Multiple sequence alignment - TraesCS2B01G369100

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 TraesCS2B01G369100 chr2B 100.000 2915 0 0 1 2915 526735381 526732467 0.000000e+00 5384.0
1 TraesCS2B01G369100 chr2B 78.977 352 48 11 2590 2915 21541430 21541079 1.760000e-52 217.0
2 TraesCS2B01G369100 chr2A 92.297 1493 69 16 671 2158 590966570 590965119 0.000000e+00 2078.0
3 TraesCS2B01G369100 chr2A 83.114 989 114 31 1197 2158 590974796 590973834 0.000000e+00 852.0
4 TraesCS2B01G369100 chr2A 79.796 1178 162 38 789 1921 590818015 590816869 0.000000e+00 787.0
5 TraesCS2B01G369100 chr2A 85.630 682 66 18 1 667 590967338 590966674 0.000000e+00 688.0
6 TraesCS2B01G369100 chr2A 90.361 415 24 3 672 1078 590975197 590974791 5.530000e-147 531.0
7 TraesCS2B01G369100 chr2A 92.149 242 18 1 428 668 590975535 590975294 1.000000e-89 340.0
8 TraesCS2B01G369100 chr2A 100.000 29 0 0 145 173 583824711 583824739 1.000000e-03 54.7
9 TraesCS2B01G369100 chr2D 91.762 1396 71 17 766 2158 446728075 446726721 0.000000e+00 1901.0
10 TraesCS2B01G369100 chr2D 91.691 1396 72 17 766 2158 446697407 446696053 0.000000e+00 1895.0
11 TraesCS2B01G369100 chr2D 84.227 970 109 30 1195 2144 446932198 446933143 0.000000e+00 904.0
12 TraesCS2B01G369100 chr2D 80.546 1172 158 34 789 1924 446653410 446652273 0.000000e+00 837.0
13 TraesCS2B01G369100 chr2D 89.340 591 48 5 62 640 446699366 446698779 0.000000e+00 728.0
14 TraesCS2B01G369100 chr2D 88.514 592 52 10 62 640 446732151 446731563 0.000000e+00 702.0
15 TraesCS2B01G369100 chr2D 89.097 321 17 5 766 1078 446931895 446932205 1.640000e-102 383.0
16 TraesCS2B01G369100 chr2D 88.672 256 29 0 416 671 446929724 446929979 2.180000e-81 313.0
17 TraesCS2B01G369100 chr2D 94.949 99 5 0 672 770 446698677 446698579 3.890000e-34 156.0
18 TraesCS2B01G369100 chr2D 94.949 99 5 0 672 770 446731461 446731363 3.890000e-34 156.0
19 TraesCS2B01G369100 chr2D 92.929 99 7 0 672 770 446930080 446930178 8.420000e-31 145.0
20 TraesCS2B01G369100 chr3D 79.506 688 92 17 2246 2915 291175382 291176038 7.410000e-121 444.0
21 TraesCS2B01G369100 chr3D 79.646 113 14 9 2360 2472 562693524 562693421 4.030000e-09 73.1
22 TraesCS2B01G369100 chr1D 78.806 670 97 30 2244 2885 469383126 469383778 2.700000e-110 409.0
23 TraesCS2B01G369100 chr3A 77.829 645 99 28 2284 2915 384190683 384191296 2.760000e-95 359.0
24 TraesCS2B01G369100 chr3A 87.500 56 5 2 2284 2338 627251258 627251204 2.430000e-06 63.9
25 TraesCS2B01G369100 chr6B 76.241 665 109 25 2297 2914 60669506 60668844 1.010000e-79 307.0
26 TraesCS2B01G369100 chr7D 77.758 553 61 27 2421 2915 5326658 5327206 1.710000e-72 283.0
27 TraesCS2B01G369100 chr7D 75.666 563 83 22 2371 2880 189914227 189914788 6.280000e-57 231.0
28 TraesCS2B01G369100 chr3B 84.791 263 35 3 2651 2909 384281160 384281421 2.880000e-65 259.0
29 TraesCS2B01G369100 chr3B 75.824 546 68 27 2424 2915 750131902 750131367 4.890000e-53 219.0
30 TraesCS2B01G369100 chr5A 78.249 377 62 14 2422 2778 117414024 117414400 1.050000e-54 224.0
31 TraesCS2B01G369100 chr5A 79.012 81 16 1 190 270 1902511 1902590 1.000000e-03 54.7
32 TraesCS2B01G369100 chr1A 82.439 205 29 6 2296 2495 586277671 586277469 3.860000e-39 172.0
33 TraesCS2B01G369100 chr6D 74.618 327 49 17 2284 2600 341389839 341390141 2.370000e-21 113.0
34 TraesCS2B01G369100 chr6D 81.818 88 14 2 189 276 436797234 436797149 4.030000e-09 73.1
35 TraesCS2B01G369100 chr7B 85.714 77 10 1 187 263 39103163 39103238 2.410000e-11 80.5
36 TraesCS2B01G369100 chr7B 83.133 83 12 2 182 263 480682593 480682674 1.120000e-09 75.0
