Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 433 of 438
Found at i:133368613 original size:75 final size:74
Alignment explanation
Indices: 133368460--133369025 Score: 638
Period size: 75 Copynumber: 7.5 Consensus size: 74
133368450 CATGTGATCC
* * * * ** *
133368460 GAGGCTCCACTCACCTCTCGCAATATGAGTTGA-TTTTCGAAA-ACGGAGATCAAAATTACCTTA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAATTACCTCA
* *
133368523 GCGTATCCT
66 GCGTGTCTT
133368532 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTATTTTGAAAGACAGAAATTGAAATTACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTTGAAAGACAGAAATTGAAATTACCTC
133368597 AGCGTGTCTT
65 AGCGTGTCTT
*
133368607 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAAATACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAATTACCTCA
*
133368672 ACGTGTCTT
66 GCGTGTCTT
* * * *
133368681 GAGGCTCAACTCACTTCTTGCAGTATGAGTTGAATTTTTTGAAAGACAGAAATTGAAAATACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTGAAAGACAGAAATTGAAATTACCTC
*
133368746 AACGTGTCTT
65 AGCGTGTCTT
* * * * * ** *
133368756 GAGGCTCAAATCACTTCTTGCAGTATGAGTTGA-ATTTTG-AA-ACAGAAATAAAAATTATCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAATTACCTCA
* **
133368818 GGGTGTCCC
66 GCGTGTCTT
* *
133368827 AAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTTTTTTTGAAAGACAGAAATTGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-------TTTTTTGAAAGACAGAAATTGAAAT
*
133368892 TACCTCAGCGTGTCCT
59 TACCTCAGCGTGTCTT
** * *
133368908 GAGGCTCAACTCACCTCTTACAATATGAGTTGATATTTTTGTGAAAGGCAGAAATTGAAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTG--ATTTTT-TGAAAGACAGAAATTGAAATTACC
* *
133368973 TCAACGTGTCAGTC
63 TCAGCGTGTC--TT
*
133368987 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
133369026 TTGAACCGTA
Statistics
Matches: 427, Mismatches: 48, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
71 49 0.11
72 34 0.08
73 6 0.01
74 74 0.17
75 131 0.31
76 6 0.01
77 37 0.09
79 34 0.08
80 2 0.00
81 53 0.12
83 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (74 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAATTACCTCA
GCGTGTCTT
Found at i:133368690 original size:149 final size:147
Alignment explanation
Indices: 133368460--133369026 Score: 645
Period size: 149 Copynumber: 3.8 Consensus size: 147
133368450 CATGTGATCC
* * * * * * *
133368460 GAGGCTCCACTCACCTCTCGCAATATGAGTTGATTTTCGAAAACGGAGATCAAAATTACCTTAGC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATGAAAATTACCTCAAC
* ** *
133368525 GTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTATTTTGAAAGACAGAAATTGAAA
66 GTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAA
133368590 TTACCTCAGCGTGTCTT
131 TTACCTCAGCGTGTCTT
133368607 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAAA-TACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAA-ACAGAAA-TGAAAATTACCTC
*** * * * *
133368671 AACGTGTCTTGAGGCTCAACTCACTTCTTGCAGTATGAGTTGAATTTTTTGAAAGACAGAAATTG
63 AACGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG
* *
133368736 AAAATACCTCAACGTGTCTT
128 AAATTACCTCAGCGTGTCTT
* * * * * * * **
133368756 GAGGCTCAAATCACTTCTTGCAGTATGAGTTGAATTTTG-AAACAGAAATAAAAATTATCTCAGG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATGAAAATTACCTCAAC
*
133368820 GTGTCCCAAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTTTTTTTGAAAGACAGAAA
66 GTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA------TTTTTTTGAAAGACAGAAA
*
133368885 TTGAAATTACCTCAGCGTGTCCT
125 TTGAAATTACCTCAGCGTGTCTT
** *
133368908 GAGGCTCAACTCACCTCTTACAATATGAGTTGATATTTTTGTGAAAGGCAGAAATTGAAAA-TAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTG--A-TTTT-TGAAA-ACAGAAA-TGAAAATTAC
*
133368972 CTCAACGTGTCAGTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
60 CTCAACGTGTC--CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
133369027 TGAACCGTAG
Statistics
Matches: 353, Mismatches: 48, Indels: 31
0.82 0.11 0.07
Matches are distributed among these distances:
145 5 0.01
146 46 0.13
147 34 0.10
148 13 0.04
149 114 0.32
150 5 0.01
152 66 0.19
154 8 0.02
155 3 0.01
156 2 0.01
157 2 0.01
158 17 0.05
159 5 0.01
160 33 0.09
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (147 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATGAAAATTACCTCAAC
GTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAA
TTACCTCAGCGTGTCTT
Found at i:133368933 original size:81 final size:81
Alignment explanation
Indices: 133368790--133369027 Score: 281
Period size: 81 Copynumber: 3.0 Consensus size: 81
133368780 ATGAGTTGAA
** * * * *
133368790 TTTTG-AA-ACAGAAATAAAAATTATCTCAGGGTGTCCCAAGGCTCAACTCACCTCTCGTAATAT
1 TTTTGAAAGACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATAT
133368853 GAGTTGATTTTTTTTT
66 GAGTTGATTTTTTTTT
* **
133368869 TTTTGAAAGACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTACAATAT
1 TTTTGAAAGACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATAT
*
133368934 GAGTTGA----TATTT
66 GAGTTGATTTTTTTTT
* * * * *
133368946 TTGTGAAAGGCAGAAATTGAAAATACCTCAACGTGTCAGTCAAGGCTCAACTCACCTCTCGCAAT
1 TTTTGAAAGACAGAAATTGAAATTACCTCAGCGTGTC-CT-AAGGCTCAACTCACCTCTCGCAAT
133369011 ATGAGTTGATTTTTTTT
64 ATGAGTTGATTTTTTTT
133369028 GAACCGTAGA
Statistics
Matches: 132, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
77 37 0.28
78 1 0.01
79 35 0.27
80 2 0.02
81 54 0.41
83 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (81 bp):
TTTTGAAAGACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTTTTT
Found at i:133370715 original size:53 final size:53
Alignment explanation
Indices: 133370627--133370776 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
133370617 CTTACACGGT
* * *
133370627 TCACATATCATACCGAAGCCATATCCCA-CACATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAGC-TATGGTCTTATACGGAATCACATTA
*
133370682 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
133370735 TCACATTGCACCGATGCCATAG-CCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
133370777 GCACACTTGT
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
52 19 0.22
53 60 0.69
54 2 0.02
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:133383224 original size:24 final size:26
Alignment explanation
Indices: 133383197--133383244 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
133383187 TATGAATACG
133383197 TACAT-ATAATATA-ATAT-TAAAATA
1 TACATAAT-ATATACATATATAAAATA
133383221 TACATAATATATACATATATAAAA
1 TACATAATATATACATATATAAAA
133383245 CATGTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
TACATAATATATACATATATAAAATA
Found at i:133385491 original size:31 final size:32
Alignment explanation
Indices: 133385453--133385512 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
133385443 AAAAAAAAAG
*
133385453 ACTTAAAT-AATAACTTTTGAATAATTTAATA
1 ACTTAAATGAAAAACTTTTGAATAATTTAATA
*
133385484 ACTTAAATGAAAAACTTTTGAATAGTTTA
1 ACTTAAATGAAAAACTTTTGAATAATTTA
133385513 GTAATTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (32 bp):
ACTTAAATGAAAAACTTTTGAATAATTTAATA
Found at i:133390051 original size:15 final size:15
Alignment explanation
Indices: 133390033--133390066 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
133390023 TCCTAAACTA
133390033 TTAAAATTATATCAT
1 TTAAAATTATATCAT
133390048 TTAAAATTATATCAT
1 TTAAAATTATATCAT
133390063 TTAA
1 TTAA
133390067 GTCCTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAAATTATATCAT
Found at i:133392753 original size:41 final size:41
Alignment explanation
Indices: 133392688--133392780 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
133392678 TAAATTATTA
*
133392688 TTTTTTGTTAATTTATTGCATATAAATTATTGAACTATTAAT
1 TTTTTTGTT-ATTTATTGCATATAAATTATTGAACGATTAAT
* ** * *
133392730 TTTTTTGTTATTTTTTGGTTATAAATTGTTGAACGATTTAT
1 TTTTTTGTTATTTATTGCATATAAATTATTGAACGATTAAT
*
133392771 TTTTATGTTA
1 TTTTTTGTTA
133392781 ATGATTTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 35 0.80
42 9 0.20
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (41 bp):
TTTTTTGTTATTTATTGCATATAAATTATTGAACGATTAAT
Found at i:133395172 original size:2 final size:2
Alignment explanation
Indices: 133395165--133395189 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
133395155 ATTTACAAAT
133395165 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
133395190 TGATTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:133406067 original size:7 final size:7
Alignment explanation
Indices: 133406057--133406081 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
133406047 TTGCAGCGTG
133406057 CATCGAT
1 CATCGAT
133406064 CATCGAT
1 CATCGAT
133406071 CATCGAT
1 CATCGAT
133406078 CATC
1 CATC
133406082 TGTATTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (7 bp):
CATCGAT
Found at i:133410943 original size:107 final size:107
Alignment explanation
Indices: 133410808--133411025 Score: 323
Period size: 107 Copynumber: 2.0 Consensus size: 107
133410798 AAGTTGTTTG
* *
133410808 AGCTGAGTATAACTGAGCTCAAATTCAGCTTGTCCAATAGTTCGAGCTTGGCTTGATAATTATTG
1 AGCTGAGTATAACTGAGCTCAAATTCAGCTTGACCAATAGTTCGAGCTTGGCTCGATAATTATTG
* *
133410873 AGTCGAGTTCAAGTTTTTCT-TCGAACATAAGTAGTTTGGGA
66 AGTCAAGTTCAAGTTTTTCTGTAGAACATAAGTAGTTTGGGA
* *
133410914 AGCTGAGTATTAC-GAAGCCTCAAATTCAGCTTGACCAATAGTTTGAGCTTGGCTCGATAATTAT
1 AGCTGAGTATAACTG-AG-CTCAAATTCAGCTTGACCAATAGTTCGAGCTTGGCTCGATAATTAT
133410978 TGAGTCAAGTTCAAGTTTTTCTCGAGTAGAACATAAGTAGTTTGGGA
64 TGAGTCAAGTTCAAGTTTTTCT---GTAGAACATAAGTAGTTTGGGA
133411025 A
1 A
133411026 CCAGTGTCTT
Statistics
Matches: 100, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
105 1 0.01
106 14 0.14
107 64 0.64
111 21 0.21
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (107 bp):
AGCTGAGTATAACTGAGCTCAAATTCAGCTTGACCAATAGTTCGAGCTTGGCTCGATAATTATTG
AGTCAAGTTCAAGTTTTTCTGTAGAACATAAGTAGTTTGGGA
Found at i:133413287 original size:27 final size:28
Alignment explanation
Indices: 133413230--133413287 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
133413220 TTAATTGGTC
*
133413230 AAATAGGTCGATTTTTTAAAAATTTAAGA
1 AAATAGGTC-ATTTTTTAAAAATGTAAGA
* *
133413259 AAATAGGTC-TTTTTTAAAAGTGTATGA
1 AAATAGGTCATTTTTTAAAAATGTAAGA
133413286 AA
1 AA
133413288 GCTCACTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 17 0.65
29 9 0.35
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (28 bp):
AAATAGGTCATTTTTTAAAAATGTAAGA
Found at i:133419551 original size:20 final size:20
Alignment explanation
Indices: 133419511--133419551 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
133419501 ATTCTAACAT
* *
133419511 AACAATCGATTTAACATAAA
1 AACAATCGATTTAAAAAAAA
*
133419531 AACAATTGATTTAAAAAAAA
