Multiple sequence alignment - TraesCS3B01G294500

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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 TraesCS3B01G294500 chr3B 100.000 3368 0 0 1 3368 473541229 473537862 0.000000e+00 6220.0
1 TraesCS3B01G294500 chr3B 80.274 365 70 2 1869 2232 237503919 237504282 1.190000e-69 274.0
2 TraesCS3B01G294500 chr3D 97.931 2562 39 8 812 3368 363514054 363511502 0.000000e+00 4425.0
3 TraesCS3B01G294500 chr3D 93.471 628 41 0 1 628 363518532 363517905 0.000000e+00 933.0
4 TraesCS3B01G294500 chr3D 81.319 364 68 0 1869 2232 160726580 160726943 2.540000e-76 296.0
5 TraesCS3B01G294500 chr3D 97.170 106 2 1 686 791 363514238 363514134 9.600000e-41 178.0
6 TraesCS3B01G294500 chr5D 87.477 543 64 1 95 633 88924409 88924951 1.030000e-174 623.0
7 TraesCS3B01G294500 chr3A 79.812 213 41 2 2021 2232 187345508 187345719 1.620000e-33 154.0
8 TraesCS3B01G294500 chr4D 91.765 85 7 0 7 91 166943386 166943470 5.900000e-23 119.0
9 TraesCS3B01G294500 chr4B 89.412 85 9 0 7 91 221702815 221702731 1.280000e-19 108.0
10 TraesCS3B01G294500 chr6B 86.047 86 12 0 6 91 39467532 39467617 3.580000e-15 93.5
11 TraesCS3B01G294500 chr5B 84.706 85 13 0 7 91 167487861 167487777 5.990000e-13 86.1
12 TraesCS3B01G294500 chr4A 83.721 86 12 2 7 91 663993496 663993412 2.790000e-11 80.5


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 TraesCS3B01G294500 chr3B 473537862 473541229 3367 True 6220.000000 6220 100.000000 1 3368 1 chr3B.!!$R1 3367
1 TraesCS3B01G294500 chr3D 363511502 363518532 7030 True 1845.333333 4425 96.190667 1 3368 3 chr3D.!!$R1 3367
2 TraesCS3B01G294500 chr5D 88924409 88924951 542 False 623.000000 623 87.477000 95 633 1 chr5D.!!$F1 538

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
800 4414 0.610785 CCGGCCCAATGTGTTTAGGT 60.611 55.000 0.0 0.0 0.0 3.08 F
1671 5344 1.499056 GTCACTGTTGCTGGCATCG 59.501 57.895 0.0 0.0 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 5435 0.318762 GGGGGCATATCTCGACAGTC 59.681 60.000 0.0 0.0 0.0 3.51 R
2686 6361 2.044551 CAAGGCAGAAGGGGGAGC 60.045 66.667 0.0 0.0 0.0 4.70 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
31 32 6.093495 AGACGAAGAACTTTCATGTTGAAACA 59.907 34.615 0.00 0.00 41.02 2.83
