Multiple sequence alignment - TraesCS3D01G269800

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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 TraesCS3D01G269800 chr3D 100.000 4650 0 0 349 4998 374355604 374360253 0.000000e+00 8588.0
1 TraesCS3D01G269800 chr3D 87.156 109 3 2 4698 4795 341843499 341843391 4.090000e-21 113.0
2 TraesCS3D01G269800 chr3D 100.000 43 0 0 1 43 374355256 374355298 4.150000e-11 80.5
3 TraesCS3D01G269800 chr3A 96.745 3933 102 14 610 4527 496987104 496991025 0.000000e+00 6530.0
4 TraesCS3D01G269800 chr3A 91.045 201 16 1 4794 4992 496994458 496994658 2.290000e-68 270.0
5 TraesCS3D01G269800 chr3A 91.566 83 6 1 4532 4614 496991239 496991320 4.090000e-21 113.0
6 TraesCS3D01G269800 chr3A 91.379 58 5 0 4698 4755 682750324 682750267 4.150000e-11 80.5
7 TraesCS3D01G269800 chr3A 94.000 50 3 0 4695 4744 55775419 55775370 5.370000e-10 76.8
8 TraesCS3D01G269800 chr3A 95.745 47 2 0 3538 3584 491189464 491189510 5.370000e-10 76.8
9 TraesCS3D01G269800 chr3A 97.674 43 1 0 1 43 496986657 496986699 1.930000e-09 75.0
10 TraesCS3D01G269800 chr3A 91.667 48 4 0 3539 3586 527938657 527938704 3.230000e-07 67.6
11 TraesCS3D01G269800 chr3B 95.327 2247 97 5 610 2853 488187260 488189501 0.000000e+00 3561.0
12 TraesCS3D01G269800 chr3B 93.636 880 43 6 3731 4600 488190552 488191428 0.000000e+00 1303.0
13 TraesCS3D01G269800 chr3B 90.838 895 56 14 2849 3731 488189592 488190472 0.000000e+00 1175.0
14 TraesCS3D01G269800 chr3B 84.477 277 26 9 349 615 488186952 488187221 1.790000e-64 257.0
15 TraesCS3D01G269800 chr3B 100.000 43 0 0 1 43 488186810 488186852 4.150000e-11 80.5
16 TraesCS3D01G269800 chr3B 86.667 60 5 3 3528 3584 691739121 691739180 4.180000e-06 63.9
17 TraesCS3D01G269800 chr5D 95.181 83 4 0 4700 4782 529278375 529278293 1.130000e-26 132.0
18 TraesCS3D01G269800 chr5D 85.321 109 5 2 4698 4795 294225270 294225378 8.850000e-18 102.0
19 TraesCS3D01G269800 chr5D 96.610 59 2 0 4737 4795 330429708 330429650 1.150000e-16 99.0
20 TraesCS3D01G269800 chr6D 86.239 109 4 2 4698 4795 331681238 331681346 1.900000e-19 108.0
21 TraesCS3D01G269800 chr6D 85.455 110 5 3 4697 4795 58439588 58439479 2.460000e-18 104.0
22 TraesCS3D01G269800 chr4A 86.239 109 4 1 4698 4795 596868395 596868503 1.900000e-19 108.0
23 TraesCS3D01G269800 chr7B 86.111 108 4 2 4700 4796 661713640 661713747 6.840000e-19 106.0
24 TraesCS3D01G269800 chr7B 90.909 55 3 2 4690 4744 662648449 662648501 6.940000e-09 73.1
25 TraesCS3D01G269800 chr7B 93.478 46 3 0 3539 3584 490685137 490685182 8.980000e-08 69.4
26 TraesCS3D01G269800 chr5B 86.598 97 10 3 4698 4793 212629490 212629396 2.460000e-18 104.0
27 TraesCS3D01G269800 chr4D 96.610 59 2 0 4737 4795 415023482 415023540 1.150000e-16 99.0
28 TraesCS3D01G269800 chr2D 83.186 113 7 3 4694 4795 612983502 612983613 5.330000e-15 93.5
29 TraesCS3D01G269800 chr7D 82.857 105 7 4 4698 4791 616886168 616886272 3.210000e-12 84.2
30 TraesCS3D01G269800 chr1D 94.118 51 3 0 4694 4744 441189344 441189294 1.490000e-10 78.7
31 TraesCS3D01G269800 chr1A 93.878 49 3 0 3539 3587 494443726 494443774 1.930000e-09 75.0
32 TraesCS3D01G269800 chr1A 95.652 46 2 0 3539 3584 567969964 567970009 1.930000e-09 75.0
