Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001991.1 Hibiscus syriacus cultivar Beakdansim tig00004072_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: 2373627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 13
Found at i:455 original size:36 final size:36
Alignment explanation
Indices: 305--458 Score: 222
Period size: 36 Copynumber: 4.3 Consensus size: 36
295 TTCACTTTTT
* * *
305 GGTGAAGACTTCAGATGGTTTGCTTCACTACTCTCT
1 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
*
341 GGTGAA-GATT-ATGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGGCTTCA-GATGGTTTGCTTCACTATTCTCC
* * *
376 GGTGAAGGCTTCAGATTGATTGCTTCACTATTTTCC
1 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
412 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
448 GGTGAAGGCTT
1 GGTGAAGGCTT
459 AGGATTGACT
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 29 0.28
36 73 0.70
37 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (36 bp):
GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
Found at i:5067 original size:20 final size:21
Alignment explanation
Indices: 5042--5178 Score: 92
Period size: 21 Copynumber: 6.6 Consensus size: 21
5032 AATGTGAAGT
5042 GGTCTTCAT-GTCGTTATG-AA
1 GGTCTTC-TCGTCGTTATGAAA
5062 GGTCTTCTCGTCGTTATGAAA
1 GGTCTTCTCGTCGTTATGAAA
*
5083 GGTCTTCTCGTC-TTGATGAAT
1 GGTCTTCTCGTCGTT-ATGAAA
* *
5104 GGCCTTCTCGTC-TTGATGAAT
1 GGTCTTCTCGTCGTT-ATGAAA
5125 GG-CATTCTCGTC-TTGATG-AA
1 GGTC-TTCTCGTCGTT-ATGAAA
* * *
5145 TGACATTCTCGTC-TTGATGAAT
1 GGTC-TTCTCGTCGTT-ATGAAA
*
5167 GCTCTTCTCGTC
1 GGTCTTCTCGTC
5179 CTTGGTACAA
Statistics
Matches: 103, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.01
20 21 0.20
21 79 0.77
22 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (21 bp):
GGTCTTCTCGTCGTTATGAAA
Found at i:5086 original size:21 final size:21
Alignment explanation
Indices: 5060--5178 Score: 127
Period size: 21 Copynumber: 5.7 Consensus size: 21
5050 TGTCGTTATG
5060 AAGGTCTTCTCGTCGTT-ATGA
1 AAGGTCTTCTCGTC-TTGATGA
5081 AAGGTCTTCTCGTCTTGATGA
1 AAGGTCTTCTCGTCTTGATGA
* *
5102 ATGGCCTTCTCGTCTTGATGA
1 AAGGTCTTCTCGTCTTGATGA
*
5123 ATGG-CATTCTCGTCTTGATG-
1 AAGGTC-TTCTCGTCTTGATGA
* *
5143 AATGACATTCTCGTCTTGATGA
1 AAGGTC-TTCTCGTCTTGATGA
* *
5165 ATGCTCTTCTCGTC
1 AAGGTCTTCTCGTC
5179 CTTGGTACAA
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.06
21 79 0.92
22 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.39
Consensus pattern (21 bp):
AAGGTCTTCTCGTCTTGATGA
Found at i:10477 original size:23 final size:23
Alignment explanation
Indices: 10433--10477 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
10423 AAAAGTATAA
* *
10433 GAAAACGTGTCATAAATGCAGAT
1 GAAAACGTGTAACAAATGCAGAT
10456 GAAAACGTGTAACACAAT-CAGA
1 GAAAACGTGTAACA-AATGCAGA
10478 CTTATTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.18
Consensus pattern (23 bp):
GAAAACGTGTAACAAATGCAGAT
Found at i:12086 original size:12 final size:13
Alignment explanation
Indices: 12061--12089 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12051 AGATATATAT
12061 AATAAATAAATAA
1 AATAAATAAATAA
12074 AATAAAT-AATAA
1 AATAAATAAATAA
12086 AATA
1 AATA
12090 CTAATAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:13915 original size:65 final size:65
Alignment explanation
Indices: 13789--13943 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
13779 AGGCCAATAT
* * * * *
13789 CCTTCGCTGTGAAGTTGAAATTG-GC-TCTGAAATTGGGAAGTTATTTGTTGACAGCCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGCTTCTGAAACTGGGAAATTATTTGTTGACAACCAGCGGCC
*
13852 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAATT-TTTGTTGACAACCAGCGGC
1 CCTTCGTTGTGAAGTTGAACTTGTGCT-TCTGAAACTGGGAAATTATTTGTTGACAACCAGCGGC
13916 C
65 C
*
13917 CCTTCGTCGTGAAGTTGAACTTGTGCT
1 CCTTCGTTGTGAAGTTGAACTTGTGCT
13944 CTCTCGAGTC
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
63 21 0.26
64 2 0.02
65 45 0.55
66 14 0.17
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (65 bp):
CCTTCGTTGTGAAGTTGAACTTGTGCTTCTGAAACTGGGAAATTATTTGTTGACAACCAGCGGCC
Found at i:14121 original size:263 final size:264
Alignment explanation
Indices: 13776--14412 Score: 807
Period size: 263 Copynumber: 2.4 Consensus size: 264
13766 TTGTGTTGCT
* * * * *
13776 TCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGAC
1 TCGAGTCCAATATCATTCGTTGTGAAGTTGAAATT-G----G-AATTGGGAAATTGTTTGTTGAC
13841 AGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTC-TTAAACTGGGAAATTTTTGTTGA
60 AGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAAACTGGGAAA-TTTTGTTGA
**
13905 CAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGTGCTCTCTCGAGTCCAATATCCTTCGCTGT
124 CAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCACTCTCTCGAGTCCAATATCCTTCGCTGT
* ** *
13970 GAAGTTGAAATTGGCTC-GAGAAATTGTTTGTTGACAGTCAGCGGCCCCTTCGTTGTGAAGTTGA
189 GAAGTTGAAATTGGCTCAGAGAAA-TGTTTGATGACAACCAGCGGCCCCTTCGTCGTGAAGTTGA
14034 ACTTGAGCTGTC
253 ACTTGAGCTGTC
*
14046 TCGAGTCCAATATCATT-TTCTGTGAAGTTGAAATTGG-ATTGGGAAATTGTTTGTTGACAGCCA
1 TCGAGTCCAATATCATTCGT-TGTGAAGTTGAAATTGGAATTGGGAAATTGTTTGTTGACAGCCA
*
14109 ACGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAAACTGGGAAATTTTGTTGACAACCA
65 GCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAAACTGGGAAATTTTGTTGACAACCA
* * * * *
14174 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
130 GCGGCCCCTTCGTCGTGAAGTTGAACTTGCACTCTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
*
14239 GAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
195 GAAATTGGCTC---A---GAGAAATGTTTGATGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAA
* *
14304 CTTGCGTTGTC
254 CTTGAGCTGTC
* * *
14315 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAA-TGTTTGATGAC
1 TCGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGG-----AATTGG-GAAATTGTTTGTTGAC
* * *
14379 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
60 AGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTG
14413 CGTTGTCTGG
Statistics
Matches: 321, Mismatches: 29, Indels: 29
0.85 0.08 0.08
Matches are distributed among these distances:
263 143 0.45
264 13 0.04
265 1 0.00
269 78 0.24
270 37 0.12
275 45 0.14
276 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (264 bp):
TCGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGAATTGGGAAATTGTTTGTTGACAGCCAG
CGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAAACTGGGAAATTTTGTTGACAACCAG
CGGCCCCTTCGTCGTGAAGTTGAACTTGCACTCTCTCGAGTCCAATATCCTTCGCTGTGAAGTTG
AAATTGGCTCAGAGAAATGTTTGATGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGAGC
TGTC
Found at i:14143 original size:99 final size:99
Alignment explanation
Indices: 13888--14145 Score: 401
Period size: 99 Copynumber: 2.6 Consensus size: 99
13878 TGTCTTAAAC
* * *
13888 TGGGAAATT-TTTGTTGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGTGCTCTCTCGAG
1 TGGGAAATTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAG
* *
13952 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT
66 TCCAATATCATTCGCTGTGAAGTTGAAATTGGAT
* * * *
13986 CGAGAAATTGTTTGTTGACAGTCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGAGCTGTCTCGAG
1 TGGGAAATTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAG
**
14051 TCCAATATCATTTTCTGTGAAGTTGAAATTGGAT
66 TCCAATATCATTCGCTGTGAAGTTGAAATTGGAT
*
14085 TGGGAAATTGTTTGTTGACAGCCAACGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
1 TGGGAAATTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
14146 TTAAACTGGG
Statistics
Matches: 143, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
98 7 0.05
99 136 0.95
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (99 bp):
TGGGAAATTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAG
TCCAATATCATTCGCTGTGAAGTTGAAATTGGAT
Found at i:14166 original size:164 final size:165
Alignment explanation
Indices: 13996--14307 Score: 407
Period size: 164 Copynumber: 1.9 Consensus size: 165
13986 CGAGAAATTG
** *
13996 TTTGTTGACAGTCAGCGGCCCCTTCGTTGTGAAGTTGAACTTG-AGCTGTCTCGAGTCCAATATC
1 TTTGTTGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCA-CTGTCTCGAGTCCAATATC
* * *
14060 ATT-TTCTGTGAAGTTGAAATTGG-ATTGG-GAAATTGTTTGTTGACAGCCAACGGCCCCTTCGT
65 ATTCGT-TGTGAAGTTGAAATTGGAATTGGAGAAA-TGTTTGATGACAACCAACGGCCCCTTCGT
*
14122 TGTGAAGTTGAACTTGTGCTGTCTTTAAACTGGGAAAT
128 CGTGAAGTTGAACTTGTGCTGTCTTTAAACTGGGAAAT
* * * *
14160 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTCGAGTCCAATATCA
* *
14225 TTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTC
66 TTCGTTGTGAAGTTGAAATTGG-----AATTGGAGAAATGTTTGATGACAACCAACGGCCCCTTC
14290 GTCGTGAAGTTGAACTTG
126 GTCGTGAAGTTGAACTTG
14308 CGTTGTCTGG
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
164 75 0.60
165 2 0.02
170 45 0.36
171 4 0.03
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (165 bp):
TTTGTTGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTCGAGTCCAATATCA
TTCGTTGTGAAGTTGAAATTGGAATTGGAGAAATGTTTGATGACAACCAACGGCCCCTTCGTCGT
GAAGTTGAACTTGTGCTGTCTTTAAACTGGGAAAT
Found at i:14210 original size:65 final size:67
Alignment explanation
Indices: 14085--14210 Score: 175
Period size: 65 Copynumber: 1.9 Consensus size: 67
14075 GAAATTGGAT
* * **
14085 TGGGAAATTGTTTGTTGACAGCCAACGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAA
1 TGGGAAATTGTTTGTTGACAACCAACGGCCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTTTAA
14150 AC
66 AC
* * *
14152 TGGGAAA-T-TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
1 TGGGAAATTGTTTGTTGACAACCAACGGCCCCTTCGTCGTGAAGTTGAACTTGCACTGTCT
14211 GGAGTCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
65 44 0.85
66 1 0.02
67 7 0.13
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (67 bp):
TGGGAAATTGTTTGTTGACAACCAACGGCCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTTTAA
AC
Found at i:14300 original size:105 final size:105
Alignment explanation
Indices: 14115--14767 Score: 1038
Period size: 105 Copynumber: 6.2 Consensus size: 105
14105 GCCAACGGCC
* *
14115 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAAACTGG-GAAAT-TTTGTTGACAACCAGCGG
1 CCTTCGTTGTGAAGTTGAAATTG-GC--TC--TAAATTGGAGAAATGTTTGTTGACAACCAGCGG
*
14178 TCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
61 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
14223 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCT
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGTTGACAACCAGCGGTCCCT
14288 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
14328 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCT
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGTTGACAACCAGCGGTCCCT
14393 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
14433 CTTTCG-T-T----TTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCT
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGTTGACAACCAGCGGTCCCT
*
14492 TCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATAT
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
14532 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATCT-GAGAAATGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAAT-TGGAGAAATGTTTGTTGACAACCAGCGGTCCC
*
14596 TTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
