Multiple sequence alignment - TraesCS5D01G232300

Loading Multiple Alignment...

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 TraesCS5D01G232300 chr5D 100.000 2303 0 0 1 2303 339111996 339114298 0.000000e+00 4253
1 TraesCS5D01G232300 chr5D 83.678 435 48 16 857 1283 384076044 384076463 2.770000e-104 388
2 TraesCS5D01G232300 chr5D 93.805 113 7 0 1438 1550 368501756 368501868 1.090000e-38 171
3 TraesCS5D01G232300 chr5D 93.636 110 7 0 1441 1550 172296557 172296448 5.090000e-37 165
4 TraesCS5D01G232300 chr5A 93.486 2011 99 12 310 2300 439877210 439879208 0.000000e+00 2959
5 TraesCS5D01G232300 chr5A 88.218 331 20 4 1 313 439876710 439877039 6.010000e-101 377
6 TraesCS5D01G232300 chr5A 82.558 430 59 14 857 1282 484559695 484560112 4.680000e-97 364
7 TraesCS5D01G232300 chr5A 93.805 113 7 0 1438 1550 479641139 479641251 1.090000e-38 171
8 TraesCS5D01G232300 chr5B 95.482 664 28 2 742 1404 398158839 398159501 0.000000e+00 1059
9 TraesCS5D01G232300 chr5B 90.909 792 58 8 1400 2183 398159812 398160597 0.000000e+00 1051
10 TraesCS5D01G232300 chr5B 91.304 322 13 8 1 313 398158338 398158653 2.110000e-115 425
11 TraesCS5D01G232300 chr5B 82.759 435 52 18 857 1283 460680577 460680996 1.300000e-97 366
12 TraesCS5D01G232300 chr5B 83.146 178 22 6 395 571 460680248 460680418 3.060000e-34 156
13 TraesCS5D01G232300 chr7A 95.413 109 5 0 1442 1550 578546619 578546727 8.460000e-40 174
14 TraesCS5D01G232300 chr4A 93.805 113 7 0 1438 1550 95706900 95707012 1.090000e-38 171
15 TraesCS5D01G232300 chr4A 94.545 110 6 0 1441 1550 254517540 254517431 1.090000e-38 171
16 TraesCS5D01G232300 chr3D 93.805 113 7 0 1438 1550 575151963 575152075 1.090000e-38 171


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 TraesCS5D01G232300 chr5D 339111996 339114298 2302 False 4253 4253 100.0000 1 2303 1 chr5D.!!$F1 2302
1 TraesCS5D01G232300 chr5A 439876710 439879208 2498 False 1668 2959 90.8520 1 2300 2 chr5A.!!$F3 2299
2 TraesCS5D01G232300 chr5B 398158338 398160597 2259 False 845 1059 92.5650 1 2183 3 chr5B.!!$F1 2182
3 TraesCS5D01G232300 chr5B 460680248 460680996 748 False 261 366 82.9525 395 1283 2 chr5B.!!$F2 888

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
983 1188 1.33726 CGTGCTTCAAGGCTGAGTAGT 60.337 52.381 0.0 0.0 31.69 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 2441 0.388659 GTTTTGTGTGCCCATGAGCA 59.611 50.0 0.0 0.0 41.46 4.26 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
35 36 3.610911 GGATCCCACCAGTTTAGACTTG 58.389 50.000 0.00 0.00 32.54 3.16
166 181 3.515502 AGCAGGCATCTAGACAGTAAACA 59.484 43.478 0.00 0.00 0.00 2.83
194 209 6.030228 CCGAGCTGAAATTTCTTTATCCAAC 58.970 40.000 18.64 0.00 0.00 3.77
262 279 3.238108 ACGCTGAATAGTTGGAGAGTG 57.762 47.619 0.00 0.00 0.00 3.51
