Multiple sequence alignment - TraesCS4A01G267400

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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 TraesCS4A01G267400 chr4A 100.000 4626 0 0 1 4626 579851633 579847008 0.000000e+00 8543
1 TraesCS4A01G267400 chr4D 96.998 3598 81 10 678 4268 22035224 22038801 0.000000e+00 6021
2 TraesCS4A01G267400 chr4D 90.421 689 44 10 1 681 22034521 22035195 0.000000e+00 887
3 TraesCS4A01G267400 chr4D 94.083 169 10 0 4354 4522 22038806 22038974 1.650000e-64 257
4 TraesCS4A01G267400 chr4D 91.509 106 4 1 4521 4626 22039048 22039148 1.740000e-29 141
5 TraesCS4A01G267400 chr4B 94.376 3627 151 10 679 4274 34052044 34055648 0.000000e+00 5518
6 TraesCS4A01G267400 chr4B 85.507 690 54 19 3 681 34051360 34052014 0.000000e+00 678
7 TraesCS4A01G267400 chr4B 92.899 169 12 0 4354 4522 34055645 34055813 3.570000e-61 246
8 TraesCS4A01G267400 chr4B 97.170 106 3 0 4521 4626 34055887 34055992 3.680000e-41 180
9 TraesCS4A01G267400 chr4B 94.624 93 4 1 4263 4355 568667428 568667519 4.820000e-30 143
10 TraesCS4A01G267400 chr7D 86.735 294 25 7 109 393 20342842 20343130 9.660000e-82 315
11 TraesCS4A01G267400 chr6B 86.532 297 21 7 109 393 542942679 542942968 4.500000e-80 309
12 TraesCS4A01G267400 chr6B 92.857 98 5 2 4266 4362 416897413 416897317 1.740000e-29 141
13 TraesCS4A01G267400 chr6A 86.195 297 22 6 109 393 265784331 265784042 2.090000e-78 303
14 TraesCS4A01G267400 chr6A 92.632 95 5 2 4265 4358 38475532 38475625 8.070000e-28 135
15 TraesCS4A01G267400 chr5A 90.991 111 9 1 284 393 162034254 162034144 1.040000e-31 148
16 TraesCS4A01G267400 chr3A 90.991 111 9 1 284 393 427381903 427381793 1.040000e-31 148
17 TraesCS4A01G267400 chr3D 97.619 84 2 0 4272 4355 411724428 411724345 1.340000e-30 145
18 TraesCS4A01G267400 chr5D 94.565 92 5 0 4272 4363 431293822 431293731 4.820000e-30 143
19 TraesCS4A01G267400 chr6D 94.505 91 5 0 4272 4362 85081785 85081875 1.740000e-29 141
20 TraesCS4A01G267400 chr1A 94.505 91 5 0 4265 4355 566298795 566298705 1.740000e-29 141
21 TraesCS4A01G267400 chr2D 91.837 98 7 1 4272 4368 15682983 15682886 8.070000e-28 135
22 TraesCS4A01G267400 chr2B 90.291 103 8 2 4272 4374 362021223 362021123 2.900000e-27 134


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 TraesCS4A01G267400 chr4A 579847008 579851633 4625 True 8543.0 8543 100.00000 1 4626 1 chr4A.!!$R1 4625
1 TraesCS4A01G267400 chr4D 22034521 22039148 4627 False 1826.5 6021 93.25275 1 4626 4 chr4D.!!$F1 4625
2 TraesCS4A01G267400 chr4B 34051360 34055992 4632 False 1655.5 5518 92.48800 3 4626 4 chr4B.!!$F2 4623

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
105 106 0.033011 GACTCAGGGAGGGAGCTGTA 60.033 60.000 0.00 0.00 35.79 2.74 F
531 548 0.096976 ATGCGATAAACTGTGCACGC 59.903 50.000 13.13 9.77 44.95 5.34 F
854 904 0.389757 GTCTCGTCTTATCCAGCCCC 59.610 60.000 0.00 0.00 0.00 5.80 F
1118 1168 0.530870 GAGATGGTACTGAAGGCCGC 60.531 60.000 0.00 0.00 0.00 6.53 F
1430 1480 1.460743 CAGCGCGTTGAAGATGAAGAA 59.539 47.619 18.92 0.00 0.00 2.52 F
3149 3206 0.122435 AAGGGACCATACCAGGGGAA 59.878 55.000 0.00 0.00 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 1158 0.393537 ATCTCTTTGGCGGCCTTCAG 60.394 55.000 21.46 12.86 0.00 3.02 R
