Multiple sequence alignment - TraesCS5D01G078900

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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 TraesCS5D01G078900 chr5D 100.000 4016 0 0 1 4016 79103952 79107967 0.000000e+00 7417.0
1 TraesCS5D01G078900 chr5D 91.571 700 53 2 2131 2824 79140013 79140712 0.000000e+00 961.0
2 TraesCS5D01G078900 chr5D 95.009 581 23 1 830 1404 79137696 79138276 0.000000e+00 907.0
3 TraesCS5D01G078900 chr5D 90.157 254 23 2 31 282 302711349 302711096 2.990000e-86 329.0
4 TraesCS5D01G078900 chr5D 76.496 468 88 16 2263 2718 76754332 76753875 6.710000e-58 235.0
5 TraesCS5D01G078900 chr5D 76.282 468 89 16 2263 2718 76690088 76689631 3.120000e-56 230.0
6 TraesCS5D01G078900 chr5D 82.609 253 24 10 287 534 79136943 79137180 5.260000e-49 206.0
7 TraesCS5D01G078900 chr5D 89.375 160 14 2 3857 4016 79166422 79166578 8.800000e-47 198.0
8 TraesCS5D01G078900 chr5D 82.775 209 26 7 352 551 76691985 76691778 1.150000e-40 178.0
9 TraesCS5D01G078900 chr5D 89.381 113 11 1 2826 2937 79149610 79149722 1.500000e-29 141.0
10 TraesCS5D01G078900 chr5B 97.035 1619 47 1 1770 3387 88737023 88738641 0.000000e+00 2723.0
11 TraesCS5D01G078900 chr5B 88.326 1679 116 30 1 1624 88703823 88705476 0.000000e+00 1941.0
12 TraesCS5D01G078900 chr5B 93.982 914 49 1 2173 3086 88705833 88706740 0.000000e+00 1378.0
13 TraesCS5D01G078900 chr5B 92.782 762 49 2 2127 2882 88781177 88781938 0.000000e+00 1098.0
14 TraesCS5D01G078900 chr5B 92.725 701 35 7 932 1624 88779920 88780612 0.000000e+00 998.0
15 TraesCS5D01G078900 chr5B 83.366 1010 104 35 665 1624 88736034 88737029 0.000000e+00 876.0
16 TraesCS5D01G078900 chr5B 92.697 356 23 1 1769 2124 88780605 88780957 9.960000e-141 510.0
17 TraesCS5D01G078900 chr5B 91.351 370 27 2 1769 2136 88705469 88705835 5.990000e-138 501.0
18 TraesCS5D01G078900 chr5B 90.523 306 22 1 3711 4016 88706738 88707036 8.090000e-107 398.0
19 TraesCS5D01G078900 chr5B 82.540 252 25 9 288 534 88778860 88779097 1.890000e-48 204.0
20 TraesCS5D01G078900 chr5B 95.935 123 5 0 3784 3906 88739717 88739839 2.450000e-47 200.0
21 TraesCS5D01G078900 chr5B 86.364 132 11 4 288 414 88735670 88735799 1.950000e-28 137.0
22 TraesCS5D01G078900 chr5B 84.733 131 17 2 365 493 85285681 85285810 1.170000e-25 128.0
23 TraesCS5D01G078900 chr5B 82.558 86 6 2 745 829 88779694 88779771 2.590000e-07 67.6
24 TraesCS5D01G078900 chr5A 90.933 1147 87 6 1769 2901 75049560 75050703 0.000000e+00 1526.0
25 TraesCS5D01G078900 chr5A 82.477 1421 126 54 288 1624 75048186 75049567 0.000000e+00 1131.0
26 TraesCS5D01G078900 chr5A 92.259 633 45 3 3083 3713 576588295 576587665 0.000000e+00 894.0
27 TraesCS5D01G078900 chr5A 90.709 635 53 3 3079 3713 573303717 573304345 0.000000e+00 841.0
28 TraesCS5D01G078900 chr1A 93.456 871 43 4 2173 3042 475710330 475711187 0.000000e+00 1280.0
29 TraesCS5D01G078900 chr1A 94.142 734 36 2 2310 3042 475616063 475616790 0.000000e+00 1110.0
30 TraesCS5D01G078900 chr1A 93.849 634 38 1 3080 3713 300564432 300565064 0.000000e+00 953.0
31 TraesCS5D01G078900 chr1A 89.373 734 52 16 899 1624 475709306 475710021 0.000000e+00 900.0
32 TraesCS5D01G078900 chr1A 91.853 626 48 3 3086 3711 469308488 469307866 0.000000e+00 870.0
33 TraesCS5D01G078900 chr1A 91.450 269 23 0 564 832 475614573 475614841 1.760000e-98 370.0
34 TraesCS5D01G078900 chr1A 91.450 269 22 1 564 832 475707882 475708149 6.340000e-98 368.0
35 TraesCS5D01G078900 chr1A 87.072 263 19 6 25 284 22350519 22350769 2.360000e-72 283.0
36 TraesCS5D01G078900 chr1A 96.491 171 6 0 1769 1939 475710014 475710184 2.360000e-72 283.0