33 TraesCS3D01G269800 chr5A 97.561 41 1 0 3544 3584 485202106 485202066 2.500000e-08 71.3


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 TraesCS3D01G269800 chr3D 374355256 374360253 4997 False 4334.25 8588 100.0000 1 4998 2 chr3D.!!$F1 4997
1 TraesCS3D01G269800 chr3A 496986657 496994658 8001 False 1747.00 6530 94.2575 1 4992 4 chr3A.!!$F3 4991
2 TraesCS3D01G269800 chr3B 488186810 488191428 4618 False 1275.30 3561 92.8556 1 4600 5 chr3B.!!$F2 4599

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
551 565 0.176449 GGGGAATTTCATGGTGCTGC 59.824 55.000 0.0 0.0 0.00 5.25 F
1371 1431 0.613012 AGGCTGGGCTTCCATTTGAC 60.613 55.000 0.0 0.0 40.27 3.18 F
1437 1497 0.329261 AGCTGGAGCCATTTGTAGCA 59.671 50.000 0.0 0.0 43.38 3.49 F
1524 1584 2.096496 GGATGACGAGGCAGATTTTGTG 59.904 50.000 0.0 0.0 0.00 3.33 F
2685 2749 2.772287 AGAGCTGACAAACTTACTGCC 58.228 47.619 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1497 0.177604 CCGCTTCAGATTCAGCCTCT 59.822 55.000 0.00 0.00 31.82 3.69 R
2654 2718 0.778815 GTCAGCTCTTTGTCGTGTCG 59.221 55.000 0.00 0.00 0.00 4.35 R
3164 3326 2.098934 CCAAAGCGCCTGCATAACATAA 59.901 45.455 2.29 0.00 46.23 1.90 R
3606 3775 5.493133 AATAACAACTGCAGTTCGTCAAA 57.507 34.783 28.97 17.38 35.83 2.69 R
4720 5708 0.032815 AAAATTGCCGTCCGTTTGGG 59.967 50.000 0.00 0.00 35.24 4.12 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
379 380 2.434331 CCAAGCCAAGAACCGGGA 59.566 61.111 6.32 0.00 0.00 5.14
405 410 2.608368 TGGGACGGACGGGGAATT 60.608 61.111 0.00 0.00 0.00 2.17
429 434 4.036498 CCTCGTGAAGTAATCCGACATACT 59.964 45.833 0.00 0.00 33.89 2.12
430 435 5.237996 CCTCGTGAAGTAATCCGACATACTA 59.762 44.000 0.00 0.00 32.24 1.82
431 436 6.052840 TCGTGAAGTAATCCGACATACTAC 57.947 41.667 0.00 0.00 32.24 2.73
432 437 4.902448 CGTGAAGTAATCCGACATACTACG 59.098 45.833 0.00 0.00 31.66 3.51
463 477 2.829720 CGAATCCCAATCCCGAGGTATA 59.170 50.000 0.00 0.00 0.00 1.47
464 478 3.451178 CGAATCCCAATCCCGAGGTATAT 59.549 47.826 0.00 0.00 0.00 0.86
490 504 4.751767 TCCATGCCTTCTGTTTGTTTTT 57.248 36.364 0.00 0.00 0.00 1.94
522 536 2.406002 AATCCAGGCGTTCCGTGGTT 62.406 55.000 2.47 0.00 37.47 3.67
531 545 2.546778 CGTTCCGTGGTTAGCATATGT 58.453 47.619 4.29 0.00 0.00 2.29
545 559 3.899360 AGCATATGTGGGGAATTTCATGG 59.101 43.478 4.29 0.00 0.00 3.66
551 565 0.176449 GGGGAATTTCATGGTGCTGC 59.824 55.000 0.00 0.00 0.00 5.25
583 597 1.002366 CGGCTTGGATCAAGAACTCG 58.998 55.000 11.35 5.62 43.42 4.18
615 629 2.289010 GCCCCTCTGTTTTGTCCATTTG 60.289 50.000 0.00 0.00 0.00 2.32
616 630 2.289010 CCCCTCTGTTTTGTCCATTTGC 60.289 50.000 0.00 0.00 0.00 3.68
617 631 2.629617 CCCTCTGTTTTGTCCATTTGCT 59.370 45.455 0.00 0.00 0.00 3.91
618 632 3.070015 CCCTCTGTTTTGTCCATTTGCTT 59.930 43.478 0.00 0.00 0.00 3.91
619 633 4.443315 CCCTCTGTTTTGTCCATTTGCTTT 60.443 41.667 0.00 0.00 0.00 3.51
648 706 6.423905 TGACATTTAGATTGGAGCGCTTATAC 59.576 38.462 13.26 3.11 0.00 1.47
669 727 3.065371 ACAGCTGTGTTTGTGTTTAGAGC 59.935 43.478 20.97 0.00 30.30 4.09
863 922 4.240096 CTGTTCTTGTTGGGCAATTGATC 58.760 43.478 10.34 0.31 36.36 2.92
892 951 2.697229 TGACTGAGCTGGTATGAGATGG 59.303 50.000 0.00 0.00 0.00 3.51
953 1013 3.259374 TGGTTCAGAGAGGTGATGTCTTC 59.741 47.826 0.00 0.00 26.31 2.87
968 1028 5.125257 TGATGTCTTCTGCTTCACTCTAGAG 59.875 44.000 18.49 18.49 0.00 2.43
