Multiple sequence alignment - TraesCS1A01G344500

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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 TraesCS1A01G344500 chr1A 100.000 3207 0 0 986 4192 532456834 532460040 0.000000e+00 5923.0
1 TraesCS1A01G344500 chr1A 95.682 1019 25 4 3179 4192 207400908 207401912 0.000000e+00 1620.0
2 TraesCS1A01G344500 chr1A 100.000 711 0 0 1 711 532455849 532456559 0.000000e+00 1314.0
3 TraesCS1A01G344500 chr1A 74.651 501 97 24 2193 2675 532435908 532436396 1.190000e-45 195.0
4 TraesCS1A01G344500 chr2A 96.256 1015 23 2 3179 4192 768243841 768242841 0.000000e+00 1650.0
5 TraesCS1A01G344500 chr2A 95.669 1016 29 2 3178 4192 526540622 526541623 0.000000e+00 1618.0
6 TraesCS1A01G344500 chr2A 95.567 1015 30 2 3179 4192 643986872 643985872 0.000000e+00 1611.0
7 TraesCS1A01G344500 chr2A 97.187 711 20 0 1 711 596415541 596416251 0.000000e+00 1203.0
8 TraesCS1A01G344500 chr2A 96.802 688 22 0 1 688 431006984 431006297 0.000000e+00 1149.0
9 TraesCS1A01G344500 chr2A 96.512 688 24 0 1 688 431013619 431012932 0.000000e+00 1138.0
10 TraesCS1A01G344500 chr6A 95.776 1018 27 2 3177 4192 94070395 94071398 0.000000e+00 1628.0
11 TraesCS1A01G344500 chr6A 95.584 1019 29 3 3176 4192 524676559 524675555 0.000000e+00 1618.0
12 TraesCS1A01G344500 chr6A 95.383 1018 27 5 3179 4192 219307971 219306970 0.000000e+00 1602.0
13 TraesCS1A01G344500 chr6A 87.923 414 40 9 1146 1554 604441737 604442145 2.930000e-131 479.0
14 TraesCS1A01G344500 chr6A 95.349 215 9 1 1768 1982 604442215 604442428 1.440000e-89 340.0
15 TraesCS1A01G344500 chr6A 97.143 70 2 0 1667 1736 604442146 604442215 7.360000e-23 119.0
16 TraesCS1A01G344500 chr7A 95.665 1015 29 2 3179 4192 489553996 489554996 0.000000e+00 1616.0
17 TraesCS1A01G344500 chr7A 95.468 1015 31 2 3178 4192 170460953 170461952 0.000000e+00 1605.0
18 TraesCS1A01G344500 chr7A 83.929 112 16 2 1869 1979 704906713 704906823 5.730000e-19 106.0
19 TraesCS1A01G344500 chr7A 90.411 73 7 0 3178 3250 590449462 590449390 3.450000e-16 97.1
20 TraesCS1A01G344500 chr3A 95.229 1027 28 10 3173 4192 28631287 28632299 0.000000e+00 1605.0
21 TraesCS1A01G344500 chr3A 95.093 1019 31 4 3179 4192 100400621 100399617 0.000000e+00 1587.0
22 TraesCS1A01G344500 chr3A 96.379 359 13 0 353 711 65819900 65820258 3.610000e-165 592.0
23 TraesCS1A01G344500 chr3A 96.508 315 11 0 1 315 65819587 65819901 4.800000e-144 521.0
24 TraesCS1A01G344500 chr3A 96.923 195 6 0 517 711 65820290 65820484 1.120000e-85 327.0
25 TraesCS1A01G344500 chr3A 82.877 146 9 6 3176 3320 73530028 73529898 2.650000e-22 117.0
26 TraesCS1A01G344500 chr2B 94.169 1029 40 7 3169 4192 34909397 34910410 0.000000e+00 1550.0
27 TraesCS1A01G344500 chr2B 87.591 411 41 9 1149 1554 790366446 790366041 6.350000e-128 468.0
28 TraesCS1A01G344500 chr2B 95.349 215 9 1 1768 1982 790365973 790365760 1.440000e-89 340.0
29 TraesCS1A01G344500 chr2B 89.513 267 22 6 1719 1983 531049517 531049779 2.420000e-87 333.0
30 TraesCS1A01G344500 chr6B 96.901 710 22 0 2 711 559465659 559464950 0.000000e+00 1190.0
31 TraesCS1A01G344500 chr6B 97.432 584 15 0 128 711 559464943 559464360 0.000000e+00 996.0
32 TraesCS1A01G344500 chr6B 83.811 593 69 14 1146 1732 46771461 46772032 4.770000e-149 538.0
33 TraesCS1A01G344500 chr6B 93.333 150 10 0 562 711 559464353 559464204 5.450000e-54 222.0
34 TraesCS1A01G344500 chr1D 91.958 858 47 7 1982 2837 434281874 434282711 0.000000e+00 1182.0
35 TraesCS1A01G344500 chr1D 88.835 618 58 6 2154 2764 434321728 434322341 0.000000e+00 749.0
36 TraesCS1A01G344500 chr1D 95.890 292 11 1 2888 3179 434282834 434283124 4.910000e-129 472.0