37 TraesCS5D01G078900 chr1A 93.919 148 9 0 1989 2136 475710185 475710332 1.450000e-54 224.0
38 TraesCS5D01G078900 chrUn 92.614 704 36 7 932 1627 227383585 227382890 0.000000e+00 998.0
39 TraesCS5D01G078900 chrUn 93.661 631 37 2 3083 3713 1908522 1907895 0.000000e+00 941.0
40 TraesCS5D01G078900 chrUn 92.697 356 23 1 1769 2124 227382900 227382548 9.960000e-141 510.0
41 TraesCS5D01G078900 chrUn 98.000 150 3 0 1618 1767 170987913 170988062 1.110000e-65 261.0
42 TraesCS5D01G078900 chrUn 98.000 150 3 0 1618 1767 171050805 171050656 1.110000e-65 261.0
43 TraesCS5D01G078900 chrUn 98.000 150 3 0 1618 1767 266527349 266527498 1.110000e-65 261.0
44 TraesCS5D01G078900 chrUn 98.000 150 3 0 1618 1767 365915370 365915221 1.110000e-65 261.0
45 TraesCS5D01G078900 chrUn 98.000 150 3 0 1618 1767 462273063 462272914 1.110000e-65 261.0
46 TraesCS5D01G078900 chrUn 82.540 252 25 9 288 534 227384645 227384408 1.890000e-48 204.0
47 TraesCS5D01G078900 chrUn 82.558 86 6 2 745 829 227383811 227383734 2.590000e-07 67.6
48 TraesCS5D01G078900 chr2D 93.250 637 40 3 3079 3713 44895718 44896353 0.000000e+00 935.0
49 TraesCS5D01G078900 chr7A 92.540 630 45 2 3084 3713 404469711 404470338 0.000000e+00 902.0
50 TraesCS5D01G078900 chr3A 92.357 628 44 3 3086 3711 508532571 508533196 0.000000e+00 891.0
51 TraesCS5D01G078900 chr4A 91.837 637 43 6 3084 3713 3341305 3340671 0.000000e+00 880.0
52 TraesCS5D01G078900 chr1D 88.627 255 16 2 31 284 391284220 391283978 8.440000e-77 298.0
53 TraesCS5D01G078900 chr1D 98.000 150 3 0 1618 1767 185776472 185776323 1.110000e-65 261.0
54 TraesCS5D01G078900 chr1D 98.000 150 3 0 1618 1767 298348007 298348156 1.110000e-65 261.0
55 TraesCS5D01G078900 chr1B 87.109 256 19 6 31 284 16662303 16662546 1.100000e-70 278.0
56 TraesCS5D01G078900 chr6D 98.000 150 3 0 1618 1767 124524602 124524453 1.110000e-65 261.0
57 TraesCS5D01G078900 chr4D 98.000 150 3 0 1618 1767 398039846 398039995 1.110000e-65 261.0


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 TraesCS5D01G078900 chr5D 79103952 79107967 4015 False 7417.000000 7417 100.000000 1 4016 1 chr5D.!!$F1 4015
1 TraesCS5D01G078900 chr5D 79136943 79140712 3769 False 691.333333 961 89.729667 287 2824 3 chr5D.!!$F4 2537
2 TraesCS5D01G078900 chr5D 76689631 76691985 2354 True 204.000000 230 79.528500 352 2718 2 chr5D.!!$R3 2366
3 TraesCS5D01G078900 chr5B 88703823 88707036 3213 False 1054.500000 1941 91.045500 1 4016 4 chr5B.!!$F2 4015
4 TraesCS5D01G078900 chr5B 88735670 88739839 4169 False 984.000000 2723 90.675000 288 3906 4 chr5B.!!$F3 3618
5 TraesCS5D01G078900 chr5B 88778860 88781938 3078 False 575.520000 1098 88.660400 288 2882 5 chr5B.!!$F4 2594
6 TraesCS5D01G078900 chr5A 75048186 75050703 2517 False 1328.500000 1526 86.705000 288 2901 2 chr5A.!!$F2 2613
7 TraesCS5D01G078900 chr5A 576587665 576588295 630 True 894.000000 894 92.259000 3083 3713 1 chr5A.!!$R1 630
8 TraesCS5D01G078900 chr5A 573303717 573304345 628 False 841.000000 841 90.709000 3079 3713 1 chr5A.!!$F1 634
9 TraesCS5D01G078900 chr1A 300564432 300565064 632 False 953.000000 953 93.849000 3080 3713 1 chr1A.!!$F2 633
10 TraesCS5D01G078900 chr1A 469307866 469308488 622 True 870.000000 870 91.853000 3086 3711 1 chr1A.!!$R1 625
11 TraesCS5D01G078900 chr1A 475614573 475616790 2217 False 740.000000 1110 92.796000 564 3042 2 chr1A.!!$F3 2478
12 TraesCS5D01G078900 chr1A 475707882 475711187 3305 False 611.000000 1280 92.937800 564 3042 5 chr1A.!!$F4 2478
13 TraesCS5D01G078900 chrUn 1907895 1908522 627 True 941.000000 941 93.661000 3083 3713 1 chrUn.!!$R1 630
