Multiple sequence alignment - TraesCS3D01G359200

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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 TraesCS3D01G359200 chr3D 100.000 7332 0 0 1 7332 472952384 472945053 0.000000e+00 13540.0
1 TraesCS3D01G359200 chr3D 92.493 3410 146 47 2523 5858 473440832 473437459 0.000000e+00 4778.0
2 TraesCS3D01G359200 chr3D 92.883 815 40 7 1724 2528 473441668 473440862 0.000000e+00 1168.0
3 TraesCS3D01G359200 chr3D 84.455 1010 58 49 733 1652 473443129 473442129 0.000000e+00 904.0
4 TraesCS3D01G359200 chr3D 90.476 630 30 10 5862 6461 473437357 473436728 0.000000e+00 804.0
5 TraesCS3D01G359200 chr3D 87.586 290 33 1 1 287 98972620 98972331 4.240000e-87 333.0
6 TraesCS3D01G359200 chr3D 92.473 93 6 1 3648 3740 570265031 570265122 1.660000e-26 132.0
7 TraesCS3D01G359200 chr3D 77.253 233 41 10 7103 7329 37768303 37768077 7.720000e-25 126.0
8 TraesCS3D01G359200 chr3B 94.596 3146 100 29 3637 6735 628120021 628116899 0.000000e+00 4804.0
9 TraesCS3D01G359200 chr3B 90.161 1992 127 28 2523 4477 628401060 628399101 0.000000e+00 2529.0
10 TraesCS3D01G359200 chr3B 96.779 1397 35 4 4469 5858 628399079 628397686 0.000000e+00 2322.0
11 TraesCS3D01G359200 chr3B 88.102 1496 99 38 14 1448 628123408 628121931 0.000000e+00 1703.0
12 TraesCS3D01G359200 chr3B 95.085 1058 34 8 2523 3567 628121094 628120042 0.000000e+00 1650.0
13 TraesCS3D01G359200 chr3B 92.778 817 39 10 1724 2528 628401898 628401090 0.000000e+00 1164.0
14 TraesCS3D01G359200 chr3B 90.820 817 31 19 1724 2521 628121922 628121131 0.000000e+00 1053.0
15 TraesCS3D01G359200 chr3B 95.175 601 28 1 6733 7332 628116818 628116218 0.000000e+00 948.0
16 TraesCS3D01G359200 chr3B 90.476 630 30 10 5862 6461 628397584 628396955 0.000000e+00 804.0
17 TraesCS3D01G359200 chr3B 90.323 620 17 22 982 1558 628403050 628402431 0.000000e+00 773.0
18 TraesCS3D01G359200 chr3B 88.172 93 11 0 6996 7088 60291958 60291866 2.160000e-20 111.0
19 TraesCS3D01G359200 chr3A 91.608 1835 100 21 2523 4330 615278643 615276836 0.000000e+00 2486.0
20 TraesCS3D01G359200 chr3A 89.550 2000 132 36 2523 4477 615705807 615703840 0.000000e+00 2464.0
21 TraesCS3D01G359200 chr3A 89.912 1695 96 36 1 1637 615281337 615279660 0.000000e+00 2113.0
22 TraesCS3D01G359200 chr3A 93.885 1390 69 8 4480 5858 615703808 615702424 0.000000e+00 2082.0
23 TraesCS3D01G359200 chr3A 93.123 1396 76 12 4469 5851 615276573 615275185 0.000000e+00 2028.0
24 TraesCS3D01G359200 chr3A 94.843 892 34 10 1625 2508 615279636 615278749 0.000000e+00 1382.0
25 TraesCS3D01G359200 chr3A 92.822 808 48 8 1724 2528 615706637 615705837 0.000000e+00 1162.0
26 TraesCS3D01G359200 chr3A 90.179 896 57 12 5857 6735 615275101 615274220 0.000000e+00 1138.0
27 TraesCS3D01G359200 chr3A 84.273 1011 71 37 719 1650 615707879 615706878 0.000000e+00 905.0
28 TraesCS3D01G359200 chr3A 89.683 630 35 10 5862 6461 615702322 615701693 0.000000e+00 776.0
