Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 127 of 259
Found at i:40999095 original size:26 final size:26
Alignment explanation
Indices: 40999056--40999108 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40999046 TTTTTTTGGG
** *
40999056 AAAAACGCTTCAAAAAGTTGAGCTAT
1 AAAAACGCCGCAAAAACTTGAGCTAT
*
40999082 AAAAACGCCGCAAAAACTTGAGTTAT
1 AAAAACGCCGCAAAAACTTGAGCTAT
40999108 A
1 A
40999109 GTGACGTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (26 bp):
AAAAACGCCGCAAAAACTTGAGCTAT
Found at i:41004868 original size:43 final size:42
Alignment explanation
Indices: 41004807--41004935 Score: 159
Period size: 43 Copynumber: 3.0 Consensus size: 42
41004797 GGCATTTGTG
*
41004807 GGAAAAGCGCCGCTAAAGGTAATGCTTTTTAGCGGCGTTTTTT
1 GGAAAAGCGCCGCTAAAGGTCATG-TTTTTAGCGGCGTTTTTT
* * * *
41004850 GGAAAAGCACCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
1 GGAAAAGCGCCGCTAAAGGTCATG-TTTTTAGCGGCGTTTTTT
* * *
41004893 GGAAAAGCGCTGCTAAAGGTCATGTTCTTTAGCGACATTTTTT
1 GGAAAAGCGCCGCTAAAGGTCATGTT-TTTAGCGGCGTTTTTT
41004936 TTCAAATAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 1 0.01
43 71 0.99
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
GGAAAAGCGCCGCTAAAGGTCATGTTTTTAGCGGCGTTTTTT
Found at i:41010500 original size:27 final size:27
Alignment explanation
Indices: 41010470--41010526 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
41010460 TGCCATAAAT
* *
41010470 AGTAAATGTGGCGA-AGCCACTAGTATC
1 AGTAAATGTGGC-ATAGCCACCAGTAAC
*
41010497 AGTAATTGTGGCATAGCCACCAGTAAC
1 AGTAAATGTGGCATAGCCACCAGTAAC
41010524 AGT
1 AGT
41010527 GCATGTGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (27 bp):
AGTAAATGTGGCATAGCCACCAGTAAC
Found at i:41010744 original size:27 final size:27
Alignment explanation
Indices: 41010706--41011012 Score: 409
Period size: 27 Copynumber: 11.4 Consensus size: 27
41010696 TACCATAGGT
*
41010706 ATTACAGTCATTTTACTCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* *
41010733 ATTATGGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* * *
41010760 ATTACGATTATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
*
41010787 ATTACGATCATTTTACTCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
*
41010814 ATTACAGTCATTTTACTCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* * *
41010841 ATTACGATTATTTTACTCTATAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* * * *
41010868 ATTACAGTTATTTTACTCTATAGAGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
*
41010895 ATTACGATCATTTTACTCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* *
41010922 ATTATGGTCATTTTACTCTACAAGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* *
41010949 ATTACGGCCATTTAACTCTACA-GGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
**
41010975 ATTACAATCATTTTACTCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
41011002 ATTACGGTCAT
1 ATTACGGTCAT
41011013 ATAACGACCT
Statistics
Matches: 245, Mismatches: 34, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 22 0.09
27 223 0.91
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
ATTACGGTCATTTTACTCTACAGGGGC
Found at i:41017109 original size:49 final size:49
Alignment explanation
Indices: 41017027--41017271 Score: 310
Period size: 49 Copynumber: 4.9 Consensus size: 49
41017017 TAGCCAAAGC
* * *
41017027 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * * *
41017076 TATCCGGTACACGTAGTAGCCTGCACTTGGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC-AAT
* * * *
41017126 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-T
** * * *
41017177 TATCAAGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
*
41017226 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC
41017272 TCACAATAGC
Statistics
Matches: 165, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
49 81 0.49
50 47 0.28
51 37 0.22
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:41027290 original size:33 final size:33
Alignment explanation
Indices: 41027248--41027310 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
41027238 AAATAACACG
*
41027248 GTCTGGGCCTAAGCCCTATTCAGTATCAGTACA
1 GTCTGGGCCTAAGCCCTATTCAGTAACAGTACA
41027281 GTCTGGGCCTAAGCCCTATTCAGTAACAGT
1 GTCTGGGCCTAAGCCCTATTCAGTAACAGT
41027311 GTGGGCCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (33 bp):
GTCTGGGCCTAAGCCCTATTCAGTAACAGTACA
Found at i:41027315 original size:28 final size:28
Alignment explanation
Indices: 41027248--41027336 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 28
41027238 AAATAACACG
41027248 GTCTGGGCCTAAGCCCTATTCAGTATCAGTACA
1 GTCTGGGCCTAAGCCCTATTCAG--T-A--ACA
41027281 GTCTGGGCCTAAGCCCTATTCAGTAACA
1 GTCTGGGCCTAAGCCCTATTCAGTAACA
* * *
41027309 GTGTGGGCCTACG-CCTAATGCAGTAACA
1 GTCTGGGCCTAAGCCCT-ATTCAGTAACA
41027337 ATACGGTACA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.06
28 24 0.46
30 1 0.02
31 1 0.02
33 23 0.44
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (28 bp):
GTCTGGGCCTAAGCCCTATTCAGTAACA
Found at i:41027734 original size:27 final size:27
Alignment explanation
Indices: 41027724--41028028 Score: 423
Period size: 27 Copynumber: 11.3 Consensus size: 27
41027714 ATATAGGGAT
41027724 ATTACGGTCATTTTACTCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
*
41027751 ATTACAGTCATTTTA-TCGTACAGGGGC
1 ATTACGGTCATTTTACTC-TACAGGGGC
* * *
41027778 ATTACGGTTATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
*
41027805 ATTACGATCATTTTACTCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* *
41027832 ATTACAGTCATTTTACTCTATAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* * * *
41027859 ATTATGCTTATTTTACTCTACAAGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* *
41027886 ATTACGGTCATTTTAGTCTACAGAGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
*
41027913 ATTACAGTCATTTTACTCTACAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* *
41027940 ATTACGGTCGTTTTACTCTATAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
*
41027967 ATTACGGTCATTTTACTCTATAGGGGC
1 ATTACGGTCATTTTACTCTACAGGGGC
* *
41027994 ATTACAGTCATTTTACTCTACAGGGGT
1 ATTACGGTCATTTTACTCTACAGGGGC
41028021 ATTACGGT
1 ATTACGGT
41028029 TATATAACGA
Statistics
Matches: 241, Mismatches: 35, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
26 2 0.01
27 238 0.99
28 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (27 bp):
ATTACGGTCATTTTACTCTACAGGGGC
Found at i:41027841 original size:81 final size:81
Alignment explanation
Indices: 41027706--41028031 Score: 483
Period size: 81 Copynumber: 4.0 Consensus size: 81
41027696 AAAAATCGTC
* **
41027706 ATTTTACCATATAGGGATATTACGGTCATTTTACTCTACAGGGGCATTACAGTCATTTTA-TCGT
1 ATTTTACCCTATAGGGGCATTACGGTCATTTTACTCTACAGGGGCATTACAGTCATTTTACTC-T
41027770 ACAGGGGCATTACGGTT
65 ACAGGGGCATTACGGTT
*
41027787 ATTTTACCCTATAGGGGCATTACGATCATTTTACTCTACAGGGGCATTACAGTCATTTTACTCTA
1 ATTTTACCCTATAGGGGCATTACGGTCATTTTACTCTACAGGGGCATTACAGTCATTTTACTCTA
* * *
41027852 TAGGGGCATTATGCTT
66 CAGGGGCATTACGGTT
* * * * *
41027868 ATTTTACTCTACAAGGGCATTACGGTCATTTTAGTCTACAGAGGCATTACAGTCATTTTACTCTA
1 ATTTTACCCTATAGGGGCATTACGGTCATTTTACTCTACAGGGGCATTACAGTCATTTTACTCTA
*
41027933 CAGGGGCATTACGGTC
66 CAGGGGCATTACGGTT
* * *
41027949 GTTTTACTCTATAGGGGCATTACGGTCATTTTACTCTATAGGGGCATTACAGTCATTTTACTCTA
1 ATTTTACCCTATAGGGGCATTACGGTCATTTTACTCTACAGGGGCATTACAGTCATTTTACTCTA
*
41028014 CAGGGGTATTACGGTT
66 CAGGGGCATTACGGTT
41028030 AT
1 AT
41028032 ATAACGACCT
Statistics
Matches: 218, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
81 216 0.99
82 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (81 bp):
ATTTTACCCTATAGGGGCATTACGGTCATTTTACTCTACAGGGGCATTACAGTCATTTTACTCTA
CAGGGGCATTACGGTT
Found at i:41029841 original size:13 final size:13
Alignment explanation
Indices: 41029823--41029898 Score: 91
Period size: 13 Copynumber: 5.9 Consensus size: 13
41029813 AGTTCTTCAT
41029823 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
41029836 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
41029849 TGCTGTGGAAGAG
1 TGCTTTTGAAAAG
*
41029862 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
41029875 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
41029888 TGC-TTTGAAAA
1 TGCTTTTGAAAA
41029899 AATTTAAGTG
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
12 7 0.13
13 46 0.87
ACGTcount: A:0.29, C:0.08, G:0.28, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:41052432 original size:44 final size:41
Alignment explanation
Indices: 41052339--41052459 Score: 111
Period size: 44 Copynumber: 2.9 Consensus size: 41
41052329 CAATGGTAAT
* * *
41052339 TGGCACTAAGTGTGAGATTTAAACTAGCTTCGGCTATATGA
1 TGGCACTAAGTGTGCGATATAAACTAGCTTCGGCTATAAGA
** *
41052380 -GGCACTAAGTGTGCGATATCGACTTAGCTTCGGTTAGTTAAGA
1 TGGCACTAAGTGTGCGATATAAAC-TAGCTTCGGCTA--TAAGA
**
41052423 TGGCACTAAGTGTGCAGA-ATCATTCTAGCTTCGGCTA
1 TGGCACTAAGTGTGC-GATAT-AAACTAGCTTCGGCTA
41052460 ACTATTGCAG
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
40 19 0.30
41 11 0.17
43 4 0.06
44 27 0.42
45 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (41 bp):
TGGCACTAAGTGTGCGATATAAACTAGCTTCGGCTATAAGA
Found at i:41067883 original size:12 final size:12
Alignment explanation
Indices: 41067877--41067901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41067867 TATTTGAATT
41067877 TGAATTTGAAAC
1 TGAATTTGAAAC
41067889 TGAATTTGAAAC
1 TGAATTTGAAAC
41067901 T
1 T
41067902 AAATCTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TGAATTTGAAAC
Found at i:41071750 original size:13 final size:13
Alignment explanation
Indices: 41071732--41071756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41071722 CGTTTCGTAT
41071732 TCATGCTTTTATA
1 TCATGCTTTTATA
41071745 TCATGCTTTTAT
1 TCATGCTTTTAT
41071757 TTCTTTCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TCATGCTTTTATA
Found at i:41071819 original size:13 final size:13
Alignment explanation
Indices: 41071791--41071829 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
41071781 AATTAGATTA
*
41071791 TGTTT-ATGTTTG
1 TGTTTCATGTTTT
*
41071803 TGTTTCGTGTTTT
1 TGTTTCATGTTTT
41071816 TGTTTCATGTTTT
1 TGTTTCATGTTTT
41071829 T
1 T
41071830 AATAATGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.05, C:0.05, G:0.21, T:0.69
Consensus pattern (13 bp):
TGTTTCATGTTTT
Found at i:41072818 original size:30 final size:30
