Multiple sequence alignment - TraesCS5A01G001900

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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 TraesCS5A01G001900 chr5A 100.000 2822 0 0 1 2822 1348486 1345665 0.000000e+00 5212.0
1 TraesCS5A01G001900 chr5A 85.714 63 9 0 374 436 445768638 445768576 1.810000e-07 67.6
2 TraesCS5A01G001900 chr5B 91.162 2874 165 31 1 2822 3473849 3476685 0.000000e+00 3818.0
3 TraesCS5A01G001900 chr5D 89.561 1322 61 34 698 1994 2512287 2511018 0.000000e+00 1605.0
4 TraesCS5A01G001900 chr5D 92.216 668 43 7 1 664 2512948 2512286 0.000000e+00 937.0
5 TraesCS5A01G001900 chr5D 78.039 765 102 43 2095 2820 2510954 2510217 3.360000e-114 422.0
6 TraesCS5A01G001900 chr4D 90.506 158 15 0 1199 1356 18464567 18464724 2.850000e-50 209.0
7 TraesCS5A01G001900 chr4A 90.385 156 15 0 1199 1354 582840677 582840522 3.680000e-49 206.0
8 TraesCS5A01G001900 chr4B 89.744 156 16 0 1199 1354 30362595 30362750 1.710000e-47 200.0
9 TraesCS5A01G001900 chr2D 73.563 435 94 16 29 451 405173217 405173642 2.270000e-31 147.0
10 TraesCS5A01G001900 chr2A 76.305 249 50 8 194 436 769525952 769526197 1.060000e-24 124.0
11 TraesCS5A01G001900 chr1A 75.177 282 60 9 194 469 84733740 84733463 1.060000e-24 124.0
12 TraesCS5A01G001900 chr7D 97.297 37 1 0 400 436 107291031 107290995 2.350000e-06 63.9


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 TraesCS5A01G001900 chr5A 1345665 1348486 2821 True 5212 5212 100.000000 1 2822 1 chr5A.!!$R1 2821
1 TraesCS5A01G001900 chr5B 3473849 3476685 2836 False 3818 3818 91.162000 1 2822 1 chr5B.!!$F1 2821
2 TraesCS5A01G001900 chr5D 2510217 2512948 2731 True 988 1605 86.605333 1 2820 3 chr5D.!!$R1 2819

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
857 872 2.202236 GAACAGCATGGCCCCTCTGA 62.202 60.0 18.4 0.0 43.62 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2650 2741 0.531657 TAAGCTAACGTTAGGCGGCA 59.468 50.0 30.94 13.92 46.52 5.69 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
110 111 4.887655 ACTAACATTGGCAGGGTAATAAGC 59.112 41.667 0.00 0.00 0.00 3.09
114 115 2.500392 TGGCAGGGTAATAAGCGTTT 57.500 45.000 0.00 0.00 0.00 3.60
230 235 3.388024 ACCTATAGCACCATGTAGTGTGG 59.612 47.826 4.35 0.00 40.04 4.17
236 242 4.917385 AGCACCATGTAGTGTGGAAATAA 58.083 39.130 0.00 0.00 40.04 1.40
282 288 9.301153 GGATTGACAAATAAATTCCACACATAC 57.699 33.333 0.00 0.00 0.00 2.39
410 416 3.261981 ACTTATTGGCTCCGTACTTGG 57.738 47.619 0.00 0.00 0.00 3.61
426 432 3.301274 ACTTGGTCTATCCTACAGAGGC 58.699 50.000 0.00 0.00 43.40 4.70
471 478 2.895372 CATCCTACCCGGTTGCGC 60.895 66.667 0.00 0.00 0.00 6.09
577 587 5.122239 CAGATGTCGGACATTAACACATTGT 59.878 40.000 23.40 0.00 39.27 2.71
582 592 4.083537 TCGGACATTAACACATTGTGCTTC 60.084 41.667 16.62 4.46 36.98 3.86
