Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 161 of 167
Found at i:53396981 original size:20 final size:20
Alignment explanation
Indices: 53396958--53397016 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
53396948 TAAACATGGT
53396958 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
53396978 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
53396998 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
53397017 GGTATTCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:53396998 original size:11 final size:11
Alignment explanation
Indices: 53396962--53397016 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
53396952 CATGGTATGT
53396962 ATGATATGCAC
1 ATGATATGCAC
* *
53396973 ATGACATG--T
1 ATGATATGCAC
53396982 ATGATATGCAC
1 ATGATATGCAC
*
53396993 ATGATATG--T
1 ATGATATGCAC
53397002 ATGATATGCAC
1 ATGATATGCAC
53397013 ATGA
1 ATGA
53397017 GGTATTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:53397094 original size:24 final size:24
Alignment explanation
Indices: 53397067--53397282 Score: 353
Period size: 24 Copynumber: 9.0 Consensus size: 24
53397057 GAGCAAGTGC
53397067 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53397091 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
53397115 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
53397139 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
53397163 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
53397187 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
53397211 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
53397235 AAAAGGGCTTTTGCCCCAGTTTTT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53397259 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53397283 ATGATAAAGC
Statistics
Matches: 183, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
24 173 0.95
25 10 0.05
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:53398755 original size:52 final size:52
Alignment explanation
Indices: 53398693--53398795 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
53398683 TGAATGTGTG
53398693 AAAGTTTTAAGCTTCGATTTAGTTAATTGCTTATGAATTTAGTTAATAGGAT
1 AAAGTTTTAAGCTTCGATTTAGTTAATTGCTTATGAATTTAGTTAATAGGAT
*
53398745 AAAGTTTTAAGCTTCGATTTAGTTAATTGCTTGTGAATTTAGTTAATAGGA
1 AAAGTTTTAAGCTTCGATTTAGTTAATTGCTTATGAATTTAGTTAATAGGA
53398796 CTTATGTGTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (52 bp):
AAAGTTTTAAGCTTCGATTTAGTTAATTGCTTATGAATTTAGTTAATAGGAT
Found at i:53400733 original size:47 final size:47
Alignment explanation
Indices: 53400680--53400996 Score: 562
Period size: 47 Copynumber: 6.7 Consensus size: 47
53400670 TTAGGATTCT
53400680 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
53400727 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
53400774 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
53400821 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
53400868 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
53400915 ATGTGATGAATGTGAAAGTGGATATATGTGACAGGGCCTAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
53400962 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
53400997 TCCCGAAGGG
Statistics
Matches: 259, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 259 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:53401171 original size:37 final size:37
Alignment explanation
Indices: 53401115--53401193 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
53401105 CCGAGCTCTA
* * *
53401115 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
53401152 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
53401189 GAGAC
1 AAGAC
53401194 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:53403202 original size:40 final size:40
Alignment explanation
Indices: 53403130--53403225 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
53403120 CTATCTTGGT
* *
53403130 ATTGCACACTTAGTGCGACATAAAACCAAAGCTATTTC-A
1 ATTGCACACTAAGTGCGACATAAAACCAAAGCTATCTCGA
* * * * *
53403169 ATTTGCACACTAAGTGCTATATATAGCCGAAGCTATCTCGA
1 A-TTGCACACTAAGTGCGACATAAAACCAAAGCTATCTCGA
*
53403210 AATGCACACTAAGTGC
1 ATTGCACACTAAGTGC
53403226 CAAACATCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.02
40 44 0.94
41 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (40 bp):
ATTGCACACTAAGTGCGACATAAAACCAAAGCTATCTCGA
Found at i:53415036 original size:13 final size:15
Alignment explanation
Indices: 53415018--53415049 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
53415008 TTTATTTATT
53415018 AATCTCTT-CCTC-G
1 AATCTCTTACCTCTG
53415031 AATCTCTTACCTCTG
1 AATCTCTTACCTCTG
53415046 AATC
1 AATC
53415050 AGCTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.22, C:0.34, G:0.06, T:0.38
Consensus pattern (15 bp):
AATCTCTTACCTCTG
Found at i:53418630 original size:46 final size:46
Alignment explanation
Indices: 53418563--53418736 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 46
53418553 TAACCCGTCA
*
53418563 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCC
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCC
* * * *
53418609 ATAAGTGAACTCAGACTCAACTCAACGAGCTC-GA-ATGC-CTAGTTAC
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--TCC
* * * *
53418655 ATCTCA-CGAACTTGGACTCAACTCAACGAGTTCGGACGTTCGCATCC
1 A--TAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCC
* *
53418702 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
53418737 TACCCAAATA
Statistics
Matches: 103, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 3 0.03
46 61 0.59
47 26 0.25
48 4 0.04
49 3 0.03
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCC
Found at i:53421499 original size:30 final size:29
Alignment explanation
Indices: 53421457--53421513 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
53421447 AAAGATAACA
53421457 AGAAAACCGAATAAAGAAATCCAAGATTG
1 AGAAAACCGAATAAAGAAATCCAAGATTG
*
53421486 AGAAACCCAGAATAAAGAAATCCAAGAT
1 AGAAAACC-GAATAAAGAAATCCAAGAT
53421514 ACGATACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (29 bp):
AGAAAACCGAATAAAGAAATCCAAGATTG
Found at i:53432677 original size:39 final size:40
Alignment explanation
Indices: 53432632--53432799 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
53432622 CGGGGTTTAG
* * *
53432632 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
53432671 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
53432711 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
53432751 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
53432792 CCGGATAT
1 CCGGATAT
53432800 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:53432782 original size:41 final size:40
Alignment explanation
Indices: 53432655--53432799 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
53432645 CTCGCACAAG
* * * * *
53432655 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
53432695 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
53432735 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
53432776 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
53432800 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:53441195 original size:79 final size:82
Alignment explanation
Indices: 53441084--53441268 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
53441074 GCTACTCGTT
* *
53441084 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
53441147 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
53441164 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
53441227 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
53441244 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53441269 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:53441268 original size:40 final size:40
Alignment explanation
Indices: 53441065--53441268 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
53441055 CGGAATTTAA
** *
53441065 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
53441105 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
53441145 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
53441184 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
53441224 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
53441264 CCGGA
1 CCGGA
53441269 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:53451051 original size:94 final size:92
Alignment explanation
Indices: 53450922--53451090 Score: 212
Period size: 94 Copynumber: 1.8 Consensus size: 92
53450912 ACATCTCGTA
* * ** * *
53450922 GCCGATGTATGTCCCAGAAATGTCTTATACTGGCTTACATCTTGAGGCCGATGCATGTCCGAGAC
1 GCCGATGCATGTCCCAGAAATGTCTTACACTGGCTTACATAATGAGGCCGATGCATGTCCCAAAC
53450987 ATGCCTTACAATAGCACTCGTCTCAAT
66 ATGCCTTACAATAGCACTCGTCTCAAT
* * * * *
53451014 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTTTCATAATGTGGCCGGTGCATGTCCCAA
1 GCCGATG-CATGTCCCAGAAAT-GTCTTACACTGGCTTACATAATGAGGCCGATGCATGTCCCAA
*
53451079 ACATGTCTTACA
64 ACATGCCTTACA
53451091 CTAGTTCACA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
92 7 0.11
93 12 0.19
94 44 0.70
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGAAATGTCTTACACTGGCTTACATAATGAGGCCGATGCATGTCCCAAAC
ATGCCTTACAATAGCACTCGTCTCAAT
Found at i:53453226 original size:24 final size:23
Alignment explanation
Indices: 53453192--53453238 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
53453182 GCTTGTATGG
*
53453192 AAAAATTTG-AAGGAAAGGGAAAAT
1 AAAAATGTGAAAGG-AA-GGAAAAT
53453216 AAAAATGTGAAAGGAAGGAAAAT
1 AAAAATGTGAAAGGAAGGAAAAT
53453239 TTGGGCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 10 0.48
25 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.15
Consensus pattern (23 bp):
AAAAATGTGAAAGGAAGGAAAAT
Found at i:53459234 original size:15 final size:15
Alignment explanation
Indices: 53459214--53459243 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53459204 GCTAGGTGAT
53459214 AACATGGTGATTGAA
1 AACATGGTGATTGAA
