Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007825.1 Hibiscus syriacus cultivar Beakdansim tig00110163_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: 2082551
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:483321 original size:36 final size:36
Alignment explanation
Indices: 483205--483321 Score: 92
Period size: 36 Copynumber: 3.1 Consensus size: 36
483195 TTATCATAAC
* *
483205 TAACAATTTGTTTTAAGTTTTAAAGAGTAATCATAT
1 TAACAATTTGTTTTAAATTTTAAAAAGTAATCATAT
** * * * *
483241 TAATTATCATAGTTTATTTAATTGTCCAAAAA-TTATCATAAT
1 TAACAAT--TTG-TT-TTAAATT-T-TAAAAAGTAATCAT-AT
483283 TAACAATTTGTTTTAAATTTTAAAAAGTAATCATAT
1 TAACAATTTGTTTTAAATTTTAAAAAGTAATCATAT
483319 TAA
1 TAA
483322 TTATCATAGT
Statistics
Matches: 59, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
36 15 0.25
37 7 0.12
38 8 0.14
39 4 0.07
40 7 0.12
41 7 0.12
42 11 0.19
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (36 bp):
TAACAATTTGTTTTAAATTTTAAAAAGTAATCATAT
Found at i:483340 original size:42 final size:42
Alignment explanation
Indices: 483215--483343 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 42
483205 TAACAATTTG
* *
483215 TTTTAAGTTTTAAAGAGTAATCATATTAATTATCATAGTTTA
1 TTTTAAATTTTAAAAAGTAATCATATTAATTATCATAGTTTA
* * * *
483257 -TTT-AATTGTCCAAAAA-TTATC--A-TAATTAACA-A-TTTG
1 TTTTAAATT-T-TAAAAAGTAATCATATTAATTATCATAGTTTA
483293 TTTTAAATTTTAAAAAGTAATCATATTAATTATCATAGTTTA
1 TTTTAAATTTTAAAAAGTAATCATATTAATTATCATAGTTTA
483335 TTTTAAATT
1 TTTTAAATT
483344 CAAATTTTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
36 8 0.12
37 9 0.13
38 12 0.18
39 2 0.03
40 11 0.16
41 9 0.13
42 16 0.24
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (42 bp):
TTTTAAATTTTAAAAAGTAATCATATTAATTATCATAGTTTA
Found at i:483465 original size:16 final size:16
Alignment explanation
Indices: 483444--483476 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
483434 CAATTACAAA
*
483444 TCAGGTTTATAACAGG
1 TCAGGTTGATAACAGG
483460 TCAGGTTGATAACAGG
1 TCAGGTTGATAACAGG
483476 T
1 T
483477 TGGGTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (16 bp):
TCAGGTTGATAACAGG
Found at i:494356 original size:81 final size:81
Alignment explanation
Indices: 494217--494372 Score: 249
Period size: 81 Copynumber: 1.9 Consensus size: 81
494207 GTCCTCCAAA
* * * *
494217 TTTTTATCATTAAAGAATAATGGGACAATTACCTATTTAGGCTTTTAAATTTTCATTTATTTTGA
1 TTTTTATCATTAAAGAATAATGAGACAACTACCTATTTAGGCCTTTAAATTTTAATTTATTTTGA
*
494282 TTTTGCCCCCAAAATT
66 TTGTGCCCCCAAAATT
* *
494298 TTTTTATTATTAAAGAATAATGAGATAACTACCTATTTAGGCCTTTAAATTTTAATTTATTTTGA
1 TTTTTATCATTAAAGAATAATGAGACAACTACCTATTTAGGCCTTTAAATTTTAATTTATTTTGA
494363 TTGTGCCCCC
66 TTGTGCCCCC
494373 TCATTTTCTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (81 bp):
TTTTTATCATTAAAGAATAATGAGACAACTACCTATTTAGGCCTTTAAATTTTAATTTATTTTGA
TTGTGCCCCCAAAATT
Found at i:503253 original size:14 final size:14
Alignment explanation
Indices: 503231--503261 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
503221 AGAATTAAAG
*
503231 TTTATAGTAAGATA
1 TTTAAAGTAAGATA
503245 TTTAAAGTAAGATA
1 TTTAAAGTAAGATA
503259 TTT
1 TTT
503262 GAATAGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (14 bp):
TTTAAAGTAAGATA
Found at i:504004 original size:19 final size:20
Alignment explanation
Indices: 503967--504004 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
503957 AGAATGTCCA
503967 GGGGGTATCGATTCTCCCTG
1 GGGGGTATCGATTCTCCCTG
503987 GGGGGTATCGATTC-CCCT
1 GGGGGTATCGATTCTCCCT
504005 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.29
Consensus pattern (20 bp):
GGGGGTATCGATTCTCCCTG
Found at i:504822 original size:3 final size:3
Alignment explanation
Indices: 504816--504848 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
504806 TATACATGGG
504816 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
504849 TTGAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:506958 original size:23 final size:23
Alignment explanation
Indices: 506932--507022 Score: 164
Period size: 23 Copynumber: 4.0 Consensus size: 23
506922 CACCACAGCT
*
506932 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
506955 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
506978 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
507001 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
507023 ATATAATAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:507260 original size:149 final size:149
Alignment explanation
Indices: 506990--507304 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
506980 TAGAATTGCA
506990 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
**
507054 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
507119 CCACAGAATATATATATATC
130 CCAAAGAATATATATATATC
*
507139 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
507204 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
507268 CCAAAGAATATATATATATC
130 CCAAAGAATATATATATATC
507288 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
507305 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
150 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:508219 original size:18 final size:18
Alignment explanation
Indices: 508198--508232 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
508188 TCCCATCTAG
508198 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
508216 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
508233 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:508822 original size:64 final size:66
Alignment explanation
Indices: 508724--508848 Score: 202
Period size: 64 Copynumber: 1.9 Consensus size: 66
508714 TAATGAAGGT
*
508724 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTTAATGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
508788 G
66 G
*
508789 ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
508849 ATTCATGCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
63 1 0.02
64 30 0.54
65 25 0.45
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (66 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
G
Found at i:508879 original size:64 final size:63
Alignment explanation
Indices: 508724--508884 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
508714 TAATGAAGGT
* * *
508724 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
* * *
508789 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGC
* * *
508853 ATGCATCGATGCACTGCATGTACATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
508885 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 57 0.68
65 24 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:512039 original size:23 final size:23
Alignment explanation
Indices: 512013--512057 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
512003 CACCACAGCT
*
512013 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
512036 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
512058 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:512278 original size:149 final size:149
Alignment explanation
Indices: 512025--512339 Score: 526
Period size: 149 Copynumber: 2.1 Consensus size: 149
512015 TATAATTGCA
512025 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
* **
512089 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
512154 CCACAGAATATATATATATC
130 CCAAAGAATATATATATATC
* * *
512174 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCTATAAGGACCACATATAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
512239 TCCTTAAGAATCATATACATATGCTAAGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAAGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
512303 CCAAAGAATATATATATATC
130 CCAAAGAATATATATATATC
512323 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
512340 CCCTCGACTC
Statistics
Matches: 156, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
148 1 0.01
149 154 0.99
150 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:513249 original size:18 final size:18
Alignment explanation
Indices: 513228--513262 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
513218 TCCTATCTAG
513228 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
513246 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
513263 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:513909 original size:64 final size:63
Alignment explanation
Indices: 513754--513914 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
513744 TAATGAAGGT
* * *
513754 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
* * * * *
513819 ATGCATCAATGCACTCCTTATGCATCGGTGCATAAATCCTATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGC
* * *