590 600 4.668576 ACACATTGTGCTTCTATCAACG 57.331 40.909 16.62 0.00 36.98 4.10
592 602 4.515191 ACACATTGTGCTTCTATCAACGTT 59.485 37.500 16.62 0.00 36.98 3.99
681 695 7.275888 TGTTTTGTCACTTCATTTGCTAGAT 57.724 32.000 0.00 0.00 0.00 1.98
750 764 6.482898 AATAATTGCCATGCCTTGTAATGA 57.517 33.333 0.00 0.00 0.00 2.57
841 856 7.421530 TTGAACAAGCATACACTAGAAGAAC 57.578 36.000 0.00 0.00 0.00 3.01
857 872 2.202236 GAACAGCATGGCCCCTCTGA 62.202 60.000 18.40 0.00 43.62 3.27
919 934 2.959484 GCAGGTCAGTGCAGCCCTA 61.959 63.158 0.00 0.00 43.41 3.53
1094 1124 2.393646 AGTACCAGATGCCTTCTCCTC 58.606 52.381 0.00 0.00 29.93 3.71
1100 1130 3.437198 CCAGATGCCTTCTCCTCCTACTA 60.437 52.174 0.00 0.00 29.93 1.82
1116 1146 5.380043 TCCTACTACTATTACCCTCCGTTG 58.620 45.833 0.00 0.00 0.00 4.10
1194 1224 0.250513 GGTCAAGGGCGTCAAGATCT 59.749 55.000 0.00 0.00 0.00 2.75
1200 1230 1.069935 GGCGTCAAGATCTAGGGCC 59.930 63.158 10.17 10.17 0.00 5.80
1202 1232 1.300233 CGTCAAGATCTAGGGCCGC 60.300 63.158 0.00 0.00 0.00 6.53
1218 1248 2.261671 GCGGCGAGGAAAGACAGA 59.738 61.111 12.98 0.00 0.00 3.41
1221 1251 1.009389 CGGCGAGGAAAGACAGACAC 61.009 60.000 0.00 0.00 0.00 3.67
1242 1272 1.523711 CAAGATATGCACGGCCGGT 60.524 57.895 31.76 12.63 0.00 5.28
1427 1457 1.977544 CCTTGTCGGAGGAGGACGT 60.978 63.158 0.00 0.00 39.25 4.34
1434 1464 3.450115 GAGGAGGACGTGGACGGG 61.450 72.222 0.00 0.00 44.95 5.28
1440 1470 2.732658 GACGTGGACGGGTCTGTT 59.267 61.111 0.00 0.00 44.95 3.16
1527 1557 1.227205 GGAGCAGGAGCATCAGACG 60.227 63.158 0.00 0.00 45.49 4.18
1583 1613 3.072944 CAAGTCCAAGGAAGAAGAGCAG 58.927 50.000 0.00 0.00 0.00 4.24
1591 1621 1.171308 GAAGAAGAGCAGCAATGGCA 58.829 50.000 0.00 0.00 44.61 4.92
1730 1769 4.643387 GCCAGTGGTTCCGGCAGT 62.643 66.667 11.74 0.00 45.52 4.40
1732 1771 1.373435 CCAGTGGTTCCGGCAGTAA 59.627 57.895 0.00 0.00 0.00 2.24
1937 1977 3.183373 GCTTTTCTATCTCGATCTTGCCG 59.817 47.826 0.00 0.00 0.00 5.69
1946 1995 3.186409 TCTCGATCTTGCCGTTTTTCTTG 59.814 43.478 0.00 0.00 0.00 3.02
1970 2019 3.420893 TCCAACAACTTCATCCATCCAC 58.579 45.455 0.00 0.00 0.00 4.02
1996 2046 9.293404 CCAGTGATGAATAATGGATTAATCAGT 57.707 33.333 17.07 5.62 44.98 3.41
2172 2242 8.679344 TGCAATCCTTCTCTATATATGGGTAA 57.321 34.615 0.00 0.00 0.00 2.85
2219 2289 3.129988 TGAGCTACCTTCCTAGCGTTTAC 59.870 47.826 0.00 0.00 43.49 2.01
2254 2324 3.385111 CACTTCTAGAGAACCGCCCTTAT 59.615 47.826 0.00 0.00 0.00 1.73
2320 2395 7.663043 TGGAAAATGTAATATTACAACCCCC 57.337 36.000 27.45 23.77 45.74 5.40
2399 2481 5.629849 CGGCTACAAGATATTCCTAGTTTCG 59.370 44.000 0.00 0.00 0.00 3.46
2406 2488 6.910536 AGATATTCCTAGTTTCGTTTGCAG 57.089 37.500 0.00 0.00 0.00 4.41
2491 2574 7.112122 TCACTTTCTACATTGCCATCAACTAT 58.888 34.615 0.00 0.00 34.60 2.12
