Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 143 of 199
Found at i:47582774 original size:49 final size:49
Alignment explanation
Indices: 47582713--47582905 Score: 323
Period size: 49 Copynumber: 3.9 Consensus size: 49
47582703 ATGTGAACAT
47582713 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
47582763 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
47582812 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
47582861 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
47582906 AGAAAACGAA
Statistics
Matches: 137, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
49 133 0.97
50 4 0.03
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:47586112 original size:46 final size:45
Alignment explanation
Indices: 47586014--47586353 Score: 338
Period size: 52 Copynumber: 7.6 Consensus size: 45
47586004 TTTGAGTACT
* *
47586014 TCTGATCAAGTGATAAAGTGATAAGTG-TAGCTT-GCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGCTACACTTA
47586057 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTC-GCTACACTTA
47586103 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTC-GCTACACTTA
* *
47586155 TCTGATCAAGTGATAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTG---A---CAAAGTGATAAGTGATAGCTTC-GCTACACTTA
* *
47586207 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGC-TTCGCTACACTTA
47586253 TCTGATCAAGTGACAAAGTGATAA--G-T-G----GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGCTACACTTA
47586290 TCTGATCAAGTGACAAAGTGATAA--G-T-G----GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGCTACACTTA
**
47586327 TCTGATCAAGAAACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
47586354 GCTACACTTA
Statistics
Matches: 267, Mismatches: 12, Indels: 40
0.84 0.04 0.13
Matches are distributed among these distances:
37 69 0.26
39 1 0.00
42 1 0.00
43 27 0.10
44 7 0.03
46 73 0.27
47 2 0.01
49 1 0.00
52 85 0.32
55 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGCTACACTTA
Found at i:47586174 original size:7 final size:7
Alignment explanation
Indices: 47586157--47586190 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
47586147 TACACTTATC
47586157 TGATCAAG
1 TGAT-AAG
47586165 TGATAAG
1 TGATAAG
*
47586172 TGAAAAG
1 TGATAAG
47586179 TGATAAG
1 TGATAAG
47586186 TGATA
1 TGATA
47586191 GCTTCGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.26
Consensus pattern (7 bp):
TGATAAG
Found at i:47586287 original size:37 final size:37
Alignment explanation
Indices: 47586243--47586425 Score: 298
Period size: 37 Copynumber: 5.0 Consensus size: 37
47586233 GATAGCTTTA
*
47586243 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
47586280 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
47586317 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
47586354 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
47586391 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
47586426 ATCATACGTA
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 11 0.08
36 4 0.03
37 125 0.89
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:47590969 original size:43 final size:43
Alignment explanation
Indices: 47590846--47590958 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 43
47590836 TTTTGGAAAT
* * *
47590846 AAACGCCGCTAAAAATCATGACCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGTGCTTTTTCCAC
* * * *
47590889 AAACGCTGCTAAAGACCATGACATTT-GCGGCGCTTTTTCTAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGTGCTTTTTCCAC
47590931 AAACGCCGCTAAAGACCATGACCTTTAG
1 AAACGCCGCTAAAGACCATGACCTTTAG
47590959 TAATGCTTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 37 0.62
43 23 0.38
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGTGCTTTTTCCAC
Found at i:47592383 original size:15 final size:17
Alignment explanation
Indices: 47592365--47592402 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
47592355 GGATAAGGAA
47592365 AAAAATTAT-AAAT-AT
1 AAAAATTATAAAATAAT
*
47592380 AAAAATTCTAAAATAAT
1 AAAAATTATAAAATAAT
47592397 AAAAAT
1 AAAAAT
47592403 AAATAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 4 0.20
17 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATTATAAAATAAT
Found at i:47593745 original size:5 final size:5
Alignment explanation
Indices: 47593735--47593759 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
47593725 TACCCAGTAT
47593735 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
47593760 TGACAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:47595226 original size:124 final size:129
Alignment explanation
Indices: 47595098--47595360 Score: 286
Period size: 139 Copynumber: 2.0 Consensus size: 129
47595088 AAAACGCCGA
* *
47595098 TATTGATTACCTTTTGCAGCGATTTT-ATAATAAACGCCG-CAAAAATTATTTCA-TT-T-CCGT
1 TATTGATTACCTTTTACAGCGATTTTCATAA-AAACGCCGTAAAAAATTATTTCATTTATGCCGT
* *
47595158 TTTACTATGCTGAAAATTTTTTATTTTATTTTTTATAAATTGATTTA-TTTTTGCGGTGTTTTTC
65 TTTACTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTC
* * * * *
47595222 TATTGCTTATCTTTTACGGTGTTTTTCATAAAAACGCCGTAAAAAATTATTTCATTTTGAACAAA
1 TATTGATTACCTTTTACAGCGATTTTCATAAAAACGCCGTAAAAAATTATTTCA-TTT-------
*
47595287 ATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGC
58 AT---GCCGTTTTACTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGC
47595352 GGCGTTTTT
120 GGCGTTTTT
47595361 ATAAAAAAAC
Statistics
Matches: 112, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
124 28 0.25
125 17 0.15
127 2 0.02
135 1 0.01
139 49 0.44
140 15 0.13
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50
Consensus pattern (129 bp):
TATTGATTACCTTTTACAGCGATTTTCATAAAAACGCCGTAAAAAATTATTTCATTTATGCCGTT
TTACTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTC
Found at i:47596053 original size:15 final size:15
Alignment explanation
Indices: 47596033--47596121 Score: 55
Period size: 15 Copynumber: 6.1 Consensus size: 15
47596023 TCGACCCCTG
47596033 AATCCCTAAACCTTA
1 AATCCCTAAACCTTA
47596048 AATCCCT-AACTCTTA
1 AATCCCTAAAC-CTTA
* *
47596063 AAT-CGT-AACATCT-
1 AATCCCTAAACCT-TA
* *
47596076 AACCCCTAAACCCCT-
1 AATCCCTAAA-CCTTA
*
47596091 AACCCCTAAACCTTA
1 AATCCCTAAACCTTA
*
47596106 AATCCC-AACCCTTA
1 AATCCCTAAACCTTA
47596120 AA
1 AA
47596122 CCATAATTGC
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.05
14 23 0.39
15 32 0.54
16 1 0.02
ACGTcount: A:0.38, C:0.37, G:0.01, T:0.24
Consensus pattern (15 bp):
AATCCCTAAACCTTA
Found at i:47596121 original size:21 final size:22
Alignment explanation
Indices: 47596082--47596123 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
47596072 ATCTAACCCC
47596082 TAAACCCCTAACCCCTAAACCT
1 TAAACCCCTAACCCCTAAACCT
* *
47596104 TAAATCCC-AACCCTTAAACC
1 TAAACCCCTAACCCCTAAACC
47596124 ATAATTGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAACCCCTAACCCCTAAACCT
Found at i:47596153 original size:15 final size:15
Alignment explanation
Indices: 47596133--47596164 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
47596123 CATAATTGCT
47596133 AATCCATAATCCCTA
1 AATCCATAATCCCTA
*
47596148 AATCCATACTCCCTA
1 AATCCATAATCCCTA
47596163 AA
1 AA
47596165 CCTTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (15 bp):
AATCCATAATCCCTA
Found at i:47596383 original size:15 final size:15
Alignment explanation
Indices: 47596363--47596421 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
47596353 CACTAACACA
*
47596363 TCTAACCCCTAAACC
1 TCTAACCCTTAAACC
*
47596378 TCTAACCCTTTAACC
1 TCTAACCCTTAAACC
* * *
47596393 CCTAAGCCTTAAATC
1 TCTAACCCTTAAACC
47596408 TC-AACCCTTAAACC
1 TCTAACCCTTAAACC
47596422 ATAATCATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
14 10 0.29
15 25 0.71
ACGTcount: A:0.32, C:0.41, G:0.02, T:0.25
Consensus pattern (15 bp):
TCTAACCCTTAAACC
Found at i:47596797 original size:41 final size:40
Alignment explanation
Indices: 47596736--47596848 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 40
47596726 TAAAATGTTT
* * * *
47596736 TTAGCGGCGATTCTAAAAAAAATCCGCTAAAGCCCTA-AGCA
1 TTAGCGGCGCTTCT-TAAAAAATCCGCTAAAG-ACTAGAGAA
*
47596777 TTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGACTAGAGAA
1 TTAGCGGCGCTTCTTAAAAAAT-CCGCTAAAGACTAGAGAA
*
47596818 TTAGCGGCGCTTCTTAAAAAACGCCGCTAAA
1 TTAGCGGCGCTTCTTAAAAAA-TCCGCTAAA
47596849 TCCCAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
40 9 0.15
41 53 0.85
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGCTTCTTAAAAAATCCGCTAAAGACTAGAGAA
Found at i:47598277 original size:19 final size:18
Alignment explanation
Indices: 47598255--47598321 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 18
47598245 ATAAAATATT
47598255 ATTTAATATTTTATGTAAA
1 ATTTAATATTTTAT-TAAA
*
47598274 ATTTAA-ATCTTTAATTGAA
1 ATTTAATAT-TTT-ATTAAA
*
47598293 A--TAATATCTTATCTAAA
1 ATTTAATATTTTAT-TAAA
*
47598310 ATTTATTATTTT
1 ATTTAATATTTT
47598322 TATTTTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
16 2 0.05
17 9 0.24
18 4 0.11
19 20 0.54
20 2 0.05
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (18 bp):
ATTTAATATTTTATTAAA
Found at i:47602033 original size:30 final size:30
Alignment explanation
Indices: 47601999--47602056 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
47601989 CTCGACATGT
47601999 TTCATAACA-TATTTTTCCATTATCATCACA
1 TTCATAACATTA-TTTTCCATTATCATCACA
47602029 TTCATAACATTATTTTCCATTATCATCA
1 TTCATAACATTATTTTCCATTATCATCA
47602057 GTTGTAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (30 bp):
TTCATAACATTATTTTCCATTATCATCACA
Found at i:47605196 original size:17 final size:17
Alignment explanation
Indices: 47605163--47605196 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47605153 GAAGTAATTA
*
47605163 AATATTATTTAACTTTG
1 AATATTATTGAACTTTG
*
47605180 AATATTATTGAATTTTG
