Multiple sequence alignment - TraesCS3A01G301500

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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 TraesCS3A01G301500 chr3A 100.000 5602 0 0 1 5602 535189864 535195465 0.000000e+00 10346.0
1 TraesCS3A01G301500 chr3A 85.934 519 60 8 67 584 498247061 498246555 4.940000e-150 542.0
2 TraesCS3A01G301500 chr3D 94.134 3273 118 24 1663 4897 415163911 415160675 0.000000e+00 4913.0
3 TraesCS3A01G301500 chr3D 90.597 1691 60 26 1 1622 415165572 415163912 0.000000e+00 2150.0
4 TraesCS3A01G301500 chr3D 81.684 748 80 37 61 777 375211237 375210516 2.260000e-158 569.0
5 TraesCS3A01G301500 chr3D 80.288 624 43 29 5017 5584 415160434 415159835 1.130000e-106 398.0
6 TraesCS3A01G301500 chr3D 98.182 55 0 1 1617 1670 66523375 66523429 1.660000e-15 95.3
7 TraesCS3A01G301500 chr3B 95.192 2496 84 10 1663 4131 541206498 541204012 0.000000e+00 3912.0
8 TraesCS3A01G301500 chr3B 88.828 1280 53 35 398 1622 541207743 541206499 0.000000e+00 1489.0
9 TraesCS3A01G301500 chr3B 91.760 716 57 2 4171 4885 541203784 541203070 0.000000e+00 994.0
10 TraesCS3A01G301500 chr3B 91.289 551 16 9 5053 5602 541085532 541085013 0.000000e+00 723.0
11 TraesCS3A01G301500 chr3B 94.554 404 18 2 6 409 541208163 541207764 6.160000e-174 621.0
12 TraesCS3A01G301500 chr3B 95.745 94 3 1 4880 4972 541091147 541091054 3.500000e-32 150.0
13 TraesCS3A01G301500 chr3B 98.182 55 0 1 1617 1670 246157450 246157504 1.660000e-15 95.3
14 TraesCS3A01G301500 chr4B 86.356 601 39 15 82 666 513100479 513101052 2.870000e-172 616.0
15 TraesCS3A01G301500 chr4B 96.040 101 4 0 666 766 513101094 513101194 1.250000e-36 165.0
16 TraesCS3A01G301500 chr4B 97.872 47 1 0 812 858 513101297 513101343 1.290000e-11 82.4
17 TraesCS3A01G301500 chr7B 86.460 517 54 13 65 578 141799005 141798502 2.280000e-153 553.0
18 TraesCS3A01G301500 chr1B 86.015 522 47 11 65 584 429584207 429583710 2.300000e-148 536.0
19 TraesCS3A01G301500 chr1B 96.364 55 0 2 1617 1670 527834238 527834291 7.730000e-14 89.8
20 TraesCS3A01G301500 chr1A 85.057 522 53 10 65 584 398448654 398448156 5.010000e-140 508.0
21 TraesCS3A01G301500 chr1A 86.008 486 44 16 189 666 508198145 508197676 3.010000e-137 499.0
22 TraesCS3A01G301500 chr1A 86.607 112 3 6 666 777 508197634 508197535 4.590000e-21 113.0
23 TraesCS3A01G301500 chr1A 93.333 60 4 0 1613 1672 23823658 23823599 7.730000e-14 89.8
24 TraesCS3A01G301500 chr4A 86.004 493 42 14 189 666 47627502 47627022 2.330000e-138 503.0
25 TraesCS3A01G301500 chr4A 88.393 112 1 6 666 777 47626970 47626871 2.120000e-24 124.0
26 TraesCS3A01G301500 chr1D 84.470 528 56 12 65 590 317427540 317427037 1.080000e-136 497.0
27 TraesCS3A01G301500 chr1D 96.364 55 0 2 1617 1670 394271204 394271151 7.730000e-14 89.8
28 TraesCS3A01G301500 chr4D 85.743 498 31 14 186 666 416450864 416451338 1.810000e-134 490.0
29 TraesCS3A01G301500 chr4D 89.916 119 9 3 650 766 416451356 416451473 3.500000e-32 150.0
30 TraesCS3A01G301500 chr4D 90.141 71 5 1 812 880 416451576 416451646 2.150000e-14 91.6
31 TraesCS3A01G301500 chr5D 83.969 524 62 13 65 584 458925969 458926474 3.030000e-132 483.0
32 TraesCS3A01G301500 chr5B 83.429 525 65 13 65 585 562979095 562979601 8.500000e-128 468.0
33 TraesCS3A01G301500 chr7D 98.113 53 1 0 1613 1665 506679541 506679489 5.980000e-15 93.5
34 TraesCS3A01G301500 chr7A 95.000 60 2 1 1612 1670 398927677 398927618 5.980000e-15 93.5
