Multiple sequence alignment - TraesCS2B01G600200

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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 TraesCS2B01G600200 chr2B 100.000 5827 0 0 1 5827 783231963 783226137 0.000000e+00 10761.0
1 TraesCS2B01G600200 chr2B 93.936 1946 82 23 515 2438 782538367 782536436 0.000000e+00 2907.0
2 TraesCS2B01G600200 chr2B 93.474 1946 89 23 515 2438 782688826 782686897 0.000000e+00 2856.0
3 TraesCS2B01G600200 chr2B 97.257 1422 29 5 1129 2541 782962119 782960699 0.000000e+00 2401.0
4 TraesCS2B01G600200 chr2B 97.115 1421 31 5 1130 2541 782836996 782835577 0.000000e+00 2388.0
5 TraesCS2B01G600200 chr2B 95.638 1490 38 11 2538 4021 782835455 782833987 0.000000e+00 2366.0
6 TraesCS2B01G600200 chr2B 93.808 1389 62 6 2434 3815 782536392 782535021 0.000000e+00 2067.0
7 TraesCS2B01G600200 chr2B 95.731 1265 36 6 2538 3802 782960577 782959331 0.000000e+00 2021.0
8 TraesCS2B01G600200 chr2B 93.165 1390 70 10 2434 3815 782686853 782685481 0.000000e+00 2017.0
9 TraesCS2B01G600200 chr2B 87.563 1391 57 33 3978 5309 782959016 782957683 0.000000e+00 1504.0
10 TraesCS2B01G600200 chr2B 90.571 1156 59 16 1 1132 782847675 782846546 0.000000e+00 1485.0
11 TraesCS2B01G600200 chr2B 90.406 1157 60 16 1 1132 782972140 782971010 0.000000e+00 1474.0
12 TraesCS2B01G600200 chr2B 87.203 1391 58 34 3978 5309 782833979 782832650 0.000000e+00 1472.0
13 TraesCS2B01G600200 chr2B 89.387 848 48 15 1 825 782987109 782986281 0.000000e+00 1029.0
14 TraesCS2B01G600200 chr2B 89.083 687 45 5 4478 5134 782684963 782684277 0.000000e+00 826.0
15 TraesCS2B01G600200 chr2B 88.792 687 47 12 4478 5134 782534502 782533816 0.000000e+00 815.0
16 TraesCS2B01G600200 chr2B 83.770 764 66 22 4403 5135 782531210 782530474 0.000000e+00 671.0
17 TraesCS2B01G600200 chr2B 83.355 763 70 19 4403 5135 782681662 782680927 0.000000e+00 652.0
18 TraesCS2B01G600200 chr2B 88.553 463 31 9 3956 4404 782685410 782684956 5.140000e-150 542.0
19 TraesCS2B01G600200 chr2B 87.931 464 33 10 3956 4404 782534950 782534495 5.170000e-145 525.0
20 TraesCS2B01G600200 chr2B 95.876 194 3 3 3833 4021 782959217 782959024 5.670000e-80 309.0
21 TraesCS2B01G600200 chr2B 78.079 479 74 15 1 461 782689916 782689451 2.070000e-69 274.0
22 TraesCS2B01G600200 chr2B 78.125 480 70 19 1 461 782539458 782538995 7.440000e-69 272.0
23 TraesCS2B01G600200 chr2B 80.370 270 42 6 251 509 683268568 683268837 1.660000e-45 195.0
24 TraesCS2B01G600200 chr2B 87.059 170 21 1 4182 4350 782682104 782681935 2.140000e-44 191.0
25 TraesCS2B01G600200 chr2B 86.471 170 22 1 4182 4350 782531652 782531483 9.970000e-43 185.0
26 TraesCS2B01G600200 chr2B 91.228 114 7 3 5311 5422 782832620 782832508 1.010000e-32 152.0
27 TraesCS2B01G600200 chr2B 91.228 114 7 3 5311 5422 782957653 782957541 1.010000e-32 152.0
28 TraesCS2B01G600200 chr2B 84.286 140 22 0 374 513 691264902 691265041 2.830000e-28 137.0
29 TraesCS2B01G600200 chr2B 95.161 62 3 0 3843 3904 782535017 782534956 1.340000e-16 99.0
30 TraesCS2B01G600200 chr2B 95.161 62 3 0 3843 3904 782685477 782685416 1.340000e-16 99.0
31 TraesCS2B01G600200 chr2D 91.540 2376 117 24 2452 4784 648240918 648238584 0.000000e+00 3197.0
32 TraesCS2B01G600200 chr2D 90.168 1546 114 17 1 1524 648243711 648242182 0.000000e+00 1978.0
