Multiple sequence alignment - TraesCS7B01G443200

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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 TraesCS7B01G443200 chr7B 100.000 4940 0 0 1 4940 708001885 707996946 0.000000e+00 9123.0
1 TraesCS7B01G443200 chr7B 82.237 304 40 6 4643 4932 712844769 712844466 2.950000e-62 250.0
2 TraesCS7B01G443200 chr7B 83.221 149 14 6 2178 2322 708102590 708102449 5.190000e-25 126.0
3 TraesCS7B01G443200 chr7B 82.734 139 12 8 2887 3025 707958242 707958116 4.040000e-21 113.0
4 TraesCS7B01G443200 chr7A 89.721 2792 151 52 653 3349 707969599 707966849 0.000000e+00 3441.0
5 TraesCS7B01G443200 chr7A 95.471 1126 41 8 3207 4329 707966849 707965731 0.000000e+00 1788.0
6 TraesCS7B01G443200 chr7A 97.425 466 9 2 4476 4940 707965709 707965246 0.000000e+00 791.0
7 TraesCS7B01G443200 chr7A 87.013 693 57 13 1 662 707972120 707971430 0.000000e+00 750.0
8 TraesCS7B01G443200 chr7D 88.591 2016 117 35 540 2488 615466645 615464676 0.000000e+00 2344.0
9 TraesCS7B01G443200 chr7D 99.360 781 4 1 3290 4070 615462243 615461464 0.000000e+00 1413.0
10 TraesCS7B01G443200 chr7D 98.855 786 7 1 2480 3263 615463025 615462240 0.000000e+00 1400.0
11 TraesCS7B01G443200 chr7D 96.989 465 12 2 4476 4940 615461073 615460611 0.000000e+00 780.0
12 TraesCS7B01G443200 chr7D 96.486 313 11 0 4070 4382 615461384 615461072 7.330000e-143 518.0
13 TraesCS7B01G443200 chr7D 88.167 431 47 3 3454 3883 614703831 614704258 1.230000e-140 510.0
14 TraesCS7B01G443200 chr7D 90.043 231 20 3 3234 3462 614702781 614703010 3.740000e-76 296.0
15 TraesCS7B01G443200 chr7D 86.567 268 18 10 286 537 615467495 615467230 3.770000e-71 279.0
16 TraesCS7B01G443200 chr7D 90.449 178 14 1 1 178 615467665 615467491 1.070000e-56 231.0
17 TraesCS7B01G443200 chr4D 81.311 305 37 13 4643 4933 393137294 393137592 3.850000e-56 230.0
18 TraesCS7B01G443200 chr6D 96.078 102 4 0 4380 4481 200398713 200398814 3.060000e-37 167.0
19 TraesCS7B01G443200 chr1D 95.146 103 5 0 4380 4482 490538115 490538217 3.960000e-36 163.0
20 TraesCS7B01G443200 chr5D 95.960 99 4 0 4381 4479 228447058 228446960 1.420000e-35 161.0
21 TraesCS7B01G443200 chr5D 100.000 28 0 0 664 691 249066219 249066192 9.000000e-03 52.8
22 TraesCS7B01G443200 chr5D 100.000 28 0 0 664 691 498655375 498655348 9.000000e-03 52.8
23 TraesCS7B01G443200 chr2D 95.146 103 4 1 4379 4480 445894882 445894984 1.420000e-35 161.0
24 TraesCS7B01G443200 chr2D 91.818 110 8 1 4381 4490 27501097 27500989 8.560000e-33 152.0
25 TraesCS7B01G443200 chr2D 79.167 192 36 4 4740 4929 14123073 14123262 4.010000e-26 130.0
26 TraesCS7B01G443200 chr2A 95.050 101 5 0 4378 4478 68155923 68155823 5.120000e-35 159.0
27 TraesCS7B01G443200 chr2A 80.447 179 31 4 4753 4929 16492422 16492598 3.100000e-27 134.0
28 TraesCS7B01G443200 chr2B 83.051 177 26 4 4754 4929 25775516 25775689 1.840000e-34 158.0
29 TraesCS7B01G443200 chr2B 93.269 104 6 1 4380 4482 230532422 230532525 8.560000e-33 152.0
30 TraesCS7B01G443200 chr2B 91.892 37 3 0 655 691 427574273 427574309 9.000000e-03 52.8
31 TraesCS7B01G443200 chr3D 93.204 103 7 0 4377 4479 448433604 448433706 8.560000e-33 152.0
