Multiple sequence alignment - TraesCS3B01G419900

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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 TraesCS3B01G419900 chr3B 100.000 4102 0 0 880 4981 656579555 656583656 0.000000e+00 7576.0
1 TraesCS3B01G419900 chr3B 100.000 643 0 0 1 643 656578676 656579318 0.000000e+00 1188.0
2 TraesCS3B01G419900 chr3D 96.149 3454 85 21 880 4300 496943622 496947060 0.000000e+00 5598.0
3 TraesCS3B01G419900 chr3D 94.163 651 35 3 2127 2776 119531032 119531680 0.000000e+00 989.0
4 TraesCS3B01G419900 chr3D 92.928 608 24 5 2 609 496942613 496943201 0.000000e+00 867.0
5 TraesCS3B01G419900 chr3D 92.697 534 28 4 4445 4977 496947319 496947842 0.000000e+00 760.0
6 TraesCS3B01G419900 chr3D 89.655 145 6 2 2808 2952 119548648 119548783 5.120000e-40 176.0
7 TraesCS3B01G419900 chr3D 97.826 46 1 0 4312 4357 496947098 496947143 4.130000e-11 80.5
8 TraesCS3B01G419900 chr3A 93.495 2306 112 26 1998 4281 637623306 637621017 0.000000e+00 3393.0
9 TraesCS3B01G419900 chr3A 94.922 1083 48 6 880 1957 637624383 637623303 0.000000e+00 1688.0
10 TraesCS3B01G419900 chr3A 95.645 643 23 2 2 643 637625056 637624418 0.000000e+00 1027.0
11 TraesCS3B01G419900 chr3A 89.922 387 28 5 4595 4980 637615520 637615144 5.800000e-134 488.0
12 TraesCS3B01G419900 chr3A 87.719 57 4 1 4531 4587 637616509 637616456 4.160000e-06 63.9
13 TraesCS3B01G419900 chr2D 93.504 508 32 1 2083 2590 474294465 474293959 0.000000e+00 754.0
14 TraesCS3B01G419900 chr2D 96.296 216 8 0 2592 2807 474252864 474252649 6.130000e-94 355.0
15 TraesCS3B01G419900 chr2D 89.655 145 6 3 2808 2952 474251008 474250873 5.120000e-40 176.0
16 TraesCS3B01G419900 chr4D 87.805 82 9 1 3304 3385 183779609 183779689 1.480000e-15 95.3
17 TraesCS3B01G419900 chr6D 86.747 83 10 1 3304 3386 46227914 46227995 1.910000e-14 91.6
18 TraesCS3B01G419900 chr5D 86.747 83 10 1 3304 3386 391825421 391825502 1.910000e-14 91.6


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 TraesCS3B01G419900 chr3B 656578676 656583656 4980 False 4382.000 7576 100.000000 1 4981 2 chr3B.!!$F1 4980
1 TraesCS3B01G419900 chr3D 496942613 496947842 5229 False 1826.375 5598 94.900000 2 4977 4 chr3D.!!$F3 4975
2 TraesCS3B01G419900 chr3D 119531032 119531680 648 False 989.000 989 94.163000 2127 2776 1 chr3D.!!$F1 649
