Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 135 of 325
Found at i:40977137 original size:19 final size:20
Alignment explanation
Indices: 40977113--40977150 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40977103 GGTACCACCA
40977113 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
40977132 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
40977151 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:40977515 original size:46 final size:46
Alignment explanation
Indices: 40977369--40977539 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
40977359 ATGTAACCCC
* * *
40977369 TAAGTGAACTCGGACTCAACTCAACGAGCT-GGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
40977414 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCA
* *
40977460 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
40977506 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40977540 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 31 0.29
46 65 0.61
47 2 0.02
48 4 0.04
49 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:40977530 original size:92 final size:91
Alignment explanation
Indices: 40977374--40977542 Score: 302
Period size: 92 Copynumber: 1.8 Consensus size: 91
40977364 ACCCCTAAGT
* *
40977374 GAACTCGGACTCAACTCAACGAGCTGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
40977439 GAGTTCGGATGCCTAGTTACATTCAC
66 GAGTTCGGATGCCTAGTTACATTCAC
*
40977465 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCT-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40977530 CGAGTTCGGATGC
65 CGAGTTCGGATGC
40977543 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 24 0.32
92 50 0.68
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTCAC
Found at i:40977558 original size:46 final size:46
Alignment explanation
Indices: 40977371--40977558 Score: 142
Period size: 46 Copynumber: 4.1 Consensus size: 46
40977361 GTAACCCCTA
* ** * *
40977371 AGTGAACTCGGACTCAACTCAACGAGCT-GGGCGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCC-T
*
40977415 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTC-
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCCT
* * * * *
40977463 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCCT
40977508 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
40977554 AGTGA
1 AGTGA
40977559 CATGTCACTT
Statistics
Matches: 115, Mismatches: 13, Indels: 29
0.73 0.08 0.18
Matches are distributed among these distances:
44 9 0.08
45 29 0.25
46 67 0.58
47 1 0.01
48 4 0.03
49 1 0.01
50 4 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:40977995 original size:30 final size:30
Alignment explanation
Indices: 40977961--40978020 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
40977951 ATTTAATACG
40977961 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
40977991 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
40978021 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:40985902 original size:29 final size:29
Alignment explanation
Indices: 40985863--40985941 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
40985853 CTTAATAATC
*
40985863 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
40985893 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
40985922 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
40985942 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:40987235 original size:10 final size:10
Alignment explanation
Indices: 40987220--40987249 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
40987210 AATTCCTTTC
40987220 TTTAATTTAT
1 TTTAATTTAT
40987230 TTTAATTTAT
1 TTTAATTTAT
40987240 TTTAATTTAT
1 TTTAATTTAT
40987250 AATAAACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTAATTTAT
Found at i:40987806 original size:19 final size:20
Alignment explanation
Indices: 40987782--40987819 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40987772 GGTACCACCA
40987782 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
40987801 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
40987820 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:40988156 original size:93 final size:93
Alignment explanation
Indices: 40988048--40988218 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
40988038 GCCCCTAAGT
* * * * *
40988048 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGAGTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
40988113 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
40988141 GAACTCAGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
40988206 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40988219 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40988215 original size:46 final size:46
Alignment explanation
Indices: 40988043--40988215 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
40988033 AACCCGCCCC
* * * * *
40988043 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCACATCCA
* *
40988089 TAAGTGAACTCAGAGTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA---C-A-TTCACATCCA
* *
40988137 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCACATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCACATCCA
*
40988182 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
40988216 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 1 0.01
45 2 0.02
46 58 0.56
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCACATCCA
Found at i:40988672 original size:30 final size:30
Alignment explanation
Indices: 40988638--40988697 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
40988628 ATTTAATACG
40988638 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
40988668 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
40988698 GTCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:40992879 original size:30 final size:30
Alignment explanation
Indices: 40992843--40993002 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
40992833 GACAAGATTG
* * * * *
40992843 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
* *
40992873 GCACTAAGTGTGCGAGTTTG---ATTATACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
40992901 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40992930 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40992960 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40992989 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40993003 GATTCACTAT
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 48 0.40
30 45 0.38
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:40992971 original size:59 final size:57
Alignment explanation
Indices: 40992843--40993002 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
40992833 GACAAGATTG
* * * * * *
40992843 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATACA
*
40992901 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATACA
40992960 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
40993003 GATTCACTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 20 0.22
59 50 0.54
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATACA
Found at i:40999335 original size:29 final size:29
Alignment explanation
Indices: 40999302--40999461 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
40999292 GTGACGAGAT
40999302 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
40999331 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
40999360 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
40999389 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
40999418 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
40999447 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
40999462 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:41007265 original size:40 final size:40
Alignment explanation
Indices: 41007210--41007360 Score: 218
Period size: 40 Copynumber: 3.8 Consensus size: 40
41007200 TGAATGATAC
* ** *
41007210 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
41007250 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
41007290 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
* *
41007330 CCGGGCTAAGA-CC-AAGGCATTTGTGCAAGTT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT
41007361 ACCAAACCGG
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
38 16 0.15
39 2 0.02
40 84 0.81
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
Found at i:41015363 original size:40 final size:39
Alignment explanation
Indices: 41015308--41015495 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 39
41015298 TGAATGATAC
* * *
41015308 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG-TTATAT
*
41015348 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
*
41015388 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* * *
41015428 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGT-TACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGT--TATAT
* * *
41015468 CTGGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGCTAAGACCCGAAGGCATTTGTGC
41015496 TTGCGGTTAT
Statistics
Matches: 134, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 130 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
Found at i:41015505 original size:80 final size:80
Alignment explanation
Indices: 41015308--41015515 Score: 249
Period size: 80 Copynumber: 2.6 Consensus size: 80
41015298 TGAATGATAC
* * * *
41015308 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
* *** *
41015373 TGCGAGTTGTTATAT
66 TGCAAGTTACCAAAT
* * *
41015388 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTC
41015452 GTGCAAGTTACCAAAT
65 GTGCAAGTTACCAAAT
* * * *
41015468 CTGGGTTAAGACCCGAAGGCAATTGTGCTTGCGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAA
41015516 ATTCCGAAGA
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 8 0.07
80 97 0.90
81 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
TGCAAGTTACCAAAT
Found at i:41017384 original size:13 final size:13
Alignment explanation
Indices: 41017366--41017407 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
41017356 CATGGCTGTA
41017366 TGGTCAGGCCGTG
1 TGGTCAGGCCGTG
41017379 TGGTCAGGCCGTG
1 TGGTCAGGCCGTG
41017392 TGGTCAGGCCGTG
1 TGGTCAGGCCGTG
41017405 TGG
1 TGG
