Multiple sequence alignment - TraesCS3D01G320600

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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 TraesCS3D01G320600 chr3D 100.000 3221 0 0 1 3221 433732127 433728907 0.000000e+00 5949.0
1 TraesCS3D01G320600 chr3A 90.355 2395 136 47 256 2609 572323525 572321185 0.000000e+00 3055.0
2 TraesCS3D01G320600 chr3A 82.143 252 24 8 1 231 572323771 572323520 2.540000e-46 196.0
3 TraesCS3D01G320600 chr3B 90.842 1092 58 15 1499 2582 566835431 566834374 0.000000e+00 1424.0
4 TraesCS3D01G320600 chr3B 87.021 470 35 10 885 1344 566836156 566835703 1.030000e-139 507.0
5 TraesCS3D01G320600 chr3B 81.781 483 39 15 297 758 566836604 566836150 3.060000e-95 359.0
6 TraesCS3D01G320600 chr2D 79.304 546 74 24 2699 3221 24865162 24864633 2.380000e-91 346.0
7 TraesCS3D01G320600 chr5D 79.249 506 65 18 2733 3214 423327592 423328081 1.870000e-82 316.0
8 TraesCS3D01G320600 chrUn 78.534 382 60 10 2699 3074 275011295 275011660 6.950000e-57 231.0
9 TraesCS3D01G320600 chrUn 79.154 331 48 9 2733 3057 315959343 315959028 3.260000e-50 209.0
10 TraesCS3D01G320600 chr2B 78.534 382 60 10 2699 3074 797551206 797551571 6.950000e-57 231.0
11 TraesCS3D01G320600 chr2B 75.741 540 73 28 2708 3221 649684700 649684193 5.410000e-53 219.0
12 TraesCS3D01G320600 chr2A 79.461 297 36 12 2698 2988 777044814 777045091 1.530000e-43 187.0
13 TraesCS3D01G320600 chr2A 79.322 295 38 9 2699 2988 777048284 777048560 5.490000e-43 185.0
14 TraesCS3D01G320600 chr2A 87.654 81 10 0 3141 3221 670688043 670687963 9.510000e-16 95.3


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 TraesCS3D01G320600 chr3D 433728907 433732127 3220 True 5949.000000 5949 100.000 1 3221 1 chr3D.!!$R1 3220
1 TraesCS3D01G320600 chr3A 572321185 572323771 2586 True 1625.500000 3055 86.249 1 2609 2 chr3A.!!$R1 2608
2 TraesCS3D01G320600 chr3B 566834374 566836604 2230 True 763.333333 1424 86.548 297 2582 3 chr3B.!!$R1 2285
3 TraesCS3D01G320600 chr2D 24864633 24865162 529 True 346.000000 346 79.304 2699 3221 1 chr2D.!!$R1 522
4 TraesCS3D01G320600 chr2B 649684193 649684700 507 True 219.000000 219 75.741 2708 3221 1 chr2B.!!$R1 513

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
241 267 0.173708 GGTTTGTTTTGTGCGGTGGA 59.826 50.0 0.0 0.0 0.0 4.02 F
249 275 0.324614 TTGTGCGGTGGATGATGAGT 59.675 50.0 0.0 0.0 0.0 3.41 F
1693 1926 0.038166 CCTCTGGTTGCCTTGCCTAA 59.962 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1904 0.255890 GGCAAGGCAACCAGAGGATA 59.744 55.000 0.00 0.0 37.17 2.59 R
2163 2400 1.073923 AGTCCAGCCTAACCAAACAGG 59.926 52.381 0.00 0.0 45.67 4.00 R
2741 2980 0.107508 CCAACGGCCACAGAGATGAT 60.108 55.000 2.24 0.0 0.00 2.45 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
71 74 3.560251 CCCCCATCGGCCGATTCT 61.560 66.667 37.36 16.83 31.62 2.40
80 83 1.149964 CGGCCGATTCTACGTTTCCC 61.150 60.000 24.07 0.00 0.00 3.97
110 113 1.209275 CGGCTCGATTTCTAGCGGTG 61.209 60.000 0.00 0.00 39.71 4.94
146 152 4.322385 GTTGTGGTTGCGCCGTCC 62.322 66.667 4.18 5.20 41.21 4.79
147 153 4.858680 TTGTGGTTGCGCCGTCCA 62.859 61.111 4.18 8.17 41.21 4.02
148 154 4.858680 TGTGGTTGCGCCGTCCAA 62.859 61.111 14.96 0.00 41.21 3.53
149 155 3.361977 GTGGTTGCGCCGTCCAAT 61.362 61.111 14.96 0.00 41.21 3.16
150 156 3.053291 TGGTTGCGCCGTCCAATC 61.053 61.111 4.18 0.00 41.21 2.67
172 198 2.958576 GCCCGCTCCTAGATCTCG 59.041 66.667 0.00 0.00 0.00 4.04
175 201 1.679336 GCCCGCTCCTAGATCTCGATA 60.679 57.143 0.00 0.00 0.00 2.92
184 210 3.192422 CCTAGATCTCGATAGGGCTGTTG 59.808 52.174 0.00 0.00 35.81 3.33
190 216 0.748005 CGATAGGGCTGTTGGGTTGG 60.748 60.000 0.00 0.00 0.00 3.77
194 220 0.326143 AGGGCTGTTGGGTTGGTTTT 60.326 50.000 0.00 0.00 0.00 2.43
196 222 1.474320 GGGCTGTTGGGTTGGTTTTTC 60.474 52.381 0.00 0.00 0.00 2.29
226 252 1.132500 TTTTTGGCCCCAATCGGTTT 58.868 45.000 0.00 0.00 35.70 3.27
227 253 0.394565 TTTTGGCCCCAATCGGTTTG 59.605 50.000 0.00 0.00 35.70 2.93
228 254 0.760945 TTTGGCCCCAATCGGTTTGT 60.761 50.000 0.00 0.00 35.70 2.83
229 255 0.760945 TTGGCCCCAATCGGTTTGTT 60.761 50.000 0.00 0.00 33.15 2.83
230 256 0.760945 TGGCCCCAATCGGTTTGTTT 60.761 50.000 0.00 0.00 33.15 2.83
231 257 0.394938 GGCCCCAATCGGTTTGTTTT 59.605 50.000 0.00 0.00 33.15 2.43
232 258 1.507562 GCCCCAATCGGTTTGTTTTG 58.492 50.000 0.00 0.00 33.15 2.44
233 259 1.202592 GCCCCAATCGGTTTGTTTTGT 60.203 47.619 0.00 0.00 33.15 2.83
234 260 2.478831 CCCCAATCGGTTTGTTTTGTG 58.521 47.619 0.00 0.00 33.15 3.33
235 261 1.864082 CCCAATCGGTTTGTTTTGTGC 59.136 47.619 0.00 0.00 33.15 4.57
236 262 1.520590 CCAATCGGTTTGTTTTGTGCG 59.479 47.619 0.00 0.00 33.15 5.34
237 263 1.520590 CAATCGGTTTGTTTTGTGCGG 59.479 47.619 0.00 0.00 0.00 5.69
238 264 0.741915 ATCGGTTTGTTTTGTGCGGT 59.258 45.000 0.00 0.00 0.00 5.68
239 265 0.179161 TCGGTTTGTTTTGTGCGGTG 60.179 50.000 0.00 0.00 0.00 4.94