35 TraesCS3A01G301500 chr6D 96.429 56 0 2 1616 1670 113614158 113614104 2.150000e-14 91.6
36 TraesCS3A01G301500 chr2D 96.429 56 1 1 1616 1670 534925460 534925515 2.150000e-14 91.6
37 TraesCS3A01G301500 chr2B 96.970 33 1 0 65 97 437091717 437091749 7.840000e-04 56.5
38 TraesCS3A01G301500 chr6B 100.000 29 0 0 65 93 643844128 643844156 3.000000e-03 54.7


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 TraesCS3A01G301500 chr3A 535189864 535195465 5601 False 10346.000000 10346 100.000000 1 5602 1 chr3A.!!$F1 5601
1 TraesCS3A01G301500 chr3A 498246555 498247061 506 True 542.000000 542 85.934000 67 584 1 chr3A.!!$R1 517
2 TraesCS3A01G301500 chr3D 415159835 415165572 5737 True 2487.000000 4913 88.339667 1 5584 3 chr3D.!!$R2 5583
3 TraesCS3A01G301500 chr3D 375210516 375211237 721 True 569.000000 569 81.684000 61 777 1 chr3D.!!$R1 716
4 TraesCS3A01G301500 chr3B 541203070 541208163 5093 True 1754.000000 3912 92.583500 6 4885 4 chr3B.!!$R3 4879
5 TraesCS3A01G301500 chr3B 541085013 541085532 519 True 723.000000 723 91.289000 5053 5602 1 chr3B.!!$R1 549
6 TraesCS3A01G301500 chr4B 513100479 513101343 864 False 287.800000 616 93.422667 82 858 3 chr4B.!!$F1 776
7 TraesCS3A01G301500 chr7B 141798502 141799005 503 True 553.000000 553 86.460000 65 578 1 chr7B.!!$R1 513
8 TraesCS3A01G301500 chr1A 508197535 508198145 610 True 306.000000 499 86.307500 189 777 2 chr1A.!!$R3 588
9 TraesCS3A01G301500 chr4A 47626871 47627502 631 True 313.500000 503 87.198500 189 777 2 chr4A.!!$R1 588
10 TraesCS3A01G301500 chr1D 317427037 317427540 503 True 497.000000 497 84.470000 65 590 1 chr1D.!!$R1 525
11 TraesCS3A01G301500 chr4D 416450864 416451646 782 False 243.866667 490 88.600000 186 880 3 chr4D.!!$F1 694
12 TraesCS3A01G301500 chr5D 458925969 458926474 505 False 483.000000 483 83.969000 65 584 1 chr5D.!!$F1 519
13 TraesCS3A01G301500 chr5B 562979095 562979601 506 False 468.000000 468 83.429000 65 585 1 chr5B.!!$F1 520

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
789 1033 0.598065 CCAGTGTTTGTTGGGCTAGC 59.402 55.0 6.04 6.04 0.00 3.42 F
1414 1724 0.036010 CGGAATCTGTGTTGCCTCCT 60.036 55.0 0.00 0.00 0.00 3.69 F
1712 2022 0.382515 CTAGCGTCTGCCTGTAGGAC 59.617 60.0 1.17 0.00 44.31 3.85 F
2781 3105 2.290071 TGGCTTTGTCCCTGTAAGCTAC 60.290 50.0 0.00 0.00 42.88 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 2022 0.179020 TCCCTGGTTGTTCAGCACTG 60.179 55.000 0.00 0.00 33.64 3.66 R
2323 2633 0.321653 AAGGAACACACGCAGATCCC 60.322 55.000 0.00 0.00 0.00 3.85 R
3088 3412 2.116238 AGTTAGGCGATGCTTCCCTTA 58.884 47.619 12.68 4.18 0.00 2.69 R
4716 5242 0.647410 CTAGCGTGACATTCGGCAAG 59.353 55.000 0.00 0.00 0.00 4.01 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
138 141 5.794687 TGACATGCCAACGTTCTAATTAG 57.205 39.130 6.11 6.11 0.00 1.73
293 305 5.527951 TGTTAATTTGTTAAGAGTGGCGTCA 59.472 36.000 0.00 0.00 0.00 4.35
316 342 8.648968 GTCATTAGAGTAACTTGTTAAGAGTGC 58.351 37.037 0.00 0.00 0.00 4.40
332 358 2.028130 AGTGCCAAACAATCGGACAAA 58.972 42.857 0.00 0.00 0.00 2.83
333 359 2.627699 AGTGCCAAACAATCGGACAAAT 59.372 40.909 0.00 0.00 0.00 2.32
334 360 2.986479 GTGCCAAACAATCGGACAAATC 59.014 45.455 0.00 0.00 0.00 2.17
335 361 2.625314 TGCCAAACAATCGGACAAATCA 59.375 40.909 0.00 0.00 0.00 2.57
336 362 3.257873 TGCCAAACAATCGGACAAATCAT 59.742 39.130 0.00 0.00 0.00 2.45
337 363 4.244862 GCCAAACAATCGGACAAATCATT 58.755 39.130 0.00 0.00 0.00 2.57