41017408 GCATTCGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.07, C:0.21, G:0.48, T:0.24
Consensus pattern (13 bp):
TGGTCAGGCCGTG
Found at i:41018346 original size:19 final size:19
Alignment explanation
Indices: 41018310--41018346 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41018300 TAATTAGGCT
* *
41018310 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
41018329 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
41018347 GAAAAATGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:41018820 original size:31 final size:32
Alignment explanation
Indices: 41018780--41018843 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
41018770 ATTTAGTAAA
*
41018780 AGATATTTAT-TAATTAAATA-ATTATATTATG
1 AGATATTTATGTAA-TAAATATATTAAATTATG
*
41018811 AGATTTTTATGTAATAAATATATTAAATTATG
1 AGATATTTATGTAATAAATATATTAAATTATG
41018843 A
1 A
41018844 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
AGATATTTATGTAATAAATATATTAAATTATG
Found at i:41018902 original size:154 final size:153
Alignment explanation
Indices: 41018622--41018902 Score: 340
Period size: 154 Copynumber: 1.8 Consensus size: 153
41018612 AATTTTAGAA
* *
41018622 TAAAAGATATTTATTAATTAAATAATTAAATAATGAGATTTTTGTTTAATAAATAAATTAAATAA
1 TAAAAGATATTTATTAATTAAATAATTAAATAATGAGATTTTTATGTAATAAATAAATTAAATAA
* * * * * *
41018687 TGAAAGTTGTAATAAATTTATTGGTACGAATGTGAAAATATAAGTGTGTACAATGTGAAAATTTA
66 TGAAAGATGTAATAAATTTAGTGGTAC-AATGTGAAAATAAAAATGTATACAATATGAAAATTTA
41018752 TTAAATAAGATATTTATTATTTAG
130 TTAAATAAGATATTTATTATTTAG
* * * *
41018776 TAAAAGATATTTATTAATTAAATAATTATATTATGAGATTTTTATGTAATAAATATATTAAATTA
1 TAAAAGATATTTATTAATTAAATAATTAAATAATGAGATTTTTATGTAATAAATAAATTAAATAA
41018841 TGACAA-ATGTATGATAAAATTT-GT-G-AC-ATGTGTAATAATAAAAATGTATACAAATAT-AA
66 TGA-AAGATGTA--AT-AAATTTAGTGGTACAATGTG-AA-AATAAAAATGTATAC-AATATGAA
41018900 AAT
124 AAT
41018903 AAATATTGAT
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
152 5 0.05
153 2 0.02
154 85 0.79
155 7 0.06
156 3 0.03
157 6 0.06
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (153 bp):
TAAAAGATATTTATTAATTAAATAATTAAATAATGAGATTTTTATGTAATAAATAAATTAAATAA
TGAAAGATGTAATAAATTTAGTGGTACAATGTGAAAATAAAAATGTATACAATATGAAAATTTAT
TAAATAAGATATTTATTATTTAG
Found at i:41018951 original size:2 final size:2
Alignment explanation
Indices: 41018939--41018973 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
41018929 ATTAACTTAT
41018939 TA TA T- 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
41018974 AAACAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41019772 original size:15 final size:15
Alignment explanation
Indices: 41019748--41019804 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
41019738 GATGAATTTC
*
41019748 TTGAATTTATATTGA
1 TTGAAATTATATTGA
*
41019763 TTGAAATTATTTTGA
1 TTGAAATTATATTGA
41019778 TTGAAATTATATTGA
1 TTGAAATTATATTGA
41019793 TTG-AATTATATT
1 TTGAAATTATATT
41019805 ATATATATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 9 0.23
15 30 0.77
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TTGAAATTATATTGA
Found at i:41019953 original size:10 final size:10
Alignment explanation
Indices: 41019938--41019965 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41019928 TGAAAAGTGA
41019938 ATTGAATTGT
1 ATTGAATTGT
41019948 ATTGAATTGT
1 ATTGAATTGT
41019958 ATTGAATT
1 ATTGAATT
41019966 ATGAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (10 bp):
ATTGAATTGT
Found at i:41020232 original size:41 final size:37
Alignment explanation
Indices: 41020186--41020295 Score: 94
Period size: 37 Copynumber: 2.8 Consensus size: 37
41020176 TCGACCTCGA
41020186 GTCGATGAGACACTGGGTGTCATTATATTTCTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA--A-ATTTCTTCGGATAG
* ** ** * * *
41020226 ATTCGATGAGGTACTGGGTACCAACTTTGTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCAAATTTCTTCGGATAG
*
41020264 GTCGATGAGACACTGGGTGTCAACTTTGCTTC
1 GTCGATGAGACACTGGGTGTCAAATTT-CTTC
41020296 AAACTATCCG
Statistics
Matches: 54, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
37 22 0.41
38 14 0.26
39 1 0.02
41 17 0.31
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAAATTTCTTCGGATAG
Found at i:41020468 original size:19 final size:20
Alignment explanation
Indices: 41020444--41020485 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
41020434 ATGAAACGAG
41020444 AAATTGA-AT-TGAGAATTGA
1 AAATTGAGATATGAG-ATTGA
41020463 AAATTGAGATATGAGATTGA
1 AAATTGAGATATGAGATTGA
41020483 AAA
1 AAA
41020486 CATGAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (20 bp):
AAATTGAGATATGAGATTGA
Found at i:41021817 original size:25 final size:25
Alignment explanation
Indices: 41021741--41021811 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
41021731 ACGAGCTATA
* * * *
41021741 AACGGAAAGCTCCTCCAAGCTTAAT
1 AACGGGAAGCTCATGCAAGCTAAAT
41021766 AACGGGAAGCTCATGCAAGCTAAAT
1 AACGGGAAGCTCATGCAAGCTAAAT
* *
41021791 AATGGGAAGCTCATGCTAGCT
1 AACGGGAAGCTCATGCAAGCT
41021812 GTATAACGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (25 bp):
AACGGGAAGCTCATGCAAGCTAAAT
Found at i:41024253 original size:18 final size:18
Alignment explanation
Indices: 41024230--41024266 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
41024220 TGATGTTAAA
41024230 AAGTATTAAAGACGATTT
1 AAGTATTAAAGACGATTT
41024248 AAGTATTAAAGACGATTT
1 AAGTATTAAAGACGATTT
41024266 A
1 A
41024267 GATTTTGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (18 bp):
AAGTATTAAAGACGATTT
Found at i:41027385 original size:39 final size:40
Alignment explanation
Indices: 41027327--41027421 Score: 158
Period size: 39 Copynumber: 2.4 Consensus size: 40
41027317 TCCTTGTTCA
41027327 GACATGTTTTTGATGATTGAACCATTATTATGGTCG-TTT
1 GACATGTTTTTGATGATTGAACCATTATTATGGTCGTTTT
*
41027366 GACATGTTTTTGATTATTGAACCATTATTATGGTCGTTTT
1 GACATGTTTTTGATGATTGAACCATTATTATGGTCGTTTT
41027406 GACAAT-TTTTTGATGA
1 GAC-ATGTTTTTGATGA
41027422 GGTAAAAGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 35 0.67
40 15 0.29
41 2 0.04
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.47
Consensus pattern (40 bp):
GACATGTTTTTGATGATTGAACCATTATTATGGTCGTTTT
Found at i:41027606 original size:20 final size:20
Alignment explanation
Indices: 41027578--41027627 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
41027568 GTGTAAATTG
41027578 GTATCGATACCATATCACGA
1 GTATCGATACCATATCACGA
*
41027598 GTATTGATACCATATCACGA
1 GTATCGATACCATATCACGA
41027618 GTATCGATAC
1 GTATCGATAC
41027628 TCAGGATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (20 bp):
GTATCGATACCATATCACGA
Found at i:41030520 original size:51 final size:51
Alignment explanation
Indices: 41030440--41030539 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
41030430 GTGCCTAAAC
* *
41030440 ATATCATGCATGCCACTTATCCATCTCAACCAGTTGATACCGAAATTACTA
1 ATATCATGCATGCAACTTATCCATCTCAACCAGTTGATACCCAAATTACTA
* *
41030491 ATATCATGCATGTAACTTATCCATTTCAACCAGTTGATACCCAAATTAC
1 ATATCATGCATGCAACTTATCCATCTCAACCAGTTGATACCCAAATTAC
41030540 CAATTCACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (51 bp):
ATATCATGCATGCAACTTATCCATCTCAACCAGTTGATACCCAAATTACTA
Found at i:41035538 original size:24 final size:23
Alignment explanation
Indices: 41035490--41035538 Score: 55
Period size: 24 Copynumber: 2.0 Consensus size: 23
41035480 TAAATTCATA
*
41035490 TTTATTATAATATTATTATAATTT
1 TTTATAATAATATTATTAT-ATTT
41035514 TTTATAATAAGTATGTATTAT-TTT
1 TTTATAATAA-TAT-TATTATATTT
41035538 T
1 T
41035539 ATTTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 13 0.59
25 3 0.14
26 6 0.27
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTATAATAATATTATTATATTT
Found at i:41037803 original size:6 final size:6
Alignment explanation
Indices: 41037794--41037832 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
41037784 TGTATTCTGC
* * *
41037794 TTCTTT TTCTTC TTCTTT TTCTTC TTCTTT TTTTTT TTC
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTC
41037833 ACATTGAGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:41037808 original size:12 final size:12
Alignment explanation
Indices: 41037788--41037825 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
41037778 ATTTGATGTA
*
41037788 TTCTGCTTCTTT
1 TTCTTCTTCTTT
41037800 TTCTTCTTCTTT
1 TTCTTCTTCTTT
41037812 TTCTTCTTCTTT
1 TTCTTCTTCTTT
41037824 TT
1 TT
41037826 TTTTTTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:41037818 original size:15 final size:14
Alignment explanation
Indices: 41037797--41037829 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41037787 ATTCTGCTTC
41037797 TTTTTCTTCTTCTT
1 TTTTTCTTCTTCTT
41037811 TTTCTTCTTCTT-TT
1 TTT-TTCTTCTTCTT
41037825 TTTTT
1 TTTTT
41037830 TTCACATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 8 0.44
15 8 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTCTTCTT
Found at i:41046337 original size:19 final size:19
Alignment explanation
Indices: 41046313--41046350 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41046303 TTGTGGGAGT
41046313 AAGGATTTTGAATGACAAA
1 AAGGATTTTGAATGACAAA
41046332 AAGGATTTTGAATGACAAA
1 AAGGATTTTGAATGACAAA
41046351 CTCTTTTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.26
Consensus pattern (19 bp):
AAGGATTTTGAATGACAAA
Found at i:41048413 original size:16 final size:17
Alignment explanation
Indices: 41048392--41048425 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41048382 ATCTGTTTGA
41048392 AATACAAG-AAAATGAT
1 AATACAAGAAAAATGAT
*
41048408 AATACATGAAAAATGAT
1 AATACAAGAAAAATGAT
41048425 A
1 A
41048426 TATGAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (17 bp):
AATACAAGAAAAATGAT
Found at i:41064419 original size:40 final size:40
Alignment explanation
Indices: 41064364--41064533 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
41064354 AACATTGGAA
41064364 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41064404 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
41064444 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
41064483 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
41064524 CTATATCCGG
1 ATATATCCGG
41064534 TTAAATCCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 109 0.98
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:41073975 original size:27 final size:27