37 TraesCS2B01G369100 chrUn 88.889 54 6 0 2285 2338 380507423 380507370 1.870000e-07 67.6
38 TraesCS2B01G369100 chr6A 88.889 54 6 0 2285 2338 546950325 546950378 1.870000e-07 67.6
39 TraesCS2B01G369100 chr6A 88.889 54 6 0 2285 2338 546959435 546959488 1.870000e-07 67.6


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 TraesCS2B01G369100 chr2B 526732467 526735381 2914 True 5384.000000 5384 100.000000 1 2915 1 chr2B.!!$R2 2914
1 TraesCS2B01G369100 chr2A 590965119 590967338 2219 True 1383.000000 2078 88.963500 1 2158 2 chr2A.!!$R2 2157
2 TraesCS2B01G369100 chr2A 590816869 590818015 1146 True 787.000000 787 79.796000 789 1921 1 chr2A.!!$R1 1132
3 TraesCS2B01G369100 chr2A 590973834 590975535 1701 True 574.333333 852 88.541333 428 2158 3 chr2A.!!$R3 1730
4 TraesCS2B01G369100 chr2D 446696053 446699366 3313 True 926.333333 1895 91.993333 62 2158 3 chr2D.!!$R2 2096
5 TraesCS2B01G369100 chr2D 446726721 446732151 5430 True 919.666667 1901 91.741667 62 2158 3 chr2D.!!$R3 2096
6 TraesCS2B01G369100 chr2D 446652273 446653410 1137 True 837.000000 837 80.546000 789 1924 1 chr2D.!!$R1 1135
7 TraesCS2B01G369100 chr2D 446929724 446933143 3419 False 436.250000 904 88.731250 416 2144 4 chr2D.!!$F1 1728
8 TraesCS2B01G369100 chr3D 291175382 291176038 656 False 444.000000 444 79.506000 2246 2915 1 chr3D.!!$F1 669
9 TraesCS2B01G369100 chr1D 469383126 469383778 652 False 409.000000 409 78.806000 2244 2885 1 chr1D.!!$F1 641
10 TraesCS2B01G369100 chr3A 384190683 384191296 613 False 359.000000 359 77.829000 2284 2915 1 chr3A.!!$F1 631
11 TraesCS2B01G369100 chr6B 60668844 60669506 662 True 307.000000 307 76.241000 2297 2914 1 chr6B.!!$R1 617
12 TraesCS2B01G369100 chr7D 5326658 5327206 548 False 283.000000 283 77.758000 2421 2915 1 chr7D.!!$F1 494
13 TraesCS2B01G369100 chr7D 189914227 189914788 561 False 231.000000 231 75.666000 2371 2880 1 chr7D.!!$F2 509
14 TraesCS2B01G369100 chr3B 750131367 750131902 535 True 219.000000 219 75.824000 2424 2915 1 chr3B.!!$R1 491

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
169 171 0.107312 CCGACGAGGAAGAGTAGGGA 60.107 60.0 0.0 0.0 45.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 6277 0.105778 AGGAGCATCGCTAGAAAGGC 59.894 55.0 0.0 0.0 39.88 4.35 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
50 51 4.572571 GCAACGGGTGGGTGGTGA 62.573 66.667 0.00 0.00 0.00 4.02
51 52 2.593436 CAACGGGTGGGTGGTGAC 60.593 66.667 0.00 0.00 0.00 3.67
52 53 3.881104 AACGGGTGGGTGGTGACC 61.881 66.667 0.00 0.00 42.27 4.02
98 99 2.351276 GTGTCGGCCTCCAACCAT 59.649 61.111 0.00 0.00 0.00 3.55
101 102 1.224592 GTCGGCCTCCAACCATGAT 59.775 57.895 0.00 0.00 0.00 2.45
110 111 3.331591 CCTCCAACCATGATGGATCCATA 59.668 47.826 27.38 15.44 45.57 2.74
129 131 1.244816 AGTCAATCTCACGTCACCGA 58.755 50.000 0.00 0.00 37.88 4.69
169 171 0.107312 CCGACGAGGAAGAGTAGGGA 60.107 60.000 0.00 0.00 45.00 4.20
173 175 3.025262 GACGAGGAAGAGTAGGGAATGT 58.975 50.000 0.00 0.00 0.00 2.71
176 178 3.181485 CGAGGAAGAGTAGGGAATGTGAC 60.181 52.174 0.00 0.00 0.00 3.67
211 213 1.133009 CCCATGCCCTACTCTACCTCT 60.133 57.143 0.00 0.00 0.00 3.69
212 214 2.683768 CCATGCCCTACTCTACCTCTT 58.316 52.381 0.00 0.00 0.00 2.85
214 216 3.571590 CATGCCCTACTCTACCTCTTCT 58.428 50.000 0.00 0.00 0.00 2.85
218 220 2.358300 CCCTACTCTACCTCTTCTGGCA 60.358 54.545 0.00 0.00 0.00 4.92
222 224 1.902508 CTCTACCTCTTCTGGCAACCA 59.097 52.381 0.00 0.00 0.00 3.67
231 233 0.478072 TCTGGCAACCACACCTTCAT 59.522 50.000 0.00 0.00 0.00 2.57
239 241 0.613260 CCACACCTTCATTCCGAGGA 59.387 55.000 0.00 0.00 0.00 3.71
291 293 0.878961 GAACAACAAGGACGGTCGCT 60.879 55.000 1.43 0.00 0.00 4.93