240 266 1.142778 CGGTTTGTTTTGTGCGGTGG 61.143 55.000 0.00 0.00 0.00 4.61
241 267 0.173708 GGTTTGTTTTGTGCGGTGGA 59.826 50.000 0.00 0.00 0.00 4.02
242 268 1.202475 GGTTTGTTTTGTGCGGTGGAT 60.202 47.619 0.00 0.00 0.00 3.41
243 269 1.857837 GTTTGTTTTGTGCGGTGGATG 59.142 47.619 0.00 0.00 0.00 3.51
244 270 1.393603 TTGTTTTGTGCGGTGGATGA 58.606 45.000 0.00 0.00 0.00 2.92
245 271 1.614996 TGTTTTGTGCGGTGGATGAT 58.385 45.000 0.00 0.00 0.00 2.45
246 272 1.269174 TGTTTTGTGCGGTGGATGATG 59.731 47.619 0.00 0.00 0.00 3.07
247 273 1.539388 GTTTTGTGCGGTGGATGATGA 59.461 47.619 0.00 0.00 0.00 2.92
248 274 1.452110 TTTGTGCGGTGGATGATGAG 58.548 50.000 0.00 0.00 0.00 2.90
249 275 0.324614 TTGTGCGGTGGATGATGAGT 59.675 50.000 0.00 0.00 0.00 3.41
250 276 0.324614 TGTGCGGTGGATGATGAGTT 59.675 50.000 0.00 0.00 0.00 3.01
251 277 1.271325 TGTGCGGTGGATGATGAGTTT 60.271 47.619 0.00 0.00 0.00 2.66
252 278 2.027653 TGTGCGGTGGATGATGAGTTTA 60.028 45.455 0.00 0.00 0.00 2.01
253 279 2.609459 GTGCGGTGGATGATGAGTTTAG 59.391 50.000 0.00 0.00 0.00 1.85
254 280 2.213499 GCGGTGGATGATGAGTTTAGG 58.787 52.381 0.00 0.00 0.00 2.69
255 281 2.420129 GCGGTGGATGATGAGTTTAGGT 60.420 50.000 0.00 0.00 0.00 3.08
264 290 3.071892 TGATGAGTTTAGGTGGTTTCCGT 59.928 43.478 0.00 0.00 0.00 4.69
270 296 2.307496 TAGGTGGTTTCCGTACCTGA 57.693 50.000 5.46 0.00 44.22 3.86
272 298 1.982958 AGGTGGTTTCCGTACCTGATT 59.017 47.619 0.00 0.00 42.95 2.57
276 302 1.339727 GGTTTCCGTACCTGATTGGCT 60.340 52.381 0.00 0.00 40.22 4.75
278 304 1.271856 TTCCGTACCTGATTGGCTGA 58.728 50.000 0.00 0.00 40.22 4.26
286 312 2.494870 ACCTGATTGGCTGATTTTCTGC 59.505 45.455 0.00 0.00 40.10 4.26
287 313 2.758979 CCTGATTGGCTGATTTTCTGCT 59.241 45.455 6.38 0.00 40.57 4.24
291 317 6.406624 CCTGATTGGCTGATTTTCTGCTAATT 60.407 38.462 15.39 4.35 46.52 1.40
292 318 6.567050 TGATTGGCTGATTTTCTGCTAATTC 58.433 36.000 15.39 10.88 46.52 2.17
295 321 3.243201 GGCTGATTTTCTGCTAATTCGGG 60.243 47.826 6.38 0.00 40.57 5.14
296 322 3.378427 GCTGATTTTCTGCTAATTCGGGT 59.622 43.478 0.00 0.00 38.17 5.28
297 323 4.731773 GCTGATTTTCTGCTAATTCGGGTG 60.732 45.833 0.00 0.00 38.17 4.61
299 325 4.394920 TGATTTTCTGCTAATTCGGGTGTC 59.605 41.667 0.00 0.00 0.00 3.67
322 348 2.561478 TATTGGGGATTCGCTTAGGC 57.439 50.000 0.40 0.00 0.00 3.93
350 376 1.005975 CGCGATTTGAACCGATCTGTC 60.006 52.381 0.00 0.00 0.00 3.51
358 384 4.847516 CCGATCTGTCCGCGCGAA 62.848 66.667 34.63 8.78 0.00 4.70
381 407 7.148787 CGAACAGTTTAGATGAGTACCTTGTTC 60.149 40.741 0.00 0.00 38.05 3.18
393 420 5.180271 AGTACCTTGTTCTTTTGTTGTCGA 58.820 37.500 0.00 0.00 0.00 4.20
395 422 5.169836 ACCTTGTTCTTTTGTTGTCGATC 57.830 39.130 0.00 0.00 0.00 3.69
409 436 1.457303 GTCGATCTATGCGATTGTGGC 59.543 52.381 0.00 0.00 40.19 5.01
416 443 0.527565 ATGCGATTGTGGCTTGGTTC 59.472 50.000 0.00 0.00 0.00 3.62
418 445 0.527565 GCGATTGTGGCTTGGTTCAT 59.472 50.000 0.00 0.00 0.00 2.57
419 446 1.468054 GCGATTGTGGCTTGGTTCATC 60.468 52.381 0.00 0.00 0.00 2.92
432 459 5.824624 GCTTGGTTCATCTATTTCCTGATGA 59.175 40.000 0.00 0.00 44.79 2.92
442 471 9.138062 CATCTATTTCCTGATGAATAGAACGAG 57.862 37.037 9.16 0.00 41.69 4.18
443 472 8.465273 TCTATTTCCTGATGAATAGAACGAGA 57.535 34.615 0.00 0.00 31.67 4.04
473 502 4.082571 AGGACATGCTGTTTGTGATTTAGC 60.083 41.667 0.00 0.00 35.06 3.09
641 689 5.022021 GCACTTAATTCGATGTTGTACTGC 58.978 41.667 0.00 0.00 0.00 4.40
679 727 5.468540 TTGCGTGACTATATCTGCCTTAT 57.531 39.130 0.00 0.00 0.00 1.73
696 744 8.702819 TCTGCCTTATATTCCATGATGATCTAG 58.297 37.037 0.00 0.00 0.00 2.43
792 840 5.128919 AGAAACTCAGATGCAACTTCTGTT 58.871 37.500 13.97 7.64 41.13 3.16
799 847 2.340210 TGCAACTTCTGTTAGCACCA 57.660 45.000 0.00 0.00 36.27 4.17
804 852 4.319549 GCAACTTCTGTTAGCACCAAGTAC 60.320 45.833 1.02 0.00 34.60 2.73
856 904 4.098654 TCAGTGGCTCAGTTCTAGCTTATC 59.901 45.833 0.00 0.00 39.97 1.75
857 905 4.099266 CAGTGGCTCAGTTCTAGCTTATCT 59.901 45.833 0.00 0.00 39.97 1.98
863 911 5.983118 GCTCAGTTCTAGCTTATCTTCTTCC 59.017 44.000 0.00 0.00 37.01 3.46
878 926 5.634118 TCTTCTTCCCAGAATGAATGTTGT 58.366 37.500 0.00 0.00 38.42 3.32
912 961 2.487762 ACGTATTGCTGGATGGTTTGTG 59.512 45.455 0.00 0.00 0.00 3.33
915 964 4.496341 CGTATTGCTGGATGGTTTGTGATC 60.496 45.833 0.00 0.00 0.00 2.92
963 1012 7.831193 ACACATCAAGACAATAAATAGAGCCTT 59.169 33.333 0.00 0.00 0.00 4.35
1089 1145 3.209410 GGAATCACACCTGCCAATCTAG 58.791 50.000 0.00 0.00 0.00 2.43
1091 1147 4.445448 GGAATCACACCTGCCAATCTAGAT 60.445 45.833 0.00 0.00 0.00 1.98
1118 1176 9.014297 CAATTTGAGTCCTTAACCTGTAGATTT 57.986 33.333 0.00 0.00 0.00 2.17
1124 1182 9.498176 GAGTCCTTAACCTGTAGATTTTGTTTA 57.502 33.333 0.00 0.00 0.00 2.01
1140 1198 9.756461 GATTTTGTTTATTTACGTTCTCTCTCC 57.244 33.333 0.00 0.00 0.00 3.71
1142 1200 5.404946 TGTTTATTTACGTTCTCTCTCCCG 58.595 41.667 0.00 0.00 0.00 5.14
1156 1214 4.028131 TCTCTCCCGCTGAATTAACCTAA 58.972 43.478 0.00 0.00 0.00 2.69
