Multiple sequence alignment - TraesCS2B01G109000

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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 TraesCS2B01G109000 chr2B 100.000 4276 0 0 1 4276 69503437 69499162 0.000000e+00 7897.0
1 TraesCS2B01G109000 chr2B 96.193 683 26 0 2132 2814 94926742 94927424 0.000000e+00 1118.0
2 TraesCS2B01G109000 chr2B 89.340 788 51 17 797 1560 94925335 94926113 0.000000e+00 959.0
3 TraesCS2B01G109000 chr2B 86.745 679 82 7 2127 2802 601333902 601334575 0.000000e+00 749.0
4 TraesCS2B01G109000 chr2B 85.517 580 63 14 183 748 94924353 94924925 1.710000e-163 586.0
5 TraesCS2B01G109000 chr2B 87.037 378 26 12 3053 3424 94927651 94928011 5.150000e-109 405.0
6 TraesCS2B01G109000 chr2B 90.584 308 19 6 1828 2128 94926370 94926674 2.400000e-107 399.0
7 TraesCS2B01G109000 chr2B 96.491 57 2 0 1556 1612 94926204 94926260 1.270000e-15 95.3
8 TraesCS2B01G109000 chr2B 92.537 67 3 2 3411 3475 601334716 601334782 1.270000e-15 95.3
9 TraesCS2B01G109000 chr2B 86.957 92 2 6 1751 1832 760860391 760860300 1.270000e-15 95.3
10 TraesCS2B01G109000 chr2D 95.982 1742 17 5 1832 3538 44088339 44086616 0.000000e+00 2780.0
11 TraesCS2B01G109000 chr2D 87.890 1412 114 35 2127 3506 60753023 60754409 0.000000e+00 1607.0
12 TraesCS2B01G109000 chr2D 90.812 1034 23 14 743 1715 44089447 44088425 0.000000e+00 1317.0
13 TraesCS2B01G109000 chr2D 94.416 770 20 3 1 748 44090730 44089962 0.000000e+00 1162.0
14 TraesCS2B01G109000 chr2D 85.664 851 53 29 743 1560 60751559 60752373 0.000000e+00 832.0
15 TraesCS2B01G109000 chr2D 83.051 767 87 25 1 748 60750720 60751462 0.000000e+00 656.0
16 TraesCS2B01G109000 chr2D 91.722 302 20 4 1828 2128 60752661 60752958 8.550000e-112 414.0
17 TraesCS2B01G109000 chr2D 96.296 243 7 2 3983 4224 44086118 44085877 8.620000e-107 398.0
18 TraesCS2B01G109000 chr2D 93.802 242 14 1 3523 3764 44086589 44086349 3.140000e-96 363.0
19 TraesCS2B01G109000 chr2D 96.045 177 6 1 3767 3943 44086285 44086110 1.950000e-73 287.0
20 TraesCS2B01G109000 chr2D 83.553 152 14 6 1607 1755 60752519 60752662 9.650000e-27 132.0
21 TraesCS2B01G109000 chr2D 93.421 76 5 0 1713 1788 44088332 44088407 3.490000e-21 113.0
22 TraesCS2B01G109000 chr2D 87.342 79 8 2 481 557 530200019 530200097 5.890000e-14 89.8
23 TraesCS2B01G109000 chr2A 96.070 1603 22 6 1962 3533 47919150 47917558 0.000000e+00 2573.0
24 TraesCS2B01G109000 chr2A 87.306 1355 112 36 2130 3466 61286455 61287767 0.000000e+00 1495.0
25 TraesCS2B01G109000 chr2A 91.823 746 9 11 743 1441 47919896 47919156 0.000000e+00 992.0
26 TraesCS2B01G109000 chr2A 86.982 845 66 20 746 1560 61285022 61285852 0.000000e+00 911.0
