Multiple sequence alignment - TraesCS2B01G309200

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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 TraesCS2B01G309200 chr2B 100.000 1413 0 0 864 2276 442323152 442321740 0.000000e+00 2610
1 TraesCS2B01G309200 chr2B 100.000 666 0 0 1 666 442324015 442323350 0.000000e+00 1230
2 TraesCS2B01G309200 chr2B 95.495 666 30 0 1 666 548635967 548635302 0.000000e+00 1064
3 TraesCS2B01G309200 chr2B 90.991 666 60 0 1 666 65438230 65437565 0.000000e+00 898
4 TraesCS2B01G309200 chr2B 92.841 433 30 1 876 1308 65437319 65436888 5.340000e-176 627
5 TraesCS2B01G309200 chr2B 94.444 378 21 0 866 1243 548634414 548634037 1.170000e-162 582
6 TraesCS2B01G309200 chr2B 95.480 177 8 0 866 1042 548635276 548635100 1.330000e-72 283
7 TraesCS2B01G309200 chr2B 96.124 129 5 0 538 666 548634569 548634441 6.370000e-51 211
8 TraesCS2B01G309200 chr2B 97.059 68 2 0 1237 1304 548632278 548632211 5.140000e-22 115
9 TraesCS2B01G309200 chrUn 90.937 982 76 10 1303 2275 52685905 52686882 0.000000e+00 1308
10 TraesCS2B01G309200 chrUn 85.495 586 83 2 3 587 335288660 335289244 5.380000e-171 610
11 TraesCS2B01G309200 chrUn 85.154 586 85 2 3 587 335285956 335286540 1.160000e-167 599
12 TraesCS2B01G309200 chr1D 91.613 775 58 7 1495 2267 376645509 376644740 0.000000e+00 1064
13 TraesCS2B01G309200 chr1D 84.151 795 116 10 1486 2276 221514742 221513954 0.000000e+00 761
14 TraesCS2B01G309200 chr4D 90.382 811 69 7 1460 2267 264819268 264818464 0.000000e+00 1057
15 TraesCS2B01G309200 chr1B 89.609 818 71 14 1440 2249 146162128 146162939 0.000000e+00 1027
16 TraesCS2B01G309200 chr3D 88.269 878 76 9 1423 2276 595370197 595371071 0.000000e+00 1026
17 TraesCS2B01G309200 chr3D 89.348 798 77 6 1481 2276 595335557 595336348 0.000000e+00 996
18 TraesCS2B01G309200 chr3D 90.526 665 63 0 1 665 127221313 127220649 0.000000e+00 880
19 TraesCS2B01G309200 chr3D 90.389 437 42 0 866 1302 127220627 127220191 1.960000e-160 575
20 TraesCS2B01G309200 chr2A 93.020 659 44 2 1619 2276 61679005 61678348 0.000000e+00 961
21 TraesCS2B01G309200 chr2A 88.350 103 12 0 1199 1301 57868079 57868181 8.540000e-25 124
22 TraesCS2B01G309200 chr1A 90.090 666 66 0 1 666 445913487 445914152 0.000000e+00 865
23 TraesCS2B01G309200 chr1A 85.171 789 106 9 1491 2276 351680948 351680168 0.000000e+00 798
24 TraesCS2B01G309200 chr4A 88.138 666 78 1 1 666 285950148 285949484 0.000000e+00 791
25 TraesCS2B01G309200 chr4A 91.116 439 39 0 866 1304 285949462 285949024 1.510000e-166 595
26 TraesCS2B01G309200 chr4A 88.584 438 42 4 866 1303 2781712 2781283 2.000000e-145 525