3 TraesCS3B01G419900 chr3A 637621017 637625056 4039 True 2036.000 3393 94.687333 2 4281 3 chr3A.!!$R2 4279
4 TraesCS3B01G419900 chr3A 637615144 637616509 1365 True 275.950 488 88.820500 4531 4980 2 chr3A.!!$R1 449
5 TraesCS3B01G419900 chr2D 474293959 474294465 506 True 754.000 754 93.504000 2083 2590 1 chr2D.!!$R1 507
6 TraesCS3B01G419900 chr2D 474250873 474252864 1991 True 265.500 355 92.975500 2592 2952 2 chr2D.!!$R2 360

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
142 143 0.319813 GTCCATGGTTTGCTGCAACC 60.320 55.000 15.72 18.50 0.0 3.77 F
1959 2330 1.067706 CGATTGAACTGCATGCCCAAA 60.068 47.619 16.68 3.05 0.0 3.28 F
2541 2912 0.179029 ACAAGTTTGGCGCTGGTAGT 60.179 50.000 7.64 0.00 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2332 0.234884 CTTCGCACGACTGGAAAACC 59.765 55.0 0.0 0.0 0.0 3.27 R
3143 5162 0.770499 TTGCATCAACTGGGGACTGA 59.230 50.0 0.0 0.0 0.0 3.41 R
4536 6734 2.235845 ACAGTCTCATCATGGCATCG 57.764 50.0 0.0 0.0 0.0 3.84 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
44 45 7.228706 TCTCTCAAGAAAATGTTCACTTTACCC 59.771 37.037 0.00 0.00 36.09 3.69
45 46 6.264518 TCTCAAGAAAATGTTCACTTTACCCC 59.735 38.462 0.00 0.00 36.09 4.95
142 143 0.319813 GTCCATGGTTTGCTGCAACC 60.320 55.000 15.72 18.50 0.00 3.77
256 257 1.686052 GCCAACAACCAACAGATCCAA 59.314 47.619 0.00 0.00 0.00 3.53
321 322 4.326227 TACGTGGGGCCAGGTCCT 62.326 66.667 10.88 0.00 42.92 3.85
329 330 2.363147 GCCAGGTCCTCCTCTCGT 60.363 66.667 0.00 0.00 43.07 4.18
613 615 2.590114 GGTGTACAAGGACCGGGCT 61.590 63.158 7.57 0.00 0.00 5.19
973 1332 2.420890 GGAGCGGCCAGATCTGAG 59.579 66.667 24.62 14.66 35.20 3.35
990 1349 2.123812 GGAGATCCGACGGAGGGT 60.124 66.667 22.99 8.93 34.05 4.34
1062 1421 4.821589 GAGGCCAGGGACTTCGCG 62.822 72.222 5.01 0.00 34.60 5.87
1400 1761 6.773976 TTTGTCTCAGAACATTGTTTTCCT 57.226 33.333 3.08 0.00 0.00 3.36
1443 1804 8.438676 TTTTCTGTTGGAAAACTTTTTGTTGA 57.561 26.923 0.00 0.00 45.54 3.18
1625 1995 2.525055 GTGTTGCTTTTGAGCGAACAA 58.475 42.857 13.73 0.00 37.46 2.83
1679 2049 4.099419 TCACAATCATACAGTAGCGGTGAT 59.901 41.667 0.00 0.00 0.00 3.06
1691 2061 3.287867 AGCGGTGATGGAATCTCATTT 57.712 42.857 0.00 0.00 45.81 2.32
1865 2235 5.261209 TCAAGGTTGGAAGAACAAACATG 57.739 39.130 0.00 0.00 40.48 3.21
1897 2267 6.094325 AGTTCTTGGACAAAACGAACATACAA 59.906 34.615 14.20 0.00 37.14 2.41