Alignment explanation
Indices: 41073940--41074225 Score: 190
Period size: 27 Copynumber: 10.6 Consensus size: 27
41073930 TACACTATAA
41073940 GGGTATTTCGATAATTTTACAAATTAC
1 GGGTATTTCGATAATTTTACAAATTAC
* * * * *
41073967 GAGTGTTTCGGTAATTTTCCAAATCGA-
1 GGGTATTTCGATAATTTTACAAAT-TAC
* *
41073994 GGGTATTTTGGTAATTTTACAAATTGA-
1 GGGTATTTCGATAATTTTACAAATT-AC
***
41074021 GGGTATTTC-AGTAATTTTACAAATCGG
1 GGGTATTTCGA-TAATTTTACAAATTAC
**
41074048 GGGTACATCGATAATTTTACAAATTGA-
1 GGGTATTTCGATAATTTTACAAATT-AC
* * *
41074075 GGGTATTTTGGTAATTTTAAAAATTGA-
1 GGGTATTTCGATAATTTTACAAATT-AC
* * ***
41074102 TGGTATTTCAATAATTTTACAAATCGG
1 GGGTATTTCGATAATTTTACAAATTAC
* **
41074129 GGGTATTTCGATAATTTTACAAACTGG
1 GGGTATTTCGATAATTTTACAAATTAC
* * **
41074156 GGGT-TTTCGGTAATTTTACAAACTGG
1 GGGTATTTCGATAATTTTACAAATTAC
* * *
41074182 GGGTATTT-TAGTAATTTTACAAACTAT
1 GGGTATTTCGA-TAATTTTACAAATTAC
*
41074209 GGGTATTTCGGTAATTT
1 GGGTATTTCGATAATTT
41074226 CTCTTTGTTA
Statistics
Matches: 208, Mismatches: 41, Indels: 20
0.77 0.15 0.07
Matches are distributed among these distances:
26 25 0.12
27 181 0.87
28 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAATTAC
Found at i:41073984 original size:54 final size:54
Alignment explanation
Indices: 41073939--41074225 Score: 294
Period size: 54 Copynumber: 5.3 Consensus size: 54
41073929 TTACACTATA
* * *
41073939 AGGGTATTTCGATAATTTTACAAATT-ACGAGTGTTTCGGTAATTTTCCAAATCG
1 AGGGTATTTCGATAATTTTACAAATTGA-GGGTATTTCGGTAATTTTACAAATCG
* * *
41073993 AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCG
* ** * * *
41074047 GGGGTACATCGATAATTTTACAAATTGAGGGTATTTTGGTAATTTTAAAAATTG
1 AGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCG
* * * * *
41074101 ATGGTATTTCAATAATTTTACAAATCGGGGGTATTTCGATAATTTTACAAA-CTG
1 AGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATC-G
* * * * ** *
41074155 GGGGT-TTTCGGTAATTTTACAAACTGGGGGTATTTTAGTAATTTTACAAA-CT
1 AGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCG
*
41074207 ATGGGTATTTCGGTAATTT
1 A-GGGTATTTCGATAATTT
41074226 CTCTTTGTTA
Statistics
Matches: 192, Mismatches: 37, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
53 43 0.22
54 148 0.77
55 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (54 bp):
AGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCG
Found at i:41074036 original size:81 final size:81
Alignment explanation
Indices: 41073939--41074225 Score: 319
Period size: 81 Copynumber: 3.6 Consensus size: 81
41073929 TTACACTATA
* * * *
41073939 AGGGTATTTC-GATAATTTTACAAATTACGAGTGTTTCGGTAATTTTCCAAATCGAGGGTATTTT
1 AGGGTATTTCAG-TAATTTTACAAATTACGGGTATTTCGATAATTTTACAAATCGAGGGTATTTT
41074003 GGTAATTTTACAAATTG
65 GGTAATTTTACAAATTG
*** ** *
41074020 AGGGTATTTCAGTAATTTTACAAATCGGGGGTACATCGATAATTTTACAAATTGAGGGTATTTTG
1 AGGGTATTTCAGTAATTTTACAAATTACGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTG
*
41074085 GTAATTTTAAAAATTG
66 GTAATTTTACAAATTG
* * *** * *
41074101 ATGGTATTTCAATAATTTTACAAATCGGGGGTATTTCGATAATTTTACAAA-CTGGGGGT-TTTC
1 AGGGTATTTCAGTAATTTTACAAATTACGGGTATTTCGATAATTTTACAAATC-GAGGGTATTTT
*
41074164 GGTAATTTTACAAACTG
65 GGTAATTTTACAAATTG
* * * * *
41074181 GGGGTATTTTAGTAATTTTACAAACTATGGGTATTTCGGTAATTT
1 AGGGTATTTCAGTAATTTTACAAATTACGGGTATTTCGATAATTT
41074226 CTCTTTGTTA
Statistics
Matches: 175, Mismatches: 29, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
80 54 0.31
81 120 0.69
82 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (81 bp):
AGGGTATTTCAGTAATTTTACAAATTACGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTG
GTAATTTTACAAATTG
Found at i:41076629 original size:47 final size:47
Alignment explanation
Indices: 41076506--41076635 Score: 151
Period size: 46 Copynumber: 2.8 Consensus size: 47
41076496 TGTAACCCGC
* * *
41076506 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-GCGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGAGCCTTTACAT
*
41076552 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA-GCCT--TTACAT
* *
41076602 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
41076636 ACTCAACCAT
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
46 36 0.48
47 28 0.37
48 5 0.07
49 1 0.01
50 5 0.07
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (47 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGAGCCTTTACAT
Found at i:41077096 original size:30 final size:30
Alignment explanation
Indices: 41077060--41077116 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41077050 TAATATGAAA
41077060 TTTTGCAAAATTACA-TTTTTGCCCCTAAAC
1 TTTTGCAAAATTACACTTTTT-CCCCTAAAC
*
41077090 TTTTGCATAATTACACTTTTTCCCCTA
1 TTTTGCAAAATTACACTTTTTCCCCTA
41077117 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.26, C:0.25, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTTGCAAAATTACACTTTTTCCCCTAAAC
Found at i:41083684 original size:40 final size:40
Alignment explanation
Indices: 41083594--41083814 Score: 245
Period size: 40 Copynumber: 5.5 Consensus size: 40
41083584 CTCAAGTAAT
* * * *
41083594 CTTCGGGATTTAG-CCGGATATA-ACTACTTGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
41083632 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
41083672 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
41083712 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
41083752 CTTC-GGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
41083793 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
41083815 CATTCGAATA
Statistics
Matches: 152, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
38 11 0.07
39 18 0.12
40 93 0.61
41 27 0.18
42 3 0.02
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:41094571 original size:40 final size:40
Alignment explanation
Indices: 41094516--41094725 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
41094506 AACATTGGAA
41094516 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41094556 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41094596 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
41094636 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
41094675 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
41094716 CTATATCCGG
1 ATATATCCGG
41094726 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:41102707 original size:40 final size:40
Alignment explanation
Indices: 41102652--41102861 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
41102642 AACATTGGAA
41102652 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41102692 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41102732 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
41102772 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
41102811 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
41102852 CTATATCCGG
1 ATATATCCGG
41102862 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:41116823 original size:37 final size:37
Alignment explanation
Indices: 41116770--41116858 Score: 137
Period size: 37 Copynumber: 2.4 Consensus size: 37
41116760 TATAAAAGAA
41116770 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
41116807 GTCTTACCCGGTCATAATCTCCACACGTAGTCATC--
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
41116842 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
41116859 TTCCAATCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
35 10 0.21
36 4 0.08
37 34 0.71
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:41117005 original size:49 final size:49
Alignment explanation
Indices: 41116950--41117216 Score: 412
Period size: 49 Copynumber: 5.4 Consensus size: 49
41116940 TTTTACATTA
41116950 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
41116999 GCCATTAGGCCTTATCACA-A-ACATACACTTTCACATTCACCACACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATT-----CACCACATCG
*
41117051 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
41117100 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
41117149 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
41117198 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
41117217 CATATATGTA
Statistics
Matches: 205, Mismatches: 6, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
47 17 0.08
48 1 0.00
49 141 0.69
52 28 0.14
53 1 0.00
54 17 0.08
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.28
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:41119981 original size:40 final size:41
Alignment explanation
Indices: 41119937--41120035 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
41119927 TCGATTGTCC
* * **
41119937 TCGGGACATAGCCCGG-TTATAGTTA-TTCGCACAATTGCCT
1 TCGGGACATAGCCCGGATT-TAGTAACTTAGCACAAAAGCCT
41119977 TCGGGA-ATTAGCCCGGATTTAGTAACTTAGCACAAAAGCCT
1 TCGGGACA-TAGCCCGGATTTAGTAACTTAGCACAAAAGCCT
*
41120018 TCGGGACTTAGCCCGGAT
1 TCGGGACATAGCCCGGAT
41120036 ACCATTCGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 1 0.02
40 19 0.38
41 30 0.60
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (41 bp):
TCGGGACATAGCCCGGATTTAGTAACTTAGCACAAAAGCCT
Found at i:41120555 original size:29 final size:29
Alignment explanation
Indices: 41120519--41120642 Score: 223
Period size: 29 Copynumber: 4.3 Consensus size: 29
41120509 TGTTGAAAAA
* *
41120519 CTCGCACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
41120548 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
41120577 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
41120606 CTCGCACACATAGTGCCTCGATTACT-AT
1 CTCGCACACATAGTGCCTCGATTACTGAT
41120634 CTCGCACAC
1 CTCGCACAC
41120643 GTAATGCCCA
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
28 11 0.12
29 82 0.88
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCGATTACTGAT
Found at i:41122735 original size:37 final size:37
Alignment explanation
Indices: 41122682--41122772 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
41122672 TATAAAAGAA
41122682 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
41122719 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
41122756 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
41122773 TTCCAAGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
37 46 0.92
38 4 0.08
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:41122922 original size:49 final size:49
