Multiple sequence alignment - TraesCS5D01G140400

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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 TraesCS5D01G140400 chr5D 100.000 7526 0 0 1 7526 223962680 223955155 0.000000e+00 13899.0
1 TraesCS5D01G140400 chr5D 92.308 338 20 3 511 843 423231675 423232011 6.830000e-130 475.0
2 TraesCS5D01G140400 chr5D 92.040 201 7 3 2167 2359 386861712 386861911 2.680000e-69 274.0
3 TraesCS5D01G140400 chr5D 85.892 241 21 7 2125 2359 277243071 277243304 2.100000e-60 244.0
4 TraesCS5D01G140400 chr5D 89.130 92 8 2 5519 5609 481427202 481427112 6.170000e-21 113.0
5 TraesCS5D01G140400 chr5D 87.000 100 9 3 5519 5615 139440916 139441014 7.980000e-20 110.0
6 TraesCS5D01G140400 chr5D 93.333 45 3 0 2358 2402 332041741 332041697 4.870000e-07 67.6
7 TraesCS5D01G140400 chr5D 92.683 41 3 0 2358 2398 387996060 387996020 8.160000e-05 60.2
8 TraesCS5D01G140400 chr5A 95.202 4189 133 22 3349 7526 298806829 298802698 0.000000e+00 6560.0
9 TraesCS5D01G140400 chr5A 95.456 2487 80 13 870 3349 298809374 298806914 0.000000e+00 3936.0
10 TraesCS5D01G140400 chr5A 85.824 522 43 19 1 513 700576978 700577477 6.690000e-145 525.0
11 TraesCS5D01G140400 chr5A 95.238 84 4 0 5526 5609 600439840 600439757 4.740000e-27 134.0
12 TraesCS5D01G140400 chr5B 96.472 3600 92 13 3424 7016 247254034 247257605 0.000000e+00 5912.0
13 TraesCS5D01G140400 chr5B 95.304 3620 113 20 1 3608 247250457 247254031 0.000000e+00 5690.0
14 TraesCS5D01G140400 chr5B 91.422 408 21 5 7131 7526 247257889 247258294 1.430000e-151 547.0
15 TraesCS5D01G140400 chr5B 84.139 517 48 16 1 510 615384421 615384910 3.180000e-128 470.0
16 TraesCS5D01G140400 chr5B 86.239 109 12 3 5512 5619 557287017 557286911 1.720000e-21 115.0
17 TraesCS5D01G140400 chr3D 91.154 520 26 8 3 513 53620790 53620282 0.000000e+00 688.0
18 TraesCS5D01G140400 chr3D 88.793 232 16 3 283 513 54001786 54002008 7.440000e-70 276.0
19 TraesCS5D01G140400 chr3D 92.857 42 3 0 7160 7201 325400907 325400866 2.270000e-05 62.1
20 TraesCS5D01G140400 chr4D 90.891 516 33 8 1 513 370067625 370068129 0.000000e+00 680.0
21 TraesCS5D01G140400 chr4D 91.133 203 11 2 2163 2359 313574197 313574398 1.240000e-67 268.0
22 TraesCS5D01G140400 chr4D 85.985 264 20 8 254 513 370055578 370055328 4.480000e-67 267.0
23 TraesCS5D01G140400 chr4D 89.756 205 18 3 7322 7526 7201981 7202182 7.490000e-65 259.0
24 TraesCS5D01G140400 chr4D 92.308 91 7 0 2077 2167 614535 614625 6.130000e-26 130.0
25 TraesCS5D01G140400 chr4D 88.421 95 10 1 5519 5612 138406357 138406263 6.170000e-21 113.0
26 TraesCS5D01G140400 chr4D 87.912 91 11 0 5519 5609 30221491 30221581 2.870000e-19 108.0
27 TraesCS5D01G140400 chr4D 88.172 93 8 3 5519 5609 414999562 414999653 2.870000e-19 108.0
28 TraesCS5D01G140400 chr4D 85.000 100 11 4 5519 5615 429472353 429472255 1.730000e-16 99.0
29 TraesCS5D01G140400 chr4D 89.655 58 2 2 5570 5625 85586342 85586287 3.770000e-08 71.3
30 TraesCS5D01G140400 chr4D 94.595 37 1 1 5577 5613 432771929 432771964 1.000000e-03 56.5
31 TraesCS5D01G140400 chr2A 87.048 525 42 14 1 513 497421472 497420962 3.050000e-158 569.0
32 TraesCS5D01G140400 chr2A 92.462 199 8 2 2167 2359 310407137 310406940 2.070000e-70 278.0
33 TraesCS5D01G140400 chr2B 85.352 512 51 18 1 508 686839466 686838975 6.740000e-140 508.0
34 TraesCS5D01G140400 chr2B 91.545 343 22 4 511 848 175454265 175454605 4.110000e-127 466.0