1 AACAATCGATTTAAAAAAAA
133419551 A
1 A
133419552 TAATATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (20 bp):
AACAATCGATTTAAAAAAAA
Found at i:133429183 original size:33 final size:33
Alignment explanation
Indices: 133429144--133429209 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
133429134 AATAACTTAG
*
133429144 TATTTTTATTATT-TT-TAATTTAATATTTTAGAT
1 TATTTTTATT-TTATTAAAATTTAA-ATTTTAGAT
*
133429177 TATTTTTCTTTTATTAAAATTTAAATTTTAGAT
1 TATTTTTATTTTATTAAAATTTAAATTTTAGAT
133429210 AAAATAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 2 0.07
33 20 0.69
34 7 0.24
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (33 bp):
TATTTTTATTTTATTAAAATTTAAATTTTAGAT
Found at i:133431218 original size:29 final size:31
Alignment explanation
Indices: 133431163--133431221 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
133431153 AATACATGTA
* *
133431163 TGTATTTACTTATTATTTAAGTAAATATTAG
1 TGTATTTACTTAATATTTAAATAAATATTAG
*
133431194 TGTATTTA-TTAATA-TTAAATTAATATTA
1 TGTATTTACTTAATATTTAAATAAATATTA
133431222 TATGATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
30 5 0.20
31 8 0.32
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (31 bp):
TGTATTTACTTAATATTTAAATAAATATTAG
Found at i:133431601 original size:15 final size:15
Alignment explanation
Indices: 133431583--133431619 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
133431573 GTATATTTAC
133431583 TTATTATATAATATA
1 TTATTATATAATATA
* *
133431598 TTATTAAATTATATA
1 TTATTATATAATATA
133431613 TTATTAT
1 TTATTAT
133431620 TAAGTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATATAATATA
Found at i:133431847 original size:16 final size:16
Alignment explanation
Indices: 133431826--133431864 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
133431816 GAAAAGCAGG
133431826 GAAAGAAA-GAGAGAAA
1 GAAAGAAAGGAGA-AAA
133431842 GAAAGAAAGGAGAAAA
1 GAAAGAAAGGAGAAAA
133431858 GAAAGAA
1 GAAAGAA
133431865 GAAAGGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGGAGAAAA
Found at i:133431882 original size:20 final size:20
Alignment explanation
Indices: 133431837--133431875 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
133431827 AAAGAAAGAG
133431837 AGAAAGAAAGAAAGGAGAAA
1 AGAAAGAAAGAAAGGAGAAA
133431857 AGAAAG-AAGAAAGG-GAAA
1 AGAAAGAAAGAAAGGAGAAA
133431875 A
1 A
133431876 TTGAAAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAAGAAAGAAAGGAGAAA
Found at i:133433217 original size:21 final size:19
Alignment explanation
Indices: 133433178--133433217 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
133433168 TGAACATGTG
*
133433178 TTTATTGTGAAATTGAATA
1 TTTATTGTGAAAGTGAATA
133433197 TTTATTAGTGAAAAGTGAATA
1 TTTATT-GTG-AAAGTGAATA
133433218 GAATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
TTTATTGTGAAAGTGAATA
Found at i:133433421 original size:12 final size:12
Alignment explanation
Indices: 133433404--133433428 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
133433394 GCCGACTACT
133433404 GTTACTGTTACC
1 GTTACTGTTACC
133433416 GTTACTGTTACC
1 GTTACTGTTACC
133433428 G
1 G
133433429 ATTCGGCACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:133433534 original size:47 final size:47
Alignment explanation
Indices: 133433459--133433575 Score: 164
Period size: 47 Copynumber: 2.5 Consensus size: 47
133433449 GATATTGTTA
* * *
133433459 CTGT-TACCGTTACTGTTACTGTTTCGAATTTGTTCTGATGAGGTATT
1 CTGTGTACCG-TACTGTTACTGTTCCGAATTTGTTCCGATGAGGTACT
133433506 CTGTGTACCGTACTGTTACTGTTCCGAATTTGTTCCGATGAGGTACT
1 CTGTGTACCGTACTGTTACTGTTCCGAATTTGTTCCGATGAGGTACT
* * *
133433553 CTGTGTAACGTATTGCTACTGTT
1 CTGTGTACCGTACTGTTACTGTT
133433576 ACTGTTACTG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
47 58 0.92
48 5 0.08
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (47 bp):
CTGTGTACCGTACTGTTACTGTTCCGAATTTGTTCCGATGAGGTACT
Found at i:133433725 original size:18 final size:18
Alignment explanation
Indices: 133433704--133433894 Score: 158
Period size: 18 Copynumber: 10.6 Consensus size: 18
133433694 TAACTGATTA
133433704 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
* *
133433722 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
*
133433740 TTACTGGAT-ATTAGACTG
1 TTACTGAATAATT-GACTG
* * *
133433758 TTACTGAATAACTGAATA
1 TTACTGAATAATTGACTG
*
133433776 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
133433794 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
* *
133433812 TCATTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* * *
133433830 CTACTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
*
133433849 TTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
133433866 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
133433884 TTACTGGATAA
1 TTACTGAATAA
133433895 CCGATCAATT
Statistics
Matches: 140, Mismatches: 23, Indels: 20
0.77 0.13 0.11
Matches are distributed among these distances:
17 20 0.14
18 103 0.74
19 17 0.12
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:133433829 original size:72 final size:72
Alignment explanation
Indices: 133433692--133433894 Score: 189
Period size: 72 Copynumber: 2.8 Consensus size: 72
133433682 AAAGGTATAA
* * * * * * * *
133433692 AATAACTGATTATTACTGAATAATTGA-CTGTTACCGGATAATTGACTGTTACTGGATATTAGAC
1 AATAACTGAATATTACTGAATAATTGATC-ATTACTGAATAACTGACTGTCACTGAATAATAGAC
*
133433756 TGTTACTG
65 TGCTACTG
* *
133433764 AATAACTGAATATTACTGAATAATTGATCATTACTGAATAACTGATTGTCATTGAATGAAT-GAC
1 AATAACTGAATATTACTGAATAATTGATCATTACTGAATAACTGACTGTCACTGAAT-AATAGAC
133433828 TGCTACTG
65 TGCTACTG
* * * * * *
133433836 AATAACTTAATTGTTACTGAAT-ATCTGAT-TTTACTGAATAATTGACTGTTACTGGATAA
1 AATAACTGAA-TATTACTGAATAAT-TGATCATTACTGAATAACTGACTGTCACTGAATAA
133433895 CCGATCAATT
Statistics
Matches: 108, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
71 2 0.02
72 89 0.82
73 17 0.16
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (72 bp):
AATAACTGAATATTACTGAATAATTGATCATTACTGAATAACTGACTGTCACTGAATAATAGACT
GCTACTG
Found at i:133433983 original size:18 final size:18
Alignment explanation
Indices: 133433692--133433987 Score: 150
Period size: 18 Copynumber: 16.1 Consensus size: 18
133433682 AAAGGTATAA
*
133433692 AATAACTGATTATTACTG
1 AATAACTGATTGTTACTG
* * *
133433710 AATAATTGACTGTTACCG
1 AATAACTGATTGTTACTG
* * *
133433728 GATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* * *
133433746 GAT-ATTAGACTGTTACTG
1 AATAACT-GATTGTTACTG
* *
133433764 AATAACTGAATATTACTG
1 AATAACTGATTGTTACTG
* **
133433782 AATAATTGATCATTACTG
1 AATAACTGATTGTTACTG
* *
133433800 AATAACTGATTGTCATTG
1 AATAACTGATTGTTACTG
* *
133433818 AATGAA-TGACTGCTACTG
1 AAT-AACTGATTGTTACTG
*
133433836 AATAACTTAATTGTTACTG
1 AATAAC-TGATTGTTACTG
*
133433855 AATATCTGATT-TTACTG
1 AATAACTGATTGTTACTG
* *
133433872 AATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
133433890 GATAACCGATCAATTGATCGATACTG
1 AATAA-C--T-GATTG-T---TACTG
* * *
133433916 AATAACTGGTTATTATTG
1 AATAACTGATTGTTACTG
* * *
133433934 AATAATTCATTGTTACCG
1 AATAACTGATTGTTACTG
* *
133433952 AATAAGTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
133433970 AATAAATAATTGTT-CTG
1 AATAACTGATTGTTACTG
133433987 A
1 A
133433988 TTGTTAATGA
Statistics
Matches: 212, Mismatches: 52, Indels: 29
0.72 0.18 0.10
Matches are distributed among these distances:
17 23 0.11
18 152 0.72
19 18 0.08
21 2 0.01
22 5 0.02
23 2 0.01
25 1 0.00
26 9 0.04
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:133436677 original size:40 final size:35
Alignment explanation
Indices: 133436552--133436657 Score: 185
Period size: 35 Copynumber: 3.0 Consensus size: 35
133436542 ATGGCAAAGT
* *
133436552 TCATCCATACTGAGTTGTGAAATTTAGGTATGGTA
1 TCATCCATACTGAGTTGTGATATGTAGGTATGGTA
*
133436587 TCATCCATATTGAGTTGTGATATGTAGGTATGGTA
1 TCATCCATACTGAGTTGTGATATGTAGGTATGGTA
133436622 TCATCCATACTGAGTTGTGATATGTAGGTATGGTA
1 TCATCCATACTGAGTTGTGATATGTAGGTATGGTA
133436657 T
1 T
133436658 TATCAAATCC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.39
Consensus pattern (35 bp):
TCATCCATACTGAGTTGTGATATGTAGGTATGGTA
Found at i:133436705 original size:75 final size:75
Alignment explanation
Indices: 133436556--133436737 Score: 196
Period size: 75 Copynumber: 2.5 Consensus size: 75
133436546 CAAAGTTCAT
* ** * *
133436556 CCATACTGAGTTGTGAAATTTAGGTATGG---TATC--ATCCATATTGAGTTGTGATATGTAGGT
1 CCATACTGAGTTGTGAAATGTAGGTATGGTATTATCAAATCCATATTGAGTTAAGAAATGTAAGT
* *
133436616 ATGGTATCAT
66 ATGGCATCAC
*
133436626 CCATACTGAGTTGTGATATGTAGGTATGGTATTATCAAATCCATATTGAGTTAAGAAATGTAAGT
1 CCATACTGAGTTGTGAAATGTAGGTATGGTATTATCAAATCCATATTGAGTTAAGAAATGTAAGT
**
133436691 ATGGCATTGC
66 ATGGCATCAC
* * * *
133436701 CCATACCGAATTGTAAAATGTAAGTATGGTATT-TCAA
1 CCATACTGAGTTGTGAAATGTAGGTATGGTATTATCAA
133436738 TGAGGAAAAC
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
70 27 0.29
73 4 0.04
74 4 0.04
75 57 0.62
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (75 bp):
CCATACTGAGTTGTGAAATGTAGGTATGGTATTATCAAATCCATATTGAGTTAAGAAATGTAAGT
ATGGCATCAC
Found at i:133443944 original size:12 final size:12
Alignment explanation
Indices: 133443929--133443959 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
133443919 TTCTCTTTTA
133443929 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
133443941 TTTTTCTTTCTC
1 TTTTTCTTTCCC
133443953 TTTTTCT
1 TTTTTCT
133443960 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:133444060 original size:16 final size:16
Alignment explanation
Indices: 133444039--133444069 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
133444029 TTTATTATTT
133444039 TATTAACATAATATAA
1 TATTAACATAATATAA
*
133444055 TATTAATATAATATA
1 TATTAACATAATATA
133444070 TTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:133446988 original size:40 final size:39
Alignment explanation
Indices: 133446909--133447025 Score: 120
Period size: 40 Copynumber: 3.1 Consensus size: 39
133446899 GTGAAATGTA
* *
133446909 GGTATGGTATCATCCATACTAAGTTGTGAA---ATGTA-
1 GGTATGGTATCATCCATACTGAGTTGTGAATGTAGGTAT
133446944 GGTATGGTATCATCCATACTGAGTTGTGATATGTAGGTAT
1 GGTATGGTATCATCCATACTGAGTTGTGA-ATGTAGGTAT
**
133446984 GGTAT--TATCAAATCCATACTGAGTTAAGAAATGTAGGTAT
1 GGTATGGTATC--ATCCATACTGAGTTGTG-AATGTAGGTAT
133447024 GG
1 GG
133447026 CATTGCCCAT
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
35 28 0.40
36 1 0.01
38 4 0.06
39 4 0.06
40 32 0.46
41 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (39 bp):
GGTATGGTATCATCCATACTGAGTTGTGAATGTAGGTAT
Found at i:133447036 original size:35 final size:35
Alignment explanation
