Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003996.1 Hibiscus syriacus cultivar Beakdansim tig00008706_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: 553326
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:1019 original size:100 final size:99
Alignment explanation
Indices: 839--1019 Score: 222
Period size: 100 Copynumber: 1.8 Consensus size: 99
829 ATATAATAAA
*
839 TAAATATTTATAAAAAAAATTATTTTAACATTTATTTTCAATATCAAAGAAAAGGGCAGTCTTAA
1 TAAATATTTATAAAAAAAATTATTTTAACATTTATTTTCAATATCAAAGAAAAGAGCAGTCTTAA
* * *
904 TACAACTGGATGTCCTACTCTGGTATTTTAAAAT
66 GACAACTAGAAGTCCTACTCTGGTATTTTAAAAT
* ** * *
938 TAAATA-TTATAAAAAATTATTA-TTTAATTTTATATTTATTAATATCAAAGAAAAGAGCTGTCT
1 TAAATATTTATAAAAAA-AATTATTTTAACATT-TATTT-TCAATATCAAAGAAAAGAGCAGTCT
* *
1001 TAAGGCACCTAGAAGTCCT
63 TAAGACAACTAGAAGTCCT
1020 TTCTGATTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
98 17 0.25
99 15 0.22
100 36 0.53
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (99 bp):
TAAATATTTATAAAAAAAATTATTTTAACATTTATTTTCAATATCAAAGAAAAGAGCAGTCTTAA
GACAACTAGAAGTCCTACTCTGGTATTTTAAAAT
Found at i:1522 original size:15 final size:17
Alignment explanation
Indices: 1502--1555 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1492 ATATTTAATT
1502 TATAAT-TT-TTTTATA
1 TATAATATTATTTTATA
1517 TATAATATTATTTTATA
1 TATAATATTATTTTATA
*
1534 GTATTTATATATATTTTA-A
1 -TA-TAATAT-TATTTTATA
1553 TAT
1 TAT
1556 TTCATTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 6 0.18
16 2 0.06
17 8 0.24
18 4 0.12
19 6 0.18
20 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TATAATATTATTTTATA
Found at i:4861 original size:15 final size:15
Alignment explanation
Indices: 4841--4872 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4831 ATCAATACCT
4841 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
4856 TTTTGCATACATTCA
1 TTTTGCATACATGCA
4871 TT
1 TT
4873 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:13541 original size:83 final size:83
Alignment explanation
Indices: 13404--13623 Score: 377
Period size: 83 Copynumber: 2.6 Consensus size: 83
13394 AACAAATGCC
* *
13404 ATGTGCTCATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
*
13469 ATTGAATTTGAAAGATAA
66 ATTGAATTTAAAAGATAA
13487 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
13552 ATTGAATTTAAAAGATAA
66 ATTGAATTTAAAAGATAA
* *
13570 AGGAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 ATGTG-C-TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
13624 AGTATGAAAC
Statistics
Matches: 130, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
83 83 0.64
84 1 0.01
85 46 0.35
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (83 bp):
ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
ATTGAATTTAAAAGATAA
Found at i:13822 original size:115 final size:115
Alignment explanation
Indices: 13573--13783 Score: 318
Period size: 115 Copynumber: 1.9 Consensus size: 115
13563 AAGATAAAGG
* *
13573 AGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTATGAAACCACG
1 AGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTATGAAACCACA
* * * * *
13638 GAACCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGG
66 GAACCAATCATTGGAATTAAAAGATGAATCTGCTCATACTAGAAATAAGA
* * *
13688 AGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GGAACTACA
1 AGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTATGAAACCACA
13752 GAACCAATCATTGGAATTAAAAGATGAA-CTGC
66 GAACCAATCATTGGAATTAAAAGATGAATCTGC
13784 ATGATCTTCA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 3 0.03
114 32 0.36
115 53 0.60
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (115 bp):
AGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTATGAAACCACA
GAACCAATCATTGGAATTAAAAGATGAATCTGCTCATACTAGAAATAAGA
Found at i:14665 original size:116 final size:113
Alignment explanation
Indices: 14478--15025 Score: 695
Period size: 116 Copynumber: 4.8 Consensus size: 113
14468 CCATCATTCA
* *
14478 ATGGATCAGCATTACCAGGTAGAGTTCATAATAAGAAGAACTCGTCATCTGAAGAAGGAAGAAGA
1 ATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGA
* *
14543 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTG
63 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
14594 ATGGATCAGCATTGT-CAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 ATGGATCAGCATT-TCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAG
14658 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAA-TCTATCACTTG
62 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTC-ATCACTTG
* ** *
14710 ATGGATTATAATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGT
1 ATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * *
14775 TCATAATGAGAAGAATTT-TTCAACTTTTTGCTCAAATCCATCACTTG
66 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
* * *
14822 ATGGGTCAGCTTTTCCA-G-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAG
1 ATGGATCAGCATTTCCAGGTA-GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
14885 TTCATAATGAGAAGAATTTGTTCAACCTTTCGCTCAAA-TCTATCACTTG
65 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTC-ATCACTTG
* ** * *
14934 ATGGATTAAAATTTCCAGAG-AAAGTTCATAATAAGAAGAACTCATCTGAAGAA-G-AG--GAAG
1 ATGGATCAGCATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* ** *
14994 TTCATAATAAGAAGAGCTTATTCAACCTTTTG
65 TTCATAATGAGAAGAATTTGTTCAACCTTTTG
15026 ACTCTGTCAC
Statistics
Matches: 389, Mismatches: 34, Indels: 25
0.87 0.08 0.06
Matches are distributed among these distances:
109 31 0.08
110 1 0.00
111 63 0.16
112 73 0.19
113 72 0.19
114 3 0.01
115 3 0.01
116 143 0.37
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
ATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
Found at i:14904 original size:224 final size:227
Alignment explanation
Indices: 14492--15025 Score: 764
Period size: 224 Copynumber: 2.4 Consensus size: 227
14482 ATCAGCATTA
*
14492 CCAGGTAGAGTTCATAATAAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 CCAGGTAGAGTTCATAATAAGAAGAA--C-TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
* * * *
14557 AGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAGCATTGTCAGGTAGAGTTCA
63 AGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTGTCAGG-AGAGTTCA
14622 TAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC
127 TAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC
* * *
14687 CTTTTGCTTAAATCTATCACTTGATGGATTATAATTT
191 CTTTCGCTCAAATCTATCACTTGATGGATTAAAATTT
*
14724 CCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
* * *
14789 ATTT-TTCAACTTTTTGCTCAAATCCATCACTTGATGGGTCAGC-TTTTCCA-GAGGAGTTCATA
66 ATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTGT-CAGGA-GAGTTCATA
*
14851 ATGAGAAGAA-C-TCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
129 ATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
14914 TCGCTCAAATCTATCACTTGATGGATTAAAATTT
194 TCGCTCAAATCTATCACTTGATGGATTAAAATTT
* *
14948 CCAGAG-AAAGTTCATAATAAGAAGAACTCATCTGAAG-AAG-AG--GAAGTTCATAATAAGAAG
1 CCAG-GTAGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAG
** *
15008 AGCTTATTCAACCTTTTG
65 AATTTGTTCAACCTTTTG
15026 ACTCTGTCAC
Statistics
Matches: 279, Mismatches: 19, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
220 20 0.07
221 11 0.04
222 2 0.01
223 3 0.01
224 115 0.41
225 2 0.01
226 1 0.00
227 23 0.08
228 35 0.13
229 41 0.15
230 1 0.00
232 25 0.09
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (227 bp):
CCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
ATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTGTCAGGAGAGTTCATAAT
GAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTC
GCTCAAATCTATCACTTGATGGATTAAAATTT
Found at i:15268 original size:6 final size:6
Alignment explanation
Indices: 15257--15334 Score: 93
Period size: 6 Copynumber: 13.0 Consensus size: 6
15247 ATTGATTTAT
* * * * *
15257 TTATTA TTATTA TAATTA TAATTA TAATTA TTATTA TAATTA TTAATA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* *
15305 TTATTA TAATTA TTATAA TTATTA TTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA
15335 AATATATTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTATTA
Found at i:15280 original size:18 final size:18
Alignment explanation
Indices: 15259--15343 Score: 93
Period size: 18 Copynumber: 4.7 Consensus size: 18
15249 TGATTTATTT
* *
15259 ATTATTATTATAATTATA
1 ATTATAATTATTATTATA
15277 ATTATAATTATTATTATA
1 ATTATAATTATTATTATA
15295 ATTATTAA-TATTATTATA
1 ATTA-TAATTATTATTATA
* * *
15313 ATTATTATAATTATTATT
1 ATTATAATTATTATTATA
15331 ATTA-AATATATTA
1 ATTATAAT-TATTA
15344 AATATATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
17 4 0.07
18 50 0.88
19 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATAATTATTATTATA
Found at i:16690 original size:19 final size:19
Alignment explanation
Indices: 16651--16690 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16641 TTATGTAGTC
* *
16651 ATAAATATATATATAATAA
1 ATAAATATATATAAAAAAA
*
16670 ATAAATATTTATAAAAAAA
1 ATAAATATATATAAAAAAA
16689 AT
1 AT
16691 TATTTTAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAATATATATAAAAAAA
Found at i:24753 original size:72 final size:72
Alignment explanation
Indices: 24668--24811 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
24658 TGAGGTCTCC
*
24668 ACCAATCTGGGGGAAGTATTTATGGATTCATAATTGTTTCTGCAGCTCCAGTATCAATGAAAGCG