513883 ATGCATCGATGCACTGCATGTACATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
513915 CCTTAAACAA
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
64 54 0.68
65 23 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:516621 original size:112 final size:112
Alignment explanation
Indices: 516419--516769 Score: 567
Period size: 112 Copynumber: 3.1 Consensus size: 112
516409 TTGTCGGTTT
* * * *
516419 GTGTTGATACTTTATAAAAATATATTGATCCATAACAATATAATAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAAAATGACAAAACC
* *
516484 GGTCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
*
516531 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAAAATGACAAAACC
*
516596 GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
* *
516643 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAAAATGACAAAACC
* * * *
516708 GGTCTATAAATGACAAAACAGGTAAAACGCTACCAAATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
*
516755 GTGTCTATACTTTAT
1 GTGTCGATACTTTAT
516770 TATAAGTATC
Statistics
Matches: 222, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 222 1.00
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
Found at i:516987 original size:162 final size:162
Alignment explanation
Indices: 516717--517231 Score: 699
Period size: 162 Copynumber: 3.1 Consensus size: 162
516707 CGGTCTATAA
* * * *
516717 ATGACAAAACAGGTAAA-ACGCTACCAAATATGTTGATAGTGTCTATACTTTATTATAAGTATCG
1 ATGACAAAACCGGTAAATA-GCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCG
* *
516781 ACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAAT
65 ACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAAT
* *
516846 ATATCGATCCATAACAATATAACATGTAAAAAT
130 GTATCGATCCATAACAATATAACAGGTAAAAAT
*
516879 ATGACAAAACCGGTAAATAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAATATCGA
1 ATGACAAAACCGGTAAATAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGA
* *
516944 CACTTTTAGAATTTAAAAGAGAATAAGTTATAACGCCAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
517009 TATCGATCCATAACAATATAACAGGTAAAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
517041 ATGACAAAACCGGTCTCGAAATGACAAAACCAGTAAAGAGCTACCAGATATGTTGAAAGTGTCGA
1 ATGACAAAACC-G----G---T-----AA--A-T----AGCTACCAGATATGTTGAAAGTGTCGA
* * *
517106 TACTTTATTATAAGTATCGACACTTATAGAATTTAAAAGAAAAGAAGTTGTAGCGCCAATAAAGT
46 TACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGT
*
517171 GTCGATACTTTATAAAAATGTATCGATCGATAACAATATAACAGGTAAAAAT
111 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAT
517223 ATGACAAAA
1 ATGACAAAA
517232 TCAGTCTCGA
Statistics
Matches: 314, Mismatches: 18, Indels: 22
0.89 0.05 0.06
Matches are distributed among these distances:
162 160 0.51
163 2 0.01
167 1 0.00
170 1 0.00
175 2 0.01
177 1 0.00
178 1 0.00
182 146 0.46
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (162 bp):
ATGACAAAACCGGTAAATAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGA
CACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAAT
Found at i:517186 original size:182 final size:182
Alignment explanation
Indices: 516879--517253 Score: 651
Period size: 182 Copynumber: 2.1 Consensus size: 182
516869 ATGTAAAAAT
* *
516879 ATGACAAAACCGGTAAATAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAATATCGA
1 ATGACAAAACCAGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAATATCGA
* * *
516944 CACTTTTAGAATTTAAAAGAGAATAAGTTATAACGCCAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTATAGAATTTAAAAGAAAAGAAGTTATAACGCCAATAAAGTGTCGATACTTTATAAAAATG
*
517009 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA
131 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAA
*
517061 ATGACAAAACCAGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACCAGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAATATCGA
* *
517126 CACTTATAGAATTTAAAAGAAAAGAAGTTGTAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTATAGAATTTAAAAGAAAAGAAGTTATAACGCCAATAAAGTGTCGATACTTTATAAAAATG
* *
517191 TATCGATCGATAACAATATAACAGGTAAAAATATGACAAAATCAGTCTCGAA
131 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAA
517243 ATGACAAAACC
1 ATGACAAAACC
517254 GATAGTAAAA
Statistics
Matches: 182, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
182 182 1.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (182 bp):
ATGACAAAACCAGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAATATCGA
CACTTATAGAATTTAAAAGAAAAGAAGTTATAACGCCAATAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAA
Found at i:517942 original size:23 final size:23
Alignment explanation
Indices: 517896--517943 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
517886 AAATAGGTTA
*
517896 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
* *
517919 ATATAAGCGCTACTTAATATATT
1 ATATAAGCGCTACCTAATACATT
517942 AT
1 AT
517944 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:529456 original size:15 final size:15
Alignment explanation
Indices: 529436--529465 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
529426 GAGCACAATT
*
529436 AATTTAATTTATAAA
1 AATTTAAATTATAAA
529451 AATTTAAATTATAAA
1 AATTTAAATTATAAA
529466 GTACTCAACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTAAATTATAAA
Found at i:531615 original size:64 final size:64
Alignment explanation
Indices: 531537--531664 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
531527 CTTTTACAAT
531537 CAAAGCGATTTCTTTTCAAAAGTGCACATTGGAATTGAAATTTGGTTTCGATTAATAGTTAGGA
1 CAAAGCGATTTCTTTTCAAAAGTGCACATTGGAATTGAAATTTGGTTTCGATTAATAGTTAGGA
531601 CAAAGCGATTTCTTTTCAAAAGTGCACATTGGAATTGAAATTTGGTTTCGATTAATAGTTAGGA
1 CAAAGCGATTTCTTTTCAAAAGTGCACATTGGAATTGAAATTTGGTTTCGATTAATAGTTAGGA
531665 GGAAGGATAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (64 bp):
CAAAGCGATTTCTTTTCAAAAGTGCACATTGGAATTGAAATTTGGTTTCGATTAATAGTTAGGA
Found at i:534566 original size:22 final size:21
Alignment explanation
Indices: 534535--534576 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
534525 TTGACAAGGT
534535 ACAACAAAT-ACTATAACAAAA
1 ACAACAAATAAC-ATAACAAAA
534556 ACAACAGAATAACATAACAAA
1 ACAACA-AATAACATAACAAA
534577 TTATCTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 11 0.58
23 2 0.11
ACGTcount: A:0.67, C:0.19, G:0.02, T:0.12
Consensus pattern (21 bp):
ACAACAAATAACATAACAAAA
Found at i:537265 original size:14 final size:14
Alignment explanation
Indices: 537238--537291 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 14
537228 TTCATTGAAA
537238 AACCGAAAAA-CCG
1 AACCGAAAAACCCG
537251 AACCGAAAAACCCG
1 AACCGAAAAACCCG
*
537265 AATCGTTAAAAAACCCG
1 AACCG---AAAAACCCG
537282 AACCGAAAAA
1 AACCGAAAAA
537292 ACCGGTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 10 0.29
14 12 0.34
17 13 0.37
ACGTcount: A:0.54, C:0.28, G:0.13, T:0.06
Consensus pattern (14 bp):
AACCGAAAAACCCG
Found at i:539723 original size:88 final size:88
Alignment explanation
Indices: 539625--539801 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
539615 TGATTAAAAG
539625 AAAATTTGTGATCCAAATTAGACCCAGAAACCCAGGAAAAATAATAGATAGGATATCCGAACAGT
1 AAAATTTGTGATCCAAATTAGACCCAGAAACCCAGGAAAAATAATAGATAGGATATCCGAACAGT
539690 AAATTCAAATATTTTAAATATAA
66 AAATTCAAATATTTTAAATATAA
539713 AAAATTTGTGATCCAAATTAGACCCAGAAACCCAGGAAAAATAATAGATAGGATATCCGAACAGT
1 AAAATTTGTGATCCAAATTAGACCCAGAAACCCAGGAAAAATAATAGATAGGATATCCGAACAGT
539778 AAATTCAAATATTTTAAATATAA
66 AAATTCAAATATTTTAAATATAA
539801 A
1 A
539802 TATCCGATAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (88 bp):
AAAATTTGTGATCCAAATTAGACCCAGAAACCCAGGAAAAATAATAGATAGGATATCCGAACAGT
AAATTCAAATATTTTAAATATAA
Found at i:540746 original size:2 final size:2
Alignment explanation
Indices: 540739--540782 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
540729 AAATACACTA
540739 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
540781 AT
1 AT
540783 TGATGGCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:543004 original size:13 final size:13
Alignment explanation
Indices: 542986--543032 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
542976 TTTTGAATAA
542986 TTTATGTAAGATT
1 TTTATGTAAGATT
*
542999 TTTATGTTAG-TGGT
1 TTTATGTAAGAT--T
*
543013 GTTATGTAAGATT
1 TTTATGTAAGATT
543026 TTTATGT
1 TTTATGT
543033 TAGTGGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 1 0.04
13 16 0.59
14 9 0.33
15 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.55
Consensus pattern (13 bp):
TTTATGTAAGATT
Found at i:543019 original size:14 final size:14
Alignment explanation
Indices: 543000--543045 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
542990 TGTAAGATTT
543000 TTATGTTAGTGGTG
1 TTATGTTAGTGGTG
* *
543014 TTATGTAAGAT--TT
1 TTATGTTAG-TGGTG
