Multiple sequence alignment - TraesCS5A01G075000

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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 TraesCS5A01G075000 chr5A 100.000 3818 0 0 1 3818 88987819 88991636 0.000000e+00 7051
1 TraesCS5A01G075000 chr5A 79.022 1125 135 47 2574 3677 559097917 559096873 0.000000e+00 676
2 TraesCS5A01G075000 chr5A 86.154 195 24 2 1469 1661 559098108 559097915 1.390000e-49 207
3 TraesCS5A01G075000 chr5B 97.774 3010 56 7 815 3818 101845406 101848410 0.000000e+00 5177
4 TraesCS5A01G075000 chr5B 91.697 819 45 4 1 818 101844408 101845204 0.000000e+00 1114
5 TraesCS5A01G075000 chr5B 79.126 709 85 31 2943 3633 539315109 539314446 7.580000e-117 431
6 TraesCS5A01G075000 chr5B 86.082 194 24 2 1470 1661 539315497 539315305 5.000000e-49 206
7 TraesCS5A01G075000 chr5D 96.966 2933 79 8 804 3730 94499832 94502760 0.000000e+00 4915
8 TraesCS5A01G075000 chr5D 95.245 673 31 1 1 673 94498518 94499189 0.000000e+00 1064
9 TraesCS5A01G075000 chr5D 94.068 118 4 3 666 780 94499723 94499840 3.920000e-40 176
10 TraesCS5A01G075000 chr5D 96.117 103 3 1 3717 3818 94502777 94502879 2.360000e-37 167
11 TraesCS5A01G075000 chr5D 86.861 137 16 1 1470 1604 443071187 443071051 6.610000e-33 152


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 TraesCS5A01G075000 chr5A 88987819 88991636 3817 False 7051.0 7051 100.0000 1 3818 1 chr5A.!!$F1 3817
1 TraesCS5A01G075000 chr5A 559096873 559098108 1235 True 441.5 676 82.5880 1469 3677 2 chr5A.!!$R1 2208
2 TraesCS5A01G075000 chr5B 101844408 101848410 4002 False 3145.5 5177 94.7355 1 3818 2 chr5B.!!$F1 3817
3 TraesCS5A01G075000 chr5B 539314446 539315497 1051 True 318.5 431 82.6040 1470 3633 2 chr5B.!!$R1 2163
4 TraesCS5A01G075000 chr5D 94498518 94502879 4361 False 1580.5 4915 95.5990 1 3818 4 chr5D.!!$F1 3817

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
130 131 1.089112 CATGACAATGCAAGCCGAGA 58.911 50.0 0.0 0.0 0.0 4.04 F
1671 2443 0.108138 GCTGGAACACCGTGCTAGAT 60.108 55.0 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 2473 0.249489 ACTGAAACAGCTCGAACGCT 60.249 50.0 0.00 0.00 41.9 5.07 R
2874 3650 1.709147 GCAATGCTAGCACCTCACGG 61.709 60.0 22.07 5.68 0.0 4.94 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
29 30 5.665916 AAAAGGGCTTAATTCATGACTGG 57.334 39.130 0.00 0.00 0.00 4.00
130 131 1.089112 CATGACAATGCAAGCCGAGA 58.911 50.000 0.00 0.00 0.00 4.04
471 472 1.938861 GTGTTTGGCACGACACGAT 59.061 52.632 15.04 0.00 38.01 3.73
495 496 3.863424 CGCACATCCACGTTTATTAGACT 59.137 43.478 0.00 0.00 0.00 3.24
504 505 3.057033 ACGTTTATTAGACTGGTCGTGCT 60.057 43.478 0.00 0.00 34.09 4.40
591 592 2.741517 GCACATTTAACATGTTTGGGCC 59.258 45.455 20.56 0.00 0.00 5.80