1164 1222 5.177696 CCGCTGAATTAACCTAATAGACTGC 59.822 44.000 0.00 0.00 0.00 4.40
1197 1255 7.558161 TCTAATCTCATTAACCAACAGCATG 57.442 36.000 0.00 0.00 46.00 4.06
1303 1361 3.458189 GTGGCACAGGTACATAGCTTAG 58.542 50.000 13.86 0.00 41.80 2.18
1314 1372 6.652481 AGGTACATAGCTTAGCTGCATTAATG 59.348 38.462 17.97 13.28 40.10 1.90
1485 1703 9.469807 CTAACAGAATACCACATCTAGTTGATC 57.530 37.037 7.81 0.00 32.05 2.92
1496 1714 8.633561 CCACATCTAGTTGATCATGAGTTAGTA 58.366 37.037 7.81 0.00 32.05 1.82
1497 1715 9.676195 CACATCTAGTTGATCATGAGTTAGTAG 57.324 37.037 7.81 5.57 32.05 2.57
1567 1785 2.696187 CCTAACCTTCTCTAGAGGTGGC 59.304 54.545 19.67 0.00 35.88 5.01
1568 1786 1.187087 AACCTTCTCTAGAGGTGGCG 58.813 55.000 19.67 5.91 35.88 5.69
1622 1849 2.932614 GTGTGTCCACAGATGACTATGC 59.067 50.000 0.00 0.00 42.74 3.14
1635 1864 2.749076 TGACTATGCCACAGAAACATGC 59.251 45.455 0.00 0.00 0.00 4.06
1651 1881 2.801679 ACATGCATCTTTTTGGTTTGCG 59.198 40.909 0.00 0.00 36.11 4.85
1693 1926 0.038166 CCTCTGGTTGCCTTGCCTAA 59.962 55.000 0.00 0.00 0.00 2.69
1694 1927 1.457346 CTCTGGTTGCCTTGCCTAAG 58.543 55.000 0.00 0.00 0.00 2.18
1699 1932 4.412199 TCTGGTTGCCTTGCCTAAGTATAT 59.588 41.667 0.00 0.00 31.80 0.86
1721 1954 3.578716 TCCTCTACCCAGAAGTTGACTTG 59.421 47.826 0.30 0.00 36.11 3.16
1852 2085 2.103263 GAGTCTGACAACTGTTCAGGGT 59.897 50.000 10.88 2.45 32.76 4.34
1853 2086 2.103263 AGTCTGACAACTGTTCAGGGTC 59.897 50.000 10.88 15.07 32.76 4.46
1965 2198 1.178276 CAGGTACAGCGAGGTTCTCT 58.822 55.000 0.00 0.00 0.00 3.10
1967 2200 2.028930 CAGGTACAGCGAGGTTCTCTTT 60.029 50.000 0.00 0.00 0.00 2.52
1994 2227 6.500684 TGTTGGTAGCAAAATTCTCTCATC 57.499 37.500 9.30 0.00 0.00 2.92
1998 2231 8.394121 GTTGGTAGCAAAATTCTCTCATCTAAG 58.606 37.037 9.30 0.00 0.00 2.18
1999 2232 7.624549 TGGTAGCAAAATTCTCTCATCTAAGT 58.375 34.615 0.00 0.00 0.00 2.24
2080 2313 6.500041 TCAGCGTAAAAATGTTGCTACTTTT 58.500 32.000 6.38 6.38 34.25 2.27
2163 2400 9.825972 TCGTTCATCTTCTTAATTTGACAATTC 57.174 29.630 0.00 0.00 34.29 2.17
2397 2635 3.698539 TGTTGATGCAAGTTGTCCTTCAA 59.301 39.130 4.48 6.28 0.00 2.69
2492 2730 4.334759 CAGGCTTATCTTCTCATGGTTGTG 59.665 45.833 0.00 0.00 0.00 3.33
2493 2731 4.018960 AGGCTTATCTTCTCATGGTTGTGT 60.019 41.667 0.00 0.00 0.00 3.72
2494 2732 4.095483 GGCTTATCTTCTCATGGTTGTGTG 59.905 45.833 0.00 0.00 0.00 3.82
2495 2733 4.437930 GCTTATCTTCTCATGGTTGTGTGC 60.438 45.833 0.00 0.00 0.00 4.57
2496 2734 2.636647 TCTTCTCATGGTTGTGTGCA 57.363 45.000 0.00 0.00 0.00 4.57
2497 2735 3.144657 TCTTCTCATGGTTGTGTGCAT 57.855 42.857 0.00 0.00 0.00 3.96
2498 2736 3.489355 TCTTCTCATGGTTGTGTGCATT 58.511 40.909 0.00 0.00 0.00 3.56
2499 2737 3.253921 TCTTCTCATGGTTGTGTGCATTG 59.746 43.478 0.00 0.00 0.00 2.82
2500 2738 2.585330 TCTCATGGTTGTGTGCATTGT 58.415 42.857 0.00 0.00 0.00 2.71
2566 2805 4.778534 ATTTTCTCATGGTTGTGCTCAG 57.221 40.909 0.00 0.00 0.00 3.35
2570 2809 0.392706 TCATGGTTGTGCTCAGTCGT 59.607 50.000 0.00 0.00 0.00 4.34
2576 2815 0.463654 TTGTGCTCAGTCGTTGCCTT 60.464 50.000 0.00 0.00 0.00 4.35
2605 2844 2.434336 GGCACTCCCTCCTTTTTGTTTT 59.566 45.455 0.00 0.00 0.00 2.43
2607 2846 3.871006 GCACTCCCTCCTTTTTGTTTTTG 59.129 43.478 0.00 0.00 0.00 2.44
2608 2847 4.382577 GCACTCCCTCCTTTTTGTTTTTGA 60.383 41.667 0.00 0.00 0.00 2.69
2609 2848 5.351458 CACTCCCTCCTTTTTGTTTTTGAG 58.649 41.667 0.00 0.00 0.00 3.02
2610 2849 4.405680 ACTCCCTCCTTTTTGTTTTTGAGG 59.594 41.667 0.00 0.00 39.25 3.86
2612 2851 4.071961 CCTCCTTTTTGTTTTTGAGGGG 57.928 45.455 0.00 0.00 36.56 4.79
2613 2852 3.454447 CCTCCTTTTTGTTTTTGAGGGGT 59.546 43.478 0.00 0.00 36.56 4.95
2614 2853 4.080582 CCTCCTTTTTGTTTTTGAGGGGTT 60.081 41.667 0.00 0.00 36.56 4.11
2615 2854 5.092554 TCCTTTTTGTTTTTGAGGGGTTC 57.907 39.130 0.00 0.00 0.00 3.62
2616 2855 4.080807 TCCTTTTTGTTTTTGAGGGGTTCC 60.081 41.667 0.00 0.00 0.00 3.62
2618 2857 5.496556 CTTTTTGTTTTTGAGGGGTTCCTT 58.503 37.500 0.00 0.00 45.05 3.36
2619 2858 5.506730 TTTTGTTTTTGAGGGGTTCCTTT 57.493 34.783 0.00 0.00 45.05 3.11
2620 2859 5.506730 TTTGTTTTTGAGGGGTTCCTTTT 57.493 34.783 0.00 0.00 45.05 2.27
2621 2860 5.506730 TTGTTTTTGAGGGGTTCCTTTTT 57.493 34.783 0.00 0.00 45.05 1.94
2645 2884 7.990541 TTTCTTTTCTTGACATGACACATTG 57.009 32.000 0.00 0.00 0.00 2.82
2646 2885 6.075762 TCTTTTCTTGACATGACACATTGG 57.924 37.500 0.00 0.00 0.00 3.16
2647 2886 5.593909 TCTTTTCTTGACATGACACATTGGT 59.406 36.000 0.00 0.00 0.00 3.67
2663 2902 7.545362 CACATTGGTGGAGATAGTTTCTTAG 57.455 40.000 0.00 0.00 41.45 2.18
2664 2903 6.540189 CACATTGGTGGAGATAGTTTCTTAGG 59.460 42.308 0.00 0.00 41.45 2.69
2665 2904 5.693769 TTGGTGGAGATAGTTTCTTAGGG 57.306 43.478 0.00 0.00 33.74 3.53
2666 2905 3.454812 TGGTGGAGATAGTTTCTTAGGGC 59.545 47.826 0.00 0.00 33.74 5.19
2667 2906 3.181453 GGTGGAGATAGTTTCTTAGGGCC 60.181 52.174 0.00 0.00 33.74 5.80
2668 2907 3.454812 GTGGAGATAGTTTCTTAGGGCCA 59.545 47.826 6.18 0.00 33.74 5.36
