Multiple sequence alignment - TraesCS3B01G472000

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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 TraesCS3B01G472000 chr3B 100.000 3842 0 0 1 3842 720264738 720268579 0.000000e+00 7095.0
1 TraesCS3B01G472000 chr3B 94.805 77 4 0 3565 3641 295692185 295692109 1.870000e-23 121.0
2 TraesCS3B01G472000 chr3B 93.333 75 4 1 3381 3454 3660787 3660861 4.060000e-20 110.0
3 TraesCS3B01G472000 chr3D 91.682 1647 84 26 137 1749 544443920 544445547 0.000000e+00 2233.0
4 TraesCS3B01G472000 chr3D 92.784 1261 77 13 1776 3026 544445617 544446873 0.000000e+00 1812.0
5 TraesCS3B01G472000 chr3D 89.368 950 53 13 771 1711 544771399 544772309 0.000000e+00 1151.0
6 TraesCS3B01G472000 chr3D 81.887 922 111 35 2203 3113 544772881 544773757 0.000000e+00 726.0
7 TraesCS3B01G472000 chr3D 90.136 294 23 6 183 473 536880751 536881041 1.010000e-100 377.0
8 TraesCS3B01G472000 chr3D 89.831 295 25 5 180 473 496742747 496743037 1.300000e-99 374.0
9 TraesCS3B01G472000 chr3D 89.456 294 27 4 182 473 536441513 536441804 6.060000e-98 368.0
10 TraesCS3B01G472000 chr3D 89.831 177 15 3 2644 2819 544791297 544791471 1.390000e-54 224.0
11 TraesCS3B01G472000 chr3D 84.579 214 23 6 3112 3323 544773810 544774015 1.810000e-48 204.0
12 TraesCS3B01G472000 chr3D 80.282 213 34 5 3108 3316 544796118 544796326 1.850000e-33 154.0
13 TraesCS3B01G472000 chr3D 87.826 115 12 2 3451 3564 544774158 544774271 2.410000e-27 134.0
14 TraesCS3B01G472000 chr3D 81.879 149 25 2 2917 3063 544795892 544796040 1.450000e-24 124.0
15 TraesCS3B01G472000 chr3D 94.366 71 4 0 66 136 544443823 544443893 4.060000e-20 110.0
16 TraesCS3B01G472000 chr3D 90.411 73 6 1 35 106 544443745 544443817 1.140000e-15 95.3
17 TraesCS3B01G472000 chr3D 83.529 85 8 5 1776 1855 544772436 544772519 1.480000e-09 75.0
18 TraesCS3B01G472000 chr3A 94.571 1271 45 10 500 1749 681398603 681399870 0.000000e+00 1943.0
19 TraesCS3B01G472000 chr3A 87.940 1393 99 36 1776 3116 681399939 681401314 0.000000e+00 1578.0
20 TraesCS3B01G472000 chr3A 94.591 869 41 4 2182 3049 681448335 681449198 0.000000e+00 1339.0
21 TraesCS3B01G472000 chr3A 91.972 872 41 10 844 1711 681446851 681447697 0.000000e+00 1195.0
22 TraesCS3B01G472000 chr3A 87.947 838 59 19 3034 3831 681449239 681450074 0.000000e+00 950.0
23 TraesCS3B01G472000 chr3A 85.906 447 39 11 35 459 681398152 681398596 4.520000e-124 455.0
24 TraesCS3B01G472000 chr3A 89.003 291 31 1 183 473 638064710 638064421 3.650000e-95 359.0
25 TraesCS3B01G472000 chr3A 83.627 397 46 10 1806 2187 681447849 681448241 4.720000e-94 355.0
26 TraesCS3B01G472000 chr3A 92.683 82 3 3 3381 3461 681449652 681449573 8.720000e-22 115.0
27 TraesCS3B01G472000 chr3A 96.875 32 1 0 633 664 681406242 681406273 2.000000e-03 54.7
28 TraesCS3B01G472000 chrUn 89.456 294 27 4 182 473 404927030 404926739 6.060000e-98 368.0
29 TraesCS3B01G472000 chrUn 89.456 294 27 4 182 473 466164180 466164471 6.060000e-98 368.0
30 TraesCS3B01G472000 chrUn 89.116 294 28 4 182 473 359852484 359852775 2.820000e-96 363.0
31 TraesCS3B01G472000 chrUn 95.946 74 3 0 3381 3454 135090734 135090807 1.870000e-23 121.0
32 TraesCS3B01G472000 chrUn 95.946 74 3 0 3381 3454 152687590 152687663 1.870000e-23 121.0