35 TraesCS5D01G140400 chr2B 83.130 409 38 18 91 491 585899289 585899674 2.010000e-90 344.0
36 TraesCS5D01G140400 chr2B 84.492 187 17 4 274 459 331027057 331026882 2.790000e-39 174.0
37 TraesCS5D01G140400 chr2B 92.157 51 2 2 2355 2404 646975939 646975988 3.770000e-08 71.3
38 TraesCS5D01G140400 chr7B 92.035 339 21 3 511 844 498599432 498599769 8.840000e-129 472.0
39 TraesCS5D01G140400 chr7B 90.217 92 9 0 5518 5609 310413162 310413071 3.690000e-23 121.0
40 TraesCS5D01G140400 chr6B 92.059 340 20 4 511 844 121524313 121523975 8.840000e-129 472.0
41 TraesCS5D01G140400 chr6B 83.815 519 56 19 1 513 633680499 633680995 1.140000e-127 468.0
42 TraesCS5D01G140400 chr6B 77.124 306 55 7 7151 7443 4568856 4569159 6.040000e-36 163.0
43 TraesCS5D01G140400 chr3B 92.059 340 20 4 511 844 745557377 745557039 8.840000e-129 472.0
44 TraesCS5D01G140400 chr3B 91.789 341 21 4 511 845 824304715 824305054 1.140000e-127 468.0
45 TraesCS5D01G140400 chr3B 88.542 96 9 2 5528 5622 821661336 821661242 1.720000e-21 115.0
46 TraesCS5D01G140400 chrUn 91.765 340 21 4 511 844 263185633 263185295 4.110000e-127 466.0
47 TraesCS5D01G140400 chrUn 97.436 39 0 1 5575 5613 75423133 75423170 1.750000e-06 65.8
48 TraesCS5D01G140400 chr7D 91.765 340 21 4 511 844 478799162 478798824 4.110000e-127 466.0
49 TraesCS5D01G140400 chr7D 90.217 92 9 0 5518 5609 336159762 336159853 3.690000e-23 121.0
50 TraesCS5D01G140400 chr1B 83.613 537 45 19 1 510 242669568 242669048 1.480000e-126 464.0
51 TraesCS5D01G140400 chr1B 87.698 252 18 7 265 513 322724207 322723966 1.600000e-71 281.0
52 TraesCS5D01G140400 chr1B 93.103 87 6 0 5519 5605 193283064 193283150 2.200000e-25 128.0
53 TraesCS5D01G140400 chr4B 86.632 389 36 8 7151 7526 13058751 13059136 4.200000e-112 416.0
54 TraesCS5D01G140400 chr2D 92.462 199 8 2 2167 2359 249891795 249891992 2.070000e-70 278.0
55 TraesCS5D01G140400 chr2D 91.919 198 8 5 2168 2359 380416529 380416724 3.460000e-68 270.0
56 TraesCS5D01G140400 chr1A 86.260 262 24 9 254 513 95532257 95532006 2.680000e-69 274.0
57 TraesCS5D01G140400 chr1A 90.805 87 8 0 5519 5605 145375861 145375775 4.770000e-22 117.0
58 TraesCS5D01G140400 chr4A 84.806 283 29 8 2084 2359 438239366 438239641 9.620000e-69 272.0
59 TraesCS5D01G140400 chr4A 95.604 91 4 0 2077 2167 477033213 477033303 6.090000e-31 147.0
60 TraesCS5D01G140400 chr7A 95.455 88 4 0 2080 2167 498590374 498590287 2.830000e-29 141.0
61 TraesCS5D01G140400 chr7A 93.333 45 3 0 2358 2402 534838639 534838595 4.870000e-07 67.6
62 TraesCS5D01G140400 chr3A 94.505 91 5 0 2077 2167 621323747 621323837 2.830000e-29 141.0
63 TraesCS5D01G140400 chr3A 88.000 100 8 3 5519 5615 470095778 470095680 1.720000e-21 115.0
64 TraesCS5D01G140400 chr3A 93.617 47 3 0 7480 7526 737594213 737594259 3.770000e-08 71.3
65 TraesCS5D01G140400 chr1D 93.103 87 6 0 5519 5605 143955470 143955556 2.200000e-25 128.0
66 TraesCS5D01G140400 chr1D 88.350 103 10 2 5508 5609 476796794 476796693 1.030000e-23 122.0
67 TraesCS5D01G140400 chr1D 87.129 101 10 3 5510 5609 34022012 34021914 2.220000e-20 111.0
68 TraesCS5D01G140400 chr1D 90.244 82 6 2 5529 5609 143955556 143955476 1.030000e-18 106.0
69 TraesCS5D01G140400 chr6A 88.421 95 11 0 5514 5608 93798345 93798439 1.720000e-21 115.0
70 TraesCS5D01G140400 chr6D 86.813 91 12 0 5519 5609 78080173 78080263 1.340000e-17 102.0
