAGAGAGTATAAGACTCG----ATCTTCAACAAACGTGTCC-A
* * * * * *
25048 CTCCCTATTCGTTCGGGGAGTATAAGACTCGAATAATCTTCAATAAACGGGTCCGCTCCCTATTC
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAAAAACGTGTCCGCTCCCTATTC
*
25113 CTTCAGAGAGTATAGGACTCGATCTTCAACAAACGTGTCCA
66 CTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTGTCCA
* * *
25154 CTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAATGTGTCCGCTCCCTATTC
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAAAAACGTGTCCGCTCCCTATTC
* * *
25219 TTTCAGAGAGTATAAGACCCGATCTTCAACAAACGTGTCCG
66 CTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTGTCCA
* * *
25260 CTCCCTATTCTTTTAGAGAGTATAGGACTCGA
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGA
25292 TCCTCATAAA
Statistics
Matches: 214, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
106 139 0.65
107 2 0.01
110 73 0.34
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (106 bp):
CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAAAAACGTGTCCGCTCCCTATTC
CTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTGTCCA
Found at i:25415 original size:37 final size:37
Alignment explanation
Indices: 25308--25417 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
25298 TAAAATAAGT
*
25308 TTGCTTCACTACTCTTCCGTGAAGGCTTATAGA-TGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATTGAA
*
25345 TTGCTTCACTACTCTTCCGTGAAGGATTAAGATTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAA
* *
25382 TTGCTTCACTGCTCTTTCGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
25418 CTTGTTTCGA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 3 0.04
37 64 0.96
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAA
Found at i:26677 original size:45 final size:45
Alignment explanation
Indices: 26610--26695 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
26600 TAAACAAAAC
* *
26610 TCAAGTCGCCCTTTGTGGGTTTTCACCTTGAGA-CCTCCTTTGGTT
1 TCAAGACGCCCTTTGTGAGTTTTCACCTTGA-ACCCTCCTTTGGTT
*
26655 TCAAGACGCCCTTT-TCGAGTTTTCATCTTGAACCCTCCTTT
1 TCAAGACGCCCTTTGT-GAGTTTTCACCTTGAACCCTCCTTT
26696 TATTTCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 2 0.06
45 34 0.94
ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40
Consensus pattern (45 bp):
TCAAGACGCCCTTTGTGAGTTTTCACCTTGAACCCTCCTTTGGTT
Found at i:26722 original size:7 final size:7
Alignment explanation
Indices: 26712--26865 Score: 108
Period size: 7 Copynumber: 21.6 Consensus size: 7
26702 TTTTTCTTTT
26712 TTTTTCA
1 TTTTTCA
26719 TTTTTCA
1 TTTTTCA
26726 TTTTTC-
1 TTTTTCA
*
26732 TCTTTCTTA
1 T-TTT-TCA
*
26741 TTTTTTCCT
1 -TTTTT-CA
26750 TCTTTTC-
1 T-TTTTCA
26757 TTTTTCA
1 TTTTTCA
*
26764 TTTTTCTT
1 TTTTTC-A
26772 TTTTTC-
1 TTTTTCA
26778 TTTTTCA
1 TTTTTCA
26785 TTTTT--
1 TTTTTCA
26790 TTTTT-A
1 TTTTTCA
26796 TTTTTCA
1 TTTTTCA
26803 TTTTTCA
1 TTTTTCA
26810 TTTTTCA
1 TTTTTCA
*
26817 TTTTTTA
1 TTTTTCA
26824 TTTTT--
1 TTTTTCA
26829 TTTCTTCA
1 TTT-TTCA
26837 TTTTTTTTCA
1 ---TTTTTCA
26847 TTTTTTCA
1 -TTTTTCA
*
26855 TTTTTCC
1 TTTTTCA
26862 TTTT
1 TTTT
26866 CTTCCTTTTT
Statistics
Matches: 124, Mismatches: 6, Indels: 34
0.76 0.04 0.21
Matches are distributed among these distances:
5 8 0.06
6 19 0.15
7 64 0.52
8 18 0.15
9 7 0.06
10 5 0.04
11 3 0.02
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:26722 original size:8 final size:8
Alignment explanation
Indices: 26711--26907 Score: 106
Period size: 8 Copynumber: 25.6 Consensus size: 8
26701 CTTTTTCTTT
26711 TTTTTTCA
1 TTTTTTCA
26719 -TTTTTCA
1 TTTTTTCA
26726 TTTTTCTC-
1 TTTTT-TCA
*
26734 TTTCTT-A
1 TTTTTTCA
*
26741 TTTTTTCC
1 TTTTTTCA
26749 TTCTTTTC-
1 TT-TTTTCA
26757 -TTTTTCA
1 TTTTTTCA
*
26764 -TTTTTCT
1 TTTTTTCA
26771 TTTTTTC-
1 TTTTTTCA
26778 -TTTTTCA
1 TTTTTTCA
**
26785 TTTTTTTTT
1 -TTTTTTCA
26794 TATTTTTCA
1 T-TTTTTCA
26803 -TTTTTCA
1 TTTTTTCA
26810 -TTTTTCA
1 TTTTTTCA
26817 TTTTTT-A
1 TTTTTTCA
26824 -TTTTT--
1 TTTTTTCA
*
26829 TTTCTTCA
1 TTTTTTCA
26837 TTTTTTTTCA
1 --TTTTTTCA
26847 TTTTTTCA
1 TTTTTTCA
*
26855 -TTTTTCC
1 TTTTTTCA
*
26862 TTTTCTTCC
1 TTTT-TTCA
26871 TTTTTTC-
1 TTTTTTCA
26878 --TTTTCA
1 TTTTTTCA
26884 TTTTTTCATCA
1 -TTTTT--TCA
26895 TTTTTTCA
1 TTTTTTCA
26903 TTTTT
1 TTTTT
26908 CTTCAAGTGA
Statistics
Matches: 153, Mismatches: 11, Indels: 50
0.71 0.05 0.23
Matches are distributed among these distances:
5 5 0.03
6 20 0.13
7 41 0.27
8 44 0.29
9 28 0.18
10 12 0.08
11 3 0.02
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCA
Found at i:26766 original size:38 final size:39
Alignment explanation
Indices: 26713--26907 Score: 120
Period size: 37 Copynumber: 4.8 Consensus size: 39
26703 TTTTCTTTTT
26713 TTTTCATTTTTCATTTTTC-TCTTTCTT-ATTTTTTCCTTC
1 TTTTC-TTTTTCATTTTTCTTCTTT-TTCATTTTTTCCTTC
** *
26752 TTTTCTTTTTCATTTTTCTTTTTTTCTTTTTCATTTTTTTTTTAT
1 TTTTCTTTTTCATTTTTC-----TTCTTTTTCATTTTTTCCTT-C
* *
26797 TTTTCATTTTTCATTTTTCAT-TTTTT-ATTTTTTTTCTTC
1 TTTTC-TTTTTCATTTTTCTTCTTTTTCA-TTTTTTCCTTC
* *
26836 ATTT-TTTTTCA-TTTT-TTCATTTTTCCTTTTCTTCCTT-
1 TTTTCTTTTTCATTTTTCTTC-TTTTTCATTTT-TTCCTTC
*
26873 TTTTC-TTTTCATTTTTTCATCATTTTTTCATTTTT
1 TTTTCTTTTTCA-TTTTTCTTC--TTTTTCATTTTT
26908 CTTCAAGTGA
Statistics
Matches: 123, Mismatches: 14, Indels: 37
0.71 0.08 0.21
Matches are distributed among these distances:
35 1 0.01
36 4 0.03
37 25 0.20
38 18 0.15
39 13 0.11
40 17 0.14
41 11 0.09
43 2 0.02
44 14 0.11
45 5 0.04
46 13 0.11
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (39 bp):
TTTTCTTTTTCATTTTTCTTCTTTTTCATTTTTTCCTTC
Found at i:26768 original size:45 final size:44
Alignment explanation
Indices: 26705--26909 Score: 185
Period size: 45 Copynumber: 4.6 Consensus size: 44
26695 TTATTTCTTT
26705 TTCTTTTTTTTTCATTTTTCATTTTTCTCTTTCTT-ATTTTTTCC
1 TTCTTTTTTTTTCATTTTTCATTTTTCTCTTT-TTCATTTTTTCC
*
26749 TTCTTTTCTTTTTCATTTTTC-TTTTTTTCTTTTTCA-TTTTT--
1 TTCTTTT-TTTTTCATTTTTCATTTTTCTCTTTTTCATTTTTTCC
* *
26790 TT-TTTATTTTTCATTTTTCATTTTTCAT-TTTTT-ATTTTTTTTC
1 TTCTTTTTTTTTCATTTTTCATTTTTC-TCTTTTTCA-TTTTTTCC
* * *
26833 TTCATTTTTTTTCATTTTTTCATTTTTC-CTTTTCTTCCTTTTTTCTT
1 TTCTTTTTTTTTCA-TTTTTCATTTTTCTC-TTT-TTCATTTTTTC-C
**
26880 TTCATTTTTTCATCATTTTTTCATTTTTCT
1 TTC-TTTTTTTTTCA-TTTTTCATTTTTCT
26910 TCAAGTGAAA
Statistics
Matches: 133, Mismatches: 11, Indels: 29
0.77 0.06 0.17
Matches are distributed among these distances:
39 14 0.11
40 13 0.10
41 8 0.06
43 9 0.07
44 27 0.20
45 29 0.22
46 8 0.06
47 3 0.02
48 22 0.17
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (44 bp):
TTCTTTTTTTTTCATTTTTCATTTTTCTCTTTTTCATTTTTTCC
Found at i:26790 original size:84 final size:87
Alignment explanation
Indices: 26702--26888 Score: 244
Period size: 84 Copynumber: 2.2 Consensus size: 87
26692 CTTTTATTTC
*
26702 TTTTTCTTTT-TTTTTCATTTTTCATTTTTC-TCTTTCTTA-TTTTTTCCTTCTTTTCTTTTTCA
1 TTTTTCTTTTATTTTTCATTTTTCATTTTTCAT-TTT-TTATTTTTTTCCTTCATTT-TTTTTCA
* *
26764 -TTTTTCTTTTTTTC-TTT-TTCAT
63 TTTTTTCATTTTTCCTTTTCTTCAT
*
26786 TTTTT-TTTTATTTTTCATTTTTCATTTTTCATTTTTTATTTTTTTTCTTCATTTTTTTTCATTT
1 TTTTTCTTTTATTTTTCATTTTTCATTTTTCATTTTTTATTTTTTTCCTTCATTTTTTTTCATTT
*
26850 TTTCATTTTTCCTTTTCTTCCT
66 TTTCATTTTTCCTTTTCTTCAT
26872 TTTTTCTTTTCATTTTT
1 TTTTTCTTTT-ATTTTT
26889 TCATCATTTT
Statistics
Matches: 90, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
83 14 0.16
84 53 0.59
85 4 0.04
86 9 0.10
87 4 0.04
88 6 0.07
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (87 bp):
TTTTTCTTTTATTTTTCATTTTTCATTTTTCATTTTTTATTTTTTTCCTTCATTTTTTTTCATTT
TTTCATTTTTCCTTTTCTTCAT
Found at i:26832 original size:76 final size:75
Alignment explanation
Indices: 26692--26888 Score: 202
Period size: 76 Copynumber: 2.5 Consensus size: 75
26682 TTGAACCCTC
* * *
26692 CTTTTATTTCTTTTTCTTTTTTTTTCATTTTTCATTTTTCTCTTTCTTATTTTTTCCTTCTTTTC
1 CTTTT-TTTCTTTTTCTTTTTTTTTTATTTTTCATTTTTCTCTTTCTCATTTTTTACTTCTTTTC
26757 TT-TTTCATTTTT
65 TTATTT--TTTTT
* *
26769 CTTTTTTTCTTTTTCATTTTTTTTTTATTTTTCATTTTTCAT-TTT-TCATTTTTTATTTTTTTT
1 CTTTTTTTCTTTTTC-TTTTTTTTTTATTTTTCATTTTTC-TCTTTCTCATTTTTTACTTCTTTT
26832 CTTCATTTTTTTT
64 CTT-ATTTTTTTT
* *
26845 CATTTTTTCATTTTTCCTTTTCTTCCTTTTTTCTTTTCATTTTT
1 CTTTTTTTC-TTTTT-CTTTT-TT--TTTTAT-TTTTCATTTTT
26889 TCATCATTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 16
0.82 0.06 0.13
