Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:2190811 original size:22 final size:22
Alignment explanation
Indices: 2190783--2190834 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2190773 TAATGATGTT
*
2190783 GAGCTAGAAGCCACTTGGCCTA
1 GAGCTAGAAGCCACTAGGCCTA
2190805 GAGCTAGAAGCCACTAGGCCTA
1 GAGCTAGAAGCCACTAGGCCTA
*
2190827 GAACTAGA
1 GAGCTAGA
2190835 CACTGATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (22 bp):
GAGCTAGAAGCCACTAGGCCTA
Found at i:2193856 original size:8 final size:8
Alignment explanation
Indices: 2193825--2193945 Score: 70
Period size: 9 Copynumber: 14.2 Consensus size: 8
2193815 ATTCATATTC
2193825 AAGACAAAA
1 AAGA-AAAA
2193834 AAG-AAAA
1 AAGAAAAA
*
2193841 GAGAAAAA
1 AAGAAAAA
2193849 ATAGAAAAA
1 A-AGAAAAA
* *
2193858 GAGAAGAAG
1 AAGAA-AAA
2193867 AAGAAAAA
1 AAGAAAAA
2193875 AAGATAAAA
1 AAGA-AAAA
2193884 AAG--AAA
1 AAGAAAAA
*
2193890 GAGAAAAGA
1 AAGAAAA-A
2193899 TAA-AAAAA
1 -AAGAAAAA
2193907 GAAGAAGAAA
1 -AAGAA-AAA
*
2193917 AGAGGAAAA
1 A-AGAAAAA
2193926 AAGAAAAA
1 AAGAAAAA
2193934 TAAGAAAGAA
1 -AAGAAA-AA
2193944 AA
1 AA
2193946 TAGAACATGT
Statistics
Matches: 88, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
6 5 0.06
7 6 0.07
8 25 0.28
9 43 0.49
10 9 0.10
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (8 bp):
AAGAAAAA
Found at i:2193876 original size:20 final size:18
Alignment explanation
Indices: 2193832--2193938 Score: 74
Period size: 21 Copynumber: 5.6 Consensus size: 18
2193822 TTCAAGACAA
2193832 AAAAGAAAAGAGAAAAAA-
1 AAAA-AAAAGAGAAAAAAG
* *
2193850 TAGAAAAAGAGAAGAAGAAG
1 AAAAAAAAGAGAA-AA-AAG
*
2193870 -AAAAAAAGATAAAAAAG
1 AAAAAAAAGAGAAAAAAG
*
2193887 AAAGAGAAAAGATAAAAAAAG
1 AAA-A-AAAAGA-GAAAAAAG
2193908 AAGAAGAAAAGAGGAAAAAAG
1 AA-AA-AAAAGA-GAAAAAAG
*
2193929 AAAAATAAGA
1 AAAAAAAAGA
2193939 AAGAAAATAG
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
17 12 0.16
18 8 0.11
19 18 0.25
20 8 0.11
21 26 0.36
22 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.04
Consensus pattern (18 bp):
AAAAAAAAGAGAAAAAAG
Found at i:2193878 original size:11 final size:11
Alignment explanation
Indices: 2193837--2193927 Score: 57
Period size: 11 Copynumber: 8.3 Consensus size: 11
2193827 GACAAAAAAG
2193837 AAAAG-AGAAA
1 AAAAGAAGAAA
2193847 AAATAGAA-AAA
1 AAA-AGAAGAAA
*
2193858 GAGAAGAAGAAGA
1 -AAAAGAAGAA-A
2193871 AAAA-AAGATAA
1 AAAAGAAGA-AA
*
2193882 AAAAGAA-AGAG
1 AAAAGAAGA-AA
*
2193893 AAAAG-ATAAA
1 AAAAGAAGAAA
*
2193903 AAAAGAAGAAG
1 AAAAGAAGAAA
*
2193914 AAAAGAGGAAA
1 AAAAGAAGAAA
2193925 AAA
1 AAA
2193928 GAAAAATAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
10 10 0.16
11 41 0.65
12 11 0.17
13 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:2193896 original size:21 final size:21
Alignment explanation
Indices: 2193851--2193931 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 21
2193841 GAGAAAAAAT
* *
2193851 AGAAAAAGA-GAAGAAG-AAG
1 AGAAAAAGATAAAAAAGAAAG
*
2193870 AAAAAAAGATAAAAAAGAAAG
1 AGAAAAAGATAAAAAAGAAAG
2193891 AG-AAAAGATAAAAAA-AGAAG
1 AGAAAAAGATAAAAAAGA-AAG
*
2193911 A-AGAAAAGAGGAAAAAAGAAA
1 AGA-AAAAGA-TAAAAAAGAAA
2193932 AATAAGAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
19 9 0.18
20 22 0.44
21 10 0.20
22 8 0.16
23 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.02
Consensus pattern (21 bp):
AGAAAAAGATAAAAAAGAAAG
Found at i:2193906 original size:49 final size:49
Alignment explanation
Indices: 2193825--2193942 Score: 150
Period size: 49 Copynumber: 2.3 Consensus size: 49
2193815 ATTCATATTC
*
2193825 AAGACAAAAAAGAAAAGAGAAAAAATAGAAAAAG-AGAAGAAGAAGA-AAAA
1 AAGA-AAAAAAG-AAAGAGAAAAAATAAAAAAAGAAGAAGAA-AAGAGAAAA
*
2193875 AAGATAAAAAAGAAAGAGAAAAGATAAAAAAAGAAGAAGAAAAGAGGAAAA
1 AAGA-AAAAAAGAAAGAGAAAAAATAAAAAAAGAAGAAGAAAAGA-GAAAA
2193926 AAGAAAAATAAGAAAGA
1 AAGAAAAA-AAGAAAGA
2193943 AAATAGAACA
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
49 23 0.38
50 22 0.36
51 16 0.26
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.03
Consensus pattern (49 bp):
AAGAAAAAAAGAAAGAGAAAAAATAAAAAAAGAAGAAGAAAAGAGAAAA
Found at i:2196207 original size:42 final size:40
Alignment explanation
Indices: 2196093--2196211 Score: 114
Period size: 42 Copynumber: 2.9 Consensus size: 40
2196083 TTTCCAAAAT
* * * *
2196093 TGATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
1 TGATAAATCCTTTGGGCCATCA-TAAGCCTTTCAAGCAAGA
* * *
2196134 TGATTAAATCCTTTGGGTCATATATAAGCCTTTTAAGCAAGA
1 TGA-TAAATCCTTTGGGCCAT-CATAAGCCTTTCAAGCAAGA
*
2196176 TGATAAGTCCTTTGGGCCATCCATAAGGCC-TTCAAG
1 TGATAAATCCTTTGGGCCAT-CATAA-GCCTTTCAAG
2196212 AAGGATGTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
41 27 0.43
42 35 0.56
43 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (40 bp):
TGATAAATCCTTTGGGCCATCATAAGCCTTTCAAGCAAGA
Found at i:2196468 original size:42 final size:42
Alignment explanation
Indices: 2196357--2196456 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
2196347 AAAAAATGGG
** * *
2196357 AAGTCCTTCGGGCCATCAATAAGTATTTCGAGCATGATGTCT
1 AAGTCCTTCGGGCCATCAATAAGCCTTTCGAGCAAGATGTAT
* * *
2196399 AAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATG-AT
1 AAGTCCTTCGGGCCATCAATAAGCCTTTCGAGCAAGATGTAT
2196440 AAGTCCTTCGGGCCATC
1 AAGTCCTTCGGGCCATC
2196457 CACAAGGCCT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (42 bp):
AAGTCCTTCGGGCCATCAATAAGCCTTTCGAGCAAGATGTAT
Found at i:2196517 original size:260 final size:259
Alignment explanation
Indices: 2196033--2196915 Score: 936
Period size: 260 Copynumber: 3.5 Consensus size: 259
2196023 ATTTTCAAAG
* * * * * *
2196033 TTTTTCAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTGATA
1 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
* * * *
2196098 AATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATATAAGC
66 AGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
** * * * * *
2196163 CTTTTAAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGGCCTTCAAGAAGGATGTTTTCACAA
131 CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGGCCTTTAGGCAGGATGCTTTCA-AA
* * * *
2196228 -GATTTTCAAAAAATGAGAAAATTATTTCCAAAGTTTATCATCTAAATCTTTTCTGAAAATTAAA
195 TGATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCAT-TAAATCTTTTCTGAAAATTGAA
2196292 A
259 A
** * * **
2196293 TTTTTGAAAAGTAAGAAAACGATTTTTAAAGTTTCTTACCTACTAAACTATTTCAAAAAATGGGA
1 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
*
2196358 AGTCCTTCGGGCCATCAATAAGTATTTCGAGCATGATG-TCTAAATCCTTCGGGTCATCTATAAG
66 AGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGAT-TAAATCCTTCGGGTCATCTATAAG
* *
2196422 CCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCACAAGGCCTTTGGGCAGGATGCTTTCAAA
130 CCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGGCCTTTAGGCAGGATGCTTTCAAA
* * * * *
2196487 TGATTTTCGAAAAATTAGAAAACGATTTCCAAAATTTCTCATTTAAATCTTTTCTAAAAATTGAT
195 TGATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCA-TTAAATCTTTTCTGAAAATTGAA
*
2196552 C
259 A
* *
2196553 TTTTT-AAAAGTGAGAAAATGATTTCCAAAG--T-TTA--T--T--AC---TT------A-G-CA
1 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
* * * * * *
2196597 AGTCCTTCGGGCCATCAATAAGTCTTTCGAACATGATGCTTAAATCCTTTGGATCATTTTTAAGC
66 AGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
* * * * *
2196662 CTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCTATAAGACCTTTAGGCAAGATGCTTTCATAT
131 CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGGCCTTTAGGCAGGATGCTTTCAAAT
* * * * * * *
2196727 GATAATTT-G-AAAATGAGAAAGTGATTTTCAACGTTTCTCATTTAGTATTTTCAGAAAA-TGAA
196 GAT--TTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCATTAAATCTTTTCTGAAAATTGAA
2196789 A
259 A
* * * *
2196790 TTTTTGAAAAGTAAGAAAATGATTTACAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTGACA
1 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
** * * * *
2196855 AGTCCTTTAGGCCATCAGTAATTCTTTCGAGCATGATGATTAAATCCTTCAGTTCATCTAT
66 AGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTAT
2196916 TAGTCTCACT
Statistics
Matches: 515, Mismatches: 81, Indels: 56
0.79 0.12 0.09
Matches are distributed among these distances:
237 8 0.02
238 36 0.07
239 144 0.28
240 4 0.01
241 7 0.01
243 1 0.00
245 1 0.00
247 3 0.01
250 4 0.01
252 1 0.00
254 1 0.00
256 3 0.01
257 2 0.00
258 52 0.10
259 24 0.05
260 223 0.43
261 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (259 bp):
TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
AGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGGCCTTTAGGCAGGATGCTTTCAAAT
GATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCATTAAATCTTTTCTGAAAATTGAAA
Found at i:2197070 original size:15 final size:15
Alignment explanation
Indices: 2197045--2197087 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2197035 TTTTCGAGTT
*
2197045 TTTAATATTATT-AA
1 TTTATTATTATTAAA
2197059 TATTATTATTATTAAA
1 T-TTATTATTATTAAA
*
2197075 TTTTTTATTATTA
1 TTTATTATTATTA
2197088 CAGGCCCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 21 0.84
16 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATTATTATTAAA
Found at i:2199930 original size:22 final size:22
Alignment explanation
Indices: 2199902--2199953 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2199892 TAATGATGTT
*
2199902 GAGCTAGAAGCCACTTGGCCTA
1 GAGCTAGAAGCCACTAGGCCTA
2199924 GAGCTAGAAGCCACTAGGCCTA
1 GAGCTAGAAGCCACTAGGCCTA
*
2199946 GAACTAGA
1 GAGCTAGA
2199954 CACTGATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (22 bp):
GAGCTAGAAGCCACTAGGCCTA
Found at i:2202972 original size:8 final size:8
Alignment explanation
Indices: 2202941--2203061 Score: 70
Period size: 9 Copynumber: 14.2 Consensus size: 8
2202931 ATTCATATTC
2202941 AAGACAAAA
1 AAGA-AAAA
2202950 AAG-AAAA
1 AAGAAAAA
*
2202957 GAGAAAAA
1 AAGAAAAA
2202965 ATAGAAAAA
1 A-AGAAAAA
* *
2202974 GAGAAGAAG
1 AAGAA-AAA
2202983 AAGAAAAA
1 AAGAAAAA
2202991 AAGATAAAA
1 AAGA-AAAA
2203000 AAG--AAA
1 AAGAAAAA
*
2203006 GAGAAAAGA
1 AAGAAAA-A
2203015 TAA-AAAAA
1 -AAGAAAAA
2203023 GAAGAAGAAA
1 -AAGAA-AAA
*
2203033 AGAGGAAAA
1 A-AGAAAAA
2203042 AAGAAAAA
1 AAGAAAAA
2203050 TAAGAAAGAA
1 -AAGAAA-AA
2203060 AA
1 AA
2203062 TAGAACATGT
Statistics
Matches: 88, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
6 5 0.06
7 6 0.07
8 25 0.28
9 43 0.49
10 9 0.10
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (8 bp):
AAGAAAAA
Found at i:2202992 original size:20 final size:18
Alignment explanation
Indices: 2202948--2203054 Score: 74
Period size: 21 Copynumber: 5.6 Consensus size: 18
2202938 TTCAAGACAA
2202948 AAAAGAAAAGAGAAAAAA-
1 AAAA-AAAAGAGAAAAAAG
* *
2202966 TAGAAAAAGAGAAGAAGAAG
1 AAAAAAAAGAGAA-AA-AAG
*
2202986 -AAAAAAAGATAAAAAAG
1 AAAAAAAAGAGAAAAAAG
*
2203003 AAAGAGAAAAGATAAAAAAAG
1 AAA-A-AAAAGA-GAAAAAAG
2203024 AAGAAGAAAAGAGGAAAAAAG
1 AA-AA-AAAAGA-GAAAAAAG
*
2203045 AAAAATAAGA
1 AAAAAAAAGA
2203055 AAGAAAATAG
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
17 12 0.16
18 8 0.11
19 18 0.25
20 8 0.11
21 26 0.36
22 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.04
Consensus pattern (18 bp):
AAAAAAAAGAGAAAAAAG
Found at i:2202994 original size:11 final size:11
Alignment explanation
Indices: 2202953--2203043 Score: 57
Period size: 11 Copynumber: 8.3 Consensus size: 11
2202943 GACAAAAAAG
2202953 AAAAG-AGAAA
1 AAAAGAAGAAA
2202963 AAATAGAA-AAA
1 AAA-AGAAGAAA
*
2202974 GAGAAGAAGAAGA
1 -AAAAGAAGAA-A
