Multiple sequence alignment - TraesCS4A01G450400

Loading Multiple Alignment...

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 TraesCS4A01G450400 chr4A 100.000 5169 0 0 1 5169 715911612 715916780 0.000000e+00 9546.0
1 TraesCS4A01G450400 chr4A 91.063 3435 218 52 1762 5169 715640991 715637619 0.000000e+00 4560.0
2 TraesCS4A01G450400 chr4A 91.039 837 40 15 742 1576 715641922 715641119 0.000000e+00 1098.0
3 TraesCS4A01G450400 chr4A 90.517 232 11 6 1 230 715643098 715642876 3.910000e-76 296.0
4 TraesCS4A01G450400 chr4A 79.279 444 68 22 1034 1460 11678368 11677932 6.550000e-74 289.0
5 TraesCS4A01G450400 chr7A 89.976 2095 178 23 2322 4399 17268735 17266656 0.000000e+00 2676.0
6 TraesCS4A01G450400 chr7A 81.775 1059 121 43 1282 2330 17271533 17270537 0.000000e+00 821.0
7 TraesCS4A01G450400 chr7A 91.886 493 36 3 742 1231 17278460 17277969 0.000000e+00 686.0
8 TraesCS4A01G450400 chr7A 82.944 727 99 16 1 714 17279726 17279012 2.630000e-177 632.0
9 TraesCS4A01G450400 chr7A 81.696 519 90 5 3621 4138 692522030 692521516 1.330000e-115 427.0
10 TraesCS4A01G450400 chr7A 81.893 486 45 25 2322 2798 17269922 17269471 2.270000e-98 370.0
11 TraesCS4A01G450400 chr7A 85.246 122 16 1 2209 2330 17269473 17269354 1.950000e-24 124.0
12 TraesCS4A01G450400 chr7D 88.320 1738 152 37 2103 3821 17761471 17759766 0.000000e+00 2037.0
13 TraesCS4A01G450400 chr7D 88.124 1482 124 31 715 2153 17762923 17761451 0.000000e+00 1714.0
14 TraesCS4A01G450400 chr7D 89.684 950 76 14 3848 4779 17759772 17758827 0.000000e+00 1192.0
15 TraesCS4A01G450400 chr7D 82.656 640 82 20 95 714 17763978 17763348 1.640000e-149 540.0
16 TraesCS4A01G450400 chr7D 92.174 115 7 2 1100 1213 600703547 600703434 1.490000e-35 161.0
17 TraesCS4A01G450400 chr7D 96.774 62 1 1 10 71 17764038 17763978 9.160000e-18 102.0
18 TraesCS4A01G450400 chr7D 100.000 29 0 0 5076 5104 195821149 195821121 3.000000e-03 54.7
19 TraesCS4A01G450400 chr3D 85.424 542 76 3 3619 4160 12299345 12298807 1.260000e-155 560.0
20 TraesCS4A01G450400 chr3D 85.529 539 75 3 3619 4157 12375490 12376025 1.260000e-155 560.0
21 TraesCS4A01G450400 chr3D 84.489 548 81 4 3599 4145 12385804 12386348 5.890000e-149 538.0
22 TraesCS4A01G450400 chr3D 86.127 173 22 2 1306 1477 12300230 12300059 8.840000e-43 185.0
23 TraesCS4A01G450400 chr3D 85.393 178 26 0 1285 1462 12374584 12374761 8.840000e-43 185.0
24 TraesCS4A01G450400 chr3D 82.011 189 34 0 2904 3092 12299982 12299794 1.490000e-35 161.0
25 TraesCS4A01G450400 chr3D 82.011 189 34 0 2901 3089 12374850 12375038 1.490000e-35 161.0
26 TraesCS4A01G450400 chr3D 93.443 61 3 1 4514 4573 463146713 463146773 7.130000e-14 89.8
27 TraesCS4A01G450400 chr3B 85.240 542 77 3 3619 4160 17989523 17990061 5.850000e-154 555.0
28 TraesCS4A01G450400 chr3B 83.091 550 84 7 3599 4146 17903505 17902963 4.650000e-135 492.0
29 TraesCS4A01G450400 chr3B 85.882 170 24 0 3176 3345 17688523 17688354 1.140000e-41 182.0
30 TraesCS4A01G450400 chr3B 82.540 189 31 2 1294 1481 17689071 17688884 1.150000e-36 165.0
31 TraesCS4A01G450400 chr3B 81.726 197 30 5 1018 1208 17689273 17689077 5.360000e-35 159.0
32 TraesCS4A01G450400 chr3B 97.059 34 1 0 4571 4604 669038316 669038283 2.010000e-04 58.4
33 TraesCS4A01G450400 chr4D 79.212 457 69 23 1025 1464 456047052 456047499 1.410000e-75 294.0
34 TraesCS4A01G450400 chr4D 79.381 97 14 5 4571 4663 484626500 484626594 4.320000e-06 63.9