29 TraesCS3D01G359200 chr3A 78.487 423 54 18 298 687 66905402 66905820 7.350000e-60 243.0
30 TraesCS3D01G359200 chr3A 90.000 130 13 0 2399 2528 615278802 615278673 1.270000e-37 169.0
31 TraesCS3D01G359200 chr7D 88.772 285 30 2 1 284 470287642 470287925 1.510000e-91 348.0
32 TraesCS3D01G359200 chr7D 88.727 275 31 0 1 275 207923725 207923999 3.280000e-88 337.0
33 TraesCS3D01G359200 chr7D 79.469 414 53 15 306 691 388908465 388908874 1.570000e-66 265.0
34 TraesCS3D01G359200 chr7D 80.597 335 57 5 7000 7330 584769746 584769416 1.220000e-62 252.0
35 TraesCS3D01G359200 chr7D 80.189 318 45 7 348 651 604999222 604998909 9.570000e-54 222.0
36 TraesCS3D01G359200 chr7D 79.221 231 27 8 349 563 188361208 188360983 2.760000e-29 141.0
37 TraesCS3D01G359200 chr4A 88.811 286 28 3 1 284 77166910 77167193 1.510000e-91 348.0
38 TraesCS3D01G359200 chr5D 88.421 285 30 3 1 284 391193229 391193511 2.530000e-89 340.0
39 TraesCS3D01G359200 chr5D 83.491 212 24 9 483 688 485269548 485269342 3.490000e-43 187.0
40 TraesCS3D01G359200 chr6D 88.153 287 31 3 3 287 16393707 16393422 9.110000e-89 339.0
41 TraesCS3D01G359200 chr2D 87.805 287 35 0 1 287 358626121 358625835 3.280000e-88 337.0
42 TraesCS3D01G359200 chr2D 91.667 96 7 1 3648 3743 578046155 578046061 1.660000e-26 132.0
43 TraesCS3D01G359200 chr2D 80.105 191 25 9 487 667 455270812 455270625 5.970000e-26 130.0
44 TraesCS3D01G359200 chr4D 81.564 358 47 12 344 687 9557126 9556774 2.010000e-70 278.0
45 TraesCS3D01G359200 chr4D 79.950 404 49 16 311 689 503448044 503447648 1.210000e-67 268.0
46 TraesCS3D01G359200 chr7B 79.665 418 49 14 304 688 699925493 699925079 1.210000e-67 268.0
47 TraesCS3D01G359200 chr2B 78.862 369 43 11 349 690 46114163 46114523 4.450000e-52 217.0
48 TraesCS3D01G359200 chr2B 97.917 48 1 0 2575 2622 282847248 282847201 4.710000e-12 84.2
49 TraesCS3D01G359200 chr1B 77.805 410 49 17 304 688 171122683 171122291 1.600000e-51 215.0
50 TraesCS3D01G359200 chr5A 75.743 404 63 14 301 688 593504625 593505009 3.520000e-38 171.0
51 TraesCS3D01G359200 chr5A 76.825 315 50 13 348 641 442503211 442503523 9.850000e-34 156.0
52 TraesCS3D01G359200 chr7A 79.061 277 33 10 348 603 556101028 556101300 4.550000e-37 167.0
53 TraesCS3D01G359200 chr5B 75.472 212 42 9 487 690 25077732 25077941 2.180000e-15 95.3


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 TraesCS3D01G359200 chr3D 472945053 472952384 7331 True 13540.000000 13540 100.000000 1 7332 1 chr3D.!!$R3 7331
1 TraesCS3D01G359200 chr3D 473436728 473443129 6401 True 1913.500000 4778 90.076750 733 6461 4 chr3D.!!$R4 5728
2 TraesCS3D01G359200 chr3B 628116218 628123408 7190 True 2031.600000 4804 92.755600 14 7332 5 chr3B.!!$R2 7318
3 TraesCS3D01G359200 chr3B 628396955 628403050 6095 True 1518.400000 2529 92.103400 982 6461 5 chr3B.!!$R3 5479
4 TraesCS3D01G359200 chr3A 615274220 615281337 7117 True 1552.666667 2486 91.610833 1 6735 6 chr3A.!!$R1 6734
