Multiple sequence alignment - TraesCS6B01G202900

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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 TraesCS6B01G202900 chr6B 100.000 4694 0 0 1 4694 248368034 248372727 0.000000e+00 8669
1 TraesCS6B01G202900 chr6B 96.429 196 5 1 1 194 315647753 315647948 5.860000e-84 322
2 TraesCS6B01G202900 chr6B 95.918 196 6 2 1 194 626213185 626213380 2.730000e-82 316
3 TraesCS6B01G202900 chr6B 95.939 197 5 3 1 194 659664024 659664220 2.730000e-82 316
4 TraesCS6B01G202900 chr6A 93.227 3957 163 43 785 4694 187900590 187904488 0.000000e+00 5725
5 TraesCS6B01G202900 chr6A 89.055 201 18 4 601 799 187900377 187900575 3.630000e-61 246
6 TraesCS6B01G202900 chr6D 92.119 2246 122 28 196 2400 142842383 142844614 0.000000e+00 3116
7 TraesCS6B01G202900 chr6D 95.763 1723 38 13 2461 4165 142844609 142846314 0.000000e+00 2745
8 TraesCS6B01G202900 chr6D 97.932 532 9 1 4163 4694 142846395 142846924 0.000000e+00 920
9 TraesCS6B01G202900 chr3B 95.567 203 7 1 1 201 800642791 800642993 1.630000e-84 324
10 TraesCS6B01G202900 chr2B 95.122 205 7 3 1 204 479849860 479849658 2.110000e-83 320
11 TraesCS6B01G202900 chr2B 94.203 207 11 1 3 208 187211134 187210928 9.800000e-82 315
12 TraesCS6B01G202900 chr5B 95.918 196 6 2 1 194 567582893 567582698 2.730000e-82 316
13 TraesCS6B01G202900 chr1B 95.918 196 6 1 1 194 626719454 626719259 2.730000e-82 316
14 TraesCS6B01G202900 chr1A 95.477 199 8 1 1 198 559297020 559296822 2.730000e-82 316


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 TraesCS6B01G202900 chr6B 248368034 248372727 4693 False 8669.000000 8669 100.000000 1 4694 1 chr6B.!!$F1 4693
1 TraesCS6B01G202900 chr6A 187900377 187904488 4111 False 2985.500000 5725 91.141000 601 4694 2 chr6A.!!$F1 4093
2 TraesCS6B01G202900 chr6D 142842383 142846924 4541 False 2260.333333 3116 95.271333 196 4694 3 chr6D.!!$F1 4498

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
298 309 0.035915 GGAAGGAGCTCAACAGGGAC 60.036 60.000 17.19 0.0 0.00 4.46 F
591 620 0.099791 CACAGTGGCGGTTCGTTTTT 59.900 50.000 0.00 0.0 0.00 1.94 F
594 623 0.812549 AGTGGCGGTTCGTTTTTGTT 59.187 45.000 0.00 0.0 0.00 2.83 F
1206 1283 1.378250 CCCGTCGGTCTACCACTCT 60.378 63.158 11.06 0.0 35.14 3.24 F
1713 1799 1.570813 GGTGTTTCAACTTGCTTGCC 58.429 50.000 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2067 0.320374 CTCCTAGTGTGCGGTTCCAA 59.680 55.000 0.00 0.00 0.00 3.53 R
2361 2449 1.490910 ACCAGGCCACTAAATCTAGCC 59.509 52.381 5.01 0.00 44.20 3.93 R
2570 2663 2.420022 ACGAGCAATTTCCGAATTCCAG 59.580 45.455 0.00 0.00 33.25 3.86 R
2602 2695 2.744202 CTGCAGTGGTGACCAGTTTATC 59.256 50.000 9.74 0.34 34.53 1.75 R
3700 3811 3.120321 TGCAAATAGTGACCGTGAAGT 57.880 42.857 0.00 0.00 0.00 3.01 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
18 19 2.643655 TGACATACGGACGTGTGGA 58.356 52.632 22.12 8.54 40.75 4.02
19 20 0.524414 TGACATACGGACGTGTGGAG 59.476 55.000 22.12 1.93 40.75 3.86
20 21 0.179145 GACATACGGACGTGTGGAGG 60.179 60.000 22.12 1.53 40.75 4.30
21 22 0.896940 ACATACGGACGTGTGGAGGT 60.897 55.000 22.12 2.14 40.75 3.85
22 23 0.245539 CATACGGACGTGTGGAGGTT 59.754 55.000 12.83 0.00 34.30 3.50
23 24 1.473677 CATACGGACGTGTGGAGGTTA 59.526 52.381 12.83 0.00 34.30 2.85
24 25 1.838112 TACGGACGTGTGGAGGTTAT 58.162 50.000 7.73 0.00 0.00 1.89
25 26 0.529378 ACGGACGTGTGGAGGTTATC 59.471 55.000 0.00 0.00 0.00 1.75
26 27 0.528924 CGGACGTGTGGAGGTTATCA 59.471 55.000 0.00 0.00 0.00 2.15
27 28 1.067425 CGGACGTGTGGAGGTTATCAA 60.067 52.381 0.00 0.00 0.00 2.57
28 29 2.344025 GGACGTGTGGAGGTTATCAAC 58.656 52.381 0.00 0.00 31.75 3.18
29 30 2.028385 GGACGTGTGGAGGTTATCAACT 60.028 50.000 0.00 0.00 32.44 3.16
30 31 3.556423 GGACGTGTGGAGGTTATCAACTT 60.556 47.826 0.00 0.00 32.44 2.66
31 32 3.660865 ACGTGTGGAGGTTATCAACTTC 58.339 45.455 0.00 0.00 36.83 3.01
32 33 2.666508 CGTGTGGAGGTTATCAACTTCG 59.333 50.000 0.00 0.00 38.29 3.79
33 34 2.415512 GTGTGGAGGTTATCAACTTCGC 59.584 50.000 0.00 0.00 38.29 4.70
34 35 2.007608 GTGGAGGTTATCAACTTCGCC 58.992 52.381 0.00 0.00 38.29 5.54
35 36 1.065709 TGGAGGTTATCAACTTCGCCC 60.066 52.381 0.00 0.00 38.29 6.13