35 TraesCS4A01G450400 chr4D 96.875 32 1 0 4571 4602 383755257 383755226 3.000000e-03 54.7
36 TraesCS4A01G450400 chr4B 81.074 391 54 17 1088 1464 570138563 570138947 1.410000e-75 294.0
37 TraesCS4A01G450400 chr5D 83.085 201 21 9 4850 5046 281168251 281168442 2.470000e-38 171.0
38 TraesCS4A01G450400 chr5D 91.935 62 3 1 4514 4573 503255301 503255362 9.220000e-13 86.1
39 TraesCS4A01G450400 chr3A 82.632 190 30 3 1024 1210 24781595 24781406 1.150000e-36 165.0
40 TraesCS4A01G450400 chrUn 82.609 184 25 6 4865 5046 88805266 88805088 6.930000e-34 156.0
41 TraesCS4A01G450400 chrUn 91.935 62 3 1 4514 4573 341018690 341018629 9.220000e-13 86.1
42 TraesCS4A01G450400 chr5A 84.024 169 20 4 4865 5031 623563078 623562915 6.930000e-34 156.0
43 TraesCS4A01G450400 chr5A 97.059 34 1 0 4571 4604 665447306 665447339 2.010000e-04 58.4
44 TraesCS4A01G450400 chr1B 82.609 184 21 6 4865 5046 487323381 487323555 8.960000e-33 152.0
45 TraesCS4A01G450400 chr1B 78.947 228 44 4 382 606 640420173 640419947 8.960000e-33 152.0
46 TraesCS4A01G450400 chr7B 81.522 184 27 6 4865 5046 745193358 745193180 1.500000e-30 145.0
47 TraesCS4A01G450400 chr7B 96.970 33 1 0 4572 4604 524773984 524774016 7.230000e-04 56.5
48 TraesCS4A01G450400 chr7B 100.000 29 0 0 5076 5104 159720743 159720715 3.000000e-03 54.7
49 TraesCS4A01G450400 chr2B 78.605 215 37 7 4869 5075 77292585 77292798 3.250000e-27 134.0
50 TraesCS4A01G450400 chr2B 94.737 76 4 0 4879 4954 473307325 473307400 9.090000e-23 119.0
51 TraesCS4A01G450400 chr2B 79.167 144 21 9 2546 2682 762352109 762351968 1.980000e-14 91.6
52 TraesCS4A01G450400 chr6B 78.140 215 38 7 4869 5075 76235432 76235645 1.510000e-25 128.0
53 TraesCS4A01G450400 chr6B 93.443 61 3 1 4514 4573 618881149 618881209 7.130000e-14 89.8
54 TraesCS4A01G450400 chr1D 81.250 144 23 4 2540 2683 464782069 464782208 4.230000e-21 113.0
55 TraesCS4A01G450400 chr1D 95.000 60 3 0 4514 4573 156906076 156906135 1.530000e-15 95.3
56 TraesCS4A01G450400 chr1D 76.471 187 28 11 2587 2763 464818640 464818820 2.560000e-13 87.9
57 TraesCS4A01G450400 chr1D 100.000 29 0 0 758 786 317121652 317121624 3.000000e-03 54.7
58 TraesCS4A01G450400 chr2A 75.463 216 42 10 4869 5075 67466445 67466232 1.530000e-15 95.3
59 TraesCS4A01G450400 chr6A 93.333 60 3 1 4514 4573 137632973 137632915 2.560000e-13 87.9
60 TraesCS4A01G450400 chr6D 91.935 62 3 2 4514 4573 431006652 431006713 9.220000e-13 86.1
61 TraesCS4A01G450400 chr6D 97.059 34 1 0 4571 4604 266771621 266771588 2.010000e-04 58.4
62 TraesCS4A01G450400 chr5B 97.143 35 0 1 4571 4604 558599160 558599194 2.010000e-04 58.4
63 TraesCS4A01G450400 chr5B 100.000 28 0 0 5077 5104 370003305 370003332 9.000000e-03 52.8


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 TraesCS4A01G450400 chr4A 715911612 715916780 5168 False 9546.000000 9546 100.000000 1 5169 1 chr4A.!!$F1 5168
1 TraesCS4A01G450400 chr4A 715637619 715643098 5479 True 1984.666667 4560 90.873000 1 5169 3 chr4A.!!$R2 5168
2 TraesCS4A01G450400 chr7A 17266656 17271533 4877 True 997.750000 2676 84.722500 1282 4399 4 chr7A.!!$R2 3117
3 TraesCS4A01G450400 chr7A 17277969 17279726 1757 True 659.000000 686 87.415000 1 1231 2 chr7A.!!$R3 1230
4 TraesCS4A01G450400 chr7A 692521516 692522030 514 True 427.000000 427 81.696000 3621 4138 1 chr7A.!!$R1 517
5 TraesCS4A01G450400 chr7D 17758827 17764038 5211 True 1117.000000 2037 89.111600 10 4779 5 chr7D.!!$R3 4769
