Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 8 of 770
Found at i:2145959 original size:25 final size:25
Alignment explanation
Indices: 2145931--2145978 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2145921 TTATACCATG
* * *
2145931 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
2145956 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
2145979 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:2146049 original size:20 final size:20
Alignment explanation
Indices: 2146024--2146080 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
2146014 AATATGGTAA
2146024 GTATGATATGCACATGAAAT
1 GTATGATATGCACATGAAAT
*
2146044 GTATGATATGCACATGATAT
1 GTATGATATGCACATGAAAT
2146064 GTATGATATGCACATGA
1 GTATGATATGCACATGA
2146081 GGTAATCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
GTATGATATGCACATGAAAT
Found at i:2146062 original size:11 final size:11
Alignment explanation
Indices: 2146026--2146080 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
2146016 TATGGTAAGT
2146026 ATGATATGCAC
1 ATGATATGCAC
* *
2146037 ATGAAATG--T
1 ATGATATGCAC
2146046 ATGATATGCAC
1 ATGATATGCAC
*
2146057 ATGATATG--T
1 ATGATATGCAC
2146066 ATGATATGCAC
1 ATGATATGCAC
2146077 ATGA
1 ATGA
2146081 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:2146158 original size:24 final size:24
Alignment explanation
Indices: 2146131--2146249 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
2146121 GAGGAAGTGA
*
2146131 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
2146155 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
2146178 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
2146202 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
2146226 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
2146250 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:2146200 original size:47 final size:48
Alignment explanation
Indices: 2146131--2146249 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
2146121 GAGGAAGTGA
2146131 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
2146178 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
2146226 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
2146250 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:2146493 original size:30 final size:31
Alignment explanation
Indices: 2146440--2146502 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
2146430 CGTTTACAGT
2146440 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
2146471 AAAGGCTTCGG-CCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
2146501 AA
1 AA
2146503 TAAGAAAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:2151901 original size:25 final size:25
Alignment explanation
Indices: 2151873--2151920 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2151863 TTATACCATG
* * *
2151873 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
2151898 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
2151921 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:2151991 original size:20 final size:20
Alignment explanation
Indices: 2151966--2152022 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
2151956 AATATGGTAA
2151966 GTATGATATGCACATGAAAT
1 GTATGATATGCACATGAAAT
*
2151986 GTATGATATGCACATGATAT
1 GTATGATATGCACATGAAAT
2152006 GTATGATATGCACATGA
1 GTATGATATGCACATGA
2152023 GGTAATCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
GTATGATATGCACATGAAAT
Found at i:2152004 original size:11 final size:11
Alignment explanation
Indices: 2151968--2152022 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
2151958 TATGGTAAGT
2151968 ATGATATGCAC
1 ATGATATGCAC
* *
2151979 ATGAAATG--T
1 ATGATATGCAC
2151988 ATGATATGCAC
1 ATGATATGCAC
*
2151999 ATGATATG--T
1 ATGATATGCAC
2152008 ATGATATGCAC
1 ATGATATGCAC
2152019 ATGA
1 ATGA
2152023 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:2152100 original size:24 final size:24
Alignment explanation
Indices: 2152073--2152191 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
2152063 GAGGAAGTGA
*
2152073 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
2152097 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
2152120 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
2152144 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
2152168 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
2152192 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:2152142 original size:47 final size:48
Alignment explanation
Indices: 2152073--2152191 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
2152063 GAGGAAGTGA
2152073 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
2152120 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
2152168 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
2152192 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:2153662 original size:25 final size:25
Alignment explanation
Indices: 2153634--2153681 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2153624 TTATACCATG
* * *
2153634 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
2153659 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
2153682 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:2163070 original size:95 final size:95
Alignment explanation
Indices: 2162889--2163174 Score: 367
Period size: 95 Copynumber: 3.0 Consensus size: 95
2162879 CAATTAATTC
* * *
2162889 ATGAATAATAGTAAAAAATGTAAAATTTCTAACTTTTTTACTAAAATTA-TAATAAATAATAAAA
1 ATGAATAATA-TTAAAAATATAAAATTTCTAAC-TTTTTAC-AAAAATAGTAATAAATAATAAAA
* * *
2162953 ACTCATACCGAAACATTATGCATCGGCTCGTGA
63 ACTTATACTGGAACATTATGCATCGGCTCGTGA
* ** * *
2162986 ATGAATAATATTAAAAATATAAAATTTCAAACTTTTTACCGAAATAGTAATAAATAACAAGAACT
1 ATGAATAATATTAAAAATATAAAATTTCTAACTTTTTACAAAAATAGTAATAAATAATAAAAACT
* * * *
2163051 TATATTGGAACATTGTGCATTGGCTCGTGT
66 TATACTGGAACATTATGCATCGGCTCGTGA
* * *
2163081 ATGAATAATATTAAAAATATAAAATTTCTAATTTTTTACAAAAATGGTAATAAATAATAAAAAAT
1 ATGAATAATATTAAAAATATAAAATTTCTAACTTTTTACAAAAATAGTAATAAATAATAAAAACT
*
2163146 TTTACTGGAACATTATGCATCGGCTCGTG
66 TATACTGGAACATTATGCATCGGCTCGTG
2163175 CATGGCTATT
Statistics
Matches: 161, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
94 4 0.02
95 128 0.80
96 19 0.12
97 10 0.06
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (95 bp):
ATGAATAATATTAAAAATATAAAATTTCTAACTTTTTACAAAAATAGTAATAAATAATAAAAACT
TATACTGGAACATTATGCATCGGCTCGTGA
Found at i:2166057 original size:68 final size:65
Alignment explanation
Indices: 2165938--2166187 Score: 183
Period size: 68 Copynumber: 3.8 Consensus size: 65
2165928 GATTGGATGA
* * ** * * *
2165938 TACAGATA-GTATGTAGCTAGGTCACATGTATGGTGCTGA-GTGCACATCATGT-GTACAAGAGA
1 TACAGATATATATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGA
2166000 GC
64 GC
*
2166002 TACAAGATATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAG
1 TAC-AGATA-TAT-ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAG
*
2166067 AGT
63 AGC
** ** * * *
2166070 TAC-GGGATATATGTAGCTAGGTCGCATGCATGGTTCTAGGTGAAGGACACCATGTAGACAAGAG
1 TACAGATATATATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAG
2166134 AGC
63 AGC
* * *
2166137 TACGAGATA-A-AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT
1 TAC-AGATATATATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGT
2166188 GTACTAGAGA
Statistics
Matches: 146, Mismatches: 28, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
63 9 0.06
64 28 0.19
65 8 0.05
66 23 0.16
67 29 0.20
68 46 0.32
69 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (65 bp):
TACAGATATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGC
Found at i:2178802 original size:16 final size:16
Alignment explanation
Indices: 2178781--2178813 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2178771 ATTCTTTTTC
2178781 ATAAAAA-AAAAATAAA
1 ATAAAAAGAAAAA-AAA
2178797 ATAAAAAGAAAAAAAA
1 ATAAAAAGAAAAAAAA
2178813 A
1 A
2178814 CAGGCCCTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (16 bp):
ATAAAAAGAAAAAAAA
Found at i:2186067 original size:24 final size:24
Alignment explanation
Indices: 2186035--2186082 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2186025 TAATTTTATA
* * *
2186035 GCTTGCACTTGCTTTTCCATGTCT
1 GCTTACACTTGATTTTCAATGTCT
2186059 GCTTACACTTGATTTTCAATGTCT
1 GCTTACACTTGATTTTCAATGTCT
2186083 ACAAATTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.46
Consensus pattern (24 bp):
GCTTACACTTGATTTTCAATGTCT
Found at i:2187579 original size:25 final size:25
Alignment explanation
Indices: 2187545--2187595 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2187535 GCCTACATAA
2187545 AGTGTAAGCATACTGCTTAAAATAT
1 AGTGTAAGCATACTGCTTAAAATAT
2187570 AGTGTAAGCATACTGCTTAAAATAT
1 AGTGTAAGCATACTGCTTAAAATAT
2187595 A
1 A
2187596 TTAATCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (25 bp):
AGTGTAAGCATACTGCTTAAAATAT
Found at i:2190452 original size:21 final size:21
Alignment explanation
Indices: 2190428--2190470 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2190418 ACCCTAGTCC
2190428 TAGTAACATAGCTCCCAACAG
1 TAGTAACATAGCTCCCAACAG
2190449 TAGTAACATAGCTCCCAACAG
1 TAGTAACATAGCTCCCAACAG
2190470 T
1 T