1899 1949 0.527565 ATGTCCTGCAATGCCGTTTC 59.472 50.000 1.53 0.00 0.00 2.78 R
2501 2553 5.248640 TCCTCTTCTTGCTATCTTTTGTGG 58.751 41.667 0.00 0.00 0.00 4.17 R
2965 3018 1.078759 GTGGATCCGTTCAGTCAGCG 61.079 60.000 7.39 0.00 0.00 5.18 R
3412 3469 0.244721 TGAGAGACTGCACATCACGG 59.755 55.000 0.00 0.00 0.00 4.94 R
4035 4096 1.275856 GCTAGCCTCTATCTGCTGCAT 59.724 52.381 2.29 0.00 38.52 3.96 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
73 74 4.329801 CCGCCCTAAAATTGAATGCTTTTC 59.670 41.667 0.00 0.00 0.00 2.29
105 106 0.033011 GACTCAGGGAGGGAGCTGTA 60.033 60.000 0.00 0.00 35.79 2.74
179 185 1.124780 GTAAAGCCCTCCTCTCCTCC 58.875 60.000 0.00 0.00 0.00 4.30
189 195 0.187361 CCTCTCCTCCCCTCGATTCT 59.813 60.000 0.00 0.00 0.00 2.40
190 196 1.327303 CTCTCCTCCCCTCGATTCTG 58.673 60.000 0.00 0.00 0.00 3.02
191 197 0.631753 TCTCCTCCCCTCGATTCTGT 59.368 55.000 0.00 0.00 0.00 3.41
240 246 0.598562 GTCACAGCCGAGAAGAGACA 59.401 55.000 0.00 0.00 0.00 3.41
250 256 3.126171 CCGAGAAGAGACAGAGTACACTG 59.874 52.174 17.49 17.49 42.78 3.66
251 257 3.126171 CGAGAAGAGACAGAGTACACTGG 59.874 52.174 22.00 6.71 41.59 4.00
252 258 4.328536 GAGAAGAGACAGAGTACACTGGA 58.671 47.826 22.00 0.00 41.59 3.86
253 259 4.730966 AGAAGAGACAGAGTACACTGGAA 58.269 43.478 22.00 0.00 41.59 3.53
254 260 5.141182 AGAAGAGACAGAGTACACTGGAAA 58.859 41.667 22.00 0.00 41.59 3.13
255 261 5.777732 AGAAGAGACAGAGTACACTGGAAAT 59.222 40.000 22.00 3.34 41.59 2.17
256 262 5.398603 AGAGACAGAGTACACTGGAAATG 57.601 43.478 22.00 0.00 41.59 2.32
274 280 6.381420 TGGAAATGTAGTTGGTTTCCTTTTCA 59.619 34.615 14.87 0.00 46.94 2.69
356 369 5.763204 TGGAGACTTTGGTTTCTGTAATGTC 59.237 40.000 0.00 0.00 0.00 3.06
362 375 9.665264 GACTTTGGTTTCTGTAATGTCTTTTAG 57.335 33.333 0.00 0.00 0.00 1.85
363 376 8.630037 ACTTTGGTTTCTGTAATGTCTTTTAGG 58.370 33.333 0.00 0.00 0.00 2.69
392 409 4.387026 AAATGTGATCTTGGACAAGGGA 57.613 40.909 11.76 0.00 38.88 4.20
454 471 4.122776 CCATGTCTAGTGATGGTTAGCAC 58.877 47.826 12.24 0.00 43.37 4.40
469 486 4.630505 GGTTAGCACCTTAGCAGTCTTTAC 59.369 45.833 0.00 0.00 40.44 2.01
482 499 4.773510 CAGTCTTTACTTTGAAACCGCTC 58.226 43.478 0.00 0.00 31.97 5.03
483 500 4.511826 CAGTCTTTACTTTGAAACCGCTCT 59.488 41.667 0.00 0.00 31.97 4.09
523 540 2.389713 GCGATTGCATGCGATAAACT 57.610 45.000 20.60 0.00 42.15 2.66
531 548 0.096976 ATGCGATAAACTGTGCACGC 59.903 50.000 13.13 9.77 44.95 5.34
533 550 1.951181 GCGATAAACTGTGCACGCGA 61.951 55.000 15.93 0.00 37.06 5.87
553 570 2.631160 TTTTGACATCTGTGGGACGT 57.369 45.000 0.00 0.00 0.00 4.34
565 582 1.067354 GTGGGACGTCGTAAATGGTCT 60.067 52.381 9.92 0.00 0.00 3.85
583 600 3.188667 GGTCTGTTGGATCGAAAAAGGTC 59.811 47.826 0.00 0.00 0.00 3.85
591 608 2.748461 TCGAAAAAGGTCGCAGTTTG 57.252 45.000 0.00 0.00 40.88 2.93
598 615 1.217882 AGGTCGCAGTTTGTCTTTCG 58.782 50.000 0.00 0.00 0.00 3.46
599 616 1.202486 AGGTCGCAGTTTGTCTTTCGA 60.202 47.619 0.00 0.00 0.00 3.71
607 624 5.679355 CGCAGTTTGTCTTTCGATTTAAACA 59.321 36.000 0.00 0.41 32.17 2.83
617 634 8.482429 GTCTTTCGATTTAAACACGTTCTAGAA 58.518 33.333 0.00 0.00 0.00 2.10
629 646 8.886816 AACACGTTCTAGAACTTATACTAACG 57.113 34.615 28.30 16.85 39.08 3.18
630 647 8.256611 ACACGTTCTAGAACTTATACTAACGA 57.743 34.615 28.30 0.00 39.08 3.85