6 TraesCS4A01G450400 chr3D 12385804 12386348 544 False 538.000000 538 84.489000 3599 4145 1 chr3D.!!$F1 546
7 TraesCS4A01G450400 chr3D 12298807 12300230 1423 True 302.000000 560 84.520667 1306 4160 3 chr3D.!!$R1 2854
8 TraesCS4A01G450400 chr3D 12374584 12376025 1441 False 302.000000 560 84.311000 1285 4157 3 chr3D.!!$F3 2872
9 TraesCS4A01G450400 chr3B 17989523 17990061 538 False 555.000000 555 85.240000 3619 4160 1 chr3B.!!$F1 541
10 TraesCS4A01G450400 chr3B 17902963 17903505 542 True 492.000000 492 83.091000 3599 4146 1 chr3B.!!$R1 547

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
682 706 0.035458 ACTGACTAAGCCTGGTGTGC 59.965 55.000 0.0 0.0 0.00 4.57 F
1244 1841 0.179026 CTGCATCACCCTGCTGCTAT 60.179 55.000 0.0 0.0 39.94 2.97 F
2468 5002 1.001120 TATCCCGCTCCCACACTCA 59.999 57.895 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2649 0.475906 AAGCAAGTTGAGCAGGGAGT 59.524 50.000 7.16 0.00 0.0 3.85 R
2931 5512 1.002659 TGTACTTTGGTCCGGTCATGG 59.997 52.381 0.00 0.69 0.0 3.66 R
4184 6781 0.263765 AACTCTAGGGCGGTGGGATA 59.736 55.000 0.00 0.00 0.0 2.59 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
70 71 1.221566 CGTGTCCATGGGAGCATCA 59.778 57.895 13.02 0.00 36.25 3.07
71 72 0.179037 CGTGTCCATGGGAGCATCAT 60.179 55.000 13.02 0.00 36.25 2.45
72 73 1.602311 GTGTCCATGGGAGCATCATC 58.398 55.000 13.02 0.00 36.25 2.92
165 167 2.237393 CAGCTGGACTAAGCAGGATC 57.763 55.000 5.57 0.00 46.08 3.36
166 168 0.749649 AGCTGGACTAAGCAGGATCG 59.250 55.000 0.00 0.00 46.08 3.69
167 169 0.461961 GCTGGACTAAGCAGGATCGT 59.538 55.000 0.00 0.00 43.01 3.73
168 170 1.804372 GCTGGACTAAGCAGGATCGTG 60.804 57.143 11.07 11.07 43.01 4.35
170 172 1.112113 GGACTAAGCAGGATCGTGGA 58.888 55.000 16.66 0.00 0.00 4.02
171 173 1.202428 GGACTAAGCAGGATCGTGGAC 60.202 57.143 16.66 1.56 0.00 4.02
172 174 0.456221 ACTAAGCAGGATCGTGGACG 59.544 55.000 16.66 0.00 41.45 4.79
173 175 0.456221 CTAAGCAGGATCGTGGACGT 59.544 55.000 16.66 0.00 40.80 4.34
194 196 1.202065 ACGGTGCGTACGTACATACAG 60.202 52.381 32.30 21.85 43.60 2.74
305 315 1.437772 GCTAGAGCGTCTACAGCCGA 61.438 60.000 0.00 0.00 34.64 5.54
359 369 3.615110 CGTGAACAGCCTAATCACTGACT 60.615 47.826 7.27 0.00 40.95 3.41
366 376 5.600069 ACAGCCTAATCACTGACTGATCATA 59.400 40.000 0.00 0.00 38.82 2.15
367 377 5.925397 CAGCCTAATCACTGACTGATCATAC 59.075 44.000 0.00 0.00 38.82 2.39
368 378 5.837979 AGCCTAATCACTGACTGATCATACT 59.162 40.000 0.00 0.00 38.82 2.12
369 379 6.015519 AGCCTAATCACTGACTGATCATACTC 60.016 42.308 0.00 0.00 38.82 2.59
374 393 5.256474 TCACTGACTGATCATACTCAGACA 58.744 41.667 22.70 7.01 44.48 3.41
379 398 5.048013 TGACTGATCATACTCAGACAAACGT 60.048 40.000 8.01 0.00 44.48 3.99
404 423 1.369625 ATCATCCTCAAACGTTCGGC 58.630 50.000 0.00 0.00 0.00 5.54
463 482 1.209747 GGATATAAGATGGTCCGGGCC 59.790 57.143 21.35 21.35 0.00 5.80
485 504 1.973281 CCACCACATCGGCTTTGCT 60.973 57.895 0.00 0.00 39.03 3.91
495 515 2.987547 GCTTTGCTCAGCCTGGCA 60.988 61.111 22.65 0.00 36.62 4.92
496 516 2.960170 CTTTGCTCAGCCTGGCAC 59.040 61.111 22.65 7.74 38.23 5.01
498 518 1.455402 TTTGCTCAGCCTGGCACAA 60.455 52.632 22.65 15.76 38.70 3.33
499 519 1.042003 TTTGCTCAGCCTGGCACAAA 61.042 50.000 22.65 20.25 38.70 2.83
504 524 2.124320 AGCCTGGCACAAACGTGT 60.124 55.556 22.65 0.00 38.70 4.49
517 537 4.688021 ACAAACGTGTGCCACAAATATTT 58.312 34.783 5.39 0.00 36.31 1.40
525 545 5.861251 GTGTGCCACAAATATTTTCATTCGA 59.139 36.000 0.00 0.00 34.08 3.71
