Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 169 of 208
Found at i:54251795 original size:21 final size:22
Alignment explanation
Indices: 54251738--54251795 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
54251728 AAATAATGTT
*
54251738 TATAC-CCAACATAATCATTTCA
1 TATACACCAAC-TAATCATTACA
* *
54251760 TAT-CACCTACAAATCA-TACA
1 TATACACCAACTAATCATTACA
54251780 TATACACCAACTAATC
1 TATACACCAACTAATC
54251796 TATGTCAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 6 0.21
21 16 0.55
22 7 0.24
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.28
Consensus pattern (22 bp):
TATACACCAACTAATCATTACA
Found at i:54270823 original size:15 final size:17
Alignment explanation
Indices: 54270803--54270849 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
54270793 ATACATATGG
*
54270803 ATATATA-AT-TATAGA
1 ATATATATATATATAAA
54270818 ATATATATATATATAAA
1 ATATATATATATATAAA
* *
54270835 ATATTTACATATATA
1 ATATATATATATATA
54270850 CGTTTATGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 7 0.26
16 2 0.07
17 18 0.67
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
ATATATATATATATAAA
Found at i:54271008 original size:3 final size:3
Alignment explanation
Indices: 54271000--54271051 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
54270990 AAAATAAAGC
* * *
54271000 TAA TAA TAA TTAA TAA TAG TAG TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54271046 TAA TAA
1 TAA TAA
54271052 CACTAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:54271030 original size:15 final size:15
Alignment explanation
Indices: 54271000--54271050 Score: 75
Period size: 15 Copynumber: 3.3 Consensus size: 15
54270990 AAAATAAAGC
*
54271000 TAATAATAATTAATAA
1 TAATAGTAA-TAATAA
*
54271016 TAGTAGTAATAATAA
1 TAATAGTAATAATAA
54271031 TAATAGTAATAATAA
1 TAATAGTAATAATAA
54271046 TAATA
1 TAATA
54271051 ACACTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 25 0.78
16 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
TAATAGTAATAATAA
Found at i:54271033 original size:18 final size:18
Alignment explanation
Indices: 54271000--54271051 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
54270990 AAAATAAAGC
54271000 TAATAATAATTAATAATAG
1 TAATAATAA-TAATAATAG
*
54271019 TAGTAATAATAATAATAG
1 TAATAATAATAATAATAG
54271037 TAATAATAATAATAA
1 TAATAATAATAATAA
54271052 CACTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATAATAG
Found at i:54271067 original size:18 final size:18
Alignment explanation
Indices: 54270999--54271063 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
54270989 GAAAATAAAG
54270999 CTAATAATAATTAATAATA
1 CTAATAATAA-TAATAATA
* *
54271018 GTAGTAATAATAATAATA
1 CTAATAATAATAATAATA
* *
54271036 GTAATAATAATAATAACA
1 CTAATAATAATAATAATA
54271054 CTAA-AATAAT
1 CTAATAATAAT
54271064 TAATTAAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
17 6 0.15
18 27 0.66
19 8 0.20
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
CTAATAATAATAATAATA
Found at i:54272683 original size:50 final size:50
Alignment explanation
Indices: 54272629--54272980 Score: 270
Period size: 50 Copynumber: 7.0 Consensus size: 50
54272619 GCTTCTTCTG
* **
54272629 TCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGTCGTCATAGCTTCAA
1 TCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAA
* * * * *
54272679 TCTGTTTGACTGCAATGTCGGGGAAGCAAAATTTGCCGTCGTAGCTTCAA
1 TCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAA
* ** * * * *
54272729 TTTGTTCCACTGC-ATCGCCTGGGAAGTGAGATTCGCCATTGTAGCTTCAA
1 TCTGTTTAACTGCAAT-GTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAA
* * *
54272779 TCTG-TT-CCGTGGC-ATCG-CTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAA
1 TCTGTTTAAC-T-GCAAT-GTC-GGGGAAGTAAGATTCGCCGTTGTAGCTTCAA
* * * *
54272829 TCT-TTTGAATTGCAATGTCAGGGAAGTGAGATTCGCCATTGTAGCTTCAA
1 TCTGTTT-AACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAA
* *** ** * *
54272879 CCTGTTCCGCTGC-ATCACTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAA
1 TCTGTTTAACTGCAATGTC-GGGGAAGTAAGATTCGCCGTTGTAGCTTCAA
* * * *
54272929 TCT-TTTGAATTGCAATGTCGGGGAAGTGAGATTCGCCATTGTAACTTCAA
1 TCTGTTT-AACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAA
54272979 TC
1 TC
54272981 ATTGTAGCTT
Statistics
Matches: 237, Mismatches: 52, Indels: 26
0.75 0.17 0.08
Matches are distributed among these distances:
48 1 0.00
49 10 0.04
50 217 0.92
51 9 0.04
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (50 bp):
TCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAA
Found at i:54272817 original size:100 final size:100
Alignment explanation
Indices: 54272749--54272980 Score: 412
Period size: 100 Copynumber: 2.3 Consensus size: 100
54272739 TGCATCGCCT
*
54272749 GGGAAGTGAGATTCGCCATTGTAGCTTCAATCTGTTCCG-TGGCATCGCTTGGGAAGTAAGATTC
1 GGGAAGTGAGATTCGCCATTGTAGCTTCAATCTGTTCCGCT-GCATCACTTGGGAAGTAAGATTC
54272813 GCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCA
65 GCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCA
*
54272849 GGGAAGTGAGATTCGCCATTGTAGCTTCAACCTGTTCCGCTGCATCACTTGGGAAGTAAGATTCG
1 GGGAAGTGAGATTCGCCATTGTAGCTTCAATCTGTTCCGCTGCATCACTTGGGAAGTAAGATTCG
*
54272914 CCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCG
66 CCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCA
*
54272949 GGGAAGTGAGATTCGCCATTGTAACTTCAATC
1 GGGAAGTGAGATTCGCCATTGTAGCTTCAATC
54272981 ATTGTAGCTT
Statistics
Matches: 126, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
100 125 0.99
101 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (100 bp):
GGGAAGTGAGATTCGCCATTGTAGCTTCAATCTGTTCCGCTGCATCACTTGGGAAGTAAGATTCG
CCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCA
Found at i:54272985 original size:15 final size:15
Alignment explanation
Indices: 54272965--54272995 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54272955 TGAGATTCGC
54272965 CATTGTAACTTCAAT
1 CATTGTAACTTCAAT
*
54272980 CATTGTAGCTTCAAT
1 CATTGTAACTTCAAT
54272995 C
1 C
54272996 TGTTCCGCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (15 bp):
CATTGTAACTTCAAT
Found at i:54273067 original size:115 final size:115
Alignment explanation
Indices: 54272865--54273095 Score: 399
Period size: 115 Copynumber: 2.0 Consensus size: 115
54272855 TGAGATTCGC
* *
54272865 CATTGTAGCTTCAACCTGTTCCGCTGCATCACTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT
1 CATTGTAGCTTCAACCTGTTCCGCTGCATCACTTAGGAAGTAAGATTCACCGTTGTGGCTTCAAT
54272930 CTTTTGAATTGCAATGTCGGGGAAGTGAGATTCGCCATTGTAACTTCAAT
66 CTTTTGAATTGCAATGTCGGGGAAGTGAGATTCGCCATTGTAACTTCAAT
* **
54272980 CATTGTAGCTTCAATCTGTTCCGCTGCATTGCTTAGGAAGTAAGATTCACCGTTGTGGCTTCAAT
1 CATTGTAGCTTCAACCTGTTCCGCTGCATCACTTAGGAAGTAAGATTCACCGTTGTGGCTTCAAT
* *
54273045 CTTTTGAATTGCAATGTCGGGGAAGTGAGATTTGCCATTGTAGCTTCAAT
66 CTTTTGAATTGCAATGTCGGGGAAGTGAGATTCGCCATTGTAACTTCAAT
54273095 C
1 C
54273096 TGTTCCGCTG
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 109 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (115 bp):
CATTGTAGCTTCAACCTGTTCCGCTGCATCACTTAGGAAGTAAGATTCACCGTTGTGGCTTCAAT
CTTTTGAATTGCAATGTCGGGGAAGTGAGATTCGCCATTGTAACTTCAAT
Found at i:54273136 original size:215 final size:215
Alignment explanation
Indices: 54272765--54273195 Score: 765
Period size: 215 Copynumber: 2.0 Consensus size: 215
54272755 TGAGATTCGC
* *
54272765 CATTGTAGCTTCAATCTGTTCCGTGGCATCGCTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT
1 CATTGTAGCTTCAATCTGTTCCGTGGCATCGCTTAGGAAGTAAGATTCACCGTTGTGGCTTCAAT
54272830 CTTTTGAATTGCAATGTCAGGGAAGTGAGATTCGCCATTGTAGCTTCAACCTGTTCCGCTGCATC
66 CTTTTGAATTGCAATGTCAGGGAAGTGAGATTCGCCATTGTAGCTTCAACCTGTTCCGCTGCATC
54272895 ACTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGA
131 ACTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGA
*
54272960 TTCGCCATTGTAACTTCAAT
196 CTCGCCATTGTAACTTCAAT
*
54272980 CATTGTAGCTTCAATCTGTTCCGCT-GCATTGCTTAGGAAGTAAGATTCACCGTTGTGGCTTCAA
1 CATTGTAGCTTCAATCTGTTCCG-TGGCATCGCTTAGGAAGTAAGATTCACCGTTGTGGCTTCAA
* * *
54273044 TCTTTTGAATTGCAATGTCGGGGAAGTGAGATTTGCCATTGTAGCTTCAATCTGTTCCGCTGCAT
65 TCTTTTGAATTGCAATGTCAGGGAAGTGAGATTCGCCATTGTAGCTTCAACCTGTTCCGCTGCAT
*
54273109 CGCTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAG
130 CACTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAG
*
54273174 ACTCGCCATTGTAGCTTCAAT
195 ACTCGCCATTGTAACTTCAAT
54273195 C
1 C
54273196 TGTTCCGCTG
Statistics
Matches: 206, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
215 205 1.00
216 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (215 bp):
CATTGTAGCTTCAATCTGTTCCGTGGCATCGCTTAGGAAGTAAGATTCACCGTTGTGGCTTCAAT
CTTTTGAATTGCAATGTCAGGGAAGTGAGATTCGCCATTGTAGCTTCAACCTGTTCCGCTGCATC
ACTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGA
CTCGCCATTGTAACTTCAAT
Found at i:54273153 original size:100 final size:100
Alignment explanation
Indices: 54272980--54273232 Score: 452
Period size: 100 Copynumber: 2.5 Consensus size: 100
54272970 TAACTTCAAT
* * *
54272980 CATTGTAGCTTCAATCTGTTCCGCTGCATTGCTTAGGAAGTAAGATTCACCGTTGTGGCTTCAAT
1 CATTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT
* *
54273045 CTTTTGAATTGCAATGTCGGGGAAGTGAGATTTGC
66 CTTTTGAATTGCAATGTCGGGGAAGTGAGACTCGC
54273080 CATTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT
1 CATTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT
54273145 CTTTTGAATTGCAATGTCGGGGAAGTGAGACTCGC
66 CTTTTGAATTGCAATGTCGGGGAAGTGAGACTCGC
*
54273180 CATTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAAGTAAGATTCGCCGT
1 CATTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGGAAGTAAGATTCGCCGT
54273233 ATGATCTGTT
Statistics
Matches: 147, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 147 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (100 bp):
CATTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT
CTTTTGAATTGCAATGTCGGGGAAGTGAGACTCGC
Found at i:54273230 original size:50 final size:49
Alignment explanation
Indices: 54272980--54273230 Score: 218
Period size: 50 Copynumber: 5.0 Consensus size: 49
54272970 TAACTTCAAT
* *
54272980 CATTGTAGCTTCAATCTGTTCCGCTGCATTGCTTAGGAAGTAAGATTCAC
1 CATTGTAGCTTCAATCTGTTCCGCTGCA-TGCTTGGGAAGTAAGATTCGC
* * * **** * * *
54273030 CGTTGTGGCTTCAATCTTTTGAATTGCAATG-TCGGGGAAGTGAGATTTGC
1 CATTGTAGCTTCAATCTGTTCCGCTGC-ATGCT-TGGGAAGTAAGATTCGC
54273080 CATTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGGAAGTAAGATTCGC
1 CATTGTAGCTTCAATCTGTTCCGCTGCAT-GCTTGGGAAGTAAGATTCGC
* * * **** * * *
54273130 CGTTGTGGCTTCAATCTTTTGAATTGCAATG-TCGGGGAAGTGAGACTCGC
1 CATTGTAGCTTCAATCTGTTCCGCTGC-ATGCT-TGGGAAGTAAGATTCGC
*
54273180 CATTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAAGTAAGATTCGC
1 CATTGTAGCTTCAATCTGTTCCGCTGCAT-GCTTGGGAAGTAAGATTCGC
54273230 C
1 C
54273231 GTATGATCTG
Statistics
Matches: 150, Mismatches: 43, Indels: 16
0.72 0.21 0.08
Matches are distributed among these distances:
49 6 0.04
50 139 0.93
51 5 0.03
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (49 bp):
CATTGTAGCTTCAATCTGTTCCGCTGCATGCTTGGGAAGTAAGATTCGC
Found at i:54285943 original size:3 final size:3
Alignment explanation
Indices: 54285935--54285986 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
54285925 AAAATAAAGC
* * *
54285935 TAA TAA TAA TTAA TAA TAG TAG TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54285981 TAA TAA
1 TAA TAA
54285987 CACTAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:54285965 original size:15 final size:15