2493 2576 8.246180 CACTTTCTACATTGCCATCAACTATTT 58.754 33.333 0.00 0.00 34.60 1.40
2501 2584 7.718753 ACATTGCCATCAACTATTTTTCCAAAA 59.281 29.630 0.00 0.00 34.60 2.44
2654 2745 3.426191 CACATGAAAAATGTTCAGTGCCG 59.574 43.478 0.00 0.00 0.00 5.69
2661 2753 1.019278 ATGTTCAGTGCCGCCTAACG 61.019 55.000 0.00 0.00 43.15 3.18
2711 2803 5.608449 TGATGACATGAAAATGTTTGGCAA 58.392 33.333 0.00 0.00 34.45 4.52
2734 2830 7.946237 GCAACAGAATTTTACATCACAAAATCG 59.054 33.333 0.00 0.00 35.15 3.34
2738 2834 8.775884 CAGAATTTTACATCACAAAATCGTACG 58.224 33.333 9.53 9.53 35.15 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.041030 TCACGTGCAAAGGTATTTTTGAGATTA 60.041 33.333 11.67 0.00 39.79 1.75
177 178 8.480501 AGCTACCTGAAAAATAATAGACCGTAA 58.519 33.333 0.00 0.00 0.00 3.18
230 235 9.203421 CCCTCAACAACTTACCAAAATTATTTC 57.797 33.333 0.00 0.00 0.00 2.17
236 242 4.810345 TCCCCTCAACAACTTACCAAAAT 58.190 39.130 0.00 0.00 0.00 1.82
246 252 4.871933 ATTTGTCAATCCCCTCAACAAC 57.128 40.909 0.00 0.00 30.14 3.32
365 371 3.434309 AGCATGAATAACCTGCAAAGGT 58.566 40.909 0.00 0.00 45.55 3.50
393 399 2.463752 AGACCAAGTACGGAGCCAATA 58.536 47.619 0.00 0.00 0.00 1.90
395 401 1.927487 TAGACCAAGTACGGAGCCAA 58.073 50.000 0.00 0.00 0.00 4.52
397 403 1.340568 GGATAGACCAAGTACGGAGCC 59.659 57.143 0.00 0.00 38.79 4.70
426 432 7.042456 CGTCATAATAAGATTTGTGTCCTCCAG 60.042 40.741 0.00 0.00 0.00 3.86
471 478 5.858381 ACAGCAATAGTACCTGGTCATATG 58.142 41.667 0.63 0.00 0.00 1.78
517 527 3.766591 ACACATCCAACAACTCCAAACAA 59.233 39.130 0.00 0.00 0.00 2.83
518 528 3.130164 CACACATCCAACAACTCCAAACA 59.870 43.478 0.00 0.00 0.00 2.83
519 529 3.705604 CACACATCCAACAACTCCAAAC 58.294 45.455 0.00 0.00 0.00 2.93
524 534 3.207474 GATGCACACATCCAACAACTC 57.793 47.619 0.00 0.00 45.94 3.01
557 567 3.058570 GCACAATGTGTTAATGTCCGACA 60.059 43.478 15.36 3.10 35.75 4.35
729 743 6.324512 AGAATCATTACAAGGCATGGCAATTA 59.675 34.615 22.64 5.86 0.00 1.40
776 790 8.768397 TCATACATACTGGTAGGAAACATCTTT 58.232 33.333 0.00 0.00 31.79 2.52
777 791 8.319057 TCATACATACTGGTAGGAAACATCTT 57.681 34.615 0.00 0.00 31.79 2.40
841 856 1.228184 GATCAGAGGGGCCATGCTG 60.228 63.158 4.39 9.55 0.00 4.41
857 872 4.785511 ACAGTGCTTACTACTTGACGAT 57.214 40.909 0.00 0.00 0.00 3.73
898 913 3.054503 GCTGCACTGACCTGCTGG 61.055 66.667 8.29 8.29 38.07 4.85
919 934 6.441604 TCATGGTCATATATACCTGCAGATGT 59.558 38.462 17.39 8.18 37.91 3.06
983 998 4.461450 TCCATCACTATCTCCTGCTAGT 57.539 45.455 0.00 0.00 0.00 2.57
1094 1124 4.522022 CCAACGGAGGGTAATAGTAGTAGG 59.478 50.000 0.00 0.00 0.00 3.18
1100 1130 0.835276 GGCCAACGGAGGGTAATAGT 59.165 55.000 0.00 0.00 0.00 2.12
1137 1167 2.505557 GGGTTGTCCGTCGTAGCG 60.506 66.667 0.00 0.00 33.83 4.26
1138 1168 1.005867 TTGGGTTGTCCGTCGTAGC 60.006 57.895 0.00 0.00 38.76 3.58