36 37 1.065709 GGAGGTTATCAACTTCGCCCA 60.066 52.381 0.00 0.00 38.29 5.36
37 38 2.007608 GAGGTTATCAACTTCGCCCAC 58.992 52.381 0.00 0.00 0.00 4.61
38 39 1.349688 AGGTTATCAACTTCGCCCACA 59.650 47.619 0.00 0.00 0.00 4.17
39 40 1.467342 GGTTATCAACTTCGCCCACAC 59.533 52.381 0.00 0.00 0.00 3.82
40 41 1.127951 GTTATCAACTTCGCCCACACG 59.872 52.381 0.00 0.00 0.00 4.49
41 42 1.017177 TATCAACTTCGCCCACACGC 61.017 55.000 0.00 0.00 0.00 5.34
42 43 3.276091 CAACTTCGCCCACACGCA 61.276 61.111 0.00 0.00 0.00 5.24
43 44 3.276846 AACTTCGCCCACACGCAC 61.277 61.111 0.00 0.00 0.00 5.34
44 45 4.539083 ACTTCGCCCACACGCACA 62.539 61.111 0.00 0.00 0.00 4.57
45 46 4.012895 CTTCGCCCACACGCACAC 62.013 66.667 0.00 0.00 0.00 3.82
60 61 1.362717 ACACGTGTGAGAGGGTTCG 59.637 57.895 22.71 0.00 0.00 3.95
61 62 1.372997 CACGTGTGAGAGGGTTCGG 60.373 63.158 7.58 0.00 0.00 4.30
62 63 2.261671 CGTGTGAGAGGGTTCGGG 59.738 66.667 0.00 0.00 0.00 5.14
63 64 2.273179 CGTGTGAGAGGGTTCGGGA 61.273 63.158 0.00 0.00 0.00 5.14
64 65 1.592223 GTGTGAGAGGGTTCGGGAG 59.408 63.158 0.00 0.00 0.00 4.30
65 66 1.609501 TGTGAGAGGGTTCGGGAGG 60.610 63.158 0.00 0.00 0.00 4.30
66 67 2.038975 TGAGAGGGTTCGGGAGGG 59.961 66.667 0.00 0.00 0.00 4.30
67 68 2.363361 GAGAGGGTTCGGGAGGGA 59.637 66.667 0.00 0.00 0.00 4.20
68 69 1.305887 GAGAGGGTTCGGGAGGGAA 60.306 63.158 0.00 0.00 0.00 3.97
69 70 0.908180 GAGAGGGTTCGGGAGGGAAA 60.908 60.000 0.00 0.00 0.00 3.13
70 71 0.475048 AGAGGGTTCGGGAGGGAAAA 60.475 55.000 0.00 0.00 0.00 2.29
71 72 0.402887 GAGGGTTCGGGAGGGAAAAA 59.597 55.000 0.00 0.00 0.00 1.94
90 91 2.675658 AAAGGTGTGTGGGCATTAGT 57.324 45.000 0.00 0.00 0.00 2.24
91 92 2.675658 AAGGTGTGTGGGCATTAGTT 57.324 45.000 0.00 0.00 0.00 2.24
92 93 1.909700 AGGTGTGTGGGCATTAGTTG 58.090 50.000 0.00 0.00 0.00 3.16
93 94 1.144913 AGGTGTGTGGGCATTAGTTGT 59.855 47.619 0.00 0.00 0.00 3.32
94 95 1.960689 GGTGTGTGGGCATTAGTTGTT 59.039 47.619 0.00 0.00 0.00 2.83
95 96 2.364002 GGTGTGTGGGCATTAGTTGTTT 59.636 45.455 0.00 0.00 0.00 2.83
96 97 3.181470 GGTGTGTGGGCATTAGTTGTTTT 60.181 43.478 0.00 0.00 0.00 2.43
97 98 3.801594 GTGTGTGGGCATTAGTTGTTTTG 59.198 43.478 0.00 0.00 0.00 2.44
98 99 2.799978 GTGTGGGCATTAGTTGTTTTGC 59.200 45.455 0.00 0.00 0.00 3.68
103 104 3.104843 GCATTAGTTGTTTTGCCCACA 57.895 42.857 0.00 0.00 0.00 4.17
104 105 2.799978 GCATTAGTTGTTTTGCCCACAC 59.200 45.455 0.00 0.00 0.00 3.82
105 106 2.853731 TTAGTTGTTTTGCCCACACG 57.146 45.000 0.00 0.00 0.00 4.49
106 107 1.752683 TAGTTGTTTTGCCCACACGT 58.247 45.000 0.00 0.00 0.00 4.49
107 108 1.752683 AGTTGTTTTGCCCACACGTA 58.247 45.000 0.00 0.00 0.00 3.57
108 109 1.673920 AGTTGTTTTGCCCACACGTAG 59.326 47.619 0.00 0.00 0.00 3.51
109 110 1.025812 TTGTTTTGCCCACACGTAGG 58.974 50.000 0.00 0.00 0.00 3.18
110 111 0.107116 TGTTTTGCCCACACGTAGGT 60.107 50.000 5.59 0.00 0.00 3.08
119 120 2.741092 CACGTAGGTGTGTGGGCT 59.259 61.111 7.41 0.00 39.38 5.19
120 121 1.667830 CACGTAGGTGTGTGGGCTG 60.668 63.158 7.41 0.00 39.38 4.85
121 122 2.047274 CGTAGGTGTGTGGGCTGG 60.047 66.667 0.00 0.00 0.00 4.85
122 123 2.879233 CGTAGGTGTGTGGGCTGGT 61.879 63.158 0.00 0.00 0.00 4.00
123 124 1.454539 GTAGGTGTGTGGGCTGGTT 59.545 57.895 0.00 0.00 0.00 3.67
124 125 0.889186 GTAGGTGTGTGGGCTGGTTG 60.889 60.000 0.00 0.00 0.00 3.77
125 126 2.690653 TAGGTGTGTGGGCTGGTTGC 62.691 60.000 0.00 0.00 41.94 4.17
126 127 2.519302 GTGTGTGGGCTGGTTGCT 60.519 61.111 0.00 0.00 42.39 3.91
127 128 2.519063 TGTGTGGGCTGGTTGCTG 60.519 61.111 0.00 0.00 42.39 4.41
128 129 2.519302 GTGTGGGCTGGTTGCTGT 60.519 61.111 0.00 0.00 42.39 4.40
129 130 2.203337 TGTGGGCTGGTTGCTGTC 60.203 61.111 0.00 0.00 42.39 3.51
130 131 2.985847 GTGGGCTGGTTGCTGTCC 60.986 66.667 0.00 0.00 42.39 4.02
131 132 3.497115 TGGGCTGGTTGCTGTCCA 61.497 61.111 0.00 0.00 42.39 4.02
132 133 2.036256 GGGCTGGTTGCTGTCCAT 59.964 61.111 0.00 0.00 42.39 3.41
133 134 2.345760 GGGCTGGTTGCTGTCCATG 61.346 63.158 0.00 0.00 42.39 3.66
134 135 2.570181 GCTGGTTGCTGTCCATGC 59.430 61.111 0.00 0.00 38.95 4.06
135 136 2.998279 GCTGGTTGCTGTCCATGCC 61.998 63.158 0.00 0.00 38.95 4.40
136 137 1.604308 CTGGTTGCTGTCCATGCCA 60.604 57.895 0.00 0.00 34.26 4.92