14637 CCTTCGTTGTGAAGTTGAAATTGACTCTGAATCT-GAGAAATGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAAT-TGGAGAAATGTTTGTTGACAACCAGCGGTCCC
14701 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
14742 CCTTCGTTGTGAAGTTGAAATTGGCT
1 CCTTCGTTGTGAAGTTGAAATTGGCT
14768 ATGGGTAAAA
Statistics
Matches: 520, Mismatches: 16, Indels: 21
0.93 0.03 0.04
Matches are distributed among these distances:
99 93 0.18
100 1 0.00
101 1 0.00
103 8 0.02
104 6 0.01
105 386 0.74
106 1 0.00
107 2 0.00
108 22 0.04
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGTTGACAACCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:14527 original size:204 final size:207
Alignment explanation
Indices: 14115--14767 Score: 1014
Period size: 204 Copynumber: 3.1 Consensus size: 207
14105 GCCAACGGCC
* *
14115 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAAACTGG-GAAAT-TTTGTTGACAACCAGCGG
1 CCTTCGTTGTGAAGTTGAAATTG-GC--TC--TAAATTGGAGAAATGTTTGTTGACAACCAGCGG
*
14178 TCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
61 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT--A-TTGAAA
*
14243 TTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
123 TTGGCTCTGAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
14308 CGTTGTCTGGAGTCCAATAT
188 CGTTGTCTGGAGTCCAATAT
*
14328 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCT
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGTTGACAACCAGCGGTCCCT
*
14393 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCG-T-T-TTGAAATTGGCTCT
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTATTGAAATTGGCTCT
*
14455 GAATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
131 GAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
14520 CGAGTCCAATAT
196 GGAGTCCAATAT
* * *
14532 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATCT-GAGAAATGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAAT-TGGAGAAATGTTTGTTGACAACCAGCGGTCCC
* *
14596 TTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGA
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT--A-TTGAAATTGG
*
14661 CTCTGAATCT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
127 CTCTGAAT-TGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
14725 TGTCTGGAGTCCAATAT
191 TGTCTGGAGTCCAATAT
14742 CCTTCGTTGTGAAGTTGAAATTGGCT
1 CCTTCGTTGTGAAGTTGAAATTGGCT
14768 ATGGGTAAAA
Statistics
Matches: 411, Mismatches: 19, Indels: 23
0.91 0.04 0.05
Matches are distributed among these distances:
204 191 0.46
205 2 0.00
206 1 0.00
208 8 0.02
209 6 0.01
210 178 0.43
211 1 0.00
212 2 0.00
213 22 0.05
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (207 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGTTGACAACCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTATTGAAATTGGCTCT
GAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
GGAGTCCAATAT
Found at i:14724 original size:309 final size:308
Alignment explanation
Indices: 14155--14754 Score: 1042
Period size: 309 Copynumber: 1.9 Consensus size: 308
14145 TTTAAACTGG
* *
14155 GAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAA
1 GAAATTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCAA
* *
14220 TATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTC
66 TATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTC
*
14285 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
131 CCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
14350 GGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
196 GACTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* *
14415 TTGTCTGGAGTCCAATATCTTTCGTTTTGAAATTGGCTCTGAATTGGA
261 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAATTGGCTCTGAATTGGA
*
14463 GAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCA
1 GAAAT-TTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCA
* *
14528 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATCT-GAGAAATGTTTGTTGACAACCAGCGG
65 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAAT-TGGAGAAATGTTTGATGACAACCAGCGG
14592 TCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
129 TCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* *
14657 TTGACTCTGAATCT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
194 TTGACTCTAAAT-TGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
14721 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
258 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
14755 GTTGAAATTG
Statistics
Matches: 276, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
308 5 0.02
309 269 0.97
310 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (308 bp):
GAAATTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCAA
TATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTC
CCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GACTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
TTGTCTGGAGTCCAATATCCTTCGTTGTGAAATTGGCTCTGAATTGGA
Found at i:26184 original size:2 final size:2
Alignment explanation
Indices: 26177--26222 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
26167 AGATAAAAAC
*
26177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26219 AT AT
1 AT AT
26223 TAACTTGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26312 original size:43 final size:40
Alignment explanation
Indices: 26265--26365 Score: 102
Period size: 43 Copynumber: 2.5 Consensus size: 40
26255 ATATAGATAT
26265 ATATAATAAATAAATAAATAAAATAA-TAA-AATACTAATAACA
1 ATAT-ATAAATAAATAAATAAAA-AACTAATAATACT-ATAA-A
*
26307 CATATATGTAA-AAATAAAATAAAAAACTAATAATACTATAAA
1 -ATATAT-AAATAAAT-AAATAAAAAACTAATAATACTATAAA
26349 ATATATAAATAAA-AAAT
1 ATATATAAATAAATAAAT
26366 TAGAATTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
39 4 0.08
40 2 0.04
41 9 0.18
42 9 0.18
43 21 0.41
44 6 0.12
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (40 bp):
ATATATAAATAAATAAATAAAAAACTAATAATACTATAAA
Found at i:28183 original size:3 final size:3
Alignment explanation
Indices: 28168--28235 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
28158 AATATAAAAT
*
28168 TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28216 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
28236 CTGGCGACTA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31201 original size:2 final size:2
Alignment explanation
Indices: 31196--31228 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31186 ACACACACAC
31196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31229 GAGAAAAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31284 original size:20 final size:20
Alignment explanation
Indices: 31259--31296 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
31249 TTTGGTTCAC
31259 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
31279 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
31297 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:31442 original size:18 final size:18
Alignment explanation
Indices: 31419--31466 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
31409 AAATTGTCCT
* *
31419 TATTATATATTTGTATAA
1 TATTATATATTTGGAAAA
*
31437 TATTATA-AGTTGGAAAA
1 TATTATATATTTGGAAAA
31454 TATTTATATATTT
1 TA-TTATATATTT
31467 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (18 bp):
TATTATATATTTGGAAAA
Found at i:34623 original size:23 final size:23
Alignment explanation
Indices: 34569--34627 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
34559 ATATTAATCC
*
34569 GTTCGTTTATGTTTGTTCATTTAA
1 GTTCATTTAT-TTTGTTCATTTAA
* *
34593 -TTAAATTTATTTTTTTCATTTAA
1 GTT-CATTTATTTTGTTCATTTAA
34616 GTTCATTTATTT
1 GTTCATTTATTT
34628 ATATTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.63
Consensus pattern (23 bp):
GTTCATTTATTTTGTTCATTTAA
Found at i:36848 original size:285 final size:285
Alignment explanation
Indices: 36333--36903 Score: 1027
Period size: 285 Copynumber: 2.0 Consensus size: 285
36323 TCAGGTTGCT
* * *
36333 TGGTTGTAAGTGTTATTTTAGGTTAATTATTAGATCCTTTGCCGTGTGTGAGGGTCTATTGTGGT
1 TGGTTATAAGTGTTATTTTAGGTTAATTATTAGATCCTTTGCAGTGTGTGAGGGTCTATTGTAGT
36398 CAATTATTAGATTATTTGCTTCAAAAGGTCATCTTGAGATCTAAAGTACTATTTGTTTCGTTAAT
66 CAATTATTAGATTATTTGCTTCAAAAGGTCATCTTGAGATCTAAAGTACTATTTGTTTCGTTAAT
36463 ATAAGATTAAAAAAATGATATAATTCTGATGTAGTTGGAAATTTTATTAATTTTTTTAGGTTGGA
131 ATAAGATTAAAAAAATGATATAATTCTGATGTAGTTGGAAATTTTATTAATTTTTTTAGGTTGGA
36528 CAATATAATATTTTATATTAAAATTAACAATATTATC-TTTTCATAACAATTTTTATACATAAAA
196 CAATATAATATTTTATATTAAAATTAACAATATTATCTTTTTCATAACAATTTTTATACATAAAA
*
36592 TTTTCATTTGTAAACACTAAACATG
261 TTTTCATTTATAAACACTAAACATG
36617 TGGTTATAAGTGTTATTTTAGGTTAATTATTAGATCCTTTGCAGTGTGTGAGGGTCTATTGTAGT
1 TGGTTATAAGTGTTATTTTAGGTTAATTATTAGATCCTTTGCAGTGTGTGAGGGTCTATTGTAGT
* * *
36682 TAATTATTAGATTATTTGCTTCAAAATGTCATCTTGAGAATCTAAAGTACTATTTGTTTTGTTAA
66 CAATTATTAGATTATTTGCTTCAAAAGGTCATCTTGAG-ATCTAAAGTACTATTTGTTTCGTTAA
* *
36747 TATAAGATTAAAAAAATGATATATTTCTGTTGTAGTTGGAAATTTTATTAATTTTTTTAGGTTGG
130 TATAAGATTAAAAAAATGATATAATTCTGATGTAGTTGGAAATTTTATTAATTTTTTTAGGTTGG
*
36812 ACAATATAATATTTTATATTAAAATTGACAATATTATCTTTTTCATAACAATTTTTATACATAAA
195 ACAATATAATATTTTATATTAAAATTAACAATATTATCTTTTTCATAACAATTTTTATACATAAA
*
36877 ATTTTCGTTTATAAACACTAAACATG
260 ATTTTCATTTATAAACACTAAACATG
36903 T
1 T
36904 TGAAATGTAA
Statistics
Matches: 274, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
284 98 0.36
285 125 0.46
286 51 0.19
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (285 bp):
TGGTTATAAGTGTTATTTTAGGTTAATTATTAGATCCTTTGCAGTGTGTGAGGGTCTATTGTAGT
CAATTATTAGATTATTTGCTTCAAAAGGTCATCTTGAGATCTAAAGTACTATTTGTTTCGTTAAT
ATAAGATTAAAAAAATGATATAATTCTGATGTAGTTGGAAATTTTATTAATTTTTTTAGGTTGGA
CAATATAATATTTTATATTAAAATTAACAATATTATCTTTTTCATAACAATTTTTATACATAAAA
TTTTCATTTATAAACACTAAACATG
Found at i:38036 original size:84 final size:84
Alignment explanation
Indices: 37884--38043 Score: 248
Period size: 84 Copynumber: 1.9 Consensus size: 84
37874 GATAATTTAG
* *
37884 TAAAATACACATTCAAGTAATCTTATGTTTCTCCAACCAAACACTGTAATTTTACATTACTACAA
1 TAAAATACACATTCAAGTAATCTTATATTCCTCCAACCAAACACTGTAATTTTACATTACTACAA
37949 AACAAACCAAACAATATAC
66 AACAAACCAAACAATATAC
* * * * * *
37968 TAAAATATACATTCAAGTAATCTTATATTCCTCCAATCAAACACTTTAATTTTATATTCCTACTA
1 TAAAATACACATTCAAGTAATCTTATATTCCTCCAACCAAACACTGTAATTTTACATTACTACAA
38033 AACAAACCAAA
66 AACAAACCAAA
38044 TAAGATATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 68 1.00
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (84 bp):
TAAAATACACATTCAAGTAATCTTATATTCCTCCAACCAAACACTGTAATTTTACATTACTACAA
AACAAACCAAACAATATAC
Found at i:38648 original size:5 final size:5
Alignment explanation
Indices: 38638--38698 Score: 63
Period size: 5 Copynumber: 12.4 Consensus size: 5
38628 TTAGATATAA
* * **
38638 AAAAT AAAAT AAAAT -AAAT AAATT CAACC AAAAT AAAA- AGAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT
38687 AAAAT AAAAT AA
1 AAAAT AAAAT AA
38699 TAAATAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 5 0.11
5 40 0.87
6 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:38712 original size:25 final size:24
Alignment explanation
Indices: 38638--38714 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 24
38628 TTAGATATAA
38638 AAAATAAAAT-AAAATAAATAAATT