1 AATATTATTGAACTTTG
47605197 CATTATTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (17 bp):
AATATTATTGAACTTTG
Found at i:47608895 original size:30 final size:30
Alignment explanation
Indices: 47608861--47608923 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
47608851 ACTTAACAAG
47608861 CAAATGCCTCTAAAACAATAACAAAATTAA
1 CAAATGCCTCTAAAACAATAACAAAATTAA
* * *
47608891 CAAATGCCTTTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAACAATAACAAAATTAA
47608921 CAA
1 CAA
47608924 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAACAATAACAAAATTAA
Found at i:47609608 original size:14 final size:14
Alignment explanation
Indices: 47609591--47609619 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47609581 TTAATTTTTT
47609591 ATCACAAATTTCTG
1 ATCACAAATTTCTG
47609605 ATCACAAATTTCTG
1 ATCACAAATTTCTG
47609619 A
1 A
47609620 ATATTATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (14 bp):
ATCACAAATTTCTG
Found at i:47613250 original size:29 final size:30
Alignment explanation
Indices: 47613192--47613250 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
47613182 GAACGAGATC
* * *
47613192 AAATCAAAATTTTATGTATAAAGTTATACA
1 AAATCAAAAGTTTATATATAAAATTATACA
*
47613222 AAAT-AAAAGTTTATATATAAAATTGTACA
1 AAATCAAAAGTTTATATATAAAATTATACA
47613251 TTATACCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.36
Consensus pattern (30 bp):
AAATCAAAAGTTTATATATAAAATTATACA
Found at i:47621423 original size:36 final size:36
Alignment explanation
Indices: 47621375--47621468 Score: 122
Period size: 36 Copynumber: 2.7 Consensus size: 36
47621365 CAAGGTCACG
* *
47621375 ATCAATAGCGTCACTATCATCAATAGCGTCATTAGT
1 ATCAATATCGTCACTATCATCAATAGCGTCACTAGT
* * *
47621411 ATCAATATCGTCACTAGCATCAATATCGTCACTATT
1 ATCAATATCGTCACTATCATCAATAGCGTCACTAGT
47621447 ATCAATATCG--A-TATCATCAATA
1 ATCAATATCGTCACTATCATCAATA
47621469 AGAAACCCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
33 10 0.19
34 1 0.02
36 41 0.79
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (36 bp):
ATCAATATCGTCACTATCATCAATAGCGTCACTAGT
Found at i:47621454 original size:18 final size:18
Alignment explanation
Indices: 47621375--47621456 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
47621365 CAAGGTCACG
* *
47621375 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTAGC
* * *
47621393 ATCAATAGCGTCATTAGT
1 ATCAATATCGTCACTAGC
47621411 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTAGC
**
47621429 ATCAATATCGTCACTATT
1 ATCAATATCGTCACTAGC
47621447 ATCAATATCG
1 ATCAATATCG
47621457 ATATCATCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (18 bp):
ATCAATATCGTCACTAGC
Found at i:47621467 original size:15 final size:17
Alignment explanation
Indices: 47621375--47621468 Score: 77
Period size: 18 Copynumber: 5.4 Consensus size: 17
47621365 CAAGGTCACG
*
47621375 ATCAATAGCGTCACTATC
1 ATCAATATCG-CACTATC
* *
47621393 ATCAATAGCGTCATTAGT-
1 ATCAATATCG-CACTA-TC
*
47621411 ATCAATATCGTCACTAGC
1 ATCAATATCG-CACTATC
*
47621429 ATCAATATCGTCACTATT
1 ATCAATATCG-CACTATC
47621447 ATCAATATCG-A-TATC
1 ATCAATATCGCACTATC
47621462 ATCAATA
1 ATCAATA
47621469 AGAAACCCTT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.15
16 1 0.01
18 55 0.82
19 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (17 bp):
ATCAATATCGCACTATC
Found at i:47628122 original size:23 final size:23
Alignment explanation
Indices: 47628096--47628145 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
47628086 AATAATAATT
47628096 TTTTATAGTAT-AAAATATGAAA-A
1 TTTTA-AGTATAAAAATAT-AAATA
*
47628119 TTTTAATTATAAAAATATAAATA
1 TTTTAAGTATAAAAATATAAATA
47628142 TTTT
1 TTTT
47628146 TTTAAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TTTTAAGTATAAAAATATAAATA
Found at i:47628297 original size:22 final size:22
Alignment explanation
Indices: 47628269--47628314 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
47628259 TAAAGTTTAT
*
47628269 ATATTATATTAATTAT-AATAAA
1 ATATTATATT-ATTATGAACAAA
*
47628291 ATATTATCTTATTATGAACAAA
1 ATATTATATTATTATGAACAAA
47628313 AT
1 AT
47628315 TCTTCTGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATTATATTATTATGAACAAA
Found at i:47638530 original size:50 final size:49
Alignment explanation
Indices: 47638476--47638600 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 49
47638466 TATGAGAGGC
* *
47638476 CCCATGTAAGACCATGTCTGGGACATGGCATGGGAACCAGTA-TGAGAAC-T
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGG---CAGTACAGAAAACAT
* * *
47638526 CCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAGAAAACAT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCAGTACAGAAAACAT
*
47638575 CCCATGTAAGACTATGTCTGGGACAT
1 CCCATGTAAGACCATGTCTGGGACAT
47638601 AGCTTTGGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
47 5 0.08
48 5 0.08
49 24 0.37
50 31 0.48
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (49 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATGGGCAGTACAGAAAACAT
Found at i:47638561 original size:56 final size:55
Alignment explanation
Indices: 47638414--47638561 Score: 134
Period size: 50 Copynumber: 2.8 Consensus size: 55
47638404 ATTTGGGTAA
* ** *
47638414 AGAGA-TCCCATGTAAGACCATATCTGAGACATGGCATTGGCATCATTGACATTATG
1 AGAGACTCCCATGTAAGACCATATCTGGGA-ATGGCATTGGCAT-AGGGACAGTATG
* *
47638470 AGAGGC-CCCATGTAAGACCATGTCTGGG-A---CA-TGGCAT-GGGAACCAGTATG
1 AGAGACTCCCATGTAAGACCATATCTGGGAATGGCATTGGCATAGGG-A-CAGTATG
47638520 AGA-ACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGACTCCCATGTAAGACCATATCTGGGA-ATGGCATTGGCA
47638562 GTACAGAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
48 1 0.01
49 2 0.03
50 36 0.49
51 2 0.03
52 1 0.01
54 1 0.01
55 2 0.03
56 29 0.39
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (55 bp):
AGAGACTCCCATGTAAGACCATATCTGGGAATGGCATTGGCATAGGGACAGTATG
Found at i:47638609 original size:49 final size:47
Alignment explanation
Indices: 47638476--47638610 Score: 153
Period size: 49 Copynumber: 2.8 Consensus size: 47
47638466 TATGAGAGGC
* * *
47638476 CCCATGTAAGACCATGTCTGGGACATGGCATGGGAACCAGTATGAGAACT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGG---CAGTAAGAAAACT
* *
47638526 CCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAGAAAACAT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCAGTA-AGAAAAC-T
* * *
47638575 CCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
47638611 TGTATTATTA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
47 5 0.07
48 5 0.07
49 32 0.44
50 31 0.42
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.23
Consensus pattern (47 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATTGGCAGTAAGAAAACT
Found at i:47638826 original size:12 final size:12
Alignment explanation
Indices: 47638809--47638847 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
47638799 ATGAGTTATT
47638809 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
47638821 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
47638833 TAAGTGAGTAAG
1 TAAGTAAGCAAG
47638845 TAA
1 TAA
47638848 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:47642818 original size:20 final size:20
Alignment explanation
Indices: 47642793--47642843 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 20
47642783 TGGCTGCGTG
47642793 ATACTGATTTGAGACAGGCC
1 ATACTGATTTGAGACAGGCC
*
47642813 ATACTGA----A-AGAGGCC
1 ATACTGATTTGAGACAGGCC
47642828 ATACTGATTTGAGACA
1 ATACTGATTTGAGACA
47642844 TGATACAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
15 13 0.54
16 1 0.04
19 1 0.04
20 9 0.38
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (20 bp):
ATACTGATTTGAGACAGGCC
Found at i:47653234 original size:12 final size:12
Alignment explanation
Indices: 47653212--47653244 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
47653202 CTTGAGCAAA
47653212 ATATATTTTTAGC
1 ATAT-TTTTTAGC
47653225 ATATTTTTTAGC
1 ATATTTTTTAGC
47653237 ATATTTTT
1 ATATTTTT
47653245 AAGTAATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (12 bp):
ATATTTTTTAGC
Found at i:47655461 original size:20 final size:19
Alignment explanation
Indices: 47655436--47655583 Score: 77
Period size: 20 Copynumber: 7.4 Consensus size: 19
47655426 TATTGAATGA
47655436 TTGTACTTACGTGCCCCTAT
1 TTGTACTT-CGTGCCCCTAT
*
47655456 TTGTACTTCTGTACCCCTGA-
1 TTGTACTTC-GTGCCCCT-AT
* * *
47655476 TTGCACTTACGTGCCCTTGT
1 TTGTACTT-CGTGCCCCTAT
* * *
47655496 TTATACTCTGGTACCCCTGA-
1 TTGTACT-TCGTGCCCCT-AT
* *
47655516 TTGTACTTGCGTGCCCTTTT
1 TTGTACTT-CGTGCCCCTAT
* *
47655536 TTGTACTTCAGTACCCCTGAA
1 TTGTACTTC-GTGCCCCT-AT
*
47655557 TT-TACATCTGTGCCCCTAT
1 TTGTACTTC-GTGCCCCTAT
47655576 TTGTACTT
1 TTGTACTT
47655584 TTTTAGCCTT
Statistics
Matches: 92, Mismatches: 25, Indels: 22
0.66 0.18 0.16
Matches are distributed among these distances:
19 6 0.07
20 81 0.88
21 5 0.05
ACGTcount: A:0.15, C:0.28, G:0.16, T:0.41
Consensus pattern (19 bp):
TTGTACTTCGTGCCCCTAT
Found at i:47655488 original size:40 final size:40
Alignment explanation
Indices: 47655433--47655643 Score: 212
Period size: 40 Copynumber: 5.3 Consensus size: 40
47655423 AATTATTGAA
*
47655433 TGATTGTACTTACGTGCCCCTATTTGTACTTCTGTACCCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCTGTACCCC
* * *
47655473 TGATTGCACTTACGTGCCCTTGTTTATAC-TCTGGTACCCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCT-GTACCCC
* * * * *
47655513 TGATTGTACTTGCGTGCCCTTTTTTGTACTTCAGTACCCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCTGTACCCC
* * * * * *
47655553 TGAATT-TACAT-CTGTGCCCCTATTTGTACTTTTTTAGCCT
1 TG-ATTGCACTTAC-GTGCCCCTATTTGTACTTCTGTACCCC
* **
47655593 TGATTGCACTTACGTGCCCCTGTTTGTACTTCAATACCCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCTGTACCCC
47655633 TGATTGCACTT
1 TGATTGCACTT
