Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008616.1 Hibiscus syriacus cultivar Beakdansim tig00111574_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: 161314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8872 original size:154 final size:154
Alignment explanation
Indices: 8654--8958 Score: 547
Period size: 154 Copynumber: 2.0 Consensus size: 154
8644 AGAATATCAT
*
8654 CATTTGTCTCAATATATGGAGCATTACTTGTAACAGAAGCATTGATTTCTTCCTCAGTTCCCAAA
1 CATTTGTCTCAATATATGGAGCATTACTTGTAACAGAAGCATTGATTTCTTCCTCAGCTCCCAAA
* *
8719 CATATCAATTAACCATCAATAACAAACTTCAGTTTTTGATTTAAAGAAGAAGGAACAACTCCTGC
66 CATATCAATTAACCATCAATAACAAACTTCAGTTTTTGATGTAAAGAAGAAGAAACAACTCCTGC
8784 AGAATGAATCCATGGCCTCCCAAA
131 AGAATGAATCCATGGCCTCCCAAA
*
8808 CATTTGTCTCAATATATGGAGCATTACTTGTAATAGAAGCATTGATTTCTTCCTCAGCTCCCAAA
1 CATTTGTCTCAATATATGGAGCATTACTTGTAACAGAAGCATTGATTTCTTCCTCAGCTCCCAAA
* *
8873 CATTTCAATTAACCGTCAATAACAAACTTCAGTTTTTGATGTAAAGAAGAAGAAACAACTCCTGC
66 CATATCAATTAACCATCAATAACAAACTTCAGTTTTTGATGTAAAGAAGAAGAAACAACTCCTGC
*
8938 ATAATGAATCCATGGCCTCCC
131 AGAATGAATCCATGGCCTCCC
8959 CTGTAAGCAA
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
154 144 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (154 bp):
CATTTGTCTCAATATATGGAGCATTACTTGTAACAGAAGCATTGATTTCTTCCTCAGCTCCCAAA
CATATCAATTAACCATCAATAACAAACTTCAGTTTTTGATGTAAAGAAGAAGAAACAACTCCTGC
AGAATGAATCCATGGCCTCCCAAA
Found at i:18977 original size:2 final size:2
Alignment explanation
Indices: 18970--19002 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18960 AACTTAATCT
18970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19003 TTGTTATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19081 original size:32 final size:32
Alignment explanation
Indices: 19045--19115 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
19035 TATTGGTGAT
19045 AATTTTTAAATTATTTTTTTACTTTACATTTA
1 AATTTTTAAATTATTTTTTTACTTTACATTTA
19077 AATTTTTAAATTATTTTTTTACTTTACATTTA
1 AATTTTTAAATTATTTTTTTACTTTACATTTA
*
19109 ATTTTTT
1 AATTTTT
19116 TATAAGACAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (32 bp):
AATTTTTAAATTATTTTTTTACTTTACATTTA
Found at i:19115 original size:19 final size:19
Alignment explanation
Indices: 19059--19115 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
19049 TTTAAATTAT
19059 TTTTTTACTTTACATTTAA
1 TTTTTTACTTTACATTTAA
* *
19078 ATTTTTA----A-A-TTAT
1 TTTTTTACTTTACATTTAA
19091 TTTTTTACTTTACATTTAA
1 TTTTTTACTTTACATTTAA
19110 TTTTTT
1 TTTTTT
19116 TATAAGACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
13 9 0.32
14 1 0.04
15 1 0.04
17 1 0.04
18 1 0.04
19 15 0.54
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTACTTTACATTTAA
Found at i:27126 original size:3 final size:3
Alignment explanation
Indices: 27120--27168 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
27110 TTATTAAAAG
* * *
27120 TAA TAA TAA TAA TTA TAA TAT TAAA TCA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA
27167 TA
1 TA
27169 TATTATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 33 0.87
4 5 0.13
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:27184 original size:22 final size:20
Alignment explanation
Indices: 27124--27187 Score: 78
Period size: 19 Copynumber: 3.2 Consensus size: 20
27114 TAAAAGTAAT
27124 AATAATAATTATAATAT-TA
1 AATAATAATTATAATATATA
* *
27143 AATCATAATAATAATA-ATA
1 AATAATAATTATAATATATA
27162 AATAATATATTATATATATATA
1 AATAATA-ATTATA-ATATATA
27184 AATA
1 AATA
27188 TTTTCAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 22 0.59
20 5 0.14
21 3 0.08
22 7 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAATAATTATAATATATA
Found at i:27208 original size:29 final size:29
Alignment explanation
Indices: 27172--27252 Score: 109
Period size: 25 Copynumber: 2.9 Consensus size: 29
27162 AATAATATAT
27172 TATATATATATAAATATTTTCAAAAACA-
1 TATATATATATAAATATTTTCAAAAACAC
27200 TATA-ATATAT-AA-ATTTTCAAAAA-AC
1 TATATATATATAAATATTTTCAAAAACAC
*
27225 TATATATTATATACATATTTTCAAAAAC
1 TATATA-TATATAAATATTTTCAAAAAC
27253 CATTTACAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
24 1 0.02
25 15 0.33
26 3 0.07
27 11 0.24
28 5 0.11
29 11 0.24
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.40
Consensus pattern (29 bp):
TATATATATATAAATATTTTCAAAAACAC
Found at i:27223 original size:27 final size:28
Alignment explanation
Indices: 27172--27251 Score: 105
Period size: 27 Copynumber: 2.9 Consensus size: 28
27162 AATAATATAT
27172 TATAT-ATATATAAATATTTTC-AAAAAC
1 TATATAATATAT-AATATTTTCAAAAAAC
27199 -ATATAATATATAA-ATTTTCAAAAAAC
1 TATATAATATATAATATTTTCAAAAAAC
*
27225 TATATATTATATACATATTTTCAAAAA
1 TATATAATATATA-ATATTTTCAAAAA
27252 CCATTTACAA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
25 6 0.13
26 12 0.26
27 17 0.36
28 1 0.02
29 11 0.23
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (28 bp):
TATATAATATATAATATTTTCAAAAAAC
Found at i:27968 original size:30 final size:30
Alignment explanation
Indices: 27925--27986 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
27915 AGGTTTTGTG
* * *
27925 TTTCAATAGAAACATTTTCCAA-GATTTTTT
1 TTTCAAGAAAAACAATTT-CAATGATTTTTT
*
27955 TTTCAAGAAAAACAATTTCAATGGTTTTTT
1 TTTCAAGAAAAACAATTTCAATGATTTTTT
27985 TT
1 TT
27987 GTGTTTCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (30 bp):
TTTCAAGAAAAACAATTTCAATGATTTTTT
Found at i:28077 original size:15 final size:15
Alignment explanation
Indices: 28059--28096 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
28049 GATTGGTGTT
28059 TCAAGAGAAAATATC
1 TCAAGAGAAAATATC
*
28074 TCAAGAGAAAATGTC
1 TCAAGAGAAAATATC
*
28089 TTAAGAGA
1 TCAAGAGA
28097 TACAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (15 bp):
TCAAGAGAAAATATC
Found at i:28132 original size:37 final size:37
Alignment explanation
Indices: 28091--28191 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 37
28081 AAAATGTCTT
* * ** *
28091 AAGAGATACAAAAATTTGTTTTAAGGGAAACTATCTC
1 AAGAGAGACAAAAATTTGTTTCAAAAGAAACTATCTA
*
28128 AAGAGAGAC-AAAATTTGTTTCAAAAGAAACTGTCTA
1 AAGAGAGACAAAAATTTGTTTCAAAAGAAACTATCTA
* * *
28164 AAGAGAGACAAAACTTAGTTCCAAAAGA
1 AAGAGAGACAAAAATTTGTTTCAAAAGA
28192 TTTTGTTTCA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 31 0.57
37 23 0.43
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.24
Consensus pattern (37 bp):
AAGAGAGACAAAAATTTGTTTCAAAAGAAACTATCTA
Found at i:28276 original size:21 final size:21
Alignment explanation
Indices: 28214--28278 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
28204 GGAAACTGTC
*
28214 TCAAGAGAGACAAAATTTATT
1 TCAAGAGAGACAAAATTTGTT
* *
28235 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
28250 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
28271 TCAAGAGA
1 TCAAGAGA
28279 AACTGTCTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.48
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:28326 original size:37 final size:37
Alignment explanation
Indices: 28205--28370 Score: 228
Period size: 37 Copynumber: 4.5 Consensus size: 37
28195 TGTTTCAAGG
* * **
28205 GAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
* * *
28241 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
28277 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
28314 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
* * *
28351 GAAATTATCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
28371 GAAATTTGTT
Statistics
Matches: 120, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
35 2 0.02
36 55 0.46
37 63 0.52
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (37 bp):
GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
Found at i:28327 original size:124 final size:124
Alignment explanation
Indices: 28072--28555 Score: 433
Period size: 124 Copynumber: 4.1 Consensus size: 124
28062 AGAGAAAATA
* * * * * *
28072 TCTCAAGAGAAAATGTCTTAAGAGATACAAAAATTTGTTTTAAGGGAAACTATCTCAAGAGAGAC
1 TCTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGGGAAACTATCTCAAGAGAGAC
* * ***
28137 AAAATTTGTTTCAAAAGAAACTGTCTAAAGAGAGACAAAACTTAGTTCCAAAAGATTTTG
65 AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTG
* *