632 649 9.713740 CACGTTCTAGAACTTATACTAACGAAT 57.286 33.333 28.30 0.00 39.08 3.34
633 650 9.713740 ACGTTCTAGAACTTATACTAACGAATG 57.286 33.333 28.30 12.53 39.08 2.67
634 651 9.713740 CGTTCTAGAACTTATACTAACGAATGT 57.286 33.333 28.30 0.00 39.08 2.71
656 674 7.561021 TGTGTCTGTGCTAATTTCTTGTTTA 57.439 32.000 0.00 0.00 0.00 2.01
798 848 5.758296 GGACTTGGTTAGCGATAATGATGAA 59.242 40.000 0.00 0.00 0.00 2.57
814 864 7.812690 AATGATGAATTCGAATTGGATGAGA 57.187 32.000 27.27 5.68 0.00 3.27
828 878 4.264253 TGGATGAGAACAATGATGGTCAC 58.736 43.478 0.00 0.00 46.21 3.67
854 904 0.389757 GTCTCGTCTTATCCAGCCCC 59.610 60.000 0.00 0.00 0.00 5.80
862 912 1.209504 CTTATCCAGCCCCGAGAAACA 59.790 52.381 0.00 0.00 0.00 2.83
921 971 5.046520 GGTAAGTGATAGAAGTGGGTGTCTT 60.047 44.000 0.00 0.00 0.00 3.01
922 972 5.568620 AAGTGATAGAAGTGGGTGTCTTT 57.431 39.130 0.00 0.00 0.00 2.52
923 973 6.681729 AAGTGATAGAAGTGGGTGTCTTTA 57.318 37.500 0.00 0.00 0.00 1.85
924 974 6.681729 AGTGATAGAAGTGGGTGTCTTTAA 57.318 37.500 0.00 0.00 0.00 1.52
972 1022 5.008019 AGTCATTGCTCGCATAAGGTTATTG 59.992 40.000 0.00 0.00 0.00 1.90
978 1028 4.798387 GCTCGCATAAGGTTATTGTTTTGG 59.202 41.667 0.00 0.00 0.00 3.28
1066 1116 1.066858 CAGCTCCTTCTGCCTCGTTAA 60.067 52.381 0.00 0.00 0.00 2.01
1108 1158 3.268330 GGTTTCCCGAAAGAGATGGTAC 58.732 50.000 0.00 0.00 0.00 3.34
1118 1168 0.530870 GAGATGGTACTGAAGGCCGC 60.531 60.000 0.00 0.00 0.00 6.53
1331 1381 1.815421 CTTCATGGCGGGAAGGACG 60.815 63.158 9.39 0.00 38.44 4.79
1430 1480 1.460743 CAGCGCGTTGAAGATGAAGAA 59.539 47.619 18.92 0.00 0.00 2.52
1529 1579 4.499183 CTTACTCTGATGGTTCTGGTGAC 58.501 47.826 0.00 0.00 0.00 3.67
1569 1619 2.105134 TCTTCAGCTTGGTAACCGGAAA 59.895 45.455 9.46 0.00 0.00 3.13
2267 2319 9.956720 CTTTGTTGATCATACTTTAATGGGATC 57.043 33.333 0.00 0.00 33.52 3.36
2381 2433 4.361451 CCATGAGGTACATTGCAGTTTC 57.639 45.455 0.00 0.00 37.07 2.78
2501 2553 3.441922 GTGGGGAGAAAGAAAGCAAGATC 59.558 47.826 0.00 0.00 0.00 2.75
2506 2558 4.520492 GGAGAAAGAAAGCAAGATCCACAA 59.480 41.667 0.00 0.00 0.00 3.33
2953 3006 5.095490 GCTCAATTGCCTACAAACATGTAC 58.905 41.667 0.00 0.00 39.77 2.90
2965 3018 1.511887 CATGTACGGCAAGCGCAAC 60.512 57.895 11.47 0.00 41.24 4.17
3047 3100 6.003326 TGTTCAGAAATATGTGCTGGAAGAA 58.997 36.000 0.00 0.00 34.07 2.52
3079 3132 3.705579 TGGAATTTGGTATGGATTGGCAG 59.294 43.478 0.00 0.00 0.00 4.85
3119 3176 4.292186 TCTCTGGAAATGGAGTTTCTGG 57.708 45.455 1.17 0.00 44.54 3.86
3149 3206 0.122435 AAGGGACCATACCAGGGGAA 59.878 55.000 0.00 0.00 0.00 3.97
3169 3226 5.641636 GGGAACTAGCAAGAAAAAGAGAGAG 59.358 44.000 0.00 0.00 0.00 3.20
3412 3469 3.196685 AGGAAGGCACACTGATAGAGTTC 59.803 47.826 0.00 0.00 29.75 3.01
3514 3571 1.203050 AGCCCATGTAACAACCTTGCT 60.203 47.619 0.00 0.00 0.00 3.91
3580 3637 3.121126 CCGTGTTGTTTCGTGACTATGTC 60.121 47.826 0.00 0.00 0.00 3.06
3598 3655 8.354711 ACTATGTCAGAATCTTGAACTCTGTA 57.645 34.615 10.73 5.09 38.20 2.74
3613 3670 5.339008 ACTCTGTAAAGTCGATTATGGCA 57.661 39.130 0.00 0.00 0.00 4.92
3638 3695 4.067192 TGTAGGATGATGATTGCATTCCG 58.933 43.478 6.16 0.00 36.79 4.30
3756 3813 5.596836 AAATTTGGAGCTCTGTGTTTGAA 57.403 34.783 14.64 0.00 0.00 2.69
3781 3838 8.678593 AGCTTATAACTATTTTCTTACCTGCC 57.321 34.615 0.00 0.00 0.00 4.85
3838 3895 7.475015 TGACAGAGAAGAAACTTGTTTTGATG 58.525 34.615 0.06 0.00 0.00 3.07
