Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 121 of 444
Found at i:31138826 original size:178 final size:177
Alignment explanation
Indices: 31138527--31138984 Score: 623
Period size: 178 Copynumber: 2.6 Consensus size: 177
31138517 TATAGTAACT
* * * * * * *
31138527 TCAAGAAGATAAGGTTTGTAACTTCAACCTGCTCCAC-TGCAACTTCAAGGAGACAA-AGCCGGT
1 TCAAGAAGATAAGATTTGTAACTTCAACCTGC-CCTCTTGCTACCTCAAAGAGATAAGA-CTGGT
* * * * *
31138590 GGCTAAAATCTGCTCTATTGCCGATACATGGAGATAAGACTAGCCATCTTCGATCTGCTTCATAG
64 GGCTAAAATCTGCTCCATAGTCGATACATGGAGATAAGATTAGCCATCTTCGATCTGCTCCATAG
* * *
31138655 CCGATACATGGAGATAAGGTCTGTAATTTTTAGTCTGCTTCCTTGCTACC
129 CCGATACATGGAGATAAGATCTGCAA-TTTCAGTCTGCTTCCTTGCTACC
* *
31138705 TCAAGAAGATAAGATTTGCACCTTCAACCTGCCCTCTTGCTACCTCAAAGAGATAAGACTGGTGG
1 TCAAGAAGATAAGATTTGTAACTTCAACCTGCCCTCTTGCTACCTCAAAGAGATAAGACTGGTGG
** *
31138770 CTAAAATCTGCTCCATAGTCGATACATAAAGATAAGATTCGCCATCTTCGATCTGCTCCATAGCC
66 CTAAAATCTGCTCCATAGTCGATACATGGAGATAAGATTAGCCATCTTCGATCTGCTCCATAGCC
31138835 GATACATGGAGATAAGATCTGCAATTTCAGTCTGCTTCCTTGCTACC
131 GATACATGGAGATAAGATCTGCAATTTCAGTCTGCTTCCTTGCTACC
* * * * * * *
31138882 TTAGGAAGATAAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGG
1 TCAAGAAGATAAGATTTGTAACTTCAACCTGCCCTCTTGCTACCTCAAAGAGATAAGACTGGTGG
*
31138947 CTAAAATATGCTCCATAGTCGATACATGGAGATAAGAT
66 CTAAAATCTGCTCCATAGTCGATACATGGAGATAAGAT
31138985 CTACAATTTC
Statistics
Matches: 247, Mismatches: 31, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
177 117 0.47
178 129 0.52
179 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (177 bp):
TCAAGAAGATAAGATTTGTAACTTCAACCTGCCCTCTTGCTACCTCAAAGAGATAAGACTGGTGG
CTAAAATCTGCTCCATAGTCGATACATGGAGATAAGATTAGCCATCTTCGATCTGCTCCATAGCC
GATACATGGAGATAAGATCTGCAATTTCAGTCTGCTTCCTTGCTACC
Found at i:31138949 original size:177 final size:178
Alignment explanation
Indices: 31138587--31138984 Score: 609
Period size: 177 Copynumber: 2.2 Consensus size: 178
31138577 AGACAAAGCC
* * * * *
31138587 GGTGGCTAAAATCTGCTCTATTGCCGATACATGGAGATAAGACTAGCCATCTTCGATCTGCTTCA
1 GGTGGCTAAAATCTGCTCCATAGTCGATACATGGAGATAAGATTAGCCATCTTCGATCTGCTCCA
* * *
31138652 TAGCCGATACATGGAGATAAGGTCTGTAATTTTTAGTCTGCTTCCTTGCTACCTCAAGAAGATAA
66 TAGCCGATACATGGAGATAAGATCTGCAATTTTCAGTCTGCTTCCTTGCTACCTCAAGAAGATAA
*
31138717 GATTTGCACCTTCAACCTGCCCTCTTGCTACCTCAAAGAGATAAGACT
131 GACTTGCACCTTCAACCTGCCCTCTTGCTACCTCAAAGAGATAAGACT
** *
31138765 GGTGGCTAAAATCTGCTCCATAGTCGATACATAAAGATAAGATTCGCCATCTTCGATCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGTCGATACATGGAGATAAGATTAGCCATCTTCGATCTGCTCCA
* *
31138830 TAGCCGATACATGGAGATAAGATCTGCAA-TTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAA
66 TAGCCGATACATGGAGATAAGATCTGCAATTTTCAGTCTGCTTCCTTGCTACCTCAAGAAGATAA
* * * * *
31138894 GACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
131 GACTTGCACCTTCAACCTGCCCTCTTGCTACCTCAAAGAGATAAGACT
*
31138942 GGTGGCTAAAATATGCTCCATAGTCGATACATGGAGATAAGAT
1 GGTGGCTAAAATCTGCTCCATAGTCGATACATGGAGATAAGAT
31138985 CTACAATTTC
Statistics
Matches: 198, Mismatches: 22, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
177 114 0.58
178 84 0.42
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (178 bp):
GGTGGCTAAAATCTGCTCCATAGTCGATACATGGAGATAAGATTAGCCATCTTCGATCTGCTCCA
TAGCCGATACATGGAGATAAGATCTGCAATTTTCAGTCTGCTTCCTTGCTACCTCAAGAAGATAA
GACTTGCACCTTCAACCTGCCCTCTTGCTACCTCAAAGAGATAAGACT
Found at i:31140457 original size:93 final size:93
Alignment explanation
Indices: 31140345--31140516 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
31140335 GCCCATAAGT
* *
31140345 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31140410 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
31140438 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31140503 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
31140517 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:31140512 original size:46 final size:46
Alignment explanation
Indices: 31140337--31140512 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
31140327 TGTAACCCGC
* * *
31140337 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
31140383 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
31140433 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
31140476 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
31140513 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:31142939 original size:30 final size:30
Alignment explanation
Indices: 31142895--31142983 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
31142885 CAAAGATAAC
31142895 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
31142924 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
31142954 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
31142984 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:31142943 original size:15 final size:15
Alignment explanation
Indices: 31142895--31142974 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
31142885 CAAAGATAAC
*
31142895 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
31142909 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
31142924 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
31142939 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
31142954 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
31142969 AAGAAA
1 AAGAAA
31142975 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:31142983 original size:15 final size:15
Alignment explanation
Indices: 31142906--31142983 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
31142896 AGAAAACCGA
31142906 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
31142921 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
31142935 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
31142950 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
31142966 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
31142981 ATA
1 ATA
31142984 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:31146043 original size:93 final size:93
Alignment explanation
Indices: 31145931--31146102 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
31145921 GCCCATAAGT
* *
31145931 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31145996 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
31146024 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31146089 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
31146103 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:31146098 original size:46 final size:46
Alignment explanation
Indices: 31145923--31146098 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
31145913 TGTAACCCGC
* * *
31145923 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
31145969 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
31146019 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
31146062 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
31146099 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:31154781 original size:9 final size:9
Alignment explanation
Indices: 31154767--31154799 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
31154757 TTTTGGATCC
31154767 AAAAAAAGG
1 AAAAAAAGG
31154776 -AAAAAAGG
1 AAAAAAAGG
31154784 AAAAAAAGG
1 AAAAAAAGG
31154793 AAAAAAA
1 AAAAAAA
31154800 TAGAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:31154787 original size:7 final size:8
Alignment explanation
Indices: 31154768--31154798 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
31154758 TTTGGATCCA
31154768 AAAAAAGG
1 AAAAAAGG
31154776 AAAAAAGG
1 AAAAAAGG
31154784 AAAAAAAGG
1 -AAAAAAGG
31154793 AAAAAA
1 AAAAAA
31154799 ATAGAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:31156691 original size:3 final size:3
Alignment explanation
Indices: 31156683--31156708 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31156673 AATCCGGTTG
31156683 CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CC
31156709 ATAATCCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CCT
Found at i:31159971 original size:50 final size:50
Alignment explanation
Indices: 31159852--31160095 Score: 247
Period size: 50 Copynumber: 4.8 Consensus size: 50
31159842 GTTGTGAGAG
* ** *
31159852 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACGGTT-TTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTG--TACCA-GATTGTTAGGT
* *
31159904 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGT
* * * * * * * *
31159954 CGCATGTGTAGTACTAAGTGCAGGATACTATGCGTGCCCGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG-TTAGGT
* * ** *
31160005 CACGTGTGTAATACTAAGTTTAGGCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGT
* * *
31160055 CGCATGTGTAATACTAAGTGCAGGCTACTATGCGTACCAGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
31160096 GAGCTTCGGT
Statistics
Matches: 155, Mismatches: 35, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
49 3 0.02