5 TraesCS3D01G359200 chr3A 615701693 615707879 6186 True 1477.800000 2464 90.042600 719 6461 5 chr3A.!!$R2 5742

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
786 808 0.877071 CCAGAAAACAGCTGATGCGT 59.123 50.000 23.35 0.00 45.42 5.24 F
1464 1589 0.108615 CGATCCAAGTGCCTCTCGTT 60.109 55.000 0.00 0.00 0.00 3.85 F
2755 3496 0.734253 CTCAACTTCACTCGAGGGCG 60.734 60.000 18.41 9.77 39.35 6.13 F
3554 4346 2.452600 AACCTGGCCAGACTTTTCAA 57.547 45.000 34.91 0.00 0.00 2.69 F
4247 5055 1.465689 CGGATGGCGAATTTGTGTGTC 60.466 52.381 0.00 0.00 0.00 3.67 F
4538 5497 3.708563 TTTATGGGCGCTTCAATTAGC 57.291 42.857 7.64 0.00 37.80 3.09 F
4567 5527 5.059833 AGCTCTCTGTTCTGTACTTTTTGG 58.940 41.667 0.00 0.00 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2755 3496 1.332997 GACTTGCATATCACCTGCTGC 59.667 52.381 0.00 0.00 40.34 5.25 R
3448 4227 0.994263 GGAAATTTCATGCACAGCGC 59.006 50.000 19.49 0.00 42.89 5.92 R
3717 4524 0.108424 CTCGCTCCACTTCCCTGAAG 60.108 60.000 2.40 2.40 44.37 3.02 R
4639 5599 0.962356 GGCCACTCCATTCACCTGTG 60.962 60.000 0.00 0.00 34.01 3.66 R
6156 7231 4.454678 TCAGCAAATCCCTGACATGATAC 58.545 43.478 0.00 0.00 34.59 2.24 R
6250 7353 1.804326 GCTGCTGAATTTGCCGCTG 60.804 57.895 11.43 3.78 37.60 5.18 R
6435 7538 2.095919 GGCTTCGTACGTTGCTTCATTT 60.096 45.455 24.93 0.00 0.00 2.32 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
69 70 8.813643 AGTAACAGTAACATCTTTGTAGTGAC 57.186 34.615 0.00 0.00 34.06 3.67
83 84 2.160822 AGTGACTGTAACAGCAGCAG 57.839 50.000 0.00 0.00 39.96 4.24
144 145 3.493176 CGTAGGCATTGGATCAGTGATGA 60.493 47.826 11.20 0.00 0.00 2.92
205 206 5.360144 ACAACCTAGAGCGATACACAATAGT 59.640 40.000 0.00 0.00 0.00 2.12
279 280 8.955388 TGTGCTTATAATAAGAACTTGCATGAA 58.045 29.630 6.60 0.00 0.00 2.57
323 330 2.480037 CGAAAATTGCTTTTGAAGGCCC 59.520 45.455 0.00 0.00 34.73 5.80
340 347 2.687610 CCAGCTCCATGGAGGCCTT 61.688 63.158 36.92 15.60 43.57 4.35
423 438 4.035558 GGAGGCATAATGTACATGTGTGTG 59.964 45.833 9.63 3.84 39.39 3.82
424 439 4.588899 AGGCATAATGTACATGTGTGTGT 58.411 39.130 9.63 0.00 39.39 3.72
444 459 8.788806 TGTGTGTAAATTTTGAGGACGAAATAT 58.211 29.630 0.00 0.00 38.65 1.28
463 478 2.363306 TGTTGAAATGAGGGCTGTGT 57.637 45.000 0.00 0.00 0.00 3.72
563 579 7.920682 GGTATTTCATCCTGAATTTTTACGCAT 59.079 33.333 0.00 0.00 36.11 4.73
678 694 2.283604 GGGCCGGGTCACCAAAAT 60.284 61.111 2.18 0.00 36.13 1.82
681 697 2.275380 GCCGGGTCACCAAAATGCT 61.275 57.895 2.18 0.00 36.13 3.79
705 721 5.878116 TCCACTCGAATAAAACCCACTATTG 59.122 40.000 0.00 0.00 0.00 1.90
735 753 6.930722 ACAAAAAGGAAAATCATCTCGCAAAT 59.069 30.769 0.00 0.00 0.00 2.32
740 759 5.039333 GGAAAATCATCTCGCAAATCAAGG 58.961 41.667 0.00 0.00 0.00 3.61
782 804 1.615384 GGAGCCCAGAAAACAGCTGAT 60.615 52.381 23.35 5.41 35.23 2.90
786 808 0.877071 CCAGAAAACAGCTGATGCGT 59.123 50.000 23.35 0.00 45.42 5.24
815 838 1.434188 TCTCCTGCTTTTGGTCCTCA 58.566 50.000 0.00 0.00 0.00 3.86
