Multiple sequence alignment - TraesCS5B01G407300

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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 TraesCS5B01G407300 chr5B 100.000 4061 0 0 781 4841 583175940 583180000 0.000000e+00 7500.0
1 TraesCS5B01G407300 chr5B 100.000 365 0 0 1 365 583175160 583175524 0.000000e+00 675.0
2 TraesCS5B01G407300 chr5A 96.393 3965 106 21 781 4740 595143929 595147861 0.000000e+00 6495.0
3 TraesCS5B01G407300 chr5A 87.838 370 20 11 1 365 595143484 595143833 1.250000e-110 411.0
4 TraesCS5B01G407300 chr5A 76.309 802 155 24 1456 2247 74478337 74479113 3.510000e-106 396.0
5 TraesCS5B01G407300 chr5D 97.335 3602 70 15 781 4378 475691901 475695480 0.000000e+00 6096.0
6 TraesCS5B01G407300 chr5D 92.212 321 14 8 4422 4740 475695468 475695779 1.240000e-120 444.0
7 TraesCS5B01G407300 chr5D 74.464 1026 210 31 1251 2247 77577765 77578767 3.510000e-106 396.0
8 TraesCS5B01G407300 chr5D 83.333 372 38 18 1 365 475691454 475691808 6.040000e-84 322.0
9 TraesCS5B01G407300 chr5D 91.000 100 8 1 4743 4841 475696085 475696184 3.040000e-27 134.0
10 TraesCS5B01G407300 chr7D 86.585 82 5 3 4181 4262 504755466 504755541 8.630000e-13 86.1


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 TraesCS5B01G407300 chr5B 583175160 583180000 4840 False 4087.5 7500 100.0000 1 4841 2 chr5B.!!$F1 4840
1 TraesCS5B01G407300 chr5A 595143484 595147861 4377 False 3453.0 6495 92.1155 1 4740 2 chr5A.!!$F2 4739
2 TraesCS5B01G407300 chr5A 74478337 74479113 776 False 396.0 396 76.3090 1456 2247 1 chr5A.!!$F1 791
3 TraesCS5B01G407300 chr5D 475691454 475696184 4730 False 1749.0 6096 90.9700 1 4841 4 chr5D.!!$F2 4840
4 TraesCS5B01G407300 chr5D 77577765 77578767 1002 False 396.0 396 74.4640 1251 2247 1 chr5D.!!$F1 996

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
972 1005 0.793250 GGAAGCTGTGTTCTTCGCTC 59.207 55.000 0.00 0.0 40.50 5.03 F
2253 2304 3.735208 CGCAGTATCTGAGTGATTCGGTT 60.735 47.826 0.66 0.0 36.65 4.44 F
3639 3693 1.078567 CCTCAGCTCTTCCCTGTGC 60.079 63.158 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2909 2960 0.040425 CCCAAAAACAGACGCCGAAG 60.04 55.0 0.00 0.00 0.00 3.79 R
3648 3702 0.389817 TCTCATGTCGGCCGTTTGAG 60.39 55.0 30.92 30.92 36.09 3.02 R
4441 4500 0.039798 GAATCCGCCGCGACAGTATA 60.04 55.0 15.93 0.00 0.00 1.47 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
39 40 5.831103 ACATTCAACAACCCTCCTGATTAT 58.169 37.500 0.00 0.00 0.00 1.28
94 95 5.221224 TGCATTTGACCTTCCTTGTGTAAAG 60.221 40.000 0.00 0.00 0.00 1.85
