Multiple sequence alignment - TraesCS5A01G397300

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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 TraesCS5A01G397300 chr5A 100.000 3885 0 0 1 3885 591677657 591681541 0 7175
1 TraesCS5A01G397300 chr5A 93.450 3252 160 32 1 3210 66106066 66109306 0 4776
2 TraesCS5A01G397300 chr5A 93.715 2116 98 21 1 2098 482761269 482759171 0 3138
3 TraesCS5A01G397300 chr5A 97.365 683 13 4 3204 3885 672587034 672586356 0 1157
4 TraesCS5A01G397300 chr5B 93.196 3263 156 23 1 3216 134559012 134555769 0 4735
5 TraesCS5A01G397300 chr5B 92.177 2889 152 44 2 2836 567614652 567611784 0 4015
6 TraesCS5A01G397300 chr3A 95.073 2111 81 12 1 2098 164756788 164754688 0 3301
7 TraesCS5A01G397300 chr3A 93.661 2114 101 23 1 2098 692602053 692599957 0 3131
8 TraesCS5A01G397300 chr3A 94.526 1224 59 7 1998 3216 164754722 164753502 0 1882
9 TraesCS5A01G397300 chr3A 97.214 682 14 3 3204 3885 88152477 88153153 0 1149
10 TraesCS5A01G397300 chr3A 97.072 683 14 6 3204 3885 482193805 482193128 0 1146
11 TraesCS5A01G397300 chr2A 94.882 2110 90 13 4 2098 560676424 560674318 0 3282
12 TraesCS5A01G397300 chr2A 94.504 1219 57 7 1998 3210 127164109 127165323 0 1871
13 TraesCS5A01G397300 chr2A 94.477 1213 58 7 2002 3211 206086189 206087395 0 1860
14 TraesCS5A01G397300 chr6A 94.371 2114 91 18 1 2098 54974564 54972463 0 3219
15 TraesCS5A01G397300 chr6A 94.073 2109 101 16 4 2098 22756721 22754623 0 3181
16 TraesCS5A01G397300 chr6A 95.000 1220 54 6 2002 3216 54972494 54971277 0 1908
17 TraesCS5A01G397300 chr6A 94.758 1221 54 9 2002 3216 22754654 22753438 0 1892
18 TraesCS5A01G397300 chr6A 87.759 964 83 22 1164 2098 116930224 116929267 0 1094
19 TraesCS5A01G397300 chr7A 93.848 2113 99 17 1 2098 67382110 67380014 0 3153
20 TraesCS5A01G397300 chr7A 93.756 2114 102 18 1 2098 67145804 67143705 0 3145
21 TraesCS5A01G397300 chr7A 94.853 1224 53 9 1993 3211 595105915 595107133 0 1903
22 TraesCS5A01G397300 chr7A 89.966 1465 101 37 2013 3444 139512704 139511253 0 1849
23 TraesCS5A01G397300 chr7A 97.365 683 13 4 3204 3885 450300385 450299707 0 1157
24 TraesCS5A01G397300 chr7A 96.930 684 14 6 3204 3885 2357803 2358481 0 1140
25 TraesCS5A01G397300 chr7B 85.056 2409 282 50 500 2874 90757557 90759921 0 2383
26 TraesCS5A01G397300 chr1A 94.431 1221 58 8 2002 3216 399817543 399816327 0 1869
27 TraesCS5A01G397300 chr1A 96.934 685 14 5 3204 3885 583692465 583693145 0 1142
28 TraesCS5A01G397300 chr4A 97.511 683 12 5 3204 3885 121226585 121225907 0 1162
29 TraesCS5A01G397300 chr4A 97.329 674 13 5 3214 3885 136456042 136456712 0 1140
30 TraesCS5A01G397300 chr4A 96.788 685 16 4 3204 3885 282583509 282584190 0 1138


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 TraesCS5A01G397300 chr5A 591677657 591681541 3884 False 7175.0 7175 100.0000 1 3885 1 chr5A.!!$F2 3884
1 TraesCS5A01G397300 chr5A 66106066 66109306 3240 False 4776.0 4776 93.4500 1 3210 1 chr5A.!!$F1 3209