2202987 AAAA-AAGATAA
1 AAAAGAAGA-AA
*
2202998 AAAAGAA-AGAG
1 AAAAGAAGA-AA
*
2203009 AAAAG-ATAAA
1 AAAAGAAGAAA
*
2203019 AAAAGAAGAAG
1 AAAAGAAGAAA
*
2203030 AAAAGAGGAAA
1 AAAAGAAGAAA
2203041 AAA
1 AAA
2203044 GAAAAATAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
10 10 0.16
11 41 0.65
12 11 0.17
13 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:2203012 original size:21 final size:21
Alignment explanation
Indices: 2202967--2203047 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 21
2202957 GAGAAAAAAT
* *
2202967 AGAAAAAGA-GAAGAAG-AAG
1 AGAAAAAGATAAAAAAGAAAG
*
2202986 AAAAAAAGATAAAAAAGAAAG
1 AGAAAAAGATAAAAAAGAAAG
2203007 AG-AAAAGATAAAAAA-AGAAG
1 AGAAAAAGATAAAAAAGA-AAG
*
2203027 A-AGAAAAGAGGAAAAAAGAAA
1 AGA-AAAAGA-TAAAAAAGAAA
2203048 AATAAGAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
19 9 0.18
20 22 0.44
21 10 0.20
22 8 0.16
23 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.02
Consensus pattern (21 bp):
AGAAAAAGATAAAAAAGAAAG
Found at i:2203022 original size:49 final size:49
Alignment explanation
Indices: 2202941--2203058 Score: 150
Period size: 49 Copynumber: 2.3 Consensus size: 49
2202931 ATTCATATTC
*
2202941 AAGACAAAAAAGAAAAGAGAAAAAATAGAAAAAG-AGAAGAAGAAGA-AAAA
1 AAGA-AAAAAAG-AAAGAGAAAAAATAAAAAAAGAAGAAGAA-AAGAGAAAA
*
2202991 AAGATAAAAAAGAAAGAGAAAAGATAAAAAAAGAAGAAGAAAAGAGGAAAA
1 AAGA-AAAAAAGAAAGAGAAAAAATAAAAAAAGAAGAAGAAAAGA-GAAAA
2203042 AAGAAAAATAAGAAAGA
1 AAGAAAAA-AAGAAAGA
2203059 AAATAGAACA
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
49 23 0.38
50 22 0.36
51 16 0.26
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.03
Consensus pattern (49 bp):
AAGAAAAAAAGAAAGAGAAAAAATAAAAAAAGAAGAAGAAAAGAGAAAA
Found at i:2205314 original size:42 final size:40
Alignment explanation
Indices: 2205200--2205318 Score: 114
Period size: 42 Copynumber: 2.9 Consensus size: 40
2205190 TTTCCAAAAT
* * * *
2205200 TGATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
1 TGATAAATCCTTTGGGCCATCA-TAAGCCTTTCAAGCAAGA
* * *
2205241 TGATTAAATCCTTTGGGTCATATATAAGCCTTTTAAGCAAGA
1 TGA-TAAATCCTTTGGGCCAT-CATAAGCCTTTCAAGCAAGA
*
2205283 TGATAAGTCCTTTGGGCCATCCATAAGGCC-TTCAAG
1 TGATAAATCCTTTGGGCCAT-CATAA-GCCTTTCAAG
2205319 AAGGATGTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
41 27 0.43
42 35 0.56
43 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (40 bp):
TGATAAATCCTTTGGGCCATCATAAGCCTTTCAAGCAAGA
Found at i:2205575 original size:42 final size:42
Alignment explanation
Indices: 2205464--2205563 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
2205454 CAAAAATGGG
** * *
2205464 AAGTCCTTCGGGCCATCAATAAGTATTTCGAGCATGATGTCT
1 AAGTCCTTCGGGCCATCAATAAGCCTTTCGAGCAAGATGTAT
* * *
2205506 AAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATG-AT
1 AAGTCCTTCGGGCCATCAATAAGCCTTTCGAGCAAGATGTAT
2205547 AAGTCCTTCGGGCCATC
1 AAGTCCTTCGGGCCATC
2205564 CACAAGGCCT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (42 bp):
AAGTCCTTCGGGCCATCAATAAGCCTTTCGAGCAAGATGTAT
Found at i:2205623 original size:260 final size:259
Alignment explanation
Indices: 2205140--2206022 Score: 954
Period size: 260 Copynumber: 3.5 Consensus size: 259
2205130 ATTTTCAAAG
* * * * * * *
2205140 TTTTTCAAAAGTAAGAGAGCAATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTGATA
1 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
* * *
2205205 AATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATATAAGC
66 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
** * * * *
2205270 CTTTTAAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGGCCTTCAAGAAGGATGTTTTCACAA
131 CTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGGCCTTTAGGCAGGATGCTTTCA-AA
* * *
2205335 -GATTTTCAAAAAATGAGAAAATGATTTCCAAAGTTTATCATCTAAATCTTTTCTGAAAATTAAA
195 TGATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCAT-TAAATCTTTTCTGAAAATTGAA
2205399 A
259 A
** * **
2205400 TTTTTGAAAAGTAAGAAAACGATTTTTAAAGTTTCTTACCTACTAAACTATTTCCAAAAATGGGA
1 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
* *
2205465 AGTCCTTCGGGCCATCAATAAGTATTTCGAGCATGATG-TCTAAATCCTTCGGGTCATCTATAAG
66 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAT-TAAATCCTTCGGGTCATCTATAAG
* * *
2205529 CCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCACAAGGCCTTTGGGCAGGATGCTTTCAAA
130 CCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGGCCTTTAGGCAGGATGCTTTCAAA
* * * * *
2205594 TGATTTTCGAAAAATTAGAAAACGATTTCCAAAATTTCTCATTTAAATCTTTTCTAAAAATTGAT
195 TGATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCA-TTAAATCTTTTCTGAAAATTGAA
*
2205659 C
259 A
* *
2205660 TTTTT-AAAAGTGAGAAAATGATTTCCAAAG--T-TTA--T--T--AC---TT------A-G-CA
1 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
* * * * *
2205704 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCGGATCATTTTTAAGC
66 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
* * * * * *
2205769 CTTTCGAGCAAGATGATAAGTCCTTTGAGCCATCTATAAGACCTTTAGGCAAGATACTTTCATAT
131 CTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGGCCTTTAGGCAGGATGCTTTCAAAT
* * * * * * *
2205834 GATAATTT-G-AAAATGAGAAAGTGATTTTCAACGTTTCTCATTTAGTATTTTCAGAAAA-TGAA
196 GAT--TTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCATTAAATCTTTTCTGAAAATTGAA
2205896 A
259 A
* * * *
2205897 TTTTTGAAAAGTAAGAAAATGATTTACAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTGACA
1 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
** * * *
2205962 AGTCCTTTAGGCCATCAGTAATTCTTTCGAGCATGATGATTAAATCCTTCAGTTCATCTAT
66 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTAT
2206023 TAGTCTCACT
Statistics
Matches: 516, Mismatches: 80, Indels: 56
0.79 0.12 0.09
Matches are distributed among these distances:
237 8 0.02
238 36 0.07
239 142 0.28
240 4 0.01
241 7 0.01
243 1 0.00
245 1 0.00
247 3 0.01
250 4 0.01
252 1 0.00
254 1 0.00
256 3 0.01
257 2 0.00
258 54 0.10
259 24 0.05
260 224 0.43
261 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (259 bp):
TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATGACA
AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
CTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGGCCTTTAGGCAGGATGCTTTCAAAT
GATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCATTAAATCTTTTCTGAAAATTGAAA
Found at i:2205771 original size:239 final size:237
Alignment explanation
Indices: 2205464--2205935 Score: 601
Period size: 239 Copynumber: 2.0 Consensus size: 237
2205454 CAAAAATGGG
* *
2205464 AAGTCCTTCGGGCCATCAATAAGTATTTCGAGCATGATGTCTAAATCCTTCGGGTCATCTATAAG
1 AAGTCCTTCGGGCCATCAATAAGTATTTCGAACATGATGTCTAAATCCTTCGGATCATCTATAAG
* * * * *
2205529 CCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCACAAGGCCTTTGGGCAGGATGCTTTCAAA
66 CCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCACAAGACCTTTAGGCAAGATACTTTCAAA
* *
2205594 TGAT-TTTCGAAAAATTAGAAAACGATTTCCAAAATTTCTCATTTAAATCTTTTCTA-AAAATTG
131 TGATATTT-G-AAAATGAGAAAACGATTTCCAAAATTTCTCATTT-AATATTTTC-AGAAAA-TG
** * *
2205657 ATCTTTTT-AAAAGTGAGAAAATGATTTCCAAAGTTTATTACTTAGC
191 AAATTTTTGAAAAGTAAGAAAATGATTTACAAAGTTTATTACTTAGC
* * * *
2205703 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAACATGATG-CTTAAATCCTTCGGATCATTTTTAA
1 AAGTCCTTCGGGCCATCAATAAGTATTTCGAACATGATGTC-TAAATCCTTCGGATCATCTATAA
* * * *
2205767 GCCTTTCGAGCAAGATGATAAGTCCTTTGAGCCATCTATAAGACCTTTAGGCAAGATACTTTCAT
65 GCCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCACAAGACCTTTAGGCAAGATACTTTCAA
** * ** *
2205832 ATGATAATTTGAAAATGAGAAAGTGATTTTCAACGTTTCTCATTTAGTATTTTCAGAAAATGAAA
130 ATGAT-ATTTGAAAATGAGAAAACGATTTCCAAAATTTCTCATTTAATATTTTCAGAAAATGAAA
*
2205897 TTTTTGAAAAGTAAGAAAATGATTTACAAAGTTTCTTAC
194 TTTTTGAAAAGTAAGAAAATGATTTACAAAGTTTATTAC
2205936 CTAGTAAATT
Statistics
Matches: 200, Mismatches: 28, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
237 9 0.05
238 42 0.21
239 145 0.73
240 1 0.00
241 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (237 bp):
AAGTCCTTCGGGCCATCAATAAGTATTTCGAACATGATGTCTAAATCCTTCGGATCATCTATAAG
CCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCACAAGACCTTTAGGCAAGATACTTTCAAA
TGATATTTGAAAATGAGAAAACGATTTCCAAAATTTCTCATTTAATATTTTCAGAAAATGAAATT
TTTGAAAAGTAAGAAAATGATTTACAAAGTTTATTACTTAGC
Found at i:2206191 original size:16 final size:16
Alignment explanation
Indices: 2206156--2206196 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2206146 GAGTTTTTAA
2206156 TATTATT-AATATTAT
1 TATTATTAAATATTAT
* *
2206171 TATTATTAAATTTTTT
1 TATTATTAAATATTAT
2206187 TATTATTAAA
1 TATTATTAAA
2206197 GGCCCAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATTAAATATTAT
Found at i:2207390 original size:2 final size:2
Alignment explanation
Indices: 2207383--2207408 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2207373 ATTTTAGTAT
2207383 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
2207409 CGTGTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2216184 original size:37 final size:39
Alignment explanation
Indices: 2216130--2216212 Score: 109
Period size: 37 Copynumber: 2.2 Consensus size: 39
2216120 ATATTATACA
* *
2216130 ATAT-TATTTATATATCCTTAATATTTTGTT-A-ATATT
1 ATATATATATATATATCCTTAATATTTTCTTAACATATT
* *
2216166 ATATATATATATATATCCTTCATTTTTTCTTAACATATT
1 ATATATATATATATATCCTTAATATTTTCTTAACATATT
2216205 ATATATAT
1 ATATATAT
2216213 CCCCATTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 4 0.10
37 22 0.55
38 1 0.03
39 13 0.32
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.55
Consensus pattern (39 bp):
ATATATATATATATATCCTTAATATTTTCTTAACATATT
Found at i:2216896 original size:34 final size:34
Alignment explanation
Indices: 2216853--2216931 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
2216843 TTTTTGGTCT
*
2216853 ACCCGACCCGAGAACAATGAATCATATACCCGAG
1 ACCCGACCCGAGAACAAGGAATCATATACCCGAG
* *
2216887 ACCCGACCCGAGAACAAGGAATCATCTACTCGAG
1 ACCCGACCCGAGAACAAGGAATCATATACCCGAG
2216921 ACCCGACCCGA
1 ACCCGACCCGA
2216932 CCCAATTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.10
Consensus pattern (34 bp):
ACCCGACCCGAGAACAAGGAATCATATACCCGAG
Found at i:2217691 original size:20 final size:20
Alignment explanation
Indices: 2217599--2217693 Score: 59
Period size: 20 Copynumber: 4.7 Consensus size: 20
2217589 AATATAACAT
* *
2217599 GTTGAAATTTGACAAATCCT
1 GTTGAAATTTGACAAAACCG
* **
2217619 GTTTAGAA-TTGACAAAAGAG
1 GTTGA-AATTTGACAAAACCG
** **
2217639 GTAACAAATTTGACAAAATTG
1 GT-TGAAATTTGACAAAACCG
*
2217660 GTTGGTAA-TTGACAAAACCG
1 GTT-GAAATTTGACAAAACCG
2217680 GTTGAAATTTGACA
1 GTTGAAATTTGACA
2217694 TAATTGATTT
Statistics
Matches: 55, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
19 3 0.05
20 35 0.64
21 17 0.31
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (20 bp):
GTTGAAATTTGACAAAACCG
Found at i:2218224 original size:199 final size:199
Alignment explanation
Indices: 2217875--2218243 Score: 587
Period size: 199 Copynumber: 1.9 Consensus size: 199
2217865 ATATATGTTA
2217875 TATATAGGTATCAATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCACGCAAAATGTATCGAT
1 TATATAGGTATCAATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCACGCAAAATGTATCGAT
* * *
2217940 ACACATGTATAAAGTATCAATACTTGGAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATT
66 ACACATATATAAAGTATCAATACTTAGAATTTCGAAACCGATTACTATAAAGTAATAGGTAAATT
* * * *
2218005 TACAATGTAAACGGTAAAAGTCTACATGTATATTGATAATGAGCGTAAATACCAAGCATCGATAT
