Multiple sequence alignment - TraesCS7D01G542200

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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 TraesCS7D01G542200 chr7D 100.000 6110 0 0 1 6110 631423356 631429465 0.000000e+00 11284.0
1 TraesCS7D01G542200 chr7D 75.740 3310 707 70 1008 4279 638670912 638667661 0.000000e+00 1576.0
2 TraesCS7D01G542200 chr7D 75.254 3047 606 102 1282 4279 631393643 631396590 0.000000e+00 1314.0
3 TraesCS7D01G542200 chr7D 91.781 73 5 1 1 72 76343261 76343189 3.900000e-17 100.0
4 TraesCS7D01G542200 chr7B 95.778 5211 185 8 5 5189 733810136 733815337 0.000000e+00 8371.0
5 TraesCS7D01G542200 chr7B 76.260 3353 691 65 987 4279 733797603 733800910 0.000000e+00 1685.0
6 TraesCS7D01G542200 chr7B 77.984 2421 448 57 997 3376 733860340 733862716 0.000000e+00 1439.0
7 TraesCS7D01G542200 chr7B 77.438 2420 472 55 997 3376 733925199 733927584 0.000000e+00 1376.0
8 TraesCS7D01G542200 chr7B 93.267 906 35 6 5210 6110 733815862 733816746 0.000000e+00 1312.0
9 TraesCS7D01G542200 chr7B 78.393 1967 373 39 991 2928 733759172 733761115 0.000000e+00 1230.0
10 TraesCS7D01G542200 chr7B 80.121 1655 278 33 1749 3376 733885724 733887354 0.000000e+00 1186.0
11 TraesCS7D01G542200 chr7B 81.030 738 130 9 4318 5053 733762331 733763060 4.110000e-161 579.0
12 TraesCS7D01G542200 chr7B 74.791 1198 260 34 3092 4274 733761336 733762506 9.140000e-138 501.0
13 TraesCS7D01G542200 chr7B 75.561 892 178 31 1076 1949 733594450 733595319 2.650000e-108 403.0
14 TraesCS7D01G542200 chr7B 90.541 74 5 2 1 72 106347523 106347450 5.040000e-16 97.1
15 TraesCS7D01G542200 chrUn 95.026 1166 58 0 4025 5190 283734458 283735623 0.000000e+00 1832.0
16 TraesCS7D01G542200 chrUn 94.597 1166 63 0 4025 5190 277754657 277755822 0.000000e+00 1805.0
17 TraesCS7D01G542200 chrUn 94.352 1080 61 0 4111 5190 304658686 304659765 0.000000e+00 1657.0
18 TraesCS7D01G542200 chrUn 94.505 1001 55 0 4190 5190 422907670 422906670 0.000000e+00 1544.0
19 TraesCS7D01G542200 chrUn 94.163 908 38 4 5210 6110 277756176 277757075 0.000000e+00 1369.0
20 TraesCS7D01G542200 chrUn 94.163 908 38 4 5210 6110 304660119 304661018 0.000000e+00 1369.0
21 TraesCS7D01G542200 chrUn 94.053 908 39 4 5210 6110 336755815 336756714 0.000000e+00 1363.0
22 TraesCS7D01G542200 chrUn 93.943 908 40 4 5210 6110 277752143 277753042 0.000000e+00 1358.0
23 TraesCS7D01G542200 chrUn 93.868 848 52 0 4343 5190 442902078 442901231 0.000000e+00 1279.0
24 TraesCS7D01G542200 chrUn 93.405 561 37 0 4630 5190 277751229 277751789 0.000000e+00 832.0
25 TraesCS7D01G542200 chrUn 93.405 561 37 0 4630 5190 336754901 336755461 0.000000e+00 832.0
26 TraesCS7D01G542200 chrUn 97.772 404 9 0 4025 4428 277754255 277754658 0.000000e+00 697.0
27 TraesCS7D01G542200 chrUn 97.337 338 9 0 4091 4428 277757952 277758289 5.310000e-160 575.0
28 TraesCS7D01G542200 chrUn 97.041 338 10 0 4091 4428 277753919 277754256 2.470000e-158 569.0
29 TraesCS7D01G542200 chrUn 98.630 292 4 0 3595 3886 88643877 88644168 9.080000e-143 518.0
30 TraesCS7D01G542200 chrUn 98.630 292 4 0 3595 3886 283733968 283734259 9.080000e-143 518.0