543027 TTATGTTAGTGGTG
1 TTATGTTAGTGGTG
543041 TTATG
1 TTATG
543046 GATTAATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 1 0.04
13 9 0.36
14 14 0.56
15 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (14 bp):
TTATGTTAGTGGTG
Found at i:543025 original size:27 final size:27
Alignment explanation
Indices: 542987--543045 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
542977 TTTGAATAAT
542987 TTATGTAAGATTTTTATGTTAGTGGTG
1 TTATGTAAGATTTTTATGTTAGTGGTG
543014 TTATGTAAGATTTTTATGTTAGTGGTG
1 TTATGTAAGATTTTTATGTTAGTGGTG
543041 TTATG
1 TTATG
543046 GATTAATTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (27 bp):
TTATGTAAGATTTTTATGTTAGTGGTG
Found at i:545667 original size:31 final size:31
Alignment explanation
Indices: 545592--545669 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
545582 TTCAAATTTC
* * *
545592 AAGTGAACAAAACCTAATAAAACGATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
545623 AAGTGACCAAAACTTAATAAAACAATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
545654 AAGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
545670 TGCTTTTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.56, C:0.17, G:0.09, T:0.18
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:563793 original size:16 final size:16
Alignment explanation
Indices: 563772--563804 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
563762 AAGTCGAGTT
563772 GATCTGGGTCAATCGG
1 GATCTGGGTCAATCGG
*
563788 GATCTGTGTCAATCGG
1 GATCTGGGTCAATCGG
563804 G
1 G
563805 TTTGGAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.27
Consensus pattern (16 bp):
GATCTGGGTCAATCGG
Found at i:564082 original size:47 final size:47
Alignment explanation
Indices: 564031--564134 Score: 149
Period size: 47 Copynumber: 2.2 Consensus size: 47
564021 CTCAAAAAAA
* * *
564031 CCGAATCGAACCGAAA-TCGACCCGAATTTTAGCC-AACCGAAAGTAAC
1 CCGAACCGAACCGAAACT-GACCCGAA-TTTAACCAAACCAAAAGTAAC
564078 CCGAACCGAACCGAAACTGACCCGAATTTAACCAAACCAAAAGTAAC
1 CCGAACCGAACCGAAACTGACCCGAATTTAACCAAACCAAAAGTAAC
564125 CCGAACCGAA
1 CCGAACCGAA
564135 AGCAACTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
46 6 0.12
47 45 0.87
48 1 0.02
ACGTcount: A:0.41, C:0.32, G:0.15, T:0.12
Consensus pattern (47 bp):
CCGAACCGAACCGAAACTGACCCGAATTTAACCAAACCAAAAGTAAC
Found at i:564086 original size:16 final size:16
Alignment explanation
Indices: 564065--564175 Score: 57
Period size: 16 Copynumber: 7.1 Consensus size: 16
564055 AATTTTAGCC
564065 AACCGAAAGTAACCCG
1 AACCGAAAGTAACCCG
* * *
564081 AACCGAACCG-AAACTG
1 AACCGAA-AGTAACCCG
* ** *
564097 ACCCGAATTTAA-CCA
1 AACCGAAAGTAACCCG
*
564112 AACCAAAAGTAACCCG
1 AACCGAAAGTAACCCG
* **
564128 AACCGAAAGCAA-CTA
1 AACCGAAAGTAACCCG
* **
564143 AACCGAAAATAACGTG
1 AACCGAAAGTAACCCG
*
564159 AACCGAAATTAACCCG
1 AACCGAAAGTAACCCG
564175 A
1 A
564176 TTTTAATTTA
Statistics
Matches: 67, Mismatches: 24, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
15 20 0.30
16 46 0.69
17 1 0.01
ACGTcount: A:0.47, C:0.29, G:0.14, T:0.10
Consensus pattern (16 bp):
AACCGAAAGTAACCCG
Found at i:564557 original size:26 final size:26
Alignment explanation
Indices: 564528--564617 Score: 153
Period size: 26 Copynumber: 3.5 Consensus size: 26
564518 AACTGAAATG
* *
564528 ACCCAAACCGAAGTGGCCCGAATCGA
1 ACCCAATCCGAAGTGGGCCGAATCGA
*
564554 ACCCAATCCGAAGTGGGCTGAATCGA
1 ACCCAATCCGAAGTGGGCCGAATCGA
564580 ACCCAATCCGAAGTGGGCCGAATCGA
1 ACCCAATCCGAAGTGGGCCGAATCGA
564606 ACCCAATCCGAA
1 ACCCAATCCGAA
564618 TGACCTATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.33, C:0.32, G:0.23, T:0.11
Consensus pattern (26 bp):
ACCCAATCCGAAGTGGGCCGAATCGA
Found at i:568761 original size:2 final size:2
Alignment explanation
Indices: 568756--568787 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
568746 TTGACGGTAC
568756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
568788 AAAGACACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:575300 original size:39 final size:39
Alignment explanation
Indices: 575241--575345 Score: 192
Period size: 39 Copynumber: 2.7 Consensus size: 39
575231 TTCTCAATAG
*
575241 TATTTCCAATACTATGTGGGATTGAGCATTACCAACACT
1 TATTCCCAATACTATGTGGGATTGAGCATTACCAACACT
575280 TATTCCCAATACTATGTGGGATTGAGCATTACCAACACT
1 TATTCCCAATACTATGTGGGATTGAGCATTACCAACACT
*
575319 TGTTCCCAATACTATGTGGGATTGAGC
1 TATTCCCAATACTATGTGGGATTGAGC
575346 TTTAAATAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 64 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (39 bp):
TATTCCCAATACTATGTGGGATTGAGCATTACCAACACT
Found at i:575678 original size:6 final size:6
Alignment explanation
Indices: 575662--575693 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
575652 GTCCGTCTCG
575662 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
575694 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:579163 original size:15 final size:15
Alignment explanation
Indices: 579143--579173 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
579133 ATGCGAAGGG
579143 CCTGAACGATACCTT
1 CCTGAACGATACCTT
579158 CCTGAACGATACCTT
1 CCTGAACGATACCTT
579173 C
1 C
579174 GAAGCATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (15 bp):
CCTGAACGATACCTT
Found at i:579675 original size:188 final size:188
Alignment explanation
Indices: 579328--579681 Score: 505
Period size: 188 Copynumber: 1.9 Consensus size: 188
579318 GTACTTTTTT
* *
579328 CCACGGAGACACTTTAAGAAAAACCATGTCGCCCACAGTAAACTCAACTTCTTTGCGCTTAAAAT
1 CCACAGAGACACTTTAAGAAAAACCATGTCGCCCACAATAAACTCAACTTCTTTGCGCTTAAAAT
* ** * * *
579393 TCTCATACGACCTTTGTTTATCCAATGCTGGTCTCACTATCTTTCACTCACTAACCTCAGTCTAA
66 TATCATACGACCTTTGCATATCCAATGCTAGTCCCACTATCTTTCACTCACTAACCTCAGTCCAA
*
579458 CAAAGGGGAGTTCTACACTTTCACCCATAAAGAGCTCCATATGGAGCCATCTAGATGC
131 CAAAGGGGAGTTATACACTTTCACCCATAAAGAGCTCCATATGGAGCCATCTAGATGC
* **
579516 CCACAGAGACACTTTAAGAAAAACCTTGTTTCCCACAATAAACTCAACTTCTTTGCGCTTCAAAA
1 CCACAGAGACACTTTAAGAAAAACCATGTCGCCCACAATAAACTCAACTTCTTTGCGCTT-AAAA
* * *
579581 -TATCATACTACTTTTGCATATCCAATGCTAGTCCCACTATCTTTC-CTTCACTAACCTCGGTCC
65 TTATCATACGACCTTTGCATATCCAATGCTAGTCCCACTATCTTTCAC-TCACTAACCTCAGTCC
* * * *
579644 AACAGAGGGTAGTTATACATTTTCGCCCATAAAGAGCT
129 AACAAAGGGGAGTTATACACTTTCACCCATAAAGAGCT
579682 TTGTATAGAG
Statistics
Matches: 145, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
187 1 0.01
188 140 0.97
189 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (188 bp):
CCACAGAGACACTTTAAGAAAAACCATGTCGCCCACAATAAACTCAACTTCTTTGCGCTTAAAAT
TATCATACGACCTTTGCATATCCAATGCTAGTCCCACTATCTTTCACTCACTAACCTCAGTCCAA
CAAAGGGGAGTTATACACTTTCACCCATAAAGAGCTCCATATGGAGCCATCTAGATGC
Found at i:582643 original size:20 final size:20
Alignment explanation
Indices: 582618--582655 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
582608 CATATTTTAA
*
582618 AGAATGCATTGATGCACTGT
1 AGAATGCATCGATGCACTGT
582638 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
582656 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:587136 original size:65 final size:65
Alignment explanation
Indices: 586997--587159 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 65
586987 AATTATTCAG
* *
586997 AGTGTATCGATGCACAGGAAGTGCATCGATGCA-CCCCTTAAAAATAGAAACATCGAATGCAGTT
1 AGTGTATCGATGCATAGGTAGTGCATCGATGCACCCCCTTAAAAATAGAAACATCGAATGCAGTT
* *
587061 AGTGCATCGATGTATTAGG-AGTGCATCGATGCACCCACCTT-AAAAT-GAAAACATCGAAGGTG
1 AGTGTATCGATGCA-TAGGTAGTGCATCGATGCACCC-CCTTAAAAATAG-AAACATCGAA--TG
587123 -A-TT
61 CAGTT
*
587126 GGTGTATCGATGCAT-GGTTAGTGCATCGATGCAC
1 AGTGTATCGATGCATAGG-TAGTGCATCGATGCAC
587160 ATGTTAAAGA
Statistics
Matches: 85, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
63 2 0.02
64 28 0.33
65 48 0.56
66 5 0.06
67 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (65 bp):
AGTGTATCGATGCATAGGTAGTGCATCGATGCACCCCCTTAAAAATAGAAACATCGAATGCAGTT
Found at i:587174 original size:24 final size:20
Alignment explanation
Indices: 587147--587204 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
587137 GCATGGTTAG
587147 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
* *
587171 TGCATCAATGTACTGTAGAA
1 TGCATCGATGCACTGTAGAA
587191 TGCATCGATGCACT
1 TGCATCGATGCACT
587205 TCAAGGGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 16 0.53
22 1 0.03
23 2 0.07
24 11 0.37
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:587883 original size:15 final size:15
Alignment explanation
Indices: 587860--587907 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
587850 CGTAGGACTC
*
587860 CTACATCCCGAAGGA
1 CTACGTCCCGAAGGA
587875 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
