Multiple sequence alignment - TraesCS4B01G067500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G067500 chr4B 100.000 3219 0 0 1 3219 60175368 60178586 0.000000e+00 5945.0
1 TraesCS4B01G067500 chr4D 90.128 2421 125 48 320 2672 41073311 41075685 0.000000e+00 3042.0
2 TraesCS4B01G067500 chr4D 91.216 148 9 1 11 158 41051361 41051504 7.040000e-47 198.0
3 TraesCS4B01G067500 chr4D 89.831 118 11 1 185 302 41072669 41072785 2.000000e-32 150.0
4 TraesCS4B01G067500 chr4A 90.051 2352 137 41 930 3218 558548475 558546158 0.000000e+00 2957.0
5 TraesCS4B01G067500 chr4A 88.333 120 5 4 612 728 558549166 558549053 5.600000e-28 135.0
6 TraesCS4B01G067500 chr4A 94.667 75 2 1 740 814 558549007 558548935 7.300000e-22 115.0
7 TraesCS4B01G067500 chr7D 87.248 149 18 1 3069 3217 82903862 82903715 5.520000e-38 169.0
8 TraesCS4B01G067500 chr7D 81.897 116 19 2 3075 3189 213516704 213516590 2.640000e-16 97.1
9 TraesCS4B01G067500 chr2B 76.991 226 34 17 58 274 72264891 72265107 2.620000e-21 113.0
10 TraesCS4B01G067500 chr3D 83.333 108 18 0 3101 3208 466291848 466291741 2.040000e-17 100.0
11 TraesCS4B01G067500 chr6A 82.203 118 15 4 3101 3217 593817619 593817507 2.640000e-16 97.1
12 TraesCS4B01G067500 chr7B 86.250 80 10 1 3112 3190 188001362 188001441 5.720000e-13 86.1
13 TraesCS4B01G067500 chr6B 81.373 102 13 4 3102 3201 676296941 676296844 9.570000e-11 78.7
14 TraesCS4B01G067500 chr3B 82.500 80 14 0 3110 3189 666473218 666473297 1.600000e-08 71.3
15 TraesCS4B01G067500 chr3A 77.778 117 25 1 3101 3217 609484024 609483909 1.600000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G067500 chr4B 60175368 60178586 3218 False 5945 5945 100.0000 1 3219 1 chr4B.!!$F1 3218
1 TraesCS4B01G067500 chr4D 41072669 41075685 3016 False 1596 3042 89.9795 185 2672 2 chr4D.!!$F2 2487
2 TraesCS4B01G067500 chr4A 558546158 558549166 3008 True 1069 2957 91.0170 612 3218 3 chr4A.!!$R1 2606

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
602 1142 0.033504 TTCGCACTGGTCCTTCACTC 59.966 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 3378 0.038526 ACTAACTTCACTCGCACCGG 60.039 55.0 0.0 0.0 0.0 5.28 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.879070 ACACAATAATCAAAGCCATATAGCTG 58.121 34.615 0.00 0.00 44.11 4.24
27 28 7.040201 ACACAATAATCAAAGCCATATAGCTGG 60.040 37.037 0.00 0.00 44.11 4.85
28 29 6.435277 ACAATAATCAAAGCCATATAGCTGGG 59.565 38.462 0.00 0.00 44.11 4.45
29 30 2.276732 TCAAAGCCATATAGCTGGGC 57.723 50.000 11.27 11.27 44.11 5.36
38 39 6.834168 GCCATATAGCTGGGCTTAATTAAA 57.166 37.500 11.78 0.00 44.32 1.52
39 40 6.856895 GCCATATAGCTGGGCTTAATTAAAG 58.143 40.000 11.78 0.00 44.32 1.85
40 41 6.434340 GCCATATAGCTGGGCTTAATTAAAGT 59.566 38.462 11.78 0.00 44.32 2.66
41 42 7.362142 GCCATATAGCTGGGCTTAATTAAAGTC 60.362 40.741 11.78 0.00 44.32 3.01
61 62 8.679344 AAAGTCCCCATTTAATTATTTCACCT 57.321 30.769 0.00 0.00 0.00 4.00
62 63 9.777008 AAAGTCCCCATTTAATTATTTCACCTA 57.223 29.630 0.00 0.00 0.00 3.08
63 64 8.996651 AGTCCCCATTTAATTATTTCACCTAG 57.003 34.615 0.00 0.00 0.00 3.02
64 65 8.787818 AGTCCCCATTTAATTATTTCACCTAGA 58.212 33.333 0.00 0.00 0.00 2.43
65 66 9.588096 GTCCCCATTTAATTATTTCACCTAGAT 57.412 33.333 0.00 0.00 0.00 1.98
66 67 9.807921 TCCCCATTTAATTATTTCACCTAGATC 57.192 33.333 0.00 0.00 0.00 2.75
67 68 9.025041 CCCCATTTAATTATTTCACCTAGATCC 57.975 37.037 0.00 0.00 0.00 3.36
68 69 9.025041 CCCATTTAATTATTTCACCTAGATCCC 57.975 37.037 0.00 0.00 0.00 3.85
69 70 9.586732 CCATTTAATTATTTCACCTAGATCCCA 57.413 33.333 0.00 0.00 0.00 4.37
72 73 9.640952 TTTAATTATTTCACCTAGATCCCAAGG 57.359 33.333 5.10 5.10 38.93 3.61
74 75 7.947782 ATTATTTCACCTAGATCCCAAGGTA 57.052 36.000 10.74 0.00 44.43 3.08
75 76 7.947782 TTATTTCACCTAGATCCCAAGGTAT 57.052 36.000 10.74 5.49 44.43 2.73
76 77 9.629649 ATTATTTCACCTAGATCCCAAGGTATA 57.370 33.333 10.74 4.73 44.43 1.47
77 78 9.629649 TTATTTCACCTAGATCCCAAGGTATAT 57.370 33.333 10.74 7.90 44.43 0.86
78 79 7.554959 TTTCACCTAGATCCCAAGGTATATC 57.445 40.000 10.74 0.00 44.43 1.63
79 80 6.227624 TCACCTAGATCCCAAGGTATATCA 57.772 41.667 10.74 0.00 44.43 2.15
80 81 6.630131 TCACCTAGATCCCAAGGTATATCAA 58.370 40.000 10.74 0.00 44.43 2.57
81 82 7.256399 TCACCTAGATCCCAAGGTATATCAAT 58.744 38.462 10.74 0.00 44.43 2.57
82 83 7.400339 TCACCTAGATCCCAAGGTATATCAATC 59.600 40.741 10.74 0.00 44.43 2.67
83 84 6.674419 ACCTAGATCCCAAGGTATATCAATCC 59.326 42.308 9.65 0.00 44.40 3.01
84 85 6.100424 CCTAGATCCCAAGGTATATCAATCCC 59.900 46.154 0.00 0.00 0.00 3.85
85 86 5.424068 AGATCCCAAGGTATATCAATCCCA 58.576 41.667 0.00 0.00 0.00 4.37
86 87 5.857283 AGATCCCAAGGTATATCAATCCCAA 59.143 40.000 0.00 0.00 0.00 4.12
87 88 6.510361 AGATCCCAAGGTATATCAATCCCAAT 59.490 38.462 0.00 0.00 0.00 3.16
88 89 6.544327 TCCCAAGGTATATCAATCCCAATT 57.456 37.500 0.00 0.00 0.00 2.32
89 90 6.932753 TCCCAAGGTATATCAATCCCAATTT 58.067 36.000 0.00 0.00 0.00 1.82