33 TraesCS3B01G472000 chr6B 96.341 82 3 0 3560 3641 408686127 408686046 6.700000e-28 135.0
34 TraesCS3B01G472000 chr5B 97.436 78 2 0 3564 3641 610346060 610345983 2.410000e-27 134.0
35 TraesCS3B01G472000 chr5B 94.805 77 4 0 3565 3641 606108925 606109001 1.870000e-23 121.0
36 TraesCS3B01G472000 chr5D 98.592 71 1 0 3381 3451 437601517 437601587 4.030000e-25 126.0
37 TraesCS3B01G472000 chr4D 94.937 79 4 0 3563 3641 360449787 360449709 1.450000e-24 124.0
38 TraesCS3B01G472000 chr4D 94.667 75 4 0 3381 3455 449455684 449455610 2.430000e-22 117.0
39 TraesCS3B01G472000 chr7D 94.805 77 4 0 3565 3641 84339385 84339461 1.870000e-23 121.0
40 TraesCS3B01G472000 chr7D 93.506 77 5 0 3381 3457 168245206 168245282 8.720000e-22 115.0
41 TraesCS3B01G472000 chr7B 94.805 77 4 0 3565 3641 136840148 136840072 1.870000e-23 121.0
42 TraesCS3B01G472000 chr4B 96.000 75 2 1 3381 3455 450316551 450316478 1.870000e-23 121.0
43 TraesCS3B01G472000 chr1B 94.805 77 4 0 3565 3641 276137561 276137637 1.870000e-23 121.0
44 TraesCS3B01G472000 chr7A 92.683 82 6 0 3560 3641 692780331 692780412 6.740000e-23 119.0
45 TraesCS3B01G472000 chr2B 83.186 113 15 1 3142 3250 548622329 548622441 2.440000e-17 100.0


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 TraesCS3B01G472000 chr3B 720264738 720268579 3841 False 7095.000000 7095 100.000000 1 3842 1 chr3B.!!$F2 3841
1 TraesCS3B01G472000 chr3D 544443745 544446873 3128 False 1062.575000 2233 92.310750 35 3026 4 chr3D.!!$F5 2991
2 TraesCS3B01G472000 chr3D 544771399 544774271 2872 False 458.000000 1151 85.437800 771 3564 5 chr3D.!!$F6 2793
3 TraesCS3B01G472000 chr3A 681398152 681401314 3162 False 1325.333333 1943 89.472333 35 3116 3 chr3A.!!$F2 3081
4 TraesCS3B01G472000 chr3A 681446851 681450074 3223 False 959.750000 1339 89.534250 844 3831 4 chr3A.!!$F3 2987

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
19 20 0.181824 ATATACCACCCGGCACCAAC 59.818 55.000 0.00 0.0 34.57 3.77 F
148 222 0.232303 CAAGCCGTCAACGAACACTC 59.768 55.000 3.71 0.0 43.02 3.51 F
606 694 0.676782 CCGGTGGGTCATGGTTTCTC 60.677 60.000 0.00 0.0 0.00 2.87 F
608 696 1.826385 GGTGGGTCATGGTTTCTCAG 58.174 55.000 0.00 0.0 0.00 3.35 F
861 976 2.549754 CCGCACAAGAACAACAAGAGAT 59.450 45.455 0.00 0.0 0.00 2.75 F
1779 1994 0.771755 GAACTTGAGGTTGAGGGGGT 59.228 55.000 0.00 0.0 38.41 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 1823 1.334869 AGGCAAAGAAAGAACAGCACG 59.665 47.619 0.0 0.0 0.0 5.34 R
1771 1986 2.382305 TCTCAAGTTCTCTACCCCCTCA 59.618 50.000 0.0 0.0 0.0 3.86 R
1772 1987 3.103080 TCTCAAGTTCTCTACCCCCTC 57.897 52.381 0.0 0.0 0.0 4.30 R
1774 1989 3.108376 ACATCTCAAGTTCTCTACCCCC 58.892 50.000 0.0 0.0 0.0 5.40 R
2733 3138 2.353704 CCAAGTCGCTACATGTTCCAGA 60.354 50.000 2.3 0.0 0.0 3.86 R
3208 3746 0.972883 AGACTCACCTCTTCAGCACC 59.027 55.000 0.0 0.0 0.0 5.01 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
17 18 4.403553 ATATACCACCCGGCACCA 57.596 55.556 0.00 0.00 34.57 4.17
18 19 2.622739 ATATACCACCCGGCACCAA 58.377 52.632 0.00 0.00 34.57 3.67
19 20 0.181824 ATATACCACCCGGCACCAAC 59.818 55.000 0.00 0.00 34.57 3.77
20 21 1.912826 TATACCACCCGGCACCAACC 61.913 60.000 0.00 0.00 34.57 3.77