137 138 1.870055 CTGGTTGCTGTCCATGCCAC 61.870 60.000 0.00 0.00 34.26 5.01
138 139 1.902918 GGTTGCTGTCCATGCCACA 60.903 57.895 0.00 0.00 0.00 4.17
139 140 1.286880 GTTGCTGTCCATGCCACAC 59.713 57.895 0.00 0.00 0.00 3.82
140 141 2.260154 TTGCTGTCCATGCCACACG 61.260 57.895 0.00 0.00 0.00 4.49
141 142 2.358615 GCTGTCCATGCCACACGA 60.359 61.111 0.00 0.00 0.00 4.35
142 143 2.393768 GCTGTCCATGCCACACGAG 61.394 63.158 0.00 0.00 0.00 4.18
143 144 1.742880 CTGTCCATGCCACACGAGG 60.743 63.158 0.00 0.00 0.00 4.63
155 156 4.539083 ACGAGGCGTGTGGCACAA 62.539 61.111 23.90 3.54 46.16 3.33
156 157 4.012895 CGAGGCGTGTGGCACAAC 62.013 66.667 23.90 17.20 44.16 3.32
157 158 2.591715 GAGGCGTGTGGCACAACT 60.592 61.111 23.90 19.95 44.16 3.16
158 159 1.301401 GAGGCGTGTGGCACAACTA 60.301 57.895 23.90 0.00 44.16 2.24
159 160 1.566018 GAGGCGTGTGGCACAACTAC 61.566 60.000 23.90 12.86 44.16 2.73
160 161 2.613506 GGCGTGTGGCACAACTACC 61.614 63.158 23.90 16.77 44.16 3.18
161 162 2.613506 GCGTGTGGCACAACTACCC 61.614 63.158 23.90 7.78 44.16 3.69
162 163 2.314647 CGTGTGGCACAACTACCCG 61.315 63.158 23.90 16.45 44.16 5.28
163 164 1.070105 GTGTGGCACAACTACCCGA 59.930 57.895 23.90 0.00 44.16 5.14
164 165 0.321298 GTGTGGCACAACTACCCGAT 60.321 55.000 23.90 0.00 44.16 4.18
165 166 1.066716 GTGTGGCACAACTACCCGATA 60.067 52.381 23.90 0.00 44.16 2.92
166 167 1.066716 TGTGGCACAACTACCCGATAC 60.067 52.381 19.74 0.00 44.16 2.24
167 168 1.066716 GTGGCACAACTACCCGATACA 60.067 52.381 13.86 0.00 44.16 2.29
168 169 1.066716 TGGCACAACTACCCGATACAC 60.067 52.381 0.00 0.00 31.92 2.90
169 170 1.648504 GCACAACTACCCGATACACC 58.351 55.000 0.00 0.00 0.00 4.16
170 171 1.066716 GCACAACTACCCGATACACCA 60.067 52.381 0.00 0.00 0.00 4.17
171 172 2.613691 CACAACTACCCGATACACCAC 58.386 52.381 0.00 0.00 0.00 4.16
172 173 2.028839 CACAACTACCCGATACACCACA 60.029 50.000 0.00 0.00 0.00 4.17
173 174 2.028748 ACAACTACCCGATACACCACAC 60.029 50.000 0.00 0.00 0.00 3.82
174 175 0.813184 ACTACCCGATACACCACACG 59.187 55.000 0.00 0.00 0.00 4.49
175 176 0.813184 CTACCCGATACACCACACGT 59.187 55.000 0.00 0.00 0.00 4.49
188 189 0.438445 CACACGTGTGGCAGTTATCG 59.562 55.000 35.65 10.61 42.10 2.92
189 190 0.669318 ACACGTGTGGCAGTTATCGG 60.669 55.000 22.71 0.00 34.19 4.18
190 191 1.079405 ACGTGTGGCAGTTATCGGG 60.079 57.895 0.00 0.00 0.00 5.14
191 192 1.216977 CGTGTGGCAGTTATCGGGA 59.783 57.895 0.00 0.00 0.00 5.14
192 193 1.082117 CGTGTGGCAGTTATCGGGAC 61.082 60.000 0.00 0.00 0.00 4.46
193 194 0.743345 GTGTGGCAGTTATCGGGACC 60.743 60.000 0.00 0.00 0.00 4.46
194 195 1.195442 TGTGGCAGTTATCGGGACCA 61.195 55.000 0.00 0.00 0.00 4.02
235 236 4.718940 ATGCCCTAAAATTTGAGAACCG 57.281 40.909 3.89 0.00 0.00 4.44
236 237 3.492337 TGCCCTAAAATTTGAGAACCGT 58.508 40.909 3.89 0.00 0.00 4.83
269 280 1.000731 GATCTCTCATTGGAGGCGGAG 59.999 57.143 0.00 0.00 41.69 4.63
291 302 2.290514 CCAATGACAGGAAGGAGCTCAA 60.291 50.000 17.19 0.00 0.00 3.02
293 304 1.423584 TGACAGGAAGGAGCTCAACA 58.576 50.000 17.19 0.63 0.00 3.33
298 309 0.035915 GGAAGGAGCTCAACAGGGAC 60.036 60.000 17.19 0.00 0.00 4.46
302 313 4.379243 AGCTCAACAGGGACGGCG 62.379 66.667 4.80 4.80 0.00 6.46
356 367 1.072852 GGGATGATGGCAGGAGCTC 59.927 63.158 4.71 4.71 41.70 4.09
389 400 3.274586 CGGTGCTCATGGATGGCG 61.275 66.667 0.00 0.00 0.00 5.69
394 405 2.124612 CTCATGGATGGCGGCACA 60.125 61.111 16.34 9.68 0.00 4.57
402 413 3.687321 ATGGCGGCACAAGCTCGAT 62.687 57.895 16.34 0.00 41.70 3.59
407 418 1.375908 GGCACAAGCTCGATGACCA 60.376 57.895 0.00 0.00 41.70 4.02
408 419 1.639298 GGCACAAGCTCGATGACCAC 61.639 60.000 0.00 0.00 41.70 4.16
412 423 0.388520 CAAGCTCGATGACCACGACA 60.389 55.000 0.00 0.00 35.88 4.35
420 431 0.241213 ATGACCACGACAGACGACAG 59.759 55.000 0.00 0.00 45.77 3.51
424 435 1.794003 CACGACAGACGACAGCGAG 60.794 63.158 0.00 0.00 45.77 5.03
426 437 2.677979 CGACAGACGACAGCGAGGA 61.678 63.158 0.00 0.00 45.77 3.71
461 490 0.682852 ACAACCGTGTAGCCAGCTTA 59.317 50.000 0.00 0.00 35.72 3.09
474 503 3.862991 GCTTAGAGGGGTCGGGGC 61.863 72.222 0.00 0.00 0.00 5.80
475 504 3.537874 CTTAGAGGGGTCGGGGCG 61.538 72.222 0.00 0.00 0.00 6.13