831 854 5.211174 GTCCTCAACCACTTACTTGTACT 57.789 43.478 0.00 0.00 0.00 2.73
833 856 6.752168 GTCCTCAACCACTTACTTGTACTAA 58.248 40.000 0.00 0.00 0.00 2.24
834 857 7.384477 GTCCTCAACCACTTACTTGTACTAAT 58.616 38.462 0.00 0.00 0.00 1.73
835 858 8.526147 GTCCTCAACCACTTACTTGTACTAATA 58.474 37.037 0.00 0.00 0.00 0.98
836 859 9.092338 TCCTCAACCACTTACTTGTACTAATAA 57.908 33.333 0.00 0.00 0.00 1.40
837 860 9.715121 CCTCAACCACTTACTTGTACTAATAAA 57.285 33.333 0.00 0.00 0.00 1.40
896 941 0.904865 ATCCGTTGCTCTCTCCACCA 60.905 55.000 0.00 0.00 0.00 4.17
974 1041 1.293498 CGAACTCACCACCTCCCAG 59.707 63.158 0.00 0.00 0.00 4.45
1334 1447 3.530564 ACTACCTGTCCATGGAGTACCTA 59.469 47.826 16.81 0.40 37.04 3.08
1464 1589 0.108615 CGATCCAAGTGCCTCTCGTT 60.109 55.000 0.00 0.00 0.00 3.85
1465 1590 1.673033 CGATCCAAGTGCCTCTCGTTT 60.673 52.381 0.00 0.00 0.00 3.60
1466 1591 2.416836 CGATCCAAGTGCCTCTCGTTTA 60.417 50.000 0.00 0.00 0.00 2.01
1468 1593 3.695830 TCCAAGTGCCTCTCGTTTAAT 57.304 42.857 0.00 0.00 0.00 1.40
1614 1820 2.477245 TCTGGTTGGCTGGCTTAGATA 58.523 47.619 2.00 0.00 0.00 1.98
1619 1825 5.022787 TGGTTGGCTGGCTTAGATATTTTT 58.977 37.500 2.00 0.00 0.00 1.94
1716 2085 8.728337 AAACCGTAATTTTATAGGAGAGAACC 57.272 34.615 0.00 0.00 0.00 3.62
1969 2600 3.539604 GCTGAAGACTGGCTTGATGTAT 58.460 45.455 0.00 0.00 36.83 2.29
2043 2677 9.109393 TCTCGATAATAGCTTTGCTGTTTAATT 57.891 29.630 6.85 0.00 40.30 1.40
2128 2764 1.776034 GCCATGTCGAGATTTCGCCC 61.776 60.000 0.00 0.00 46.28 6.13
2150 2786 5.308825 CCGATGGAAAGTAAGCCATAGATT 58.691 41.667 0.00 0.00 44.60 2.40
2170 2806 1.977854 TGACACCTGGACAAGTGCTAT 59.022 47.619 0.00 0.00 37.51 2.97
2315 2953 5.313280 TCTAGGATCTTCTCTGTAGTCCC 57.687 47.826 0.00 0.00 0.00 4.46
2330 2968 2.508526 AGTCCCTGCTTGTTTGATCAC 58.491 47.619 0.00 0.00 0.00 3.06
2392 3033 7.177498 TGAGCGTATATGAATGAATGTTCAC 57.823 36.000 0.00 0.00 40.60 3.18
2494 3200 7.421530 TGCTTTAATCAGAGTTCTTGTACAC 57.578 36.000 0.00 0.00 0.00 2.90
2755 3496 0.734253 CTCAACTTCACTCGAGGGCG 60.734 60.000 18.41 9.77 39.35 6.13
2832 3573 6.222038 ACATTAGCCGAGACTAAATGAAGA 57.778 37.500 0.00 0.00 35.82 2.87
2924 3665 8.130469 TCTTTTATTTAAAGGAAACACGTCCAC 58.870 33.333 0.00 0.00 42.88 4.02
2974 3715 7.624360 TGTTTTTCTATAGATTTCCACGCAT 57.376 32.000 2.58 0.00 0.00 4.73
2983 3724 3.312421 AGATTTCCACGCATTAACCATCG 59.688 43.478 0.00 0.00 0.00 3.84
3203 3961 9.613428 TCTGATTTCGTCATTTATGAATTAGGT 57.387 29.630 0.00 0.00 38.75 3.08
3447 4226 8.848474 ATACTTGCAACAGTATTCTTACAGTT 57.152 30.769 5.40 0.00 36.72 3.16
3451 4230 4.394795 CAACAGTATTCTTACAGTTGCGC 58.605 43.478 0.00 0.00 43.96 6.09
3554 4346 2.452600 AACCTGGCCAGACTTTTCAA 57.547 45.000 34.91 0.00 0.00 2.69
3562 4354 3.368739 GGCCAGACTTTTCAATCCCATTG 60.369 47.826 0.00 0.00 41.57 2.82
3567 4359 6.351202 CCAGACTTTTCAATCCCATTGCATTA 60.351 38.462 0.00 0.00 40.05 1.90
3568 4360 7.270047 CAGACTTTTCAATCCCATTGCATTAT 58.730 34.615 0.00 0.00 40.05 1.28
