Multiple sequence alignment - TraesCS5D01G230600

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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 TraesCS5D01G230600 chr5D 100.000 3960 0 0 1 3960 337680220 337684179 0.000000e+00 7313.0
1 TraesCS5D01G230600 chr5D 90.583 446 34 3 3282 3719 427568852 427569297 5.700000e-163 584.0
2 TraesCS5D01G230600 chr5D 82.069 145 23 3 270 413 32158951 32158809 1.930000e-23 121.0
3 TraesCS5D01G230600 chr5D 78.363 171 32 5 513 681 457659348 457659515 5.410000e-19 106.0
4 TraesCS5D01G230600 chr5B 90.413 1648 89 20 1452 3036 396432691 396434332 0.000000e+00 2104.0
5 TraesCS5D01G230600 chr5B 94.684 602 21 1 834 1424 396432022 396432623 0.000000e+00 924.0
6 TraesCS5D01G230600 chr5B 87.268 754 76 13 1 746 396394306 396395047 0.000000e+00 843.0
7 TraesCS5D01G230600 chr5B 88.689 557 48 5 3282 3832 517215591 517216138 0.000000e+00 665.0
8 TraesCS5D01G230600 chr5B 87.013 231 27 3 3046 3273 347991385 347991155 1.410000e-64 257.0
9 TraesCS5D01G230600 chr5A 89.507 1096 61 13 1422 2482 438823785 438824861 0.000000e+00 1338.0
10 TraesCS5D01G230600 chr5A 93.154 891 58 2 3049 3936 643297404 643298294 0.000000e+00 1304.0
11 TraesCS5D01G230600 chr5A 93.097 507 29 4 919 1424 438823236 438823737 0.000000e+00 737.0
12 TraesCS5D01G230600 chr5A 87.257 565 58 10 3282 3832 542062914 542063478 2.010000e-177 632.0
13 TraesCS5D01G230600 chr5A 91.085 258 17 4 2561 2815 438842346 438842600 1.050000e-90 344.0
14 TraesCS5D01G230600 chr5A 88.933 253 14 4 2812 3050 438843676 438843928 2.310000e-77 300.0
15 TraesCS5D01G230600 chr5A 94.444 90 5 0 2472 2561 438837264 438837353 5.340000e-29 139.0
16 TraesCS5D01G230600 chr5A 90.909 77 3 1 748 820 438823053 438823129 2.520000e-17 100.0
17 TraesCS5D01G230600 chr5A 84.783 92 13 1 3870 3960 436905494 436905403 1.520000e-14 91.6
18 TraesCS5D01G230600 chr2B 92.274 919 65 6 3047 3960 408096277 408097194 0.000000e+00 1299.0
19 TraesCS5D01G230600 chr2B 82.121 1622 176 52 1432 2966 158431582 158433176 0.000000e+00 1284.0
20 TraesCS5D01G230600 chr2B 86.386 617 56 11 827 1424 158430917 158431524 0.000000e+00 649.0
21 TraesCS5D01G230600 chr2B 85.022 227 21 6 3047 3270 200084658 200084442 6.660000e-53 219.0
22 TraesCS5D01G230600 chr2B 82.581 155 25 2 501 654 444613168 444613015 6.900000e-28 135.0
23 TraesCS5D01G230600 chr1A 92.039 917 61 5 3047 3960 86559070 86559977 0.000000e+00 1279.0
24 TraesCS5D01G230600 chr1A 79.355 155 29 3 501 653 243605748 243605595 5.410000e-19 106.0
25 TraesCS5D01G230600 chr2D 87.520 617 49 10 827 1424 108769784 108770391 0.000000e+00 688.0
26 TraesCS5D01G230600 chr2D 82.759 638 78 6 1421 2028 108770438 108771073 1.250000e-149 540.0
27 TraesCS5D01G230600 chr2D 87.872 437 46 4 2033 2463 108771107 108771542 1.270000e-139 507.0
28 TraesCS5D01G230600 chr2D 83.227 471 52 16 2483 2941 108771611 108772066 1.320000e-109 407.0
29 TraesCS5D01G230600 chr2D 89.496 238 21 3 3047 3281 370957202 370957438 8.320000e-77 298.0
30 TraesCS5D01G230600 chr2A 85.714 623 53 16 827 1424 104787241 104787852 3.360000e-175 625.0
31 TraesCS5D01G230600 chr2A 84.041 589 65 7 1471 2032 104787949 104788535 1.250000e-149 540.0
32 TraesCS5D01G230600 chr2A 86.726 452 53 4 2035 2480 104788567 104789017 2.750000e-136 496.0
33 TraesCS5D01G230600 chr2A 82.627 472 50 17 2483 2951 104789079 104789521 4.800000e-104 388.0
34 TraesCS5D01G230600 chr2A 81.333 150 26 2 273 420 66805926 66805777 1.930000e-23 121.0