123 124 8.469200 CAGCAAAATCATCTAAAAATGGAGGTA 58.531 33.333 0.00 0.00 0.00 3.08
132 133 9.090692 CATCTAAAAATGGAGGTAAAAATGCAG 57.909 33.333 0.00 0.00 0.00 4.41
150 151 8.483307 AAATGCAGGCTGTAAAAATTCTATTG 57.517 30.769 17.16 0.00 0.00 1.90
270 296 6.602410 TTAATTTGGTTGCATTGGAGATGA 57.398 33.333 0.00 0.00 0.00 2.92
275 301 3.760151 TGGTTGCATTGGAGATGAGAAAG 59.240 43.478 0.00 0.00 0.00 2.62
321 352 4.311816 CATTAAATGCTGTGGGATGGAC 57.688 45.455 0.00 0.00 0.00 4.02
944 977 3.873812 GATGGTGTAGGGGCGGGG 61.874 72.222 0.00 0.00 0.00 5.73
972 1005 0.793250 GGAAGCTGTGTTCTTCGCTC 59.207 55.000 0.00 0.00 40.50 5.03
2169 2220 4.488879 TCATCAAGAAGTCAGTGATGTCG 58.511 43.478 17.61 0.00 45.75 4.35
2253 2304 3.735208 CGCAGTATCTGAGTGATTCGGTT 60.735 47.826 0.66 0.00 36.65 4.44
2909 2960 1.805428 AATGGCCGCACACAAGGAAC 61.805 55.000 0.00 0.00 0.00 3.62
2971 3022 3.551259 TCCACTTCGGAGATTTGCC 57.449 52.632 0.00 0.00 39.64 4.52
3102 3153 2.811873 GCTCTTTGGAGTGGAAGAAGCA 60.812 50.000 0.00 0.00 41.38 3.91
3150 3201 3.392616 AGGTATCATTCACCATGGAGGAC 59.607 47.826 21.47 4.41 41.22 3.85
3453 3507 4.083484 GGCCCGAAGATAAAATATGAACGG 60.083 45.833 0.00 0.00 37.98 4.44
3639 3693 1.078567 CCTCAGCTCTTCCCTGTGC 60.079 63.158 0.00 0.00 0.00 4.57
3717 3771 0.039437 TCGAAGTCGTCACTGCTTCC 60.039 55.000 0.00 0.00 40.80 3.46
3792 3846 4.853743 GCAAAATTTCTGGACTCATCGTTC 59.146 41.667 0.00 0.00 0.00 3.95
3940 3994 1.352622 ACAGAAGGAAGGTGGTGGCA 61.353 55.000 0.00 0.00 0.00 4.92
3959 4013 4.216042 TGGCAACAGTGTAATTGTGATGAG 59.784 41.667 0.00 0.00 46.17 2.90
3962 4016 4.640771 ACAGTGTAATTGTGATGAGGGT 57.359 40.909 0.00 0.00 34.53 4.34
3976 4030 3.776731 TGAGGGTTGGAAGAGGAGATA 57.223 47.619 0.00 0.00 0.00 1.98
4136 4194 4.348656 TCGTAGATTTTGGTCGAGATTCG 58.651 43.478 0.00 0.00 42.10 3.34
4171 4229 4.813161 CACCTGATTATTTGATGAGCGTCT 59.187 41.667 0.00 0.00 0.00 4.18
4172 4230 5.050499 CACCTGATTATTTGATGAGCGTCTC 60.050 44.000 0.58 0.58 0.00 3.36
4296 4354 4.089839 GGTGATCCATCCACCCCT 57.910 61.111 0.00 0.00 46.30 4.79
4299 4358 1.410224 GGTGATCCATCCACCCCTTTC 60.410 57.143 0.00 0.00 46.30 2.62
4333 4392 3.057596 TGTCAAACTTGAAATCATCCGCC 60.058 43.478 0.00 0.00 39.21 6.13
4335 4394 0.451783 AACTTGAAATCATCCGCCGC 59.548 50.000 0.00 0.00 0.00 6.53
4382 4441 2.029918 GGTTTGTTGGTCAATGAGCTCC 60.030 50.000 12.15 4.70 35.84 4.70
4402 4461 5.164620 TCCTCATGCTGTGTCTGATTTTA 57.835 39.130 0.00 0.00 0.00 1.52
4403 4462 5.748402 TCCTCATGCTGTGTCTGATTTTAT 58.252 37.500 0.00 0.00 0.00 1.40
