Multiple sequence alignment - TraesCS3D01G304600

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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 TraesCS3D01G304600 chr3D 100.000 4910 0 0 1 4910 418726288 418731197 0.000000e+00 9068.0
1 TraesCS3D01G304600 chr3D 97.917 48 1 0 2437 2484 418728636 418728683 3.150000e-12 84.2
2 TraesCS3D01G304600 chr3D 97.917 48 1 0 2349 2396 418728724 418728771 3.150000e-12 84.2
3 TraesCS3D01G304600 chr3B 90.351 4923 309 97 99 4910 545065420 545070287 0.000000e+00 6307.0
4 TraesCS3D01G304600 chr3B 100.000 46 0 0 2348 2393 545067784 545067829 8.760000e-13 86.1
5 TraesCS3D01G304600 chr3A 91.553 4120 210 70 856 4910 532451462 532447416 0.000000e+00 5553.0
6 TraesCS3D01G304600 chr5D 82.516 612 92 10 1 599 333989761 333989152 1.570000e-144 523.0
7 TraesCS3D01G304600 chr5A 81.076 576 98 9 69 636 435686712 435686140 2.700000e-122 449.0
8 TraesCS3D01G304600 chr5A 78.862 246 36 9 1 239 333403917 333403681 8.510000e-33 152.0
9 TraesCS3D01G304600 chr1D 78.003 591 101 17 1 585 134685228 134684661 1.310000e-90 344.0
10 TraesCS3D01G304600 chr1D 91.083 157 14 0 1135 1291 423043280 423043124 3.850000e-51 213.0
11 TraesCS3D01G304600 chr1D 93.182 44 3 0 562 605 73668699 73668742 1.140000e-06 65.8
12 TraesCS3D01G304600 chr7B 75.427 761 122 40 1 722 622804882 622804148 4.770000e-80 309.0
13 TraesCS3D01G304600 chr7B 75.743 639 100 30 1 621 380505746 380506347 2.250000e-68 270.0
14 TraesCS3D01G304600 chr7D 76.056 639 111 31 1 605 571237973 571238603 1.340000e-75 294.0
15 TraesCS3D01G304600 chr7D 75.753 631 125 19 1 620 568036832 568036219 4.810000e-75 292.0
16 TraesCS3D01G304600 chr7D 73.844 627 97 44 1 604 30483735 30484317 2.330000e-43 187.0
17 TraesCS3D01G304600 chr7D 83.908 174 23 3 1 169 209835464 209835637 1.410000e-35 161.0
18 TraesCS3D01G304600 chr1A 92.357 157 12 0 1135 1291 518974118 518973962 1.780000e-54 224.0
19 TraesCS3D01G304600 chr1B 91.083 157 14 0 1135 1291 572295414 572295258 3.850000e-51 213.0
20 TraesCS3D01G304600 chr1B 74.390 246 47 9 204 446 615752998 615753230 1.880000e-14 91.6
21 TraesCS3D01G304600 chr2D 81.022 274 41 8 1 266 605383908 605383638 1.790000e-49 207.0
22 TraesCS3D01G304600 chr2D 75.676 407 65 24 221 605 632130849 632130455 6.530000e-39 172.0
23 TraesCS3D01G304600 chr5B 73.731 670 115 37 1 654 2548749 2549373 6.440000e-49 206.0
24 TraesCS3D01G304600 chr5B 74.234 555 103 27 1 545 429099478 429100002 3.880000e-46 196.0
25 TraesCS3D01G304600 chr4B 73.623 599 111 34 2 568 39296304 39296887 2.330000e-43 187.0


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 TraesCS3D01G304600 chr3D 418726288 418731197 4909 False 3078.80 9068 98.611333 1 4910 3 chr3D.!!$F1 4909
1 TraesCS3D01G304600 chr3B 545065420 545070287 4867 False 3196.55 6307 95.175500 99 4910 2 chr3B.!!$F1 4811
2 TraesCS3D01G304600 chr3A 532447416 532451462 4046 True 5553.00 5553 91.553000 856 4910 1 chr3A.!!$R1 4054
3 TraesCS3D01G304600 chr5D 333989152 333989761 609 True 523.00 523 82.516000 1 599 1 chr5D.!!$R1 598
4 TraesCS3D01G304600 chr5A 435686140 435686712 572 True 449.00 449 81.076000 69 636 1 chr5A.!!$R2 567
5 TraesCS3D01G304600 chr1D 134684661 134685228 567 True 344.00 344 78.003000 1 585 1 chr1D.!!$R1 584
6 TraesCS3D01G304600 chr7B 622804148 622804882 734 True 309.00 309 75.427000 1 722 1 chr7B.!!$R1 721
7 TraesCS3D01G304600 chr7B 380505746 380506347 601 False 270.00 270 75.743000 1 621 1 chr7B.!!$F1 620