35 TraesCS5D01G230600 chr7D 94.618 353 18 1 3608 3960 555876791 555876440 2.690000e-151 545.0
36 TraesCS5D01G230600 chr7D 82.394 142 21 4 272 411 84247484 84247623 1.930000e-23 121.0
37 TraesCS5D01G230600 chr7D 78.947 152 19 7 513 663 235571487 235571626 1.520000e-14 91.6
38 TraesCS5D01G230600 chr6D 84.400 250 23 7 3047 3281 352758648 352758400 8.560000e-57 231.0
39 TraesCS5D01G230600 chr6D 82.979 141 22 2 271 410 89701000 89700861 4.150000e-25 126.0
40 TraesCS5D01G230600 chr3A 85.650 223 28 4 3049 3268 660904941 660904720 8.560000e-57 231.0
41 TraesCS5D01G230600 chr3A 79.268 164 31 3 501 662 529183784 529183622 1.160000e-20 111.0
42 TraesCS5D01G230600 chr6A 83.628 226 33 4 3038 3260 564086037 564086261 4.010000e-50 209.0
43 TraesCS5D01G230600 chr3B 83.772 228 25 3 3048 3273 808853161 808852944 5.190000e-49 206.0
44 TraesCS5D01G230600 chr3B 89.706 136 11 3 3825 3958 808851985 808851851 1.890000e-38 171.0
45 TraesCS5D01G230600 chr4A 91.818 110 8 1 3852 3960 650905238 650905129 6.850000e-33 152.0
46 TraesCS5D01G230600 chr4A 83.333 138 19 3 273 410 198122214 198122347 1.490000e-24 124.0
47 TraesCS5D01G230600 chr3D 85.075 134 17 2 270 403 516673290 516673160 2.480000e-27 134.0
48 TraesCS5D01G230600 chr3D 83.108 148 18 6 272 416 607008277 607008420 1.160000e-25 128.0
49 TraesCS5D01G230600 chr7B 83.108 148 17 6 270 410 21662687 21662541 1.160000e-25 128.0
50 TraesCS5D01G230600 chr1B 90.909 44 4 0 502 545 44588086 44588129 4.270000e-05 60.2


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 TraesCS5D01G230600 chr5D 337680220 337684179 3959 False 7313.00 7313 100.0000 1 3960 1 chr5D.!!$F1 3959
1 TraesCS5D01G230600 chr5B 396432022 396434332 2310 False 1514.00 2104 92.5485 834 3036 2 chr5B.!!$F3 2202
2 TraesCS5D01G230600 chr5B 396394306 396395047 741 False 843.00 843 87.2680 1 746 1 chr5B.!!$F1 745
3 TraesCS5D01G230600 chr5B 517215591 517216138 547 False 665.00 665 88.6890 3282 3832 1 chr5B.!!$F2 550
4 TraesCS5D01G230600 chr5A 643297404 643298294 890 False 1304.00 1304 93.1540 3049 3936 1 chr5A.!!$F3 887
5 TraesCS5D01G230600 chr5A 438823053 438824861 1808 False 725.00 1338 91.1710 748 2482 3 chr5A.!!$F4 1734
6 TraesCS5D01G230600 chr5A 542062914 542063478 564 False 632.00 632 87.2570 3282 3832 1 chr5A.!!$F2 550
7 TraesCS5D01G230600 chr5A 438842346 438843928 1582 False 322.00 344 90.0090 2561 3050 2 chr5A.!!$F5 489
8 TraesCS5D01G230600 chr2B 408096277 408097194 917 False 1299.00 1299 92.2740 3047 3960 1 chr2B.!!$F1 913
9 TraesCS5D01G230600 chr2B 158430917 158433176 2259 False 966.50 1284 84.2535 827 2966 2 chr2B.!!$F2 2139
10 TraesCS5D01G230600 chr1A 86559070 86559977 907 False 1279.00 1279 92.0390 3047 3960 1 chr1A.!!$F1 913
11 TraesCS5D01G230600 chr2D 108769784 108772066 2282 False 535.50 688 85.3445 827 2941 4 chr2D.!!$F2 2114
12 TraesCS5D01G230600 chr2A 104787241 104789521 2280 False 512.25 625 84.7770 827 2951 4 chr2A.!!$F1 2124

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
25 26 0.036010 AAGTGGCCAAGATCGACCAG 60.036 55.0 7.24 0.0 31.46 4.00 F
333 334 0.252103 GAGGTGGTCACAGGGGTAGA 60.252 60.0 3.40 0.0 0.00 2.59 F
375 377 0.790207 GGTGAGTGTGTGTGCGTATG 59.210 55.0 0.00 0.0 0.00 2.39 F
1687 1837 0.036732 TGGTTGCTTGAAGCCTCGAT 59.963 50.0 15.43 0.0 41.51 3.59 F
1783 1945 0.535553 TTGGTCGGCCAGTGTTTACC 60.536 55.0 9.61 0.0 46.91 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 1393 0.179015 TTAAACAGCCGGCAGGAACA 60.179 50.000 31.54 5.06 41.02 3.18 R