28197 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TCTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTATCTCAAGAGAGACA
28262 AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC------AA---
66 AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTG
* * ** * *
28312 ----AA--GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTATCTCAAGGGAGAC
1 TCTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTATCTCAAGAGAGAC
* * * * * * * **
28371 GAAATTTGTTTCATGGGAAACAGAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACTG
65 AAAATTTGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTG
* * * * ** *
28423 TTTCAAGGGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAA-GGAACCCGTGTCAAGAGAGACA
1 TCTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTATCTCAAGAGAGACA
* *
28487 AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAAGAAACTG
66 AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTG
28546 TCTCAAGGGA
1 TCTCAAGGGA
28556 GAATAAATTT
Statistics
Matches: 288, Mismatches: 45, Indels: 54
0.74 0.12 0.14
Matches are distributed among these distances:
102 7 0.02
107 2 0.01
108 3 0.01
109 28 0.10
110 43 0.15
111 3 0.01
114 1 0.00
115 37 0.13
116 6 0.02
117 26 0.09
118 2 0.01
123 27 0.09
124 80 0.28
125 23 0.08
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.25
Consensus pattern (124 bp):
TCTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTATCTCAAGAGAGACA
AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTG
Found at i:28391 original size:73 final size:72
Alignment explanation
Indices: 28205--28391 Score: 230
Period size: 73 Copynumber: 2.6 Consensus size: 72
28195 TGTTTCAAGG
* * *
28205 GAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
1 GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTAGT
* *
28270 TTCAAGA
66 TCCAAAA
* * * **
28277 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTA
1 GAAACTATCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTA
28342 GTTCCAAAA
64 GTTCCAAAA
* * * *
28351 GAAATTATCTCAAGGGAGACGAAATTTGTTTCATGGGAAAC
1 GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
28392 AGATTCAAAG
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
72 24 0.25
73 43 0.45
74 29 0.30
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (72 bp):
GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTAGT
TCCAAAA
Found at i:28426 original size:15 final size:15
Alignment explanation
Indices: 28406--28438 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28396 TCAAAGATTT
28406 TGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAAC
28421 TGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAAC
28436 TGT
1 TGT
28439 CTTAAGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (15 bp):
TGTTTCAAGGGAAAC
Found at i:28522 original size:36 final size:36
Alignment explanation
Indices: 28421--28806 Score: 371
Period size: 36 Copynumber: 11.1 Consensus size: 36
28411 CAAGGGAAAC
*
28421 TGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
28457 TGTTTCAA-GGAACCCGTGTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
28492 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
** *
28529 TGTTTCAAAAGAAACTGTCTCAAGGGAGA-ATAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACA-AAATT
* * * *
28565 TGTTTCAAGGAAAACAGAT-T-TA-A-AG----ATTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* * * *
28594 TGTTTTAAGGAAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
*
28623 TGTTTCAAGGGAAACTGTCTCAAGAGAGACCAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
28659 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
28693 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
28729 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
28765 TGTTTCAAGGGAAACTGTCTCAGGAAAGACTAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATT
28802 TGTTT
1 TGTTT
28807 TGAGTAAATT
Statistics
Matches: 301, Mismatches: 33, Indels: 31
0.82 0.09 0.08
Matches are distributed among these distances:
28 1 0.00
29 46 0.15
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
34 32 0.11
35 32 0.11
36 141 0.47
37 43 0.14
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:28552 original size:37 final size:36
Alignment explanation
Indices: 28193--28383 Score: 247
Period size: 36 Copynumber: 5.2 Consensus size: 36
28183 TCCAAAAGAT
*
28193 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
28229 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
28265 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
28301 CTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * * * *
28338 CTTAGTTCCAAAAGAAATTATCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
28375 TTTGTTTCA
1 TTTGTTTCA
28384 TGGGAAACAG
Statistics
Matches: 142, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
36 76 0.54
37 66 0.46
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:28552 original size:188 final size:192
Alignment explanation
Indices: 28074--28779 Score: 728
Period size: 188 Copynumber: 3.6 Consensus size: 192
28064 AGAAAATATC
* * * * * *
28074 TCAAGAGAAAATGTCTTAAGAGATACAAAAATTTGTTTTAAGGGAAACTATCTCAAGAGAGACAA
1 TCAAG-GAAACTGTCTCAAGAGAGAC-AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* * * * * ** **** *
28139 AA-TTTGTTTCAAAAGAAACTGTCTAAAGAGAGACAAAACTTAGTTCCAAAAGATTTTGTTTCAA
64 AACTTTGTTTCAAAAGAAACTATCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACAGATTCAA
* *** * * * *
28203 GGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
128 -AGATTTTGTTTCAAG-GAGA-AAGATCTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
28268 GTT
190 GTT
* * *
28271 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAA
1 TCAAG-GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* * * * *
28336 AACTTAGTTCCAAAAGAAATTATCTCAAGGGAGACGAAATTTGTTTCATGGGAAACAGATTCAAA
64 AACTTTGTTTCAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAA
*
28401 GATTTTGTTTCAAGG-G-AA-A-CTGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAATTTGTT
129 GATTTTGTTTCAAGGAGAAAGATCTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
* * *
28461 TCAAGGAACCCGTGTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TCAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
28526 CTTTGTTTCAAAAGAAACTGTCTCAAGGGAGA-ATAAATTTGTTTCAAGGAAAACAGATTTAAAG
66 CTTTGTTTCAAAAGAAACTATCTCAAGGGAGACA-AAATTTGTTTCAAGGGAAACAGATTCAAAG
* * *
28590 ATTTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACCA
130 ATTTTGTTTCAAGG-----AG----AAAGA-TCTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
28655 AATTTGTT
185 AATTTGTT
* * *
28663 TCAAGGGAAACTATCTCAAGAGAGAC--AATTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAA
1 TCAA-GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
* *
28726 A-TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
65 ACTTTGTTTCAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
28780 TGTCTCAGGA
Statistics
Matches: 428, Mismatches: 62, Indels: 35
0.82 0.12 0.07
Matches are distributed among these distances:
188 101 0.24
189 21 0.05
190 43 0.10
191 1 0.00
192 2 0.00
194 2 0.00
195 1 0.00
196 14 0.03
197 68 0.16
198 29 0.07
199 2 0.00
200 48 0.11
201 37 0.09
202 42 0.10
203 17 0.04
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (192 bp):
TCAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
CTTTGTTTCAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGA
TTTTGTTTCAAGGAGAAAGATCTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
Found at i:28645 original size:29 final size:29
Alignment explanation
Indices: 28563--28637 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
28553 GGAGAATAAA
*
28563 TTTGTTTCAAGGAAAACAGATTTAAAGAT
1 TTTGTTTCAAGGAAAACAGATTCAAAGAT
*
28592 TTTGTTTTAAGGAAAACAGATTCAAAGAT
1 TTTGTTTCAAGGAAAACAGATTCAAAGAT
*
28621 TTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGGAAAAC
28638 TGTCTCAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.35
Consensus pattern (29 bp):
TTTGTTTCAAGGAAAACAGATTCAAAGAT
Found at i:28702 original size:70 final size:71
Alignment explanation
Indices: 28621--28806 Score: 293
Period size: 70 Copynumber: 2.6 Consensus size: 71
28611 ATTCAAAGAT
* *
