Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 161 of 284
Found at i:53964969 original size:39 final size:38
Alignment explanation
Indices: 53964818--53964985 Score: 135
Period size: 40 Copynumber: 4.2 Consensus size: 38
53964808 GGACTAAGAT
* *
53964818 CCGAAGGCATT-TGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTCTGT--GAGTTACTAA-ACCGGGTTAAGTC
* * *
53964858 CCGAAGGCCTT-TGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTCTGT--GAGTTACTAA-ACCGGGTTAAGTC
* *
53964898 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTC-TGTGAGTTACT-AAA-CCGGGTTAAGTC
* * *
53964938 CCGAAGGCATTCTATGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTCTGTGAGTTACTA-AACCGGGTTAAGTC
53964977 CCGAAGGCA
1 CCGAAGGCA
53964986 CTTGAACGAG
Statistics
Matches: 109, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
39 27 0.25
40 80 0.73
42 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (38 bp):
CCGAAGGCATTCTGTGAGTTACTAAACCGGGTTAAGTC
Found at i:53977144 original size:31 final size:31
Alignment explanation
Indices: 53977074--53977145 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
53977064 TTGGAGGATT
*
53977074 ACACGCCCATGTGGGTGGGCCGTGTAGTTCC
1 ACACGCCCGTGTGGGTGGGCCGTGTAGTTCC
*
53977105 ACACGCCCGTGTGGGTGGGCCGTGTGGTTCC
1 ACACGCCCGTGTGGGTGGGCCGTGTAGTTCC
*
53977136 ACATGCCCGT
1 ACACGCCCGT
53977146 ATCTTCAGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.11, C:0.31, G:0.36, T:0.22
Consensus pattern (31 bp):
ACACGCCCGTGTGGGTGGGCCGTGTAGTTCC
Found at i:53978410 original size:42 final size:42
Alignment explanation
Indices: 53978247--53978413 Score: 144
Period size: 42 Copynumber: 4.0 Consensus size: 42
53978237 AATCATACCA
* * ** *
53978247 ATGCCATATCCTAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGACATGGTCTTACATGAAATCTCATAACG
* * * * *
53978289 AAGCCAATAACCCAG-CAATGGTCTTACACG-ATTTTCATATA-G
1 ATGCC-ATATCCCAGAC-ATGGTCTTACATGAAATCTCATA-ACG
*
53978331 ATGCCATGTCCCAGACATGGTCTTACATGAAATCTCATAACG
1 ATGCCATATCCCAGACATGGTCTTACATGAAATCTCATAACG
* * *
53978373 ATGTCATATCCCAGATATGGTCTTACACTTAAA-CTCATAAC
1 ATGCCATATCCCAGACATGGTCTTACA-TGAAATCTCATAAC
53978414 CCTAATGTCA
Statistics
Matches: 99, Mismatches: 19, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
41 20 0.20
42 56 0.57
43 23 0.23
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACATGAAATCTCATAACG
Found at i:53978411 original size:84 final size:84
Alignment explanation
Indices: 53978247--53978411 Score: 181
Period size: 84 Copynumber: 2.0 Consensus size: 84
53978237 AATCATACCA
* * ** *
53978247 ATGCCATATCCTAGATATGGTCTTACATGGGATCTCATATCGAAGCCAATAACCCAGCAATGGTC
1 ATGCCATATCCCAGACATGGTCTTACATGAAATCTCATAACGAAGCCAATAACCCAGCAATGGTC
***
53978312 TTACACGATTTTCATATAG
66 TTACACGAAACTCATATAG
* * * *
53978331 ATGCCATGTCCCAGACATGGTCTTACATGAAATCTCATAACGATGTC-ATATCCCAG-ATATGGT
1 ATGCCATATCCCAGACATGGTCTTACATGAAATCTCATAACGAAGCCAATAACCCAGCA-ATGGT
*
53978394 CTTACACTTAAACTCATA
65 CTTACAC-GAAACTCATA
53978412 ACCCTAATGT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
82 1 0.02
83 20 0.30
84 45 0.68
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.30
Consensus pattern (84 bp):
ATGCCATATCCCAGACATGGTCTTACATGAAATCTCATAACGAAGCCAATAACCCAGCAATGGTC
TTACACGAAACTCATATAG
Found at i:53981955 original size:2 final size:2
Alignment explanation
Indices: 53981948--53982011 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
53981938 TTTATGGTTT
53981948 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
53981990 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
53982012 AAGAAATACA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:53987667 original size:39 final size:40
Alignment explanation
Indices: 53987582--53987667 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 40
53987572 AAAATAACTC
**
53987582 TTAATTTAAAGAAAATAAATGTAATTATCTAAAAAAGATT
1 TTAATTTAAAGAAAATAAACATAATTATCTAAAAAAGATT
*
53987622 TCAATTTAAA-AAAATAAACATAATTATCTAAAAAA-AGTT
1 TTAATTTAAAGAAAATAAACATAATTATCTAAAAAAGA-TT
53987661 TTAATTT
1 TTAATTT
53987668 TTTAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
38 1 0.02
39 31 0.76
40 9 0.22
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (40 bp):
TTAATTTAAAGAAAATAAACATAATTATCTAAAAAAGATT
Found at i:53987803 original size:14 final size:15
Alignment explanation
Indices: 53987786--53987822 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
53987776 ATAATGAATT
53987786 ATATTTCACTTA-AA
1 ATATTTCACTTATAA
*
53987800 ATATTTTACTTATAA
1 ATATTTCACTTATAA
53987815 A-ATTTCAC
1 ATATTTCAC
53987823 ATCAACTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATTTCACTTATAA
Found at i:53989311 original size:15 final size:15
Alignment explanation
Indices: 53989291--53989319 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53989281 ATAAAAGATA
53989291 AAAATTATAATAATG
1 AAAATTATAATAATG
53989306 AAAATTATAATAAT
1 AAAATTATAATAAT
53989320 TTATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATTATAATAATG
Found at i:53990981 original size:79 final size:78
Alignment explanation
Indices: 53990879--53991102 Score: 281
Period size: 79 Copynumber: 2.8 Consensus size: 78
53990869 GCTCCTCGTT
* *
53990879 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
53990944 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
53990959 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
53991023 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
53991037 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
53991101 GA
63 GA
53991103 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
78 36 0.29
79 56 0.44
80 34 0.27
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:53990996 original size:39 final size:40
Alignment explanation
Indices: 53990879--53991102 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
53990869 GCTCCTCGTT
* *
53990879 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
53990919 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
53990959 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
53990998 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
53991037 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
53991078 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53991103 CATCATTCAA
Statistics
Matches: 166, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.45
40 77 0.46
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:53998864 original size:40 final size:39
Alignment explanation
Indices: 53998827--53998918 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
53998817 GCTACTCGTT
*
53998827 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
53998867 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
53998906 CAAATGCCTTCGG
1 CAAATGCCTTCGG
53998919 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:53998898 original size:39 final size:40
Alignment explanation
Indices: 53998808--53998971 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
53998798 CGGAATTTAA
** *
53998808 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
53998848 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
53998887 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
53998927 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
53998967 CCGGA
1 CCGGA
53998972 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54007591 original size:57 final size:57
Alignment explanation
Indices: 54007523--54007630 Score: 198
Period size: 57 Copynumber: 1.9 Consensus size: 57
54007513 TTTCTGATTC
*
54007523 GGCCCCACTTTATTGATTGTGCTGCAAATTGGTCCTTTTCTGCTTATTTTTTACTTT
1 GGCCCCACTTTATTGACTGTGCTGCAAATTGGTCCTTTTCTGCTTATTTTTTACTTT
*
54007580 GGCCCCACTTTATTGACTGTGCTGCAAATTGGTCCTTTTCTGCTTGTTTTT
1 GGCCCCACTTTATTGACTGTGCTGCAAATTGGTCCTTTTCTGCTTATTTTT
54007631 GACTCACAGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (57 bp):
GGCCCCACTTTATTGACTGTGCTGCAAATTGGTCCTTTTCTGCTTATTTTTTACTTT
Found at i:54013796 original size:25 final size:25
Alignment explanation
Indices: 54013732--54013826 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
54013722 TCATGTACAT
* *
54013732 GTATGCTCATATGAGCTGTGAATCA
1 GTATGCTCACACGAGCTGTGAATCA
*
54013757 GTATGCTCACTCGAGCTGT-AGATCA
1 GTATGCTCACACGAGCTGTGA-ATCA
* ** *
54013782 GTATGCTCTCACGAGCAATAAATC-
1 GTATGCTCACACGAGCTGTGAATCA
*
54013806 GATATTCTCACACGAGCTGTG
1 G-TATGCTCACACGAGCTGTG
54013827 GGTTGGAACA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
24 2 0.04
25 52 0.95
26 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAATCA
Found at i:54015651 original size:50 final size:50
Alignment explanation
Indices: 54015585--54015983 Score: 474
Period size: 50 Copynumber: 7.9 Consensus size: 50
54015575 TAAGACGGTT
* *
54015585 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCACATTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* * * * * *
54015635 TTAGGTCGCATGTGTAGTACTAAATGCAGGCTACTATGCGTACCTGATAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* * ** *
54015685 CTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATTAGATGG
1 -TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* * *
54015736 TTAGGTCACGTGTGTAATACTAAGTGCAGACTACTACGTGTACCAGATTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
** ** * *
54015786 TTAGGTCATATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* * * * * *
54015836 CTTCGATCACGTATGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGG
1 -TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* * *
54015887 TTAGGTCACGTGTGTAGTACTAGGCGTAGGCTACTATGTGTACCAGATTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* * *
54015937 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGAGTACCAGA
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
54015984 GAGCTCCGGT
Statistics
Matches: 286, Mismatches: 61, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
50 207 0.72
51 79 0.28
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
Found at i:54015716 original size:101 final size:99
Alignment explanation