53459229 AACATGGTGATTGAA
1 AACATGGTGATTGAA
53459244 GTATGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (15 bp):
AACATGGTGATTGAA
Found at i:53465837 original size:53 final size:54
Alignment explanation
Indices: 53465769--53465908 Score: 165
Period size: 54 Copynumber: 2.6 Consensus size: 54
53465759 CTTACCATTG
* * * *
53465769 CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCATTA
1 CCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAACTCACCAATA
* * * * * * *
53465822 TCATGCCTTGGCATGGTCTTACATGATTTGCTTGCCTTGTAGAACTTACCAATG
1 CCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAACTCACCAATA
*
53465876 CCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 CCATGCCTTGGCATGGTCTTACATGGTATCCTT
53465909 AAACCCTAAT
Statistics
Matches: 70, Mismatches: 16, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
53 32 0.46
54 38 0.54
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (54 bp):
CCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAACTCACCAATA
Found at i:53465890 original size:54 final size:53
Alignment explanation
Indices: 53465757--53465908 Score: 178
Period size: 53 Copynumber: 2.8 Consensus size: 53
53465747 TTCCTTTTTA
* * * *
53465757 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
1 AACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATG
* ** * * *
53465810 AACTCACCATTATCATGCCTTGGCATGGTCTTACATGATTTGCTTGCCTTGTAG
1 AACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTAT-G
* * *
53465864 AACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATCCTT
53465909 AAACCCTAAT
Statistics
Matches: 80, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
53 42 0.52
54 38 0.47
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (53 bp):
AACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATG
Found at i:53468226 original size:43 final size:43
Alignment explanation
Indices: 53468128--53468229 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
53468118 ATCGAGATGT
* * *
53468128 GATTACATGTAAGACCATGTCTGGGAAATTGGCATTGTATTGA
1 GATTACGTGTAAGACCATGTCTGGGAAATTGGCATCGTAATGA
* * *
53468171 GATTACGAGTAAGACCATGTCTGGGACATTGGCATCGTTAAT-C
1 GATTACGTGTAAGACCATGTCTGGGAAATTGGCATCG-TAATGA
*
53468214 GATTTCGTGTAAGACC
1 GATTACGTGTAAGACC
53468230 CTGTTAGGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
43 47 0.94
44 3 0.06
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGAAATTGGCATCGTAATGA
Found at i:53474378 original size:41 final size:40
Alignment explanation
Indices: 53474226--53474395 Score: 143
Period size: 41 Copynumber: 4.2 Consensus size: 40
53474216 GCTAATCGGG
*
53474226 GTCTAAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGT
1 GTCT-AATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
* * * *
53474267 G-CTAATAACCGAACTTATTTTCGAAGGGCTTTTTAGAGCCAAT
1 GTCTAAT--CCGAGCTTAGTCTCGAAGGGC-TTTT-GAGCCAGT
* *
53474310 GTCATAA-CCG-GACTTAGT-TCTGAAGGGCCTTCGAGCCAGT
1 GTC-TAATCCGAG-CTTAGTCTC-GAAGGGCTTTTGAGCCAGT
* *
53474350 AGTCTAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCGGT
1 -GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
53474391 G-CTAA
1 GTCTAA
53474396 GAGTCAAACT
Statistics
Matches: 103, Mismatches: 14, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
39 7 0.07
40 13 0.13
41 49 0.48
42 22 0.21
43 8 0.08
44 1 0.01
45 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (40 bp):
GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
Found at i:53494316 original size:42 final size:41
Alignment explanation
Indices: 53494240--53494374 Score: 134
Period size: 42 Copynumber: 3.3 Consensus size: 41
53494230 NNNNNNNNNN
*
53494240 AAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTTTCG
1 AAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTTCCG
* *
53494281 AAGGGCTTTTTAGAGCCAGTG-TCATAACCGGACTTAGTTCCG
1 AAGGGC-TTTT-GAGCCAGTGCTAATAACCGAACTTAGTTCCG
* * * *
53494323 AAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTT-GGTCTCG
1 AAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTTC-CG
53494364 AAGGGCTTTTG
1 AAGGGCTTTTG
53494375 CGCTGGTGCT
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
40 11 0.14
41 26 0.34
42 28 0.36
43 12 0.16
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (41 bp):
AAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTTCCG
Found at i:53501873 original size:46 final size:46
Alignment explanation
Indices: 53501800--53501993 Score: 185
Period size: 46 Copynumber: 4.2 Consensus size: 46
53501790 CAGATCAATT
* * * *
53501800 GATTGAAGAA-ACCACAAATCCTGTACCCCTGAGTTATAGTGGGATG
1 GATTGAAGAAGA-TACAAATCTTATACCCCTGAGTTACAGTGGGATG
* * *
53501846 TATTGAGGAAGATACAAATCTTATACCCCTGAGTTGCAGTGGGATG
1 GATTGAAGAAGATACAAATCTTATACCCCTGAGTTACAGTGGGATG
* * * *
53501892 GATTGAAGATGATAAAAATCTTATACCCTTGAGTTACAATGGGATG
1 GATTGAAGAAGATACAAATCTTATACCCCTGAGTTACAGTGGGATG
* * * * * * *
53501938 GATGGAAGAA-ACCAAAAATTTTATACCCTTAAGTTACAATGGGATG
1 GATTGAAGAAGA-TACAAATCTTATACCCCTGAGTTACAGTGGGATG
*
53501984 GATGGAAGAA
1 GATTGAAGAA
53501994 ACCACAAATT
Statistics
Matches: 127, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
45 1 0.01
46 125 0.98
47 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (46 bp):
GATTGAAGAAGATACAAATCTTATACCCCTGAGTTACAGTGGGATG
Found at i:53501994 original size:46 final size:46
Alignment explanation
Indices: 53501861--53502007 Score: 188
Period size: 46 Copynumber: 3.2 Consensus size: 46
53501851 AGGAAGATAC
* * * * * *
53501861 AAATCTTATACCCCTGAGTTGCAGTGGGATGGATTGAAGATGA-TAA
1 AAATCTTATACCCTTGAGTTACAATGGGATGGATGGAAGA-AACCAA
53501907 AAATCTTATACCCTTGAGTTACAATGGGATGGATGGAAGAAACCAA
1 AAATCTTATACCCTTGAGTTACAATGGGATGGATGGAAGAAACCAA
* * *
53501953 AAATTTTATACCCTTAAGTTACAATGGGATGGATGGAAGAAACCAC
1 AAATCTTATACCCTTGAGTTACAATGGGATGGATGGAAGAAACCAA
*
53501999 AAATTTTAT
1 AAATCTTAT
53502008 CTCCCTAAAG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 90 0.99
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (46 bp):
AAATCTTATACCCTTGAGTTACAATGGGATGGATGGAAGAAACCAA
Found at i:53502286 original size:21 final size:21
Alignment explanation
Indices: 53502257--53502298 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
53502247 ATTTGGCATA
53502257 AGCAATGGAGTAGATTGAAGT
1 AGCAATGGAGTAGATTGAAGT
*
53502278 AGCAGTGGAGTAGATTGAAGT
1 AGCAATGGAGTAGATTGAAGT
53502299 CGTAGATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.24
Consensus pattern (21 bp):
AGCAATGGAGTAGATTGAAGT
Found at i:53502775 original size:45 final size:46
Alignment explanation
Indices: 53502663--53502777 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 46
53502653 AGATCGAAGC
53502663 CACAATCCTTATC-TCTTTGAAGTTGTAGTAGAGCAGGATAAAAATA
1 CACAATCCTTATCTTC-TTGAAGTTGTAGTAGAGCAGGATAAAAATA
* * * * * * * *
53502709 CACAAACCTTATCTCCCTGAAGTTGTAGTGGAGTAGGTTGAAATTA
1 CACAATCCTTATCTTCTTGAAGTTGTAGTAGAGCAGGATAAAAATA
*
53502755 C-CAATTCTTATCTTCTTGAAGTT
1 CACAATCCTTATCTTCTTGAAGTT
53502778 TCAGCAGAGT
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
45 18 0.32
46 37 0.66
47 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (46 bp):
CACAATCCTTATCTTCTTGAAGTTGTAGTAGAGCAGGATAAAAATA
Found at i:53505575 original size:30 final size:29
Alignment explanation
Indices: 53505539--53505599 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
53505529 AAACAAAAGT
*
53505539 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGAGATTT-AACTAGC
53505569 TTTGGCACTAAGTGTGAGATTTAACTAGC
1 TTTGGCACTAAGTGTGAGATTTAACTAGC
53505598 TT
1 TT
53505600 CGGCTACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGAGATTTAACTAGC
Found at i:53518300 original size:49 final size:49
Alignment explanation
Indices: 53518228--53518371 Score: 200
Period size: 49 Copynumber: 2.9 Consensus size: 49
53518218 GCCGAAGCTA
53518228 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG-
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-ACAGT
* * * * *
53518277 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTT
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCACAG--T
*
53518328 TCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
53518372 TCACAATAGA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
48 4 0.05
49 39 0.48
51 38 0.47
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (49 bp):
TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCACAGT
Found at i:53518356 original size:51 final size:49
Alignment explanation
Indices: 53518231--53518371 Score: 185
Period size: 51 Copynumber: 2.8 Consensus size: 49
53518221 GAAGCTATCT
* *
53518231 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCG
* * * *
53518280 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCG
*
53518331 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACC
53518372 TCACAATAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 4 0.05
49 36 0.46
51 38 0.49
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (49 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCG
Found at i:53521189 original size:46 final size:46
Alignment explanation
Indices: 53521091--53521310 Score: 232
Period size: 46 Copynumber: 4.8 Consensus size: 46
53521081 TAACCGTGCT
* *
53521091 GATGCATGTCCCAAACATGTCTTACACTAG--CACATCTCGTA-GCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTCG-AGGCC
* * *
53521135 GACGCATGTCCCAGACATGTCTGACACTGGCTAACATCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTCGAGGCC
* * *
53521181 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATACT-GTGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCACAT-CTCGAGGCC
* * * * * * *
53521227 GATGCATGTCCTAGACATGTCTTACACTAGCCCTCGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTCGAGGCC
*
53521273 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCACA
53521311 AATCTCATGT
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
44 26 0.18