Alignment explanation
Indices: 41122867--41123129 Score: 465
Period size: 49 Copynumber: 5.4 Consensus size: 49
41122857 ATTTACATTA
41122867 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
41122916 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
41122965 GCCATTAGGCC-TATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
41123013 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
41123062 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
41123111 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
41123130 CATATATGTA
Statistics
Matches: 207, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
48 48 0.23
49 159 0.77
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:41122993 original size:97 final size:98
Alignment explanation
Indices: 41122867--41123129 Score: 465
Period size: 97 Copynumber: 2.7 Consensus size: 98
41122857 ATTTACATTA
41122867 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
41122932 ACATATACATACACTTTCACATTCACCACATCG
66 ACATATACATACACTTTCACATTCACCACATCG
*
41122965 GCCATTAGGCC-TATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATC
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
*
41123029 ACATATACATACACTTTCACATTCATCACATCG
66 ACATATACATACACTTTCACATTCACCACATCG
* * * *
41123062 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTGGCCATTCGGCCTTATC
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
41123127 ACA
66 ACA
41123130 CATATATGTA
Statistics
Matches: 157, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
97 95 0.61
98 62 0.39
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.29
Consensus pattern (98 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
ACATATACATACACTTTCACATTCACCACATCG
Found at i:41125894 original size:40 final size:41
Alignment explanation
Indices: 41125850--41125948 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
41125840 TCGATTGTCC
* * **
41125850 TCGGGACATAGCCCGG-TTATAGTTA-TTCGCACAATTGCCT
1 TCGGGACATAGCCCGGATT-TAGTAACTTAGCACAAAAGCCT
41125890 TCGGGA-ATTAGCCCGGATTTAGTAACTTAGCACAAAAGCCT
1 TCGGGACA-TAGCCCGGATTTAGTAACTTAGCACAAAAGCCT
*
41125931 TCGGGACTTAGCCCGGAT
1 TCGGGACATAGCCCGGAT
41125949 ACCATTCGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 1 0.02
40 19 0.38
41 30 0.60
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (41 bp):
TCGGGACATAGCCCGGATTTAGTAACTTAGCACAAAAGCCT
Found at i:41126467 original size:29 final size:29
Alignment explanation
Indices: 41126432--41126557 Score: 216
Period size: 29 Copynumber: 4.3 Consensus size: 29
41126422 TGTTGAAAAA
* * *
41126432 CTCGCACACACATTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
41126461 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
41126490 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
41126519 CTCGCACACATAGTGCCTCGATTACTGATT
1 CTCGCACACATAGTGCCTCGATTACTGA-T
41126549 CTCGCACAC
1 CTCGCACAC
41126558 GTAATGCCCA
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 83 0.89
30 10 0.11
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.27
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCGATTACTGAT
Found at i:41129226 original size:37 final size:37
Alignment explanation
Indices: 41129138--41129257 Score: 192
Period size: 36 Copynumber: 3.3 Consensus size: 37
41129128 TATAAAAGAA
*
41129138 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
41129175 G-CTTACCCGGTCATAATCTCC-CACCGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACA-CGTAGTCATCGG
41129211 GTCTTACCCGGTCATAATCTCCACACGTAGTCATC-G
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
41129247 GTCTCACCCGG
1 GTCTTACCCGG
41129258 AACATATTCC
Statistics
Matches: 78, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
35 2 0.03
36 43 0.55
37 31 0.40
38 2 0.03
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:41129414 original size:49 final size:49
Alignment explanation
Indices: 41129359--41129572 Score: 367
Period size: 49 Copynumber: 4.4 Consensus size: 49
41129349 CATTACATTA
41129359 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
41129408 GCCATTAGGCC-TATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
41129456 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
41129505 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
41129554 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
41129573 CATATATGTA
Statistics
Matches: 158, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
48 48 0.30
49 110 0.70
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:41129460 original size:97 final size:98
Alignment explanation
Indices: 41129359--41129572 Score: 367
Period size: 97 Copynumber: 2.2 Consensus size: 98
41129349 CATTACATTA
41129359 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCC-TATC
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
41129423 ACATATACATACACTTTCACATTCACCACATCG
66 ACATATACATACACTTTCACATTCACCACATCG
* *
41129456 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
* * *
41129521 ACATATACATACACTTTCACATTCATCGCATTG
66 ACATATACATACACTTTCACATTCACCACATCG
*
41129554 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
41129573 CATATATGTA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
97 58 0.53
98 51 0.47
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.29
Consensus pattern (98 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
ACATATACATACACTTTCACATTCACCACATCG
Found at i:41131473 original size:29 final size:29
Alignment explanation
Indices: 41131408--41131505 Score: 182
Period size: 28 Copynumber: 3.4 Consensus size: 29
41131398 GACGAGATTA
41131408 GCACTAAGTGTGCATGCTGGAAA-ATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
41131436 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
41131465 GCACTAAGTGTGC-TGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
41131493 GCACTAAGTGTGC
1 GCACTAAGTGTGC
41131506 GAGCTCGAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
28 51 0.74
29 18 0.26
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.27
Consensus pattern (29 bp):
GCACTAAGTGTGCATGCTGGAAATATATG
Found at i:41131522 original size:57 final size:59
Alignment explanation
Indices: 41131408--41131565 Score: 182
Period size: 57 Copynumber: 2.7 Consensus size: 59
41131398 GACGAGATTA
* *
41131408 GCACTAAGTGTGCATGCTGGAAA-ATATGGCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAGATATG
* *
41131465 GCACTAAGTGTGC-TGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAAGGGTATG
1 GCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAGATATG
* ** * **
41131522 GCACTATGTGTGCGGGCT-TAAATCGCATGGCACTAAGTGTGCGA
1 GCACTAAGTGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
41131566 AATCGAGTAT
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
56 9 0.10
57 57 0.65
58 22 0.25
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (59 bp):
GCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAGATATG
Found at i:41138882 original size:29 final size:29
Alignment explanation
Indices: 41138840--41138968 Score: 206
Period size: 29 Copynumber: 4.4 Consensus size: 29
41138830 GACGAGATTA
41138840 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
41138869 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
41138898 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
* ***
41138927 GCACTAAGTGTGCGA-GCTCGAAGGGTATG
1 GCACTAAGTGTGC-ATGCTGGAAATATATG
41138956 GCACTAAGTGTGC
1 GCACTAAGTGTGC
41138969 GAGCTCGAAG
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 94 0.99
30 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.26
Consensus pattern (29 bp):
GCACTAAGTGTGCATGCTGGAAATATATG
Found at i:41138969 original size:29 final size:29
Alignment explanation
Indices: 41138840--41139028 Score: 170
Period size: 29 Copynumber: 6.5 Consensus size: 29
41138830 GACGAGATTA
* **
41138840 GCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCGA-GCTCGAAAGGTATG
* **
41138869 GCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCGA-GCTCGAAAGGTATG
* **
41138898 GCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCGA-GCTCGAAAGGTATG
*
41138927 GCACTAAGTGTGCGAGCTCGAAGGGTATG
1 GCACTAAGTGTGCGAGCTCGAAAGGTATG
*
41138956 GCACTAAGTGTGCGAGCTCGAAGGGTATG
1 GCACTAAGTGTGCGAGCTCGAAAGGTATG
* * * * *
41138985 GCACTATGTGTGCGGGCT-TAAATCGCATG
1 GCACTAAGTGTGCGAGCTCGAAA-GGTATG
41139014 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
41139029 AATCGAGTAT
Statistics
Matches: 146, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
28 2 0.01
29 143 0.98
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTCGAAAGGTATG
Found at i:41138985 original size:58 final size:59
Alignment explanation
Indices: 41138840--41139028 Score: 190
Period size: 58 Copynumber: 3.3 Consensus size: 59
41138830 GACGAGATTA
* * * **
41138840 GCACTAAGTGTGC-ATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCGATGCTCGAAAGATATGGCACTAAGTGTGCGA-GCTCGAAACGTATG
* * **
41138898 GCACTAAGTGTGC-ATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAAGGGTATG
1 GCACTAAGTGTGCGATGCTCGAAAGATATGGCACTAAGTGTGCGAGCTCGAAACGTATG
* * * * * *
41138956 GCACTAAGTGTGCGA-GCTCGAAGGGTATGGCACTATGTGTGCGGGCT-TAAATCGCATG
1 GCACTAAGTGTGCGATGCTCGAAAGATATGGCACTAAGTGTGCGAGCTCGAAA-CGTATG
41139014 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
41139029 AATCGAGTAT
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
57 2 0.02
58 110 0.96
59 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (59 bp):
GCACTAAGTGTGCGATGCTCGAAAGATATGGCACTAAGTGTGCGAGCTCGAAACGTATG
Found at i:41138986 original size:87 final size:87
Alignment explanation
Indices: 41138865--41139028 Score: 206
Period size: 87 Copynumber: 1.9 Consensus size: 87
41138855 GCTGGAAATA
* * * *
41138865 TATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAAT-ATATGGC
1 TATGGCACTAAGTGTGCATGCTCGAAAGATATGGCACTAAGTGTGCAGGCT-GAAATCACATGGC
41138929 ACTAAGTGTGCGAGCTCGAAGGG
65 ACTAAGTGTGCGAGCTCGAAGGG
* * * * * *
41138952 TATGGCACTAAGTGTGCGA-GCTCGAAGGGTATGGCACTATGTGTGCGGGCTTAAATCGCATGGC
1 TATGGCACTAAGTGTGC-ATGCTCGAAAGATATGGCACTAAGTGTGCAGGCTGAAATCACATGGC
41139016 ACTAAGTGTGCGA
65 ACTAAGTGTGCGA