71 TraesCS5D01G140400 chr6D 91.304 46 4 0 2358 2403 462207614 462207569 6.300000e-06 63.9


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 TraesCS5D01G140400 chr5D 223955155 223962680 7525 True 13899.000000 13899 100.000000 1 7526 1 chr5D.!!$R1 7525
1 TraesCS5D01G140400 chr5A 298802698 298809374 6676 True 5248.000000 6560 95.329000 870 7526 2 chr5A.!!$R2 6656
2 TraesCS5D01G140400 chr5B 247250457 247258294 7837 False 4049.666667 5912 94.399333 1 7526 3 chr5B.!!$F2 7525
3 TraesCS5D01G140400 chr3D 53620282 53620790 508 True 688.000000 688 91.154000 3 513 1 chr3D.!!$R1 510
4 TraesCS5D01G140400 chr4D 370067625 370068129 504 False 680.000000 680 90.891000 1 513 1 chr4D.!!$F5 512
5 TraesCS5D01G140400 chr2A 497420962 497421472 510 True 569.000000 569 87.048000 1 513 1 chr2A.!!$R2 512
6 TraesCS5D01G140400 chr1B 242669048 242669568 520 True 464.000000 464 83.613000 1 510 1 chr1B.!!$R1 509

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
596 634 0.313672 TTCAACGGCAATGGCTTCAC 59.686 50.000 5.02 0.0 40.87 3.18 F
602 640 1.000385 CGGCAATGGCTTCACTTTTGA 60.000 47.619 5.02 0.0 40.87 2.69 F
618 656 1.361204 TTGATGAGCCACCTTGGAGA 58.639 50.000 0.00 0.0 40.96 3.71 F
1806 1849 1.407936 AGCATCGTCTCATAGCCTGT 58.592 50.000 0.00 0.0 0.00 4.00 F
3639 3962 1.298340 CCCATGGTACTGGTGCGAA 59.702 57.895 11.73 0.0 34.23 4.70 F
4164 4487 1.725066 CGAACACTTGGCGTGGTTT 59.275 52.632 0.00 0.0 45.50 3.27 F
4525 4848 0.320421 TGGCTCGTACAGAAAGGCAC 60.320 55.000 6.69 0.0 40.24 5.01 F
4530 4853 1.675219 GTACAGAAAGGCACGGGGA 59.325 57.895 0.00 0.0 0.00 4.81 F
4607 4930 3.355626 GTGGAACCTTTTTGTCTGCTC 57.644 47.619 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2247 0.691413 AGCTCTAGCCTACCCCAACC 60.691 60.000 0.0 0.0 43.38 3.77 R
2379 2426 2.172717 ACTCCCTCCATCCCAAATTACG 59.827 50.000 0.0 0.0 0.00 3.18 R
2786 2833 2.816087 CAGGAACTAATGCAGTGTTGCT 59.184 45.455 14.2 14.2 45.05 3.91 R
3929 4252 2.489722 GCAGGAAAGCAAGGAAGTTAGG 59.510 50.000 0.0 0.0 0.00 2.69 R
4493 4816 1.013596 CGAGCCACAACAAAGTGACA 58.986 50.000 0.0 0.0 42.05 3.58 R
5304 5627 1.293062 ACATGCCCTCCTGTGAATCT 58.707 50.000 0.0 0.0 0.00 2.40 R
6209 6537 1.629861 TGATGCTGATCTTCCACCACA 59.370 47.619 0.0 0.0 0.00 4.17 R
6222 6550 5.823209 TGAAATGAACAGGTATGATGCTG 57.177 39.130 0.0 0.0 0.00 4.41 R
6713 7044 5.437060 ACCAAGCAAGTTCTACAAAGAGAA 58.563 37.500 0.0 0.0 31.96 2.87 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
84 87 4.337177 TCCCAAATGGCGCGGACA 62.337 61.111 8.83 0.00 0.00 4.02
164 167 3.509137 GACGTCGAGGCAACCACCA 62.509 63.158 4.75 0.00 37.17 4.17
265 292 2.758327 CGATCCGACCAGGTGGGA 60.758 66.667 24.64 24.64 44.00 4.37
281 315 5.828328 CAGGTGGGAGGATCTTTTAATAACC 59.172 44.000 0.00 0.00 33.73 2.85
361 397 2.682856 GTGGCAGTCAAAGAACACTTGA 59.317 45.455 0.00 0.00 0.00 3.02
392 428 0.534873 TAGCGCCAACTCAGCACATA 59.465 50.000 2.29 0.00 0.00 2.29
393 429 0.742281 AGCGCCAACTCAGCACATAG 60.742 55.000 2.29 0.00 0.00 2.23
394 430 1.717937 CGCCAACTCAGCACATAGC 59.282 57.895 0.00 0.00 46.19 2.97
484 522 2.730382 GGGTATTTGTAACCACAGGGG 58.270 52.381 0.00 0.00 44.81 4.79
526 564 1.551883 GTAATAGTCGTGGTGGGGTGT 59.448 52.381 0.00 0.00 0.00 4.16
528 566 0.543410 ATAGTCGTGGTGGGGTGTCA 60.543 55.000 0.00 0.00 0.00 3.58
551 589 1.078759 CTGGAGTTCGATGGCGTGTC 61.079 60.000 0.00 0.00 38.98 3.67
572 610 4.268720 GGTGTTGCCCCTGTTTGA 57.731 55.556 0.00 0.00 0.00 2.69
