Multiple sequence alignment - TraesCS5A01G206100

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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 TraesCS5A01G206100 chr5A 100.000 2439 0 0 766 3204 416123200 416125638 0.000000e+00 4505.0
1 TraesCS5A01G206100 chr5A 100.000 350 0 0 1 350 416122435 416122784 0.000000e+00 647.0
2 TraesCS5A01G206100 chr5A 80.537 745 133 9 2308 3043 605025870 605026611 2.160000e-156 562.0
3 TraesCS5A01G206100 chr4B 82.314 2437 357 66 809 3204 620106354 620103951 0.000000e+00 2045.0
4 TraesCS5A01G206100 chr4B 82.215 2429 355 68 818 3204 620190295 620187902 0.000000e+00 2021.0
5 TraesCS5A01G206100 chr4B 82.042 2439 359 68 809 3204 620139847 620137445 0.000000e+00 2004.0
6 TraesCS5A01G206100 chr3A 92.617 1368 70 14 766 2128 721505770 721504429 0.000000e+00 1938.0
7 TraesCS5A01G206100 chr3A 82.666 1823 271 30 1413 3204 288603970 288605778 0.000000e+00 1574.0
8 TraesCS5A01G206100 chr3A 93.447 351 22 1 1 350 721506169 721505819 1.320000e-143 520.0
9 TraesCS5A01G206100 chr7B 86.272 1792 222 16 1421 3204 700727493 700729268 0.000000e+00 1925.0
10 TraesCS5A01G206100 chr7B 82.489 1639 247 31 767 2394 700632879 700634488 0.000000e+00 1400.0
11 TraesCS5A01G206100 chr7B 87.226 822 90 10 2389 3204 700666725 700667537 0.000000e+00 922.0
12 TraesCS5A01G206100 chr7B 77.064 654 124 23 771 1416 700726806 700727441 1.410000e-93 353.0
13 TraesCS5A01G206100 chr7D 92.210 1027 66 6 1931 2945 185916689 185915665 0.000000e+00 1441.0
14 TraesCS5A01G206100 chr1B 79.581 1577 274 39 1480 3043 553889489 553891030 0.000000e+00 1085.0
15 TraesCS5A01G206100 chr1B 81.780 236 42 1 1465 1699 29583133 29582898 2.520000e-46 196.0
16 TraesCS5A01G206100 chr5B 79.201 1577 276 39 1483 3043 704546509 704544969 0.000000e+00 1048.0
17 TraesCS5A01G206100 chr5B 78.858 648 122 13 2563 3204 704536832 704536194 1.060000e-114 424.0
18 TraesCS5A01G206100 chr5B 83.772 228 35 2 1467 1693 595294475 595294249 6.960000e-52 215.0
19 TraesCS5A01G206100 chr1A 80.820 1293 214 29 822 2101 299295342 299296613 0.000000e+00 983.0
20 TraesCS5A01G206100 chr1A 80.952 84 15 1 810 893 71425591 71425509 7.420000e-07 65.8
21 TraesCS5A01G206100 chr6D 80.217 920 158 17 1459 2374 447920712 447919813 0.000000e+00 669.0
22 TraesCS5A01G206100 chr3B 75.857 671 129 19 1465 2126 809220619 809219973 8.630000e-81 311.0
23 TraesCS5A01G206100 chr3B 76.000 125 27 2 772 893 743521636 743521760 9.600000e-06 62.1
24 TraesCS5A01G206100 chr2B 79.683 379 61 12 809 1180 556706243 556706612 3.170000e-65 259.0
25 TraesCS5A01G206100 chr2D 76.852 432 79 14 1543 1962 119819958 119819536 1.160000e-54 224.0
26 TraesCS5A01G206100 chr1D 95.455 44 2 0 851 894 16712666 16712709 1.590000e-08 71.3


