Multiple sequence alignment - TraesCS3A01G163400

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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 TraesCS3A01G163400 chr3A 100.000 2883 0 0 1 2883 165842496 165845378 0.000000e+00 5325.0
1 TraesCS3A01G163400 chr3A 90.674 2284 183 15 1 2267 165818940 165821210 0.000000e+00 3011.0
2 TraesCS3A01G163400 chr3A 87.785 614 74 1 925 1537 534808261 534808874 0.000000e+00 717.0
3 TraesCS3A01G163400 chr3A 77.151 709 106 39 1 680 332142772 332142091 7.590000e-96 361.0
4 TraesCS3A01G163400 chr3A 89.764 254 24 2 728 981 226629696 226629445 9.960000e-85 324.0
5 TraesCS3A01G163400 chr3A 77.522 565 98 22 1589 2142 247683691 247684237 2.160000e-81 313.0
6 TraesCS3A01G163400 chr3A 75.983 712 110 41 1 680 332132928 332132246 7.760000e-81 311.0
7 TraesCS3A01G163400 chr3A 85.590 229 24 7 547 769 123815892 123816117 6.210000e-57 231.0
8 TraesCS3A01G163400 chr2A 91.802 1232 82 11 1053 2266 216321232 216322462 0.000000e+00 1698.0
9 TraesCS3A01G163400 chr2A 92.973 1110 76 2 1053 2161 216158391 216159499 0.000000e+00 1616.0
10 TraesCS3A01G163400 chr2A 92.765 622 41 4 2263 2883 306075526 306074908 0.000000e+00 896.0
11 TraesCS3A01G163400 chr2A 76.869 709 127 33 1589 2273 233615786 233615091 1.630000e-97 366.0
12 TraesCS3A01G163400 chr2A 78.608 589 99 24 1589 2162 233705577 233705001 5.870000e-97 364.0
13 TraesCS3A01G163400 chr6A 87.375 800 90 9 760 1550 370120149 370119352 0.000000e+00 907.0
14 TraesCS3A01G163400 chr6A 84.043 564 73 17 1 555 259824456 259823901 7.080000e-146 527.0
15 TraesCS3A01G163400 chr6A 90.947 243 22 0 739 981 259284664 259284422 7.700000e-86 327.0
16 TraesCS3A01G163400 chr6A 75.912 685 107 36 1570 2227 411633448 411634101 6.040000e-77 298.0
17 TraesCS3A01G163400 chr6A 86.066 122 14 2 560 680 65417173 65417292 8.380000e-26 128.0
18 TraesCS3A01G163400 chr2B 92.084 619 46 3 2267 2883 608260051 608260668 0.000000e+00 869.0
19 TraesCS3A01G163400 chr2D 91.814 623 48 3 2263 2883 559118562 559117941 0.000000e+00 865.0
20 TraesCS3A01G163400 chr2D 91.640 622 51 1 2263 2883 50565547 50564926 0.000000e+00 859.0
21 TraesCS3A01G163400 chr2D 78.732 757 88 42 1 697 505974353 505973610 3.410000e-119 438.0
22 TraesCS3A01G163400 chr2D 77.097 751 96 43 1 697 515675875 515675147 5.870000e-97 364.0
23 TraesCS3A01G163400 chr2D 76.431 751 101 45 1 697 515683698 515682970 1.280000e-88 337.0
24 TraesCS3A01G163400 chr2D 87.692 195 24 0 790 984 484556276 484556082 8.040000e-56 228.0
25 TraesCS3A01G163400 chr1D 91.801 622 50 1 2263 2883 419981195 419980574 0.000000e+00 865.0
26 TraesCS3A01G163400 chr1D 91.640 622 51 1 2263 2883 115997620 115996999 0.000000e+00 859.0