28 29 3.134127 GGCACCAACCGCATCCTC 61.134 66.667 0.00 0.00 0.00 3.71
29 30 3.134127 GCACCAACCGCATCCTCC 61.134 66.667 0.00 0.00 0.00 4.30
30 31 2.350895 CACCAACCGCATCCTCCA 59.649 61.111 0.00 0.00 0.00 3.86
31 32 2.040544 CACCAACCGCATCCTCCAC 61.041 63.158 0.00 0.00 0.00 4.02
32 33 2.438434 CCAACCGCATCCTCCACC 60.438 66.667 0.00 0.00 0.00 4.61
33 34 2.350895 CAACCGCATCCTCCACCA 59.649 61.111 0.00 0.00 0.00 4.17
50 51 1.075482 CACCCAGGAGCACCAACAT 59.925 57.895 2.07 0.00 38.94 2.71
51 52 0.540365 CACCCAGGAGCACCAACATT 60.540 55.000 2.07 0.00 38.94 2.71
52 53 0.540365 ACCCAGGAGCACCAACATTG 60.540 55.000 2.07 0.00 38.94 2.82
53 54 0.540365 CCCAGGAGCACCAACATTGT 60.540 55.000 2.07 0.00 38.94 2.71
61 63 3.023119 AGCACCAACATTGTCTGTTTCA 58.977 40.909 0.00 0.00 45.98 2.69
97 99 2.256158 CCAACCTGTACGACGCGA 59.744 61.111 15.93 0.00 0.00 5.87
118 166 3.685214 GAGCAGATCGACACGGCGT 62.685 63.158 6.77 6.77 34.06 5.68
140 214 0.250513 AGGGAGATCAAGCCGTCAAC 59.749 55.000 0.00 0.00 0.00 3.18
141 215 1.084370 GGGAGATCAAGCCGTCAACG 61.084 60.000 0.00 0.00 39.44 4.10
148 222 0.232303 CAAGCCGTCAACGAACACTC 59.768 55.000 3.71 0.00 43.02 3.51
170 244 6.040209 TCAATTCCAGCTGCATTTAACAAT 57.960 33.333 8.66 0.00 0.00 2.71
172 246 6.591062 TCAATTCCAGCTGCATTTAACAATTC 59.409 34.615 8.66 0.00 0.00 2.17
178 253 8.313292 TCCAGCTGCATTTAACAATTCTTTTAT 58.687 29.630 8.66 0.00 0.00 1.40
311 386 6.976636 TTTAATATCGTTGTGAGCACATGA 57.023 33.333 0.00 6.37 41.52 3.07
498 573 2.288025 GGGGTGAACTGGCTCCGTA 61.288 63.158 0.00 0.00 0.00 4.02
529 604 2.469516 CCTCGCATGGGCCGTAAAC 61.470 63.158 4.59 0.00 36.38 2.01
534 609 1.734388 GCATGGGCCGTAAACATCCC 61.734 60.000 0.00 0.00 39.22 3.85
604 692 1.074248 ACCGGTGGGTCATGGTTTC 59.926 57.895 6.12 0.00 46.01 2.78
605 693 1.378762 CCGGTGGGTCATGGTTTCT 59.621 57.895 0.00 0.00 0.00 2.52
606 694 0.676782 CCGGTGGGTCATGGTTTCTC 60.677 60.000 0.00 0.00 0.00 2.87
608 696 1.826385 GGTGGGTCATGGTTTCTCAG 58.174 55.000 0.00 0.00 0.00 3.35
612 700 2.978978 TGGGTCATGGTTTCTCAGAAGA 59.021 45.455 0.00 0.00 0.00 2.87
701 812 6.321181 ACTTTTACCAGCTGATGAAAACTCAA 59.679 34.615 17.39 0.00 0.00 3.02
703 814 2.555757 ACCAGCTGATGAAAACTCAAGC 59.444 45.455 17.39 0.00 0.00 4.01
737 848 5.065218 GTGAAAAGAACAAGACTGAAGCTGA 59.935 40.000 0.00 0.00 0.00 4.26
861 976 2.549754 CCGCACAAGAACAACAAGAGAT 59.450 45.455 0.00 0.00 0.00 2.75
1347 1476 2.896854 GCGATCCTCGGCATGCAA 60.897 61.111 21.36 5.89 40.84 4.08
1694 1823 5.998363 AGATCGCCAAAGGTATAATTTCTCC 59.002 40.000 0.00 0.00 0.00 3.71
1695 1824 4.124238 TCGCCAAAGGTATAATTTCTCCG 58.876 43.478 0.00 0.00 0.00 4.63
1743 1892 6.996509 ACTCTGCCAAAATGTTTAACATGAT 58.003 32.000 11.60 1.26 37.97 2.45
1769 1984 4.035675 GTGTTTGGAGTTGAGAACTTGAGG 59.964 45.833 0.00 0.00 43.03 3.86
1770 1985 4.200092 GTTTGGAGTTGAGAACTTGAGGT 58.800 43.478 0.00 0.00 43.03 3.85
1771 1986 4.503714 TTGGAGTTGAGAACTTGAGGTT 57.496 40.909 0.00 0.00 43.03 3.50
1772 1987 3.808728 TGGAGTTGAGAACTTGAGGTTG 58.191 45.455 0.00 0.00 43.03 3.77
1773 1988 3.454447 TGGAGTTGAGAACTTGAGGTTGA 59.546 43.478 0.00 0.00 43.03 3.18
1774 1989 4.061596 GGAGTTGAGAACTTGAGGTTGAG 58.938 47.826 0.00 0.00 43.03 3.02
1775 1990 4.061596 GAGTTGAGAACTTGAGGTTGAGG 58.938 47.826 0.00 0.00 43.03 3.86