31 TraesCS7D01G542200 chrUn 98.396 187 3 0 4025 4211 88644367 88644553 4.570000e-86 329.0
32 TraesCS7D01G542200 chrUn 98.396 187 3 0 4025 4211 277758288 277758474 4.570000e-86 329.0
33 TraesCS7D01G542200 chrUn 79.412 170 30 3 377 545 131922755 131922590 1.390000e-21 115.0
34 TraesCS7D01G542200 chrUn 86.022 93 10 2 4409 4501 422907670 422907581 5.040000e-16 97.1
35 TraesCS7D01G542200 chrUn 89.041 73 8 0 1 73 221313529 221313457 2.350000e-14 91.6
36 TraesCS7D01G542200 chrUn 89.041 73 8 0 1 73 244820832 244820760 2.350000e-14 91.6
37 TraesCS7D01G542200 chr7A 76.357 3354 672 86 987 4279 726686234 726682941 0.000000e+00 1688.0
38 TraesCS7D01G542200 chr7A 77.663 2422 466 55 997 3376 727228717 727231105 0.000000e+00 1406.0
39 TraesCS7D01G542200 chr7A 77.685 2039 386 46 1748 3757 726814168 726812170 0.000000e+00 1181.0
40 TraesCS7D01G542200 chr7A 80.390 872 153 14 4288 5154 726683151 726682293 0.000000e+00 647.0
41 TraesCS7D01G542200 chr7A 75.797 1223 235 37 1010 2200 727215337 727214144 4.140000e-156 562.0
42 TraesCS7D01G542200 chr7A 78.750 640 111 20 992 1614 726816232 726815601 7.370000e-109 405.0
43 TraesCS7D01G542200 chr7A 79.259 405 80 3 999 1401 726770308 726769906 4.660000e-71 279.0
44 TraesCS7D01G542200 chr6D 72.679 2833 656 86 994 3758 468910533 468913315 0.000000e+00 835.0
45 TraesCS7D01G542200 chr6D 78.125 288 49 6 304 590 68091300 68091026 2.930000e-38 171.0
46 TraesCS7D01G542200 chr6D 77.931 290 49 7 304 592 89301097 89301372 3.790000e-37 167.0
47 TraesCS7D01G542200 chr6D 94.915 59 2 1 1 58 460642124 460642182 2.350000e-14 91.6
48 TraesCS7D01G542200 chr6D 100.000 28 0 0 73 100 22078576 22078603 1.100000e-02 52.8
49 TraesCS7D01G542200 chr3D 81.739 230 33 6 364 588 58538940 58539165 3.760000e-42 183.0
50 TraesCS7D01G542200 chr3D 77.934 213 41 5 378 588 143951899 143951691 1.790000e-25 128.0
51 TraesCS7D01G542200 chr3D 90.541 74 6 1 1 73 1610256 1610183 5.040000e-16 97.1
52 TraesCS7D01G542200 chr1D 78.125 288 49 6 304 590 370915392 370915118 2.930000e-38 171.0
53 TraesCS7D01G542200 chr1D 94.915 59 2 1 1 58 288009622 288009680 2.350000e-14 91.6
54 TraesCS7D01G542200 chr1D 100.000 28 0 0 73 100 1572228 1572201 1.100000e-02 52.8
55 TraesCS7D01G542200 chr1D 100.000 28 0 0 73 100 415043564 415043537 1.100000e-02 52.8
56 TraesCS7D01G542200 chr2B 82.703 185 29 1 407 588 10870264 10870080 1.760000e-35 161.0
57 TraesCS7D01G542200 chr1B 80.288 208 40 1 381 588 10935966 10935760 8.200000e-34 156.0
58 TraesCS7D01G542200 chr3B 78.346 254 37 12 293 544 536793672 536793435 1.370000e-31 148.0
59 TraesCS7D01G542200 chr4D 77.512 209 45 2 378 585 305964400 305964607 2.310000e-24 124.0
60 TraesCS7D01G542200 chr4D 91.781 73 5 1 1 72 30555417 30555489 3.900000e-17 100.0
61 TraesCS7D01G542200 chr2A 76.526 213 46 4 378 588 262331350 262331140 5.010000e-21 113.0
62 TraesCS7D01G542200 chr2A 90.541 74 6 1 1 73 235280971 235280898 5.040000e-16 97.1
63 TraesCS7D01G542200 chr2A 90.541 74 6 1 1 73 613040574 613040647 5.040000e-16 97.1
