Multiple sequence alignment - TraesCS2B01G265100

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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 TraesCS2B01G265100 chr2B 100.000 2646 0 0 1 2646 357518483 357521128 0 4887
1 TraesCS2B01G265100 chr2B 97.203 2610 72 1 1 2610 391167714 391165106 0 4414
2 TraesCS2B01G265100 chrUn 97.854 2610 55 1 1 2610 186201715 186204323 0 4508
3 TraesCS2B01G265100 chr7B 97.778 2610 57 1 1 2610 742996151 742993543 0 4497
4 TraesCS2B01G265100 chr7B 97.663 2610 59 2 1 2610 716872076 716874683 0 4481
5 TraesCS2B01G265100 chr1A 97.778 2610 54 3 1 2610 498684525 498687130 0 4495
6 TraesCS2B01G265100 chr5A 97.548 2610 63 1 1 2610 492862433 492859825 0 4464
7 TraesCS2B01G265100 chr4A 97.281 2611 68 3 1 2610 67603672 67601064 0 4425
8 TraesCS2B01G265100 chr4B 97.241 2610 69 3 1 2610 209306366 209303760 0 4418
9 TraesCS2B01G265100 chr3A 97.165 2610 73 1 1 2610 725803458 725800850 0 4409


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 TraesCS2B01G265100 chr2B 357518483 357521128 2645 False 4887 4887 100.000 1 2646 1 chr2B.!!$F1 2645
1 TraesCS2B01G265100 chr2B 391165106 391167714 2608 True 4414 4414 97.203 1 2610 1 chr2B.!!$R1 2609
2 TraesCS2B01G265100 chrUn 186201715 186204323 2608 False 4508 4508 97.854 1 2610 1 chrUn.!!$F1 2609
3 TraesCS2B01G265100 chr7B 742993543 742996151 2608 True 4497 4497 97.778 1 2610 1 chr7B.!!$R1 2609
4 TraesCS2B01G265100 chr7B 716872076 716874683 2607 False 4481 4481 97.663 1 2610 1 chr7B.!!$F1 2609
5 TraesCS2B01G265100 chr1A 498684525 498687130 2605 False 4495 4495 97.778 1 2610 1 chr1A.!!$F1 2609
6 TraesCS2B01G265100 chr5A 492859825 492862433 2608 True 4464 4464 97.548 1 2610 1 chr5A.!!$R1 2609
7 TraesCS2B01G265100 chr4A 67601064 67603672 2608 True 4425 4425 97.281 1 2610 1 chr4A.!!$R1 2609
8 TraesCS2B01G265100 chr4B 209303760 209306366 2606 True 4418 4418 97.241 1 2610 1 chr4B.!!$R1 2609
9 TraesCS2B01G265100 chr3A 725800850 725803458 2608 True 4409 4409 97.165 1 2610 1 chr3A.!!$R1 2609

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
711 715 1.279271 GCTCTGCTCCTCCTAAAACCA 59.721 52.381 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1698 0.250038 AGCATGTCCCGATGATTCCG 60.25 55.0 0.0 0.0 0.0 4.3 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
78 79 8.088981 TGAACAAGAAGGACAGTAACTAGAATC 58.911 37.037 0.00 0.00 0.00 2.52
283 286 4.922206 TGCAAGGATGTAAAGAATGAGGT 58.078 39.130 0.00 0.00 0.00 3.85
553 557 7.256083 GCATATTGAAGGGAAGGCTATGAAAAT 60.256 37.037 0.00 0.00 0.00 1.82
