Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005300.1 Hibiscus syriacus cultivar Beakdansim tig00011997_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: 114328
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:133 original size:35 final size:36
Alignment explanation
Indices: 68--168 Score: 93
Period size: 37 Copynumber: 2.8 Consensus size: 36
58 ACTATACTTT
* * *
68 TTCAAAAAACGTATT-T-AAAACCATACTATATAT-A
1 TTCAAAAACCGTTTTCTAAAAACTATA-TATATATCA
* * *
102 TTC-AAAATCGATTTTTTAAAAACTATATATATATGCT
1 TTCAAAAACCG-TTTTCTAAAAACTATATATATAT-CA
139 TTCAAAAACCGTTTTCTAAAAACTATATAT
1 TTCAAAAACCGTTTTCTAAAAACTATATAT
169 TCATGTTTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
33 6 0.11
34 6 0.11
35 8 0.15
36 8 0.15
37 21 0.38
38 6 0.11
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.38
Consensus pattern (36 bp):
TTCAAAAACCGTTTTCTAAAAACTATATATATATCA
Found at i:144 original size:37 final size:35
Alignment explanation
Indices: 102--181 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 35
92 ACTATATATA
* *
102 TTCAAAATCGATTTTTTAAAAACTATATATAT-ATGCT
1 TTCAAAACCG-TTTTCTAAAAACTATATAT-TCATG-T
139 TTCAAAAACCGTTTTCTAAAAACTATATATTCATGT
1 TTC-AAAACCGTTTTCTAAAAACTATATATTCATGT
175 TTCAAAA
1 TTCAAAA
182 ATATTCCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 4 0.10
36 5 0.13
37 24 0.62
38 6 0.15
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (35 bp):
TTCAAAACCGTTTTCTAAAAACTATATATTCATGT
Found at i:1800 original size:20 final size:20
Alignment explanation
Indices: 1770--1815 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1760 TTAATTTTTG
*
1770 AATTTATTTTAAAAATATTA
1 AATTTACTTTAAAAATATTA
* * *
1790 TATTTACTTTATACATATTA
1 AATTTACTTTAAAAATATTA
1810 AATTTA
1 AATTTA
1816 TTATTATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (20 bp):
AATTTACTTTAAAAATATTA
Found at i:1831 original size:24 final size:23
Alignment explanation
Indices: 1804--1851 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1794 TACTTTATAC
* *
1804 ATATTAAATTTATTATTATTTTAA
1 ATATTAAATTAACTA-TATTTTAA
*
1828 ATATTATATTAACTATATTTTAA
1 ATATTAAATTAACTATATTTTAA
1851 A
1 A
1852 ATATATATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTAAATTAACTATATTTTAA
Found at i:7757 original size:34 final size:35
Alignment explanation
Indices: 7666--7759 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
7656 TTCATTGTTC
* * *
7666 AAACAGTGCAGAAAAATATAGTGCATATTTGGTTA
1 AAACAGTGCAGAAAAATACAGTGCAGATTTGCTTA
* * * *
7701 AAACAATGCAGAAAAATGCAGTGTAGATTTGCTTC
1 AAACAGTGCAGAAAAATACAGTGCAGATTTGCTTA
*
7736 GAACAGTGCAG-AAAATACAGTGCA
1 AAACAGTGCAGAAAAATACAGTGCA
7760 ATGCAGATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 11 0.23
35 37 0.77
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (35 bp):
AAACAGTGCAGAAAAATACAGTGCAGATTTGCTTA
Found at i:9940 original size:23 final size:23
Alignment explanation
Indices: 9901--9954 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
9891 TAATAAAACA
9901 TTTTTTT-CTTTCTTTTTATAATT
1 TTTTTTTACTTTCTTTTTA-AATT
* *
9924 TTTTTTTATTTTC-TTTTAAGTT
1 TTTTTTTACTTTCTTTTTAAATT
9946 TTGTTTTTA
1 TT-TTTTTA
9955 AAATGCTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
23 18 0.67
24 4 0.15
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTTTTACTTTCTTTTTAAATT
Found at i:11673 original size:13 final size:13
Alignment explanation
Indices: 11657--11682 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11647 CTCTATTAGT
11657 TTTTTTATTTTTA
1 TTTTTTATTTTTA
11670 TTTTTTATTTTTA
1 TTTTTTATTTTTA
11683 ATCACTAATA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:12817 original size:19 final size:19
Alignment explanation
Indices: 12793--12832 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12783 TAAACCTTAA
*
12793 AACTTAAACCATAAACTCT
1 AACTTAAACCACAAACTCT
*
12812 AACTTAAACCCCAAACTCT
1 AACTTAAACCACAAACTCT
12831 AA
1 AA
12833 ACCCTAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (19 bp):
AACTTAAACCACAAACTCT
Found at i:12874 original size:20 final size:22
Alignment explanation
Indices: 12824--12874 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
12814 CTTAAACCCC
12824 AAACTCTAAACCCTAAACTTTA
1 AAACTCTAAACCCTAAACTTTA
*
12846 ACACT-TAAACCCT-AAC-TTA
1 AAACTCTAAACCCTAAACTTTA
*
12865 AAATTCTAAA
1 AAACTCTAAA
12875 ATTAATAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 6 0.24
20 7 0.28
21 8 0.32
22 4 0.16
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (22 bp):
AAACTCTAAACCCTAAACTTTA
Found at i:14066 original size:22 final size:22
Alignment explanation
Indices: 14038--14122 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
14028 TTACGTAACA
**
14038 CTGCAACACGCTATAAATTGAG
1 CTGCAACAAACTATAAATTGAG
14060 CTGCAACAAACTATAAATTGAG
1 CTGCAACAAACTATAAATTGAG
*
14082 CCGCAACAAACTATAAATTGAG
1 CTGCAACAAACTATAAATTGAG
** *
14104 CCACAACAAACTTTAAATT
1 CTGCAACAAACTATAAATT
14123 ATTTGAAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (22 bp):
CTGCAACAAACTATAAATTGAG
Found at i:14291 original size:16 final size:17
Alignment explanation
Indices: 14270--14305 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
14260 TAAACGTTAT
14270 TTTAAAATTAAATT-AA
1 TTTAAAATTAAATTGAA
*
14286 TTTAAATTTAAATTGAA
1 TTTAAAATTAAATTGAA
14303 TTT
1 TTT
14306 TTCTCATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAATTAAATTGAA
Found at i:25737 original size:17 final size:16
Alignment explanation
Indices: 25715--25764 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 16
25705 GTTTATTTTA
25715 TTTTA-TATTTGTAATGT
1 TTTTATTATTT-TAAT-T
25732 TTTTATTATTTTATATT
1 TTTTATTATTTTA-ATT
25749 TTTTATTATTTTAATT
1 TTTTATTATTTTAATT
25765 AAGCTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.10
17 21 0.68
18 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (16 bp):
TTTTATTATTTTAATT
Found at i:30666 original size:39 final size:39
Alignment explanation
Indices: 30588--30666 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
30578 TTGTTTTTAA
* * *