3596 4402 5.050567 CCTTTCAGTTACAACGTGGTCTTAC 60.051 44.000 0.00 0.00 0.00 2.34
3600 4406 5.045215 CAGTTACAACGTGGTCTTACTTCA 58.955 41.667 0.00 0.00 0.00 3.02
3605 4411 4.989168 ACAACGTGGTCTTACTTCATCTTC 59.011 41.667 0.00 0.00 0.00 2.87
3607 4413 6.015688 ACAACGTGGTCTTACTTCATCTTCTA 60.016 38.462 0.00 0.00 0.00 2.10
3654 4460 4.853196 CCGTCATAAATGTTTGACAAGCAG 59.147 41.667 10.58 0.00 41.85 4.24
3667 4474 5.213891 TGACAAGCAGAACTGACTATGAA 57.786 39.130 5.97 0.00 0.00 2.57
3717 4524 3.949132 AGGAAAGGAAATCTGACAGAGC 58.051 45.455 11.52 3.03 0.00 4.09
3733 4540 4.310288 GCTTCAGGGAAGTGGAGC 57.690 61.111 7.71 0.00 41.90 4.70
4139 4947 2.288948 TGCCATTTGCTTGCAGTTTAGG 60.289 45.455 0.00 0.00 42.00 2.69
4247 5055 1.465689 CGGATGGCGAATTTGTGTGTC 60.466 52.381 0.00 0.00 0.00 3.67
4501 5445 6.884280 ACTTGCTTCTTTATGCTAACTTGT 57.116 33.333 0.00 0.00 0.00 3.16
4538 5497 3.708563 TTTATGGGCGCTTCAATTAGC 57.291 42.857 7.64 0.00 37.80 3.09
4567 5527 5.059833 AGCTCTCTGTTCTGTACTTTTTGG 58.940 41.667 0.00 0.00 0.00 3.28
4608 5568 6.639632 TTGCTTTCCTTTATCATATGAGGC 57.360 37.500 11.78 0.00 0.00 4.70
6250 7353 1.009829 CTATCTTGAACACGGCTGGC 58.990 55.000 0.00 0.00 0.00 4.85
6435 7538 2.224185 TGCTTCCGTTGTAGCTGAGAAA 60.224 45.455 0.00 0.00 36.02 2.52
6535 7650 3.203716 CCATAGGAGAGCCCGTTTTAAC 58.796 50.000 0.00 0.00 40.87 2.01
6557 7673 5.600696 ACTTTTGGTGCTCATTTGGTTAAG 58.399 37.500 0.00 0.00 0.00 1.85
6631 7748 7.001674 TGTTTGGTGAATAGTTTCATGTAGGT 58.998 34.615 0.00 0.00 43.49 3.08
6632 7749 7.174253 TGTTTGGTGAATAGTTTCATGTAGGTC 59.826 37.037 0.00 0.00 43.49 3.85
6633 7750 6.620877 TGGTGAATAGTTTCATGTAGGTCT 57.379 37.500 0.00 0.00 43.49 3.85
6634 7751 7.727578 TGGTGAATAGTTTCATGTAGGTCTA 57.272 36.000 0.00 0.00 43.49 2.59
6635 7752 8.319057 TGGTGAATAGTTTCATGTAGGTCTAT 57.681 34.615 0.00 0.00 43.49 1.98
6636 7753 8.204160 TGGTGAATAGTTTCATGTAGGTCTATG 58.796 37.037 0.00 0.00 43.49 2.23
6637 7754 7.657761 GGTGAATAGTTTCATGTAGGTCTATGG 59.342 40.741 0.00 0.00 43.49 2.74
6638 7755 7.171678 GTGAATAGTTTCATGTAGGTCTATGGC 59.828 40.741 0.00 0.00 43.49 4.40
6739 7939 9.232082 CTCTCTTCTCATTAGAAACTACAATCG 57.768 37.037 0.00 0.00 41.19 3.34
6769 7969 2.112279 AAGGGTCACAACACCTAGGA 57.888 50.000 17.98 0.00 36.57 2.94
6788 7988 8.275040 ACCTAGGATGCAATTAGTAACTGATTT 58.725 33.333 17.98 0.00 0.00 2.17
6838 8038 8.997621 TCACTAACCTGTATTAACATCAAGTC 57.002 34.615 0.00 0.00 34.37 3.01
6879 8079 1.628846 TCCCTCCTGGTAGAGTTTTGC 59.371 52.381 0.00 0.00 34.77 3.68
6884 8084 2.979678 TCCTGGTAGAGTTTTGCTCCTT 59.020 45.455 0.00 0.00 45.21 3.36
6920 8120 3.390280 AGTCCTTGACTCCCTCCAG 57.610 57.895 0.00 0.00 38.71 3.86
6933 8133 0.179000 CCTCCAGTCAATCTTCCCCG 59.821 60.000 0.00 0.00 0.00 5.73
6961 8161 0.179084 CTCCGCTCGGGCTGATTAAA 60.179 55.000 5.36 0.00 36.09 1.52
7013 8213 4.621034 GGTGCGGATAAAATCACTGTTTTG 59.379 41.667 0.00 0.00 33.62 2.44
7052 8252 0.667184 CACAAAATGAACCCCGCTGC 60.667 55.000 0.00 0.00 0.00 5.25