64 TraesCS7D01G542200 chr4B 91.892 74 5 1 1 73 651630443 651630370 1.080000e-17 102.0
65 TraesCS7D01G542200 chr4B 93.103 58 4 0 1 58 56974922 56974979 1.090000e-12 86.1
66 TraesCS7D01G542200 chr4B 100.000 28 0 0 73 100 39255937 39255910 1.100000e-02 52.8
67 TraesCS7D01G542200 chr5D 91.781 73 5 1 1 72 445132060 445132132 3.900000e-17 100.0
68 TraesCS7D01G542200 chr5D 100.000 28 0 0 73 100 393620850 393620823 1.100000e-02 52.8
69 TraesCS7D01G542200 chr5D 100.000 28 0 0 73 100 484559946 484559973 1.100000e-02 52.8
70 TraesCS7D01G542200 chr1A 75.472 212 49 3 378 588 559836429 559836638 3.900000e-17 100.0
71 TraesCS7D01G542200 chr4A 84.444 90 8 4 510 595 111061126 111061213 3.920000e-12 84.2
72 TraesCS7D01G542200 chr5B 100.000 28 0 0 73 100 547491512 547491539 1.100000e-02 52.8
73 TraesCS7D01G542200 chr5B 100.000 28 0 0 73 100 699562077 699562104 1.100000e-02 52.8


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 TraesCS7D01G542200 chr7D 631423356 631429465 6109 False 11284.00 11284 100.000000 1 6110 1 chr7D.!!$F2 6109
1 TraesCS7D01G542200 chr7D 638667661 638670912 3251 True 1576.00 1576 75.740000 1008 4279 1 chr7D.!!$R2 3271
2 TraesCS7D01G542200 chr7D 631393643 631396590 2947 False 1314.00 1314 75.254000 1282 4279 1 chr7D.!!$F1 2997
3 TraesCS7D01G542200 chr7B 733810136 733816746 6610 False 4841.50 8371 94.522500 5 6110 2 chr7B.!!$F7 6105
4 TraesCS7D01G542200 chr7B 733797603 733800910 3307 False 1685.00 1685 76.260000 987 4279 1 chr7B.!!$F2 3292
5 TraesCS7D01G542200 chr7B 733860340 733862716 2376 False 1439.00 1439 77.984000 997 3376 1 chr7B.!!$F3 2379
6 TraesCS7D01G542200 chr7B 733925199 733927584 2385 False 1376.00 1376 77.438000 997 3376 1 chr7B.!!$F5 2379
7 TraesCS7D01G542200 chr7B 733885724 733887354 1630 False 1186.00 1186 80.121000 1749 3376 1 chr7B.!!$F4 1627
8 TraesCS7D01G542200 chr7B 733759172 733763060 3888 False 770.00 1230 78.071333 991 5053 3 chr7B.!!$F6 4062
9 TraesCS7D01G542200 chr7B 733594450 733595319 869 False 403.00 403 75.561000 1076 1949 1 chr7B.!!$F1 873
10 TraesCS7D01G542200 chrUn 304658686 304661018 2332 False 1513.00 1657 94.257500 4111 6110 2 chrUn.!!$F4 1999
11 TraesCS7D01G542200 chrUn 442901231 442902078 847 True 1279.00 1279 93.868000 4343 5190 1 chrUn.!!$R4 847
12 TraesCS7D01G542200 chrUn 283733968 283735623 1655 False 1175.00 1832 96.828000 3595 5190 2 chrUn.!!$F3 1595
13 TraesCS7D01G542200 chrUn 336754901 336756714 1813 False 1097.50 1363 93.729000 4630 6110 2 chrUn.!!$F5 1480
14 TraesCS7D01G542200 chrUn 277751229 277758474 7245 False 941.75 1805 95.831750 4025 6110 8 chrUn.!!$F2 2085
15 TraesCS7D01G542200 chrUn 422906670 422907670 1000 True 820.55 1544 90.263500 4190 5190 2 chrUn.!!$R5 1000
16 TraesCS7D01G542200 chrUn 88643877 88644553 676 False 423.50 518 98.513000 3595 4211 2 chrUn.!!$F1 616
17 TraesCS7D01G542200 chr7A 727228717 727231105 2388 False 1406.00 1406 77.663000 997 3376 1 chr7A.!!$F1 2379
18 TraesCS7D01G542200 chr7A 726682293 726686234 3941 True 1167.50 1688 78.373500 987 5154 2 chr7A.!!$R3 4167