Indices: 54015585--54015983 Score: 449
Period size: 101 Copynumber: 4.0 Consensus size: 99
54015575 TAAGACGGTT
* *
54015585 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCACATTGTTAGGTCGCATGTGT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCACATTGTTAGGTCACATGTGT
* * * *
54015650 AGTACTAAATGCAGGCTACTATGCGTACCTGATAG
66 AGTACTAAGTGCAGGCTACTACGTGTACCAGAT-G
* * ** * * *
54015685 CTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATTAGATGGTTAGGTCACGTGTG
1 -TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCACATTGTTAGGTCACATGTG
* *
54015750 TAATACTAAGTGCAGACTACTACGTGTACCAGATTG
65 TAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TG
** ** * * * * *
54015786 TTAGGTCATATGTGTAGTACTAAGTGCAGGCTACTATGCATACC-CGATAGCTTCGATCACGTAT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAC-ATTG-TTAGGTCACATGT
*
54015850 GTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGG
64 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-G
* * * * *
54015887 TTAGGTCACGTGTGTAGTACTAGGCGTAGGCTACTATGTGTACCAGATTGTTAGGTCGCATGTGT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCACATTGTTAGGTCACATGTGT
* *
54015952 AGTACTAAGTGCAGGCTACTATGAGTACCAGA
66 AGTACTAAGTGCAGGCTACTACGTGTACCAGA
54015984 GAGCTCCGGT
Statistics
Matches: 245, Mismatches: 48, Indels: 11
0.81 0.16 0.04
Matches are distributed among these distances:
100 79 0.32
101 165 0.67
102 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (99 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCACATTGTTAGGTCACATGTGT
AGTACTAAGTGCAGGCTACTACGTGTACCAGATG
Found at i:54015819 original size:151 final size:151
Alignment explanation
Indices: 54015556--54015980 Score: 645
Period size: 151 Copynumber: 2.8 Consensus size: 151
54015546 GTTGTCCTAT
* *
54015556 GTGCAGACTACTATGTGT-TTAAGACGGTTTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACT
1 GTGCAGGCTACTATGTGTATT-AGATGG--TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
54015620 ACGTGTACCACATTGTTAGGTCGCATGTGTAGTACTAAATGCAGGCTACTATGCGTACCTGATAG
63 ACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAG
* *
54015685 CTTTGATCACGTGTGTAGTACTAA
128 CTTCGATCACGTATGTAGTACTAA
* *
54015709 GTGCAGGCTACTATGTGTATTAGATGGTTAGGTCACGTGTGTAATACTAAGTGCAGACTACTACG
1 GTGCAGGCTACTATGTGTATTAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACG
** *
54015774 TGTACCAGATTGTTAGGTCATATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAGCTT
66 TGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTT
54015839 CGATCACGTATGTAGTACTAA
131 CGATCACGTATGTAGTACTAA
* * * * * *
54015860 GTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAGGCGTAGGCTACTATG
1 GTGCAGGCTACTATGTGTATTAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACG
*
54015925 TGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGAGTACC
66 TGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
54015981 AGAGAGCTCC
Statistics
Matches: 247, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
151 223 0.90
153 22 0.09
154 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (151 bp):
GTGCAGGCTACTATGTGTATTAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACG
TGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTT
CGATCACGTATGTAGTACTAA
Found at i:54018020 original size:30 final size:30
Alignment explanation
Indices: 54017984--54018044 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
54017974 AAAGTGTGAT
54017984 TTGAGTTTCGTAGACCCAAATAAGGGACTA
1 TTGAGTTTCGTAGACCCAAATAAGGGACTA
54018014 TTGAGTTTCGTAGACCCAAATAAGGGACTA
1 TTGAGTTTCGTAGACCCAAATAAGGGACTA
54018044 T
1 T
54018045 GTACATGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (30 bp):
TTGAGTTTCGTAGACCCAAATAAGGGACTA
Found at i:54026085 original size:8 final size:8
Alignment explanation
Indices: 54026072--54026102 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
54026062 ATTTTTATCA
*
54026072 TTAATTAT
1 TTAATTAC
54026080 TTAATTAC
1 TTAATTAC
54026088 TTAATTAC
1 TTAATTAC
54026096 TTAATTA
1 TTAATTA
54026103 ACCTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (8 bp):
TTAATTAC
Found at i:54026860 original size:27 final size:28
Alignment explanation
Indices: 54026830--54026895 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
54026820 CGTTCCTTTT
*
54026830 GAGTTTGCCATGAA-TACCATTCATTTA
1 GAGTTCGCCATGAAGTACCATTCATTTA
* *
54026857 GAGTTCACCAT-AAGTACCATTCCTTTA
1 GAGTTCGCCATGAAGTACCATTCATTTA
54026884 GAGTTCGCCATG
1 GAGTTCGCCATG
54026896 GTGGTGTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (28 bp):
GAGTTCGCCATGAAGTACCATTCATTTA
Found at i:54027817 original size:165 final size:166
Alignment explanation
Indices: 54027542--54027873 Score: 603
Period size: 165 Copynumber: 2.0 Consensus size: 166
54027532 CCAGACTTCC
54027542 ACCTCGATATTAGCAGCAAGCACTTGACATGGAGTAATTACTGGTGAGGACCCAGATCTACAACT
1 ACCTCGATATTAGCAGCAAGCACTTGACATGGAGTAATTACTGGTGAGGACCCAGATCTACAACT
*
54027607 CCAGCTTGAAAGGGAAAGAAATATAACAAGTTCTTTAATATTCAGCAATAATACTTCTTGAAGAA
66 CCAGCTTGAAAGGGAAAGAAATATAACAAGTTCTTTAAGATTCAGCAATAATACTTCTTGAAGAA
*
54027672 GGAAAACTCCCTCTTTTTAGACCCGAATATCAATAT
131 GGAAAACTCCCTCTTTTTAGACCCGAAAATCAATAT
54027708 ACCTCGATATTAGCAG-AAGCACTTGACATGGAGTAATTACTGGTGAGGACCCAGATCTACAACT
1 ACCTCGATATTAGCAGCAAGCACTTGACATGGAGTAATTACTGGTGAGGACCCAGATCTACAACT
* *
54027772 CCAGCTTGAAGGGGAAAGAAATATAACAAGTTCTTTAAGATTCAGCGATAATACTTCTTGAAGAA
66 CCAGCTTGAAAGGGAAAGAAATATAACAAGTTCTTTAAGATTCAGCAATAATACTTCTTGAAGAA
**
54027837 GGAAAACTCCCTCTTTTTAGATTCGAAAATCAATAT
131 GGAAAACTCCCTCTTTTTAGACCCGAAAATCAATAT
54027873 A
1 A
54027874 TGTAACCTAC
Statistics
Matches: 160, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
165 144 0.90
166 16 0.10
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (166 bp):
ACCTCGATATTAGCAGCAAGCACTTGACATGGAGTAATTACTGGTGAGGACCCAGATCTACAACT
CCAGCTTGAAAGGGAAAGAAATATAACAAGTTCTTTAAGATTCAGCAATAATACTTCTTGAAGAA
GGAAAACTCCCTCTTTTTAGACCCGAAAATCAATAT
Found at i:54028691 original size:13 final size:13
Alignment explanation
Indices: 54028673--54028698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54028663 GTATACACAA
54028673 CATACTCATACAC
1 CATACTCATACAC
54028686 CATACTCATACAC
1 CATACTCATACAC
54028699 AATAATGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
CATACTCATACAC
Found at i:54031467 original size:47 final size:47
Alignment explanation
Indices: 54031379--54031496 Score: 161
Period size: 47 Copynumber: 2.5 Consensus size: 47
54031369 TCGAGACGTA
*
54031379 AGCCAGTGTAAGA-CATGTCTAGGACATGCATCGACTATGAGATGAT-
1 AGCCAATGTAAGACCATGTCTAGGACATGCATCGACTATGAGAT-ATG
*
54031425 AGTCAATGTAAGACCATGTCTAGGACATGGCATCGACT-TGAGATATG
1 AGCCAATGTAAGACCATGTCTAGGACAT-GCATCGACTATGAGATATG
* *
54031472 AGCCAGTATAAGACCATGTCTAGGA
1 AGCCAATGTAAGACCATGTCTAGGA
54031497 AACGACATCA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
46 13 0.20
47 42 0.66
48 9 0.14
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (47 bp):
AGCCAATGTAAGACCATGTCTAGGACATGCATCGACTATGAGATATG
Found at i:54036170 original size:50 final size:50
Alignment explanation
Indices: 54036006--54036346 Score: 360
Period size: 50 Copynumber: 6.8 Consensus size: 50
54035996 TGAGAACACA
* * * ***
54036006 TGTGTAGTACTATGTGCAGGCTACCATGTGTTTAAGATGGTTTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGG--TTAGGTCACG
* * * *** *
54036058 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TGGTTAGGTCACG
* * *
54036109 TGTGTAATACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACG
* * * *** *
54036159 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TGGTTAGGTCACG
* * *
54036210 TGTGTAATACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACG
* * *
54036260 TGTGTAGTACTAAGTGCAGGCTACTGCGTGTACCAGATTGTT-GGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACG
* *
54036309 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
54036347 AGCTTCGGTT
Statistics
Matches: 237, Mismatches: 50, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
49 41 0.17
50 86 0.36
51 80 0.34
52 30 0.13
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACG
Found at i:54036293 original size:101 final size:101
Alignment explanation
Indices: 54036006--54036284 Score: 477
Period size: 101 Copynumber: 2.7 Consensus size: 101
54035996 TGAGAACACA
* * ** * * *
54036006 TGTGTAGTACTATGTGCAGGCTACCATGTGTTTAAGATGGTTTTAGGTCACGTGTGTAGTACTAA
1 TGTGTAATACTAAGTGCAGGCTATTACGTGTATCAGATGG--TTAGGTCACGTGTGTAGTACTAA
54036071 GTGCAGGCTACTATGCGTACCCGACAACTTCGGTCACG
64 GTGCAGGCTACTATGCGTACCCGACAACTTCGGTCACG
54036109 TGTGTAATACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGT
1 TGTGTAATACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGT
54036174 GCAGGCTACTATGCGTACCCGACAACTTCGGTCACG
66 GCAGGCTACTATGCGTACCCGACAACTTCGGTCACG
54036210 TGTGTAATACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGT
1 TGTGTAATACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGT
54036275 GCAGGCTACT
66 GCAGGCTACT
54036285 GCGTGTACCA
Statistics
Matches: 169, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
101 136 0.80
103 33 0.20
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TGTGTAATACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGT
GCAGGCTACTATGCGTACCCGACAACTTCGGTCACG
Found at i:54036566 original size:16 final size:15
Alignment explanation
Indices: 54036545--54036575 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
54036535 GGAATGGAGT
54036545 AAGTGAAATTATGTAA
1 AAGTGAAATT-TGTAA
54036561 AAGTGAAATTTGTAA
1 AAGTGAAATTTGTAA
54036576 TAAAACAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (15 bp):
AAGTGAAATTTGTAA
Found at i:54037086 original size:34 final size:34
Alignment explanation
Indices: 54037046--54037114 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
54037036 GTGAGTCTAG
54037046 TTTCTGGAAAAATTATCAGATCTTAATTTGGAGT
1 TTTCTGGAAAAATTATCAGATCTTAATTTGGAGT
54037080 TTTCTGGAAAAATTATCAGATCTTAATTTGGAGT
1 TTTCTGGAAAAATTATCAGATCTTAATTTGGAGT
54037114 T
1 T
54037115 CCGTATCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (34 bp):
TTTCTGGAAAAATTATCAGATCTTAATTTGGAGT