1021 1081 2.038269 GCACGAAGAAATGCCGGGA 61.038 57.895 2.18 0.00 35.73 5.14
1095 1155 1.008327 TCTCCCAAGATGGCCTACTCA 59.992 52.381 3.32 0.00 35.79 3.41
1161 1221 2.550855 GCTTGACCTTGTCCTGATGTCA 60.551 50.000 0.00 0.00 34.38 3.58
1272 1332 7.126115 TGGAAAAAGGCCATGATCAATCTATTT 59.874 33.333 5.01 0.00 0.00 1.40
1371 1431 0.613012 AGGCTGGGCTTCCATTTGAC 60.613 55.000 0.00 0.00 40.27 3.18
1401 1461 5.937540 TGTGATTGATAGACGACAAATGGTT 59.062 36.000 0.00 0.00 0.00 3.67
1413 1473 4.023279 CGACAAATGGTTGAACATCAAGGA 60.023 41.667 0.00 0.00 37.00 3.36
1437 1497 0.329261 AGCTGGAGCCATTTGTAGCA 59.671 50.000 0.00 0.00 43.38 3.49
1509 1569 2.821969 AGTTCCTGCAATGTTGGATGAC 59.178 45.455 0.00 0.00 0.00 3.06
1524 1584 2.096496 GGATGACGAGGCAGATTTTGTG 59.904 50.000 0.00 0.00 0.00 3.33
2204 2268 9.289303 CTGCGTAATGTTTTAAATGCTAGAATT 57.711 29.630 0.00 0.00 0.00 2.17
2685 2749 2.772287 AGAGCTGACAAACTTACTGCC 58.228 47.619 0.00 0.00 0.00 4.85
2784 2848 6.647334 TCTACATTTGCCATTCTTTTGACA 57.353 33.333 0.00 0.00 0.00 3.58
2803 2867 3.088532 ACAGCCAAACAGAAGTTGTCAA 58.911 40.909 0.00 0.00 39.73 3.18
3063 3225 9.743057 TTACAATTTCACATCAAAAGTCGAAAT 57.257 25.926 0.00 0.00 35.25 2.17
3154 3316 9.208022 TCATTGAACAGTTAAGATGTTACTCAG 57.792 33.333 6.08 0.00 40.86 3.35
3164 3326 6.560253 AAGATGTTACTCAGAATTTTGCGT 57.440 33.333 0.00 0.00 0.00 5.24
3606 3775 5.497474 AGTTCTTTGTAATTGCCGTCCTAT 58.503 37.500 0.00 0.00 0.00 2.57
3703 3875 9.662947 CATATGAATATCCATGAGAGCAAGTAA 57.337 33.333 0.00 0.00 0.00 2.24
3974 4226 1.679311 CCTACTGGCTGGTTGCTGA 59.321 57.895 0.00 0.00 42.39 4.26
4133 4385 7.538678 CAGAATAATGTCACACCAGTAAAAAGC 59.461 37.037 0.00 0.00 0.00 3.51
4198 4450 7.040132 ACTCTCCATTCTTTCCAAAGTTCATTC 60.040 37.037 0.00 0.00 37.31 2.67
4359 4619 6.883217 ACACTCTCTTGATACATGAGCAAAAT 59.117 34.615 0.00 0.00 36.16 1.82
4377 4637 5.910723 GCAAAATCAAAAGCAAAATCACAGG 59.089 36.000 0.00 0.00 0.00 4.00
4381 4641 5.336150 TCAAAAGCAAAATCACAGGTTGA 57.664 34.783 0.00 0.00 39.11 3.18
4453 4720 5.104900 AGCTTAATTCTCCCTATGACGTTGT 60.105 40.000 0.00 0.00 0.00 3.32
4458 4725 4.451629 TCTCCCTATGACGTTGTTCTTC 57.548 45.455 0.00 0.00 0.00 2.87
4469 4736 5.297527 TGACGTTGTTCTTCTCTGTGTACTA 59.702 40.000 0.00 0.00 0.00 1.82
4482 4749 6.014070 TCTCTGTGTACTAAGTTTGGCCATAA 60.014 38.462 6.09 0.49 0.00 1.90
4574 5048 0.946221 CGGAGTGGTGTCTGCTTGTC 60.946 60.000 0.00 0.00 0.00 3.18
4577 5051 2.139118 GAGTGGTGTCTGCTTGTCTTC 58.861 52.381 0.00 0.00 0.00 2.87
4588 5062 1.501337 CTTGTCTTCGCACTGCAGCA 61.501 55.000 15.27 0.00 0.00 4.41
4600 5074 1.081094 CTGCAGCATCGTGATTCACA 58.919 50.000 16.61 4.75 33.40 3.58
4610 5084 5.643664 CATCGTGATTCACATTTGGATGTT 58.356 37.500 16.61 0.00 43.92 2.71
4611 5085 5.295431 TCGTGATTCACATTTGGATGTTC 57.705 39.130 16.61 0.00 43.92 3.18
4612 5086 4.759183 TCGTGATTCACATTTGGATGTTCA 59.241 37.500 16.61 0.00 43.92 3.18
4643 5631 4.932268 GGACGTATGAAATCCGACAAAA 57.068 40.909 0.00 0.00 0.00 2.44
4646 5634 5.277601 ACGTATGAAATCCGACAAAACAG 57.722 39.130 0.00 0.00 0.00 3.16
4647 5635 4.992319 ACGTATGAAATCCGACAAAACAGA 59.008 37.500 0.00 0.00 0.00 3.41
4648 5636 5.120208 ACGTATGAAATCCGACAAAACAGAG 59.880 40.000 0.00 0.00 0.00 3.35
4659 5647 1.336755 CAAAACAGAGTGAAACCGGGG 59.663 52.381 6.32 0.00 37.80 5.73