1959 2330 1.067706 CGATTGAACTGCATGCCCAAA 60.068 47.619 16.68 3.05 0.00 3.28
1961 2332 2.459060 TTGAACTGCATGCCCAAATG 57.541 45.000 16.68 0.97 0.00 2.32
1991 2362 3.059597 AGTCGTGCGAAGTTCTTGAATTG 60.060 43.478 0.56 0.00 0.00 2.32
2004 2375 2.307496 TGAATTGGTTCAGCCCATGT 57.693 45.000 0.00 0.00 39.36 3.21
2342 2713 1.522668 TACTGCTGTTGATGGTGCAC 58.477 50.000 8.80 8.80 0.00 4.57
2383 2754 5.957168 TGACCATTATTCAAACACCATCCAT 59.043 36.000 0.00 0.00 0.00 3.41
2420 2791 2.432146 GAGAATTCCATTTGGCCCCTTC 59.568 50.000 0.00 0.00 34.44 3.46
2502 2873 1.039233 CCATCACAACTGGGCATCCC 61.039 60.000 0.00 0.00 45.71 3.85
2541 2912 0.179029 ACAAGTTTGGCGCTGGTAGT 60.179 50.000 7.64 0.00 0.00 2.73
2556 2927 3.857052 TGGTAGTTTTGCTCATACCTCG 58.143 45.455 0.00 0.00 38.78 4.63
2574 2945 0.469331 CGGATACCTACCAGGAGGCA 60.469 60.000 0.00 0.00 40.65 4.75
2578 2949 3.573695 GATACCTACCAGGAGGCAGTTA 58.426 50.000 0.00 0.00 40.65 2.24
2826 4838 3.503363 TCTGCATGTGGACAAATGAAGAC 59.497 43.478 8.78 0.00 34.18 3.01
2838 4850 3.340814 AATGAAGACATCAACCGAGCT 57.659 42.857 0.00 0.00 42.54 4.09
3053 5066 7.060633 CGCAATTGAATACAGGTAAACTTTGTC 59.939 37.037 10.34 0.00 0.00 3.18
3143 5162 4.613437 ACAGGCTGGAAACATATTCCAAT 58.387 39.130 20.34 0.00 46.85 3.16
3238 5257 1.074405 TGCTCTGCTGAACCCAGAAAT 59.926 47.619 0.00 0.00 43.02 2.17
3329 5348 4.222114 GCAAGCAGTTCATCAAACACTAC 58.778 43.478 0.00 0.00 40.56 2.73
3554 5573 1.004745 GAACAGCTCCCTGAATTCCCA 59.995 52.381 2.27 0.00 41.77 4.37
3779 5798 3.238232 GCACACAAGATGCTCAGGA 57.762 52.632 0.00 0.00 40.08 3.86
4026 6045 3.660970 ATACTGAGAGCTGAGAGTGGA 57.339 47.619 0.00 0.00 0.00 4.02
4185 6204 7.772332 AATAGTGAGATGACACGAATAAACC 57.228 36.000 0.00 0.00 44.35 3.27
4354 6441 9.263538 TGTAACTACTGGTTATGTGTTTAACTG 57.736 33.333 0.00 0.00 41.68 3.16
4364 6451 9.953697 GGTTATGTGTTTAACTGTGTGAAAATA 57.046 29.630 0.00 0.00 33.49 1.40
4410 6522 7.221452 GCTAGGCACATCTGAAACATAAAAATG 59.779 37.037 0.00 0.00 0.00 2.32
4411 6523 7.230849 AGGCACATCTGAAACATAAAAATGA 57.769 32.000 0.00 0.00 0.00 2.57
4412 6524 7.844009 AGGCACATCTGAAACATAAAAATGAT 58.156 30.769 0.00 0.00 0.00 2.45
4413 6525 8.970020 AGGCACATCTGAAACATAAAAATGATA 58.030 29.630 0.00 0.00 0.00 2.15
4414 6526 9.754382 GGCACATCTGAAACATAAAAATGATAT 57.246 29.630 0.00 0.00 0.00 1.63
4465 6663 6.182627 TCATGATAAGCTGTGAACTTCCATT 58.817 36.000 0.00 0.00 0.00 3.16
