Multiple sequence alignment - TraesCS4A01G412400

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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 TraesCS4A01G412400 chr4A 100.000 3073 0 0 1 3073 684268665 684265593 0.000000e+00 5675
1 TraesCS4A01G412400 chr4A 99.660 1177 3 1 1730 2905 684285811 684284635 0.000000e+00 2150
2 TraesCS4A01G412400 chr4A 92.799 611 38 5 1 608 684398757 684399364 0.000000e+00 880
3 TraesCS4A01G412400 chr4A 89.583 96 10 0 33 128 494048069 494048164 4.160000e-24 122
4 TraesCS4A01G412400 chr2D 94.905 2473 111 7 609 3073 645763082 645765547 0.000000e+00 3855
5 TraesCS4A01G412400 chr2D 92.432 2471 168 8 609 3073 596264569 596262112 0.000000e+00 3509
6 TraesCS4A01G412400 chr2D 90.476 315 30 0 609 923 640823570 640823256 1.700000e-112 416
7 TraesCS4A01G412400 chr2B 90.045 2210 182 17 833 3037 765751962 765754138 0.000000e+00 2828
8 TraesCS4A01G412400 chr2A 96.584 1054 29 4 2022 3073 87816272 87815224 0.000000e+00 1740
9 TraesCS4A01G412400 chr2A 95.880 801 32 1 609 1409 87850533 87849734 0.000000e+00 1295
10 TraesCS4A01G412400 chr2A 96.629 623 21 0 1405 2027 87841069 87840447 0.000000e+00 1035
11 TraesCS4A01G412400 chr2A 89.583 96 10 0 33 128 682500765 682500670 4.160000e-24 122
12 TraesCS4A01G412400 chr7A 95.014 1083 52 2 609 1691 624799959 624798879 0.000000e+00 1700
13 TraesCS4A01G412400 chr7A 71.769 1091 257 46 1876 2944 471819496 471820557 8.450000e-66 261
14 TraesCS4A01G412400 chr7A 89.623 106 11 0 23 128 650413560 650413455 5.340000e-28 135
15 TraesCS4A01G412400 chr5A 93.932 791 42 1 609 1399 705356518 705355734 0.000000e+00 1190
16 TraesCS4A01G412400 chr5A 90.836 371 30 2 609 975 601349172 601349542 7.650000e-136 494
17 TraesCS4A01G412400 chr6A 90.418 407 37 1 609 1015 547339557 547339153 4.510000e-148 534
18 TraesCS4A01G412400 chr6A 90.541 370 30 3 609 975 144017658 144017291 4.610000e-133 484
19 TraesCS4A01G412400 chr6A 89.623 106 8 1 23 128 596770078 596770180 6.910000e-27 132
20 TraesCS4A01G412400 chr7B 74.975 1007 191 42 610 1603 39957712 39956754 1.030000e-109 407
21 TraesCS4A01G412400 chr7B 71.968 1113 235 65 1857 2938 425412031 425413097 3.930000e-64 255
22 TraesCS4A01G412400 chr7B 81.683 202 37 0 140 341 490306373 490306574 5.270000e-38 169
23 TraesCS4A01G412400 chr6D 88.732 142 16 0 252 393 202968058 202968199 1.130000e-39 174