304 318 3.740397 TCGCTGGCAGTTGCATGC 61.740 61.111 17.16 11.82 45.74 4.06
378 392 4.703645 TTTTTGTGTGTTGATCGGTCAA 57.296 36.364 7.11 7.11 41.89 3.18
382 396 2.547634 TGTGTGTTGATCGGTCAATGTG 59.452 45.455 15.35 0.00 45.46 3.21
391 405 2.549282 GTCAATGTGCGCGAACGT 59.451 55.556 12.10 8.81 42.83 3.99
394 408 1.368731 CAATGTGCGCGAACGTGTT 60.369 52.632 13.94 4.51 42.83 3.32
426 440 6.560711 GGATTTTGCGATTTATGGTTGTAGT 58.439 36.000 0.00 0.00 0.00 2.73
434 448 6.250819 CGATTTATGGTTGTAGTTGCTCTTG 58.749 40.000 0.00 0.00 0.00 3.02
528 542 5.986501 TGAAGAGTCTTCCTTTCTAGACC 57.013 43.478 26.37 2.14 41.31 3.85
660 697 6.014669 AGAGAAGAAATGACTACTGAGCAGTT 60.015 38.462 8.60 0.00 42.54 3.16
723 861 1.226323 CCTGCCGAACTCTCGTACG 60.226 63.158 9.53 9.53 43.87 3.67
741 879 2.553268 GCGAGACAGCAAGTGCAC 59.447 61.111 9.40 9.40 45.16 4.57
784 5046 6.054941 TCAGACTAAGCTTTGAAACATGACA 58.945 36.000 14.98 0.00 0.00 3.58
801 5063 3.351740 TGACACCTGCAAAGAAAAGTCA 58.648 40.909 0.00 0.00 32.91 3.41
813 5075 6.128553 GCAAAGAAAAGTCATGATAGTCGACA 60.129 38.462 19.50 4.13 31.92 4.35
840 5104 3.560068 GTGTGAATCTGTGAACGAAGGTT 59.440 43.478 0.00 0.00 39.63 3.50
890 5157 2.767505 AGTCGTCCACAAGATCAAACC 58.232 47.619 0.00 0.00 0.00 3.27
899 5166 2.880890 ACAAGATCAAACCTGCTGTGTC 59.119 45.455 0.00 0.00 0.00 3.67
900 5167 3.144506 CAAGATCAAACCTGCTGTGTCT 58.855 45.455 0.00 0.00 0.00 3.41
901 5168 4.202357 ACAAGATCAAACCTGCTGTGTCTA 60.202 41.667 0.00 0.00 0.00 2.59
902 5169 4.833478 AGATCAAACCTGCTGTGTCTAT 57.167 40.909 0.00 0.00 0.00 1.98
903 5170 5.171339 AGATCAAACCTGCTGTGTCTATT 57.829 39.130 0.00 0.00 0.00 1.73
904 5171 6.299805 AGATCAAACCTGCTGTGTCTATTA 57.700 37.500 0.00 0.00 0.00 0.98
905 5172 6.893583 AGATCAAACCTGCTGTGTCTATTAT 58.106 36.000 0.00 0.00 0.00 1.28
906 5173 7.341805 AGATCAAACCTGCTGTGTCTATTATT 58.658 34.615 0.00 0.00 0.00 1.40
1011 5298 4.590487 TTCGACATGGCGAAGTCC 57.410 55.556 31.87 0.00 44.43 3.85
1143 5439 2.593468 ATTGCGGGACCGATGACAGG 62.593 60.000 15.99 0.00 42.83 4.00
1227 5532 2.762234 GGAGAGCGTCGTCACCGAT 61.762 63.158 0.00 0.00 46.30 4.18
1389 5703 1.068250 GATAGCCGCCTTCTTCGCT 59.932 57.895 0.00 0.00 0.00 4.93
1397 5711 1.731720 GCCTTCTTCGCTCACTTCAT 58.268 50.000 0.00 0.00 0.00 2.57
1428 5742 1.439679 GGCGTAAGTTCACCTCCAAG 58.560 55.000 0.00 0.00 41.68 3.61
1429 5743 0.796927 GCGTAAGTTCACCTCCAAGC 59.203 55.000 0.00 0.00 41.68 4.01
1431 5745 2.338500 CGTAAGTTCACCTCCAAGCTC 58.662 52.381 0.00 0.00 0.00 4.09
1435 5749 1.202818 AGTTCACCTCCAAGCTCCAAC 60.203 52.381 0.00 0.00 0.00 3.77
1436 5750 1.140312 TTCACCTCCAAGCTCCAACT 58.860 50.000 0.00 0.00 0.00 3.16
1437 5751 2.024176 TCACCTCCAAGCTCCAACTA 57.976 50.000 0.00 0.00 0.00 2.24
1439 5753 2.038557 TCACCTCCAAGCTCCAACTAAC 59.961 50.000 0.00 0.00 0.00 2.34
1440 5754 2.039084 CACCTCCAAGCTCCAACTAACT 59.961 50.000 0.00 0.00 0.00 2.24
1459 5773 5.979288 AACTACTACTACCAACACTGGAG 57.021 43.478 0.00 0.00 46.92 3.86
1947 6277 1.834178 GAATTGATCGACGCGCAAAAG 59.166 47.619 5.73 0.00 0.00 2.27
1955 6285 0.515564 GACGCGCAAAAGCCTTTCTA 59.484 50.000 5.73 0.00 0.00 2.10
1983 6320 2.712087 CTCCTACTGCTCTACCTCCCTA 59.288 54.545 0.00 0.00 0.00 3.53
2158 6505 8.603242 TGGAGAAGTGAGTTTAACTATTTCAC 57.397 34.615 0.00 2.42 38.68 3.18
2174 6521 9.936759 AACTATTTCACTTTGTTTTGAGGAAAA 57.063 25.926 0.00 0.00 0.00 2.29
2191 6538 5.736486 GGAAAACTTCCGGTCTATTCATC 57.264 43.478 0.00 0.00 40.59 2.92
2192 6539 5.183228 GGAAAACTTCCGGTCTATTCATCA 58.817 41.667 0.00 0.00 40.59 3.07
2193 6540 5.064834 GGAAAACTTCCGGTCTATTCATCAC 59.935 44.000 0.00 0.00 40.59 3.06