2190471 TTCAAATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (21 bp):
TAGTAACATAGCTCCCAACAG
Found at i:2196066 original size:19 final size:20
Alignment explanation
Indices: 2196042--2196087 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2196032 ATTTTATAAA
2196042 TATTTTGAA-TTTTAAATTT
1 TATTTTGAATTTTTAAATTT
*
2196061 TATTTTGAATTTTTGAATTT
1 TATTTTGAATTTTTAAATTT
*
2196081 TTTTTTG
1 TATTTTG
2196088 TAAAATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (20 bp):
TATTTTGAATTTTTAAATTT
Found at i:2197994 original size:24 final size:24
Alignment explanation
Indices: 2197960--2198013 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2197950 TTTTAATTAA
* *
2197960 ATTTTATAAATAATTAATATTTAT
1 ATTTTAAAAATAATTAAAATTTAT
* *
2197984 TTTTTAAAAATATTTAAAATTTAT
1 ATTTTAAAAATAATTAAAATTTAT
2198008 ATTTTA
1 ATTTTA
2198014 TATATTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTAAAAATAATTAAAATTTAT
Found at i:2199896 original size:23 final size:22
Alignment explanation
Indices: 2199866--2199910 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
2199856 TTACAAATTT
2199866 AAATTTTAAAAACAACATCATTC
1 AAATTTTAAAAACAACAT-ATTC
*
2199889 AAATTTTAAAGACAACATATTC
1 AAATTTTAAAAACAACATATTC
2199911 GATCCGACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTTTAAAAACAACATATTC
Found at i:2201247 original size:7 final size:7
Alignment explanation
Indices: 2201233--2201270 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2201223 CCCAGCGTTT
2201233 AACCTTC
1 AACCTTC
*
2201240 AGCCTTC
1 AACCTTC
2201247 AACCTTC
1 AACCTTC
2201254 AACCTTC
1 AACCTTC
2201261 AACCTTC
1 AACCTTC
2201268 AAC
1 AAC
2201271 TTCTTGTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.29, C:0.42, G:0.03, T:0.26
Consensus pattern (7 bp):
AACCTTC
Found at i:2202308 original size:95 final size:95
Alignment explanation
Indices: 2202145--2202335 Score: 364
Period size: 95 Copynumber: 2.0 Consensus size: 95
2202135 CAAATAATAA
*
2202145 CTATTAAATTCATTATGTTATTTTCAAAATTTGATGTGTCAAACATATTATCGCATGTGTACCGC
1 CTATTAAATTCATTATGTTATTTTCAAAATTTGATATGTCAAACATATTATCGCATGTGTACCGC
2202210 TATGTTTGTTTGTTATTTTTACATATTACT
66 TATGTTTGTTTGTTATTTTTACATATTACT
*
2202240 CTATTAAATTCATTATGTTTTTTTCAAAATTTGATATGTCAAACATATTATCGCATGTGTACCGC
1 CTATTAAATTCATTATGTTATTTTCAAAATTTGATATGTCAAACATATTATCGCATGTGTACCGC
2202305 TATGTTTGTTTGTTATTTTTACATATTACT
66 TATGTTTGTTTGTTATTTTTACATATTACT
2202335 C
1 C
2202336 ACAAAAAAAA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (95 bp):
CTATTAAATTCATTATGTTATTTTCAAAATTTGATATGTCAAACATATTATCGCATGTGTACCGC
TATGTTTGTTTGTTATTTTTACATATTACT
Found at i:2203279 original size:18 final size:18
Alignment explanation
Indices: 2203225--2203282 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 18
2203215 TTACTTTCCA
2203225 TATATATATTAATTATT-AT
1 TATAT-TATTAATT-TTAAT
*
2203244 TATATTACTAATTTTTAAT
1 TATATTATTAA-TTTTAAT
2203263 TATATTATTAATTTTAAT
1 TATATTATTAATTTTAAT
2203281 TA
1 TA
2203283 ATCATGCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 16 0.46
19 19 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTATTAATTTTAAT
Found at i:2205446 original size:307 final size:307
Alignment explanation
Indices: 2204875--2205633 Score: 1010
Period size: 307 Copynumber: 2.5 Consensus size: 307
2204865 ACCCATATGG
* * * *
2204875 TGAAATCACTTTCATGGCAAGACCTTAACAAGAATGCGACAATGGAAAAGCTCAAAATGAATTCA
1 TGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGAGCTCAAAATGAATTCA
* * * * * * *
2204940 AGATTCTGATTAAAAGGAAAATAAGATTATTCGGACAAGATATCTGAGAAGAGGTCATGATGTAA
66 AGATTTTGATTAAAAGGAAAATAAGATTATTTGGACAAGACATTTGGGGAGAGGTCATGGTGTAA
** * * **
2205005 ATTGTCAAAAGTTTTTTACACCATTGTTAGGGGGAGCCATTAGAAAATAAGAGTAGGTACTAAAG
131 ATTACCAAAAGCTTTTTACACCATTGTTAGGGGGAACCATTAGAAAATAAGAACAGGTACTAAAG
* * *
2205070 CTATGTCTTTCATGTCCTGAATATTTCTTCATATTGAATAAAACCCGTGGTTTCAAATATATATT
196 CTATGTCTTTCATATCCTAAATATTTCTTCATACTGAATAAAACCCGTGGTTTCAAATATATATT
*
2205135 AATTATCTTCTCTCTTTTATTCATTACAAATATTGGCTACAATATAA
261 AATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATAA
* * * * *
2205182 TGAAATCACTCTCATGGCAAGACCTCGACATGAAGGCGACAATGG-AGTGCCTCAGAATGAATTT
1 TGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGAG-CTCAAAATGAATTC
* * *
2205246 AAGATTTTTATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGGAGAGGTCATGGTGT
65 AAGATTTTGATTAAAAGGAAAATAAGATTATTTGGACAAGACA-TTTGGGGAGAGGTCATGGTGT
*
2205311 AAATTACCAAAAGCTTTTTA-AGCCATTGTTGGGGGGAACCATTAGAAAATAAGAACAGGTACTA
129 AAATTACCAAAAGCTTTTTACA-CCATTGTTAGGGGGAACCATTAGAAAATAAGAACAGGTACTA
* * *
2205375 AAGTTATGTCTTTCATATACC-AAATGTTT-TCTCATACTGAATAAAACTCGTGG-TTCAAATAT
193 AAGCTATGTCTTTCATAT-CCTAAATATTTCT-TCATACTGAATAAAACCCGTGGTTTCAAATAT
* *
2205437 ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCATATGA
256 ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATAA
* *
2205489 CGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGC-AGCAATGGAAAGAGC-CAAAATAAATT
1 TGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGA-CAATGG-AAGAGCTCAAAATGAATT
* * * * *
2205552 CAAGGTTTTGATTAAAAGAAAAATAAGATTATTTGGATAAGACATTTGGGGAGAGGTTATCGTGT
64 CAAGATTTTGATTAAAAGGAAAATAAGATTATTTGGACAAGACATTTGGGGAGAGGTCATGGTGT
*
2205617 AAATTACTAAAAAGCTT
129 AAATTAC-CAAAAGCTT
2205634 CATTTGAAGA
Statistics
Matches: 392, Mismatches: 51, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
306 29 0.07
307 243 0.62
308 115 0.29
309 5 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (307 bp):
TGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGAGCTCAAAATGAATTCA
AGATTTTGATTAAAAGGAAAATAAGATTATTTGGACAAGACATTTGGGGAGAGGTCATGGTGTAA
ATTACCAAAAGCTTTTTACACCATTGTTAGGGGGAACCATTAGAAAATAAGAACAGGTACTAAAG
CTATGTCTTTCATATCCTAAATATTTCTTCATACTGAATAAAACCCGTGGTTTCAAATATATATT
AATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATAA
Found at i:2209801 original size:31 final size:31
Alignment explanation
Indices: 2209734--2209821 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 31
2209724 AACTTAATGT
* * *
2209734 TGTTTTAAATTCAGTTTGAAATATTTTATGTTTA
1 TGTTCTAAACTCAGTTTGAAA-A--TTAAGTTTA
2209768 TGTTCTAAACTCAGTTTGAAAATTAAGTTTA
1 TGTTCTAAACTCAGTTTGAAAATTAAGTTTA
* *
2209799 TGTTCTAAGCTGAGTTTGAAAAT
1 TGTTCTAAACTCAGTTTGAAAAT
2209822 AAAAAATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 29 0.59
33 1 0.02
34 19 0.39
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (31 bp):
TGTTCTAAACTCAGTTTGAAAATTAAGTTTA
Found at i:2212157 original size:31 final size:31
Alignment explanation
Indices: 2212119--2212180 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2212109 AATAAAATTA
2212119 TTAGCCAATGTTTCCCAATTTTATTGTGATC
1 TTAGCCAATGTTTCCCAATTTTATTGTGATC
* *
2212150 TTAGCCAATGTTTGCCAATTTTCTTGTGATC
1 TTAGCCAATGTTTCCCAATTTTATTGTGATC
2212181 ATATTCTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (31 bp):
TTAGCCAATGTTTCCCAATTTTATTGTGATC
Found at i:2212211 original size:14 final size:14
Alignment explanation
Indices: 2212192--2212218 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2212182 TATTCTTCCA
2212192 TGATCCAACTATGG
1 TGATCCAACTATGG
2212206 TGATCCAACTATG
1 TGATCCAACTATG
2212219 CTAGGCAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (14 bp):
TGATCCAACTATGG
Found at i:2212707 original size:21 final size:21
Alignment explanation
Indices: 2212683--2212722 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2212673 ATTATTCCCT
2212683 TTTTGATGATATGACATTTCA
1 TTTTGATGATATGACATTTCA
2212704 TTTTGATGATATGACATTT
1 TTTTGATGATATGACATTT
2212723 TTATGTTAAA
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:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (21 bp):
TTTTGATGATATGACATTTCA
Found at i:2214972 original size:48 final size:48
Alignment explanation
Indices: 2214896--2214993 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
2214886 CATGAGCAGA
* *
2214896 TTTGAACCACTCATACAATCTAGCACATTACAACAAATATGAAGAAAT
1 TTTGAACCACTCATACAATCTAGCACATTACAACAAATAGGAAAAAAT
*
2214944 TTTGTACCACTCATACAATCTAGCACATTACAACAAATAGGAAAAAAT
1 TTTGAACCACTCATACAATCTAGCACATTACAACAAATAGGAAAAAAT
2214992 TT
1 TT
2214994 CAACAAGTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (48 bp):
TTTGAACCACTCATACAATCTAGCACATTACAACAAATAGGAAAAAAT
Found at i:2220595 original size:43 final size:43
Alignment explanation
Indices: 2220547--2220634 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
2220537 CTAATTATCG
2220547 AACATGCCATTTCATATGCTTATGTACATTCTCATATCAAATC
1 AACATGCCATTTCATATGCTTATGTACATTCTCATATCAAATC
2220590 AACATGCCATTTCATATGCTTATGTACATTCTCATATCAAATC
1 AACATGCCATTTCATATGCTTATGTACATTCTCATATCAAATC
2220633 AA
1 AA
2220635 AACAAGCCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (43 bp):
AACATGCCATTTCATATGCTTATGTACATTCTCATATCAAATC
Found at i:2221395 original size:2 final size:2
Alignment explanation
Indices: 2221388--2221425 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2221378 GAGCTAACTT
*
2221388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2221426 AAATAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2221825 original size:43 final size:43
Alignment explanation
Indices: 2221724--2221826 Score: 102