7078 8278 6.670695 ACTTTAGCATGATTTGACCCTTTT 57.329 33.333 0.00 0.00 0.00 2.27
7096 8296 8.250538 ACCCTTTTTAAAAATGCACAATATCG 57.749 30.769 13.55 0.00 0.00 2.92
7173 8373 0.692476 AGCATCAGCCACCACTACAA 59.308 50.000 0.00 0.00 43.56 2.41
7219 8419 1.317613 TGCACAAAGATGAAACGCCT 58.682 45.000 0.00 0.00 0.00 5.52
7226 8426 4.097892 ACAAAGATGAAACGCCTTGAACTT 59.902 37.500 0.00 0.00 0.00 2.66
7261 8461 2.347490 CAGCAACGCCAGGTAGGT 59.653 61.111 0.00 0.00 40.61 3.08
7273 8473 3.279434 CCAGGTAGGTACTTTGGCATTC 58.721 50.000 0.00 0.00 41.75 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.703001 ATTGCTACTGTTACCACTGCT 57.297 42.857 0.00 0.00 0.00 4.24
37 38 8.372459 ACAAAGATGTTACTGTTACTATCACCA 58.628 33.333 0.00 0.00 35.91 4.17
57 58 5.270893 TGCTGTTACAGTCACTACAAAGA 57.729 39.130 14.23 0.00 33.43 2.52
69 70 3.005554 ACTATTGCTGCTGCTGTTACAG 58.994 45.455 17.00 8.18 40.80 2.74
83 84 9.314321 TGATCTTTGCTAAGTTACTACTATTGC 57.686 33.333 7.77 0.00 33.17 3.56
144 145 6.567687 TGAACGTCATCCAACACAAATATT 57.432 33.333 0.00 0.00 0.00 1.28
253 254 8.504812 TCATGCAAGTTCTTATTATAAGCACA 57.495 30.769 14.95 4.89 31.79 4.57
323 330 1.153005 GAAGGCCTCCATGGAGCTG 60.153 63.158 32.97 22.26 40.69 4.24
395 410 4.823442 ACATGTACATTATGCCTCCATGTG 59.177 41.667 5.37 0.00 39.73 3.21
423 438 9.834628 TCAACATATTTCGTCCTCAAAATTTAC 57.165 29.630 0.00 0.00 0.00 2.01
444 459 2.363306 ACACAGCCCTCATTTCAACA 57.637 45.000 0.00 0.00 0.00 3.33
463 478 3.838565 TCATGTGCTGAAAAACCCCTTA 58.161 40.909 0.00 0.00 0.00 2.69
524 540 8.739039 CAGGATGAAATACCTTAAAATGTGACA 58.261 33.333 0.00 0.00 39.69 3.58
607 623 6.803154 AAATTCAGACTTTCCGGTTTAGAG 57.197 37.500 0.00 0.00 0.00 2.43
662 678 2.969827 CATTTTGGTGACCCGGCC 59.030 61.111 0.00 0.00 0.00 6.13
663 679 2.212900 GAGCATTTTGGTGACCCGGC 62.213 60.000 0.00 0.00 0.00 6.13
678 694 2.039216 TGGGTTTTATTCGAGTGGAGCA 59.961 45.455 0.00 0.00 0.00 4.26
681 697 5.687166 ATAGTGGGTTTTATTCGAGTGGA 57.313 39.130 0.00 0.00 0.00 4.02
705 721 6.346040 CGAGATGATTTTCCTTTTTGTTGTGC 60.346 38.462 0.00 0.00 0.00 4.57
735 753 3.513912 TGATAGTTTCTTCGGCTCCTTGA 59.486 43.478 0.00 0.00 0.00 3.02
740 759 3.623510 CCCTTTGATAGTTTCTTCGGCTC 59.376 47.826 0.00 0.00 0.00 4.70
782 804 2.426522 CAGGAGAAAATGAAGGACGCA 58.573 47.619 0.00 0.00 0.00 5.24
786 808 4.281688 CCAAAAGCAGGAGAAAATGAAGGA 59.718 41.667 0.00 0.00 0.00 3.36
862 906 1.557832 ACGGATCCGAGAAATTTGGGA 59.442 47.619 39.55 0.00 42.83 4.37
896 941 0.404426 GGGGCTCCTTTTGTAGTGGT 59.596 55.000 0.00 0.00 0.00 4.16
974 1041 2.750237 GGGGAATGGCGGTGTGTC 60.750 66.667 0.00 0.00 0.00 3.67
1437 1550 1.086634 GCACTTGGATCGCTCACCTC 61.087 60.000 0.00 0.00 0.00 3.85
1468 1593 7.066525 CCCAAGAGTACGAAAATAAATAGCCAA 59.933 37.037 0.00 0.00 0.00 4.52
1509 1666 3.690139 TCACGGTCAAACAAAGCACTAAA 59.310 39.130 0.00 0.00 0.00 1.85
1619 1825 7.450014 TGCTTGGTTAAGTAATGGATCAGAAAA 59.550 33.333 0.00 0.00 36.27 2.29
1623 1861 6.757897 TTGCTTGGTTAAGTAATGGATCAG 57.242 37.500 0.00 0.00 34.25 2.90