574 612 1.047801 GGTGTTGCCCCTGTTTGATT 58.952 50.000 0.00 0.00 0.00 2.57
575 613 1.416030 GGTGTTGCCCCTGTTTGATTT 59.584 47.619 0.00 0.00 0.00 2.17
596 634 0.313672 TTCAACGGCAATGGCTTCAC 59.686 50.000 5.02 0.00 40.87 3.18
602 640 1.000385 CGGCAATGGCTTCACTTTTGA 60.000 47.619 5.02 0.00 40.87 2.69
618 656 1.361204 TTGATGAGCCACCTTGGAGA 58.639 50.000 0.00 0.00 40.96 3.71
688 726 3.146847 GAGGTGACCCGTCATTCTTTTT 58.853 45.455 0.00 0.00 42.18 1.94
701 739 2.341846 TCTTTTTCTTCGGTGGCTGT 57.658 45.000 0.00 0.00 0.00 4.40
715 753 3.286751 CTGTTGTGGTGGTGCCGG 61.287 66.667 0.00 0.00 41.21 6.13
731 769 3.695606 GGAGGCAGGTGACGAGCA 61.696 66.667 0.00 0.00 37.88 4.26
765 803 4.100808 GCTCAGAGATGTTCTACCATCCTT 59.899 45.833 0.00 0.00 41.79 3.36
779 817 7.685481 TCTACCATCCTTTCAGTTTTGTCATA 58.315 34.615 0.00 0.00 0.00 2.15
786 824 5.163754 CCTTTCAGTTTTGTCATATCGGTCC 60.164 44.000 0.00 0.00 0.00 4.46
794 832 3.281158 TGTCATATCGGTCCTTACGTGA 58.719 45.455 0.00 0.00 0.00 4.35
833 876 9.438228 TTTTTATGAATGAGACACGTATTACCA 57.562 29.630 0.00 0.00 0.00 3.25
877 920 5.705441 TGTAGTGAATTTTTCTCCAGCGAAT 59.295 36.000 0.00 0.00 0.00 3.34
963 1006 4.609018 CATTCCTCCGGCCGCGAT 62.609 66.667 22.85 5.34 0.00 4.58
1537 1580 4.560856 AGCTCGTCGATGCGCTCC 62.561 66.667 16.17 0.00 0.00 4.70
1806 1849 1.407936 AGCATCGTCTCATAGCCTGT 58.592 50.000 0.00 0.00 0.00 4.00
1895 1939 8.940768 ACAAAACTTTTGCATGTATTGTACTT 57.059 26.923 13.22 0.00 0.00 2.24
1987 2032 5.054390 TCAATCGGCAGAAAATGGTTAAC 57.946 39.130 0.00 0.00 0.00 2.01
2010 2055 4.917906 AGACTCAAGGCTATCTTTGGTT 57.082 40.909 0.00 0.00 32.41 3.67
2019 2064 6.567602 AGGCTATCTTTGGTTGAGTCTTAT 57.432 37.500 0.00 0.00 0.00 1.73
2020 2065 6.963322 AGGCTATCTTTGGTTGAGTCTTATT 58.037 36.000 0.00 0.00 0.00 1.40
2179 2226 8.609176 TCTAGACAAATCTACAACAACAACAAC 58.391 33.333 0.00 0.00 36.29 3.32
2180 2227 7.151999 AGACAAATCTACAACAACAACAACA 57.848 32.000 0.00 0.00 31.46 3.33
2181 2228 7.598278 AGACAAATCTACAACAACAACAACAA 58.402 30.769 0.00 0.00 31.46 2.83
2200 2247 4.145052 ACAAAGCCTTTAGTCCCAAAGAG 58.855 43.478 0.00 0.00 37.66 2.85
2349 2396 1.946984 TTACGGACTCCTCCCATGTT 58.053 50.000 0.00 0.00 31.93 2.71
2379 2426 7.928103 TCGGTATCTAGACAAATCTAAGACAC 58.072 38.462 0.00 0.00 36.98 3.67
2975 3026 5.361285 CACATACTAACAGAAGGGCTAGAGT 59.639 44.000 0.00 0.00 0.00 3.24
3205 3256 7.655236 TCATTGCACATCCTTACAAATTTTG 57.345 32.000 7.59 7.59 0.00 2.44
3293 3344 3.262405 ACCTCTTTCGTAGTATTGCCCAA 59.738 43.478 0.00 0.00 0.00 4.12
3535 3672 4.925068 ACAACTTGTGTGAATGAAGCTTC 58.075 39.130 19.89 19.89 39.72 3.86
3546 3869 5.181009 TGAATGAAGCTTCACATCCACTAG 58.819 41.667 30.66 0.00 40.49 2.57
3574 3897 8.625786 TCAGTTTGGACATGATATGAATATGG 57.374 34.615 0.00 0.00 0.00 2.74
3639 3962 1.298340 CCCATGGTACTGGTGCGAA 59.702 57.895 11.73 0.00 34.23 4.70
3894 4217 3.931578 ACACATCTCAGTTGCTTAGTCC 58.068 45.455 0.00 0.00 0.00 3.85
3895 4218 3.324846 ACACATCTCAGTTGCTTAGTCCA 59.675 43.478 0.00 0.00 0.00 4.02
4023 4346 8.713971 TGGATTCCATATACTGATACAGTTGTT 58.286 33.333 9.63 0.00 42.59 2.83
4057 4380 6.418101 TGTAATCCTCCTTCAAGATGGAAAG 58.582 40.000 6.22 2.04 34.70 2.62
4164 4487 1.725066 CGAACACTTGGCGTGGTTT 59.275 52.632 0.00 0.00 45.50 3.27
4225 4548 8.868522 ATGGAAACTTCATCATAACTCTTTCA 57.131 30.769 0.00 0.00 0.00 2.69
4226 4549 8.099364 TGGAAACTTCATCATAACTCTTTCAC 57.901 34.615 0.00 0.00 0.00 3.18
