Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 19
Found at i:1339729 original size:24 final size:24
Alignment explanation
Indices: 1339719--1339833 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
1339709 CATAATTCAC
* *
1339719 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAT
* *
1339743 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
* *
1339767 GTCAAGTATCAGATCATAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
1339791 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
*
1339815 GTCAAATATCATATCAGAA
1 GTCAAGTATCATATCAGAA
1339834 ATCAAATCGA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.02
24 78 0.96
25 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:1339850 original size:72 final size:71
Alignment explanation
Indices: 1339699--1339850 Score: 173
Period size: 72 Copynumber: 2.1 Consensus size: 71
1339689 GGATATATCA
* * *
1339699 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
1 AAAATCAGATCATAATCCACGTCAAGTATCATATCAAAATCCAGGTCAAATATCAGATCAGAATC
*
1339764 CAAGTC
66 CAAATC
* * * * *
1339770 AAGTATCAGATCATAATCCATGTC-AGATATCATATCAGAATCCATGTCAAATATCATATCAGAA
1 AA-AATCAGATCATAATCCACGTCAAG-TATCATATCAAAATCCAGGTCAAATATCAGATCAG-A
1339834 AT-CAAATC
63 ATCCAAATC
1339842 GAAAATCAG
1 -AAAATCAG
1339851 GTAAAATATT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
71 4 0.06
72 58 0.87
73 5 0.07
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (71 bp):
AAAATCAGATCATAATCCACGTCAAGTATCATATCAAAATCCAGGTCAAATATCAGATCAGAATC
CAAATC
Found at i:1342304 original size:18 final size:18
Alignment explanation
Indices: 1342283--1342341 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
1342273 CAGCGGTTAA
*
1342283 CGGGTCAACCGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1342301 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
* *
1342319 CAGGTCAATGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1342337 CGGGT
1 CGGGT
1342342 TATGACCGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:1342312 original size:13 final size:13
Alignment explanation
Indices: 1342296--1342320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1342286 GTCAACCGGT
1342296 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1342309 CGGGTCGGGTCA
1 CGGGTCGGGTCA
1342321 GGTCAATGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1349070 original size:2 final size:2
Alignment explanation
Indices: 1349063--1349088 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1349053 TATTATAATG
1349063 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
1349089 TAAGAATCAA
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):
AT
Found at i:1349189 original size:4 final size:4
Alignment explanation
Indices: 1349180--1349214 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
1349170 CTTCTCATCC
1349180 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1349215 GTATTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:1349255 original size:12 final size:12
Alignment explanation
Indices: 1349234--1349270 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
1349224 TTATTAATAA
1349234 TTTT-TATATAT
1 TTTTATATATAT
1349245 TTTTATATATAT
1 TTTTATATATAT
1349257 TTTTATTATATAT
1 TTTTA-TATATAT
1349270 T
1 T
1349271 CATCTACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.17
12 12 0.50
13 8 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTATATATAT
Found at i:1349470 original size:2 final size:2
Alignment explanation
Indices: 1349339--1349456 Score: 154
Period size: 2 Copynumber: 61.0 Consensus size: 2
1349329 TTAATCATAC
* * * * *
1349339 AT AT AT AC AT AC AT AT AT AC AT TT AT AT -T AT -T AT A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1349378 TT AT AT -T 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
1349419 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
1349457 CTTTAAGTAT
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
1 4 0.04
2 98 0.96
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1350204 original size:21 final size:21
Alignment explanation
Indices: 1350178--1350217 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1350168 ACCATTACAG
*
1350178 TGCTGATGTGGCAGTCCACAA
1 TGCTGACGTGGCAGTCCACAA
1350199 TGCTGACGTGGCAGTCCAC
1 TGCTGACGTGGCAGTCCAC
1350218 TATGACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.23
Consensus pattern (21 bp):
TGCTGACGTGGCAGTCCACAA
Found at i:1350528 original size:21 final size:21
Alignment explanation
Indices: 1350502--1350566 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1350492 GTTGAGCGTT
*
1350502 ACAGTGCTGACGTGACAGTCT
1 ACAGTGCTGACGTGACAGTCC
* * *
1350523 ATAGTGTTGACGTGACGGTCC
1 ACAGTGCTGACGTGACAGTCC
* *
1350544 ACAGTGCTTACGCGACAGTCC
1 ACAGTGCTGACGTGACAGTCC
1350565 AC
1 AC
1350567 TATGGCTGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (21 bp):
ACAGTGCTGACGTGACAGTCC
Found at i:1350676 original size:24 final size:24
Alignment explanation
Indices: 1350649--1350705 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
1350639 TTTTTAAAAA
* * **
1350649 ATAAAAATATTCTATATTATAAAT
1 ATAAAAATATTCAAAAAAATAAAT
*
1350673 ATAAAATTATTCAAAAAAATAAAT
1 ATAAAAATATTCAAAAAAATAAAT
1350697 ATAAAAATA
1 ATAAAAATA
1350706 CGAAAAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAAAATATTCAAAAAAATAAAT
Found at i:1350712 original size:24 final size:24
Alignment explanation
Indices: 1350667--1350712 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1350657 ATTCTATATT
* ***
1350667 ATAAATATAAAATTATTCAAAAAA
1 ATAAATATAAAAATACGAAAAAAA
1350691 ATAAATATAAAAATACGAAAAA
1 ATAAATATAAAAATACGAAAAA
1350713 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
ATAAATATAAAAATACGAAAAAAA
Found at i:1351206 original size:2 final size:2
Alignment explanation
Indices: 1351187--1351239 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
1351177 AGCATTAGTA
* *
1351187 AT AT GT AT AT AT GT -T AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1351227 AT TT AT A- AT AT AT
1 AT AT AT AT AT AT AT
1351240 TTTTAAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1351240 original size:14 final size:13
Alignment explanation
Indices: 1351200--1351256 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
1351190 TGTATATATG
*
1351200 TTATATATATATAT
1 TTATA-ATATATTT
*
1351214 ATATATATATATTAT
1 TTATA-ATATATT-T
1351229 TTATAATATATTT
1 TTATAATATATTT
*
1351242 TTA-AAAATATTT
1 TTATAATATATTT
1351254 TTA
1 TTA
1351257 ATTTTTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.29
13 4 0.11
14 18 0.47
15 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATAATATATTT
Found at i:1351420 original size:32 final size:32
Alignment explanation
Indices: 1351384--1351459 Score: 75
Period size: 32 Copynumber: 2.4 Consensus size: 32
1351374 ATTTAATTTT
* *
1351384 TATTTTATTATTTTTATATTAAATTTTTTAAA-
1 TATTTTATTATTTGTATATT-AATTATTTAAAC
* * * *
1351416 TATTTGAATAATTGTATATTTATTATTTAAAC
1 TATTTTATTATTTGTATATTAATTATTTAAAC
1351448 TATTTT-TTATTT
1 TATTTTATTATTT
1351460 CTAAAACAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (32 bp):
TATTTTATTATTTGTATATTAATTATTTAAAC
Found at i:1353858 original size:30 final size:29
Alignment explanation
Indices: 1353823--1353924 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 29
1353813 AGTTAAAGTA
*
1353823 AAAATAAGATACATTTTTAAAAATTAAGAT
1 AAAATAA-ATATATTTTTAAAAATTAAGAT
1353853 AAAAT--ATATATTTTT--AAATTAAGAT
1 AAAATAAATATATTTTTAAAAATTAAGAT
* * *
1353878 AAGATTAAAATATATTTTT--AAGTTAAAAT
1 AA-AAT-AAATATATTTTTAAAAATTAAGAT
1353907 AAAAATAAAATATATTTT
1 -AAAAT-AAATATATTTT
1353925 ACTTGGTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
25 12 0.19
26 2 0.03
27 9 0.15
29 32 0.52
30 7 0.11
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (29 bp):
AAAATAAATATATTTTTAAAAATTAAGAT
Found at i:1353897 original size:29 final size:29
Alignment explanation
Indices: 1353842--1353924 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
1353832 TACATTTTTA
*
1353842 AAAATTAAGATAAAATATATATTTTTAAATT
1 AAAA-TAAGATTAAA-ATATATTTTTAAATT
* *
1353873 AAGATAAGATTAAAATATATTTTTAAGTT
1 AAAATAAGATTAAAATATATTTTTAAATT
* *
1353902 AAAATAAAAATAAAATATATTTT
1 AAAATAAGATTAAAATATATTTT
1353925 ACTTGGTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 34 0.74
30 9 0.20
31 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (29 bp):
AAAATAAGATTAAAATATATTTTTAAATT
Found at i:1355841 original size:31 final size:31
Alignment explanation
Indices: 1355803--1355877 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
1355793 TAGTCAGGTG
*
1355803 TGCATTCAGATAATGA-ACAGTATGTCAAGTT
1 TGCATTCAGATAAT-ACACAATATGTCAAGTT
*
1355834 TGCATTCAGATAATACATAATATGTCAAGTT
1 TGCATTCAGATAATACACAATATGTCAAGTT
* *
1355865 CGCATTTAGATAA
1 TGCATTCAGATAA
1355878 AGCATAGCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.03
31 38 0.97
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (31 bp):
TGCATTCAGATAATACACAATATGTCAAGTT
Found at i:1357205 original size:29 final size:29
Alignment explanation
Indices: 1357151--1357207 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1357141 GACCACTTTC
*
1357151 GTTTTTATTTAATTAAAATATTGTCACTT
1 GTTTTTATTTAATTAAAATATAGTCACTT
* *
1357180 GTTTTTATTTAATTAAGATGTAGTCACT
1 GTTTTTATTTAATTAAAATATAGTCACT
1357208 AAGGGTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.53
Consensus pattern (29 bp):
GTTTTTATTTAATTAAAATATAGTCACTT
Found at i:1357453 original size:15 final size:15
Alignment explanation
Indices: 1357420--1357462 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1357410 AACTTATTTT
1357420 AATTAAAAT-AAATA
1 AATTAAAATAAAATA
*
1357434 TATTAAAATAAAATA
1 AATTAAAATAAAATA
1357449 AATTAAAATAAAAT
1 AATTAAAATAAAAT