340 366 6.534793 GCCAAACAATCGGACAAATCATTATT 59.465 34.615 0.00 0.00 0.00 1.40
386 420 7.264373 AGTACTGGATAGCAAAATTATGTGC 57.736 36.000 0.00 1.44 41.22 4.57
417 485 2.731451 CAGGACTGTGTGTTCATGTACG 59.269 50.000 0.00 0.00 0.00 3.67
493 566 5.416639 TGATTGATGCAATAGACAGCAAAGT 59.583 36.000 0.00 0.00 45.45 2.66
787 1031 3.430473 CCCAGTGTTTGTTGGGCTA 57.570 52.632 0.00 0.00 46.96 3.93
788 1032 1.247567 CCCAGTGTTTGTTGGGCTAG 58.752 55.000 0.00 0.00 46.96 3.42
789 1033 0.598065 CCAGTGTTTGTTGGGCTAGC 59.402 55.000 6.04 6.04 0.00 3.42
790 1034 0.598065 CAGTGTTTGTTGGGCTAGCC 59.402 55.000 26.55 26.55 0.00 3.93
791 1035 0.889186 AGTGTTTGTTGGGCTAGCCG 60.889 55.000 27.24 0.00 36.85 5.52
792 1036 1.602323 TGTTTGTTGGGCTAGCCGG 60.602 57.895 27.24 0.00 36.85 6.13
793 1037 2.675075 TTTGTTGGGCTAGCCGGC 60.675 61.111 27.24 21.89 36.85 6.13
794 1038 3.204467 TTTGTTGGGCTAGCCGGCT 62.204 57.895 34.85 34.85 38.46 5.52
1413 1723 0.036388 TCGGAATCTGTGTTGCCTCC 60.036 55.000 0.00 0.00 0.00 4.30
1414 1724 0.036010 CGGAATCTGTGTTGCCTCCT 60.036 55.000 0.00 0.00 0.00 3.69
1415 1725 1.743996 GGAATCTGTGTTGCCTCCTC 58.256 55.000 0.00 0.00 0.00 3.71
1479 1789 6.636454 ACTAGGTGATTTCTGATTTGGGTA 57.364 37.500 0.00 0.00 0.00 3.69
1569 1879 1.701847 AGTGACCTTGACATGCCTCTT 59.298 47.619 0.00 0.00 0.00 2.85
1581 1891 0.967887 TGCCTCTTAGTGAGCGAGCT 60.968 55.000 0.00 0.00 41.35 4.09
1602 1912 7.490725 CGAGCTATGCTTAGATTATTAGTGCAT 59.509 37.037 10.67 0.00 39.88 3.96
1603 1913 8.715191 AGCTATGCTTAGATTATTAGTGCATC 57.285 34.615 10.67 0.00 39.79 3.91
1622 1932 4.513318 GCATCTAACCTGCTTGGAAGATAC 59.487 45.833 13.52 8.44 38.82 2.24
1623 1933 5.686124 GCATCTAACCTGCTTGGAAGATACT 60.686 44.000 13.52 0.00 38.82 2.12
1624 1934 5.599999 TCTAACCTGCTTGGAAGATACTC 57.400 43.478 3.40 0.00 39.71 2.59
1625 1935 3.636153 AACCTGCTTGGAAGATACTCC 57.364 47.619 3.40 0.00 39.71 3.85
1626 1936 1.840635 ACCTGCTTGGAAGATACTCCC 59.159 52.381 3.40 0.00 39.71 4.30
1627 1937 2.122768 CCTGCTTGGAAGATACTCCCT 58.877 52.381 0.00 0.00 38.35 4.20
1628 1938 2.103941 CCTGCTTGGAAGATACTCCCTC 59.896 54.545 0.00 0.00 38.35 4.30
1629 1939 3.037549 CTGCTTGGAAGATACTCCCTCT 58.962 50.000 0.00 0.00 34.22 3.69
1630 1940 2.768527 TGCTTGGAAGATACTCCCTCTG 59.231 50.000 0.00 0.00 34.22 3.35
1631 1941 2.769095 GCTTGGAAGATACTCCCTCTGT 59.231 50.000 0.00 0.00 34.22 3.41
1632 1942 3.961408 GCTTGGAAGATACTCCCTCTGTA 59.039 47.826 0.00 0.00 34.22 2.74
1633 1943 4.406003 GCTTGGAAGATACTCCCTCTGTAA 59.594 45.833 0.00 0.00 34.22 2.41
1634 1944 5.104900 GCTTGGAAGATACTCCCTCTGTAAA 60.105 44.000 0.00 0.00 34.22 2.01
1635 1945 6.546428 TTGGAAGATACTCCCTCTGTAAAG 57.454 41.667 0.00 0.00 34.22 1.85
1636 1946 5.838955 TGGAAGATACTCCCTCTGTAAAGA 58.161 41.667 0.00 0.00 34.22 2.52
1637 1947 6.261435 TGGAAGATACTCCCTCTGTAAAGAA 58.739 40.000 0.00 0.00 34.22 2.52
1638 1948 6.729100 TGGAAGATACTCCCTCTGTAAAGAAA 59.271 38.462 0.00 0.00 34.22 2.52
1639 1949 7.403231 TGGAAGATACTCCCTCTGTAAAGAAAT 59.597 37.037 0.00 0.00 34.22 2.17
1640 1950 8.925338 GGAAGATACTCCCTCTGTAAAGAAATA 58.075 37.037 0.00 0.00 0.00 1.40
1647 1957 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
1648 1958 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
1649 1959 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
1650 1960 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
1697 2007 4.830046 TGGGTCTGATTGATAGTCTCTAGC 59.170 45.833 0.00 0.00 0.00 3.42