33 TraesCS2B01G600200 chr2D 85.169 890 81 26 4979 5827 648238584 648237705 0.000000e+00 865.0
34 TraesCS2B01G600200 chr2D 87.892 669 55 11 1703 2366 648241570 648240923 0.000000e+00 763.0
35 TraesCS2B01G600200 chr2D 86.188 362 42 7 5465 5819 598722448 598722808 9.160000e-103 385.0
36 TraesCS2B01G600200 chr2D 83.469 369 51 6 5468 5826 309090783 309090415 9.360000e-88 335.0
37 TraesCS2B01G600200 chr2D 91.946 149 7 2 1524 1668 648242105 648241958 2.750000e-48 204.0
38 TraesCS2B01G600200 chrUn 84.845 2481 227 68 2433 4869 31206695 31209070 0.000000e+00 2361.0
39 TraesCS2B01G600200 chrUn 88.099 1126 91 22 251 1353 31203930 31205035 0.000000e+00 1297.0
40 TraesCS2B01G600200 chrUn 91.712 736 55 2 1700 2435 31205899 31206628 0.000000e+00 1016.0
41 TraesCS2B01G600200 chrUn 91.429 455 22 7 3318 3772 476027389 476027826 4.990000e-170 608.0
42 TraesCS2B01G600200 chrUn 97.041 169 5 0 1356 1524 31205158 31205326 9.560000e-73 285.0
43 TraesCS2B01G600200 chrUn 91.096 146 11 2 1524 1668 31205401 31205545 4.610000e-46 196.0
44 TraesCS2B01G600200 chr5B 86.193 1253 129 25 2566 3814 593211126 593209914 0.000000e+00 1315.0
45 TraesCS2B01G600200 chr5B 84.511 736 105 5 1703 2438 593211991 593211265 0.000000e+00 719.0
46 TraesCS2B01G600200 chr5B 84.976 619 55 13 4548 5147 593233148 593232549 1.400000e-165 593.0
47 TraesCS2B01G600200 chr5B 79.401 568 80 22 975 1522 593213155 593212605 3.320000e-97 366.0
48 TraesCS2B01G600200 chr5B 83.333 342 39 4 4737 5061 593216768 593216428 3.410000e-77 300.0
49 TraesCS2B01G600200 chr5B 78.936 451 67 14 4425 4873 593209183 593208759 1.240000e-71 281.0
50 TraesCS2B01G600200 chr5B 77.465 497 85 20 36 512 577359648 577360137 7.440000e-69 272.0
51 TraesCS2B01G600200 chr5B 79.557 406 54 22 3923 4320 593209839 593209455 4.480000e-66 263.0
52 TraesCS2B01G600200 chr5D 84.169 379 51 7 5457 5826 417598399 417598021 5.550000e-95 359.0
53 TraesCS2B01G600200 chr6A 83.651 367 52 6 5468 5826 147155349 147155715 7.230000e-89 339.0
54 TraesCS2B01G600200 chr6A 77.987 477 79 15 37 495 6997343 6996875 5.750000e-70 276.0
55 TraesCS2B01G600200 chr2A 83.113 379 50 12 5447 5815 601673859 601674233 3.370000e-87 333.0
56 TraesCS2B01G600200 chr3A 83.333 366 53 7 5468 5826 523306038 523305674 1.210000e-86 331.0
57 TraesCS2B01G600200 chr3A 90.566 53 5 0 5160 5212 647185887 647185939 2.910000e-08 71.3
58 TraesCS2B01G600200 chr1D 83.106 367 53 7 5468 5826 132873104 132873469 5.630000e-85 326.0
59 TraesCS2B01G600200 chr1D 77.673 318 58 9 208 512 314058783 314059100 1.290000e-41 182.0
60 TraesCS2B01G600200 chr1B 83.060 366 54 6 5468 5826 505096109 505095745 5.630000e-85 326.0
61 TraesCS2B01G600200 chr6D 78.411 491 79 16 37 508 320111068 320111550 1.590000e-75 294.0
62 TraesCS2B01G600200 chr6D 77.104 511 80 22 37 512 103205820 103205312 1.610000e-65 261.0
63 TraesCS2B01G600200 chr6D 93.478 46 2 1 5172 5216 17134723 17134678 3.770000e-07 67.6
64 TraesCS2B01G600200 chr4A 77.847 483 89 10 38 505 536775362 536775841 3.440000e-72 283.0
65 TraesCS2B01G600200 chr4A 77.273 132 27 3 210 339 706430724 706430854 2.250000e-09 75.0
66 TraesCS2B01G600200 chr7A 77.339 481 85 14 37 496 641971435 641971912 4.480000e-66 263.0