Indices: 133446898--133447051 Score: 155
Period size: 35 Copynumber: 4.3 Consensus size: 35
133446888 CATGGGAAAG
* *
133446898 TGTGAAATGTAGGTATGGTATCATCCATACTAAGT
1 TGTGAAATGTAGGTATGGTATCACCCATACTGAGT
*
133446933 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCACCCATACTGAGT
* *
133446968 TGTGATATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ACCCATACTGAGT
** * ** *
133447008 TAAGAAATGTAGGTATGGCATTGCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCACCCATACTGAGT
*
133447043 TGTAAAATG
1 TGTGAAATG
133447052 CAAGTATCGT
Statistics
Matches: 101, Mismatches: 13, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
35 67 0.66
37 2 0.02
38 4 0.04
40 28 0.28
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCACCCATACTGAGT
Found at i:133447036 original size:75 final size:70
Alignment explanation
Indices: 133446898--133447051 Score: 173
Period size: 75 Copynumber: 2.1 Consensus size: 70
133446888 CATGGGAAAG
** * *
133446898 TGTGAAATGTAGGTATGGTATCATCCATACTAAGTTGTGAAATGTAGGTATGGTATCATCCATAC
1 TGTGAAATGTAGGTATGGTATCATCCATACTAAGTTAAGAAATGTAGGTATGGCATCACCCATAC
*
133446963 TGAGT
66 CGAGT
* * **
133446968 TGTGATATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTGCC
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTAAGTTAAGAAATGTAGGTATGGCATCACC
133447033 CATACCGAGT
61 CATACCGAGT
*
133447043 TGTAAAATG
1 TGTGAAATG
133447052 CAAGTATCGT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
70 17 0.25
73 4 0.06
75 47 0.69
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (70 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTAAGTTAAGAAATGTAGGTATGGCATCACCCATAC
CGAGT
Found at i:133447064 original size:75 final size:74
Alignment explanation
Indices: 133446920--133447068 Score: 172
Period size: 75 Copynumber: 2.0 Consensus size: 74
133446910 GTATGGTATC
** * * * * * * * *
133446920 ATCCATACTAAGTTGTGAAATGTAGGTATGGTATCATCCATACTGAGTTGTGATATGTAGGTATG
1 ATCCATACTAAGTTAAGAAATGTAGGTATGGCATCACCCATACCGAGTTGTAAAATGCAAGTATC
133446985 GTATTATCAA
66 GTATT-TCAA
* **
133446995 ATCCATACTGAGTTAAGAAATGTAGGTATGGCATTGCCCATACCGAGTTGTAAAATGCAAGTATC
1 ATCCATACTAAGTTAAGAAATGTAGGTATGGCATCACCCATACCGAGTTGTAAAATGCAAGTATC
133447060 GTATTTCAA
66 GTATTTCAA
133447069 TGAAGAAAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
74 4 0.07
75 57 0.93
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33
Consensus pattern (74 bp):
ATCCATACTAAGTTAAGAAATGTAGGTATGGCATCACCCATACCGAGTTGTAAAATGCAAGTATC
GTATTTCAA
Found at i:133448923 original size:29 final size:29
Alignment explanation
Indices: 133448891--133448971 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 29
133448881 ACTGAATCTA
133448891 AAATTTAAAATTTAAAAAATAAAAAGACT
1 AAATTTAAAATTTAAAAAATAAAAAGACT
* * *
133448920 AAATTTTTAAAA-AT-AAAAGTATAAAGACT
1 AAA--TTTAAAATTTAAAAAATAAAAAGACT
*
133448949 AAATTTTAAATTTACGAAAAATA
1 AAATTTAAAATTTA--AAAAATA
133448972 TATAAACTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
27 6 0.15
28 1 0.03
29 19 0.47
30 1 0.03
31 13 0.32
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (29 bp):
AAATTTAAAATTTAAAAAATAAAAAGACT
Found at i:133452289 original size:3 final size:3
Alignment explanation
Indices: 133452269--133452361 Score: 65
Period size: 3 Copynumber: 32.7 Consensus size: 3
133452259 ACGCCCTTAG
* * * *
133452269 AAT AAT AAC AA- AATT AAT AAT AA- AAT AAG AAT TAT -AT AAT ATCT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
133452313 AA- AAG AAT AAT AAT AA- AAT AAT AAT AAT -AT AAT AAC AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
133452357 AAT AA
1 AAT AA
133452362 AGTAGCAACA
Statistics
Matches: 73, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
2 14 0.19
3 55 0.75
4 4 0.05
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:133452334 original size:11 final size:11
Alignment explanation
Indices: 133452269--133452362 Score: 82
Period size: 11 Copynumber: 8.1 Consensus size: 11
133452259 ACGCCCTTAG
*
133452269 AATAATAACAA
1 AATAATAATAA
133452280 AATTAATAATAA
1 AA-TAATAATAA
*
133452292 AATAAGAATTATA
1 AATAATAA-TA-A
*
133452305 TAATATCTAA-AA
1 -AATA-ATAATAA
133452317 GAATAATAATAA
1 -AATAATAATAA
133452329 AATAATAATAA
1 AATAATAATAA
* *
133452340 TATAATAACAA
1 AATAATAATAA
133452351 AATAATAATAA
1 AATAATAATAA
133452362 A
1 A
133452363 GTAGCAACAA
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
11 40 0.60
12 19 0.28
13 2 0.03
14 4 0.06
15 2 0.03
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (11 bp):
AATAATAATAA
Found at i:133452371 original size:22 final size:22
Alignment explanation
Indices: 133452327--133452374 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
133452317 GAATAATAAT
*
133452327 AAAATAATAATAATATAATAAC
1 AAAATAATAATAATATAACAAC
*
133452349 AAAATAATAATAA-AGTAGCAAC
1 AAAATAATAATAATA-TAACAAC
133452371 AAAA
1 AAAA
133452375 CAGCTAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (22 bp):
AAAATAATAATAATATAACAAC
Found at i:133475328 original size:381 final size:381
Alignment explanation
Indices: 133474712--133475600 Score: 1616
Period size: 381 Copynumber: 2.3 Consensus size: 381
133474702 AGAAAGCTTG
*
133474712 AGGACAGAATGAAGATGGCTGACGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
* *
133474777 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGCACGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACAA
**
133474842 ACAACTTGCAGAATCAGCAAAGGCAATCTTGAGTAAGGATGCTCTTTTGATTGACCAAGCTACCA
131 ACAACTTGCAGAATCAGCAAAGGCAATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
*
133474907 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAATCT
196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
133474972 TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCATGCTGCTGCTATTGAACAAAAGCT
261 TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCATGCTGCTGCTATTGAACAAAAGCT
*
133475037 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAATCTTA
326 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAAACTTA
*
133475093 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACCGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
133475158 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACAA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACAA
* *
133475223 ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
131 ACAACTTGCAGAATCAGCAAAGGCAATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
* *
133475288 TGATTGAAGAAGCAGAAACACGTATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
* **
133475353 TGCACTGAACTTCGCCAGAGGCTTCTGGAGGAGGAGCAGTGTGCTGCTGCTATTGAACAAAAGCT
261 TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCATGCTGCTGCTATTGAACAAAAGCT
* *
133475418 TGAAGATATGGTGGAGAATGACTTTTTGAAGACACAGGAGGAGCTGTCTAAACTTG
326 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAAACTTA
*
133475474 AGGACAGAATGAAGATGGCTGAAGATGACCTAAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
133475539 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGA
133475601 TGCTCTTCTA
Statistics
Matches: 489, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
381 489 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (381 bp):
AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACAA
ACAACTTGCAGAATCAGCAAAGGCAATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCATGCTGCTGCTATTGAACAAAAGCT
TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAAACTTA
Found at i:133478179 original size:222 final size:221
Alignment explanation
Indices: 133477899--133478458 Score: 823
Period size: 222 Copynumber: 2.5 Consensus size: 221
133477889 CCACTTAACC
*
133477899 GACTCTGGGAAAAAGCTTACCAATGCTTATGCTGTCCTTGATGGTTTAAAGAAAGAAATGACTTT
1 GACTCTGGGAAAAAGCTTACCAATGCTTATGCTGTCC-TGATGGTTTAAAGAAAGAAATGATTTT
* * *
133477964 TACAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCGGGAAAGTGAGTTGTCTTTTC
65 TGCAAAATTAGATGCATATTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTCTTTTC
* ** * * *
133478029 TCCAAGAAAAAGTTGAAGAAGCACAGGTTGAGCAAAGAATGTTGAAGAAAGAGAACTGTCTACTT
130 TACAAGAAAAAGTTGAAGAAGCACAAATTGAGCAAAGAAAGATGAAGAAAGAAAACTGTCTACTT
* * * *
133478094 CTCCAGGATTTGGAGGAGCAGAAAGCT
195 CTCCAGAATTTGGACGAGAAGAAAGCA
* *
133478121 GACTCTGGGAAAAAGCTTGCCAATGCTTATTCTGTCGCTGATGGTTTAAAGAAAGAAATGATTTT
1 GACTCTGGGAAAAAGCTTACCAATGCTTATGCTGTC-CTGATGGTTTAAAGAAAGAAATGATTTT
* *
133478186 TGCAAAATTAGATGCATACTTGAAAGGGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTCTTTTC
65 TGCAAAATTAGATGCATATTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTCTTTTC
** *
133478251 TACAAGAAAAAGTTGAAGAAGCACAAATTGAGTTAAGAAAGATGAAGAAAGAAAACTGTCTGCTT
130 TACAAGAAAAAGTTGAAGAAGCACAAATTGAGCAAAGAAAGATGAAGAAAGAAAACTGTCTACTT
*
133478316 CTCCAGAATTTGGACGAGAAGGAAGCA
195 CTCCAGAATTTGGACGAGAAGAAAGCA
* * * * *
133478343 GACACCGGAAAAAAGCTTACCAATGCTTATGCTGTCATTGATGGTTTAAAGAAAGAAATAATTTT
1 GACTCTGGGAAAAAGCTTACCAATGCTTATGCTGTC-CTGATGGTTTAAAGAAAGAAATGATTTT
* * *
133478408 TGCAAAAGTAGATGCATTTTTGAAAGAGCAGCTATTGGAGGAGCAGGAAAG
65 TGCAAAATTAGATGCATATTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAG
133478459 GATATCAAAG
Statistics
Matches: 302, Mismatches: 35, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
222 301 1.00
223 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (221 bp):
GACTCTGGGAAAAAGCTTACCAATGCTTATGCTGTCCTGATGGTTTAAAGAAAGAAATGATTTTT
GCAAAATTAGATGCATATTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTCTTTTCT
ACAAGAAAAAGTTGAAGAAGCACAAATTGAGCAAAGAAAGATGAAGAAAGAAAACTGTCTACTTC
TCCAGAATTTGGACGAGAAGAAAGCA
Found at i:133491338 original size:33 final size:31
Alignment explanation
Indices: 133491292--133491377 Score: 75
Period size: 31 Copynumber: 2.7 Consensus size: 31
133491282 CTGTTTGATC
*
133491292 CACTTATTT-TTAATATTTGGTACATGAACTTAA
1 CACTT-TTTCTTAAT-TTT-GTACATAAACTTAA
* * *
133491325 CACTTTTTCTTAATTTTGTACTTAAATTTGA
1 CACTTTTTCTTAATTTTGTACATAAACTTAA
* * *
133491356 CAGTTTTTCTTAAGTTGGTACA
1 CACTTTTTCTTAATTTTGTACA
133491378 ATTTGGTACA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 28 0.64
32 6 0.14
33 10 0.23
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (31 bp):
CACTTTTTCTTAATTTTGTACATAAACTTAA
Found at i:133491922 original size:60 final size:60
Alignment explanation
Indices: 133491840--133491977 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
133491830 AAGCTTAGGG
* *
133491840 ACCAAATTAAGAAAAAAATGTCAAGTTCAGGAA-CTAAACTGGGCTAAA-AAAAGGTTTAGAT
1 ACCAAATT-AGAAAAAAATGTCAAGTTCAAGAATC-AAACTGGGCCAAATAAAA-GTTTAGAT
* * * * *
133491901 ACCAAATTAGGAAAAAGTGTCAAGTTCAAGTATCAAATTGGGCCAAATAAAAGTTTATAT
