Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 70 of 290
Found at i:23126964 original size:107 final size:108
Alignment explanation
Indices: 23126834--23127242 Score: 488
Period size: 107 Copynumber: 3.8 Consensus size: 108
23126824 AGTATTTCGA
* *
23126834 TAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGAGGGTATTTTAATAATTTTACAA
1 TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAA
*
23126899 ATCGAGGGTGTTTCATTAATTTCAC-AATCGAGGGTATTTTAG
66 ATCGAGGGTGTTTCAGTAATTTCACAAATCGAGGGTATTTTAG
* * *
23126941 TAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGAGGGTGTTTCGATAATTTTACAA
1 TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAA
* *
23127006 ATCGAGGGTGTTTTAGTAATTTTACAAATCGAGGGTATTTT-G
66 ATCGAGGGTGTTTCAGTAATTTCACAAATCGAGGGTATTTTAG
* * * * *
23127048 TTAATTTTACAAATCGAGGGTATTTCAGTAATTTCAC-AATCGAGGATATTTTGGTAATTTTATA
1 -TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACA
* * * * * *
23127112 AATTGGGGGTATTT-TGATAATTTTACAAATTGAGGGTATTTTAG
65 AATCGAGGGTGTTTCAG-TAATTTCACAAATCGAGGGTATTTTAG
* * * * * * * *
23127156 TAATTTCAC-AATTGAGGGTATTTCGATAATTTTATAAAT-TAGGCGCATTTTGGTAATTTTAAA
1 TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCGAGG-GTATTTTGATAATTTTACA
* *
23127219 AATTGAGGGTATTTCAGTAATTTC
65 AATCGAGGGTGTTTCAGTAATTTC
23127243 TCTTTATTAT
Statistics
Matches: 263, Mismatches: 32, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
106 25 0.10
107 188 0.71
108 50 0.19
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.41
Consensus pattern (108 bp):
TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAA
ATCGAGGGTGTTTCAGTAATTTCACAAATCGAGGGTATTTTAG
Found at i:23127046 original size:161 final size:161
Alignment explanation
Indices: 23126828--23127242 Score: 532
Period size: 161 Copynumber: 2.6 Consensus size: 161
23126818 TACAACAGTA
*
23126828 TTTCGATAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGAGGGTATTTTAATAATT
1 TTTCGATAATTTTACAAATCGAGGGTGTTTCAGTAATTTTACAAATCGAGGGTATTTTAATAATT
* * *
23126893 TTACAAATCGAGGGTGTTTCATTAATTTCACAATCGAGGGTATTTTAGTAATTTTACAAATCGAG
66 TTACAAATCGAGGGTATTTCAGTAATTTCACAATCGAGGATATTTTAGTAATTTTACAAATCGAG
* *
23126958 GGTGTTTCGGTAATTTTACAAATCGAGGGTG
131 GGTATTTCGATAATTTTACAAATCGAGGGTG
* **
23126989 TTTCGATAATTTTACAAATCGAGGGTGTTTTAGTAATTTTACAAATCGAGGGTATTTTGTTAATT
1 TTTCGATAATTTTACAAATCGAGGGTGTTTCAGTAATTTTACAAATCGAGGGTATTTTAATAATT
* * * *
23127054 TTACAAATCGAGGGTATTTCAGTAATTTCACAATCGAGGATATTTTGGTAATTTTATAAATTGGG
66 TTACAAATCGAGGGTATTTCAGTAATTTCACAATCGAGGATATTTTAGTAATTTTACAAATCGAG
* * *
23127119 GGTATTTTGATAATTTTACAAATTGAGGGTA
131 GGTATTTCGATAATTTTACAAATCGAGGGTG
* * * * * * * **
23127150 TTT-TAGTAATTTCAC-AATTGAGGGTATTTC-GATAATTTTATAAAT-TAGGCGCATTTTGGTA
1 TTTCGA-TAATTTTACAAATCGAGGGTGTTTCAG-TAATTTTACAAATCGAGG-GTATTTTAATA
* *
23127211 ATTTTAAAAATTGAGGGTATTTCAGTAATTTC
63 ATTTTACAAATCGAGGGTATTTCAGTAATTTC
23127243 TCTTTATTAT
Statistics
Matches: 224, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
159 4 0.02
160 64 0.29
161 156 0.70
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.41
Consensus pattern (161 bp):
TTTCGATAATTTTACAAATCGAGGGTGTTTCAGTAATTTTACAAATCGAGGGTATTTTAATAATT
TTACAAATCGAGGGTATTTCAGTAATTTCACAATCGAGGATATTTTAGTAATTTTACAAATCGAG
GGTATTTCGATAATTTTACAAATCGAGGGTG
Found at i:23130913 original size:47 final size:47
Alignment explanation
Indices: 23130840--23131044 Score: 302
Period size: 47 Copynumber: 4.4 Consensus size: 47
23130830 GATGTACAAG
* * * *
23130840 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTAATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
23130887 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * * * *
23130934 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAT
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
23130981 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
23131028 GTGTATAAATGTGATAA
1 GTGTATATATGTGATAA
23131045 TTCTCGAAGG
Statistics
Matches: 142, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 142 1.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
Found at i:23130958 original size:94 final size:94
Alignment explanation
Indices: 23130840--23131044 Score: 338
Period size: 94 Copynumber: 2.2 Consensus size: 94
23130830 GATGTACAAG
* *
23130840 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTAATGAATGTGAAAGTGTATATATGTGATAAG
1 GTGTATATATGTGATAAGACCTAATGGCCGATGTAATGAATGTGAAAGTGTATATATGTGATAAG
23130905 GCCGAATGGCCAATGTGATGAATGTGAAA
66 GCCGAATGGCCAATGTGATGAATGTGAAA
* * * *
23130934 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAATGTGTATATATGTGATAAG
1 GTGTATATATGTGATAAGACCTAATGGCCGATGTAATGAATGTGAAAGTGTATATATGTGATAAG
*
23130999 GCCGAATGGCCAATGTGATGGATGTGAAA
66 GCCGAATGGCCAATGTGATGAATGTGAAA
*
23131028 GTGTATAAATGTGATAA
1 GTGTATATATGTGATAA
23131045 TTCTCGAAGG
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 102 1.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (94 bp):
GTGTATATATGTGATAAGACCTAATGGCCGATGTAATGAATGTGAAAGTGTATATATGTGATAAG
GCCGAATGGCCAATGTGATGAATGTGAAA
Found at i:23134152 original size:93 final size:93
Alignment explanation
Indices: 23134024--23134194 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
23134014 GCCCATAACT
* *
23134024 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
23134089 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * * *
23134117 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTGAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
23134182 CGAGTTCGGATGC
66 CGAGCTCGGATGC
23134195 TCAAACATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:23134191 original size:46 final size:46
Alignment explanation
Indices: 23134016--23134191 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
23134006 TGTAACCCGC
* * *
23134016 CCATAACTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAACTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
23134062 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAACTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* ** * *
23134108 ACATCTCTCGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATAACT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* * *
23134155 CCATAAGTGAACTCGGACTCAACTGAACGAGTTCGGA
1 CCATAACTGAACTCGGACTCAACTCAACGAGCTCGGA
23134192 TGCTCAAACA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 66 0.62
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAACTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:23134210 original size:46 final size:45
Alignment explanation
Indices: 23134023--23134210 Score: 125
Period size: 46 Copynumber: 4.1 Consensus size: 45
23134013 CGCCCATAAC
* * ** * *
23134023 TGAACTCAGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACATCC-T-AG
*
23134069 TGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTACATCTCT--
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACATC-CTAG
* * *** *
23134116 CGAACTCGGACTCAACTCAATGAGTTCGGACATTC-GCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACATCC-T-AG
*
23134162 TGAACTCGGACTCAACTGAACGAGTTCGGATGCTCAAACATCCTAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-AACATCCTAG
23134208 TGA
1 TGA
23134211 CATGTCACTT
Statistics
Matches: 110, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
42 1 0.01
43 5 0.05
45 1 0.01
46 63 0.57
47 28 0.25
48 6 0.05
50 5 0.05
51 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACATCCTAG
Found at i:23135680 original size:27 final size:27
Alignment explanation
Indices: 23135615--23135681 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
23135605 TATAATCATA
*
23135615 TATCTCATAGGGGCATAACAGTCATTT
1 TATCACATAGGGGCATAACAGTCATTT
* *
23135642 TATCACACAGGGGCATAATAGTCATTT
1 TATCACATAGGGGCATAACAGTCATTT
23135669 TATCA-ATTAGGGG
1 TATCACA-TAGGGG
23135682 GTCTAGGTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.03
27 34 0.97
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (27 bp):
TATCACATAGGGGCATAACAGTCATTT
Found at i:23138142 original size:39 final size:40
Alignment explanation
Indices: 23137999--23138165 Score: 243
Period size: 40 Copynumber: 4.2 Consensus size: 40
23137989 CCTTTGGAAT
* *
23137999 TTAG-CCGGATATAGCT-ACTTGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
*
23138038 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
23138078 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-C
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
23138117 TTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGAC
23138157 TTAGCCCGG
1 TTAGCCCGG
23138166 TTATCATCCG
Statistics
Matches: 118, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.01
39 40 0.34
40 77 0.65
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:23138145 original size:79 final size:80
Alignment explanation
Indices: 23137999--23138165 Score: 243
Period size: 79 Copynumber: 2.1 Consensus size: 80
23137989 CCTTTGGAAT
* * * *
23137999 TTAG-CCGGATATAGCTACTTGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
1 TTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCAC
23138063 AAATGCCTTCGGGAC
66 AAATGCCTTCGGGAC
*
23138078 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGC
1 TTAGCCCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTAGC
23138140 ACAAATGCCTTCGGGAC
64 ACAAATGCCTTCGGGAC
23138157 TTAGCCCGG
1 TTAGCCCGG
23138166 TTATCATCCG
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
78 1 0.01
79 50 0.62
80 29 0.36
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCAC
AAATGCCTTCGGGAC