4662 5650 0.396811 ACAGAGTGAAACCGGGGAAG 59.603 55.000 6.32 0.00 37.80 3.46
4665 5653 0.605589 GAGTGAAACCGGGGAAGGTG 60.606 60.000 6.32 0.00 45.21 4.00
4666 5654 2.114411 TGAAACCGGGGAAGGTGC 59.886 61.111 6.32 0.00 45.21 5.01
4669 5657 2.406002 GAAACCGGGGAAGGTGCAGA 62.406 60.000 6.32 0.00 45.21 4.26
4670 5658 2.692273 AAACCGGGGAAGGTGCAGAC 62.692 60.000 6.32 0.00 45.21 3.51
4671 5659 3.322466 CCGGGGAAGGTGCAGACT 61.322 66.667 0.00 0.00 0.00 3.24
4673 5661 1.550130 CCGGGGAAGGTGCAGACTAA 61.550 60.000 0.00 0.00 0.00 2.24
4674 5662 0.391263 CGGGGAAGGTGCAGACTAAC 60.391 60.000 0.00 0.00 0.00 2.34
4675 5663 0.035343 GGGGAAGGTGCAGACTAACC 60.035 60.000 0.00 0.00 36.66 2.85
4676 5664 0.690762 GGGAAGGTGCAGACTAACCA 59.309 55.000 8.75 0.00 39.05 3.67
4677 5665 1.073284 GGGAAGGTGCAGACTAACCAA 59.927 52.381 8.75 0.00 39.05 3.67
4678 5666 2.290960 GGGAAGGTGCAGACTAACCAAT 60.291 50.000 8.75 0.00 39.05 3.16
4679 5667 3.421844 GGAAGGTGCAGACTAACCAATT 58.578 45.455 8.75 0.00 39.05 2.32
4680 5668 4.566907 GGGAAGGTGCAGACTAACCAATTA 60.567 45.833 8.75 0.00 39.05 1.40
4681 5669 5.193679 GGAAGGTGCAGACTAACCAATTAT 58.806 41.667 8.75 0.00 39.05 1.28
4682 5670 6.354130 GGAAGGTGCAGACTAACCAATTATA 58.646 40.000 8.75 0.00 39.05 0.98
4684 5672 6.561519 AGGTGCAGACTAACCAATTATACT 57.438 37.500 8.75 0.00 39.05 2.12
4686 5674 6.070194 AGGTGCAGACTAACCAATTATACTGT 60.070 38.462 8.75 0.00 39.05 3.55
4687 5675 7.125204 AGGTGCAGACTAACCAATTATACTGTA 59.875 37.037 8.75 0.00 39.05 2.74
4688 5676 7.438459 GGTGCAGACTAACCAATTATACTGTAG 59.562 40.741 0.00 0.00 36.41 2.74
4689 5677 7.438459 GTGCAGACTAACCAATTATACTGTAGG 59.562 40.741 0.00 0.00 31.58 3.18
4690 5678 6.929606 GCAGACTAACCAATTATACTGTAGGG 59.070 42.308 0.00 0.00 31.58 3.53
4691 5679 7.442656 CAGACTAACCAATTATACTGTAGGGG 58.557 42.308 0.00 0.00 0.00 4.79
4692 5680 7.070821 CAGACTAACCAATTATACTGTAGGGGT 59.929 40.741 0.00 0.00 0.00 4.95
4693 5681 7.626487 AGACTAACCAATTATACTGTAGGGGTT 59.374 37.037 12.65 12.65 40.27 4.11
4694 5682 7.799081 ACTAACCAATTATACTGTAGGGGTTC 58.201 38.462 11.87 0.00 38.29 3.62
4695 5683 5.641789 ACCAATTATACTGTAGGGGTTCC 57.358 43.478 0.00 0.00 0.00 3.62
4696 5684 5.294473 ACCAATTATACTGTAGGGGTTCCT 58.706 41.667 0.00 0.00 46.96 3.36
4698 5686 6.218938 ACCAATTATACTGTAGGGGTTCCTTT 59.781 38.462 0.00 0.00 41.56 3.11
4699 5687 7.406739 ACCAATTATACTGTAGGGGTTCCTTTA 59.593 37.037 0.00 0.00 41.56 1.85
4702 5690 7.909485 TTATACTGTAGGGGTTCCTTTAGAG 57.091 40.000 0.00 0.00 41.56 2.43
4703 5691 2.838813 ACTGTAGGGGTTCCTTTAGAGC 59.161 50.000 0.00 0.00 41.56 4.09
4704 5692 2.838202 CTGTAGGGGTTCCTTTAGAGCA 59.162 50.000 0.00 0.00 41.56 4.26
4705 5693 3.253220 TGTAGGGGTTCCTTTAGAGCAA 58.747 45.455 0.00 0.00 41.56 3.91
4706 5694 2.881111 AGGGGTTCCTTTAGAGCAAC 57.119 50.000 0.00 0.00 41.56 4.17
4707 5695 2.349445 AGGGGTTCCTTTAGAGCAACT 58.651 47.619 0.00 0.00 41.56 3.16
4708 5696 2.306219 AGGGGTTCCTTTAGAGCAACTC 59.694 50.000 0.00 0.00 41.56 3.01
4709 5697 2.618302 GGGGTTCCTTTAGAGCAACTCC 60.618 54.545 0.00 0.00 32.23 3.85
4710 5698 2.039879 GGGTTCCTTTAGAGCAACTCCA 59.960 50.000 0.00 0.00 0.00 3.86
4711 5699 3.497942 GGGTTCCTTTAGAGCAACTCCAA 60.498 47.826 0.00 0.00 0.00 3.53
4712 5700 4.336280 GGTTCCTTTAGAGCAACTCCAAT 58.664 43.478 0.00 0.00 0.00 3.16
