Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001985.1 Hibiscus syriacus cultivar Beakdansim tig00004046_pilon, whole genome shotgun sequence
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: 712196
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:162349 original size:54 final size:54
Alignment explanation
Indices: 162262--162625 Score: 308
Period size: 54 Copynumber: 6.6 Consensus size: 54
162252 CTATGTGTAC
* * * *
162262 TTTTAGCACTATTTGTGTAACCCACATAATTCATCAAAAGTTGATGAACAACCG
1 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCAAAAGTTGATGAACAACCG
* *
162316 TTTTGGCACTATGTGTACAACCCACAGAATTCATCATAAGTTGATGAACAACCG
1 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCAAAAGTTGATGAACAACCG
* * *
162370 TTTTGGAACTATGTGTGCAACCCAC-GAAATTCATCATAAGTTGATGAACAACCA
1 TTTTGGCACTATGTGTGCAACCCACAG-AATTCATCAAAAGTTGATGAACAACCG
* *
162424 TTTTGGCACTATGCCACTATGTGTGCAACCCACATAATTCATCATATA-TTGATGAACAACCG
1 TTTT-G------G-CACTATGTGTGCAACCCACAGAATTCATCA-AAAGTTGATGAACAACCG
* * * * * * *
162486 TATAGGCACTATATGT--TACCCAC-GAAATTCATCATATGTTGATGAACGACCG
1 TTTTGGCACTATGTGTGCAACCCACAG-AATTCATCAAAAGTTGATGAACAACCG
* * * * ** * *
162538 TATAGGCACTATGTGTGCAAACCACATAATTCAT-AATGTGTTTATGAACGACCG
1 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCAA-AAGTTGATGAACAACCG
* * * *
162592 TATAGGCACTAAGTGTGTAACCCACAGAATTCAT
1 TTTTGGCACTATGTGTGCAACCCACAGAATTCAT
162626 AATGAGATTA
Statistics
Matches: 259, Mismatches: 34, Indels: 34
0.79 0.10 0.10
Matches are distributed among these distances:
52 43 0.17
53 2 0.01
54 167 0.64
55 2 0.01
61 2 0.01
62 42 0.16
63 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (54 bp):
TTTTGGCACTATGTGTGCAACCCACAGAATTCATCAAAAGTTGATGAACAACCG
Found at i:162602 original size:168 final size:169
Alignment explanation
Indices: 162268--162602 Score: 417
Period size: 168 Copynumber: 2.0 Consensus size: 169
162258 GTACTTTTAG
* * * * *
162268 CACTATTTGTGTAACCCACATAATTCATCAAAAGTTGATGAACAACCGTTTTGGCACTATGTGTA
1 CACTATGTGTGCAACCCACATAATTCATCAAAAGTTGATGAACAACCGTATAGGCACTATATGTA
* * *
162333 CAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGGAACTATGTGTGCAACCCACGAA
66 -AACCCACAGAATTCATCATAAGTTGATGAACAACCGTATAGGAACTATGTGTGCAAACCACGAA
* * *
162398 ATTCATCATAAGTTGATGAACAACCATTTTGGCACTATGC
130 ATTCATAATAAGTTGATGAACAACCATATAGGCACTATGC
*
162438 CACTATGTGTGCAACCCACATAATTCATCATATA-TTGATGAACAACCGTATAGGCACTATATGT
1 CACTATGTGTGCAACCCACATAATTCATCA-AAAGTTGATGAACAACCGTATAGGCACTATATGT
* * * *
162502 -TACCCAC-GAAATTCATCATATGTTGATGAACGACCGTATAGGCACTATGTGTGCAAACCAC-A
65 AAACCCACAG-AATTCATCATAAGTTGATGAACAACCGTATAGGAACTATGTGTGCAAACCACGA
** * * *
162564 TAATTCATAATGTGTTTATGAACGACCGTATAGGCACTA
129 -AATTCATAATAAGTTGATGAACAACCATATAGGCACTA
162603 AGTGTGTAAC
Statistics
Matches: 141, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
167 2 0.01
168 82 0.58
170 55 0.39
171 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (169 bp):
CACTATGTGTGCAACCCACATAATTCATCAAAAGTTGATGAACAACCGTATAGGCACTATATGTA
AACCCACAGAATTCATCATAAGTTGATGAACAACCGTATAGGAACTATGTGTGCAAACCACGAAA
TTCATAATAAGTTGATGAACAACCATATAGGCACTATGC
Found at i:166571 original size:21 final size:21
Alignment explanation
Indices: 166547--166586 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
166537 CAATGGGATT
*
166547 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTGGATTTTG
*
166568 AGGATTTGGAAGTGGATTT
1 AGGATTAGGAAGTGGATTT
166587 GGTTGACGGT
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:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTGGATTTTG
Found at i:171131 original size:22 final size:21
Alignment explanation
Indices: 171089--171128 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
171079 GAGCTTATTT
*
171089 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
171110 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
171129 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:177850 original size:54 final size:54
Alignment explanation
Indices: 177782--178129 Score: 337
Period size: 54 Copynumber: 6.4 Consensus size: 54
177772 CTATGTGTAC
* *
177782 TTTTGGCACTATGTGTGCAACCCACGTAATTCATCATAAGTTGATGAACAACCG
1 TTTTAGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCG
177836 TTTTAGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCG
1 TTTTAGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCG
* * * *
177890 TTTTGGCACTATGTGTGCAACCCACAGAATTCTTCATATGTTGATGAACAACC-
1 TTTTAGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCG
* * * ** * *
177943 ATATAGGCATTATGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACC-
1 TTTTA-GCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCG
* * * * * ** *
177997 ATATAGGCACTAAGTGTGCAAACCACGGAATTCATAATGTGCTT-ATGAACGACCG
1 TTTTA-GCACTATGTGTGCAACCCACGGAATTCATCATAAG-TTGATGAACAACCG
* * * * * *
178052 -TATAGGCACTAAGTGTGCAACCCACGGAATTCATAATGAGATT-ATGAATAACTG
1 TTTTA-GCACTATGTGTGCAACCCACGGAATTCATCATAAG-TTGATGAACAACCG
* * * *
178106 TATCAGCACTACGTGTGCACCCCA
1 TTTTAGCACTATGTGTGCAACCCA
178130 AAGAACGTAT
Statistics
Matches: 259, Mismatches: 31, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
53 2 0.01
54 254 0.98
55 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (54 bp):
TTTTAGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCG
Found at i:178062 original size:162 final size:162
Alignment explanation
Indices: 177786--178083 Score: 411
Period size: 162 Copynumber: 1.8 Consensus size: 162
177776 GTGTACTTTT
** * * *
177786 GGCACTATGTGTGCAACCCACGTAATTCATCATAAGTTGATGAACAACCGTTTTAGCACTATGTG
1 GGCACTATGTGTGCAACCCACAAAATTCATCATAAGTTGATGAACAACCGATATAGCACTAAGTG
* * * * *
177851 TGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATGTGTGCAACCCACA
66 TGCAAACCACGGAATTCATAATAAGTTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACA
177916 GAATTCTTCATATGTTGATGAACAACCATATA
131 GAATTCTTCATATGTTGATGAACAACCATATA
* * *
177948 GGCATTATGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACC-ATATAGGCACTAAGT
1 GGCACTATGTGTGCAACCCACAAAATTCATCATAAGTTGATGAACAACCGATATA-GCACTAAGT
** *
178012 GTGCAAACCACGGAATTCATAATGTGCTT-ATGAACGACCGTATAGGCACTAAGTGTGCAACCCA
65 GTGCAAACCACGGAATTCATAATAAG-TTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCA
*
178076 CGGAATTC
129 CAGAATTC
178084 ATAATGAGAT
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
161 3 0.03
162 112 0.96
163 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (162 bp):
GGCACTATGTGTGCAACCCACAAAATTCATCATAAGTTGATGAACAACCGATATAGCACTAAGTG
TGCAAACCACGGAATTCATAATAAGTTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACA
GAATTCTTCATATGTTGATGAACAACCATATA
Found at i:178099 original size:108 final size:107
Alignment explanation
Indices: 177786--178085 Score: 379
Period size: 108 Copynumber: 2.8 Consensus size: 107
177776 GTGTACTTTT
* * *
177786 GGCACTATGTGTGCAACCCACGTAATTCATCATAAGTTGATGAACAACCGTTTTA-GCACTATGT
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG-TATAGGCACTATGT
* * *
177850 GTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTT
65 GTGCAACCCACGGAATTCATCAT-AGTTGATGAACAACCATATA
* * * *
177894 GGCACTATGTGTGCAACCCACAGAATTCTTCATATGTTGATGAACAACCATATAGGCATTATGTG
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTG
** *
177959 TGCAACCCACAAAATTCATCATATGTTGATGAACGACCATATA
66 TGCAACCCACGGAATTCATCATA-GTTGATGAACAACCATATA
* * * * * *
178002 GGCACTAAGTGTGCAAACCACGGAATTCATAATGTGCTT-ATGAACGACCGTATAGGCACTAAGT
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATG-TTGATGAACAACCGTATAGGCACTATGT
178066 GTGCAACCCACGGAATTCAT
65 GTGCAACCCACGGAATTCAT
178086 AATGAGATTA
Statistics
Matches: 164, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
107 4 0.02
108 158 0.96
109 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (107 bp):
GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTG
TGCAACCCACGGAATTCATCATAGTTGATGAACAACCATATA
Found at i:179671 original size:2 final size:2
Alignment explanation
Indices: 179664--179691 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
179654 CCCCCATTAC
179664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
179692 CATTGTCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:191408 original size:3 final size:3
Alignment explanation
Indices: 191400--191469 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
191390 TTCATCCTTC
* * *
191400 TAT TAT TAT TAT TAT CAA TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
191448 AAT TAT GAT TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
191470 TTTTATTTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:201226 original size:13 final size:13
Alignment explanation
Indices: 201210--201239 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
201200 TATATATATA
*
201210 AAAAAGAAAAAAC
1 AAAAACAAAAAAC
201223 AAAAACAAAAAAC
1 AAAAACAAAAAAC
201236 AAAA
1 AAAA
201240 TGTGGTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAC
Found at i:202991 original size:134 final size:135
Alignment explanation
Indices: 202489--203049 Score: 487
Period size: 134 Copynumber: 4.2 Consensus size: 135
202479 TTTAAACTTC
* ** *
202489 CCTG-AAGAACAGTGGAATGAATCAATGTCCCCAGATATGATTTTCCCTGAAGAAACAGTGGAAC
1 CCTGAAAGAACAATGGAATGAATCAATGTCCCCAGATATGATTTTCCCCAAAGAAACAGCGGAAC
* * * *
202553 ATATCCCCTCTCTTTCCATATTT-ATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCCTAGATTCA
66 AGAT-CCCTCTCTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTACCTCGATTCA
202617 TTC-TT
130 TTCTTT
* * ** * * ** *** * * * *
202622 CCTTAAAGTACAATGGAATGAATCAACATCCACATATATGATTAACCATGAAGAAATAACAGAAT
1 CCTGAAAGAACAATGGAATGAATCAATGTCCCCAGATATGATTTTCCCCAAAGAAACAGCGGAAC
* * *
202687 ATG-TCCCATCTCTTTCCAGATTTGATATTCCCTGAGTAGCAGTGGAATAAGTCTACCTCAATTC
66 A-GATCCC-TCTCTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTACCTCGATTC
*
202751 ATTCTTC
129 ATTCTTT
* * * * * * * * ** * * *
202758 CCTG-AAGAATAGTAGAATCAATTAACGTCCCCATATCTGA-TTTCCCTGAAGAAACAGTGAAAT
1 CCTGAAAGAACAATGGAATGAATCAATGTCCCCAGATATGATTTTCCCCAAAGAAACAGCGGAAC
* * * * * *
202821 AAATCCC-CTATTTTTCAGATTTGATCTTCCTTGAGTAGTAGTGGAACAAGTCTGCCTCGATTCA
66 AGATCCCTCT-CTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTACCTCGATTCA
202885 TTCTTT
130 TTCTTT
* * * * *
202891 TCTGAAAGAACAATGGAGTGAATCAATGTCTCCAGATCT-ATTTTCCCCCAAAGAAGCAGCGGAA
1 CCTGAAAGAACAATGGAATGAATCAATGTCCCCAGATATGATTTT-CCCCAAAGAAACAGCGGAA
*
202955 CAGATCCC-CTCTTTCCAGATTTGATCTTCCCTGAGTAGTAGTGGAACAAGTCTACCTCGATTCA
65 CAGATCCCTCTCTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTACCTCGATTCA
*
203019 ATC-TT
130 TTCTTT
* * *
203024 CCTTGAAA-AATAATGAAATAAATCAA
1 CC-TGAAAGAACAATGGAATGAATCAA
203050 CGTTTCTCGA
Statistics
Matches: 339, Mismatches: 78, Indels: 22
0.77 0.18 0.05
Matches are distributed among these distances:
132 2 0.01
133 78 0.23
134 167 0.49
135 88 0.26
136 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (135 bp):
CCTGAAAGAACAATGGAATGAATCAATGTCCCCAGATATGATTTTCCCCAAAGAAACAGCGGAAC
AGATCCCTCTCTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTACCTCGATTCAT
TCTTT
Found at i:204833 original size:27 final size:26
Alignment explanation
Indices: 204762--204836 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
204752 TCACTTTTGC
*
204762 ATTTTATTTTTTTTAATTTTTGACATG
1 ATTTTATTTTTTTT-ATTTTAGACATG
*
204789 ATGTTT-TTTGTTTATATTTTAGACAT-
1 AT-TTTATTT-TTTTTATTTTAGACATG
204815 ATTTTCATTTTATTTTATTTTA
1 ATTTT-ATTTT-TTTTATTTTA
204837 ATTTTTGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
25 3 0.08
26 3 0.08
27 27 0.68
28 7 0.17
ACGTcount: A:0.23, C:0.04, G:0.07, T:0.67
Consensus pattern (26 bp):
ATTTTATTTTTTTTATTTTAGACATG
Found at i:206174 original size:94 final size:95
Alignment explanation
Indices: 206031--206270 Score: 256
Period size: 95 Copynumber: 2.5 Consensus size: 95
206021 GATTCAATCA
* * * *
206031 GTATCGATACCGAA-T-GAAGTGGTATCGATACCATGGTGAGGGTATCGATACCGGGTAACATCG
1 GTATCGATACCAAAGTAG-AGTAGTATCGATACCATGGTAAGGGTATCGATACCGGGCAACATCG
*
206094 AACCTAA-TTTGGTATCGATACCATATA-GGG
65 AACCTAATTTTGGTATCGATACCAGA-AGGGG
* * * * * *
206124 GTATC-AGTACCATAGTATATTAGTATCGATACCATGGTAAGGGTAGCGATACTGGGCCACATCG
1 GTATCGA-TACCAAAGTAGAGTAGTATCGATACCATGGTAAGGGTATCGATACCGGGCAACATCG
* * **
206188 AATCTAATTTTGGTATTGATACTGGAAGGGG
65 AACCTAATTTTGGTATCGATACCAGAAGGGG
* * *
206219 GTATCGATACCAAAGTAGAGTAATATTGATACCATGGTAGGGGTATCGATAC
1 GTATCGATACCAAAGTAGAGTAGTATCGATACCATGGTAAGGGTATCGATAC
206271 TGAACGGCCA
Statistics
Matches: 119, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
92 1 0.01
93 10 0.08
94 47 0.39
95 60 0.50
96 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (95 bp):
GTATCGATACCAAAGTAGAGTAGTATCGATACCATGGTAAGGGTATCGATACCGGGCAACATCGA
ACCTAATTTTGGTATCGATACCAGAAGGGG
Found at i:206667 original size:59 final size:59
Alignment explanation
Indices: 206596--206872 Score: 455
Period size: 59 Copynumber: 4.7 Consensus size: 59
206586 TAGCAAATGA
* * * *
206596 CACTTTGTGTGCTAAAAGGGTAAGGAAATCATACTAAGTGTATAAATTTTCAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* *
206655 CACTTCGTGTGCTAAAATGGTAAGAAAATCATGCTAAGTGTATGAATTTCCAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* * *
206714 TACTTTGTGTACTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAAATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* *
206773 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATATGG
1 CACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGATAGGG
206832 CACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGT
1 CACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGT
206873 CTAATCATGA
Statistics
Matches: 201, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 201 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (59 bp):
CACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGATAGGG
Found at i:212035 original size:22 final size:23
Alignment explanation
Indices: 211996--212040 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
211986 CTGGAAGGGG
211996 GTATCGATACCAACGTAG-GGTA
1 GTATCGATACCAACGTAGAGGTA
**
212018 GTATCGATACCATGGTAGAGGTA
1 GTATCGATACCAACGTAGAGGTA
212041 TCGATATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (23 bp):
GTATCGATACCAACGTAGAGGTA
Found at i:212043 original size:20 final size:20
Alignment explanation
Indices: 211995--212046 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
211985 ACTGGAAGGG
*
211995 GGTATCGATACCAACGTAGG
1 GGTATCGATACCAACGTAGA
**
212015 GTAGTATCGATACCATGGTAGA
1 G--GTATCGATACCAACGTAGA
212037 GGTATCGATA
1 GGTATCGATA
212047 TTGAAGGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCAACGTAGA
Found at i:212046 original size:95 final size:96
Alignment explanation
Indices: 211828--212046 Score: 259
Period size: 95 Copynumber: 2.3 Consensus size: 96
211818 ATTCAATTTA
*
211828 TATCGATACCATGGGT-GAGGGTATCGATACCGGGTAACATCGAACCTAATTTTGGTATCGATAC
1 TATCGATACCAT-GGTAGAGGGTATCGATACCGGGTAACACCGAACCTAATTTTGGTATCGATAC
* * * *
211892 CATATAGGGGTATCGGTACCATAGTATAGTAT
65 CAGATAGGGGTATCGATACCATAGTAGAGTAG
* * * * * *
211924 TATCGATACCATGGTA-AGGGTAGCGATACTGGGTCACACCGAATCTAATTTTGGTATTGATACT
1 TATCGATACCATGGTAGAGGGTATCGATACCGGGTAACACCGAACCTAATTTTGGTATCGATACC
* *
211988 GGA-AGGGGGTATCGATACCA-ACGTAGGGTAG
66 AGATA-GGGGTATCGATACCATA-GTAGAGTAG
212019 TATCGATACCATGGTAGA-GGTATCGATA
1 TATCGATACCATGGTAGAGGGTATCGATA
212047 TTGAAGGGCC
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
94 2 0.02
95 90 0.86
96 13 0.12
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (96 bp):
TATCGATACCATGGTAGAGGGTATCGATACCGGGTAACACCGAACCTAATTTTGGTATCGATACC
AGATAGGGGTATCGATACCATAGTAGAGTAG
Found at i:212444 original size:59 final size:59
Alignment explanation
Indices: 212373--212836 Score: 646
Period size: 59 Copynumber: 7.9 Consensus size: 59
212363 TACCAAATGA
*
212373 CACTTCGTGTGCTAAAA-GGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAAGG
1 CACTTTGTGTGCTAAAATGG-TAAGGAAATCATACTAAGTGTATGAATTTCCAGATAAGG
* * *
212432 CAATTTGTGTGCTAAGATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAAGG
* * *
212491 CACTTTGTCTGCTAAAATGGTAAGGAAATCATACTAAGTGTATAAATTTCCAGATATGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAAGG
* *
212550 CACTTTGTGTGCTAAAATGGTAAGGAAATAATACTAAGTGTATGAATTTCTAGAT-AGAG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAAG-G
* * *
212609 CACTTTGTGTGTTAAAATGGTAAGGAAACCATACTAAGTGTATGAATTTCTAGAT-AGAG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAAG-G
* * * **
212668 CACTTTGTGCGCTAAAATGGTAAGGAAATCATACCAAGTGTATGAATTTCCCGATTGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAAGG
* * *
212727 CACTTTGTGTGCTAAAATGGTAAGGAAAGCATACTAAGTGTATGAATTTCTAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAAGG
* * * * * *
212786 CACTTCGTGTGCTAAAATGATAAGGAAATTATATTAATTGTATTAATTTCC
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCC
212837 TATTGAAATT
Statistics
Matches: 364, Mismatches: 38, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
58 1 0.00
59 360 0.99
60 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (59 bp):
CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAAGG
Found at i:214886 original size:36 final size:35
Alignment explanation
Indices: 214777--214908 Score: 194
Period size: 35 Copynumber: 3.7 Consensus size: 35
214767 AACACAATCA
214777 TCAATTACATTCTAAACC-CTAAATTCCAAAATACT
1 TCAATTACATTCTAAACCTC-AAATTCCAAAATACT
* *
214812 TCAATTACATTCTAAACCTCAAAATCCAAAATGCT
1 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
214847 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCTCAAATTCC-AAAATACT
** *
214883 TCAATTACATTCCCAACCCCAAATTC
1 TCAATTACATTCTAAACCTCAAATTC
214909 ATAATCCATT
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
35 57 0.65
36 31 0.35
ACGTcount: A:0.42, C:0.28, G:0.01, T:0.30
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAATACT
Found at i:215579 original size:148 final size:142
Alignment explanation
Indices: 215396--215675 Score: 470
Period size: 148 Copynumber: 1.9 Consensus size: 142
215386 TATTTAAATG
* *
215396 AGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCGAAAATT
1 AGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTC--AAA--
215461 CAATTAAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTTGAGTCAACTATTT
62 -AATTAAATTCGACTTGATTTAAATTTTACAAACTCAAATCG-AAAAATTTTGAGTCAACTATTT
215526 TATAAACTAAACTGAATC
125 TATAAACTAAACTGAATC
215544 AGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAAATT
1 AGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAAATT
* *
215609 CAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAATTTTGAGTCAACTATTTTATAAA
66 AAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAATTTTGAGTCAACTATTTTATAAA
215674 CT
131 CT
215676 GAATTGAGTA
Statistics
Matches: 128, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
142 30 0.23
143 39 0.30
146 3 0.02
148 56 0.44
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.36
Consensus pattern (142 bp):
AGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAAATT
AAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAATTTTGAGTCAACTATTTTATAAA
CTAAACTGAATC
Found at i:215874 original size:35 final size:35
Alignment explanation
Indices: 215834--215929 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 35
215824 AATGGATTAT
* *
215834 GAATTTGGGGTTGGGT-ATGTAATTGAAGTATTTTA
1 GAATTTGGGGTT-GATAATGTAATTAAAGTATTTTA
* * *
215869 GAATTTGAGGTTTATAATGTAATTAAAGTATTTTG
1 GAATTTGGGGTTGATAATGTAATTAAAGTATTTTA
* * *
215904 GATTTTGGGGTTTAGAATGTAATTAA
1 GAATTTGGGGTTGATAATGTAATTAA
215930 TGACTGTGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
34 1 0.02
35 51 0.98
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (35 bp):
GAATTTGGGGTTGATAATGTAATTAAAGTATTTTA
Found at i:217497 original size:53 final size:53
Alignment explanation
Indices: 217417--217522 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
217407 AAACAAAAAA
*
217417 CTGTCGGGTCGGGTGTTACATTATAAGTGGATGCGTACATGACCGAATTTAAT
1 CTGTCGGGTCGGGTGTTACATTATAAGTGGATGCGTACATGACCGAATCTAAT
*
217470 CTGTCGGGTCGTGTGTTACATTATAAGTGGATGCGTACATGACCGAATCTAAT
1 CTGTCGGGTCGGGTGTTACATTATAAGTGGATGCGTACATGACCGAATCTAAT
217523 GTTGTTTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (53 bp):
CTGTCGGGTCGGGTGTTACATTATAAGTGGATGCGTACATGACCGAATCTAAT
Found at i:217939 original size:14 final size:15
Alignment explanation
Indices: 217922--217950 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
217912 TTAAATTCTA
217922 ATTATTATTT-TATT
1 ATTATTATTTATATT
217936 ATTATTATTTATATT
1 ATTATTATTTATATT
217951 TATCCTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTATTATTTATATT
Found at i:219271 original size:16 final size:18
Alignment explanation
Indices: 219247--219279 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
219237 AAATCTTTAT
219247 TTATCTCGAA-TATGAAA
1 TTATCTCGAATTATGAAA
219264 TTAT-TCGAATTATGAA
1 TTATCTCGAATTATGAA
219280 TCTAACGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (18 bp):
TTATCTCGAATTATGAAA