Matches are distributed among these distances:
76 40 0.39
77 40 0.39
78 7 0.07
80 5 0.05
81 11 0.11
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (75 bp):
CTTTTTTTCTTTTTCTTTTTTTTTTATTTTTCATTTTTCTCTTTCTCATTTTTTACTTCTTTTCT
TATTTTTTTT
Found at i:26882 original size:37 final size:32
Alignment explanation
Indices: 26709--26901 Score: 118
Period size: 32 Copynumber: 5.9 Consensus size: 32
26699 TTCTTTTTCT
26709 TTTTTTTTCA-TTTTTCATTTTTCTCTTTCTT-A
1 TTTTTTTTCATTTTTTCATTTTT-T-TTTCTTCA
* * **
26741 --TTTTTTCCTTCTTTTCTTTTTCATTTTTCTTTT
1 TTTTTTTTCATT-TTTTCATTTT--TTTTTCTTCA
26774 TTTCTTTTTCATTTTTT--TTTTATTTTTCATT--
1 TTT-TTTTTCATTTTTTCATTTT-TTTTTC-TTCA
26805 TTTCATTTTTCATTTTTT-A-TTTTTTTTCTTCA
1 TTT--TTTTTCATTTTTTCATTTTTTTTTCTTCA
*
26837 TTTTTTTTCATTTTTTCATTTTTCCTTTTCTTCCTT
1 TTTTTTTTCATTTTTTCATTTTT--TTTTCTT-C-A
**
26873 TTTTCTTTTCATTTTTTCATCATTTTTTC
1 TTTT-TTTTCATTTTTTCATTTTTTTTTC
26902 ATTTTTCTTC
Statistics
Matches: 133, Mismatches: 8, Indels: 37
0.75 0.04 0.21
Matches are distributed among these distances:
30 22 0.17
31 11 0.08
32 45 0.34
33 7 0.05
34 8 0.06
35 11 0.08
36 12 0.09
37 17 0.13
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTTTTTCATTTTTTCATTTTTTTTTCTTCA
Found at i:34011 original size:64 final size:64
Alignment explanation
Indices: 33937--34098 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
33927 ATTGTTTGAA
* **
33937 GGTGTATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAAT
34000 T
64 T
* * * *
34001 GGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGTATTT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATT
** * *
34065 TATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCAT
34099 ACCTTCATTA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
63 3 0.04
64 70 0.86
65 8 0.10
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (64 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATT
Found at i:40927 original size:64 final size:64
Alignment explanation
Indices: 40853--41014 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 64
40843 ATTGTTTGAA
* * *
40853 GGTGTATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTAAAAATAAAAACATCGAATGCAATT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCATCCCATTAAAAAT-AAAACATCGAATGCAATT
* * * * *
40917 GGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGTATTT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAAAAATAAAACATCGAATGCAATT
** * *
40981 TATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCAT
41015 ACCTTCATTA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 3 0.04
64 65 0.80
65 13 0.16
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (64 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCATCCCATTAAAAATAAAACATCGAATGCAATT
Found at i:45820 original size:2 final size:2
Alignment explanation
Indices: 45815--45845 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45805 TTAATCATTA
45815 AT AT 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 AT AT A
45846 ATTACTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48097 original size:22 final size:22
Alignment explanation
Indices: 48066--48107 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
48056 ATATGTGTTC
48066 AATTCATTTATGTTCATAAATA
1 AATTCATTTATGTTCATAAATA
*
48088 AATTCGTTTATGTTCATAAA
1 AATTCATTTATGTTCATAAA
48108 CCAGCTCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (22 bp):
AATTCATTTATGTTCATAAATA
Found at i:48116 original size:22 final size:22
Alignment explanation
Indices: 48072--48119 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
48062 GTTCAATTCA
* *
48072 TTTATGTTCATAAATAAATTCG
1 TTTATGTTCATAAACAAACTCG
* *
48094 TTTATGTTCATAAACCAGCTCG
1 TTTATGTTCATAAACAAACTCG
48116 TTTA
1 TTTA
48120 GAATACCGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (22 bp):
TTTATGTTCATAAACAAACTCG
Found at i:49599 original size:15 final size:15
Alignment explanation
Indices: 49579--49614 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
49569 TTTCAGAAAA
* *
49579 TGAATTATTGTAATT
1 TGAATTACTGGAATT
49594 TGAATTACTGGAATT
1 TGAATTACTGGAATT
49609 TGAATT
1 TGAATT
49615 CTAGAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:49671 original size:14 final size:14
Alignment explanation
Indices: 49632--49672 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
49622 ATAAATTGTA
* *
49632 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
49646 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
49660 TTTCCGTAAAATG
1 TTTCCGGAAAATG
49673 AATTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:49847 original size:21 final size:21
Alignment explanation
Indices: 49821--49881 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
49811 ATCATAAAAC
49821 TTATTTATTATTAAAAATAAT
1 TTATTTATTATTAAAAATAAT
*
49842 TTATTTATTATTAAATAGT-AT
1 TTATTTATTATTAAA-AATAAT
*
49863 TT-TTATATTAATAAAAATA
1 TTATT-TATTATTAAAAATA
49882 TTAATTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.12
21 28 0.82
22 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATTTATTATTAAAAATAAT
Found at i:50005 original size:23 final size:23
Alignment explanation
Indices: 49956--50018 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
49946 GTGTTATATT
* **
49956 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
*
49979 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTAATTAAA
50002 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
50019 AAATAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 22 0.65
24 1 0.03
25 11 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:50012 original size:12 final size:12
Alignment explanation
Indices: 49978--50018 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
49968 TATTAATTAG
49978 TATA-TTTTAAA
1 TATATTTTTAAA
49989 TATATTTATTAAA
1 TATATTT-TTAAA
50002 -ATATTATTTAAA
1 TATATT-TTTAAA
50014 TATAT
1 TATAT
50019 AAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.15
12 12 0.46
13 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATTTTTAAA
Found at i:50046 original size:19 final size:20
Alignment explanation
Indices: 49994--50046 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
49984 TTAAATATAT
49994 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
50013 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
50034 TTATTAAATATAT
1 TTATTAAATATAT
50047 AAAATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:50051 original size:29 final size:28
Alignment explanation
Indices: 50002--50079 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
49992 ATTTATTAAA
50002 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAATAATATTAT
**
50031 -TCATTATTAAATATATAAAATTTTATTAT
1 AT-ATTATTAAATATAT-AAATAATATTAT
50060 ATATTATTAAA-ATA-AAATAA
1 ATATTATTAAATATATAAATAA
50080 AAATATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
26 4 0.10
28 14 0.33
29 23 0.55
30 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATTATTAAATATATAAATAATATTAT
Found at i:50141 original size:21 final size:22
Alignment explanation
Indices: 50115--50176 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
50105 TTGATTATTT
50115 TATATAATATTAAAAATA-TAA
1 TATATAATATTAAAAATATTAA
* *
50136 TATATATTATTATAAATATTAA
1 TATATAATATTAAAAATATTAA
*
50158 TAAATAA-A-TAAATAATATT
1 TATATAATATTAAA-AATATT
50177 TTGATGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.09
21 23 0.68
22 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATAATATTAAAAATATTAA
Found at i:50145 original size:33 final size:33
Alignment explanation
Indices: 50098--50178 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 33
50088 TATCTTATAT
50098 TATAATAT-TGATTATTTTATATAATATTAA-AAA
1 TATAATATAT-ATTATTTTATA-AATATTAATAAA
50131 TATAATATATATTA--TTATAAATATTAATAAA
1 TATAATATATATTATTTTATAAATATTAATAAA
* *
50162 TA-AATAAATAATATTTT
1 TATAATATATATTATTTT
50179 GATGAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
30 17 0.40
31 10 0.24
32 2 0.05
33 12 0.29
34 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
TATAATATATATTATTTTATAAATATTAATAAA
Found at i:50413 original size:42 final size:41
Alignment explanation
Indices: 50360--50467 Score: 153
Period size: 42 Copynumber: 2.6 Consensus size: 41