1 ACCAATCTGGGGGAAGTATTTATGGATTCATAATTGTTTCTACAGCTCCAGTATCAATGAAAGCG
24733 ATTACTG
66 ATTACTG
24740 ACCAATCTGGGGGAAGTATTTATGGATTCATAATTGTTTCTACAGCTCCAGTATCAATGAAAGCG
1 ACCAATCTGGGGGAAGTATTTATGGATTCATAATTGTTTCTACAGCTCCAGTATCAATGAAAGCG
24805 ATTACTG
66 ATTACTG
24812 GAATTGGTTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (72 bp):
ACCAATCTGGGGGAAGTATTTATGGATTCATAATTGTTTCTACAGCTCCAGTATCAATGAAAGCG
ATTACTG
Found at i:30191 original size:23 final size:23
Alignment explanation
Indices: 30161--30244 Score: 150
Period size: 23 Copynumber: 3.7 Consensus size: 23
30151 TATGGTACTA
30161 CGGTGCAATTCTACGTGGCACTC
1 CGGTGCAATTCTACGTGGCACTC
30184 CGGTGCAATTCTACGTGGCACTC
1 CGGTGCAATTCTACGTGGCACTC
*
30207 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGTGGCACTC
*
30230 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
30245 AGATGGGGTG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.27
Consensus pattern (23 bp):
CGGTGCAATTCTACGTGGCACTC
Found at i:31634 original size:23 final size:23
Alignment explanation
Indices: 31602--31708 Score: 178
Period size: 23 Copynumber: 4.7 Consensus size: 23
31592 TATGGTACTA
* *
31602 CGGTGTAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGTGGCACTC
31625 CGGTGCAATTCTACGTGGCACTC
1 CGGTGCAATTCTACGTGGCACTC
31648 CGGTGCAATTCTACGTGGCACTC
1 CGGTGCAATTCTACGTGGCACTC
*
31671 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGTGGCACTC
*
31694 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
31709 AGCTGTGGTG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 80 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (23 bp):
CGGTGCAATTCTACGTGGCACTC
Found at i:36154 original size:23 final size:23
Alignment explanation
Indices: 36112--36170 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
36102 TGGCACTACA
36112 GTGCAATTCTACGCGACAC-TCTG
1 GTGCAATTCTACGCGACACTTC-G
* * *
36135 GTGCAATTCTATGTGGCACTTCG
1 GTGCAATTCTACGCGACACTTCG
*
36158 GTGCAATTATACG
1 GTGCAATTCTACG
36171 AGCTGTGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
GTGCAATTCTACGCGACACTTCG
Found at i:44805 original size:26 final size:25
Alignment explanation
Indices: 44748--44814 Score: 116
Period size: 25 Copynumber: 2.6 Consensus size: 25
44738 GAGATGGGCA
44748 AGAGGAAAAAGGGAATCGTGGGAAC
1 AGAGGAAAAAGGGAATCGTGGGAAC
44773 AGAGGAAAAAGGGAATCGTGGGAAC
1 AGAGGAAAAAGGGAATCGTGGGAAC
*
44798 AGATGGAAAAGGGGAAT
1 AGA-GGAAAAAGGGAAT
44815 GGGATTTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 28 0.70
26 12 0.30
ACGTcount: A:0.45, C:0.06, G:0.40, T:0.09
Consensus pattern (25 bp):
AGAGGAAAAAGGGAATCGTGGGAAC
Found at i:45123 original size:81 final size:83
Alignment explanation
Indices: 44932--45153 Score: 261
Period size: 81 Copynumber: 2.7 Consensus size: 83
44922 TTTTGCAGCG
* * * * *
44932 TTTGTGTAAAAATGCCGCTACAGT-CTAATATTTTGCGGCGTTTGTTTGAAAAAACGCCACTATA
1 TTTGTATAAAAATGCCGCTAAAGTACTAATCTATTGCGGCGTTTGTAT--AAAAACGCCACTATA
**
44996 GATGAACCCTATTGTGGCTT
64 GATGAACCCTATTACGGCTT
* * * * *
45016 TTTTTATCAAAATGCCGCTAAAGTACTAATCTGTTGTGGCGTTTGTCTAAAAACGCCACTATAGA
1 TTTGTATAAAAATGCCGCTAAAGTACTAATCTATTGCGGCGTTTGTATAAAAACGCCACTATAGA
*
45081 TGGA-CCTATTACGGC-T
66 TGAACCCTATTACGGCTT
* * *
45097 TTTGTATAAAAACGCCGCTAAAGTACTATTCTATTGCGGCGTTTATATAAAAACGCC
1 TTTGTATAAAAATGCCGCTAAAGTACTAATCTATTGCGGCGTTTGTATAAAAACGCC
45154 GCTAAAGTAC
Statistics
Matches: 118, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
81 50 0.42
82 9 0.08
83 20 0.17
84 20 0.17
85 19 0.16
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (83 bp):
TTTGTATAAAAATGCCGCTAAAGTACTAATCTATTGCGGCGTTTGTATAAAAACGCCACTATAGA
TGAACCCTATTACGGCTT
Found at i:45204 original size:42 final size:41
Alignment explanation
Indices: 45024--45204 Score: 188
Period size: 41 Copynumber: 4.4 Consensus size: 41
45014 TTTTTTTATC
* * * * * *
45024 AAAATGCCGCTAAAGTACTAATCTGTTGTGGCGTTTGTCTA
1 AAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTTATATA
* * * * *
45065 AAAACGCCACTATAG-A-TGGAC-CTATTACGGCTTTTGTATA
1 AAAACGCCGCTAAAGTACT--ACTCTATTGCGGCGTTTATATA
*
45105 AAAACGCCGCTAAAGTACTATTCTATTGCGGCGTTTATATA
1 AAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTTATATA
*
45146 AAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTTATTTAA
1 AAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTTATAT-A
*
45188 AAAACGACGCTAAAGTA
1 AAAACGCCGCTAAAGTA
45205 TCATTTTATG
Statistics
Matches: 116, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
39 1 0.01
40 29 0.25
41 68 0.59
42 18 0.16
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (41 bp):
AAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTTATATA
Found at i:48806 original size:11 final size:11
Alignment explanation
Indices: 48786--48819 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
48776 TAAGTATTAA
48786 TTTTTAAATAT
1 TTTTTAAATAT
*
48797 TTTTTGAATAT
1 TTTTTAAATAT
48808 TTTTTAAATAT
1 TTTTTAAATAT
48819 T
1 T
48820 ATGAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:54179 original size:45 final size:45
Alignment explanation
Indices: 54115--54205 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
54105 CACAATTACC
54115 TCATAAACTATATCGTTTATACTTAGTTGCCTTTTAAAGTATTTT
1 TCATAAACTATATCGTTTATACTTAGTTGCCTTTTAAAGTATTTT
54160 TCATAAACTATATCGTTTATACTTAGTTGCCTTTTAAAGTATTTT
1 TCATAAACTATATCGTTTATACTTAGTTGCCTTTTAAAGTATTTT
54205 T
1 T
54206 TGAGACGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (45 bp):
TCATAAACTATATCGTTTATACTTAGTTGCCTTTTAAAGTATTTT
Found at i:63178 original size:29 final size:29
Alignment explanation
Indices: 63136--63201 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
63126 TTAAATCCCT
*
63136 CGACTATCAAAAGTTACAAAAAGATCATC
1 CGACTATTAAAAGTTACAAAAAGATCATC
* *
63165 CGACTATTAAAAGTTACAAAATGATTATC
1 CGACTATTAAAAGTTACAAAAAGATCATC
*
63194 TGACTATT
1 CGACTATT
63202 CATTATTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (29 bp):
CGACTATTAAAAGTTACAAAAAGATCATC
Found at i:68334 original size:27 final size:27
Alignment explanation
Indices: 68295--68360 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
68285 GGGCAACCCG
* * * *
68295 ACCCGACCTGAAAATTTTACATCCTTC
1 ACCCGACCCGAAAAATATACACCCTTC
*
68322 ACCCGACCCGAAAAATATATACCCTTC
1 ACCCGACCCGAAAAATATACACCCTTC
*
68349 AACCGACCCGAA
1 ACCCGACCCGAA
68361 TCCGATCCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.35, C:0.36, G:0.09, T:0.20
Consensus pattern (27 bp):
ACCCGACCCGAAAAATATACACCCTTC
Found at i:69011 original size:6 final size:6
Alignment explanation
Indices: 69000--69024 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
68990 GTATGATAAA
69000 AAAATC AAAATC AAAATC AAAATC A
1 AAAATC AAAATC AAAATC AAAATC A
69025 TGTCTAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:70934 original size:2 final size:2
Alignment explanation
Indices: 70927--70951 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70917 AACACGGATC
70927 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
70952 TGACTTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71772 original size:2 final size:2
Alignment explanation
Indices: 71765--71791 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71755 TAGGTATTGG
71765 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
71792 AATTTCGATC
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:73161 original size:83 final size:81
Alignment explanation
Indices: 73018--73465 Score: 341
Period size: 81 Copynumber: 5.4 Consensus size: 81
73008 CGATATCCTA
* * * * * *
73018 ATATATAGTGGCGTTTTTGTGAGAACCCCGCTAAAAACGCATACTTTAGTAG-TTTATATGTTAA
1 ATATATAGTGGC-TTTTTGTAAAAACGCCGCTAAAAATGCATACTTTAGTGGCATT-TATG-T-A
* * *
73082 AAAAAAG-CTACTATAGACAT
62 AAAAAAGTC-GCTATAGCCAG
* * *
73102 ATATATAGTGACATTTTGTAAAAACGCCGCTAAAAATGCATACTTTAGTGGCATTTATGTAAACA
1 ATATATAGTGGCTTTTTGTAAAAACGCCGCTAAAAATGCATACTTTAGTGGCATTTATGTAAAAA
* *
73167 ACGTCGCTATATCCAG
66 AAGTCGCTATAGCCAG
* * * * * ** *
73183 ATATATAGCGGCGTCTATGTAAAAAATGCTGCTAAAAATGCGCACTTTAGTGGCATTTATGTAAC
1 ATATATAGTGGC-TTTTTGT-AAAAACGCCGCTAAAAATGCATACTTTAGTGGCATTTATGTAAA
*
73248 AAATGTCGCTATAGCCAG
64 AAAAGTCGCTATAGCCAG
* * * * *
73266 ATATAGTGGT-GTTTTTTGTGAAAACGCCGCTAAAAATGCATACTTTGGTGGCGTTTATGTAAAA
1 ATATA-TAGTGGCTTTTTGTAAAAACGCCGCTAAAAATGCATACTTTAGTGGCATTTATGTAAAA
* *
73330 AATGGCGCTATAGCCAG
65 AAAGTCGCTATAGCCAG
** * * * * *
73347 ATATATAGTGGCGTTTTTGTGTATA--CCACTAAAGTAA-GCGTACTTTAGCGGCATTTATGTTA
1 ATATATAGTGGC-TTTTTGTAAAAACGCCGCTAAA--AATGCATACTTTAGTGGCATTTATGTAA
* * *
73409 AAAACGTCGCGATAGCCCG
63 AAAAAGTCGCTATAGCCAG
* * * *
73428 ATATATCGTGGCGTTTATGTTAAAAACACCGTTAAAAA
1 ATATATAGTGGC-TTTTTG-TAAAAACGCCGCTAAAAA
73466 CGCAACATTA
Statistics
Matches: 290, Mismatches: 62, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
80 10 0.03
81 134 0.46
82 28 0.10
83 97 0.33
84 21 0.07
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (81 bp):
ATATATAGTGGCTTTTTGTAAAAACGCCGCTAAAAATGCATACTTTAGTGGCATTTATGTAAAAA
AAGTCGCTATAGCCAG
Found at i:84360 original size:21 final size:21
Alignment explanation
Indices: 84334--84380 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
84324 CTAATATTGT
84334 AATGTCAAAATTAGGTGCAAC
1 AATGTCAAAATTAGGTGCAAC
*
84355 AATGTCAAAATTAGGTGCAAT