24 TraesCS4A01G412400 chr3B 95.789 95 4 0 33 127 29352563 29352657 1.480000e-33 154
25 TraesCS4A01G412400 chr3A 80.583 206 34 4 189 392 261345376 261345577 1.480000e-33 154
26 TraesCS4A01G412400 chr3D 88.596 114 11 1 15 128 14825966 14825855 1.490000e-28 137
27 TraesCS4A01G412400 chr4D 87.931 116 11 2 13 128 49782854 49782742 1.920000e-27 134
28 TraesCS4A01G412400 chrUn 89.583 96 10 0 33 128 431971619 431971714 4.160000e-24 122


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 TraesCS4A01G412400 chr4A 684265593 684268665 3072 True 5675 5675 100.000 1 3073 1 chr4A.!!$R1 3072
1 TraesCS4A01G412400 chr4A 684284635 684285811 1176 True 2150 2150 99.660 1730 2905 1 chr4A.!!$R2 1175
2 TraesCS4A01G412400 chr4A 684398757 684399364 607 False 880 880 92.799 1 608 1 chr4A.!!$F2 607
3 TraesCS4A01G412400 chr2D 645763082 645765547 2465 False 3855 3855 94.905 609 3073 1 chr2D.!!$F1 2464
4 TraesCS4A01G412400 chr2D 596262112 596264569 2457 True 3509 3509 92.432 609 3073 1 chr2D.!!$R1 2464
5 TraesCS4A01G412400 chr2B 765751962 765754138 2176 False 2828 2828 90.045 833 3037 1 chr2B.!!$F1 2204
6 TraesCS4A01G412400 chr2A 87815224 87816272 1048 True 1740 1740 96.584 2022 3073 1 chr2A.!!$R1 1051
7 TraesCS4A01G412400 chr2A 87849734 87850533 799 True 1295 1295 95.880 609 1409 1 chr2A.!!$R3 800
8 TraesCS4A01G412400 chr2A 87840447 87841069 622 True 1035 1035 96.629 1405 2027 1 chr2A.!!$R2 622
9 TraesCS4A01G412400 chr7A 624798879 624799959 1080 True 1700 1700 95.014 609 1691 1 chr7A.!!$R1 1082
10 TraesCS4A01G412400 chr7A 471819496 471820557 1061 False 261 261 71.769 1876 2944 1 chr7A.!!$F1 1068
11 TraesCS4A01G412400 chr5A 705355734 705356518 784 True 1190 1190 93.932 609 1399 1 chr5A.!!$R1 790
12 TraesCS4A01G412400 chr7B 39956754 39957712 958 True 407 407 74.975 610 1603 1 chr7B.!!$R1 993
13 TraesCS4A01G412400 chr7B 425412031 425413097 1066 False 255 255 71.968 1857 2938 1 chr7B.!!$F1 1081

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
554 555 0.251121 TATGTGTGGGCACTGGGTTG 60.251 55.000 0.0 0.0 45.44 3.77 F
597 600 1.133915 TGTTGGTGTGGGAGGTTTCTC 60.134 52.381 0.0 0.0 39.25 2.87 F
868 871 1.139853 GCATCCCATCTCCTCTTTCGT 59.860 52.381 0.0 0.0 0.00 3.85 F
1674 1685 1.160137 GCTTCCACCAGTGCTTAGTG 58.840 55.000 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1538 3.169908 TGCTAAGTGTGTCTGTATCCCA 58.830 45.455 0.0 0.0 0.0 4.37 R