32 TraesCS7B01G443200 chr3B 93.204 103 7 0 4377 4479 588476640 588476742 8.560000e-33 152.0
33 TraesCS7B01G443200 chr6A 100.000 30 0 0 662 691 250609531 250609502 6.910000e-04 56.5
34 TraesCS7B01G443200 chr6A 100.000 30 0 0 662 691 250692320 250692291 6.910000e-04 56.5
35 TraesCS7B01G443200 chr5A 100.000 28 0 0 664 691 474916880 474916907 9.000000e-03 52.8
36 TraesCS7B01G443200 chr5A 100.000 28 0 0 664 691 594576270 594576243 9.000000e-03 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 TraesCS7B01G443200 chr7B 707996946 708001885 4939 True 9123.0 9123 100.000000 1 4940 1 chr7B.!!$R2 4939
1 TraesCS7B01G443200 chr7A 707965246 707972120 6874 True 1692.5 3441 92.407500 1 4940 4 chr7A.!!$R1 4939
2 TraesCS7B01G443200 chr7D 615460611 615467665 7054 True 995.0 2344 93.899571 1 4940 7 chr7D.!!$R1 4939
3 TraesCS7B01G443200 chr7D 614702781 614704258 1477 False 403.0 510 89.105000 3234 3883 2 chr7D.!!$F1 649

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
953 3418 1.247567 AGGAACAAATTCACCCAGCG 58.752 50.0 0.00 0.0 36.46 5.18 F
1596 4133 0.036483 TTTATGGCGCTGCTCACTCA 60.036 50.0 7.64 0.0 0.00 3.41 F
1610 4147 0.387878 CACTCAGTGTCAGAGCCGTC 60.388 60.0 0.00 0.0 36.58 4.79 F
3375 7776 0.394488 TTTTGGGTGTCAACGAGCCA 60.394 50.0 0.00 0.0 39.23 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 4667 0.674581 TGGTGCACTGCAGAGCATAC 60.675 55.000 35.68 29.96 43.06 2.39 R
3139 7392 6.453922 GGTGTTCGACTCAGACGATAAAATTC 60.454 42.308 0.00 0.00 39.45 2.17 R
3651 8883 9.700831 GAGCCATATACCCTGGAAATAATAAAT 57.299 33.333 0.00 0.00 35.70 1.40 R
4461 9774 1.854939 TCTTATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37 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
43 44 4.387559 CCGATTGTCGTGAATCTTAACACA 59.612 41.667 0.00 0.00 38.40 3.72
49 50 5.989168 TGTCGTGAATCTTAACACAGACAAT 59.011 36.000 3.61 0.00 41.75 2.71
76 77 1.284111 TGCTGAAGATGCCCAGGGAT 61.284 55.000 10.89 0.00 0.00 3.85
105 106 2.418777 CGATGCATCAGGCTCCGA 59.581 61.111 25.70 0.00 45.15 4.55
127 128 6.095947 GACAGGTCGACAATGATAAAACTC 57.904 41.667 22.39 7.58 0.00 3.01
159 160 5.120830 ACTCTGATTAGTGCTTGTTTTAGCG 59.879 40.000 0.00 0.00 44.18 4.26
182 183 6.460763 GCGTAAATGTAGCTCGTTTTAACTTC 59.539 38.462 0.00 0.00 36.72 3.01
193 194 7.173390 AGCTCGTTTTAACTTCAATTTAGCTCT 59.827 33.333 0.00 0.00 29.94 4.09
285 305 8.964476 CCATGTGGTCTTAGTATACTTTCAAT 57.036 34.615 11.40 0.00 0.00 2.57
344 364 8.704849 TGGATTTGAGGAGTTAAATTTGAGAA 57.295 30.769 0.00 0.00 0.00 2.87
362 383 3.753272 GAGAATTGGCTAGCTTCACACAA 59.247 43.478 15.72 9.42 0.00 3.33
366 387 6.434028 AGAATTGGCTAGCTTCACACAATTTA 59.566 34.615 20.88 0.00 38.29 1.40
409 445 9.049523 GCAGAGAAAATTGAAAGGAAATCTTTT 57.950 29.630 0.00 0.00 45.00 2.27
476 512 8.659925 TTAATTGTGTTTGTGAGCATGATTTT 57.340 26.923 0.00 0.00 0.00 1.82
478 514 5.970140 TGTGTTTGTGAGCATGATTTTTG 57.030 34.783 0.00 0.00 0.00 2.44
479 515 4.809958 TGTGTTTGTGAGCATGATTTTTGG 59.190 37.500 0.00 0.00 0.00 3.28
487 524 1.799994 GCATGATTTTTGGTGTGCCAC 59.200 47.619 0.00 0.00 46.01 5.01
504 541 5.220381 GTGCCACGATTAGAATTAGATCGA 58.780 41.667 18.65 0.00 43.86 3.59
507 544 5.864474 GCCACGATTAGAATTAGATCGATGT 59.136 40.000 18.65 0.00 43.86 3.06