131 TACAATGAAAACGATAAAAGTCTACAGGTATAATGATAATGAGCGTAAATACCAAGCATCGATAT
2218070 TGTC
196 TGTC
* *
2218074 TATATAGGTATCGATAC-TTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATGTATCGA
1 TATATAGGTATCAATACTTTTAGTCCAGTATGCTTCTC-AACAATTTGCACGCAAAATGTATCGA
* * * * *
2218138 TACACATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTATAAAGTAATATGTTAAT
65 TACACATATATAAAGTATCAATACTTAGAATTTCGAAACCGATTACTATAAAGTAATAGGTAAAT
*
2218203 TTACAATGAAAACGATAAAAGTCTACCGGTATAATGATAAT
130 TTACAATGAAAACGATAAAAGTCTACAGGTATAATGATAAT
2218244 AGGTTTAAAC
Statistics
Matches: 154, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
198 19 0.12
199 135 0.88
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (199 bp):
TATATAGGTATCAATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCACGCAAAATGTATCGAT
ACACATATATAAAGTATCAATACTTAGAATTTCGAAACCGATTACTATAAAGTAATAGGTAAATT
TACAATGAAAACGATAAAAGTCTACAGGTATAATGATAATGAGCGTAAATACCAAGCATCGATAT
TGTC
Found at i:2218286 original size:199 final size:199
Alignment explanation
Indices: 2217875--2218289 Score: 550
Period size: 199 Copynumber: 2.1 Consensus size: 199
2217865 ATATATGTTA
* *
2217875 TATATAGGTATCAATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCACGCAAAATGTATCGAT
1 TATATAAGTATCGATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCACGCAAAATGTATCGAT
* * *
2217940 ACACATGTATAAAGTATCAATACTTGGAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATT
66 ACACATATATAAAGTATCAATACTTAGAATTTCGAAACCGATTACTATAAAGTAATAGGTAAATT
* * * * * *
2218005 TACAATGTAAACGGTAAAAGTCTACATGTATATTGATAATGAGCGTAAATACCAAGCATCGATAT
131 TACAATGAAAACGATAAAAGTCTACAGGTATAATGATAATGAGCGTAAACACCAAGCATCGATAA
**
2218070 TGTC
196 CATC
* *
2218074 TATATAGGTATCGATAC-TTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATGTATCGA
1 TATATAAGTATCGATACTTTTAGTCCAGTATGCTTCTC-AACAATTTGCACGCAAAATGTATCGA
* * * * *
2218138 TACACATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTATAAAGTAATATGTTAAT
65 TACACATATATAAAGTATCAATACTTAGAATTTCGAAACCGATTACTATAAAGTAATAGGTAAAT
* * *
2218203 TTACAATGAAAACGATAAAAGTCTACCGGTATAATGATAAT-AG-GTTTAAACATCAAGTATCGA
130 TTACAATGAAAACGATAAAAGTCTACAGGTATAATGATAATGAGCG--TAAACACCAAGCATCGA
*
2218266 TACACATG
193 TA-ACATC
2218274 TATA-AAGTATCGATAC
1 TATATAAGTATCGATAC
2218290 GTGAAATTTC
Statistics
Matches: 189, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
197 1 0.01
198 21 0.11
199 162 0.86
200 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (199 bp):
TATATAAGTATCGATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCACGCAAAATGTATCGAT
ACACATATATAAAGTATCAATACTTAGAATTTCGAAACCGATTACTATAAAGTAATAGGTAAATT
TACAATGAAAACGATAAAAGTCTACAGGTATAATGATAATGAGCGTAAACACCAAGCATCGATAA
CATC
Found at i:2218654 original size:118 final size:113
Alignment explanation
Indices: 2218492--2218885 Score: 319
Period size: 118 Copynumber: 3.5 Consensus size: 113
2218482 AAATAAATCA
* *
2218492 AGTAATTAACATATTTTATTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAACAGACACTACA
1 AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGC-TTAAACAGACA-TACA
2218557 TATTACATTAAATAAATGGTACTTGTTAGGTTATTATGGTTGATAATATTTCC
64 TATTACATTAAATAAAT--TACTTGTTA-GTTATTATGGTTGATAATATTTCC
* * * * **
2218610 AGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTA-ACA
1 AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAAAC--AGACATACA
* ** ** * * * ** *
2218674 TTTTAGGCGCTACCT-AA-TA-TT-TT-G--ATAAT-ATTGATAACAAATCA
64 TATTA--CATTAAATAAATTACTTGTTAGTTATTATGGTTGATAATATTTCC
* * * *
2218718 AGTAATTAA-C-A--TTGTTATCGTTGGATTTCTAAAGCCCCATCAGCTTTAAACAGACGTTACC
1 AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGC-TTAAACAGAC-ATACA
* *
2218779 TATTATATTAAATAAATACTACTTGTTATGTTATTATGGTTGATAATGTTTCC
64 TATTACATTAAATAAAT--TACTTGTTA-GTTATTATGGTTGATAATATTTCC
* * *
2218832 AGTAATTAACTTATTTTGTTATCGTCGGATTTATAAGGCTCCATCAGCTTAAAC
1 AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAAAC
2218886 TTTGGTAACA
Statistics
Matches: 207, Mismatches: 47, Indels: 45
0.69 0.16 0.15
Matches are distributed among these distances:
103 4 0.02
104 30 0.14
105 12 0.06
106 1 0.00
107 3 0.01
108 21 0.10
109 6 0.03
111 2 0.01
113 6 0.03
114 20 0.10
115 2 0.01
116 1 0.00
117 19 0.09
118 74 0.36
119 6 0.03
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (113 bp):
AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAAACAGACATACATA
TTACATTAAATAAATTACTTGTTAGTTATTATGGTTGATAATATTTCC
Found at i:2218871 original size:222 final size:223
Alignment explanation
Indices: 2218469--2219064 Score: 874
Period size: 222 Copynumber: 2.7 Consensus size: 223
2218459 TGGTAATAAA
* * *
2218469 TTGATAATATTGAAAATAAATCAAGTAATTAACATATTTTATTATCGTCGGATTTCTAAGGCCCC
1 TTGATAATATTGATAACAAATCAAGTAATTAAC-TA-TTTGTTATCGTCGGATTTCTAAGGCCCC
* * *
2218534 ATCAGCTTTAAACAGACACTACATATTACATTAAATAAATGGTACTTGTTAGGTTATTATGGTTG
64 ATCAGCTTTAAACAGACGCTACATATTA-ATTAAATAAATGCTACTTGTTATGTTATTATGGTTG
* *
2218599 ATAATATTTCCAGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGCTCCATCAGCTTAAAC
128 ATAATGTTTCCAGTAATTAACCTATTTTGTTATCATCAGATTTATAAGGCTCCATCAGCTTAAAC
*
2218664 TTTGGTAACATTTTAGGCGCTACCTAATATT
193 TTTGGTAACATTTTAGGCGCTACCTAATATG
* *
2218695 TTGATAATATTGATAACAAATCAAGTAATTAAC-A-TTGTTATCGTTGGATTTCTAAAGCCCCAT
1 TTGATAATATTGATAACAAATCAAGTAATTAACTATTTGTTATCGTCGGATTTCTAAGGCCCCAT
* * *
2218758 CAGCTTTAAACAGACGTTACCTATTATATTAAATAAATACTACTTGTTATGTTATTATGGTTGAT
66 CAGCTTTAAACAGACGCTACATATTA-ATTAAATAAATGCTACTTGTTATGTTATTATGGTTGAT
* * *
2218823 AATGTTTCCAGTAATTAACTTATTTTGTTATCGTCGGATTTATAAGGCTCCATCAGCTTAAACTT
130 AATGTTTCCAGTAATTAACCTATTTTGTTATCATCAGATTTATAAGGCTCCATCAGCTTAAACTT
*
2218888 TGGTAACATTTTAGGCGGTACCTAATATG
195 TGGTAACATTTTAGGCGCTACCTAATATG
*
2218917 TTGATAATATTGATAACAAATAAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCC
1 TTGATAATATTGATAACAAATCAAGTAATTAA-CTA-TTTGTTATCGTCGGATTTCTAAGGCCCC
** * * * *
2218982 ATCAGCTTTAATA-AGACGCTATTTATTAAGTTACATAAGTGCTACCTGTTATGTTGTTATGGTT
64 ATCAGCTTTAA-ACAGACGCTACATATTAA-TTAAATAAATGCTACTTGTTATGTTATTATGGTT
2219046 GATAATGTTTCCAGTAATT
127 GATAATGTTTCCAGTAATT
2219065 CACCGGTTAT
Statistics
Matches: 334, Mismatches: 30, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
222 202 0.60
223 1 0.00
224 2 0.01
225 1 0.00
226 127 0.38
227 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (223 bp):
TTGATAATATTGATAACAAATCAAGTAATTAACTATTTGTTATCGTCGGATTTCTAAGGCCCCAT
CAGCTTTAAACAGACGCTACATATTAATTAAATAAATGCTACTTGTTATGTTATTATGGTTGATA
ATGTTTCCAGTAATTAACCTATTTTGTTATCATCAGATTTATAAGGCTCCATCAGCTTAAACTTT
GGTAACATTTTAGGCGCTACCTAATATG
Found at i:2221565 original size:113 final size:113
Alignment explanation
Indices: 2221367--2221578 Score: 320
Period size: 113 Copynumber: 1.9 Consensus size: 113
2221357 ATTAAGATTG
* *
2221367 TTTCCCTAGAAACCCCAATCTTGAATCTCTTAGGACTTGTATCCTAAAATTCTTAATCTAGTTTT
1 TTTCCCTAGAAACCCCAATCTTGAATCTCTTAGGACTTGTATCCTAAAATGCTTAATCTAGCTTT
* *
2221432 TCTTAAGATTATTTCTCTAGAAAGCTCAACTTTTTCTTTCATAGATAC
66 TCTTAAGATCATTTCTCTAGAAACCTCAACTTTTTCTTTCATAGATAC
* * *
2221480 TTTCCCTAGAAACCTCAATCTTGACTCTCTTAGGATTTGTATCCTAGAAA-GCTTAATCTAGACT
1 TTTCCCTAGAAACCCCAATCTTGAATCTCTTAGGACTTGTATCCTA-AAATGCTTAATCTAG-CT
*
2221544 TTT-TTAGGATCATTTCTCTAGAAACCTCAACTTTT
64 TTTCTTAAGATCATTTCTCTAGAAACCTCAACTTTT
2221579 CCTGACCATC
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
113 82 0.92
114 7 0.08
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.41
Consensus pattern (113 bp):
TTTCCCTAGAAACCCCAATCTTGAATCTCTTAGGACTTGTATCCTAAAATGCTTAATCTAGCTTT
TCTTAAGATCATTTCTCTAGAAACCTCAACTTTTTCTTTCATAGATAC
Found at i:2231158 original size:5 final size:5
Alignment explanation
Indices: 2231132--2231178 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
2231122 TTCTATTACT
* * *
2231132 TATTA TAATA TAAATA TATTA TGTTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA T-ATTA TATTA TATTA TATTA TATTA TATTA TATTA T
2231179 GTATTACAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 32 0.86
6 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
TATTA
Found at i:2232363 original size:90 final size:90
Alignment explanation
Indices: 2232210--2232387 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
2232200 CCTAACACAC
* * * *
2232210 CCTTTTATAGCCAAGTTACGCTAGTCATATTAGGGGTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
2232275 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
2232300 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
2232365 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
2232388 TTCGGGATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:2234049 original size:19 final size:18
Alignment explanation
Indices: 2234015--2234057 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
2234005 TTAGCATTGT
2234015 GAAAAGAAAATAATGAAA
1 GAAAAGAAAATAATGAAA
2234033 GAAAAGTAAAA-AGATGAAA
1 GAAAAG-AAAATA-ATGAAA
2234052 GAAAAG
1 GAAAAG
2234058 GAGAACTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (18 bp):
GAAAAGAAAATAATGAAA
Found at i:2234220 original size:19 final size:19
Alignment explanation
Indices: 2234196--2234233 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2234186 CTACCAAGAA
2234196 TCCT-AACAAAATAACTAAT
1 TCCTAAACAAAATAA-TAAT
*
2234215 TCCTAAATAAAATAATAAT
1 TCCTAAACAAAATAATAAT
2234234 AAAATTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (19 bp):
TCCTAAACAAAATAATAAT
Found at i:2234274 original size:3 final size:3
Alignment explanation
Indices: 2234266--2234378 Score: 145
Period size: 3 Copynumber: 37.3 Consensus size: 3
2234256 CATTCCACCA
2234266 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
2234314 TAT TAT TAT TATT TAT TAT TAT TAC TAG TAC TAC TAC TAC TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2234360 TTT TAT TAT TAT TGT TAT T
1 TAT TAT TAT TAT TAT TAT T
2234379 TACAAGCTAC
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
3 98 0.97
4 3 0.03
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2239127 original size:11 final size:11
Alignment explanation
Indices: 2239113--2239155 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2239103 TCAACTTGTA
*
2239113 ATTAGTTTGTT
1 ATTAGTTAGTT
*
2239124 ATTAGTTAGTCC
1 ATTAGTTAGT-T
2239136 ATTAGTTAGTT
1 ATTAGTTAGTT
*
2239147 GTTAGTTAG
1 ATTAGTTAG
2239156 CTGTTGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (11 bp):
ATTAGTTAGTT
Found at i:2254837 original size:20 final size:20
Alignment explanation
Indices: 2254812--2254878 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
2254802 CGCAACGGTC
2254812 ATCGCAATGCGATTGATAGA
1 ATCGCAATGCGATTGATAGA
2254832 ATCGCAATGCGATTGATAGA
1 ATCGCAATGCGATTGATAGA
2254852 ATCGCAATGCGATTGATAGA
1 ATCGCAATGCGATTGATAGA
2254872 ATCGCAA
1 ATCGCAA
2254879 CGTTGAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATTGATAGA
Found at i:2254984 original size:6 final size:6
Alignment explanation
Indices: 2254973--2255042 Score: 105
Period size: 6 Copynumber: 12.5 Consensus size: 6
2254963 GACACGTATT
2254973 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2255020 ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
2255043 CGAGACGAGA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 25 0.39
6 39 0.61
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2255717 original size:6 final size:6
Alignment explanation