3867 3928 9.844790 TGTGAATACTGAATTTATTGCTTTCTG 57.155 29.630 0.00 0.00 0.00 3.02
3872 3933 9.941664 ATACTGAATTTATTGCTTTCTGATTCG 57.058 29.630 0.00 0.00 0.00 3.34
3873 3934 7.820648 ACTGAATTTATTGCTTTCTGATTCGT 58.179 30.769 0.00 0.00 0.00 3.85
3874 3935 8.299570 ACTGAATTTATTGCTTTCTGATTCGTT 58.700 29.630 0.00 0.00 0.00 3.85
3997 4058 1.202394 TGCAAAGTCAAAGTGCGCATT 60.202 42.857 15.91 6.43 41.27 3.56
4035 4096 3.115390 AGCTTTAGGGCAAGGACTCATA 58.885 45.455 0.00 0.00 34.17 2.15
4039 4100 1.216064 AGGGCAAGGACTCATATGCA 58.784 50.000 0.00 0.00 40.51 3.96
4167 4252 3.157087 TCTTGCATTTGTTCTCCTTCCC 58.843 45.455 0.00 0.00 0.00 3.97
4168 4253 2.673775 TGCATTTGTTCTCCTTCCCA 57.326 45.000 0.00 0.00 0.00 4.37
4270 4357 2.417719 AGCTTTCGTGGAAGACATGTC 58.582 47.619 18.47 18.47 37.38 3.06
4273 4360 3.393800 CTTTCGTGGAAGACATGTCACT 58.606 45.455 27.02 13.98 37.38 3.41
4274 4361 2.724977 TCGTGGAAGACATGTCACTC 57.275 50.000 27.02 20.86 37.38 3.51
4275 4362 1.272490 TCGTGGAAGACATGTCACTCC 59.728 52.381 27.98 27.98 37.38 3.85
4276 4363 1.673033 CGTGGAAGACATGTCACTCCC 60.673 57.143 29.92 22.69 34.67 4.30
4277 4364 1.625818 GTGGAAGACATGTCACTCCCT 59.374 52.381 29.92 10.07 34.67 4.20
4278 4365 1.902508 TGGAAGACATGTCACTCCCTC 59.097 52.381 29.92 16.68 34.67 4.30
4279 4366 1.208293 GGAAGACATGTCACTCCCTCC 59.792 57.143 27.02 16.91 31.42 4.30
4280 4367 0.898320 AAGACATGTCACTCCCTCCG 59.102 55.000 27.02 0.00 0.00 4.63
4281 4368 0.251832 AGACATGTCACTCCCTCCGT 60.252 55.000 27.02 0.00 0.00 4.69
4282 4369 0.173708 GACATGTCACTCCCTCCGTC 59.826 60.000 21.07 0.00 0.00 4.79
4283 4370 1.258445 ACATGTCACTCCCTCCGTCC 61.258 60.000 0.00 0.00 0.00 4.79
4284 4371 1.686110 ATGTCACTCCCTCCGTCCC 60.686 63.158 0.00 0.00 0.00 4.46
4285 4372 2.283676 GTCACTCCCTCCGTCCCA 60.284 66.667 0.00 0.00 0.00 4.37
4286 4373 1.686110 GTCACTCCCTCCGTCCCAT 60.686 63.158 0.00 0.00 0.00 4.00
4287 4374 0.396695 GTCACTCCCTCCGTCCCATA 60.397 60.000 0.00 0.00 0.00 2.74
4288 4375 0.337082 TCACTCCCTCCGTCCCATAA 59.663 55.000 0.00 0.00 0.00 1.90
4289 4376 1.062428 TCACTCCCTCCGTCCCATAAT 60.062 52.381 0.00 0.00 0.00 1.28
4290 4377 2.178325 TCACTCCCTCCGTCCCATAATA 59.822 50.000 0.00 0.00 0.00 0.98
4291 4378 3.173965 CACTCCCTCCGTCCCATAATAT 58.826 50.000 0.00 0.00 0.00 1.28
4292 4379 3.055819 CACTCCCTCCGTCCCATAATATG 60.056 52.174 0.00 0.00 0.00 1.78
4293 4380 3.181410 ACTCCCTCCGTCCCATAATATGA 60.181 47.826 1.10 0.00 0.00 2.15
4294 4381 3.441101 TCCCTCCGTCCCATAATATGAG 58.559 50.000 1.10 0.00 0.00 2.90
4295 4382 3.076937 TCCCTCCGTCCCATAATATGAGA 59.923 47.826 1.10 0.00 0.00 3.27
4296 4383 3.449018 CCCTCCGTCCCATAATATGAGAG 59.551 52.174 1.10 0.73 0.00 3.20
4297 4384 4.090090 CCTCCGTCCCATAATATGAGAGT 58.910 47.826 1.10 0.00 0.00 3.24
4298 4385 4.081972 CCTCCGTCCCATAATATGAGAGTG 60.082 50.000 1.10 0.00 0.00 3.51
4299 4386 4.480115 TCCGTCCCATAATATGAGAGTGT 58.520 43.478 1.10 0.00 0.00 3.55
4300 4387 4.899457 TCCGTCCCATAATATGAGAGTGTT 59.101 41.667 1.10 0.00 0.00 3.32
4301 4388 5.365605 TCCGTCCCATAATATGAGAGTGTTT 59.634 40.000 1.10 0.00 0.00 2.83
4302 4389 6.055588 CCGTCCCATAATATGAGAGTGTTTT 58.944 40.000 1.10 0.00 0.00 2.43
4303 4390 6.542370 CCGTCCCATAATATGAGAGTGTTTTT 59.458 38.462 1.10 0.00 0.00 1.94