90 91 7.369434 TCCCAAGGTATATCAATCCCAATTTT 58.631 34.615 0.00 0.00 0.00 1.82
91 92 7.848875 TCCCAAGGTATATCAATCCCAATTTTT 59.151 33.333 0.00 0.00 0.00 1.94
92 93 9.153479 CCCAAGGTATATCAATCCCAATTTTTA 57.847 33.333 0.00 0.00 0.00 1.52
107 108 9.844257 TCCCAATTTTTAATATTAAAGGCATGG 57.156 29.630 22.08 22.08 34.45 3.66
108 109 9.065798 CCCAATTTTTAATATTAAAGGCATGGG 57.934 33.333 27.26 27.26 37.52 4.00
109 110 9.625747 CCAATTTTTAATATTAAAGGCATGGGT 57.374 29.630 17.71 0.98 34.45 4.51
115 116 9.482175 TTTAATATTAAAGGCATGGGTGTAAGT 57.518 29.630 15.19 0.00 0.00 2.24
117 118 8.691661 AATATTAAAGGCATGGGTGTAAGTAG 57.308 34.615 0.00 0.00 0.00 2.57
118 119 5.765576 TTAAAGGCATGGGTGTAAGTAGA 57.234 39.130 0.00 0.00 0.00 2.59
119 120 3.914426 AAGGCATGGGTGTAAGTAGAG 57.086 47.619 0.00 0.00 0.00 2.43
120 121 3.116096 AGGCATGGGTGTAAGTAGAGA 57.884 47.619 0.00 0.00 0.00 3.10
121 122 3.034635 AGGCATGGGTGTAAGTAGAGAG 58.965 50.000 0.00 0.00 0.00 3.20
122 123 2.483889 GGCATGGGTGTAAGTAGAGAGC 60.484 54.545 0.00 0.00 0.00 4.09
123 124 2.168521 GCATGGGTGTAAGTAGAGAGCA 59.831 50.000 0.00 0.00 0.00 4.26
124 125 3.786635 CATGGGTGTAAGTAGAGAGCAC 58.213 50.000 0.00 0.00 0.00 4.40
125 126 2.884320 TGGGTGTAAGTAGAGAGCACA 58.116 47.619 0.00 0.00 0.00 4.57
126 127 3.236047 TGGGTGTAAGTAGAGAGCACAA 58.764 45.455 0.00 0.00 0.00 3.33
127 128 3.838317 TGGGTGTAAGTAGAGAGCACAAT 59.162 43.478 0.00 0.00 0.00 2.71
128 129 4.184629 GGGTGTAAGTAGAGAGCACAATG 58.815 47.826 0.00 0.00 0.00 2.82
129 130 4.322801 GGGTGTAAGTAGAGAGCACAATGT 60.323 45.833 0.00 0.00 0.00 2.71
130 131 5.105473 GGGTGTAAGTAGAGAGCACAATGTA 60.105 44.000 0.00 0.00 0.00 2.29
131 132 6.395629 GGTGTAAGTAGAGAGCACAATGTAA 58.604 40.000 0.00 0.00 0.00 2.41
132 133 6.310711 GGTGTAAGTAGAGAGCACAATGTAAC 59.689 42.308 0.00 0.00 0.00 2.50
133 134 6.866770 GTGTAAGTAGAGAGCACAATGTAACA 59.133 38.462 0.00 0.00 0.00 2.41
134 135 7.545965 GTGTAAGTAGAGAGCACAATGTAACAT 59.454 37.037 0.00 0.00 0.00 2.71
135 136 8.745590 TGTAAGTAGAGAGCACAATGTAACATA 58.254 33.333 0.00 0.00 0.00 2.29
136 137 9.239002 GTAAGTAGAGAGCACAATGTAACATAG 57.761 37.037 0.00 0.00 0.00 2.23
137 138 7.646548 AGTAGAGAGCACAATGTAACATAGA 57.353 36.000 0.00 0.00 0.00 1.98
138 139 8.243961 AGTAGAGAGCACAATGTAACATAGAT 57.756 34.615 0.00 0.00 0.00 1.98
139 140 8.356657 AGTAGAGAGCACAATGTAACATAGATC 58.643 37.037 0.00 0.00 0.00 2.75
140 141 7.117285 AGAGAGCACAATGTAACATAGATCA 57.883 36.000 0.00 0.00 0.00 2.92
141 142 7.733969 AGAGAGCACAATGTAACATAGATCAT 58.266 34.615 0.00 0.00 0.00 2.45
142 143 8.864087 AGAGAGCACAATGTAACATAGATCATA 58.136 33.333 0.00 0.00 0.00 2.15
143 144 9.650539 GAGAGCACAATGTAACATAGATCATAT 57.349 33.333 0.00 0.00 0.00 1.78
168 169 7.696992 AACAACAAAGTCTAAACCTCTTTCA 57.303 32.000 0.00 0.00 30.41 2.69
169 170 7.696992 ACAACAAAGTCTAAACCTCTTTCAA 57.303 32.000 0.00 0.00 30.41 2.69
170 171 8.293699 ACAACAAAGTCTAAACCTCTTTCAAT 57.706 30.769 0.00 0.00 30.41 2.57
171 172 8.190784 ACAACAAAGTCTAAACCTCTTTCAATG 58.809 33.333 0.00 0.00 30.41 2.82
172 173 6.739112 ACAAAGTCTAAACCTCTTTCAATGC 58.261 36.000 0.00 0.00 30.41 3.56
173 174 6.321181 ACAAAGTCTAAACCTCTTTCAATGCA 59.679 34.615 0.00 0.00 30.41 3.96
174 175 7.014615 ACAAAGTCTAAACCTCTTTCAATGCAT 59.985 33.333 0.00 0.00 30.41 3.96
175 176 7.530426 AAGTCTAAACCTCTTTCAATGCATT 57.470 32.000 5.99 5.99 0.00 3.56
176 177 6.917533 AGTCTAAACCTCTTTCAATGCATTG 58.082 36.000 29.75 29.75 39.10 2.82
177 178 6.716628 AGTCTAAACCTCTTTCAATGCATTGA 59.283 34.615 33.08 33.08 44.42 2.57
178 179 6.803807 GTCTAAACCTCTTTCAATGCATTGAC 59.196 38.462 35.75 19.20 45.63 3.18
179 180 5.534207 AAACCTCTTTCAATGCATTGACA 57.466 34.783 35.75 29.24 45.63 3.58
180 181 5.733620 AACCTCTTTCAATGCATTGACAT 57.266 34.783 35.75 15.92 45.63 3.06
181 182 5.068234 ACCTCTTTCAATGCATTGACATG 57.932 39.130 35.75 27.02 45.63 3.21
182 183 4.525487 ACCTCTTTCAATGCATTGACATGT 59.475 37.500 35.75 25.00 45.63 3.21
183 184 5.100259 CCTCTTTCAATGCATTGACATGTC 58.900 41.667 35.75 19.27 45.63 3.06
222 223 5.643379 TTAGAAGCAAGTAAAGCCCAATG 57.357 39.130 0.00 0.00 0.00 2.82
226 227 2.093869 AGCAAGTAAAGCCCAATGCATG 60.094 45.455 0.00 0.00 44.83 4.06
240 241 5.510671 CCAATGCATGGTATAAGTCGTTTC 58.489 41.667 0.00 0.00 44.85 2.78
244 245 6.897259 TGCATGGTATAAGTCGTTTCTTAC 57.103 37.500 0.00 0.00 33.56 2.34
247 248 7.551262 TGCATGGTATAAGTCGTTTCTTACAAT 59.449 33.333 0.00 0.00 33.56 2.71
274 275 9.967451 CTTACCATATTAGAGACATAGAGAGGA 57.033 37.037 0.00 0.00 0.00 3.71
290 291 9.528018 CATAGAGAGGACACTTATTTCTTTCTC 57.472 37.037 0.00 0.00 0.00 2.87
294 295 7.836842 AGAGGACACTTATTTCTTTCTCTCTC 58.163 38.462 0.00 0.00 0.00 3.20
305 306 7.807687 TTTCTTTCTCTCTCGTAATAAACCG 57.192 36.000 0.00 0.00 0.00 4.44
307 308 6.549952 TCTTTCTCTCTCGTAATAAACCGAC 58.450 40.000 0.00 0.00 0.00 4.79
308 309 6.373774 TCTTTCTCTCTCGTAATAAACCGACT 59.626 38.462 0.00 0.00 0.00 4.18
309 310 7.550551 TCTTTCTCTCTCGTAATAAACCGACTA 59.449 37.037 0.00 0.00 0.00 2.59
