Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 139 of 211
Found at i:41329409 original size:16 final size:16
Alignment explanation
Indices: 41329388--41329454 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 16
41329378 ATATAAATAT
41329388 AAATAATTATATAAAC
1 AAATAATTATATAAAC
41329404 AAATAAGACAACTTAATATAAAC
1 AAAT-----AA-TTA-TATAAAC
*
41329427 AAATATTTATATAAAC
1 AAATAATTATATAAAC
*
41329443 AAATATTTATAT
1 AAATAATTATAT
41329455 TTAAAGAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
16 23 0.53
17 3 0.07
18 1 0.02
21 2 0.05
22 3 0.07
23 11 0.26
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.33
Consensus pattern (16 bp):
AAATAATTATATAAAC
Found at i:41329437 original size:14 final size:16
Alignment explanation
Indices: 41329419--41329454 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
41329409 AGACAACTTA
41329419 ATATAAACAAATATTT
1 ATATAAACAAATATTT
41329435 ATATAAACAAATATTT
1 ATATAAACAAATATTT
41329451 ATAT
1 ATAT
41329455 TTAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAACAAATATTT
Found at i:41329956 original size:29 final size:29
Alignment explanation
Indices: 41329924--41329995 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
41329914 AAAAATAAAA
41329924 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
41329953 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
41329982 ATTTACCAAAATAT
1 ATTTACCAAAATAT
41329996 ATAAAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:41330018 original size:28 final size:28
Alignment explanation
Indices: 41329978--41330033 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
41329968 ACAACTTTTT
41329978 TTTTATTTACCAAAATATATAAAAAAAA
1 TTTTATTTACCAAAATATATAAAAAAAA
41330006 TTTTATTTACCAAAATATATAAAAAAAA
1 TTTTATTTACCAAAATATATAAAAAAAA
41330034 CTAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (28 bp):
TTTTATTTACCAAAATATATAAAAAAAA
Found at i:41330132 original size:26 final size:27
Alignment explanation
Indices: 41330059--41330132 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
41330049 CTGACACTTC
*
41330059 GCGGCACCAAAGGTGCCAAA-TAAGTTG
1 GCGGCACC-ATGGTGCCAAAGTAAGTTG
* *
41330086 GTGGCACCATTGGTGCCAAAGTCA-TTG
1 GCGGCACCA-TGGTGCCAAAGTAAGTTG
41330113 GCGGCACCATGGTGCCAAAG
1 GCGGCACCATGGTGCCAAAG
41330133 GAAAAAAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 12 0.29
27 27 0.66
28 2 0.05
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (27 bp):
GCGGCACCATGGTGCCAAAGTAAGTTG
Found at i:41330513 original size:57 final size:55
Alignment explanation
Indices: 41330447--41330557 Score: 168
Period size: 57 Copynumber: 2.0 Consensus size: 55
41330437 AGATAGTCAC
* *
41330447 TTAATTAGAATTCTCTCTTTTAATAACTCTATTTTAATTTAATAAACTATTAAGTAA
1 TTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTAA-AAA-AATTAAGTAA
* *
41330504 TTAATTAGAATTCTTTCATTTCATAACTCTATTTTAATTTAAAAAAATTAAGTA
1 TTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTAAAAAAATTAAGTA
41330558 TTACTTAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
55 8 0.16
56 3 0.06
57 39 0.78
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.47
Consensus pattern (55 bp):
TTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTAAAAAAATTAAGTAA
Found at i:41330606 original size:37 final size:37
Alignment explanation
Indices: 41330564--41330634 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
41330554 AGTATTACTT
41330564 AATAGTTTATTAAATTAAAATAGAGTTACTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTACTAAATGAG
*
41330601 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTACTAAAT
41330635 AAAAAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.38
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTACTAAATGAG
Found at i:41330639 original size:19 final size:19
Alignment explanation
Indices: 41330570--41330638 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
41330560 ACTTAATAGT
41330570 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * * *
41330589 TTACTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
41330607 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
41330626 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
41330639 AAATGAGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 19 0.46
19 22 0.54
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.36
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:41330646 original size:20 final size:19
Alignment explanation
Indices: 41330570--41330647 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
41330560 ACTTAATAGT
* *
41330570 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
* * * * *
41330589 TTACTAAATGAGAATAG-T
1 TTATTAAATAAAAAAAGAG
* *
41330607 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
41330626 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
41330646 TT
1 TT
41330648 GAAGGGGAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
18 14 0.30
19 28 0.60
20 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:41330769 original size:27 final size:26
Alignment explanation
Indices: 41330713--41330798 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
41330703 TTTTTTTTCC
*
41330713 TTTGGCACCATGGTGCCGCCAA-TGA
1 TTTGGCACCATGGTGCCGCCAATTTA
*
41330738 CTTTGGCACCAATGGTGCCACCAATTTA
1 -TTTGGCACC-ATGGTGCCGCCAATTTA
* *
41330766 TTTGACACCTTTGGTGCCGCCAATTTA
1 TTTGGCACC-ATGGTGCCGCCAATTTA
*
41330793 ATTGGC
1 TTTGGC
41330799 TGGTGTTAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.18
27 39 0.78
28 2 0.04
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (26 bp):
TTTGGCACCATGGTGCCGCCAATTTA
Found at i:41330869 original size:28 final size:28
Alignment explanation
Indices: 41330840--41330937 Score: 180
Period size: 28 Copynumber: 3.5 Consensus size: 28
41330830 TTTTTTTGAT
41330840 ATATTTTGGTAAATAAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
41330867 TATATTTTGGTAAATAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
41330896 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
41330924 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
41330938 TTTTATTTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
28 67 0.97
29 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:41339189 original size:28 final size:26
Alignment explanation
Indices: 41339155--41339223 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 26
41339145 TCCATATTAT
41339155 TTTTTAAAATTTTAAAAAATATTTATA
1 TTTTTAAAATTTTAAAAAATATTT-TA
* *
41339182 TTATTTAATAATTTT-ATATATATTTTA
1 TT-TTTAA-AATTTTAAAAAATATTTTA
41339209 TTTATTAAAATTTTA
1 TTT-TTAAAATTTTA
41339224 TATATAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
26 7 0.19
27 10 0.28
28 13 0.36
29 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTTTAAAATTTTAAAAAATATTTTA
Found at i:41339209 original size:24 final size:25
Alignment explanation
Indices: 41339173--41339229 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
41339163 ATTTTAAAAA
* *
41339173 ATATTTATATTATTTA-ATAATTTT
1 ATATATATATTATTTATAAAATTTT
*
41339197 ATATATATTTTATTTATTAAAATTTT
1 ATATATATATTATTTA-TAAAATTTT
41339223 ATATATA
1 ATATATA
41339230 AACAACTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 14 0.50
26 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATATATATATTATTTATAAAATTTT
Found at i:41339227 original size:28 final size:27
Alignment explanation
Indices: 41339151--41339229 Score: 90
Period size: 26 Copynumber: 2.9 Consensus size: 27
41339141 CACATCCATA
* * *
41339151 TTATTTTTTAAAATTTTA-AAAAATAT
1 TTATTTATTAAAATTTTATATATATAT
41339177 TTATATTATTTAATAATTTTATATATAT-T
1 TTAT-TTA-TTAA-AATTTTATATATATAT
41339206 TTATTTATTAAAATTTTATATATA
1 TTATTTATTAAAATTTTATATATA
41339230 AACAACTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
26 17 0.37
27 6 0.13
28 7 0.15
29 12 0.26
30 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATTTATTAAAATTTTATATATATAT
Found at i:41339974 original size:24 final size:24
Alignment explanation
Indices: 41339953--41340001 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
41339943 AGTTAAAATG
*
41339953 TATATATAATTAAATATCAAAATAT
1 TATATA-AATTAAATAACAAAATAT
*
41339978 TTTATAAATTAAATAACAAAATAT
1 TATATAAATTAAATAACAAAATAT
41340002 AATTATGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
TATATAAATTAAATAACAAAATAT
Found at i:41340085 original size:35 final size:35
Alignment explanation
Indices: 41340036--41340102 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
41340026 ATTATAAAAA
* *
41340036 ATTATTTATATTATATTATATAATAATATATTAGG
1 ATTATTTATATTATATTAAATAAAAATATATTAGG
41340071 ATTATGTTAT-TTATATTAAATAAAAATATATT
1 ATTAT-TTATATTATATTAAATAAAAATATATT
41340103 TATATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 25 0.86
36 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (35 bp):
ATTATTTATATTATATTAAATAAAAATATATTAGG
Found at i:41343341 original size:132 final size:132
Alignment explanation
Indices: 41343096--41343369 Score: 314
Period size: 132 Copynumber: 2.1 Consensus size: 132
41343086 TTCGTAGATC
*** * * * *
41343096 CATCATATCGAGTTTAAATGTGGCTTGTTAGGTATGCTGCGAGCTGTTAGAACATGACGTCTTCC
1 CATCATATCGAGTTTAAATGCAACTTGTTAGGTACGCTGCGAGCTATTAGAACATAACGTCTACC
* * * * * *
41343161 TTGTCACTTGTATGGGTGGATCGTGCTCGCATGAATCTGGCCGCTGAGACTCTTTGGTTATTAGA
66 TTGCCACATGTATGGGTAGATCGTGCTCGCATGAATCTGACCACTGAGACTCTTTCGTTATTAGA
41343226 AT
131 AT
* * * *
41343228 CATCATGTCGAGTTTAAATGCAACTTGTTGGGTACGCTGCGAGTTATTAGAACCTAACGTCTACC
1 CATCATATCGAGTTTAAATGCAACTTGTTAGGTACGCTGCGAGCTATTAGAACATAACGTCTACC
* * * * * * *
41343293 TTGCCACATGTATGGGTAGATCGTGCTTGCATGGATCTGATCATTGAGATTTTTTCGTTATTGGA
66 TTGCCACATGTATGGGTAGATCGTGCTCGCATGAATCTGACCACTGAGACTCTTTCGTTATTAGA
41343358 AT
131 AT
**
41343360 TGTCATATCG
1 CATCATATCG
41343370 CAAAAAAAAA
Statistics
Matches: 115, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
132 115 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (132 bp):
CATCATATCGAGTTTAAATGCAACTTGTTAGGTACGCTGCGAGCTATTAGAACATAACGTCTACC
TTGCCACATGTATGGGTAGATCGTGCTCGCATGAATCTGACCACTGAGACTCTTTCGTTATTAGA
AT
Found at i:41345704 original size:27 final size:27
Alignment explanation
Indices: 41345674--41345754 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
41345664 GACAGCTTGA
41345674 CCCCTCCTGTCGAGAATGACAATGTGG
1 CCCCTCCTGTCGAGAATGACAATGTGG
* ** *
41345701 CCCCTCCTATTAAGAATGATAATGTGG
1 CCCCTCCTGTCGAGAATGACAATGTGG
* *
41345728 CCCTTCCTG-CTGAGAATGACAAAGTGG
1 CCCCTCCTGTC-GAGAATGACAATGTGG
41345755 GCCAAGATGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (27 bp):
CCCCTCCTGTCGAGAATGACAATGTGG
Found at i:41346288 original size:72 final size:70
Alignment explanation
Indices: 41346216--41346655 Score: 278
Period size: 72 Copynumber: 6.1 Consensus size: 70
41346206 CCTGCAAGCC
*
41346216 TTAATAATAACAGCTGAGAGCTTTTAACTCTCGCTAACTATTTAGAGAGCTGCGATTTTAATCCT
1 TTAATAATAACAG-TGAGAGCTTTTAACTCTCGCTAACTATTT-GAGGGCTGCGATTTTAATCCT
*
41346281 GTGAGCC
64 GTGAGCT
* * * * * * ** * *
41346288 TTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTGCTTGGAGGGCTGC-AGCCTAAAACC
1 TTAATAATAACAGTGA-GAGCTTTTAACTCTCGCTAACT-ATTTGAGGGCTGCGA-TTTTAATCC
*
41346352 TATGAGCT
63 TGTGAGCT
* * * * * *
41346360 TTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGAGGGGGTAC-ATTTTTAATCA
1 TTAATAATAACAG-TGAGAGCTTTTAACTCTCGCTAACTATTTGA-GGGCTGCGA-TTTTAATCC