Alignment explanation
Indices: 41072782--41072843 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
41072772 ATTCCCAAGC
*
41072782 TTAGGGGTAAAAGTGTAAATATGCAAAAGT
1 TTAGGGGCAAAAGTGTAAATATGCAAAAGT
* * * *
41072812 TTAGGGGCAAAATTGTAATTTTGCCAAAGT
1 TTAGGGGCAAAAGTGTAAATATGCAAAAGT
41072842 TT
1 TT
41072844 GAGTTAACGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (30 bp):
TTAGGGGCAAAAGTGTAAATATGCAAAAGT
Found at i:41075160 original size:71 final size:71
Alignment explanation
Indices: 41075044--41075182 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
41075034 ATGTATAAGT
*
41075044 GTGTAAGAGATTAAGGTTGACCAAAGCTTGGAAAATAGTCTAGGTATATTCCACACAGGCTGAGA
1 GTGTAAGAGATTAAGGTTGACCAAAGCTTGGAAAATAGTCTAGGTATATTCCACACAGGCAGAGA
41075109 CACATG
66 CACATG
41075115 GTGTAAGAGATTAAGGTTGACCAAAGCTTGGAAAATAGTCTAGGTATATTCCACACAGGCAGAGA
1 GTGTAAGAGATTAAGGTTGACCAAAGCTTGGAAAATAGTCTAGGTATATTCCACACAGGCAGAGA
41075180 CAC
66 CAC
41075183 GACCATGTGT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (71 bp):
GTGTAAGAGATTAAGGTTGACCAAAGCTTGGAAAATAGTCTAGGTATATTCCACACAGGCAGAGA
CACATG
Found at i:41082802 original size:27 final size:26
Alignment explanation
Indices: 41082754--41082813 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
41082744 GCAAGGCTGC
*
41082754 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
41082781 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
41082807 CAAATAT
1 CAGATAT
41082814 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41095722 original size:44 final size:44
Alignment explanation
Indices: 41095643--41096121 Score: 385
Period size: 44 Copynumber: 10.9 Consensus size: 44
41095633 NNNNNNNNNN
* * * *
41095643 TCTTCGATCTGCTTCGCTGTAAGCACA-GGAGTGCCAGATCTGCTA
1 TCTTCGATCTG-TTCCCTATAAACACAGGGA-TGCCAAATCTGCTA
* *
41095688 TCTTCGACCTGTTCCCTATAAACACAGGGATGCCAAATATGCTA
1 TCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTA
* **
41095732 TCTTC-AACTTGTT-CCTATAAACACAGGGATGCC--ATGCTGAAA
1 TCTTCGATC-TGTTCCCTATAAACACAGGGATGCCAAAT-CTGCTA
** * * * *
41095774 TCTTCGATCTGCTTTGCTGTAAGCACA-GGAGTGTCAGATCTGCTA
1 TCTTCGATCTG-TTCCCTATAAACACAGGGA-TGCCAAATCTGCTA
*
41095819 TCTTCGATCT-TTCCCTATAAACACAGGGATACCAAATCTGCTA
1 TCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTA
* * **
41095862 TCTTC-AACTTGTTCCCAATAAACACAGGGATGCC--ATGCTGAAA
1 TCTTCGATC-TGTTCCCTATAAACACAGGGATGCCAAAT-CTGCTA
* * * * ** *
41095905 TCTTCGATCTGCTTCACTGTAAGCACA-AGAGTGTTAGATCTGCTA
1 TCTTCGATCTG-TTCCCTATAAACACAGGGA-TGCCAAATCTGCTA
* *
41095950 TCTTCGATCTGTTCCCTATAAACTCAGGGATGCCAAATATGCTA
1 TCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTA
* **
41095994 TCTTC-AACTTGTTCCCTATAAACACAGGGATGCC--ATGCTGAAA
1 TCTTCGATC-TGTTCCCTATAAACACAGGGATGCCAAAT-CTGCTA
* * * * *
41096037 TCTTCGATCTGCTTCGCTGTAAGCACA-GGAGTGTCATATCTGCTA
1 TCTTCGATCTG-TTCCCTATAAACACAGGGA-TGCCAAATCTGCTA
*
41096082 TCTTCGATCTGTTCCCTATAAACACAAGGATGCCAAATCT
1 TCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCT
41096122 TGTTTCTTTG
Statistics
Matches: 342, Mismatches: 65, Indels: 55
0.74 0.14 0.12
Matches are distributed among these distances:
41 2 0.01
42 16 0.05
43 85 0.25
44 171 0.50
45 62 0.18
46 6 0.02
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
TCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTA
Found at i:41096041 original size:132 final size:132
Alignment explanation
Indices: 41095643--41096119 Score: 832
Period size: 132 Copynumber: 3.6 Consensus size: 132
41095633 NNNNNNNNNN
* *
41095643 TCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGCCAGATCTGCTATCTTCGACCTGTTCCCTATA
1 TCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
41095708 AACACAGGGATGCCAAATATGCTATCTTCAACTTGTT-CCTATAAACACAGGGATGCCATGCTGA
66 AACACAGGGATGCCAAATATGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGA
41095772 AA
131 AA
*
41095774 TCTTCGATCTGCTTTGCTGTAAGCACAGGAGTGTCAGATCTGCTATCTTCGATCT-TTCCCTATA
1 TCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
* * *
41095838 AACACAGGGATACCAAATCTGCTATCTTCAACTTGTTCCCAATAAACACAGGGATGCCATGCTGA
66 AACACAGGGATGCCAAATATGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGA
41095903 AA
131 AA
* * *
41095905 TCTTCGATCTGCTTCACTGTAAGCACAAGAGTGTTAGATCTGCTATCTTCGATCTGTTCCCTATA
1 TCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
*
41095970 AACTCAGGGATGCCAAATATGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGA
66 AACACAGGGATGCCAAATATGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGA
41096035 AA
131 AA
*
41096037 TCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGTCATATCTGCTATCTTCGATCTGTTCCCTATA
1 TCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
*
41096102 AACACAAGGATGCCAAAT
66 AACACAGGGATGCCAAAT
41096120 CTTGTTTCTT
Statistics
Matches: 324, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
130 44 0.14
131 131 0.40
132 149 0.46
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (132 bp):
TCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
AACACAGGGATGCCAAATATGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGA
AA
Found at i:41096932 original size:11 final size:10
Alignment explanation
Indices: 41096906--41096931 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41096896 TGCCTCTCTA
41096906 TTTTTTCTTT
1 TTTTTTCTTT
41096916 TTTTTTCTTT
1 TTTTTTCTTT
41096926 TTTTTT
1 TTTTTT
41096932 TTGAATAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:41101353 original size:39 final size:39
Alignment explanation
Indices: 41101294--41101386 Score: 159
Period size: 39 Copynumber: 2.4 Consensus size: 39
41101284 CGGATGTAAC
* *
41101294 AACCAGCACGAATGCCTTCGGGAGTTAACCCGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGTTATAAT
*
41101333 AACCCGCACGAATGCCTTCGGGACTTAACCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGTTATAAT
41101372 AACCCGCACGAATGC
1 AACCCGCACGAATGC
41101387 TATGCACATA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (39 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGTTATAAT
Found at i:41109439 original size:39 final size:40
Alignment explanation
Indices: 41109305--41109438 Score: 252
Period size: 40 Copynumber: 3.4 Consensus size: 40
41109295 CGGATGTAAC
*
41109305 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
41109345 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
41109385 AACCCGCACGAATG-CTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
41109424 AACCCGCACGAATGC
1 AACCCGCACGAATGC
41109439 TATGCACATA
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
39 39 0.42
40 53 0.58
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:41110109 original size:16 final size:16
Alignment explanation
Indices: 41110088--41110122 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
41110078 ATAATTATAA
41110088 CATAACATCAAGTACT
1 CATAACATCAAGTACT
41110104 CATAACATCAAGTACT
1 CATAACATCAAGTACT
41110120 CAT
1 CAT
41110123 TTTACTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.26
Consensus pattern (16 bp):
CATAACATCAAGTACT
Found at i:41114473 original size:27 final size:26
Alignment explanation
Indices: 41114425--41114484 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
41114415 ACGAGGCTGC
*
41114425 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
41114452 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
41114478 TAGATAT
1 CAGATAT
41114485 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41116656 original size:27 final size:27
Alignment explanation
Indices: 41116626--41116802 Score: 219
Period size: 27 Copynumber: 6.6 Consensus size: 27
41116616 ACATAAAAGA
* **
41116626 AAAATAGCCATTTTACCTCACGAGGGC
1 AAAATAGTCATTTTACCTCATAAGGGC
* * *
41116653 AAAACAGTCATTTTACCTTATGAGGGC
1 AAAATAGTCATTTTACCTCATAAGGGC
* *
41116680 AAAATAGCCATTTTACCTTATAAGGGC
1 AAAATAGTCATTTTACCTCATAAGGGC
* *
41116707 AAAATAATCATTTTACCTCATGAGGGC
1 AAAATAGTCATTTTACCTCATAAGGGC
* *
41116734 AAAATAGTTATTTTACCTCAAAAGGGC
1 AAAATAGTCATTTTACCTCATAAGGGC
* * *
41116761 AAAACAGTCATTTCACCTCACAAGGGC
1 AAAATAGTCATTTTACCTCATAAGGGC
41116788 AAAATAGTCATTTTA
1 AAAATAGTCATTTTA
41116803 TCAATTAGGG
Statistics
Matches: 129, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 129 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (27 bp):
AAAATAGTCATTTTACCTCATAAGGGC
Found at i:41118958 original size:10 final size:10
Alignment explanation
Indices: 41118943--41118967 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41118933 TCAAGACAAA
41118943 ACATTTTCAC
1 ACATTTTCAC
41118953 ACATTTTCAC
1 ACATTTTCAC
41118963 ACATT
1 ACATT
41118968 CAAACATGCC
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:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
ACATTTTCAC
Found at i:41124219 original size:47 final size:47
Alignment explanation
Indices: 41124168--41124272 Score: 174
Period size: 47 Copynumber: 2.2 Consensus size: 47
41124158 TAGTATTAAT
* * *
41124168 TATGTGATAAGGCCGAATGGGCAATGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTAAAAGTGTATA
41124215 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTAAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTAAAAGTGTATA
*
41124262 AATGTGATAAG
1 TATGTGATAAG
41124273 TCCCGAAGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (47 bp):
TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTAAAAGTGTATA
Found at i:41134349 original size:45 final size:45
Alignment explanation
Indices: 41134285--41134411 Score: 184
Period size: 45 Copynumber: 2.8 Consensus size: 45
41134275 ATGGTTGAAG
* *
41134285 GATGCCATGGTGTTTTTCAACCATGGTCTTATTCATTCCTGACTA
1 GATGCAATGGTGTCTTTCAACCATGGTCTTATTCATTCCTGACTA
* * *
41134330 GATGCTATGGTGTCTTTCAACCATGGTCTTATTCATTCCTGATTT
1 GATGCAATGGTGTCTTTCAACCATGGTCTTATTCATTCCTGACTA
*
41134375 GATGCCAAT-GTGTCTTTCTACCATGGTCTTATTCATT
1 GATG-CAATGGTGTCTTTCAACCATGGTCTTATTCATT
41134412 TTACGTCGTG
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
45 72 0.96
46 3 0.04
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (45 bp):
GATGCAATGGTGTCTTTCAACCATGGTCTTATTCATTCCTGACTA
Found at i:41134484 original size:45 final size:45
Alignment explanation
Indices: 41134423--41134529 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 45
41134413 TACGTCGTGT
** *
41134423 TGCCATAATGTCTTTCAACCATGGAT-TTA-TTCGTCT-GATTCATGA