310 311 6.841443 TCTCTCTCGTAATAAACCGACTAG 57.159 41.667 0.00 0.00 0.00 2.57
311 312 6.344500 TCTCTCTCGTAATAAACCGACTAGT 58.656 40.000 0.00 0.00 0.00 2.57
312 313 7.492524 TCTCTCTCGTAATAAACCGACTAGTA 58.507 38.462 0.00 0.00 0.00 1.82
313 314 8.147058 TCTCTCTCGTAATAAACCGACTAGTAT 58.853 37.037 0.00 0.00 0.00 2.12
314 315 9.416794 CTCTCTCGTAATAAACCGACTAGTATA 57.583 37.037 0.00 0.00 0.00 1.47
315 316 9.935241 TCTCTCGTAATAAACCGACTAGTATAT 57.065 33.333 0.00 0.00 0.00 0.86
318 319 9.970243 CTCGTAATAAACCGACTAGTATATCAG 57.030 37.037 0.00 0.00 0.00 2.90
406 920 7.946381 AAAAAGGGAAGGTTAAAAATTGCAA 57.054 28.000 0.00 0.00 0.00 4.08
415 929 2.162319 AAAAATTGCAAACGGGCGAT 57.838 40.000 1.71 0.00 39.59 4.58
416 930 1.427435 AAAATTGCAAACGGGCGATG 58.573 45.000 1.71 0.00 37.93 3.84
417 931 0.600557 AAATTGCAAACGGGCGATGA 59.399 45.000 1.71 0.00 37.93 2.92
431 945 2.163509 GCGATGAGATACTAGCCTCCA 58.836 52.381 0.00 0.00 0.00 3.86
436 950 4.160642 TGAGATACTAGCCTCCACGTTA 57.839 45.455 0.00 0.00 0.00 3.18
438 952 3.220940 AGATACTAGCCTCCACGTTACC 58.779 50.000 0.00 0.00 0.00 2.85
439 953 2.512692 TACTAGCCTCCACGTTACCA 57.487 50.000 0.00 0.00 0.00 3.25
445 980 2.028385 AGCCTCCACGTTACCAAGTAAG 60.028 50.000 0.00 0.00 0.00 2.34
448 983 4.828829 CCTCCACGTTACCAAGTAAGAAT 58.171 43.478 0.00 0.00 0.00 2.40
451 986 5.613329 TCCACGTTACCAAGTAAGAATGTT 58.387 37.500 0.00 0.00 0.00 2.71
458 993 4.906618 ACCAAGTAAGAATGTTCGTCCAT 58.093 39.130 0.00 0.00 0.00 3.41
464 999 2.359900 AGAATGTTCGTCCATTGGCTC 58.640 47.619 0.00 0.00 35.24 4.70
483 1018 1.388768 TCGATTGTCGATTCAACGTGC 59.611 47.619 0.00 0.00 44.82 5.34
489 1024 0.599991 TCGATTCAACGTGCTGCAGT 60.600 50.000 16.64 0.23 34.70 4.40
497 1032 1.898574 CGTGCTGCAGTCCCCTTTT 60.899 57.895 16.64 0.00 0.00 2.27
511 1046 6.481976 CAGTCCCCTTTTAAAATGACCAAAAC 59.518 38.462 15.92 3.95 0.00 2.43
517 1052 2.928801 AAAATGACCAAAACAGGGGC 57.071 45.000 0.00 0.00 0.00 5.80
522 1057 0.469144 GACCAAAACAGGGGCCTTGA 60.469 55.000 23.86 0.00 0.00 3.02
532 1067 3.023832 CAGGGGCCTTGATTAATTCGTT 58.976 45.455 10.68 0.00 0.00 3.85
539 1074 4.929211 GCCTTGATTAATTCGTTTTTGGCT 59.071 37.500 0.00 0.00 33.45 4.75
553 1088 4.751767 TTTTGGCTGAAGTTTGTTGGAT 57.248 36.364 0.00 0.00 0.00 3.41
566 1106 7.346751 AGTTTGTTGGATCACATACAAAACT 57.653 32.000 12.45 7.79 39.45 2.66
585 1125 3.915536 ACTAGTGCTTCCTCGAACTTTC 58.084 45.455 0.00 0.00 0.00 2.62
602 1142 0.033504 TTCGCACTGGTCCTTCACTC 59.966 55.000 0.00 0.00 0.00 3.51
604 1144 1.666011 GCACTGGTCCTTCACTCGA 59.334 57.895 0.00 0.00 0.00 4.04
609 1149 1.733399 GGTCCTTCACTCGACGCAC 60.733 63.158 0.00 0.00 0.00 5.34
610 1150 1.286260 GTCCTTCACTCGACGCACT 59.714 57.895 0.00 0.00 0.00 4.40
678 1221 2.459060 TGAAAAATGGGTACGCGAGA 57.541 45.000 15.93 0.00 0.00 4.04
679 1222 2.343101 TGAAAAATGGGTACGCGAGAG 58.657 47.619 15.93 0.00 0.00 3.20
684 1232 2.829458 GGGTACGCGAGAGAGCCT 60.829 66.667 15.93 0.00 35.98 4.58
686 1234 2.278271 GTACGCGAGAGAGCCTGC 60.278 66.667 15.93 0.00 0.00 4.85
787 1369 3.760035 CGACCACCGACCTCCCAG 61.760 72.222 0.00 0.00 41.76 4.45
788 1370 3.391382 GACCACCGACCTCCCAGG 61.391 72.222 0.00 0.00 42.49 4.45
1002 1945 2.027073 CACACCACACACCGATCCG 61.027 63.158 0.00 0.00 0.00 4.18
1003 1946 3.118454 CACCACACACCGATCCGC 61.118 66.667 0.00 0.00 0.00 5.54
1004 1947 3.621805 ACCACACACCGATCCGCA 61.622 61.111 0.00 0.00 0.00 5.69
1013 1956 1.889105 CCGATCCGCACCAATCAGG 60.889 63.158 0.00 0.00 45.67 3.86
1018 1961 3.803082 CGCACCAATCAGGCACCG 61.803 66.667 0.00 0.00 43.14 4.94
1020 1963 3.443045 CACCAATCAGGCACCGGC 61.443 66.667 0.00 0.00 43.14 6.13
1023 1966 1.152984 CCAATCAGGCACCGGCATA 60.153 57.895 0.00 0.00 43.71 3.14
1024 1967 1.447317 CCAATCAGGCACCGGCATAC 61.447 60.000 0.00 0.00 43.71 2.39
1025 1968 1.523711 AATCAGGCACCGGCATACG 60.524 57.895 0.00 0.00 43.71 3.06
1180 2123 1.135960 CTTCCCCTTCCTCCATCTCC 58.864 60.000 0.00 0.00 0.00 3.71
1203 2146 2.268298 CCTATTTGTACGCGCAACTCT 58.732 47.619 5.73 0.00 0.00 3.24
1264 2213 4.166888 AGCTGCCATCGTCGCCAT 62.167 61.111 0.00 0.00 0.00 4.40
1265 2214 3.643978 GCTGCCATCGTCGCCATC 61.644 66.667 0.00 0.00 0.00 3.51
1266 2215 3.333189 CTGCCATCGTCGCCATCG 61.333 66.667 0.00 0.00 0.00 3.84
1311 2260 4.477975 GGCGTCCGTCCGTCAGAG 62.478 72.222 0.00 0.00 31.49 3.35
1451 2411 3.288308 CTGCAGCGGTCGTCCTTCT 62.288 63.158 0.00 0.00 0.00 2.85
1609 2575 2.294078 GGAGGTGGAGGAGGTGGTG 61.294 68.421 0.00 0.00 0.00 4.17
2190 3165 3.135348 AGCATGAAGATTCATCGGGAAGA 59.865 43.478 5.09 0.00 45.62 2.87
2192 3167 4.518211 GCATGAAGATTCATCGGGAAGAAT 59.482 41.667 5.09 0.00 45.62 2.40
2204 3179 1.186200 GGAAGAATGCAAGAACCCCC 58.814 55.000 0.00 0.00 0.00 5.40
2205 3180 1.549950 GGAAGAATGCAAGAACCCCCA 60.550 52.381 0.00 0.00 0.00 4.96
2207 3182 2.629017 AGAATGCAAGAACCCCCATT 57.371 45.000 0.00 0.00 0.00 3.16
2208 3183 2.181975 AGAATGCAAGAACCCCCATTG 58.818 47.619 0.00 0.00 0.00 2.82