2669 2908 4.103311 GTGGAGATAGTTTCTTAGGGCCAT 59.897 45.833 6.18 0.00 33.74 4.40
2670 2909 4.348168 TGGAGATAGTTTCTTAGGGCCATC 59.652 45.833 6.18 0.00 33.74 3.51
2671 2910 4.595350 GGAGATAGTTTCTTAGGGCCATCT 59.405 45.833 6.18 0.97 33.74 2.90
2672 2911 5.780793 GGAGATAGTTTCTTAGGGCCATCTA 59.219 44.000 6.18 0.00 33.74 1.98
2673 2912 6.071051 GGAGATAGTTTCTTAGGGCCATCTAG 60.071 46.154 6.18 0.00 33.74 2.43
2674 2913 6.386284 AGATAGTTTCTTAGGGCCATCTAGT 58.614 40.000 6.18 0.00 0.00 2.57
2675 2914 6.847036 AGATAGTTTCTTAGGGCCATCTAGTT 59.153 38.462 6.18 0.00 0.00 2.24
2676 2915 5.780958 AGTTTCTTAGGGCCATCTAGTTT 57.219 39.130 6.18 0.00 0.00 2.66
2677 2916 6.140968 AGTTTCTTAGGGCCATCTAGTTTT 57.859 37.500 6.18 0.00 0.00 2.43
2678 2917 7.266905 AGTTTCTTAGGGCCATCTAGTTTTA 57.733 36.000 6.18 0.00 0.00 1.52
2679 2918 7.696017 AGTTTCTTAGGGCCATCTAGTTTTAA 58.304 34.615 6.18 0.00 0.00 1.52
2680 2919 7.829706 AGTTTCTTAGGGCCATCTAGTTTTAAG 59.170 37.037 6.18 1.47 0.00 1.85
2681 2920 5.681639 TCTTAGGGCCATCTAGTTTTAAGC 58.318 41.667 6.18 0.00 0.00 3.09
2682 2921 5.428783 TCTTAGGGCCATCTAGTTTTAAGCT 59.571 40.000 6.18 0.00 0.00 3.74
2683 2922 4.592997 AGGGCCATCTAGTTTTAAGCTT 57.407 40.909 6.18 3.48 0.00 3.74
2684 2923 4.273318 AGGGCCATCTAGTTTTAAGCTTG 58.727 43.478 9.86 0.00 0.00 4.01
2685 2924 3.381590 GGGCCATCTAGTTTTAAGCTTGG 59.618 47.826 9.86 0.00 0.00 3.61
2686 2925 3.181486 GGCCATCTAGTTTTAAGCTTGGC 60.181 47.826 9.86 12.54 45.92 4.52
2687 2926 3.443681 GCCATCTAGTTTTAAGCTTGGCA 59.556 43.478 15.01 0.00 45.93 4.92
2688 2927 4.082245 GCCATCTAGTTTTAAGCTTGGCAA 60.082 41.667 15.01 0.00 45.93 4.52
2689 2928 5.394553 GCCATCTAGTTTTAAGCTTGGCAAT 60.395 40.000 15.01 0.00 45.93 3.56
2690 2929 6.038356 CCATCTAGTTTTAAGCTTGGCAATG 58.962 40.000 9.86 2.44 0.00 2.82
2691 2930 6.350445 CCATCTAGTTTTAAGCTTGGCAATGT 60.350 38.462 9.86 0.00 0.00 2.71
2692 2931 6.648879 TCTAGTTTTAAGCTTGGCAATGTT 57.351 33.333 9.86 0.00 0.00 2.71
2693 2932 7.049799 TCTAGTTTTAAGCTTGGCAATGTTT 57.950 32.000 9.86 2.42 0.00 2.83
2694 2933 8.172352 TCTAGTTTTAAGCTTGGCAATGTTTA 57.828 30.769 9.86 1.45 0.00 2.01
2695 2934 8.802267 TCTAGTTTTAAGCTTGGCAATGTTTAT 58.198 29.630 9.86 0.00 0.00 1.40
2696 2935 7.889589 AGTTTTAAGCTTGGCAATGTTTATC 57.110 32.000 9.86 0.01 0.00 1.75
2697 2936 7.441017 AGTTTTAAGCTTGGCAATGTTTATCA 58.559 30.769 9.86 0.00 0.00 2.15
2704 2943 5.521372 GCTTGGCAATGTTTATCAGGAAATC 59.479 40.000 0.00 0.00 0.00 2.17
2717 2956 3.528905 TCAGGAAATCATTGGGATCACCT 59.471 43.478 0.00 0.00 40.03 4.00
2720 2959 3.633986 GGAAATCATTGGGATCACCTGAC 59.366 47.826 0.00 0.00 41.11 3.51
2724 2963 0.833287 ATTGGGATCACCTGACGGAG 59.167 55.000 0.00 0.00 41.11 4.63
2749 2988 0.179127 CACGTGCGTCCATCATCTCT 60.179 55.000 0.82 0.00 0.00 3.10
2782 3021 6.367161 TGGATCAGATTTTAATGAGATGGCA 58.633 36.000 0.00 0.00 0.00 4.92
2802 3041 5.789710 GCAAGAAGCAACGTATTACCTAA 57.210 39.130 0.00 0.00 44.79 2.69
2820 3064 3.989817 CCTAATTTTTGCAACTGAGTGGC 59.010 43.478 4.67 4.67 32.23 5.01
2825 3069 1.473258 TTGCAACTGAGTGGCTGTTT 58.527 45.000 13.90 0.00 36.64 2.83
2826 3070 1.473258 TGCAACTGAGTGGCTGTTTT 58.527 45.000 13.90 0.00 36.64 2.43
2850 3094 1.525995 CTCCCACCGCAACAACTGT 60.526 57.895 0.00 0.00 0.00 3.55
2851 3095 1.785041 CTCCCACCGCAACAACTGTG 61.785 60.000 0.00 0.00 35.14 3.66
2852 3096 2.118404 CCCACCGCAACAACTGTGT 61.118 57.895 0.00 0.00 40.75 3.72
2853 3097 1.063972 CCACCGCAACAACTGTGTG 59.936 57.895 0.00 0.00 38.27 3.82
2854 3098 1.653094 CCACCGCAACAACTGTGTGT 61.653 55.000 0.00 0.00 38.27 3.72
2855 3099 0.170116 CACCGCAACAACTGTGTGTT 59.830 50.000 3.57 3.57 42.48 3.32
2862 3106 3.597072 AACTGTGTGTTGCGGCAA 58.403 50.000 12.11 12.11 37.52 4.52
2863 3107 1.138671 AACTGTGTGTTGCGGCAAC 59.861 52.632 32.94 32.94 43.78 4.17
2864 3108 1.312371 AACTGTGTGTTGCGGCAACT 61.312 50.000 36.75 19.44 43.85 3.16
2884 3128 3.136443 ACTGTGTGTTGAGGGATCTGAAA 59.864 43.478 0.00 0.00 0.00 2.69
2896 3140 3.941704 GATCTGAAACTGGATCCCCTT 57.058 47.619 9.90 0.00 34.09 3.95
2937 3181 1.376037 CCTCCAAAGCACTCCCGAC 60.376 63.158 0.00 0.00 0.00 4.79
2939 3183 3.423154 CCAAAGCACTCCCGACGC 61.423 66.667 0.00 0.00 0.00 5.19
2940 3184 3.777925 CAAAGCACTCCCGACGCG 61.778 66.667 3.53 3.53 0.00 6.01
2984 3240 3.283684 CGTCTTGCCACCGCCAAA 61.284 61.111 0.00 0.00 0.00 3.28
3001 3257 2.937959 AAACACCCCCGTTGTGCCAT 62.938 55.000 0.00 0.00 37.22 4.40
3008 3264 2.108514 CCGTTGTGCCATCGCTGAT 61.109 57.895 0.00 0.00 35.36 2.90
3010 3266 1.638388 CGTTGTGCCATCGCTGATGT 61.638 55.000 14.50 0.00 38.28 3.06
3013 3270 2.891936 TGCCATCGCTGATGTCGC 60.892 61.111 14.50 12.35 38.28 5.19
3022 3279 3.971453 CTGATGTCGCCGAGCACGT 62.971 63.158 2.18 0.00 37.88 4.49
3045 3302 4.955774 GCCGTCGTGGTTGTCGGT 62.956 66.667 0.00 0.00 44.07 4.69
3049 3306 4.986587 TCGTGGTTGTCGGTCGCG 62.987 66.667 0.00 0.00 35.98 5.87