45 3 0.02
46 87 0.60
47 15 0.10
48 14 0.10
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTCGAGGCC
Found at i:53528238 original size:43 final size:43
Alignment explanation
Indices: 53528191--53528295 Score: 149
Period size: 43 Copynumber: 2.4 Consensus size: 43
53528181 TTTTAGACAG
* * *
53528191 GGTCTTACATGAAATC-GAATAACGATGCCAATGTCCCAAACAT
1 GGTCTTACATGTAATCACAAT-ACAATGCCAATGTCCCAAACAT
* *
53528234 GGTCTTACACGTAATCACAATACAATGCCAATGTCCCAAACTT
1 GGTCTTACATGTAATCACAATACAATGCCAATGTCCCAAACAT
53528277 GGTCTTACATGTAATCACA
1 GGTCTTACATGTAATCACA
53528296 TATCGGTAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 52 0.95
44 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (43 bp):
GGTCTTACATGTAATCACAATACAATGCCAATGTCCCAAACAT
Found at i:53529439 original size:216 final size:216
Alignment explanation
Indices: 53529065--53529496 Score: 864
Period size: 216 Copynumber: 2.0 Consensus size: 216
53529055 ACATGAAATA
53529065 GGTGAAATAGAATATTTTTAAGTTAGGGGCATTTTGATCATTTAGTAATTAAAATGAATTAAAAA
1 GGTGAAATAGAATATTTTTAAGTTAGGGGCATTTTGATCATTTAGTAATTAAAATGAATTAAAAA
53529130 CAAAGTAAAAGCCAAAATTTCTTGTCCATCTTCTTCCTTGGACGAATTTTACATGAATAAACCAT
66 CAAAGTAAAAGCCAAAATTTCTTGTCCATCTTCTTCCTTGGACGAATTTTACATGAATAAACCAT
53529195 CGCTAGGGTTTTCCAAGCTTCCAAGTTCGATTGTAAGTCCGTTCTTGCCCCGTTTTTAATGATTT
131 CGCTAGGGTTTTCCAAGCTTCCAAGTTCGATTGTAAGTCCGTTCTTGCCCCGTTTTTAATGATTT
53529260 TTACGTTTTTGAAATCTTTAC
196 TTACGTTTTTGAAATCTTTAC
53529281 GGTGAAATAGAATATTTTTAAGTTAGGGGCATTTTGATCATTTAGTAATTAAAATGAATTAAAAA
1 GGTGAAATAGAATATTTTTAAGTTAGGGGCATTTTGATCATTTAGTAATTAAAATGAATTAAAAA
53529346 CAAAGTAAAAGCCAAAATTTCTTGTCCATCTTCTTCCTTGGACGAATTTTACATGAATAAACCAT
66 CAAAGTAAAAGCCAAAATTTCTTGTCCATCTTCTTCCTTGGACGAATTTTACATGAATAAACCAT
53529411 CGCTAGGGTTTTCCAAGCTTCCAAGTTCGATTGTAAGTCCGTTCTTGCCCCGTTTTTAATGATTT
131 CGCTAGGGTTTTCCAAGCTTCCAAGTTCGATTGTAAGTCCGTTCTTGCCCCGTTTTTAATGATTT
53529476 TTACGTTTTTGAAATCTTTAC
196 TTACGTTTTTGAAATCTTTAC
53529497 AACAAGATCT
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 216 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (216 bp):
GGTGAAATAGAATATTTTTAAGTTAGGGGCATTTTGATCATTTAGTAATTAAAATGAATTAAAAA
CAAAGTAAAAGCCAAAATTTCTTGTCCATCTTCTTCCTTGGACGAATTTTACATGAATAAACCAT
CGCTAGGGTTTTCCAAGCTTCCAAGTTCGATTGTAAGTCCGTTCTTGCCCCGTTTTTAATGATTT
TTACGTTTTTGAAATCTTTAC
Found at i:53533493 original size:45 final size:45
Alignment explanation
Indices: 53533442--53533532 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
53533432 CCAAAACATG
* *
53533442 TGTCACATACATCATGAACTCAGACCGCAACTTAACGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAACGAGTTCAGA
* *
53533487 TGTCACATATATCATGAACTCAGACCACAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAACGAGTTCAGA
53533532 T
1 T
53533533 CACATAATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (45 bp):
TGTCACATACATCATGAACTCAGACCACAACTCAACGAGTTCAGA
Found at i:53535466 original size:43 final size:43
Alignment explanation
Indices: 53535405--53535487 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
53535395 ACATGAATCA
* * *
53535405 CATCCATTATGAACTCGAACCTGTCAACAAGCTCGGATGCTTG
1 CATCCATAATGAACTCGAACCTATCAACAAGCTCCGATGCTTG
*
53535448 CATCCATAATGAACTCGAACCTATCAACGAGCTCCGATGC
1 CATCCATAATGAACTCGAACCTATCAACAAGCTCCGATGC
53535488 CACATATCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
CATCCATAATGAACTCGAACCTATCAACAAGCTCCGATGCTTG
Found at i:53552696 original size:22 final size:20
Alignment explanation
Indices: 53552648--53552696 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 20
53552638 TCTTAACTAC
*
53552648 TCAAATCCATAGCCAAAACA
1 TCAAATCAATAGCCAAAACA
53552668 TACCAAATCAATATGCCAAAATCA
1 T--CAAATCAATA-GCCAAAA-CA
53552692 TCAAA
1 TCAAA
53552697 CTTACATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
22 13 0.54
23 7 0.29
24 3 0.12
ACGTcount: A:0.51, C:0.27, G:0.04, T:0.18
Consensus pattern (20 bp):
TCAAATCAATAGCCAAAACA
Found at i:53553510 original size:43 final size:43
Alignment explanation
Indices: 53553445--53553614 Score: 148
Period size: 43 Copynumber: 4.0 Consensus size: 43
53553435 AGCTCGTACA
* * * * *
53553445 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGTAATCACATATCG
* * * *
53553487 ATGCCACTGTCCCAGACAAGGTCTTACACGAAATCAAATAACG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGTAATCACATATCG
* * *
53553530 ATGCAAATGTCCCA-AAAATGGTCTTACACGTAATCACA-ATACA
1 ATGCCAATGTCCCAGACAA-GGTCTTACACGTAATCACATAT-CG
*** * *
53553573 ATGCCAATGTCATGGACATGGTCTTACATGTAATCACATATC
1 ATGCCAATGTCCCAGACAAGGTCTTACACGTAATCACATATC
53553615 AGTAACCTAA
Statistics
Matches: 100, Mismatches: 23, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
42 9 0.09
43 87 0.87
44 4 0.04
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAAGGTCTTACACGTAATCACATATCG
Found at i:53554268 original size:65 final size:65
Alignment explanation
Indices: 53554186--53554447 Score: 488
Period size: 65 Copynumber: 4.0 Consensus size: 65
53554176 GATATCTATC
*
53554186 ACTAAGCTTTCATAATTCATCATCAAACATTCAAAAACACATGAATTCATCAACGAAAATTCACA
1 ACTAAGCTTTCACAATTCATCATCAAACATTCAAAAACACATGAATTCATCAACGAAAATTCACA
53554251 ACTAAGCTTTCACAATTCATCATCAAACATTCAAAAACACATGAATTCATCAACGAAAATTCACA
1 ACTAAGCTTTCACAATTCATCATCAAACATTCAAAAACACATGAATTCATCAACGAAAATTCACA
53554316 ACTAAGCTTTCACAATTCATCATCAAACATTCAAAAACACATGAATTCATCAACGAAAATTCACA
1 ACTAAGCTTTCACAATTCATCATCAAACATTCAAAAACACATGAATTCATCAACGAAAATTCACA
* **
53554381 ACTAAGCTTTCACAATTCATCATCAAACATTCAAAAACACATGAATTCATCAATGGCAATTCACA
1 ACTAAGCTTTCACAATTCATCATCAAACATTCAAAAACACATGAATTCATCAACGAAAATTCACA
53554446 AC
1 AC
53554448 ATCATCAATA
Statistics
Matches: 193, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 193 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.25
Consensus pattern (65 bp):
ACTAAGCTTTCACAATTCATCATCAAACATTCAAAAACACATGAATTCATCAACGAAAATTCACA
Found at i:53555903 original size:21 final size:22
Alignment explanation
Indices: 53555871--53555911 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
53555861 TTTTTTTTAT
*
53555871 ATAAATTGTGATGTTTAGAAGC
1 ATAAATTGTGATGTTAAGAAGC
53555893 ATAAA-TGTGATGTTAAGAA
1 ATAAATTGTGATGTTAAGAA
53555912 AACCATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (22 bp):
ATAAATTGTGATGTTAAGAAGC
Found at i:53563079 original size:47 final size:47
Alignment explanation
Indices: 53563028--53563160 Score: 171
Period size: 46 Copynumber: 2.9 Consensus size: 47
53563018 GAATTATAAG
* *
53563028 GCATCCGAACTCGTTGAATTGCGTTCTGAGTTCACTTATGGATG-CAA
1 GCATCCGAACTCGTTGAGTTGTGTTCTGAGTTCA-TTATGGATGTCAA
* * *
53563075 GCATCCGAACTCATTGCGTTGTGTTCTGAGTTCATTATGGATGTGAA
1 GCATCCGAACTCGTTGAGTTGTGTTCTGAGTTCATTATGGATGTCAA
* * *
53563122 -CACCCGAGCTCGTTGAGTTGTGTTCCGAGTTCATTATGG
1 GCATCCGAACTCGTTGAGTTGTGTTCTGAGTTCATTATGG
53563161 GTGAAATTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
46 43 0.57
47 32 0.43
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGTGTTCTGAGTTCATTATGGATGTCAA
Found at i:53570127 original size:47 final size:47
Alignment explanation
Indices: 53570076--53570208 Score: 180
Period size: 46 Copynumber: 2.9 Consensus size: 47
53570066 GAATTATGAG
*
53570076 GCATCCGAACTCGTTGAGTTGTGTTCCGAGTTCACTTATGGATG-CAA
1 GCATCCGAACTCATTGAGTTGTGTTCCGAGTTCA-TTATGGATGTCAA
* *
53570123 GCATCCGAACTCATTCAGTTGTGTTCCGAGTTCATTATGGATGTGAA
1 GCATCCGAACTCATTGAGTTGTGTTCCGAGTTCATTATGGATGTCAA
* * * *
53570170 -CACCCGAGCTCTTTGAGTTGCGTTCCGAGTTCATTATGG
1 GCATCCGAACTCATTGAGTTGTGTTCCGAGTTCATTATGG
53570209 GTGAAATTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
46 43 0.56
47 34 0.44
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (47 bp):
GCATCCGAACTCATTGAGTTGTGTTCCGAGTTCATTATGGATGTCAA
Found at i:53573954 original size:17 final size:17
Alignment explanation
Indices: 53573932--53573965 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53573922 TGGTAAAGAG
*
53573932 CCATGTCATCATATGAC
1 CCATGTCAACATATGAC
53573949 CCATGTCAACATATGAC
1 CCATGTCAACATATGAC
53573966 AATGAGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (17 bp):
CCATGTCAACATATGAC
Found at i:53587841 original size:45 final size:45
Alignment explanation
Indices: 53587777--53587866 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
53587767 ACAGGTGGTT
*
53587777 CAGCAGCACGATTATGTATATAATAACTTTGATTTCTAATTGTTA
1 CAGCAGCACCATTATGTATATAATAACTTTGATTTCTAATTGTTA
53587822 CAGCAGCACCATTATGTATATAATAACTTTGATTTCTAATTGTTA
1 CAGCAGCACCATTATGTATATAATAACTTTGATTTCTAATTGTTA
53587867 TGTTTGATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (45 bp):
CAGCAGCACCATTATGTATATAATAACTTTGATTTCTAATTGTTA
Found at i:53594507 original size:16 final size:16
Alignment explanation
Indices: 53594486--53594521 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53594476 AATTCCTAAC
*
53594486 AATCTTCAAATCCCTA
1 AATCTTCAAATACCTA
*
53594502 AATCTTGAAATACCTA
1 AATCTTCAAATACCTA
53594518 AATC
1 AATC
53594522 GTTAGCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.31
Consensus pattern (16 bp):
AATCTTCAAATACCTA
Found at i:53600048 original size:43 final size:44
Alignment explanation
Indices: 53599969--53600103 Score: 175
Period size: 43 Copynumber: 3.1 Consensus size: 44
53599959 TATCGAAATG
* *
53599969 TGATATTCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
1 TGATATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
* * * *
53600013 TGATA-TCGGGCTTTGAGCTTAGTAGGCCATGATGCCGGTGAAA
1 TGATATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
*
53600056 T-ATTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TGA-TATTCG-GGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
53600101 TGA
1 TGA
53600104 AATGTTATGT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 1 0.01
43 35 0.46
44 8 0.11
45 31 0.41
46 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (44 bp):
TGATATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