2209 3184 2.178580 GAATGCAAGAACCCCCATTGA 58.821 47.619 0.00 0.00 0.00 2.57
2210 3185 2.555732 ATGCAAGAACCCCCATTGAT 57.444 45.000 0.00 0.00 0.00 2.57
2211 3186 1.851304 TGCAAGAACCCCCATTGATC 58.149 50.000 0.00 0.00 0.00 2.92
2393 3378 4.451900 TGAAGTTCTCCTTGTTCTTGGTC 58.548 43.478 4.17 0.00 32.03 4.02
2502 3492 2.688446 TCAGTGACGGCTCGAATATTCT 59.312 45.455 13.45 0.00 0.00 2.40
2518 3508 1.186200 TTCTGATGCGAGTAGGCTGT 58.814 50.000 0.00 0.00 0.00 4.40
2537 3527 1.591594 CGTCGGCGGCAACATAGAT 60.592 57.895 13.62 0.00 0.00 1.98
2601 3595 4.573900 GGTGATGAAGAGTGTGAGACATT 58.426 43.478 0.00 0.00 0.00 2.71
2630 3624 2.332654 AAGAACGTGGATTGCCGGC 61.333 57.895 22.73 22.73 36.79 6.13
2701 3707 1.470805 CGACGGCATGATTAGTGGTGA 60.471 52.381 0.00 0.00 0.00 4.02
2720 3726 6.263168 GTGGTGATATAATCTTGTTCCCAAGG 59.737 42.308 2.88 0.00 46.65 3.61
2727 3733 0.310854 CTTGTTCCCAAGGTCGCAAC 59.689 55.000 0.00 0.00 43.62 4.17
2728 3734 0.106918 TTGTTCCCAAGGTCGCAACT 60.107 50.000 0.00 0.00 0.00 3.16
2729 3735 0.534203 TGTTCCCAAGGTCGCAACTC 60.534 55.000 0.00 0.00 0.00 3.01
2730 3736 1.301401 TTCCCAAGGTCGCAACTCG 60.301 57.895 0.00 0.00 40.15 4.18
2731 3737 3.423154 CCCAAGGTCGCAACTCGC 61.423 66.667 0.00 0.00 38.27 5.03
2732 3738 2.664851 CCAAGGTCGCAACTCGCA 60.665 61.111 0.00 0.00 42.60 5.10
2733 3739 2.250939 CCAAGGTCGCAACTCGCAA 61.251 57.895 0.00 0.00 42.60 4.85
2734 3740 1.205064 CAAGGTCGCAACTCGCAAG 59.795 57.895 0.00 0.00 42.60 4.01
2735 3741 1.227556 AAGGTCGCAACTCGCAAGT 60.228 52.632 0.00 0.00 42.60 3.16
2736 3742 1.222115 AAGGTCGCAACTCGCAAGTC 61.222 55.000 0.00 0.00 42.60 3.01
2737 3743 2.465920 GTCGCAACTCGCAAGTCG 59.534 61.111 0.00 0.00 42.60 4.18
2738 3744 2.027024 TCGCAACTCGCAAGTCGT 59.973 55.556 0.00 0.00 42.60 4.34
2739 3745 1.590525 TCGCAACTCGCAAGTCGTT 60.591 52.632 0.00 0.00 42.60 3.85
2747 3753 1.798223 CTCGCAAGTCGTTTTCATCCA 59.202 47.619 0.00 0.00 39.67 3.41
2750 3756 1.606668 GCAAGTCGTTTTCATCCACCA 59.393 47.619 0.00 0.00 0.00 4.17
2752 3758 3.670627 GCAAGTCGTTTTCATCCACCATC 60.671 47.826 0.00 0.00 0.00 3.51
2756 3762 3.016031 TCGTTTTCATCCACCATCCATG 58.984 45.455 0.00 0.00 0.00 3.66
2766 3772 2.264124 CCATCCATGGCAGCATAGC 58.736 57.895 6.96 0.00 41.75 2.97
2794 3800 5.010213 GTGGTGGTAGTAATTTGCTTCCAAA 59.990 40.000 13.05 4.25 44.39 3.28
2821 3827 1.264288 GGTTCTTTGTCACAAGCGAGG 59.736 52.381 0.00 0.00 0.00 4.63
2827 3833 1.581934 TGTCACAAGCGAGGAAACAG 58.418 50.000 0.00 0.00 0.00 3.16
2830 3836 1.347707 TCACAAGCGAGGAAACAGGAT 59.652 47.619 0.00 0.00 0.00 3.24
2839 3845 7.304497 AGCGAGGAAACAGGATTATATAACT 57.696 36.000 0.00 0.00 0.00 2.24
2841 3847 8.305317 AGCGAGGAAACAGGATTATATAACTAC 58.695 37.037 0.00 0.00 0.00 2.73
2880 3886 4.536295 TCCACCATCCATAGTAGACTGA 57.464 45.455 0.00 0.00 0.00 3.41
2882 3888 6.214177 TCCACCATCCATAGTAGACTGATA 57.786 41.667 0.00 0.00 0.00 2.15
2901 3907 9.856488 GACTGATAGTAGTCTATTGTGACAAAA 57.144 33.333 0.62 0.00 42.93 2.44
2917 3923 7.551585 TGTGACAAAAATACAGTCAATTTGGT 58.448 30.769 0.00 0.00 43.16 3.67
2922 3928 7.867403 ACAAAAATACAGTCAATTTGGTAGCAG 59.133 33.333 0.00 0.00 35.77 4.24
2978 3984 1.691434 GGCTTCCACATTTGGTTGGAA 59.309 47.619 0.00 3.17 44.35 3.53
2979 3985 2.289010 GGCTTCCACATTTGGTTGGAAG 60.289 50.000 21.16 21.16 46.44 3.46
2981 3987 3.069443 GCTTCCACATTTGGTTGGAAGAA 59.931 43.478 27.07 0.00 46.53 2.52
2982 3988 4.442753 GCTTCCACATTTGGTTGGAAGAAA 60.443 41.667 27.07 0.00 46.53 2.52
2983 3989 4.935352 TCCACATTTGGTTGGAAGAAAG 57.065 40.909 0.00 0.00 44.35 2.62
3024 4030 6.672593 AGGGTGCTTCCAATTATCTCATTTA 58.327 36.000 1.43 0.00 38.11 1.40
3054 4060 7.919690 TCAAAAGATAATAATCCTGTTCGCTG 58.080 34.615 0.00 0.00 31.98 5.18
3055 4061 7.552687 TCAAAAGATAATAATCCTGTTCGCTGT 59.447 33.333 0.00 0.00 31.98 4.40
3062 4068 1.672030 CCTGTTCGCTGTGGCATCA 60.672 57.895 0.00 0.00 38.60 3.07
3075 4081 6.261118 GCTGTGGCATCAGTAGATTAAAAAG 58.739 40.000 15.25 0.00 37.70 2.27
3121 4128 2.000447 GTACGAGAACATGGCAACTCC 59.000 52.381 0.00 0.00 37.61 3.85
3125 4132 1.734465 GAGAACATGGCAACTCCGAAG 59.266 52.381 0.00 0.00 37.80 3.79
3143 4150 2.699251 AGGTTTTCGACGGCAAATTC 57.301 45.000 0.00 0.00 0.00 2.17
3150 4157 0.865111 CGACGGCAAATTCAGTGACA 59.135 50.000 0.00 0.00 0.00 3.58
3151 4158 1.398451 CGACGGCAAATTCAGTGACAC 60.398 52.381 0.00 0.00 0.00 3.67
3159 4166 3.961480 AATTCAGTGACACGAGGATGA 57.039 42.857 0.00 0.00 0.00 2.92
3184 4194 3.826157 ACTTTAGTTGCTAAGCATGCCAA 59.174 39.130 15.66 8.61 38.76 4.52
3185 4195 4.463891 ACTTTAGTTGCTAAGCATGCCAAT 59.536 37.500 15.66 3.55 38.76 3.16
3186 4196 5.047092 ACTTTAGTTGCTAAGCATGCCAATT 60.047 36.000 15.66 10.54 38.76 2.32
3190 4200 4.453136 AGTTGCTAAGCATGCCAATTTTTG 59.547 37.500 15.66 3.89 38.76 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.355169 CAGCTATATGGCTTTGATTATTGTGTT 58.645 33.333 11.40 0.00 41.00 3.32
1 2 7.040201 CCAGCTATATGGCTTTGATTATTGTGT 60.040 37.037 11.40 0.00 41.00 3.72