4235 4558 5.240121 TCATAACTCTTTCACGGTTAACCC 58.760 41.667 19.09 1.64 0.00 4.11
4259 4582 6.404403 CCGAGAGCACATTACAAGTACTCTTA 60.404 42.308 0.00 0.00 39.27 2.10
4403 4726 3.074538 ACTGAAATGGTAGGGAGCAAGTT 59.925 43.478 0.00 0.00 36.46 2.66
4451 4774 4.568152 TGGTGTTTTTAGCTTGCTCTTC 57.432 40.909 0.00 0.00 0.00 2.87
4493 4816 1.074566 CCTTTCCAGCTTGAGACCCTT 59.925 52.381 0.00 0.00 0.00 3.95
4525 4848 0.320421 TGGCTCGTACAGAAAGGCAC 60.320 55.000 6.69 0.00 40.24 5.01
4530 4853 1.675219 GTACAGAAAGGCACGGGGA 59.325 57.895 0.00 0.00 0.00 4.81
4589 4912 8.873830 CATAAGTTATACAAGAAGTGTCAGGTG 58.126 37.037 0.00 0.00 41.98 4.00
4607 4930 3.355626 GTGGAACCTTTTTGTCTGCTC 57.644 47.619 0.00 0.00 0.00 4.26
4650 4973 9.679661 TGCTACCTTGAAATGATAGACAAATTA 57.320 29.630 0.00 0.00 0.00 1.40
4676 4999 5.590259 AGGTGTATGCAGCCAAGTAAAATAG 59.410 40.000 9.50 0.00 43.61 1.73
5276 5599 6.761731 TGTTGTGTTAATTAATGTTGCTGC 57.238 33.333 0.31 0.00 0.00 5.25
5291 5614 4.333095 TGTTGCTGCGAGTTACAAAAGTTA 59.667 37.500 0.00 0.00 0.00 2.24
5405 5728 4.081309 AGGCAAATGCTTACCGAGTTACTA 60.081 41.667 5.25 0.00 41.70 1.82
5524 5847 9.613428 CATGTTCTATTCTTATTTGGTACTCCA 57.387 33.333 0.00 0.00 42.66 3.86
5536 5859 5.623956 TTGGTACTCCATACGATCCAAAT 57.376 39.130 0.00 0.00 43.91 2.32
5729 6056 8.807667 ATGAAAAACTTTGCTATTCTCAACAG 57.192 30.769 0.00 0.00 0.00 3.16
5839 6167 4.887071 ACTTTGGTTCATGCTACTTTGTCA 59.113 37.500 0.00 0.00 0.00 3.58
5844 6172 7.701539 TGGTTCATGCTACTTTGTCAAATAT 57.298 32.000 0.00 0.00 0.00 1.28
5921 6249 8.643324 ACAAGGTTTTATGCAGTTTTTACCATA 58.357 29.630 0.00 0.00 0.00 2.74
6222 6550 2.286872 CTGCAGATGTGGTGGAAGATC 58.713 52.381 8.42 0.00 0.00 2.75
6544 6872 5.880901 AGTAAAGGTGTTCTGATTGATGGT 58.119 37.500 0.00 0.00 0.00 3.55
6876 7208 9.224267 TCTTCTGTTGAAATAAATTCTGAGGAG 57.776 33.333 0.00 0.00 38.92 3.69
6877 7209 7.928307 TCTGTTGAAATAAATTCTGAGGAGG 57.072 36.000 0.00 0.00 38.92 4.30
6878 7210 7.689299 TCTGTTGAAATAAATTCTGAGGAGGA 58.311 34.615 0.00 0.00 38.92 3.71
6919 7254 5.633830 TCAATGTGAAGCTGGAGAATTTC 57.366 39.130 0.00 0.00 0.00 2.17
7020 7356 1.198178 GCTGCGGTGGATTTTCGTAAA 59.802 47.619 0.00 0.00 0.00 2.01
7026 7362 4.790444 GCGGTGGATTTTCGTAAACTTGTT 60.790 41.667 0.00 0.00 0.00 2.83
7027 7363 5.275494 CGGTGGATTTTCGTAAACTTGTTT 58.725 37.500 4.14 4.14 0.00 2.83
7028 7364 5.172411 CGGTGGATTTTCGTAAACTTGTTTG 59.828 40.000 8.79 0.00 0.00 2.93
7029 7365 5.051307 GGTGGATTTTCGTAAACTTGTTTGC 60.051 40.000 8.79 6.63 0.00 3.68
7030 7366 5.044558 TGGATTTTCGTAAACTTGTTTGCC 58.955 37.500 8.79 0.00 0.00 4.52
7031 7367 4.446385 GGATTTTCGTAAACTTGTTTGCCC 59.554 41.667 8.79 0.52 0.00 5.36
7032 7368 2.759538 TTCGTAAACTTGTTTGCCCG 57.240 45.000 8.79 8.20 0.00 6.13
7033 7369 1.950828 TCGTAAACTTGTTTGCCCGA 58.049 45.000 8.79 10.01 0.00 5.14
7034 7370 1.868498 TCGTAAACTTGTTTGCCCGAG 59.132 47.619 8.79 0.00 0.00 4.63
7035 7371 1.069500 CGTAAACTTGTTTGCCCGAGG 60.069 52.381 8.79 0.00 0.00 4.63
7036 7372 1.268625 GTAAACTTGTTTGCCCGAGGG 59.731 52.381 3.22 3.22 38.57 4.30
7037 7373 0.106419 AAACTTGTTTGCCCGAGGGA 60.106 50.000 13.28 0.00 37.50 4.20
7038 7374 0.106419 AACTTGTTTGCCCGAGGGAA 60.106 50.000 13.28 0.00 37.50 3.97
7039 7375 0.537371 ACTTGTTTGCCCGAGGGAAG 60.537 55.000 13.28 8.55 33.87 3.46
7040 7376 0.250727 CTTGTTTGCCCGAGGGAAGA 60.251 55.000 13.28 0.00 33.87 2.87
7041 7377 0.183971 TTGTTTGCCCGAGGGAAGAA 59.816 50.000 13.28 0.16 33.87 2.52