1525 1671 1.064758 AGCCTGACACAACCAAACTGA 60.065 47.619 0.00 0.00 0.00 3.41 R
2298 2511 1.213678 TGCTAGGCAATCCAGCATCTT 59.786 47.619 0.00 0.00 39.70 2.40 R
2767 3077 0.177836 ACCTGGTTTGGTTTGCTTGC 59.822 50.000 0.00 0.00 36.89 4.01 R
3014 4425 0.320374 AAACGAAGACGGATGGAGCA 59.680 50.000 0.00 0.00 44.46 4.26 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
25 26 0.036010 AAGTGGCCAAGATCGACCAG 60.036 55.000 7.24 0.00 31.46 4.00
34 35 2.947652 CAAGATCGACCAGCAAATCCAT 59.052 45.455 0.00 0.00 0.00 3.41
35 36 2.569059 AGATCGACCAGCAAATCCATG 58.431 47.619 0.00 0.00 0.00 3.66
37 38 0.394216 TCGACCAGCAAATCCATGGG 60.394 55.000 13.02 0.00 38.48 4.00
57 58 3.837355 GGAAGCCCCAAATATGATGACT 58.163 45.455 0.00 0.00 34.14 3.41
78 79 3.274095 AGAGAACCCAAAGCATAGAGC 57.726 47.619 0.00 0.00 46.19 4.09
88 89 3.193471 GCATAGAGCTCGAGGAAGC 57.807 57.895 15.58 6.76 42.82 3.86
94 95 2.202864 GCTCGAGGAAGCTGAGGC 60.203 66.667 15.58 0.00 39.27 4.70
116 117 3.681897 CGATAGCAGTGGGAGATAAATGC 59.318 47.826 0.00 0.00 0.00 3.56
125 126 3.938963 TGGGAGATAAATGCGTCAAACTC 59.061 43.478 0.00 0.00 0.00 3.01
128 129 5.112686 GGAGATAAATGCGTCAAACTCTCT 58.887 41.667 0.00 0.00 0.00 3.10
129 130 5.006165 GGAGATAAATGCGTCAAACTCTCTG 59.994 44.000 0.00 0.00 0.00 3.35
153 154 1.400113 GGTAAAAGCGGGCACGTAAAC 60.400 52.381 11.45 1.29 43.45 2.01
160 161 3.060000 GGCACGTAAACAGGGGGC 61.060 66.667 0.00 0.00 0.00 5.80
177 178 2.345244 CAGGAGGAGCACGCAACT 59.655 61.111 0.00 0.00 0.00 3.16
182 183 1.287730 GAGGAGCACGCAACTGACTG 61.288 60.000 0.00 0.00 0.00 3.51
193 194 4.211389 CGCAACTGACTGAACAAATACAC 58.789 43.478 0.00 0.00 0.00 2.90
198 199 3.799366 TGACTGAACAAATACACACGGT 58.201 40.909 0.00 0.00 0.00 4.83
217 218 4.202578 GGTAGTAGACAACCGTATCGAC 57.797 50.000 0.00 0.00 0.00 4.20
237 238 3.898529 ACGATCGGATAGACGGAAAATC 58.101 45.455 20.98 0.00 0.00 2.17
249 250 1.201921 CGGAAAATCTGGCGAGAAACG 60.202 52.381 1.37 0.00 45.66 3.60
268 269 3.259064 ACGAGACATGGTCATAAAACCG 58.741 45.455 0.00 0.00 42.62 4.44
277 278 1.395954 GTCATAAAACCGGGCGACTTC 59.604 52.381 6.32 0.00 0.00 3.01
278 279 0.372334 CATAAAACCGGGCGACTTCG 59.628 55.000 6.32 0.00 43.27 3.79
310 311 0.689055 TGATGTGCCAGCTCAGTCTT 59.311 50.000 0.65 0.00 0.00 3.01
313 314 0.469494 TGTGCCAGCTCAGTCTTTCA 59.531 50.000 0.00 0.00 0.00 2.69
314 315 1.155042 GTGCCAGCTCAGTCTTTCAG 58.845 55.000 0.00 0.00 0.00 3.02
324 325 2.365617 TCAGTCTTTCAGAGGTGGTCAC 59.634 50.000 0.00 0.00 0.00 3.67
333 334 0.252103 GAGGTGGTCACAGGGGTAGA 60.252 60.000 3.40 0.00 0.00 2.59
335 336 1.597461 GTGGTCACAGGGGTAGAGC 59.403 63.158 0.00 0.00 0.00 4.09
336 337 0.905337 GTGGTCACAGGGGTAGAGCT 60.905 60.000 0.00 0.00 0.00 4.09
337 338 0.904865 TGGTCACAGGGGTAGAGCTG 60.905 60.000 0.00 0.00 0.00 4.24
338 339 1.219393 GTCACAGGGGTAGAGCTGC 59.781 63.158 0.00 0.00 0.00 5.25
339 340 1.229177 TCACAGGGGTAGAGCTGCA 60.229 57.895 1.02 0.00 0.00 4.41
354 356 1.600957 GCTGCATGCGTGAGTTCATAT 59.399 47.619 14.09 0.00 0.00 1.78
375 377 0.790207 GGTGAGTGTGTGTGCGTATG 59.210 55.000 0.00 0.00 0.00 2.39
378 380 2.407361 GTGAGTGTGTGTGCGTATGTAC 59.593 50.000 0.00 0.00 0.00 2.90
405 407 4.511734 GTCTGCGTTTGTACTGTGTTTAC 58.488 43.478 0.00 0.00 0.00 2.01
410 412 6.323266 TGCGTTTGTACTGTGTTTACAAAAT 58.677 32.000 8.78 0.00 46.08 1.82
411 413 7.470079 TGCGTTTGTACTGTGTTTACAAAATA 58.530 30.769 8.78 0.00 46.08 1.40
412 414 7.966753 TGCGTTTGTACTGTGTTTACAAAATAA 59.033 29.630 8.78 0.00 46.08 1.40
413 415 8.796278 GCGTTTGTACTGTGTTTACAAAATAAA 58.204 29.630 8.78 0.00 46.08 1.40