1776 1991 3.142174 GTTGAGAACTTGAGGTTGAGGG 58.858 50.000 0.00 0.00 38.41 4.30
1777 1992 1.699634 TGAGAACTTGAGGTTGAGGGG 59.300 52.381 0.00 0.00 38.41 4.79
1778 1993 1.003696 GAGAACTTGAGGTTGAGGGGG 59.996 57.143 0.00 0.00 38.41 5.40
1779 1994 0.771755 GAACTTGAGGTTGAGGGGGT 59.228 55.000 0.00 0.00 38.41 4.95
1780 1995 1.982958 GAACTTGAGGTTGAGGGGGTA 59.017 52.381 0.00 0.00 38.41 3.69
1781 1996 1.657804 ACTTGAGGTTGAGGGGGTAG 58.342 55.000 0.00 0.00 0.00 3.18
1782 1997 1.151413 ACTTGAGGTTGAGGGGGTAGA 59.849 52.381 0.00 0.00 0.00 2.59
1783 1998 1.834263 CTTGAGGTTGAGGGGGTAGAG 59.166 57.143 0.00 0.00 0.00 2.43
1784 1999 1.089978 TGAGGTTGAGGGGGTAGAGA 58.910 55.000 0.00 0.00 0.00 3.10
1785 2000 1.435563 TGAGGTTGAGGGGGTAGAGAA 59.564 52.381 0.00 0.00 0.00 2.87
1786 2001 1.832366 GAGGTTGAGGGGGTAGAGAAC 59.168 57.143 0.00 0.00 0.00 3.01
1787 2002 1.437547 AGGTTGAGGGGGTAGAGAACT 59.562 52.381 0.00 0.00 0.00 3.01
1788 2003 2.157989 AGGTTGAGGGGGTAGAGAACTT 60.158 50.000 0.00 0.00 0.00 2.66
1789 2004 2.027100 GGTTGAGGGGGTAGAGAACTTG 60.027 54.545 0.00 0.00 0.00 3.16
1790 2005 2.904434 GTTGAGGGGGTAGAGAACTTGA 59.096 50.000 0.00 0.00 0.00 3.02
1791 2006 2.821437 TGAGGGGGTAGAGAACTTGAG 58.179 52.381 0.00 0.00 0.00 3.02
1960 2218 4.142534 CCAGCAGATCACCAATTGTTAGTG 60.143 45.833 4.43 5.88 0.00 2.74
2043 2315 4.728534 GCATGGATTGCGTTTTAAGTACA 58.271 39.130 0.00 0.00 42.54 2.90
2089 2381 4.274459 AGTCAGCTTAAACTTTGCACAGAG 59.726 41.667 6.92 0.00 0.00 3.35
2107 2399 6.205658 GCACAGAGTTTCTAGAATTCCAACTT 59.794 38.462 5.89 0.00 0.00 2.66
2206 2597 6.542370 TCCTATAAGTGCAGGCTTAAATGTTC 59.458 38.462 1.33 0.00 34.98 3.18
2310 2701 2.031870 AGTGAACTGGAAAGTTTGGGC 58.968 47.619 0.00 0.00 31.35 5.36
2369 2760 5.176223 CACTTGAATCAATCCAACAAAGCAC 59.824 40.000 0.00 0.00 0.00 4.40
2445 2837 4.889409 TCAGAAGCAAGTTGGATTTGTTCT 59.111 37.500 4.75 0.00 31.90 3.01
2498 2890 5.013079 AGGTCTGACTGTTCCATGTTCATAA 59.987 40.000 7.85 0.00 0.00 1.90
2585 2988 2.678336 GCCTACCACTTTTTCTCCATCG 59.322 50.000 0.00 0.00 0.00 3.84
2733 3138 4.141041 AGAGATATCACAGTAGAGCAGGGT 60.141 45.833 5.32 0.00 0.00 4.34
2739 3144 1.203187 ACAGTAGAGCAGGGTCTGGAA 60.203 52.381 11.04 0.00 31.21 3.53
2757 3162 3.270877 GGAACATGTAGCGACTTGGAAT 58.729 45.455 15.49 3.57 35.53 3.01
2849 3254 9.559732 TGTTTTCTCTAAACTCTGATGATCAAA 57.440 29.630 0.00 0.00 45.18 2.69
3018 3446 5.722021 TTTTCTGGAATTTCCTTAGCACC 57.278 39.130 16.25 0.00 37.46 5.01
3039 3467 6.293626 GCACCACTGATGTCCATATTGATTAC 60.294 42.308 0.00 0.00 0.00 1.89
3151 3689 2.441375 TCTGGATTGGGTGAACAAGACA 59.559 45.455 0.00 0.00 33.23 3.41
3208 3746 8.328864 GCTTGTCTAGGTATAAGTTGAATTTCG 58.671 37.037 0.00 0.00 0.00 3.46
3258 3798 4.534500 TGATATTCACACTACCACAACCCT 59.466 41.667 0.00 0.00 0.00 4.34
3259 3799 2.631160 TTCACACTACCACAACCCTG 57.369 50.000 0.00 0.00 0.00 4.45
3280 3820 7.945664 ACCCTGTTTGGTTACTATGTTAATTGA 59.054 33.333 0.00 0.00 33.91 2.57
3558 4199 3.070878 CCATTGCCTTAACTGTTGGGTTT 59.929 43.478 2.69 0.00 0.00 3.27
3573 4214 7.783119 ACTGTTGGGTTTTTAAATACTTCCTCT 59.217 33.333 8.42 0.00 0.00 3.69
3576 4217 7.754851 TGGGTTTTTAAATACTTCCTCTGTC 57.245 36.000 8.42 0.00 0.00 3.51
3579 4220 6.717997 GGTTTTTAAATACTTCCTCTGTCCCA 59.282 38.462 8.42 0.00 0.00 4.37