2194 6541 5.422214 AAACTTCCGGTCTATTCATCACT 57.578 39.130 0.00 0.00 0.00 3.41
2195 6542 6.540438 AAACTTCCGGTCTATTCATCACTA 57.460 37.500 0.00 0.00 0.00 2.74
2196 6543 6.540438 AACTTCCGGTCTATTCATCACTAA 57.460 37.500 0.00 0.00 0.00 2.24
2197 6544 6.732896 ACTTCCGGTCTATTCATCACTAAT 57.267 37.500 0.00 0.00 0.00 1.73
2198 6545 6.750148 ACTTCCGGTCTATTCATCACTAATC 58.250 40.000 0.00 0.00 0.00 1.75
2199 6546 6.323996 ACTTCCGGTCTATTCATCACTAATCA 59.676 38.462 0.00 0.00 0.00 2.57
2200 6547 6.918067 TCCGGTCTATTCATCACTAATCAT 57.082 37.500 0.00 0.00 0.00 2.45
2201 6548 6.691508 TCCGGTCTATTCATCACTAATCATG 58.308 40.000 0.00 0.00 0.00 3.07
2202 6549 5.871524 CCGGTCTATTCATCACTAATCATGG 59.128 44.000 0.00 0.00 0.00 3.66
2203 6550 5.349817 CGGTCTATTCATCACTAATCATGGC 59.650 44.000 0.00 0.00 0.00 4.40
2204 6551 6.233434 GGTCTATTCATCACTAATCATGGCA 58.767 40.000 0.00 0.00 0.00 4.92
2205 6552 6.370994 GGTCTATTCATCACTAATCATGGCAG 59.629 42.308 0.00 0.00 0.00 4.85
2206 6553 7.157347 GTCTATTCATCACTAATCATGGCAGA 58.843 38.462 0.00 0.00 0.00 4.26
2207 6554 7.823310 GTCTATTCATCACTAATCATGGCAGAT 59.177 37.037 0.00 0.00 0.00 2.90
2208 6555 8.380867 TCTATTCATCACTAATCATGGCAGATT 58.619 33.333 13.90 13.90 40.99 2.40
2209 6556 7.834881 ATTCATCACTAATCATGGCAGATTT 57.165 32.000 14.42 1.73 38.97 2.17
2210 6557 6.872628 TCATCACTAATCATGGCAGATTTC 57.127 37.500 14.42 0.00 38.97 2.17
2211 6558 6.598503 TCATCACTAATCATGGCAGATTTCT 58.401 36.000 14.42 2.19 38.97 2.52
2212 6559 6.485648 TCATCACTAATCATGGCAGATTTCTG 59.514 38.462 14.42 3.13 46.40 3.02
2222 6569 0.332632 CAGATTTCTGCCCCAAGGGA 59.667 55.000 6.74 0.00 46.48 4.20
2234 6581 1.276421 CCCAAGGGAGATAGGTATGCG 59.724 57.143 0.00 0.00 37.50 4.73
2235 6582 1.338200 CCAAGGGAGATAGGTATGCGC 60.338 57.143 0.00 0.00 0.00 6.09
2236 6583 1.620819 CAAGGGAGATAGGTATGCGCT 59.379 52.381 9.73 0.00 0.00 5.92
2237 6584 2.016905 AGGGAGATAGGTATGCGCTT 57.983 50.000 9.73 4.59 0.00 4.68
2238 6585 1.620819 AGGGAGATAGGTATGCGCTTG 59.379 52.381 9.73 0.00 0.00 4.01
2239 6586 1.344763 GGGAGATAGGTATGCGCTTGT 59.655 52.381 9.73 0.00 0.00 3.16
2240 6587 2.224305 GGGAGATAGGTATGCGCTTGTT 60.224 50.000 9.73 0.00 0.00 2.83
2241 6588 3.006537 GGGAGATAGGTATGCGCTTGTTA 59.993 47.826 9.73 0.00 0.00 2.41
2242 6589 4.238514 GGAGATAGGTATGCGCTTGTTAG 58.761 47.826 9.73 0.00 0.00 2.34
2261 6608 3.458872 GGCATCTCCAACGATGACA 57.541 52.632 5.07 0.00 46.46 3.58
2264 6611 2.283298 GCATCTCCAACGATGACATGT 58.717 47.619 0.00 0.00 42.63 3.21
2269 6616 6.653183 CATCTCCAACGATGACATGTAAATC 58.347 40.000 0.00 4.60 42.63 2.17
2270 6617 5.116180 TCTCCAACGATGACATGTAAATCC 58.884 41.667 0.00 0.00 0.00 3.01
2271 6618 3.868661 TCCAACGATGACATGTAAATCCG 59.131 43.478 0.00 0.00 0.00 4.18
2276 6623 1.934589 TGACATGTAAATCCGCTCCG 58.065 50.000 0.00 0.00 0.00 4.63
2277 6625 1.206132 TGACATGTAAATCCGCTCCGT 59.794 47.619 0.00 0.00 0.00 4.69
2281 6629 3.069016 ACATGTAAATCCGCTCCGTCATA 59.931 43.478 0.00 0.00 0.00 2.15
2282 6630 4.245660 CATGTAAATCCGCTCCGTCATAT 58.754 43.478 0.00 0.00 0.00 1.78
2320 6672 0.603065 CAGTCCACGGACACTGATGA 59.397 55.000 18.21 0.00 46.76 2.92
2321 6673 1.000843 CAGTCCACGGACACTGATGAA 59.999 52.381 18.21 0.00 46.76 2.57
2326 6678 1.546029 CACGGACACTGATGAAGGAGA 59.454 52.381 0.00 0.00 0.00 3.71
2339 6691 0.625849 AAGGAGACCGCCATCCAATT 59.374 50.000 0.00 0.00 38.12 2.32
2345 6701 2.069273 GACCGCCATCCAATTCTATCG 58.931 52.381 0.00 0.00 0.00 2.92
2356 6712 8.253810 CCATCCAATTCTATCGTGTATATGTCT 58.746 37.037 0.00 0.00 0.00 3.41
2366 6722 5.345702 TCGTGTATATGTCTGCCAGTAAAC 58.654 41.667 0.00 0.00 0.00 2.01