4713 5701 4.156739 GGTTCCTTTAGAGCAACTCCAATG 59.843 45.833 0.00 0.00 0.00 2.82
4714 5702 3.955471 TCCTTTAGAGCAACTCCAATGG 58.045 45.455 0.00 0.00 31.45 3.16
4715 5703 3.019564 CCTTTAGAGCAACTCCAATGGG 58.980 50.000 0.00 0.00 28.44 4.00
4717 5705 0.255890 TAGAGCAACTCCAATGGGCC 59.744 55.000 0.00 0.00 0.00 5.80
4718 5706 2.361610 AGCAACTCCAATGGGCCG 60.362 61.111 0.00 0.00 0.00 6.13
4720 5708 2.700773 GCAACTCCAATGGGCCGAC 61.701 63.158 0.00 0.00 0.00 4.79
4734 5722 4.973055 CGACCCAAACGGACGGCA 62.973 66.667 0.00 0.00 44.72 5.69
4735 5723 2.592287 GACCCAAACGGACGGCAA 60.592 61.111 0.00 0.00 34.64 4.52
4736 5724 1.969589 GACCCAAACGGACGGCAAT 60.970 57.895 0.00 0.00 34.64 3.56
4738 5726 1.110518 ACCCAAACGGACGGCAATTT 61.111 50.000 0.00 0.00 34.64 1.82
4750 6891 2.075338 CGGCAATTTTGTCCATTTGGG 58.925 47.619 0.00 0.00 35.41 4.12
4751 6892 2.549778 CGGCAATTTTGTCCATTTGGGT 60.550 45.455 0.00 0.00 38.11 4.51
4752 6893 3.073678 GGCAATTTTGTCCATTTGGGTC 58.926 45.455 0.00 0.00 38.11 4.46
4753 6894 2.736192 GCAATTTTGTCCATTTGGGTCG 59.264 45.455 0.00 0.00 38.11 4.79
4754 6895 3.324993 CAATTTTGTCCATTTGGGTCGG 58.675 45.455 0.00 0.00 38.11 4.79
4755 6896 0.676736 TTTTGTCCATTTGGGTCGGC 59.323 50.000 0.00 0.00 38.11 5.54
4756 6897 1.182385 TTTGTCCATTTGGGTCGGCC 61.182 55.000 0.00 0.00 38.11 6.13
4757 6898 2.034999 GTCCATTTGGGTCGGCCA 59.965 61.111 9.07 0.00 38.11 5.36
4758 6899 2.046285 GTCCATTTGGGTCGGCCAG 61.046 63.158 9.07 0.00 38.11 4.85
4759 6900 2.755469 CCATTTGGGTCGGCCAGG 60.755 66.667 9.07 0.00 36.17 4.45
4802 8234 1.310904 GTTTGGGTCGGCAAGTGTTA 58.689 50.000 0.00 0.00 0.00 2.41
4805 8237 0.470766 TGGGTCGGCAAGTGTTAGTT 59.529 50.000 0.00 0.00 0.00 2.24
4816 8248 5.932303 GGCAAGTGTTAGTTCAAGATGTAGA 59.068 40.000 0.00 0.00 0.00 2.59
4890 8324 5.345202 GCAAACAAATGAAGAAGATGCAGAG 59.655 40.000 0.00 0.00 0.00 3.35
4891 8325 4.698583 ACAAATGAAGAAGATGCAGAGC 57.301 40.909 0.00 0.00 0.00 4.09
4893 8327 4.395542 ACAAATGAAGAAGATGCAGAGCTC 59.604 41.667 5.27 5.27 0.00 4.09
4895 8329 5.611128 AATGAAGAAGATGCAGAGCTCTA 57.389 39.130 17.75 1.39 0.00 2.43
4900 8334 5.874897 AGAAGATGCAGAGCTCTAGAATT 57.125 39.130 17.75 7.95 0.00 2.17
4901 8335 6.237887 AGAAGATGCAGAGCTCTAGAATTT 57.762 37.500 17.75 8.70 0.00 1.82
4949 8383 6.262273 CCAGTCCTTGTTTCAGCTAAAGTTTA 59.738 38.462 0.00 0.00 0.00 2.01
4970 8404 8.931385 GTTTATGAAACTTATTCCATGCACAT 57.069 30.769 0.00 0.00 38.35 3.21
4978 8412 5.645929 ACTTATTCCATGCACATACGAAACA 59.354 36.000 0.00 0.00 0.00 2.83
4985 8419 6.364706 TCCATGCACATACGAAACAAAATTTC 59.635 34.615 0.00 0.00 0.00 2.17
4992 8426 9.993881 CACATACGAAACAAAATTTCTTTGATC 57.006 29.630 4.32 0.00 33.83 2.92
4993 8427 9.743057 ACATACGAAACAAAATTTCTTTGATCA 57.257 25.926 4.32 0.00 33.83 2.92
4997 8431 9.097257 ACGAAACAAAATTTCTTTGATCAATGT 57.903 25.926 17.97 10.35 33.83 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
388 389 2.608368 AATTCCCCGTCCGTCCCA 60.608 61.111 0.00 0.00 0.00 4.37
403 408 3.446161 TGTCGGATTACTTCACGAGGAAT 59.554 43.478 0.00 0.00 41.80 3.01
405 410 2.439409 TGTCGGATTACTTCACGAGGA 58.561 47.619 0.00 0.00 35.88 3.71
446 460 6.069847 GGAATAAATATACCTCGGGATTGGGA 60.070 42.308 0.00 0.00 0.00 4.37
463 477 6.610075 ACAAACAGAAGGCATGGAATAAAT 57.390 33.333 0.00 0.00 0.00 1.40