Found at i:54045454 original size:46 final size:46
Alignment explanation
Indices: 54045404--54045625 Score: 288
Period size: 46 Copynumber: 4.8 Consensus size: 46
54045394 TGGTTGAGCA
54045404 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
*
54045450 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * * *
54045496 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
54045541 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
54045589 CCCAAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54045626 GCAGATTACA
Statistics
Matches: 155, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
43 6 0.04
45 4 0.03
46 108 0.70
47 28 0.18
48 4 0.03
50 5 0.03
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:54050457 original size:39 final size:39
Alignment explanation
Indices: 54050379--54050544 Score: 244
Period size: 39 Copynumber: 4.3 Consensus size: 39
54050369 TAATTTATTT
*
54050379 TGAGTCTTTAATTATGTCATAA-TTGAACATCATTAATA
1 TGAGTTTTTAATTATGTCATAATTTGAACATCATTAATA
* *
54050417 TGAGTTTTTAATTATGTCACAATTTGAACATCATTGATA
1 TGAGTTTTTAATTATGTCATAATTTGAACATCATTAATA
*
54050456 TGAGTTTTTAATTATGTCATAATCTGAACATCATTAATA
1 TGAGTTTTTAATTATGTCATAATTTGAACATCATTAATA
* * * *
54050495 AGAGTTTTTAATTATGTCATAGTTTGGACATCTTTAATA
1 TGAGTTTTTAATTATGTCATAATTTGAACATCATTAATA
*
54050534 TGTGTTTTTAA
1 TGAGTTTTTAA
54050545 GTGTGTTTAA
Statistics
Matches: 114, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
38 20 0.18
39 94 0.82
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (39 bp):
TGAGTTTTTAATTATGTCATAATTTGAACATCATTAATA
Found at i:54052891 original size:11 final size:11
Alignment explanation
Indices: 54052869--54052908 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
54052859 TTATTGGCTT
54052869 ATTTATTGACTC
1 ATTTA-TGACTC
54052881 ATTTATGACTC
1 ATTTATGACTC
*
54052892 GTTTATGACTC
1 ATTTATGACTC
*
54052903 GTTTAT
1 ATTTAT
54052909 TTATTAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 22 0.81
12 5 0.19
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (11 bp):
ATTTATGACTC
Found at i:54055698 original size:335 final size:335
Alignment explanation
Indices: 54055088--54055760 Score: 1247
Period size: 335 Copynumber: 2.0 Consensus size: 335
54055078 TTATTATCCC
54055088 GATAGACTGTATTAGTTGTCATAGCTGAGTTATGATCTTGTCGTTCCATAAGACCTTACCGCCAT
1 GATAGACTGTATTAGTTGTCATAGCTGAGTTATGATCTTGTCGTTCCATAAGACCTTACCGCCAT
*
54055153 CGCGGTGTAGCTCCATAGAGCTCGTTGATCACTATCACAGTATTGTTCTATGAAACCTAATAACT
66 CGCGGTGTAGCTCCATAGAGCTCGTTGATCACCATCACAGTATTGTTCTATGAAACCTAATAACT
54055218 TTTGTCACGATGTAGCCTCAAAAGACCAGTTGATAACATTTCATTTCATTTATAACCTTGATGCT
131 TTTGTCACGATGTAGCCTCAAAAGACCAGTTGATAACATTTCATTTCATTTATAACCTTGATGCT
* * * *
54055283 CGAACACTGCAGTGTCTCTTCCACAAGGCCAGGAGCTTTGTACATCACGATTTGCAGCCAGGACA
196 CGAACACTGCAGTGTCTCCTCCACAAGGCCAGGAGCTTTGCACATCACGATTTACAGCCAGAACA
* *
54055348 TTGTATGGCGAAATCTTAATGGAAATCCATTTCTCTATTCATCTGCCTATACCTTTAGTTCACTA
261 TTGTATGGCGAAATCTTAATAGAAATCCATTTCTCTATTCATCTGCCTATACCTTCAGTTCACTA
54055413 TACATACAAT
326 TACATACAAT
54055423 GATAGACTGTATTAGTTGTCATAGCTGAGTTATGATCTTGTCGTTCCATAAGACCTTACCGCCAT
1 GATAGACTGTATTAGTTGTCATAGCTGAGTTATGATCTTGTCGTTCCATAAGACCTTACCGCCAT
* * *
54055488 CGCGGTGTAGCTCCATAGAGCTCGTTGATCACCATCGCGGTGTTGTTCTATGAAACCTAATAACT
66 CGCGGTGTAGCTCCATAGAGCTCGTTGATCACCATCACAGTATTGTTCTATGAAACCTAATAACT
54055553 TTTGTCACGATGTAGCCTCAAAAGACCAGTTGATAACATTTCATTTCATTTATAACCTTGATGCT
131 TTTGTCACGATGTAGCCTCAAAAGACCAGTTGATAACATTTCATTTCATTTATAACCTTGATGCT
*
54055618 CGAACACTGCAGTGTCTCCTCCACAAGGCCCGGAGCTTTGCACATCACGATTTACAGCCAGAACA
196 CGAACACTGCAGTGTCTCCTCCACAAGGCCAGGAGCTTTGCACATCACGATTTACAGCCAGAACA
54055683 TTGTATGGCGAAATCTTAATAGAAATCCATTTCTCTATTCATCTGCCTATACCTTCAGTTCACTA
261 TTGTATGGCGAAATCTTAATAGAAATCCATTTCTCTATTCATCTGCCTATACCTTCAGTTCACTA
54055748 TACATACAAT
326 TACATACAAT
54055758 GAT
1 GAT
54055761 GCTTGAACAC
Statistics
Matches: 327, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
335 327 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (335 bp):
GATAGACTGTATTAGTTGTCATAGCTGAGTTATGATCTTGTCGTTCCATAAGACCTTACCGCCAT
CGCGGTGTAGCTCCATAGAGCTCGTTGATCACCATCACAGTATTGTTCTATGAAACCTAATAACT
TTTGTCACGATGTAGCCTCAAAAGACCAGTTGATAACATTTCATTTCATTTATAACCTTGATGCT
CGAACACTGCAGTGTCTCCTCCACAAGGCCAGGAGCTTTGCACATCACGATTTACAGCCAGAACA
TTGTATGGCGAAATCTTAATAGAAATCCATTTCTCTATTCATCTGCCTATACCTTCAGTTCACTA
TACATACAAT
Found at i:54059974 original size:16 final size:16
Alignment explanation
Indices: 54059955--54059985 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54059945 CTTCTTCACT
54059955 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
54059971 TACTTACTTACTTAA
1 TACTCACTTACTTAA
54059986 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:54059991 original size:20 final size:20
Alignment explanation
Indices: 54059952--54059991 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54059942 AAACTTCTTC
* *
54059952 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
54059972 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
54059992 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:54060102 original size:23 final size:24
Alignment explanation
Indices: 54060064--54060108 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
54060054 TTTTCTCTTC
*
54060064 TAGCATGAACTTGTCTTACCTTTT
1 TAGCATGAACTCGTCTTACCTTTT
54060088 TAGCAT-AACTCGTCTTACCTT
1 TAGCATGAACTCGTCTTACCTT
54060109 ACCTTACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (24 bp):
TAGCATGAACTCGTCTTACCTTTT
Found at i:54062401 original size:828 final size:827
Alignment explanation
Indices: 54060805--54062466 Score: 3306
Period size: 828 Copynumber: 2.0 Consensus size: 827
54060795 GACTCAAACT
54060805 TTGGCAAAATTACATTTTTGCCCCTAAACTTTTACATATTTACACTTTTCCCCAATGCTCGGAAA
1 TTGGCAAAATTACATTTTTGCCCCTAAACTTTTACATATTTACACTTTTCCCCAATGCTCGGAAA
54060870 TTAAAAGTCATCCTATTTTATTATGTTTTATGACATGCTGGTCATTTTCCCCTTCTATGAAAACA
66 TTAAAAGTCATCCTATTTTATTATGTTTTATGACATGCTGGTCATTTTCCCCTTCTATGAAAACA
54060935 TCAAATTCTCACTCTAACATGTACTTATGAACATTGGGTATTTTTACCGATTATGTCATTTTACT
131 TCAAATTCTCACTCTAACATGTACTTATGAACATTGGGTATTTTTACCGATTATGTCATTTTACT
54061000 CGTTTTCACGTAAAATTGCTTAGCAAAAGTTGTTTAACACAATTTCAAGCTTCATATTCTACCAT
196 CGTTTTCACGTAAAATTGCTTAGCAAAAGTTGTTTAACACAATTTCAAGCTTCATATTCTACCAT
54061065 AAAACATCAAAATAAACACATTTCACATATGGGTACTTTTCCAAATATAAACCCTAGGTTAAATT
261 AAAACATCAAAATAAACACATTTCACATATGGGTACTTTTCCAAATATAAACCCTAGGTTAAATT
54061130 ATTGCTAGAATAAGCTTAATCAAGTTACCAGACTCTAAAAACATAAAGAACATTAAAAACAGGGC
326 ATTGCTAGAATAAGCTTAATCAAGTTACCAGACTCTAAAAACATAAAGAACATTAAAAACAGGGC
54061195 TAAAACGGACTTACAATCGAGCTTGGAAGCTTGAAAAACCCTAGATATGTCTTCCTCATGTGAAA
391 TAAAACGGACTTACAATCGAGCTTGGAAGCTTGAAAAACCCTAGATATGTCTTCCTCATGTGAAA
54061260 TTCGGCCAAGGGGTTGAAGATGGACAAAAATTGGCTTTTAATTTTATTTTTAATTCATTTTAGTA
456 TTCGGCCAAGGGGTTGAAGATGGACAAAAATTGGCTTTTAATTTTATTTTTAATTCATTTTAGTA
54061325 ACTAAATGACCAAAATGCCCTTAATTAAAAACTATGGTGTTTTATCTTCCTTTAGGTATTTTTGT
521 ACTAAATGACCAAAATGCCCTTAATTAAAAACTATGGTGTTTTATCTTCCTTTAGGTATTTTTGT
54061390 CCAAACTAGTATAATGGTCTAATTACTATCCAAGGACCTCCACTTTAAAAACTCATTACTCACAA
586 CCAAACTAGTATAATGGTCTAATTACTATCCAAGGACCTCCACTTTAAAAACTCATTACTCACAA
54061455 GTACTTAGTACCTTTGTGAACTAGAACACACTTTTTACAACTTTTGCAATTTAGTCTTAAATATC
651 GTACTTAGTACCTTTGTGAACTAGAACACACTTTTTACAACTTTTGCAATTTAGTCTTAAATATC
54061520 AAATTGGACCCTCTATCGACAAAATTTCTAAATAAAATTGTCACACAATCATGCAATCATGTCAT
716 AAATTGGACCCTCTATCGACAAAATTTCTAAATAAAATTGTCACACAATCATGCAATCATGTCAT
54061585 AGACCTTAAAATGATAATAAAATAAATTTTTCTACCTGGATTTGTGG
781 AGACCTTAAAATGATAATAAAATAAATTTTTCTACCTGGATTTGTGG
54061632 NTTGGCAAAATTACATTTTTGCCCCTAAACTTTTACATATTTACACTTTTCCCCAATGCTCGGAA
1 -TTGGCAAAATTACATTTTTGCCCCTAAACTTTTACATATTTACACTTTTCCCCAATGCTCGGAA
54061697 ATTAAAAGTCATCCTATTTTATTATGTTTTATGACATGCTGGTCATTTTCCCCTTCTATGAAAAC
65 ATTAAAAGTCATCCTATTTTATTATGTTTTATGACATGCTGGTCATTTTCCCCTTCTATGAAAAC
54061762 ATCAAATTCTCACTCTAACATGTACTTATGAACATTGGGTATTTTTACCGATTATGTCATTTTAC
130 ATCAAATTCTCACTCTAACATGTACTTATGAACATTGGGTATTTTTACCGATTATGTCATTTTAC
54061827 TCGTTTTCACGTAAAATTGCTTAGCAAAAGTTGTTTAACACAATTTCAAGCTTCATATTCTACCA
195 TCGTTTTCACGTAAAATTGCTTAGCAAAAGTTGTTTAACACAATTTCAAGCTTCATATTCTACCA
54061892 TAAAACATCAAAATAAACACATTTCACATATGGGTACTTTTCCAAATATAAACCCTAGGTTAAAT
260 TAAAACATCAAAATAAACACATTTCACATATGGGTACTTTTCCAAATATAAACCCTAGGTTAAAT
54061957 TATTGCTAGAATAAGCTTAATCAAGTTACCAGACTCTAAAAACATAAAGAACATTAAAAACAGGG
325 TATTGCTAGAATAAGCTTAATCAAGTTACCAGACTCTAAAAACATAAAGAACATTAAAAACAGGG
54062022 CTAAAACGGACTTACAATCGAGCTTGGAAGCTTGAAAAACCCTAGATATGTCTTCCTCATGTGAA
390 CTAAAACGGACTTACAATCGAGCTTGGAAGCTTGAAAAACCCTAGATATGTCTTCCTCATGTGAA
54062087 ATTCGGCCAAGGGGTTGAAGATGGACAAAAATTGGCTTTTAATTTTATTTTTAATTCATTTTAGT
455 ATTCGGCCAAGGGGTTGAAGATGGACAAAAATTGGCTTTTAATTTTATTTTTAATTCATTTTAGT
54062152 AACTAAATGACCAAAATGCCCTTAATTAAAAACTATGGTGTTTTATCTTCCTTTAGGTATTTTTG
520 AACTAAATGACCAAAATGCCCTTAATTAAAAACTATGGTGTTTTATCTTCCTTTAGGTATTTTTG
54062217 TCCAAACTAGTATAATGGTCTAATTACTATCCAAGGACCTCCACTTTAAAAACTCATTACTCACA
585 TCCAAACTAGTATAATGGTCTAATTACTATCCAAGGACCTCCACTTTAAAAACTCATTACTCACA
54062282 AGTACTTAGTACCTTTGTGAACTAGAACACACTTTTTACAACTTTTGCAATTTAGTCTTAAATAT
650 AGTACTTAGTACCTTTGTGAACTAGAACACACTTTTTACAACTTTTGCAATTTAGTCTTAAATAT
54062347 CAAATTGGACCCTCTATCGACAAAATTTCTAAATAAAATTGTCACACAATCATGCAATCATGTCA
715 CAAATTGGACCCTCTATCGACAAAATTTCTAAATAAAATTGTCACACAATCATGCAATCATGTCA
54062412 TAGACCTTAAAATGATAATAAAATAAATTTTTCTACCTGGATTTGTGG
780 TAGACCTTAAAATGATAATAAAATAAATTTTTCTACCTGGATTTGTGG
*
54062460 TTCGCAA
1 TTGGCAA
54062467 CCACTATTCC
Statistics
Matches: 833, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
827 6 0.01
828 827 0.99
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (827 bp):
TTGGCAAAATTACATTTTTGCCCCTAAACTTTTACATATTTACACTTTTCCCCAATGCTCGGAAA
TTAAAAGTCATCCTATTTTATTATGTTTTATGACATGCTGGTCATTTTCCCCTTCTATGAAAACA
TCAAATTCTCACTCTAACATGTACTTATGAACATTGGGTATTTTTACCGATTATGTCATTTTACT
CGTTTTCACGTAAAATTGCTTAGCAAAAGTTGTTTAACACAATTTCAAGCTTCATATTCTACCAT