37 TraesCS1A01G344500 chr1D 81.757 296 42 9 2885 3179 434322426 434322710 1.950000e-58 237.0
38 TraesCS1A01G344500 chr1D 93.893 131 8 0 1018 1148 434281745 434281875 9.190000e-47 198.0
39 TraesCS1A01G344500 chr1D 76.836 354 62 16 2193 2533 434274202 434274548 9.260000e-42 182.0
40 TraesCS1A01G344500 chr1D 75.397 252 54 4 2888 3132 434368668 434368918 9.520000e-22 115.0
41 TraesCS1A01G344500 chr1B 90.187 856 62 7 1982 2836 587989225 587990059 0.000000e+00 1096.0
42 TraesCS1A01G344500 chr1B 87.988 666 65 8 2154 2811 588002990 588003648 0.000000e+00 773.0
43 TraesCS1A01G344500 chr1B 95.205 292 13 1 2888 3179 587990185 587990475 1.060000e-125 460.0
44 TraesCS1A01G344500 chr1B 93.333 165 9 1 986 1148 587989062 587989226 4.190000e-60 243.0
45 TraesCS1A01G344500 chr1B 89.109 202 8 2 3179 3380 563975807 563975620 5.420000e-59 239.0
46 TraesCS1A01G344500 chr1B 77.119 354 61 14 2193 2533 587981999 587982345 1.990000e-43 187.0
47 TraesCS1A01G344500 chr1B 75.502 249 53 4 2888 3129 588151701 588151948 9.520000e-22 115.0
48 TraesCS1A01G344500 chr4B 82.796 837 100 18 1146 1978 584504873 584505669 0.000000e+00 708.0
49 TraesCS1A01G344500 chr4B 82.114 123 20 2 2345 2466 5406456 5406577 2.060000e-18 104.0
50 TraesCS1A01G344500 chr3B 88.302 530 52 7 1149 1675 609325482 609324960 9.890000e-176 627.0
51 TraesCS1A01G344500 chr3B 84.559 544 40 16 2 503 134243875 134243334 2.250000e-137 499.0
52 TraesCS1A01G344500 chr3B 91.628 215 18 0 1768 1982 609324609 609324395 8.810000e-77 298.0
53 TraesCS1A01G344500 chr3B 91.244 217 15 4 498 711 134241920 134241705 4.100000e-75 292.0
54 TraesCS1A01G344500 chr3D 82.392 744 82 20 1 711 95584637 95583910 1.670000e-168 603.0
55 TraesCS1A01G344500 chr3D 81.989 744 83 24 1 711 264682392 264681667 6.040000e-163 584.0
56 TraesCS1A01G344500 chr3D 82.883 222 15 9 1719 1939 604231778 604231977 1.200000e-40 178.0
57 TraesCS1A01G344500 chr2D 85.131 612 49 18 1149 1736 7406497 7405904 4.670000e-164 588.0
58 TraesCS1A01G344500 chr2D 87.261 157 14 3 383 538 642357093 642356942 1.550000e-39 174.0
59 TraesCS1A01G344500 chr5A 85.017 594 61 14 1146 1732 193922331 193922903 2.810000e-161 579.0
60 TraesCS1A01G344500 chr5A 87.348 411 42 9 1149 1554 93189763 93189358 2.950000e-126 462.0
61 TraesCS1A01G344500 chr5A 89.811 265 23 4 1719 1983 193922919 193923179 1.870000e-88 337.0
62 TraesCS1A01G344500 chr5A 94.884 215 10 1 1768 1982 93189288 93189075 6.720000e-88 335.0
63 TraesCS1A01G344500 chr5A 97.143 70 2 0 1667 1736 93189357 93189288 7.360000e-23 119.0
64 TraesCS1A01G344500 chr7B 84.286 560 63 16 1136 1691 80075678 80075140 1.340000e-144 523.0
65 TraesCS1A01G344500 chr7B 89.121 239 13 4 1758 1985 80071367 80071131 6.860000e-73 285.0
66 TraesCS1A01G344500 chr7B 84.459 148 9 2 3179 3326 3042966 3042833 2.630000e-27 134.0
67 TraesCS1A01G344500 chr5B 82.168 572 63 23 1 548 469969175 469968619 4.940000e-124 455.0
68 TraesCS1A01G344500 chr4A 100.000 29 0 0 2821 2849 735370157 735370185 2.000000e-03 54.7


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 TraesCS1A01G344500 chr1A 532455849 532460040 4191 False 3618.500000 5923 100.000000 1 4192 2 chr1A.!!$F3 4191
1 TraesCS1A01G344500 chr1A 207400908 207401912 1004 False 1620.000000 1620 95.682000 3179 4192 1 chr1A.!!$F1 1013
2 TraesCS1A01G344500 chr2A 768242841 768243841 1000 True 1650.000000 1650 96.256000 3179 4192 1 chr2A.!!$R4 1013
3 TraesCS1A01G344500 chr2A 526540622 526541623 1001 False 1618.000000 1618 95.669000 3178 4192 1 chr2A.!!$F1 1014