464 478 6.418057 AACAAACAGAAGGCATGGAATAAA 57.582 33.333 0.00 0.00 0.00 1.40
490 504 1.339055 CCTGGATTGGCTCTGTTCGAA 60.339 52.381 0.00 0.00 0.00 3.71
522 536 5.078949 CCATGAAATTCCCCACATATGCTA 58.921 41.667 1.58 0.00 0.00 3.49
531 545 1.559368 CAGCACCATGAAATTCCCCA 58.441 50.000 0.00 0.00 0.00 4.96
545 559 2.257676 GGCAGAGCAAAGCAGCAC 59.742 61.111 0.00 0.00 36.85 4.40
551 565 4.729918 AGCCGGGGCAGAGCAAAG 62.730 66.667 12.97 0.00 44.88 2.77
619 633 5.048083 AGCGCTCCAATCTAAATGTCAAAAA 60.048 36.000 2.64 0.00 0.00 1.94
648 706 3.313526 AGCTCTAAACACAAACACAGCTG 59.686 43.478 13.48 13.48 34.68 4.24
669 727 3.181520 CGCGATAACAACAAAGGAGGAAG 60.182 47.826 0.00 0.00 0.00 3.46
863 922 1.066143 ACCAGCTCAGTCATAAACCGG 60.066 52.381 0.00 0.00 0.00 5.28
892 951 2.191128 AGTTGTGGCTCCAATCACTC 57.809 50.000 0.00 0.00 35.15 3.51
953 1013 3.441922 TGTACAGCTCTAGAGTGAAGCAG 59.558 47.826 20.75 6.69 0.00 4.24
968 1028 3.555547 TCAATATGTCACGCATGTACAGC 59.444 43.478 0.33 4.52 38.47 4.40
1017 1077 2.125552 TCTCGCTGCATTGTCCCG 60.126 61.111 0.00 0.00 0.00 5.14
1021 1081 2.270205 CCCCTCTCGCTGCATTGT 59.730 61.111 0.00 0.00 0.00 2.71
1089 1149 4.456280 TGCAACATAGGACTGTGAGTAG 57.544 45.455 2.99 0.00 0.00 2.57
1095 1155 4.511527 CTCTCATTGCAACATAGGACTGT 58.488 43.478 0.00 0.00 0.00 3.55
1272 1332 4.603989 AATGCCAATCATGAAACACACA 57.396 36.364 0.00 0.00 35.13 3.72
1357 1417 2.052104 CCCCGTCAAATGGAAGCCC 61.052 63.158 0.00 0.00 0.00 5.19
1371 1431 2.296190 TCGTCTATCAATCACATCCCCG 59.704 50.000 0.00 0.00 0.00 5.73
1401 1461 2.886523 CAGCTTGGTTCCTTGATGTTCA 59.113 45.455 0.00 0.00 0.00 3.18
1413 1473 0.971386 CAAATGGCTCCAGCTTGGTT 59.029 50.000 0.00 0.00 39.03 3.67
1437 1497 0.177604 CCGCTTCAGATTCAGCCTCT 59.822 55.000 0.00 0.00 31.82 3.69
1467 1527 2.730524 GGGACTCTCCTCAGCCTGC 61.731 68.421 0.00 0.00 36.57 4.85
1509 1569 1.135575 GCTTCCACAAAATCTGCCTCG 60.136 52.381 0.00 0.00 0.00 4.63
1524 1584 2.999331 TGTACAATAGGCAAGGCTTCC 58.001 47.619 0.00 1.96 0.00 3.46
2016 2078 8.906867 AGTTTTGATGATAAAGTATGATGGTGG 58.093 33.333 0.00 0.00 0.00 4.61
2592 2656 5.592688 ACAGAGTTTAGTGCAAAGCCTTTAA 59.407 36.000 0.00 0.00 0.00 1.52
2654 2718 0.778815 GTCAGCTCTTTGTCGTGTCG 59.221 55.000 0.00 0.00 0.00 4.35
2685 2749 5.032863 GCATCAGCACAGCAACTTATAAAG 58.967 41.667 0.00 0.00 41.58 1.85
2784 2848 3.620488 TCTTGACAACTTCTGTTTGGCT 58.380 40.909 0.00 0.00 38.84 4.75
2907 3067 7.775093 TCAGAAAAGAAAAGAACTCCTGATGAA 59.225 33.333 0.00 0.00 0.00 2.57
2908 3068 7.282585 TCAGAAAAGAAAAGAACTCCTGATGA 58.717 34.615 0.00 0.00 0.00 2.92
2959 3119 9.613428 CCTTTGTACTTCATCATATCTTAACCA 57.387 33.333 0.00 0.00 0.00 3.67
3154 3316 5.276348 GCCTGCATAACATAACGCAAAATTC 60.276 40.000 0.00 0.00 33.21 2.17
3164 3326 2.098934 CCAAAGCGCCTGCATAACATAA 59.901 45.455 2.29 0.00 46.23 1.90
3606 3775 5.493133 AATAACAACTGCAGTTCGTCAAA 57.507 34.783 28.97 17.38 35.83 2.69
3703 3875 9.193806 AGTTCATTTAGATCATTGTATTGGCTT 57.806 29.630 0.00 0.00 0.00 4.35
3724 3896 6.461092 CGGAATGGCTATGTTCTACTAGTTCA 60.461 42.308 0.00 0.00 0.00 3.18
3974 4226 6.380095 CTACGTAGCATCTAGGTTCTTCTT 57.620 41.667 10.14 0.00 0.00 2.52
4133 4385 5.505173 TTTGTCAGGCTTCTTTCTTTGAG 57.495 39.130 0.00 0.00 0.00 3.02