67 TraesCS2B01G600200 chr3B 75.403 496 93 15 36 513 1337342 1336858 4.570000e-51 213.0
68 TraesCS2B01G600200 chr4B 76.000 325 65 9 201 513 294139846 294139523 7.820000e-34 156.0
69 TraesCS2B01G600200 chr7B 96.078 51 1 1 5165 5215 552775277 552775326 1.350000e-11 82.4
70 TraesCS2B01G600200 chr7B 90.909 55 4 1 5160 5214 552789831 552789884 8.100000e-09 73.1
71 TraesCS2B01G600200 chr7D 96.000 50 1 1 5163 5212 506139846 506139798 4.840000e-11 80.5
72 TraesCS2B01G600200 chr7D 90.909 55 4 1 5160 5214 519676521 519676574 8.100000e-09 73.1


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 TraesCS2B01G600200 chr2B 783226137 783231963 5826 True 10761.000000 10761 100.000000 1 5827 1 chr2B.!!$R4 5826
1 TraesCS2B01G600200 chr2B 782832508 782836996 4488 True 1594.500000 2388 92.796000 1130 5422 4 chr2B.!!$R7 4292
2 TraesCS2B01G600200 chr2B 782846546 782847675 1129 True 1485.000000 1485 90.571000 1 1132 1 chr2B.!!$R1 1131
3 TraesCS2B01G600200 chr2B 782971010 782972140 1130 True 1474.000000 1474 90.406000 1 1132 1 chr2B.!!$R2 1131
4 TraesCS2B01G600200 chr2B 782957541 782962119 4578 True 1277.400000 2401 93.531000 1129 5422 5 chr2B.!!$R8 4293
5 TraesCS2B01G600200 chr2B 782986281 782987109 828 True 1029.000000 1029 89.387000 1 825 1 chr2B.!!$R3 824
6 TraesCS2B01G600200 chr2B 782530474 782539458 8984 True 942.625000 2907 88.499250 1 5135 8 chr2B.!!$R5 5134
7 TraesCS2B01G600200 chr2B 782680927 782689916 8989 True 932.125000 2856 88.491125 1 5135 8 chr2B.!!$R6 5134
8 TraesCS2B01G600200 chr2D 648237705 648243711 6006 True 1401.400000 3197 89.343000 1 5827 5 chr2D.!!$R2 5826
9 TraesCS2B01G600200 chrUn 31203930 31209070 5140 False 1031.000000 2361 90.558600 251 4869 5 chrUn.!!$F2 4618
10 TraesCS2B01G600200 chr5B 593232549 593233148 599 True 593.000000 593 84.976000 4548 5147 1 chr5B.!!$R1 599
11 TraesCS2B01G600200 chr5B 593208759 593216768 8009 True 540.666667 1315 81.988500 975 5061 6 chr5B.!!$R2 4086
12 TraesCS2B01G600200 chr6D 103205312 103205820 508 True 261.000000 261 77.104000 37 512 1 chr6D.!!$R2 475

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
894 1543 1.133181 TTCTCATCCCACCACCAGCA 61.133 55.000 0.0 0.0 0.00 4.41 F
1269 3906 2.431683 GGTGCCTCCACTTCAGCA 59.568 61.111 0.0 0.0 41.75 4.41 F
1892 5154 4.929479 TGGGCATGAAAGTGTATAGGTTT 58.071 39.130 0.0 0.0 0.00 3.27 F
3123 6588 1.418334 ACCCCTTCTCCATGAGATCG 58.582 55.000 0.0 0.0 38.56 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 5092 3.209410 CATCCTCCTGTCAGCCATAAAC 58.791 50.000 0.0 0.0 0.00 2.01 R
3123 6588 1.198178 GGTAGACGATCTCCGATCAGC 59.802 57.143 4.9 0.0 41.76 4.26 R
3814 7397 0.871057 CACACACACACACACACACA 59.129 50.000 0.0 0.0 0.00 3.72 R
4994 8960 0.035458 GCAGCATAGGTAAGCCCGAT 59.965 55.000 0.0 0.0 38.74 4.18 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
110 113 6.101997 CCACATTAAAAAGAAAGCCCATCTC 58.898 40.000 0.00 0.00 0.00 2.75
124 127 1.495878 CATCTCCTGCATAGCACGAC 58.504 55.000 0.00 0.00 33.79 4.34
160 163 4.737765 CACGTCCAACACAACCAAAAATAG 59.262 41.667 0.00 0.00 0.00 1.73
193 219 9.227777 GTTCTACAACAGTAATAAAAGGTCCAT 57.772 33.333 0.00 0.00 32.14 3.41
218 245 2.071372 AGGTGGGTAGATCCTATCCGA 58.929 52.381 0.00 0.00 36.25 4.55