Indices: 2255706--2255762 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
2255696 TCTCGTCTCG
*
2255706 GGTCGT GGTCGT TGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2255754 GGTCGT GGT
1 GGTCGT GGT
2255763 AATACGTGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
GGTCGT
Found at i:2255841 original size:20 final size:20
Alignment explanation
Indices: 2255818--2255864 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2255808 AAAATTCGTA
2255818 TGCGATTCTATAAATCGCAT
1 TGCGATTCTATAAATCGCAT
*
2255838 TGCGATTCTATCAATCGCAT
1 TGCGATTCTATAAATCGCAT
2255858 TGCGATT
1 TGCGATT
2255865 TTCTTCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
TGCGATTCTATAAATCGCAT
Found at i:2258694 original size:15 final size:16
Alignment explanation
Indices: 2258674--2258707 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2258664 CTATGTATGA
*
2258674 ATTTTTTCCG-AAAAT
1 ATTTTTTACGTAAAAT
2258689 ATTTTTTACGTAAAAT
1 ATTTTTTACGTAAAAT
2258705 ATT
1 ATT
2258708 GATATCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTTTTACGTAAAAT
Found at i:2259012 original size:30 final size:30
Alignment explanation
Indices: 2258976--2259054 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 30
2258966 AAAACCGAAT
*
2258976 TAAACGGGGATGGGGAAAAACTGTTTATGC
1 TAAACGGGGATGGGGAAAAACCGTTTATGC
*
2259006 TAAACGGAGACGGGGATGGGGAAAAACCGTTTATGT
1 T--A---A-ACGGGGATGGGGAAAAACCGTTTATGC
2259042 TAAACGGGGATGG
1 TAAACGGGGATGG
2259055 AGACGGGGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
30 11 0.27
31 1 0.02
32 1 0.02
34 1 0.02
35 1 0.02
36 26 0.63
ACGTcount: A:0.33, C:0.10, G:0.37, T:0.20
Consensus pattern (30 bp):
TAAACGGGGATGGGGAAAAACCGTTTATGC
Found at i:2259063 original size:36 final size:36
Alignment explanation
Indices: 2258987--2259063 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
2258977 AAACGGGGAT
* * *
2258987 GGGGAAAAACTGTTTATGCTAAACGGAGACGGGGAT
1 GGGGAAAAACCGTTTATGCTAAACGGAGACGGAGAC
* * *
2259023 GGGGAAAAACCGTTTATGTTAAACGGGGATGGAGAC
1 GGGGAAAAACCGTTTATGCTAAACGGAGACGGAGAC
2259059 GGGGA
1 GGGGA
2259064 CGGGTTTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.10, G:0.39, T:0.18
Consensus pattern (36 bp):
GGGGAAAAACCGTTTATGCTAAACGGAGACGGAGAC
Found at i:2259063 original size:42 final size:36
Alignment explanation
Indices: 2258979--2259048 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
2258969 ACCGAATTAA
*
2258979 ACGGGGATGGGGAAAAACTGTTTATGCTAAACGGAG
1 ACGGGGATGGGGAAAAACCGTTTATGCTAAACGGAG
*
2259015 ACGGGGATGGGGAAAAACCGTTTATGTTAAACGG
1 ACGGGGATGGGGAAAAACCGTTTATGCTAAACGG
2259049 GGATGGAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.33, C:0.11, G:0.36, T:0.20
Consensus pattern (36 bp):
ACGGGGATGGGGAAAAACCGTTTATGCTAAACGGAG
Found at i:2259106 original size:12 final size:12
Alignment explanation
Indices: 2259078--2259114 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
2259068 TTTAGTAATC
*
2259078 CCCGCCCCGATTA
1 CCCGGCCCGA-TA
2259091 CCCGGCCCGATA
1 CCCGGCCCGATA
2259103 CCCGGCCCGATA
1 CCCGGCCCGATA
2259115 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (12 bp):
CCCGGCCCGATA
Found at i:2259205 original size:2 final size:2
Alignment explanation
Indices: 2259133--2259187 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
2259123 AAATAATTTT
2259133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2259174 TA -A TA TT TA TA TA T
1 TA TA TA TA TA TA TA T
2259188 TTCATTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2265098 original size:18 final size:18
Alignment explanation
Indices: 2265075--2265110 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2265065 TGTAAAATTG
2265075 TAATAATTAAT-TATAATA
1 TAATAA-TAATATATAATA
2265093 TAATAATAATATATAATA
1 TAATAATAATATATAATA
2265111 ATATTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATATATAATA
Found at i:2265347 original size:36 final size:36
Alignment explanation
Indices: 2265307--2265397 Score: 164
Period size: 36 Copynumber: 2.5 Consensus size: 36
2265297 TGATATGTTC
2265307 TTGCTTCACTACTTTTTTGTGAAGGCTTGATTTGCA
1 TTGCTTCACTACTTTTTTGTGAAGGCTTGATTTGCA
*
2265343 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
1 TTGCTTCACTACTTTTTTGTGAAGGCTTGATTTGCA
2265379 TTGCTTCACTACTCTTTTT
1 TTGCTTCACTACT-TTTTT
2265398 TGTAGGTTGG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
36 48 0.92
37 4 0.08
ACGTcount: A:0.15, C:0.20, G:0.16, T:0.48
Consensus pattern (36 bp):
TTGCTTCACTACTTTTTTGTGAAGGCTTGATTTGCA
Found at i:2269917 original size:21 final size:21
Alignment explanation
Indices: 2269891--2269933 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2269881 ATATCAATTA
*
2269891 TGCATCGATGCACTTCTACAG
1 TGCATCGATGCACTGCTACAG
2269912 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTGCTACAG
2269933 T
1 T
2269934 AACTTCGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCACTGCTACAG
Found at i:2270623 original size:31 final size:31
Alignment explanation
Indices: 2270578--2270720 Score: 250
Period size: 31 Copynumber: 4.6 Consensus size: 31
2270568 TTCATAGATT
* *
2270578 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* *
2270609 CTGAAGAACATAGGTAAACAGTCCATATGTT
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2270640 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2270671 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2270702 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
2270721 CCTCGACCCT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:2275226 original size:31 final size:31
Alignment explanation
Indices: 2275201--2275370 Score: 277
Period size: 31 Copynumber: 5.5 Consensus size: 31
2275191 TTCATAGATT
* * *
2275201 CCGAAGAACCTAGGTAATCAGTTCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
2275232 CCGAAGAACATAGGTAAATAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
2275263 CCGAAGAACATAGATAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2275294 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* *
2275325 CCGAAGAACATAGGTAAACATTCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2275356 CCGAAGAACATAGGT
1 CCGAAGAACATAGGT
2275371 TAACCCTCGA
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 130 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:2276336 original size:20 final size:20
Alignment explanation
Indices: 2276307--2276357 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2276297 CGAAATATCC
2276307 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
*
2276327 ATGCACCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
2276347 ATGCATCGATG
1 ATGCATCGATG
2276358 TACCTACCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:2279908 original size:31 final size:31
Alignment explanation
Indices: 2279870--2280012 Score: 232
Period size: 31 Copynumber: 4.6 Consensus size: 31
2279860 TTCATAGATT
* *
2279870 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
2279901 CCGAAGAACATAGGTAAACAGTCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
2279932 CCAAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2279963 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
**
2279994 CTAAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
2280013 CCTCGACCCT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:2283818 original size:21 final size:21
Alignment explanation
Indices: 2283792--2283834 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2283782 ATATCAATTA
2283792 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTGCTACAG
2283813 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTGCTACAG
2283834 T
1 T
2283835 AACTTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (21 bp):
TGCATCGATGCACTGCTACAG
Found at i:2284516 original size:31 final size:31
Alignment explanation
Indices: 2284471--2284582 Score: 188
Period size: 31 Copynumber: 3.6 Consensus size: 31
2284461 TTCATAGATT
* *
2284471 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
2284502 CCGAATAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
2284533 CCGAAGAACATAGGTAAACAGTCCATATATC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2284564 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
2284583 CCTCGACCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:2285586 original size:20 final size:20
Alignment explanation
Indices: 2285512--2285573 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
2285502 CGAAATATCC
*
2285512 ATGCATCGATGCACCCCTTA
1 ATGCCTCGATGCACCCCTTA
2285532 ATGCCTCGATGCACCCCTTA
1 ATGCCTCGATGCACCCCTTA
2285552 ATGCCTCGATGCACCCCTTA
1 ATGCCTCGATGCACCCCTTA
2285572 AT
1 AT
2285574 TCATTGATGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.23, C:0.37, G:0.15, T:0.26
Consensus pattern (20 bp):
ATGCCTCGATGCACCCCTTA
Found at i:2291327 original size:13 final size:13
Alignment explanation
Indices: 2291311--2291337 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2291301 TTGTGGCCCA
2291311 CTCTTCACTCATT
1 CTCTTCACTCATT
2291324 CTCTTCACTCATT
1 CTCTTCACTCATT
2291337 C
1 C
2291338 CAGTCAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.41, G:0.00, T:0.44
Consensus pattern (13 bp):
CTCTTCACTCATT
Found at i:2291683 original size:359 final size:359
Alignment explanation
Indices: 2291024--2291683 Score: 1196
Period size: 359 Copynumber: 1.8 Consensus size: 359
2291014 GAGGTGCACA
* * * *
2291024 ACCTATAAAATATCCCTCTCATTCACGTCTGCGGGAATTCAAGGAACTAAATGTTTCAGCTAGAA
1 ACCTATAAAACATCCCTCTCATTCACGTCTACGGGAATTCAAGGAACTAAATGTTTCAACTAAAA
*
2291089 TAGCAGGAACCAGATTTGCATTATTGTTCAATCTTTCAAATAGGTCTATAGTTGATATATCCACA
66 TAGCAGGAACCAGATTTGCATTATTGTTCAATCTTTCAAATAGATCTATAGTTGATATATCCACA
*
2291154 TGCCCCAGGATCTTCGAAAAAATGACCATTCCATAAATACCTAAAGCCAACATATCAATCTTCTT
131 TGCCCCAGGATCTTCGAAAAAATGACCATTCCATAAATACCTAAAGCCAACATATCAATCTTATT
*
2291219 TCTTTTGTCTGGATGACGGTAAATTACTTCTCTAAGAGCCGTCCAAGTGATACATTCACTATTAC
196 TATTTTGTCTGGATGACGGTAAATTACTTCTCTAAGAGCCGTCCAAGTGATACATTCACTATTAC
2291284 CCTATTTTTTATATTTCTTGTGGCCCACTCTTCACTCATTCTCTTCACTCATTCCAGTCAGTAAG
261 CCTATTTTTTATATTTCTTGTGGCCCACTCTTCACTCATTCTCTTCACTCATTCCAGTCAGTAAG
2291349 AGCACTTTCTTCTTAAAAGGAGTAGTATTAGGTG
326 AGCACTTTCTTCTTAAAAGGAGTAGTATTAGGTG
*
2291383 ACCTATAAAACATCCCTCTCATTCACGTCTACGGGGATTCAAGGAACTAAATGTTTCAACTAAAA
1 ACCTATAAAACATCCCTCTCATTCACGTCTACGGGAATTCAAGGAACTAAATGTTTCAACTAAAA
*
2291448 TAGCAGGAACC-GAATTTGCATTCTTGTTCAATCTTTCAAATAGATCTATAGTTGATATATCCAC
66 TAGCAGGAACCAG-ATTTGCATTATTGTTCAATCTTTCAAATAGATCTATAGTTGATATATCCAC
2291512 ATGCCCCAGGATCTTCGAAAAAATGACCATTCCATAAATACCTAAAGCCAACATATCAATCTTAT
130 ATGCCCCAGGATCTTCGAAAAAATGACCATTCCATAAATACCTAAAGCCAACATATCAATCTTAT
*
2291577 TTATTTTGTCTGGATGACGGTAAATTACTTCTCTCAGAGCCGTCCAAGTGATACATTCACTATTA
195 TTATTTTGTCTGGATGACGGTAAATTACTTCTCTAAGAGCCGTCCAAGTGATACATTCACTATTA
* *
2291642 CCTTATTTTTTATTTTTCTTGTGGCCCACTCTTCACTCATTC
260 CCCTATTTTTTATATTTCTTGTGGCCCACTCTTCACTCATTC
2291684 CAGTCAGTAA
Statistics
Matches: 288, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
358 1 0.00
359 287 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (359 bp):
ACCTATAAAACATCCCTCTCATTCACGTCTACGGGAATTCAAGGAACTAAATGTTTCAACTAAAA
TAGCAGGAACCAGATTTGCATTATTGTTCAATCTTTCAAATAGATCTATAGTTGATATATCCACA
TGCCCCAGGATCTTCGAAAAAATGACCATTCCATAAATACCTAAAGCCAACATATCAATCTTATT
TATTTTGTCTGGATGACGGTAAATTACTTCTCTAAGAGCCGTCCAAGTGATACATTCACTATTAC