2 TraesCS5A01G397300 chr5A 482759171 482761269 2098 True 3138.0 3138 93.7150 1 2098 1 chr5A.!!$R1 2097
3 TraesCS5A01G397300 chr5A 672586356 672587034 678 True 1157.0 1157 97.3650 3204 3885 1 chr5A.!!$R2 681
4 TraesCS5A01G397300 chr5B 134555769 134559012 3243 True 4735.0 4735 93.1960 1 3216 1 chr5B.!!$R1 3215
5 TraesCS5A01G397300 chr5B 567611784 567614652 2868 True 4015.0 4015 92.1770 2 2836 1 chr5B.!!$R2 2834
6 TraesCS5A01G397300 chr3A 692599957 692602053 2096 True 3131.0 3131 93.6610 1 2098 1 chr3A.!!$R2 2097
7 TraesCS5A01G397300 chr3A 164753502 164756788 3286 True 2591.5 3301 94.7995 1 3216 2 chr3A.!!$R3 3215
8 TraesCS5A01G397300 chr3A 88152477 88153153 676 False 1149.0 1149 97.2140 3204 3885 1 chr3A.!!$F1 681
9 TraesCS5A01G397300 chr3A 482193128 482193805 677 True 1146.0 1146 97.0720 3204 3885 1 chr3A.!!$R1 681
10 TraesCS5A01G397300 chr2A 560674318 560676424 2106 True 3282.0 3282 94.8820 4 2098 1 chr2A.!!$R1 2094
11 TraesCS5A01G397300 chr2A 127164109 127165323 1214 False 1871.0 1871 94.5040 1998 3210 1 chr2A.!!$F1 1212
12 TraesCS5A01G397300 chr2A 206086189 206087395 1206 False 1860.0 1860 94.4770 2002 3211 1 chr2A.!!$F2 1209
13 TraesCS5A01G397300 chr6A 54971277 54974564 3287 True 2563.5 3219 94.6855 1 3216 2 chr6A.!!$R3 3215
14 TraesCS5A01G397300 chr6A 22753438 22756721 3283 True 2536.5 3181 94.4155 4 3216 2 chr6A.!!$R2 3212
15 TraesCS5A01G397300 chr6A 116929267 116930224 957 True 1094.0 1094 87.7590 1164 2098 1 chr6A.!!$R1 934
16 TraesCS5A01G397300 chr7A 67380014 67382110 2096 True 3153.0 3153 93.8480 1 2098 1 chr7A.!!$R2 2097
17 TraesCS5A01G397300 chr7A 67143705 67145804 2099 True 3145.0 3145 93.7560 1 2098 1 chr7A.!!$R1 2097
18 TraesCS5A01G397300 chr7A 595105915 595107133 1218 False 1903.0 1903 94.8530 1993 3211 1 chr7A.!!$F2 1218
19 TraesCS5A01G397300 chr7A 139511253 139512704 1451 True 1849.0 1849 89.9660 2013 3444 1 chr7A.!!$R3 1431
20 TraesCS5A01G397300 chr7A 450299707 450300385 678 True 1157.0 1157 97.3650 3204 3885 1 chr7A.!!$R4 681
21 TraesCS5A01G397300 chr7A 2357803 2358481 678 False 1140.0 1140 96.9300 3204 3885 1 chr7A.!!$F1 681
22 TraesCS5A01G397300 chr7B 90757557 90759921 2364 False 2383.0 2383 85.0560 500 2874 1 chr7B.!!$F1 2374
23 TraesCS5A01G397300 chr1A 399816327 399817543 1216 True 1869.0 1869 94.4310 2002 3216 1 chr1A.!!$R1 1214
24 TraesCS5A01G397300 chr1A 583692465 583693145 680 False 1142.0 1142 96.9340 3204 3885 1 chr1A.!!$F1 681
25 TraesCS5A01G397300 chr4A 121225907 121226585 678 True 1162.0 1162 97.5110 3204 3885 1 chr4A.!!$R1 681
26 TraesCS5A01G397300 chr4A 136456042 136456712 670 False 1140.0 1140 97.3290 3214 3885 1 chr4A.!!$F1 671
27 TraesCS5A01G397300 chr4A 282583509 282584190 681 False 1138.0 1138 96.7880 3204 3885 1 chr4A.!!$F2 681

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
416 420 2.157668 GTCTGTTGCCATGTTACAGTCG 59.842 50.0 14.81 0.0 40.08 4.18 F
1127 1169 0.107654 GGTTGCCACCTCGAGCTTAT 60.108 55.0 6.99 0.0 40.44 1.73 F