27 TraesCS2B01G109000 chr2A 82.764 615 69 23 956 1555 62918801 62919393 8.200000e-142 514.0
28 TraesCS2B01G109000 chr2A 89.514 391 24 4 3888 4273 47917186 47916808 2.990000e-131 479.0
29 TraesCS2B01G109000 chr2A 79.340 576 75 24 875 1427 753270683 753271237 8.740000e-97 364.0
30 TraesCS2B01G109000 chr2A 93.388 242 12 2 3523 3764 47917526 47917289 5.260000e-94 355.0
31 TraesCS2B01G109000 chr2A 87.713 293 22 10 1837 2128 61286110 61286389 3.190000e-86 329.0
32 TraesCS2B01G109000 chr2A 86.765 272 32 4 1 270 61280573 61280842 2.500000e-77 300.0
33 TraesCS2B01G109000 chr2A 83.010 206 11 5 1556 1741 62919463 62919664 9.510000e-37 165.0
34 TraesCS2B01G109000 chr2A 95.556 45 0 2 3767 3809 47917224 47917180 2.130000e-08 71.3
35 TraesCS2B01G109000 chr5B 91.857 614 45 4 2217 2828 457989916 457990526 0.000000e+00 852.0
36 TraesCS2B01G109000 chr5B 93.846 65 4 0 3415 3479 457990595 457990659 9.790000e-17 99.0
37 TraesCS2B01G109000 chr5B 87.059 85 2 1 1754 1829 36808601 36808517 2.120000e-13 87.9
38 TraesCS2B01G109000 chr5B 96.154 52 2 0 1778 1829 621238755 621238806 7.620000e-13 86.1
39 TraesCS2B01G109000 chr5B 96.154 52 2 0 1778 1829 704531977 704532028 7.620000e-13 86.1
40 TraesCS2B01G109000 chr5B 80.769 78 13 2 1 76 202772076 202772153 4.620000e-05 60.2
41 TraesCS2B01G109000 chr6B 86.654 547 67 5 2277 2821 157480015 157479473 6.120000e-168 601.0
42 TraesCS2B01G109000 chr6B 96.721 61 2 0 3415 3475 157476418 157476358 7.560000e-18 102.0
43 TraesCS2B01G109000 chr6B 96.721 61 2 0 3415 3475 157478548 157478488 7.560000e-18 102.0
44 TraesCS2B01G109000 chr6B 96.721 61 2 0 3415 3475 157479397 157479337 7.560000e-18 102.0
45 TraesCS2B01G109000 chr6B 86.747 83 10 1 476 557 647694445 647694527 1.640000e-14 91.6
46 TraesCS2B01G109000 chr3D 84.051 627 65 20 956 1555 473415338 473414720 4.800000e-159 571.0
47 TraesCS2B01G109000 chr3D 80.316 569 76 22 875 1427 275444650 275445198 8.620000e-107 398.0
48 TraesCS2B01G109000 chr4D 83.280 628 67 25 956 1555 499921221 499920604 1.050000e-150 544.0
49 TraesCS2B01G109000 chr4A 91.557 379 29 3 2452 2828 703283578 703283201 1.760000e-143 520.0
50 TraesCS2B01G109000 chr4A 90.062 161 13 3 985 1144 196571415 196571573 5.600000e-49 206.0
51 TraesCS2B01G109000 chr4A 100.000 34 0 0 2290 2323 703283638 703283605 3.570000e-06 63.9
52 TraesCS2B01G109000 chr5A 82.212 624 78 21 956 1555 612651936 612652550 1.370000e-139 507.0
53 TraesCS2B01G109000 chr5A 86.207 87 3 2 1752 1829 612161472 612161558 7.620000e-13 86.1
54 TraesCS2B01G109000 chr7B 81.616 631 73 23 956 1555 629199523 629200141 2.310000e-132 483.0
55 TraesCS2B01G109000 chr7B 81.458 631 74 23 956 1555 629183109 629183727 1.080000e-130 477.0