Found at i:53600093 original size:45 final size:43
Alignment explanation
Indices: 53599986--53600103 Score: 157
Period size: 45 Copynumber: 2.7 Consensus size: 43
53599976 CGGGCTTCGG
*
53599986 GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
* * * *
53600029 GCTTAGTAGGCCATGATGCCGGTGAAAT-ATTATTCGAGCCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TCG-GCCTTTGA
53600074 GCCTAGCAGGCTATAATGCCGGTGAAATGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA
53600104 AATGTTATGT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
42 1 0.02
43 26 0.42
44 3 0.05
45 31 0.50
46 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (43 bp):
GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
Found at i:53600593 original size:114 final size:114
Alignment explanation
Indices: 53600363--53600586 Score: 315
Period size: 114 Copynumber: 2.0 Consensus size: 114
53600353 ATGATATTTG
53600363 TATCCGGCTTAAAGACCGCAGACTATATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TATCCGGCTTAAAGACCGCAGACTATATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
53600428 TGCTGGTAATATATCCAGGTTAATTCCCGCAGGCTTCGTGCTGGTAATA
66 TGCTGGTAATATATCCAGGTTAAATCCCGCAGGCCTAGTGCTGGTAATA
* ** * * * *
53600477 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAA-TATATCCGGGTTAATTCCCGCAGGCTTC
1 TATCCGGCTTAAAGACCGCAGACTATATGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTC
* * *
53600541 GTGCTGGTATTATATTCGGGTTAAATCCCGCAGGCCTAGTGCTGGT
65 GTGCTGGTAATATATCCAGGTTAAATCCCGCAGGCCTAGTGCTGGT
53600587 GTTATATTCG
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
114 94 0.98
115 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.30
Consensus pattern (114 bp):
TATCCGGCTTAAAGACCGCAGACTATATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
TGCTGGTAATATATCCAGGTTAAATCCCGCAGGCCTAGTGCTGGTAATA
Found at i:53600596 original size:38 final size:38
Alignment explanation
Indices: 53600390--53600586 Score: 306
Period size: 38 Copynumber: 5.2 Consensus size: 38
53600380 GCAGACTATA
53600390 TGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCG
* *
53600428 TGCTGGTAATATATCCAGGTTAATTCCCGCAGGCTTCG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
*
53600466 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTTG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
*
53600504 TGCTGGTAATATATCCGGGTTAATTCCCGCAGGCTTCG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
* * * *
53600542 TGCTGGTATTATATTCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
53600580 TGCTGGT
1 TGCTGGT
53600587 GTTATATTCG
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
38 144 0.99
39 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (38 bp):
TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:53600688 original size:45 final size:45
Alignment explanation
Indices: 53600600--53600714 Score: 121
Period size: 45 Copynumber: 2.6 Consensus size: 45
53600590 ATATTCGAGC
* * * * *
53600600 CTTT-GAGCCTAGCAGGCTATTATGCCGGTGAGATACTATTCGGG
1 CTTTCGAGCCTAGCAGGCTATAATGCCGATAAAATACTAATCGGG
53600644 CTTTCGAGCCTAGCAGGCTATAATGCCGATAAAATGA-TAATCGGG
1 CTTTCGAGCCTAGCAGGCTATAATGCCGATAAAAT-ACTAATCGGG
* * *
53600689 C-CTCGATCCTAGCAGGCGA-AATGCCG
1 CTTTCGAGCCTAGCAGGCTATAATGCCG
53600715 GTGATTTGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
43 7 0.11
44 19 0.31
45 34 0.56
46 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (45 bp):
CTTTCGAGCCTAGCAGGCTATAATGCCGATAAAATACTAATCGGG
Found at i:53601724 original size:14 final size:14
Alignment explanation
Indices: 53601705--53601734 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53601695 TCAGACAAAA
53601705 TAAAATAAAAAATT
1 TAAAATAAAAAATT
*
53601719 TAAAATAAAAACTT
1 TAAAATAAAAAATT
53601733 TA
1 TA
53601735 CTTAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAATAAAAAATT
Found at i:53603891 original size:28 final size:28
Alignment explanation
Indices: 53603859--53603928 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
53603849 TATTGTACTC
* * *
53603859 AGTGTACGAAATATTGAGAATGGCTCTT
1 AGTGTGCGAAATATTGAGAATGACACTT
* *
53603887 AGTGTGTGAGATATTGAGAATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
*
53603915 AGTGTGCAAAATAT
1 AGTGTGCGAAATAT
53603929 CGAATGATTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (28 bp):
AGTGTGCGAAATATTGAGAATGACACTT
Found at i:53605933 original size:28 final size:28
Alignment explanation
Indices: 53605902--53606083 Score: 170
Period size: 28 Copynumber: 6.4 Consensus size: 28
53605892 TGAACATAGA
* * *
53605902 CACTGTGTGTGTGAGTTCCTTAATCGAG
1 CACTGTGTGTGCGAGTTCCGTAACCGAG
* * ****
53605930 CACTGTGTGTGCAAGAT-CGATTGTTGAGG
1 CACTGTGTGTGCGAGTTCCG-TAACCGA-G
*
53605959 CACTGTGTGTGTGAGTTCCGTAACCGAG
1 CACTGTGTGTGCGAGTTCCGTAACCGAG
53605987 CACTGTGTGTGCGAGTTCCGTAACCGAG
1 CACTGTGTGTGCGAGTTCCGTAACCGAG
* ****
53606015 CACTGTGTGTGCGAGATT-GGTTGTTGAGG
1 CACTGTGTGTGCGAG-TTCCGTAACCGA-G
*
53606044 CACTGTGTGTGCGAGTTCCGTAACCAAG
1 CACTGTGTGTGCGAGTTCCGTAACCGAG
53606072 CACTGTGTGTGC
1 CACTGTGTGTGC
53606084 AAGATCGGTT
Statistics
Matches: 122, Mismatches: 26, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
27 1 0.01
28 80 0.66
29 39 0.32
30 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (28 bp):
CACTGTGTGTGCGAGTTCCGTAACCGAG
Found at i:53606045 original size:85 final size:85
Alignment explanation
Indices: 53605902--53606083 Score: 292
Period size: 85 Copynumber: 2.1 Consensus size: 85
53605892 TGAACATAGA
* * *
53605902 CACTGTGTGTGTGAGTTCCTTAATCGAGCACTGTGTGTGCAAGATCGATTGTTGAGGCACTGTGT
1 CACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCAAGATCGATTGTTGAGGCACTGTGT
* *
53605967 GTGTGAGTTCCGTAACCGAG
66 GTGCGAGTTCCGTAACCAAG
* * *
53605987 CACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATTGGTTGTTGAGGCACTGTGT
1 CACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCAAGATCGATTGTTGAGGCACTGTGT
53606052 GTGCGAGTTCCGTAACCAAG
66 GTGCGAGTTCCGTAACCAAG
53606072 CACTGTGTGTGC
1 CACTGTGTGTGC
53606084 AAGATCGGTT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (85 bp):
CACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCAAGATCGATTGTTGAGGCACTGTGT
GTGCGAGTTCCGTAACCAAG
Found at i:53606047 original size:57 final size:57
Alignment explanation
Indices: 53605986--53606113 Score: 202
Period size: 57 Copynumber: 2.2 Consensus size: 57
53605976 CCGTAACCGA
* * *
53605986 GCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATTGGTTGTTGAG
1 GCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTGAG
*
53606043 GCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTGGG
1 GCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTGAG
53606100 GCACTAAGTGTGTG
1 GCACT--GTGTGTG
53606114 AAATGAGATC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
57 58 0.89
59 7 0.11
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.29
Consensus pattern (57 bp):
GCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTGAG
Found at i:53611104 original size:28 final size:28
Alignment explanation
Indices: 53611043--53611104 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
53611033 TCAGTGTACG
* * *
53611043 AAATATTGAGAATGGCTCTTAGTATGCG
1 AAATATTGAGAATGACACTTAGTATGCA
* *
53611071 AGATATTGAGAATGACACTTAGTGTGCA
1 AAATATTGAGAATGACACTTAGTATGCA
53611099 AAATAT
1 AAATAT
53611105 CGAATGATTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAGTATGCA
Found at i:53617847 original size:45 final size:45
Alignment explanation
Indices: 53617790--53617881 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
53617780 GGAATTATGT
53617790 CATTTGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGA
1 CATTTGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGA
*
53617835 CATTTGAACTCATTGAGTTGTGGTCTGAGTTCATGATGTATGTGA
1 CATTTGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGA
53617880 CA
1 CA
53617882 CATGTTTTGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (45 bp):
CATTTGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGA
Found at i:53617868 original size:21 final size:21
Alignment explanation
Indices: 53617799--53617868 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
53617789 TCATTTGAAC
53617799 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
* * * **
53617820 TCA-TGATATATGTGACATTTGAAC
1 TCATTGA-GT-TGTG--GTCTGAGT
53617844 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
53617865 TCAT
1 TCAT
53617869 GATGTATGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
22 4 0.12
23 4 0.12
24 8 0.24
25 3 0.09
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.41
Consensus pattern (21 bp):
TCATTGAGTTGTGGTCTGAGT
Found at i:53623390 original size:15 final size:15
Alignment explanation
Indices: 53623370--53623406 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
53623360 TATTGTAATT
53623370 TGGATTTACTTATCA
1 TGGATTTACTTATCA
* *
53623385 TGGATTTATTTATCT
1 TGGATTTACTTATCA
53623400 TGGATTT
1 TGGATTT
53623407 CTTTATTCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (15 bp):
TGGATTTACTTATCA
Found at i:53623411 original size:15 final size:15
Alignment explanation
Indices: 53623369--53623412 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
53623359 GTATTGTAAT
53623369 TTGGATTTAC-TTATC
1 TTGGATTT-CTTTATC
* *
53623384 ATGGATTTATTTATC
1 TTGGATTTCTTTATC
53623399 TTGGATTTCTTTAT
1 TTGGATTTCTTTAT
53623413 TCTGGGCTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (15 bp):
TTGGATTTCTTTATC
Found at i:53627118 original size:49 final size:47
Alignment explanation
Indices: 53627052--53627214 Score: 245
Period size: 47 Copynumber: 3.4 Consensus size: 47
53627042 ATTGATGTAC
* *
53627052 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
53627099 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTATATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