303 322 8.485578 AGGGACCAATAAAACACAGAATTAAA 57.514 30.769 0.00 0.00 0.00 1.52
304 323 8.364894 AGGGACCAATAAAACACAGAATTAAAC 58.635 33.333 0.00 0.00 0.00 2.01
305 324 8.145122 GGGACCAATAAAACACAGAATTAAACA 58.855 33.333 0.00 0.00 0.00 2.83
391 585 6.868864 ACCAATGCATATTAAGCTACTCGTAG 59.131 38.462 0.00 0.00 36.29 3.51
577 771 8.813643 TCTTTACTGCTGTTAAGACTTAAGAC 57.186 34.615 17.78 2.62 37.05 3.01
667 861 9.177608 GGATTAGCAGATAAAATGGCATATGTA 57.822 33.333 0.00 0.00 0.00 2.29
763 958 4.622220 GCATTCCTGATTGTTTGCTCCATT 60.622 41.667 0.00 0.00 0.00 3.16
975 1180 1.452145 TTTGACCCGTGCTTCAAGGC 61.452 55.000 0.00 0.00 33.36 4.35
983 1188 1.337260 CGTGCTTCAAGGCTGAGTAGT 60.337 52.381 0.00 0.00 31.69 2.73
996 1201 3.775654 GTAGTGGCGGCTCTGGCT 61.776 66.667 22.18 9.27 38.73 4.75
1013 1218 1.089920 GCTGCGATGGACAGAACAAT 58.910 50.000 0.00 0.00 37.32 2.71
1020 1225 0.605319 TGGACAGAACAATCGGTGGC 60.605 55.000 0.00 0.00 33.93 5.01
1038 1243 2.671682 GGTGTCAGAGGGGAAGGC 59.328 66.667 0.00 0.00 0.00 4.35
1131 1336 0.111061 TCAAGTGCCAGGCTCACATT 59.889 50.000 14.15 0.00 36.93 2.71
1190 1395 3.147595 CTCCGACGGCCATCCTGA 61.148 66.667 9.66 0.00 0.00 3.86
1217 1422 1.734655 TCTTCCACTTCTTGGCTCCT 58.265 50.000 0.00 0.00 46.47 3.69
1291 1496 4.536090 ACATTCTTCCTACCCAGATTGACA 59.464 41.667 0.00 0.00 0.00 3.58
1292 1497 4.826274 TTCTTCCTACCCAGATTGACAG 57.174 45.455 0.00 0.00 0.00 3.51
1293 1498 3.107601 TCTTCCTACCCAGATTGACAGG 58.892 50.000 0.00 0.00 0.00 4.00
1294 1499 2.642171 TCCTACCCAGATTGACAGGT 57.358 50.000 0.00 0.00 36.36 4.00
1295 1500 2.467880 TCCTACCCAGATTGACAGGTC 58.532 52.381 0.00 0.00 33.70 3.85
1436 1967 3.381949 AGGTCTTCGAGACAAACGAAAG 58.618 45.455 14.26 0.00 46.79 2.62
1453 1984 2.664402 AAGAGCTGCTTTGGGAAGAA 57.336 45.000 2.53 0.00 34.71 2.52
1511 2042 6.950619 ACATGCAGATAGATCCTACATACAGA 59.049 38.462 0.00 0.00 0.00 3.41
1516 2047 8.748412 GCAGATAGATCCTACATACAGAGAAAT 58.252 37.037 0.00 0.00 0.00 2.17
1583 2114 5.239525 AGTTGGTAGAGTTTCAAGTGCAATC 59.760 40.000 0.00 0.00 0.00 2.67
1664 2195 1.610886 GGTTCTGTTGCTGGGGTAGTC 60.611 57.143 0.00 0.00 0.00 2.59
1860 2393 2.871633 GGTTGTCAACTTTTTGGCATGG 59.128 45.455 15.17 0.00 46.64 3.66
1878 2411 1.256812 GGCAATGGCTTGTTACCACT 58.743 50.000 0.00 0.00 40.82 4.00
1933 2466 1.561643 TGGGCACACAAAACCTTGAA 58.438 45.000 0.00 0.00 36.33 2.69
2054 2590 4.202253 GGAAAGAACCATTGGCAAAACTCT 60.202 41.667 3.01 1.30 0.00 3.24
2060 2596 3.450457 ACCATTGGCAAAACTCTGAAACA 59.550 39.130 3.01 0.00 0.00 2.83
2063 2599 3.731652 TGGCAAAACTCTGAAACATGG 57.268 42.857 0.00 0.00 0.00 3.66
2083 2619 8.125978 ACATGGATGTTAATGTTGTCTTCAAT 57.874 30.769 0.00 0.00 37.90 2.57
2087 2623 7.665145 TGGATGTTAATGTTGTCTTCAATGAGA 59.335 33.333 0.00 0.00 35.92 3.27