1670 2038 7.064134 CGGTTTCACATCTAAAATACTACAGCA 59.936 37.037 0.00 0.00 0.00 4.41
1688 2056 8.937634 TCTCTCCTATAAAATTACGGTTTCAC 57.062 34.615 0.00 0.00 0.00 3.18
1700 2068 9.595823 CAAATCTTACGGTTCTCTCCTATAAAA 57.404 33.333 0.00 0.00 0.00 1.52
1707 2076 6.106673 TCAATCAAATCTTACGGTTCTCTCC 58.893 40.000 0.00 0.00 0.00 3.71
1716 2085 6.015504 CCAGACGTTTCAATCAAATCTTACG 58.984 40.000 0.00 0.00 0.00 3.18
2043 2677 4.283212 CCCATGGGCTAAACTTCTGAAAAA 59.717 41.667 20.41 0.00 0.00 1.94
2128 2764 5.991606 TCAATCTATGGCTTACTTTCCATCG 59.008 40.000 0.00 0.00 41.81 3.84
2150 2786 1.419381 TAGCACTTGTCCAGGTGTCA 58.581 50.000 10.67 0.00 40.13 3.58
2211 2848 5.065090 TGAATTTAGAAGGCATCACGTCATG 59.935 40.000 0.00 0.00 0.00 3.07
2306 2944 3.126001 TCAAACAAGCAGGGACTACAG 57.874 47.619 0.00 0.00 36.02 2.74
2307 2945 3.072330 TGATCAAACAAGCAGGGACTACA 59.928 43.478 0.00 0.00 36.02 2.74
2315 2953 5.749588 TCAAAACATGTGATCAAACAAGCAG 59.250 36.000 0.00 0.00 32.81 4.24
2375 3016 6.622833 TCATGCGTGAACATTCATTCATAT 57.377 33.333 6.04 0.00 40.60 1.78
2392 3033 2.159585 TCGCCAAATGTAGTTTCATGCG 60.160 45.455 0.00 0.00 39.11 4.73
2457 3106 5.974300 TGATTAAAGCATCGCGAAATCTAC 58.026 37.500 22.46 7.60 31.90 2.59
2465 3171 3.553511 AGAACTCTGATTAAAGCATCGCG 59.446 43.478 0.00 0.00 0.00 5.87
2467 3173 6.414408 ACAAGAACTCTGATTAAAGCATCG 57.586 37.500 0.00 0.00 0.00 3.84
2494 3200 5.240623 GTCTGTGATAGTGGATCCAGTCTAG 59.759 48.000 25.66 18.01 35.74 2.43
2755 3496 1.332997 GACTTGCATATCACCTGCTGC 59.667 52.381 0.00 0.00 40.34 5.25
2832 3573 6.072452 GCAGTATTCACAAAGTTAAAGGCTCT 60.072 38.462 0.00 0.00 0.00 4.09
2924 3665 6.013725 TGGTTATCACATAGGGCAGGTTATAG 60.014 42.308 0.00 0.00 0.00 1.31
2974 3715 4.377943 CGAGTTGTTTGATGCGATGGTTAA 60.378 41.667 0.00 0.00 0.00 2.01
2983 3724 6.695292 ATTTTTCATCGAGTTGTTTGATGC 57.305 33.333 0.00 0.00 44.33 3.91
3047 3788 5.717178 ACCTCACTTATCAGTCAGAGCTAAA 59.283 40.000 0.00 0.00 0.00 1.85
3048 3789 5.126222 CACCTCACTTATCAGTCAGAGCTAA 59.874 44.000 0.00 0.00 0.00 3.09
3360 4139 1.661341 GACATAGGTGCAGCTTCCTG 58.339 55.000 25.47 19.94 42.13 3.86
3448 4227 0.994263 GGAAATTTCATGCACAGCGC 59.006 50.000 19.49 0.00 42.89 5.92
3450 4229 2.288948 TGGTGGAAATTTCATGCACAGC 60.289 45.455 19.49 15.96 0.00 4.40
3451 4230 3.319755 GTGGTGGAAATTTCATGCACAG 58.680 45.455 19.49 0.00 0.00 3.66
3459 4251 4.016444 TCATGCTAGGTGGTGGAAATTTC 58.984 43.478 9.83 9.83 0.00 2.17
3519 4311 7.172342 TGGCCAGGTTAATAATAATAGCGATT 58.828 34.615 0.00 0.00 0.00 3.34
3523 4315 7.168905 AGTCTGGCCAGGTTAATAATAATAGC 58.831 38.462 32.23 3.77 0.00 2.97
3536 4328 2.519013 GATTGAAAAGTCTGGCCAGGT 58.481 47.619 32.23 17.48 0.00 4.00
3538 4330 1.821136 GGGATTGAAAAGTCTGGCCAG 59.179 52.381 27.87 27.87 0.00 4.85
3541 4333 3.853475 CAATGGGATTGAAAAGTCTGGC 58.147 45.455 0.00 0.00 42.83 4.85
3554 4346 7.731688 ACTGAAAGGATAATAATGCAATGGGAT 59.268 33.333 0.00 0.00 39.30 3.85