Period size: 43 Copynumber: 2.4 Consensus size: 43
2221714 TACTCAGAAT
* *
2221724 CACATATATTACATA-CAATGCCATATCCCAGATATGGTACCTTA
1 CACATA-ATCACATATCAATGCCATATCCCAGATAGGGTA-CTTA
** * *
2221768 CATGTTATCACATATCAATGCCTCTATCCCAGATAGGGT-CTTA
1 CACATAATCACATATCAATGCC-ATATCCCAGATAGGGTACTTA
*
2221811 CACATAATCTCATATC
1 CACATAATCACATATC
2221827 GATACCAATG
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
43 23 0.49
44 10 0.21
45 14 0.30
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (43 bp):
CACATAATCACATATCAATGCCATATCCCAGATAGGGTACTTA
Found at i:2225589 original size:19 final size:18
Alignment explanation
Indices: 2225565--2225608 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
2225555 CATTTATATA
2225565 TTAATTATATTACTAATTT
1 TTAATTATATTACTAA-TT
*
2225584 TTAATTATATTATTAATT
1 TTAATTATATTACTAATT
2225602 TTAATTA
1 TTAATTA
2225609 ATCATGCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATTATATTACTAATT
Found at i:2226070 original size:84 final size:84
Alignment explanation
Indices: 2225929--2226098 Score: 268
Period size: 84 Copynumber: 2.0 Consensus size: 84
2225919 ATCAATAATA
** *
2225929 TCCATAAAAAACAAACGTCATTCTTGAAACTCGAAAAATGAAGCAACAGACATGAAAGGGAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAAATCGAAAAATGAAGCAACAGACATGAAAGGGAAAAA
*
2225994 TAGTATGCATCGTTCTACT
66 CAGTATGCATCGTTCTACT
* * *
2226013 TCCATGAAAAACAAACACCATTCTTGAAAATTGAAAAATGCAGCAACAGACATGAAAGGGAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAAATCGAAAAATGAAGCAACAGACATGAAAGGGAAAAA
*
2226078 CGGTATGCATCGTTCTACT
66 CAGTATGCATCGTTCTACT
2226097 TC
1 TC
2226099 GCTTTGAATC
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (84 bp):
TCCATAAAAAACAAACACCATTCTTGAAAATCGAAAAATGAAGCAACAGACATGAAAGGGAAAAA
CAGTATGCATCGTTCTACT
Found at i:2231951 original size:25 final size:22
Alignment explanation
Indices: 2231900--2231952 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
2231890 TATTATTTTA
* *
2231900 TGTAAATATTTTCTAAATTTAT
1 TGTATATATTTTCTAAAATTAT
2231922 TGTATATATTTTCTTTAAAATTAT
1 TGTATATATTTTC--TAAAATTAT
2231946 TCGTATA
1 T-GTATA
2231953 AAGCTTGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 12 0.46
24 9 0.35
25 5 0.19
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.55
Consensus pattern (22 bp):
TGTATATATTTTCTAAAATTAT
Found at i:2234120 original size:19 final size:19
Alignment explanation
Indices: 2234079--2234120 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2234069 TCTTTCTTTT
**
2234079 TGCATTCATTTCATGCATT
1 TGCATTCATTTCATGCACA
2234098 TGCATTGCATTTCAT-CACA
1 TGCATT-CATTTCATGCACA
2234117 TGCA
1 TGCA
2234121 CTAGATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (19 bp):
TGCATTCATTTCATGCACA
Found at i:2235953 original size:16 final size:16
Alignment explanation
Indices: 2235916--2235953 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2235906 TAAAAGTTCC
2235916 AAAAAAAAAGAGAAAA
1 AAAAAAAAAGAGAAAA
2235932 ATAAAAAAAA-AGAAAA
1 A-AAAAAAAAGAGAAAA
*
2235948 GAAAAA
1 AAAAAA
2235954 GAAACTGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAGAAAA
Found at i:2237155 original size:64 final size:65
Alignment explanation
Indices: 2237043--2237171 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 65
2237033 TATACAATAG
* * *
2237043 CACATCTAGTTAGGAGCATTTGATTTTATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGGTAGGAGCATTTGATTTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
* * * *
2237108 CACATTTAGGTAGGAGCATTTGA-TTCATTTCAATCATTGCATCCTAATTATTTGGCATAGGCAT
1 CACATCTAGGTAGGAGCATTTGATTTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
2237172 AGATACATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
64 36 0.63
65 21 0.37
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (65 bp):
CACATCTAGGTAGGAGCATTTGATTTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:2237441 original size:85 final size:85
Alignment explanation
Indices: 2237233--2237449 Score: 208
Period size: 85 Copynumber: 2.5 Consensus size: 85
2237223 GGAATCGGTG
** **
2237233 AATTCACAGATCTTATCTTCCTAAGCAATAGTGGAGCAGATCAAAGATACAAGCCTTAACCTTCT
1 AATT-ACAGATCTTATCTTCCTAAGCAGGAGTGGAGCAGATCAAAGA-ACAAGCCTTAACCCCCT
* *
2237298 GAGCAGTAGGGTAACAGGCTAA
64 AAGAAGTAGGGTAACAGGCTAA
** * * * **
2237320 AATTTACAGATCTTGGC-T-CTATGAGTAGTG-GTGGAGCAGGTCGAAG-ACCCGCCTTAACCCC
1 AA-TTACAGATCTTATCTTCCTA--AGCAG-GAGTGGAGCAGATCAAAGAACAAGCCTTAACCCC
*
2237381 CTAAGAAGTAGGGTAATAGGCTAA
62 CTAAGAAGTAGGGTAACAGGCTAA
*
2237405 AATTACAGATCTTATCTTCGCTAAGCAGGAGCGGAGCAGATCAAA
1 AATTACAGATCTTATCTTC-CTAAGCAGGAGTGGAGCAGATCAAA
2237450 TTTTGGTGAA
Statistics
Matches: 102, Mismatches: 20, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
84 13 0.13
85 54 0.53
86 1 0.01
87 32 0.31
88 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (85 bp):
AATTACAGATCTTATCTTCCTAAGCAGGAGTGGAGCAGATCAAAGAACAAGCCTTAACCCCCTAA
GAAGTAGGGTAACAGGCTAA
Found at i:2237557 original size:135 final size:132
Alignment explanation
Indices: 2237398--2237894 Score: 592
Period size: 135 Copynumber: 3.7 Consensus size: 132
2237388 GTAGGGTAAT
* * * *
2237398 AGGCTAAAATTA-CAGATCTTATCTTCGCTAAGCAGGAGCGGAGCAGATCAAATTTTGGTGAATC
1 AGGCTAAAA-TACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGG-GAATC
2237462 TTATCTCCATGTATCAGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGT
64 TTATCTCCATGTATC-GCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGT
2237527 GGAGC
128 GGAGC
*
2237532 AGGCTAAACATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTC
1 AGGCTAAA-ATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGGAA-TC
* * * **
2237597 TTATCTTCATGTATCGTCAATGGAGCAAATTTCAGCCATCAGCCTTATCTTCACTGAGCAGGAGT
64 TTATCTCCATGTATCG-CAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGT
*
2237662 GGAGT
128 GGAGC
* * *
2237667 AGGCT-AAATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGGTCGAACTTTGGAGAATCT
1 AGGCTAAAATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGG-GAATCT
** * * *
2237731 TATCTCCACATACCGGTAATGGAGCAGATTCTAATCATCAGCCTTATCTTCACTGAGCAGGAGTG
65 TATCTCCATGTATC-GCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTG
2237796 GAGC
129 GAGC
* * * * *
2237800 AGGCTAAACATACCAGATCTTATCTCCA-TGTATCAGCTA-TGGAGCAGATCAGAA--ATGGCGA
1 AGGCTAAA-ATACCAGATCTTATCTTCACTG-AGCAG-GAGTGAAGCAGATCA-AATTTTGG-GA
* *
2237861 GTCTTATCTCCATGTATCGGCTATGGAGCAGATT
61 ATCTTATCTCCATGTATC-GCAATGGAGCAGATT
2237895 TTAGCCACAA
Statistics
Matches: 312, Mismatches: 40, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
133 111 0.36
134 55 0.18
135 143 0.46
136 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (132 bp):
AGGCTAAAATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGGAATCTT
ATCTCCATGTATCGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGA
GC
Found at i:2237952 original size:268 final size:268
Alignment explanation
Indices: 2237401--2237957 Score: 680
Period size: 268 Copynumber: 2.1 Consensus size: 268
2237391 GGGTAATAGG
* * * *
2237401 CTAAAATTACAGATCTTATCTTCGCTAAGCAGGAGCGGAGCAGATCAAATTTTGGTGAATCTTAT
1 CTAAAATTACAGATCTTATCTTCACTAAGCAGGAGCGAAGCAGATCAAACTTTGGAGAATCTTAT
** *
2237466 CTCCATGTATCAGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAG
66 CTCCACATACCAGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAG
* *
2237531 CAGGCTAAACATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGT
131 CAGGCTAAACATACCAGATCTTATCTCCACTGAGCAGGAGTGAAGCAGATCAAA-TATGGCAAGT
* * *
2237596 CTTATCTTCATGTATCGTCAATGGAGCAAATTTCAGCCATCAGCCTTATCTTCACTGAGCAGGAG
195 CTTATCTCCATGTATCGGCAATGGAGCAAATTTCAGCCATCAGCCTTATCTTCACTGAGCAGCAG
* * **
2237661 TGGAGTAGG
260 TGAAGCAAA
* * * *
2237670 CT-AAA-TACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGGTCGAACTTTGGAGAATCTTA
1 CTAAAATTA-CAGATCTTATCTTCACTAAGCAGGAGCGAAGCAGATCAAACTTTGGAGAATCTTA
* * *
2237733 TCTCCACATACCGGTAATGGAGCAGATTCTAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGA
65 TCTCCACATACCAGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGA
* * * *
2237798 GCAGGCTAAACATACCAGATCTTATCTCCA-TGTATCAGCTA-TGGAGCAGATCAGAA-ATGGCG
130 GCAGGCTAAACATACCAGATCTTATCTCCACTG-AGCAG-GAGTGAAGCAGATCA-AATATGGCA
* * * * * *
2237860 AGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA-CAAGTCTTATCTT-TCTGAAGT
192 AGTCTTATCTCCATGTATCGGCAATGGAGCAAATTTCAGCCATC-AGCCTTATCTTCACTG-AGC
*
2237923 TGCAG-GAAGCAAA
255 AGCAGTGAAGCAAA
2237936 CTGAAAATTACAGATCTTATCT
1 CT-AAAATTACAGATCTTATCT
2237958 CCATGTATCG
Statistics
Matches: 245, Mismatches: 34, Indels: 19
0.82 0.11 0.06
Matches are distributed among these distances:
266 10 0.04
267 60 0.24
268 168 0.69
269 7 0.03
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (268 bp):
CTAAAATTACAGATCTTATCTTCACTAAGCAGGAGCGAAGCAGATCAAACTTTGGAGAATCTTAT
CTCCACATACCAGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAG
CAGGCTAAACATACCAGATCTTATCTCCACTGAGCAGGAGTGAAGCAGATCAAATATGGCAAGTC
TTATCTCCATGTATCGGCAATGGAGCAAATTTCAGCCATCAGCCTTATCTTCACTGAGCAGCAGT
GAAGCAAA
Found at i:2237978 original size:133 final size:133
Alignment explanation
Indices: 2237813--2238133 Score: 527
Period size: 133 Copynumber: 2.4 Consensus size: 133
2237803 CTAAACATAC
*
2237813 CAGATCTTATCTCCATGTATCAGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTAT
1 CAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTAT
* * * *
2237878 CGGCTATGGAGCAGATTTTAGCCACAAGTCTTATCTTTCTGAAGTTGCAGGAAGCAAACTGAAAA
66 CAGATATGGAGCAGATTTTAGCCACAAGTCTTATCTTCCTAAAGTTGCAGGAAGCAAACTGAAAA
2237943 TTA
131 TTA
* * *
2237946 CAGATCTTATCTCCATGTATCGGCTATAGAGCAAATCAGAAATGGCGAGTCTTATCTCTATGTAT
1 CAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTAT
* *
2238011 CAGATATGGAGCAGATTTTAGCCACAAGTCTTATCTTCCTAAAGTTGTAGGAAGCAGACTGAAAA
66 CAGATATGGAGCAGATTTTAGCCACAAGTCTTATCTTCCTAAAGTTGCAGGAAGCAAACTGAAAA
2238076 TTA
131 TTA
* *
2238079 CAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAGGAATGG-TAGTCTTATC
1 CAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTCTTATC
2238134 GCTATGAAGC
Statistics
Matches: 174, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
132 9 0.05
133 165 0.95
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (133 bp):
CAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTAT
CAGATATGGAGCAGATTTTAGCCACAAGTCTTATCTTCCTAAAGTTGCAGGAAGCAAACTGAAAA
TTA
Found at i:2239140 original size:27 final size:25
Alignment explanation
Indices: 2239089--2239141 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
2239079 TTGTTAAAGG
*
2239089 TGATTTTTTAGTTTCTTTCCCTTTC
1 TGATTTTTTAGTTTCTTTCACTTTC
* *
2239114 TGATTTTGTTATTATTCTTTCATTTTC
1 TGATTTT-TTAGT-TTCTTTCACTTTC
2239141 T
1 T
2239142 TCTTGTGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.11, C:0.15, G:0.08, T:0.66
Consensus pattern (25 bp):
TGATTTTTTAGTTTCTTTCACTTTC
Found at i:2241137 original size:308 final size:307
Alignment explanation
Indices: 2240565--2241408 Score: 864
Period size: 308 Copynumber: 2.7 Consensus size: 307
2240555 GACTAAAATC
** * * * * * *
2240565 ATATGATGAAATCACTTTCATGGA-AAGATCTTAACAAGAATGCGACAATAAAGAGG-CTCAGAA
1 ATATGATGAAATCACTCCCAT-GACAAGACCTCAACAAGAAGGAGGCAATGAAG-GGCCTCAGAA
* * * * **** * * *
2240628 TGAATTCAA-ATTCTAATTAAAAGGAAAATAAGATTGTTCATAC-AGAATATTTGGGGATAGGTC
64 AGAATTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAG-ACATTTGGAGAAAGGTC
* * * * * * * *
2240691 ATGATGTAAATTGTCAAAAA-A-ATTTTATGCCACTGTTGGGGGGGGAGCCATTAGAAAATAAAA
128 ATGGTGTAAATT-ACAAAAAGACTTTTTACGCCATTATT---GGGGGAGCCACTAGAAAATAAGA
* * * * * * * * *
2240754 ATAGGTATTAAAACTATGTCTTTCATGTATCGAATATTTCATCATATTGAATATAACTCTTTATT
189 ACAGGTACTAAAGCTATGTCTTTCATGTACCAAATGTTTCATCATATTGAATAAAACTCGTGATT
2240819 CCAAATATATATTAATTATCTTCTCCCTTTTACTCATTACAAATATTGGCTACA
254 CCAAATATATATTAATTATCTTCTCCCTTTTACTCATTACAAATATTGGCTACA
** *
2240873 ATATGATGAAATCACTCCCATGGTAAGACCTCAAC-AGAAAGGCA-GCAATGGAGGGCCTCA-AA
1 ATATGATGAAATCACTCCCATGACAAGACCTCAACAAG-AAGG-AGGCAATGAAGGGCCTCAGAA
* *
2240935 ATGAATTCAAGGTTTTCATTAAAAGGAAAGTAAGATTGTTTGGGCAAGACATTGTGGAGAGAGGT
64 A-GAATTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATT-TGGAGAAAGGT
* * * * *
2241000 CATTGTGTAAATTACCAAAAG-CTTTTTACGTCATTGTTGAGGGGAGCCACTAGAAAGTAAGAAC
127 CATGGTGTAAATTACAAAAAGACTTTTTACGCCATTATTG-GGGGAGCCACTAGAAAATAAGAAC
* ** *
2241064 AGGTACTAAAGCTATGTC-TTCTATATACCAAATGTTTTTTCATATTGAATAAAACTCGTGGTTC
191 AGGTACTAAAGCTATGTCTTTC-ATGTACCAAATGTTTCATCATATTGAATAAAACTCGTGATTC
* * * *
2241128 CAGATATATATTAATTATTTTCTCCCTTTTATTCATTACAAATATTGGCTACG
255 CAAATATATATTAATTATCTTCTCCCTTTTACTCATTACAAATATTGGCTACA
* * *
2241181 ATATGATGAAGTCACTCTCATGACAATACCTCAACAAGAAGGAGGCAATGAAGGGCCTCAGAAAG
1 ATATGATGAAATCACTCCCATGACAAGACCTCAACAAGAAGGAGGCAATGAAGGGCCTCAGAAAG
* * *
2241246 AATTCAAGGTTTTGATTAAAAGGAAAATAATATTGTTTGGGCAAGACATTTGGGGAAAGGTCATG
66 AATTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTGGAGAAAGGTCATG
* * * * *
2241311 GTGTAAATTACAAAAAGAAACTTTTTACGCCATTATTGGTGGTAGGCGCTAGAAAATAAGAAGAA
131 GTGTAAATTACAAAAAG--ACTTTTTACGCCATTATTGG-GGGAGCCACTAGAAAATAAGAACAG
* *
2241376 ATACTAAAGTTATGTCTTTCATGTACCAAATGT
193 GTACTAAAGCTATGTCTTTCATGTACCAAATGT
2241409 GAAATATAAA
Statistics
Matches: 442, Mismatches: 74, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
307 40 0.09
308 263 0.60
309 41 0.09
310 95 0.21
311 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (307 bp):
ATATGATGAAATCACTCCCATGACAAGACCTCAACAAGAAGGAGGCAATGAAGGGCCTCAGAAAG
AATTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTGGAGAAAGGTCATG
GTGTAAATTACAAAAAGACTTTTTACGCCATTATTGGGGGAGCCACTAGAAAATAAGAACAGGTA
CTAAAGCTATGTCTTTCATGTACCAAATGTTTCATCATATTGAATAAAACTCGTGATTCCAAATA
TATATTAATTATCTTCTCCCTTTTACTCATTACAAATATTGGCTACA
Found at i:2242801 original size:27 final size:27
Alignment explanation
Indices: 2242763--2242819 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
2242753 CCCAGGACTA
*
2242763 AGGCGAATGATACAATGAAAATATTTG
1 AGGCGAATGATACAATGAAAAGATTTG
*
2242790 AGGCGAATGATACCATGAAAAGATTTG
1 AGGCGAATGATACAATGAAAAGATTTG
2242817 AGG
1 AGG
2242820 TAAGGAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.26, T:0.23
Consensus pattern (27 bp):
AGGCGAATGATACAATGAAAAGATTTG
Found at i:2252393 original size:22 final size:21
Alignment explanation
Indices: 2252368--2252424 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2252358 TAACTAAGGC
*
2252368 ATGTCTCGAGACAAAAGCTCTT
1 ATGTCTCGAGACAAAA-CTCAT
* * *
2252390 ATGTCTTGAGACCTATACTCAT
1 ATGTCTCGAGA-CAAAACTCAT
2252412 ATGTCTCGAGACA
1 ATGTCTCGAGACA
2252425 GGGTACCTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 1 0.04
22 24 0.86
23 3 0.11
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGTCTCGAGACAAAACTCAT
Found at i:2253841 original size:17 final size:17
Alignment explanation
Indices: 2253819--2253852 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2253809 ACAAAATTTT
* *
2253819 TTAAAATGATAGAAGAG
1 TTAAAAAGATAAAAGAG
2253836 TTAAAAAGATAAAAGAG
1 TTAAAAAGATAAAAGAG
2253853 AGAATAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (17 bp):
TTAAAAAGATAAAAGAG
Found at i:2255737 original size:101 final size:101
Alignment explanation
Indices: 2255562--2255764 Score: 309
Period size: 101 Copynumber: 2.0 Consensus size: 101
2255552 ATTTTCCATA
* * * * *
2255562 ATAAATTGAATGGCTAAACAAGATATGAAAGCAGAAGCAACTTGGCTTCTAGCACCTATTAAAAC
1 ATAAATTGAAAGGCTAAACAAGATATAAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAAC
* *
2255627 AGTATAGACTAGGATGGAACTATATCTAAAGATGAC
66 AGTATAGACTAAGATGGAACTATAACTAAAGATGAC
2255663 ATAAATTGAAAGGCTAAACAAGAT-TCAAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAA
1 ATAAATTGAAAGGCTAAACAAGATAT-AAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAA
* *
2255727 CAGTATAGACTAAGATGGAATTATAAGTAAAGATGAC
65 CAGTATAGACTAAGATGGAACTATAACTAAAGATGAC
2255764 A
1 A
2255765 AACTAAAAAG
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 1 0.01
101 91 0.99
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (101 bp):
ATAAATTGAAAGGCTAAACAAGATATAAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAAC
AGTATAGACTAAGATGGAACTATAACTAAAGATGAC
Found at i:2260003 original size:22 final size:21
Alignment explanation
Indices: 2259978--2260034 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
2259968 TAACTGAGGC
*
2259978 ATGTCTCGAGACAAAAGCTCTT
1 ATGTCTCGAGACAAAA-CTCAT
* *
2260000 ATGTCTCGAGACTTATACTCAT
1 ATGTCTCGAGAC-AAAACTCAT
2260022 ATGTCTCGAGACA
1 ATGTCTCGAGACA
2260035 GGGTACCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGTCTCGAGACAAAACTCAT
Found at i:2260918 original size:68 final size:68
Alignment explanation
Indices: 2260818--2260948 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 68
2260808 ATTGCAATAC
* * * *
2260818 TTAGTTCTTAAAACCATTGTGAGAAGATAGTTTTGACTTGTCATTATGCGCCACGCGATTTTTTA
1 TTAGCTCTTAAAACCATTATGAGAAGATAGTTTTCACTAGTCATTATGCGCCACGCGATTTTTTA
2260883 GTG
66 GTG
* * *
2260886 TTAGCTCTTAAAACC-TTATTAGAAATATAGTTTTCACTAGTCATTATGCGCCATGCGATTTTT
1 TTAGCTCTTAAAACCATTATGAG-AAGATAGTTTTCACTAGTCATTATGCGCCACGCGATTTTT
2260949 GGGAGGAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 5 0.09
68 50 0.91
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (68 bp):
TTAGCTCTTAAAACCATTATGAGAAGATAGTTTTCACTAGTCATTATGCGCCACGCGATTTTTTA
GTG
Found at i:2261449 original size:17 final size:17
Alignment explanation
Indices: 2261427--2261460 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2261417 ACAAAAATTT
*
2261427 TTAAAAAGATAGAAGAG
1 TTAAAAAGATAAAAGAG
2261444 TTAAAAAGATAAAAGAG
1 TTAAAAAGATAAAAGAG
2261461 AGAATAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (17 bp):
TTAAAAAGATAAAAGAG
Found at i:2264727 original size:5 final size:5
Alignment explanation
Indices: 2264678--2264709 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2264668 AATTTAGCCA
*
2264678 TTATT TTATT TTATT TTATT TTATT TTGTT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
2264710 TTGTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:2265748 original size:40 final size:40
Alignment explanation
Indices: 2265688--2265767 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
2265678 GACAATACCT
*
2265688 AAGGAAAAATCCACCTAGACTTTACTTGTTATTCTGGCTC
1 AAGGAAAAATCCACCAAGACTTTACTTGTTATTCTGGCTC
2265728 AAGGAAAAATCCACCAAGACTTTACTTGTTATTCTGGCTC
1 AAGGAAAAATCCACCAAGACTTTACTTGTTATTCTGGCTC
2265768 CGAATCGGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (40 bp):