27 TraesCS3A01G163400 chr1D 87.741 571 55 14 4 564 208615212 208614647 0.000000e+00 652.0
28 TraesCS3A01G163400 chr1D 81.918 636 81 28 1650 2267 242606020 242605401 9.220000e-140 507.0
29 TraesCS3A01G163400 chr1D 84.564 149 21 2 833 979 455056525 455056377 2.310000e-31 147.0
30 TraesCS3A01G163400 chr4D 91.479 622 50 3 2263 2883 333077422 333078041 0.000000e+00 852.0
31 TraesCS3A01G163400 chr4D 91.318 622 53 1 2263 2883 422499212 422498591 0.000000e+00 848.0
32 TraesCS3A01G163400 chr4D 80.763 629 99 22 1649 2268 314700805 314701420 3.360000e-129 472.0
33 TraesCS3A01G163400 chr4D 87.179 195 25 0 790 984 103646364 103646170 3.740000e-54 222.0
34 TraesCS3A01G163400 chr4D 86.408 206 24 3 780 984 103654557 103654355 3.740000e-54 222.0
35 TraesCS3A01G163400 chr4D 86.667 195 26 0 790 984 114518671 114518477 1.740000e-52 217.0
36 TraesCS3A01G163400 chr4D 86.528 193 26 0 790 982 228644172 228643980 2.250000e-51 213.0
37 TraesCS3A01G163400 chr4D 82.822 163 23 5 821 979 232992726 232992565 1.080000e-29 141.0
38 TraesCS3A01G163400 chr4D 89.474 95 8 2 887 979 37162217 37162311 5.050000e-23 119.0
39 TraesCS3A01G163400 chr5D 91.200 625 53 2 2260 2883 100011521 100010898 0.000000e+00 848.0
40 TraesCS3A01G163400 chr5D 77.205 737 103 42 1 697 110315751 110316462 1.260000e-98 370.0
41 TraesCS3A01G163400 chr5D 88.050 159 15 2 543 697 421944528 421944686 4.910000e-43 185.0
42 TraesCS3A01G163400 chr5D 87.097 155 16 2 547 697 130547918 130548072 3.820000e-39 172.0
43 TraesCS3A01G163400 chr5D 90.400 125 12 0 573 697 79510729 79510605 6.390000e-37 165.0
44 TraesCS3A01G163400 chr5D 90.400 125 12 0 573 697 79518379 79518255 6.390000e-37 165.0
45 TraesCS3A01G163400 chr5D 86.755 151 16 3 551 697 130556345 130556495 6.390000e-37 165.0
46 TraesCS3A01G163400 chr5D 85.256 156 18 3 543 694 438250510 438250664 3.850000e-34 156.0
47 TraesCS3A01G163400 chr5D 90.099 101 10 0 580 680 237765231 237765331 6.480000e-27 132.0
48 TraesCS3A01G163400 chr4A 76.873 1388 244 62 925 2267 359960036 359961391 0.000000e+00 713.0
49 TraesCS3A01G163400 chr4A 82.960 581 72 9 925 1501 391105683 391105126 1.540000e-137 499.0
50 TraesCS3A01G163400 chr4A 82.069 580 76 13 925 1501 392815086 392815640 1.210000e-128 470.0
51 TraesCS3A01G163400 chr4A 88.068 176 19 2 522 697 226512553 226512726 1.050000e-49 207.0
52 TraesCS3A01G163400 chr7A 85.036 695 77 16 1 680 358339230 358339912 0.000000e+00 682.0
53 TraesCS3A01G163400 chr7A 85.000 80 10 2 1261 1339 481275413 481275491 2.380000e-11 80.5
54 TraesCS3A01G163400 chr7D 87.219 579 56 12 1 564 241480237 241479662 0.000000e+00 643.0
