Multiple sequence alignment - TraesCS2B01G478500

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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 TraesCS2B01G478500 chr2B 100.000 4118 0 0 1 4118 675533085 675537202 0.000000e+00 7605.0
1 TraesCS2B01G478500 chr2B 82.747 2730 378 53 436 3118 675524272 675526955 0.000000e+00 2346.0
2 TraesCS2B01G478500 chr2B 87.611 1235 129 12 1896 3118 675334063 675332841 0.000000e+00 1411.0
3 TraesCS2B01G478500 chr2B 81.604 212 35 2 287 494 675524348 675524559 5.470000e-39 172.0
4 TraesCS2B01G478500 chr2B 92.157 51 3 1 4068 4117 450521859 450521809 2.050000e-08 71.3
5 TraesCS2B01G478500 chr2D 92.363 3195 197 22 1 3184 564475305 564478463 0.000000e+00 4505.0
6 TraesCS2B01G478500 chr2D 92.021 2519 175 17 769 3278 564438197 564440698 0.000000e+00 3515.0
7 TraesCS2B01G478500 chr2D 81.255 2422 337 61 436 2807 564418102 564420456 0.000000e+00 1849.0
8 TraesCS2B01G478500 chr2D 87.893 1239 121 12 1896 3118 564071994 564070769 0.000000e+00 1430.0
9 TraesCS2B01G478500 chr2D 94.580 738 33 3 1 732 564437457 564438193 0.000000e+00 1134.0
10 TraesCS2B01G478500 chr2D 87.177 889 82 7 3189 4075 564478574 564479432 0.000000e+00 981.0
11 TraesCS2B01G478500 chr2D 89.212 482 43 4 3277 3755 564440780 564441255 9.860000e-166 593.0
12 TraesCS2B01G478500 chr2D 94.488 127 3 2 3907 4033 564441269 564441391 4.200000e-45 193.0
13 TraesCS2B01G478500 chr2A 94.320 1743 88 6 18 1750 705267577 705269318 0.000000e+00 2660.0
14 TraesCS2B01G478500 chr2A 83.260 2724 373 46 436 3118 705264052 705266733 0.000000e+00 2427.0
15 TraesCS2B01G478500 chr2A 87.500 1240 124 16 1896 3118 704754679 704753454 0.000000e+00 1402.0
16 TraesCS2B01G478500 chr2A 89.103 624 55 8 2052 2670 705342857 705343472 0.000000e+00 763.0
17 TraesCS2B01G478500 chr4B 90.159 2012 166 18 2064 4066 22488520 22486532 0.000000e+00 2590.0
18 TraesCS2B01G478500 chr4B 90.968 1085 84 7 1955 3037 22438650 22437578 0.000000e+00 1448.0
19 TraesCS2B01G478500 chr4B 86.233 1046 133 7 917 1959 22440902 22439865 0.000000e+00 1123.0
20 TraesCS2B01G478500 chr4B 93.344 631 33 5 1 629 22442708 22442085 0.000000e+00 924.0
21 TraesCS2B01G478500 chr4B 93.664 363 15 4 623 981 22441257 22440899 1.680000e-148 536.0
22 TraesCS2B01G478500 chr4A 77.951 1220 209 43 606 1791 729654105 729655298 0.000000e+00 708.0
23 TraesCS2B01G478500 chr7D 78.141 1194 200 42 631 1791 10056654 10057819 0.000000e+00 702.0
24 TraesCS2B01G478500 chr3B 79.195 149 28 3 3540 3686 70907172 70907319 2.620000e-17 100.0
25 TraesCS2B01G478500 chr3B 96.154 52 2 0 4066 4117 819958737 819958788 7.330000e-13 86.1
26 TraesCS2B01G478500 chr3D 74.894 235 49 9 3314 3542 411008138 411007908 9.420000e-17 99.0
27 TraesCS2B01G478500 chr6D 91.071 56 4 1 4063 4117 172602517 172602462 1.590000e-09 75.0