19 TraesCS7D01G542200 chr7A 726812170 726816232 4062 True 793.00 1181 78.217500 992 3757 2 chr7A.!!$R4 2765
20 TraesCS7D01G542200 chr7A 727214144 727215337 1193 True 562.00 562 75.797000 1010 2200 1 chr7A.!!$R2 1190
21 TraesCS7D01G542200 chr6D 468910533 468913315 2782 False 835.00 835 72.679000 994 3758 1 chr6D.!!$F4 2764

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
926 949 0.178947 TTCCCAGCCCCACGAAAAAT 60.179 50.000 0.0 0.0 0.00 1.82 F
927 950 0.610785 TCCCAGCCCCACGAAAAATC 60.611 55.000 0.0 0.0 0.00 2.17 F
928 951 1.506262 CCAGCCCCACGAAAAATCG 59.494 57.895 0.0 0.0 39.31 3.34 F
933 956 1.528292 CCCCACGAAAAATCGCCCAA 61.528 55.000 0.0 0.0 36.44 4.12 F
1699 3048 1.942657 CATTGTATGGAAGGGCAGACG 59.057 52.381 0.0 0.0 0.00 4.18 F
3041 4507 1.959042 AGCACACTGTCCAGACTTTG 58.041 50.000 0.4 0.0 0.00 2.77 F
3879 5353 0.402121 GCCCAAAGTTGTCTCTCCCT 59.598 55.000 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 3616 0.613777 GGTCACCTTGGTACTCAGGG 59.386 60.000 13.51 11.69 46.90 4.45 R
2343 3737 1.066858 TCGAGAACTTCCATCCAGTGC 60.067 52.381 0.00 0.00 0.00 4.40 R
2856 4265 2.417339 TCTCACGAACTGTTTCTCCG 57.583 50.000 0.00 0.00 0.00 4.63 R
3041 4507 5.801380 TCAGGTCCAATAGTTTTAGGTGAC 58.199 41.667 0.00 0.00 0.00 3.67 R
3513 4982 6.293462 GGTGAAGATACTCCAACAACTCAAAC 60.293 42.308 0.00 0.00 0.00 2.93 R
4496 6249 0.039074 ACAAGTGAGGTTCGAGAGCG 60.039 55.000 0.00 0.00 39.35 5.03 R
5484 7742 1.526917 GGATGGCAGACCCCAATCG 60.527 63.158 0.00 0.00 38.61 3.34 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
18 19 2.609534 AACCGGGACTAAAGGCCCC 61.610 63.158 15.63 7.40 41.50 5.80
62 63 2.524306 CATTTGGTGGGCCTTTAGTGA 58.476 47.619 4.53 0.00 35.27 3.41
82 104 2.346365 GTTCGTGAGTCCCCACCC 59.654 66.667 0.00 0.00 33.67 4.61
91 113 1.001269 GTCCCCACCCTTTAGTGCC 60.001 63.158 0.00 0.00 36.38 5.01
97 119 0.536460 CACCCTTTAGTGCCGGTTGT 60.536 55.000 1.90 0.00 0.00 3.32
140 162 3.065510 GCTCGATTCTGCACTAGTGTCTA 59.934 47.826 23.44 10.04 0.00 2.59
168 190 2.562912 GGTGCAGCAATGGTGACG 59.437 61.111 17.33 0.00 32.22 4.35
223 245 2.317609 CGGGCTTCTGTGTTGACCG 61.318 63.158 0.00 0.00 0.00 4.79
280 302 2.434359 GGCCGGGACAAGACGAAG 60.434 66.667 2.18 0.00 0.00 3.79
290 312 4.359706 GGACAAGACGAAGCAATGTTTTT 58.640 39.130 0.00 0.00 0.00 1.94
383 405 2.442188 CGTCCTAGCAAACGTCGCC 61.442 63.158 6.32 0.00 34.30 5.54
439 461 2.122144 ACTGGCGGGCCCCATATA 60.122 61.111 18.66 0.00 33.64 0.86
471 493 6.553852 TCTCTCTTAACCAAACTAGAACCACT 59.446 38.462 0.00 0.00 0.00 4.00
472 494 6.522054 TCTCTTAACCAAACTAGAACCACTG 58.478 40.000 0.00 0.00 0.00 3.66
474 496 7.016268 TCTCTTAACCAAACTAGAACCACTGAT 59.984 37.037 0.00 0.00 0.00 2.90
476 498 4.974645 ACCAAACTAGAACCACTGATCA 57.025 40.909 0.00 0.00 0.00 2.92
477 499 4.899502 ACCAAACTAGAACCACTGATCAG 58.100 43.478 21.37 21.37 0.00 2.90
478 500 4.348168 ACCAAACTAGAACCACTGATCAGT 59.652 41.667 22.89 22.89 43.61 3.41
479 501 4.932200 CCAAACTAGAACCACTGATCAGTC 59.068 45.833 25.58 14.22 40.20 3.51
509 531 6.598525 TGCAAATTGATTACACAAGACGTAG 58.401 36.000 0.00 0.00 33.22 3.51
539 561 6.227522 TCTGCAACAAAAGTGTAGCATAGTA 58.772 36.000 0.00 0.00 36.80 1.82