53627148 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGG
1 AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
53627195 AAGTGTATAAATGTGATAAG
1 AAGTATATATATGTGATAAG
53627215 TCCCGAAGGG
Statistics
Matches: 108, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
47 64 0.59
49 44 0.41
ACGTcount: A:0.34, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:53627136 original size:40 final size:44
Alignment explanation
Indices: 53627052--53627185 Score: 151
Period size: 49 Copynumber: 2.9 Consensus size: 44
53627042 ATTGATGTAC
* * *
53627052 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGT
1 AAGTATATATACGTGATAAGGCCGAATGGCCAATGTGA-GAATGT
53627097 GAAAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGT
1 --AAGTATATATA--CGTGATAAGGCCGAATGGCCAATGTGA-GAATGT
* *
53627146 GAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGA
1 --AAGTATATATACGTGATAAGGCCGAATGGCCAATGTGA
53627186 TGGATGTGGA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
47 37 0.46
49 43 0.54
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.27
Consensus pattern (44 bp):
AAGTATATATACGTGATAAGGCCGAATGGCCAATGTGAGAATGT
Found at i:53627186 original size:22 final size:22
Alignment explanation
Indices: 53627113--53627186 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
53627103 ATATATATGC
53627113 GTGATAAGGCCGAATGGCCAAT
1 GTGATAAGGCCGAATGGCCAAT
* * ***
53627135 GTGATGAATG-TGAAAGTGTATATAT
1 GTGAT-AAGGCCG-AA-TGGCCA-AT
53627160 GTGATAAGGCCGAATGGCCAAT
1 GTGATAAGGCCGAATGGCCAAT
53627182 GTGAT
1 GTGAT
53627187 GGATGTGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
22 13 0.35
23 8 0.22
24 8 0.22
25 8 0.22
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.26
Consensus pattern (22 bp):
GTGATAAGGCCGAATGGCCAAT
Found at i:53637535 original size:24 final size:23
Alignment explanation
Indices: 53637479--53637535 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 23
53637469 GATTTTTTAC
*
53637479 ATATATATTTTAAATTTTTAGAA
1 ATATATATTTTAAATTTTTAAAA
* * *
53637502 CTATTTTATTTATAATTTTTTAAAA
1 ATA-TATATTT-TAAATTTTTAAAA
53637527 ATATATATT
1 ATATATATT
53637536 AACATAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
23 2 0.08
24 11 0.42
25 13 0.50
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATATATTTTAAATTTTTAAAA
Found at i:53641844 original size:12 final size:13
Alignment explanation
Indices: 53641816--53641848 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
53641806 AAATGAAGAG
53641816 AGAAGAAACATGA
1 AGAAGAAACATGA
*
53641829 AGAAGAAGCA-GA
1 AGAAGAAACATGA
53641841 AGAAGAAA
1 AGAAGAAA
53641849 AGCTTGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.64, C:0.06, G:0.27, T:0.03
Consensus pattern (13 bp):
AGAAGAAACATGA
Found at i:53650206 original size:28 final size:28
Alignment explanation
Indices: 53650166--53650221 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
53650156 TTCTTGGCCT
* *
53650166 GTGTCTCTCACATGGCCTAGACACGCCC
1 GTGTCCCTCACATGGCCTAAACACGCCC
53650194 GTGTCCCTCACATGGCCTAAACACGCCC
1 GTGTCCCTCACATGGCCTAAACACGCCC
53650222 ATGTTATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.41, G:0.20, T:0.20
Consensus pattern (28 bp):
GTGTCCCTCACATGGCCTAAACACGCCC
Found at i:53650448 original size:42 final size:42
Alignment explanation
Indices: 53650390--53650482 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
53650380 AAGTGCAGAG
* * ** *
53650390 ACACACGGCTGGGCAACATGCCCATAGGGTTGACCGTGTGTC
1 ACACATGGCCGGGCAACACACCCATAGGGCTGACCGTGTGTC
53650432 ACACATGGCCGGGCAACACACCCATAGGGCTGACCGTGTGTC
1 ACACATGGCCGGGCAACACACCCATAGGGCTGACCGTGTGTC
*
53650474 AGACATGGC
1 ACACATGGC
53650483 TTAGACACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (42 bp):
ACACATGGCCGGGCAACACACCCATAGGGCTGACCGTGTGTC
Found at i:53653119 original size:20 final size:19
Alignment explanation
Indices: 53653091--53653149 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
53653081 TGATGTGTTA
*
53653091 AAATGATTTTAACTTGATT
1 AAATCATTTTAACTTGATT
* *
53653110 GAAATCATTTTGACTTGGTT
1 -AAATCATTTTAACTTGATT
* *
53653130 AAACTTATTCTAACTTGATT
1 AAA-TCATTTTAACTTGATT
53653150 TTAAAATTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (19 bp):
AAATCATTTTAACTTGATT
Found at i:53653131 original size:40 final size:40
Alignment explanation
Indices: 53653062--53653149 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
53653052 AACAATTATG
* *
53653062 ACTTGTTTGAAAATCATTTTGATGTGTTAAAATGATTTTA
1 ACTTGATTGAAAATCATTTTGATGTGTTAAAATGATTCTA
* *
53653102 ACTTGATTG-AAATCATTTTGACT-TGGTTAAACTTATTCTA
1 ACTTGATTGAAAATCATTTTGA-TGT-GTTAAAATGATTCTA
53653142 ACTTGATT
1 ACTTGATT
53653150 TTAAAATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 13 0.31
40 29 0.69
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.47
Consensus pattern (40 bp):
ACTTGATTGAAAATCATTTTGATGTGTTAAAATGATTCTA
Found at i:53655389 original size:20 final size:21
Alignment explanation
Indices: 53655364--53655403 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53655354 AAAATGGTAT
* *
53655364 ATATTTTTAACTAA-GTATCG
1 ATATTTGTAAATAAGGTATCG
53655384 ATATTTGTAAATAAGGTATC
1 ATATTTGTAAATAAGGTATC
53655404 AATACCGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (21 bp):
ATATTTGTAAATAAGGTATCG
Found at i:53659460 original size:17 final size:17
Alignment explanation
Indices: 53659438--53659472 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
53659428 TTTGCATGGG
53659438 GACATGGGTTATATTTT
1 GACATGGGTTATATTTT
53659455 GACATGGGTTATATTTT
1 GACATGGGTTATATTTT
53659472 G
1 G
53659473 GAGGAAGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.46
Consensus pattern (17 bp):
GACATGGGTTATATTTT
Found at i:53659524 original size:27 final size:27
Alignment explanation
Indices: 53659484--53659595 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
53659474 AGGAAGCGTC
*
53659484 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
53659511 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
53659538 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
53659566 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
53659592 CTGG
1 CTGG
53659596 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:53659590 original size:54 final size:54
Alignment explanation
Indices: 53659484--53659595 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
53659474 AGGAAGCGTC
* *
53659484 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
53659538 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
53659592 CTGG
1 CTGG
53659596 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:53660603 original size:56 final size:56
Alignment explanation
Indices: 53660517--53660629 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
53660507 TACATAGTCA
53660517 AAGTGGAATGAAAGATTTTACAGTTAGATCTGAAGCTCGGGAACCAACTAGGGTCT
1 AAGTGGAATGAAAGATTTTACAGTTAGATCTGAAGCTCGGGAACCAACTAGGGTCT
53660573 AAGTGGAATGAAAGATTTTACAGTTAGATCTGAAGCTCGGGAACCAACTAGGGTCT
1 AAGTGGAATGAAAGATTTTACAGTTAGATCTGAAGCTCGGGAACCAACTAGGGTCT
53660629 A
1 A
53660630 TGTAATTCGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.25
Consensus pattern (56 bp):
AAGTGGAATGAAAGATTTTACAGTTAGATCTGAAGCTCGGGAACCAACTAGGGTCT
Found at i:53666504 original size:21 final size:21
Alignment explanation
Indices: 53666460--53666508 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
53666450 ATGCCAAAAT
*
53666460 GGTATC-A-ATTTTTAACTAA
1 GGTATCGATATTTTTAAATAA
*
53666479 -TTATCGATATTTTTAAATAA
1 GGTATCGATATTTTTAAATAA
53666499 GGTATCGATA
1 GGTATCGATA
53666509 CCATGTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.17
19 1 0.04
20 11 0.46
21 8 0.33
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (21 bp):
GGTATCGATATTTTTAAATAA
Found at i:53668290 original size:11 final size:11
Alignment explanation
Indices: 53668215--53668290 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
53668205 ATTTCAAAAA
*
53668215 TAATATTATTT
1 TAATATTAATT
53668226 TAATAGTTTAATAT
1 TAATA--TTAAT-T
53668240 TAA-ATTAAATT
1 TAATATT-AATT
*
53668251 TAATATTTATAT
1 TAATATTAAT-T
*
53668263 TAATAGT-ATT
1 TAATATTAATT
53668273 T--TATTAATT
1 TAATATTAATT
53668282 TAATATTAA
1 TAATATTAA
53668291 AGTGATTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 2 0.04
11 21 0.40
12 13 0.25
13 5 0.10
14 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Found at i:53668298 original size:25 final size:24
Alignment explanation
Indices: 53668221--53668299 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
53668211 AAAATAATAT
* *
53668221 TATTTTAATAGTTTAATATTAAAT
1 TATTTTAATAATTTAATATTAAAG
*
53668245 TAAATTTAAT-ATTT-ATATTAATAG
1 T-ATTTTAATAATTTAATATTAA-AG
*
53668269 TATTTTATTAATTTAATATTAAAG
1 TATTTTAATAATTTAATATTAAAG
53668293 TGATTTT
1 T-ATTTT
53668300 CTTTATATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
23 13 0.29
24 13 0.29
25 19 0.42
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (24 bp):
TATTTTAATAATTTAATATTAAAG
Found at i:53670135 original size:35 final size:35
Alignment explanation
Indices: 53670063--53670146 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
53670053 TCAAGGCCTT
* *
53670063 ACCCCAAAGGACCTAATAATCGTTTTCACAGTATC
1 ACCCCAAAGGACCTAATAATCATTTTAACAGTATC
* ** *
53670098 ACCCTAAAGGACCTAATAATCATTTTAATGGTGTC
1 ACCCCAAAGGACCTAATAATCATTTTAACAGTATC
*
53670133 ACCCCGAAGGACCT
1 ACCCCAAAGGACCT
53670147 TACCATCGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.25
Consensus pattern (35 bp):
ACCCCAAAGGACCTAATAATCATTTTAACAGTATC
Found at i:53670953 original size:96 final size:95
Alignment explanation
Indices: 53670780--53671102 Score: 339
Period size: 96 Copynumber: 3.4 Consensus size: 95
53670770 GGGTGAATTA
* * * * * * *
53670780 CCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACAGGTCGA-GGCCGATGCCATGTCCCA
1 CCGATGTCATGTCCCAAACAT-GTCTTACACTAGCTCTCA-TTAGATTGTCGATGCCATGTCCCA
*