1 ACCAAATTAGAAAAAAATGTCAAGTTCAAGAATCAAACTGGGCCAAATAAAAGTTTAGAT
*
133491961 GCCAAATTAGAAAAAAA
1 ACCAAATTAGAAAAAAA
133491978 ACCAAGTTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
60 52 0.80
61 13 0.20
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (60 bp):
ACCAAATTAGAAAAAAATGTCAAGTTCAAGAATCAAACTGGGCCAAATAAAAGTTTAGAT
Found at i:133497066 original size:66 final size:66
Alignment explanation
Indices: 133496960--133497152 Score: 275
Period size: 66 Copynumber: 3.0 Consensus size: 66
133496950 TGAAGACAAC
* * *
133496960 GATGATTCTGCATCCATGAATGCTGAAAGTGCAAAGGGAGAAGTGAAAGAAGAGGAAAAGGAGGA
1 GATGATTCTGAATCCATGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGA
133497025 A
66 A
* *
133497026 GATGATTCTGTATCCATGAATGCTGAAAGTGCAAAGGGAGAAGAGAATGAAGAGGAAAAGGAAGA
1 GATGATTCTGAATCCATGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGA
133497091 A
66 A
** * * *
133497092 GATGATTCTGAATCTTTAAATGCTGAAAATTCAAA---AGAAGAGAAAGAAGAGGAAAAGGAAG
1 GATGATTCTGAATCCATGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAG
133497153 GGGAGCAGGA
Statistics
Matches: 116, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
63 25 0.22
66 91 0.78
ACGTcount: A:0.45, C:0.08, G:0.30, T:0.17
Consensus pattern (66 bp):
GATGATTCTGAATCCATGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGA
A
Found at i:133509811 original size:28 final size:28
Alignment explanation
Indices: 133509771--133509826 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
133509761 ATAGAAAAAC
133509771 AACTTTGTATAAACTAACAAGTTGCTTT
1 AACTTTGTATAAACTAACAAGTTGCTTT
133509799 AACTTTGTATAAACTAACAAGTTGCTTT
1 AACTTTGTATAAACTAACAAGTTGCTTT
133509827 GCCTTATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (28 bp):
AACTTTGTATAAACTAACAAGTTGCTTT
Found at i:133510133 original size:18 final size:20
Alignment explanation
Indices: 133510099--133510149 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
133510089 AAAATTACAA
133510099 AAAAATTT-AAATAATTT-T
1 AAAAATTTAAAATAATTTAT
*
133510117 TAAAATTTAAAAT-ATTTAT
1 AAAAATTTAAAATAATTTAT
133510136 AAAAATTTCAAAAT
1 AAAAATTT-AAAAT
133510150 TTATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.39
19 12 0.43
20 5 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTTAAAATAATTTAT
Found at i:133510133 original size:27 final size:27
Alignment explanation
Indices: 133510098--133510152 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
133510088 AAAAATTACA
* *
133510098 AAAAAATTTA-AATAATTTTTAAAATTT
1 AAAAAATTTATAA-AAATTTCAAAATTT
*
133510125 AAAATATTTATAAAAATTTCAAAATTT
1 AAAAAATTTATAAAAATTTCAAAATTT
133510152 A
1 A
133510153 TATTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAAAATTTATAAAAATTTCAAAATTT
Found at i:133510151 original size:18 final size:18
Alignment explanation
Indices: 133510099--133510185 Score: 70
Period size: 18 Copynumber: 4.7 Consensus size: 18
133510089 AAAATTACAA
133510099 AAAAATTTAAATAATTT-T
1 AAAAATTTAAA-AATTTAT
*
133510117 TAAAATTTAAAATATTTAT
1 AAAAATTTAAAA-ATTTAT
*
133510136 AAAAATTTCAAAATTTAT
1 AAAAATTTAAAAATTTAT
*** *
133510154 -ATTTTTTAAAAAAATTAT
1 AAAAATTT-AAAAATTTAT
133510172 AAAAATTTTAAAAA
1 AAAAA-TTTAAAAA
133510186 AATTCTAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
17 5 0.09
18 28 0.53
19 17 0.32
20 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAAATTTAAAAATTTAT
Found at i:133510151 original size:36 final size:36
Alignment explanation
Indices: 133510099--133510185 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
133510089 AAAATTACAA
* * *
133510099 AAAAATTTAAATAATTTTTAAAATTTAAAATATTTAT
1 AAAAATTTAAA-AATTTATAAAATTTAAAAAAATTAT
* ***
133510136 AAAAATTTCAAAATTTATATTTTTTAAAAAAATTAT
1 AAAAATTTAAAAATTTATAAAATTTAAAAAAATTAT
133510172 AAAAATTTTAAAAA
1 AAAAA-TTTAAAAA
133510186 AATTCTAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
36 24 0.59
37 17 0.41
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
AAAAATTTAAAAATTTATAAAATTTAAAAAAATTAT
Found at i:133512495 original size:14 final size:13
Alignment explanation
Indices: 133512457--133512500 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
133512447 TTTCACTTTG
*
133512457 TTTTTTTATGAAT
1 TTTTTTTATGATT
*
133512470 TTTTTATATGATT
1 TTTTTTTATGATT
133512483 TTTTTTTCATGATCT
1 TTTTTTT-ATGAT-T
133512498 TTT
1 TTT
133512501 CTCTTTGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 17 0.65
14 5 0.19
15 4 0.15
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTTTTATGATT
Found at i:133512518 original size:2 final size:2
Alignment explanation
Indices: 133512511--133512549 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
133512501 CTCTTTGGAT
133512511 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
133512550 TTACACAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:133513121 original size:26 final size:26
Alignment explanation
Indices: 133513092--133513170 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 26
133513082 AAAATAACTC
133513092 TTCAATTTTTATAAAATAAAAAAAAA
1 TTCAATTTTTATAAAATAAAAAAAAA
* * * *
133513118 TTCACA-TGTCAAAATAATAAAAAAAAT
1 TTCA-ATTTTTATAA-AATAAAAAAAAA
* *
133513145 TCTCAATATTTATAAAATTAAAAAAA
1 T-TCAATTTTTATAAAATAAAAAAAA
133513171 TCAAATTAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
26 9 0.22
27 24 0.60
28 7 0.17
ACGTcount: A:0.59, C:0.08, G:0.01, T:0.32
Consensus pattern (26 bp):
TTCAATTTTTATAAAATAAAAAAAAA
Found at i:133516665 original size:46 final size:44
Alignment explanation
Indices: 133516580--133516666 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 44
133516570 TACAAAAATA
133516580 GGAAGATAGAAAATATAAAATTTCTTTCCATAATTTTGTTTGGTT
1 GGAAGATAGAAAATATAAAATTTCTTTCCAT-ATTTTGTTTGGTT
*
133516625 GGAATGATAGAAAA-ATTATAATTTTCTTTCCAT-TTATTGTTT
1 GGAA-GATAGAAAATA-TA-AAATTTCTTTCCATATT-TTGTTT
133516667 AGCAGATTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
45 7 0.19
46 17 0.46
47 13 0.35
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (44 bp):
GGAAGATAGAAAATATAAAATTTCTTTCCATATTTTGTTTGGTT
Found at i:133520518 original size:31 final size:30
Alignment explanation
Indices: 133520461--133520518 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
133520451 ACGATTTAAT
*
133520461 TTGAATTTTAAAAACTAAAAAGTAGAGGGA
1 TTGAATTTTAAAAACTAAAAAATAGAGGGA
* *
133520491 TTGAATTTTTAAAATTAAAAATATAGAG
1 TTGAATTTTAAAAACTAAAAA-ATAGAG
133520519 ACTAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.33
Consensus pattern (30 bp):
TTGAATTTTAAAAACTAAAAAATAGAGGGA
Found at i:133529338 original size:19 final size:19
Alignment explanation
Indices: 133529310--133529346 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
133529300 TCAATTTTGA
133529310 AAAAACTTATTTTAGTATTT
1 AAAAACTTATTTTA-TATTT
133529330 AAAAA-TTATTTTATATT
1 AAAAACTTATTTTATATT
133529347 AATATTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
AAAAACTTATTTTATATTT
Found at i:133531628 original size:3 final size:3
Alignment explanation
Indices: 133531620--133531667 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
133531610 CTTTCTTTCT
** * *
133531620 TTC TTC TTC TTC TTC TTC TAG ATC TTC TTC TTC TTC TTC TTC TAC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
133531668 CTTTACAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.06, C:0.31, G:0.02, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:133533153 original size:207 final size:205
Alignment explanation
Indices: 133532797--133533359 Score: 753
Period size: 207 Copynumber: 2.7 Consensus size: 205
133532787 GCTCAGCCGA
* * *
133532797 AAAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAACCATTATCTGGGTTTGGTACCATT
1 AAAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCATTATCCGGGTTTGGTACCGTT
* *
133532862 CATTCGTATGATAAAAGTG--TGTGTTTTTAGTAGTCGAGGTGTCCGTTTATTCTAGGAAATAAA
66 CATTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGT-CG-TTATTCTAGGAAATAAA
* * *
133532925 CGACATTGTTGTGATAATTATAGCCTGTTAACCAATTCGGTGTTTTC-TTTTACCAGCTTGTACT
129 GGACGTTGTTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTTACCAGCTTGTACT
133532989 TACGGCTTAACCC
194 TACGGCTTAA-CC
*** *
133533002 CCCAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCGTT
1 AAAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCATTATCCGGGTTTGGTACCGTT
133533067 CATTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCAGATTATTCTAGGAAATAAA
66 CATTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTC-G-TTATTCTAGGAAATAAA
* **
133533132 GGACGTTGTTGTGATAATTATAGCCTGTTAACTAATACGGTGTTTTCTTTTATTTTACTGGCTTG
129 GGACGTTGTTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTC---T-TTTTACCAGCTTG
*
133533197 TACTTATGGCTTAACC
190 TACTTACGGCTTAACC
* * * *
133533213 AAAAAAAAAAAGAAATGGTTTGTGTTGTAGTTGATTGCGAATCATTATCCGGGTTTGGTATCG-G
1 AAAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCATTATCCGGGTTTGGTACCGTT
* * * *
133533277 CATTCACATGATAAAAGTGTTTGTGTTTTTTGCTAGTCGAGGTATC--CATT-TAGGAAATAAAG
66 CATTCATATGATAAAAGTGTTTGTG-TTTTTGGTAGTCGAGGTGTCGTTATTCTAGGAAATAAAG
* *
133533339 GATGTTGTTGCGATAATTATA
130 GACGTTGTTGTGATAATTATA
133533360 ATGATGAATT
Statistics
Matches: 318, Mismatches: 31, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
205 76 0.24
206 32 0.10
207 86 0.27
210 24 0.08
211 76 0.24
212 24 0.08
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (205 bp):
AAAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCATTATCCGGGTTTGGTACCGTT
CATTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCGTTATTCTAGGAAATAAAGG
ACGTTGTTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTTACCAGCTTGTACTTA
CGGCTTAACC
Found at i:133542504 original size:22 final size:24
Alignment explanation
Indices: 133542457--133542517 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 24
133542447 GTAGCGAGGA
*
133542457 AAGAA-AGGAGAGAAGCGAGAGTG
1 AAGAAGAGGAGAGAAGCGAGAGCG
*
133542480 AAGAAGAGGAGAGGAGC-AG-GCG
1 AAGAAGAGGAGAGAAGCGAGAGCG
* *
133542502 AAGAAGATGAAAGAAG
1 AAGAAGAGGAGAGAAG
133542518 AGAAGATGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 15 0.47
23 7 0.22
24 10 0.31
ACGTcount: A:0.49, C:0.05, G:0.43, T:0.03
Consensus pattern (24 bp):
AAGAAGAGGAGAGAAGCGAGAGCG
Found at i:133543353 original size:5 final size:5
Alignment explanation
Indices: 133543343--133543367 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
133543333 TAAATTTCTA
133543343 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
133543368 TATATATCTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:133545906 original size:35 final size:35
Alignment explanation