4406 4465 6.971184 CCTCATGCTGTGTCTGATTTTATTTC 59.029 38.462 0.00 0.00 0.00 2.17
4407 4466 7.362315 CCTCATGCTGTGTCTGATTTTATTTCA 60.362 37.037 0.00 0.00 0.00 2.69
4408 4467 8.058667 TCATGCTGTGTCTGATTTTATTTCAT 57.941 30.769 0.00 0.00 0.00 2.57
4434 4493 6.698008 TTCAAGAATGTGTTGTGTCTGATT 57.302 33.333 0.00 0.00 0.00 2.57
4435 4494 6.304356 TCAAGAATGTGTTGTGTCTGATTC 57.696 37.500 0.00 0.00 0.00 2.52
4436 4495 6.057533 TCAAGAATGTGTTGTGTCTGATTCT 58.942 36.000 0.00 0.00 32.75 2.40
4437 4496 5.936686 AGAATGTGTTGTGTCTGATTCTG 57.063 39.130 0.00 0.00 30.75 3.02
4438 4497 5.614308 AGAATGTGTTGTGTCTGATTCTGA 58.386 37.500 0.00 0.00 30.75 3.27
4439 4498 6.236409 AGAATGTGTTGTGTCTGATTCTGAT 58.764 36.000 0.00 0.00 30.75 2.90
4440 4499 5.874895 ATGTGTTGTGTCTGATTCTGATG 57.125 39.130 0.00 0.00 0.00 3.07
4441 4500 4.707105 TGTGTTGTGTCTGATTCTGATGT 58.293 39.130 0.00 0.00 0.00 3.06
4442 4501 5.852827 TGTGTTGTGTCTGATTCTGATGTA 58.147 37.500 0.00 0.00 0.00 2.29
4448 4507 7.410120 TGTGTCTGATTCTGATGTATACTGT 57.590 36.000 4.17 0.00 0.00 3.55
4486 4545 6.294955 GCTGGTAGTACATGATGATCATCTGA 60.295 42.308 30.65 16.12 34.28 3.27
4528 4587 0.319555 GCACTAGCCACAGTGTTCGA 60.320 55.000 11.16 0.00 46.31 3.71
4569 4628 4.981806 TGTTGTGTTTCTGCTTTTAGCT 57.018 36.364 0.00 0.00 42.97 3.32
4571 4630 5.719173 TGTTGTGTTTCTGCTTTTAGCTTT 58.281 33.333 0.00 0.00 42.97 3.51
4572 4631 5.576384 TGTTGTGTTTCTGCTTTTAGCTTTG 59.424 36.000 0.00 0.00 42.97 2.77
4573 4632 5.574891 TGTGTTTCTGCTTTTAGCTTTGA 57.425 34.783 0.00 0.00 42.97 2.69
4587 4646 6.494893 TTAGCTTTGATGATGTTGTGTACC 57.505 37.500 0.00 0.00 0.00 3.34
4671 4730 2.558554 TAGAACGGCCTGCTCGCTTC 62.559 60.000 0.00 0.00 0.00 3.86
4695 4754 2.057137 TGCTCTGTTGCTTTCTGGTT 57.943 45.000 0.00 0.00 0.00 3.67
4780 5142 4.261994 GGCAAAAACTCCAGAATACTTGCA 60.262 41.667 5.89 0.00 39.67 4.08
4791 5153 1.710013 ATACTTGCACCGAAGTCGTG 58.290 50.000 0.00 0.19 37.38 4.35
4810 5172 3.136123 CAGCCATGGCCCGTGAAG 61.136 66.667 33.14 10.55 43.17 3.02
4812 5174 4.424711 GCCATGGCCCGTGAAGGA 62.425 66.667 27.24 0.00 45.00 3.36
4828 5191 7.201705 CCCGTGAAGGAAACTATAAAAATCCTC 60.202 40.741 0.00 0.00 45.00 3.71
4831 5194 8.184848 GTGAAGGAAACTATAAAAATCCTCTGC 58.815 37.037 0.00 0.00 42.68 4.26
4835 5198 6.238402 GGAAACTATAAAAATCCTCTGCGACC 60.238 42.308 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.814504 ATCAGGAGGGTTGTTGAATGT 57.185 42.857 0.00 0.00 0.00 2.71
17 18 6.780457 AATAATCAGGAGGGTTGTTGAATG 57.220 37.500 0.00 0.00 0.00 2.67
94 95 7.322664 TCCATTTTTAGATGATTTTGCTGACC 58.677 34.615 0.00 0.00 0.00 4.02