Found at i:23142216 original size:43 final size:42
Alignment explanation
Indices: 23142058--23142218 Score: 148
Period size: 43 Copynumber: 3.7 Consensus size: 42
23142048 AATGGCAACA
* * *
23142058 TCCCAGACGTGGTCTTACATGTAATCACATGTCGATGCCACTG
1 TCCCAGACGTGGTCTTACATG-AAACACATATCGATGCCAATG
* * * *
23142101 TCCCAGGCAG-GGTCTTACACGAATCACA-ATTACGATGCCGATG
1 TCCCAGAC-GTGGTCTTACATGAAACACATA-T-CGATGCCAATG
* * *
23142144 TCCCAGACATGGTGTTAC-TCAAAATCACATATCGATGCCAATG
1 TCCCAGACGTGGTCTTACAT-GAAA-CACATATCGATGCCAATG
23142187 TCCCAGACGTGGTCTTACATGAGAACACATAT
1 TCCCAGACGTGGTCTTACATGA-AACACATAT
23142219 TGGAAATCCT
Statistics
Matches: 94, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
42 8 0.09
43 76 0.81
44 9 0.10
45 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.25
Consensus pattern (42 bp):
TCCCAGACGTGGTCTTACATGAAACACATATCGATGCCAATG
Found at i:23147111 original size:31 final size:31
Alignment explanation
Indices: 23147050--23147113 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
23147040 TCATTTCGGG
*
23147050 GAATGCCGAATGAAGAGTGGGGCATATTTTA
1 GAATGCCGAATGAAGAGTGGGGCAGATTTTA
* * *
23147081 GAATGCCGAATTAAGAGTGGGGTAGGTTTTA
1 GAATGCCGAATGAAGAGTGGGGCAGATTTTA
23147112 GA
1 GA
23147114 TGTGGTTCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.08, G:0.34, T:0.27
Consensus pattern (31 bp):
GAATGCCGAATGAAGAGTGGGGCAGATTTTA
Found at i:23148581 original size:52 final size:52
Alignment explanation
Indices: 23148503--23148604 Score: 186
Period size: 52 Copynumber: 2.0 Consensus size: 52
23148493 TAAGTTTGGA
*
23148503 AAGAGTGAGTTTTGGCTTCAAGAAGTCAGATTTCTCGGTCATATTGTGTCAG
1 AAGAGTGAGTTTTGGCTTCAAGAAGTCAAATTTCTCGGTCATATTGTGTCAG
*
23148555 AAGAGTGAGTTTTGGCTTTAAGAAGTCAAATTTCTCGGTCATATTGTGTC
1 AAGAGTGAGTTTTGGCTTCAAGAAGTCAAATTTCTCGGTCATATTGTGTC
23148605 GGGTGATGGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (52 bp):
AAGAGTGAGTTTTGGCTTCAAGAAGTCAAATTTCTCGGTCATATTGTGTCAG
Found at i:23150669 original size:29 final size:29
Alignment explanation
Indices: 23150635--23150708 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
23150625 TAATCAACCG
*
23150635 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
23150664 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
23150693 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
23150709 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:23178221 original size:41 final size:41
Alignment explanation
Indices: 23178170--23178249 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
23178160 GGTTCTTTTC
23178170 TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAGAT
1 TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAGAT
23178211 TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAG
1 TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAG
23178250 CTTTCACTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (41 bp):
TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAGAT
Found at i:23179128 original size:12 final size:11
Alignment explanation
Indices: 23179105--23179135 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
23179095 GGGTTAATAA
23179105 ATAAAAAAAAT
1 ATAAAAAAAAT
23179116 ATAAAATAAAAT
1 ATAAAA-AAAAT
23179128 ATAAAAAA
1 ATAAAAAA
23179136 TAGGCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAAAAAT
Found at i:23180958 original size:58 final size:57
Alignment explanation
Indices: 23180887--23181008 Score: 208
Period size: 58 Copynumber: 2.1 Consensus size: 57
23180877 AGCTAAACTG
*
23180887 CGATTGAGCGAGAATAACTCTGAAACTTTATCTGTTCATAAGATATTCTGTAATAAA
1 CGATTGAGCGAGAACAACTCTGAAACTTTATCTGTTCATAAGATATTCTGTAATAAA
*
23180944 NCGATTGCGCGAGAACAACTCTGAAACTTTATCTGTTCATAAGATATTCTGTAATAAA
1 -CGATTGAGCGAGAACAACTCTGAAACTTTATCTGTTCATAAGATATTCTGTAATAAA
*
23181002 CAATTGA
1 CGATTGA
23181009 AACAATAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 5 0.08
58 55 0.92
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (57 bp):
CGATTGAGCGAGAACAACTCTGAAACTTTATCTGTTCATAAGATATTCTGTAATAAA
Found at i:23186990 original size:14 final size:14
Alignment explanation
Indices: 23186971--23187003 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
23186961 AGGTTAACAA
23186971 ATAAAAAATATAAT
1 ATAAAAAATATAAT
23186985 ATAAAAAATATAAT
1 ATAAAAAATATAAT
23186999 ATAAA
1 ATAAA
23187004 GAAAAGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAAAATATAAT
Found at i:23206757 original size:30 final size:30
Alignment explanation
Indices: 23206712--23206771 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
23206702 ATTTAATAAG
*
23206712 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
23206742 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
23206772 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:23217138 original size:29 final size:29
Alignment explanation
Indices: 23217105--23217180 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
23217095 TATCGATGAT
*
23217105 CATCGATCAATGAAAAGGGAT-GTTTTGAC
1 CATCGATCTATGAAAAGGGATAGTTTT-AC
*
23217134 CATCGAT-TATGAAAATGGATAGTTTTAC
1 CATCGATCTATGAAAAGGGATAGTTTTAC
*
23217162 TATCGA-CTATGAAAAGGGA
1 CATCGATCTATGAAAAGGGA
23217181 CGATGACGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 29 0.71
29 12 0.29
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (29 bp):
CATCGATCTATGAAAAGGGATAGTTTTAC
Found at i:23229284 original size:41 final size:41
Alignment explanation
Indices: 23229233--23229312 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
23229223 GGTTCTTTTC
23229233 TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAGAT
1 TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAGAT
23229274 TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAG
1 TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAG
23229313 CTTTCACTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (41 bp):
TTTTTCTATCTTGGAGAATTAGGGTTAGCCACCTGAAAGAT
Found at i:23230191 original size:12 final size:11
Alignment explanation
Indices: 23230168--23230198 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
23230158 GGGTTAATAA
23230168 ATAAAAAAAAT
1 ATAAAAAAAAT
23230179 ATAAAATAAAAT
1 ATAAAA-AAAAT
23230191 ATAAAAAA
1 ATAAAAAA
23230199 TAGGCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAAAAAT
Found at i:23231916 original size:18 final size:18
Alignment explanation
Indices: 23231893--23231937 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
23231883 TTAAGGCTAC
*
23231893 AAAACTGAGACTGTAGGG
1 AAAACTAAGACTGTAGGG
* *
23231911 AAAACTAAGCCTTTAGGG
1 AAAACTAAGACTGTAGGG
23231929 AAAACTAAG
1 AAAACTAAG
23231938 CCCTAGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.18
Consensus pattern (18 bp):
AAAACTAAGACTGTAGGG
Found at i:23238013 original size:14 final size:14
Alignment explanation
Indices: 23237994--23238026 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
23237984 AGGTTAACAA
23237994 ATAAAAAATATAAT
1 ATAAAAAATATAAT
23238008 ATAAAAAATATAAT
1 ATAAAAAATATAAT
23238022 ATAAA
1 ATAAA
23238027 GAAAAGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAAAATATAAT
Found at i:23257781 original size:30 final size:30
Alignment explanation
Indices: 23257736--23257795 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
23257726 ATTTAATAAG
*
23257736 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
23257766 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
23257796 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:23268162 original size:29 final size:29
Alignment explanation
Indices: 23268129--23268204 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
23268119 TATCGATGAT
*
23268129 CATCGATCAATGAAAAGGGAT-GTTTTGAC
1 CATCGATCTATGAAAAGGGATAGTTTT-AC
*
23268158 CATCGAT-TATGAAAATGGATAGTTTTAC
1 CATCGATCTATGAAAAGGGATAGTTTTAC
*
23268186 TATCGA-CTATGAAAAGGGA
1 CATCGATCTATGAAAAGGGA
23268205 CGATGACGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 29 0.71
29 12 0.29
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (29 bp):
CATCGATCTATGAAAAGGGATAGTTTTAC
Found at i:23286014 original size:24 final size:24
Alignment explanation
Indices: 23286003--23286148 Score: 251
Period size: 24 Copynumber: 6.1 Consensus size: 24
23285993 GCCTAGCCTC
23286003 TTTAATAACTGGGGCA-AAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
*
23286026 TTTAATAA-TAGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
23286049 TTTAATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
*
23286073 TTTAACAACTGGGGCATAAGCCCTT
1 TTTAATAACTGGGGCATAAGCCC-T
23286098 TTTAATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
23286122 TTTAATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
23286146 TTT
1 TTT
23286149 GCACTTCCTC
Statistics
Matches: 116, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
22 6 0.05
23 23 0.20
24 64 0.55
25 23 0.20
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (24 bp):
TTTAATAACTGGGGCATAAGCCCT
Found at i:23286112 original size:49 final size:49
Alignment explanation
Indices: 23286003--23286148 Score: 253
Period size: 49 Copynumber: 3.0 Consensus size: 49
23285993 GCCTAGCCTC
*
23286003 TTTAATAACTGGGGCA-AAGCCCTTTTAATAA-TAGGGCATAAGCCC-T
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
*
23286049 TTTAATAACTGGGGCATAAGCCCTTTTAACAACTGGGGCATAAGCCCTT
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
23286098 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
23286147 TT
1 TT
23286149 GCACTTCCTC
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
46 16 0.17
47 14 0.15
