Multiple sequence alignment - TraesCS5A01G187600

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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 TraesCS5A01G187600 chr5A 100.000 2717 0 0 1 2717 389158674 389161390 0.000000e+00 5018.0
1 TraesCS5A01G187600 chr5D 95.157 2044 74 7 685 2717 308633430 308631401 0.000000e+00 3203.0
2 TraesCS5A01G187600 chr5D 89.812 638 55 5 1 636 308634044 308633415 0.000000e+00 809.0
3 TraesCS5A01G187600 chr5B 93.919 1924 91 12 803 2717 353938166 353936260 0.000000e+00 2881.0
4 TraesCS5A01G187600 chr5B 87.591 137 15 1 1 135 353983325 353983189 1.010000e-34 158.0
5 TraesCS5A01G187600 chr5B 86.555 119 7 5 521 636 353938344 353938232 3.670000e-24 122.0
6 TraesCS5A01G187600 chr5B 92.500 80 5 1 129 208 353941216 353941138 2.210000e-21 113.0
7 TraesCS5A01G187600 chr4A 97.500 40 1 0 369 408 667788145 667788184 4.850000e-08 69.4
8 TraesCS5A01G187600 chr6B 90.385 52 4 1 361 411 530560470 530560419 1.750000e-07 67.6
9 TraesCS5A01G187600 chr7A 95.000 40 2 0 369 408 85209303 85209342 2.260000e-06 63.9
10 TraesCS5A01G187600 chr7A 95.000 40 2 0 369 408 143359405 143359444 2.260000e-06 63.9
11 TraesCS5A01G187600 chr3D 95.000 40 2 0 369 408 389633131 389633170 2.260000e-06 63.9
12 TraesCS5A01G187600 chr2D 93.023 43 3 0 369 411 169042548 169042506 2.260000e-06 63.9
13 TraesCS5A01G187600 chr1B 93.023 43 3 0 369 411 442949271 442949229 2.260000e-06 63.9
14 TraesCS5A01G187600 chr7B 97.222 36 1 0 369 404 106602246 106602281 8.120000e-06 62.1


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 TraesCS5A01G187600 chr5A 389158674 389161390 2716 False 5018.000000 5018 100.000000 1 2717 1 chr5A.!!$F1 2716
1 TraesCS5A01G187600 chr5D 308631401 308634044 2643 True 2006.000000 3203 92.484500 1 2717 2 chr5D.!!$R1 2716
2 TraesCS5A01G187600 chr5B 353936260 353941216 4956 True 1038.666667 2881 90.991333 129 2717 3 chr5B.!!$R2 2588

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
823 3322 1.066143 AGTAGTCAGCAATTCACCCGG 60.066 52.381 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 4415 3.510388 TGCAAACACAAAAATGACCGA 57.49 38.095 0.0 0.0 0.0 4.69 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
42 43 9.791820 CAATTTATGCATTAGTTGACTCAATGA 57.208 29.630 13.77 0.00 32.54 2.57
93 96 8.920665 CGAATTTTGAAATAATGCAACAACCTA 58.079 29.630 0.00 0.00 0.00 3.08
102 105 3.157932 TGCAACAACCTAGTTTTGCAC 57.842 42.857 17.82 0.24 40.58 4.57
116 119 8.500773 CCTAGTTTTGCACGTAGAATTTAGAAA 58.499 33.333 0.00 0.00 0.00 2.52
118 121 7.699566 AGTTTTGCACGTAGAATTTAGAAACA 58.300 30.769 0.00 0.00 0.00 2.83
124 127 6.183360 GCACGTAGAATTTAGAAACATCGACA 60.183 38.462 0.00 0.00 0.00 4.35