363 392 5.606505 TCGCTTACATGCATGAATAACCTA 58.393 37.500 32.75 10.14 0.00 3.08
364 393 6.052360 TCGCTTACATGCATGAATAACCTAA 58.948 36.000 32.75 16.71 0.00 2.69
372 417 8.965819 ACATGCATGAATAACCTAACACATTTA 58.034 29.630 32.75 0.00 0.00 1.40
572 1204 6.388435 AAGATAAGAAGGATTTCAGCATGC 57.612 37.500 10.51 10.51 35.70 4.06
635 1267 7.867909 AGTTTGGCAATTTCTCTTTAACTTAGC 59.132 33.333 0.00 0.00 0.00 3.09
717 1351 8.880878 TCTCTTTAATATGTACAAAGCGCATA 57.119 30.769 11.47 0.00 30.91 3.14
894 1543 1.133181 TTCTCATCCCACCACCAGCA 61.133 55.000 0.00 0.00 0.00 4.41
1269 3906 2.431683 GGTGCCTCCACTTCAGCA 59.568 61.111 0.00 0.00 41.75 4.41
1565 4432 5.330271 ACTCATATTATTCTTTCGTGCGC 57.670 39.130 0.00 0.00 0.00 6.09
1830 5092 7.632721 TGTTGTCATCATTATTCATGTCATCG 58.367 34.615 0.00 0.00 34.06 3.84
1892 5154 4.929479 TGGGCATGAAAGTGTATAGGTTT 58.071 39.130 0.00 0.00 0.00 3.27
3123 6588 1.418334 ACCCCTTCTCCATGAGATCG 58.582 55.000 0.00 0.00 38.56 3.69
3146 6611 2.228059 GATCGGAGATCGTCTACCCAA 58.772 52.381 0.00 0.00 45.12 4.12
3237 6702 6.196918 TCCAGATTCTCCAAGCATATTGAT 57.803 37.500 0.00 0.00 0.00 2.57
3258 6723 5.462068 TGATATTTCATCAGACTTTACGCCG 59.538 40.000 0.00 0.00 0.00 6.46
3566 7037 6.485648 TCAGCCAGGACTTTAGTTAAACTTTC 59.514 38.462 0.00 0.00 0.00 2.62
3606 7078 7.226441 AGTGGCATAGACATGATAATGCTTTA 58.774 34.615 21.37 11.53 43.33 1.85
3634 7106 9.762933 TTCTGCAATAAAGCTTAAACAAATCTT 57.237 25.926 0.00 0.00 34.99 2.40
3635 7107 9.762933 TCTGCAATAAAGCTTAAACAAATCTTT 57.237 25.926 0.00 0.00 37.33 2.52
3814 7397 6.395629 GGTAAGTAGTGATATGTGTGTGTGT 58.604 40.000 0.00 0.00 0.00 3.72
3816 7399 5.468540 AGTAGTGATATGTGTGTGTGTGT 57.531 39.130 0.00 0.00 0.00 3.72
3818 7401 4.071961 AGTGATATGTGTGTGTGTGTGT 57.928 40.909 0.00 0.00 0.00 3.72
3820 7403 3.559655 GTGATATGTGTGTGTGTGTGTGT 59.440 43.478 0.00 0.00 0.00 3.72
3822 7405 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
3823 7406 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3824 7407 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3825 7408 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3826 7409 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3827 7410 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3828 7411 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3829 7412 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3830 7413 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3831 7414 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3832 7415 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3833 7416 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3834 7417 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3835 7418 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3836 7419 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3952 7560 3.715638 AGGGGTTGCTTAGGTAGTTTC 57.284 47.619 0.00 0.00 0.00 2.78
4020 7697 9.699410 AGTTAAATTTCCATGATCCTCATTACA 57.301 29.630 0.00 0.00 34.28 2.41
4118 7822 9.167311 GAACCTAATCCATGGATATGATGTAAC 57.833 37.037 27.54 13.18 36.36 2.50
4187 7893 2.378038 ACTTGTGTGTGTGCAGGAATT 58.622 42.857 0.00 0.00 0.00 2.17
4300 8006 5.828859 AGGACGCAATAGAGTAACTACAGAT 59.171 40.000 0.00 0.00 33.62 2.90
4355 8071 9.609346 ATTTTGTACTCTTACCCACATACATAC 57.391 33.333 0.00 0.00 0.00 2.39