4304 4391 7.409697 CGTCCCATAATATGAGAGTGTTTTTG 58.590 38.462 1.10 0.00 0.00 2.44
4305 4392 7.279981 CGTCCCATAATATGAGAGTGTTTTTGA 59.720 37.037 1.10 0.00 0.00 2.69
4306 4393 8.398665 GTCCCATAATATGAGAGTGTTTTTGAC 58.601 37.037 1.10 0.00 0.00 3.18
4307 4394 8.106462 TCCCATAATATGAGAGTGTTTTTGACA 58.894 33.333 1.10 0.00 35.42 3.58
4308 4395 8.400947 CCCATAATATGAGAGTGTTTTTGACAG 58.599 37.037 1.10 0.00 39.39 3.51
4309 4396 8.950210 CCATAATATGAGAGTGTTTTTGACAGT 58.050 33.333 1.10 0.00 44.58 3.55
4313 4400 6.851222 ATGAGAGTGTTTTTGACAGTAGTG 57.149 37.500 0.00 0.00 41.98 2.74
4314 4401 5.730550 TGAGAGTGTTTTTGACAGTAGTGT 58.269 37.500 1.90 1.90 41.98 3.55
4315 4402 6.869695 TGAGAGTGTTTTTGACAGTAGTGTA 58.130 36.000 2.39 0.00 41.98 2.90
4316 4403 6.978659 TGAGAGTGTTTTTGACAGTAGTGTAG 59.021 38.462 2.39 0.00 41.98 2.74
4317 4404 6.875076 AGAGTGTTTTTGACAGTAGTGTAGT 58.125 36.000 2.39 0.00 41.98 2.73
4318 4405 6.757010 AGAGTGTTTTTGACAGTAGTGTAGTG 59.243 38.462 2.39 0.00 41.98 2.74
4319 4406 6.403878 AGTGTTTTTGACAGTAGTGTAGTGT 58.596 36.000 2.39 0.00 44.60 3.55
4320 4407 7.549839 AGTGTTTTTGACAGTAGTGTAGTGTA 58.450 34.615 2.39 0.00 42.13 2.90
4321 4408 8.036575 AGTGTTTTTGACAGTAGTGTAGTGTAA 58.963 33.333 2.39 0.00 42.13 2.41
4322 4409 8.658609 GTGTTTTTGACAGTAGTGTAGTGTAAA 58.341 33.333 2.39 0.00 42.13 2.01
4323 4410 9.217278 TGTTTTTGACAGTAGTGTAGTGTAAAA 57.783 29.630 2.39 4.63 42.13 1.52
4345 4432 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
4346 4433 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
4347 4434 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
4348 4435 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
4349 4436 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
4350 4437 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
4351 4438 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
4352 4439 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4353 4440 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4354 4441 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4355 4442 2.852714 TTATGGGACGGAGGGAGTAA 57.147 50.000 0.00 0.00 0.00 2.24
4408 4495 4.082026 AGGTGCAGATTTTGGTGCTATTTC 60.082 41.667 0.00 0.00 40.54 2.17
4413 4500 6.380846 TGCAGATTTTGGTGCTATTTCCTTAT 59.619 34.615 0.00 0.00 40.54 1.73
4460 4547 4.795795 CGATGTCTGCTTACTAGTCTGTTG 59.204 45.833 0.00 0.00 0.00 3.33
4472 4559 4.528596 ACTAGTCTGTTGTTGTAGATGGCT 59.471 41.667 0.00 0.00 0.00 4.75
4526 4688 5.633830 TGGAATTCAGTCAAGCAAATCTC 57.366 39.130 7.93 0.00 0.00 2.75
4569 4731 5.942826 TGCATACACCTGTCAATCAAATGTA 59.057 36.000 0.00 0.00 33.73 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 0.694444 ATCACCCGGCCAAGTCCTAT 60.694 55.000 2.24 0.00 0.00 2.57
179 185 4.615949 CAGAACATCTACAGAATCGAGGG 58.384 47.826 0.00 0.00 0.00 4.30
189 195 4.565022 TCGTTTCATGCAGAACATCTACA 58.435 39.130 9.97 0.00 36.64 2.74
190 196 5.725110 ATCGTTTCATGCAGAACATCTAC 57.275 39.130 9.97 1.46 36.64 2.59
191 197 6.108687 AGAATCGTTTCATGCAGAACATCTA 58.891 36.000 8.83 0.00 36.64 1.98
240 246 5.307196 ACCAACTACATTTCCAGTGTACTCT 59.693 40.000 0.00 0.00 0.00 3.24
251 257 8.141268 TGATGAAAAGGAAACCAACTACATTTC 58.859 33.333 0.00 0.00 0.00 2.17
252 258 8.017418 TGATGAAAAGGAAACCAACTACATTT 57.983 30.769 0.00 0.00 0.00 2.32