55 TraesCS3A01G163400 chr7D 87.928 555 53 12 1 544 148055625 148056176 2.420000e-180 641.0
56 TraesCS3A01G163400 chr7D 86.585 574 63 12 1 564 317737828 317738397 3.160000e-174 621.0
57 TraesCS3A01G163400 chr7D 83.148 629 81 20 1643 2258 547109443 547110059 4.200000e-153 551.0
58 TraesCS3A01G163400 chr7D 81.511 622 94 17 1657 2267 343666072 343666683 2.580000e-135 492.0
59 TraesCS3A01G163400 chr7D 82.308 520 74 16 1659 2169 343674302 343674812 4.410000e-118 435.0
60 TraesCS3A01G163400 chr7D 76.716 743 102 41 1 697 482360911 482361628 5.910000e-92 348.0
61 TraesCS3A01G163400 chr7D 89.308 159 13 3 543 697 492179677 492179519 2.270000e-46 196.0
62 TraesCS3A01G163400 chr3D 87.326 576 55 12 4 564 581952961 581952389 0.000000e+00 643.0
63 TraesCS3A01G163400 chr3D 88.214 543 48 8 1 536 259696219 259696752 4.050000e-178 634.0
64 TraesCS3A01G163400 chr3D 81.616 631 93 19 1649 2268 407239636 407239018 4.290000e-138 501.0
65 TraesCS3A01G163400 chr3D 76.735 735 110 39 4 697 411482097 411481383 1.270000e-93 353.0
66 TraesCS3A01G163400 chr3D 89.231 195 21 0 790 984 268766587 268766393 7.980000e-61 244.0
67 TraesCS3A01G163400 chr3D 87.745 204 22 2 780 982 268774298 268774097 4.800000e-58 235.0
68 TraesCS3A01G163400 chr3D 76.715 481 69 30 1 464 227804334 227804788 8.040000e-56 228.0
69 TraesCS3A01G163400 chr3D 88.679 159 14 3 543 697 460207428 460207586 1.050000e-44 191.0
70 TraesCS3A01G163400 chr3D 88.050 159 15 2 543 697 283364811 283364653 4.910000e-43 185.0
71 TraesCS3A01G163400 chr3D 86.792 159 17 1 543 697 170692362 170692204 1.060000e-39 174.0
72 TraesCS3A01G163400 chr1A 90.260 462 43 2 709 1169 141259578 141259118 1.140000e-168 603.0
73 TraesCS3A01G163400 chr1A 84.103 195 29 2 790 983 188566091 188565898 1.360000e-43 187.0
74 TraesCS3A01G163400 chr5A 83.628 623 77 20 1650 2258 347071198 347070587 1.940000e-156 562.0
75 TraesCS3A01G163400 chr5A 87.298 496 50 13 1650 2141 347065165 347064679 3.250000e-154 555.0
76 TraesCS3A01G163400 chr5A 76.923 520 75 33 209 697 183812551 183812046 1.330000e-63 254.0
77 TraesCS3A01G163400 chr5A 81.905 210 30 5 2062 2266 229099286 229099080 1.370000e-38 171.0
78 TraesCS3A01G163400 chr6D 80.811 641 92 25 1649 2271 125394548 125395175 9.350000e-130 473.0
79 TraesCS3A01G163400 chr6D 80.255 628 102 22 1649 2267 179555301 179555915 1.220000e-123 453.0
80 TraesCS3A01G163400 chr6D 86.979 192 25 0 790 981 143527502 143527311 1.740000e-52 217.0
81 TraesCS3A01G163400 chr7B 79.605 608 93 25 1679 2267 402964128 402963533 9.620000e-110 407.0
82 TraesCS3A01G163400 chr7B 77.385 650 94 38 1650 2267 277894191 277893563 1.280000e-88 337.0
83 TraesCS3A01G163400 chr7B 77.217 654 94 39 1648 2267 277878980 277878348 5.950000e-87 331.0