1712 2022 0.382515 CTAGCGTCTGCCTGTAGGAC 59.617 60.000 1.17 0.00 44.31 3.85
1785 2095 6.370718 CCCGTAATCCCTGTAACTATAATTGC 59.629 42.308 0.00 0.00 0.00 3.56
1846 2156 8.951243 TGATATCAAGATCGTAATAGTCCTCTG 58.049 37.037 1.98 0.00 0.00 3.35
1972 2282 4.689345 GCTACAAGAATTTCAGTACGGTGT 59.311 41.667 0.00 0.00 0.00 4.16
2022 2332 7.070198 TGGATATCGTAACTTCCAGTTCCATAA 59.930 37.037 0.00 0.00 39.51 1.90
2179 2489 8.470805 AGGTACACTACATAGAAATGAAGACTG 58.529 37.037 0.00 0.00 36.54 3.51
2238 2548 5.680619 TCATGGTAACCTGTCATTATGGTC 58.319 41.667 0.00 0.00 33.42 4.02
2332 2642 4.916983 TTATTTTTCCATGGGATCTGCG 57.083 40.909 13.02 0.00 0.00 5.18
2459 2772 3.877559 TCAATGACCTGACCAGCTTATG 58.122 45.455 0.00 0.00 0.00 1.90
2781 3105 2.290071 TGGCTTTGTCCCTGTAAGCTAC 60.290 50.000 0.00 0.00 42.88 3.58
2805 3129 6.212791 ACTGCACCTTAGGTTCTTGAGTAATA 59.787 38.462 0.00 0.00 31.02 0.98
2849 3173 4.453478 TGATCTAAGTTTGCAGCTCAAGTG 59.547 41.667 0.00 0.00 35.84 3.16
2860 3184 5.296748 TGCAGCTCAAGTGCGATAATTATA 58.703 37.500 0.00 0.00 44.35 0.98
2955 3279 5.437289 TTGTTTACATGGAGCTTTCACTG 57.563 39.130 0.00 0.00 0.00 3.66
3076 3400 3.808174 AGCTCGGACAGTTTTTCAGTAAC 59.192 43.478 0.00 0.00 0.00 2.50
3082 3406 6.068931 CGGACAGTTTTTCAGTAACGTTATG 58.931 40.000 11.86 10.66 0.00 1.90
3088 3412 9.878599 CAGTTTTTCAGTAACGTTATGAGAATT 57.121 29.630 11.86 8.74 0.00 2.17
3125 3451 5.507482 GCCTAACTTCCACCTGTTCTTTTTC 60.507 44.000 0.00 0.00 0.00 2.29
3293 3619 3.719268 AGATTCACATACAGGTTGGCA 57.281 42.857 0.00 0.00 0.00 4.92
3676 4013 2.663196 CGTCCTCCAACTGACCCC 59.337 66.667 0.00 0.00 0.00 4.95
3900 4237 5.222048 ACAAGGCAACAGAAAAGGAGGTATA 60.222 40.000 0.00 0.00 41.41 1.47
4025 4362 7.147976 AGGTTGAACATAGCAATTTCAAGTTC 58.852 34.615 0.00 0.00 39.34 3.01
4096 4433 4.715534 TGATTTCCCAAGTGACAACCTA 57.284 40.909 0.00 0.00 0.00 3.08
4099 4436 5.710099 TGATTTCCCAAGTGACAACCTAATC 59.290 40.000 0.00 0.00 0.00 1.75
4102 4439 6.381498 TTCCCAAGTGACAACCTAATCATA 57.619 37.500 0.00 0.00 0.00 2.15
4106 4443 5.064707 CCAAGTGACAACCTAATCATAACCG 59.935 44.000 0.00 0.00 0.00 4.44
4162 4499 1.207791 GGGAAATGCTCTGAGGGAGA 58.792 55.000 6.83 0.00 44.45 3.71
4329 4854 2.049433 GTAGCCGCACACGACACT 60.049 61.111 0.00 0.00 43.93 3.55
4430 4955 6.989169 GTGTGAATATTTCCTCTGCTCATACT 59.011 38.462 0.00 0.00 0.00 2.12
4436 4961 8.894768 ATATTTCCTCTGCTCATACTGTAAAC 57.105 34.615 0.00 0.00 0.00 2.01
4470 4995 6.228273 ACGATAACTAAATTCATGATGCGG 57.772 37.500 0.00 0.00 0.00 5.69
4487 5012 2.223386 TGCGGCAGTACAGTTTTTGTTC 60.223 45.455 0.00 0.00 41.29 3.18
4608 5133 2.550978 GCGCTGCCAAATAGAGTTCTA 58.449 47.619 0.00 0.00 0.00 2.10
4611 5136 3.739519 CGCTGCCAAATAGAGTTCTAGCT 60.740 47.826 0.00 0.00 0.00 3.32
4632 5157 4.023707 GCTACAGAACAGAAGCAACACAAT 60.024 41.667 0.00 0.00 35.05 2.71
4682 5208 2.097954 GCATTGATGTTCGCCAGATGAA 59.902 45.455 0.00 0.00 0.00 2.57
4685 5211 4.844998 TTGATGTTCGCCAGATGAAAAA 57.155 36.364 0.00 0.00 0.00 1.94
4716 5242 6.238130 GGTTTATTCCTACTGCGATCACTTTC 60.238 42.308 0.00 0.00 0.00 2.62
4721 5248 1.160137 ACTGCGATCACTTTCTTGCC 58.840 50.000 0.00 0.00 0.00 4.52
4737 5264 0.812549 TGCCGAATGTCACGCTAGTA 59.187 50.000 0.00 0.00 0.00 1.82
4747 5274 3.503827 TCACGCTAGTATTGTGACCAG 57.496 47.619 5.52 0.00 37.69 4.00
4768 5296 5.932303 CCAGTGGTAATACCTCCATTTATCG 59.068 44.000 11.16 0.00 39.58 2.92
4782 5310 4.332819 CCATTTATCGGAGAACACAGAACC 59.667 45.833 0.00 0.00 43.58 3.62