56 TraesCS2B01G109000 chr7B 85.823 395 41 5 1175 1555 619205893 619206286 5.150000e-109 405.0
57 TraesCS2B01G109000 chr7B 89.412 85 0 1 1754 1829 60366479 60366563 9.790000e-17 99.0
58 TraesCS2B01G109000 chr7B 85.000 80 10 2 480 557 577671578 577671499 3.540000e-11 80.5
59 TraesCS2B01G109000 chr3A 80.423 567 77 21 876 1427 596107659 596108206 6.660000e-108 401.0
60 TraesCS2B01G109000 chr3A 87.209 86 2 2 1753 1829 663575411 663575326 5.890000e-14 89.8
61 TraesCS2B01G109000 chr3A 86.517 89 3 2 1750 1829 696373429 696373517 5.890000e-14 89.8
62 TraesCS2B01G109000 chr3A 96.154 52 2 0 1778 1829 69643805 69643856 7.620000e-13 86.1
63 TraesCS2B01G109000 chr1D 92.093 215 17 0 875 1089 269496886 269496672 1.930000e-78 303.0
64 TraesCS2B01G109000 chr1D 83.140 172 27 2 31 201 214403136 214402966 5.720000e-34 156.0
65 TraesCS2B01G109000 chr4B 89.412 85 0 1 1754 1829 59873819 59873735 9.790000e-17 99.0
66 TraesCS2B01G109000 chr4B 82.051 78 12 2 1 76 647574050 647574127 9.920000e-07 65.8
67 TraesCS2B01G109000 chr4B 79.747 79 13 3 1 76 515450823 515450745 2.000000e-03 54.7
68 TraesCS2B01G109000 chr7D 88.462 78 8 1 481 557 134766288 134766211 4.550000e-15 93.5
69 TraesCS2B01G109000 chr7D 96.154 52 2 0 1778 1829 180444960 180445011 7.620000e-13 86.1
70 TraesCS2B01G109000 chr6A 87.342 79 8 2 481 557 463531367 463531289 5.890000e-14 89.8
71 TraesCS2B01G109000 chr1B 87.805 82 2 1 1754 1827 32770929 32770848 5.890000e-14 89.8
72 TraesCS2B01G109000 chr1B 86.585 82 3 5 1756 1829 32770848 32770929 2.740000e-12 84.2
73 TraesCS2B01G109000 chr1B 97.297 37 1 0 1752 1788 32770803 32770839 3.570000e-06 63.9
74 TraesCS2B01G109000 chrUn 87.059 85 2 1 1754 1829 314542752 314542668 2.120000e-13 87.9


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 TraesCS2B01G109000 chr2B 69499162 69503437 4275 True 7897.000000 7897 100.000000 1 4276 1 chr2B.!!$R1 4275
1 TraesCS2B01G109000 chr2B 94924353 94928011 3658 False 593.716667 1118 90.860333 183 3424 6 chr2B.!!$F1 3241
2 TraesCS2B01G109000 chr2B 601333902 601334782 880 False 422.150000 749 89.641000 2127 3475 2 chr2B.!!$F2 1348
3 TraesCS2B01G109000 chr2D 44085877 44090730 4853 True 1051.166667 2780 94.558833 1 4224 6 chr2D.!!$R1 4223
4 TraesCS2B01G109000 chr2D 60750720 60754409 3689 False 728.200000 1607 86.376000 1 3506 5 chr2D.!!$F3 3505
5 TraesCS2B01G109000 chr2A 61285022 61287767 2745 False 911.666667 1495 87.333667 746 3466 3 chr2A.!!$F3 2720
6 TraesCS2B01G109000 chr2A 47916808 47919896 3088 True 894.060000 2573 93.270200 743 4273 5 chr2A.!!$R1 3530
7 TraesCS2B01G109000 chr2A 753270683 753271237 554 False 364.000000 364 79.340000 875 1427 1 chr2A.!!$F2 552