Alignment explanation
Indices: 54285935--54285985 Score: 75
Period size: 15 Copynumber: 3.3 Consensus size: 15
54285925 AAAATAAAGC
*
54285935 TAATAATAATTAATAA
1 TAATAGTAA-TAATAA
*
54285951 TAGTAGTAATAATAA
1 TAATAGTAATAATAA
54285966 TAATAGTAATAATAA
1 TAATAGTAATAATAA
54285981 TAATA
1 TAATA
54285986 ACACTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 25 0.78
16 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
TAATAGTAATAATAA
Found at i:54285968 original size:18 final size:18
Alignment explanation
Indices: 54285935--54285986 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
54285925 AAAATAAAGC
54285935 TAATAATAATTAATAATAG
1 TAATAATAA-TAATAATAG
*
54285954 TAGTAATAATAATAATAG
1 TAATAATAATAATAATAG
54285972 TAATAATAATAATAA
1 TAATAATAATAATAA
54285987 CACTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATAATAG
Found at i:54286002 original size:18 final size:18
Alignment explanation
Indices: 54285934--54285998 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
54285924 GAAAATAAAG
54285934 CTAATAATAATTAATAATA
1 CTAATAATAA-TAATAATA
* *
54285953 GTAGTAATAATAATAATA
1 CTAATAATAATAATAATA
* *
54285971 GTAATAATAATAATAACA
1 CTAATAATAATAATAATA
54285989 CTAA-AATAAT
1 CTAATAATAAT
54285999 TAATTAAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
17 6 0.15
18 27 0.66
19 8 0.20
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
CTAATAATAATAATAATA
Found at i:54286516 original size:21 final size:21
Alignment explanation
Indices: 54286490--54286529 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
54286480 CAGCCATGTG
54286490 GGGTTCCTTGGCCCCTGTTAC
1 GGGTTCCTTGGCCCCTGTTAC
54286511 GGGTTCCTTGGCCCCTGTT
1 GGGTTCCTTGGCCCCTGTT
54286530 GCGCCGCCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.03, C:0.33, G:0.30, T:0.35
Consensus pattern (21 bp):
GGGTTCCTTGGCCCCTGTTAC
Found at i:54287754 original size:30 final size:31
Alignment explanation
Indices: 54287715--54287774 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
54287705 AGAGGTGGGA
*
54287715 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
54287746 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
54287775 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:54288002 original size:9 final size:9
Alignment explanation
Indices: 54287988--54288024 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54287978 TATAGTTTGA
54287988 TATTCGAAT
1 TATTCGAAT
54287997 TATTCGAAT
1 TATTCGAAT
*
54288006 TATTCGAGT
1 TATTCGAAT
54288015 TATTCGAAT
1 TATTCGAAT
54288024 T
1 T
54288025 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54288094 original size:9 final size:9
Alignment explanation
Indices: 54288077--54288107 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
54288067 TCGAGTTGAT
54288077 TCGAATAAC
1 TCGAATAAC
*
54288086 TCGATTAAC
1 TCGAATAAC
54288095 TCGAATAAC
1 TCGAATAAC
54288104 TCGA
1 TCGA
54288108 TCCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:54291914 original size:44 final size:42
Alignment explanation
Indices: 54291846--54292000 Score: 136
Period size: 44 Copynumber: 3.5 Consensus size: 42
54291836 TTTAATTCGA
* *
54291846 TCCACTGCAACTTCAGAGG-TATAGGATTCATCGTTTTAATCTGC
1 TCCACTGCAACTTTAG-GGAGATAGGATT-ATCG-TTTAATCTGC
* * *
54291890 TCCACTGTAACTTTAGGGAGATAGGATTAGTAGCTTCAATCTGC
1 TCCACTGCAACTTTAGGGAGATAGGATTA-TCG-TTTAATCTGC
* *
54291934 TCCACTGCAA-TTTCAGGGAGATAAGATTGGTATC-TTTAACCTGC
1 TCCACTGCAACTTT-AGGGAGATAGGA-T--TATCGTTTAATCTGC
*
54291978 TCCACTGCAACTTCAGGGAGATA
1 TCCACTGCAACTTTAGGGAGATA
54292001 AGGTTTGCTA
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.07
44 80 0.87
45 3 0.03
46 1 0.01
47 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
TCCACTGCAACTTTAGGGAGATAGGATTATCGTTTAATCTGC
Found at i:54292001 original size:44 final size:44
Alignment explanation
Indices: 54291883--54292674 Score: 426
Period size: 44 Copynumber: 17.7 Consensus size: 44
54291873 TCATCGTTTT
* * * * *
54291883 AATCTGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
* *
54291927 AATCTGCTCCACTGCAATTTCAGGGAGATAAGATTGGTATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
* * *
54291971 AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAA-GATTGGTATCTTC
* * * * * **
54292016 AGTCTACTCCACTACAACTTCAGTGAGATAAGGTCTGCAAT-TTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGGTATCTTC
* * * * * *
54292060 AACCTGC-CCTACTGCAACTTGAGGGGGATAAGGTTTG-AT-AT-
1 AATCTGCTCC-ACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
* * *
54292101 GATCTGCTCTACTGCAACTTCAGTGAGATAAGATCTGCAATGTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG----GTAT--CTTC
* * * * * * * * *
54292152 AATTTGTTCCACTACAACTTCAAGGAAATAAGGTTCGATATATTA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GGTATCTTC
* * *
54292197 AATCTGCTCCACTACAACTTCAGGAAGATAAGATTTGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
* * * * *
54292241 AACCTGCTCCACTACAACTTTAGGGAGATAAGGTTTGTTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAA-GATTGGTATCTTC
* * * *
54292286 AGTCTACTCCACTGCAACTTTAGTGAGATAAGAGTT-GTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATCTTC
* * * * ****
54292330 AACCTGCTCTACTGTAACTTTCA-GGAGATAAGGTCCACAAT-TTC
1 AATCTGCTCCACTGCAAC-TTCAGGGAGATAAGAT-TGGTATCTTC
* * * * *
54292374 AATCTGC-CCTACTGCAACTTGAGGGGGATAAGGTTTG-AT-AT-
1 AATCTGCTCC-ACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
* * * *
54292415 GATTTGCTCTACTGCAACTTCAGTGAGATAAGATCTGCAATGTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG----GTAT--CTTC
* * ** * * * *
54292466 AATCCGTTCCACCACAACTTCAAGGAAATAAGATTCGATATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GGTATCTTC
** * * *
54292511 GGTCTTCTCCACTCCAACTTCAGGGAGATAAGATTTGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
* * **
54292555 AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTCTGCAAT-TTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGGTATCTTC
* * * * *
54292599 AACCTACCCCACTGCAACTTCAAGGG-GATAAGGTTTGTCA-CTTC
1 AATCTGCTCCACTGCAACTTC-AGGGAGATAAGATTGGT-ATCTTC
* * * *
54292643 AACCTGCTCTACTCCAACTTCAGAGAGATAAG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG
54292675 GTTTGTGGCT
Statistics
Matches: 564, Mismatches: 145, Indels: 78
0.72 0.18 0.10
Matches are distributed among these distances:
41 50 0.09
42 10 0.02
43 12 0.02
44 274 0.49
45 151 0.27
46 2 0.00
47 10 0.02
50 4 0.01
51 51 0.09
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
Found at i:54292211 original size:181 final size:184
Alignment explanation
Indices: 54291978--54292318 Score: 424
Period size: 181 Copynumber: 1.9 Consensus size: 184
54291968 TTTAACCTGC
* * * * * * * *
54291978 TCCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTCAGTCTACTCCACTACAACTTCAGTG-A
1 TCCACTACAACTTCAAGGAAATAAGGTTCGATATATTAAATCTACTCCACTACAACTTCAG-GAA
* * * *
54292042 GATAAGGTCTGCAAT-TTCAACCTGC-CCTACTGCAACTTGAGGGGGATAAGGTTTG-AT-ATGA
65 GATAAGATCTG-AATCTTCAACCTGCTCC-ACTACAACTTGAGGGAGATAAGGTTTGTATCATCA
* *
54292103 -TCTGCTCTACTGCAACTTCAGTGAGATAAGATCTGCAATGTATAGCTTCAATTTGT
128 GTCTACTCCACTGCAACTTCAGTGAGATAAGATCTGCAATGTATAGCTTCAATTTGT
*
54292159 TCCACTACAACTTCAAGGAAATAAGGTTCGATATATTAAATCTGCTCCACTACAACTTCAGGAAG
1 TCCACTACAACTTCAAGGAAATAAGGTTCGATATATTAAATCTACTCCACTACAACTTCAGGAAG
* * * *
54292224 ATAAGATTTGTATCTTCAACCTGCTCCACTACAACTTTAGGGAGATAAGGTTTGTTATCTTCAGT
66 ATAAGATCTGAATCTTCAACCTGCTCCACTACAACTTGAGGGAGATAAGGTTTG-TATCATCAGT
*
54292289 CTACTCCACTGCAACTTTAGTGAGATAAGA
130 CTACTCCACTGCAACTTCAGTGAGATAAGA
54292319 GTTGTATCTT
Statistics
Matches: 133, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
180 3 0.02
181 96 0.72
182 2 0.02
183 2 0.02
184 2 0.02
185 28 0.21
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (184 bp):
TCCACTACAACTTCAAGGAAATAAGGTTCGATATATTAAATCTACTCCACTACAACTTCAGGAAG
ATAAGATCTGAATCTTCAACCTGCTCCACTACAACTTGAGGGAGATAAGGTTTGTATCATCAGTC
TACTCCACTGCAACTTCAGTGAGATAAGATCTGCAATGTATAGCTTCAATTTGT
Found at i:54292329 original size:314 final size:315
Alignment explanation
Indices: 54291883--54292676 Score: 1059
Period size: 314 Copynumber: 2.5 Consensus size: 315
54291873 TCATCGTTTT
** * * * * *
54291883 AATCTGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCACTGCAA-TTT
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCTCCACTGCAACTTT
* * *
54291947 CAGGGAGATAA-GATTGGTATCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTA
66 -AGGGAGATAAGGTTTGGTATCTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTGCTA
** **
54292011 TCTTCAGTCTACTCCACTACAAC-TTCAGTGAGATAAGGTCTGCAATTTCAACCTGCCCTACTGC
130 TCTTCAACCTACTCCACTACAACTTTCAG-GAGATAAGGTCCACAATTTCAACCTGCCCTACTGC
54292075 AACTTGAGGGGGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGTGAGATAAGATCTGCA
194 AACTTGAGGGGGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGTGAGATAAGATCTGCA
** * *
54292140 ATGTATAGCTTCAATTTGTTCCACTACAACTTCAAGGAAATAAGGTTCGATATATTA
259 ATGTATAGCTTCAATCCGTTCCACCACAACTTCAAGGAAATAAGATTCGATATATTA
* *
54292197 AATCTGCTCCACTACAACTTCAGGAAGATAAGATTTGTATCTTCAACCTGCTCCACTACAACTTT
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCTCCACTGCAACTTT
* ** * *
54292262 AGGGAGATAAGGTTTGTTATCTTCAGTCTACTCCACTGCAACTTTAGTGAGATAAGAG-TTG-TA
66 AGGGAGATAAGGTTTGGTATCTTCAACCTACTCCACTGCAACTTCAGGGAGATAAG-GTTTGCTA
* * ** *
54292325 TCTTCAACCTGCTCTACTGTAACTTTCAGGAGATAAGGTCCACAATTTCAATCTGCCCTACTGCA
130 TCTTCAACCTACTCCACTACAACTTTCAGGAGATAAGGTCCACAATTTCAACCTGCCCTACTGCA
*
54292390 ACTTGAGGGGGATAAGGTTTGATATGATTTGCTCTACTGCAACTTCAGTGAGATAAGATCTGCAA
195 ACTTGAGGGGGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGTGAGATAAGATCTGCAA
* *
54292455 TGTATAGCTTCAATCCGTTCCACCACAACTTCAAGGAAATAAGATTCGATATCTTT
260 TGTATAGCTTCAATCCGTTCCACCACAACTTCAAGGAAATAAGATTCGATATATTA
** * * *
54292511 GGTCTTCTCCACTCCAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCTCCACTGCAACTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCTCCACTGCAACTTT
* ** *
54292576 AGGGAGATAAGGTCTGCAAT-TTCAACCTACCCCACTGCAACTTCAAGGG-GATAAGGTTTG-TC
66 AGGGAGATAAGGTTTGGTATCTTCAACCTACTCCACTGCAACTTC-AGGGAGATAAGGTTTGCT-
* * *
54292638 A-CTTCAACCTGCTCTACTCCAAC-TTCAGAGAGATAAGGT
129 ATCTTCAACCTACTCCACTACAACTTTCAG-GAGATAAGGT
54292677 TTGTGGCTTT
Statistics
Matches: 422, Mismatches: 50, Indels: 17
0.86 0.10 0.03
Matches are distributed among these distances:
312 6 0.01
313 60 0.14
314 307 0.73
315 48 0.11
316 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (315 bp):
AATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCTCCACTGCAACTTT
AGGGAGATAAGGTTTGGTATCTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTGCTAT
CTTCAACCTACTCCACTACAACTTTCAGGAGATAAGGTCCACAATTTCAACCTGCCCTACTGCAA
CTTGAGGGGGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGTGAGATAAGATCTGCAAT
GTATAGCTTCAATCCGTTCCACCACAACTTCAAGGAAATAAGATTCGATATATTA
Found at i:54292846 original size:51 final size:51
Alignment explanation
Indices: 54292749--54292862 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
54292739 ATCCGCTCTA
* * * *
54292749 CTTCAGCTTTCATCTATTCCACTACAACACTAGGGAAACAATATTCGCTAC
1 CTTCAGCTTTAATCTATTCCACTACAACACTAGAGAAACAAGATTCGCCAC
* * ** * * *
54292800 CTTTAGCTTTAATCTGTTCCACTGGAACGCTAGAGAAATAAGATTCGCCGC
1 CTTCAGCTTTAATCTATTCCACTACAACACTAGAGAAACAAGATTCGCCAC
54292851 CTTCAGCTTTAA
1 CTTCAGCTTTAA
54292863 CGATAGGGAC
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (51 bp):
CTTCAGCTTTAATCTATTCCACTACAACACTAGAGAAACAAGATTCGCCAC