50350 TCGGAAAATC
*
50360 AATTACGTGAAACAAACACTGGAAAATATTTTCCGAAAAACG
1 AATTACGTGAAACAAACAC-GGAAAATATTTTCCGAAAAACA
* * *
50402 AATTACTTGAAACAAACACGGGAAAATATTTTTCGGAAAACA
1 AATTACGTGAAACAAACAC-GGAAAATATTTTCCGAAAAACA
*
50444 AATTACGTAAAACAAACACGGAAA
1 AATTACGTGAAACAAACACGGAAA
50468 TTCGGAAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
41 5 0.08
42 54 0.92
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (41 bp):
AATTACGTGAAACAAACACGGAAAATATTTTCCGAAAAACA
Found at i:50817 original size:17 final size:17
Alignment explanation
Indices: 50797--50839 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
50787 AATCCAGATA
50797 TTTGCCGAA-TCTTGGCG
1 TTTGCCGAATTC-TGGCG
50814 TTTGCCGAATTCTGGCG
1 TTTGCCGAATTCTGGCG
50831 TTTG-CGAAT
1 TTTGCCGAAT
50840 AGAACAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 18 0.72
18 2 0.08
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.37
Consensus pattern (17 bp):
TTTGCCGAATTCTGGCG
Found at i:55587 original size:31 final size:29
Alignment explanation
Indices: 55551--55636 Score: 77
Period size: 31 Copynumber: 2.9 Consensus size: 29
55541 AAACAATTTA
*
55551 TTTAGTCACTTAACTATTATCATATTTATGT
1 TTTAGTCACTTAACTATTA-AAT-TTTATGT
* * *
55582 TTTAGTTAATTAACTTTTAAATTTTATGT
1 TTTAGTCACTTAACTATTAAATTTTATGT
* *
55611 TTTAATCAC-TAAC-GTTATAATTTTAT
1 TTTAGTCACTTAACTATTA-AATTTTAT
55637 TCTATTTTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.07
28 12 0.26
29 13 0.28
30 2 0.04
31 16 0.35
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (29 bp):
TTTAGTCACTTAACTATTAAATTTTATGT
Found at i:59090 original size:29 final size:27
Alignment explanation
Indices: 59044--59099 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
59034 TAATTGAATG
59044 AAACGTTAGGCACCAAACTAGAACAAAAT
1 AAACGTTAGGCACCAAACT-GAA-AAAAT
* *
59073 AAACTTTAGGCACTAAACTGAAAAAAT
1 AAACGTTAGGCACCAAACTGAAAAAAT
59100 GAGCATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 3 0.12
29 17 0.68
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (27 bp):
AAACGTTAGGCACCAAACTGAAAAAAT
Found at i:67058 original size:28 final size:28
Alignment explanation
Indices: 66998--67059 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
66988 TTATCATCAT
*
66998 TTTCAATTTTCTGGGCCTATCTTTTACA
1 TTTCGATTTTCTGGGCCTATCTTTTACA
67026 TTTCGATTTTCTGGGCCTATCTTTTACA
1 TTTCGATTTTCTGGGCCTATCTTTTACA
67054 TTTCGA
1 TTTCGA
67060 GACATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (28 bp):
TTTCGATTTTCTGGGCCTATCTTTTACA
Found at i:69109 original size:60 final size:60
Alignment explanation
Indices: 69036--69155 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
69026 AGGCCATTAT
69036 ACGTCCTTCTGTTGGTCCTTTGATGTACTAACACCGGTTTCCGTTTGGTCTTGTTGTTTG
1 ACGTCCTTCTGTTGGTCCTTTGATGTACTAACACCGGTTTCCGTTTGGTCTTGTTGTTTG
69096 ACGTCCTTCTGTTGGTCCTTTGATGTACTAACACCGGTTTCCGTTTGGTCTTGTTGTTTG
1 ACGTCCTTCTGTTGGTCCTTTGATGTACTAACACCGGTTTCCGTTTGGTCTTGTTGTTTG
69156 GTTCACTTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.45
Consensus pattern (60 bp):
ACGTCCTTCTGTTGGTCCTTTGATGTACTAACACCGGTTTCCGTTTGGTCTTGTTGTTTG
Found at i:70091 original size:276 final size:276
Alignment explanation
Indices: 69593--70148 Score: 1103
Period size: 276 Copynumber: 2.0 Consensus size: 276
69583 TAAACAAGCC
69593 TTGGCCTGAGAATAGAAGAAGCGGCTTCCTATTTCATCGATTTGGTGGGCAAAACTCTTGTGTCT
1 TTGGCCTGAGAATAGAAGAAGCGGCTTCCTATTTCATCGATTTGGTGGGCAAAACTCTTGTGTCT
69658 CAGTGCATCATTGCATTAACAATGCTCTCAGTTCAGCAATTCTGGCTAATTACATAATGTATGGA
66 CAGTGCATCATTGCATTAACAATGCTCTCAGTTCAGCAATTCTGGCTAATTACATAATGTATGGA
69723 AGAACAAAGTAAACCAAGGGAGGATGCAAGCGTACAGGCCAAATTAAAGATAGTGTTTCCTTCTC
131 AGAACAAAGTAAACCAAGGGAGGATGCAAGCGTACAGGCCAAATTAAAGATAGTGTTTCCTTCTC
69788 TTGTTGTTTTAGTCTCTGTCACAAGGCTTCAAGCCTATCTTATGTCCCATTAAGCCATGAGGAGC
196 TTGTTGTTTTAGTCTCTGTCACAAGGCTTCAAGCCTATCTTATGTCCCATTAAGCCATGAGGAGC
69853 TTCCATTAATAAGAAG
261 TTCCATTAATAAGAAG
*
69869 TTGGTCTGAGAATAGAAGAAGCGGCTTCCTATTTCATCGATTTGGTGGGCAAAACTCTTGTGTCT
1 TTGGCCTGAGAATAGAAGAAGCGGCTTCCTATTTCATCGATTTGGTGGGCAAAACTCTTGTGTCT
69934 CAGTGCATCATTGCATTAACAATGCTCTCAGTTCAGCAATTCTGGCTAATTACATAATGTATGGA
66 CAGTGCATCATTGCATTAACAATGCTCTCAGTTCAGCAATTCTGGCTAATTACATAATGTATGGA
69999 AGAACAAAGTAAACCAAGGGAGGATGCAAGCGTACAGGCCAAATTAAAGATAGTGTTTCCTTCTC
131 AGAACAAAGTAAACCAAGGGAGGATGCAAGCGTACAGGCCAAATTAAAGATAGTGTTTCCTTCTC
70064 TTGTTGTTTTAGTCTCTGTCACAAGGCTTCAAGCCTATCTTATGTCCCATTAAGCCATGAGGAGC
196 TTGTTGTTTTAGTCTCTGTCACAAGGCTTCAAGCCTATCTTATGTCCCATTAAGCCATGAGGAGC
70129 TTCCATTAATAAGAAG
261 TTCCATTAATAAGAAG
70145 TTGG
1 TTGG
70149 ACTTGGAGGA
Statistics
Matches: 279, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
276 279 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (276 bp):
TTGGCCTGAGAATAGAAGAAGCGGCTTCCTATTTCATCGATTTGGTGGGCAAAACTCTTGTGTCT
CAGTGCATCATTGCATTAACAATGCTCTCAGTTCAGCAATTCTGGCTAATTACATAATGTATGGA
AGAACAAAGTAAACCAAGGGAGGATGCAAGCGTACAGGCCAAATTAAAGATAGTGTTTCCTTCTC
TTGTTGTTTTAGTCTCTGTCACAAGGCTTCAAGCCTATCTTATGTCCCATTAAGCCATGAGGAGC
TTCCATTAATAAGAAG
Found at i:80908 original size:143 final size:139
Alignment explanation
Indices: 80583--81000 Score: 477
Period size: 144 Copynumber: 2.9 Consensus size: 139
80573 TTCCAGAAAT
* * * * *
80583 ACCTTTTATTTAATATAACTATAATTATTATTTTTATATATTTCTGTTCTATTATTGAAAAATTT
1 ACCTTTTATTTAATATAATTAAAATTATTATTTTTATATATTTCTGTTTTATCATT-TAAAATTT
* * *
80648 GTTAGCAATAATTTTTTATTGACGAGAAAGATACAATAAAAGTTATTTTAATTTTATATAAAAAA
65 -TTAGTAATAATTTTTTCTTGACGAGAAAGATACAATATAAGTTATTTTAA-TTTATAT-AAAAA
*
80713 GTATTAAGATAAAA
127 -TATTAAAATAAAA
* * * *
80727 ACCTTTTATTTAATATAATTAAAATTACTGTTTTTATATGTTTCTGTTTTATCATTTAACATTTA
1 ACCTTTTATTTAATATAATTAAAATTATTATTTTTATATATTTCTGTTTTATCATTTAAAATTT-
* *
80792 ATAGTAATAATTTTTTTTCTTGACGAGAAAGATACAATATAAGTTATTTTAATTTGATATATAAA
65 TTAGTAATAA--TTTTTTCTTGACGAGAAAGATACAATATAAGTTATTTTAATTT-ATATAAAAA
80857 TATTAAAAT-AAA
127 TATTAAAATAAAA
* * * * *
80869 TCATTTTTATTTAACATAATTAAAATTATTATTTCTATATATTTATGTTTTAATC-TTTAAAAAT
1 AC-CTTTTATTTAATATAATTAAAATTATTATTTTTATATATTTCTGTTTT-ATCATTT-AAAAT
* *
80933 CTTTTAGTAAT-ATTTTTTCTTGA-GTAGAAAGACACATTATAAGTTATTTTAATTT-TATAAAA
63 -TTTTAGTAATAATTTTTTCTTGACG-AGAAAGATACAATATAAGTTATTTTAATTTATATAAAA
80995 ATATTA
126 ATATTA
81001 CAAGCTATAA
Statistics
Matches: 237, Mismatches: 29, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
139 12 0.05
140 1 0.00
141 39 0.16
142 4 0.02
143 67 0.28
144 70 0.30
145 44 0.19
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (139 bp):
ACCTTTTATTTAATATAATTAAAATTATTATTTTTATATATTTCTGTTTTATCATTTAAAATTTT
TAGTAATAATTTTTTCTTGACGAGAAAGATACAATATAAGTTATTTTAATTTATATAAAAATATT
AAAATAAAA
Found at i:81011 original size:143 final size:141
Alignment explanation
Indices: 80583--81011 Score: 453
Period size: 143 Copynumber: 3.0 Consensus size: 141
80573 TTCCAGAAAT
* * * * * *
80583 ACCTTTTATTTAATATAACTATAATTATTATTTTTATATATTTCTGTTCTATTATTGAAAAATTT
1 ACCTTTTATTTAATATAATTAAAATTATTATTTTTATATATTTCTGTTTTAATCTTTAAAAATTT
* * * *
80648 GTTAGCAATAATTTTTTATTGACGAGAAAGATACAATAAAAGTTATTTTAATTTTATATAAAAAA
66 ATTAGTAATAATTTTTTCTTGACGAGAAAGATACAATATAAGTTATTTTAA-TTT-TAT-AAAAA
80713 GTATT-AAG-ATAAAA
128 -TATTAAAGTAT-AAA
* * * *
80727 ACCTTTTATTTAATATAATTAAAATTACTGTTTTTATATGTTTCTGTTTT-ATCATTT-AACATT
1 ACCTTTTATTTAATATAATTAAAATTATTATTTTTATATATTTCTGTTTTAATC-TTTAAAAATT
* *
80790 TAATAGTAATAATTTTTTTTCTTGACGAGAAAGATACAATATAAGTTATTTTAATTTGATATATA
65 TATTAGTAATAA--TTTTTTCTTGACGAGAAAGATACAATATAAGTTATTTTAATTT--TATAAA
80855 AATATTAAA--ATAAA
126 AATATTAAAGTATAAA
* * * * *
80869 TCATTTTTATTTAACATAATTAAAATTATTATTTCTATATATTTATGTTTTAATCTTTAAAAATC
1 AC-CTTTTATTTAATATAATTAAAATTATTATTTTTATATATTTCTGTTTTAATCTTTAAAAAT-
* *
80934 TT-TTAGTAAT-ATTTTTTCTTGA-GTAGAAAGACACATTATAAGTTATTTTAATTTTATAAAAA
64 TTATTAGTAATAATTTTTTCTTGACG-AGAAAGATACAATATAAGTTATTTTAATTTTATAAAAA
80996 TATTACAAGCTATAAA
128 TATTA-AAG-TATAAA
81012 CACACAAGCG
Statistics
Matches: 242, Mismatches: 29, Indels: 29
0.81 0.10 0.10
Matches are distributed among these distances:
139 12 0.05
140 3 0.01
141 39 0.16
142 4 0.02
143 71 0.29
144 69 0.29
145 44 0.18
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (141 bp):