2 3 7.310664 CCAGCTATATGGCTTTGATTATTGTG 58.689 38.462 11.40 0.00 41.00 3.33
3 4 6.435277 CCCAGCTATATGGCTTTGATTATTGT 59.565 38.462 11.40 0.00 41.00 2.71
4 5 6.626623 GCCCAGCTATATGGCTTTGATTATTG 60.627 42.308 11.40 0.00 41.00 1.90
5 6 5.420104 GCCCAGCTATATGGCTTTGATTATT 59.580 40.000 11.40 0.00 41.00 1.40
6 7 4.952335 GCCCAGCTATATGGCTTTGATTAT 59.048 41.667 11.40 0.00 41.00 1.28
7 8 4.335416 GCCCAGCTATATGGCTTTGATTA 58.665 43.478 11.40 0.00 41.00 1.75
8 9 3.160269 GCCCAGCTATATGGCTTTGATT 58.840 45.455 11.40 0.00 41.00 2.57
9 10 2.800250 GCCCAGCTATATGGCTTTGAT 58.200 47.619 11.40 0.00 41.00 2.57
10 11 2.276732 GCCCAGCTATATGGCTTTGA 57.723 50.000 11.40 0.00 41.00 2.69
15 16 6.434340 ACTTTAATTAAGCCCAGCTATATGGC 59.566 38.462 2.23 2.23 45.70 4.40
16 17 7.121315 GGACTTTAATTAAGCCCAGCTATATGG 59.879 40.741 0.00 0.00 38.25 2.74
17 18 7.121315 GGGACTTTAATTAAGCCCAGCTATATG 59.879 40.741 19.84 0.00 43.78 1.78
18 19 7.175797 GGGACTTTAATTAAGCCCAGCTATAT 58.824 38.462 19.84 0.00 43.78 0.86
19 20 6.466759 GGGGACTTTAATTAAGCCCAGCTATA 60.467 42.308 23.34 0.00 45.00 1.31
20 21 5.386060 GGGACTTTAATTAAGCCCAGCTAT 58.614 41.667 19.84 0.00 43.78 2.97
21 22 4.385977 GGGGACTTTAATTAAGCCCAGCTA 60.386 45.833 23.34 0.36 45.00 3.32
22 23 3.627492 GGGGACTTTAATTAAGCCCAGCT 60.627 47.826 23.34 0.00 45.00 4.24
23 24 2.693591 GGGGACTTTAATTAAGCCCAGC 59.306 50.000 23.34 11.31 45.00 4.85
24 25 3.976015 TGGGGACTTTAATTAAGCCCAG 58.024 45.455 23.34 11.89 45.00 4.45
25 26 4.618378 ATGGGGACTTTAATTAAGCCCA 57.382 40.909 23.34 17.39 44.99 5.36
26 27 5.950544 AAATGGGGACTTTAATTAAGCCC 57.049 39.130 17.90 17.90 43.68 5.19
35 36 9.777008 AGGTGAAATAATTAAATGGGGACTTTA 57.223 29.630 0.00 0.00 0.00 1.85
36 37 8.679344 AGGTGAAATAATTAAATGGGGACTTT 57.321 30.769 0.00 0.00 0.00 2.66
37 38 9.421399 CTAGGTGAAATAATTAAATGGGGACTT 57.579 33.333 0.00 0.00 0.00 3.01
38 39 8.787818 TCTAGGTGAAATAATTAAATGGGGACT 58.212 33.333 0.00 0.00 0.00 3.85
39 40 8.990163 TCTAGGTGAAATAATTAAATGGGGAC 57.010 34.615 0.00 0.00 0.00 4.46
40 41 9.807921 GATCTAGGTGAAATAATTAAATGGGGA 57.192 33.333 0.00 0.00 0.00 4.81
41 42 9.025041 GGATCTAGGTGAAATAATTAAATGGGG 57.975 37.037 0.00 0.00 0.00 4.96
42 43 9.025041 GGGATCTAGGTGAAATAATTAAATGGG 57.975 37.037 0.00 0.00 0.00 4.00
43 44 9.586732 TGGGATCTAGGTGAAATAATTAAATGG 57.413 33.333 0.00 0.00 0.00 3.16
46 47 9.640952 CCTTGGGATCTAGGTGAAATAATTAAA 57.359 33.333 0.00 0.00 32.39 1.52
47 48 8.787818 ACCTTGGGATCTAGGTGAAATAATTAA 58.212 33.333 12.06 0.00 45.12 1.40
48 49 8.344939 ACCTTGGGATCTAGGTGAAATAATTA 57.655 34.615 12.06 0.00 45.12 1.40
49 50 7.226059 ACCTTGGGATCTAGGTGAAATAATT 57.774 36.000 12.06 0.00 45.12 1.40
50 51 6.848562 ACCTTGGGATCTAGGTGAAATAAT 57.151 37.500 12.06 0.00 45.12 1.28
51 52 7.947782 ATACCTTGGGATCTAGGTGAAATAA 57.052 36.000 18.78 4.63 46.03 1.40
52 53 9.268282 GATATACCTTGGGATCTAGGTGAAATA 57.732 37.037 18.78 12.01 46.03 1.40
53 54 7.739444 TGATATACCTTGGGATCTAGGTGAAAT 59.261 37.037 18.78 11.87 46.03 2.17
54 55 7.079700 TGATATACCTTGGGATCTAGGTGAAA 58.920 38.462 18.78 8.89 46.03 2.69
55 56 6.630131 TGATATACCTTGGGATCTAGGTGAA 58.370 40.000 18.78 10.62 46.03 3.18
56 57 6.227624 TGATATACCTTGGGATCTAGGTGA 57.772 41.667 18.78 10.74 46.03 4.02
57 58 6.935240 TTGATATACCTTGGGATCTAGGTG 57.065 41.667 18.78 0.00 46.03 4.00
59 60 6.100424 GGGATTGATATACCTTGGGATCTAGG 59.900 46.154 7.31 7.31 40.88 3.02
60 61 6.673978 TGGGATTGATATACCTTGGGATCTAG 59.326 42.308 0.00 0.00 35.55 2.43
61 62 6.580167 TGGGATTGATATACCTTGGGATCTA 58.420 40.000 0.00 0.00 35.55 1.98
62 63 5.424068 TGGGATTGATATACCTTGGGATCT 58.576 41.667 0.00 0.00 35.55 2.75
63 64 5.779241 TGGGATTGATATACCTTGGGATC 57.221 43.478 0.00 0.00 35.55 3.36
64 65 6.741500 ATTGGGATTGATATACCTTGGGAT 57.259 37.500 0.00 0.00 35.55 3.85
65 66 6.544327 AATTGGGATTGATATACCTTGGGA 57.456 37.500 0.00 0.00 35.55 4.37
66 67 7.616528 AAAATTGGGATTGATATACCTTGGG 57.383 36.000 0.00 0.00 35.55 4.12
81 82 9.844257 CCATGCCTTTAATATTAAAAATTGGGA 57.156 29.630 18.74 17.08 32.73 4.37
82 83 9.065798 CCCATGCCTTTAATATTAAAAATTGGG 57.934 33.333 25.15 25.15 35.14 4.12
83 84 9.625747 ACCCATGCCTTTAATATTAAAAATTGG 57.374 29.630 18.74 19.35 32.73 3.16
89 90 9.482175 ACTTACACCCATGCCTTTAATATTAAA 57.518 29.630 17.54 17.54 0.00 1.52
91 92 9.787435 CTACTTACACCCATGCCTTTAATATTA 57.213 33.333 0.00 0.00 0.00 0.98
92 93 8.499406 TCTACTTACACCCATGCCTTTAATATT 58.501 33.333 0.00 0.00 0.00 1.28
93 94 8.041143 TCTACTTACACCCATGCCTTTAATAT 57.959 34.615 0.00 0.00 0.00 1.28
94 95 7.346175 TCTCTACTTACACCCATGCCTTTAATA 59.654 37.037 0.00 0.00 0.00 0.98
95 96 6.157994 TCTCTACTTACACCCATGCCTTTAAT 59.842 38.462 0.00 0.00 0.00 1.40
96 97 5.486063 TCTCTACTTACACCCATGCCTTTAA 59.514 40.000 0.00 0.00 0.00 1.52
97 98 5.027460 TCTCTACTTACACCCATGCCTTTA 58.973 41.667 0.00 0.00 0.00 1.85
98 99 3.844211 TCTCTACTTACACCCATGCCTTT 59.156 43.478 0.00 0.00 0.00 3.11