8 TraesCS3D01G304600 chr7D 571237973 571238603 630 False 294.00 294 76.056000 1 605 1 chr7D.!!$F3 604
9 TraesCS3D01G304600 chr7D 568036219 568036832 613 True 292.00 292 75.753000 1 620 1 chr7D.!!$R1 619
10 TraesCS3D01G304600 chr5B 2548749 2549373 624 False 206.00 206 73.731000 1 654 1 chr5B.!!$F1 653

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
760 897 0.179020 TATGGATGCGGGCCTTTGAG 60.179 55.0 0.84 0.0 0.00 3.02 F
908 1045 0.471022 AACTGGAACGGGGGCAAAAT 60.471 50.0 0.00 0.0 40.47 1.82 F
1629 1790 1.033574 CGTTGCAAGTTGGGGGTAAA 58.966 50.0 0.00 0.0 0.00 2.01 F
2374 2568 0.178990 AGTCCTGGCTGAAACCAACC 60.179 55.0 0.00 0.0 39.86 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 2549 0.178990 GGTTGGTTTCAGCCAGGACT 60.179 55.000 0.0 0.0 42.87 3.85 R
2356 2550 0.178990 AGGTTGGTTTCAGCCAGGAC 60.179 55.000 0.0 0.0 45.35 3.85 R
3282 3508 1.103803 TCTCAGGCGTCACATACTCC 58.896 55.000 0.0 0.0 32.72 3.85 R
3964 4197 1.347378 TGGTGCTGCTCTGAACATACA 59.653 47.619 0.0 0.0 0.00 2.29 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
29 30 0.916358 CCACATCCACCTCCTCCCTT 60.916 60.000 0.00 0.00 0.00 3.95
31 32 1.355720 CACATCCACCTCCTCCCTTTT 59.644 52.381 0.00 0.00 0.00 2.27
44 45 3.357079 CTTTTCGTGCCGCCAGCT 61.357 61.111 0.00 0.00 44.23 4.24
59 63 2.233566 AGCTCAAGCCCATCCACCA 61.234 57.895 0.00 0.00 43.38 4.17
60 64 1.076485 GCTCAAGCCCATCCACCAT 60.076 57.895 0.00 0.00 34.31 3.55
62 71 0.549950 CTCAAGCCCATCCACCATCT 59.450 55.000 0.00 0.00 0.00 2.90
67 76 0.396060 GCCCATCCACCATCTCTCTC 59.604 60.000 0.00 0.00 0.00 3.20
81 90 1.684049 CTCTCCCGCTCTTCCCACT 60.684 63.158 0.00 0.00 0.00 4.00
84 93 3.003173 CCCGCTCTTCCCACTCCA 61.003 66.667 0.00 0.00 0.00 3.86
169 178 5.679601 GGTTCTAGATTGAGCAGGAGATTT 58.320 41.667 0.00 0.00 0.00 2.17
242 289 1.049855 CAGGAGGATGAGGAGCAGCT 61.050 60.000 0.00 0.00 32.29 4.24
301 394 2.363795 AGGTGCCGGATCCGAAGA 60.364 61.111 35.42 15.30 42.83 2.87
355 466 0.389817 CAACATGAAGGACGCGGAGA 60.390 55.000 12.47 0.00 0.00 3.71
412 523 1.751927 CAACAGGCCATCCCAGAGC 60.752 63.158 5.01 0.00 35.39 4.09
463 583 2.807676 ACCTCAGTTAATTTGGCAGGG 58.192 47.619 0.00 0.00 0.00 4.45
611 732 3.857052 GTGGACATCACCGACAAAGATA 58.143 45.455 0.00 0.00 40.39 1.98
622 747 6.435277 TCACCGACAAAGATAAAGGTAGTACT 59.565 38.462 0.00 0.00 0.00 2.73
664 801 6.984740 TTTATTGTTTGCACGCTTTTCTAG 57.015 33.333 0.00 0.00 0.00 2.43
665 802 4.829064 ATTGTTTGCACGCTTTTCTAGA 57.171 36.364 0.00 0.00 0.00 2.43
668 805 5.181690 TGTTTGCACGCTTTTCTAGAAAT 57.818 34.783 18.37 0.94 0.00 2.17
673 810 4.694982 TGCACGCTTTTCTAGAAATGATCA 59.305 37.500 26.83 17.00 0.00 2.92
752 889 3.748048 CAGTCACTATTTATGGATGCGGG 59.252 47.826 0.00 0.00 0.00 6.13
753 890 2.484264 GTCACTATTTATGGATGCGGGC 59.516 50.000 0.00 0.00 0.00 6.13
754 891 1.812571 CACTATTTATGGATGCGGGCC 59.187 52.381 0.00 0.00 0.00 5.80
755 892 1.705186 ACTATTTATGGATGCGGGCCT 59.295 47.619 0.84 0.00 0.00 5.19
756 893 2.108250 ACTATTTATGGATGCGGGCCTT 59.892 45.455 0.84 0.00 0.00 4.35
757 894 2.086610 ATTTATGGATGCGGGCCTTT 57.913 45.000 0.84 0.00 0.00 3.11
758 895 1.110442 TTTATGGATGCGGGCCTTTG 58.890 50.000 0.84 0.00 0.00 2.77
759 896 0.257328 TTATGGATGCGGGCCTTTGA 59.743 50.000 0.84 0.00 0.00 2.69
760 897 0.179020 TATGGATGCGGGCCTTTGAG 60.179 55.000 0.84 0.00 0.00 3.02
761 898 2.830370 GGATGCGGGCCTTTGAGG 60.830 66.667 0.84 0.00 38.80 3.86
773 910 0.947244 CTTTGAGGCGTTGCAAGTCT 59.053 50.000 0.00 0.31 0.00 3.24