50 84 0.54
51 37 0.24
52 31 0.20
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGT
Found at i:31160034 original size:101 final size:101
Alignment explanation
Indices: 31159903--31160103 Score: 330
Period size: 101 Copynumber: 2.0 Consensus size: 101
31159893 CGGTTTTAGG
* *
31159903 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAATACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAATAC
* * *
31159968 TAAGTGCAGGATACTATGCGTGCCCGATAGCTTCGA
66 TAAGTGCAGGATACTATGCGTACCAGAGAGCTTCGA
**
31160004 TCACGTGTGTAATACTAAGTTTAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAATAC
1 TCACGTGTGTAATACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAATAC
*
31160069 TAAGTGCAGGCTACTATGCGTACCAGAGAGCTTCG
66 TAAGTGCAGGATACTATGCGTACCAGAGAGCTTCG
31160104 GTTACAAGGG
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (101 bp):
TCACGTGTGTAATACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAATAC
TAAGTGCAGGATACTATGCGTACCAGAGAGCTTCGA
Found at i:31163055 original size:16 final size:16
Alignment explanation
Indices: 31163034--31163064 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31163024 TTTTGTATTA
*
31163034 TTTTAATATTAAATAT
1 TTTTAAAATTAAATAT
31163050 TTTTAAAATTAAATA
1 TTTTAAAATTAAATA
31163065 ACATTAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAAATTAAATAT
Found at i:31169102 original size:2 final size:2
Alignment explanation
Indices: 31169095--31169121 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31169085 GACAAGATAA
31169095 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31169122 CTAATTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31170552 original size:17 final size:17
Alignment explanation
Indices: 31170527--31170561 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31170517 TAAAGAAAAA
*
31170527 ACTTAAATTTGAATATT
1 ACTTAAATTTAAATATT
*
31170544 ACTTGAATTTAAATATT
1 ACTTAAATTTAAATATT
31170561 A
1 A
31170562 GAATTATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (17 bp):
ACTTAAATTTAAATATT
Found at i:31170812 original size:2 final size:2
Alignment explanation
Indices: 31170805--31170830 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31170795 TGAAGGCTAA
31170805 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
31170831 TGGTCTAAAA
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:31178288 original size:13 final size:11
Alignment explanation
Indices: 31178262--31178291 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
31178252 TGTATATCCA
31178262 ATATAAATATT
1 ATATAAATATT
*
31178273 ATATAAATATC
1 ATATAAATATT
31178284 ATATAAAT
1 ATATAAAT
31178292 TAATTTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATAAATATT
Found at i:31179287 original size:10 final size:10
Alignment explanation
Indices: 31179260--31179309 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
31179250 TTAAATTCTA
*
31179260 AAAGATGAAT
1 AAAGATAAAT
31179270 ACAA-ATAAAT
1 A-AAGATAAAT
*
31179280 AAAGATAATT
1 AAAGATAAAT
31179290 AAAGATAAAT
1 AAAGATAAAT
31179300 AAAGATAAAT
1 AAAGATAAAT
31179310 GTTAAATCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:31180139 original size:99 final size:99
Alignment explanation
Indices: 31179964--31180152 Score: 281
Period size: 99 Copynumber: 1.9 Consensus size: 99
31179954 GTTTTTGTTT
* * *
31179964 TTTTTCTTAAGAATATATTGAACCTTTTGACGCAAAGAGAGATGACAGCCAAGCACCCCACCCCG
1 TTTTTCTTAAGAACATATCGAACCTTTTGACGCAAAGAGAGATGACAGCCAAACACCCCACCCCG
31180029 GTTACTCAGCCCAACATACTCCTAACTTATTATA
66 GTTACTCAGCCCAACATACTCCTAACTTATTATA
* ** *
31180063 TTTTTCTTAAGAACATATCGAACCTTTTGACGTTAAA-AGAGATGACAGCCAAACACCTTACCTC
1 TTTTTCTTAAGAACATATCGAACCTTTTGACG-CAAAGAGAGATGACAGCCAAACACCCCACCCC
* *
31180127 GGTTACTTAGCCCAACATATTCCTAA
65 GGTTACTCAGCCCAACATACTCCTAA
31180153 AAAAAATTAT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 77 0.96
100 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.29
Consensus pattern (99 bp):
TTTTTCTTAAGAACATATCGAACCTTTTGACGCAAAGAGAGATGACAGCCAAACACCCCACCCCG
GTTACTCAGCCCAACATACTCCTAACTTATTATA
Found at i:31181301 original size:5 final size:5
Alignment explanation
Indices: 31181291--31181364 Score: 60
Period size: 5 Copynumber: 13.6 Consensus size: 5
31181281 ATTAATATCC
*
31181291 AAATA AAATA AAGTAA TAAATAA AAATAA ATAATA AAATA AAATA AAA-A
1 AAATA AAATA AAAT-A -AAAT-A AAAT-A A-AATA AAATA AAATA AAATA
*
31181340 GAAGAAA AAATA AAATA AAATA AAA
1 -AA-ATA AAATA AAATA AAATA AAA
31181365 ATTGGGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
4 1 0.02
5 37 0.62
6 13 0.22
7 9 0.15
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:31181313 original size:17 final size:17
Alignment explanation
Indices: 31181291--31181364 Score: 77
Period size: 17 Copynumber: 4.5 Consensus size: 17
31181281 ATTAATATCC
31181291 AAATAAAATAAAGTAAT-
1 AAATAAAATAAA-TAATA
31181308 AAATAAAAATAAATAATA
1 AAAT-AAAATAAATAATA
*
31181326 AAATAAAATAAA-AAGA
1 AAATAAAATAAATAATA
31181342 AGAA-AAAAT-AA-AATA
1 A-AATAAAATAAATAATA
31181357 AAATAAAA
1 AAATAAAA
31181365 ATTGGGTTGC
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.04
15 10 0.20
16 9 0.18
17 18 0.35
18 12 0.24
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (17 bp):
AAATAAAATAAATAATA
Found at i:31182761 original size:33 final size:33
Alignment explanation
Indices: 31182719--31182795 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
31182709 TTGTTTCCTT
* * * *
31182719 TTGGAAATCAAGAGTTTGTTGTAGTATTTGCTG
1 TTGGAAATCAAGAATTTCTTGTAGTATCTGCTA
* *
31182752 TTGGAAATCAATAATTTCTTGTTGTATCTGCTA
1 TTGGAAATCAAGAATTTCTTGTAGTATCTGCTA
31182785 TTGGAAATCAA
1 TTGGAAATCAA
31182796 ACATATTAGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (33 bp):
TTGGAAATCAAGAATTTCTTGTAGTATCTGCTA
Found at i:31184304 original size:29 final size:29
Alignment explanation
Indices: 31184262--31184319 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
31184252 GAGAAAAGAA
31184262 AAAACAAAAATAGAATTAAAAGTTTTGAT
1 AAAACAAAAATAGAATTAAAAGTTTTGAT
*
31184291 AAAATAAAAATAGAATTAAAAGTTTTGAT
1 AAAACAAAAATAGAATTAAAAGTTTTGAT
31184320 TGAAATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (29 bp):
AAAACAAAAATAGAATTAAAAGTTTTGAT
Found at i:31187116 original size:29 final size:29
Alignment explanation
Indices: 31187084--31187218 Score: 119
Period size: 29 Copynumber: 4.7 Consensus size: 29
31187074 ATACCCTCCG
** *
31187084 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACATAGTGCCATATTTTTCC
* *
31187113 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACATAGTGCCATATTTTTCC
* * *
31187142 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACATAGTGCCATATTTTTCC
* * * *
31187171 AGCACGCACACTTAGTGCCATATATTTCT
1 AGCTCGCACACATAGTGCCATATTTTTCC
* * *
31187200 TGCACGCACACTTAGTGCC
1 AGCTCGCACACATAGTGCC
31187219 GATCTCGTCA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
29 90 0.99
30 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (29 bp):
AGCTCGCACACATAGTGCCATATTTTTCC
Found at i:31187209 original size:58 final size:58
Alignment explanation
Indices: 31187030--31187219 Score: 161
Period size: 58 Copynumber: 3.3 Consensus size: 58
31187020 TACTCGATTT
* * * *** *
31187030 CGCACACTTAGTGCCACGTA-ATTT-AAGCCCGCACACACAGTGCCATA-CCCTCCGAGCT
1 CGCACACTTAGTG-C-CGTATATTTCCAGCACGCACACATAGTGCCATATATTTCC-AGCA
** * ** * *
31187088 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
* * * **
31187146 TGCACACTTAGTGCCTTATATTTCCAGCACGCACACTTAGTGCCATATATTTCTTGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
31187204 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
31187220 ATCTCGTCAC
Statistics
Matches: 103, Mismatches: 26, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
56 4 0.04
57 4 0.04
58 92 0.89
59 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (58 bp):
CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
Found at i:31193850 original size:29 final size:29
Alignment explanation
Indices: 31193763--31193952 Score: 172
Period size: 29 Copynumber: 6.6 Consensus size: 29
31193753 CTACTCGATT
*
31193763 TCGCACACTTAGTGCCACGTA-ATTT-AAGC
1 TCGCACACTTAGTGCCA--TATATTTCCAGC
* * ***
31193792 CCGCACACATAGTGCCATA-CCCTCCGAGC
1 TCGCACACTTAGTGCCATATATTTCC-AGC
** *
31193821 TCGCACACCCAGTGCCATATTTTTCCAGC
1 TCGCACACTTAGTGCCATATATTTCCAGC
* * * *
31193850 TTGCACACATAGTGTCATATTTTTCCAGC
1 TCGCACACTTAGTGCCATATATTTCCAGC
*
31193879 AT-GCACACTTAGTGCCTTATATTTCCAGC
1 -TCGCACACTTAGTGCCATATATTTCCAGC
*
31193908 ACGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATATATTTCCAGC
*
31193937 ACGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
31193953 GATCTCGTCA
Statistics
Matches: 134, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
27 3 0.02
29 127 0.95
30 4 0.03
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.27
Consensus pattern (29 bp):
TCGCACACTTAGTGCCATATATTTCCAGC
Found at i:31203303 original size:43 final size:42