3076 3347 1.759445 ACCATCCATCCTCTTCTCACG 59.241 52.381 0.00 0.00 0.00 4.35
3082 3353 3.515502 TCCATCCTCTTCTCACGTTCATT 59.484 43.478 0.00 0.00 0.00 2.57
3093 3365 0.606604 ACGTTCATTAGACCAGGCGT 59.393 50.000 0.00 0.00 0.00 5.68
3172 3447 2.631984 CTCCATCGCGATCGTCGA 59.368 61.111 27.58 27.58 43.74 4.20
3173 3448 1.207848 CTCCATCGCGATCGTCGAT 59.792 57.895 28.93 28.93 46.27 3.59
3203 3478 1.912043 CACCATCAACCCTCTCTCCTT 59.088 52.381 0.00 0.00 0.00 3.36
3214 3489 2.297701 CTCTCTCCTTCTCCCTCTTCG 58.702 57.143 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.798682 GGAGGGCGAGGAGGGGAA 62.799 72.222 0.00 0.00 0.00 3.97
59 62 1.537562 GGAAACGTAGAATCGGCCGAT 60.538 52.381 34.60 34.60 36.23 4.18
71 74 2.295602 GGGGGAGCAGGGAAACGTA 61.296 63.158 0.00 0.00 0.00 3.57
91 94 1.065928 ACCGCTAGAAATCGAGCCG 59.934 57.895 9.48 6.22 40.78 5.52
94 97 1.405821 AGTCCACCGCTAGAAATCGAG 59.594 52.381 0.00 0.00 0.00 4.04
146 152 2.142357 TAGGAGCGGGCGATCGATTG 62.142 60.000 21.57 8.40 0.00 2.67
147 153 1.867919 CTAGGAGCGGGCGATCGATT 61.868 60.000 21.57 0.00 0.00 3.34
148 154 2.282251 TAGGAGCGGGCGATCGAT 60.282 61.111 21.57 0.00 0.00 3.59
149 155 2.749706 ATCTAGGAGCGGGCGATCGA 62.750 60.000 21.57 0.00 0.00 3.59
150 156 2.259875 GATCTAGGAGCGGGCGATCG 62.260 65.000 11.69 11.69 0.00 3.69
172 198 0.331616 ACCAACCCAACAGCCCTATC 59.668 55.000 0.00 0.00 0.00 2.08
175 201 0.326143 AAAACCAACCCAACAGCCCT 60.326 50.000 0.00 0.00 0.00 5.19
184 210 0.528901 GCACACCGAAAAACCAACCC 60.529 55.000 0.00 0.00 0.00 4.11
226 252 1.269174 CATCATCCACCGCACAAAACA 59.731 47.619 0.00 0.00 0.00 2.83
227 253 1.539388 TCATCATCCACCGCACAAAAC 59.461 47.619 0.00 0.00 0.00 2.43
228 254 1.811965 CTCATCATCCACCGCACAAAA 59.188 47.619 0.00 0.00 0.00 2.44
229 255 1.271325 ACTCATCATCCACCGCACAAA 60.271 47.619 0.00 0.00 0.00 2.83
230 256 0.324614 ACTCATCATCCACCGCACAA 59.675 50.000 0.00 0.00 0.00 3.33
231 257 0.324614 AACTCATCATCCACCGCACA 59.675 50.000 0.00 0.00 0.00 4.57
232 258 1.453155 AAACTCATCATCCACCGCAC 58.547 50.000 0.00 0.00 0.00 5.34
233 259 2.419990 CCTAAACTCATCATCCACCGCA 60.420 50.000 0.00 0.00 0.00 5.69
234 260 2.213499 CCTAAACTCATCATCCACCGC 58.787 52.381 0.00 0.00 0.00 5.68
235 261 3.198068 CACCTAAACTCATCATCCACCG 58.802 50.000 0.00 0.00 0.00 4.94
236 262 3.054361 ACCACCTAAACTCATCATCCACC 60.054 47.826 0.00 0.00 0.00 4.61
237 263 4.222124 ACCACCTAAACTCATCATCCAC 57.778 45.455 0.00 0.00 0.00 4.02
238 264 4.927267 AACCACCTAAACTCATCATCCA 57.073 40.909 0.00 0.00 0.00 3.41
239 265 4.640647 GGAAACCACCTAAACTCATCATCC 59.359 45.833 0.00 0.00 0.00 3.51
240 266 4.332819 CGGAAACCACCTAAACTCATCATC 59.667 45.833 0.00 0.00 0.00 2.92
241 267 4.261801 CGGAAACCACCTAAACTCATCAT 58.738 43.478 0.00 0.00 0.00 2.45
242 268 3.071892 ACGGAAACCACCTAAACTCATCA 59.928 43.478 0.00 0.00 0.00 3.07
243 269 3.671716 ACGGAAACCACCTAAACTCATC 58.328 45.455 0.00 0.00 0.00 2.92
244 270 3.782656 ACGGAAACCACCTAAACTCAT 57.217 42.857 0.00 0.00 0.00 2.90
245 271 3.244181 GGTACGGAAACCACCTAAACTCA 60.244 47.826 0.00 0.00 39.50 3.41
246 272 3.007290 AGGTACGGAAACCACCTAAACTC 59.993 47.826 6.63 0.00 42.40 3.01
247 273 2.974794 AGGTACGGAAACCACCTAAACT 59.025 45.455 6.63 0.00 42.40 2.66
248 274 3.069289 CAGGTACGGAAACCACCTAAAC 58.931 50.000 6.63 0.00 42.40 2.01
249 275 2.971330 TCAGGTACGGAAACCACCTAAA 59.029 45.455 6.63 0.00 42.40 1.85
250 276 2.607499 TCAGGTACGGAAACCACCTAA 58.393 47.619 6.63 0.00 42.40 2.69
251 277 2.307496 TCAGGTACGGAAACCACCTA 57.693 50.000 6.63 0.00 42.40 3.08
252 278 1.652947 ATCAGGTACGGAAACCACCT 58.347 50.000 6.63 0.00 42.40 4.00
253 279 2.081462 CAATCAGGTACGGAAACCACC 58.919 52.381 6.63 0.00 42.40 4.61
254 280 2.081462 CCAATCAGGTACGGAAACCAC 58.919 52.381 6.63 0.00 42.40 4.16
255 281 1.612199 GCCAATCAGGTACGGAAACCA 60.612 52.381 6.63 0.00 42.40 3.67
264 290 3.696051 GCAGAAAATCAGCCAATCAGGTA 59.304 43.478 0.00 0.00 40.61 3.08
270 296 5.450965 CCGAATTAGCAGAAAATCAGCCAAT 60.451 40.000 0.00 0.00 28.14 3.16
272 298 3.378112 CCGAATTAGCAGAAAATCAGCCA 59.622 43.478 0.00 0.00 28.14 4.75
276 302 4.331968 ACACCCGAATTAGCAGAAAATCA 58.668 39.130 0.00 0.00 0.00 2.57
278 304 4.396166 CAGACACCCGAATTAGCAGAAAAT 59.604 41.667 0.00 0.00 0.00 1.82
286 312 4.997395 CCCAATATCAGACACCCGAATTAG 59.003 45.833 0.00 0.00 0.00 1.73
287 313 4.202419 CCCCAATATCAGACACCCGAATTA 60.202 45.833 0.00 0.00 0.00 1.40
291 317 1.128200 CCCCAATATCAGACACCCGA 58.872 55.000 0.00 0.00 0.00 5.14
292 318 1.128200 TCCCCAATATCAGACACCCG 58.872 55.000 0.00 0.00 0.00 5.28
295 321 2.808543 GCGAATCCCCAATATCAGACAC 59.191 50.000 0.00 0.00 0.00 3.67
296 322 2.705658 AGCGAATCCCCAATATCAGACA 59.294 45.455 0.00 0.00 0.00 3.41
297 323 3.409026 AGCGAATCCCCAATATCAGAC 57.591 47.619 0.00 0.00 0.00 3.51
299 325 4.256920 CCTAAGCGAATCCCCAATATCAG 58.743 47.826 0.00 0.00 0.00 2.90
323 349 4.096558 TTCAAATCGCGGCCGCAC 62.097 61.111 45.26 21.62 42.06 5.34