7042 7378 0.250727 TGTTTGCCCGAGGGAAGAAG 60.251 55.000 13.28 0.00 33.87 2.85
7043 7379 0.960861 GTTTGCCCGAGGGAAGAAGG 60.961 60.000 13.28 0.00 33.87 3.46
7044 7380 1.423794 TTTGCCCGAGGGAAGAAGGT 61.424 55.000 13.28 0.00 33.87 3.50
7045 7381 1.838073 TTGCCCGAGGGAAGAAGGTC 61.838 60.000 13.28 0.00 37.50 3.85
7078 7414 5.300286 AGTGTTTGCTTGATCTACTTTGCTT 59.700 36.000 0.00 0.00 0.00 3.91
7191 7696 2.301870 TGTTGGCGACTACTCCAGAATT 59.698 45.455 4.09 0.00 36.98 2.17
7193 7698 1.134367 TGGCGACTACTCCAGAATTCG 59.866 52.381 0.00 0.00 0.00 3.34
7201 7707 3.601443 ACTCCAGAATTCGGACTCTTG 57.399 47.619 7.20 4.56 0.00 3.02
7210 7727 7.313646 CAGAATTCGGACTCTTGTTCTTAGTA 58.686 38.462 0.00 0.00 0.00 1.82
7249 7766 3.906218 TGGAGATATACTCAATGCAGGCT 59.094 43.478 0.00 0.00 46.54 4.58
7254 7771 7.308450 AGATATACTCAATGCAGGCTCTAAA 57.692 36.000 0.00 0.00 0.00 1.85
7265 7782 3.574396 GCAGGCTCTAAAAAGGGTTCTTT 59.426 43.478 0.00 0.00 44.40 2.52
7353 7871 4.321156 GCACTGGCTCACAAATTAACATCA 60.321 41.667 0.00 0.00 36.96 3.07
7360 7878 5.512788 GCTCACAAATTAACATCATGGAACG 59.487 40.000 0.00 0.00 0.00 3.95
7439 7957 3.230134 TGTTGGGGAAAGTGGAAGAATG 58.770 45.455 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 292 5.112129 ACTGCCGGTTATTAAAAGATCCT 57.888 39.130 1.90 0.00 0.00 3.24
361 397 2.432628 GCGCTAGTCAACCGCTGT 60.433 61.111 0.00 0.00 43.95 4.40
392 428 2.360801 GGTTTTGTGTATGTGTGTGGCT 59.639 45.455 0.00 0.00 0.00 4.75
393 429 2.738135 GGTTTTGTGTATGTGTGTGGC 58.262 47.619 0.00 0.00 0.00 5.01
394 430 2.356382 ACGGTTTTGTGTATGTGTGTGG 59.644 45.455 0.00 0.00 0.00 4.17
395 431 3.684103 ACGGTTTTGTGTATGTGTGTG 57.316 42.857 0.00 0.00 0.00 3.82
396 432 7.361371 CCATTATACGGTTTTGTGTATGTGTGT 60.361 37.037 0.00 0.00 33.54 3.72
397 433 6.964370 CCATTATACGGTTTTGTGTATGTGTG 59.036 38.462 0.00 0.00 33.54 3.82
398 434 6.879993 TCCATTATACGGTTTTGTGTATGTGT 59.120 34.615 0.00 0.00 33.54 3.72
399 435 7.184106 GTCCATTATACGGTTTTGTGTATGTG 58.816 38.462 0.00 0.00 33.54 3.21
484 522 1.912371 GCGCTGGTGTCCACTTTAGC 61.912 60.000 0.00 9.95 33.15 3.09
526 564 1.410517 GCCATCGAACTCCAGATCTGA 59.589 52.381 24.62 9.26 0.00 3.27
528 566 0.387202 CGCCATCGAACTCCAGATCT 59.613 55.000 0.00 0.00 38.10 2.75
568 606 7.923973 AGCCATTGCCGTTGAACAAATCAAA 62.924 40.000 0.00 0.00 43.65 2.69
570 608 2.865670 GCCATTGCCGTTGAACAAATCA 60.866 45.455 0.00 0.00 35.85 2.57
572 610 1.344114 AGCCATTGCCGTTGAACAAAT 59.656 42.857 0.00 0.00 38.69 2.32
574 612 0.749649 AAGCCATTGCCGTTGAACAA 59.250 45.000 0.00 0.00 38.69 2.83
575 613 0.313672 GAAGCCATTGCCGTTGAACA 59.686 50.000 0.00 0.00 38.69 3.18
596 634 2.490903 CTCCAAGGTGGCTCATCAAAAG 59.509 50.000 0.00 0.00 37.47 2.27
602 640 0.842635 GGATCTCCAAGGTGGCTCAT 59.157 55.000 0.00 0.00 37.47 2.90
666 704 0.246635 AAGAATGACGGGTCACCTCG 59.753 55.000 3.22 0.00 43.11 4.63
674 712 2.812011 ACCGAAGAAAAAGAATGACGGG 59.188 45.455 0.00 0.00 42.73 5.28
688 726 1.227823 CCACAACAGCCACCGAAGA 60.228 57.895 0.00 0.00 0.00 2.87
701 739 4.263572 CCTCCGGCACCACCACAA 62.264 66.667 0.00 0.00 39.03 3.33
715 753 1.078848 AATGCTCGTCACCTGCCTC 60.079 57.895 0.00 0.00 0.00 4.70
722 760 1.195448 CTTGACACCAATGCTCGTCAC 59.805 52.381 0.00 0.00 38.07 3.67
727 765 1.467734 CTGAGCTTGACACCAATGCTC 59.532 52.381 15.76 15.76 44.46 4.26
728 766 1.072806 TCTGAGCTTGACACCAATGCT 59.927 47.619 0.00 0.00 38.51 3.79
731 769 3.008813 ACATCTCTGAGCTTGACACCAAT 59.991 43.478 12.47 0.00 0.00 3.16