AAGGAAAAATCCACCAAGACTTTACTTGTTATTCTGGCTC
Found at i:2267454 original size:231 final size:231
Alignment explanation
Indices: 2267036--2267493 Score: 783
Period size: 231 Copynumber: 2.0 Consensus size: 231
2267026 GAAAAGTCAT
* * * *
2267036 GAGGACGAAGCCTAATAGAGCAGCCAGTGTTTTCAATCTAGATGTAGTCACCATATTATCAAACC
1 GAGGACGAAGCCTAACAGACCAACCAATGTTTTCAATCTAGATGTAGTCACCATATTATCAAACC
*** *
2267101 AGATAGAATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTATGTAGGTACATCCGGTGATG
66 AGATAGAATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTACACAAGTACATCCGGTGATG
* *
2267166 CAGTGTGATACAAATGGAGGAGGAATGAACAATTCAGAATATTTACCCTAAGGTCCTAGCACAGA
131 CAGTGTGATACAAACGGAGGAGGAATGAACAATTCAGAATATTTACCCTAAGGTCCTAACACAGA
2267231 GAACAAACAAGTCAACTATATGGGTAATAATTATCA
196 GAACAAACAAGTCAACTATATGGGTAATAATTATCA
*
2267267 GAGGATGAAGCCTAACAGACCAACCAATGTTTTCAATCTAGATGTAGTCACCATATTATCAAACC
1 GAGGACGAAGCCTAACAGACCAACCAATGTTTTCAATCTAGATGTAGTCACCATATTATCAAACC
2267332 AGATAGAATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTACACAAGTACATCCGGTGATG
66 AGATAGAATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTACACAAGTACATCCGGTGATG
*
2267397 CAGTGTGATACAAACGGAGGAGGAATGAACAATTCAGAATATTTACACC-ACGGTCCTAACACAG
131 CAGTGTGATACAAACGGAGGAGGAATGAACAATTCAGAATATTTAC-CCTAAGGTCCTAACACAG
*
2267461 AGAATAAACAAGTCAACTATATGGGTAATAATT
195 AGAACAAACAAGTCAACTATATGGGTAATAATT
2267494 CTACGTCTCA
Statistics
Matches: 213, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
231 211 0.99
232 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (231 bp):
GAGGACGAAGCCTAACAGACCAACCAATGTTTTCAATCTAGATGTAGTCACCATATTATCAAACC
AGATAGAATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTACACAAGTACATCCGGTGATG
CAGTGTGATACAAACGGAGGAGGAATGAACAATTCAGAATATTTACCCTAAGGTCCTAACACAGA
GAACAAACAAGTCAACTATATGGGTAATAATTATCA
Found at i:2270404 original size:3 final size:3
Alignment explanation
Indices: 2270387--2270448 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
2270377 TTTTCTTGGT
2270387 TTA TT- TTA TTA -TA TTA TTTA TTTA TTCA TT- TT- TCTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA -TTA TT-A TTA TTA T-TA TTA TTA TTA
*
2270432 TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
2270449 CTTGTTATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
2 7 0.14
3 33 0.65
4 11 0.22
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2272140 original size:6 final size:6
Alignment explanation
Indices: 2272125--2272164 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
2272115 ATTGAGTCTA
* *
2272125 TTTA-T TTTATT TTTATT TCTAGT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
2272165 GATTATTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:2277113 original size:17 final size:15
Alignment explanation
Indices: 2277083--2277139 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 15
2277073 TATTTCCCAC
**
2277083 AAAAAAAATGATAAA
1 AAAAAAAAAAATAAA
2277098 AAAAGTAAAAAAATAAA
1 AAAA--AAAAAAATAAA
2277115 ATACAAAAAAAAATAAA
1 A-A-AAAAAAAAATAAA
2277132 TAAAAAAA
1 -AAAAAAA
2277140 TTTGTGGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 4 0.11
16 5 0.14
17 22 0.63
18 2 0.06
19 2 0.06
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.12
Consensus pattern (15 bp):
AAAAAAAAAAATAAA
Found at i:2277123 original size:16 final size:15
Alignment explanation
Indices: 2277104--2277139 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
2277094 TAAAAAAAGT
2277104 AAAAAAATAAAATACAA
1 AAAAAAAT-AAATA-AA
2277121 AAAAAAATAAATAAA
1 AAAAAAATAAATAAA
2277136 AAAA
1 AAAA
2277140 TTTGTGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAAATAAATAAA
Found at i:2277140 original size:12 final size:12
Alignment explanation
Indices: 2277084--2277140 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
2277074 ATTTCCCACA
*
2277084 AAAAAAAT-GAT
1 AAAAAAATAAAT
*
2277095 AAAAAAAGTAAAA
1 AAAAAAA-TAAAT
2277108 AAATAAAATACAA-
1 AAA-AAAATA-AAT
2277121 AAAAAAATAAAT
1 AAAAAAATAAAT
2277133 AAAAAAAT
1 AAAAAAAT
2277141 TTGTGGTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 9 0.23
12 15 0.38
13 9 0.23
14 6 0.15
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.14
Consensus pattern (12 bp):
AAAAAAATAAAT
Found at i:2283382 original size:29 final size:30
Alignment explanation
Indices: 2283345--2283411 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
2283335 TAAAAAATTA
* *
2283345 TTAATCGACCCCTT-ACCGAAT-TAATTCGG
1 TTAACCGACCACTTAACCGAATAT-ATTCGG
* *
2283374 TTAACCGACCATTTAACCGAATATGTTCGG
1 TTAACCGACCACTTAACCGAATATATTCGG
2283404 TTAACCGA
1 TTAACCGA
2283412 ATTTGTTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 11 0.34
30 20 0.62
31 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (30 bp):
TTAACCGACCACTTAACCGAATATATTCGG
Found at i:2293441 original size:45 final size:45
Alignment explanation
Indices: 2293372--2293490 Score: 143
Period size: 45 Copynumber: 2.6 Consensus size: 45
2293362 TTAAAGGATA
* * *
2293372 CCATAGTGTCTTTCAAC-AATGGTCTTA-TTCGTCAGATTCATGATG
1 CCATAGCGTCTTTCAGCTAA-GGTCTTACTT-GTCAGAATCATGATG
* *
2293417 CCATAGCGTCTTTCAGCTAAGGTCTTACTTGTTAGAATCGTGATG
1 CCATAGCGTCTTTCAGCTAAGGTCTTACTTGTCAGAATCATGATG
* *
2293462 CCATAACGTCTTTCAGCTATGGTCTTACT
1 CCATAGCGTCTTTCAGCTAAGGTCTTACT
2293491 CATTTCTAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
45 61 0.94
46 4 0.06
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (45 bp):
CCATAGCGTCTTTCAGCTAAGGTCTTACTTGTCAGAATCATGATG
Found at i:2294147 original size:25 final size:25
Alignment explanation
Indices: 2294101--2294244 Score: 155
Period size: 25 Copynumber: 5.8 Consensus size: 25
2294091 GAGCGGTAAA
* * * *
2294101 CGGTAAGATCATCCGAGTTGAATAT
1 CGGTAAGCTCTTCTGAGCTGAATAT
*
2294126 TGGTAAGCTCTTCTGAGCTGAATAT
1 CGGTAAGCTCTTCTGAGCTGAATAT
*
2294151 CGGTAAGCTCTTTTGAGCTGAATAT
1 CGGTAAGCTCTTCTGAGCTGAATAT
* ** *
2294176 CGGTAAGCTTTTCCAAGCTGACTAT
1 CGGTAAGCTCTTCTGAGCTGAATAT
*
2294201 CAGTAAGCTCTTCTGAGCTGAATAT
1 CGGTAAGCTCTTCTGAGCTGAATAT
* *
2294226 TGATAAGCTCATT-TGAGCT
1 CGGTAAGCTC-TTCTGAGCT
2294245 ATGGTGAATC
Statistics
Matches: 98, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
25 96 0.98
26 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (25 bp):
CGGTAAGCTCTTCTGAGCTGAATAT
Found at i:2298922 original size:61 final size:60
Alignment explanation
Indices: 2298854--2298979 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 60
2298844 CTTCAAACCG
* * *
2298854 TGTTAGAGTCTGTTGAATAA-ACACAGGCGTATGGTCTACCCGTGTAAGGAAGTCTAGGCCA
1 TGTTAGAGTCTGCT-AA-AACACACAGGCATATGGTCTACCCGTGTAAGGAAGTCCAGGCCA
* * * * *
2298915 TGTTAGAGTCTGCTAAAACTACACGGGCATGTGGTCTGCTCGTGTAAGGAAGTCCAGGCCG
1 TGTTAGAGTCTGCTAAAAC-ACACAGGCATATGGTCTACCCGTGTAAGGAAGTCCAGGCCA
2298976 TGTT
1 TGTT
2298980 GATTTCTCAC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.04
60 2 0.04
61 51 0.93
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (60 bp):
TGTTAGAGTCTGCTAAAACACACAGGCATATGGTCTACCCGTGTAAGGAAGTCCAGGCCA
Found at i:2301578 original size:22 final size:22
Alignment explanation
Indices: 2301543--2301584 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2301533 TCATCGAAAT
*
2301543 GAGGCACTATAGTGCAAATACA
1 GAGGCACTATAGTGAAAATACA
2301565 GAGGCACTGA-AGTGAAAATA
1 GAGGCACT-ATAGTGAAAATA
2301585 GAGACACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (22 bp):
GAGGCACTATAGTGAAAATACA
Found at i:2302695 original size:23 final size:22
Alignment explanation
Indices: 2302643--2302700 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
2302633 AATCTTCACG
*
2302643 GATATGCAATCTTAG---ATAT
1 GATATGTAATCTTAGAACATAT
2302662 GATATGTAATCTTAGAACATAT
1 GATATGTAATCTTAGAACATAT
*
2302684 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
2302701 GATTTGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.42
22 6 0.18
23 13 0.39
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (22 bp):
GATATGTAATCTTAGAACATAT
Found at i:2307783 original size:27 final size:28
Alignment explanation
Indices: 2307717--2307791 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
2307707 TATTCTTATG
* **
2307717 ATTTAT-TTCAAATTTTTATATGTATTA
1 ATTTATCTTTAAATTTTTATACATATTA
2307744 A-TTA-CTTTAAAATTTTTATACATA-TA
1 ATTTATCTTT-AAATTTTTATACATATTA
2307770 ATTTATCTTTAAATGTTTTATA
1 ATTTATCTTTAAAT-TTTTATA
2307792 TATTGCTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
26 8 0.20
27 21 0.52
28 11 0.28
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (28 bp):
ATTTATCTTTAAATTTTTATACATATTA
Found at i:2310479 original size:93 final size:93
Alignment explanation
Indices: 2310366--2310536 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
2310356 GCCCCTAAGT
* *
2310366 GAACTCGGACTCAACTCAACGAGCTCA-AGCGTTCGTATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCAGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
2310430 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
2310459 GAACTGGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2310524 CGAGTTCGGATGC
66 CGAGTTCGGATGC
2310537 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 71 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:2310531 original size:46 final size:47