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 TraesCS5A01G206100 chr5A 416122435 416125638 3203 False 2576 4505 100.000 1 3204 2 chr5A.!!$F2 3203
1 TraesCS5A01G206100 chr5A 605025870 605026611 741 False 562 562 80.537 2308 3043 1 chr5A.!!$F1 735
2 TraesCS5A01G206100 chr4B 620103951 620106354 2403 True 2045 2045 82.314 809 3204 1 chr4B.!!$R1 2395
3 TraesCS5A01G206100 chr4B 620187902 620190295 2393 True 2021 2021 82.215 818 3204 1 chr4B.!!$R3 2386
4 TraesCS5A01G206100 chr4B 620137445 620139847 2402 True 2004 2004 82.042 809 3204 1 chr4B.!!$R2 2395
5 TraesCS5A01G206100 chr3A 288603970 288605778 1808 False 1574 1574 82.666 1413 3204 1 chr3A.!!$F1 1791
6 TraesCS5A01G206100 chr3A 721504429 721506169 1740 True 1229 1938 93.032 1 2128 2 chr3A.!!$R1 2127
7 TraesCS5A01G206100 chr7B 700632879 700634488 1609 False 1400 1400 82.489 767 2394 1 chr7B.!!$F1 1627
8 TraesCS5A01G206100 chr7B 700726806 700729268 2462 False 1139 1925 81.668 771 3204 2 chr7B.!!$F3 2433
9 TraesCS5A01G206100 chr7B 700666725 700667537 812 False 922 922 87.226 2389 3204 1 chr7B.!!$F2 815
10 TraesCS5A01G206100 chr7D 185915665 185916689 1024 True 1441 1441 92.210 1931 2945 1 chr7D.!!$R1 1014
11 TraesCS5A01G206100 chr1B 553889489 553891030 1541 False 1085 1085 79.581 1480 3043 1 chr1B.!!$F1 1563
12 TraesCS5A01G206100 chr5B 704544969 704546509 1540 True 1048 1048 79.201 1483 3043 1 chr5B.!!$R3 1560
13 TraesCS5A01G206100 chr5B 704536194 704536832 638 True 424 424 78.858 2563 3204 1 chr5B.!!$R2 641
14 TraesCS5A01G206100 chr1A 299295342 299296613 1271 False 983 983 80.820 822 2101 1 chr1A.!!$F1 1279
15 TraesCS5A01G206100 chr6D 447919813 447920712 899 True 669 669 80.217 1459 2374 1 chr6D.!!$R1 915
16 TraesCS5A01G206100 chr3B 809219973 809220619 646 True 311 311 75.857 1465 2126 1 chr3B.!!$R1 661

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
150 152 0.038251 TTCTGTACGACAGCTGGCTG 60.038 55.0 19.55 19.42 45.54 4.85 F
285 287 1.017177 GTCACCGCCGCAGTAAATGA 61.017 55.0 0.00 0.00 0.00 2.57 F
1117 1123 0.176910 TGGTCATATCGGCGCTTCAA 59.823 50.0 7.64 0.00 0.00 2.69 F
2155 2265 0.741915 TCAACAAAACCCTTGCCGTC 59.258 50.0 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 1069 0.322975 AAGATGAGTCGGCAGTTGCT 59.677 50.0 3.88 0.0 41.70 3.91 R
1166 1172 0.617413 CTTCCCAGTGGACTCAGCAT 59.383 55.0 11.95 0.0 41.57 3.79 R
2201 2311 0.895530 CTGCTTTCCTCGTCACCCTA 59.104 55.0 0.00 0.0 0.00 3.53 R
3119 3274 0.758734 CCACTCTGTGACAGGACCAA 59.241 55.0 13.33 0.0 35.23 3.67 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
46 47 6.151648 CACTTTATCATGTTCATTGGTCCACT 59.848 38.462 0.00 0.00 0.00 4.00
111 113 3.485216 CGTGGTAAAACGAATCTGATGCC 60.485 47.826 0.00 0.00 46.49 4.40