Indices: 133545860--133545931 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
133545850 TGTTCTTAAC
133545860 CAGGCTGAAATATTACTTTTGATTTACAATTAAGG
1 CAGGCTGAAATATTACTTTTGATTTACAATTAAGG
133545895 CAGGCTGAAATATTACTTTTGATTTACAATTAAGG
1 CAGGCTGAAATATTACTTTTGATTTACAATTAAGG
133545930 CA
1 CA
133545932 TATGAAATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (35 bp):
CAGGCTGAAATATTACTTTTGATTTACAATTAAGG
Found at i:133547831 original size:30 final size:30
Alignment explanation
Indices: 133547795--133547854 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
133547785 GTTGCTAATG
133547795 CGATAAGAGGTGGTTTGGTTCGTCGAATCT
1 CGATAAGAGGTGGTTTGGTTCGTCGAATCT
133547825 CGATAAGAGGTGGTTTGGTTCGTCGAATCT
1 CGATAAGAGGTGGTTTGGTTCGTCGAATCT
133547855 TACATTCTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (30 bp):
CGATAAGAGGTGGTTTGGTTCGTCGAATCT
Found at i:133548621 original size:19 final size:19
Alignment explanation
Indices: 133548572--133548621 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
133548562 ATATATAAAC
*
133548572 AAAACATGAAAAATAGTTT
1 AAAACATGAAAAATAGTTA
* *
133548591 AAAGCATTAAAAATA-TATA
1 AAAACATGAAAAATAGT-TA
133548610 AAAACATGAAAA
1 AAAACATGAAAA
133548622 TCTCTTTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAACATGAAAAATAGTTA
Found at i:133549901 original size:96 final size:96
Alignment explanation
Indices: 133549733--133549920 Score: 241
Period size: 96 Copynumber: 2.0 Consensus size: 96
133549723 AAACTAAACT
* * * * * *
133549733 GATACTCTCAGTAGACCGGAAGCTTGCATTTTTCACATCCTCCGATTCTTTCCTAGACAAAACGG
1 GATACTCTCAGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCTAGACAAAACAG
*
133549798 CACAATTCAACTCGTGAACCAAAACCGAACC
66 CAAAATTCAACTCGTGAACCAAAACCGAACC
* * * * * *
133549829 GATACTCTCGGTAGACCGAAAACTTGCACTCTGCACATCCTCTGGTTCTTTCCTATACAGAACAT
1 GATACTCTCAGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCTAGACAAAACAG
* *
133549894 CAAAATTCAACTCGTGAGCCGAAACCG
66 CAAAATTCAACTCGTGAACCAAAACCG
133549921 GTCTTCTCCT
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 77 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.24
Consensus pattern (96 bp):
GATACTCTCAGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCTAGACAAAACAG
CAAAATTCAACTCGTGAACCAAAACCGAACC
Found at i:133550118 original size:120 final size:123
Alignment explanation
Indices: 133549819--133550212 Score: 501
Period size: 123 Copynumber: 3.2 Consensus size: 123
133549809 TCGTGAACCA
* * * * *
133549819 AAACCGAACCGATACTCTCGGTAGACCGAAAACTTGCACTCTGCACATCCTCTGGTTCTTTCCTA
1 AAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCCA
*
133549884 TACAGAACATCAAAATTCAACTCGTGAGCCGAAACCGGTCTTCTCCTCCTCGAGT-TAG
66 TACAAAACATCAAAATTCAACTCGTGAGCCGAAACCGGTC-TCTCCTCCTCGAGTCTAG
* * * * * * *
133549942 AAACCAAACCGATACTCTCACTAGACCGAAAGCTTACATTTTTTACATCCTTCGGTTCTTTCCCA
1 AAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCCA
* * * * *
133550007 TGCAAAACAGCACAATTCAGCTCGTGAGCCGAATCCGGTC-CT-CTCCTCG-GTCTAG
66 TACAAAACATCAAAATTCAACTCGTGAGCCGAAACCGGTCTCTCCTCCTCGAGTCTAG
* *
133550062 AAACCGAACCGATGCTCTCAGTAGACCGAAAACTTGCATTCTTCACGTCCTCCGGTTCTTTCCCA
1 AAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCCA
** *
133550127 TACAAAACATCATGATTCAACTCGTGAGCCGAAACCGGTCCTCTCCTCCTCGAG-CTCG
66 TACAAAACATCAAAATTCAACTCGTGAGCCGAAACCGGT-CTCTCCTCCTCGAGTCTAG
** *
133550185 AAACCGAACCGACGCTCTCAGTGGACCG
1 AAACCGAACCGATACTCTCAGTAGACCG
133550213 GAAGCTTACA
Statistics
Matches: 230, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
119 2 0.01
120 99 0.43
121 3 0.01
122 2 0.01
123 123 0.53
124 1 0.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (123 bp):
AAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCCA
TACAAAACATCAAAATTCAACTCGTGAGCCGAAACCGGTCTCTCCTCCTCGAGTCTAG
Found at i:133550943 original size:7 final size:7
Alignment explanation
Indices: 133550931--133550975 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
133550921 AATGCAATAC
133550931 TCAACAG
1 TCAACAG
133550938 TCAACAG
1 TCAACAG
133550945 TCAACAG
1 TCAACAG
*
133550952 TCAATAG
1 TCAACAG
*
133550959 TCAATAG
1 TCAACAG
*
133550966 TCAATAG
1 TCAACAG
133550973 TCA
1 TCA
133550976 TGGATGCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.22
Consensus pattern (7 bp):
TCAACAG
Found at i:133550950 original size:14 final size:14
Alignment explanation
Indices: 133550925--133550975 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
133550915 TTTTATAATG
*
133550925 CAATACTCAACAGT
1 CAATAGTCAACAGT
*
133550939 CAACAGTCAACAGT
1 CAATAGTCAACAGT
*
133550953 CAATAGTCAATAGT
1 CAATAGTCAACAGT
133550967 CAATAGTCA
1 CAATAGTCA
133550976 TGGATGCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.22
Consensus pattern (14 bp):
CAATAGTCAACAGT
Found at i:133551586 original size:21 final size:20
Alignment explanation
Indices: 133551562--133551613 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
133551552 TTTTAAATGC
133551562 AATATTAAAAAATTAGATAAA
1 AATATTAAAAAA-TAGATAAA
* *
133551583 AATATTTAAAAAATAGTTTAA
1 AATA-TTAAAAAATAGATAAA
133551604 AATATTAAAA
1 AATATTAAAA
133551614 TCTTGTACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 14 0.50
22 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AATATTAAAAAATAGATAAA
Found at i:133559527 original size:11 final size:11
Alignment explanation
Indices: 133559463--133559536 Score: 51
Period size: 12 Copynumber: 6.4 Consensus size: 11
133559453 ATTCCAGACA
*
133559463 ATTTAAAAATT
1 ATTTAAAAAAT
133559474 ATTCTTAATAAAAT
1 A-T-TTAA-AAAAT
*
133559488 ATAATAAAAAAT
1 AT-TTAAAAAAT
* * *
133559500 ATTTTACAATT
1 ATTTAAAAAAT
133559511 ATTTTAAAAAAT
1 A-TTTAAAAAAT
133559523 ATTT-AAAAAT
1 ATTTAAAAAAT
133559533 ATTT
1 ATTT
133559537 TTACACCACA
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
10 10 0.20
11 10 0.20
12 16 0.33
13 8 0.16
14 5 0.10
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (11 bp):
ATTTAAAAAAT
Found at i:133559532 original size:10 final size:11
Alignment explanation
Indices: 133559494--133559537 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
133559484 AAATATAATA
133559494 AAAAATATTTT
1 AAAAATATTTT
* *
133559505 ACAATTATTTT
1 AAAAATATTTT
133559516 AAAAA-ATATTT
1 AAAAATAT-TTT
133559527 AAAAATATTTT
1 AAAAATATTTT
133559538 TACACCACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:133559539 original size:23 final size:23
Alignment explanation
Indices: 133559492--133559537 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
133559482 TAAAATATAA
* *
133559492 TAAAAAATATTTTACAATTATTT
1 TAAAAAATATTTAAAAATTATTT
133559515 TAAAAAATATTTAAAAA-TATTT
1 TAAAAAATATTTAAAAATTATTT
133559537 T
1 T
133559538 TACACCACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAAAATATTTAAAAATTATTT
Found at i:133559803 original size:90 final size:93
Alignment explanation
Indices: 133559648--133559898 Score: 264
Period size: 93 Copynumber: 2.7 Consensus size: 93
133559638 ACTCAAAGCT
* * * * * **
133559648 CAAGTGCTCCAAAAGTGAAATAAAATAAATAATAATTTTAACAGTTA-TCCCGAAAATTTTCAAA
1 CAAGTGCTCCAAAAATGAAATATAATAAATAATAATTTTTATAATTATTCCCGAAAATTTAAAAA
133559712 AA-AAAATTGGAC-ACTATACTAAAATC-
66 AATAAAATTGGACGACTATACTAAAA-CA
*
133559738 CAAGTGCTCCAAAAATGAAATATAATAAATAATAATTTTTATAATTATTCCGGAAAA-TTAAAAA
1 CAAGTGCTCCAAAAATGAAATATAATAAATAATAATTTTTATAATTATTCCCGAAAATTTAAAAA
* ** * * *
133559802 AATTATTTTTGACGTGCTATACTCAAACA
66 AATAAAATTGGACG-ACTATACTAAAACA
* * * *
133559831 CAAGTGC-CCTAAAAATAAAATATATTAAATAATAATTTTTATAATTA-TCTCGAAAATTTTAAA
1 CAAGTGCTCC-AAAAATGAAATATAATAAATAATAATTTTTATAATTATTCCCGAAAATTTAAAA
133559894 AAATA
65 AAATA
133559899 TTTTTACACC
Statistics
Matches: 134, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
90 49 0.37
91 14 0.10
92 10 0.07
93 61 0.46
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (93 bp):
CAAGTGCTCCAAAAATGAAATATAATAAATAATAATTTTTATAATTATTCCCGAAAATTTAAAAA
AATAAAATTGGACGACTATACTAAAACA
Found at i:133559852 original size:93 final size:92
Alignment explanation
Indices: 133559567--133559903 Score: 284
Period size: 91 Copynumber: 3.7 Consensus size: 92
133559557 TTAAGCGCCT
* * * * ***
133559567 AAAAATAAAATATAATAAATAACAAATTTTACAATTATCTCGAAATGTTTTAAAAAAA-ATTGCA
1 AAAAATAAAATATAATAAATAATAATTTTTATAATTATCTCGAAA--ATTTAAAAAAATATTTTT
* * *
133559631 G-CAT-C-ATACTCAAAGCTCAAGTGCTCC
64 GACGTGCTATACTAAAATC-CAAGTGCTCC
* * * * * * * * *
133559658 AAAAGTGAAATAAAATAAATAATAATTTTAACAGTTATCCCGAAAATTTTCAAAAAAA-A-ATTG
1 AAAAATAAAATATAATAAATAATAATTTTTATAATTATCTCGAAAA-TTT-AAAAAAATATTTTT
*
133559721 GAC--ACTATACTAAAATCCAAGTGCTCC
64 GACGTGCTATACTAAAATCCAAGTGCTCC
*
133559748 AAAAATGAAATATAATAAATAATAATTTTTATAATTAT-TCCGGAAAA-TTAAAAAAATTATTTT
1 AAAAATAAAATATAATAAATAATAATTTTTATAATTATCT-C-GAAAATTTAAAAAAA-TATTTT
*
133559811 TGACGTGCTATACTCAAA-CACAAGTGC-CC
63 TGACGTGCTATACTAAAATC-CAAGTGCTCC
* *
133559840 TAAAAATAAAATATATTAAATAATAATTTTTATAATTATCTCGAAAATTTTAAAAAATATTTTT
1 -AAAAATAAAATATAATAAATAATAATTTTTATAATTATCTCGAAAATTTAAAAAAATATTTTT
133559904 ACACCACTAT
Statistics
Matches: 202, Mismatches: 28, Indels: 31
0.77 0.11 0.12
Matches are distributed among these distances:
88 7 0.03
89 2 0.01
90 50 0.25
91 65 0.32
92 15 0.07
93 62 0.31
94 1 0.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (92 bp):
AAAAATAAAATATAATAAATAATAATTTTTATAATTATCTCGAAAATTTAAAAAAATATTTTTGA
CGTGCTATACTAAAATCCAAGTGCTCC
Found at i:133560399 original size:94 final size:93
Alignment explanation
Indices: 133560255--133560498 Score: 260
Period size: 94 Copynumber: 2.6 Consensus size: 93
133560245 GTGCCTCAAT
** * * * * *
133560255 AATGAAATATTAA-AAATAATTTTTTTTACAGTTATCTTAGAATATATAAAAAATTTATTTTTGC
1 AATGAAATA-TAATAAATAATAATTTTTACAGTTATCTTAAAAAATTTAAAAAATATATTTTTAC
* * *
133560319 AACAAC-ATACTCAAACCCAAGTTCTCCGGA
65 -ACAACAATACTC-AACCCAAATGCTCCGAA
* *
133560349 AATGAAATATAATAAATAATAAATTTTACAGTTATCTCAAAAAATTTAAAAAAATATATTTTTAC
1 AATGAAATATAATAAATAATAATTTTTACAGTTATCTTAAAAAATTT-AAAAAATATATTTTTAC
* ** *
133560414 ACAACAATCCTCTGCCCAAATGCTTCGAA
65 ACAACAATACTCAACCCAAATGCTCCGAA
**
133560443 AATGAAATATAATAAATAATAATTTTTACAACTATCCTTAAAAAA-TTAAAAAATAT
1 AATGAAATATAATAAATAATAATTTTTACAGTTAT-CTTAAAAAATTTAAAAAATAT
133560499 CACCACCATA
Statistics
Matches: 126, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
93 12 0.10
94 86 0.68
95 28 0.22
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (93 bp):
AATGAAATATAATAAATAATAATTTTTACAGTTATCTTAAAAAATTTAAAAAATATATTTTTACA
CAACAATACTCAACCCAAATGCTCCGAA
Found at i:133560845 original size:16 final size:17
Alignment explanation