523 560 3.756963 TCGATGTATTATCTCGGTGAGGG 59.243 47.826 0.00 0.00 33.38 4.30
537 1156 1.255667 TGAGGGGGTAGTCGAGTTGC 61.256 60.000 0.00 0.00 0.00 4.17
538 1157 1.957765 GAGGGGGTAGTCGAGTTGCC 61.958 65.000 0.00 1.31 0.00 4.52
555 1174 1.384222 GCCCCGCCACAAGGAATTAG 61.384 60.000 0.00 0.00 36.89 1.73
599 1218 3.224884 GGCTGCGCCTTTTTGTTATTA 57.775 42.857 4.18 0.00 46.69 0.98
638 1257 5.600908 TTCAAGGTATTTTTCGGTTCTCG 57.399 39.130 0.00 0.00 40.90 4.04
648 1267 2.433868 TCGGTTCTCGGAGAAGTTTG 57.566 50.000 20.23 10.54 34.42 2.93
773 3234 8.445193 CTGATTTACTCAGCAAAAGAAATGAC 57.555 34.615 0.00 0.00 44.73 3.06
811 3272 9.566530 TGAAAATACATCATGATACAAAAACCG 57.433 29.630 8.15 0.00 0.00 4.44
826 3287 1.787057 AACCGGACGCATTTTTCGCA 61.787 50.000 9.46 0.00 0.00 5.10
846 3307 1.271652 ACACCACCACCGCAAATATCA 60.272 47.619 0.00 0.00 0.00 2.15
864 3325 7.722949 AATATCATTTTCCACTGGACATTGT 57.277 32.000 0.00 0.00 0.00 2.71
869 3330 7.206687 TCATTTTCCACTGGACATTGTAAAAC 58.793 34.615 0.00 0.00 0.00 2.43
953 3418 1.247567 AGGAACAAATTCACCCAGCG 58.752 50.000 0.00 0.00 36.46 5.18
998 3463 4.968719 ACCAAGGGGACAAGAAAAGAAAAT 59.031 37.500 0.00 0.00 38.05 1.82
1136 3622 2.525381 CCATCCTCCTCCCCCTCG 60.525 72.222 0.00 0.00 0.00 4.63
1354 3861 1.555075 CCTCCTACAGCTTTGCCACTA 59.445 52.381 0.00 0.00 0.00 2.74
1369 3876 3.392285 TGCCACTATCATGCCTCTGTATT 59.608 43.478 0.00 0.00 0.00 1.89
1372 3879 5.049129 GCCACTATCATGCCTCTGTATTTTC 60.049 44.000 0.00 0.00 0.00 2.29
1379 3902 4.746535 TGCCTCTGTATTTTCGGTATGA 57.253 40.909 0.00 0.00 0.00 2.15
1411 3934 1.634973 TCATGGTGATGGCTTCTTGGA 59.365 47.619 1.86 0.00 0.00 3.53
1413 3936 3.459227 TCATGGTGATGGCTTCTTGGATA 59.541 43.478 1.86 0.00 0.00 2.59
1418 3941 5.721000 TGGTGATGGCTTCTTGGATATTTTT 59.279 36.000 1.86 0.00 0.00 1.94
1504 4027 5.120053 TCTGTACGTGATGCAGTTTTATGTG 59.880 40.000 0.00 0.00 41.52 3.21
1505 4028 4.752604 TGTACGTGATGCAGTTTTATGTGT 59.247 37.500 0.00 0.00 0.00 3.72
1509 4032 5.458452 ACGTGATGCAGTTTTATGTGTTTTG 59.542 36.000 0.00 0.00 0.00 2.44
1512 4035 7.118724 GTGATGCAGTTTTATGTGTTTTGTTG 58.881 34.615 0.00 0.00 0.00 3.33
1513 4036 6.815641 TGATGCAGTTTTATGTGTTTTGTTGT 59.184 30.769 0.00 0.00 0.00 3.32
1515 4038 6.825584 TGCAGTTTTATGTGTTTTGTTGTTG 58.174 32.000 0.00 0.00 0.00 3.33
1516 4039 6.646653 TGCAGTTTTATGTGTTTTGTTGTTGA 59.353 30.769 0.00 0.00 0.00 3.18
1517 4040 6.953189 GCAGTTTTATGTGTTTTGTTGTTGAC 59.047 34.615 0.00 0.00 0.00 3.18
1572 4109 8.722342 TTGTGTCGTTTCTTAAAATTATCAGC 57.278 30.769 0.00 0.00 0.00 4.26
1593 4130 0.804989 AGTTTTATGGCGCTGCTCAC 59.195 50.000 7.64 0.00 0.00 3.51
1594 4131 0.804989 GTTTTATGGCGCTGCTCACT 59.195 50.000 7.64 0.00 0.00 3.41
1595 4132 1.086696 TTTTATGGCGCTGCTCACTC 58.913 50.000 7.64 0.00 0.00 3.51
1596 4133 0.036483 TTTATGGCGCTGCTCACTCA 60.036 50.000 7.64 0.00 0.00 3.41
1609 4146 0.823769 TCACTCAGTGTCAGAGCCGT 60.824 55.000 4.28 0.00 36.58 5.68
1610 4147 0.387878 CACTCAGTGTCAGAGCCGTC 60.388 60.000 0.00 0.00 36.58 4.79
1611 4148 1.214062 CTCAGTGTCAGAGCCGTCC 59.786 63.158 0.00 0.00 0.00 4.79
1647 4184 1.135460 GTCTTGCATTGGAAGCTCTGC 60.135 52.381 12.62 0.00 35.21 4.26
1655 4192 2.175878 TGGAAGCTCTGCTCTGAAAC 57.824 50.000 0.00 0.00 38.25 2.78