Alignment explanation
Indices: 2310361--2310533 Score: 196
Period size: 46 Copynumber: 3.7 Consensus size: 47
2310351 AACCCGCCCC
* * * *
2310361 TAAGTGAACTCGGACTCAACTCAACGAGCTC-AAGCGTTCGTATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCA
*
2310407 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCATCCA
* * *
2310455 TCA-CGAACTGGGACTCAACTCAACGAGTTCGGA-CATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCA
2310500 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
2310534 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 58 0.55
47 29 0.27
48 3 0.03
49 2 0.02
50 2 0.02
51 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCA
Found at i:2310552 original size:46 final size:44
Alignment explanation
Indices: 2310409--2310552 Score: 132
Period size: 46 Copynumber: 3.1 Consensus size: 44
2310399 CGTATCCATA
2310409 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * * *
2310456 CA-CGAACTGGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
2310502 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
2310548 AGTGA
1 AGTGA
2310553 CATGTCACTT
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.41
47 30 0.38
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:2312797 original size:23 final size:22
Alignment explanation
Indices: 2312756--2312798 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2312746 GCAATCTTAG
*
2312756 ATATGATATGTAATCTTAGAAC
1 ATATGATATGTAATATTAGAAC
*
2312778 ATATGATTTTGTAATATTAGA
1 ATATGA-TATGTAATATTAGA
2312799 GATTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (22 bp):
ATATGATATGTAATATTAGAAC
Found at i:2313048 original size:15 final size:16
Alignment explanation
Indices: 2313030--2313059 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2313020 GTCGTTTGGC
2313030 TTTGAGTT-GTTTTCA
1 TTTGAGTTGGTTTTCA
2313045 TTTGAGTTGGTTTTC
1 TTTGAGTTGGTTTTC
2313060 GTAGAGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.07, G:0.23, T:0.60
Consensus pattern (16 bp):
TTTGAGTTGGTTTTCA
Found at i:2315099 original size:4 final size:4
Alignment explanation
Indices: 2315090--2315125 Score: 54
Period size: 4 Copynumber: 8.5 Consensus size: 4
2315080 TGAACAGGGG
2315090 AGAA AGAA AGGAA AGAA AGGAA AGAA AGAA AGAA AG
1 AGAA AGAA A-GAA AGAA A-GAA AGAA AGAA AGAA AG
2315126 GGAGAAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 22 0.73
5 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2315105 original size:9 final size:9
Alignment explanation
Indices: 2315091--2315126 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2315081 GAACAGGGGA
2315091 GAAAGAAAG
1 GAAAGAAAG
2315100 GAAAGAAAG
1 GAAAGAAAG
2315109 GAAAGAAA-
1 GAAAGAAAG
2315117 GAAAGAAAG
1 GAAAGAAAG
2315126 G
1 G
2315127 GAGAAAAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (9 bp):
GAAAGAAAG
Found at i:2315106 original size:13 final size:13
Alignment explanation
Indices: 2315090--2315126 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2315080 TGAACAGGGG
2315090 AGAAAGAAAGGAA
1 AGAAAGAAAGGAA
2315103 AGAAAGGAAA-GAA
1 AGAAA-GAAAGGAA
2315116 AGAAAGAAAGG
1 AGAAAGAAAGG
2315127 GAGAAAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGGAA
Found at i:2315134 original size:13 final size:12
Alignment explanation
Indices: 2315090--2315132 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
2315080 TGAACAGGGG
2315090 AGAAAGAAAGGAA
1 AGAAAGAAAGG-A
*
2315103 AGAAAGGAAAGAA
1 AGAAA-GAAAGGA
*
2315116 AGAAAGAAAGGG
1 AGAAAGAAAGGA
2315128 AGAAA
1 AGAAA
2315133 AGGGAAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.38
13 11 0.42
14 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAGGA
Found at i:2315495 original size:10 final size:10
Alignment explanation
Indices: 2315482--2315516 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2315472 AAGTGAATTT
*
2315482 GAATTGAATT
1 GAATTGAATG
2315492 GAATTGAATG
1 GAATTGAATG
*
2315502 GAATGGAATG
1 GAATTGAATG
2315512 GAATT
1 GAATT
2315517 ATGATTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (10 bp):
GAATTGAATG
Found at i:2315989 original size:45 final size:45
Alignment explanation
Indices: 2315925--2316117 Score: 287
Period size: 45 Copynumber: 4.3 Consensus size: 45
2315915 CTGTTACCGC
* *
2315925 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAGTATTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* *
2315970 TACTGCTACTGTTACCGATTCGGCACTTTGTATGTCGAATATTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * *
2316015 TACTGTTACCGTTACCGATTCGGTACTTTGTGTGTGGAATATTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * * *
2316060 TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
2316105 TACTGTTACTGTT
1 TACTGTTACTGTT
2316118 CCAGATTTGT
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:2316561 original size:18 final size:18
Alignment explanation
Indices: 2316281--2316563 Score: 137
Period size: 18 Copynumber: 15.3 Consensus size: 18
2316271 AAAGGTATAA
* *
2316281 AATAACTGATTATTACTG
1 AATAACTGACTGTTACTG
* *
2316299 AATAATTGACTGTTACCG
1 AATAACTGACTGTTACTG
* *
2316317 GATAATTGACTGTTACTG
1 AATAACTGACTGTTACTG
* *
2316335 GAT-ATTAGACTGTTACTG
1 AATAACT-GACTGTTACTG
* *
2316353 AATAACTGAATATTACTG
1 AATAACTGACTGTTACTG
* * *
2316371 AATAATTGA-TCATTATTG
1 AATAACTGACT-GTTACTG
* * *
2316389 AATAACTAATTGTCACTG
1 AATAACTGACTGTTACTG
*
2316407 AATGAA-TGACTGCTACTG
1 AAT-AACTGACTGTTACTG
* * *
2316425 AATAACTTAATAGTTATTG
1 AATAACTGACT-GTTACTG
* *
2316444 AATATCTGA-TTTTACTG
1 AATAACTGACTGTTACTG
*
2316461 AATAATTGACTGTTACTG
1 AATAACTGACTGTTACTG
* *
2316479 GATAACCGATCAATTGATCGATACTG
1 AATAACTGA-C---TG-T---TACTG
* *
2316505 AATAACTGA-TAATTATTG
1 AATAACTGACT-GTTACTG
* *
2316523 AATAATTGATTGTTA-TCG
1 AATAACTGACTGTTACT-G
2316541 AATAACTGACTGTTACTG
1 AATAACTGACTGTTACTG
2316559 AATAA
1 AATAA
2316564 ATAATTATTC
Statistics
Matches: 202, Mismatches: 43, Indels: 40
0.71 0.15 0.14
Matches are distributed among these distances:
17 19 0.09
18 146 0.72
19 20 0.10
21 2 0.01
22 2 0.01
23 1 0.00
26 12 0.06
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
AATAACTGACTGTTACTG
Found at i:2316561 original size:36 final size:36
Alignment explanation
Indices: 2316281--2316563 Score: 164
Period size: 36 Copynumber: 7.6 Consensus size: 36
2316271 AAAGGTATAA
* * * *
2316281 AATAACTGATTATTACTGAATAATTGACTGTTACCG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
* * * *
2316317 GATAATTGACTGTTACTGGAT-ATTAGACTGTTACTG
1 AATAACTGACTGTTACTGAATAATT-GATTGTTACTG
* * ** *
2316353 AATAACTGAATATTACTGAATAATTGATCATTATTG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
* * * * *
2316389 AATAACTAATTGTCACTGAATGAA-TGACTGCTACTG
1 AATAACTGACTGTTACTGAAT-AATTGATTGTTACTG
* * *
2316425 AATAACTTAATAGTTATTGAAT-ATCTGATT-TTACTG
1 AATAACTGACT-GTTACTGAATAAT-TGATTGTTACTG
* * *
2316461 AATAATTGACTGTTACTGGATAACCGATCAATTGATCGATACTG
1 AATAACTGACTGTTACT-G---A---AT-AATTGATTGTTACTG
* *
2316505 AATAACTGA-TAATTATTGAATAATTGATTGTTA-TCG
1 AATAACTGACT-GTTACTGAATAATTGATTGTTACT-G
2316541 AATAACTGACTGTTACTGAATAA
1 AATAACTGACTGTTACTGAATAA
2316564 ATAATTATTC
Statistics
Matches: 185, Mismatches: 43, Indels: 38
0.70 0.16 0.14
Matches are distributed among these distances:
35 10 0.05
36 126 0.68
37 20 0.11
39 1 0.01
40 1 0.01
42 2 0.01
43 6 0.03
44 19 0.10
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (36 bp):
AATAACTGACTGTTACTGAATAATTGATTGTTACTG
Found at i:2316709 original size:2 final size:2
Alignment explanation
Indices: 2316702--2316764 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
2316692 TGAATAGTTC
2316702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2316744 TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2316765 GTTTTATAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2317181 original size:25 final size:21
Alignment explanation
Indices: 2317136--2317177 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2317126 AACTAGGATG
2317136 AGTGTGAATATTTATTTTAAT
1 AGTGTGAATATTTATTTTAAT
2317157 AGTGTGAATATTTATTTTAAT
1 AGTGTGAATATTTATTTTAAT
2317178 TAATGACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (21 bp):
AGTGTGAATATTTATTTTAAT
Found at i:2321435 original size:15 final size:15
Alignment explanation
Indices: 2321412--2321446 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2321402 AAGTGAATTT
*
2321412 GAATTGAATTGAATG
1 GAATTGAATGGAATG
*
2321427 GAATGGAATGGAATG
1 GAATTGAATGGAATG
2321442 GAATT
1 GAATT
2321447 ATGATTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (15 bp):
GAATTGAATGGAATG
Found at i:2321864 original size:18 final size:19
Alignment explanation
Indices: 2321836--2321871 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2321826 GGCACTTATG
2321836 TACTAGTTACTGTTACCGC
1 TACTAGTTACTGTTACCGC
2321855 TACT-GTTACTGTTACCG
1 TACTAGTTACTGTTACCG
2321872 ATTCTGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (19 bp):
TACTAGTTACTGTTACCGC
Found at i:2321919 original size:45 final size:45
Alignment explanation
Indices: 2321855--2322094 Score: 383
Period size: 45 Copynumber: 5.3 Consensus size: 45
2321845 CTGTTACCGC
* *
2321855 TACTGTTACTGTTACCGATTCTGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