1 AAAATAAAATAAAAATAAATAAA-T
* ** *
38662 CAACCAAAATAAAAAGAAATAAAAT
1 AAAATAAAATAAAAATAAAT-AAAT
38687 AAAATAAAATAATAAATAAATAAAT
1 AAAATAAAATAA-AAATAAATAAAT
38712 AAA
1 AAA
38715 GAATAGAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
24 7 0.17
25 25 0.60
26 10 0.24
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.19
Consensus pattern (24 bp):
AAAATAAAATAAAAATAAATAAAT
Found at i:39476 original size:37 final size:36
Alignment explanation
Indices: 39426--39527 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
39416 ATAGTAGAAC
*
39426 TCTATCATATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
* *
39463 TTTATCCTGTTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
39497 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
39528 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 32 0.55
37 26 0.45
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:40377 original size:105 final size:105
Alignment explanation
Indices: 40075--40735 Score: 924
Period size: 105 Copynumber: 6.3 Consensus size: 105
40065 CATTGTTCCA
* * ** * *
40075 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGAGAAGTTG-TTGTTGACAA
* * * *
40139 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* **
40181 AGTCCAATATACTTCGTTGTGAAGTTGAAATTGAATCTGA-A-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
*
40241 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
40281 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
*
40346 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
40386 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
* *
40451 AGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
40491 AATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
*
40556 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
40596 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTG-TTGTTGACAAG
* * *
40661 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
40702 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
40736 CGCGGATGGC
Statistics
Matches: 510, Mismatches: 33, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
99 1 0.00
100 82 0.16
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.01
105 305 0.60
106 84 0.16
107 4 0.01
109 22 0.04
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:41430 original size:68 final size:65
Alignment explanation
Indices: 41339--41496 Score: 199
Period size: 68 Copynumber: 2.4 Consensus size: 65
41329 AAGATATCTG
* * * *
41339 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGGTTTAAGGGAAATAAATTTAAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGGTTTAAGGGAAATAAATTCAAAG-G
41404 TT
64 TT
* * * *
41406 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGGTTTAAGGGAAATAAATTCAAAGGT
41471 T
65 T
* *
41472 TTGTTTCAAGGGAAAATGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
41497 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 21 0.27
66 3 0.04
67 23 0.29
68 32 0.41
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGGTTTAAGGGAAATAAATTCAAAGGTT
Found at i:41523 original size:65 final size:67
Alignment explanation
Indices: 41340--41661 Score: 160
Period size: 65 Copynumber: 4.7 Consensus size: 67
41330 AGATATCTGT
* ** * * * * * *
41340 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAA-TTATGGTTTAAGGGAAATAAATTTAAAGAT
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTAT--TTCAAGAGAAATAAATTCAAAGAG
41404 TTTG
64 TTTG
* * * * * * *
41408 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAATAAATTCAAAGAGTT
41472 T-
66 TG
* * **
41473 TGTTTCAAGGGAAAATGTCTCAAGATAGACGAAAA-TTATTTCAAGAGAAAT-TGTCTCAAGAGA
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAATAAAT-TCAA-AGA
*
41536 GACAAAACTT-
63 G------TTTG
* * * * * ** * *
41546 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAA-AGAAA-ACATATTCAAATA-
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAATA-A-ATTCAAAGAG
41608 TTT-
64 TTTG
* *
41611 TGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTAATTTCAAGGGAAA
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTT-ATTTCAAGAGAAA
41662 CTGTCTCAAG
Statistics
Matches: 193, Mismatches: 44, Indels: 35
0.71 0.16 0.13
Matches are distributed among these distances:
64 1 0.01
65 72 0.37
66 15 0.08
67 25 0.13
68 30 0.16
69 3 0.02
72 9 0.05
73 37 0.19
74 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (67 bp):
TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAATAAATTCAAAGAGTT
TG
Found at i:41528 original size:36 final size:36
Alignment explanation
Indices: 41475--41753 Score: 245
Period size: 36 Copynumber: 7.9 Consensus size: 36
41465 AAAGGTTTTG
* * *
41475 TTTCAAGGGAAAATGTCTCAAGATAGACGAAAA-TTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTA
* *
41511 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
* * * ** *
41547 GTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTG
1 -TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
* * * *
41584 TTTCAA-AGAAAACATAT-TC-----A-A-ATATTTTG
1 TTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTTA
* *
41613 TTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT-A
* * *
41650 TTTCAAGGGAAACTGTCTCAAGATAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
*
41686 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTC
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
*
41722 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
41754 CTCTTCTAGT
Statistics
Matches: 200, Mismatches: 29, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 2 0.01
31 1 0.00
34 1 0.00
35 7 0.04
36 108 0.54
37 63 0.31
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:41574 original size:138 final size:138
Alignment explanation
Indices: 41420--41727 Score: 413
Period size: 138 Copynumber: 2.2 Consensus size: 138
41410 TTTCAAGAGT
* ** * * *
41420 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
41485 AAATGTCTCAAGATAGACGAAAA-TT-ATTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAG
66 AAATGTCTCAAGAGAGAC-AAAATTTAATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAG
41548 TTCCAAAAGA
129 TTCCAAAAGA
** * *
41558 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * *
41623 AAATGTCTCAAGAGAGACAAAATTTAATTTCAAGGGAAACTGTCTCAAGATAGACAAAATTTGTT
66 AAATGTCTCAAGAGAGACAAAATTTAATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTT
* *
41688 TCAAGAGA
131 CCAAAAGA
* *
41696 AACTGTCTCAAGAGAGACAAAATTTCTTTCAA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAA
41728 GGGAAACTGT
Statistics
Matches: 147, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
137 4 0.03
138 113 0.77
139 30 0.20
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (138 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
AAATGTCTCAAGAGAGACAAAATTTAATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTT
CCAAAAGA
Found at i:41639 original size:102 final size:103
Alignment explanation
Indices: 41511--41697 Score: 268
Period size: 102 Copynumber: 1.8 Consensus size: 103
41501 ACGAAAATTA
* * *
41511 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGAC
1 TTTCAAGAGAAAATGTCTCAAGAGAGACAAAACTTAATTCCAAAAGAAACTGTCTCAAGAGAGAC
**
41576 GGAATTTGTTTCAA-AGAAAACATATTCAAATATTTTG
66 AAAATTTGTTTCAAGAGAAAACATATTCAAATATTTTG
* * * ** *
41613 TTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTAATTTCAAGGGAAACTGTCTCAAGATAGAC
1 TTTCAAGAGAAAATGTCTCAAGAGAGACAAAACTTAATTCCAAAAGAAACTGTCTCAAGAGAGAC
41678 AAAATTTGTTTCAAGAGAAA
66 AAAATTTGTTTCAAGAGAAA
41698 CTGTCTCAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
102 68 0.93
103 5 0.07
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (103 bp):
TTTCAAGAGAAAATGTCTCAAGAGAGACAAAACTTAATTCCAAAAGAAACTGTCTCAAGAGAGAC
AAAATTTGTTTCAAGAGAAAACATATTCAAATATTTTG
Found at i:41775 original size:35 final size:36
Alignment explanation
Indices: 41613--41787 Score: 187
Period size: 36 Copynumber: 4.9 Consensus size: 36
41603 AAATATTTTG
* *
41613 TTTCAAGGGAAAA-TGTCTCAAGAGAGACAAAATTTAA
1 TTTCAA-GGAAAACTGTCTCAAGAGAGACAAAATCT-C
* * * *
41650 TTTCAAGGGAAACTGTCTCAAGATAGACAAAATTTG
1 TTTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTC
*
41686 TTTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTC
1 TTTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTC
*
41722 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CTC
1 TTTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTC
* * *
41757 -TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTTCAAG-GAAAACTGTCTCAAGAGAGACAAA
41788 TCTTGTTTTA
Statistics
Matches: 122, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
34 5 0.04
35 24 0.20
36 65 0.53
37 28 0.23
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.23
Consensus pattern (36 bp):
TTTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTC
Found at i:42260 original size:18 final size:18
Alignment explanation
Indices: 42233--42268 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42223 TATTGAATCC
* *
42233 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
42251 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
42269 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:42708 original size:22 final size:22
Alignment explanation
Indices: 42682--42730 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
42672 TTGTGTTTGG
* *
42682 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
42704 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
42726 TCAAA
1 TCAAA
42731 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:42737 original size:22 final size:22
Alignment explanation
Indices: 42694--42737 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42684 AAAGGTTTGG
* * *
42694 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
42716 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
42738 TGGGGTGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:43401 original size:31 final size:29
Alignment explanation
Indices: 43354--43438 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 29
43344 TCTTTACATG
* *
43354 TGCTTTTTGTCCCTTTTTCTTTTTGATTTT
1 TGCTTTTTTTCTCTTTTTCTTTTT-ATTTT
*
43384 TG-TTCTTGTTTCTCTTTTTCTTTGTTTTTTT
1 TGCTT-TT-TTTCTCTTTTTCTTT-TTATTTT
43415 TGCTTTTTTTCT-TCTTTTCTTTTT
1 TGCTTTTTTTCTCT-TTTTCTTTTT
43439 TGTTCTTGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
29 5 0.11
30 17 0.36
31 21 0.45
32 4 0.09
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.75
Consensus pattern (29 bp):
TGCTTTTTTTCTCTTTTTCTTTTTATTTT
Found at i:46919 original size:5 final size:5
Alignment explanation
Indices: 46909--46992 Score: 56
Period size: 5 Copynumber: 17.6 Consensus size: 5
46899 TAGATATAAA
* * **
46909 AAAAT AAAAT -AAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT AAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
46955 AGAAAT AAAAT AAAAT AATAA- ATAAAT -AAAT -AAAT AAA
1 A-AAAT AAAAT AAAAT AA-AAT A-AAAT AAAAT AAAAT AAA
46993 GCATAGAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
4 21 0.33
5 39 0.61
6 4 0.06
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:46924 original size:4 final size:4
Alignment explanation
Indices: 46904--46992 Score: 60
Period size: 4 Copynumber: 21.2 Consensus size: 4