1786 4357 4.220821 CACATGTTAGGGAGTAGTGACACT 59.779 45.833 13.68 13.68 0.00 3.55
1814 4385 1.725641 TTTGCGACTGTATGGAGCAG 58.274 50.000 0.00 0.00 39.11 4.24
1937 4511 3.809279 TGAGTGCACAAGATGTACAGTTG 59.191 43.478 21.04 15.80 45.74 3.16
1940 4514 5.793817 AGTGCACAAGATGTACAGTTGATA 58.206 37.500 21.04 8.89 45.74 2.15
1945 4519 6.797033 GCACAAGATGTACAGTTGATAAACAC 59.203 38.462 21.68 5.02 0.00 3.32
1973 4547 7.391833 AGAACTTGGAATTCCTGATGTTAGAAC 59.608 37.037 24.73 11.40 36.82 3.01
2008 4582 5.083821 ACTTATGGTGCCATTGGTTTAGTT 58.916 37.500 9.19 0.00 37.82 2.24
2220 4796 5.360591 AGGTGAACGATGTGATATTTCCTC 58.639 41.667 0.00 0.00 0.00 3.71
2221 4797 5.129485 AGGTGAACGATGTGATATTTCCTCT 59.871 40.000 0.00 0.00 0.00 3.69
2222 4798 5.817816 GGTGAACGATGTGATATTTCCTCTT 59.182 40.000 0.00 0.00 0.00 2.85
2263 4839 7.399765 AGGATATCTCATTAGATTGGTCTCCTG 59.600 40.741 2.05 0.00 39.55 3.86
2354 4930 1.152984 TGATATGGCTGGCCGTTGG 60.153 57.895 11.79 0.00 39.42 3.77
3139 7392 4.337274 TGTTATTCAGGCATCTGCATTCTG 59.663 41.667 4.33 2.88 44.36 3.02
3166 7419 2.174363 TCGTCTGAGTCGAACACCTA 57.826 50.000 0.00 0.00 34.36 3.08
3375 7776 0.394488 TTTTGGGTGTCAACGAGCCA 60.394 50.000 0.00 0.00 39.23 4.75
3586 8816 3.591527 TCTCATGTGGGAAGTTTGGGTAT 59.408 43.478 0.00 0.00 0.00 2.73
4289 9602 3.434319 CGAGTGTGTGCATGCCCC 61.434 66.667 16.68 6.36 0.00 5.80
4356 9669 3.483869 GATGGGGAAGAGGCGGCT 61.484 66.667 13.09 13.09 0.00 5.52
4380 9693 5.046159 TGTTGTTCTTCCCAACTACGGATAT 60.046 40.000 5.07 0.00 42.09 1.63
4381 9694 6.154877 TGTTGTTCTTCCCAACTACGGATATA 59.845 38.462 5.07 0.00 42.09 0.86
4382 9695 6.152932 TGTTCTTCCCAACTACGGATATAC 57.847 41.667 0.00 0.00 0.00 1.47
4383 9696 5.895534 TGTTCTTCCCAACTACGGATATACT 59.104 40.000 0.00 0.00 0.00 2.12
4384 9697 6.040166 TGTTCTTCCCAACTACGGATATACTC 59.960 42.308 0.00 0.00 0.00 2.59
4385 9698 5.075493 TCTTCCCAACTACGGATATACTCC 58.925 45.833 0.00 0.00 41.07 3.85
4386 9699 3.771216 TCCCAACTACGGATATACTCCC 58.229 50.000 0.00 0.00 41.49 4.30
4387 9700 3.400322 TCCCAACTACGGATATACTCCCT 59.600 47.826 0.00 0.00 41.49 4.20
4388 9701 3.762823 CCCAACTACGGATATACTCCCTC 59.237 52.174 0.00 0.00 41.49 4.30
4389 9702 3.762823 CCAACTACGGATATACTCCCTCC 59.237 52.174 0.00 0.00 41.49 4.30
4393 9706 1.461559 CGGATATACTCCCTCCGTCC 58.538 60.000 3.95 0.00 45.30 4.79
4394 9707 1.849977 GGATATACTCCCTCCGTCCC 58.150 60.000 0.00 0.00 38.19 4.46
4395 9708 1.076677 GGATATACTCCCTCCGTCCCA 59.923 57.143 0.00 0.00 38.19 4.37
4396 9709 2.492196 GGATATACTCCCTCCGTCCCAA 60.492 54.545 0.00 0.00 38.19 4.12
4397 9710 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
4398 9711 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
4399 9712 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4400 9713 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4401 9714 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4402 9715 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4403 9716 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4404 9717 3.452878 TCCCTCCGTCCCAAAATAAGTA 58.547 45.455 0.00 0.00 0.00 2.24
4405 9718 4.042174 TCCCTCCGTCCCAAAATAAGTAT 58.958 43.478 0.00 0.00 0.00 2.12