1 AATGTCAAAATTAGGTGCAAC
84376 AATGT
1 AATGT
84381 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (21 bp):
AATGTCAAAATTAGGTGCAAC
Found at i:86182 original size:17 final size:17
Alignment explanation
Indices: 86157--86191 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
86147 GCTATCCCTT
86157 AGTAACAATGGAGCTTC
1 AGTAACAATGGAGCTTC
*
86174 AGTAGCAATGGAGCTTC
1 AGTAACAATGGAGCTTC
86191 A
1 A
86192 ATTTCCCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (17 bp):
AGTAACAATGGAGCTTC
Found at i:96377 original size:28 final size:28
Alignment explanation
Indices: 96345--96402 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
96335 TTAAAGAAAA
96345 TTTGAGTCATAAAATACGACATATTAAC
1 TTTGAGTCATAAAATACGACATATTAAC
96373 TTTGAGTCATAAAATACGACATATTAAC
1 TTTGAGTCATAAAATACGACATATTAAC
96401 TT
1 TT
96403 GACTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (28 bp):
TTTGAGTCATAAAATACGACATATTAAC
Found at i:110833 original size:37 final size:37
Alignment explanation
Indices: 110744--110825 Score: 164
Period size: 37 Copynumber: 2.2 Consensus size: 37
110734 TGCCGAATGA
110744 GACGCCGAGGTTGGGAGGCTGTGAGGTGTCTTCTTGC
1 GACGCCGAGGTTGGGAGGCTGTGAGGTGTCTTCTTGC
110781 GACGCCGAGGTTGGGAGGCTGTGAGGTGTCTTCTTGC
1 GACGCCGAGGTTGGGAGGCTGTGAGGTGTCTTCTTGC
110818 GACGCCGA
1 GACGCCGA
110826 CGATGGGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.12, C:0.21, G:0.43, T:0.24
Consensus pattern (37 bp):
GACGCCGAGGTTGGGAGGCTGTGAGGTGTCTTCTTGC
Found at i:111424 original size:35 final size:36
Alignment explanation
Indices: 111348--111425 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
111338 AAAATATTTT
* ** *
111348 AATTTAGGGTTTAGAATGTAATTCAAGTATTTTTGA
1 AATTTTGGGTTTAGAATACAATTCAAGTAGTTTTGA
* *
111384 AATTTTGGGTTTAGAATACAATTGAAGT-GTTTTGG
1 AATTTTGGGTTTAGAATACAATTCAAGTAGTTTTGA
111419 AATTTTG
1 AATTTTG
111426 AGCATGAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 12 0.33
36 24 0.67
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.45
Consensus pattern (36 bp):
AATTTTGGGTTTAGAATACAATTCAAGTAGTTTTGA
Found at i:118744 original size:15 final size:15
Alignment explanation
Indices: 118724--118773 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
118714 TATGTCAACG
118724 AAATTTGATATTGAA
1 AAATTTGATATTGAA
* *
118739 AAATTT-A-ATGGGAG
1 AAATTTGATAT-TGAA
118753 AAATTTGATATTGAA
1 AAATTTGATATTGAA
118768 AAATTT
1 AAATTT
118774 AATGGGAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (15 bp):
AAATTTGATATTGAA
Found at i:118758 original size:14 final size:14
Alignment explanation
Indices: 118739--118787 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
118729 TGATATTGAA
118739 AAATTTAATGGGAG
1 AAATTTAATGGGAG
* *
118753 AAATTTGATAT-TGAA
1 AAATTT-A-ATGGGAG
118768 AAATTTAATGGGAG
1 AAATTTAATGGGAG
118782 AAATTT
1 AAATTT
118788 CTCATTGTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 2 0.07
14 15 0.54
15 9 0.32
16 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (14 bp):
AAATTTAATGGGAG
Found at i:118794 original size:29 final size:29
Alignment explanation
Indices: 118723--118787 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
118713 CTATGTCAAC
118723 GAAATTTGATATTGAAAAATTTAATGGGA
1 GAAATTTGATATTGAAAAATTTAATGGGA
118752 GAAATTTGATATTGAAAAATTTAATGGGA
1 GAAATTTGATATTGAAAAATTTAATGGGA
118781 GAAATTT
1 GAAATTT
118788 CTCATTGTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (29 bp):
GAAATTTGATATTGAAAAATTTAATGGGA
Found at i:126331 original size:14 final size:14
Alignment explanation
Indices: 126312--126339 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
126302 TATGTATGTA
126312 TGTATGTGTGTGTG
1 TGTATGTGTGTGTG
126326 TGTATGTGTGTGTG
1 TGTATGTGTGTGTG
126340 ATTTTGGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (14 bp):
TGTATGTGTGTGTG
Found at i:128430 original size:197 final size:191
Alignment explanation
Indices: 128175--128644 Score: 475
Period size: 195 Copynumber: 2.4 Consensus size: 191
128165 GTGTGTGTGC
* * * *
128175 GCTTCTTTTTTACTCACATCCATAATTGGTCTTTTCAGTTCT-TTAATTGATATTTTTTATATTT
1 GCTTCTTTTTCACTCACATCCATAATTAGTCGTTTCAATTCTCTT-ATTGATATTTTTTATATTT
* * *
128239 TGAATCGAGTTTAAACCGACCCAAAATAAAAAAACCAAATAACTTACAGAGTCATGTA-ACATA-
65 TGAATCAAGTTTAAACCAACCCAAAAT--AAAAACC-AATAACTTACAGAATCATG-ACAC-TAC
* * * ***** *
128302 ATAGAAATTAGTCGTTTCGATTCTCTCTTTTTAATTATCTTTAAAACTCTATCACGAACA-TTTC
125 A-AAAAATTA-TCATTTAGATTCTCT-TTTTTAATTAAAACGAAAA-TCTATCACAAACATTTTC
128366 TTTTTGT
186 -TTTTGT
* *
128373 GCTTC-TTTTCACTCGCATCCATAACTAGTCGTTTCAATTCTCTTATTGATATTTTTTATATATA
1 GCTTCTTTTTCACTCACATCCATAATTAGTCGTTTCAATTCTCTTATTGATA-TTTTT-TATAT-
* * * * * *
128437 TTTCGAATCAAGTTTAGACTAACTCAAAATAAAAAGCAATGACTTACATAATCATGACACTACAA
63 TTT-GAATCAAGTTTAAACCAACCCAAAATAAAAACCAATAACTTACAGAATCATGACACTACAA
* * *
128502 AAAATTATCATTTAGATTCTCTTTTTTAATTAAAACGAAAATTTGTCACAAACGTTTTCTTTTGT
127 AAAATTATCATTTAGATTCTCTTTTTTAATTAAAACGAAAATCTATCACAAACATTTTCTTTTGT
* * *
128567 GTTTCTTTTTCACTCACATCCATAATTAGTCGTTTTAATTCTCCTATTGATATTGTTTTAT-TTT
1 GCTTCTTTTTCACTCACATCCATAATTAGTCGTTTCAATTCTCTTATTGATATT-TTTTATATTT
*
128631 TAAATCAAGTTTAA
65 TGAATCAAGTTTAA
128645 CCGGTGACGG
Statistics
Matches: 228, Mismatches: 34, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
191 11 0.05
192 3 0.01
193 1 0.00
194 24 0.11
195 63 0.28
196 13 0.06
197 47 0.21
198 31 0.14
199 11 0.05
200 3 0.01
201 21 0.09
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (191 bp):
GCTTCTTTTTCACTCACATCCATAATTAGTCGTTTCAATTCTCTTATTGATATTTTTTATATTTT
GAATCAAGTTTAAACCAACCCAAAATAAAAACCAATAACTTACAGAATCATGACACTACAAAAAA
TTATCATTTAGATTCTCTTTTTTAATTAAAACGAAAATCTATCACAAACATTTTCTTTTGT
Found at i:128924 original size:121 final size:122
Alignment explanation
Indices: 128808--129043 Score: 341
Period size: 121 Copynumber: 1.9 Consensus size: 122
128798 TTTTTTGTCA
* * *
128808 TTGTTTTCGTTTATCTTTTTTCTCAGGGTTAGATTTGACATCCCCGCGACTGATCAAGATGACAC
1 TTGTTTTCGTTTATCTTTTTTCTCAAGGTTAGATTTGACATCCCCACGACTGATCAAAATGACAC
*
128873 TTATTTGTTATCATGTTGATCTTCTCTACTTTGGA-CTCTCGAATT-ATTTTTTGAAG
66 TCATTTGTTATCATGTTGATCTTCTCTACTTTGGACCT-TCGAATTGATTTTTTGAAG
* ** * *
128929 TTGTTTTCGTTTATCTTTTTTCTCAAGGTTGGATTTGACATTGCCACGACTGATTAAAATGACGC
1 TTGTTTTCGTTTATCTTTTTTCTCAAGGTTAGATTTGACATCCCCACGACTGATCAAAATGACAC
* * *
128994 TCATTTGTTATCATGTTGATTTTTTCTGCTTTGGACCTTCGAATTGATTT
66 TCATTTGTTATCATGTTGATCTTCTCTACTTTGGACCTTCGAATTGATTT
129044 GGATACACGT
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
121 95 0.94
122 6 0.06
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGTTTTCGTTTATCTTTTTTCTCAAGGTTAGATTTGACATCCCCACGACTGATCAAAATGACAC
TCATTTGTTATCATGTTGATCTTCTCTACTTTGGACCTTCGAATTGATTTTTTGAAG
Found at i:130969 original size:23 final size:23
Alignment explanation
Indices: 130933--130978 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
130923 ACATATTATA
*
130933 TGGCACTACGGTGCAAT-TCTACG
1 TGGCACTACAGTGC-ATCTCTACG
*
130956 TGGCACTTCAGTGCATCTCTACG
1 TGGCACTACAGTGCATCTCTACG
130979 CGGGTCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (23 bp):
TGGCACTACAGTGCATCTCTACG
Found at i:131599 original size:21 final size:22
Alignment explanation
Indices: 131559--131600 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
131549 ACGGAAGTAC
*
131559 TGTAGCAGGGGAATCGATTCCT
1 TGTAGCAGGGGAACCGATTCCT
*
131581 TGTAGCA-GGGTACCGATTCC
1 TGTAGCAGGGGAACCGATTCC
131601 CTATTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.26
Consensus pattern (22 bp):
TGTAGCAGGGGAACCGATTCCT
Found at i:138115 original size:23 final size:23
Alignment explanation
Indices: 138081--138166 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
138071 ACATATTATA
*
138081 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
138104 TGGCACTTCGGTGC-ATCTCTACG
1 TGGCACTTCGGTGCAAT-TCTACG
* * *
138127 CGGTC-CTTTAGG-ACAAATTCTACG
1 TGG-CAC-TTCGGTGC-AATTCTACG
138151 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
138167 ATTTATATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
22 2 0.04
23 30 0.61
24 15 0.31
25 2 0.04
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:141131 original size:12 final size:12
Alignment explanation
Indices: 141114--141138 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
141104 CTCAAACAGA
141114 GAGAATGAACGT
1 GAGAATGAACGT
141126 GAGAATGAACGT
1 GAGAATGAACGT
141138 G
1 G
141139 TTGCATGGCA
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:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:141211 original size:29 final size:29
Alignment explanation
Indices: 141167--141222 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
141157 TCCCAACACA
* *
141167 TAGGTCGTCATTCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
141196 TAGGTCGCCATGCCCTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
141223 ACCCTCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.11, C:0.38, G:0.29, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:141263 original size:33 final size:33
Alignment explanation
Indices: 141226--141300 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
141216 GCGACCTACC
* *
141226 CTCGCTCGGCTT-CCCTCAGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCAGATGCCCTCACATAG
* *
141259 CTCGCTCGGTTGCTCTCGGATGCCCTCACATAG