46894 CATGTTAGAT
*
46904 ATAA AAAA ATAAA ATAA ATAAA ATAA ATAA ATAA ATTCAA CCA-AA AT-A
1 ATAA ATAA AT-AA ATAA AT-AA ATAA ATAA ATAA A-T-AA --ATAA ATAA
*
46952 A-AA AGAA ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA A
46993 GCATAGAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
3 6 0.09
4 45 0.64
5 16 0.23
6 2 0.03
8 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:47015 original size:54 final size:55
Alignment explanation
Indices: 46900--47016 Score: 126
Period size: 50 Copynumber: 2.2 Consensus size: 55
46890 GAAACATGTT
*
46900 AGATA-TAAA-AAAATAAAATAAATAAAATAAATAAATAAATTCAACCAAAATAA
1 AGATAGTAAATAAAATAAAATAAATAAAATAAATAAATAAATTAAACCAAAATAA
*
46953 A-A-AG-AAATAAAATAAAAT-AAT-AAATAAATAAATAAA-TAAAGCATAGAA-AA
1 AGATAGTAAATAAAATAAAATAAATAAAATAAATAAATAAATTAAACCA-A-AATAA
47003 ATGATAGTAAATAA
1 A-GATAGTAAATAA
47017 TAGTATAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
49 5 0.09
50 19 0.35
51 9 0.17
52 12 0.22
53 3 0.06
54 6 0.11
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (55 bp):
AGATAGTAAATAAAATAAAATAAATAAAATAAATAAATAAATTAAACCAAAATAA
Found at i:47783 original size:34 final size:34
Alignment explanation
Indices: 47706--47806 Score: 148
Period size: 34 Copynumber: 2.9 Consensus size: 34
47696 ATAGTAGAAC
*
47706 TCTATCATATTTTTAGAAGTTTGAATCCTAGCAAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCT---AAAAT
*
47743 TTTATCATATTTTTAGGAGTTTGAATCCTAAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCTAAAAT
*
47777 TCTATCATATTTTTAAGAGTTTGAATCCTA
1 TCTATCATATTTTTAGGAGTTTGAATCCTA
47807 GTAGGACGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 33 0.55
37 27 0.45
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (34 bp):
TCTATCATATTTTTAGGAGTTTGAATCCTAAAAT
Found at i:52983 original size:35 final size:39
Alignment explanation
Indices: 52944--53021 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
52934 AACTTGTCGT
52944 TAAAGTTTT-AC-A-GA-GTACCAAAATAAAACAAAAAC
1 TAAAGTTTTAACAACGAGGTACCAAAATAAAACAAAAAC
* * *
52979 TAAAGTTTTAACAACGAGGTACTAAAATGAAATAAAAAC
1 TAAAGTTTTAACAACGAGGTACCAAAATAAAACAAAAAC
53018 TAAA
1 TAAA
53022 CTTTAGATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 9 0.25
36 2 0.06
37 1 0.03
38 2 0.06
39 22 0.61
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (39 bp):
TAAAGTTTTAACAACGAGGTACCAAAATAAAACAAAAAC
Found at i:61402 original size:23 final size:23
Alignment explanation
Indices: 61372--61442 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
61362 AAAAATTCAG
61372 GAGCTTGATTGAAGCTAGATTTT
1 GAGCTTGATTGAAGCTAGATTTT
61395 GAGCTTGATTGAAGCTAGATTTT
1 GAGCTTGATTGAAGCTAGATTTT
* * * *
61418 GAGCTCGATTCAAGCTCGAATTT
1 GAGCTTGATTGAAGCTAGATTTT
61441 GA
1 GA
61443 ACATACAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (23 bp):
GAGCTTGATTGAAGCTAGATTTT
Found at i:61518 original size:26 final size:25
Alignment explanation
Indices: 61488--61538 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
61478 TTTTTAAAAT
*
61488 TTATAATTATCAATAATGTATTTTTA
1 TTAT-ATTATCAATAATGTAATTTTA
* *
61514 TTATATTTTTAATAATGTAATTTTA
1 TTATATTATCAATAATGTAATTTTA
61539 AAAAATCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
TTATATTATCAATAATGTAATTTTA
Found at i:62484 original size:23 final size:23
Alignment explanation
Indices: 62458--62505 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
62448 ATAAAGTACA
*
62458 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
62481 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
62504 AT
1 AT
62506 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:63247 original size:39 final size:39
Alignment explanation
Indices: 63193--63274 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
63183 CAAGTTGTAG
*
63193 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
63232 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
63271 ATTT
1 ATTT
63275 GATGAGCATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:63560 original size:18 final size:18
Alignment explanation
Indices: 63537--63572 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
63527 CGAAATATAT
63537 TTGAAATTCAAACTCAAA
1 TTGAAATTCAAACTCAAA
* *
63555 TTGAAATTTAAATTCAAA
1 TTGAAATTCAAACTCAAA
63573 CTCCAATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
TTGAAATTCAAACTCAAA
Found at i:64069 original size:23 final size:23
Alignment explanation
Indices: 63998--64069 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
63988 ATACTTTACA
* *
63998 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
64021 ATATAAACGATACATA-TACATT
1 ATATAAACGCTACCTATTACATT
* *
64043 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
64066 ATAT
1 ATAT
64070 GTTTACCTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 19 0.47
23 21 0.52
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:64466 original size:25 final size:25
Alignment explanation
Indices: 64409--64474 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
64399 CACTCAAAAG
*
64409 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
64434 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
64459 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
64475 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:66753 original size:19 final size:19
Alignment explanation
Indices: 66675--66755 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
66665 AACGCAAGCG
66675 AAAA-TATAAATCGTATAC
1 AAAATTATAAATCGTATAC
* **
66693 AAAATTAT-ATTCACATAC
1 AAAATTATAAATCGTATAC
*
66711 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
66730 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
66749 AAAATTA
1 AAAATTA
66756 ACCCTACATT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
18 18 0.35
19 34 0.65
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:68575 original size:32 final size:33
Alignment explanation
Indices: 68539--68603 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
68529 CATCTTAATA
*
68539 TCACCCCTTAACACC-CAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
68571 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
68604 CCATCTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:68679 original size:21 final size:21
Alignment explanation
Indices: 68637--68701 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
68627 CCCCTTATGC
* * *
68637 CTATCAAGTGTATCTTCGACT
1 CTATCAAGTTTCTCTACGACT
* *
68658 CTCTCGAGTTTCTCTACGACT
1 CTATCAAGTTTCTCTACGACT
* *
68679 CGATCAAGTTTCTCTTCGACT
1 CTATCAAGTTTCTCTACGACT
68700 CT
1 CT
68702 TGATTGTCTT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.29, G:0.14, T:0.38
Consensus pattern (21 bp):
CTATCAAGTTTCTCTACGACT
Found at i:71113 original size:22 final size:22
Alignment explanation
Indices: 71088--71133 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
71078 TCCAGTAACG
*
71088 TTTTACCGGTTTTATCATTTTT
1 TTTTACCGGTTTTATCATATTT
71110 TTTTACCGGTTTTATCATATTT
1 TTTTACCGGTTTTATCATATTT
71132 TT
1 TT
71134 ACCTGGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.13, G:0.09, T:0.63
Consensus pattern (22 bp):
TTTTACCGGTTTTATCATATTT
Found at i:71824 original size:229 final size:228
Alignment explanation
Indices: 71419--71901 Score: 885
Period size: 229 Copynumber: 2.1 Consensus size: 228
71409 ACTTTTATAT
*
71419 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCAATTT
*
71484 ATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAAATAT
66 ATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAAAAAT
71549 TATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
* *
71614 TATAATAATAAATATGTTTTCAACAGTGAAATAA
196 GATAATAATAAATATATTTTC-ACAGTGAAATAA
71648 GTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCAATTT
* *
71713 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
66 ATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAAAAAT
* *
71778 TATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAACTAAA
131 TATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
71843 GATAATAATAAATATATTTTCACAGTGAAATAA
196 GATAATAATAAATATATTTTCACAGTGAAATAA
71876 GTATGGACACTTTTATAAAAATGATA
1 GTATGGACACTTTTATAAAAATGATA
71902 GATAATTTAC
Statistics
Matches: 246, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
228 38 0.15
229 208 0.85
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (228 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCAATTT
ATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAAAAAT
TATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
GATAATAATAAATATATTTTCACAGTGAAATAA
Found at i:72566 original size:15 final size:15
Alignment explanation
Indices: 72548--72579 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
72538 TTTTTTTAAG
*
72548 TTGTTTTTTATAAAA
1 TTGTATTTTATAAAA
72563 TTGTATTTTATAAAA
1 TTGTATTTTATAAAA
72578 TT
1 TT
72580 TTGAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
TTGTATTTTATAAAA
Found at i:74843 original size:34 final size:33
Alignment explanation
Indices: 74794--74882 Score: 124
Period size: 34 Copynumber: 2.7 Consensus size: 33
74784 AAAGAAGGAA
* * *
74794 GCGAGGAGAAAAGAAGGCAAGATGGTGCCGCCG
1 GCGAGGAGAAGAGAAGGCAAGATAGTACCGCCG
* *
74827 GTGAGGGAGAAGAGAAGACAAGATAGTACCGCCG
1 GCGA-GGAGAAGAGAAGGCAAGATAGTACCGCCG
74861 GCGAGGAGAAGAGAAGGCAAGA
1 GCGAGGAGAAGAGAAGGCAAGA
74883 AAATATTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 20 0.42
34 28 0.58
ACGTcount: A:0.38, C:0.15, G:0.42, T:0.06
Consensus pattern (33 bp):
GCGAGGAGAAGAGAAGGCAAGATAGTACCGCCG
Found at i:78809 original size:9 final size:9
Alignment explanation
Indices: 78797--78848 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
78787 TATTATTTTA
78797 TATTTAATT
1 TATTTAATT
*
78806 TATTTAA-G
1 TATTTAATT
78814 TATTTAATT
1 TATTTAATT
78823 TATTTAA--
1 TATTTAATT
*
78830 TATTTTATT
1 TATTTAATT
*
78839 TAATTAATT
1 TATTTAATT
78848 T
1 T
78849 TTTGCATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:78819 original size:17 final size:16
Alignment explanation
Indices: 78789--78846 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
78779 TATATTTTTA
*
78789 TTATTTTATATTTAAT
1 TTATTTAATATTTAAT
78805 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTAAT
*
78822 TTATTTAATATTTTAT
1 TTATTTAATATTTAAT
*
78838 TTAATTAAT
1 TTATTTAAT
78847 TTTTTGCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 22 0.58
17 16 0.42
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTATTTAATATTTAAT
Found at i:87527 original size:24 final size:24
Alignment explanation
Indices: 87495--87557 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
87485 ATGTGTCAAG
*
87495 ATATTTAATTGGAATCTTTAATTT
1 ATATTTAATTGAAATCTTTAATTT
87519 ATATTTAATTGAAATCTTTAATTT
1 ATATTTAATTGAAATCTTTAATTT
87543 ATATTTAATTGAAAT
1 ATATTTAATTGAAAT
87558 GTTTTCCTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.52
Consensus pattern (24 bp):
ATATTTAATTGAAATCTTTAATTT
Found at i:89315 original size:109 final size:108
Alignment explanation
Indices: 89100--89315 Score: 252
Period size: 108 Copynumber: 2.0 Consensus size: 108
89090 GATAATTTAA
* * * *
89100 AAATGATGGTCAAAATAAAAATGAACTATAATTAGGTAGTAATTGATATAGTTCACCTAAAATAT