41139029 AATCGAGTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
86 4 0.06
87 60 0.92
88 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.25
Consensus pattern (87 bp):
TATGGCACTAAGTGTGCATGCTCGAAAGATATGGCACTAAGTGTGCAGGCTGAAATCACATGGCA
CTAAGTGTGCGAGCTCGAAGGG
Found at i:41139066 original size:2 final size:2
Alignment explanation
Indices: 41139061--41139095 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41139051 GTGCGTACTC
41139061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41139096 CCGATCGGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41144122 original size:29 final size:29
Alignment explanation
Indices: 41144021--41144114 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
41144011 GTGATGAGAT
41144021 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
41144050 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
41144079 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
41144108 CGGCACT
1 TGGCACT
41144115 GGGTGTGCGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:41144139 original size:58 final size:58
Alignment explanation
Indices: 41144017--41144151 Score: 175
Period size: 58 Copynumber: 2.3 Consensus size: 58
41144007 TACGGTGATG
* *
41144017 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
* **
41144074 ATATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGC-ATGCTCGAA
* * *
41144132 GGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
41144152 GGGCTTAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.04
58 63 0.94
59 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.26
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
Found at i:41144220 original size:2 final size:2
Alignment explanation
Indices: 41144215--41144251 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41144205 GTGCGTACTC
41144215 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
41144252 CTCCGATCGA
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:41146615 original size:25 final size:24
Alignment explanation
Indices: 41146566--41146759 Score: 216
Period size: 25 Copynumber: 8.0 Consensus size: 24
41146556 TGCTTTACCA
*
41146566 TATAACTGGAGGCCT-AG-CCTCTTT
1 TATAACTGG-GGCATAAGCCCT-TTT
* *
41146590 TAGTAACTGGGGCAAAAACCCTTTT
1 TA-TAACTGGGGCATAAGCCCTTTT
*
41146615 TATAACTGGGGCATAAGCCCTTCAT
1 TATAACTGGGGCATAAGCCCTT-TT
*
41146640 CATAACTGGGGCATAAGCCCTTTAT
1 TATAACTGGGGCATAAGCCCTTT-T
*
41146665 CATAACTGGGGCATAAGCCCTTTAT
1 TATAACTGGGGCATAAGCCCTTT-T
*
41146690 CATAACTGGGGCATAAGCCC-TTT
1 TATAACTGGGGCATAAGCCCTTTT
* *
41146713 AATAACTGGGGCATAAGGCC-TTT
1 TATAACTGGGGCATAAGCCCTTTT
*
41146736 AATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTT
41146760 GCACTTCCTC
Statistics
Matches: 153, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
23 41 0.27
24 28 0.18
25 81 0.53
26 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (24 bp):
TATAACTGGGGCATAAGCCCTTTT
Found at i:41146721 original size:23 final size:23
Alignment explanation
Indices: 41146588--41146758 Score: 225
Period size: 25 Copynumber: 7.1 Consensus size: 23
41146578 CCTAGCCTCT
* * *
41146588 TTTAGTAACTGGGGCAAAAACCC
1 TTTAATAACTGGGGCATAAGCCC
*
41146611 TTTTTATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
41146635 TTCATCATAACTGGGGCATAAGCCC
1 TT--TAATAACTGGGGCATAAGCCC
41146660 TTTATCATAACTGGGGCATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
41146685 TTTATCATAACTGGGGCATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
*
41146710 TTTAATAACTGGGGCATAAGGCC
1 TTTAATAACTGGGGCATAAGCCC
41146733 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
41146756 TTT
1 TTT
41146759 TGCACTTCCT
Statistics
Matches: 135, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
23 46 0.34
24 19 0.14
25 70 0.52
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:41146831 original size:9 final size:9
Alignment explanation
Indices: 41146817--41146873 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
41146807 ATCTCATGTG
41146817 CATATCATA
1 CATATCATA
*
41146826 CATATCATGTG
1 CATATCA--TA
41146837 CATATCATA
1 CATATCATA
* *
41146846 CATGTCATGTG
1 CATATCA--TA
41146857 CATATCATA
1 CATATCATA
41146866 CATATCAT
1 CATATCAT
41146874 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:41146833 original size:20 final size:20
Alignment explanation
Indices: 41146805--41146875 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
41146795 GCATTTATGA
*
41146805 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
41146825 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
41146845 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
41146865 ACATATCATGT
1 ACATATCATGT
41146876 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:41146840 original size:11 final size:11
Alignment explanation
Indices: 41146810--41146864 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
41146800 TATGAACATC
41146810 TCATGTGCATA
1 TCATGTGCATA
*
41146821 TCA--TACATA
1 TCATGTGCATA
41146830 TCATGTGCATA
1 TCATGTGCATA
* *
41146841 TCA--TACATG
1 TCATGTGCATA
41146850 TCATGTGCATA
1 TCATGTGCATA
41146861 TCAT
1 TCAT
41146865 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:41146940 original size:25 final size:25
Alignment explanation
Indices: 41146912--41146959 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41146902 ATATATAAAC
* * *
41146912 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
41146937 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
41146960 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:41148303 original size:20 final size:19
Alignment explanation
Indices: 41148261--41148310 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
41148251 AACAATTGGC
41148261 AAGAGGAGAAAGAAAAGAA
1 AAGAGGAGAAAGAAAAGAA
* * *
41148280 AAGAGGGGAATAGATAAGAG
1 AAGAGGAGAA-AGAAAAGAA
*
41148300 AAGAGAAGAAA
1 AAGAGGAGAAA
41148311 ATAATTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.04
Consensus pattern (19 bp):
AAGAGGAGAAAGAAAAGAA
Found at i:41152817 original size:14 final size:14
Alignment explanation
Indices: 41152793--41152831 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
41152783 AATTTTTATT
41152793 TTTATTTTTATTTTA
1 TTTA-TTTTATTTTA
*
41152808 TTTATTTTATCTTA
1 TTTATTTTATTTTA
41152822 -TTATTTTATT
1 TTTATTTTATT
41152832 ATTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 9 0.41
14 9 0.41
15 4 0.18
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:41152828 original size:22 final size:20
Alignment explanation
Indices: 41152787--41152835 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
41152777 CAACCCAATT
41152787 TTTATTTTTATTTTTATTTTA
1 TTTA-TTTTATTTTTATTTTA
41152808 TTTATTTTATCTTATTATTTTA
1 TTTATTTTAT-TT-TTATTTTA
41152830 -TTATTT
1 TTTATTT
41152836 ATTATTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTATTTTATTTTTATTTTA
Found at i:41152839 original size:15 final size:15
Alignment explanation
Indices: 41152792--41152843 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
41152782 CAATTTTTAT
41152792 TTTTATT-TTTATTTTA
1 TTTTATTATTTA--TTA
*
41152808 TTTATTTTATCTTATTA
1 TTT-TATTAT-TTATTA
41152825 TTTTATTATTTATTA
1 TTTTATTATTTATTA
41152840 TTTT
1 TTTT
41152844 CAGATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 10 0.32
16 8 0.26
17 9 0.29
18 1 0.03
19 3 0.10
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTATTTATTA
Found at i:41154405 original size:15 final size:15
Alignment explanation
Indices: 41154385--41154414 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41154375 CATTTTATTT
*
41154385 ATATTAGGATAATTA
1 ATATTAAGATAATTA
41154400 ATATTAAGATAATTA
1 ATATTAAGATAATTA
41154415 TTAGGATTAT
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:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:41154442 original size:27 final size:26
Alignment explanation
Indices: 41154381--41154443 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
41154371 ACTCCATTTT
41154381 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * * *
41154408 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
41154436 ATTTTATT
1 ATTTTATT
41154444 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:41166618 original size:46 final size:47
Alignment explanation
Indices: 41166400--41166765 Score: 199
Period size: 46 Copynumber: 7.7 Consensus size: 47
41166390 GGGCTATTGT
* * * *
41166400 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA-CATTATGA
1 GAGC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGA-GATGA
*
41166446 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-TATTGAGACGA
1 GAGC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-TGAGATGA
* * * *
41166494 GAGCTAATGTAAG-GCATGCCTGGGACAT-GCATCGGCT-TCGTA-AGGTA
1 GAGC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCTAT-G-AGATG-A
* ** *
41166541 -AGCCAGTATAAGA-CATGTCAAGGACAT-GCATCGGCTATGAGATGT
1 GAG-CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGAGATGA
* * *
41166586 GA-CAGTGTAAGACCATGTCTGGGACATGGCATCAGC-ACGGATATGCGA
1 GAGCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-TGAGAT--GA
* * *
41166634 GAGCTAGTGTAAGACCATGTTTGGGACATGGCGTCGGCCTCGATGACA-GTA
1 GAGC-AGTGTAAGACCATGTCTGGGACATGGCATCGG-CT--ATGAGATG-A
* * * * *
41166685 -ATCAGTGTAAGACTATATCTGGGACGTGGCATCGACT-TGAGACATGA
1 GAGCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGAG--ATGA
* * *
41166732 G-CCAATGTAAGACCATGTCTAGGACATGGCATCG
1 GAGCAGTGTAAGACCATGTCTGGGACATGGCATCG
41166766 TCATCATACC
Statistics
Matches: 249, Mismatches: 42, Indels: 57
0.72 0.12 0.16
Matches are distributed among these distances:
44 9 0.04
45 18 0.07
46 67 0.27
47 62 0.25
48 27 0.11
49 28 0.11
50 32 0.13
51 2 0.01
53 3 0.01
54 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (47 bp):
GAGCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGAGATGA
Found at i:41172973 original size:48 final size:47
Alignment explanation
Indices: 41172920--41173347 Score: 324
Period size: 48 Copynumber: 9.0 Consensus size: 47
41172910 GGGTGAATTA
* * * *
41172920 CCGATGCCATGTTCTAAACATGGTCTTACACTGGCTCACATGTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC-AGG
* * * * * * * *
41172968 CCGATGGCATGTCCCAAACATGGTCTTATACTAGCTCTCATCTTAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-ATCAGG