28621 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACCAAATTTGTTTCAAGGGAAACTATCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
28686 GAC-AA
66 GACAAA
*
28691 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
28756 GACAAAA
66 GAC-AAA
* * *
28763 TTTGTTTCAAGGGAAACTGTCTCAGGAAAGACTAAACTTTGTTT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTTGTTT
28807 TGAGTAAATT
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
70 65 0.61
72 31 0.29
73 10 0.09
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (71 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
GACAAA
Found at i:28736 original size:21 final size:20
Alignment explanation
Indices: 28642--28740 Score: 67
Period size: 21 Copynumber: 5.4 Consensus size: 20
28632 GGAAACTGTC
28642 TCAAGAGAGACCAAATTTGTT
1 TCAAGAGAGA-CAAATTTGTT
* * *
28663 TCAAG-G-G--AAA-CTATC
1 TCAAGAGAGACAAATTTGTT
28678 TCAAGAGAGAC-AATTTGTT
1 TCAAGAGAGACAAATTTGTT
*
28697 TCAAG-G-G--AAA-TTGTC
1 TCAAGAGAGACAAATTTGTT
28712 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGAC-AAATTTGTT
28733 TCAAGAGA
1 TCAAGAGA
28741 AACTATCTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 24
0.64 0.09 0.27
Matches are distributed among these distances:
15 16 0.28
16 7 0.12
17 3 0.05
18 3 0.05
19 8 0.14
20 4 0.07
21 17 0.29
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (20 bp):
TCAAGAGAGACAAATTTGTT
Found at i:34998 original size:3 final size:3
Alignment explanation
Indices: 34981--35018 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
34971 AGGTCTACAA
34981 AAT AAT AA- AAGT AAT AAT AAT AAT AAT AAAT AAT AAT A
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT A
35019 TATTATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 25 0.78
4 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:35062 original size:35 final size:37
Alignment explanation
Indices: 35016--35100 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 37
35006 ATAAATAATA
35016 ATATATTATATATA-TATAAAAAT-ATTTTTAAAAAC-
1 ATATATTATATATATTATAAAAATGA-TTTTAAAAACT
* * * *
35051 ATATAATATATAAATTTTCAAAATGATTTTAAAAACT
1 ATATATTATATATATTATAAAAATGATTTTAAAAACT
35088 ATATATTATATAT
1 ATATATTATATAT
35101 GTATTTTCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 12 0.29
36 17 0.41
37 12 0.29
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
ATATATTATATATATTATAAAAATGATTTTAAAAACT
Found at i:36835 original size:21 final size:21
Alignment explanation
Indices: 36811--36863 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
36801 GGACTGTCAT
*
36811 GTCAACACTGTGGACTACCAC
1 GTCAACACTGTGAACTACCAC
** *
36832 GTCAGTACCGTGAACTACCAC
1 GTCAACACTGTGAACTACCAC
* *
36853 ATCCACACTGT
1 GTCAACACTGT
36864 AACGGTTAAC
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (21 bp):
GTCAACACTGTGAACTACCAC
Found at i:37556 original size:2 final size:2
Alignment explanation
Indices: 37551--37586 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
37541 GCTTATAATG
37551 AT AT AT AT 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 AT AT AT AT
37587 TGTAGATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39616 original size:21 final size:21
Alignment explanation
Indices: 39583--39836 Score: 304
Period size: 21 Copynumber: 12.2 Consensus size: 21
39573 GATTCACAAC
* *
39583 GCGAACTTCGACTATTGCAAT
1 GCGAACTTGGACTATCGCAAT
*
39604 GCGAGCTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
39625 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
*
39646 GCAAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
* *
39667 GCGAA-TATGTA-AATCGCAAT
1 GCGAACT-TGGACTATCGCAAT
* * *
39687 GTGATA-GTCGACTATCGCAAT
1 GCGA-ACTTGGACTATCGCAAT
39708 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
39729 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
39750 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
* * *
39771 GCGAACATGTA-AATCGCAAT
1 GCGAACTTGGACTATCGCAAT
* *
39791 G-TAA-TAGTCGACTATCGCAAT
1 GCGAACT--TGGACTATCGCAAT
39812 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
39833 GCGA
1 GCGA
39837 TTCGACTGGT
Statistics
Matches: 198, Mismatches: 26, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.01
20 26 0.13
21 167 0.84
22 2 0.01
23 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAT
Found at i:39721 original size:104 final size:104
Alignment explanation
Indices: 39590--39836 Score: 449
Period size: 104 Copynumber: 2.4 Consensus size: 104
39580 AACGCGAACT
* *
39590 TCGACTATTGCAATGCGAGCTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCAAACTTG
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCAAACTTG
* *
39655 GACTATCGCAATGCGAATATGTAAATCGCAATGTGATAG
66 GACTATCGCAATGCGAACATGTAAATCGCAATGTAATAG
*
39694 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTG
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCAAACTTG
39759 GACTATCGCAATGCGAACATGTAAATCGCAATGTAATAG
66 GACTATCGCAATGCGAACATGTAAATCGCAATGTAATAG
39798 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGA
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGA
39837 TTCGACTGGT
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 138 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (104 bp):
TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCAAACTTG
GACTATCGCAATGCGAACATGTAAATCGCAATGTAATAG
Found at i:39787 original size:83 final size:84
Alignment explanation
Indices: 39583--39836 Score: 297
Period size: 83 Copynumber: 3.0 Consensus size: 84
39573 GATTCACAAC
* * * * *
39583 GCGAACTTCGACTATTGCAATGCGAGCTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGC
1 GCGAACTTGGACTATCGCAATGCGAACATGTACTATCGCAATGCGAACTTGGACTATCGCAATGC
*
39648 AAACTTGGACTATCGCAAT
66 GAACTTGGACTATCGCAAT
* * * *
39667 GCGAA-TATGTA-AATCGCAATGTG-ATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAA
1 GCGAACT-TGGACTATCGCAATGCGAACATGT--ACTATCGCAATGCGAACTTGGACTATCGCAA
39728 TGCGAACTTGGACTATCGCAAT
63 TGCGAACTTGGACTATCGCAAT
* * *
39750 GCGAACTTGGACTATCGCAATGCGAACATGTA-AATCGCAATG-TAA-TAGTCGACTATCGCAAT
1 GCGAACTTGGACTATCGCAATGCGAACATGTACTATCGCAATGCGAACT--TGGACTATCGCAAT
39812 GCGAACTTGGACTATCGCAAT
64 GCGAACTTGGACTATCGCAAT
39833 GCGA
1 GCGA
39837 TTCGACTGGT
Statistics
Matches: 144, Mismatches: 17, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
81 2 0.01
82 2 0.01
83 117 0.81
84 19 0.13
85 2 0.01
86 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (84 bp):
GCGAACTTGGACTATCGCAATGCGAACATGTACTATCGCAATGCGAACTTGGACTATCGCAATGC
GAACTTGGACTATCGCAAT
Found at i:39950 original size:5 final size:5
Alignment explanation
Indices: 39924--39968 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
39914 CGTATTACCA
*
39924 CGACC ACGACC ACGAAC CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGA
39969 GACGAGACGA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
5 27 0.73
6 10 0.27
ACGTcount: A:0.27, C:0.53, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:40657 original size:42 final size:42
Alignment explanation
Indices: 40608--40786 Score: 195
Period size: 42 Copynumber: 4.2 Consensus size: 42
40598 ATTTTGGACT
* *
40608 ATCGCAACGAACATAGAATAAATCACAACGAATTTGGAATAA
1 ATCGCAACGAACTTAGAATAAATCGCAACGAATTTGGAATAA
* *
40650 ATCGCAACGCGAACTTCGACT--ATCGCAACGAATTTGGAATAA
1 ATCGCAA--CGAACTTAGAATAAATCGCAACGAATTTGGAATAA
*
40692 ATCGCAACACGAACTTGGAATAAATCGCAACGAATTTGGAATAA
1 ATCGC-A-ACGAACTTAGAATAAATCGCAACGAATTTGGAATAA
* * * *
40736 ATCGCAACGCGAACTTCGACT--ATCGCAACAAACTTGGAATAA
1 ATCGCAA--CGAACTTAGAATAAATCGCAACGAATTTGGAATAA
40778 ATCGCAACG
1 ATCGCAACG
40787 CGAACTTGGA
Statistics
Matches: 119, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
40 2 0.02
42 69 0.58
43 2 0.02
44 46 0.39
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (42 bp):
ATCGCAACGAACTTAGAATAAATCGCAACGAATTTGGAATAA
Found at i:40674 original size:21 final size:21
Alignment explanation
Indices: 40608--40805 Score: 142
Period size: 21 Copynumber: 9.3 Consensus size: 21
40598 ATTTTGGACT
* *
40608 ATCGCAA-CGAACATAGAATAA
1 ATCGCAACCGAACTTGGAAT-A
* *
40629 ATCACAA-CGAATTTGGAATAA
1 ATCGCAACCGAACTTGGAAT-A
* *
40650 ATCGCAACGCGAACTTCGACT-
1 ATCGCAAC-CGAACTTGGAATA
*