30588 AGAATATTTTATCTCACTTAAGATGGTTTCTCTCGAAAC
1 AGAATATTTTATCTCACTTAAGATAGTTTCACTCAAAAC
* * *
30627 AGAATATTTTA-CTCCGCTTGAGATAGTTTCACTTAAAAC
1 AGAATATTTTATCT-CACTTAAGATAGTTTCACTCAAAAC
30666 A
1 A
30667 AGAGTTGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (39 bp):
AGAATATTTTATCTCACTTAAGATAGTTTCACTCAAAAC
Found at i:30823 original size:77 final size:76
Alignment explanation
Indices: 30727--30902 Score: 193
Period size: 76 Copynumber: 2.4 Consensus size: 76
30717 CTTGAAACAG
* * *
30727 AAGATTTTGTCTCGCTTGAGACAGTTTTTTACTCGAAACAAGAAGATTT-ATTTCACTCAATATT
1 AAGATTTTGTCTCGCTTGAGACAG-TTTTTACTCAAAACAAG-ACATTTCATTTCACTCAAGATT
30791 GTTTTTCTTAAAAC
64 -TTTTTCTTAAAAC
* * *
30805 AAGA-TTTGTCTTGCTTGAGACAGTTTTTACTCAAAAGAAGACATTTCTTTTCACTCAAGA---T
1 AAGATTTTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAGACATTTCATTTCACTCAAGATTTT
* *
30866 TTT-TTGAAAG
66 TTTCTTAAAAC
* *
30876 AAGATTTTATCTCGCTTGAGATAGTTT
1 AAGATTTTGTCTCGCTTGAGACAGTTT
30903 CCCTTGAAAC
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
71 9 0.11
72 23 0.27
75 5 0.06
76 26 0.31
77 18 0.21
78 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (76 bp):
AAGATTTTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAGACATTTCATTTCACTCAAGATTTT
TTTCTTAAAAC
Found at i:30921 original size:39 final size:39
Alignment explanation
Indices: 30874--31267 Score: 421
Period size: 39 Copynumber: 10.5 Consensus size: 39
30864 ATTTTTTGAA
* *
30874 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
30913 AGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
30952 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
30991 AGAAGATTTTTATCTCGCTT-ATGATAGTTTTCCTCGAAAT
1 AGAAGA-TTTTGTCTCGCTTGA-GATAGTTTCCCTCGAAAC
*
31031 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
31070 AAAAGATTTTGTCT--C-----AT--TTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
31100 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
31139 AGAAGATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
31178 -G-A-ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
31213 TG-A-ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
31250 --AA-ATTTTGTCTCTCTTGA
1 AGAAGATTTTGTCTCGCTTGA
31268 AACAAATTTT
Statistics
Matches: 320, Mismatches: 20, Indels: 33
0.86 0.05 0.09
Matches are distributed among these distances:
30 25 0.08
32 3 0.01
36 85 0.27
37 4 0.01
38 1 0.00
39 166 0.52
40 36 0.11
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:31062 original size:79 final size:76
Alignment explanation
Indices: 30874--31204 Score: 394
Period size: 79 Copynumber: 4.4 Consensus size: 76
30864 ATTTTTTGAA
*
30874 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTGTCTCACTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTC-CTT-AGATAG
30939 TTTCCCTCGAAAC
64 TTTCCCTCGAAAC
* *
30952 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTTATCTCGCTTATGATA
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA-TTTTGTCTC-CTTA-GATA
* *
31017 GTTTTCCTCGAAAT
63 GTTTCCCTCGAAAC
* * *
31031 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAAGATTTTGTCT-C----AT--TT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCCTTAGATAGTT
31089 TCCCTCGAAAC
66 TCCCTCGAAAC
* *
31100 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCTCTTGAGACAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTC-CTT-AGATAG
* *
31165 TTTCTCTTGAAAC
64 TTTCCCTCGAAAC
* * *
31178 -G-A-ATTTTGTCTCTCTTGAGACAGTTTC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTC
31205 TCTTGAAATG
Statistics
Matches: 222, Mismatches: 20, Indels: 25
0.83 0.07 0.09
Matches are distributed among these distances:
69 62 0.28
71 3 0.01
75 23 0.10
76 3 0.01
77 1 0.00
78 62 0.28
79 68 0.31
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (76 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCCTTAGATAGTT
TCCCTCGAAAC
Found at i:31093 original size:30 final size:30
Alignment explanation
Indices: 31057--31114 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
31047 CTTGAGATAG
*
31057 TTTCCCTTGAAACAAAAGATTTTGTCTCAT
1 TTTCCCTCGAAACAAAAGATTTTGTCTCAT
*
31087 TTTCCCTCGAAACAGAAGATTTTGTCTC
1 TTTCCCTCGAAACAAAAGATTTTGTCTC
31115 GCTTGAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (30 bp):
TTTCCCTCGAAACAAAAGATTTTGTCTCAT
Found at i:31122 original size:187 final size:180
Alignment explanation
Indices: 30900--31252 Score: 476
Period size: 187 Copynumber: 1.9 Consensus size: 180
30890 CTTGAGATAG
* *
30900 TTTCCCTTGAAACAGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAACATAAGATTTTATC
1 TTTCCCTCGAAACAGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATC
* *
30965 TCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTTATCTCGCTT-ATGATAGTTT-TCCTCGA
66 TCGCTTGAGACAGTTTCCCTCGAAAC-G-A-A-TTTTATCTCGCTTGA-GACAGTTTCT-CTCGA
*
31028 AATAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAAGATTTTGTCTCAT
125 AAT-G-A-ATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAAAAGATTTTGTCTCAT
* *
31087 TTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTC
1 TTTCCCTCGAAACAGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATC
* * * * * *
31152 TCTCTTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATGAA
66 TCGCTTGAGACAGTTTCCCTCGAAACGAATTTTATCTCGCTTGAGACAGTTTCTCTCGAAATGAA
* *
31217 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
131 TTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAAA
31253 TTTTGTCTCT
Statistics
Matches: 149, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
180 34 0.23
181 1 0.01
182 1 0.01
183 25 0.17
184 3 0.02
185 1 0.01
186 1 0.01
187 83 0.56
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (180 bp):
TTTCCCTCGAAACAGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATC
TCGCTTGAGACAGTTTCCCTCGAAACGAATTTTATCTCGCTTGAGACAGTTTCTCTCGAAATGAA
TTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAAAAGATTTTGTCTCAT
Found at i:31138 original size:69 final size:68
Alignment explanation
Indices: 31018--31153 Score: 236
Period size: 69 Copynumber: 2.0 Consensus size: 68