4406 9719 4.102054 TCCCTCCGTCCCAAAATAAGTATC 59.898 45.833 0.00 0.00 0.00 2.24
4407 9720 4.102681 CCCTCCGTCCCAAAATAAGTATCT 59.897 45.833 0.00 0.00 0.00 1.98
4408 9721 5.298347 CCTCCGTCCCAAAATAAGTATCTC 58.702 45.833 0.00 0.00 0.00 2.75
4409 9722 5.163343 CCTCCGTCCCAAAATAAGTATCTCA 60.163 44.000 0.00 0.00 0.00 3.27
4410 9723 6.302535 TCCGTCCCAAAATAAGTATCTCAA 57.697 37.500 0.00 0.00 0.00 3.02
4411 9724 6.110707 TCCGTCCCAAAATAAGTATCTCAAC 58.889 40.000 0.00 0.00 0.00 3.18
4412 9725 6.070424 TCCGTCCCAAAATAAGTATCTCAACT 60.070 38.462 0.00 0.00 0.00 3.16
4413 9726 6.598064 CCGTCCCAAAATAAGTATCTCAACTT 59.402 38.462 0.00 0.00 42.31 2.66
4414 9727 7.120726 CCGTCCCAAAATAAGTATCTCAACTTT 59.879 37.037 0.00 0.00 40.20 2.66
4415 9728 7.962918 CGTCCCAAAATAAGTATCTCAACTTTG 59.037 37.037 0.00 0.00 40.20 2.77
4416 9729 8.793592 GTCCCAAAATAAGTATCTCAACTTTGT 58.206 33.333 0.00 0.00 40.20 2.83
4430 9743 8.361592 TCTCAACTTTGTACTAACTTTAGTGC 57.638 34.615 11.24 10.37 43.44 4.40
4449 9762 9.781633 TTTAGTGCAAAGTAGTATTAAGGTTGA 57.218 29.630 0.00 0.00 0.00 3.18
4450 9763 7.907214 AGTGCAAAGTAGTATTAAGGTTGAG 57.093 36.000 0.00 0.00 0.00 3.02
4451 9764 7.676947 AGTGCAAAGTAGTATTAAGGTTGAGA 58.323 34.615 0.00 0.00 0.00 3.27
4452 9765 7.603024 AGTGCAAAGTAGTATTAAGGTTGAGAC 59.397 37.037 0.00 0.00 0.00 3.36
4453 9766 7.386848 GTGCAAAGTAGTATTAAGGTTGAGACA 59.613 37.037 0.00 0.00 0.00 3.41
4454 9767 7.386848 TGCAAAGTAGTATTAAGGTTGAGACAC 59.613 37.037 0.00 0.00 0.00 3.67
4455 9768 7.603024 GCAAAGTAGTATTAAGGTTGAGACACT 59.397 37.037 0.00 0.00 0.00 3.55
4456 9769 9.490379 CAAAGTAGTATTAAGGTTGAGACACTT 57.510 33.333 0.00 0.00 0.00 3.16
4464 9777 7.519032 TTAAGGTTGAGACACTTATTTTGGG 57.481 36.000 0.00 0.00 0.00 4.12
4465 9778 5.319043 AGGTTGAGACACTTATTTTGGGA 57.681 39.130 0.00 0.00 0.00 4.37
4466 9779 5.070685 AGGTTGAGACACTTATTTTGGGAC 58.929 41.667 0.00 0.00 0.00 4.46
4467 9780 4.083484 GGTTGAGACACTTATTTTGGGACG 60.083 45.833 0.00 0.00 0.00 4.79
4468 9781 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
4469 9782 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
4470 9783 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
4471 9784 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4472 9785 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
4473 9786 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4474 9787 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4574 9887 5.068987 CCAAGTGTCATACAATATTTGGGGG 59.931 44.000 0.00 0.00 30.58 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.228228 GCATCCCTGGGCATCTTCA 59.772 57.895 8.22 0.00 0.00 3.02
105 106 4.625742 CGAGTTTTATCATTGTCGACCTGT 59.374 41.667 14.12 4.69 0.00 4.00
113 114 8.204836 AGAGTTATAGCCGAGTTTTATCATTGT 58.795 33.333 0.00 0.00 0.00 2.71
127 128 5.127693 AGCACTAATCAGAGTTATAGCCG 57.872 43.478 0.00 0.00 0.00 5.52
159 160 9.821662 ATTGAAGTTAAAACGAGCTACATTTAC 57.178 29.630 0.00 0.00 0.00 2.01
285 305 7.117523 CACAAACACCTCATTCAAAACTCAAAA 59.882 33.333 0.00 0.00 0.00 2.44
344 364 6.377996 TCATAAATTGTGTGAAGCTAGCCAAT 59.622 34.615 12.13 9.81 0.00 3.16
347 367 5.220931 CCTCATAAATTGTGTGAAGCTAGCC 60.221 44.000 12.13 0.00 0.00 3.93
362 383 7.175104 TCTGCAAACCTTAACTCCTCATAAAT 58.825 34.615 0.00 0.00 0.00 1.40