2367 6723 5.105675 TCGTGTATATGTCTGCCAGTAAACA 60.106 40.000 0.00 0.00 0.00 2.83
2368 6724 5.579119 CGTGTATATGTCTGCCAGTAAACAA 59.421 40.000 0.00 0.00 0.00 2.83
2408 6764 0.747255 AGTCTGATCCATAACGCGCT 59.253 50.000 5.73 0.00 0.00 5.92
2409 6765 1.954382 AGTCTGATCCATAACGCGCTA 59.046 47.619 5.73 0.00 0.00 4.26
2410 6766 2.030717 AGTCTGATCCATAACGCGCTAG 60.031 50.000 5.73 0.00 0.00 3.42
2411 6767 2.031069 GTCTGATCCATAACGCGCTAGA 60.031 50.000 5.73 0.00 0.00 2.43
2412 6768 2.820197 TCTGATCCATAACGCGCTAGAT 59.180 45.455 5.73 1.10 0.00 1.98
2413 6769 3.119814 TCTGATCCATAACGCGCTAGATC 60.120 47.826 5.73 11.80 0.00 2.75
2414 6770 2.177977 GATCCATAACGCGCTAGATCG 58.822 52.381 5.73 0.00 0.00 3.69
2445 6811 2.289631 GGATCACATGCCCGATCACATA 60.290 50.000 17.38 0.00 39.88 2.29
2504 6871 4.570772 CGTGACAAAAGAATATCCATCCGT 59.429 41.667 0.00 0.00 0.00 4.69
2506 6873 4.808895 TGACAAAAGAATATCCATCCGTCG 59.191 41.667 0.00 0.00 0.00 5.12
2508 6875 2.457366 AAGAATATCCATCCGTCGGC 57.543 50.000 6.34 0.00 0.00 5.54
2555 6930 1.306141 TGCCGATCTGACCCTCCTT 60.306 57.895 0.00 0.00 0.00 3.36
2574 6949 1.299850 CACGCTCAAGGTGTCGTCA 60.300 57.895 0.00 0.00 36.40 4.35
2584 6960 4.325304 TGTCGTCACGCCGCGTAA 62.325 61.111 19.71 0.00 38.32 3.18
2599 6980 1.040339 CGTAAGCAGCCTCCTCCTCT 61.040 60.000 0.00 0.00 0.00 3.69
2665 7082 2.711311 CGGACGGCTTGCATGATG 59.289 61.111 3.33 0.00 0.00 3.07
2669 7086 1.268896 GGACGGCTTGCATGATGATTG 60.269 52.381 3.33 0.00 0.00 2.67
2677 7094 2.086094 TGCATGATGATTGTTGCGTCT 58.914 42.857 0.00 0.00 37.92 4.18
2710 7128 3.650942 ACTCCACCTTCAAGGACAACATA 59.349 43.478 11.59 0.00 37.67 2.29
2742 7160 1.869754 CGCATCGGTTCCGATCTTCAT 60.870 52.381 21.61 0.61 45.80 2.57
2772 7212 0.813210 CGAGCATGGCCTTCTTCTCC 60.813 60.000 3.32 0.00 0.00 3.71
2775 7215 0.254178 GCATGGCCTTCTTCTCCTCA 59.746 55.000 3.32 0.00 0.00 3.86
2779 7219 1.208052 TGGCCTTCTTCTCCTCAATCG 59.792 52.381 3.32 0.00 0.00 3.34
2797 7237 0.037232 CGAGGCCCTTTTCTCTTCGT 60.037 55.000 0.00 0.00 0.00 3.85
2813 7253 1.446099 CGTGCGCCAGCTTCTTCTA 60.446 57.895 4.18 0.00 45.42 2.10
2838 7278 5.817816 GGTCGTCTCCATCAATAGTTTGAAT 59.182 40.000 0.00 0.00 44.70 2.57
2885 7328 0.104120 TCGGACCGCTTGACATATGG 59.896 55.000 9.66 0.00 0.00 2.74
2886 7329 0.104120 CGGACCGCTTGACATATGGA 59.896 55.000 7.80 0.00 0.00 3.41
2891 7334 2.224378 ACCGCTTGACATATGGATCCTG 60.224 50.000 14.23 5.56 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.800863 GCGACTCTGCCTCGACGA 61.801 66.667 0.00 0.00 32.65 4.20
33 34 4.572571 TCACCACCCACCCGTTGC 62.573 66.667 0.00 0.00 0.00 4.17
98 99 5.279156 CGTGAGATTGACTATGGATCCATCA 60.279 44.000 30.61 20.53 37.82 3.07
101 102 3.960755 ACGTGAGATTGACTATGGATCCA 59.039 43.478 18.88 18.88 0.00 3.41
129 131 4.457496 CCGGAGCCTGCACATCGT 62.457 66.667 0.00 0.00 0.00 3.73
169 171 0.602638 ATGCACCGACGTGTCACATT 60.603 50.000 3.42 0.00 42.39 2.71
173 175 2.419620 ACATGCACCGACGTGTCA 59.580 55.556 0.00 0.00 42.39 3.58
176 178 3.118454 GGGACATGCACCGACGTG 61.118 66.667 0.00 0.00 43.35 4.49
211 213 0.257328 TGAAGGTGTGGTTGCCAGAA 59.743 50.000 0.00 0.00 32.34 3.02
212 214 0.478072 ATGAAGGTGTGGTTGCCAGA 59.522 50.000 0.00 0.00 32.34 3.86
214 216 1.327303 GAATGAAGGTGTGGTTGCCA 58.673 50.000 0.00 0.00 0.00 4.92
218 220 1.271379 CCTCGGAATGAAGGTGTGGTT 60.271 52.381 0.00 0.00 0.00 3.67
222 224 0.250513 GCTCCTCGGAATGAAGGTGT 59.749 55.000 0.00 0.00 0.00 4.16
291 293 1.033202 ATGATCGCATGCAACTGCCA 61.033 50.000 19.57 6.58 39.00 4.92
378 392 2.549282 GAACACGTTCGCGCACAT 59.451 55.556 10.01 0.00 46.04 3.21
391 405 1.238625 GCAAAATCCGTCCCCGAACA 61.239 55.000 0.00 0.00 35.63 3.18