587890 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
587905 CTA
1 CTA
587908 TTATACCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (15 bp):
CTACGTCCCGAAGGA
Found at i:588038 original size:29 final size:29
Alignment explanation
Indices: 587992--588069 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
587982 TTTCATATGT
*
587992 TCATGTA-CTCATGTCATTTTTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
588020 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
588049 TCATGTAGCTCATGTCATTTC
1 TCATGTAGCTCATGTCATTTC
588070 ATATCATGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.15
29 41 0.85
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:588098 original size:12 final size:12
Alignment explanation
Indices: 588081--588128 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
588071 TATCATGTTC
588081 TCATATCACATG
1 TCATATCACATG
*
588093 TCATATCACATA
1 TCATATCACATG
588105 TCATATCACATAG
1 TCATATCACAT-G
588118 -CATATCACATG
1 TCATATCACATG
588129 AACATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 1 0.03
12 32 0.97
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATG
Found at i:594074 original size:21 final size:22
Alignment explanation
Indices: 594037--594080 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
594027 TCCAAAATGA
594037 AAAAGGATACTCTATCACTAGTG
1 AAAAGGATAC-CTATCACTAGTG
594060 AAAAGGATA-CTATCACTAGTG
1 AAAAGGATACCTATCACTAGTG
594081 TTAGAAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.57
23 9 0.43
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (22 bp):
AAAAGGATACCTATCACTAGTG
Found at i:605766 original size:6 final size:6
Alignment explanation
Indices: 605747--605780 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
605737 TTCCTTCACA
* *
605747 CTCTTT CCCTTT CTCCTT CTCTTT CTCTTT CTCT
1 CTCTTT CTCTTT CTCTTT CTCTTT CTCTTT CTCT
605781 GTGCAAGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (6 bp):
CTCTTT
Found at i:610528 original size:2 final size:2
Alignment explanation
Indices: 610521--610551 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
610511 CTTAAGATAC
610521 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
610552 ACATTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:614751 original size:32 final size:32
Alignment explanation
Indices: 614715--614782 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
614705 ACGAGCATTT
614715 ATAAAATCCAAAATTCAAGTCTCAAAATCCAA
1 ATAAAATCCAAAATTCAAGTCTCAAAATCCAA
614747 ATAAAATCCAAAATTCAAGTCTCAAAATCCAA
1 ATAAAATCCAAAATTCAAGTCTCAAAATCCAA
614779 ATAA
1 ATAA
614783 CGTTTAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.54, C:0.21, G:0.03, T:0.22
Consensus pattern (32 bp):
ATAAAATCCAAAATTCAAGTCTCAAAATCCAA
Found at i:616301 original size:20 final size:20
Alignment explanation
Indices: 616278--616327 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
616268 GAATATGTAA
*
616278 ATCGCAACGCGATTCTGACT
1 ATCGCAACACGATTCTGACT
616298 ATCGCAACACGATTCTGACT
1 ATCGCAACACGATTCTGACT
616318 ATCGCAACAC
1 ATCGCAACAC
616328 TGAATTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (20 bp):
ATCGCAACACGATTCTGACT
Found at i:616487 original size:22 final size:21
Alignment explanation
Indices: 616462--616512 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 21
616452 CTCTCTCCGG
616462 CGACATCCGTTCCTATATCCAA
1 CGACATCC-TTCCTATATCCAA
616484 CGACA----TCCTATATCCAA
1 CGACATCCTTCCTATATCCAA
616501 CGACATCCTTCC
1 CGACATCCTTCC
616513 CCATCCGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
17 17 0.68
21 3 0.12
22 5 0.20
ACGTcount: A:0.27, C:0.39, G:0.08, T:0.25
Consensus pattern (21 bp):
CGACATCCTTCCTATATCCAA
Found at i:616494 original size:17 final size:17
Alignment explanation
Indices: 616472--616509 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
616462 CGACATCCGT
616472 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
616489 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
616506 TCCT
1 TCCT
616510 TCCCCATCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.26
Consensus pattern (17 bp):
TCCTATATCCAACGACA
Found at i:619467 original size:18 final size:18
Alignment explanation
Indices: 619444--619478 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
619434 AGCAAAAGGC
619444 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
619462 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
619479 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:619674 original size:20 final size:20
Alignment explanation
Indices: 619649--619725 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
619639 TTACACATTC
619649 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
619669 ATTTGACTATCGCAACGTGA
1 ATTTGAATATCGCAACGCGA
* * *
619689 ATTTGATTATCTCAACGGGA
1 ATTTGAATATCGCAACGCGA
619709 ATTT-AACTATCGCAACG
1 ATTTGAA-TATCGCAACG
619726 AGAAAATCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:619705 original size:40 final size:40
Alignment explanation
Indices: 619649--619725 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
619639 TTACACATTC
*
619649 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGTGA
1 ATTTGAATATCGCAACGCGAATTTAACTATCGCAACGTGA
* * *
619689 ATTTGATTATCTCAACGGGAATTTAACTATCGCAACG
1 ATTTGAATATCGCAACGCGAATTTAACTATCGCAACG
619726 AGAAAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (40 bp):
ATTTGAATATCGCAACGCGAATTTAACTATCGCAACGTGA
Found at i:619774 original size:19 final size:20
Alignment explanation
Indices: 619731--619774 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
619721 CAACGAGAAA
*
619731 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
619751 ATCGCAACGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
619770 TTCGC
1 ATCGC
619775 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:619794 original size:20 final size:20
Alignment explanation
Indices: 619769--619841 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
619759 GCGAATTGAC
*
619769 TTTCGCGTTGCGATTTTGGT
1 TTTCGCATTGCGATTTTGGT
**
619789 TTTCGCATTGCGATTTTGAC
1 TTTCGCATTGCGATTTTGGT
619809 TTTCGCATTGCGATTTTGAG-
1 TTTCGCATTGCGATTTTG-GT
*
619829 TTTAGCATTGCGA
1 TTTCGCATTGCGA
619842 AAGTGTACCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTGGT
Found at i:619808 original size:40 final size:40
Alignment explanation
Indices: 619764--619841 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
619754 GCAACGCGAA
* *
619764 TTGACTTTCGCGTTGCGATTTTG-GTTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATTTTGAG-TTTAGCATTGCGATT
619804 TTGACTTTCGCATTGCGATTTTGAGTTTAGCATTGCGA
1 TTGACTTTCGCATTGCGATTTTGAGTTTAGCATTGCGA
619842 AAGTGTACCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (40 bp):
TTGACTTTCGCATTGCGATTTTGAGTTTAGCATTGCGATT
Found at i:620005 original size:67 final size:68
Alignment explanation
Indices: 619889--620071 Score: 184
Period size: 71 Copynumber: 2.7 Consensus size: 68
619879 TGCAGATTGA
* *
619889 AATT-AACAAATCAAATTTTACATTTCAATCAATTAAACAAGC---ACAAATAAGAA-TTATTTA
1 AATTAAACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAAAAATAAGAATTTATTT-
619949 T-ACATC
62 TCACATC
*
619955 AATTAAACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTT
1 AATTAAACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAA-AATAAGAA-T-TTATTTT
*
620019 CCTCATC
63 -CACATC
* *
620026 AATTAAACAAATCAACTTTTA-AGAATCAATTAAACAATCAAAAAAA
1 AATTAAACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAA
620072 GTGTACCCCA
Statistics
Matches: 101, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
63 16 0.16
66 6 0.06
67 24 0.24
69 1 0.01
70 8 0.08
71 46 0.46
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.30
Consensus pattern (68 bp):
AATTAAACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAAATAAGAATTTATTTTCAC
ATC
Found at i:621342 original size:21 final size:21
Alignment explanation
Indices: 621318--621415 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
621308 GGGAGGAACA
*
621318 TCTTCAACGATGACAGAGGCC
1 TCTTGAACGATGACAGAGGCC
* ** * *
621339 TCTTGAACGGTGGGAGGGGAC
1 TCTTGAACGATGACAGAGGCC
* * *
621360 TCTTG-AGGATGATAGTGGCC
1 TCTTGAACGATGACAGAGGCC
*
621380 TCTTGAACGAT-AGGAGAGGCC
1 TCTTGAACGATGA-CAGAGGCC
621401 TCTTGAACGATGACA
1 TCTTGAACGATGACA
621416 TGTGATTCAG
Statistics
Matches: 58, Mismatches: 16, Indels: 6
0.73 0.20 0.08
Matches are distributed among these distances:
20 15 0.26
21 42 0.72
22 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (21 bp):
TCTTGAACGATGACAGAGGCC
Found at i:621383 original size:41 final size:41
Alignment explanation
Indices: 621326--621415 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