366 387 4.287067 TCTCTGCAAACCTTAACTCCTCAT 59.713 41.667 0.00 0.00 0.00 2.90
409 445 8.707796 ATTAGGATATCTCTAACCGAACTCAA 57.292 34.615 12.90 0.00 30.61 3.02
504 541 3.173965 CCCCCTCACCGAGATAATACAT 58.826 50.000 0.00 0.00 0.00 2.29
507 544 3.400322 ACTACCCCCTCACCGAGATAATA 59.600 47.826 0.00 0.00 0.00 0.98
523 560 2.582978 GGGGCAACTCGACTACCC 59.417 66.667 0.00 0.00 40.05 3.69
537 1156 0.751643 CCTAATTCCTTGTGGCGGGG 60.752 60.000 0.00 0.00 0.00 5.73
538 1157 1.384222 GCCTAATTCCTTGTGGCGGG 61.384 60.000 0.00 0.00 33.96 6.13
545 1164 7.987458 TCACTTTAGATAGTGCCTAATTCCTTG 59.013 37.037 0.00 0.00 44.10 3.61
546 1165 8.090788 TCACTTTAGATAGTGCCTAATTCCTT 57.909 34.615 0.00 0.00 44.10 3.36
599 1218 9.959721 ATACCTTGAATATAAAAGCCATACGAT 57.040 29.630 0.00 0.00 0.00 3.73
638 1257 4.123506 GCCTATGTCTAGCAAACTTCTCC 58.876 47.826 0.00 0.00 0.00 3.71
648 1267 8.138712 GGAGTATAATATGTGCCTATGTCTAGC 58.861 40.741 0.00 0.00 0.00 3.42
811 3272 1.001745 GGTGTGCGAAAAATGCGTCC 61.002 55.000 0.00 0.00 34.24 4.79
826 3287 1.271652 TGATATTTGCGGTGGTGGTGT 60.272 47.619 0.00 0.00 0.00 4.16
846 3307 7.069331 TCTGTTTTACAATGTCCAGTGGAAAAT 59.931 33.333 15.09 8.16 46.53 1.82
869 3330 9.434420 TTTTGGCCACTCAAAAATAATAATCTG 57.566 29.630 3.88 0.00 41.76 2.90
878 3339 8.922931 AAAATCTATTTTGGCCACTCAAAAAT 57.077 26.923 3.88 11.44 45.79 1.82
890 3351 7.775120 AGCATCCACTGTAAAATCTATTTTGG 58.225 34.615 10.26 4.38 40.00 3.28
922 3386 9.143631 GGTGAATTTGTTCCTATTTCTTTCATG 57.856 33.333 0.00 0.00 0.00 3.07
953 3418 6.156519 GGTTTGTGTGGGTCTGAATTTTATC 58.843 40.000 0.00 0.00 0.00 1.75
1072 3558 2.742372 GCGTGCATGGTCGGACTT 60.742 61.111 8.27 0.00 0.00 3.01
1121 3607 4.565850 GCCGAGGGGGAGGAGGAT 62.566 72.222 0.00 0.00 38.47 3.24
1354 3861 4.156455 ACCGAAAATACAGAGGCATGAT 57.844 40.909 0.00 0.00 0.00 2.45
1369 3876 9.051679 CATGACCAATTTACTATCATACCGAAA 57.948 33.333 0.00 0.00 0.00 3.46
1372 3879 6.934645 ACCATGACCAATTTACTATCATACCG 59.065 38.462 0.00 0.00 0.00 4.02
1379 3902 5.536161 GCCATCACCATGACCAATTTACTAT 59.464 40.000 0.00 0.00 30.57 2.12
1392 3915 2.133281 TCCAAGAAGCCATCACCATG 57.867 50.000 0.00 0.00 0.00 3.66
1411 3934 4.273235 TCGCGTGCATGATCTGAAAAATAT 59.727 37.500 10.93 0.00 0.00 1.28
1413 3936 2.419673 TCGCGTGCATGATCTGAAAAAT 59.580 40.909 10.93 0.00 0.00 1.82
1418 3941 0.102844 TGATCGCGTGCATGATCTGA 59.897 50.000 20.32 9.51 41.24 3.27
1504 4027 6.858993 TGTCTACAACAAGTCAACAACAAAAC 59.141 34.615 0.00 0.00 34.03 2.43
1505 4028 6.971602 TGTCTACAACAAGTCAACAACAAAA 58.028 32.000 0.00 0.00 34.03 2.44
1572 4109 1.199789 TGAGCAGCGCCATAAAACTTG 59.800 47.619 2.29 0.00 0.00 3.16
1593 4130 1.214062 GGACGGCTCTGACACTGAG 59.786 63.158 0.00 0.00 33.52 3.35
1594 4131 2.626780 CGGACGGCTCTGACACTGA 61.627 63.158 0.00 0.00 0.00 3.41
1595 4132 2.126307 CGGACGGCTCTGACACTG 60.126 66.667 0.00 0.00 0.00 3.66
1596 4133 3.374402 CCGGACGGCTCTGACACT 61.374 66.667 0.00 0.00 0.00 3.55
1609 4146 0.402504 ACAACATTTACCCAGCCGGA 59.597 50.000 5.05 0.00 34.64 5.14
1610 4147 0.808755 GACAACATTTACCCAGCCGG 59.191 55.000 0.00 0.00 37.81 6.13
1611 4148 1.821216 AGACAACATTTACCCAGCCG 58.179 50.000 0.00 0.00 0.00 5.52