1 CTCGCTCGGTTGCCCTCAGATGCCCTCACATAG
*
141292 CTCGTTCGG
1 CTCGCTCGG
141301 ATGGCCTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 2 0.06
33 34 0.94
ACGTcount: A:0.11, C:0.39, G:0.23, T:0.28
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCAGATGCCCTCACATAG
Found at i:141310 original size:33 final size:32
Alignment explanation
Indices: 141239--141310 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
141229 GCTCGGCTTC
* * * *
141239 CCTCAGATTCCCTCGCATAGCTCGCTCGGTTG
1 CCTCGGATGCCCTCACATAGCTCGCTCGGTGG
*
141271 CTCTCGGATGCCCTCACATAGCTCGTTCGGATGG
1 C-CTCGGATGCCCTCACATAGCTCGCTCGG-TGG
141305 CCTCGG
1 CCTCGG
141311 TCGGATGGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
32 1 0.03
33 29 0.88
34 3 0.09
ACGTcount: A:0.12, C:0.36, G:0.25, T:0.26
Consensus pattern (32 bp):
CCTCGGATGCCCTCACATAGCTCGCTCGGTGG
Found at i:141314 original size:14 final size:14
Alignment explanation
Indices: 141292--141324 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
141282 CCTCACATAG
*
141292 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
141306 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
141320 CTCGG
1 CTCGG
141325 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:141928 original size:16 final size:18
Alignment explanation
Indices: 141895--141933 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
141885 TCTCTCTGAA
141895 ATTTTAAAATTATTATAT
1 ATTTTAAAATTATTATAT
141913 ATTTT-AAATT-TTATAT
1 ATTTTAAAATTATTATAT
141929 ATTTT
1 ATTTT
141934 TGTGAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.52
17 5 0.24
18 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTAAAATTATTATAT
Found at i:144297 original size:25 final size:22
Alignment explanation
Indices: 144266--144333 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
144256 TAAGGAGTTG
*
144266 TAATATTATTAACTATATATTA
1 TAATATTATTAACTATAAATTA
*
144288 TCCTTATATT-TTAAC-ATAAATTA
1 ---TAATATTATTAACTATAAATTA
*
144311 TAATATTATTAACTATAATTTA
1 TAATATTATTAACTATAAATTA
144333 T
1 T
144334 TTATTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 6 0.16
21 5 0.14
22 8 0.22
23 7 0.19
24 5 0.14
25 6 0.16
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATTATTAACTATAAATTA
Found at i:149715 original size:66 final size:66
Alignment explanation
Indices: 149632--149764 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
149622 TTGAAGAGAG
* *
149632 AGATGGTGTTCTTTATCTCGGCTGGATGAATCGAGCCATTGTTGCCTCCTGCGCATGGAGATGTT
1 AGATGGCGTTCTTTATCTCGGCTGGATGAATCGAGCCATTGTCGCCTCCTGCGCATGGAGATGTT
149697 A
66 A
149698 AGATGGCGTTCTTTATCTCGGCTGGATGAATCGAGCCATTGTCGCCTCCTGCGCATGGAGATGTT
1 AGATGGCGTTCTTTATCTCGGCTGGATGAATCGAGCCATTGTCGCCTCCTGCGCATGGAGATGTT
149763 A
66 A
149764 A
1 A
149765 CCGATCGATA
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:0.19, C:0.21, G:0.29, T:0.32
Consensus pattern (66 bp):
AGATGGCGTTCTTTATCTCGGCTGGATGAATCGAGCCATTGTCGCCTCCTGCGCATGGAGATGTT
A
Found at i:158568 original size:13 final size:13
Alignment explanation
Indices: 158550--158608 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
158540 TCAAGGTCGC
*
158550 AATAAACGAACAT
1 AATAAACAAACAT
158563 AATAAACAAACAT
1 AATAAACAAACAT
*
158576 AAAGAACAACACAAACAT
1 ----AATAA-ACAAACAT
158594 AATAAACAAACAT
1 AATAAACAAACAT
158607 AA
1 AA
158609 ACGAACAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
13 22 0.58
14 4 0.11
17 4 0.11
18 8 0.21
ACGTcount: A:0.68, C:0.17, G:0.03, T:0.12
Consensus pattern (13 bp):
AATAAACAAACAT
Found at i:158591 original size:18 final size:18
Alignment explanation
Indices: 158568--158624 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
158558 AACATAATAA
158568 ACAAACATAAAGAACAAC
1 ACAAACATAAAGAACAAC
*
158586 ACAAACAT----AATAA-
1 ACAAACATAAAGAACAAC
158599 ACAAACATAAACGAACAAC
1 ACAAACATAAA-GAACAAC
158618 ACAAACA
1 ACAAACA
158625 CACAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 8 0.26
14 4 0.13
18 12 0.39
19 7 0.23
ACGTcount: A:0.67, C:0.23, G:0.04, T:0.07
Consensus pattern (18 bp):
ACAAACATAAAGAACAAC
Found at i:158596 original size:31 final size:32
Alignment explanation
Indices: 158558--158624 Score: 127
Period size: 31 Copynumber: 2.1 Consensus size: 32
158548 GCAATAAACG
158558 AACATAATAAACAAACATAAA-GAACAACACA
1 AACATAATAAACAAACATAAACGAACAACACA
158589 AACATAATAAACAAACATAAACGAACAACACA
1 AACATAATAAACAAACATAAACGAACAACACA
158621 AACA
1 AACA
158625 CACAAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.67, C:0.21, G:0.03, T:0.09
Consensus pattern (32 bp):
AACATAATAAACAAACATAAACGAACAACACA
Found at i:158926 original size:26 final size:24
Alignment explanation
Indices: 158876--158940 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 24
158866 GTCCTCTGTT
*
158876 CGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACACAAA
**
158900 CGAACATATAATCGAACGTTCAC--A
1 CGAACATA-AAT-GAACGAACACAAA
158924 --AACATAAATGAACGAAC
1 CGAACATAAATGAACGAAC
158941 GAGCCCTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 6 0.18
21 3 0.09
22 6 0.18
24 9 0.26
25 3 0.09
26 7 0.21
ACGTcount: A:0.52, C:0.20, G:0.12, T:0.15
Consensus pattern (24 bp):
CGAACATAAATGAACGAACACAAA
Found at i:174386 original size:2 final size:2
Alignment explanation
Indices: 174379--174403 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
174369 GTTCATATGC
174379 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 A
174404 CATACTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:177793 original size:42 final size:43
Alignment explanation
Indices: 177747--177827 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
177737 AAGAAAAATA
* *
177747 TGCAAGAGTAAACAAATAAAATTTGCTAAGGC-AAAAATTAAT
1 TGCAAGAATAAACAAATAAAAGTTGCTAAGGCGAAAAATTAAT
**
177789 TGCAAGAATAAGTAAATAAAAGTTGCTAAGGCGAAAAAT
1 TGCAAGAATAAACAAATAAAAGTTGCTAAGGCGAAAAAT
177828 GTTCAATTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 28 0.82
43 6 0.18
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (43 bp):
TGCAAGAATAAACAAATAAAAGTTGCTAAGGCGAAAAATTAAT
Found at i:185555 original size:25 final size:26
Alignment explanation
Indices: 185525--185586 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
185515 TTTATTTCTA
185525 TTTTAATCATTAAAATCTAAA-TATT
1 TTTTAATCATTAAAATCTAAATTATT
* *
185550 TTTTAATCACTAAAATTTAAATTATT
1 TTTTAATCATTAAAATCTAAATTATT
*
185576 TATTTATTCAT
1 T-TTTAATCAT
185587 ACTTTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 19 0.61
26 5 0.16
27 7 0.23
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTTAATCATTAAAATCTAAATTATT
Found at i:186334 original size:4 final size:4
Alignment explanation
Indices: 186325--186351 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
186315 TATTTGAGTT
186325 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
186352 GTATGCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:187943 original size:23 final size:23
Alignment explanation
Indices: 187917--187961 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
187907 CACCACAGCT
*
187917 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
187940 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
187962 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:188210 original size:149 final size:149
Alignment explanation
Indices: 187940--188243 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
187930 CGAAGTGCCC
187940 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* *
188005 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
188070 CATATGTCCTAAAGAACCG
131 CATATGTCCCAAAGAACCG
188089 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
188154 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
188219 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
188238 CGTAGA
1 CGTAGA
188244 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:188756 original size:19 final size:20
Alignment explanation
Indices: 188719--188756 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
188709 TTTTTTCTCA
188719 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGGTTCCCCCC
*
188739 TGGGGGTATCGGTTCCCC
1 TGGGGGAATCGGTTCCCC
188757 TCTAGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.32, G:0.37, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGGTTCCCCCC
Found at i:195173 original size:149 final size:149
Alignment explanation
Indices: 194903--195204 Score: 577
Period size: 149 Copynumber: 2.0 Consensus size: 149
194893 AAGTGCCCCA
194903 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
* *
194968 TATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATACA
66 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
*
195033 TATGTCCTAAAGAACCGCG
131 TATGTCCCAAAGAACCGCG
195052 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
195117 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
195182 TATGTCCCAAAGAACCGCG
131 TATGTCCCAAAGAACCGCG
195201 TAGA
1 TAGA
195205 CCCTCTACCC
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCAAAGAACCGCG
Found at i:195719 original size:19 final size:20
Alignment explanation
Indices: 195682--195719 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
195672 TTTTTTCTCA
195682 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGGTTCCCCCC
*
195702 TGGGGGTATCGGTTCCCC