4401 8164 6.179756 TGGCACACTGATTACTCAAATGTAT 58.820 36.000 0.88 0.00 32.31 2.29
4488 8415 5.502382 CGCGCTTTCATTTATGTATCTGTGT 60.502 40.000 5.56 0.00 0.00 3.72
4709 8639 3.365976 AACGCAACGGTGACAGTTA 57.634 47.368 3.55 0.00 0.00 2.24
4843 8779 0.608035 TGAAGGGATGTGGCCGTTTC 60.608 55.000 0.00 0.00 36.26 2.78
4844 8780 0.608035 GAAGGGATGTGGCCGTTTCA 60.608 55.000 0.00 0.00 36.26 2.69
4845 8781 0.609131 AAGGGATGTGGCCGTTTCAG 60.609 55.000 0.00 0.00 32.46 3.02
4846 8782 1.303317 GGGATGTGGCCGTTTCAGT 60.303 57.895 0.00 0.00 0.00 3.41
4885 8849 3.004326 GCCATGGCGGATGTTTGCA 62.004 57.895 23.48 0.00 36.56 4.08
4888 8852 0.173935 CATGGCGGATGTTTGCATGT 59.826 50.000 0.00 0.00 35.07 3.21
4899 8863 1.081556 TTTGCATGTCGTCGGGATCG 61.082 55.000 0.00 0.00 37.82 3.69
4985 8951 3.457198 GCTCCGTAGCTTGTTTTCTTC 57.543 47.619 0.00 0.00 45.85 2.87
4994 8960 8.932791 CCGTAGCTTGTTTTCTTCTTCTTTATA 58.067 33.333 0.00 0.00 0.00 0.98
5007 8974 7.727186 TCTTCTTCTTTATATCGGGCTTACCTA 59.273 37.037 0.00 0.00 36.97 3.08
5062 9032 3.058293 TGCTTGCTGAACCTTTGTATTCG 60.058 43.478 0.00 0.00 0.00 3.34
5246 9226 6.303839 AGCTAATGTCAAGGGAAAACTTGTA 58.696 36.000 5.92 0.00 46.11 2.41
5347 9355 2.957402 TGGAGGCATGTTCTCTTTGT 57.043 45.000 14.67 0.00 0.00 2.83
5356 9364 4.781071 CATGTTCTCTTTGTTCACTGCTC 58.219 43.478 0.00 0.00 0.00 4.26
5388 9398 8.792633 AGCAATAACAATGTGTAATGTGTTACT 58.207 29.630 0.00 0.00 38.79 2.24
5408 9418 7.450014 TGTTACTGACTTCATCTCTTCTTCTCT 59.550 37.037 0.00 0.00 0.00 3.10
5409 9419 8.952278 GTTACTGACTTCATCTCTTCTTCTCTA 58.048 37.037 0.00 0.00 0.00 2.43
5439 9449 4.968719 TCAGCCTTAGGATCTGGAATTACA 59.031 41.667 0.69 0.00 0.00 2.41
5444 9458 6.651225 GCCTTAGGATCTGGAATTACATGTAC 59.349 42.308 4.68 0.00 0.00 2.90
5466 9480 0.689412 TAGATCCGGCACATGGGTCA 60.689 55.000 0.00 0.00 39.20 4.02
5518 9532 1.924731 TGACCTATGATCGCCTAGGG 58.075 55.000 11.72 0.44 39.10 3.53
5528 9542 3.964688 TGATCGCCTAGGGACAATAAGAA 59.035 43.478 11.72 0.00 0.00 2.52
5535 9549 5.440610 CCTAGGGACAATAAGAAGCATTGT 58.559 41.667 0.00 0.56 46.58 2.71
5604 10046 2.218302 CGAGTCGGTGTAGATCGTACTC 59.782 54.545 4.10 12.15 33.30 2.59
5610 10052 2.543430 GGTGTAGATCGTACTCGGAGTC 59.457 54.545 15.05 5.79 37.69 3.36
5615 10057 0.532417 ATCGTACTCGGAGTCCCTCG 60.532 60.000 15.05 14.50 37.69 4.63
5620 10062 0.617413 ACTCGGAGTCCCTCGAACTA 59.383 55.000 4.45 0.00 34.87 2.24
5629 10071 5.712917 GGAGTCCCTCGAACTATAGATGAAT 59.287 44.000 6.78 0.00 0.00 2.57
5637 10079 5.710567 TCGAACTATAGATGAATGATCCCGT 59.289 40.000 6.78 0.00 0.00 5.28
5643 10085 1.867233 GATGAATGATCCCGTGAACCG 59.133 52.381 0.00 0.00 0.00 4.44
5644 10086 0.742990 TGAATGATCCCGTGAACCGC 60.743 55.000 0.00 0.00 34.38 5.68
5645 10087 1.436983 GAATGATCCCGTGAACCGCC 61.437 60.000 0.00 0.00 34.38 6.13
5646 10088 2.886730 AATGATCCCGTGAACCGCCC 62.887 60.000 0.00 0.00 34.38 6.13
5647 10089 4.090588 GATCCCGTGAACCGCCCA 62.091 66.667 0.00 0.00 34.38 5.36
5654 10096 2.280524 TGAACCGCCCACGAACAG 60.281 61.111 0.00 0.00 43.93 3.16
5655 10097 2.280592 GAACCGCCCACGAACAGT 60.281 61.111 0.00 0.00 43.93 3.55
5656 10098 2.280592 AACCGCCCACGAACAGTC 60.281 61.111 0.00 0.00 43.93 3.51
5658 10100 3.041940 CCGCCCACGAACAGTCAC 61.042 66.667 0.00 0.00 43.93 3.67