84 TraesCS3A01G163400 chr7B 78.976 371 55 13 1 357 378104789 378105150 6.210000e-57 231.0
85 TraesCS3A01G163400 chr3B 78.889 540 76 28 1755 2267 127351769 127352297 5.950000e-87 331.0
86 TraesCS3A01G163400 chr3B 75.993 604 72 44 2 563 279135047 279135619 7.980000e-61 244.0
87 TraesCS3A01G163400 chr3B 78.195 399 43 24 1 361 27724033 27724425 6.260000e-52 215.0
88 TraesCS3A01G163400 chr3B 83.402 241 20 13 1 223 518397305 518397067 3.770000e-49 206.0
89 TraesCS3A01G163400 chr3B 82.988 241 21 13 1 223 518836255 518836017 1.750000e-47 200.0
90 TraesCS3A01G163400 chr1B 82.114 246 27 11 1 231 456234922 456234679 8.150000e-46 195.0


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 TraesCS3A01G163400 chr3A 165842496 165845378 2882 False 5325 5325 100.000 1 2883 1 chr3A.!!$F3 2882
1 TraesCS3A01G163400 chr3A 165818940 165821210 2270 False 3011 3011 90.674 1 2267 1 chr3A.!!$F2 2266
2 TraesCS3A01G163400 chr3A 534808261 534808874 613 False 717 717 87.785 925 1537 1 chr3A.!!$F5 612
3 TraesCS3A01G163400 chr3A 332142091 332142772 681 True 361 361 77.151 1 680 1 chr3A.!!$R3 679
4 TraesCS3A01G163400 chr3A 247683691 247684237 546 False 313 313 77.522 1589 2142 1 chr3A.!!$F4 553
5 TraesCS3A01G163400 chr3A 332132246 332132928 682 True 311 311 75.983 1 680 1 chr3A.!!$R2 679
6 TraesCS3A01G163400 chr2A 216321232 216322462 1230 False 1698 1698 91.802 1053 2266 1 chr2A.!!$F2 1213
7 TraesCS3A01G163400 chr2A 216158391 216159499 1108 False 1616 1616 92.973 1053 2161 1 chr2A.!!$F1 1108
8 TraesCS3A01G163400 chr2A 306074908 306075526 618 True 896 896 92.765 2263 2883 1 chr2A.!!$R3 620
9 TraesCS3A01G163400 chr2A 233615091 233615786 695 True 366 366 76.869 1589 2273 1 chr2A.!!$R1 684
10 TraesCS3A01G163400 chr2A 233705001 233705577 576 True 364 364 78.608 1589 2162 1 chr2A.!!$R2 573
11 TraesCS3A01G163400 chr6A 370119352 370120149 797 True 907 907 87.375 760 1550 1 chr6A.!!$R3 790
12 TraesCS3A01G163400 chr6A 259823901 259824456 555 True 527 527 84.043 1 555 1 chr6A.!!$R2 554
13 TraesCS3A01G163400 chr6A 411633448 411634101 653 False 298 298 75.912 1570 2227 1 chr6A.!!$F2 657
14 TraesCS3A01G163400 chr2B 608260051 608260668 617 False 869 869 92.084 2267 2883 1 chr2B.!!$F1 616
15 TraesCS3A01G163400 chr2D 559117941 559118562 621 True 865 865 91.814 2263 2883 1 chr2D.!!$R6 620
16 TraesCS3A01G163400 chr2D 50564926 50565547 621 True 859 859 91.640 2263 2883 1 chr2D.!!$R1 620
17 TraesCS3A01G163400 chr2D 505973610 505974353 743 True 438 438 78.732 1 697 1 chr2D.!!$R3 696
18 TraesCS3A01G163400 chr2D 515675147 515675875 728 True 364 364 77.097 1 697 1 chr2D.!!$R4 696