123 124 9.506018 AATAGAATTTTTACAGCCTGCATTTTT 57.494 25.926 0.00 0.00 0.00 1.94
174 181 9.320295 TCATTTATAATCAACCAAAGTTCCCTT 57.680 29.630 0.00 0.00 32.45 3.95
175 182 8.893563 TCATTTATAATCAACCAAAGTTCCCT 57.106 30.769 0.00 0.00 32.45 4.20
253 279 3.438216 TTCTCATCTCCAATGCAACCA 57.562 42.857 0.00 0.00 0.00 3.67
254 280 3.760684 ACTTTCTCATCTCCAATGCAACC 59.239 43.478 0.00 0.00 0.00 3.77
270 296 5.085219 CCCGTATATCTTCCCCTACTTTCT 58.915 45.833 0.00 0.00 0.00 2.52
275 301 4.097589 CGATTCCCGTATATCTTCCCCTAC 59.902 50.000 0.00 0.00 0.00 3.18
321 352 2.351726 CGGAATTAAAAGCAGAGGTCCG 59.648 50.000 0.00 0.00 40.61 4.79
914 947 1.762460 ACCATCCGATTCGCCTCCT 60.762 57.895 0.00 0.00 0.00 3.69
917 950 0.389391 CTACACCATCCGATTCGCCT 59.611 55.000 0.00 0.00 0.00 5.52
2253 2304 0.251916 GGACACCATCGAACCCATCA 59.748 55.000 0.00 0.00 0.00 3.07
2909 2960 0.040425 CCCAAAAACAGACGCCGAAG 60.040 55.000 0.00 0.00 0.00 3.79
2971 3022 2.310538 AGCTTCAACCTGGTTTTCTGG 58.689 47.619 9.90 0.00 39.98 3.86
3102 3153 1.066143 CCCATACTTGGCACTCGTTCT 60.066 52.381 0.00 0.00 42.15 3.01
3123 3174 2.779755 TGGTGAATGATACCTTGCGT 57.220 45.000 0.00 0.00 39.01 5.24
3639 3693 2.125269 CCGTTTGAGGTAGGCCGG 60.125 66.667 0.00 0.00 40.50 6.13
3648 3702 0.389817 TCTCATGTCGGCCGTTTGAG 60.390 55.000 30.92 30.92 36.09 3.02
3717 3771 4.647399 TCAAAGTTTGTAAGGAACCCAAGG 59.353 41.667 15.08 0.00 0.00 3.61
3940 3994 4.985538 ACCCTCATCACAATTACACTGTT 58.014 39.130 0.00 0.00 0.00 3.16
3959 4013 4.202409 CCTTGATATCTCCTCTTCCAACCC 60.202 50.000 3.98 0.00 0.00 4.11
3962 4016 4.040047 TGCCTTGATATCTCCTCTTCCAA 58.960 43.478 3.98 0.00 0.00 3.53
4016 4070 1.002069 ATTCATGCCAAGGGGAGACA 58.998 50.000 0.00 0.00 35.59 3.41
4017 4071 1.396653 CATTCATGCCAAGGGGAGAC 58.603 55.000 0.00 0.00 35.59 3.36
4171 4229 2.158871 ACAAGCAAGTACAAGGAACGGA 60.159 45.455 0.00 0.00 0.00 4.69
4172 4230 2.218603 ACAAGCAAGTACAAGGAACGG 58.781 47.619 0.00 0.00 0.00 4.44
4293 4351 4.708177 TGACAAAGAGAACTGAGAAAGGG 58.292 43.478 0.00 0.00 0.00 3.95
4296 4354 7.390440 TCAAGTTTGACAAAGAGAACTGAGAAA 59.610 33.333 0.00 0.00 33.02 2.52
4299 4358 6.668541 TCAAGTTTGACAAAGAGAACTGAG 57.331 37.500 0.00 0.00 33.02 3.35
4333 4392 0.742505 TACAGAACATACCGAGGGCG 59.257 55.000 0.00 0.00 37.24 6.13
4335 4394 2.963101 TCCATACAGAACATACCGAGGG 59.037 50.000 0.00 0.00 0.00 4.30
4348 4407 3.119388 CCAACAAACCAGCATCCATACAG 60.119 47.826 0.00 0.00 0.00 2.74
4382 4441 7.532571 TGAAATAAAATCAGACACAGCATGAG 58.467 34.615 0.00 0.00 39.69 2.90