765 803 5.160607 AGGACCGATATGACAAAACTGAA 57.839 39.130 0.00 0.00 0.00 3.02
779 817 1.891150 ACAAGTCACGTAAGGACCGAT 59.109 47.619 1.21 0.00 46.39 4.18
847 890 4.156739 GGAGAAAAATTCACTACAGGGCTG 59.843 45.833 0.00 0.00 0.00 4.85
848 891 4.202567 TGGAGAAAAATTCACTACAGGGCT 60.203 41.667 0.00 0.00 0.00 5.19
849 892 4.079253 TGGAGAAAAATTCACTACAGGGC 58.921 43.478 0.00 0.00 0.00 5.19
1503 1546 3.802008 CTCGGCGACACGTATCCCG 62.802 68.421 15.02 15.02 44.03 5.14
1806 1849 2.665165 AGTGTGTTTGAATCCCTGCAA 58.335 42.857 0.00 0.00 0.00 4.08
1845 1889 5.950965 AACGTCGATGTCTAAAGCAATAG 57.049 39.130 11.41 0.00 0.00 1.73
1846 1890 5.865013 TCAAACGTCGATGTCTAAAGCAATA 59.135 36.000 11.41 0.00 0.00 1.90
1847 1891 4.688879 TCAAACGTCGATGTCTAAAGCAAT 59.311 37.500 11.41 0.00 0.00 3.56
1895 1939 3.932710 GCAAGGACATGAACGAATCTACA 59.067 43.478 0.00 0.00 0.00 2.74
1987 2032 4.583871 ACCAAAGATAGCCTTGAGTCTTG 58.416 43.478 0.00 0.00 34.79 3.02
2065 2110 2.157640 TTGGGATGGGTTGCATTAGG 57.842 50.000 0.00 0.00 0.00 2.69
2179 2226 3.507622 CCTCTTTGGGACTAAAGGCTTTG 59.492 47.826 22.32 13.97 38.04 2.77
2180 2227 3.140332 ACCTCTTTGGGACTAAAGGCTTT 59.860 43.478 17.76 17.76 41.11 3.51
2181 2228 2.716969 ACCTCTTTGGGACTAAAGGCTT 59.283 45.455 8.07 0.00 41.11 4.35
2200 2247 0.691413 AGCTCTAGCCTACCCCAACC 60.691 60.000 0.00 0.00 43.38 3.77
2259 2306 4.122776 CGTAGAAGCTTGCTATCCATGTT 58.877 43.478 2.10 0.00 0.00 2.71
2379 2426 2.172717 ACTCCCTCCATCCCAAATTACG 59.827 50.000 0.00 0.00 0.00 3.18
2786 2833 2.816087 CAGGAACTAATGCAGTGTTGCT 59.184 45.455 14.20 14.20 45.05 3.91
2804 2851 7.693952 TCTAGCTTTTATGCGAATAAAACAGG 58.306 34.615 15.96 9.03 38.13 4.00
2975 3026 5.304357 TGATGTGTCTGAACTAGAAAGACCA 59.696 40.000 16.27 14.27 39.69 4.02
3205 3256 6.500041 TGTCAAAAACATTTGTAGCTGGTAC 58.500 36.000 9.96 9.96 31.20 3.34
3535 3672 5.049405 GTCCAAACTGAAACTAGTGGATGTG 60.049 44.000 0.00 0.00 28.98 3.21
3639 3962 3.101437 TGCTCATCAATTGGAGGCAATT 58.899 40.909 5.42 0.00 35.37 2.32
3929 4252 2.489722 GCAGGAAAGCAAGGAAGTTAGG 59.510 50.000 0.00 0.00 0.00 2.69
4023 4346 4.927267 AGGAGGATTACATTGGACAACA 57.073 40.909 0.00 0.00 0.00 3.33
4164 4487 8.570488 CAAGGAAGCAGTGCAATTTATATATCA 58.430 33.333 19.20 0.00 0.00 2.15
4403 4726 5.741011 CCAGTTGGTAGCCAGAGTAAAATA 58.259 41.667 0.00 0.00 33.81 1.40
4451 4774 7.219484 AGGTCAAATTCAGACTAAAACATGG 57.781 36.000 0.00 0.00 36.29 3.66
4493 4816 1.013596 CGAGCCACAACAAAGTGACA 58.986 50.000 0.00 0.00 42.05 3.58
4530 4853 2.301870 TCTTCCTACAAACATCACGGCT 59.698 45.455 0.00 0.00 0.00 5.52
4589 4912 1.947456 ACGAGCAGACAAAAAGGTTCC 59.053 47.619 0.00 0.00 0.00 3.62
4607 4930 1.806542 AGCACAACTGAATGCCTAACG 59.193 47.619 0.00 0.00 43.12 3.18
4650 4973 2.292828 ACTTGGCTGCATACACCTTT 57.707 45.000 0.50 0.00 0.00 3.11
4676 4999 8.208718 TGCAAGTGGTTCTAACATATATTCAC 57.791 34.615 0.00 0.00 0.00 3.18
5200 5523 8.133627 CCCATGAAAATATGTCATCTTCTTCAC 58.866 37.037 0.00 0.00 33.37 3.18
5291 5614 8.432805 CCTCCTGTGAATCTGGTATAACTTTAT 58.567 37.037 0.00 0.00 36.66 1.40
5304 5627 1.293062 ACATGCCCTCCTGTGAATCT 58.707 50.000 0.00 0.00 0.00 2.40
5361 5684 7.037438 TGCCTTTTTGATATCTTGCAAATCTC 58.963 34.615 0.00 1.04 34.36 2.75
5405 5728 5.650266 TGGAACTGTGACAGTGTTATTGTTT 59.350 36.000 20.19 0.00 44.62 2.83
5524 5847 5.113383 TGCGACACTTAATTTGGATCGTAT 58.887 37.500 0.00 0.00 0.00 3.06