8 TraesCS2B01G109000 chr2A 62918801 62919664 863 False 339.500000 514 82.887000 956 1741 2 chr2A.!!$F4 785
9 TraesCS2B01G109000 chr5B 457989916 457990659 743 False 475.500000 852 92.851500 2217 3479 2 chr5B.!!$F4 1262
10 TraesCS2B01G109000 chr6B 157476358 157480015 3657 True 226.750000 601 94.204250 2277 3475 4 chr6B.!!$R1 1198
11 TraesCS2B01G109000 chr3D 473414720 473415338 618 True 571.000000 571 84.051000 956 1555 1 chr3D.!!$R1 599
12 TraesCS2B01G109000 chr3D 275444650 275445198 548 False 398.000000 398 80.316000 875 1427 1 chr3D.!!$F1 552
13 TraesCS2B01G109000 chr4D 499920604 499921221 617 True 544.000000 544 83.280000 956 1555 1 chr4D.!!$R1 599
14 TraesCS2B01G109000 chr5A 612651936 612652550 614 False 507.000000 507 82.212000 956 1555 1 chr5A.!!$F2 599
15 TraesCS2B01G109000 chr7B 629199523 629200141 618 False 483.000000 483 81.616000 956 1555 1 chr7B.!!$F4 599
16 TraesCS2B01G109000 chr7B 629183109 629183727 618 False 477.000000 477 81.458000 956 1555 1 chr7B.!!$F3 599
17 TraesCS2B01G109000 chr3A 596107659 596108206 547 False 401.000000 401 80.423000 876 1427 1 chr3A.!!$F2 551

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
103 105 0.250166 AACCGTCTTGTGCCACTACC 60.250 55.000 0.00 0.00 0.00 3.18 F
737 810 0.958822 ACGGTGCTTTTTGGCTAAGG 59.041 50.000 0.00 0.00 0.00 2.69 F
1123 1944 1.229400 AACTCCCGTAAGAGCCCCA 60.229 57.895 0.00 0.00 37.39 4.96 F
1366 2232 1.273606 CCGTGATAGCTATGGGACTGG 59.726 57.143 11.94 7.15 0.00 4.00 F
2052 3079 1.672881 AGTTGTTGCTTCAGTCTGTGC 59.327 47.619 11.68 11.68 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 2232 1.203052 CACCATCAAAGTGGCACATCC 59.797 52.381 21.41 0.00 44.52 3.51 R
2730 3827 3.657835 CTTGCTCTTGGCGCGCTTC 62.658 63.158 32.29 16.28 45.43 3.86 R
2751 3848 1.126488 CATGCTTCCTCTCCCTGCTA 58.874 55.000 0.00 0.00 0.00 3.49 R
3081 7256 2.165641 GCCCTGTTTGCCAAATAGTACC 59.834 50.000 12.17 0.00 0.00 3.34 R
3810 8108 2.664402 ACACTGGAAATGCTTCTGGT 57.336 45.000 0.00 0.00 0.00 4.00 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
103 105 0.250166 AACCGTCTTGTGCCACTACC 60.250 55.000 0.00 0.00 0.00 3.18
140 142 4.957296 AGTTCAAACACACGATTAGTCCT 58.043 39.130 0.00 0.00 0.00 3.85
205 215 1.771854 TGCCCTTTAAGAGGTGACACA 59.228 47.619 8.08 0.00 44.71 3.72
232 242 2.350498 CGTCCGGTCACATTTACCAATC 59.650 50.000 0.00 0.00 36.78 2.67
335 345 7.776969 CCCATGGGTCCTTTATATATGAATCAG 59.223 40.741 23.93 0.00 0.00 2.90
415 425 3.184379 GCGCGCATAGTTTTAGATCATCA 59.816 43.478 29.10 0.00 0.00 3.07
474 506 1.603172 GCGGGAATGTCATAGGACTCG 60.603 57.143 9.22 6.32 44.61 4.18
487 519 5.472478 TCATAGGACTCGTATGTGGATGTAC 59.528 44.000 15.25 0.00 34.87 2.90