3582 4223 8.770010 TTTTAAATACTTCCTCTGTCCCAAAA 57.230 30.769 0.00 0.00 0.00 2.44
3586 4227 8.581253 AAATACTTCCTCTGTCCCAAAATAAG 57.419 34.615 0.00 0.00 0.00 1.73
3590 4231 4.906618 TCCTCTGTCCCAAAATAAGTGTC 58.093 43.478 0.00 0.00 0.00 3.67
3591 4232 4.597507 TCCTCTGTCCCAAAATAAGTGTCT 59.402 41.667 0.00 0.00 0.00 3.41
3596 4237 4.518970 TGTCCCAAAATAAGTGTCTCAAGC 59.481 41.667 0.00 0.00 0.00 4.01
3597 4238 4.762251 GTCCCAAAATAAGTGTCTCAAGCT 59.238 41.667 0.00 0.00 0.00 3.74
3599 4240 6.430000 GTCCCAAAATAAGTGTCTCAAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
3601 4242 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
3602 4243 7.606456 CCCAAAATAAGTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
3603 4244 8.443937 CCAAAATAAGTGTCTCAAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
3604 4245 8.988934 CAAAATAAGTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 0.36 0.00 2.90
3607 4248 9.726438 AATAAGTGTCTCAAGCTTAGTACAATT 57.274 29.630 17.97 17.97 0.00 2.32
3609 4250 8.451908 AAGTGTCTCAAGCTTAGTACAATTTT 57.548 30.769 0.00 0.00 0.00 1.82
3611 4252 7.499232 AGTGTCTCAAGCTTAGTACAATTTTGT 59.501 33.333 0.00 1.08 44.86 2.83
3612 4253 8.770828 GTGTCTCAAGCTTAGTACAATTTTGTA 58.229 33.333 0.00 0.00 42.35 2.41
3638 4279 8.895737 ACTAGCTCTAGTATAAAGTTGAGACAC 58.104 37.037 7.73 0.00 43.98 3.67
3640 4281 8.356000 AGCTCTAGTATAAAGTTGAGACACTT 57.644 34.615 0.00 0.00 38.74 3.16
3641 4282 8.247562 AGCTCTAGTATAAAGTTGAGACACTTG 58.752 37.037 0.00 0.00 37.07 3.16
3643 4284 8.645814 TCTAGTATAAAGTTGAGACACTTGGA 57.354 34.615 0.00 0.00 37.07 3.53
3645 4286 6.702329 AGTATAAAGTTGAGACACTTGGAGG 58.298 40.000 0.00 0.00 37.07 4.30
3646 4287 2.938956 AAGTTGAGACACTTGGAGGG 57.061 50.000 0.00 0.00 35.57 4.30
3647 4288 2.103153 AGTTGAGACACTTGGAGGGA 57.897 50.000 0.00 0.00 0.00 4.20
3648 4289 1.974236 AGTTGAGACACTTGGAGGGAG 59.026 52.381 0.00 0.00 0.00 4.30
3649 4290 1.694696 GTTGAGACACTTGGAGGGAGT 59.305 52.381 0.00 0.00 0.00 3.85
3650 4291 2.897969 GTTGAGACACTTGGAGGGAGTA 59.102 50.000 0.00 0.00 0.00 2.59
3651 4292 3.474798 TGAGACACTTGGAGGGAGTAT 57.525 47.619 0.00 0.00 0.00 2.12
3655 4312 4.684724 AGACACTTGGAGGGAGTATGTAA 58.315 43.478 0.00 0.00 0.00 2.41
3677 4334 8.202137 TGTAATATGGTTAGCACTTCCTAAGAC 58.798 37.037 0.00 0.00 0.00 3.01
3719 4376 3.412237 TGTAAACTTGGTGGTAGCCTC 57.588 47.619 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.181824 GTTGGTGCCGGGTGGTATAT 59.818 55.000 2.18 0.00 37.67 0.86
1 2 1.603306 GTTGGTGCCGGGTGGTATA 59.397 57.895 2.18 0.00 37.67 1.47
2 3 2.353573 GTTGGTGCCGGGTGGTAT 59.646 61.111 2.18 0.00 37.67 2.73
3 4 3.956314 GGTTGGTGCCGGGTGGTA 61.956 66.667 2.18 0.00 37.67 3.25
11 12 3.134127 GAGGATGCGGTTGGTGCC 61.134 66.667 0.00 0.00 0.00 5.01
12 13 3.134127 GGAGGATGCGGTTGGTGC 61.134 66.667 0.00 0.00 0.00 5.01
13 14 2.040544 GTGGAGGATGCGGTTGGTG 61.041 63.158 0.00 0.00 0.00 4.17
14 15 2.351276 GTGGAGGATGCGGTTGGT 59.649 61.111 0.00 0.00 0.00 3.67
15 16 2.438434 GGTGGAGGATGCGGTTGG 60.438 66.667 0.00 0.00 0.00 3.77
16 17 2.040544 GTGGTGGAGGATGCGGTTG 61.041 63.158 0.00 0.00 0.00 3.77
17 18 2.351276 GTGGTGGAGGATGCGGTT 59.649 61.111 0.00 0.00 0.00 4.44
18 19 3.717294 GGTGGTGGAGGATGCGGT 61.717 66.667 0.00 0.00 0.00 5.68