1 AAATGATGATCAAAATAAAAATGAACTATAATTAGGTAGTAACTAATATAATTCACCTAAAATAT
* *
89165 ATTACTACAAGTAAACATATAAGAAATTGGGTATTTGTATTAG
66 ACTACTACAAGTAAACATATAAGAAATTAGGTATTTGTATTAG
* * * * * * *
89208 AAATGTTGATCAAAATGAAAATGGATTATAATTAGGTGGTTACTAATATAATTTACCCTAAAATA
1 AAATGATGATCAAAATAAAAATGAACTATAATTAGGTAGTAACTAATATAATTCA-CCTAAAATA
* * * * * *
89273 TACTATTACAATTCAACATTTAATAGATTAGGTATTTGTATTA
65 TACTACTACAAGTAAACATATAAGAAATTAGGTATTTGTATTA
89316 AAGGTAAAAT
Statistics
Matches: 88, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
108 44 0.50
109 44 0.50
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (108 bp):
AAATGATGATCAAAATAAAAATGAACTATAATTAGGTAGTAACTAATATAATTCACCTAAAATAT
ACTACTACAAGTAAACATATAAGAAATTAGGTATTTGTATTAG
Found at i:92645 original size:29 final size:31
Alignment explanation
Indices: 92577--92642 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
92567 TGTTCAAAGT
* *
92577 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATAAAATTTCC-A-AAC
*
92610 TTGGCCACCAACCAAGATAAAATTTTC-AAC
1 TTGGCCACCAACCAAGATAAAATTTCCAAAC
92640 TTG
1 TTG
92643 CCAATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.17
33 25 0.83
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATAAAATTTCCAAAC
Found at i:98907 original size:20 final size:21
Alignment explanation
Indices: 98882--98923 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
98872 TTACGCATAT
* *
98882 TACTAATAATATTATAA-AAA
1 TACTAAAAATATAATAATAAA
98902 TACTAAAAATATAATAATAAA
1 TACTAAAAATATAATAATAAA
98923 T
1 T
98924 CATAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TACTAAAAATATAATAATAAA
Found at i:99349 original size:2 final size:2
Alignment explanation
Indices: 99344--99371 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
99334 TGGTTTTTTC
99344 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
99372 GAAAGGTGTA
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:102049 original size:18 final size:16
Alignment explanation
Indices: 102010--102050 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
102000 GAACTTGTGC
102010 TCTT-TATTCAATGGT
1 TCTTATATTCAATGGT
102025 T-TTATATTCAATGTGGT
1 TCTTATATTCAA--TGGT
102042 TCTTATATT
1 TCTTATATT
102051 AAGTGTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 8 0.36
17 5 0.23
18 7 0.32
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (16 bp):
TCTTATATTCAATGGT
Found at i:108248 original size:3 final size:3
Alignment explanation
Indices: 108240--108264 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
108230 GAAGTTTTTC
108240 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
108265 GAAGAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:111152 original size:30 final size:30
Alignment explanation
Indices: 111118--111176 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
111108 ATTAAATTTT
* *
111118 TTTATTTATA-AATATTTAAAATAATATTAG
1 TTTATTAATATAATAATT-AAATAATATTAG
*
111148 TTTATTAATATAATAATTAATTAATATTA
1 TTTATTAATATAATAATTAAATAATATTA
111177 TAAAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
TTTATTAATATAATAATTAAATAATATTAG
Found at i:111406 original size:15 final size:13
Alignment explanation
Indices: 111360--111406 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
111350 TATGATTTCA
*
111360 TAAATTATTTTTA
1 TAAATTATTTTTG
111373 TAAATTATTTTTG
1 TAAATTATTTTTG
111386 TAAAATTTATTTTATG
1 T-AAA-TTATTTT-TG
111402 TAAAT
1 TAAAT
111407 AACTTTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 13 0.43
14 4 0.13
15 10 0.33
16 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (13 bp):
TAAATTATTTTTG
Found at i:114078 original size:30 final size:30
Alignment explanation
Indices: 114042--114107 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
114032 AGAGAACCGA
* *
114042 CGGTTCACACCGGTTTTACCGGTTTTTAGC
1 CGGTTCACACCGGTTTTACCGGTTCTCAGC
*
114072 CGGTTCACACCGGTTTTGCCGGTTCTCAGC
1 CGGTTCACACCGGTTTTACCGGTTCTCAGC
114102 CGGTTC
1 CGGTTC
114108 TTCTGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.11, C:0.30, G:0.26, T:0.33
Consensus pattern (30 bp):
CGGTTCACACCGGTTTTACCGGTTCTCAGC
Found at i:114094 original size:19 final size:20
Alignment explanation
Indices: 114059--114106 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
114049 CACCGGTTTT
114059 ACCGGTTTTTAGCCGGTTCAC
1 ACCGG-TTTTAGCCGGTTCAC
*
114080 ACCGGTTTT-GCCGGTTCTC
1 ACCGGTTTTAGCCGGTTCAC
114099 AGCCGGTT
1 A-CCGGTT
114107 CTTCTGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
20 10 0.40
21 5 0.20
ACGTcount: A:0.10, C:0.29, G:0.27, T:0.33
Consensus pattern (20 bp):
ACCGGTTTTAGCCGGTTCAC
Found at i:114615 original size:12 final size:12
Alignment explanation
Indices: 114598--114622 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
114588 ATATATATAG
114598 TTTTTGAAAACA
1 TTTTTGAAAACA
114610 TTTTTGAAAACA
1 TTTTTGAAAACA
114622 T
1 T
114623 ATATATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:114638 original size:35 final size:36
Alignment explanation
Indices: 114456--114881 Score: 333
Period size: 37 Copynumber: 12.0 Consensus size: 36
114446 TTATATATAT
* * *
114456 ACATATTTTGAAACTACGTATATAATATATAGTTTTTAAT
1 ACAT-TTTTGAAA--ACATATAT-ATATATAGTTTTGAAA
* *
114496 A-GTTTTT-AAAACTATATA-ATATATAGTTTTAAAAAA
1 ACATTTTTGAAAAC-ATATATATATATAGTTTT--GAAA
* * * *
114532 GACATTTTAGAAAATATATATAATATATAATTTTTAAA
1 -ACATTTTTGAAAACATATAT-ATATATAGTTTTGAAA
*
114570 ATCA-TTTTGAAAACTTATATATATATAGTTTTTGAAA
1 A-CATTTTTGAAAACATATATATATATAG-TTTTGAAA
114607 ACATTTTTGAAAACATATATAT-TATAGTTTTGAAA
1 ACATTTTTGAAAACATATATATATATAGTTTTGAAA
114642 ACATTTTTTTGAAAACATATATATTATATAGTTTT-AAA
1 ACA--TTTTTGAAAACATATATA-TATATAGTTTTGAAA
**
114680 ATCA-TTTTG-AAATTTATATAATATATAG--TTGAAA
1 A-CATTTTTGAAAACATATAT-ATATATAGTTTTGAAA
***
114714 TTTTTTTTG-AAAC--ATATA-ATATAGTTTTGAAA
1 ACATTTTTGAAAACATATATATATATAGTTTTGAAA
*
114746 ACATTTTTGAAAA-TTATA-ATATATAGTTTTGAAA
1 ACATTTTTGAAAACATATATATATATAGTTTTGAAA
*
114780 ACA-TTTTGAAAA-TTATA-ATATATAGTTTTGAAA
1 ACATTTTTGAAAACATATATATATATAGTTTTGAAA
* * *
114813 ACATTTTTGAAAACATTTATATAT-TA--TAT-AAG
1 ACATTTTTGAAAACATATATATATATAGTTTTGAAA
* *
114845 ACA-TTTTGAAAATATATATAATATATAGTTTTTAAA
1 ACATTTTTGAAAACATATAT-ATATATAGTTTTGAAA
114881 A
1 A
114882 AATATTTTTG
Statistics
Matches: 321, Mismatches: 32, Indels: 70
0.76 0.08 0.17
Matches are distributed among these distances:
30 6 0.02
31 15 0.05
32 25 0.08
33 43 0.13
34 52 0.16
35 35 0.11
36 33 0.10
37 61 0.19
38 23 0.07
39 16 0.05
40 12 0.04
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ACATTTTTGAAAACATATATATATATAGTTTTGAAA
Found at i:114704 original size:33 final size:34
Alignment explanation
Indices: 114498--114825 Score: 262
Period size: 33 Copynumber: 9.3 Consensus size: 34
114488 TTTTTAATAG
* *
114498 TTTTT-AAAACTATATAATATATAGTTTTAAAAAAGACA
1 TTTTTGAAAATTATAT-A-ATATAGTTTT--GAAA-ACA
* * *
114536 TTTTAGAAAATATATATAATATATAATTTTTAAAATCA
1 TTTTTGAAAAT-TATAT-A-ATATAGTTTTGAAAA-CA
114574 -TTTTGAAAACTTATATATATATAGTTTTTGAAAACA
1 TTTTTGAAAA-TTATATA-ATATAG-TTTTGAAAACA
* *
114610 TTTTTGAAAACATATATATTATAGTTTTGAAAACA
1 TTTTTGAAAA-TTATATAATATAGTTTTGAAAACA
*
114645 TTTTTTTGAAAACATATATATTATATAGTTTT-AAAATCA
1 --TTTTTG-AAA-AT-TATATAATATAGTTTTGAAAA-CA
* * ***
114684 -TTTTGAAATTTATATAATATA-TAGTTGAAATTT
1 TTTTTGAAAATTATATAATATAGT-TTTGAAAACA
*
114717 TTTTTG-AAA-CATATAATATAGTTTTGAAAACA
1 TTTTTGAAAATTATATAATATAGTTTTGAAAACA
114749 TTTTTGAAAATTATA-ATATATAGTTTTGAAAACA
1 TTTTTGAAAATTATATA-ATATAGTTTTGAAAACA
114783 -TTTTGAAAATTATA-ATATATAGTTTTGAAAACA
1 TTTTTGAAAATTATATA-ATATAGTTTTGAAAACA
114816 TTTTTGAAAA
1 TTTTTGAAAA
114826 CATTTATATA
Statistics
Matches: 245, Mismatches: 25, Indels: 44
0.78 0.08 0.14
Matches are distributed among these distances:
32 23 0.09
33 52 0.21
34 38 0.16
35 14 0.06
36 19 0.08
37 44 0.18
38 17 0.07
39 21 0.09
40 17 0.07
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (34 bp):
TTTTTGAAAATTATATAATATAGTTTTGAAAACA
Found at i:114822 original size:12 final size:12
Alignment explanation
Indices: 114805--114830 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
114795 TAATATATAG
114805 TTTTGAAAACAT
1 TTTTGAAAACAT
114817 TTTTGAAAACAT
1 TTTTGAAAACAT
114829 TT
1 TT
114831 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:114900 original size:39 final size:38
Alignment explanation
Indices: 114474--114953 Score: 227
Period size: 37 Copynumber: 13.5 Consensus size: 38
114464 TGAAACTACG
*
114474 TATATAATATATAGTTTTT---AATAGTTTTT-AAAA-C
1 TATATAATATATAGTTTTTAAAAATA-TTTTTGAAAATA
* * *
114508 TATATAATATATAGTTTTAAAAAAGACATTTTAGAAAATA
1 TATATAATATATAGTTTT-TAAAA-ATATTTTTGAAAATA
*
114548 TATATAATATATAATTTTT-AAAATCA-TTTTGAAAACT-
1 TATATAATATATAGTTTTTAAAAAT-ATTTTTGAAAA-TA
* * *
114585 TATAT-ATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATAATATATAGTTTTTAAAAATATTTTTGAAAATA
* * *
114622 TATAT-AT-TATAGTTTTGAAAACATTTTTTTGAAAACA
1 TATATAATATATAGTTTTTAAAA-ATATTTTTGAAAATA
* *
114659 TATATATTATATAG-TTTT-AAAATCA-TTTTG-AAATT
1 TATATAATATATAGTTTTTAAAAAT-ATTTTTGAAAATA
* * *
114694 TATATAATATATAG---TTGAAATTTTTTTTG--AA-A
1 TATATAATATATAGTTTTTAAAAATATTTTTGAAAATA
* * *
114726 CATAT-A-ATATAG-TTTTGAAAACATTTTTG-AAA-A
1 TATATAATATATAGTTTTTAAAAATATTTTTGAAAATA
* *
114759 T-TATAATATATAG-TTTTGAAAACA-TTTTG-AAA-A
1 TATATAATATATAGTTTTTAAAAATATTTTTGAAAATA
* * *
114792 T-TATAATATATAG-TTTTGAAAACATTTTTGAAAACA
1 TATATAATATATAGTTTTTAAAAATATTTTTGAAAATA
* * * * **
114828 T-T-T-ATATAT--TATAT-AAGACATTTTGAAAATATA
1 TATATAATATATAGTTTTTAAAAATATTTTTGAAA-ATA
* **
114861 TATA-ATATATAGT--TTTTAAAAAATATTTTTGAAGTTA
1 TATATA-ATATA-TAGTTTTTAAAAATATTTTTGAAAATA
** *
114898 TATATTGTATAT-GTTTTTAAAAATGTTTTTGAAAATA
1 TATATAATATATAGTTTTTAAAAATATTTTTGAAAATA
**
114935 CGTATAATATATAGTTTTT
1 TATATAATATATAGTTTTT
114954 TTTTAAAAAA
Statistics
Matches: 355, Mismatches: 54, Indels: 70
0.74 0.11 0.15
Matches are distributed among these distances:
30 6 0.02
31 1 0.00
32 31 0.09
33 46 0.13
34 56 0.16
35 20 0.06
36 41 0.12
37 96 0.27
38 30 0.08
39 11 0.03
40 17 0.05
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (38 bp):
TATATAATATATAGTTTTTAAAAATATTTTTGAAAATA
Found at i:114909 original size:68 final size:64
Alignment explanation
Indices: 114732--114893 Score: 166
Period size: 67 Copynumber: 2.4 Consensus size: 64
114722 GAAACATATA
* * *
114732 ATATAGTTTTGAAAACATTTTTGAAA-A-TTATAATATATAGTTTTGAAAACATTTTGAAAATTA
1 ATATAGTTTTAAAAACATTTTTGAAACATTTAT-ATAT-TA--TAT-AAGACATTTTGAAAATTA
114795 TAAT
61 TAAT
*
114799 ATATAGTTTTGAAAACATTTTTGAAAACATTTATATATTATATAAGACATTTTGAAAATATATAT
1 ATATAGTTTTAAAAACATTTTTG-AAACATTTATATATTATATAAGACATTTTG-AAA-AT-TAT
114864 AAT
62 AAT
*
114867 ATATAGTTTTTAAAAAATATTTTTGAA
1 ATATAG-TTTT-AAAAACATTTTTGAA
114894 GTTATATATT
Statistics
Matches: 83, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
65 10 0.12
66 5 0.06
67 25 0.30
68 17 0.20
69 11 0.13
70 15 0.18
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (64 bp):
ATATAGTTTTAAAAACATTTTTGAAACATTTATATATTATATAAGACATTTTGAAAATTATAAT
Found at i:115023 original size:3 final size:3
Alignment explanation
Indices: 115015--115085 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
115005 TTTTATATAG