Found at i:54293030 original size:21 final size:21
Alignment explanation
Indices: 54292989--54293031 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54292979 GATTCGCTGC
* *
54292989 CTTCAGCTTTAATCTGCTCCA
1 CTTCAACTTTAATCTACTCCA
*
54293010 CTTCAACTTTAATCTATTCCA
1 CTTCAACTTTAATCTACTCCA
54293031 C
1 C
54293032 CGCAACGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.05, T:0.40
Consensus pattern (21 bp):
CTTCAACTTTAATCTACTCCA
Found at i:54293037 original size:21 final size:21
Alignment explanation
Indices: 54292995--54293037 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
54292985 CTGCCTTCAG
* **
54292995 CTTTAATCTGCTCCACTTCAA
1 CTTTAATCTACTCCACCGCAA
*
54293016 CTTTAATCTATTCCACCGCAA
1 CTTTAATCTACTCCACCGCAA
54293037 C
1 C
54293038 GCTAGGGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.35, G:0.05, T:0.35
Consensus pattern (21 bp):
CTTTAATCTACTCCACCGCAA
Found at i:54293898 original size:27 final size:27
Alignment explanation
Indices: 54293868--54293932 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
54293858 AAACTTCTAG
54293868 AGTAATATGC-AAAACATCCATTGTGAA
1 AGTAATAT-CAAAAACATCCATTGTGAA
*
54293895 AGTATTATCAGAAAACATCCATTGTGAA
1 AGTAATATCA-AAAACATCCATTGTGAA
*
54293923 AGTATTATCA
1 AGTAATATCA
54293933 GTCCATTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 7 0.20
28 27 0.77
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (27 bp):
AGTAATATCAAAAACATCCATTGTGAA
Found at i:54293910 original size:28 final size:28
Alignment explanation
Indices: 54293878--54293933 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
54293868 AGTAATATGC
54293878 AAAACATCCATTGTGAAAGTATTATCAG
1 AAAACATCCATTGTGAAAGTATTATCAG
54293906 AAAACATCCATTGTGAAAGTATTATCAG
1 AAAACATCCATTGTGAAAGTATTATCAG
54293934 TCCATTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (28 bp):
AAAACATCCATTGTGAAAGTATTATCAG
Found at i:54304351 original size:44 final size:44
Alignment explanation
Indices: 54304288--54304652 Score: 401
Period size: 44 Copynumber: 8.3 Consensus size: 44
54304278 TGCACTCTTG
* * *
54304288 AAGTTACAGTGGAGTAGATTGAAGCTACCAATCTTATCTTCCTA
1 AAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTA
* * * *
54304332 AAGTTGCAGTGGAGTAGATTAAAGCCACAAATTTTATCTCCCTG
1 AAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTA
*
54304376 AAGTTGCAGTGGAGTAGACTGAAG-TCACAAATCTTATCTCCCTA
1 AAGTTGCAGTGGAGTAGATTGAAGCT-ACAAATCTTATCTCCCTA
* * * * * * * * * *
54304420 AAGTTACACTAGAGCATATTAAAACCACAAATCTTATCTTCCTG
1 AAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTA
* * *
54304464 AAGTTGCAGTGGAGTAGATTAAAGCTAAAAATCTTATCTCCCTG
1 AAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTA
* * * *
54304508 AAGTTTCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTA
1 AAGTTGCAGTGGAGTAGATTGAAGCTA-CAAATCTTATCTCCCTA
* *
54304553 AAGTTGCAGTGGAATAGATTGAAGCTACAAATCTTATCTCCTTA
1 AAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTA
* ** * *
54304597 AAGTTGCAGTGGAGCAGATTGAAGAGACAAATCATATGC-CTCTA
1 AAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTAT-CTCCCTA
54304641 AAGTTGCAGTGG
1 AAGTTGCAGTGG
54304653 GTCGAATTAA
Statistics
Matches: 265, Mismatches: 52, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
44 227 0.86
45 38 0.14
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
AAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTA
Found at i:54304697 original size:13 final size:13
Alignment explanation
Indices: 54304679--54304741 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 13
54304669 ATTCTTCATA
54304679 GCTTTTGAAAAGT
1 GCTTTTGAAAAGT
54304692 GCTTTTGAAAAGT
1 GCTTTTGAAAAGT
* *
54304705 -ATTGTGGAAAAGT
1 GCTT-TTGAAAAGT
* *
54304718 ACTTTTGAGAAGT
1 GCTTTTGAAAAGT
54304731 GCTTTTGAAAA
1 GCTTTTGAAAA
54304742 ATTTGAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
12 2 0.05
13 37 0.90
14 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (13 bp):
GCTTTTGAAAAGT
Found at i:54305663 original size:14 final size:13
Alignment explanation
Indices: 54305627--54305672 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
54305617 CGTCCAGATC
54305627 AAAACCAAAAATA
1 AAAACCAAAAATA
*
54305640 AATAAACAAAATATA
1 AA-AACCAAAA-ATA
54305655 AAAACCAAAAAATA
1 AAAACC-AAAAATA
54305669 AAAA
1 AAAA
54305673 AGTCCATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 17 0.61
15 9 0.32
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAACCAAAAATA
Found at i:54305672 original size:15 final size:15
Alignment explanation
Indices: 54305627--54305673 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
54305617 CGTCCAGATC
54305627 AAAACC-AAAAATAA
1 AAAACCAAAAAATAA
*
54305641 ATAAA-CAAAATAT-A
1 A-AAACCAAAAAATAA
54305655 AAAACCAAAAAATAA
1 AAAACCAAAAAATAA
54305670 AAAA
1 AAAA
54305674 GTCCATTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 3 0.11
14 11 0.41
15 13 0.48
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAACCAAAAAATAA
Found at i:54306002 original size:22 final size:24
Alignment explanation
Indices: 54305956--54306009 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
54305946 ATAGAAACAT
*
54305956 GAAGCAAAAATAGTAAAAAAGACA
1 GAAGCAAAAATAGTAAAAAACACA
*
54305980 GAAGCAAAAA-A-TAGAAAACACA
1 GAAGCAAAAATAGTAAAAAACACA
54306002 GAAGCAAA
1 GAAGCAAA
54306010 CACGAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 17 0.61
23 1 0.04
24 10 0.36
ACGTcount: A:0.67, C:0.11, G:0.17, T:0.06
Consensus pattern (24 bp):
GAAGCAAAAATAGTAAAAAACACA
Found at i:54320710 original size:28 final size:28
Alignment explanation
Indices: 54320630--54320712 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 28
54320620 CATGGGATTG
* * *
54320630 ATTTGCTCACACAAGTTGTAATATTCAA
1 ATTTGCTCACACAAGCTGTGATATTTAA
* * * * *
54320658 ATTTTCTCACACGAGCTATGGTATTTGA
1 ATTTGCTCACACAAGCTGTGATATTTAA
*
54320686 ATTTGCTCACACAAGGTGTGATATTTA
1 ATTTGCTCACACAAGCTGTGATATTTA
54320713 GGCTACTCAC
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (28 bp):
ATTTGCTCACACAAGCTGTGATATTTAA
Found at i:54321930 original size:17 final size:17
Alignment explanation
Indices: 54321885--54321931 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
54321875 TTCCACCCAG
*
54321885 TTTCATCTTTTATTAGT
1 TTTCATATTTTATTAGT
*
54321902 TTTCTTTATTTTACTTA-T
1 TTTC-ATATTTTA-TTAGT
54321920 TTTCATATTTTA
1 TTTCATATTTTA
54321932 ATTTTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 11 0.44
18 11 0.44
19 3 0.12
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTCATATTTTATTAGT
Found at i:54322056 original size:4 final size:4
Alignment explanation
Indices: 54322047--54322093 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
54322037 TAAGTCTTTT
54322047 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
54322094 GATTGGGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:54330193 original size:21 final size:21
Alignment explanation
Indices: 54330167--54330207 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54330157 AGACGAGCAA
* *
54330167 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
54330188 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
54330208 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:54337159 original size:24 final size:25
Alignment explanation
Indices: 54337113--54337160 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
54337103 TACCCATAAT
*
54337113 AATATTAAACAATTATAATATTGAA
1 AATATTAAACAATTATAACATTGAA
* *
54337138 AATATTGAA-AATTATTACATTGA
1 AATATTAAACAATTATAACATTGA
54337161 CATTAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (25 bp):
AATATTAAACAATTATAACATTGAA
Found at i:54341252 original size:20 final size:20
Alignment explanation
Indices: 54341227--54341265 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
54341217 GCTGACATGG
54341227 TGGTTGGACACAACGATTAA
1 TGGTTGGACACAACGATTAA
54341247 TGGTTGGACACAACGATTA
1 TGGTTGGACACAACGATTA
54341266 CAACAATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (20 bp):
TGGTTGGACACAACGATTAA
Found at i:54347317 original size:891 final size:893
Alignment explanation
Indices: 54344957--54348526 Score: 7008
Period size: 892 Copynumber: 4.0 Consensus size: 893
54344947 GAAACCTAAG
54344957 CCTTCAGAAACTTATATTTGACCAATATATCCCTTAATTAATCACTTGATTCATCAACCAACAAA
1 CCTTCAGAAACTTATATTTGACCAATATATCCCTTAATTAATCACTTGATTCATCAACCAACAAA
* *
54345022 ATATCTCCAACATAAAACTCGAAAAACTAAACCAATGAAGATTTGAAAACTTACCATGACGAGTT
66 ATATCTCCAACATAAAACTCGAGAAACTAAACCAACGAAGATTTGAAAACTTACCATGACGAGTT
*
54345087 CGATAACCAGTCATCTCTATACACTGGAATATCAGCTTAAAACCTTTGAACAGCACCTAAACGAG
131 CGATAACCAGTCATCTCTATACACTGGAATATCCGCTTAAAACCTTTGAACAGCACCTAAACGAG
54345152 AGTAAAACGAACCCTTTATTAACTGTCTAATCAAAATACGATAACTAAGGGGGGAAATTCCACTT
196 AGTAAAACGAACCCTTTATTAACTGTCTAATCAAAATACGATAACTAAGGGGGGAAATTCCACTT
*
54345217 ACAGAAATAGATAAATCAAAATTTACAGCCAAAGAGATGACTCCCAAAAAAATACAGAAACGAAA
261 ACAGAAATAGATAAATAAAAATTTACAGCCAAAGAGATGACTCCCAAAAAAATACAGAAACGAAA
54345282 AGAGAGGGCAAAGAGAAGAAACAAGATTCGACCAAAGGGGAACAAAAACCAAAAGTGAACAAGAA
326 AGAGAGGGCAAAGAGAAGAAACAAGATTCGACCAAAGGGGAACAAAAACCAAAAGTGAACAAGAA
54345347 GGGAGAAAACACGGCAGAGAAACAAAAGTCTAATGCCAGAAAATTTGTTGGGAAAAGAAAGAAAT
391 GGGAGAAAACACGGCAGAGAAACAAAAGTCTAATGCCAGAAAATTTGTTGGGAAAAGAAAGAAAT
54345412 AGAAAATAGAAAACTGATAAGGAGAAAATCTTATTTTGATAACTTCTCCCCAATTATCTCCTAAA
456 AGAAAATAGAAAACTGATAAGGAGAAAATCTTATTTTGATAACTTCTCCCCAATTATCTCCTAAA
54345477 AACACTCCCTATTAACCCACTAAAACACAACTACTCAGCAGTCTAATTTAATTTGAACTCCACCA
521 AACACTCCCTATTAACCCACTAAAACACAACTACTCAGCAGTCTAATTTAATTTGAACTCCACCA
54345542 CGCCACACACATAAAAAAAATTAATTCCCCTGCTTGCGCAAGGACTCGAACACAAGATCTCCTAC
586 CGCCACACACATAAAAAAAATTAATTCCCCTGCTTGCGCAAGGACTCGAACACAAGATCTCCTAC
54345607 ACGCTACCACTCCGCTTAACCACTAGACCAGCAGCCCCATTCTGATAAATTTTTACCAACAATCA
651 ACGCTACCACTCCGCTTAACCACTAGACCAGCAGCCCCATTCTGATAAATTTTTACCAACAATCA
54345672 AATAAAAGCCTACTGAACAAGAGTAAGACCTAATTCATTCAAAATACCAAAATTTCCCAAGCGAA
716 AATAAAAGCCTACTGAACAAGAGTAAGACCTAATTCATTCAAAATACCAAAATTTCCCAAGCGAA
54345737 GACTTGAACTTGGGACCTCCCAAACACTTCCAGAACTCATAACCACTAAAGCTAACAGATATTTG
781 GACTTGAACTTGGGACCTCCCAAACACTTCCAGAACTCATAACCACTAAAGCTAACAGATATTTG
54345802 TGTCATATTTTCACAACAACAAAATTAGAAATTTTGGGGCGTTACACT
846 TGTCATATTTTCACAACAACAAAATTAGAAATTTTGGGGCGTTACACT
54345850 CCTTCAGAAACTTATATTTGACCAATATATCCCTTAATTAATCACTTGATTCATCAACCAACAAA
1 CCTTCAGAAACTTATATTTGACCAATATATCCCTTAATTAATCACTTGATTCATCAACCAACAAA
54345915 ATATCTCCAACATAAAACTCGAGAAACTAAACCAACGAAGATTTGAAAACTTACCATGACGAGTT
66 ATATCTCCAACATAAAACTCGAGAAACTAAACCAACGAAGATTTGAAAACTTACCATGACGAGTT
54345980 CGATAACCAGTCATCTCTATACACTGGAATATCCGCTTAAAACCTTTGAACAGCACCTAAACGAG
131 CGATAACCAGTCATCTCTATACACTGGAATATCCGCTTAAAACCTTTGAACAGCACCTAAACGAG
54346045 AGTAAAACGAACCCTTTATTAACTGTCTAATCAAAATACGATAACTAAGGGGGGAAATTCCACTT
196 AGTAAAACGAACCCTTTATTAACTGTCTAATCAAAATACGATAACTAAGGGGGGAAATTCCACTT
54346110 ACAGAAATAGATAAAT-AAAATTTACAGCCAAAGAGATGACTCCCAAAAAAATACAGAAACGAAA
261 ACAGAAATAGATAAATAAAAATTTACAGCCAAAGAGATGACTCCCAAAAAAATACAGAAACGAAA
54346174 AGAGAGGGCAAAGAGAAGAAACAAGATTCGACCAAAGGGGAACAAAAACCAAAAGTGAACAAGAA
326 AGAGAGGGCAAAGAGAAGAAACAAGATTCGACCAAAGGGGAACAAAAACCAAAAGTGAACAAGAA
54346239 GGGAGAAAACACGGCAGAGAAACAAAAGTCTAATGCCAGAAAATTTGTTGGGAAAAGAAAGAAAT
391 GGGAGAAAACACGGCAGAGAAACAAAAGTCTAATGCCAGAAAATTTGTTGGGAAAAGAAAGAAAT
54346304 AGAAAATAGAAAACTGATAAGGAGAAAATCTTATTTTGATAACTTCTCCCCAATTATCTCCTAAA