394 408 2.246761 ATCGCAAAATCCGTCCCCGA 62.247 55.000 0.00 0.00 35.63 5.14
401 415 4.420168 ACAACCATAAATCGCAAAATCCG 58.580 39.130 0.00 0.00 0.00 4.18
434 448 2.608752 CCTGTTGCTGTCAAAGATTGCC 60.609 50.000 0.00 0.00 33.37 4.52
528 542 2.225019 ACAGCAGAAAACAGCTTGATCG 59.775 45.455 0.00 0.00 39.50 3.69
550 564 4.976116 GCGAATTTATTGATACCCAGCAAC 59.024 41.667 0.00 0.00 31.78 4.17
660 697 1.412710 GATCGGGGAACATCTGTGCTA 59.587 52.381 0.00 0.00 0.00 3.49
667 704 1.006832 CGTGTTGATCGGGGAACATC 58.993 55.000 0.27 0.00 34.69 3.06
723 861 2.666190 TGCACTTGCTGTCTCGCC 60.666 61.111 2.33 0.00 42.66 5.54
784 5046 6.006449 ACTATCATGACTTTTCTTTGCAGGT 58.994 36.000 0.00 0.00 0.00 4.00
801 5063 1.476891 ACACGGCTTGTCGACTATCAT 59.523 47.619 17.92 0.00 29.79 2.45
813 5075 1.873591 GTTCACAGATTCACACGGCTT 59.126 47.619 0.00 0.00 0.00 4.35
899 5166 9.378551 TGGCAAGCGGTTTATATAGAATAATAG 57.621 33.333 0.00 0.00 0.00 1.73
900 5167 9.158233 GTGGCAAGCGGTTTATATAGAATAATA 57.842 33.333 0.00 0.00 0.00 0.98
901 5168 7.120726 GGTGGCAAGCGGTTTATATAGAATAAT 59.879 37.037 0.00 0.00 0.00 1.28
902 5169 6.428771 GGTGGCAAGCGGTTTATATAGAATAA 59.571 38.462 0.00 0.00 0.00 1.40
903 5170 5.935789 GGTGGCAAGCGGTTTATATAGAATA 59.064 40.000 0.00 0.00 0.00 1.75
904 5171 4.760204 GGTGGCAAGCGGTTTATATAGAAT 59.240 41.667 0.00 0.00 0.00 2.40
905 5172 4.131596 GGTGGCAAGCGGTTTATATAGAA 58.868 43.478 0.00 0.00 0.00 2.10
906 5173 3.735591 GGTGGCAAGCGGTTTATATAGA 58.264 45.455 0.00 0.00 0.00 1.98
1011 5298 2.908940 GCCAAGATCGCCATGGGG 60.909 66.667 22.46 22.46 34.71 4.96
1227 5532 1.153901 GATCCCGTCGAAGAACGCA 60.154 57.895 0.00 0.00 39.69 5.24
1389 5703 1.546029 CCAGTCTCGTGGATGAAGTGA 59.454 52.381 0.00 0.00 40.44 3.41
1397 5711 1.592400 CTTACGCCCAGTCTCGTGGA 61.592 60.000 0.00 0.00 40.44 4.02
1428 5742 6.071728 TGTTGGTAGTAGTAGTTAGTTGGAGC 60.072 42.308 0.00 0.00 0.00 4.70
1429 5743 7.176340 AGTGTTGGTAGTAGTAGTTAGTTGGAG 59.824 40.741 0.00 0.00 0.00 3.86
1431 5745 7.088905 CAGTGTTGGTAGTAGTAGTTAGTTGG 58.911 42.308 0.00 0.00 0.00 3.77
1435 5749 6.095160 CCTCCAGTGTTGGTAGTAGTAGTTAG 59.905 46.154 0.00 0.00 45.26 2.34
1436 5750 5.948162 CCTCCAGTGTTGGTAGTAGTAGTTA 59.052 44.000 0.00 0.00 45.26 2.24
1437 5751 4.771054 CCTCCAGTGTTGGTAGTAGTAGTT 59.229 45.833 0.00 0.00 45.26 2.24
1439 5753 4.597004 TCCTCCAGTGTTGGTAGTAGTAG 58.403 47.826 0.00 0.00 45.26 2.57
1440 5754 4.662966 TCCTCCAGTGTTGGTAGTAGTA 57.337 45.455 0.00 0.00 45.26 1.82
1459 5773 7.001073 AGCTTAATCATGGAGAGGTAAATTCC 58.999 38.462 0.00 0.00 0.00 3.01
1476 5801 6.316390 ACAAGTTACATACAGCCAGCTTAATC 59.684 38.462 0.00 0.00 0.00 1.75
1882 6212 1.688269 TTGTTCCCTGGGTCGACGTT 61.688 55.000 13.56 0.00 0.00 3.99
1883 6213 2.135581 TTGTTCCCTGGGTCGACGT 61.136 57.895 13.56 0.00 0.00 4.34
1947 6277 0.105778 AGGAGCATCGCTAGAAAGGC 59.894 55.000 0.00 0.00 39.88 4.35
1955 6285 0.754957 AGAGCAGTAGGAGCATCGCT 60.755 55.000 0.00 0.00 43.88 4.93
2074 6416 6.401047 CATCATTTGGATGTTGCCTAGAAT 57.599 37.500 0.00 0.00 46.81 2.40
2169 6516 5.064834 GTGATGAATAGACCGGAAGTTTTCC 59.935 44.000 9.46 0.00 46.62 3.13
2170 6517 5.875359 AGTGATGAATAGACCGGAAGTTTTC 59.125 40.000 9.46 5.22 0.00 2.29
2171 6518 5.805728 AGTGATGAATAGACCGGAAGTTTT 58.194 37.500 9.46 0.00 0.00 2.43
2172 6519 5.422214 AGTGATGAATAGACCGGAAGTTT 57.578 39.130 9.46 0.00 0.00 2.66
2173 6520 6.540438 TTAGTGATGAATAGACCGGAAGTT 57.460 37.500 9.46 0.00 0.00 2.66
2174 6521 6.323996 TGATTAGTGATGAATAGACCGGAAGT 59.676 38.462 9.46 0.00 0.00 3.01
2175 6522 6.749139 TGATTAGTGATGAATAGACCGGAAG 58.251 40.000 9.46 0.00 0.00 3.46
2176 6523 6.724893 TGATTAGTGATGAATAGACCGGAA 57.275 37.500 9.46 0.00 0.00 4.30