4 TraesCS1A01G344500 chr2A 643985872 643986872 1000 True 1611.000000 1611 95.567000 3179 4192 1 chr2A.!!$R3 1013
5 TraesCS1A01G344500 chr2A 596415541 596416251 710 False 1203.000000 1203 97.187000 1 711 1 chr2A.!!$F2 710
6 TraesCS1A01G344500 chr2A 431006297 431006984 687 True 1149.000000 1149 96.802000 1 688 1 chr2A.!!$R1 687
7 TraesCS1A01G344500 chr2A 431012932 431013619 687 True 1138.000000 1138 96.512000 1 688 1 chr2A.!!$R2 687
8 TraesCS1A01G344500 chr6A 94070395 94071398 1003 False 1628.000000 1628 95.776000 3177 4192 1 chr6A.!!$F1 1015
9 TraesCS1A01G344500 chr6A 524675555 524676559 1004 True 1618.000000 1618 95.584000 3176 4192 1 chr6A.!!$R2 1016
10 TraesCS1A01G344500 chr6A 219306970 219307971 1001 True 1602.000000 1602 95.383000 3179 4192 1 chr6A.!!$R1 1013
11 TraesCS1A01G344500 chr6A 604441737 604442428 691 False 312.666667 479 93.471667 1146 1982 3 chr6A.!!$F2 836
12 TraesCS1A01G344500 chr7A 489553996 489554996 1000 False 1616.000000 1616 95.665000 3179 4192 1 chr7A.!!$F2 1013
13 TraesCS1A01G344500 chr7A 170460953 170461952 999 False 1605.000000 1605 95.468000 3178 4192 1 chr7A.!!$F1 1014
14 TraesCS1A01G344500 chr3A 28631287 28632299 1012 False 1605.000000 1605 95.229000 3173 4192 1 chr3A.!!$F1 1019
15 TraesCS1A01G344500 chr3A 100399617 100400621 1004 True 1587.000000 1587 95.093000 3179 4192 1 chr3A.!!$R2 1013
16 TraesCS1A01G344500 chr3A 65819587 65820484 897 False 480.000000 592 96.603333 1 711 3 chr3A.!!$F2 710
17 TraesCS1A01G344500 chr2B 34909397 34910410 1013 False 1550.000000 1550 94.169000 3169 4192 1 chr2B.!!$F1 1023
18 TraesCS1A01G344500 chr2B 790365760 790366446 686 True 404.000000 468 91.470000 1149 1982 2 chr2B.!!$R1 833
19 TraesCS1A01G344500 chr6B 559464204 559465659 1455 True 802.666667 1190 95.888667 2 711 3 chr6B.!!$R1 709
20 TraesCS1A01G344500 chr6B 46771461 46772032 571 False 538.000000 538 83.811000 1146 1732 1 chr6B.!!$F1 586
21 TraesCS1A01G344500 chr1D 434281745 434283124 1379 False 617.333333 1182 93.913667 1018 3179 3 chr1D.!!$F3 2161
22 TraesCS1A01G344500 chr1D 434321728 434322710 982 False 493.000000 749 85.296000 2154 3179 2 chr1D.!!$F4 1025
23 TraesCS1A01G344500 chr1B 588002990 588003648 658 False 773.000000 773 87.988000 2154 2811 1 chr1B.!!$F2 657
24 TraesCS1A01G344500 chr1B 587989062 587990475 1413 False 599.666667 1096 92.908333 986 3179 3 chr1B.!!$F4 2193
25 TraesCS1A01G344500 chr4B 584504873 584505669 796 False 708.000000 708 82.796000 1146 1978 1 chr4B.!!$F2 832
26 TraesCS1A01G344500 chr3B 609324395 609325482 1087 True 462.500000 627 89.965000 1149 1982 2 chr3B.!!$R2 833
27 TraesCS1A01G344500 chr3B 134241705 134243875 2170 True 395.500000 499 87.901500 2 711 2 chr3B.!!$R1 709
28 TraesCS1A01G344500 chr3D 95583910 95584637 727 True 603.000000 603 82.392000 1 711 1 chr3D.!!$R1 710
29 TraesCS1A01G344500 chr3D 264681667 264682392 725 True 584.000000 584 81.989000 1 711 1 chr3D.!!$R2 710
30 TraesCS1A01G344500 chr2D 7405904 7406497 593 True 588.000000 588 85.131000 1149 1736 1 chr2D.!!$R1 587
31 TraesCS1A01G344500 chr5A 193922331 193923179 848 False 458.000000 579 87.414000 1146 1983 2 chr5A.!!$F1 837
32 TraesCS1A01G344500 chr5A 93189075 93189763 688 True 305.333333 462 93.125000 1149 1982 3 chr5A.!!$R1 833
33 TraesCS1A01G344500 chr7B 80071131 80075678 4547 True 404.000000 523 86.703500 1136 1985 2 chr7B.!!$R2 849
34 TraesCS1A01G344500 chr5B 469968619 469969175 556 True 455.000000 455 82.168000 1 548 1 chr5B.!!$R1 547

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
433 2234 0.179227 CGAACGAATGCATGCGAACA 60.179 50.0 33.39 0.0 0.00 3.18 F