47655644 TTATCCCTTG
Statistics
Matches: 140, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
39 7 0.05
40 127 0.91
41 6 0.04
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.41
Consensus pattern (40 bp):
TGATTGCACTTACGTGCCCCTATTTGTACTTCTGTACCCC
Found at i:47655614 original size:60 final size:60
Alignment explanation
Indices: 47655446--47655617 Score: 149
Period size: 60 Copynumber: 2.9 Consensus size: 60
47655436 TTGTACTTAC
* * * *
47655446 GTGCCCCTATTTGTACTTCTGTACCCCTGATTGCACTTACGTGCCCTTGTTTATACTCTG
1 GTGCCCCTATTTGTACTTCTGTAGCCTTGATTGCACTTACGTGCCCCTGTTTACACTCTG
* ** * *
47655506 GTACCCCTGA-TTGTACTTGC-GT-GCCCTTTTTTGTACTT-CAGTACCCCTGAATTTACA-TCT
1 GTGCCCCT-ATTTGTACTT-CTGTAG-CCTTGATTGCACTTAC-GTGCCCCTG--TTTACACTCT
47655566 -
60 G
* *
47655566 GTGCCCCTATTTGTACTTTTTTAGCCTTGATTGCACTTACGTGCCCCTGTTT
1 GTGCCCCTATTTGTACTTCTGTAGCCTTGATTGCACTTACGTGCCCCTGTTT
47655618 GTACTTCAAT
Statistics
Matches: 86, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
58 3 0.03
59 2 0.02
60 69 0.80
61 7 0.08
62 5 0.06
ACGTcount: A:0.14, C:0.28, G:0.16, T:0.41
Consensus pattern (60 bp):
GTGCCCCTATTTGTACTTCTGTAGCCTTGATTGCACTTACGTGCCCCTGTTTACACTCTG
Found at i:47655632 original size:20 final size:19
Alignment explanation
Indices: 47655609--47655663 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
47655599 CACTTACGTG
47655609 CCCCTGTTTGTACTTCAAT
1 CCCCTGTTTGTACTTCAAT
* * **
47655628 ACCCCTGATTGCACTTTTAT
1 -CCCCTGTTTGTACTTCAAT
*
47655648 CCCTTGTTTGTACTTC
1 CCCCTGTTTGTACTTC
47655664 GGTGCCCCTG
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.15, C:0.31, G:0.11, T:0.44
Consensus pattern (19 bp):
CCCCTGTTTGTACTTCAAT
Found at i:47657796 original size:21 final size:21
Alignment explanation
Indices: 47657757--47657796 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
47657747 CTCCTACAGT
** *
47657757 ATGAAATTTTCTATCTTTTCC
1 ATGAAATTTTAAATATTTTCC
47657778 ATGAAATTTTAAATATTTT
1 ATGAAATTTTAAATATTTT
47657797 TTATTTAGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
ATGAAATTTTAAATATTTTCC
Found at i:47662205 original size:26 final size:27
Alignment explanation
Indices: 47662176--47662242 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
47662166 CCCGATATAT
47662176 GGCTCTTCGTGAGCTTTC-CAATTAAA
1 GGCTCTTCGTGAGCTTTCTCAATTAAA
* ** *
47662202 GGCTCTTTGTGAGC-TTCTTGATTAAT
1 GGCTCTTCGTGAGCTTTCTCAATTAAA
47662228 GGCTCTTCG-GAGCTT
1 GGCTCTTCGTGAGCTT
47662243 CCCGATATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 7 0.21
26 27 0.79
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (27 bp):
GGCTCTTCGTGAGCTTTCTCAATTAAA
Found at i:47662338 original size:49 final size:49
Alignment explanation
Indices: 47662285--47662392 Score: 130
Period size: 49 Copynumber: 2.2 Consensus size: 49
47662275 TGGCTATCTA
**
47662285 GAGCTTCCTGATTAATGACTCTT-CGAAGCTACCCATTAT-TGGCTCACAT
1 GAGCTTCCTGATT-ATGACTCTTACG-AGCTACCCATTATACAGCTCACAT
* * * *
47662334 GAGCTTCCCGATTATGACTCTTATGAGCTTCCCGTTATACAGCTCACAT
1 GAGCTTCCTGATTATGACTCTTACGAGCTACCCATTATACAGCTCACAT
47662383 GAGCTTCCTG
1 GAGCTTCCTG
47662393 TAATATGGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 20 0.40
49 30 0.60
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (49 bp):
GAGCTTCCTGATTATGACTCTTACGAGCTACCCATTATACAGCTCACAT
Found at i:47662347 original size:25 final size:25
Alignment explanation
Indices: 47662311--47662390 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 25
47662301 GACTCTTCGA
*
47662311 AGCTACCC-ATTATTGGCTCACATG
1 AGCTTCCCGATTATTGGCTCACATG
* **
47662335 AGCTTCCCGATTA-TGACTCTTATG
1 AGCTTCCCGATTATTGGCTCACATG
**
47662359 AGCTTCCCG-TTATACAGCTCACATG
1 AGCTTCCCGATTAT-TGGCTCACATG
47662384 AGCTTCC
1 AGCTTCC
47662391 TGTAATATGG
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
23 3 0.07
24 24 0.55
25 17 0.39
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (25 bp):
AGCTTCCCGATTATTGGCTCACATG
Found at i:47662362 original size:73 final size:74
Alignment explanation
Indices: 47662211--47662365 Score: 183
Period size: 73 Copynumber: 2.1 Consensus size: 74
47662201 AGGCTCTTTG
* * * * *
47662211 TGAGCTTCTTGATTAATGGCTCTTCGGAGCTTCCCGATATGACTCGCATGAACTTCCCGATATAT
1 TGAGCTTCCTGATTAATGACTCTTCGAAGCTACCCGATATGACTCACATGAACTTCCCGATATAT
*
47662276 GGCTATCTA
66 GACTATCTA
* *
47662285 -GAGCTTCCTGATTAATGACTCTTCGAAGCTACCC-ATTATTGGCTCACATGAGCTTCCCGAT-T
1 TGAGCTTCCTGATTAATGACTCTTCGAAGCTACCCGA-TA-TGACTCACATGAACTTCCCGATAT
*
47662347 ATGACTCT-TA
64 ATGACTATCTA
47662357 TGAGCTTCC
1 TGAGCTTCC
47662366 CGTTATACAG
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
72 3 0.04
73 47 0.68
74 19 0.28
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.34
Consensus pattern (74 bp):
TGAGCTTCCTGATTAATGACTCTTCGAAGCTACCCGATATGACTCACATGAACTTCCCGATATAT
GACTATCTA
Found at i:47662403 original size:25 final size:25
Alignment explanation
Indices: 47662324--47662403 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
47662314 TACCCATTAT
*
47662324 TGGCTCACATGAGCTTCCCG-ATTA
1 TGGCTCACATGAGCTTCCCGTAATA
* ** *
47662348 TGACTCTTATGAGCTTCCCGTTATA
1 TGGCTCACATGAGCTTCCCGTAATA
** *
47662373 CAGCTCACATGAGCTTCCTGTAATA
1 TGGCTCACATGAGCTTCCCGTAATA
47662398 TGGCTC
1 TGGCTC
47662404 GAGAGAGGGC
Statistics
Matches: 41, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
24 17 0.41
25 24 0.59
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCGTAATA
Found at i:47665863 original size:30 final size:31
Alignment explanation
Indices: 47665829--47665902 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
47665819 AGAAGTTACA
*
47665829 ATTT-AGTCATTGAACTATTTGAAAGTTTTT
1 ATTTAAGTCATTGAACTATTTAAAAGTTTTT
* *
47665859 ATTTAAGTCACTAAACTATTTAAAAGTTTTT
1 ATTTAAGTCATTGAACTATTTAAAAGTTTTT
47665890 ATTTAAGTCATTG
1 ATTTAAGTCATTG
47665903 TGCTATTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (31 bp):
ATTTAAGTCATTGAACTATTTAAAAGTTTTT
Found at i:47665909 original size:31 final size:30
Alignment explanation
Indices: 47665829--47665925 Score: 110
Period size: 31 Copynumber: 3.3 Consensus size: 30
47665819 AGAAGTTACA
47665829 ATTT-AGTCATTGAACTATTTGAAAGTTTTT
1 ATTTAAGTCATTGAACTATTT-AAAGTTTTT
* *
47665859 ATTTAAGTCACTAAACTATTTAAAAGTTTTT
1 ATTTAAGTCATTGAACTATTT-AAAGTTTTT
**
47665890 ATTTAAGTCATTGTGCTA-TT-AAGTTTTT
1 ATTTAAGTCATTGAACTATTTAAAGTTTTT
*
47665918 CTTTAAGT
1 ATTTAAGT
47665926 TCCGCCAATG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 15 0.26
30 6 0.10
31 37 0.64
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.49
Consensus pattern (30 bp):
ATTTAAGTCATTGAACTATTTAAAGTTTTT
Found at i:47668729 original size:11 final size:11
Alignment explanation
Indices: 47668674--47668749 Score: 68
Period size: 12 Copynumber: 6.6 Consensus size: 11
47668664 AAATAAATGA
47668674 AAGAAAAAGA-
1 AAGAAAAAGAG
47668684 ATAG-AAAA-AG
1 A-AGAAAAAGAG
47668694 AAGAACAAAGTAG
1 AAGAA-AAAG-AG
*
47668707 AACGAAACAGAG
1 AA-GAAAAAGAG
47668719 AAGAAAAAGAG
1 AAGAAAAAGAG
47668730 AAAGAAAAAGGAG
1 -AAGAAAAA-GAG
47668743 AAGAAAA
1 AAGAAAA
47668750 TTAGGGTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
9 3 0.05
10 7 0.13
11 13 0.24
12 19 0.35
13 10 0.18
14 3 0.05
ACGTcount: A:0.70, C:0.04, G:0.24, T:0.03
Consensus pattern (11 bp):
AAGAAAAAGAG
Found at i:47671113 original size:89 final size:91
Alignment explanation
Indices: 47670939--47671134 Score: 263
Period size: 89 Copynumber: 2.2 Consensus size: 91
47670929 TTTAAGGGTG
* * *** * *
47670939 CAAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCTTGTTTTTCTTTTTGCACTCATT
1 CAAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTGACCTTCTTTTTGCACCCAAT
*
47671003 TGGGTACTTGAACTTTCAAAATGCAT
66 TAGGTACTTGAACTTTCAAAATGCAT
*
47671029 CAAAAAGATCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCT-ACCTT-TTTTTGCACCCAAT
1 CAAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTGACCTTCTTTTTGCACCCAAT
**
47671092 TAGGTACTTGAGTTTTCAAAATGCAT
66 TAGGTACTTGAACTTTCAAAATGCAT
*
47671118 TAAAAAGACCCTCAAAC
1 CAAAAAGACCCTCAAAC
47671135 TTAAAAAAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
89 50 0.54
90 9 0.10
91 33 0.36
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (91 bp):
CAAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTGACCTTCTTTTTGCACCCAAT
TAGGTACTTGAACTTTCAAAATGCAT
Found at i:47671266 original size:17 final size:18
Alignment explanation
Indices: 47671244--47671286 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
47671234 AGAAATTTAT
47671244 TAAAAATTAGAAAAAA-A
1 TAAAAATTAGAAAAAATA
* *
47671261 TAAAAATCATAAAAAATA
1 TAAAAATTAGAAAAAATA
47671279 TAAAAATT
1 TAAAAATT
47671287 TGTAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAAATTAGAAAAAATA
Found at i:47671303 original size:55 final size:54
Alignment explanation
Indices: 47671239--47671357 Score: 152
Period size: 55 Copynumber: 2.1 Consensus size: 54
47671229 ATATTAGAAA
* *
47671239 TTTATTAAAAAT-TAGAAAAAAATAAAA-ATCATAAAAAATATAAAAATTTGTAAAAT
1 TTTA-TAAAAATCTA-AAAAAAATAAAATAT-AT-AAAAATATAAAAAATTATAAAAT
*
47671295 TTTATAAAAATCGTAAAAAAAATAAAATATATAGAAATATAAAAAATTATAAAAT
1 TTTATAAAAATC-TAAAAAAAATAAAATATATAAAAATATAAAAAATTATAAAAT
47671350 TTTATAAA
1 TTTATAAA
47671358 GTCGTAAGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
55 35 0.61
56 18 0.32
57 4 0.07
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (54 bp):
TTTATAAAAATCTAAAAAAAATAAAATATATAAAAATATAAAAAATTATAAAAT
Found at i:47671348 original size:9 final size:9
Alignment explanation
Indices: 47671244--47671348 Score: 54
Period size: 9 Copynumber: 11.6 Consensus size: 9
47671234 AGAAATTTAT
47671244 TAAAAATTA
1 TAAAAATTA
* *
47671253 GAAAAA-AA
1 TAAAAATTA
*
47671261 TAAAAATCA
1 TAAAAATTA
*
47671270 TAAAAAATA