* * * * **
41173016 TCGATGCCATATCCCAGACATGGTCTTACATTGGCTCTCATAATGTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-ATCAGG
** * **
41173064 CCGATATCATG-CCCTAGACATGGTCTTACACTAG-TGCACATAATGTGG
1 CCGATGCCATGTCCC-AGACATGGTCTTACACTGGCT-CACAT-ATCAGG
* * *
41173112 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC-AGG
* * * * ** *
41173160 TCGATGCCATGTTCCAGACTTGGTCTTTCACCAGCTTCACA-A-CATCG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCACATATCA-GG
* * * * * *
41173207 CCGATGCCATGTTCCAAACATGGTCTTACAATGGCTCTCATAACATCG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCA-GG
* * * *
41173255 TCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCATGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCA-GG
* *
41173303 CAGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCA
41173348 CCCAAATGGC
Statistics
Matches: 311, Mismatches: 59, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
46 5 0.02
47 37 0.12
48 261 0.84
49 8 0.03
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (47 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAGG
Found at i:41173275 original size:23 final size:23
Alignment explanation
Indices: 41173200--41173275 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
41173190 CCAGCTTCAC
*
41173200 AACATCGCCGATGCCATGTTCCA
1 AACATCGTCGATGCCATGTTCCA
* * * * *
41173223 AACATGGTC-TTACAATGGCTCTCA
1 AACATCGTCGATGCCAT-GTTC-CA
41173247 TAACATCGTCGATGCCATGTTCCA
1 -AACATCGTCGATGCCATGTTCCA
41173271 AACAT
1 AACAT
41173276 GGTCTTACAC
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
22 4 0.11
23 15 0.39
24 4 0.11
25 11 0.29
26 4 0.11
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (23 bp):
AACATCGTCGATGCCATGTTCCA
Found at i:41181048 original size:48 final size:47
Alignment explanation
Indices: 41180720--41181049 Score: 275
Period size: 48 Copynumber: 6.9 Consensus size: 47
41180710 TGAACTGGCT
* * * *
41180720 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTTCAGGCCG
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCAT-ATCATGCCG
* * * * * * *
41180768 ATACCATG-ACCTAGACATGGTCTTACACTAGCTCTCATCTCAATGTCA
1 ATGCCATGTTCC-AAACATGGTCTTACACTGGCTCTCATATC-ATGCCG
* * * * * ** *
41180816 ATGCTACGTTCCAGACTTGGTCTTACACTAGAGCACATATCAATGCCG
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATC-ATGCCG
* * * * * * *
41180864 ATGTCATGTTCTAGACATGGTCTTACACTGGCTCTCACAACATCACCA
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCAT-GCCG
* * *
41180912 ATGCCATGTTCCAAACATGGACTTACACTGGCTCTCATAACATCACCG
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCAT-GCCG
* * *
41180960 ATGCCATGTTCCAAACATGGTCTTACACTGGATCTTATATCGTGGCCG
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCAT-GCCG
* * *
41181008 ATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCA
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCA
41181050 CCCAAATGGC
Statistics
Matches: 227, Mismatches: 51, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
47 6 0.03
48 219 0.96
49 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (47 bp):
ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCATGCCG
Found at i:41183833 original size:34 final size:31
Alignment explanation
Indices: 41183765--41183837 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
41183755 TATTTGATTT
* *
41183765 AAGAACAAGAATCAAAGAACAACATTTAAGG
1 AAGAAGAAGAATCAAAGAAAAACATTTAAGG
* *
41183796 AAGAAGAAGAATGAAAGAAAAACATTTAAGA
1 AAGAAGAAGAATCAAAGAAAAACATTTAAGG
41183827 AAGAAGAAGAA
1 AAGAAGAAGAA
41183838 CCTCTTGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.63, C:0.07, G:0.19, T:0.11
Consensus pattern (31 bp):
AAGAAGAAGAATCAAAGAAAAACATTTAAGG
Found at i:41186879 original size:206 final size:206
Alignment explanation
Indices: 41186614--41187019 Score: 650
Period size: 206 Copynumber: 2.0 Consensus size: 206
41186604 CCCTCCTGAT
* *
41186614 GCAATACATCTCACCTTACTTGAAACATAAATATAACATTTTTGTAAGTTCAAGAGAACTTAATA
1 GCAATACATCCCACCTTACTTGAAACATAAATATAACATTTTTGAAAGTTCAAGAGAACTTAATA
* * * *
41186679 AGCTTTAATCCAAAATATACCTTGGCGGATATTAATTATGACTAATGAACATTTGTGCACCAATT
66 AGCTTTAATCCAAAATATACCTTGACGAATATTAATTATGACTAATGAACATCTATGCACCAATT
* * * * * *
41186744 ATTCTTTTTAGACCACTTTCTTCTACCTCGGGTGGATACCACTATAGTTTTGGTATACAGTTACA
131 ATCCTTTTTAGACCACTTTCTTCTACCTCGGGCGGATACCACTACAATTTTGGTACACACTTACA
41186809 TGCCACCTAGC
196 TGCCACCTAGC
* * *
41186820 GCAATACATCCCACTTTACTTGAAACATAAATATAACATTTTTGAAAGTTCAGGAGAACTTAATG
1 GCAATACATCCCACCTTACTTGAAACATAAATATAACATTTTTGAAAGTTCAAGAGAACTTAATA
* * *
41186885 AGCTTTAATCCAAAATATACCTTGACGAATATTGATTATGATTAATGAACATCTATGCGCCAATT
66 AGCTTTAATCCAAAATATACCTTGACGAATATTAATTATGACTAATGAACATCTATGCACCAATT
41186950 ATCCTTTTTAGACCACTTTCTTCTACCTCGGGCGGATACCACTACAATTTTGGTACACACTTACA
131 ATCCTTTTTAGACCACTTTCTTCTACCTCGGGCGGATACCACTACAATTTTGGTACACACTTACA
41187015 TGCCA
196 TGCCA
41187020 ACTATCATAC
Statistics
Matches: 182, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
206 182 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (206 bp):
GCAATACATCCCACCTTACTTGAAACATAAATATAACATTTTTGAAAGTTCAAGAGAACTTAATA
AGCTTTAATCCAAAATATACCTTGACGAATATTAATTATGACTAATGAACATCTATGCACCAATT
ATCCTTTTTAGACCACTTTCTTCTACCTCGGGCGGATACCACTACAATTTTGGTACACACTTACA
TGCCACCTAGC
Found at i:41187797 original size:25 final size:25
Alignment explanation
Indices: 41187769--41187821 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
41187759 GGCCAAACAG
*
41187769 AATATGCCACAAAGGCATCATACAA
1 AATACGCCACAAAGGCATCATACAA
*
41187794 AATACGCCACTAAGGCATCATACAA
1 AATACGCCACAAAGGCATCATACAA
41187819 AAT
1 AAT
41187822 CTCATGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.25, G:0.11, T:0.17
Consensus pattern (25 bp):
AATACGCCACAAAGGCATCATACAA
Found at i:41190024 original size:40 final size:40
Alignment explanation
Indices: 41189918--41190124 Score: 242
Period size: 40 Copynumber: 5.2 Consensus size: 40
41189908 TGAATGATAC
* ** *
41189918 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
41189958 CCGGGCTAAGA-CCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
41189997 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
* * *** *
41190037 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
* ** *
41190077 CCGGGTTAAGACCCGAAGGCAATT-GTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTTATAT
41190117 CC-GGCTAA
1 CCGGGCTAA
41190125 ATTCGAAGAA
Statistics
Matches: 145, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 38 0.26
40 104 0.72
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
Found at i:41203286 original size:29 final size:29
Alignment explanation
Indices: 41203265--41203347 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
41203255 GTGCTGTATT
** *
41203265 TTTCCAGCTTGCACACTTAGTGCCAAATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
41203294 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
41203323 TTTCCAGCACGCACACTTAGTGCCA
1 TTTCCAGCACGCACACTTAGTGCCA
41203348 ATCTCGTCAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCATATA
Found at i:41207787 original size:29 final size:28
Alignment explanation
Indices: 41207699--41207801 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 28
41207689 TACTCAATCA
* *
41207699 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATA-CATTCAAGCT
* * * * *
41207728 CGTACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATACA-TTCAAGCT
*
41207757 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATACATT-CAAGCT
*
41207786 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
41207802 ATCTCGTCAC
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
28 2 0.03
29 56 0.97
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
CGCACACTTAGTGCCATACATTCAAGCT
Found at i:41219111 original size:24 final size:24
Alignment explanation
Indices: 41219084--41219290 Score: 315
Period size: 24 Copynumber: 8.6 Consensus size: 24
41219074 CTTATTATGT
* * *
41219084 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
* *
41219108 TCGCACACGTAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
41219132 TCGCACACTTAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
41219156 TCGCACACTTAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
41219180 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
41219204 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
41219228 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
41219252 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
41219276 TCGCACACATAGTGC
1 TCGCACACATAGTGC
41219291 ATTTGAGATA
Statistics
Matches: 176, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 176 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:41232106 original size:28 final size:28
Alignment explanation
Indices: 41232037--41232137 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
41232027 GACAAGATTG
* * * *
41232037 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
41232067 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41232095 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
41232124 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41232138 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:41241784 original size:25 final size:27
Alignment explanation
Indices: 41241700--41241798 Score: 94
Period size: 29 Copynumber: 3.6 Consensus size: 27
41241690 TACTCAATCA
* * *
41241700 CGCACACTTAATGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCATAT-A-TCAAGCT
* *
41241729 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-T-CAAGCT
41241758 CGCACACTTAGTGCCAT-TA-CAAGCT
1 CGCACACTTAGTGCCATATATCAAGCT
*
41241783 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
41241799 ATCTCGTCCC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
25 20 0.33
28 4 0.07
29 36 0.60
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATATATCAAGCT
Found at i:41245269 original size:22 final size:22
Alignment explanation
Indices: 41245235--41245296 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
41245225 AATACGTTTT
*
41245235 GCACACAGCCATAATCAGGTTG
1 GCACAAAGCCATAATCAGGTTG
* * *
41245257 GCATAGAGCCATATAT-AGTTTG
1 GCACAAAGCCATA-ATCAGGTTG