Alignment explanation
Indices: 31203256--31203395 Score: 115
Period size: 43 Copynumber: 3.3 Consensus size: 42
31203246 TCCCGGACGT
* * **
31203256 GGTCTTACATGTAATCAAATATCGATGCCTCTGTCCCAAACAG
1 GGTCTTACACGAAATCAAATA-CGATGCCGATGTCCCAAACAG
* * *
31203299 GGTCTTACACGAAATCAGATACGATGTCGATGTCCCAAACAT
1 GGTCTTACACGAAATCAAATACGATGCCGATGTCCCAAACAG
* * * *
31203341 GGTCTTATACGTAAAT-ATCAAT-CGAGGCCTG-TGTCCCACACAC
1 GGTCTTACACG-AAATCA--AATACGATGCC-GATGTCCCAAACAG
31203384 GGTCTTACACGA
1 GGTCTTACACGA
31203396 TGTCTCAGAC
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
42 29 0.37
43 47 0.59
44 3 0.04
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACGATGCCGATGTCCCAAACAG
Found at i:31204858 original size:20 final size:20
Alignment explanation
Indices: 31204835--31204884 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
31204825 TTAAATTCGA
31204835 AAAGATGAATACAA-ATAAAT
1 AAAGATGAATA-AAGATAAAT
31204855 AAAGAT-AATTAAAGATAAAT
1 AAAGATGAA-TAAAGATAAAT
31204875 AAAGATGAAT
1 AAAGATGAAT
31204885 GTTAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 4 0.15
20 21 0.78
21 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.22
Consensus pattern (20 bp):
AAAGATGAATAAAGATAAAT
Found at i:31204862 original size:10 final size:10
Alignment explanation
Indices: 31204835--31204880 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
31204825 TTAAATTCGA
*
31204835 AAAGATGAAT
1 AAAGATAAAT
31204845 ACAA-ATAAAT
1 A-AAGATAAAT
*
31204855 AAAGATAATT
1 AAAGATAAAT
31204865 AAAGATAAAT
1 AAAGATAAAT
31204875 AAAGAT
1 AAAGAT
31204881 GAATGTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 2 0.06
10 27 0.87
11 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:31204898 original size:6 final size:6
Alignment explanation
Indices: 31204887--31204915 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31204877 AGATGAATGT
31204887 TAAATC TAAATC TAAATC TAAATC TAAAT
1 TAAATC TAAATC TAAATC TAAATC TAAAT
31204916 AATAATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
TAAATC
Found at i:31206307 original size:7 final size:7
Alignment explanation
Indices: 31206295--31206335 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
31206285 AATTTATACC
31206295 AAAAGCG
1 AAAAGCG
31206302 AAAAGCG
1 AAAAGCG
31206309 AAAAGCG
1 AAAAGCG
31206316 AAAAGCG
1 AAAAGCG
31206323 AAAAGCG
1 AAAAGCG
31206330 AAAAGC
1 AAAAGC
31206336 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.15, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAAGCG
Found at i:31209660 original size:3 final size:3
Alignment explanation
Indices: 31209647--31209694 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
31209637 CTTTCGTAGC
*
31209647 ATT ATTT ATT ATT A-T ATT AATT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
31209693 AT
1 AT
31209695 ATATATACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:31209736 original size:25 final size:24
Alignment explanation
Indices: 31209680--31209747 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
31209670 TTATTATTAT
*
31209680 TATTATTATTATTATATATATACATG
1 TATT-TTATTATTAT-TATATACATA
**
31209706 CCTTTTATTATTATTCATATACATA
1 TATTTTATTATTATT-ATATACATA
*
31209731 TATTTTAAATATTATTA
1 TATTTT-ATTATTATTA
31209748 CCATTATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 1 0.03
25 23 0.68
26 10 0.29
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (24 bp):
TATTTTATTATTATTATATACATA
Found at i:31209875 original size:25 final size:23
Alignment explanation
Indices: 31209847--31209892 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
31209837 TGTATAGTAT
*
31209847 TATTTTAATTACTTATTTACTATCA
1 TATTATAATTACTT-TTT-CTATCA
*
31209872 TATTATATTTACTTTTTCTAT
1 TATTATAATTACTTTTTCTAT
31209893 TTTAACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 3 0.16
25 12 0.63
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATAATTACTTTTTCTATCA
Found at i:31210125 original size:2 final size:2
Alignment explanation
Indices: 31210118--31210153 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
31210108 TCACTAACGC
31210118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
31210154 ATTTTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31222526 original size:42 final size:43
Alignment explanation
Indices: 31222479--31222713 Score: 223
Period size: 42 Copynumber: 5.4 Consensus size: 43
31222469 ATGATGGGCT
31222479 TTAACCCCCTAAGCAGTAGGGT-ACAAGCCAA-ATTTACAAGCC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAGATTTAC-AGCC
* * *
31222521 TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGC-CAAGATTTACAG-CC
* * * ** *
31222566 TTAACCCCTCTAAGCAGTAGGGAAAC-AGATCAAGATAT-GGGCT
1 TTAACCCC-CTAAGCAGTAGGGTAACAAG-CCAAGATTTACAGCC
*
31222609 TTAACCCCCTAAGCAGTA-GGTAACAAGCTAA-ATTTACAAGCC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAGATTTAC-AGCC
* * * *
31222651 TTAA-ACCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGC-CAAGATTTACAG-CC
31222695 TTAACCCCCTAAGCAGTAG
1 TTAACCCCCTAAGCAGTAG
31222714 TGGAGCAGAT
Statistics
Matches: 155, Mismatches: 24, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
40 3 0.02
41 19 0.12
42 49 0.32
43 17 0.11
44 16 0.10
45 35 0.23
46 16 0.10
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (43 bp):
TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAGATTTACAGCC
Found at i:31222695 original size:129 final size:131
Alignment explanation
Indices: 31222349--31222762 Score: 516
Period size: 129 Copynumber: 3.2 Consensus size: 131
31222339 CAAACACCAA
* * * *
31222349 GCTTTAACCCCCTAAGCAGTAGGGTAACAAGCT-GATGTTCATAAGATCTTAAACCCCTAAGAAG
1 GCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTAAAT-TT-ACAAG-CCTTAAA-CCCTAAGCAG
* * * *
31222413 TAGGGTAACA-GC--AA-A-TTGCAGATCTTAATCCCC-AAGTAGTA-GGAAATAGATCGAAGAT
62 TAGGGTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGAT
31222471 GATGG
127 GATGG
* *
31222476 GCTTTAACCCCCTAAGCAGTAGGGT-ACAAGCCAAATTTACAAGCCTTAACCCCCTAAGCAGTAG
1 GCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTAAATTTACAAGCCTTAA-ACCCTAAGCAGTAG
31222540 GGTAACAGGCTGAAGATTTACAGATCTTAACCCCTCTAAGCAGTAGGGAAACAGATC-AAGAT-A
65 GGTAACAGGCTGAAGATTTACAGATCTTAACCCC-CTAAGCAGTAGGGAAACAGATCGAAGATGA
31222603 TGG
129 TGG
31222606 GCTTTAACCCCCTAAGCAGTA-GGTAACAAGCTAAATTTACAAGCCTTAAACCCTAAGCAGTAGG
1 GCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTAAATTTACAAGCCTTAAACCCTAAGCAGTAGG
* * *
31222670 GTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAGTGG-AGCAGATCGAAGACGAA
66 GTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAG-GGAAACAGATCGAAGATGAT
*
31222734 GA
130 GG
* *
31222736 ACCTTAA--CCCTAAGCAGTAGGGTAACA
1 GCTTTAACCCCCTAAGCAGTAGGGTAACA
31222763 GGTTGAATTG
Statistics
Matches: 254, Mismatches: 18, Indels: 28
0.85 0.06 0.09
Matches are distributed among these distances:
124 24 0.09
125 6 0.02
126 8 0.03
127 29 0.11
128 31 0.12
129 78 0.31
130 56 0.22
131 12 0.05
132 10 0.04
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (131 bp):
GCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTAAATTTACAAGCCTTAAACCCTAAGCAGTAGG
GTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATG
G
Found at i:31222799 original size:84 final size:86
Alignment explanation
Indices: 31222649--31222881 Score: 343
Period size: 84 Copynumber: 2.7 Consensus size: 86
31222639 AATTTACAAG
*
31222649 CCTTAAACCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAG
1 CCTTAAACCCTAAGCAGTAGGGTAACAGGTTG-AGATTTACAGATCTTAACCCCCTAAGCAGTAG
31222714 TGGAGCAGATCGAAGACGAAGAA
65 TGGAGCAGA-CGAAGACGAAGAA
* * *
31222737 CCTT-AACCCTAAGCAGTAGGGTAACAGGTTGA-A-TTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CCTTAAACCCTAAGCAGTAGGGTAACAGGTTGAGATTTACAGATCTTAACCCCCTAAGCAGTAGT
31222799 GGAGCAGACGAAGACGAAGAA
66 GGAGCAGACGAAGACGAAGAA
**
31222820 CCTTAAACCCCTAAGCAGTA-GGTAACAGGTTGAG-TTTACAGATC-TAAAACCCTAAGCAGTAG
1 CCTTAAA-CCCTAAGCAGTAGGGTAACAGGTTGAGATTTACAGATCTTAACCCCCTAAGCAGTAG
31222882 GGAAATAGAT
Statistics
Matches: 133, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
83 17 0.13
84 64 0.48
85 21 0.16
86 1 0.01
87 26 0.20
88 4 0.03
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (86 bp):
CCTTAAACCCTAAGCAGTAGGGTAACAGGTTGAGATTTACAGATCTTAACCCCCTAAGCAGTAGT
GGAGCAGACGAAGACGAAGAA
Found at i:31230454 original size:20 final size:20
Alignment explanation
Indices: 31230396--31230441 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
31230386 TGGTCCATAA
*
31230396 GCCCATTGGGCCCAGTTTTG
1 GCCCATTGGGCCCAATTTTG
31230416 GCCCATTGGGCCCAATTTTG
1 GCCCATTGGGCCCAATTTTG
31230436 GCCCAT
1 GCCCAT
31230442 CTGGCCCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.33, G:0.26, T:0.28
Consensus pattern (20 bp):
GCCCATTGGGCCCAATTTTG
Found at i:31237610 original size:28 final size:28
Alignment explanation
Indices: 31237545--31237645 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
31237535 ATAGTGAATC