1 TAAAAATTA
*
47671279 TAAAAATTTG
1 TAAAAA-TTA
*
47671289 TAAAATTTTA
1 TAAAA-ATTA
**
47671299 TAAAAATCG
1 TAAAAATTA
**
47671308 TAAAAAAAA
1 TAAAAATTA
47671317 T-AAAATATA
1 TAAAAAT-TA
*
47671326 TAGAAA-TA
1 TAAAAATTA
47671334 TAAAAAATTA
1 T-AAAAATTA
47671344 TAAAA
1 TAAAA
47671349 TTTTATAAAG
Statistics
Matches: 69, Mismatches: 20, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
8 13 0.19
9 37 0.54
10 19 0.28
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (9 bp):
TAAAAATTA
Found at i:47671857 original size:88 final size:90
Alignment explanation
Indices: 47671667--47671864 Score: 235
Period size: 90 Copynumber: 2.2 Consensus size: 90
47671657 AAGAGCATGG
* * ** *
47671667 GCTTAATTGC-TTTTTTGAAA-AA-TTTGGAGGGTGTTTTTGATGCATTTTAAAAGTTCAAGTAC
1 GCTTAATTGCTTTTTTTTAAAGAAGTTT-GAAGGCCTTTTTGATGCATTTGAAAAGTTCAAGTAC
* *
47671729 CCAATTGAGTGATAGAAAAAGCCGGA
65 CCAATTGAGTGATAAAAAAAGACGGA
* * *
47671755 GCTTAATTGCTTTTTTTTAAAGAAGTTTGAAGGCCTTTTTGATGCATTTGGAAAGTTCAAGTGCT
1 GCTTAATTGCTTTTTTTTAAAGAAGTTTGAAGGCCTTTTTGATGCATTTGAAAAGTTCAAGTACC
* *
47671820 CAATTGAGT-ATAAAAAAATAGGGA
66 CAATTGAGTGATAAAAAAAGACGGA
*
47671844 -CTTAATTGTTTTTTTTTAAAG
1 GCTTAATTGCTTTTTTTTAAAG
47671865 TTTGAGGGCT
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
88 30 0.32
89 20 0.21
90 41 0.44
91 3 0.03
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (90 bp):
GCTTAATTGCTTTTTTTTAAAGAAGTTTGAAGGCCTTTTTGATGCATTTGAAAAGTTCAAGTACC
CAATTGAGTGATAAAAAAAGACGGA
Found at i:47674743 original size:16 final size:16
Alignment explanation
Indices: 47674722--47674757 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
47674712 TTTGGTTCGC
47674722 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
47674738 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
47674754 TGTA
1 TGTA
47674758 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:47675015 original size:18 final size:17
Alignment explanation
Indices: 47674994--47675028 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
47674984 TTATTATTAA
*
47674994 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
47675012 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
47675029 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:47675080 original size:157 final size:157
Alignment explanation
Indices: 47674880--47675196 Score: 546
Period size: 157 Copynumber: 2.0 Consensus size: 157
47674870 TAGAATACCT
*
47674880 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTATAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTATAATAAGATTATTA
* * ** *
47674945 TTATCAGTAATAAATTTTTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAA
66 ATATCAATAATAAA-TAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAA
47675010 ATATATAATTTAATAAAATTCTT-ATAA
130 ATATATAATTTAATAAAATTCTTAATAA
* *
47675037 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTATAATAAGATTATTA
47675102 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
47675167 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
47675194 TTA
1 TTA
47675197 ATATTCTTAT
Statistics
Matches: 151, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
156 70 0.46
157 81 0.54
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTATAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:47675167 original size:16 final size:16
Alignment explanation
Indices: 47675130--47675171 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
47675120 TTAATCATAT
*
47675130 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
47675146 TT-AAATATATTATAA
1 TTAAAATATATTATAA
47675161 TTAAAATATAT
1 TTAAAATATAT
47675172 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:47675178 original size:14 final size:15
Alignment explanation
Indices: 47675139--47675180 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
47675129 TTTAAACATA
*
47675139 ATTATTATTAAATAT
1 ATTATAATTAAATAT
47675154 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
47675168 A-TATAATTTAATA
1 ATTATAATTAAATA
47675181 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:47675267 original size:120 final size:120
Alignment explanation
Indices: 47675128--47675417 Score: 480
Period size: 120 Copynumber: 2.4 Consensus size: 120
47675118 ATTTAATCAT
*
47675128 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
47675193 ATTAATATTCTTATACGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATACGAATTTACT-AAATCATAATATATGATACTGT-AAATGA-AA
47675250 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
47675313 ATTAATATTCTTATATGAATTTACTAAATCATAATATATGATACTGTAAATGAAA
66 ATTAATATTCTTATACGAATTTACTAAATCATAATATATGATACTGTAAATGAAA
* * *
47675368 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAA
47675418 AATAATTTAA
Statistics
Matches: 161, Mismatches: 4, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
118 7 0.04
119 65 0.40
120 86 0.53
121 2 0.01
122 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (120 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATACGAATTTACTAAATCATAATATATGATACTGTAAATGAAA
Found at i:47675298 original size:14 final size:15
Alignment explanation
Indices: 47675249--47675300 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
47675239 GTAAAATATA
47675249 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
47675264 TATTAAATATATTAT
1 AATTAAATATATTAT
47675279 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
47675292 AATTTAATA
1 AATTAAATA
47675301 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:47675511 original size:24 final size:25
Alignment explanation
Indices: 47675465--47675512 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
47675455 TATGAATTTG
47675465 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
47675491 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
47675513 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:47675536 original size:92 final size:88
Alignment explanation
Indices: 47675440--47675645 Score: 254
Period size: 92 Copynumber: 2.3 Consensus size: 88
47675430 TAATTATAAC
* * * *
47675440 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATT-T-TTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAAT-A
* *
47675504 TTAATAT-TAAATTTCATAAAATTCTTGA
62 GTAATATAT-AATTT-ATAAAATTCTTAA
47675532 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAA-TTT-TTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
*
47675597 GATATATAATTTATAAAATTCTTAA
64 AATATATAATTTATAAAATTCTTAA
47675622 TAATAAAATTTTTATATGAATTTA
1 TAAT-AAATTTTTATATGAATTTA
47675646 CTAAAATCAA
Statistics
Matches: 102, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
89 13 0.13
90 19 0.19
91 14 0.14
92 51 0.50
93 5 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (88 bp):
TAATAAATTTTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGTAA
TATATAATTTATAAAATTCTTAA
Found at i:47678979 original size:97 final size:97
Alignment explanation
Indices: 47678868--47679103 Score: 463
Period size: 97 Copynumber: 2.4 Consensus size: 97
47678858 TTTAATAATA
47678868 ATTATATAAGCATCGAAATTGGAACTTGATTGATTGTTTATATAAGTACCGAATTATATTTTAAT
1 ATTATATAAGCATCGAAATTGGAACTTGATTGATTGTTTATATAAGTACCGAATTATATTTTAAT
*
47678933 TAAAATATGCAGATTTAATCTTAAATTTGGAT
66 TAAAATATGCAGATTTAATCTTAAATTTGGAC
47678965 ATTATATAAGCATCGAAATTGGAACTTGATTGATTGTTTATATAAGTACCGAATTATATTTTAAT
1 ATTATATAAGCATCGAAATTGGAACTTGATTGATTGTTTATATAAGTACCGAATTATATTTTAAT
47679030 TAAAATATGCAGATTTAATCTTAAATTTGGAC
66 TAAAATATGCAGATTTAATCTTAAATTTGGAC
47679062 ATTATATAAGCATCGAAATTGGAACTTGATTGATTGTTTATA
1 ATTATATAAGCATCGAAATTGGAACTTGATTGATTGTTTATA
47679104 CATAATTTAA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 138 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (97 bp):
ATTATATAAGCATCGAAATTGGAACTTGATTGATTGTTTATATAAGTACCGAATTATATTTTAAT
TAAAATATGCAGATTTAATCTTAAATTTGGAC
Found at i:47679205 original size:13 final size:13
Alignment explanation
Indices: 47679187--47679213 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47679177 TAAAAACAAC
47679187 TATATTGTTTAAA
1 TATATTGTTTAAA
47679200 TATATTGTTTAAA
1 TATATTGTTTAAA
47679213 T
1 T
47679214 TAAACCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TATATTGTTTAAA
Found at i:47685842 original size:20 final size:21
Alignment explanation
Indices: 47685790--47685843 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
47685780 ATCAATATGC
*
47685790 AAAAATAATATTTCTTAGATCG
1 AAAATTAAT-TTTCTTAGATCG
*
47685812 AAAATTGATTTTC-TAGATC-
1 AAAATTAATTTTCTTAGATCG
47685831 AAAACTTAATTTT
1 AAAA-TTAATTTT
47685844 AAAAGCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 4 0.14
22 7 0.25
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (21 bp):
AAAATTAATTTTCTTAGATCG
Found at i:47694048 original size:2 final size:2
Alignment explanation
Indices: 47694041--47694080 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47694031 GGGAATTATG
47694041 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
47694081 ACGAACGGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47701473 original size:25 final size:25
Alignment explanation
Indices: 47701445--47701495 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
47701435 TGATGTAAAC
47701445 TCATCCACAATGCTCATTTGACACA
1 TCATCCACAATGCTCATTTGACACA
*
47701470 TCATCCATAATGCTCATTTGACACA
1 TCATCCACAATGCTCATTTGACACA
47701495 T
1 T
47701496 AAATCCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (25 bp):
TCATCCACAATGCTCATTTGACACA
Found at i:47702387 original size:28 final size:26
Alignment explanation
Indices: 47702343--47702412 Score: 63
Period size: 28 Copynumber: 2.6 Consensus size: 26
47702333 AATTATTCTG
*
47702343 CAAAAA-AAAGAAGTAAAACAAACATGAA
1 CAAAAATAAA-AAATAAAACAAA-AT-AA