99 100 3.450904 TCTCTACTTACACCCATGCCTT 58.549 45.455 0.00 0.00 0.00 4.35
100 101 3.034635 CTCTCTACTTACACCCATGCCT 58.965 50.000 0.00 0.00 0.00 4.75
101 102 2.483889 GCTCTCTACTTACACCCATGCC 60.484 54.545 0.00 0.00 0.00 4.40
102 103 2.168521 TGCTCTCTACTTACACCCATGC 59.831 50.000 0.00 0.00 0.00 4.06
103 104 3.195610 TGTGCTCTCTACTTACACCCATG 59.804 47.826 0.00 0.00 0.00 3.66
104 105 3.441101 TGTGCTCTCTACTTACACCCAT 58.559 45.455 0.00 0.00 0.00 4.00
105 106 2.884320 TGTGCTCTCTACTTACACCCA 58.116 47.619 0.00 0.00 0.00 4.51
106 107 3.955650 TTGTGCTCTCTACTTACACCC 57.044 47.619 0.00 0.00 0.00 4.61
107 108 4.822026 ACATTGTGCTCTCTACTTACACC 58.178 43.478 0.00 0.00 0.00 4.16
108 109 6.866770 TGTTACATTGTGCTCTCTACTTACAC 59.133 38.462 0.00 0.00 0.00 2.90
109 110 6.988522 TGTTACATTGTGCTCTCTACTTACA 58.011 36.000 0.00 0.00 0.00 2.41
110 111 9.239002 CTATGTTACATTGTGCTCTCTACTTAC 57.761 37.037 2.23 0.00 0.00 2.34
111 112 9.185680 TCTATGTTACATTGTGCTCTCTACTTA 57.814 33.333 2.23 0.00 0.00 2.24
112 113 8.067751 TCTATGTTACATTGTGCTCTCTACTT 57.932 34.615 2.23 0.00 0.00 2.24
113 114 7.646548 TCTATGTTACATTGTGCTCTCTACT 57.353 36.000 2.23 0.00 0.00 2.57
114 115 8.138074 TGATCTATGTTACATTGTGCTCTCTAC 58.862 37.037 2.23 0.00 0.00 2.59
115 116 8.237811 TGATCTATGTTACATTGTGCTCTCTA 57.762 34.615 2.23 0.00 0.00 2.43
116 117 7.117285 TGATCTATGTTACATTGTGCTCTCT 57.883 36.000 2.23 0.00 0.00 3.10
117 118 7.959689 ATGATCTATGTTACATTGTGCTCTC 57.040 36.000 2.23 0.00 0.00 3.20
142 143 9.403583 TGAAAGAGGTTTAGACTTTGTTGTTAT 57.596 29.630 0.00 0.00 34.63 1.89
143 144 8.795842 TGAAAGAGGTTTAGACTTTGTTGTTA 57.204 30.769 0.00 0.00 34.63 2.41
144 145 7.696992 TGAAAGAGGTTTAGACTTTGTTGTT 57.303 32.000 0.00 0.00 34.63 2.83
145 146 7.696992 TTGAAAGAGGTTTAGACTTTGTTGT 57.303 32.000 0.00 0.00 34.63 3.32
146 147 7.168135 GCATTGAAAGAGGTTTAGACTTTGTTG 59.832 37.037 0.00 0.00 34.63 3.33
147 148 7.147915 TGCATTGAAAGAGGTTTAGACTTTGTT 60.148 33.333 0.00 0.00 34.63 2.83
148 149 6.321181 TGCATTGAAAGAGGTTTAGACTTTGT 59.679 34.615 0.00 0.00 34.63 2.83
149 150 6.738114 TGCATTGAAAGAGGTTTAGACTTTG 58.262 36.000 0.00 0.00 34.63 2.77
150 151 6.959639 TGCATTGAAAGAGGTTTAGACTTT 57.040 33.333 0.00 0.00 36.71 2.66
151 152 7.231317 TCAATGCATTGAAAGAGGTTTAGACTT 59.769 33.333 34.23 0.00 43.26 3.01
152 153 6.716628 TCAATGCATTGAAAGAGGTTTAGACT 59.283 34.615 34.23 0.00 43.26 3.24
153 154 6.913170 TCAATGCATTGAAAGAGGTTTAGAC 58.087 36.000 34.23 0.00 43.26 2.59
166 167 6.072064 TGTTGTATGACATGTCAATGCATTGA 60.072 34.615 33.08 33.08 43.58 2.57
167 168 6.094061 TGTTGTATGACATGTCAATGCATTG 58.906 36.000 31.00 29.75 43.58 2.82
168 169 6.270156 TGTTGTATGACATGTCAATGCATT 57.730 33.333 31.00 16.56 43.58 3.56
169 170 5.900865 TGTTGTATGACATGTCAATGCAT 57.099 34.783 31.00 17.27 43.58 3.96
170 171 5.900865 ATGTTGTATGACATGTCAATGCA 57.099 34.783 31.00 24.28 43.58 3.96
171 172 8.686397 TTTAATGTTGTATGACATGTCAATGC 57.314 30.769 31.00 22.28 43.58 3.56
222 223 6.897259 TGTAAGAAACGACTTATACCATGC 57.103 37.500 0.00 0.00 35.32 4.06
232 233 9.886132 AATATGGTAAGATTGTAAGAAACGACT 57.114 29.630 0.00 0.00 0.00 4.18
247 248 9.967451 CCTCTCTATGTCTCTAATATGGTAAGA 57.033 37.037 0.00 0.00 0.00 2.10
252 253 7.888021 AGTGTCCTCTCTATGTCTCTAATATGG 59.112 40.741 0.00 0.00 0.00 2.74
338 849 9.232082 CTTCAACAATTGTTTACAATCGAAGAA 57.768 29.630 25.94 18.75 45.06 2.52
340 851 8.781067 TCTTCAACAATTGTTTACAATCGAAG 57.219 30.769 25.01 25.01 45.06 3.79
341 852 9.743057 AATCTTCAACAATTGTTTACAATCGAA 57.257 25.926 21.10 16.75 45.06 3.71
387 901 4.212425 CCGTTTGCAATTTTTAACCTTCCC 59.788 41.667 0.00 0.00 0.00 3.97
393 907 2.795470 TCGCCCGTTTGCAATTTTTAAC 59.205 40.909 0.00 0.00 0.00 2.01
406 920 1.269998 GCTAGTATCTCATCGCCCGTT 59.730 52.381 0.00 0.00 0.00 4.44
415 929 2.730934 ACGTGGAGGCTAGTATCTCA 57.269 50.000 10.47 0.36 0.00 3.27
416 930 3.252944 GGTAACGTGGAGGCTAGTATCTC 59.747 52.174 0.00 0.00 0.00 2.75
417 931 3.220940 GGTAACGTGGAGGCTAGTATCT 58.779 50.000 0.00 0.00 0.00 1.98
431 945 5.291971 ACGAACATTCTTACTTGGTAACGT 58.708 37.500 0.00 0.00 42.51 3.99
436 950 4.345859 TGGACGAACATTCTTACTTGGT 57.654 40.909 0.00 0.00 0.00 3.67
438 952 5.631026 CCAATGGACGAACATTCTTACTTG 58.369 41.667 0.00 0.00 38.94 3.16
439 953 4.156008 GCCAATGGACGAACATTCTTACTT 59.844 41.667 2.05 0.00 38.94 2.24
445 980 1.062587 CGAGCCAATGGACGAACATTC 59.937 52.381 2.05 0.00 38.94 2.67
448 983 0.249120 ATCGAGCCAATGGACGAACA 59.751 50.000 20.84 4.47 36.88 3.18
451 986 0.249120 ACAATCGAGCCAATGGACGA 59.751 50.000 19.74 19.74 37.41 4.20
464 999 1.390123 AGCACGTTGAATCGACAATCG 59.610 47.619 1.14 0.00 42.10 3.34
483 1018 4.321974 GGTCATTTTAAAAGGGGACTGCAG 60.322 45.833 13.48 13.48 42.68 4.41
489 1024 6.408662 CCTGTTTTGGTCATTTTAAAAGGGGA 60.409 38.462 12.28 4.53 0.00 4.81
497 1032 2.635427 GGCCCCTGTTTTGGTCATTTTA 59.365 45.455 0.00 0.00 0.00 1.52
511 1046 2.654863 ACGAATTAATCAAGGCCCCTG 58.345 47.619 0.00 0.00 0.00 4.45