Found at i:226013 original size:16 final size:16
Alignment explanation
Indices: 225981--226013 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
225971 TTTGACAAAT
225981 AATAAAACAACATATA
1 AATAAAACAACATATA
225997 AATAATAACAACA-ATA
1 AATAA-AACAACATATA
226013 A
1 A
226014 CAATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AATAAAACAACATATA
Found at i:228518 original size:3 final size:3
Alignment explanation
Indices: 228510--228540 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
228500 TTTTTTATCT
*
228510 TTA TTA TTA TTC TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
228541 ATATACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:229103 original size:28 final size:28
Alignment explanation
Indices: 229068--229133 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
229058 CCAACTCCAT
**
229068 ACTAACATTCTTGTTGTTGTTCATATAC
1 ACTAACATTCTTCATGTTGTTCATATAC
229096 ACTAACATTCTTCATGTTGTTCATATAC
1 ACTAACATTCTTCATGTTGTTCATATAC
229124 ACTAACATTC
1 ACTAACATTC
229134 CCCATGCAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (28 bp):
ACTAACATTCTTCATGTTGTTCATATAC
Found at i:229139 original size:28 final size:28
Alignment explanation
Indices: 229082--229139 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
229072 ACATTCTTGT
**
229082 TGTTGTTCATATACACTAACATTCTTCA
1 TGTTGTTCATATACACTAACATTCCCCA
229110 TGTTGTTCATATACACTAACATTCCCCA
1 TGTTGTTCATATACACTAACATTCCCCA
229138 TG
1 TG
229140 CAGTCCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.40
Consensus pattern (28 bp):
TGTTGTTCATATACACTAACATTCCCCA
Found at i:229148 original size:28 final size:28
Alignment explanation
Indices: 229089--229149 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
229079 TGTTGTTGTT
** ** *
229089 CATATACACTAACATTCTTCATGTTGTT
1 CATATACACTAACATTCCCCATGCAGTC
229117 CATATACACTAACATTCCCCATGCAGTC
1 CATATACACTAACATTCCCCATGCAGTC
229145 CATAT
1 CATAT
229150 CTTCAGCTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (28 bp):
CATATACACTAACATTCCCCATGCAGTC
Found at i:237928 original size:31 final size:31
Alignment explanation
Indices: 237893--237958 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
237883 AGTTACGTCG
*
237893 GGGACCATATTGAAAATAGACTAAATGTTGC
1 GGGACCATATTGAAAACAGACTAAATGTTGC
* * *
237924 GGGACCATATTGCAAACGGACTAAATGTTGG
1 GGGACCATATTGAAAACAGACTAAATGTTGC
237955 GGGA
1 GGGA
237959 TTGTATTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.23
Consensus pattern (31 bp):
GGGACCATATTGAAAACAGACTAAATGTTGC
Found at i:238985 original size:19 final size:19
Alignment explanation
Indices: 238963--239000 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
238953 TCTTTTCATC
*
238963 TATTTTTATTATAAAATAT
1 TATTTTTATAATAAAATAT
238982 TATTTTTATAATAAAATAT
1 TATTTTTATAATAAAATAT
239001 AATATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTATAATAAAATAT
Found at i:239008 original size:19 final size:19
Alignment explanation
Indices: 238967--239008 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
238957 TTCATCTATT
* * *
238967 TTTATTATAAAATATTATT
1 TTTATAATAAAATATAATA
238986 TTTATAATAAAATATAATA
1 TTTATAATAAAATATAATA
239005 TTTA
1 TTTA
239009 ATTTAGTCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATAATAAAATATAATA
Found at i:239386 original size:31 final size:31
Alignment explanation
Indices: 239351--239418 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
239341 TTACAATACA
239351 ATCCCCCAACATTTAGTCCGTTTGCAATATG
1 ATCCCCCAACATTTAGTCCGTTTGCAATATG
*
239382 ATCCCTCAACATTTAGTCCGTTTGCAATATG
1 ATCCCCCAACATTTAGTCCGTTTGCAATATG
*
239413 GTCCCC
1 ATCCCC
239419 GACGTAACTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32
Consensus pattern (31 bp):
ATCCCCCAACATTTAGTCCGTTTGCAATATG
Found at i:239667 original size:59 final size:60
Alignment explanation
Indices: 239573--239702 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 60
239563 AATTTAGGGT
* * * * * *
239573 AAAG-TACAAAAATGGTCCCTCGATTGTAGGTTGTTGCTTTGTTGAGTCATC-ACTATTA
1 AAAGTTACAAAAATAGTCCCTCGACTATAGGGTGTTGCTTTGTTGAATCACCAACTATTA
* *
239631 AAAGTTACAAAAATAGTCCTTCGACTATAGGGTGTTGCTTTGTTGAATCGCCAACTATTA
1 AAAGTTACAAAAATAGTCCCTCGACTATAGGGTGTTGCTTTGTTGAATCACCAACTATTA
239691 AAAGTTACAAAA
1 AAAGTTACAAAA
239703 TAATCACCCG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 4 0.06
59 39 0.63
60 19 0.31
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (60 bp):
AAAGTTACAAAAATAGTCCCTCGACTATAGGGTGTTGCTTTGTTGAATCACCAACTATTA
Found at i:239715 original size:59 final size:59
Alignment explanation
Indices: 239599--239717 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 59
239589 CCCTCGATTG
* * * * *
239599 TAGGTTGTTGCTTTGTTGAGTCATCACTATTAAAAGTTACAAAAATAGTCCTTCGACTA
1 TAGGGTGTTGCTTTGTTGAATCACCACTATTAAAAGTTACAAAAATAATCCTCCGACTA
*
239658 TAGGGTGTTGCTTTGTTGAATCGCCAACTATTAAAAGTTAC-AAAATAATCAC-CCGACTA
1 TAGGGTGTTGCTTTGTTGAATCACC-ACTATTAAAAGTTACAAAAATAATC-CTCCGACTA
239717 T
1 T
239718 TCATATGTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 36 0.69
60 16 0.31
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (59 bp):
TAGGGTGTTGCTTTGTTGAATCACCACTATTAAAAGTTACAAAAATAATCCTCCGACTA
Found at i:241151 original size:15 final size:14
Alignment explanation
Indices: 241113--241162 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
241103 AAAAAGGAAA
241113 AAATGAATAATAAAT
1 AAAT-AATAATAAAT
241128 -AATAA-AATAAAT
1 AAATAATAATAAAT
241140 AAATACATAATAAAT
1 AAATA-ATAATAAAT
241155 -AATAATAA
1 AAATAATAA
241163 ATAATGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 7 0.22
13 10 0.31
14 8 0.25
15 7 0.22
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (14 bp):
AAATAATAATAAAT
Found at i:241167 original size:7 final size:7
Alignment explanation
Indices: 241118--241159 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
241108 GGAAAAAATG
241118 AATAATA
1 AATAATA
241125 AATAAT-
1 AATAATA
241131 AA-AATA
1 AATAATA
241137 AATAAATA
1 AAT-AATA
*
241145 CATAATA
1 AATAATA
241152 AATAATA
1 AATAATA
241159 A
1 A
241160 TAAATAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 3 0.10
6 4 0.13
7 17 0.57
8 6 0.20
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:241674 original size:33 final size:33
Alignment explanation
Indices: 241637--241718 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
241627 AGTCCTACTT
* * *
241637 GGACTCAAATGCTTTGGTTTTAGTATTTTAATA
1 GGACTCAAATACGTTGGTTTTAGTATTTCAATA
*
241670 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTTGGTTTTAGTATTTCAATA
*
241703 AGACTCAAATACGTTG
1 GGACTCAAATACGTTG
241719 ATTTATTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (33 bp):
GGACTCAAATACGTTGGTTTTAGTATTTCAATA
Found at i:241786 original size:3 final size:3
Alignment explanation
Indices: 241772--241830 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
241762 GGCCTACAAA
241772 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
241816 AAT -AT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AA
241831 AATGTTTTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 7 0.14
3 43 0.84
4 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:243019 original size:110 final size:110
Alignment explanation
Indices: 242816--243073 Score: 389
Period size: 110 Copynumber: 2.4 Consensus size: 110
242806 GTATTGCTCC
* * * * * * * *
242816 GAGTCCAATATCCTCCGCCGTGAATTTGAAATTGGCTCTG---GAACTGGGAAA-TTATTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTAAATTGAAAAGTTGTTTGTTG
*
242877 ACAATCAGCCGCCCCTTCGTCTTGAAGTTGAGCTTGTGTTGTCTT
66 ACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
*
242922 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTAAATTGAAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTAAATTGAAAAGTTGTTTGTTG
242987 ACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
66 ACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
*
243032 GGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
243074 ATTGGGAAGC
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
106 36 0.26
109 7 0.05
110 93 0.68
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (110 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTAAATTGAAAAGTTGTTTGTTG
ACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:247078 original size:7 final size:7
Alignment explanation
Indices: 247068--247117 Score: 66
Period size: 7 Copynumber: 6.9 Consensus size: 7
247058 AGGAAAAATG
247068 AATAATA
1 AATAATA
247075 AATAATAA
1 AATAAT-A
247083 AATAAATA
1 AAT-AATA
247091 AATAATA
1 AATAATA
247098 AATAA-A
1 AATAATA
247104 TAATAATA
1 -AATAATA
247112 AATAAT
1 AATAAT
247118 GTATTATCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 26 0.67
8 9 0.23
9 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:247084 original size:27 final size:27
Alignment explanation
Indices: 247063--247116 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
247053 CAAAAAGGAA
247063 AAATGAAT-AATAAATAATAAAATAAAT
1 AAAT-AATAAATAAATAATAAAATAAAT
247090 AAATAATAAATAAATAAT--AATAAAT
1 AAATAATAAATAAATAATAAAATAAAT
247115 AA
1 AA
247117 TGTATTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 9 0.35
26 3 0.12
27 14 0.54
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (27 bp):
AAATAATAAATAAATAATAAAATAAAT
Found at i:247089 original size:4 final size:4
Alignment explanation
Indices: 247071--247116 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
247061 AAAAATGAAT
247071 AATA AAT- AATAA AATA AATA AAT- AATA AATA AAT- AAT- AATA AATA
1 AATA AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA AATA
247116 A
1 A
247117 TGTATTATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.32
4 23 0.61
5 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:247626 original size:33 final size:33
Alignment explanation
Indices: 247589--247670 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
247579 AGTCCTACTT
* *
247589 GGACTCAAATGC-TTCGGTTTTAGTGTTTTAATA
1 GGACTCAAATACGTT-GGTTTTAGTGTTTCAATA
247622 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
*
247655 AGACTCAAATACGTTG
1 GGACTCAAATACGTTG
247671 ATTTATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (33 bp):
GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
Found at i:247735 original size:3 final size:3
Alignment explanation
Indices: 247729--247769 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
247719 ACAAAAAAAA
247729 AAT AAT AAT AAT AAT AAT AAT AA- ATAT AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A