19 TraesCS3A01G163400 chr2D 515682970 515683698 728 True 337 337 76.431 1 697 1 chr2D.!!$R5 696
20 TraesCS3A01G163400 chr1D 419980574 419981195 621 True 865 865 91.801 2263 2883 1 chr1D.!!$R4 620
21 TraesCS3A01G163400 chr1D 115996999 115997620 621 True 859 859 91.640 2263 2883 1 chr1D.!!$R1 620
22 TraesCS3A01G163400 chr1D 208614647 208615212 565 True 652 652 87.741 4 564 1 chr1D.!!$R2 560
23 TraesCS3A01G163400 chr1D 242605401 242606020 619 True 507 507 81.918 1650 2267 1 chr1D.!!$R3 617
24 TraesCS3A01G163400 chr4D 333077422 333078041 619 False 852 852 91.479 2263 2883 1 chr4D.!!$F3 620
25 TraesCS3A01G163400 chr4D 422498591 422499212 621 True 848 848 91.318 2263 2883 1 chr4D.!!$R6 620
26 TraesCS3A01G163400 chr4D 314700805 314701420 615 False 472 472 80.763 1649 2268 1 chr4D.!!$F2 619
27 TraesCS3A01G163400 chr5D 100010898 100011521 623 True 848 848 91.200 2260 2883 1 chr5D.!!$R3 623
28 TraesCS3A01G163400 chr5D 110315751 110316462 711 False 370 370 77.205 1 697 1 chr5D.!!$F1 696
29 TraesCS3A01G163400 chr4A 359960036 359961391 1355 False 713 713 76.873 925 2267 1 chr4A.!!$F2 1342
30 TraesCS3A01G163400 chr4A 391105126 391105683 557 True 499 499 82.960 925 1501 1 chr4A.!!$R1 576
31 TraesCS3A01G163400 chr4A 392815086 392815640 554 False 470 470 82.069 925 1501 1 chr4A.!!$F3 576
32 TraesCS3A01G163400 chr7A 358339230 358339912 682 False 682 682 85.036 1 680 1 chr7A.!!$F1 679
33 TraesCS3A01G163400 chr7D 241479662 241480237 575 True 643 643 87.219 1 564 1 chr7D.!!$R1 563
34 TraesCS3A01G163400 chr7D 148055625 148056176 551 False 641 641 87.928 1 544 1 chr7D.!!$F1 543
35 TraesCS3A01G163400 chr7D 317737828 317738397 569 False 621 621 86.585 1 564 1 chr7D.!!$F2 563
36 TraesCS3A01G163400 chr7D 547109443 547110059 616 False 551 551 83.148 1643 2258 1 chr7D.!!$F6 615
37 TraesCS3A01G163400 chr7D 343666072 343666683 611 False 492 492 81.511 1657 2267 1 chr7D.!!$F3 610
38 TraesCS3A01G163400 chr7D 343674302 343674812 510 False 435 435 82.308 1659 2169 1 chr7D.!!$F4 510
39 TraesCS3A01G163400 chr7D 482360911 482361628 717 False 348 348 76.716 1 697 1 chr7D.!!$F5 696
40 TraesCS3A01G163400 chr3D 581952389 581952961 572 True 643 643 87.326 4 564 1 chr3D.!!$R7 560
41 TraesCS3A01G163400 chr3D 259696219 259696752 533 False 634 634 88.214 1 536 1 chr3D.!!$F2 535
42 TraesCS3A01G163400 chr3D 407239018 407239636 618 True 501 501 81.616 1649 2268 1 chr3D.!!$R5 619
43 TraesCS3A01G163400 chr3D 411481383 411482097 714 True 353 353 76.735 4 697 1 chr3D.!!$R6 693
44 TraesCS3A01G163400 chr5A 347070587 347071198 611 True 562 562 83.628 1650 2258 1 chr5A.!!$R4 608