*
31237545 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
31237574 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
31237602 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
31237632 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31237646 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:31239559 original size:31 final size:30
Alignment explanation
Indices: 31239523--31239623 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 30
31239513 TAATCACATT
31239523 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATATTATCTA-ATA
** *
31239554 AATATTAAATTTAATTTAATATCT-TATAAT-
1 AATATTAAA-TTAATAAAATAT-TATCTAATA
*
31239584 AATATTAAATTAATAAAATACTATCTATATA
1 AATATTAAATTAATAAAATATTATCTA-ATA
31239615 AATATTAAA
1 AATATTAAA
31239624 GTAAAGTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
28 1 0.02
29 12 0.21
30 11 0.19
31 20 0.34
32 13 0.22
33 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (30 bp):
AATATTAAATTAATAAAATATTATCTAATA
Found at i:31239592 original size:61 final size:61
Alignment explanation
Indices: 31239522--31239648 Score: 191
Period size: 61 Copynumber: 2.1 Consensus size: 61
31239512 TTAATCACAT
* * * * *
31239522 TAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTTAATTTAATATCTTATAA
1 TAATATTAAATTAATAAAATACTATCTAGATAAATATTAAAGTAAAGTTAATATCTCATAA
* *
31239583 TAATATTAAATTAATAAAATACTATCTATATAAATATTAAAGTAAAGTTAATATCTCATAT
1 TAATATTAAATTAATAAAATACTATCTAGATAAATATTAAAGTAAAGTTAATATCTCATAA
31239644 TAATA
1 TAATA
31239649 AATAGATAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (61 bp):
TAATATTAAATTAATAAAATACTATCTAGATAAATATTAAAGTAAAGTTAATATCTCATAA
Found at i:31239690 original size:15 final size:16
Alignment explanation
Indices: 31239657--31239690 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
31239647 TAAATAGATA
31239657 AATATTAAATTAGCTTT
1 AATATTAAATTA-CTTT
31239674 AATATTAAATT-CTTT
1 AATATTAAATTACTTT
31239689 AA
1 AA
31239691 AACAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
17 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
AATATTAAATTACTTT
Found at i:31240025 original size:22 final size:21
Alignment explanation
Indices: 31239986--31240026 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
31239976 ACTAGACACA
31239986 AGGGGCACACACCCGTGTGGG
1 AGGGGCACACACCCGTGTGGG
31240007 AGGGGCA-ACACGCCTGTGTG
1 AGGGGCACACAC-CC-GTGTG
31240027 ACCAATCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.20, C:0.27, G:0.41, T:0.12
Consensus pattern (21 bp):
AGGGGCACACACCCGTGTGGG
Found at i:31254048 original size:46 final size:46
Alignment explanation
Indices: 31253995--31254170 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
31253985 TATTTGGGCA
31253995 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
31254041 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
31254088 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
31254134 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31254171 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:31254150 original size:93 final size:93
Alignment explanation
Indices: 31253991--31254162 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
31253981 GGGATATTTG
* *
31253991 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31254056 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
31254084 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31254149 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
31254163 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:31257173 original size:6 final size:6
Alignment explanation
Indices: 31257154--31257197 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
31257144 GTAATAATAA
31257154 TTATATT TTA-TT TTATTT TTATTT TTATTT TTATTT TTATTT TT
1 TTAT-TT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TT
31257198 GAAATAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.14
6 28 0.78
7 3 0.08
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTATTT
Found at i:31257268 original size:49 final size:49
Alignment explanation
Indices: 31257204--31257302 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
31257194 TTTTGAAATA
31257204 ATTATAATAATTTTTATTTTTATTTGCATCTGAATTGTTTTATGGGAAT
1 ATTATAATAATTTTTATTTTTATTTGCATCTGAATTGTTTTATGGGAAT
31257253 ATTATAATAATTTTTATTTTTATTTGCATCTGAATTGTTTTATGGGAAT
1 ATTATAATAATTTTTATTTTTATTTGCATCTGAATTGTTTTATGGGAAT
31257302 A
1 A
31257303 ACATAACTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (49 bp):
ATTATAATAATTTTTATTTTTATTTGCATCTGAATTGTTTTATGGGAAT
Found at i:31261110 original size:47 final size:47
Alignment explanation
Indices: 31261041--31261134 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
31261031 ATTCTCACAC
31261041 TAAGAAAAAAAAAGTCTAAGACGGCGGATTCTACGATTGATCCTGTT
1 TAAGAAAAAAAAAGTCTAAGACGGCGGATTCTACGATTGATCCTGTT
31261088 TAAGAAAAAAAAAGTCTAAGACGGCGGATTCTACGATTGATCCTGTT
1 TAAGAAAAAAAAAGTCTAAGACGGCGGATTCTACGATTGATCCTGTT
31261135 GAAACATCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (47 bp):
TAAGAAAAAAAAAGTCTAAGACGGCGGATTCTACGATTGATCCTGTT
Found at i:31261274 original size:66 final size:65
Alignment explanation
Indices: 31261164--31261290 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 65
31261154 AAGCTCTTAC
* * *
31261164 TGGAGTTCATCATATTTCTTGTTGCCTTTGCTTCCCTCGCTGCTGCCT-TCGCTTTAAGTTGGAG
1 TGGAGTTCATCATATTTCTTGTAGCCTCTGCTTCCCTCGATGCTGCCTCT-GCTTTAAGTTGGAG
31261228 T
65 T
* *
31261229 TGGAGTTCATCATATTTTCTT-TGAGCCTCTGCTTCTCTCGATGCTGCCTCTGCTTTGAGTTG
1 TGGAGTTCATCATA-TTTCTTGT-AGCCTCTGCTTCCCTCGATGCTGCCTCTGCTTTAAGTTG
31261291 AGCAATTTGC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
65 15 0.28
66 38 0.70
67 1 0.02
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.43
Consensus pattern (65 bp):
TGGAGTTCATCATATTTCTTGTAGCCTCTGCTTCCCTCGATGCTGCCTCTGCTTTAAGTTGGAGT
Found at i:31264105 original size:37 final size:37
Alignment explanation
Indices: 31264053--31264228 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
31264043 GAATAATCCT
* *
31264053 CACACGTAGTTATCGGGTCTTACCCAGACAAAATCTC
1 CACACGTAGTCATCGGGTCTTACCCGGACAAAATCTC
31264090 CACACGTAGTCATCGGGTCTTACCCGGACAAAATCTC
1 CACACGTAGTCATCGGGTCTTACCCGGACAAAATCTC
* *
31264127 CACACATAGTCATCGGGTCTTACCCGGACATAATCTC
1 CACACGTAGTCATCGGGTCTTACCCGGACAAAATCTC
* *
31264164 CACACGTAGTCATCGGGTCTTACCCGGACATAATCTT
1 CACACGTAGTCATCGGGTCTTACCCGGACAAAATCTC
31264201 CACACGTAGTCATCGGGTCTTACCCGGA
1 CACACGTAGTCATCGGGTCTTACCCGGA
31264229 ATATATTTCC
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 133 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
CACACGTAGTCATCGGGTCTTACCCGGACAAAATCTC
Found at i:31264421 original size:48 final size:48
Alignment explanation
Indices: 31264361--31264756 Score: 621
Period size: 48 Copynumber: 8.2 Consensus size: 48
31264351 CGGCCACAAT
*
31264361 ATATACACATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* *
31264409 ATATACATATCTCATACATATTTCTCATTAGCCATTCGGATTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* **
31264457 ATATATATATATCTCATACATATTTCATGTTAGCCATTCGGCTTTACCAC
1 --ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* *
31264507 ATATACATATCTCATACATAGTTCACATTAGCTATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* *
31264555 ATATATATATCTCATACATATTTCATATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
*
31264603 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* *
31264651 ATATATATATCTCATACATATTTCATATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* *
31264699 ATATACATATCTCATACATATTTCACACTAGCCATTCGTCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* *
31264747 ACATATATAT
1 ATATACATAT
31264757 TTATCTTGTA
Statistics
Matches: 317, Mismatches: 29, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
48 274 0.86
50 43 0.14
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (48 bp):
ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
Found at i:31265955 original size:2 final size:2
Alignment explanation
Indices: 31265918--31265946 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31265908 TACATAAGGC
31265918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31265947 CCTATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31269739 original size:15 final size:15
Alignment explanation
Indices: 31269716--31269754 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
31269706 CTTGGCTTGC
*
31269716 ATTTTGAAATGCAAA
1 ATTTAGAAATGCAAA
31269731 ATTTAGAAATGCAAA
1 ATTTAGAAATGCAAA
31269746 ATTTAGAAA
1 ATTTAGAAA
31269755 AGTTTGTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (15 bp):
ATTTAGAAATGCAAA
Found at i:31270189 original size:35 final size:35
Alignment explanation
Indices: 31270145--31270211 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
31270135 TTTTTATATT
31270145 CTTTAAATGTTTATGAAAGTTATGATAATCATAAA
1 CTTTAAATGTTTATGAAAGTTATGATAATCATAAA