28 TraesCS2B01G478500 chr5A 91.071 56 4 1 4063 4117 327339598 327339653 1.590000e-09 75.0
29 TraesCS2B01G478500 chr3A 91.071 56 4 1 4063 4117 431575665 431575720 1.590000e-09 75.0
30 TraesCS2B01G478500 chr6A 95.652 46 1 1 4066 4110 356612291 356612336 5.710000e-09 73.1
31 TraesCS2B01G478500 chr7B 92.157 51 3 1 4068 4117 410700733 410700683 2.050000e-08 71.3
32 TraesCS2B01G478500 chr1B 95.349 43 1 1 4071 4112 243518445 243518487 2.660000e-07 67.6
33 TraesCS2B01G478500 chr1A 97.436 39 1 0 4069 4107 449023852 449023890 2.660000e-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 TraesCS2B01G478500 chr2B 675533085 675537202 4117 False 7605.00 7605 100.00000 1 4118 1 chr2B.!!$F1 4117
1 TraesCS2B01G478500 chr2B 675332841 675334063 1222 True 1411.00 1411 87.61100 1896 3118 1 chr2B.!!$R2 1222
2 TraesCS2B01G478500 chr2B 675524272 675526955 2683 False 1259.00 2346 82.17550 287 3118 2 chr2B.!!$F2 2831
3 TraesCS2B01G478500 chr2D 564475305 564479432 4127 False 2743.00 4505 89.77000 1 4075 2 chr2D.!!$F3 4074
4 TraesCS2B01G478500 chr2D 564418102 564420456 2354 False 1849.00 1849 81.25500 436 2807 1 chr2D.!!$F1 2371
5 TraesCS2B01G478500 chr2D 564070769 564071994 1225 True 1430.00 1430 87.89300 1896 3118 1 chr2D.!!$R1 1222
6 TraesCS2B01G478500 chr2D 564437457 564441391 3934 False 1358.75 3515 92.57525 1 4033 4 chr2D.!!$F2 4032
7 TraesCS2B01G478500 chr2A 705264052 705269318 5266 False 2543.50 2660 88.79000 18 3118 2 chr2A.!!$F2 3100
8 TraesCS2B01G478500 chr2A 704753454 704754679 1225 True 1402.00 1402 87.50000 1896 3118 1 chr2A.!!$R1 1222
9 TraesCS2B01G478500 chr2A 705342857 705343472 615 False 763.00 763 89.10300 2052 2670 1 chr2A.!!$F1 618
10 TraesCS2B01G478500 chr4B 22486532 22488520 1988 True 2590.00 2590 90.15900 2064 4066 1 chr4B.!!$R1 2002
11 TraesCS2B01G478500 chr4B 22437578 22442708 5130 True 1007.75 1448 91.05225 1 3037 4 chr4B.!!$R2 3036
12 TraesCS2B01G478500 chr4A 729654105 729655298 1193 False 708.00 708 77.95100 606 1791 1 chr4A.!!$F1 1185
13 TraesCS2B01G478500 chr7D 10056654 10057819 1165 False 702.00 702 78.14100 631 1791 1 chr7D.!!$F1 1160

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
687 1566 1.122019 ACAGCCTCGTTGTTCCTCCT 61.122 55.000 0.0 0.0 0.00 3.69 F
1128 2100 1.008538 CAACGCAAGCAACAGGGAC 60.009 57.895 0.0 0.0 45.62 4.46 F
1912 2909 0.036952 CATGTGGAGAAGGCTGACGT 60.037 55.000 0.0 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 2591 1.171308 AACAGCAGTGATGCACCATC 58.829 50.0 8.62 0.0 40.88 3.51 R
2687 4918 1.132199 GTCGCTGTCGTGGATGTACG 61.132 60.0 0.00 0.0 44.98 3.67 R
3403 5830 0.040058 ATGCTCAAAGGCCACCATCA 59.960 50.0 5.01 0.0 0.00 3.07 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
66 67 7.040617 GGAGAACGAAAAAGGGAGACTTAATTT 60.041 37.037 0.00 0.00 38.85 1.82
78 79 5.393461 GGAGACTTAATTTGGCCTCATGTTG 60.393 44.000 3.32 0.00 0.00 3.33