830 967 4.527427 ACTTGTACCTCTTCTACCCTTCAC 59.473 45.833 0.00 0.00 0.00 3.18
837 974 4.284746 CCTCTTCTACCCTTCACTTTCACT 59.715 45.833 0.00 0.00 0.00 3.41
845 982 3.741344 CCCTTCACTTTCACTTGTAGACG 59.259 47.826 0.00 0.00 0.00 4.18
879 1016 4.115199 AGATTGGCCGCCCACTCC 62.115 66.667 7.03 0.00 40.64 3.85
908 1045 0.471022 AACTGGAACGGGGGCAAAAT 60.471 50.000 0.00 0.00 40.47 1.82
942 1079 3.382803 GAGCTCATCGCCTGCACCT 62.383 63.158 9.40 0.00 40.39 4.00
977 1120 1.662629 CTAGACAAGCCTGTGCAATCG 59.337 52.381 0.00 0.00 41.13 3.34
1377 1523 2.165641 TGCCTAGCATAATACGATCGGG 59.834 50.000 20.98 7.68 31.71 5.14
1393 1539 2.781911 GGGACGAGGAATTTCTGCC 58.218 57.895 0.00 0.00 0.00 4.85
1502 1663 1.078072 TATTGCCACGGCGACCATT 60.078 52.632 16.62 6.38 45.51 3.16
1532 1693 3.186047 GATACTTGCACGCGCGGT 61.186 61.111 35.22 23.24 42.97 5.68
1629 1790 1.033574 CGTTGCAAGTTGGGGGTAAA 58.966 50.000 0.00 0.00 0.00 2.01
1639 1800 3.161866 GTTGGGGGTAAATTTCTGCTGA 58.838 45.455 0.00 0.00 0.00 4.26
1651 1814 6.519679 AATTTCTGCTGATTGCTCATACAA 57.480 33.333 0.00 0.00 43.37 2.41
1696 1859 6.975197 TCATCTTTGAGCGACTGATTTAGTAG 59.025 38.462 0.00 0.00 40.53 2.57
1702 1865 5.417894 TGAGCGACTGATTTAGTAGGAAGAA 59.582 40.000 0.00 0.00 40.53 2.52
1714 1877 4.504858 AGTAGGAAGAAATAACGGTGCAG 58.495 43.478 0.00 0.00 0.00 4.41
1733 1896 7.375053 GGTGCAGTTTATGAAGTTTGGATTTA 58.625 34.615 0.00 0.00 0.00 1.40
1781 1944 7.734924 ACGATGCATGATTACACAGAATATT 57.265 32.000 2.46 0.00 0.00 1.28
1977 2145 8.319057 TGCTAAAGATTTCTGGACTTCCTATA 57.681 34.615 0.00 0.00 36.82 1.31
2022 2190 2.421529 GGTGGAATGCTTAACCTCGGAT 60.422 50.000 0.00 0.00 0.00 4.18
2152 2320 3.136443 TCGAGCAGGGTAATTTGATCCAT 59.864 43.478 0.00 0.00 0.00 3.41
2168 2336 7.894753 TTGATCCATTGATTTTAGTGGCATA 57.105 32.000 0.00 0.00 0.00 3.14
2228 2399 5.206905 AGCACCAATAACTTAATTCCCCT 57.793 39.130 0.00 0.00 0.00 4.79
2270 2441 3.417069 ACCACTCATCAACAATTCCGA 57.583 42.857 0.00 0.00 0.00 4.55
2286 2459 4.966965 TTCCGAAACAGCAAGTACAAAA 57.033 36.364 0.00 0.00 0.00 2.44
2347 2541 3.476552 TGGCTAGAGGTTTGAAACACTG 58.523 45.455 10.53 5.40 0.00 3.66
2350 2544 5.221843 TGGCTAGAGGTTTGAAACACTGTAT 60.222 40.000 10.53 0.00 0.00 2.29
2351 2545 5.122396 GGCTAGAGGTTTGAAACACTGTATG 59.878 44.000 10.53 4.12 0.00 2.39
2352 2546 5.390991 GCTAGAGGTTTGAAACACTGTATGC 60.391 44.000 10.53 8.87 0.00 3.14
2353 2547 4.460263 AGAGGTTTGAAACACTGTATGCA 58.540 39.130 10.53 0.00 0.00 3.96
2354 2548 5.072741 AGAGGTTTGAAACACTGTATGCAT 58.927 37.500 10.53 3.79 0.00 3.96
2355 2549 6.237901 AGAGGTTTGAAACACTGTATGCATA 58.762 36.000 10.53 1.16 0.00 3.14
2356 2550 6.372659 AGAGGTTTGAAACACTGTATGCATAG 59.627 38.462 6.67 0.01 0.00 2.23
2357 2551 6.003950 AGGTTTGAAACACTGTATGCATAGT 58.996 36.000 6.67 0.76 0.00 2.12
2358 2552 6.149474 AGGTTTGAAACACTGTATGCATAGTC 59.851 38.462 6.67 0.00 0.00 2.59
2359 2553 6.314784 GTTTGAAACACTGTATGCATAGTCC 58.685 40.000 6.67 0.00 0.00 3.85
2360 2554 5.420725 TGAAACACTGTATGCATAGTCCT 57.579 39.130 6.67 0.00 0.00 3.85
2362 2556 3.827008 ACACTGTATGCATAGTCCTGG 57.173 47.619 6.67 0.00 0.00 4.45
2363 2557 2.158900 ACACTGTATGCATAGTCCTGGC 60.159 50.000 6.67 0.00 0.00 4.85
2364 2558 2.103771 CACTGTATGCATAGTCCTGGCT 59.896 50.000 6.67 0.00 0.00 4.75
2365 2559 2.103771 ACTGTATGCATAGTCCTGGCTG 59.896 50.000 6.67 0.48 0.00 4.85
2366 2560 2.366590 CTGTATGCATAGTCCTGGCTGA 59.633 50.000 6.67 0.00 0.00 4.26