209 676 2.024176 ATAAAGTCTTGCCGCGATGT 57.976 45.000 8.23 0.00 0.00 3.06
226 693 3.684305 CGATGTCATTGGAGCTTGTGTTA 59.316 43.478 0.00 0.00 0.00 2.41
252 719 4.445879 CCATCTCACATCCATCATCTTGGT 60.446 45.833 0.00 0.00 38.01 3.67
330 797 4.332543 TGCTCATTTAGTCGGCTAAACATG 59.667 41.667 23.55 18.34 46.27 3.21
333 800 6.564873 GCTCATTTAGTCGGCTAAACATGATC 60.565 42.308 23.55 15.58 46.27 2.92
347 814 8.090831 GCTAAACATGATCACCTATGTCTCATA 58.909 37.037 0.00 0.00 36.56 2.15
375 842 2.560981 CCAAATAAAACGGCACTCCCTT 59.439 45.455 0.00 0.00 0.00 3.95
402 869 7.360017 CGATCCATATTAATTGTCGCTGCTTTA 60.360 37.037 0.00 0.00 0.00 1.85
404 871 6.989759 TCCATATTAATTGTCGCTGCTTTAGA 59.010 34.615 0.00 0.00 0.00 2.10
408 2786 4.410492 AATTGTCGCTGCTTTAGAACAG 57.590 40.909 0.00 0.00 36.96 3.16
429 2807 2.671632 GCTCTCCGAGCGAGTAGTTTTT 60.672 50.000 0.00 0.00 45.85 1.94
474 2852 5.898174 ACATGTATCAATGCATTTCCACAG 58.102 37.500 9.83 9.58 30.47 3.66
557 3048 2.009774 CAGAAGGCAATCTTACACCGG 58.990 52.381 0.00 0.00 35.50 5.28
563 3054 4.389374 AGGCAATCTTACACCGGAATATG 58.611 43.478 9.46 0.00 0.00 1.78
577 3068 5.163205 ACCGGAATATGATCAGATGGTTTGA 60.163 40.000 9.46 0.00 0.00 2.69
645 3136 3.618171 GGTAACTCTCACCCGCAAA 57.382 52.632 0.00 0.00 0.00 3.68
646 3137 1.886886 GGTAACTCTCACCCGCAAAA 58.113 50.000 0.00 0.00 0.00 2.44
647 3138 2.223745 GGTAACTCTCACCCGCAAAAA 58.776 47.619 0.00 0.00 0.00 1.94
677 3168 3.618171 GGTAACTCTCACCCGCAAA 57.382 52.632 0.00 0.00 0.00 3.68
678 3169 1.886886 GGTAACTCTCACCCGCAAAA 58.113 50.000 0.00 0.00 0.00 2.44
679 3170 2.223745 GGTAACTCTCACCCGCAAAAA 58.776 47.619 0.00 0.00 0.00 1.94
823 3322 1.066143 AGTAGTCAGCAATTCACCCGG 60.066 52.381 0.00 0.00 0.00 5.73
949 3448 4.400251 CCACTCCTCCGACCCCCT 62.400 72.222 0.00 0.00 0.00 4.79
950 3449 2.760385 CACTCCTCCGACCCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
951 3450 4.444081 ACTCCTCCGACCCCCTCG 62.444 72.222 0.00 0.00 42.54 4.63
985 3484 2.279517 GAATCGCGCATCCGGAGT 60.280 61.111 11.34 0.00 34.32 3.85
1015 3514 2.045438 CCATGGCGCAAGGTACCA 60.045 61.111 15.94 0.00 37.99 3.25
1674 4173 1.884444 GGTGGTCAGAGAGGTCGTC 59.116 63.158 0.00 0.00 0.00 4.20
1736 4235 7.519008 CGATTGAGAGGTAAGATATTGTTTGCC 60.519 40.741 0.00 0.00 0.00 4.52
1741 4240 9.174166 GAGAGGTAAGATATTGTTTGCCTTTAA 57.826 33.333 6.64 0.00 39.15 1.52
1779 4278 8.405531 TCTTGTAGTGAAATTTTTGAACCTCTG 58.594 33.333 0.00 0.00 0.00 3.35
1791 4290 7.439157 TTTTGAACCTCTGTATGAGATTGTG 57.561 36.000 0.00 0.00 45.39 3.33
1795 4294 5.091261 ACCTCTGTATGAGATTGTGGTTC 57.909 43.478 0.00 0.00 45.39 3.62
1857 4357 7.817418 TCTTTTTGGTGAATTAGTAGCAACT 57.183 32.000 0.00 0.00 39.91 3.16
1858 4358 8.232913 TCTTTTTGGTGAATTAGTAGCAACTT 57.767 30.769 0.00 0.00 37.15 2.66