66 67 6.165700 AGGCCATCTTAATTATGCTTTTGG 57.834 37.500 5.01 0.00 0.00 3.28
98 99 0.956633 CTGGTGTCAACAGCTTGCAT 59.043 50.000 4.61 0.00 44.12 3.96
143 144 1.908344 TTGGCTGTAGCTGAATTGCA 58.092 45.000 0.00 0.00 41.70 4.08
170 171 1.842562 CACAGATTCCCAGTCCTCCAT 59.157 52.381 0.00 0.00 0.00 3.41
187 188 8.323567 AGTCCTCCATAAAATTTGCAATGAAAT 58.676 29.630 0.00 0.00 0.00 2.17
266 267 3.820467 CACCATATTGCCCACATCGTTAT 59.180 43.478 0.00 0.00 0.00 1.89
274 275 2.420129 GCCCACATCGTTATGAAGACCT 60.420 50.000 0.00 0.00 36.54 3.85
277 278 3.261580 CACATCGTTATGAAGACCTGCA 58.738 45.455 0.00 0.00 36.54 4.41
325 330 4.729868 AGCCAGAACATCCAAAACTTAGT 58.270 39.130 0.00 0.00 0.00 2.24
349 354 2.223294 CCTCACTACGGTTCGAGATGAC 60.223 54.545 0.00 0.00 0.00 3.06
368 373 2.497675 GACCACATCAGTAAGCTCCTCA 59.502 50.000 0.00 0.00 0.00 3.86
406 411 2.105128 CCTCGCCATCCGACAGTC 59.895 66.667 0.00 0.00 41.89 3.51
424 429 2.505819 AGTCAAATAGGGAATGACGCCT 59.494 45.455 0.00 0.00 46.19 5.52
477 482 7.138736 GCAAGCTGTTGTTTAAGACATCTTTA 58.861 34.615 0.00 0.00 38.26 1.85
613 618 2.821366 CACATGAGAGTGGCCCGC 60.821 66.667 0.00 0.00 35.88 6.13
652 817 4.943373 TTTTTGGAGGGGGTGCTC 57.057 55.556 0.00 0.00 0.00 4.26
653 818 1.155155 TTTTTGGAGGGGGTGCTCC 59.845 57.895 0.00 0.00 40.05 4.70
654 819 1.660019 TTTTTGGAGGGGGTGCTCCA 61.660 55.000 7.20 0.00 46.84 3.86
657 822 4.048470 GGAGGGGGTGCTCCAACC 62.048 72.222 7.20 8.31 41.21 3.77
658 823 3.256960 GAGGGGGTGCTCCAACCA 61.257 66.667 16.96 0.00 44.30 3.67
659 824 3.260100 AGGGGGTGCTCCAACCAG 61.260 66.667 16.96 0.00 44.30 4.00
732 4346 0.817654 GGTTGGCCAATTAGGAGCAC 59.182 55.000 23.66 5.56 41.22 4.40
757 4371 2.026301 CCGGCTAGTAGCGAGCAC 59.974 66.667 15.85 0.85 43.62 4.40
770 4384 1.219124 GAGCACGATTCTGGGCTGA 59.781 57.895 9.45 0.00 36.59 4.26
794 4408 4.740822 GAGCCCGGCCCAATGTGT 62.741 66.667 5.55 0.00 0.00 3.72
795 4409 4.299796 AGCCCGGCCCAATGTGTT 62.300 61.111 5.55 0.00 0.00 3.32
796 4410 3.310307 GCCCGGCCCAATGTGTTT 61.310 61.111 0.00 0.00 0.00 2.83
798 4412 1.944234 GCCCGGCCCAATGTGTTTAG 61.944 60.000 0.00 0.00 0.00 1.85
799 4413 1.319614 CCCGGCCCAATGTGTTTAGG 61.320 60.000 0.00 0.00 0.00 2.69
800 4414 0.610785 CCGGCCCAATGTGTTTAGGT 60.611 55.000 0.00 0.00 0.00 3.08
803 4417 3.020984 CGGCCCAATGTGTTTAGGTTAT 58.979 45.455 0.00 0.00 0.00 1.89