40671 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAACCGAACTTGGAAT-A
40692 ATCGCAACACGAACTTGGAATAA
1 ATCGCAAC-CGAACTTGGAAT-A
*
40715 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAACCGAACTTGGAAT-A
* *
40736 ATCGCAACGCGAACTTCGACT-
1 ATCGCAAC-CGAACTTGGAATA
*
40757 ATCGCAA-CAAACTTGGAATAA
1 ATCGCAACCGAACTTGGAAT-A
*
40778 ATCGCAACGCGAACTTGGACT-
1 ATCGCAAC-CGAACTTGGAATA
40799 ATCGCAA
1 ATCGCAA
40806 TACGAATATG
Statistics
Matches: 144, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
19 18 0.12
21 78 0.54
23 48 0.33
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACCGAACTTGGAATA
Found at i:40759 original size:86 final size:86
Alignment explanation
Indices: 40614--40796 Score: 312
Period size: 86 Copynumber: 2.1 Consensus size: 86
40604 GACTATCGCA
* *
40614 ACGAACATAGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC
1 ACGAACTTGGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC
* *
40679 GAATTTGGAATAAATCGCAAC
66 AAACTTGGAATAAATCGCAAC
*
40700 ACGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC
1 ACGAACTTGGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC
40765 AAACTTGGAATAAATCGCAAC
66 AAACTTGGAATAAATCGCAAC
*
40786 GCGAACTTGGA
1 ACGAACTTGGA
40797 CTATCGCAAT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 91 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (86 bp):
ACGAACTTGGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC
AAACTTGGAATAAATCGCAAC
Found at i:40787 original size:42 final size:42
Alignment explanation
Indices: 40633--40805 Score: 274
Period size: 42 Copynumber: 4.1 Consensus size: 42
40623 GAATAAATCA
40633 CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
* * *
40675 CAACGAATTTGGAATAAATCGCAACACGAACTTGGAATAAATCG
1 CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT--ATCG
40719 CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
* * *
40761 CAACAAACTTGGAATAAATCGCAACGCGAACTTGGACTATCG
1 CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
40803 CAA
1 CAA
40806 TACGAATATG
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
42 81 0.68
44 39 0.32
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (42 bp):
CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
Found at i:43088 original size:130 final size:131
Alignment explanation
Indices: 42871--43233 Score: 394
Period size: 130 Copynumber: 2.8 Consensus size: 131
42861 AATGAGAATG
** * *
42871 GTAATATC-CTTTCATTTCGGTCGGAGTAATAAATGAATGCTTTAAGGCAT-AAGAGGTCATTTA
1 GTAATATCTCTTT-ATTTCAATTGGAGTAATAAATGAATGCTTTAATGCATGAA-AGGTCATTTA
* * * * * * * * * *
42934 TTTTCAATTGGAAATAATTTGATATTGCCT-TTTTCTCTCGAATTAATATCGATTTTTTAGACGG
64 TTCTCGATTGGAAATAATTAGATATT-ACTATTTTCACTCGAATCAATATCAAATTTTAAGACGA
42998 AATA
128 AATA
* * * *
43002 TTAATATCTCTTTATTTCAATTGGGGTAATAAATAAATG-TTTAATGCATGAAAGGTCGTTTATT
1 GTAATATCTCTTTATTTCAATTGGAGTAATAAATGAATGCTTTAATGCATGAAAGGTCATTTATT
* * * * * *
43066 CTCGATTGGAAATCATTAGATATTATTATTTTCACTTGAATCGATATTAAATTTTAAGATGAAAT
66 CTCGATTGGAAATAATTAGATATTACTATTTTCACTCGAATCAATATCAAATTTTAAGACGAAAT
43131 A
131 A
* * *
43132 GTAATATCTCTTTATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAAAGGTCATTTATT
1 GTAATATCTCTTTATTTCAATTGGAGTAATAAATGAATGCTTTAATGCATGAAAGGTCATTTATT
* *
43197 CTCGATTGGAAGTAATTATATATTA-TCATTTTCACTC
66 CTCGATTGGAAATAATTAGATATTACT-ATTTTCACTC
43234 TTAAAATTAT
Statistics
Matches: 193, Mismatches: 34, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
129 1 0.01
130 104 0.54
131 84 0.44
132 4 0.02
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (131 bp):
GTAATATCTCTTTATTTCAATTGGAGTAATAAATGAATGCTTTAATGCATGAAAGGTCATTTATT
CTCGATTGGAAATAATTAGATATTACTATTTTCACTCGAATCAATATCAAATTTTAAGACGAAAT
A
Found at i:44187 original size:2 final size:2
Alignment explanation
Indices: 44055--44168 Score: 90
Period size: 2 Copynumber: 57.0 Consensus size: 2
44045 ACAGCCATTT
* * * * *
44055 TA TA TCA TA TA GTA TA TA TA TG CA TG TA TA TA CA TA TA TG TA TA
1 TA TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
44099 TA CT- TA TA CA TA TA TA TC T- TA TA TG CA 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
*
44140 TA TA TA TA TA TA TA TA T- TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44169 AAAGTACATA
Statistics
Matches: 87, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
1 3 0.03
2 79 0.91
3 5 0.06
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:44711 original size:21 final size:21
Alignment explanation
Indices: 44652--44712 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
44642 ATGTTAAATT
*
44652 ATATTTAAATT-ATTATATGAA
1 ATATTTAAATTAATTTTAT-AA
** **
44673 A-AAATAAATTAAACTTATAA
1 ATATTTAAATTAATTTTATAA
44693 ATATTTAAATTAATTTTATA
1 ATATTTAAATTAATTTTATA
44713 TAATCTAATA
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATTTAAATTAATTTTATAA
Found at i:58136 original size:47 final size:47
Alignment explanation
Indices: 58083--58248 Score: 246
Period size: 47 Copynumber: 3.6 Consensus size: 47
58073 TATATATGAT
* *
58083 ATCCTTTCATGCATTTTCAATTATGGA-ATCCTTTCTTGCCTTAATGC
1 ATCCTTTCATGCATTTTCAATTAT-GACATCATTTCATGCCTTAATGC
* * * *
58130 ATCCTTTCATGCATTTTCAATTATGACATAATTTCAGGCCTGATTGC
1 ATCCTTTCATGCATTTTCAATTATGACATCATTTCATGCCTTAATGC
*
58177 ATCCGTTCATGCATTTTCAATTATGACATCATTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTCAATTATGACATCATTTCATGCCTTAATGC
58224 ATCC-TTCATGCATTTTCAATTATGA
1 ATCCTTTCATGCATTTTCAATTATGA
58249 ATTCGATTTA
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
46 23 0.21
47 84 0.79
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (47 bp):
ATCCTTTCATGCATTTTCAATTATGACATCATTTCATGCCTTAATGC
Found at i:58804 original size:96 final size:95
Alignment explanation
Indices: 58659--58858 Score: 276
Period size: 95 Copynumber: 2.1 Consensus size: 95
58649 ACCTTGGTAC
* *
58659 CGATACTTCTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAAATTAGCTTCGATG
1 CGATACTACTATACTATGGTACCGATACCCCCTTCCAGTATCGATACC-AAAATTAGATTCGATG
* *
58724 -TTGCTTGATATCGATACCCTTACCATGGCAT
65 ATTAC-TGATATCGACACCCTTACCATGGCAT
* ** * *
58755 CGATACTACTATACTATTGTACCGATACCCGTTTCTAGTATCGATACCAAAATTATATTCGATGA
1 CGATACTACTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCGATGA
* *
58820 TTACTGGTATCGACACCCTTACCATGGTAT
66 TTACTGATATCGACACCCTTACCATGGCAT
58850 CGATACTAC
1 CGATACTAC
58859 ACAGCTAAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
95 46 0.50
96 46 0.50
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (95 bp):
CGATACTACTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCGATGA
TTACTGATATCGACACCCTTACCATGGCAT
Found at i:58857 original size:95 final size:96
Alignment explanation
Indices: 58648--58858 Score: 282
Period size: 96 Copynumber: 2.2 Consensus size: 96
58638 TTGATACTAC
* * *
58648 TACCTTGGTACCGATACTTCTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAAAT
1 TACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAAAT
* * *
58713 TAGCTTCGATGTTGCTTGATATCGATACCCT
66 TAGATTCGATGTTACTTGATATCGACACCCT
* * ** *
58744 TACCATGGCATCGATACTACTATACTATTGTACCGATACCCGTTTCTAGTATCGATACC-AAAAT
1 TACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAAAT
* *
58808 TATATTCGATGATTAC-TGGTATCGACACCCT
66 TAGATTCGATG-TTACTTGATATCGACACCCT
58839 TACCATGGTATCGATACTAC
1 TACCATGGTATCGATACTAC
58859 ACAGCTAAAT
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
95 46 0.46
96 54 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (96 bp):
TACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAAAT
TAGATTCGATGTTACTTGATATCGACACCCT
Found at i:59763 original size:81 final size:81
Alignment explanation
Indices: 59674--60310 Score: 904
Period size: 81 Copynumber: 7.9 Consensus size: 81
59664 AATTTTCATC
** * * *
59674 TTTACTCAACATTGTTTATCCGTTCATGTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
59739 GTTAGGCCATTATTCT
66 GTTAGGCCATTATTCT
* *
59755 TTTACTCAACCGTATTTAACCGTTCATCTAACTGACATAATTGGCACCTTTCTACCAATTGCACA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
** *
59820 -TATAAACCATTACTCT
66 GT-TAGGCCATTATTCT
* * * *
59836 TTTTCTCAACGGTATTTAACCGTTCATCTGACTGGCATAATTGGCACCTTTCAACCAATTGCATA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