CCTATTTTTTATATTTCTTGTGGCCCACTCTTCACTCATTCTCTTCACTCATTCCAGTCAGTAAG
AGCACTTTCTTCTTAAAAGGAGTAGTATTAGGTG
Found at i:2293467 original size:18 final size:18
Alignment explanation
Indices: 2293444--2293481 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2293434 AACATAAGAT
2293444 ATAAATAATAATAGT-ATA
1 ATAAATAAT-ATAGTAATA
*
2293462 ATAAATACTATAGTAATA
1 ATAAATAATATAGTAATA
2293480 AT
1 AT
2293482 TAATTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
ATAAATAATATAGTAATA
Found at i:2294441 original size:3 final size:3
Alignment explanation
Indices: 2294435--2294475 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2294425 TAATTAGAAT
2294435 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2294476 TACTTATAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2294461 original size:26 final size:27
Alignment explanation
Indices: 2294418--2294475 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
2294408 TGTAAAATTG
*
2294418 TAATAATTAATTAGAATATAATAATAA
1 TAATAATTAATAAGAATATAATAATAA
*
2294445 TAATAA-TAATAATAATATAATAATAA
1 TAATAATTAATAAGAATATAATAATAA
2294471 TAATA
1 TAATA
2294476 TACTTATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
TAATAATTAATAAGAATATAATAATAA
Found at i:2294484 original size:20 final size:20
Alignment explanation
Indices: 2294418--2294477 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
2294408 TGTAAAATTG
* *
2294418 TAATAATTAATTAGAATATAA
1 TAATAA-TAATAATAATATAA
2294439 TAATAATAATAATAATAATAA
1 TAATAATAATAATAAT-ATAA
2294460 T-ATAATAATAATAATATA
1 TAATAATAATAATAATATA
2294478 CTTATAACGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.08
20 22 0.61
21 11 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TAATAATAATAATAATATAA
Found at i:2295894 original size:13 final size:13
Alignment explanation
Indices: 2295876--2295901 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2295866 CTTTGGCCCA
2295876 TTGACTTTGACCG
1 TTGACTTTGACCG
2295889 TTGACTTTGACCG
1 TTGACTTTGACCG
2295902 AAAAGTCAAA
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:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
TTGACTTTGACCG
Found at i:2297809 original size:16 final size:16
Alignment explanation
Indices: 2297773--2297822 Score: 73
Period size: 16 Copynumber: 3.0 Consensus size: 16
2297763 TGTTTCTGAG
2297773 GGAATTGGAATCTATGAA
1 GGAATTGGAA--TATGAA
*
2297791 GGAATTGGAATATGTA
1 GGAATTGGAATATGAA
2297807 GGAATTGGAATATGAA
1 GGAATTGGAATATGAA
2297823 TCTGAAACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 20 0.67
18 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.30, T:0.28
Consensus pattern (16 bp):
GGAATTGGAATATGAA
Found at i:2298444 original size:33 final size:33
Alignment explanation
Indices: 2298407--2298475 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
2298397 CTAAACCTGA
2298407 ACCCGACCCAAATATCACACTTAAAAAAACCCG
1 ACCCGACCCAAATATCACACTTAAAAAAACCCG
* *
2298440 ACCCGACCCGAATATCATACTTAAAAAAACCCG
1 ACCCGACCCAAATATCACACTTAAAAAAACCCG
2298473 ACC
1 ACC
2298476 TGAATATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.36, G:0.07, T:0.13
Consensus pattern (33 bp):
ACCCGACCCAAATATCACACTTAAAAAAACCCG
Found at i:2298474 original size:28 final size:28
Alignment explanation
Indices: 2298406--2298495 Score: 99
Period size: 28 Copynumber: 3.0 Consensus size: 28
2298396 CCTAAACCTG
* *
2298406 AACCCGACCCAAATATCACACTTAAAAAA
1 AACCCGACCCGAATATCAAACTT-AAAAA
*
2298435 ACCCGACCCGACCCGAATATCATACTTAAAAA
1 A----ACCCGACCCGAATATCAAACTTAAAAA
*
2298467 AACCCGACCTGAATATCAAACTTAAAAA
1 AACCCGACCCGAATATCAAACTTAAAAA
2298495 A
1 A
2298496 CCTGACCTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
28 26 0.49
29 1 0.02
32 6 0.11
33 20 0.38
ACGTcount: A:0.48, C:0.30, G:0.07, T:0.16
Consensus pattern (28 bp):
AACCCGACCCGAATATCAAACTTAAAAA
Found at i:2298502 original size:27 final size:28
Alignment explanation
Indices: 2298440--2298506 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
2298430 AAAAAACCCG
* *
2298440 ACCCGACCCGAATATCATACTTAAAAAA
1 ACCCGACCTGAATATCAAACTTAAAAAA
2298468 ACCCGACCTGAATATCAAACTT-AAAAA
1 ACCCGACCTGAATATCAAACTTAAAAAA
*
2298495 ACCTGACCTGAA
1 ACCCGACCTGAA
2298507 CCCGAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 16 0.44
28 20 0.56
ACGTcount: A:0.45, C:0.28, G:0.09, T:0.18
Consensus pattern (28 bp):
ACCCGACCTGAATATCAAACTTAAAAAA
Found at i:2308254 original size:2 final size:2
Alignment explanation
Indices: 2308249--2308305 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2308239 AAATAAATAA
2308249 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
2308291 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2308306 AACAAGAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2309997 original size:136 final size:136
Alignment explanation
Indices: 2309751--2310076 Score: 492
Period size: 136 Copynumber: 2.4 Consensus size: 136
2309741 GGTACCTAGG
* * *
2309751 CAAGTTCTTCTCATTATGAGCTTCTTCTCCCTCTATT-GAATGAGTTATTCTCATTATGAACTCT
1 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTCT-TTCGGATGAGTTCTTCTCATTATGAACTCT
* * * * ** * *
2309815 CCATCGAAATTGTCAATCCCTTAAGCGAGGCGTTGCTGGTTTGAAGTGTTGTGAATTAAGCAATA
65 CCACCAAAAATGTCAATCCCTCAAGCGAGGCGTTGCTCATTCGAAGTGTGGTGAATTAAGCAATA
2309880 GGTCGAA
130 GGTCGAA
*
2309887 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTT
1 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTC
* * *
2309952 CACCAAAAATGTCAATCCCTCAAGTGAGGTGTTGCTCATTCGAAGTGTGGTGAATTGAGCAATAG
66 CACCAAAAATGTCAATCCCTCAAGCGAGGCGTTGCTCATTCGAAGTGTGGTGAATTAAGCAATAG
2310017 GTCGAA
131 GTCGAA
*
2310023 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCAT
1 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCAT
2310077 GATTAACTGT
Statistics
Matches: 173, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
135 2 0.01
136 171 0.99
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (136 bp):
CAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTC
CACCAAAAATGTCAATCCCTCAAGCGAGGCGTTGCTCATTCGAAGTGTGGTGAATTAAGCAATAG
GTCGAA
Found at i:2311046 original size:12 final size:12
Alignment explanation
Indices: 2311031--2311092 Score: 74
Period size: 12 Copynumber: 5.1 Consensus size: 12
2311021 GAACCTCTCC
2311031 TTTTCTTTTTCT
1 TTTTCTTTTTCT
2311043 TTTTCTTTTTCTT
1 TTTTCTTTTTC-T
2311056 TTTTCTTTTTTCT
1 TTTTC-TTTTTCT
2311069 TTCTT-TTTTTCT
1 TT-TTCTTTTTCT
*
2311081 TCTT-TTTTTCT
1 TTTTCTTTTTCT
2311092 T
1 T
2311093 CTTAGACGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
11 10 0.22
12 19 0.41
13 9 0.20
14 8 0.17
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:2311060 original size:19 final size:18
Alignment explanation
Indices: 2311031--2311092 Score: 81
Period size: 19 Copynumber: 3.4 Consensus size: 18
2311021 GAACCTCTCC
2311031 TTTTC-TTTTTCTTTTTCT
1 TTTTCTTTTTTCTTTTT-T
2311049 TTTTCTTTTTTCTTTTTT
1 TTTTCTTTTTTCTTTTTT
* *
2311067 CTTTCTTTTTTTCTTCTTT
1 TTTTC-TTTTTTCTTTTTT
2311086 TTTTCTT
1 TTTTCTT
2311093 CTTAGACGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 12 0.31
19 27 0.69
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTTTT
Found at i:2311093 original size:11 final size:11
Alignment explanation
Indices: 2311031--2311095 Score: 73
Period size: 11 Copynumber: 5.9 Consensus size: 11
2311021 GAACCTCTCC
*
2311031 TTTTCTTTTTCT
1 TTTTCTTCTT-T
2311043 TTTTCTT-TTT
1 TTTTCTTCTTT
2311053 CTTTT-TTC-TT
1 -TTTTCTTCTTT
2311063 TTTTCTTTCTTT
1 TTTTC-TTCTTT
2311075 TTTTCTTCTTT
1 TTTTCTTCTTT
2311086 TTTTCTTCTT
1 TTTTCTTCTT
2311096 AGACGTAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.08
10 5 0.10
11 25 0.52
12 14 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTCTTT
Found at i:2314838 original size:15 final size:15
Alignment explanation
Indices: 2314820--2314850 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2314810 AAAGAAGAAC
2314820 AAGATCAAGAAAAGA
1 AAGATCAAGAAAAGA
*
2314835 AAGATGAAGAAAAGA
1 AAGATCAAGAAAAGA
2314850 A
1 A
2314851 GAAAATGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.23, T:0.06
Consensus pattern (15 bp):
AAGATCAAGAAAAGA
Found at i:2322214 original size:20 final size:20
Alignment explanation
Indices: 2322189--2322239 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2322179 CAAAACCAAC
*
2322189 GGTATCGATACCGGCCAGGG
1 GGTATCGATACCGGCCAAGG
2322209 GGTATCGATACCGGCCAAGG
1 GGTATCGATACCGGCCAAGG
2322229 GGTATCGATAC
1 GGTATCGATAC
2322240 TACTATGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (20 bp):
GGTATCGATACCGGCCAAGG
Found at i:2322382 original size:24 final size:24
Alignment explanation
Indices: 2322347--2322400 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2322337 CATTGGTTAT
* *
2322347 GGTATCGGTACTACTATGTATAAG
1 GGTATCGATACTACTAGGTATAAG
2322371 GGTATCGATACTACTAGGTATAAG
1 GGTATCGATACTACTAGGTATAAG
2322395 GGTATC
1 GGTATC
2322401 AGTACCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (24 bp):
GGTATCGATACTACTAGGTATAAG
Found at i:2331121 original size:18 final size:18
Alignment explanation
Indices: 2331067--2331121 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
2331057 GTACTACTAT
*
2331067 GTGTAAGGGTATCGGTACT
1 GTGT-AGGGTATCGGTACC
*
2331086 GTGTAAGGTATCGGTACC
1 GTGTAGGGTATCGGTACC
*
2331104 GTGTAGGGTATTGGTACC
1 GTGTAGGGTATCGGTACC
2331122 CAAATTAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.20, C:0.13, G:0.36, T:0.31
Consensus pattern (18 bp):
GTGTAGGGTATCGGTACC
Found at i:2331169 original size:20 final size:20
Alignment explanation
Indices: 2331144--2331195 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2331134 GATGTTTGGG
2331144 AGTATCGATACTGTTGAGGC
1 AGTATCGATACTGTTGAGGC
2331164 AGTATCGATACTGTTGAGGC
1 AGTATCGATACTGTTGAGGC
2331184 AGTATCGATACT
1 AGTATCGATACT
2331196 ACCCTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTGTTGAGGC
Found at i:2331376 original size:18 final size:18
Alignment explanation
Indices: 2331353--2331388 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2331343 ATTTGAATAA
2331353 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
2331371 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
2331389 CTTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (18 bp):
TTGAATCGAATATAAAAT
Found at i:2342131 original size:46 final size:46
Alignment explanation
Indices: 2342080--2342197 Score: 168
Period size: 46 Copynumber: 2.6 Consensus size: 46
2342070 ACCGCTATGT
2342080 ATTTTCATTTATGGTATCCTTTCATG-CAGAGTATACACTGTTATAC
1 ATTTTCATTTATGGTATCCTTTCATGCCA-AGTATACACTGTTATAC
* * * *
2342126 ATTTTCATTTATGGCATCATTTCATGCCAATTATGCACTGTTATAC
1 ATTTTCATTTATGGTATCCTTTCATGCCAAGTATACACTGTTATAC
2342172 ATTTTCATTTAT-GTCATCCTTTCATG
1 ATTTTCATTTATGGT-ATCCTTTCATG
2342198 TCATTTATAG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
45 1 0.02
46 61 0.95
47 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (46 bp):
ATTTTCATTTATGGTATCCTTTCATGCCAAGTATACACTGTTATAC
Found at i:2342654 original size:57 final size:57
Alignment explanation
Indices: 2342508--2343065 Score: 872
Period size: 57 Copynumber: 9.8 Consensus size: 57
2342498 CCCGCTACCA
* *
2342508 ATACAAAAATTCATATACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
** *
2342565 ATACG-AAATTCATAAACTTATTATGAATTTCTTAGTTTTTTGCACACAAAGTACCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