1 TGCCATAACATCTTTCAACCATGG-TCTTACTT-GT-TAGAATCATGA
* * *
41134468 TGCCATAGCATCTTTCAACTATGGTCTTACTTGTTAGAATCGTGA
1 TGCCATAACATCTTTCAACCATGGTCTTACTTGTTAGAATCATGA
41134513 TGCCATAACATCTTTCA
1 TGCCATAACATCTTTCA
41134530 GCTCTAGTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
44 2 0.04
45 48 0.92
46 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCCATAACATCTTTCAACCATGGTCTTACTTGTTAGAATCATGA
Found at i:41134540 original size:45 final size:45
Alignment explanation
Indices: 41134465--41134571 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
41134455 GTCTGATTCA
* * *
41134465 TGATGCCATAGCATCTTTCAACTATGGTCTTACTT-GTT-AGAATCG
1 TGATGCCATAACATCTTTCAACTATAGTCTTA-TTCATTGA-AATCG
* *
41134510 TGATGCCATAACATCTTTCAGCTCTAGTCTTATTCATTGAAATCG
1 TGATGCCATAACATCTTTCAACTATAGTCTTATTCATTGAAATCG
*
41134555 TGATGCCATAACGTCTT
1 TGATGCCATAACATCTT
41134572 CCAGATATTG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
44 2 0.04
45 51 0.94
46 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (45 bp):
TGATGCCATAACATCTTTCAACTATAGTCTTATTCATTGAAATCG
Found at i:41134585 original size:45 final size:45
Alignment explanation
Indices: 41134465--41134592 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 45
41134455 GTCTGATTCA
* * * **
41134465 TGATGCCATAGCATCTTTCA-ACTATGGTCTTACTTGTT-AGAATCG
1 TGATGCCATAACATCTTCCAGA-TATAGTCTTACTCATTGA-AATCG
* * * *
41134510 TGATGCCATAACATCTTTCAGCTCTAGTCTTATTCATTGAAATCG
1 TGATGCCATAACATCTTCCAGATATAGTCTTACTCATTGAAATCG
* *
41134555 TGATGCCATAACGTCTTCCAGATATTGTCTTACTCATT
1 TGATGCCATAACATCTTCCAGATATAGTCTTACTCATT
41134593 TTCGATATGA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
45 67 0.99
46 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (45 bp):
TGATGCCATAACATCTTCCAGATATAGTCTTACTCATTGAAATCG
Found at i:41135950 original size:77 final size:77
Alignment explanation
Indices: 41135864--41136016 Score: 243
Period size: 77 Copynumber: 2.0 Consensus size: 77
41135854 TCTGAAACCA
* * *
41135864 CCATTTTCGACACTACTAAAAAATGGGTTATTACAGCTCTCCCATTTTTAAGAAAATTCCATCAT
1 CCATTTTCGACACTACTAAAAAATAGGCTATGACAGCTCTCCCATTTTTAAGAAAATTCCATCAT
*
41135929 CGAAACCTCTCT
66 CAAAACCTCTCT
* *
41135941 CCATTTTCGACACTACTAAAAAATAGGCTATGACAGCTCTCCCTTTTTTAAGAAAATTTCATCAT
1 CCATTTTCGACACTACTAAAAAATAGGCTATGACAGCTCTCCCATTTTTAAGAAAATTCCATCAT
*
41136006 CAAAATCTCTC
66 CAAAACCTCTC
41136017 CCCTGTAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.33
Consensus pattern (77 bp):
CCATTTTCGACACTACTAAAAAATAGGCTATGACAGCTCTCCCATTTTTAAGAAAATTCCATCAT
CAAAACCTCTCT
Found at i:41138983 original size:27 final size:26
Alignment explanation
Indices: 41138953--41139129 Score: 120
Period size: 27 Copynumber: 6.5 Consensus size: 26
41138943 AAATTGTACA
* *
41138953 GCACTAAGTGTGCGATTCTACTTTGTT
1 GCACTAAGTGTGCGATT-GACTATGTT
* * *
41138980 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCG-ATTGACTATGTT
* ***
41139007 GCACTAAGTGTGCGAATTGACCATACG
1 GCACTAAGTGTGCG-ATTGACTATGTT
* *
41139034 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTT
* * *
41139062 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTT
* * * *
41139089 GCACTAAATGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGA-TTGACTATGTT
*
41139116 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
41139130 GGCTCAATAT
Statistics
Matches: 119, Mismatches: 28, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
26 1 0.01
27 95 0.80
28 23 0.19
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTT
Found at i:41139076 original size:55 final size:53
Alignment explanation
Indices: 41139007--41139129 Score: 140
Period size: 55 Copynumber: 2.3 Consensus size: 53
41138997 TGAATATGAT
* *
41139007 GCACTAAGTGTGCGAATTGACCATAC-GGCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAATTGA--ATACGGGCACTAAATGTGCGAGT-TAACTATATA
* * * *
41139062 GCACTAAGTGTGCGATTTGATTACGTGGCACTAAATGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAATTGAATACG-GGCACTAAATGTGCGAGTTAACTATATA
*
41139116 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
41139130 GGCTCAATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
53 3 0.05
54 20 0.34
55 36 0.61
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (53 bp):
GCACTAAGTGTGCGAATTGAATACGGGCACTAAATGTGCGAGTTAACTATATA
Found at i:41139120 original size:82 final size:81
Alignment explanation
Indices: 41138949--41139129 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
41138939 GATTAAATTG
* * * *
41138949 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
*
41139014 GTGTGCGAATTGACCA
66 ATGTGCGAATTGACCA
* ** *
41139030 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41139094 AAATGTGCGAGTTGATTA
64 AAATGTGCGAATTGACCA
* *
41139112 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41139130 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 22 0.27
82 61 0.73
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
ATGTGCGAATTGACCA
Found at i:41147903 original size:31 final size:31
Alignment explanation
Indices: 41147861--41147970 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
41147851 TCTAACGGTT
41147861 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
41147892 ACTAGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
41147923 ACTGGGCCAAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
41147954 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
41147971 ACTGTAAACG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:41148039 original size:42 final size:42
Alignment explanation
Indices: 41147992--41148085 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
41147982 TATGGCCCAT
* * *
41147992 AAGCCCATTTCAATATCACATGTAAT-GTCAATGGATGTATGC
1 AAGCCCATTTCAATATCACATGAAATACT-AATGAATGTATGC
*
41148034 AAGCCCATTTCAATATGACATGAAATACTAATGAATGTATGC
1 AAGCCCATTTCAATATCACATGAAATACTAATGAATGTATGC
41148076 AAGCCCATTT
1 AAGCCCATTT
41148086 GGGGAGACTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (42 bp):
AAGCCCATTTCAATATCACATGAAATACTAATGAATGTATGC
Found at i:41148260 original size:25 final size:26
Alignment explanation
Indices: 41148231--41148378 Score: 257
Period size: 26 Copynumber: 5.8 Consensus size: 26
41148221 CTCTTTTAAT
41148231 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
41148256 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
**
41148281 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
41148306 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
41148332 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
41148358 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
41148379 GCACTTCCTC
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
25 58 0.49
26 60 0.51
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:41148473 original size:39 final size:40
Alignment explanation
Indices: 41148428--41148513 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 40
41148418 TTATGAATAC
*
41148428 ATCATGTGCATTTCATACATAT-ATGTGCATTTCATA-CA
1 ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
*
41148466 TATCATGTGCATTTTATACATATCATGTGCATATCATATCA
1 -ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
41148507 ATCATGT
1 ATCATGT
41148514 ATATCATATC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 21 0.49
40 20 0.47
41 2 0.05
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (40 bp):
ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
Found at i:41148475 original size:20 final size:20
Alignment explanation
Indices: 41148428--41148513 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
41148418 TTATGAATAC
41148428 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
41148448 AT-ATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
41148467 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
41148487 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
41148507 ATCATGT
1 ATCATGT
41148514 ATATCATATC
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
19 19 0.31
20 40 0.66
21 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:41149282 original size:27 final size:27
Alignment explanation
Indices: 41149221--41149284 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
41149211 GGCGTATTCA
41149221 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGGTATTACGG
* * *
41149248 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAAGGG-TATTACGG
*
41149275 TCTTTTTACC
1 TCATTTTACC
41149285 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAAGGGTATTACGG
Found at i:41149368 original size:27 final size:27
Alignment explanation
Indices: 41149338--41149415 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
41149328 GTAAATCTAC
*
41149338 AAATTAAGGGTATTTCTGTAATTTTGT
1 AAATTAAGGGTATTTCTGTAATTTTAT
* *
41149365 AAATCAGGGGTATTT-TGGTAATTTTAT
1 AAATTAAGGGTATTTCT-GTAATTTTAT
*
41149392 AAATTGAGGGTATTTC-GATAATTT
1 AAATTAAGGGTATTTCTG-TAATTT
41149416 CACAAACCAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.05
27 40 0.95
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.45
Consensus pattern (27 bp):
AAATTAAGGGTATTTCTGTAATTTTAT
Found at i:41149384 original size:54 final size:54
Alignment explanation
Indices: 41149318--41149448 Score: 156
Period size: 54 Copynumber: 2.4 Consensus size: 54
41149308 CATCCTACAA
* * * *** *
41149318 GGGTGTTTTGGTAAATCTACAAATTAAGGGTATTTCTG-TAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTC-GATAATTTCACAAACCAG
* *
41149372 GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGATAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGATAATTTCACAAACCAG
*
41149426 TGGTATTTTGGTAATTTTACAAA
1 GGGTATTTTGGTAATTTTACAAA
41149449 CAAGGGTGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.02
54 64 0.98
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGATAATTTCACAAACCAG
Found at i:41149529 original size:27 final size:27
Alignment explanation
Indices: 41149499--41149753 Score: 126
Period size: 27 Copynumber: 9.4 Consensus size: 27
41149489 GTAATTTCAC
* *
41149499 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATAGTAATTTTATA
* * *
41149526 AATC-AGGGGTAAAACAGCAATTTTGTA
1 AATCGA-GGGTAAAATAGTAATTTTATA
*
41149553 AATCGAGGGTAAAATAGTAA-TCTATA
1 AATCGAGGGTAAAATAGTAATTTTATA
* *** *
41149579 AATTGAGGGTACTTTGGTAATTTT-TA
1 AATCGAGGGTAAAATAGTAATTTTATA