144 146 2.471743 GTGAACAGTTCTGTACGACAGC 59.528 50.000 14.51 0.00 45.54 4.40
150 152 0.038251 TTCTGTACGACAGCTGGCTG 60.038 55.000 19.55 19.42 45.54 4.85
159 161 2.116772 AGCTGGCTGGCACATTGT 59.883 55.556 0.00 0.00 38.20 2.71
175 177 1.884075 TTGTAGGAGCGTGCCGTGAT 61.884 55.000 0.00 0.00 0.00 3.06
209 211 3.426568 GTGGCTCAGCTCCGTTGC 61.427 66.667 0.00 0.00 0.00 4.17
243 245 2.964925 GAACAGACACGCACGGCA 60.965 61.111 0.00 0.00 0.00 5.69
261 263 1.200020 GCACCGTCTGATGGAAAAAGG 59.800 52.381 22.36 5.71 0.00 3.11
272 274 3.588891 GAAAAAGGCGCCGTCACCG 62.589 63.158 23.20 0.00 0.00 4.94
285 287 1.017177 GTCACCGCCGCAGTAAATGA 61.017 55.000 0.00 0.00 0.00 2.57
289 291 1.134640 ACCGCCGCAGTAAATGATGTA 60.135 47.619 0.00 0.00 0.00 2.29
340 342 3.385111 AGATATGACGGTCTTCTCCCAAC 59.615 47.826 9.88 0.00 0.00 3.77
804 806 1.959226 TGAAGACGGCGCAAGTTCC 60.959 57.895 10.83 0.00 41.68 3.62
806 808 2.171489 GAAGACGGCGCAAGTTCCAC 62.171 60.000 10.83 0.00 41.68 4.02
943 945 3.123804 GTCGCATAGATGAACAACCGAT 58.876 45.455 0.00 0.00 0.00 4.18
965 969 3.638160 TGGAAAAATGCTGACTGCTTCTT 59.362 39.130 5.87 0.00 43.37 2.52
972 976 2.358898 TGCTGACTGCTTCTTGTTTTCC 59.641 45.455 5.87 0.00 43.37 3.13
1117 1123 0.176910 TGGTCATATCGGCGCTTCAA 59.823 50.000 7.64 0.00 0.00 2.69
1161 1167 4.379243 AGGCCGCTCTCACCAACG 62.379 66.667 0.00 0.00 0.00 4.10
1166 1172 2.004583 CCGCTCTCACCAACGAAATA 57.995 50.000 0.00 0.00 0.00 1.40
1238 1244 6.386927 AGGAGGTACATAACTGAATCATGGAA 59.613 38.462 0.00 0.00 0.00 3.53
1291 1300 8.100791 AGTAGAGTAGTAGATAATCCTCTGCAG 58.899 40.741 7.63 7.63 35.12 4.41
1323 1355 3.191162 GTGTCAGCTATGGTGATGCAAAA 59.809 43.478 0.00 0.00 42.05 2.44
1457 1541 1.069358 GCTCCCCTTGATAGAGTTCCG 59.931 57.143 0.00 0.00 0.00 4.30
1708 1799 4.346129 GTCAGCAACAAGAAACTCACTTG 58.654 43.478 0.00 0.00 46.69 3.16
1756 1860 4.318333 CGTGACCTCTGCAATTTCATATCG 60.318 45.833 0.00 0.00 0.00 2.92
1757 1861 4.811024 GTGACCTCTGCAATTTCATATCGA 59.189 41.667 0.00 0.00 0.00 3.59
1773 1877 3.942130 ATCGAACTGTCTGACATGTGA 57.058 42.857 11.45 7.65 0.00 3.58
1797 1906 3.711190 AGAAAATGTTTGCAGGGGAAACT 59.289 39.130 13.21 0.00 34.88 2.66
1962 2072 1.112315 TGGCCATCCCACAAACACAC 61.112 55.000 0.00 0.00 39.18 3.82
2009 2119 5.920840 GTGAAACAGCTTAGGGAAAACAATC 59.079 40.000 0.00 0.00 36.32 2.67
2114 2224 0.901827 TCTGTGCGGGAGAATAAGCA 59.098 50.000 0.00 0.00 37.26 3.91
2155 2265 0.741915 TCAACAAAACCCTTGCCGTC 59.258 50.000 0.00 0.00 0.00 4.79
2201 2311 3.583086 CCCGGAATTCACATATAGGGTCT 59.417 47.826 0.73 0.00 33.22 3.85
2344 2454 2.215907 TGCCATTTGGTTTGTTCGTG 57.784 45.000 0.00 0.00 37.57 4.35
2587 2721 5.682943 TGTACAATTTGTAGACCAAGCAC 57.317 39.130 9.49 0.00 32.84 4.40