48 13 0.14
49 51 0.54
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (49 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
Found at i:23286123 original size:73 final size:70
Alignment explanation
Indices: 23286003--23286148 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 70
23285993 GCCTAGCCTC
*
23286003 TTTAATAACTGGGGCAAAGCCCTTTTAATAATAGGGCATAAGCCCTTTTAATAACTGGGGCATAA
1 TTTAACAACTGGGGCAAAGCCCTTTTAATAATAGGGCATAAGCCCTTTTAATAACTGGGGCATAA
23286068 GCCCT
66 GCCCT
*
23286073 TTTAACAACTGGGGCATAAGCCCTTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCA
1 TTTAACAACTGGGGCA-AAGCCC-TTTTAATAA-TAGGGCATAAGCCCTTTTAATAACTGGGGCA
23286138 TAAGCCCT
63 TAAGCCCT
23286146 TTT
1 TTT
23286149 GCACTTCCTC
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
70 15 0.21
71 6 0.08
72 9 0.13
73 41 0.58
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (70 bp):
TTTAACAACTGGGGCAAAGCCCTTTTAATAATAGGGCATAAGCCCTTTTAATAACTGGGGCATAA
GCCCT
Found at i:23286222 original size:20 final size:20
Alignment explanation
Indices: 23286197--23286263 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
23286187 TTATGAATAC
*
23286197 ATCATGTGCATATCATATAT
1 ATCATGTGCATATCATACAT
*
23286217 ATCATGCGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
23286237 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
23286257 ACCATGT
1 ATCATGT
23286264 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:23288041 original size:37 final size:37
Alignment explanation
Indices: 23287980--23288058 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
23287970 TTATTACGAA
* * *
23287980 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCTCCACACGAAGTCATCGG
*
23288017 GTCTTACCCAGACAAAAT-TCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCT-CCACACGAAGTCATCGG
23288054 GTCTT
1 GTCTT
23288059 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCTCCACACGAAGTCATCGG
Found at i:23288255 original size:47 final size:47
Alignment explanation
Indices: 23288177--23288475 Score: 490
Period size: 47 Copynumber: 6.3 Consensus size: 47
23288167 CCCTTCGGGA
* * * * * *
23288177 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23288224 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23288271 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23288318 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23288365 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23288412 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23288461 CTTATCACATATATA
1 CTTATCACATATATA
23288476 TACTNNNNNN
Statistics
Matches: 239, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
47 192 0.80
49 47 0.20
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:23291611 original size:40 final size:40
Alignment explanation
Indices: 23291581--23291751 Score: 263
Period size: 40 Copynumber: 4.3 Consensus size: 40
23291571 CTTCGGGACC
* * * ****
23291581 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGAAACT
*
23291621 TAG-CAGGATATATCACTAGCACGAATGCTCCTCGAAACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGAAACT
23291660 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGAAACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGAAACT
23291700 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGAAACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGAAACT
23291740 TAGCCCGGATAT
1 TAGCCCGGATAT
23291752 GGAACTTAGT
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
39 31 0.26
40 90 0.74
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
TAGCCCGGATATATCACTAGCACGAATGCTCCTCGAAACT
Found at i:23291786 original size:58 final size:58
Alignment explanation
Indices: 23291696--23291820 Score: 187
Period size: 58 Copynumber: 2.1 Consensus size: 58
23291686 TGCTCCTCGA
*
23291696 AACTTAGCCCGGATATATCACTAGCACGAATGCTCCTCGAAACTTAGCCCGGATATGG
1 AACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGAAACTTAGCCCGGATATGG
* * * *
23291754 AACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATGG
1 AACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGAAACTTAGCCCGGATATGG
*
23291812 TCACTTAGC
1 -AACTTAGC
23291821 ACAAAGCCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
58 53 0.90
59 6 0.10
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (58 bp):
AACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGAAACTTAGCCCGGATATGG
Found at i:23291832 original size:40 final size:40
Alignment explanation
Indices: 23291752--23291846 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
23291742 GCCCGGATAT
*
23291752 GGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTC
1 GGAACTTAGTCCGGATACATCACTAGCACGAAAGCTCTTC
**
23291792 GGAACTTAGTCCGGATATGGTCACTTAGCAC-AAAGC-CTTC
1 GGAACTTAGTCCGGATA-CATCAC-TAGCACGAAAGCTCTTC
* *
23291832 GGGACTTAGCCCGGA
1 GGAACTTAGTCCGGA
23291847 CATCATTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 34 0.71
41 8 0.17
42 6 0.12
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.23
Consensus pattern (40 bp):
GGAACTTAGTCCGGATACATCACTAGCACGAAAGCTCTTC
Found at i:23291839 original size:98 final size:98
Alignment explanation
Indices: 23291656--23291846 Score: 260
Period size: 98 Copynumber: 1.9 Consensus size: 98
23291646 TGCTCCTCGA
*
23291656 AACTTAGCCCGGATATATCACTAGCACGAATGCTCCTCGAAACTTAGCCCGGATATATCACTAGC
1 AACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGAAACTTAGCCCGGATATATCACTAGC
*
23291721 ACGAATGCTCCTCGAAACTTAGCCCGGATATGG
66 ACGAAAGCTCCTCGAAACTTAGCCCGGATATGG
* * * * *
23291754 AACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATGGTCACTTA
1 AACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGAAACTTAGCCCGGATAT-ATCAC-TA
* **
23291819 GCAC-AAAGC-CTTCGGGACTTAGCCCGGA
64 GCACGAAAGCTCCTCGAAACTTAGCCCGGA
23291847 CATCATTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
98 67 0.83
99 8 0.10
100 6 0.07
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (98 bp):
AACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGAAACTTAGCCCGGATATATCACTAGC
ACGAAAGCTCCTCGAAACTTAGCCCGGATATGG
Found at i:23292191 original size:29 final size:29
Alignment explanation
Indices: 23292152--23292230 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
23292142 CTTAATAATC
*
23292152 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
23292182 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
23292211 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
23292231 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:23292273 original size:43 final size:43
Alignment explanation
Indices: 23292212--23292314 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
23292202 TGCATTTCAA
*
23292212 GCCCGCACACTTAGTGCCAATCTCACAACTGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
23292255 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
23292298 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
23292315 TGAAAACCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:23293051 original size:45 final size:45
Alignment explanation
Indices: 23292995--23293084 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
23292985 ACATTCAAAA
*
23292995 GATGCCATTTTCGCGTGGCTTATATACAGTAACCAAAAATATTCT
1 GATGCCATTTTCGCATGGCTTATATACAGTAACCAAAAATATTCT
* *
23293040 GATGTCATTTTCGCATGGCTTATATACATTAACCAAAAATATTCT
1 GATGCCATTTTCGCATGGCTTATATACAGTAACCAAAAATATTCT
23293085 TCCGCCACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (45 bp):
GATGCCATTTTCGCATGGCTTATATACAGTAACCAAAAATATTCT
Found at i:23299652 original size:37 final size:37
Alignment explanation
Indices: 23299588--23299733 Score: 220
Period size: 37 Copynumber: 3.9 Consensus size: 37
23299578 AGCTCGGATG
* * *
23299588 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
23299625 AAATCTCCACGCGTAGTCATCGAGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
23299662 TAATCTCCACACGTAGTCATCGGGTCTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
23299699 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
23299734 ATATATTTCC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 99 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:23300006 original size:47 final size:47
Alignment explanation
Indices: 23299942--23301127 Score: 2093
Period size: 47 Copynumber: 25.1 Consensus size: 47
23299932 ACACGTTTCG
* * * * ** *
23299942 CATTAGCCATTCAGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
* * * *
23299989 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300036 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300083 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300130 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300177 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300224 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300271 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300318 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300365 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300412 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300459 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300506 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300553 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300600 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300647 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300694 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300741 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23300788 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
