Multiple sequence alignment - TraesCS4D01G090500

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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 TraesCS4D01G090500 chr4D 100.000 3383 0 0 1 3383 65579216 65575834 0.000000e+00 6248.0
1 TraesCS4D01G090500 chr4D 79.508 244 41 6 2687 2925 467241680 467241441 7.510000e-37 165.0
2 TraesCS4D01G090500 chr4D 86.022 93 12 1 2756 2847 69402003 69402095 7.730000e-17 99.0
3 TraesCS4D01G090500 chr4A 94.467 3416 127 29 1 3383 530120787 530124173 0.000000e+00 5204.0
4 TraesCS4D01G090500 chr4B 95.572 2507 78 10 364 2866 96273102 96270625 0.000000e+00 3984.0
5 TraesCS4D01G090500 chr4B 87.842 329 27 8 2860 3182 96270008 96269687 1.150000e-99 374.0
6 TraesCS4D01G090500 chr4B 83.951 243 20 8 26 260 96273379 96273148 7.350000e-52 215.0
7 TraesCS4D01G090500 chr4B 87.831 189 13 5 3174 3362 96268361 96268183 2.640000e-51 213.0
8 TraesCS4D01G090500 chr4B 78.161 261 43 11 2674 2926 585030102 585029848 1.630000e-33 154.0
9 TraesCS4D01G090500 chr5D 91.743 218 18 0 1365 1582 205995758 205995975 1.530000e-78 303.0
10 TraesCS4D01G090500 chr5D 83.957 187 26 4 1384 1568 539014529 539014713 3.470000e-40 176.0
11 TraesCS4D01G090500 chr5A 91.284 218 19 0 1365 1582 264421478 264421695 7.100000e-77 298.0
12 TraesCS4D01G090500 chr5B 90.826 218 20 0 1365 1582 206102422 206102205 3.300000e-75 292.0
13 TraesCS4D01G090500 chr5B 83.854 192 25 5 2674 2860 245968606 245968796 9.650000e-41 178.0
14 TraesCS4D01G090500 chr5B 91.667 48 3 1 2676 2722 491037861 491037908 7.840000e-07 65.8
15 TraesCS4D01G090500 chr6D 84.937 239 31 4 1363 1597 393936217 393935980 1.570000e-58 237.0
16 TraesCS4D01G090500 chr6A 84.937 239 31 4 1363 1597 540145669 540145432 1.570000e-58 237.0
17 TraesCS4D01G090500 chr2D 81.553 206 33 5 1384 1586 520537008 520536805 7.510000e-37 165.0
18 TraesCS4D01G090500 chr1A 77.992 259 45 9 2676 2926 23815575 23815829 5.850000e-33 152.0
19 TraesCS4D01G090500 chr2B 77.381 168 31 6 2760 2926 117930662 117930501 3.590000e-15 93.5
20 TraesCS4D01G090500 chr1B 79.310 116 18 4 2698 2810 671181087 671180975 3.620000e-10 76.8
21 TraesCS4D01G090500 chr6B 100.000 32 0 0 1716 1747 12118379 12118348 3.650000e-05 60.2


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 TraesCS4D01G090500 chr4D 65575834 65579216 3382 True 6248.0 6248 100.000 1 3383 1 chr4D.!!$R1 3382
1 TraesCS4D01G090500 chr4A 530120787 530124173 3386 False 5204.0 5204 94.467 1 3383 1 chr4A.!!$F1 3382
2 TraesCS4D01G090500 chr4B 96268183 96273379 5196 True 1196.5 3984 88.799 26 3362 4 chr4B.!!$R2 3336