* *
31270180 CTTTAAATGTTTATGTAAGTTATGATTATCAT
1 CTTTAAATGTTTATGAAAGTTATGATAATCAT
31270212 CTTTAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (35 bp):
CTTTAAATGTTTATGAAAGTTATGATAATCATAAA
Found at i:31270522 original size:16 final size:15
Alignment explanation
Indices: 31270501--31270534 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
31270491 TTTTTCTCGA
31270501 TTTTATTTTGCTATTT
1 TTTTATTTT-CTATTT
*
31270517 TTTTATTTTTTATTT
1 TTTTATTTTCTATTT
31270532 TTT
1 TTT
31270535 AAGAATGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTATTTTCTATTT
Found at i:31270739 original size:13 final size:13
Alignment explanation
Indices: 31270721--31270748 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31270711 ATTATAAAAG
31270721 TTAGTTACAAATA
1 TTAGTTACAAATA
31270734 TTAGTTACAAATA
1 TTAGTTACAAATA
31270747 TT
1 TT
31270749 TTGTCAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (13 bp):
TTAGTTACAAATA
Found at i:31273794 original size:20 final size:20
Alignment explanation
Indices: 31273769--31273845 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
31273759 GCAGCAGACG
31273769 TTGGGGAAAAACTAAGGGAT
1 TTGGGGAAAAACTAAGGGAT
**
31273789 TTGGGG---AA-T--TTGAT
1 TTGGGGAAAAACTAAGGGAT
31273803 TTGGGGAAAAAACTAAGGGAT
1 TTGGGG-AAAAACTAAGGGAT
* *
31273824 TTGGAGAAAAAATAAGGGAT
1 TTGGGGAAAAACTAAGGGAT
31273844 TT
1 TT
31273846 TAAGAAACTG
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.20
16 1 0.02
17 2 0.05
18 2 0.05
19 1 0.02
20 21 0.48
21 8 0.18
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (20 bp):
TTGGGGAAAAACTAAGGGAT
Found at i:31273824 original size:21 final size:20
Alignment explanation
Indices: 31273800--31273845 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
31273790 TGGGGAATTT
*
31273800 GATTTGGGGAAAAAACTAAGG
1 GATTTGGAGAAAAAA-TAAGG
31273821 GATTTGGAGAAAAAATAAGG
1 GATTTGGAGAAAAAATAAGG
31273841 GATTT
1 GATTT
31273846 TAAGAAACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.43, C:0.02, G:0.30, T:0.24
Consensus pattern (20 bp):
GATTTGGAGAAAAAATAAGG
Found at i:31273851 original size:20 final size:21
Alignment explanation
Indices: 31273808--31273852 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
31273798 TTGATTTGGG
*
31273808 GAAAAAACTAAGGGATTTGGA
1 GAAAAAACTAAGGGATTTGAA
*
31273829 GAAAAAA-TAAGGGATTTTAA
1 GAAAAAACTAAGGGATTTGAA
31273849 GAAA
1 GAAA
31273853 CTGAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.53, C:0.02, G:0.24, T:0.20
Consensus pattern (21 bp):
GAAAAAACTAAGGGATTTGAA
Found at i:31273990 original size:40 final size:41
Alignment explanation
Indices: 31273919--31274021 Score: 129
Period size: 40 Copynumber: 2.5 Consensus size: 41
31273909 AGTCGCGACA
*
31273919 TTTATGAGAAAAACGCCGTTATTGCTTTATCTTTAGCAGCG
1 TTTATGAGAAAAACGCCGCTATTGCTTTATCTTTAGCAGCG
* * * *
31273960 TTTATGAGAAAATA-G-CGCTATTGTTTTATCTTTTGTAGTG
1 TTTATGAGAAAA-ACGCCGCTATTGCTTTATCTTTAGCAGCG
*
31274000 TTTATGAGAAAAACGCCACTAT
1 TTTATGAGAAAAACGCCGCTAT
31274022 ATTTTTAACC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 1 0.02
40 33 0.62
41 18 0.34
42 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (41 bp):
TTTATGAGAAAAACGCCGCTATTGCTTTATCTTTAGCAGCG
Found at i:31278836 original size:12 final size:12
Alignment explanation
Indices: 31278821--31278861 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
31278811 TTTTTAGAGG
31278821 TTTTTTCTTTTC
1 TTTTTTCTTTTC
31278833 TTTTTTCTTTTC
1 TTTTTTCTTTTC
*
31278845 TTATTTTGTTTTC
1 TT-TTTTCTTTTC
31278858 TTTT
1 TTTT
31278862 ATCCTTAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:31279079 original size:31 final size:31
Alignment explanation
Indices: 31279020--31279081 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
31279010 AATACAAAGA
*
31279020 ATTCTTTCAATACTCAAATACATTTCATTCT
1 ATTCTTTCAATACTCAAATACATCTCATTCT
*
31279051 ATTCTTTCAATACTC-AGTACAGTCTCATTCT
1 ATTCTTTCAATACTCAAATACA-TCTCATTCT
31279082 TTCAGTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTCTTTCAATACTCAAATACATCTCATTCT
Found at i:31284192 original size:26 final size:26
Alignment explanation
Indices: 31284117--31284194 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 26
31284107 AATACAAAGA
*
31284117 ATTCTTTCAATACTCAATACATTTTC
1 ATTCTTTCAATACTCAATACAGTTTC
31284143 ATTCTATTATTTCAATACTCAATACAGTTTC
1 ATTC-----TTTCAATACTCAATACAGTTTC
31284174 ATTCTTTCAATACAT-AATACA
1 ATTCTTTCAATAC-TCAATACA
31284195 TTAACAACTC
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
26 19 0.42
27 1 0.02
31 25 0.56
ACGTcount: A:0.35, C:0.21, G:0.01, T:0.44
Consensus pattern (26 bp):
ATTCTTTCAATACTCAATACAGTTTC
Found at i:31297976 original size:13 final size:13
Alignment explanation
Indices: 31297958--31298010 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
31297948 GTTCGGCAGG
31297958 GACACGCCCGTGT
1 GACACGCCCGTGT
*
31297971 GACACGCCCATGT
1 GACACGCCCGTGT
*
31297984 GACACGCCTGTGT
1 GACACGCCCGTGT
*
31297997 GACACGCTCGTGT
1 GACACGCCCGTGT
31298010 G
1 G
31298011 CGATTACTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.17, C:0.34, G:0.30, T:0.19
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:31308448 original size:48 final size:48
Alignment explanation
Indices: 31308314--31308440 Score: 166
Period size: 48 Copynumber: 2.6 Consensus size: 48
31308304 CTGGGCTATC
*
31308314 GGCATCAATATCTGATCCCATGTAAGACCATGTCTGGGACAAAGCATT
1 GGCATCAATATATGATCCCATGTAAGACCATGTCTGGGACAAAGCATT
** * ** * *
31308362 GGCATTGATCTACAATCCCACGTAAGACCATGTCTGGGA-AATGGCATT
1 GGCATCAATATATGATCCCATGTAAGACCATGTCTGGGACAA-AGCATT
31308410 GGCATCAATATATGATCCCATGTAAGACCAT
1 GGCATCAATATATGATCCCATGTAAGACCAT
31308441 ATTTGGGATA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
47 2 0.03
48 62 0.97
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (48 bp):
GGCATCAATATATGATCCCATGTAAGACCATGTCTGGGACAAAGCATT
Found at i:31308463 original size:48 final size:47
Alignment explanation
Indices: 31308314--31308463 Score: 149
Period size: 48 Copynumber: 3.1 Consensus size: 47
31308304 CTGGGCTATC
*
31308314 GGCATCAATATCTGATCCCATGTAAGACCATGTCTGGGACAA-AGCATT
1 GGCATCAATATATGATCCCATGTAAGACCATGTCTGGGA-AAGA-CATT
** * ** * *
31308362 GGCATTGATCTACAATCCCACGTAAGACCATGTCTGGGAAATGGCATT
1 GGCATCAATATATGATCCCATGTAAGACCATGTCTGGGAAA-GACATT
* * *
31308410 GGCATCAATATATGATCCCATGTAAGACCATATTTGGGATACGACATT
1 GGCATCAATATATGATCCCATGTAAGACCATGTCTGGGA-AAGACATT
*
31308458 AGCATC
1 GGCATC
31308464 CTACCATGTG
Statistics
Matches: 80, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
47 2 0.03
48 77 0.96
49 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (47 bp):
GGCATCAATATATGATCCCATGTAAGACCATGTCTGGGAAAGACATT
Found at i:31309575 original size:38 final size:38
Alignment explanation
Indices: 31309512--31309673 Score: 191
Period size: 38 Copynumber: 4.2 Consensus size: 38
31309502 CAGCATAAAA
* * * * *
31309512 CCTGCGGGACTTTAAGCTCAGATATAATACCGGCACTAGG
1 CCTGCGGGA-TTTAA-CCCGGATATAATACCAGCACGAAG
*
31309552 CCTGCGAGATTTAACCCGGATATAATACCAGCACGAAG
1 CCTGCGGGATTTAACCCGGATATAATACCAGCACGAAG
* * *
31309590 CTTGCGGGATTTAACCCGGATATATTACCAGCGCGAAG
1 CCTGCGGGATTTAACCCGGATATAATACCAGCACGAAG
* *
31309628 CCTGCGGGATTTAACCCGGATATAATTCCAGCA-TATAG
1 CCTGCGGGATTTAACCCGGATATAATACCAGCACGA-AG
31309666 CCTGCGGG
1 CCTGCGGG
31309674 TCTTTAAGCC
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
37 1 0.01
38 92 0.87
39 5 0.05
40 8 0.08
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (38 bp):
CCTGCGGGATTTAACCCGGATATAATACCAGCACGAAG
Found at i:31309672 original size:76 final size:77
Alignment explanation
Indices: 31309500--31309683 Score: 210
Period size: 76 Copynumber: 2.4 Consensus size: 77
31309490 AAATCCAGTC
* * * * *
31309500 ACCAGCATAAAACCTGCGGGACTTTAAGCTCAGATATAATACCGGCACTAGGCCTGCGAGATTTA
1 ACCAGCAT-AAGCCTGCGGGACTTTAAGCCCAGATATAATACCAGCACGAAGCCTGCGAGATTTA
31309565 ACCCGGATATAAT
65 ACCCGGATATAAT
* * * * * *
31309578 ACCAGCACGAAGCTTGCGGGA-TTTAA-CCCGGATATATTACCAGCGCGAAGCCTGCGGGATTTA
1 ACCAGCA-TAAGCCTGCGGGACTTTAAGCCCAGATATAATACCAGCACGAAGCCTGCGAGATTTA
31309641 ACCCGGATATAAT
65 ACCCGGATATAAT
* *
31309654 TCCAGCATATAGCCTGCGGGTCTTTAAGCC
1 ACCAGCATA-AGCCTGCGGGACTTTAAGCC
31309684 TGGATACACA
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
75 1 0.01
76 57 0.66
77 10 0.11
78 19 0.22
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (77 bp):
ACCAGCATAAGCCTGCGGGACTTTAAGCCCAGATATAATACCAGCACGAAGCCTGCGAGATTTAA
CCCGGATATAAT
Found at i:31315186 original size:46 final size:46
Alignment explanation
Indices: 31315038--31315256 Score: 252
Period size: 46 Copynumber: 4.7 Consensus size: 46
31315028 GGGTGTAATA
31315038 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCGTA-
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGC-TT-ACATAT-CGTAG
* *
31315088 CCGATGCATGTTCCAGACATGTCTTACACTAGC--ACATCTCGTAG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATATCGTAG
* *
31315132 CCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCG-AGG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATATCGTA-G
* * *
31315178 CCGATGCATATCCCAGACATGTCTTACACTGGCTCT-CATAAT-GTGG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCT-TACAT-ATCGTAG
*
31315224 CCGATGCATGTCCTAGACATGTCTTACACTAGC
1 CCGATGCATGTCCCAGACATGTCTTACACTAGC
31315257 ACACACACAT
Statistics
Matches: 152, Mismatches: 10, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
43 4 0.03
44 36 0.24
45 1 0.01
46 77 0.51
47 2 0.01
48 13 0.09
49 13 0.09
50 6 0.04
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATATCGTAG
Found at i:31321502 original size:19 final size:20
Alignment explanation
Indices: 31321478--31321515 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
31321468 GGTACCACCA
31321478 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
31321497 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
31321516 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:31321856 original size:93 final size:93
Alignment explanation
Indices: 31321745--31321915 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
31321735 GCCCCTAAGT
* *
31321745 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
31321810 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
31321838 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
31321903 CGAGTTCGGATGC
66 CGAGTTCGGATGC
31321916 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:31321912 original size:46 final size:46
Alignment explanation
Indices: 31321740--31321912 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
31321730 AACCCGCCCC
* * * * *
31321740 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
31321786 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
31321834 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
31321879 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
31321913 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:31322369 original size:31 final size:30
Alignment explanation
Indices: 31322334--31322394 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
31322324 ATTTAATACG
31322334 AACTTTAAAAAAAATTACACTTTTGCCCCTA
1 AACTTT-AAAAAAATTACACTTTTGCCCCTA
*** *
31322365 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
31322395 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:31335043 original size:40 final size:39
Alignment explanation
Indices: 31334878--31335061 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
31334868 AAATTGAATG
* * *
31334878 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
31334918 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
31334958 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
31334998 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
31335037 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
31335062 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:31335086 original size:80 final size:81
Alignment explanation
Indices: 31334918--31335106 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
31334908 GCTGGAAATT
* * * *
31334918 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
31334983 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
31334999 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
31335062 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
31335078 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
31335107 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:31343160 original size:40 final size:39
Alignment explanation
Indices: 31342995--31343178 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
31342985 AAATTGAATG
* * *
31342995 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
31343035 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
31343075 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
31343115 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
31343154 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
31343179 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:31343203 original size:80 final size:81
Alignment explanation
Indices: 31343035--31343223 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
31343025 GCTGGAAATT
* * * *
31343035 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
31343100 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
31343116 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
31343179 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
31343195 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
31343224 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:31345535 original size:5 final size:5
Alignment explanation
Indices: 31345525--31345555 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
31345515 TCGTGATTAA
31345525 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
31345556 GAGCACATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:31351187 original size:6 final size:6
Alignment explanation
Indices: 31351172--31351210 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
31351162 TAAGTAAAGG
31351172 AAAA-T AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
31351211 GCGACTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:31364786 original size:25 final size:28
Alignment explanation
Indices: 31364734--31364787 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
31364724 TTATCGTTAT
* *
31364734 TATGTGTTGAATGATCGATTTTGCATAA
1 TATGTGTTGAATGATCGATTATGAATAA
31364762 TATG-GTTGAAT-AT-GATTATGAATAA
1 TATGTGTTGAATGATCGATTATGAATAA
31364787 T
1 T
31364788 GCGTGATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.46
26 2 0.08
27 7 0.29
28 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (28 bp):
TATGTGTTGAATGATCGATTATGAATAA
Found at i:31364934 original size:48 final size:48
Alignment explanation
Indices: 31364876--31365147 Score: 268
Period size: 48 Copynumber: 5.7 Consensus size: 48
31364866 TATGTGCGCT
* * * * *
31364876 AGTGTAAGACCGTGTATGGGACACGGCATTGGCCATGATATGAGAGCC
1 AGTGTAAGACCATGTCTGGAACATGGCATCGGCCATGATATGAGAGCC
* * * * *
31364924 AATGTAAGACCATGTTTGGAACATGGCATCGG-CAAGGTAATAAGAGCC
1 AGTGTAAGACCATGTCTGGAACATGGCATCGGCCATGAT-ATGAGAGCC
* * * * *
31364972 AGTGTAAGACC-TTTCTGGAACATGGCATCGG-TATTGATATGTGTGCT
1 AGTGTAAGACCATGTCTGGAACATGGCATCGGCCA-TGATATGAGAGCC
* *
31365019 AGTGTAAGACCATGTCTAGG-ACATGGCACCGGCCA-CATTATGAGAGCC
1 AGTGTAAGACCATGTCT-GGAACATGGCATCGGCCATGA-TATGAGAGCC
* * *
31365067 AGTGTAAGACCATGTCTGGGACATGGCATCGGCC-TCGACATGTGAGCC
1 AGTGTAAGACCATGTCTGGAACATGGCATCGGCCAT-GATATGAGAGCC
*
31365115 AGTGTAAGACCATGTTTGGAACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGAACATGGCATCGGC
31365148 AATTCACCCT
Statistics
Matches: 183, Mismatches: 32, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
47 42 0.23
48 137 0.75
49 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGAACATGGCATCGGCCATGATATGAGAGCC
Found at i:31365121 original size:143 final size:144
Alignment explanation
Indices: 31364863--31365146 Score: 369
Period size: 143 Copynumber: 2.0 Consensus size: 144
31364853 GACATTTGGG
* * ** *
31364863 TGATATGTGCGCTAGTGTAAGACCGTGTATGGGACACGGCATTGGCCATGATATGAGAGCCAATG
1 TGATATGTGCGCTAGTGTAAGACCATGTATAGGACACGGCACCGGCCATCATATGAGAGCCAATG
* *
31364928 TAAGACCATGTTTGGAACATGGCATCGGCAAGGTAATAAGAGCCAGTGTAAGACC-T-TTCTGGA
66 TAAGACCATGTCTGGAACATGGCATCGGCAACGTAATAAGAGCCAGTGTAAGACCATGTT-TGGA
31364991 ACATGGCATCGGTAT
130 ACATGGCATCGGTAT
* * * *
31365006 TGATATGTGTGCTAGTGTAAGACCATGTCTAGGACATGGCACCGGCCA-CATTATGAGAGCCAGT
1 TGATATGTGCGCTAGTGTAAGACCATGTATAGGACACGGCACCGGCCATCA-TATGAGAGCCAAT
* ** **
31365070 GTAAGACCATGTCTGGGACATGGCATCGGCCTCG-ACATGTGAGCCAGTGTAAGACCATGTTTGG
65 GTAAGACCATGTCTGGAACATGGCATCGGCAACGTA-ATAAGAGCCAGTGTAAGACCATGTTTGG
31365134 AACATGGCATCGG
129 AACATGGCATCGG
31365147 CAATTCACCC
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
142 2 0.02
143 100 0.83
144 17 0.14
145 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (144 bp):
TGATATGTGCGCTAGTGTAAGACCATGTATAGGACACGGCACCGGCCATCATATGAGAGCCAATG
TAAGACCATGTCTGGAACATGGCATCGGCAACGTAATAAGAGCCAGTGTAAGACCATGTTTGGAA
CATGGCATCGGTAT
Found at i:31365912 original size:45 final size:45
Alignment explanation
Indices: 31365848--31365938 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
31365838 AAGTAAGGGT
* *
31365848 GGCAAAAAGGCTTGGTACATAGCCCTATTTTTGTCCACATGGGCA
1 GGCAAAAAGGCTTCGTACATAGCCCTATTTTTGTCCACATAGGCA
*
31365893 GGCAAAAAGGCTTCGTACATAGCCCTATTTTTTTCCACATAGGCA
1 GGCAAAAAGGCTTCGTACATAGCCCTATTTTTGTCCACATAGGCA
31365938 G
1 G
31365939 ACACACGGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (45 bp):
GGCAAAAAGGCTTCGTACATAGCCCTATTTTTGTCCACATAGGCA
Found at i:31369986 original size:20 final size:21
Alignment explanation
Indices: 31369969--31370016 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31369959 CCAGACATAG