31008 CTTATGATAG
* *
31018 TTTTCCTCGAAATAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAAGATTTTGTC
1 TTTTCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGTC
31083 TCA
66 TCA
*
31086 TTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGT
1 TTTT-CCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGT
31151 CTC
65 CTC
31154 TCTTGAGACA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 4 0.06
69 60 0.94
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (68 bp):
TTTTCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGTC
TCA
Found at i:31168 original size:108 final size:109
Alignment explanation
Indices: 30978--31177 Score: 323
Period size: 108 Copynumber: 1.8 Consensus size: 109
30968 CTTGAGATAG
* *
30978 TTTCCCTCGAAACAGAAGATTTTTATCTCGCTTATGATAGTTTTCCTCGAAATAGAAGATTTTGT
1 TTTCCCTCGAAACAGAAGATTTTTATCTCGCTTATGATAGTTTCCCTCGAAACAGAAGATTTTGT
*
31043 CTCGCTTGAGATAGTTTCCCTTGAAACAAAAGATTTTGTCTCAT
66 CTCGCTTGAGACAGTTTCCCTTGAAACAAAAGATTTTGTCTCAT
*
31087 TTTCCCTCGAAACAGAAGA-TTTTGTCTCGCTTGA-GATAGTTTCCCTCGAAACAGAAGATTTTG
1 TTTCCCTCGAAACAGAAGATTTTTATCTCGCTT-ATGATAGTTTCCCTCGAAACAGAAGATTTTG
* *
31150 TCTCTCTTGAGACAGTTTCTCTTGAAAC
65 TCTCGCTTGAGACAGTTTCCCTTGAAAC
31178 GAATTTTGTC
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
108 64 0.76
109 20 0.24
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (109 bp):
TTTCCCTCGAAACAGAAGATTTTTATCTCGCTTATGATAGTTTCCCTCGAAACAGAAGATTTTGT
CTCGCTTGAGACAGTTTCCCTTGAAACAAAAGATTTTGTCTCAT
Found at i:31191 original size:36 final size:36
Alignment explanation
Indices: 31105--31267 Score: 245
Period size: 36 Copynumber: 4.4 Consensus size: 36
31095 GAAACAGAAG
* * * *
31105 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-G-A
31143 GATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGA
1 -ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGA
*
31180 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATGA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGA
*
31216 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGA
31252 ATTTTGTCTCTCTTGA
1 ATTTTGTCTCTCTTGA
31268 AACAAATTTT
Statistics
Matches: 117, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
36 85 0.73
37 1 0.01
38 1 0.01
39 30 0.26
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.42
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGA
Found at i:31192 original size:21 final size:20
Alignment explanation
Indices: 31167--31288 Score: 93
Period size: 21 Copynumber: 6.4 Consensus size: 20
31157 TGAGACAGTT
31167 TCTCTTGAAACGAATTTTGTC
1 TCTCTTGAAAC-AATTTTGTC
* *
31188 TCTCTTGAGAC-A----GTT
1 TCTCTTGAAACAATTTTGTC
*
31203 TCTCTTGAAATGAATTTTGTC
1 TCTCTTGAAA-CAATTTTGTC
* *
31224 TCTCTTGAGAC-A----GTT
1 TCTCTTGAAACAATTTTGTC
31239 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAAC-AATTTTGTC
31260 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAAC-AATTTTGTC
31281 TCTCTTGA
1 TCTCTTGA
31289 GACAGTTTCC
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
15 23 0.29
17 2 0.03
19 2 0.03
21 52 0.66
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (20 bp):
TCTCTTGAAACAATTTTGTC
Found at i:31264 original size:57 final size:57
Alignment explanation
Indices: 31203--31324 Score: 190
Period size: 57 Copynumber: 2.1 Consensus size: 57
31193 TGAGACAGTT
** * *
31203 TCTCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
*
31260 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGAATTTTATC
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
*
31317 TATCTTGA
1 TCTCTTGA
31325 GACATTTCCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (57 bp):
TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
Found at i:31276 original size:93 final size:92
Alignment explanation
Indices: 31167--31359 Score: 307
Period size: 93 Copynumber: 2.1 Consensus size: 92
31157 TGAGACAGTT
* * * * *
31167 TCTCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATGAATTTTGTCTCTCTTGA
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGAATTTTATCTATCTTGA
*
31232 GACAGTTTCTC-TTGAAACAAATTTTGTC
66 GACA-TTTC-CATTGAAACAAATTCTGTC
31260 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGAATTTTATCTATCTTGA
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGAATTTTATCTATCTTGA
31325 GACATTTCCATTGAAACAAATTCTGTC
66 GACATTTCCATTGAAACAAATTCTGTC
31352 TCTCTTGA
1 TCTCTTGA
31360 GATATTCCCT
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
91 1 0.01
92 28 0.30
93 64 0.69
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (92 bp):
TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGAATTTTATCTATCTTGA
GACATTTCCATTGAAACAAATTCTGTC
Found at i:31340 original size:35 final size:35
Alignment explanation
Indices: 31263--31377 Score: 160
Period size: 35 Copynumber: 3.3 Consensus size: 35
31253 TTTTGTCTCT
31263 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACA-TTTCC
* * *
31299 CTTGAAACGAATTTTATCTATCTTGAGACATTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACATTTCC
* * *
31334 ATTGAAACAAATTCTGTCTCTCTTGAGATA-TTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACATTTCC
31368 CTTGAAACAA
1 CTTGAAACAA
31378 GAAATGTATC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
34 13 0.19
35 29 0.42
36 27 0.39
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (35 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACATTTCC
Found at i:31388 original size:71 final size:73
Alignment explanation
Indices: 31264--31473 Score: 216
Period size: 71 Copynumber: 2.9 Consensus size: 73
31254 TTTGTCTCTC
* * *
31264 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC--GAATTTTATCT-ATCTTGAG
1 TTGAAACAAATTTTGTCTCTCTTGAGATA-TTTCCCTTGAAACAAGAAATGTATCTCA-CTTGAG
31326 A-CATTTCCA
64 AGCATTTCCA
*
31335 TTGAAACAAATTCTGTCTCTCTTGAGATA-TTCCCTTGAAACAAGAAATGTATCTCACTTGAGAT
1 TTGAAACAAATTTTGTCTCTCTTGAGATATTTCCCTTGAAACAAGAAATGTATCTCACTTGAGA-
** *
31399 GGTTTTTCA
65 GCATTTCCA
* * * * *
31408 -TAAAACCAATTTTGTCTCGCTTGAGATAATTTTCCCTTGAAACAAGAAATTTTATCTCACTCGA