4498 6696 7.048512 ACCAAAAAGTCATAGCAGTACCTATC 58.951 38.462 0.00 0.00 0.00 2.08
4536 6734 9.899226 ATCATCTTACTGCTTAAACAAAGAAAC 57.101 29.630 0.00 0.00 37.38 2.78
4618 7744 4.509970 GCACAAACCCCAAACAGATTAAAC 59.490 41.667 0.00 0.00 0.00 2.01
4655 7781 7.034685 ACTTACCACAAGTTTGTTGGATAAC 57.965 36.000 15.56 0.00 39.91 1.89
4679 7805 3.489785 AGTTAAAGCTTGTCTTGACGACG 59.510 43.478 0.00 0.00 45.87 5.12
4694 7820 7.744715 GTCTTGACGACGTTTGAAATGATAAAT 59.255 33.333 0.13 0.00 32.04 1.40
4744 7870 8.699215 ACTTTAAGCATGAAAGCAGAGGTACTG 61.699 40.741 0.00 0.00 40.39 2.74
4810 7936 7.063074 GCACATACCTATACCTTATTTACGCTG 59.937 40.741 0.00 0.00 0.00 5.18
4831 7957 1.807142 CAAAAAGAGCTTCCTCGGGTC 59.193 52.381 0.00 0.00 43.05 4.46
4834 7960 1.280457 AAGAGCTTCCTCGGGTCATT 58.720 50.000 0.00 0.00 43.05 2.57
4843 7969 4.561500 TCCTCGGGTCATTGATTAACAA 57.438 40.909 0.00 0.00 42.95 2.83
4877 8003 3.402110 ACGAACATGAAATCTGCACAGA 58.598 40.909 0.00 2.25 42.37 3.41
4925 8052 7.821359 GCATTTATGAGGACTAATAGCAGATGA 59.179 37.037 0.00 0.00 0.00 2.92
4950 8077 7.793902 ACAGTAGTTACAAATCAAACATCGTC 58.206 34.615 0.00 0.00 0.00 4.20
4977 8104 5.123979 GGATGTTAAAGCTACTCCAAGTTGG 59.876 44.000 16.36 16.36 39.43 3.77
4980 8107 2.457366 AAGCTACTCCAAGTTGGACG 57.543 50.000 21.05 17.81 42.67 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.658190 TGAGAGAATGATCATGTGGTGACTA 59.342 40.000 9.46 0.00 40.28 2.59
71 72 8.119226 GTGACCATTTTCTTGAGAGAATAATCG 58.881 37.037 0.00 0.00 41.35 3.34
142 143 9.401058 AGAGATCAAAATAGTGGTAAGGATTTG 57.599 33.333 0.00 0.00 0.00 2.32
256 257 1.407618 GTCTTGGGGTTCGCACTTTTT 59.592 47.619 0.00 0.00 0.00 1.94
316 317 1.603326 GACGATTACGAGAGGAGGACC 59.397 57.143 0.00 0.00 42.66 4.46
321 322 2.485124 GGAGAGGACGATTACGAGAGGA 60.485 54.545 0.00 0.00 42.66 3.71
370 371 1.664873 GGAATAAAGACTCGGGGCAC 58.335 55.000 0.00 0.00 0.00 5.01
378 380 5.760131 CAGAAATGGGAGGGAATAAAGACT 58.240 41.667 0.00 0.00 0.00 3.24
973 1332 2.123812 ACCCTCCGTCGGATCTCC 60.124 66.667 15.81 0.00 0.00 3.71
990 1349 2.284625 ACCACCATCTCCGCTCCA 60.285 61.111 0.00 0.00 0.00 3.86
1266 1625 1.007734 GACGACGTTGAGCTCCACA 60.008 57.895 17.31 0.00 0.00 4.17
1427 1788 9.325198 AGGACATTATTCAACAAAAAGTTTTCC 57.675 29.630 0.32 0.00 38.74 3.13
1527 1889 1.476833 CCATACAGGCGGCATTTACCT 60.477 52.381 13.08 0.00 0.00 3.08