577 598 1.306141 TTCAGCCCCTCTCCGTCAT 60.306 57.895 0.00 0.00 0.00 3.06
600 621 1.137872 CACTTCTGATCCCCTCCGAAG 59.862 57.143 5.26 5.26 45.60 3.79
628 652 2.281484 GCCGGTGACCAAAGCAGA 60.281 61.111 1.90 0.00 0.00 4.26
641 665 2.978824 GCAGAGTTGCCTCCGGTA 59.021 61.111 0.00 0.00 44.74 4.02
656 680 0.538118 CGGTAGGGAATCCGGTTTCA 59.462 55.000 23.29 3.97 42.61 2.69
661 685 1.280998 AGGGAATCCGGTTTCAACGAT 59.719 47.619 23.29 4.81 38.33 3.73
669 693 2.404215 CGGTTTCAACGATGACTGACT 58.596 47.619 0.00 0.00 34.61 3.41
677 701 1.478510 ACGATGACTGACTAAGCCTGG 59.521 52.381 0.00 0.00 0.00 4.45
682 706 0.035458 ACTGACTAAGCCTGGTGTGC 59.965 55.000 0.00 0.00 0.00 4.57
730 1303 2.310233 CGAATATGAGGCGTGCCCG 61.310 63.158 7.39 0.00 39.21 6.13
740 1325 4.457496 CGTGCCCGATCAGTGCCT 62.457 66.667 0.00 0.00 35.63 4.75
744 1329 4.100084 CCCGATCAGTGCCTGGCA 62.100 66.667 19.30 19.30 35.60 4.92
748 1333 1.667236 CGATCAGTGCCTGGCATTTA 58.333 50.000 26.22 12.95 41.91 1.40
872 1458 9.084533 ACTCCTTTTGTAAATAAATGTAAGCCA 57.915 29.630 0.00 0.00 0.00 4.75
948 1542 0.808755 CATCGCCAACCCAACTAACC 59.191 55.000 0.00 0.00 0.00 2.85
1243 1840 1.222661 CTGCATCACCCTGCTGCTA 59.777 57.895 0.00 0.00 39.94 3.49
1244 1841 0.179026 CTGCATCACCCTGCTGCTAT 60.179 55.000 0.00 0.00 39.94 2.97
1245 1842 1.071228 CTGCATCACCCTGCTGCTATA 59.929 52.381 0.00 0.00 39.94 1.31
1246 1843 1.202687 TGCATCACCCTGCTGCTATAC 60.203 52.381 0.00 0.00 39.94 1.47
1247 1844 1.202687 GCATCACCCTGCTGCTATACA 60.203 52.381 0.00 0.00 36.64 2.29
1300 1908 6.436027 TCTCTATACAGGAGTTTGATGGACT 58.564 40.000 0.00 0.00 33.06 3.85
1426 2034 2.016961 CCGCCAAGGACATCAATCG 58.983 57.895 0.00 0.00 45.00 3.34
1434 2042 4.437239 CAAGGACATCAATCGCTTCTACT 58.563 43.478 0.00 0.00 0.00 2.57
1437 2045 3.001736 GGACATCAATCGCTTCTACTTGC 59.998 47.826 0.00 0.00 0.00 4.01
1572 2180 5.317808 ACTGCGAGTGAGTCCATATACTAT 58.682 41.667 0.00 0.00 0.00 2.12
1573 2181 6.473758 ACTGCGAGTGAGTCCATATACTATA 58.526 40.000 0.00 0.00 0.00 1.31
1574 2182 7.113437 ACTGCGAGTGAGTCCATATACTATAT 58.887 38.462 0.00 0.00 0.00 0.86
1575 2183 8.265764 ACTGCGAGTGAGTCCATATACTATATA 58.734 37.037 0.00 0.00 0.00 0.86
1576 2184 9.110502 CTGCGAGTGAGTCCATATACTATATAA 57.889 37.037 0.00 0.00 0.00 0.98
1577 2185 9.628500 TGCGAGTGAGTCCATATACTATATAAT 57.372 33.333 0.00 0.00 0.00 1.28
1698 2335 4.032960 ACATGAATGTGAGCCCTTTGTA 57.967 40.909 0.00 0.00 40.03 2.41
1701 2338 2.224744 TGAATGTGAGCCCTTTGTAGCA 60.225 45.455 0.00 0.00 0.00 3.49
1723 2360 5.067805 GCACTATTCTTTATTTGGGGGTCTG 59.932 44.000 0.00 0.00 0.00 3.51
1727 2364 2.110899 TCTTTATTTGGGGGTCTGGCAA 59.889 45.455 0.00 0.00 0.00 4.52
1728 2365 2.230130 TTATTTGGGGGTCTGGCAAG 57.770 50.000 0.00 0.00 0.00 4.01
1735 2372 1.005450 GGGGGTCTGGCAAGTTATTGA 59.995 52.381 0.00 0.00 38.83 2.57
1757 2394 4.729227 AGTGGATTGTTTCGTTTTGGTT 57.271 36.364 0.00 0.00 0.00 3.67
1759 2396 4.867608 AGTGGATTGTTTCGTTTTGGTTTG 59.132 37.500 0.00 0.00 0.00 2.93
1760 2397 4.865365 GTGGATTGTTTCGTTTTGGTTTGA 59.135 37.500 0.00 0.00 0.00 2.69
1886 2566 2.691011 AGTTGTTTGGTGCGTGGTTATT 59.309 40.909 0.00 0.00 0.00 1.40
1909 2591 4.875536 TGTGTCCATACATTTCGATCTTGG 59.124 41.667 0.00 0.00 38.08 3.61
1916 2598 6.038603 CCATACATTTCGATCTTGGTGTGATT 59.961 38.462 0.00 0.00 0.00 2.57
1919 2601 5.106555 ACATTTCGATCTTGGTGTGATTGTC 60.107 40.000 0.00 0.00 0.00 3.18
1936 2618 1.490490 TGTCTGTGAGACTTTTGGGCT 59.510 47.619 5.39 0.00 45.27 5.19