1 TTGAAACAAATTTTGTCTCTCTTGAGAT-A-TTTCCCTTGAAACAAGAAA-TGTATCTCACTTGA
31472 GA
63 GA
31474 TAGCTTCTCT
Statistics
Matches: 117, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
69 12 0.10
71 43 0.37
72 24 0.21
73 6 0.05
75 18 0.15
76 14 0.12
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (73 bp):
TTGAAACAAATTTTGTCTCTCTTGAGATATTTCCCTTGAAACAAGAAATGTATCTCACTTGAGAG
CATTTCCA
Found at i:31924 original size:64 final size:64
Alignment explanation
Indices: 31817--31942 Score: 207
Period size: 64 Copynumber: 2.0 Consensus size: 64
31807 AGTTCATAAC
* * *
31817 GAGAAGAACTTGTTCAACCTTGCATCAACATTTCTAGCAGGGAGTTCATAATGAGAAAAACTAT
1 GAGAAAAACTTGTTCAACCTTGAATCAACATTTCCAGCAGGGAGTTCATAATGAGAAAAACTAT
* *
31881 GAGAAAAACTTGTTCAACCTTGAATCAACATTTCCAGCGGGGAGTTCATAATGAGAAGAACT
1 GAGAAAAACTTGTTCAACCTTGAATCAACATTTCCAGCAGGGAGTTCATAATGAGAAAAACT
31943 CATCCAATGA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (64 bp):
GAGAAAAACTTGTTCAACCTTGAATCAACATTTCCAGCAGGGAGTTCATAATGAGAAAAACTAT
Found at i:32034 original size:91 final size:91
Alignment explanation
Indices: 31879--32085 Score: 324
Period size: 91 Copynumber: 2.3 Consensus size: 91
31869 GAGAAAAACT
* *
31879 ATGAGAAAAACTTGTTCAACCTTGAATCAACATTTCCAGCGGGGAGTTCATAATGAGAAGAACTC
1 ATGAGAAAAACTTGTTCAACCTTGGATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTC
*
31944 ATCCAATGAGGGAAAAGAAGTTCATA
66 ATCCAACGAGGGAAAAGAAGTTCATA
* * * *
31970 ATGAGAAAAACGTGTTCAACCTTGGCTCAGCATTTCCAGTGGAGAGTTCATAATGAGAAGAACTC
1 ATGAGAAAAACTTGTTCAACCTTGGATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTC
* *
32035 ATCCAACGGGGGAGAAGAAGTTCATA
66 ATCCAACGAGGGAAAAGAAGTTCATA
*
32061 ATGAGAAGAACTTGTTCAACCTTGG
1 ATGAGAAAAACTTGTTCAACCTTGG
32086 TTCGATTTCA
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 105 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (91 bp):
ATGAGAAAAACTTGTTCAACCTTGGATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTC
ATCCAACGAGGGAAAAGAAGTTCATA
Found at i:37866 original size:19 final size:17
Alignment explanation
Indices: 37846--37896 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 17
37836 TTTGAATTCT
37846 TTTTCTTTTCTTTTCTTC
1 TTTTCTTTTCTTTT-TTC
37864 TTTTCTTCTTCTTTTTGTC
1 TTTTCTT-TTCTTTTT-TC
37883 TTTTC-TTTCTTTTT
1 TTTTCTTTTCTTTTT
37897 GCACTCCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.26
18 9 0.29
19 14 0.45
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTTC
Found at i:39772 original size:7 final size:8
Alignment explanation
Indices: 39754--39797 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 8
39744 TTTATATTGT
39754 TTTTATTA
1 TTTTATTA
39762 TTTTA-TA
1 TTTTATTA
39769 TTTTAATTA
1 TTTT-ATTA
39778 TTTTAATTA
1 TTTT-ATTA
39787 TGTTTATTA
1 T-TTTATTA
39796 TT
1 TT
39798 ATTTAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 6 0.18
8 7 0.21
9 17 0.52
10 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
TTTTATTA
Found at i:39772 original size:16 final size:18
Alignment explanation
Indices: 39739--39810 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 18
39729 GGTTTTTATT
*
39739 TTATGTTTATATTGTTTTTA
1 TTAT-TTTA-ATTATTTTTA
*
39759 TTATTTT-A-TATTTTAA
1 TTATTTTAATTATTTTTA
*
39775 TTATTTTAATTATGTTTA
1 TTATTTTAATTATTTTTA
39793 TTATTATTTAATT-TTTTT
1 TTA-T-TTTAATTATTTTT
39811 GTAATTTCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
16 13 0.30
17 2 0.05
18 9 0.21
19 8 0.19
20 11 0.26
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (18 bp):
TTATTTTAATTATTTTTA
Found at i:39779 original size:9 final size:9
Alignment explanation
Indices: 39739--39797 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
39729 GGTTTTTATT
39739 TTATGTTTATA
1 TTAT-TTTA-A
* *
39750 TTGTTTTTA
1 TTATTTTAA
39759 TTATTTT-A
1 TTATTTTAA
39767 -TATTTTAA
1 TTATTTTAA
39775 TTATTTTAA
1 TTATTTTAA
39784 TTATGTTT-A
1 TTAT-TTTAA
39793 TTATT
1 TTATT
39798 ATTTAATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
7 6 0.14
8 3 0.07
9 24 0.57
10 6 0.14
11 3 0.07
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (9 bp):
TTATTTTAA
Found at i:39781 original size:25 final size:25
Alignment explanation
Indices: 39707--39810 Score: 70
Period size: 25 Copynumber: 4.0 Consensus size: 25
39697 TTAATTATGG
**
39707 TTATTTTATATTTATACAATTAGGTTT-
1 TTATTTTATATTT-T--AATTATTTTTA
* *
39734 TTATTTTAT-GTTTATATTGTTTTTA
1 TTATTTTATATTTTA-ATTATTTTTA
*
39759 TTATTTTATATTTTAATTATTTTAA
1 TTATTTTATATTTTAATTATTTTTA
39784 TTATGTTTATTATTATTTAATT-TTTTT
1 TTAT-TTTA-TA-T-TTTAATTATTTTT
39811 GTAATTTCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
23 1 0.02
24 6 0.10
25 22 0.35
26 10 0.16
27 11 0.18
28 5 0.08
29 7 0.11
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.68
Consensus pattern (25 bp):
TTATTTTATATTTTAATTATTTTTA
Found at i:42811 original size:13 final size:13
Alignment explanation
Indices: 42795--42851 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
42785 AGAAATAAAT
*
42795 AAAATAATGAAAG
1 AAAATAAGGAAAG
42808 AAAATAAGGAAA-
1 AAAATAAGGAAAG
* *
42820 CAAATAAGCAAAGAG
1 AAAATAAG-GAA-AG
*
42835 AAAATAAGCAAAG
1 AAAATAAGGAAAG
42848 AAAA
1 AAAA
42852 AAACAAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 7 0.19
13 19 0.53
14 3 0.08
15 7 0.19
ACGTcount: A:0.70, C:0.05, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAATAAGGAAAG
Found at i:42836 original size:27 final size:27
Alignment explanation
Indices: 42806--42869 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
42796 AAATAATGAA
* *
42806 AGAAAATAAGGAAACAAATAAGCAAAG
1 AGAAAATAAGGAAACAAAAAAACAAAG
* *
42833 AGAAAATAAGCAAAGAAAAAAACAAAG
1 AGAAAATAAGGAAACAAAAAAACAAAG
*
42860 A-AAAAAAAGG
1 AGAAAATAAGG
42870 GACAAGAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.72, C:0.06, G:0.17, T:0.05
Consensus pattern (27 bp):
AGAAAATAAGGAAACAAAAAAACAAAG
Found at i:42841 original size:15 final size:14
Alignment explanation
Indices: 42821--42864 Score: 65
Period size: 15 Copynumber: 3.2 Consensus size: 14
42811 ATAAGGAAAC
42821 AAATAAGCAAAGAGA