53670844 GACATGGTCTTACACTAGCTCTCATCTCAATG
64 GACATGGTCTTACACTAGCTCTCATATCAATG
* * *
53670876 CCAATGTCATGTCCCAACCATAGTCTTACACTGGCTCTCA-TA-ATGTGGTCGATGCCATGTCCC
1 CCGATGTCATGTCCCAAACAT-GTCTTACACTAGCTCTCATTAGAT-T-GTCGATGCCATGTCCC
* * * *
53670939 AGACATGGTTTTACACTAGCGCACATATTAATG
63 AGACATGGTCTTACACTAGCTCTCATATCAATG
* * *
53670972 CCGATGTCATGTCCCAAACATGATCTTACACTAGCTCTCATTAGATTGTTGATGCCATGTTCCAA
1 CCGATGTCATGTCCCAAACATG-TCTTACACTAGCTCTCATTAGATTGTCGATGCCATGTCCCAG
* *
53671037 ACATGGTCCTACACTGGCTCTCATATC-ATGG
65 ACATGGTCTTACACTAGCTCTCATATCAAT-G
* * *
53671068 CTGATGCCATGTCCCAAACATGGTCTTAGACTAGC
1 CCGATGTCATGTCCCAAACAT-GTCTTACACTAGC
53671103 ACACATATCA
Statistics
Matches: 189, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
93 1 0.01
94 1 0.01
95 3 0.02
96 178 0.94
97 4 0.02
98 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (95 bp):
CCGATGTCATGTCCCAAACATGTCTTACACTAGCTCTCATTAGATTGTCGATGCCATGTCCCAGA
CATGGTCTTACACTAGCTCTCATATCAATG
Found at i:53671050 original size:144 final size:143
Alignment explanation
Indices: 53670781--53671112 Score: 391
Period size: 144 Copynumber: 2.3 Consensus size: 143
53670771 GGTGAATTAC
* * ** * *
53670781 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACAGGTCGAGGCCGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAAGGCCGATGCCATGTCCCAAA
* * * *
53670846 CATGGTCTTACACTAGCTCTCATCTCAATGCCAATGTCATGTCCCAACCATAGTCTTACACTGGC
66 CATGATCTTACACTAGCTCTCATCTCAATGCCAATGCCATGTCCCAAACATAGTCCTACACTGGC
*
53670911 TCTCATAAT-GTGG
131 TCTCAT-ATCATGG
* * * * * *
53670924 TCGATGCCATGTCCCAGACATGGTTTTACACTAGCGCACATATTAATGCCGATGTCATGTCCCAA
1 -CGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAAGGCCGATGCCATGTCCCAA
*** * *
53670989 ACATGATCTTACACTAGCTCTCAT-T-AGATTGTTGATGCCATGTTCCAAACATGGTCCTACACT
65 ACATGATCTTACACTAGCTCTCATCTCA-A-TGCCAATGCCATGTCCCAAACATAGTCCTACACT
53671052 GGCTCTCATATCATGG
128 GGCTCTCATATCATGG
*
53671068 CTGATGCCATGTCCCAAACATGGTCTTAGACTAGCACACATATCA
1 C-GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCA
53671113 CCCAAATGTC
Statistics
Matches: 158, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
142 1 0.01
143 5 0.03
144 152 0.96
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (143 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAAGGCCGATGCCATGTCCCAAA
CATGATCTTACACTAGCTCTCATCTCAATGCCAATGCCATGTCCCAAACATAGTCCTACACTGGC
TCTCATATCATGG
Found at i:53671112 original size:48 final size:48
Alignment explanation
Indices: 53670780--53671112 Score: 307
Period size: 48 Copynumber: 6.9 Consensus size: 48
53670770 GGGTGAATTA
* * **
53670780 CCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACAGGTCGA-GG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATC-ATGG
* *
53670828 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAAT-G
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATC-ATGG
* * * * * *
53670876 CCAATGTCATGTCCCAACCATAGTCTTACACTGGCTCTCATAAT-GTGG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCAT-ATCATGG
* * * * * *
53670924 TCGATGCCATGTCCCAGACATGGTTTTACACTAGCGCACATATTAAT-G
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATA-TCATGG
* * * *
53670972 CCGATGTCATGTCCCAAACATGATCTTACACTAGCTCTCAT-TAGATTG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATAT-CATGG
** * * *
53671020 TTGATGCCATGTTCCAAACATGGTCCTACACTGGCTCTCATATCATGG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCATGG
* * * *
53671068 CTGATGCCATGTCCCAAACATGGTCTTAGACTAGCACACATATCA
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCA
53671113 CCCAAATGTC
Statistics
Matches: 228, Mismatches: 49, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
46 1 0.00
47 4 0.02
48 220 0.96
49 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28
Consensus pattern (48 bp):
CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCATGG
Found at i:53678712 original size:96 final size:95
Alignment explanation
Indices: 53678545--53678862 Score: 383
Period size: 96 Copynumber: 3.3 Consensus size: 95
53678535 GAGGGTGAAT
* * * * *
53678545 TGCTGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACAT-GTCGAGGCCGATGCCATGTCC
1 TGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCCATGTCC
* *
53678609 TAGACATGGTCTTACACTAGCTCCTATCTCAA
65 CAGACATGGTCTTACACTAGCTCC-ATATCAA
* * *
53678641 TGTTGATGCCATGTCCCAGACATGGTCTTCCACTGGCTCTCATAATGTGGCTGATGCCATGTCCC
1 TGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATGTCCC
*
53678706 AGACATGGTCTTACACTAGCGTACATATCAA
66 AGACATGGTCTTACACTAGC-TCCATATCAA
* *
53678737 TGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATTACAT-T-ACCGATGCCATGTT
1 TGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-TA-ATGTGGCCGATGCCATGTC
* * *
53678800 CCAAACATGGTCTTACACTGGCTCTCATATC-G
64 CCAGACATGGTCTTACACTAGCTC-CATATCAA
* *
53678832 TGGCCGATGCCATGTCCTAGACATGGTCTTA
1 T-GCTGATGCCATGTCCCAGACATGGTCTTA
53678863 TACTAGTGCA
Statistics
Matches: 194, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
95 2 0.01
96 184 0.95
97 6 0.03
98 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (95 bp):
TGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATGTCCC
AGACATGGTCTTACACTAGCTCCATATCAA
Found at i:53678808 original size:144 final size:144
Alignment explanation
Indices: 53678546--53678879 Score: 415
Period size: 144 Copynumber: 2.3 Consensus size: 144
53678536 AGGGTGAATT
* * * * * *
53678546 GCTGATGCCATGTTCCAAACATGGTCTTACACTGGC-TCACATGTCGAGGCCGATGCCATGTCCT
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCGT-ACATATCAAGGCCGATGCCATGTCCC
*** * *
53678610 AGACATGGTCTTACACTAGCTCCTATCTCAATGTTGATGCCATGTCCCAGACATGGTCTTCCACT
65 AGACATGGTCTTACACTAGCTCCTATCTCAATACCGATGCCATGTCCCAAACATGGTCTTACACT
53678675 GGCTCTCATAAT-GTG
130 GGCTCTCAT-ATCGTG
* *
53678690 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCGTACATATCAATGCTGATGCCATGTCCCA
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCGTACATATCAAGGCCGATGCCATGTCCCA
* * *
53678755 GACATGGTCTTACACTGGCT-CTCAT-TACATTACCGATGCCATGTTCCAAACATGGTCTTACAC
66 GACATGGTCTTACACTAGCTCCT-ATCT-CAATACCGATGCCATGTCCCAAACATGGTCTTACAC
53678818 TGGCTCTCATATCGTG
129 TGGCTCTCATATCGTG
* * * * *
53678834 GCCGATGCCATGTCCTAGACATGGTCTTATACTAGTGCACATATCA
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCGTACATATCA
53678880 CCCAAATGTC
Statistics
Matches: 165, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
143 5 0.03
144 159 0.96
145 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (144 bp):
GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCGTACATATCAAGGCCGATGCCATGTCCCA
GACATGGTCTTACACTAGCTCCTATCTCAATACCGATGCCATGTCCCAAACATGGTCTTACACTG
GCTCTCATATCGTG
Found at i:53678877 original size:48 final size:48
Alignment explanation
Indices: 53678549--53678879 Score: 318
Period size: 48 Copynumber: 6.9 Consensus size: 48
53678539 GTGAATTGCT
* * *
53678549 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGA-GGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC-ATGGCC
* * * **
53678597 GATGCCATGTCCTAGACATGGTCTTACACTAGCTC-CTATCTCAAT-GTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCAC-ATATC-ATGGCC
* * * *
53678645 GATGCCATGTCCCAGACATGGTCTTCCACTGGCTCTCATAAT-GTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-ATCATGGCC
* *
53678693 GATGCCATGTCCCAGACATGGTCTTACACTAGCGT-ACATATCAAT-GCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TCACATATC-ATGGCC
* **
53678741 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-TACATTACC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAT-CATGGCC
* * * *
53678789 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCATGGCC
* * *
53678837 GATGCCATGTCCTAGACATGGTCTTATACTAG-TGCACATATCA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-CACATATCA
53678880 CCCAAATGTC
Statistics
Matches: 236, Mismatches: 34, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
47 9 0.04
48 222 0.94
49 5 0.02
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCATGGCC
Found at i:53683501 original size:17 final size:17
Alignment explanation
Indices: 53683462--53683501 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
53683452 AAATAGCATA
*
53683462 TTATTTGAATTTTTTTG
1 TTATTTGAATTTTTTTC
**
53683479 AAATTTGAATTTTTTTC
1 TTATTTGAATTTTTTTC
53683496 TTATTT
1 TTATTT
53683502 CTTAAAATTA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.68
Consensus pattern (17 bp):
TTATTTGAATTTTTTTC
Found at i:53683532 original size:15 final size:16
Alignment explanation
Indices: 53683512--53683545 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
53683502 CTTAAAATTA
*
53683512 TTTAAAATAATTTT-T
1 TTTAAAAAAATTTTAT
53683527 TTTAAAAAAATTTTAT
1 TTTAAAAAAATTTTAT
53683543 TTT
1 TTT
53683546 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAAAAAAATTTTAT
Found at i:53684645 original size:14 final size:13
Alignment explanation
Indices: 53684619--53684658 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
53684609 TTTGGGGTCA
53684619 TGAGTTTAGGTTT
1 TGAGTTTAGGTTT
53684632 TGAGTTTGAGGTTT
1 TGAGTTT-AGGTTT
*
53684646 GGAGTTTA-GTTT
1 TGAGTTTAGGTTT
53684658 T
1 T
53684659 TATGGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 12 0.50
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.53
Consensus pattern (13 bp):
TGAGTTTAGGTTT
Found at i:53684729 original size:12 final size:12
Alignment explanation
Indices: 53684712--53684742 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
53684702 AGGCTTCGAT
53684712 GTTCGAGTTCAA
1 GTTCGAGTTCAA
53684724 GTTCGAGTTCAA
1 GTTCGAGTTCAA
53684736 GTTCGAG
1 GTTCGAG
53684743 GTTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (12 bp):
GTTCGAGTTCAA
Found at i:53684999 original size:19 final size:19
Alignment explanation
Indices: 53684975--53685013 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
53684965 GTTTCTAATG
53684975 TCACATGTGTTGTACGTGA
1 TCACATGTGTTGTACGTGA