19 20 4.489771 GGGTGGTGGAGGATGCGG 62.490 72.222 0.00 0.00 0.00 5.69
20 21 3.687321 CTGGGTGGTGGAGGATGCG 62.687 68.421 0.00 0.00 0.00 4.73
21 22 2.273449 CTGGGTGGTGGAGGATGC 59.727 66.667 0.00 0.00 0.00 3.91
22 23 1.616327 TCCTGGGTGGTGGAGGATG 60.616 63.158 0.00 0.00 37.07 3.51
23 24 1.307343 CTCCTGGGTGGTGGAGGAT 60.307 63.158 0.00 0.00 44.44 3.24
24 25 2.122729 CTCCTGGGTGGTGGAGGA 59.877 66.667 0.00 0.00 44.44 3.71
27 28 3.249189 GTGCTCCTGGGTGGTGGA 61.249 66.667 0.00 0.00 37.07 4.02
28 29 4.351054 GGTGCTCCTGGGTGGTGG 62.351 72.222 0.00 0.00 37.07 4.61
29 30 3.132029 TTGGTGCTCCTGGGTGGTG 62.132 63.158 6.34 0.00 37.07 4.17
30 31 2.776526 TTGGTGCTCCTGGGTGGT 60.777 61.111 6.34 0.00 37.07 4.16
31 32 2.282462 GTTGGTGCTCCTGGGTGG 60.282 66.667 6.34 0.00 34.23 4.61
32 33 0.540365 AATGTTGGTGCTCCTGGGTG 60.540 55.000 6.34 0.00 34.23 4.61
33 34 0.540365 CAATGTTGGTGCTCCTGGGT 60.540 55.000 6.34 0.00 34.23 4.51
50 51 2.821546 CCTGAGTCGTGAAACAGACAA 58.178 47.619 0.00 0.00 40.87 3.18
51 52 1.538204 GCCTGAGTCGTGAAACAGACA 60.538 52.381 0.00 0.00 40.87 3.41
52 53 1.140816 GCCTGAGTCGTGAAACAGAC 58.859 55.000 0.00 0.00 39.48 3.51
53 54 0.318699 CGCCTGAGTCGTGAAACAGA 60.319 55.000 0.00 0.00 35.74 3.41
61 63 4.363990 CACCAGCGCCTGAGTCGT 62.364 66.667 2.29 0.00 32.44 4.34
118 166 0.537188 GACGGCTTGATCTCCCTCAA 59.463 55.000 0.00 0.00 34.14 3.02
140 214 1.135859 GCAGCTGGAATTGAGTGTTCG 60.136 52.381 17.12 0.00 0.00 3.95
141 215 1.881973 TGCAGCTGGAATTGAGTGTTC 59.118 47.619 17.12 0.00 0.00 3.18
148 222 6.592607 AGAATTGTTAAATGCAGCTGGAATTG 59.407 34.615 17.82 0.00 0.00 2.32
170 244 7.445707 GCACCCCAACCAAATTAAATAAAAGAA 59.554 33.333 0.00 0.00 0.00 2.52
172 246 6.128418 CGCACCCCAACCAAATTAAATAAAAG 60.128 38.462 0.00 0.00 0.00 2.27
178 253 1.270358 GCGCACCCCAACCAAATTAAA 60.270 47.619 0.30 0.00 0.00 1.52
303 378 2.773661 TCTGATATGTGGGTCATGTGCT 59.226 45.455 0.00 0.00 37.91 4.40
304 379 3.198409 TCTGATATGTGGGTCATGTGC 57.802 47.619 0.00 0.00 37.91 4.57
498 573 3.854669 CGAGGGGATTGCCGAGCT 61.855 66.667 0.00 0.00 33.83 4.09
534 609 1.502190 GAAAGAAAGGCCCGCTTCG 59.498 57.895 0.00 0.00 0.00 3.79
625 713 3.399181 GACCCATGACCCGCTGGA 61.399 66.667 0.00 0.00 34.24 3.86
703 814 5.743398 TCTTGTTCTTTTCACAGCGATTTTG 59.257 36.000 0.00 0.00 0.00 2.44
737 848 2.437716 CCCGGCCGCAGTACAATT 60.438 61.111 22.85 0.00 0.00 2.32
767 878 6.534475 TTAACCTATCGAAAGCTCCTAACA 57.466 37.500 0.00 0.00 0.00 2.41
797 908 0.942962 GCAGCTCGGAAATCATCAGG 59.057 55.000 0.00 0.00 0.00 3.86
861 976 5.941058 TCATGGTAAAAACCGAAGCTAATCA 59.059 36.000 0.00 0.00 0.00 2.57
945 1074 3.118738 CGTGTGGGGATTAAACTCTAGCT 60.119 47.826 0.00 0.00 0.00 3.32
1694 1823 1.334869 AGGCAAAGAAAGAACAGCACG 59.665 47.619 0.00 0.00 0.00 5.34
1695 1824 2.620585 AGAGGCAAAGAAAGAACAGCAC 59.379 45.455 0.00 0.00 0.00 4.40
1743 1892 5.475220 TCAAGTTCTCAACTCCAAACACAAA 59.525 36.000 0.00 0.00 41.91 2.83
1769 1984 2.904434 TCAAGTTCTCTACCCCCTCAAC 59.096 50.000 0.00 0.00 0.00 3.18
1770 1985 3.173965 CTCAAGTTCTCTACCCCCTCAA 58.826 50.000 0.00 0.00 0.00 3.02
1771 1986 2.382305 TCTCAAGTTCTCTACCCCCTCA 59.618 50.000 0.00 0.00 0.00 3.86
1772 1987 3.103080 TCTCAAGTTCTCTACCCCCTC 57.897 52.381 0.00 0.00 0.00 4.30