* *
41346424 AGTGAGCC
63 TGTGAGCT
* * * * * * *
41346432 TTAATAATGACAATTGGGAGTTTTTAACTCTCGTTAACTATTTAAGGGGCTGCGGTTTTAGA-CC
1 TTAATAATAAC-AGTGAGAGCTTTTAACTCTCGCTAACTATTTGA-GGGCTGCGATTTTA-ATCC
* *
41346496 TGCGAGAT
63 TGTGAGCT
* * * * * * * *
41346504 TTAATGATGACAGTTAGGAGCTTTTAACTCCCGCTAACTATTTGGGGGGTTGTGATATTGAA-CC
1 TTAATAATAACAGTGA-GAGCTTTTAACTCTCGCTAACTATTT-GAGGGCTGCGAT-TTTAATCC
**
41346568 TACGAGCT
63 TGTGAGCT
** * * *
41346576 TTAATAATAATTGTTGGGAGCTTTTAACTCTCGTTAACTATTTGAGGGACTACGATTTTAAT-CT
1 TTAATAATAACAG-TGAGAGCTTTTAACTCTCGCTAACTATTTGAGGG-CTGCGATTTTAATCCT
*
41346640 CGTGAGGT
64 -GTGAGCT
41346648 TTAATAAT
1 TTAATAAT
41346656 GACATTTGAC
Statistics
Matches: 274, Mismatches: 79, Indels: 30
0.72 0.21 0.08
Matches are distributed among these distances:
71 19 0.07
72 246 0.90
73 9 0.03
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (70 bp):
TTAATAATAACAGTGAGAGCTTTTAACTCTCGCTAACTATTTGAGGGCTGCGATTTTAATCCTGT
GAGCT
Found at i:41346352 original size:144 final size:142
Alignment explanation
Indices: 41346139--41346470 Score: 362
Period size: 144 Copynumber: 2.3 Consensus size: 142
41346129 TTAAAGCTAC
* * * * **
41346139 GAGCCTTAATGATGACATCTGAGAGCTTTTAACTCCCGTTAATTGTTTGGAGGGATGCAGTATTG
1 GAGCCTTAATGATGACAT-TG-GAGCTTTTAACTCTCGTTAACTGCTTGGAGGGATGCAGCATAA
* * * *
41346204 AACCTGCAAGCCTTAATAATAACAGCTGAGAGCTTTTAACTCTCGCTAACTATTT-AGAGAGCTG
64 AACCTACAAGCCTTAATAATAACAGCTGAGAGCTTTTAACTCTCACCAACTATTTGAG-GAGCTA
**
41346268 CGA-TTTTAATCCTGT
128 C-ATTTTTAATCAAGT
* * * *
41346283 GAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTGCTTGGAGGGCTGCAGCCTAA
1 GAGCCTTAATGATGACA-TT-GGAGCTTTTAACTCTCGTTAACTGCTTGGAGGGATGCAGCATAA
** * * * *
41346348 AACCTATGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGAGGGGGTAC
64 AACCTACAAGCCTTAATAATAACAGCTGAGAGCTTTTAACTCTCACCAACTATTTGAGGAGCTAC
41346413 ATTTTTAATCAAGT
129 ATTTTTAATCAAGT
* *
41346427 GAGCCTTAATAATGACAATTGGGAGTTTTTAACTCTCGTTAACT
1 GAGCCTTAATGATGAC-ATT-GGAGCTTTTAACTCTCGTTAACT
41346471 ATTTAAGGGG
Statistics
Matches: 156, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
143 1 0.01
144 150 0.96
145 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (142 bp):
GAGCCTTAATGATGACATTGGAGCTTTTAACTCTCGTTAACTGCTTGGAGGGATGCAGCATAAAA
CCTACAAGCCTTAATAATAACAGCTGAGAGCTTTTAACTCTCACCAACTATTTGAGGAGCTACAT
TTTTAATCAAGT
Found at i:41346507 original size:144 final size:144
Alignment explanation
Indices: 41346216--41346553 Score: 351
Period size: 144 Copynumber: 2.4 Consensus size: 144
41346206 CCTGCAAGCC
* * * * *
41346216 TTAATAATAACAGCTGAGAGCTTTTAACTCTCGCTAACTATTT-AGAGAGCTGCGATTTTAATCC
1 TTAATAATAACAGCTGGGAGCTTTTAACTCTCGCTAACTATTTGAG-GGGGTACGATTTTAATCA
* * * * * *
41346280 TGTGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTGCTTGGAGGGCTGCAGCC
65 AGTGAGCCTTAATAATGACAATTAGGAGCTTTTAACTCTCGCTAACTACTTAGAGGGCTGCAGCC
* *
41346345 TAAAACCTATGAGCT
130 TAAAACCTACGAGAT
* *
41346360 TTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGAGGGGGTAC-ATTTTTAATCA
1 TTAATAATAACAGCTGGGAGCTTTTAACTCTCGCTAACTATTTGAGGGGGTACGA-TTTTAATCA
* * * * * *
41346424 AGTGAGCCTTAATAATGACAATTGGGAGTTTTTAACTCTCGTTAACTATTTA-AGGGGCTGCGGT
65 AGTGAGCCTTAATAATGACAATTAGGAGCTTTTAACTCTCGCTAACTACTTAGA-GGGCTGCAGC
* * * *
41346488 TTTAGACCTGCGAGAT
129 CTAAAACCTACGAGAT
* * * * *
41346504 TTAATGATGACAGTTAGGAGCTTTTAACTCCCGCTAACTATTTG-GGGGGT
1 TTAATAATAACAGCTGGGAGCTTTTAACTCTCGCTAACTATTTGAGGGGGT
41346554 TGTGATATTG
Statistics
Matches: 159, Mismatches: 32, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
143 8 0.05
144 149 0.94
145 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (144 bp):
TTAATAATAACAGCTGGGAGCTTTTAACTCTCGCTAACTATTTGAGGGGGTACGATTTTAATCAA
GTGAGCCTTAATAATGACAATTAGGAGCTTTTAACTCTCGCTAACTACTTAGAGGGCTGCAGCCT
AAAACCTACGAGAT
Found at i:41346510 original size:216 final size:215
Alignment explanation
Indices: 41346212--41346659 Score: 517
Period size: 216 Copynumber: 2.1 Consensus size: 215
41346202 TGAACCTGCA
* *
41346212 AGCCTTAATAATAACAGCTGAGAGCTTTTAACTCTCGCTAACTATTTAGAGAGCTGCGATTTTAA
1 AGCCTTAATAATGACAACTGAGAGCTTTTAACTCTCGCTAACTATTTAGAGAGCTGCGATTTTAA
* * * * *
41346277 TCCTGTGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTGCTTGGAGGGCTGCA
66 TCCTGCGAGACTTAATGATGACAGTTAGGAGCTTTTAACTCCCGCTAACTACTTGGAGGGCTG-A
* *
41346342 GCCTA-AAACCTATGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGAG
130 G-ATATAAACCTACGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGAG
**
41346406 GGGGTAC-ATTTTTAATCAAGTG
194 GGACTACGA-TTTTAATCAAGTG
* * * * * *
41346428 AGCCTTAATAATGACAATTGGGAGTTTTTAACTCTCGTTAACTATTTA-AGGGGCTGCGGTTTTA
1 AGCCTTAATAATGACAACTGAGAGCTTTTAACTCTCGCTAACTATTTAGA-GAGCTGCGATTTTA
* * * *
41346492 GA-CCTGCGAGATTTAATGATGACAGTTAGGAGCTTTTAACTCCCGCTAACTATTTGGGGGGTTG
65 -ATCCTGCGAGACTTAATGATGACAGTTAGGAGCTTTTAACTCCCGCTAACTACTTGGAGGGCTG
* * ** * ***
41346556 TGATATTGAACCTACGAGCTTTAATAATAATTGTTGGGAGCTTTTAACTCTCGTTAACTATTTGA
129 AGATA-TAAACCTACGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGA
**
41346621 GGGACTACGATTTTAATCTCGTG
193 GGGACTACGATTTTAATCAAGTG
**
41346644 AGGTTTAATAATGACA
1 AGCCTTAATAATGACA
41346660 TTTGACTACG
Statistics
Matches: 194, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
214 2 0.01
215 2 0.01
216 188 0.97
217 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (215 bp):
AGCCTTAATAATGACAACTGAGAGCTTTTAACTCTCGCTAACTATTTAGAGAGCTGCGATTTTAA
TCCTGCGAGACTTAATGATGACAGTTAGGAGCTTTTAACTCCCGCTAACTACTTGGAGGGCTGAG
ATATAAACCTACGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGAGGG
ACTACGATTTTAATCAAGTG
Found at i:41346674 original size:40 final size:40
Alignment explanation
Indices: 41346623--41346704 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
41346613 CTATTTGAGG
41346623 GACTACGATTTTAATCTCGTGAGGTTTAATAATGACATTT
1 GACTACGATTTTAATCTCGTGAGGTTTAATAATGACATTT
41346663 GACTACGATTTTAATCTCGTGAGGTTTAATAATGACATTT
1 GACTACGATTTTAATCTCGTGAGGTTTAATAATGACATTT
41346703 GA
1 GA
41346705 GAGCTTTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (40 bp):
GACTACGATTTTAATCTCGTGAGGTTTAATAATGACATTT
Found at i:41346791 original size:71 final size:72
Alignment explanation
Indices: 41346688--41347019 Score: 309
Period size: 72 Copynumber: 4.7 Consensus size: 72
41346678 CTCGTGAGGT
* * * * ***
41346688 TTAATAATGACA-TTTGAGAGCTTTTCAA-TCTCGCTAATTGTTTGGGGGCTGCAATTTTAAACC
1 TTAATAATGACAGCTAGAGAGCTTTT-AACTCTCGCTAACTGTTTGGGGGTTGTGGTTTTAAACC
*
41346751 TGCAAGCC
65 TGCGAGCC
* * * *
41346759 TTAATGATGATAGCTAG-GAGCTTTTAACTCTCGCTAACTATTTGGAGGTTGTGGTTTTAAACCT
1 TTAATAATGACAGCTAGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGTTGTGGTTTTAAACCT
41346823 GCGAGCC
66 GCGAGCC
* * * * *
41346830 TTAATAATGACA-ATTGAGAGCTTTTAACTCTCACTAATTGTTTGGGTGGTTGTGGTTTTAAACT
1 TTAATAATGACAGCTAGAGAGCTTTTAACTCTCGCTAACTGTTTGGG-GGTTGTGGTTTTAAACC
* *
41346894 TACGAGTC
65 TGCGAGCC
* * * * * * *
41346902 TGAATGAA-GACAGCTAG-GAGTTTTTAACTCTCGCTAAATATTTAAGGGGTTGTGGTATTGAAC
1 TTAAT-AATGACAGCTAGAGAGCTTTTAACTCTCGCTAACTGTTT-GGGGGTTGTGGTTTTAAAC
41346965 CTGCGAGCC
64 CTGCGAGCC
** * *
41346974 TTAATAATGGTAGCT-GAAAGCTTTTAACTCTCACTAACTGTTTGGG
1 TTAATAATGACAGCTAGAGAGCTTTTAACTCTCGCTAACTGTTTGGG
41347020 TTTTTTATGA
Statistics
Matches: 207, Mismatches: 45, Indels: 18
0.77 0.17 0.07
Matches are distributed among these distances:
70 4 0.02
71 93 0.45
72 104 0.50
73 6 0.03
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (72 bp):
TTAATAATGACAGCTAGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGTTGTGGTTTTAAACCT
GCGAGCC
Found at i:41347004 original size:144 final size:143
Alignment explanation
Indices: 41346761--41347020 Score: 387
Period size: 144 Copynumber: 1.8 Consensus size: 143
41346751 TGCAAGCCTT
* * * *
41346761 AATGATGATAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGGAGGTTGTGGTTTTAAACCTGCG
1 AATGAAGACAGCTAGGAGCTTTTAACTCTCGCTAAATATTTGGAGGTTGTGGTATTAAACCTGCG
* * *
41346826 AGCCTTAATAATGACAATTGAGAGCTTTTAACTCTCACTAATTGTTTGGGTGGTTGTGGTTTTAA
66 AGCCTTAATAATGACAACTGAAAGCTTTTAACTCTCACTAACTGTTTGGGTGGTTGTGGTTTTAA
41346891 ACTTACGAGTCTG
131 ACTTACGAGTCTG
* *
41346904 AATGAAGACAGCTAGGAGTTTTTAACTCTCGCTAAATATTTAAGG-GGTTGTGGTATTGAACCTG
1 AATGAAGACAGCTAGGAGCTTTTAACTCTCGCTAAATATTT--GGAGGTTGTGGTATTAAACCTG
** *
41346968 CGAGCCTTAATAATGGTAGCTGAAAGCTTTTAACTCTCACTAACTGTTTGGGT
64 CGAGCCTTAATAATGACAACTGAAAGCTTTTAACTCTCACTAACTGTTTGGGT
41347021 TTTTTATGAG
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
143 37 0.36
144 64 0.62
145 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (143 bp):
AATGAAGACAGCTAGGAGCTTTTAACTCTCGCTAAATATTTGGAGGTTGTGGTATTAAACCTGCG
AGCCTTAATAATGACAACTGAAAGCTTTTAACTCTCACTAACTGTTTGGGTGGTTGTGGTTTTAA
ACTTACGAGTCTG
Found at i:41347348 original size:13 final size:13
Alignment explanation
Indices: 41347330--41347357 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41347320 TAAGTACGTG
41347330 TTGTATTTTTGAC
1 TTGTATTTTTGAC
41347343 TTGTATTTTTGAC
1 TTGTATTTTTGAC
41347356 TT
1 TT
41347358 TAGCTATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (13 bp):
TTGTATTTTTGAC
Found at i:41355041 original size:22 final size:22
Alignment explanation
Indices: 41355015--41355061 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
41355005 TTTATATTAA
41355015 ATTATTTTATGATGATTGATTT
1 ATTATTTTATGATGATTGATTT
41355037 ATTATTTTATGATGATTGATTT
1 ATTATTTTATGATGATTGATTT
41355059 ATT
1 ATT
41355062 GCGCTCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.60
Consensus pattern (22 bp):
ATTATTTTATGATGATTGATTT
Found at i:41355926 original size:10 final size:9
Alignment explanation
Indices: 41355891--41355928 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
41355881 TTTAGATTAA
41355891 AAATTAATT
1 AAATTAATT
41355900 -AATTAAGTT
1 AAATTAA-TT
41355909 AAATTAATT
1 AAATTAATT
41355918 AAGATTAATT
1 AA-ATTAATT
41355928 A
1 A
41355929 GTTTAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 6 0.23
9 6 0.23
10 14 0.54
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (9 bp):
AAATTAATT
Found at i:41355927 original size:14 final size:14
Alignment explanation
Indices: 41355893--41355928 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
41355883 TAGATTAAAA
41355893 ATTAATTAATTAAG
1 ATTAATTAATTAAG
41355907 -TTAAATTAATTAAG
1 ATT-AATTAATTAAG
41355921 ATTAATTA
1 ATTAATTA
41355929 GTTTAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 16 0.80
15 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
ATTAATTAATTAAG
Found at i:41359667 original size:47 final size:47
Alignment explanation
Indices: 41359544--41359667 Score: 220
Period size: 43 Copynumber: 2.7 Consensus size: 47
41359534 ATGAATTAGG
41359544 ACCAAATTGAATAAGATAAGAATTATGAGGGACTAAATCATAATTTT
1 ACCAAATTGAATAAGATAAGAATTATGAGGGACTAAATCATAATTTT
41359591 ACCAAA-T---TAAGATAAGAATTATGAGGGACTAAATCATAATTTT
1 ACCAAATTGAATAAGATAAGAATTATGAGGGACTAAATCATAATTTT
41359634 ACCAAATTGAATAAGATAAGAATTATGAGGGACT
1 ACCAAATTGAATAAGATAAGAATTATGAGGGACT
41359668 CAATGATGGA
Statistics
Matches: 73, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
43 42 0.58
44 1 0.01
46 1 0.01
47 29 0.40
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (47 bp):
ACCAAATTGAATAAGATAAGAATTATGAGGGACTAAATCATAATTTT
Found at i:41359817 original size:11 final size:13
Alignment explanation