560 564 9.574516 GAAGGGAAGGCTATGAAAATAATTCTA 57.425 33.333 0.00 0.00 0.00 2.10
711 715 1.279271 GCTCTGCTCCTCCTAAAACCA 59.721 52.381 0.00 0.00 0.00 3.67
886 890 6.991938 AGCAAAGCAATTCCAACATAAACTA 58.008 32.000 0.00 0.00 0.00 2.24
903 907 8.265764 ACATAAACTAACACTTTAGGATCCTCC 58.734 37.037 20.22 0.00 39.36 4.30
1014 1018 3.825908 TTAAAGATGTGGCCTTCCCTT 57.174 42.857 3.32 0.00 0.00 3.95
1271 1276 9.529325 GAAAGCCATATTTTCCACCTTATTTAC 57.471 33.333 0.00 0.00 0.00 2.01
1290 1295 6.653526 TTTACATATTCCATTCCAGCCATG 57.346 37.500 0.00 0.00 0.00 3.66
1393 1399 8.192774 GCAGGATAAATCACAGAATTCAAATGA 58.807 33.333 8.44 8.34 0.00 2.57
1433 1439 4.943093 GCAATTCAAACCTAATGGCCAAAT 59.057 37.500 10.96 4.19 36.63 2.32
1509 1515 4.475016 ACAACTCCATATTCTACTGGCCTT 59.525 41.667 3.32 0.00 32.30 4.35
1534 1540 6.068010 CCTCTCTGATCTACTATCCAACTGT 58.932 44.000 0.00 0.00 0.00 3.55
1570 1576 2.375174 TGTTCACCCTAGGCTCACATTT 59.625 45.455 2.05 0.00 0.00 2.32
1580 1586 1.340889 GGCTCACATTTTGGCACTTCA 59.659 47.619 0.00 0.00 0.00 3.02
1615 1621 5.885912 ACTCAAAGGACTTGCTTGTCTTTTA 59.114 36.000 15.12 7.34 41.93 1.52
1692 1698 1.369321 CTGGCCTTCTCCTATCCGC 59.631 63.158 3.32 0.00 0.00 5.54
1752 1758 3.871594 CCACATAGTTTAGGGAAGCGAAG 59.128 47.826 0.00 0.00 0.00 3.79
1846 1852 7.308435 CGCAAAAGATTTCTATTTGGAGTTCT 58.692 34.615 12.70 0.00 35.21 3.01
1847 1853 7.809806 CGCAAAAGATTTCTATTTGGAGTTCTT 59.190 33.333 12.70 0.00 35.21 2.52
1952 1958 3.222173 ACTTGTCCACACTGGCATAAA 57.778 42.857 0.00 0.00 37.47 1.40
1981 1987 0.541863 CCCGGAACTAAGAGGCATGT 59.458 55.000 0.73 0.00 0.00 3.21
1984 1990 3.393800 CCGGAACTAAGAGGCATGTATG 58.606 50.000 0.00 0.00 0.00 2.39
2029 2035 4.607293 ATGAATAAGTATCAGCGAGGCA 57.393 40.909 0.00 0.00 0.00 4.75
2165 2171 5.542635 ACCAATGTCCTAGACTACAAGTTCA 59.457 40.000 0.00 0.00 33.15 3.18
2230 2236 3.329542 TTGCCCTCTGGATCACGCC 62.330 63.158 0.00 0.00 0.00 5.68
2250 2256 1.632589 GGGTCCTTGCTTGTTCCAAT 58.367 50.000 0.00 0.00 0.00 3.16
2419 2425 0.600255 CAACGCTTCTGGTCGGAAGT 60.600 55.000 17.68 1.16 43.13 3.01
2433 2439 0.458669 GGAAGTTGGTCGATCGCCTA 59.541 55.000 22.99 15.99 0.00 3.93
2610 2616 4.662278 TGATCGGAAAAAGGACCTCAAAT 58.338 39.130 0.00 0.00 0.00 2.32
2611 2617 5.076873 TGATCGGAAAAAGGACCTCAAATT 58.923 37.500 0.00 0.00 0.00 1.82
2612 2618 6.242396 TGATCGGAAAAAGGACCTCAAATTA 58.758 36.000 0.00 0.00 0.00 1.40
2613 2619 6.374333 TGATCGGAAAAAGGACCTCAAATTAG 59.626 38.462 0.00 0.00 0.00 1.73
2614 2620 5.007682 TCGGAAAAAGGACCTCAAATTAGG 58.992 41.667 0.00 0.00 42.82 2.69
2615 2621 4.157840 CGGAAAAAGGACCTCAAATTAGGG 59.842 45.833 0.00 0.00 41.32 3.53