2709 3010 0.107361 ACTATAGCGTGTTTGGGGGC 60.107 55.0 0.00 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 1453 1.145377 AACGGCAGTCTTCCACGTT 59.855 52.632 0.0 0.0 42.17 3.99 R
2870 3175 0.610232 GATGCTCAACAGGTGCCCTT 60.610 55.000 0.0 0.0 35.15 3.95 R
3641 3964 4.122337 TCCTTTATATACGGAGGCAGGA 57.878 45.455 0.0 0.0 0.00 3.86 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
227 230 2.523245 TGCATGTTGCCACTTGGATAA 58.477 42.857 0.00 0.00 44.23 1.75
316 320 3.523547 GCAAATTGGCTGCATAACATGA 58.476 40.909 0.00 0.00 39.69 3.07
370 374 6.483405 TGCCATATATATGCTTTCCATGTGA 58.517 36.000 16.08 0.00 35.34 3.58
416 420 2.157668 GTCTGTTGCCATGTTACAGTCG 59.842 50.000 14.81 0.00 40.08 4.18
568 595 9.369904 GAATTCTATGTTGCATTTTAACATGGT 57.630 29.630 10.54 0.00 45.49 3.55
784 821 7.938563 TTTCAAATGTAACCAATGTGCTTAC 57.061 32.000 0.00 0.00 0.00 2.34
813 850 7.463119 GCCACATTTATGTTTTCGACAATCATG 60.463 37.037 8.62 0.00 42.62 3.07
875 916 6.363357 GCATTCACTAGTTGACATTTTTCACC 59.637 38.462 0.00 0.00 32.26 4.02
909 950 3.559171 GGCAAGGACATTCTGTTAGGTGA 60.559 47.826 0.00 0.00 0.00 4.02
937 979 5.472148 TGCTTACTTCCTGCATTTTCATTG 58.528 37.500 0.00 0.00 0.00 2.82
969 1011 4.755123 ACAATTTGGTCTGTTCTTACCTCG 59.245 41.667 0.78 0.00 36.67 4.63
1036 1078 1.065199 GGATCCACCACAGCAGAATCA 60.065 52.381 6.95 0.00 38.79 2.57
1037 1079 2.618816 GGATCCACCACAGCAGAATCAA 60.619 50.000 6.95 0.00 38.79 2.57
1126 1168 1.295423 GGTTGCCACCTCGAGCTTA 59.705 57.895 6.99 0.00 40.44 3.09
1127 1169 0.107654 GGTTGCCACCTCGAGCTTAT 60.108 55.000 6.99 0.00 40.44 1.73
1219 1267 4.316205 TGCAGAAGAAGAAACGTACTCA 57.684 40.909 0.00 0.00 0.00 3.41
1285 1333 0.323542 ACCGACGATCAGAAGGGAGT 60.324 55.000 0.00 0.00 0.00 3.85
1356 1404 3.825014 TCTAGTCAACCCTATATGCGACC 59.175 47.826 0.00 0.00 0.00 4.79
1405 1453 3.778075 TCTAGGGAATTTGTGATTCCGGA 59.222 43.478 0.00 0.00 46.46 5.14
1513 1561 1.997669 AACAAGATCGAGGAAGCGTC 58.002 50.000 0.00 0.00 0.00 5.19
1704 1755 3.073411 TCCCCATCCTGGTGAATGATA 57.927 47.619 0.00 0.00 35.17 2.15
1772 1828 0.325933 TGCAAGCTAGTCACTGCCAT 59.674 50.000 3.48 0.00 0.00 4.40
1846 1907 2.025767 AATTTTGTGCGGTGCAGGCA 62.026 50.000 8.22 8.22 40.08 4.75
1946 2007 0.393077 CCAGAAGGGTTGTCGACTGT 59.607 55.000 17.92 0.00 0.00 3.55
2018 2175 2.578786 TGCATGGCAACCTGATCATAG 58.421 47.619 0.00 0.00 34.76 2.23
2512 2803 1.876322 GCCATGGCTGTCTGAGTATC 58.124 55.000 29.98 0.00 38.26 2.24
2709 3010 0.107361 ACTATAGCGTGTTTGGGGGC 60.107 55.000 0.00 0.00 0.00 5.80
2825 3129 7.792374 ATATTTTTGATGTCGTGCTAGTGAT 57.208 32.000 0.00 0.00 0.00 3.06
2867 3172 1.675483 TGCTTCTTGTTTCGTGCACAT 59.325 42.857 18.64 0.00 0.00 3.21
2907 3212 4.399303 AGCATCTAATTGGGTAGTTTGCAC 59.601 41.667 0.00 0.00 35.56 4.57
2995 3301 2.034879 CGGTTGCGAGGCAGTTCAT 61.035 57.895 0.00 0.00 40.61 2.57
3359 3678 4.193826 ACGTAGAGGAAGTAGTCGTACA 57.806 45.455 0.00 0.00 0.00 2.90
3479 3801 2.162681 CAAAGCTTCGGGGATGAGTTT 58.837 47.619 0.00 0.00 0.00 2.66