14 TraesCS5D01G078900 chrUn 227382548 227384645 2097 True 444.900000 998 87.602250 288 2124 4 chrUn.!!$R5 1836
15 TraesCS5D01G078900 chr2D 44895718 44896353 635 False 935.000000 935 93.250000 3079 3713 1 chr2D.!!$F1 634
16 TraesCS5D01G078900 chr7A 404469711 404470338 627 False 902.000000 902 92.540000 3084 3713 1 chr7A.!!$F1 629
17 TraesCS5D01G078900 chr3A 508532571 508533196 625 False 891.000000 891 92.357000 3086 3711 1 chr3A.!!$F1 625
18 TraesCS5D01G078900 chr4A 3340671 3341305 634 True 880.000000 880 91.837000 3084 3713 1 chr4A.!!$R1 629

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
253 255 0.107508 AACATCTGGCCTCGTCCATG 60.108 55.0 3.32 0.0 35.22 3.66 F
1657 4211 0.112025 AGAGAGCTGCCTTGGCTTTT 59.888 50.0 13.18 0.0 40.40 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 4554 0.234884 GAGGACGTCGCCAAAAAGTG 59.765 55.0 9.92 0.0 0.00 3.16 R
3409 6971 0.321564 CGCCTCATCAGGGTTGAACA 60.322 55.0 0.00 0.0 40.75 3.18 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
28 29 9.874215 GTTCAGGTTTAGTAAGATTAACACAAC 57.126 33.333 0.00 0.00 0.00 3.32
37 38 3.951663 AGATTAACACAACAGGCCCTAC 58.048 45.455 0.00 0.00 0.00 3.18
60 61 3.989817 GGCCGCATTTCATTGATTAATCC 59.010 43.478 12.90 0.00 0.00 3.01
85 86 4.526262 ACAGAGAGAATGCTGTTACAGAGT 59.474 41.667 17.40 0.04 42.33 3.24
103 104 4.154918 CAGAGTTACAGAACAATGGAAGGC 59.845 45.833 0.00 0.00 38.10 4.35
106 107 3.057526 GTTACAGAACAATGGAAGGCCAC 60.058 47.826 5.01 0.00 40.30 5.01
129 130 4.081972 CCTATGGCGATACTACAAGCATCT 60.082 45.833 0.00 0.00 0.00 2.90
138 139 6.198029 CGATACTACAAGCATCTCTGTTTCAG 59.802 42.308 0.00 0.00 0.00 3.02
139 140 5.474578 ACTACAAGCATCTCTGTTTCAGA 57.525 39.130 0.00 0.00 38.25 3.27
140 141 5.233988 ACTACAAGCATCTCTGTTTCAGAC 58.766 41.667 0.00 0.00 35.39 3.51
141 142 3.062763 ACAAGCATCTCTGTTTCAGACG 58.937 45.455 0.00 0.00 35.39 4.18
152 153 1.040646 TTTCAGACGGAGCAGTCACT 58.959 50.000 9.16 0.00 43.24 3.41
178 180 4.869861 CAGTTTTAGCAAAATACATGGGGC 59.130 41.667 0.00 0.00 32.22 5.80
192 194 1.456331 GGGGCATTGATCAGGGTGG 60.456 63.158 0.00 0.00 0.00 4.61
210 212 1.768275 TGGCTCAAAGAGTCTGTCCAA 59.232 47.619 0.00 0.00 35.05 3.53
222 224 2.039084 GTCTGTCCAACTGGTGAATCCT 59.961 50.000 0.00 0.00 37.07 3.24
253 255 0.107508 AACATCTGGCCTCGTCCATG 60.108 55.000 3.32 0.00 35.22 3.66
261 263 2.107750 CTCGTCCATGATGCGGCT 59.892 61.111 0.00 0.00 0.00 5.52
280 282 2.954753 GACGACTTGCTTGGGCGTG 61.955 63.158 9.44 0.00 42.25 5.34
285 287 2.282391 TTGCTTGGGCGTGCAGAT 60.282 55.556 0.00 0.00 40.46 2.90
339 344 7.064966 AACAAGCAAGGATTGTTCTTGAAAAAG 59.935 33.333 6.76 0.00 46.91 2.27
458 479 3.459145 GGGAGCGAGGAAAAATAGAGAC 58.541 50.000 0.00 0.00 0.00 3.36
466 487 5.480205 GAGGAAAAATAGAGACGAAGGTGT 58.520 41.667 0.00 0.00 0.00 4.16
478 499 1.336517 CGAAGGTGTAGGAAGCAACGA 60.337 52.381 0.00 0.00 0.00 3.85
500 525 8.772306 ACGATTGACATGAAATATGAAATTCG 57.228 30.769 0.00 0.38 0.00 3.34
524 550 4.021925 GCACCGGTGGAGGAAGCT 62.022 66.667 34.58 0.00 34.68 3.74
541 578 4.019860 GGAAGCTATGCCCTTCTCATGATA 60.020 45.833 0.00 0.00 38.91 2.15
554 591 7.151308 CCTTCTCATGATACTTCTCATACCAC 58.849 42.308 0.00 0.00 34.11 4.16
557 594 4.280929 TCATGATACTTCTCATACCACCGG 59.719 45.833 0.00 0.00 34.11 5.28
558 595 3.638860 TGATACTTCTCATACCACCGGT 58.361 45.455 0.00 0.00 40.16 5.28
559 596 3.383505 TGATACTTCTCATACCACCGGTG 59.616 47.826 28.26 28.26 36.19 4.94
682 1338 1.677966 CGTCCTCTTCCTGTCCCGA 60.678 63.158 0.00 0.00 0.00 5.14
716 1412 1.691976 TCAAGTCTGGTGGTGTAGTGG 59.308 52.381 0.00 0.00 0.00 4.00
724 1420 1.270678 GGTGGTGTAGTGGTGGAGAAC 60.271 57.143 0.00 0.00 0.00 3.01