4198 4450 7.473735 TCTAGCTGGATGAATATGAGTAAGG 57.526 40.000 0.00 0.00 0.00 2.69
4359 4619 5.105392 ACTCAACCTGTGATTTTGCTTTTGA 60.105 36.000 0.00 0.00 35.07 2.69
4377 4637 2.420022 AGCACACACTGTCAAACTCAAC 59.580 45.455 0.00 0.00 0.00 3.18
4453 4720 5.989777 GCCAAACTTAGTACACAGAGAAGAA 59.010 40.000 0.00 0.00 0.00 2.52
4458 4725 4.002906 TGGCCAAACTTAGTACACAGAG 57.997 45.455 0.61 0.00 0.00 3.35
4512 4779 0.320771 TTTTCAGAGAGTGGCCGAGC 60.321 55.000 0.00 0.00 0.00 5.03
4519 4786 4.446719 GCAAAGGCAATTTTTCAGAGAGTG 59.553 41.667 0.00 0.00 40.72 3.51
4574 5048 2.385875 ACGATGCTGCAGTGCGAAG 61.386 57.895 24.34 4.21 35.36 3.79
4577 5051 1.974249 AATCACGATGCTGCAGTGCG 61.974 55.000 16.64 17.86 35.97 5.34
4588 5062 5.415389 TGAACATCCAAATGTGAATCACGAT 59.585 36.000 9.00 2.17 45.48 3.73
4600 5074 2.618045 GGACCGGTCTGAACATCCAAAT 60.618 50.000 32.52 0.00 0.00 2.32
4626 5614 6.147164 TCACTCTGTTTTGTCGGATTTCATAC 59.853 38.462 0.00 0.00 0.00 2.39
4627 5615 6.227522 TCACTCTGTTTTGTCGGATTTCATA 58.772 36.000 0.00 0.00 0.00 2.15
4628 5616 5.063204 TCACTCTGTTTTGTCGGATTTCAT 58.937 37.500 0.00 0.00 0.00 2.57
4643 5631 0.396811 CTTCCCCGGTTTCACTCTGT 59.603 55.000 0.00 0.00 0.00 3.41
4646 5634 0.605589 CACCTTCCCCGGTTTCACTC 60.606 60.000 0.00 0.00 34.29 3.51
4647 5635 1.454539 CACCTTCCCCGGTTTCACT 59.545 57.895 0.00 0.00 34.29 3.41
4648 5636 2.265904 GCACCTTCCCCGGTTTCAC 61.266 63.158 0.00 0.00 34.29 3.18
4659 5647 7.011482 CAGTATAATTGGTTAGTCTGCACCTTC 59.989 40.741 5.00 0.00 33.76 3.46
4662 5650 6.113411 ACAGTATAATTGGTTAGTCTGCACC 58.887 40.000 0.00 0.00 32.57 5.01
4665 5653 6.929606 CCCTACAGTATAATTGGTTAGTCTGC 59.070 42.308 0.00 0.00 32.57 4.26
4666 5654 7.070821 ACCCCTACAGTATAATTGGTTAGTCTG 59.929 40.741 0.00 0.00 34.05 3.51
4669 5657 7.147426 GGAACCCCTACAGTATAATTGGTTAGT 60.147 40.741 0.00 0.00 35.13 2.24
4670 5658 7.072076 AGGAACCCCTACAGTATAATTGGTTAG 59.928 40.741 0.00 0.00 42.15 2.34
4671 5659 6.910290 AGGAACCCCTACAGTATAATTGGTTA 59.090 38.462 0.00 0.00 42.15 2.85
4673 5661 5.294473 AGGAACCCCTACAGTATAATTGGT 58.706 41.667 0.00 0.00 42.15 3.67
4674 5662 5.906772 AGGAACCCCTACAGTATAATTGG 57.093 43.478 0.00 0.00 42.15 3.16
4675 5663 8.711170 TCTAAAGGAACCCCTACAGTATAATTG 58.289 37.037 0.00 0.00 43.48 2.32
4676 5664 8.865244 TCTAAAGGAACCCCTACAGTATAATT 57.135 34.615 0.00 0.00 43.48 1.40
4677 5665 7.016366 GCTCTAAAGGAACCCCTACAGTATAAT 59.984 40.741 0.00 0.00 43.48 1.28
4678 5666 6.325804 GCTCTAAAGGAACCCCTACAGTATAA 59.674 42.308 0.00 0.00 43.48 0.98
4679 5667 5.837438 GCTCTAAAGGAACCCCTACAGTATA 59.163 44.000 0.00 0.00 43.48 1.47
4680 5668 4.654724 GCTCTAAAGGAACCCCTACAGTAT 59.345 45.833 0.00 0.00 43.48 2.12
4681 5669 4.028825 GCTCTAAAGGAACCCCTACAGTA 58.971 47.826 0.00 0.00 43.48 2.74
4682 5670 2.838813 GCTCTAAAGGAACCCCTACAGT 59.161 50.000 0.00 0.00 43.48 3.55
4684 5672 2.910544 TGCTCTAAAGGAACCCCTACA 58.089 47.619 0.00 0.00 43.48 2.74
4686 5674 3.994931 GTTGCTCTAAAGGAACCCCTA 57.005 47.619 0.00 0.00 45.29 3.53
4687 5675 2.881111 GTTGCTCTAAAGGAACCCCT 57.119 50.000 0.00 0.00 45.29 4.79
4692 5680 4.335416 CCATTGGAGTTGCTCTAAAGGAA 58.665 43.478 9.80 0.00 40.54 3.36
4693 5681 3.308402 CCCATTGGAGTTGCTCTAAAGGA 60.308 47.826 14.94 0.00 40.54 3.36
4694 5682 3.019564 CCCATTGGAGTTGCTCTAAAGG 58.980 50.000 3.62 8.78 38.78 3.11