41245279 GCACAAAGCCATAATCAG
1 GCACAAAGCCATAATCAG
41245297 AATAATTGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (22 bp):
GCACAAAGCCATAATCAGGTTG
Found at i:41245535 original size:40 final size:41
Alignment explanation
Indices: 41245438--41245559 Score: 183
Period size: 41 Copynumber: 3.0 Consensus size: 41
41245428 TAAAAGCCAC
* *
41245438 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTTAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT
* *
41245479 CGGTGGATCCATGGTCGTCAAGCAGCCATACGATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT
* *
41245520 -GGTGGAGCCACGGTCGTCAAGCAACCATTCGATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT
41245560 TTCTTCCTCC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 36 0.49
41 37 0.51
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.21
Consensus pattern (41 bp):
CGGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT
Found at i:41245849 original size:27 final size:27
Alignment explanation
Indices: 41245817--41246036 Score: 131
Period size: 27 Copynumber: 8.0 Consensus size: 27
41245807 TTGGTAAATC
41245817 TACAAACTAAGGGTATTTCGATAATTT
1 TACAAACTAAGGGTATTTCGATAATTT
* * * *
41245844 TGCAAACCAATGGTATTTCTATAATTT
1 TACAAACTAAGGGTATTTCGATAATTT
** * * * *
41245871 TTGATAGTCACGGGTGTATTTCTATAATTT
1 TACAAACT-A-AGG-GTATTTCGATAATTT
*
41245901 TCCAAA-TCAAGGGTATTTCGATAATTT
1 TACAAACT-AAGGGTATTTCGATAATTT
* * *
41245928 TCCAAATTAAGGGTATTT-TAGTAATTT
1 TACAAACTAAGGGTATTTCGA-TAATTT
* * * *
41245955 TACAAATTGAGGGTATTTAGGTAATTT
1 TACAAACTAAGGGTATTTCGATAATTT
* * * *
41245982 CACAAA-TTAGAGGTATTTAGGTAATTT
1 TACAAACTAAG-GGTATTTCGATAATTT
* * * *
41246009 TACAAACCAGGGGTATTTTGGTAATTT
1 TACAAACTAAGGGTATTTCGATAATTT
41246036 T
1 T
41246037 TCTATTTGAG
Statistics
Matches: 157, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.03
27 126 0.80
28 5 0.03
29 4 0.03
30 18 0.11
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (27 bp):
TACAAACTAAGGGTATTTCGATAATTT
Found at i:41245961 original size:54 final size:53
Alignment explanation
Indices: 41245886--41246089 Score: 182
Period size: 54 Copynumber: 3.8 Consensus size: 53
41245876 AGTCACGGGT
* * * *
41245886 GTATTTCTA-TAATTTTCCAAATCAAGGGTATTTCGATAATTTTCCAAATTAAGG
1 GTATTT-TAGTAATTTTACAAACCAAGGGTATTTAGGTAATTTTCCAAATT-AGG
***
41245940 GTATTTTAGTAATTTTACAAATTGAGGGTATTTAGGTAA-TTTCACAAATTAGAG
1 GTATTTTAGTAATTTTACAAACCAAGGGTATTTAGGTAATTTTC-CAAATTAG-G
* * * * *
41245994 GTA-TTTAGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTTCTATTTGAGG
1 GTATTTTA-GTAATTTTACAAACCAAGGGTATTTAGGTAATTTTCCAAATT-AGG
* ** *
41246048 GTATTTTGGTAATTTTGTAAACCAAGGGTATTCAGG-AATTTT
1 GTATTTTAGTAATTTTACAAACCAAGGGTATTTAGGTAATTTT
41246090 GTAAACCATC
Statistics
Matches: 124, Mismatches: 19, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
53 18 0.15
54 98 0.79
55 8 0.06
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (53 bp):
GTATTTTAGTAATTTTACAAACCAAGGGTATTTAGGTAATTTTCCAAATTAGG
Found at i:41246075 original size:27 final size:27
Alignment explanation
Indices: 41245993--41246097 Score: 88
Period size: 27 Copynumber: 3.9 Consensus size: 27
41245983 ACAAATTAGA
** *
41245993 GGTATTTAGGTAATTTTACAAACCAGG
1 GGTATTTAGGTAATTTTGTAAACCAAG
* * ****
41246020 GGTATTTTGGTAATTTT-TCTATTTGAG
1 GGTATTTAGGTAATTTTGT-AAACCAAG
*
41246047 GGTATTTTGGTAATTTTGTAAACCAAG
1 GGTATTTAGGTAATTTTGTAAACCAAG
*
41246074 GGTATTCAGG-AATTTTGTAAACCA
1 GGTATTTAGGTAATTTTGTAAACCA
41246098 TCCCAGTCCA
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
26 14 0.23
27 46 0.75
28 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
GGTATTTAGGTAATTTTGTAAACCAAG
Found at i:41246078 original size:81 final size:80
Alignment explanation
Indices: 41245899--41246089 Score: 188
Period size: 81 Copynumber: 2.4 Consensus size: 80
41245889 TTTCTATAAT
* * * **
41245899 TTTC-CAAATCAAGGGTATTTCGATAATTTTCCAAATTAAGGGTATTTTAGTAATTTTACAAATT
1 TTTCACAAA-CAAGGGTATTTAGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAATT
41245963 GAGGGTATTTAGGTAA
65 GAGGGTATTTAGGTAA
** * * * * *
41245979 TTTCACAAATTAGAGGTATTTAGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTTCTATTT
1 TTTCACAAACAAG-GGTATTTAGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAATT
*
41246044 GAGGGTATTTTGGTAA
65 GAGGGTATTTAGGTAA
*** *
41246060 TTTTGTAAACCAAGGGTATTCAGG-AATTTT
1 TTTCACAAA-CAAGGGTATTTAGGTAATTTT
41246090 GTAAACCATC
Statistics
Matches: 89, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
80 12 0.13
81 75 0.84
82 2 0.02
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.41
Consensus pattern (80 bp):
TTTCACAAACAAGGGTATTTAGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAATTG
AGGGTATTTAGGTAA
Found at i:41246489 original size:22 final size:22
Alignment explanation
Indices: 41246458--41246519 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
41246448 AATACGTTTT
*
41246458 GCACACAGCCATAATCAGGTTG
1 GCACAAAGCCATAATCAGGTTG
* *
41246480 GCACAGAGCCAT-ATGTAGGTTG
1 GCACAAAGCCATAAT-CAGGTTG
* *
41246502 TCGCAAAGCCATAATCAG
1 GCACAAAGCCATAATCAG
41246520 AATAATTGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (22 bp):
GCACAAAGCCATAATCAGGTTG
Found at i:41246758 original size:40 final size:41
Alignment explanation
Indices: 41246661--41246782 Score: 183
Period size: 41 Copynumber: 3.0 Consensus size: 41
41246651 TAAAAGCCAC
* *
41246661 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTTAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT
* *
41246702 CGGTGGATCCATGGTCGTCAAGCAGCCATACGATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT
* *
41246743 -GGTGGAGCCACGGTCGTCAAGCAACCATTCGATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT
41246783 TTCTTCCTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 36 0.49
41 37 0.51
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.21
Consensus pattern (41 bp):
CGGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT
Found at i:41247071 original size:26 final size:27
Alignment explanation
Indices: 41247042--41247093 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
41247032 GGTAAATCTA
41247042 CAAACCAAAGGCA-TTCGGTAATTTTG
1 CAAACCAAAGGCATTTCGGTAATTTTG
* * *
41247068 CAAACCAATGGTATTTCTGTAATTTT
1 CAAACCAAAGGCATTTCGGTAATTTT
41247094 TGAAAGTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (27 bp):
CAAACCAAAGGCATTTCGGTAATTTTG
Found at i:41247093 original size:27 final size:26
Alignment explanation
Indices: 41247042--41247153 Score: 102
Period size: 27 Copynumber: 4.2 Consensus size: 26
41247032 GGTAAATCTA
* *
41247042 CAAACCAAAGGCA-TTCGGTAATTTTG
1 CAAACC-AAGGTATTTCTGTAATTTTG
41247068 CAAACCAATGGTATTTCTGTAATTTTTG
1 CAAACCAA-GGTATTTCTGTAA-TTTTG
*
41247096 -AAAGTCAAGGGTATTTCTGTAATTTTG
1 CAAA-CCAA-GGTATTTCTGTAATTTTG
* * *
41247123 TAAATCAAGAGTATTTCTGTAATTTTC
1 CAAACCAAG-GTATTTCTGTAATTTTG
41247150 CAAA
1 CAAA
41247154 ATAGAGGTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
25 2 0.03
26 10 0.14
27 38 0.51
28 24 0.32
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (26 bp):
CAAACCAAGGTATTTCTGTAATTTTG
Found at i:41247208 original size:81 final size:81
Alignment explanation
Indices: 41247103--41247309 Score: 238
Period size: 81 Copynumber: 2.6 Consensus size: 81
41247093 TTGAAAGTCA
** * * *
41247103 AGGGTATTTCTGTAATTTTGTAAATCAAGAGTATTTCTGTAATTTTCCAAAATAGAGGTATTTTA
1 AGGGTATTTAGGTAATTTTGTAAATCAAGGGTATTTCTGTAATTTTACAAAACAGAGGTATTTTA
41247168 GAAATTTTACAAATTG
66 GAAATTTTACAAATTG
** * * *
41247184 AGGGTATTTAGGTAATTTCATAAATCAAGGGTATTT-TGTTAATTATACAAACCAGGGGTATTTT
1 AGGGTATTTAGGTAATTTTGTAAATCAAGGGTATTTCTG-TAATTTTACAAAACAGAGGTATTTT
* * * *
41247248 GGTAATTTTGCTAATTG
65 AGAAATTTTACAAATTG
* * *
41247265 AGGGTATTTTGGTAATTTTGTAAACCAAGGGTA-TTCAGTAATTTT
1 AGGGTATTTAGGTAATTTTGTAAATCAAGGGTATTTCTGTAATTTT
41247310 GTAAACCAAC
Statistics
Matches: 104, Mismatches: 20, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
80 10 0.10
81 94 0.90
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (81 bp):
AGGGTATTTAGGTAATTTTGTAAATCAAGGGTATTTCTGTAATTTTACAAAACAGAGGTATTTTA
GAAATTTTACAAATTG
Found at i:41247295 original size:27 final size:27
Alignment explanation
Indices: 41247058--41247314 Score: 152
Period size: 27 Copynumber: 9.5 Consensus size: 27
41247048 AAAGGCATTC
* * *
41247058 GGTAATTTTGCAAACCAATGGTATTTCT
1 GGTAATTTTGTAAATCAAGGGTATTT-T
41247086 -GTAATTTT-TGAAAGTCAAGGGTATTTCT
1 GGTAATTTTGT-AAA-TCAAGGGTATTT-T
*
41247114 -GTAATTTTGTAAATCAAGAGTATTTCT
1 GGTAATTTTGTAAATCAAGGGTATTT-T
**
41247141 -GTAATTTTCCAAA--ATAGAGGTATTTT
1 GGTAATTTTGTAAATCA-AG-GGTATTTT
* * ** ** *
41247167 AGAAATTTTACAAATTGAGGGTATTTA
1 GGTAATTTTGTAAATCAAGGGTATTTT
**
41247194 GGTAATTTCATAAATCAAGGGTATTTT
1 GGTAATTTTGTAAATCAAGGGTATTTT
* * ** * *
41247221 GTTAATTATACAAACCAGGGGTATTTT
1 GGTAATTTTGTAAATCAAGGGTATTTT
**
41247248 GGTAATTTTGCT-AATTGAGGGTATTTT
1 GGTAATTTTG-TAAATCAAGGGTATTTT
* *
41247275 GGTAATTTTGTAAACCAAGGGTA-TTC
1 GGTAATTTTGTAAATCAAGGGTATTTT
*
41247301 AGTAATTTTGTAAA
1 GGTAATTTTGTAAA
41247315 CCAACCCAGT
Statistics
Matches: 182, Mismatches: 37, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
25 1 0.01
26 19 0.10
27 136 0.75
28 25 0.14
29 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (27 bp):
GGTAATTTTGTAAATCAAGGGTATTTT
Found at i:41247718 original size:22 final size:22
Alignment explanation
Indices: 41247674--41247738 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
41247664 GCAAATACGT
*
41247674 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
*
41247696 TTGGCACAAAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
** *
41247718 TTGGTGCAAACCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
41247739 AATAATTGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:41247978 original size:40 final size:41
Alignment explanation
Indices: 41247883--41248001 Score: 177
Period size: 40 Copynumber: 2.9 Consensus size: 41
41247873 AAGCCACCGA
* *
41247883 TGGATCCACGGTCGTCAAGCAACCATGCGATCCTTAATCGG
1 TGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATCGG
41247924 TGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT-GG
1 TGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATCGG
* * **