734 1430 1.616865 TGGTGGAGAACGAAGACGAAT 59.383 47.619 0.00 0.00 42.66 3.34
742 1438 4.377897 AGAACGAAGACGAATGGAAGTTT 58.622 39.130 0.00 0.00 42.66 2.66
752 1448 7.992008 AGACGAATGGAAGTTTCTTTTTAACA 58.008 30.769 0.00 0.00 0.00 2.41
847 1615 0.533531 GGGACCGAGAACCAACGTTT 60.534 55.000 0.00 0.00 30.30 3.60
882 1650 2.029623 ACAGTATCTACGCCGTCCAAT 58.970 47.619 0.00 0.00 0.00 3.16
1082 2955 1.826096 ACTACGAGGAAGAGGAAAGCC 59.174 52.381 0.00 0.00 0.00 4.35
1274 3159 4.162690 GCTCGCACCCGGATCCTT 62.163 66.667 10.75 0.00 34.56 3.36
1617 4171 5.352293 GCCACCATCCAAAGATTTCATTTTC 59.648 40.000 0.00 0.00 0.00 2.29
1618 4172 5.876460 CCACCATCCAAAGATTTCATTTTCC 59.124 40.000 0.00 0.00 0.00 3.13
1619 4173 5.876460 CACCATCCAAAGATTTCATTTTCCC 59.124 40.000 0.00 0.00 0.00 3.97
1620 4174 5.045651 ACCATCCAAAGATTTCATTTTCCCC 60.046 40.000 0.00 0.00 0.00 4.81
1621 4175 4.799564 TCCAAAGATTTCATTTTCCCCG 57.200 40.909 0.00 0.00 0.00 5.73
1622 4176 3.513515 TCCAAAGATTTCATTTTCCCCGG 59.486 43.478 0.00 0.00 0.00 5.73
1623 4177 3.261580 CAAAGATTTCATTTTCCCCGGC 58.738 45.455 0.00 0.00 0.00 6.13
1624 4178 1.102978 AGATTTCATTTTCCCCGGCG 58.897 50.000 0.00 0.00 0.00 6.46
1625 4179 0.815095 GATTTCATTTTCCCCGGCGT 59.185 50.000 6.01 0.00 0.00 5.68
1627 4181 1.579084 TTTCATTTTCCCCGGCGTCG 61.579 55.000 0.29 0.29 0.00 5.12
1639 4193 3.834799 GCGTCGGTAGGGACCCAG 61.835 72.222 14.60 0.86 43.64 4.45
1640 4194 2.044650 CGTCGGTAGGGACCCAGA 60.045 66.667 14.60 3.52 43.64 3.86
1641 4195 2.119655 CGTCGGTAGGGACCCAGAG 61.120 68.421 14.60 0.85 43.64 3.35
1642 4196 1.305623 GTCGGTAGGGACCCAGAGA 59.694 63.158 14.60 3.52 43.64 3.10
1643 4197 0.752376 GTCGGTAGGGACCCAGAGAG 60.752 65.000 14.60 0.00 43.64 3.20
1645 4199 1.311747 GGTAGGGACCCAGAGAGCT 59.688 63.158 14.60 0.00 40.23 4.09
1646 4200 1.045911 GGTAGGGACCCAGAGAGCTG 61.046 65.000 14.60 0.00 40.23 4.24
1647 4201 1.381872 TAGGGACCCAGAGAGCTGC 60.382 63.158 14.60 0.00 40.91 5.25
1648 4202 2.880629 TAGGGACCCAGAGAGCTGCC 62.881 65.000 14.60 0.00 40.91 4.85
1650 4204 2.297129 GGACCCAGAGAGCTGCCTT 61.297 63.158 0.00 0.00 40.91 4.35
1651 4205 1.078567 GACCCAGAGAGCTGCCTTG 60.079 63.158 0.00 0.00 40.91 3.61
1652 4206 2.271497 CCCAGAGAGCTGCCTTGG 59.729 66.667 0.00 0.00 40.91 3.61
1654 4208 2.669849 CAGAGAGCTGCCTTGGCT 59.330 61.111 13.18 0.00 43.26 4.75
1656 4210 0.608582 CAGAGAGCTGCCTTGGCTTT 60.609 55.000 13.18 0.00 40.40 3.51
1657 4211 0.112025 AGAGAGCTGCCTTGGCTTTT 59.888 50.000 13.18 0.00 40.40 2.27
1659 4213 1.183676 AGAGCTGCCTTGGCTTTTGG 61.184 55.000 13.18 0.10 40.40 3.28
1660 4214 2.357881 GCTGCCTTGGCTTTTGGC 60.358 61.111 13.18 0.00 46.26 4.52
1669 4425 1.081442 GGCTTTTGGCGTTCCTTCG 60.081 57.895 0.00 0.00 42.94 3.79
1673 4429 2.409975 CTTTTGGCGTTCCTTCGTAGA 58.590 47.619 0.00 0.00 0.00 2.59
1677 4433 2.646930 TGGCGTTCCTTCGTAGATCTA 58.353 47.619 0.00 0.00 35.04 1.98
1678 4434 2.357009 TGGCGTTCCTTCGTAGATCTAC 59.643 50.000 21.00 21.00 35.04 2.59
1691 4447 3.047695 AGATCTACGGATTTCACCCCT 57.952 47.619 0.00 0.00 31.46 4.79
1692 4448 4.194678 AGATCTACGGATTTCACCCCTA 57.805 45.455 0.00 0.00 31.46 3.53
1693 4449 3.896272 AGATCTACGGATTTCACCCCTAC 59.104 47.826 0.00 0.00 31.46 3.18
1696 4452 4.806892 TCTACGGATTTCACCCCTACATA 58.193 43.478 0.00 0.00 0.00 2.29
1698 4454 2.101917 ACGGATTTCACCCCTACATACG 59.898 50.000 0.00 0.00 0.00 3.06
1700 4456 3.181473 CGGATTTCACCCCTACATACGAA 60.181 47.826 0.00 0.00 0.00 3.85
1702 4458 5.374071 GGATTTCACCCCTACATACGAAAT 58.626 41.667 0.00 0.00 36.17 2.17
1726 4527 3.153130 CACTCTCCTCTGTCTCACTCAA 58.847 50.000 0.00 0.00 0.00 3.02