** *
41149605 CAAGTCGAGGGT-ATTTCAGTAATTTTACA
1 -AA-TCGAGGGTAAAAT-AGTAATTTTATA
* *** *
41149634 AATCAGGGGGTATTTTAGTAATTTTACA
1 AATC-GAGGGTAAAATAGTAATTTTATA
* *** *
41149662 AA-CTAGGGGTATTTTAGTAATTTTGTA
1 AATCGA-GGGTAAAATAGTAATTTTATA
* * *
41149689 AATTGAGGGTAAAA-CGATAATTCTATA
1 AATCGAGGGTAAAATAG-TAATTTTATA
* * * *
41149716 AATTGAAGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATAGTAATTTTATA
41149743 AATCGAGGGTA
1 AATCGAGGGTA
41149754 GGACGGTAAT
Statistics
Matches: 180, Mismatches: 35, Indels: 26
0.75 0.15 0.11
Matches are distributed among these distances:
26 23 0.13
27 114 0.63
28 39 0.22
29 4 0.02
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (27 bp):
AATCGAGGGTAAAATAGTAATTTTATA
Found at i:41149615 original size:28 final size:27
Alignment explanation
Indices: 41149583--41149685 Score: 104
Period size: 28 Copynumber: 3.7 Consensus size: 27
41149573 TCTATAAATT
* *
41149583 GAGGGTACTTTGGTAATTTTTACAAGTC-
1 GAGGGTA-TTTAGTAA-TTTTACAAATCA
41149611 GAGGGTATTTCAGTAATTTTACAAATCA
1 GAGGGTATTT-AGTAATTTTACAAATCA
*
41149639 GGGGGTATTTTAGTAATTTTACAAA-CTA
1 GAGGGTA-TTTAGTAATTTTACAAATC-A
41149667 G-GGGTATTTTAGTAATTTT
1 GAGGGTA-TTTAGTAATTTT
41149686 GTAAATTGAG
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
27 32 0.47
28 33 0.49
29 3 0.04
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (27 bp):
GAGGGTATTTAGTAATTTTACAAATCA
Found at i:41149697 original size:28 final size:28
Alignment explanation
Indices: 41149567--41149697 Score: 103
Period size: 28 Copynumber: 4.8 Consensus size: 28
41149557 GAGGGTAAAA
* *
41149567 TAGTAA-TCTATAAATTGA-GGGTACTT
1 TAGTAATTTTATAAATTGAGGGGTATTT
* *
41149593 TGGTAATTTT-TACAAGTCGA-GGGTATTT
1 TAGTAATTTTATA-AA-TTGAGGGGTATTT
* * *
41149621 CAGTAATTTTACAAA-TCAGGGGGTATTT
1 TAGTAATTTTATAAATTGA-GGGGTATTT
* *
41149649 TAGTAATTTTACAAACT-AGGGGTATTT
1 TAGTAATTTTATAAATTGAGGGGTATTT
*
41149676 TAGTAATTTTGTAAATTGAGGG
1 TAGTAATTTTATAAATTGAGGG
41149698 TAAAACGATA
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
26 8 0.10
27 27 0.32
28 47 0.56
29 2 0.02
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (28 bp):
TAGTAATTTTATAAATTGAGGGGTATTT
Found at i:41149761 original size:27 final size:27
Alignment explanation
Indices: 41149678--41149780 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 27
41149668 GGGTATTTTA
* *
41149678 GTAATTTTGTAAATTGAGGGTAAAACG
1 GTAATTCTATAAATTGAGGGTAAAACG
* * *
41149705 ATAATTCTATAAATTGAAGGTAAAATG
1 GTAATTCTATAAATTGAGGGTAAAACG
* **
41149732 GTAATTCTATAAATCGAGGGTAGGACG
1 GTAATTCTATAAATTGAGGGTAAAACG
* * *
41149759 GTAATTTTGTAAATTGGGGGTA
1 GTAATTCTATAAATTGAGGGTA
41149781 CTTTGGTAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (27 bp):
GTAATTCTATAAATTGAGGGTAAAACG
Found at i:41151133 original size:45 final size:45
Alignment explanation
Indices: 41151053--41151165 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 45
41151043 CCGTGGCATT
* * ***
41151053 TTTCAACCATGGTCTTATTCATTCTCGACTAGATGCCATGGTGTC
1 TTTCAACCATGGTCTTATTCATTCCCAACTAGATGCCACAATGTC
* *
41151098 TTTCAACCATGGTCTTATTCATTCCCAATTTGATGCCACAATGTC
1 TTTCAACCATGGTCTTATTCATTCCCAACTAGATGCCACAATGTC
* * *
41151143 TCTCTACCATGGTCTTAATCATT
1 TTTCAACCATGGTCTTATTCATT
41151166 TTACGTTGTG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (45 bp):
TTTCAACCATGGTCTTATTCATTCCCAACTAGATGCCACAATGTC
Found at i:41155916 original size:48 final size:48
Alignment explanation
Indices: 41155840--41156153 Score: 146
Period size: 49 Copynumber: 6.6 Consensus size: 48
41155830 ATTACGGGAA
** * * * *
41155840 CCAGTGTAATTCATATCTGGGACTTGCATCAGCCTCAAGATATACGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACGAG
* * **
41155888 CCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA-CGA-GAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACGAG
* * *
41155934 CTAGTGTAAGACATGTTTGGGACATGCATCGGCC-CTGAGATATACAAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTC-GAGATATACGAG
* * * * * * * * ** *
41155982 CTACTGTAAGACCTGTCTAGAACATGGCGTCAG-CT--TG-T-TGTGTG
1 CCAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGATATACGAG
* * * * * *
41156026 TCAGTGTAAGACCTATCTGGGACATGGCATCGACAC-CGATAGATGA-GAG
1 CCAGTGTAAGACATGTCTGGGACAT-GCATCGGC-CTCGAGATAT-ACGAG
* * * * *
41156075 CCAGTGTAAGACTTGTCTAGGACATGGCATTGGCCTCGAAATATGA-AAG
1 CCAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGATAT-ACGAG
* *
41156124 TCAGTGTAAGACTTGTCTGGGACATAGCAT
1 CCAGTGTAAGACATGTCTGGGACAT-GCAT
41156154 TGACTTTGAT
Statistics
Matches: 198, Mismatches: 55, Indels: 25
0.71 0.20 0.09
Matches are distributed among these distances:
44 26 0.13
45 1 0.01
46 40 0.20
47 2 0.01
48 56 0.28
49 73 0.37
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (48 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACGAG
Found at i:41155973 original size:46 final size:46
Alignment explanation
Indices: 41155885--41155973 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
41155875 CAAGATATAC
*
41155885 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACTGAGACGA
* * *
41155931 GAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCCTGAGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACTGAGA
41155974 TATACAAGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACTGAGACGA
Found at i:41156154 original size:49 final size:49
Alignment explanation
Indices: 41156025--41156157 Score: 160
Period size: 49 Copynumber: 2.7 Consensus size: 49
41156015 CTTGTTGTGT
* * * * *
41156025 GTCAGTGTAAGACCTATCTGGGACATGGCATCGACACCGATAGATGAGA
1 GTCAGTGTAAGACTTGTCTGGGACATGGCATTGACACCGAAAGATGAAA
* * * *
41156074 GCCAGTGTAAGACTTGTCTAGGACATGGCATTGGC-CTCGAAATATGAAA
1 GTCAGTGTAAGACTTGTCTGGGACATGGCATTGACAC-CGAAAGATGAAA
*
41156123 GTCAGTGTAAGACTTGTCTGGGACATAGCATTGAC
1 GTCAGTGTAAGACTTGTCTGGGACATGGCATTGAC
41156158 TTTGATGTGC
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
48 1 0.01
49 69 0.99
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (49 bp):
GTCAGTGTAAGACTTGTCTGGGACATGGCATTGACACCGAAAGATGAAA
Found at i:41161626 original size:16 final size:18
Alignment explanation
Indices: 41161595--41161627 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
41161585 CCCCTATGTG
41161595 ATGTATGGACCTATATTC
1 ATGTATGGACCTATATTC
41161613 ATGTAT-GA-CTATATT
1 ATGTATGGACCTATATT
41161628 ATAGCATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (18 bp):
ATGTATGGACCTATATTC
Found at i:41164502 original size:40 final size:40
Alignment explanation
Indices: 41164447--41164702 Score: 440
Period size: 40 Copynumber: 6.4 Consensus size: 40
41164437 AGCATTGGAT
*
41164447 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGGGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
41164487 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
41164527 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
41164567 TATATCTGGGCTAAGACCCGAAGGCAACTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
** *
41164607 TATATCCGGGCTGTGACCCGAAGGCAATTATGCGAGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
41164647 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
41164687 TATGTCCGGGTTAAGA
1 TATATCCGGGCTAAGA
41164703 ACATATCAAC
Statistics
Matches: 203, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 203 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:41175453 original size:27 final size:26
Alignment explanation
Indices: 41175433--41175593 Score: 142
Period size: 27 Copynumber: 6.1 Consensus size: 26
41175423 ATTTTACCCT
*
41175433 ACAGGGGTATTTCGGTAATTTTACACT
1 ACAGGGGTATTTCGGTAATTTTACA-A
** * *
41175460 ACAAAGGTATCTAGGTAATTTTACAA
1 ACAGGGGTATTTCGGTAATTTTACAA
* * *
41175486 ACTGGGGTATGTCGATAATTTTACAA
1 ACAGGGGTATTTCGGTAATTTTACAA
* *
41175512 ATCGGGGGTATTTCGGTAATTTTATAA
1 A-CAGGGGTATTTCGGTAATTTTACAA
* * * **
41175539 TCTGAGGTATTTTAGTAATTTTACAA
1 ACAGGGGTATTTCGGTAATTTTACAA
**
41175565 ACTAATGGTATTTCGGTAATTTTACAA
1 AC-AGGGGTATTTCGGTAATTTTACAA
41175592 AC
1 AC
41175594 CGTGGTCTTC
Statistics
Matches: 105, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
26 42 0.40
27 63 0.60
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (26 bp):
ACAGGGGTATTTCGGTAATTTTACAA
Found at i:41175548 original size:53 final size:53
Alignment explanation
Indices: 41175438--41175593 Score: 140
Period size: 53 Copynumber: 2.9 Consensus size: 53
41175428 ACCCTACAGG
* * * * *
41175438 GGTATTTCG-GTAATTTTACACTAC-AAAGGTATCTAGGTAATTTTACAAACTGG
1 GGTA-TTCGAGTAATTTTACA-AACTAAGGGTATTTCGGTAATTTTACAAACTGA
** * *
41175491 GGTATGTCGA-TAATTTTACAAA-TCGGGGGTATTTCGGTAATTTTATAATCTGA
1 GGTAT-TCGAGTAATTTTACAAACT-AAGGGTATTTCGGTAATTTTACAAACTGA
** *
41175544 GGTATTTTAGTAATTTTACAAACTAATGGTATTTCGGTAATTTTACAAAC
1 GGTATTCGAGTAATTTTACAAACTAAGGGTATTTCGGTAATTTTACAAAC
41175594 CGTGGTCTTC
Statistics
Matches: 81, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
52 4 0.05
53 76 0.94
54 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (53 bp):
GGTATTCGAGTAATTTTACAAACTAAGGGTATTTCGGTAATTTTACAAACTGA
Found at i:41179281 original size:40 final size:40
Alignment explanation
Indices: 41179226--41179532 Score: 560
Period size: 40 Copynumber: 7.7 Consensus size: 40
41179216 AGCATTGGAT
*
41179226 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
41179266 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
41179306 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
41179346 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
41179386 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
41179426 TATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
41179466 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
41179506 TATGTCCGGGTTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
41179533 ATGTGTTTGC
Statistics
Matches: 260, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 260 1.00
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:41182110 original size:2 final size:2
Alignment explanation
Indices: 41182103--41182135 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41182093 AGGAAAAAGG
41182103 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
41182136 GGGGTAAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41182643 original size:90 final size:90
Alignment explanation
Indices: 41182487--41182653 Score: 219