59901 GTTAGGCCATTATTCT
66 GTTAGGCCATTATTCT
*
59917 TTTACTCAACGGTATTTAACCGTTCATCTAATTGGCATAATTGGCACCTTTCTACCAATTGCACA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
59982 GTTAGGCCATTATTCT
66 GTTAGGCCATTATTCT
* * * * * *
59998 TTTACTC-A--TTATTTAATCGTTCACCTAATTGGCATAATTTGCACCTTTCTACCAATTACACA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
*
60060 GTTAGACCATTATTCT
66 GTTAGGCCATTATTCT
* * * *
60076 TTTACTCAACTGTATTTAACCGTTCATATAACTGGCATAATTGACACCTTTCTACCAATTGCATA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
* * *
60141 GTTATGTCACTATTCT
66 GTTAGGCCATTATTCT
* * * *
60157 TTTACTCAACGGTATTTTACTGTTCATCTAACTGGCATAATTGGAACCTTTCTACCAATTACACA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
*
60222 ATTAGGCCATTATTCT
66 GTTAGGCCATTATTCT
* * *
60238 TTTACTCAATGGTATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGCACA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
60303 GTTAGGCC
66 GTTAGGCC
60311 TTAAAGGCAC
Statistics
Matches: 489, Mismatches: 62, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
78 71 0.15
79 1 0.00
80 2 0.00
81 414 0.85
82 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (81 bp):
TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACA
GTTAGGCCATTATTCT
Found at i:60288 original size:321 final size:321
Alignment explanation
Indices: 59706--60310 Score: 960
Period size: 321 Copynumber: 1.9 Consensus size: 321
59696 TTCATGTAAC
* *
59706 TGGCATAATTGGCACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACCGTATT
1 TGGCATAATTGGCACCTTTCTACCAATTACACAGTTAGACCATTATTCTTTTACTCAACCGTATT
* * *
59771 TAACCGTTCATCTAACTGACATAATTGGCACCTTTCTACCAATTGCACATATAAACCATTACTCT
66 TAACCGTTCATATAACTGACATAATTGACACCTTTCTACCAATTGCACATATAAACCACTACTCT
* * * * *
59836 TTTTCTCAACGGTATTTAACCGTTCATCTGACTGGCATAATTGGCACCTTTCAACCAATTGCATA
131 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGAACCTTTCAACCAATTACACA
* * * *
59901 GTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAATTGGCATAATTGGCACCT
196 ATTAGGCCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACCT
59966 TTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCATTATTTAATCGTTCACCTAAT
261 TTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCATTATTTAATCGTTCACCTAAT
* *
60027 TGGCATAATTTGCACCTTTCTACCAATTACACAGTTAGACCATTATTCTTTTACTCAACTGTATT
1 TGGCATAATTGGCACCTTTCTACCAATTACACAGTTAGACCATTATTCTTTTACTCAACCGTATT
* * *** *
60092 TAACCGTTCATATAACTGGCATAATTGACACCTTTCTACCAATTGCATAGT-TATGTCACTATTC
66 TAACCGTTCATATAACTGACATAATTGACACCTTTCTACCAATTGCACA-TATAAACCACTACTC
* * *
60156 TTTTACTCAACGGTATTTTACTGTTCATCTAACTGGCATAATTGGAACCTTTCTACCAATTACAC
130 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGAACCTTTCAACCAATTACAC
*
60221 AATTAGGCCATTATTCTTTTACTCAATGGTATTTAACCATTCATCTAACTGGCATAATTGACACC
195 AATTAGGCCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACC
60286 TTTCTACCAATTGCACAGTTAGGCC
260 TTTCTACCAATTGCACAGTTAGGCC
60311 TTAAAGGCAC
Statistics
Matches: 257, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
321 256 1.00
322 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (321 bp):
TGGCATAATTGGCACCTTTCTACCAATTACACAGTTAGACCATTATTCTTTTACTCAACCGTATT
TAACCGTTCATATAACTGACATAATTGACACCTTTCTACCAATTGCACATATAAACCACTACTCT
TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGAACCTTTCAACCAATTACACA
ATTAGGCCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACCT
TTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCATTATTTAATCGTTCACCTAAT
Found at i:60408 original size:67 final size:67
Alignment explanation
Indices: 60260--60443 Score: 273
Period size: 67 Copynumber: 2.7 Consensus size: 67
60250 TATTTAACCA
* * * *
60260 TTCATCTAACTGGCATAATTGACACCTTTCTACCA-ATTGCACAGTTAGGCCTTAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATA-AGCACAGTTAGG-CTCAAAGGCACTTA
60324 GCCT
64 GCCT
**
60328 TTCATCT-GTTGGCATAAATGACACCTTTCTATCATAAGCACAGTTAGGCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATAAGCACAGTTAGGCTCAAAGGCACTTAGC
60392 CT
66 CT
*
60394 TTCATCTAACTGGCATAAATGACCCCTTTCTATCATAAGCACAGTTAGGC
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATAAGCACAGTTAGGC
60444 CTATTAATCT
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
66 24 0.23
67 73 0.70
68 8 0.08
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (67 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTATCATAAGCACAGTTAGGCTCAAAGGCACTTAGC
CT
Found at i:60731 original size:54 final size:56
Alignment explanation
Indices: 60658--60798 Score: 173
Period size: 55 Copynumber: 2.6 Consensus size: 56
60648 CATATATTTT
* * * * *
60658 CCCATAC-GAACATTCATACAGTTGGTATGGATTT-TTTA-GTTCGCACACATAGTA
1 CCCATACAGAA-ATTCATACACTTAGTATGAATTTCCTTATGTTCGCACACAAAGTA
* * *
60712 CCCATACAGAAATTCATACACTTAGTATGAATTTCCTTATTTTTGCACACAAAGTT
1 CCCATACAGAAATTCATACACTTAGTATGAATTTCCTTATGTTCGCACACAAAGTA
60768 CCC-TACAGAAATTCATACACTTAGTATGAAT
1 CCCATACAGAAATTCATACACTTAGTATGAAT
60799 ATCTTACAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
54 27 0.36
55 34 0.45
56 15 0.20
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (56 bp):
CCCATACAGAAATTCATACACTTAGTATGAATTTCCTTATGTTCGCACACAAAGTA
Found at i:64432 original size:17 final size:17
Alignment explanation
Indices: 64410--64442 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
64400 AAACGCATAT
64410 CGATTTTGTCTTAAAAA
1 CGATTTTGTCTTAAAAA
*
64427 CGATTTTTTCTTAAAA
1 CGATTTTGTCTTAAAA
64443 TTAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (17 bp):
CGATTTTGTCTTAAAAA
Found at i:67613 original size:18 final size:19
Alignment explanation
Indices: 67565--67613 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 19
67555 AAGATCAAAT
67565 CAAAGGAAAAAATAAAGAG
1 CAAAGGAAAAAATAAAGAG
67584 CAAAGGAAAAAATAAAGAG
1 CAAAGGAAAAAATAAAGAG
67603 CAAAGAGAAAA
1 CAAAG-GAAAA
67614 GAAAAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.69, C:0.06, G:0.20, T:0.04
Consensus pattern (19 bp):
CAAAGGAAAAAATAAAGAG
Found at i:67635 original size:28 final size:27
Alignment explanation
Indices: 67590--67667 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
67580 AGAGCAAAGG
67590 AAAAAATAAAGAGCAAAGAGAAAAGAAA
1 AAAAAATAAAGAGCAAAGA-AAAAGAAA
*
67618 AAAAGAATAAA-ATCAAAGAAAAAGAAA
1 AAAA-AATAAAGAGCAAAGAAAAAGAAA
* *
67645 AAAAAAGAAAAAAG-AAAGAAAAA
1 AAAAAA-TAAAGAGCAAAGAAAAA
67668 AGACAAGAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 2 0.05
27 24 0.55
28 12 0.27
29 6 0.14
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.04
Consensus pattern (27 bp):
AAAAAATAAAGAGCAAAGAAAAAGAAA
Found at i:67645 original size:16 final size:17
Alignment explanation
Indices: 67610--67670 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 17
67600 GAGCAAAGAG
67610 AAAAGAAAAAAAGAATAAA
1 AAAAG-AAAAAAGAA-AAA
67629 ATCAAAG-AAAAAGAAAAA
1 A--AAAGAAAAAAGAAAAA
67647 AAAAGAAAAAAGAAAGAA
1 AAAAGAAAAAAGAAA-AA
67665 AAAAGA
1 AAAAGA
67671 CAAGAAGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.11
17 9 0.24
18 12 0.32
19 9 0.24
21 4 0.11
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAA
Found at i:67649 original size:10 final size:10
Alignment explanation
Indices: 67636--67668 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
67626 AAAATCAAAG
67636 AAAAAGAAAA
1 AAAAAGAAAA
67646 AAAAAGAAAA
1 AAAAAGAAAA
67656 AAGAAAGAAAA
1 AA-AAAGAAAA
67667 AA
1 AA
67669 GACAAGAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:67650 original size:21 final size:20
Alignment explanation
Indices: 67611--67668 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
67601 AGCAAAGAGA
*
67611 AAAGAAAAA-AAGAATAAAATC
1 AAAGAAAAAGAA-AA-AAAAAC
*
67632 AAAGAAAAAGAAAAAAAAAG
1 AAAGAAAAAGAAAAAAAAAC
*
67652 AAAAAAGAAAGAAAAAA
1 AAAGAA-AAAGAAAAAA
67669 GACAAGAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 9 0.28
21 21 0.66
22 2 0.06
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAAAAC
Found at i:67669 original size:11 final size:11
Alignment explanation
Indices: 67638--67676 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
67628 AATCAAAGAA
67638 AAAGAAAAAA-
1 AAAGAAAAAAG
67648 AAAGAAAAAAG
1 AAAGAAAAAAG
67659 AAAGAAAAAAG
1 AAAGAAAAAAG