45 TraesCS3A01G163400 chr5A 183812046 183812551 505 True 254 254 76.923 209 697 1 chr5A.!!$R1 488
46 TraesCS3A01G163400 chr6D 125394548 125395175 627 False 473 473 80.811 1649 2271 1 chr6D.!!$F1 622
47 TraesCS3A01G163400 chr6D 179555301 179555915 614 False 453 453 80.255 1649 2267 1 chr6D.!!$F2 618
48 TraesCS3A01G163400 chr7B 402963533 402964128 595 True 407 407 79.605 1679 2267 1 chr7B.!!$R3 588
49 TraesCS3A01G163400 chr7B 277893563 277894191 628 True 337 337 77.385 1650 2267 1 chr7B.!!$R2 617
50 TraesCS3A01G163400 chr7B 277878348 277878980 632 True 331 331 77.217 1648 2267 1 chr7B.!!$R1 619
51 TraesCS3A01G163400 chr3B 127351769 127352297 528 False 331 331 78.889 1755 2267 1 chr3B.!!$F2 512
52 TraesCS3A01G163400 chr3B 279135047 279135619 572 False 244 244 75.993 2 563 1 chr3B.!!$F3 561

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
433 529 1.225855 TGCATTCGTTCACTGGTCAC 58.774 50.0 0.0 0.0 0.00 3.67 F
1007 1202 0.319211 CACCACAACAGCATGGCAAG 60.319 55.0 0.0 0.0 43.62 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1767 0.338814 ACCTAACCCTCACCCGATCT 59.661 55.0 0.0 0.0 0.0 2.75 R
2478 2816 0.606401 ACGGTTCTGAATGTGGCAGG 60.606 55.0 0.0 0.0 34.2 4.85 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
87 101 9.495754 TTTAATGCAAACACAATTTTTAAGCAC 57.504 25.926 0.00 0.00 31.79 4.40
343 424 2.000701 TTCCCATGGGTCGATGGCT 61.001 57.895 30.28 0.00 41.59 4.75
433 529 1.225855 TGCATTCGTTCACTGGTCAC 58.774 50.000 0.00 0.00 0.00 3.67
650 845 3.428870 CGTTCATAGTCGCACAAGTTTCT 59.571 43.478 0.00 0.00 0.00 2.52
669 864 1.548719 CTGTAGATGTTCGGGGTCACA 59.451 52.381 0.00 0.00 0.00 3.58
697 892 2.816083 CGGCATTTCGGTGCGGTA 60.816 61.111 7.42 0.00 45.97 4.02
714 909 1.535437 GGTACTTGCCATCGGTAGTCG 60.535 57.143 0.00 0.00 40.90 4.18
774 969 2.579207 ATCATACACGGGTCTTGTCG 57.421 50.000 0.00 0.00 0.00 4.35
784 979 2.317040 GGGTCTTGTCGGATCCATAGA 58.683 52.381 13.41 5.34 36.55 1.98
828 1023 3.209410 GGACTTGGCGATCTTGATGAAT 58.791 45.455 0.00 0.00 0.00 2.57
840 1035 6.566187 CGATCTTGATGAATTGAAGGAGCATC 60.566 42.308 0.00 0.00 36.71 3.91
842 1037 2.615447 TGATGAATTGAAGGAGCATCGC 59.385 45.455 0.00 0.00 38.48 4.58
1007 1202 0.319211 CACCACAACAGCATGGCAAG 60.319 55.000 0.00 0.00 43.62 4.01
1019 1214 4.664062 GGCAAGGAGGCAATGCTA 57.336 55.556 4.82 0.00 43.51 3.49
1103 1298 2.846532 CTGGGCTTGGGGAGTTGT 59.153 61.111 0.00 0.00 0.00 3.32
1120 1315 2.084610 TGTCGAACTTGCTGGATCTG 57.915 50.000 0.00 0.00 0.00 2.90
1131 1326 2.122989 GGATCTGGCGGGGTCCTA 60.123 66.667 10.32 0.00 0.00 2.94
1214 1410 2.118076 CCAAGGAAGCAGGGCCAA 59.882 61.111 6.18 0.00 0.00 4.52
1242 1438 3.005539 ACATGGCAGCGAGGAGGT 61.006 61.111 0.00 0.00 0.00 3.85