Period size: 90 Copynumber: 1.9 Consensus size: 90
41182477 CAAATAGGGT
* * * * *
41182487 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCACACATTGATGCCATATCTCAGATATG
1 GCCAAAGCCATGTACCAGACATGATCTTACACGGGACCACACATCGATGCCATATCTCAGACATG
41182552 GTCTTATACGAAGTCTGGAATCAGC
66 GTCTTATACGAAGTCTGGAATCAGC
* * * * * *
41182577 GCCAACGCCATGTACCAGACATGATCTTATACGGGACCTCATATCGATGCCATGTC-CTGGACAT
1 GCCAAAGCCATGTACCAGACATGATCTTACACGGGACCACACATCGATGCCATATCTC-AGACAT
41182641 GGTCTTATACGAA
65 GGTCTTATACGAA
41182654 ATCATTTATT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
89 1 0.02
90 64 0.98
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (90 bp):
GCCAAAGCCATGTACCAGACATGATCTTACACGGGACCACACATCGATGCCATATCTCAGACATG
GTCTTATACGAAGTCTGGAATCAGC
Found at i:41182894 original size:33 final size:33
Alignment explanation
Indices: 41182852--41182918 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
41182842 TTATTAAATC
41182852 ATTTCATATAACATCAAGCATTAAATACACGAT
1 ATTTCATATAACATCAAGCATTAAATACACGAT
41182885 ATTTCATATAACATCAAGCATTAAATACACGAT
1 ATTTCATATAACATCAAGCATTAAATACACGAT
41182918 A
1 A
41182919 ATGAAATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (33 bp):
ATTTCATATAACATCAAGCATTAAATACACGAT
Found at i:41209988 original size:26 final size:26
Alignment explanation
Indices: 41209959--41210013 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
41209949 TCCAAAGTTG
41209959 CCTTATGCTTGGTCAACCAATCCATC
1 CCTTATGCTTGGTCAACCAATCCATC
41209985 CCTTATGCTTGGTCAACCAATCCATC
1 CCTTATGCTTGGTCAACCAATCCATC
41210011 CCT
1 CCT
41210014 AGTATCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.36, G:0.11, T:0.31
Consensus pattern (26 bp):
CCTTATGCTTGGTCAACCAATCCATC
Found at i:41223940 original size:7 final size:7
Alignment explanation
Indices: 41223928--41223952 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41223918 ATTCATATAA
41223928 ATGAAAT
1 ATGAAAT
41223935 ATGAAAT
1 ATGAAAT
41223942 ATGAAAT
1 ATGAAAT
41223949 ATGA
1 ATGA
41223953 TAGTTGAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
ATGAAAT
Found at i:41224579 original size:18 final size:19
Alignment explanation
Indices: 41224552--41224592 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
41224542 TATTTTGTAA
* *
41224552 TTTTATAAAATT-TTAATT
1 TTTTAAAAAATTAATAATT
41224570 TTTTAAAAAATTAATAATT
1 TTTTAAAAAATTAATAATT
41224589 TTTT
1 TTTT
41224593 TGAATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAAAATTAATAATT
Found at i:41224614 original size:24 final size:26
Alignment explanation
Indices: 41224583--41224663 Score: 98
Period size: 25 Copynumber: 3.2 Consensus size: 26
41224573 TAAAAAATTA
41224583 ATAATTTTTT-TGAA-TTAT-TTTTAT
1 ATAATTTTTTAT-AATTTATATTTTAT
*
41224607 ATAATTTTTTATAATTTTTATTTTAT
1 ATAATTTTTTATAATTTATATTTTAT
* *
41224633 ATAAATTTTTAT-ATTTTTATTTTAT
1 ATAATTTTTTATAATTTATATTTTAT
41224658 ATAATT
1 ATAATT
41224664 GGCATGTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
24 12 0.24
25 22 0.43
26 17 0.33
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (26 bp):
ATAATTTTTTATAATTTATATTTTAT
Found at i:41224630 original size:26 final size:25
Alignment explanation
Indices: 41224601--41224663 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
41224591 TTTGAATTAT
41224601 TTTTATATAATTTTTTATAATTTTTA
1 TTTTATATAATTTTTTAT-ATTTTTA
*
41224627 TTTTATATAAATTTTTATATTTTTA
1 TTTTATATAATTTTTTATATTTTTA
41224652 TTTTATATAATT
1 TTTTATATAATT
41224664 GGCATGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 18 0.51
26 17 0.49
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTATATAATTTTTTATATTTTTA
Found at i:41224635 original size:16 final size:17
Alignment explanation
Indices: 41224610--41224644 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41224600 TTTTTATATA
*
41224610 ATTTTTTAT-AATTTTT
1 ATTTTATATAAATTTTT
41224626 ATTTTATATAAATTTTT
1 ATTTTATATAAATTTTT
41224643 AT
1 AT
41224645 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTATATAAATTTTT
Found at i:41224740 original size:19 final size:19
Alignment explanation
Indices: 41224718--41224756 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41224708 TATTTTGAAT
41224718 TTTTAGA-TTTTATATATTA
1 TTTTAGACTTTT-TATATTA
*
41224737 TTTTATACTTTTTATATTA
1 TTTTAGACTTTTTATATTA
41224756 T
1 T
41224757 ATAATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTAGACTTTTTATATTA
Found at i:41229297 original size:39 final size:40
Alignment explanation
Indices: 41229202--41229424 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
41229192 TTGAATGATG
*
41229202 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
41229240 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
41229281 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
41229320 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
41229359 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
41229398 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41229425 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:41229388 original size:79 final size:81
Alignment explanation
Indices: 41229202--41229424 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
41229192 TTGAATGATG
* * *
41229202 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
41229264 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
41229281 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
41229342 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
41229359 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
41229423 TG
66 TG
41229425 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:41229446 original size:79 final size:79
Alignment explanation
Indices: 41229202--41229457 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
41229192 TTGAATGATG
* * * *
41229202 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
41229263 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
41229281 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
41229345 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
41229359 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
41229422 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
41229439 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
41229458 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:41237185 original size:39 final size:40
Alignment explanation
Indices: 41237088--41237310 Score: 239
Period size: 39 Copynumber: 5.7 Consensus size: 40
41237078 TTGAATGATG
*
41237088 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
41237126 ATCCGGACTAAGAT-CTGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
41237167 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
41237206 TCTGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
41237245 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* * *
41237284 AACCGGGATATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41237311 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
39 89 0.56
40 59 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:41237332 original size:79 final size:79
Alignment explanation
Indices: 41237142--41237343 Score: 191
Period size: 79 Copynumber: 2.6 Consensus size: 79
41237132 ACTAAGATCT
** * *
41237142 GAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAA
1 GAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
* * *
41237205 TTCTGGGCTAAGCCC
65 TACCGGGATAAGCCC
** *
41237220 GAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-A
1 GAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAA
*
41237283 TAACCGGGATATGTCCC
65 T-ACCGGGATAAG-CCC
* * *
41237300 GAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 GAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
41237344 TACTGATTTG
Statistics
Matches: 106, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
77 1 0.01
78 35 0.33
79 45 0.42
80 25 0.24
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (79 bp):
GAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
ACCGGGATAAGCCC
Found at i:41240079 original size:50 final size:50
Alignment explanation
Indices: 41239905--41240200 Score: 292
Period size: 50 Copynumber: 5.9 Consensus size: 50
41239895 ATCTATTGTG
* * * * * *
41239905 AGGTCACGTGTTTAGTACTAAGTACAGGATACTACATGTACCGGATTATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
41239955 -GGTCGCATGTATAGTACTAAGTGCAGGCTACTATGCT-TACCCGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACG-TGTACCAGATAA-TT
* * * * **
41240005 CGATCACGTGTGCAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * **
41240055 AGGTCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* **
41240105 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACTGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * ** *
41240155 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTGTGCGTACCAGATA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
41240201 GCTTTGGCTA
Statistics
Matches: 204, Mismatches: 38, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
49 74 0.36
50 95 0.47
51 35 0.17
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:41241538 original size:49 final size:48
Alignment explanation
Indices: 41241482--41241655 Score: 169
Period size: 49 Copynumber: 3.6 Consensus size: 48
41241472 GAGGTGTGTT
* * *
41241482 AGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATAAGTGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGGCATCGACTCAGAT-AGTGAGAGCC
* *
41241531 AGTGTAAGACATGTCTAGGACATGGCATCAGCCTC-GAT-GT-ATGTAAGTC
1 AGTGTAAGACATGTCTAGGACATGGCATC-GACTCAGATAGTGA-G--AGCC
* * * * *
41241580 AGTGTAAGACCTGT-TCGGGACATGGCATCAACTTAGAT-GTGAGAGCT
1 AGTGTAAGACATGTCT-AGGACATGGCATCGACTCAGATAGTGAGAGCC
41241627 AGTGTAAGACATGTCTAGGACATGGCATC
1 AGTGTAAGACATGTCTAGGACATGGCATC
41241656 AACCTCAATG
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
46 1 0.01
47 30 0.29
48 4 0.04
49 64 0.62
50 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACATGTCTAGGACATGGCATCGACTCAGATAGTGAGAGCC
Found at i:41241648 original size:96 final size:96
Alignment explanation
Indices: 41241482--41241729 Score: 363
Period size: 96 Copynumber: 2.6 Consensus size: 96
41241472 GAGGTGTGTT
**
41241482 AGTGTAAGACCTG-TCTGGGACATGGCATCGACACAGATAAGTGAGAGCCAGTGTAAGACATGTC