2608 2742 2.709213 GAGCCATGGAGATAGCAATCC 58.291 52.381 18.40 0.00 36.05 3.01
2748 2882 5.824904 AAGTGGTGAATCACATGATAAGC 57.175 39.130 15.86 0.00 39.93 3.09
2784 2921 0.774276 TGGCATGGGGTTCACTTGTA 59.226 50.000 0.00 0.00 0.00 2.41
2850 2987 1.204941 GAGATACGACACAAGTGGGCT 59.795 52.381 5.08 0.00 34.19 5.19
2871 3008 3.356529 AAGCCATACTTCAAGGGAGTG 57.643 47.619 0.00 0.00 30.77 3.51
2880 3017 0.836606 TCAAGGGAGTGTTCTGTGCA 59.163 50.000 0.00 0.00 0.00 4.57
2925 3062 1.174712 AGAGCGCCAACAACATGCTT 61.175 50.000 2.29 0.00 35.73 3.91
3009 3147 3.586100 TTCGACCGTGAATCAGATGAA 57.414 42.857 0.00 0.00 0.00 2.57
3066 3221 7.497909 AGCTAGCTTTACTTGTGTTTTTGTAGA 59.502 33.333 12.68 0.00 0.00 2.59
3067 3222 7.798982 GCTAGCTTTACTTGTGTTTTTGTAGAG 59.201 37.037 7.70 0.00 0.00 2.43
3080 3235 8.062448 GTGTTTTTGTAGAGTGTGTGATTCTAC 58.938 37.037 4.40 4.40 41.91 2.59
3083 3238 5.547181 TGTAGAGTGTGTGATTCTACTCG 57.453 43.478 10.98 0.00 42.02 4.18
3178 3333 0.672091 TTGCTATCGAAAGGCACGCA 60.672 50.000 9.28 0.00 35.62 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.330250 ACATGATAAAGTGTTCAGCTGCT 58.670 39.130 9.47 0.00 0.00 4.24
36 37 5.279206 CGCATATCTCTAGAAGTGGACCAAT 60.279 44.000 0.00 0.00 0.00 3.16
46 47 3.759086 CCCACTAGCGCATATCTCTAGAA 59.241 47.826 11.47 0.00 34.53 2.10
74 75 2.376109 ACCACGACCGTATTCTCTGAT 58.624 47.619 0.00 0.00 0.00 2.90
111 113 2.409975 ACTGTTCACAACCGTATTCCG 58.590 47.619 0.00 0.00 0.00 4.30
122 124 3.786516 TGTCGTACAGAACTGTTCACA 57.213 42.857 21.50 12.92 41.83 3.58
144 146 0.035152 TCCTACAATGTGCCAGCCAG 60.035 55.000 0.00 0.00 0.00 4.85
150 152 2.089854 CACGCTCCTACAATGTGCC 58.910 57.895 0.00 0.00 0.00 5.01
179 181 4.778143 GCCACGGACCGGCTCATT 62.778 66.667 20.00 0.00 46.56 2.57
209 211 0.530744 TTCGGAGGACCACATTCTCG 59.469 55.000 0.00 0.00 35.59 4.04
243 245 1.534729 GCCTTTTTCCATCAGACGGT 58.465 50.000 0.00 0.00 0.00 4.83
272 274 2.662791 CGCATACATCATTTACTGCGGC 60.663 50.000 6.83 0.00 46.18 6.53
312 314 2.757894 AGACCGTCATATCTCTGGGT 57.242 50.000 0.40 0.00 0.00 4.51
316 318 3.117474 TGGGAGAAGACCGTCATATCTCT 60.117 47.826 19.78 7.48 37.33 3.10
768 770 2.354328 TCACTTGGTAGGGTTTGGGAT 58.646 47.619 0.00 0.00 0.00 3.85
804 806 0.329261 TCCCTCCTCTGCCATTTGTG 59.671 55.000 0.00 0.00 0.00 3.33
806 808 1.005215 ACTTCCCTCCTCTGCCATTTG 59.995 52.381 0.00 0.00 0.00 2.32
982 986 4.503817 CCTCATTCAGCGGAAATCTATGGA 60.504 45.833 2.68 0.00 36.43 3.41
1034 1038 4.626081 ACGTCCACCAGCACCAGC 62.626 66.667 0.00 0.00 42.56 4.85
1065 1069 0.322975 AAGATGAGTCGGCAGTTGCT 59.677 50.000 3.88 0.00 41.70 3.91
1117 1123 1.207791 GGGGATCTGACATGGTGAGT 58.792 55.000 0.00 0.00 0.00 3.41
1161 1167 3.118261 TCCCAGTGGACTCAGCATATTTC 60.118 47.826 11.95 0.00 35.03 2.17