804 4418 4.200874 CGGCCCAATGTGTTTAGGTTATA 58.799 43.478 0.00 0.00 0.00 0.98
805 4419 4.825085 CGGCCCAATGTGTTTAGGTTATAT 59.175 41.667 0.00 0.00 0.00 0.86
806 4420 5.048991 CGGCCCAATGTGTTTAGGTTATATC 60.049 44.000 0.00 0.00 0.00 1.63
807 4421 5.243060 GGCCCAATGTGTTTAGGTTATATCC 59.757 44.000 0.00 0.00 0.00 2.59
823 4496 1.566298 ATCCTTCCAGCCTCACCACC 61.566 60.000 0.00 0.00 0.00 4.61
973 4646 4.873129 CAGGGTCCATCGTCGCCG 62.873 72.222 0.00 0.00 0.00 6.46
976 4649 4.137872 GGTCCATCGTCGCCGGAA 62.138 66.667 5.05 0.00 33.95 4.30
1098 4771 3.261580 CATACGTGTCCTGCTTGATCAA 58.738 45.455 8.12 8.12 0.00 2.57
1230 4903 3.012518 CTCCAACATCATCCTCAACACC 58.987 50.000 0.00 0.00 0.00 4.16
1259 4932 4.697756 TCCTTCGCCGTTGCCCAG 62.698 66.667 0.00 0.00 0.00 4.45
1671 5344 1.499056 GTCACTGTTGCTGGCATCG 59.501 57.895 0.00 0.00 0.00 3.84
1703 5376 8.399425 GGGTAATGTATCTGAGTATCTACATCG 58.601 40.741 2.36 0.00 34.56 3.84
1762 5435 1.805869 CCAGTGGCTCAGTCTTCAAG 58.194 55.000 0.00 0.00 0.00 3.02
1855 5528 4.349365 GAAGAGGAAGGAGAAGAAGGAGA 58.651 47.826 0.00 0.00 0.00 3.71
1857 5530 4.959080 AGAGGAAGGAGAAGAAGGAGAAT 58.041 43.478 0.00 0.00 0.00 2.40
1859 5532 5.897250 AGAGGAAGGAGAAGAAGGAGAATAC 59.103 44.000 0.00 0.00 0.00 1.89
1860 5533 5.849140 AGGAAGGAGAAGAAGGAGAATACT 58.151 41.667 0.00 0.00 0.00 2.12
1877 5550 7.823310 GGAGAATACTACGTCTGGATATACAGA 59.177 40.741 14.00 14.00 44.74 3.41
1911 5584 2.370281 TGCTTCTCGACAAGATCCAC 57.630 50.000 4.45 0.00 32.82 4.02
1942 5615 4.657969 ACCTAGATGCTCTTTCCAAGCTAT 59.342 41.667 0.00 0.00 40.50 2.97
2168 5841 1.745115 GCCTCGTTGCCTACATGCA 60.745 57.895 0.00 0.00 40.07 3.96
2413 6087 1.007271 CGACTCTTGCACTCACGGT 60.007 57.895 0.00 0.00 0.00 4.83
2468 6142 2.041216 ACCCAATCCTTCACCTACCAAC 59.959 50.000 0.00 0.00 0.00 3.77
2490 6164 4.774726 ACTCAAGCTCAGAGACCTTATCAA 59.225 41.667 19.59 0.00 36.91 2.57
2534 6208 4.745620 CGGGCGGTTCAAAAGAAATTTAAA 59.254 37.500 0.00 0.00 0.00 1.52
2543 6217 8.878769 GTTCAAAAGAAATTTAAAGCTGACCAA 58.121 29.630 0.00 0.00 0.00 3.67
2544 6218 8.647143 TCAAAAGAAATTTAAAGCTGACCAAG 57.353 30.769 0.00 0.00 0.00 3.61
2545 6219 7.710475 TCAAAAGAAATTTAAAGCTGACCAAGG 59.290 33.333 0.00 0.00 0.00 3.61
2546 6220 6.976934 AAGAAATTTAAAGCTGACCAAGGA 57.023 33.333 0.00 0.00 0.00 3.36