Indices: 41359793--41359824 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41359783 TAGTTTATTA
41359793 ATATTTTAATATG
1 ATATTTTAATATG
41359806 AT-TTTTAA-ATG
1 ATATTTTAATATG
41359817 ATATTTTA
1 ATATTTTA
41359825 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:41362507 original size:20 final size:20
Alignment explanation
Indices: 41362484--41362530 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
41362474 TGATTAAATG
41362484 ATTTAAAATATGTTTAATTC
1 ATTTAAAATATGTTTAATTC
41362504 ATTTAAAATATGTTTAATTC
1 ATTTAAAATATGTTTAATTC
41362524 ATTTAAA
1 ATTTAAA
41362531 TATTAAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (20 bp):
ATTTAAAATATGTTTAATTC
Found at i:41364694 original size:20 final size:20
Alignment explanation
Indices: 41364669--41364707 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41364659 TAGTGGATCA
*
41364669 TCGAGGGGCTCACACTATCG
1 TCGAGGAGCTCACACTATCG
41364689 TCGAGGAGCTCACACTATC
1 TCGAGGAGCTCACACTATC
41364708 TTATTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (20 bp):
TCGAGGAGCTCACACTATCG
Found at i:41366405 original size:5 final size:5
Alignment explanation
Indices: 41366395--41366427 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
41366385 AAAACTCATA
41366395 AAAAT AAAAT AAAAT AAAAT AAAAT AAATAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA
41366428 CTAGTCAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:41368007 original size:42 final size:42
Alignment explanation
Indices: 41367918--41368058 Score: 212
Period size: 42 Copynumber: 3.4 Consensus size: 42
41367908 GATCTCGGTA
* * *
41367918 TCGCACATTTAGTGCCCGTTATTC-ACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
* *
41367959 TCGCACACTTAATGCCTGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
*
41368001 TTGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
*
41368043 TCCCACACTTAGTGCC
1 TCGCACACTTAGTGCC
41368059 ATTCATACAG
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 21 0.24
42 68 0.76
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
Found at i:41375199 original size:42 final size:41
Alignment explanation
Indices: 41375113--41375253 Score: 187
Period size: 42 Copynumber: 3.4 Consensus size: 41
41375103 GATCTCGGTA
* * * *
41375113 TCGCACATTTAGTGCCCGTTATTCACATCGTCATTTTAGA-T
1 TCGCACACTTAGTGTCTGTTATTCACATCATCATTTTA-ATT
*
41375154 TCGCACACTTAGTGTCTGTTATTTCACATCATCATTATAATT
1 TCGCACACTTAGTGTCTGTTA-TTCACATCATCATTTTAATT
41375196 TCGCACACTTAGTG-CTCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGTCT-GTTATTC-ACATCATCATTTTAATT
41375238 TCGCACACTTAGTGTC
1 TCGCACACTTAGTGTC
41375254 ATTCATATAG
Statistics
Matches: 89, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
41 24 0.27
42 64 0.72
43 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (41 bp):
TCGCACACTTAGTGTCTGTTATTCACATCATCATTTTAATT
Found at i:41387581 original size:11 final size:12
Alignment explanation
Indices: 41387561--41387586 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41387551 CTAAATAACC
41387561 AAAAGAAAAAAA
1 AAAAGAAAAAAA
41387573 AAAAGAAAAAAA
1 AAAAGAAAAAAA
41387585 AA
1 AA
41387587 GGTGAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:41395581 original size:17 final size:19
Alignment explanation
Indices: 41395536--41395583 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
41395526 GTATTTTATT
*
41395536 AATTTAATATTAAAGTGAT
1 AATTTAATATTAAAGTGAA
*
41395555 TATCTTAATATTAAA-T-AA
1 AAT-TTAATATTAAAGTGAA
41395573 AATTTAATATT
1 AATTTAATATT
41395584 TATCTTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 3 0.12
20 11 0.44
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
AATTTAATATTAAAGTGAA
Found at i:41395630 original size:16 final size:16
Alignment explanation
Indices: 41395606--41395646 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
41395596 AAATATTCTA
41395606 TTAAT-TTAA-TAAGAT
1 TTAATATTAATTAA-AT
*
41395621 TTAATATTAATTTAAT
1 TTAATATTAATTAAAT
41395637 TTAATATTAA
1 TTAATATTAA
41395647 AGTGATTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 16 0.70
17 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TTAATATTAATTAAAT
Found at i:41398512 original size:16 final size:16
Alignment explanation
Indices: 41398491--41398522 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41398481 CATTCTGCAT
41398491 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
41398507 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
41398523 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:41400579 original size:18 final size:18
Alignment explanation
Indices: 41400558--41400617 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
41400548 GACCTCACTC
41400558 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
41400576 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
41400594 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
41400615 TCT
1 TCT
41400618 CGCTCGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:41401575 original size:12 final size:13
Alignment explanation
Indices: 41401551--41401580 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41401541 CAAAAAAAAA
41401551 TTTTTGAATTTTT
1 TTTTTGAATTTTT
41401564 TTTTTGAATTTTT
1 TTTTTGAATTTTT
41401577 TTTT
1 TTTT
41401581 CAAATTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTGAATTTTT
Found at i:41403112 original size:16 final size:16
Alignment explanation
Indices: 41403091--41403122 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41403081 CATTCTGCAT
*
41403091 TTAAACAACAGCAGCA
1 TTAAACAACAACAGCA
41403107 TTAAACAACAACAGCA
1 TTAAACAACAACAGCA
41403123 AAACACATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.25, G:0.09, T:0.12
Consensus pattern (16 bp):
TTAAACAACAACAGCA
Found at i:41411890 original size:34 final size:34
Alignment explanation
Indices: 41411777--41411900 Score: 124
Period size: 34 Copynumber: 3.6 Consensus size: 34
41411767 ACATATACGA
* * * *
41411777 ATATCATATCAGAATATCACATTACCAAAAACAT
1 ATATCATATCAGAATGTCATATTTCCATAAACAT
* *
41411811 ATATCAAACCAGAATGTCATATTTCCATAAACAT
1 ATATCATATCAGAATGTCATATTTCCATAAACAT
* * * * *
41411845 A-AACTAGATCAGAGTGTCATATTTTCATAAATAT
1 ATATC-ATATCAGAATGTCATATTTCCATAAACAT
*
41411879 ATATCATATCAGAATGTTATAT
1 ATATCATATCAGAATGTCATAT
41411901 CAGATCAAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
33 2 0.03
34 68 0.94
35 2 0.03
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.32
Consensus pattern (34 bp):
ATATCATATCAGAATGTCATATTTCCATAAACAT
Found at i:41412607 original size:23 final size:23
Alignment explanation
Indices: 41412547--41412609 Score: 90
Period size: 25 Copynumber: 2.7 Consensus size: 23
41412537 TGAGCTATGA
*
41412547 ATTCCACTGTTGCTAGTAAAGTC
1 ATTCCACTGTTGCTAGTAAAGCC
*
41412570 ATGTCATACTGTTGCTAGTAAAGCC
1 AT-TC-CACTGTTGCTAGTAAAGCC
41412595 ATTCCACTGTTGCTA
1 ATTCCACTGTTGCTA
41412610 CAATATGGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.34
24 4 0.11
25 19 0.54
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (23 bp):
ATTCCACTGTTGCTAGTAAAGCC
Found at i:41416206 original size:22 final size:23
Alignment explanation
Indices: 41416178--41416224 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
41416168 TAACGGTGTT
*
41416178 AATAACTAGA-TCCAAAAAATAA
1 AATAACTAAATTCCAAAAAATAA
*
41416200 AATAACTAAATTCCTAAAAATAA
1 AATAACTAAATTCCAAAAAATAA
41416223 AA
1 AA
41416225 ATATAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.21
Consensus pattern (23 bp):
AATAACTAAATTCCAAAAAATAA
Found at i:41416227 original size:29 final size:28
Alignment explanation
Indices: 41416192--41416250 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
41416182 ACTAGATCCA
41416192 AAAAATAAAATAACTAAATTCCTAAAAAT
1 AAAAATAAAATAACTAAATTCC-AAAAAT
* * * *
41416221 AAAAATATAATCATTAAATTCCAAATAT
1 AAAAATAAAATAACTAAATTCCAAAAAT
41416249 AA
1 AA
41416251 GAATTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAAATAAAATAACTAAATTCCAAAAAT
Found at i:41422616 original size:39 final size:39
Alignment explanation
Indices: 41422555--41422634 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
41422545 GTGTTACAAT
* * *
41422555 TTATATTAAAAAATTACCATAAATGTAATAAATA-TTTTA
1 TTATATTAAAAAATCACAATAAATATAATAAA-AGTTTTA
41422594 TTATATTAAAAAA-CACAAATAAATATAATAAAAGTTTTA
1 TTATATTAAAAAATCAC-AATAAATATAATAAAAGTTTTA
41422633 TT
1 TT
41422635 GTATCAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 3 0.08
39 33 0.92
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.39
Consensus pattern (39 bp):
TTATATTAAAAAATCACAATAAATATAATAAAAGTTTTA
Found at i:41427252 original size:21 final size:21
Alignment explanation
Indices: 41427222--41427261 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41427212 TTAATGCTAA
41427222 TATTAATATAAAATTTAAATT
1 TATTAATATAAAATTTAAATT
* *
41427243 TATTACTATAAATTTTAAA
1 TATTAATATAAAATTTAAA
41427262 AATTTTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTAATATAAAATTTAAATT
Found at i:41427331 original size:21 final size:20
Alignment explanation
Indices: 41427275--41427323 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
41427265 TTTATGTATT
**
41427275 TTTATATATTTTTAAATTTA
1 TTTATATATTTTTAAAAATA
*
41427295 TTAATATATTTTTTAAAAATA
1 TTTATATA-TTTTTAAAAATA
41427316 TTTATATA
1 TTTATATA
41427324 CTTATTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATATTTTTAAAAATA
Found at i:41427337 original size:50 final size:50
Alignment explanation
Indices: 41427235--41427338 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
41427225 TAATATAAAA
* * *
41427235 TTTAAATTTATTACTATAAATTTTAAAAATTTTATGTATTTTTATATATT
1 TTTAAATTTATTAATATAAATTTTAAAAATTTTATATATTATTATATATT
** *
41427285 TTTAAATTTATTAATATATTTTTTAAAAATATTTATATACTTATTA-ATTTT
1 TTTAAATTTATTAATATAAATTTTAAAAAT-TTTATATA-TTATTATATATT
41427336 TTT
1 TTT
41427339 TAGAATTGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 27 0.59
51 14 0.30
52 5 0.11
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (50 bp):
TTTAAATTTATTAATATAAATTTTAAAAATTTTATATATTATTATATATT
Found at i:41428510 original size:98 final size:98
Alignment explanation
Indices: 41428336--41428532 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
41428326 GTACAATAAA
*
41428336 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * *
41428401 CCTCTAGAATCCTAAACTCGGAATATTTCTTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
*
41428434 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
41428499 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
41428532 A
1 A
41428533 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:41430050 original size:19 final size:19
Alignment explanation
Indices: 41429994--41430148 Score: 139
Period size: 19 Copynumber: 7.8 Consensus size: 19
41429984 AAATTAAATC
*
41429994 TCTAAGATTACAAAATCATATA
1 TCTAAGATTAC-ATATC--ATA
* *
41430016 TTCTAATATTGCATATCATA
1 -TCTAAGATTACATATCATA
*
41430036 TCTAAGATTATATATCATA
1 TCTAAGATTACATATCATA
*
41430055 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
41430074 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
41430095 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
* * *
41430114 TCTAGGATTGCATATTATA
1 TCTAAGATTACATATCATA
* * *
41430133 TATAATATTGCATATC
1 TCTAAGATTACATATC
41430149 CTCAAAAATT
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