445 447 2.537143 ACGGACAGAATAAGGTGGACT 58.463 47.619 0.00 0.00 0.00 3.85
464 466 1.077429 GACCAGGCTGGCCCTTAAG 60.077 63.158 33.04 7.53 43.06 1.85
496 499 6.037720 CCAAAAACAAAATCCACCACTAAACC 59.962 38.462 0.00 0.00 0.00 3.27
505 508 2.486592 CCACCACTAAACCGGAATTGAC 59.513 50.000 9.46 0.00 0.00 3.18
510 513 1.020333 TAAACCGGAATTGACGCGGG 61.020 55.000 9.46 0.80 0.00 6.13
511 514 2.734948 AAACCGGAATTGACGCGGGA 62.735 55.000 9.46 0.00 0.00 5.14
544 547 3.115554 AGTTTGCAAGCACGACAATTTC 58.884 40.909 16.04 0.00 0.00 2.17
561 565 8.202697 CGACAATTTCGTGGTAAACAAATAAAC 58.797 33.333 2.97 0.00 43.24 2.01
580 584 9.520515 AAATAAACTGAGTCAGATTTACCATGT 57.479 29.630 26.86 4.04 35.18 3.21
590 594 6.007076 TCAGATTTACCATGTTTGCCAACTA 58.993 36.000 2.01 0.00 33.58 2.24
597 601 4.161377 ACCATGTTTGCCAACTAAACTTGT 59.839 37.500 2.01 0.00 39.54 3.16
617 621 3.065233 TGTCATCATCGGCAAGCATAAAC 59.935 43.478 0.00 0.00 0.00 2.01
645 650 6.313411 CCATAAAAATGTTCGATTTGCCATGT 59.687 34.615 0.00 0.00 0.00 3.21
650 655 4.313277 TGTTCGATTTGCCATGTCAAAA 57.687 36.364 5.94 0.00 39.13 2.44
651 656 4.686972 TGTTCGATTTGCCATGTCAAAAA 58.313 34.783 5.94 0.00 39.13 1.94
692 697 5.088739 GCAGTCGAGTCCAATGTAAAAATG 58.911 41.667 0.00 0.00 0.00 2.32
693 698 5.088739 CAGTCGAGTCCAATGTAAAAATGC 58.911 41.667 0.00 0.00 0.00 3.56
694 699 4.759693 AGTCGAGTCCAATGTAAAAATGCA 59.240 37.500 0.00 0.00 0.00 3.96
695 700 5.415701 AGTCGAGTCCAATGTAAAAATGCAT 59.584 36.000 0.00 0.00 0.00 3.96
696 701 6.071952 AGTCGAGTCCAATGTAAAAATGCATT 60.072 34.615 5.99 5.99 35.91 3.56
698 703 7.116233 GTCGAGTCCAATGTAAAAATGCATTTT 59.884 33.333 27.73 27.73 43.52 1.82
700 705 8.920665 CGAGTCCAATGTAAAAATGCATTTTTA 58.079 29.630 36.46 36.46 45.24 1.52
730 739 6.500400 ACATTTCCTTGGGCCTTACTATTTTT 59.500 34.615 4.53 0.00 0.00 1.94
763 772 4.434545 AATAGCAGATGCACTCCTCATT 57.565 40.909 7.68 0.00 45.16 2.57
764 773 2.328819 AGCAGATGCACTCCTCATTC 57.671 50.000 7.68 0.00 45.16 2.67
776 789 1.546029 TCCTCATTCAGACCACTCACG 59.454 52.381 0.00 0.00 0.00 4.35
806 819 2.273449 CCTAGCCCAACCCAGCAG 59.727 66.667 0.00 0.00 0.00 4.24
900 976 1.529226 AAACAATCCGAATCGCCACA 58.471 45.000 0.00 0.00 0.00 4.17
929 1005 1.644786 CTCCAATGCCGAAACCGTCC 61.645 60.000 0.00 0.00 0.00 4.79
1086 1176 4.200283 GAGCTCCGACGCCTCTGG 62.200 72.222 0.87 0.00 0.00 3.86
1183 1278 1.612463 ACCTCTCTGTTGTACGTGTCC 59.388 52.381 0.00 0.00 0.00 4.02
1229 1324 1.408683 GGTGTGCAAGGCCATCATCTA 60.409 52.381 5.01 0.00 0.00 1.98
1298 1393 1.402787 GACGGATTGCCCATTTGGAT 58.597 50.000 0.00 0.00 37.39 3.41
1336 1432 4.175337 GCATGCCTGACCCGCCTA 62.175 66.667 6.36 0.00 0.00 3.93
1448 1594 8.523523 TTGCATTTCTGTTTCACTAATTCATG 57.476 30.769 0.00 0.00 0.00 3.07
1513 1659 1.060937 GACGACATTGGATGTGCGC 59.939 57.895 0.00 0.00 45.03 6.09
1534 1680 2.029110 CGAATTGGGCATTCAGTTTGGT 60.029 45.455 0.00 0.00 41.51 3.67
1570 1716 2.893489 ACCTTTTGTGCAGAAGGGATTC 59.107 45.455 20.80 0.00 44.45 2.52
1578 1724 1.081892 CAGAAGGGATTCGTGCTGTG 58.918 55.000 0.00 0.00 31.49 3.66
1609 1759 2.293399 CCTTTGGTAGTTCTGTTGTGCC 59.707 50.000 0.00 0.00 0.00 5.01
1610 1760 3.214328 CTTTGGTAGTTCTGTTGTGCCT 58.786 45.455 0.00 0.00 0.00 4.75
1646 1796 5.651576 TGCTATTGATGTCTGGTTATGCAAA 59.348 36.000 0.00 0.00 0.00 3.68
1650 1800 5.327616 TGATGTCTGGTTATGCAAATTGG 57.672 39.130 0.00 0.00 0.00 3.16
1655 1805 1.066286 TGGTTATGCAAATTGGCCTGC 60.066 47.619 3.32 5.93 39.09 4.85