491 520 2.335011 CGGCCGCGACATAGATCA 59.665 61.111 14.67 0.00 0.00 2.92
493 522 0.667487 CGGCCGCGACATAGATCATT 60.667 55.000 14.67 0.00 0.00 2.57
494 523 1.512926 GGCCGCGACATAGATCATTT 58.487 50.000 8.23 0.00 0.00 2.32
500 529 4.321304 CCGCGACATAGATCATTTAGGAGT 60.321 45.833 8.23 0.00 0.00 3.85
528 557 0.326264 GTGAGAGGCTTCATGGTGGT 59.674 55.000 0.00 0.00 0.00 4.16
530 559 0.460987 GAGAGGCTTCATGGTGGTCG 60.461 60.000 0.00 0.00 0.00 4.79
538 567 3.399181 ATGGTGGTCGGCGTGGAT 61.399 61.111 6.85 0.00 0.00 3.41
550 579 2.273449 GTGGATGCAGGGTGAGGG 59.727 66.667 0.00 0.00 0.00 4.30
585 614 1.002792 GAAAGTTCACAGTGGCGGTTC 60.003 52.381 0.00 0.00 0.00 3.62
587 616 1.885850 GTTCACAGTGGCGGTTCGT 60.886 57.895 0.00 0.00 0.00 3.85
590 619 0.745128 TCACAGTGGCGGTTCGTTTT 60.745 50.000 0.00 0.00 0.00 2.43
591 620 0.099791 CACAGTGGCGGTTCGTTTTT 59.900 50.000 0.00 0.00 0.00 1.94
592 621 0.099791 ACAGTGGCGGTTCGTTTTTG 59.900 50.000 0.00 0.00 0.00 2.44
593 622 0.099791 CAGTGGCGGTTCGTTTTTGT 59.900 50.000 0.00 0.00 0.00 2.83
594 623 0.812549 AGTGGCGGTTCGTTTTTGTT 59.187 45.000 0.00 0.00 0.00 2.83
596 625 1.584761 GTGGCGGTTCGTTTTTGTTTC 59.415 47.619 0.00 0.00 0.00 2.78
629 661 6.375945 TGCTAGTGGTGTTGCAAATATATG 57.624 37.500 0.00 0.00 32.12 1.78
654 688 5.894393 TCACTTGGAGTTAAAATTTGGGACA 59.106 36.000 0.00 0.00 0.00 4.02
680 714 4.816385 TGCAAAATTTTCGGCACCAAATAA 59.184 33.333 10.87 0.00 0.00 1.40
716 750 6.922247 TGTTGAAGGTCGTTGTTTTACATA 57.078 33.333 0.00 0.00 0.00 2.29
742 776 2.741759 TGAAGATGCTCTTACACGCA 57.258 45.000 0.00 0.00 36.73 5.24
754 788 5.381174 TCTTACACGCACATACAGTACTT 57.619 39.130 0.00 0.00 0.00 2.24
850 913 2.386661 AACCAACGCTTGAGATCGAT 57.613 45.000 0.00 0.00 0.00 3.59
867 930 8.300286 TGAGATCGATCAGGACATAAATAAGTC 58.700 37.037 26.47 10.11 0.00 3.01
915 992 4.003648 AGATCTAAACGGCCTCTTTGTTG 58.996 43.478 0.00 0.00 0.00 3.33
982 1059 1.979155 CACTCCCTCGCTCCACTCA 60.979 63.158 0.00 0.00 0.00 3.41
983 1060 1.979693 ACTCCCTCGCTCCACTCAC 60.980 63.158 0.00 0.00 0.00 3.51
984 1061 1.979155 CTCCCTCGCTCCACTCACA 60.979 63.158 0.00 0.00 0.00 3.58
1074 1151 3.141488 CTCCTCGCCGTGGTAGCT 61.141 66.667 4.98 0.00 0.00 3.32
1175 1252 2.520741 CCCGCTCTCCTCTCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
1206 1283 1.378250 CCCGTCGGTCTACCACTCT 60.378 63.158 11.06 0.00 35.14 3.24
1448 1525 4.101448 CGGCAAGGTCCCTCCCTG 62.101 72.222 0.00 0.00 34.19 4.45
1478 1555 6.704310 TCTTTAACCCTACTGCTCGTTTTAT 58.296 36.000 0.00 0.00 0.00 1.40
1487 1564 5.083136 ACTGCTCGTTTTATCGCATTATG 57.917 39.130 0.00 0.00 0.00 1.90
1490 1567 4.808895 TGCTCGTTTTATCGCATTATGACT 59.191 37.500 0.00 0.00 0.00 3.41
1494 1571 6.741109 TCGTTTTATCGCATTATGACTCCTA 58.259 36.000 0.00 0.00 0.00 2.94
1526 1604 5.573337 ACTGTTCTTGGTATACTCGGTAC 57.427 43.478 2.25 0.00 0.00 3.34
1548 1626 2.510238 GTGTGGCTGGCGAGCTAG 60.510 66.667 20.62 3.99 45.44 3.42
1602 1681 8.507249 GGATTCTCATGGTATGTTAGTTAATGC 58.493 37.037 0.00 0.00 0.00 3.56
1603 1682 7.801716 TTCTCATGGTATGTTAGTTAATGCC 57.198 36.000 0.00 0.00 0.00 4.40
1713 1799 1.570813 GGTGTTTCAACTTGCTTGCC 58.429 50.000 0.00 0.00 0.00 4.52
1779 1867 8.751302 TGGTTGAACTGTTCTTTTTAAAGTTC 57.249 30.769 20.18 6.86 44.45 3.01
1820 1908 5.829924 ACCAGAAGTGACTTGAATTTCACAT 59.170 36.000 0.90 0.00 43.94 3.21
1850 1938 8.303876 AGTTATTTTGTGTGTGTTGTTCTTCTT 58.696 29.630 0.00 0.00 0.00 2.52
1853 1941 4.678509 TGTGTGTGTTGTTCTTCTTGTC 57.321 40.909 0.00 0.00 0.00 3.18
1892 1980 9.511272 TGCTCTGATAATTATTTACATGCATCT 57.489 29.630 0.00 0.00 0.00 2.90
2117 2205 7.929245 TCGCCAAGCTATAATGTTGACTTTATA 59.071 33.333 0.00 8.37 31.39 0.98
2200 2288 5.922544 GGAATGACATTGAAAACAGGTTGAG 59.077 40.000 5.14 0.00 0.00 3.02
2324 2412 8.014322 TGAAACACGTCAGAAATTCATAGTAC 57.986 34.615 0.00 0.00 0.00 2.73
2354 2442 5.885912 TGTTTGGAACTCTTGAGTAGCTTTT 59.114 36.000 3.52 0.00 0.00 2.27
2583 2676 3.950397 AGTGCATACTGGAATTCGGAAA 58.050 40.909 0.00 0.00 35.34 3.13
2602 2695 5.140177 GGAAATTGCTCGTAATTGATAGCG 58.860 41.667 0.00 0.00 37.80 4.26
2624 2717 0.255890 AAACTGGTCACCACTGCAGT 59.744 50.000 15.25 15.25 29.09 4.40
2994 3087 4.412060 TTGTTATTCCCCTTTCATGGGT 57.588 40.909 0.00 0.00 45.70 4.51