3492 3814 2.309528 TGAGTTTCGTCAGCACAACT 57.690 45.000 0.00 0.00 32.02 3.16
3627 3949 2.221749 CACGAGGATCAACTTGTGTGTG 59.778 50.000 9.92 0.00 44.34 3.82
3628 3950 2.158957 ACGAGGATCAACTTGTGTGTGT 60.159 45.455 0.00 0.00 33.85 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 80 8.370182 ACAATCATTCAGGAAAAATTAGTTGCT 58.630 29.630 0.00 0.00 0.00 3.91
111 114 4.349930 ACTTTACCATTCCTACAGTGTGGT 59.650 41.667 5.88 6.05 44.75 4.16
316 320 6.147864 ACAGTTGATGTGCAAATTAGTTGT 57.852 33.333 0.00 0.00 41.91 3.32
370 374 4.022416 TGCTGTGTTCAGACAAAAACTTGT 60.022 37.500 0.00 0.00 43.76 3.16
416 420 7.378461 CGTACAATGAATTTGCCACATTATACC 59.622 37.037 0.00 0.00 39.03 2.73
549 575 9.499479 TGAAATTACCATGTTAAAATGCAACAT 57.501 25.926 0.00 0.00 45.23 2.71
568 595 6.648725 GGCAAAAATGTGCTAGGTTGAAATTA 59.351 34.615 0.00 0.00 44.31 1.40
784 821 5.218885 TGTCGAAAACATAAATGTGGCAAG 58.781 37.500 0.00 0.00 41.61 4.01
909 950 2.638480 TGCAGGAAGTAAGCAGTTGT 57.362 45.000 0.00 0.00 33.75 3.32
937 979 0.039527 GACCAAATTGTCACGGTGGC 60.040 55.000 5.63 5.63 35.29 5.01
1036 1078 2.158813 TCTTTTCTCCGTCCAGTTGCTT 60.159 45.455 0.00 0.00 0.00 3.91
1037 1079 1.416401 TCTTTTCTCCGTCCAGTTGCT 59.584 47.619 0.00 0.00 0.00 3.91
1127 1169 9.872757 GAAATTTTAGTTCATGACAAACGACTA 57.127 29.630 0.00 0.00 0.00 2.59
1219 1267 3.260100 CCTGGGAGGCCCTGTTGT 61.260 66.667 0.00 0.00 45.70 3.32
1285 1333 1.748244 GCATACCCATCTCAGCAGCAA 60.748 52.381 0.00 0.00 0.00 3.91
1356 1404 1.659098 GTCGTAAATCTCACCAAGCCG 59.341 52.381 0.00 0.00 0.00 5.52
1405 1453 1.145377 AACGGCAGTCTTCCACGTT 59.855 52.632 0.00 0.00 42.17 3.99
1513 1561 1.272212 CAGGAAACAAATGGGGGAACG 59.728 52.381 0.00 0.00 0.00 3.95
1846 1907 9.434420 TTCATGTTCTTCACATTTTTCAGTTTT 57.566 25.926 0.00 0.00 44.40 2.43
1878 1939 3.941483 CAGGAAGTCGGCAATGAACTTAT 59.059 43.478 0.00 0.00 0.00 1.73
2220 2499 3.756963 AGACAGTCAACGTACATGAGCTA 59.243 43.478 0.00 0.00 0.00 3.32
2234 2513 2.300152 GGTGGACAGATCAAGACAGTCA 59.700 50.000 2.66 0.00 0.00 3.41
2372 2652 3.058914 CAGAACTAACCTGCAGTTTTCCG 60.059 47.826 13.81 0.00 40.05 4.30
2512 2803 2.427095 TGTGGAGTGAGACATGGATACG 59.573 50.000 0.00 0.00 42.51 3.06
2709 3010 3.704061 TCCACTTTCCAAAGTTTTGAGGG 59.296 43.478 6.18 0.63 46.52 4.30
2736 3037 1.748329 AAGACGGAGCTGAGTGCACA 61.748 55.000 21.04 0.00 45.94 4.57
2825 3129 5.124776 GCAGCAGTAACCAACCATATTACAA 59.875 40.000 0.00 0.00 32.33 2.41
2870 3175 0.610232 GATGCTCAACAGGTGCCCTT 60.610 55.000 0.00 0.00 35.15 3.95
2907 3212 2.409870 GCAAGCTGGTCATTCCGGG 61.410 63.158 0.00 0.00 42.62 5.73
2995 3301 3.773418 TCCGTTCTGGGACAAATGTAA 57.227 42.857 0.00 0.00 38.70 2.41
3359 3678 1.041437 GGTCGGATCGGGAAGAAGAT 58.959 55.000 0.00 0.00 0.00 2.40
3458 3780 0.693049 ACTCATCCCCGAAGCTTTGT 59.307 50.000 12.77 0.00 0.00 2.83
3492 3814 2.215196 CATCATCATCGTCACCATGCA 58.785 47.619 0.00 0.00 0.00 3.96
3641 3964 4.122337 TCCTTTATATACGGAGGCAGGA 57.878 45.455 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.