1671 1821 3.019964 TGCGATGCAGAGTTTTGGT 57.980 47.368 0.00 0.00 33.32 3.67
1687 1837 0.036732 TGGTTGCTTGAAGCCTCGAT 59.963 50.000 15.43 0.00 41.51 3.59
1705 1855 6.459066 CCTCGATTGATGTACTGATGGTAAT 58.541 40.000 0.00 0.00 31.56 1.89
1707 1857 7.542477 CCTCGATTGATGTACTGATGGTAATAC 59.458 40.741 0.00 0.00 31.56 1.89
1783 1945 0.535553 TTGGTCGGCCAGTGTTTACC 60.536 55.000 9.61 0.00 46.91 2.85
1791 1953 0.884704 CCAGTGTTTACCGCAGCAGT 60.885 55.000 0.00 0.00 0.00 4.40
1835 1997 4.641989 GGCATAAGGTGACAACAGAATCAT 59.358 41.667 0.00 0.00 35.22 2.45
1964 2145 5.163509 TGTGTGGTACATCTAGCTCTGAATC 60.164 44.000 0.00 0.00 44.52 2.52
2003 2184 7.434307 GGACTTGATTTGTCATATCTTTGCATG 59.566 37.037 5.10 0.00 36.26 4.06
2010 2191 3.795101 GTCATATCTTTGCATGCAGTTGC 59.205 43.478 21.50 5.31 43.07 4.17
2091 2303 0.602562 TGTTATTTGTGCTGGCTGCC 59.397 50.000 12.87 12.87 42.00 4.85
2252 2465 2.463047 AAAAGTTTGTGGGCTGGGTA 57.537 45.000 0.00 0.00 0.00 3.69
2286 2499 3.992643 TGCAACAGCTTGTAATTTGCAT 58.007 36.364 3.28 0.00 45.70 3.96
2573 2870 8.874816 GCAGCTAGTAATATTGTTATAGCTTCC 58.125 37.037 16.49 10.67 42.37 3.46
2583 2884 4.839121 TGTTATAGCTTCCCGTTTCACAT 58.161 39.130 0.00 0.00 0.00 3.21
2605 2906 1.336440 TGTGGATGCTGGTTTTTGTCG 59.664 47.619 0.00 0.00 0.00 4.35
2628 2931 4.843147 CATAGTTTGCAGTTCGTTGTTCA 58.157 39.130 0.00 0.00 0.00 3.18
2639 2949 4.264380 AGTTCGTTGTTCAACGCATTTTTC 59.736 37.500 26.36 9.30 45.06 2.29
2647 2957 6.329496 TGTTCAACGCATTTTTCTTCTTTCT 58.671 32.000 0.00 0.00 0.00 2.52
2666 2976 6.818644 TCTTTCTATATCCTTGTTGTGACTGC 59.181 38.462 0.00 0.00 0.00 4.40
2667 2977 5.939764 TCTATATCCTTGTTGTGACTGCT 57.060 39.130 0.00 0.00 0.00 4.24
2684 2994 1.375098 GCTCTGCCTGATTCCTGCAC 61.375 60.000 0.00 0.00 0.00 4.57
2767 3077 5.413309 AAGTCTTCAGTTATCTCCACCAG 57.587 43.478 0.00 0.00 0.00 4.00
2878 4275 3.620966 GCTAAAATGACCTCTCTGGCTGT 60.621 47.826 0.00 0.00 40.22 4.40
2937 4334 4.576463 TCAGCTGAACTTCAAGAAGAAACC 59.424 41.667 15.67 3.51 40.79 3.27
2966 4377 1.940613 CCGCCACCAGCTAACTAAATC 59.059 52.381 0.00 0.00 40.39 2.17
2987 4398 2.099263 CAGCATGAAAGGAATGGAGCTG 59.901 50.000 0.00 0.00 39.69 4.24
3014 4425 2.699846 TGATGCAAAAAGGGCACTTCTT 59.300 40.909 0.00 0.00 45.23 2.52
3028 4439 1.625818 ACTTCTTGCTCCATCCGTCTT 59.374 47.619 0.00 0.00 0.00 3.01
3086 4497 2.882137 GAGACCCATTTTGTCCGTTTGA 59.118 45.455 0.00 0.00 33.09 2.69
3205 4620 0.390735 AATGGGTACGAAGCGGACAC 60.391 55.000 4.46 0.46 45.45 3.67
3272 4687 2.122729 TCCCACCTAGCAGTGCCT 59.877 61.111 12.58 1.64 36.38 4.75
3273 4688 1.538876 TCCCACCTAGCAGTGCCTT 60.539 57.895 12.58 0.00 36.38 4.35
3545 4967 4.514577 CTCTTCACGGCCGCGGAT 62.515 66.667 33.48 10.83 0.00 4.18
3690 5124 2.282958 AGAAGGAGCGGGTCGTCA 60.283 61.111 2.62 0.00 0.00 4.35
3772 5206 2.418910 CGTGCCTCGAGGACCTCAT 61.419 63.158 35.69 0.00 42.86 2.90
3888 5323 1.266989 CTGTCCGCTTTTGGGTTCTTC 59.733 52.381 0.00 0.00 0.00 2.87
3894 5329 1.679153 GCTTTTGGGTTCTTCCGTTGA 59.321 47.619 0.00 0.00 37.00 3.18
3909 5344 1.073025 TTGAATGCCCGCAGTGTCT 59.927 52.632 0.00 0.00 0.00 3.41
3922 5357 4.408821 TGTCTGCCCCATGTCCGC 62.409 66.667 0.00 0.00 0.00 5.54
3925 5360 4.738998 CTGCCCCATGTCCGCCAA 62.739 66.667 0.00 0.00 0.00 4.52
3928 5363 4.738998 CCCCATGTCCGCCAAGCA 62.739 66.667 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.123248 TTGCTGGTCGATCTTGGCCA 62.123 55.000 0.00 0.00 0.00 5.36
10 11 0.960364 TTTGCTGGTCGATCTTGGCC 60.960 55.000 0.00 0.00 0.00 5.36
25 26 1.825341 GGGCTTCCCATGGATTTGC 59.175 57.895 15.22 11.57 44.65 3.68