1 AGTGTAAGACCTGTTC-GGGACATGGCATCGACTTAGAT--GTGAGAGCCAGTGTAAGACATGTC
* * *
41241546 TAGGACATGGCATCAGCCTCGATGTATGTAAGTC
63 TAGGACATGGCATCAACCTCAATGTATGTAAGCC
* *
41241580 AGTGTAAGACCTGTTCGGGACATGGCATCAACTTAGATGTGAGAGCTAGTGTAAGACATGTCTAG
1 AGTGTAAGACCTGTTCGGGACATGGCATCGACTTAGATGTGAGAGCCAGTGTAAGACATGTCTAG
41241645 GACATGGCATCAACCTCAATGTATGTAAGCC
66 GACATGGCATCAACCTCAATGTATGTAAGCC
* * * *
41241676 AGTGTAAGACCTGTTCGGGATATGGCATTGACTTAGACGTGAAAGCCAGTGTAA
1 AGTGTAAGACCTGTTCGGGACATGGCATCGACTTAGATGTGAGAGCCAGTGTAA
41241730 AACCATGTTT
Statistics
Matches: 136, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
96 102 0.75
98 32 0.24
99 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (96 bp):
AGTGTAAGACCTGTTCGGGACATGGCATCGACTTAGATGTGAGAGCCAGTGTAAGACATGTCTAG
GACATGGCATCAACCTCAATGTATGTAAGCC
Found at i:41241703 original size:49 final size:49
Alignment explanation
Indices: 41241527--41241685 Score: 193
Period size: 49 Copynumber: 3.3 Consensus size: 49
41241517 GATAAGTGAG
* *
41241527 AGCCAGTGTAAGACATGTCTAGGACATGGCATCAGCCTCGATGTATGTA
1 AGCCAGTGTAAGACATGTCTAGGACATGGCATCAACCTCAATGTATGTA
* * * *
41241576 AGTCAGTGTAAGACCTGT-TCGGGACATGGCATCAA-CT-TA-G-ATGTGA
1 AGCCAGTGTAAGACATGTCT-AGGACATGGCATCAACCTCAATGTATGT-A
*
41241622 GAGCTAGTGTAAGACATGTCTAGGACATGGCATCAACCTCAATGTATGTA
1 -AGCCAGTGTAAGACATGTCTAGGACATGGCATCAACCTCAATGTATGTA
41241672 AGCCAGTGTAAGAC
1 AGCCAGTGTAAGAC
41241686 CTGTTCGGGA
Statistics
Matches: 91, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
45 4 0.04
46 2 0.02
47 30 0.33
48 6 0.07
49 43 0.47
50 2 0.02
51 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (49 bp):
AGCCAGTGTAAGACATGTCTAGGACATGGCATCAACCTCAATGTATGTA
Found at i:41241986 original size:62 final size:62
Alignment explanation
Indices: 41241915--41242043 Score: 240
Period size: 62 Copynumber: 2.1 Consensus size: 62
41241905 ATTCTTGTTG
*
41241915 TATGAATAGCGAGGAATGAACATGAGTAAGATTTGTTATGAACATTTACTCTTTGTGTGAGT
1 TATGAATAGCGAGGAATGAACATGAGTAAGATTTGTTATGAACATTTACTCTTTGTGCGAGT
*
41241977 TATGAATAGCGAGGAATGAACATGAGTAAGATTTTTTATGAACATTTACTCTTTGTGCGAGT
1 TATGAATAGCGAGGAATGAACATGAGTAAGATTTGTTATGAACATTTACTCTTTGTGCGAGT
41242039 TATGA
1 TATGA
41242044 TATATTGGGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.36
Consensus pattern (62 bp):
TATGAATAGCGAGGAATGAACATGAGTAAGATTTGTTATGAACATTTACTCTTTGTGCGAGT
Found at i:41242514 original size:37 final size:37
Alignment explanation
Indices: 41242471--41242543 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
41242461 TGAATTCATG
* * *
41242471 TTGTGGTTGATTTAGTCTTATATTGTTGTGTGAATTA
1 TTGTGGTTGATTTAGCCTTATATTGCTGTGAGAATTA
41242508 TTGTGGTTGATTTAGCCTTATATTGCTGTGAGAATT
1 TTGTGGTTGATTTAGCCTTATATTGCTGTGAGAATT
41242544 GGAGATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.19, C:0.05, G:0.25, T:0.51
Consensus pattern (37 bp):
TTGTGGTTGATTTAGCCTTATATTGCTGTGAGAATTA
Found at i:41243181 original size:21 final size:22
Alignment explanation
Indices: 41243140--41243181 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41243130 GTCAAGAAGG
41243140 CCACACGGGAGTGTCACCCCTT
1 CCACACGGGAGTGTCACCCCTT
*
41243162 CCACACGGGCGTGT-ACCCCT
1 CCACACGGGAGTGTCACCCCT
41243182 GTTTCAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.17
Consensus pattern (22 bp):
CCACACGGGAGTGTCACCCCTT
Found at i:41248055 original size:48 final size:46
Alignment explanation
Indices: 41247975--41248095 Score: 154
Period size: 47 Copynumber: 2.6 Consensus size: 46
41247965 AAGGCTGATG
* ** *
41247975 CATGTCCCAAACATGTCTTACACTGGCACTCATCTCTGT-TCCGATAC
1 CATGTCCCAGACATGTCTTACACTGGCACTCAT-AATGTAGCCGA-AC
* *
41248022 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCCGAAG
1 CATGTCCCAGACAT-GTCTTACACTGGCACTCATAATGTAGCCGAAC
41248069 CATGTCCCAGACATGTCTTACACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
41248096 GCACAAATCA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
46 13 0.20
47 31 0.47
48 22 0.33
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.27
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCACTCATAATGTAGCCGAAC
Found at i:41248074 original size:94 final size:92
Alignment explanation
Indices: 41247827--41248095 Score: 287
Period size: 94 Copynumber: 2.9 Consensus size: 92
41247817 TATATATATT
* * *
41247827 GCCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCTCATATATGCATGCTGATGCATGTCCC
1 GCCGAT-CCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTAGGCTGATGCATGTCCC
*
41247892 AGACATGTCTTACACTAGCACAACTCTTA
64 AGACATGTCTTACACTGGCACAACTCTTA
* * * * * * *
41247921 GCCGATGCGTGTCCCAAACA-CGTCTTACATTGGCTATC-T-TTGTCAAGGCTGATGCATGTCCC
1 GCCGATCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT--AGGCTGATGCATGTCCC
* *
41247983 AAACATGTCTTACACTGGCACTCATCTCTGT-
64 AGACATGTCTTACACTGGCA--CAACTCT-TA
* * *
41248014 TCCGATACCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTA-GCCGAAGCATGTCCCA
1 GCCGAT-CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGGCTGATGCATGTCCCA
41248078 GACATGTCTTACACTGGC
65 GACATGTCTTACACTGGC
41248096 GCACAAATCA
Statistics
Matches: 142, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
89 2 0.01
91 35 0.25
92 15 0.11
93 21 0.15
94 49 0.35
95 16 0.11
96 1 0.01
97 3 0.02
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (92 bp):
GCCGATCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGGCTGATGCATGTCCCAG
ACATGTCTTACACTGGCACAACTCTTA
Found at i:41248471 original size:30 final size:30
Alignment explanation
Indices: 41248435--41248493 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
41248425 TAAATTTACA
* *
41248435 ACTTTGGTAAAATGACCATTTTGCCCCTAG
1 ACTTTGGCAAAATGACCATTTTACCCCTAG
41248465 ACTTTGGCAAAATGACCATTTTACCCCTA
1 ACTTTGGCAAAATGACCATTTTACCCCTA
41248494 TGCCCGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (30 bp):
ACTTTGGCAAAATGACCATTTTACCCCTAG
Found at i:41249544 original size:44 final size:44
Alignment explanation
Indices: 41249478--41249563 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
41249468 TACATGTATT
* * *
41249478 GCATCCATTATGAACTCAGACCAATTCAACGAGTTCGGATGCTG
1 GCATCCATAATGAACTCAGACCAATTCAACGAGCTCAGATGCTG
*
41249522 GCATCCATAATGAACTCGGACCAATTCAACGAGCTCAGATGC
1 GCATCCATAATGAACTCAGACCAATTCAACGAGCTCAGATGC
41249564 CTCATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (44 bp):
GCATCCATAATGAACTCAGACCAATTCAACGAGCTCAGATGCTG
Found at i:41250317 original size:20 final size:20
Alignment explanation
Indices: 41250292--41250330 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41250282 ATAATTTCAA
41250292 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
41250312 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
41250331 AATAGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:41252278 original size:24 final size:24
Alignment explanation
Indices: 41252248--41252301 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
41252238 AATCAAGTAA
41252248 AATTAAATTAATCAAATTAATTAG
1 AATTAAATTAATCAAATTAATTAG
41252272 AATTAAATTAATCAAATTAATTAG
1 AATTAAATTAATCAAATTAATTAG
41252296 AATTAA
1 AATTAA
41252302 TATGACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (24 bp):
AATTAAATTAATCAAATTAATTAG
Found at i:41256431 original size:21 final size:21
Alignment explanation
Indices: 41256405--41256447 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41256395 ACTAATAGTG
41256405 TTAGATTACAAGTTATTTGCA
1 TTAGATTACAAGTTATTTGCA
41256426 TTAGATTACAAGTTATTTGCA
1 TTAGATTACAAGTTATTTGCA
41256447 T
1 T
41256448 GCAAATATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (21 bp):
TTAGATTACAAGTTATTTGCA
Found at i:41271901 original size:32 final size:32
Alignment explanation
Indices: 41271865--41271928 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
41271855 AGGTTAGCAT
41271865 CTTTCATAGCTTGAAAGTTTTCCATTTGTCTA
1 CTTTCATAGCTTGAAAGTTTTCCATTTGTCTA
41271897 CTTTCATAGCTTGAAAGTTTTCCATTTGTCTA
1 CTTTCATAGCTTGAAAGTTTTCCATTTGTCTA
41271929 TCTCGGAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (32 bp):
CTTTCATAGCTTGAAAGTTTTCCATTTGTCTA
Found at i:41282770 original size:51 final size:51
Alignment explanation
Indices: 41282645--41282840 Score: 270
Period size: 51 Copynumber: 3.9 Consensus size: 51
41282635 TAGATAAGGC
* * *
41282645 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACACGTGACCT-AA-C
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGT
* * * *
41282695 CATCTGATACACATAGTAGCCTGCACTTAGTACTACACACATGATTGAAGT
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGT
* * *
41282746 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGT
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGT
*
41282797 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
41282841 CCTCACAATA
Statistics
Matches: 128, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
49 1 0.01
50 41 0.32
51 86 0.67
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (51 bp):
TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGT
Found at i:41282788 original size:101 final size:102
Alignment explanation
Indices: 41282645--41282836 Score: 287
Period size: 101 Copynumber: 1.9 Consensus size: 102
41282635 TAGATAAGGC
* * *
41282645 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACACGTGACCTAA-CCATCTGATACACAT
1 TATCAGGTACGCATAGTAGCCTGCACATAGTACTACACACGTGACCGAAGCCATCGGATACACAT
41282709 AGTAGCCTGCACTTAGTACTACACACATGATTGAAGT
66 AGTAGCCTGCACTTAGTACTACACACATGATTGAAGT
* * * ** * *
41282746 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGTTATCGGGTACGCAT
1 TATCAGGTACGCATAGTAGCCTGCACATAGTACTACACACGTGACCGAAGCCATCGGATACACAT
41282811 AGTAGCCTGCACTTAGTACTACACAC
66 AGTAGCCTGCACTTAGTACTACACAC
41282837 GTGACCTCAC
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 44 0.55
102 36 0.45
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (102 bp):
TATCAGGTACGCATAGTAGCCTGCACATAGTACTACACACGTGACCGAAGCCATCGGATACACAT
AGTAGCCTGCACTTAGTACTACACACATGATTGAAGT
Found at i:41283119 original size:27 final size:27
Alignment explanation
Indices: 41283089--41283142 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
41283079 TCATACAACC
* *
41283089 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
41283116 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
41283143 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:41289170 original size:28 final size:28