2342621 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
** *
2342678 ATAC-AGAAATTCATAAACTTATTATGAATTTCTT-TGTTTTTGTACACAAAGTGCCC
1 ATACGA-AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
2342734 ATACGAAAATTCATAAACGTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * *
2342791 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTCTTTGCACACAAAGTGCCT
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
2342848 ATACAAAAATTCATAAACTTATTATGAATTTCTT-AGTTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * *
2342904 ATAGGGAAATTCATAAACTTATTATGAATTCCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * **
2342961 ATATGGAAATTCATAAACTTAGAATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
2343018 ATACGGAAATTAATAAACTTATTATGAATTTCTTAACTTTTTGCACAC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACAC
2343066 TCAGTGTCAT
Statistics
Matches: 459, Mismatches: 37, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
56 152 0.33
57 307 0.67
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (57 bp):
ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:2342718 original size:113 final size:114
Alignment explanation
Indices: 2342508--2343065 Score: 906
Period size: 113 Copynumber: 4.9 Consensus size: 114
2342498 CCCGCTACCA
* *
2342508 ATACAAAAATTCATATACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATAC-GAA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAA
** *
2342572 ATTCATAAACTTATTATGAATTTCTTAGTTTTTTGCACACAAAGTACCC
66 ATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
2342621 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAGAA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAA
** *
2342686 ATTCATAAACTTATTATGAATTTCTT-TGTTTTTGTACACAAAGTGCCC
66 ATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
2342734 ATACGAAAATTCATAAACGTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAA
* *
2342799 ATTCATAAACTTATTATGAATTTCTTAACTCTTTGCACACAAAGTGCCT
66 ATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * *
2342848 ATACAAAAATTCATAAACTTATTATGAATTTCTT-AGTTTTTGCACACAAAGTGCCCATAGGGAA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAA
*
2342912 ATTCATAAACTTATTATGAATTCCTTAACTTTTTGCACACAAAGTGCCC
66 ATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * **
2342961 ATATGGAAATTCATAAACTTAGAATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAA
*
2343026 ATTAATAAACTTATTATGAATTTCTTAACTTTTTGCACAC
66 ATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACAC
2343066 TCAGTGTCAT
Statistics
Matches: 413, Mismatches: 29, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
113 269 0.65
114 144 0.35
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (114 bp):
ATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAA
ATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:2342803 original size:170 final size:169
Alignment explanation
Indices: 2342508--2343065 Score: 891
Period size: 170 Copynumber: 3.3 Consensus size: 169
2342498 CCCGCTACCA
* *
2342508 ATACAAAAATTCATATACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGAAA
1 ATACAAAAATTCATAAACTTATTATGAATTTCTT-AGTTTTTGCACACAAAGTGCCCATACGAAA
** * *
2342573 TTCATAAACTTATTATGAATTTCTTAGTTTTTTGCACACAAAGTACCCATACGAAAATTCATAAA
65 TTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAA
2342638 CTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
130 CTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * *
2342678 ATACAGAAATTCATAAACTTATTATGAATTTCTTTGTTTTTGTACACAAAGTGCCCATACGAAAA
1 ATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACG-AAA
*
2342743 TTCATAAACGTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAA
65 TTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAA
* *
2342808 CTTATTATGAATTTCTTAACTCTTTGCACACAAAGTGCCT
130 CTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
2342848 ATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATAGGGAAA
1 ATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATA-CGAAA
* *
2342913 TTCATAAACTTATTATGAATTCCTTAACTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAA
65 TTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAA
**
2342978 CTTAGAATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
130 CTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
** * *
2343018 ATACGGAAATTAATAAACTTATTATGAATTTCTTAACTTTTTGCACAC
1 ATACAAAAATTCATAAACTTATTATGAATTTCTT-AGTTTTTGCACAC
2343066 TCAGTGTCAT
Statistics
Matches: 358, Mismatches: 27, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
169 24 0.07
170 321 0.90
171 13 0.04
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (169 bp):
ATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAT
TCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAC
TTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:2346219 original size:77 final size:76
Alignment explanation
Indices: 2346082--2346289 Score: 267
Period size: 77 Copynumber: 2.7 Consensus size: 76
2346072 CAAAGCCAAA
* * * * **
2346082 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCTCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
2346147 TTTGGC-CCTGAG
66 TTT-GCTCC-GAG
* *
2346159 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCAATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
2346224 TTTGCTCCGAG
66 TTTGCTCCGAG
* * * * *
2346235 AATTCCAGTATGCTCGAAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
2346290 TTGTACAACG
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
75 16 0.14
76 37 0.32
77 62 0.54
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGCTCCGAG
Found at i:2352123 original size:21 final size:21
Alignment explanation
Indices: 2352066--2352136 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
2352056 GGGAATCGAT
*
2352066 CCCCCACTGAGGGAACCGATTC
1 CCCCCACAG-GGGAACCGATTC
*
2352088 CCCCTTTGA-AGGGGAACCGATTC
1 CCCC---CACAGGGGAACCGATTC
* *
2352111 CCCCCACAGGGGAATCGATAC
1 CCCCCACAGGGGAACCGATTC
2352132 CCCCC
1 CCCCC
2352137 TAGGGTTCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.03
21 17 0.43
22 4 0.10
23 16 0.40
24 1 0.03
25 1 0.03
ACGTcount: A:0.23, C:0.41, G:0.23, T:0.14
Consensus pattern (21 bp):
CCCCCACAGGGGAACCGATTC
Found at i:2354891 original size:76 final size:77
Alignment explanation
Indices: 2354722--2354922 Score: 271
Period size: 76 Copynumber: 2.6 Consensus size: 77
2354712 AATTACAGAT
* * **
2354722 TGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCTCCCTAAATGGTTTTGGCCCC
1 TGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCC
*
2354787 GAGATTTCCAAAA
65 GAGAATTCCAAAA
* *
2354800 TGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTT-GCTCTG
1 TGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCG
**
2354864 AGAATTCCAGTA
66 AGAATTCCAAAA
* * *
2354876 TGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 TGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
2354923 TGTACAACGA
Statistics
Matches: 111, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
75 19 0.17
76 38 0.34
77 36 0.32
78 18 0.16
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.20
Consensus pattern (77 bp):
TGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCG
AGAATTCCAAAA
Found at i:2357374 original size:22 final size:22
Alignment explanation
Indices: 2357349--2357420 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
2357339 ACATTTTCAT
2357349 TTATGGCATCCTTTCATGTCAA
1 TTATGGCATCCTTTCATGTCAA
* * * *
2357371 TTAT-GCAATGCTATACATTTCAT
1 TTATGGC-ATCCT-TTCATGTCAA
* *
2357394 TTATGGCATCCTTTCATGCCAG
1 TTATGGCATCCTTTCATGTCAA
2357416 TTATG
1 TTATG
2357421 CACTAATCTT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
21 2 0.05
22 19 0.50
23 15 0.39
24 2 0.05
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.42
Consensus pattern (22 bp):
TTATGGCATCCTTTCATGTCAA
Found at i:2357407 original size:45 final size:46
Alignment explanation
Indices: 2357289--2357422 Score: 164
Period size: 46 Copynumber: 2.9 Consensus size: 46
2357279 TAATATACCA
* * * * * *
2357289 CTATGCATTTTCAATTGTGGTATCCTTTCATGT-AGATTATACACTG
1 CTATACATTTTCATTTATGGCATCCTTTCATGTCA-ATTATGCAATG
*
2357335 TTATACATTTTCATTTATGGCATCCTTTCATGTCAATTATGCAATG
1 CTATACATTTTCATTTATGGCATCCTTTCATGTCAATTATGCAATG
* *
2357381 CTATACA-TTTCATTTATGGCATCCTTTCATGCCAGTTATGCA
1 CTATACATTTTCATTTATGGCATCCTTTCATGTCAATTATGCA
2357423 CTAATCTTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
45 33 0.43
46 43 0.56
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (46 bp):
CTATACATTTTCATTTATGGCATCCTTTCATGTCAATTATGCAATG
Found at i:2357799 original size:57 final size:59
Alignment explanation
Indices: 2357722--2358310 Score: 568
Period size: 57 Copynumber: 9.8 Consensus size: 59
2357712 CCCGCTACCA
* * *
2357722 ATACAGAAATTCATATACTTATTATGAATTTCTTAAC-T-TTTTGCACACAAAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTCTTTTGCACACAAAGTGCCC
**
2357779 ATACGGAAATTCATAAACTTATTATGAATTTCTTTTCTTTTCTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAAC--TTCTTTTGCACACAAAGTGCCC
* * * * * * **
2357840 ATACGGAAATTCATAAACTTGTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAACTT
1 ATACGGAAATTCATAAACTTAT-----TAT-GAATTTC-TTAACTTCTTTTGCA---C---ACAA
**
2357905 TTTGCACAC
53 AGTGC-C-C
* * *
2357914 A-AAGTGCCCATACGAAAATTCATAAACTTATTATGGATTTCTT-A-GT-TTTTGCACACAAAGT
1 ATACG-G---A-A-----ATTCATAAACTTATTATGAATTTCTTAACTTCTTTTGCACACAAAGT
*
2357975 GCAC
56 GCCC
2357979 ATACGGAAATTCATAAACTTATTATGAATTTCTTAAC-T-TTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTCTTTTGCACACAAAGTGCCC
*
2358036 ATATGGAAATTCATAAACTTATTATGAATTTCTTAAC-T-TTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTCTTTTGCACACAAAGTGCCC
* * * * *
2358093 ATACGAAAATTTATAAACTTATTATGGATTTCTT-A-GT-TTTTGCACACAAAGTGCAC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTCTTTTGCACACAAAGTGCCC
2358149 ATACGGAAATTCATAAACTTATTATGAATTTCTTAAC-T-TTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTCTTTTGCACACAAAGTGCCC
*
2358206 ATGCGGAAATTCATAAACTTATTATGAATTTCTTAAC-T-TTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTCTTTTGCACACAAAGTGCCC
2358263 ATACGGAAATTCATAAACTTATTATGAATTTCTTAAC-T-TTTTGCACAC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTCTTTTGCACAC
2358311 TCAATGCCAT
Statistics
Matches: 452, Mismatches: 45, Indels: 70
0.80 0.08 0.12
Matches are distributed among these distances:
56 76 0.17
57 262 0.58
60 1 0.00
61 40 0.09
62 1 0.00
65 3 0.01
66 12 0.03
67 11 0.02
68 2 0.00
69 1 0.00
70 1 0.00
72 5 0.01
73 8 0.02
74 4 0.01
75 1 0.00
76 1 0.00
77 6 0.01
78 4 0.01
83 13 0.03
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (59 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTCTTTTGCACACAAAGTGCCC
Found at i:2357850 original size:61 final size:57
Alignment explanation
Indices: 2357722--2357859 Score: 195
Period size: 61 Copynumber: 2.4 Consensus size: 57
2357712 CCCGCTACCA
* * *
2357722 ATACAGAAATTCATATACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
**
2357779 ATACGGAAATTCATAAACTTATTATGAATTTCTTTTCTTTTCTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAAC---T-TTTTGCACACAAAGTGCCC
2357840 ATACGGAAATTCATAAACTT
1 ATACGGAAATTCATAAACTT
2357860 GTGCCCATAT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
57 33 0.46
60 1 0.01
61 38 0.53
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (57 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:2357873 original size:26 final size:26