517 1052 6.155827 TCAGCCAAAAACGAATTAATCAAGG 58.844 36.000 0.00 0.00 0.00 3.61
522 1057 7.494298 ACAAACTTCAGCCAAAAACGAATTAAT 59.506 29.630 0.00 0.00 0.00 1.40
532 1067 4.161189 TGATCCAACAAACTTCAGCCAAAA 59.839 37.500 0.00 0.00 0.00 2.44
539 1074 6.951062 TTGTATGTGATCCAACAAACTTCA 57.049 33.333 0.00 0.00 32.81 3.02
553 1088 5.865085 AGGAAGCACTAGTTTTGTATGTGA 58.135 37.500 0.00 0.00 0.00 3.58
585 1125 1.734477 CGAGTGAAGGACCAGTGCG 60.734 63.158 0.00 0.00 0.00 5.34
590 1130 2.197605 TGCGTCGAGTGAAGGACCA 61.198 57.895 0.00 0.00 0.00 4.02
591 1131 1.733399 GTGCGTCGAGTGAAGGACC 60.733 63.158 0.00 0.00 38.61 4.46
602 1142 0.163788 GTTTCCATGTCAGTGCGTCG 59.836 55.000 0.00 0.00 0.00 5.12
604 1144 1.227999 CGGTTTCCATGTCAGTGCGT 61.228 55.000 0.00 0.00 0.00 5.24
609 1149 1.227999 ACGTGCGGTTTCCATGTCAG 61.228 55.000 0.00 0.00 0.00 3.51
610 1150 1.225376 GACGTGCGGTTTCCATGTCA 61.225 55.000 0.00 0.00 44.61 3.58
657 1200 4.116961 CTCTCGCGTACCCATTTTTCATA 58.883 43.478 5.77 0.00 0.00 2.15
661 1204 2.618053 CTCTCTCGCGTACCCATTTTT 58.382 47.619 5.77 0.00 0.00 1.94
729 1277 4.179579 GTGATTCCTTGCGGGCGC 62.180 66.667 0.00 0.00 42.35 6.53
730 1278 3.864686 CGTGATTCCTTGCGGGCG 61.865 66.667 0.00 0.00 34.39 6.13
731 1279 2.435938 TCGTGATTCCTTGCGGGC 60.436 61.111 0.00 0.00 34.39 6.13
732 1280 1.815421 CCTCGTGATTCCTTGCGGG 60.815 63.158 0.00 0.00 0.00 6.13
734 1282 0.391130 TTCCCTCGTGATTCCTTGCG 60.391 55.000 0.00 0.00 0.00 4.85
735 1283 1.468914 GTTTCCCTCGTGATTCCTTGC 59.531 52.381 0.00 0.00 0.00 4.01
737 1285 1.621814 TCGTTTCCCTCGTGATTCCTT 59.378 47.619 0.00 0.00 0.00 3.36
738 1286 1.204941 CTCGTTTCCCTCGTGATTCCT 59.795 52.381 0.00 0.00 0.00 3.36
788 1370 4.424711 TGGGGATTGAGGCGTGGC 62.425 66.667 0.00 0.00 0.00 5.01
789 1371 2.124570 CTGGGGATTGAGGCGTGG 60.125 66.667 0.00 0.00 0.00 4.94
790 1372 2.124570 CCTGGGGATTGAGGCGTG 60.125 66.667 0.00 0.00 0.00 5.34
791 1373 4.115199 GCCTGGGGATTGAGGCGT 62.115 66.667 0.00 0.00 45.25 5.68
794 1376 3.023116 TGGGCCTGGGGATTGAGG 61.023 66.667 4.53 0.00 0.00 3.86
795 1377 2.276740 GTGGGCCTGGGGATTGAG 59.723 66.667 4.53 0.00 0.00 3.02
796 1378 3.727258 CGTGGGCCTGGGGATTGA 61.727 66.667 4.53 0.00 0.00 2.57
797 1379 3.704231 CTCGTGGGCCTGGGGATTG 62.704 68.421 4.53 0.00 0.00 2.67
798 1380 3.411517 CTCGTGGGCCTGGGGATT 61.412 66.667 4.53 0.00 0.00 3.01
982 1925 2.281484 ATCGGTGTGTGGTGTGGC 60.281 61.111 0.00 0.00 0.00 5.01
991 1934 1.705337 GATTGGTGCGGATCGGTGTG 61.705 60.000 1.93 0.00 0.00 3.82
1002 1945 3.443045 CCGGTGCCTGATTGGTGC 61.443 66.667 0.00 0.00 38.35 5.01
1003 1946 3.443045 GCCGGTGCCTGATTGGTG 61.443 66.667 1.90 0.00 38.35 4.17
1004 1947 1.920734 TATGCCGGTGCCTGATTGGT 61.921 55.000 1.90 0.00 38.35 3.67
1020 1963 1.819632 GCTTCCCTGTGGGCGTATG 60.820 63.158 0.00 0.00 43.94 2.39
1029 1972 4.021925 GTCTGCGGGCTTCCCTGT 62.022 66.667 0.00 0.00 42.67 4.00
1062 2005 1.814169 GACGCTGTTTCGGGATCCC 60.814 63.158 22.12 22.12 0.00 3.85
1098 2041 2.357517 CTTCACACGCTTCCGCCT 60.358 61.111 0.00 0.00 38.22 5.52
1122 2065 2.431942 AGCCGTAACGACTTGCCG 60.432 61.111 0.00 0.00 0.00 5.69
1180 2123 0.993532 TTGCGCGTACAAATAGGTCG 59.006 50.000 8.43 0.00 0.00 4.79
1261 2210 3.378339 GTCGGTGGTAAATAGACGATGG 58.622 50.000 0.00 0.00 32.73 3.51
1264 2213 1.401552 CGGTCGGTGGTAAATAGACGA 59.598 52.381 0.00 0.00 33.04 4.20
1265 2214 1.401552 TCGGTCGGTGGTAAATAGACG 59.598 52.381 0.00 0.00 33.04 4.18
1266 2215 3.551659 GGATCGGTCGGTGGTAAATAGAC 60.552 52.174 0.00 0.00 0.00 2.59
1326 2283 2.517402 CGACCTCCCTCCTCCTCG 60.517 72.222 0.00 0.00 0.00 4.63
1433 2393 2.771763 AAGAAGGACGACCGCTGCAG 62.772 60.000 10.11 10.11 41.83 4.41
1582 2545 4.361971 TCCACCTCCTCGCCGTCT 62.362 66.667 0.00 0.00 0.00 4.18
1609 2575 3.695825 TCCACCCTCTCCTCCCCC 61.696 72.222 0.00 0.00 0.00 5.40
2190 3165 2.323999 TCAATGGGGGTTCTTGCATT 57.676 45.000 0.00 0.00 0.00 3.56
2192 3167 1.851304 GATCAATGGGGGTTCTTGCA 58.149 50.000 0.00 0.00 0.00 4.08
2204 3179 7.008992 GGAAAGCAAGAAAAGAATCGATCAATG 59.991 37.037 0.00 0.00 0.00 2.82
2205 3180 7.031975 GGAAAGCAAGAAAAGAATCGATCAAT 58.968 34.615 0.00 0.00 0.00 2.57
2207 3182 5.390885 CGGAAAGCAAGAAAAGAATCGATCA 60.391 40.000 0.00 0.00 0.00 2.92
2208 3183 5.024555 CGGAAAGCAAGAAAAGAATCGATC 58.975 41.667 0.00 0.00 0.00 3.69
2209 3184 4.974591 CGGAAAGCAAGAAAAGAATCGAT 58.025 39.130 0.00 0.00 0.00 3.59
2210 3185 4.404507 CGGAAAGCAAGAAAAGAATCGA 57.595 40.909 0.00 0.00 0.00 3.59
2361 3338 7.856145 ACAAGGAGAACTTCATGATCAATAC 57.144 36.000 0.00 0.00 37.29 1.89
2362 3339 8.324306 AGAACAAGGAGAACTTCATGATCAATA 58.676 33.333 0.00 0.00 37.29 1.90
2363 3340 7.173722 AGAACAAGGAGAACTTCATGATCAAT 58.826 34.615 0.00 0.00 37.29 2.57
2393 3378 0.038526 ACTAACTTCACTCGCACCGG 60.039 55.000 0.00 0.00 0.00 5.28
2502 3492 1.313091 ACGACAGCCTACTCGCATCA 61.313 55.000 0.00 0.00 32.98 3.07
2518 3508 2.011741 ATCTATGTTGCCGCCGACGA 62.012 55.000 0.00 0.00 43.93 4.20