456 AGAAAATAGAAAACTGATAAGGAGAAAATCTTATTTTGATAACTTCTCCCCAATTATCTCCTAAA
54346369 AACACTCCCTATTAACCCACTAAAACACAACTACTCAGCAGTCTAATTTAATTTGAACTCCACCA
521 AACACTCCCTATTAACCCACTAAAACACAACTACTCAGCAGTCTAATTTAATTTGAACTCCACCA
54346434 CGCCACACACATAAAAAAAATTAATTCCCCTGCTTGCGCAAGGACTCGAACACAAGATCTCCTAC
586 CGCCACACACATAAAAAAAATTAATTCCCCTGCTTGCGCAAGGACTCGAACACAAGATCTCCTAC
*
54346499 ACGCTACCACTCCACTTAACCACTAGACCAGCAGCCCCATTCTGATAAATTTTTACCAACAATCA
651 ACGCTACCACTCCGCTTAACCACTAGACCAGCAGCCCCATTCTGATAAATTTTTACCAACAATCA
54346564 AATAAAAGCCTACTGAACAAGAGTAAGACCTAATTCATTCAAAATACCAAAATTTCCCAAGCGAA
716 AATAAAAGCCTACTGAACAAGAGTAAGACCTAATTCATTCAAAATACCAAAATTTCCCAAGCGAA
54346629 GACTTGAACTTGGGACCTCCCAAACACTTCCAGAACTCATAACCACTAAAGCTAACAGATATTTG
781 GACTTGAACTTGGGACCTCCCAAACACTTCCAGAACTCATAACCACTAAAGCTAACAGATATTTG
54346694 TGTCATATTTTCACAACAACAAAATTAGAAATTTTGGGGCGTTACACT
846 TGTCATATTTTCACAACAACAAAATTAGAAATTTTGGGGCGTTACACT
54346742 CCTTCAGAAACTTATATTTGACCAATATATCCCTTAATTAATCACTTGATTCATCAACCAACAAA
1 CCTTCAGAAACTTATATTTGACCAATATATCCCTTAATTAATCACTTGATTCATCAACCAACAAA
54346807 ATATCTCCAACATAAAACTCGAGAAACTAAACCAACGAAGATTTGAAAACTTACCATGACGAGTT
66 ATATCTCCAACATAAAACTCGAGAAACTAAACCAACGAAGATTTGAAAACTTACCATGACGAGTT
54346872 CGATAACCAGTCATCTCTATACACTGGAATATCCGCTTAAAACCTTTGAACAGCACCTAAACGAG
131 CGATAACCAGTCATCTCTATACACTGGAATATCCGCTTAAAACCTTTGAACAGCACCTAAACGAG
54346937 AGTAAAACGAACCCTTTATTAACTGTCTAATCAAAATACGATAACTAA-GGGGGAAATTCCACTT
196 AGTAAAACGAACCCTTTATTAACTGTCTAATCAAAATACGATAACTAAGGGGGGAAATTCCACTT
54347001 ACAGAAATAGATAAAT-AAAATTTACAGCCAAAGAGATGACTCCCAAAAAAATACAGAAACGAAA
261 ACAGAAATAGATAAATAAAAATTTACAGCCAAAGAGATGACTCCCAAAAAAATACAGAAACGAAA
54347065 AGAGAGGGCAAAGAGAAGAAACAAGATTCGACCAAAGGGGAACAAAAACCAAAAGTGAACAAGAA
326 AGAGAGGGCAAAGAGAAGAAACAAGATTCGACCAAAGGGGAACAAAAACCAAAAGTGAACAAGAA
54347130 GGGAGAAAACACGGCAGAGAAACAAAAGTCTAATGCCAGAAAATTTGTTGGGAAAAGAAAGAAAT
391 GGGAGAAAACACGGCAGAGAAACAAAAGTCTAATGCCAGAAAATTTGTTGGGAAAAGAAAGAAAT
54347195 AGAAAATAGAAAACTGATAAGGAGAAAATCTTATTTTGATAACTTCTCCCCAATTATCTCCTAAA
456 AGAAAATAGAAAACTGATAAGGAGAAAATCTTATTTTGATAACTTCTCCCCAATTATCTCCTAAA
54347260 AACACTCCCTATTAACCCACTAAAACACAACTACTCAGCAGTCTAATTTAATTTGAACTCCACCA
521 AACACTCCCTATTAACCCACTAAAACACAACTACTCAGCAGTCTAATTTAATTTGAACTCCACCA
54347325 CGCCACACACATAAAAAAAATTAATTCCCCTGCTTGCGCAAGGACTCGAACACAAGATCTCCTAC
586 CGCCACACACATAAAAAAAATTAATTCCCCTGCTTGCGCAAGGACTCGAACACAAGATCTCCTAC
54347390 ACGCTACCACTCCGCTTAACCACTAGACCAGCAGCCCCATTCTGATAAATTTTTACCAACAATCA
651 ACGCTACCACTCCGCTTAACCACTAGACCAGCAGCCCCATTCTGATAAATTTTTACCAACAATCA
54347455 AATAAAAGCCTACTGAACAAGAGTAAGACCTAATTCATTCAAAATACCAAAATTTCCCAAGCGAA
716 AATAAAAGCCTACTGAACAAGAGTAAGACCTAATTCATTCAAAATACCAAAATTTCCCAAGCGAA
54347520 GACTTGAACTTGGGACCTCCCAAACACTTCCAGAACTCATAACCACTAAAGCTAACAGATATTTG
781 GACTTGAACTTGGGACCTCCCAAACACTTCCAGAACTCATAACCACTAAAGCTAACAGATATTTG
54347585 TGTCATATTTTCACAACAACAAAATTAGAAATTTTGGGGCGTTACACT
846 TGTCATATTTTCACAACAACAAAATTAGAAATTTTGGGGCGTTACACT
54347633 CCTTCAGAAACTTATATTTGACCAATATATCCCTTAATTAATCACTTGATTCATCAACCAACAAA
1 CCTTCAGAAACTTATATTTGACCAATATATCCCTTAATTAATCACTTGATTCATCAACCAACAAA
54347698 ATATCTCCAACATAAAACTCGAGAAACTAAACCAACGAAGATTTGAAAACTTACCATGACGAGTT
66 ATATCTCCAACATAAAACTCGAGAAACTAAACCAACGAAGATTTGAAAACTTACCATGACGAGTT
54347763 CGATAACCAGTCATCTCTATACACTGGAATATCCGCTTAAAACCTTTGAACAGCACCTAAACGAG
131 CGATAACCAGTCATCTCTATACACTGGAATATCCGCTTAAAACCTTTGAACAGCACCTAAACGAG
54347828 AGTAAAACGAACCCTTTATTAACTGTCTAATCAAAATACGATAACTAAGGGGGGAAATTCCACTT
196 AGTAAAACGAACCCTTTATTAACTGTCTAATCAAAATACGATAACTAAGGGGGGAAATTCCACTT
54347893 ACAGAAATAGATAAATAAAAATTTACAGCCAAAGAGATGACTCCCAAAAAAATACAGAAACGAAA
261 ACAGAAATAGATAAATAAAAATTTACAGCCAAAGAGATGACTCCCAAAAAAATACAGAAACGAAA
54347958 AGAGAGGGCAAAGAGAAGAAACAAGATTCGACCAAAGGGGAACAAAAACCAAAAGTGAACAAGAA
326 AGAGAGGGCAAAGAGAAGAAACAAGATTCGACCAAAGGGGAACAAAAACCAAAAGTGAACAAGAA
54348023 GGGAGAAAACACGGCAGAGAAACAAAAGTCTAATGCCAGAAAATTTGTTGGGAAAAGAAAGAAAT
391 GGGAGAAAACACGGCAGAGAAACAAAAGTCTAATGCCAGAAAATTTGTTGGGAAAAGAAAGAAAT
54348088 AGAAAATAGAAAACTGATAAGGAGAAAATCTTATTTTGATAACTTCTCCCCAATTATCTCCTAAA
456 AGAAAATAGAAAACTGATAAGGAGAAAATCTTATTTTGATAACTTCTCCCCAATTATCTCCTAAA
*
54348153 AACACTCCCTATTAACCCACTAAAACACAACTACTCAGCAGTCTGATTTAATTTGAACTCCACCA
521 AACACTCCCTATTAACCCACTAAAACACAACTACTCAGCAGTCTAATTTAATTTGAACTCCACCA
54348218 CGCCACACACATAAAAAAAATTAATTCCCCTGCTTGCGCAAGGACTCGAACACAAGATCTCCTAC
586 CGCCACACACATAAAAAAAATTAATTCCCCTGCTTGCGCAAGGACTCGAACACAAGATCTCCTAC
*
54348283 ATGCTACC-CTCCGCTTAACCACTAGACCAGCAGCCCCATTCTGATAAATTTTTACCAACAATCA
651 ACGCTACCACTCCGCTTAACCACTAGACCAGCAGCCCCATTCTGATAAATTTTTACCAACAATCA
* *
54348347 AATAAAAGCCTGCTGAA-AAGAGTAAGACCTAATTCATTCTAAATACCAAAATTTCCCAAGC-AA
716 AATAAAAGCCTACTGAACAAGAGTAAGACCTAATTCATTCAAAATACCAAAATTTCCCAAGCGAA
54348410 GACTTGAACTTGGGACCTCCCAAACACTTCCAGAACTCATAACCACTAAAGCTAACAGATATTTG
781 GACTTGAACTTGGGACCTCCCAAACACTTCCAGAACTCATAACCACTAAAGCTAACAGATATTTG
*
54348475 TGTCATATTTTCACAACAACGAAATTAGAAATTTTGGGGCGTTACACT
846 TGTCATATTTTCACAACAACAAAATTAGAAATTTTGGGGCGTTACACT
54348523 CCTT
1 CCTT
54348527 TACTATCTCC
Statistics
Matches: 2665, Mismatches: 10, Indels: 7
0.99 0.00 0.00
Matches are distributed among these distances:
890 118 0.04
891 933 0.35
892 962 0.36
893 652 0.24
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22
Consensus pattern (893 bp):
CCTTCAGAAACTTATATTTGACCAATATATCCCTTAATTAATCACTTGATTCATCAACCAACAAA
ATATCTCCAACATAAAACTCGAGAAACTAAACCAACGAAGATTTGAAAACTTACCATGACGAGTT
CGATAACCAGTCATCTCTATACACTGGAATATCCGCTTAAAACCTTTGAACAGCACCTAAACGAG
AGTAAAACGAACCCTTTATTAACTGTCTAATCAAAATACGATAACTAAGGGGGGAAATTCCACTT
ACAGAAATAGATAAATAAAAATTTACAGCCAAAGAGATGACTCCCAAAAAAATACAGAAACGAAA
AGAGAGGGCAAAGAGAAGAAACAAGATTCGACCAAAGGGGAACAAAAACCAAAAGTGAACAAGAA
GGGAGAAAACACGGCAGAGAAACAAAAGTCTAATGCCAGAAAATTTGTTGGGAAAAGAAAGAAAT
AGAAAATAGAAAACTGATAAGGAGAAAATCTTATTTTGATAACTTCTCCCCAATTATCTCCTAAA
AACACTCCCTATTAACCCACTAAAACACAACTACTCAGCAGTCTAATTTAATTTGAACTCCACCA
CGCCACACACATAAAAAAAATTAATTCCCCTGCTTGCGCAAGGACTCGAACACAAGATCTCCTAC
ACGCTACCACTCCGCTTAACCACTAGACCAGCAGCCCCATTCTGATAAATTTTTACCAACAATCA
AATAAAAGCCTACTGAACAAGAGTAAGACCTAATTCATTCAAAATACCAAAATTTCCCAAGCGAA
GACTTGAACTTGGGACCTCCCAAACACTTCCAGAACTCATAACCACTAAAGCTAACAGATATTTG
TGTCATATTTTCACAACAACAAAATTAGAAATTTTGGGGCGTTACACT
Found at i:54355911 original size:29 final size:31
Alignment explanation
Indices: 54355860--54355921 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
54355850 AGCCTATATC
*
54355860 TTTATAATTTTTAAAGAATTAAA-TGAAATT
1 TTTATAATTTTTAAAGAACTAAAGTGAAATT
*
54355890 TTTAT-ATTTTT-AAGAAGCTAAAGTGTAATT
1 TTTATAATTTTTAAAGAA-CTAAAGTGAAATT
54355920 TT
1 TT
54355922 ACCTTTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.18
29 10 0.36
30 13 0.46
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (31 bp):
TTTATAATTTTTAAAGAACTAAAGTGAAATT
Found at i:54357740 original size:17 final size:17
Alignment explanation
Indices: 54357720--54357757 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
54357710 AAAAAAAGCA
54357720 AAAAGAAAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
* *
54357737 AAAAGAAAAAGGAAGAG
1 AAAAGAAAAAAGAAAAG
54357754 AAAA
1 AAAA
54357758 ACCTCTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:54358800 original size:12 final size:12
Alignment explanation
Indices: 54358785--54358817 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54358775 ATAGTTCGAT
54358785 TTAGTCATTTAA
1 TTAGTCATTTAA
*
54358797 TTAGTCAATTAA
1 TTAGTCATTTAA
54358809 TT-GTCATTT
1 TTAGTCATTT
54358818 TAGGTTTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (12 bp):
TTAGTCATTTAA
Found at i:54363127 original size:19 final size:19
Alignment explanation
Indices: 54363105--54363181 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
54363095 AAGGAGTAGT
*
54363105 TTTTCATTTGATTTAAAAA
1 TTTTCATTCGATTTAAAAA
* *
54363124 TTTTCAATT-TATTTAAAAC
1 TTTTC-ATTCGATTTAAAAA
* *
54363143 TGTTCCATTCGATTTTAAAAT
1 T-TTTCATTCGA-TTTAAAAA
*
54363164 TTTTCACTCGATTTAAAA
1 TTTTCATTCGATTTAAAA
54363182 CTATTTCACA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 24 0.51
20 15 0.32
21 8 0.17
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTTCATTCGATTTAAAAA
Found at i:54363174 original size:20 final size:20
Alignment explanation
Indices: 54363151--54363224 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
54363141 ACTGTTCCAT
54363151 TCGATTTTAAAATTTTTCAC
1 TCGATTTTAAAATTTTTCAC
*
54363171 TCGA-TTTAAAACTATTTCAC
1 TCGATTTTAAAA-TTTTTCAC
* *
54363191 ACGATTTTATAATTGTTTCAC
1 TCGATTTTAAAATT-TTTCAC
* *
54363212 TTGAGTTTAAAAT
1 TCGATTTTAAAAT
54363225 ACTTGAAGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 7 0.16
20 15 0.35
21 21 0.49
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (20 bp):
TCGATTTTAAAATTTTTCAC
Found at i:54363196 original size:40 final size:40
Alignment explanation
Indices: 54363116--54363223 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
54363106 TTTCATTTGA
* * * * **
54363116 TTTAAAAATTTTCAATTTATTTAAAACTGTTCCATTCGAT
1 TTTAAAATTTTTCACTTGATTTAAAACTATTCCACACGAT
* *
54363156 TTTAAAATTTTTCACTCGATTTAAAACTATTTCACACGAT
1 TTTAAAATTTTTCACTTGATTTAAAACTATTCCACACGAT
*
54363196 TTTATAATTGTTTCACTTGAGTTTAAAA
1 TTTAAAATT-TTTCACTTGA-TTTAAAA
54363224 TACTTGAAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 40 0.71
41 9 0.16
42 7 0.12
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.46
Consensus pattern (40 bp):
TTTAAAATTTTTCACTTGATTTAAAACTATTCCACACGAT
Found at i:54363209 original size:21 final size:20
Alignment explanation
Indices: 54363152--54363211 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
54363142 CTGTTCCATT
*
54363152 CGATTTTAAAATTTTTCACT
1 CGATTTTAAAATTTTTCACA
*
54363172 CGA-TTTAAAACTATTTCACA
1 CGATTTTAAAA-TTTTTCACA
*
54363192 CGATTTTATAATTGTTTCAC
1 CGATTTTAAAATT-TTTCAC
54363212 TTGAGTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 7 0.21
20 14 0.42
21 12 0.36
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.45
Consensus pattern (20 bp):
CGATTTTAAAATTTTTCACA
Found at i:54364701 original size:16 final size:18
Alignment explanation
Indices: 54364668--54364707 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
54364658 ATGGAATTAG
*
54364668 AATTTGATTGAGGAAATT
1 AATTTAATTGAGGAAATT
54364686 -ATTTAATTGA-GAAATT
1 AATTTAATTGAGGAAATT
54364702 AATTTA
1 AATTTA
54364708 TTTTGGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (18 bp):
AATTTAATTGAGGAAATT
Found at i:54368905 original size:4 final size:4
Alignment explanation
Indices: 54368896--54368957 Score: 88
Period size: 4 Copynumber: 15.5 Consensus size: 4
54368886 TTTCAATTCA
* * *
54368896 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
54368944 ATAC ATGC ATAC AT
1 ATAC ATAC ATAC AT
54368958 GATTACTGCT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:54369389 original size:49 final size:50
Alignment explanation
Indices: 54369286--54369394 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 50
54369276 GGCTATTCAG
* * *
54369286 GATGGTAGAATATCAAAACAGTGAAAGCCATTGTTATCTGGCCATCCGAA
1 GATGGTAGAATATCAAAACAGTGAAAACCATTATTATCTGGCAATCCGAA
* * *
54369336 -ATGGTAGAATATCGAAATAGTGAAAACCATTATTGT-TGGGCAATCC-AA
1 GATGGTAGAATATCAAAACAGTGAAAACCATTATTATCT-GGCAATCCGAA
54369384 GATGGTAGAAT
1 GATGGTAGAAT
54369395 TTGTAAATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.06
49 48 0.94
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (50 bp):