1587 1957 5.529060 GCAACACCCCAACAATAAAATTTGA 59.471 36.000 0.00 0.00 0.00 2.69
1625 1995 6.319658 AGGAGAACGAAAATAATCATGCACAT 59.680 34.615 0.00 0.00 0.00 3.21
1679 2049 7.558807 ACAGATGCATTAGAAAATGAGATTCCA 59.441 33.333 0.00 0.00 44.50 3.53
1833 2203 1.074405 TCCAACCTTGATTCTGCAGCT 59.926 47.619 9.47 0.00 0.00 4.24
1865 2235 5.088739 CGTTTTGTCCAAGAACTGATATGC 58.911 41.667 0.00 0.00 0.00 3.14
1959 2330 0.250124 TCGCACGACTGGAAAACCAT 60.250 50.000 0.00 0.00 0.00 3.55
1961 2332 0.234884 CTTCGCACGACTGGAAAACC 59.765 55.000 0.00 0.00 0.00 3.27
1971 2342 2.223144 CCAATTCAAGAACTTCGCACGA 59.777 45.455 0.00 0.00 0.00 4.35
1972 2343 2.032030 ACCAATTCAAGAACTTCGCACG 60.032 45.455 0.00 0.00 0.00 5.34
2004 2375 7.530863 TGTAAAATAAAATCGCACATACAGCA 58.469 30.769 0.00 0.00 0.00 4.41
2146 2517 4.970711 AGGAATCATCAAGATGCAGGTAG 58.029 43.478 5.19 0.00 38.65 3.18
2342 2713 3.055167 TGGTCATGTCATGTCACCCTAAG 60.055 47.826 17.04 0.00 0.00 2.18
2383 2754 3.701205 TTCTCAGTGCTATTGCTGGAA 57.299 42.857 0.00 0.00 40.48 3.53
2420 2791 1.339438 CCATGACAGTGACCTTCCTGG 60.339 57.143 0.00 0.00 42.93 4.45
2457 2828 1.840635 AGAAGCCTGTAGTCCATTCCC 59.159 52.381 0.00 0.00 0.00 3.97
2502 2873 3.394274 TGTATCCCCATTCACCATACCAG 59.606 47.826 0.00 0.00 0.00 4.00
2541 2912 3.709653 AGGTATCCGAGGTATGAGCAAAA 59.290 43.478 0.00 0.00 0.00 2.44
2556 2927 1.343069 CTGCCTCCTGGTAGGTATCC 58.657 60.000 12.01 0.00 41.57 2.59
2574 2945 4.647853 TGTATACCGGAGAGCACATTAACT 59.352 41.667 9.46 0.00 0.00 2.24
2578 2949 2.102588 GGTGTATACCGGAGAGCACATT 59.897 50.000 9.46 0.00 37.19 2.71
2838 4850 0.885879 CCTTGAGCATTGCAGCTTCA 59.114 50.000 11.91 2.73 46.75 3.02
3053 5066 4.676196 GCAAATTGGAGCAACATACTGGAG 60.676 45.833 0.00 0.00 0.00 3.86
3143 5162 0.770499 TTGCATCAACTGGGGACTGA 59.230 50.000 0.00 0.00 0.00 3.41
3238 5257 2.076100 CTGGTTGCGAAGACAGCATTA 58.924 47.619 0.00 0.00 44.74 1.90
3329 5348 2.361757 AGATTCTGGAGCACTCTCATCG 59.638 50.000 0.00 0.00 41.13 3.84
3554 5573 3.951680 CAGGGGTTGTGTCACTTAAGTTT 59.048 43.478 5.07 0.00 0.00 2.66
3779 5798 6.208204 CAGGGACTTCTTCAAAATCACTGATT 59.792 38.462 0.00 0.00 42.34 2.57
3875 5894 3.626996 CTCCATTCTGCCGCCACCA 62.627 63.158 0.00 0.00 0.00 4.17
4159 6178 8.665685 GGTTTATTCGTGTCATCTCACTATTTT 58.334 33.333 0.00 0.00 36.33 1.82
4185 6204 6.662414 ATGTGTAATTACTGAACCGTCATG 57.338 37.500 16.33 0.00 31.85 3.07