2131 2667 5.772672 TGCTAGGCTATTTCAAAAGTTGGAA 59.227 36.000 0.00 0.00 31.53 3.53
2148 2684 2.950309 TGGAATCGGTCTAGTCTAGTGC 59.050 50.000 6.77 1.97 0.00 4.40
2153 2689 2.753452 TCGGTCTAGTCTAGTGCTTTGG 59.247 50.000 6.77 0.00 0.00 3.28
2173 2709 5.233083 TGGATAATAGGCACCTGATTCAG 57.767 43.478 6.70 6.70 0.00 3.02
2179 2715 9.289782 GATAATAGGCACCTGATTCAGTAAAAT 57.710 33.333 12.54 0.00 0.00 1.82
2190 2726 8.454106 CCTGATTCAGTAAAATCTTGTAAGGTG 58.546 37.037 12.54 0.00 36.73 4.00
2232 2768 2.774687 TCTTCCACTTTTCGTTAGGGC 58.225 47.619 0.00 0.00 0.00 5.19
2255 2791 6.593770 GGCTTTGGTTGAATAAAATGGTTAGG 59.406 38.462 0.00 0.00 0.00 2.69
2260 2796 8.429237 TGGTTGAATAAAATGGTTAGGTGATT 57.571 30.769 0.00 0.00 0.00 2.57
2261 2797 8.310382 TGGTTGAATAAAATGGTTAGGTGATTG 58.690 33.333 0.00 0.00 0.00 2.67
2263 2799 6.559810 TGAATAAAATGGTTAGGTGATTGCG 58.440 36.000 0.00 0.00 0.00 4.85
2267 2803 3.558931 ATGGTTAGGTGATTGCGATCA 57.441 42.857 12.88 12.88 39.92 2.92
2277 2813 4.260375 GGTGATTGCGATCAACTCATACAC 60.260 45.833 22.66 6.43 44.86 2.90
2300 2836 9.028284 ACACTACTTGTAGCTAGTTGGTTTATA 57.972 33.333 7.62 0.00 36.32 0.98
2301 2837 9.865321 CACTACTTGTAGCTAGTTGGTTTATAA 57.135 33.333 7.62 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.210722 CCCTCTAACCCAAAGCCTCTC 59.789 57.143 0.00 0.00 0.00 3.20
60 75 1.443407 CGTCCTGGTGAGGCATAGG 59.557 63.158 0.00 0.00 39.57 2.57
166 181 6.484977 GGATAAAGAAATTTCAGCTCGGAGAT 59.515 38.462 19.99 0.00 33.89 2.75
194 209 4.174411 TGAGGTACACAAGTGATCTTCG 57.826 45.455 7.28 0.00 0.00 3.79
262 279 0.107654 CCCTAAGCACCAGCACTACC 60.108 60.000 0.00 0.00 45.49 3.18
303 322 7.047891 ACGTGTGTATCCAATTGAGAATATGT 58.952 34.615 7.12 0.00 0.00 2.29
304 323 7.482654 ACGTGTGTATCCAATTGAGAATATG 57.517 36.000 7.12 0.00 0.00 1.78
305 324 8.201464 TGTACGTGTGTATCCAATTGAGAATAT 58.799 33.333 7.12 0.00 32.11 1.28
307 326 6.403049 TGTACGTGTGTATCCAATTGAGAAT 58.597 36.000 7.12 0.23 32.11 2.40
345 539 6.611381 TGGTATGACGTACACTACTGTTAAC 58.389 40.000 7.13 0.00 34.87 2.01
360 554 6.486253 AGCTTAATATGCATTGGTATGACG 57.514 37.500 3.54 0.00 33.37 4.35
391 585 7.280428 GGGAGTTATGTTAGGCTTTCTAGAAAC 59.720 40.741 13.99 10.70 0.00 2.78
530 724 7.429636 AGACCGAAGACAATTAAAATTCGAA 57.570 32.000 0.00 0.00 44.01 3.71
550 744 7.871463 TCTTAAGTCTTAACAGCAGTAAAGACC 59.129 37.037 14.59 2.80 45.75 3.85
571 765 7.719633 AGCTTCTAAAAGTCCATTGTGTCTTAA 59.280 33.333 0.00 0.00 34.79 1.85
572 766 7.173218 CAGCTTCTAAAAGTCCATTGTGTCTTA 59.827 37.037 0.00 0.00 34.79 2.10
573 767 6.016777 CAGCTTCTAAAAGTCCATTGTGTCTT 60.017 38.462 0.00 0.00 34.79 3.01
574 768 5.471456 CAGCTTCTAAAAGTCCATTGTGTCT 59.529 40.000 0.00 0.00 34.79 3.41
575 769 5.335191 CCAGCTTCTAAAAGTCCATTGTGTC 60.335 44.000 0.00 0.00 34.79 3.67