*
23300835 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
*** *
23300882 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATCCATCA
23300933 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
*
23300980 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
* *** *
23301027 CATTGGCCATTCAGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATCCATCA
*
23301078 CATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
23301125 CAT
1 CAT
23301128 AAAATCCTAA
Statistics
Matches: 1105, Mismatches: 26, Indels: 16
0.96 0.02 0.01
Matches are distributed among these distances:
47 1017 0.92
51 88 0.08
ACGTcount: A:0.26, C:0.33, G:0.12, T:0.29
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
Found at i:23301657 original size:76 final size:76
Alignment explanation
Indices: 23301566--23301718 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
23301556 CTACGAATCA
* *
23301566 AATTTCTCATTTTACAGAATTCGAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAA
1 AATTTCTCATTTTACAGAATTCAAAATGTGTTCTATTTGATTTCATTTGAAACTAGACTCATTAA
23301631 GGAGTCTAAGC
66 GGAGTCTAAGC
*
23301642 AATTTCTCATTTTACAGAATTCAAAATGTGTTCTATTTGATTTCATTTGAAACTAGATTCATTAA
1 AATTTCTCATTTTACAGAATTCAAAATGTGTTCTATTTGATTTCATTTGAAACTAGACTCATTAA
23301707 GGAGTCTAAGC
66 GGAGTCTAAGC
23301718 A
1 A
23301719 TATAAATTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (76 bp):
AATTTCTCATTTTACAGAATTCAAAATGTGTTCTATTTGATTTCATTTGAAACTAGACTCATTAA
GGAGTCTAAGC
Found at i:23305133 original size:40 final size:40
Alignment explanation
Indices: 23305101--23305452 Score: 497
Period size: 40 Copynumber: 8.8 Consensus size: 40
23305091 CCAACATGAT
* * *
23305101 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** *
23305141 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
23305181 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
23305221 TGCTCCTCAGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
23305261 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** * *
23305301 AACTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* **
23305341 TGCTCCTCGAAACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** * *
23305381 AACTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
23305421 TGCTCCTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
23305453 CTCAATTCTC
Statistics
Matches: 280, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 280 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:23306777 original size:37 final size:37
Alignment explanation
Indices: 23306724--23306826 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
23306714 CGAATAGTCC
* *
23306724 CCACACGTAGTTATCGGGTCTTACTCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
23306761 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
23306798 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
23306827 ATATATTTCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:23307025 original size:48 final size:48
Alignment explanation
Indices: 23306967--23307151 Score: 343
Period size: 48 Copynumber: 3.9 Consensus size: 48
23306957 ATATACACAC
*
23306967 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
23307015 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
23307063 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
23307111 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACA
23307152 CACATATATA
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 135 1.00
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.34
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:23310508 original size:40 final size:40
Alignment explanation
Indices: 23310476--23311180 Score: 1095
Period size: 40 Copynumber: 17.6 Consensus size: 40
23310466 CCAGCATGAT
* * * *
23310476 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
23310516 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
23310556 TGCTCTTCAGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
23310596 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
23310636 TGCTCTTCGGGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
23310676 TGCTCTTCAGGACTTTGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
23310716 TGCTCTTCGGGACTTAGCCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
23310756 TGCTCTTCAGGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
23310796 TGCTCTTCGGGACTTAGCCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
23310836 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
23310876 TGCTCTTCAGGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
23310916 TGCTCTTCGGGACTTAGCCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
23310956 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
23310996 TGCTCTTTGGGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
23311036 TGATCTTCAGAACTTAGCCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
23311076 TGCTCTTCAGGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
23311116 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
23311156 TGCTCTTCGGGACTTAGCCCAGATA
1 TGCTCTTCGGGACTTAGCCCGGATA
23311181 TATATAACTC
Statistics
Matches: 606, Mismatches: 59, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 606 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:23320828 original size:46 final size:46
Alignment explanation
Indices: 23320737--23320955 Score: 144
Period size: 46 Copynumber: 4.7 Consensus size: 46
23320727 GGGGTAGGGT
* *
23320737 GCCGATGCCATATTCCAAACATGGTCTTACACTGACTATCATCTCGTA-
1 GCCGATG-CATGTTCCAGACAT-GTCTTACACTGACTATCATCTCG-AG
* * *
23320785 GCCGATGCATGTTCCAGACATGTTTTACACTGGCT-TACGTCTCGAG
1 GCCGATGCATGTTCCAGACATGTCTTACACTGACTAT-CATCTCGAG
* * * * *
23320831 GCTGATGCATGTCCCGGATATGTCTTACACT-AGC-ACTCATCTCGAT
1 GCCGATGCATGTTCCAGACATGTCTTACACTGA-CTA-TCATCTCGAG
* * * * *
23320877 GCCGATGCCATG-TCTCAGACATGGTCTTACACAGGCTCTCATAAT-GTG
1 GCCGATG-CATGTTC-CAGACAT-GTCTTACACTGACTATCAT-CTCGAG
* * *
23320925 GCCGAAGCATGTCCCAAACATGTCTTACACT
1 GCCGATGCATGTTCCAGACATGTCTTACACT
23320956 AGCCTTCAAT
Statistics
Matches: 132, Mismatches: 27, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
45 2 0.02
46 68 0.52
47 32 0.24
48 29 0.22
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTTCCAGACATGTCTTACACTGACTATCATCTCGAG
Found at i:23321929 original size:45 final size:45
Alignment explanation
Indices: 23321865--23321953 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
23321855 CCCTATCTCG
*
23321865 TAACCGTCGCCAGAATAGGTAAGGGGCATTACCGGACTTGTAACC
1 TAACCGTCGCCAGAATAGGTAAGGGGCATTAACGGACTTGTAACC
*
23321910 TAACCGTCGCCGGAATAGGTAAGGGGCATTAACGGACTTGTAAC
1 TAACCGTCGCCAGAATAGGTAAGGGGCATTAACGGACTTGTAAC
23321954 TCATGTCAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.20
Consensus pattern (45 bp):
TAACCGTCGCCAGAATAGGTAAGGGGCATTAACGGACTTGTAACC
Found at i:23324126 original size:40 final size:40
Alignment explanation
Indices: 23324080--23324166 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
23324070 CTCGCACAAG
* * *
23324080 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAAT
* *
23324120 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAAT
23324160 GCCTTCG
1 GCCTTCG
23324167 AATCTNNNNN
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAAT
Found at i:23324546 original size:24 final size:23
Alignment explanation
Indices: 23324514--23324614 Score: 98
Period size: 23 Copynumber: 4.4 Consensus size: 23
23324504 GTCGTGGTCG
23324514 GTAAGCTCTATTGAGCTGAAAACA
1 GTAAGCTCTATTGAGCTG-AAACA
*
23324538 GTAAGCTCTATTGAGCT-AAATA
1 GTAAGCTCTATTGAGCTGAAACA
** * *
23324560 GTAAGCTCCT-TCAAGCTGAATCG
1 GTAAGCT-CTATTGAGCTGAAACA
* * *
23324583 GTAAGCTCCAATGAGCTGAAATA
1 GTAAGCTCTATTGAGCTGAAACA
23324606 GTAAGCTCT
1 GTAAGCTCT
23324615 CCCGAGCTAT
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
22 17 0.28
23 26 0.43
24 17 0.28
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (23 bp):
GTAAGCTCTATTGAGCTGAAACA
Found at i:23327385 original size:40 final size:40
Alignment explanation
Indices: 23327298--23327439 Score: 180
Period size: 40 Copynumber: 3.6 Consensus size: 40
23327288 ATTCCCAAAC
* * * *
23327298 CAAATGCCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAG-TAACTCGCA
** *
23327337 CATTTGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
**
23327377 CAAATGCCTTCAAGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
23327417 CAAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
23327440 NNNNNNNNNN
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 17 0.20
40 70 0.80
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:23346624 original size:56 final size:52
Alignment explanation
Indices: 23346511--23346624 Score: 124
Period size: 56 Copynumber: 2.1 Consensus size: 52
23346501 TGTTTATTTA
** **
23346511 TTTATTTTCATTTTTTCTTGTTAGTTATTATTATTTGTTATTTTATTTTTCT
1 TTTATTTTCATTTTTTCTTGTTAGTTATTATTATTTGTTATACTATTTTGAT
23346563 TTTATTTTCATTTTTTATCATTAGTTTA-TTATTATTATTTGTT-TACTATTTTGAT
1 TTTATTTTCA-TTTTT-TC-TT-G-TTAGTTATTATTATTTGTTATACTATTTTGAT
23346618 TATTATT
1 T-TTATT
23346625 ATTATTTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
52 10 0.19
53 5 0.10
54 2 0.04
55 11 0.21
56 21 0.40
57 3 0.06
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (52 bp):
TTTATTTTCATTTTTTCTTGTTAGTTATTATTATTTGTTATACTATTTTGAT
Found at i:23346708 original size:22 final size:21
Alignment explanation
Indices: 23346683--23346738 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 21
23346673 TGTTTATTCA