ACCTTTTATTTAATATAATTAAAATTATTATTTTTATATATTTCTGTTTTAATCTTTAAAAATTT
ATTAGTAATAATTTTTTCTTGACGAGAAAGATACAATATAAGTTATTTTAATTTTATAAAAATAT
TAAAGTATAAA
Found at i:95033 original size:178 final size:176
Alignment explanation
Indices: 94630--95092 Score: 809
Period size: 176 Copynumber: 2.6 Consensus size: 176
94620 AACAAAAATG
* * * *
94630 AGAAGACAGGGAGAAGGAATTGTACCTGTCAATTCGTTATGGCAAAGAAGAATGTGTGTGAGGGA
1 AGAAGAGAGGGAGATGGAATTGTACCTGTCAACTCGTTATGGGAAAGAAGAATGTGTGTGAGGGA
*
94695 TGTCAGGTTTCCAATAACGGGAGGAATTGGACCTGAAACATATATATACTTACCGTTATAAGCTA
66 TGTCAGGTTTCCAATAACGGGAGGAATTGGACCTGAAACATATATATACTTACCCTTATAAGCTA
* *
94760 TCTGTCTTTTACATTTAAAAGAAAAAGAAAGAAAATTGAATGGAAA
131 TCTGTCTTTTACACTTAAAAGAAAAAGAAAGAAAAGTGAATGGAAA
* * *
94806 AGAGGAGAGGGAGATGGAATTGTACCTGTCAACTTGTTATGGGAAAGAAGAATGTGTCTGAGGGA
1 AGAAGAGAGGGAGATGGAATTGTACCTGTCAACTCGTTATGGGAAAGAAGAATGTGTGTGAGGGA
94871 TGTCAGGTTTCCAATAACGGGAGGAATTGGACCTGAAACATATATATACTTACCCTTATAAGCTA
66 TGTCAGGTTTCCAATAACGGGAGGAATTGGACCTGAAACATATATATACTTACCCTTATAAGCTA
*
94936 TCTGTCTTTTACACTTAAAAGAAAAAAAGAAAGAAAAGTGTATGGAAA
131 TCTGTCTTTTACACTTAAAAG--AAAAAGAAAGAAAAGTGAATGGAAA
94984 AGAAGAGAGGGAGATGGAATTGTACCTGTCAACTCGTTATGGGAAAGAAGAATGTGTGTGAGGGA
1 AGAAGAGAGGGAGATGGAATTGTACCTGTCAACTCGTTATGGGAAAGAAGAATGTGTGTGAGGGA
95049 TGTCAGGTTTCCAATAACGGGAGGAATTGGACCTGAAACATATA
66 TGTCAGGTTTCCAATAACGGGAGGAATTGGACCTGAAACATATA
95093 CTTACCATTA
Statistics
Matches: 271, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
176 142 0.52
178 129 0.48
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.25
Consensus pattern (176 bp):
AGAAGAGAGGGAGATGGAATTGTACCTGTCAACTCGTTATGGGAAAGAAGAATGTGTGTGAGGGA
TGTCAGGTTTCCAATAACGGGAGGAATTGGACCTGAAACATATATATACTTACCCTTATAAGCTA
TCTGTCTTTTACACTTAAAAGAAAAAGAAAGAAAAGTGAATGGAAA
Found at i:100903 original size:34 final size:29
Alignment explanation
Indices: 100838--100898 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
100828 ATTTACAGCC
100838 TATCCCTGATTGTGGCATTCCTTTTCTTT
1 TATCCCTGATTGTGGCATTCCTTTTCTTT
100867 TATCCCTGATTGTGGCATTCCTTTTCTTT
1 TATCCCTGATTGTGGCATTCCTTTTCTTT
100896 TAT
1 TAT
100899 TTTATTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.11, C:0.23, G:0.13, T:0.52
Consensus pattern (29 bp):
TATCCCTGATTGTGGCATTCCTTTTCTTT
Found at i:109211 original size:20 final size:20
Alignment explanation
Indices: 109186--109224 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
109176 CCACATGCAA
*
109186 CTATATGCTCCTAAATGAAT
1 CTATATGATCCTAAATGAAT
*
109206 CTATATGATCCTATATGAA
1 CTATATGATCCTAAATGAA
109225 CTTTTAGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (20 bp):
CTATATGATCCTAAATGAAT
Found at i:114947 original size:3 final size:3
Alignment explanation
Indices: 114933--114985 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
114923 GAAAGAGCAG
114933 AGA AGCA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
114979 AGA AGA A
1 AGA AGA A
114986 AGAGATCGCC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:118074 original size:18 final size:18
Alignment explanation
Indices: 118048--118085 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
118038 TCGAAAGGAC
*
118048 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
118066 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
118084 TG
1 TG
118086 GATGGAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:123784 original size:18 final size:18
Alignment explanation
Indices: 123758--123792 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
123748 TCGAAAGGAC
*
123758 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
123776 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
123793 CTGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:131737 original size:20 final size:18
Alignment explanation
Indices: 131704--131749 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
131694 ATGAAATGTA
131704 TTTTCTTCCTCTCCTCTC
1 TTTTCTTCCTCTCCTCTC
131722 TTTTCTTTCTCTCTCCTCTC
1 TTTTC-TTC-CTCTCCTCTC
131742 -TTTCTTCC
1 TTTTCTTCC
131750 ATAGTCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.31
19 7 0.27
20 10 0.38
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTCTTCCTCTCCTCTC
Found at i:132388 original size:15 final size:15
Alignment explanation
Indices: 132368--132400 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
132358 TTAATAAAAA
132368 TAACCTCTCTCTTTT
1 TAACCTCTCTCTTTT
132383 TAACCTCTCTCTTTT
1 TAACCTCTCTCTTTT
132398 TAA
1 TAA
132401 TTTAGTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.30, G:0.00, T:0.52
Consensus pattern (15 bp):
TAACCTCTCTCTTTT
Found at i:132545 original size:14 final size:14
Alignment explanation
Indices: 132526--132552 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
132516 AAAAACACCT
132526 TATTTGAAATATAA
1 TATTTGAAATATAA
132540 TATTTGAAATATA
1 TATTTGAAATATA
132553 TTTTATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
TATTTGAAATATAA
Found at i:137323 original size:53 final size:54
Alignment explanation
Indices: 137162--138092 Score: 968
Period size: 54 Copynumber: 17.5 Consensus size: 54
137152 CTCTCTACTC
*
137162 CTTCA-GAGAGTAT-GAGACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 CTTCAGGA-AGTATGGA-ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * * ** * *
137216 TTTCAGGAAGTATAGAACTCAAAAATCTT-TCTCTTACGGGTTTGCTCCTTCTTT
1 CTTCAGGAAGTATGGAACTCGAAAATCTTCT-TCAAACGGGTTCGCTCCCTCTTT
* * * * *
137270 CTTCAGGGAGTATAGAACTC-AGACAT-TTCTTCAAACGGGTTTGCTCCTTCTTT
1 CTTCAGGAAGTATGGAACTCGA-AAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * * * *
137323 CTTTAAGG-AGTATGGAACTCG--GAT-ATCTTCACACGGGTTCGCTCTCTCTTT
1 C-TTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
137374 C-TCTAGGGAGTATGGAACTCG--AA-CATCTTCAAACAGGTTCGCTCCCTCTTT
1 CTTC-AGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * * * *
137425 CTTTAGGGAGTATGGAACTCG--AAT-ATCTTCACATGGGTTCGCTCCCTCTTT
1 CTTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
137476 -TTCAGGAAGTATAGAACTCGAAAATCTTCTTCAAATGGG-TCGCTTCCTCTTT
1 CTTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * * * *
137528 CTTTCAGGAAGTATAGAACTCGGATATCTTCTTCAAATGGGTTCGCTCTCTCTTT
1 C-TTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
*
137583 C-TCTAGGAAGTATGGAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 CTTC-AGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* *
137637 -TTCAGGAAGTACGGAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 CTTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * ** *
137690 -TTCAGGAAGTATAGAACTCAAAAATCTTCTTCAAATAGGTTCGCTTCCTCTTT
1 CTTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
137743 CTTTCAGGAAGTATAGAACTCGAATATATTCTTCAAACGGGTTCGCTCCCTCTTT
1 C-TTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* *
137798 C-TCTAGGAAGTATGGAACTCGAAAATCTTCTTAAAATGGGTTCGCTCCCTCTTT
1 CTTC-AGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* ** *
137852 -TTCAGGAAGTATAGAACTCGAAAATCTTCTTCAAATAGGTTCGCTTCCTCTTT
1 CTTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
137905 CTTTCAGGAAGTATAGAACTCGGATATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 C-TTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * * * *
137960 TTTTAGGGAGTATGGAACTCGAACA--GTCTTCAAACGGGTTCGCTCCCTCTTT
1 CTTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* *
138012 C-TCTAGGGAGTATGGAACTCG--AA-CATCTTCAAACGGGTTCGCTCCCTCTTT
1 CTTC-AGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
*
138063 CTCTAAGG-AGTATGGAACTCGAACAATCTT
1 CT-TCAGGAAGTATGGAACTCGAA-AATCTT
138093 TACTTGCTTC
Statistics
Matches: 759, Mismatches: 84, Indels: 67
0.83 0.09 0.07
Matches are distributed among these distances:
49 1 0.00
50 21 0.03
51 148 0.19
52 62 0.08
53 194 0.26
54 219 0.29
55 114 0.15
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (54 bp):
CTTCAGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTT
Found at i:139400 original size:10 final size:9
Alignment explanation
Indices: 139387--139443 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
139377 TTGTTCTCTT
139387 TTTTTTAATC
1 TTTTTT-ATC
139397 TTTTTTATC
1 TTTTTTATC
*
139406 CTTTTTATC
1 TTTTTTATC
*
139415 ATTTTT-TC
1 TTTTTTATC
*
139423 TTTTTTTTTC
1 -TTTTTTATC
*