AAAACATCAAAATAAACACATTTCACATATGGGTACTTTTCCAAATATAAACCCTAGGTTAAATT
ATTGCTAGAATAAGCTTAATCAAGTTACCAGACTCTAAAAACATAAAGAACATTAAAAACAGGGC
TAAAACGGACTTACAATCGAGCTTGGAAGCTTGAAAAACCCTAGATATGTCTTCCTCATGTGAAA
TTCGGCCAAGGGGTTGAAGATGGACAAAAATTGGCTTTTAATTTTATTTTTAATTCATTTTAGTA
ACTAAATGACCAAAATGCCCTTAATTAAAAACTATGGTGTTTTATCTTCCTTTAGGTATTTTTGT
CCAAACTAGTATAATGGTCTAATTACTATCCAAGGACCTCCACTTTAAAAACTCATTACTCACAA
GTACTTAGTACCTTTGTGAACTAGAACACACTTTTTACAACTTTTGCAATTTAGTCTTAAATATC
AAATTGGACCCTCTATCGACAAAATTTCTAAATAAAATTGTCACACAATCATGCAATCATGTCAT
AGACCTTAAAATGATAATAAAATAAATTTTTCTACCTGGATTTGTGG
Found at i:54062942 original size:18 final size:18
Alignment explanation
Indices: 54062919--54062960 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
54062909 AAATCTAAGA
*
54062919 ACTTTCTTCCACGGGGAT
1 ACTTTCTTCCACGAGGAT
54062937 ACTTTCTTCCACGAGGAT
1 ACTTTCTTCCACGAGGAT
54062955 ACTTTC
1 ACTTTC
54062961 AAAACTACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.36
Consensus pattern (18 bp):
ACTTTCTTCCACGAGGAT
Found at i:54068478 original size:16 final size:16
Alignment explanation
Indices: 54068459--54068489 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54068449 CTTCTTCATT
54068459 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
54068475 TACTTACTTACTTAA
1 TACTCACTTACTTAA
54068490 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:54068871 original size:55 final size:53
Alignment explanation
Indices: 54068728--54068935 Score: 195
Period size: 55 Copynumber: 3.8 Consensus size: 53
54068718 ATCCTTTTGA
* * * *
54068728 AACTCACCATTACCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* *
54068781 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G
* * ***
54068835 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-G
1 -AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * * * * *
54068888 AAACCTTACCAGTTGTCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -AA-CTCACCA-ATGCCATGTCTTGACATGGTCTTACATGGGATCCTT
54068936 AAACCCTAAT
Statistics
Matches: 128, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
52 2 0.02
53 46 0.36
54 7 0.05
55 71 0.55
56 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (53 bp):
AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:54069470 original size:23 final size:23
Alignment explanation
Indices: 54069443--54069488 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
54069433 ATGAACATTA
54069443 GGTATTTTTACCGATTATGTCGT
1 GGTATTTTTACCGATTATGTCGT
*
54069466 GGTATTTTTATCGATTATGTCGT
1 GGTATTTTTACCGATTATGTCGT
54069489 TTTACTCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (23 bp):
GGTATTTTTACCGATTATGTCGT
Found at i:54071528 original size:11 final size:11
Alignment explanation
Indices: 54071512--54071544 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
54071502 AGAAAACCCT
54071512 TAAACACACAA
1 TAAACACACAA
54071523 TAAACACACAA
1 TAAACACACAA
*
54071534 TAAACAAACAA
1 TAAACACACAA
54071545 AAAAATACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.67, C:0.24, G:0.00, T:0.09
Consensus pattern (11 bp):
TAAACACACAA
Found at i:54076149 original size:12 final size:12
Alignment explanation
Indices: 54076121--54076153 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
54076111 GACTTAGTTA
54076121 TTTATG-TTTTC
1 TTTATGTTTTTC
54076132 -TTATGTTTTTC
1 TTTATGTTTTTC
54076143 TTTATGTTTTT
1 TTTATGTTTTT
54076154 ATTTGCGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 5 0.25
12 10 0.50
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTATGTTTTTC
Found at i:54091969 original size:19 final size:18
Alignment explanation
Indices: 54091941--54091992 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
54091931 ATCCGACAAA
54091941 GCCT-AATAAATGATAAT
1 GCCTGAATAAATGATAAT
*
54091958 GCTTGAAATAAATGATAAT
1 GCCTG-AATAAATGATAAT
54091977 GCCTG-ATAAATGATAA
1 GCCTGAATAAATGATAA
54091993 ATGATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 14 0.45
19 17 0.55
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (18 bp):
GCCTGAATAAATGATAAT
Found at i:54092811 original size:23 final size:21
Alignment explanation
Indices: 54092775--54092825 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
54092765 TCTGCTTGAA
54092775 ATATATGAAAATGATGATACATG
1 ATATATGAAAATGA-GAT-CATG
*
54092798 ATATAT-AAATATGAGATGATG
1 ATATATGAAA-ATGAGATCATG
54092819 ATATATG
1 ATATATG
54092826 TACATGGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.36
22 6 0.24
23 10 0.40
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (21 bp):
ATATATGAAAATGAGATCATG
Found at i:54094109 original size:25 final size:21
Alignment explanation
Indices: 54094049--54094103 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
54094039 GTCCTATGGT
54094049 CACACGGGTGTGTCCCTTGAC
1 CACACGGGTGTGTCCCTTGAC
54094070 CACACGGGTGTGTCCCTTGAC
1 CACACGGGTGTGTCCCTTGAC
* *
54094091 CACATGGGCGTGT
1 CACACGGGTGTGT
54094104 TTGTCCTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.24
Consensus pattern (21 bp):
CACACGGGTGTGTCCCTTGAC
Found at i:54096989 original size:8 final size:8
Alignment explanation
Indices: 54096976--54097006 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
54096966 TTTTTATTTT
54096976 TATTTAAA
1 TATTTAAA
54096984 TATTTAAA
1 TATTTAAA
54096992 TATTTAAA
1 TATTTAAA
54097000 TATTTAA
1 TATTTAA
54097007 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TATTTAAA
Found at i:54097034 original size:6 final size:7
Alignment explanation
Indices: 54097008--54097033 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54096998 AATATTTAAT
54097008 TTTTTTA
1 TTTTTTA
54097015 TTTTTTA
1 TTTTTTA
54097022 TTTTTTA
1 TTTTTTA
54097029 TTTTT
1 TTTTT
54097034 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:54097040 original size:13 final size:13
Alignment explanation
Indices: 54097010--54097067 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
54097000 TATTTAATTT
**
54097010 TTTTATTTTTTATT
1 TTTTA-TTTTTAAA
54097024 TTTTATTTTTAAA
1 TTTTATTTTTAAA
*
54097037 TTTTAATTTTAAA
1 TTTTATTTTTAAA
* *
54097050 TTTAATTATTAATA
1 TTTTATTTTTAA-A
54097064 TTTT
1 TTTT
54097068 TTATTAAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
13 27 0.75
14 9 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTTTTAAA
Found at i:54108193 original size:32 final size:32
Alignment explanation
Indices: 54108157--54108217 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
54108147 TTGATGTGTT
54108157 TATGTGTTATATGTTTGATCACTCACTAATCA
1 TATGTGTTATATGTTTGATCACTCACTAATCA
54108189 TATGTGTTATATGTTTGATCACTCACTAA
1 TATGTGTTATATGTTTGATCACTCACTAA
54108218 ACATCAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (32 bp):
TATGTGTTATATGTTTGATCACTCACTAATCA
Found at i:54119446 original size:20 final size:20
Alignment explanation
Indices: 54119417--54119462 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
54119407 AATAGTGGAG
*
54119417 GGGTTTGAATGCAAATTCAA
1 GGGTTCGAATGCAAATTCAA
54119437 GGGTTCGAATGCAAATTCAA
1 GGGTTCGAATGCAAATTCAA
54119457 GGGTTC
1 GGGTTC
54119463 TTCAAGGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (20 bp):
GGGTTCGAATGCAAATTCAA
Found at i:54122459 original size:14 final size:14
Alignment explanation
Indices: 54122442--54122475 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54122432 ACCACGGTCA
54122442 ATAAAACATAAATC
1 ATAAAACATAAATC
**
54122456 ATAAATTATAAATC
1 ATAAAACATAAATC
54122470 ATAAAA
1 ATAAAA
54122476 GTCCAAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAACATAAATC
Found at i:54122666 original size:6 final size:6
Alignment explanation
Indices: 54122655--54122679 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54122645 TAAGCACCTT
54122655 TCAGTA TCAGTA TCAGTA TCAGTA T
1 TCAGTA TCAGTA TCAGTA TCAGTA T
54122680 GCACAAGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (6 bp):
TCAGTA
Found at i:54124498 original size:24 final size:25
Alignment explanation
Indices: 54124471--54124525 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
54124461 GCAGCAGCTA
*
54124471 ATTAATT-TGTTCTAA-ATTAGACAC
1 ATTAATTATGTCCTAAGA-TAGACAC
54124495 ATTAAATTATGTCCTAAGATAGACAC
1 ATT-AATTATGTCCTAAGATAGACAC
54124521 ATTAA
1 ATTAA
54124526 ACACATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 3 0.11
25 6 0.22
26 17 0.63
27 1 0.04
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (25 bp):
ATTAATTATGTCCTAAGATAGACAC
Found at i:54127689 original size:11 final size:10
Alignment explanation
Indices: 54127660--54127688 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54127650 TTCTTCACAA
54127660 AATTTTTTTG
1 AATTTTTTTG
54127670 AATTTTTTTG
1 AATTTTTTTG
54127680 AATTTTTTT
1 AATTTTTTT
54127689 TTACAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (10 bp):
AATTTTTTTG
Found at i:54128461 original size:22 final size:20
Alignment explanation
Indices: 54128422--54128461 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
54128412 GCTGGAAATT
*
54128422 TCCTTGAAGTTTCTTGAACG
1 TCCTTGAAGTTCCTTGAACG
54128442 TCCTTGCAAGCTTCCTTGAA
1 TCCTTG-AAG-TTCCTTGAA
54128462 GTTTCCTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 3 0.18
22 8 0.47
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (20 bp):
TCCTTGAAGTTCCTTGAACG
Found at i:54131681 original size:21 final size:22
Alignment explanation
Indices: 54131646--54131686 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
54131636 CTACATCAAT
54131646 AATTGCAAACATAT-ACCAACC
1 AATTGCAAACATATAACCAACC
54131667 AATT-CAAACAGTATAACCAA
1 AATTGCAAACA-TATAACCAA
54131687 GCAACTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.20
Consensus pattern (22 bp):
AATTGCAAACATATAACCAACC
Found at i:54138743 original size:42 final size:43
Alignment explanation
Indices: 54138644--54138781 Score: 122
Period size: 43 Copynumber: 3.2 Consensus size: 43
54138634 TGAGACATCG
* * * * *
54138644 TGTAAGACCGTGTCTAGGACACAAGCCTCG--ATTGATATTTACG
1 TGTAAGACCATGTCTAGGACAGAGGCATCGATATTGA-A-TTACA
* ** *
54138687 TATAAGACCATGTCTAGGACATTGGCATCG-TATCT-AATTTCA
1 TGTAAGACCATGTCTAGGACAGAGGCATCGATAT-TGAATTACA