2321900 TACTGCTACCGTTACCGATTCGGCACTTTGTGTGTC-AGATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGA-ATATTGT
*
2321945 TACTGTTACCGTTACCGATTCGGCACTGTGTGTGTCGAATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
2321990 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTGGAATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * *
2322035 TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
2322080 TACTGTTACTGTTAC
1 TACTGTTACCGTTAC
2322095 TGTTACTGTT
Statistics
Matches: 182, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
44 1 0.01
45 180 0.99
46 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (45 bp):
TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:2322085 original size:6 final size:6
Alignment explanation
Indices: 2322074--2322143 Score: 131
Period size: 6 Copynumber: 11.7 Consensus size: 6
2322064 GTGTGTTGAA
*
2322074 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTAT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT
2322122 TACTGT TACTGT TACTGT TACT
1 TACTGT TACTGT TACTGT TACT
2322144 ATTCCAGATT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (6 bp):
TACTGT
Found at i:2322343 original size:18 final size:18
Alignment explanation
Indices: 2322322--2322512 Score: 151
Period size: 18 Copynumber: 10.6 Consensus size: 18
2322312 TAACTGATTA
2322322 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
* *
2322340 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
*
2322358 TTACTGGAT-ATTAGACTG
1 TTACTGAATAATT-GACTG
* * *
2322376 TTACTGAATAACTGAATT
1 TTACTGAATAATTGACTG
*
2322394 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* * *
2322412 TTACTAAATAACTGATTG
1 TTACTGAATAATTGACTG
*
2322430 TCACTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* *
2322448 CTACTGAATAACTT-AATAG
1 TTACTGAATAA-TTGACT-G
*
2322467 TTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
2322484 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
2322502 TTACTGGATAA
1 TTACTGAATAA
2322513 CCGATCAATT
Statistics
Matches: 139, Mismatches: 22, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
17 19 0.14
18 104 0.75
19 16 0.12
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:2322398 original size:36 final size:36
Alignment explanation
Indices: 2322310--2322592 Score: 164
Period size: 36 Copynumber: 7.6 Consensus size: 36
2322300 AAAGGTATAA
* * *
2322310 AATAACTGATTATTACTGAATAATTGACTGTTACCG
1 AATAACTGAATGTTACTGAATAATTGACTGTTACTG
* * * *
2322346 GATAATTGACTGTTACTGGAT-ATTAGACTGTTACTG
1 AATAACTGAATGTTACTGAATAATT-GACTGTTACTG
* * *
2322382 AATAACTGAATTTTACTGAATAATTGA-TCATTACTA
1 AATAACTGAATGTTACTGAATAATTGACT-GTTACTG
* * *
2322418 AATAACTGATTGTCACTGAATGAA-TGACTGCTACTG
1 AATAACTGAATGTTACTGAAT-AATTGACTGTTACTG
* *
2322454 AATAACTTAATAGTTACTGAAT-ATCTGA-TTTTACTG
1 AATAACTGAAT-GTTACTGAATAAT-TGACTGTTACTG
* * *
2322490 AATAATTGACTGTTACTGGATAACCGATCAATTGA-TCGATACTG
1 AATAACTGAATGTTACT-G---A---AT-AATTGACT-GTTACTG
** * * * *
2322534 AATAACTGGTTATTATTGAATAATTGATTGTTACCG
1 AATAACTGAATGTTACTGAATAATTGACTGTTACTG
* *
2322570 AATAACTGACTGTTACTAAATAA
1 AATAACTGAATGTTACTGAATAA
2322593 ATAATTATTC
Statistics
Matches: 187, Mismatches: 41, Indels: 38
0.70 0.15 0.14
Matches are distributed among these distances:
35 11 0.06
36 127 0.68
37 21 0.11
39 1 0.01
40 1 0.01
42 2 0.01
43 5 0.03
44 19 0.10
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (36 bp):
AATAACTGAATGTTACTGAATAATTGACTGTTACTG
Found at i:2322572 original size:18 final size:18
Alignment explanation
Indices: 2322551--2322585 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2322541 GGTTATTATT
* *
2322551 GAATAATTGATTGTTACC
1 GAATAACTGACTGTTACC
2322569 GAATAACTGACTGTTAC
1 GAATAACTGACTGTTAC
2322586 TAAATAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
GAATAACTGACTGTTACC
Found at i:2322739 original size:2 final size:2
Alignment explanation
Indices: 2322732--2322760 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2322722 GAATAGTTCA
2322732 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2322761 TAATATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2324189 original size:13 final size:13
Alignment explanation
Indices: 2324171--2324196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2324161 GTAAATGATG
2324171 TTAAAATAAATAT
1 TTAAAATAAATAT
2324184 TTAAAATAAATAT
1 TTAAAATAAATAT
2324197 ATTATAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAATAAATAT
Found at i:2325327 original size:39 final size:40
Alignment explanation
Indices: 2325221--2325330 Score: 109
Period size: 38 Copynumber: 2.8 Consensus size: 40
2325211 ACCTTGAGTA
* **
2325221 GATGAGACACTGGGTGTC-ACTAAATTTCTTCGGATAGATTC
1 GATGAGACACTGGGTGTCAACT--ATTACTTCGGATAGAGCC
** ** *
2325262 GATGAGGTACTGGGTACCAACT-TTACTTCGGCTAG-GCC
1 GATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGCC
2325300 GATGAGACACTGGGTGTCAACTATTACTTCG
1 GATGAGACACTGGGTGTCAACTATTACTTCG
2325331 AACTATCCGA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
38 19 0.35
39 19 0.35
41 14 0.25
42 3 0.05
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGCC
Found at i:2325341 original size:39 final size:39
Alignment explanation
Indices: 2325221--2325354 Score: 96
Period size: 39 Copynumber: 3.4 Consensus size: 39
2325211 ACCTTGAGTA
* * *
2325221 GATGAGACACTGGGTGTC-ACTAAATTTCTTCGGATA-GATTC
1 GATGAGACACTGGGTGTCAACT--ATTACTTC-GA-ACTATCC
** ** * *
2325262 GATGAGGTACTGGGTACCAACT-TTACTTCG-GCTAGGCC
1 GATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TCC
2325300 GATGAGACACTGGGTGTCAACTATTACTTCGAACTATCC
1 GATGAGACACTGGGTGTCAACTATTACTTCGAACTATCC
* *
2325339 GATGAGGCATTGGGTG
1 GATGAGACACTGGGTG
2325355 CCATATTGGT
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
37 1 0.01
38 20 0.28
39 30 0.42
40 3 0.04
41 14 0.20
42 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (39 bp):
GATGAGACACTGGGTGTCAACTATTACTTCGAACTATCC
Found at i:2327256 original size:21 final size:20
Alignment explanation
Indices: 2327193--2327252 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
2327183 TTATAAGTAT
2327193 TTTTTATACATATATTAAATA
1 TTTTT-TACATATATTAAATA
2327214 -TTTTTA-ATAT-TTATAAGTA
1 TTTTTTACATATATTA-AA-TA
2327233 TTTTTTACATATATTAAATA
1 TTTTTTACATATATTAAATA
2327253 ATTTAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
17 3 0.09
18 6 0.18
19 4 0.12
20 12 0.35
21 6 0.18
22 3 0.09
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTTACATATATTAAATA
Found at i:2334122 original size:19 final size:19
Alignment explanation
Indices: 2334100--2334156 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
2334090 AGTTTTGAAG
2334100 AAAATATTAAAAATATTAT
1 AAAATATTAAAAATATTAT
* * * *
2334119 AAAAAATAAAAAAAATCAT
1 AAAATATTAAAAATATTAT
*
2334138 ATAATATTTAAAGAATATT
1 AAAATA-TTAAA-AATATT
2334157 TTAAGATTCT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 19 0.70
20 4 0.15
21 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATATTAAAAATATTAT
Found at i:2334361 original size:2 final size:2
Alignment explanation
Indices: 2334354--2334379 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2334344 TTAAATTTTA
2334354 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2334380 CAATTAAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2334727 original size:18 final size:19
Alignment explanation
Indices: 2334670--2334734 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 19
2334660 AAATTTATAT
2334670 TTATAAAAATATTATTAAAAA
1 TTATAAAAATA--ATTAAAAA
* *
2334691 TTATAAAAATTATT-TAAA
1 TTATAAAAATAATTAAAAA
2334709 TTATAAAAA-AATTAAAAA
1 TTATAAAAATAATTAAAAA
*
2334727 TCATAAAA
1 TTATAAAA
2334735 GTGTTCACCT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.08
18 22 0.58
19 3 0.08
21 10 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TTATAAAAATAATTAAAAA
Found at i:2334734 original size:9 final size:9
Alignment explanation
Indices: 2334670--2334717 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
2334660 AAATTTATAT
2334670 TTATAAAAATA
1 TTAT-AAAA-A
2334681 TTATTAAAAA
1 TTA-TAAAAA
2334691 TTATAAAAA
1 TTATAAAAA
**
2334700 TTATTTAAA
1 TTATAAAAA
2334709 TTATAAAAA
1 TTATAAAAA
2334718 AATTAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 20 0.62
10 4 0.12
11 7 0.22
12 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TTATAAAAA
Found at i:2338597 original size:2 final size:2
Alignment explanation
Indices: 2338590--2338623 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2338580 TATACAAATT
2338590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2338624 AACAAATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2339572 original size:21 final size:22
Alignment explanation
Indices: 2339543--2339596 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2339533 AGTCTATATC
*
2339543 ATTATAATTTTTAAAAAATTAA
1 ATTATAATTTTCAAAAAATTAA
*
2339565 ATTA-AATTTTCATAAAATTAAA
1 ATTATAATTTTCAAAAAATT-AA
*
2339587 AGTATAATTT
1 ATTATAATTT
2339597 CACTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.48
22 9 0.33
23 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTATAATTTTCAAAAAATTAA
Found at i:2343423 original size:14 final size:15