2613 6287 0.829990 AACAGGGGTTTGTGCCTTTG 59.170 50.000 0.00 0.00 31.83 2.77
2617 6291 1.912731 AGGGGTTTGTGCCTTTGTTTT 59.087 42.857 0.00 0.00 0.00 2.43
2619 6293 2.421775 GGGGTTTGTGCCTTTGTTTTTG 59.578 45.455 0.00 0.00 0.00 2.44
2620 6294 3.078097 GGGTTTGTGCCTTTGTTTTTGT 58.922 40.909 0.00 0.00 0.00 2.83
2657 6332 6.841601 TGCTTTCTACTATATTTCCTGCCAT 58.158 36.000 0.00 0.00 0.00 4.40
2686 6361 9.859427 TTTGCTTAAATGTCCTTTATTGATCTG 57.141 29.630 0.00 0.00 0.00 2.90
2687 6362 7.483307 TGCTTAAATGTCCTTTATTGATCTGC 58.517 34.615 0.00 0.00 0.00 4.26
2688 6363 7.340232 TGCTTAAATGTCCTTTATTGATCTGCT 59.660 33.333 0.00 0.00 0.00 4.24
2696 6372 3.864789 TTATTGATCTGCTCCCCCTTC 57.135 47.619 0.00 0.00 0.00 3.46
3038 6714 5.874810 TGCATGGTCTTTGAGTAGTCAATAC 59.125 40.000 13.69 13.84 42.41 1.89
3066 6742 2.168326 TGCCATGCATATGACTACCG 57.832 50.000 6.97 0.00 36.36 4.02
3197 6873 3.244078 TGAACAAACGAGTGCCTCACTAT 60.244 43.478 0.00 0.00 45.44 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.731976 ACATGAAAGTTCTTCGTCTCGC 59.268 45.455 0.00 0.00 0.00 5.03
31 32 3.303351 AGATGGCCTCGGATGAAAAAT 57.697 42.857 3.32 0.00 0.00 1.82
40 41 3.679389 AGCATAATTAAGATGGCCTCGG 58.321 45.455 3.32 0.00 0.00 4.63
66 67 2.288948 TGACACCAGATTTTTGCATGGC 60.289 45.455 1.60 0.00 36.21 4.40
98 99 1.202867 TGCATGTAACAACCAGAGGCA 60.203 47.619 0.00 0.00 0.00 4.75
143 144 2.237392 GACTGGGAATCTGTGCCTACTT 59.763 50.000 0.00 0.00 38.91 2.24
170 171 8.431593 GCACGTCTTATTTCATTGCAAATTTTA 58.568 29.630 1.71 0.00 0.00 1.52
187 188 1.476891 GAGTCCCATGAGCACGTCTTA 59.523 52.381 0.00 0.00 0.00 2.10
274 275 2.659063 CCTCGGTGGACCTCATGCA 61.659 63.158 0.00 0.00 38.35 3.96
277 278 3.461773 CGCCTCGGTGGACCTCAT 61.462 66.667 0.00 0.00 38.35 2.90
325 330 3.548745 TCTCGAACCGTAGTGAGGATA 57.451 47.619 0.00 0.00 0.00 2.59
349 354 3.494048 GGATGAGGAGCTTACTGATGTGG 60.494 52.174 0.00 0.00 0.00 4.17
368 373 4.148825 GTGTGGGCTCTCGCGGAT 62.149 66.667 6.13 0.00 36.88 4.18
406 411 3.278574 TCAAGGCGTCATTCCCTATTTG 58.721 45.455 0.00 0.00 0.00 2.32
424 429 1.540363 GCCACTCCGACTTTGACTCAA 60.540 52.381 0.00 0.00 0.00 3.02
477 482 3.118261 ACTGGTGATGTTCGGAAGCATAT 60.118 43.478 0.00 0.00 0.00 1.78
613 618 5.649782 AAAAGACTGGTTGGAGCATATTG 57.350 39.130 0.00 0.00 0.00 1.90