5660 10102 2.022129 CGCCCACGAACAGTCACTC 61.022 63.158 0.00 0.00 43.93 3.51
5664 10106 1.537348 CCCACGAACAGTCACTCGAAA 60.537 52.381 0.08 0.00 38.43 3.46
5681 10123 2.132762 GAAAGAAGACCGAAAGCACGA 58.867 47.619 0.00 0.00 35.09 4.35
5689 10132 1.199558 ACCGAAAGCACGACTCTCTAC 59.800 52.381 0.00 0.00 35.09 2.59
5717 10161 3.274393 GCGTATGGCTTCACGATCT 57.726 52.632 9.64 0.00 40.56 2.75
5719 10163 1.536072 GCGTATGGCTTCACGATCTGA 60.536 52.381 9.64 0.00 40.56 3.27
5729 10173 0.733909 CACGATCTGACAGCGCTTCA 60.734 55.000 7.50 14.34 0.00 3.02
5730 10174 0.734253 ACGATCTGACAGCGCTTCAC 60.734 55.000 7.50 2.25 0.00 3.18
5739 10183 1.373497 AGCGCTTCACCGTCAAGAG 60.373 57.895 2.64 0.00 0.00 2.85
5773 10523 4.591072 CCGAAGAATTAGAGGGAGGAGATT 59.409 45.833 0.00 0.00 0.00 2.40
5779 10529 0.719015 AGAGGGAGGAGATTGGACCA 59.281 55.000 0.00 0.00 0.00 4.02
5780 10530 0.833949 GAGGGAGGAGATTGGACCAC 59.166 60.000 0.00 0.00 0.00 4.16
5781 10531 0.119155 AGGGAGGAGATTGGACCACA 59.881 55.000 0.00 0.00 0.00 4.17
5782 10532 0.253327 GGGAGGAGATTGGACCACAC 59.747 60.000 0.00 0.00 0.00 3.82
5784 10534 0.108138 GAGGAGATTGGACCACACCG 60.108 60.000 0.00 0.00 0.00 4.94
5787 10537 2.750237 GATTGGACCACACCGGGC 60.750 66.667 6.32 0.00 45.59 6.13
5791 10541 3.637273 GGACCACACCGGGCTTCT 61.637 66.667 6.32 0.00 45.62 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 113 2.509111 TGCGTCGTGCTATGCAGG 60.509 61.111 5.97 5.97 46.63 4.85
124 127 0.384230 GGACGTGTTGATTGTGTGCG 60.384 55.000 0.00 0.00 0.00 5.34
187 213 2.047830 CTACCCACCTAAGGATGGACC 58.952 57.143 3.64 0.00 38.34 4.46
193 219 4.045590 GGATAGGATCTACCCACCTAAGGA 59.954 50.000 0.00 0.00 39.30 3.36
197 223 3.262842 TCGGATAGGATCTACCCACCTA 58.737 50.000 0.00 0.00 39.99 3.08
218 245 7.578310 CATTCATGGATGGTGAAGTAATCTT 57.422 36.000 6.03 0.00 38.81 2.40
248 276 1.686325 GAGCATACGGCCAGGGAGAA 61.686 60.000 2.24 0.00 46.50 2.87
514 1146 5.595542 ACAGTAGTTTCAAAGTTTTACCCCC 59.404 40.000 0.00 0.00 0.00 5.40
515 1147 6.704289 ACAGTAGTTTCAAAGTTTTACCCC 57.296 37.500 0.00 0.00 0.00 4.95
560 1192 3.255149 CCCTAATCTGGCATGCTGAAATC 59.745 47.826 18.92 0.00 0.00 2.17
572 1204 8.837099 ATATCAATCTCTCTACCCTAATCTGG 57.163 38.462 0.00 0.00 0.00 3.86
635 1267 6.089476 TGGCACACATATAAATTTGAACACG 58.911 36.000 0.00 0.00 0.00 4.49
776 1416 2.425143 ACCACCATGCATTCCTGTAG 57.575 50.000 0.00 0.00 0.00 2.74
894 1543 3.054802 GGATGGAGAATCTGTCAAGTGGT 60.055 47.826 0.00 0.00 35.43 4.16
1565 4432 9.799106 ATATACACATGAAATTAAGGAGAAGGG 57.201 33.333 0.00 0.00 0.00 3.95
1634 4505 6.360370 TCATATAGATGGTAGGAGTTTGCC 57.640 41.667 0.00 0.00 33.49 4.52
1830 5092 3.209410 CATCCTCCTGTCAGCCATAAAC 58.791 50.000 0.00 0.00 0.00 2.01
1892 5154 7.872962 CAGTATTCTGGACCAAGCGATGGAA 62.873 48.000 17.19 2.51 43.59 3.53
1961 5226 7.042335 AGAGGACATCTTTATTGTTCCTAACG 58.958 38.462 0.00 0.00 32.99 3.18
3123 6588 1.198178 GGTAGACGATCTCCGATCAGC 59.802 57.143 4.90 0.00 41.76 4.26
3146 6611 3.511477 TCTTGCTCCTCCTTAGTGAACT 58.489 45.455 0.00 0.00 0.00 3.01
3237 6702 5.001237 TCGGCGTAAAGTCTGATGAAATA 57.999 39.130 6.85 0.00 0.00 1.40
3258 6723 1.606350 CGTCGTCGGTGTTCAGCTTC 61.606 60.000 0.00 0.00 0.00 3.86
3566 7037 4.035278 TGCCACTTAACCTTTTTGTTCG 57.965 40.909 0.00 0.00 0.00 3.95