1727 4528 3.191162 CACTCTCCTCTGTCTCACTCAAG 59.809 52.174 0.00 0.00 0.00 3.02
1729 4530 3.153130 TCTCCTCTGTCTCACTCAAGTG 58.847 50.000 3.69 3.69 46.91 3.16
1745 4546 3.498397 TCAAGTGAATTGGTTTCGAGAGC 59.502 43.478 0.00 0.00 39.54 4.09
1746 4547 3.126001 AGTGAATTGGTTTCGAGAGCA 57.874 42.857 3.40 3.40 37.13 4.26
1749 4550 4.154918 AGTGAATTGGTTTCGAGAGCATTC 59.845 41.667 8.79 13.61 37.13 2.67
1753 4554 1.706287 GGTTTCGAGAGCATTCCGCC 61.706 60.000 0.00 0.00 44.04 6.13
1754 4555 1.019278 GTTTCGAGAGCATTCCGCCA 61.019 55.000 0.00 0.00 44.04 5.69
1755 4556 1.019278 TTTCGAGAGCATTCCGCCAC 61.019 55.000 0.00 0.00 44.04 5.01
1756 4557 1.888436 TTCGAGAGCATTCCGCCACT 61.888 55.000 0.00 0.00 44.04 4.00
1757 4558 1.448540 CGAGAGCATTCCGCCACTT 60.449 57.895 0.00 0.00 44.04 3.16
1758 4559 1.021390 CGAGAGCATTCCGCCACTTT 61.021 55.000 0.00 0.00 44.04 2.66
1759 4560 1.168714 GAGAGCATTCCGCCACTTTT 58.831 50.000 0.00 0.00 44.04 2.27
1760 4561 1.541588 GAGAGCATTCCGCCACTTTTT 59.458 47.619 0.00 0.00 44.04 1.94
1761 4562 1.270550 AGAGCATTCCGCCACTTTTTG 59.729 47.619 0.00 0.00 44.04 2.44
2124 5386 9.667107 CTTTGGTTCTACAGATATTCAGGTAAA 57.333 33.333 0.00 0.00 0.00 2.01
2333 5856 7.725397 CCATGGTTATTGGATTGATAAGAAGGA 59.275 37.037 2.57 0.00 36.26 3.36
2519 6053 6.366332 GTCATAAATACCGCGATCTTCTCAAT 59.634 38.462 8.23 0.00 0.00 2.57
2558 6092 7.410728 CGTCTGAAAATTATGGTGTTGAATTGC 60.411 37.037 0.00 0.00 0.00 3.56
2572 6106 2.945008 TGAATTGCTATTCCGGCAGAAG 59.055 45.455 16.61 0.00 39.56 2.85
2582 6116 4.580835 GGCAGAAGACCTGACGTC 57.419 61.111 9.11 9.11 45.78 4.34
2645 6179 1.148310 CGATGACACTTGTGGTCCAC 58.852 55.000 15.64 15.64 34.36 4.02
2760 6300 2.150611 CGACGCTACGAATTTGGATACG 59.849 50.000 0.00 0.00 35.39 3.06
2807 6347 6.438259 TTGAAAATACTTCGTGTTTGGTCA 57.562 33.333 0.00 0.00 28.05 4.02
2875 6422 8.347035 GTTTTGTCCAACAACAATAAGCTACTA 58.653 33.333 0.00 0.00 37.90 1.82
2928 6475 5.688823 TCGAACATGTTCAAACAAGCTATG 58.311 37.500 32.06 15.04 43.03 2.23
2949 6496 6.826893 ATGTATTTAAATGATGTTTGCGGC 57.173 33.333 11.05 0.00 0.00 6.53
3074 6621 8.477419 TTTGTGGAAGAGTGGATTTTCTAAAT 57.523 30.769 0.00 0.00 0.00 1.40
3190 6740 3.506067 CCTAAGTTTTCCAGCGGATTGTT 59.494 43.478 0.00 0.00 0.00 2.83
3378 6940 1.275291 TCAGCACTAGCAACACCCTAC 59.725 52.381 0.00 0.00 45.49 3.18
3491 7053 4.410400 CCTCCCTGCCAACGTCCC 62.410 72.222 0.00 0.00 0.00 4.46
3581 7143 2.616842 GGTTGTCCAAATGTGAACGACT 59.383 45.455 0.00 0.00 0.00 4.18
3611 7173 8.515414 AGCTAGTTTGGACATTGTCTAAATTTC 58.485 33.333 25.05 17.26 42.89 2.17
3636 7198 2.076863 GACGCAATAGACAAGCCACTT 58.923 47.619 0.00 0.00 0.00 3.16
3647 7209 4.035208 AGACAAGCCACTTAAGACGTTTTG 59.965 41.667 10.09 9.17 0.00 2.44
3659 7221 4.339872 AGACGTTTTGTGGTATGTGGTA 57.660 40.909 0.00 0.00 0.00 3.25
3715 7278 5.467035 AGCCACTAGAGATGCTCTAATTC 57.533 43.478 0.00 0.00 41.74 2.17
3748 7311 1.006832 CACGGCAAGCATGTAGTACC 58.993 55.000 0.00 0.00 0.00 3.34
3761 7324 5.300752 CATGTAGTACCAAATAGCCTGAGG 58.699 45.833 0.00 0.00 0.00 3.86
3786 8164 1.859427 CTGCATTTGTCTGCGCACCT 61.859 55.000 5.66 0.00 45.30 4.00
3802 8180 1.691976 CACCTAAGGTCACCACTCACA 59.308 52.381 0.00 0.00 31.02 3.58
3839 8217 2.042162 AGGCAATTCACTCCTCAATGGT 59.958 45.455 0.00 0.00 37.07 3.55
3845 8223 0.037303 CACTCCTCAATGGTGGCTGT 59.963 55.000 0.00 0.00 37.07 4.40
3914 8292 2.103941 GAGAGCATGTAAGGAGGAAGGG 59.896 54.545 0.00 0.00 0.00 3.95
3923 8301 2.690510 GAGGAAGGGGAGCAGGCT 60.691 66.667 0.00 0.00 0.00 4.58
3951 8329 6.256321 GCCTTGTTATCAATTGTAAGCAATGG 59.744 38.462 5.13 11.93 43.89 3.16
3971 8349 8.188531 CAATGGAAGTGCCTTGTAAATAATTG 57.811 34.615 0.00 0.00 37.63 2.32