2616 2622 4.081642 GGAAAAAGGACCTCAAATTAGGGC 60.082 45.833 0.00 0.00 44.87 5.19
2620 2626 5.466127 AAGGACCTCAAATTAGGGCATTA 57.534 39.130 0.00 0.00 46.68 1.90
2621 2627 5.837829 AAGGACCTCAAATTAGGGCATTAA 58.162 37.500 0.00 0.00 46.68 1.40
2622 2628 6.260663 AAGGACCTCAAATTAGGGCATTAAA 58.739 36.000 0.00 0.00 46.68 1.52
2623 2629 6.902974 AAGGACCTCAAATTAGGGCATTAAAT 59.097 34.615 0.00 0.00 46.68 1.40
2624 2630 8.065007 AAGGACCTCAAATTAGGGCATTAAATA 58.935 33.333 0.00 0.00 46.68 1.40
2627 2633 9.914131 GACCTCAAATTAGGGCATTAAATAATC 57.086 33.333 0.00 0.00 44.97 1.75
2628 2634 9.660544 ACCTCAAATTAGGGCATTAAATAATCT 57.339 29.630 0.00 0.00 41.32 2.40
2637 2643 7.457561 AGGGCATTAAATAATCTCTCTCTTCC 58.542 38.462 0.00 0.00 0.00 3.46
2638 2644 7.072961 AGGGCATTAAATAATCTCTCTCTTCCA 59.927 37.037 0.00 0.00 0.00 3.53
2639 2645 7.887495 GGGCATTAAATAATCTCTCTCTTCCAT 59.113 37.037 0.00 0.00 0.00 3.41
2640 2646 8.945057 GGCATTAAATAATCTCTCTCTTCCATC 58.055 37.037 0.00 0.00 0.00 3.51
2641 2647 8.945057 GCATTAAATAATCTCTCTCTTCCATCC 58.055 37.037 0.00 0.00 0.00 3.51
2642 2648 9.447157 CATTAAATAATCTCTCTCTTCCATCCC 57.553 37.037 0.00 0.00 0.00 3.85
2643 2649 8.805145 TTAAATAATCTCTCTCTTCCATCCCT 57.195 34.615 0.00 0.00 0.00 4.20
2644 2650 6.684897 AATAATCTCTCTCTTCCATCCCTG 57.315 41.667 0.00 0.00 0.00 4.45
2645 2651 2.468301 TCTCTCTCTTCCATCCCTGG 57.532 55.000 0.00 0.00 44.64 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
283 286 1.888436 CGGGCCAGTCTGTTCTAGCA 61.888 60.000 4.39 0.00 0.00 3.49
397 400 6.346518 CGCTTTGCTTTCATTTACCGAAAATT 60.347 34.615 0.00 0.00 35.54 1.82
553 557 4.035324 CAGGCGTTCGAGAGACTAGAATTA 59.965 45.833 0.00 0.00 41.84 1.40
560 564 2.995872 GCCAGGCGTTCGAGAGACT 61.996 63.158 0.00 0.00 41.84 3.24
903 907 3.821421 ACGGGTCTATAGAAAGGCTTG 57.179 47.619 3.40 0.00 0.00 4.01
1014 1018 6.070078 TGCTCCATATCCATATATGTGCTTGA 60.070 38.462 11.73 1.93 42.33 3.02
1160 1165 7.752239 CGAGTTTGAAAGCATTAATGAAGTGAT 59.248 33.333 19.73 0.00 0.00 3.06
1262 1267 7.451255 TGGCTGGAATGGAATATGTAAATAAGG 59.549 37.037 0.00 0.00 0.00 2.69
1290 1295 2.221981 CGAAAAGAGTGAGTTGCTGTCC 59.778 50.000 0.00 0.00 0.00 4.02
1393 1399 5.829924 TGAATTGCCTTCTCTTTCTGTCTTT 59.170 36.000 0.00 0.00 34.75 2.52
1433 1439 9.547753 GCTATAAGTATTTCTGTCTTGGATTCA 57.452 33.333 0.00 0.00 0.00 2.57
1509 1515 6.126332 ACAGTTGGATAGTAGATCAGAGAGGA 60.126 42.308 0.00 0.00 0.00 3.71
1570 1576 2.653726 ACACAGTGAATGAAGTGCCAA 58.346 42.857 7.81 0.00 35.47 4.52
1580 1586 5.552870 AGTCCTTTGAGTACACAGTGAAT 57.447 39.130 7.81 0.00 0.00 2.57