2034 2716 3.362237 CGCTGCTATCGTACAATAAGCTC 59.638 47.826 0.00 1.14 0.00 4.09
2094 2777 9.733219 TTAAAGACGTTCACGGATTTTAATTTT 57.267 25.926 4.07 0.00 44.95 1.82
2434 4968 1.085501 AACCAACGACACACACCGTC 61.086 55.000 0.00 0.00 38.13 4.79
2456 4990 1.819632 GTTGTGGCCAGCTATCCCG 60.820 63.158 5.11 0.00 0.00 5.14
2465 4999 2.109181 GCTATCCCGCTCCCACAC 59.891 66.667 0.00 0.00 0.00 3.82
2466 5000 2.435693 GCTATCCCGCTCCCACACT 61.436 63.158 0.00 0.00 0.00 3.55
2468 5002 1.001120 TATCCCGCTCCCACACTCA 59.999 57.895 0.00 0.00 0.00 3.41
2535 5074 8.349568 ACTAGGATTTAGAAAATGTTCCAACC 57.650 34.615 0.00 0.00 33.92 3.77
2536 5075 7.947890 ACTAGGATTTAGAAAATGTTCCAACCA 59.052 33.333 0.00 0.00 33.92 3.67
2537 5076 6.993079 AGGATTTAGAAAATGTTCCAACCAC 58.007 36.000 0.00 0.00 33.92 4.16
2538 5077 5.861787 GGATTTAGAAAATGTTCCAACCACG 59.138 40.000 0.00 0.00 33.92 4.94
2541 5080 6.642707 TTAGAAAATGTTCCAACCACGAAT 57.357 33.333 0.00 0.00 33.92 3.34
2542 5081 5.529581 AGAAAATGTTCCAACCACGAATT 57.470 34.783 0.00 0.00 33.92 2.17
2543 5082 5.288804 AGAAAATGTTCCAACCACGAATTG 58.711 37.500 0.00 0.00 33.92 2.32
2545 5084 5.776173 AAATGTTCCAACCACGAATTGTA 57.224 34.783 0.00 0.00 0.00 2.41
2675 5223 9.942850 TGTTCATGAACTTCAGAAATACTCATA 57.057 29.630 32.57 9.20 41.67 2.15
2718 5266 9.321590 GAATTTGCAAAAATGTTCATAGCTTTC 57.678 29.630 17.19 6.32 0.00 2.62
2809 5365 1.472480 GCAACAACACACAACCTCACT 59.528 47.619 0.00 0.00 0.00 3.41
2848 5404 1.153046 CAAACCACGACCCACCTGT 60.153 57.895 0.00 0.00 0.00 4.00
2920 5501 1.001393 TAGCAAAGGGCCTTTCGGG 60.001 57.895 28.29 18.22 46.50 5.14
2931 5512 1.001706 GCCTTTCGGGTTGTTGAAGAC 60.002 52.381 0.00 0.00 37.43 3.01
2944 5525 0.834261 TGAAGACCATGACCGGACCA 60.834 55.000 9.46 6.03 0.00 4.02
3052 5633 2.618045 CCCCACCTTCGACATAAAGCTT 60.618 50.000 0.00 0.00 0.00 3.74
3089 5670 8.873830 CAATCTTCTCAACTTACGATGTATGTT 58.126 33.333 0.00 3.28 0.00 2.71
3284 5865 5.392380 CCATTTTGAAACGAAGGATGAGGAG 60.392 44.000 0.00 0.00 0.00 3.69
3368 5950 1.197492 GCATGCATGTCAACTCGAACA 59.803 47.619 26.79 0.00 0.00 3.18
3401 5983 5.046376 TGTGATTGAGGCTTGATGAGACTTA 60.046 40.000 0.00 0.00 46.50 2.24
3523 6105 3.455177 TGTGTGTCAACCCACCTTACTTA 59.545 43.478 0.00 0.00 34.35 2.24
3530 6120 3.216230 ACCCACCTTACTTACATCCCT 57.784 47.619 0.00 0.00 0.00 4.20
3532 6122 4.702196 ACCCACCTTACTTACATCCCTAA 58.298 43.478 0.00 0.00 0.00 2.69
3535 6125 5.607171 CCCACCTTACTTACATCCCTAATCT 59.393 44.000 0.00 0.00 0.00 2.40
3536 6126 6.785963 CCCACCTTACTTACATCCCTAATCTA 59.214 42.308 0.00 0.00 0.00 1.98
3537 6127 7.256225 CCCACCTTACTTACATCCCTAATCTAC 60.256 44.444 0.00 0.00 0.00 2.59
3538 6128 7.289317 CCACCTTACTTACATCCCTAATCTACA 59.711 40.741 0.00 0.00 0.00 2.74
3539 6129 8.701895 CACCTTACTTACATCCCTAATCTACAA 58.298 37.037 0.00 0.00 0.00 2.41
3540 6130 8.702819 ACCTTACTTACATCCCTAATCTACAAC 58.297 37.037 0.00 0.00 0.00 3.32
3581 6171 7.861630 ACGATTATATGTTGTGGTATCAAAGC 58.138 34.615 0.00 0.00 0.00 3.51
3592 6184 6.472016 TGTGGTATCAAAGCATTGTTCTCTA 58.528 36.000 1.04 0.00 38.03 2.43
3652 6249 0.865111 CAATGACCGACGTGAGCAAA 59.135 50.000 0.00 0.00 0.00 3.68
4062 6659 1.227853 AAACCGGCAAGAACGAGCT 60.228 52.632 0.00 0.00 0.00 4.09
4112 6709 3.316283 GAGGAGCTGATCTATTTCGCAG 58.684 50.000 0.00 0.00 0.00 5.18
4240 6837 4.101119 AGTGCTAATGTTTATACCTCGCCT 59.899 41.667 0.00 0.00 0.00 5.52
4643 7262 0.600255 AAACTGACCGGCTCTGTTCG 60.600 55.000 20.80 4.61 39.46 3.95