41247964 TGGAGCCACAGTCGTCAAGCAACCATTTGATCCTCAAT
1 TGGATCCACGGTCGTCAAGCAACCATACGATCCTCAAT
41248002 TTCTTCCTCC
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 36 0.50
41 36 0.50
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (41 bp):
TGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATCGG
Found at i:41248291 original size:27 final size:27
Alignment explanation
Indices: 41248261--41248573 Score: 202
Period size: 27 Copynumber: 11.6 Consensus size: 27
41248251 GGTAAATCTA
* *
41248261 CAAACCAAGGGCATTTCGGTAATTTTG
1 CAAATCAAGGGTATTTCGGTAATTTTG
* ** * *
41248288 CAAACCAATAGTATATCTGTAATATTTG
1 CAAATCAAGGGTATTTCGGTAAT-TTTG
**
41248316 -AAAGTCAAGGGTATTTCTATAATTTTG
1 CAAA-TCAAGGGTATTTCGGTAATTTTG
* * * *
41248343 TAAATCAAGAGTATTTCTGTAATTTTC
1 CAAATCAAGGGTATTTCGGTAATTTTG
* * *
41248370 CAAATTAAGTGTATTTCAGTAATTTT-
1 CAAATCAAGGGTATTTCGGTAATTTTG
* * ** *
41248396 CTAAATTAGGGGTATTTTAGTAATTTTA
1 C-AAATCAAGGGTATTTCGGTAATTTTG
** * **
41248424 CAAATTGAGGGTATTTAGGTAATTTCA
1 CAAATCAAGGGTATTTCGGTAATTTTG
* *
41248451 CAAATCAAGGGTATTTTGGTAATTTTA
1 CAAATCAAGGGTATTTCGGTAATTTTG
* * *
41248478 CAAA-CTAGGGATATTTTGGTAATTTTA
1 CAAATCAAGGG-TATTTCGGTAATTTTG
* *
41248505 CAAA-CTAGAGGTATTTTGGTAATTTTG
1 CAAATCAAG-GGTATTTCGGTAATTTTG
* ** *
41248532 CTAATTGAGGGTATTTTGGTAATTTTG
1 CAAATCAAGGGTATTTCGGTAATTTTG
* *
41248559 TAAACCAAGGGTATT
1 CAAATCAAGGGTATT
41248574 CAGGAATTTT
Statistics
Matches: 239, Mismatches: 39, Indels: 16
0.81 0.13 0.05
Matches are distributed among these distances:
26 6 0.03
27 207 0.87
28 26 0.11
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCGGTAATTTTG
Found at i:41248438 original size:81 final size:80
Alignment explanation
Indices: 41248353--41248563 Score: 230
Period size: 81 Copynumber: 2.6 Consensus size: 80
41248343 TAAATCAAGA
* ** * *
41248353 GTATTTCTGTAATTTTCCAAATTAAGTGTATTTCAGTAATTTTCTAAATTAGGGGTATTTTAGTA
1 GTATTT-TGTAATTTTCCAAATTAAGGGTATTTTGGTAATTTTCTAAACTAGGGATATTTTAGTA
*
41248418 ATTTTACAAA-TTGAGG
65 ATTTTACAAACTAGA-G
* * *
41248434 GTATTTAGGTAA-TTTCACAAATCAAGGGTATTTTGGTAATTTTAC-AAACTAGGGATATTTTGG
1 GTATTT-TGTAATTTTC-CAAATTAAGGGTATTTTGGTAATTTT-CTAAACTAGGGATATTTTAG
41248497 TAATTTTACAAACTAGAG
63 TAATTTTACAAACTAGAG
* * * *
41248515 GTATTTTGGTAATTTTGCTAATTGAGGGTATTTTGGTAATTTTGTAAAC
1 GTATTTT-GTAATTTTCCAAATTAAGGGTATTTTGGTAATTTTCTAAAC
41248564 CAAGGGTATT
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
80 4 0.04
81 97 0.90
82 7 0.06
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (80 bp):
GTATTTTGTAATTTTCCAAATTAAGGGTATTTTGGTAATTTTCTAAACTAGGGATATTTTAGTAA
TTTTACAAACTAGAG
Found at i:41248617 original size:21 final size:22
Alignment explanation
Indices: 41248588--41248634 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
41248578 AATTTTGTAA
41248588 ACCAGCCCAGT-CCAACCAACAC
1 ACCAGCCCA-TACCAACCAACAC
41248610 ACCA-CCCATACCAACCAACAC
1 ACCAGCCCATACCAACCAACAC
41248631 ACCA
1 ACCA
41248635 AGTGAGGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.40, C:0.51, G:0.04, T:0.04
Consensus pattern (22 bp):
ACCAGCCCATACCAACCAACAC
Found at i:41248977 original size:22 final size:22
Alignment explanation
Indices: 41248949--41249013 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
41248939 GCAAATACGT
*
41248949 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
*
41248971 TTGGCACAAAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
41248993 TTGGCGCAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
41249014 AATAATTGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.05
22 33 0.89
23 2 0.05
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:41249214 original size:41 final size:41
Alignment explanation
Indices: 41249157--41249278 Score: 181
Period size: 41 Copynumber: 3.0 Consensus size: 41
41249147 AAAGCCACCA
* *
41249157 GTGGATCCACGGTCGTCAAGCAACCATGCGATCCTTAATTG
1 GTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATTG
* *
41249198 GTGGATCCACGGTCGTCAAGCAACGATACGATCCTCAATCG
1 GTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATTG
* * *
41249239 GTGGATCCCCAGTCGTCAAGCAACCATTCGATCCTCAATT
1 GTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATT
41249279 TCTTCCTCCG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (41 bp):
GTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATTG
Found at i:41249557 original size:27 final size:27
Alignment explanation
Indices: 41249527--41249585 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
41249517 AAGGTGTTTT
41249527 GGTAAATCTACAAACCAAGGGCATTTC
1 GGTAAATCTACAAACCAAGGGCATTTC
* * * * *
41249554 GGTAATTTTGCAAACCAATGGTATTTC
1 GGTAAATCTACAAACCAAGGGCATTTC
*
41249581 TGTAA
1 GGTAA
41249586 TTTTTGAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTAAATCTACAAACCAAGGGCATTTC
Found at i:41249586 original size:27 final size:27
Alignment explanation
Indices: 41249537--41249830 Score: 197
Period size: 27 Copynumber: 10.9 Consensus size: 27
41249527 GGTAAATCTA
* * *
41249537 CAAACCAAGGGCATTTCGGTAATTTTG
1 CAAATCAAGGGTATTTCTGTAATTTTG
* *
41249564 CAAACCAATGGTATTTCTGTAATTTTTG
1 CAAATCAAGGGTATTTCTGTAA-TTTTG
*
41249592 -AAAGTCAAGAGTATTTCTGTAATTTTG
1 CAAA-TCAAGGGTATTTCTGTAATTTTG
* * * *
41249619 TAAATCAAGAGTATTTCTGGAATTTTC
1 CAAATCAAGGGTATTTCTGTAATTTTG
*
41249646 CAAATCAAGGGTATTTC-GATAATTTTC
1 CAAATCAAGGGTATTTCTG-TAATTTTG
* * *
41249673 CAAATTAGGGGTATTT-TAGTAATTTTA
1 CAAATCAAGGGTATTTCT-GTAATTTTG
** ** **
41249700 CAAATTGAGGGTATTTAGGTAATTTCA
1 CAAATCAAGGGTATTTCTGTAATTTTG
* *
41249727 CAAA-CTAGGGGTATTT-TGGTAATTTTT
1 CAAATC-AAGGGTATTTCT-GTAATTTTG
* **
41249754 CTAATTGAGGGTATTT-TGGTAATTTTG
1 CAAATCAAGGGTATTTCT-GTAATTTTG
* * *
41249781 TAAACCAAGGGTA-TTCAGTAATTTTG
1 CAAATCAAGGGTATTTCTGTAATTTTG
* * *
41249807 TAAACCAAGGGTATTTCAGTAATT
1 CAAATCAAGGGTATTTCTGTAATT
41249831 CTACCTTACA
Statistics
Matches: 220, Mismatches: 35, Indels: 24
0.79 0.13 0.09
Matches are distributed among these distances:
26 25 0.11
27 171 0.78
28 24 0.11
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCTGTAATTTTG
Found at i:41249633 original size:55 final size:53
Alignment explanation
Indices: 41249549--41249676 Score: 141
Period size: 55 Copynumber: 2.3 Consensus size: 53
41249539 AACCAAGGGC
* **
41249549 ATTTCGGTAATTTTGCAAACCAATGGTATTTCTGTAATTTTTGAAAGTCAAGAGT
1 ATTTC-GTAATTTTGCAAACCAATGGTATTTCTGGAATTTTCCAAA-TCAAGAGT
* * *
41249604 ATTTCTGTAATTTTGTAAATCAA-GAGTATTTCTGGAATTTTCCAAATCAAGGGT
1 ATTTC-GTAATTTTGCAAACCAATG-GTATTTCTGGAATTTTCCAAATCAAGAGT
*
41249658 ATTTCGATAATTTTCCAAA
1 ATTTCG-TAATTTTGCAAA
41249677 TTAGGGGTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
53 1 0.02
54 23 0.37
55 38 0.61
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (53 bp):
ATTTCGTAATTTTGCAAACCAATGGTATTTCTGGAATTTTCCAAATCAAGAGT
Found at i:41249903 original size:27 final size:27
Alignment explanation
Indices: 41249812--41249910 Score: 114
Period size: 27 Copynumber: 3.7 Consensus size: 27
41249802 TTTTGTAAAC
41249812 CAAGGGTATTTCAGTAATTCTAC-CTTA
1 CAAGGGTATTTCAGTAATTCTACTC-TA
*
41249839 C-AGGGAAATTTCAGTAATTCTA-TCCTA
1 CAAGGG-TATTTCAGTAATTCTACT-CTA
* *
41249866 CAGGGGCATTTCAGTAATTCTACTCTA
1 CAAGGGTATTTCAGTAATTCTACTCTA
*
41249893 CAAGGGTATTTCGGTAAT
1 CAAGGGTATTTCAGTAAT
41249911 ACTAGCCTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.07
27 52 0.85
28 5 0.08
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (27 bp):
CAAGGGTATTTCAGTAATTCTACTCTA
Found at i:41251097 original size:26 final size:24
Alignment explanation
Indices: 41251005--41251100 Score: 140
Period size: 24 Copynumber: 3.9 Consensus size: 24
41250995 GAGGTTCTTG
*
41251005 TTCAGCTCAATAGAGCTCACCGTT
1 TTCAGCTCAATAGAGCTTACCGTT
41251029 TTCAGCTCAATAGAGCTTACCGTT
1 TTCAGCTCAATAGAGCTTACCGTT
*
41251053 TTCAGCTCAATAGAGCTTACTGTT
1 TTCAGCTCAATAGAGCTTACCGTT
41251077 TATCAGCTC-ATGAAGAGCTTACCG
1 T-TCAGCTCAAT--AGAGCTTACCG
41251101 ACCATGTCTC
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
24 49 0.74
25 7 0.11
26 10 0.15
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (24 bp):
TTCAGCTCAATAGAGCTTACCGTT
Found at i:41257094 original size:46 final size:46
Alignment explanation
Indices: 41257041--41257214 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
41257031 TTTGGGCATT
*
41257041 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTC
* * *
41257087 CGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTC
* *
41257134 CGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG-C
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTC
*
41257179 TCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 -CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41257215 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
43 6 0.05
45 4 0.04
46 62 0.56
47 30 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTC
Found at i:41257188 original size:93 final size:93
Alignment explanation
Indices: 41257035--41257207 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
41257025 GGGATATTTG
* * *
41257035 GGCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCGTTGAG
41257100 TTGAGTCCGAGTTCATGAGATGTAACTA
66 TTGAGTCCGAGTTCATGAGATGTAACTA
* *
41257128 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG-CTCGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTC-CGAACTCGTTGA
41257192 GTTGAGTCCGAGTTCA
65 GTTGAGTCCGAGTTCA
41257208 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
92 1 0.01
93 73 0.99
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCATGAGATGTAACTA
Found at i:41261309 original size:24 final size:24
Alignment explanation
Indices: 41261243--41261347 Score: 83
Period size: 24 Copynumber: 4.4 Consensus size: 24
41261233 ATAGCTCGTA
** *
41261243 AGAGCTTACTATTTT-AGCTCATT
1 AGAGCTTACCGTTTTCAGCTCAAT
* * *
41261266 AGAGGTTA-C-TGTTCATCTCAAT
1 AGAGCTTACCGTTTTCAGCTCAAT
41261288 AGAGCTTACCGTTTTCAGCTCAAT
1 AGAGCTTACCGTTTTCAGCTCAAT
* *
41261312 AGAGCTTACTGTTTATCAACTC-AT
1 AGAGCTTACCGTTT-TCAGCTCAAT
41261336 GAAGAGCTTACC
1 --AGAGCTTACC
41261348 AACCATGTCT
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
21 3 0.05
22 13 0.20
23 8 0.12
24 26 0.40
25 6 0.09
26 9 0.14
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (24 bp):
AGAGCTTACCGTTTTCAGCTCAAT
Done.