* *
54138729 TGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGAATTACA
1 TGTAAGACCATGTCTAGGACAGAGGCATCGATATTGAATTACA
54138772 TGTAAGACCA
1 TGTAAGACCA
54138782 CATCTGGGAC
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
42 29 0.38
43 43 0.57
44 3 0.04
45 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACAGAGGCATCGATATTGAATTACA
Found at i:54138799 original size:43 final size:42
Alignment explanation
Indices: 54138710--54138791 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 42
54138700 CTAGGACATT
* *
54138710 GGCATCGTATCTAATTTCATGTAAGACCCTGTCTGGGACAGA
1 GGCATCGTATCTAATTACATGTAAGACCCTATCTGGGACAGA
54138752 GGCATCGATAT-TGAATTACATGTAAGACCAC-ATCTGGGAC
1 GGCATCG-TATCT-AATTACATGTAAGACC-CTATCTGGGAC
54138792 GTCGGCATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
42 8 0.23
43 26 0.74
44 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (42 bp):
GGCATCGTATCTAATTACATGTAAGACCCTATCTGGGACAGA
Found at i:54145853 original size:27 final size:26
Alignment explanation
Indices: 54145818--54145926 Score: 137
Period size: 27 Copynumber: 4.0 Consensus size: 26
54145808 AGCATGGCTG
*
54145818 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
*
54145844 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGACAGAGCCA
54145872 CCAGAACAGATATATGTGACAGAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
* * *
54145899 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGACAGAGCCA
54145926 C
1 C
54145927 TAGGACGCTT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 50 0.68
28 17 0.23
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:54145882 original size:54 final size:54
Alignment explanation
Indices: 54145818--54145926 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 54
54145808 AGCATGGCTG
*
54145818 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* *
54145872 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
54145926 C
1 C
54145927 TAGGACGCTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 32 0.63
55 19 0.37
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:54147317 original size:24 final size:24
Alignment explanation
Indices: 54147282--54147382 Score: 157
Period size: 24 Copynumber: 4.2 Consensus size: 24
54147272 CCAACACTAT
* *
54147282 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
54147306 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
54147330 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
54147354 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
54147378 TCTCC
1 TCTCC
54147383 TGACAAACTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.25, C:0.41, G:0.02, T:0.33
Consensus pattern (24 bp):
TCTCCCTTATCAACTCCTAAATCC
Found at i:54148891 original size:43 final size:42
Alignment explanation
Indices: 54148802--54148883 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
54148792 TTGGGACATT
* ** *
54148802 GGCATCGTATCTGATTTCATGTAAGACCGTGTCTGGGACAGA
1 GGCATCGTATCTGATTACATGTAAGACCACGTCTAGGACAGA
54148844 GGCATCGATAT-TGAATTACATGTAAGACCACGTCTAGGAC
1 GGCATCG-TATCTG-ATTACATGTAAGACCACGTCTAGGAC
54148884 GTCGGCATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 9 0.26
43 25 0.74
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (42 bp):
GGCATCGTATCTGATTACATGTAAGACCACGTCTAGGACAGA
Found at i:54153536 original size:30 final size:30
Alignment explanation
Indices: 54153479--54153537 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
54153469 TGCCTTTGAA
* *
54153479 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACACCAAATTTTT
54153509 AATATTTACAAAAAGAG-CAACCAAATTTT
1 AATATTTACAAAAAGAGAC-ACCAAATTTT
54153538 GAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTTT
Found at i:54157250 original size:115 final size:115
Alignment explanation
Indices: 54157048--54157623 Score: 1118
Period size: 115 Copynumber: 5.0 Consensus size: 115
54157038 TATTCCAAAG
54157048 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
1 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
54157113 AATCCTCGTAAACTTTGTTCTTACCTCGATCAAGACCCGAATCACATTTC
66 AATCCTCGTAAACTTTGTTCTTACCTCGATCAAGACCCGAATCACATTTC
54157163 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
1 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
54157228 AATCCTCGTAAACTTTGTTCTTACCTCGATCAAGACCCGAATCACATTTC
66 AATCCTCGTAAACTTTGTTCTTACCTCGATCAAGACCCGAATCACATTTC
54157278 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
1 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
54157343 AATCCTCGTAAACTTTGTTCTTACCTCGATCAAGACCCGAATCACATTTC
66 AATCCTCGTAAACTTTGTTCTTACCTCGATCAAGACCCGAATCACATTTC
54157393 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
1 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
54157458 AATCCTCGTAAACTTTGTTCTTACCTCGATCAAGACCCGAATCACATTTC
66 AATCCTCGTAAACTTTGTTCTTACCTCGATCAAGACCCGAATCACATTTC
54157508 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
1 TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
* *
54157573 AATTCTTGTAAACTTTGTTCTTATCC-CGATCAAGACCCGAATCACATTTC
66 AATCCTCGTAAACTTTGTTCTTA-CCTCGATCAAGACCCGAATCACATTTC
54157623 T
1 T
54157624 CTTGATCTAA
Statistics
Matches: 458, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
115 456 1.00
116 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (115 bp):
TAAGCTTTAATAACACATTATTCACATATGTACTTACCTCGATACAAAATGATGAAGATGAGCTT
AATCCTCGTAAACTTTGTTCTTACCTCGATCAAGACCCGAATCACATTTC
Found at i:54159046 original size:54 final size:54
Alignment explanation
Indices: 54158964--54159072 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
54158954 GCGGACTCAG
*
54158964 TTTACCCTTTTTACCGAATCTAAGAACCTTCCTCCATGGGGATACTTTTAGAAA
1 TTTACCCTTTTTACCGAATCTAAGAACCTTCCTCCACGGGGATACTTTTAGAAA
*
54159018 TTTACCCTTTTTACTGAATCTAAGAACCTTCCTCCACGGGGATACTTTTAGAAA
1 TTTACCCTTTTTACCGAATCTAAGAACCTTCCTCCACGGGGATACTTTTAGAAA
54159072 T
1 T
54159073 ACCTTATCAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (54 bp):
TTTACCCTTTTTACCGAATCTAAGAACCTTCCTCCACGGGGATACTTTTAGAAA
Found at i:54163654 original size:21 final size:22
Alignment explanation
Indices: 54163628--54163669 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
54163618 CACTTAGCAT
54163628 AGGGGC-ACACGCCCGTGTGAG
1 AGGGGCAACACGCCCGTGTGAG
54163649 AGGGGCAACACGCCCGTGTGA
1 AGGGGCAACACGCCCGTGTGA
54163670 CCATTTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.21, C:0.29, G:0.40, T:0.10
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGAG
Found at i:54179366 original size:27 final size:28
Alignment explanation
Indices: 54179282--54179379 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
54179272 CATGAGATTG
* * * *
54179282 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
54179311 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
54179339 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
54179366 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
54179380 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:54179390 original size:27 final size:27
Alignment explanation
Indices: 54179310--54179392 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
54179300 TAAATTGTAC
* *
54179310 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
54179338 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
54179365 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
54179392 A
1 A
54179393 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:54179393 original size:29 final size:27
Alignment explanation
Indices: 54179282--54179393 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
54179272 CATGAGATTG
** * *
54179282 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
54179311 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
54179339 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
54179366 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
54179394 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:54194936 original size:12 final size:12
Alignment explanation
Indices: 54194916--54194952 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
54194906 AAATTAAACT
*
54194916 TATTAAATCAAA
1 TATTCAATCAAA
54194928 TATTCAATCAAA
1 TATTCAATCAAA
*
54194940 TATTCAGTCAAA
1 TATTCAATCAAA
54194952 T
1 T
54194953 TCATCCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (12 bp):
TATTCAATCAAA
Found at i:54198532 original size:37 final size:37
Alignment explanation
Indices: 54198482--54198560 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54198472 TTATTACGAA
* * *
54198482 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
54198519 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
54198556 GTCTT
1 GTCTT
54198561 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:54198853 original size:49 final size:49
Alignment explanation
Indices: 54198679--54199189 Score: 894
Period size: 49 Copynumber: 10.6 Consensus size: 49
54198669 CCCTTCGGGA
* * * * *
54198679 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
54198726 CCTGTCAC--ATATATACACTTTCACATCCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54198773 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54198820 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54198869 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54198918 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54198967 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54199016 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54199065 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54199114 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54199163 CTTATCAC--ATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
54199190 ACCAACCCTT
Statistics
Matches: 451, Mismatches: 9, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
46 1 0.00
47 109 0.24
49 341 0.76
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54199505 original size:40 final size:40
Alignment explanation
Indices: 54199416--54199514 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