253 259 7.595819 TGATGAAAAGGAAACCAACTACATT 57.404 32.000 0.00 0.00 0.00 2.71
254 260 7.233348 ACATGATGAAAAGGAAACCAACTACAT 59.767 33.333 0.00 0.00 0.00 2.29
255 261 6.549364 ACATGATGAAAAGGAAACCAACTACA 59.451 34.615 0.00 0.00 0.00 2.74
256 262 6.981722 ACATGATGAAAAGGAAACCAACTAC 58.018 36.000 0.00 0.00 0.00 2.73
274 280 4.141642 TGGCAGCACATCTAACTACATGAT 60.142 41.667 0.00 0.00 0.00 2.45
356 369 7.373493 AGATCACATTTTGCAACTCCTAAAAG 58.627 34.615 0.00 0.00 0.00 2.27
362 375 4.022068 TCCAAGATCACATTTTGCAACTCC 60.022 41.667 0.00 0.00 0.00 3.85
363 376 4.919754 GTCCAAGATCACATTTTGCAACTC 59.080 41.667 0.00 0.00 0.00 3.01
392 409 5.063817 GCCGCATTTAAGAATGAATTTGCTT 59.936 36.000 3.47 0.00 44.37 3.91
454 471 6.565999 CGGTTTCAAAGTAAAGACTGCTAAGG 60.566 42.308 0.00 0.00 35.52 2.69
469 486 1.069906 CCGTCAAGAGCGGTTTCAAAG 60.070 52.381 0.00 0.00 43.84 2.77
482 499 1.134401 ACCATAGCATCCACCGTCAAG 60.134 52.381 0.00 0.00 0.00 3.02
483 500 0.908910 ACCATAGCATCCACCGTCAA 59.091 50.000 0.00 0.00 0.00 3.18
489 506 1.597742 ATCGCAACCATAGCATCCAC 58.402 50.000 0.00 0.00 0.00 4.02
492 509 2.042104 GCAATCGCAACCATAGCATC 57.958 50.000 0.00 0.00 38.36 3.91
523 540 0.590682 ATGTCAAAATCGCGTGCACA 59.409 45.000 18.64 0.00 0.00 4.57
531 548 2.094258 CGTCCCACAGATGTCAAAATCG 59.906 50.000 0.00 0.00 0.00 3.34
533 550 3.140325 ACGTCCCACAGATGTCAAAAT 57.860 42.857 0.00 0.00 40.99 1.82
553 570 3.193903 TCGATCCAACAGACCATTTACGA 59.806 43.478 0.00 0.00 0.00 3.43
565 582 1.533731 GCGACCTTTTTCGATCCAACA 59.466 47.619 0.00 0.00 41.78 3.33
583 600 5.679355 TGTTTAAATCGAAAGACAAACTGCG 59.321 36.000 0.00 0.00 46.97 5.18
591 608 8.000285 TCTAGAACGTGTTTAAATCGAAAGAC 58.000 34.615 17.88 0.00 46.97 3.01
607 624 9.713740 CATTCGTTAGTATAAGTTCTAGAACGT 57.286 33.333 25.92 25.06 45.50 3.99
617 634 6.530534 GCACAGACACATTCGTTAGTATAAGT 59.469 38.462 0.00 0.00 0.00 2.24
628 645 5.536554 AGAAATTAGCACAGACACATTCG 57.463 39.130 0.00 0.00 0.00 3.34
629 646 6.672147 ACAAGAAATTAGCACAGACACATTC 58.328 36.000 0.00 0.00 0.00 2.67
630 647 6.639632 ACAAGAAATTAGCACAGACACATT 57.360 33.333 0.00 0.00 0.00 2.71
632 649 6.449635 AAACAAGAAATTAGCACAGACACA 57.550 33.333 0.00 0.00 0.00 3.72
633 650 7.591426 CCTTAAACAAGAAATTAGCACAGACAC 59.409 37.037 0.00 0.00 0.00 3.67
634 651 7.648142 CCTTAAACAAGAAATTAGCACAGACA 58.352 34.615 0.00 0.00 0.00 3.41
635 652 6.582672 GCCTTAAACAAGAAATTAGCACAGAC 59.417 38.462 0.00 0.00 0.00 3.51
636 653 6.490040 AGCCTTAAACAAGAAATTAGCACAGA 59.510 34.615 0.00 0.00 0.00 3.41
656 674 1.160137 GACATCGCAAGTGAAGCCTT 58.840 50.000 0.00 0.00 39.48 4.35
798 848 7.423199 CATCATTGTTCTCATCCAATTCGAAT 58.577 34.615 4.39 4.39 0.00 3.34
814 864 1.885887 CCCAACGTGACCATCATTGTT 59.114 47.619 0.00 0.00 31.11 2.83
828 878 1.202382 GGATAAGACGAGACCCCAACG 60.202 57.143 0.00 0.00 0.00 4.10
854 904 1.998315 CAGGAGCATCAGTGTTTCTCG 59.002 52.381 0.00 0.00 36.25 4.04
862 912 3.790437 CGGGCCAGGAGCATCAGT 61.790 66.667 4.39 0.00 46.50 3.41
921 971 6.384258 TCTTGTGCACTTGTGCTTAATTAA 57.616 33.333 23.53 0.00 35.49 1.40
922 972 5.562696 GCTCTTGTGCACTTGTGCTTAATTA 60.563 40.000 23.53 2.57 35.49 1.40
923 973 4.794003 GCTCTTGTGCACTTGTGCTTAATT 60.794 41.667 23.53 0.00 35.49 1.40
924 974 3.304928 GCTCTTGTGCACTTGTGCTTAAT 60.305 43.478 23.53 0.00 35.49 1.40