1614 4151 4.789012 ATGCAAGACAACATTTACCCAG 57.211 40.909 0.00 0.00 0.00 4.45
1616 4153 4.021544 TCCAATGCAAGACAACATTTACCC 60.022 41.667 0.00 0.00 34.32 3.69
1655 4192 7.083858 TCATCGTTAAAAGCTTTGAAATCTGG 58.916 34.615 13.54 1.64 0.00 3.86
1692 4259 6.721318 ACTTGGAGCAATTCTTATAGTTCCA 58.279 36.000 0.00 0.00 0.00 3.53
1786 4357 1.317613 ACAGTCGCAAATTGCTCCAA 58.682 45.000 16.42 0.00 42.25 3.53
1910 4483 5.606505 TGTACATCTTGTGCACTCAGTTTA 58.393 37.500 19.41 0.13 38.04 2.01
1926 4500 7.387948 AGTTCTGGTGTTTATCAACTGTACATC 59.612 37.037 0.00 0.00 36.20 3.06
1937 4511 6.434340 AGGAATTCCAAGTTCTGGTGTTTATC 59.566 38.462 26.22 0.00 46.51 1.75
1940 4514 4.342092 CAGGAATTCCAAGTTCTGGTGTTT 59.658 41.667 26.22 0.00 46.51 2.83
1955 4529 7.409465 GGATACGTTCTAACATCAGGAATTC 57.591 40.000 0.00 0.00 0.00 2.17
1981 4555 4.584638 ACCAATGGCACCATAAGTTCTA 57.415 40.909 1.81 0.00 35.31 2.10
2008 4582 7.290110 TCAGATACTCTCACTTCACTCAAAA 57.710 36.000 0.00 0.00 0.00 2.44
2049 4625 6.998968 TGAAAAACAATGGAAACTGCATTT 57.001 29.167 0.00 0.00 36.23 2.32
2091 4667 0.674581 TGGTGCACTGCAGAGCATAC 60.675 55.000 35.68 29.96 43.06 2.39
2263 4839 7.731054 ACCCTAATTACAATCAGACAGAGATC 58.269 38.462 0.00 0.00 0.00 2.75
2354 4930 7.964604 ATAAGAACACTGTAACAAGGAAGAC 57.035 36.000 0.00 0.00 0.00 3.01
2718 6956 9.965824 GAATTCTGAAGACAAAGGAAAAATGTA 57.034 29.630 0.00 0.00 0.00 2.29
3139 7392 6.453922 GGTGTTCGACTCAGACGATAAAATTC 60.454 42.308 0.00 0.00 39.45 2.17
3651 8883 9.700831 GAGCCATATACCCTGGAAATAATAAAT 57.299 33.333 0.00 0.00 35.70 1.40
4176 9489 3.971245 ACCACTTCCTCATCTGAAGAC 57.029 47.619 6.99 0.00 41.38 3.01
4178 9491 2.746362 GCAACCACTTCCTCATCTGAAG 59.254 50.000 0.00 0.00 43.82 3.02
4380 9693 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4381 9694 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
4382 9695 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4383 9696 2.271777 ACTTATTTTGGGACGGAGGGA 58.728 47.619 0.00 0.00 0.00 4.20
4384 9697 2.801077 ACTTATTTTGGGACGGAGGG 57.199 50.000 0.00 0.00 0.00 4.30
4385 9698 5.163343 TGAGATACTTATTTTGGGACGGAGG 60.163 44.000 0.00 0.00 0.00 4.30
4386 9699 5.914033 TGAGATACTTATTTTGGGACGGAG 58.086 41.667 0.00 0.00 0.00 4.63
4387 9700 5.943349 TGAGATACTTATTTTGGGACGGA 57.057 39.130 0.00 0.00 0.00 4.69
4388 9701 6.113411 AGTTGAGATACTTATTTTGGGACGG 58.887 40.000 0.00 0.00 0.00 4.79
4389 9702 7.611213 AAGTTGAGATACTTATTTTGGGACG 57.389 36.000 0.00 0.00 36.62 4.79
4390 9703 8.793592 ACAAAGTTGAGATACTTATTTTGGGAC 58.206 33.333 0.00 0.00 37.37 4.46
4391 9704 8.934023 ACAAAGTTGAGATACTTATTTTGGGA 57.066 30.769 0.00 0.00 37.37 4.37
4404 9717 8.989980 GCACTAAAGTTAGTACAAAGTTGAGAT 58.010 33.333 3.46 0.00 41.82 2.75
4405 9718 7.982919 TGCACTAAAGTTAGTACAAAGTTGAGA 59.017 33.333 3.46 0.00 41.82 3.27
4406 9719 8.138365 TGCACTAAAGTTAGTACAAAGTTGAG 57.862 34.615 3.46 0.00 41.82 3.02
4407 9720 8.495361 TTGCACTAAAGTTAGTACAAAGTTGA 57.505 30.769 12.43 0.00 41.56 3.18
4423 9736 9.781633 TCAACCTTAATACTACTTTGCACTAAA 57.218 29.630 0.00 0.00 0.00 1.85
4424 9737 9.431887 CTCAACCTTAATACTACTTTGCACTAA 57.568 33.333 0.00 0.00 0.00 2.24
4425 9738 8.809066 TCTCAACCTTAATACTACTTTGCACTA 58.191 33.333 0.00 0.00 0.00 2.74