Indices: 133560805--133560846 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
133560795 GCAATTAAGG
133560805 TTAGGGTTTTGGAAATT
1 TTAGGGTTTTGGAAATT
* *
133560822 TT-GAGTTTT-TAAATT
1 TTAGGGTTTTGGAAATT
133560837 TTAGGGTTTT
1 TTAGGGTTTT
133560847 AAGGAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.33
16 12 0.57
17 2 0.10
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (17 bp):
TTAGGGTTTTGGAAATT
Found at i:133560960 original size:96 final size:96
Alignment explanation
Indices: 133560836--133561038 Score: 243
Period size: 96 Copynumber: 2.1 Consensus size: 96
133560826 GTTTTTAAAT
* * ** *
133560836 TTTAGGG-TTTTAAGGAAAAAAATTAAATAAATTAAGGTTTAATGTTTGTTAATTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAAATCAAATAAATTAAGGTTTAAGGTTACTTAAGTAAATTAATTA
* *
133560900 CTAATTTTAAAAAAA-TAGATTATGG-TTTAGTG
66 -TAA-ATTAAAAAAATTAGATTA-GGATTTAGGG
* * * *
133560932 TTTATGGTTTTTAAGG-AAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAAATCAAATAAATTAAGGTTTAAGGTTACTTAAGTAAATTAATTA
133560996 TAAATTAAAAAAATTAGATTAGGATTTTAGGG
66 TAAATTAAAAAAATTAGATTAGGA-TTTAGGG
133561028 TTTAGGGTTTT
1 TTTAGGGTTTT
133561039 AGGGTATTTA
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
94 11 0.12
95 10 0.11
96 62 0.68
97 8 0.09
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.41
Consensus pattern (96 bp):
TTTAGGGTTTTTAAGGAAAAAAATCAAATAAATTAAGGTTTAAGGTTACTTAAGTAAATTAATTA
TAAATTAAAAAAATTAGATTAGGATTTAGGG
Found at i:133561038 original size:15 final size:15
Alignment explanation
Indices: 133561014--133561043 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
133561004 AAAAATTAGA
133561014 TTAGGATTTTAGGGT
1 TTAGGATTTTAGGGT
*
133561029 TTAGGGTTTTAGGGT
1 TTAGGATTTTAGGGT
133561044 ATTTAAGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (15 bp):
TTAGGATTTTAGGGT
Found at i:133561344 original size:126 final size:126
Alignment explanation
Indices: 133561127--133561399 Score: 449
Period size: 126 Copynumber: 2.2 Consensus size: 126
133561117 AAAAGCTTCT
*
133561127 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCACAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAAATTTGAGAAGACGTGTCTGCACAA
* *
133561192 ATAGTGTCAAAAATGCTTCAAACAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAACAGGATGCATTGTCAGCAAAAGTACTGAAAGAAACTCCC
* **
133561253 ACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAAATTTGAGAAGACGTGTCTGCACAA
* *
133561318 ATAGTGT-AAAAAGCGCTTCAATCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAACTTCC
66 ATAGTGTCAAAAA-CGCTTCAAACAGGATGCATTGTCAGCAAAAGTACTGAAAGAAACTCCC
*
133561379 ACGTGGATGCTCTTTTGCTAC
1 ACGTGGACGCTCTTTTGCTAC
133561400 TAGCATTGTC
Statistics
Matches: 137, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 5 0.04
126 132 0.96
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAAATTTGAGAAGACGTGTCTGCACAA
ATAGTGTCAAAAACGCTTCAAACAGGATGCATTGTCAGCAAAAGTACTGAAAGAAACTCCC
Found at i:133561432 original size:56 final size:56
Alignment explanation
Indices: 133561346--133561455 Score: 220
Period size: 56 Copynumber: 2.0 Consensus size: 56
133561336 CAATCAGGAT
133561346 GCATTGTCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACTA
1 GCATTGTCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACTA
133561402 GCATTGTCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTAC
1 GCATTGTCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTAC
133561456 AGTAGTCTCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (56 bp):
GCATTGTCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACTA
Found at i:133561484 original size:56 final size:56
Alignment explanation
Indices: 133561352--133561474 Score: 167
Period size: 56 Copynumber: 2.2 Consensus size: 56
133561342 GGATGCATTG
* * * *
133561352 TCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACTAGCATTG
1 TCAGAAAAAATACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACTAGCAGTC
* * *
133561408 TCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTAC-AGTAGTC
1 TCAGAAAAAATACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACTAGCAGTC
*
133561463 TCTGAAAAAATA
1 TCAGAAAAAATA
133561475 ATTTTAAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
55 13 0.21
56 48 0.79
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (56 bp):
TCAGAAAAAATACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACTAGCAGTC
Found at i:133561532 original size:182 final size:182
Alignment explanation
Indices: 133561220--133561581 Score: 564
Period size: 182 Copynumber: 2.0 Consensus size: 182
133561210 CAAACAGGAT
*
133561220 GCATTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTG
1 GCATTGTCAGCAAAAGTACTGAAAGAAACTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTG
* * * * *
133561285 AAAAAATAATTTTGAGAAGACGTGTCTGTGCAAATAGTGTAAAAAGCGCTTCAATCAGGATGCAT
66 AAAAAATAATTTTAAGAAGACGTGTCTGCGCAAATAGTGTAAAAAGCACTTCAAGCAGAATGCAT
*
133561350 TGTCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACTA
131 TGTCAGCAAAAGTACTGAAAGAAACTCCCACGTGGATGCTCTTTTGCTACTA
* * *
133561402 GCATTGTCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACAGTAGTCTCTG
1 GCATTGTCAGCAAAAGTACTGAAAGAAACTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTG
* *
133561467 AAAAAATAATTTTAAGAAGATGTGTCTGCGCAAATAGTGGTAAAGA-CACTTCAAGCAGAATGCA
66 AAAAAATAATTTTAAGAAGACGTGTCTGCGCAAATAGT-GTAAAAAGCACTTCAAGCAGAATGCA
* * * *
133561531 TTTTCAGCAAAATTACTGGAAGAAGCTCCCACGTGGATGCTCTTTTGCTAC
130 TTGTCAGCAAAAGTACTGAAAGAAACTCCCACGTGGATGCTCTTTTGCTAC
133561582 AGTGGTTTCT
Statistics
Matches: 163, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
182 157 0.96
183 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (182 bp):
GCATTGTCAGCAAAAGTACTGAAAGAAACTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTG
AAAAAATAATTTTAAGAAGACGTGTCTGCGCAAATAGTGTAAAAAGCACTTCAAGCAGAATGCAT
TGTCAGCAAAAGTACTGAAAGAAACTCCCACGTGGATGCTCTTTTGCTACTA
Found at i:133561628 original size:126 final size:126
Alignment explanation
Indices: 133561402--133561721 Score: 489
Period size: 126 Copynumber: 2.5 Consensus size: 126
133561392 TTTGCTACTA
* * * * *
133561402 GCATTGTCAGCAAAAGTACTGAAAGAAACTTCCACGTGGATGCTCTTTTGCTACAGTAGTCTCTG
1 GCATTTTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGATGCTCTTTTGCTACAGTGGTTTCTG
* * *
133561467 AAAAAATAATTTTAAGAAGATGTGTCTGCGCAAATAGTGGT-AAAGACACTTCAAGCAGAAT
66 AAAAAATAATTTTAAGAAGACGTGTCTGCACAAATAGT-GTCAAAAACACTTCAAGCAGAAT
* *
133561528 GCATTTTCAGCAAAATTACTGGAAGAAGCTCCCACGTGGATGCTCTTTTGCTACAGTGGTTTCTG
1 GCATTTTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGATGCTCTTTTGCTACAGTGGTTTCTG
* * * *
133561593 AAAAAATAATTTTGAGAAGACGTGTCTGCATAAATAGTGTCAAAAACGCTTCAAGCAGGAT
66 AAAAAATAATTTTAAGAAGACGTGTCTGCACAAATAGTGTCAAAAACACTTCAAGCAGAAT
*
133561654 GCATTTTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGACGCTCTTTTGCTACAGTGGTTTCTG
1 GCATTTTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGATGCTCTTTTGCTACAGTGGTTTCTG
133561719 AAA
66 AAA
133561722 TAACTTGAGC
Statistics
Matches: 176, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
125 2 0.01
126 174 0.99
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (126 bp):
GCATTTTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGATGCTCTTTTGCTACAGTGGTTTCTG
AAAAAATAATTTTAAGAAGACGTGTCTGCACAAATAGTGTCAAAAACACTTCAAGCAGAAT
Found at i:133561691 original size:308 final size:308
Alignment explanation
Indices: 133561122--133561707 Score: 915
Period size: 308 Copynumber: 1.9 Consensus size: 308
133561112 TCTAAAAAAG
* *
133561122 CTTCTACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTG
1 CTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTAAGAAGACGTGTCTG
** *
133561187 CACAAATAGTGTCAAAAATGCTTCAAACAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCC
66 CACAAATAGTGTCAAAAACACTTCAAACAGAATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCC
**
133561252 CACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGTGCA
131 CACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACA
* *
133561317 AATAGTGTAAAAAGCGCTTCAATCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAACTTCCACG
196 AATAGTGTAAAAAGCGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAACTCCCACG
*
133561382 TGGATGCTCTTTTGCTACTAGCATTGTCAGCAAAAGTACTGAAAGAAA
261 TGGACGCTCTTTTGCTACTAGCATTGTCAGCAAAAGTACTGAAAGAAA
* * *
133561430 CTTCCACGTGGATGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTAAGAAGATGTGTCTG
1 CTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTAAGAAGACGTGTCTG
* * * * * *
133561495 CGCAAATAGTGGT-AAAGACACTTCAAGCAGAATGCATTTTCAGCAAAATTACTGGAAGAAGCTC
66 CACAAATAGT-GTCAAAAACACTTCAAACAGAATGCATTGTCAGCAAAAGTACTGAAAGAAGCTC
* * * *
133561559 CCACGTGGATGCTCTTTTGCTACAGTGGTTTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCAT
130 CCACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGCAC
* *
133561624 AAATAGTGTCAAAAA-CGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCCA
195 AAATAGTGT-AAAAAGCGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAACTCCCA
133561688 CGTGGACGCTCTTTTGCTAC
259 CGTGGACGCTCTTTTGCTAC
133561708 AGTGGTTTCT
Statistics
Matches: 251, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
308 244 0.97
309 7 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (308 bp):
CTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTAAGAAGACGTGTCTG
CACAAATAGTGTCAAAAACACTTCAAACAGAATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCC
CACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACA
AATAGTGTAAAAAGCGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAACTCCCACG
TGGACGCTCTTTTGCTACTAGCATTGTCAGCAAAAGTACTGAAAGAAA
Found at i:133564903 original size:116 final size:116
Alignment explanation
Indices: 133564727--133565340 Score: 1068
Period size: 116 Copynumber: 5.3 Consensus size: 116
133564717 TTTATATTTT
* * *
133564727 ATTACATGAAATAATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
* * *
133564792 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATATT
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
* * * * *
133564843 ATCACATGAAATAATATAAAAATATTCAAAATGTTGCCTTGTTTAAAACAATTTCTATTTTACTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
133564908 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
133564959 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
133565024 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
133565075 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
*
133565140 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
* *
133565191 ATTACATGAAATAATAT-AAAAGATTCAAAATGTTGTCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