562 613 2.624364 TGACCTAGAACTACGCACACAA 59.376 45.455 0.00 0.00 0.00 3.33
735 808 1.681538 TCACGGTGCTTTTTGGCTAA 58.318 45.000 2.51 0.00 0.00 3.09
737 810 0.958822 ACGGTGCTTTTTGGCTAAGG 59.041 50.000 0.00 0.00 0.00 2.69
738 811 1.243902 CGGTGCTTTTTGGCTAAGGA 58.756 50.000 0.00 0.00 0.00 3.36
739 812 1.818674 CGGTGCTTTTTGGCTAAGGAT 59.181 47.619 0.00 0.00 0.00 3.24
740 813 3.013921 CGGTGCTTTTTGGCTAAGGATA 58.986 45.455 0.00 0.00 0.00 2.59
741 814 3.065371 CGGTGCTTTTTGGCTAAGGATAG 59.935 47.826 0.00 0.00 0.00 2.08
772 1529 3.594603 AGAGACACGTGGTTTCATAGG 57.405 47.619 21.57 0.00 33.18 2.57
1123 1944 1.229400 AACTCCCGTAAGAGCCCCA 60.229 57.895 0.00 0.00 37.39 4.96
1294 2147 2.966516 GGGATGAGTCTTCTTCGGGTAT 59.033 50.000 6.04 0.00 0.00 2.73
1313 2166 6.002704 GGGTATCTGAGTATCTAGACGGAAA 58.997 44.000 0.00 0.00 34.92 3.13
1315 2168 7.361894 GGTATCTGAGTATCTAGACGGAAAAC 58.638 42.308 0.00 0.00 34.92 2.43
1318 2171 5.125097 TCTGAGTATCTAGACGGAAAACCAC 59.875 44.000 0.00 0.00 34.92 4.16
1319 2172 5.014858 TGAGTATCTAGACGGAAAACCACT 58.985 41.667 0.00 0.00 34.92 4.00
1321 2174 5.262804 AGTATCTAGACGGAAAACCACTCT 58.737 41.667 0.00 0.00 0.00 3.24
1366 2232 1.273606 CCGTGATAGCTATGGGACTGG 59.726 57.143 11.94 7.15 0.00 4.00
1649 2631 7.819900 AGTACAAGTTGAGTCATAAGGAACATC 59.180 37.037 10.54 0.00 0.00 3.06
1721 2706 5.073311 AGCTAATCGAGTTGCTTGTTCTA 57.927 39.130 15.78 0.00 30.96 2.10
1747 2732 6.007076 TGTTCCTTTACCTTCACATGCAATA 58.993 36.000 0.00 0.00 0.00 1.90
1753 2741 7.094205 CCTTTACCTTCACATGCAATAACTTCT 60.094 37.037 0.00 0.00 0.00 2.85
1754 2742 8.856153 TTTACCTTCACATGCAATAACTTCTA 57.144 30.769 0.00 0.00 0.00 2.10
1755 2743 6.743575 ACCTTCACATGCAATAACTTCTAC 57.256 37.500 0.00 0.00 0.00 2.59
1756 2744 6.476378 ACCTTCACATGCAATAACTTCTACT 58.524 36.000 0.00 0.00 0.00 2.57
1757 2745 6.595716 ACCTTCACATGCAATAACTTCTACTC 59.404 38.462 0.00 0.00 0.00 2.59
1758 2746 6.037610 CCTTCACATGCAATAACTTCTACTCC 59.962 42.308 0.00 0.00 0.00 3.85
1759 2747 5.428253 TCACATGCAATAACTTCTACTCCC 58.572 41.667 0.00 0.00 0.00 4.30
1760 2748 5.189736 TCACATGCAATAACTTCTACTCCCT 59.810 40.000 0.00 0.00 0.00 4.20
1761 2749 5.525378 CACATGCAATAACTTCTACTCCCTC 59.475 44.000 0.00 0.00 0.00 4.30
1762 2750 5.426833 ACATGCAATAACTTCTACTCCCTCT 59.573 40.000 0.00 0.00 0.00 3.69
1763 2751 5.344743 TGCAATAACTTCTACTCCCTCTG 57.655 43.478 0.00 0.00 0.00 3.35
1764 2752 4.777896 TGCAATAACTTCTACTCCCTCTGT 59.222 41.667 0.00 0.00 0.00 3.41
1765 2753 5.955959 TGCAATAACTTCTACTCCCTCTGTA 59.044 40.000 0.00 0.00 0.00 2.74
1766 2754 6.127423 TGCAATAACTTCTACTCCCTCTGTAC 60.127 42.308 0.00 0.00 0.00 2.90