247770 TTTTTGTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 5 0.15
3 28 0.82
4 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:248099 original size:23 final size:23
Alignment explanation
Indices: 248071--248143 Score: 146
Period size: 23 Copynumber: 3.2 Consensus size: 23
248061 GTAAGAAAAG
248071 GCTTCTAAATGAATTTATAAGAA
1 GCTTCTAAATGAATTTATAAGAA
248094 GCTTCTAAATGAATTTATAAGAA
1 GCTTCTAAATGAATTTATAAGAA
248117 GCTTCTAAATGAATTTATAAGAA
1 GCTTCTAAATGAATTTATAAGAA
248140 GCTT
1 GCTT
248144 TTCCTTACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (23 bp):
GCTTCTAAATGAATTTATAAGAA
Found at i:248560 original size:21 final size:21
Alignment explanation
Indices: 248514--248560 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
248504 ACAAATGAAT
* *
248514 TTACAGCAGTTATTCGAATTG
1 TTACAGCAGCTATTCGAATAG
*
248535 GTACAGCAGCTATTAC-AATAG
1 TTACAGCAGCTATT-CGAATAG
248556 TTACA
1 TTACA
248561 ACTTTTATCC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (21 bp):
TTACAGCAGCTATTCGAATAG
Found at i:250106 original size:16 final size:16
Alignment explanation
Indices: 250085--250127 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
250075 TAAAATAAGA
*
250085 TTAATTAATAATTCGT
1 TTAATTAATAATTCAT
** *
250101 TTAATTTTTAATTTAT
1 TTAATTAATAATTCAT
250117 TTAATTAATAA
1 TTAATTAATAA
250128 ATAAAAGTAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TTAATTAATAATTCAT
Found at i:250667 original size:35 final size:37
Alignment explanation
Indices: 250604--250678 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 37
250594 TTTCGTCCTA
250604 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
* *
250641 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
250676 CTA
1 CTA
250679 TGTTTTAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 22 0.61
36 5 0.14
37 9 0.25
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:253163 original size:8 final size:8
Alignment explanation
Indices: 253150--253188 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
253140 GAACATTTCA
*
253150 TGCATTCT
1 TGCATTTT
253158 TGCA-TTT
1 TGCATTTT
253165 TGCATTTT
1 TGCATTTT
*
253173 TGCCTTTT
1 TGCATTTT
253181 TGCATTTT
1 TGCATTTT
253189 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:254336 original size:22 final size:22
Alignment explanation
Indices: 254313--254374 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
254303 CAAAAAGGGC
254313 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
254336 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
254357 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
254375 TAAAAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:254365 original size:20 final size:20
Alignment explanation
Indices: 254313--254381 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
254303 CAAAAAGGGC
*
254313 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
254336 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
254357 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
254377 AAAAA
1 AAAAA
254382 AGGGGACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 10 0.24
24 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:255020 original size:22 final size:22
Alignment explanation
Indices: 254992--255042 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
254982 CCCCATCAAT
254992 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
255014 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
255036 CCTTTGA
1 CCTTTGA
255043 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:255478 original size:18 final size:18
Alignment explanation
Indices: 255455--255490 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
255445 TCAACATCAA
*
255455 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
255473 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
255491 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:256119 original size:36 final size:36
Alignment explanation
Indices: 256021--256178 Score: 262
Period size: 36 Copynumber: 4.3 Consensus size: 36
256011 ATTGAAAACA
* *
256021 TTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATAA
1 TTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAG
*
256058 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACAG
*
256095 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAT
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
256131 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
256167 TTTCCCTTGAAA
1 TTTCCCTTGAAA
256179 CAAAATATTT
Statistics
Matches: 114, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
36 69 0.61
37 38 0.33
38 7 0.06
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
Found at i:256211 original size:138 final size:138
Alignment explanation
Indices: 256064--256318 Score: 368
Period size: 138 Copynumber: 1.8 Consensus size: 138
256054 ATAATTTCCC
* * *
256064 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGA
1 TTGAAAC-AAATTTCGTCCCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGA
* * * *
256128 CATTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTAAAT
65 CAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACAAAATATTTAAAT
256193 ATGTTTTCT
130 ATGTTTTCT
* ** * *
256202 TTGAAACAAATTTCGTCCCCCTTGAGTCAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCGTCCCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
* *
256267 AGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
66 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACA
256319 TAAAATCTTC
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
137 25 0.25
138 77 0.75
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
TTGAAACAAATTTCGTCCCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACAAAATATTTAAATA
TGTTTTCT
Found at i:256258 original size:174 final size:175
Alignment explanation
Indices: 255972--256303 Score: 454
Period size: 174 Copynumber: 1.9 Consensus size: 175
255962 ACTAGAAGAG
* *
255972 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAACATTTCCCTTGAAACAAA
* *
256037 TTTTCGTCTCTCTTGAGATAATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCT
66 TTTTCGTCCCCCTTGAGATAATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCT
* *
256102 TGAAATAAATTTTGTCTCTCTTGAGACATTTTCCCTTGAAATAAA
131 TGAAACAAATTTTGTCTCCCTTGAGACATTTTCCCTTGAAATAAA
* * ** * *
256147 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATATTTAAATATGTTTTCTTTGAAACAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAA-ACATTTCCCTTGAAACAA
* ** * * * *
256211 A-TTTCGTCCCCCTTGAG-TCAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCT
65 ATTTTCGTCCCCCTTGAGAT-AATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCC
256274 CTTGAAACAAATTTTGTCTCCCTTGAGACA
129 CTTGAAACAAATTTTGTCTCCCTTGAGACA
256304 GTTACTCTTG
Statistics
Matches: 136, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
173 1 0.01
174 88 0.65
175 47 0.35
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (175 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAACATTTCCCTTGAAACAAA
TTTTCGTCCCCCTTGAGATAATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCT
TGAAACAAATTTTGTCTCCCTTGAGACATTTTCCCTTGAAATAAA
Found at i:256270 original size:37 final size:36
Alignment explanation
Indices: 256197--256318 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 36
256187 TTAAATATGT
* * *
256197 TTTCT-TTGAAACAAATTTCGTCCCCCTTGAGTCAG
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * * *
256232 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
256269 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
256305 TTACTCTTGAAACA
1 TTTCTCTTGAAACA
256319 TAAAATCTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
35 5 0.07
36 40 0.54
37 29 0.39
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:257224 original size:105 final size:105
Alignment explanation
Indices: 256991--258384 Score: 1411
Period size: 105 Copynumber: 13.3 Consensus size: 105
256981 GCCATCCGCG
* * *
256991 ATTTCAACTCCAC-GACGGAGGATATTGTGGCACTCGAGACAACGCAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATA-T-TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGA
* *
257055 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
62 AGGGACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * * *
257100 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
257165 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * *
257205 ATTTTAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAGG
* *
257269 GACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
65 GACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * ** *
257310 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
257375 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
257415 ATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
257480 ACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * * * *
257520 ATTTCAACTTCACAGCGAAGGATATTGTACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
257585 GCGGCTGAC-TGT---CGACAA----GCAATTTCGGAGCCA
66 ACGGCTG-CTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
257618 ATCTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
257683 ACGGCTGGTTGTCAACAAATAATTTCCCAGTTTCAGGGCCA
66 ACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * * * *
257724 ATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
257789 GCGGCTGAC-TGT---CGACAA----GCAATTTCGGAGCCA
66 ACGGCTG-CTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
257822 ATCTCAACTTCACAGCGAAGGATATTGGACTTGAGACAACACAAGTTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
257887 ACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCG
66 ACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * * *
257928 ATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAACGA
* * * ** * ** *
257992 AGGGATGACTGGTTGTCAACGAACAACTTTTCAGTTTCA-TCCGCG
62 AGGGACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGC-CA
* * *
258037 ATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAACGA
* ** * *
258101 AGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
62 AGGGACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
**
258146 ATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * * * *
258211 ATGACTGATTGTCAACAA-GA-TT-TC--GTTCAGAGTCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * ** * * * *
258246 ATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGTACAAGCTCAACTTCATAGCAAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * * *
258311 GCGACTGAC-TGTCAACAAACAATTTCCCAGTTCCAGAACCA
66 ACGGCTG-CTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
*
258352 ATTTCAACTTCACAGCGGAGGATATTGGACTCG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCG
258385 GAACAATATT
Statistics
Matches: 1101, Mismatches: 147, Indels: 77
0.83 0.11 0.06
Matches are distributed among these distances:
98 157 0.14
100 76 0.07
101 4 0.00
102 15 0.01
103 5 0.00
104 3 0.00
105 386 0.35
106 248 0.23
107 5 0.00
108 4 0.00
109 196 0.18
110 2 0.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:258908 original size:35 final size:37
Alignment explanation
Indices: 258845--258919 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 37
258835 TTTCGTCCTA
258845 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
* *
258882 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
258917 CTA
1 CTA
258920 TGTTTTAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 22 0.61
36 5 0.14
37 9 0.25
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:269742 original size:58 final size:55
Alignment explanation
Indices: 269605--269759 Score: 152
Period size: 57 Copynumber: 2.7 Consensus size: 55
269595 TCAAATGAGC
* * * *
269605 TTTT-AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATAATTCCCAAAGAAT
1 TTTTAAGAAACTAAGCCTGATTTT-AAGGGTTTCTTGATGATAACTCCAAAAGAAA
* * * *
269660 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGATTTCTTGATGATAACT-GAAAATGAGAGA
1 TTTT-AAGAAACTAAGCCTGATTTTAAGGG-TTTCTTGATGATAACTCCAAAA-GA-A-A
*
269719 TTTTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 TTTTAAGAAACTAAGCCTGATTTT-AAGGGTTTCTTGATGA
269760 GTAAGTCTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
55 4 0.05
56 6 0.07
57 34 0.42
58 29 0.36
59 8 0.10
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (55 bp):
TTTTAAGAAACTAAGCCTGATTTTAAGGGTTTCTTGATGATAACTCCAAAAGAAA
Found at i:269742 original size:115 final size:109
Alignment explanation
Indices: 269547--269759 Score: 275
Period size: 115 Copynumber: 1.9 Consensus size: 109
269537 ATTTTTAAAT
* * ** *
269547 GAATTTTTCAAATAAGCTAAGCCTAATTTATAAGGTTTCTTGATGTTTTCAAATGAGCTTTTAGA
1 GAATTTTTCAAAGAAGCTAAGCCTAATTTATAAGGTTTCTTGATGTCTGAAAATGAGATTTTAGA
*
269612 AACTAAGCCTGATTTTCAGGGGTTTCTTGATGATAATTCCCAAA
66 AACTAAGCCTGATTTTCAAGGGTTTCTTGATGATAATTCCCAAA
* *
269656 GAATTTTT-AAAGAAGCTAAGCCTAATTTTTAGGGATTTCTTGATGATAACTGAAAATGAGAGAT
1 GAATTTTTCAAAGAAGCTAAGCCTAATTTATAAGG-TTTCTTGATG-T--CTGAAAAT--GAGAT
*
269720 TTTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
60 TTT-AGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGA
269760 GTAAGTCTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
108 23 0.26
109 18 0.20
110 1 0.01
112 5 0.06
114 7 0.08
115 34 0.39
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (109 bp):
GAATTTTTCAAAGAAGCTAAGCCTAATTTATAAGGTTTCTTGATGTCTGAAAATGAGATTTTAGA
AACTAAGCCTGATTTTCAAGGGTTTCTTGATGATAATTCCCAAA
Found at i:270178 original size:227 final size:227
Alignment explanation
Indices: 269779--270393 Score: 795
Period size: 227 Copynumber: 2.7 Consensus size: 227
269769 TCGGGCAATT
* *
269779 AGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGTCTTTTGAGCAAGATGA
1 AGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATGA
* *
269844 TAAGTCCTTCGGGCCATCCATAAGACCTTT-GGACATGATGTTTTCAAAATTTCCTTTGCTCGAT
66 TAAGTCCTTC-GGCCATCCATAAGACCTTTAGG-CAGGATGTTTTCAACATTTCCTTTGCTCGAT
* * * * * *
269908 TCAGAACACTTGGAATCAACAATGCCCCACTAGAGGGGTTAACATTTCCTATTGCTTGATTCATA
129 TCACAACACTTCGAATCAACAACGCCCCACTAGAGGGGTTAACATTTCCTATTGCTCGATTAACA
* * *
269973 ACATTTCAAATCAGCAAAAGTCCTTCAGGCCATC
194 ACACTTCAAATAAGCAAAAGTCCTTCAGACCATC
* * *
270007 AGTAAGTCTTTCGAGCATGATGCTTAAATCCTTTAGGTCATCTATAAGTATTTCGAACAAGATGA
1 AGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATGA
* *
270072 TAAGTCCTTCGACCATCCATAAGACCTTTAGGCAGGATGTTTTCAACATTTCCTTTACTCGATTC
66 TAAGTCCTTCGGCCATCCATAAGACCTTTAGGCAGGATGTTTTCAACATTTCCTTTGCTCGATTC
* * ** *
270137 ATAACACTTCAAATCAGTAACGCCCCACTAGAGGGGTTAACATTTTCTATTGCTCGATTAACAAC
131 ACAACACTTCGAATCAACAACGCCCCACTAGAGGGGTTAACATTTCCTATTGCTCGATTAACAAC
* * **
270202 ACTTCGAATAAGTAAAAGTCCTTCTTACCATC
196 ACTTCAAATAAGCAAAAGTCCTTCAGACCATC
* * * *
270234 AGTAAGACTTTCGAGCTTTCGAGCATGTTGCTTAAATCCTTCGGGTCATCTATAAATCCTTCGAG
1 AGTAAG----T----CTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGTCTTTCGAG
** * *
270299 CAAGATGATAAGTTATTAAGGCCATCCATAAGACCTTCAGGCAGGATG-TTTC-ACATTTCCTTT
58 CAAGATGATAAGTCCTT-CGGCCATCCATAAGACCTTTAGGCAGGATGTTTTCAACATTTCCTTT
270362 GCTCGATTCACAACACTTCGAATCAACAACGC
122 GCTCGATTCACAACACTTCGAATCAACAACGC
270394 ATCACTTGAG
Statistics
Matches: 334, Mismatches: 43, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
227 134 0.40
228 72 0.22
231 1 0.00
234 38 0.11
235 62 0.19
236 27 0.08
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (227 bp):
AGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATGA
TAAGTCCTTCGGCCATCCATAAGACCTTTAGGCAGGATGTTTTCAACATTTCCTTTGCTCGATTC
ACAACACTTCGAATCAACAACGCCCCACTAGAGGGGTTAACATTTCCTATTGCTCGATTAACAAC
ACTTCAAATAAGCAAAAGTCCTTCAGACCATC
Found at i:271846 original size:2 final size:2
Alignment explanation
Indices: 271839--271870 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
271829 ACTTTTGTTG
*
271839 AT AT AT AT AT AT AC 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
271871 TTGGGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:272357 original size:12 final size:11
Alignment explanation
Indices: 272328--272379 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
272318 TGCAAGTATA
*
272328 TTTTATTTTTT
1 TTTTGTTTTTT
*
272339 ATGTTGTGTTTTT
1 -TTTTGT-TTTTT
272352 TTTTGTTTTTGT
1 TTTTGTTTTT-T
272364 TTTTGTTTTTT
1 TTTTGTTTTTT
272375 ATTTT
1 -TTTT
272380 CATTTTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 5 0.15
12 24 0.71
13 5 0.15
ACGTcount: A:0.06, C:0.00, G:0.12, T:0.83
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:274085 original size:21 final size:21
Alignment explanation
Indices: 274033--274088 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
274023 CCAAAATGCA
* *
274033 TAAAATAAAAT-AACAGTGGC
1 TAAATTAAAATAAACAGTGAC
* *
274053 TAAATCAGAAATAAACATTGAC
1 TAAATTA-AAATAAACAGTGAC
274075 TAAATTAAAATAAA
1 TAAATTAAAATAAA
274089 ATAAAAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.17
21 11 0.38
22 13 0.45
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.23
Consensus pattern (21 bp):
TAAATTAAAATAAACAGTGAC
Found at i:275697 original size:92 final size:92
Alignment explanation
Indices: 275286--275732 Score: 389
Period size: 92 Copynumber: 4.9 Consensus size: 92
275276 TGATCTGTCC
* * * * ** * * * * *
275286 ACTGGAAATGTTTGTCTCTCGAGTGAGGAGTCACTGATTCTAAATGTCGTGAATCGAACAAAGGT
1 ACTGGAAATGTTGGTCCCTCGAGTAAGGCGTTGCTGATTCGAAATGACATGAATCGAGCCAAGGT
* * *
275351 TGAACAAGCTCTTCACTATGAATTCTCT
66 TGAATAAGTTCTTCTC-ATGAATTCTCT
* * * *
275379 ACTGGAAATATTGGTCCCTCGAGTAAGGCGTTGCTGATTC-AAA--ACTGTGAATCAAGCTAAGG
1 ACTGGAAATGTTGGTCCCTCGAGTAAGGCGTTGCTGATTCGAAATGAC-ATGAATCGAGCCAAGG
* *
275441 TTGAATAAGTTCTTCTAATGAATTCTTT
65 TTGAATAAGTTCTTCTCATGAATTCTCT
* * * * * * *
275469 ATTGGAAATGTTGGTCCCTCTAGTGAGGTGTTGCTGATTCGAAATGTCATGAATCAAGCCAAAGT
1 ACTGGAAATGTTGGTCCCTCGAGTAAGGCGTTGCTGATTCGAAATGACATGAATCGAGCCAAGGT
* * * * *
275534 TGAATAATTTTTTCTTATGAATTATTT
66 TGAATAAGTTCTTCTCATGAATTCTCT
* * * * *
275561 ACTAGAAATTTTGGTCCCTCGAGTGAGGCGTTACTGATTTGAAATGACATGAATCGAGCCAAGGT
1 ACTGGAAATGTTGGTCCCTCGAGTAAGGCGTTGCTGATTCGAAATGACATGAATCGAGCCAAGGT
*
275626 TGAATAAGTTATTCTCATGAATTCTCT
66 TGAATAAGTTCTTCTCATGAATTCTCT
* * * * * * *** *
275653 ACTGGAAATGTTAGTACTTCGAGTAAGGCATT-TTCAATTCGAAATGTTGTGAATCGAGTCAAGG
1 ACTGGAAATGTTGGTCCCTCGAGTAAGGCGTTGCT-GATTCGAAATGACATGAATCGAGCCAAGG
* *
275717 TTTAATAATTTCTTCT
65 TTGAATAAGTTCTTCT
275733 ATTTCGAGTG
Statistics
Matches: 288, Mismatches: 61, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
90 46 0.16
91 30 0.10
92 178 0.62
93 34 0.12
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (92 bp):
ACTGGAAATGTTGGTCCCTCGAGTAAGGCGTTGCTGATTCGAAATGACATGAATCGAGCCAAGGT
TGAATAAGTTCTTCTCATGAATTCTCT
Found at i:275770 original size:39 final size:39
Alignment explanation
Indices: 275727--275802 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
275717 TTTAATAATT
* *
275727 TCTTCTATTTCGAGTGAAAATATCTCAAGC-GAGATAAAA
1 TCTTCTATTTCAAGTGAAAACATCTCAA-CTGAGATAAAA
*
275766 TCTTCTATTTCAAGTGAAACCATCTCAACTGAGATAA
1 TCTTCTATTTCAAGTGAAAACATCTCAACTGAGATAA
275803 TCCCTTGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (39 bp):
TCTTCTATTTCAAGTGAAAACATCTCAACTGAGATAAAA
Found at i:278136 original size:14 final size:15
Alignment explanation
Indices: 278116--278152 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
278106 GCAAATGCAA
278116 AGATGCAAAAATGAG
1 AGATGCAAAAATGAG
*
278131 AG-TGC-AAAATGCG
1 AGATGCAAAAATGAG
278144 AGATGCAAA
1 AGATGCAAA
278153 TGCAACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.49, C:0.11, G:0.27, T:0.14
Consensus pattern (15 bp):
AGATGCAAAAATGAG
Found at i:278136 original size:28 final size:29
Alignment explanation
Indices: 278081--278152 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
278071 TATATATACT
* *
278081 AATGCAAAAATGCAAAGATGCACATGC-A
1 AATGCAAAGATGCAAAAATGCACATGCAA
*
278109 AATGCAAAGATGCAAAAATG-AGAGTGCAA
1 AATGCAAAGATGCAAAAATGCACA-TGCAA
*
278138 AATGC-GAGATGCAAA
1 AATGCAAAGATGCAAA
278153 TGCAACAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 2 0.05
28 30 0.79
29 6 0.16
ACGTcount: A:0.50, C:0.14, G:0.22, T:0.14
Consensus pattern (29 bp):
AATGCAAAGATGCAAAAATGCACATGCAA
Found at i:278155 original size:13 final size:14
Alignment explanation
Indices: 278090--278152 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
278080 TAATGCAAAA
*
278090 ATGCAAAGATGC-AC
1 ATGCAAA-ATGCGAG
*
278104 ATGC-AAATGCAAAG
1 ATGCAAAATGC-GAG
*
278118 ATGCAAAAATGAGAG
1 ATGC-AAAATGCGAG
278133 -TGCAAAATGCGAG
1 ATGCAAAATGCGAG
278146 ATGCAAA
1 ATGCAAA
278153 TGCAACAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 4 0.10
13 11 0.28
14 18 0.45
15 2 0.05
16 5 0.12
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (14 bp):
ATGCAAAATGCGAG
Found at i:279486 original size:3 final size:3
Alignment explanation
Indices: 279480--279509 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
279470 CTCATCATCC
*
279480 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
279510 GCATCATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:279791 original size:21 final size:21