4668 7287 4.820897 TGAATCTCGTTAAGCTCATGTGT 58.179 39.130 0.00 0.00 0.00 3.72
4760 7379 0.865769 GAAGTAATATGGCGGCCACG 59.134 55.000 26.48 0.00 44.63 4.94
5035 7654 8.831000 AACAAAACTAACAAATTACAGTCGAC 57.169 30.769 7.70 7.70 0.00 4.20
5049 7668 3.131223 ACAGTCGACCATTCTATCACCAG 59.869 47.826 13.01 0.00 0.00 4.00
5147 7766 2.291741 CTCTGTTTCTCCACTGTTTGCC 59.708 50.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.905429 TCACAAGGTACGTAGGTGTAGTA 58.095 43.478 15.57 0.28 0.00 1.82
70 71 2.737359 CGTACGTAGCCATGGTGTTGAT 60.737 50.000 14.67 0.00 0.00 2.57
71 72 1.403116 CGTACGTAGCCATGGTGTTGA 60.403 52.381 14.67 0.00 0.00 3.18
72 73 0.996462 CGTACGTAGCCATGGTGTTG 59.004 55.000 14.67 4.13 0.00 3.33
135 137 2.607811 TCCAGCTGGATCCAATCGT 58.392 52.632 32.00 0.00 39.78 3.73
157 159 1.807886 GTACGTCCACGATCCTGCT 59.192 57.895 6.03 0.00 43.02 4.24
158 160 1.585521 CGTACGTCCACGATCCTGC 60.586 63.158 7.22 0.00 44.69 4.85
159 161 1.063649 CCGTACGTCCACGATCCTG 59.936 63.158 15.21 0.00 44.69 3.86
163 165 2.180017 GCACCGTACGTCCACGAT 59.820 61.111 15.21 0.00 44.69 3.73
164 166 4.388080 CGCACCGTACGTCCACGA 62.388 66.667 15.21 0.00 44.69 4.35
165 167 3.307505 TACGCACCGTACGTCCACG 62.308 63.158 15.21 14.09 43.88 4.94
166 168 2.560861 TACGCACCGTACGTCCAC 59.439 61.111 15.21 0.00 43.88 4.02
173 175 2.003301 TGTATGTACGTACGCACCGTA 58.997 47.619 20.18 5.99 41.54 4.02
194 196 1.067495 CGCCTCGGAGGAAGGAATATC 60.067 57.143 27.95 5.40 37.67 1.63
305 315 4.636435 CGGTTTGAGGTGCCCGGT 62.636 66.667 0.00 0.00 36.84 5.28
338 348 3.681897 CAGTCAGTGATTAGGCTGTTCAC 59.318 47.826 18.56 18.56 40.00 3.18
359 369 8.596271 TTAAAACGTTTGTCTGAGTATGATCA 57.404 30.769 15.46 0.00 0.00 2.92
366 376 7.228706 AGGATGATTTAAAACGTTTGTCTGAGT 59.771 33.333 15.46 0.00 0.00 3.41
367 377 7.584987 AGGATGATTTAAAACGTTTGTCTGAG 58.415 34.615 15.46 0.00 0.00 3.35
368 378 7.227711 TGAGGATGATTTAAAACGTTTGTCTGA 59.772 33.333 15.46 0.00 0.00 3.27
369 379 7.359595 TGAGGATGATTTAAAACGTTTGTCTG 58.640 34.615 15.46 0.00 0.00 3.51
374 393 7.617533 CGTTTGAGGATGATTTAAAACGTTT 57.382 32.000 7.96 7.96 37.54 3.60
379 398 6.375377 CCGAACGTTTGAGGATGATTTAAAA 58.625 36.000 17.38 0.00 0.00 1.52
404 423 2.901338 TATGAGAGGGGTCGGATAGG 57.099 55.000 0.00 0.00 0.00 2.57
463 482 3.605749 AAGCCGATGTGGTGGACGG 62.606 63.158 0.00 0.00 46.74 4.79
469 488 0.957395 CTGAGCAAAGCCGATGTGGT 60.957 55.000 0.00 0.00 41.21 4.16
485 504 2.186160 CACGTTTGTGCCAGGCTGA 61.186 57.895 17.94 0.00 39.67 4.26
504 524 7.953158 TTTTCGAATGAAAATATTTGTGGCA 57.047 28.000 0.39 0.00 46.38 4.92
517 537 3.998341 CGGTCTAGGGTTTTTCGAATGAA 59.002 43.478 0.00 0.00 0.00 2.57
525 545 4.961438 TTGACTACGGTCTAGGGTTTTT 57.039 40.909 0.00 0.00 42.54 1.94
577 598 1.584724 GGAGGGGATCAGAAGTGGAA 58.415 55.000 0.00 0.00 0.00 3.53
641 665 0.688487 TCGTTGAAACCGGATTCCCT 59.312 50.000 20.46 0.00 0.00 4.20
652 676 3.994392 GGCTTAGTCAGTCATCGTTGAAA 59.006 43.478 0.00 0.00 32.48 2.69
654 678 2.826128 AGGCTTAGTCAGTCATCGTTGA 59.174 45.455 0.00 0.00 0.00 3.18
656 680 2.093973 CCAGGCTTAGTCAGTCATCGTT 60.094 50.000 0.00 0.00 0.00 3.85
661 685 1.344438 CACACCAGGCTTAGTCAGTCA 59.656 52.381 0.00 0.00 0.00 3.41
669 693 1.671054 GCTTCGCACACCAGGCTTA 60.671 57.895 0.00 0.00 0.00 3.09
677 701 2.375766 CGAGGTCTGCTTCGCACAC 61.376 63.158 0.00 0.00 37.40 3.82
682 706 0.863538 CATCGTCGAGGTCTGCTTCG 60.864 60.000 4.85 0.00 44.19 3.79