54199406 GCTACTCGTT
* * * *
54199416 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
* *
54199456 CAAATGCCTTCGGGACTTAACCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAAC-TAGCA
54199497 CAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
54199515 GCCCAGACAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 44 0.85
41 8 0.15
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
Found at i:54204270 original size:3 final size:3
Alignment explanation
Indices: 54204262--54204286 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54204252 TATTTACTTC
54204262 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
54204287 ATTTTATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54207669 original size:50 final size:50
Alignment explanation
Indices: 54207592--54207697 Score: 185
Period size: 50 Copynumber: 2.1 Consensus size: 50
54207582 CCAGTGCCAT
* *
54207592 ATATATATATCTAATATGGGCTTACATGGCTCATTCCTATCTCCAAAGCC
1 ATATATATATCTAATATGGGCTGACATGGCTAATTCCTATCTCCAAAGCC
*
54207642 ATATATATATCTAATATGGGCTGACATGGCTAATTCCTGTCTCCAAAGCC
1 ATATATATATCTAATATGGGCTGACATGGCTAATTCCTATCTCCAAAGCC
54207692 ATATAT
1 ATATAT
54207698 CTGATATGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (50 bp):
ATATATATATCTAATATGGGCTGACATGGCTAATTCCTATCTCCAAAGCC
Found at i:54207715 original size:46 final size:47
Alignment explanation
Indices: 54207596--54207728 Score: 178
Period size: 50 Copynumber: 2.8 Consensus size: 47
54207586 TGCCATATAT
*
54207596 ATATATCTAATATGGGCTTACATGGCTCATTCCTATCTCCAAAGCCATA
1 ATATATCTAATATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC--A
* *
54207645 TATATATCTAATATGGGCTGACATGGCTAATTCCTGTCTCCAAAGCC-
1 -ATATATCTAATATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCA
* * *
54207692 ATATATCTGATATGGACTTACATGGCTCATTTCTGTC
1 ATATATCTAATATGGGCTTACATGGCTCATTCCTGTC
54207729 CTGTCCTGTC
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
46 32 0.43
50 43 0.57
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (47 bp):
ATATATCTAATATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCA
Found at i:54212057 original size:46 final size:47
Alignment explanation
Indices: 54211951--54212072 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 47
54211941 TGTCTTCGAC
** * *
54211951 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
54212001 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
54212047 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
54212073 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 34 0.53
50 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:54229368 original size:22 final size:22
Alignment explanation
Indices: 54229325--54229368 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
54229315 AAAAATAATC
**
54229325 AAAATTAATTAAAATTTGACAT
1 AAAATTAATTAAAATTCAACAT
54229347 AAAATTAATTAAAATTCAACAT
1 AAAATTAATTAAAATTCAACAT
54229369 GTTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATTAATTAAAATTCAACAT
Found at i:54230906 original size:30 final size:30
Alignment explanation
Indices: 54230872--54230928 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
54230862 ATGAATTGGA
54230872 AGCTTTGGCACTAAGTGTGCGATTTAACCT
1 AGCTTTGGCACTAAGTGTGCGATTTAACCT
54230902 AGCTTTGGCACTAAGTGTGCGATTTAA
1 AGCTTTGGCACTAAGTGTGCGATTTAA
54230929 GGTCTCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (30 bp):
AGCTTTGGCACTAAGTGTGCGATTTAACCT
Found at i:54237014 original size:30 final size:29
Alignment explanation
Indices: 54236980--54237044 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 29
54236970 ATGAATCGGA
54236980 AGCTTTGGCACTAAGTGTGCGATTTAAACT
1 AGCTTTGGCACTAAGTGTGCGATTT-AACT
*
54237010 AGCTTTGGCACTAAGTGTGTGATTTAACT
1 AGCTTTGGCACTAAGTGTGCGATTTAACT
54237039 AGCTTT
1 AGCTTT
54237045 AGCTACTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTGTGCGATTTAACT
Found at i:54239524 original size:49 final size:49
Alignment explanation
Indices: 54239445--54239539 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
54239435 TAGGACTATC
* * *
54239445 TTATTCTATCATCTCAAGTTGCCTGACAACAGTGAATTTTAGTATTCAT
1 TTATTCTATCATCCCAAATTGCCTGACAACAATGAATTTTAGTATTCAT
* **
54239494 TTATTCTATCATCCCAAATTTCCT-ACCAACAATGGTTTTTAGTATT
1 TTATTCTATCATCCCAAATTGCCTGA-CAACAATGAATTTTAGTATT
54239540 TTCCCACATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.03
49 38 0.97
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.42
Consensus pattern (49 bp):
TTATTCTATCATCCCAAATTGCCTGACAACAATGAATTTTAGTATTCAT
Found at i:54240809 original size:16 final size:16
Alignment explanation
Indices: 54240788--54240820 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54240778 CAGGGTCTGT
54240788 TTCTTATTCTCCATCA
1 TTCTTATTCTCCATCA
54240804 TTCTTATTCTCCATCA
1 TTCTTATTCTCCATCA
54240820 T
1 T
54240821 CTAGTACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.30, G:0.00, T:0.52
Consensus pattern (16 bp):
TTCTTATTCTCCATCA
Found at i:54264165 original size:48 final size:48
Alignment explanation
Indices: 54264109--54264377 Score: 278
Period size: 48 Copynumber: 5.6 Consensus size: 48
54264099 GAATTTGTCA
* * * *
54264109 ATGCCATGTCTCAGACATGGTCTTACATTGACTCACATGTCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCGAGGCCG
* * *
54264157 ATGCCATGTCCTAGACATGGTCTTACAC-CAGCTCTCATGTCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATCGAGGCCG
* ** *
54264205 ATGCCATGTCCTAGACATGGTCTTACACT-AGCTCTCATAAGGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATCGAGGCCG
* * **
54264253 ATGCCATGTCCCAGACATGGTCTTACACTAGGA--CACATATCAATACCG
1 ATGCCATGTCCCAGACATGGTCTTACACT--GACTCTCATATCGAGGCCG
* * * *
54264301 ATGCCATGTCCCAAACATGGTCTTACACTGGCTTTCATAAT-GTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCAT-ATCGAGGCCG
*
54264349 ATGTCATGTCCCAGACATGGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
54264378 AGCACACATA
Statistics
Matches: 186, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
46 1 0.01
47 1 0.01
48 181 0.97
49 2 0.01
51 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCGAGGCCG
Found at i:54264273 original size:96 final size:96
Alignment explanation
Indices: 54264109--54264390 Score: 334
Period size: 96 Copynumber: 2.9 Consensus size: 96
54264099 GAATTTGTCA
* * ** * *
54264109 ATGCCATGT-CTCAGACATGGTCTTACA-TTGACTCACATGTCGAGGCCGATGCCATGTCCTAGA
1 ATGCCATGTCCT-AGACATGGTCTTACACTAG-CTCTCATAACGTGGCCGATGCCATGTCCCAGA
* * * * *
54264172 CATGGTCTTACACCAGCTCTCATGTCGAGGCCG
64 CATGGTCTTACACCAGCACACATATCAAGACCG
*
54264205 ATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAAGGTGGCCGATGCCATGTCCCAGACA
1 ATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAACGTGGCCGATGCCATGTCCCAGACA
* * *
54264270 TGGTCTTACACTAGGACACATATCAATACCG
66 TGGTCTTACACCAGCACACATATCAAGACCG
* * * * * *
54264301 ATGCCATGTCCCAAACATGGTCTTACACTGGCTTTCATAATGTGGCCGATGTCATGTCCCAGACA
1 ATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAACGTGGCCGATGCCATGTCCCAGACA
*
54264366 TGGTCTTACACTAGCACACATATCA
66 TGGTCTTACACCAGCACACATATCA
54264391 CCCAAATGTC
Statistics
Matches: 162, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
96 158 0.98
97 4 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (96 bp):
ATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAACGTGGCCGATGCCATGTCCCAGACA
TGGTCTTACACCAGCACACATATCAAGACCG
Found at i:54264369 original size:144 final size:143
Alignment explanation
Indices: 54264109--54264380 Score: 359
Period size: 144 Copynumber: 1.9 Consensus size: 143
54264099 GAATTTGTCA
* * * * * * *
54264109 ATGCCATGTCTCAGACATGGTCTTACATTGACTCACATGTCGAGGCCGATGCCATGTCCTAGACA
1 ATGCCATGTCCCAGACATGGTCTTACATGGAC-CACATATCAAGACCGATGCCATGTCCCAAACA
* *
54264174 TGGTCTTACACCAGCTCTCATGTCGAGGCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTC
65 TGGTCTTACACCAGCTCTCATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC
54264239 TCATAAGGTGGCCG
130 TCATAAGGTGGCCG
*
54264253 ATGCCATGTCCCAGACATGGTCTTACACTAGGA-CACATATCAATACCGATGCCATGTCCCAAAC
1 ATGCCATGTCCCAGACATGGTCTTACA-T-GGACCACATATCAAGACCGATGCCATGTCCCAAAC
** * * *
54264317 ATGGTCTTACACTGGCTTTCATAAT-GTGGCCGATGTCATGTCCCAGACATGGTCTTACACTAGC
64 ATGGTCTTACACCAGCTCTCAT-ATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
54264381 ACACATATCA
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
144 106 0.96
145 2 0.02
146 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (143 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGACCACATATCAAGACCGATGCCATGTCCCAAACAT
GGTCTTACACCAGCTCTCATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT
CATAAGGTGGCCG
Found at i:54268348 original size:80 final size:79
Alignment explanation
Indices: 54268264--54268435 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
54268254 GGACTAAGAT
*
54268264 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
54268328 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
54268344 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
54268409 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
54268423 CCGAAGGCATTTG
1 CCGAAGGCATTTG
54268436 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:54268415 original size:39 final size:39
Alignment explanation
Indices: 54268211--54268433 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
54268201 TTGAATGCTG
* * * * *
54268211 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
54268251 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
54268290 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
54268331 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
54268371 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
54268410 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
54268434 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:54268453 original size:79 final size:80
Alignment explanation
Indices: 54268291--54268468 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
54268281 AGATACAAAT
* * * *
54268291 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