5536 5859 6.535865 TCTTAGTTCAAAACTGCGACACTTAA 59.464 34.615 2.65 0.00 42.84 1.85
5646 5973 5.677319 TGAACTGAGTTATACAGGGGAAG 57.323 43.478 0.00 0.00 39.38 3.46
5687 6014 9.705290 AGTTTTTCATCGGCTTGTAAAATAATT 57.295 25.926 5.58 0.00 31.47 1.40
5729 6056 9.935241 AGGTATCTATGATCACAAATGACATAC 57.065 33.333 0.00 0.00 37.79 2.39
5870 6198 7.704472 GTGTCATGGTTAACAATTGAGTTTTGA 59.296 33.333 13.59 3.66 33.07 2.69
6169 6497 6.290605 ACTAACAAACACCAAACGGTAGTAT 58.709 36.000 0.00 0.00 33.92 2.12
6209 6537 1.629861 TGATGCTGATCTTCCACCACA 59.370 47.619 0.00 0.00 0.00 4.17
6222 6550 5.823209 TGAAATGAACAGGTATGATGCTG 57.177 39.130 0.00 0.00 0.00 4.41
6630 6961 7.815840 TTGACTTTTGATCCAACTATCAACA 57.184 32.000 0.00 0.00 43.69 3.33
6713 7044 5.437060 ACCAAGCAAGTTCTACAAAGAGAA 58.563 37.500 0.00 0.00 31.96 2.87
6715 7046 5.506317 CCAACCAAGCAAGTTCTACAAAGAG 60.506 44.000 0.00 0.00 31.96 2.85
6852 7184 8.163408 TCCTCCTCAGAATTTATTTCAACAGAA 58.837 33.333 0.00 0.00 36.75 3.02
6876 7208 5.768317 TGAACCGAATCAATTTGTTCTTCC 58.232 37.500 14.67 0.00 35.09 3.46
6877 7209 7.382218 ACATTGAACCGAATCAATTTGTTCTTC 59.618 33.333 11.46 2.91 45.39 2.87
6878 7210 7.169645 CACATTGAACCGAATCAATTTGTTCTT 59.830 33.333 15.39 5.66 45.39 2.52
6905 7240 7.791029 TGGTTTAAAAAGAAATTCTCCAGCTT 58.209 30.769 0.00 0.00 0.00 3.74
7020 7356 0.537371 CTTCCCTCGGGCAAACAAGT 60.537 55.000 0.00 0.00 34.68 3.16
7026 7362 1.838073 GACCTTCTTCCCTCGGGCAA 61.838 60.000 0.00 0.00 34.68 4.52
7027 7363 2.203938 ACCTTCTTCCCTCGGGCA 60.204 61.111 0.00 0.00 34.68 5.36
7028 7364 2.585153 GACCTTCTTCCCTCGGGC 59.415 66.667 0.00 0.00 34.68 6.13
7029 7365 3.310652 GGACCTTCTTCCCTCGGG 58.689 66.667 0.00 0.00 0.00 5.14
7035 7371 6.063496 ACACTAAAATAGGGACCTTCTTCC 57.937 41.667 0.00 0.00 32.21 3.46
7036 7372 7.575155 GCAAACACTAAAATAGGGACCTTCTTC 60.575 40.741 0.00 0.00 32.21 2.87
7037 7373 6.208797 GCAAACACTAAAATAGGGACCTTCTT 59.791 38.462 0.00 0.00 32.21 2.52
7038 7374 5.710567 GCAAACACTAAAATAGGGACCTTCT 59.289 40.000 0.00 0.00 32.21 2.85
7039 7375 5.710567 AGCAAACACTAAAATAGGGACCTTC 59.289 40.000 0.00 0.00 32.21 3.46
7040 7376 5.641155 AGCAAACACTAAAATAGGGACCTT 58.359 37.500 0.00 0.00 32.21 3.50
7041 7377 5.256806 AGCAAACACTAAAATAGGGACCT 57.743 39.130 0.00 0.00 32.21 3.85
7042 7378 5.475564 TCAAGCAAACACTAAAATAGGGACC 59.524 40.000 0.00 0.00 32.21 4.46
7043 7379 6.569179 TCAAGCAAACACTAAAATAGGGAC 57.431 37.500 0.00 0.00 32.21 4.46
7044 7380 7.175104 AGATCAAGCAAACACTAAAATAGGGA 58.825 34.615 0.00 0.00 32.21 4.20
7045 7381 7.396540 AGATCAAGCAAACACTAAAATAGGG 57.603 36.000 0.00 0.00 34.64 3.53
7118 7454 6.426937 GGCTCAGTTTGTACTTGTTGAATCTA 59.573 38.462 0.00 0.00 30.26 1.98
7125 7461 6.546034 ACTTTATGGCTCAGTTTGTACTTGTT 59.454 34.615 0.00 0.00 30.26 2.83
7191 7696 6.395426 TTTGTACTAAGAACAAGAGTCCGA 57.605 37.500 0.00 0.00 38.05 4.55
7193 7698 9.708092 AGTATTTTGTACTAAGAACAAGAGTCC 57.292 33.333 0.00 0.00 38.05 3.85
7221 7738 5.781818 TGCATTGAGTATATCTCCATCTGGA 59.218 40.000 0.00 0.00 42.12 3.86
7265 7782 5.631512 GCGACAATACTTTGCCATGTAAAAA 59.368 36.000 0.00 0.00 36.22 1.94
7353 7871 2.509548 TGGAATCCAAGGATCGTTCCAT 59.490 45.455 15.38 0.00 45.30 3.41
7360 7878 5.359194 TCACTAGTTGGAATCCAAGGATC 57.641 43.478 16.05 3.49 44.82 3.36
7439 7957 1.718757 GCCAGTGTGCGGATCAATCC 61.719 60.000 0.00 0.00 43.65 3.01
7466 7984 5.864474 ACACAGAACGTATAAAGAGCTTCAG 59.136 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.