1 TGGGGGAATCGGTTCCCC
195720 TCTAGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.32, G:0.37, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGGTTCCCCCC
Found at i:202877 original size:21 final size:21
Alignment explanation
Indices: 202853--202894 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
202843 AGTTTATTTT
202853 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
* *
202874 TAAATTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
202895 AATTTGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:202925 original size:32 final size:32
Alignment explanation
Indices: 202883--202958 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 32
202873 GTAAATTTTG
* *
202883 TTTCAATTATCGAA-TTTGAAGTTTTTAAGTA
1 TTTCAATTATCGAACTTGGAAGTATTTAAGTA
* *
202914 TTTGAATTTATCAAACTTGGAAGTATTTAAGTA
1 TTTCAA-TTATCGAACTTGGAAGTATTTAAGTA
202947 TTTCAATTATCG
1 TTTCAATTATCG
202959 TAAACTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 5 0.14
32 12 0.32
33 20 0.54
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGGAAGTATTTAAGTA
Found at i:203833 original size:2 final size:2
Alignment explanation
Indices: 203826--203865 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
203816 TTTGTTTTAT
203826 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
203866 ATGAACTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:220004 original size:2 final size:2
Alignment explanation
Indices: 219999--220028 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
219989 ATATACTTGG
219999 AT 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
220029 TTGCTACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220156 original size:28 final size:28
Alignment explanation
Indices: 220124--220181 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
220114 TTCGGGTAAA
220124 TTACATAAATGATCACCCAATTATAGGT
1 TTACATAAATGATCACCCAATTATAGGT
220152 TTACATAAATGATCACCCAATTATAGGT
1 TTACATAAATGATCACCCAATTATAGGT
220180 TT
1 TT
220182 TGTCTCTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (28 bp):
TTACATAAATGATCACCCAATTATAGGT
Found at i:221638 original size:8 final size:8
Alignment explanation
Indices: 221627--221654 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
221617 GCATACCCAT
221627 GGTGCATC
1 GGTGCATC
221635 GGTGCATC
1 GGTGCATC
221643 GGTGCATC
1 GGTGCATC
221651 GGTG
1 GGTG
221655 TAAAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.21, G:0.43, T:0.25
Consensus pattern (8 bp):
GGTGCATC
Found at i:221741 original size:18 final size:17
Alignment explanation
Indices: 221687--221735 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
221677 TTGGACCCTT
* *
221687 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
221705 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
221723 AGTGCATTCGATG
1 AGTGCA-TCGATG
221736 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:221822 original size:56 final size:55
Alignment explanation
Indices: 221716--221823 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 55
221706 AGTGCATCGA
* *
221716 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
221771 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 TGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGG
221824 TAAGTGCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
55 19 0.41
56 24 0.52
57 3 0.07
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (55 bp):
TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:221839 original size:56 final size:54
Alignment explanation
Indices: 221716--221840 Score: 137
Period size: 56 Copynumber: 2.2 Consensus size: 54
221706 AGTGCATCGA
*
221716 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 TGCATCAA-TGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
221771 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TAAG
1 TGCATC-AATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCT--G
*
221828 TGCATCGATGCAT
1 TGCATCAATGCAT
221841 GAAATGCATT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
55 18 0.30
56 32 0.53
57 10 0.17
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (54 bp):
TGCATCAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:230585 original size:65 final size:65
Alignment explanation
Indices: 230451--230611 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
230441 GTGCACTAAG
* * *
230451 AGTGTATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
* * * * *
230515 GGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGC
230578 T
65 T
*
230579 AAGTGCATCGATGCATGAAATGCATTCGATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
230612 CAATTTAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 27 0.33
65 53 0.64
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
Found at i:230650 original size:65 final size:63
Alignment explanation
Indices: 230456--230653 Score: 188
Period size: 65 Copynumber: 3.1 Consensus size: 63
230446 CTAAGAGTGT
* * *
230456 ATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCTGGTG
1 ATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTTGGTG
230519 C
63 C
* * **
230520 ATCGATGCATCAAATGCATTTGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAAGTGC
1 ATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTTGGTGC
* ** *
230585 ATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATTGATGCATGGATTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGT
230648 GC
62 GC
230650 ATCG
1 ATCG
230654 GTGTATCACT
Statistics
Matches: 111, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 42 0.38
65 58 0.52
66 4 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGC
Found at i:231191 original size:2 final size:2
Alignment explanation
Indices: 231182--231219 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
231172 TATCATTAAC
231182 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA GTA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T
231220 TTGATTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 29 0.88
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:233859 original size:33 final size:33
Alignment explanation
Indices: 233813--233884 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
233803 ATGATGCAGT
*
233813 TGATGACCCTGAGCTAGATGATTCCAACCATAA
1 TGATGACCATGAGCTAGATGATTCCAACCATAA
* * *
233846 TGATGACCATGAGCTGGATGATTCCAATCATGA
1 TGATGACCATGAGCTAGATGATTCCAACCATAA
233879 TGATGA
1 TGATGA
233885 TGAAGATGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (33 bp):
TGATGACCATGAGCTAGATGATTCCAACCATAA
Found at i:237581 original size:2 final size:2
Alignment explanation
Indices: 237574--237607 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
237564 AGTATTTTCA
237574 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
237608 AAACACTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:238203 original size:51 final size:51
Alignment explanation
Indices: 238138--238279 Score: 212
Period size: 51 Copynumber: 2.8 Consensus size: 51
238128 TGCTCACCTC
* * *
238138 ATCAGCAAAGTGATGAGAAGAACCAATCCAGGAAAACCTCGAGTAAGACTC
1 ATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAATAAGACTA
* * * *
238189 CTCAGCAAAATGATGAGAAGAACCAATCCAGGGAGACCTCGAATAAGAGTA
1 ATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAATAAGACTA
*
238240 ATCAGCAAAGTGATGAGAAGAACCAGTCCAGGGAAACCTC
1 ATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTC
238280 ATGTAAGCTT
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 80 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.13
Consensus pattern (51 bp):
ATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAATAAGACTA
Found at i:241582 original size:46 final size:46
Alignment explanation
Indices: 241515--241643 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
241505 AAATAAATCA
*
241515 CTAAATAATTCACCATAATTTGGCAATAAATTAATGAATCATTAAT
1 CTAAATAATTCACCATAATTTGGCAATAGATTAATGAATCATTAAT
* *
241561 CTAAATAATTCACCATAATTTGGCAATAGATTAAGGAATCATTACT
1 CTAAATAATTCACCATAATTTGGCAATAGATTAATGAATCATTAAT
241607 CTAAATAATTCACCATAATTTGGCAATAGATTAATGA
1 CTAAATAATTCACCATAATTTGGCAATAGATTAATGA
241644 TTCACTAAAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.33
Consensus pattern (46 bp):
CTAAATAATTCACCATAATTTGGCAATAGATTAATGAATCATTAAT
Found at i:252962 original size:260 final size:260
Alignment explanation
Indices: 252501--253028 Score: 986
Period size: 260 Copynumber: 2.0 Consensus size: 260
252491 AAGTCAGGTC
*
252501 ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTATGGAACTAAAGGGAAACTGATC
1 ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTATGGAACCAAAGGGAAACTGATC
*
252566 AAGCATACTAGTAGAAATTTGGCTTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
66 AAGCATACTAGTAGAAATTTGGATTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
*
252631 TCAGTAAGTTGTTGCAAAATCAACAGCAATTCAGCATTGAAAAAATATGTTGAACTTCTTCATCC
131 TCAGTAAGTTGTTGCAAAATCAACAGCAATTCAGAATTGAAAAAATATGTTGAACTTCTTCATCC
252696 TCACATTCCTCGCTCAACAACCAAAGAAACCCTTACTTTGATTCACTAAAACCGAACAATCAGCT
196 TCACATTCCTCGCTCAACAACCAAAGAAACCCTTACTTTGATTCACTAAAACCGAACAATCAGCT
* *
252761 ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTGTGGAACCAAAGGGCAACTGATC
1 ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTATGGAACCAAAGGGAAACTGATC
252826 AAGCATACTAGTAGAAATTTGGATTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
66 AAGCATACTAGTAGAAATTTGGATTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
*
252891 TCGGTAAGTTGTTGCAAAATCAACAGCAATTCAGAATTGAAAAAATATGTTGAACTTCTTCATCC
131 TCAGTAAGTTGTTGCAAAATCAACAGCAATTCAGAATTGAAAAAATATGTTGAACTTCTTCATCC
252956 TCACATTCCTCGCTCAACAACCAAAGAAACCCTTACTTTGATTCACTAAAACCGAACAATCAGCT
196 TCACATTCCTCGCTCAACAACCAAAGAAACCCTTACTTTGATTCACTAAAACCGAACAATCAGCT
*
253021 -TAACAAAA
1 ATACCAAAA
253029 TAATCAACTT
Statistics
Matches: 261, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
259 7 0.03
260 254 0.97
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (260 bp):
ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTATGGAACCAAAGGGAAACTGATC
AAGCATACTAGTAGAAATTTGGATTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
TCAGTAAGTTGTTGCAAAATCAACAGCAATTCAGAATTGAAAAAATATGTTGAACTTCTTCATCC
TCACATTCCTCGCTCAACAACCAAAGAAACCCTTACTTTGATTCACTAAAACCGAACAATCAGCT
Found at i:254937 original size:32 final size:32
Alignment explanation
Indices: 254891--254955 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
254881 AACTGAGTAT
254891 CGGGTACCCAATTACC-GAGTACCCGTAAAATC
1 CGGGTACCCAATTACCGGA-TACCCGTAAAATC
* *
254923 CGGGTACCCGATTACCGGATACCCGTAACATC
1 CGGGTACCCAATTACCGGATACCCGTAAAATC
254955 C
1 C
254956 AGATCGAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.28, C:0.34, G:0.20, T:0.18
Consensus pattern (32 bp):
CGGGTACCCAATTACCGGATACCCGTAAAATC
Found at i:255766 original size:26 final size:26
Alignment explanation
Indices: 255730--255793 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
255720 CCGTGACCCG
255730 ACCCGACCCGACAAAATTAATGTTTC
1 ACCCGACCCGACAAAATTAATGTTTC
255756 ACCCGACCCGACAAAATTAATGTTTC
1 ACCCGACCCGACAAAATTAATGTTTC
255782 ACCCGACCCGAC
1 ACCCGACCCGAC
255794 CTGACCCGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.33, C:0.36, G:0.12, T:0.19
Consensus pattern (26 bp):
ACCCGACCCGACAAAATTAATGTTTC
Found at i:268840 original size:20 final size:20
Alignment explanation
Indices: 268801--268840 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
268791 TTTAAGTAGT
* **
268801 AAAATTAATATTTTCGATAA
1 AAAAATAATATTTTAAATAA
268821 AAAAATAATATTTTAAATAA
1 AAAAATAATATTTTAAATAA
268841 TCTTTACCGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAAATAATATTTTAAATAA
Found at i:275482 original size:20 final size:20
Alignment explanation
Indices: 275459--275499 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
275449 CATGTGACTA
275459 CCCCGATCACGATGCGTCTC
1 CCCCGATCACGATGCGTCTC
275479 CCCCGATCACGATGCGTCTC
1 CCCCGATCACGATGCGTCTC
275499 C
1 C
275500 ATGGCGCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.46, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCCGATCACGATGCGTCTC
Found at i:275892 original size:114 final size:114
Alignment explanation
Indices: 275678--275892 Score: 315
Period size: 114 Copynumber: 1.9 Consensus size: 114
275668 ATAAATTTTG
* *
275678 AAAATCAATTTTTTTCTCACAATTCTTATGTTTTCTTTATATTTTATATTTTTCTTTAGCCAATT
1 AAAATCAATTTTTTTCTCACAATTATTATGTTTTCTTTATATTTTATATTTTTCTTTAACCAATT
* ** * *
275743 AAACTTAATTTGATTGTTATCGTTATCAACGTTGCACATAATTCTGAAA
66 AAACTTAATTCGATTGGCATCATTACCAACGTTGCACATAATTCTGAAA
* **
275792 AAAATCAA-TTTTTTCTCCCAATTATTATGTTTTCTTTATATTTTATATTTTTCCTTTAACCTCT
1 AAAATCAATTTTTTTCTCACAATTATTATGTTTTCTTTATATTTTATATTTTT-CTTTAACCAAT
*
275856 TAAACTTAATTCGATTGGCATCATTACCAGCGTTGCA
65 TAAACTTAATTCGATTGGCATCATTACCAACGTTGCA
275893 TAAAATACGT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
113 42 0.47
114 47 0.53
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.48
Consensus pattern (114 bp):
AAAATCAATTTTTTTCTCACAATTATTATGTTTTCTTTATATTTTATATTTTTCTTTAACCAATT
AAACTTAATTCGATTGGCATCATTACCAACGTTGCACATAATTCTGAAA
Found at i:286080 original size:2 final size:2
Alignment explanation
Indices: 286073--286133 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
286063 TATTCGATCA
286073 AT AT AT AT AT AT AT 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 AT AT AT AT
286115 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
286134 CTAGGACCCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:293503 original size:2 final size:2
Alignment explanation
Indices: 293496--293532 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
293486 ACTTAATCTC
293496 AT AT AT 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 AT AT AT A
293533 CCACTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:294282 original size:26 final size:26
Alignment explanation
Indices: 294247--294356 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
294237 TAGCAGTAGT
*
294247 GGTGGCTGTTGAGTGGTCCAAGCGAC
1 GGTGGCTGTTGAGCGGTCCAAGCGAC
* **
294273 GGTGGTTGTTGAGCGGTCCAAGCGGT
1 GGTGGCTGTTGAGCGGTCCAAGCGAC
*
294299 GGTGGCTGTTGAGCGGTCCAAGCGAT
1 GGTGGCTGTTGAGCGGTCCAAGCGAC
*
294325 GGTGGCTGTTGAGCGGTCCAAGCGGC
1 GGTGGCTGTTGAGCGGTCCAAGCGAC
294351 GGTGGC
1 GGTGGC
294357 ATGAGTGGTC
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.13, C:0.19, G:0.45, T:0.23
Consensus pattern (26 bp):
GGTGGCTGTTGAGCGGTCCAAGCGAC
Found at i:294322 original size:52 final size:52
Alignment explanation
Indices: 294245--294356 Score: 188
Period size: 52 Copynumber: 2.2 Consensus size: 52
294235 GTTAGCAGTA
* *
294245 GTGGTGGCTGTTGAGTGGTCCAAGCGACGGTGGTTGTTGAGCGGTCCAAGCG
1 GTGGTGGCTGTTGAGCGGTCCAAGCGACGGTGGCTGTTGAGCGGTCCAAGCG
*
294297 GTGGTGGCTGTTGAGCGGTCCAAGCGATGGTGGCTGTTGAGCGGTCCAAGCG
1 GTGGTGGCTGTTGAGCGGTCCAAGCGACGGTGGCTGTTGAGCGGTCCAAGCG
*
294349 GCGGTGGC
1 GTGGTGGC
294357 ATGAGTGGTC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.46, T:0.23
Consensus pattern (52 bp):
GTGGTGGCTGTTGAGCGGTCCAAGCGACGGTGGCTGTTGAGCGGTCCAAGCG
Found at i:299335 original size:21 final size:21
Alignment explanation
Indices: 299310--299356 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
299300 AAATAATTTT
*
299310 ATTTTAATATTTAAAATATTA
1 ATTTTAATACTTAAAATATTA
**
299331 ATTTTGTTACTTAAAATATTA
1 ATTTTAATACTTAAAATATTA
299352 ATTTT
1 ATTTT
299357 TTAACATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTAATACTTAAAATATTA
Found at i:300604 original size:26 final size:27
Alignment explanation
Indices: 300559--300610 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
300549 TTATCTTACT
* *
300559 TGAAAATTTTATATCCTCCACCCGACC
1 TGAAAATTATATATCATCCACCCGACC
*
300586 TGAAAA-TATATATCATCCATCCGAC
1 TGAAAATTATATATCATCCACCCGAC
300611 TTAAACTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.29
Consensus pattern (27 bp):
TGAAAATTATATATCATCCACCCGACC
Found at i:301649 original size:28 final size:29
Alignment explanation
Indices: 301610--301666 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
301600 TAACAATTAT
* *
301610 TTTTCTTTCAAGTATATATATAGTAAATA
1 TTTTCTTTCAAGAATATATATAATAAATA
301639 TTTT-TTTCAAGAATATATATAATAAATA
1 TTTTCTTTCAAGAATATATATAATAAATA
301667 ATTATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (29 bp):
TTTTCTTTCAAGAATATATATAATAAATA
Found at i:310076 original size:24 final size:24
Alignment explanation
Indices: 310030--310076 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
310020 CGCCGCCGCC
* *
310030 GCCGCCGTCTCGGTCGTGGTCGTG
1 GCCGCCGTCTCGCTCGTGCTCGTG
310054 GCCGCCGTCTCGTCTCGT-CTCGT
1 GCCGCCGTCTCG-CTCGTGCTCGT
310077 CTCGGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.00, C:0.38, G:0.34, T:0.28
Consensus pattern (24 bp):
GCCGCCGTCTCGCTCGTGCTCGTG
Found at i:310243 original size:21 final size:19
Alignment explanation
Indices: 310191--310245 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
310181 CGTTGCGATT
*
310191 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
310210 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
310233 TTGGACTATCGCA
1 TTGGACTATCGCA
310246 GTGCGAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 6 0.21
21 13 0.45
23 10 0.34
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:311193 original size:22 final size:22
Alignment explanation
Indices: 311165--311209 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
311155 GGTAAAAATT
* *
311165 ACCTAAAACATTATTTTTTTTA
1 ACCTAAAACATTAATGTTTTTA
*
311187 ACCTAAAATATTAATGTTTTTA
1 ACCTAAAACATTAATGTTTTTA
311209 A
1 A
311210 TAAAGTGCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (22 bp):
ACCTAAAACATTAATGTTTTTA
Found at i:338081 original size:13 final size:13
Alignment explanation
Indices: 338060--338092 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
338050 AAGACTCAAG
338060 AAAAA-AATATAA
1 AAAAATAATATAA
*
338072 AAATATAATATAA
1 AAAAATAATATAA
338085 AAAAATAA
1 AAAAATAA
338093 GAGAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAATAATATAA
Found at i:338255 original size:19 final size:19
Alignment explanation
Indices: 338212--338249 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
338202 GATTAGGTTG
*
338212 AGAAAAAATAGAGGCGACT
1 AGAAAAAAGAGAGGCGACT
*
338231 AGAAAAAAGAGAGGTGACT
1 AGAAAAAAGAGAGGCGACT
338250 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.29, T:0.11
Consensus pattern (19 bp):
AGAAAAAAGAGAGGCGACT
Found at i:350949 original size:2 final size:2
Alignment explanation