1250 1446 2.279408 GCGAGGAGGTAGAGGGGT 59.721 66.667 0.00 0.00 0.00 4.95
1252 1448 1.306970 CGAGGAGGTAGAGGGGTGT 59.693 63.158 0.00 0.00 0.00 4.16
1258 1454 3.066814 GTAGAGGGGTGTCGGCGT 61.067 66.667 6.85 0.00 0.00 5.68
1259 1455 2.283388 TAGAGGGGTGTCGGCGTT 60.283 61.111 6.85 0.00 0.00 4.84
1350 1548 2.825836 CCATGGCAAGGTCGAGGC 60.826 66.667 0.00 0.00 0.00 4.70
1371 1569 3.399181 GGAGGTCGGACATGGGCA 61.399 66.667 10.76 0.00 0.00 5.36
1397 1598 2.027192 GCCACTGTAGATGACCCTTTCA 60.027 50.000 0.00 0.00 39.11 2.69
1561 1767 0.854218 AGCGAGGGAGATAAGGAGGA 59.146 55.000 0.00 0.00 0.00 3.71
1996 2288 4.943093 GGCATTGGGATTTATTTGCAAGTT 59.057 37.500 0.00 0.00 0.00 2.66
2170 2499 3.786516 AATGACATGATGCGATGCAAA 57.213 38.095 0.00 0.00 43.62 3.68
2259 2595 4.021925 GAGCGCTGGTCTTGGGGT 62.022 66.667 18.48 0.00 0.00 4.95
2281 2617 7.275920 GGGTGTCACAAGAGTCAATAATCTAT 58.724 38.462 5.12 0.00 0.00 1.98
2310 2646 7.701924 CACATCACCATATGATTTAACACCAAC 59.298 37.037 3.65 0.00 46.54 3.77
2434 2770 9.672673 ATGTGATTAACAAGCAAAGAGTACTAT 57.327 29.630 0.00 0.00 43.61 2.12
2446 2782 7.069950 AGCAAAGAGTACTATGGTGTGATCATA 59.930 37.037 0.00 0.00 0.00 2.15
2458 2795 4.563976 GGTGTGATCATATTTTGCTTGTGC 59.436 41.667 0.00 0.00 40.20 4.57
2478 2816 2.280628 CGAGAGGTTTAGTCAATGGGC 58.719 52.381 0.00 0.00 0.00 5.36
2599 2937 9.237187 GTATCCAGATTGAGATACTGAGTCATA 57.763 37.037 0.00 0.00 41.01 2.15
2621 2960 1.802960 AGATCAGTGTCAAAGCTTGCG 59.197 47.619 0.00 0.00 0.00 4.85
2640 2979 1.585214 CGTCGATGTAACCCTTTACGC 59.415 52.381 0.00 0.00 40.61 4.42
2767 3107 1.080638 ACCCCCTTGCCAAACTCATA 58.919 50.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 101 7.463544 TCTGCATCGTGATAACAACATTTAAG 58.536 34.615 0.00 0.00 0.00 1.85
104 127 6.775939 AACTTGTATATGTCATCTGCATCG 57.224 37.500 0.00 0.00 0.00 3.84
291 368 1.379044 CACCCCACCATCTCTTGCC 60.379 63.158 0.00 0.00 0.00 4.52
343 424 2.011222 GTTGTTCCCTCGTTTGACACA 58.989 47.619 0.00 0.00 0.00 3.72
433 529 0.966920 AGGTATAACCGCCGAGATGG 59.033 55.000 0.00 0.00 44.90 3.51
484 583 4.380550 CGTCTACTTCCTCTACATTGCACA 60.381 45.833 0.00 0.00 0.00 4.57
650 845 1.634960 TGTGACCCCGAACATCTACA 58.365 50.000 0.00 0.00 0.00 2.74
697 892 2.575108 TCGACTACCGATGGCAAGT 58.425 52.632 0.00 0.00 43.23 3.16
714 909 1.376037 CCTCCGGACTGCCAAGTTC 60.376 63.158 0.00 0.00 36.52 3.01
722 917 1.305887 AAGTACCCCCTCCGGACTG 60.306 63.158 0.00 0.00 0.00 3.51
758 953 1.407979 GATCCGACAAGACCCGTGTAT 59.592 52.381 0.00 0.00 0.00 2.29
774 969 2.599677 AGTTCCCGTCTCTATGGATCC 58.400 52.381 4.20 4.20 33.01 3.36
784 979 3.254024 ATGCGCCAAGTTCCCGTCT 62.254 57.895 4.18 0.00 0.00 4.18
828 1023 2.125147 CCCGCGATGCTCCTTCAA 60.125 61.111 8.23 0.00 0.00 2.69