329 355 0.301687 CAGATCGGTTCAAATCGCGG 59.698 55.000 6.13 0.00 31.28 6.46
350 376 0.025001 CATCTAAACTGTTCGCGCGG 59.975 55.000 31.69 16.53 0.00 6.46
358 384 7.304497 AGAACAAGGTACTCATCTAAACTGT 57.696 36.000 0.00 0.00 38.49 3.55
381 407 4.840401 TCGCATAGATCGACAACAAAAG 57.160 40.909 0.00 0.00 0.00 2.27
393 420 2.224606 CCAAGCCACAATCGCATAGAT 58.775 47.619 0.00 0.00 42.43 1.98
395 422 1.382522 ACCAAGCCACAATCGCATAG 58.617 50.000 0.00 0.00 0.00 2.23
416 443 9.138062 CTCGTTCTATTCATCAGGAAATAGATG 57.862 37.037 5.84 0.00 42.25 2.90
418 445 8.465273 TCTCGTTCTATTCATCAGGAAATAGA 57.535 34.615 1.67 1.67 39.39 1.98
419 446 9.534565 TTTCTCGTTCTATTCATCAGGAAATAG 57.465 33.333 0.00 0.00 39.39 1.73
432 459 9.209175 GCATGTCCTAATATTTCTCGTTCTATT 57.791 33.333 0.00 0.00 0.00 1.73
473 502 5.550290 ACCTAAAATCAGCCCACAAATTTG 58.450 37.500 16.67 16.67 0.00 2.32
641 689 2.427453 ACGCAATACAGAGGGTACTCAG 59.573 50.000 0.00 0.00 46.44 3.35
653 701 4.280929 AGGCAGATATAGTCACGCAATACA 59.719 41.667 0.00 0.00 31.24 2.29
760 808 9.160496 AGTTGCATCTGAGTTTCTTCTTATAAG 57.840 33.333 6.11 6.11 0.00 1.73
761 809 9.507329 AAGTTGCATCTGAGTTTCTTCTTATAA 57.493 29.630 0.00 0.00 0.00 0.98
762 810 9.155975 GAAGTTGCATCTGAGTTTCTTCTTATA 57.844 33.333 0.00 0.00 0.00 0.98
763 811 7.882271 AGAAGTTGCATCTGAGTTTCTTCTTAT 59.118 33.333 0.00 0.00 37.63 1.73
764 812 7.172190 CAGAAGTTGCATCTGAGTTTCTTCTTA 59.828 37.037 9.76 0.00 45.74 2.10
774 822 3.999001 TGCTAACAGAAGTTGCATCTGAG 59.001 43.478 20.01 10.40 45.74 3.35
792 840 7.986704 AGATAGTAGGATAGTACTTGGTGCTA 58.013 38.462 0.00 0.28 35.45 3.49
804 852 9.688091 TGCAATAGTTCCTAGATAGTAGGATAG 57.312 37.037 1.61 0.00 42.74 2.08
856 904 5.972107 ACAACATTCATTCTGGGAAGAAG 57.028 39.130 0.00 0.00 0.00 2.85
857 905 8.421249 AATTACAACATTCATTCTGGGAAGAA 57.579 30.769 0.00 0.00 0.00 2.52
863 911 9.865321 AATTCTGAATTACAACATTCATTCTGG 57.135 29.630 13.69 0.00 41.36 3.86
878 926 8.725405 TCCAGCAATACGTTAATTCTGAATTA 57.275 30.769 16.71 16.71 32.38 1.40
912 961 3.244976 CTGCAAAACATCCCAAACGATC 58.755 45.455 0.00 0.00 0.00 3.69
915 964 1.139163 GCTGCAAAACATCCCAAACG 58.861 50.000 0.00 0.00 0.00 3.60
963 1012 0.187117 TGATTGGCCCCAAACAGACA 59.813 50.000 0.00 0.00 39.55 3.41
1089 1145 8.041323 TCTACAGGTTAAGGACTCAAATTGATC 58.959 37.037 0.00 0.00 0.00 2.92
1091 1147 7.311092 TCTACAGGTTAAGGACTCAAATTGA 57.689 36.000 0.00 0.00 0.00 2.57
1118 1176 5.865552 CGGGAGAGAGAACGTAAATAAACAA 59.134 40.000 0.00 0.00 0.00 2.83
1124 1182 2.100989 AGCGGGAGAGAGAACGTAAAT 58.899 47.619 0.00 0.00 0.00 1.40
1139 1197 5.696724 CAGTCTATTAGGTTAATTCAGCGGG 59.303 44.000 0.00 0.00 0.00 6.13
1140 1198 5.177696 GCAGTCTATTAGGTTAATTCAGCGG 59.822 44.000 0.00 0.00 0.00 5.52
1142 1200 7.213678 AGAGCAGTCTATTAGGTTAATTCAGC 58.786 38.462 0.00 0.00 0.00 4.26
1156 1214 9.752228 TGAGATTAGATATTGAGAGCAGTCTAT 57.248 33.333 0.00 0.00 30.97 1.98
1314 1372 3.370366 GTGATCTGTGACTGTGCATCTTC 59.630 47.826 0.00 0.00 0.00 2.87
1567 1785 7.767745 AATACAGATAAGATATGCATCAGCG 57.232 36.000 0.19 0.00 46.23 5.18
1607 1834 2.169144 TCTGTGGCATAGTCATCTGTGG 59.831 50.000 11.19 0.00 34.16 4.17
1615 1842 2.749076 TGCATGTTTCTGTGGCATAGTC 59.251 45.455 11.19 4.43 0.00 2.59
1622 1849 4.449743 CCAAAAAGATGCATGTTTCTGTGG 59.550 41.667 20.80 21.38 0.00 4.17
1635 1864 4.606961 ACTGTACGCAAACCAAAAAGATG 58.393 39.130 0.00 0.00 0.00 2.90
1671 1904 0.255890 GGCAAGGCAACCAGAGGATA 59.744 55.000 0.00 0.00 37.17 2.59
1693 1926 6.778559 GTCAACTTCTGGGTAGAGGATATACT 59.221 42.308 0.00 0.00 34.38 2.12
1694 1927 6.778559 AGTCAACTTCTGGGTAGAGGATATAC 59.221 42.308 0.00 0.00 34.38 1.47
1699 1932 3.544698 AGTCAACTTCTGGGTAGAGGA 57.455 47.619 0.00 0.00 34.38 3.71
1721 1954 3.798202 ACGGATCTACAAAGAAGATGCC 58.202 45.455 0.00 0.00 38.25 4.40
1852 2085 6.040504 TGTTGTAGCTGTAGTCTTTCTTCAGA 59.959 38.462 0.00 0.00 41.89 3.27
1853 2086 6.216569 TGTTGTAGCTGTAGTCTTTCTTCAG 58.783 40.000 0.00 0.00 42.11 3.02
1967 2200 7.551585 TGAGAGAATTTTGCTACCAACAAAAA 58.448 30.769 5.83 0.00 46.67 1.94
1976 2209 8.386606 CACACTTAGATGAGAGAATTTTGCTAC 58.613 37.037 0.00 0.00 0.00 3.58
1977 2210 8.097038 ACACACTTAGATGAGAGAATTTTGCTA 58.903 33.333 0.00 0.00 0.00 3.49
1978 2211 6.939163 ACACACTTAGATGAGAGAATTTTGCT 59.061 34.615 0.00 0.00 0.00 3.91
1979 2212 7.138692 ACACACTTAGATGAGAGAATTTTGC 57.861 36.000 0.00 0.00 0.00 3.68
1984 2217 9.087871 AGCATATACACACTTAGATGAGAGAAT 57.912 33.333 0.00 0.00 0.00 2.40
1994 2227 9.920133 ATAACTCATCAGCATATACACACTTAG 57.080 33.333 0.00 0.00 0.00 2.18
1998 2231 8.824159 AAGATAACTCATCAGCATATACACAC 57.176 34.615 0.00 0.00 35.96 3.82
1999 2232 8.864087 AGAAGATAACTCATCAGCATATACACA 58.136 33.333 0.00 0.00 35.96 3.72
2080 2313 7.398829 TGGCATTGTAAATTACCTGAACTAGA 58.601 34.615 0.00 0.00 0.00 2.43
2120 2353 1.393539 ACGACGCAACAGTCAATATGC 59.606 47.619 0.00 0.00 40.98 3.14