4800 5328 5.468746 CAGAACCTTCCTTTGTGATTTACGA 59.531 40.000 0.00 0.00 0.00 3.43
4863 5400 4.578928 AGTGTGTGGTGGATTTTCTGTAAC 59.421 41.667 0.00 0.00 0.00 2.50
4864 5401 4.578928 GTGTGTGGTGGATTTTCTGTAACT 59.421 41.667 0.00 0.00 0.00 2.24
4917 5510 5.741388 AAGTATTTGCCGAGCTGAAATAG 57.259 39.130 0.00 0.00 0.00 1.73
4920 5513 1.737838 TTGCCGAGCTGAAATAGTGG 58.262 50.000 0.00 0.00 0.00 4.00
4921 5514 0.613260 TGCCGAGCTGAAATAGTGGT 59.387 50.000 0.00 0.00 0.00 4.16
4923 5516 2.235155 TGCCGAGCTGAAATAGTGGTTA 59.765 45.455 0.00 0.00 0.00 2.85
4925 5518 3.309954 GCCGAGCTGAAATAGTGGTTAAG 59.690 47.826 0.00 0.00 0.00 1.85
4927 5520 4.806247 CCGAGCTGAAATAGTGGTTAAGAG 59.194 45.833 0.00 0.00 0.00 2.85
4928 5521 5.411781 CGAGCTGAAATAGTGGTTAAGAGT 58.588 41.667 0.00 0.00 0.00 3.24
4930 5523 6.183360 CGAGCTGAAATAGTGGTTAAGAGTTG 60.183 42.308 0.00 0.00 0.00 3.16
4931 5524 6.769512 AGCTGAAATAGTGGTTAAGAGTTGA 58.230 36.000 0.00 0.00 0.00 3.18
4932 5525 6.876257 AGCTGAAATAGTGGTTAAGAGTTGAG 59.124 38.462 0.00 0.00 0.00 3.02
4933 5526 6.874134 GCTGAAATAGTGGTTAAGAGTTGAGA 59.126 38.462 0.00 0.00 0.00 3.27
4934 5527 7.387948 GCTGAAATAGTGGTTAAGAGTTGAGAA 59.612 37.037 0.00 0.00 0.00 2.87
4952 5545 7.652909 AGTTGAGAAAAATCATTTGCAAATCGA 59.347 29.630 21.70 20.41 0.00 3.59
4987 5580 9.632807 TTTTTGATAGTTTGATAATGGGAAACG 57.367 29.630 0.00 0.00 35.23 3.60
4990 5583 7.981142 TGATAGTTTGATAATGGGAAACGAAC 58.019 34.615 0.00 0.00 35.23 3.95
5002 5595 1.947456 GAAACGAACTGAAGGCAAGGT 59.053 47.619 0.00 0.00 0.00 3.50
5031 5695 1.466866 GGTCGCGGCAGAAATTTAACC 60.467 52.381 14.93 0.41 0.00 2.85
5032 5696 0.444651 TCGCGGCAGAAATTTAACCG 59.555 50.000 17.30 17.30 46.50 4.44
5048 5712 0.945813 ACCGCGAATTCCACGAAAAA 59.054 45.000 8.23 0.00 0.00 1.94
5195 5867 1.287730 GAGACAGAGCGCAACACCAG 61.288 60.000 11.47 0.00 0.00 4.00
5399 6116 0.679505 TACTTGAGCGCCTGTTCTGT 59.320 50.000 2.29 1.53 0.00 3.41
5493 6213 7.549488 TCTCTAGCACTGCTTTTAAATAGGAAC 59.451 37.037 9.30 0.00 40.44 3.62
5512 6232 9.941325 ATAGGAACATGCATTTGTTAATTTTCA 57.059 25.926 5.69 0.00 39.85 2.69
5513 6233 8.314143 AGGAACATGCATTTGTTAATTTTCAG 57.686 30.769 5.69 0.00 39.85 3.02
5514 6234 8.149647 AGGAACATGCATTTGTTAATTTTCAGA 58.850 29.630 5.69 0.00 39.85 3.27
5516 6236 9.749490 GAACATGCATTTGTTAATTTTCAGATG 57.251 29.630 5.69 7.96 39.85 2.90
5518 6238 9.926158 ACATGCATTTGTTAATTTTCAGATGTA 57.074 25.926 0.00 9.10 31.63 2.29
5592 6312 1.392853 GCTTCAGTTGATGTCAGAGCG 59.607 52.381 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.822990 TCTCTCCAATTAGACGCCGTT 59.177 47.619 0.00 0.00 0.00 4.44
293 305 7.676947 TGGCACTCTTAACAAGTTACTCTAAT 58.323 34.615 0.00 0.00 0.00 1.73
316 342 8.477984 AAATAATGATTTGTCCGATTGTTTGG 57.522 30.769 0.00 0.00 33.86 3.28
332 358 7.613022 ACACCTGATCAGTGACAAAATAATGAT 59.387 33.333 21.11 0.00 34.69 2.45
333 359 6.942005 ACACCTGATCAGTGACAAAATAATGA 59.058 34.615 21.11 0.00 0.00 2.57
334 360 7.149569 ACACCTGATCAGTGACAAAATAATG 57.850 36.000 21.11 3.84 0.00 1.90
335 361 7.448161 TGAACACCTGATCAGTGACAAAATAAT 59.552 33.333 21.11 0.00 0.00 1.28
336 362 6.770303 TGAACACCTGATCAGTGACAAAATAA 59.230 34.615 21.11 0.00 0.00 1.40
337 363 6.295249 TGAACACCTGATCAGTGACAAAATA 58.705 36.000 21.11 0.00 0.00 1.40
340 366 4.149511 TGAACACCTGATCAGTGACAAA 57.850 40.909 21.11 0.44 0.00 2.83
417 485 0.252197 ACAACCGGACTTGCTATCCC 59.748 55.000 9.46 0.00 31.99 3.85
610 713 2.281484 TGCAAGAAGACACCGGCC 60.281 61.111 0.00 0.00 0.00 6.13