1357463 TAGTCCTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTAAAATAAAATA
Found at i:1360167 original size:175 final size:174
Alignment explanation
Indices: 1359876--1360224 Score: 689
Period size: 175 Copynumber: 2.0 Consensus size: 174
1359866 ACGGCTGCTA
1359876 TTGACCGACAAACGACAATACTTACTGCTCTACAATAGCAAACAACATTAATACAAAGACAAATG
1 TTGACCGACAAACGACAATACTTACTGCTCTACAATAGCAAACAACATTAATACAAAGACAAATG
1359941 TCCGATCTTACCATTAAAAGACAACAACAAGCAAATCTGAATGATGATAATCAAACCAAGAGAAG
66 TCCGATCTTACCATTAAAAGACAACAACAAGCAAATCTGAATGATGATAATC-AACCAAGAGAAG
1360006 CCGTAGGAGATTATCAACATAATCCAATACAAACTGGAAGTGTAC
130 CCGTAGGAGATTATCAACATAATCCAATACAAACTGGAAGTGTAC
1360051 TTGACCGACAAACGACAATACTTACTGCTCTACAATAGCAAACAACATTAATACAAAGACAAATG
1 TTGACCGACAAACGACAATACTTACTGCTCTACAATAGCAAACAACATTAATACAAAGACAAATG
1360116 TCCGATCTTACCATTAAAAGACAACAACAAGCAAATCTGAATGATGATAATCAACCAAGAGAAGC
66 TCCGATCTTACCATTAAAAGACAACAACAAGCAAATCTGAATGATGATAATCAACCAAGAGAAGC
1360181 CGTAGGAGATTATCAACATAATCCAATACAAACTGGAAGTGTAC
131 CGTAGGAGATTATCAACATAATCCAATACAAACTGGAAGTGTAC
1360225 AACTTCGACT
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
174 57 0.33
175 117 0.67
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (174 bp):
TTGACCGACAAACGACAATACTTACTGCTCTACAATAGCAAACAACATTAATACAAAGACAAATG
TCCGATCTTACCATTAAAAGACAACAACAAGCAAATCTGAATGATGATAATCAACCAAGAGAAGC
CGTAGGAGATTATCAACATAATCCAATACAAACTGGAAGTGTAC
Found at i:1368668 original size:20 final size:21
Alignment explanation
Indices: 1368630--1368669 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1368620 TTTCACAGTG
* *
1368630 AAAAAGTATGGACACTTTTAT
1 AAAAAGGATAGACACTTTTAT
1368651 AAAAAGGATAGACA-TTTTA
1 AAAAAGGATAGACACTTTTA
1368670 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
AAAAAGGATAGACACTTTTAT
Found at i:1368734 original size:23 final size:22
Alignment explanation
Indices: 1368672--1368743 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
1368662 ACATTTTACA
*
1368672 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
1368695 ATATAACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
1368717 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
1368740 ATAT
1 ATAT
1368744 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 20 0.45
23 24 0.55
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:1369130 original size:23 final size:23
Alignment explanation
Indices: 1369104--1369166 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1369094 ATATAACCAC
1369104 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* **
1369127 TACCTATTACATTATATAAGCTC
1 TACCTATTACATTATATAAACGA
*
1369150 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1369167 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1369164 original size:423 final size:424
Alignment explanation
Indices: 1368332--1369363 Score: 1842
Period size: 423 Copynumber: 2.5 Consensus size: 424
1368322 TATTACATTA
*
1368332 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATTGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1368397 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTCCACCTACAATATTAA-TT--TAATTTCA
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTCCACCTACAATATTAATTTAATAATTTCA
1368458 TTTGCACAAAAAATTATTTGA-TTTTTGATATTTTATAAAATATTATTTAGAATTTTAA-TTAAT
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTAATTTAAT
1368521 AATAATATATATCGTAACGTAAAAAATAAATCATTAAACGCCTATAATTACTAAATTAATATCTT
196 AATAATATATATCGTAACGTAAAAAATAAATCATTAAACGCCTATAATTACTAAATTAATATCTT
*
1368586 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTTCACAGTGAAAAAGTATGGACACTTTTAT
261 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGA-ACTTTTAT
*
1368651 AAAAAGGATAGACATTTTACAATATAACCACTACCTATTACATTATATAACGATACCTATTACAT
325 AAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAACGATACCTATTACAT
1368716 TATATAAGCGCTACCTATTACATCATATTTTTACC
390 TATATAAGCGCTACCTATTACATCATATTTTTACC
*
1368751 TATTATATTGAAATTGTCCATAC-TTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
* *
1368815 TTATGTTTCAATTTTTTTTAATAGTGTTTTATGTTTTCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTCCACCTACAATATTAATTTAATAATTTCA
1368880 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTAATTTAAT
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTAATTTAAT
*
1368945 AATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTT
196 AATAATATATATCGTAACGTAAAAAATAAATCATTAAACGCCTATAATTACTAAATTAATATCTT
1369010 AAAACTCACTCAAAAGATAACCTTAAATTAA-G-TTTCCACAGTGAAAAAAGTATGG-ACTTTTA
261 -AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATGGAACTTTTA
1369072 TAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTAC
324 TAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATAT-AACGATACCTATTAC
*
1369137 ATTATATAAGCTCTACCTATTACATCATATTTTTACC
388 ATTATATAAGCGCTACCTATTACATCATATTTTTACC
1369174 TATTATATTGAAAGTGTCCATACTTTTTATAAAAA-GATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1369238 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTCCACCTACAATA-TAATTTAATAA-TTCA
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTCCACCTACAATATTAATTTAATAATTTCA
1369301 TTTGCAC-AAAAATTATTTGATTTTTTGATATTTTAT-AAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAA-TTTTAATTTAA
1369364 CAACATTAAC
Statistics
Matches: 591, Mismatches: 11, Indels: 21
0.95 0.02 0.03
Matches are distributed among these distances:
418 51 0.09
419 75 0.13
420 42 0.07
421 11 0.02
422 95 0.16
423 195 0.33
424 92 0.16
425 30 0.05
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (424 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTAATTTAAT
AATAATATATATCGTAACGTAAAAAATAAATCATTAAACGCCTATAATTACTAAATTAATATCTT
AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGAACTTTTATA
AAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAACGATACCTATTACATT
ATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:1369628 original size:39 final size:39
Alignment explanation
Indices: 1369574--1369659 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
1369564 TCAAGTGTAG
*
1369574 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
1369613 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
1369652 ATTTTGAT
1 ATTTTGAT
1369660 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:1369931 original size:18 final size:18
Alignment explanation
Indices: 1369918--1369954 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1369908 CGAAATATAT
1369918 ATTGAAATTCAAATTCAA
1 ATTGAAATTCAAATTCAA
*
1369936 ATTGAAATTGAAATTCAA
1 ATTGAAATTCAAATTCAA
1369954 A
1 A
1369955 CTCCAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAATTCAA
Found at i:1370414 original size:23 final size:23
Alignment explanation
Indices: 1370388--1370450 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1370378 ATATAACCAC
1370388 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1370411 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1370434 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1370451 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1370912 original size:39 final size:39
Alignment explanation
Indices: 1370858--1370943 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
1370848 CAAGTTGTAG
* *
1370858 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTACTTGGCACCATATGAGATTTGA
* *
1370897 ATTTTGATTTCCTTTTACTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTACTTGGCACCATATGAGATTTGA
1370936 ATTTTGAT
1 ATTTTGAT
1370944 GAGCATCGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTACTTGGCACCATATGAGATTTGA
Found at i:1371225 original size:18 final size:18
Alignment explanation
Indices: 1371202--1371238 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1371192 CGAAATATAT
1371202 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1371220 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1371238 A
1 A
1371239 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1371712 original size:23 final size:23
Alignment explanation
Indices: 1371654--1371725 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1371644 ATACTTTACA
* *
1371654 ATATAATCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1371677 A-ATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
1371699 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1371722 ATAT
1 ATAT
1371726 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 19 0.45
23 23 0.55
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1371766 original size:20 final size:21
Alignment explanation
Indices: 1371743--1371789 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
1371733 TATTATATTG
1371743 AAAGTTTCCATAC-TTTTATA
1 AAAGTTTCCATACTTTTTATA
** * *
1371763 AAAGGATCGATACTTTTTTTA
1 AAAGTTTCCATACTTTTTATA
1371784 AAAGTT
1 AAAGTT
1371790 ATGTAATTTA
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (21 bp):
AAAGTTTCCATACTTTTTATA
Found at i:1372122 original size:24 final size:24
Alignment explanation
Indices: 1372066--1372128 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
1372056 CACTCAAAAT
*
1372066 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCT-AATATGTAGTTA
***
1372091 ACAAACATACCTAATATGTAGTTA
1 ATGTACATACCTAATATGTAGTTA
*
1372115 TTGTACATACCTAA
1 ATGTACATACCTAA
1372129 ATTTAATGAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (24 bp):
ATGTACATACCTAATATGTAGTTA
Found at i:1375063 original size:175 final size:179
Alignment explanation
Indices: 1374573--1375046 Score: 720
Period size: 176 Copynumber: 2.7 Consensus size: 179
1374563 TTAAAATTAC
* *
1374573 CGACACTTTTTAAATGGTATCGACACATTTCTTCCAATCTGGACAT-AAGTATCGACACAATATT
1 CGACACTTTTTAAATCGTATCGACACATTTCTTCCAATCTGGACATAAAGTACCGACACAATATT
* *
1374637 ATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATA
66 AAAAAGTGTCGA-ATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATA
*
1374702 TTACAAA-TTATCTATTACA-TA-AA-TCTGAGTTCCGATGTGTAAATGT
130 TTACAAATTTATCTATTACATTATAATTATGAGTTCCGATGTGTAAATGT
* * *
1374748 CGATACTTTTTTAATCG--TCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATA
1 CGACACTTTTTAAATCGTATCGACACA--TTTCTTCCAATCTGGACATAAAGTACCGACACAATA
1374811 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
64 TTAAAAAGTGTCGA-ATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
*
1374876 TATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
128 TATTACAAATTTATCTATTACATTATAATTATGAGTTCCGATGTGTAAATGT
* *
1374928 CGACAC-TTTTAACATTGTATCGACACATTT-TTCCAATCTGGACATAAAGTACCGACAC-AGAT
1 CGACACTTTTTAA-ATCGTATCGACACATTTCTTCCAATCTGGACATAAAGTACCGACACAATAT
1374990 TAAAAAGTGTCG-ATAGG-TGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
65 TAAAAAGTGTCGAATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
1375047 ATAGCATTGC
Statistics
Matches: 275, Mismatches: 14, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
173 8 0.03
175 72 0.26
176 92 0.33
177 12 0.04
178 17 0.06
179 34 0.12
180 32 0.12
182 8 0.03
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (179 bp):
CGACACTTTTTAAATCGTATCGACACATTTCTTCCAATCTGGACATAAAGTACCGACACAATATT
AAAAAGTGTCGAATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATAT
TACAAATTTATCTATTACATTATAATTATGAGTTCCGATGTGTAAATGT
Found at i:1375078 original size:175 final size:179
Alignment explanation
Indices: 1374573--1375079 Score: 698
Period size: 175 Copynumber: 2.9 Consensus size: 179
1374563 TTAAAATTAC
* *
1374573 CGACACTTTTTAAATGGTATCGACACATTTCTTCCAATCTGGACAT-AAGTATCGACACAATATT
1 CGACACTTTTTAAATCGTATCGACACATTTCTTCCAATCTGGACATAAAGTACCGACACAATATT
* *
1374637 ATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATA
66 AAAAAGTGTCGA-ATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATA
* * *
1374702 TTACAAA-TTATCTA--TTA-CATAAATCTGAGTTCCGATGTGTAAATGT
130 TTACAAATTTATCTATTTTATTATAATTATGAGTTCCGATGTGTAAATGT
* * *
1374748 CGATACTTTTTTAATCG--TCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATA
1 CGACACTTTTTAAATCGTATCGACACA--TTTCTTCCAATCTGGACATAAAGTACCGACACAATA
1374811 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
64 TTAAAAAGTGTCGA-ATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
** *
1374876 TATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
128 TATTACAAATTTATCTATTTTATTATAATTATGAGTTCCGATGTGTAAATGT
* *
1374928 CGACAC-TTTTAACATTGTATCGACACATTT-TTCCAATCTGGACATAAAGTACCGACAC-AGAT
1 CGACACTTTTTAA-ATCGTATCGACACATTTCTTCCAATCTGGACATAAAGTACCGACACAATAT
* *
1374990 TAAAAAGTGTCG-ATAGG-TGTAGACCTATTCGCGCATAAAACCGGTATATTTATACC-GATAGC
65 TAAAAAGTGTCGAATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA-T
* *
1375052 ATTGCAAATTTACCTATTTTATTATAAT
129 ATTACAAATTTATCTATTTTATTATAAT
1375080 ATGTTGAAAG
Statistics
Matches: 297, Mismatches: 24, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
173 8 0.03
174 3 0.01
175 95 0.32
176 92 0.31
177 7 0.02
178 15 0.05
179 33 0.11
180 36 0.12
182 8 0.03
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (179 bp):
CGACACTTTTTAAATCGTATCGACACATTTCTTCCAATCTGGACATAAAGTACCGACACAATATT
AAAAAGTGTCGAATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATAT
TACAAATTTATCTATTTTATTATAATTATGAGTTCCGATGTGTAAATGT
Found at i:1376240 original size:21 final size:21
Alignment explanation
Indices: 1376214--1376255 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1376204 CCCCCTATGC
1376214 CTCAAGTGTATATTCGACTCT
1 CTCAAGTGTATATTCGACTCT
* * *
1376235 CTCAAGTTTCTCTTCGACTCT
1 CTCAAGTGTATATTCGACTCT
1376256 TGATTGTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.40
Consensus pattern (21 bp):
CTCAAGTGTATATTCGACTCT
Found at i:1378516 original size:19 final size:18
Alignment explanation
Indices: 1378462--1378507 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
1378452 ATCCGGTATC
1378462 ATTTTACCGGTTTTATCAT
1 ATTTTACCGG-TTTATCAT
1378481 -TTTGATACCGGTTTATCAT
1 ATTT--TACCGGTTTATCAT
1378500 ATTTTACC
1 ATTTTACC
1378508 TGTTATATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 7 0.29
19 8 0.33
20 9 0.38
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (18 bp):
ATTTTACCGGTTTATCAT
Found at i:1379113 original size:228 final size:229
Alignment explanation
Indices: 1378715--1379433 Score: 1318
Period size: 228 Copynumber: 3.1 Consensus size: 229
1378705 ACTTTTATAC
1378715 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
*
1378780 TTTTTAATAGCGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-AAAAA
1378845 ATTATTTGATTATTTGATA-TTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
130 ATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
1378909 AGATAATAATAAATATGTTTTTCACAGTGAAATAA
195 AGATAATAATAAATATGTTTTTCACAGTGAAATAA
*
1378944 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTTAA-TT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1379008 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
1379073 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
*
1379138 GATAATAATAAATATGTTTTCCACAGTGAAATAA
196 GATAATAATAAATATGTTTTTCACAGTGAAATAA
*
1379172 GTATGGACACTTTTATAAAAATAATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
*
1379237 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
*
1379302 TTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
*
1379367 GATAATAATAAATAT-ATTTTCACAGTGAAATAA
196 GATAATAATAAATATGTTTTTCACAGTGAAATAA
* * *
1379400 GTATGAACACTTTTATAAAAAGGATAGATACTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTT
1379434 ACAATATAAC
Statistics
Matches: 475, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
227 24 0.05
228 245 0.52
229 206 0.43
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (229 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
GATAATAATAAATATGTTTTTCACAGTGAAATAA
Found at i:1384240 original size:342 final size:342
Alignment explanation
Indices: 1383614--1384255 Score: 794
Period size: 342 Copynumber: 1.9 Consensus size: 342
1383604 ACAATCGACC
* *
1383614 GAACACCCAACGGCGTGTCTTCGACCAACCACCCATGACCAAAAGCCCCATAATTTTGCAACCAA
1 GAACACCCAACGACGTGTCCTCGACCAACCACCCATGACCAAAAGCCCCATAATTTTGCAACCAA
* * * * * * *
1383679 TCGAGCTCCCAAAAATTGTGTAAATGAAAATTTTTATTTTAGGGTTTTGAAACCATAAAAATCTC
66 TCGAACACCCAAAAATCGTGTAAATGAAAACTTTTATTTTAAGGTTTCGAAACCATAAAAATCCC
* * *
1383744 TTAGATCAATCGTGGTAATCAGTCGTTTGATCGGATGTGGTGGTCGGTCGTTTGTCGTTTGGTCG
131 TTAGATCAATCGTGGTAATCAGTCGTTTGATCAGATGTGGTGGTCGGTCATTTATCGTTTGGTCG
* * * * * * * * * **
1383809 GCAGTAGTATTCGGACTTTGACCTTGGTAGTTGGTCGTGGTAGGGGAGGGGAGAAGGGAGAAAAG
196 GCAGTAGCAGTCGGACTTTGACCGTGGCAGTGGGACGGGGAAGGGAAAAGGAGAAGGGAGAAAA-
** *
1383874 GGGGGAGGGAGAAAGGGGAGTTGGCGTTGTTCTCTTTTTTTAATTTTTAATATAATTTTTTTAAA
260 GGGGGAGGGAGAAAGGGGAGTTGGCACTGTTCCCTTTTTTTAATTTTTAATATAATTTTTTTAAA
1383939 AAAAATTCCAAAATACCA
325 AAAAATTCCAAAATACCA
* * * * *
1383957 GAACACCCAACGACGTGTCACT-GGCCAACCACCTATGACCAAAAGCCTCATACTTTTGTAACCA
1 GAACACCCAACGACGTGTC-CTCGACCAACCACCCATGACCAAAAGCCCCATAATTTTGCAACCA
* *
1384021 ATCGAACACCC-AAAATCGTGTAAATGAAAACTTTTGTTTTAAGGTTTCGAAACTATAAAAATCC
65 ATCGAACACCCAAAAATCGTGTAAATGAAAACTTTTATTTTAAGGTTTCGAAACCATAAAAATCC
** *
1384085 CTTAGATTGATCGTGGTAATCAGTCGTTTGATCAGATGTGGTGGTCGGTTATTTATCGTTTGGTC
130 CTTAGATCAATCGTGGTAATCAGTCGTTTGATCAGATGTGGTGGTCGGTCATTTATCGTTTGGTC
** * **
1384150 GGTTGTGGCAGTCGGACTAGTTGGTCGTGGCAG-GGGACGGGGGAAAGGAGAAAAGG-GAAGGGA
195 GGCAGTAGCAGTCGGACT--TTGACCGTGGCAGTGGGAC-GGGG-AAGG-GAAAAGGAGAAGGGA
1384213 G-AAA-GGGGAGGGA-AATAGGGGAGTTGGCACTGTTCCCTTTTTT
255 GAAAAGGGGGAGGGAGAA-AGGGGAGTTGGCACTGTTCCCTTTTTT
1384256 GTTTTAATTT
Statistics
Matches: 251, Mismatches: 41, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
341 2 0.01
342 151 0.60
343 67 0.27
344 16 0.06
345 11 0.04
346 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (342 bp):
GAACACCCAACGACGTGTCCTCGACCAACCACCCATGACCAAAAGCCCCATAATTTTGCAACCAA
TCGAACACCCAAAAATCGTGTAAATGAAAACTTTTATTTTAAGGTTTCGAAACCATAAAAATCCC
TTAGATCAATCGTGGTAATCAGTCGTTTGATCAGATGTGGTGGTCGGTCATTTATCGTTTGGTCG
GCAGTAGCAGTCGGACTTTGACCGTGGCAGTGGGACGGGGAAGGGAAAAGGAGAAGGGAGAAAAG
GGGGAGGGAGAAAGGGGAGTTGGCACTGTTCCCTTTTTTTAATTTTTAATATAATTTTTTTAAAA
AAAATTCCAAAATACCA
Found at i:1385678 original size:30 final size:30
Alignment explanation
Indices: 1385607--1385679 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1385597 ACATTCTGAA
* *
1385607 ACATTCAGAGCCATTATCAAACAGCATGTC
1 ACATTCAGAGCTATTATCAAACAACATGTC
*
1385637 ACATTCAGAGCTATTATCAAACAACATGTT
1 ACATTCAGAGCTATTATCAAACAACATGTC
1385667 ACATTCAGAGCTA
1 ACATTCAGAGCTA
1385680 ATTCATACAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.26
Consensus pattern (30 bp):
ACATTCAGAGCTATTATCAAACAACATGTC
Found at i:1390638 original size:16 final size:15
Alignment explanation
Indices: 1390611--1390652 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1390601 CGTACAAAGT
1390611 ATATAAATAAAATAC
1 ATATAAATAAAATAC
*
1390626 ATATAATATAAAATGC
1 ATATAA-ATAAAATAC
*
1390642 ATATACATAAA
1 ATATAAATAAA
1390653 TATAACTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (15 bp):
ATATAAATAAAATAC
Found at i:1390671 original size:2 final size:2
Alignment explanation
Indices: 1390664--1390690 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1390654 ATAACTACAT
1390664 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1390691 TACCAATGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1392131 original size:3 final size:3
Alignment explanation
Indices: 1392104--1392152 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
1392094 TGGTCTGAAA
* * *
1392104 AAT AAT AAA AAT ATT ATT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1392151 AA
1 AA