139433 TTTTTCATC
1 TTTTTTATC
139442 TT
1 TT
139444 CAAGCAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 2 0.05
9 30 0.75
10 8 0.20
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTATC
Found at i:148783 original size:25 final size:25
Alignment explanation
Indices: 148749--148824 Score: 125
Period size: 25 Copynumber: 3.0 Consensus size: 25
148739 GAACATTAGA
148749 AACCTAACCACATGATATCTAGTTC
1 AACCTAACCACATGATATCTAGTTC
* *
148774 AACCTAACCACATGGTATCTAATTC
1 AACCTAACCACATGATATCTAGTTC
*
148799 AACCTAACCACATGATCTCTAGTTC
1 AACCTAACCACATGATATCTAGTTC
148824 A
1 A
148825 CATGCATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.36, C:0.29, G:0.08, T:0.28
Consensus pattern (25 bp):
AACCTAACCACATGATATCTAGTTC
Found at i:154022 original size:169 final size:172
Alignment explanation
Indices: 153690--154023 Score: 647
Period size: 169 Copynumber: 2.0 Consensus size: 172
153680 CTTCCAAATG
153690 CATGGAGGTTTGAATAATCAGCTGGTTTACCAGTCCACATCTCCATTGGTGTCTTCAGCTCTATT
1 CATGGAGGTTTGAATAATCAGCTGGTTTACCAGTCCACATCTCCATTGGTGTCTTCAGCTCTATT
153755 GCAGTTAATGGAGCTCAATTCACCAAATAACAGGCGGTATTGACTGCTTCTGCCCAGAATGATTT
66 GCAGTTAATGGAGCTCAATTCACCAAATAACAGGCGGTATTGACTGCTTCTGCCCAGAATGATTT
153820 TTCTAGGCCTGCATCCCTCAACATTGCTCTTGTTATTTCTAA
131 TTCTAGGCCTGCATCCCTCAACATTGCTCTTGTTATTTCTAA
153862 CATGGAGGTTTGAATAATCAGCTGGTTTACCA-TCCACATCTCCATTGGTGTCTTCAGCTCTATT
1 CATGGAGGTTTGAATAATCAGCTGGTTTACCAGTCCACATCTCCATTGGTGTCTTCAGCTCTATT
153926 GCAGTTAATGGAGCTC-ATTCACCAAATAACAGGCGGTATTGACTGCTT-TGCCCAGAATGATTT
66 GCAGTTAATGGAGCTCAATTCACCAAATAACAGGCGGTATTGACTGCTTCTGCCCAGAATGATTT
153989 TTCTAGGCCTGCATCCCTCAACATTGCTCTTGTTA
131 TTCTAGGCCTGCATCCCTCAACATTGCTCTTGTTA
154024 GTTAAAGTTT
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
169 50 0.31
170 32 0.20
171 48 0.30
172 32 0.20
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (172 bp):
CATGGAGGTTTGAATAATCAGCTGGTTTACCAGTCCACATCTCCATTGGTGTCTTCAGCTCTATT
GCAGTTAATGGAGCTCAATTCACCAAATAACAGGCGGTATTGACTGCTTCTGCCCAGAATGATTT
TTCTAGGCCTGCATCCCTCAACATTGCTCTTGTTATTTCTAA
Found at i:158681 original size:19 final size:19
Alignment explanation
Indices: 158650--158696 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
158640 AATATAAAAT
*
158650 ATAA-ATTTTTATTTTATA
1 ATAATATTTATATTTTATA
158668 ATAATATTTATATTTTATA
1 ATAATATTTATATTTTATA
* *
158687 GTCATATTTA
1 ATAATATTTA
158697 AATAAAAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
ATAATATTTATATTTTATA
Found at i:158876 original size:28 final size:28
Alignment explanation
Indices: 158845--158901 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
158835 TTTTAATAAT
*
158845 AAAAATATT-ATTTTTTTA-AAAAAACTC
1 AAAAA-ATTAATTTATTTATAAAAAACTC
*
158872 AAAAAGTTAATTTATTTATAAAAAACTC
1 AAAAAATTAATTTATTTATAAAAAACTC
158900 AA
1 AA
158902 GCATTTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 2 0.08
27 13 0.50
28 11 0.42
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (28 bp):
AAAAAATTAATTTATTTATAAAAAACTC
Found at i:159267 original size:7 final size:7
Alignment explanation
Indices: 159255--159291 Score: 53
Period size: 6 Copynumber: 5.7 Consensus size: 7
159245 CGGCGATCGT
159255 GGAAAGG
1 GGAAAGG
159262 GGAAA-G
1 GGAAAGG
159268 GGAAAGG
1 GGAAAGG
159275 GG-AAGG
1 GGAAAGG
159281 GG-AAGG
1 GGAAAGG
159287 GGAAA
1 GGAAA
159292 AAGAGAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 18 0.64
7 10 0.36
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (7 bp):
GGAAAGG
Found at i:159876 original size:21 final size:21
Alignment explanation
Indices: 159850--159889 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
159840 TGATATTTTT
159850 TATTATCAT-TTTATTTTTTAA
1 TATTAT-ATCTTTATTTTTTAA
159871 TATTATATCTTTATTTTTT
1 TATTATATCTTTATTTTTT
159890 TTAATAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (21 bp):
TATTATATCTTTATTTTTTAA
Found at i:159965 original size:23 final size:23
Alignment explanation
Indices: 159906--159963 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
159896 AGTATGTTTA
159906 TATGATACGTTTTCATCTGCCTT
1 TATGATACGTTTTCATCTGCCTT
* * *
159929 TATGATACGTTTTCTTTTGTCTT
1 TATGATACGTTTTCATCTGCCTT
159952 T-TGATACGTTTT
1 TATGATACGTTTT
159964 TCAGTCGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.55
Consensus pattern (23 bp):
TATGATACGTTTTCATCTGCCTT
Found at i:160673 original size:15 final size:14
Alignment explanation
Indices: 160647--160688 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
160637 CCTATAGAGT
160647 CATACTATATATAC
1 CATACTATATATAC
*
160661 CATAGTATGATATAC
1 CATACTAT-ATATAC
160676 CATACTATATATA
1 CATACTATATATA
160689 ATAGAGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (14 bp):
CATACTATATATAC
Found at i:163186 original size:58 final size:59
Alignment explanation
Indices: 163073--163202 Score: 167
Period size: 58 Copynumber: 2.2 Consensus size: 59
163063 TTTATTGGGT
* * * *
163073 AAAGTGTAC-AAATGGTCCTCTAATTATAGGTGTTATTTTGCTGAGTCATTCGACTATTA
1 AAAGT-TACAAAATAGTCCTCTAACTATAGGCGTTATTTTGCTGAGTCATTAGACTATTA
* *
163132 AAA-TTATAAAATAGTCCTCTAACTATAGAGCGTTATTTTGTTGAGTCA-TAGACTATTA
1 AAAGTTACAAAATAGTCCTCTAACTATAG-GCGTTATTTTGCTGAGTCATTAGACTATTA
163190 AAAGTTACAAAAT
1 AAAGTTACAAAAT
163203 TGTCATCCGA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
57 2 0.03
58 31 0.51
59 28 0.46
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (59 bp):
AAAGTTACAAAATAGTCCTCTAACTATAGGCGTTATTTTGCTGAGTCATTAGACTATTA
Found at i:163216 original size:59 final size:59
Alignment explanation
Indices: 163104--163216 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
163094 AATTATAGGT
* * * *
163104 GTTATTTTGCTGAGTCATTCGACTATTAAAATTATAAAATAGTCCTCTAACTATAGAGC
1 GTTATTTTGCTGAGTCATTAGACTATTAAAATTACAAAATAGTCATCCAACTATAGAGC
* * *
163163 GTTATTTTGTTGAGTCA-TAGACTATTAAAAGTTACAAAATTGTCATCCGACTAT
1 GTTATTTTGCTGAGTCATTAGACTATTAAAA-TTACAAAATAGTCATCCAACTAT
163217 TCATATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
58 12 0.26
59 34 0.74
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (59 bp):
GTTATTTTGCTGAGTCATTAGACTATTAAAATTACAAAATAGTCATCCAACTATAGAGC
Found at i:163856 original size:18 final size:19
Alignment explanation
Indices: 163835--163875 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
163825 TGATTTTTGG
163835 TTTTGTTATTTT-TTTTTC
1 TTTTGTTATTTTATTTTTC
163853 TTTTGTTATTTTATTTTTC
1 TTTTGTTATTTTATTTTTC
163872 TTTT
1 TTTT
163876 CCTTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (19 bp):
TTTTGTTATTTTATTTTTC
Found at i:173533 original size:16 final size:16
Alignment explanation
Indices: 173509--173552 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
173499 TAAACAAATA
*
173509 AATTTATTGTTATATT
1 AATTAATTGTTATATT
**
173525 AATTAATTGAAATATT
1 AATTAATTGTTATATT
*
173541 AATAAATTGTTA
1 AATTAATTGTTA
173553 ACTAAAAATG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
AATTAATTGTTATATT
Found at i:174401 original size:18 final size:18
Alignment explanation
Indices: 174378--174412 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
174368 AAGTTTTCTT
174378 TTTGGTATT-TTTAAGTTG
1 TTTGGT-TTGTTTAAGTTG
174396 TTTGGTTTGTTTAAGTT
1 TTTGGTTTGTTTAAGTT
174413 CTTTTTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (18 bp):
TTTGGTTTGTTTAAGTTG
Found at i:178284 original size:3 final size:3
Alignment explanation
Indices: 178276--178304 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
178266 TCCCGTGTGG
178276 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
178305 ATAAAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:183523 original size:2 final size:2
Alignment explanation
Indices: 183516--183571 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
183506 CACGCACGCG
183516 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
183558 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
183572 ATTTTTATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:186327 original size:13 final size:13
Alignment explanation
Indices: 186309--186334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
186299 CTTTAAAGGT
186309 ATAATCTCTTTTG
1 ATAATCTCTTTTG
186322 ATAATCTCTTTTG
1 ATAATCTCTTTTG
186335 TAACAACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