37 38 5.869579 TCTAGTCATCATATTTGGGGCTTC 58.130 41.667 0.00 0.00 0.00 3.86
57 58 4.408182 GCTCTATGCTTTGGGTTCTCTA 57.592 45.455 0.00 0.00 38.95 2.43
78 79 1.733402 ATCGCCTCAGCTTCCTCGAG 61.733 60.000 5.13 5.13 36.60 4.04
88 89 1.068753 CCCACTGCTATCGCCTCAG 59.931 63.158 0.00 0.00 34.43 3.35
94 95 3.681897 GCATTTATCTCCCACTGCTATCG 59.318 47.826 0.00 0.00 0.00 2.92
108 109 6.244275 GTTCAGAGAGTTTGACGCATTTATC 58.756 40.000 0.00 0.00 0.00 1.75
110 111 4.149922 CGTTCAGAGAGTTTGACGCATTTA 59.850 41.667 0.00 0.00 0.00 1.40
116 117 2.135664 ACCGTTCAGAGAGTTTGACG 57.864 50.000 0.00 0.00 0.00 4.35
125 126 1.076332 CCCGCTTTTACCGTTCAGAG 58.924 55.000 0.00 0.00 0.00 3.35
128 129 1.227883 TGCCCGCTTTTACCGTTCA 60.228 52.632 0.00 0.00 0.00 3.18
129 130 1.208358 GTGCCCGCTTTTACCGTTC 59.792 57.895 0.00 0.00 0.00 3.95
160 161 2.031516 CAGTTGCGTGCTCCTCCTG 61.032 63.158 0.00 0.00 0.00 3.86
177 178 3.799366 ACCGTGTGTATTTGTTCAGTCA 58.201 40.909 0.00 0.00 0.00 3.41
182 183 6.151691 TGTCTACTACCGTGTGTATTTGTTC 58.848 40.000 0.00 0.00 0.00 3.18
198 199 4.445718 GATCGTCGATACGGTTGTCTACTA 59.554 45.833 7.93 0.00 44.12 1.82
217 218 3.914966 CAGATTTTCCGTCTATCCGATCG 59.085 47.826 8.51 8.51 0.00 3.69
222 223 2.135933 CGCCAGATTTTCCGTCTATCC 58.864 52.381 0.00 0.00 0.00 2.59
228 229 1.804748 GTTTCTCGCCAGATTTTCCGT 59.195 47.619 0.00 0.00 0.00 4.69
237 238 0.994995 CATGTCTCGTTTCTCGCCAG 59.005 55.000 0.00 0.00 39.67 4.85
249 250 2.943033 CCCGGTTTTATGACCATGTCTC 59.057 50.000 0.00 0.00 39.78 3.36
277 278 3.002042 GGCACATCATCTTGAGATTGACG 59.998 47.826 0.90 0.00 31.21 4.35
278 279 3.943381 TGGCACATCATCTTGAGATTGAC 59.057 43.478 0.90 0.00 31.21 3.18
310 311 1.127567 CCCCTGTGACCACCTCTGAA 61.128 60.000 0.00 0.00 0.00 3.02
313 314 0.252284 CTACCCCTGTGACCACCTCT 60.252 60.000 0.00 0.00 0.00 3.69
314 315 0.252103 TCTACCCCTGTGACCACCTC 60.252 60.000 0.00 0.00 0.00 3.85
324 325 1.525535 GCATGCAGCTCTACCCCTG 60.526 63.158 14.21 0.00 41.15 4.45
333 334 0.675837 ATGAACTCACGCATGCAGCT 60.676 50.000 19.57 0.00 42.61 4.24
335 336 2.032290 CCATATGAACTCACGCATGCAG 60.032 50.000 19.57 12.98 0.00 4.41
336 337 1.941975 CCATATGAACTCACGCATGCA 59.058 47.619 19.57 0.00 0.00 3.96
337 338 1.265095 CCCATATGAACTCACGCATGC 59.735 52.381 7.91 7.91 0.00 4.06
338 339 2.288729 CACCCATATGAACTCACGCATG 59.711 50.000 3.65 0.00 0.00 4.06
339 340 2.170397 TCACCCATATGAACTCACGCAT 59.830 45.455 3.65 0.00 0.00 4.73
354 356 1.677637 TACGCACACACACTCACCCA 61.678 55.000 0.00 0.00 0.00 4.51
375 377 1.273455 ACAAACGCAGACGCTCGTAC 61.273 55.000 0.00 0.00 45.53 3.67
378 380 1.002250 AGTACAAACGCAGACGCTCG 61.002 55.000 0.00 0.00 45.53 5.03
385 387 4.523853 TGTAAACACAGTACAAACGCAG 57.476 40.909 0.00 0.00 0.00 5.18
414 416 4.759516 ATTCTGTCCGTTGCGTATTTTT 57.240 36.364 0.00 0.00 0.00 1.94
415 417 5.163794 CCTTATTCTGTCCGTTGCGTATTTT 60.164 40.000 0.00 0.00 0.00 1.82
416 418 4.331717 CCTTATTCTGTCCGTTGCGTATTT 59.668 41.667 0.00 0.00 0.00 1.40
417 419 3.869246 CCTTATTCTGTCCGTTGCGTATT 59.131 43.478 0.00 0.00 0.00 1.89
418 420 3.118884 ACCTTATTCTGTCCGTTGCGTAT 60.119 43.478 0.00 0.00 0.00 3.06
419 421 2.231964 ACCTTATTCTGTCCGTTGCGTA 59.768 45.455 0.00 0.00 0.00 4.42
420 422 1.001633 ACCTTATTCTGTCCGTTGCGT 59.998 47.619 0.00 0.00 0.00 5.24
421 423 1.393539 CACCTTATTCTGTCCGTTGCG 59.606 52.381 0.00 0.00 0.00 4.85
422 424 1.737793 CCACCTTATTCTGTCCGTTGC 59.262 52.381 0.00 0.00 0.00 4.17
427 429 3.369576 GGTCAGTCCACCTTATTCTGTCC 60.370 52.174 0.00 0.00 35.97 4.02