612 715 1.672356 CCCTGCAAGAAGACACCGG 60.672 63.158 0.00 0.00 34.07 5.28
618 721 4.722700 GGCGCCCCTGCAAGAAGA 62.723 66.667 18.11 0.00 37.32 2.87
807 1051 0.586802 GCCCAACAAACTCGTCACTC 59.413 55.000 0.00 0.00 0.00 3.51
808 1052 0.818040 GGCCCAACAAACTCGTCACT 60.818 55.000 0.00 0.00 0.00 3.41
809 1053 0.818040 AGGCCCAACAAACTCGTCAC 60.818 55.000 0.00 0.00 0.00 3.67
810 1054 0.106918 AAGGCCCAACAAACTCGTCA 60.107 50.000 0.00 0.00 0.00 4.35
1029 1332 1.358725 GCTTAACGATGCAGCGGACA 61.359 55.000 29.52 10.09 35.12 4.02
1115 1419 0.910513 CAGAGTTCGTCGAATCAGCG 59.089 55.000 11.45 0.00 0.00 5.18
1260 1570 1.124477 GCTCCAGTCCATCCCCCTAG 61.124 65.000 0.00 0.00 0.00 3.02
1413 1723 1.988956 AGAGAGCCAGTGCCCAGAG 60.989 63.158 0.00 0.00 38.69 3.35
1414 1724 2.121385 AGAGAGCCAGTGCCCAGA 59.879 61.111 0.00 0.00 38.69 3.86
1415 1725 2.268280 CAGAGAGCCAGTGCCCAG 59.732 66.667 0.00 0.00 38.69 4.45
1479 1789 7.341030 TGTTCATCAGTTCATGTGGATTCTAT 58.659 34.615 0.00 0.00 0.00 1.98
1560 1870 1.850377 CTCGCTCACTAAGAGGCATG 58.150 55.000 0.00 0.00 44.86 4.06
1569 1879 3.477530 TCTAAGCATAGCTCGCTCACTA 58.522 45.455 10.74 0.47 38.25 2.74
1602 1912 4.406003 GGAGTATCTTCCAAGCAGGTTAGA 59.594 45.833 0.00 0.00 37.20 2.10
1603 1913 4.443598 GGGAGTATCTTCCAAGCAGGTTAG 60.444 50.000 0.00 0.00 39.09 2.34
1622 1932 9.757227 CACTCTTATATTTCTTTACAGAGGGAG 57.243 37.037 0.00 0.00 32.92 4.30
1623 1933 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
1624 1934 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
1642 1952 9.310449 TCCTAAAGTAGTGATCTAAACACTCTT 57.690 33.333 0.00 0.00 45.58 2.85
1643 1953 8.880991 TCCTAAAGTAGTGATCTAAACACTCT 57.119 34.615 0.00 0.00 45.58 3.24
1646 1956 9.021863 CGAATCCTAAAGTAGTGATCTAAACAC 57.978 37.037 0.00 0.00 38.38 3.32
1647 1957 8.963725 TCGAATCCTAAAGTAGTGATCTAAACA 58.036 33.333 0.00 0.00 0.00 2.83
1648 1958 9.968870 ATCGAATCCTAAAGTAGTGATCTAAAC 57.031 33.333 0.00 0.00 0.00 2.01
1649 1959 9.967346 CATCGAATCCTAAAGTAGTGATCTAAA 57.033 33.333 0.00 0.00 0.00 1.85
1650 1960 8.577296 CCATCGAATCCTAAAGTAGTGATCTAA 58.423 37.037 0.00 0.00 0.00 2.10
1651 1961 7.176865 CCCATCGAATCCTAAAGTAGTGATCTA 59.823 40.741 0.00 0.00 0.00 1.98
1652 1962 6.015010 CCCATCGAATCCTAAAGTAGTGATCT 60.015 42.308 0.00 0.00 0.00 2.75
1653 1963 6.159988 CCCATCGAATCCTAAAGTAGTGATC 58.840 44.000 0.00 0.00 0.00 2.92
1654 1964 5.602978 ACCCATCGAATCCTAAAGTAGTGAT 59.397 40.000 0.00 0.00 0.00 3.06
1655 1965 4.960469 ACCCATCGAATCCTAAAGTAGTGA 59.040 41.667 0.00 0.00 0.00 3.41
1656 1966 5.069251 AGACCCATCGAATCCTAAAGTAGTG 59.931 44.000 0.00 0.00 0.00 2.74
1657 1967 5.069251 CAGACCCATCGAATCCTAAAGTAGT 59.931 44.000 0.00 0.00 0.00 2.73
1658 1968 5.302059 TCAGACCCATCGAATCCTAAAGTAG 59.698 44.000 0.00 0.00 0.00 2.57
1659 1969 5.205821 TCAGACCCATCGAATCCTAAAGTA 58.794 41.667 0.00 0.00 0.00 2.24
1660 1970 4.030913 TCAGACCCATCGAATCCTAAAGT 58.969 43.478 0.00 0.00 0.00 2.66
1661 1971 4.672587 TCAGACCCATCGAATCCTAAAG 57.327 45.455 0.00 0.00 0.00 1.85
1667 1977 5.788450 ACTATCAATCAGACCCATCGAATC 58.212 41.667 0.00 0.00 0.00 2.52
1670 1980 4.474394 AGACTATCAATCAGACCCATCGA 58.526 43.478 0.00 0.00 0.00 3.59
1712 2022 0.179020 TCCCTGGTTGTTCAGCACTG 60.179 55.000 0.00 0.00 33.64 3.66
1785 2095 2.802816 ACAAACTCAAACTCTAGCAGCG 59.197 45.455 0.00 0.00 0.00 5.18
1832 2142 8.407064 AGTAAATTCAGACAGAGGACTATTACG 58.593 37.037 0.00 0.00 0.00 3.18