1773 1988 3.246167 ACATCTCAAGTTCTCTACCCCCT 60.246 47.826 0.00 0.00 0.00 4.79
1774 1989 3.108376 ACATCTCAAGTTCTCTACCCCC 58.892 50.000 0.00 0.00 0.00 5.40
1775 1990 3.181485 CGACATCTCAAGTTCTCTACCCC 60.181 52.174 0.00 0.00 0.00 4.95
1776 1991 3.695060 TCGACATCTCAAGTTCTCTACCC 59.305 47.826 0.00 0.00 0.00 3.69
1777 1992 4.966965 TCGACATCTCAAGTTCTCTACC 57.033 45.455 0.00 0.00 0.00 3.18
1778 1993 9.176181 GATTTATCGACATCTCAAGTTCTCTAC 57.824 37.037 0.00 0.00 0.00 2.59
1779 1994 9.126151 AGATTTATCGACATCTCAAGTTCTCTA 57.874 33.333 0.00 0.00 0.00 2.43
1780 1995 7.920151 CAGATTTATCGACATCTCAAGTTCTCT 59.080 37.037 0.00 0.00 0.00 3.10
1781 1996 7.704472 ACAGATTTATCGACATCTCAAGTTCTC 59.296 37.037 0.00 0.00 0.00 2.87
1782 1997 7.551585 ACAGATTTATCGACATCTCAAGTTCT 58.448 34.615 0.00 0.00 0.00 3.01
1783 1998 7.763172 ACAGATTTATCGACATCTCAAGTTC 57.237 36.000 0.00 0.00 0.00 3.01
1784 1999 8.470805 ACTACAGATTTATCGACATCTCAAGTT 58.529 33.333 0.00 0.00 0.00 2.66
1785 2000 8.001881 ACTACAGATTTATCGACATCTCAAGT 57.998 34.615 0.00 0.00 0.00 3.16
1886 2144 5.873712 AGTTAGATCAACTGCAATCAGAGTG 59.126 40.000 9.00 0.00 46.01 3.51
1948 2206 4.034285 AGGGGTTCTCACTAACAATTGG 57.966 45.455 10.83 0.00 0.00 3.16
1983 2255 9.485206 GTTACTAACATGAAGTTTAACCTCTCA 57.515 33.333 0.00 0.00 41.64 3.27
2065 2357 4.273480 TCTGTGCAAAGTTTAAGCTGACTC 59.727 41.667 3.21 0.00 0.00 3.36
2066 2358 4.199310 TCTGTGCAAAGTTTAAGCTGACT 58.801 39.130 3.21 0.00 0.00 3.41
2089 2381 6.570571 GCTGGGAAAGTTGGAATTCTAGAAAC 60.571 42.308 9.71 6.86 0.00 2.78
2107 2399 5.191727 TGGATCTTTATGAAAGCTGGGAA 57.808 39.130 0.00 0.00 38.39 3.97
2206 2597 6.985188 TTTGCTGCTTAATGTAGTAAGAGG 57.015 37.500 0.00 0.00 34.98 3.69
2310 2701 8.942338 TCAAACTAACAGCACTAACTATATGG 57.058 34.615 0.00 0.00 0.00 2.74
2369 2760 7.531716 TGCGAACCTTTTAAACCATTATACAG 58.468 34.615 0.00 0.00 0.00 2.74
2386 2778 4.689345 GTGACACTAGTAAATTGCGAACCT 59.311 41.667 0.00 0.00 0.00 3.50
2445 2837 6.701145 TGTGCATTTACTTACAACTTGGAA 57.299 33.333 0.00 0.00 0.00 3.53
2585 2988 4.201628 CGCAGCTTGTTGAGTTACATAGTC 60.202 45.833 0.00 0.00 0.00 2.59
2733 3138 2.353704 CCAAGTCGCTACATGTTCCAGA 60.354 50.000 2.30 0.00 0.00 3.86
2739 3144 3.935203 CAGAATTCCAAGTCGCTACATGT 59.065 43.478 2.69 2.69 0.00 3.21
2757 3162 6.286758 GTCATTAGATCTCAGCATTCCAGAA 58.713 40.000 0.00 0.00 0.00 3.02
2835 3240 4.639310 GCCTGTGATTTTGATCATCAGAGT 59.361 41.667 16.47 0.00 39.38 3.24
2849 3254 6.061441 TCACATATAAATTCCGCCTGTGATT 58.939 36.000 0.00 0.00 37.27 2.57
2947 3358 9.577110 CATACAAGATACAATCAACAAAAGCAT 57.423 29.630 0.00 0.00 0.00 3.79
3018 3446 8.442632 AACAGTAATCAATATGGACATCAGTG 57.557 34.615 0.00 0.00 0.00 3.66
3039 3467 5.178061 TCTACAGGCATCACAACATAACAG 58.822 41.667 0.00 0.00 0.00 3.16
3103 3588 2.479656 GCTTGAGTGAACTTCTCTGCAG 59.520 50.000 7.63 7.63 34.81 4.41
3208 3746 0.972883 AGACTCACCTCTTCAGCACC 59.027 55.000 0.00 0.00 0.00 5.01
3422 4061 3.583086 CCCTCCGTCCCATAATGTAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
3428 4067 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3521 4162 2.626266 GCAATGGCCTGAATGATCATGA 59.374 45.455 9.46 0.00 34.37 3.07
3548 4189 8.082242 CAGAGGAAGTATTTAAAAACCCAACAG 58.918 37.037 0.00 0.00 0.00 3.16