31369969 CCGTGTGACTA-TCCACATGC
1 CCGTGTGACTACTCCACATGC
*
31369989 CCGTGTGACTACTCCACACGC
1 CCGTGTGACTACTCCACATGC
*
31370010 CCATGTG
1 CCGTGTG
31370017 CGCAAACCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.23
Consensus pattern (21 bp):
CCGTGTGACTACTCCACATGC
Found at i:31370614 original size:19 final size:21
Alignment explanation
Indices: 31370592--31370632 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
31370582 CATACTAGTC
31370592 AAACATA-TCAA-CCATATAT
1 AAACATACTCAAGCCATATAT
31370611 AAACATACCTCAAGCCATATAT
1 AAACATA-CTCAAGCCATATAT
31370633 TACAAAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
AAACATACTCAAGCCATATAT
Found at i:31386050 original size:39 final size:39
Alignment explanation
Indices: 31386004--31386143 Score: 226
Period size: 39 Copynumber: 3.6 Consensus size: 39
31385994 AGACTAAGAT
*
31386004 CCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGTTAAGC
1 CCGAAGGCATTCGTGCGAGTTAATAAATCCGGGTTAAGC
*
31386043 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGC
1 CCGAAGGCATTCGTGCGAGTTAATAAATCCGGGTTAAGC
* * *
31386082 CCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTAATAAATCCGGGTTAAG-C
31386122 CCGAAGGCATTCGTGCGAGTTA
1 CCGAAGGCATTCGTGCGAGTTA
31386144 CTATAACCGG
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 73 0.77
40 22 0.23
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTAATAAATCCGGGTTAAGC
Found at i:31386138 original size:40 final size:39
Alignment explanation
Indices: 31386004--31386172 Score: 223
Period size: 39 Copynumber: 4.3 Consensus size: 39
31385994 AGACTAAGAT
* *
31386004 CCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGTTAAGC
1 CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGTTAAGC
* *
31386043 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGC
1 CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGTTAAGC
* *
31386082 CCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGTTAAG-C
* * *
31386122 CCGAAGGCATTCGTGCGAGTTACTATAACCGGGGTT-TGTC
1 CCGAAGGCATTCGTGCGAGTTAATA-AACCCGGGTTAAG-C
31386162 CCGAAGGCATT
1 CCGAAGGCATT
31386173 TGAGCTAGTC
Statistics
Matches: 121, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
39 73 0.60
40 39 0.32
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGTTAAGC
Found at i:31390973 original size:6 final size:5
Alignment explanation
Indices: 31390944--31391034 Score: 82
Period size: 5 Copynumber: 17.8 Consensus size: 5
31390934 GATGTCTTTC
* *
31390944 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT CAAAAGA AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAA-T AAAAT
31390992 AAAAAT AAAAT AAAAT -AAAT AAAAT AAAAT AAAAT -AAAT AAAA
1 -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
31391035 ATAATGATTC
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
3 3 0.04
4 8 0.11
5 35 0.49
6 26 0.36
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:31391013 original size:14 final size:14
Alignment explanation
Indices: 31390994--31391034 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
31390984 AGAAAAATAA
31390994 AAATAAAATAAAAT
1 AAATAAAATAAAAT
31391008 AAATAAAATAAAAT
1 AAATAAAATAAAAT
31391022 AAA-ATAAATAAAA
1 AAATA-AAATAAAA
31391035 ATAATGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 1 0.04
14 25 0.96
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:31391015 original size:19 final size:19
Alignment explanation
Indices: 31390944--31391034 Score: 86
Period size: 19 Copynumber: 4.9 Consensus size: 19
31390934 GATGTCTTTC
31390944 AAAATAAAAT-AATAAAATT
1 AAAATAAAATAAATAAAA-T
*
31390963 GAAATGAAAAT--A-AAAAT
1 AAAAT-AAAATAAATAAAAT
* *
31390980 CAAA-AGAA-AAATAAAAAT
1 AAAATAAAATAAAT-AAAAT
31390998 AAAATAAAATAAATAAAAT
1 AAAATAAAATAAATAAAAT
31391017 AAAATAAAATAAATAAAA
1 AAAATAAAATAAATAAAA
31391035 ATAATGATTC
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.05
16 1 0.02
17 4 0.07
18 12 0.20
19 31 0.52
20 9 0.15
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (19 bp):
AAAATAAAATAAATAAAAT
Found at i:31391020 original size:24 final size:24
Alignment explanation
Indices: 31390944--31391033 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
31390934 GATGTCTTTC
*
31390944 AAAATAAAAT-AATAAAATTGAAAT
1 AAAATAAAATAAATAAAA-TAAAAT
*
31390968 GAAAATAAAAATCAAAAGAAAAATAAAAAT
1 -AAAAT-AAAAT--AAA-TAAAAT-AAAAT
31390998 AAAATAAAATAAATAAAATAAAAT
1 AAAATAAAATAAATAAAATAAAAT
31391022 AAAAT-AAATAAA
1 AAAATAAAATAAA
31391034 AATAATGATT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
23 7 0.12
24 10 0.18
25 10 0.18
26 8 0.14
28 5 0.09
29 8 0.14
30 8 0.14
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (24 bp):
AAAATAAAATAAATAAAATAAAAT
Found at i:31396335 original size:13 final size:13
Alignment explanation
Indices: 31396313--31396345 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
31396303 AAGGATTTGT
31396313 TTAT-TAAACTAA
1 TTATCTAAACTAA
31396325 TTATCTAAACTAA
1 TTATCTAAACTAA
*
31396338 TTAACTAA
1 TTATCTAA
31396346 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:31398973 original size:150 final size:150
Alignment explanation
Indices: 31398702--31399001 Score: 591
Period size: 150 Copynumber: 2.0 Consensus size: 150
31398692 ACAGCTTCAT
*
31398702 CGTCACATACACTATTCGCCGTCTTGCTGTTGGACTGACCTTACGGCGAGCACGGTTCCCTACAA
1 CGTCACATACACTATTCGCCATCTTGCTGTTGGACTGACCTTACGGCGAGCACGGTTCCCTACAA
31398767 TGAAAGTCGCTCGAAGGCAACTTCTCTCCCTCTAGCACTATGCTACATTTCATGCCATCTTGGCT
66 TGAAAGTCGCTCGAAGGCAACTTCTCTCCCTCTAGCACTATGCTACATTTCATGCCATCTTGGCT
31398832 CATACTTTAACTGGAAGGAG
131 CATACTTTAACTGGAAGGAG
31398852 CGTCACATACACTATTCGCCATCTTGCTGTTGGACTGACCTTACGGCGAGCACGGTTCCCTACAA
1 CGTCACATACACTATTCGCCATCTTGCTGTTGGACTGACCTTACGGCGAGCACGGTTCCCTACAA
31398917 TGAAAGTCGCTCGAAGGCAACTTCTCTCCCTCTAGCACTATGCTACATTTCATGCCATCTTGGCT
66 TGAAAGTCGCTCGAAGGCAACTTCTCTCCCTCTAGCACTATGCTACATTTCATGCCATCTTGGCT
31398982 CATACTTTAACTGGAAGGAG
131 CATACTTTAACTGGAAGGAG
31399002 AGAGAGCACC
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (150 bp):
CGTCACATACACTATTCGCCATCTTGCTGTTGGACTGACCTTACGGCGAGCACGGTTCCCTACAA
TGAAAGTCGCTCGAAGGCAACTTCTCTCCCTCTAGCACTATGCTACATTTCATGCCATCTTGGCT
CATACTTTAACTGGAAGGAG
Found at i:31407429 original size:13 final size:12
Alignment explanation
Indices: 31407411--31407440 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
31407401 TGCTCGATTT
31407411 AAAAAAAAAAGA
1 AAAAAAAAAAGA
31407423 GAAAAAAAAAAGA
1 -AAAAAAAAAAGA
31407436 AAAAA
1 AAAAA
31407441 GAGCATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:31411383 original size:17 final size:17
Alignment explanation
Indices: 31411361--31411437 Score: 52
Period size: 17 Copynumber: 4.5 Consensus size: 17
31411351 GCAAGACTGT
31411361 GAGCTCACCAAATGCGC
1 GAGCTCACCAAATGCGC
*
31411378 GAGCTCTA-CAAA-GCTTC
1 GAGCTC-ACCAAATGC-GC
*
31411395 GAGCTCACCCAAAAT-TGC
1 GAGCTCA-CC-AAATGCGC
* * *
31411413 TAGCTCATCAAATGTGC
1 GAGCTCACCAAATGCGC
31411430 GAGCTCAC
1 GAGCTCAC
31411438 TAAGACTGCG
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
16 7 0.15
17 27 0.59
18 9 0.20
19 3 0.07
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.19
Consensus pattern (17 bp):
GAGCTCACCAAATGCGC
Found at i:31411864 original size:20 final size:20
Alignment explanation
Indices: 31411839--31411886 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
31411829 CCAAAAATGT
*
31411839 TTGAACTATATAGTCTAAAC
1 TTGAACCATATAGTCTAAAC
31411859 TTGAACCATATAGTCTAAAC
1 TTGAACCATATAGTCTAAAC
31411879 TTGAACCA
1 TTGAACCA
31411887 ACTTATGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (20 bp):
TTGAACCATATAGTCTAAAC
Found at i:31413220 original size:15 final size:15
Alignment explanation
Indices: 31413200--31413233 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
31413190 AGCTTGCATG
31413200 AGGAAAGACATAATA
1 AGGAAAGACATAATA
31413215 AGGAAAGACATAATA
1 AGGAAAGACATAATA
31413230 AGGA
1 AGGA
31413234 GAGTGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.24, T:0.12
Consensus pattern (15 bp):
AGGAAAGACATAATA
Found at i:31413525 original size:31 final size:31
Alignment explanation
Indices: 31413489--31413551 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
31413479 TTAGTACTTG
*
31413489 AACTTGATACTTTTTCTTAAATTGACACCTA
1 AACTTGACACTTTTTCTTAAATTGACACCTA
* *
31413520 AACTTGACACTTTTTCTTAATTTGGCACCTA
1 AACTTGACACTTTTTCTTAAATTGACACCTA
31413551 A
1 A
31413552 TCTTTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (31 bp):
AACTTGACACTTTTTCTTAAATTGACACCTA
Found at i:31425860 original size:29 final size:29
Alignment explanation
Indices: 31425810--31425885 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
31425800 TTTGAAAAAA
* *
31425810 AATA-TTTTTTATAGTTTTAAA-TACTTTT
1 AATATTTTTTTA-ATTTTTAAATTAATTTT
31425838 AATATTTTTTTAATTTTTAAAATTAATTTT
1 AATATTTTTTTAATTTTT-AAATTAATTTT
31425868 -ATAATTTTTTTGAATTTT
1 AAT-ATTTTTTT-AATTTT