23346683 TATTATTTTTAGTTAGTATTTT
1 TATTATTTTTAG-TAGTATTTT
*
23346705 TATTATTTTTAGTATTATTTT
1 TATTATTTTTAGTAGTATTTT
23346726 TACTTATTATTTA
1 TA-TTATT-TTTA
23346739 CTTATTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 10 0.32
22 17 0.55
23 4 0.13
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
TATTATTTTTAGTAGTATTTT
Found at i:23346738 original size:11 final size:10
Alignment explanation
Indices: 23346699--23346746 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
23346689 TTTTAGTTAG
23346699 TATTTTTA-T
1 TATTTTTACT
*
23346708 TATTTTTAGTAT
1 TATTTTTA--CT
23346720 TATTTTTACT
1 TATTTTTACT
23346730 TATTATTTACT
1 TATT-TTTACT
23346741 TATTTT
1 TATTTT
23346747 CTTATTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 8 0.24
10 7 0.21
11 10 0.29
12 9 0.26
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (10 bp):
TATTTTTACT
Found at i:23352756 original size:30 final size:29
Alignment explanation
Indices: 23352704--23352763 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
23352694 TATGATATGG
23352704 TATCTTGGATTTCTGTACCTTGGATATCTT
1 TATCTTGGATTTCTGTA-CTTGGATATCTT
*
23352734 TATCTTGGATTCTTCTGT-CTTGGATTTCTT
1 TATCTTGGA-T-TTCTGTACTTGGATATCTT
23352764 CATTCTGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 20 0.74
31 1 0.04
32 6 0.22
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (29 bp):
TATCTTGGATTTCTGTACTTGGATATCTT
Found at i:23352764 original size:16 final size:16
Alignment explanation
Indices: 23352704--23352764 Score: 65
Period size: 15 Copynumber: 4.0 Consensus size: 16
23352694 TATGATATGG
*
23352704 TATCTTGGATTTC-TG
1 TATCTTGGATTTCTTC
* *
23352719 TACCTTGGATATCTT-
1 TATCTTGGATTTCTTC
23352734 TATCTTGGA-TTCTTC
1 TATCTTGGATTTCTTC
*
23352749 TGTCTTGGATTTCTTC
1 TATCTTGGATTTCTTC
23352765 ATTCTGGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.11
15 27 0.71
16 7 0.18
ACGTcount: A:0.13, C:0.18, G:0.16, T:0.52
Consensus pattern (16 bp):
TATCTTGGATTTCTTC
Found at i:23362487 original size:37 final size:37
Alignment explanation
Indices: 23362437--23362510 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
23362427 ACATTCTAGA
*
23362437 AAAGGTAGATAAGCTGCATTTATCAATTGGGGTTATC
1 AAAGGTAGATAAGCTGCATTTATCAACTGGGGTTATC
23362474 AAAGGTAGATAAGCTGCATTTATCAACTGGGGTTATC
1 AAAGGTAGATAAGCTGCATTTATCAACTGGGGTTATC
23362511 TACGTGTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.31
Consensus pattern (37 bp):
AAAGGTAGATAAGCTGCATTTATCAACTGGGGTTATC
Found at i:23362662 original size:20 final size:20
Alignment explanation
Indices: 23362637--23362687 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
23362627 ATATTCTGGT
*
23362637 TTAGCCTTTGTGGTATTC-TG
1 TTAGCCTTTGTGGCA-TCATG
*
23362657 TTAGCCTTCGTGGCATCATG
1 TTAGCCTTTGTGGCATCATG
23362677 TTAGCCTTTGT
1 TTAGCCTTTGT
23362688 CGCGTACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.45
Consensus pattern (20 bp):
TTAGCCTTTGTGGCATCATG
Found at i:23362717 original size:25 final size:25
Alignment explanation
Indices: 23362680--23362745 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
23362670 CATCATGTTA
*
23362680 GCCTTTGTCGCGTACTT-TATATATT
1 GCCTTTGTGGCGTA-TTATATATATT
* *
23362705 GCCTTTGTGGCGTATTATGTATGTT
1 GCCTTTGTGGCGTATTATATATATT
*
23362730 GCCTTTGTGGCATATT
1 GCCTTTGTGGCGTATT
23362746 CTGTCTAGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 2 0.06
25 34 0.94
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.47
Consensus pattern (25 bp):
GCCTTTGTGGCGTATTATATATATT
Found at i:23365234 original size:13 final size:13
Alignment explanation
Indices: 23365216--23365250 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
23365206 GGACACGCGC
23365216 CCATGTGGCCAGG
1 CCATGTGGCCAGG
*
23365229 CCATGTGGTCAGG
1 CCATGTGGCCAGG
23365242 CCATGTGGC
1 CCATGTGGC
23365251 TCACACAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.29, G:0.37, T:0.20
Consensus pattern (13 bp):
CCATGTGGCCAGG
Found at i:23366542 original size:25 final size:24
Alignment explanation
Indices: 23366434--23366596 Score: 107
Period size: 25 Copynumber: 6.6 Consensus size: 24
23366424 ATTAGAGAAT
* * *
23366434 GCTCATACGAGCACATAAACGGGAA
1 GCTCATAAGAGC-CATTATCGGGAA
** * *
23366459 GCTCATGTGAGCCAATATCGAGAA
1 GCTCATAAGAGCCATTATCGGGAA
* * * *
23366483 GTTCA-AGCGAGCCAATATCAGGAA
1 GCTCATA-AGAGCCATTATCGGGAA
* *
23366507 GCTCCA-GAGAGCCATTAATTGGGAA
1 GCT-CATAAGAGCCATT-ATCGGGAA
*
23366532 GCTCATAAGAGTCAGTTATCGGGAA
1 GCTCATAAGAGCCA-TTATCGGGAA
*
23366557 GCTC-TGAAGAGCCAATTATCGAGAA
1 GCTCAT-AAGAGCC-ATTATCGGGAA
23366582 GCTCATAAGAGCCAT
1 GCTCATAAGAGCCAT
23366597 AACGGAAGCT
Statistics
Matches: 108, Mismatches: 22, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
24 40 0.37
25 64 0.59
26 4 0.04
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (24 bp):
GCTCATAAGAGCCATTATCGGGAA
Found at i:23366796 original size:105 final size:104
Alignment explanation
Indices: 23366614--23366809 Score: 261
Period size: 105 Copynumber: 1.9 Consensus size: 104
23366604 GCTCGAAATA
* * *
23366614 ATTAACGGGAAGCTCCGGAGAGCCATATATCAAGACGCTCATAAGAGTTGCAGTGTGTCCACAAC
1 ATTAACGGGAAGCTCCGGAAAGCCAAATATCAAGACGCTCATAACAGTTG-AGTGTGTCCACAAC
*
23366679 ACATGCAGGATCACAACCAATCGGGATGCTTTGAAGAGCT
65 ACATGCAGGATCACAACCAATAGGGATGCTTTGAAGAGCT
* * * *
23366719 ATTAACGGGAAGCT-TGTGAAAGCCAAATATCAAGATGCTCGTAACAGCTATG-GTGTGTCCGCA
1 ATTAACGGGAAGCTCCG-GAAAGCCAAATATCAAGACGCTCATAACAG-T-TGAGTGTGTCCACA
*
23366782 ACACATGCAGGATCACAGCCAATAGGGA
63 ACACATGCAGGATCACAACCAATAGGGA
23366810 ACCCCGTATC
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
104 1 0.01
105 75 0.95
106 1 0.01
107 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (104 bp):
ATTAACGGGAAGCTCCGGAAAGCCAAATATCAAGACGCTCATAACAGTTGAGTGTGTCCACAACA
CATGCAGGATCACAACCAATAGGGATGCTTTGAAGAGCT
Found at i:23367116 original size:21 final size:21
Alignment explanation
Indices: 23367090--23367140 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
23367080 TATGCGAATG
*
23367090 AATTTA-ATATCAATTTAATAC
1 AATTTACAT-TCAATTCAATAC
*
23367111 AATTTACATTCAATTCAATCC
1 AATTTACATTCAATTCAATAC
*
23367132 AATTCACAT
1 AATTTACAT
23367141 ATTAGGCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTTACATTCAATTCAATAC
Found at i:23379860 original size:15 final size:15
Alignment explanation
Indices: 23379842--23379872 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23379832 TGATCGATAG
*
23379842 TATGATGACGTTTCC
1 TATGATAACGTTTCC
23379857 TATGATAACGTTTCC
1 TATGATAACGTTTCC
23379872 T
1 T
23379873 GACGATCCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (15 bp):
TATGATAACGTTTCC
Found at i:23393402 original size:3 final size:3
Alignment explanation
Indices: 23393394--23393425 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
23393384 TACATTCCAA
23393394 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
23393426 GTAAATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:23393573 original size:27 final size:29
Alignment explanation
Indices: 23393523--23393587 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
23393513 TTCTATATTG
23393523 TATATATATTGCTTTTGTATGTATTATGTA
1 TATATATATT-CTTTTGTATGTATTATGTA
* *
23393553 TATATATATT-TTTTTTA-GTATTATGTT
1 TATATATATTCTTTTGTATGTATTATGTA
*
23393580 TTTATATA
1 TATATATA
23393588 CTATTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 16 0.50
28 6 0.19
30 10 0.31
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (29 bp):
TATATATATTCTTTTGTATGTATTATGTA
Found at i:23393642 original size:23 final size:24
Alignment explanation
Indices: 23393591--23393633 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
23393581 TTATATACTA
23393591 TTATATA--TTTTAATATTATTAG
1 TTATATACCTTTTAATATTATTAG
23393613 TTATATACCTTTT-ATATTATT
1 TTATATACCTTTTAATATTATT
23393634 GTATGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (24 bp):
TTATATACCTTTTAATATTATTAG
Found at i:23394472 original size:37 final size:39
Alignment explanation
Indices: 23394430--23394509 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
23394420 TGTTTTCATG
* * *
23394430 TATATA-CCTTTAATACCA-TATTATTTGTATATTTATA
1 TATATATCCTTAAATACCATTATTATTTATATATATATA
* *
23394467 TATATATTCTTAAATATCATTATTATTTATATATATATA
1 TATATATCCTTAAATACCATTATTATTTATATATATATA
23394506 TATA
1 TATA
23394510 CTTTATGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 6 0.17
38 9 0.25
39 21 0.58
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (39 bp):
TATATATCCTTAAATACCATTATTATTTATATATATATA
Found at i:23394522 original size:39 final size:37
Alignment explanation
Indices: 23394439--23394522 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 37
23394429 GTATATACCT
* * * *
23394439 TTAATACCATATTATTTGTATATTTATATATATATTC
1 TTAATATCATATTATTTATATATATATATATATATTA
23394476 TTAAATATCATTATTATTTATATATATATATATACT-TTA
1 TT-AATATCA-TATTATTTATATATATATATATA-TATTA
23394515 TGTAATAT
1 T-TAATAT
23394523 ATCAATAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 2 0.05
38 6 0.15
39 29 0.74
40 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (37 bp):
TTAATATCATATTATTTATATATATATATATATATTA
Found at i:23394644 original size:17 final size:17
Alignment explanation
Indices: 23394607--23394649 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
23394597 TGCTACGTAT
* *
23394607 ATATATGTATTTTTATT
1 ATATATGTATATTTATA
*
23394624 ATATATGTATATTTCTA
1 ATATATGTATATTTATA
23394641 ATATTATGT
1 ATA-TATGT
23394650 TACGTTGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (17 bp):
ATATATGTATATTTATA