544 566 8.850452 GCAACAAAAGTGTAGCATAGTATTTTC 58.150 33.333 0.00 0.00 36.80 2.29
574 596 3.801114 AGCCTTCAAAGTGGTTGTTTC 57.199 42.857 0.00 0.00 38.47 2.78
575 597 2.430694 AGCCTTCAAAGTGGTTGTTTCC 59.569 45.455 0.00 0.00 38.47 3.13
721 744 5.480073 ACCCAACATGTAAATGTAGCAATGT 59.520 36.000 0.00 0.00 33.81 2.71
731 754 6.534475 AAATGTAGCAATGTCAATGGATGT 57.466 33.333 0.00 0.00 0.00 3.06
745 768 3.530265 TGGATGTACGGGATACACAAC 57.470 47.619 0.00 0.00 46.65 3.32
750 773 5.220777 GGATGTACGGGATACACAACAATTG 60.221 44.000 3.24 3.24 46.65 2.32
755 778 3.623060 CGGGATACACAACAATTGAGAGG 59.377 47.826 13.59 1.54 39.74 3.69
764 787 1.076024 ACAATTGAGAGGGCACATGGT 59.924 47.619 13.59 0.00 0.00 3.55
818 841 3.064820 ACATGACGGGATGCGTATTTTTC 59.935 43.478 0.00 0.00 0.00 2.29
919 942 3.645268 ATTCGCTTCCCAGCCCCAC 62.645 63.158 0.00 0.00 44.06 4.61
926 949 0.178947 TTCCCAGCCCCACGAAAAAT 60.179 50.000 0.00 0.00 0.00 1.82
927 950 0.610785 TCCCAGCCCCACGAAAAATC 60.611 55.000 0.00 0.00 0.00 2.17
928 951 1.506262 CCAGCCCCACGAAAAATCG 59.494 57.895 0.00 0.00 39.31 3.34
932 955 1.974343 CCCCACGAAAAATCGCCCA 60.974 57.895 0.00 0.00 36.44 5.36
933 956 1.528292 CCCCACGAAAAATCGCCCAA 61.528 55.000 0.00 0.00 36.44 4.12
1430 1465 8.839310 ACTATGAAAGATGATAATAGTGGTGC 57.161 34.615 0.00 0.00 33.81 5.01
1593 1643 5.471456 CCTATGTGAGCCTGTATCCAAATTC 59.529 44.000 0.00 0.00 0.00 2.17
1699 3048 1.942657 CATTGTATGGAAGGGCAGACG 59.057 52.381 0.00 0.00 0.00 4.18
1746 3101 4.423625 AACCAGTGGCAGATTCTATACC 57.576 45.455 9.78 0.00 0.00 2.73
1829 3185 7.200455 GCCCAACACCTGTATAATGATAAAAC 58.800 38.462 0.00 0.00 0.00 2.43
1869 3226 2.569853 TGTTAGGGTCTGGGTATGTGTG 59.430 50.000 0.00 0.00 0.00 3.82
2002 3389 4.757149 CACAGGAACTCAAGTCTAAAAGGG 59.243 45.833 0.00 0.00 34.60 3.95
2191 3581 4.367450 CCTCGAGTCTGATGAATTCTTCC 58.633 47.826 12.31 4.08 0.00 3.46
2282 3676 5.009010 CACGGGCTATTGCTAAGAAATTGAT 59.991 40.000 0.00 0.00 39.59 2.57
2343 3737 3.449018 TGAGGAAGGAGATTTCTCGGAAG 59.551 47.826 1.67 0.00 45.48 3.46
2783 4192 9.725019 TGAAGACAACTATGATGTGACTTTTAT 57.275 29.630 0.00 0.00 0.00 1.40
2856 4265 7.857885 CGGGCTTTGATGATTTTTAGAAGATAC 59.142 37.037 0.00 0.00 0.00 2.24
2866 4275 9.151471 TGATTTTTAGAAGATACGGAGAAACAG 57.849 33.333 0.00 0.00 0.00 3.16
2869 4278 8.530269 TTTTAGAAGATACGGAGAAACAGTTC 57.470 34.615 0.00 0.00 0.00 3.01
3041 4507 1.959042 AGCACACTGTCCAGACTTTG 58.041 50.000 0.40 0.00 0.00 2.77
3127 4596 4.323417 CCGCCTTATCAGTTTATGCCATA 58.677 43.478 0.00 0.00 0.00 2.74
3513 4982 4.338118 AGTTGGTTGTGTGGTGACATTAAG 59.662 41.667 0.00 0.00 46.14 1.85
3879 5353 0.402121 GCCCAAAGTTGTCTCTCCCT 59.598 55.000 0.00 0.00 0.00 4.20
3957 5437 2.162408 GCTGACTTATGCAGGGAACAAC 59.838 50.000 0.00 0.00 34.00 3.32
4264 5798 1.153208 GGAGAGTCAGGCATGCAGG 60.153 63.158 21.36 10.88 0.00 4.85
4272 5806 3.467226 GGCATGCAGGCAATGGCT 61.467 61.111 26.25 2.53 43.51 4.75
4419 5953 1.746615 GCCCATCGAAGCAGCTCAA 60.747 57.895 0.00 0.00 0.00 3.02
4445 6198 3.167485 TCATCAATCCTTTGCCTGCTTT 58.833 40.909 0.00 0.00 32.61 3.51