3001 3095 1.620524 CCCCTTTCATGGGTGCTCAAT 60.621 52.381 0.00 0.00 45.70 2.57
3261 3355 7.823745 AAGTGAGTAGGTGATTTTGTCATTT 57.176 32.000 0.00 0.00 39.48 2.32
3264 3358 9.349713 AGTGAGTAGGTGATTTTGTCATTTTAA 57.650 29.630 0.00 0.00 39.48 1.52
3273 3367 8.272866 GTGATTTTGTCATTTTAAAACTTCCGG 58.727 33.333 1.97 0.00 39.48 5.14
3404 3503 7.686434 TCAGGGTATAAAGTAACAAGAGCTTT 58.314 34.615 0.00 0.00 36.54 3.51
3700 3811 8.122472 TCATGTGATCAAGTACTAACTCAAGA 57.878 34.615 0.00 0.00 33.75 3.02
3820 3931 4.674475 GCTCTTGTAGTTAGTAGCTGGAC 58.326 47.826 0.00 0.00 0.00 4.02
3925 4036 5.353394 TCATTAGCCATTCTTCGGTTAGT 57.647 39.130 0.00 0.00 0.00 2.24
3988 4099 9.736023 GCTTTTGTAGTTTGCTTTGCTATATAT 57.264 29.630 0.00 0.00 0.00 0.86
4006 4117 9.829507 GCTATATATTGATCTGCCTGAGTAATT 57.170 33.333 0.00 0.00 0.00 1.40
4124 4235 3.181440 TGATCACCTCTTTTTGCTCCTGT 60.181 43.478 0.00 0.00 0.00 4.00
4144 4255 5.330455 TGTGAGACATGATCCAACTACTC 57.670 43.478 0.00 0.00 0.00 2.59
4321 4522 9.905713 ACTTTTGTAATACTATCATCCATGTGT 57.094 29.630 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.524414 CTCCACACGTCCGTATGTCA 59.476 55.000 0.00 0.00 0.00 3.58
1 2 0.179145 CCTCCACACGTCCGTATGTC 60.179 60.000 0.00 0.00 0.00 3.06
2 3 0.896940 ACCTCCACACGTCCGTATGT 60.897 55.000 0.00 0.00 0.00 2.29
3 4 0.245539 AACCTCCACACGTCCGTATG 59.754 55.000 0.00 0.00 0.00 2.39
4 5 1.838112 TAACCTCCACACGTCCGTAT 58.162 50.000 0.00 0.00 0.00 3.06
5 6 1.745087 GATAACCTCCACACGTCCGTA 59.255 52.381 0.00 0.00 0.00 4.02
6 7 0.529378 GATAACCTCCACACGTCCGT 59.471 55.000 0.00 0.00 0.00 4.69
7 8 0.528924 TGATAACCTCCACACGTCCG 59.471 55.000 0.00 0.00 0.00 4.79
8 9 2.028385 AGTTGATAACCTCCACACGTCC 60.028 50.000 0.00 0.00 0.00 4.79
9 10 3.314541 AGTTGATAACCTCCACACGTC 57.685 47.619 0.00 0.00 0.00 4.34
10 11 3.660865 GAAGTTGATAACCTCCACACGT 58.339 45.455 0.00 0.00 0.00 4.49
11 12 2.666508 CGAAGTTGATAACCTCCACACG 59.333 50.000 0.00 0.00 0.00 4.49
12 13 2.415512 GCGAAGTTGATAACCTCCACAC 59.584 50.000 0.00 0.00 0.00 3.82
13 14 2.614481 GGCGAAGTTGATAACCTCCACA 60.614 50.000 0.00 0.00 0.00 4.17
14 15 2.007608 GGCGAAGTTGATAACCTCCAC 58.992 52.381 0.00 0.00 0.00 4.02
15 16 1.065709 GGGCGAAGTTGATAACCTCCA 60.066 52.381 0.00 0.00 0.00 3.86
16 17 1.065709 TGGGCGAAGTTGATAACCTCC 60.066 52.381 0.00 0.00 0.00 4.30
17 18 2.007608 GTGGGCGAAGTTGATAACCTC 58.992 52.381 0.00 0.00 0.00 3.85
18 19 1.349688 TGTGGGCGAAGTTGATAACCT 59.650 47.619 0.00 0.00 0.00 3.50
19 20 1.467342 GTGTGGGCGAAGTTGATAACC 59.533 52.381 0.00 0.00 0.00 2.85
20 21 1.127951 CGTGTGGGCGAAGTTGATAAC 59.872 52.381 0.00 0.00 0.00 1.89
21 22 1.434555 CGTGTGGGCGAAGTTGATAA 58.565 50.000 0.00 0.00 0.00 1.75
22 23 1.017177 GCGTGTGGGCGAAGTTGATA 61.017 55.000 0.00 0.00 0.00 2.15
23 24 2.325082 GCGTGTGGGCGAAGTTGAT 61.325 57.895 0.00 0.00 0.00 2.57
24 25 2.970324 GCGTGTGGGCGAAGTTGA 60.970 61.111 0.00 0.00 0.00 3.18
25 26 3.276091 TGCGTGTGGGCGAAGTTG 61.276 61.111 0.00 0.00 35.06 3.16
26 27 3.276846 GTGCGTGTGGGCGAAGTT 61.277 61.111 0.00 0.00 35.06 2.66
27 28 4.539083 TGTGCGTGTGGGCGAAGT 62.539 61.111 0.00 0.00 35.06 3.01
28 29 4.012895 GTGTGCGTGTGGGCGAAG 62.013 66.667 0.00 0.00 35.06 3.79
39 40 2.734723 CCCTCTCACACGTGTGCG 60.735 66.667 37.70 33.02 45.25 5.34
40 41 1.222115 GAACCCTCTCACACGTGTGC 61.222 60.000 37.70 20.63 45.25 4.57
41 42 0.939577 CGAACCCTCTCACACGTGTG 60.940 60.000 37.04 37.04 46.91 3.82
42 43 1.362717 CGAACCCTCTCACACGTGT 59.637 57.895 17.22 17.22 0.00 4.49
43 44 1.372997 CCGAACCCTCTCACACGTG 60.373 63.158 15.48 15.48 0.00 4.49
44 45 2.571216 CCCGAACCCTCTCACACGT 61.571 63.158 0.00 0.00 0.00 4.49
45 46 2.214181 CTCCCGAACCCTCTCACACG 62.214 65.000 0.00 0.00 0.00 4.49
46 47 1.592223 CTCCCGAACCCTCTCACAC 59.408 63.158 0.00 0.00 0.00 3.82
47 48 1.609501 CCTCCCGAACCCTCTCACA 60.610 63.158 0.00 0.00 0.00 3.58
48 49 2.359967 CCCTCCCGAACCCTCTCAC 61.360 68.421 0.00 0.00 0.00 3.51
49 50 2.038975 CCCTCCCGAACCCTCTCA 59.961 66.667 0.00 0.00 0.00 3.27
50 51 0.908180 TTTCCCTCCCGAACCCTCTC 60.908 60.000 0.00 0.00 0.00 3.20
51 52 0.475048 TTTTCCCTCCCGAACCCTCT 60.475 55.000 0.00 0.00 0.00 3.69