1011 3049 2.143008 TGTACGCACGTCACTGAAAT 57.857 45.0 0.00 0.0 0.00 2.17 F
2094 8222 0.179225 CACAAATCACGGCGCAGTAC 60.179 55.0 14.13 0.0 0.00 2.73 F
2131 8259 0.323816 TTTGTGCCCTTGTCCACACA 60.324 50.0 0.00 0.0 41.26 3.72 F
2639 8771 0.389948 GACGCCCTTCATGTCTTCGT 60.390 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 3693 0.037326 TCCTCGCTTCGAATTGCAGT 60.037 50.0 9.70 0.00 34.74 4.40 R
2881 9168 0.030369 GGATACCTGATCGAACGCGT 59.970 55.0 5.58 5.58 38.98 6.01 R
2957 9244 0.591741 CTTGCTCGTCGTCGATACCC 60.592 60.0 5.00 0.00 45.21 3.69 R
3060 9347 0.606673 GCTCAGGGTCCCAAGACAAC 60.607 60.0 11.55 0.00 45.48 3.32 R
3577 9877 0.887247 TGTTGTTGTGTGCTGCTGTT 59.113 45.0 0.00 0.00 0.00 3.16 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
35 36 1.499368 TCCATCCAGCTGTCTGCATA 58.501 50.000 13.81 0.00 45.94 3.14
211 239 4.617223 CGTCATCGTCGCATAGATGTAATT 59.383 41.667 10.69 0.00 43.34 1.40
433 2234 0.179227 CGAACGAATGCATGCGAACA 60.179 50.000 33.39 0.00 0.00 3.18
648 2686 4.513692 CGTGAGGTGGTATTTTGTCTTGAA 59.486 41.667 0.00 0.00 0.00 2.69
669 2707 5.733572 TGAATGTTTCGTGTACGTGTTTTTC 59.266 36.000 0.00 5.18 40.80 2.29
685 2723 4.094590 TGTTTTTCGGTGCGTTTAGAGAAA 59.905 37.500 0.00 0.00 0.00 2.52
1011 3049 2.143008 TGTACGCACGTCACTGAAAT 57.857 45.000 0.00 0.00 0.00 2.17
1320 3415 6.441093 TGCAAGAATATAGCCAGAAACAAG 57.559 37.500 0.00 0.00 0.00 3.16
1334 3429 6.150140 GCCAGAAACAAGATTGAACTCTACAT 59.850 38.462 0.00 0.00 0.00 2.29
1405 3500 9.002600 TCAATCGATGAACTTATGGGATAAATG 57.997 33.333 0.00 0.00 34.30 2.32
1433 3528 5.833131 TCCCCTATACTGAATTGGCAATTTC 59.167 40.000 25.02 17.82 0.00 2.17
1435 3530 5.299279 CCCTATACTGAATTGGCAATTTCGT 59.701 40.000 25.02 23.61 0.00 3.85
1522 3619 3.869272 CGGTTGATCGCTGCCTGC 61.869 66.667 0.00 0.00 38.57 4.85
1559 3667 4.821589 CCGAGGACGAGGGCAAGC 62.822 72.222 0.00 0.00 42.66 4.01
1585 3693 1.798223 GCAAGACAAGCACACACGATA 59.202 47.619 0.00 0.00 0.00 2.92
1597 3705 3.122780 CACACACGATACTGCAATTCGAA 59.877 43.478 16.59 0.00 36.73 3.71
1602 3710 2.097685 CGATACTGCAATTCGAAGCGAG 60.098 50.000 3.35 5.79 37.14 5.03
1665 3775 0.528924 AACGTACTGGTGCGCTGATA 59.471 50.000 9.73 0.00 42.39 2.15
1744 7862 2.042464 CCAGACCTAGGCTGCTATCAA 58.958 52.381 21.26 0.00 32.06 2.57
1747 7865 2.962421 AGACCTAGGCTGCTATCAACTC 59.038 50.000 9.30 0.00 0.00 3.01
1750 7868 3.230134 CCTAGGCTGCTATCAACTCTCT 58.770 50.000 0.00 0.00 0.00 3.10
1764 7882 3.823281 ACTCTCTCTGGATGATTGCAG 57.177 47.619 0.00 0.00 42.29 4.41
1767 7885 4.099266 ACTCTCTCTGGATGATTGCAGTAC 59.901 45.833 0.00 0.00 41.68 2.73
1814 7932 2.125106 CCAGCGAGCCCAGGTAAC 60.125 66.667 0.00 0.00 0.00 2.50
1894 8012 9.871175 AAATGATGGCCATGCTTGATATATATA 57.129 29.630 26.56 0.00 35.24 0.86
2021 8149 1.004918 AGCCTGACAGCAACGGTAC 60.005 57.895 0.00 0.00 34.23 3.34
2054 8182 6.854496 TGCGTTCTCAAAATTTACTACAGT 57.146 33.333 0.00 0.00 0.00 3.55
2058 8186 8.706035 GCGTTCTCAAAATTTACTACAGTAGAA 58.294 33.333 14.94 0.00 0.00 2.10
2069 8197 2.949451 ACAGTAGAAGATCACCGCAG 57.051 50.000 0.00 0.00 0.00 5.18
2084 8212 2.036556 CGCAGGTTGACACAAATCAC 57.963 50.000 0.00 0.00 0.00 3.06
2085 8213 1.660052 CGCAGGTTGACACAAATCACG 60.660 52.381 0.00 0.00 0.00 4.35
2086 8214 1.334960 GCAGGTTGACACAAATCACGG 60.335 52.381 0.00 0.00 0.00 4.94
2087 8215 0.951558 AGGTTGACACAAATCACGGC 59.048 50.000 0.00 0.00 0.00 5.68
2088 8216 0.385473 GGTTGACACAAATCACGGCG 60.385 55.000 4.80 4.80 0.00 6.46
2089 8217 0.996727 GTTGACACAAATCACGGCGC 60.997 55.000 6.90 0.00 0.00 6.53
2090 8218 1.440145 TTGACACAAATCACGGCGCA 61.440 50.000 10.83 0.00 0.00 6.09
2091 8219 1.154413 GACACAAATCACGGCGCAG 60.154 57.895 10.83 8.25 0.00 5.18