4402 4461 9.165035 ACACAACACATTCTTGAAAAATGAAAT 57.835 25.926 0.00 0.00 37.51 2.17
4403 4462 8.545229 ACACAACACATTCTTGAAAAATGAAA 57.455 26.923 0.00 0.00 37.51 2.69
4406 4465 7.488792 TCAGACACAACACATTCTTGAAAAATG 59.511 33.333 0.00 0.00 39.50 2.32
4407 4466 7.546358 TCAGACACAACACATTCTTGAAAAAT 58.454 30.769 0.00 0.00 0.00 1.82
4408 4467 6.918626 TCAGACACAACACATTCTTGAAAAA 58.081 32.000 0.00 0.00 0.00 1.94
4434 4493 1.001706 GCCGCGACAGTATACATCAGA 60.002 52.381 8.23 0.00 0.00 3.27
4435 4494 1.409412 GCCGCGACAGTATACATCAG 58.591 55.000 8.23 0.20 0.00 2.90
4436 4495 0.317519 CGCCGCGACAGTATACATCA 60.318 55.000 8.23 0.00 0.00 3.07
4437 4496 1.002250 CCGCCGCGACAGTATACATC 61.002 60.000 15.93 1.47 0.00 3.06
4438 4497 1.007734 CCGCCGCGACAGTATACAT 60.008 57.895 15.93 0.00 0.00 2.29
4439 4498 1.449726 ATCCGCCGCGACAGTATACA 61.450 55.000 15.93 0.00 0.00 2.29
4440 4499 0.318445 AATCCGCCGCGACAGTATAC 60.318 55.000 15.93 0.00 0.00 1.47
4441 4500 0.039798 GAATCCGCCGCGACAGTATA 60.040 55.000 15.93 0.00 0.00 1.47
4442 4501 1.299926 GAATCCGCCGCGACAGTAT 60.300 57.895 15.93 0.00 0.00 2.12
4467 4526 4.839550 AGCCTCAGATGATCATCATGTACT 59.160 41.667 31.99 21.42 37.20 2.73
4468 4527 5.149973 AGCCTCAGATGATCATCATGTAC 57.850 43.478 31.99 19.84 37.20 2.90
4469 4528 5.820404 AAGCCTCAGATGATCATCATGTA 57.180 39.130 31.99 15.90 37.20 2.29
4470 4529 4.708576 AAGCCTCAGATGATCATCATGT 57.291 40.909 31.99 13.41 37.20 3.21
4528 4587 4.451900 ACAACAGTGAGTCGGAAAGAAAT 58.548 39.130 0.00 0.00 0.00 2.17
4569 4628 4.023279 GTGCAGGTACACAACATCATCAAA 60.023 41.667 0.00 0.00 40.40 2.69
4571 4630 3.073678 GTGCAGGTACACAACATCATCA 58.926 45.455 0.00 0.00 40.40 3.07
4572 4631 3.338249 AGTGCAGGTACACAACATCATC 58.662 45.455 0.00 0.00 43.23 2.92
4573 4632 3.423539 AGTGCAGGTACACAACATCAT 57.576 42.857 0.00 0.00 43.23 2.45
4587 4646 1.066303 CTACTCGGAGGCTTAGTGCAG 59.934 57.143 10.23 0.00 45.15 4.41
4671 4730 2.161808 CAGAAAGCAACAGAGCATCAGG 59.838 50.000 0.00 0.00 37.82 3.86
4674 4733 2.157738 ACCAGAAAGCAACAGAGCATC 58.842 47.619 0.00 0.00 36.85 3.91
4695 4754 5.590259 AGAAAAGAAGCAACTTAGAACAGCA 59.410 36.000 0.00 0.00 0.00 4.41
4780 5142 1.816863 ATGGCTGACACGACTTCGGT 61.817 55.000 3.30 0.00 44.95 4.69
4791 5153 3.918253 TTCACGGGCCATGGCTGAC 62.918 63.158 34.70 23.29 41.60 3.51
4810 5172 6.238402 GGTCGCAGAGGATTTTTATAGTTTCC 60.238 42.308 0.00 0.00 36.95 3.13
4812 5174 5.589050 GGGTCGCAGAGGATTTTTATAGTTT 59.411 40.000 0.00 0.00 36.95 2.66


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

AutoCloner maintained by Alex Coulton.