52 53 0.402887 TTTTTCCCTCCCGAACCCTC 59.597 55.000 0.00 0.00 0.00 4.30
53 54 2.559285 TTTTTCCCTCCCGAACCCT 58.441 52.632 0.00 0.00 0.00 4.34
69 70 3.304829 ACTAATGCCCACACACCTTTTT 58.695 40.909 0.00 0.00 0.00 1.94
70 71 2.957474 ACTAATGCCCACACACCTTTT 58.043 42.857 0.00 0.00 0.00 2.27
71 72 2.627699 CAACTAATGCCCACACACCTTT 59.372 45.455 0.00 0.00 0.00 3.11
72 73 2.238521 CAACTAATGCCCACACACCTT 58.761 47.619 0.00 0.00 0.00 3.50
73 74 1.144913 ACAACTAATGCCCACACACCT 59.855 47.619 0.00 0.00 0.00 4.00
74 75 1.616159 ACAACTAATGCCCACACACC 58.384 50.000 0.00 0.00 0.00 4.16
75 76 3.726291 AAACAACTAATGCCCACACAC 57.274 42.857 0.00 0.00 0.00 3.82
76 77 3.739519 GCAAAACAACTAATGCCCACACA 60.740 43.478 0.00 0.00 32.73 3.72
77 78 2.799978 GCAAAACAACTAATGCCCACAC 59.200 45.455 0.00 0.00 32.73 3.82
78 79 3.104843 GCAAAACAACTAATGCCCACA 57.895 42.857 0.00 0.00 32.73 4.17
83 84 2.799978 GTGTGGGCAAAACAACTAATGC 59.200 45.455 0.00 0.00 38.06 3.56
84 85 3.049206 CGTGTGGGCAAAACAACTAATG 58.951 45.455 0.00 0.00 0.00 1.90
85 86 2.691011 ACGTGTGGGCAAAACAACTAAT 59.309 40.909 0.00 0.00 0.00 1.73
86 87 2.093106 ACGTGTGGGCAAAACAACTAA 58.907 42.857 0.00 0.00 0.00 2.24
87 88 1.752683 ACGTGTGGGCAAAACAACTA 58.247 45.000 0.00 0.00 0.00 2.24
88 89 1.673920 CTACGTGTGGGCAAAACAACT 59.326 47.619 0.00 0.00 0.00 3.16
89 90 1.268845 CCTACGTGTGGGCAAAACAAC 60.269 52.381 0.00 0.00 0.00 3.32
90 91 1.025812 CCTACGTGTGGGCAAAACAA 58.974 50.000 0.00 0.00 0.00 2.83
91 92 0.107116 ACCTACGTGTGGGCAAAACA 60.107 50.000 12.88 0.00 34.14 2.83
92 93 0.309612 CACCTACGTGTGGGCAAAAC 59.690 55.000 12.88 0.00 35.10 2.43
93 94 2.709170 CACCTACGTGTGGGCAAAA 58.291 52.632 12.88 0.00 35.10 2.44
94 95 4.466133 CACCTACGTGTGGGCAAA 57.534 55.556 12.88 0.00 35.10 3.68
102 103 1.667830 CAGCCCACACACCTACGTG 60.668 63.158 0.00 0.00 46.11 4.49
103 104 2.741092 CAGCCCACACACCTACGT 59.259 61.111 0.00 0.00 0.00 3.57
104 105 2.047274 CCAGCCCACACACCTACG 60.047 66.667 0.00 0.00 0.00 3.51
105 106 0.889186 CAACCAGCCCACACACCTAC 60.889 60.000 0.00 0.00 0.00 3.18
106 107 1.454104 CAACCAGCCCACACACCTA 59.546 57.895 0.00 0.00 0.00 3.08
107 108 2.195683 CAACCAGCCCACACACCT 59.804 61.111 0.00 0.00 0.00 4.00
108 109 3.605664 GCAACCAGCCCACACACC 61.606 66.667 0.00 0.00 37.23 4.16
117 118 2.570181 GCATGGACAGCAACCAGC 59.430 61.111 0.00 0.00 40.89 4.85
118 119 1.604308 TGGCATGGACAGCAACCAG 60.604 57.895 0.00 0.00 40.89 4.00
119 120 1.902918 GTGGCATGGACAGCAACCA 60.903 57.895 0.00 0.00 41.83 3.67
120 121 1.902918 TGTGGCATGGACAGCAACC 60.903 57.895 0.00 0.00 35.00 3.77
121 122 1.286880 GTGTGGCATGGACAGCAAC 59.713 57.895 0.00 0.00 36.45 4.17
122 123 2.260154 CGTGTGGCATGGACAGCAA 61.260 57.895 0.00 0.00 0.00 3.91
123 124 2.669229 CGTGTGGCATGGACAGCA 60.669 61.111 0.00 0.00 0.00 4.41
124 125 2.358615 TCGTGTGGCATGGACAGC 60.359 61.111 0.00 0.00 0.00 4.40
125 126 1.742880 CCTCGTGTGGCATGGACAG 60.743 63.158 0.00 0.00 0.00 3.51
126 127 2.347114 CCTCGTGTGGCATGGACA 59.653 61.111 0.00 0.00 0.00 4.02
138 139 4.539083 TTGTGCCACACGCCTCGT 62.539 61.111 0.00 0.00 42.36 4.18
139 140 4.012895 GTTGTGCCACACGCCTCG 62.013 66.667 0.00 0.00 37.14 4.63
140 141 1.301401 TAGTTGTGCCACACGCCTC 60.301 57.895 0.00 0.00 37.14 4.70
141 142 1.597027 GTAGTTGTGCCACACGCCT 60.597 57.895 0.00 0.00 37.14 5.52
142 143 2.613506 GGTAGTTGTGCCACACGCC 61.614 63.158 0.00 0.00 37.14 5.68
143 144 2.613506 GGGTAGTTGTGCCACACGC 61.614 63.158 0.00 0.00 37.14 5.34
144 145 2.314647 CGGGTAGTTGTGCCACACG 61.315 63.158 0.00 0.00 37.14 4.49
145 146 0.321298 ATCGGGTAGTTGTGCCACAC 60.321 55.000 0.00 0.00 34.56 3.82
146 147 1.066716 GTATCGGGTAGTTGTGCCACA 60.067 52.381 0.00 0.00 0.00 4.17
147 148 1.066716 TGTATCGGGTAGTTGTGCCAC 60.067 52.381 0.00 0.00 0.00 5.01
148 149 1.066716 GTGTATCGGGTAGTTGTGCCA 60.067 52.381 0.00 0.00 0.00 4.92
149 150 1.648504 GTGTATCGGGTAGTTGTGCC 58.351 55.000 0.00 0.00 0.00 5.01
150 151 1.066716 TGGTGTATCGGGTAGTTGTGC 60.067 52.381 0.00 0.00 0.00 4.57
151 152 2.028839 TGTGGTGTATCGGGTAGTTGTG 60.029 50.000 0.00 0.00 0.00 3.33
152 153 2.028748 GTGTGGTGTATCGGGTAGTTGT 60.029 50.000 0.00 0.00 0.00 3.32
153 154 2.613691 GTGTGGTGTATCGGGTAGTTG 58.386 52.381 0.00 0.00 0.00 3.16