84 85 7.834181 ACTTAATTTGGCCTCATGTTGTATAGT 59.166 33.333 3.32 0.00 0.00 2.12
90 91 3.736252 GCCTCATGTTGTATAGTGTAGCG 59.264 47.826 0.00 0.00 0.00 4.26
100 101 6.699895 TGTATAGTGTAGCGTGAAAAACTG 57.300 37.500 0.00 0.00 0.00 3.16
110 111 3.371168 CGTGAAAAACTGTGGTCCAATG 58.629 45.455 0.00 0.00 0.00 2.82
176 177 2.536365 TCAAAATACGCGCACTAGAGG 58.464 47.619 5.73 0.00 0.00 3.69
206 213 9.774742 CATTTAAGCAAACTAGATTACTCCAAC 57.225 33.333 0.00 0.00 0.00 3.77
233 240 9.503399 AAATTGTAATCGTAGAGAAACTTTCCT 57.497 29.630 0.00 0.00 43.63 3.36
306 314 5.664457 TGATTGTAACAGCTCCATAGACAG 58.336 41.667 0.00 0.00 0.00 3.51
322 330 7.618117 TCCATAGACAGGTTCTACATTGACTAA 59.382 37.037 0.00 0.00 39.78 2.24
368 376 8.576442 GTTAGATGAAAGAAATTTTGACCCAGA 58.424 33.333 0.00 0.00 0.00 3.86
480 490 2.664851 CCTCGCTGTTCCGCACAA 60.665 61.111 0.00 0.00 33.87 3.33
629 1507 5.395435 GGATCAGTTTCCTGTACCCTCTTAC 60.395 48.000 0.00 0.00 39.82 2.34
687 1566 1.122019 ACAGCCTCGTTGTTCCTCCT 61.122 55.000 0.00 0.00 0.00 3.69
895 1792 6.483307 TGTCTCTTCCAAGTATTTGTCAACTG 59.517 38.462 0.00 0.00 32.21 3.16
900 1797 3.191371 CCAAGTATTTGTCAACTGCTCCC 59.809 47.826 0.00 0.00 32.21 4.30
901 1798 3.788227 AGTATTTGTCAACTGCTCCCA 57.212 42.857 0.00 0.00 0.00 4.37
902 1799 3.679389 AGTATTTGTCAACTGCTCCCAG 58.321 45.455 0.00 0.00 44.80 4.45
961 1924 7.786943 TCATATGAACTGGTATCTTCCTCTTCT 59.213 37.037 1.98 0.00 0.00 2.85
1128 2100 1.008538 CAACGCAAGCAACAGGGAC 60.009 57.895 0.00 0.00 45.62 4.46
1148 2120 1.676916 CGATTTCAGCTTCAGCCCTGA 60.677 52.381 0.00 0.00 43.38 3.86
1228 2200 2.526432 GGTCAGGAAGAGTGGTCTACA 58.474 52.381 0.00 0.00 30.45 2.74
1268 2240 3.345808 GAACAGCAAGCGCACGGA 61.346 61.111 11.47 0.00 42.27 4.69
1317 2305 2.356535 GCTCAACATCCTCCCACAGAAT 60.357 50.000 0.00 0.00 0.00 2.40
1336 2327 2.940514 TGGGACTGGAGAAGGTATGA 57.059 50.000 0.00 0.00 0.00 2.15
1362 2353 7.002879 CCTTCATCCTCACAAATAATCCATCT 58.997 38.462 0.00 0.00 0.00 2.90
1435 2426 1.289109 CGGCGTGAAGACAAACCGAT 61.289 55.000 0.00 0.00 44.32 4.18
1529 2520 8.390354 CGACTTAAATAGCATCAAATCTGTTCA 58.610 33.333 0.00 0.00 0.00 3.18
1534 2525 4.170292 AGCATCAAATCTGTTCAGCAAC 57.830 40.909 0.00 0.00 0.00 4.17
1539 2530 2.361757 CAAATCTGTTCAGCAACACCCA 59.638 45.455 0.00 0.00 37.61 4.51
1559 2550 3.119291 CACTCAGTAATCAGTCCATCGC 58.881 50.000 0.00 0.00 0.00 4.58
1583 2574 4.163078 CCTCTCAAGTGGGTCTGATGTATT 59.837 45.833 0.00 0.00 0.00 1.89
1588 2579 2.168521 AGTGGGTCTGATGTATTGGTCG 59.831 50.000 0.00 0.00 0.00 4.79
1590 2581 1.202651 GGGTCTGATGTATTGGTCGGG 60.203 57.143 0.00 0.00 0.00 5.14
1595 2586 3.709141 TCTGATGTATTGGTCGGGATCAA 59.291 43.478 0.00 0.00 35.67 2.57
1600 2591 4.373527 TGTATTGGTCGGGATCAAATACG 58.626 43.478 0.00 0.00 34.74 3.06
1606 2597 2.800544 GTCGGGATCAAATACGATGGTG 59.199 50.000 0.00 0.00 37.69 4.17
1613 2604 3.872696 TCAAATACGATGGTGCATCACT 58.127 40.909 0.00 0.00 40.54 3.41