54268356 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
54268371 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
54268435 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
54268450 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
54268469 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:54276202 original size:40 final size:40
Alignment explanation
Indices: 54276119--54276421 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
54276109 TTGAATGCTG
* * * * * *
54276119 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
54276159 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
54276199 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
54276239 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
54276279 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
54276319 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
54276359 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
54276398 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
54276422 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:54283017 original size:48 final size:48
Alignment explanation
Indices: 54282954--54283179 Score: 215
Period size: 48 Copynumber: 4.7 Consensus size: 48
54282944 GTGAATTTTT
* *
54282954 CGATGCCCTGTCCCAGACATGGTCTTACACTAGGTCACATGTCAAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGC
* * ** *
54283002 CGATGCCGTGCCCCAGACATGGTCTTACACTAGCTCTTATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGC
* * * * *
54283050 TGATGCCATGTCCTAGACACGGTCTTACACTAGCTCTCA--T-AAGGTGTT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAA-G-G-C
* * ***** *
54283098 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAGGTGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGC
*
54283146 CGATGCCATGTCCTAGACATGGTCTTACACTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGC
54283180 ATACATATCA
Statistics
Matches: 149, Mismatches: 23, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
45 1 0.01
46 2 0.01
47 1 0.01
48 143 0.96
49 1 0.01
50 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGC
Found at i:54283119 original size:96 final size:96
Alignment explanation
Indices: 54283002--54283179 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
54282992 ATGTCAAGGC
* * **
54283002 CGATGCCGTGCCCCAGACATGGTCTTACACTAGCTCTTATGTCGAGG-CTGATGCCATGTCCTAG
1 CGATGCCATGCCCCAGACATGGTCTTACACTAGCTCTCATAACGAGGTC-GATGCCATGTCCTAG
54283066 ACACGGTCTTACACTAGCTCTCATAAGGTGTT
65 ACACGGTCTTACACTAGCTCTCATAAGGTGTT
* * * *
54283098 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAGGTGGTCGATGCCATGTCCTAGA
1 CGATGCCATGCCCCAGACATGGTCTTACACTAGCTCTCATAACGAGGTCGATGCCATGTCCTAGA
*
54283163 CATGGTCTTACACTAGC
66 CACGGTCTTACACTAGC
54283180 ATACATATCA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 71 0.99
97 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (96 bp):
CGATGCCATGCCCCAGACATGGTCTTACACTAGCTCTCATAACGAGGTCGATGCCATGTCCTAGA
CACGGTCTTACACTAGCTCTCATAAGGTGTT
Found at i:54294767 original size:40 final size:40
Alignment explanation
Indices: 54294723--54294984 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
54294713 GCTCCTCGTT
* *
54294723 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
54294763 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54294803 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54294842 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54294881 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
54294920 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
54294961 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54294985 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:54296081 original size:14 final size:14
Alignment explanation
Indices: 54296062--54296088 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54296052 AGGATGAGCA
54296062 TTTTTTTTTCTTTG
1 TTTTTTTTTCTTTG
54296076 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
54296089 CTAGTTTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.04, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Found at i:54302956 original size:29 final size:29
Alignment explanation
Indices: 54302893--54302960 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
54302883 TAATCAACCG
54302893 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
54302922 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
54302951 CGCACACTTA
1 CGCACACTTA
54302961 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:54303073 original size:174 final size:174
Alignment explanation
Indices: 54302782--54303109 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
54302772 AACTCAAGGT
* *
54302782 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
54302847 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
54302912 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
54302956 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
54303021 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
54303086 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
54303110 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:54303101 original size:29 final size:30
Alignment explanation
Indices: 54303062--54303140 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
54303052 CTTAATAATC
54303062 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
54303092 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
54303121 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
54303141 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:54304269 original size:46 final size:46
Alignment explanation
Indices: 54304216--54304307 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
54304206 AGGATGAAAA
*
54304216 AGGATGAACAAGTTTTTCTTTTCCTTTCTTTAGCTCACGGTAATGG
1 AGGATGAACAAGTTTTTCTTTTCCTTTCTTTAGCTCACGGCAATGG
54304262 AGGATGAACAAGTTTTTCTTTTCCTTTCTTTAGCTCACGGCAATGG
1 AGGATGAACAAGTTTTTCTTTTCCTTTCTTTAGCTCACGGCAATGG
54304308 GGGGGGAAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (46 bp):
AGGATGAACAAGTTTTTCTTTTCCTTTCTTTAGCTCACGGCAATGG
Found at i:54316403 original size:38 final size:38
Alignment explanation
Indices: 54316354--54316432 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
54316344 TATTTGATAG
*
54316354 TGAATGACTTTTCATGAAGGAAGATGTAATGGTTACAA
1 TGAATGACTTTTCATGAAGGAAGATGTAATCGTTACAA
*
54316392 TGAATGACTTTTCATGAAGGAATATGTAATCGTTACAA
1 TGAATGACTTTTCATGAAGGAAGATGTAATCGTTACAA
54316430 TGA
1 TGA
54316433 GAGGATCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.33
Consensus pattern (38 bp):
TGAATGACTTTTCATGAAGGAAGATGTAATCGTTACAA
Found at i:54321868 original size:27 final size:27
Alignment explanation
Indices: 54321838--54322015 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54321828 ATATTGAGTC
* * * *
54321838 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54321865 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54321892 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54321920 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54321947 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54321974 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54322001 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54322016 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54321977 original size:82 final size:81
Alignment explanation
Indices: 54321859--54322014 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54321849 TGCTATATAA
* *
54321859 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54321924 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54321941 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54322005 CACTTAGTGC
65 CACTTAGTGC
54322015 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54329933 original size:27 final size:27
Alignment explanation
Indices: 54329903--54330080 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54329893 ATATTGAGTC
* * * *
54329903 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54329930 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54329957 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54329985 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54330012 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54330039 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54330066 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54330081 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54330042 original size:82 final size:81
Alignment explanation
Indices: 54329924--54330079 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54329914 TGCTATATAA
* *
54329924 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54329989 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54330006 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54330070 CACTTAGTGC
65 CACTTAGTGC
54330080 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54333221 original size:52 final size:52
Alignment explanation
Indices: 54333137--54333246 Score: 134
Period size: 52 Copynumber: 2.1 Consensus size: 52
54333127 GGGGTTTGCT
* ** *
54333137 AAGAGAGTTTCAGTAAGGAGTTCTACTGAGATTC-AGCAAAGTAGTGTACACA
1 AAGAGAGTTTCAGCAAGGAGTTCTACCAAGATTCGA-CAAAGCAGTGTACACA
* *
54333189 AAGAGAGTTTCAGCAAGGAGTTC-ACCCAAGATTCGACAAAGCAGTGTACGCC
1 AAGAGAGTTTCAGCAAGGAGTTCTA-CCAAGATTCGACAAAGCAGTGTACACA
54333241 AAGAGA
1 AAGAGA
54333247 ACATCAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
51 1 0.02
52 48 0.96
53 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (52 bp):
AAGAGAGTTTCAGCAAGGAGTTCTACCAAGATTCGACAAAGCAGTGTACACA
Found at i:54334959 original size:29 final size:29
Alignment explanation
Indices: 54334911--54334989 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
54334901 TATGGCGTAC
*
54334911 TAGGCCC-AATCTCATTCATATTGCCCAT
1 TAGGCCCAAATCTCATTCATATGGCCCAT
54334939 TAGGCCCAAATCTCATTCATATGGCCCAT
1 TAGGCCCAAATCTCATTCATATGGCCCAT
*
54334968 TAGGCCCAAATCACATTCATAT
1 TAGGCCCAAATCTCATTCATAT