1139 1169 1.005294 CGTTGGGTTGTCCGTCGTAG 61.005 60.000 0.00 0.00 38.76 3.51
1140 1170 1.007502 CGTTGGGTTGTCCGTCGTA 60.008 57.895 0.00 0.00 38.76 3.43
1200 1230 3.181967 CTGTCTTTCCTCGCCGCG 61.182 66.667 6.39 6.39 0.00 6.46
1202 1232 1.009389 GTGTCTGTCTTTCCTCGCCG 61.009 60.000 0.00 0.00 0.00 6.46
1239 1269 3.849951 CGGTCCCTCATCCCACCG 61.850 72.222 0.00 0.00 45.38 4.94
1427 1457 1.155390 AGGAGAACAGACCCGTCCA 59.845 57.895 0.00 0.00 0.00 4.02
1434 1464 0.610687 CCAGGTCCAGGAGAACAGAC 59.389 60.000 0.00 0.00 33.03 3.51
1440 1470 0.105194 TGTTGTCCAGGTCCAGGAGA 60.105 55.000 2.57 0.00 35.42 3.71
1527 1557 2.299867 TGATCTTCTTTTTGCCTTGGCC 59.700 45.455 9.35 0.00 0.00 5.36
1591 1621 3.394836 GAGGAGAACAGGGGCGCT 61.395 66.667 7.64 0.00 0.00 5.92
1730 1769 3.485463 AGTAGTTGTTGCTGCAGGTTA 57.515 42.857 17.12 0.00 0.00 2.85
1732 1771 2.767505 GTAGTAGTTGTTGCTGCAGGT 58.232 47.619 17.12 0.00 0.00 4.00
1946 1995 5.066505 GTGGATGGATGAAGTTGTTGGATAC 59.933 44.000 0.00 0.00 0.00 2.24
1970 2019 9.293404 ACTGATTAATCCATTATTCATCACTGG 57.707 33.333 12.90 0.00 34.65 4.00
1996 2046 2.240414 AGAGGAACATGGCATGTGATGA 59.760 45.455 31.99 0.00 44.07 2.92
1997 2047 2.651455 AGAGGAACATGGCATGTGATG 58.349 47.619 31.99 8.79 44.07 3.07
2260 2330 2.858787 AAAAACTTCCCTCCCCACAA 57.141 45.000 0.00 0.00 0.00 3.33
2293 2368 9.758651 GGGGTTGTAATATTACATTTTCCATTC 57.241 33.333 25.09 14.74 42.66 2.67
2375 2457 5.629849 CGAAACTAGGAATATCTTGTAGCCG 59.370 44.000 0.00 0.00 0.00 5.52
2399 2481 8.854979 TTATCATGTAATTATGTGCTGCAAAC 57.145 30.769 2.77 0.00 0.00 2.93
2465 2547 5.413833 AGTTGATGGCAATGTAGAAAGTGAG 59.586 40.000 0.00 0.00 36.22 3.51
2466 2548 5.316167 AGTTGATGGCAATGTAGAAAGTGA 58.684 37.500 0.00 0.00 36.22 3.41
2491 2574 9.072375 AGAACAAACAGGAAAATTTTGGAAAAA 57.928 25.926 8.47 0.00 35.03 1.94
2493 2576 9.898152 ATAGAACAAACAGGAAAATTTTGGAAA 57.102 25.926 8.47 0.00 35.03 3.13
2501 2584 8.463930 TCAACTGATAGAACAAACAGGAAAAT 57.536 30.769 0.00 0.00 35.08 1.82
2557 2643 7.750458 CACACTAATTACTTGATTGAACGCAAT 59.250 33.333 0.00 0.00 47.00 3.56
2561 2649 6.598525 TGCACACTAATTACTTGATTGAACG 58.401 36.000 0.00 0.00 0.00 3.95
2579 2667 8.514136 TGCTTTGTTAACTATTATTTGCACAC 57.486 30.769 7.22 0.00 0.00 3.82
2650 2741 0.531657 TAAGCTAACGTTAGGCGGCA 59.468 50.000 30.94 13.92 46.52 5.69
2654 2745 4.564940 TCTAGCTAAGCTAACGTTAGGC 57.435 45.455 30.94 25.20 40.82 3.93
2706 2798 5.781210 TGTGATGTAAAATTCTGTTGCCA 57.219 34.783 0.00 0.00 0.00 4.92
2711 2803 9.607285 GTACGATTTTGTGATGTAAAATTCTGT 57.393 29.630 0.00 0.00 37.73 3.41
2734 2830 9.101655 AGTATTTGGTTAAATGTGTATCCGTAC 57.898 33.333 0.00 0.00 37.12 3.67


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

AutoCloner maintained by Alex Coulton.