1929 4429 6.025896 CAGAAGATGATCGGTCATTTTTGTG 58.974 40.000 13.46 14.41 44.96 3.33
2038 4538 2.135933 GCTACCTGATTGTACGGATGC 58.864 52.381 0.00 0.00 0.00 3.91
2434 4942 8.826710 TGACGCTAATTATTTGTTATGAAGAGG 58.173 33.333 0.00 0.00 0.00 3.69
2545 5053 9.800572 AGATCTAGAGTAATGAGTGTTATAGCA 57.199 33.333 0.00 0.00 0.00 3.49
2701 5209 7.225538 CCAACTATGAAAGTGTAGGATTAGCTG 59.774 40.741 0.00 0.00 38.88 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 70 7.795859 AGGTTGTTGCATTATTTCAAAATTCG 58.204 30.769 0.00 0.00 0.00 3.34
93 96 7.699566 TGTTTCTAAATTCTACGTGCAAAACT 58.300 30.769 0.00 0.00 0.00 2.66
102 105 7.895870 ACATGTCGATGTTTCTAAATTCTACG 58.104 34.615 0.00 0.00 40.05 3.51
116 119 5.344743 AGTCTTATCCAACATGTCGATGT 57.655 39.130 15.34 0.00 45.24 3.06
118 121 7.782049 TCTTTAGTCTTATCCAACATGTCGAT 58.218 34.615 0.00 6.22 0.00 3.59
124 127 8.560124 AGATCCTCTTTAGTCTTATCCAACAT 57.440 34.615 0.00 0.00 0.00 2.71
131 134 7.510685 TGCACCATAGATCCTCTTTAGTCTTAT 59.489 37.037 0.00 0.00 0.00 1.73
209 676 4.661222 TGGAATAACACAAGCTCCAATGA 58.339 39.130 0.00 0.00 33.25 2.57
226 693 5.844773 AGATGATGGATGTGAGATGGAAT 57.155 39.130 0.00 0.00 0.00 3.01
330 797 7.014711 TGGAAAGACTATGAGACATAGGTGATC 59.985 40.741 18.69 12.54 0.00 2.92
333 800 6.471233 TGGAAAGACTATGAGACATAGGTG 57.529 41.667 18.69 0.99 0.00 4.00
347 814 4.583073 AGTGCCGTTTTATTTGGAAAGACT 59.417 37.500 0.00 0.00 0.00 3.24
375 842 4.388773 GCAGCGACAATTAATATGGATCGA 59.611 41.667 9.55 0.00 0.00 3.59
518 2896 9.040939 GCCTTCTGTTTTAAAAACACACATAAT 57.959 29.630 1.31 0.00 0.00 1.28
557 3048 9.894783 CAAATCTCAAACCATCTGATCATATTC 57.105 33.333 0.00 0.00 0.00 1.75
563 3054 8.734386 ACTTTACAAATCTCAAACCATCTGATC 58.266 33.333 0.00 0.00 0.00 2.92
577 3068 8.796475 ACATAGCATGTCAAACTTTACAAATCT 58.204 29.630 0.00 0.00 39.92 2.40
613 3104 7.760340 GGTGAGAGTTACCTGAGTTATTAACAG 59.240 40.741 9.15 0.00 35.30 3.16
616 3107 6.127535 CGGGTGAGAGTTACCTGAGTTATTAA 60.128 42.308 0.00 0.00 45.55 1.40
618 3109 4.159879 CGGGTGAGAGTTACCTGAGTTATT 59.840 45.833 0.00 0.00 45.55 1.40
620 3111 3.087031 CGGGTGAGAGTTACCTGAGTTA 58.913 50.000 0.00 0.00 45.55 2.24
621 3112 1.893801 CGGGTGAGAGTTACCTGAGTT 59.106 52.381 0.00 0.00 45.55 3.01
622 3113 1.546961 CGGGTGAGAGTTACCTGAGT 58.453 55.000 0.00 0.00 45.55 3.41
623 3114 0.173708 GCGGGTGAGAGTTACCTGAG 59.826 60.000 7.16 0.00 45.55 3.35
624 3115 0.541063 TGCGGGTGAGAGTTACCTGA 60.541 55.000 7.16 0.00 45.55 3.86
625 3116 0.320374 TTGCGGGTGAGAGTTACCTG 59.680 55.000 0.00 0.00 45.48 4.00
626 3117 1.053424 TTTGCGGGTGAGAGTTACCT 58.947 50.000 0.00 0.00 38.30 3.08
627 3118 1.886886 TTTTGCGGGTGAGAGTTACC 58.113 50.000 0.00 0.00 37.48 2.85
647 3138 6.940867 GGGTGAGAGTTACCTGAGTTATTTTT 59.059 38.462 0.00 0.00 38.30 1.94