GATGGTAGAATATCAAAACAGTGAAAACCATTATTATCTGGCAATCCGAA
Found at i:54377858 original size:57 final size:58
Alignment explanation
Indices: 54377711--54377851 Score: 248
Period size: 57 Copynumber: 2.4 Consensus size: 58
54377701 GACATTCCCC
* * *
54377711 TGTTTGATTTAAGGGTGATTGTTTGATTGTATTAACATTTTTTTTCTAACCGAATAGG
1 TGTTTGATTTAAGGGTGATTGTTTGATTGAATTAACATGTTTTTTCTAACCCAATAGG
54377769 TGTTTGATTTAAGGGTGATTGTTTGATTGAATTAACA-GTTTTTTCTAACCCAATAGG
1 TGTTTGATTTAAGGGTGATTGTTTGATTGAATTAACATGTTTTTTCTAACCCAATAGG
54377826 TGTTTGATTTAAGGGTGATTGTTTGA
1 TGTTTGATTTAAGGGTGATTGTTTGA
54377852 AAGAATTGAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
57 44 0.55
58 36 0.45
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.47
Consensus pattern (58 bp):
TGTTTGATTTAAGGGTGATTGTTTGATTGAATTAACATGTTTTTTCTAACCCAATAGG
Found at i:54378279 original size:13 final size:11
Alignment explanation
Indices: 54378251--54378280 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
54378241 AATATTTTAC
54378251 ATTTTTTTTGA
1 ATTTTTTTTGA
54378262 ATTTTATTTTGA
1 ATTTT-TTTTGA
54378274 ATTTTTT
1 ATTTTTT
54378281 GAGTGGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:54387671 original size:26 final size:26
Alignment explanation
Indices: 54387642--54387705 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
54387632 TACCTACGGT
54387642 AGTTTCAGAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* * *
54387668 AGTTTCAGGATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
*
54387694 AGTTTTAGAATA
1 AGTTTCAGAATA
54387706 CTTACAGGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:54395008 original size:29 final size:31
Alignment explanation
Indices: 54394957--54395018 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
54394947 AGCCTATATC
*
54394957 TTTATAATTTTTAAAGAATTAAA-TGAAATT
1 TTTATAATTTTTAAAGAACTAAAGTGAAATT
*
54394987 TTTAT-ATTTTT-AAGAAGCTAAAGTGTAATT
1 TTTATAATTTTTAAAGAA-CTAAAGTGAAATT
54395017 TT
1 TT
54395019 ACCTTTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.18
29 10 0.36
30 13 0.46
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (31 bp):
TTTATAATTTTTAAAGAACTAAAGTGAAATT
Found at i:54396833 original size:12 final size:12
Alignment explanation
Indices: 54396807--54396857 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
54396797 ATTATCGAGC
*
54396807 AAAA-AAAAGCA
1 AAAAGAAAAGAA
54396818 AAAAGAAAA-AA
1 AAAAGAAAAGAA
54396829 GAAAAGAAAAGAA
1 -AAAAGAAAAGAA
*
54396842 AAAAGGAAGAGAA
1 AAAA-GAAAAGAA
54396855 AAA
1 AAA
54396858 CCTCTATTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 5 0.15
12 17 0.50
13 12 0.35
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:54396838 original size:17 final size:18
Alignment explanation
Indices: 54396818--54396856 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
54396808 AAAAAAAGCA
54396818 AAAAGAAAAAA-GAAAAG
1 AAAAGAAAAAAGGAAAAG
*
54396835 AAAAGAAAAAAGGAAGAG
1 AAAAGAAAAAAGGAAAAG
54396853 AAAA
1 AAAA
54396857 ACCTCTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAGGAAAAG
Found at i:54396838 original size:18 final size:18
Alignment explanation
Indices: 54396807--54396857 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
54396797 ATTATCGAGC
54396807 AAAA-AAAAGCAAAAAGAA
1 AAAAGAAAAG-AAAAAGAA
54396825 AAAAGAAAAG-AAAAGAA
1 AAAAGAAAAGAAAAAGAA
*
54396842 AAAAGGAAGAGAAAAA
1 AAAA-GAAAAGAAAAA
54396858 CCTCTATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 11 0.38
18 9 0.31
19 9 0.31
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAGAA
Found at i:54397901 original size:12 final size:12
Alignment explanation
Indices: 54397886--54397918 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54397876 ATAGTTCGAT
54397886 TTAGTCATTTAA
1 TTAGTCATTTAA
*
54397898 TTAGTCAATTAA
1 TTAGTCATTTAA
54397910 TT-GTCATTT
1 TTAGTCATTT
54397919 TAGGTTTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (12 bp):
TTAGTCATTTAA
Found at i:54402235 original size:19 final size:19
Alignment explanation
Indices: 54402213--54402289 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
54402203 AAGGAGTAGT
*
54402213 TTTTCATTTGATTTAAAAA
1 TTTTCATTCGATTTAAAAA
* *
54402232 TTTTCAATT-TATTTAAAAC
1 TTTTC-ATTCGATTTAAAAA
* *
54402251 TGTTCCATTCGATTTTAAAAT
1 T-TTTCATTCGA-TTTAAAAA
*
54402272 TTTTCACTCGATTTAAAA
1 TTTTCATTCGATTTAAAA
54402290 CTATTTCACA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 24 0.51
20 15 0.32
21 8 0.17
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTTCATTCGATTTAAAAA
Found at i:54402282 original size:20 final size:20
Alignment explanation
Indices: 54402259--54402332 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
54402249 ACTGTTCCAT
54402259 TCGATTTTAAAATTTTTCAC
1 TCGATTTTAAAATTTTTCAC
*
54402279 TCGA-TTTAAAACTATTTCAC
1 TCGATTTTAAAA-TTTTTCAC
* *
54402299 ACGATTTTATAATTGTTTCAC
1 TCGATTTTAAAATT-TTTCAC
* *
54402320 TTGAGTTTAAAAT
1 TCGATTTTAAAAT
54402333 ACTTGAAGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 7 0.16
20 15 0.35
21 21 0.49
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (20 bp):
TCGATTTTAAAATTTTTCAC
Found at i:54402304 original size:40 final size:40
Alignment explanation
Indices: 54402224--54402331 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
54402214 TTTCATTTGA
* * * * **
54402224 TTTAAAAATTTTCAATTTATTTAAAACTGTTCCATTCGAT
1 TTTAAAATTTTTCACTTGATTTAAAACTATTCCACACGAT
* *
54402264 TTTAAAATTTTTCACTCGATTTAAAACTATTTCACACGAT
1 TTTAAAATTTTTCACTTGATTTAAAACTATTCCACACGAT
*
54402304 TTTATAATTGTTTCACTTGAGTTTAAAA
1 TTTAAAATT-TTTCACTTGA-TTTAAAA
54402332 TACTTGAAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 40 0.71
41 9 0.16
42 7 0.12
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.46
Consensus pattern (40 bp):
TTTAAAATTTTTCACTTGATTTAAAACTATTCCACACGAT
Found at i:54402317 original size:21 final size:20
Alignment explanation
Indices: 54402260--54402319 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
54402250 CTGTTCCATT
*
54402260 CGATTTTAAAATTTTTCACT
1 CGATTTTAAAATTTTTCACA
*
54402280 CGA-TTTAAAACTATTTCACA
1 CGATTTTAAAA-TTTTTCACA
*
54402300 CGATTTTATAATTGTTTCAC
1 CGATTTTAAAATT-TTTCAC
54402320 TTGAGTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 7 0.21
20 14 0.42
21 12 0.36
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.45
Consensus pattern (20 bp):
CGATTTTAAAATTTTTCACA
Found at i:54403809 original size:16 final size:18
Alignment explanation
Indices: 54403776--54403815 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
54403766 ATGGAATTAG
*
54403776 AATTTGATTGAGGAAATT
1 AATTTAATTGAGGAAATT
54403794 -ATTTAATTGA-GAAATT
1 AATTTAATTGAGGAAATT
54403810 AATTTA
1 AATTTA
54403816 TTTTGGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (18 bp):
AATTTAATTGAGGAAATT
Found at i:54408025 original size:4 final size:4
Alignment explanation
Indices: 54408016--54408073 Score: 80
Period size: 4 Copynumber: 14.5 Consensus size: 4
54408006 TTTCAATTCA
* * *
54408016 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
54408064 ATGC ATAC AT
1 ATAC ATAC AT
54408074 GATTACTGCT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:54408507 original size:49 final size:50
Alignment explanation
Indices: 54408404--54408512 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 50
54408394 GGCTATTCAG
* * *
54408404 GATGGTAGAATATCAAAACAGTGAAAGCCATTGTTATCTGGCCATCCGAA
1 GATGGTAGAATATCAAAACAGTGAAAACCATTATTATCTGGCAATCCGAA
* * *
54408454 -ATGGTAGAATATCGAAATAGTGAAAACCATTATTGT-TGGGCAATCC-AA
1 GATGGTAGAATATCAAAACAGTGAAAACCATTATTATCT-GGCAATCCGAA
54408502 GATGGTAGAAT
1 GATGGTAGAAT
54408513 TTGTAAATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.06
49 48 0.94
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (50 bp):
GATGGTAGAATATCAAAACAGTGAAAACCATTATTATCTGGCAATCCGAA
Found at i:54416978 original size:57 final size:58
Alignment explanation
Indices: 54416831--54416971 Score: 248
Period size: 57 Copynumber: 2.4 Consensus size: 58
54416821 GACATTCCCC
* *
54416831 TGTTTGATTTAAGGGTGATTGTTTGATTGTATTAACATTTTTTTTCTAACCAAATAGG
1 TGTTTGATTTAAGGGTGATTGTTTGATTGAATTAACATGTTTTTTCTAACCAAATAGG
*
54416889 TGTTTGATTTAAGGGTGATTGTTTGATTGAATTAACA-GTTTTTTCTAACCCAATAGG
1 TGTTTGATTTAAGGGTGATTGTTTGATTGAATTAACATGTTTTTTCTAACCAAATAGG
54416946 TGTTTGATTTAAGGGTGATTGTTTGA
1 TGTTTGATTTAAGGGTGATTGTTTGA
54416972 AAGAATTGAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
57 44 0.55
58 36 0.45
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (58 bp):
TGTTTGATTTAAGGGTGATTGTTTGATTGAATTAACATGTTTTTTCTAACCAAATAGG
Found at i:54417400 original size:13 final size:11
Alignment explanation
Indices: 54417372--54417401 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
54417362 AATATTTTAC
54417372 ATTTTTTTTGA
1 ATTTTTTTTGA
54417383 ATTTTATTTTGA
1 ATTTT-TTTTGA
54417395 ATTTTTT
1 ATTTTTT
54417402 GAGTGGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:54421376 original size:61 final size:61
Alignment explanation
Indices: 54421322--54421509 Score: 156
Period size: 61 Copynumber: 3.1 Consensus size: 61
54421312 TTATAGTATT
*
54421322 ATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
1 ATATATTATGATTTAAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
* * * * * * * *
54421383 ATATATT-TTA-ATAAAAATATATTTAATATTA-ATTATTTCAA-ATT-A-TATTTTA-TAGTAT
1 ATATATTATGATTTAAGAA-A-A-TTCATATAAGAATATTT-AATATTAAGAATTTTATTA-AAT
54421441 C
61 C
* * * * *
54421442 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTAAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
54421503 ATATATT
1 ATATATT
54421510 TTAATTAAAA
Statistics
Matches: 93, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
58 10 0.11
59 29 0.31
60 8 0.09
61 35 0.38
62 11 0.12
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (61 bp):
ATATATTATGATTTAAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
Found at i:54421410 original size:120 final size:120
Alignment explanation
Indices: 54421257--54421544 Score: 463
Period size: 120 Copynumber: 2.4 Consensus size: 120
54421247 AGTATGATGA
*
54421257 TAAATTATATATTATT-ATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
1 TAAATTATATATT-TTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
* * *
54421321 TATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
65 CATATATTATGATTTGAGAAAATTCATATAAGAATATTGAATATTAAGAATTTTAT
* * *
54421377 TAAATCATATATTTTAATAAAAATATATTTAATATTAATTAT-TTCAAATTATATTTTATAGTAT
1 TAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTAT
* *
54421441 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
65 CATATATTATGATTTGAGAAAATTCATATAAGAATATTGAATATTAAGAATTTTAT
54421497 TAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 TAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
54421545 ATATGATTAA
Statistics
Matches: 153, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
119 4 0.03
120 147 0.96
121 2 0.01
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATC
ATATATTATGATTTGAGAAAATTCATATAAGAATATTGAATATTAAGAATTTTAT
Found at i:54421518 original size:18 final size:17
Alignment explanation
Indices: 54421490--54421524 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54421480 ATTATTAAGA
*
54421490 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54421507 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54421525 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54421778 original size:16 final size:16