Alignment explanation
Indices: 2357834--2357885 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2357824 TGCACACAAA
2357834 GTGCCCATACGGAAATTCATAAACTT
1 GTGCCCATACGGAAATTCATAAACTT
*
2357860 GTGCCCATATGGAAATTCATAAACTT
1 GTGCCCATACGGAAATTCATAAACTT
2357886 ATTATGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (26 bp):
GTGCCCATACGGAAATTCATAAACTT
Found at i:2358068 original size:113 final size:114
Alignment explanation
Indices: 2357860--2358310 Score: 780
Period size: 113 Copynumber: 4.0 Consensus size: 114
2357850 TCATAAACTT
*
2357860 GTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
1 GTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
* * *
2357925 ACGAAAATTCATAAACTTATTATGGATTTCTT-AGTTTTTGCACACAAA
66 ACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
*
2357973 GTGCACATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
1 GTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
*
2358038 ATGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
66 ACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
* * * * *
2358087 GTGCCCATACGAAAATTTATAAACTTATTATGGATTTCTT-AGTTTTTGCACACAAAGTGCACAT
1 GTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
2358151 ACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
66 ACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
*
2358200 GTGCCCATGCGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
1 GTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
2358265 ACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACAC
66 ACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACAC
2358311 TCAATGCCAT
Statistics
Matches: 317, Mismatches: 19, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
113 198 0.62
114 119 0.38
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (114 bp):
GTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
ACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
Found at i:2358142 original size:170 final size:170
Alignment explanation
Indices: 2357860--2358310 Score: 839
Period size: 170 Copynumber: 2.6 Consensus size: 170
2357850 TCATAAACTT
2357860 GTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
1 GTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
2357925 ACGAAAATTCATAAACTTATTATGGATTTCTTAGTTTTTGCACACAAAGTGCACATACGGAAATT
66 ACGAAAATTCATAAACTTATTATGGATTTCTTAGTTTTTGCACACAAAGTGCACATACGGAAATT
2357990 CATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
131 CATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
2358030 GTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
1 GTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
*
2358095 ACGAAAATTTATAAACTTATTATGGATTTCTTAGTTTTTGCACACAAAGTGCACATACGGAAATT
66 ACGAAAATTCATAAACTTATTATGGATTTCTTAGTTTTTGCACACAAAGTGCACATACGGAAATT
2358160 CATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
131 CATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
**
2358200 GTGCCCATGCGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
1 GTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
* * *
2358265 ACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACAC
66 ACGAAAATTCATAAACTTATTATGGATTTCTT-AGTTTTTGCACAC
2358311 TCAATGCCAT
Statistics
Matches: 273, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
170 261 0.96
171 12 0.04
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (170 bp):
GTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAT
ACGAAAATTCATAAACTTATTATGGATTTCTTAGTTTTTGCACACAAAGTGCACATACGGAAATT
CATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAA
Found at i:2359069 original size:9 final size:10
Alignment explanation
Indices: 2359055--2359079 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2359045 AAACTGAATT
2359055 AAAAAAAGAA
1 AAAAAAAGAA
2359065 AAAAAAAGAA
1 AAAAAAAGAA
2359075 AAAAA
1 AAAAA
2359080 CAACATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:2360154 original size:6 final size:6
Alignment explanation
Indices: 2360145--2360245 Score: 193
Period size: 6 Copynumber: 16.8 Consensus size: 6
2360135 ACCAAAATGA
2360145 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
1 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
*
2360193 GTATGC GTATGC GTATGC GTATGC GTATGC ATATGC GTATGC GTATGC
1 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
2360241 GTATG
1 GTATG
2360246 ATAGCTATTC
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.34
Consensus pattern (6 bp):
GTATGC
Found at i:2362275 original size:85 final size:85
Alignment explanation
Indices: 2362176--2362493 Score: 309
Period size: 85 Copynumber: 3.7 Consensus size: 85
2362166 GTCATCGTCA
* * * * * * * *
2362176 ATGGTTGATTTGCTCCTTTCTCTGAATGACGTCAAACTGGAAAATGATCTTGATCCTTTCTCTGA
1 ATGGTTGATCTGCTCCTTTCTCTGAAGGACGCCAAATTGGGAAACGATCTTGATCATTTCTCTAA
* * *
2362241 AGGACGCTAAGTTGAGATTG
66 AGGACGCCAAGTCGAGATAG
* * * *
2362261 ATGGTTGATCTGCTCCTTTCTTTGAAGGATGTCAAATTGGGAAACGATCTTGATCATTTCTCCAA
1 ATGGTTGATCTGCTCCTTTCTCTGAAGGACGCCAAATTGGGAAACGATCTTGATCATTTCTCTAA
* *
2362326 AGGACGCCAAG-CCAGGATCG
66 AGGACGCCAAGTCGA-GATAG
* * * * * * *
2362346 ATGGTTGTTCTACTCATTTCTCTGAAGGACACCAAATTGGGAAACGATCTTGCTCATTTCTTTCA
1 ATGGTTGATCTGCTCCTTTCTCTGAAGGACGCCAAATTGGGAAACGATCTTGATCATTTCTCTAA
*
2362411 AGGACGCCAAGTCGGGATAG
66 AGGACGCCAAGTCGAGATAG
* * * * * *
2362431 ATGGTTGATATGCTCAC-TTCTTTGAATGACGCCAAATCGGGGAACAATCTT-ACTCATTTCTCT
1 ATGGTTGATCTGCTC-CTTTCTCTGAAGGACGCCAAATTGGGAAACGATCTTGA-TCATTTCTCT
2362494 GGATGACGCT
Statistics
Matches: 189, Mismatches: 40, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
84 1 0.01
85 187 0.99
86 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (85 bp):
ATGGTTGATCTGCTCCTTTCTCTGAAGGACGCCAAATTGGGAAACGATCTTGATCATTTCTCTAA
AGGACGCCAAGTCGAGATAG
Found at i:2362519 original size:170 final size:170
Alignment explanation
Indices: 2362163--2362520 Score: 364
Period size: 170 Copynumber: 2.1 Consensus size: 170
2362153 ACGGATACGT
* * * * * ** *
2362163 CAAGTCATCGTCAATGGTTGATTTGCTCCTTTCTCTGAATGACGTCAAACTGGAAAATGATCTTG
1 CAAGTCATAGTCGATGGTTGATTTACTCATTTCTCTGAAGGACACCAAACTGGAAAACGATCTTG
* * * * * * * *
2362228 ATCCTTTCTCTGAAGGACGCTAAGTTGAGATTGATGGTTGATCTGCTCCTTTCTTTGAAGGATGT
66 ATCATTTCTCTCAAGGACGCCAAGTCGAGATAGATGGTTGATATGCTCCTTTCTTTGAAGGACGC
* *
2362293 CAAATTGGGAAACGATCTTGATCATTTCTCCAAAGGACGC
131 CAAATCGGGAAACAATCTTGATCATTTCTCCAAAGGACGC
* * * *
2362333 CAAGCCA-GGATCGATGGTTG-TTCTACTCATTTCTCTGAAGGACACCAAATTGGGAAACGATCT
1 CAAGTCATAG-TCGATGGTTGATT-TACTCATTTCTCTGAAGGACACCAAACTGGAAAACGATCT
* * * *
2362396 TGCTCATTTCTTTCAAGGACGCCAAGTCGGGATAGATGGTTGATATGCTCAC-TTCTTTGAATGA
64 TGATCATTTCTCTCAAGGACGCCAAGTCGAGATAGATGGTTGATATGCTC-CTTTCTTTGAAGGA
* *** *
2362460 CGCCAAATCGGGGAACAATCTT-ACTCATTTCTCTGGATGACGC
128 CGCCAAATCGGGAAACAATCTTGA-TCATTTCTCCAAAGGACGC
*
2362503 TAAGTCATAGTCGATGGT
1 CAAGTCATAGTCGATGGT
2362521 GATATGCTCA
Statistics
Matches: 150, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
169 4 0.03
170 144 0.96
171 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (170 bp):
CAAGTCATAGTCGATGGTTGATTTACTCATTTCTCTGAAGGACACCAAACTGGAAAACGATCTTG
ATCATTTCTCTCAAGGACGCCAAGTCGAGATAGATGGTTGATATGCTCCTTTCTTTGAAGGACGC
CAAATCGGGAAACAATCTTGATCATTTCTCCAAAGGACGC
Found at i:2363614 original size:21 final size:21
Alignment explanation
Indices: 2363590--2363632 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2363580 ATCGCTGTTC
*
2363590 GTTTATCATTGGTGCATTTGG
1 GTTTAACATTGGTGCATTTGG
2363611 GTTTAACATTGGTGCATTTGG
1 GTTTAACATTGGTGCATTTGG
2363632 G
1 G
2363633 GCAGGGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.30, T:0.44
Consensus pattern (21 bp):
GTTTAACATTGGTGCATTTGG
Found at i:2364044 original size:40 final size:42
Alignment explanation
Indices: 2364000--2364091 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 42
2363990 AATTTTCTAA
* * *
2364000 TTTATATAAAAATTAAATATTTTATAATTA-AAAA-AAACAG
1 TTTATATAAAAATTAAATAATATATAATTATAAAATAAAAAG
* * *
2364040 TTTATA-ATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 TTTATATA-AAAATTAAATAATATATAATTATAAAATAAAAAG
2364082 TTTATATAAA
1 TTTATATAAA
2364092 TTTTTAATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
39 1 0.02
40 24 0.59
41 4 0.10
42 11 0.27
43 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (42 bp):
TTTATATAAAAATTAAATAATATATAATTATAAAATAAAAAG
Found at i:2364329 original size:186 final size:185
Alignment explanation
Indices: 2364002--2364392 Score: 667
Period size: 186 Copynumber: 2.1 Consensus size: 185
2363992 TTTTCTAATT
* * *
2364002 TATATAA-AAATTAAATATTTTATAATTAAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
2364066 ATTATAAAATAAAAATTTTATATAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 ATTATAAAATAAAAAATTTATATAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
* *
2364131 TGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGTCCATATGTTA
131 TGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* * *
2364186 TATATAATATATTTAATATTTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
2364251 ATTATAAAATAAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAAATTTATATAAA-TTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
*
2364316 TTGGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
130 TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
2364372 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
2364393 AAAATTTTAT
Statistics
Matches: 194, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
184 7 0.04
185 76 0.39
186 111 0.57
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTATAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAAATTTATATAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:2365127 original size:6 final size:7
Alignment explanation
Indices: 2365111--2365135 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2365101 TTTTGATCTG
2365111 TTTTAAT
1 TTTTAAT
2365118 TTTTAAT
1 TTTTAAT
2365125 TTTTAAT
1 TTTTAAT
2365132 TTTT
1 TTTT
2365136 TCAAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:2365233 original size:30 final size:28
Alignment explanation
Indices: 2365191--2365252 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
2365181 TAAAAATTAA
2365191 TATTTTTTATACCTAAACTATCAGTTTT
1 TATTTTTTATACCTAAACTATCAGTTTT
*
2365219 TATTCTTTTAATACCTAAACTCTCA-TTTT
1 TATT-TTTT-ATACCTAAACTATCAGTTTT
2365248 T-TTTT
1 TATTTT
2365253 CAAAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 2 0.06
28 6 0.19
29 9 0.29
30 14 0.45
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (28 bp):
TATTTTTTATACCTAAACTATCAGTTTT
Found at i:2370145 original size:27 final size:27
Alignment explanation
Indices: 2370114--2370181 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
2370104 TCTATTTACA
*
2370114 AAATCATATTTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
*
2370141 AAATCATATCTCTATAGGAATGGTAAT
1 AAATCATATCTCTATAGGAATGGTAAC
2370168 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
2370182 ATTCCTACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 9 0.23
27 30 0.77
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:2379435 original size:4 final size:4
Alignment explanation
Indices: 2379426--2379453 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2379416 TAATCGTATT