ATAATCTCTTTTG
Found at i:191887 original size:62 final size:62
Alignment explanation
Indices: 191785--191909 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
191775 ACCGTCGGAG
** ** *
191785 AAAACAACTTCTCAGGCATGCTTAATGACTCATCGTGCTTTAATAATGTATTTAAATGTAAT
1 AAAACAACTTCTCAGGCAAACTTAATGACTCATCACGCTTTAATAATGTACTTAAATGTAAT
*
191847 AAAACAACTTCTCAGGTAAACTTAATGACTCATCACGCTTTAATAATGTACTTAAATGTAAT
1 AAAACAACTTCTCAGGCAAACTTAATGACTCATCACGCTTTAATAATGTACTTAAATGTAAT
191909 A
1 A
191910 GAGTTATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (62 bp):
AAAACAACTTCTCAGGCAAACTTAATGACTCATCACGCTTTAATAATGTACTTAAATGTAAT
Found at i:192418 original size:41 final size:41
Alignment explanation
Indices: 192361--192444 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
192351 TTCTGCGTTC
* *
192361 TACGGGATTATAAAAACTTTTAAATTGAAGGTTATTTTATT
1 TACGGGATTATAAAAACTTTTAAATTAAAGGTTATTGTATT
192402 TACGGGATTATAAAAACTTTTAAATTAAAGGTTATTGTATT
1 TACGGGATTATAAAAACTTTTAAATTAAAGGTTATTGTATT
192443 TA
1 TA
192445 TTTTTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (41 bp):
TACGGGATTATAAAAACTTTTAAATTAAAGGTTATTGTATT
Found at i:205027 original size:13 final size:13
Alignment explanation
Indices: 205008--205076 Score: 93
Period size: 13 Copynumber: 5.3 Consensus size: 13
204998 GTCATAACTC
205008 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
205021 TACCCGACCTGTT
1 GACCCGACCCGTT
*
205034 GACCCGACCCTTT
1 GACCCGACCCGTT
*
205047 GACTCGACCCGTT
1 GACCCGACCCGTT
*
205060 GATCCGACCCGTT
1 GACCCGACCCGTT
205073 GACC
1 GACC
205077 GTTGACCGGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.16, C:0.42, G:0.20, T:0.22
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:207623 original size:24 final size:24
Alignment explanation
Indices: 207578--207649 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
207568 GATACATAAC
* * *
207578 CTGAATTCTGTTCTAATTTCTGAT
1 CTGAATTCTGTTATGATATCTGAT
* * *
207602 CTGGATTTTGTTATGATATCTGTT
1 CTGAATTCTGTTATGATATCTGAT
* *
207626 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATATCTGAT
207650 ATCTCCGCTT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.53
Consensus pattern (24 bp):
CTGAATTCTGTTATGATATCTGAT
Found at i:207635 original size:12 final size:12
Alignment explanation
Indices: 207578--207647 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
207568 GATACATAAC
207578 CTGAATTCTGTT
1 CTGAATTCTGTT
*
207590 CT-AATTTCTGAT
1 CTGAA-TTCTGTT
* *
207602 CTGGATTTTGTT
1 CTGAATTCTGTT
*
207614 ATG-ATATCTGTT
1 CTGAAT-TCTGTT
207626 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
207638 TTGATTTCTG
1 CTGAATTCTG
207648 ATATCTCCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 4 0.09
12 38 0.84
13 3 0.07
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:209861 original size:36 final size:36
Alignment explanation
Indices: 209789--209860 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
209779 TTAAGGTTTC
* *
209789 ACCCGACCCGACCCGACCCGAATATATGACTTAAAA
1 ACCCGACCCGACCCGACCCGAATATATGAATAAAAA
209825 ACCCGACCCGACCCGACCCGAA-ATAAT-AATAAAAA
1 ACCCGACCCGACCCGACCCGAATAT-ATGAATAAAAA
209860 A
1 A
209861 AATTTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.42, C:0.35, G:0.12, T:0.11
Consensus pattern (36 bp):
ACCCGACCCGACCCGACCCGAATATATGAATAAAAA
Found at i:214532 original size:14 final size:14
Alignment explanation
Indices: 214503--214543 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
214493 ATTTTGTTTG
214503 AATAAAAAAATA-AA
1 AATAAAAAAA-AGAA
214517 AATAAAAAAAAGAA
1 AATAAAAAAAAGAA
*
214531 AA-AAGAAAAAGAA
1 AATAAAAAAAAGAA
214544 TAAAAGGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (14 bp):
AATAAAAAAAAGAA
Found at i:214548 original size:16 final size:15
Alignment explanation
Indices: 214506--214548 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
214496 TTGTTTGAAT
214506 AAAAAAATAAAAATA
1 AAAAAAATAAAAATA
*
214521 AAAAAAAGAAAAA-A
1 AAAAAAATAAAAATA
214535 GAAAAAGAATAAAA
1 -AAAAA-AATAAAA
214549 GGGGGTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 17 0.71
16 6 0.25
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAAAATAAAAATA
Found at i:214549 original size:14 final size:13
Alignment explanation
Indices: 214502--214548 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
214492 TATTTTGTTT
214502 GAATAAAAAAATAA
1 GAATAAAAAAA-AA
*
214516 AAAT-AAAAAAAA
1 GAATAAAAAAAAA
214528 GAA-AAAAGAAAAA
1 GAATAAAA-AAAAA
214541 GAATAAAA
1 GAATAAAA
214549 GGGGGTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 7 0.25
13 14 0.50
14 7 0.25
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (13 bp):
GAATAAAAAAAAA
Found at i:215828 original size:37 final size:37
Alignment explanation
Indices: 215773--215934 Score: 191
Period size: 37 Copynumber: 4.4 Consensus size: 37
215763 TCTGACCTTC
* *
215773 GAAGCAAATCAATATTAAGCCTTCACGAAAAAGTAGT
1 GAAGCAAATCAATCTTAAGCCTTCACGAAAGAGTAGT
*
215810 GAAGCAAATCAATCTTAAGCCTTCATGAAAGAGTAGT
1 GAAGCAAATCAATCTTAAGCCTTCACGAAAGAGTAGT
* * * * *
215847 GAAGTAAGTCGATCTTAAGCCTTCACGGAAGAGTATT
1 GAAGCAAATCAATCTTAAGCCTTCACGAAAGAGTAGT
* * * * *
215884 GAAACAAATCAATCTT-AGCCTTCAAGGAACAGTAGC
1 GAAGCAAATCAATCTTAAGCCTTCACGAAAGAGTAGT
*
215920 GAAGCAAATAAATCT
1 GAAGCAAATCAATCT
215935 CGAGTCTGAT
Statistics
Matches: 106, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
36 29 0.27
37 77 0.73
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (37 bp):
GAAGCAAATCAATCTTAAGCCTTCACGAAAGAGTAGT
Found at i:216259 original size:27 final size:26
Alignment explanation
Indices: 216222--216295 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 26
216212 TTTATTTGGG
*
216222 TTTATATTATTATTA-ATTATATTATA
1 TTTATATTATTATTATA-TATATGATA
*
216248 TTTATATATATTGTTATATATATGATA
1 TTTATAT-TATTATTATATATATGATA
* *
216275 TTATGTAATCATTATTATATA
1 TT-TAT-ATTATTATTATATA
216296 CATGTCATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 7 0.18
27 17 0.44
28 13 0.33
29 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTATATTATTATTATATATATGATA
Found at i:226554 original size:109 final size:109
Alignment explanation
Indices: 226363--226568 Score: 340
Period size: 109 Copynumber: 1.9 Consensus size: 109
226353 TAAGAATAGA
* * **
226363 TTCTATAGTCTATGCTTTGGGGAACAGAATGAGGTTCCTAATGTTTTTCTTAGCTGGGCCATTTA
1 TTCTATAGTCTATGCTTTGGGGAACAGAACGAGGTTCCAAATGTTTTTCTTAGCTAAGCCATTTA
* *
226428 TATTAGTCAAAACCGGCACATAGAATCTATCAAAATATATTCAT
66 TATTAATCAAAAACGGCACATAGAATCTATCAAAATATATTCAT
* *
226472 TTCTATAGTCTGTGCTTTGGGGAACAGAACGGGGTTCCAAATGTTTTTCTTAGCTAAGCCATTTA
1 TTCTATAGTCTATGCTTTGGGGAACAGAACGAGGTTCCAAATGTTTTTCTTAGCTAAGCCATTTA
226537 TATTAATCAAAAACGGCACATAGAATCTATCA
66 TATTAATCAAAAACGGCACATAGAATCTATCA
226569 TACAAAATCA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 89 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (109 bp):
TTCTATAGTCTATGCTTTGGGGAACAGAACGAGGTTCCAAATGTTTTTCTTAGCTAAGCCATTTA
TATTAATCAAAAACGGCACATAGAATCTATCAAAATATATTCAT
Found at i:250139 original size:12 final size:12
Alignment explanation
Indices: 250122--250146 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
250112 ATTCGATTAA
250122 AGCTTGAATTTG
1 AGCTTGAATTTG
250134 AGCTTGAATTTG
1 AGCTTGAATTTG
250146 A
1 A
250147 ACATTAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (12 bp):
AGCTTGAATTTG
Found at i:252532 original size:2 final size:2
Alignment explanation
Indices: 252520--252553 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
252510 CTTCTAAAAC
*
252520 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
252554 GCCCCCATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:252744 original size:24 final size:24
Alignment explanation
Indices: 252717--252788 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
252707 AAACGGAGAT
252717 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
252741 ATCAGATATCATAACAGAATTCAT
1 ATCAGAAATCAAAACAGAATTCAG
*
252765 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
252789 GTAATGTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:252746 original size:12 final size:12
Alignment explanation
Indices: 252719--252788 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