154 155 1.203052 CGTGTGGTGTATCGGGTAGTT 59.797 52.381 0.00 0.00 0.00 2.24
155 156 0.813184 CGTGTGGTGTATCGGGTAGT 59.187 55.000 0.00 0.00 0.00 2.73
156 157 0.813184 ACGTGTGGTGTATCGGGTAG 59.187 55.000 0.00 0.00 0.00 3.18
157 158 0.527113 CACGTGTGGTGTATCGGGTA 59.473 55.000 7.58 0.00 41.89 3.69
158 159 1.290955 CACGTGTGGTGTATCGGGT 59.709 57.895 7.58 0.00 41.89 5.28
159 160 4.178861 CACGTGTGGTGTATCGGG 57.821 61.111 7.58 0.00 41.89 5.14
169 170 0.438445 CGATAACTGCCACACGTGTG 59.562 55.000 36.13 36.13 45.23 3.82
170 171 0.669318 CCGATAACTGCCACACGTGT 60.669 55.000 17.22 17.22 0.00 4.49
171 172 1.358725 CCCGATAACTGCCACACGTG 61.359 60.000 15.48 15.48 0.00 4.49
172 173 1.079405 CCCGATAACTGCCACACGT 60.079 57.895 0.00 0.00 0.00 4.49
173 174 1.082117 GTCCCGATAACTGCCACACG 61.082 60.000 0.00 0.00 0.00 4.49
174 175 0.743345 GGTCCCGATAACTGCCACAC 60.743 60.000 0.00 0.00 0.00 3.82
175 176 1.195442 TGGTCCCGATAACTGCCACA 61.195 55.000 0.00 0.00 0.00 4.17
176 177 0.180406 ATGGTCCCGATAACTGCCAC 59.820 55.000 0.00 0.00 0.00 5.01
177 178 0.916086 AATGGTCCCGATAACTGCCA 59.084 50.000 0.00 0.00 0.00 4.92
178 179 2.052782 AAATGGTCCCGATAACTGCC 57.947 50.000 0.00 0.00 0.00 4.85
179 180 5.767816 ATTTAAATGGTCCCGATAACTGC 57.232 39.130 0.00 0.00 0.00 4.40
180 181 8.846211 ACATTATTTAAATGGTCCCGATAACTG 58.154 33.333 11.05 0.00 32.14 3.16
181 182 8.990163 ACATTATTTAAATGGTCCCGATAACT 57.010 30.769 11.05 0.00 32.14 2.24
186 187 9.245481 ACTTTTACATTATTTAAATGGTCCCGA 57.755 29.630 11.05 0.00 32.14 5.14
235 236 6.922247 ATGAGAGATCATCATGTTTCACAC 57.078 37.500 11.46 0.00 36.07 3.82
236 237 6.317893 CCAATGAGAGATCATCATGTTTCACA 59.682 38.462 12.62 0.00 37.46 3.58
252 253 1.227497 GCTCCGCCTCCAATGAGAG 60.227 63.158 0.00 0.00 41.42 3.20
254 255 2.203126 GGCTCCGCCTCCAATGAG 60.203 66.667 0.00 0.00 46.69 2.90
269 280 0.034670 AGCTCCTTCCTGTCATTGGC 60.035 55.000 0.00 0.00 0.00 4.52
274 285 1.345741 CTGTTGAGCTCCTTCCTGTCA 59.654 52.381 12.15 0.00 0.00 3.58
302 313 1.278238 CAAAGTCCGCTATCACCGTC 58.722 55.000 0.00 0.00 0.00 4.79
329 340 3.392616 CCTGCCATCATCCCTAAACTACT 59.607 47.826 0.00 0.00 0.00 2.57
356 367 4.907034 CGCTCATCGTCGTCCCCG 62.907 72.222 0.00 0.00 0.00 5.73
380 391 3.142838 GCTTGTGCCGCCATCCAT 61.143 61.111 0.00 0.00 0.00 3.41
389 400 1.375908 TGGTCATCGAGCTTGTGCC 60.376 57.895 0.00 5.70 40.80 5.01
394 405 0.109086 CTGTCGTGGTCATCGAGCTT 60.109 55.000 0.00 0.00 37.99 3.74
402 413 1.652563 CTGTCGTCTGTCGTGGTCA 59.347 57.895 0.00 0.00 40.80 4.02
407 418 2.556792 CTCGCTGTCGTCTGTCGT 59.443 61.111 0.00 0.00 40.80 4.34
408 419 2.202362 CCTCGCTGTCGTCTGTCG 60.202 66.667 0.00 0.00 41.41 4.35
412 423 3.805307 CGCTCCTCGCTGTCGTCT 61.805 66.667 0.00 0.00 36.13 4.18
432 443 2.282180 ACGGTTGTGCCATCCCAC 60.282 61.111 0.00 0.00 36.97 4.61
447 476 0.103208 CCCTCTAAGCTGGCTACACG 59.897 60.000 0.00 0.00 0.00 4.49
474 503 0.667487 AATGATCTATGTCGCGGCCG 60.667 55.000 24.05 24.05 0.00 6.13
475 504 1.512926 AAATGATCTATGTCGCGGCC 58.487 50.000 8.89 0.00 0.00 6.13
484 513 6.445139 CCCCATACCACTCCTAAATGATCTAT 59.555 42.308 0.00 0.00 0.00 1.98
491 520 3.716872 CTCACCCCATACCACTCCTAAAT 59.283 47.826 0.00 0.00 0.00 1.40
493 522 2.316677 TCTCACCCCATACCACTCCTAA 59.683 50.000 0.00 0.00 0.00 2.69
494 523 1.934480 TCTCACCCCATACCACTCCTA 59.066 52.381 0.00 0.00 0.00 2.94
500 529 0.253160 AAGCCTCTCACCCCATACCA 60.253 55.000 0.00 0.00 0.00 3.25
530 559 4.408821 TCACCCTGCATCCACGCC 62.409 66.667 0.00 0.00 0.00 5.68
541 570 3.637273 GTTGCGTCCCCTCACCCT 61.637 66.667 0.00 0.00 0.00 4.34
550 579 1.336755 ACTTTCACCATTGTTGCGTCC 59.663 47.619 0.00 0.00 0.00 4.79
575 604 0.812549 AACAAAAACGAACCGCCACT 59.187 45.000 0.00 0.00 0.00 4.00
585 614 2.293399 AGCTGCCCTAGAAACAAAAACG 59.707 45.455 0.00 0.00 0.00 3.60
587 616 2.035832 GCAGCTGCCCTAGAAACAAAAA 59.964 45.455 28.76 0.00 34.31 1.94
590 619 0.401738 AGCAGCTGCCCTAGAAACAA 59.598 50.000 34.39 0.00 43.38 2.83
591 620 1.208052 CTAGCAGCTGCCCTAGAAACA 59.792 52.381 34.39 8.05 43.38 2.83
592 621 1.208293 ACTAGCAGCTGCCCTAGAAAC 59.792 52.381 34.39 4.46 43.38 2.78
593 622 1.208052 CACTAGCAGCTGCCCTAGAAA 59.792 52.381 34.39 10.77 43.38 2.52