Alignment explanation
Indices: 279767--279806 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
279757 ACTTAGACTT
*
279767 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAAGACCACATAGA
279788 TGTCCCGAAAGACCACATA
1 TGTCCCGAAAGACCACATA
279807 TAACATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (21 bp):
TGTCCCGAAAGACCACATAGA
Found at i:282665 original size:20 final size:20
Alignment explanation
Indices: 282636--282673 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
282626 TTTCAAAGGG
282636 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
282656 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
282674 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:282836 original size:64 final size:65
Alignment explanation
Indices: 282684--282842 Score: 203
Period size: 65 Copynumber: 2.5 Consensus size: 65
282674 GAATAAATTG
* * * * * *
282684 AACATCAAATGCAGTTTATGCATCGATGCACTCTCAATCCATTGATGCACTCAGGTTTTAATGAA
1 AACATCAAATGCATTTTATGCATCGATGCACACACAATCCATCGATGCACTCAGGTCTTAATCAA
* * * * *
282749 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTTATTCAA
1 AACATCAAATGCATTTTATGCATCGATGCACACACAATCCATCGATGCACTCAGGTCTTAATCAA
*
282813 AACATCCAATGCATTTTATGCATCGATGCA
1 AACATCAAATGCATTTTATGCATCGATGCA
282843 AGCTTAGTGC
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 35 0.43
65 47 0.57
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (65 bp):
AACATCAAATGCATTTTATGCATCGATGCACACACAATCCATCGATGCACTCAGGTCTTAATCAA
Found at i:282859 original size:64 final size:63
Alignment explanation
Indices: 282684--282863 Score: 182
Period size: 64 Copynumber: 2.8 Consensus size: 63
282674 GAATAAATTG
* * * * * *
282684 AACATCAAATGCAGTTTATGCATCGATGCACTCTCAATCCATTGATGCACTCAGGTTTTAATGAA
1 AACATCAAATGCATTTTATGCATCGATGCA-ACTC-ATGCATCGATGCACTCAGGTCTTAATCAA
* * * *
282749 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTTATTCAA
1 AACATCAAATGCATTTTATGCATCGATGCA-AC-TCATGCATCGATGCACTCAGGTCTTAATCAA
* * *
282813 AACATCCAATGCATTTTATGCATCGATGCAAGCTTAGTGCACCGATGCACT
1 AACATCAAATGCATTTTATGCATCGATGCAA-CTCA-TGCATCGATGCACT
282864 AAGTGTTTCA
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 49 0.50
65 46 0.47
66 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (63 bp):
AACATCAAATGCATTTTATGCATCGATGCAACTCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:290403 original size:64 final size:65
Alignment explanation
Indices: 290244--290405 Score: 245
Period size: 65 Copynumber: 2.5 Consensus size: 65
290234 GAATAAATTG
* * * * * *
290244 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCAATGCACTCAGGTCTTAATCAA
* *
290309 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCAATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCAATGCACTCAGGTCTTAATCAA
290373 AACATCGAATGCATTTTATGCATCGATGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
290406 TTAGTGCACC
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 39 0.44
65 50 0.56
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCAATGCACTCAGGTCTTAATCAA
Found at i:290421 original size:64 final size:64
Alignment explanation
Indices: 290244--290423 Score: 236
Period size: 64 Copynumber: 2.8 Consensus size: 64
290234 GAATAAATTG
* * * *
290244 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACT-CATGCATCGATGCACTCAGGTCTTAATCAA
* * * *
290309 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCAATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACAC-TCATGCATCGATGCACTCAGGTCTTAATCAA
* *
290373 AACATCGAATGCATTTTATGCATCGATGCACACTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACACTCA-TGCATCGATGCACT
290424 AAGTGCTCCA
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
63 1 0.01
64 51 0.50
65 49 0.49
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACTCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:291766 original size:21 final size:23
Alignment explanation
Indices: 291729--291785 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
291719 ACAAAATGCG
* *
291729 TAAAATAAAATAAAATAACAATGGC
1 TAAAATAAAA-AATA-AACAATGAC
*
291754 T-AAATAAAAAATAAACAGTGAC
1 TAAAATAAAAAATAAACAATGAC
291776 TAAAATAAAA
1 TAAAATAAAA
291786 TGGTAAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 8 0.29
23 11 0.39
24 8 0.29
25 1 0.04
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (23 bp):
TAAAATAAAAAATAAACAATGAC
Found at i:291778 original size:22 final size:22
Alignment explanation
Indices: 291740--291785 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
291730 AAAATAAAAT
*
291740 AAAATAACAATGGCT-AAATAA
1 AAAATAACAATGACTAAAATAA
*
291761 AAAATAAACAGTGACTAAAATAA
1 AAAAT-AACAATGACTAAAATAA
291784 AA
1 AA
291786 TGGTAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 8 0.38
23 8 0.38
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.17
Consensus pattern (22 bp):
AAAATAACAATGACTAAAATAA
Found at i:311544 original size:2 final size:2
Alignment explanation
Indices: 311533--311578 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
311523 ACGTTTGCAT
311533 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
311574 TA TA T
1 TA TA T
311579 GCTTATTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:313036 original size:15 final size:15
Alignment explanation
Indices: 313016--313051 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
313006 GCCTCCACTT
313016 TTAGTTAGATTTCAA
1 TTAGTTAGATTTCAA
313031 TTAGTTAGATTTCAA
1 TTAGTTAGATTTCAA
313046 TCTAGT
1 T-TAGT
313052 CCTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (15 bp):
TTAGTTAGATTTCAA
Found at i:319358 original size:54 final size:53
Alignment explanation
Indices: 319204--319449 Score: 213
Period size: 53 Copynumber: 4.6 Consensus size: 53
319194 TTTTATTAGA
* *
319204 AACTAAGACA-GATTTTT-GAAAGTTTCTTGATGATTTTAAATGAATTTTGAATA-
1 AACTAAG-CATGATTTTTAG-AAGTTTCTTGATGATTTTAAATGAGTTTTCAA-AG
* * *
319257 AGCTAAG-ACCGATTTTCAGAAGTTTC-TGATGATTTTTAAATGAGTTTTCAAAG
1 AACTAAGCA-TGATTTTTAGAAGTTTCTTGATGA-TTTTAAATGAGTTTTCAAAG
319310 AACTAAGCATGATTTTTAGAAGTTTCTTGATGATTTATAAATGAGTTTTCAAAG
1 AACTAAGCATGATTTTTAGAAGTTTCTTGATGATTT-TAAATGAGTTTTCAAAG
* * * ** * *
319364 AAGCTAAGCCTGGTTTTCAGGGGTTTCTTGATG-TTTCAAATGAATTTTTC-AAG
1 AA-CTAAGCATGATTTTTAGAAGTTTCTTGATGATTTTAAATG-AGTTTTCAAAG
* **
319417 AAGCTAAGC-T-AATTTTAGGTGTTTCTTGATGAT
1 AA-CTAAGCATGATTTTTAGAAGTTTCTTGATGAT
319450 AACCTTAAAT
Statistics
Matches: 164, Mismatches: 18, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
51 18 0.11
52 9 0.05
53 76 0.46
54 36 0.22
55 25 0.15
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (53 bp):
AACTAAGCATGATTTTTAGAAGTTTCTTGATGATTTTAAATGAGTTTTCAAAG
Found at i:319447 original size:106 final size:105
Alignment explanation
Indices: 319223--319449 Score: 257
Period size: 106 Copynumber: 2.1 Consensus size: 105
319213 AGATTTTTGA
* *
319223 AAGTTTCTTGATGATTTTAAATGAATTTTGAATAAGCTAAGACCGATTTTCAGAAGTTTCTGATG
1 AAGTTTCTTGATGATTTTAAATGAATTTTAAAGAAGCTAAGACCGATTTTCAGAAGTTTCTGATG
* *
319288 ATTTTTAAATGAGTTTTCAAAGAACTAAGCATGATTTTTAG
66 A-TTTCAAATGAGTTTTCAAAGAACTAAGCATGAATTTTAG
* * **
319329 AAGTTTCTTGATGATTTATAAATGAGTTTTCAAAGAAGCTAAG-CCTGGTTTTCAGGGGTTTCTT
1 AAGTTTCTTGATGATTT-TAAATGAATTTT-AAAGAAGCTAAGACC-GATTTTCAGAAGTTTC-T
*
319393 GATG-TTTCAAATGAATTTTTC-AAGAAGCTAAGC-T-AATTTTAG
62 GATGATTTCAAATG-AGTTTTCAAAGAA-CTAAGCATGAATTTTAG
**
319435 GTGTTTCTTGATGAT
1 AAGTTTCTTGATGAT
319450 AACCTTAAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
106 37 0.36
107 27 0.26
108 35 0.34
109 5 0.05
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (105 bp):
AAGTTTCTTGATGATTTTAAATGAATTTTAAAGAAGCTAAGACCGATTTTCAGAAGTTTCTGATG
ATTTCAAATGAGTTTTCAAAGAACTAAGCATGAATTTTAG
Found at i:320099 original size:18 final size:18
Alignment explanation
Indices: 320076--320113 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
320066 CTGGGAAGAG
320076 AATGAAGACTCCTCTAGC
1 AATGAAGACTCCTCTAGC
* *
320094 AATGAAGACTGCTCTTGC
1 AATGAAGACTCCTCTAGC
320112 AA
1 AA
320114 CTATTCCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (18 bp):
AATGAAGACTCCTCTAGC
Found at i:321287 original size:121 final size:121
Alignment explanation
Indices: 320926--321321 Score: 295
Period size: 121 Copynumber: 3.3 Consensus size: 121
320916 TTTGCTTGAA
* * *
320926 TCCATCATAGAATGAGGTGGATCAATATTTCCAATGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 TCCATCACAGAAGGAGGTGGATCAACATTTCCAATGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * *
320991 AAACACTTTGTTCATCCATCGC--ATGGAGTTGGATCAGCATCATCAC--TATTCTAT
66 -ATC-CTTGGATCATCCATTGCATATGGAGTTGGATCAACATCATCACTTTGTTCTAT
* * ** * *
321045 TCCATCACAGAAGGAAGTGGATCAACATTACCAGGGGAG-AGCTCATAATGAGAAGAAC----TC
1 TCCATCACAGAAGGAGGTGGATCAACATTTCCAATGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * * * ** *
321105 ATCCGATGGGGAGAAT-AAGTT-CATGAT-GA---GAAT-AACTTGTTCAACCTTTGTTC-AGC
66 ATCC--T-TGGATCATCCA-TTGCAT-ATGGAGTTGGATCAACATCATC-A-CTTTGTTCTA-T
* *
321161 TCCATCATAGAAGGAGGTGGATCAACATTTCCAATGAAGAAGTTTATAATGAGAAGAACTTGTTC
1 TCCATCACAGAAGGAGGTGGATCAACATTTCCAATGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
321226 ATCCTTGGCTCATCCATTGCATATGGAGTTGGATCAACATCATCACTTTGTTCTAT
66 ATCCTTGGATCATCCATTGCATATGGAGTTGGATCAACATCATCACTTTGTTCTAT
* * ** *
321282 TCCATCACAGAATGAGTTGGAGAAAAATTTCCAATGAAGA
1 TCCATCACAGAAGGAGGTGGATCAACATTTCCAATGAAGA
321322 GTTAATGAAA
Statistics
Matches: 204, Mismatches: 48, Indels: 48
0.68 0.16 0.16
Matches are distributed among these distances:
112 6 0.03
113 6 0.03
114 6 0.03
115 5 0.02
116 39 0.19
117 19 0.09
118 26 0.13
119 38 0.19
121 48 0.24
122 5 0.02
123 6 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (121 bp):
TCCATCACAGAAGGAGGTGGATCAACATTTCCAATGAAGAAGTTCATAATGAGAAGAACTTGTTC
ATCCTTGGATCATCCATTGCATATGGAGTTGGATCAACATCATCACTTTGTTCTAT
Found at i:321460 original size:23 final size:23
Alignment explanation
Indices: 321434--321478 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
321424 TTGGCTCATC
*
321434 CATCACATAAGGAGTTGGATCAG
1 CATCACATAAAGAGTTGGATCAG
321457 CATCACATAAAGAGTTGGATCA
1 CATCACATAAAGAGTTGGATCA
321479 ACGTTTCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (23 bp):
CATCACATAAAGAGTTGGATCAG
Found at i:321905 original size:21 final size:23
Alignment explanation
Indices: 321863--321943 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 23
321853 CATTTTCATC
321863 AAAATATTAATTATTAAATATT-T
1 AAAATA-TAATTATTAAATATTAT
*
321886 AAAATATATTTATT-AATATTAT