4426 9739 7.603024 GTCTCAACCTTAATACTACTTTGCACT 59.397 37.037 0.00 0.00 0.00 4.40
4427 9740 7.386848 TGTCTCAACCTTAATACTACTTTGCAC 59.613 37.037 0.00 0.00 0.00 4.57
4428 9741 7.386848 GTGTCTCAACCTTAATACTACTTTGCA 59.613 37.037 0.00 0.00 0.00 4.08
4429 9742 7.603024 AGTGTCTCAACCTTAATACTACTTTGC 59.397 37.037 0.00 0.00 0.00 3.68
4430 9743 9.490379 AAGTGTCTCAACCTTAATACTACTTTG 57.510 33.333 0.00 0.00 0.00 2.77
4438 9751 9.238368 CCCAAAATAAGTGTCTCAACCTTAATA 57.762 33.333 0.00 0.00 0.00 0.98
4439 9752 7.947890 TCCCAAAATAAGTGTCTCAACCTTAAT 59.052 33.333 0.00 0.00 0.00 1.40
4440 9753 7.229907 GTCCCAAAATAAGTGTCTCAACCTTAA 59.770 37.037 0.00 0.00 0.00 1.85
4441 9754 6.713450 GTCCCAAAATAAGTGTCTCAACCTTA 59.287 38.462 0.00 0.00 0.00 2.69
4442 9755 5.535030 GTCCCAAAATAAGTGTCTCAACCTT 59.465 40.000 0.00 0.00 0.00 3.50
4443 9756 5.070685 GTCCCAAAATAAGTGTCTCAACCT 58.929 41.667 0.00 0.00 0.00 3.50
4444 9757 4.083484 CGTCCCAAAATAAGTGTCTCAACC 60.083 45.833 0.00 0.00 0.00 3.77
4445 9758 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
4446 9759 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4447 9760 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
4448 9761 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
4449 9762 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
4450 9763 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
4451 9764 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
4452 9765 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4453 9766 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4454 9767 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4455 9768 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4456 9769 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4457 9770 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4458 9771 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
4459 9772 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
4460 9773 2.245546 TCTTATACTCCCTCCGTCCCAA 59.754 50.000 0.00 0.00 0.00 4.12
4461 9774 1.854939 TCTTATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37
4462 9775 2.671896 TCTTATACTCCCTCCGTCCC 57.328 55.000 0.00 0.00 0.00 4.46
4463 9776 3.190953 CGATTCTTATACTCCCTCCGTCC 59.809 52.174 0.00 0.00 0.00 4.79
4464 9777 4.070716 TCGATTCTTATACTCCCTCCGTC 58.929 47.826 0.00 0.00 0.00 4.79
4465 9778 4.096190 TCGATTCTTATACTCCCTCCGT 57.904 45.455 0.00 0.00 0.00 4.69
4466 9779 5.449107 TTTCGATTCTTATACTCCCTCCG 57.551 43.478 0.00 0.00 0.00 4.63
4467 9780 6.651225 CCAATTTCGATTCTTATACTCCCTCC 59.349 42.308 0.00 0.00 0.00 4.30
4468 9781 7.171678 CACCAATTTCGATTCTTATACTCCCTC 59.828 40.741 0.00 0.00 0.00 4.30
4469 9782 6.992715 CACCAATTTCGATTCTTATACTCCCT 59.007 38.462 0.00 0.00 0.00 4.20
4470 9783 6.204882 CCACCAATTTCGATTCTTATACTCCC 59.795 42.308 0.00 0.00 0.00 4.30
4471 9784 6.766467 ACCACCAATTTCGATTCTTATACTCC 59.234 38.462 0.00 0.00 0.00 3.85
4472 9785 7.254795 CCACCACCAATTTCGATTCTTATACTC 60.255 40.741 0.00 0.00 0.00 2.59
4473 9786 6.542370 CCACCACCAATTTCGATTCTTATACT 59.458 38.462 0.00 0.00 0.00 2.12
4474 9787 6.540914 TCCACCACCAATTTCGATTCTTATAC 59.459 38.462 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.