2532 3522 2.152830 GAGGAGACGTACCGCATCTAT 58.847 52.381 9.39 0.00 0.00 1.98
2533 3523 1.590932 GAGGAGACGTACCGCATCTA 58.409 55.000 9.39 0.00 0.00 1.98
2537 3527 2.046988 TCGAGGAGACGTACCGCA 60.047 61.111 13.36 1.35 34.70 5.69
2601 3595 4.274602 TCCACGTTCTTGCCATTAACTA 57.725 40.909 0.00 0.00 0.00 2.24
2680 3686 0.535335 ACCACTAATCATGCCGTCGT 59.465 50.000 0.00 0.00 0.00 4.34
2713 3719 2.342279 CGAGTTGCGACCTTGGGA 59.658 61.111 0.00 0.00 44.57 4.37
2714 3720 3.423154 GCGAGTTGCGACCTTGGG 61.423 66.667 0.00 0.00 44.57 4.12
2727 3733 1.798223 TGGATGAAAACGACTTGCGAG 59.202 47.619 0.00 0.00 44.57 5.03
2728 3734 1.529438 GTGGATGAAAACGACTTGCGA 59.471 47.619 0.00 0.00 44.57 5.10
2730 3736 1.606668 TGGTGGATGAAAACGACTTGC 59.393 47.619 0.00 0.00 0.00 4.01
2731 3737 3.119849 GGATGGTGGATGAAAACGACTTG 60.120 47.826 0.00 0.00 0.00 3.16
2732 3738 3.081804 GGATGGTGGATGAAAACGACTT 58.918 45.455 0.00 0.00 0.00 3.01
2733 3739 2.039746 TGGATGGTGGATGAAAACGACT 59.960 45.455 0.00 0.00 0.00 4.18
2734 3740 2.432444 TGGATGGTGGATGAAAACGAC 58.568 47.619 0.00 0.00 0.00 4.34
2735 3741 2.869101 TGGATGGTGGATGAAAACGA 57.131 45.000 0.00 0.00 0.00 3.85
2736 3742 2.099592 CCATGGATGGTGGATGAAAACG 59.900 50.000 5.56 0.00 43.05 3.60
2737 3743 3.806625 CCATGGATGGTGGATGAAAAC 57.193 47.619 5.56 0.00 43.05 2.43
2750 3756 1.545841 CATGCTATGCTGCCATGGAT 58.454 50.000 18.40 1.82 32.15 3.41
2752 3758 0.826256 ACCATGCTATGCTGCCATGG 60.826 55.000 24.78 24.78 42.13 3.66
2756 3762 1.454479 ACCACCATGCTATGCTGCC 60.454 57.895 0.00 0.00 0.00 4.85
2757 3763 1.731433 CCACCACCATGCTATGCTGC 61.731 60.000 0.00 0.00 0.00 5.25
2761 3767 4.415881 TTACTACCACCACCATGCTATG 57.584 45.455 0.00 0.00 0.00 2.23
2763 3769 5.189928 CAAATTACTACCACCACCATGCTA 58.810 41.667 0.00 0.00 0.00 3.49
2766 3772 4.016444 AGCAAATTACTACCACCACCATG 58.984 43.478 0.00 0.00 0.00 3.66
2794 3800 4.202050 GCTTGTGACAAAGAACCAGTCAAT 60.202 41.667 0.00 0.00 43.16 2.57
2800 3806 1.939934 CTCGCTTGTGACAAAGAACCA 59.060 47.619 0.00 0.00 0.00 3.67
2821 3827 8.362639 TGGTCCGTAGTTATATAATCCTGTTTC 58.637 37.037 0.00 0.00 0.00 2.78
2827 3833 7.025963 CGACTTGGTCCGTAGTTATATAATCC 58.974 42.308 0.00 0.00 0.00 3.01
2830 3836 6.767902 AGACGACTTGGTCCGTAGTTATATAA 59.232 38.462 0.00 0.00 39.30 0.98
2839 3845 1.608055 TGAAGACGACTTGGTCCGTA 58.392 50.000 4.51 0.00 39.30 4.02
2841 3847 1.630148 GATGAAGACGACTTGGTCCG 58.370 55.000 4.51 0.00 37.66 4.79
2882 3888 9.998106 ACTGTATTTTTGTCACAATAGACTACT 57.002 29.630 0.00 0.00 39.27 2.57
2901 3907 7.629222 GCAATCTGCTACCAAATTGACTGTATT 60.629 37.037 0.00 0.00 40.96 1.89
2903 3909 5.123820 GCAATCTGCTACCAAATTGACTGTA 59.876 40.000 0.00 0.00 40.96 2.74
2917 3923 0.393402 CAGCCTGGTGCAATCTGCTA 60.393 55.000 0.00 0.00 45.31 3.49
2922 3928 2.882876 CAGCAGCCTGGTGCAATC 59.117 61.111 21.79 0.00 46.60 2.67
2965 3971 5.893824 AGTCTTCTTTCTTCCAACCAAATGT 59.106 36.000 0.00 0.00 0.00 2.71
2978 3984 4.503714 TTGGTGGACAAGTCTTCTTTCT 57.496 40.909 0.00 0.00 33.18 2.52
2979 3985 4.036852 CCTTTGGTGGACAAGTCTTCTTTC 59.963 45.833 0.00 0.00 40.82 2.62
2981 3987 3.555966 CCTTTGGTGGACAAGTCTTCTT 58.444 45.455 0.00 0.00 40.82 2.52
2982 3988 2.158608 CCCTTTGGTGGACAAGTCTTCT 60.159 50.000 0.00 0.00 40.82 2.85
2983 3989 2.230660 CCCTTTGGTGGACAAGTCTTC 58.769 52.381 0.00 0.00 40.82 2.87
3030 4036 7.641411 CACAGCGAACAGGATTATTATCTTTTG 59.359 37.037 0.00 0.00 0.00 2.44
3037 4043 3.202906 GCCACAGCGAACAGGATTATTA 58.797 45.455 0.00 0.00 0.00 0.98
3038 4044 2.017049 GCCACAGCGAACAGGATTATT 58.983 47.619 0.00 0.00 0.00 1.40
3039 4045 1.065491 TGCCACAGCGAACAGGATTAT 60.065 47.619 0.00 0.00 44.31 1.28
3040 4046 0.323302 TGCCACAGCGAACAGGATTA 59.677 50.000 0.00 0.00 44.31 1.75
3048 4054 0.894835 TCTACTGATGCCACAGCGAA 59.105 50.000 7.07 0.00 44.31 4.70
3051 4057 5.818136 TTTTAATCTACTGATGCCACAGC 57.182 39.130 7.07 0.00 41.06 4.40
3054 4060 7.391148 TTCCTTTTTAATCTACTGATGCCAC 57.609 36.000 0.00 0.00 32.44 5.01
3055 4061 8.055181 AGATTCCTTTTTAATCTACTGATGCCA 58.945 33.333 0.00 0.00 40.93 4.92
3075 4081 6.196724 CGAACGTTCAGTACTTATCAGATTCC 59.803 42.308 26.71 0.00 0.00 3.01
3102 4108 1.403647 CGGAGTTGCCATGTTCTCGTA 60.404 52.381 0.00 0.00 35.94 3.43
3107 4113 0.804989 CCTTCGGAGTTGCCATGTTC 59.195 55.000 0.00 0.00 35.94 3.18
3110 4116 1.247567 AAACCTTCGGAGTTGCCATG 58.752 50.000 0.00 0.00 35.94 3.66
3111 4117 1.886542 GAAAACCTTCGGAGTTGCCAT 59.113 47.619 0.00 0.00 35.94 4.40
3125 4132 2.287368 ACTGAATTTGCCGTCGAAAACC 60.287 45.455 0.00 0.00 0.00 3.27
3132 4139 1.398451 CGTGTCACTGAATTTGCCGTC 60.398 52.381 0.65 0.00 0.00 4.79
3135 4142 1.197721 CCTCGTGTCACTGAATTTGCC 59.802 52.381 0.65 0.00 0.00 4.52
3137 4144 3.996363 TCATCCTCGTGTCACTGAATTTG 59.004 43.478 0.65 0.00 0.00 2.32
3140 4147 2.562738 TGTCATCCTCGTGTCACTGAAT 59.437 45.455 0.65 0.00 0.00 2.57
3143 4150 2.061773 GTTGTCATCCTCGTGTCACTG 58.938 52.381 0.65 0.00 0.00 3.66


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.