1392153 ACAATTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1394625 original size:31 final size:30
Alignment explanation
Indices: 1394581--1394643 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
1394571 TATGATAAAT
1394581 TTTGAAAAGTTTAAAGACCATTTTATAATAG
1 TTTGAAAAGTTTAAAGACCA-TTTATAATAG
* * *
1394612 TTTGATAAA-TTTAATGACTATTTGTAATAG
1 TTTGA-AAAGTTTAAAGACCATTTATAATAG
1394642 TT
1 TT
1394644 AATAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.39
31 14 0.50
32 3 0.11
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (30 bp):
TTTGAAAAGTTTAAAGACCATTTATAATAG
Found at i:1399059 original size:23 final size:23
Alignment explanation
Indices: 1399033--1399076 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1399023 CACCACAGCT
1399033 CATATAATTGCACCGAAGTGCAA
1 CATATAATTGCACCGAAGTGCAA
*
1399056 CATATAATTGCACCGGAGTGC
1 CATATAATTGCACCGAAGTGC
1399077 CGCGTAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCAA
Found at i:1399087 original size:23 final size:23
Alignment explanation
Indices: 1399033--1399101 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
1399023 CACCACAGCT
* *
1399033 CATATAATTGCACCGAAGTGCAA
1 CATAGAATTGCACCGAAGTGCCA
* * *
1399056 CATATAATTGCACCGGAGTGCCG
1 CATAGAATTGCACCGAAGTGCCA
* * *
1399079 CGTAGAATTACACCGTAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
1399102 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
CATAGAATTGCACCGAAGTGCCA
Found at i:1399354 original size:103 final size:103
Alignment explanation
Indices: 1399117--1399434 Score: 561
Period size: 103 Copynumber: 3.1 Consensus size: 103
1399107 TAATGTCCAT
* * * *
1399117 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAATATG-GTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1399181 GACTTCACACATGTTCCAAAGAATAC--ATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1399217 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1399282 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1399320 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1399385 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1399423 AAAGACCACATA
1 AAGGACCACATA
1399435 GTCCCTCGAC
Statistics
Matches: 209, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
100 51 0.24
101 35 0.17
103 123 0.59
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1402035 original size:206 final size:206
Alignment explanation
Indices: 1401652--1402065 Score: 764
Period size: 206 Copynumber: 2.0 Consensus size: 206
1401642 TAAAACACAT
1401652 AAATATTTATCTCCTTGCCTATATCATTTATATGATCAAAATACACAACACCAATCCAGATTCGT
1 AAATATTTATCTCCTTGCCTATATCATTTATATGATCAAAATACACAACACCAATCCAGATTCGT
1401717 ATCTCATTTGATTAACTTACTTTATGTTTCCTTCCAATCTGCTAATTCTAACATCCTGCCATTAC
66 ATCTCATTTGATTAACTTACTTTATGTTTCCTTCCAATCTGCTAATTCTAACATCCTGCCATTAC
1401782 GCTAATTAATAAAACTTTTCAATCTAGGGCGTAAGCCCTGATCAAATTAATCATACACATCATTT
131 GCTAATTAATAAAACTTTTCAATCTAGGGCGTAAGCCCTGATCAAATTAATCATACACATCATTT
1401847 CAGTTAAAATC
196 CAGTTAAAATC
1401858 AAATATTTATCTCCTTGCCTATAT-A-TTATATGATCAAAATACAC-A-ACCACATCCAGATTCG
1 AAATATTTATCTCCTTGCCTATATCATTTATATGATCAAAATACACAACACCA-ATCCAGATTCG
1401919 TATCTCATTTGATTAACTTACTTTATGTTTCCTTCCAATCTGCTAATTCTAACATCCATGCCATT
65 TATCTCATTTGATTAACTTACTTTATGTTTCCTTCCAATCTGCTAATTCTAACATCC-TGCCATT
1401984 ACAGCTAATTAATAACAACTTTTCAATCTAGGGCGTAAGCCCTGATCAAATTAATCATACACATC
129 AC-GCTAATTAATAA-AACTTTTCAATCTAGGGCGTAAGCCCTGATCAAATTAATCATACACATC
1402049 ATTTCAGTTAAAATC
192 ATTTCAGTTAAAATC
1402064 AA
1 AA
1402066 CCCAGTGTAA
Statistics
Matches: 204, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
202 4 0.02
203 69 0.34
204 28 0.14
205 13 0.06
206 90 0.44
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.36
Consensus pattern (206 bp):
AAATATTTATCTCCTTGCCTATATCATTTATATGATCAAAATACACAACACCAATCCAGATTCGT
ATCTCATTTGATTAACTTACTTTATGTTTCCTTCCAATCTGCTAATTCTAACATCCTGCCATTAC
GCTAATTAATAAAACTTTTCAATCTAGGGCGTAAGCCCTGATCAAATTAATCATACACATCATTT
CAGTTAAAATC
Found at i:1405105 original size:23 final size:23
Alignment explanation
Indices: 1405079--1405203 Score: 108
Period size: 23 Copynumber: 5.3 Consensus size: 23
1405069 CACCACAGCT
*
1405079 CATATAATTGCACTGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
1405102 CATATAATTGCATC-AGAGTGCCG
1 CATATAATTGCACCGA-AGTGCCA
* *
1405125 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
1405148 TATAATAATTGCACCGGAGTGCCG
1 CAT-ATAATTGCACCGAAGTGCCA
* * *
1405172 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
1405195 TATAATAAT
1 CAT-ATAAT
1405204 GTCCATAAGG
Statistics
Matches: 79, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.01
23 56 0.71
24 22 0.28
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1405169 original size:47 final size:47
Alignment explanation
Indices: 1405079--1405203 Score: 180
Period size: 47 Copynumber: 2.7 Consensus size: 47
1405069 CACCACAGCT
* * * * *
1405079 CATATAATTGCACTGAAGTGCCACAT-ATAATTGCATCAGAGTGCCG
1 CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCAGAGTGCCG
*
1405125 CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCG
1 CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCAGAGTGCCG
*
1405172 CGTAGAATTGCACCGTAGTGCCATATAATAAT
1 CATAGAATTGCACCGTAGTGCCATATAATAAT
1405204 GTCCATAAGG
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
46 22 0.31
47 49 0.69
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (47 bp):
CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCAGAGTGCCG
Found at i:1405379 original size:103 final size:102
Alignment explanation
Indices: 1405213--1405517 Score: 500
Period size: 103 Copynumber: 3.0 Consensus size: 102
1405203 TGTCCATAAG
* * *
1405213 GACCACATATCATTCTTTAAG-A--ATATACATA--CTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1405273 TTCACACATGTTCCAAAGAATACATATATGTCCTGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCC-GAAA
1405311 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
1405376 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGT-CCGAAA
1405414 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG--TCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1405477 TTCACACATGTTCCAAAGAATAC-TATATGTCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCGAAA
1405513 GACCA
1 GACCA
1405518 AATAACCCTC
Statistics
Matches: 196, Mismatches: 5, Indels: 11
0.92 0.02 0.05
Matches are distributed among these distances:
98 20 0.10
99 11 0.06
100 7 0.04
101 41 0.21
103 115 0.59
104 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (102 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCGAAA
Found at i:1409021 original size:3 final size:3
Alignment explanation
Indices: 1409013--1409052 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
1409003 TGTAAATTAA
1409013 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A
1409053 TTTTTTTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1409524 original size:127 final size:130
Alignment explanation
Indices: 1409248--1409596 Score: 392
Period size: 127 Copynumber: 2.7 Consensus size: 130
1409238 GTCGTCTAAC
*
1409248 GGTGACATGGCTCCTACGTGATGA-GA--TCTGGTCGGTGGATGACACGGTTCCTACGCGATGAG
1 GGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTA--CGATGAG
* * * *
1409310 GATGGCTGACCATCTTTAGGGAGGGTAATAACACGGTTCATACTCGATGAGGATGTCTGGTTATC
64 GATGGATGACCATATTTAGGGA--GTAATAACACGGTTCATACTCGATGAGGACGACTGGTTATC
1409375 TAGG
127 TAGG
** * * *
1409379 GGTGACACAACTCCTACGTGACGAGGAGGTCTGGTTGGTGGATGACACGGTTCCTAC-ATGATGA
1 GGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGATGAGGA
* * *
1409443 -GGATGACCATATTTAGGGA-TGATAACATGGTTTC-TA-TGTGATGAGGACGACTGGTTATCTA
66 TGGATGACCATATTTAGGGAGTAATAACACGG-TTCATACT-CGATGAGGACGACTGGTTATCTA
1409504 GG
129 GG
* * * *
1409506 GGTGACACGGCTCATACGTGATGAGGAGGTCTGGGCGGGGGATGACACGGTTCCTACGCGATAAG
1 GGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTA--CGATGAG
* *
1409571 GACGGCTGACCATATTTAGGGA-TAAT
64 GATGGATGACCATATTTAGGGAGTAAT
1409597 GTTTCAAGGG
Statistics
Matches: 185, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
126 1 0.01
127 82 0.44
128 3 0.02
129 1 0.01
130 22 0.12
131 47 0.25
132 3 0.02
134 26 0.14
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (130 bp):
GGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGATGAGGA
TGGATGACCATATTTAGGGAGTAATAACACGGTTCATACTCGATGAGGACGACTGGTTATCTAGG
Found at i:1409731 original size:66 final size:66
Alignment explanation
Indices: 1409596--1409975 Score: 331
Period size: 66 Copynumber: 5.8 Consensus size: 66
1409586 TTAGGGATAA
* * * * * * *
1409596 TGTTTCAAGGGAAACCGTCTCAAGAGATACAAACTT-GTTTCAAGGGAAACAAACTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGAAG-
*
1409660 TG
65 GG
* * * *
1409662 TGTTTCAAGAGAAATTGTCTCAAGAGAGATAAAATTCGTTTCGAGGGAAACAATCTCAAAGAAGG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGAAGG
1409727 G
66 G
*
1409728 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-AGATCTCAAAGATA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACA-ATCTCAAAGA-A
1409792 -GG
64 GGG
* ** * **
1409794 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGATTTCAAAGATTG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGAAGG
1409859 G
66 G
* * * * * ** * * *
1409860 TGTTCCATGAGAAAC-GATCTCAAGGGAGA-TAATTTTTTTTCAAGAGAAACAGA-CTTAAAGAT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACA-ATCTCAAAGAA
*
1409922 TGG
64 GGG
* * * * ** *
1409925 TGTTTTATGAGAAACTATCTCAAAGGGAGACAAAATTTGTTTCAAGAGAAA
1 TGTTTCAAGAGAAACTGTCTC-AAGAGAGACAAAATTCATTTCAAGGGAAA
1409976 TAGACTCAAA
Statistics
Matches: 265, Mismatches: 39, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
65 44 0.17
66 179 0.68
67 42 0.16
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGAAGG
G