1 AAATAAGCAAAGA-A
42836 AAATAAGCAAAGAA
1 AAATAAGCAAAGAA
42850 AAA-AA-CAAAGAA
1 AAATAAGCAAAGAA
42862 AAA
1 AAA
42865 AAAGGGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.34
13 2 0.07
14 4 0.14
15 13 0.45
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.05
Consensus pattern (14 bp):
AAATAAGCAAAGAA
Found at i:42860 original size:12 final size:13
Alignment explanation
Indices: 42825--42866 Score: 59
Period size: 12 Copynumber: 3.2 Consensus size: 13
42815 GGAAACAAAT
42825 AAGCAAAGAGAAAA
1 AAGCAAAGA-AAAA
42839 TAAGCAAAGAAAAA
1 -AAGCAAAGAAAAA
42853 AA-CAAAGAAAAA
1 AAGCAAAGAAAAA
42865 AA
1 AA
42867 AGGGACAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.44
13 2 0.07
14 4 0.15
15 9 0.33
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.02
Consensus pattern (13 bp):
AAGCAAAGAAAAA
Found at i:44376 original size:67 final size:67
Alignment explanation
Indices: 44296--44484 Score: 280
Period size: 65 Copynumber: 2.9 Consensus size: 67
44286 TTTTTACTCA
* * *
44296 AAACAAA--TTTGTCTCTCTTTAGACATTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCTCT
1 AAACAAAGTTTTGTCTCTCTTTAGACAGTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCCCC
44359 TG
66 TG
*
44361 AAACAAAGTTTTGTCTCTCTTTAGACAGTTTCTCTT-AAA-AATAATCTTTGAGT-TGTTTCCCC
1 AAACAAAGTTTTGTCTCTCTTTAGACAGTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCCCC
44423 TG
66 TG
* *
44425 AAACAAAGTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGT
1 AAACAAAG-TTTTGTCTCTCTTTAGACAGTTTCTCTTGAAATAAAAATCTTTGAGTATGT
44485 AGTTTTGTCT
Statistics
Matches: 111, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
64 17 0.15
65 47 0.42
66 6 0.05
67 38 0.34
68 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (67 bp):
AAACAAAGTTTTGTCTCTCTTTAGACAGTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCCCC
TG
Found at i:44562 original size:120 final size:118
Alignment explanation
Indices: 44367--44585 Score: 359
Period size: 120 Copynumber: 1.8 Consensus size: 118
44357 CTTGAAACAA
* * *
44367 AGTTTTGTCTCTCTTTAGACAGTTTCTCTTAAAAATAATCTTTGAGTTGTTTCCCCTGAAACAAA
1 AGTTTTGTCTCTCTTGAGACAGTTACTCTTAAAAAAAATCTTTGAGTTGTTTCCCCTGAAACAAA
44432 GTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGT
66 GTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGT
* *
44485 AGTTTTGTCTCTCTTGAGACGGTTACTCTTAAAACAAAAGTCTTTGAGTTTGTTTCCCTTGAAAC
1 AGTTTTGTCTCTCTTGAGACAGTTACTCTTAAAA-AAAA-TCTTTGAG-TTGTTTCCCCTGAAAC
44550 AAAG-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
63 AAAGTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
44586 CATCATCTTT
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
118 31 0.33
119 3 0.03
120 40 0.43
121 19 0.20
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (118 bp):
AGTTTTGTCTCTCTTGAGACAGTTACTCTTAAAAAAAATCTTTGAGTTGTTTCCCCTGAAACAAA
GTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGT
Found at i:44564 original size:67 final size:65
Alignment explanation
Indices: 44487--44717 Score: 329
Period size: 65 Copynumber: 3.5 Consensus size: 65
44477 GTGTATGTAG
* * * **
44487 TTTTGTCTCTCTTGAGACGGTTACTCTTAAAACAAAAGTCTTTGAGTTTGTTTCCCTTGAAACAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCA-TCTTTGAGTTTGTTTCCCTTGAAACAA
44552 A
65 A
* * *
44553 GTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGA
1 -TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTTTGTTTCCCTTGAAACAA
44618 A
65 A
* * *
44619 TTTTGTCTCTCTTGAGATAGTTTCTCATGAAACATCATCTTTGAGTTTGTTTCCCTTG-AAGAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTTTGTTTCCCTTGAAACAAA
*
44683 TTTTGTCTCTCTTGAGACAGCTTCTCTTGAAACAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAT
44718 TATCCCTATA
Statistics
Matches: 147, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
64 36 0.24
65 54 0.37
66 25 0.17
67 32 0.22
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTTTGTTTCCCTTGAAACAAA
Found at i:44605 original size:29 final size:29
Alignment explanation
Indices: 44565--44678 Score: 79
Period size: 29 Copynumber: 3.7 Consensus size: 29
44555 TTTGTCTCTC
*
44565 TTGAGA-CAGTTTCTCTTGAAACATCATCT
1 TTGAGATC-GTTTCCCTTGAAACATCATCT
44594 TTGAGATCGTTTCCCTTGAAACGAATTTTGTC-TCT
1 TTGAGATCGTTTCCCTTGAAAC--A-----TCATCT
* * *
44629 CTTGAGATAGTTTCTCATGAAACATCATCT
1 -TTGAGATCGTTTCCCTTGAAACATCATCT
* *
44659 TTGAGTTTGTTTCCCTTGAA
1 TTGAGATCGTTTCCCTTGAA
44679 GAAATTTTGT
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
29 37 0.55
30 4 0.06
31 1 0.01
34 1 0.01
35 3 0.04
36 21 0.31
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (29 bp):
TTGAGATCGTTTCCCTTGAAACATCATCT
Found at i:44625 original size:185 final size:184
Alignment explanation
Indices: 44303--44650 Score: 509
Period size: 185 Copynumber: 1.9 Consensus size: 184
44293 TCAAAACAAA
* * * * * *
44303 TTTGTCTCTCTTTAGACATTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCTCTTGAAACAAA
1 TTTGTCTCTCTTGAGACAGTTACTCTTAAAACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAA
* *
44368 GTTTTGTCTCTCTTTAGACAGTTTCTCTTAAAAATAATCTTTGAGTTGTTTCCCCTGAAACAAAG
66 GTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAATAATCTTTGAGTCGTTTCCCCTGAAACAAAG
*
44433 TTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGTAGT
131 -TTTTGTCTCTCTTGAGACAGTTTCTCATGAAATAAAAATCTTTGTGTATGTAGT
* * *
44488 TTTGTCTCTCTTGAGACGGTTACTCTTAAAACAAAAGTCTTTGAGTTTGTTTCCCTTGAAACAAA
1 TTTGTCTCTCTTGAGACAGTTACTCTTAAAACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAA
* * * *
44553 GTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGA
66 GTTTTGTCTCTCTTGAGACAGTTTCTCTT-AAAAATAATCTTTGAG-TCGTTTCCCCTGAAACAA
*
44618 A-TTTTGTCTCTCTTGAGATAGTTTCTCATGAAA
129 AGTTTTGTCTCTCTTGAGACAGTTTCTCATGAAA
44651 CATCATCTTT
Statistics
Matches: 144, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
185 114 0.79
186 14 0.10
187 16 0.11
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (184 bp):
TTTGTCTCTCTTGAGACAGTTACTCTTAAAACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAA
GTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAATAATCTTTGAGTCGTTTCCCCTGAAACAAAG
TTTTGTCTCTCTTGAGACAGTTTCTCATGAAATAAAAATCTTTGTGTATGTAGT
Found at i:44953 original size:131 final size:133
Alignment explanation
Indices: 44740--45111 Score: 464
Period size: 134 Copynumber: 2.8 Consensus size: 133
44730 TGGCTAGCAG
* * * *
44740 TCCTCATCGCATAGGAATCGTGTCATCCACCGACCAGATATCCTCATCACATAGGAGCAGTGTCA
1 TCCTCATCGCATAGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACATAGGAGCAGCGTCA
* *
44805 CCCTTAGATAACCAGTCGTCCTTATCAAATAGGAATCGTG-TTATCATC-CCTAAAGATGG-CAT
66 CCCTTAGATAACCAGTCGTCCTCATCAAATAGGAACCGTGTTTATCATCACCTAAAGATGGCCA-
*
44867 GTCA
130 GCCA
* * * *
44871 TCCTCATCACATTGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACATAGGAGCCGCATCA
1 TCCTCATCGCATAGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACATAGGAGCAGCGTCA
*
44936 CCCTTAGATAACCAGTCGTCCTCATCAAGTAGGAACCGTGTTTATCATCATCCTAAAGATGGCCA
66 CCCTTAGATAACCAGTCGTCCTCATCAAATAGGAACCGTGTTTATCATCA-CCTAAAGATGGCCA
*
45001 GCCG
130 GCCA
* * * * **
45005 TCCTCATCGCATAGGAACTGTGTCATCCACCAACCATATCTCCTCATCACGTAGGAGTTGCGTCA
1 TCCTCATCGCATAGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACATAGGAGCAGCGTCA
* * * * **
45070 ACCTTAGATAATCA-TCTGTCATAATCACGTAGGAACCGTGTT
66 CCCTTAGATAACCAGTC-GTCCTCATCAAATAGGAACCGTGTT
45112 ATCTCCAACT
Statistics
Matches: 209, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
131 94 0.45
132 8 0.04
133 2 0.01
134 103 0.49
135 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (133 bp):
TCCTCATCGCATAGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACATAGGAGCAGCGTCA
CCCTTAGATAACCAGTCGTCCTCATCAAATAGGAACCGTGTTTATCATCACCTAAAGATGGCCAG
CCA
Found at i:45060 original size:134 final size:132
Alignment explanation
Indices: 44719--45111 Score: 472
Period size: 131 Copynumber: 3.0 Consensus size: 132
44709 TTGAAACATT
* * * *
44719 ATCCCTATAA-ATGGCTAGCAGTCCTCATCGCATAGGAA-TCGTGTCATCCACCGACCAGATATC
1 ATCCCTA-AAGATGGCCAGCCGTCCTCATCGCATAGGAACT-GTGTCATCCACCGACCAAATCTC
* * * *
44782 CTCATCACATAGGAGCAGTGTCACCCTTAGATAACCAGTCGTCCTTATCAAATAGGAATCGTG-T
64 CTCATCACATAGGAGCAGCGTCACCCTTAGATAACCAGTCGTCCTAATCAAGTAGGAACCGTGTT
44846 TATC
129 TATC
* * * * *
44850 ATCCCTAAAGATGG-CATGTCATCCTCATCACATTGGAACCGTGTCATCCACCGACCAAATCTCC
1 ATCCCTAAAGATGGCCA-GCCGTCCTCATCGCATAGGAACTGTGTCATCCACCGACCAAATCTCC
* * *
44914 TCATCACATAGGAGCCGCATCACCCTTAGATAACCAGTCGTCCTCATCAAGTAGGAACCGTGTTT
65 TCATCACATAGGAGCAGCGTCACCCTTAGATAACCAGTCGTCCTAATCAAGTAGGAACCGTGTTT
44979 ATC
130 ATC
* *
44982 ATCATCCTAAAGATGGCCAGCCGTCCTCATCGCATAGGAACTGTGTCATCCACCAACCATATCTC
1 ATC--CCTAAAGATGGCCAGCCGTCCTCATCGCATAGGAACTGTGTCATCCACCGACCAAATCTC
* ** * * * *
45047 CTCATCACGTAGGAGTTGCGTCAACCTTAGATAATCA-TCTGTCATAATCACGTAGGAACCGTGT
64 CTCATCACATAGGAGCAGCGTCACCCTTAGATAACCAGTC-GTCCTAATCAAGTAGGAACCGTGT
45111 T
128 T
45112 ATCTCCAACT
Statistics
Matches: 223, Mismatches: 31, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
130 3 0.01
131 105 0.47
132 8 0.04
133 2 0.01
134 103 0.46
135 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (132 bp):
ATCCCTAAAGATGGCCAGCCGTCCTCATCGCATAGGAACTGTGTCATCCACCGACCAAATCTCCT
CATCACATAGGAGCAGCGTCACCCTTAGATAACCAGTCGTCCTAATCAAGTAGGAACCGTGTTTA
TC
Found at i:54403 original size:20 final size:20
Alignment explanation
Indices: 54378--54416 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54368 CTTAGTTGCG
* *
54378 AAAAATTGAAATTTAAATTA
1 AAAAATTAAAAATTAAATTA
54398 AAAAATTAAAAATTAAATT
1 AAAAATTAAAAATTAAATT
54417 CAAATTACTT
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:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAATTAAAAATTAAATTA
Found at i:56627 original size:24 final size:25
Alignment explanation
Indices: 56575--56628 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
56565 TCGGCCTACA
* *
56575 AAATAATTGTAATATATAAATTAAT
1 AAATAATAGTAATATATAAATAAAT
56600 -AATAATAGTAATA-ATAAATAAAT
1 AAATAATAGTAATATATAAATAAAT
56623 AAATAA
1 AAATAA
56629 ATACATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (25 bp):
AAATAATAGTAATATATAAATAAAT
Found at i:57398 original size:86 final size:86
Alignment explanation
Indices: 57285--57497 Score: 365
Period size: 86 Copynumber: 2.5 Consensus size: 86
57275 GACAATTTTT
* *
57285 TTTGACAAATAACCCTTCTTG-CATTAAGCTATGCTGTAAATCTGGTTTGCCTCTGAGCTAATTG
1 TTTGACAGATAACCCTTCTCGAC-TTAAGCTATGCTGTAAATCTGGTTTGCCTCTGAGCTAATTG
57349 TAATCGAACTTGAAGGTCTTTG
65 TAATCGAACTTGAAGGTCTTTG
* *
57371 TTTGACAGATAACCCTTCTCGACTTAAGCTATGTTGTAAATCTGGTTTGCCTCTGAGCTGATTGT
1 TTTGACAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATCTGGTTTGCCTCTGAGCTAATTGT
57436 AATCGAACTTGAAGGTCTTTG
66 AATCGAACTTGAAGGTCTTTG
*
57457 TTTGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
1 TTTGACAGATAACCCTTCTCGACTTAAGCTATGCTGTAAAT
57498 GATGTGCCTT
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
86 119 0.99
87 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (86 bp):
TTTGACAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATCTGGTTTGCCTCTGAGCTAATTGT
AATCGAACTTGAAGGTCTTTG
Found at i:58067 original size:106 final size:106
Alignment explanation
Indices: 57757--58897 Score: 1848
Period size: 106 Copynumber: 11.0 Consensus size: 106
57747 ATTGTGAAGT
* *
57757 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
57822 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* *
57863 TGAAATT-GGGAATTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
57927 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
57968 TGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
58033 CTGGAGTCCAATACCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
58074 TGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
58139 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
58180 TGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
58245 CTGGAGTCCAATATCCTTCG-TGCGAAGTTGAAATTGG---
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
58282 -G--A--A-G---TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