53684994 TCACATGTGTTGTACGTGA
1 TCACATGTGTTGTACGTGA
53685013 T
1 T
53685014 TTTACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (19 bp):
TCACATGTGTTGTACGTGA
Found at i:53687093 original size:12 final size:12
Alignment explanation
Indices: 53687052--53687093 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
53687042 AATGAATGTA
53687052 AAGAAGAATAAT
1 AAGAAGAATAAT
* *
53687064 AAAAATAATAAT
1 AAGAAGAATAAT
*
53687076 AA-AAGAATAAG
1 AAGAAGAATAAT
53687087 AAGAAGA
1 AAGAAGA
53687094 CGATAGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (12 bp):
AAGAAGAATAAT
Found at i:53691837 original size:36 final size:36
Alignment explanation
Indices: 53691795--53691867 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
53691785 AATATTCAAA
53691795 AATTCAATATTTCATCAAATCCAATAAGAGAAATTT
1 AATTCAATATTTCATCAAATCCAATAAGAGAAATTT
53691831 AATTCAATATTTCATCAAATCCAATAAGAGAAATTT
1 AATTCAATATTTCATCAAATCCAATAAGAGAAATTT
53691867 A
1 A
53691868 TAAAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (36 bp):
AATTCAATATTTCATCAAATCCAATAAGAGAAATTT
Found at i:53692476 original size:65 final size:67
Alignment explanation
Indices: 53692378--53692504 Score: 213
Period size: 65 Copynumber: 1.9 Consensus size: 67
53692368 TGAAATAAGC
* *
53692378 CAACCATATGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAAAAAAATGGC
1 CAACCATATGTTTTGAAGAAGAAAAATGGTGTTTCGCAAGAGAAAAAATGAGAGAAAAAAATGGC
53692443 AG
66 AG
*
53692445 CAACCATGTGTTTTGAAG-A-AAAAATGGTGTTTCGCAAGAGAAAAAATGAGAGAAAAAAAT
1 CAACCATATGTTTTGAAGAAGAAAAATGGTGTTTCGCAAGAGAAAAAATGAGAGAAAAAAAT
53692505 TTGTTAAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 39 0.68
66 1 0.02
67 17 0.30
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.20
Consensus pattern (67 bp):
CAACCATATGTTTTGAAGAAGAAAAATGGTGTTTCGCAAGAGAAAAAATGAGAGAAAAAAATGGC
AG
Found at i:53695862 original size:27 final size:27
Alignment explanation
Indices: 53695832--53695886 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
53695822 TAGACTAAGT
53695832 GGTTAAGTGTTAGTGTTCCTCTTTAGA
1 GGTTAAGTGTTAGTGTTCCTCTTTAGA
53695859 GGTTAAGTGTTAGTGTTCCTCTTTAGA
1 GGTTAAGTGTTAGTGTTCCTCTTTAGA
53695886 G
1 G
53695887 AGCTTAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.11, G:0.27, T:0.44
Consensus pattern (27 bp):
GGTTAAGTGTTAGTGTTCCTCTTTAGA
Found at i:53697153 original size:28 final size:27
Alignment explanation
Indices: 53697112--53697209 Score: 110
Period size: 28 Copynumber: 3.6 Consensus size: 27
53697102 GTGTATCCTC
53697112 TATTTTTCAGATTTTACACTTTTGCCT
1 TATTTTTCAGATTTTACACTTTTGCCT
* * *
53697139 ATATTTTTCAAATTTTACAGTTTTACCCT
1 -TATTTTTCAGATTTTACACTTTT-GCCT
*
53697168 T-TTTTT-AGATTTTACATTTTTGCCCT
1 TATTTTTCAGATTTTACACTTTTG-CCT
*
53697194 TATTTTTCATATTTTA
1 TATTTTTCAGATTTTA
53697210 TAGTTTAATC
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
26 17 0.29
27 10 0.17
28 29 0.49
29 3 0.05
ACGTcount: A:0.21, C:0.15, G:0.05, T:0.58
Consensus pattern (27 bp):
TATTTTTCAGATTTTACACTTTTGCCT
Found at i:53702301 original size:11 final size:11
Alignment explanation
Indices: 53702287--53702321 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
53702277 GATTAATGAT
*
53702287 GATTCGATGAA
1 GATTCGACGAA
*
53702298 GATTCGACGAC
1 GATTCGACGAA
53702309 GATTCGACGAA
1 GATTCGACGAA
53702320 GA
1 GA
53702322 ATTGATACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (11 bp):
GATTCGACGAA
Found at i:53702451 original size:48 final size:47
Alignment explanation
Indices: 53702399--53702624 Score: 192
Period size: 48 Copynumber: 4.8 Consensus size: 47
53702389 TATGCATGAA
*
53702399 CCATGTAAGACCATGTTTGGGACATGGCATTGGCATCGAAATATGATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATC-AAATATGATC
* * *
53702447 CCATGTAAGACCATGTTTGAGACATGGCATTGGCATC-AATATGAGAC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAATATGA-TC
* * ** * ***
53702494 ATCGTGTAAGACCATAG-CTGGGTTATCGGC-TTCG-AT-ATGCATGATC
1 -CCATGTAAGACCAT-GTCTGGGACAT-GGCATTGGCATCAAATATGATC
* * * *
53702540 CGATGTAAGACCATGTCTAGGACATGGCTTTGGCATCAATATGTGATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAA-ATATGATC
* * *
53702588 CCATGTAAGACCATATCCGGGATATGGCATTGGCATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
53702625 CGACTATGTG
Statistics
Matches: 138, Mismatches: 30, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
44 4 0.03
45 20 0.14
46 10 0.07
47 8 0.06
48 92 0.67
49 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (47 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAATATGATC
Found at i:53704787 original size:40 final size:40
Alignment explanation
Indices: 53704743--53704890 Score: 260
Period size: 40 Copynumber: 3.7 Consensus size: 40
53704733 GCAAACACAT
* *
53704743 TTGCCTTCGGGTCTTAACCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53704783 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
53704823 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53704863 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
53704891 TCCAATGCTC
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:53709145 original size:22 final size:22
Alignment explanation
Indices: 53709120--53709163 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53709110 TAGTCATATA
53709120 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
53709142 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
53709164 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:53709208 original size:16 final size:16
Alignment explanation
Indices: 53709186--53709222 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
53709176 CAATTTTATT
53709186 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
53709203 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
53709218 TAATA
1 TAATA
53709223 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:53709275 original size:15 final size:15
Alignment explanation
Indices: 53709255--53709311 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
53709245 ATTCAATATT
53709255 AATATTTTAATAATA
1 AATATTTTAATAATA
*
53709270 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
53709289 AATATATTAATAATA
1 AATATTTTAATAATA
*
53709304 AATGTTTT
1 AATATTTT
53709312 GTAATAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:53709779 original size:14 final size:14
Alignment explanation
Indices: 53709760--53709798 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
53709750 CCAGAAAAGT
53709760 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
53709774 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
53709788 AAGTCATTTTC
1 AAATCATTTTC
53709799 AGTGAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:53711580 original size:8 final size:8
Alignment explanation
Indices: 53711549--53711573 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53711539 AATTATAAAA
53711549 TATTTTAT
1 TATTTTAT
53711557 TATTTTAT
1 TATTTTAT
53711565 TATTTTAT
1 TATTTTAT
53711573 T
1 T
53711574 GTATTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:53711722 original size:33 final size:32
Alignment explanation
Indices: 53711680--53711753 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 32
53711670 AAATAAGTAC
53711680 ATTTGTATTATTTA-TATATAATTAGTAAAAAGAT
1 ATTT-TATTATTTACTAT-TAATTAGT-AAAAGAT
53711714 ATTTTATTATTTACTATTAATTAGTAAAAGAT
1 ATTTTATTATTTACTATTAATTAGTAAAAGAT
53711746 -TTTT-TTAT
1 ATTTTATTAT
53711754 GATAAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
30 4 0.10
31 4 0.10
32 7 0.18
33 17 0.44
34 7 0.18
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (32 bp):
ATTTTATTATTTACTATTAATTAGTAAAAGAT
Found at i:53714390 original size:48 final size:48
Alignment explanation
Indices: 53714336--53714501 Score: 206
Period size: 48 Copynumber: 3.5 Consensus size: 48
53714326 AATCCGGACG
*
53714336 TGGTCTTACAGTAGCTCTCATATAAATGTCAATGCCATGTTCCAAACA
1 TGGTCTTACACTAGCTCTCATATAAATGTCAATGCCATGTTCCAAACA
* * ** * * * * *
53714384 TGGTCTTACACTGGCTCACATATCGAGGCCAGTGCCATGTCCCAGACA
1 TGGTCTTACACTAGCTCTCATATAAATGTCAATGCCATGTTCCAAACA
* *
53714432 TGGTTTTACACTAGCTCTCATATAAATGTCGATGCCATGTTCCAAACA
1 TGGTCTTACACTAGCTCTCATATAAATGTCAATGCCATGTTCCAAACA
* *
53714480 TGGTCTTACACTGGCTCACATA
1 TGGTCTTACACTAGCTCTCATA
53714502 ACCTTAGTAT
Statistics
Matches: 94, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 94 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (48 bp):
TGGTCTTACACTAGCTCTCATATAAATGTCAATGCCATGTTCCAAACA
Found at i:53716288 original size:36 final size:36
Alignment explanation
Indices: 53716205--53716288 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 36
53716195 ATTTTTCACT
*
53716205 ATTTATTT-A-TTAAAAATTTAAAAGAAACATGTTA
1 ATTTATTTAATTTTAAAATTTAAAAGAAACATGTTA
* * *
53716239 ATTT-TTTATATTTTAAAA-TTATAAAGAAACTTTTTC
1 ATTTATTTA-ATTTTAAAATTTA-AAAGAAACATGTTA
53716275 ATTTATTTAATTTT
1 ATTTATTTAATTTT
53716289 TCAACTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
33 3 0.07
34 4 0.10
35 4 0.10
36 26 0.63
37 4 0.10
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (36 bp):
ATTTATTTAATTTTAAAATTTAAAAGAAACATGTTA
Found at i:53716649 original size:8 final size:7
Alignment explanation
Indices: 53716640--53716696 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
53716630 TAAAACAAAT
53716640 TTTTATA
1 TTTTATA
53716647 TTTTATTA
1 TTTTA-TA
53716655 GTTTTATA
1 -TTTTATA
53716663 -TTTATA
1 TTTTATA
53716669 TTTTATA
1 TTTTATA
53716676 GTTTTTATA
1 --TTTTATA
*
53716685 ATTT-TA
1 TTTTATA
53716691 TTTTAT
1 TTTTAT
53716697 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
6 11 0.26
7 15 0.36
8 4 0.10
9 12 0.29
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (7 bp):
TTTTATA
Found at i:53716669 original size:22 final size:24
Alignment explanation
Indices: 53716641--53716697 Score: 86
Period size: 22 Copynumber: 2.5 Consensus size: 24
53716631 AAAACAAATT