883 1078 4.074526 GCTCGAGCTGCCTCCACA 62.075 66.667 29.88 0.00 38.21 4.17
902 1097 2.563798 CCATGCGCCAACAACCAGT 61.564 57.895 4.18 0.00 0.00 4.00
995 1190 2.362120 GCCTCCTTGCCATGCTGT 60.362 61.111 0.00 0.00 0.00 4.40
1007 1202 1.227674 CCCGAGTAGCATTGCCTCC 60.228 63.158 4.70 0.00 0.00 4.30
1100 1295 2.416747 CAGATCCAGCAAGTTCGACAA 58.583 47.619 0.00 0.00 0.00 3.18
1103 1298 0.391661 GCCAGATCCAGCAAGTTCGA 60.392 55.000 0.00 0.00 0.00 3.71
1131 1326 2.883828 CGTCACCTCAAGCCCCACT 61.884 63.158 0.00 0.00 0.00 4.00
1183 1378 1.817099 CTTGGCTGCCCTGTCGATC 60.817 63.158 17.53 0.00 0.00 3.69
1188 1383 2.437897 CTTCCTTGGCTGCCCTGT 59.562 61.111 17.53 0.00 0.00 4.00
1242 1438 2.283388 AACGCCGACACCCCTCTA 60.283 61.111 0.00 0.00 0.00 2.43
1250 1446 2.915659 ACCTCCTCAACGCCGACA 60.916 61.111 0.00 0.00 0.00 4.35
1252 1448 3.744719 CGACCTCCTCAACGCCGA 61.745 66.667 0.00 0.00 0.00 5.54
1258 1454 3.379445 GTCGCCCGACCTCCTCAA 61.379 66.667 9.53 0.00 39.08 3.02
1350 1548 4.873129 CATGTCCGACCTCCGCCG 62.873 72.222 0.00 0.00 36.84 6.46
1371 1569 1.305802 TCATCTACAGTGGCCCGGT 60.306 57.895 0.00 0.74 0.00 5.28
1397 1598 4.517934 TAGCCTCCTACGCCGCCT 62.518 66.667 0.00 0.00 0.00 5.52
1561 1767 0.338814 ACCTAACCCTCACCCGATCT 59.661 55.000 0.00 0.00 0.00 2.75
1656 1919 6.605119 AGAAATAAGAGAGAGGGAGAGAGAG 58.395 44.000 0.00 0.00 0.00 3.20
1996 2288 6.968263 TTGATGTGGAATTACCTTTGACAA 57.032 33.333 0.00 0.00 39.86 3.18
2185 2514 6.201997 GTGTGACTTGTTTGTTTGTTCCTTTT 59.798 34.615 0.00 0.00 0.00 2.27
2259 2595 9.942850 TGAAATAGATTATTGACTCTTGTGACA 57.057 29.630 0.00 0.00 0.00 3.58
2281 2617 8.465999 GGTGTTAAATCATATGGTGATGTGAAA 58.534 33.333 2.13 0.00 46.80 2.69
2295 2631 6.707440 TGTGAACTGTTGGTGTTAAATCAT 57.293 33.333 0.00 0.00 0.00 2.45
2333 2669 1.693083 GCGATGTGAACTACGGGTGC 61.693 60.000 0.00 0.00 0.00 5.01
2421 2757 5.419542 TGATCACACCATAGTACTCTTTGC 58.580 41.667 0.00 0.00 0.00 3.68
2434 2770 5.712004 CACAAGCAAAATATGATCACACCA 58.288 37.500 0.00 0.00 0.00 4.17
2446 2782 1.609208 ACCTCTCGCACAAGCAAAAT 58.391 45.000 0.00 0.00 42.27 1.82
2458 2795 2.280628 GCCCATTGACTAAACCTCTCG 58.719 52.381 0.00 0.00 0.00 4.04
2478 2816 0.606401 ACGGTTCTGAATGTGGCAGG 60.606 55.000 0.00 0.00 34.20 4.85
2599 2937 2.551459 GCAAGCTTTGACACTGATCTGT 59.449 45.455 0.00 0.00 0.00 3.41
2621 2960 1.929169 GGCGTAAAGGGTTACATCGAC 59.071 52.381 0.00 0.00 39.78 4.20
2640 2979 2.930950 TGGAGGTGACAAAGAGTTTGG 58.069 47.619 4.52 0.00 44.81 3.28
2714 3054 3.360867 CAGGAGTAGATCACTGGACAGT 58.639 50.000 0.00 0.00 43.61 3.55
2767 3107 5.137551 ACCAAACTTATTGTGTACCTTGCT 58.862 37.500 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.