3814 7397 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3816 7399 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3818 7401 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3820 7403 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3822 7405 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3823 7406 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3824 7407 2.342179 CTACACACACACACACACACA 58.658 47.619 0.00 0.00 0.00 3.72
3825 7408 1.062002 GCTACACACACACACACACAC 59.938 52.381 0.00 0.00 0.00 3.82
3826 7409 1.338200 TGCTACACACACACACACACA 60.338 47.619 0.00 0.00 0.00 3.72
3827 7410 1.364721 TGCTACACACACACACACAC 58.635 50.000 0.00 0.00 0.00 3.82
3828 7411 2.323968 ATGCTACACACACACACACA 57.676 45.000 0.00 0.00 0.00 3.72
3829 7412 2.286950 CCAATGCTACACACACACACAC 60.287 50.000 0.00 0.00 0.00 3.82
3830 7413 1.946081 CCAATGCTACACACACACACA 59.054 47.619 0.00 0.00 0.00 3.72
3831 7414 2.217750 TCCAATGCTACACACACACAC 58.782 47.619 0.00 0.00 0.00 3.82
3832 7415 2.629336 TCCAATGCTACACACACACA 57.371 45.000 0.00 0.00 0.00 3.72
3833 7416 4.503741 AAATCCAATGCTACACACACAC 57.496 40.909 0.00 0.00 0.00 3.82
3834 7417 4.340666 ACAAAATCCAATGCTACACACACA 59.659 37.500 0.00 0.00 0.00 3.72
3835 7418 4.870363 ACAAAATCCAATGCTACACACAC 58.130 39.130 0.00 0.00 0.00 3.82
3836 7419 5.767665 ACTACAAAATCCAATGCTACACACA 59.232 36.000 0.00 0.00 0.00 3.72
4020 7697 8.321353 TGTGTGTTAATCTTCATGAGGATTAGT 58.679 33.333 28.63 15.04 39.48 2.24
4154 7860 7.254795 GCACACACACAAGTTAAGAAGTAATCT 60.255 37.037 0.00 0.00 41.32 2.40
4355 8071 8.264347 TGCCATTAGGGTATGTATGTATGTATG 58.736 37.037 0.00 0.00 39.65 2.39
4401 8164 1.735018 GTGCATGCATGGTAACGTACA 59.265 47.619 25.64 11.60 42.51 2.90
4846 8782 4.081087 GGCTACTAGTTCAACATCCCTGAA 60.081 45.833 0.00 0.00 0.00 3.02
4861 8805 0.681733 ACATCCGCCATGGCTACTAG 59.318 55.000 33.07 20.53 36.72 2.57
4880 8839 1.081556 CGATCCCGACGACATGCAAA 61.082 55.000 0.00 0.00 38.22 3.68
4882 8841 2.104132 CGATCCCGACGACATGCA 59.896 61.111 0.00 0.00 38.22 3.96
4885 8849 4.266070 CCGCGATCCCGACGACAT 62.266 66.667 8.23 0.00 37.45 3.06
4944 8910 2.750350 CCGGAGCAGGAAACAGGT 59.250 61.111 0.00 0.00 0.00 4.00
4947 8913 4.697756 CGGCCGGAGCAGGAAACA 62.698 66.667 20.10 0.00 42.56 2.83
4985 8951 6.535508 GCATAGGTAAGCCCGATATAAAGAAG 59.464 42.308 0.00 0.00 38.74 2.85
4994 8960 0.035458 GCAGCATAGGTAAGCCCGAT 59.965 55.000 0.00 0.00 38.74 4.18
5020 8990 2.823154 CAAAAGGGAAATAGTTCGGGCA 59.177 45.455 0.00 0.00 34.28 5.36
5111 9081 5.065346 TCAACATTAGAAAACAAGCACACGA 59.935 36.000 0.00 0.00 0.00 4.35
5113 9083 7.698836 ATTCAACATTAGAAAACAAGCACAC 57.301 32.000 0.00 0.00 0.00 3.82
5244 9224 7.547227 AGGCAGAATCCAACAACAAATAATAC 58.453 34.615 0.00 0.00 0.00 1.89
5246 9226 6.610075 AGGCAGAATCCAACAACAAATAAT 57.390 33.333 0.00 0.00 0.00 1.28
5309 9289 7.147213 TGCCTCCAATGGATACTAATTTTCCTA 60.147 37.037 0.87 0.00 37.61 2.94
5356 9364 7.814107 ACATTACACATTGTTATTGCTCAAAGG 59.186 33.333 0.00 0.00 0.00 3.11
5388 9398 6.186957 AGCTAGAGAAGAAGAGATGAAGTCA 58.813 40.000 0.00 0.00 0.00 3.41
5439 9449 2.235891 TGTGCCGGATCTATCGTACAT 58.764 47.619 5.05 0.00 0.00 2.29
5444 9458 0.390340 CCCATGTGCCGGATCTATCG 60.390 60.000 5.05 0.00 0.00 2.92
5466 9480 3.495434 TTCCACTACGTTTCCCAACAT 57.505 42.857 0.00 0.00 32.54 2.71