2092 8220 1.841663 GACACAAATCACGGCGCAGT 61.842 55.000 10.83 9.16 0.00 4.40
2093 8221 0.601576 ACACAAATCACGGCGCAGTA 60.602 50.000 14.13 2.53 0.00 2.74
2094 8222 0.179225 CACAAATCACGGCGCAGTAC 60.179 55.000 14.13 0.00 0.00 2.73
2119 8247 5.527951 TCATGTACAATTTCACTTTGTGCC 58.472 37.500 0.00 0.00 38.45 5.01
2120 8248 4.314740 TGTACAATTTCACTTTGTGCCC 57.685 40.909 0.00 0.00 38.45 5.36
2128 8256 0.385390 CACTTTGTGCCCTTGTCCAC 59.615 55.000 0.00 0.00 0.00 4.02
2131 8259 0.323816 TTTGTGCCCTTGTCCACACA 60.324 50.000 0.00 0.00 41.26 3.72
2132 8260 1.304617 TGTGCCCTTGTCCACACAA 59.695 52.632 0.00 0.00 39.91 3.33
2136 8264 2.423538 GTGCCCTTGTCCACACAATATC 59.576 50.000 0.00 0.00 41.82 1.63
2239 8371 2.623513 CAGGGGGAGGAGGGCTAT 59.376 66.667 0.00 0.00 0.00 2.97
2331 8463 4.067972 ACATTTCGGCCGACTACATAAT 57.932 40.909 31.19 20.80 0.00 1.28
2536 8668 2.032799 GCACACCGTGAACATCTCAAAA 59.967 45.455 5.28 0.00 35.22 2.44
2632 8764 2.825836 GCTGGGACGCCCTTCATG 60.826 66.667 14.76 0.00 45.70 3.07
2639 8771 0.389948 GACGCCCTTCATGTCTTCGT 60.390 55.000 0.00 0.00 0.00 3.85
2757 8892 2.910688 AACAACGTCATCAGGTGAGT 57.089 45.000 0.00 0.00 37.56 3.41
2798 8952 7.573710 ACTTCCCTATGTTGTTTCTATGCATA 58.426 34.615 6.20 6.20 0.00 3.14
2809 9096 9.056005 GTTGTTTCTATGCATATCATGACCTTA 57.944 33.333 6.92 0.00 36.63 2.69
2811 9098 9.797642 TGTTTCTATGCATATCATGACCTTAAT 57.202 29.630 6.92 0.00 36.63 1.40
2816 9103 9.896645 CTATGCATATCATGACCTTAATTAGGT 57.103 33.333 6.92 6.37 46.93 3.08
2843 9130 9.760077 AATACCTCTGTTCCTAAATATAACACG 57.240 33.333 0.00 0.00 0.00 4.49
2844 9131 7.179076 ACCTCTGTTCCTAAATATAACACGT 57.821 36.000 0.00 0.00 0.00 4.49
2845 9132 7.618137 ACCTCTGTTCCTAAATATAACACGTT 58.382 34.615 0.00 0.00 0.00 3.99
2846 9133 8.098912 ACCTCTGTTCCTAAATATAACACGTTT 58.901 33.333 0.00 0.00 0.00 3.60
2847 9134 8.943002 CCTCTGTTCCTAAATATAACACGTTTT 58.057 33.333 0.00 0.00 0.00 2.43
2848 9135 9.755064 CTCTGTTCCTAAATATAACACGTTTTG 57.245 33.333 0.00 0.00 0.00 2.44
2849 9136 9.491675 TCTGTTCCTAAATATAACACGTTTTGA 57.508 29.630 0.00 0.00 0.00 2.69
2850 9137 9.537848 CTGTTCCTAAATATAACACGTTTTGAC 57.462 33.333 0.00 0.00 0.00 3.18
2851 9138 8.222433 TGTTCCTAAATATAACACGTTTTGACG 58.778 33.333 0.00 0.00 39.31 4.35
2852 9139 7.293402 TCCTAAATATAACACGTTTTGACGG 57.707 36.000 0.00 0.00 37.45 4.79
2853 9140 6.873076 TCCTAAATATAACACGTTTTGACGGT 59.127 34.615 0.00 0.00 37.45 4.83
2854 9141 7.387397 TCCTAAATATAACACGTTTTGACGGTT 59.613 33.333 0.00 7.29 37.45 4.44
2855 9142 7.479291 CCTAAATATAACACGTTTTGACGGTTG 59.521 37.037 0.00 0.00 37.45 3.77
2856 9143 6.542574 AATATAACACGTTTTGACGGTTGA 57.457 33.333 0.00 0.19 37.45 3.18
2857 9144 4.879104 ATAACACGTTTTGACGGTTGAA 57.121 36.364 0.00 0.00 37.45 2.69
2858 9145 3.555917 AACACGTTTTGACGGTTGAAA 57.444 38.095 3.90 0.00 37.45 2.69
2859 9146 3.555917 ACACGTTTTGACGGTTGAAAA 57.444 38.095 3.90 0.00 37.45 2.29
2860 9147 3.494232 ACACGTTTTGACGGTTGAAAAG 58.506 40.909 3.90 2.01 37.45 2.27
2861 9148 2.849473 CACGTTTTGACGGTTGAAAAGG 59.151 45.455 13.17 13.17 37.45 3.11
2862 9149 2.159352 ACGTTTTGACGGTTGAAAAGGG 60.159 45.455 16.53 8.53 37.45 3.95
2863 9150 2.159352 CGTTTTGACGGTTGAAAAGGGT 60.159 45.455 9.42 0.00 0.00 4.34
2864 9151 3.183754 GTTTTGACGGTTGAAAAGGGTG 58.816 45.455 0.00 0.00 0.00 4.61
2865 9152 2.131776 TTGACGGTTGAAAAGGGTGT 57.868 45.000 0.00 0.00 0.00 4.16
2866 9153 3.278668 TTGACGGTTGAAAAGGGTGTA 57.721 42.857 0.00 0.00 0.00 2.90
2867 9154 3.495434 TGACGGTTGAAAAGGGTGTAT 57.505 42.857 0.00 0.00 0.00 2.29
2868 9155 3.142951 TGACGGTTGAAAAGGGTGTATG 58.857 45.455 0.00 0.00 0.00 2.39