*
133565255 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAATAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
* *
133565306 ATTATATGAAATAATATAAAAAGATTCAAAATGTT
1 ATTACATGAAATAATATAAAAATATTCAAAATGTT
133565341 TGCACAAATA
Statistics
Matches: 475, Mismatches: 22, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
115 110 0.23
116 365 0.77
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (116 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
Found at i:133565751 original size:18 final size:18
Alignment explanation
Indices: 133565725--133565767 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
133565715 GACTAGAAAA
* * *
133565725 AGGAAACATATAAGGGCT
1 AGGATACATAAAAGGCCT
133565743 AGGATACATAAAAGGCCT
1 AGGATACATAAAAGGCCT
133565761 AGGATAC
1 AGGATAC
133565768 GTACTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGCCT
Found at i:133565878 original size:30 final size:30
Alignment explanation
Indices: 133565821--133565886 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
133565811 GTTGAACTGT
* *
133565821 TGGGCCTGGTGACTGTGTAGGTCCTGTT-A
1 TGGGCCGGGTGACTGTGTAGGGCCTGTTGA
*
133565850 CTGGGCCGGGTGATTGTGT-GGGCGCTGTTGA
1 -TGGGCCGGGTGACTGTGTAGGGC-CTGTTGA
133565881 TGGGCC
1 TGGGCC
133565887 TGCGCTGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.10
30 27 0.87
31 1 0.03
ACGTcount: A:0.08, C:0.18, G:0.44, T:0.30
Consensus pattern (30 bp):
TGGGCCGGGTGACTGTGTAGGGCCTGTTGA
Found at i:133569163 original size:46 final size:46
Alignment explanation
Indices: 133569096--133569276 Score: 186
Period size: 46 Copynumber: 3.8 Consensus size: 46
133569086 TGTAACCCGC
*
133569096 CCATAAGTAAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
133569142 CCATAAGTGAACTCAGACTCAACTCAACGAGCTTGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * *
133569192 CTC-TCGAACTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CAT--AAGT-GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
133569241 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
133569277 ATGCCCAAAT
Statistics
Matches: 112, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
46 61 0.54
47 3 0.03
48 4 0.04
49 6 0.05
50 6 0.05
51 4 0.04
52 3 0.03
53 25 0.22
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:133571676 original size:30 final size:29
Alignment explanation
Indices: 133571632--133571700 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
133571622 AAAGATAATA
133571632 AGAAAACCAAATAAAGAAATCCAAGATAG
1 AGAAAACCAAATAAAGAAATCCAAGATAG
* * * *
133571661 AGAAACCCAGAATAAAGAGATCCAGGATAT
1 AGAAAACCA-AATAAAGAAATCCAAGATAG
133571691 AGAAAACCAA
1 AGAAAACCAA
133571701 GATACGATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (29 bp):
AGAAAACCAAATAAAGAAATCCAAGATAG
Found at i:133571704 original size:15 final size:15
Alignment explanation
Indices: 133571631--133571704 Score: 62
Period size: 15 Copynumber: 5.0 Consensus size: 15
133571621 CAAAGATAAT
133571631 AAGAAAACCAA-ATA
1 AAGAAAACCAAGATA
*
133571645 AAGAAATCCAAGATA
1 AAGAAAACCAAGATA
* *
133571660 GAG-AAACCCAGAATA
1 AAGAAAACCAAG-ATA
* * *
133571675 AAGAGATCCAGGATA
1 AAGAAAACCAAGATA
*
133571690 TAGAAAACCAAGATA
1 AAGAAAACCAAGATA
133571705 CGATATTATG
Statistics
Matches: 44, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
14 16 0.36
15 24 0.55
16 4 0.09
ACGTcount: A:0.58, C:0.15, G:0.16, T:0.11
Consensus pattern (15 bp):
AAGAAAACCAAGATA
Found at i:133574515 original size:46 final size:46
Alignment explanation
Indices: 133574448--133574628 Score: 186
Period size: 46 Copynumber: 3.8 Consensus size: 46
133574438 TGTAACCCGC
*
133574448 CCATAAGTAAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
133574494 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * *
133574544 CTC-TCGAACTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CAT--AAGT-GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
133574593 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG
133574629 ATGCCCAAAT
Statistics
Matches: 115, Mismatches: 9, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
46 63 0.55
47 3 0.03
48 4 0.03
49 6 0.05
50 6 0.05
51 4 0.03
52 3 0.03
53 26 0.23
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:133577393 original size:30 final size:30
Alignment explanation
Indices: 133577354--133577410 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
133577344 TTTTATAAAT
133577354 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
133577384 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
133577411 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:133577605 original size:13 final size:13
Alignment explanation
Indices: 133577587--133577637 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
133577577 CTTAAACCAA
133577587 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
133577600 ACTTTTCTATAA-C
1 ACTTTTC-AAAAGC
*
133577613 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
133577626 ACTTTTCAAAAG
1 ACTTTTCAAAAG
133577638 TATTGCTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 3 0.09
13 26 0.81
14 3 0.09
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:133578586 original size:13 final size:13
Alignment explanation
Indices: 133578568--133578598 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
133578558 GCTGGGTACC
133578568 TTCTTTTTTTTTG
1 TTCTTTTTTTTTG
*
133578581 TTCTTTTTTTTTT
1 TTCTTTTTTTTTG
133578594 TTCTT
1 TTCTT
133578599 ATAAATGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (13 bp):
TTCTTTTTTTTTG
Found at i:133578716 original size:2 final size:2
Alignment explanation
Indices: 133578709--133578734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
133578699 CTGTTTTATA
133578709 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
133578735 TTATTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:133579610 original size:2 final size:2
Alignment explanation
Indices: 133579603--133579635 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
133579593 TTAAAACCCC
133579603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
133579636 GCTTGTTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:133580486 original size:31 final size:31
Alignment explanation
Indices: 133580406--133580488 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
133580396 CATTTACTGT
* *
133580406 AAGTACTAATTTGGACAAAAAAGCAAAGTTT
1 AAGTACTAATTTGGACCAAAAAGCAAAGTTC
* * * *
133580437 AGGTACTAATTTGAACCAAGAAGCTAAGTTC
1 AAGTACTAATTTGGACCAAAAAGCAAAGTTC
133580468 AAGTACCTAA-TTGGACCAAAA
1 AAGTA-CTAATTTGGACCAAAA
133580489 TAAACTTTAG
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 38 0.90
32 4 0.10
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (31 bp):
AAGTACTAATTTGGACCAAAAAGCAAAGTTC
Found at i:133582945 original size:23 final size:24
Alignment explanation
Indices: 133582919--133582963 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
133582909 AAAAAATTTA
133582919 AAATAACATAAAA-GAAAAAAAAT
1 AAATAACATAAAATGAAAAAAAAT
** *
133582942 AAATTTCTTAAAATGAAAAAAA
1 AAATAACATAAAATGAAAAAAA
133582964 TATAGGGACC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (24 bp):
AAATAACATAAAATGAAAAAAAAT
Found at i:133584458 original size:46 final size:47
Alignment explanation
Indices: 133584398--133584625 Score: 331
Period size: 46 Copynumber: 5.0 Consensus size: 47
133584388 TTTGACATGA
* * * * * *
133584398 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*** *
133584444 TGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
133584490 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
133584536 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTT-ATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
133584582 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAG
133584626 AGAGCACACT
Statistics
Matches: 168, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
45 7 0.04
46 158 0.94
47 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
Found at i:133588136 original size:2 final size:2
Alignment explanation
Indices: 133588065--133588117 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
133588055 TGATCCAGTG
* *
133588065 AT AT AT AA AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
133588107 AT AT AT AT AT A
1 AT AT AT AT AT A
133588118 GTAGAATTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:133597203 original size:26 final size:26
Alignment explanation
Indices: 133597167--133597219 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
133597157 AAAGGTAAAA
133597167 AAAAAAACTTTAATCCACCGTTGATC
1 AAAAAAACTTTAATCCACCGTTGATC
133597193 AAAAAAACTTTAATCCACCGTTGATC
1 AAAAAAACTTTAATCCACCGTTGATC
133597219 A
1 A
133597220 TGCTACGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (26 bp):
AAAAAAACTTTAATCCACCGTTGATC
Found at i:133601738 original size:21 final size:21
Alignment explanation
Indices: 133601693--133601732 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
133601683 CCCCAAACCT
* *
133601693 GTTTAGGATTCAAGATTTAAA
1 GTTTAAGATTCAAAATTTAAA
133601714 GTTTAAGATTCAAAATTTA
1 GTTTAAGATTCAAAATTTA
133601733 GGGTTTTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (21 bp):
GTTTAAGATTCAAAATTTAAA
Found at i:133604733 original size:30 final size:31
Alignment explanation
Indices: 133604664--133604734 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
133604654 CTTAAGGGTC
** *
133604664 AGAACTAAAATTTTAAATTTCAAAAAGTATA
1 AGAACTAAAATGATAAATTACAAAAAGTATA
* *
133604695 ATG-TCTAAAATGATAAATTAGAAAAA-TATA
1 A-GAACTAAAATGATAAATTACAAAAAGTATA
133604725 AGAACTAAAA
1 AGAACTAAAA
133604735 CTAACCAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
29 1 0.03
30 11 0.34
31 19 0.59
32 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (31 bp):
AGAACTAAAATGATAAATTACAAAAAGTATA
Found at i:133606889 original size:13 final size:14
Alignment explanation
Indices: 133606871--133606903 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
133606861 AAGTTAATAA
*
133606871 TTGAATT-TATCTC
1 TTGAATTATATATC
133606884 TTGAATTATATATC
1 TTGAATTATATATC
133606898 TTGAAT
1 TTGAAT
133606904 ATTTATCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (14 bp):
TTGAATTATATATC
Found at i:133614468 original size:23 final size:23
Alignment explanation
Indices: 133614425--133614469 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
133614415 ATTTTTCTAA
*
133614425 ACAAAAAACAACTCAATAAAAAG
1 ACAAAAAACAACTCAACAAAAAG
*
133614448 ACAAATAAACAA-TTAACAAAAA
1 ACAAA-AAACAACTCAACAAAAA