1628 2619 4.222114 GCATCACTGCTGTTTCAAGTAAC 58.778 43.478 0.00 0.00 45.32 2.50
1632 2623 5.050490 TCACTGCTGTTTCAAGTAACTCTC 58.950 41.667 0.00 0.00 0.00 3.20
1663 2654 0.319211 CACAAGTGGGCAGCATGTTG 60.319 55.000 5.00 5.00 39.31 3.33
1664 2655 1.373748 CAAGTGGGCAGCATGTTGC 60.374 57.895 24.73 24.73 45.46 4.17
1675 2672 3.243201 GCAGCATGTTGCCCTATTAAGTC 60.243 47.826 22.63 0.00 46.52 3.01
1676 2673 3.002656 CAGCATGTTGCCCTATTAAGTCG 59.997 47.826 0.00 0.00 46.52 4.18
1686 2683 6.282930 TGCCCTATTAAGTCGGTACATTAAC 58.717 40.000 0.00 0.00 0.00 2.01
1694 2691 3.830755 AGTCGGTACATTAACCTGTCACT 59.169 43.478 0.00 0.00 37.39 3.41
1792 2789 3.659786 TGGAACTTCACCACAATAGACG 58.340 45.455 0.00 0.00 32.03 4.18
1820 2817 3.370527 GCCACAGTTAGAAGAGGGCATTA 60.371 47.826 0.00 0.00 39.66 1.90
1821 2818 4.192317 CCACAGTTAGAAGAGGGCATTAC 58.808 47.826 0.00 0.00 0.00 1.89
1822 2819 4.080863 CCACAGTTAGAAGAGGGCATTACT 60.081 45.833 0.00 0.00 0.00 2.24
1823 2820 4.872691 CACAGTTAGAAGAGGGCATTACTG 59.127 45.833 0.00 0.00 38.12 2.74
1824 2821 4.080863 ACAGTTAGAAGAGGGCATTACTGG 60.081 45.833 0.00 0.00 36.86 4.00
1825 2822 4.162320 CAGTTAGAAGAGGGCATTACTGGA 59.838 45.833 0.00 0.00 0.00 3.86
1912 2909 0.036952 CATGTGGAGAAGGCTGACGT 60.037 55.000 0.00 0.00 0.00 4.34
1968 4184 1.153647 GATCGACGCACATGGTCCA 60.154 57.895 0.00 0.00 0.00 4.02
1989 4205 4.766891 CCAGTCAAATTTAAGCTCAGGGAA 59.233 41.667 0.00 0.00 0.00 3.97
2031 4247 1.448540 CAGTCCTACCCGCAAGCTG 60.449 63.158 0.00 0.00 0.00 4.24
2094 4310 0.038166 GGATGAACTTGGAGGTGGCA 59.962 55.000 0.00 0.00 0.00 4.92
2235 4451 1.302832 CCACAAGAAGGGCGAGCTT 60.303 57.895 0.00 0.00 0.00 3.74
2292 4508 0.321653 ACAAGCTCCTTTACGCCAGG 60.322 55.000 0.00 0.00 0.00 4.45
2523 4748 2.261671 GTCATCCAGCACGACGGT 59.738 61.111 0.00 0.00 0.00 4.83
2592 4817 1.401148 GCGTACGAGAGCTTCTTCACA 60.401 52.381 21.65 0.00 0.00 3.58
2650 4875 0.895530 GGTCTTCGTCATGGAGGTGA 59.104 55.000 0.00 0.00 0.00 4.02
2775 5012 0.680601 TGCCGATGCACATTGTGGAT 60.681 50.000 21.89 21.89 46.66 3.41
2802 5039 4.124943 AGGCTCTACGGCGAGGGA 62.125 66.667 16.62 7.47 44.22 4.20
2838 5075 4.778143 GACCCATTGCTCGGCGGT 62.778 66.667 7.21 0.00 0.00 5.68
2904 5141 3.645660 TGCTGCCATCCGAACCCA 61.646 61.111 0.00 0.00 0.00 4.51
2959 5196 2.363172 TTGATCGATGGTGCCCCGA 61.363 57.895 0.54 5.55 36.72 5.14
3030 5269 2.906458 CAGCGGGAGATGGAGCTT 59.094 61.111 0.00 0.00 43.79 3.74
3036 5275 1.745264 GGAGATGGAGCTTCCGGAG 59.255 63.158 3.34 0.00 40.17 4.63
3289 5716 8.647796 CCCTAATGACAGATAGTTGGTTATACA 58.352 37.037 0.00 0.00 0.00 2.29
3313 5740 2.920227 GCATTGTCGGCATTTTTCGTCA 60.920 45.455 0.00 0.00 0.00 4.35
3388 5815 4.216687 TGAAAACCCACGTTATAGCCTTTG 59.783 41.667 0.00 0.00 0.00 2.77
3391 5818 5.362105 AACCCACGTTATAGCCTTTGATA 57.638 39.130 0.00 0.00 0.00 2.15
3403 5830 2.421529 GCCTTTGATAGTTGGATCCGGT 60.422 50.000 7.39 0.00 0.00 5.28