Alignment explanation
Indices: 41289105--41289228 Score: 194
Period size: 28 Copynumber: 4.4 Consensus size: 28
41289095 GAGATTGGCG
* * * *
41289105 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
41289134 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
41289162 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
41289190 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41289218 CTGAGTGTGCG
1 CTAAGTGTGCG
41289229 GACTTAATAT
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
28 75 0.83
29 15 0.17
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:41297586 original size:38 final size:39
Alignment explanation
Indices: 41297535--41297611 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
41297525 TTCTTAGGAG
41297535 TTTAATTTAATGTAACATTTC-AAAAAAATATTTTTCTA
1 TTTAATTTAATGTAACATTTCAAAAAAAATATTTTTCTA
**
41297573 TTTAATTTAATGTAATTTTTCAAAAAAAATATTTTTCTA
1 TTTAATTTAATGTAACATTTCAAAAAAAATATTTTTCTA
41297612 AGTAGCCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 19 0.53
39 17 0.47
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (39 bp):
TTTAATTTAATGTAACATTTCAAAAAAAATATTTTTCTA
Found at i:41301179 original size:120 final size:119
Alignment explanation
Indices: 41300957--41301219 Score: 316
Period size: 120 Copynumber: 2.2 Consensus size: 119
41300947 TCCTCGTTCA
* * **
41300957 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
* * * *
41301022 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCAC
66 TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATAC-ACTTAGCAC
* *
41301075 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACCCGGA
** * ** *
41301140 TTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
64 TTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATATACACTTAGCAC
*
41301196 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41301220 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 36 0.30
120 80 0.66
121 6 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATACACTTAGCAC
Found at i:41301180 original size:40 final size:40
Alignment explanation
Indices: 41300957--41301166 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
41300947 TCCTCGTTCA
* * * ** *
41300957 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
41300996 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
41301036 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
41301076 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
41301116 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
41301156 AAGGCCTTCGG
1 AATGCCTTCGG
41301167 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:41301203 original size:80 final size:80
Alignment explanation
Indices: 41300960--41301219 Score: 267
Period size: 80 Copynumber: 3.3 Consensus size: 80
41300950 TCGTTCAAAT
* * * ** * * *
41300960 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
41301024 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
* * *
41301039 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
41301104 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
** * **
41301119 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
*
41301183 ATTC-ACTTAGCAC-AAA
65 A-ACAAC-TAGCACGAAA
*
41301199 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
41301220 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
79 33 0.21
80 120 0.75
81 6 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ACAACTAGCACGAAA
Found at i:41301228 original size:41 final size:41
Alignment explanation
Indices: 41301151--41301228 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41301141 TTAGTATCTC
* * *
41301151 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41301192 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41301229 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41303020 original size:22 final size:21
Alignment explanation
Indices: 41302994--41303042 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
41302984 TTTGTACTTA
*
41302994 AATTATTCACATAATGAATTTT
1 AATTATT-ACATAATAAATTTT
*
41303016 AATTAATTTCATAATAAATTTT
1 AATT-ATTACATAATAAATTTT
41303038 AATTA
1 AATTA
41303043 ATTTTGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
AATTATTACATAATAAATTTT
Found at i:41303023 original size:10 final size:10
Alignment explanation
Indices: 41303005--41303052 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
41302995 ATTATTCACA
*
41303005 TAATGAATTT
1 TAATTAATTT
41303015 TAATTAATTT
1 TAATTAATTT
*
41303025 CATAATAAATTT
1 --TAATTAATTT
41303037 TAATTAATTT
1 TAATTAATTT
*
41303047 TGATTA
1 TAATTA
41303053 CTTTCGATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 23 0.72
12 9 0.28
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (10 bp):
TAATTAATTT
Found at i:41303043 original size:22 final size:22
Alignment explanation
Indices: 41303003--41303046 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41302993 AAATTATTCA
*
41303003 CATAATGAATTTTAATTAATTT
1 CATAATAAATTTTAATTAATTT
41303025 CATAATAAATTTTAATTAATTT
1 CATAATAAATTTTAATTAATTT
41303047 TGATTACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
CATAATAAATTTTAATTAATTT
Found at i:41314827 original size:5 final size:5
Alignment explanation
Indices: 41314813--41314842 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
41314803 TTTTTTAATC
*
41314813 TATAA AATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA
41314843 AAATAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
TATAA
Found at i:41317647 original size:29 final size:29
Alignment explanation
Indices: 41317614--41317673 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
41317604 TAAGGTAAAA
41317614 TTAAAGTAGTTTTACACTATTTTTTATCT
1 TTAAAGTAGTTTTACACTATTTTTTATCT
41317643 TTAAAGTAGTTTTACACTATTTTTTATCT
1 TTAAAGTAGTTTTACACTATTTTTTATCT
41317672 TT
1 TT
41317674 TTGTATGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (29 bp):
TTAAAGTAGTTTTACACTATTTTTTATCT
Found at i:41319288 original size:6 final size:6
Alignment explanation
Indices: 41319273--41319306 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
41319263 GATCATTCTT
* *
41319273 ATTTTC ATTTCT ATTTCC ATTTCC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
41319307 TTGGAAACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (6 bp):
ATTTCC
Found at i:41325326 original size:50 final size:49
Alignment explanation
Indices: 41325251--41325512 Score: 157
Period size: 46 Copynumber: 5.6 Consensus size: 49
41325241 GTATAATACG
* *
41325251 GATGCCATATCCCAGACATGGTCTTACACTAG-C-TCTCATATATTCGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGACACCTC-TATA-T-GTGCC
* * * *
41325301 GATGCCATGTCCCAAACATAGTCTTACA-TTGACACCTCTATATGTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGACACCTCTATATGTGCC
* *
41325349 GATGCCATGTCCCAGACATGGTCTTACACTA-ACACATCT-TGTG-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGACACCTCTATATGTGCC
* * * * * * **
41325395 GATG-TATATTCTAGACAT-GTCTTACACT-GGCTTACATCTCGA-G-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGAC--ACCTCTATATGTGCC
* *
41325441 GAT-ACATGTCCCAGACAT-GTCTTACACT-G-C-TCTC-ATAATGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGACACCTCTAT-ATGT-GCC
*
41325486 AATG-CATGTCCCAGACAT-GTCTTACAC
1 GATGCCATGTCCCAGACATGGTCTTACAC
41325513 CGACACACAA
Statistics
Matches: 171, Mismatches: 28, Indels: 31
0.74 0.12 0.13
Matches are distributed among these distances:
42 3 0.02
43 1 0.01
44 11 0.06
45 39 0.23
46 40 0.23
47 3 0.02
48 37 0.22
49 4 0.02
50 30 0.18
51 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGACACCTCTATATGTGCC
Found at i:41325373 original size:48 final size:50
Alignment explanation
Indices: 41325251--41325379 Score: 158
Period size: 48 Copynumber: 2.6 Consensus size: 50
41325241 GTATAATACG
* *
41325251 GATGCCATATCCCAGACATGGTCTTACACTAGCTCTCATATATTCGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCCCTCATATATTCGTGCC
* * * *
41325301 GATGCCATGTCCCAAACATAGTCTTACA-TTGACACCTC-TATA-T-GTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAG-C-CCTCATATATTCGTGCC
41325349 GATGCCATGTCCCAGACATGGTCTTACACTA
1 GATGCCATGTCCCAGACATGGTCTTACACTA
41325380 ACACATCTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
48 30 0.45
49 4 0.06
50 30 0.45
51 3 0.04
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (50 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCCCTCATATATTCGTGCC
Found at i:41325432 original size:46 final size:46
Alignment explanation
Indices: 41325251--41325512 Score: 178
Period size: 45 Copynumber: 5.6 Consensus size: 46
41325241 GTATAATACG
* * *
41325251 GATGCCATATCCCAGACATGGTCTTACACTAGCTCTCATATATTCGT-GCC
1 GATG-CATGTCCCAGACAT-GTCTTACACT-GCTCT-ACATCTT-GTGGCC
* * * * * *
41325301 GATGCCATGTCCCAAACATAGTCTTACATTG-AC-ACCTCTATATGTGTC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGCTCTACATCT-TGTG-GCC
**
41325349 GATGCCATGTCCCAGACATGGTCTTACACT-AAC-ACATCTTGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGCTCTACATCTTGTGGCC
* * * * * *
41325395 GATGTATATTCTAGACATGTCTTACACTGGCT-TACATCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACT-GCTCTACATCTTGTGGCC
* **
41325441 GATACATGTCCCAGACATGTCTTACACTGCTCT-CATAATGTGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGCTCTACATCTTGTGGCC
*
41325486 AATGCATGTCCCAGACATGTCTTACAC
1 GATGCATGTCCCAGACATGTCTTACAC
41325513 CGACACACAA
Statistics
Matches: 169, Mismatches: 35, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
44 10 0.06
45 46 0.27
46 45 0.27
47 4 0.02
48 37 0.22
49 1 0.01
50 26 0.15
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGCTCTACATCTTGTGGCC
Found at i:41330854 original size:79 final size:81
Alignment explanation
Indices: 41330712--41330894 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 81
41330702 TACTCGTTCA
* * * *
41330712 AATGCCTTCGGGACATAGCCCCG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGGA
* *
41330776 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
* **
41330792 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCTTTC-AGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGAGA-CTTAACCCGG
* *
41330854 ATATGGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
*