2379426 TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2379454 GCATCTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:2379902 original size:82 final size:83
Alignment explanation
Indices: 2379803--2380024 Score: 389
Period size: 82 Copynumber: 2.7 Consensus size: 83
2379793 CGTGCAAAAA
2379803 AAGTATGCAAATCTTGCAAAAAAAAAGTATAATTAGTGTAGTTTAATAATGTGTGTGTGTGTGTG
1 AAGTATGCAAATCTTGCAAAAAAAAAGTATAATTAGTGTAGTTTAATAATGTGTGTGTGTGTGTG
2379868 -GCTTGAACGCCACCTAT
66 TGCTTGAACGCCACCTAT
2379885 AAGTATGCAAATCTTGCAAAAAAAAAGTATAATTAGTGTAGTTTAATAATGTGTGTGTGTGTGTG
1 AAGTATGCAAATCTTGCAAAAAAAAAGTATAATTAGTGTAGTTTAATAATGTGTGTGTGTGTGTG
2379950 TTATGCTTGAACGCCACCTAT
66 ---TGCTTGAACGCCACCTAT
2379971 AAGTATGCAAATCTTGC--AAAAAAAGTATAATTAGTGTAGTTTAATAATGT-TGTG
1 AAGTATGCAAATCTTGCAAAAAAAAAGTATAATTAGTGTAGTTTAATAATGTGTGTG
2380025 GGTGGATGAG
Statistics
Matches: 136, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
82 65 0.48
83 4 0.03
84 33 0.24
86 34 0.25
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (83 bp):
AAGTATGCAAATCTTGCAAAAAAAAAGTATAATTAGTGTAGTTTAATAATGTGTGTGTGTGTGTG
TGCTTGAACGCCACCTAT
Found at i:2387052 original size:16 final size:16
Alignment explanation
Indices: 2387028--2387059 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2387018 TATCGCCGAC
*
2387028 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2387044 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2387060 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2389474 original size:21 final size:21
Alignment explanation
Indices: 2389430--2389474 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2389420 ACTTAACACA
* *
2389430 TTTAGTATCTAAACTATCCGT
1 TTTAGTACCTAAACTATCAGT
* *
2389451 TTTAGTACCTAAACTTTCATT
1 TTTAGTACCTAAACTATCAGT
2389472 TTT
1 TTT
2389475 TTTAAAAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAGT
Found at i:2389677 original size:147 final size:146
Alignment explanation
Indices: 2389493--2389801 Score: 564
Period size: 147 Copynumber: 2.1 Consensus size: 146
2389483 TGAAGTATGA
*
2389493 TTTAGGTACTAAATGTGTTTTGGTAGCTAAACTTTTAACTTTTTCAACACTTAAGTTTTGGTACT
1 TTTAGGTACTAAATGCGTTTTGGTAGCTAAACTTTTAACTTTTTCAACACTTAAGTTTTGGTACT
2389558 AAAAATGAAATAAAAATTAAACTTTAGGAATGATTTTGAAAAAATTGAAAGTTTAGGTACTAAAA
66 AAAAATGAAATAAAAATTAAACTTTAGGAATGATTTTG-AAAAATTGAAAGTTTAGGTACTAAAA
*
2389623 AGGATCAAAATTGATAG
130 AGGATCAAAACTGATAG
*
2389640 TTTGGGTACTAAATGCGTTTTGGTAGCTAAACTTTTAACTTTTTCAACACTTAAGTTTTGGTACT
1 TTTAGGTACTAAATGCGTTTTGGTAGCTAAACTTTTAACTTTTTCAACACTTAAGTTTTGGTACT
* *
2389705 AAAAATGAAATAAAAATTAAACTTTAGGTATGATTTTGAAAAATTGAAAGTTTAGGTATTAAAAA
66 AAAAATGAAATAAAAATTAAACTTTAGGAATGATTTTGAAAAATTGAAAGTTTAGGTACTAAAAA
2389770 GGATCAAAACTGATAG
131 GGATCAAAACTGATAG
2389786 TTTAGGTACTAAATGC
1 TTTAGGTACTAAATGC
2389802 ATAGTTTACC
Statistics
Matches: 156, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
146 56 0.36
147 100 0.64
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.36
Consensus pattern (146 bp):
TTTAGGTACTAAATGCGTTTTGGTAGCTAAACTTTTAACTTTTTCAACACTTAAGTTTTGGTACT
AAAAATGAAATAAAAATTAAACTTTAGGAATGATTTTGAAAAATTGAAAGTTTAGGTACTAAAAA
GGATCAAAACTGATAG
Found at i:2391738 original size:2 final size:2
Alignment explanation
Indices: 2391709--2391757 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
2391699 GGAATATTTT
* *
2391709 TA TA CA TA TA CTA TA TT TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2391751 TA TA TA T
1 TA TA TA T
2391758 GTATTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2395068 original size:32 final size:31
Alignment explanation
Indices: 2395039--2395119 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 31
2395029 TTTATTTAAT
*
2395039 TTTTAAAAAATAAAAATTATTTCAAATTTAAAA
1 TTTT-AAAAATAAAAAATA-TTCAAATTTAAAA
* *
2395072 TTTTAAATATAAAAAATATTCAAATGTTCAATA
1 TTTTAAAAATAAAAAATATTCAAAT-TT-AAAA
* *
2395105 TATTAAATATAAAAA
1 TTTTAAAAATAAAAA
2395120 TACTAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 7 0.17
32 14 0.33
33 21 0.50
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (31 bp):
TTTTAAAAATAAAAAATATTCAAATTTAAAA
Found at i:2395087 original size:33 final size:33
Alignment explanation
Indices: 2395048--2395119 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
2395038 TTTTTAAAAA
* *
2395048 ATAAAAATTATTTCAAAT-TT-AAAATTTTAAAT
1 ATAAAAAATA-TTCAAATGTTCAAAATATTAAAT
*
2395080 ATAAAAAATATTCAAATGTTCAATATATTAAAT
1 ATAAAAAATATTCAAATGTTCAAAATATTAAAT
2395113 ATAAAAA
1 ATAAAAA
2395120 TACTAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 7 0.20
32 11 0.31
33 17 0.49
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (33 bp):
ATAAAAAATATTCAAATGTTCAAAATATTAAAT
Found at i:2395147 original size:15 final size:14
Alignment explanation
Indices: 2395106--2395181 Score: 59
Period size: 15 Copynumber: 5.3 Consensus size: 14
2395096 TGTTCAATAT
2395106 ATTAAATA-TAAAA
1 ATTAAATACTAAAA
*
2395119 ATACTAAA-AATAAAA
1 AT--TAAATACTAAAA
2395134 ATTAAATTACTAAAA
1 ATTAAA-TACTAAAA
*
2395149 ATTAAATA-TATAA
1 ATTAAATACTAAAA
*
2395162 TTTAAAATACTATAAA
1 ATT-AAATACTA-AAA
2395178 ATTA
1 ATTA
2395182 TTAAAGATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
13 12 0.24
14 8 0.16
15 26 0.52
16 4 0.08
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTAAATACTAAAA
Found at i:2395154 original size:28 final size:27
Alignment explanation
Indices: 2395106--2395181 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
2395096 TGTTCAATAT
2395106 ATTAAATA-TAAAAATACTAAAAATAAAA
1 ATTAAATACTAAAAAT--TAAAAATAAAA
* *
2395134 ATTAAATTACTAAAAATTAAATATATAA
1 ATTAAA-TACTAAAAATTAAAAATAAAA
*
2395162 TTTAAAATACTATAAAATTA
1 ATT-AAATACTA-AAAATTA
2395182 TTAAAGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 22 0.54
29 12 0.29
30 7 0.17
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (27 bp):
ATTAAATACTAAAAATTAAAAATAAAA
Found at i:2395163 original size:22 final size:22
Alignment explanation
Indices: 2395106--2395163 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
2395096 TGTTCAATAT
* *
2395106 ATTAAATATAAAAATACTAAAA
1 ATTAAATATATAATTACTAAAA
*
2395128 A-TAAAAAT-TAAATTACTAAAA
1 ATTAAATATAT-AATTACTAAAA
2395149 ATTAAATATATAATT
1 ATTAAATATATAATT
2395164 TAAAATACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 17 0.59
22 11 0.38
23 1 0.03
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (22 bp):
ATTAAATATATAATTACTAAAA
Found at i:2395808 original size:17 final size:17
Alignment explanation
Indices: 2395752--2395809 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
2395742 AGTATTGCAG
2395752 TATTTTTAATATATATTAA
1 TATTTTTAATAT-T-TTAA
* **
2395771 T-TTTTTAGTAATTTTTT
1 TATTTTTAAT-ATTTTAA
2395788 TATTTTTAATATTTTAA
1 TATTTTTAATATTTTAA
2395805 TATTT
1 TATTT
2395810 ATTTTTTTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 13 0.42
18 15 0.48
19 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTTTTAATATTTTAA
Found at i:2402533 original size:22 final size:22
Alignment explanation
Indices: 2402505--2402692 Score: 222
Period size: 22 Copynumber: 8.7 Consensus size: 22
2402495 GGACCATTAC
*
2402505 GTCCCTAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* *
2402527 GTCCCTAAGGAACACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* *
2402549 GTCCCTAAGAACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* *
2402571 GTCCCGAAGAACCAC----TAC
1 GTCCCGAAGGACCACTGGATAT
*
2402589 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAT
*
2402611 ATCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* *
2402633 GTCCCGAAGGACCATTGGATAC
1 GTCCCGAAGGACCACTGGATAT
* *
2402655 GTCCTGAAGGGCCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
*
2402677 GTCCCGAATGACCACT
1 GTCCCGAAGGACCACT
2402693 ATAAACTCTC
Statistics
Matches: 144, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
18 16 0.11
22 128 0.89
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAT
Found at i:2402593 original size:62 final size:62
Alignment explanation
Indices: 2402527--2402646 Score: 177
Period size: 62 Copynumber: 1.9 Consensus size: 62
2402517 CACTGGATAT
* ** *
2402527 GTCCCTAAGGAACACTGGATATGTCCCTAAGAACCACTGGATATGTCCCGAAGAACCACTAC
1 GTCCCGAAGGAACACTGGATACATCCCGAAGAACCACTGGATATGTCCCGAAGAACCACTAC
* * *
2402589 GTCCCGAAGGACCACTGGATACATCCCGAAGGACCACTGGATATGTCCCGAAGGACCA
1 GTCCCGAAGGAACACTGGATACATCCCGAAGAACCACTGGATATGTCCCGAAGAACCA
2402647 TTGGATACGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.17
Consensus pattern (62 bp):
GTCCCGAAGGAACACTGGATACATCCCGAAGAACCACTGGATATGTCCCGAAGAACCACTAC
Found at i:2402670 original size:84 final size:84
Alignment explanation
Indices: 2402487--2402670 Score: 242
Period size: 84 Copynumber: 2.2 Consensus size: 84
2402477 GTGAATATTT
* * * ** *
2402487 GTCCCAAAGGACCATTACGTCCCTAAGGACCACTGGATATGTCCCTAAGGAACACTGGATATGTC
1 GTCCCGAAGGACCACTACGTCCCGAAGGACCACTGGATACATCCCGAAGGAACACTGGATATGTC
* *
2402552 CCTAAGAACCACTGGATAT
66 CCGAAGAACCACTGGATAC
* *
2402571 GTCCCGAAGAACCACTACGTCCCGAAGGACCACTGGATACATCCCGAAGGACCACTGGATATGTC
1 GTCCCGAAGGACCACTACGTCCCGAAGGACCACTGGATACATCCCGAAGGAACACTGGATATGTC
* *
2402636 CCGAAGGACCATTGGATAC
66 CCGAAGAACCACTGGATAC
* *
2402655 GTCCTGAAGGGCCACT
1 GTCCCGAAGGACCACT
2402671 GGATATGTCC
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.18
Consensus pattern (84 bp):
GTCCCGAAGGACCACTACGTCCCGAAGGACCACTGGATACATCCCGAAGGAACACTGGATATGTC
CCGAAGAACCACTGGATAC
Found at i:2403724 original size:86 final size:86
Alignment explanation
Indices: 2403579--2403751 Score: 337
Period size: 86 Copynumber: 2.0 Consensus size: 86
2403569 AAGAATTATA
2403579 CCAACTTTGCAACATGATTTAATTCCACTTCTAACACTTAATATGTCTTAACTAGATTGATGACA
1 CCAACTTTGCAACATGATTTAATTCCACTTCTAACACTTAATATGTCTTAACTAGATTGATGACA
2403644 AATCAAATTTAACTTCCAATT
66 AATCAAATTTAACTTCCAATT
*
2403665 CCAACTTTGTAACATGATTTAATTCCACTTCTAACACTTAATATGTCTTAACTAGATTGATGACA
1 CCAACTTTGCAACATGATTTAATTCCACTTCTAACACTTAATATGTCTTAACTAGATTGATGACA
2403730 AATCAAATTTAACTTCCAATT
66 AATCAAATTTAACTTCCAATT
2403751 C
1 C
2403752 TAGATATGAA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (86 bp):
CCAACTTTGCAACATGATTTAATTCCACTTCTAACACTTAATATGTCTTAACTAGATTGATGACA
AATCAAATTTAACTTCCAATT
Found at i:2409008 original size:22 final size:22
Alignment explanation
Indices: 2408983--2409045 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
2408973 GACTGACCAC
2408983 TACGTCCCAAAGGACCACTGGA
1 TACGTCCCAAAGGACCACTGGA
*
2409005 TACGTCCCGAAA-AACCACTGGA
1 TACGTCCC-AAAGGACCACTGGA
* **
2409027 TATGTCCTGAAGGACCACT
1 TACGTCCCAAAGGACCACT
2409046 ATAAACCCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.06
22 29 0.85
23 3 0.09
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.17
Consensus pattern (22 bp):
TACGTCCCAAAGGACCACTGGA
Found at i:2409023 original size:40 final size:40
Alignment explanation
Indices: 2408927--2409015 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
2408917 AGTGAATATT
* *
2408927 CGTCCCGAATGACCATTACGTCCCTAAGGACCACTAGATA
1 CGTCCCGAATGACCACTACGTCCCAAAGGACCACTAGATA
* * *
2408967 TGTCCCGACTGACCACTACGTCCCAAAGGACCACTGGATA
1 CGTCCCGAATGACCACTACGTCCCAAAGGACCACTAGATA
2409007 CGTCCCGAA
1 CGTCCCGAA
2409016 AAACCACTGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.28, C:0.35, G:0.19, T:0.18
Consensus pattern (40 bp):
CGTCCCGAATGACCACTACGTCCCAAAGGACCACTAGATA
Done.