67670 ACAAGAA
1 A-AAGAA
67677 GCACACACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.37
11 12 0.44
12 5 0.19
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:73337 original size:18 final size:18
Alignment explanation
Indices: 73311--73345 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
73301 TCGAAAGGAC
*
73311 TGAAATAAATGATAAGAT
1 TGAAATAAATAATAAGAT
*
73329 TGAATTAAATAATAAGA
1 TGAAATAAATAATAAGA
73346 CCAGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (18 bp):
TGAAATAAATAATAAGAT
Found at i:76553 original size:32 final size:32
Alignment explanation
Indices: 76501--76570 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
76491 TGAAGCAAGA
* * * *
76501 AACATTGAATGTTGGGGCATCTTT-GGAGATTT
1 AACATCGAATATTGGAGCATCTTTAGG-GATTC
76533 AACATCGAATATTGGAGCATCTTTAGGGATTC
1 AACATCGAATATTGGAGCATCTTTAGGGATTC
76565 AACATC
1 AACATC
76571 CTGATACGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (32 bp):
AACATCGAATATTGGAGCATCTTTAGGGATTC
Found at i:77167 original size:129 final size:129
Alignment explanation
Indices: 76825--77181 Score: 398
Period size: 133 Copynumber: 2.7 Consensus size: 129
76815 GAAACCATTA
* * *
76825 TCCCTAAAGATGGTCTGCCATCTCATCATGTAGGAACCATGTCATCCCTCGACCAAACCTCCTCA
1 TCCCTAAAGATGGTCTTCCGTCTCATCATGTAGGAACCATGTCATCCCT-GACCAGACCTCCTCA
** * * * * *
76890 TCACATAAGATTCGTGTCACCCTTGATAACCAACCGTCCTTATCGCGTAGGAACTGTGTTATCAC
65 TCACATAAGAACCGTGTCACCCTTGATAAACAACCATCCTTATCACATAGGAACCGTGTTATCA-
76955 CC
129 -C
*
76957 TCCCTAAAGATGGTCTAT-CGTTCTCATCATGTAGGAACCGTGTCATCCCTTGACCAGACCTCCT
1 TCCCTAAAGATGGTCT-TCCG-TCTCATCATGTAGGAACCATGTCATCCC-TGACCAGACCTCCT
* * * *
77021 CATCACGTAAGAGCCGTGTCACCCTTGATAAACAACCATCTTTATCATATAGGAACCGTGTTATC
63 CATCACATAAGAACCGTGTCACCCTTGATAAACAACCATCCTTATCACATAGGAACCGTGTTATC
77086 A-
128 AC
* * * *
77087 T-CCTAAAGATGGTGTTCCGTCCTCATCACGTAGGAACCATGTCATCAACTGACCAGACCAT-GT
1 TCCCTAAAGATGGTCTTCCGT-CTCATCATGTAGGAACCATGTCATC-CCTGACCAGACC-TCCT
* * *
77150 CATCATATAGGAACCGTGTCATCCCTAGATAA
63 CATCACATAAGAACCGTGTCA-CCCTTGATAA
77182 CAGCTGCCCT
Statistics
Matches: 193, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
128 2 0.01
129 66 0.34
130 12 0.06
132 17 0.09
133 95 0.49
134 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (129 bp):
TCCCTAAAGATGGTCTTCCGTCTCATCATGTAGGAACCATGTCATCCCTGACCAGACCTCCTCAT
CACATAAGAACCGTGTCACCCTTGATAAACAACCATCCTTATCACATAGGAACCGTGTTATCAC
Found at i:77510 original size:3 final size:3
Alignment explanation
Indices: 77502--77539 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
77492 CTACCAAAAA
77502 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
77540 ATTTACATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:80117 original size:13 final size:13
Alignment explanation
Indices: 80110--80150 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
80100 TCTTTTCTTC
80110 TTAACTTTTCACT
1 TTAACTTTTCACT
80123 TTAACTTTTCACACT
1 TTAACTTTT--CACT
80138 TTAACTTTTCACT
1 TTAACTTTTCACT
80151 CTTCCCCTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAACTTTTCACT
Found at i:80139 original size:15 final size:15
Alignment explanation
Indices: 80110--80149 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
80100 TCTTTTCTTC
80110 TTAACTTTT--CACT
1 TTAACTTTTCACACT
80123 TTAACTTTTCACACT
1 TTAACTTTTCACACT
80138 TTAACTTTTCAC
1 TTAACTTTTCAC
80150 TCTTCCCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 9 0.36
15 16 0.64
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAACTTTTCACACT
Found at i:80492 original size:20 final size:22
Alignment explanation
Indices: 80467--80514 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
80457 CAATTTCTAA
* *
80467 TTTTTTACTAAA-CATTGTT-G
1 TTTTTTACAAAATAATTGTTAG
80487 TTTTTTACAAAATAATTGTTAG
1 TTTTTTACAAAATAATTGTTAG
80509 TTTTTT
1 TTTTTT
80515 CTTTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
21 6 0.25
22 7 0.29
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.58
Consensus pattern (22 bp):
TTTTTTACAAAATAATTGTTAG
Found at i:80597 original size:53 final size:54
Alignment explanation
Indices: 80469--80598 Score: 185
Period size: 53 Copynumber: 2.4 Consensus size: 54
80459 ATTTCTAATT
* *
80469 TTTTACTAAAC-ATTGTTGTTTTTTACAAAATAATTGTTAGTTTTTTCTTTTAAA
1 TTTTGCTAAACGA-TGTTGCTTTTTACAAAATAATTGTTAGTTTTTTCTTTTAAA
**
80523 TTTTGCTAAACGATGCCGCTTTTTAC-AAA-AATTGTTAGTTTTCTTCTTTTAAA
1 TTTTGCTAAACGATGTTGCTTTTTACAAAATAATTGTTAGTTTT-TTCTTTTAAA
80576 TTTTGCTAAACGATGTTGCTTTT
1 TTTTGCTAAACGATGTTGCTTTT
80599 ATTATTCGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
52 13 0.19
53 34 0.50
54 20 0.29
55 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.52
Consensus pattern (54 bp):
TTTTGCTAAACGATGTTGCTTTTTACAAAATAATTGTTAGTTTTTTCTTTTAAA
Found at i:82270 original size:17 final size:18
Alignment explanation
Indices: 82239--82273 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
82229 AAATCGAAAA
*
82239 AAATAGAGGGGTCTCGGG
1 AAATAGAGGGCTCTCGGG
82257 AAATA-AGGGCTCTCGGG
1 AAATAGAGGGCTCTCGGG
82274 TTTTCCAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.29, C:0.14, G:0.40, T:0.17
Consensus pattern (18 bp):
AAATAGAGGGCTCTCGGG
Found at i:89344 original size:35 final size:34
Alignment explanation
Indices: 89295--89412 Score: 114
Period size: 35 Copynumber: 3.4 Consensus size: 34
89285 GTTGGAAATC
*
89295 TATCTCTAAAGAGATGAAAATTTTTCAAGAGAAAA
1 TATCTC-AATGAGATGAAAATTTTTCAAGAGAAAA
* * *
89330 TATCTCAAGTGAGAT-ACAATTTTTCAAGGGAAAC
1 TATCTCAA-TGAGATGAAAATTTTTCAAGAGAAAA
* * *
89364 TGTCTCGAATGAGACGAAATTTGTTTCAAGA-AAAA
1 TATCTC-AATGAGATGAAAATT-TTTCAAGAGAAAA
89399 TATCTCCAATGAGA
1 TATCT-CAATGAGA
89413 AAAAAAATAT
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
34 28 0.42
35 31 0.46
36 8 0.12
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.29
Consensus pattern (34 bp):
TATCTCAATGAGATGAAAATTTTTCAAGAGAAAA
Found at i:89356 original size:34 final size:33
Alignment explanation
Indices: 89312--89412 Score: 98
Period size: 34 Copynumber: 2.9 Consensus size: 33
89302 AAAGAGATGA
*
89312 AAATTTTTCAAGAGAAAATATCTCAAGTGAGA-T
1 AAATTTTTCAAGAGAAAATATCTCAA-TGAGACG
* * *
89345 ACAATTTTTCAAGGGAAACTGTCTCGAATGAGACG
1 A-AATTTTTCAAGAGAAAATATCTC-AATGAGACG
89380 AAATTTGTTTCAAGA-AAAATATCTCCAATGAGA
1 AAA-TT-TTTCAAGAGAAAATATCT-CAATGAGA
89413 AAAAAAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
33 1 0.02
34 27 0.49
35 19 0.35
36 8 0.15
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.29
Consensus pattern (33 bp):
AAATTTTTCAAGAGAAAATATCTCAATGAGACG
Found at i:89677 original size:36 final size:35
Alignment explanation
Indices: 89577--89692 Score: 105
Period size: 36 Copynumber: 3.3 Consensus size: 35
89567 AGGGAAAATG
* * *
89577 TCTCAAGTGAGATAAA-TTGTGTTTAAAGAACACTA
1 TCTCAAGTGAGA-AAATTTATGTTTAAAGAAAATTA
* * * * *
89612 TCTCAAGT--GATATTTTAT-TTCGAAGGAAAATTG
1 TCTCAAGTGAGAAAATTTATGTT-TAAAGAAAATTA
89645 TCTCAAGTGAGACAAATTTATGTTTAAAGAAAATTA
1 TCTCAAGTGAGA-AAATTTATGTTTAAAGAAAATTA
89681 TCTCAAGTGAGA
1 TCTCAAGTGAGA
89693 TAAAAAAATT
Statistics
Matches: 62, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
32 3 0.05
33 20 0.32
35 10 0.16
36 27 0.44
37 2 0.03
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (35 bp):
TCTCAAGTGAGAAAATTTATGTTTAAAGAAAATTA
Found at i:89688 original size:69 final size:66
Alignment explanation
Indices: 89510--89693 Score: 226
Period size: 67 Copynumber: 2.7 Consensus size: 66
89500 AGAGAAACTA
* * * * *
89510 TCTCAAGTG-GACAAAATTTGTTTTAAGGAGAATAATCTCAAGTGAGCTTTTATTTCGAGGGAAA
1 TCTCAAGTGAGAC-AAATTTG-TTTAAAGAAAATTATCTCAAGTGAGATTTTATTTCGAAGGAAA
89574 ATG
64 ATG
* * * *
89577 TCTCAAGTGAGATAAATTGTGTTTAAAGAACACTATCTCAAGTGATATTTTATTTCGAAGGAAAA
1 TCTCAAGTGAGACAAATT-TGTTTAAAGAAAATTATCTCAAGTGAGATTTTATTTCGAAGGAAAA
89642 TTG
65 -TG
89645 TCTCAAGTGAGACAAATTTATGTTTAAAGAAAATTATCTCAAGTGAGAT
1 TCTCAAGTGAGACAAA-TT-TGTTTAAAGAAAATTATCTCAAGTGAGAT
89694 AAAAAAATTT
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
67 50 0.51
68 21 0.21
69 28 0.28
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (66 bp):
TCTCAAGTGAGACAAATTTGTTTAAAGAAAATTATCTCAAGTGAGATTTTATTTCGAAGGAAAAT
G