1 AAAATATAATTATTAAATATTAT
*
321908 AATAATATAATATATTTTAATATTAT
1 AA-AATATAAT-TA-TTAAATATTAT
321934 ATAAA-ATAAT
1 A-AAATATAAT
321944 AATTTATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.12
22 10 0.20
23 13 0.26
24 2 0.04
25 7 0.14
26 11 0.22
27 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATATAATTATTAAATATTAT
Found at i:321936 original size:28 final size:28
Alignment explanation
Indices: 321888--321957 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 28
321878 AAATATTTAA
321888 AATATATTTATTAATATTATAATAAT-AT
1 AATATATTTATTAATATTATAA-AATAAT
*
321916 AATATA-TT-TTAATATTATATAA-AAT
1 AATATATTTATTAATATTATAAAATAAT
321941 AATA-ATTTATATAATAT
1 AATATATTTAT-TAATAT
321958 AAGATATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 1 0.03
25 10 0.27
26 12 0.32
27 8 0.22
28 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AATATATTTATTAATATTATAAAATAAT
Found at i:321952 original size:17 final size:18
Alignment explanation
Indices: 321925--321969 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
321915 TAATATATTT
321925 TAATATTATATAAAATAA
1 TAATATTATATAAAATAA
*
321943 TAAT-TTATATAATATAA
1 TAATATTATATAAAATAA
*
321960 -GATATTATAT
1 TAATATTATAT
321970 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 18 0.75
18 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TAATATTATATAAAATAA
Found at i:322033 original size:27 final size:27
Alignment explanation
Indices: 321966--322035 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 27
321956 ATAAGATATT
* *
321966 ATATTTTTTTTTAATAAT--ATAATAA
1 ATATTTATATTTAATAATGAATAATAA
*
321991 ATTTTTATATTTAATAATGAATAAT-A
1 ATATTTATATTTAATAATGAATAATAA
322017 ATATTTATATTTAAATAAT
1 ATATTTATATTT-AATAAT
322036 ATTTTAGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 15 0.39
26 12 0.32
27 11 0.29
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
ATATTTATATTTAATAATGAATAATAA
Found at i:322094 original size:22 final size:22
Alignment explanation
Indices: 322051--322094 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
322041 AGTAAAGATA
*
322051 TTTAAAATATACTAATAATATT
1 TTTAAAATATAATAATAATATT
322073 TTTAAAATATAAT-ATAACTATT
1 TTTAAAATATAATAATAA-TATT
322095 ACTTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAAATATAATAATAATATT
Found at i:322108 original size:24 final size:22
Alignment explanation
Indices: 322073--322124 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
322063 TAATAATATT
*
322073 TTTAA-AATATAATATAACTATTAC
1 TTTAATAATATAAT-TAA-TA-TAA
322097 TTTAATAA-ATAATTAATATAA
1 TTTAATAATATAATTAATATAA
322118 TTTAATA
1 TTTAATA
322125 TTTTATTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.35
22 2 0.08
23 3 0.12
24 10 0.38
25 2 0.08
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAATAATATAATTAATATAA
Found at i:322191 original size:17 final size:17
Alignment explanation
Indices: 322169--322202 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
322159 TATTAAAATT
322169 ATAAAA-AATATTTAATA
1 ATAAAATAAT-TTTAATA
322186 ATAAAATAATTTTAATA
1 ATAAAATAATTTTAATA
322203 TTTTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAATAATTTTAATA
Found at i:322216 original size:21 final size:22
Alignment explanation
Indices: 322186--322242 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
322176 ATATTTAATA
*
322186 ATAA-AATAATTTTAATA-TTTT
1 ATAATAATAATATTAA-AGTTTT
322207 A-AATAATAATATTAAAGTTTT
1 ATAATAATAATATTAAAGTTTT
*
322228 ATGATAATAATATTA
1 ATAATAATAATATTA
322243 TTTAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 3 0.10
21 16 0.52
22 12 0.39
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
ATAATAATAATATTAAAGTTTT
Found at i:322257 original size:22 final size:22
Alignment explanation
Indices: 322190--322270 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 22
322180 TTAATAATAA
322190 AATAAT-TTTAATATTT-TAAAT
1 AATAATATTTAATATTTGT-AAT
* *
322211 AATAATATTAAAGTTTTATGATAAT
1 AATAATATTTAA-TATT-TG-TAAT
*
322236 AATATTATTTAATATTTGTAAT
1 AATAATATTTAATATTTGTAAT
*
322258 AAATAATTTTTAA
1 -AATAATATTTAA
322271 AAAAACTCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
21 6 0.13
22 8 0.17
23 15 0.32
24 4 0.09
25 13 0.28
26 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
AATAATATTTAATATTTGTAAT
Found at i:322364 original size:19 final size:18
Alignment explanation
Indices: 322340--322417 Score: 95
Period size: 19 Copynumber: 4.2 Consensus size: 18
322330 TTTCCAGATG
*
322340 TTTTCCAGAAATTAATTCT
1 TTTT-CAGAAATTAATTCA
322359 TTTTCCAGAAATTTAATTCA
1 TTTT-CAGAAA-TTAATTCA
322379 TTTTCAGAAATGTAATTCA
1 TTTTCAGAAAT-TAATTCA
*
322398 TTTTCAGAATTTAA-TCA
1 TTTTCAGAAATTAATTCA
322415 TTT
1 TTT
322418 ATTTTTCAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.11
18 4 0.07
19 34 0.62
20 11 0.20
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.47
Consensus pattern (18 bp):
TTTTCAGAAATTAATTCA
Found at i:322406 original size:38 final size:37
Alignment explanation
Indices: 322340--322417 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 37
322330 TTTCCAGATG
*
322340 TTTTCCAGAAATTAATTCTTTTTCCAGAAATTTAATTCA
1 TTTTCCAGAAATTAATTCATTTTCCAG-AATTTAA-TCA
322379 TTTT-CAGAAATGTAATTCATTTT-CAGAATTTAATCA
1 TTTTCCAGAAAT-TAATTCATTTTCCAGAATTTAATCA
322415 TTT
1 TTT
322418 ATTTTTCAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 6 0.16
37 7 0.19
38 10 0.27
39 14 0.38
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.47
Consensus pattern (37 bp):
TTTTCCAGAAATTAATTCATTTTCCAGAATTTAATCA
Found at i:323923 original size:21 final size:20
Alignment explanation
Indices: 323894--323936 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
323884 AATCCTTGCA
*
323894 TATTTTTATTTTAATTTTTT
1 TATTTTTATTTTAATTTATT
323914 TATTTATTATTTTAATTTATT
1 TATTT-TTATTTTAATTTATT
323935 TA
1 TA
323937 ATTGTGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTTTTATTTTAATTTATT
Found at i:325316 original size:157 final size:157
Alignment explanation
Indices: 325032--325346 Score: 573
Period size: 157 Copynumber: 2.0 Consensus size: 157
325022 TATAAAAATA
*
325032 AAATGTTTTATTAAAATCACACTTTTATGTGTCCCGATCGCACCTTAAAATGATTGGTGGCGACT
1 AAATGTTTTATTAAAATCACACATTTATGTGTCCCGATCGCACCTTAAAATGATTGGTGGCGACT
325097 CCTCACATTTAAAATCTTTTCAAAAAAAAACCCCAAGTTGTACGACTTTTTTTCCACCCGGGCGA
66 CCTCACATTTAAAATCTTTTCAAAAAAAAACCCCAAGTTGTACGACTTTTTTTCCACCCGGGCGA
325162 AAAAC-GTGTCGAC-ATATTTAATGTT
131 AAAACGGTGTCGACAATATTTAATGTT
325187 AAATGTTTTATTAAAATCACACAATTTATGGTGTCCCGATCGCACCTTAAAATGATTGGTGGCGA
1 AAATGTTTTATTAAAATCACAC-ATTTAT-GTGTCCCGATCGCACCTTAAAATGATTGGTGGCGA
325252 CTCCTCACATTTAAAAATCTTTTC-AAAAAAAACCCCAAGTTGTACGACTTTTTTTCCACCCGGG
64 CTCCTCACATTT-AAAATCTTTTCAAAAAAAAACCCCAAGTTGTACGACTTTTTTTCCACCCGGG
325316 CGAAAAACGGTGTCGACAATATTTAATGTT
128 CGAAAAACGGTGTCGACAATATTTAATGTT
325346 A
1 A
325347 CGATTTGGCT
Statistics
Matches: 154, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
155 22 0.14
156 5 0.03
157 95 0.62
158 19 0.12
159 13 0.08
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (157 bp):
AAATGTTTTATTAAAATCACACATTTATGTGTCCCGATCGCACCTTAAAATGATTGGTGGCGACT
CCTCACATTTAAAATCTTTTCAAAAAAAAACCCCAAGTTGTACGACTTTTTTTCCACCCGGGCGA
AAAACGGTGTCGACAATATTTAATGTT
Found at i:334608 original size:38 final size:36
Alignment explanation
Indices: 334566--334908 Score: 122
Period size: 38 Copynumber: 9.2 Consensus size: 36
334556 TTTTCACTCG
*
334566 AAACATAAATTTTATCTCATTTGATATTATTTTTCTTA
1 AAACA-AAATTTTATCTCACTTGA-ATTATTTTTCTTA
* ** * ** ** *
334604 AAAC-AAACTTCGTCTCGCTTGAAACAGTTTCACTTG
1 AAACAAAATTTTATCTCACTTGAATTA-TTTTTCTTA
*
334640 AAACATAAATTTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACA-AAATTTTATCTCACTTGA-ATTATTTTTCTTA
** * ** ** **
334678 AAACAAAA-TTTGGCTCGCTT-AAGACAGTTTCACTCG
1 AAACAAAATTTTATCTCACTTGAA-TTA-TTTTTCTTA
* *
334714 AAACAGAAATTTTATCTCACTTGAGATTGTTTTTCCTA
1 AAACA-AAATTTTATCTCACTTGA-ATTATTTTTCTTA
* * * ** ** *
334752 AAA-ACAAACTTTGTCTCGCTTGAGACAATTTCCCTCA
1 AAACA-AAATTTTATCTCACTTGA-ATTATTTTTCTTA
*
334789 AAACAGAAATTTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACA-AAATTTTATCTCACTTGA-ATTATTTTTCTTA
* ** * * * **
334827 AAAC-AAACTTCGTCTCGCTTGAGA-CAGTTTTCACTCG
1 AAACAAAATTTTATCTCACTTGA-ATTA-TTTT-TCTTA
*
334864 AAACAGAAATTTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACA-AAATTTTATCTCACTTGA-ATTATTTTTCTTA
334902 AAACAAA
1 AAACAAA
334909 CTTCGCCTCG
Statistics
Matches: 209, Mismatches: 80, Indels: 33
0.65 0.25 0.10
Matches are distributed among these distances:
34 1 0.00
35 3 0.01
36 62 0.30
37 40 0.19
38 80 0.38
39 22 0.11
40 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (36 bp):
AAACAAAATTTTATCTCACTTGAATTATTTTTCTTA
Found at i:334673 original size:74 final size:74
Alignment explanation
Indices: 334501--334988 Score: 699
Period size: 74 Copynumber: 6.6 Consensus size: 74
334491 AATACAAAAA
* *
334501 TTTATCTCACTCT-AGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAATTTTCACTC
1 TTTATCTCACT-TGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGAC-AGTTTCACTC
*
334565 GAAACATAAAT
64 GAAACAGAAAT
* * * * *
334576 TTTATCTCATTTGATATTATTTTTCTTAAAACAAACTTCGTCTCGCTTGAAACAGTTTCACTTGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTCACTCGA
*
334641 AACATAAAT
66 AACAGAAAT
* * * *
334650 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGGCTCGCTTAAGACAGTTTCACTCGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTCACTCGA
334715 AACAGAAAT
66 AACAGAAAT
* * * * *
334724 TTTATCTCACTTGAGATTGTTTTTCCTAAAAACAAACTTTGTCTCGCTTGAGACAATTTCCCTCA
1 TTTATCTCACTTGAGATTGTTTTT-CTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTCACTCG
334789 AAACAGAAAT
65 AAACAGAAAT
334799 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACTCG
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAG-TTTCACTCG
334864 AAACAGAAAT
65 AAACAGAAAT
* * * *
334874 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGCCTCGCTCGATACAATTTCACTCGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTCACTCGA
*
334939 AATAGAAAT
66 AACAGAAAT
** *
334948 TTTATCTCACTTGAGAGAGTTTTTCTTAAAACAAAGTTCGT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGT
334989 GCAACACCCC
Statistics
Matches: 372, Mismatches: 38, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
74 191 0.51
75 181 0.49
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (74 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTCACTCGA
AACAGAAAT
Found at i:334756 original size:149 final size:148
Alignment explanation