3558 4199 8.950007 ATTTTGGGACAGAGGAAGTATTTAAA 57.050 30.769 0.00 0.00 42.39 1.52
3568 4209 4.597507 AGACACTTATTTTGGGACAGAGGA 59.402 41.667 0.00 0.00 42.39 3.71
3573 4214 4.518970 GCTTGAGACACTTATTTTGGGACA 59.481 41.667 0.00 0.00 0.00 4.02
3576 4217 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
3579 4220 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
3582 4223 9.726438 AAATTGTACTAAGCTTGAGACACTTAT 57.274 29.630 9.86 0.00 0.00 1.73
3585 4226 7.499232 ACAAAATTGTACTAAGCTTGAGACACT 59.501 33.333 9.86 1.62 40.16 3.55
3586 4227 7.639945 ACAAAATTGTACTAAGCTTGAGACAC 58.360 34.615 9.86 7.18 40.16 3.67
3613 4254 9.116067 AGTGTCTCAACTTTATACTAGAGCTAG 57.884 37.037 0.00 3.06 39.04 3.42
3616 4257 7.489757 CCAAGTGTCTCAACTTTATACTAGAGC 59.510 40.741 0.00 0.00 38.34 4.09
3617 4258 8.740906 TCCAAGTGTCTCAACTTTATACTAGAG 58.259 37.037 0.00 0.00 38.34 2.43
3619 4260 7.976734 CCTCCAAGTGTCTCAACTTTATACTAG 59.023 40.741 0.00 0.00 38.34 2.57
3620 4261 7.093465 CCCTCCAAGTGTCTCAACTTTATACTA 60.093 40.741 0.00 0.00 38.34 1.82
3621 4262 6.295916 CCCTCCAAGTGTCTCAACTTTATACT 60.296 42.308 0.00 0.00 38.34 2.12
3622 4263 5.875359 CCCTCCAAGTGTCTCAACTTTATAC 59.125 44.000 0.00 0.00 38.34 1.47
3624 4265 4.597507 TCCCTCCAAGTGTCTCAACTTTAT 59.402 41.667 0.00 0.00 38.34 1.40
3627 4268 2.370189 CTCCCTCCAAGTGTCTCAACTT 59.630 50.000 0.00 0.00 41.08 2.66
3629 4270 1.694696 ACTCCCTCCAAGTGTCTCAAC 59.305 52.381 0.00 0.00 0.00 3.18
3630 4271 2.103153 ACTCCCTCCAAGTGTCTCAA 57.897 50.000 0.00 0.00 0.00 3.02
3631 4272 2.992847 TACTCCCTCCAAGTGTCTCA 57.007 50.000 0.00 0.00 0.00 3.27
3632 4273 3.100671 ACATACTCCCTCCAAGTGTCTC 58.899 50.000 0.00 0.00 0.00 3.36
3633 4274 3.191888 ACATACTCCCTCCAAGTGTCT 57.808 47.619 0.00 0.00 0.00 3.41
3634 4275 5.615925 ATTACATACTCCCTCCAAGTGTC 57.384 43.478 0.00 0.00 0.00 3.67
3635 4276 6.043243 CCATATTACATACTCCCTCCAAGTGT 59.957 42.308 0.00 0.00 0.00 3.55
3636 4277 6.043243 ACCATATTACATACTCCCTCCAAGTG 59.957 42.308 0.00 0.00 0.00 3.16
3637 4278 6.151049 ACCATATTACATACTCCCTCCAAGT 58.849 40.000 0.00 0.00 0.00 3.16
3638 4279 6.688073 ACCATATTACATACTCCCTCCAAG 57.312 41.667 0.00 0.00 0.00 3.61
3640 4281 6.212791 GCTAACCATATTACATACTCCCTCCA 59.787 42.308 0.00 0.00 0.00 3.86
3641 4282 6.212791 TGCTAACCATATTACATACTCCCTCC 59.787 42.308 0.00 0.00 0.00 4.30
3643 4284 6.787957 AGTGCTAACCATATTACATACTCCCT 59.212 38.462 0.00 0.00 0.00 4.20
3645 4286 7.603024 GGAAGTGCTAACCATATTACATACTCC 59.397 40.741 0.00 0.00 0.00 3.85
3646 4287 8.368668 AGGAAGTGCTAACCATATTACATACTC 58.631 37.037 0.00 0.00 0.00 2.59
3647 4288 8.263854 AGGAAGTGCTAACCATATTACATACT 57.736 34.615 0.00 0.00 0.00 2.12
3648 4289 9.991906 TTAGGAAGTGCTAACCATATTACATAC 57.008 33.333 0.00 0.00 0.00 2.39
3650 4291 8.934697 TCTTAGGAAGTGCTAACCATATTACAT 58.065 33.333 0.00 0.00 0.00 2.29
3651 4292 8.202137 GTCTTAGGAAGTGCTAACCATATTACA 58.798 37.037 0.00 0.00 0.00 2.41
3655 4312 6.611642 TCTGTCTTAGGAAGTGCTAACCATAT 59.388 38.462 0.00 0.00 0.00 1.78
3677 4334 1.815003 GGGACATTTTGGTGAGCTCTG 59.185 52.381 16.19 5.28 0.00 3.35
3719 4376 2.218603 AGCTTGGTAAAGTCAACCACG 58.781 47.619 0.00 0.00 46.56 4.94


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

AutoCloner maintained by Alex Coulton.