1927 2237 1.905354 AAAGCCAGCCTTCACCAGC 60.905 57.895 0.00 0.00 31.99 4.85
2036 2346 2.642427 AGCATGGCATACATCGACAAA 58.358 42.857 0.00 0.00 37.84 2.83
2313 2623 2.428171 CACGCAGATCCCATGGAAAAAT 59.572 45.455 15.22 0.55 34.34 1.82
2322 2632 1.003839 GGAACACACGCAGATCCCA 60.004 57.895 0.00 0.00 0.00 4.37
2323 2633 0.321653 AAGGAACACACGCAGATCCC 60.322 55.000 0.00 0.00 0.00 3.85
2332 2642 3.476552 TCATCCAGACAAAGGAACACAC 58.523 45.455 0.00 0.00 38.93 3.82
2519 2832 7.759489 AGCACTTCCACAAGTCATTTATTAA 57.241 32.000 0.00 0.00 41.24 1.40
2781 3105 3.409026 ACTCAAGAACCTAAGGTGCAG 57.591 47.619 0.00 0.00 35.34 4.41
2849 3173 7.689812 GCCGCATATGATTCATATAATTATCGC 59.310 37.037 16.82 13.28 35.18 4.58
2860 3184 5.603596 ACATTTTTGCCGCATATGATTCAT 58.396 33.333 6.97 4.28 0.00 2.57
2931 3255 6.939730 TCAGTGAAAGCTCCATGTAAACAATA 59.060 34.615 0.00 0.00 0.00 1.90
2955 3279 3.302365 TTGCAGCTTACCAAAAGCATC 57.698 42.857 11.90 3.97 45.30 3.91
3076 3400 6.346919 CGATGCTTCCCTTAATTCTCATAACG 60.347 42.308 0.00 0.00 0.00 3.18
3082 3406 2.550180 GGCGATGCTTCCCTTAATTCTC 59.450 50.000 0.00 0.00 0.00 2.87
3088 3412 2.116238 AGTTAGGCGATGCTTCCCTTA 58.884 47.619 12.68 4.18 0.00 2.69
3293 3619 8.988934 CAGTACAAGTGAACAAATAGTGTGTAT 58.011 33.333 0.00 0.00 40.60 2.29
3676 4013 6.981762 ATCTCTTTGAGAAGTACTGCATTG 57.018 37.500 3.00 0.00 42.27 2.82
3900 4237 3.267812 ACACATGGAAGGGAGACATGATT 59.732 43.478 10.47 0.00 43.46 2.57
4063 4400 4.487714 TGGGAAATCATCACTGACTACC 57.512 45.455 0.00 0.00 33.22 3.18
4096 4433 6.866480 ACAAAGAATGCATTCGGTTATGATT 58.134 32.000 28.88 15.17 41.56 2.57
4099 4436 6.324819 AGAACAAAGAATGCATTCGGTTATG 58.675 36.000 29.77 25.31 41.56 1.90
4102 4439 4.853924 AGAACAAAGAATGCATTCGGTT 57.146 36.364 29.96 29.96 41.56 4.44
4106 4443 9.162793 CGATACATAAGAACAAAGAATGCATTC 57.837 33.333 28.44 28.44 37.06 2.67
4153 4490 8.206867 TCATGTTACAGATAATTTCTCCCTCAG 58.793 37.037 0.00 0.00 29.93 3.35
4162 4499 6.818644 ACAGCGACTCATGTTACAGATAATTT 59.181 34.615 0.00 0.00 0.00 1.82
4221 4746 7.572724 GCAGTACATCTGGATCATGAAATTAGC 60.573 40.741 0.00 0.00 43.78 3.09
4279 4804 2.479275 CTGCAGTGAATCGCTGGATATG 59.521 50.000 23.22 7.22 41.08 1.78
4329 4854 2.940514 TGGTCTCCATTCCTCCAGTA 57.059 50.000 0.00 0.00 0.00 2.74
4464 4989 2.031157 ACAAAAACTGTACTGCCGCATC 60.031 45.455 0.00 0.00 36.10 3.91
4470 4995 6.944557 ACTTTTGAACAAAAACTGTACTGC 57.055 33.333 12.61 0.00 39.49 4.40
4608 5133 3.134458 GTGTTGCTTCTGTTCTGTAGCT 58.866 45.455 0.00 0.00 34.77 3.32
4611 5136 6.449635 AAATTGTGTTGCTTCTGTTCTGTA 57.550 33.333 0.00 0.00 0.00 2.74
4632 5157 2.667481 CGAACCCTACGCGACATAAAAA 59.333 45.455 15.93 0.00 0.00 1.94
4657 5183 1.469703 CTGGCGAACATCAATGCTCAA 59.530 47.619 0.00 0.00 0.00 3.02
4682 5208 8.044908 TCGCAGTAGGAATAAACCTCTAATTTT 58.955 33.333 0.00 0.00 41.00 1.82
4685 5211 6.726490 TCGCAGTAGGAATAAACCTCTAAT 57.274 37.500 0.00 0.00 41.00 1.73
4716 5242 0.647410 CTAGCGTGACATTCGGCAAG 59.353 55.000 0.00 0.00 0.00 4.01
4721 5248 4.102649 TCACAATACTAGCGTGACATTCG 58.897 43.478 0.00 0.00 34.83 3.34
4737 5264 4.080526 GGAGGTATTACCACTGGTCACAAT 60.081 45.833 15.19 1.99 41.95 2.71
4747 5274 6.105397 TCCGATAAATGGAGGTATTACCAC 57.895 41.667 15.19 8.59 41.95 4.16
4768 5296 3.493767 AAGGAAGGTTCTGTGTTCTCC 57.506 47.619 0.00 0.00 0.00 3.71
4782 5310 6.978343 TGGTATCGTAAATCACAAAGGAAG 57.022 37.500 0.00 0.00 0.00 3.46
4824 5361 2.032550 CACACTCCAGCTGACAAACAAG 59.967 50.000 17.39 3.33 0.00 3.16