Found at i:89786 original size:57 final size:55
Alignment explanation
Indices: 89724--89833 Score: 139
Period size: 57 Copynumber: 2.0 Consensus size: 55
89714 AAGCTATCTC
* * * *
89724 GAGTGAGAAGAAACTTGTTTTAAGAAAAACTATGTCAAGTGGTATATTTTTTTTTCT
1 GAGTGAGAAGAAACTTGATATAAGAAAAACTATCTCAA-TGATA-ATTTTTTTTTCT
* * *
89781 GAGTGAGACGATACTTGATATAAGGAAAACTATCTCAATGATAATTTTTTTTT
1 GAGTGAGAAGAAACTTGATATAAGAAAAACTATCTCAATGATAATTTTTTTTT
89834 GTTTCAAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
55 10 0.22
56 4 0.09
57 32 0.70
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (55 bp):
GAGTGAGAAGAAACTTGATATAAGAAAAACTATCTCAATGATAATTTTTTTTTCT
Found at i:96134 original size:17 final size:17
Alignment explanation
Indices: 96112--96144 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
96102 GAACTAAAAT
96112 CTAAAAAAACAAAGAAA
1 CTAAAAAAACAAAGAAA
*
96129 CTAAAAAAATAAAGAA
1 CTAAAAAAACAAAGAA
96145 GAAAACAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (17 bp):
CTAAAAAAACAAAGAAA
Found at i:100096 original size:15 final size:16
Alignment explanation
Indices: 100076--100111 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
100066 TGATTGAAAC
*
100076 AATAAG-AAGGAAAAA
1 AATAAGAAAAGAAAAA
100091 AATAAGAAAAGAAAAA
1 AATAAGAAAAGAAAAA
100107 AATAA
1 AATAA
100112 TTACCTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (16 bp):
AATAAGAAAAGAAAAA
Found at i:114324 original size:23 final size:23
Alignment explanation
Indices: 114296--114367 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
114286 AAGATGATTT
114296 TAAAAACGAATGGATGTGTTTTA
1 TAAAAACGAATGGATGTGTTTTA
* ** * *
114319 TAAAAATG-ATTTATAAATGATTTA
1 TAAAAACGAATGGAT--GTGTTTTA
114343 TAAAAACGAATGGATGTGTTTTA
1 TAAAAACGAATGGATGTGTTTTA
114366 TA
1 TA
114368 CAAATTATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
22 4 0.11
23 15 0.42
24 13 0.36
25 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.38
Consensus pattern (23 bp):
TAAAAACGAATGGATGTGTTTTA
Found at i:114333 original size:13 final size:13
Alignment explanation
Indices: 114315--114348 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
114305 ATGGATGTGT
114315 TTTATAAAAATGA
1 TTTATAAAAATGA
114328 TTTAT--AAATGA
1 TTTATAAAAATGA
114339 TTTATAAAAA
1 TTTATAAAAA
114349 CGAATGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (13 bp):
TTTATAAAAATGA
Found at i:124072 original size:19 final size:19
Alignment explanation
Indices: 124048--124100 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
124038 TCAACTCTAG
124048 TCAAAGTCAACGGATCAGA
1 TCAAAGTCAACGGATCAGA
* * * *
124067 TCAAAGACAACGGGT-GGG
1 TCAAAGTCAACGGATCAGA
124085 TCAAAGTCAACGGATC
1 TCAAAGTCAACGGATC
124101 GGGTCGTGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (19 bp):
TCAAAGTCAACGGATCAGA
Found at i:132788 original size:15 final size:15
Alignment explanation
Indices: 132770--132799 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
132760 CCACGGTGCT
132770 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
*
132785 CCCGGAATCTTGCGC
1 CCCGGAATCCTGCGC
132800 GATTGTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.43, G:0.27, T:0.17
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:135060 original size:23 final size:23
Alignment explanation
Indices: 135013--135060 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
135003 AATAACATAT
**
135013 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
135036 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
135059 TA
1 TA
135061 TGCATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:135117 original size:23 final size:23
Alignment explanation
Indices: 135091--135138 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
135081 ATCAAGTACA
135091 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
135114 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
135137 AT
1 AT
135139 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:135122 original size:87 final size:87
Alignment explanation
Indices: 134971--135138 Score: 293
Period size: 87 Copynumber: 1.9 Consensus size: 87
134961 CGGTTATGTT
* *
134971 ATATCATTTAACTGGAAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAA
1 ATATCATTTAACCGGAAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAA
135036 TAGGTAGCGCTTATATAATAAA
66 TAGGTAGCGCTTATATAATAAA
*
135058 ATATGCATTTAACCGG-AAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTA
1 ATAT-CATTTAACCGGAAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTA
135122 ATAGGTAGCGCTTATAT
65 ATAGGTAGCGCTTATAT
135139 TGACCTATTT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
87 67 0.87
88 10 0.13
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (87 bp):
ATATCATTTAACCGGAAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAA
TAGGTAGCGCTTATATAATAAA
Found at i:135542 original size:198 final size:196
Alignment explanation
Indices: 135133--135654 Score: 540
Period size: 198 Copynumber: 2.6 Consensus size: 196
135123 TAGGTAGCGC
* * * *
135133 TTATATTGACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTATAAATTGACCTAT
1 TTATGTTGACCTA-TTTCTCAT-AAACCGGTATATTTTAACCGGTTACATTATAAATTTACCTAT
* *
135198 TACATTAT-GTATATCGGTTTCGATGTTTTCGGGATCGATACAATTTTAAATGTATCGACACTTT
64 TACATTATAAT-TATCGATTTCGATGTTTTCGGGATCGATACAATTTTAAATGTATCGACACTTT
* * * * * * *
135262 ATGCATGCAACTCGTTTGTGCTTTATTTTGGAAAAAAGTATCGACACATATTTAAAGAGTGTCGA
128 ATGCATACAACTCGTTTGTCCTTCATTTTGGAAAAAAGTATCAACACAAATTAAAAAAGTGTCGA
135327 TACA
193 TACA
** * * * *
135331 CAATGTAGACCTATTTGCTAATTAACCGGTATATTTTAACCGGTTACATTATAAATTTACCTGTT
1 TTATGTTGACCTATTT-CTCATAAACCGGTATATTTTAACCGGTTACATTATAAATTTACCTATT
* * **
135396 ACATAATAATTATCGATTTCGATG-TTTCGATGATCGATA-TTTTTTACAAATGTATCGACACTT
65 ACATTATAATTATCGATTTCGATGTTTTCG-GGATCGATACAATTTT--AAATGTATCGACACTT
* *
135459 TATGCTTACACCTCGTTT-TCCATTCATTTT-GAAAAAATGTATCAACACAAATTAAAAAAGTGT
127 TATGCATACAACTCGTTTGTCC-TTCATTTTGGAAAAAA-GTATCAACACAAATTAAAAAAGTGT
*
135522 CGATACT
190 CGATACA
* **
135529 TTATGTTGACCTATTCTCTCATGAACCCGGTATATTTCT-ACC-GTTACATTGGAAATTTACCTA
1 TTATGTTGACCTATT-TCTCAT-AAACCGGTATATTT-TAACCGGTTACATTATAAATTTACCTA
* * ** *
135592 TTACATTATAATTATCGGTCTCTTTGATTTT-GGGATCGATAC-TTGTTATAAATGTATCGACAC
63 TTACATTATAATTATCGATTTCGATG-TTTTCGGGATCGATACAAT-TT-TAAATGTATCGACAC
135655 AAAATCTAAT
Statistics
Matches: 268, Mismatches: 41, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
196 9 0.03
197 77 0.29
198 158 0.59
199 19 0.07
200 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (196 bp):
TTATGTTGACCTATTTCTCATAAACCGGTATATTTTAACCGGTTACATTATAAATTTACCTATTA
CATTATAATTATCGATTTCGATGTTTTCGGGATCGATACAATTTTAAATGTATCGACACTTTATG
CATACAACTCGTTTGTCCTTCATTTTGGAAAAAAGTATCAACACAAATTAAAAAAGTGTCGATAC
A
Found at i:136377 original size:18 final size:19
Alignment explanation
Indices: 136338--136388 Score: 77
Period size: 18 Copynumber: 2.6 Consensus size: 19
136328 TTAGTGACAT
136338 TCTTTCTCTTCATTTCCTCCA
1 TCTTT-TCTTC-TTTCCTCCA
136359 TCTTTTCTTCTTT-CTCCA
1 TCTTTTCTTCTTTCCTCCA
136377 TCTTTTCTTCTT
1 TCTTTTCTTCTT
136389 CAAATTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.57
19 3 0.10
20 5 0.17
21 5 0.17
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (19 bp):
TCTTTTCTTCTTTCCTCCA
Found at i:136765 original size:15 final size:15
Alignment explanation
Indices: 136745--136774 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
136735 ACTCTGTTTT
136745 CCCTGACCGTAATCC
1 CCCTGACCGTAATCC
*
136760 CCCTGACCGTCATCC
1 CCCTGACCGTAATCC
136775 ACCCCTCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.50, G:0.13, T:0.20
Consensus pattern (15 bp):
CCCTGACCGTAATCC
Found at i:137091 original size:22 final size:24
Alignment explanation
Indices: 137063--137118 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
137053 AACCTGCATT
137063 TATAATAAAAT-TA-ATCATTTTA
1 TATAATAAAATATACATCATTTTA
*
137085 TATAAT-AACTATACCATCATTTTA
1 TATAATAAAATATA-CATCATTTTA
*
137109 TATAAAAAAA
1 TATAATAAAA
137119 CAAAAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
24 14 0.52
25 2 0.07
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (24 bp):
TATAATAAAATATACATCATTTTA