576 770 4.520492 CCAGCTTCTAAAAGTCCATTGTGT 59.480 41.667 0.00 0.00 34.79 3.72
577 771 4.082571 CCCAGCTTCTAAAAGTCCATTGTG 60.083 45.833 0.00 0.00 34.79 3.33
763 958 5.531198 TCTGCCCTTAAACTATGGTACCTA 58.469 41.667 14.36 0.00 0.00 3.08
975 1180 1.140589 CAGAGCCGCCACTACTCAG 59.859 63.158 0.00 0.00 32.71 3.35
996 1201 1.358877 CGATTGTTCTGTCCATCGCA 58.641 50.000 0.00 0.00 0.00 5.10
1013 1218 3.680786 CTCTGACACCGCCACCGA 61.681 66.667 0.00 0.00 36.29 4.69
1020 1225 2.982130 CCTTCCCCTCTGACACCG 59.018 66.667 0.00 0.00 0.00 4.94
1038 1243 3.191539 GCAGCCGCCTTCTTCTCG 61.192 66.667 0.00 0.00 0.00 4.04
1131 1336 1.071228 CATGAGGATCGGAAGGCATCA 59.929 52.381 0.00 0.00 38.61 3.07
1269 1474 5.102953 TGTCAATCTGGGTAGGAAGAATG 57.897 43.478 0.00 0.00 0.00 2.67
1331 1547 5.691754 GTCCATGTTTGCCTTTTAACTTGAG 59.308 40.000 0.00 0.00 33.61 3.02
1436 1967 2.821969 TGATTTCTTCCCAAAGCAGCTC 59.178 45.455 0.00 0.00 32.18 4.09
1486 2017 6.950619 TCTGTATGTAGGATCTATCTGCATGT 59.049 38.462 10.02 0.00 37.91 3.21
1583 2114 1.901591 AGCACCATGTTTCAGTCCTG 58.098 50.000 0.00 0.00 0.00 3.86
1629 2160 5.596836 ACAGAACCATTGTGTTTCACATT 57.403 34.783 3.43 0.00 44.16 2.71
1664 2195 7.383102 AGTATTCCATGCAGTTTCTTGTAAG 57.617 36.000 0.00 0.00 0.00 2.34
1706 2237 3.500014 CACATATGTTGCATTTGCGTCA 58.500 40.909 5.37 0.48 45.83 4.35
1831 2364 5.821995 CCAAAAAGTTGACAACCATCCAAAT 59.178 36.000 14.72 0.00 36.83 2.32
1908 2441 0.388659 GTTTTGTGTGCCCATGAGCA 59.611 50.000 0.00 0.00 41.46 4.26
1972 2505 2.091555 AGGGTAAGTTTGGTTTGAGCCA 60.092 45.455 0.00 0.00 36.62 4.75
2030 2566 3.454082 AGTTTTGCCAATGGTTCTTTCCA 59.546 39.130 0.00 0.00 42.01 3.53
2060 2596 8.352137 TCATTGAAGACAACATTAACATCCAT 57.648 30.769 0.00 0.00 38.90 3.41
2063 2599 8.886816 GTCTCATTGAAGACAACATTAACATC 57.113 34.615 9.82 0.00 44.20 3.06
2083 2619 2.489971 CCCGTAGCAAAAAGTGTCTCA 58.510 47.619 0.00 0.00 0.00 3.27
2131 2667 3.381908 CCAAAGCACTAGACTAGACCGAT 59.618 47.826 16.55 0.34 0.00 4.18
2148 2684 6.064060 TGAATCAGGTGCCTATTATCCAAAG 58.936 40.000 0.00 0.00 0.00 2.77
2153 2689 8.677148 TTTTACTGAATCAGGTGCCTATTATC 57.323 34.615 15.38 0.00 35.51 1.75
2225 2761 6.593770 CCATTTTATTCAACCAAAGCCCTAAC 59.406 38.462 0.00 0.00 0.00 2.34
2232 2768 8.364142 TCACCTAACCATTTTATTCAACCAAAG 58.636 33.333 0.00 0.00 0.00 2.77
2255 2791 4.568359 AGTGTATGAGTTGATCGCAATCAC 59.432 41.667 0.00 0.00 41.62 3.06
2260 2796 4.983671 AGTAGTGTATGAGTTGATCGCA 57.016 40.909 0.00 0.00 0.00 5.10
2261 2797 5.103000 ACAAGTAGTGTATGAGTTGATCGC 58.897 41.667 0.00 0.00 39.29 4.58
2263 2799 7.484975 AGCTACAAGTAGTGTATGAGTTGATC 58.515 38.462 8.85 0.00 41.93 2.92
2267 2803 7.941431 ACTAGCTACAAGTAGTGTATGAGTT 57.059 36.000 8.85 0.00 41.93 3.01


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

AutoCloner maintained by Alex Coulton.