3972 8350 6.279513 TGGAAGTGCCTTGTAAATAATTGG 57.720 37.500 0.00 0.00 37.63 3.16
3973 8351 5.186797 TGGAAGTGCCTTGTAAATAATTGGG 59.813 40.000 0.00 0.00 37.63 4.12
3979 8357 5.777732 TGCCTTGTAAATAATTGGGTGACTT 59.222 36.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.249852 AGGGCCTGTTGTGTTAATCTTACTA 59.750 40.000 4.50 0.00 0.00 1.82
37 38 2.772568 TAATCAATGAAATGCGGCCG 57.227 45.000 24.05 24.05 0.00 6.13
60 61 3.838120 TGTAACAGCATTCTCTCTGTCG 58.162 45.455 0.00 0.00 42.19 4.35
85 86 3.153919 GTGGCCTTCCATTGTTCTGTAA 58.846 45.455 3.32 0.00 45.62 2.41
106 107 3.660501 TGCTTGTAGTATCGCCATAGG 57.339 47.619 0.00 0.00 0.00 2.57
108 109 4.767409 AGAGATGCTTGTAGTATCGCCATA 59.233 41.667 5.25 0.00 41.40 2.74
116 117 6.390721 GTCTGAAACAGAGATGCTTGTAGTA 58.609 40.000 1.53 0.00 41.46 1.82
117 118 5.233988 GTCTGAAACAGAGATGCTTGTAGT 58.766 41.667 1.53 0.00 41.46 2.73
118 119 4.325741 CGTCTGAAACAGAGATGCTTGTAG 59.674 45.833 1.53 0.00 41.46 2.74
119 120 4.237724 CGTCTGAAACAGAGATGCTTGTA 58.762 43.478 1.53 0.00 41.46 2.41
120 121 3.062763 CGTCTGAAACAGAGATGCTTGT 58.937 45.455 1.53 0.00 41.46 3.16
121 122 2.414481 CCGTCTGAAACAGAGATGCTTG 59.586 50.000 1.53 0.00 41.46 4.01
122 123 2.300152 TCCGTCTGAAACAGAGATGCTT 59.700 45.455 1.53 0.00 41.46 3.91
129 130 1.000163 GACTGCTCCGTCTGAAACAGA 60.000 52.381 0.00 0.00 38.25 3.41
138 139 1.983972 CTGTAAGTGACTGCTCCGTC 58.016 55.000 0.00 0.00 34.52 4.79
152 153 7.607250 CCCCATGTATTTTGCTAAAACTGTAA 58.393 34.615 0.00 0.00 32.37 2.41
178 180 2.133281 TTGAGCCACCCTGATCAATG 57.867 50.000 0.00 0.00 0.00 2.82
192 194 2.805099 CAGTTGGACAGACTCTTTGAGC 59.195 50.000 0.00 0.00 32.04 4.26
210 212 1.001641 GCAGCCAGGATTCACCAGT 60.002 57.895 0.00 0.00 42.04 4.00
222 224 0.607217 CAGATGTTGGTCTGCAGCCA 60.607 55.000 21.35 21.35 39.19 4.75
244 246 2.107750 AGCCGCATCATGGACGAG 59.892 61.111 0.00 0.00 0.00 4.18
253 255 3.084579 CAAGTCGTCAGCCGCATC 58.915 61.111 0.00 0.00 36.19 3.91
261 263 2.664851 CGCCCAAGCAAGTCGTCA 60.665 61.111 0.00 0.00 39.83 4.35
272 274 4.932789 GAGTATCTGCACGCCCAA 57.067 55.556 0.00 0.00 0.00 4.12
313 315 5.596836 TTCAAGAACAATCCTTGCTTGTT 57.403 34.783 1.04 1.04 46.55 2.83
339 344 1.553704 CCGGCTGGGGTATATACTTCC 59.446 57.143 12.54 13.81 0.00 3.46
458 479 1.068474 CGTTGCTTCCTACACCTTCG 58.932 55.000 0.00 0.00 0.00 3.79
466 487 4.200838 TCATGTCAATCGTTGCTTCCTA 57.799 40.909 0.00 0.00 0.00 2.94
500 525 0.955919 CCTCCACCGGTGCTTCTTTC 60.956 60.000 29.75 0.00 0.00 2.62
524 550 5.840693 TGAGAAGTATCATGAGAAGGGCATA 59.159 40.000 0.09 0.00 0.00 3.14
541 578 0.902531 CCACCGGTGGTATGAGAAGT 59.097 55.000 40.44 0.00 45.53 3.01
554 591 0.098728 GACAATCGCAAATCCACCGG 59.901 55.000 0.00 0.00 0.00 5.28
557 594 1.526986 CGTCGACAATCGCAAATCCAC 60.527 52.381 17.16 0.00 40.21 4.02
558 595 0.718904 CGTCGACAATCGCAAATCCA 59.281 50.000 17.16 0.00 40.21 3.41
559 596 3.491934 CGTCGACAATCGCAAATCC 57.508 52.632 17.16 0.00 40.21 3.01
682 1338 0.399454 ACTTGATCTGCAGTGGCTGT 59.601 50.000 14.67 6.14 41.91 4.40
716 1412 1.993370 CCATTCGTCTTCGTTCTCCAC 59.007 52.381 0.00 0.00 38.33 4.02
724 1420 4.992381 AAGAAACTTCCATTCGTCTTCG 57.008 40.909 0.00 0.00 38.55 3.79
734 1430 7.607250 TGCTTTCTGTTAAAAAGAAACTTCCA 58.393 30.769 9.47 4.38 38.43 3.53
742 1438 5.833131 ACCTCCATGCTTTCTGTTAAAAAGA 59.167 36.000 2.90 0.00 36.09 2.52
752 1448 0.040204 CCCCAACCTCCATGCTTTCT 59.960 55.000 0.00 0.00 0.00 2.52
847 1615 7.063544 CGTAGATACTGTCTGATGTATCGATCA 59.936 40.741 18.85 0.03 45.58 2.92
1457 3357 4.787280 AGAGCGGGGGACAGGAGG 62.787 72.222 0.00 0.00 0.00 4.30
1599 4153 4.162131 CCGGGGAAAATGAAATCTTTGGAT 59.838 41.667 0.00 0.00 0.00 3.41