4890 5483 7.618502 TTTCAGCTCGGCAAATACTTATTTA 57.381 32.000 0.00 0.00 34.36 1.40
4892 5485 6.699575 ATTTCAGCTCGGCAAATACTTATT 57.300 33.333 0.00 0.00 0.00 1.40
4894 5487 6.257849 CACTATTTCAGCTCGGCAAATACTTA 59.742 38.462 0.00 0.00 0.00 2.24
4895 5488 5.065218 CACTATTTCAGCTCGGCAAATACTT 59.935 40.000 0.00 0.00 0.00 2.24
4896 5489 4.572389 CACTATTTCAGCTCGGCAAATACT 59.428 41.667 0.00 0.00 0.00 2.12
4897 5490 4.260784 CCACTATTTCAGCTCGGCAAATAC 60.261 45.833 0.00 0.00 0.00 1.89
4899 5492 2.684881 CCACTATTTCAGCTCGGCAAAT 59.315 45.455 0.00 0.00 0.00 2.32
4900 5493 2.083774 CCACTATTTCAGCTCGGCAAA 58.916 47.619 0.00 0.00 0.00 3.68
4903 5496 1.739067 AACCACTATTTCAGCTCGGC 58.261 50.000 0.00 0.00 0.00 5.54
4905 5498 5.411781 ACTCTTAACCACTATTTCAGCTCG 58.588 41.667 0.00 0.00 0.00 5.03
4908 5501 6.874134 TCTCAACTCTTAACCACTATTTCAGC 59.126 38.462 0.00 0.00 0.00 4.26
4917 5510 9.750125 AAATGATTTTTCTCAACTCTTAACCAC 57.250 29.630 0.00 0.00 0.00 4.16
4920 5513 9.248291 TGCAAATGATTTTTCTCAACTCTTAAC 57.752 29.630 0.00 0.00 0.00 2.01
4921 5514 9.814899 TTGCAAATGATTTTTCTCAACTCTTAA 57.185 25.926 0.00 0.00 0.00 1.85
4923 5516 8.721019 TTTGCAAATGATTTTTCTCAACTCTT 57.279 26.923 8.05 0.00 0.00 2.85
4925 5518 7.948363 CGATTTGCAAATGATTTTTCTCAACTC 59.052 33.333 28.67 8.59 0.00 3.01
4927 5520 7.786114 TCGATTTGCAAATGATTTTTCTCAAC 58.214 30.769 28.67 8.73 0.00 3.18
4928 5521 7.652909 ACTCGATTTGCAAATGATTTTTCTCAA 59.347 29.630 28.67 0.00 0.00 3.02
4930 5523 7.572502 ACTCGATTTGCAAATGATTTTTCTC 57.427 32.000 28.67 11.05 0.00 2.87
4931 5524 8.915654 GTTACTCGATTTGCAAATGATTTTTCT 58.084 29.630 28.67 2.32 0.00 2.52
4932 5525 8.162245 GGTTACTCGATTTGCAAATGATTTTTC 58.838 33.333 28.67 12.47 0.00 2.29
4933 5526 7.872483 AGGTTACTCGATTTGCAAATGATTTTT 59.128 29.630 28.67 3.95 0.00 1.94
4934 5527 7.378181 AGGTTACTCGATTTGCAAATGATTTT 58.622 30.769 28.67 11.37 0.00 1.82
4977 5570 1.886542 GCCTTCAGTTCGTTTCCCATT 59.113 47.619 0.00 0.00 0.00 3.16
4978 5571 1.202879 TGCCTTCAGTTCGTTTCCCAT 60.203 47.619 0.00 0.00 0.00 4.00
4979 5572 0.181587 TGCCTTCAGTTCGTTTCCCA 59.818 50.000 0.00 0.00 0.00 4.37
4980 5573 1.266989 CTTGCCTTCAGTTCGTTTCCC 59.733 52.381 0.00 0.00 0.00 3.97
4981 5574 1.266989 CCTTGCCTTCAGTTCGTTTCC 59.733 52.381 0.00 0.00 0.00 3.13
4982 5575 1.947456 ACCTTGCCTTCAGTTCGTTTC 59.053 47.619 0.00 0.00 0.00 2.78
4985 5578 2.104281 AGTTACCTTGCCTTCAGTTCGT 59.896 45.455 0.00 0.00 0.00 3.85
4987 5580 6.049790 CCTATAGTTACCTTGCCTTCAGTTC 58.950 44.000 0.00 0.00 0.00 3.01
4990 5583 4.409247 ACCCTATAGTTACCTTGCCTTCAG 59.591 45.833 0.00 0.00 0.00 3.02
5002 5595 0.956633 CTGCCGCGACCCTATAGTTA 59.043 55.000 8.23 0.00 0.00 2.24
5006 5599 1.045407 ATTTCTGCCGCGACCCTATA 58.955 50.000 8.23 0.00 0.00 1.31
5014 5607 2.924713 CGGTTAAATTTCTGCCGCG 58.075 52.632 12.74 0.00 35.90 6.46
5122 5793 3.845259 GTGGATAGACGGCGCCCA 61.845 66.667 23.46 8.21 0.00 5.36
5399 6116 7.581213 ATGTTGGTCAATCTGTTTTGAGTTA 57.419 32.000 0.00 0.00 36.34 2.24
5458 6178 4.940483 AGCAGTGCTAGAGATCCCATATA 58.060 43.478 18.11 0.00 36.99 0.86
5460 6180 3.251016 AGCAGTGCTAGAGATCCCATA 57.749 47.619 18.11 0.00 36.99 2.74
5461 6181 2.100128 AGCAGTGCTAGAGATCCCAT 57.900 50.000 18.11 0.00 36.99 4.00
5462 6182 1.871418 AAGCAGTGCTAGAGATCCCA 58.129 50.000 20.09 0.00 38.25 4.37
5463 6183 2.998316 AAAGCAGTGCTAGAGATCCC 57.002 50.000 20.09 0.00 38.25 3.85


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

AutoCloner maintained by Alex Coulton.