252709 ACGGAGATAT
* *
252719 CAGAAATCAAAA
1 CAGAATTCAGAA
*
252731 CAGAATTCAGAT
1 CAGAATTCAGAA
*
252743 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
252755 CAGAATTCATAT
1 CAGAATTCAGAA
*
252767 CAGAAATCAGAA
1 CAGAATTCAGAA
252779 CAGAATTCAG
1 CAGAATTCAG
252789 GTAATGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:252786 original size:48 final size:48
Alignment explanation
Indices: 252715--252825 Score: 145
Period size: 48 Copynumber: 2.3 Consensus size: 48
252705 GTAAACGGAG
* * *
252715 ATATCAGAAATCAAAACAGAATTCAGATCA-GATATCATAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGATAATG-TATCAGAACAGAATTC
*
252763 ATATCAGAAATCAGAACAGAATTCAGGTAATGTATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGATAATGTATCAGAACAGAATTC
*
252811 A-AGTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
252826 TAAAATATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 1 0.02
48 54 0.96
49 1 0.02
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGATAATGTATCAGAACAGAATTC
Found at i:252823 original size:24 final size:24
Alignment explanation
Indices: 252718--252825 Score: 105
Period size: 24 Copynumber: 4.5 Consensus size: 24
252708 AACGGAGATA
*
252718 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* *
252741 ATCAGATATCATAACAGAATTCATA-
1 -TCAGAAATCAGAACAGAATTCA-AG
*
252766 TCAGAAATCAGAACAGAATTCAGG
1 TCAGAAATCAGAACAGAATTCAAG
* *
252790 TAATG-TATCAGAACAGAATTCAAG
1 TCA-GAAATCAGAACAGAATTCAAG
*
252814 TCGGAAATCAGA
1 TCAGAAATCAGA
252826 TAAAATATTT
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
23 1 0.01
24 65 0.96
25 1 0.01
26 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:255427 original size:29 final size:29
Alignment explanation
Indices: 255394--255490 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
255384 ATTTTACACA
*
255394 AATAGCACCAAACA-GAAATTAATTCCCAG
1 AATAGCACCAAAAACG-AATTAATTCCCAG
* *
255423 GATAGCA-CAAAAATCGAATTAATTCCCAT
1 AATAGCACCAAAAA-CGAATTAATTCCCAG
** *
255452 AATAGCACCAAATTCGAATTAATTACCAG
1 AATAGCACCAAAAACGAATTAATTCCCAG
*
255481 AATAACACCA
1 AATAGCACCA
255491 TTTTCGAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 5 0.09
29 46 0.82
30 5 0.09
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.21
Consensus pattern (29 bp):
AATAGCACCAAAAACGAATTAATTCCCAG
Found at i:255472 original size:58 final size:58
Alignment explanation
Indices: 255393--255535 Score: 137
Period size: 58 Copynumber: 2.5 Consensus size: 58
255383 AATTTTACAC
* *
255393 AAATAGCACCAAA--CAGAAATTAATTCCCAGGATAGCACAAAAATCGAATTAATTCCCA
1 AAATAGCACCAAATTC-G-AATTAATTCCCAGAATAACACAAAAATCGAATTAATTCCCA
* * * *** *
255451 TAATAGCACCAAATTCGAATTAATTACCAGAATAACACCATTTTCGAATTATTTCCCA
1 AAATAGCACCAAATTCGAATTAATTCCCAGAATAACACAAAAATCGAATTAATTCCCA
* ** *
255509 AAATATCACCACTTTCGAATTATTTCC
1 AAATAGCACCAAATTCGAATTAATTCC
255536 GTGCGACGGT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
58 66 0.97
59 1 0.01
60 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (58 bp):
AAATAGCACCAAATTCGAATTAATTCCCAGAATAACACAAAAATCGAATTAATTCCCA
Found at i:255496 original size:29 final size:29
Alignment explanation
Indices: 255436--255535 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
255426 AGCACAAAAA
* * *
255436 TCGAATTAATTCCCATAATAGCACCAAAT
1 TCGAATTAATTCCCAAAATAACACCAATT
* * *
255465 TCGAATTAATTACCAGAATAACACCATTT
1 TCGAATTAATTCCCAAAATAACACCAATT
* * *
255494 TCGAATTATTTCCCAAAATATCACCACTT
1 TCGAATTAATTCCCAAAATAACACCAATT
*
255523 TCGAATTATTTCC
1 TCGAATTAATTCC
255536 GTGCGACGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (29 bp):
TCGAATTAATTCCCAAAATAACACCAATT
Found at i:256508 original size:11 final size:10
Alignment explanation
Indices: 256482--256513 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
256472 CTGGTTCACT
256482 GGTTCAACCG
1 GGTTCAACCG
256492 GGTTCAACCG
1 GGTTCAACCG
256502 CGGTTCAACCG
1 -GGTTCAACCG
256513 G
1 G
256514 ATTTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.19
Consensus pattern (10 bp):
GGTTCAACCG
Found at i:256993 original size:20 final size:21
Alignment explanation
Indices: 256968--257019 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
256958 TTTTCCCAAT
*
256968 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
256988 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
257009 TCGCAATGCGA
1 TCGCAATGCGA
257020 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:257032 original size:41 final size:41
Alignment explanation
Indices: 257005--257136 Score: 133
Period size: 41 Copynumber: 3.2 Consensus size: 41
256995 GCGAATTGGG
* * *
257005 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* * *
257046 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAAT-AC
** * * *
257088 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
257127 ATAATCGCAA
1 AAAATCGCAA
257137 TGCGATTTTC
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.42
41 39 0.53
42 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:257033 original size:20 final size:20
Alignment explanation
Indices: 257008--257122 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
256998 AATTGGGAAA
*
257008 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
257028 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
257049 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
257069 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
257089 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
257109 TTCGCAACGCGATA
1 ATCGCAACGCGATA
257123 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:257340 original size:22 final size:22
Alignment explanation
Indices: 257312--257353 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
257302 CTCTCTCACT
257312 CATCTCCGACGAAATCCGTCCC
1 CATCTCCGACGAAATCCGTCCC
*
257334 CATCTCCGGCGAAATCCGTC
1 CATCTCCGACGAAATCCGTC
257354 TATCTCCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.43, G:0.17, T:0.19
Consensus pattern (22 bp):
CATCTCCGACGAAATCCGTCCC
Found at i:257641 original size:20 final size:20
Alignment explanation
Indices: 257597--257660 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
257587 GCGATTTTAG
257597 TTTCGCGTTGCGATAGTCGA-
1 TTTCGCGTTGCGATAGTC-AT
*
257617 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
257637 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
257657 TTTC
1 TTTC
257661 AGAAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:259000 original size:18 final size:18
Alignment explanation
Indices: 258979--259023 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
258969 TCCACTTCGG
*
258979 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
258997 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
259015 GAGCCATCA
1 GAGCCATCA
259024 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:259578 original size:14 final size:14
Alignment explanation
Indices: 259559--259616 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
259549 ATGCGAAATG
259559 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
259573 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
259589 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
259605 AAAATCGCAACG
1 AAAATCGCAACG
259617 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:259601 original size:32 final size:33
Alignment explanation
Indices: 259543--259633 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
259533 CGGAATGGCT
259543 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
259576 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
259608 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
259634 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:259627 original size:19 final size:19
Alignment explanation
Indices: 259505--259638 Score: 74
Period size: 19 Copynumber: 7.6 Consensus size: 19
259495 TAGTTTACTT
* **
259505 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
* ***
259525 TCGCAACGCGGAATGGCTA
1 TCGCAACGCGAAATGAAAA
*
259544 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
259563 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
259577 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
259595 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