Found at i:1409785 original size:36 final size:36
Alignment explanation
Indices: 1409745--1409852 Score: 95
Period size: 36 Copynumber: 3.2 Consensus size: 36
1409735 AAAGAAACTG
*
1409745 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAAGA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGA
* ** * *
1409781 TCTC-A-A-AG--ATAGGT-GTTTCAAGAGAAATTG-
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-TGA
1409811 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGA
*
1409847 TTTCAA
1 TCTCAA
1409853 AGATTGGTGT
Statistics
Matches: 52, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
30 15 0.29
31 5 0.10
32 1 0.02
33 4 0.08
34 1 0.02
35 6 0.12
36 20 0.38
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGA
Found at i:1409841 original size:132 final size:130
Alignment explanation
Indices: 1409596--1409975 Score: 402
Period size: 132 Copynumber: 2.9 Consensus size: 130
1409586 TTAGGGATAA
* * * * * *
1409596 TGTTTCAAGGGAAACCGTCTCAAGAGATACAAACTTGTTTCAAGGGAAACAAACTCAAAGATGAT
1 TGTTTCAAGAGAAA-CGTCTCAAGAGAGACAAAATTATTTCAAGGGAAACAGACTCAAAGAT-AG
* *
1409661 GTGTTTCAAGAGAAATTGTCTCAAGAGAGATAAAATTCGTTTCGAGGGAAACAATCTCAAAGAAG
64 GTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAAG
1409726 GG
129 GG
*
1409728 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-AGATCTCAAAGATA
1 TGTTTCAAGAGAAAC-GTCTCAAGAGAGACAAAATT-ATTTCAAGGGAAACAGA-CTCAAAGATA
* ** * *
1409792 GGTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGATTTCAAAGAT
63 GGTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAA
*
1409857 TGG
128 GGG
* * * * ** * * * *
1409860 TGTTCCATGAGAAACGATCTCAAGGGAGATAATTTTTTTTCAAGAGAAACAGACTTAAAGATTGG
1 TGTTTCAAGAGAAACG-TCTCAAGAGAGACAAAATTATTTCAAGGGAAACAGACTCAAAGATAGG
* * * * * * *
1409925 TGTTTTATGAGAAACTATCTCAAAGGGAGACAAAATTTGTTTCAAGAGAAA
65 TGTTTCAAGAGAAATTGTCTC-AAGAGAGACAAAATTCGTTTCAAGGGAAA
1409976 TAGACTCAAA
Statistics
Matches: 208, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
131 40 0.19
132 147 0.71
133 21 0.10
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (130 bp):
TGTTTCAAGAGAAACGTCTCAAGAGAGACAAAATTATTTCAAGGGAAACAGACTCAAAGATAGGT
GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAAGGG
Found at i:1410170 original size:36 final size:36
Alignment explanation
Indices: 1410127--1410252 Score: 157
Period size: 36 Copynumber: 3.5 Consensus size: 36
1410117 TTTGTATTCC
* *
1410127 GAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTT
1 GAGAGAAACTATCTCAAGCGAGACAAAATTTGTTTT
*
1410163 GAGAGAAATTATCTCAAGCGAGACAAAATTTGTTTT
1 GAGAGAAACTATCTCAAGCGAGACAAAATTTGTTTT
* * *
1410199 TAAAAAAACTATCTCAAGCGAGACAAAATTTGATTTT
1 GAGAGAAACTATCTCAAGCGAGACAAAATTTG-TTTT
*
1410236 -A-AGAAAATAATCTCAAG
1 GAGAGAAACT-ATCTCAAG
1410253 GTAGATAGAC
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
35 5 0.06
36 70 0.89
37 4 0.05
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (36 bp):
GAGAGAAACTATCTCAAGCGAGACAAAATTTGTTTT
Found at i:1411330 original size:2 final size:2
Alignment explanation
Indices: 1411323--1411359 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1411313 ATCTTTATTG
1411323 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1411360 TGTCTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1414196 original size:18 final size:18
Alignment explanation
Indices: 1414173--1414210 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1414163 AAAAGAAAAG
*
1414173 AAATGAGTTAGTACATAC
1 AAATGAGTTAGTACAAAC
1414191 AAATGAGTTAGTACAAAC
1 AAATGAGTTAGTACAAAC
1414209 AA
1 AA
1414211 GATAATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.24
Consensus pattern (18 bp):
AAATGAGTTAGTACAAAC
Found at i:1417627 original size:3 final size:3
Alignment explanation
Indices: 1417619--1417679 Score: 106
Period size: 3 Copynumber: 20.3 Consensus size: 3
1417609 TGTAAATTAA
1417619 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1417667 -AT AATT AAT AAT A
1 AAT AA-T AAT AAT A
1417680 TTTTTTTAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1423222 original size:60 final size:60
Alignment explanation
Indices: 1423146--1423281 Score: 209
Period size: 60 Copynumber: 2.3 Consensus size: 60
1423136 GCGATTTTCC
*
1423146 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGAGTAT
* * * * *
1423206 GACTATCGCAACGCGAATATGTAAATCGCAATGCGATTCTGACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGAGTAT
*
1423266 GACTGTCGCAATGCGA
1 GACTATCGCAATGCGA
1423282 TTTTCAAAGC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (60 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGAGTAT
Found at i:1423282 original size:20 final size:20
Alignment explanation
Indices: 1423146--1423283 Score: 145
Period size: 20 Copynumber: 6.9 Consensus size: 20
1423136 GCGATTTTCC
*
1423146 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
1423166 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGATTAT
*
1423186 GACTATCGCAATGCGAGTAT
1 GACTATCGCAATGCGATTAT
* *
1423206 GACTATCGCAACGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
1423226 GTA-AATCGCAATGCGATTCT
1 G-ACTATCGCAATGCGATTAT
* *
1423246 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
1423266 GACTGTCGCAATGCGATT
1 GACTATCGCAATGCGATT
1423284 TTCAAAGCGC
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
19 2 0.02
20 97 0.96
21 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:1423938 original size:20 final size:20
Alignment explanation
Indices: 1423913--1423964 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1423903 GCTGCGATTC
1423913 TCGCGTTGCGATAGTCAAAT
1 TCGCGTTGCGATAGTCAAAT
**
1423933 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCAAAT
*
1423953 TCGTGTTGCGAT
1 TCGCGTTGCGAT
1423965 TTTCATTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATAGTCAAAT
Found at i:1423970 original size:20 final size:20
Alignment explanation
Indices: 1423917--1423985 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
1423907 CGATTCTCGC
* ** *
1423917 GTTGCGATAGTCAAATTCGC
1 GTTGCGATTGTCATTTTCGT
*
1423937 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTGTCATTTTCGT
*
1423957 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTGTCATTTTCGT
*
1423977 GTTGAGATT
1 GTTGCGATT
1423986 ATAAGTTTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.43
Consensus pattern (20 bp):
GTTGCGATTGTCATTTTCGT
Found at i:1423994 original size:20 final size:20
Alignment explanation
Indices: 1423951--1423994 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1423941 CGATAGTCAT
* * * *
1423951 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGAGATTATAAG
1423971 TTTCGTGTTGAGATTATAAG
1 TTTCGTGTTGAGATTATAAG
1423991 TTTC
1 TTTC
1423995 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGAGATTATAAG
Found at i:1425919 original size:20 final size:20
Alignment explanation
Indices: 1425894--1425961 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
1425884 TAGTTTACTT
1425894 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1425914 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
1425934 TCGCAACGC-GAATTTAACTA
1 TCGCAACGCGGAA-ATGACTA
1425954 TCGCAACG
1 TCGCAACG
1425962 AAAGAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 2 0.05
20 41 0.95
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1426032 original size:20 final size:20
Alignment explanation
Indices: 1426004--1426079 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1425994 GCGATTCTCT
**
1426004 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
* *
1426024 CGTTACGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCG
1426044 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1426064 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
1426080 CGTGTTGCGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1426667 original size:21 final size:21
Alignment explanation
Indices: 1426580--1426678 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
1426570 GACTCATCTG
1426580 TCATCGTTCAAGAGGCCTC-C
1 TCATCGTTCAAGAGGCCTCTC
* *
1426600 CCTATCGTTCAAGAGGCCTCTA
1 TC-ATCGTTCAAGAGGCCTCTC
** * *
1426622 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCTCTC
* *
1426643 TCATCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCTCTC
* *
1426664 TCATTGTTGAAGAGG
1 TCATCGTTCAAGAGG
1426679 TCCCTCCCAA
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.02
21 60 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCTCTC
Found at i:1426677 original size:42 final size:41
Alignment explanation
Indices: 1426577--1426682 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 41
1426567 TCCGACTCAT
* *
1426577 CTGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCT
1 CTGTCATCGTTCAAGAGTCC-CCCCTATCGTTCAAGAGGCCA
* ** *
1426619 CTATCATCCCTCAAGAGTCCCCTCTCATCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCCCT-ATCGTTCAAGAGGCCA
* *
1426661 CTGTCATTGTTGAAGAGGTCCC
1 CTGTCATCGTTCAAGA-GTCCC
1426683 TCCCAACATT
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 4 0.08
42 42 0.82
43 5 0.10
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (41 bp):
CTGTCATCGTTCAAGAGTCCCCCCTATCGTTCAAGAGGCCA
Found at i:1428069 original size:36 final size:30
Alignment explanation
Indices: 1427989--1428054 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
1427979 ATAAGAGTTG
1427989 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
1428019 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
1428049 ATTTGT
1 ATTTGT
1428055 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:1428231 original size:20 final size:20
Alignment explanation
Indices: 1428204--1428541 Score: 277
Period size: 20 Copynumber: 17.9 Consensus size: 20
1428194 ACGATTTTCT
1428204 CGTTGCGATAGTCAAATTC-
1 CGTTGCGATAGTCAAATTCG
* *