594 623 0.826715 CACTAGCAGCTGCCCTAGAA 59.173 55.000 34.39 12.51 43.38 2.10
596 625 1.333636 ACCACTAGCAGCTGCCCTAG 61.334 60.000 34.39 29.24 43.38 3.02
629 661 6.183360 TGTCCCAAATTTTAACTCCAAGTGAC 60.183 38.462 0.00 0.00 0.00 3.67
654 688 2.209273 GGTGCCGAAAATTTTGCAGTT 58.791 42.857 14.30 0.00 33.80 3.16
655 689 1.137872 TGGTGCCGAAAATTTTGCAGT 59.862 42.857 14.30 0.00 33.80 4.40
663 697 7.033185 GTGTATCTTTATTTGGTGCCGAAAAT 58.967 34.615 0.00 0.00 0.00 1.82
680 714 5.181245 CGACCTTCAACAAATGGTGTATCTT 59.819 40.000 0.00 0.00 40.60 2.40
742 776 7.425606 CAAGCCAAAGAAAAAGTACTGTATGT 58.574 34.615 0.00 0.00 0.00 2.29
754 788 2.093553 ACAGCAAGCAAGCCAAAGAAAA 60.094 40.909 0.00 0.00 34.23 2.29
867 930 5.768317 TGCGATCCTTTTGTTTTCCTAAAG 58.232 37.500 0.00 0.00 0.00 1.85
915 992 1.149148 GACTCGAGGGTGTTTTCTGC 58.851 55.000 18.41 0.00 0.00 4.26
1074 1151 6.011981 GGGAGAGGAAGGATATAGAGAAGAGA 60.012 46.154 0.00 0.00 0.00 3.10
1187 1264 1.377725 GAGTGGTAGACCGACGGGA 60.378 63.158 20.00 0.00 39.43 5.14
1443 1520 1.628846 GGGTTAAAGAGAGTGCAGGGA 59.371 52.381 0.00 0.00 0.00 4.20
1448 1525 3.055747 AGCAGTAGGGTTAAAGAGAGTGC 60.056 47.826 0.00 0.00 34.23 4.40
1478 1555 6.040504 ACAATACTGTAGGAGTCATAATGCGA 59.959 38.462 0.00 0.00 35.96 5.10
1526 1604 1.446792 CTCGCCAGCCACACAGTAG 60.447 63.158 0.00 0.00 0.00 2.57
1548 1626 3.316308 ACTTCAGAGTTTGACAATGTGCC 59.684 43.478 0.00 0.00 34.94 5.01
1602 1681 3.868077 GCTTTAGCTGTGATCTGTGTAGG 59.132 47.826 0.00 0.00 38.21 3.18
1603 1682 4.498241 TGCTTTAGCTGTGATCTGTGTAG 58.502 43.478 0.00 0.00 42.66 2.74
1820 1908 6.443934 ACAACACACACAAAATAACTAGCA 57.556 33.333 0.00 0.00 0.00 3.49
1850 1938 5.065235 TCAGAGCAATTCAATCACAAGACA 58.935 37.500 0.00 0.00 0.00 3.41
1901 1989 6.509418 TTTTCATATGAAGTACCCTGCAAC 57.491 37.500 17.28 0.00 35.21 4.17
1979 2067 0.320374 CTCCTAGTGTGCGGTTCCAA 59.680 55.000 0.00 0.00 0.00 3.53
2117 2205 3.683847 GCAGAGCAACATCCTTATGAGGT 60.684 47.826 3.04 0.00 43.97 3.85
2200 2288 4.439289 GCTCAACAAATAGGAAGTGCCATC 60.439 45.833 0.00 0.00 40.02 3.51
2324 2412 6.927294 ACTCAAGAGTTCCAAACAGTTAAG 57.073 37.500 0.00 0.00 38.83 1.85
2361 2449 1.490910 ACCAGGCCACTAAATCTAGCC 59.509 52.381 5.01 0.00 44.20 3.93
2377 2465 3.118112 AGAGTCATATTGGAAGGCACCAG 60.118 47.826 3.88 0.00 41.19 4.00
2419 2507 9.897744 TTTCTGACACAAAACAGATATCATTTC 57.102 29.630 5.32 0.00 41.71 2.17
2426 2514 9.299963 CACAAAATTTCTGACACAAAACAGATA 57.700 29.630 0.00 0.00 41.71 1.98
2520 2613 6.424509 CACACCTTAAAATCATGTGCACAAAT 59.575 34.615 25.72 17.34 34.76 2.32
2541 2634 8.289618 TGCACTAGAAGAAAACATTTATCACAC 58.710 33.333 0.00 0.00 0.00 3.82
2570 2663 2.420022 ACGAGCAATTTCCGAATTCCAG 59.580 45.455 0.00 0.00 33.25 3.86
2583 2676 7.385205 AGTTTATCGCTATCAATTACGAGCAAT 59.615 33.333 0.00 0.00 38.04 3.56
2602 2695 2.744202 CTGCAGTGGTGACCAGTTTATC 59.256 50.000 9.74 0.34 34.53 1.75
3247 3341 8.272866 CCGGAAGTTTTAAAATGACAAAATCAC 58.727 33.333 3.52 0.00 41.24 3.06
3248 3342 7.982354 ACCGGAAGTTTTAAAATGACAAAATCA 59.018 29.630 9.46 0.00 43.13 2.57
3261 3355 6.982852 TGAATGCATAAACCGGAAGTTTTAA 58.017 32.000 9.46 0.00 46.79 1.52
3533 3633 9.226606 CCACACTAGAACTTTGATAACCATTTA 57.773 33.333 0.00 0.00 0.00 1.40
3534 3634 7.724061 ACCACACTAGAACTTTGATAACCATTT 59.276 33.333 0.00 0.00 0.00 2.32
3557 3668 8.145767 CCAACTTAACATATTAGTATCGGACCA 58.854 37.037 0.00 0.00 0.00 4.02
3700 3811 3.120321 TGCAAATAGTGACCGTGAAGT 57.880 42.857 0.00 0.00 0.00 3.01
3820 3931 0.893270 TTCCTTGCACCAATGACCCG 60.893 55.000 0.00 0.00 0.00 5.28
3988 4099 4.226427 AGCAATTACTCAGGCAGATCAA 57.774 40.909 0.00 0.00 0.00 2.57
4006 4117 7.277539 GGTGCAAAATTTGTATAAGCATAAGCA 59.722 33.333 7.60 0.00 45.49 3.91
4124 4235 6.427441 AGTAGAGTAGTTGGATCATGTCTCA 58.573 40.000 0.00 0.00 0.00 3.27
4304 4505 6.322931 TCTGGGTACACATGGATGATAGTAT 58.677 40.000 0.00 0.00 0.00 2.12
4305 4506 5.711698 TCTGGGTACACATGGATGATAGTA 58.288 41.667 0.00 0.00 0.00 1.82
4321 4522 4.168101 AGTTCTCATGTTTCCTCTGGGTA 58.832 43.478 0.00 0.00 0.00 3.69
4572 4773 4.458989 TCTGTACTGCCAAATCAACATTCC 59.541 41.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.