Indices: 350942--350966 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
350932 CCAAAGCATT
350942 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
350967 GCATATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:354627 original size:87 final size:87
Alignment explanation
Indices: 354481--354645 Score: 294
Period size: 87 Copynumber: 1.9 Consensus size: 87
354471 GTTTGGAGAC
* *
354481 ACATGTATGGAAGCAACCTTGACCCGTAAATTATTTTTGCTGTTACTATCAAAACCCTGGTCGCT
1 ACATGTATGGAAGCAACCTTGACCCGTAAATCATTTTCGCTGTTACTATCAAAACCCTGGTCGCT
*
354546 TCCCCGTAAAGCAGCTCCAGAG
66 TCCACGTAAAGCAGCTCCAGAG
*
354568 ACATGTATGGAAGCAACCTTGACCCGTAAATCCTTTTCGCTGTTACTATCAAAACCCTGGTCGCT
1 ACATGTATGGAAGCAACCTTGACCCGTAAATCATTTTCGCTGTTACTATCAAAACCCTGGTCGCT
354633 TCCACGTAAAGCA
66 TCCACGTAAAGCA
354646 ATTCCAGCCA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (87 bp):
ACATGTATGGAAGCAACCTTGACCCGTAAATCATTTTCGCTGTTACTATCAAAACCCTGGTCGCT
TCCACGTAAAGCAGCTCCAGAG
Found at i:359830 original size:11 final size:11
Alignment explanation
Indices: 359814--359841 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
359804 TAAAAATTAT
359814 AAATTAGTTAA
1 AAATTAGTTAA
359825 AAATTAGTTAA
1 AAATTAGTTAA
359836 AAATTA
1 AAATTA
359842 TGGATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (11 bp):
AAATTAGTTAA
Found at i:362568 original size:25 final size:25
Alignment explanation
Indices: 362534--362587 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
362524 GAGTGGATGG
362534 TTATTAAAGTAGATCTTGAAAAAGC
1 TTATTAAAGTAGATCTTGAAAAAGC
362559 TTATTAAAGTAGATCTTGAAAAAGC
1 TTATTAAAGTAGATCTTGAAAAAGC
362584 TTAT
1 TTAT
362588 GACTGATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (25 bp):
TTATTAAAGTAGATCTTGAAAAAGC
Found at i:363862 original size:15 final size:16
Alignment explanation
Indices: 363835--363865 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
363825 ATATACTTTT
363835 TTTAAAAATAATATAA
1 TTTAAAAATAATATAA
363851 TTTAAAAA-AATATAA
1 TTTAAAAATAATATAA
363866 AAAAATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTAAAAATAATATAA
Found at i:363933 original size:26 final size:23
Alignment explanation
Indices: 363918--363962 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
363908 TATAATTATA
363918 TATATATTAACTTTAAAATATTT
1 TATATATTAACTTTAAAATATTT
* *
363941 TTTATATTAACTTATTAAATAT
1 TATATATTAACTT-TAAAATAT
363963 ATTTCATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATATTAACTTTAAAATATTT
Found at i:364180 original size:31 final size:31
Alignment explanation
Indices: 364145--364212 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
364135 GGGTGACCAC
*
364145 ATCTTAATTAAATAAAAACGAAAGTGATCAT
1 ATCTTAATTAAATAAAAAAGAAAGTGATCAT
364176 ATCTTAATTAAATAAAAAAGAAAGTGATCAT
1 ATCTTAATTAAATAAAAAAGAAAGTGATCAT
364207 ATCTTA
1 ATCTTA
364213 TATTTTTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAAAGAAAGTGATCAT
Found at i:374983 original size:15 final size:15
Alignment explanation
Indices: 374963--374995 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
374953 AGAATATTAT
374963 TCAATGTTATAGATG
1 TCAATGTTATAGATG
374978 TCAATGTTATAGATG
1 TCAATGTTATAGATG
374993 TCA
1 TCA
374996 GGTGTAAGCG
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:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (15 bp):
TCAATGTTATAGATG
Found at i:375298 original size:36 final size:36
Alignment explanation
Indices: 375258--375328 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
375248 ATTTGGTAAT
*
375258 TCATATATTAAAATATTACT-TTT-ATATTTTATTATG
1 TCATA-ATTAAAATATTAATGTTTAATATTTT-TTATG
* *
375294 TCATAATTTAAATTTTAATGTTTAATATTTTTTAT
1 TCATAATTAAAATATTAATGTTTAATATTTTTTAT
375329 TATATAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
35 11 0.37
36 12 0.40
37 7 0.23
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (36 bp):
TCATAATTAAAATATTAATGTTTAATATTTTTTATG
Found at i:380388 original size:13 final size:14
Alignment explanation
Indices: 380370--380400 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
380360 GTTCATGCCC
380370 TAAAATTA-TTTCA
1 TAAAATTATTTTCA
380383 TAAAATTATTTTCA
1 TAAAATTATTTTCA
380397 TAAA
1 TAAA
380401 CTTTATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAATTATTTTCA
Found at i:395955 original size:21 final size:21
Alignment explanation
Indices: 395931--396104 Score: 99
Period size: 21 Copynumber: 7.9 Consensus size: 21
395921 GCGTAGAATT
*
395931 TGTCCCGAAGGACTACATAGA
1 TGTCCCGAAGGACCACATAGA
*
395952 TGTCCCGAAGGACCACATATAACACATA
1 TGTCCCGAAGGACCAC--AT-----AGA
**
395980 TGTATCGAAGGACCAC-T--A
1 TGTCCCGAAGGACCACATAGA
* *
395998 TGTCCCGAATGACCACGTAGA
1 TGTCCCGAAGGACCACATAGA
*
396019 TGTCCCGAAGGACCACATATAACACATA
1 TGTCCCGAAGGACCAC--AT-----AGA
396047 TGTCCCGAAGGACCAC-T--A
1 TGTCCCGAAGGACCACATAGA
* *
396065 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACATAGA
396086 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
396105 TAACACATAT
Statistics
Matches: 120, Mismatches: 13, Indels: 40
0.69 0.08 0.23
Matches are distributed among these distances:
18 30 0.25
19 2 0.02
21 49 0.41
23 3 0.03
25 2 0.02
28 34 0.28
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:396019 original size:67 final size:67
Alignment explanation
Indices: 395931--396152 Score: 363
Period size: 67 Copynumber: 3.3 Consensus size: 67
395921 GCGTAGAATT
* * **
395931 TGTCCCGAAGGACTACATAGATGTCCCGAAGGACCACATATAACACATATGTATCGAAGGACCAC
1 TGTCCCGAAGGACCACGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAGGACCAC
395996 TA
66 TA
*
395998 TGTCCCGAATGACCACGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCACGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAGGACCAC
396063 TA
66 TA
* *
396065 TGTCCCGAAGGACCGCGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAAGACCAC
1 TGTCCCGAAGGACCACGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAGGACCAC
396130 TA
66 TA
* *
396132 TGTCCCAAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
396153 CCCTCGACTC
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 146 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (67 bp):
TGTCCCGAAGGACCACGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAGGACCAC
TA
Found at i:397013 original size:24 final size:20
Alignment explanation
Indices: 396960--397017 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
396950 TTCCCATTGA
*
396960 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
396980 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
397003 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
397018 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:400215 original size:18 final size:18
Alignment explanation
Indices: 400192--400230 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
400182 AATAATAATA
* *
400192 AAATAAGTTATGGTGATT
1 AAATAAATTATAGTGATT
*
400210 AAATAAATTTTAGTGATT
1 AAATAAATTATAGTGATT
400228 AAA
1 AAA
400231 ATAGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (18 bp):
AAATAAATTATAGTGATT
Found at i:410250 original size:26 final size:27
Alignment explanation
Indices: 410186--410251 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
410176 CCCTAAACTC
410186 AAACCCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGAATATCACACTTAAA
* *
410213 AAACCCGTCCCGAATATCACATTTAAA
1 AAACCCGACCCGAATATCACACTTAAA
410240 AAA-CCGACCCGA
1 AAACCCGACCCGA
410252 CTCGACCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 8 0.22
27 28 0.78
ACGTcount: A:0.42, C:0.33, G:0.09, T:0.15
Consensus pattern (27 bp):
AAACCCGACCCGAATATCACACTTAAA
Found at i:414760 original size:18 final size:18
Alignment explanation
Indices: 414724--414761 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
414714 TCTAGGAACA
*
414724 TTTTATTTATTTATTTAT
1 TTTTATTTATTTATATAT
414742 TTTTA-TTATTTCATATAT
1 TTTTATTTATTT-ATATAT
414760 TT
1 TT
414762 GGTTTTAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTATTTATATAT
Found at i:417543 original size:23 final size:23
Alignment explanation
Indices: 417496--417539 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
417486 TTGAATCATA
417496 TTAAATTAACTAAAAAACTTAAT
1 TTAAATTAACTAAAAAACTTAAT
*
417519 TTAAA-TAA-TAAACAACTTAAT
1 TTAAATTAACTAAAAAACTTAAT
417540 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 3 0.15
23 5 0.25
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (23 bp):
TTAAATTAACTAAAAAACTTAAT
Found at i:422069 original size:102 final size:102
Alignment explanation
Indices: 421953--422149 Score: 376
Period size: 102 Copynumber: 1.9 Consensus size: 102
421943 GTATCAAATT
421953 TCATCATTAATATAATATCATGATGACCATTCTATAATGATCTTATAAATTTAATGATAAAAAAT
1 TCATCATTAATATAATATCATGATGACCATTCTATAATGATCTTATAAATTTAATGATAAAAAAT
422018 TATTCAAATATAATTCAATGACTTGTGATATAGTTTA
66 TATTCAAATATAATTCAATGACTTGTGATATAGTTTA
* *
422055 TCATCATTAATATAATATCATGATGACCATTCTGTAATGATCTTATAAATTTAATGATAGAAAAT
1 TCATCATTAATATAATATCATGATGACCATTCTATAATGATCTTATAAATTTAATGATAAAAAAT
422120 TATTCAAATATAATTCAATGACTTGTGATA
66 TATTCAAATATAATTCAATGACTTGTGATA
422150 GTTTACTCTA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 93 1.00
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.40
Consensus pattern (102 bp):
TCATCATTAATATAATATCATGATGACCATTCTATAATGATCTTATAAATTTAATGATAAAAAAT