688 712 1.032657 CCTCCACATCGTCGAGGTCT 61.033 60.000 10.00 0.00 36.44 3.85
691 715 1.729470 CCTCCTCCACATCGTCGAGG 61.729 65.000 5.17 5.17 41.26 4.63
744 1329 2.466846 AGCAAATTCGGGCCCTTAAAT 58.533 42.857 22.43 13.88 0.00 1.40
748 1333 1.341976 ACATAGCAAATTCGGGCCCTT 60.342 47.619 22.43 4.16 0.00 3.95
755 1340 4.346734 ACAGCAAGACATAGCAAATTCG 57.653 40.909 0.00 0.00 0.00 3.34
830 1416 6.441088 AAAGGAGTATATTCCATCCTGGTC 57.559 41.667 15.98 0.00 41.36 4.02
831 1417 6.160459 ACAAAAGGAGTATATTCCATCCTGGT 59.840 38.462 15.98 4.31 41.36 4.00
872 1458 7.284034 GCGGATGGATGGATAATGATCTAAAAT 59.716 37.037 0.00 0.00 32.15 1.82
891 1479 2.149803 TTATACCCTCGCGCGGATGG 62.150 60.000 31.69 27.46 36.58 3.51
988 1585 0.524392 CGTCGCATCCTCACTCAGAC 60.524 60.000 0.00 0.00 0.00 3.51
1215 1812 1.815003 GGGTGATGCAGGTCAGAAAAG 59.185 52.381 0.00 0.00 0.00 2.27
1218 1815 0.325933 CAGGGTGATGCAGGTCAGAA 59.674 55.000 0.00 0.00 0.00 3.02
1243 1840 5.361285 GTCCATCAACAGTAGACTCCTGTAT 59.639 44.000 0.53 0.00 42.17 2.29
1244 1841 4.705507 GTCCATCAACAGTAGACTCCTGTA 59.294 45.833 0.53 0.00 42.17 2.74
1245 1842 3.511934 GTCCATCAACAGTAGACTCCTGT 59.488 47.826 0.00 0.00 44.80 4.00
1246 1843 3.118956 GGTCCATCAACAGTAGACTCCTG 60.119 52.174 0.00 0.00 36.01 3.86
1247 1844 3.100671 GGTCCATCAACAGTAGACTCCT 58.899 50.000 0.00 0.00 0.00 3.69
1248 1845 2.159226 CGGTCCATCAACAGTAGACTCC 60.159 54.545 0.00 0.00 0.00 3.85
1249 1846 2.492484 ACGGTCCATCAACAGTAGACTC 59.508 50.000 0.00 0.00 0.00 3.36
1250 1847 2.492484 GACGGTCCATCAACAGTAGACT 59.508 50.000 0.00 0.00 0.00 3.24
1300 1908 1.077716 TCTGAGATCCTCGCGTCCA 60.078 57.895 5.77 0.00 32.35 4.02
1437 2045 3.131046 GGGAAGATATTTGGGCAGTGTTG 59.869 47.826 0.00 0.00 0.00 3.33
1523 2131 4.631377 TGTGCACACATCTTAGTTATGAGC 59.369 41.667 17.42 0.00 36.21 4.26
1540 2148 1.010797 CACTCGCAGTTGTGTGCAC 60.011 57.895 10.75 10.75 44.21 4.57
1691 2328 8.190784 CCCAAATAAAGAATAGTGCTACAAAGG 58.809 37.037 0.00 0.00 0.00 3.11
1698 2335 5.044105 AGACCCCCAAATAAAGAATAGTGCT 60.044 40.000 0.00 0.00 0.00 4.40
1701 2338 5.766590 CCAGACCCCCAAATAAAGAATAGT 58.233 41.667 0.00 0.00 0.00 2.12
1723 2360 5.391312 ACAATCCACTTCAATAACTTGCC 57.609 39.130 0.00 0.00 32.11 4.52
1727 2364 6.877611 ACGAAACAATCCACTTCAATAACT 57.122 33.333 0.00 0.00 0.00 2.24
1728 2365 7.924103 AAACGAAACAATCCACTTCAATAAC 57.076 32.000 0.00 0.00 0.00 1.89
1735 2372 4.729227 ACCAAAACGAAACAATCCACTT 57.271 36.364 0.00 0.00 0.00 3.16
1757 2394 8.698973 TTAAAACCCAAGACAACATAGATCAA 57.301 30.769 0.00 0.00 0.00 2.57
1803 2482 7.295340 CACCCCCATCATGATATATGAATGAT 58.705 38.462 8.15 12.00 40.77 2.45
1886 2566 4.875536 CCAAGATCGAAATGTATGGACACA 59.124 41.667 0.00 0.00 38.76 3.72
1919 2601 1.242076 CCAGCCCAAAAGTCTCACAG 58.758 55.000 0.00 0.00 0.00 3.66
1953 2635 3.444805 GAGTCGAGCTGAGCGGGT 61.445 66.667 0.00 0.00 0.00 5.28
1967 2649 0.475906 AAGCAAGTTGAGCAGGGAGT 59.524 50.000 7.16 0.00 0.00 3.85
2013 2695 3.362237 CGAGCTTATTGTACGATAGCAGC 59.638 47.826 15.07 15.07 42.67 5.25
2058 2741 8.557864 TCCGTGAACGTCTTTAAATTTAATGAA 58.442 29.630 21.56 8.72 37.74 2.57
2226 2949 6.484364 AAGGTTCATGAACATTTCCAAAGT 57.516 33.333 33.42 11.67 41.79 2.66
2409 4943 1.305201 GTGTGTCGTTGGTTGATGGT 58.695 50.000 0.00 0.00 0.00 3.55
2434 4968 1.027357 GATAGCTGGCCACAACCATG 58.973 55.000 0.00 0.00 39.54 3.66
2439 4973 2.589540 CGGGATAGCTGGCCACAA 59.410 61.111 0.00 0.00 0.00 3.33