54334990 ACATGCTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.15
29 41 0.85
ACGTcount: A:0.29, C:0.30, G:0.11, T:0.29
Consensus pattern (29 bp):
TAGGCCCAAATCTCATTCATATGGCCCAT
Found at i:54335212 original size:8 final size:8
Alignment explanation
Indices: 54335199--54335228 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
54335189 GTAGCCAAAC
54335199 TTTTGGCT
1 TTTTGGCT
*
54335207 TTTTGGCA
1 TTTTGGCT
54335215 TTTTGGCT
1 TTTTGGCT
54335223 TTTTGG
1 TTTTGG
54335229 GATTTGCCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.10, G:0.27, T:0.60
Consensus pattern (8 bp):
TTTTGGCT
Found at i:54335220 original size:16 final size:16
Alignment explanation
Indices: 54335199--54335233 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
54335189 GTAGCCAAAC
54335199 TTTTGGCTTTTTGGCA
1 TTTTGGCTTTTTGGCA
*
54335215 TTTTGGCTTTTTGGGA
1 TTTTGGCTTTTTGGCA
54335231 TTT
1 TTT
54335234 GCCGATCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.09, G:0.26, T:0.60
Consensus pattern (16 bp):
TTTTGGCTTTTTGGCA
Found at i:54339369 original size:57 final size:59
Alignment explanation
Indices: 54339308--54339427 Score: 131
Period size: 57 Copynumber: 2.1 Consensus size: 59
54339298 CCCTTACAGA
*
54339308 GCCCAAACAAGTCCACA-T-ACATGCATATGGCCCACTAGGCCC-AATCTCATTCATATG
1 GCCCAAACAAGTCCA-AGTCACATGCATATGGCCCACTAGGCCCAAATCACATTCATATG
** * * * * *
54339365 GCCC-ATTAGGTCCAAGTCTCATTCGTATGGCCCATTAGGCCCAAATCACATTCATATG
1 GCCCAAACAAGTCCAAGTCACATGCATATGGCCCACTAGGCCCAAATCACATTCATATG
54339423 GCCCA
1 GCCCA
54339428 TTAGTCCCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
55 1 0.02
56 8 0.16
57 24 0.47
58 18 0.35
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (59 bp):
GCCCAAACAAGTCCAAGTCACATGCATATGGCCCACTAGGCCCAAATCACATTCATATG
Found at i:54339394 original size:29 final size:28
Alignment explanation
Indices: 54339331--54339447 Score: 153
Period size: 29 Copynumber: 4.1 Consensus size: 28
54339321 CACATACATG
*
54339331 CATATGGCCCACTAGGCCCAATCTCATT
1 CATATGGCCCATTAGGCCCAATCTCATT
*
54339359 CATATGGCCCATTAGGTCCAAGTCTCATT
1 CATATGGCCCATTAGGCCCAA-TCTCATT
* *
54339388 CGTATGGCCCATTAGGCCCAAATCACATT
1 CATATGGCCCATTAGGCCC-AATCTCATT
* *
54339417 CATATGGCCCATTAGTCCCAAATCACATT
1 CATATGGCCCATTAGGCCC-AATCTCATT
54339446 CA
1 CA
54339448 AATACATGCT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
28 19 0.24
29 59 0.74
30 2 0.03
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (28 bp):
CATATGGCCCATTAGGCCCAATCTCATT
Found at i:54341262 original size:22 final size:21
Alignment explanation
Indices: 54341237--54341278 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54341227 AGTAAAATTT
54341237 TCTATAAAATCTATTTTCAAGC
1 TCTA-AAAATCTATTTTCAAGC
* *
54341259 TCTAAGACTCTATTTTCAAG
1 TCTAAAAATCTATTTTCAAG
54341279 TTATGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (21 bp):
TCTAAAAATCTATTTTCAAGC
Found at i:54345648 original size:50 final size:52
Alignment explanation
Indices: 54345571--54345702 Score: 180
Period size: 50 Copynumber: 2.6 Consensus size: 52
54345561 ATGTGTTCTA
* * * *
54345571 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTTAGTT-AAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAAGTTTCCAT
*
54345622 CA-TAAATTATGAT-ATGCATTATGTAACTCCCATGTTAGTTAAAGTTTCCAT
1 CATTAAATTAAG-TCATGCATTATGTAACTCCCATGTTAGTTAAAGTTTCCAT
*
54345673 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
54345703 ATTTGTTCAT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
50 32 0.46
51 15 0.21
52 23 0.33
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (52 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAAGTTTCCAT
Found at i:54352475 original size:67 final size:67
Alignment explanation
Indices: 54352361--54352493 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 67
54352351 CAGCTCCTGC
* *
54352361 TGAAGGGGCAGTGCTGACTGAAAATCGACCTCCTACTGTTGTCCAAGGAGGAGGAGAAAGGGCTC
1 TGAAGGGGCAGTGCCGACTGAAAATCGACCTCCTACTGTTGTCCAAGGAAGAGGAGAAAGGGCTC
54352426 GA
66 GA
** *
54352428 TGAAGGGGTGGTGCCGACTGAAATTCGACCTCCTACTGTTGGT-CAAGGAAGAGGAGAAAGGGCT
1 TGAAGGGGCAGTGCCGACTGAAAATCGACCTCCTACTGTT-GTCCAAGGAAGAGGAGAAAGGGCT
54352492 CG
65 CG
54352494 GGAATCCTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 58 0.97
68 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.35, T:0.19
Consensus pattern (67 bp):
TGAAGGGGCAGTGCCGACTGAAAATCGACCTCCTACTGTTGTCCAAGGAAGAGGAGAAAGGGCTC
GA
Found at i:54359257 original size:16 final size:16
Alignment explanation
Indices: 54359236--54359268 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54359226 TTGTAAAGCC
54359236 CCAAAAATCCTGAAAT
1 CCAAAAATCCTGAAAT
*
54359252 CCAAAAATCTTGAAAT
1 CCAAAAATCCTGAAAT
54359268 C
1 C
54359269 TTGAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.21
Consensus pattern (16 bp):
CCAAAAATCCTGAAAT
Found at i:54362872 original size:30 final size:30
Alignment explanation
Indices: 54362829--54362917 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
54362819 CAAAAATAAC
54362829 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
54362858 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * *
54362888 AAGAGATCCA-AGATAAAGAAACCCAAGATA
1 AAGAAAACCAGA-ATAAAGAAATCCAAGATA
54362918 TGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 10 0.20
30 38 0.76
31 2 0.04
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:54362877 original size:15 final size:15
Alignment explanation
Indices: 54362829--54362908 Score: 85
Period size: 15 Copynumber: 5.4 Consensus size: 15
54362819 CAAAAATAAC
*
54362829 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
54362843 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
54362858 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
54362873 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
*
54362888 AAGAGATCCA-AGATA
1 AAGAAATCCAGA-ATA
54362903 AAGAAA
1 AAGAAA
54362909 CCCAAGATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
14 10 0.18
15 44 0.80
16 1 0.02
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:54362913 original size:15 final size:15
Alignment explanation
Indices: 54362840--54362917 Score: 88
Period size: 15 Copynumber: 5.2 Consensus size: 15
54362830 AGAAAACCGA
54362840 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
54362855 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
54362869 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
*
54362884 AATAAAGAGATCCAAG
1 -ATAAAGAAATCCAAG
*
54362900 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
54362915 ATA
1 ATA
54362918 TGATACTATG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.07
15 46 0.85
16 4 0.07
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:54365958 original size:93 final size:93
Alignment explanation
Indices: 54365845--54366015 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
54365835 GCCCATAAGT
**
54365845 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGAAATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54365910 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
54365938 GAACTTGGACTCAACTCAACGAGTTCGGAAATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGAAATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
54366003 CGAGTTCGGATGC
66 CGAGCTCGGATGC
54366016 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGAAATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:54366012 original size:46 final size:45
Alignment explanation
Indices: 54365837--54366012 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
54365827 TGTAACCCGC
*
54365837 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGAATTCGCAT
*
54365883 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAATTCGC-A--T
* *** * *
54365929 ACATCTCTCGAACTTGGACTCAACTCAACGAGTTCGGAAATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-AATTCGCAT
*
54365976 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
54366013 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 3 0.03
46 66 0.60
47 31 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAATTCGCAT
Found at i:54367527 original size:29 final size:29
Alignment explanation
Indices: 54367494--54367595 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 29
54367484 TGAATGTGAC
*
54367494 TGGGCCTAACGGGCCATATAAATATGATT
1 TGGGCCTAATGGGCCATATAAATATGATT
* *
54367523 TGGGCCTAATGGGCCATATATAA-GTGGTT
1 TGGGCCTAATGGGCCATATA-AATATGATT
* *
54367552 TGGGCCTAATTGGCCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAATATGATT
*
54367580 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
54367596 AATACAGGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
28 17 0.27
29 43 0.69
30 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATATGATT
Found at i:54372140 original size:16 final size:16
Alignment explanation
Indices: 54372119--54372151 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54372109 TTGTAACGCC
54372119 CCAAAAATCCCGAAAT
1 CCAAAAATCCCGAAAT
*
54372135 CCAAAAATCTCGAAAT
1 CCAAAAATCCCGAAAT
54372151 C
1 C
54372152 TTGAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.30, G:0.06, T:0.15
Consensus pattern (16 bp):
CCAAAAATCCCGAAAT
Found at i:54373382 original size:8 final size:8
Alignment explanation
Indices: 54373369--54373407 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
54373359 ATCGACAAAA
54373369 GCTGAAAT
1 GCTGAAAT
54373377 GCTGAAAT
1 GCTGAAAT
** *
54373385 GCCAAAAA
1 GCTGAAAT
54373393 GCTGAAAT
1 GCTGAAAT
54373401 GCTGAAA
1 GCTGAAA
54373408 AGCCAAAAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (8 bp):
GCTGAAAT
Found at i:54373397 original size:24 final size:24
Alignment explanation
Indices: 54373365--54373415 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
54373355 ATGAATCGAC
*
54373365 AAAAGCTGAAATGCTGAAATGCCA
1 AAAAGCTGAAATGCTGAAAAGCCA
54373389 AAAAGCTGAAATGCTGAAAAGCCA
1 AAAAGCTGAAATGCTGAAAAGCCA
54373413 AAA
1 AAA
54373416 GTTTGGCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.14
Consensus pattern (24 bp):
AAAAGCTGAAATGCTGAAAAGCCA
Done.