1009 1059 3.068732 CCATCAGCGTCCTTTAGATCAGA 59.931 47.826 0.00 0.00 0.00 3.27
1066 1116 6.279813 ACCCATTTCTACATACATCCCAAT 57.720 37.500 0.00 0.00 0.00 3.16
1108 1158 0.393537 ATCTCTTTGGCGGCCTTCAG 60.394 55.000 21.46 12.86 0.00 3.02
1147 1197 7.713734 ATGAAATGATCAAATGGAACTGACT 57.286 32.000 0.00 0.00 42.54 3.41
1148 1198 7.219535 CGAATGAAATGATCAAATGGAACTGAC 59.780 37.037 0.00 0.00 42.54 3.51
1149 1199 7.094248 ACGAATGAAATGATCAAATGGAACTGA 60.094 33.333 0.00 0.00 42.54 3.41
1331 1381 6.811253 TCACACAACCAATCTTAACATACC 57.189 37.500 0.00 0.00 0.00 2.73
1430 1480 7.550196 GCATCATCTTCTTCTTCTTCTTCTTCT 59.450 37.037 0.00 0.00 0.00 2.85
1529 1579 8.231837 GCTGAAGATAAGTAAGTATCTACCTCG 58.768 40.741 0.00 0.00 39.44 4.63
1899 1949 0.527565 ATGTCCTGCAATGCCGTTTC 59.472 50.000 1.53 0.00 0.00 2.78
2267 2319 8.832521 TGAACCAAATATAAAGCATAAGGTACG 58.167 33.333 0.00 0.00 0.00 3.67
2408 2460 8.400947 CAGTGTCAATCCATCGAAATTAAGAAT 58.599 33.333 0.00 0.00 0.00 2.40
2501 2553 5.248640 TCCTCTTCTTGCTATCTTTTGTGG 58.751 41.667 0.00 0.00 0.00 4.17
2506 2558 9.389755 GTATCTTTTCCTCTTCTTGCTATCTTT 57.610 33.333 0.00 0.00 0.00 2.52
2965 3018 1.078759 GTGGATCCGTTCAGTCAGCG 61.079 60.000 7.39 0.00 0.00 5.18
3047 3100 2.893424 ACCAAATTCCACTTCCTGCAT 58.107 42.857 0.00 0.00 0.00 3.96
3079 3132 5.045872 AGAGAAATGCAGCAACTTTGTTTC 58.954 37.500 0.00 3.88 0.00 2.78
3149 3206 7.094848 GCATTTCTCTCTCTTTTTCTTGCTAGT 60.095 37.037 0.00 0.00 0.00 2.57
3360 3417 1.815003 CCCACCAAGTTCTCAAGATGC 59.185 52.381 0.00 0.00 0.00 3.91
3412 3469 0.244721 TGAGAGACTGCACATCACGG 59.755 55.000 0.00 0.00 0.00 4.94
3580 3637 6.863645 TCGACTTTACAGAGTTCAAGATTCTG 59.136 38.462 9.31 9.31 43.04 3.02
3598 3655 6.119536 TCCTACATTTGCCATAATCGACTTT 58.880 36.000 0.00 0.00 0.00 2.66
3613 3670 6.294342 CGGAATGCAATCATCATCCTACATTT 60.294 38.462 3.77 0.00 30.72 2.32
3638 3695 8.522542 TCTAAGGATAAGGACTAGAAGAACAC 57.477 38.462 0.00 0.00 0.00 3.32
3756 3813 7.441458 CGGCAGGTAAGAAAATAGTTATAAGCT 59.559 37.037 0.00 0.00 0.00 3.74
3772 3829 0.394352 AATGAAGGCCGGCAGGTAAG 60.394 55.000 30.85 0.00 40.50 2.34
3781 3838 1.098050 CTTCTCCCAAATGAAGGCCG 58.902 55.000 0.00 0.00 36.84 6.13
3871 3932 7.533900 CCACAAGTGTAGAATGAAAATACAACG 59.466 37.037 0.00 0.00 31.61 4.10
3872 3933 7.807907 CCCACAAGTGTAGAATGAAAATACAAC 59.192 37.037 0.00 0.00 31.61 3.32
3873 3934 7.504238 ACCCACAAGTGTAGAATGAAAATACAA 59.496 33.333 0.00 0.00 31.61 2.41
3874 3935 7.001674 ACCCACAAGTGTAGAATGAAAATACA 58.998 34.615 0.00 0.00 0.00 2.29
3997 4058 5.489792 AAAGCTCTGAGATGTACCTTTCA 57.510 39.130 9.28 0.00 0.00 2.69
4035 4096 1.275856 GCTAGCCTCTATCTGCTGCAT 59.724 52.381 2.29 0.00 38.52 3.96
4039 4100 3.420893 CAGTAGCTAGCCTCTATCTGCT 58.579 50.000 12.13 0.00 41.57 4.24
4270 4357 1.424638 ATTATGGGACGGAGGGAGTG 58.575 55.000 0.00 0.00 0.00 3.51
4273 4360 3.076937 TCTCATATTATGGGACGGAGGGA 59.923 47.826 1.94 0.00 34.11 4.20
4274 4361 3.441101 TCTCATATTATGGGACGGAGGG 58.559 50.000 1.94 0.00 34.11 4.30
4275 4362 4.081972 CACTCTCATATTATGGGACGGAGG 60.082 50.000 1.94 0.00 34.11 4.30
4276 4363 4.524714 ACACTCTCATATTATGGGACGGAG 59.475 45.833 1.94 6.21 34.11 4.63
4277 4364 4.480115 ACACTCTCATATTATGGGACGGA 58.520 43.478 1.94 0.00 34.11 4.69