1428223 CTATTGCGATAATCAAATTCG
1 C-GTTGCGATAGTCAAATTCG
*
1428244 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
1428263 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
1428277 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1428297 CATTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1428317 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1428337 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* **
1428357 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
**
1428377 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
1428397 CATTGCGAT--T---A-TC-
1 CGTTGCGATAGTCAAATTCG
1428410 CTGTTGCGATAGTCAAATTCG
1 C-GTTGCGATAGTCAAATTCG
* ** *
1428431 CGTTGCGATAATCATTTTTG
1 CGTTGCGATAGTCAAATTCG
* * *
1428451 CATTGAGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
1428465 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
1428485 CGTTGCGATAGTCATATTTG
1 CGTTGCGATAGTCAAATTCG
*
1428505 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
1428525 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
1428542 GAATGTGTAA
Statistics
Matches: 260, Mismatches: 37, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
13 1 0.00
14 28 0.11
16 3 0.01
17 1 0.00
18 2 0.01
19 18 0.07
20 205 0.79
21 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1428286 original size:73 final size:73
Alignment explanation
Indices: 1428160--1428345 Score: 248
Period size: 73 Copynumber: 2.5 Consensus size: 73
1428150 TTCAATCTGC
* * * * * *
1428160 ATCATATTCGCGTTGCGATAGTCTAATACACTTTACGATTTTCTCGTTGCGATAGTCAAATTC-C
1 ATCAAATTCGCGTTGCGATAGTC-AATTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGC
1428224 TATTGCGATA
65 -ATTGCGATA
*
1428234 ATCAAATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCA
1 ATCAAATTCGCGTTGCGATAGTCAATTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCA
1428299 TTGCGATA
66 TTGCGATA
* * *
1428307 GTTAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGAT
1 ATCAAATTCGCGTTGCGATAG-TCAATTCGCGTTGCGAT
1428346 AGTCATATTC
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
73 61 0.62
74 38 0.38
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.36
Consensus pattern (73 bp):
ATCAAATTCGCGTTGCGATAGTCAATTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCA
TTGCGATA
Found at i:1428303 original size:34 final size:34
Alignment explanation
Indices: 1428170--1428305 Score: 114
Period size: 34 Copynumber: 3.9 Consensus size: 34
1428160 ATCATATTCG
* * * * * *
1428170 CGTTGCGATAGTCTAATACACTTTACGATTTTCT
1 CGTTGCGATAGTCAAATTCGCATTGCGATTATCT
*
1428204 CGTTGCGATAGTCAAATTC-CTATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGC-ATTGCGAT--T---A-TCT
* *
1428244 CGTTGCGATAGTC-ATTTCGCGTTGCGATTATCT
1 CGTTGCGATAGTCAAATTCGCATTGCGATTATCT
1428277 CGTTGCGATAGTCAAATTCGCATTGCGAT
1 CGTTGCGATAGTCAAATTCGCATTGCGAT
1428306 AGTTAAATTC
Statistics
Matches: 82, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
33 16 0.20
34 37 0.45
36 1 0.01
37 1 0.01
39 11 0.13
40 16 0.20
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCATTGCGATTATCT
Found at i:1428446 original size:54 final size:53
Alignment explanation
Indices: 1428359--1428513 Score: 211
Period size: 54 Copynumber: 2.9 Consensus size: 53
1428349 CATATTCGCA
** *
1428359 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCTG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTT-GCATTGCGATTATCCCG
* *
1428413 TTGCGATAGTCAAATTCGCGTTGCGATAATCATTTTTGCATTGAGATTATCCCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCA-TTTTGCATTGCGATTATCCCG
* * *
1428467 TTGCGATATTCAAATTCACGTTGCGATAGTCATATTTGCGTTGCGAT
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAT-TTTGCATTGCGAT
1428514 AGTCATATTC
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 84 0.94
55 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (53 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTGCATTGCGATTATCCCG
Found at i:1428739 original size:18 final size:18
Alignment explanation
Indices: 1428716--1428750 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1428706 AAGCCGGTTG
*
1428716 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1428734 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1428751 GCCTTTTGCT
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:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1430806 original size:14 final size:14
Alignment explanation
Indices: 1430787--1430813 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1430777 TCCCGTGGCA
1430787 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
1430801 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
1430814 TTTCTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1431047 original size:24 final size:24
Alignment explanation
Indices: 1431013--1431066 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1431003 CTGAAACATC
1431013 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1431037 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1431061 ATCAAA
1 ATCAAA
1431067 TTTCAAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1431934 original size:20 final size:20
Alignment explanation
Indices: 1431885--1431998 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
1431875 TTGAAATTCA
* *
1431885 GCATTGCGACAGTCAGAATC
1 GCATTGCGATAGTCATAATC
*
1431905 GCGTTGCGATAGTCATAATC
1 GCATTGCGATAGTCATAATC
* *
1431925 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CATAATC
* *
1431945 GCGTTGCGATAGTCATACTC
1 GCATTGCGATAGTCATAATC
* *
1431965 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CATAATC
1431985 GCATTGCGATAGTC
1 GCATTGCGATAGTC
1431999 GGAAAATTGC
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 73 0.95
21 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (20 bp):
GCATTGCGATAGTCATAATC
Found at i:1432567 original size:30 final size:30
Alignment explanation
Indices: 1432533--1432594 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1432523 TAAAGATTTT
* *
1432533 GATTTGAGCATAACGTCAATAA-AAGTATTG
1 GATTTAAGCACAACGTCAATAAGAA-TATTG
*
1432563 GATTTAAGCACAACGTCTATAAGAATATTG
1 GATTTAAGCACAACGTCAATAAGAATATTG
1432593 GA
1 GA
1432595 ATGTTCATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (30 bp):
GATTTAAGCACAACGTCAATAAGAATATTG
Found at i:1436830 original size:6 final size:6
Alignment explanation
Indices: 1436819--1436978 Score: 141
Period size: 6 Copynumber: 27.3 Consensus size: 6
1436809 AGTTACTATG
** **
1436819 TACATA TACATA TACATA TATGTA TA-AGTA TATGTA TACATA T--ATA
1 TACATA TACATA TACATA TACATA TACA-TA TACATA TACATA TACATA
* * * * ** * *
1436865 TACATA TACGTA TATATA TAC--A CACGTA TATGTA TACGTA TACGTA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* * *
1436911 TACATA TACGTA TACGTA TACGTA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1436959 TACATA TACATA TACATA TA
1 TACATA TACATA TACATA TA
1436979 ATTTGATCTG
Statistics
Matches: 131, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
4 7 0.05
6 124 0.95
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (6 bp):
TACATA
Found at i:1436836 original size:12 final size:12
Alignment explanation
Indices: 1436819--1436978 Score: 168
Period size: 12 Copynumber: 13.7 Consensus size: 12
1436809 AGTTACTATG
*
1436819 TACATATACATA
1 TACATATACGTA
*
1436831 TACATATATGTA
1 TACATATACGTA
*
1436843 TA-AGTATATGTA
1 TACA-TATACGTA
1436855 TACATATA--TA
1 TACATATACGTA
1436865 TACATATACGTA
1 TACATATACGTA
*
1436877 TATATATAC--A
1 TACATATACGTA
* * *
1436887 CACGTATATGTA
1 TACATATACGTA
*
1436899 TACGTATACGTA
1 TACATATACGTA
1436911 TACATATACGTA
1 TACATATACGTA
*
1436923 TACGTATACGTA
1 TACATATACGTA
*
1436935 TACATATACATA
1 TACATATACGTA
*
1436947 TACATATACATA
1 TACATATACGTA
*
1436959 TACATATACATA
1 TACATATACGTA
1436971 TACATATA
1 TACATATA
1436979 ATTTGATCTG
Statistics
Matches: 129, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
10 16 0.12
11 1 0.01
12 111 0.86
13 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (12 bp):
TACATATACGTA
Found at i:1445433 original size:33 final size:30
Alignment explanation
Indices: 1445396--1445483 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 30
1445386 TGGAAATTTC
1445396 ATCTTGGTTGGTGGCCAACTTATTGAAAAATTA
1 ATCTTGGTTGGTGGCCAACTTATTG-AAAA--A
* * *
1445429 ATCTTGGTTGGTGGTCAACTCATTGGAAAA
1 ATCTTGGTTGGTGGCCAACTTATTGAAAAA
*
1445459 ATCTTTGGTAGGTGGCCAACTTATT
1 ATC-TTGGTTGGTGGCCAACTTATT
1445484 TTTTCATGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.08
31 18 0.38
32 3 0.06
33 23 0.48
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (30 bp):
ATCTTGGTTGGTGGCCAACTTATTGAAAAA
Found at i:1447208 original size:35 final size:35
Alignment explanation
Indices: 1447169--1447342 Score: 190
Period size: 35 Copynumber: 5.0 Consensus size: 35
1447159 TGACTGATTG
*
1447169 TTATGCA-TACTCTAAATGCTACACATGACACATTA
1 TTATGCATTA-TCTAAATGCGACACATGACACATTA
* *
1447204 TTATGCA-TACTCTAAATGCTACACATGATACATTA
1 TTATGCATTA-TCTAAATGCGACACATGACACATTA
* * *
1447239 TTATGCATTATTTGAATGCGACACATGACACATTG
1 TTATGCATTATCTAAATGCGACACATGACACATTA
* * * *
1447274 TTGTGCATTATCTAAATGCGACACATGACATACTC
1 TTATGCATTATCTAAATGCGACACATGACACATTA
* * * *
1447309 TTGTGCATTATTTGAATGAGACACATGACACATT
1 TTATGCATTATCTAAATGCGACACATGACACATT
1447343 GTTAGTATCT
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
35 119 0.98
36 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (35 bp):
TTATGCATTATCTAAATGCGACACATGACACATTA
Found at i:1447288 original size:70 final size:70
Alignment explanation
Indices: 1447183--1447346 Score: 222
Period size: 70 Copynumber: 2.3 Consensus size: 70
1447173 GCATACTCTA
* * * * *
1447183 AATGCTACACATGACACATTATTATGCATACTCTAAATGCTACACATGATACATTATTATGCATT