Alignment explanation
Indices: 54421757--54421810 Score: 99
Period size: 16 Copynumber: 3.4 Consensus size: 16
54421747 TTGATTTGCT
54421757 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
54421773 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
54421789 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
54421805 ATTACA
1 ATTACA
54421811 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.26, C:0.35, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:54422724 original size:34 final size:31
Alignment explanation
Indices: 54422661--54422729 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 31
54422651 TTTTTTAAGT
54422661 TTTTTTAAAAATAATTTTTATATAATTATAAA
1 TTTTTTAAAAATAATTTTTATATAATTAT-AA
* *
54422693 TTTTTTGAAAA-AATATTTTATAATATTTTATAA
1 TTTTTTAAAAATAAT-TTTTAT-ATA-ATTATAA
54422726 TTTT
1 TTTT
54422730 ATTTTGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 3 0.09
32 16 0.50
33 9 0.28
34 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTTTTAAAAATAATTTTTATATAATTATAA
Found at i:54427499 original size:77 final size:77
Alignment explanation
Indices: 54427372--54427526 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
54427362 TAGCTATTAG
54427372 AACTCTACTTTTGCACCTTTTTTGATTTAGTCATTTTTGCTAAATATTAAAAAATAAAAAATATA
1 AACTCTACTTTTGCACCTTTTTTGATTTAGTCATTTTTGCTAAATATTAAAAAATAAAAAATATA
54427437 TTGTGTGTTTAT
66 TTGTGTGTTTAT
54427449 AACTCTACTTTTGCACCTTTTTTGATTTAGTCATTTTTGCTAAATATTAAAAAATAAAAAATATA
1 AACTCTACTTTTGCACCTTTTTTGATTTAGTCATTTTTGCTAAATATTAAAAAATAAAAAATATA
*
54427514 TTTTGTGTTTAT
66 TTGTGTGTTTAT
54427526 A
1 A
54427527 TTGATTTAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.47
Consensus pattern (77 bp):
AACTCTACTTTTGCACCTTTTTTGATTTAGTCATTTTTGCTAAATATTAAAAAATAAAAAATATA
TTGTGTGTTTAT
Found at i:54428381 original size:267 final size:267
Alignment explanation
Indices: 54427906--54428439 Score: 1059
Period size: 267 Copynumber: 2.0 Consensus size: 267
54427896 AGTTTAAAAT
54427906 TAACGGGTAACCAGACACTATTATTTTCACCTGTATATTGAAATCTTTTACGAGGTTTCATCAGG
1 TAACGGGTAACCAGACACTATTATTTTCACCTGTATATTGAAATCTTTTACGAGGTTTCATCAGG
54427971 TAAAATTTTGATTGAAGAATGAGAGATATGTCATTTGAGATTGGTTATGTGGCTAGTTGTGTTGG
66 TAAAATTTTGATTGAAGAATGAGAGATATGTCATTTGAGATTGGTTATGTGGCTAGTTGTGTTGG
54428036 GTTTTGAGATCTAAATTGGCTTGATTGGAAATGAAGATGATTATGGTTATTCATATGATTGAAAT
131 GTTTTGAGATCTAAATTGGCTTGATTGGAAATGAAGATGATTATGGTTATTCATATGATTGAAAT
54428101 CAAAGCTTTGTATATTAATGTTGTGGTTTGAATCTTGATATGTATATTTGTATTTATAATGATTT
196 CAAAGCTTTGTATATTAATGTTGTGGTTTGAATCTTGATATGTATATTTGTATTTATAATGATTT
54428166 ATATGTG
261 ATATGTG
*
54428173 TAACGGGTAACCAGACACTATTATTTTCACCTGTATATTGAGATCTTTTACGAGGTTTCATCAGG
1 TAACGGGTAACCAGACACTATTATTTTCACCTGTATATTGAAATCTTTTACGAGGTTTCATCAGG
54428238 TAAAATTTTGATTGAAGAATGAGAGATATGTCATTTGAGATTGGTTATGTGGCTAGTTGTGTTGG
66 TAAAATTTTGATTGAAGAATGAGAGATATGTCATTTGAGATTGGTTATGTGGCTAGTTGTGTTGG
54428303 GTTTTGAGATCTAAATTGGCTTGATTGGAAATGAAGATGATTATGGTTATTCATATGATTGAAAT
131 GTTTTGAGATCTAAATTGGCTTGATTGGAAATGAAGATGATTATGGTTATTCATATGATTGAAAT
54428368 CAAAGCTTTGTATATTAATGTTGTGGTTTGAATCTTGATATGTATATTTGTATTTATAATGATTT
196 CAAAGCTTTGTATATTAATGTTGTGGTTTGAATCTTGATATGTATATTTGTATTTATAATGATTT
54428433 ATATGTG
261 ATATGTG
54428440 AATAGAAATT
Statistics
Matches: 266, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
267 266 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (267 bp):
TAACGGGTAACCAGACACTATTATTTTCACCTGTATATTGAAATCTTTTACGAGGTTTCATCAGG
TAAAATTTTGATTGAAGAATGAGAGATATGTCATTTGAGATTGGTTATGTGGCTAGTTGTGTTGG
GTTTTGAGATCTAAATTGGCTTGATTGGAAATGAAGATGATTATGGTTATTCATATGATTGAAAT
CAAAGCTTTGTATATTAATGTTGTGGTTTGAATCTTGATATGTATATTTGTATTTATAATGATTT
ATATGTG
Found at i:54430437 original size:17 final size:17
Alignment explanation
Indices: 54430396--54430446 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
54430386 CCGATAGAGG
* *
54430396 TTTTTATTATTATTATTGG
1 TTTTTTTTATT-TT-TTGA
54430415 TTTTTTTTATTTTTTGA
1 TTTTTTTTATTTTTTGA
*
54430432 TTTTTTTAATTTTTT
1 TTTTTTTTATTTTTT
54430447 TGTTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 17 0.59
18 2 0.07
19 10 0.34
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTTTTTATTTTTTGA
Found at i:54435123 original size:13 final size:13
Alignment explanation
Indices: 54435105--54435129 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54435095 ACACTTAAAG
54435105 CAATTTGTGGTAA
1 CAATTTGTGGTAA
54435118 CAATTTGTGGTA
1 CAATTTGTGGTA
54435130 CGAGAATAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (13 bp):
CAATTTGTGGTAA
Found at i:54440340 original size:14 final size:14
Alignment explanation
Indices: 54440321--54440350 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54440311 CTCTTATTAA
54440321 AATATTTTATACAC
1 AATATTTTATACAC
54440335 AATATTTTATACAC
1 AATATTTTATACAC
54440349 AA
1 AA
54440351 ATAAATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATTTTATACAC
Found at i:54440374 original size:22 final size:22
Alignment explanation
Indices: 54440349--54440396 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
54440339 TTTTATACAC
54440349 AAATAAATGTTA-ACTCTTATCA
1 AAATAAA-GTTATACTCTTATCA
* *
54440371 AAAT-TAGTTATACTCTTATTA
1 AAATAAAGTTATACTCTTATCA
54440392 AAATA
1 AAATA
54440397 TTTTATACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.18
21 14 0.64
22 4 0.18
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (22 bp):
AAATAAAGTTATACTCTTATCA
Found at i:54440404 original size:21 final size:21
Alignment explanation
Indices: 54440357--54440395 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54440347 ACAAATAAAT
54440357 GTTA-ACTCTTATCAAAATTA
1 GTTATACTCTTATCAAAATTA
*
54440377 GTTATACTCTTATTAAAAT
1 GTTATACTCTTATCAAAAT
54440396 ATTTTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (21 bp):
GTTATACTCTTATCAAAATTA
Found at i:54452660 original size:12 final size:12
Alignment explanation
Indices: 54452643--54452674 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
54452633 ATATTTTATA
54452643 ATCTATATACAT
1 ATCTATATACAT
54452655 ATCTATAT--AT
1 ATCTATATACAT
54452665 ATCTATATAC
1 ATCTATATAC
54452675 TTTTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.56
12 8 0.44
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
ATCTATATACAT
Found at i:54452732 original size:15 final size:16
Alignment explanation
Indices: 54452707--54452736 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54452697 TAAATACATA
54452707 TTTATATATATATATT
1 TTTATATATATATATT
54452723 TTTA-ATATATATAT
1 TTTATATATATATAT
54452737 GTACATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATATATATATATT
Found at i:54453516 original size:109 final size:109
Alignment explanation
Indices: 54453320--54453759 Score: 688
Period size: 109 Copynumber: 4.1 Consensus size: 109
54453310 AGATGCGGAT
* *
54453320 TTTTCAAAATAAGGCAATGTTCTGCGTTTGGAAATTCAAGGAAACGTGCCCTAATGTGCTGGGTT
1 TTTT-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTT
* *
54453385 TCGATTGTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
65 TCGATTTTTCCCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
54453430 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTT
54453495 CGATTTTTCCCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
66 CGATTTTTCCCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* * *
54453539 TTTCAAAATAAGGCAATGGTTTGCGTTTGGAAGTTCGAGGAAACGTGCCCTAATGTGCTGGGTTT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTT
*
54453604 CGAGTTTTCCCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
66 CGATTTTTCCCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* *
54453648 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGG-AACGTGCCCTAATGTGCTGGGTTT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTT
* * * * * * *
54453712 TGA--TTTCTCGTTTAACCAAATAGCCAAACATCCTCTTGAAAA
66 CGATTTTTCCCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
*
54453754 TCTTAA
1 TTTTAA
54453760 TCCATGTCAT
Statistics
Matches: 310, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
106 37 0.12
108 26 0.08
109 243 0.78
110 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (109 bp):
TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCCCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
Found at i:54455179 original size:19 final size:19
Alignment explanation
Indices: 54455155--54455201 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54455145 AACGTCTCTT
*
54455155 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
54455174 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
54455193 TATGCATTA
1 TTTGCATTA
54455202 GATTTTCACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:54458034 original size:10 final size:9
Alignment explanation
Indices: 54458019--54458091 Score: 67
Period size: 10 Copynumber: 7.7 Consensus size: 9
54458009 CAGATTCAAT
54458019 AAAAAAAGAG
1 AAAAAAA-AG
54458029 AAAAAAAAG
1 AAAAAAAAG
54458038 AAAAAAAAG
1 AAAAAAAAG
*
54458047 AAAAAAAAAT
1 -AAAAAAAAG
54458057 AAGAAAAAAG
1 AA-AAAAAAG
*
54458067 AAGAAGAGAA-
1 AA-AA-AAAAG
*
54458077 AAGAAAAAG
1 AAAAAAAAG
54458086 AAAAAA
1 AAAAAA
54458092 TGAGAGGCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
8 3 0.06
9 19 0.36
10 28 0.53
11 3 0.06
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:54458043 original size:18 final size:18
Alignment explanation
Indices: 54458019--54458091 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
54458009 CAGATTCAAT
54458019 AAAAAAAGAGAAAAAAAAG
1 AAAAAAA-AGAAAAAAAAG
*
54458038 AAAAAAAAGAAAAAAAAAT
1 AAAAAAAAG-AAAAAAAAG
*
54458057 AAGAAAAAAGAAGAAGAGAA-
1 AA-AAAAAAGAA-AA-AAAAG
*
54458077 AAGAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
54458092 TGAGAGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
17 1 0.02
18 4 0.09
19 27 0.59
20 11 0.24
21 3 0.07
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAAG
Found at i:54458044 original size:20 final size:20
Alignment explanation
Indices: 54458019--54458084 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
54458009 CAGATTCAAT
54458019 AAAAAAAGAGAAAAAAAAGA
1 AAAAAAAGAGAAAAAAAAGA
*
54458039 AAAAAAAGA-AAAAAAAATA
1 AAAAAAAGAGAAAAAAAAGA
*
54458058 AGAAAAAAGAAGAAGAGAAAAGA
1 A-AAAAAAG-AGAA-AAAAAAGA
54458081 AAAA
1 AAAA
54458085 GAAAAAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 10 0.26
20 16 0.41
21 1 0.03
22 5 0.13
23 7 0.18
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAGAAAAAAAAGA
Found at i:54458045 original size:13 final size:13
Alignment explanation
Indices: 54458019--54458091 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
54458009 CAGATTCAAT
54458019 AAAAAAAGAGAAAA-
1 AAAAAAA-A-AAAAG
54458033 AAAAGAAAAAAAAG
1 AAAA-AAAAAAAAG
*
54458047 AAAAAAAAATAAG
1 AAAAAAAAAAAAG
* *
54458060 AAAAAAGAAGAAG
1 AAAAAAAAAAAAG
* *
54458073 AGAAAAGAAAAAG
1 AAAAAAAAAAAAG
54458086 AAAAAA
1 AAAAAA
54458092 TGAGAGGCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
13 39 0.76
14 9 0.18
15 3 0.06
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:54459509 original size:50 final size:50
Alignment explanation
Indices: 54459374--54459877 Score: 250
Period size: 50 Copynumber: 10.1 Consensus size: 50
54459364 GAAACTACAG
* ** * **
54459374 ATTGCAATTCAAAAGATTGAAGCCACAACGACGAATCTTACTTCCAAG-C
1 ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTCCCCGAC
* ** * ** * * * * *