5499 9513 1.427753 TCCCTAGGCGATCATAGGTCA 59.572 52.381 2.05 0.19 37.45 4.02
5501 9515 1.147191 TGTCCCTAGGCGATCATAGGT 59.853 52.381 2.05 0.00 37.45 3.08
5506 9520 3.572642 TCTTATTGTCCCTAGGCGATCA 58.427 45.455 2.05 1.57 0.00 2.92
5511 9525 3.560636 TGCTTCTTATTGTCCCTAGGC 57.439 47.619 2.05 0.00 0.00 3.93
5518 9532 6.146021 CCAAACCAACAATGCTTCTTATTGTC 59.854 38.462 4.09 0.00 45.28 3.18
5528 9542 4.686191 TCAAATCCAAACCAACAATGCT 57.314 36.364 0.00 0.00 0.00 3.79
5535 9549 5.379732 GGTAACGATCAAATCCAAACCAA 57.620 39.130 0.00 0.00 0.00 3.67
5566 9580 2.028930 ACTCGTCTTCTTCCGCTTCAAT 60.029 45.455 0.00 0.00 0.00 2.57
5610 10052 6.406400 GGGATCATTCATCTATAGTTCGAGGG 60.406 46.154 0.00 0.00 0.00 4.30
5615 10057 6.925211 TCACGGGATCATTCATCTATAGTTC 58.075 40.000 0.00 0.00 0.00 3.01
5620 10062 4.561530 CGGTTCACGGGATCATTCATCTAT 60.562 45.833 0.00 0.00 39.42 1.98
5629 10071 4.090588 GGGCGGTTCACGGGATCA 62.091 66.667 0.00 0.00 44.51 2.92
5637 10079 2.280524 CTGTTCGTGGGCGGTTCA 60.281 61.111 0.00 0.00 38.89 3.18
5643 10085 2.022129 CGAGTGACTGTTCGTGGGC 61.022 63.158 0.00 0.00 32.44 5.36
5644 10086 0.031585 TTCGAGTGACTGTTCGTGGG 59.968 55.000 0.00 0.00 37.99 4.61
5645 10087 1.787155 CTTTCGAGTGACTGTTCGTGG 59.213 52.381 0.00 0.00 37.99 4.94
5646 10088 2.727777 TCTTTCGAGTGACTGTTCGTG 58.272 47.619 0.00 0.00 37.99 4.35
5647 10089 3.066342 TCTTCTTTCGAGTGACTGTTCGT 59.934 43.478 0.00 0.00 37.99 3.85
5649 10091 3.736759 GGTCTTCTTTCGAGTGACTGTTC 59.263 47.826 0.00 0.00 0.00 3.18
5650 10092 3.718815 GGTCTTCTTTCGAGTGACTGTT 58.281 45.455 0.00 0.00 0.00 3.16
5651 10093 2.287668 CGGTCTTCTTTCGAGTGACTGT 60.288 50.000 0.00 0.00 31.76 3.55
5652 10094 2.031069 TCGGTCTTCTTTCGAGTGACTG 60.031 50.000 0.00 0.00 34.75 3.51
5654 10096 2.701073 TCGGTCTTCTTTCGAGTGAC 57.299 50.000 0.00 0.00 0.00 3.67
5655 10097 3.639538 CTTTCGGTCTTCTTTCGAGTGA 58.360 45.455 0.00 0.00 34.33 3.41
5656 10098 2.155924 GCTTTCGGTCTTCTTTCGAGTG 59.844 50.000 0.00 0.00 34.33 3.51
5658 10100 2.155924 GTGCTTTCGGTCTTCTTTCGAG 59.844 50.000 0.00 0.00 34.33 4.04
5660 10102 1.136611 CGTGCTTTCGGTCTTCTTTCG 60.137 52.381 0.00 0.00 0.00 3.46
5664 10106 0.674534 AGTCGTGCTTTCGGTCTTCT 59.325 50.000 0.00 0.00 0.00 2.85
5701 10144 3.119291 CTGTCAGATCGTGAAGCCATAC 58.881 50.000 0.00 0.00 36.74 2.39
5717 10161 2.355837 GACGGTGAAGCGCTGTCA 60.356 61.111 12.58 14.40 46.03 3.58
5719 10163 1.956170 CTTGACGGTGAAGCGCTGT 60.956 57.895 12.58 3.09 36.07 4.40
5729 10173 2.607187 CGACAATTAGCTCTTGACGGT 58.393 47.619 18.91 0.45 37.85 4.83
5730 10174 1.324736 GCGACAATTAGCTCTTGACGG 59.675 52.381 23.99 12.99 40.42 4.79
5739 10183 3.675467 AATTCTTCGGCGACAATTAGC 57.325 42.857 19.32 0.00 0.00 3.09
5773 10523 3.948719 GAAGCCCGGTGTGGTCCA 61.949 66.667 0.00 0.00 35.15 4.02
5779 10529 3.181454 CCTCATAATTAGAAGCCCGGTGT 60.181 47.826 0.00 0.00 0.00 4.16
5780 10530 3.071023 TCCTCATAATTAGAAGCCCGGTG 59.929 47.826 0.00 0.00 0.00 4.94
5781 10531 3.314693 TCCTCATAATTAGAAGCCCGGT 58.685 45.455 0.00 0.00 0.00 5.28
5782 10532 4.559862 ATCCTCATAATTAGAAGCCCGG 57.440 45.455 0.00 0.00 0.00 5.73
5784 10534 7.181125 TCCTCTAATCCTCATAATTAGAAGCCC 59.819 40.741 6.93 0.00 42.31 5.19


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

AutoCloner maintained by Alex Coulton.