259609 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
259628 TCGCAATGCGA
1 TCGCAACGCGA
259639 TTTGTGTTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 23
0.71 0.10 0.18
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 41 0.46
20 9 0.10
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:259679 original size:19 final size:19
Alignment explanation
Indices: 259664--259767 Score: 111
Period size: 19 Copynumber: 5.4 Consensus size: 19
259654 GCGATTTTGT
259664 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
259682 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
259701 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
259721 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
259740 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
259760 TGTTGCGA
1 CGTTGCGA
259768 AAGTAAACTA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 8 0.11
19 36 0.49
20 29 0.40
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:259725 original size:39 final size:38
Alignment explanation
Indices: 259675--259748 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
259665 GTTGCGATTT
**
259675 CATTTCGCGTTGCGATTTTCATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
*
259713 CATTTCCGCGTTGCGATAGTCATTTCGCGTTGCGAT
1 CATTT-CGCGTTGCGATAGTCATTTCGCATTGCGAT
259749 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.16
39 27 0.84
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (38 bp):
CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
Found at i:261776 original size:14 final size:14
Alignment explanation
Indices: 261757--261812 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
261747 CGAAATGGCT
261757 ATCGCAATGAGAAA
1 ATCGCAATGAGAAA
261771 ATCGCAATGCGAAATGAAA
1 ATCGCAAT--G--A-GAAA
*
261790 ATCGCAACGAGAAA
1 ATCGCAATGAGAAA
261804 ATCGCAATG
1 ATCGCAATG
261813 CGATTTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (14 bp):
ATCGCAATGAGAAA
Found at i:261789 original size:19 final size:17
Alignment explanation
Indices: 261766--261815 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
261756 TATCGCAATG
261766 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
261784 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
261799 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
261816 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:261828 original size:33 final size:33
Alignment explanation
Indices: 261738--261815 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
261728 AAAACAGACT
* *** *
261738 ATCGCAACGCGAAATGGCTATCGCAATGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
261771 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
261804 ATCGCAATGCGA
1 ATCGCAATGCGA
261816 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:261859 original size:20 final size:20
Alignment explanation
Indices: 261834--261891 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
261824 TCGCATTGCG
*
261834 ATTTTCTCGTTGTGATAGCC
1 ATTTTCTCGTTGCGATAGCC
261854 ATTTTCGT-GTTGCGATAGCC
1 ATTTTC-TCGTTGCGATAGCC
*
261874 ATTTTCGCGTTGCGATAG
1 ATTTTCTCGTTGCGATAG
261892 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTTCTCGTTGCGATAGCC
Found at i:262975 original size:24 final size:24
Alignment explanation
Indices: 262948--263001 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
262938 GTATTCGAAA
* *
262948 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
262972 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
262996 TTTGAT
1 TTTGAT
263002 GATGTTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:265513 original size:19 final size:19
Alignment explanation
Indices: 265491--265621 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
265481 GGAAATTACT
265491 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
265510 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
265524 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
265543 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
265557 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
265576 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
265590 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
265609 ATCGCAACGCGAA
1 ATCGCAATGCGAA
265622 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:265533 original size:33 final size:33
Alignment explanation
Indices: 265491--265617 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
265481 GGAAATTACT
265491 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
265524 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
265556 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
265590 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
265618 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:265598 original size:66 final size:66
Alignment explanation
Indices: 265492--265624 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
265482 GAAATTACTA
*
265492 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
265557 T
66 T
*
265558 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
265623 T
66 T
265624 T
1 T
265625 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:265639 original size:19 final size:20
Alignment explanation
Indices: 265617--265659 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
265607 AAATCGCAAC
265617 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* * *
265636 GCGATTTTCATTTTTGCGTT
1 GCGAATTTCAATTTCGCGTT
265656 GCGA
1 GCGA
265660 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:265819 original size:14 final size:14
Alignment explanation
Indices: 265800--265836 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
265790 CATCAATTAA
265800 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
265814 ACAAATCACCTTTT
1 ACAAATCAACTTTT
265828 ACAAATCAA
1 ACAAATCAA
265837 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:267187 original size:21 final size:21
Alignment explanation
Indices: 267121--267187 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
267111 GTGAATCGGG
*
267121 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
267141 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
267163 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
267184 CTCT
1 CTCT
267188 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:267206 original size:42 final size:41
Alignment explanation
Indices: 267121--267243 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
267111 GTGAATCGGG
* * * *
267121 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
267163 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
267205 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
267244 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:269328 original size:33 final size:33
Alignment explanation
Indices: 269271--269369 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
269261 ACGAGATAAT
*
269271 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
269305 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
269338 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
269370 GCGAAATGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:269363 original size:19 final size:19
Alignment explanation
Indices: 269246--269430 Score: 183
Period size: 19 Copynumber: 10.1 Consensus size: 19
269236 TCTTTTGGTT
*
269246 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
269265 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
269285 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
269303 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
269319 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
269337 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
269352 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
269372 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
269391 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
269410 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
269429 GA
1 GA
269431 TTTTTGTTTC
Statistics
Matches: 140, Mismatches: 13, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 63 0.45
20 46 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Done.