3562 4354 8.395633 ACGTTGTAACTGAAAGGATAATAATGC 58.604 33.333 0.00 0.00 39.30 3.56
3567 4359 6.235664 ACCACGTTGTAACTGAAAGGATAAT 58.764 36.000 0.00 0.00 39.30 1.28
3568 4360 5.613329 ACCACGTTGTAACTGAAAGGATAA 58.387 37.500 0.00 0.00 39.30 1.75
3635 4441 7.113965 GTCAGTTCTGCTTGTCAAACATTTATG 59.886 37.037 0.00 0.00 0.00 1.90
3654 4460 7.687941 TCCTGGAAAAATTCATAGTCAGTTC 57.312 36.000 0.00 0.00 0.00 3.01
3703 4510 3.055530 TCCCTGAAGCTCTGTCAGATTTC 60.056 47.826 14.28 15.38 44.44 2.17
3717 4524 0.108424 CTCGCTCCACTTCCCTGAAG 60.108 60.000 2.40 2.40 44.37 3.02
3733 4540 1.266989 GCAACTTTGGAAGGGAACTCG 59.733 52.381 0.00 0.00 42.68 4.18
4139 4947 2.572290 CGGGTGGAGATTACCATTTCC 58.428 52.381 0.00 0.00 42.17 3.13
4247 5055 2.377628 ATACCGTATGCCCAGCCACG 62.378 60.000 4.42 4.42 36.32 4.94
4538 5497 2.170166 ACAGAACAGAGAGCTCCAGAG 58.830 52.381 10.93 0.49 0.00 3.35
4608 5568 9.931210 GAATTTAGTAAACTTCATTATGGTCCG 57.069 33.333 0.00 0.00 0.00 4.79
4639 5599 0.962356 GGCCACTCCATTCACCTGTG 60.962 60.000 0.00 0.00 34.01 3.66
4802 5762 6.267471 TCCACTGATCTGTTTTTAGCCATTTT 59.733 34.615 1.95 0.00 0.00 1.82
6156 7231 4.454678 TCAGCAAATCCCTGACATGATAC 58.545 43.478 0.00 0.00 34.59 2.24
6250 7353 1.804326 GCTGCTGAATTTGCCGCTG 60.804 57.895 11.43 3.78 37.60 5.18
6435 7538 2.095919 GGCTTCGTACGTTGCTTCATTT 60.096 45.455 24.93 0.00 0.00 2.32
6535 7650 4.990426 CCTTAACCAAATGAGCACCAAAAG 59.010 41.667 0.00 0.00 0.00 2.27
6557 7673 6.147864 TGCTGCACTCCATATTTTATTTCC 57.852 37.500 0.00 0.00 0.00 3.13
6739 7939 7.773690 AGGTGTTGTGACCCTTTATTATGTATC 59.226 37.037 0.00 0.00 36.56 2.24
6753 7953 1.003118 TGCATCCTAGGTGTTGTGACC 59.997 52.381 9.08 0.00 36.09 4.02
6836 8036 7.258441 GGAAAAGGTTGGCTCTTTATTATGAC 58.742 38.462 0.00 0.00 33.80 3.06
6838 8038 6.381133 AGGGAAAAGGTTGGCTCTTTATTATG 59.619 38.462 0.00 0.00 33.80 1.90
6920 8120 2.115291 GCCTGCGGGGAAGATTGAC 61.115 63.158 15.02 0.00 37.23 3.18
6933 8133 4.577246 CGAGCGGAGGTAGCCTGC 62.577 72.222 6.21 6.21 39.88 4.85
6941 8141 2.028125 TTAATCAGCCCGAGCGGAGG 62.028 60.000 11.05 0.00 46.59 4.30
6945 8145 1.160329 CCCTTTAATCAGCCCGAGCG 61.160 60.000 0.00 0.00 46.67 5.03
6973 8173 3.058160 CAAGGCCGGGAAGCAGTG 61.058 66.667 2.18 0.00 0.00 3.66
6974 8174 4.351054 CCAAGGCCGGGAAGCAGT 62.351 66.667 10.74 0.00 0.00 4.40
7013 8213 9.791820 TTTTGTGCTAAAGTTACTAAAAAGGTC 57.208 29.630 0.00 0.00 0.00 3.85
7052 8252 6.029346 AGGGTCAAATCATGCTAAAGTTTG 57.971 37.500 0.00 0.00 0.00 2.93
7078 8278 6.682746 ACACCACGATATTGTGCATTTTTAA 58.317 32.000 16.58 0.00 38.55 1.52
7096 8296 3.125316 GCATAGTGTAGCAGAAACACCAC 59.875 47.826 2.90 0.00 46.77 4.16
7173 8373 2.434774 GGGTTGGCGTTTCTCCCT 59.565 61.111 0.00 0.00 35.63 4.20
7219 8419 4.936411 TCACTACGAAACACCAAAGTTCAA 59.064 37.500 0.00 0.00 0.00 2.69
7226 8426 2.828877 CTGGTCACTACGAAACACCAA 58.171 47.619 0.00 0.00 36.69 3.67
7301 8502 8.474025 ACTTTAACACAAAATGAACATTCCTGA 58.526 29.630 13.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.