648 3139 6.473758 GGGTGAGAGTTACCTGAGTTATTTT 58.526 40.000 0.00 0.00 38.30 1.82
649 3140 5.337330 CGGGTGAGAGTTACCTGAGTTATTT 60.337 44.000 0.00 0.00 45.55 1.40
650 3141 4.159879 CGGGTGAGAGTTACCTGAGTTATT 59.840 45.833 0.00 0.00 45.55 1.40
651 3142 3.700038 CGGGTGAGAGTTACCTGAGTTAT 59.300 47.826 0.00 0.00 45.55 1.89
652 3143 3.087031 CGGGTGAGAGTTACCTGAGTTA 58.913 50.000 0.00 0.00 45.55 2.24
653 3144 1.893801 CGGGTGAGAGTTACCTGAGTT 59.106 52.381 0.00 0.00 45.55 3.01
654 3145 1.546961 CGGGTGAGAGTTACCTGAGT 58.453 55.000 0.00 0.00 45.55 3.41
655 3146 0.173708 GCGGGTGAGAGTTACCTGAG 59.826 60.000 7.16 0.00 45.55 3.35
656 3147 0.541063 TGCGGGTGAGAGTTACCTGA 60.541 55.000 7.16 0.00 45.55 3.86
657 3148 0.320374 TTGCGGGTGAGAGTTACCTG 59.680 55.000 0.00 0.00 45.48 4.00
658 3149 1.053424 TTTGCGGGTGAGAGTTACCT 58.947 50.000 0.00 0.00 38.30 3.08
659 3150 1.886886 TTTTGCGGGTGAGAGTTACC 58.113 50.000 0.00 0.00 37.48 2.85
743 3236 4.365514 TGAGAGCTTTGATGTTTACCCA 57.634 40.909 0.00 0.00 0.00 4.51
949 3448 2.106938 GACAGGGATGCGATGCGA 59.893 61.111 0.00 0.00 0.00 5.10
950 3449 3.333189 CGACAGGGATGCGATGCG 61.333 66.667 0.00 0.00 0.00 4.73
951 3450 2.923426 TTCCGACAGGGATGCGATGC 62.923 60.000 0.00 0.00 46.62 3.91
952 3451 0.250038 ATTCCGACAGGGATGCGATG 60.250 55.000 0.00 0.00 46.62 3.84
953 3452 0.034059 GATTCCGACAGGGATGCGAT 59.966 55.000 0.00 0.00 46.62 4.58
1736 4235 8.660373 CACTACAAGATTAAGCTGGAGTTAAAG 58.340 37.037 1.14 0.00 0.00 1.85
1741 4240 6.360370 TTCACTACAAGATTAAGCTGGAGT 57.640 37.500 1.14 2.39 0.00 3.85
1779 4278 6.978659 TCGTATCAAGAACCACAATCTCATAC 59.021 38.462 0.00 0.00 0.00 2.39
1791 4290 6.927294 AAGGAAATCATCGTATCAAGAACC 57.073 37.500 0.00 0.00 0.00 3.62
1795 4294 9.708222 CAGTAAAAAGGAAATCATCGTATCAAG 57.292 33.333 0.00 0.00 0.00 3.02
1849 4349 3.975168 TCCACCTCCTAAAGTTGCTAC 57.025 47.619 0.00 0.00 0.00 3.58
1857 4357 6.840090 TTATCATTCCATCCACCTCCTAAA 57.160 37.500 0.00 0.00 0.00 1.85
1858 4358 6.332635 ACATTATCATTCCATCCACCTCCTAA 59.667 38.462 0.00 0.00 0.00 2.69
1915 4415 3.510388 TGCAAACACAAAAATGACCGA 57.490 38.095 0.00 0.00 0.00 4.69
1929 4429 9.830294 ACGGTTAACTAGTTTATATTTGCAAAC 57.170 29.630 15.41 7.63 35.36 2.93
2038 4538 7.420800 ACTTAGTCACAAGAAGAAAGCAATTG 58.579 34.615 0.00 0.00 0.00 2.32
2103 4608 6.479972 TTGACGATATCCAAACCATCTACT 57.520 37.500 0.00 0.00 0.00 2.57
2106 4611 6.826668 TGTATTGACGATATCCAAACCATCT 58.173 36.000 0.00 0.00 0.00 2.90
2191 4698 9.768662 AACACTTTCTAATCAATTGCTTGAATT 57.231 25.926 4.80 0.26 44.29 2.17
2545 5053 4.640201 GTGGACATGTGGCACAATATAAGT 59.360 41.667 25.95 15.33 44.16 2.24


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

AutoCloner maintained by Alex Coulton.