1166 1172 0.617413 CTTCCCAGTGGACTCAGCAT 59.383 55.000 11.95 0.00 41.57 3.79
1207 1213 2.033049 CAGTTATGTACCTCCTCGTCCG 59.967 54.545 0.00 0.00 0.00 4.79
1343 1377 8.593679 TCAGGAGTTTATCACTAGTCATGAAAA 58.406 33.333 0.00 0.00 35.01 2.29
1347 1381 7.340122 TCTCAGGAGTTTATCACTAGTCATG 57.660 40.000 0.00 0.00 35.01 3.07
1457 1541 2.561419 TGGAGTTACTCTACCAGCACAC 59.439 50.000 12.41 0.00 0.00 3.82
1595 1680 2.507407 TACCAAATCCAAGCTCCCAC 57.493 50.000 0.00 0.00 0.00 4.61
1729 1825 4.769688 TGAAATTGCAGAGGTCACGATAT 58.230 39.130 0.00 0.00 0.00 1.63
1731 1827 3.057969 TGAAATTGCAGAGGTCACGAT 57.942 42.857 0.00 0.00 0.00 3.73
1756 1860 5.991328 TTCTTTCACATGTCAGACAGTTC 57.009 39.130 9.64 0.00 0.00 3.01
1757 1861 6.757897 TTTTCTTTCACATGTCAGACAGTT 57.242 33.333 9.64 0.00 0.00 3.16
1773 1877 4.769345 TTCCCCTGCAAACATTTTCTTT 57.231 36.364 0.00 0.00 0.00 2.52
1797 1906 3.134262 AGATCTGCTATTCTGCTGCTCAA 59.866 43.478 0.00 0.00 32.21 3.02
1962 2072 4.564372 CGAGATCCTTTGTGTACACATCTG 59.436 45.833 28.35 19.50 41.52 2.90
2114 2224 3.455177 ACATCATCATCAGCTTGGTCTCT 59.545 43.478 0.00 0.00 0.00 3.10
2155 2265 4.687948 TCGTTCTGCTGAATCTCTTTGAAG 59.312 41.667 9.40 0.00 34.40 3.02
2201 2311 0.895530 CTGCTTTCCTCGTCACCCTA 59.104 55.000 0.00 0.00 0.00 3.53
2253 2363 3.475566 AGAACTTGTACTGCAGCTTGA 57.524 42.857 15.27 0.00 0.00 3.02
2305 2415 3.426159 GCATGTCATACAAGTTTGTCCGG 60.426 47.826 0.00 0.00 42.35 5.14
2559 2683 8.458843 GCTTGGTCTACAAATTGTACAACATAT 58.541 33.333 11.22 0.00 38.91 1.78
2568 2692 3.472652 TCGTGCTTGGTCTACAAATTGT 58.527 40.909 3.43 3.43 38.91 2.71
2587 2721 2.344950 GATTGCTATCTCCATGGCTCG 58.655 52.381 6.96 0.00 37.40 5.03
2608 2742 3.126831 CAGTATTAGGGAGCTCGCTTTG 58.873 50.000 34.77 21.10 39.91 2.77
2655 2789 5.095691 GGCTTTCTTTTGCCTTTTTAAGC 57.904 39.130 0.00 0.00 45.26 3.09
2748 2882 1.672881 GCCATCTCAAATTCCTCCACG 59.327 52.381 0.00 0.00 0.00 4.94
2850 2987 3.844211 ACACTCCCTTGAAGTATGGCTTA 59.156 43.478 0.00 0.00 37.59 3.09
2871 3008 2.796593 GCTGGTCATTTTTGCACAGAAC 59.203 45.455 1.24 0.00 0.00 3.01
2880 3017 1.267806 CGCTGAGTGCTGGTCATTTTT 59.732 47.619 0.00 0.00 40.11 1.94
2925 3062 1.946768 GCTGGCGGCATGTAAATCTTA 59.053 47.619 13.85 0.00 41.35 2.10
3066 3221 6.459024 GCTTCTATCGAGTAGAATCACACACT 60.459 42.308 13.91 0.00 45.78 3.55
3067 3222 5.683743 GCTTCTATCGAGTAGAATCACACAC 59.316 44.000 13.91 0.00 45.78 3.82
3080 3235 9.176181 GATAAGTTAGTCTTTGCTTCTATCGAG 57.824 37.037 0.00 0.00 37.56 4.04
3119 3274 0.758734 CCACTCTGTGACAGGACCAA 59.241 55.000 13.33 0.00 35.23 3.67
3130 3285 1.001746 CTCATGACAGCACCACTCTGT 59.998 52.381 0.00 0.00 46.46 3.41


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

AutoCloner maintained by Alex Coulton.