Found at i:23402016 original size:14 final size:14
Alignment explanation
Indices: 23401997--23402031 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
23401987 GCCCTTTCCC
*
23401997 GGCCTTCAGACATA
1 GGCCTTCAAACATA
23402011 GGCCTTCAAACATA
1 GGCCTTCAAACATA
23402025 GGCCTTC
1 GGCCTTC
23402032 TACTACTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (14 bp):
GGCCTTCAAACATA
Found at i:23404586 original size:23 final size:23
Alignment explanation
Indices: 23404560--23404611 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
23404550 TTCTAACAGG
*
23404560 CACACCAGAATTTCCAACCCAAA
1 CACACCAGAATATCCAACCCAAA
23404583 CACACCAGAATATCCAACCCAAA
1 CACACCAGAATATCCAACCCAAA
23404606 CACACC
1 CACACC
23404612 CGGAATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.44, C:0.42, G:0.04, T:0.10
Consensus pattern (23 bp):
CACACCAGAATATCCAACCCAAA
Found at i:23404898 original size:8 final size:10
Alignment explanation
Indices: 23404869--23404909 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
23404859 ATTCTAATAA
*
23404869 TCACATATTT
1 TCACACATTT
23404879 TCACACATTT
1 TCACACATTT
23404889 TCACA-A-TT
1 TCACACATTT
*
23404897 TCATACATTT
1 TCACACATTT
23404907 TCA
1 TCA
23404910 TTCAATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 6 0.22
9 2 0.07
10 19 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (10 bp):
TCACACATTT
Found at i:23405132 original size:15 final size:15
Alignment explanation
Indices: 23405108--23405160 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
23405098 ATATATATAT
*
23405108 TATAATTTCAATCAA
1 TATAAATTCAATCAA
23405123 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* * *
23405138 AATGATTTCAATCAA
1 TATAAATTCAATCAA
23405153 TATAAATT
1 TATAAATT
23405161 TGATAAATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:23411255 original size:17 final size:17
Alignment explanation
Indices: 23411221--23411258 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
23411211 TGTGTACACG
23411221 TGTAAAAATAAAATATA
1 TGTAAAAATAAAATATA
23411238 TGTATAAAATAATAATATA
1 TGTA-AAAATAA-AATATA
23411257 TG
1 TG
23411259 AAATACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (17 bp):
TGTAAAAATAAAATATA
Found at i:23411287 original size:5 final size:5
Alignment explanation
Indices: 23411277--23411309 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
23411267 AATATTTAAG
*
23411277 TATAT TATAT TATTT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
23411310 TATAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATAT
Found at i:23411405 original size:17 final size:18
Alignment explanation
Indices: 23411380--23411422 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
23411370 AACGAAACAG
23411380 AGAAGAAAGAGAAAGAAA
1 AGAAGAAAGAGAAAGAAA
23411398 AGAA-AAAGAGAAAGAAA
1 AGAAGAAAGAGAAAGAAA
*
23411415 AGGAGAAA
1 AGAAGAAA
23411423 AGCTAGGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAGAAAGAGAAAGAAA
Found at i:23411413 original size:12 final size:12
Alignment explanation
Indices: 23411383--23411422 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
23411373 GAAACAGAGA
*
23411383 AGAAAGAGAAAG
1 AGAAAGAAAAAG
23411395 A-AAAGAAAAAG
1 AGAAAGAAAAAG
*
23411406 AGAAAGAAAAGG
1 AGAAAGAAAAAG
23411418 AGAAA
1 AGAAA
23411423 AGCTAGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAG
Found at i:23413882 original size:22 final size:22
Alignment explanation
Indices: 23413841--23413946 Score: 97
Period size: 22 Copynumber: 4.7 Consensus size: 22
23413831 TCAGCTTGTA
*
23413841 AGAGCTTACTGGCTTCAGCTCATT
1 AGAGCTTACT-G-TTCAGCTCAAT
* **
23413865 GGAGCTTACTGTTCAGCT-TGT
1 AGAGCTTACTGTTCAGCTCAAT
* * *
23413886 ATTAGCTTAGTATTCAGCTCAAT
1 A-GAGCTTACTGTTCAGCTCAAT
*
23413909 AGAGCTTACCGTTTCAGCTCAAT
1 AGAGCTTACTG-TTCAGCTCAAT
23413932 AGAGCTTACTGTTCA
1 AGAGCTTACTGTTCA
23413947 TCAACTCAGG
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
21 1 0.02
22 31 0.48
23 24 0.37
24 9 0.14
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (22 bp):
AGAGCTTACTGTTCAGCTCAAT
Found at i:23417473 original size:17 final size:17
Alignment explanation
Indices: 23417447--23417483 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
23417437 TTAAAACCCT
23417447 AAACCCTAATTCTTAAA
1 AAACCCTAATTCTTAAA
*
23417464 AAACCTTAATTCTTAAA
1 AAACCCTAATTCTTAAA
23417481 AAA
1 AAA
23417484 ATCCTAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (17 bp):
AAACCCTAATTCTTAAA
Found at i:23418738 original size:31 final size:30
Alignment explanation
Indices: 23418677--23418760 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
23418667 AAAATTTGAG
*
23418677 AAAAGTATTTAAATTTTAAATTTTTGAAAA
1 AAAAGTATTTAAATTTTAAAATTTTGAAAA
**
23418707 AAAAGTATTTAGTTTTTAAAATTTTGAAAA
1 AAAAGTATTTAAATTTTAAAATTTTGAAAA
* *
23418737 AAGAA-AACTTAAATTTTCAAAATT
1 AA-AAGTATTTAAATTTT-AAAATT
23418761 ATATATTCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 37 0.82
31 8 0.18
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (30 bp):
AAAAGTATTTAAATTTTAAAATTTTGAAAA
Found at i:23420176 original size:17 final size:18
Alignment explanation
Indices: 23420146--23420179 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
23420136 ATGCCATGTG
23420146 AAAAACATAAATAAAAAT
1 AAAAACATAAATAAAAAT
*
23420164 AAAAA-ATACATAAAAA
1 AAAAACATAAATAAAAA
23420180 GATATAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAACATAAATAAAAAT
Found at i:23421334 original size:16 final size:18
Alignment explanation
Indices: 23421313--23421349 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23421303 TTTTATATAT
23421313 TATAAAT-T-ACATAATA
1 TATAAATATAACATAATA
*
23421329 TATAAATATAATATAATA
1 TATAAATATAACATAATA
23421347 TAT
1 TAT
23421350 TACAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAATATAACATAATA
Found at i:23424613 original size:17 final size:16
Alignment explanation
Indices: 23424591--23424637 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
23424581 AATCGCCACC
23424591 AATATTCTTTGGTTTGT
1 AATATTCTTTGGTTT-T
23424608 AATATTCTATTTGG-TTT
1 AATATTC--TTTGGTTTT
*
23424625 CATATTCTTTGGT
1 AATATTCTTTGGT
23424638 ATGCGATCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 5 0.19
17 14 0.54
18 2 0.08
19 5 0.19
ACGTcount: A:0.19, C:0.09, G:0.15, T:0.57
Consensus pattern (16 bp):
AATATTCTTTGGTTTT
Found at i:23425621 original size:32 final size:32
Alignment explanation
Indices: 23425552--23425657 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 32
23425542 CAGTTCTGTG
* * * * *
23425552 AAATGATAACAAATATTAGCTTTTCATTTTATG
1 AAATGATAACAAATATCAAC-TTTAATTTTGTA
23425585 AAATGATAACAAAT-TACAACTTTAATTTTGTA
1 AAATGATAACAAATAT-CAACTTTAATTTTGTA
* *
23425617 AAATGATAACAAATATCAATTTTAATTTTGTT
1 AAATGATAACAAATATCAACTTTAATTTTGTA
23425649 AAATGATAA
1 AAATGATAA
23425658 TTATATTCCT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
32 47 0.73
33 17 0.27
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (32 bp):
AAATGATAACAAATATCAACTTTAATTTTGTA
Found at i:23426720 original size:47 final size:47
Alignment explanation
Indices: 23426651--23426740 Score: 180
Period size: 47 Copynumber: 1.9 Consensus size: 47
23426641 GAGGTCCATA
23426651 AATGGTAATTAGACCATTAGGTTTTCATGGACAAAAATGGACACATC
1 AATGGTAATTAGACCATTAGGTTTTCATGGACAAAAATGGACACATC
23426698 AATGGTAATTAGACCATTAGGTTTTCATGGACAAAAATGGACA
1 AATGGTAATTAGACCATTAGGTTTTCATGGACAAAAATGGACA
23426741 TACATAGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (47 bp):
AATGGTAATTAGACCATTAGGTTTTCATGGACAAAAATGGACACATC
Found at i:23427834 original size:53 final size:53
Alignment explanation
Indices: 23427754--23427858 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
23427744 ATAAACTACG
* ** * *
23427754 ATAAGGCAAAGATCCCATGTAACACCATGCCAAGGCATGGAAATGGTGAGTTC
1 ATAAGGCAAAGATACCACATAACACCATGCCAAGACATGGAAATGGTAAGTTC
* * *
23427807 ATAAGGCAAGGATACCACATAAGACCATGTCAAGACATGGAAATGGTAAGTT
1 ATAAGGCAAAGATACCACATAACACCATGCCAAGACATGGAAATGGTAAGTT
23427859 TAAAAAGGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (53 bp):
ATAAGGCAAAGATACCACATAACACCATGCCAAGACATGGAAATGGTAAGTTC
Found at i:23434220 original size:40 final size:40
Alignment explanation
Indices: 23434165--23434369 Score: 349
Period size: 40 Copynumber: 5.1 Consensus size: 40
23434155 ATTTGAATTT
*
23434165 TATCCGGGCTAAGTCTCGAAGGGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATG
* *
23434205 TATCCGGGCTAAGTCTCGAAGGGCATTCATGCTAGTGATG
1 TATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATG
23434245 TATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATG
*
23434285 TATCCGGACTAAGTCTCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATG
*
23434325 TATCCGGACTAAGT-TCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCT-CGAAGAGCATTCGTGCTAGTGATG
23434365 TATCC
1 TATCC
23434370 NNNNNNNNNN
Statistics
Matches: 160, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
39 1 0.01
40 159 0.99
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATG
Found at i:23437237 original size:47 final size:47
Alignment explanation
Indices: 23437163--23437459 Score: 459
Period size: 47 Copynumber: 6.3 Consensus size: 47
23437153 NNNNNNNNNN
* * *
23437163 TATATATGTGATAAGGCCTAATAGCCGATGTGACGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG
*
23437210 TATATATGTGATAAGGCCTAATGGCCGACGTGACGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG
* * *
23437257 TATATATGTGAGAAGGCCTAATAGCCGACGTGAGGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG
*
23437304 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG
*
23437351 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG
* * * * *
23437398 TATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG
*
23437445 TATAAATGTGATAAG
1 TATATATGTGATAAG
23437460 TCCCGAAGGG
Statistics
Matches: 233, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 233 1.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG
Found at i:23439103 original size:21 final size:21
Alignment explanation
Indices: 23439077--23439134 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
23439067 GTACAAACAA
23439077 GGGCACGTAAGTGCAATTTAG
1 GGGCACGTAAGTGCAATTTAG
* *
23439098 GGGCACCG-AAGTACAA-ATAG
1 GGGCA-CGTAAGTGCAATTTAG
23439118 GGGCAC-TAAGTGCAATT
1 GGGCACGTAAGTGCAATT
23439135 CAAAGGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 8 0.27
20 8 0.27
21 12 0.40
22 2 0.07
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (21 bp):
GGGCACGTAAGTGCAATTTAG
Found at i:23439149 original size:40 final size:41
Alignment explanation
Indices: 23439061--23439175 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 41
23439051 ATTTAGGGGT
* * **
23439061 ACCGAAGTACAAACAAGGGCACGTAAGTGCAATTTAGGGGC
1 ACCGAAGTACAAACAAGGGCACATAAGTGCAATTCAAAGGC
* * *
23439102 ACCGAAGTACAAATAGGGGCAC-TAAGTGCAATTCAAAGGT
1 ACCGAAGTACAAACAAGGGCACATAAGTGCAATTCAAAGGC
** *
23439142 ATTGAAGTGCAAACAAGGGCACATAAGTGCAATT
1 ACCGAAGTACAAACAAGGGCACATAAGTGCAATT
23439176 TAGGGTATAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
40 31 0.50
41 31 0.50
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (41 bp):
ACCGAAGTACAAACAAGGGCACATAAGTGCAATTCAAAGGC
Found at i:23439183 original size:40 final size:40
Alignment explanation
Indices: 23439046--23439180 Score: 171
Period size: 41 Copynumber: 3.3 Consensus size: 40
23439036 GAGCATGTAT
23439046 GTGCAATTTAGGGGTACCGAAGTACAAACAAGGGCACGTAA
1 GTGCAATTTAGGGGTACCGAAGTACAAACAAGGGCAC-TAA
* * *
23439087 GTGCAATTTAGGGGCACCGAAGTACAAATAGGGGCACTAA
1 GTGCAATTTAGGGGTACCGAAGTACAAACAAGGGCACTAA
* ** ** *
23439127 GTGCAATTCAAAGGTATTGAAGTGCAAACAAGGGCACATAA
1 GTGCAATTTAGGGGTACCGAAGTACAAACAAGGGCAC-TAA
23439168 GTGCAATTTAGGG
1 GTGCAATTTAGGG
23439181 TATAATTAAG
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 31 0.40
41 47 0.60
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (40 bp):
GTGCAATTTAGGGGTACCGAAGTACAAACAAGGGCACTAA
Found at i:23440685 original size:21 final size:22
Alignment explanation
Indices: 23440660--23440708 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
23440650 ATATAATTTT
23440660 TAAATATATAAAATACAT-AAAA
1 TAAATATATAAAA-ACATCAAAA
*
23440682 -AAATA-CTAAAAACATCAAAA
1 TAAATATATAAAAACATCAAAA
23440702 TAAATAT
1 TAAATAT
23440709 TTTCTAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.17
20 9 0.39
21 10 0.43
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAATATATAAAAACATCAAAA
Found at i:23445603 original size:18 final size:18
Alignment explanation
Indices: 23445568--23445610 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
23445558 TTATTAACAA
*
23445568 TTTAATATATATATTTAT
1 TTTAATATATATAGTTAT
23445586 TTTAATATCATAT-GTTAT
1 TTTAATAT-ATATAGTTAT
23445604 TATTAAT
1 T-TTAAT
23445611 TAATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTAATATATATAGTTAT
Found at i:23450299 original size:28 final size:29
Alignment explanation
Indices: 23450245--23450301 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
23450235 TAAAAAGTAA
*
23450245 AAAGACTAAATTATTAAAAATAAAAAAAT
1 AAAGACTAAATTACTAAAAATAAAAAAAT
*
23450274 AAAGACTAAATT-CTAAAAGTAAAAAAAT
1 AAAGACTAAATTACTAAAAATAAAAAAAT
23450302 CTTAAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (29 bp):
AAAGACTAAATTACTAAAAATAAAAAAAT
Found at i:23451117 original size:30 final size:30
Alignment explanation
Indices: 23451081--23451140 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
23451071 CTGGGTTAAT
* *
23451081 CTAATATTTTTCTCATTAAAATATTGAAAA
1 CTAATATTTTTCCCATTAAAATATTAAAAA
23451111 CTAATATTTTTCCCATTAAAATATTAAAAA
1 CTAATATTTTTCCCATTAAAATATTAAAAA
23451141 ATTATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.42
Consensus pattern (30 bp):
CTAATATTTTTCCCATTAAAATATTAAAAA
Found at i:23451149 original size:9 final size:9
Alignment explanation
Indices: 23451127--23451388 Score: 99
Period size: 9 Copynumber: 27.7 Consensus size: 9
23451117 TTTTTCCCAT
23451127 TAAAATATTA
1 TAAAA-ATTA
23451137 -AAAAATTA
1 TAAAAATTA
*
23451145 TAAAAATCAGA
1 TAAAAAT--TA
*
23451156 AAAAAATTA
1 TAAAAATTA
23451165 TAAAAA-TA
1 TAAAAATTA
23451173 GTAAAAA-TA
1 -TAAAAATTA
*
23451182 TCAAAAAAATA
1 T--AAAAATTA
23451193 TAAAAATTA
1 TAAAAATTA
23451202 -AAAAATATA
1 TAAAAAT-TA
*
23451211 TGAAAATTGA
1 TAAAAATT-A
* * *
23451221 TTTAAACTTT
1 -TAAAAATTA
23451231 TAAAAATTA
1 TAAAAATTA
23451240 TAAAAATTAA
1 TAAAAATT-A
* *
23451250 TAAATACTA
1 TAAAAATTA
23451259 TCAAAAA-TA
1 T-AAAAATTA
23451268 TAATAAATCTA
1 TAA-AAAT-TA
*
23451279 -ATAAATTA
1 TAAAAATTA
23451287 T--AAATTAA
1 TAAAAATT-A
*
23451295 TAAAACATATT
1 TAAAA-AT-TA
*
23451306 TAAAATTTCA
1 TAAAAATT-A
23451316 TAAAAATGTA
1 TAAAAAT-TA
* *
23451326 TTAAAATTC
1 TAAAAATTA
*
23451335 TATAAAATCA
1 TA-AAAATTA
**
23451345 TAAAAAGAA
1 TAAAAATTA
*
23451354 TAAAAAGTA
1 TAAAAATTA
*
23451363 TTAAAATTTA
1 -TAAAAATTA
*
23451373 TATAAAATCA
1 TA-AAAATTA
23451383 TAAAAA
1 TAAAAA
23451389 CCTGAATTGA
Statistics
Matches: 193, Mismatches: 32, Indels: 55
0.69 0.11 0.20
Matches are distributed among these distances:
7 5 0.03
8 19 0.10
9 82 0.42
10 60 0.31
11 26 0.13
12 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:23451178 original size:20 final size:20
Alignment explanation
Indices: 23451136--23451198 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
23451126 TTAAAATATT
23451136 AAAAAATTATAAAAATCAG-A
1 AAAAAATTATAAAAAT-AGTA
23451156 AAAAAATTATAAAAATAGTA
1 AAAAAATTATAAAAATAGTA
* * *
23451176 AAAATATCAAAAAAATA-TA
1 AAAAAATTATAAAAATAGTA
23451195 AAAA
1 AAAA
23451199 TTAAAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 8 0.21
20 31 0.79
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAAAATTATAAAAATAGTA
Found at i:23451211 original size:29 final size:29
Alignment explanation
Indices: 23451155--23451209 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
23451145 TAAAAATCAG
*
23451155 AAAAAAATTATAAAAATAGTAAAAATATC
1 AAAAAAATTATAAAAATAGAAAAAATATC
*
23451184 AAAAAAA-TATAAAAAT-TAAAAAATAT
1 AAAAAAATTATAAAAATAGAAAAAATAT
23451210 ATGAAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 9 0.38
29 7 0.29
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (29 bp):
AAAAAAATTATAAAAATAGAAAAAATATC
Found at i:23451216 original size:29 final size:28
Alignment explanation
Indices: 23451128--23451216 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 28
23451118 TTTTCCCATT
23451128 AAAATATTAAAAAATTATAAAAATCA-GAAA
1 AAAATA-T-AAAAATTATAAAAAT-ATGAAA
*
23451158 AAAATTATAAAAA-TAGTAAAAATATCAAA
1 AAAA-TATAAAAATTA-TAAAAATATGAAA
*
23451187 AAAATATAAAAATTAAAAAATATATGAAA
1 AAAATATAAAAATTATAAAA-ATATGAAA
23451216 A
1 A
23451217 TTGATTTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
28 15 0.29
29 29 0.57
30 5 0.10
31 2 0.04
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (28 bp):
AAAATATAAAAATTATAAAAATATGAAA
Found at i:23451308 original size:75 final size:74
Alignment explanation
Indices: 23451157--23451331 Score: 171
Period size: 75 Copynumber: 2.3 Consensus size: 74
23451147 AAAATCAGAA
*
23451157 AAAAATTATAAAAA-TAGTAAAAATATCAAAAAAATATAAAAATTAAAAAATATATGAAAATTGA
1 AAAAATTATAAAAATTAATAAAAATATC-AAAAAATATAAAAATTAAAAAATATAT-AAAATTGA
* *
23451221 TTTAAACTTTT
64 ATAAAACTTTT
* *
23451232 AAAAATTATAAAAATTAATAAATACTATC-AAAAATATAATAAATCTAATAAAT-TAT-AAATT-
1 AAAAATTATAAAAATTAATAAA-AATATCAAAAAATATAA-AAAT-TAAAAAATATATAAAATTG
23451293 AATAAAACATATTT
63 AATAAAAC-T-TTT
* *
23451307 AAAATTTCATAAAAATGTATTAAAA
1 AAAAATT-ATAAAAAT-TAATAAAA
23451332 TTCTATAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
73 6 0.07
74 6 0.07
75 33 0.39
76 22 0.26
77 18 0.21
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (74 bp):
AAAAATTATAAAAATTAATAAAAATATCAAAAAATATAAAAATTAAAAAATATATAAAATTGAAT
AAAACTTTT
Found at i:23451320 original size:21 final size:22
Alignment explanation
Indices: 23451294--23451346 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
23451284 TTATAAATTA
23451294 ATAAAACATAT-TTAAAATT-T
1 ATAAAACATATATTAAAATTCT
*
23451314 CATAAAA-ATGTATTAAAATTCT
1 -ATAAAACATATATTAAAATTCT
23451336 ATAAAATCATA
1 ATAAAA-CATA
23451347 AAAAGAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.12
21 20 0.77
22 1 0.04
23 2 0.08
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAAACATATATTAAAATTCT
Found at i:23451358 original size:38 final size:38
Alignment explanation
Indices: 23451315--23451388 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 38
23451305 TTAAAATTTC
*
23451315 ATAAAAATGTATTAAAA-TTCTATAAAATCATAAAAAGA
1 ATAAAAA-GTATTAAAATTTATATAAAATCATAAAAAGA
23451353 ATAAAAAGTATTAAAATTTATATAAAATCATAAAAA
1 ATAAAAAGTATTAAAATTTATATAAAATCATAAAAA
23451389 CCTGAATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 9 0.26
38 25 0.74
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (38 bp):
ATAAAAAGTATTAAAATTTATATAAAATCATAAAAAGA
Found at i:23451972 original size:18 final size:19
Alignment explanation
Indices: 23451944--23451979 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
23451934 AAACAGTTAA
*
23451944 ATATGTTTTTTTTAATTTT
1 ATATGTTTTTTATAATTTT
23451963 ATAT-TTTTTTATAATTT