2367 2561 2.771372 TGTATGCATAGTCCTGGCTGAA 59.229 45.455 6.67 0.00 0.00 3.02
2368 2562 3.199727 TGTATGCATAGTCCTGGCTGAAA 59.800 43.478 6.67 0.00 0.00 2.69
2369 2563 2.113860 TGCATAGTCCTGGCTGAAAC 57.886 50.000 0.00 0.00 0.00 2.78
2370 2564 1.340017 TGCATAGTCCTGGCTGAAACC 60.340 52.381 0.00 0.00 0.00 3.27
2371 2565 1.340017 GCATAGTCCTGGCTGAAACCA 60.340 52.381 0.00 0.00 38.29 3.67
2372 2566 2.879756 GCATAGTCCTGGCTGAAACCAA 60.880 50.000 0.00 0.00 39.86 3.67
2373 2567 2.561478 TAGTCCTGGCTGAAACCAAC 57.439 50.000 0.00 0.00 39.86 3.77
2374 2568 0.178990 AGTCCTGGCTGAAACCAACC 60.179 55.000 0.00 0.00 39.86 3.77
2375 2569 0.178990 GTCCTGGCTGAAACCAACCT 60.179 55.000 0.00 0.00 39.86 3.50
2376 2570 1.073284 GTCCTGGCTGAAACCAACCTA 59.927 52.381 0.00 0.00 39.86 3.08
2377 2571 1.777878 TCCTGGCTGAAACCAACCTAA 59.222 47.619 0.00 0.00 39.86 2.69
2378 2572 1.886542 CCTGGCTGAAACCAACCTAAC 59.113 52.381 0.00 0.00 39.86 2.34
2379 2573 2.582052 CTGGCTGAAACCAACCTAACA 58.418 47.619 0.00 0.00 39.86 2.41
2380 2574 2.955660 CTGGCTGAAACCAACCTAACAA 59.044 45.455 0.00 0.00 39.86 2.83
2381 2575 3.366396 TGGCTGAAACCAACCTAACAAA 58.634 40.909 0.00 0.00 36.55 2.83
2382 2576 3.383185 TGGCTGAAACCAACCTAACAAAG 59.617 43.478 0.00 0.00 36.55 2.77
2383 2577 3.383505 GGCTGAAACCAACCTAACAAAGT 59.616 43.478 0.00 0.00 0.00 2.66
2384 2578 4.142026 GGCTGAAACCAACCTAACAAAGTT 60.142 41.667 0.00 0.00 0.00 2.66
2385 2579 5.068067 GGCTGAAACCAACCTAACAAAGTTA 59.932 40.000 0.00 0.00 0.00 2.24
2386 2580 6.406065 GGCTGAAACCAACCTAACAAAGTTAA 60.406 38.462 0.00 0.00 0.00 2.01
2387 2581 7.036829 GCTGAAACCAACCTAACAAAGTTAAA 58.963 34.615 0.00 0.00 0.00 1.52
2388 2582 7.009815 GCTGAAACCAACCTAACAAAGTTAAAC 59.990 37.037 0.00 0.00 0.00 2.01
2389 2583 7.893658 TGAAACCAACCTAACAAAGTTAAACA 58.106 30.769 0.00 0.00 0.00 2.83
2390 2584 8.365647 TGAAACCAACCTAACAAAGTTAAACAA 58.634 29.630 0.00 0.00 0.00 2.83
2391 2585 9.205719 GAAACCAACCTAACAAAGTTAAACAAA 57.794 29.630 0.00 0.00 0.00 2.83
2392 2586 9.727859 AAACCAACCTAACAAAGTTAAACAAAT 57.272 25.926 0.00 0.00 0.00 2.32
2441 2637 7.959733 TGTCTTGTTTACTTGACTAATATGCG 58.040 34.615 0.00 0.00 0.00 4.73
2543 2739 7.666804 TCAGTTCTACCACATAACTGTACTACA 59.333 37.037 12.61 0.00 46.49 2.74
2580 2782 2.703536 TCAGGCAGTGTTTTAGTCTGGA 59.296 45.455 0.00 0.00 35.77 3.86
2621 2823 4.713814 TGACCTCTGAGCAACTATGAATCT 59.286 41.667 0.00 0.00 0.00 2.40
2637 2839 9.941325 ACTATGAATCTAATTTCTATCCAGCTG 57.059 33.333 6.78 6.78 0.00 4.24
2649 2851 2.584835 TCCAGCTGCACAAACCTTAT 57.415 45.000 8.66 0.00 0.00 1.73
2654 2856 4.501229 CCAGCTGCACAAACCTTATCAAAA 60.501 41.667 8.66 0.00 0.00 2.44
2655 2857 5.232463 CAGCTGCACAAACCTTATCAAAAT 58.768 37.500 0.00 0.00 0.00 1.82
2656 2858 5.119588 CAGCTGCACAAACCTTATCAAAATG 59.880 40.000 0.00 0.00 0.00 2.32
2657 2859 4.990426 GCTGCACAAACCTTATCAAAATGT 59.010 37.500 0.00 0.00 0.00 2.71
2658 2860 5.466393 GCTGCACAAACCTTATCAAAATGTT 59.534 36.000 0.00 0.00 0.00 2.71
2659 2861 6.346838 GCTGCACAAACCTTATCAAAATGTTC 60.347 38.462 0.00 0.00 0.00 3.18
2660 2862 6.815089 TGCACAAACCTTATCAAAATGTTCT 58.185 32.000 0.00 0.00 0.00 3.01
2661 2863 6.922957 TGCACAAACCTTATCAAAATGTTCTC 59.077 34.615 0.00 0.00 0.00 2.87
2662 2864 6.922957 GCACAAACCTTATCAAAATGTTCTCA 59.077 34.615 0.00 0.00 0.00 3.27
2685 2888 5.302823 CAGATGTGTACCATATCAGAGACCA 59.697 44.000 4.20 0.00 35.03 4.02
2717 2924 6.128445 CGATCAAAAGCAGAATGTTACTGTCT 60.128 38.462 0.00 0.00 39.31 3.41