621316 CATCTTCAAC
* * *
621326 GATGACAGAGGCCTCTTGAACGGTGGGAGGGGACTCTTGAG
1 GATGACAGAGGCCTCTTGAACGATAGGAGAGGACTCTTGAG
* * * *
621367 GATGATAGTGGCCTCTTGAACGATAGGAGAGGCCTCTTGAAC
1 GATGACAGAGGCCTCTTGAACGATAGGAGAGGACTCTTG-AG
621409 GATGACA
1 GATGACA
621416 TGTGATTCAG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 33 0.82
42 7 0.17
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.21
Consensus pattern (41 bp):
GATGACAGAGGCCTCTTGAACGATAGGAGAGGACTCTTGAG
Found at i:621930 original size:20 final size:20
Alignment explanation
Indices: 621907--621951 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
621897 CTTAAAATCA
621907 CAACGCGAAA-ATGACTATCG
1 CAACGCGAAATA-GACTATCG
*
621927 CAACGCGAATTAGACTATCG
1 CAACGCGAAATAGACTATCG
621947 CAACG
1 CAACG
621952 GGATAATCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAATAGACTATCG
Found at i:621980 original size:19 final size:19
Alignment explanation
Indices: 621956--622013 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
621946 GCAACGGGAT
*
621956 AATCGCAATGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
621975 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
621994 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAA-TAAA
622014 TTCGTTTTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 31 0.94
20 2 0.06
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:624071 original size:20 final size:20
Alignment explanation
Indices: 624031--624071 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
624021 TATGAAACTT
* *
624031 AAAATCGCAACACGAATATG
1 AAAATCGCAACACAAAAATG
624051 AAAATCGCAACACAAAAATG
1 AAAATCGCAACACAAAAATG
624071 A
1 A
624072 CTATTGCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACAAAAATG
Found at i:624135 original size:33 final size:33
Alignment explanation
Indices: 624094--624164 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
624084 GAATTTGACT
624094 ATCGCAACGAGATAATCACAACGCGAAA-TGAAA
1 ATCGCAACGAGATAATCACAACGCGAAACT-AAA
* *
624127 ATCGCAACGAGATAATCGCAATGCGAAACTAAA
1 ATCGCAACGAGATAATCACAACGCGAAACTAAA
624160 ATCGC
1 ATCGC
624165 GTTGCGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGATAATCACAACGCGAAACTAAA
Found at i:624572 original size:20 final size:21
Alignment explanation
Indices: 624547--624586 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
624537 TCTGAGAGAT
624547 GGAGATA-GACGGATTTCGCC
1 GGAGATAGGACGGATTTCGCC
624567 GGAGATAGGGACGGATTTCG
1 GGAGATA-GGACGGATTTCG
624587 TCGAAGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.20
Consensus pattern (21 bp):
GGAGATAGGACGGATTTCGCC
Found at i:624594 original size:22 final size:22
Alignment explanation
Indices: 624554--624599 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
624544 GATGGAGATA
*
624554 GACGGATTTCGCCGGAGATAGG
1 GACGGATTTCGCCGAAGATAGG
* *
624576 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGCCGAAGATAGG
624598 GA
1 GA
624600 TAGATGTCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.41, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATAGG
Found at i:624777 original size:20 final size:20
Alignment explanation
Indices: 624749--624862 Score: 147
Period size: 20 Copynumber: 5.7 Consensus size: 20
624739 GCGCTTTAAA
624749 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
624769 AATCACGTTGCGGTAGTCAG
1 AATCGCGTTGCGATAGTCAG
624789 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* * *
624809 AATCGTGCTACGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*** *
624829 AATCGTACTACGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
624849 AATCGCGTTGCGAT
1 AATCGCGTTGCGAT
624863 TTACATATTC
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:633158 original size:3 final size:3
Alignment explanation
Indices: 633152--633250 Score: 146
Period size: 3 Copynumber: 33.0 Consensus size: 3
633142 TTCATTTAAA
* * *
633152 ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
633200 ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT AAT ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
633245 ATT ATT
1 ATT ATT
633251 TAATAAATAA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.02
3 81 0.94
4 3 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:635805 original size:244 final size:242
Alignment explanation
Indices: 635376--635861 Score: 945
Period size: 244 Copynumber: 2.0 Consensus size: 242
635366 ATACCATCGT
635376 TTGCATCAATTTCACATCGTTAAAGAAGAGGCCTTGTGAGTTTCAAAACCCATTCCTTATTCCAC
1 TTGCATCAATTTCACATCGTTAAAGAAGAGGCCTTGTGAGTTTCAAAACCCATTCCTTATTCCAC
635441 AATTCTAGTTAAGAGTATATGAATACCATATTGAGGCTGCGTGGTGATGAACAGCATAGGGGCAT
66 AATTCTAGTTAAGAGTATATGAATACCATATTGAGGCTGCGTGGTGATGAACAGCATAGGGGCAT
635506 GAACATATGTCGACGACACTGCCAGTGAGTATTGCCGGATAATCATAGCTATAGCTATTTTCATC
131 GAACATATGTCGACGACACTGCCAGTGAGTATTGCCGGATAATCATAGCTATAGCTATTTTCATC
635571 TCAACCATGGCTAAATTCTGGCCGACACAAATTCTAGGCCATAAACCGA
196 TCAACCATGGCTAAATTCTGGCCG--ACAAATTCTAGGCCATAAACCGA
635620 TTGCATCAATTTCACATCGTTAAAGAAGAGGCCTTGTGAGTTTCAAAACCCATTCCTTATTCCAC
1 TTGCATCAATTTCACATCGTTAAAGAAGAGGCCTTGTGAGTTTCAAAACCCATTCCTTATTCCAC
635685 AATTCTAGTTAAGAGTATATGAATACCATATTGAGGCTGCGTGGTGATGAACAGCATAGGGGCAT
66 AATTCTAGTTAAGAGTATATGAATACCATATTGAGGCTGCGTGGTGATGAACAGCATAGGGGCAT
635750 GAACATATGTCGACGACACTGCCAGTGAGTATTGCCGGATAATCATAGCTATAGCTATTTTCATC
131 GAACATATGTCGACGACACTGCCAGTGAGTATTGCCGGATAATCATAGCTATAGCTATTTTCATC
*
635815 TCAACCATGGCTAAATTCTGGCCGACAAATTCTAGGCCCTAAACCGA
196 TCAACCATGGCTAAATTCTGGCCGACAAATTCTAGGCCATAAACCGA
635862 GTGGAATAAA
Statistics
Matches: 241, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
242 22 0.09
244 219 0.91
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (242 bp):
TTGCATCAATTTCACATCGTTAAAGAAGAGGCCTTGTGAGTTTCAAAACCCATTCCTTATTCCAC
AATTCTAGTTAAGAGTATATGAATACCATATTGAGGCTGCGTGGTGATGAACAGCATAGGGGCAT
GAACATATGTCGACGACACTGCCAGTGAGTATTGCCGGATAATCATAGCTATAGCTATTTTCATC
TCAACCATGGCTAAATTCTGGCCGACAAATTCTAGGCCATAAACCGA
Found at i:636975 original size:26 final size:26
Alignment explanation
Indices: 636939--636992 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
636929 ATTTCAGGTA
636939 CCCAACCCTGCAATTAAAGTATACTT
1 CCCAACCCTGCAATTAAAGTATACTT
636965 CCCAACCCTGCAATTAAAGTATACTT
1 CCCAACCCTGCAATTAAAGTATACTT
636991 CC
1 CC
636993 ATAGAGGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.26
Consensus pattern (26 bp):
CCCAACCCTGCAATTAAAGTATACTT
Found at i:637796 original size:7 final size:7
Alignment explanation
Indices: 637784--637819 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
637774 ATAAGTAGAA
637784 AATATTT
1 AATATTT
637791 AATATTT
1 AATATTT
637798 AATATTT
1 AATATTT
*
637805 AATATAT
1 AATATTT
*
637812 ATTATTT
1 AATATTT
637819 A
1 A
637820 TAAACTTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATATTT
Found at i:645050 original size:2 final size:2
Alignment explanation
Indices: 645043--645069 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
645033 CGATACATAC
645043 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
645070 AGTATTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:645710 original size:75 final size:75
Alignment explanation
Indices: 645587--645844 Score: 327
Period size: 75 Copynumber: 3.4 Consensus size: 75
645577 CTTAATCGGT
* * * * *
645587 TAAAATAAAATAGGCGCTAACTATTATGTTAAACTACCTACCAGTTTGTTTAAAGGTTATTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTATCTATCAGTTTGTTTAAAGGTTACTAATA
* *
645652 ATGTAAAAGA
66 ATGTAAACGG
* * * *
645662 TAAAATAAAATAGGTGCTACCTATTACGTTAAAATATATGTCAGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTATCTATCAGTTTGTTTAAAGGTTACTAATA
645727 ATGTAAACGG
66 ATGTAAACGG
* * * ** **
645737 TAAAATAAAATAGACACTACATATTACGTTAAACTATCTATTGGTTTGTTTAAAGGTTACCGATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTATCTATCAGTTTGTTTAAAGGTTACTAATA
*
645802 ATGTTAACGG
66 ATGTAAACGG
* *
645812 TAAAATAAAATAAGTGCTACCTATTACGTTAAA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAA
645845 TAAGCGTTAC
Statistics
Matches: 155, Mismatches: 28, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 155 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAACTATCTATCAGTTTGTTTAAAGGTTACTAATA
ATGTAAACGG
Found at i:645845 original size:23 final size:23
Alignment explanation
Indices: 645819--645890 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
645809 CGGTAAAATA
* *
645819 AAATAAGTGCTACCTATTACGTT
1 AAATAAGCGCTACATATTACGTT
*
645842 AAATAAGCGTTACATATTACGTT
1 AAATAAGCGCTACATATTACGTT
*
645865 AAATAAGCGCTACATATTATGTT
1 AAATAAGCGCTACATATTACGTT
645888 AAA
1 AAA
645891 CTAACTACTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (23 bp):