2869 9156 3.143728 GACGGTTGAAAAGGGTGTATGT 58.856 45.455 0.00 0.00 0.00 2.29
2870 9157 3.558033 ACGGTTGAAAAGGGTGTATGTT 58.442 40.909 0.00 0.00 0.00 2.71
2871 9158 3.955551 ACGGTTGAAAAGGGTGTATGTTT 59.044 39.130 0.00 0.00 0.00 2.83
2872 9159 4.403113 ACGGTTGAAAAGGGTGTATGTTTT 59.597 37.500 0.00 0.00 0.00 2.43
2873 9160 5.593502 ACGGTTGAAAAGGGTGTATGTTTTA 59.406 36.000 0.00 0.00 0.00 1.52
2874 9161 6.096564 ACGGTTGAAAAGGGTGTATGTTTTAA 59.903 34.615 0.00 0.00 0.00 1.52
2875 9162 6.418523 CGGTTGAAAAGGGTGTATGTTTTAAC 59.581 38.462 0.00 0.00 0.00 2.01
2876 9163 6.702723 GGTTGAAAAGGGTGTATGTTTTAACC 59.297 38.462 6.08 6.08 0.00 2.85
2877 9164 6.074544 TGAAAAGGGTGTATGTTTTAACCG 57.925 37.500 0.00 0.00 33.24 4.44
2878 9165 4.508461 AAAGGGTGTATGTTTTAACCGC 57.492 40.909 0.00 0.00 33.24 5.68
2879 9166 2.439409 AGGGTGTATGTTTTAACCGCC 58.561 47.619 0.00 0.00 33.24 6.13
2880 9167 2.161030 GGGTGTATGTTTTAACCGCCA 58.839 47.619 0.00 0.00 33.24 5.69
2881 9168 2.557490 GGGTGTATGTTTTAACCGCCAA 59.443 45.455 0.00 0.00 33.24 4.52
2882 9169 3.567530 GGTGTATGTTTTAACCGCCAAC 58.432 45.455 0.00 0.00 0.00 3.77
2883 9170 3.227948 GTGTATGTTTTAACCGCCAACG 58.772 45.455 0.00 0.00 39.67 4.10
2884 9171 2.244251 GTATGTTTTAACCGCCAACGC 58.756 47.619 0.00 0.00 38.22 4.84
2957 9244 2.628178 TCAGCTCTGGAACATATACCGG 59.372 50.000 0.00 0.00 38.20 5.28
3012 9299 1.546476 CTCTTTGAGGTACCGACAGCT 59.454 52.381 6.18 0.00 0.00 4.24
3060 9347 1.788258 ATGTCTCAAGCGGCATATCG 58.212 50.000 1.45 0.00 0.00 2.92
3162 9449 1.195448 CTCCTGTTCAATGTCACACGC 59.805 52.381 0.00 0.00 0.00 5.34
3207 9494 2.076863 GAAAAGTCATGCTAGTGGCGT 58.923 47.619 0.00 0.00 45.43 5.68
3249 9536 1.153529 CATTACCGGTGCGCCACTA 60.154 57.895 19.93 1.08 34.40 2.74
3250 9537 1.153509 ATTACCGGTGCGCCACTAC 60.154 57.895 19.93 0.00 34.40 2.73
3251 9538 2.582734 ATTACCGGTGCGCCACTACC 62.583 60.000 19.93 4.43 34.40 3.18
3262 9549 4.373116 CACTACCGGTGCGCCACT 62.373 66.667 19.93 2.18 39.22 4.00
3263 9550 4.373116 ACTACCGGTGCGCCACTG 62.373 66.667 19.93 8.41 40.14 3.66
3498 9785 0.462375 TAGTGTCTTGTGTGGTGCGT 59.538 50.000 0.00 0.00 0.00 5.24
3611 9911 6.017192 ACACAACAACATCAGATTCATCGAAA 60.017 34.615 0.00 0.00 0.00 3.46
3688 9989 7.698970 TCAAAAGACCGAACAAAGATAAAACAC 59.301 33.333 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.116300 CGCGCATACACAAGAAGTAGAT 58.884 45.455 8.75 0.00 0.00 1.98
100 118 3.936566 ACCCTCTTCCCCCGGACA 61.937 66.667 0.73 0.00 0.00 4.02
433 2234 1.750193 CCCACGTTCAGCATTATGGT 58.250 50.000 0.00 0.00 0.00 3.55
648 2686 4.265371 CGAAAAACACGTACACGAAACAT 58.735 39.130 9.04 0.00 43.02 2.71
669 2707 5.864986 ACATATTTTTCTCTAAACGCACCG 58.135 37.500 0.00 0.00 0.00 4.94
990 3028 2.143008 TTCAGTGACGTGCGTACAAT 57.857 45.000 4.09 0.00 0.00 2.71
993 3031 3.515071 AAATTTCAGTGACGTGCGTAC 57.485 42.857 0.00 0.00 0.00 3.67
1109 3184 0.394080 GGCAGAGAAGAAGCAGCCAT 60.394 55.000 0.00 0.00 41.63 4.40
1161 3236 3.815401 GCTTCGCATACCCATGTTAGAAT 59.185 43.478 0.00 0.00 34.40 2.40
1166 3241 3.275617 TTAGCTTCGCATACCCATGTT 57.724 42.857 0.00 0.00 34.40 2.71
1320 3415 6.890293 AGAAGGGGTTATGTAGAGTTCAATC 58.110 40.000 0.00 0.00 0.00 2.67
1334 3429 1.695242 TGTCGCTTTGAGAAGGGGTTA 59.305 47.619 3.83 0.00 43.77 2.85
1405 3500 5.876357 TGCCAATTCAGTATAGGGGATTAC 58.124 41.667 0.00 0.00 0.00 1.89
1441 3536 5.507077 TCGCACTGTGAGTTTTGTAATTTC 58.493 37.500 12.86 0.00 0.00 2.17
1554 3662 4.451652 GTCTTGCCTCGCGCTTGC 62.452 66.667 5.56 5.71 38.78 4.01
1559 3667 3.043713 TGCTTGTCTTGCCTCGCG 61.044 61.111 0.00 0.00 0.00 5.87
1567 3675 3.059884 CAGTATCGTGTGTGCTTGTCTT 58.940 45.455 0.00 0.00 0.00 3.01