3406 5833 4.444876 CCTTTGATAGTTGGATCCGGTGAT 60.445 45.833 7.39 0.00 0.00 3.06
3413 5840 2.203209 GATCCGGTGATGGTGGCC 60.203 66.667 0.00 0.00 0.00 5.36
3481 5908 4.174411 TCTCATAGTCCTTGTGTTGTCG 57.826 45.455 0.00 0.00 0.00 4.35
3497 5924 4.158579 TGTTGTCGAGAGATAGTTGATGCT 59.841 41.667 0.00 0.00 45.19 3.79
3550 5992 2.338500 GTTCGCTTGAGAACTAGGTGG 58.662 52.381 9.41 0.00 45.07 4.61
3551 5993 1.629043 TCGCTTGAGAACTAGGTGGT 58.371 50.000 0.00 0.00 0.00 4.16
3552 5994 2.799017 TCGCTTGAGAACTAGGTGGTA 58.201 47.619 0.00 0.00 0.00 3.25
3553 5995 2.753452 TCGCTTGAGAACTAGGTGGTAG 59.247 50.000 0.00 0.00 34.52 3.18
3554 5996 2.735762 CGCTTGAGAACTAGGTGGTAGC 60.736 54.545 0.00 0.00 30.92 3.58
3555 5997 2.418884 GCTTGAGAACTAGGTGGTAGCC 60.419 54.545 0.00 0.00 30.92 3.93
3556 5998 2.921834 TGAGAACTAGGTGGTAGCCT 57.078 50.000 0.00 0.00 42.43 4.58
3557 5999 4.279145 CTTGAGAACTAGGTGGTAGCCTA 58.721 47.826 0.00 0.00 39.94 3.93
3609 6051 2.147958 CCAAAGTTTGAATCCCGTCGA 58.852 47.619 17.33 0.00 0.00 4.20
3640 6082 1.207089 CTAGTGCTTCAATCGGGTGGA 59.793 52.381 0.00 0.00 0.00 4.02
3686 6128 3.072944 GGTGCTAATGCTCATGGATCTC 58.927 50.000 0.00 0.00 40.48 2.75
3689 6131 4.451774 GTGCTAATGCTCATGGATCTCTTC 59.548 45.833 0.00 0.00 40.48 2.87
3735 6178 9.827198 TTTCCTTTTTATCCATCCTATGCATAT 57.173 29.630 6.92 0.00 0.00 1.78
3788 6231 2.575532 CAGGATCCTTTGTGTGTGTGT 58.424 47.619 13.00 0.00 0.00 3.72
3795 6238 6.128282 GGATCCTTTGTGTGTGTGTACTAATG 60.128 42.308 3.84 0.00 0.00 1.90
3855 6679 7.201776 GGTGTGTGTTTATTATGCATGTATCCA 60.202 37.037 10.16 0.00 0.00 3.41
3936 6952 8.162880 CACACTAGAGATAGCGTTTAACAAAAG 58.837 37.037 0.00 0.00 0.00 2.27
3970 6988 2.062773 TAAAGGAGGTTAAGCCCCCA 57.937 50.000 13.90 0.00 38.26 4.96
3971 6989 0.704664 AAAGGAGGTTAAGCCCCCAG 59.295 55.000 13.90 0.00 38.26 4.45
3973 6991 1.208165 AGGAGGTTAAGCCCCCAGTG 61.208 60.000 13.90 0.00 38.26 3.66
3974 6992 1.205460 GGAGGTTAAGCCCCCAGTGA 61.205 60.000 0.00 0.00 38.26 3.41
3983 7001 1.271840 GCCCCCAGTGAGTGATGGTA 61.272 60.000 0.00 0.00 34.58 3.25
4067 8186 1.688197 CAAAACAATCAGCCAGTGGGT 59.312 47.619 8.42 8.42 36.17 4.51
4071 8190 0.037303 CAATCAGCCAGTGGGTCACT 59.963 55.000 11.93 0.00 46.51 3.41
4078 8197 3.138625 AGTGGGTCACTGTCGGTG 58.861 61.111 5.35 5.35 43.63 4.94
4079 8198 1.760875 AGTGGGTCACTGTCGGTGT 60.761 57.895 11.59 0.00 43.63 4.16
4083 8202 0.179067 GGGTCACTGTCGGTGTCAAA 60.179 55.000 11.59 0.00 45.50 2.69
4084 8203 1.658994 GGTCACTGTCGGTGTCAAAA 58.341 50.000 11.59 0.00 45.50 2.44
4085 8204 1.329599 GGTCACTGTCGGTGTCAAAAC 59.670 52.381 11.59 2.22 45.50 2.43
4086 8205 1.329599 GTCACTGTCGGTGTCAAAACC 59.670 52.381 11.59 0.00 45.50 3.27
4092 8211 4.150994 GGTGTCAAAACCGGCTGA 57.849 55.556 0.00 0.00 0.00 4.26
4094 8213 0.521735 GGTGTCAAAACCGGCTGATC 59.478 55.000 0.00 0.33 0.00 2.92