4447 6200 2.596346 TCAATCCTTTGCCTGCTTTCA 58.404 42.857 0.00 0.00 32.61 2.69
4496 6249 1.436336 GCATGCAGTCAATGGCTCC 59.564 57.895 14.21 0.00 0.00 4.70
4561 6314 7.939039 TGAACTCTGAGAATTTAACAGTGGATT 59.061 33.333 12.44 0.00 33.93 3.01
4697 6450 4.137543 ACTAACCTAATATTGCCTGCAGC 58.862 43.478 8.66 4.57 44.14 5.25
5130 6883 2.949644 GCACAAGGTAACACAACTCCTT 59.050 45.455 0.00 0.00 40.38 3.36
5131 6884 4.131596 GCACAAGGTAACACAACTCCTTA 58.868 43.478 0.00 0.00 38.09 2.69
5159 6912 7.391620 TCTATGTATTCCTTCTTTTCCAACGT 58.608 34.615 0.00 0.00 0.00 3.99
5161 6914 7.989416 ATGTATTCCTTCTTTTCCAACGTAA 57.011 32.000 0.00 0.00 0.00 3.18
5184 6937 2.606275 GGAGTCGATCCCGCAATTC 58.394 57.895 0.00 0.00 43.01 2.17
5201 7448 7.066163 CCCGCAATTCTCTATCATTTATATGCA 59.934 37.037 0.00 0.00 0.00 3.96
5203 7450 8.663025 CGCAATTCTCTATCATTTATATGCACT 58.337 33.333 0.00 0.00 0.00 4.40
5372 7630 2.743636 TCAAAGGTCAGTCGATCACC 57.256 50.000 0.00 0.00 0.00 4.02
5388 7646 4.216257 CGATCACCCTGTCACTTTCATTTT 59.784 41.667 0.00 0.00 0.00 1.82
5453 7711 1.423056 CAGTTTGCTCGCTGCTAGC 59.577 57.895 18.17 18.17 43.37 3.42
5457 7715 0.532573 TTTGCTCGCTGCTAGCTACT 59.467 50.000 23.94 0.00 39.60 2.57
5469 7727 3.515502 TGCTAGCTACTCTCCACACATTT 59.484 43.478 17.23 0.00 0.00 2.32
5484 7742 5.455392 CACACATTTGAGTCTTGGAATGAC 58.545 41.667 12.67 0.00 40.96 3.06
5522 7786 0.250553 CGGCCTCAAGGGTTACACAA 60.251 55.000 0.00 0.00 37.43 3.33
5725 7989 8.760980 TTCTCACCATTTTCCTTTCTTTTCTA 57.239 30.769 0.00 0.00 0.00 2.10
5741 8005 3.639672 TTCTAAAGGAAATCGACCCCC 57.360 47.619 0.00 0.00 0.00 5.40
5803 8070 5.930135 ACTAACTTGTGAAATCTGACAGGT 58.070 37.500 1.81 0.00 34.15 4.00
5820 8087 4.406456 ACAGGTTTGATGGCAGAATTACA 58.594 39.130 0.00 0.00 0.00 2.41
5832 8099 5.304101 TGGCAGAATTACACATTTCCAAAGT 59.696 36.000 0.00 0.00 0.00 2.66
5906 8173 1.676014 GCAAGTTGTCGGCCTATCTGT 60.676 52.381 0.00 0.00 0.00 3.41
5982 8251 6.886178 AATACAGCTACCTTCCTTTCCTAA 57.114 37.500 0.00 0.00 0.00 2.69
6028 8297 4.945246 AGTCGTGTGTCCCATATTACATC 58.055 43.478 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.609534 GGGGCCTTTAGTCCCGGTT 61.610 63.158 0.84 0.00 43.55 4.44
1 2 3.013327 GGGGCCTTTAGTCCCGGT 61.013 66.667 0.84 0.00 43.55 5.28
3 4 2.590092 CTGGGGCCTTTAGTCCCG 59.410 66.667 0.84 0.00 43.55 5.14
62 63 2.522436 TGGGGACTCACGAACCGT 60.522 61.111 0.00 0.00 42.36 4.83
82 104 1.084289 GGCTACAACCGGCACTAAAG 58.916 55.000 0.00 0.00 0.00 1.85
91 113 1.353076 GGTTCGTAAGGCTACAACCG 58.647 55.000 0.00 0.00 33.48 4.44
97 119 1.488390 ATTCCCGGTTCGTAAGGCTA 58.512 50.000 0.00 0.00 38.47 3.93
140 162 3.023949 GCTGCACCGAGGATGAGGT 62.024 63.158 0.00 0.00 42.34 3.85
168 190 3.155167 CCGGGGTAGAGGCCTGTC 61.155 72.222 12.00 0.00 0.00 3.51
207 229 1.966451 CCCGGTCAACACAGAAGCC 60.966 63.158 0.00 0.00 0.00 4.35
337 359 5.348724 GGTAGCGTTATATCATCATGTGTGG 59.651 44.000 0.00 0.00 0.00 4.17
339 361 6.096673 TGGTAGCGTTATATCATCATGTGT 57.903 37.500 0.00 0.00 0.00 3.72
381 403 4.494199 GCTTAACATCTCACATGTAACGGC 60.494 45.833 0.00 0.00 0.00 5.68
383 405 4.259810 CCGCTTAACATCTCACATGTAACG 60.260 45.833 0.00 0.00 0.00 3.18