622 633 4.785511 TCGGTCTGCTAGGCTATATTTC 57.214 45.455 0.00 0.00 0.00 2.17
623 634 4.408276 TCGGTCTGCTAGGCTATATTTCT 58.592 43.478 0.00 0.00 0.00 2.52
624 635 4.218635 TCGGTCTGCTAGGCTATATTTCTG 59.781 45.833 0.00 0.00 0.00 3.02
625 636 4.619394 CGGTCTGCTAGGCTATATTTCTGG 60.619 50.000 0.00 0.00 0.00 3.86
626 637 4.323104 GGTCTGCTAGGCTATATTTCTGGG 60.323 50.000 0.00 0.00 0.00 4.45
627 638 3.261897 TCTGCTAGGCTATATTTCTGGGC 59.738 47.826 0.00 0.00 0.00 5.36
628 639 2.305927 TGCTAGGCTATATTTCTGGGCC 59.694 50.000 0.00 0.00 42.74 5.80
629 640 2.305927 GCTAGGCTATATTTCTGGGCCA 59.694 50.000 5.85 5.85 44.60 5.36
630 641 3.054065 GCTAGGCTATATTTCTGGGCCAT 60.054 47.826 6.72 0.00 44.60 4.40
631 642 4.568592 GCTAGGCTATATTTCTGGGCCATT 60.569 45.833 6.72 0.00 44.60 3.16
637 648 2.043307 ATTTCTGGGCCATTTTGGGT 57.957 45.000 6.72 0.00 38.19 4.51
659 670 6.890268 GGGTCTATTGGATTGTTTCTTAGGTT 59.110 38.462 0.00 0.00 0.00 3.50
1395 2165 0.972471 TCATCAAGGCGCTCTCCTCA 60.972 55.000 7.64 0.00 34.82 3.86
1407 2177 2.604686 TCCTCAGCGGGCTTGACT 60.605 61.111 0.00 0.00 0.00 3.41
1599 2371 3.740128 GATGGTGCGACAGGGCGAT 62.740 63.158 0.00 0.00 35.06 4.58
1604 2376 4.760047 GCGACAGGGCGATGTGGT 62.760 66.667 0.00 0.00 32.25 4.16
1668 2440 0.970640 TAAGCTGGAACACCGTGCTA 59.029 50.000 0.00 0.00 35.98 3.49
1671 2443 0.108138 GCTGGAACACCGTGCTAGAT 60.108 55.000 0.00 0.00 0.00 1.98
1701 2473 0.253347 AGGCTGGGAAGATGGAGGAA 60.253 55.000 0.00 0.00 0.00 3.36
1803 2575 1.957177 GACATGGAGATGGCTCGAGTA 59.043 52.381 15.13 4.02 42.25 2.59
1922 2694 4.478206 TTACTCAGATGAAGGAAGCTGG 57.522 45.455 0.00 0.00 0.00 4.85
2088 2860 3.132646 ACATGTTTTGCAAGTGTGGATGT 59.867 39.130 0.00 1.47 0.00 3.06
2314 3086 0.974010 AGAGGGACGCCGGTATTTCA 60.974 55.000 1.90 0.00 0.00 2.69
2315 3087 0.108041 GAGGGACGCCGGTATTTCAA 60.108 55.000 1.90 0.00 0.00 2.69
2439 3211 4.032310 TGATAAAAAGCATGCCTTGGGAT 58.968 39.130 15.66 2.21 33.01 3.85
3059 3861 3.807622 CAGGTTTGCTCTGTCGAAAACTA 59.192 43.478 7.78 0.00 33.90 2.24
3530 4350 8.213679 AGTGTCATGCTATGTTATGAGGTTTAT 58.786 33.333 0.00 0.00 34.25 1.40
3633 4454 6.932356 AGGTTGCTGTGATGTTTATGATAG 57.068 37.500 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.153958 GCTTTGTTGCGCCATCCTC 60.154 57.895 4.18 0.00 0.00 3.71
49 50 2.108168 GGTATGCTAGAGGGTGACACA 58.892 52.381 8.08 0.00 0.00 3.72
81 82 2.817844 GTTTAAGGGTGGGTCATGTCAC 59.182 50.000 0.00 0.49 0.00 3.67
368 369 1.626356 ATGCATGACCTAGCCCACGT 61.626 55.000 0.00 0.00 0.00 4.49
471 472 2.102070 AATAAACGTGGATGTGCGGA 57.898 45.000 0.00 0.00 0.00 5.54
544 545 2.159114 GGTCGGCCGGTTACTAAATGTA 60.159 50.000 27.83 0.00 0.00 2.29
591 592 2.170985 CAGACCGAAAAGCACGCG 59.829 61.111 3.53 3.53 0.00 6.01