1692 1698 0.250038 AGCATGTCCCGATGATTCCG 60.250 55.000 0.00 0.00 0.00 4.30
1752 1758 2.934553 GTGAACTAACCCGAACTATGGC 59.065 50.000 0.00 0.00 0.00 4.40
1846 1852 5.390885 GCAGTGATCGAGCAACTAAATGAAA 60.391 40.000 4.22 0.00 0.00 2.69
1847 1853 4.093408 GCAGTGATCGAGCAACTAAATGAA 59.907 41.667 4.22 0.00 0.00 2.57
1952 1958 3.053095 TCTTAGTTCCGGGGAGATACTGT 60.053 47.826 0.00 0.00 0.00 3.55
1981 1987 7.223584 TCTTTGAATCGATAAAGATGGGCATA 58.776 34.615 16.04 0.00 37.83 3.14
1984 1990 6.377327 TTCTTTGAATCGATAAAGATGGGC 57.623 37.500 19.20 0.00 41.15 5.36
2029 2035 3.393743 TACCGGGCCCGTATTCCCT 62.394 63.158 40.52 16.67 40.41 4.20
2165 2171 0.396556 ACCCAAGCCGGAAGTTTGTT 60.397 50.000 5.05 0.00 36.56 2.83
2230 2236 1.228124 TGGAACAAGCAAGGACCCG 60.228 57.895 0.00 0.00 31.92 5.28
2250 2256 4.099419 ACGTGATACATTCCTAGCATGACA 59.901 41.667 0.00 2.89 0.00 3.58
2419 2425 1.721664 CCGACTAGGCGATCGACCAA 61.722 60.000 22.46 5.23 40.86 3.67
2454 2460 1.963515 ACAGAAATCCCACTGGCAAAC 59.036 47.619 0.00 0.00 38.30 2.93
2513 2519 3.626930 ACGCTGTTCTTAGAGATCTCCT 58.373 45.455 19.30 9.22 0.00 3.69
2519 2525 3.126514 CCGTAGAACGCTGTTCTTAGAGA 59.873 47.826 22.58 7.63 40.91 3.10
2526 2532 0.458025 CTCCCCGTAGAACGCTGTTC 60.458 60.000 11.79 11.79 40.91 3.18
2611 2617 8.598041 GGAAGAGAGAGATTATTTAATGCCCTA 58.402 37.037 0.00 0.00 0.00 3.53
2612 2618 7.072961 TGGAAGAGAGAGATTATTTAATGCCCT 59.927 37.037 0.00 0.00 0.00 5.19
2613 2619 7.227156 TGGAAGAGAGAGATTATTTAATGCCC 58.773 38.462 0.00 0.00 0.00 5.36
2614 2620 8.860780 ATGGAAGAGAGAGATTATTTAATGCC 57.139 34.615 0.00 0.00 0.00 4.40
2615 2621 8.945057 GGATGGAAGAGAGAGATTATTTAATGC 58.055 37.037 0.00 0.00 0.00 3.56
2616 2622 9.447157 GGGATGGAAGAGAGAGATTATTTAATG 57.553 37.037 0.00 0.00 0.00 1.90
2617 2623 9.404077 AGGGATGGAAGAGAGAGATTATTTAAT 57.596 33.333 0.00 0.00 0.00 1.40
2618 2624 8.654997 CAGGGATGGAAGAGAGAGATTATTTAA 58.345 37.037 0.00 0.00 0.00 1.52
2619 2625 7.236432 CCAGGGATGGAAGAGAGAGATTATTTA 59.764 40.741 0.00 0.00 0.00 1.40
2620 2626 6.044171 CCAGGGATGGAAGAGAGAGATTATTT 59.956 42.308 0.00 0.00 0.00 1.40
2621 2627 5.547276 CCAGGGATGGAAGAGAGAGATTATT 59.453 44.000 0.00 0.00 0.00 1.40
2622 2628 5.092968 CCAGGGATGGAAGAGAGAGATTAT 58.907 45.833 0.00 0.00 0.00 1.28
2623 2629 4.487804 CCAGGGATGGAAGAGAGAGATTA 58.512 47.826 0.00 0.00 0.00 1.75
2624 2630 3.316501 CCAGGGATGGAAGAGAGAGATT 58.683 50.000 0.00 0.00 0.00 2.40
2625 2631 2.975075 CCAGGGATGGAAGAGAGAGAT 58.025 52.381 0.00 0.00 0.00 2.75
2626 2632 2.468301 CCAGGGATGGAAGAGAGAGA 57.532 55.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.