1767 2755 6.683360 GCAATAACTTCTACTCCCTCTGTACC 60.683 46.154 0.00 0.00 0.00 3.34
1768 2756 4.399483 AACTTCTACTCCCTCTGTACCA 57.601 45.455 0.00 0.00 0.00 3.25
1769 2757 4.611564 ACTTCTACTCCCTCTGTACCAT 57.388 45.455 0.00 0.00 0.00 3.55
1770 2758 5.728937 ACTTCTACTCCCTCTGTACCATA 57.271 43.478 0.00 0.00 0.00 2.74
1771 2759 6.088541 ACTTCTACTCCCTCTGTACCATAA 57.911 41.667 0.00 0.00 0.00 1.90
1772 2760 6.684538 ACTTCTACTCCCTCTGTACCATAAT 58.315 40.000 0.00 0.00 0.00 1.28
1773 2761 7.823635 ACTTCTACTCCCTCTGTACCATAATA 58.176 38.462 0.00 0.00 0.00 0.98
1774 2762 7.945664 ACTTCTACTCCCTCTGTACCATAATAG 59.054 40.741 0.00 0.00 0.00 1.73
1775 2763 7.403837 TCTACTCCCTCTGTACCATAATAGT 57.596 40.000 0.00 0.00 0.00 2.12
1776 2764 7.823635 TCTACTCCCTCTGTACCATAATAGTT 58.176 38.462 0.00 0.00 0.00 2.24
1777 2765 6.732896 ACTCCCTCTGTACCATAATAGTTG 57.267 41.667 0.00 0.00 0.00 3.16
1778 2766 6.203072 ACTCCCTCTGTACCATAATAGTTGT 58.797 40.000 0.00 0.00 0.00 3.32
1779 2767 6.324254 ACTCCCTCTGTACCATAATAGTTGTC 59.676 42.308 0.00 0.00 0.00 3.18
1780 2768 5.301045 TCCCTCTGTACCATAATAGTTGTCG 59.699 44.000 0.00 0.00 0.00 4.35
1781 2769 4.982916 CCTCTGTACCATAATAGTTGTCGC 59.017 45.833 0.00 0.00 0.00 5.19
1782 2770 5.221263 CCTCTGTACCATAATAGTTGTCGCT 60.221 44.000 0.00 0.00 0.00 4.93
1783 2771 5.588240 TCTGTACCATAATAGTTGTCGCTG 58.412 41.667 0.00 0.00 0.00 5.18
1784 2772 5.358725 TCTGTACCATAATAGTTGTCGCTGA 59.641 40.000 0.00 0.00 0.00 4.26
1785 2773 5.968254 TGTACCATAATAGTTGTCGCTGAA 58.032 37.500 0.00 0.00 0.00 3.02
1786 2774 6.040247 TGTACCATAATAGTTGTCGCTGAAG 58.960 40.000 0.00 0.00 0.00 3.02
1825 2813 4.603131 ACAACTATTACGGTACAGAGGGA 58.397 43.478 0.00 0.00 0.00 4.20
1960 2985 6.326323 ACTCCCATGTAAATGTTTTTCCACTT 59.674 34.615 0.00 0.00 0.00 3.16
2052 3079 1.672881 AGTTGTTGCTTCAGTCTGTGC 59.327 47.619 11.68 11.68 0.00 4.57
2287 3383 2.123248 TTGCAGGGCAGAACATCCGA 62.123 55.000 0.00 0.00 40.61 4.55
2446 3542 8.715998 GCATGATAGTATTCATCTTTGTAGGTG 58.284 37.037 0.00 0.00 34.09 4.00
2730 3827 2.538437 CTCTCTGATCAGTTTGAGGCG 58.462 52.381 21.92 4.53 0.00 5.52
3564 7800 8.905702 GCACAAAAAGTAGATTTACATCACAAG 58.094 33.333 0.00 0.00 31.96 3.16
3657 7893 5.754406 TGAAACCATTGCAAACTTGATCAAG 59.246 36.000 29.74 29.74 43.79 3.02
3702 7938 6.169419 TGAACAACAAATCTCTATGCTTCG 57.831 37.500 0.00 0.00 0.00 3.79
3715 7951 1.592064 TGCTTCGTCTGTGATTGCAA 58.408 45.000 0.00 0.00 0.00 4.08
3764 8000 9.704098 CTAAAAGAACAAGAACAGTGTAAAGTC 57.296 33.333 0.00 0.00 0.00 3.01
3765 8001 7.681939 AAAGAACAAGAACAGTGTAAAGTCA 57.318 32.000 0.00 0.00 0.00 3.41
3825 8123 2.238521 GAACCACCAGAAGCATTTCCA 58.761 47.619 0.00 0.00 33.64 3.53
3833 8131 4.460382 ACCAGAAGCATTTCCAGTGTATTG 59.540 41.667 0.00 0.00 33.64 1.90