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
740 753 1.201429 GGTCATGACCCTCACCCAGT 61.201 60.0 31.37 0.0 45.68 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2685 2700 3.057548 CCCTGCTGCAACGCATGA 61.058 61.111 3.02 0.0 39.52 3.07 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
71 72 3.007614 AGGTTGTAGGACGTACTTGCAAT 59.992 43.478 5.12 0.00 33.65 3.56
225 234 8.665906 TCTCTAAGAAATTGAGAAAAGGGGTAA 58.334 33.333 0.00 0.00 37.05 2.85
268 277 8.018537 AGATTATAAGGTTTAAACATTGCCCC 57.981 34.615 24.36 11.73 34.45 5.80
275 284 7.177832 AGGTTTAAACATTGCCCCTATAAAC 57.822 36.000 19.57 0.00 33.32 2.01
298 307 8.593945 AACAATAATAGGATGAACAACATGGT 57.406 30.769 0.00 0.00 39.56 3.55
299 308 9.693739 AACAATAATAGGATGAACAACATGGTA 57.306 29.630 0.00 0.00 39.56 3.25
300 309 9.120538 ACAATAATAGGATGAACAACATGGTAC 57.879 33.333 0.00 0.00 39.56 3.34
426 439 4.389890 TGTAATGGATTTGCAATGCTCC 57.610 40.909 6.82 5.89 0.00 4.70
482 495 1.464608 CAGACAAACTACCACGCCATG 59.535 52.381 0.00 0.00 0.00 3.66
494 507 2.086869 CACGCCATGGAGAGAAATTGT 58.913 47.619 23.45 0.00 0.00 2.71
505 518 3.067106 AGAGAAATTGTCATGCGTTCGT 58.933 40.909 0.00 0.00 0.00 3.85
506 519 4.242475 AGAGAAATTGTCATGCGTTCGTA 58.758 39.130 0.00 0.00 0.00 3.43
507 520 4.870426 AGAGAAATTGTCATGCGTTCGTAT 59.130 37.500 0.00 0.00 0.00 3.06
508 521 5.005779 AGAGAAATTGTCATGCGTTCGTATC 59.994 40.000 0.00 0.00 0.00 2.24
509 522 4.629634 AGAAATTGTCATGCGTTCGTATCA 59.370 37.500 0.00 0.00 0.00 2.15
514 527 4.119136 TGTCATGCGTTCGTATCATGATT 58.881 39.130 14.65 0.00 45.43 2.57
541 554 1.819632 CCGAGGAAATTCGCTGGGG 60.820 63.158 5.19 0.00 39.19 4.96
542 555 1.819632 CGAGGAAATTCGCTGGGGG 60.820 63.158 0.00 0.00 33.39 5.40
729 742 1.838112 TTGATTGGCCAGGTCATGAC 58.162 50.000 17.91 17.91 0.00 3.06
740 753 1.201429 GGTCATGACCCTCACCCAGT 61.201 60.000 31.37 0.00 45.68 4.00
881 896 3.501568 GGTGGTTTTCTGGGGTTTAGGAT 60.502 47.826 0.00 0.00 0.00 3.24
1092 1107 0.610687 ACTGTGCCTAGCTGTCTTCC 59.389 55.000 0.00 0.00 0.00 3.46
1225 1240 1.442148 CCCTTCTACTACGCTGCCC 59.558 63.158 0.00 0.00 0.00 5.36
1845 1860 2.267642 CGCCATCAAGACCCGGAA 59.732 61.111 0.73 0.00 0.00 4.30
1905 1920 2.113139 CCCACTGCTGTTTCGGGT 59.887 61.111 8.90 0.00 31.80 5.28
2611 2626 6.759497 AGTAATCCATGTTTAGAACAAGGC 57.241 37.500 9.54 0.00 46.88 4.35
2619 2634 6.381801 CATGTTTAGAACAAGGCGATTTTCT 58.618 36.000 0.00 1.48 45.86 2.52
2685 2700 7.661847 AGCACTTTAACAGAACTAGCTAATTGT 59.338 33.333 0.00 0.00 0.00 2.71
2697 2712 2.159476 AGCTAATTGTCATGCGTTGCAG 60.159 45.455 0.00 0.00 43.65 4.41
2763 2808 8.701895 CCCGACATATATACACCTACCATATTT 58.298 37.037 0.00 0.00 0.00 1.40
2872 2917 7.906199 TTAATTTGATTTAGGTATGGGTGGG 57.094 36.000 0.00 0.00 0.00 4.61
3004 3674 0.388659 TTGTGTGCCAATGGTTGAGC 59.611 50.000 0.00 0.00 0.00 4.26
3038 3708 4.725490 TCAACAGAAAACTAAAGAGGGGG 58.275 43.478 0.00 0.00 0.00 5.40
3101 3776 4.441217 GCGAACCTACTAACCCTCCTTTAG 60.441 50.000 0.00 0.00 33.46 1.85
3128 3803 7.019388 AGTAGAGATTGGGGAAGCAAGATATA 58.981 38.462 0.00 0.00 0.00 0.86