4095 8214 0.521735 GTGTCAAAACCGGCTGATCC 59.478 55.000 0.00 0.00 0.00 3.36
4096 8215 0.608035 TGTCAAAACCGGCTGATCCC 60.608 55.000 0.00 0.00 0.00 3.85
4103 8222 3.616721 CGGCTGATCCCGGGTAGG 61.617 72.222 22.86 10.59 44.46 3.18
4115 8234 4.129148 GGTAGGGGGCCCAAGCTG 62.129 72.222 26.86 0.00 39.73 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 4.442893 GCTACACTATACAACATGAGGCCA 60.443 45.833 5.01 0.00 0.00 5.36
78 79 6.400727 CCACAGTTTTTCACGCTACACTATAC 60.401 42.308 0.00 0.00 0.00 1.47
84 85 2.610374 GACCACAGTTTTTCACGCTACA 59.390 45.455 0.00 0.00 0.00 2.74
90 91 4.111916 CACATTGGACCACAGTTTTTCAC 58.888 43.478 0.00 0.00 0.00 3.18
100 101 3.071874 TGGAAGATCACATTGGACCAC 57.928 47.619 0.00 0.00 0.00 4.16
110 111 2.939103 AGCGCTTAACATGGAAGATCAC 59.061 45.455 2.64 0.00 0.00 3.06
206 213 9.543018 GGAAAGTTTCTCTACGATTACAATTTG 57.457 33.333 15.05 0.00 0.00 2.32
218 225 4.523173 CCCCCAAAAGGAAAGTTTCTCTAC 59.477 45.833 15.05 0.00 38.24 2.59
306 314 6.818644 TGAAGATGCTTAGTCAATGTAGAACC 59.181 38.462 0.00 0.00 0.00 3.62
368 376 0.698238 TAGTGCCAGCCCTGAACAAT 59.302 50.000 0.00 0.00 0.00 2.71
480 490 6.043938 TGGTACCAGATTAAAAGAGGAGTGTT 59.956 38.462 11.60 0.00 0.00 3.32
629 1507 9.950680 ACAGTGACATTAACATAAGAAAAACAG 57.049 29.630 0.00 0.00 0.00 3.16
687 1566 4.098894 ACGGATTAAAAGAGGGGTGTCTA 58.901 43.478 0.00 0.00 0.00 2.59
830 1716 2.299297 AGGTACAGCGGCCAATACTATC 59.701 50.000 2.24 0.00 0.00 2.08
900 1797 2.709125 TTTCACCACGGACGAGGCTG 62.709 60.000 8.09 6.33 0.00 4.85
901 1798 2.035237 TTTTCACCACGGACGAGGCT 62.035 55.000 8.09 0.00 0.00 4.58
902 1799 1.566018 CTTTTCACCACGGACGAGGC 61.566 60.000 8.09 0.00 0.00 4.70
961 1924 1.271054 GCTTCCTGCAACCTTCTCAGA 60.271 52.381 0.00 0.00 42.31 3.27
1128 2100 0.731417 CAGGGCTGAAGCTGAAATCG 59.269 55.000 1.74 0.00 41.70 3.34
1148 2120 3.406764 GAGTTGTTGGAGATTGCTGAGT 58.593 45.455 0.00 0.00 0.00 3.41
1268 2240 1.286260 GTCCTGAACGACGTGAGCT 59.714 57.895 0.00 0.00 0.00 4.09
1317 2305 2.467880 GTCATACCTTCTCCAGTCCCA 58.532 52.381 0.00 0.00 0.00 4.37
1336 2327 6.078456 TGGATTATTTGTGAGGATGAAGGT 57.922 37.500 0.00 0.00 0.00 3.50
1344 2335 5.452356 GGGCAAAGATGGATTATTTGTGAGG 60.452 44.000 0.00 0.00 36.52 3.86
1435 2426 3.998341 GTGTCAAATTCCACGGCTACTAA 59.002 43.478 0.00 0.00 0.00 2.24
1500 2491 7.766278 ACAGATTTGATGCTATTTAAGTCGAGT 59.234 33.333 0.00 0.00 0.00 4.18
1501 2492 8.136057 ACAGATTTGATGCTATTTAAGTCGAG 57.864 34.615 0.00 0.00 0.00 4.04
1509 2500 6.519679 TGCTGAACAGATTTGATGCTATTT 57.480 33.333 5.97 0.00 0.00 1.40
1512 2503 4.761227 TGTTGCTGAACAGATTTGATGCTA 59.239 37.500 5.97 0.00 37.15 3.49
1529 2520 2.371841 TGATTACTGAGTGGGTGTTGCT 59.628 45.455 0.00 0.00 0.00 3.91
1534 2525 2.567169 TGGACTGATTACTGAGTGGGTG 59.433 50.000 0.00 0.00 0.00 4.61
1539 2530 2.101582 GGCGATGGACTGATTACTGAGT 59.898 50.000 0.00 0.00 0.00 3.41