AAATAAGCGCTACATATTACGTT
Found at i:645957 original size:120 final size:121
Alignment explanation
Indices: 645753--646228 Score: 512
Period size: 121 Copynumber: 4.0 Consensus size: 121
645743 AAAATAGACA
* ** *** *
645753 CTACATATTACGTTAAACTATCTATTGGTTTGTTTAAAGGTTACCGATAATGTTAACGGTAAAAT
1 CTACATATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAAT
* * * *
645818 AAAATA-AGTGCTACCTATTACGTTAAATAAGCGTTA-CATATTACGTTAAATAAGCG
66 AAAATAGA-CGCTACATATTACGTTAAATAAGCGCTATC-TATTACGTTAAATAAGTG
* * *
645874 CTACATATTATGTTAAACTAACTACTGGTTTGTTTAAATGTTAAT-ATAATGTAAACGGTAAAAT
1 CTACATATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAAT
* * * * *
645938 AAAATAGACGCTACATATTATGTTAAATAGGCGTTATCTATTAGGTTAAATAAGTA
66 AAAATAGACGCTACATATTACGTTAAATAAGCGCTATCTATTACGTTAAATAAGTG
* * ** * *
645994 CTACCTATTGCGTTAAACTAGTTACCGATTTGTTTAAAGGTTAATAATAATATAAACGGTAAAAT
1 CTACATATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAAT
* * * * * * *
646059 AAAATAGGCGTTGCCTATTATGTTAAAT-AGACGCCATCTATTAGGTTAAATAAGTG
66 AAAATAGACGCTACATATTACGTTAAATAAG-CGCTATCTATTACGTTAAATAAGTG
* * * *
646115 TTACCTATTAGGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAACT
1 CTACATATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAAT
* * * * * *
646180 AAAATAGGCGTTGCATATTACATTAAATAACCGCTA-CAATTACGTTAAA
66 AAAATAGACGCTACATATTACGTTAAATAAGCGCTATCTATTACGTTAAA
646229 CTAGCTACCG
Statistics
Matches: 304, Mismatches: 46, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
120 112 0.37
121 191 0.63
122 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (121 bp):
CTACATATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAAT
AAAATAGACGCTACATATTACGTTAAATAAGCGCTATCTATTACGTTAAATAAGTG
Found at i:646709 original size:28 final size:28
Alignment explanation
Indices: 646677--646734 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
646667 TAAAATATCA
646677 AACATCATAGATGATATTAATATTTGCT
1 AACATCATAGATGATATTAATATTTGCT
*
646705 AACATCATAGATGATATTGATATTTGCT
1 AACATCATAGATGATATTAATATTTGCT
646733 AA
1 AA
646735 AGTATTGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (28 bp):
AACATCATAGATGATATTAATATTTGCT
Found at i:647114 original size:108 final size:108
Alignment explanation
Indices: 646922--647198 Score: 383
Period size: 108 Copynumber: 2.6 Consensus size: 108
646912 TATTTATTAG
* * * * * * *
646922 AAAATAAGAAATTAACATATATTGTTGTCGTCGGATTCCGAAGGCCCCATCAGCTTAAACTTTGG
1 AAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAACTTAAACTTTGG
* **
646987 TAACATTTTAGGAGTTACCTAATGTGTTGATAATATTAATAAC
66 TAACATTTTAGGAGCTACCTAATACGTTGATAATATTAATAAC
*
647030 AAAATAAGTAATTAACCTATTTTGTTATCGTTGGATTTCTAAGGCCCCATCAACTTAAACTTTGG
1 AAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAACTTAAACTTTGG
* *
647095 TAATATTTTAGGCGCTACCTAATACGTTGATAATATTAATAAC
66 TAACATTTTAGGAGCTACCTAATACGTTGATAATATTAATAAC
* * * **
647138 AAATTAAATAATTAAACTATTTTGTTATCGTCATATTTCTAAGGCCCCATCAACTTTAAAC
1 AAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAAC-TTAAAC
647199 ATGCACTATT
Statistics
Matches: 149, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
108 143 0.96
109 6 0.04
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (108 bp):
AAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAACTTAAACTTTGG
TAACATTTTAGGAGCTACCTAATACGTTGATAATATTAATAAC
Found at i:650463 original size:14 final size:13
Alignment explanation
Indices: 650416--650455 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
650406 TTTAGCCTCA
650416 AATT-TATTTATT
1 AATTATATTTATT
*
650428 AATTATAGTTATAT
1 AATTATATTTAT-T
650442 AATTATATTTATT
1 AATTATATTTATT
650455 A
1 A
650456 TTTAATATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
AATTATATTTATT
Found at i:650922 original size:31 final size:29
Alignment explanation
Indices: 650860--650922 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
650850 TGATTGAGTA
**
650860 ACTTGTTTATAACTTTTTAAAATTGAATG
1 ACTTGTTTATAACTTACTAAAATTGAATG
*
650889 ACTTGTTTATAATCTTACTAATAATTGATTG
1 ACTTGTTTATAA-CTTACTAA-AATTGAATG
650920 ACT
1 ACT
650923 CGTGATGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.41
30 6 0.21
31 11 0.38
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (29 bp):
ACTTGTTTATAACTTACTAAAATTGAATG
Found at i:655166 original size:40 final size:40
Alignment explanation
Indices: 655110--655209 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
655100 AGGCCCCCGT
* *
655110 GTCATTAGTCGATGGTGGGTGCGGAATAAACCCCAGATCG
1 GTCATTAGTCGATGGTGGGCGCAGAATAAACCCCAGATCG
* *
655150 GTCATTAGTCGGTGGTGGGCGCATAATAAACCCCAGATCG
1 GTCATTAGTCGATGGTGGGCGCAGAATAAACCCCAGATCG
*
655190 GTCATTATTCGATGGTGGGC
1 GTCATTAGTCGATGGTGGGC
655210 ACAGCATGTC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (40 bp):
GTCATTAGTCGATGGTGGGCGCAGAATAAACCCCAGATCG
Found at i:655487 original size:16 final size:16
Alignment explanation
Indices: 655439--655478 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
655429 ACGTGGTCCT
655439 TCGGGACAATAATATG
1 TCGGGACAATAATATG
655455 TCGGGACAATAATATG
1 TCGGGACAATAATATG
655471 TCGGGACA
1 TCGGGACA
655479 TTTCTATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (16 bp):
TCGGGACAATAATATG
Found at i:656021 original size:37 final size:37
Alignment explanation
Indices: 655937--656021 Score: 113
Period size: 36 Copynumber: 2.3 Consensus size: 37
655927 ATTAAACCTT
655937 TTTTACAATTTTAATTTTGTAAAAAAATTATATAAATA
1 TTTTACAA-TTTAATTTTGTAAAAAAATTATATAAATA
*
655975 --TTACGAATTTAATTTTTTAAAGAAAA-TATATAAATA
1 TTTTAC-AATTTAATTTTGTAAA-AAAATTATATAAATA
656011 TTTTACAATTT
1 TTTTACAATTT
656022 GTAATATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
36 27 0.64
37 11 0.26
38 4 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTTACAATTTAATTTTGTAAAAAAATTATATAAATA
Found at i:662601 original size:3 final size:3
Alignment explanation
Indices: 662593--662633 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
662583 AATAAAATGG
* *
662593 AAT AAT AAT ATT AAT AAT AAT AGT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
662634 TAAATTTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:662610 original size:12 final size:11
Alignment explanation
Indices: 662593--662633 Score: 64
Period size: 12 Copynumber: 3.5 Consensus size: 11
662583 AATAAAATGG
662593 AATAATAATATT
1 AATAATAATA-T
662605 AATAATAATAGT
1 AATAATAATA-T
662617 AATAATAATAT
1 AATAATAATAT
662628 AATAAT
1 AATAAT
662634 TAAATTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AATAATAATAT
Found at i:662733 original size:22 final size:24
Alignment explanation
Indices: 662682--662735 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 24
662672 CTGAAAATTT
* *
662682 TGATTTATTGATTTACTGGTTAAA
1 TGATTTATGGATTTACTGGTGAAA
*
662706 -GGTTTATGGA-TTAC-GGTGAAA
1 TGATTTATGGATTTACTGGTGAAA
662727 TGATTTATG
1 TGATTTATG
662736 TTATTTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 6 0.24
22 11 0.44
23 8 0.32
ACGTcount: A:0.28, C:0.04, G:0.24, T:0.44
Consensus pattern (24 bp):
TGATTTATGGATTTACTGGTGAAA
Found at i:662950 original size:23 final size:23
Alignment explanation
Indices: 662917--662960 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
662907 ATAGGCTCTG
*
662917 AGGCCCCGAAAACGTTCTTGGAT
1 AGGCCCAGAAAACGTTCTTGGAT
*
662940 AGGCCCAGAAAACTTTCTTGG
1 AGGCCCAGAAAACGTTCTTGG
662961 GTAAGCTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
AGGCCCAGAAAACGTTCTTGGAT
Found at i:666759 original size:31 final size:31
Alignment explanation
Indices: 666724--666826 Score: 161
Period size: 31 Copynumber: 3.3 Consensus size: 31
666714 TGAAGTGATC
666724 ATTTTATTACAAATCGATAACGTTAGTGACT
1 ATTTTATTACAAATCGATAACGTTAGTGACT
666755 ATTTTATTACAAATCGATAACGTTAGTGACT
1 ATTTTATTACAAATCGATAACGTTAGTGACT
* * *
666786 ATTTTATTACAAATCAATAATGTTAGCGACT
1 ATTTTATTACAAATCGATAACGTTAGTGACT
* *
666817 AATTTGTTAC
1 ATTTTATTAC
666827 TTTTGAGACT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (31 bp):
ATTTTATTACAAATCGATAACGTTAGTGACT
Found at i:667422 original size:50 final size:52
Alignment explanation
Indices: 667321--667428 Score: 202
Period size: 50 Copynumber: 2.1 Consensus size: 52
667311 AATAGTAAAA
667321 AATACTAATAAACAAACAACCTTAATATATATATATATATATATATTATGTT
1 AATACTAATAAACAAACAACCTTAATATATATATATATATATATATTATGTT
667373 AATACTAATAAACAAACAACCTT-A-ATATATATATATATATATATTATGTT
1 AATACTAATAAACAAACAACCTTAATATATATATATATATATATATTATGTT
667423 AATACT
1 AATACT
667429 TGCCAATCTC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
50 32 0.57
51 1 0.02
52 23 0.41
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (52 bp):