4695 5683 2.424956 GCCCATTGGAGTTGCTCTAAAG 59.575 50.000 3.62 0.00 34.82 1.85
4696 5684 2.446435 GCCCATTGGAGTTGCTCTAAA 58.554 47.619 3.62 0.00 34.82 1.85
4698 5686 0.255890 GGCCCATTGGAGTTGCTCTA 59.744 55.000 3.62 0.00 0.00 2.43
4699 5687 1.000396 GGCCCATTGGAGTTGCTCT 60.000 57.895 3.62 0.00 0.00 4.09
4702 5690 2.361104 TCGGCCCATTGGAGTTGC 60.361 61.111 3.62 0.00 0.00 4.17
4703 5691 2.046285 GGTCGGCCCATTGGAGTTG 61.046 63.158 3.62 0.00 0.00 3.16
4704 5692 2.355115 GGTCGGCCCATTGGAGTT 59.645 61.111 3.62 0.00 0.00 3.01
4717 5705 4.973055 TGCCGTCCGTTTGGGTCG 62.973 66.667 0.00 0.00 45.31 4.79
4718 5706 1.520600 AATTGCCGTCCGTTTGGGTC 61.521 55.000 0.00 0.00 37.00 4.46
4720 5708 0.032815 AAAATTGCCGTCCGTTTGGG 59.967 50.000 0.00 0.00 35.24 4.12
4722 5710 1.784283 GACAAAATTGCCGTCCGTTTG 59.216 47.619 0.00 0.00 35.72 2.93
4723 5711 1.269361 GGACAAAATTGCCGTCCGTTT 60.269 47.619 5.67 0.00 39.86 3.60
4724 5712 0.312729 GGACAAAATTGCCGTCCGTT 59.687 50.000 5.67 0.00 39.86 4.44
4725 5713 1.953772 GGACAAAATTGCCGTCCGT 59.046 52.632 5.67 0.00 39.86 4.69
4728 5716 2.736192 CCAAATGGACAAAATTGCCGTC 59.264 45.455 0.00 0.00 37.39 4.79
4729 5717 2.549778 CCCAAATGGACAAAATTGCCGT 60.550 45.455 0.00 0.00 37.39 5.68
4732 5720 2.736192 CGACCCAAATGGACAAAATTGC 59.264 45.455 0.00 0.00 37.39 3.56
4733 5721 3.324993 CCGACCCAAATGGACAAAATTG 58.675 45.455 0.00 0.00 37.39 2.32
4734 5722 2.289382 GCCGACCCAAATGGACAAAATT 60.289 45.455 0.00 0.00 37.39 1.82
4735 5723 1.275010 GCCGACCCAAATGGACAAAAT 59.725 47.619 0.00 0.00 37.39 1.82
4736 5724 0.676736 GCCGACCCAAATGGACAAAA 59.323 50.000 0.00 0.00 37.39 2.44
4738 5726 1.605165 GGCCGACCCAAATGGACAA 60.605 57.895 0.00 0.00 37.39 3.18
4777 6918 3.652000 GCCGACCCAAACGCGAAA 61.652 61.111 15.93 0.00 0.00 3.46
4778 6919 4.912485 TGCCGACCCAAACGCGAA 62.912 61.111 15.93 0.00 0.00 4.70
4780 6921 4.383602 CTTGCCGACCCAAACGCG 62.384 66.667 3.53 3.53 0.00 6.01
4781 6922 3.284449 ACTTGCCGACCCAAACGC 61.284 61.111 0.00 0.00 0.00 4.84
4782 6923 1.720694 AACACTTGCCGACCCAAACG 61.721 55.000 0.00 0.00 0.00 3.60
4783 6924 1.265905 CTAACACTTGCCGACCCAAAC 59.734 52.381 0.00 0.00 0.00 2.93
4784 6925 1.134037 ACTAACACTTGCCGACCCAAA 60.134 47.619 0.00 0.00 0.00 3.28
4785 6926 0.470766 ACTAACACTTGCCGACCCAA 59.529 50.000 0.00 0.00 0.00 4.12
4786 6927 0.470766 AACTAACACTTGCCGACCCA 59.529 50.000 0.00 0.00 0.00 4.51
4787 6928 1.154197 GAACTAACACTTGCCGACCC 58.846 55.000 0.00 0.00 0.00 4.46
4789 6930 3.128349 TCTTGAACTAACACTTGCCGAC 58.872 45.455 0.00 0.00 0.00 4.79
4790 6931 3.462483 TCTTGAACTAACACTTGCCGA 57.538 42.857 0.00 0.00 0.00 5.54
4791 6932 3.498397 ACATCTTGAACTAACACTTGCCG 59.502 43.478 0.00 0.00 0.00 5.69
4802 8234 6.155393 CCTTTCCCTACTCTACATCTTGAACT 59.845 42.308 0.00 0.00 0.00 3.01
4805 8237 5.838955 TCCTTTCCCTACTCTACATCTTGA 58.161 41.667 0.00 0.00 0.00 3.02
4816 8248 5.664815 AGTTCCTTTTTCCTTTCCCTACT 57.335 39.130 0.00 0.00 0.00 2.57
4914 8348 6.361433 TGAAACAAGGACTGGAACATCTAAA 58.639 36.000 0.00 0.00 38.20 1.85
4924 8358 4.137543 ACTTTAGCTGAAACAAGGACTGG 58.862 43.478 0.00 0.00 0.00 4.00
4949 8383 6.542005 TCGTATGTGCATGGAATAAGTTTCAT 59.458 34.615 0.00 0.00 33.69 2.57


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

AutoCloner maintained by Alex Coulton.