1583 2574 2.224185 CCATCGTATTTGATCCCGACCA 60.224 50.000 0.00 0.00 31.43 4.02
1588 2579 2.571212 TGCACCATCGTATTTGATCCC 58.429 47.619 0.00 0.00 0.00 3.85
1590 2581 4.512944 AGTGATGCACCATCGTATTTGATC 59.487 41.667 0.00 0.00 43.14 2.92
1595 2586 1.942657 GCAGTGATGCACCATCGTATT 59.057 47.619 0.00 0.00 43.14 1.89
1600 2591 1.171308 AACAGCAGTGATGCACCATC 58.829 50.000 8.62 0.00 40.88 3.51
1606 2597 4.023707 AGTTACTTGAAACAGCAGTGATGC 60.024 41.667 8.62 0.00 0.00 3.91
1613 2604 4.054780 ACGAGAGTTACTTGAAACAGCA 57.945 40.909 0.00 0.00 46.40 4.41
1628 2619 2.654749 TGTGCTGTATTGGACGAGAG 57.345 50.000 0.00 0.00 0.00 3.20
1632 2623 1.464608 CCACTTGTGCTGTATTGGACG 59.535 52.381 0.00 0.00 0.00 4.79
1663 2654 5.698089 GGTTAATGTACCGACTTAATAGGGC 59.302 44.000 0.00 0.00 0.00 5.19
1664 2655 6.927381 CAGGTTAATGTACCGACTTAATAGGG 59.073 42.308 0.00 0.00 43.21 3.53
1665 2656 7.495055 ACAGGTTAATGTACCGACTTAATAGG 58.505 38.462 0.00 0.00 43.21 2.57
1666 2657 8.192774 TGACAGGTTAATGTACCGACTTAATAG 58.807 37.037 0.00 0.00 43.21 1.73
1667 2658 7.975616 GTGACAGGTTAATGTACCGACTTAATA 59.024 37.037 0.00 0.00 43.21 0.98
1670 2661 5.477984 AGTGACAGGTTAATGTACCGACTTA 59.522 40.000 0.00 0.00 43.21 2.24
1675 2672 5.320549 ACTAGTGACAGGTTAATGTACCG 57.679 43.478 0.00 0.00 43.21 4.02
1676 2673 6.932947 AGAACTAGTGACAGGTTAATGTACC 58.067 40.000 0.00 0.00 38.53 3.34
1686 2683 3.127203 CGTCCAGTAGAACTAGTGACAGG 59.873 52.174 15.60 2.12 38.45 4.00
1694 2691 7.606839 CCAGATATATGTCGTCCAGTAGAACTA 59.393 40.741 0.00 0.00 0.00 2.24
1792 2789 3.182967 CTCTTCTAACTGTGGCATCGTC 58.817 50.000 0.00 0.00 0.00 4.20
1820 2817 3.584733 AAAGCACCTTTCTTCTCCAGT 57.415 42.857 0.00 0.00 0.00 4.00
1821 2818 3.005155 CCAAAAGCACCTTTCTTCTCCAG 59.995 47.826 0.00 0.00 31.99 3.86
1822 2819 2.958355 CCAAAAGCACCTTTCTTCTCCA 59.042 45.455 0.00 0.00 31.99 3.86
1823 2820 2.288457 GCCAAAAGCACCTTTCTTCTCC 60.288 50.000 0.00 0.00 42.97 3.71
1824 2821 3.018598 GCCAAAAGCACCTTTCTTCTC 57.981 47.619 0.00 0.00 42.97 2.87
1968 4184 5.635120 AGTTCCCTGAGCTTAAATTTGACT 58.365 37.500 0.00 0.00 0.00 3.41
2094 4310 2.338984 GTCGACACCCGCTTGACT 59.661 61.111 11.55 0.00 38.37 3.41
2235 4451 3.439476 GGAAGTACTCGTAGACAAGCAGA 59.561 47.826 0.00 0.00 0.00 4.26
2292 4508 2.808321 GACGACGCGGTCCTTTCC 60.808 66.667 12.47 0.00 0.00 3.13
2523 4748 2.108157 GTGGAGTGGTGCGTGACA 59.892 61.111 0.00 0.00 0.00 3.58
2687 4918 1.132199 GTCGCTGTCGTGGATGTACG 61.132 60.000 0.00 0.00 44.98 3.67
2775 5012 2.248248 CCGTAGAGCCTCCATATCCAA 58.752 52.381 0.00 0.00 0.00 3.53
2826 5063 1.302511 AAACTCACCGCCGAGCAAT 60.303 52.632 0.00 0.00 36.42 3.56
2838 5075 1.962822 CTGCGCCTGCTCAAACTCA 60.963 57.895 4.18 0.00 43.34 3.41
2895 5132 1.612442 CCTCTCCCTTGGGTTCGGA 60.612 63.158 5.51 0.54 0.00 4.55
2904 5141 2.041265 ATGGACGGCCTCTCCCTT 59.959 61.111 9.82 0.00 34.31 3.95
3036 5275 2.604174 CGTGAACAGCAACCCGACC 61.604 63.158 0.00 0.00 0.00 4.79