2163 2400 1.073923 AGTCCAGCCTAACCAAACAGG 59.926 52.381 0.00 0.00 45.67 4.00
2312 2550 0.037882 ACACAGATGCCTCACACGAG 60.038 55.000 0.00 0.00 39.16 4.18
2397 2635 0.525761 GTGGCGCATACAAACCATGT 59.474 50.000 10.83 0.00 46.36 3.21
2495 2733 3.338818 AAACGAACAGAGCACACAATG 57.661 42.857 0.00 0.00 0.00 2.82
2496 2734 4.370364 AAAAACGAACAGAGCACACAAT 57.630 36.364 0.00 0.00 0.00 2.71
2497 2735 3.840890 AAAAACGAACAGAGCACACAA 57.159 38.095 0.00 0.00 0.00 3.33
2530 2769 9.624697 CCATGAGAAAATAAACAAATTCGAGAA 57.375 29.630 0.00 0.00 0.00 2.87
2531 2770 8.792633 ACCATGAGAAAATAAACAAATTCGAGA 58.207 29.630 0.00 0.00 0.00 4.04
2566 2805 3.365265 CCTGGCCAAGGCAACGAC 61.365 66.667 7.01 0.00 44.11 4.34
2585 2824 3.819564 AAAACAAAAAGGAGGGAGTGC 57.180 42.857 0.00 0.00 0.00 4.40
2592 2831 4.753516 ACCCCTCAAAAACAAAAAGGAG 57.246 40.909 0.00 0.00 0.00 3.69
2619 2858 8.871862 CAATGTGTCATGTCAAGAAAAGAAAAA 58.128 29.630 0.00 0.00 0.00 1.94
2620 2859 7.492020 CCAATGTGTCATGTCAAGAAAAGAAAA 59.508 33.333 0.00 0.00 0.00 2.29
2621 2860 6.979817 CCAATGTGTCATGTCAAGAAAAGAAA 59.020 34.615 0.00 0.00 0.00 2.52
2622 2861 6.096705 ACCAATGTGTCATGTCAAGAAAAGAA 59.903 34.615 0.00 0.00 0.00 2.52
2623 2862 5.593909 ACCAATGTGTCATGTCAAGAAAAGA 59.406 36.000 0.00 0.00 0.00 2.52
2624 2863 5.688621 CACCAATGTGTCATGTCAAGAAAAG 59.311 40.000 0.00 0.00 37.72 2.27
2625 2864 5.451659 CCACCAATGTGTCATGTCAAGAAAA 60.452 40.000 0.00 0.00 41.09 2.29
2626 2865 4.037803 CCACCAATGTGTCATGTCAAGAAA 59.962 41.667 0.00 0.00 41.09 2.52
2627 2866 3.569277 CCACCAATGTGTCATGTCAAGAA 59.431 43.478 0.00 0.00 41.09 2.52
2628 2867 3.148412 CCACCAATGTGTCATGTCAAGA 58.852 45.455 0.00 0.00 41.09 3.02
2629 2868 3.148412 TCCACCAATGTGTCATGTCAAG 58.852 45.455 0.00 0.00 41.09 3.02
2630 2869 3.148412 CTCCACCAATGTGTCATGTCAA 58.852 45.455 0.00 0.00 41.09 3.18
2631 2870 2.371510 TCTCCACCAATGTGTCATGTCA 59.628 45.455 0.00 0.00 41.09 3.58
2632 2871 3.057969 TCTCCACCAATGTGTCATGTC 57.942 47.619 0.00 0.00 41.09 3.06
2633 2872 3.726557 ATCTCCACCAATGTGTCATGT 57.273 42.857 0.00 0.00 41.09 3.21
2634 2873 4.774124 ACTATCTCCACCAATGTGTCATG 58.226 43.478 0.00 0.00 41.09 3.07
2635 2874 5.441718 AACTATCTCCACCAATGTGTCAT 57.558 39.130 0.00 0.00 41.09 3.06
2636 2875 4.908601 AACTATCTCCACCAATGTGTCA 57.091 40.909 0.00 0.00 41.09 3.58
2637 2876 5.491982 AGAAACTATCTCCACCAATGTGTC 58.508 41.667 0.00 0.00 41.09 3.67
2638 2877 5.505181 AGAAACTATCTCCACCAATGTGT 57.495 39.130 0.00 0.00 41.09 3.72
2639 2878 6.540189 CCTAAGAAACTATCTCCACCAATGTG 59.460 42.308 0.00 0.00 37.42 3.21
2640 2879 6.353082 CCCTAAGAAACTATCTCCACCAATGT 60.353 42.308 0.00 0.00 37.42 2.71
2641 2880 6.058183 CCCTAAGAAACTATCTCCACCAATG 58.942 44.000 0.00 0.00 37.42 2.82
2642 2881 5.398012 GCCCTAAGAAACTATCTCCACCAAT 60.398 44.000 0.00 0.00 37.42 3.16
2643 2882 4.080526 GCCCTAAGAAACTATCTCCACCAA 60.081 45.833 0.00 0.00 37.42 3.67
2644 2883 3.454812 GCCCTAAGAAACTATCTCCACCA 59.545 47.826 0.00 0.00 37.42 4.17
2645 2884 3.181453 GGCCCTAAGAAACTATCTCCACC 60.181 52.174 0.00 0.00 37.42 4.61
2646 2885 3.454812 TGGCCCTAAGAAACTATCTCCAC 59.545 47.826 0.00 0.00 37.42 4.02
2647 2886 3.731431 TGGCCCTAAGAAACTATCTCCA 58.269 45.455 0.00 0.00 37.42 3.86
2648 2887 4.595350 AGATGGCCCTAAGAAACTATCTCC 59.405 45.833 0.00 0.00 37.42 3.71
2649 2888 5.816955 AGATGGCCCTAAGAAACTATCTC 57.183 43.478 0.00 0.00 37.42 2.75
2650 2889 6.386284 ACTAGATGGCCCTAAGAAACTATCT 58.614 40.000 0.00 0.00 41.32 1.98
2651 2890 6.673839 ACTAGATGGCCCTAAGAAACTATC 57.326 41.667 0.00 0.00 0.00 2.08
2652 2891 7.453141 AAACTAGATGGCCCTAAGAAACTAT 57.547 36.000 0.00 0.00 0.00 2.12
2653 2892 6.886178 AAACTAGATGGCCCTAAGAAACTA 57.114 37.500 0.00 0.00 0.00 2.24
2654 2893 5.780958 AAACTAGATGGCCCTAAGAAACT 57.219 39.130 0.00 0.00 0.00 2.66
2655 2894 7.415318 GCTTAAAACTAGATGGCCCTAAGAAAC 60.415 40.741 0.00 0.00 0.00 2.78
2656 2895 6.602009 GCTTAAAACTAGATGGCCCTAAGAAA 59.398 38.462 0.00 0.00 0.00 2.52
2657 2896 6.069615 AGCTTAAAACTAGATGGCCCTAAGAA 60.070 38.462 0.00 0.00 0.00 2.52
2658 2897 5.428783 AGCTTAAAACTAGATGGCCCTAAGA 59.571 40.000 0.00 0.00 0.00 2.10
2659 2898 5.685728 AGCTTAAAACTAGATGGCCCTAAG 58.314 41.667 0.00 0.00 0.00 2.18
2660 2899 5.710409 AGCTTAAAACTAGATGGCCCTAA 57.290 39.130 0.00 0.00 0.00 2.69
2661 2900 5.437060 CAAGCTTAAAACTAGATGGCCCTA 58.563 41.667 0.00 0.00 0.00 3.53
2662 2901 4.273318 CAAGCTTAAAACTAGATGGCCCT 58.727 43.478 0.00 0.00 0.00 5.19
2663 2902 3.381590 CCAAGCTTAAAACTAGATGGCCC 59.618 47.826 0.00 0.00 0.00 5.80
2664 2903 3.181486 GCCAAGCTTAAAACTAGATGGCC 60.181 47.826 0.00 0.00 33.07 5.36
2665 2904 3.443681 TGCCAAGCTTAAAACTAGATGGC 59.556 43.478 11.01 11.01 38.99 4.40
2666 2905 5.643379 TTGCCAAGCTTAAAACTAGATGG 57.357 39.130 0.00 0.00 0.00 3.51
2667 2906 6.624423 ACATTGCCAAGCTTAAAACTAGATG 58.376 36.000 0.00 0.00 0.00 2.90
2668 2907 6.840780 ACATTGCCAAGCTTAAAACTAGAT 57.159 33.333 0.00 0.00 0.00 1.98