133614470 TTAAAGAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.71, C:0.16, G:0.02, T:0.11
Consensus pattern (23 bp):
ACAAAAAACAACTCAACAAAAAG
Found at i:133617841 original size:8 final size:8
Alignment explanation
Indices: 133617818--133617857 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
133617808 TCCATACATA
*
133617818 TATATATA
1 TATATATG
133617826 TATATATG
1 TATATATG
133617834 TATATATG
1 TATATATG
*
133617842 TATGTATG
1 TATATATG
133617850 TATA-ATG
1 TATATATG
133617857 T
1 T
133617858 CTTTTCTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:133617845 original size:12 final size:12
Alignment explanation
Indices: 133617815--133617857 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
133617805 TTTTCCATAC
*
133617815 ATATATATATAT
1 ATATATGTATAT
133617827 ATATATGTATAT
1 ATATATGTATAT
* *
133617839 ATGTATGTATGT
1 ATATATGTATAT
133617851 ATA-ATGT
1 ATATATGT
133617858 CTTTTCTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 4 0.15
12 23 0.85
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:133627817 original size:30 final size:30
Alignment explanation
Indices: 133627783--133627849 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
133627773 CTTTGACCTT
133627783 TTAAAAATGAAAAAAA-ATATTTTTAATCTC
1 TTAAAAATGAAAAAAATATA-TTTTAATCTC
* * *
133627813 TTAAACATGATAAAATTATATTTTAATCTC
1 TTAAAAATGAAAAAAATATATTTTAATCTC
*
133627843 TAAAAAA
1 TTAAAAA
133627850 ATTACAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.37
Consensus pattern (30 bp):
TTAAAAATGAAAAAAATATATTTTAATCTC
Found at i:133628693 original size:31 final size:31
Alignment explanation
Indices: 133628607--133628693 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
133628597 TTATAAAATG
* * *
133628607 GTCATTGAATTATTCGAAAGTTTTCATTTAA
1 GTCATTGAACTATTTGAAAGTTTTTATTTAA
* *
133628638 GTTATTGAACTATTTAAAAGTTTTTATTTAA
1 GTCATTGAACTATTTGAAAGTTTTTATTTAA
**
133628669 GTCATT-AGGTATTTGAAAGCTTTTT
1 GTCATTGAACTATTTGAAAG-TTTTT
133628694 TGTTAAAGCC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
30 10 0.22
31 36 0.78
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (31 bp):
GTCATTGAACTATTTGAAAGTTTTTATTTAA
Found at i:133630074 original size:31 final size:30
Alignment explanation
Indices: 133629993--133630100 Score: 119
Period size: 31 Copynumber: 3.6 Consensus size: 30
133629983 TATACCTTAT
* * *
133629993 AAAATTTTAAAAAAATTAATTATGCC-CCC
1 AAAATTTTAAAAAATTTAATTAAGCCTTCC
* *
133630022 AAAAATTTAAAAAGTTCTAATTAAGCCTTCC
1 AAAATTTTAAAAAATT-TAATTAAGCCTTCC
*
133630053 AAAAGTTTTAAAAAATTTAATTAAACCTTCC
1 AAAA-TTTTAAAAAATTTAATTAAGCCTTCC
* *
133630084 AATATTTTTAAAAATTT
1 AAAATTTTAAAAAATTT
133630101 CTCATCAATC
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
29 13 0.20
30 21 0.32
31 22 0.33
32 10 0.15
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTTTAAAAAATTTAATTAAGCCTTCC
Found at i:133630626 original size:31 final size:31
Alignment explanation
Indices: 133630553--133630611 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
133630543 TTTAATTTGA
* *
133630553 TCAA-TTTAGTCCCTATACTTTTTGAATTAG
1 TCAATTTTAGTCCCCATACTTTTTAAATTAG
133630583 TCAATTTTAGTCCCCATACTTTTTAAATT
1 TCAATTTTAGTCCCCATACTTTTTAAATT
133630612 TTTAACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (31 bp):
TCAATTTTAGTCCCCATACTTTTTAAATTAG
Found at i:133638616 original size:24 final size:22
Alignment explanation
Indices: 133638576--133638621 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
133638566 AAAATTCTTA
*
133638576 TTTTTAATTTAATATTTAATAT
1 TTTTTAATTTAAAATTTAATAT
*
133638598 TTTTTAATTATTAAAATTTTATAT
1 TTTTTAA-T-TTAAAATTTAATAT
133638622 ACATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 1 0.05
24 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTAATTTAAAATTTAATAT
Found at i:133638785 original size:14 final size:14
Alignment explanation
Indices: 133638766--133638812 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
133638756 TATATTTACA
133638766 AATATTAAATAAAT
1 AATATTAAATAAAT
133638780 AATATTAAATAAAT
1 AATATTAAATAAAT
133638794 --T-TTAAATATAA-
1 AATATTAAATA-AAT
133638805 AATATTAA
1 AATATTAA
133638813 TGCACAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 7 0.24
12 3 0.10
13 1 0.03
14 18 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATTAAATAAAT
Found at i:133638798 original size:25 final size:25
Alignment explanation
Indices: 133638765--133638812 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
133638755 ATATATTTAC
133638765 AAATATTAAATA-AATAATATTAAAT
1 AAATATTAAATATAA-AATATTAAAT
*
133638790 AAATTTTAAATATAAAATATTAA
1 AAATATTAAATATAAAATATTAA
133638813 TGCACAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATATTAAATATAAAATATTAAAT
Found at i:133638958 original size:38 final size:38
Alignment explanation
Indices: 133638914--133638988 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
133638904 CGTACAATTA
*
133638914 AAATTAAACGCGACCAATACAAATCGAAATTTTAATCG
1 AAATTAAACGCGACAAATACAAATCGAAATTTTAATCG
* * *
133638952 AAATTAAACGCGATAAATACGAATTGAAATTTTAATC
1 AAATTAAACGCGACAAATACAAATCGAAATTTTAATC
133638989 TATGCAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.27
Consensus pattern (38 bp):
AAATTAAACGCGACAAATACAAATCGAAATTTTAATCG
Found at i:133639179 original size:7 final size:7
Alignment explanation
Indices: 133639167--133639196 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
133639157 TTAATTTATG
133639167 TTAAATT
1 TTAAATT
133639174 TTAAATT
1 TTAAATT
*
133639181 TTGAATT
1 TTAAATT
133639188 TTAAATT
1 TTAAATT
133639195 TT
1 TT
133639197 TTATAGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (7 bp):
TTAAATT
Found at i:133640525 original size:10 final size:10
Alignment explanation
Indices: 133640510--133640539 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
133640500 GATGAAATTA
133640510 TTTTTATATT
1 TTTTTATATT
*
133640520 TTTTTATAAT
1 TTTTTATATT
133640530 TTTTTATATT
1 TTTTTATATT
133640540 ATTAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTATATT
Found at i:133644755 original size:21 final size:21
Alignment explanation
Indices: 133644731--133644795 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
133644721 AAGTCTAGCT
*
133644731 GAAGCACATAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAACG
*
133644752 GAAGC-C-CGAAG-GCT-AACT
1 GAAGCACAC-AAGTGCTAAACG
133644770 GAAGCACACAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAACG
133644791 GAAGC
1 GAAGC
133644796 CCGAAGGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 8 0.22
19 7 0.19
20 8 0.22
21 13 0.36
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAGCACACAAGTGCTAAACG
Found at i:133644772 original size:39 final size:39
Alignment explanation
Indices: 133644713--133644813 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
133644703 ATCGTGATCT
* * *
133644713 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
133644752 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
133644791 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
133644814 TAATCAGAGC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.37, C:0.25, G:0.27, T:0.12
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:133644826 original size:39 final size:39
Alignment explanation
Indices: 133644713--133644828 Score: 164
Period size: 39 Copynumber: 3.0 Consensus size: 39
133644703 ATCGTGATCT
* * *
133644713 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATCAGTGCTAAACG
133644752 GAAGCCCGAAGGCTAACTGAAGCACA-CAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATC-AGTGCTAAACG
*
133644791 GAAGCCCGAAGGCTAACTGAAGCTA-ATCAGAGCTAAAC
1 GAAGCCCGAAGGCTAACTGAAGC-ACATCAGTGCTAAAC
133644829 TGAAACCCCA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
39 68 0.97
40 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.25, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATCAGTGCTAAACG
Found at i:133647617 original size:5 final size:5
Alignment explanation
Indices: 133647593--133647634 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
133647583 ATTTATTTAA
*
133647593 ATTAT A-TAT ATATGT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT AT-TAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
133647635 AATTGATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.12
5 25 0.76
6 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
ATTAT
Found at i:133647655 original size:3 final size:3
Alignment explanation
Indices: 133647593--133647708 Score: 100
Period size: 3 Copynumber: 38.3 Consensus size: 3
133647583 ATTTATTTAA
*
133647593 ATT ATAT ATAT ATGT ATT A-T ATT A-T ATT A-T ATT A-T ATT A-T ATA
1 ATT AT-T AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
133647636 ATT GATT ATT ATA ATT ATT AATT GTT ATGGT -TT ATT ATT ATT ATT ATT
1 ATT -ATT ATT ATT ATT ATT -ATT ATT AT--T ATT ATT ATT ATT ATT ATT
133647684 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
133647709 AATAAATTAA
Statistics
Matches: 95, Mismatches: 7, Indels: 22
0.77 0.06 0.18
Matches are distributed among these distances:
2 11 0.12
3 66 0.69
4 17 0.18
5 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:133647994 original size:33 final size:33
Alignment explanation
Indices: 133647957--133648023 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
133647947 TATTTATACA
*
133647957 ATTATAATATT-TTATTTAAATT-AGTAGATATTT
1 ATTAT-ATATTATTATTAAAATTAAG-AGATATTT
*
133647990 ATTATTTATTATTATTAAAATTAAGAGATATTT
1 ATTATATATTATTATTAAAATTAAGAGATATTT
133648023 A
1 A
133648024 ATAATTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 4 0.13
33 24 0.80
34 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (33 bp):
ATTATATATTATTATTAAAATTAAGAGATATTT
Found at i:133648169 original size:17 final size:18
Alignment explanation
Indices: 133648147--133648182 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
133648137 TATATATAAA
133648147 ATAAAAAGAAATA-AAAC
1 ATAAAAAGAAATAGAAAC
*
133648164 ATAAAAATAAATAGAAAC
1 ATAAAAAGAAATAGAAAC
133648182 A
1 A
133648183 AAACAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (18 bp):
ATAAAAAGAAATAGAAAC
Found at i:133648172 original size:23 final size:23
Alignment explanation
Indices: 133648144--133648187 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
133648134 ATATATATAT
*
133648144 AAAATAAAAAGAAATAAAACATA
1 AAAATAAAAAGAAACAAAACATA
*
133648167 AAAATAAATAGAAACAAAACA
1 AAAATAAAAAGAAACAAAACA
133648188 AACAGAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.77, C:0.07, G:0.05, T:0.11
Consensus pattern (23 bp):
AAAATAAAAAGAAACAAAACATA
Done.