3854 8152 9.428097 GTATTGAAGTCAGATATATGCACATCA 57.572 33.333 0.00 0.00 0.00 3.07
4109 8412 2.093658 AGGCACAAGAATCCGTTCGTAT 60.094 45.455 0.00 0.00 39.38 3.06
4124 8427 4.495184 CGTTCGTATAAACCAAATGGCTCC 60.495 45.833 0.00 0.00 39.32 4.70
4129 8432 4.824479 ATAAACCAAATGGCTCCAAAGG 57.176 40.909 0.00 0.00 39.32 3.11
4238 8541 4.694760 CATGACATGGAAGTAGGGATGA 57.305 45.455 7.60 0.00 0.00 2.92
4260 8563 1.368579 CCGTCAGGTTTGGGTACGT 59.631 57.895 0.00 0.00 31.87 3.57
4263 8566 1.223187 GTCAGGTTTGGGTACGTGTG 58.777 55.000 0.00 0.00 35.85 3.82
4273 8576 1.338769 GGGTACGTGTGAAGGCTTCAT 60.339 52.381 30.70 18.18 42.47 2.57
4274 8577 2.423577 GGTACGTGTGAAGGCTTCATT 58.576 47.619 30.70 18.00 42.47 2.57
4275 8578 2.415512 GGTACGTGTGAAGGCTTCATTC 59.584 50.000 30.70 23.41 42.47 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 40 3.917329 TGAAGACAGAGATTTCGACGT 57.083 42.857 0.00 0.00 0.00 4.34
103 105 6.519761 GTGTTTGAACTACACAAGCATATTCG 59.480 38.462 0.00 0.00 44.08 3.34
193 203 0.393077 CGACCCTTGTGTCACCTCTT 59.607 55.000 0.00 0.00 34.88 2.85
205 215 1.477685 AATGTGACCGGACGACCCTT 61.478 55.000 9.46 0.00 0.00 3.95
232 242 8.815141 TGAGTTTTAATTGATTGGATTGTGTG 57.185 30.769 0.00 0.00 0.00 3.82
335 345 5.227908 TCATCTTCTACAAAAGTCCACGAC 58.772 41.667 0.00 0.00 0.00 4.34
467 499 3.899726 AGTACATCCACATACGAGTCCT 58.100 45.455 0.00 0.00 0.00 3.85
474 506 8.542497 TGTGTTTAGAAAGTACATCCACATAC 57.458 34.615 0.00 0.00 0.00 2.39
562 613 8.602472 ATGAGGTAGAGAGATTTTGAGTACTT 57.398 34.615 0.00 0.00 0.00 2.24
735 808 6.540914 CGTGTCTCTAGAGAAACTTCTATCCT 59.459 42.308 31.34 0.00 42.25 3.24
737 810 7.184106 CACGTGTCTCTAGAGAAACTTCTATC 58.816 42.308 31.34 15.24 42.25 2.08
738 811 6.094325 CCACGTGTCTCTAGAGAAACTTCTAT 59.906 42.308 31.34 14.82 42.25 1.98
739 812 5.411977 CCACGTGTCTCTAGAGAAACTTCTA 59.588 44.000 31.34 5.58 42.25 2.10
740 813 4.216687 CCACGTGTCTCTAGAGAAACTTCT 59.783 45.833 31.34 16.51 42.25 2.85
741 814 4.023021 ACCACGTGTCTCTAGAGAAACTTC 60.023 45.833 31.34 17.67 42.25 3.01
772 1529 2.737252 AGCGATGTCCGACTTTTCTTTC 59.263 45.455 0.00 0.00 41.76 2.62
1123 1944 2.201771 GGGAGAGCGGATAGGGGT 59.798 66.667 0.00 0.00 0.00 4.95
1245 2098 1.863267 GAGGCTGTTCATCCGATCTG 58.137 55.000 0.00 0.00 0.00 2.90
1294 2147 5.125097 GTGGTTTTCCGTCTAGATACTCAGA 59.875 44.000 0.00 0.00 44.36 3.27
1315 2168 4.370917 CACAAAATCAAACCCAAGAGTGG 58.629 43.478 0.00 0.00 45.53 4.00
1318 2171 4.053295 CAGCACAAAATCAAACCCAAGAG 58.947 43.478 0.00 0.00 0.00 2.85
1319 2172 3.703556 TCAGCACAAAATCAAACCCAAGA 59.296 39.130 0.00 0.00 0.00 3.02
1321 2174 3.740764 GCTCAGCACAAAATCAAACCCAA 60.741 43.478 0.00 0.00 0.00 4.12