431 433 2.840651 CCTGGTCAGTCCACCTTATTCT 59.159 50.000 0.00 0.00 41.93 2.40
445 447 1.850289 TTAAGGGCCAGCCTGGTCA 60.850 57.895 18.72 0.00 45.98 4.02
471 474 6.037720 GGTTTAGTGGTGGATTTTGTTTTTGG 59.962 38.462 0.00 0.00 0.00 3.28
488 491 1.201877 CGCGTCAATTCCGGTTTAGTG 60.202 52.381 0.00 0.00 0.00 2.74
496 499 1.087202 TCATTCCCGCGTCAATTCCG 61.087 55.000 4.92 0.00 0.00 4.30
505 508 3.757745 ACTAAATTTGTCATTCCCGCG 57.242 42.857 0.00 0.00 0.00 6.46
537 540 9.026074 CAGTTTATTTGTTTACCACGAAATTGT 57.974 29.630 0.00 0.00 32.08 2.71
544 547 6.950545 TGACTCAGTTTATTTGTTTACCACG 58.049 36.000 0.00 0.00 0.00 4.94
553 557 9.778993 CATGGTAAATCTGACTCAGTTTATTTG 57.221 33.333 5.94 6.37 32.61 2.32
556 560 9.520515 AAACATGGTAAATCTGACTCAGTTTAT 57.479 29.630 5.94 0.00 32.61 1.40
558 562 7.651808 CAAACATGGTAAATCTGACTCAGTTT 58.348 34.615 5.94 8.37 32.61 2.66
561 565 5.392380 GGCAAACATGGTAAATCTGACTCAG 60.392 44.000 0.00 0.00 0.00 3.35
590 594 2.095059 GCTTGCCGATGATGACAAGTTT 60.095 45.455 0.00 0.00 41.22 2.66
597 601 3.313249 CAGTTTATGCTTGCCGATGATGA 59.687 43.478 0.00 0.00 0.00 2.92
617 621 5.220453 GGCAAATCGAACATTTTTATGGCAG 60.220 40.000 0.00 0.00 0.00 4.85
629 634 3.998099 TTTGACATGGCAAATCGAACA 57.002 38.095 22.97 0.00 33.16 3.18
670 675 5.088739 GCATTTTTACATTGGACTCGACTG 58.911 41.667 0.00 0.00 0.00 3.51
692 697 7.529158 CCCAAGGAAATGTCAAATAAAAATGC 58.471 34.615 0.00 0.00 0.00 3.56
693 698 7.361971 GGCCCAAGGAAATGTCAAATAAAAATG 60.362 37.037 0.00 0.00 0.00 2.32
694 699 6.658816 GGCCCAAGGAAATGTCAAATAAAAAT 59.341 34.615 0.00 0.00 0.00 1.82
695 700 6.000840 GGCCCAAGGAAATGTCAAATAAAAA 58.999 36.000 0.00 0.00 0.00 1.94
696 701 5.309282 AGGCCCAAGGAAATGTCAAATAAAA 59.691 36.000 0.00 0.00 0.00 1.52
698 703 4.424842 AGGCCCAAGGAAATGTCAAATAA 58.575 39.130 0.00 0.00 0.00 1.40
700 705 2.906568 AGGCCCAAGGAAATGTCAAAT 58.093 42.857 0.00 0.00 0.00 2.32
702 707 2.397044 AAGGCCCAAGGAAATGTCAA 57.603 45.000 0.00 0.00 0.00 3.18
704 709 3.087370 AGTAAGGCCCAAGGAAATGTC 57.913 47.619 0.00 0.00 0.00 3.06
712 721 6.339587 TCAACAAAAATAGTAAGGCCCAAG 57.660 37.500 0.00 0.00 0.00 3.61
730 739 6.200665 GTGCATCTGCTATTTGTTTTTCAACA 59.799 34.615 3.53 0.00 40.55 3.33
746 755 1.941294 CTGAATGAGGAGTGCATCTGC 59.059 52.381 0.00 0.00 42.50 4.26
763 772 2.276116 GGGCTCGTGAGTGGTCTGA 61.276 63.158 0.00 0.00 0.00 3.27
764 773 2.262915 GGGCTCGTGAGTGGTCTG 59.737 66.667 0.00 0.00 0.00 3.51
776 789 3.541713 CTAGGCTCGGGTGGGCTC 61.542 72.222 0.00 0.00 40.13 4.70
900 976 3.420893 TCGGCATTGGAGTGAAGAAATT 58.579 40.909 0.00 0.00 0.00 1.82
1086 1176 2.417515 GGAGGAGTCGAAGTTGATGTCC 60.418 54.545 0.00 0.00 0.00 4.02
1142 1234 1.419381 GAGGGAGAGGAGGTGATTCC 58.581 60.000 0.00 0.00 37.52 3.01
1183 1278 2.787249 CGCGAAACCAGCATCAGG 59.213 61.111 0.00 0.00 34.19 3.86
1298 1393 0.179015 TTAAACAGCCGGCAGGAACA 60.179 50.000 31.54 5.06 41.02 3.18
1333 1429 7.284034 ACCTGCTCAATTATCAGACAAAATAGG 59.716 37.037 0.00 0.00 0.00 2.57
1336 1432 7.472334 AACCTGCTCAATTATCAGACAAAAT 57.528 32.000 3.25 0.00 0.00 1.82
1448 1594 1.081094 AATACCCGTTACTTGCACGC 58.919 50.000 0.00 0.00 36.27 5.34
1513 1659 2.029110 ACCAAACTGAATGCCCAATTCG 60.029 45.455 0.00 0.00 46.68 3.34
1525 1671 1.064758 AGCCTGACACAACCAAACTGA 60.065 47.619 0.00 0.00 0.00 3.41
1534 1680 3.788227 AAAGGTATCAGCCTGACACAA 57.212 42.857 5.36 0.00 39.17 3.33
1570 1716 1.735920 GGAGCAGACTCACAGCACG 60.736 63.158 0.00 0.00 45.42 5.34
1578 1724 1.903183 ACTACCAAAGGGAGCAGACTC 59.097 52.381 0.00 0.00 42.66 3.36