27 TraesCS2B01G309200 chr5A 84.615 624 95 1 1 624 69221197 69221819 8.930000e-174 619
28 TraesCS2B01G309200 chr5B 84.983 586 86 2 3 587 688966338 688966922 5.410000e-166 593
29 TraesCS2B01G309200 chr5B 73.171 369 93 6 920 1285 41967556 41967191 6.600000e-26 128
30 TraesCS2B01G309200 chr5B 73.139 309 83 0 920 1228 21381788 21381480 6.650000e-21 111
31 TraesCS2B01G309200 chr7A 83.193 238 36 4 1070 1305 7510392 7510157 4.920000e-52 215
32 TraesCS2B01G309200 chr6B 72.494 389 103 4 896 1282 504165642 504166028 3.070000e-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 TraesCS2B01G309200 chr2B 442321740 442324015 2275 True 1920.0 2610 100.0000 1 2276 2 chr2B.!!$R2 2275
1 TraesCS2B01G309200 chr2B 65436888 65438230 1342 True 762.5 898 91.9160 1 1308 2 chr2B.!!$R1 1307
2 TraesCS2B01G309200 chr2B 548632211 548635967 3756 True 451.0 1064 95.7204 1 1304 5 chr2B.!!$R3 1303
3 TraesCS2B01G309200 chrUn 52685905 52686882 977 False 1308.0 1308 90.9370 1303 2275 1 chrUn.!!$F1 972
4 TraesCS2B01G309200 chrUn 335285956 335289244 3288 False 604.5 610 85.3245 3 587 2 chrUn.!!$F2 584
5 TraesCS2B01G309200 chr1D 376644740 376645509 769 True 1064.0 1064 91.6130 1495 2267 1 chr1D.!!$R2 772
6 TraesCS2B01G309200 chr1D 221513954 221514742 788 True 761.0 761 84.1510 1486 2276 1 chr1D.!!$R1 790
7 TraesCS2B01G309200 chr4D 264818464 264819268 804 True 1057.0 1057 90.3820 1460 2267 1 chr4D.!!$R1 807
8 TraesCS2B01G309200 chr1B 146162128 146162939 811 False 1027.0 1027 89.6090 1440 2249 1 chr1B.!!$F1 809
9 TraesCS2B01G309200 chr3D 595370197 595371071 874 False 1026.0 1026 88.2690 1423 2276 1 chr3D.!!$F2 853
10 TraesCS2B01G309200 chr3D 595335557 595336348 791 False 996.0 996 89.3480 1481 2276 1 chr3D.!!$F1 795
11 TraesCS2B01G309200 chr3D 127220191 127221313 1122 True 727.5 880 90.4575 1 1302 2 chr3D.!!$R1 1301
12 TraesCS2B01G309200 chr2A 61678348 61679005 657 True 961.0 961 93.0200 1619 2276 1 chr2A.!!$R1 657
13 TraesCS2B01G309200 chr1A 445913487 445914152 665 False 865.0 865 90.0900 1 666 1 chr1A.!!$F1 665
14 TraesCS2B01G309200 chr1A 351680168 351680948 780 True 798.0 798 85.1710 1491 2276 1 chr1A.!!$R1 785
15 TraesCS2B01G309200 chr4A 285949024 285950148 1124 True 693.0 791 89.6270 1 1304 2 chr4A.!!$R2 1303
16 TraesCS2B01G309200 chr5A 69221197 69221819 622 False 619.0 619 84.6150 1 624 1 chr5A.!!$F1 623
17 TraesCS2B01G309200 chr5B 688966338 688966922 584 False 593.0 593 84.9830 3 587 1 chr5B.!!$F1 584

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
233 2938 1.402852 CCAGACGAATGCACTCTTCGA 60.403 52.381 23.58 0.0 46.36 3.71 F