2456 4990 2.103042 GCATCGTGAGTGTGGGAGC 61.103 63.158 0.00 0.00 0.00 4.70
2465 4999 4.838152 CCCCCGGTGCATCGTGAG 62.838 72.222 19.62 6.46 0.00 3.51
2520 5059 5.163457 ACAATTCGTGGTTGGAACATTTTCT 60.163 36.000 0.00 0.00 39.30 2.52
2521 5060 5.047188 ACAATTCGTGGTTGGAACATTTTC 58.953 37.500 0.00 0.00 39.30 2.29
2534 5073 7.010552 TCCAAACATTTGTTTTACAATTCGTGG 59.989 33.333 5.95 2.31 45.07 4.94
2535 5074 7.899974 TCCAAACATTTGTTTTACAATTCGTG 58.100 30.769 5.95 0.00 45.07 4.35
2536 5075 8.655651 ATCCAAACATTTGTTTTACAATTCGT 57.344 26.923 5.95 0.00 45.07 3.85
2646 5194 9.766277 GAGTATTTCTGAAGTTCATGAACATTC 57.234 33.333 33.92 29.70 43.47 2.67
2698 5246 9.667989 ATTTTTGAAAGCTATGAACATTTTTGC 57.332 25.926 0.00 0.00 0.00 3.68
2824 5380 2.511900 GGTCGTGGTTTGTGGGGA 59.488 61.111 0.00 0.00 0.00 4.81
2920 5501 1.535462 CCGGTCATGGTCTTCAACAAC 59.465 52.381 0.00 0.00 0.00 3.32
2931 5512 1.002659 TGTACTTTGGTCCGGTCATGG 59.997 52.381 0.00 0.69 0.00 3.66
2944 5525 1.589803 GGTGCTCACCGTTGTACTTT 58.410 50.000 2.97 0.00 42.29 2.66
3052 5633 2.833943 TGAGAAGATTGTAGGCTGCAGA 59.166 45.455 20.43 0.00 0.00 4.26
3089 5670 5.987019 AGCCCCATAGGTTTCTGTTTATA 57.013 39.130 0.00 0.00 38.26 0.98
3092 5673 3.621461 CGTAGCCCCATAGGTTTCTGTTT 60.621 47.826 0.00 0.00 38.26 2.83
3320 5901 1.561717 CCGGATTGTTTGACGCGACA 61.562 55.000 15.93 11.23 0.00 4.35
3368 5950 5.244402 TCAAGCCTCAATCACATTCATTGTT 59.756 36.000 0.00 0.00 36.00 2.83
3401 5983 8.035448 AGCCTAATTAATAGAGGTTGTTAGCT 57.965 34.615 14.74 0.00 33.04 3.32
3432 6014 7.181418 TGATGTGTTTTAACAGAACAACGTAC 58.819 34.615 0.00 0.00 40.05 3.67
3437 6019 9.243637 GCTAATTGATGTGTTTTAACAGAACAA 57.756 29.630 14.57 14.57 44.60 2.83
3523 6105 5.452917 GGTTAGCGTTGTAGATTAGGGATGT 60.453 44.000 0.00 0.00 0.00 3.06
3530 6120 6.509656 CCACATAGGTTAGCGTTGTAGATTA 58.490 40.000 0.00 0.00 0.00 1.75
3532 6122 4.945246 CCACATAGGTTAGCGTTGTAGAT 58.055 43.478 0.00 0.00 0.00 1.98
3557 6147 7.860613 TGCTTTGATACCACAACATATAATCG 58.139 34.615 0.00 0.00 0.00 3.34
3564 6154 5.726980 ACAATGCTTTGATACCACAACAT 57.273 34.783 18.35 0.00 36.64 2.71
4062 6659 2.093658 GTGCCCCTATTCTTCGAGTCAA 60.094 50.000 0.00 0.00 0.00 3.18
4112 6709 0.861837 CGCTCTTCCGATAACATGCC 59.138 55.000 0.00 0.00 0.00 4.40
4184 6781 0.263765 AACTCTAGGGCGGTGGGATA 59.736 55.000 0.00 0.00 0.00 2.59
4568 7172 1.901591 CAGCTCATTAATCCGCCCAT 58.098 50.000 0.00 0.00 0.00 4.00
4623 7242 1.594331 GAACAGAGCCGGTCAGTTTT 58.406 50.000 1.90 0.00 35.16 2.43
4624 7243 0.600255 CGAACAGAGCCGGTCAGTTT 60.600 55.000 1.90 0.00 35.16 2.66
4625 7244 1.006102 CGAACAGAGCCGGTCAGTT 60.006 57.895 7.97 7.97 37.59 3.16
4626 7245 1.745320 AACGAACAGAGCCGGTCAGT 61.745 55.000 1.90 0.00 0.00 3.41
4631 7250 1.128692 GATTCAAACGAACAGAGCCGG 59.871 52.381 0.00 0.00 0.00 6.13
4643 7262 6.017933 CACATGAGCTTAACGAGATTCAAAC 58.982 40.000 0.00 0.00 0.00 2.93
4668 7287 5.010719 GTCTATTAACGACTGATCATGGGGA 59.989 44.000 0.00 0.00 0.00 4.81
4699 7318 2.621998 CTGATCCCGTAGACCGTAACAT 59.378 50.000 0.00 0.00 33.66 2.71
4760 7379 1.324736 CAAATTAGCGCGTCACCTCTC 59.675 52.381 8.43 0.00 0.00 3.20
4863 7482 1.065928 CGCGGGACACCATCTAGTC 59.934 63.158 0.00 0.00 36.13 2.59
5035 7654 4.405680 TGGAGTGTACTGGTGATAGAATGG 59.594 45.833 0.00 0.00 0.00 3.16
5049 7668 6.072673 CCTTATTTGTTCCTGTTGGAGTGTAC 60.073 42.308 0.00 0.00 44.24 2.90
5147 7766 1.336440 TGAGTTTGCAATTGACCCACG 59.664 47.619 10.34 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.