1568 3676 2.677199 CAGTATCGTGTGTGCTTGTCT 58.323 47.619 0.00 0.00 0.00 3.41
1569 3677 1.126846 GCAGTATCGTGTGTGCTTGTC 59.873 52.381 0.00 0.00 32.97 3.18
1570 3678 1.148310 GCAGTATCGTGTGTGCTTGT 58.852 50.000 0.00 0.00 32.97 3.16
1571 3679 1.147473 TGCAGTATCGTGTGTGCTTG 58.853 50.000 0.00 0.00 36.84 4.01
1572 3680 1.877637 TTGCAGTATCGTGTGTGCTT 58.122 45.000 0.00 0.00 36.84 3.91
1585 3693 0.037326 TCCTCGCTTCGAATTGCAGT 60.037 50.000 9.70 0.00 34.74 4.40
1597 3705 4.615815 GCATCCGGCATCCTCGCT 62.616 66.667 0.00 0.00 43.97 4.93
1665 3775 5.238583 GGTAGTTTGCATCGCTAATAGGAT 58.761 41.667 0.00 0.00 0.00 3.24
1717 7835 0.400670 AGCCTAGGTCTGGGAATCCC 60.401 60.000 12.39 12.39 45.71 3.85
1744 7862 3.106054 ACTGCAATCATCCAGAGAGAGT 58.894 45.455 0.00 0.00 33.40 3.24
1747 7865 3.494048 GGGTACTGCAATCATCCAGAGAG 60.494 52.174 0.00 0.00 33.40 3.20
1750 7868 2.195727 TGGGTACTGCAATCATCCAGA 58.804 47.619 0.00 0.00 33.40 3.86
1764 7882 0.109723 TGACTTGGCCTGTTGGGTAC 59.890 55.000 3.32 0.00 37.43 3.34
1767 7885 1.181098 CCTTGACTTGGCCTGTTGGG 61.181 60.000 3.32 3.54 38.36 4.12
1831 7949 2.292016 TGAAATTTCGGCAAAGAAGCGA 59.708 40.909 13.34 0.00 34.64 4.93
1920 8048 7.326789 CGCATACCCAATATTTTCTGCTAATTG 59.673 37.037 0.00 0.00 0.00 2.32
2051 8179 1.478510 ACCTGCGGTGATCTTCTACTG 59.521 52.381 0.00 0.00 32.98 2.74
2053 8181 2.094182 TCAACCTGCGGTGATCTTCTAC 60.094 50.000 0.94 0.00 35.34 2.59
2054 8182 2.094182 GTCAACCTGCGGTGATCTTCTA 60.094 50.000 0.94 0.00 35.34 2.10
2058 8186 0.320771 GTGTCAACCTGCGGTGATCT 60.321 55.000 0.94 0.00 35.34 2.75
2062 8190 0.667993 ATTTGTGTCAACCTGCGGTG 59.332 50.000 0.94 0.00 35.34 4.94
2065 8193 1.660052 CGTGATTTGTGTCAACCTGCG 60.660 52.381 0.00 0.00 0.00 5.18
2069 8197 0.385473 CGCCGTGATTTGTGTCAACC 60.385 55.000 0.00 0.00 0.00 3.77
2080 8208 0.104855 ATGATGTACTGCGCCGTGAT 59.895 50.000 15.24 6.38 0.00 3.06
2081 8209 0.805711 CATGATGTACTGCGCCGTGA 60.806 55.000 15.24 1.23 0.00 4.35
2082 8210 1.083806 ACATGATGTACTGCGCCGTG 61.084 55.000 15.24 6.48 0.00 4.94
2083 8211 0.458260 TACATGATGTACTGCGCCGT 59.542 50.000 10.01 10.01 0.00 5.68
2084 8212 3.266282 TACATGATGTACTGCGCCG 57.734 52.632 4.18 0.00 0.00 6.46
2091 8219 9.117145 CACAAAGTGAAATTGTACATGATGTAC 57.883 33.333 24.78 24.78 43.34 2.90
2092 8220 7.807433 GCACAAAGTGAAATTGTACATGATGTA 59.193 33.333 0.23 0.23 38.90 2.29
2093 8221 6.642131 GCACAAAGTGAAATTGTACATGATGT 59.358 34.615 2.65 2.65 38.90 3.06
2094 8222 6.089820 GGCACAAAGTGAAATTGTACATGATG 59.910 38.462 0.00 0.00 38.90 3.07
2103 8231 3.795877 ACAAGGGCACAAAGTGAAATTG 58.204 40.909 0.58 4.62 35.23 2.32
2117 8245 2.722094 TGATATTGTGTGGACAAGGGC 58.278 47.619 0.00 0.00 45.29 5.19
2119 8247 6.704289 ATTGATGATATTGTGTGGACAAGG 57.296 37.500 0.00 0.00 45.29 3.61
2136 8264 8.002665 CGCGCAGATATATGAGATAAATTGATG 58.997 37.037 8.75 0.00 0.00 3.07
2331 8463 2.186160 CACTTGCACAAGGACGGCA 61.186 57.895 14.51 0.00 42.53 5.69
2473 8605 3.621805 TCAAAGACAGGCGGCCGA 61.622 61.111 33.48 0.00 0.00 5.54
2482 8614 1.001974 CCGATGTGGAGGTCAAAGACA 59.998 52.381 0.00 0.00 42.00 3.41
2483 8615 1.726853 CCGATGTGGAGGTCAAAGAC 58.273 55.000 0.00 0.00 42.00 3.01
2536 8668 0.036952 CAGACTTCTCCACATGCGGT 60.037 55.000 0.00 0.00 0.00 5.68
2570 8702 1.734477 CGAAGTCGTCTGGCACCAG 60.734 63.158 10.60 10.60 44.86 4.00
2632 8764 1.016653 GCCTGAGCTCCAACGAAGAC 61.017 60.000 12.15 0.00 35.50 3.01
2757 8892 2.478894 GGAAGTTTGCGATCGTCTTTGA 59.521 45.455 17.81 0.00 0.00 2.69
2820 9107 7.179076 ACGTGTTATATTTAGGAACAGAGGT 57.821 36.000 0.00 0.00 33.91 3.85
2822 9109 9.755064 CAAAACGTGTTATATTTAGGAACAGAG 57.245 33.333 0.00 0.00 33.91 3.35