AATACTAATAAACAAACAACCTTAATATATATATATATATATATATTATGTT
Found at i:670952 original size:29 final size:29
Alignment explanation
Indices: 670918--671079 Score: 105
Period size: 29 Copynumber: 5.5 Consensus size: 29
670908 GTTGACTGGA
*
670918 TGATATTTTAGTAATTATTTTGAAAATGG
1 TGATATTTTAGTAATTATTTTGAAAAAGG
* * * *
670947 TGATATTTTGGTAATTATTTTTAAAATGA
1 TGATATTTTAGTAATTATTTTGAAAAAGG
* * * *
670976 TGCTATTTTCA-AAATTGTTTTTTAAAAAGG
1 TGATATTTT-AGTAATT-ATTTTGAAAAAGG
* ** * * *
671006 TGATAAATTCTA-TTTTTTTTTTAAAAAAAAG
1 TGAT--ATTTTAGTAATTATTTT-GAAAAAGG
*
671037 TGATATTTTAGTAATTATTTTGAAAAGGG
1 TGATATTTTAGTAATTATTTTGAAAAAGG
671066 TGATATATTT-GTAA
1 TGATAT-TTTAGTAA
671080 ATTGTTTTTA
Statistics
Matches: 103, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
29 58 0.56
30 28 0.27
31 13 0.13
32 4 0.04
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (29 bp):
TGATATTTTAGTAATTATTTTGAAAAAGG
Found at i:685002 original size:33 final size:34
Alignment explanation
Indices: 684965--685072 Score: 98
Period size: 33 Copynumber: 3.2 Consensus size: 34
684955 AGTAAGAAAT
* * *
684965 TTATTTTTATGTTAGTAT-TTT-TTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
684998 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATATATTTATGTAAATATTA
* * *
685032 TT-TTTTTAT-TAAAATAATATTTATATAATTATTA
1 TTATTTTTATAT-TAAT-ATATTTATGTAAATATTA
685066 TTTATTT
1 -TTATTT
685073 AGAATTATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
32 1 0.02
33 26 0.41
34 24 0.38
35 9 0.14
36 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:685034 original size:31 final size:33
Alignment explanation
Indices: 684996--685068 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
684986 TTTAAATAGT
*
684996 TATTATTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTATATTAAATAATATTTATATAAA
* *
685027 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTATATT-AAATAATATTTATATAAA
685061 TATTATTT
1 TATTATTT
685069 ATTTAGAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 14 0.39
33 3 0.08
34 19 0.53
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTATATTAAATAATATTTATATAAA
Found at i:685235 original size:17 final size:17
Alignment explanation
Indices: 685213--685266 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
685203 AATGTTAATA
685213 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
685230 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
685247 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
685264 TTT
1 TTT
685267 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:686837 original size:21 final size:21
Alignment explanation
Indices: 686813--686898 Score: 120
Period size: 21 Copynumber: 4.1 Consensus size: 21
686803 GCCCACCAGT
686813 TTACATTCCGAGCCCGCAGGG
1 TTACATTCCGAGCCCGCAGGG
686834 TTACATTCCGAGCCCGCAGGG
1 TTACATTCCGAGCCCGCAGGG
**
686855 TTACATTCATAGCCCGCCA-GG
1 TTACATTCCGAGCCCG-CAGGG
* *
686876 TTACATGCCTAGCCCGCAGGG
1 TTACATTCCGAGCCCGCAGGG
686897 TT
1 TT
686899 TTATACCATA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.03
21 55 0.93
22 2 0.03
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.22
Consensus pattern (21 bp):
TTACATTCCGAGCCCGCAGGG
Found at i:687460 original size:34 final size:34
Alignment explanation
Indices: 687421--687518 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
687411 AAATTTTTTT
* *
687421 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
687455 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
687489 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
687519 CATTAAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:688147 original size:128 final size:128
Alignment explanation
Indices: 687919--688672 Score: 1320
Period size: 128 Copynumber: 5.9 Consensus size: 128
687909 TTACCTGATT
*
687919 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
687984 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCT-GAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* * *
688047 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
*
688111 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
65 CTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
688175 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
688240 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
688303 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
688368 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
688431 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
688496 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCACCTTCATGTCAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
688559 TACTGATATATCTAGTGTCACCGAGGGACATGAGTGACATAATAGGGTAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
688624 TG---AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
688673 ACTCCGATTA
Statistics
Matches: 603, Mismatches: 20, Indels: 9
0.95 0.03 0.01
Matches are distributed among these distances:
125 45 0.07
127 2 0.00
128 555 0.92
129 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:688754 original size:8 final size:8
Alignment explanation
Indices: 688743--688783 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
688733 TCACAAACTT
688743 TCAAATTC
1 TCAAATTC
688751 TCAAATT-
1 TCAAATTC
*
688758 TCCAAACTC
1 T-CAAATTC
688767 T-AAATTC
1 TCAAATTC
688774 TCAAATTC
1 TCAAATTC
688782 TC
1 TC
688784 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 7 0.25
8 20 0.71
9 1 0.04
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (8 bp):
TCAAATTC
Found at i:688759 original size:15 final size:15
Alignment explanation
Indices: 688736--688783 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
688726 CTTCAGTTCA
688736 CAAACTTTCAAATTCT
1 CAAA-TTTCAAATTCT
*
688752 CAAATTTCCAAACTCT
1 CAAATTT-CAAATTCT
688768 -AAATTCTCAAATTCT
1 CAAATT-TCAAATTCT
688783 C
1 C
688784 TGAAAATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (15 bp):
CAAATTTCAAATTCT
Found at i:694625 original size:2 final size:2
Alignment explanation
Indices: 694618--694646 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
694608 CAGAATCGTA
694618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
694647 GATTAACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:696234 original size:15 final size:15
Alignment explanation
Indices: 696214--696244 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
696204 TTTATTCTTA
696214 TACCATTACATAATT
1 TACCATTACATAATT
696229 TACCATTACATAATT
1 TACCATTACATAATT
696244 T
1 T
696245 TTATTCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (15 bp):
TACCATTACATAATT
Found at i:699016 original size:17 final size:17
Alignment explanation
Indices: 698974--699016 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
698964 TGAGAATGAG
* *
698974 GGAACTGTTTGTTTCGT
1 GGAACTTTTTATTTCGT
*
698991 GGAAGTTTTTATTTCGT
1 GGAACTTTTTATTTCGT
*
699008 TGAACTTTT
1 GGAACTTTT
699017 GTTAGTTTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.23, T:0.51
Consensus pattern (17 bp):
GGAACTTTTTATTTCGT
Found at i:702705 original size:30 final size:30
Alignment explanation
Indices: 702664--702741 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
702654 GTCTCGTGCT
*
702664 TATAT-TATTTTTTTGAACCCTAGTGATTA
1 TATATATATTTTTTTGAACCCGAGTGATTA
* *
702693 TATATATA-TTTTTTGAAACTCGCGTGATTA
1 TATATATATTTTTTTG-AACCCGAGTGATTA
702723 TAT-TATTATTATTTTTGAA
1 TATATA-TATT-TTTTTGAA
702742 ACCCCTCGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 14 0.34
30 18 0.44
31 3 0.07
32 6 0.15
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (30 bp):
TATATATATTTTTTTGAACCCGAGTGATTA
Found at i:707778 original size:11 final size:11
Alignment explanation
Indices: 707762--707824 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
707752 AAAATTACAT
707762 TATTAAAAATA
1 TATTAAAAATA
707773 TATTAAAAATA
1 TATTAAAAATA
* * ***
707784 CACTATTGATA
1 TATTAAAAATA
707795 -ATTATAAAA-A
1 TATTA-AAAATA
707805 T-TTAAAAATA
1 TATTAAAAATA
707815 TATTAAAAAT
1 TATTAAAAAT
707825 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 4 0.10
10 9 0.23
11 26 0.67
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:707891 original size:14 final size:14
Alignment explanation
Indices: 707869--707901 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
707859 GTCCTTGTAA
*
707869 TAAACCTTAAACCC
1 TAAATCTTAAACCC
707883 TAAATCTTAAACCC
1 TAAATCTTAAACCC
707897 TAAAT
1 TAAAT
707902 AATAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAATCTTAAACCC
Found at i:707927 original size:21 final size:22
Alignment explanation
Indices: 707868--707927 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