2725 2932 8.798859 AGCAGAATGTTACTGTCTATTTGATT 57.201 30.769 0.00 0.00 39.31 2.57
2732 2939 8.703604 TGTTACTGTCTATTTGATTAGTGAGC 57.296 34.615 0.00 0.00 0.00 4.26
2806 3016 3.883489 GGCCAATTGTCATTCCCTAGTAC 59.117 47.826 4.43 0.00 0.00 2.73
2863 3073 9.928236 TGTTTTATTTGAGTTTTGCTAAAATGC 57.072 25.926 0.00 0.00 38.43 3.56
2869 3079 4.915085 TGAGTTTTGCTAAAATGCTAACGC 59.085 37.500 0.00 0.00 35.23 4.84
2870 3080 5.121221 AGTTTTGCTAAAATGCTAACGCT 57.879 34.783 0.00 0.00 35.23 5.07
2871 3081 6.072948 TGAGTTTTGCTAAAATGCTAACGCTA 60.073 34.615 0.00 0.00 35.23 4.26
2872 3082 6.674066 AGTTTTGCTAAAATGCTAACGCTAA 58.326 32.000 0.00 0.00 35.23 3.09
2873 3083 7.312899 AGTTTTGCTAAAATGCTAACGCTAAT 58.687 30.769 0.00 0.00 35.23 1.73
2874 3084 7.273381 AGTTTTGCTAAAATGCTAACGCTAATG 59.727 33.333 0.00 0.00 35.23 1.90
2875 3085 6.429791 TTGCTAAAATGCTAACGCTAATGA 57.570 33.333 0.00 0.00 36.97 2.57
2876 3086 6.618287 TGCTAAAATGCTAACGCTAATGAT 57.382 33.333 0.00 0.00 36.97 2.45
2940 3165 5.104900 TCCAGTTAGCCCTTGTATCTTCTTC 60.105 44.000 0.00 0.00 0.00 2.87
2962 3187 6.627087 TCTTCTTTTCTCATGGTATCTGGT 57.373 37.500 0.00 0.00 0.00 4.00
3122 3347 4.091549 AGGTGAAACAAGCCATGATTGAT 58.908 39.130 15.07 3.32 39.98 2.57
3167 3392 5.341872 TTCTCACATTGGGCCAATATTTG 57.658 39.130 30.26 24.63 32.35 2.32
3282 3508 5.827666 ACAGAAAAACATTTGACGGTTAGG 58.172 37.500 0.00 0.00 0.00 2.69
3520 3747 8.097662 CAGTTCTGGTCCTATTTCTAGTTCTTT 58.902 37.037 0.00 0.00 0.00 2.52
3527 3754 8.047310 GGTCCTATTTCTAGTTCTTTGATCCAA 58.953 37.037 0.00 0.00 0.00 3.53
3549 3776 1.705186 AGTGGAGTGGGCATGTAGTTT 59.295 47.619 0.00 0.00 0.00 2.66
3596 3823 7.921786 TTTTATAAGATGAACAGGTGGACAG 57.078 36.000 0.00 0.00 0.00 3.51
3806 4037 5.581126 TGCATGAACTCACTTTCTTTGTT 57.419 34.783 0.00 0.00 0.00 2.83
3883 4114 7.878127 TCGAGAATTTGGTCAGAAATAAGAAGT 59.122 33.333 0.00 0.00 0.00 3.01
3897 4128 2.593346 AGAAGTCTAAGCCTGCATCG 57.407 50.000 0.00 0.00 0.00 3.84
3964 4197 4.510167 ATCCATCGGATTCTTCCACTTT 57.490 40.909 0.00 0.00 39.79 2.66
3997 4230 2.115266 CACCAGAAAAGCGGGGGT 59.885 61.111 0.00 0.00 35.99 4.95
4037 4273 1.494721 TCTGAAAGTTTGTCCCCTGCT 59.505 47.619 0.00 0.00 33.76 4.24
4198 4441 6.085458 GTCGTTTGATTATGCGATGCTTTATG 59.915 38.462 0.00 0.00 35.78 1.90
4313 4556 8.870160 TTTTTGGAGATAAAATCACAACACTG 57.130 30.769 0.00 0.00 31.32 3.66
4385 4628 5.243426 TGTAGCTTGAGGAACAAAAACAC 57.757 39.130 0.00 0.00 38.08 3.32
4388 4631 6.600032 TGTAGCTTGAGGAACAAAAACACTTA 59.400 34.615 0.00 0.00 38.08 2.24
4413 4656 5.659440 AGTGTTAAATTGGCCGAATTCAT 57.341 34.783 6.22 3.13 32.76 2.57
4516 4759 6.047870 TGGATTTGAAATTTTGTGACACAGG 58.952 36.000 8.55 0.00 0.00 4.00
4517 4760 6.048509 GGATTTGAAATTTTGTGACACAGGT 58.951 36.000 8.55 0.00 0.00 4.00
4524 4767 8.511321 TGAAATTTTGTGACACAGGTGATATAC 58.489 33.333 8.55 0.74 0.00 1.47
4529 4772 6.650427 TGTGACACAGGTGATATACTATCC 57.350 41.667 3.56 0.00 0.00 2.59
4553 4796 6.490040 CCTGTCTTTGTTCCTAGAATTTTCCA 59.510 38.462 0.00 0.00 0.00 3.53
4577 4820 7.551974 CCATGACTCTTATTGTGAAGTTCTCAT 59.448 37.037 8.37 0.61 36.14 2.90
4620 4863 6.980593 TGGAATTTTGGTCACTCTTATTGTG 58.019 36.000 0.00 0.00 36.82 3.33
4629 4872 6.042093 TGGTCACTCTTATTGTGAAGTTCTCT 59.958 38.462 4.17 0.00 44.63 3.10
4723 4969 7.371159 GCTTGCTTTATCTTTACTGTTCCTTT 58.629 34.615 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.548031 GAGATGGTGGATGGGCTTGA 59.452 55.000 0.00 0.00 0.00 3.02
59 63 0.469144 GGGAAGAGCGGGAGAGAGAT 60.469 60.000 0.00 0.00 0.00 2.75