54459423 AATGCGGTGGAGCAGATTGAAGCTACGATGGCGAATCTCACTTCCTCGAC
1 ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTCCCCGAC
* * * ** ** **
54459473 ATTGCAATTCAAAAGATTGAAACCACAACAGTGAATCTTGCTTCTCAGGTG
1 ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTC-CCCGAC
* ** * * * ***
54459524 A-TACAGCGGAATAGATTGAAGCCACGACGACAAATCTCACTTCCCCGAC
1 ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTCCCCGAC
* * * * ** * *
54459573 ATTGTAATTCAAAAGATTGAAGCCGCAACGATGAATCTTGCTTCCCAGGC
1 ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTCCCCGAC
* * * * *
54459623 GA-TGCAGTGGAACAGATTGAAGCTACGACGGTGAATCTCACTTCCCCGAC
1 -ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTCCCCGAC
* * * * * *
54459673 ATTGCAATGCAAAAGATTGAAGCCACAATGGCGAATCTTACTTCTCAGGC
1 ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTCCCCGAC
* * *
54459723 GATGTAGC-A-G-AACAGATTGAAGTCACAATGGTGAATCTCACTTCCCCGAC
1 -AT-T-GCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTCCCCGAC
* * * * * *
54459773 ATTGCAAT-TAAAAGATTGAGGCCACAACGGTGAATCTTACTTTTCCAGGC
1 ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCAC-TTCCCCGAC
* * * * * ** *
54459823 GA-TGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTGCTTCCCTGAC
1 -ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTCCCCGAC
54459873 ATTGC
1 ATTGC
54459878 GGTTAAATAG
Statistics
Matches: 325, Mismatches: 115, Indels: 29
0.69 0.25 0.06
Matches are distributed among these distances:
47 2 0.01
48 2 0.01
49 67 0.21
50 216 0.66
51 34 0.10
52 2 0.01
53 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (50 bp):
ATTGCAATGCAAAAGATTGAAGCCACAACGGTGAATCTCACTTCCCCGAC
Found at i:54459582 original size:100 final size:100
Alignment explanation
Indices: 54459374--54459913 Score: 600
Period size: 100 Copynumber: 5.4 Consensus size: 100
54459364 GAAACTACAG
** * * * * *
54459374 ATTGCAATTCAAAAGATTGAAGCCACAACGACGAATCTTACTTC-CAAGCAATGCGGTGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
* * *
54459438 ATTGAAGCTACGATGGCGAATCTCACTTCCTCGAC
66 ATTGAAGCCACGACGGCGAATCTCACTTCCCCGAC
* * * * * *
54459473 ATTGCAATTCAAAAGATTGAAACCACAACAGTGAATCTTGCTTCTCAGGTGATACAGCGGAATAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
* *
54459538 ATTGAAGCCACGACGACAAATCTCACTTCCCCGAC
66 ATTGAAGCCACGACGGCGAATCTCACTTCCCCGAC
* * * * * *
54459573 ATTGTAATTCAAAAGATTGAAGCCGCAACGATGAATCTTGCTTCCCAGGCGATGCAGTGGAACAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
* *
54459638 ATTGAAGCTACGACGGTGAATCTCACTTCCCCGAC
66 ATTGAAGCCACGACGGCGAATCTCACTTCCCCGAC
* * * * *
54459673 ATTGCAATGCAAAAGATTGAAGCCACAATGGCGAATCTTACTTCTCAGGCGATGTAGCAGAACAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
* * * *
54459738 ATTGAAGTCACAATGGTGAATCTCACTTCCCCGAC
66 ATTGAAGCCACGACGGCGAATCTCACTTCCCCGAC
* * * *
54459773 ATTGCAATT-AAAAGATTGAGGCCACAACGGTGAATCTTACTTTTCCAGGCGATGCAGTGGAATA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCT-CAGGCGATGCAGCGGAACA
* * ** *
54459837 GATTGAAGCTACAACGGCGAATCTTGCTTCCCTGAC
65 GATTGAAGCCACGACGGCGAATCTCACTTCCCCGAC
** * * *
54459873 ATTGCGGTT-AAATAGATTGAAGCTACAACAGCGAATCTTAC
1 ATTGCAATTCAAA-AGATTGAAGCCACAACGGTGAATCTTAC
54459914 ATCCCTGATG
Statistics
Matches: 369, Mismatches: 69, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
99 70 0.19
100 275 0.75
101 24 0.07
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (100 bp):
ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
ATTGAAGCCACGACGGCGAATCTCACTTCCCCGAC
Found at i:54459721 original size:200 final size:198
Alignment explanation
Indices: 54459374--54459913 Score: 677
Period size: 200 Copynumber: 2.7 Consensus size: 198
54459364 GAAACTACAG
* * * * *
54459374 ATTGCAATTCAAAAGATTGAAGCCACAACGACGAATCTTACTTCCAAGCAATGCGGTGGAGCAGA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGATGAATCTTACTTCCAGGCGATGCAGTGGAACAGA
* * *
54459439 TTGAAGCTACGATGGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTGAAACCACAACAG
66 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACATTGCAA-TCAAAAGATTGAAGCCACAACAG
* * * * * *
54459504 TGAATCTTGCTTCTCAGGTGATACAGCGGAATAGATTGAAGCCACGACGACAAATCTCACTTCCC
130 CGAATCTTACTTCTCAGGCGATACAGCAGAACAGATTGAAGCCACAACGACAAATCTCACTTCCC
54459569 CGAC
195 CGAC
* * *
54459573 ATTGTAATTCAAAAGATTGAAGCCGCAACGATGAATCTTGCTTCCCAGGCGATGCAGTGGAACAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGATGAATCTTACTT-CCAGGCGATGCAGTGGAACAG
* **
54459638 ATTGAAGCTACGACGGTGAATCTCACTTCCCCGACATTGCAATGCAAAAGATTGAAGCCACAATG
65 ATTGAAGCTACGACGGCGAATCTCACTTCCCCGACATTGCAAT-CAAAAGATTGAAGCCACAACA
** * * ***
54459703 GCGAATCTTACTTCTCAGGCGATGTAGCAGAACAGATTGAAGTCACAATGGTGAATCTCACTTCC
129 GCGAATCTTACTTCTCAGGCGATACAGCAGAACAGATTGAAGCCACAACGACAAATCTCACTTCC
54459768 CCGAC
194 CCGAC
* * *
54459773 ATTGCAATT-AAAAGATTGAGGCCACAACGGTGAATCTTACTTTTCCAGGCGATGCAGTGGAATA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGATGAATCTTAC--TTCCAGGCGATGCAGTGGAACA
* ** * ** * *
54459837 GATTGAAGCTACAACGGCGAATCTTGCTTCCCTGACATTGCGGTTAAATAGATTGAAGCTACAAC
64 GATTGAAGCTACGACGGCGAATCTCACTTCCCCGACATTGCAATCAAA-AGATTGAAGCCACAAC
54459902 AGCGAATCTTAC
128 AGCGAATCTTAC
54459914 ATCCCTGATG
Statistics
Matches: 292, Mismatches: 44, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
199 70 0.24
200 220 0.75
201 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (198 bp):
ATTGCAATTCAAAAGATTGAAGCCACAACGATGAATCTTACTTCCAGGCGATGCAGTGGAACAGA
TTGAAGCTACGACGGCGAATCTCACTTCCCCGACATTGCAATCAAAAGATTGAAGCCACAACAGC
GAATCTTACTTCTCAGGCGATACAGCAGAACAGATTGAAGCCACAACGACAAATCTCACTTCCCC
GAC
Found at i:54459936 original size:50 final size:50
Alignment explanation
Indices: 54459833--54459948 Score: 142
Period size: 50 Copynumber: 2.3 Consensus size: 50
54459823 GATGCAGTGG
* * * * ** *
54459833 AATAGATTGAAGCTACAACGGCGAATCTTGCTTCCCTGACATTGCGGTTA
1 AATAGATTGAAGCTACAACAGCGAATCTTACATCCCTGACAGTGCAATGA
** *
54459883 AATAGATTGAAGCTACAACAGCGAATCTTACATCCCTGATGGTGTAATGA
1 AATAGATTGAAGCTACAACAGCGAATCTTACATCCCTGACAGTGCAATGA
54459933 AATAGATTGAAGCTAC
1 AATAGATTGAAGCTAC
54459949 GACGACGAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (50 bp):
AATAGATTGAAGCTACAACAGCGAATCTTACATCCCTGACAGTGCAATGA
Found at i:54460129 original size:44 final size:45
Alignment explanation
Indices: 54460079--54460275 Score: 113
Period size: 44 Copynumber: 4.5 Consensus size: 45
54460069 TCTCTGGTTG
54460079 GCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG-CA
1 GCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGACA
* ** * ** * * **
54460123 GTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGACTA
1 GCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGAC-A
* * * * ***
54460169 -CAGTGGAGTACATTGAAG---CCAGTAAT-TCTATCTCCCT-GGTTG
1 GCAGTGGAATAGATTGAAGATTTCAG--ATCT-TATCTCCCTAAGACA
*
54460211 GCAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAG-CA
1 GCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGACA
* * *
54460255 GTAGTGGAACAGATCGAAGAT
1 GCAGTGGAATAGATTGAAGAT
54460276 GGTAGATTTT
Statistics
Matches: 112, Mismatches: 30, Indels: 22
0.68 0.18 0.13
Matches are distributed among these distances:
42 3 0.03
43 18 0.16
44 71 0.63
45 17 0.15
46 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (45 bp):
GCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGACA
Found at i:54460303 original size:132 final size:132
Alignment explanation
Indices: 54460066--54460410 Score: 534
Period size: 132 Copynumber: 2.6 Consensus size: 132
54460056 AAACAGTCCA
* *
54460066 ATCTCTCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
1 ATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGGA
* *
54460131 GCAGATCGAAGATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCAGTAATT
66 GCAGATCGAAGATGGTAGATTTTACCTCCCTATGACTACAGTGGAGTACATTGAAGCCAGTAATT
54460196 CT
131 CT
54460198 ATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGGA
1 ATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGGA
* *
54460263 ACAGATCGAAGATGGTAGATTTTACCTCCCTATGATTACAGTGGAGTACATTGAAGCCAGTAATT
66 GCAGATCGAAGATGGTAGATTTTACCTCCCTATGACTACAGTGGAGTACATTGAAGCCAGTAATT
54460328 CT
131 CT
* * * *
54460330 ATCTCCGTGATTGGCAGTAGAATAGATTGAAGATTGT-AGATTCTGTA--TCCCTAAGCAGTAGT
1 ATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATT-TCA-AATCT-TATCTCCCTAAGCAGTAGT
* *
54460392 GGAGTAGATCAAAGATGGT
63 GGAGCAGATCGAAGATGGT
54460411 GAATCTTATC
Statistics
Matches: 197, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
132 190 0.96
133 5 0.03
134 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (132 bp):
ATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGGA
GCAGATCGAAGATGGTAGATTTTACCTCCCTATGACTACAGTGGAGTACATTGAAGCCAGTAATT
CT
Found at i:54461946 original size:20 final size:18
Alignment explanation
Indices: 54461909--54461948 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
54461899 ATTTATTTAC
*
54461909 TTTTTTTTTTCTTTTTCA
1 TTTTTCTTTTCTTTTTCA
54461927 TTTTTCTTTTCATTTCTTCA
1 TTTTTCTTTTC-TTT-TTCA
54461947 TT
1 TT
54461949 ATTTATGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTTCA
Found at i:54462810 original size:19 final size:19
Alignment explanation
Indices: 54462783--54462819 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54462773 TGCGTTCATT
54462783 TCAAAAAAACAATTTTGAA
1 TCAAAAAAACAATTTTGAA
* *
54462802 TCAAGAAAATAATTTTGA
1 TCAAAAAAACAATTTTGA
54462820 TACATTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (19 bp):
TCAAAAAAACAATTTTGAA
Found at i:54463780 original size:17 final size:17
Alignment explanation
Indices: 54463760--54463792 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54463750 GCAATATTTA
*
54463760 TAAAATAATAGAATATG
1 TAAAATAATAAAATATG
54463777 TAAAATAATAAAATAT
1 TAAAATAATAAAATAT
54463793 TTATAATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAAATAATAAAATATG
Found at i:54465918 original size:21 final size:21
Alignment explanation
Indices: 54465876--54465918 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
54465866 ACCACACATT
* *
54465876 TTTTTTAATGAATATTTTAGA
1 TTTTTTAATGAATATCTAAGA
54465897 TTTTTTAA-GAAATATCTAAGA
1 TTTTTTAATG-AATATCTAAGA
54465918 T
1 T
54465919 ATATGTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTTTTAATGAATATCTAAGA
Found at i:54487142 original size:37 final size:37
Alignment explanation
Indices: 54487081--54487226 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
54487071 TACGTATGAT
* *
54487081 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
54487116 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
54487153 CACTTATCACTTTGTTTCTTGATCAGATAAGTGCAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
54487190 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
54487227 TAAAGCTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 90 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:54487243 original size:46 final size:46
Alignment explanation
Indices: 54487190--54487556 Score: 437
Period size: 46 Copynumber: 7.6 Consensus size: 46
54487180 TAAGTGCAGC
* * **
54487190 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
54487236 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
54487282 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
54487334 CACTTATCACTTTATTACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
54487380 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
54487432 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