707858 TGTCCTTGTA
* *
707868 ATAAACCTTAAACCCTAAATCT
1 ATAAACCATAAACCATAAATCT
* **
707890 -TAAACCCTAAATAATAAAT-T
1 ATAAACCATAAACCATAAATCT
707910 ATAAACCATAAACCATAA
1 ATAAACCATAAACCATAA
707928 GCCCTAAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (22 bp):
ATAAACCATAAACCATAAATCT
Found at i:711987 original size:28 final size:27
Alignment explanation
Indices: 711956--712022 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
711946 CTTTAAAAAT
* * *
711956 ATATTTTATTTTTATCTTAATGTATTA-A
1 ATATTTTATTATTAACTTAAT-T-TAAGA
711984 ATATTTTTATTATTAACTTAATTTAAGA
1 ATA-TTTTATTATTAACTTAATTTAAGA
712012 ATATTTTATTA
1 ATATTTTATTA
712023 ATATTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 10 0.29
28 8 0.24
29 16 0.47
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (27 bp):
ATATTTTATTATTAACTTAATTTAAGA
Found at i:712200 original size:127 final size:128
Alignment explanation
Indices: 712053--712293 Score: 394
Period size: 127 Copynumber: 1.9 Consensus size: 128
712043 AAATTTATTT
* * *
712053 TATTTTATTAGATATATATTTAATAACATTTTATTATTAATTTAAAAATATTTTTAAAATTTAAA
1 TATTTTATTAGATACATATTTAAGAAAATTTTATTATTAATTTAAAAATATTTTTAAAATTTAAA
*
712118 ATAAAAATATAATATAT-TTAAGCTAAGCTAAGAATAAAATATATATTTTAATTTTAAAAATA
66 ATAAAAACATAATATATATTAAGCTAAGCTAAGAATAAAATATATATTTTAATTTTAAAAATA
*
712180 TATTTTATTAGATACATATTTAAGAAAATTTTATTATTGATTTAAAAATATTTTTAAAATTTAAA
1 TATTTTATTAGATACATATTTAAGAAAATTTTATTATTAATTTAAAAATATTTTTAAAATTTAAA
** * *
712245 ATAAGCACATAATATATATTAAGCTAAGCTAATAATAAAATATGTATTT
66 ATAAAAACATAATATATATTAAGCTAAGCTAAGAATAAAATATATATTT
712294 CTAAATTAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
127 75 0.72
128 29 0.28
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (128 bp):
TATTTTATTAGATACATATTTAAGAAAATTTTATTATTAATTTAAAAATATTTTTAAAATTTAAA
ATAAAAACATAATATATATTAAGCTAAGCTAAGAATAAAATATATATTTTAATTTTAAAAATA
Found at i:712325 original size:27 final size:27
Alignment explanation
Indices: 712275--712351 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
712265 AAGCTAAGCT
*
712275 AATAATAA-AATATGTATTTCTAAATTAA
1 AATAATAATAA-A-GTATTTTTAAATTAA
*
712303 AATAGTAATAAAGTATTTTTAAATTAA
1 AATAATAATAAAGTATTTTTAAATTAA
* * *
712330 ATTAATAATAAAATATATTTAA
1 AATAATAATAAAGTATTTTTAA
712352 TAAGATAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 32 0.76
28 8 0.19
29 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (27 bp):
AATAATAATAAAGTATTTTTAAATTAA
Found at i:715099 original size:15 final size:15
Alignment explanation
Indices: 715079--715116 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
715069 GTTTACTTCA
715079 GAATGATTAAGCGCT
1 GAATGATTAAGCGCT
715094 GAATGATTAAGCGCT
1 GAATGATTAAGCGCT
715109 GAATGATT
1 GAATGATT
715117 CAAATATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (15 bp):
GAATGATTAAGCGCT
Found at i:723608 original size:23 final size:23
Alignment explanation
Indices: 723581--723636 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
723571 TTTTATAAGG
* *
723581 TTGAATTGAAGTTGATTTCATTC
1 TTGAATCGAAGTTGATTTCATGC
723604 TTGAATCGAAGTTGATTTCATGC
1 TTGAATCGAAGTTGATTTCATGC
723627 TTGAATCGAA
1 TTGAATCGAA
723637 TCAAAATCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.41
Consensus pattern (23 bp):
TTGAATCGAAGTTGATTTCATGC
Found at i:726867 original size:16 final size:15
Alignment explanation
Indices: 726842--726875 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
726832 TTGTAATTTC
*
726842 TTAATATAATTAGTA
1 TTAATATAATTAATA
726857 TTAATTATAATTAATA
1 TTAA-TATAATTAATA
726873 TTA
1 TTA
726876 TGATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:727264 original size:6 final size:6
Alignment explanation
Indices: 727249--727288 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
727239 CATATCTCAT
727249 TTTCATC TTTCAC TTTCAC TTTCA- TATTCAC TTTCAC TTT
1 TTTCA-C TTTCAC TTTCAC TTTCAC T-TTCAC TTTCAC TTT
727289 TGATTTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.03
6 24 0.77
7 6 0.19
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTCAC
Found at i:727377 original size:19 final size:19
Alignment explanation
Indices: 727316--727399 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 19
727306 ACTTTCACAT
*
727316 TTCATAAC-TCATTCTCAGA
1 TTCATAACTTAATT-TCAGA
* * *
727335 TTCAGAACTT-TTTTCTGGA
1 TTCATAACTTAATTTC-AGA
*
727354 CTCATAACTTAATTTCAGA
1 TTCATAACTTAATTTCAGA
* *
727373 TTCATAGCTTATTTTCA-A
1 TTCATAACTTAATTTCAGA
727391 GTTCATAAC
1 -TTCATAAC
727400 CCAATGCATA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
18 3 0.06
19 42 0.84
20 5 0.10
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (19 bp):
TTCATAACTTAATTTCAGA
Found at i:728459 original size:21 final size:21
Alignment explanation
Indices: 728433--728474 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
728423 CCACGATGGG
*
728433 GGGTATCGATACCCCTTCATA
1 GGGTATCAATACCCCTTCATA
*
728454 GGGTATCAATACTCCTTCATA
1 GGGTATCAATACCCCTTCATA
728475 AAATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (21 bp):
GGGTATCAATACCCCTTCATA
Found at i:728692 original size:30 final size:30
Alignment explanation
Indices: 728658--728717 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
728648 AACTTTGAAT
728658 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAGTCCAAAAACATTTTGC
728688 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAGTCCAAAAACATTTTGC
728718 CTTAAATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAGTCCAAAAACATTTTGC
Found at i:731371 original size:18 final size:17
Alignment explanation
Indices: 731314--731380 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 17
731304 GTTGTAGCCA
*
731314 GGGGGTATAGATACCCT
1 GGGGGTATAGATACCAT
* * *
731331 AGGGGTATCGATACTAT
1 GGGGGTATAGATACCAT
*
731348 --GGGTATCGATACCAT
1 GGGGGTATAGATACCAT
731363 GGGGGGTATAGATACCAT
1 -GGGGGTATAGATACCAT
731381 CCGAGCAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
15 14 0.34
17 13 0.32
18 14 0.34
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (17 bp):
GGGGGTATAGATACCAT
Found at i:731551 original size:30 final size:30
Alignment explanation
Indices: 731517--731574 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
731507 AACTTTGAAT
*
731517 AAATTCAATTTAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAGTCCAAAAACATTTTGC
731547 AAATTCAATTCAAGTCCAAAAACATTTT
1 AAATTCAATTCAAGTCCAAAAACATTTT
731575 ACCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (30 bp):
AAATTCAATTCAAGTCCAAAAACATTTTGC
Found at i:742274 original size:16 final size:17
Alignment explanation
Indices: 742255--742287 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
742245 TGAATATAAT
742255 TTTAAAAAT-ATATTAA
1 TTTAAAAATAATATTAA
742271 TTTAAAAATAATATTAA
1 TTTAAAAATAATATTAA
742288 AAAAGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAAAATAATATTAA
Found at i:743479 original size:12 final size:12
Alignment explanation
Indices: 743461--743491 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
743451 AATAAAAATA
743461 TTAAAAATTTATT
1 TTAAAAATTTA-T
743474 TTAAAAATTTAT
1 TTAAAAATTTAT
743486 TTAAAA
1 TTAAAA
743492 TAAAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTAAAAATTTAT
Found at i:746164 original size:198 final size:198
Alignment explanation
Indices: 745826--746221 Score: 792
Period size: 198 Copynumber: 2.0 Consensus size: 198
745816 GAAATGTACC
745826 ATGAAATAGTAATGAAGGATGTCGCTTACTCTTACCTACTTGATGCCTGCTTCATCACCTTTTCT
1 ATGAAATAGTAATGAAGGATGTCGCTTACTCTTACCTACTTGATGCCTGCTTCATCACCTTTTCT
745891 GTTTACTTTATCCCAAGGGGGTAAAAATCCTTTGTCCTTTTGACAGATCTGCCCTATCCAGTTGT
66 GTTTACTTTATCCCAAGGGGGTAAAAATCCTTTGTCCTTTTGACAGATCTGCCCTATCCAGTTGT
745956 TCTTACGTCTAGTCTGAATAGTATTTCGTCCGGTGTGGTAGTTGATGGATTTTCACTAACTGGAA
131 TCTTACGTCTAGTCTGAATAGTATTTCGTCCGGTGTGGTAGTTGATGGATTTTCACTAACTGGAA
746021 ATT
196 ATT
746024 ATGAAATAGTAATGAAGGATGTCGCTTACTCTTACCTACTTGATGCCTGCTTCATCACCTTTTCT
1 ATGAAATAGTAATGAAGGATGTCGCTTACTCTTACCTACTTGATGCCTGCTTCATCACCTTTTCT
746089 GTTTACTTTATCCCAAGGGGGTAAAAATCCTTTGTCCTTTTGACAGATCTGCCCTATCCAGTTGT
66 GTTTACTTTATCCCAAGGGGGTAAAAATCCTTTGTCCTTTTGACAGATCTGCCCTATCCAGTTGT
746154 TCTTACGTCTAGTCTGAATAGTATTTCGTCCGGTGTGGTAGTTGATGGATTTTCACTAACTGGAA
131 TCTTACGTCTAGTCTGAATAGTATTTCGTCCGGTGTGGTAGTTGATGGATTTTCACTAACTGGAA
746219 ATT
196 ATT
746222 TATTTTTACT
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 198 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (198 bp):
ATGAAATAGTAATGAAGGATGTCGCTTACTCTTACCTACTTGATGCCTGCTTCATCACCTTTTCT
GTTTACTTTATCCCAAGGGGGTAAAAATCCTTTGTCCTTTTGACAGATCTGCCCTATCCAGTTGT
TCTTACGTCTAGTCTGAATAGTATTTCGTCCGGTGTGGTAGTTGATGGATTTTCACTAACTGGAA
ATT
Done.