58338 TTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * *
58379 TGAAATTGGGAATTTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
58444 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* *
58485 TGAAATTAAGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
58550 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
58591 TGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
58656 CTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGG---
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * *
58694 -G--A--A-G---TTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAGCTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
58750 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * *
58791 TGAAATTGGGAATTTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
58856 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
58897 T
1 T
58898 CGAGCAATAT
Statistics
Matches: 972, Mismatches: 37, Indels: 52
0.92 0.03 0.05
Matches are distributed among these distances:
93 69 0.07
94 100 0.10
96 1 0.00
97 2 0.00
98 3 0.00
99 1 0.00
100 3 0.00
101 1 0.00
102 1 0.00
103 2 0.00
105 119 0.12
106 670 0.69
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
TGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
Found at i:58327 original size:411 final size:412
Alignment explanation
Indices: 57578--58897 Score: 2152
Period size: 411 Copynumber: 3.2 Consensus size: 412
57568 TTGAAACCGT
*
57578 GGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
1 GGAAATTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
* *
57643 CAATATTCTTCGTTGTGAAGTTGAAATTGG----G-AA--AGG------TTTATTGACAACCAGC
66 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGC
* * * *
57695 GGTCACTTCGTCGTGAGGATGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGA
131 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
*
57760 AATTGG----GAAATT--G------TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
196 AATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
57813 TTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTT
261 TTGCGTTGTCTGGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGG----G-AA----G--TTG
57878 TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
315 TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*
57943 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTA
380 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* *
57976 GGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
1 GGAAATTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
* *
58041 CAATACCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGC
66 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGC
58106 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
131 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
58171 AATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
196 AATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
58236 TTGCGTTGTCTGGAGTCCAATATCCTTCG-TGCGAAGTTGAAATTGGGAAGTTGTTTATTGACAA
261 TTGCGTTGTCTGGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGGAAGTTGTTTATTGACAA
*
58300 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATATCCTTCGCTGTGAA
326 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
58365 GTTGAAATTGGCTCTGAAATTG
391 GTTGAAATTGGCTCTGAAATTG
*
58387 GGAATTTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
1 GGAAATTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
*
58452 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAATTATTTGTTGACAACCAGC
66 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGC
*
58517 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGA
131 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
58582 AATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
196 AATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
58647 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGGAAGTTGTTTATTGACAA
261 TTGCGTTGTCTGGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGGAAGTTGTTTATTGACAA
* *
58712 CCAGTGGTCCCTTCGTCGTGAAGTTGAGCTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
326 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
58777 GTTGAAATTGGCTCTGAAATTG
391 GTTGAAATTGGCTCTGAAATTG
*
58799 GGAATTTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
1 GGAAATTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
58864 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
66 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
58898 CGAGCAATAT
Statistics
Matches: 871, Mismatches: 25, Indels: 38
0.93 0.03 0.04
Matches are distributed among these distances:
398 90 0.10
402 1 0.00
403 2 0.00
405 3 0.00
411 462 0.53
412 218 0.25
413 1 0.00
415 6 0.01
417 3 0.00
418 1 0.00
422 16 0.02
423 68 0.08
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (412 bp):
GGAAATTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
AATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTG
Found at i:58748 original size:200 final size:200
Alignment explanation
Indices: 58505--58893 Score: 715
Period size: 200 Copynumber: 1.9 Consensus size: 200
58495 AAATTATTTG
58505 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
58570 CTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTC
66 CTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTC
58635 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGGAAGTT
131 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGGAAGTT
58700 GTTTA
196 GTTTA
* *
58705 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAGCTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * *
58770 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTTTTTATTGACAACCAGCGGTCCCTTCGTC
66 CTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTC
*
58835 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
131 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGG
58894 CTCTCGAGCA
Statistics