1627 4181 1.045911 CAGCTCTCTGGGTCCCTACC 61.046 65.000 10.00 0.00 45.97 3.18
1628 4182 1.681486 GCAGCTCTCTGGGTCCCTAC 61.681 65.000 10.00 0.00 40.65 3.18
1629 4183 1.381872 GCAGCTCTCTGGGTCCCTA 60.382 63.158 10.00 0.00 40.65 3.53
1630 4184 2.686835 GCAGCTCTCTGGGTCCCT 60.687 66.667 10.00 0.00 40.65 4.20
1631 4185 3.791586 GGCAGCTCTCTGGGTCCC 61.792 72.222 0.00 0.00 40.65 4.46
1632 4186 2.297129 AAGGCAGCTCTCTGGGTCC 61.297 63.158 0.00 0.00 40.65 4.46
1633 4187 1.078567 CAAGGCAGCTCTCTGGGTC 60.079 63.158 0.00 0.00 40.65 4.46
1634 4188 2.600729 CCAAGGCAGCTCTCTGGGT 61.601 63.158 0.00 0.00 40.65 4.51
1635 4189 2.271497 CCAAGGCAGCTCTCTGGG 59.729 66.667 0.00 0.00 40.65 4.45
1639 4193 0.243095 CAAAAGCCAAGGCAGCTCTC 59.757 55.000 14.40 0.00 44.88 3.20
1640 4194 1.183676 CCAAAAGCCAAGGCAGCTCT 61.184 55.000 14.40 0.00 44.88 4.09
1641 4195 1.291272 CCAAAAGCCAAGGCAGCTC 59.709 57.895 14.40 0.00 44.88 4.09
1642 4196 3.463345 CCAAAAGCCAAGGCAGCT 58.537 55.556 14.40 0.00 44.88 4.24
1646 4200 1.664649 GAACGCCAAAAGCCAAGGC 60.665 57.895 2.02 2.02 44.89 4.35
1647 4201 1.006220 GGAACGCCAAAAGCCAAGG 60.006 57.895 0.00 0.00 38.78 3.61
1648 4202 0.389025 AAGGAACGCCAAAAGCCAAG 59.611 50.000 0.00 0.00 38.78 3.61
1650 4204 1.791103 CGAAGGAACGCCAAAAGCCA 61.791 55.000 0.00 0.00 38.78 4.75
1651 4205 1.081442 CGAAGGAACGCCAAAAGCC 60.081 57.895 0.00 0.00 38.78 4.35
1652 4206 0.869730 TACGAAGGAACGCCAAAAGC 59.130 50.000 0.00 0.00 36.29 3.51
1654 4208 2.529780 TCTACGAAGGAACGCCAAAA 57.470 45.000 0.00 0.00 36.29 2.44
1656 4210 1.822990 AGATCTACGAAGGAACGCCAA 59.177 47.619 0.00 0.00 36.29 4.52
1657 4211 1.471119 AGATCTACGAAGGAACGCCA 58.529 50.000 0.00 0.00 36.29 5.69
1669 4425 3.896272 AGGGGTGAAATCCGTAGATCTAC 59.104 47.826 21.00 21.00 0.00 2.59
1673 4429 3.649843 TGTAGGGGTGAAATCCGTAGAT 58.350 45.455 0.00 0.00 0.00 1.98
1677 4433 2.101917 CGTATGTAGGGGTGAAATCCGT 59.898 50.000 0.00 0.00 0.00 4.69
1678 4434 2.363038 TCGTATGTAGGGGTGAAATCCG 59.637 50.000 0.00 0.00 0.00 4.18
1679 4435 4.411256 TTCGTATGTAGGGGTGAAATCC 57.589 45.455 0.00 0.00 0.00 3.01
1681 4437 5.826208 GGAATTTCGTATGTAGGGGTGAAAT 59.174 40.000 0.00 0.00 37.57 2.17
1682 4438 5.187687 GGAATTTCGTATGTAGGGGTGAAA 58.812 41.667 0.00 0.00 0.00 2.69
1683 4439 4.225492 TGGAATTTCGTATGTAGGGGTGAA 59.775 41.667 0.00 0.00 0.00 3.18
1684 4440 3.775866 TGGAATTTCGTATGTAGGGGTGA 59.224 43.478 0.00 0.00 0.00 4.02
1686 4442 3.778629 AGTGGAATTTCGTATGTAGGGGT 59.221 43.478 0.00 0.00 0.00 4.95
1688 4444 5.277857 AGAGTGGAATTTCGTATGTAGGG 57.722 43.478 0.00 0.00 0.00 3.53
1691 4447 5.892119 AGAGGAGAGTGGAATTTCGTATGTA 59.108 40.000 0.00 0.00 0.00 2.29
1692 4448 4.712337 AGAGGAGAGTGGAATTTCGTATGT 59.288 41.667 0.00 0.00 0.00 2.29
1693 4449 5.046529 CAGAGGAGAGTGGAATTTCGTATG 58.953 45.833 0.00 0.00 0.00 2.39
1696 4452 2.900546 ACAGAGGAGAGTGGAATTTCGT 59.099 45.455 0.00 0.00 0.00 3.85
1698 4454 4.221703 TGAGACAGAGGAGAGTGGAATTTC 59.778 45.833 0.00 0.00 0.00 2.17
1700 4456 3.513515 GTGAGACAGAGGAGAGTGGAATT 59.486 47.826 0.00 0.00 0.00 2.17
1702 4458 2.109128 AGTGAGACAGAGGAGAGTGGAA 59.891 50.000 0.00 0.00 0.00 3.53
1726 4527 3.126001 TGCTCTCGAAACCAATTCACT 57.874 42.857 0.00 0.00 37.96 3.41
1727 4528 4.406943 GAATGCTCTCGAAACCAATTCAC 58.593 43.478 0.00 0.00 37.96 3.18
1729 4530 3.485877 CGGAATGCTCTCGAAACCAATTC 60.486 47.826 0.00 0.00 34.52 2.17
1730 4531 2.420022 CGGAATGCTCTCGAAACCAATT 59.580 45.455 0.00 0.00 0.00 2.32
1731 4532 2.009774 CGGAATGCTCTCGAAACCAAT 58.990 47.619 0.00 0.00 0.00 3.16
1733 4534 1.019278 GCGGAATGCTCTCGAAACCA 61.019 55.000 0.00 0.00 41.73 3.67