115015 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
115062 ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
115086 TCCTATTTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:116149 original size:2 final size:2
Alignment explanation
Indices: 116137--116186 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
116127 TGTTTTAGTC
116137 TA TA T- 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
116178 TA TA TA TA T
1 TA TA TA TA T
116187 TCCGAATTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:118221 original size:19 final size:19
Alignment explanation
Indices: 118187--118231 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
118177 ATTTAGACAT
118187 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
118205 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
118224 TTTGCATT
1 TTTGCATT
118232 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:121770 original size:165 final size:164
Alignment explanation
Indices: 121584--122123 Score: 893
Period size: 165 Copynumber: 3.3 Consensus size: 164
121574 TACCTGCCAC
* *
121584 AAAGACTTTTGAGTTCGACTACGATCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTGCAGTATAGCTTAAGTCGA
121649 GAAGAGCTATATGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
65 GAAGAGCTATATGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
*
121714 ACATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
130 GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
121749 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTGCAGTATAGCTTAAGTCGA
121814 GAAGAGCTATATGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
65 GAAGAGCTATATGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
* *
121879 GCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
130 GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
*
121914 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCATATCATTTGCAGTATAGCTTAAGTCGA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTGCAGTATAGCTTAAGTCGA
* *** ** * *
121979 GAAG-GACTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTAC
65 GAAGAG-CTATATGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTAC
122043 AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
129 AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
*
122079 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTC-AAGGCACATCATT
122124 CACAATATAA
Statistics
Matches: 353, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
164 4 0.01
165 344 0.97
166 5 0.01
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (164 bp):
AAAGACCTTTGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
AAGAGCTATATGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
CATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
Found at i:121856 original size:80 final size:80
Alignment explanation
Indices: 121583--122023 Score: 384
Period size: 80 Copynumber: 5.4 Consensus size: 80
121573 CTACCTGCCA
** *
121583 CAAAGACTTTTGAGTTCGACTACGA-TCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTC
1 CAAAGACCCTTGAGTTCGACTAC-ACTCAGCTCAACGGCATATCATTTGCAGTATAGCTTAAGTC
121647 GAGAAGAGCTATATGC
65 GAGAAGAGCTATATGC
* * * * * ** * * *
121663 CAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAACATAACTCAAGGC
1 CAAAGACCCTTGAGTTCGACTACACTCAGC-TCAACGGCATATCATTTGCAGTATAGCTTAAGTC
* * * *
121728 TAGAAGGGTTATCTGTGAC
65 GAGAAGAGCTA--TATG-C
* * *
121747 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGTATAGCTTAAGT
1 C-AAAGACCCTTGAGTTCGACTACACTCAGCT-CAACGGCATATCATTTGCAGTATAGCTTAAGT
121811 CGAGAAGAGCTATATGC
64 CGAGAAGAGCTATATGC
* * * * * * * * *
121828 CAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGC
1 CAAAGACCCTTGAGTTCGACTACACTCAGC-TCAACGGCATATCATTTGCAGTATAGCTTAAGTC
* * * *
121893 TAGAAGGGTTATCTGTTAGC
65 GAGAAGAGCTA--T-AT-GC
* * *
121913 AAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCATATCATTTGCAGTATAGCTTAAGTCG
1 CAAAGACCCTTGAGTTCGACTACACTCAGCTCAACGGCATATCATTTGCAGTATAGCTTAAGTCG
*
121978 AGAAG-GACTATCTGC
66 AGAAGAG-CTATATGC
** *
121993 CAAAGACCCCCGAGTTCGATTACACTCAGCT
1 CAAAGACCCTTGAGTTCGACTACACTCAGCT
122024 TTGAGGGCAC
Statistics
Matches: 278, Mismatches: 69, Indels: 28
0.74 0.18 0.07
Matches are distributed among these distances:
79 1 0.00
80 79 0.28
81 67 0.24
82 4 0.01
83 5 0.02
84 67 0.24
85 55 0.20
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (80 bp):
CAAAGACCCTTGAGTTCGACTACACTCAGCTCAACGGCATATCATTTGCAGTATAGCTTAAGTCG
AGAAGAGCTATATGC
Found at i:122134 original size:84 final size:85
Alignment explanation
Indices: 121662--122180 Score: 451
Period size: 84 Copynumber: 6.2 Consensus size: 85
121652 GAGCTATATG
* * * * *
121662 CCAAAGACCCTT-AAGTTCGATTACACTCAGCT-TCAAGGGCATAACATTTACAACATAACTCAA
1 CCAAAGA-CCTTCGAGTTCGACTACACTCAGCTCTCAAGGGCACATCATTTACAGCATAACTCAA
121725 GGCTAGAAGGGTTATCTGTGA
65 GGCTAGAAGGGTTATCTGTGA
* * * * * *
121746 CCAAAAGACCTTTGAGTTCGACTACGCTCAGCTC-CAA-GGCACATCATTTGCAGTATAGCTTAA
1 CC-AAAGACCTTCGAGTTCGACTACACTCAGCTCTCAAGGGCACATCATTTACAGCATAACTCAA
* * * * *
121809 GTCGAGAAGAGCTA--TATG-
65 GGCTAGAAGGGTTATCTGTGA
* * * *
121827 CCAAAGACCCTT-AAGTTCGATTACACTCAGCT-TCAAGGGCATAACATTTACAGCATAACTCAA
1 CCAAAGA-CCTTCGAGTTCGACTACACTCAGCTCTCAAGGGCACATCATTTACAGCATAACTCAA
*
121890 GGCTAGAAGGGTTATCTGTTA
65 GGCTAGAAGGGTTATCTGTGA
* * * * * * * * *
121911 GCAAAAGACCTTTGAGTTCGACTACGCTCAG--CTCAACGGCATATCATTTGCAGTATAGCTTAA
1 -CCAAAGACCTTCGAGTTCGACTACACTCAGCTCTCAAGGGCACATCATTTACAGCATAACTCAA
* * **
121974 GTCGAGAAGGACTATC--TG-
65 GGCTAGAAGGGTTATCTGTGA
** * **
121992 CCAAAGACCCCCGAGTTCGATTACACTCAGCT-TTGAGGGCACATCATTTACAGCATAACTCAAG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCTCAAGGGCACATCATTTACAGCATAACTCAAG
122056 GCTAGAAGGGTTATCTGTGA
66 GCTAGAAGGGTTATCTGTGA
* * **
122076 CCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCT-AA-GGCACATCATTCACAATATAACTCAA
1 CC-AAAGACCTTCGAGTTCGACTACACTCAGCTCTCAAGGGCACATCATTTACAGCATAACTCAA
*
122139 GGCTAGAAGGGTTATCTGTCAA
65 GGCTAGAAGGGTTATCTGT-GA
* *
122161 CCGAAGACCTCCGAGTTCGA
1 CCAAAGACCTTCGAGTTCGA
122181 TTATATTCAA
Statistics
Matches: 341, Mismatches: 74, Indels: 40
0.75 0.16 0.09
Matches are distributed among these distances:
80 49 0.14
81 71 0.21
82 4 0.01
83 4 0.01
84 136 0.40
85 76 0.22
86 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (85 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCTCAAGGGCACATCATTTACAGCATAACTCAAG
GCTAGAAGGGTTATCTGTGA
Found at i:122926 original size:33 final size:33
Alignment explanation
Indices: 122823--123210 Score: 283
Period size: 33 Copynumber: 11.7 Consensus size: 33
122813 TGAAACTACG
* * *
122823 TATATAATATATAGTTTTAATA-GTTTTTAAAA
1 TATATAATATATAGTTTTAAAACATTTTGAAAA
122855 CTATATAATATATAGTTTTAAAAAAGACATTTTAGAAAA
1 -TATATAATATATAGTTTT---AAA-ACATTTT-GAAAA
*
122894 TATATAATATATAATTTTAAAATCA-TTTGAAAA
1 TATATAATATATAGTTTTAAAA-CATTTTGAAAA
*
122927 -CT-T-ATATATAGTTTTTGAAAACATTTTTGAAAA
1 TATATAATATATAG-TTTT-AAAACA-TTTTGAAAA
*
122960 CATAT-AT-TATAGTTTTGAAAACATTTTTTTGAAAACA
1 TATATAATATATAGTTTT-AAAACA---TTTTG-AAA-A
* *
122997 TATATATTATATAGTTTTAAAATCATTTTGAAAT
1 TATATAATATATAGTTTTAAAA-CATTTTGAAAA
* ***
123031 TATTATAATATATAG-TTGAAATTTTTTTG-AAA
1 TA-TATAATATATAGTTTTAAAACATTTTGAAAA
*
123063 CATAT-A-ATATAGTTTTGAAAACATTTTG-AAA
1 TATATAATATATAGTTTT-AAAACATTTTGAAAA
*
123094 -ATAT-ATATATAG-TTTGAAACATTTTGAAAA
1 TATATAATATATAGTTTTAAAACATTTTGAAAA
123124 T-TATAATATATAGTTTTGAAAACATTTTTGAAAA
1 TATATAATATATAGTTTT-AAAACA-TTTTGAAAA
* * * *
123158 CAT-TTATATATA--TATAAGACATTTTGAAAA
1 TATATAATATATAGTTTTAAAACATTTTGAAAA
123188 TATATAATATATAGTTTTTAAAA
1 TATATAATATATAG-TTTTAAAA
123211 AATATTTTTG
Statistics
Matches: 289, Mismatches: 31, Indels: 69
0.74 0.08 0.18
Matches are distributed among these distances:
29 16 0.06
30 35 0.12
31 48 0.17
32 13 0.04
33 52 0.18
34 39 0.13
35 29 0.10
36 10 0.03
37 6 0.02
38 26 0.09
39 15 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (33 bp):
TATATAATATATAGTTTTAAAACATTTTGAAAA
Found at i:122955 original size:12 final size:12
Alignment explanation
Indices: 122938--122962 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
122928 TTATATATAG
122938 TTTTTGAAAACA
1 TTTTTGAAAACA
122950 TTTTTGAAAACA
1 TTTTTGAAAACA
122962 T
1 T
122963 ATATTATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:122965 original size:31 final size:31
Alignment explanation
Indices: 122900--123199 Score: 183
Period size: 31 Copynumber: 9.3 Consensus size: 31
122890 AAAATATATA
122900 ATATATA-ATTTT-AAAATCA--TTTGAAAAC
1 ATATATATATTTTGAAAA-CATTTTTGAAAAC
*
122928 TTATATATAGTTTTTGAAAACATTTTTGAAAAC
1 ATATATATA--TTTTGAAAACATTTTTGAAAAC
122961 ATATATTATAGTTTTGAAAACATTTTTTTGAAAAC
1 ATATA-TATA-TTTTGAAAACA--TTTTTGAAAAC
* **
122996 ATATATATTATATAGTTTTAAAATCA-TTTTGAAATT
1 --ATATA-TATAT--TTTGAAAA-CATTTTTGAAAAC
* **
123032 ATTATAATATATAGTTG-AAATTTTTTTG-AAAC
1 A-TAT-ATATAT-TTTGAAAACATTTTTGAAAAC
*
123064 ATATAATATAGTTTTGAAAACA-TTTTGAAAAT
1 ATAT-ATATA-TTTTGAAAACATTTTTGAAAAC
* *
123096 ATATATATAGTTTG-AAACA-TTTTGAAAATT
1 ATATATATATTTTGAAAACATTTTTGAAAA-C
123126 ATAATATATAGTTTTGAAAACATTTTTGAAAAC
1 AT-ATATATA-TTTTGAAAACATTTTTGAAAAC
* * * *
123159 ATTTATATATATAT-AAGACA-TTTTGAAAAT
1 ATATATATAT-TTTGAAAACATTTTTGAAAAC
123189 ATATAATATAT
1 ATAT-ATATAT
123200 AGTTTTTAAA
Statistics
Matches: 220, Mismatches: 25, Indels: 51
0.74 0.08 0.17
Matches are distributed among these distances:
28 6 0.03
29 15 0.07
30 19 0.09
31 47 0.21
32 30 0.14
33 39 0.18
34 16 0.07
35 19 0.09
36 10 0.05
37 10 0.05
38 7 0.03
39 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (31 bp):
ATATATATATTTTGAAAACATTTTTGAAAAC
Found at i:123008 original size:103 final size:96
Alignment explanation
Indices: 122973--123157 Score: 95
Period size: 94 Copynumber: 1.9 Consensus size: 96
122963 ATATTATAGT
122973 TTTGAAAACATTTTTTTGAAAACATATATATTATATAGTTTT-AAAATCATTTTGAAAT-TAT-T
1 TTTGAAAACA--TTTTTGAAAAC--ATATA-T-TATAGTTTTGAAAA-CATTTTGAAATATATAT
* * **
123035 ATAATATATAGTTGAAATTTTTTTGAAACA-TATAATATAG-T
59 AT-ATA-AT-TTTAAAATCATTTTGAAA-ATTAT-ATATAGTT
*
123076 TTTGAAAACA-TTTTGAAAATATATA-TATAG-TTTG-AAACATTTTGAAA-ATTATAATATATA
1 TTTGAAAACATTTTTGAAAACATATATTATAGTTTTGAAAACATTTTGAAATA-TAT-ATATATA
*
123136 GTTTTGAAAA-CATTTTTGAAAA
64 ATTTT-AAAATCA-TTTTGAAAA
123158 CATTTATATA
Statistics
Matches: 69, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
93 13 0.19
94 21 0.30
95 8 0.12
96 3 0.04
98 5 0.07
100 9 0.13
103 10 0.14
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (96 bp):
TTTGAAAACATTTTTGAAAACATATATTATAGTTTTGAAAACATTTTGAAATATATATATATAAT
TTTAAAATCATTTTGAAAATTATATATAGTT
Found at i:123117 original size:93 final size:96
Alignment explanation
Indices: 122825--123198 Score: 315
Period size: 103 Copynumber: 3.8 Consensus size: 96
122815 AAACTACGTA
* * * *
122825 TATAATATATAGTTTTAATA-GTTTTT-AAAACTATATAATATATAGTTTTAAAAAAGACATTTT
1 TATAATATATAGTTTGAAAACATTTTTGAAAAC-ATAT-A-ATATAGTTTT--GAAA-ACATTTT
*
122888 AGAAAATATATAATATATAATTTTAAAATCA-TTTGAAAACT
60 -G-AAA-ATAT-ATATATAGTTTTAAAATCATTTTGAAAA-T
* *
122929 TAT-ATATAGT-TTTTGAAAACATTTTTGAAAACATATATTATAGTTTTGAAAACATTTTTTTGA
1 TATAATATA-TAGTTTGAAAACATTTTTGAAAACATATAATATAGTTTTGAAAACA---TTTTG-