3239 5583 6.489022 GGTAGATTACAAACTTTGTTCCCAGT 59.511 38.462 12.35 0.00 42.22 4.00
3289 5716 2.620242 GAAAAATGCCGACAATGCCAT 58.380 42.857 0.00 0.00 0.00 4.40
3313 5740 4.506758 GGCAATGCCTTCAACAATGTAAT 58.493 39.130 18.47 0.00 46.69 1.89
3388 5815 2.368875 ACCATCACCGGATCCAACTATC 59.631 50.000 9.46 0.00 0.00 2.08
3391 5818 0.253044 CACCATCACCGGATCCAACT 59.747 55.000 9.46 0.00 0.00 3.16
3403 5830 0.040058 ATGCTCAAAGGCCACCATCA 59.960 50.000 5.01 0.00 0.00 3.07
3406 5833 0.040058 ATGATGCTCAAAGGCCACCA 59.960 50.000 5.01 0.00 0.00 4.17
3413 5840 9.084164 CCTTCATAAAAGAAATGATGCTCAAAG 57.916 33.333 0.00 0.00 33.52 2.77
3497 5924 5.413309 ACAAGGAAAAACAACAACCATGA 57.587 34.783 0.00 0.00 0.00 3.07
3554 5996 1.003580 ACTGTGACCATTGCCACTAGG 59.996 52.381 0.00 0.00 34.57 3.02
3555 5997 2.079158 CACTGTGACCATTGCCACTAG 58.921 52.381 0.32 0.00 34.57 2.57
3556 5998 1.271325 CCACTGTGACCATTGCCACTA 60.271 52.381 9.86 0.00 34.57 2.74
3557 5999 0.538057 CCACTGTGACCATTGCCACT 60.538 55.000 9.86 0.00 34.57 4.00
3558 6000 0.823356 ACCACTGTGACCATTGCCAC 60.823 55.000 9.86 0.00 0.00 5.01
3565 6007 2.191908 GGTGCACCACTGTGACCA 59.808 61.111 31.23 0.21 45.76 4.02
3592 6034 2.225727 GCTTTCGACGGGATTCAAACTT 59.774 45.455 0.00 0.00 0.00 2.66
3609 6051 5.689383 TTGAAGCACTAGAAATTCGCTTT 57.311 34.783 7.15 0.00 42.69 3.51
3672 6114 5.950549 ACAAAAAGAAGAGATCCATGAGCAT 59.049 36.000 0.00 0.00 0.00 3.79
3686 6128 9.783425 GAAAAATATGAAGCGAACAAAAAGAAG 57.217 29.630 0.00 0.00 0.00 2.85
3689 6131 8.298030 AGGAAAAATATGAAGCGAACAAAAAG 57.702 30.769 0.00 0.00 0.00 2.27
3721 6164 6.906157 AAACCAAAGATATGCATAGGATGG 57.094 37.500 20.48 20.48 0.00 3.51
3729 6172 8.579850 AAGTCATAGAAAACCAAAGATATGCA 57.420 30.769 0.00 0.00 0.00 3.96
3735 6178 6.959639 AGCAAAGTCATAGAAAACCAAAGA 57.040 33.333 0.00 0.00 0.00 2.52
3855 6679 6.822667 TTGATTCACAATGTAGCATCAAGT 57.177 33.333 8.92 0.00 33.18 3.16
3970 6988 5.965033 AATTCAGGATACCATCACTCACT 57.035 39.130 0.00 0.00 37.17 3.41
3983 7001 6.959044 GGTTTGCACCCCCTAATTCAGGAT 62.959 50.000 0.00 0.00 41.40 3.24
4075 8194 0.521735 GATCAGCCGGTTTTGACACC 59.478 55.000 1.90 0.00 0.00 4.16
4077 8196 0.608035 GGGATCAGCCGGTTTTGACA 60.608 55.000 1.90 0.00 37.63 3.58
4078 8197 1.644786 CGGGATCAGCCGGTTTTGAC 61.645 60.000 1.90 0.88 37.63 3.18
4079 8198 1.376683 CGGGATCAGCCGGTTTTGA 60.377 57.895 1.90 5.56 37.63 2.69
4083 8202 3.988050 TACCCGGGATCAGCCGGTT 62.988 63.158 32.02 14.76 46.79 4.44
4084 8203 4.468769 TACCCGGGATCAGCCGGT 62.469 66.667 32.02 15.33 46.79 5.28
4086 8205 3.616721 CCTACCCGGGATCAGCCG 61.617 72.222 32.02 6.45 37.63 5.52
4098 8217 4.129148 CAGCTTGGGCCCCCTACC 62.129 72.222 22.27 2.81 39.73 3.18
4099 8218 1.999002 TACAGCTTGGGCCCCCTAC 60.999 63.158 22.27 6.16 39.73 3.18


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

AutoCloner maintained by Alex Coulton.