1626 1776 6.342906 CCAATTTGCATAACCAGACATCAAT 58.657 36.000 0.00 0.00 0.00 2.57
1655 1805 1.267806 AGCAACCAAAACTCTGCATCG 59.732 47.619 0.00 0.00 37.26 3.84
1662 1812 2.101415 AGGCTTCAAGCAACCAAAACTC 59.899 45.455 12.53 0.00 44.75 3.01
1671 1821 2.183478 TCAATCGAGGCTTCAAGCAA 57.817 45.000 12.53 0.00 44.75 3.91
1687 1837 9.981114 CATACAGTATTACCATCAGTACATCAA 57.019 33.333 0.00 0.00 0.00 2.57
1705 1855 5.020795 TCCTTGTACCTGAAGCATACAGTA 58.979 41.667 0.00 0.00 34.04 2.74
1707 1857 4.437239 CTCCTTGTACCTGAAGCATACAG 58.563 47.826 0.00 0.00 30.82 2.74
1783 1945 4.581493 CACATAAATAGAACACTGCTGCG 58.419 43.478 0.00 0.00 0.00 5.18
1791 1953 5.709631 TGCCTCTTTGCACATAAATAGAACA 59.290 36.000 0.00 0.00 36.04 3.18
1835 1997 1.602668 GCTTCCAACGAGCATGCAAAA 60.603 47.619 21.98 2.17 39.89 2.44
1964 2145 6.148811 ACAAATCAAGTCCATTACCGTTGTAG 59.851 38.462 0.00 0.00 0.00 2.74
2010 2191 6.044682 TGTATATATGAGATGCAGGAATGCG 58.955 40.000 0.00 0.00 37.69 4.73
2027 2208 9.845740 AACAGCACCAATCTAAACATGTATATA 57.154 29.630 0.00 0.00 0.00 0.86
2091 2303 2.361119 TCTCCCATAGATGTCGAAACCG 59.639 50.000 0.00 0.00 0.00 4.44
2252 2465 6.707161 ACAAGCTGTTGCAATAAATGACAATT 59.293 30.769 0.59 0.00 42.74 2.32
2298 2511 1.213678 TGCTAGGCAATCCAGCATCTT 59.786 47.619 0.00 0.00 39.70 2.40
2301 2514 3.909587 TTGCTAGGCAATCCAGCAT 57.090 47.368 0.51 0.00 43.99 3.79
2437 2655 7.915293 TTACGTCATGAATTCCACAACTAAT 57.085 32.000 2.27 0.00 0.00 1.73
2447 2665 8.280497 ACACTTGTAGTTTTACGTCATGAATTC 58.720 33.333 0.00 0.00 32.21 2.17
2583 2884 3.190327 CGACAAAAACCAGCATCCACATA 59.810 43.478 0.00 0.00 0.00 2.29
2628 2931 9.178758 AGGATATAGAAAGAAGAAAAATGCGTT 57.821 29.630 0.00 0.00 0.00 4.84
2639 2949 8.877779 CAGTCACAACAAGGATATAGAAAGAAG 58.122 37.037 0.00 0.00 0.00 2.85
2647 2957 5.664457 CAGAGCAGTCACAACAAGGATATA 58.336 41.667 0.00 0.00 0.00 0.86
2666 2976 0.252479 AGTGCAGGAATCAGGCAGAG 59.748 55.000 0.00 0.00 38.38 3.35
2667 2977 0.694771 AAGTGCAGGAATCAGGCAGA 59.305 50.000 0.00 0.00 38.38 4.26
2684 2994 5.499139 TTTTGTGAGTTGGTAGCTGAAAG 57.501 39.130 0.00 0.00 0.00 2.62
2767 3077 0.177836 ACCTGGTTTGGTTTGCTTGC 59.822 50.000 0.00 0.00 36.89 4.01
2966 4377 2.099263 CAGCTCCATTCCTTTCATGCTG 59.901 50.000 0.00 0.00 40.17 4.41
2987 4398 3.538379 CCTTTTTGCATCAAGGGCC 57.462 52.632 14.26 0.00 36.62 5.80
3014 4425 0.320374 AAACGAAGACGGATGGAGCA 59.680 50.000 0.00 0.00 44.46 4.26
3028 4439 7.866729 TGCTCTTACAAACATATCAAAAACGA 58.133 30.769 0.00 0.00 0.00 3.85
3086 4497 2.878406 CAAGTTTTGTGTCCGGATGACT 59.122 45.455 7.81 2.97 44.75 3.41
3173 4586 9.059260 GCTTCGTACCCATTTTTCCTATATTTA 57.941 33.333 0.00 0.00 0.00 1.40
3189 4603 1.005867 TTGTGTCCGCTTCGTACCC 60.006 57.895 0.00 0.00 0.00 3.69
3336 4753 2.027285 TGGATGCGGATGAGAAGAAACA 60.027 45.455 0.00 0.00 0.00 2.83
3389 4809 4.342378 CGAGGAGTAGGATTGAGATGGAAA 59.658 45.833 0.00 0.00 0.00 3.13
3690 5124 4.394712 CAAGGGCGCCGTCTCCTT 62.395 66.667 23.85 15.61 41.15 3.36
3847 5282 2.815647 GGACAGCAGCTACACCGC 60.816 66.667 0.00 0.00 0.00 5.68
3888 5323 3.055719 ACTGCGGGCATTCAACGG 61.056 61.111 0.00 0.00 0.00 4.44
3909 5344 4.738998 CTTGGCGGACATGGGGCA 62.739 66.667 0.00 1.43 36.89 5.36
3922 5357 0.325933 TGGGTCTCATGTCTGCTTGG 59.674 55.000 0.00 0.00 0.00 3.61
3925 5360 1.609061 CGTTTGGGTCTCATGTCTGCT 60.609 52.381 0.00 0.00 0.00 4.24
3928 5363 1.002087 GTCCGTTTGGGTCTCATGTCT 59.998 52.381 0.00 0.00 37.00 3.41


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

AutoCloner maintained by Alex Coulton.