1 ATATGTTTTTTATAATTT
23451980 ATTAGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
ATATGTTTTTTATAATTTT
Found at i:23452008 original size:29 final size:27
Alignment explanation
Indices: 23451959--23452038 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
23451949 TTTTTTTTAA
**
23451959 TTTTATATTTTTTTATAATTTATTAGAGT
1 TTTTATATTTTTCAATAATTTA-TA-AGT
23451988 TTTTATATTTTTACAAT-ATTTATAAGT
1 TTTTATATTTTT-CAATAATTTATAAGT
**
23452015 TTTTATAAATTT-AATAAGTTTATA
1 TTTTATATTTTTCAATAA-TTTATA
23452039 TTAATTTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.07
26 1 0.02
27 19 0.43
28 2 0.05
29 17 0.39
30 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (27 bp):
TTTTATATTTTTCAATAATTTATAAGT
Found at i:23452015 original size:27 final size:29
Alignment explanation
Indices: 23451959--23452021 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
23451949 TTTTTTTTAA
**
23451959 TTTTATATTTTTTTATAATTTATTAGAGT
1 TTTTATATTTTTCAATAATTTATTAGAGT
23451988 TTTTATATTTTTACAAT-ATTTA-TA-AGT
1 TTTTATATTTTT-CAATAATTTATTAGAGT
23452015 TTTTATA
1 TTTTATA
23452022 AATTTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 10 0.32
28 2 0.06
29 17 0.55
30 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (29 bp):
TTTTATATTTTTCAATAATTTATTAGAGT
Found at i:23452019 original size:19 final size:19
Alignment explanation
Indices: 23451995--23452035 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
23451985 AGTTTTTATA
23451995 TTTTTACAATATTT-ATAAG
1 TTTTTACAA-ATTTAATAAG
*
23452014 TTTTTATAAATTTAATAAG
1 TTTTTACAAATTTAATAAG
23452033 TTT
1 TTT
23452036 ATATTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTTACAAATTTAATAAG
Found at i:23452044 original size:19 final size:18
Alignment explanation
Indices: 23452005--23452045 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
23451995 TTTTTACAAT
*
23452005 ATTTATAAGTTTTTATAA
1 ATTTATAAGTTTATATAA
*
23452023 ATTTAATAAGTTTATATTA
1 ATTT-ATAAGTTTATATAA
23452042 ATTT
1 ATTT
23452046 CAATGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
ATTTATAAGTTTATATAA
Found at i:23457068 original size:9 final size:9
Alignment explanation
Indices: 23457048--23457103 Score: 60
Period size: 9 Copynumber: 6.2 Consensus size: 9
23457038 TAAGAGTTAA
23457048 TTTTAA-TT
1 TTTTAATTT
23457056 TTTTAATTT
1 TTTTAATTT
23457065 TTTTAATTT
1 TTTTAATTT
*
23457074 TTTTCATTT
1 TTTTAATTT
* *
23457083 ATGTAATTT
1 TTTTAATTT
*
23457092 TAATTAATTT
1 T-TTTAATTT
23457102 TT
1 TT
23457104 ATTTTATAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
8 6 0.16
9 25 0.66
10 7 0.18
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTAATTT
Found at i:23459193 original size:62 final size:59
Alignment explanation
Indices: 23459077--23459197 Score: 140
Period size: 62 Copynumber: 2.0 Consensus size: 59
23459067 TTGTACAAAC
* **
23459077 TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTGAATATTCTAATAGTAAAT
1 TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAACTAATAG-AAAT
23459137 TATTTTTATATT-TTGTCCTATTTAATAAAATAGAAA-TTCTTTTGAATAAAAC-AATAGAAAT
1 TATTTTTATATTGTT-T-C-ATTTAATAAAATA-AAAGTTCTTTTGAAT-AAACTAATAGAAAT
23459198 AACGCGACAC
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
59 2 0.04
60 13 0.25
61 5 0.09
62 28 0.53
63 5 0.09
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (59 bp):
TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAACTAATAGAAAT
Found at i:23461791 original size:49 final size:49
Alignment explanation
Indices: 23461729--23461851 Score: 158
Period size: 49 Copynumber: 2.5 Consensus size: 49
23461719 TTTGTTGTGT
* * *
23461729 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGA
1 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACACCAATAGATAAAA
* * ** *
23461778 G-CAAGTGTAAGACCTGTTTGGGACATGGCATCGGCGTCAATATATAAAA
1 GTC-AGTGTAAGACCTGTCTGGGACATGGCATCGACACCAATAGATAAAA
23461827 GTCAGTGTAAGACCTGTCTGGGACA
1 GTCAGTGTAAGACCTGTCTGGGACA
23461852 CTGTATCGAC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.02
49 61 0.97
50 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (49 bp):
GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACACCAATAGATAAAA
Found at i:23469571 original size:49 final size:48
Alignment explanation
Indices: 23469504--23469679 Score: 198
Period size: 49 Copynumber: 3.6 Consensus size: 48
23469494 GTTGTGCGTT
23469504 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATA-ATGAGAGCC
* * *
23469553 AGTGTAAGACCTGTCTGGGACATGACATCGAC-CTTGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACAC-TGATA-ATGAGAGCC
* * * *
23469602 AGTGTAAGACCTGTCTGGGGCATGGCATCGA-A-T-TTAATGTGCTAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATAATGAG--AGCC
*
23469649 AGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGTGTAAGACC-TGTCTGGGACATGGCATCG
23469680 GCATTTTATC
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
45 3 0.03
46 2 0.02
47 14 0.13
48 18 0.17
49 72 0.66
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATAATGAGAGCC
Found at i:23470385 original size:25 final size:25
Alignment explanation
Indices: 23470351--23470401 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
23470341 ATCATGTTGA
23470351 GATAGAATAGATTGTGTTTTAGGGT
1 GATAGAATAGATTGTGTTTTAGGGT
23470376 GATAGAATAGATTGTGTTTTAGGGT
1 GATAGAATAGATTGTGTTTTAGGGT
23470401 G
1 G
23470402 GCAAGGGGCT
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:0.27, C:0.00, G:0.33, T:0.39
Consensus pattern (25 bp):
GATAGAATAGATTGTGTTTTAGGGT
Found at i:23470924 original size:20 final size:21
Alignment explanation
Indices: 23470885--23470924 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23470875 GTCACAATGG
23470885 CCACACGAGCGTGTTGCCCTT
1 CCACACGAGCGTGTTGCCCTT
23470906 CCACACG-GACGTG-TGCCCT
1 CCACACGAG-CGTGTTGCCCT
23470925 GCTTCAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (21 bp):
CCACACGAGCGTGTTGCCCTT
Found at i:23471770 original size:21 final size:20
Alignment explanation
Indices: 23471745--23471841 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
23471735 GAATCCCAAC
23471745 CCTTGAACCTTAAGCCATGAA
1 CCTTGAACCTTAA-CCATGAA
* * * *
23471766 TCTTGAACCTCAAACATCACA
1 CCTTGAACCTTAACCATGA-A
23471787 CCTTGAACCTTAAACC-TCGAA
1 CCTTGAACCTT-AACCAT-GAA
* *
23471808 CCTTGAACCTTGCACCTTGAA
1 CCTTGAACCTT-AACCATGAA
* *
23471829 CCATGAACTTTAA
1 CCTTGAACCTTAA
23471842 ACCTCAACCC
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
20 5 0.08
21 49 0.83
22 5 0.08
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.26
Consensus pattern (20 bp):
CCTTGAACCTTAACCATGAA
Found at i:23471802 original size:7 final size:7
Alignment explanation
Indices: 23471786--23471836 Score: 66
Period size: 7 Copynumber: 7.3 Consensus size: 7
23471776 CAAACATCAC
23471786 ACCTTGA
1 ACCTTGA
*
23471793 ACCTTAA
1 ACCTTGA
*
23471800 ACCTCGA
1 ACCTTGA
23471807 ACCTTGA
1 ACCTTGA
*
23471814 ACCTTGC
1 ACCTTGA
23471821 ACCTTGA
1 ACCTTGA
*
23471828 ACCATGA
1 ACCTTGA
23471835 AC
1 AC
23471837 TTTAAACCTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.31, C:0.33, G:0.12, T:0.24
Consensus pattern (7 bp):
ACCTTGA
Found at i:23471803 original size:14 final size:14
Alignment explanation
Indices: 23471745--23471845 Score: 67
Period size: 14 Copynumber: 7.2 Consensus size: 14
23471735 GAATCCCAAC
*
23471745 CCTTGAACCTTAAG
1 CCTTGAACCTTAAA
* * *
23471759 CCATGAATCTTGAA
1 CCTTGAACCTTAAA
** * * *
23471773 CCTCAAACATCACA
1 CCTTGAACCTTAAA
23471787 CCTTGAACCTTAAA
1 CCTTGAACCTTAAA
* *
23471801 CCTCGAACCTTGAA
1 CCTTGAACCTTAAA
* *
23471815 CCTTGCACCTTGAA
1 CCTTGAACCTTAAA
* *
23471829 CCATGAACTTTAAA
1 CCTTGAACCTTAAA
23471843 CCT
1 CCT
23471846 CAACCCTCAA
Statistics
Matches: 61, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
14 61 1.00
ACGTcount: A:0.33, C:0.32, G:0.10, T:0.26
Consensus pattern (14 bp):
CCTTGAACCTTAAA
Found at i:23471845 original size:21 final size:21
Alignment explanation
Indices: 23471790--23471850 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
23471780 CATCACACCT
*
23471790 TGAACCTTAAACCTCGAACCT
1 TGAACCTTAAACCTCGAACCA
** *
23471811 TGAACCTTGCACCTTGAACCA
1 TGAACCTTAAACCTCGAACCA
*
23471832 TGAACTTTAAACCTC-AACC
1 TGAACCTTAAACCTCGAACC
23471851 CTCAAGTTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.25
Consensus pattern (21 bp):
TGAACCTTAAACCTCGAACCA
Found at i:23472461 original size:7 final size:7
Alignment explanation
Indices: 23472376--23472460 Score: 116
Period size: 7 Copynumber: 12.1 Consensus size: 7
23472366 TGTCTTAAAT
23472376 CCCAAAC
1 CCCAAAC
23472383 CCCAAAC
1 CCCAAAC
23472390 CCCAAAC
1 CCCAAAC
23472397 CCCAAAC
1 CCCAAAC
*
23472404 ACCAAAC
1 CCCAAAC
23472411 CCCAAAC
1 CCCAAAC
*
23472418 CCTAAAC
1 CCCAAAC
23472425 CCCAAAC
1 CCCAAAC
*
23472432 CTCAAAC
1 CCCAAAC
**
23472439 CTTAAAC
1 CCCAAAC
23472446 CCCAAAC
1 CCCAAAC
*
23472453 CTCAAAC
1 CCCAAAC
23472460 C
1 C
23472461 TTGAACCTAG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 69 1.00
ACGTcount: A:0.44, C:0.51, G:0.00, T:0.06
Consensus pattern (7 bp):
CCCAAAC
Found at i:23472467 original size:14 final size:14
Alignment explanation
Indices: 23472450--23472496 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
23472440 TTAAACCCCA
23472450 AACCTCAAACCTTG
1 AACCTCAAACCTTG
23472464 AACCT-AGAACCTTG
1 AACCTCA-AACCTTG
* * *
23472478 AACCCCAACCCTCG
1 AACCTCAAACCTTG
23472492 AACCT
1 AACCT
23472497 TGACTATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.34, C:0.40, G:0.09, T:0.17
Consensus pattern (14 bp):
AACCTCAAACCTTG
Done.