53716641 TTTATATTTTATTAG-TTTTAT-A
1 TTTATATTTTATTAGTTTTTATAA
53716663 TTTATATTTTA-TAGTTTTTATAA
1 TTTATATTTTATTAGTTTTTATAA
53716686 TTT-TATTTTATT
1 TTTATATTTTATT
53716698 TAATAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.09
22 24 0.75
23 5 0.16
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTATATTTTATTAGTTTTTATAA
Found at i:53716672 original size:29 final size:29
Alignment explanation
Indices: 53716640--53716696 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
53716630 TAAAACAAAT
*
53716640 TTTTATA--TTTTATTAGTTTTATATTTATA
1 TTTTATAGTTTTTA-TAATTTTAT-TTTATA
53716669 TTTTATAGTTTTTATAATTTTATTTTAT
1 TTTTATAGTTTTTATAATTTTATTTTAT
53716697 TTAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 12 0.48
30 8 0.32
31 5 0.20
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (29 bp):
TTTTATAGTTTTTATAATTTTATTTTATA
Found at i:53722183 original size:18 final size:18
Alignment explanation
Indices: 53722160--53722195 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53722150 AAATTGAGTT
53722160 TCGTAAACAACTACTAAA
1 TCGTAAACAACTACTAAA
53722178 TCGTAAACAACTACTAAA
1 TCGTAAACAACTACTAAA
53722196 GACAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (18 bp):
TCGTAAACAACTACTAAA
Found at i:53731841 original size:47 final size:47
Alignment explanation
Indices: 53731787--53731878 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
53731777 AGTGCATTCT
53731787 GAAGAAGATGCTTATAATCTTTATAATCAGTTTGCTTTGAGTAAGGC
1 GAAGAAGATGCTTATAATCTTTATAATCAGTTTGCTTTGAGTAAGGC
*
53731834 GAAGAAGATGCTTATAATCTTTATAATTAGTTTGCTTTGAGTAAG
1 GAAGAAGATGCTTATAATCTTTATAATCAGTTTGCTTTGAGTAAG
53731879 TGGTTTAGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (47 bp):
GAAGAAGATGCTTATAATCTTTATAATCAGTTTGCTTTGAGTAAGGC
Found at i:53743361 original size:22 final size:22
Alignment explanation
Indices: 53743335--53743377 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
53743325 TGCATCAGGC
*
53743335 AAAAATTTTTAAAAATTATTATT
1 AAAAA-TTATAAAAATTATTATT
53743358 AAAAATTATAAAAATTATTA
1 AAAAATTATAAAAATTATTA
53743378 GATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATTATAAAAATTATTATT
Found at i:53743571 original size:20 final size:20
Alignment explanation
Indices: 53743546--53743602 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
53743536 ATAAATAATC
53743546 AAAAAATTCAAAAATTGCAA
1 AAAAAATTCAAAAATTGCAA
*
53743566 AAAAAATTCAAAAATTGTAA
1 AAAAAATTCAAAAATTGCAA
***
53743586 AACTTATTCAAAAATTG
1 AAAAAATTCAAAAATTG
53743603 TGAAAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAAAATTCAAAAATTGCAA
Found at i:53743603 original size:20 final size:19
Alignment explanation
Indices: 53743551--53743618 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
53743541 TAATCAAAAA
* **
53743551 ATTCAAAAATTGCAAAAAAA
1 ATTCAAAAATTG-TAAAATT
53743571 ATTCAAAAATTGTAAAACTT
1 ATTCAAAAATTGTAAAA-TT
53743591 ATTCAAAAATTGTGAAAATT
1 ATTCAAAAATTGT-AAAATT
53743611 ATT-AAAAA
1 ATTCAAAAA
53743619 AATCTTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.21
20 30 0.70
21 4 0.09
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.29
Consensus pattern (19 bp):
ATTCAAAAATTGTAAAATT
Found at i:53747037 original size:13 final size:13
Alignment explanation
Indices: 53747030--53747094 Score: 80
Period size: 13 Copynumber: 5.0 Consensus size: 13
53747020 TTTATTATAA
*
53747030 TATATTATTTTAT
1 TATATTATATTAT
53747043 TATATTA-A-TAT
1 TATATTATATTAT
*
53747054 TACATTATATTAT
1 TATATTATATTAT
53747067 TATATTATATTATAT
1 TATATTATA-T-TAT
53747082 TATATTATATTAT
1 TATATTATATTAT
53747095 ATTATATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
11 9 0.20
12 1 0.02
13 21 0.47
14 2 0.04
15 12 0.27
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTATATTAT
Found at i:53747045 original size:8 final size:8
Alignment explanation
Indices: 53747021--53747099 Score: 58
Period size: 8 Copynumber: 9.5 Consensus size: 8
53747011 GTTAAGATTT
53747021 TTATTATAA
1 TTATTAT-A
*
53747030 TATATTATT
1 T-TATTATA
53747039 TTATTATA
1 TTATTATA
53747047 TTA--ATA
1 TTATTATA
53747053 TTACATTATA
1 TT--ATTATA
53747063 TTATTATA
1 TTATTATA
53747071 TTA-TAT-
1 TTATTATA
53747077 TATATTATA
1 T-TATTATA
53747086 TTATATTATA
1 -T-TATTATA
53747096 TTAT
1 TTAT
53747100 ATAAAACAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 19
0.74 0.03 0.24
Matches are distributed among these distances:
6 6 0.10
7 5 0.08
8 25 0.42
9 3 0.05
10 20 0.34
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTATA
Found at i:53747049 original size:5 final size:5
Alignment explanation
Indices: 53747022--53747101 Score: 105
Period size: 5 Copynumber: 16.6 Consensus size: 5
53747012 TTAAGATTTT
* *
53747022 TATTA TAATA TATTA T-TT- TATTA TATTAA TATTA CATTA TA-T- TATTA
1 TATTA TATTA TATTA TATTA TATTA TATT-A TATTA TATTA TATTA TATTA
53747069 TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TAT
53747102 AAAACAAAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
3 3 0.05
4 6 0.09
5 52 0.79
6 5 0.08
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:53751324 original size:29 final size:28
Alignment explanation
Indices: 53751278--53751375 Score: 160
Period size: 29 Copynumber: 3.4 Consensus size: 28
53751268 AGAGGTATAT
*
53751278 TTATAATAGAGATTGCCACAAAGGCTTTC
1 TTATAATAGAG-TTGCCATAAAGGCTTTC
53751307 TTATAATAGAGTTCGCCATAAAGGCTTTC
1 TTATAATAGAGTT-GCCATAAAGGCTTTC
53751336 TTATAATAGAGTTTGCCATAAAGGCTTTC
1 TTATAATAGAG-TTGCCATAAAGGCTTTC
53751365 TTATAATAGAG
1 TTATAATAGAG
53751376 ATCACTACAA
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
28 2 0.03
29 62 0.94
30 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (28 bp):
TTATAATAGAGTTGCCATAAAGGCTTTC
Found at i:53751417 original size:29 final size:29
Alignment explanation
Indices: 53751377--53751460 Score: 123
Period size: 29 Copynumber: 2.9 Consensus size: 29
53751367 ATAATAGAGA
* * *
53751377 TCACTACAAAAGCTTCCATTTTAACAAATT
1 TCACCACAAAGGCTTCCA-TTTAACAAAGT
53751407 TCACCACAAAGGCTTCCATTTAACAAAGT
1 TCACCACAAAGGCTTCCATTTAACAAAGT
*
53751436 TCACCATAAAGGCTTCCATTTAACA
1 TCACCACAAAGGCTTCCATTTAACA
53751461 GAGATAGCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 34 0.68
30 16 0.32
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (29 bp):
TCACCACAAAGGCTTCCATTTAACAAAGT
Found at i:53751618 original size:46 final size:45
Alignment explanation
Indices: 53751468--53751621 Score: 134
Period size: 46 Copynumber: 3.4 Consensus size: 45
53751458 ACAGAGATAG
* * * * * *
53751468 CCAAACAATTCAAGACAAATAAATCAATTTCTATCATGTACAATAA
1 CCAAACAATTTAATACAAACAAACCCA-TTCTGTCATGTACAATAA
* *
53751514 CCAAACAATTTAATACAAACAAATCCATTCTGTCA--TACACAT-G
1 CCAAACAATTTAATACAAACAAACCCATTCTGTCATGTACA-ATAA
* * ** * *
53751557 GCAGACAATAAAATACAAAGAAACCCATGTTTGTCATGTACAATAA
1 CCAAACAATTTAATACAAACAAACCCAT-TCTGTCATGTACAATAA
53751603 CCAAACAATTTAATACAAA
1 CCAAACAATTTAATACAAA
53751622 TAAATCCAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
43 26 0.31
44 8 0.09
45 9 0.11
46 42 0.49
ACGTcount: A:0.49, C:0.21, G:0.06, T:0.24
Consensus pattern (45 bp):
CCAAACAATTTAATACAAACAAACCCATTCTGTCATGTACAATAA
Found at i:53752156 original size:202 final size:201
Alignment explanation
Indices: 53751810--53752281 Score: 640
Period size: 202 Copynumber: 2.3 Consensus size: 201
53751800 ATAGGAATTG
* *
53751810 ATTTGTCTCTTTCCTAAGGTTATTAGTATGCACATGGCAGACAATAACTTTAGAAAAATCCAAAC
1 ATTTGTCT-TTTCCTAAGGCTATTAGTATGCACATGGTAGACAATAACTTTAGAAAAATCCAAAC
* * * *
53751875 CTGCAATTCAATTTGATACAAACAACGATCCTATTTGAACCAACATTTAAAAAATGTTTTGGATC
65 CTACAATTCAATTTGATACAAACAACAATCATATTTGAACCAACATTTAAAAAATGTTTTGAATC
* * * * *
53751940 ATATTTAAATAATTCAATGACATACATAGTTTCGAATAATTCAATACAAATTGATTTGTCAAATA
130 ATATTTAAATAATTCAATCACATACACAATTTCGAATAATTCAATAAAAACTGATTTGTCAAATA
53752005 GAAACTA
195 GAAACTA
* * *
53752012 ATTTGTCTATTTCCTAAGGCTAGTAGTATGCACATGGTAGACAACAAC-TTAGAAAAATCTAAAC
1 ATTTGTCT-TTTCCTAAGGCTATTAGTATGCACATGGTAGACAATAACTTTAGAAAAATCCAAAC
* *
53752076 CTACAATTCAATTTGATATAAACAATAATCATATTTGAACCAACATTTAAAAAAATGTTTTGAAT
65 CTACAATTCAATTTGATACAAACAACAATCATATTTGAACCAACATTT-AAAAAATGTTTTGAAT
* * *
53752141 CGTATTTGAATAATTCAATCACATACACAATTTTGAATAATTCAATAAAAACTGATTTGTCAAAT
129 CATATTTAAATAATTCAATCACATACACAATTTCGAATAATTCAATAAAAACTGATTTGTCAAAT
* *
53752206 AGGAACTG
194 AGAAACTA
** ** * * *
53752214 ATTTAACCTTAAACCTAAGGCTATTTGTATGCACATGGTAGACCATGACTTTAGAAAAATCCAAA
1 ATTT-GTCTT-TTCCTAAGGCTATTAGTATGCACATGGTAGACAATAACTTTAGAAAAATCCAAA
53752279 CCT
64 CCT
53752282 TCCATTTACT
Statistics
Matches: 234, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
201 58 0.25
202 126 0.54
203 33 0.14
204 17 0.07
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (201 bp):
ATTTGTCTTTTCCTAAGGCTATTAGTATGCACATGGTAGACAATAACTTTAGAAAAATCCAAACC
TACAATTCAATTTGATACAAACAACAATCATATTTGAACCAACATTTAAAAAATGTTTTGAATCA
TATTTAAATAATTCAATCACATACACAATTTCGAATAATTCAATAAAAACTGATTTGTCAAATAG
AAACTA
Found at i:53753627 original size:15 final size:16
Alignment explanation
Indices: 53753607--53753649 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
53753597 TTTTTCTTTT
*
53753607 TTTTTATAATTTT-CA
1 TTTTTAAAATTTTACA
*
53753622 TTTTTAAAATTTTATA
1 TTTTTAAAATTTTACA
53753638 TTTTTAAAATTT
1 TTTTTAAAATTT
53753650 ATTTTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAAAATTTTACA
Found at i:53753640 original size:16 final size:16
Alignment explanation
Indices: 53753607--53753662 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
53753597 TTTTTCTTTT
* *
53753607 TTTTTATAATTTT-CA
1 TTTTTAAAATTTTATA
53753622 TTTTTAAAATTTTATA
1 TTTTTAAAATTTTATA
53753638 TTTTTAAAA-TTTAT-
1 TTTTTAAAATTTTATA
53753652 TTTTTATAAAT
1 TTTTTA-AAAT
53753663 AATTCAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 6 0.17
15 20 0.56
16 10 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTAAAATTTTATA
Done.