Matches: 182, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 182 1.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (200 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTC
GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGGAAGTT
GTTTA
Found at i:62565 original size:19 final size:19
Alignment explanation
Indices: 62541--62578 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
62531 CTTAGTTGCG
* *
62541 AAAAATTGAAATTTAAATT
1 AAAAATTAAAAATTAAATT
62560 AAAAATTAAAAATTAAATT
1 AAAAATTAAAAATTAAATT
62579 CAAATTACTT
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:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AAAAATTAAAAATTAAATT
Found at i:64791 original size:24 final size:25
Alignment explanation
Indices: 64739--64791 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
64729 TCGGCCTACA
* *
64739 AAATAATTGTAATATATAAATTAAT
1 AAATAATAGTAATATATAAATAAAT
64764 -AATAATAGTAATA-ATAAATAAAT
1 AAATAATAGTAATATATAAATAAAT
64787 AAATA
1 AAATA
64792 CATAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (25 bp):
AAATAATAGTAATATATAAATAAAT
Found at i:68759 original size:16 final size:15
Alignment explanation
Indices: 68740--68781 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
68730 TTATAATGTG
68740 AAAATATTATTATTAT
1 AAAATATTATTATT-T
*
68756 AAAATATAATTATTT
1 AAAATATTATTATTT
*
68771 AAAATAATATT
1 AAAATATTATT
68782 TAATTTTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATATTATTATTT
Found at i:68775 original size:15 final size:16
Alignment explanation
Indices: 68740--68776 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
68730 TTATAATGTG
*
68740 AAAATATTATTATTAT
1 AAAATATAATTATTAT
68756 AAAATATAATTATT-T
1 AAAATATAATTATTAT
68771 AAAATA
1 AAAATA
68777 ATATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATATAATTATTAT
Found at i:69204 original size:19 final size:19
Alignment explanation
Indices: 69164--69210 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
69154 AACTAAATAA
* *
69164 AATAATATAATATTCACTT
1 AATAATATTATATTCACGT
69183 AATAATATTATATTTCA-GT
1 AATAATATTATA-TTCACGT
*
69202 AATATTATT
1 AATAATATT
69211 TCTAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (19 bp):
AATAATATTATATTCACGT
Found at i:71997 original size:36 final size:36
Alignment explanation
Indices: 71956--72031 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
71946 ATTTTCGGGA
*
71956 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
71992 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
72028 TTTT
1 TTTT
72032 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:74413 original size:18 final size:20
Alignment explanation
Indices: 74369--74414 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
74359 AGTATTTAGT
*
74369 AAAAACTAAATTATACATTA
1 AAAAATTAAATTATACATTA
**
74389 ATTAATTAAATTA-A-ATTA
1 AAAAATTAAATTATACATTA
74407 AAAAATTA
1 AAAAATTA
74415 TATATTTATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTAAATTATACATTA
Found at i:88582 original size:4 final size:4
Alignment explanation
Indices: 88573--88617 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
88563 GATCAGATGT
88573 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
88618 CAGACAGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:88622 original size:4 final size:4
Alignment explanation
Indices: 88615--88649 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
88605 ATAGATAGAT
88615 AGAC AGAC AGAC AGAC AGAC AGAC A-AGC AGAC AGA
1 AGAC AGAC AGAC AGAC AGAC AGAC AGA-C AGAC AGA
88650 TAGAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.03
4 27 0.93
5 1 0.03
ACGTcount: A:0.51, C:0.23, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:91000 original size:11 final size:11
Alignment explanation
Indices: 90984--91008 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
90974 TGTCATGTCA
90984 ATGCTAACAAT
1 ATGCTAACAAT
90995 ATGCTAACAAT
1 ATGCTAACAAT
91006 ATG
1 ATG
91009 GTGTTGCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (11 bp):
ATGCTAACAAT
Found at i:93409 original size:2 final size:2
Alignment explanation
Indices: 93398--93426 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
93388 TATACTTGTG
93398 TA TA -A 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
93427 AATGCACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:93495 original size:24 final size:24
Alignment explanation
Indices: 93459--93524 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
93449 TATGCATATG
* *
93459 TATA-ATATATATGTGTGTGTATT
1 TATATATACATATGTATGTGTATT
93482 TATATATACATATGTATGTGTATT
1 TATATATACATATGTATGTGTATT
93506 TATATATACATATGTATGT
1 TATATATACATATGTATGT
93525 TTGTGTGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 4 0.10
24 36 0.90
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (24 bp):
TATATATACATATGTATGTGTATT
Found at i:93562 original size:20 final size:20
Alignment explanation
Indices: 93515--93579 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
93505 TTATATATAC
* *
93515 ATATGTATGTT-TGTGTGAT
1 ATATGTATATTATGTGTTAT
* *
93534 ACATATATATTATGTGTTAT
1 ATATGTATATTATGTGTTAT
*
93554 ATATGTATATGA-GTGTATAT
1 ATATGTATATTATGTGT-TAT
93574 ATATGT
1 ATATGT
93580 TACACTTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.32
20 25 0.68
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (20 bp):
ATATGTATATTATGTGTTAT
Found at i:94724 original size:16 final size:16
Alignment explanation
Indices: 94705--94738 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
94695 TCAATTACAG
94705 GTCAGATTCATAACAA
1 GTCAGATTCATAACAA
* *
94721 GTCAGGTTGATAACAA
1 GTCAGATTCATAACAA
94737 GT
1 GT
94739 TAGGTAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (16 bp):
GTCAGATTCATAACAA
Found at i:107117 original size:13 final size:13
Alignment explanation
Indices: 107087--107117 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
107077 GATTTTCTTG
107087 GAAAATCAATTTT
1 GAAAATCAATTTT
107100 G-AAATCAATTTT
1 GAAAATCAATTTT
107112 GAAAAT
1 GAAAAT
107118 GTGAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (13 bp):
GAAAATCAATTTT
Done.