460 482 6.365970 AAATGACTGATCAGTGGTTCTAGT 57.634 37.500 32.50 5.57 42.66 2.57
461 483 7.524912 CAAAAATGACTGATCAGTGGTTCTAG 58.475 38.462 32.50 13.42 42.66 2.43
464 486 4.919754 GCAAAAATGACTGATCAGTGGTTC 59.080 41.667 32.50 18.01 42.66 3.62
466 488 3.890756 TGCAAAAATGACTGATCAGTGGT 59.109 39.130 32.50 17.31 42.66 4.16
467 489 4.508461 TGCAAAAATGACTGATCAGTGG 57.492 40.909 32.50 13.06 42.66 4.00
468 490 7.170151 TCAATTTGCAAAAATGACTGATCAGTG 59.830 33.333 32.50 16.81 42.66 3.66
471 493 8.610248 AATCAATTTGCAAAAATGACTGATCA 57.390 26.923 24.71 8.76 39.83 2.92
472 494 9.962759 GTAATCAATTTGCAAAAATGACTGATC 57.037 29.630 24.71 14.14 0.00 2.92
474 496 8.763356 GTGTAATCAATTTGCAAAAATGACTGA 58.237 29.630 24.71 16.54 31.34 3.41
476 498 8.659925 TGTGTAATCAATTTGCAAAAATGACT 57.340 26.923 24.71 19.47 31.34 3.41
477 499 9.372541 CTTGTGTAATCAATTTGCAAAAATGAC 57.627 29.630 24.71 17.60 31.34 3.06
478 500 9.322773 TCTTGTGTAATCAATTTGCAAAAATGA 57.677 25.926 24.53 24.53 31.34 2.57
479 501 9.372541 GTCTTGTGTAATCAATTTGCAAAAATG 57.627 29.630 17.19 17.48 31.34 2.32
509 531 6.317910 CTACACTTTTGTTGCAGAAAACAC 57.682 37.500 2.46 0.00 39.70 3.32
539 561 9.247861 ACTTTGAAGGCTATGTCAATAGAAAAT 57.752 29.630 1.23 0.00 38.49 1.82
544 566 5.882557 ACCACTTTGAAGGCTATGTCAATAG 59.117 40.000 1.23 5.07 39.12 1.73
552 574 4.280929 GGAAACAACCACTTTGAAGGCTAT 59.719 41.667 0.00 0.00 38.73 2.97
574 596 5.234329 ACGAATATGACGAGTAAATTGCAGG 59.766 40.000 9.07 0.00 34.70 4.85
575 597 6.274001 ACGAATATGACGAGTAAATTGCAG 57.726 37.500 9.07 0.00 34.70 4.41
615 638 2.189833 CGGATGAGAGAACCGGTCA 58.810 57.895 8.04 0.07 42.48 4.02
721 744 3.707102 TGTGTATCCCGTACATCCATTGA 59.293 43.478 0.00 0.00 44.65 2.57
731 754 5.408880 TCTCAATTGTTGTGTATCCCGTA 57.591 39.130 5.13 0.00 0.00 4.02
745 768 1.475280 CACCATGTGCCCTCTCAATTG 59.525 52.381 0.00 0.00 0.00 2.32
750 773 4.308526 CACACCATGTGCCCTCTC 57.691 61.111 0.00 0.00 41.89 3.20
764 787 4.497984 AGCACCGCCACCAACACA 62.498 61.111 0.00 0.00 0.00 3.72
818 841 1.866853 GCGTTTCCAAGCCAAGGAGG 61.867 60.000 0.00 0.00 36.33 4.30
919 942 2.267426 GGGATTTTGGGCGATTTTTCG 58.733 47.619 0.00 0.00 0.00 3.46
926 949 1.304052 CAGGTGGGATTTTGGGCGA 60.304 57.895 0.00 0.00 0.00 5.54
927 950 3.005540 GCAGGTGGGATTTTGGGCG 62.006 63.158 0.00 0.00 0.00 6.13
928 951 2.659063 GGCAGGTGGGATTTTGGGC 61.659 63.158 0.00 0.00 0.00 5.36
932 955 2.110578 GCTTATGGCAGGTGGGATTTT 58.889 47.619 0.00 0.00 41.35 1.82
933 956 1.689258 GGCTTATGGCAGGTGGGATTT 60.689 52.381 0.00 0.00 44.01 2.17
1107 1130 3.489180 TCTTTCTTGATCTCGACGGAC 57.511 47.619 0.00 0.00 0.00 4.79
1430 1465 1.747709 AATAGGAACAGCAGCAGCAG 58.252 50.000 3.17 0.00 45.49 4.24
1593 1643 1.278985 TGGTGTGGAGTTATGCAGAGG 59.721 52.381 0.00 0.00 0.00 3.69
1699 3048 3.818773 TCATCTTTGGTTCCCTCGAAAAC 59.181 43.478 0.00 0.00 0.00 2.43
1746 3101 2.618709 AGCAAGAACTGAAAGGGTTTCG 59.381 45.455 0.00 0.00 42.55 3.46
1869 3226 4.410492 AAGCACATCAAAATCAGTCGAC 57.590 40.909 7.70 7.70 0.00 4.20
2031 3418 2.733956 TCCCAACCCTGATTATTGCAC 58.266 47.619 0.00 0.00 0.00 4.57
2191 3581 8.936070 TCAAATATGAATGCTTCAAAGAATGG 57.064 30.769 3.27 0.00 43.95 3.16