19 79 0.71
20 3 0.03
21 17 0.15
22 4 0.04
23 9 0.08
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:41430100 original size:40 final size:40
Alignment explanation
Indices: 41430017--41430148 Score: 200
Period size: 38 Copynumber: 3.4 Consensus size: 40
41430007 AATCATATAT
*
41430017 TCTAATATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
41430055 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
*
41430095 TCTAAGATTGCATATCATATCTAGGATTGCATAT-T-ATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
* *
41430133 TATAATATTGCATATC
1 TCTAAGATTGCATATC
41430149 CTCAAAAATT
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
38 44 0.50
39 1 0.01
40 43 0.49
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:41430100 original size:59 final size:59
Alignment explanation
Indices: 41430028--41430147 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 59
41430018 CTAATATTGC
* *
41430028 ATATCATATCTAAGATTATATATCATATCTAAGATTGCATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATATATAAGATTGCAT
* * * *
41430087 ATATCATATCTAAGATTGCATATCATATCTAGGATTGCATATTATATATAATATTGCAT
1 ATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATATATAAGATTGCAT
41430146 AT
1 AT
41430148 CCTCAAAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (59 bp):
ATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATATATAAGATTGCAT
Found at i:41430380 original size:44 final size:43
Alignment explanation
Indices: 41430324--41430836 Score: 289
Period size: 44 Copynumber: 11.8 Consensus size: 43
41430314 TGCCATCTTC
41430324 AGTCTGC-CTCACTGCAACTTCAGGAGGATAAGACTTGCTTATTT
1 AGTCTGCTC-CACTGCAACTTCAGGAGGATAAGACTTGC-TATTT
* * * * *
41430368 AGTCTACTTCACTGCAACTTCAGGAAGATAAGACTAG--A-TG
1 AGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGCTATTT
* * * *
41430408 CGATCTGCT-CTCTGCAACTTCA-GAGAGATAAGATCTAAGGT-TTT
1 AG-TCTGCTCCACTGCAACTTCAGGAG-GATAAGA-CT-TGCTATTT
* * * * * *
41430452 AATCCGCCCCACTGCAACTTCAAGGA-GATAGGATTATCGGC--GTT
1 AGTCTGCTCCACTGCAACTTC-AGGAGGATAAGACT-T--GCTATTT
* *
41430496 AATCTGCTCCACTGCAACTTCAGG-GAGATAAGACTTGCCATCTT
1 AGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACTTGCTAT-TT
* *
41430540 CAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT
1 -AGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGC-TATTT
* *
41430585 AGTCTGCTCCACTGCAACTTCAGG-GAGATAAGACTAG--A-TG
1 AGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACTTGCTATTT
* * * * *
41430625 CGATCTGCT-CTCTGCAAATTCA-GAGAGATAAGATCTGAGGT-TTT
1 AG-TCTGCTCCACTGCAACTTCAGGAG-GATAAGA-CT-TGCTATTT
* * * * *
41430669 AATCCGCTCCAATGCAACTTCAGG-GAGATAGGATTATCGGC--TTT
1 AGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACT-T--GCTATTT
* *
41430713 AATCTGCTCCACTGCAACTTCAGG-GAGATAAGACTTGCGATCTCT
1 AGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACTTGCTAT-T-T
* * *
41430758 AGTCTGCCCCACTGCAACTTTAGGAGGATAAGACTTGCTTACTT
1 AGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGC-TATTT
41430802 AGTCTGCTCCACTGCAACTTCAGG-GAGATAAGACT
1 AGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACT
41430837 AGATGCGATC
Statistics
Matches: 371, Mismatches: 58, Indels: 80
0.73 0.11 0.16
Matches are distributed among these distances:
39 3 0.01
40 43 0.12
41 21 0.06
42 4 0.01
43 20 0.05
44 199 0.54
45 75 0.20
46 6 0.02
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (43 bp):
AGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGCTATTT
Found at i:41430595 original size:89 final size:88
Alignment explanation
Indices: 41430324--41430836 Score: 305
Period size: 89 Copynumber: 5.9 Consensus size: 88
41430314 TGCCATCTTC
* * * * **
41430324 AGTCTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTATTTAGTCTACTTCACTGCAACT
1 AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCATCTTCAGTCTGCCCCACTGCAACT
* * * * *
41430387 TCAGGAAGATAAGACTAG-ATGC-G
64 TCAGGGAGATAAGACTTGCTTACTT
* * * * * * *
41430410 A-TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAG-GT-TTTAATCCGCCCCACTGCAACT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCATCTTCAGTCTGCCCCACTGCAACT
* * * **
41430471 TCAAGGAGATAGGA-TT-ATCGGCGTT
64 TCAGGGAGATAAGACTTGCT-TAC-TT
*
41430496 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATCTTCAGTCTGCCCCACTGCAACTT
41430561 CA-GGAGGATAAGACTTGCTTACTT
65 CAGGGA-GATAAGACTTGCTTACTT
* * * * *
41430585 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-A--TGC-GATCTG-CTCTCTGCAAATT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAG-TCTGCCCCACTGCAACTT
* * *
41430645 CAGAGAGATAAGATCTGAGGTT--TT
65 CAGGGAGATAAGA-CT-TGCTTACTT
* * * * * ** * * *
41430669 AATCCGCTCCAATGCAACTTCAGGGAGATAGGA-TTATCGGCTTTAATCTGCTCCACTGCAACTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCATCTTCAGTCTGCCCCACTGCAACTT
*
41430733 CAGGGAGATAAGACTTGC-GATCTCT
65 CAGGGAGATAAGACTTGCTTA-CT-T
* * * *
41430758 AGTCTGCCCCACTGCAACTTTA-GGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACT
1 AGTCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCAT-CTTCAGTCTGCCCCACTGCAACT
41430821 TCAGGGAGATAAGACT
64 TCAGGGAGATAAGACT
41430837 AGATGCGATC
Statistics
Matches: 330, Mismatches: 64, Indels: 63
0.72 0.14 0.14
Matches are distributed among these distances:
83 2 0.01
84 100 0.30
85 20 0.06
86 8 0.02
87 16 0.05
88 51 0.15
89 124 0.38
90 8 0.02
91 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (88 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAGTCTGCCCCACTGCAACTTC
AGGGAGATAAGACTTGCTTACTT
Found at i:41430689 original size:217 final size:217
Alignment explanation
Indices: 41430314--41430915 Score: 999
Period size: 217 Copynumber: 2.8 Consensus size: 217
41430304 TAGGAATTAG
* * * *
41430314 TGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTACTTCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
*
41430379 CTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
* * *
41430444 AAGGTTTTAATCCGCCCCACTGCAACTTCAAGGAGATAGGATTATCGGCGTTAATCTGCTCCACT
131 GAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCGTTAATCTGCTCCACT
41430509 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
41430531 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
*
41430596 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAAATTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
* *
41430661 GAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
131 GAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCGTTAATCTGCTCCACT
41430726 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
* *
41430748 TGCGATC-TCTAGTCTGCCCCACTGCAACTTTAGGAGGATAAGACTTGCTTACTTAGTCTGCTCC
1 TGCCATCTTC-AGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCC
* * * * * *
41430812 ACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTATCTACAACTTCAAAAAGATAAGATT
65 ACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATC
* *
41430877 TGAGGTTTTAATTCACTCCACTGCAACTTCAGGGAGATA
130 TGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
41430916 AGACTTGCCA
Statistics
Matches: 361, Mismatches: 23, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
216 2 0.01
217 359 0.99
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
GAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCGTTAATCTGCTCCACT
GCAACTTCAGGGAGATAAGACT
Found at i:41431047 original size:132 final size:131
Alignment explanation
Indices: 41430907--41431559 Score: 1081
Period size: 132 Copynumber: 4.9 Consensus size: 131
41430897 CTGCAACTTC
* * * * *
41430907 AGGGAGATAAGACTTGCCATCTTCAACCTTCTCCGCTGCTGCTTAGGGATACAAGGCTTAGTGGC
1 AGGGAGATAAGA-TTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
* *
41430972 TTAAATCTGCTTCCCACTATCTTGGAAAGAAAAGATTCGCCATCTTCGATCTGCTCCACTACTGC
65 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
41431037 TT
130 TT
41431039 AGGGAGATAAGATTTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGA-TTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
*
41431104 TTAAATCTGCTTTCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
65 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
41431169 TT
130 TT
* * *
41431171 AGGGAGATAAGATCTACAATCTTCAACCTTCTCTGCTGCTGCTGAGAGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGAT-TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
* *
41431236 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGT
65 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
41431301 TT
130 TT
* * * *
41431303 AGGGAGATAAGATCTACAATCTTTAACCTTCTCCGCTACTGCTCAGAGAGACAATGCTTGGTGGC
1 AGGGAGATAAGAT-TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
**
41431368 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCATCGTCTTCGATCTGCTCCACTACTGC
65 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
41431433 TT
130 TT
*
41431435 AGAGAGATAAGATTTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGA-TTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
41431500 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
65 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
41431560 GTCAATGCAA
Statistics
Matches: 488, Mismatches: 31, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 486 1.00
133 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (131 bp):
AGGGAGATAAGATTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
T
Found at i:41431458 original size:44 final size:44
Alignment explanation
Indices: 41431014--41431460 Score: 163
Period size: 44 Copynumber: 10.2 Consensus size: 44
41431004 AGATTCGCCA
* * *
41431014 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATTTACAG
* * * * * * * ** ***
41431058 TCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATTTACAG
* * * * ** *
41431102 GCTTAAATCTGCTTTCCACTA-T-CTTGGAAAGATAAGATTCGCCG
1 TCTTCAATCTGC--TCCACTACTGCTTAGAGAGATAAGATTTACAG
* * * *
41431146 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATTTACAG
* * ** * * * ** ***
41431190 TCTTCAACCTTCTCTGCTGCTGCTGAGAGAGACAAGGCTTGGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATTTACAG
* * * * ** *
41431234 GCTTAAATCTGCTTCCCACTA-T-CTTGGAAAGATAAGATTCGCTG
1 TCTTCAATCTGC-T-CCACTACTGCTTAGAGAGATAAGATTTACAG
* * * * *
41431278 TCTTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATTTACAG
* * * * * * * ***
41431322 TCTTTAACCTTCTCCGCTACTGCTCAGAGAGACAATG-CTTGGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAA-GATTTACAG
* * * * *
41431366 GCTTAAATCTGCTTCCCACTA-T-CTTGGAAAGATAAGATTCATC-G
1 TCTTCAATCTGC-T-CCACTACTGCTTAGAGAGATAAGATTTA-CAG
* *
41431410 TCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATTTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATTTACAG
41431454 TCTTCAA
1 TCTTCAA
41431461 CCTTCTCCGC
Statistics
Matches: 268, Mismatches: 119, Indels: 32
0.64 0.28 0.08
Matches are distributed among these distances:
42 19 0.07
43 7 0.03
44 223 0.83
45 6 0.02
46 13 0.05
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATTTACAG
Found at i:41433576 original size:180 final size:180
Alignment explanation
Indices: 41433274--41433626 Score: 625
Period size: 180 Copynumber: 2.0 Consensus size: 180
41433264 TGCACGTTCC
*
41433274 CTTCAGGCCACAATCTCCATTGTCCCCTTATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
1 CTTCAGGCCACAATCTCCATTGTCCCCTCATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
*
41433339 ACAAGTATGAAAATAGGCTACAATCTATGTCATCTTTAAAGTCATGAGATCCCTCTAAACACAGA