1 AATGCGACACATGACACATTGTTATGCATACTCTAAATGCGACACATGACACACTATTATGCATT
1447248 ATTTG
66 ATTTG
* * * *
1447253 AATGCGACACATGACACATTGTTGTGCATTA-TCTAAATGCGACACATGACATACTCTTGTGCAT
1 AATGCGACACATGACACATTGTTATGCA-TACTCTAAATGCGACACATGACACACTATTATGCAT
1447317 TATTTG
65 TATTTG
*
1447323 AATGAGACACATGACACATTGTTA
1 AATGCGACACATGACACATTGTTA
1447347 GTATCTAGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
70 80 0.98
71 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (70 bp):
AATGCGACACATGACACATTGTTATGCATACTCTAAATGCGACACATGACACACTATTATGCATT
ATTTG
Found at i:1449954 original size:13 final size:13
Alignment explanation
Indices: 1449936--1449972 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1449926 AATTTACAAT
1449936 GCCCAAAAGAATA
1 GCCCAAAAGAATA
1449949 GCCCAAAAGAATA
1 GCCCAAAAGAATA
*
1449962 ACCCAAAAGAA
1 GCCCAAAAGAA
1449973 AGGACGACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.57, C:0.24, G:0.14, T:0.05
Consensus pattern (13 bp):
GCCCAAAAGAATA
Found at i:1451685 original size:18 final size:17
Alignment explanation
Indices: 1451625--1451685 Score: 68
Period size: 18 Copynumber: 3.5 Consensus size: 17
1451615 ATATAAAGAG
*
1451625 CTAGTTTAATTATTGAA
1 CTAGTTTAATTAGTGAA
* * *
1451642 CCAGTTTAAATGGATGAA
1 CTAGTTTAATTAG-TGAA
1451660 CTAGTTTAATTAGTGAA
1 CTAGTTTAATTAGTGAA
1451677 CTAGCTTTA
1 CTAG-TTTA
1451686 TTGAATGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
17 17 0.49
18 18 0.51
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (17 bp):
CTAGTTTAATTAGTGAA
Found at i:1451694 original size:18 final size:17
Alignment explanation
Indices: 1451625--1451694 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
1451615 ATATAAAGAG
*
1451625 CTAGTTTAATTATTGAA
1 CTAGTTTAATTAATGAA
* **
1451642 CCAGTTTAAATGGATGAA
1 CTAGTTT-AATTAATGAA
*
1451660 CTAGTTTAATTAGTGAA
1 CTAGTTTAATTAATGAA
1451677 CTAGCTTT-ATTGAATGAA
1 CTAG-TTTAATT-AATGAA
1451695 AGATGATACT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
17 20 0.49
18 21 0.51
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (17 bp):
CTAGTTTAATTAATGAA
Found at i:1451694 original size:35 final size:35
Alignment explanation
Indices: 1451625--1451694 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
1451615 ATATAAAGAG
* *
1451625 CTAGTTTAATTATTGAACCAGTTTAAATGGATGAA
1 CTAGTTTAATTAGTGAACCAGTTTAAATGAATGAA
* *
1451660 CTAGTTTAATTAGTGAACTAGCTTT-ATTGAATGAA
1 CTAGTTTAATTAGTGAACCAG-TTTAAATGAATGAA
1451695 AGATGATACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (35 bp):
CTAGTTTAATTAGTGAACCAGTTTAAATGAATGAA
Found at i:1453911 original size:21 final size:21
Alignment explanation
Indices: 1453887--1453931 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1453877 TACTGCTCAA
* *
1453887 CTCGACTTGTTGGTCGTTAAG
1 CTCGACTCGTTGCTCGTTAAG
1453908 CTCGACTCGTTGCTCGTTAAG
1 CTCGACTCGTTGCTCGTTAAG
1453929 CTC
1 CTC
1453932 ACTAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.27, G:0.24, T:0.36
Consensus pattern (21 bp):
CTCGACTCGTTGCTCGTTAAG
Found at i:1462496 original size:29 final size:29
Alignment explanation
Indices: 1462450--1462519 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
1462440 GAGCCAAACC
1462450 GAGAT-AGG-GAGGTTCTAACCCACCTTA
1 GAGATAAGGAGAGGTTCTAACCCACCTTA
1462477 GAGATAAGGAGAGGTTCTAACCCACCTTA
1 GAGATAAGGAGAGGTTCTAACCCACCTTA
1462506 GAGATAAGGAGAGG
1 GAGATAAGGAGAGG
1462520 GTTTCATTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 5 0.12
28 3 0.07
29 33 0.80
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (29 bp):
GAGATAAGGAGAGGTTCTAACCCACCTTA
Found at i:1463722 original size:20 final size:22
Alignment explanation
Indices: 1463699--1463738 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1463689 TTTTTTCAAT
1463699 TATG-TAAC-TTTTAGGTTGAA
1 TATGATAACATTTTAGGTTGAA
*
1463719 TATGATAGCATTTTAGGTTG
1 TATGATAACATTTTAGGTTG
1463739 GATAATGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.45
Consensus pattern (22 bp):
TATGATAACATTTTAGGTTGAA
Found at i:1466098 original size:56 final size:56
Alignment explanation
Indices: 1466033--1466226 Score: 212
Period size: 56 Copynumber: 3.5 Consensus size: 56
1466023 CCCTATTTTC
*
1466033 TAGATATATTCGATTTCGGGACCCCTATTTTTATGATTCTTAATGGCAACAACTGA
1 TAGATATATTCGATTTCGGGACCCCTATTTTTATGATTCTTAATGACAACAACTGA
* * * * * *
1466089 TAAATATATTCGATTTTGGGGCCCCTATTTTTAT-ATTTCTTAGTGACAACAATTAA
1 TAGATATATTCGATTTCGGGACCCCTATTTTTATGA-TTCTTAATGACAACAACTGA
* * * * * * *
1466145 TAGATATACTT-AATTCCGGGACCCTTTTTTTTATGTTTATTAATGACAATAACTGA
1 TAGATATA-TTCGATTTCGGGACCCCTATTTTTATGATTCTTAATGACAACAACTGA
* *
1466201 TAGATATATTCGATTTTGGGGCCCCT
1 TAGATATATTCGATTTCGGGACCCCT
1466227 GCACGGTCGC
Statistics
Matches: 109, Mismatches: 25, Indels: 8
0.77 0.18 0.06
Matches are distributed among these distances:
55 3 0.03
56 104 0.95
57 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (56 bp):
TAGATATATTCGATTTCGGGACCCCTATTTTTATGATTCTTAATGACAACAACTGA
Found at i:1467815 original size:26 final size:26
Alignment explanation
Indices: 1467786--1467836 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1467776 CAAAAATTTA
1467786 AAGATTTGATCCTTA-AGTAAATTTTT
1 AAGATTTGATCCTTACA-TAAATTTTT
* *
1467812 AAGATTTTATTCTTACATAAATTTT
1 AAGATTTGATCCTTACATAAATTTT
1467837 AATTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (26 bp):
AAGATTTGATCCTTACATAAATTTTT
Found at i:1469283 original size:41 final size:41
Alignment explanation
Indices: 1469226--1469308 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1469216 CCATCCTGAT
*
1469226 ATGTATGTGTTATATGTGTGTAATGAATGCATGCAAGTCTC
1 ATGTATGTGTTATATGTGTGTAATGAATGCATGCAAGCCTC
* *
1469267 ATGTATGTGTTATATGTGTGTATTGTATGCATGCAAGCCTC
1 ATGTATGTGTTATATGTGTGTAATGAATGCATGCAAGCCTC
1469308 A
1 A
1469309 CAGTTAGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (41 bp):
ATGTATGTGTTATATGTGTGTAATGAATGCATGCAAGCCTC
Found at i:1469777 original size:6 final size:6
Alignment explanation
Indices: 1469766--1469830 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
1469756 CCACATATTT
* * * * *
1469766 TATATA TATATA TATATA TATACA TATACA TATACA TATACA TATACA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
1469814 TCTATG TATATA T-TATA
1 TATATA TATATA TATATA
1469831 GTTCGCAAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
5 4 0.08
6 49 0.92
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (6 bp):
TATATA
Found at i:1469783 original size:12 final size:12
Alignment explanation
Indices: 1469766--1469814 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
1469756 CCACATATTT
*
1469766 TATATATATATA
1 TATATATATACA
1469778 TATATATATACA
1 TATATATATACA
*
1469790 TATACATATACA
1 TATATATATACA
*
1469802 TATACATATACA
1 TATATATATACA
1469814 T
1 T
1469815 CTATGTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
TATATATATACA
Found at i:1469823 original size:18 final size:18
Alignment explanation
Indices: 1469766--1469814 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1469756 CCACATATTT
* * *
1469766 TATATATATATATATATA
1 TATACATATACATATACA
1469784 TATACATATACATATACA
1 TATACATATACATATACA
1469802 TATACATATACAT
1 TATACATATACAT
1469815 CTATGTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (18 bp):
TATACATATACATATACA
Found at i:1469917 original size:38 final size:37
Alignment explanation
Indices: 1469875--1470097 Score: 197
Period size: 36 Copynumber: 5.8 Consensus size: 37
1469865 TATAGGTTTT
1469875 TTTTTAAAAAGCA-TTTTGAAAA-TGAATATAGTATATAG
1 TTTTT-AAAA-CATTTTTGAAAACT-AATATAGTATATAG
*
1469913 TTTTTAAAACAGTTTTGAAAACT-ATAT-GATATATAG
1 TTTTTAAAACATTTTTGAAAACTAATATAG-TATATAG
* **
1469949 TTTTTAAGACATTTTTAGAAAAAAAATATA-TAATATATGG
1 TTTTTAAAACATTTTT-GAAAACTAATATAGT-ATATA--G
* *
1469989 TTTTTAAAATCATTTTTTGAAAACTTATATAATATATAG
1 TTTTTAAAA-CA-TTTTTGAAAACTAATATAGTATATAG
* * *
1470028 TTTTTTAAAGCATTTTTGAAAACTTATATATAATATATAA
1 -TTTTTAAAACATTTTTGAAAAC-TA-ATATAGTATATAG
*
1470068 TTTTTAAAACATTTTTGAAAA-TTATATAGT
1 TTTTTAAAACATTTTTGAAAACTAATATAGT
1470098 TTTTTGAAAA
Statistics
Matches: 156, Mismatches: 14, Indels: 32
0.77 0.07 0.16
Matches are distributed among these distances:
35 1 0.01
36 33 0.21
37 20 0.13
38 26 0.17
39 24 0.15
40 29 0.19
41 17 0.11
42 6 0.04
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (37 bp):
TTTTTAAAACATTTTTGAAAACTAATATAGTATATAG
Found at i:1469939 original size:79 final size:74
Alignment explanation
Indices: 1469856--1470095 Score: 236
Period size: 79 Copynumber: 3.1 Consensus size: 74
1469846 TAAAAATACA
*
1469856 TATATAATATATAGGTTTTTTTTTAAAAAGCA-TTTTGAAAATGAATATAGTATATAGTTTTTAA
1 TATATAATATATA-G---TTTTTT-AAAAGCATTTTTGAAAATAAATATA-TATATAGTTTTTAA
*
1469920 AACAGTTTTGAAAAC
60 AACATTTTTGAAAAC
* * *
1469935 TATATGATATATAG-TTTTTAAGA-CATTTTTAGAAAAAAAATATATAATATATGGTTTTTAAAA
1 TATATAATATATAGTTTTTTAAAAGCATTTTT-GAAAATAAATATAT-ATATA--GTTTTTAAAA
1469998 TCATTTTTTGAAAAC
62 -CA-TTTTTGAAAAC
* *
1470013 TTATATAATATATAGTTTTTT-AAAGCATTTTTGAAAACTTATATATAATATATAATTTTTAAAA
1 -TATATAATATATAGTTTTTTAAAAGCATTTTTGAAAA--TAAATAT-ATATATAGTTTTTAAAA
*
1470077 CATTTTTGAAAAT
62 CATTTTTGAAAAC
1470090 TATATA
1 TATATA
1470096 GTTTTTTGAA
Statistics
Matches: 137, Mismatches: 11, Indels: 29
0.77 0.06 0.16
Matches are distributed among these distances:
72 2 0.01
73 8 0.06
74 21 0.15
76 16 0.12
77 12 0.09
78 13 0.09
79 41 0.30
80 12 0.09
81 10 0.07
82 2 0.01
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (74 bp):
TATATAATATATAGTTTTTTAAAAGCATTTTTGAAAATAAATATATATATAGTTTTTAAAACATT
TTTGAAAAC
Found at i:1469992 original size:40 final size:40
Alignment explanation
Indices: 1469875--1470088 Score: 180
Period size: 40 Copynumber: 5.5 Consensus size: 40
1469865 TATAGGTTTT
** *
1469875 TTTTTAAAAAGCA-TTTTG-AAAATGA-ATATAGTATATAG