1366 2232 1.203052 CACCATCAAAGTGGCACATCC 59.797 52.381 21.41 0.00 44.52 3.51
1649 2631 4.956075 ACCATGGTTAGGCTAATGGAAAAG 59.044 41.667 25.01 9.30 41.84 2.27
1721 2706 4.832266 TGCATGTGAAGGTAAAGGAACATT 59.168 37.500 0.00 0.00 0.00 2.71
1747 2732 4.399483 TGGTACAGAGGGAGTAGAAGTT 57.601 45.455 0.00 0.00 0.00 2.66
1763 2751 6.040878 ACTTCAGCGACAACTATTATGGTAC 58.959 40.000 0.00 0.00 0.00 3.34
1764 2752 6.216801 ACTTCAGCGACAACTATTATGGTA 57.783 37.500 0.00 0.00 0.00 3.25
1765 2753 5.086104 ACTTCAGCGACAACTATTATGGT 57.914 39.130 0.00 0.00 0.00 3.55
1766 2754 5.580691 TGAACTTCAGCGACAACTATTATGG 59.419 40.000 0.00 0.00 0.00 2.74
1767 2755 6.647212 TGAACTTCAGCGACAACTATTATG 57.353 37.500 0.00 0.00 0.00 1.90
1768 2756 6.893958 CTGAACTTCAGCGACAACTATTAT 57.106 37.500 5.84 0.00 37.72 1.28
1825 2813 5.413833 CACTGAAACCAGCTTCATCATTACT 59.586 40.000 0.00 0.00 34.86 2.24
1960 2985 4.087182 ACACCTAAAGCAGCTACTCTGTA 58.913 43.478 0.00 0.00 44.66 2.74
2052 3079 4.051922 GCTAGGTCCACGAGATTAACATG 58.948 47.826 0.00 0.00 0.00 3.21
2128 3156 8.586273 CACAAATAAGAGTTCAAACAAACACAG 58.414 33.333 0.00 0.00 0.00 3.66
2287 3383 4.479158 TGAAACCATCCTTTACCAGCTTT 58.521 39.130 0.00 0.00 0.00 3.51
2446 3542 5.518487 CCAAATCACAGGTTACAACACAAAC 59.482 40.000 0.00 0.00 0.00 2.93
2730 3827 3.657835 CTTGCTCTTGGCGCGCTTC 62.658 63.158 32.29 16.28 45.43 3.86
2751 3848 1.126488 CATGCTTCCTCTCCCTGCTA 58.874 55.000 0.00 0.00 0.00 3.49
3081 7256 2.165641 GCCCTGTTTGCCAAATAGTACC 59.834 50.000 12.17 0.00 0.00 3.34
3657 7893 5.234757 TCAAAACTTCAAATGTCTTGCATGC 59.765 36.000 11.82 11.82 37.96 4.06
3702 7938 4.453478 TCAGAATGACTTGCAATCACAGAC 59.547 41.667 0.00 0.26 42.56 3.51
3753 7989 8.613060 ATGGCATATTATCTGACTTTACACTG 57.387 34.615 0.00 0.00 0.00 3.66
3759 7995 9.797642 TGTATCAATGGCATATTATCTGACTTT 57.202 29.630 0.00 0.00 0.00 2.66
3764 8000 8.652810 TCGATGTATCAATGGCATATTATCTG 57.347 34.615 0.00 0.00 0.00 2.90
3765 8001 9.269453 CATCGATGTATCAATGGCATATTATCT 57.731 33.333 17.50 0.00 0.00 1.98
3810 8108 2.664402 ACACTGGAAATGCTTCTGGT 57.336 45.000 0.00 0.00 0.00 4.00
3825 8123 8.424133 TGTGCATATATCTGACTTCAATACACT 58.576 33.333 0.00 0.00 0.00 3.55
3859 8157 9.252962 CACAGGAAATATGAATAAAATGCCTTC 57.747 33.333 0.00 0.00 0.00 3.46
3947 8245 8.429493 TCAAGATACATGTCATCTCATTTGAC 57.571 34.615 0.00 0.00 43.04 3.18
3948 8246 9.623000 AATCAAGATACATGTCATCTCATTTGA 57.377 29.630 0.00 9.88 31.45 2.69
4109 8412 3.850752 TCCTTTGGAGCCATTTGGTTTA 58.149 40.909 0.00 0.00 37.57 2.01
4129 8432 7.970614 AGCATAGAATTTTCGAAGGAAACATTC 59.029 33.333 0.00 1.84 41.66 2.67
4246 8549 1.871039 CTTCACACGTACCCAAACCTG 59.129 52.381 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.