2177 6524 6.295292 CCATGATTAGTGATGAATAGACCGGA 60.295 42.308 9.46 0.00 0.00 5.14
2178 6525 5.871524 CCATGATTAGTGATGAATAGACCGG 59.128 44.000 0.00 0.00 0.00 5.28
2179 6526 5.349817 GCCATGATTAGTGATGAATAGACCG 59.650 44.000 0.00 0.00 0.00 4.79
2180 6527 6.233434 TGCCATGATTAGTGATGAATAGACC 58.767 40.000 0.00 0.00 0.00 3.85
2181 6528 7.157347 TCTGCCATGATTAGTGATGAATAGAC 58.843 38.462 0.00 0.00 0.00 2.59
2182 6529 7.307131 TCTGCCATGATTAGTGATGAATAGA 57.693 36.000 0.00 0.00 0.00 1.98
2183 6530 8.563123 AATCTGCCATGATTAGTGATGAATAG 57.437 34.615 0.00 0.00 35.18 1.73
2184 6531 8.929260 AAATCTGCCATGATTAGTGATGAATA 57.071 30.769 0.00 0.00 35.82 1.75
2185 6532 7.724506 AGAAATCTGCCATGATTAGTGATGAAT 59.275 33.333 0.00 0.00 35.82 2.57
2186 6533 7.012989 CAGAAATCTGCCATGATTAGTGATGAA 59.987 37.037 0.00 0.00 35.82 2.57
2187 6534 6.485648 CAGAAATCTGCCATGATTAGTGATGA 59.514 38.462 0.00 0.00 35.82 2.92
2188 6535 6.669278 CAGAAATCTGCCATGATTAGTGATG 58.331 40.000 0.00 0.00 35.82 3.07
2189 6536 6.879276 CAGAAATCTGCCATGATTAGTGAT 57.121 37.500 0.00 0.00 35.82 3.06
2203 6550 0.332632 TCCCTTGGGGCAGAAATCTG 59.667 55.000 5.78 6.05 43.94 2.90
2204 6551 0.627986 CTCCCTTGGGGCAGAAATCT 59.372 55.000 5.78 0.00 43.94 2.40
2205 6552 0.625849 TCTCCCTTGGGGCAGAAATC 59.374 55.000 5.78 0.00 43.94 2.17
2206 6553 1.312884 ATCTCCCTTGGGGCAGAAAT 58.687 50.000 5.78 0.00 43.94 2.17
2207 6554 1.846439 CTATCTCCCTTGGGGCAGAAA 59.154 52.381 5.78 0.00 43.94 2.52
2208 6555 1.511613 CTATCTCCCTTGGGGCAGAA 58.488 55.000 5.78 0.00 43.94 3.02
2209 6556 0.400525 CCTATCTCCCTTGGGGCAGA 60.401 60.000 5.78 2.78 43.94 4.26
2210 6557 0.695803 ACCTATCTCCCTTGGGGCAG 60.696 60.000 5.78 0.00 43.94 4.85
2211 6558 0.645496 TACCTATCTCCCTTGGGGCA 59.355 55.000 5.78 0.00 43.94 5.36
2212 6559 1.630878 CATACCTATCTCCCTTGGGGC 59.369 57.143 5.78 0.00 43.94 5.80
2213 6560 1.630878 GCATACCTATCTCCCTTGGGG 59.369 57.143 5.78 0.00 46.11 4.96
2214 6561 1.276421 CGCATACCTATCTCCCTTGGG 59.724 57.143 0.00 0.00 0.00 4.12
2215 6562 1.338200 GCGCATACCTATCTCCCTTGG 60.338 57.143 0.30 0.00 0.00 3.61
2216 6563 1.620819 AGCGCATACCTATCTCCCTTG 59.379 52.381 11.47 0.00 0.00 3.61
2217 6564 2.016905 AGCGCATACCTATCTCCCTT 57.983 50.000 11.47 0.00 0.00 3.95
2218 6565 1.620819 CAAGCGCATACCTATCTCCCT 59.379 52.381 11.47 0.00 0.00 4.20
2219 6566 1.344763 ACAAGCGCATACCTATCTCCC 59.655 52.381 11.47 0.00 0.00 4.30
2220 6567 2.821991 ACAAGCGCATACCTATCTCC 57.178 50.000 11.47 0.00 0.00 3.71
2221 6568 4.238514 CCTAACAAGCGCATACCTATCTC 58.761 47.826 11.47 0.00 0.00 2.75
2222 6569 3.006967 CCCTAACAAGCGCATACCTATCT 59.993 47.826 11.47 0.00 0.00 1.98
2223 6570 3.326747 CCCTAACAAGCGCATACCTATC 58.673 50.000 11.47 0.00 0.00 2.08
2224 6571 2.550208 GCCCTAACAAGCGCATACCTAT 60.550 50.000 11.47 0.00 0.00 2.57
2225 6572 1.202604 GCCCTAACAAGCGCATACCTA 60.203 52.381 11.47 0.00 0.00 3.08
2226 6573 0.463833 GCCCTAACAAGCGCATACCT 60.464 55.000 11.47 0.00 0.00 3.08
2227 6574 0.746563 TGCCCTAACAAGCGCATACC 60.747 55.000 11.47 0.00 0.00 2.73
2228 6575 1.264288 GATGCCCTAACAAGCGCATAC 59.736 52.381 11.47 0.00 41.85 2.39
2229 6576 1.140852 AGATGCCCTAACAAGCGCATA 59.859 47.619 11.47 0.00 41.85 3.14
2230 6577 0.107017 AGATGCCCTAACAAGCGCAT 60.107 50.000 11.47 0.00 44.36 4.73
2231 6578 0.744414 GAGATGCCCTAACAAGCGCA 60.744 55.000 11.47 0.00 35.35 6.09
2232 6579 1.440145 GGAGATGCCCTAACAAGCGC 61.440 60.000 0.00 0.00 0.00 5.92
2233 6580 0.107703 TGGAGATGCCCTAACAAGCG 60.108 55.000 0.00 0.00 34.97 4.68
2234 6581 1.745653 GTTGGAGATGCCCTAACAAGC 59.254 52.381 0.00 0.00 34.97 4.01
2235 6582 2.009774 CGTTGGAGATGCCCTAACAAG 58.990 52.381 0.00 0.00 34.97 3.16