122992 AAACATATATATTATATAGTTTTAAAATCATTTTGAAATTAT
61 -AA-A-ATATA-TATATAGTTTTAAAATCATTTTGAAA--AT
**
123034 TATAATATATAG-TTG-AAATTTTTTTG-AAACATATAATATAGTTTTGAAAACATTTTGAAAAT
1 TATAATATATAGTTTGAAAACATTTTTGAAAACATATAATATAGTTTTGAAAACATTTTGAAAAT
*
123096 ATATATATAG-TTTGAAA-CATTTTGAAAAT
66 ATATATATAGTTTTAAAATCATTTTGAAAAT
* * *
123125 TATAATATATAGTTTTGAAAACATTTTTGAAAACAT-TTATATA-TATAT-AAGACATTTTGAAA
1 TATAATATATAG-TTTGAAAACATTTTTGAAAACATATAATATAGT-TTTGAAAACATTTTGAAA
123187 ATATATAATATA
64 ATATAT-ATATA
123199 TAGTTTTTAA
Statistics
Matches: 233, Mismatches: 17, Indels: 50
0.78 0.06 0.17
Matches are distributed among these distances:
91 14 0.06
93 33 0.14
94 28 0.12
95 13 0.06
96 5 0.02
97 1 0.00
98 2 0.01
99 3 0.01
100 8 0.03
101 1 0.00
102 17 0.07
103 60 0.26
104 29 0.12
105 13 0.06
106 6 0.03
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (96 bp):
TATAATATATAGTTTGAAAACATTTTTGAAAACATATAATATAGTTTTGAAAACATTTTGAAAAT
ATATATATAGTTTTAAAATCATTTTGAAAAT
Found at i:123154 original size:12 final size:12
Alignment explanation
Indices: 123137--123162 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
123127 TAATATATAG
123137 TTTTGAAAACAT
1 TTTTGAAAACAT
123149 TTTTGAAAACAT
1 TTTTGAAAACAT
123161 TT
1 TT
123163 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:123237 original size:67 final size:64
Alignment explanation
Indices: 122858--123222 Score: 191
Period size: 64 Copynumber: 5.5 Consensus size: 64
122848 TTTAAAACTA
* * * * *
122858 TATAATATATAGTTTTAAAAAAGACATTTTAGAAAATATATAATATATAATTTTAAAATCA-TTT
1 TATAATATATAGTTTT--AAAA-ACATTTTTGAAAACAT-TTATATAT-A-TATAAGA-CATTTT
*
122922 GAAAAC
59 GAAAAT
* * * *
122928 T-T-ATATATAGTTTTTGAAAACATTTTTGAAAACATATAT-TATAGTTTTGAAAACATTTTTTT
1 TATAATATATAG-TTTTAAAAACATTTTTGAAAACATTTATATATA--TAT-AAGACA---TTTT
122990 GAAAACAT
59 G-AAA-AT
* * ** **
122998 ATATATTATATAGTTTTAAAATCA-TTTTGAAATTA-TTATAATATATAGTTGAA-ATTTTTTTG
1 -TATAATATATAGTTTTAAAAACATTTTTGAAAACATTTAT-ATATATA--T-AAGA-CATTTTG
123060 AAACA-
60 AAA-AT
* * *
123065 TAT-A-ATATAGTTTTGAAAACA-TTTTG-AAA-ATATATATATAGTTTGAA-ACATTTTGAAAA
1 TATAATATATAGTTTTAAAAACATTTTTGAAAACATTTATATATA-TAT-AAGACATTTTGAAAA
123124 T
64 T
*
123125 TATAATATATAGTTTTGAAAACATTTTTGAAAACATTTATATATATATAAGACATTTTGAAAAT
1 TATAATATATAGTTTTAAAAACATTTTTGAAAACATTTATATATATATAAGACATTTTGAAAAT
*
123189 ATATAATATATAGTTTTTAAAAAATATTTTTGAA
1 -TATAATATATAG-TTTT-AAAAACATTTTTGAA
123223 GTTATATTTG
Statistics
Matches: 239, Mismatches: 27, Indels: 61
0.73 0.08 0.19
Matches are distributed among these distances:
59 1 0.00
60 11 0.05
61 6 0.03
62 23 0.10
63 14 0.06
64 47 0.20
65 28 0.12
66 21 0.09
67 16 0.07
68 17 0.07
69 13 0.05
70 6 0.03
71 11 0.05
72 18 0.08
73 7 0.03
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (64 bp):
TATAATATATAGTTTTAAAAACATTTTTGAAAACATTTATATATATATAAGACATTTTGAAAAT
Found at i:123346 original size:3 final size:3
Alignment explanation
Indices: 123334--123404 Score: 114
Period size: 3 Copynumber: 25.0 Consensus size: 3
123324 ATTTTTATAG
123334 ATT A-T ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
123379 ATT ATT ATT ATT ATT ATT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
123405 TCCTATTTAT
Statistics
Matches: 64, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 8 0.12
3 56 0.88
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:123363 original size:20 final size:20
Alignment explanation
Indices: 123334--123404 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
123324 ATTTTTATAG
123334 ATTATATTATTATTA-TATT
1 ATTATATTATTATTATTATT
123353 A-T-TATTATTATTATTATT
1 ATTATATTATTATTATTATT
123371 ATTATATTATTATTATTATT
1 ATTATATTATTATTATTATT
*
123391 ATTATTTTATTATT
1 ATTATATTATTATT
123405 TCCTATTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
17 11 0.23
18 6 0.12
19 2 0.04
20 29 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTATATTATTATTATTATT
Found at i:123364 original size:23 final size:22
Alignment explanation
Indices: 123334--123404 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 22
123324 ATTTTTATAG
123334 ATTA-TATTATTATTATATTATT
1 ATTATTATTATTATTAT-TTATT
123356 ATTATTATTATTATTATTATATT
1 ATTATTATTATTATTATT-TATT
123379 ATTATTATTATTATTATTTTATT
1 ATTATTATTATTATTA-TTTATT
123402 ATT
1 ATT
123405 TCCTATTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
22 5 0.11
23 39 0.85
24 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTATTATTATTATTATTTATT
Found at i:124453 original size:2 final size:2
Alignment explanation
Indices: 124446--124500 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
124436 GTTTTAGTCC
124446 TA TA TA 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
124488 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
124501 TCCGAATTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:126564 original size:17 final size:18
Alignment explanation
Indices: 126525--126564 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
126515 TGATAAACTC
126525 ATATAAGTGATTTAAGAT
1 ATATAAGTGATTTAAGAT
*
126543 A-ATAAGTGA-TTAATAT
1 ATATAAGTGATTTAAGAT
126559 ATATAA
1 ATATAA
126565 ATTCATAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 12 0.60
18 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (18 bp):
ATATAAGTGATTTAAGAT
Found at i:127130 original size:23 final size:23
Alignment explanation
Indices: 127094--127150 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
127084 TAAGCTACCA
* *
127094 AAAGACATAG-AAAACGTGTCAC
1 AAAGACAGAGAAAAACGTATCAC
* *
127116 AAAGACAGAGAAAAATGTATCAT
1 AAAGACAGAGAAAAACGTATCAC
127139 AAAGACAGAGAA
1 AAAGACAGAGAA
127151 CATTTCACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.12
Consensus pattern (23 bp):
AAAGACAGAGAAAAACGTATCAC
Found at i:133288 original size:72 final size:73
Alignment explanation
Indices: 133124--133308 Score: 250
Period size: 72 Copynumber: 2.5 Consensus size: 73
133114 ACAGAAAGCT
** *
133124 GAAAGCCTATCATGCATGTGTATAAGTAAAGAAATGAATGAGAAAATACCAACACACTCTAATGC
1 GAAAGCCTATCATGCATGCATATAAGTAAACAAATGAATGAGAAAATACCAACACAC-CTAATGC
*
133189 CTACAAACA
65 CCACAAACA
* * * *
133198 GAAAGCTTATCATGCATGCATAAAAGTACAA-AAATGAATGAGAGAAA-ACCGATACA-CTAATG
1 GAAAGCCTATCATGCATGCATATAAGTA-AACAAATGAATGAGA-AAATACCAACACACCTAATG
133260 CCCACAAACA
64 CCCACAAACA
133270 GAAAGCCTATCATGCATGCATATAAGTAAACAAATGAAT
1 GAAAGCCTATCATGCATGCATATAAGTAAACAAATGAAT
133309 TGAGTGAATA
Statistics
Matches: 99, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
71 2 0.02
72 49 0.49
74 43 0.43
75 5 0.05
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.19
Consensus pattern (73 bp):
GAAAGCCTATCATGCATGCATATAAGTAAACAAATGAATGAGAAAATACCAACACACCTAATGCC
CACAAACA
Found at i:134384 original size:105 final size:104
Alignment explanation
Indices: 134203--134411 Score: 400
Period size: 105 Copynumber: 2.0 Consensus size: 104
134193 AACATAAGAA
134203 ACTAATATATTAAAACGATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCAA
1 ACTAATATATTAAAACGATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCAA
134268 CATCATACAAAACCAAAGAAAAAGAGAATGAATCAAAAG
66 CATCATACAAAACCAAAGAAAAAGAGAATGAATCAAAAG
134307 ACTAATATATTAAAACAGATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCA
1 ACTAATATATTAAAAC-GATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCA
*
134372 ACATCATACAAAACCAAAGAAAAAGGGAATGAATCAAAAG
65 ACATCATACAAAACCAAAGAAAAAGAGAATGAATCAAAAG
134412 TCAAAGTTCA
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 16 0.16
105 87 0.84
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.19
Consensus pattern (104 bp):
ACTAATATATTAAAACGATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCAA
CATCATACAAAACCAAAGAAAAAGAGAATGAATCAAAAG
Found at i:134564 original size:2 final size:2
Alignment explanation
Indices: 134557--134583 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
134547 GGAAGATAAA
134557 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
134584 AAACACTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:137510 original size:11 final size:12
Alignment explanation
Indices: 137470--137513 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
137460 TATTTAAACG
*
137470 GGTATTGGGCCA
1 GGTATTGGGTCA
*
137482 GGTATTGGGTCG
1 GGTATTGGGTCA
137494 GGTATTGGGTC-
1 GGTATTGGGTCA
137505 GGTATTGGG
1 GGTATTGGG
137514 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:137512 original size:23 final size:24
Alignment explanation
Indices: 137468--137513 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
137458 ATTATTTAAA
137468 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
137492 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
137514 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:137640 original size:12 final size:13
Alignment explanation
Indices: 137624--137668 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
137614 TTTAATATTT
137624 ATCGGGTCGGGT-
1 ATCGGGTCGGGTA
*
137636 ATCGGGGCGGGTA
1 ATCGGGTCGGGTA
137649 ATCGGGGT-GGGTA
1 ATC-GGGTCGGGTA
137662 ATCGGGT
1 ATCGGGT
137669 AATCGGGGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 15 0.52
13 11 0.38
14 3 0.10
ACGTcount: A:0.13, C:0.13, G:0.51, T:0.22
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:137680 original size:13 final size:13
Alignment explanation
Indices: 137624--137667 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
137614 TTTAATATTT
*
137624 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
137636 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
*
137649 ATCGGGGTGGGTA
1 ATCGGGGCGGGTA
137662 ATCGGG
1 ATCGGG
137668 TAATCGGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.14, C:0.14, G:0.52, T:0.20
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:138683 original size:18 final size:18
Alignment explanation
Indices: 138646--138689 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
138636 ACTTTCTTAG
138646 CATTATCA-TATATATAT
1 CATTATCATTATATATAT
* *
138663 CATTATCATTATCTCTAT
1 CATTATCATTATATATAT
138681 CATTATCAT
1 CATTATCAT
138690 CGAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (18 bp):
CATTATCATTATATATAT
Found at i:139173 original size:149 final size:149
Alignment explanation
Indices: 138901--139206 Score: 594
Period size: 149 Copynumber: 2.1 Consensus size: 149
138891 CACCGAAGTG
138901 CACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGA
1 CACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGA
138966 ATCATATACATATACTAGGGATCAAGTATGTATCTTACAAGACTTCACACATGTTCCACAGAATA
66 ATCATATACATATACTAGGGATCAAGTATGTATCTTACAAGACTTCACACATGTTCCACAGAATA
139031 TATATATATCCCGAAGGAC
131 TATATATATCCCGAAGGAC
*
139050 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGA
1 CACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGA
*
139115 ATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATA
66 ATCATATACATATACTAGGGATCAAGTATGTATCTTACAAGACTTCACACATGTTCCACAGAATA
139180 TATATATATCCCGAAGGAC
131 TATATATATCCCGAAGGAC
139199 CACGTAGA
1 CACGTAGA
139207 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (149 bp):
CACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGA
ATCATATACATATACTAGGGATCAAGTATGTATCTTACAAGACTTCACACATGTTCCACAGAATA