2824 9111 9.537848 GTCAAAACGTGTTATATTTAGGAACAG 57.462 33.333 0.00 0.00 33.91 3.16
2843 9130 3.183754 CACCCTTTTCAACCGTCAAAAC 58.816 45.455 0.00 0.00 0.00 2.43
2844 9131 2.826725 ACACCCTTTTCAACCGTCAAAA 59.173 40.909 0.00 0.00 0.00 2.44
2845 9132 2.448453 ACACCCTTTTCAACCGTCAAA 58.552 42.857 0.00 0.00 0.00 2.69
2846 9133 2.131776 ACACCCTTTTCAACCGTCAA 57.868 45.000 0.00 0.00 0.00 3.18
2847 9134 3.142951 CATACACCCTTTTCAACCGTCA 58.857 45.455 0.00 0.00 0.00 4.35
2848 9135 3.143728 ACATACACCCTTTTCAACCGTC 58.856 45.455 0.00 0.00 0.00 4.79
2849 9136 3.217681 ACATACACCCTTTTCAACCGT 57.782 42.857 0.00 0.00 0.00 4.83
2850 9137 4.577834 AAACATACACCCTTTTCAACCG 57.422 40.909 0.00 0.00 0.00 4.44
2851 9138 6.702723 GGTTAAAACATACACCCTTTTCAACC 59.297 38.462 0.00 0.00 0.00 3.77
2852 9139 6.418523 CGGTTAAAACATACACCCTTTTCAAC 59.581 38.462 0.00 0.00 0.00 3.18
2853 9140 6.505272 CGGTTAAAACATACACCCTTTTCAA 58.495 36.000 0.00 0.00 0.00 2.69
2854 9141 5.507650 GCGGTTAAAACATACACCCTTTTCA 60.508 40.000 0.00 0.00 0.00 2.69
2855 9142 4.919168 GCGGTTAAAACATACACCCTTTTC 59.081 41.667 0.00 0.00 0.00 2.29
2856 9143 4.262121 GGCGGTTAAAACATACACCCTTTT 60.262 41.667 0.00 0.00 0.00 2.27
2857 9144 3.256383 GGCGGTTAAAACATACACCCTTT 59.744 43.478 0.00 0.00 0.00 3.11
2858 9145 2.821378 GGCGGTTAAAACATACACCCTT 59.179 45.455 0.00 0.00 0.00 3.95
2859 9146 2.224818 TGGCGGTTAAAACATACACCCT 60.225 45.455 0.00 0.00 0.00 4.34
2860 9147 2.161030 TGGCGGTTAAAACATACACCC 58.839 47.619 0.00 0.00 0.00 4.61
2861 9148 3.567530 GTTGGCGGTTAAAACATACACC 58.432 45.455 0.00 0.00 0.00 4.16
2862 9149 3.227948 CGTTGGCGGTTAAAACATACAC 58.772 45.455 0.00 0.00 0.00 2.90
2863 9150 2.350580 GCGTTGGCGGTTAAAACATACA 60.351 45.455 0.00 0.00 38.78 2.29
2864 9151 2.244251 GCGTTGGCGGTTAAAACATAC 58.756 47.619 0.00 0.00 38.78 2.39
2865 9152 2.615489 GCGTTGGCGGTTAAAACATA 57.385 45.000 0.00 0.00 38.78 2.29
2866 9153 3.482765 GCGTTGGCGGTTAAAACAT 57.517 47.368 0.00 0.00 38.78 2.71
2877 9164 2.395690 CTGATCGAACGCGTTGGC 59.604 61.111 31.89 16.40 38.98 4.52
2878 9165 0.457166 TACCTGATCGAACGCGTTGG 60.457 55.000 31.89 28.43 38.98 3.77
2879 9166 1.517276 GATACCTGATCGAACGCGTTG 59.483 52.381 31.89 20.72 38.98 4.10
2880 9167 1.535437 GGATACCTGATCGAACGCGTT 60.535 52.381 26.97 26.97 38.98 4.84
2881 9168 0.030369 GGATACCTGATCGAACGCGT 59.970 55.000 5.58 5.58 38.98 6.01
2882 9169 2.797515 GGATACCTGATCGAACGCG 58.202 57.895 3.53 3.53 35.12 6.01
2957 9244 0.591741 CTTGCTCGTCGTCGATACCC 60.592 60.000 5.00 0.00 45.21 3.69
3009 9296 2.435586 GCCGTCTGCATCACAGCT 60.436 61.111 0.00 0.00 46.76 4.24
3012 9299 1.810853 CATCGCCGTCTGCATCACA 60.811 57.895 0.00 0.00 41.33 3.58
3060 9347 0.606673 GCTCAGGGTCCCAAGACAAC 60.607 60.000 11.55 0.00 45.48 3.32
3162 9449 7.032580 CCTAGTAGTGTTGATTGAGAACTCAG 58.967 42.308 4.72 0.00 41.13 3.35
3253 9540 4.107051 GTGATGGCAGTGGCGCAC 62.107 66.667 21.02 21.02 42.47 5.34
3262 9549 7.946917 GAATTTAATTCTAATGGCGTGATGGCA 60.947 37.037 10.15 2.57 45.60 4.92
3263 9550 4.829064 TTAATTCTAATGGCGTGATGGC 57.171 40.909 0.00 0.00 45.12 4.40
3264 9551 7.858052 GAATTTAATTCTAATGGCGTGATGG 57.142 36.000 10.15 0.00 36.37 3.51
3522 9816 9.612066 ACCTATGCAAAAATCAGAAAAGAAAAA 57.388 25.926 0.00 0.00 0.00 1.94
3577 9877 0.887247 TGTTGTTGTGTGCTGCTGTT 59.113 45.000 0.00 0.00 0.00 3.16
3611 9911 9.250624 GTATTCGCAGACTAATCTTCTATTGTT 57.749 33.333 0.00 0.00 34.32 2.83
3688 9989 3.253677 ACTCACGGTCTTGAGACTTGTAG 59.746 47.826 10.76 6.78 45.19 2.74
3892 10193 6.882678 GGTAACAGTTACAAAGGATACACCAT 59.117 38.462 22.34 0.00 38.30 3.55


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

AutoCloner maintained by Alex Coulton.