2236 6583 1.626321 TCGTTGGAGATGCCCTAACAA 59.374 47.619 0.00 0.00 34.97 2.83
2237 6584 1.271856 TCGTTGGAGATGCCCTAACA 58.728 50.000 0.00 0.00 34.97 2.41
2238 6585 2.158957 TCATCGTTGGAGATGCCCTAAC 60.159 50.000 2.38 0.00 45.57 2.34
2239 6586 2.115427 TCATCGTTGGAGATGCCCTAA 58.885 47.619 2.38 0.00 45.57 2.69
2240 6587 1.412710 GTCATCGTTGGAGATGCCCTA 59.587 52.381 2.38 0.00 45.57 3.53
2241 6588 0.179000 GTCATCGTTGGAGATGCCCT 59.821 55.000 2.38 0.00 45.57 5.19
2242 6589 0.107703 TGTCATCGTTGGAGATGCCC 60.108 55.000 2.38 0.00 45.57 5.36
2261 6608 2.910688 ATGACGGAGCGGATTTACAT 57.089 45.000 0.00 0.00 0.00 2.29
2264 6611 3.305813 GGACATATGACGGAGCGGATTTA 60.306 47.826 10.38 0.00 0.00 1.40
2269 6616 1.371758 CGGACATATGACGGAGCGG 60.372 63.158 10.38 0.00 0.00 5.52
2270 6617 2.016704 GCGGACATATGACGGAGCG 61.017 63.158 20.14 10.49 0.00 5.03
2271 6618 0.941463 CTGCGGACATATGACGGAGC 60.941 60.000 23.57 17.09 39.08 4.70
2307 6659 1.546476 GTCTCCTTCATCAGTGTCCGT 59.454 52.381 0.00 0.00 0.00 4.69
2320 6672 0.625849 AATTGGATGGCGGTCTCCTT 59.374 50.000 0.00 0.00 32.47 3.36
2321 6673 0.181350 GAATTGGATGGCGGTCTCCT 59.819 55.000 0.00 0.00 32.47 3.69
2326 6678 1.416401 ACGATAGAATTGGATGGCGGT 59.584 47.619 0.00 0.00 41.38 5.68
2339 6691 5.070685 ACTGGCAGACATATACACGATAGA 58.929 41.667 23.66 0.00 41.38 1.98
2345 6701 6.370442 TGTTGTTTACTGGCAGACATATACAC 59.630 38.462 23.66 10.08 0.00 2.90
2356 6712 7.550551 TGAATTTCAAATTGTTGTTTACTGGCA 59.449 29.630 0.00 0.00 36.07 4.92
2408 6764 1.099295 ATCCGACGTGGTGCGATCTA 61.099 55.000 0.00 0.00 44.77 1.98
2409 6765 2.337749 GATCCGACGTGGTGCGATCT 62.338 60.000 0.00 0.00 44.77 2.75
2410 6766 1.944676 GATCCGACGTGGTGCGATC 60.945 63.158 0.00 0.00 44.77 3.69
2411 6767 2.104331 GATCCGACGTGGTGCGAT 59.896 61.111 0.00 0.00 44.77 4.58
2412 6768 3.366915 TGATCCGACGTGGTGCGA 61.367 61.111 0.00 0.00 44.77 5.10
2414 6770 1.447838 ATGTGATCCGACGTGGTGC 60.448 57.895 0.00 0.00 39.52 5.01
2418 6774 2.173669 GGGCATGTGATCCGACGTG 61.174 63.158 0.00 1.86 36.16 4.49
2419 6775 2.186903 GGGCATGTGATCCGACGT 59.813 61.111 0.00 0.00 0.00 4.34
2475 6841 4.819630 GGATATTCTTTTGTCACGGGCATA 59.180 41.667 0.00 0.00 0.00 3.14
2532 6901 4.554036 GGTCAGATCGGCAGGGCC 62.554 72.222 0.00 0.00 46.75 5.80
2533 6902 4.554036 GGGTCAGATCGGCAGGGC 62.554 72.222 0.00 0.00 0.00 5.19
2535 6904 2.801631 GGAGGGTCAGATCGGCAGG 61.802 68.421 0.00 0.00 0.00 4.85
2545 6920 1.118965 TTGAGCGTGAAGGAGGGTCA 61.119 55.000 0.00 0.00 43.39 4.02
2555 6930 1.007734 GACGACACCTTGAGCGTGA 60.008 57.895 0.00 0.00 33.78 4.35
2584 6960 0.839853 ACAAAGAGGAGGAGGCTGCT 60.840 55.000 8.79 8.79 0.00 4.24
2615 7032 1.354040 CAGCGACAACATGAGGAGTC 58.646 55.000 0.00 0.68 0.00 3.36
2677 7094 1.067295 AGGTGGAGTCTTTGGATGCA 58.933 50.000 0.00 0.00 0.00 3.96
2772 7212 2.093235 AGAGAAAAGGGCCTCGATTGAG 60.093 50.000 6.46 2.59 42.18 3.02
2775 7215 2.678190 CGAAGAGAAAAGGGCCTCGATT 60.678 50.000 6.46 2.12 34.75 3.34
2779 7219 1.443802 CACGAAGAGAAAAGGGCCTC 58.556 55.000 6.46 0.00 0.00 4.70
2787 7227 2.317609 GCTGGCGCACGAAGAGAAA 61.318 57.895 10.83 0.00 35.78 2.52
2797 7237 1.219124 CCTAGAAGAAGCTGGCGCA 59.781 57.895 10.83 0.00 39.10 6.09
2813 7253 4.466370 TCAAACTATTGATGGAGACGACCT 59.534 41.667 0.00 0.00 40.59 3.85
2838 7278 2.826725 GGAGGAGAAAAAGACGGAGAGA 59.173 50.000 0.00 0.00 0.00 3.10
2885 7328 2.863137 GACATCTTGTCGAAGCAGGATC 59.137 50.000 0.00 0.00 37.67 3.36
2886 7329 2.898705 GACATCTTGTCGAAGCAGGAT 58.101 47.619 0.00 0.00 37.67 3.24


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

AutoCloner maintained by Alex Coulton.