Alignment explanation
Indices: 2343404--2343444 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2343394 TTAGCCCAAT
2343404 ATTTTATTTATTAA-
1 ATTTTATTTATTAAC
*
2343418 ATTTTATATTTTTAAC
1 ATTTTAT-TTATTAAC
2343434 A-TTTATTTATT
1 ATTTTATTTATT
2343445 CTGAATTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.48
15 11 0.48
16 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTATTTATTAAC
Found at i:2344426 original size:20 final size:20
Alignment explanation
Indices: 2344383--2344425 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2344373 CAGTAAAATA
*
2344383 TTTTCTGGAAAATAATTTTC
1 TTTTCTGGAAAATAATTTAC
*
2344403 TTTTCTGG-AAATGATTTAC
1 TTTTCTGGAAAATAATTTAC
2344422 TTTT
1 TTTT
2344426 TTGGTGTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (20 bp):
TTTTCTGGAAAATAATTTAC
Found at i:2344537 original size:22 final size:22
Alignment explanation
Indices: 2344510--2344551 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2344500 TTGTTTTTAC
2344510 ATATATTAATAAATTTATATAT
1 ATATATTAATAAATTTATATAT
2344532 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
2344552 TTTAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATATTAATAAATTTATATAT
Found at i:2344770 original size:14 final size:14
Alignment explanation
Indices: 2344751--2344778 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2344741 TTTTTTGATT
2344751 ATCATCCATCCACA
1 ATCATCCATCCACA
2344765 ATCATCCATCCACA
1 ATCATCCATCCACA
2344779 CCTCTCTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (14 bp):
ATCATCCATCCACA
Found at i:2345548 original size:24 final size:24
Alignment explanation
Indices: 2345514--2345566 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2345504 GAATACCTCA
2345514 CACACTCATCTCTAACATTCAACC
1 CACACTCATCTCTAACATTCAACC
*
2345538 CACACTTATCTCTAACATTCAACC
1 CACACTCATCTCTAACATTCAACC
2345562 CACAC
1 CACAC
2345567 CATAAGAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.42, G:0.00, T:0.25
Consensus pattern (24 bp):
CACACTCATCTCTAACATTCAACC
Found at i:2347395 original size:9 final size:9
Alignment explanation
Indices: 2347381--2347414 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2347371 ATTTTCTAAT
*
2347381 TCGAATAAC
1 TCGAATAAA
2347390 TCGAATAAA
1 TCGAATAAA
2347399 TCGAATAAA
1 TCGAATAAA
*
2347408 CCGAATA
1 TCGAATA
2347415 TAAGCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.21
Consensus pattern (9 bp):
TCGAATAAA
Found at i:2347722 original size:12 final size:12
Alignment explanation
Indices: 2347707--2347739 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2347697 TATTTTTTAG
2347707 TTATTTACTCAC
1 TTATTTACTCAC
*
2347719 TTATTTATTCAC
1 TTATTTACTCAC
2347731 TTATTTACT
1 TTATTTACT
2347740 TCAATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATTTACTCAC
Found at i:2348554 original size:41 final size:40
Alignment explanation
Indices: 2348498--2348583 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
2348488 CAAATACATT
* *
2348498 TAAAACAAATATTAAAATAAGAAACAAATAAAAAATGATAC
1 TAAAACAAATATTAAAACAAGAAACAAATAAAAAAT-ATAA
* * * * *
2348539 TAAAACAATTCTTAAAACAATATACAAATTAAAAATATAA
1 TAAAACAAATATTAAAACAAGAAACAAATAAAAAATATAA
2348579 TAAAA
1 TAAAA
2348584 AGTGATTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.23
Consensus pattern (40 bp):
TAAAACAAATATTAAAACAAGAAACAAATAAAAAATATAA
Found at i:2348634 original size:28 final size:27
Alignment explanation
Indices: 2348566--2348634 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
2348556 CAATATACAA
* * *
2348566 ATTAAAAATATAATAAAAAGTGATTAT
1 ATTAAAAATAAAATAAAAAGTAAATAT
* *
2348593 ATTAAAATTGAAAATAAAATGTAAATAT
1 ATTAAAAAT-AAAATAAAAAGTAAATAT
2348621 GATTAAAAATAAAA
1 -ATTAAAAATAAAA
2348635 AATATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 8 0.24
28 18 0.53
29 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (27 bp):
ATTAAAAATAAAATAAAAAGTAAATAT
Found at i:2349041 original size:18 final size:18
Alignment explanation
Indices: 2348998--2349032 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2348988 TTTCTACTAG
2348998 AATT-TTATTTATCTTTT
1 AATTATTATTTATCTTTT
2349015 AATTATTATTTAT-TTTT
1 AATTATTATTTATCTTTT
2349032 A
1 A
2349033 TGTTATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
AATTATTATTTATCTTTT
Found at i:2358127 original size:14 final size:15
Alignment explanation
Indices: 2358110--2358138 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2358100 TTATATCACG
2358110 AATCA-TATAAAATT
1 AATCATTATAAAATT
2358124 AATCATTATAAAATT
1 AATCATTATAAAATT
2358139 CAGTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
AATCATTATAAAATT
Found at i:2359558 original size:44 final size:44
Alignment explanation
Indices: 2359504--2359592 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
2359494 AAGTAACAGA
*
2359504 AACAGTACGACACATG-AAGTGCCTCATCGACACAAAGTCGAAGT
1 AACAATACGACAC-TGTAAGTGCCTCATCGACACAAAGTCGAAGT
* * *
2359548 AACAATACGACACTGTTAGTGCCTCATCGACTCAAGGTCGAAGT
1 AACAATACGACACTGTAAGTGCCTCATCGACACAAAGTCGAAGT
2359592 A
1 A
2359593 TCCCTGTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 2 0.05
44 38 0.95
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (44 bp):
AACAATACGACACTGTAAGTGCCTCATCGACACAAAGTCGAAGT
Found at i:2364650 original size:14 final size:15
Alignment explanation
Indices: 2364633--2364661 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2364623 TTATATCACG
2364633 AATCA-TATAAAATT
1 AATCATTATAAAATT
2364647 AATCATTATAAAATT
1 AATCATTATAAAATT
2364662 CAGTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
AATCATTATAAAATT
Found at i:2365296 original size:18 final size:18
Alignment explanation
Indices: 2365273--2365308 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2365263 TCAGTAACAA
2365273 GCAAAATTTAAATCCAAT
1 GCAAAATTTAAATCCAAT
2365291 GCAAAATTTAAATCCAAT
1 GCAAAATTTAAATCCAAT
2365309 CTTTCAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (18 bp):
GCAAAATTTAAATCCAAT
Found at i:2366100 original size:44 final size:44
Alignment explanation
Indices: 2366045--2366133 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
2366035 AAGTAACAGA
2366045 AACACTACGACAC-ACGAAGTGCCTCATCGACACAAAGTCGAAGT
1 AACACTACGACACTA-GAAGTGCCTCATCGACACAAAGTCGAAGT
* ** * * *
2366089 AACAGTACGACACTATTAGTGCCTCGTCGACTCAAGGTCGAAGT
1 AACACTACGACACTAGAAGTGCCTCATCGACACAAAGTCGAAGT
2366133 A
1 A
2366134 TCCCTATACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (44 bp):
AACACTACGACACTAGAAGTGCCTCATCGACACAAAGTCGAAGT
Found at i:2370217 original size:40 final size:41
Alignment explanation
Indices: 2370173--2370265 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
2370163 ACTAGTTTGG
*
2370173 CACCCAGTGTCTTATCGGAT-AATTCGAAGTAGTAAATTAA
1 CACCCAGTGTCTTATCGAATAAATTCGAAGTAGTAAATTAA
* *
2370213 CACCCAGTGTCTTATCGAATAAATTCGAAGTCGTAAATTGA
1 CACCCAGTGTCTTATCGAATAAATTCGAAGTAGTAAATTAA
2370254 CACCCAGTGTCT
1 CACCCAGTGTCT
2370266 CATCAGTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 19 0.39
41 30 0.61
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (41 bp):
CACCCAGTGTCTTATCGAATAAATTCGAAGTAGTAAATTAA
Found at i:2371292 original size:19 final size:19
Alignment explanation
Indices: 2371257--2371314 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2371247 ATATACTTAA
* *
2371257 ATATTAAGTAAACATAT-T
1 ATATTAAATATACATATGT
*
2371275 TTATTAATATATACATATGT
1 ATATTAA-ATATACATATGT
*
2371295 ATATTAAATTTACATATGT
1 ATATTAAATATACATATGT
2371314 A
1 A
2371315 ATCACTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 6 0.18
19 20 0.61
20 7 0.21
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
ATATTAAATATACATATGT
Found at i:2373199 original size:51 final size:50
Alignment explanation
Indices: 2373137--2373310 Score: 285
Period size: 51 Copynumber: 3.4 Consensus size: 50
2373127 CTGATCACAT
2373137 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
* *
2373188 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
* * *
2373238 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
2373289 TTATCACTTGTCACTGATCAGA
1 TTATCACTTGTCACTGATCAGA
2373311 AGTACTCAAA
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 46 0.41
51 67 0.59
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
Found at i:2373342 original size:12 final size:12
Alignment explanation
Indices: 2373325--2373349 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2373315 CTCAAATCCA
2373325 TTCCACTCAATT
1 TTCCACTCAATT
2373337 TTCCACTCAATT
1 TTCCACTCAATT
2373349 T
1 T
2373350 GATCATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TTCCACTCAATT
Found at i:2380909 original size:51 final size:50
Alignment explanation
Indices: 2380838--2381011 Score: 285
Period size: 51 Copynumber: 3.4 Consensus size: 50
2380828 CTGATCACAT
2380838 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
* *
2380889 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
* * *
2380939 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
2380990 TTATCACTTGTCACTGATCAGA
1 TTATCACTTGTCACTGATCAGA
2381012 AGTACTCAAA
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 46 0.41
51 67 0.59
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
Done.