54487478 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
54487530 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
54487557 AGTACTCAAA
Statistics
Matches: 284, Mismatches: 19, Indels: 36
0.84 0.06 0.11
Matches are distributed among these distances:
46 153 0.54
48 2 0.01
49 2 0.01
50 2 0.01
52 125 0.44
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:54487309 original size:52 final size:52
Alignment explanation
Indices: 54487233--54487550 Score: 444
Period size: 52 Copynumber: 6.3 Consensus size: 52
54487223 TAGCTAAAGC
* *
54487233 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
54487286 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
54487338 TATCAC-TTT-A--T-T-ACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
54487384 TATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
54487436 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
54487482 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
54487534 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
54487551 ATCAGAAGTA
Statistics
Matches: 238, Mismatches: 14, Indels: 26
0.86 0.05 0.09
Matches are distributed among these distances:
46 80 0.34
47 5 0.02
48 3 0.01
50 3 0.01
51 6 0.03
52 123 0.52
53 18 0.08
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:54487355 original size:98 final size:98
Alignment explanation
Indices: 54487201--54487556 Score: 595
Period size: 98 Copynumber: 3.6 Consensus size: 98
54487191 ACTTATCACT
* * * * *
54487201 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACTTGATCAGATAA
* *
54487266 GTATAGCCGAAGCTATCACTTATCACTTTTCAC
66 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
* *
54487299 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTATTACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACTTGATCAGATAA
54487364 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
66 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
*
54487397 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTATCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACTTGATCAGATAA
54487462 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
66 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
* * *
54487495 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGA
1 TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACTTGATCAGA
54487557 AGTACTCAAA
Statistics
Matches: 244, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 244 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACTTGATCAGATAA
GTATAGCCGAAGCTATTACTTATCACTTTCCAC
Found at i:54494929 original size:82 final size:82
Alignment explanation
Indices: 54494808--54494965 Score: 196
Period size: 82 Copynumber: 1.9 Consensus size: 82
54494798 TTGTATAAAA
*
54494808 CACCGGCATAAAGCCTCCTAGGCACAAAGCCCGATACATTTCACCAGCA-CAAAGCCTAC-TAGA
1 CACCGGCATAAAGCCTCCTAGACACAAAGCCCGATACATTTCACCAGCATC-AAGCCT-CTTAGA
54494871 CATAAAGTCTGAAGTAATT
64 CATAAAGTCTGAAGTAATT
* * * * * *
54494890 CACCGGCATCAAGCCTGCTAGACATAAAGCCTG-TAACATTTCATCGGCATCAAGCCTCTTAGAC
1 CACCGGCATAAAGCCTCCTAGACACAAAGCCCGAT-ACATTTCACCAGCATCAAGCCTCTTAGAC
*
54494954 GTAAAGTCTGAA
65 ATAAAGTCTGAA
54494966 ACATCTTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
81 2 0.03
82 62 0.95
83 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.20
Consensus pattern (82 bp):
CACCGGCATAAAGCCTCCTAGACACAAAGCCCGATACATTTCACCAGCATCAAGCCTCTTAGACA
TAAAGTCTGAAGTAATT
Found at i:54494969 original size:41 final size:41
Alignment explanation
Indices: 54494808--54494969 Score: 148
Period size: 41 Copynumber: 4.0 Consensus size: 41
54494798 TTGTATAAAA
* * * * * * *
54494808 CACCGGCATAAAGCCTCCTAGGCACAAAGCCCGATACATTT
1 CACCGGCATCAAGCCTACTAGACATAAAGTCTGAAACATTT
* ** *
54494849 CACCAGCA-CAAAGCCTACTAGACATAAAGTCTGAAGTAATT
1 CACCGGCATC-AAGCCTACTAGACATAAAGTCTGAAACATTT
* * *
54494890 CACCGGCATCAAGCCTGCTAGACATAAAGCCTGTAACATTT
1 CACCGGCATCAAGCCTACTAGACATAAAGTCTGAAACATTT
* *
54494931 CATCGGCATCAAGCCT-CTTAGACGTAAAGTCTGAAACAT
1 CACCGGCATCAAGCCTAC-TAGACATAAAGTCTGAAACAT
54494970 CTTATTTTCA
Statistics
Matches: 96, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
40 1 0.01
41 94 0.98
42 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (41 bp):
CACCGGCATCAAGCCTACTAGACATAAAGTCTGAAACATTT
Found at i:54497478 original size:2 final size:2
Alignment explanation
Indices: 54497471--54497591 Score: 242
Period size: 2 Copynumber: 60.5 Consensus size: 2
54497461 AAAGTAGAAC
54497471 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
54497513 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
54497555 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
54497592 GGGAACCTTT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 119 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:54499806 original size:9 final size:9
Alignment explanation
Indices: 54499792--54499850 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
54499782 AAAAATTTTT
54499792 GTTAAATCG
1 GTTAAATCG
*
54499801 GTTAAACCG
1 GTTAAATCG
*
54499810 GTGAAATCG
1 GTTAAATCG
54499819 GTTAAATCG
1 GTTAAATCG
**
54499828 GTTAAGCCG
1 GTTAAATCG
*
54499837 GTTAAATTG
1 GTTAAATCG
54499846 GTTAA
1 GTTAA
54499851 TTTTTAACCA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (9 bp):
GTTAAATCG
Found at i:54499822 original size:27 final size:27
Alignment explanation
Indices: 54499792--54499850 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
54499782 AAAAATTTTT
54499792 GTTAAATCGGTTAAACCGGTGAAATCG
1 GTTAAATCGGTTAAACCGGTGAAATCG
* * *
54499819 GTTAAATCGGTTAAGCCGGTTAAATTG
1 GTTAAATCGGTTAAACCGGTGAAATCG
54499846 GTTAA
1 GTTAA
54499851 TTTTTAACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (27 bp):
GTTAAATCGGTTAAACCGGTGAAATCG
Found at i:54509142 original size:14 final size:14
Alignment explanation
Indices: 54509125--54509170 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
54509115 TTAAAATGAA
54509125 ATAAATATTTAAAC
1 ATAAATATTTAAAC
* *
54509139 ATAATTCTTTAAA-
1 ATAAATATTTAAAC
54509152 A-AAACTATTTAAAC
1 ATAAA-TATTTAAAC
54509166 ATAAA
1 ATAAA
54509171 ATATATAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
12 2 0.08
13 8 0.32
14 12 0.48
15 3 0.12
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAAATATTTAAAC
Found at i:54512315 original size:32 final size:34
Alignment explanation
Indices: 54512269--54512332 Score: 80
Period size: 32 Copynumber: 1.9 Consensus size: 34
54512259 ATATGCGTGT
54512269 ATATGCATAAATATA-ATAAT-AA-AAAATATAAA
1 ATATGCATAAATATATA-AATAAATAAAATATAAA
* *
54512301 ATATGTATATATATATAAATAAATAAAATATA
1 ATATGCATAAATATATAAATAAATAAAATATA
54512333 TATAATAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 16 0.59
33 3 0.11
34 8 0.30
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (34 bp):
ATATGCATAAATATATAAATAAATAAAATATAAA
Found at i:54512336 original size:27 final size:26
Alignment explanation
Indices: 54512279--54512339 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
54512269 ATATGCATAA
54512279 ATATAATAATAAAAAATATAAAATAT
1 ATATAATAATAAAAAATATAAAATAT
* *
54512305 GTATATATATATAAATAA-ATAAAATAT
1 ATATA-ATA-ATAAAAAATATAAAATAT
54512332 ATATAATA
1 ATATAATA
54512340 GGATACATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 7 0.23
27 16 0.53
28 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
ATATAATAATAAAAAATATAAAATAT
Found at i:54514702 original size:30 final size:30
Alignment explanation
Indices: 54514666--54514725 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
54514656 TTGAAAAATG
54514666 TAGTTATTAATCCCAAACATGGATCGTAAA
1 TAGTTATTAATCCCAAACATGGATCGTAAA
54514696 TAGTTATTAATCCCAAACATGGATCGTAAA
1 TAGTTATTAATCCCAAACATGGATCGTAAA
54514726 ATGAACATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (30 bp):
TAGTTATTAATCCCAAACATGGATCGTAAA
Found at i:54522108 original size:22 final size:22
Alignment explanation
Indices: 54522083--54522124 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54522073 GAAACATAGA
*
54522083 ATATCATATCCAGATGCAGAAC
1 ATATCAAATCCAGATGCAGAAC
*
54522105 ATATCAAATGCAGATGCAGA
1 ATATCAAATCCAGATGCAGA
54522125 TTTCCACCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (22 bp):
ATATCAAATCCAGATGCAGAAC
Found at i:54538842 original size:20 final size:20
Alignment explanation
Indices: 54538805--54538865 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
54538795 TATGCACGTG
* **
54538805 TATTATATTGTAGGTATAAA
1 TATTATATAGTATATATAAA
*
54538825 TATTATATAGTATATATATA
1 TATTATATAGTATATATAAA
*
54538845 TAAATATATAG-ATAT-TAAA
1 T-ATTATATAGTATATATAAA
54538864 TA
1 TA
54538866 AATAAAAAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 21 0.62
21 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
TATTATATAGTATATATAAA
Found at i:54538843 original size:16 final size:16
Alignment explanation
Indices: 54538818--54538865 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
54538808 TATATTGTAG
*
54538818 GTATAAATATTATATA
1 GTATAAATATTAAATA
*
54538834 GTATATATATATAAATA
1 GTATAAATAT-TAAATA
*
54538851 -TATAGATATTAAATA
1 GTATAAATATTAAATA
54538866 AATAAAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 17 0.61
17 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
GTATAAATATTAAATA
Found at i:54538866 original size:19 final size:21
Alignment explanation
Indices: 54538819--54538869 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
54538809 ATATTGTAGG
*
54538819 TATAAAT-ATTATATAGTATA
1 TATAAATAAATATATAGTATA
*
54538839 TATATATAAATATATAG-ATA
1 TATAAATAAATATATAGTATA
54538859 T-TAAATAAATA
1 TATAAATAAATA
54538870 AAAAGCGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 10 0.37
21 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TATAAATAAATATATAGTATA
Found at i:54546747 original size:20 final size:20
Alignment explanation
Indices: 54546709--54546747 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54546699 AAATTGTTTC
*
54546709 AAATCATAAAGAATTATAAA
1 AAATCATAAAGAATCATAAA
54546729 AAATCATACAA-AATCATAA
1 AAATCATA-AAGAATCATAA
54546748 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (20 bp):
AAATCATAAAGAATCATAAA
Found at i:54546780 original size:33 final size:33
Alignment explanation
Indices: 54546723--54546788 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
54546713 CATAAAGAAT
*
54546723 TATAAAAAATCATACAAAATCATAATATATATA
1 TATAAAAAATCATACAAAACCATAATATATATA
* * *
54546756 TATAGAAAATTATATAAAACCATAATATATATA
1 TATAAAAAATCATACAAAACCATAATATATATA
54546789 AATATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.32
Consensus pattern (33 bp):
TATAAAAAATCATACAAAACCATAATATATATA
Found at i:54548738 original size:24 final size:24
Alignment explanation
Indices: 54548706--54548752 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
54548696 CATAATCAAA
* *
54548706 TACAAATGCGGACACAGATTTAGT
1 TACAAATGCAGACACAAATTTAGT
* *
54548730 TACAGATGCAGCCACAAATTTAG
1 TACAAATGCAGACACAAATTTAG
54548753 ATATATATGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (24 bp):
TACAAATGCAGACACAAATTTAGT
Found at i:54551322 original size:20 final size:20
Alignment explanation
Indices: 54551297--54551338 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
54551287 TAAAAAAACA
54551297 TTATTTCTAGGTTAACTTAT
1 TTATTTCTAGGTTAACTTAT
54551317 TTATTTCTAGGTTAACTTAT
1 TTATTTCTAGGTTAACTTAT
54551337 TT
1 TT
54551339 CTACAACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (20 bp):
TTATTTCTAGGTTAACTTAT
Done.