641 806 3.256960 TGGTTGGAGCACCCCCTC 61.257 66.667 0.00 0.00 35.73 4.30
642 807 3.260100 CTGGTTGGAGCACCCCCT 61.260 66.667 0.00 0.00 35.73 4.79
645 810 0.178990 AAAGACTGGTTGGAGCACCC 60.179 55.000 0.00 0.00 35.73 4.61
646 811 1.692411 AAAAGACTGGTTGGAGCACC 58.308 50.000 0.00 0.00 37.34 5.01
669 834 2.708861 TGGAGCACCCTCTACTCAAAAA 59.291 45.455 0.00 0.00 38.21 1.94
675 840 0.178903 TGGTTGGAGCACCCTCTACT 60.179 55.000 0.00 0.00 38.21 2.57
676 841 0.250513 CTGGTTGGAGCACCCTCTAC 59.749 60.000 0.00 0.00 38.21 2.59
677 842 0.178903 ACTGGTTGGAGCACCCTCTA 60.179 55.000 0.00 0.00 38.21 2.43
678 843 1.462238 ACTGGTTGGAGCACCCTCT 60.462 57.895 0.00 0.00 38.21 3.69
680 845 1.462238 AGACTGGTTGGAGCACCCT 60.462 57.895 0.00 0.00 35.73 4.34
681 846 1.302832 CAGACTGGTTGGAGCACCC 60.303 63.158 0.00 0.00 35.73 4.61
682 847 0.603975 GACAGACTGGTTGGAGCACC 60.604 60.000 7.51 0.00 37.34 5.01
683 848 0.603975 GGACAGACTGGTTGGAGCAC 60.604 60.000 7.51 0.00 0.00 4.40
732 4346 1.006102 CTACTAGCCGGCCCAATCG 60.006 63.158 26.15 7.77 0.00 3.34
757 4371 1.668337 CGCTCTATCAGCCCAGAATCG 60.668 57.143 0.00 0.00 46.74 3.34
791 4405 5.763698 GGCTGGAAGGATATAACCTAAACAC 59.236 44.000 1.35 0.00 39.62 3.32
792 4406 5.670361 AGGCTGGAAGGATATAACCTAAACA 59.330 40.000 1.35 1.72 39.62 2.83
793 4407 6.183361 TGAGGCTGGAAGGATATAACCTAAAC 60.183 42.308 1.35 0.00 39.62 2.01
794 4408 5.908831 TGAGGCTGGAAGGATATAACCTAAA 59.091 40.000 1.35 0.00 39.62 1.85
795 4409 5.307196 GTGAGGCTGGAAGGATATAACCTAA 59.693 44.000 1.35 0.00 39.62 2.69
796 4410 4.838986 GTGAGGCTGGAAGGATATAACCTA 59.161 45.833 1.35 0.00 39.62 3.08
798 4412 3.244596 GGTGAGGCTGGAAGGATATAACC 60.245 52.174 0.00 0.00 0.00 2.85
799 4413 3.391296 TGGTGAGGCTGGAAGGATATAAC 59.609 47.826 0.00 0.00 0.00 1.89
800 4414 3.391296 GTGGTGAGGCTGGAAGGATATAA 59.609 47.826 0.00 0.00 0.00 0.98
803 4417 1.204146 GTGGTGAGGCTGGAAGGATA 58.796 55.000 0.00 0.00 0.00 2.59
804 4418 1.566298 GGTGGTGAGGCTGGAAGGAT 61.566 60.000 0.00 0.00 0.00 3.24
805 4419 2.224159 GGTGGTGAGGCTGGAAGGA 61.224 63.158 0.00 0.00 0.00 3.36
806 4420 2.352805 GGTGGTGAGGCTGGAAGG 59.647 66.667 0.00 0.00 0.00 3.46
807 4421 2.352805 GGGTGGTGAGGCTGGAAG 59.647 66.667 0.00 0.00 0.00 3.46
973 4646 2.982744 GCGCACTTGCTCCCTTTCC 61.983 63.158 0.30 0.00 39.32 3.13