1 TTTTT-AAAAGCATTTTTGAAAAAAAATATATAATATATAG
* * *
1469913 TTTTTAAAA-CAGTTTTG---AAAACTATATGATATATAG
1 TTTTTAAAAGCATTTTTGAAAAAAAATATATAATATATAG
* *
1469949 TTTTTAAGA-CATTTTTAGAAAAAAAATATATAATATATGG
1 TTTTTAAAAGCATTTTT-GAAAAAAAATATATAATATATAG
* **
1469989 TTTTTAAAATCATTTTTTG--AAAACTTATATAATATATAG
1 TTTTTAAAAGCA-TTTTTGAAAAAAAATATATAATATATAG
* *** *
1470028 TTTTTTAAAGCATTTTTGAAAACTTATATATAATATATAA
1 TTTTTAAAAGCATTTTTGAAAAAAAATATATAATATATAG
1470068 TTTTTAAAA-CATTTTTGAAAA
1 TTTTTAAAAGCATTTTTGAAAA
1470089 TTATATAGTT
Statistics
Matches: 144, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
35 2 0.01
36 27 0.19
37 10 0.07
38 11 0.08
39 39 0.27
40 47 0.33
41 3 0.02
42 5 0.03
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (40 bp):
TTTTTAAAAGCATTTTTGAAAAAAAATATATAATATATAG
Found at i:1470108 original size:31 final size:31
Alignment explanation
Indices: 1470068--1470139 Score: 119
Period size: 33 Copynumber: 2.3 Consensus size: 31
1470058 TAATATATAA
1470068 TTTTTAAAACA-TTTTTGAAAATTATATAGT
1 TTTTTAAAACATTTTTTGAAAATTATATAGT
1470098 TTTTTGAAAACATTTTTTTGAAAATTATATAGT
1 TTTTT-AAAACA-TTTTTTGAAAATTATATAGT
1470131 TTTTTAAAA
1 TTTTTAAAA
1470140 AAAATTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
30 5 0.13
31 6 0.15
32 4 0.10
33 24 0.62
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (31 bp):
TTTTTAAAACATTTTTTGAAAATTATATAGT
Found at i:1470232 original size:3 final size:3
Alignment explanation
Indices: 1470224--1470291 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
1470214 ATTTATTTAT
* * *
1470224 TTA TTA TTA TTA TTA TTA TCA TTA TCA TTA TTTA TTA TTA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1470270 TTA TTA CTTA TT- TTA TT- TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TT
1470292 TTTCCCGTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 4 0.07
3 45 0.82
4 6 0.11
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1470286 original size:31 final size:31
Alignment explanation
Indices: 1470219--1470287 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
1470209 GTTTTATTTA
1470219 TTTATTTATTATTATTATTATTATCATTATC
1 TTTATTTATTATTATTATTATTATCATTATC
* * *
1470250 ATTATTTATTATTATTATTTTTATTACTTAT-
1 TTTATTTATTATTATTATTATTATCA-TTATC
1470281 TTTATTT
1 TTTATTT
1470288 TATTTTTCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (31 bp):
TTTATTTATTATTATTATTATTATCATTATC
Found at i:1472777 original size:17 final size:18
Alignment explanation
Indices: 1472757--1472803 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
1472747 AGTTTAATTT
1472757 TTTTTTATTTTTTTCT-A
1 TTTTTTATTTTTTTCTCA
1472774 TTTTTTATTTTTTTCTCA
1 TTTTTTATTTTTTTCTCA
1472792 -TTTTTATTTTTT
1 TTTTTTATTTTTT
1472804 AACTAACCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 28 0.97
18 1 0.03
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTATTTTTTTCTCA
Found at i:1472851 original size:28 final size:31
Alignment explanation
Indices: 1472820--1472896 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
1472810 CCCTTTTACC
1472820 TTTTTTATTTTTTATTCA-TTTTGT-T-TTA
1 TTTTTTATTTTTTATTCACTTTTGTATATTA
* *
1472848 TTTTATAATTTTTTTATTTACTTTTGTATATTA
1 TTTT-TTA-TTTTTTATTCACTTTTGTATATTA
* *
1472881 TTATTTATTTATTATT
1 TTTTTTATTTTTTATT
1472897 TTTTACTAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 4 0.10
29 2 0.05
30 10 0.26
31 14 0.36
32 3 0.08
33 6 0.15
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (31 bp):
TTTTTTATTTTTTATTCACTTTTGTATATTA
Found at i:1472867 original size:20 final size:23
Alignment explanation
Indices: 1472844--1472893 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
1472834 TTCATTTTGT
1472844 TTTATTTTATA-ATT-TT-TTTA
1 TTTATTTTATATATTATTATTTA
*
1472864 TTTACTTTTGTATATTATTATTTA
1 TTTA-TTTTATATATTATTATTTA
1472888 TTTATT
1 TTTATT
1472894 ATTTTTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 6 0.24
22 3 0.12
23 4 0.16
24 8 0.32
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTATTTTATATATTATTATTTA
Found at i:1472900 original size:28 final size:27
Alignment explanation
Indices: 1472824--1472900 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 27
1472814 TTTACCTTTT
* *
1472824 TTATTTTTTATTCATTTTGTTTTATTTTA
1 TTATTTTTTATT-ATTTT-TTGTATATTA
* *
1472853 TAATTTTTTTATT-TACTTTTGTATATTA
1 TTA-TTTTTTATTAT-TTTTTGTATATTA
1472881 TTATTTATTTATTATTTTTT
1 TTATTT-TTTATTATTTTTT
1472901 ACTAACTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
27 3 0.08
28 21 0.55
29 5 0.13
30 9 0.24
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (27 bp):
TTATTTTTTATTATTTTTTGTATATTA
Found at i:1474364 original size:5 final size:5
Alignment explanation
Indices: 1474354--1474382 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1474344 ATTAATGGTC
1474354 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1474383 ATAACAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1474762 original size:8 final size:8
Alignment explanation
Indices: 1474749--1474774 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1474739 CTAACTTAGA
1474749 GAGAAAGG
1 GAGAAAGG
1474757 GAGAAAGG
1 GAGAAAGG
1474765 GAGAAAGG
1 GAGAAAGG
1474773 GA
1 GA
1474775 AAATCGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (8 bp):
GAGAAAGG
Found at i:1475420 original size:20 final size:20
Alignment explanation
Indices: 1475395--1475437 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1475385 TTTAAGAGCT
1475395 CATTTAGAACCATGTAGATG
1 CATTTAGAACCATGTAGATG
* * *
1475415 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATGTAGATG
1475435 CAT
1 CAT
1475438 GCGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATGTAGATG
Found at i:1477380 original size:3 final size:3
Alignment explanation
Indices: 1477365--1477450 Score: 91
Period size: 3 Copynumber: 27.7 Consensus size: 3
1477355 GTAACCTGAA
* * * *
1477365 AAT AAT AAA AAT AAT ATT AGT AAT AAT AAT AAT GAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
1477414 AAT AAT AAAT AAT TAT AATT AAT AAT AAC AAT AAT AA
1 AAT AAT -AAT AAT AAT AA-T AAT AAT AAT AAT AAT AA
1477451 ACAATTAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
3 60 0.87
4 9 0.13
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1481665 original size:16 final size:16
Alignment explanation
Indices: 1481644--1481680 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1481634 ACCTATTCGA
1481644 ATAAATAAATAAATAT
1 ATAAATAAATAAATAT
*
1481660 ATAAATAAATAGATAT
1 ATAAATAAATAAATAT
1481676 ATAAA
1 ATAAA
1481681 AATTACCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAAATAAATAAATAT
Found at i:1482657 original size:2 final size:2
Alignment explanation
Indices: 1482650--1482692 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1482640 CAAATTCTTT
1482650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1482692 T
1 T
1482693 CTAAATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1484401 original size:16 final size:15
Alignment explanation
Indices: 1484383--1484427 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1484373 CGCCCTATAA
1484383 AACACGAGGTCTATT
1 AACACGAGGTCTATT
*
1484398 AA-ACG-CGTCCTA-T
1 AACACGAGGT-CTATT
1484411 AACACGAGGTCTATT
1 AACACGAGGTCTATT
1484426 AA
1 AA
1484428 ACGCGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
13 5 0.21
14 12 0.50
15 7 0.29
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (15 bp):
AACACGAGGTCTATT
Found at i:1487185 original size:2 final size:2
Alignment explanation
Indices: 1487175--1487218 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1487165 ATTTAAAAAA
1487175 AT AT A- 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
1487216 AT A
1 AT A
1487219 CTTTCTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1487623 original size:31 final size:31
Alignment explanation
Indices: 1487585--1487650 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1487575 CAGTTAAGTC
* *
1487585 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATAGCAAAAGGACTAAATGTTGA
*
1487616 GGGACCATATAGCAAAAGGACTAAATGTTGG
1 GGGACCATATAGCAAAAGGACTAAATGTTGA
1487647 GGGA
1 GGGA
1487651 TTGTATTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (31 bp):
GGGACCATATAGCAAAAGGACTAAATGTTGA
Found at i:1496500 original size:2 final size:2
Alignment explanation
Indices: 1496493--1496521 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1496483 AGTTATTAAT
1496493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1496522 TAAATGTGTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1497998 original size:2 final size:2
Alignment explanation
Indices: 1497991--1498017 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1497981 TCAATCTACA
1497991 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
1498018 ATTTACGACA
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:1502260 original size:24 final size:24
Alignment explanation
Indices: 1502228--1502278 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1502218 AAAATTTTAT
* * *
1502228 TTACATCTTTCTAAATTTCTATGC
1 TTACATCTTTATAAACTTCTAAGC
*
1502252 TTACGTCTTTATAAACTTCTAAGC
1 TTACATCTTTATAAACTTCTAAGC
1502276 TTA
1 TTA
1502279 GAATAGTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (24 bp):
TTACATCTTTATAAACTTCTAAGC
Found at i:1508398 original size:45 final size:45
Alignment explanation
Indices: 1508343--1508430 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
1508333 CATCTTGAGC
1508343 TGGCAAGTTCATTCGGATATAATTTTTAAATGGTCTTTGAGCATG
1 TGGCAAGTTCATTCGGATATAATTTTTAAATGGTCTTTGAGCATG
1508388 TGGCAAGTTCATTCGGATATAATTTTTAAATGGTCTTTGAGCA
1 TGGCAAGTTCATTCGGATATAATTTTTAAATGGTCTTTGAGCA
1508431 GTGAGCCTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (45 bp):
TGGCAAGTTCATTCGGATATAATTTTTAAATGGTCTTTGAGCATG
Done.