2063 2077 3.812156 TGTCCTTCACTTCAACTTCGA 57.188 42.857 0.0 0.0 0.0 3.71 R
2064 2078 4.094294 TGTTTGTCCTTCACTTCAACTTCG 59.906 41.667 0.0 0.0 0.0 3.79 R
3044 3074 5.241506 CAGCATCAGGGAAAACAACTTCTAA 59.758 40.000 0.0 0.0 0.0 2.10 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
106 107 0.863144 CGACCCGAAACAACGACATT 59.137 50.000 0.00 0.00 35.09 2.71
142 143 6.373005 TGTGACATGGAAGAAAGGAGATTA 57.627 37.500 0.00 0.00 0.00 1.75
201 202 0.323178 CAACTTGCATCCCTCCAGCT 60.323 55.000 0.00 0.00 0.00 4.24
272 273 1.608283 GCCTGGCTCGTTAGAAACTGT 60.608 52.381 12.43 0.00 0.00 3.55
282 283 6.911511 GCTCGTTAGAAACTGTCGATATAAGT 59.088 38.462 0.00 0.00 0.00 2.24
288 289 6.338937 AGAAACTGTCGATATAAGTGTTCCC 58.661 40.000 0.00 0.00 0.00 3.97
304 305 2.191375 CCAGCGAGACATGCCCAT 59.809 61.111 0.00 0.00 0.00 4.00
307 308 0.390492 CAGCGAGACATGCCCATAGA 59.610 55.000 0.00 0.00 0.00 1.98
317 318 5.533903 AGACATGCCCATAGATGCTTTAAAG 59.466 40.000 11.02 11.02 0.00 1.85
377 378 1.747444 ATAGGCCGGATTCTTCCCAT 58.253 50.000 5.05 0.00 39.01 4.00
417 418 1.188219 GGCTCCCGCATCTCTATCCA 61.188 60.000 0.00 0.00 38.10 3.41
440 441 0.767375 ACTGGTCTGCATTGGTCAGT 59.233 50.000 0.00 0.00 33.48 3.41
455 456 2.615493 GGTCAGTTGACGGATCCAATGT 60.615 50.000 13.41 0.79 45.65 2.71
457 458 2.567169 TCAGTTGACGGATCCAATGTCT 59.433 45.455 13.41 1.25 33.81 3.41
464 465 4.881273 TGACGGATCCAATGTCTAATTTGG 59.119 41.667 13.41 0.00 43.10 3.28
465 466 4.207165 ACGGATCCAATGTCTAATTTGGG 58.793 43.478 13.41 0.00 42.21 4.12
541 542 9.181061 CTATGAGAGATGAGAGATGATATGTGT 57.819 37.037 0.00 0.00 0.00 3.72
550 551 2.158711 AGATGATATGTGTGGGCACTGG 60.159 50.000 0.00 0.00 45.44 4.00
554 555 0.251121 TATGTGTGGGCACTGGGTTG 60.251 55.000 0.00 0.00 45.44 3.77
561 562 2.360475 GCACTGGGTTGCCTCCTC 60.360 66.667 0.00 0.00 36.42 3.71
567 568 2.285743 GGTTGCCTCCTCCTCCCT 60.286 66.667 0.00 0.00 0.00 4.20
568 569 2.371259 GGTTGCCTCCTCCTCCCTC 61.371 68.421 0.00 0.00 0.00 4.30
569 570 1.613630 GTTGCCTCCTCCTCCCTCA 60.614 63.158 0.00 0.00 0.00 3.86
586 589 2.872245 CCTCACTAGTTGTGTTGGTGTG 59.128 50.000 4.63 0.00 46.27 3.82
597 600 1.133915 TGTTGGTGTGGGAGGTTTCTC 60.134 52.381 0.00 0.00 39.25 2.87
868 871 1.139853 GCATCCCATCTCCTCTTTCGT 59.860 52.381 0.00 0.00 0.00 3.85
1185 1194 4.774124 CATGCTCTGATTTGAGGTTAGGA 58.226 43.478 0.00 0.00 34.82 2.94
1203 1212 7.125963 AGGTTAGGATTAGGGTTTCAGTTCTAG 59.874 40.741 0.00 0.00 0.00 2.43