Indices: 334501--334988 Score: 708
Period size: 149 Copynumber: 3.3 Consensus size: 148
334491 AATACAAAAA
*
334501 TTTATCTCACTCT-AGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAATTTTCACTC
1 TTTATCTCACT-TGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGAC-AGTTTCACTC
* * * *
334565 GAAACATAAATTTTATCTCATTTGATATTATTTTTCTTAAAACAAACTTCGTCTCGCTTGAAACA
64 GAAACAGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAAACA
* * *
334630 GTTTCACTTGAAACATAAAT
129 ATTTCACTCGAAACAGAAAT
* * * * *
334650 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGGCTCGCTTAAGACAGTTTCACTCGA
1 TTTATCTCACTTGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTCACTCGA
* * *
334715 AACAGAAATTTTATCTCACTTGAGATTGTTTTTCCTAAAAACAAACTTTGTCTCGCTTGAGACAA
66 AACAGAAATTTTATCTCACTTGAGATTGTTTTT-CTTAAAACAAACTTCGTCTCGCTTGAAACAA
* *
334780 TTTCCCTCAAAACAGAAAT
130 TTTCACTCGAAACAGAAAT
*
334799 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACTCG
1 TTTATCTCACTTGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAG-TTTCACTCG
* * *
334864 AAACAGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGCCTCGCTCGATACAA
65 AAACAGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAAACAA
*
334929 TTTCACTCGAAATAGAAAT
130 TTTCACTCGAAACAGAAAT
* *
334948 TTTATCTCACTTGAGAGAGTTTTTCTTAAAACAAAGTTCGT
1 TTTATCTCACTTGAGATAGTTTTTCTTAAAACAAACTTCGT
334989 GCAACACCCC
Statistics
Matches: 303, Mismatches: 33, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
148 41 0.14
149 219 0.72
150 43 0.14
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (148 bp):
TTTATCTCACTTGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTCACTCGA
AACAGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAAACAAT
TTCACTCGAAACAGAAAT
Found at i:335757 original size:21 final size:21
Alignment explanation
Indices: 335726--335776 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
335716 ATATAAAATT
*
335726 TGTCCCGAAGGACCACATAGA
1 TGTCCCAAAGGACCACATAGA
* * *
335747 TGTCTCAAAGGACCATATATA
1 TGTCCCAAAGGACCACATAGA
335768 TGTCCCAAA
1 TGTCCCAAA
335777 TGAACACTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
TGTCCCAAAGGACCACATAGA
Found at i:336225 original size:27 final size:30
Alignment explanation
Indices: 336168--336227 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
336158 CATATGTTCG
*
336168 TATAACATATAGATCATCACCATATAACATA
1 TATAACATATACATCATCACCA-ATAACATA
336199 TATAACATATACAT-ATCA-C-ATAACATA
1 TATAACATATACATCATCACCAATAACATA
336226 TA
1 TA
336228 ATACATACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 10 0.36
29 1 0.04
30 4 0.14
31 13 0.46
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (30 bp):
TATAACATATACATCATCACCAATAACATA
Found at i:336389 original size:22 final size:23
Alignment explanation
Indices: 336345--336389 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
336335 TTTTTCACTT
*
336345 ATTCATATAATTTCATTATACCA
1 ATTCATATAATTTCATTACACCA
*
336368 ATTCCTATAATTT-ATTACACCA
1 ATTCATATAATTTCATTACACCA
336390 TCATGTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTCATATAATTTCATTACACCA
Found at i:337820 original size:17 final size:16
Alignment explanation
Indices: 337789--337822 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
337779 CACGTGAGGA
337789 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
337805 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
337822 T
1 T
337823 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:344217 original size:19 final size:21
Alignment explanation
Indices: 344180--344222 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
344170 TAACTTTTTC
344180 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
344200 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
344220 TTT
1 TTT
344223 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:344228 original size:19 final size:20
Alignment explanation
Indices: 344179--344228 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
344169 TTAACTTTTT
*
344179 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
344199 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
344218 CTTTTACCTTT
1 CTTTTACCTTT
344229 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:348024 original size:17 final size:16
Alignment explanation
Indices: 347993--348026 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
347983 CACGTGAGGA
347993 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
348009 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
348026 T
1 T
348027 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:350419 original size:37 final size:36
Alignment explanation
Indices: 350331--350441 Score: 116
Period size: 36 Copynumber: 3.1 Consensus size: 36
350321 AAACAAGAAG
* * * * * * *
350331 TTTATCTCACTTAAGATTGTTTTTCTTAAAATAAAC
1 TTTATCTCACCTGAGATAGTTTCTCTTCAAACAAAT
* *
350367 TTCATCTCACTTGAGATAGTTT-TCTCTCGAAACAAAT
1 TTTATCTCACCTGAGATAGTTTCTCT-TC-AAACAAAT
350404 TTTATCTCACCTGAGATAGTTTCTCTTCAAACAAAT
1 TTTATCTCACCTGAGATAGTTTCTCTTCAAACAAAT
350440 TT
1 TT
350442 CTTTTCGTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 3 0.05
36 30 0.47
37 28 0.44
38 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (36 bp):
TTTATCTCACCTGAGATAGTTTCTCTTCAAACAAAT
Found at i:350436 original size:36 final size:35
Alignment explanation
Indices: 350331--350441 Score: 123
Period size: 37 Copynumber: 3.1 Consensus size: 35
350321 AAACAAGAAG
* * * * *
350331 TTTATCTCACTTAAGATTGTTTTTCTTAAAATAAAC
1 TTTATCTCACTTGAGATAG-TTTTCTTCAAACAAAT
*
350367 TTCATCTCACTTGAGATAGTTTTCTCTCGAAACAAAT
1 TTTATCTCACTTGAGATAGTTTTCT-TC-AAACAAAT
*
350404 TTTATCTCACCTGAGATAGTTTCTCTTCAAACAAAT
1 TTTATCTCACTTGAGATAGTTT-TCTTCAAACAAAT
350440 TT
1 TT
350442 CTTTTCGTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 6 0.09
36 27 0.42
37 28 0.44
38 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (35 bp):
TTTATCTCACTTGAGATAGTTTTCTTCAAACAAAT
Found at i:350784 original size:99 final size:96
Alignment explanation
Indices: 350583--350788 Score: 218
Period size: 98 Copynumber: 2.1 Consensus size: 96
350573 ATAAACCAAT
** *
350583 CAACATTTCCAATGGAGAAGAAGTTCGTAATGAAGAACTTGTTCAACTTTTGCTAGATTCACGAC
1 CAACATTTCCAATAAAGAAGAAGTTCATAATGAAGAACTTGTTCAACTTTTGCTAGATTCACGAC
* * * *
350648 ATTTGAATCAGCGAAACTTCACTTGAGGGAT
66 ATTTGAATCAGCGAAACCTCACTCGAGGCAC
* ** * *
350679 TAACATTTCCAATAAAGACTAAGTTCATAATGAGAATAACTTGTTCAAAC-TTTGCTCGATTCAC
1 CAACATTTCCAATAAAGAAGAAGTTCATAAT--GAAGAACTTGTTC-AACTTTTGCTAGATTCAC
** *
350743 GGTATTTCGAATCAGC-AATGCCTCACTCGAGGCAC
63 GACATTT-GAATCAGCGAA-ACCTCACTCGAGGCAC
350778 CAACATTTCCA
1 CAACATTTCCA
350789 GTGGAAAGAT
Statistics
Matches: 89, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
96 25 0.28
98 32 0.36
99 32 0.36
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (96 bp):
CAACATTTCCAATAAAGAAGAAGTTCATAATGAAGAACTTGTTCAACTTTTGCTAGATTCACGAC
ATTTGAATCAGCGAAACCTCACTCGAGGCAC
Found at i:352413 original size:22 final size:21
Alignment explanation
Indices: 352387--352447 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
352377 TTTACACTTA
352387 TTTTTTTTTATTTTTTAAGC-
1 TTTTTTTTTATTTTTTAAGCT
* * **
352407 TTGTTTTTT-CTTTTTAATAT
1 TTTTTTTTTATTTTTTAAGCT
352427 TTTTCTTTTTATTTTTTAAGC
1 TTTT-TTTTTATTTTTTAAGC
352448 AATGTTCATT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
19 7 0.23
20 11 0.37
21 5 0.17
22 7 0.23
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTTTTTTATTTTTTAAGCT
Found at i:354151 original size:22 final size:22
Alignment explanation
Indices: 354126--354167 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
354116 ATAAAAGGCT
*
354126 AAATTAAAAAAAGAAATAAATG
1 AAATAAAAAAAAGAAATAAATG
354148 AAATAAAAAAAAGAAATAAA
1 AAATAAAAAAAAGAAATAAA
354168 AAAACTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (22 bp):
AAATAAAAAAAAGAAATAAATG
Found at i:354170 original size:13 final size:13
Alignment explanation
Indices: 354147--354171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
354137 AGAAATAAAT
354147 GAAATAAAAAAAA
1 GAAATAAAAAAAA
354160 GAAATAAAAAAA
1 GAAATAAAAAAA
354172 CTAGCTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
GAAATAAAAAAAA
Found at i:354190 original size:32 final size:30
Alignment explanation
Indices: 354154--354236 Score: 78
Period size: 33 Copynumber: 2.6 Consensus size: 30
354144 AATGAAATAA
* **
354154 AAAAAAGAAATAAAAAAACTAGCTAAAATTAG
1 AAAAAAGAAATAAAAAAA-T-GCAAAAAGAAG
*
354186 -AAAAAGTAAAATAAAAACAATTCAAAAAGAAG
1 AAAAAAG--AAATAAAAA-AATGCAAAAAGAAG
354218 AAAAAAGAAATAAAAAAAT
1 AAAAAAGAAATAAAAAAAT
354237 AAAGATAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
30 3 0.07
31 15 0.35
32 7 0.16
33 16 0.37
34 2 0.05
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.13
Consensus pattern (30 bp):
AAAAAAGAAATAAAAAAATGCAAAAAGAAG
Found at i:354359 original size:10 final size:10
Alignment explanation
Indices: 354344--354370 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
354334 AAAAGAAATA
354344 AATTAAAAAC
1 AATTAAAAAC
354354 AATTAAAAAC
1 AATTAAAAAC
354364 AATTAAA
1 AATTAAA
354371 TTAAAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (10 bp):
AATTAAAAAC
Found at i:357490 original size:54 final size:54
Alignment explanation
Indices: 357377--357490 Score: 131
Period size: 53 Copynumber: 2.1 Consensus size: 54
357367 TTTTTTTTTT
* * ** *
357377 TTTTTTCTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACGTTTC
1 TTTTTTCTTTTTTCAATTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGAATA
* * * *
357431 CTTTTTC-TTTTTCAATTTAGGATGCCCTCTCGGGTTTTCATCCTAAGCGAAATA
1 TTTTTTCTTTTTTCAATTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG-AATA
357485 TTTTTT
1 TTTTTT
357491 GAATACATCT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
53 37 0.76
54 12 0.24
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (54 bp):
TTTTTTCTTTTTTCAATTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGAATA
Found at i:361402 original size:46 final size:46
Alignment explanation
Indices: 361335--361430 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
361325 AACTTTGGCA
* *
361335 AGGTGATTTTGAATACATAACCACCTGATTTAAATGTGTCATAAAG
1 AGGTGATTTCGAACACATAACCACCTGATTTAAATGTGTCATAAAG
* *
361381 AGGTGGTTTCGAACACATAACCACCTGATTTAAATGTGTCGTAAAG
1 AGGTGATTTCGAACACATAACCACCTGATTTAAATGTGTCATAAAG
361427 AGGT
1 AGGT
361431 AGGAATACCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (46 bp):
AGGTGATTTCGAACACATAACCACCTGATTTAAATGTGTCATAAAG
Done.