2226 3616 0.613777 GGTCACCTTGGTACTCAGGG 59.386 60.000 13.51 11.69 46.90 4.45
2282 3676 1.553690 GCCTGCTAGAGGTGAACCCA 61.554 60.000 0.00 0.00 44.97 4.51
2343 3737 1.066858 TCGAGAACTTCCATCCAGTGC 60.067 52.381 0.00 0.00 0.00 4.40
2540 3934 7.870509 TCCATGTAATCCTCATCTTTTTCTG 57.129 36.000 0.00 0.00 0.00 3.02
2783 4192 8.849168 TGCTCTTCAACTTAATCATTTCTTCAA 58.151 29.630 0.00 0.00 0.00 2.69
2856 4265 2.417339 TCTCACGAACTGTTTCTCCG 57.583 50.000 0.00 0.00 0.00 4.63
3041 4507 5.801380 TCAGGTCCAATAGTTTTAGGTGAC 58.199 41.667 0.00 0.00 0.00 3.67
3513 4982 6.293462 GGTGAAGATACTCCAACAACTCAAAC 60.293 42.308 0.00 0.00 0.00 2.93
3879 5353 2.673200 GGAGCTGTGAGGCATGGGA 61.673 63.158 0.00 0.00 34.17 4.37
4027 5513 5.184287 TCATTGAAATGTGTGATGCATCTGT 59.816 36.000 26.32 1.53 37.65 3.41
4028 5514 5.515270 GTCATTGAAATGTGTGATGCATCTG 59.485 40.000 26.32 12.17 37.65 2.90
4034 5568 5.093457 GCTCTGTCATTGAAATGTGTGATG 58.907 41.667 3.10 0.00 37.65 3.07
4419 5953 3.449737 CAGGCAAAGGATTGATGATGGTT 59.550 43.478 0.00 0.00 38.94 3.67
4445 6198 5.405935 TTCAATCTCAAGTTCCTCGATGA 57.594 39.130 0.00 0.00 0.00 2.92
4447 6200 4.467795 TCCTTCAATCTCAAGTTCCTCGAT 59.532 41.667 0.00 0.00 0.00 3.59
4496 6249 0.039074 ACAAGTGAGGTTCGAGAGCG 60.039 55.000 0.00 0.00 39.35 5.03
4561 6314 8.999431 GTTGACTGTGATAAGAGGATTAAAACA 58.001 33.333 0.00 0.00 0.00 2.83
4697 6450 1.892819 TTCTCGCAGCTGGAAGGAGG 61.893 60.000 17.12 0.00 0.00 4.30
5007 6760 3.441101 ACCCTGCACTAATAGACACTCA 58.559 45.455 0.00 0.00 0.00 3.41
5201 7448 7.308830 GCAGAAACAGAGTAATGAATCCAAAGT 60.309 37.037 0.00 0.00 0.00 2.66
5203 7450 6.489700 TGCAGAAACAGAGTAATGAATCCAAA 59.510 34.615 0.00 0.00 0.00 3.28
5206 7453 5.877012 TCTGCAGAAACAGAGTAATGAATCC 59.123 40.000 15.67 0.00 41.72 3.01
5207 7454 6.974932 TCTGCAGAAACAGAGTAATGAATC 57.025 37.500 15.67 0.00 41.72 2.52
5208 7455 6.128445 CGTTCTGCAGAAACAGAGTAATGAAT 60.128 38.462 29.99 0.00 46.85 2.57
5388 7646 8.314021 TGTTGAGATGCTGAACTAAGAATAAGA 58.686 33.333 0.00 0.00 29.40 2.10
5453 7711 5.398603 AGACTCAAATGTGTGGAGAGTAG 57.601 43.478 0.00 0.00 39.47 2.57
5457 7715 3.390967 TCCAAGACTCAAATGTGTGGAGA 59.609 43.478 0.00 0.00 31.21 3.71
5469 7727 3.599343 CCAATCGTCATTCCAAGACTCA 58.401 45.455 0.00 0.00 33.89 3.41
5484 7742 1.526917 GGATGGCAGACCCCAATCG 60.527 63.158 0.00 0.00 38.61 3.34
5522 7786 1.912043 CTCCCATGAGTGAGGAAAGGT 59.088 52.381 0.00 0.00 33.70 3.50
5590 7854 3.533606 ATCTAGCTGTCGCAGTGAAAT 57.466 42.857 0.00 0.00 39.10 2.17
5779 8046 5.992217 ACCTGTCAGATTTCACAAGTTAGTC 59.008 40.000 0.00 0.00 0.00 2.59
5794 8061 1.699083 TCTGCCATCAAACCTGTCAGA 59.301 47.619 0.00 0.00 0.00 3.27
5796 8063 2.655090 TTCTGCCATCAAACCTGTCA 57.345 45.000 0.00 0.00 0.00 3.58
5803 8070 6.014755 TGGAAATGTGTAATTCTGCCATCAAA 60.015 34.615 0.00 0.00 0.00 2.69
5820 8087 3.132925 GCACATTGCACTTTGGAAATGT 58.867 40.909 0.00 0.00 44.26 2.71
5906 8173 2.547299 AAAACCCATGTACGAACCGA 57.453 45.000 0.00 0.00 0.00 4.69
5982 8251 2.057137 TGAGAGCTGCCAAAACTGTT 57.943 45.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.