66 ACAAGTATGAAAATAGGCTACAATCTATGTCATCTTTAAAGCCATGAGATCCCTCTAAACACAGA
* * *
41433404 TCTCACTCAAAAGGAACTTCTGAGTTCGTAACAACATCACTCAAAAGGAA
131 TCCCAATCAAAAGGAACTTCTGAGTCCGTAACAACATCACTCAAAAGGAA
*
41433454 CTTCAGGCCATAATCTCCATTGTCCCCTCATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
1 CTTCAGGCCACAATCTCCATTGTCCCCTCATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
*
41433519 ACAAGTCTGAAAATAGGCTACAATCTATGTCATCTTTAAAGCCATGAGATCCCTCTAAACACAGA
66 ACAAGTATGAAAATAGGCTACAATCTATGTCATCTTTAAAGCCATGAGATCCCTCTAAACACAGA
* *
41433584 TCCCAATTAAAAGGAACTTCTGAGTCCGTAACAGCATCACTCA
131 TCCCAATCAAAAGGAACTTCTGAGTCCGTAACAACATCACTCA
41433627 TGTCATTGAT
Statistics
Matches: 164, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
180 164 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (180 bp):
CTTCAGGCCACAATCTCCATTGTCCCCTCATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
ACAAGTATGAAAATAGGCTACAATCTATGTCATCTTTAAAGCCATGAGATCCCTCTAAACACAGA
TCCCAATCAAAAGGAACTTCTGAGTCCGTAACAACATCACTCAAAAGGAA
Found at i:41437706 original size:98 final size:98
Alignment explanation
Indices: 41437534--41437730 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
41437524 ACAATAAAAC
* *
41437534 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACATCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* *
41437599 TCTAGAATCCCAAACTCGGAATATTTCCTTTAT
66 TCTAAAATCCCAAACACGGAATATTTCCTTTAT
* *
41437632 TTTAAAAGAACATCCACTTATCTAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
41437697 TTTAAAATCCCAAACACGGAATATTTCCTTTAT
66 TCTAAAATCCCAAACACGGAATATTTCCTTTAT
41437730 T
1 T
41437731 ATTTTTAAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.29
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACACGGAATATTTCCTTTAT
Found at i:41438429 original size:25 final size:26
Alignment explanation
Indices: 41438392--41438448 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
41438382 ATATACATAT
41438392 AAATAT-GAAAATATTC-ATT-AAAA
1 AAATATAGAAAATATTCGATTAAAAA
*
41438415 AAATATAGAAAAATATTCGTTTAAAAA
1 AAATATAG-AAAATATTCGATTAAAAA
41438442 AAATATA
1 AAATATA
41438449 TACATGTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 6 0.21
24 1 0.03
25 9 0.31
26 2 0.07
27 11 0.38
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (26 bp):
AAATATAGAAAATATTCGATTAAAAA
Found at i:41438548 original size:10 final size:10
Alignment explanation
Indices: 41438533--41438557 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41438523 AAAAAAATAA
41438533 ATATACATAT
1 ATATACATAT
41438543 ATATACATAT
1 ATATACATAT
41438553 ATATA
1 ATATA
41438558 TGAGAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATACATAT
Found at i:41439235 original size:19 final size:19
Alignment explanation
Indices: 41439211--41439302 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
41439201 AATCATATAT
41439211 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
41439230 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
41439249 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
41439268 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
41439287 TATAAGATTGCATATC
1 TCTAAGATTGCATATC
41439303 CTCAAAAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:41439258 original size:38 final size:38
Alignment explanation
Indices: 41439188--41439302 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 38
41439178 AAATTAAATC
*
41439188 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
*
41439230 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* * *
41439268 TCTAGGATTGCATATCATATATAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
41439303 CTCAAAAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 50 0.75
39 3 0.04
41 4 0.06
42 10 0.15
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:41439913 original size:80 final size:81
Alignment explanation
Indices: 41439820--41439968 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 81
41439810 AATAGGACCC
* * * * *
41439820 CACTTAATTATATTTAAAATTTAACAAAAAAATGATACTC-ACTTTGAACATAATTAAAA-ATAT
1 CACTTAATCATATTTAAAACTTAACAAAAAAATAAGA-TCAACTTTAAACATAATTAAAATATAT
41439883 ATATTACAGATAGGATT
65 ATATTACAGATAGGATT
*** *
41439900 CACTTAATCATATTTAAAACTTAATTTAAAAATAAGATCAACTTTAAATATAATTAAAATATATA
1 CACTTAATCATATTTAAAACTTAACAAAAAAATAAGATCAACTTTAAACATAATTAAAATATATA
41439965 TATT
66 TATT
41439969 TTGGAACTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
79 2 0.03
80 47 0.81
81 9 0.16
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (81 bp):
CACTTAATCATATTTAAAACTTAACAAAAAAATAAGATCAACTTTAAACATAATTAAAATATATA
TATTACAGATAGGATT
Found at i:41458760 original size:21 final size:20
Alignment explanation
Indices: 41458736--41458780 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
41458726 TAACTTAAGG
41458736 GAAACAATCTTAAAATCGAGT
1 GAAACAAT-TTAAAATCGAGT
* * *
41458757 GAAACAGTTTTAAATCGATT
1 GAAACAATTTAAAATCGAGT
41458777 GAAA
1 GAAA
41458781 ATTTTTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (20 bp):
GAAACAATTTAAAATCGAGT
Found at i:41460212 original size:12 final size:10
Alignment explanation
Indices: 41460167--41460209 Score: 59
Period size: 11 Copynumber: 4.0 Consensus size: 10
41460157 AACTAAATCC
41460167 TTTCTCTCAA
1 TTTCTCTCAA
41460177 TTTCTCTCTAA
1 TTTCTCTC-AA
41460188 TATTCTCTCAA
1 T-TTCTCTCAA
41460199 TTTCCTCTCAA
1 TTT-CTCTCAA
41460210 ATTCCTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.33
11 13 0.43
12 7 0.23
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:41460246 original size:11 final size:11
Alignment explanation
Indices: 41460232--41460287 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
41460222 AAAAACTTTA
41460232 ATTTTTAAATT
1 ATTTTTAAATT
*
41460243 ATTTTTAAA-A
1 ATTTTTAAATT
*
41460253 AGTTTTAAATTTT
1 ATTTTTAAA--TT
41460266 ATTTTTTAAATT
1 A-TTTTTAAATT
*
41460278 TTTTTTAAAT
1 ATTTTTAAAT
41460288 CGTAAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 8 0.22
11 18 0.50
12 2 0.06
13 1 0.03
14 7 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
ATTTTTAAATT
Found at i:41460279 original size:21 final size:19
Alignment explanation
Indices: 41460228--41460279 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
41460218 TTAAAAAAAC
*
41460228 TTTAATTTTTAAATTATTT
1 TTTAAATTTTAAATTATTT
*
41460247 TTAAAAAGTTTTAAATTTTATTT
1 TT-TAAA-TTTTAAA--TTATTT
41460270 TTTAAATTTT
1 TTTAAATTTT
41460280 TTTTAAATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 11 0.42
22 3 0.12
23 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTAAATTTTAAATTATTT
Found at i:41460281 original size:23 final size:21
Alignment explanation
Indices: 41460231--41460281 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
41460221 AAAAAACTTT
41460231 AATTTTTAAATTATTTTTAAA
1 AATTTTTAAATTATTTTTAAA
* *
41460252 AAGTTTTAAATTTTATTTTTTAA
1 AATTTTTAAA--TTATTTTTAAA
*
41460275 ATTTTTT
1 AATTTTT
41460282 TTAAATCGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 9 0.38
23 15 0.62
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
AATTTTTAAATTATTTTTAAA
Found at i:41460283 original size:13 final size:14
Alignment explanation
Indices: 41460255--41460283 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41460245 TTTTAAAAAG
41460255 TTTTAAATTTTATT
1 TTTTAAATTTTATT
41460269 TTTTAAATTTT-TT
1 TTTTAAATTTTATT
41460282 TT
1 TT
41460284 AAATCGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTAAATTTTATT
Found at i:41463621 original size:96 final size:95
Alignment explanation
Indices: 41463457--41463736 Score: 357
Period size: 95 Copynumber: 2.9 Consensus size: 95
41463447 AGTAACCCTA
* * *
41463457 AACCCCAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTT-AATTTTTTCTTAAAAACCCTAAACACTAAA-CCTAATCTAAT
*
41463522 TTTTTAAAAATTTATAATTAATTTACTCAAGT
64 TTTTAAAAAATTTATAATTAATTTACTCAAGT
* * * *
41463554 AACCCTGAACCCTAATTTATTTAATTTTTTCATAAAAACCCTTAACTCTAAACTCTAATCTAATT
1 AACCCTAAACCCTAATTTATTTAATTTTTTCTTAAAAACCCTAAACACTAAAC-CTAATCTAATT
* *
41463619 TTTAAAAAAATT-TAATTAAATTACTCAAGT
65 TTTAAAAAATTTATAATTAATTTACTCAAGT
* ** ** * *
41463649 AACCCTAAACCCTAATTTAATTGCTTTTTTCTTAAAAAACAATAAACACGAAACCTAATCCAA-T
1 AACCCTAAACCCTAATTTATTTAATTTTTTCTT-AAAAACCCTAAACACTAAACCTAATCTAATT
41463713 TTTAAAAAATTTATAATTAATTTA
65 TTTAAAAAATTTATAATTAATTTA
41463737 ATTGACAAAC
Statistics
Matches: 157, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
94 12 0.08
95 64 0.41
96 61 0.39
97 20 0.13
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (95 bp):
AACCCTAAACCCTAATTTATTTAATTTTTTCTTAAAAACCCTAAACACTAAACCTAATCTAATTT
TTAAAAAATTTATAATTAATTTACTCAAGT
Found at i:41463662 original size:95 final size:96
Alignment explanation
Indices: 41463457--41463732 Score: 342
Period size: 96 Copynumber: 2.9 Consensus size: 96
41463447 AGTAACCCTA
* * *
41463457 AACCCCAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTT-AATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAAT
* * *
41463522 TTTTTAAAAATTTATAATTAATTTACTCAAGT
65 TTTTAAAAAAATTATAATTAAATTACTCAAGT
* * * * *
41463554 AACCCTGAACCCTAATTTATTTAATTTTTTCATAAAAACCCTTAACTCTAAACTCTAATCTAATT
1 AACCCTAAACCCTAATTTATTTAATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATT
41463619 TTTAAAAAAATT-TAATTAAATTACTCAAGT
66 TTTAAAAAAATTATAATTAAATTACTCAAGT
* ** ** * *
41463649 AACCCTAAACCCTAATTTAATTGCTTTTTTCTTAAAAAACAATAAACACGAAA-CCTAATCCAA-
1 AACCCTAAACCCTAATTTATTTAATTTTTTCTT-AAAAACCCTAAACACTAAACCCTAATCTAAT
*
41463712 TTTTAAAAAATTTATAATTAA
65 TTTTAAAAAAATTATAATTAA
41463733 TTTAATTGAC
Statistics
Matches: 153, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
94 12 0.08
95 60 0.39
96 61 0.40
97 20 0.13
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (96 bp):
AACCCTAAACCCTAATTTATTTAATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATT
TTTAAAAAAATTATAATTAAATTACTCAAGT
Found at i:41465987 original size:20 final size:19
Alignment explanation
Indices: 41465950--41465988 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
41465940 TTTTTGGGTG
*
41465950 ATTTAATAGAGAAGTAAAA
1 ATTTAATAGAGAACTAAAA
*
41465969 ATTTAAATAGAGGACTAAAA
1 ATTT-AATAGAGAACTAAAA
41465989 TGATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (19 bp):
ATTTAATAGAGAACTAAAA
Found at i:41467048 original size:23 final size:24
Alignment explanation
Indices: 41466993--41467048 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
41466983 TTGATTTGTA
* *
41466993 ATATATCATTATTTCAAATTTATC
1 ATATATTATTATTTCAAACTTATC
*
41467017 ATGTATTATTATTT-AAACTTATC
1 ATATATTATTATTTCAAACTTATC
*
41467040 ATATTTTAT
1 ATATATTAT
41467049 GTAAATTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATATTATTATTTCAAACTTATC
Found at i:41467641 original size:52 final size:52
Alignment explanation
Indices: 41467578--41467681 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
41467568 GTCTATTTCG
41467578 AACTTTCGCATATATTATTTATTTTTATACTTTTTGGATTTACAATTTCCTT
1 AACTTTCGCATATATTATTTATTTTTATACTTTTTGGATTTACAATTTCCTT
41467630 AACTTTCGCATATATTATTTATTTTTATACTTTTTGGATTTACAATTTCCTT
1 AACTTTCGCATATATTATTTATTTTTATACTTTTTGGATTTACAATTTCCTT
41467682 TCTTCCATGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.25, C:0.13, G:0.06, T:0.56
Consensus pattern (52 bp):
AACTTTCGCATATATTATTTATTTTTATACTTTTTGGATTTACAATTTCCTT
Found at i:41467677 original size:28 final size:28