31425886 GAATTTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 9 0.22
29 12 0.29
30 14 0.34
31 6 0.15
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (29 bp):
AATATTTTTTTAATTTTTAAATTAATTTT
Found at i:31425903 original size:30 final size:31
Alignment explanation
Indices: 31425825--31425903 Score: 72
Period size: 31 Copynumber: 2.5 Consensus size: 31
31425815 TTTTTATAGT
*
31425825 TTTAAATACTTTTAATATTTTTTTAATTTTTAAA
1 TTTAAA-A-TTTTAAT-TTTTTTGAATTTTTAAA
* * *
31425859 ATT-AATTTTATAATTTTTTTGAA-TTTTGAA
1 TTTAAAATTT-TAATTTTTTTGAATTTTTAAA
31425889 TTTAAAATTTTAATT
1 TTTAAAATTTTAATT
31425904 AATCATTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
30 13 0.35
31 16 0.43
32 4 0.11
33 2 0.05
34 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAAAATTTTAATTTTTTTGAATTTTTAAA
Found at i:31426264 original size:13 final size:13
Alignment explanation
Indices: 31426246--31426270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31426236 AATGGAGAAC
31426246 TAAAATCAACCAT
1 TAAAATCAACCAT
31426259 TAAAATCAACCA
1 TAAAATCAACCA
31426271 AAAAATTCCC
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:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAATCAACCAT
Found at i:31426529 original size:20 final size:19
Alignment explanation
Indices: 31426504--31426541 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
31426494 AAAATAAGAG
31426504 GAAAAATAAATGAATTTTTT
1 GAAAAATAAAT-AATTTTTT
*
31426524 GAAAAATATATAATTTTT
1 GAAAAATAAATAATTTTT
31426542 AACTACCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
GAAAAATAAATAATTTTTT
Found at i:31426653 original size:5 final size:6
Alignment explanation
Indices: 31426636--31426663 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31426626 TAGTCATCTC
31426636 TCTTTT TCTTTT TCTTTT TCTTTT TCTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT
31426664 CCTCTCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:31438770 original size:41 final size:41
Alignment explanation
Indices: 31438725--31438842 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
31438715 TGAAAGATAA
31438725 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
31438766 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
31438796 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
31438837 ATGTAG
1 ATGTAG
31438843 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:31438781 original size:71 final size:71
Alignment explanation
Indices: 31438693--31438856 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
31438683 GAGATGTATC
31438693 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
31438758 AGGACA
66 AGGACA
31438764 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
31438829 AGGACA
66 AGGACA
31438835 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
31438857 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:31446351 original size:41 final size:41
Alignment explanation
Indices: 31446306--31446423 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
31446296 TGAAAGATAA
31446306 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
31446347 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
31446377 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
31446418 ATGTAG
1 ATGTAG
31446424 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:31446362 original size:71 final size:71
Alignment explanation
Indices: 31446274--31446437 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
31446264 GAGATGTATC
31446274 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
31446339 AGGACA
66 AGGACA
31446345 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
31446410 AGGACA
66 AGGACA
31446416 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
31446438 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:31451857 original size:40 final size:37
Alignment explanation
Indices: 31451791--31451925 Score: 143
Period size: 35 Copynumber: 3.7 Consensus size: 37
31451781 CATGGAAAAG
* **
31451791 TGTGAAATGGAGGTATGGTA--TCATCCATACCAAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
31451826 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATT-TC--ATCCATACTGAGT
** * *
31451866 TAAGAAATGTAGGCATGGCATTTC--CCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
*
31451901 TGTAAAATGTAGGTATGGTATTTCA
1 TGTGAAATGTAGGTATGGTATTTCA
31451926 ATGAGGAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
35 49 0.60
38 2 0.02
39 2 0.02
40 29 0.35
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
Found at i:31454664 original size:13 final size:13
Alignment explanation
Indices: 31454646--31454671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31454636 CGTGTTTCCA
31454646 AAAACCATTTGTT
1 AAAACCATTTGTT
31454659 AAAACCATTTGTT
1 AAAACCATTTGTT
31454672 TCCATAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:31455622 original size:20 final size:20
Alignment explanation
Indices: 31455594--31455642 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
31455584 ACAAGGCTAG
* *
31455594 CCATATGGCCAGACATGCGT
1 CCATGTGGCCAGACACGCGT
31455614 CCATGTGGCCAGACACGCGT
1 CCATGTGGCCAGACACGCGT
31455634 CCATGTGGC
1 CCATGTGGC
31455643 GTCGACAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.33, G:0.29, T:0.18
Consensus pattern (20 bp):
CCATGTGGCCAGACACGCGT
Found at i:31459381 original size:20 final size:21
Alignment explanation
Indices: 31459352--31459400 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
31459342 ATATTCTATG
*
31459352 ATTA-TTTAATTAGATA-TAT
1 ATTATTTTAATAAGATATTAT
*
31459371 ATTATTTTAATAAGATATTTT
1 ATTATTTTAATAAGATATTAT
31459392 ATTATTTTA
1 ATTATTTTA
31459401 TTATTATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
21 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTATTTTAATAAGATATTAT
Found at i:31459404 original size:3 final size:3
Alignment explanation
Indices: 31459386--31459434 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
31459376 TTTAATAAGA
*
31459386 TAT T-T TAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
31459431 TAT T
1 TAT T
31459435 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:31459406 original size:11 final size:11
Alignment explanation
Indices: 31459390--31459428 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
31459380 ATAAGATATT
31459390 TTATTATTTTA
1 TTATTATTTTA
*
31459401 TTATTATTTCA
1 TTATTATTTTA
31459412 TTATTATTTTA
1 TTATTATTTTA
31459423 TTATTA
1 TTATTA
31459429 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:31459414 original size:19 final size:19
Alignment explanation
Indices: 31459386--31459427 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
31459376 TTTAATAAGA
*
31459386 TATTTTATTATT-TTATTAT
1 TATTTCATTATTATT-TTAT
31459405 TATTTCATTATTATTTTAT
1 TATTTCATTATTATTTTAT
31459424 TATT
1 TATT
31459428 AATTATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTCATTATTATTTTAT
Found at i:31461585 original size:46 final size:46
Alignment explanation
Indices: 31461532--31461749 Score: 294
Period size: 46 Copynumber: 4.7 Consensus size: 46
31461522 ATGAATTGTG
* *
31461532 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
**
31461578 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
* * * *
31461624 TAGGACCATGGTTAAAAGATACCATGGCAGCGTGACATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
* *
31461670 TAAGACCATGGTTGAAAGATAACATGGCAACATGACA-GAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAA
* * * *
31461716 TAAGACCATAGTTGAAAGACACTATGGCATCATG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATG
31461750 TCAAAGATAA
Statistics
Matches: 150, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 1 0.01
46 149 0.99
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
Found at i:31461696 original size:92 final size:92
Alignment explanation
Indices: 31461532--31461744 Score: 327
Period size: 92 Copynumber: 2.3 Consensus size: 92
31461522 ATGAATTGTG
*
31461532 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGA
* * *
31461597 TACCATGGCAACATGACGGGAAATGAA
66 TAACATGGCAACATGACAGAAAATGAA
* * *
31461624 TAGGACCATGGTTAAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGA
*
31461689 TAACATGGCAACATGACAGAAAATGAG
66 TAACATGGCAACATGACAGAAAATGAA
* * *
31461716 TAAGACCATAGTTGAAAGACACTATGGCA
1 TAAGACCATGGTTGAAAGATACCATGGCA
31461745 TCATGTCAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 108 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGA
TAACATGGCAACATGACAGAAAATGAA
Found at i:31467874 original size:28 final size:28
Alignment explanation
Indices: 31467838--31467895 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
31467828 TCTTTTGAAG
31467838 ATAGAATTTCTTGATCTATTGCATGATA
1 ATAGAATTTCTTGATCTATTGCATGATA
31467866 ATAGAATTTCTTGATCTATTGCATGATA
1 ATAGAATTTCTTGATCTATTGCATGATA
31467894 AT
1 AT
31467896 GCTTACCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (28 bp):
ATAGAATTTCTTGATCTATTGCATGATA
Done.