*
47702371 CAAAAATAAAAAATAAAATAAAATAA
1 CAAAAATAAAAAATAAAACAAAATAA
*
47702397 -AATAATAATAAAATAA
1 CAAAAATAA-AAAATAA
47702413 TAATAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 7 0.19
26 9 0.24
27 2 0.05
28 16 0.43
29 3 0.08
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (26 bp):
CAAAAATAAAAAATAAAACAAAATAA
Found at i:47702388 original size:5 final size:5
Alignment explanation
Indices: 47702380--47702419 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
47702370 ACAAAAATAA
47702380 AAAAT AAAAT AAAAT AAAAT AATAAT AAAAT AATAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AA-AAT AAA
47702420 TTTAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 23 0.70
6 10 0.30
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:47702398 original size:22 final size:22
Alignment explanation
Indices: 47702373--47702419 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
47702363 AACATGAACA
47702373 AAAATAAAAAATAAAATAA-AAT
1 AAAAT-AAAAATAAAATAATAAT
*
47702395 AAAATAATAATAAAATAATAAT
1 AAAATAAAAATAAAATAATAAT
47702417 AAA
1 AAA
47702420 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAATAAAAATAAAATAATAAT
Found at i:47702406 original size:11 final size:11
Alignment explanation
Indices: 47702382--47702419 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
47702372 AAAAATAAAA
47702382 AATAAAATAA-
1 AATAAAATAAT
47702392 AATAAAATAAT
1 AATAAAATAAT
47702403 AATAAAATAAT
1 AATAAAATAAT
47702414 AATAAA
1 AATAAA
47702420 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:47705037 original size:52 final size:51
Alignment explanation
Indices: 47704939--47705043 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
47704929 TTATAAAACT
* * *
47704939 TATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATA
1 TATAAATATAAAATACATAATGCATTTATCAAAAAAAGGAAAATATAAATA
* * * *
47704990 TATAAATATAAAATATATTCATGCATTTA-CAAAAAAATGAAATATATAAGTA
1 TATAAATATAAAATACA-TAATGCATTTATCAAAAAAAGGAAA-ATATAAATA
47705042 TA
1 TA
47705044 ATATAAAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
51 25 0.56
52 20 0.44
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (51 bp):
TATAAATATAAAATACATAATGCATTTATCAAAAAAAGGAAAATATAAATA
Found at i:47705355 original size:24 final size:27
Alignment explanation
Indices: 47705309--47705359 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
47705299 ATATGTAGGT
*
47705309 ATAATAATAATATATAATATAATAAAA
1 ATAATAATAACATATAATATAATAAAA
47705336 ATAATAATAACA-A-AAT-TAATAAAA
1 ATAATAATAACATATAATATAATAAAA
47705360 TAGACTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 3 0.13
26 1 0.04
27 11 0.48
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (27 bp):
ATAATAATAACATATAATATAATAAAA
Found at i:47705805 original size:23 final size:22
Alignment explanation
Indices: 47705762--47705819 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
47705752 AAAGGGTATC
* *
47705762 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
47705783 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
47705806 TACATATCATATCT
1 TACAAATCATATCT
47705820 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:47705822 original size:19 final size:19
Alignment explanation
Indices: 47705775--47705853 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 19
47705765 AAATTAAATC
*
47705775 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
47705795 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
47705817 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
* *
47705838 TCTAATATTGCATATC
1 TCTAAGATTACATATC
47705854 CTCGAAGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 14 0.29
21 17 0.35
22 7 0.14
23 11 0.22
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:47705835 original size:21 final size:21
Alignment explanation
Indices: 47705809--47705852 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
47705799 CTAAGATTAC
47705809 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
47705830 ATATCATATCTAATATTGCAT
1 ATATCATATCTAAGATTGCAT
47705851 AT
1 AT
47705853 CCTCGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:47714035 original size:22 final size:23
Alignment explanation
Indices: 47714003--47714054 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
47713993 GGTATGGGAC
47714003 AGGCAGAGGTGCTAGTCAGACTG
1 AGGCAGAGGTGCTAGTCAGACTG
*
47714026 AGGCA-AGGTGCTAGTCAGATTG
1 AGGCAGAGGTGCTAGTCAGACTG
47714048 AGG-AGAG
1 AGGCAGAG
47714055 ACAGCCTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.78
23 5 0.19
ACGTcount: A:0.29, C:0.13, G:0.40, T:0.17
Consensus pattern (23 bp):
AGGCAGAGGTGCTAGTCAGACTG
Found at i:47717273 original size:40 final size:40
Alignment explanation
Indices: 47717229--47717311 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
47717219 GAACTTTAAT
*
47717229 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTCGAC
* *
47717269 TTTATTAAACTCATCTTAGTTAGTAATTGAGTTGGTCGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTCGAC
47717309 TTT
1 TTT
47717312 CTTTTATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (40 bp):
TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTCGAC
Found at i:47721900 original size:40 final size:40
Alignment explanation
Indices: 47721856--47721938 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
47721846 GAACTTTAAT
47721856 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCAGGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCAGGAC
* **
47721896 TTTATTAAACTCATCTTAGTTAGTAATTGAGTTGTTGGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCAGGAC
47721936 TTT
1 TTT
47721939 CTTTTATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (40 bp):
TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCAGGAC
Found at i:47723783 original size:34 final size:34
Alignment explanation
Indices: 47723745--47723841 Score: 83
Period size: 34 Copynumber: 3.1 Consensus size: 34
47723735 TAAAGTAATG
47723745 CATTATGTAAGTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAAGTTTCATGTTAGTTAAGTTTGCAT
47723779 CATTAAAT-TAAG--TCA---T-GTT-AGTTT--A-
1 CATT--ATGTAAGTTTCATGTTAGTTAAGTTTGCAT
*
47723804 -ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAAGTTTCATGTTAGTTAAGTTTGCAT
47723837 CATTA
1 CATTA
47723842 AAATTAATTC
Statistics
Matches: 48, Mismatches: 1, Indels: 28
0.62 0.01 0.36
Matches are distributed among these distances:
22 2 0.04
23 3 0.06
24 3 0.06
25 3 0.06
26 1 0.02
28 6 0.12
29 6 0.12
30 6 0.12
32 1 0.02
33 3 0.06
34 8 0.17
35 4 0.08
36 2 0.04
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.46
Consensus pattern (34 bp):
CATTATGTAAGTTTCATGTTAGTTAAGTTTGCAT
Found at i:47723954 original size:9 final size:9
Alignment explanation
Indices: 47723940--47723982 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
47723930 TGCTTATTAA
47723940 GTTTAATGT
1 GTTTAATGT
47723949 GTTTAATGT
1 GTTTAATGT
47723958 GTTTTTAATGT
1 G--TTTAATGT
47723969 GTTT--TGT
1 GTTTAATGT
47723976 GTTTAAT
1 GTTTAAT
47723983 ATGAGTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.23
9 14 0.47
11 9 0.30
ACGTcount: A:0.19, C:0.00, G:0.21, T:0.60
Consensus pattern (9 bp):
GTTTAATGT
Found at i:47723966 original size:11 final size:11
Alignment explanation
Indices: 47723941--47723973 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
47723931 GCTTATTAAG
47723941 TTTAATGTG--
1 TTTAATGTGTT
47723950 TTTAATGTGTT
1 TTTAATGTGTT
47723961 TTTAATGTGTT
1 TTTAATGTGTT
47723972 TT
1 TT
47723974 GTGTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
11 13 0.59
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (11 bp):
TTTAATGTGTT
Found at i:47744207 original size:25 final size:25
Alignment explanation
Indices: 47744141--47744209 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
47744131 CTCTATATGT
47744141 ATGCTCACACGAGCTGT-AATCAGA
1 ATGCTCACACGAGCTGTGAATCAGA
* *
47744165 ATGCTCAGACGAGTTGTGAATCAGA
1 ATGCTCACACGAGCTGTGAATCAGA
*
47744190 ATGCTCACATGAGCTGTGAA
1 ATGCTCACACGAGCTGTGAA
47744210 AATGGGTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 15 0.38
25 24 0.62
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAATCAGA
Found at i:47749046 original size:38 final size:38
Alignment explanation
Indices: 47748894--47749025 Score: 115
Period size: 38 Copynumber: 3.5 Consensus size: 38
47748884 GGAATGGGAA
* * **
47748894 GATTATCTACTAGTCCTTCG-GAACAACACCGTGTAATT
1 GATTATCTACTAGTCCTTCGAG-GCTACACCGTGTAAAC
* * * ** * * *
47748932 GATTATCTATTGGTCCTTTGAGGAGACATCATGTAAGTC
1 GATTATCTACTAGTCCTTCGAGGCTACACCGTGTAA-AC
*
47748971 -ATTATCTACTAGTCCTTCGAGGCTACACTGTGTAAAC
1 GATTATCTACTAGTCCTTCGAGGCTACACCGTGTAAAC
47749008 GATTATCTACTAGTCCTT
1 GATTATCTACTAGTCCTT
47749026 TGGGGTGGCA
Statistics
Matches: 73, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
37 1 0.01
38 70 0.96
39 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (38 bp):
GATTATCTACTAGTCCTTCGAGGCTACACCGTGTAAAC
Found at i:47762618 original size:50 final size:50
Alignment explanation
Indices: 47762511--47762957 Score: 484
Period size: 50 Copynumber: 8.8 Consensus size: 50
47762501 ATTTGGGTAA
* *
47762511 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
** *
47762567 AGATTTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
47762617 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
47762667 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** *
47762717 AGAGGTCCCATGTAAGACCATGTCTGGTACATGGGGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
47762767 AGAGGTCTCATGTAAGACCATCTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * ** *
47762817 AGAGGTCCCCCGTAAGACCATGTCAGGGACATGGCATGGGCACTTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