4278 4365 4.873746 ACACTCTCATATTATGGGACGG 57.126 45.455 1.94 1.00 34.11 4.79
4279 4366 7.279981 TCAAAAACACTCTCATATTATGGGACG 59.720 37.037 1.94 2.61 34.11 4.79
4280 4367 8.398665 GTCAAAAACACTCTCATATTATGGGAC 58.601 37.037 1.94 0.00 34.11 4.46
4281 4368 8.106462 TGTCAAAAACACTCTCATATTATGGGA 58.894 33.333 6.10 6.10 33.65 4.37
4282 4369 8.279970 TGTCAAAAACACTCTCATATTATGGG 57.720 34.615 3.89 0.31 31.20 4.00
4283 4370 8.950210 ACTGTCAAAAACACTCTCATATTATGG 58.050 33.333 3.89 0.00 33.24 2.74
4287 4374 8.993121 CACTACTGTCAAAAACACTCTCATATT 58.007 33.333 0.00 0.00 33.24 1.28
4288 4375 8.150945 ACACTACTGTCAAAAACACTCTCATAT 58.849 33.333 0.00 0.00 33.24 1.78
4289 4376 7.497595 ACACTACTGTCAAAAACACTCTCATA 58.502 34.615 0.00 0.00 33.24 2.15
4290 4377 6.349300 ACACTACTGTCAAAAACACTCTCAT 58.651 36.000 0.00 0.00 33.24 2.90
4291 4378 5.730550 ACACTACTGTCAAAAACACTCTCA 58.269 37.500 0.00 0.00 33.24 3.27
4292 4379 6.979238 ACTACACTACTGTCAAAAACACTCTC 59.021 38.462 0.00 0.00 33.24 3.20
4293 4380 6.757010 CACTACACTACTGTCAAAAACACTCT 59.243 38.462 0.00 0.00 33.24 3.24
4294 4381 6.534079 ACACTACACTACTGTCAAAAACACTC 59.466 38.462 0.00 0.00 33.24 3.51
4295 4382 6.403878 ACACTACACTACTGTCAAAAACACT 58.596 36.000 0.00 0.00 33.24 3.55
4296 4383 6.657836 ACACTACACTACTGTCAAAAACAC 57.342 37.500 0.00 0.00 33.24 3.32
4297 4384 8.774890 TTTACACTACACTACTGTCAAAAACA 57.225 30.769 0.00 0.00 36.18 2.83
4321 4408 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
4322 4409 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
4323 4410 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
4324 4411 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
4325 4412 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
4326 4413 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4327 4414 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4328 4415 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4329 4416 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4330 4417 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4331 4418 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4332 4419 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4333 4420 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4334 4421 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
4335 4422 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
4336 4423 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
4337 4424 3.659195 TCTATTACTCCCTCCGTCCCATA 59.341 47.826 0.00 0.00 0.00 2.74
4338 4425 2.449730 TCTATTACTCCCTCCGTCCCAT 59.550 50.000 0.00 0.00 0.00 4.00
4339 4426 1.854939 TCTATTACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37
4340 4427 2.671896 TCTATTACTCCCTCCGTCCC 57.328 55.000 0.00 0.00 0.00 4.46
4341 4428 6.854091 AAATATCTATTACTCCCTCCGTCC 57.146 41.667 0.00 0.00 0.00 4.79
4355 4442 9.882996 CATGAACGTGCACATAAAAATATCTAT 57.117 29.630 18.64 0.00 0.00 1.98
4460 4547 4.473477 AGGTTACTGAGCCATCTACAAC 57.527 45.455 0.00 0.00 0.00 3.32
4472 4559 7.997773 AGTATAAGCGATGATAGGTTACTGA 57.002 36.000 0.00 0.00 34.90 3.41
4526 4688 5.242069 TGCATATAACCACGGTGATTTTG 57.758 39.130 10.28 0.00 0.00 2.44
4569 4731 8.109634 ACAGTGGTATTCATTTGTCCTTCTATT 58.890 33.333 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.