60 64 1.076632 GGGAAGAGCGGGAGAGAGA 60.077 63.158 0.00 0.00 0.00 3.10
62 71 1.682684 GTGGGAAGAGCGGGAGAGA 60.683 63.158 0.00 0.00 0.00 3.10
67 76 2.317149 GATGGAGTGGGAAGAGCGGG 62.317 65.000 0.00 0.00 0.00 6.13
81 90 0.107268 CCATGGCGATGTCAGATGGA 59.893 55.000 7.98 0.00 36.45 3.41
84 93 1.807755 CGAACCATGGCGATGTCAGAT 60.808 52.381 13.04 0.00 0.00 2.90
184 193 3.197790 GTCGGCTGCGATGCATGT 61.198 61.111 2.46 0.00 38.13 3.21
187 201 3.120385 CAAGTCGGCTGCGATGCA 61.120 61.111 0.00 0.00 36.92 3.96
242 289 2.367377 CATCCTCCCCTGCCTCCA 60.367 66.667 0.00 0.00 0.00 3.86
289 364 0.755698 TCCTCCTTCTTCGGATCCGG 60.756 60.000 32.79 18.56 40.25 5.14
355 466 0.473755 TGCACACCCATGAACTCTGT 59.526 50.000 0.00 0.00 0.00 3.41
412 523 1.365293 TATGCCTCATCCTGGATGGG 58.635 55.000 30.88 28.81 39.99 4.00
611 732 9.344772 CAGTAGATCAGATACAGTACTACCTTT 57.655 37.037 0.00 0.00 32.14 3.11
690 827 2.723273 TCTCTGCGTCCAGATACTTCA 58.277 47.619 0.00 0.00 46.44 3.02
691 828 3.701241 CTTCTCTGCGTCCAGATACTTC 58.299 50.000 0.00 0.00 46.44 3.01
692 829 2.159170 GCTTCTCTGCGTCCAGATACTT 60.159 50.000 0.00 0.00 46.44 2.24
693 830 1.407258 GCTTCTCTGCGTCCAGATACT 59.593 52.381 0.00 0.00 46.44 2.12
703 840 3.599514 CGTGTTAAATTTGCTTCTCTGCG 59.400 43.478 0.00 0.00 35.36 5.18
753 890 0.040067 GACTTGCAACGCCTCAAAGG 60.040 55.000 0.00 0.00 38.80 3.11
754 891 0.947244 AGACTTGCAACGCCTCAAAG 59.053 50.000 0.00 0.00 0.00 2.77
755 892 1.333619 GAAGACTTGCAACGCCTCAAA 59.666 47.619 0.00 0.00 0.00 2.69
756 893 0.944386 GAAGACTTGCAACGCCTCAA 59.056 50.000 0.00 0.00 0.00 3.02
757 894 0.884704 GGAAGACTTGCAACGCCTCA 60.885 55.000 1.24 0.00 0.00 3.86
758 895 0.603975 AGGAAGACTTGCAACGCCTC 60.604 55.000 9.55 0.00 0.00 4.70
759 896 0.179018 AAGGAAGACTTGCAACGCCT 60.179 50.000 9.55 0.00 38.21 5.52
760 897 2.331265 AAGGAAGACTTGCAACGCC 58.669 52.632 9.55 0.00 38.21 5.68
773 910 1.522668 CTGCCGATGAACACAAGGAA 58.477 50.000 0.00 0.00 0.00 3.36
830 967 3.664486 CACGAGACGTCTACAAGTGAAAG 59.336 47.826 25.61 9.10 38.32 2.62
837 974 2.734670 CAAACCACGAGACGTCTACAA 58.265 47.619 20.09 0.00 38.32 2.41
879 1016 1.435577 CGTTCCAGTTTTACCCCTCG 58.564 55.000 0.00 0.00 0.00 4.63
908 1045 2.679092 TCGGAGCGAGGGGTAAGA 59.321 61.111 0.00 0.00 0.00 2.10
1197 1343 3.823330 CGCGCGTACTTCTCCCCT 61.823 66.667 24.19 0.00 0.00 4.79
1377 1523 0.741221 AGCGGCAGAAATTCCTCGTC 60.741 55.000 1.45 0.00 0.00 4.20
1393 1539 1.219522 AAACCCGACACTCGAAAGCG 61.220 55.000 0.00 0.00 43.74 4.68
1478 1639 3.199891 GCCGTGGCAATACCGTCC 61.200 66.667 5.89 0.00 43.94 4.79
1484 1645 0.178301 TAATGGTCGCCGTGGCAATA 59.822 50.000 12.06 0.00 42.06 1.90
1502 1663 1.037493 AAGTATCGCCGAGCACCATA 58.963 50.000 0.00 0.00 0.00 2.74
1532 1693 2.048597 ACGGCGCAGAATCGACAA 60.049 55.556 16.26 0.00 37.32 3.18
1535 1696 1.805539 CTTCACGGCGCAGAATCGA 60.806 57.895 16.26 2.05 0.00 3.59
1696 1859 4.499037 AAACTGCACCGTTATTTCTTCC 57.501 40.909 0.00 0.00 0.00 3.46
1702 1865 6.569179 AACTTCATAAACTGCACCGTTATT 57.431 33.333 0.00 0.00 0.00 1.40
1781 1944 5.885352 TCTGGAAAGAACAACATTCTGTCAA 59.115 36.000 8.68 0.00 35.07 3.18
1792 1955 7.540474 ACATAGTCTACTCTGGAAAGAACAA 57.460 36.000 1.26 0.00 0.00 2.83
1909 2072 8.918202 ATAAATGAAAGACACACCAAACTAGA 57.082 30.769 0.00 0.00 0.00 2.43
1913 2076 8.871686 AAAGATAAATGAAAGACACACCAAAC 57.128 30.769 0.00 0.00 0.00 2.93
1977 2145 0.768221 TCCCAGGTTTGAGCTCCTGT 60.768 55.000 12.15 0.00 46.79 4.00