3156 3831 9.810545 GATCTAGCATTCCAAATAGACCTATAC 57.189 37.037 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
264 273 8.957466 GTTCATCCTATTATTGTTTATAGGGGC 58.043 37.037 0.00 0.00 42.37 5.80
275 284 8.282592 CGTACCATGTTGTTCATCCTATTATTG 58.717 37.037 0.00 0.00 34.09 1.90
426 439 4.383649 CACAAGATGGCAAATTTCACTTCG 59.616 41.667 0.00 0.00 0.00 3.79
482 495 3.484229 CGAACGCATGACAATTTCTCTCC 60.484 47.826 0.00 0.00 0.00 3.71
505 518 2.825532 TCGGAGCCATCGAATCATGATA 59.174 45.455 9.04 0.00 33.42 2.15
506 519 1.620323 TCGGAGCCATCGAATCATGAT 59.380 47.619 1.18 1.18 33.42 2.45
507 520 1.000171 CTCGGAGCCATCGAATCATGA 60.000 52.381 0.00 0.00 36.15 3.07
508 521 1.426423 CTCGGAGCCATCGAATCATG 58.574 55.000 0.00 0.00 36.15 3.07
509 522 0.319728 CCTCGGAGCCATCGAATCAT 59.680 55.000 0.00 0.00 36.15 2.45
514 527 0.830648 AATTTCCTCGGAGCCATCGA 59.169 50.000 0.00 0.00 35.24 3.59
541 554 1.227973 CGCCAGATTTCTAGGGCCC 60.228 63.158 16.46 16.46 43.50 5.80
542 555 0.107165 AACGCCAGATTTCTAGGGCC 60.107 55.000 0.00 0.00 43.50 5.80
543 556 1.300481 GAACGCCAGATTTCTAGGGC 58.700 55.000 0.00 0.00 42.98 5.19
591 604 4.749245 ACAGCTGTTTGTTAGCATGTAC 57.251 40.909 15.25 0.00 43.53 2.90
644 657 4.580580 GTGGTAATCATGAGGTTGGGATTC 59.419 45.833 0.09 0.00 32.62 2.52
729 742 0.397816 AGCTAGCTACTGGGTGAGGG 60.398 60.000 17.69 0.00 0.00 4.30
740 753 2.357952 CGTGGTGTGTATCAGCTAGCTA 59.642 50.000 18.86 6.64 43.97 3.32
881 896 5.640147 AGGTTTGGATTTTGAGTATGACCA 58.360 37.500 0.00 0.00 0.00 4.02
1072 1087 1.404851 GGAAGACAGCTAGGCACAGTC 60.405 57.143 0.00 0.00 0.00 3.51
1092 1107 0.107312 CCTGCTGGTCCATGAGAAGG 60.107 60.000 0.51 0.00 0.00 3.46
2423 2438 4.562394 CACAAACCATGGATTAATGAACGC 59.438 41.667 21.47 0.00 0.00 4.84
2611 2626 8.930760 CCCTAGCAAGAATTCTATAGAAAATCG 58.069 37.037 18.79 9.66 37.61 3.34
2685 2700 3.057548 CCCTGCTGCAACGCATGA 61.058 61.111 3.02 0.00 39.52 3.07
2697 2712 4.020218 TCACTAGAATATGTATGCCCCTGC 60.020 45.833 0.00 0.00 38.26 4.85
2732 2747 4.894784 AGGTGTATATATGTCGGGCAAAG 58.105 43.478 0.00 0.00 0.00 2.77
2866 2911 3.782656 TTTACTTGACTTCTCCCACCC 57.217 47.619 0.00 0.00 0.00 4.61
2867 2912 6.650427 AAATTTTACTTGACTTCTCCCACC 57.350 37.500 0.00 0.00 0.00 4.61
2868 2913 7.712797 TCAAAATTTTACTTGACTTCTCCCAC 58.287 34.615 2.44 0.00 0.00 4.61
2914 3583 7.703058 ATCGGTACTTTTCCAAATCAAATCT 57.297 32.000 0.00 0.00 0.00 2.40
3043 3713 2.508407 TTTTTCCTCCCCGCATCCCC 62.508 60.000 0.00 0.00 0.00 4.81
3044 3714 1.000145 TTTTTCCTCCCCGCATCCC 60.000 57.895 0.00 0.00 0.00 3.85
3101 3776 4.406003 TCTTGCTTCCCCAATCTCTACTAC 59.594 45.833 0.00 0.00 0.00 2.73
3128 3803 5.305644 AGGTCTATTTGGAATGCTAGATCGT 59.694 40.000 0.00 0.00 0.00 3.73
3156 3831 4.331717 ACATAAAAGCATTAGGAACGACGG 59.668 41.667 0.00 0.00 0.00 4.79
3268 5277 9.981114 CATTTTATTAAACAACCCTTCAAGAGT 57.019 29.630 0.00 0.00 0.00 3.24
3329 5338 9.454859 CAGTTTTCTAGTTTATGAGGATTCCTT 57.545 33.333 6.68 0.00 31.76 3.36


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

AutoCloner maintained by Alex Coulton.