47762867 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
47762916 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
47762958 TGTTATATTC
Statistics
Matches: 340, Mismatches: 50, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
49 36 0.11
50 261 0.77
53 3 0.01
55 1 0.00
56 39 0.11
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:47766716 original size:6 final size:6
Alignment explanation
Indices: 47766705--47766729 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47766695 ATACCACTTA
47766705 AGGAAG AGGAAG AGGAAG AGGAAG A
1 AGGAAG AGGAAG AGGAAG AGGAAG A
47766730 AGAAAGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AGGAAG
Found at i:47788509 original size:140 final size:140
Alignment explanation
Indices: 47788255--47788818 Score: 713
Period size: 140 Copynumber: 4.0 Consensus size: 140
47788245 AGGCTTACCG
* * *
47788255 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTAGGATAGACTTG-TCGATATATGCTTTGGCCA
1 CGACACTTTTGGGCCAACACTTTCCTAAGTGTTAGGATAGACTTGCT-GACATACGCTTTGGCCA
* * *
47788319 ACTCTTTGTATAAGGGTTGGGGTATGCATGCCTAAGGCAATACTTAAATAAGAGTCGGCTTTGTC
65 ACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACAATTAAATAAGAGTCGGCTTTGTC
*
47788384 CAACATTATGC
130 CAACACTATGC
* * *
47788395 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTAGTATAGACTTGCTGACATACGCTTTGGTCAA
1 CGACACTTTTGGGCCAACACTTTCCTAAGTGTTAGGATAGACTTGCTGACATACGCTTTGGCCAA
* * * * **
47788460 CTCTTTGTATAAGGGTTGGAATATACATGCCTAAGGCAACAATTTAATAAGATTCAACTTTG-CA
66 CTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACAATTAAATAAGAGTCGGCTTTGTC-
47788524 CAACACTATGC
130 CAACACTATGC
* * * *
47788535 CGACACATTTGGGCCAACACTTTCCTAATTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAA
1 CGACACTTTTGGGCCAACACTTTCCTAAGTGTTAGGATAGACTTGCTGACATACGCTTTGGCCAA
* * * * **
47788600 CTCGTTGTATAAGGGTTAGGG-TATGCATGCTTCAGGTAACTCTTAAATAAGAGTCGGCTTTGTC
66 CTCTTTGTATAAGGGTT-GGGATATGCATGCCTAAGGCAACAATTAAATAAGAGTCGGCTTTGTC
*
47788664 CAACACTATGT
130 CAACACTATGC
* * * * ***
47788675 CGACACTTTTGGGCCAACATTTTCTTAAGTGTT-GAGATAGACTTGTTGACATATGCTTTGAAAA
1 CGACACTTTTGGGCCAACACTTTCCTAAGTGTTAG-GATAGACTTGCTGACATACGCTTTGGCCA
* * * * *
47788739 ACTCTTTATATAAGGGTTGGGATATGCATGCCTAAGGCAACAATTAGACAAGAGTTGGGTTTGTC
65 ACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACAATTAAATAAGAGTCGGCTTTGTC
47788804 CAACACTATGC
130 CAACACTATGC
47788815 CGAC
1 CGAC
47788819 TTTTGTTATA
Statistics
Matches: 362, Mismatches: 56, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
139 5 0.01
140 353 0.98
141 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (140 bp):
CGACACTTTTGGGCCAACACTTTCCTAAGTGTTAGGATAGACTTGCTGACATACGCTTTGGCCAA
CTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACAATTAAATAAGAGTCGGCTTTGTCC
AACACTATGC
Found at i:47788771 original size:280 final size:280
Alignment explanation
Indices: 47788255--47788783 Score: 801
Period size: 280 Copynumber: 1.9 Consensus size: 280
47788245 AGGCTTACCG
* * * * *
47788255 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTAGGATAGACTTGTCGATATATGCTTTGGCCAA
1 CGACACATTTGGGCCAACACTTTCCTAAGTGTTAGGATAGACTTGCCGACATACGCTTTGGCCAA
* *
47788320 CTCTTTGTATAAGGGTTGGGGTATGCATGCCTAAGGCAATACTTAAATAAGAGTCGGCTTTGTCC
66 CTCGTTGTATAAGGGTTAGGGTATGCATGCCTAAGGCAATACTTAAATAAGAGTCGGCTTTGTCC
* *
47788385 AACATTATGCCGACACTTTTGGGCCGACACTTTCCTAAGTGTTAGTATAGACTTGCTGACATACG
131 AACACTATGCCGACACTTTTGGGCCAACACTTTCCTAAGTGTTAGTATAGACTTGCTGACATACG
*** *
47788450 CTTTGGTCAACTCTTTGTATAAGGGTTGGAATATACATGCCTAAGGCAACAATTTAATAAGATTC
196 CTTTGAAAAACTCTTTATATAAGGGTTGGAATATACATGCCTAAGGCAACAATTTAATAAGATTC
47788515 AACTTTGCACAACACTATGC
261 AACTTTGCACAACACTATGC
* *
47788535 CGACACATTTGGGCCAACACTTTCCTAATTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAA
1 CGACACATTTGGGCCAACACTTTCCTAAGTGTTAGGATAGACTTGCCGACATACGCTTTGGCCAA
* * *
47788600 CTCGTTGTATAAGGGTTAGGGTATGCATGCTTCAGGTAACT-CTTAAATAAGAGTCGGCTTTGTC
66 CTCGTTGTATAAGGGTTAGGGTATGCATGCCTAAGGCAA-TACTTAAATAAGAGTCGGCTTTGTC
* * * *
47788664 CAACACTATGTCGACACTTTTGGGCCAACATTTTCTTAAGTGTTGAG-ATAGACTTGTTGACATA
130 CAACACTATGCCGACACTTTTGGGCCAACACTTTCCTAAGTGTT-AGTATAGACTTGCTGACATA
* * *
47788728 TGCTTTGAAAAACTCTTTATATAAGGGTTGGGATATGCATGCCTAAGGCAACAATT
194 CGCTTTGAAAAACTCTTTATATAAGGGTTGGAATATACATGCCTAAGGCAACAATT
47788784 AGACAAGAGT
Statistics
Matches: 222, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
280 219 0.99
281 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (280 bp):
CGACACATTTGGGCCAACACTTTCCTAAGTGTTAGGATAGACTTGCCGACATACGCTTTGGCCAA
CTCGTTGTATAAGGGTTAGGGTATGCATGCCTAAGGCAATACTTAAATAAGAGTCGGCTTTGTCC
AACACTATGCCGACACTTTTGGGCCAACACTTTCCTAAGTGTTAGTATAGACTTGCTGACATACG
CTTTGAAAAACTCTTTATATAAGGGTTGGAATATACATGCCTAAGGCAACAATTTAATAAGATTC
AACTTTGCACAACACTATGC
Found at i:47790500 original size:36 final size:35
Alignment explanation
Indices: 47790409--47790690 Score: 294
Period size: 36 Copynumber: 7.9 Consensus size: 35
47790399 AAAAAAATTA
* *
47790409 CCTTAGATGTGTCTAACCCAACCTTTTTAAGGTTG
1 CCTTAGATGGGTCTATCCCAACCTTTTTAAGGTTG
47790444 CCTTAGATGGGTCTATCCCAACCTTTTTAAGGTTG
1 CCTTAGATGGGTCTATCCCAACCTTTTTAAGGTTG
* *
47790479 CCTTAGATAAGGTCTATCCCAACTTTATTTAAAGGTTG
1 CCTTAGAT-GGGTCTATCCCAACCTT-TTT-AAGGTTG
* ** * * *
47790517 CCTTAAACACGGCCTATCCCAACCTTTCTAAGGTTA
1 CCTTAGA-TGGGTCTATCCCAACCTTTTTAAGGTTG
* * *
47790553 TCTTAGATGGGTTTATCTCAACCTTTTATAAGGTTG
1 CCTTAGATGGGTCTATCCCAACCTTTT-TAAGGTTG
* *
47790589 TCTTAGATGGGTCTATCACAACCTTTTTAAAGGTTG
1 CCTTAGATGGGTCTATCCCAACCTTTTT-AAGGTTG
* ***
47790625 TCTTAGACAAAGTCTATCCCAACCTTTTTAAGGTTG
1 CCTTAGA-TGGGTCTATCCCAACCTTTTTAAGGTTG
* * **
47790661 CCTCAGATGGGTTTATCCCAATTTTTTTAA
1 CCTTAGATGGGTCTATCCCAACCTTTTTAA
47790691 ATGTTGACCT
Statistics
Matches: 206, Mismatches: 34, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
35 73 0.35
36 84 0.41
37 22 0.11
38 27 0.13
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (35 bp):
CCTTAGATGGGTCTATCCCAACCTTTTTAAGGTTG
Found at i:47790657 original size:108 final size:109
Alignment explanation
Indices: 47790419--47790690 Score: 359
Period size: 108 Copynumber: 2.5 Consensus size: 109
47790409 CCTTAGATGT
* *
47790419 GTCTAACCCAACCTTTTTAAGGTTGCCTTAGATGGGTCTATCCCAACCTTTTTAAGGTTGCCTTA
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGATGGGTTTATCCCAACCTTTTTAAGGTTGCCTTA
* * **
47790484 GATAAGGTCTATCCCAACTTTATTTAAAGGTTGCCTTAAACACG
66 GATAAGGTCTATCACAACCTTATTTAAAGGTTGCCTTAAACAAA
* * ** * *
47790528 GCCTATCCCAACCTTTCTAAGGTTATCTTAGATGGGTTTATCTCAACCTTTTATAAGGTTGTCTT
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGATGGGTTTATCCCAACCTTTT-TAAGGTTGCCTT
* * *
47790593 AGAT-GGGTCTATCACAACCTT-TTTAAAGGTTGTCTTAGACAAA
65 AGATAAGGTCTATCACAACCTTATTTAAAGGTTGCCTTAAACAAA
* **
47790636 GTCTATCCCAACCTTTTTAAGGTTGCCTCAGATGGGTTTATCCCAATTTTTTTAA
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGATGGGTTTATCCCAACCTTTTTAA
47790691 ATGTTGACCT
Statistics
Matches: 139, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
107 3 0.02
108 62 0.45
109 59 0.42
110 15 0.11
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (109 bp):
GTCTATCCCAACCTTTTTAAGGTTGCCTTAGATGGGTTTATCCCAACCTTTTTAAGGTTGCCTTA
GATAAGGTCTATCACAACCTTATTTAAAGGTTGCCTTAAACAAA
Found at i:47819094 original size:13 final size:13
Alignment explanation
Indices: 47819076--47819100 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47819066 AATGCTAGGT
47819076 TGGGCACAAAAAG
1 TGGGCACAAAAAG
47819089 TGGGCACAAAAA
1 TGGGCACAAAAA
47819101 CTGAGACAGC
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:0.48, C:0.16, G:0.28, T:0.08
Consensus pattern (13 bp):
TGGGCACAAAAAG
Found at i:47820278 original size:15 final size:16
Alignment explanation
Indices: 47820250--47820279 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47820240 TAAATTCATA
47820250 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
47820266 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
47820280 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:47820299 original size:18 final size:17
Alignment explanation
Indices: 47820271--47820305 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
47820261 ATTATTAAGA
*
47820271 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
47820288 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
47820306 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:47820398 original size:14 final size:16
Alignment explanation
Indices: 47820369--47820401 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
47820359 TAAATTCATA
47820369 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
47820385 TAAGAAT-TTT-TTAT
1 TAAGAATATTTATTAT
47820399 TAA
1 TAA
47820402 ATTATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:47820418 original size:18 final size:18
Alignment explanation
Indices: 47820392--47820426 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47820382 TATTAAGAAT
* *
47820392 TTTTTATTAAATTATATA
1 TTTTAATTAAAATATATA
47820410 TTTTAATTAAAATATAT
1 TTTTAATTAAAATATAT
47820427 TTAATAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATTAAAATATATA
Found at i:47820506 original size:122 final size:120
Alignment explanation
Indices: 47820208--47820560 Score: 663
Period size: 121 Copynumber: 2.9 Consensus size: 120
47820198 TTAATTAAAA
47820208 ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
1 ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
47820273 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
66 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
47820328 ATATTTTATA-TATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
1 ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAA-