1373 1383 6.202954 GGTCGAACAAGTCTTATATTGATGGG 59.797 42.308 0.00 0.00 0.00 4.00
1374 1384 5.758296 TCGAACAAGTCTTATATTGATGGGC 59.242 40.000 0.00 0.00 0.00 5.36
1416 1427 4.422073 TGTGAAGTTGAGACATGGTCTT 57.578 40.909 0.00 0.00 43.53 3.01
1484 1495 4.642885 GCCCAGTGTAATGTTTATTGGCTA 59.357 41.667 0.00 0.00 29.77 3.93
1488 1499 6.238103 CCAGTGTAATGTTTATTGGCTACTCG 60.238 42.308 0.00 0.00 0.00 4.18
1523 1534 3.449377 TGGATACAGGACTGCGAATTGTA 59.551 43.478 0.00 0.00 46.17 2.41
1527 1538 2.563179 ACAGGACTGCGAATTGTAGACT 59.437 45.455 0.00 0.00 33.97 3.24
1565 1576 1.603802 AGCATGTCTGTTGTTGTTCCG 59.396 47.619 0.00 0.00 0.00 4.30
1674 1685 1.160137 GCTTCCACCAGTGCTTAGTG 58.840 55.000 0.00 0.00 0.00 2.74
2062 2076 8.156820 TGTTGAGGATGTTAAATCTGAAGAAGA 58.843 33.333 0.00 0.00 39.94 2.87
2064 2078 8.954950 TGAGGATGTTAAATCTGAAGAAGATC 57.045 34.615 0.00 0.00 45.37 2.75
2065 2079 7.708322 TGAGGATGTTAAATCTGAAGAAGATCG 59.292 37.037 0.00 0.00 45.37 3.69
2137 2155 6.602009 GGTAAAGCTTAAAAGATTCAGGCCTA 59.398 38.462 3.98 0.00 32.73 3.93
2982 3012 7.865385 TGCACACTTCCTTTATTATTTGTGTTC 59.135 33.333 0.00 0.00 36.36 3.18
2991 3021 9.559958 CCTTTATTATTTGTGTTCTCATGTGTC 57.440 33.333 0.00 0.00 0.00 3.67
3044 3074 1.117150 GCAGGGGTTGATCAATGCAT 58.883 50.000 21.32 0.00 33.92 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 5.809051 GGGTCGATCGTAACAAACTCTATTT 59.191 40.000 15.94 0.00 0.00 1.40
73 74 1.916000 CGGGTCGATCGTAACAAACTC 59.084 52.381 15.94 3.47 0.00 3.01
106 107 8.539544 TCTTCCATGTCACAAGAGTAATAATCA 58.460 33.333 0.00 0.00 0.00 2.57
119 120 4.916041 ATCTCCTTTCTTCCATGTCACA 57.084 40.909 0.00 0.00 0.00 3.58
142 143 2.012236 ACCTCCTCTAACCTCTTCCCT 58.988 52.381 0.00 0.00 0.00 4.20
201 202 3.068881 CCCCTTGCACGAGAGGAA 58.931 61.111 3.60 0.00 34.91 3.36
253 254 2.338500 GACAGTTTCTAACGAGCCAGG 58.662 52.381 0.00 0.00 36.23 4.45
256 257 2.342910 TCGACAGTTTCTAACGAGCC 57.657 50.000 0.00 0.00 36.23 4.70
272 273 2.953648 TCGCTGGGAACACTTATATCGA 59.046 45.455 0.00 0.00 35.60 3.59
282 283 1.375908 GCATGTCTCGCTGGGAACA 60.376 57.895 10.38 10.38 39.59 3.18
288 289 0.390492 TCTATGGGCATGTCTCGCTG 59.610 55.000 0.00 0.00 0.00 5.18
304 305 4.239304 TCGCACGAACTTTAAAGCATCTA 58.761 39.130 15.24 0.00 0.00 1.98
307 308 3.747193 CATCGCACGAACTTTAAAGCAT 58.253 40.909 15.24 4.48 0.00 3.79
317 318 4.166011 GGCCTGCATCGCACGAAC 62.166 66.667 0.00 0.00 33.79 3.95