2669 2908 6.648879 AACATTGCCAAGCTTAAAACTAGA 57.351 33.333 0.00 0.00 0.00 2.43
2670 2909 8.986477 ATAAACATTGCCAAGCTTAAAACTAG 57.014 30.769 0.00 0.00 0.00 2.57
2671 2910 8.580720 TGATAAACATTGCCAAGCTTAAAACTA 58.419 29.630 0.00 0.00 0.00 2.24
2672 2911 7.441017 TGATAAACATTGCCAAGCTTAAAACT 58.559 30.769 0.00 0.00 0.00 2.66
2673 2912 7.148590 CCTGATAAACATTGCCAAGCTTAAAAC 60.149 37.037 0.00 0.00 0.00 2.43
2674 2913 6.873076 CCTGATAAACATTGCCAAGCTTAAAA 59.127 34.615 0.00 0.00 0.00 1.52
2675 2914 6.210385 TCCTGATAAACATTGCCAAGCTTAAA 59.790 34.615 0.00 0.00 0.00 1.52
2676 2915 5.714333 TCCTGATAAACATTGCCAAGCTTAA 59.286 36.000 0.00 0.00 0.00 1.85
2677 2916 5.260424 TCCTGATAAACATTGCCAAGCTTA 58.740 37.500 0.00 0.00 0.00 3.09
2678 2917 4.088634 TCCTGATAAACATTGCCAAGCTT 58.911 39.130 0.00 0.00 0.00 3.74
2679 2918 3.700538 TCCTGATAAACATTGCCAAGCT 58.299 40.909 0.00 0.00 0.00 3.74
2680 2919 4.454728 TTCCTGATAAACATTGCCAAGC 57.545 40.909 0.00 0.00 0.00 4.01
2681 2920 6.632909 TGATTTCCTGATAAACATTGCCAAG 58.367 36.000 0.00 0.00 0.00 3.61
2682 2921 6.602410 TGATTTCCTGATAAACATTGCCAA 57.398 33.333 0.00 0.00 0.00 4.52
2683 2922 6.795144 ATGATTTCCTGATAAACATTGCCA 57.205 33.333 0.00 0.00 0.00 4.92
2684 2923 6.480981 CCAATGATTTCCTGATAAACATTGCC 59.519 38.462 0.00 0.00 37.03 4.52
2685 2924 6.480981 CCCAATGATTTCCTGATAAACATTGC 59.519 38.462 0.00 0.00 37.03 3.56
2686 2925 7.784037 TCCCAATGATTTCCTGATAAACATTG 58.216 34.615 0.00 0.00 37.45 2.82
2687 2926 7.976414 TCCCAATGATTTCCTGATAAACATT 57.024 32.000 0.00 0.00 0.00 2.71
2688 2927 7.785985 TGATCCCAATGATTTCCTGATAAACAT 59.214 33.333 0.00 0.00 32.41 2.71
2689 2928 7.068593 GTGATCCCAATGATTTCCTGATAAACA 59.931 37.037 0.00 0.00 32.41 2.83
2690 2929 7.428826 GTGATCCCAATGATTTCCTGATAAAC 58.571 38.462 0.00 0.00 32.41 2.01
2691 2930 6.550854 GGTGATCCCAATGATTTCCTGATAAA 59.449 38.462 0.00 0.00 32.41 1.40
2692 2931 6.070656 GGTGATCCCAATGATTTCCTGATAA 58.929 40.000 0.00 0.00 32.41 1.75
2693 2932 5.373555 AGGTGATCCCAATGATTTCCTGATA 59.626 40.000 3.45 0.00 36.31 2.15
2694 2933 4.169461 AGGTGATCCCAATGATTTCCTGAT 59.831 41.667 3.45 0.00 36.31 2.90
2695 2934 3.528905 AGGTGATCCCAATGATTTCCTGA 59.471 43.478 3.45 0.00 36.31 3.86
2696 2935 3.635373 CAGGTGATCCCAATGATTTCCTG 59.365 47.826 10.08 10.08 42.48 3.86
2697 2936 3.528905 TCAGGTGATCCCAATGATTTCCT 59.471 43.478 3.45 0.00 37.34 3.36
2704 2943 0.541392 TCCGTCAGGTGATCCCAATG 59.459 55.000 3.45 0.00 39.05 2.82
2717 2956 3.588906 ACGTGTCGTGCTCCGTCA 61.589 61.111 0.00 0.00 39.18 4.35
2731 2970 0.179127 CAGAGATGATGGACGCACGT 60.179 55.000 0.00 0.00 0.00 4.49
2741 2980 0.107508 CCAACGGCCACAGAGATGAT 60.108 55.000 2.24 0.00 0.00 2.45
2742 2981 1.191489 TCCAACGGCCACAGAGATGA 61.191 55.000 2.24 0.00 0.00 2.92
2749 2988 0.327924 AATCTGATCCAACGGCCACA 59.672 50.000 2.24 0.00 0.00 4.17
2782 3021 9.620660 CAAAAATTAGGTAATACGTTGCTTCTT 57.379 29.630 0.00 0.00 0.00 2.52
2802 3041 2.431782 ACAGCCACTCAGTTGCAAAAAT 59.568 40.909 0.00 0.00 0.00 1.82
2820 3064 2.351738 GCGGTGGGAGAAATCAAAACAG 60.352 50.000 0.00 0.00 0.00 3.16
2825 3069 1.243902 GTTGCGGTGGGAGAAATCAA 58.756 50.000 0.00 0.00 0.00 2.57
2826 3070 0.109532 TGTTGCGGTGGGAGAAATCA 59.890 50.000 0.00 0.00 0.00 2.57
2850 3094 2.043405 ACACAGTTGCCGCAACACA 61.043 52.632 32.22 0.00 45.66 3.72
2851 3095 1.586042 CACACAGTTGCCGCAACAC 60.586 57.895 32.22 12.56 45.66 3.32
2852 3096 1.590610 AACACACAGTTGCCGCAACA 61.591 50.000 32.22 0.00 45.66 3.33
2853 3097 1.138671 AACACACAGTTGCCGCAAC 59.861 52.632 25.74 25.74 43.83 4.17
2854 3098 3.597072 AACACACAGTTGCCGCAA 58.403 50.000 0.38 0.38 39.49 4.85
2861 3105 2.705658 TCAGATCCCTCAACACACAGTT 59.294 45.455 0.00 0.00 42.42 3.16
2862 3106 2.329267 TCAGATCCCTCAACACACAGT 58.671 47.619 0.00 0.00 0.00 3.55
2863 3107 3.407424 TTCAGATCCCTCAACACACAG 57.593 47.619 0.00 0.00 0.00 3.66
2864 3108 3.136443 AGTTTCAGATCCCTCAACACACA 59.864 43.478 0.00 0.00 0.00 3.72
2884 3128 0.252881 TGCTCTCAAGGGGATCCAGT 60.253 55.000 15.23 0.00 34.83 4.00
2896 3140 3.640407 GGGTGGTGGCTGCTCTCA 61.640 66.667 0.00 0.00 0.00 3.27
2971 3227 3.532155 GGTGTTTGGCGGTGGCAA 61.532 61.111 1.29 1.29 46.03 4.52
3001 3257 4.854784 GCTCGGCGACATCAGCGA 62.855 66.667 4.99 0.00 35.00 4.93
3026 3283 4.986587 CGACAACCACGACGGCGA 62.987 66.667 22.49 0.00 41.64 5.54
3045 3302 4.077184 GGATGGTGGTGGACGCGA 62.077 66.667 15.93 0.00 0.00 5.87
3049 3306 0.181350 GAGGATGGATGGTGGTGGAC 59.819 60.000 0.00 0.00 0.00 4.02
3076 3347 1.737793 CCAACGCCTGGTCTAATGAAC 59.262 52.381 0.00 0.00 40.78 3.18
3156 3431 3.340789 ATCGACGATCGCGATGGA 58.659 55.556 33.43 21.00 45.74 3.41
3165 3440 2.722487 GTGGAGGCGATCGACGAT 59.278 61.111 21.57 10.78 45.77 3.73
3172 3447 1.561769 TTGATGGTGGTGGAGGCGAT 61.562 55.000 0.00 0.00 0.00 4.58
3173 3448 2.220586 TTGATGGTGGTGGAGGCGA 61.221 57.895 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.