TATATATATCCCGAAGGAC
Found at i:141487 original size:35 final size:36
Alignment explanation
Indices: 141429--141522 Score: 104
Period size: 35 Copynumber: 2.6 Consensus size: 36
141419 GGGATGTTAC
*
141429 AAATTCGGGTATTTTT-TTATTATTTAATGTTTCATAAAA
1 AAATT-GGGTATTTTTCTTATTA---AAGGTTTCATAAAA
*
141468 AAATT-GGTATTTTTCTTATTAAAGGTTTCATAATA
1 AAATTGGGTATTTTTCTTATTAAAGGTTTCATAAAA
*
141503 AATTTGGGTA-TTTTCTTATT
1 AAATTGGGTATTTTTCTTATT
141523 GAAGATTAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
35 26 0.52
36 4 0.08
37 9 0.18
38 6 0.12
39 5 0.10
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (36 bp):
AAATTGGGTATTTTTCTTATTAAAGGTTTCATAAAA
Found at i:146375 original size:37 final size:37
Alignment explanation
Indices: 146302--146376 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
146292 GTTGGAAAAT
* * *
146302 ATTTATATATTTTCTTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTATAAAAATTGAAAATCATAAA
146339 ATTTATATAATTTT-TTATACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTATA-AAAATTGAAAATCATAAA
146376 A
1 A
146377 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 18 0.55
38 15 0.45
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTATAAAAATTGAAAATCATAAA
Found at i:147033 original size:37 final size:37
Alignment explanation
Indices: 146960--147034 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
146950 GTTGGAAAAT
* *
146960 ATTTATATATTTTCTTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTTAAAAATTAAAAATCATAAA
*
146997 ATTTATATAATTTT-TTTTACTAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTTA-AAAATTAAAAATCATAAA
147034 A
1 A
147035 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 19 0.58
38 14 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTATATATTTTCTTTTAAAAATTAAAAATCATAAA
Found at i:148467 original size:29 final size:29
Alignment explanation
Indices: 148425--148511 Score: 158
Period size: 29 Copynumber: 3.0 Consensus size: 29
148415 TCTCCATCCA
148425 TTAACATATTGAATTATATTTAATAACTT
1 TTAACATATTGAATTATATTTAATAACTT
148454 TTAACATATTGAATTATATTTAATAACTT
1 TTAACATATTGAATTATATTTAATAACTT
148483 TTAACATATT-AGATTATATTTAATAACTT
1 TTAACATATTGA-ATTATATTTAATAACTT
148512 ATCCAAAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
28 1 0.02
29 56 0.98
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (29 bp):
TTAACATATTGAATTATATTTAATAACTT
Found at i:148865 original size:2 final size:2
Alignment explanation
Indices: 148858--148882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
148848 GTAATTGGAT
148858 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
148883 GCACACTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:151537 original size:60 final size:60
Alignment explanation
Indices: 151463--151624 Score: 162
Period size: 61 Copynumber: 2.7 Consensus size: 60
151453 ATTTTAAGTT
* *
151463 GGTCCTTAAACTTTTAAATATTCTAATTTCATTTCTAAATTATGAATATCATTCTAAATA
1 GGTCCTTAAACTTTTAAATATTCTAATTTAATTTCTAAATTATGAACATCATTCTAAATA
* * * * * * ** *
151523 GTTCCTTAAACTTTTAAACATTCTATTTTTAATCTCTAAACTATGACCATGTTTCTAAATT
1 GGTCCTTAAACTTTTAAATATTCTA-ATTTAATTTCTAAATTATGAACATCATTCTAAATA
** * * * *
151584 GGTCCCCAAACTTTTGAATCTTCTAATTTTATTACTAAATT
1 GGTCCTTAAACTTTTAAATATTCTAATTTAATTTCTAAATT
151625 CATCCAAATA
Statistics
Matches: 79, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
60 34 0.43
61 45 0.57
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.45
Consensus pattern (60 bp):
GGTCCTTAAACTTTTAAATATTCTAATTTAATTTCTAAATTATGAACATCATTCTAAATA
Found at i:151741 original size:2 final size:2
Alignment explanation
Indices: 151734--151762 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
151724 GATGTGATTA
151734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
151763 ATTTGGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:158210 original size:59 final size:59
Alignment explanation
Indices: 158112--158232 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 59
158102 AGCAGGCTGT
** * *
158112 ATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTAGG-CACAACCTTGTGTGTC
1 ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGT-GGACACAACCTTATGTGTC
* ** * *
158171 ATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTC
1 ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGTC
158230 ATA
1 ATA
158233 CTCGAGATTG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 2 0.04
59 50 0.96
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (59 bp):
ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGTC
Found at i:158791 original size:13 final size:13
Alignment explanation
Indices: 158771--158832 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
158761 AGTACTGTTC
*
158771 ACTGTTCACGGGT
1 ACTGTTCACGGTT
* *
158784 ATTGTTCACTGTT
1 ACTGTTCACGGTT
*
158797 ACTGTTCACAGTTT
1 ACTGTTCAC-GGTT
* *
158811 ATTGTTCACGGAT
1 ACTGTTCACGGTT
158824 ACTGTTCAC
1 ACTGTTCAC
158833 TATTCATATA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 28 0.74
14 10 0.26
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (13 bp):
ACTGTTCACGGTT
Found at i:158813 original size:27 final size:26
Alignment explanation
Indices: 158764--158832 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
158754 TTTCGGAAGT
158764 ACTGTTCACTGTTCACGGGTATTGTTC
1 ACTGTT-ACTGTTCACGGGTATTGTTC
**
158791 ACTGTTACTGTTCACAGTTTATTGTTC
1 ACTGTTACTGTTCAC-GGGTATTGTTC
* *
158818 ACGGATACTGTTCAC
1 ACTGTTACTGTTCAC
158833 TATTCATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 9 0.24
27 28 0.76
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (26 bp):
ACTGTTACTGTTCACGGGTATTGTTC
Found at i:159160 original size:19 final size:19
Alignment explanation
Indices: 159136--159198 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
159126 CAAGCGCTCA
159136 GGTCGGACACATGTCAACG
1 GGTCGGACACATGTCAACG
* ***
159155 GGTCGGGTCAGGCGCTC-A-G
1 GGTC-GGACACATG-TCAACG
159174 -GTCGGACACATGTCAACG
1 GGTCGGACACATGTCAACG
159192 GGTCGGA
1 GGTCGGA
159199 TTAACTTGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
16 2 0.06
17 6 0.19
18 4 0.13
19 11 0.35
20 6 0.19
21 2 0.06
ACGTcount: A:0.21, C:0.25, G:0.38, T:0.16
Consensus pattern (19 bp):
GGTCGGACACATGTCAACG
Found at i:159170 original size:37 final size:37
Alignment explanation
Indices: 159117--159197 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
159107 GAGTAAGGTA
159117 GGGTCGGGTCAAGCGCTCAGGTCGGACACATGTCAAC
1 GGGTCGGGTCAAGCGCTCAGGTCGGACACATGTCAAC
*
159154 GGGTCGGGTCAGGCGCTCAGGTCGGACACATGTCAAC
1 GGGTCGGGTCAAGCGCTCAGGTCGGACACATGTCAAC
159191 GGGTCGG
1 GGGTCGG
159198 ATTAACTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.19, C:0.26, G:0.40, T:0.16
Consensus pattern (37 bp):
GGGTCGGGTCAAGCGCTCAGGTCGGACACATGTCAAC
Found at i:167563 original size:29 final size:29
Alignment explanation
Indices: 167517--167601 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
167507 TCCCAACACA
* * *
167517 TAGGTCGCCATACCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTCG
* *
167546 TAGGTCGCCATGCTCTCCGGGCAACCTCG
1 TAGGTCGCCATGCACTCCGGGCGACCTCG
167575 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
167602 ACCCTCGCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.14, C:0.38, G:0.28, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTCG
Found at i:170858 original size:20 final size:20
Alignment explanation
Indices: 170833--170872 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
170823 TCCAAATTCT
170833 CAACGCGAATATGTAAATCG
1 CAACGCGAATATGTAAATCG
*
170853 CAACGCGAATTTGTAAATCG
1 CAACGCGAATATGTAAATCG
170873 TAACACAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
CAACGCGAATATGTAAATCG
Found at i:170907 original size:20 final size:20
Alignment explanation
Indices: 170882--171055 Score: 142
Period size: 20 Copynumber: 8.8 Consensus size: 20
170872 GTAACACAGA
*
170882 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCAAT
* *
170902 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCAAT
* *
170922 AGTCAATTTCTCAACGCAAT
1 AGTCAAATTCGCAACGCAAT
170942 AGTCAAATTCGCAACGCGAATT
1 AGTCAAATTCGCAACGC-AA-T
* * *
170964 TGT-TAA-TCGCAACAC-AT
1 AGTCAAATTCGCAACGCAAT
* * *
170981 AAGTCAAATTCGTAATGCGAT
1 -AGTCAAATTCGCAACGCAAT
* *
171002 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCAAT
*
171022 AGTTAAATTCGCAACTG-AAT
1 AGTCAAATTCGCAAC-GCAAT
*
171042 -TTCAAATTCGCAAC
1 AGTCAAATTCGCAAC
171056 ACGAATTTAC
Statistics
Matches: 120, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
17 1 0.01
18 3 0.03
19 14 0.12
20 93 0.77
21 6 0.05
22 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCAAT
Found at i:170946 original size:60 final size:59
Alignment explanation
Indices: 170882--171036 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 59
170872 GTAACACAGA
*
170882 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAATTTC-TCAACGCAAT
1 AGTCAAATTCGCAACGCGATAGT-AAATTCGCAACACAAAAGTCAAATTCGT-AACGCAAT
* * * * *
170942 AGTCAAATTCGCAACGCGAATTTGTTAA-TCGCAACACATAAGTCAAATTCGTAATGCGAT
1 AGTCAAATTCGCAACGCG-A-TAGTAAATTCGCAACACAAAAGTCAAATTCGTAACGCAAT
* * *
171002 AGTCAAATTCGCAACACAAAAGTTAAATTCGCAAC
1 AGTCAAATTCGCAACGCGATAG-TAAATTCGCAAC
171037 TGAATTTCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
58 1 0.01
59 4 0.05
60 67 0.85
61 4 0.05
62 3 0.04
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (59 bp):
AGTCAAATTCGCAACGCGATAGTAAATTCGCAACACAAAAGTCAAATTCGTAACGCAAT
Found at i:170962 original size:100 final size:100
Alignment explanation
Indices: 170825--171063 Score: 333
Period size: 100 Copynumber: 2.4 Consensus size: 100
170815 TTAGATTTTC
*
170825 CAAATTCTCAACGCGAATATGT-AAA-TCGCAACGCGAATTTGTAAATCGTAACACAGAAGTCAA
1 CAAATTCTCAACGC-AATA-GTCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAA
170888 ATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
64 ATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
* * *
170925 CAATTTCTCAACGCAATAGTCAAATTCGCAACGCGAATTTGTTAATCGCAACACATAAGTCAAAT
1 CAAATTCTCAACGCAATAGTCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
* *
170990 TCGTAATGCGATAGTCAAATTCGCAACACAAAAGT
66 TCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
* * * *
171025 TAAATTCGCAACTG-AAT-TTCAAATTCGCAACACGAATTT
1 CAAATTCTCAAC-GCAATAGTCAAATTCGCAACGCGAATTT
171064 ACTTTCGCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
98 2 0.02
99 27 0.22
100 95 0.76
101 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (100 bp):
CAAATTCTCAACGCAATAGTCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
TCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
Found at i:171063 original size:20 final size:20
Alignment explanation
Indices: 171004--171063 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
170994 AATGCGATAG
* *
171004 TCAAATTCGCAACACAAAAGT
1 TCAAATTCGCAACAC-GAATT
*
171025 T-AAATTCGCAAC-TGAATT
1 TCAAATTCGCAACACGAATT
171043 TCAAATTCGCAACACGAATT
1 TCAAATTCGCAACACGAATT
171063 T
1 T
171064 ACTTTCGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 4 0.12
19 11 0.33
20 17 0.52
21 1 0.03
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.27
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Done.