622 633 2.431782 CAATAGACCCAAAATGGCCCAG 59.568 50.000 0.00 0.00 35.79 4.45
623 634 2.465813 CAATAGACCCAAAATGGCCCA 58.534 47.619 0.00 0.00 35.79 5.36
624 635 1.762370 CCAATAGACCCAAAATGGCCC 59.238 52.381 0.00 0.00 35.79 5.80
625 636 2.745968 TCCAATAGACCCAAAATGGCC 58.254 47.619 0.00 0.00 35.79 5.36
626 637 4.162131 ACAATCCAATAGACCCAAAATGGC 59.838 41.667 0.00 0.00 35.79 4.40
627 638 5.937975 ACAATCCAATAGACCCAAAATGG 57.062 39.130 0.00 0.00 37.25 3.16
628 639 7.614494 AGAAACAATCCAATAGACCCAAAATG 58.386 34.615 0.00 0.00 0.00 2.32
629 640 7.797121 AGAAACAATCCAATAGACCCAAAAT 57.203 32.000 0.00 0.00 0.00 1.82
630 641 7.610580 AAGAAACAATCCAATAGACCCAAAA 57.389 32.000 0.00 0.00 0.00 2.44
631 642 7.396055 CCTAAGAAACAATCCAATAGACCCAAA 59.604 37.037 0.00 0.00 0.00 3.28
708 1272 3.953300 GCCTAAATGGGCCATGCA 58.047 55.556 22.01 10.01 45.92 3.96
803 1369 3.430929 GCAGTGTGCTACAAGGTATAGCT 60.431 47.826 0.00 0.00 44.52 3.32
986 1756 0.108520 GGACATTGGCGTTCGGACTA 60.109 55.000 0.00 0.00 0.00 2.59
1231 2001 0.914417 TTGGGGAAGGAGGCGAAGAT 60.914 55.000 0.00 0.00 0.00 2.40
1320 2090 1.587043 CGGAGAAGACAGAGACCGCA 61.587 60.000 0.00 0.00 34.36 5.69
1599 2371 0.541063 TCCTCCTCGCACTTACCACA 60.541 55.000 0.00 0.00 0.00 4.17
1604 2376 2.565391 TCAAACATCCTCCTCGCACTTA 59.435 45.455 0.00 0.00 0.00 2.24
1668 2440 0.620556 CAGCCTTGGTGTACCCATCT 59.379 55.000 4.19 1.03 44.74 2.90
1671 2443 2.534396 CCCAGCCTTGGTGTACCCA 61.534 63.158 0.00 0.00 43.40 4.51
1701 2473 0.249489 ACTGAAACAGCTCGAACGCT 60.249 50.000 0.00 0.00 41.90 5.07
1824 2596 2.473984 CGTCCACGTTACCAAGTTCTTC 59.526 50.000 0.00 0.00 34.11 2.87
1922 2694 1.267806 CAGCCACATCAAGTTCCACAC 59.732 52.381 0.00 0.00 0.00 3.82
2088 2860 3.199071 AGACATAATCAGCCCGGTTTACA 59.801 43.478 0.00 0.00 0.00 2.41
2314 3086 4.042187 GCCATAGTCCCTCTCCATATTGTT 59.958 45.833 0.00 0.00 0.00 2.83
2315 3087 3.584848 GCCATAGTCCCTCTCCATATTGT 59.415 47.826 0.00 0.00 0.00 2.71
2439 3211 8.946746 GGGACCCCCATATTACCTCATTAGGA 62.947 50.000 0.00 0.00 44.21 2.94
2874 3650 1.709147 GCAATGCTAGCACCTCACGG 61.709 60.000 22.07 5.68 0.00 4.94
3059 3861 5.408604 CCAGCTTTCGTCTTAACATAGTTGT 59.591 40.000 0.00 0.00 37.82 3.32
3288 4105 9.975218 ACTAATCTACTTTTCCAACATAACCAT 57.025 29.630 0.00 0.00 0.00 3.55
3310 4127 6.812656 TGAACGACTGTAAAACACTCAACTAA 59.187 34.615 0.00 0.00 0.00 2.24
3408 4228 6.935208 GGAGATACAAGCTTAATACCCGAATT 59.065 38.462 0.00 0.00 0.00 2.17
3472 4292 7.793902 TCTAAGAAGCGTGAAATACAAACTTC 58.206 34.615 0.00 0.00 40.22 3.01
3562 4382 7.801716 AGCAGTGAGTTATAAGTTGAAACAA 57.198 32.000 0.00 0.00 0.00 2.83
3698 4523 7.063308 CCAATTATTGAAGTTCCAAACATTCCG 59.937 37.037 6.50 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.