Alignment explanation
Indices: 41467594--41467677 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 28
41467584 CGCATATATT
41467594 ATTTATTTTTATACTTTTTGGATTTACA
1 ATTTATTTTTATACTTTTTGGATTTACA
** * * * **
41467622 A-TT-TCCTTA-AC-TTTCGCATATATT
1 ATTTATTTTTATACTTTTTGGATTTACA
41467646 ATTTATTTTTATACTTTTTGGATTTACA
1 ATTTATTTTTATACTTTTTGGATTTACA
41467674 ATTT
1 ATTT
41467678 CCTTTCTTCC
Statistics
Matches: 38, Mismatches: 14, Indels: 8
0.63 0.23 0.13
Matches are distributed among these distances:
24 9 0.24
25 4 0.11
26 8 0.21
27 4 0.11
28 13 0.34
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (28 bp):
ATTTATTTTTATACTTTTTGGATTTACA
Found at i:41472939 original size:3 final size:3
Alignment explanation
Indices: 41472931--41473011 Score: 90
Period size: 3 Copynumber: 27.0 Consensus size: 3
41472921 TTTTTTAGCT
* *
41472931 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
41472979 TTG TTG TTG TTA TTA TCA ATA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41473012 ATTTTATTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:41473217 original size:17 final size:17
Alignment explanation
Indices: 41473195--41473230 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
41473185 TTTATTTACG
41473195 TTTCATTATTGA-TATTA
1 TTTCATTATT-ATTATTA
41473212 TTTCATTATTATTATTA
1 TTTCATTATTATTATTA
41473229 TT
1 TT
41473231 ATTGTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTCATTATTATTATTA
Found at i:41496489 original size:50 final size:50
Alignment explanation
Indices: 41496364--41496807 Score: 301
Period size: 50 Copynumber: 9.0 Consensus size: 50
41496354 AAACCATAGT
* * * * ** *
41496364 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT--TTGGCA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACA
* ** * * * *
41496412 ATGCAGCGGAACAGATTGAAGCTACAACAGCAAATCTCACTTCCCCGACA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACA
* * * * **
41496462 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT-CTGGTA-A
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCCG-ACA
*** * * * *
41496511 -TGCAACGGAACATATTGAAGCTACAACAGCGAATCTCACTTCCCCGACA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACA
* * * *** **
41496560 TTGCAATTTAAAAGATCGAAGCCACAAC-GACGAATCTTACTT-TTGGGGA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAG-CGAATCTTACTTCCCCGACA
** * * * *
41496609 -TGCAGCGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACA
* * * *
41496658 TTGCAGTTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACA
** * * * *
41496708 TTGCAGCGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACA
* * * * * *
41496758 TTGCAGTTTAAAGGATCGAAGCCACAACGGCGAATCTTATTTCCTCGACA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACA
41496808 AGACCGGGCA
Statistics
Matches: 292, Mismatches: 94, Indels: 18
0.72 0.23 0.04
Matches are distributed among these distances:
48 95 0.33
49 12 0.04
50 185 0.63
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (50 bp):
TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACA
Found at i:41496533 original size:98 final size:98
Alignment explanation
Indices: 41496364--41496796 Score: 650
Period size: 98 Copynumber: 4.4 Consensus size: 98
41496354 AAACCATAGT
*
41496364 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTTGGCAATGCAGCGGAACAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCAATGCAGCGGAACAGATT
*
41496429 GAAGCTACAACAGCAAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * *
41496462 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGTAATGCAACGGAACATATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCAATGCAGCGGAACAGATT
41496527 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * **
41496560 TTGCAATTTAAAAGATCGAAGCCACAACGACGAATCTTACTTTTGGGGATGCAGCGGAACAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCAATGCAGCGGAACAGATT
* * *
41496625 GAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * * * *
41496658 TTGCAGTTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCATTGCAGCGGAACAGA
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT--CTGGCAATGCAGCGGAACAGA
* * *
41496723 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
64 TTGAAGCTACAACAGCGAATCTCACTTCCCCGACA
* *
41496758 TTGCAGTTTAAAGGATCGAAGCCACAACGGCGAATCTTA
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTA
41496797 TTTCCTCGAC
Statistics
Matches: 307, Mismatches: 26, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
98 220 0.72
100 87 0.28
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (98 bp):
TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCAATGCAGCGGAACAGATT
GAAGCTACAACAGCGAATCTCACTTCCCCGACA
Found at i:41497657 original size:10 final size:10
Alignment explanation
Indices: 41497618--41497657 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
41497608 CTCTGTTCTC
41497618 TTTTCTTATTT
1 TTTTCTT-TTT
* *
41497629 CTTTCTTTAT
1 TTTTCTTTTT
41497639 TTTTCTTTTT
1 TTTTCTTTTT
41497649 TTTTCTTTT
1 TTTTCTTTT
41497658 CATTAGAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 19 0.76
11 6 0.24
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:41498379 original size:17 final size:17
Alignment explanation
Indices: 41498347--41498391 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
41498337 TTTATTTACG
41498347 TTTCATTATTGA-TATTA
1 TTTCATTATT-ATTATTA
*
41498364 TTTCATTATTATTATTG
1 TTTCATTATTATTATTA
41498381 TTT--TTATTATT
1 TTTCATTATTATT
41498392 TATTCTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 8 0.31
16 1 0.04
17 17 0.65
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTCATTATTATTATTA
Found at i:41504157 original size:27 final size:26
Alignment explanation
Indices: 41504116--41504229 Score: 93
Period size: 27 Copynumber: 4.2 Consensus size: 26
41504106 AAAAGGCAAC
* *
41504116 AAAGAATATTCTTTGTGGCGAACTCTG
1 AAAGAATA-ACTTTGTGGCGAACTCTA
* ** *
41504143 AAAGAATAACTTTTGCGGTAAATTCTA
1 AAAGAATAAC-TTTGTGGCGAACTCTA
* *
41504170 AAAGAATAAACTCTATGGCGAACTCTA
1 AAAGAAT-AACTTTGTGGCGAACTCTA
* **
41504197 AAAGAATAGCCTTTGTCACGAACTCTA
1 AAAGAATA-ACTTTGTGGCGAACTCTA
41504224 AAAGAA
1 AAAGAA
41504230 CTCTAAAAGA
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
26 2 0.03
27 62 0.93
28 3 0.04
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (26 bp):
AAAGAATAACTTTGTGGCGAACTCTA
Found at i:41504247 original size:14 final size:11
Alignment explanation
Indices: 41504216--41504240 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41504206 CCTTTGTCAC
41504216 GAACTCTAAAA
1 GAACTCTAAAA
41504227 GAACTCTAAAA
1 GAACTCTAAAA
41504238 GAA
1 GAA
41504241 TAACTCTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (11 bp):
GAACTCTAAAA
Found at i:41508128 original size:18 final size:19
Alignment explanation
Indices: 41508105--41508145 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
41508095 CAATTTCCCA
*
41508105 AAATAAATATTACTT-ATT
1 AAATAAATATTAATTAATT
*
41508123 AAATAAATTTTAATTAATT
1 AAATAAATATTAATTAATT
41508142 AAAT
1 AAAT
41508146 TTTCAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAAATATTAATTAATT
Found at i:41508155 original size:16 final size:16
Alignment explanation
Indices: 41508120--41508164 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
41508110 AATATTACTT
41508120 ATTAAATAAATTTT-A
1 ATTAAATAAATTTTCA
*
41508135 ATTAATTAAATTTTCA
1 ATTAAATAAATTTTCA
41508151 ATTAAAT-AATTTTC
1 ATTAAATAAATTTTC
41508165 TCAATCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAATAAATTTTCA
Found at i:41521517 original size:24 final size:24
Alignment explanation
Indices: 41521468--41521514 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
41521458 TATCAATTTA
*
41521468 TTTATTACATAAATTATTATTAAT
1 TTTATTAAATAAATTATTATTAAT
41521492 TTTATTTAAATAAA-TATTGATTA
1 TTTA-TTAAATAAATTATT-ATTA
41521515 TTTAATTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTATTAAATAAATTATTATTAAT
Found at i:41523034 original size:22 final size:22
Alignment explanation
Indices: 41522991--41523061 Score: 83
Period size: 22 Copynumber: 3.1 Consensus size: 22
41522981 TTCACAAACT
41522991 AATTCTCTCTCAAATTTTCTCTCA
1 AATTC-CTCTCAAA-TTTCTCTCA
*
41523015 ATTTCCTCTC-AATTTGCTCTCA
1 AATTCCTCTCAAATTT-CTCTCA
41523037 AATTCCT-TCCAAATTTCTCTCA
1 AATTCCTCT-CAAATTTCTCTCA
41523059 AAT
1 AAT
41523062 CCATATTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.10
22 24 0.57
23 10 0.24
24 4 0.10
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.44
Consensus pattern (22 bp):
AATTCCTCTCAAATTTCTCTCA
Found at i:41523060 original size:11 final size:11
Alignment explanation
Indices: 41522991--41523061 Score: 67
Period size: 11 Copynumber: 6.3 Consensus size: 11
41522981 TTCACAAACT
41522991 AATTCTCTCTCA
1 AATT-TCTCTCA
41523003 AATTTTCTCTC-
1 AA-TTTCTCTCA
41523014 AATTTCCTCTC-
1 AATTT-CTCTCA
41523025 AATTTGCTCTCA
1 AATTT-CTCTCA
*
41523037 AATTCCT-TCCA
1 AATTTCTCT-CA
41523048 AATTTCTCTCA
1 AATTTCTCTCA
41523059 AAT
1 AAT
41523062 CCATATTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
10 4 0.08
11 32 0.63
12 13 0.25
13 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.44
Consensus pattern (11 bp):
AATTTCTCTCA
Found at i:41523086 original size:51 final size:50
Alignment explanation
Indices: 41523021--41523119 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 50
41523011 CTCAATTTCC
41523021 TCTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAATTTCTCTCAAATCC-TATTTAA
* * * * *
41523072 TCTCAATTTTCTCTCAAGTTCCTCTTAGATTTCTCTTAAATCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCTATTT
41523120 TTAAATATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 5 0.12
51 36 0.86
52 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.03, T:0.45
Consensus pattern (50 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCTATTTAA
Found at i:41523130 original size:10 final size:10
Alignment explanation
Indices: 41523115--41523154 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
41523105 TCTTAAATCC
41523115 TATTTTTAAA
1 TATTTTTAAA
41523125 TATTTTTAAA
1 TATTTTTAAA
* *
41523135 AATTTTTTAA
1 TATTTTTAAA
*
41523145 TTTTTTTAAA
1 TATTTTTAAA
41523155 CCGTAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:41523141 original size:20 final size:20
Alignment explanation
Indices: 41523116--41523154 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41523106 CTTAAATCCT
41523116 ATTTTTAAATATTTTTAAAA
1 ATTTTTAAATATTTTTAAAA
* *
41523136 ATTTTTTAATTTTTTTAAA
1 ATTTTTAAATATTTTTAAA
41523155 CCGTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTAAATATTTTTAAAA
Found at i:41524935 original size:18 final size:18
Alignment explanation
Indices: 41524908--41524947 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41524898 CAGGTGCGTT
* *
41524908 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
41524926 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
41524944 TCCT
1 TCCT
41524948 TTTCCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:41525529 original size:43 final size:42
Alignment explanation
Indices: 41525482--41525836 Score: 273
Period size: 43 Copynumber: 8.0 Consensus size: 42
41525472 TTTAATTGGC
* *
41525482 AAACCCCAACCCTTAACTTAAAAATCATAACACCTTAACCTAA
1 AAACCCCAACCCTTAACTTAAAAACCCTAAC-CCTTAACCTAA
41525525 AAACCCTAACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAA
1 AAA--C---CCC-AACCCTTAACTTAAAAACCCTAAC-CCTTAACCTAA
41525574 AAACCCCAACGCTAACCGTTAACTT-AAAACCTCTAACCCCTTAACCTAA
1 AAACCCCAA--C---CC-TTAACTTAAAAACC-CTAA-CCCTTAACCTAA
* * *
41525623 AAACCCTAACCCTTAACTTAAAAACCCTAGCCCATTCACCTAA
1 AAACCCCAACCCTTAACTTAAAAACCCTAACCC-TTAACCTAA
* ** * * *
41525666 AAATCATAACCCTTAACTTTAAAACCATAACCCTTAACTTAA
1 AAACCCCAACCCTTAACTTAAAAACCCTAACCCTTAACCTAA
* * * * ** **
41525708 AAACCCTAAACTCTTTACTTTAAAACTGTAACCCTTAAATTAA
1 AAACCC-CAACCCTTAACTTAAAAACCCTAACCCTTAACCTAA
* * ** *
41525751 AAACCCTAAACCCTTAACTTTAAAACTGTAACCCTTAA-ATAAA
1 AAACCC-CAACCCTTAACTTAAAAACCCTAACCCTTAACCT-AA
* * *
41525794 AAACCCTAACACTTAACTTAAAAACCCTAACCCTTAACTTAA
1 AAACCCCAACCCTTAACTTAAAAACCCTAACCCTTAACCTAA
41525836 A
1 A
41525837 TATAATTTGA
Statistics
Matches: 264, Mismatches: 29, Indels: 39
0.80 0.09 0.12
Matches are distributed among these distances:
42 44 0.17
43 126 0.48
44 11 0.04
45 2 0.01
47 2 0.01
48 11 0.04
49 67 0.25
50 1 0.00
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.24
Consensus pattern (42 bp):
AAACCCCAACCCTTAACTTAAAAACCCTAACCCTTAACCTAA
Found at i:41525557 original size:21 final size:21
Alignment explanation
Indices: 41525482--41525836 Score: 298
Period size: 21 Copynumber: 16.0 Consensus size: 21
41525472 TTTAATTGGC
*
41525482 AAACCCCAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* * *
41525503 AAATCATAACACCTTAACCTAAAA
1 AAACCCTAAC-CCTTAA-CT-TAA
41525527 ACCCTAACCCTAACCCTTAACTTAA
1 A----AACCCTAACCCTTAACTTAA
*
41525552 AAACCCTAACACCTTAACCTAA
1 AAACCCTAAC-CCTTAACTTAA
*
41525574 AAACCCCAACGCTAACCGTTAACTT-A
1 AAA---C--C-CTAACCCTTAACTTAA
*
41525600 AAACCTCTAACCCCTTAACCTAA
1 AAACC-CTAA-CCCTTAACTTAA
41525623 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* * *
41525644 AAACCCTAGCCCATTCACCTAA
1 AAACCCTAACCC-TTAACTTAA
* * *
41525666 AAATCATAACCCTTAACTTTA
1 AAACCCTAACCCTTAACTTAA
*
41525687 AAACCATAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* * *
41525708 AAACCCTAAACTCTTTACTTTA
1 AAACCCT-AACCCTTAACTTAA
** *
41525730 AAACTGTAACCCTTAAATTAA
1 AAACCCTAACCCTTAACTTAA
*
41525751 AAACCCTAAACCCTTAACTTTA
1 AAACCCT-AACCCTTAACTTAA
** * *
41525773 AAACTGTAACCCTTAAATAAA
1 AAACCCTAACCCTTAACTTAA
*
41525794 AAACCCTAACACTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
41525815 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
41525836 A
1 A
41525837 TATAATTTGA
Statistics
Matches: 265, Mismatches: 50, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
21 137 0.52
22 80 0.30
23 9 0.03
24 3 0.01
25 4 0.02
26 6 0.02
27 14 0.05
28 12 0.05
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.24
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:41525740 original size:64 final size:63
Alignment explanation
Indices: 41525536--41525836 Score: 282
Period size: 64 Copynumber: 4.6 Consensus size: 63
41525526 AACCCTAACC
* * *
41525536 CTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCCAACGCTAACCGTTAACTTAA
1 CTAACCCTTAACTTAAAAACCCTAAC-CCTTAACTTAAAAACCCTAA--C---CCATTAACTTAA
41525601 AACCT
60 AA-CT
* * * * *
41525606 CTAACCCCTTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAGCCCATTCACCTAAAAAT
1 CTAA-CCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCATTAACTTAAAACT
* * * *
41525670 CATAACCCTTAACTTTAAAACCATAACCCTTAACTTAAAAACCCTAAACTC-TTTACTTTAAAAC
1 C-TAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCT-AACCCATTAAC-TTAAAAC
41525734 T
63 T
* * * ** * * *
41525735 GTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTTAAAACTGTAACCC-TTAAATAAAAAACC
1 CTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACCCATTAACT-TAAAACT
*
41525799 CTAACACTTAACTTAAAAACCCTAACCCTTAACTTAAA
1 CTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
41525837 TATAATTTGA
Statistics
Matches: 193, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
63 15 0.08
64 94 0.49
65 41 0.21
68 1 0.01
70 21 0.11
71 21 0.11
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.25
Consensus pattern (63 bp):
CTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCATTAACTTAAAACT
Found at i:41526660 original size:126 final size:126
Alignment explanation
Indices: 41526434--41527022 Score: 966
Period size: 126 Copynumber: 4.7 Consensus size: 126
41526424 ACTAGAAGCG
* * *
41526434 ATTTTATACTGTTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAGGACCTACTGTAGCAAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
* *
41526499 GCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATATCATCCTGCTTGCAGCGTT
66 GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
* * *
41526560 GTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTATTGTAGCAAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
*
41526625 GCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
66 GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
*
41526686 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCGAGGACCTACTGTAGCAAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
41526751 GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
66 GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
* * *
41526812 ATTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACAGTAGCAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCTACTGTAGCAAA
* * * *
41526877 AGCGCGTCCACGAGGGCGCAATTTCAAAAATTCTTCTCATAA-AGCATCCTGCTTGAAGCATT
65 AGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTGCAGCGTT
*
41526939 -TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
* *
41527003 GCGCGTACACGTGGGCGCGA
66 GCGCGTCCACGAGGGCGCGA
41527023 CTTAAAAAAT
Statistics
Matches: 432, Mismatches: 29, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
125 38 0.09
126 318 0.74
127 74 0.17
128 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (126 bp):
ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
Found at i:41528462 original size:27 final size:27
Alignment explanation
Indices: 41528430--41528484 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
41528420 GTTTATAAAT
*
41528430 TTTTAAAATTTATATTTTAATGTGTAA
1 TTTTAAAATTTATATTTTAATGTATAA
* *
41528457 TTTTAAATTTTATGTTTTAATGTATAA
1 TTTTAAAATTTATATTTTAATGTATAA
41528484 T
1 T
41528485 GATTGAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTTAAAATTTATATTTTAATGTATAA
Found at i:41528688 original size:13 final size:12
Alignment explanation
Indices: 41528650--41528681 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
41528640 CCGCATGTAT
41528650 TAATTTTTTATA
1 TAATTTTTTATA
*
41528662 TTATTTTTTATA
1 TAATTTTTTATA
41528674 TAATTTTT
1 TAATTTTT
41528682 AAATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:41528951 original size:22 final size:22
Alignment explanation
Indices: 41528904--41528951 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
41528894 CAATAACAAC
* * *
41528904 AAAATAGTAGTAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
41528926 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
41528948 AAAA
1 AAAA
41528952 CAAATAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:41529517 original size:40 final size:40
Alignment explanation
Indices: 41529429--41529558 Score: 104
Period size: 40 Copynumber: 3.2 Consensus size: 40
41529419 ATTTTCTGCG
* ** * *
41529429 AAATCGCGTCCACATCAGCGCGATGTCAGGGTACGT-GTCAGG
1 AAATCGCGTCCACATCAGCGCGAT-T-TGCTTACGTGGACA-C
*
41529471 ACATCGCGTCCACATCAGCGCGATTTGCTTACGTGGACAC
1 AAATCGCGTCCACATCAGCGCGATTTGCTTACGTGGACAC
** * *
41529511 AAATCGCG-CCTACGAGGA-TGCGATTTGCTTAAGTGGACAC
1 AAATCGCGTCC-AC-ATCAGCGCGATTTGCTTACGTGGACAC
41529551 AAATCGCG
1 AAATCGCG
41529559 CCTACGAGGA
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
39 2 0.03
40 43 0.58
41 6 0.08
42 23 0.31
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (40 bp):
AAATCGCGTCCACATCAGCGCGATTTGCTTACGTGGACAC
Found at i:41529559 original size:40 final size:40
Alignment explanation
Indices: 41529489--41529587 Score: 164
Period size: 40 Copynumber: 2.5 Consensus size: 40
41529479 TCCACATCAG
*
41529489 CGCGATTTGCTTACGTGGACACAAATCGCGCCTACGAGGA
1 CGCGATTTGCTTAAGTGGACACAAATCGCGCCTACGAGGA
*
41529529 TGCGATTTGCTTAAGTGGACACAAATCGCGCCTACGAGGA
1 CGCGATTTGCTTAAGTGGACACAAATCGCGCCTACGAGGA
41529569 CGCGATTTGC-TAACGTGGA
1 CGCGATTTGCTTAA-GTGGA
41529588 TGAACAGTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 3 0.05
40 52 0.95
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.22
Consensus pattern (40 bp):
CGCGATTTGCTTAAGTGGACACAAATCGCGCCTACGAGGA
Found at i:41542130 original size:12 final size:12
Alignment explanation
Indices: 41542113--41542153 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
41542103 CACCTAGGCA
41542113 CGCCTAGGCGCT
1 CGCCTAGGCGCT
41542125 CGCCTAGGCGCT
1 CGCCTAGGCGCT
*
41542137 TGCCTAGGCGCT
1 CGCCTAGGCGCT
*
41542149 TGCCT
1 CGCCT
41542154 TGACATCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.07, C:0.39, G:0.32, T:0.22
Consensus pattern (12 bp):
CGCCTAGGCGCT
Found at i:41549277 original size:2 final size:2
Alignment explanation
Indices: 41549272--41549296 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41549262 GTGTCAAAAA
41549272 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41549297 ATCAGAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41549829 original size:25 final size:26
Alignment explanation
Indices: 41549780--41549830 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
41549770 AGGTATAATT
**
41549780 ACGTTTATATATTTCACTCTTAATTTC
1 ACGTTTATATATAGCACTC-TAATTTC
41549807 ACGTTTATATATAGCACTC-AATTT
1 ACGTTTATATATAGCACTCTAATTT
41549831 TTTCACTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
27 17 0.77
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (26 bp):
ACGTTTATATATAGCACTCTAATTTC
Found at i:41551787 original size:7 final size:7
Alignment explanation
Indices: 41551777--41551819 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
41551767 ATTATATAAT
41551777 GTGCATG
1 GTGCATG
41551784 GTGCATG
1 GTGCATG
41551791 GTGCATG
1 GTGCATG
41551798 GTGCATG
1 GTGCATG
41551805 GTGCATG
1 GTGCATG
41551812 GTGCATG
1 GTGCATG
41551819 G
1 G
41551820 AAACATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.14, C:0.14, G:0.44, T:0.28
Consensus pattern (7 bp):
GTGCATG
Found at i:41552703 original size:40 final size:40
Alignment explanation
Indices: 41552641--41552734 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
41552631 TTTGGATTAC
* *
41552641 AAACGCCCCTAAAAATCGAGCATTAGCGGCGCAAAC-CATA
1 AAACGCCGCTAAAAATCGAGCATTAGCGGCG-AAACTAATA
* **
41552681 AAACGCCGCTAAAGAT-GTAGCATTAGCGGCGATTCTAATA
1 AAACGCCGCTAAAAATCG-AGCATTAGCGGCGAAACTAATA
41552721 AAACGCCGCTAAAA
1 AAACGCCGCTAAAA
41552735 GTCGGACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 3 0.07
40 43 0.93
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (40 bp):
AAACGCCGCTAAAAATCGAGCATTAGCGGCGAAACTAATA
Found at i:41553068 original size:186 final size:186
Alignment explanation
Indices: 41552837--41553185 Score: 522
Period size: 187 Copynumber: 1.9 Consensus size: 186
41552827 AACGCAGAGT
*
41552837 TTGGTCTTAAGGTACACTAGCATTAGTGGCGCTTATACGAAAACGCCGCTAAAGCATAGTATTAG
1 TTGGTCTTAAGGTACACTAACATTAGTGGCGCTTATACGAAAACGCCGCTAAAGCATAGTATTAG
* * *
41552902 CGGCGAGTA-GAGAAAGCGCCGCAATATTTCTTAACCAAAATGCAGAGTTTGGTCTTGAGGTATA
66 CGGCGAGTACGA-AAAACGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACA
*
41552966 TTAGGATTAGTGGCGCTTAT-TGGAAAACACCGCAAAATATTAACCAAAACGTGCGCA
130 TTACGATTAGTGGCGCTTATAT-GAAAACACCGCAAAATATTAACCAAAACGTGCGCA
* * * * * *
41553023 TTGGTCTTAATGTATAGTAACATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGTATAGTATTAG
1 TTGGTCTTAAGGTACACTAACATTAGTGGCGCTTATACGAAAACGCCGCTAAAGCATAGTATTAG
* * *
41553088 CGGCGAGTACTTAAAAACGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACA
66 CGGCGAGTAC-GAAAAACGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACA
*
41553153 TTACGATTAGTGGCGCTTATATGAAAACGCCGC
130 TTACGATTAGTGGCGCTTATATGAAAACACCGC
41553186 TAAAGCATAG
Statistics
Matches: 145, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
186 67 0.46
187 76 0.52
188 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (186 bp):
TTGGTCTTAAGGTACACTAACATTAGTGGCGCTTATACGAAAACGCCGCTAAAGCATAGTATTAG
CGGCGAGTACGAAAAACGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACAT
TACGATTAGTGGCGCTTATATGAAAACACCGCAAAATATTAACCAAAACGTGCGCA
Found at i:41553316 original size:73 final size:74
Alignment explanation
Indices: 41553209--41553357 Score: 192
Period size: 73 Copynumber: 2.0 Consensus size: 74
41553199 TAGCAGCGCG
* * * * *
41553209 TATTGTAAAGTGCCACAAAATATGAACCAAAACGCAGAG-TTTGGTCTTGCGGTATATTAGGATT
1 TATTGGAAAATGCCACAAAATATGAACCAAAACGCAGAGCTTTGGTCTTGAGGTATAGTAGCATT
41553273 AGTGGCACT
66 AGTGGCACT
* * * * *
41553282 TATTGGAAAATGCCGCAAAATATTAACCAAAACGCTGCGCTTTGGTCTTGATGTATAGTAGCATT
1 TATTGGAAAATGCCACAAAATATGAACCAAAACGCAGAGCTTTGGTCTTGAGGTATAGTAGCATT
*
41553347 AGTGGCGCT
66 AGTGGCACT
41553356 TA
1 TA
41553358 AGCTAAAATG
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
73 33 0.52
74 31 0.48
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (74 bp):
TATTGGAAAATGCCACAAAATATGAACCAAAACGCAGAGCTTTGGTCTTGAGGTATAGTAGCATT
AGTGGCACT
Found at i:41553329 original size:300 final size:298
Alignment explanation
Indices: 41552817--41553565 Score: 1131
Period size: 300 Copynumber: 2.5 Consensus size: 298
41552807 CCGCAATACA
* * * * *
41552817 TCTTAACGAAAACGCAGAGTTTGGTCTTAAGGTACACTAGCATTAGTGGCGCTTATACGAAAACG
1 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAG-ATTAGTGGCGCTTATATGAAAACG
* ** * * *
41552882 CCGCTAAAGCATAGTATTAGCGGCGAGTAGAG-AAAGCGCCGCAATATTTCTTAACCAAAATGCA
65 CCGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGCGCCGCAA-A-ATATTAACCAAAACGCA
*
41552946 GAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAACACCGCAAAATATTAACC
128 GAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCACTTATTGGAAAACACCGCAAAATATTAACC
*
41553011 AAAACGTGCGCATTGGTCTTAATGTATAGTAACATTAGTGGCGCTTATGCTAAAACGCCGCTAAA
193 AAAACGTGCGCATTGGTCTTAATGTATAGTAACATTAGTGGCGCTTAAGCTAAAACGCCGCTAAA
* * * *
41553076 GTATAGTATTAGCGGCGAGTACTTAAAAACGCCGCAATCTT
258 GTATAGTATTAGCAGCGAGTACTGAAAAACACAGCAATCTT
41553117 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTACGATTAGTGGCGCTTATATGAAAACG
1 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTA-GATTAGTGGCGCTTATATGAAAACG
* * * *
41553182 CCGCTAAAGCATAGTATTAGCAGCGCGTATTGTAAAGTGCCACAAAATATGAACCAAAACGCAGA
65 CCGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGA
* **
41553247 GTTTGGTCTTGCGGTATATTAGGATTAGTGGCACTTATTGGAAAATGCCGCAAAATATTAACCAA
130 GTTTGGTCTTGAGGTATATTAGGATTAGTGGCACTTATTGGAAAACACCGCAAAATATTAACCAA
* * * *
41553312 AACGCTGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTAAGCTAAAATGCCGCTAAAG
195 AACG-TGCGCATTGGTCTTAATGTATAGTAACATTAGTGGCGCTTAAGCTAAAACGCCGCTAAAG
*
41553377 TATAGTATTAGCAGCGAGTACTGAAAAGCACAGCAATCTT
259 TATAGTATTAGCAGCGAGTACTGAAAAACACAGCAATCTT
*
41553417 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAGGATTAGTGGCGCTTATTTGAAAACG
1 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTA-GATTAGTGGCGCTTATATGAAAACG
* *
41553482 CCGCTAAAGCAAAGTATTAGCGGCGCGTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGC
65 CCGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGA
*
41553547 GTTTTGGTCTTGATGTATA
130 G-TTTGGTCTTGAGGTATA
41553566 CTAGCAGTTG
Statistics
Matches: 406, Mismatches: 39, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
299 80 0.20
300 300 0.74
301 26 0.06
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (298 bp):
TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAGATTAGTGGCGCTTATATGAAAACGC
CGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGAG
TTTGGTCTTGAGGTATATTAGGATTAGTGGCACTTATTGGAAAACACCGCAAAATATTAACCAAA
ACGTGCGCATTGGTCTTAATGTATAGTAACATTAGTGGCGCTTAAGCTAAAACGCCGCTAAAGTA
TAGTATTAGCAGCGAGTACTGAAAAACACAGCAATCTT
Found at i:41553366 original size:74 final size:73
Alignment explanation
Indices: 41553213--41553371 Score: 185
Period size: 74 Copynumber: 2.2 Consensus size: 73
41553203 AGCGCGTATT
* * * * *
41553213 GTAAAGTGCCACAAAATATGAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGATTAGTGG
1 GTAAAATGCCGCAAAATATGAACCAAAACGCAGAGTTTGGTCTTGAGGTATAGTAGCATTAGTGG
*
41553278 CACTTATT
66 CACTTATA
* * * * *
41553286 GGAAAATGCCGCAAAATATTAACCAAAACGCTGCGCTTTGGTCTTGATGTATAGTAGCATTAGTG
1 GTAAAATGCCGCAAAATATGAACCAAAACGCAGAG-TTTGGTCTTGAGGTATAGTAGCATTAGTG
*
41553351 GCGCTTA-A
65 GCACTTATA
41553359 GCTAAAATGCCGC
1 G-TAAAATGCCGC
41553372 TAAAGTATAG
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
73 30 0.42
74 41 0.58
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (73 bp):
GTAAAATGCCGCAAAATATGAACCAAAACGCAGAGTTTGGTCTTGAGGTATAGTAGCATTAGTGG
CACTTATA
Found at i:41553595 original size:113 final size:112
Alignment explanation
Indices: 41553293--41553622 Score: 367
Period size: 114 Copynumber: 2.9 Consensus size: 112
41553283 ATTGGAAAAT
* *
41553293 GCCGCAAAATATTAACCAAAACGCTGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTA
1 GCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATGTATACTAGCATTAGTGGCGCTTA
* * * * *
41553358 AGCTAAAATGCCGCTAAAGTATAGTATTAGCAGCGAGTACTGAAAAGC
65 TGCTAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTACTGAAAAGC
* * ** * * * * * * *
41553406 ACAGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAGGATTAGTGGCGCTT
1 GCCGCAA--AATATTAACCAAAACGCAGCGTTTGGTCTTGATGTATACTAGCATTAGTGGCGCTT
* * * *
41553471 AT-TTGAAAACGCCGCTAAAGCAAAGTATTAGCGGCGCGTATTGTAAAGC
64 ATGCT-AAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTACTGAAAAGC
41553520 GCCGCAAAATATTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGCAGTT-GTGGCGCTT
1 GCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATGTATACTAGCA-TTAGTGGCGCTT
* * *
41553584 ATGGTAAAACGCCGCTAAAACATATTATTAGCGGCGCGT
64 ATGCTAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGT
41553623 TGTGGGAAGC
Statistics
Matches: 175, Mismatches: 36, Indels: 12
0.78 0.16 0.05
Matches are distributed among these distances:
112 17 0.10
113 66 0.38
114 76 0.43
115 16 0.09
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (112 bp):
GCCGCAAAATATTAACCAAAACGCAGCGTTTGGTCTTGATGTATACTAGCATTAGTGGCGCTTAT
GCTAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTACTGAAAAGC
Found at i:41553676 original size:16 final size:17
Alignment explanation
Indices: 41553642--41553716 Score: 127
Period size: 16 Copynumber: 4.5 Consensus size: 17
41553632 CACCGCTAGG
41553642 TTATTATATAATGTAGT
1 TTATTATATAATGTAGT
*
41553659 TTATTATAT-ATTTAGT
1 TTATTATATAATGTAGT
41553675 TTATTATAT-ATGTAGT
1 TTATTATATAATGTAGT
41553691 TTATTATATAATGTAGT
1 TTATTATATAATGTAGT
41553708 TTATTATAT
1 TTATTATAT
41553717 TATATAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
16 30 0.55
17 25 0.45
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.57
Consensus pattern (17 bp):
TTATTATATAATGTAGT
Found at i:41553680 original size:33 final size:33
Alignment explanation
Indices: 41553642--41553716 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
41553632 CACCGCTAGG
*
41553642 TTATTATATAATGTAGTTTATTATAT-ATTTAGT
1 TTATTATAT-ATGTAGTTTATTATATAATGTAGT
41553675 TTATTATATATGTAGTTTATTATATAATGTAGT
1 TTATTATATATGTAGTTTATTATATAATGTAGT
41553708 TTATTATAT
1 TTATTATAT
41553717 TATATAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 16 0.40
33 24 0.60
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.57
Consensus pattern (33 bp):
TTATTATATATGTAGTTTATTATATAATGTAGT
Found at i:41553758 original size:7 final size:7
Alignment explanation
Indices: 41553746--41553771 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41553736 TTGAATTATA
41553746 GTTTAGG
1 GTTTAGG
41553753 GTTTAGG
1 GTTTAGG
41553760 GTTTAGG
1 GTTTAGG
41553767 GTTTA
1 GTTTA
41553772 CGATGTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:41556885 original size:25 final size:25
Alignment explanation
Indices: 41556851--41556990 Score: 86
Period size: 25 Copynumber: 5.4 Consensus size: 25
41556841 TATCTTAGAC
* *
41556851 AACTTACATAATACATAGCATACAT
1 AACTTACATAATACAAAACATACAT
* *
41556876 AACTTGCATAATACAAAACTTACAT
1 AACTTACATAATACAAAACATACAT
* * * *
41556901 AACTTAAATATCTTACACAACTTACAT
1 AACTTACATA--ATACAAAACATACAT
* * * *
41556928 AACCTACATAATATATTTAACTTACAT
1 AACTTACATAATACA--AAACATACAT
* *
41556955 AACTTACATAACTTAC-ATA-ATACAA
1 AACTTACATAA--TACAAAACATACAT
41556980 AACTTACATAA
1 AACTTACATAA
41556991 CTTAAATATC
Statistics
Matches: 90, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
25 47 0.52
26 1 0.01
27 40 0.44
29 2 0.02
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (25 bp):
AACTTACATAATACAAAACATACAT
Found at i:41556899 original size:9 final size:9
Alignment explanation
Indices: 41556851--41557255 Score: 317
Period size: 9 Copynumber: 46.0 Consensus size: 9
41556841 TATCTTAGAC
41556851 AACTTACAT
1 AACTTACAT
41556860 AA--TACAT
1 AACTTACAT
* *
41556867 AGCATACAT
1 AACTTACAT
*
41556876 AACTTGCAT
1 AACTTACAT
*
41556885 AA--TACAA
1 AACTTACAT
41556892 AACTTACAT
1 AACTTACAT
*
41556901 AACTTAAAT
1 AACTTACAT
* *
41556910 ATCTTACAC
1 AACTTACAT
41556919 AACTTACAT
1 AACTTACAT
*
41556928 AACCTACAT
1 AACTTACAT
**
41556937 AA-TATATTT
1 AACT-TACAT
41556946 AACTTACAT
1 AACTTACAT
41556955 AACTTACAT
1 AACTTACAT
41556964 AACTTACAT
1 AACTTACAT
*
41556973 AA--TACAA
1 AACTTACAT
41556980 AACTTACAT
1 AACTTACAT
*
41556989 AACTTAAAT
1 AACTTACAT
* *
41556998 ATCTTACAC
1 AACTTACAT
41557007 AACTTACAT
1 AACTTACAT
*
41557016 AACCTACAT
1 AACTTACAT
41557025 AA--TACATTT
1 AACTTACA--T
41557034 AACTTACAT
1 AACTTACAT
*
41557043 AACTTACGT
1 AACTTACAT
41557052 AACTTACAT
1 AACTTACAT
*
41557061 AA--TACAA
1 AACTTACAT
41557068 AAC-TACAT
1 AACTTACAT
*
41557076 AACTTAAAT
1 AACTTACAT
* *
41557085 ATCTTACAC
1 AACTTACAT
41557094 AACTTACAT
1 AACTTACAT
*
41557103 AACCTACAT
1 AACTTACAT
41557112 AA--TACATTT
1 AACTTACA--T
41557121 AACTTACAT
1 AACTTACAT
41557130 AACTTACAT
1 AACTTACAT
*
41557139 AA--TACAA
1 AACTTACAT
41557146 AACTTACAT
1 AACTTACAT
*
41557155 AACTTAAAT
1 AACTTACAT
* *
41557164 ATCTTACAC
1 AACTTACAT
41557173 AACTTACAT
1 AACTTACAT
*
41557182 AACCTACAT
1 AACTTACAT
41557191 AA--TACATTT
1 AACTTACA--T
*
41557200 AACTTATAT
1 AACTTACAT
*
41557209 AACTTATAT
1 AACTTACAT
41557218 AACTTACAT
1 AACTTACAT
*
41557227 AA-TAACTTAT
1 AACTTAC--AT
*
41557237 ACACGTACAT
1 A-ACTTACAT
41557247 AACTTACAT
1 AACTTACAT
41557256 TTAACTTACC
Statistics
Matches: 314, Mismatches: 54, Indels: 56
0.74 0.13 0.13
Matches are distributed among these distances:
7 41 0.13
8 10 0.03
9 242 0.77
10 7 0.02
11 12 0.04
12 2 0.01
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Done.