1734 4535 1.706287 GGCGGAATGCTCTCGAAACC 61.706 60.000 0.00 0.00 45.43 3.27
1735 4536 1.019278 TGGCGGAATGCTCTCGAAAC 61.019 55.000 0.00 0.00 45.43 2.78
1737 4538 1.447838 GTGGCGGAATGCTCTCGAA 60.448 57.895 0.00 0.00 45.43 3.71
1740 4541 1.168714 AAAAGTGGCGGAATGCTCTC 58.831 50.000 0.00 0.00 45.43 3.20
1742 4543 1.669795 CCAAAAAGTGGCGGAATGCTC 60.670 52.381 0.00 0.00 41.72 4.26
1753 4554 0.234884 GAGGACGTCGCCAAAAAGTG 59.765 55.000 9.92 0.00 0.00 3.16
1754 4555 1.219522 CGAGGACGTCGCCAAAAAGT 61.220 55.000 9.92 0.00 43.03 2.66
1755 4556 1.491563 CGAGGACGTCGCCAAAAAG 59.508 57.895 9.92 0.00 43.03 2.27
1756 4557 3.632700 CGAGGACGTCGCCAAAAA 58.367 55.556 9.92 0.00 43.03 1.94
1764 4565 2.507324 GCTGAAGCCGAGGACGTC 60.507 66.667 7.13 7.13 37.88 4.34
1765 4566 4.421479 CGCTGAAGCCGAGGACGT 62.421 66.667 0.00 0.00 37.91 4.34
2124 5386 3.137360 GGTAAGGATGAAGAAGGCTGGAT 59.863 47.826 0.00 0.00 0.00 3.41
2333 5856 2.154462 CAACTTCTCCAAGCACGGAAT 58.846 47.619 0.00 0.00 33.65 3.01
2389 5914 0.031178 GAGCAGCCAAACACAAGGTG 59.969 55.000 0.00 0.00 39.75 4.00
2558 6092 1.757118 TCAGGTCTTCTGCCGGAATAG 59.243 52.381 5.05 0.00 43.06 1.73
2572 6106 2.155155 GTGACAAAATCGACGTCAGGTC 59.845 50.000 17.16 12.59 40.17 3.85
2582 6116 3.674753 GGGCAAAGAATGTGACAAAATCG 59.325 43.478 0.00 0.00 26.43 3.34
2645 6179 0.811915 AGAAGTCCTCATCGTCGGTG 59.188 55.000 0.00 0.00 0.00 4.94
2760 6300 9.626045 CAAAACTACCACTCAAAAGGATAATTC 57.374 33.333 0.00 0.00 0.00 2.17
2807 6347 6.497259 TGGTTGGATAGAGTAACTTCTCACTT 59.503 38.462 0.00 0.00 36.97 3.16
2928 6475 8.574196 AATAGCCGCAAACATCATTTAAATAC 57.426 30.769 0.00 0.00 0.00 1.89
2998 6545 3.111838 CGCCACGCATGCAAATAATTTA 58.888 40.909 19.57 0.00 0.00 1.40
3074 6621 6.040278 CACTAGAGATGCTCTTACAATCCAGA 59.960 42.308 1.88 0.00 41.50 3.86
3303 6863 2.355756 CCTTTGTATGTCTTGCGGATGG 59.644 50.000 0.00 0.00 0.00 3.51
3409 6971 0.321564 CGCCTCATCAGGGTTGAACA 60.322 55.000 0.00 0.00 40.75 3.18
3491 7053 2.940410 GCATCAATTTGGAGCAATTGGG 59.060 45.455 7.72 2.88 0.00 4.12
3581 7143 4.286032 AGACAATGTCCAAACTAGCTACCA 59.714 41.667 10.12 0.00 32.18 3.25
3611 7173 1.321743 GCTTGTCTATTGCGTCGTCTG 59.678 52.381 0.00 0.00 0.00 3.51
3636 7198 4.706035 ACCACATACCACAAAACGTCTTA 58.294 39.130 0.00 0.00 0.00 2.10
3647 7209 7.627726 GCCAAATTTAGACTTACCACATACCAC 60.628 40.741 0.00 0.00 0.00 4.16
3659 7221 4.694037 GTGGTCTACGCCAAATTTAGACTT 59.306 41.667 14.61 0.00 41.00 3.01
3715 7278 2.493035 TGCCGTGACATATAATGCCAG 58.507 47.619 0.00 0.00 0.00 4.85
3761 7324 0.109412 GCAGACAAATGCAGACCAGC 60.109 55.000 0.00 0.00 45.77 4.85
3786 8164 2.615391 TGGATGTGAGTGGTGACCTTA 58.385 47.619 2.11 0.00 0.00 2.69
3839 8217 2.500392 AAAAAGCCGGTATACAGCCA 57.500 45.000 1.90 0.00 0.00 4.75
3923 8301 5.709631 TGCTTACAATTGATAACAAGGCAGA 59.290 36.000 13.59 0.00 39.46 4.26
3963 8341 6.187682 CCTCACCTAAGTCACCCAATTATTT 58.812 40.000 0.00 0.00 0.00 1.40
3967 8345 2.290960 GCCTCACCTAAGTCACCCAATT 60.291 50.000 0.00 0.00 0.00 2.32
3968 8346 1.282157 GCCTCACCTAAGTCACCCAAT 59.718 52.381 0.00 0.00 0.00 3.16
3969 8347 0.690762 GCCTCACCTAAGTCACCCAA 59.309 55.000 0.00 0.00 0.00 4.12
3970 8348 1.198759 GGCCTCACCTAAGTCACCCA 61.199 60.000 0.00 0.00 34.51 4.51
3971 8349 1.602771 GGCCTCACCTAAGTCACCC 59.397 63.158 0.00 0.00 34.51 4.61
3972 8350 0.910088 AGGGCCTCACCTAAGTCACC 60.910 60.000 0.00 0.00 39.65 4.02
3973 8351 0.250513 CAGGGCCTCACCTAAGTCAC 59.749 60.000 0.95 0.00 39.34 3.67
3979 8357 1.003442 ATGCTCAGGGCCTCACCTA 59.997 57.895 0.95 0.00 39.34 3.08


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

AutoCloner maintained by Alex Coulton.