2022 2190 1.066143 GCCTCCAGATCACCTCGAAAA 60.066 52.381 0.00 0.00 0.00 2.29
2152 2320 9.800433 CATACAATGTTATGCCACTAAAATCAA 57.200 29.630 0.00 0.00 0.00 2.57
2228 2399 8.038944 GTGGTAATCTAACAGGTCAGTTAATCA 58.961 37.037 0.00 0.00 33.89 2.57
2286 2459 7.039313 AGAAAGAAACCGAAAGTAGCAATTT 57.961 32.000 0.00 0.00 0.00 1.82
2290 2463 4.879545 ACAAGAAAGAAACCGAAAGTAGCA 59.120 37.500 0.00 0.00 0.00 3.49
2298 2471 7.874016 TGTATAGCTAAACAAGAAAGAAACCGA 59.126 33.333 0.00 0.00 0.00 4.69
2347 2541 3.475566 TTCAGCCAGGACTATGCATAC 57.524 47.619 1.16 0.00 0.00 2.39
2350 2544 1.340017 GGTTTCAGCCAGGACTATGCA 60.340 52.381 0.00 0.00 0.00 3.96
2351 2545 1.340017 TGGTTTCAGCCAGGACTATGC 60.340 52.381 0.00 0.00 33.97 3.14
2352 2546 2.749621 GTTGGTTTCAGCCAGGACTATG 59.250 50.000 0.00 0.00 40.01 2.23
2353 2547 2.290960 GGTTGGTTTCAGCCAGGACTAT 60.291 50.000 0.00 0.00 42.87 2.12
2354 2548 1.073284 GGTTGGTTTCAGCCAGGACTA 59.927 52.381 0.00 0.00 42.87 2.59
2355 2549 0.178990 GGTTGGTTTCAGCCAGGACT 60.179 55.000 0.00 0.00 42.87 3.85
2356 2550 0.178990 AGGTTGGTTTCAGCCAGGAC 60.179 55.000 0.00 0.00 45.35 3.85
2357 2551 1.440618 TAGGTTGGTTTCAGCCAGGA 58.559 50.000 0.00 0.00 45.35 3.86
2358 2552 1.886542 GTTAGGTTGGTTTCAGCCAGG 59.113 52.381 2.37 0.00 45.35 4.45
2359 2553 2.582052 TGTTAGGTTGGTTTCAGCCAG 58.418 47.619 2.37 0.00 45.35 4.85
2360 2554 2.738587 TGTTAGGTTGGTTTCAGCCA 57.261 45.000 2.37 0.00 45.35 4.75
2362 2556 4.649088 ACTTTGTTAGGTTGGTTTCAGC 57.351 40.909 0.00 0.00 0.00 4.26
2363 2557 8.030106 TGTTTAACTTTGTTAGGTTGGTTTCAG 58.970 33.333 0.00 0.00 0.00 3.02
2364 2558 7.893658 TGTTTAACTTTGTTAGGTTGGTTTCA 58.106 30.769 0.00 0.00 0.00 2.69
2365 2559 8.760103 TTGTTTAACTTTGTTAGGTTGGTTTC 57.240 30.769 0.00 0.00 0.00 2.78
2366 2560 9.727859 ATTTGTTTAACTTTGTTAGGTTGGTTT 57.272 25.926 0.00 0.00 0.00 3.27
2407 2601 9.520204 AGTCAAGTAAACAAGACAAATGAAATG 57.480 29.630 0.00 0.00 33.56 2.32
2417 2611 7.960793 ACGCATATTAGTCAAGTAAACAAGAC 58.039 34.615 0.00 0.00 0.00 3.01
2426 2620 5.221263 CCAGGACTACGCATATTAGTCAAGT 60.221 44.000 12.82 0.71 45.02 3.16
2427 2621 5.223382 CCAGGACTACGCATATTAGTCAAG 58.777 45.833 12.82 6.33 45.02 3.02
2428 2622 4.500887 GCCAGGACTACGCATATTAGTCAA 60.501 45.833 12.82 0.00 45.02 3.18
2429 2623 3.005472 GCCAGGACTACGCATATTAGTCA 59.995 47.826 12.82 0.00 45.02 3.41
2430 2624 3.256136 AGCCAGGACTACGCATATTAGTC 59.744 47.826 4.96 4.96 43.27 2.59
2431 2625 3.005897 CAGCCAGGACTACGCATATTAGT 59.994 47.826 0.00 0.00 32.23 2.24
2441 2637 2.152016 GTTGGTTTCAGCCAGGACTAC 58.848 52.381 0.00 0.00 40.01 2.73
2481 2677 9.107177 CAGAACACTAGAATGAATAGAAGCAAT 57.893 33.333 0.00 0.00 0.00 3.56
2543 2739 2.719739 CCTGAGGTTGATCACATTGCT 58.280 47.619 0.00 0.00 0.00 3.91
2580 2782 8.900781 CAGAGGTCAAATTTGAAGATACATCAT 58.099 33.333 22.07 5.32 39.21 2.45
2621 2823 5.125417 GGTTTGTGCAGCTGGATAGAAATTA 59.875 40.000 17.12 0.00 0.00 1.40
2637 2839 6.922957 TGAGAACATTTTGATAAGGTTTGTGC 59.077 34.615 0.00 0.00 0.00 4.57
2649 2851 6.295249 TGGTACACATCTGAGAACATTTTGA 58.705 36.000 0.00 0.00 0.00 2.69
2654 2856 7.288621 TCTGATATGGTACACATCTGAGAACAT 59.711 37.037 0.00 0.00 43.42 2.71
2655 2857 6.607198 TCTGATATGGTACACATCTGAGAACA 59.393 38.462 0.00 0.00 43.42 3.18
2656 2858 7.043961 TCTGATATGGTACACATCTGAGAAC 57.956 40.000 0.00 0.00 43.42 3.01
2660 2862 5.536538 GGTCTCTGATATGGTACACATCTGA 59.463 44.000 0.00 3.13 45.44 3.27
2661 2863 5.302823 TGGTCTCTGATATGGTACACATCTG 59.697 44.000 0.00 0.00 43.67 2.90