Found at i:139627 original size:182 final size:182
Alignment explanation
Indices: 138967--139610 Score: 884
Period size: 182 Copynumber: 3.6 Consensus size: 182
138957 ATTAAAGTAC
* * * * *
138967 CGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCGG-TTT-TCATA
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * *
139030 TTTTTACCTATTATATTGTTATGGATCGATACGTTT-TCATAAAGTATCGACACTTTTTAGGCGC
66 TTATTACCTATTATATTGCTATGGATCGATACATTTGT-ATAAAGTATCGACACTTTTTAGGCGC
*
139094 TATAATTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
130 TATAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
* * * * *
139147 CGACACTTTCAATATATCTGATATCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * *
139212 TTATTACTTGTTATATTGCTATAGATCGATACATTTGTATAAAGTATAGACACTTTTTA-GCGCT
66 TTATTACCTATTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
* * *
139276 ATTACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATACTAATGTAT
131 ATAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
** * * **
139328 CGACACTTTCAATATATATGGTATCTTTTTACCGGTTTTATCATTTCGAGACTTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* *
139393 TTATTACCTATTCTATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGTGCT
66 TTATTACCTATTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
* *
139458 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
* * * *
139510 CGACACTTTCAATATATCCGGTAGCGGTTTACCGGTTTTATCATAAT-GACACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCAT-TTCGAGACCGGTTTTGTCAT
* * * *
139574 ATTTTTATCTGTTATATTGCTATGGATCCATACATTT
65 ATTATTACCTATTATATTGCTATGGATCGATACATTT
139611 TTAATTTGTA
Statistics
Matches: 409, Mismatches: 50, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
180 45 0.11
181 172 0.42
182 190 0.46
183 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
TTATTACCTATTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
ATAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
Found at i:141673 original size:15 final size:16
Alignment explanation
Indices: 141636--141666 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
141626 TTTCATGTTA
*
141636 ATATCATTTTAAATTC
1 ATATCATTTAAAATTC
141652 ATATCATTTAAAATT
1 ATATCATTTAAAATT
141667 TATTCATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATCATTTAAAATTC
Found at i:146448 original size:3 final size:3
Alignment explanation
Indices: 146422--146531 Score: 172
Period size: 3 Copynumber: 37.7 Consensus size: 3
146412 CTTATTCTTC
* * *
146422 TTA TTC TTA TTC TTA TTC TTA TTA TTA -TA TTA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
146468 TTA TTA TTA TTA -TA 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
146515 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
146532 CTTCACGTTG
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
2 6 0.06
3 92 0.94
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:146737 original size:79 final size:79
Alignment explanation
Indices: 146599--146848 Score: 294
Period size: 79 Copynumber: 3.2 Consensus size: 79
146589 TTCCTTAAAT
* * * **
146599 TATGGGTGCATTATCGGCATAAAATAATAATGCATATAGG-TGAATTATTAGCATGAAAGGATTT
1 TATGGGTGCATTATCGACATAAAAGAATAATGCATAT-GGATGCATTATTAGCATGAAAGGATGC
146663 CATAGCTGAAATGCA
65 CATAGCTGAAATGCA
*
146678 TATGGGTGCATTATCGACATAAAAGAATAATGCATATGGATGCATTATTGAG-ATTAAAGGATGC
1 TATGGGTGCATTATCGACATAAAAGAATAATGCATATGGATGCATTATT-AGCATGAAAGGATGC
146742 CATAGCTGAAATGCA
65 CATAGCTGAAATGCA
* * * * * ** *
146757 TATAGGTGTATTATCAATATAAAAGAATAATGCATAT-GAGTGCA-T-TTGGCATGAAATAAGGC
1 TATGGGTGCATTATCGACATAAAAGAATAATGCATATGGA-TGCATTATTAGCATGAAAGGATGC
* *
146819 CATAACTGAAATGAA
65 CATAGCTGAAATGCA
146834 TATGGGTGCATTATC
1 TATGGGTGCATTATC
146849 AGTATAAATA
Statistics
Matches: 148, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
76 1 0.01
77 36 0.24
78 5 0.03
79 104 0.70
80 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (79 bp):
TATGGGTGCATTATCGACATAAAAGAATAATGCATATGGATGCATTATTAGCATGAAAGGATGCC
ATAGCTGAAATGCA
Found at i:149501 original size:45 final size:43
Alignment explanation
Indices: 149437--149580 Score: 137
Period size: 45 Copynumber: 3.5 Consensus size: 43
149427 ATAAAAGAAT
*
149437 AATGCATAT-GGATGAATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATAGG-TGCATTATTGGCATGAAA-GATGCCATAG-TGA
*
149482 AATGCATATAGGTGCATTATTAGCAT-AAA-AT---A-A-T--
1 AATGCATATAGGTGCATTATTGGCATGAAAGATGCCATAGTGA
*
149516 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGTTGA
1 AATGCATATAGGTGCATTATTGGCATGAAAG-ATGCCATAG-TGA
*
149561 AATACATATAGGTGCATTAT
1 AATGCATATAGGTGCATTAT
149581 CAGCATAAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
34 24 0.30
35 3 0.04
36 1 0.01
37 2 0.02
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 2 0.02
43 1 0.01
44 3 0.04
45 39 0.48
46 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (43 bp):
AATGCATATAGGTGCATTATTGGCATGAAAGATGCCATAGTGA
Found at i:149509 original size:79 final size:79
Alignment explanation
Indices: 149335--149589 Score: 368
Period size: 79 Copynumber: 3.2 Consensus size: 79
149325 TTAAATTATG
* * * * *
149335 GGTGAATTATCGGCATAAACGAATAATGTATATGGGTGCTTTATTGGCATG-AAGGATGCCATAG
1 GGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG
*
149399 TTGAAATACATATG
66 TTGAAATACATATA
* * * *
149413 GGTGAATTATCGGCATAAAAGAATAATGCATATGGATGAATTATTGGCATGAAAGGATGCCATAG
1 GGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG
* *
149478 CTGAAATGCATATA
66 TTGAAATACATATA
* * *
149492 GGTGCATTATTAGCATAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAG
1 GGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG
149557 TTGAAATACATATA
66 TTGAAATACATATA
149571 GGTGCATTATCAGCATAAA
1 GGTGCATTATCAGCATAAA
149590 TGTATGTTAT
Statistics
Matches: 158, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 46 0.29
79 112 0.71
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (79 bp):
GGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG
TTGAAATACATATA
Found at i:154924 original size:95 final size:95
Alignment explanation
Indices: 154750--154931 Score: 226
Period size: 95 Copynumber: 1.9 Consensus size: 95
154740 TTTTCCTATC
* *
154750 TGACCTACAATGAAGAGTAGATGAGAAGATCCTTATTTCTTTGAATCTGACCTACCCCAAAGAGC
1 TGACCTACAATGAAGAGTAGA-GAGAAGATCCCTATTTCTTTGAATCTGACCTACCCCAAAGAAC
*
154815 ACCGAAGAAGATTCCAATTTTTCTTTAGATT
65 ACAGAAGAAGATTCCAATTTTTCTTTAGATT
* * * **
154846 TGACCTACCATGAAGAGTAGCA-AGAAGATCCCTCTTTCTTTGAATTTGACCTACCCTTAAGAAC
1 TGACCTACAATGAAGAGTAG-AGAGAAGATCCCTATTTCTTTGAATCTGACCTACCCCAAAGAAC
*
154910 AACAG-AGCAA-ATTCCATTTTTT
65 -ACAGAAG-AAGATTCCAATTTTT
154932 TTTCTTATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
95 49 0.66
96 24 0.32
97 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (95 bp):
TGACCTACAATGAAGAGTAGAGAGAAGATCCCTATTTCTTTGAATCTGACCTACCCCAAAGAACA
CAGAAGAAGATTCCAATTTTTCTTTAGATT
Found at i:155965 original size:24 final size:24
Alignment explanation
Indices: 155933--155978 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
155923 TCTTCCAGAT
155933 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
155957 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
155979 CATATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:157840 original size:31 final size:32
Alignment explanation
Indices: 157797--157861 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
157787 TTTAAAGCAT
* * *
157797 ATAGTTCATTTAGGAAG-TAGTTCATTTATGC
1 ATAGATCATTTAGGAAGCTACTTCATTCATGC
*
157828 ATAGATCATTTAGTAAGCTACTTCATTCATGC
1 ATAGATCATTTAGGAAGCTACTTCATTCATGC
157860 AT
1 AT
157862 CTAGTTCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (32 bp):
ATAGATCATTTAGGAAGCTACTTCATTCATGC
Found at i:157931 original size:17 final size:17
Alignment explanation
Indices: 157881--157933 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
157871 TGAATAAAGT
*
157881 TAGTTCATTAATTAAAC
1 TAGTTCGTTAATTAAAC
* *
157898 TAGTT-GATTCATCAAAC
1 TAGTTCG-TTAATTAAAC
*
157915 TAGTTCGTTTATTAAAC
1 TAGTTCGTTAATTAAAC
157932 TA
1 TA
157934 ACTCTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 28 0.97
18 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (17 bp):
TAGTTCGTTAATTAAAC
Done.