975 4648 2.203337 TGCGCACTTGCTCCCTTT 60.203 55.556 5.66 0.00 39.32 3.11
976 4649 2.980233 GTGCGCACTTGCTCCCTT 60.980 61.111 32.55 0.00 39.32 3.95
1094 4767 7.123247 CCTTCTTGTAGAAACCATGGATTTGAT 59.877 37.037 21.47 6.05 33.19 2.57
1098 4771 4.706962 GCCTTCTTGTAGAAACCATGGATT 59.293 41.667 21.47 14.05 33.19 3.01
1140 4813 0.676782 CCAACGAGCGAATCCCCTTT 60.677 55.000 0.00 0.00 0.00 3.11
1230 4903 1.067821 GGCGAAGGACAGTAGGAGATG 59.932 57.143 0.00 0.00 0.00 2.90
1262 4935 1.681327 GCCAGTACACCCTCCTCGA 60.681 63.158 0.00 0.00 0.00 4.04
1308 4981 1.973281 GGGGTCGTCAGTGTCGGTA 60.973 63.158 9.84 0.00 0.00 4.02
1651 5324 1.227943 ATGCCAGCAACAGTGACGT 60.228 52.632 0.00 0.00 0.00 4.34
1671 5344 3.068307 ACTCAGATACATTACCCAGCGAC 59.932 47.826 0.00 0.00 0.00 5.19
1762 5435 0.318762 GGGGGCATATCTCGACAGTC 59.681 60.000 0.00 0.00 0.00 3.51
1859 5532 7.226918 TCAAAGACTCTGTATATCCAGACGTAG 59.773 40.741 0.00 0.00 36.57 3.51
1860 5533 7.052248 TCAAAGACTCTGTATATCCAGACGTA 58.948 38.462 0.00 0.00 36.57 3.57
1942 5615 0.401356 TTGCACAAGCCATCTCCAGA 59.599 50.000 0.00 0.00 41.13 3.86
2162 5835 1.805869 GCTGAAGAGAGTGTGCATGT 58.194 50.000 0.00 0.00 0.00 3.21
2168 5841 1.827681 TAGAGCGCTGAAGAGAGTGT 58.172 50.000 18.48 0.00 0.00 3.55
2413 6087 0.960364 GAGCCGCTCAATTCCACCAA 60.960 55.000 15.78 0.00 0.00 3.67
2490 6164 5.757808 CCCGAATGAACATTTTCTGGTTTTT 59.242 36.000 1.56 0.00 32.36 1.94
2534 6208 3.515602 ACAAAGAATCCTTGGTCAGCT 57.484 42.857 0.00 0.00 30.87 4.24
2543 6217 5.066593 GTGACTTTCCTGACAAAGAATCCT 58.933 41.667 0.02 0.00 36.92 3.24
2544 6218 5.049129 CAGTGACTTTCCTGACAAAGAATCC 60.049 44.000 0.02 0.00 36.92 3.01
2545 6219 5.561725 GCAGTGACTTTCCTGACAAAGAATC 60.562 44.000 0.00 0.00 36.92 2.52
2546 6220 4.276926 GCAGTGACTTTCCTGACAAAGAAT 59.723 41.667 0.00 0.00 36.92 2.40
2686 6361 2.044551 CAAGGCAGAAGGGGGAGC 60.045 66.667 0.00 0.00 0.00 4.70
2687 6362 2.044551 GCAAGGCAGAAGGGGGAG 60.045 66.667 0.00 0.00 0.00 4.30
2688 6363 2.532715 AGCAAGGCAGAAGGGGGA 60.533 61.111 0.00 0.00 0.00 4.81
2696 6372 2.283298 CACCTATACACAGCAAGGCAG 58.717 52.381 0.00 0.00 31.98 4.85
3038 6714 4.207635 GTCATATGCATGGCAAACAATTCG 59.792 41.667 10.16 0.00 43.62 3.34
3324 7000 3.577415 ACTACTTGGAGTTGGAGGTACAC 59.423 47.826 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.