2662 2864 5.458595 TGGTCTCTGATATGGTACACATCT 58.541 41.667 0.00 0.00 43.67 2.90
2685 2888 7.383102 ACATTCTGCTTTTGATCGAAACTAT 57.617 32.000 3.86 0.00 0.00 2.12
2782 2992 1.856629 AGGGAATGACAATTGGCCAG 58.143 50.000 9.30 0.00 0.00 4.85
2806 3016 2.507484 TGCAAACTGAAGACATCCAGG 58.493 47.619 0.00 0.00 34.85 4.45
2862 3072 3.303395 GCACCTTCATCATTAGCGTTAGC 60.303 47.826 0.00 0.00 45.58 3.09
2863 3073 3.248602 GGCACCTTCATCATTAGCGTTAG 59.751 47.826 0.00 0.00 0.00 2.34
2865 3075 2.017049 GGCACCTTCATCATTAGCGTT 58.983 47.619 0.00 0.00 0.00 4.84
2867 3077 1.959042 AGGCACCTTCATCATTAGCG 58.041 50.000 0.00 0.00 0.00 4.26
2869 3079 6.040955 TCTGTACTAGGCACCTTCATCATTAG 59.959 42.308 0.00 0.00 0.00 1.73
2870 3080 5.897250 TCTGTACTAGGCACCTTCATCATTA 59.103 40.000 0.00 0.00 0.00 1.90
2871 3081 4.716784 TCTGTACTAGGCACCTTCATCATT 59.283 41.667 0.00 0.00 0.00 2.57
2872 3082 4.290093 TCTGTACTAGGCACCTTCATCAT 58.710 43.478 0.00 0.00 0.00 2.45
2873 3083 3.708451 TCTGTACTAGGCACCTTCATCA 58.292 45.455 0.00 0.00 0.00 3.07
2874 3084 4.160626 ACTTCTGTACTAGGCACCTTCATC 59.839 45.833 0.00 0.00 0.00 2.92
2875 3085 4.097418 ACTTCTGTACTAGGCACCTTCAT 58.903 43.478 0.00 0.00 0.00 2.57
2876 3086 3.507411 ACTTCTGTACTAGGCACCTTCA 58.493 45.455 0.00 0.00 0.00 3.02
2940 3165 7.065563 CAGAACCAGATACCATGAGAAAAGAAG 59.934 40.741 0.00 0.00 0.00 2.85
2962 3187 5.533112 AGGTCATAAGAGATCCTTCCAGAA 58.467 41.667 0.38 0.00 36.34 3.02
3122 3347 3.019799 TCAACACCAACTGCCCTTAAA 57.980 42.857 0.00 0.00 0.00 1.52
3282 3508 1.103803 TCTCAGGCGTCACATACTCC 58.896 55.000 0.00 0.00 32.72 3.85
3527 3754 2.764269 ACTACATGCCCACTCCACTAT 58.236 47.619 0.00 0.00 0.00 2.12
3549 3776 3.568443 TCACTGGTACGGGCTATTATGA 58.432 45.455 0.00 0.00 40.47 2.15
3596 3823 3.857157 TCACTATATGAAACAGGGGCC 57.143 47.619 0.00 0.00 33.02 5.80
3659 3887 6.791887 TTGAGCTCAGTCTGTTCTTTATTG 57.208 37.500 17.43 0.00 0.00 1.90
3718 3946 1.883275 CCAAGGCGTTTGACCATTGTA 59.117 47.619 3.76 0.00 39.21 2.41
3806 4037 1.608025 GGACCTGACAAGAATCGCACA 60.608 52.381 0.00 0.00 0.00 4.57
3897 4128 2.093394 GGTTGAGACTTAAGAGGAGGCC 60.093 54.545 10.09 0.00 0.00 5.19
3963 4196 2.224499 TGGTGCTGCTCTGAACATACAA 60.224 45.455 0.00 0.00 0.00 2.41
3964 4197 1.347378 TGGTGCTGCTCTGAACATACA 59.653 47.619 0.00 0.00 0.00 2.29
3997 4230 8.750515 TTCAGAATAATAGAATGATTGTGCCA 57.249 30.769 0.00 0.00 0.00 4.92
4198 4441 2.010145 TGCGTTCTCCTAAGTGATGC 57.990 50.000 0.00 0.00 0.00 3.91
4368 4611 9.450807 CACTATTAAGTGTTTTTGTTCCTCAAG 57.549 33.333 0.00 0.00 46.76 3.02
4385 4628 9.233232 GAATTCGGCCAATTTAACACTATTAAG 57.767 33.333 2.24 0.00 34.60 1.85
4388 4631 7.164230 TGAATTCGGCCAATTTAACACTATT 57.836 32.000 2.24 0.00 34.60 1.73
4431 4674 8.646004 AGAGACAAATCTAGCTATGAATAGCAA 58.354 33.333 21.23 9.09 45.84 3.91
4465 4708 9.956720 AATTCAAAACATCACTCAGAAAACTAG 57.043 29.630 0.00 0.00 0.00 2.57
4516 4759 8.643324 AGGAACAAAGACAGGATAGTATATCAC 58.357 37.037 0.00 0.00 0.00 3.06
4517 4760 8.783660 AGGAACAAAGACAGGATAGTATATCA 57.216 34.615 0.00 0.00 0.00 2.15
4524 4767 9.454859 AAAATTCTAGGAACAAAGACAGGATAG 57.545 33.333 0.00 0.00 0.00 2.08
4529 4772 7.510549 TGGAAAATTCTAGGAACAAAGACAG 57.489 36.000 0.00 0.00 0.00 3.51
4577 4820 2.569853 CCAGCACCCCCGTATATGATTA 59.430 50.000 0.00 0.00 0.00 1.75
4620 4863 5.563867 CGGCACTCCTATATCAGAGAACTTC 60.564 48.000 8.52 0.00 34.13 3.01
4629 4872 5.084519 AGTATTTCCGGCACTCCTATATCA 58.915 41.667 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.