41330871 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41330895 CATCATTCGA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
78 2 0.02
79 57 0.66
80 28 0.32
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:41330894 original size:40 final size:40
Alignment explanation
Indices: 41330691--41330894 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
41330681 CGGAATTTAA
** *
41330691 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
41330731 CCCGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41330771 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
41330810 CCGGA-ATTAGTAACTCGCACAAATGCTTTC-AGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
41330850 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41330890 CCGGA
1 CCGGA
41330895 CATCATTCGA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
38 1 0.01
39 32 0.24
40 91 0.67
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41338022 original size:79 final size:80
Alignment explanation
Indices: 41337924--41338106 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
41337914 TACTCGTTCA
* *
41337924 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
*
41337987 ATTTAGTAACTCA-CATC
64 ATATAGTAACTCAGCA-C
* **
41338004 AATGCCTTCGGG-CTTAGCCTGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* * *
41338068 ATGGTCACTTAGCAC
66 ATAGTAACTCAGCAC
*
41338083 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41338107 CATCATTCGA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.68
80 25 0.28
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTCAGCAC
Found at i:41338047 original size:39 final size:40
Alignment explanation
Indices: 41337922--41338106 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
41337912 GCTACTCGTT
*
41337922 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
41337962 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
41338002 TC-AATGCCTTCGGG-CTTAGCCTGGAATTAGTAACTCGCA
1 -CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
41338041 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
41338082 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41338107 CATCATTCGA
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 3 0.02
39 30 0.24
40 76 0.62
41 14 0.11
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:41341983 original size:18 final size:18
Alignment explanation
Indices: 41341957--41341995 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
41341947 AGGCATTAAC
* *
41341957 TCATTCATGAAAATTTCA
1 TCATCCATGAAAATATCA
41341975 TCATCCATGAAAATATCA
1 TCATCCATGAAAATATCA
41341993 TCA
1 TCA
41341996 ATTGCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (18 bp):
TCATCCATGAAAATATCA
Found at i:41342662 original size:48 final size:50
Alignment explanation
Indices: 41342540--41342668 Score: 158
Period size: 48 Copynumber: 2.6 Consensus size: 50
41342530 GTATAATGCA
*
41342540 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATTCGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCCCTCACATATTCGTGCC
* * * * *
41342590 GATGCCATGTCCCAAACATAGTCTTACA-TTGACACCTC-TATA-T-GTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAG-C-CCTCACATATTCGTGCC
41342638 GATGCCATGTCCCAGACATGGTCTTACACTA
1 GATGCCATGTCCCAGACATGGTCTTACACTA
41342669 ACACATCTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
48 30 0.45
49 4 0.06
50 30 0.45
51 3 0.04
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (50 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCCCTCACATATTCGTGCC
Found at i:41342721 original size:46 final size:46
Alignment explanation
Indices: 41342540--41342854 Score: 203
Period size: 46 Copynumber: 6.7 Consensus size: 46
41342530 GTATAATGCA
* * *
41342540 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATTCGT-GCC
1 GATG-CATATCCCAGACAT-GTCTTACACTGGCTCT--CATCTT-GTGGCC
* * * * * * *
41342590 GATGCCATGTCCCAAACATAGTCTTACATTGACAC-C-TCTATATGTGTC
1 GATG-CATATCCCAGACAT-GTCTTACACTGGCTCTCATCT-TGTG-GCC
* ** *
41342638 GATGCCATGTCCCAGACATGGTCTTACACT--AACACATCTTGTGGCC
1 GATG-CATATCCCAGACAT-GTCTTACACTGGCTCTCATCTTGTGGCC
* * *
41342684 GATGCATATTCCAGACATGTCTTACACTGGCT-TACATCTTGAGGTC
1 GATGCATATCCCAGACATGTCTTACACTGGCTCT-CATCTTGTGGCC
* * **
41342730 GATACATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAT-GCC
1 GATGCATATCCCAGACATGTCTTACACTGGCTCTCATCT-TGTGGCC
* **
41342776 GATACCATATCCCAGACATAGTCTTACACTGGCTCTCATAATGTGGCC
1 GAT-GCATATCCCAGACAT-GTCTTACACTGGCTCTCATCTTGTGGCC
* * *
41342824 AATGCATGTCCCAGACATGTTTTACACTGGC
1 GATGCATATCCCAGACATGTCTTACACTGGC
41342855 ACACAAATAA
Statistics
Matches: 213, Mismatches: 39, Indels: 30
0.76 0.14 0.11
Matches are distributed among these distances:
44 10 0.05
45 12 0.06
46 72 0.34
47 34 0.16
48 56 0.26
50 29 0.14
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (46 bp):
GATGCATATCCCAGACATGTCTTACACTGGCTCTCATCTTGTGGCC
Found at i:41342832 original size:94 final size:93
Alignment explanation
Indices: 41342540--41342854 Score: 277
Period size: 94 Copynumber: 3.3 Consensus size: 93
41342530 GTATAATGCA
* * * *
41342540 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATTCGTGCCGATGCCATGTCCCAA
1 GATG-CATGTCCCAGACATGGTCTTACACTGGCTCT--CAT-CTCGTGCCGAT-CCATATCCCAG
* * *
41342605 ACATAGTCTTACATTGACACCTC-TATATGT-GTC
61 ACATAGTCTTACACTGGC-TCTCATA-ATGTGGTC
** * * * *
41342638 GATGCCATGTCCCAGACATGGTCTTACACT--AACACATCTTGTGGCCGATGCATATTCCAGACA
1 GATG-CATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCGT-GCCGATCCATATCCCAGACA
** *
41342701 T-GTCTTACACTGGCT-TACATCTTGAGGTC
64 TAGTCTTACACTGGCTCT-CATAATGTGGTC
* *
41342730 GATACATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCAATGCCGATACCATATCCCAGACA
1 GATGCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTC-GTGCCGAT-CCATATCCCAGACA
*
41342794 TAGTCTTACACTGGCTCTCATAATGTGGCC
64 TAGTCTTACACTGGCTCTCATAATGTGGTC
* *
41342824 AATGCATGTCCCAGACAT-GTTTTACACTGGC
1 GATGCATGTCCCAGACATGGTCTTACACTGGC
41342855 ACACAAATAA
Statistics
Matches: 177, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
90 11 0.06
91 17 0.10
92 30 0.17
93 28 0.16
94 59 0.33
95 1 0.01
96 1 0.01
98 30 0.17
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (93 bp):
GATGCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCGTGCCGATCCATATCCCAGACATA
GTCTTACACTGGCTCTCATAATGTGGTC
Found at i:41352922 original size:27 final size:27
Alignment explanation
Indices: 41352884--41352964 Score: 153
Period size: 27 Copynumber: 3.0 Consensus size: 27
41352874 TAAGCATTTT
41352884 CATGCTTAGTAACCTCGAATAACCAGA
1 CATGCTTAGTAACCTCGAATAACCAGA
*
41352911 CATGCTTAGTAACCTCGAATAACCGGA
1 CATGCTTAGTAACCTCGAATAACCAGA
41352938 CATGCTTAGTAACCTCGAATAACCAGA
1 CATGCTTAGTAACCTCGAATAACCAGA
41352965 AAGTAAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (27 bp):
CATGCTTAGTAACCTCGAATAACCAGA
Found at i:41355028 original size:37 final size:38
Alignment explanation
Indices: 41354987--41355061 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 38
41354977 CCTATCATAC
41354987 GAGGATAACAAATATAAAATGACTAAATAT-AATTTAT
1 GAGGATAACAAATATAAAATGACTAAATATAAATTTAT
**
41355024 GAGGATAATGAATATAAAATGACTAAATATAAATTTAT
1 GAGGATAACAAATATAAAATGACTAAATATAAATTTAT
41355062 TCCTTACTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 28 0.80
38 7 0.20
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (38 bp):
GAGGATAACAAATATAAAATGACTAAATATAAATTTAT
Found at i:41357494 original size:36 final size:36
Alignment explanation
Indices: 41357447--41357518 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
41357437 CGTATCTTAG
*
41357447 ACACTTCGCCACATCTACGAGTTTGATCCTTACTTT
1 ACACCTCGCCACATCTACGAGTTTGATCCTTACTTT
**
41357483 ACACCTCGCCACATCTGTGAGTTTGATCCTTACTTT
1 ACACCTCGCCACATCTACGAGTTTGATCCTTACTTT
41357519 TTGTCTCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (36 bp):
ACACCTCGCCACATCTACGAGTTTGATCCTTACTTT
Found at i:41365881 original size:43 final size:43
Alignment explanation
Indices: 41365833--41365921 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
41365823 TGGTAGGAAC
41365833 GCTAAAAAAATGAAAAGAAAAAGTATTATTATTTTCATCCATT
1 GCTAAAAAAATGAAAAGAAAAAGTATTATTATTTTCATCCATT
41365876 GCTAAAAAAATGAAAAGAAAAAGTATTATTATTTTCATCCATT
1 GCTAAAAAAATGAAAAGAAAAAGTATTATTATTTTCATCCATT
41365919 GCT
1 GCT
41365922 TGGTTAACTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (43 bp):
GCTAAAAAAATGAAAAGAAAAAGTATTATTATTTTCATCCATT
Found at i:41367140 original size:4 final size:4
Alignment explanation
Indices: 41367131--41367159 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
41367121 AACTTGTGAA
41367131 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
41367160 CTACCAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:41368252 original size:17 final size:18
Alignment explanation
Indices: 41368218--41368262 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
41368208 GTCCTAGATA
41368218 TTAT-TTTTTTATAAAATT
1 TTATATTTTTTAT-AAATT
41368236 TTATATTTTTTAT-AATT
1 TTATATTTTTTATAAATT
41368253 TTATATTTTT
1 TTATATTTTT
41368263 ACGACTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.54
18 4 0.15
19 8 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATTTTTTATAAATT
Found at i:41368253 original size:10 final size:10
Alignment explanation
Indices: 41368222--41368313 Score: 52
Period size: 10 Copynumber: 9.6 Consensus size: 10
41368212 TAGATATTAT
41368222 TTTTTTATAA
1 TTTTTTATAA
**
41368232 AATTTTAT-A
1 TTTTTTATAA
41368241 TTTTTTATAA
1 TTTTTTATAA
41368251 --TTTTAT-A
1 TTTTTTATAA
**
41368258 -TTTTTACGA
1 TTTTTTATAA
*
41368267 CTTTTTATAAA
1 TTTTTTAT-AA
*
41368278 TTTTTTACAA
1 TTTTTTATAA
*
41368288 -CTTTTATAA
1 TTTTTTATAA
*
41368297 TTCTTTTATGA
1 TT-TTTTATAA
41368308 TTTTTT
1 TTTTTT
41368314 TCTATAGTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 14
0.70 0.15 0.16
Matches are distributed among these distances:
7 1 0.02
8 11 0.18
9 15 0.24
10 19 0.31
11 16 0.26
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:41368282 original size:20 final size:20
Alignment explanation
Indices: 41368258--41368296 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
41368248 TAATTTTATA
*
41368258 TTTTTACGACTTTTTATAAAT
1 TTTTTACAAC-TTTTATAAAT
41368279 TTTTTACAACTTTTATAA
1 TTTTTACAACTTTTATAA
41368297 TTCTTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTACAACTTTTATAAAT
Done.