4230 6291 9.996554 TGAATTTAATCTGTCTTGTGAAGTAGA 57.003 29.630 0.00 0.00 0.00 2.59
4335 6422 6.116806 TCACACAGTTAAACACATAACCAGT 58.883 36.000 0.00 0.00 36.62 4.00
4371 6458 7.389884 CAGATGTGCCTAGCTTATGAACATAAT 59.610 37.037 7.55 0.00 33.29 1.28
4372 6459 6.707608 CAGATGTGCCTAGCTTATGAACATAA 59.292 38.462 0.00 6.99 0.00 1.90
4373 6460 6.041979 TCAGATGTGCCTAGCTTATGAACATA 59.958 38.462 0.00 0.00 0.00 2.29
4374 6461 5.061853 CAGATGTGCCTAGCTTATGAACAT 58.938 41.667 0.00 0.00 0.00 2.71
4376 6463 4.697514 TCAGATGTGCCTAGCTTATGAAC 58.302 43.478 0.00 0.00 0.00 3.18
4379 6466 4.877823 TGTTTCAGATGTGCCTAGCTTATG 59.122 41.667 0.00 0.00 0.00 1.90
4436 6548 6.882610 AGTTCACAGCTTATCATGAAACAA 57.117 33.333 0.00 0.00 33.09 2.83
4465 6663 9.073475 ACTGCTATGACTTTTTGGTATTTTGTA 57.927 29.630 0.00 0.00 0.00 2.41
4516 6714 6.635239 GCATCGTTTCTTTGTTTAAGCAGTAA 59.365 34.615 0.00 0.00 33.66 2.24
4517 6715 6.140110 GCATCGTTTCTTTGTTTAAGCAGTA 58.860 36.000 0.00 0.00 33.66 2.74
4520 6718 4.202060 TGGCATCGTTTCTTTGTTTAAGCA 60.202 37.500 0.00 0.00 33.66 3.91
4521 6719 4.295051 TGGCATCGTTTCTTTGTTTAAGC 58.705 39.130 0.00 0.00 33.66 3.09
4524 6722 5.697473 TCATGGCATCGTTTCTTTGTTTA 57.303 34.783 0.00 0.00 0.00 2.01
4525 6723 4.582701 TCATGGCATCGTTTCTTTGTTT 57.417 36.364 0.00 0.00 0.00 2.83
4526 6724 4.218200 TCATCATGGCATCGTTTCTTTGTT 59.782 37.500 0.00 0.00 0.00 2.83
4527 6725 3.758023 TCATCATGGCATCGTTTCTTTGT 59.242 39.130 0.00 0.00 0.00 2.83
4528 6726 4.095334 TCTCATCATGGCATCGTTTCTTTG 59.905 41.667 0.00 0.00 0.00 2.77
4529 6727 4.095483 GTCTCATCATGGCATCGTTTCTTT 59.905 41.667 0.00 0.00 0.00 2.52
4536 6734 2.235845 ACAGTCTCATCATGGCATCG 57.764 50.000 0.00 0.00 0.00 3.84
4618 7744 6.257193 ACTTGTGGTAAGTAAGTTCTTTCACG 59.743 38.462 0.00 0.00 35.41 4.35
4744 7870 4.332819 ACACTTACCATTCGCTAATTGCTC 59.667 41.667 0.00 0.00 40.11 4.26
4810 7936 0.523519 CCCGAGGAAGCTCTTTTTGC 59.476 55.000 0.00 0.00 0.00 3.68
4831 7957 5.156355 GCACACCTGTCTTGTTAATCAATG 58.844 41.667 0.00 0.00 35.35 2.82
4834 7960 2.805671 CGCACACCTGTCTTGTTAATCA 59.194 45.455 0.00 0.00 0.00 2.57
4843 7969 1.299926 GTTCGTCGCACACCTGTCT 60.300 57.895 0.00 0.00 0.00 3.41
4925 8052 7.439955 TGACGATGTTTGATTTGTAACTACTGT 59.560 33.333 0.00 0.00 0.00 3.55
4950 8077 5.940470 ACTTGGAGTAGCTTTAACATCCTTG 59.060 40.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.