TATTCAAATATAATTCAATGACTTGTGATATAGTTTA
Found at i:426568 original size:26 final size:26
Alignment explanation
Indices: 426529--426584 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
426519 AGGTTAGATT
426529 TTTTTTTAAATGAT-TTTGGG-TCGAA
1 TTTTTTTAAATGATGTTTGGGTTCG-A
*
426554 TTTTTTTAATGTGATGTTTGGGTTCGA
1 TTTTTTTAA-ATGATGTTTGGGTTCGA
426581 TTTT
1 TTTT
426585 AGGATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 9 0.33
26 4 0.15
27 11 0.41
28 3 0.11
ACGTcount: A:0.18, C:0.04, G:0.21, T:0.57
Consensus pattern (26 bp):
TTTTTTTAAATGATGTTTGGGTTCGA
Found at i:428520 original size:2 final size:2
Alignment explanation
Indices: 428513--428546 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
428503 TAAGGCCCAA
428513 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
428547 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:428595 original size:2 final size:2
Alignment explanation
Indices: 428546--428580 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
428536 TCTCTCTCTC
428546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
428581 CGTTTGTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:429865 original size:105 final size:105
Alignment explanation
Indices: 429661--429868 Score: 233
Period size: 105 Copynumber: 2.0 Consensus size: 105
429651 GTCAATGATA
* *
429661 TTGATTCCAGGTCAAAAGAGAATGAAGGCTCTGAAATGGATGGAGCTGGTGCCAGTGATTGCAAT
1 TTGATTCCAGGTCAAAAGAGAATGAAGGCTCTGAAATGGATGGAGCTGCTGACAGTGATTGCAAT
* * **
429726 GGAGTCGGTTTAGCTAATTGTACTGCCATGGCCAATGTTC
66 GGAGTCGGTTTAGCCAAATGTACTGCCAACGCCAATGTTC
* * * * **
429766 TTGATTTCAGGTCAAAAGAGAATG-AGGACTCTGAAATGGCTGTAGCTTCTGATGGTGATTGCAA
1 TTGATTCCAGGTCAAAAGAGAATGAAGG-CTCTGAAATGGATGGAGCTGCTGACAGTGATTGCAA
** *
429830 TGGAGAT-GGTTTA-CCAAATGATGGTGCTAACGCCAATGT
65 TGGAG-TCGGTTTAGCCAAATG-TACTGCCAACGCCAATGT
429869 GTCTGATCCC
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
104 8 0.09
105 76 0.89
106 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (105 bp):
TTGATTCCAGGTCAAAAGAGAATGAAGGCTCTGAAATGGATGGAGCTGCTGACAGTGATTGCAAT
GGAGTCGGTTTAGCCAAATGTACTGCCAACGCCAATGTTC
Found at i:430124 original size:120 final size:120
Alignment explanation
Indices: 429756--430572 Score: 653
Period size: 120 Copynumber: 6.9 Consensus size: 120
429746 TACTGCCATG
* * **
429756 GCCAATGTTCT-TGATTTCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTTCTGATG
1 GCCAATGTTATCT-ATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATG
* * * * * *
429820 GTGATTGCAATGGAGATGGTTTACCAAATGATGGTGCTAA-CGCCAATGTGTCTGAT
65 GCGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGC-CCAATGTCTCTGAA
* * * * * * * * *
429876 CCCAATGTTCTCGATTTCAGGTCAAAAGAGAACGAGGGCCCTGAAAAGGCTCTAGCTAATGATGA
1 GCCAATGTTATCTATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGC---TGATGA
* * * *
429941 TGGCGATTGCAATGGAGAAGGTTTAGTTAATGATAGTGCTAAGGCCACTGTCTCTGAA
63 TGGCGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGCCCAATGTCTCTGAA
* * * * *
429999 ACCAATATTATCTATTCCAGGTCAAAAGAGAATG-GAGACTCTGAAACGGCTTTAGCTGATGATA
1 GCCAATGTTATCTATTCCAGGTCAAAAGAGAATGAG-GACTCTGAAATGGCTGTAGCTGATGATG
* * * * ** *
430063 GTGATTGCAATGGAAATGCTTTAGCTGATGATAGTGCCGAGCCCAATGTCCCTGAA
65 GCGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGCCCAATGTCTCTGAA
*** * * * * *
430119 GCCAATGTTAT-TGATTCCAGGTCAAAAGAGTCCGAGGGCTCTGAAATGGTTTTTGCTGATCATG
1 GCCAATGTTATCT-ATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATG
** * *
430183 AAGATTGCAATGGAGATGGTTTAGCTAATGATATTGCTAAG-GCAACTGTCTCTGAA
65 GCGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGCCCAA-TGTCTCTGAA
* * * ** * * * * *
430239 GACAAAGTTCTGGATCCCGGGTCGAGAGAGAATGAGGACTCTGGAATGGCTGTAGCTGATGATGG
1 GCCAATGTTATCTATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGG
* * * *
430304 CGATTGCAATCGAGATGGTTTAGCTAATGATATTGCTAAGGCCACTGTCTCTGAA
66 CGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGCCCAATGTCTCTGAA
* * ** * ** *
430359 GCCAATGTTATCAATTCCAAGTCAAAAGAGAATGAGGGTTCTCAAATGGCCATAGCTGATGATGA
1 GCCAATGTTATCTATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGG
* * * * * *
430424 C-AGTTGCTATGGAGATGGTTTAGCAAATGATAGTGGT--G-CTACTGTTTCTGAA
66 CGA-TTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGCCCAATGTCTCTGAA
** * * * * * * *
430476 GCCAATGTTATGGACTT-CAGTTCGAAAGATAATGA-G-TTCTGAACTAGTTGTAGC---TGAT-
1 GCCAATGTTATCTA-TTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATG
*
430534 --GATTGCAATGGAGATGGTTTAGCTTATGATAGTGCTAAG
65 GCGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAG
430573 GCACTGTTTC
Statistics
Matches: 557, Mismatches: 124, Indels: 41
0.77 0.17 0.06
Matches are distributed among these distances:
109 30 0.05
110 1 0.00
111 1 0.00
112 4 0.01
115 12 0.02
116 1 0.00
117 38 0.07
118 3 0.01
119 5 0.01
120 363 0.65
121 3 0.01
122 1 0.00
123 95 0.17
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (120 bp):
GCCAATGTTATCTATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGG
CGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGCCCAATGTCTCTGAA
Found at i:430281 original size:240 final size:240
Alignment explanation
Indices: 429773--430458 Score: 754
Period size: 240 Copynumber: 2.8 Consensus size: 240
429763 TTCTTGATTT
**
429773 CAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTTCTGATGGTGATTGCAATGGAGATG
1 CAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAGATG
* * * * * ** * *
429838 GTTTACCAAATGATGGTGCTAA-CGCCAATGTGTCTGATCCCAATGTTCTCGATTTCAGGTCAAA
66 GTTTAGCTAATGATAGTGCCAAGC-CCAATGTCTCTGAAGCCAATGTTATCGATTCCAGGTCAAA
* * * ** *
429902 AGAGAACGAGGGCCCTGAAAAGGCTCTAGCTAATGATGATGGCGATTGCAATGGAGAAGGTTTAG
130 AGAGAACGAGGGCTCTGAAATGGCTATAGC---TGATGATGAAGATTGCAATGGAGATGGTTTAG
* * * *
429967 TTAATGATAGTGCTAAGGCCACTGTCTCTGAAACCAATATTATCTATTC
192 CTAATGATAGTGCTAAGGCAACTGTCTCTGAAACCAATAGTATCTATCC
* * * *
430016 CAGGTCAAAAGAGAATG-GAGACTCTGAAACGGCTTTAGCTGATGATAGTGATTGCAATGGAAAT
1 CAGGTCAAAAGAGAATGAG-GACTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAGAT
* * * * *
430080 GCTTTAGCTGATGATAGTGCCGAGCCCAATGTCCCTGAAGCCAATGTTATTGATTCCAGGTCAAA
65 GGTTTAGCTAATGATAGTGCCAAGCCCAATGTCTCTGAAGCCAATGTTATCGATTCCAGGTCAAA
** * * * *
430145 AGAGTCCGAGGGCTCTGAAATGGTTTTTGCTGATCATGAAGATTGCAATGGAGATGGTTTAGCTA
130 AGAGAACGAGGGCTCTGAAATGGCTATAGCTGATGATGAAGATTGCAATGGAGATGGTTTAGCTA
*
430210 ATGATATTGCTAAGGCAACTGTCTCTGAAGA-CAA-AGT-TCTGGATCC
195 ATGATAGTGCTAAGGCAACTGTCTCTGAA-ACCAATAGTATCT--ATCC
* * * * * *
430256 CGGGTCGAGAGAGAATGAGGACTCTGGAATGGCTGTAGCTGATGATGGCGATTGCAATCGAGATG
1 CAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAGATG
* * * * * *
430321 GTTTAGCTAATGATATTGCTAAGGCCACTGTCTCTGAAGCCAATGTTATCAATTCCAAGTCAAAA
66 GTTTAGCTAATGATAGTGCCAAGCCCAATGTCTCTGAAGCCAATGTTATCGATTCCAGGTCAAAA
* * * * * *
430386 GAGAATGAGGGTTCTCAAATGGCCATAGCTGATGATGACAG-TTGCTATGGAGATGGTTTAGCAA
131 GAGAACGAGGGCTCTGAAATGGCTATAGCTGATGATGA-AGATTGCAATGGAGATGGTTTAGCTA
430450 ATGATAGTG
195 ATGATAGTG
430459 GTGCTACTGT
Statistics
Matches: 366, Mismatches: 70, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
238 3 0.01
239 2 0.01
240 227 0.62
241 4 0.01
242 1 0.00
243 128 0.35
244 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (240 bp):
CAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAGATG
GTTTAGCTAATGATAGTGCCAAGCCCAATGTCTCTGAAGCCAATGTTATCGATTCCAGGTCAAAA
GAGAACGAGGGCTCTGAAATGGCTATAGCTGATGATGAAGATTGCAATGGAGATGGTTTAGCTAA
TGATAGTGCTAAGGCAACTGTCTCTGAAACCAATAGTATCTATCC
Found at i:438616 original size:163 final size:163
Alignment explanation
Indices: 438348--438673 Score: 604
Period size: 163 Copynumber: 2.0 Consensus size: 163
438338 GTGTCCCATT
438348 TTCTCTCGTCGTATCAATATCAAACAAAATTTCTTGCTCTCCAAACAAGTTCGGATTCTTATCCA
1 TTCTCTCGTCGTATCAATATCAAACAAAATTTCTTGCTCTCCAAACAAGTTCGGATTCTTATCCA
438413 ATACCCTTTTCGTTTCTCAACTAAATTATCATGTTTGCTGTG-TTTTTT-TCATCGAATCATGAA
66 ATACCCTTTTCGTTTCTCAACTAAATTATCATGTTTGCTGTGTTTTTTTATCATCGAATCATGAA
438476 AATAGGATTCTTTTTTGAAGTTTCTTCTCGTTG
131 AATAGGATTCTTTTTTGAAGTTTCTTCTCGTTG
438509 TTCTCTCGTCGTATC-ATATCAAACAAAATTTCTTGCTCTCCAAACAAGGTTCGGATTCTTATAT
1 TTCTCTCGTCGTATCAATATCAAACAAAATTTCTTGCTCTCCAAACAA-GTTCGGATTC-T-TAT
438573 CCAATACCCTTTTCGTTTCTCAACTAAATTATCATGTTTGCTGTGTTTTTTTATCATCGAATCAT
63 CCAATACCCTTTTCGTTTCTCAACTAAATTATCATGTTTGCTGTGTTTTTTTATCATCGAATCAT
438638 GAAAATAGGATTCTTTTTTGAAGTTTCTTCTCGTTG
128 GAAAATAGGATTCTTTTTTGAAGTTTCTTCTCGTTG
438674 ATCATACGCA
Statistics
Matches: 160, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
160 32 0.20
161 25 0.16
162 1 0.01
163 48 0.30
164 6 0.04
165 48 0.30
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (163 bp):
TTCTCTCGTCGTATCAATATCAAACAAAATTTCTTGCTCTCCAAACAAGTTCGGATTCTTATCCA
ATACCCTTTTCGTTTCTCAACTAAATTATCATGTTTGCTGTGTTTTTTTATCATCGAATCATGAA
AATAGGATTCTTTTTTGAAGTTTCTTCTCGTTG
Found at i:443473 original size:18 final size:18
Alignment explanation
Indices: 443452--443490 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
443442 ATATTGATGT
*
443452 GGATCAAAAT-AGATTTAG
1 GGATC-AAATCAGAATTAG
443470 GGATCAAATCAGAATTAG
1 GGATCAAATCAGAATTAG
443488 GGA
1 GGA
443491 CTAAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.44, C:0.08, G:0.26, T:0.23
Consensus pattern (18 bp):
GGATCAAATCAGAATTAG
Done.