47820392 TTTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
65 -TTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
*
47820449 ATATTTTATAGTACCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
1 ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
*
47820514 TTTATTAAATTATATATTTTAATTAATATATATTTAATAATAATTAT
66 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
47820561 GTTAAAATAT
Statistics
Matches: 228, Mismatches: 2, Indels: 6
0.97 0.01 0.03
Matches are distributed among these distances:
119 53 0.23
120 57 0.25
121 66 0.29
122 52 0.23
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
Found at i:47820519 original size:15 final size:16
Alignment explanation
Indices: 47820491--47820520 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47820481 TAAATTCATA
47820491 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
47820507 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
47820521 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:47820542 original size:14 final size:15
Alignment explanation
Indices: 47820516--47820555 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
47820506 TTAAGAATTT
*
47820516 TATTAAATT-ATATA
1 TATTTAATTAATATA
47820530 T-TTTAATTAATATA
1 TATTTAATTAATATA
47820544 TATTTAA-TAATA
1 TATTTAATTAATA
47820556 ATTATGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATTAATATA
Found at i:47820545 original size:18 final size:17
Alignment explanation
Indices: 47820512--47820548 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
47820502 ATTATTAAGA
47820512 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
47820529 ATTTTAATT-AA-TATAT
1 ATTTT-ATTAAATTATAT
47820545 ATTT
1 ATTT
47820549 AATAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
17 7 0.37
18 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:47820736 original size:39 final size:40
Alignment explanation
Indices: 47820693--47820798 Score: 133
Period size: 44 Copynumber: 2.5 Consensus size: 40
47820683 TTTCCTTATG
47820693 CTATTACACCTCTATTTCATTCAACCAAACACAAGAA-TA
1 CTATTACACCTCTATTTCATTCAACCAAACACAAGAATTA
*
47820732 CTATTACACCTCTATTCCATTCCATTCAACCAAACAGAAGAATTA
1 CTATTACACCTCTA-T---TT-CATTCAACCAAACACAAGAATTA
*
47820777 CATATTACACCTCTATTCCATT
1 C-TATTACACCTCTATTTCATT
47820799 ACACATCTAC
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
39 14 0.24
40 1 0.02
41 4 0.07
42 1 0.02
43 2 0.03
44 19 0.33
45 4 0.07
46 13 0.22
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (40 bp):
CTATTACACCTCTATTTCATTCAACCAAACACAAGAATTA
Found at i:47820773 original size:44 final size:46
Alignment explanation
Indices: 47820710--47820798 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
47820700 ACCTCTATTT
47820710 CATTCAACCAAACACAAGAA-TAC-TATTACACCTCTATTCCATTC
1 CATTCAACCAAACACAAGAATTACATATTACACCTCTATTCCATTC
*
47820754 CATTCAACCAAACAGAAGAATTACATATTACACCTCTATTCCATT
1 CATTCAACCAAACACAAGAATTACATATTACACCTCTATTCCATT
47820799 ACACATCTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 19 0.45
45 3 0.07
46 20 0.48
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.28
Consensus pattern (46 bp):
CATTCAACCAAACACAAGAATTACATATTACACCTCTATTCCATTC
Found at i:47820801 original size:16 final size:16
Alignment explanation
Indices: 47820780--47820833 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
47820770 AGAATTACAT
47820780 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* **
47820796 ATTACACATCTACCCC
1 ATTACACCTCTATTCC
47820812 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
47820828 ATTACA
1 ATTACA
47820834 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:47837455 original size:20 final size:20
Alignment explanation
Indices: 47837407--47837456 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
47837397 ATGTCAAAAG
* *
47837407 AAGCCACAAAGAATAACAGA
1 AAGCCACAGAGAACAACAGA
47837427 AAGCCACAGAGAACAACAGA
1 AAGCCACAGAGAACAACAGA
47837447 AAGCCACAGA
1 AAGCCACAGA
47837457 AAAGAATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.56, C:0.24, G:0.18, T:0.02
Consensus pattern (20 bp):
AAGCCACAGAGAACAACAGA
Found at i:47841073 original size:23 final size:23
Alignment explanation
Indices: 47841041--47841098 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
47841031 AGCTAGGGAG
*
47841041 GTGCGGCGATAGGGTGTGGTGAT
1 GTGCGACGATAGGGTGTGGTGAT
47841064 GTGCGACGATAGGGTGTGGTGAT
1 GTGCGACGATAGGGTGTGGTGAT
47841087 GTGCGACGATAG
1 GTGCGACGATAG
47841099 ATGTGCTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.17, C:0.10, G:0.48, T:0.24
Consensus pattern (23 bp):
GTGCGACGATAGGGTGTGGTGAT
Found at i:47842659 original size:8 final size:8
Alignment explanation
Indices: 47842646--47842672 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
47842636 ATATTATTGA
47842646 ATTTTATT
1 ATTTTATT
47842654 ATTTTATT
1 ATTTTATT
47842662 ATTTTATT
1 ATTTTATT
47842670 ATT
1 ATT
47842673 ATAATTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTATT
Found at i:47845048 original size:51 final size:50
Alignment explanation
Indices: 47844981--47845174 Score: 205
Period size: 51 Copynumber: 3.9 Consensus size: 50
47844971 CAATGATATT
* * * *
47844981 TGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGGCCATTACCATC
1 TGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * *
47845032 TGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 TGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* ** * * * *
47845083 CGGTATGCATAGTAGCCTGCAC--AGTACTACACATGCGACC-TATCATCC
1 TGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCAT-C
47845131 TGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
47845175 CACTTTCACT
Statistics
Matches: 113, Mismatches: 25, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
47 3 0.03
48 20 0.18
49 14 0.12
50 16 0.14
51 58 0.51
52 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (50 bp):
TGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:47845149 original size:99 final size:100
Alignment explanation
Indices: 47844988--47845170 Score: 289
Period size: 99 Copynumber: 1.8 Consensus size: 100
47844978 ATTTGGTTCA
* *
47844988 CATAGTAGCCTGCACATAGTACTACACATGTGGCCATTACCATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACA-AGTACTACACATGCGACCA-TACCATCTGATACACGTAGTAGCCTGCA
47845053 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
64 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* *
47845090 CATAGTAGCCTGCAC-AGTACTACACATGCGACC-TATCATCCTGGTACACGTAGTAGCCTGCAC
1 CATAGTAGCCTGCACAAGTACTACACATGCGACCATACCAT-CTGATACACGTAGTAGCCTGCAC
47845153 ATAGTACTACACACGTGA
65 ATAGTACTACACACGTGA
47845171 CCATCACTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
98 5 0.07
99 40 0.53
100 16 0.21
102 15 0.20
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (100 bp):
CATAGTAGCCTGCACAAGTACTACACATGCGACCATACCATCTGATACACGTAGTAGCCTGCACA
TAGTACTACACACGTGATCGAAACTATCCGGTATG
Found at i:47854686 original size:28 final size:28
Alignment explanation
Indices: 47854643--47854712 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
47854633 AAATAAAAAT
47854643 TTACCAAAATAT-TATAACTTTTTTTAG
1 TTACCAAAATATATATAACTTTTTTTAG
* *
47854670 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAG
47854698 TTACCAAAATATATA
1 TTACCAAAATATATA
47854713 AAAAAAACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 12 0.30
28 28 0.70
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAG
Found at i:47854792 original size:27 final size:27
Alignment explanation
Indices: 47854762--47854819 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
47854752 CCTTGGTCAC
*
47854762 GCCAATGGCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
47854789 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
47854816 GCCA
1 GCCA
47854820 TATTGATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.17
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAATGGT
Found at i:47854944 original size:3 final size:3
Alignment explanation
Indices: 47854886--47854925 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
47854876 AAAATCAAAA
47854886 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
47854926 GTTGTTGCGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:47855015 original size:19 final size:21
Alignment explanation
Indices: 47854976--47855017 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
47854966 AAATTTTTGA
*
47854976 TTATATTGTTGTTATTATTTT
1 TTATATTGTTGTTAATATTTT
47854997 TTATATT-TTG-TAATATTTT
1 TTATATTGTTGTTAATATTTT
47855016 TT
1 TT
47855018 GTTTTAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 3 0.15
21 7 0.35
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (21 bp):
TTATATTGTTGTTAATATTTT
Found at i:47860446 original size:160 final size:158
Alignment explanation
Indices: 47860272--47860700 Score: 378
Period size: 159 Copynumber: 2.7 Consensus size: 158
47860262 AACCATTTAT
47860272 TCGTATTTTTTTCTCCACATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTA
1 TCGTATTTTTTTCTCCACATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTA
* *
47860337 CATTATTTCAGTGCATAATGTTTGAAATTTATTACTCTAGTGT-ATTATTTAAATTAATTTGGTG
66 CATTATTTCAGTGCATAATGTTTGAAATTTATTA-T-TAGTGTAATTATTT--ATGAATTT--TA
*
47860401 TAAAA-A-AATA-ACCCTTACCCCTGCCCTTTGC
125 TAAAATAGAATACACCCTTACCCCTGCCATTTGC
* * * * * **
47860432 TCGTATTATTTTCTCGA-TTTTTATTACTTTAAATAAAAATAT-TTTATTCTCGT-ATTTTATTG
1 TCGTATTTTTTTCTCCACATTTTATTACTTT--A-AAAAATATCATAATT-TC-TAATTTTATAA
* * ** * *
47860494 TTTTATATTATTTCAGTACATTTTCTTTGAAATATT-TT-TTA-T-TAATTATTTCTGAATTTTA
61 TTTTACATTATTTCAGTGCATAATGTTTGAAAT-TTATTATTAGTGTAATTATTTATGAATTTTA
* ** *
47860555 TAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGT
125 TAAAA--TAG-AATACACCCTTACCCCTGCCATTTGC
* ** *
47860592 TCGTATTTTTTTCTCCGCATTTTATTACTTTAAAAAATATCATAAACT-TAGTCTTTTATAATTT
1 TCGTATTTTTTTCTCCACATTTTATTACTTTAAAAAATATCATAATTTCTA--ATTTTATAATTT
*
47860656 TACATTATTTCAGTGCATCATGTTTGAAATTTATTAATTTAGTGT
64 TACATTATTTCAGTGCATAATGTTTGAAATTTATT-A-TTAGTGT
47860701 GTTAAGGAGG
Statistics
Matches: 209, Mismatches: 36, Indels: 44
0.72 0.12 0.15
Matches are distributed among these distances:
154 6 0.03
156 7 0.03
157 2 0.01
158 19 0.09
159 57 0.27
160 46 0.22
161 17 0.08
162 50 0.24
163 4 0.02
164 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (158 bp):
TCGTATTTTTTTCTCCACATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTA
CATTATTTCAGTGCATAATGTTTGAAATTTATTATTAGTGTAATTATTTATGAATTTTATAAAAT
AGAATACACCCTTACCCCTGCCATTTGC
Found at i:47861134 original size:15 final size:16
Alignment explanation
Indices: 47861114--47861155 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
47861104 AGAAATATCG
47861114 TAATTTTTTATT-TTA
1 TAATTTTTTATTATTA
* *
47861129 TAATTTTATATTATTT
1 TAATTTTTTATTATTA
*
47861145 TAATTTATTAT
1 TAATTTTTTAT
47861156 GTTTGAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATTTTTTATTATTA
Found at i:47861588 original size:4 final size:4
Alignment explanation
Indices: 47861572--47861711 Score: 105
Period size: 4 Copynumber: 34.0 Consensus size: 4
47861562 CTCCTTTCCT
*
47861572 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTT-C TTTC T-TTC
*
47861618 -TTC TTT- TTT- TTCTC TTCTCC TTTCC TTTTC TTTC CTTC -TT- TTTC
1 TTTC TTTC TTTC TT-TC TT-T-C TTT-C -TTTC TTTC TTTC TTTC TTTC
*
47861662 TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
47861712 CCTCTCCTTT
Statistics
Matches: 116, Mismatches: 5, Indels: 30
0.77 0.03 0.20
Matches are distributed among these distances:
3 16 0.14
4 72 0.62
5 18 0.16
6 10 0.09
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:47861589 original size:28 final size:27
Alignment explanation
Indices: 47861510--47861707 Score: 98
Period size: 28 Copynumber: 7.5 Consensus size: 27
47861500 ATTACCTTTT
*
47861510 TTTCTTTTTTTTCCTTCTTTCCTTC-CC
1 TTTCTTTTCTTTCCTTCTTT-CTTCTCC
* *
47861537 TCTTCTTCTTC-TTCTTTTTTCTCTTCTCC
1 T-TTCTT-TTCTTTCCTTCTT-TCTTCTCC
**
47861566 TTTCCTTTTCTTTCCTTCTTTCTTTCTTT
1 TTT-CTTTTCTTTCCTTCTTTC-TTCTCC
* *
47861595 TTTCTTCTCTTTTCC-T-TTTCTTCTTC
1 TTTCTTTTC-TTTCCTTCTTTCTTCTCC
* * *
47861621 TTTTTTTTCTCTT-CTCCTTTCCTT-TTC
1 TTTCTTTTCT-TTCCTTCTTT-CTTCTCC
*
47861648 TTTC-CTTCTTT--TTCTTTCTT-TCC
1 TTTCTTTTCTTTCCTTCTTTCTTCTCC
* * *
47861671 TCTCCTTTCTTTCTTTCTTTCTT-T-C
1 TTTCTTTTCTTTCCTTCTTTCTTCTCC
47861696 TTTC-TTTCTTTC
1 TTTCTTTTCTTTC
47861708 TTTCCCTCTC
Statistics
Matches: 137, Mismatches: 19, Indels: 33
0.72 0.10 0.17
Matches are distributed among these distances:
23 8 0.06
24 19 0.14
25 8 0.06
26 28 0.20
27 14 0.10
28 32 0.23
29 28 0.20
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCTTTTCTTTCCTTCTTTCTTCTCC
Found at i:47861607 original size:33 final size:32
Alignment explanation
Indices: 47861547--47861707 Score: 129
Period size: 33 Copynumber: 5.0 Consensus size: 32
47861537 TCTTCTTCTT
* *
47861547 CTTCTTT-TTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTCT-TTTTTCTTT-CTTTTCTTTC
*
47861580 CTTCTTTCTTTCTTTTTTCTTCTCTTTTCCTTTT
1 CTTCTTTCTTTCTTTTTTCTT-TCTTTT-CTTTC
* *
47861614 CTTC-TTCTTT-TTTTTCTCTTCTCCTTTCCTT-
1 CTTCTTTCTTTCTTTTT-TCTT-TCTTTTCTTTC
* * *
47861645 -TTCTTTCCTTC-TTTTTCTTTCTTTCCTCTC
1 CTTCTTTCTTTCTTTTTTCTTTCTTTTCTTTC
47861675 CTTTCTTTCTTTCTTTCTTTCTTTC-TTTCTTTC
1 C-TTCTTTCTTTCTTT-TTTCTTTCTTTTCTTTC
47861708 TTTCCCTCTC
Statistics
Matches: 104, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
29 6 0.06
30 7 0.07
31 9 0.09
32 18 0.17
33 42 0.40
34 22 0.21
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (32 bp):
CTTCTTTCTTTCTTTTTTCTTTCTTTTCTTTC
Found at i:47861829 original size:27 final size:27
Alignment explanation
Indices: 47861754--47861821 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
47861744 TATTATTAAC
*
47861754 TGGTGCTGCCAATAATATTGGCACCAT
1 TGGTGCCGCCAATAATATTGGCACCAT
** * *
47861781 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATAATATTGGCACCAT
47861808 TGGTGCCGCCAATA
1 TGGTGCCGCCAATA
47861822 CCATTGGCGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.29
Consensus pattern (27 bp):
TGGTGCCGCCAATAATATTGGCACCAT
Found at i:47861907 original size:23 final size:23
Alignment explanation
Indices: 47861875--47861920 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
47861865 TTTATTTTTT
47861875 TATATATTTTGGTAAATAAAAAA
1 TATATATTTTGGTAAATAAAAAA
* *
47861898 TATATTTTTTGTTAAATAAAAAA
1 TATATATTTTGGTAAATAAAAAA
47861921 AGTTATAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (23 bp):
TATATATTTTGGTAAATAAAAAA
Found at i:47863888 original size:43 final size:43
Alignment explanation
Indices: 47863835--47863960 Score: 207
Period size: 43 Copynumber: 2.9 Consensus size: 43
47863825 GTATTTTGTT
*
47863835 TGAACGTGAGTATTAAATATGTCCTTTTCAGGGACTATTTTAA
1 TGAATGTGAGTATTAAATATGTCCTTTTCAGGGACTATTTTAA
* *
47863878 TGAATGTGAGTATTAAATATGTCCTTTTTAGGGACTGTTTTAA
1 TGAATGTGAGTATTAAATATGTCCTTTTCAGGGACTATTTTAA
*
47863921 TGAATGTGAGTATTAAATATGTCCTTTTGAGGGACATATT
1 TGAATGTGAGTATTAAATATGTCCTTTTCAGGGAC-TATT
47863961 GTTTGAACGT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
43 74 0.96
44 3 0.04
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (43 bp):
TGAATGTGAGTATTAAATATGTCCTTTTCAGGGACTATTTTAA
Found at i:47870065 original size:54 final size:50
Alignment explanation
Indices: 47869983--47870225 Score: 186
Period size: 48 Copynumber: 4.9 Consensus size: 50
47869973 TGACATTAGG
**
47869983 GATGAGA--TCCCATGTAAGACCATGTCTGGG-CATGGCATTGGCATTATTGA
1 GATGAGAGGTCCCA-GTAAGACCATGTCTGGGACATGGCATTGGCA--ACCGA
*
47870033 GGTTATGAGAGGTCCCAGTAAGACCATGTCTGGGACATGGCGTTGG--ACCGA
1 -G--ATGAGAGGTCCCAGTAAGACCATGTCTGGGACATGGCATTGGCAACCGA
* *
47870084 GATGAGAGGTCCCCGTAAGACCATGTCTGGGACATGGCATGGGC-ACCGA
1 GATGAGAGGTCCCAGTAAGACCATGTCTGGGACATGGCATTGGCAACCGA
* ** * *
47870133 TATGAGAACT-CCATGTAAGACCATATCTGGGATATGGCATT-GCAGTA-C-A
1 GATGAGAGGTCCCA-GTAAGACCATGTCTGGGACATGGCATTGGCA--ACCGA
* ** *
47870182 G--GAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GATGAGAGGTCCCA-GTAAGACCATGTCTGGGACATGGCATTGGCA
47870226 TGTTATTATC
Statistics
Matches: 160, Mismatches: 20, Indels: 26
0.78 0.10 0.13
Matches are distributed among these distances:
47 4 0.03
48 71 0.44
49 40 0.25
50 2 0.01
51 5 0.03
53 6 0.04
54 17 0.11
55 15 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCAGTAAGACCATGTCTGGGACATGGCATTGGCAACCGA
Found at i:47878072 original size:50 final size:50
Alignment explanation
Indices: 47877967--47878073 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
47877957 TTATTGAGGT
* * * * *
47877967 TATGAGAGGTCCCACGTAAGACAATGTCTGGGACATGGCGTTGGTACCTA
1 TATGAGAGGTCCCACGTAAGACAATGTCAGGGACATGGCATGGGCACCGA
* * *
47878017 GATGAGAGGTCCCCCGTAAGACCATGTCAGGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCACGTAAGACAATGTCAGGGACATGGCATGGGCACCGA
47878067 TATGAGA
1 TATGAGA
47878074 ACTCTCATGT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.27, C:0.21, G:0.32, T:0.20
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACAATGTCAGGGACATGGCATGGGCACCGA
Found at i:47878389 original size:20 final size:20
Alignment explanation
Indices: 47878364--47878402 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
47878354 TAAGTTATTT
47878364 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
47878384 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
47878403 GAATAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:47880255 original size:24 final size:25
Alignment explanation
Indices: 47880215--47880286 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 25
47880205 AGCTCATATG
* *
47880215 AGCTAAGAATCGGTAAGCTCTCACA
1 AGCTGAGAATCGATAAGCTCTCACA
*
47880240 AGCTGA-AATCGATAAGCTCAT-ACG
1 AGCTGAGAATCGATAAGCTC-TCACA
*
47880264 AGCTGAGAATCAATAAGCTCTCA
1 AGCTGAGAATCGATAAGCTCTCA
47880287 TGATCTGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 21 0.52
25 19 0.47
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (25 bp):
AGCTGAGAATCGATAAGCTCTCACA
Found at i:47880273 original size:49 final size:49
Alignment explanation
Indices: 47880151--47880286 Score: 150
Period size: 50 Copynumber: 2.7 Consensus size: 49
47880141 TTCTTGTACA
* * * *
47880151 TGTATGCTCATATGAGCTATGAATCGGTATGCTCTCACGAGTTGTAAATC
1 TGTAAGCTCATATGAGCTA-GAATCGGTAAGCTCTCACAAGCTGTAAATC
*
47880201 TGTCAGCTCATATGAGCTAAGAATCGGTAAGCTCTCACAAGCTG-AAATC
1 TGTAAGCTCATATGAGCT-AGAATCGGTAAGCTCTCACAAGCTGTAAATC
* **
47880250 -GATAAGCTCATACGAGCTGAGAATCAATAAGCTCTCA
1 TG-TAAGCTCATATGAGCT-AGAATCGGTAAGCTCTCA
47880287 TGATCTGAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.47
50 37 0.50
51 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (49 bp):
TGTAAGCTCATATGAGCTAGAATCGGTAAGCTCTCACAAGCTGTAAATC
Found at i:47880298 original size:49 final size:49
Alignment explanation
Indices: 47880156--47880286 Score: 129
Period size: 49 Copynumber: 2.7 Consensus size: 49
47880146 GTACATGTAT
* * ** * * * *
47880156 GCTCATATGAGCTATGAATCGGTATGCTCTCACGAGTTGTAAATCTG-TCA
1 GCTCATACGAGCTAAGAATCAATAAGCTCTCACAAGCTG-AAATC-GATAA
* **
47880206 GCTCATATGAGCTAAGAATCGGTAAGCTCTCACAAGCTGAAATCGATAA
1 GCTCATACGAGCTAAGAATCAATAAGCTCTCACAAGCTGAAATCGATAA
*
47880255 GCTCATACGAGCTGAGAATCAATAAGCTCTCA
1 GCTCATACGAGCTAAGAATCAATAAGCTCTCA
47880287 TGATCTGAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
48 1 0.01
49 35 0.49
50 35 0.49
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (49 bp):
GCTCATACGAGCTAAGAATCAATAAGCTCTCACAAGCTGAAATCGATAA
Done.