338 339 1.240641 TTGGTTGCCCGCATACACTG 61.241 55.000 0.00 0.00 0.00 3.66
377 378 4.738998 CATCCAACCAGGCCCGCA 62.739 66.667 0.00 0.00 37.29 5.69
440 441 6.435430 CAAATTAGACATTGGATCCGTCAA 57.565 37.500 17.39 11.14 31.92 3.18
464 465 1.382146 TATCTCCACCGTGACCCCC 60.382 63.158 0.00 0.00 0.00 5.40
465 466 1.683418 GGTATCTCCACCGTGACCCC 61.683 65.000 0.00 0.00 35.97 4.95
550 551 2.285743 AGGGAGGAGGAGGCAACC 60.286 66.667 0.00 0.00 37.17 3.77
554 555 0.469144 CTAGTGAGGGAGGAGGAGGC 60.469 65.000 0.00 0.00 0.00 4.70
557 558 1.717077 ACAACTAGTGAGGGAGGAGGA 59.283 52.381 0.00 0.00 0.00 3.71
558 559 2.239681 ACAACTAGTGAGGGAGGAGG 57.760 55.000 0.00 0.00 0.00 4.30
569 570 1.841277 TCCCACACCAACACAACTAGT 59.159 47.619 0.00 0.00 0.00 2.57
578 581 1.605753 GAGAAACCTCCCACACCAAC 58.394 55.000 0.00 0.00 0.00 3.77
603 606 3.482436 TCCAGTGCATTTAACTCCGTTT 58.518 40.909 0.00 0.00 0.00 3.60
868 871 1.409064 CTAGTGTCGCCAGATTAGCCA 59.591 52.381 0.00 0.00 0.00 4.75
951 957 0.749049 CAGATCACCTCCGCTCATCA 59.251 55.000 0.00 0.00 0.00 3.07
1028 1035 0.033306 ACCGTAAGAGGGAGGAGGAC 60.033 60.000 0.00 0.00 43.02 3.85
1185 1194 7.510675 TGGAATCTAGAACTGAAACCCTAAT 57.489 36.000 0.00 0.00 0.00 1.73
1373 1383 6.415867 CACATCCATCAAAATACTCGATTTGC 59.584 38.462 4.66 0.00 37.82 3.68
1374 1384 7.696755 TCACATCCATCAAAATACTCGATTTG 58.303 34.615 3.35 3.35 37.82 2.32
1416 1427 5.048504 GCAGAAAGTCATTGATCCAAAGTGA 60.049 40.000 0.00 0.00 0.00 3.41
1484 1495 3.627395 TCCAAATTCATACCAGCGAGT 57.373 42.857 0.00 0.00 0.00 4.18
1488 1499 5.239525 GTCCTGTATCCAAATTCATACCAGC 59.760 44.000 0.00 0.00 0.00 4.85
1523 1534 3.176924 AGTGTGTCTGTATCCCAGTCT 57.823 47.619 0.00 0.00 42.19 3.24
1527 1538 3.169908 TGCTAAGTGTGTCTGTATCCCA 58.830 45.455 0.00 0.00 0.00 4.37
1565 1576 8.186821 ACATATAGCTGAAAATGCTGAAACTTC 58.813 33.333 0.00 0.00 41.32 3.01
1674 1685 5.442402 CAAATTAACACCATGCTTTGTTGC 58.558 37.500 13.12 0.00 36.61 4.17
2062 2076 4.336889 TGTCCTTCACTTCAACTTCGAT 57.663 40.909 0.00 0.00 0.00 3.59
2063 2077 3.812156 TGTCCTTCACTTCAACTTCGA 57.188 42.857 0.00 0.00 0.00 3.71
2064 2078 4.094294 TGTTTGTCCTTCACTTCAACTTCG 59.906 41.667 0.00 0.00 0.00 3.79
2065 2079 5.560966 TGTTTGTCCTTCACTTCAACTTC 57.439 39.130 0.00 0.00 0.00 3.01
2137 2155 6.550854 TGGAAATCAAGTTCCTTCATGTTCTT 59.449 34.615 10.28 0.00 46.29 2.52
3044 3074 5.241506 CAGCATCAGGGAAAACAACTTCTAA 59.758 40.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.