1026 4419 1.142748 GGACTGCCTGGAGATCGTG 59.857 63.158 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 4444 0.108585 GGTGCCACCACTGAAAGAGA 59.891 55.0 9.55 0.0 41.75 3.1 R
2077 7266 0.179084 ACGGGTTGCGTATCCAGATG 60.179 55.0 7.67 0.0 0.00 2.9 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
233 2938 1.402852 CCAGACGAATGCACTCTTCGA 60.403 52.381 23.58 0.00 46.36 3.71
258 2963 5.591643 ACGGCATATCAAAGTTATAAGCG 57.408 39.130 0.00 0.00 0.00 4.68
406 3111 2.550978 CACATGGTCTCGGGACATTAC 58.449 52.381 18.98 0.00 43.77 1.89
452 3157 2.753296 GAGAGGGCTCAAATGATCTCG 58.247 52.381 0.00 0.00 40.96 4.04
491 3196 3.565482 GGCACTCAAGAAACAGAATCACA 59.435 43.478 0.00 0.00 0.00 3.58
498 3203 5.821995 TCAAGAAACAGAATCACACATGACA 59.178 36.000 0.00 0.00 37.79 3.58
523 3228 5.543507 GATCAGCTGGATCCTTTCTCTTA 57.456 43.478 15.13 0.00 45.58 2.10
587 3292 2.959030 ACAGGCTCATGCTTCGATACTA 59.041 45.455 0.00 0.00 39.59 1.82
1026 4419 1.142748 GGACTGCCTGGAGATCGTG 59.857 63.158 0.00 0.00 0.00 4.35
1051 4444 3.960102 TCTCTGGAAAAATTGCCACACTT 59.040 39.130 0.00 0.00 0.00 3.16
1059 4452 5.596836 AAAATTGCCACACTTCTCTTTCA 57.403 34.783 0.00 0.00 0.00 2.69
1134 4527 9.853555 GATTTATTTGATGTTCAACATGTACCA 57.146 29.630 8.05 0.00 39.27 3.25
1149 4542 0.107831 TACCAAGAGCAGCCAACGTT 59.892 50.000 0.00 0.00 0.00 3.99
1167 4560 0.539438 TTTCGGCCCATCTTTGTGCT 60.539 50.000 0.00 0.00 0.00 4.40
1176 4569 4.202441 CCCATCTTTGTGCTAAGTATGCT 58.798 43.478 0.00 0.00 0.00 3.79
1186 4579 2.096496 GCTAAGTATGCTTGCACACTGG 59.904 50.000 7.32 5.34 36.22 4.00
1193 4586 1.968017 CTTGCACACTGGCGGTCAT 60.968 57.895 0.00 0.00 36.28 3.06
1266 6424 4.082354 GCTGATGATGCAAGGAGTTCTTTT 60.082 41.667 0.00 0.00 32.41 2.27
1317 6475 2.113562 AAAAACGCCCACGCCCTA 59.886 55.556 0.00 0.00 45.53 3.53
1322 6480 4.609018 CGCCCACGCCCTATCCTG 62.609 72.222 0.00 0.00 0.00 3.86
1367 6525 2.799207 GCTGCTACTCTGCTTCTAGCTG 60.799 54.545 0.00 0.00 42.97 4.24
1376 6534 4.527944 TCTGCTTCTAGCTGCTACTTCTA 58.472 43.478 5.02 0.00 42.97 2.10
1396 6554 1.338200 ACTGCTACCAAGTACTGCTGC 60.338 52.381 0.00 0.00 0.00 5.25
1399 6557 1.338200 GCTACCAAGTACTGCTGCTGT 60.338 52.381 16.37 16.37 0.00 4.40
1667 6853 0.906775 CGCTAACCTTTCCCCCACTA 59.093 55.000 0.00 0.00 0.00 2.74
1739 6925 3.314357 GCTAATTACCCCTAAAACAGCCG 59.686 47.826 0.00 0.00 0.00 5.52
1742 6928 0.251073 TACCCCTAAAACAGCCGCTC 59.749 55.000 0.00 0.00 0.00 5.03
1825 7011 1.000739 CAATGACATGTGGGGCCCT 59.999 57.895 25.93 1.41 0.00 5.19
1826 7012 1.000739 AATGACATGTGGGGCCCTG 59.999 57.895 25.93 16.72 0.00 4.45
1827 7013 3.667217 ATGACATGTGGGGCCCTGC 62.667 63.158 25.93 17.09 0.00 4.85
1877 7064 5.700832 CACAGTCAGCCATTAACTTTGACTA 59.299 40.000 11.24 0.00 44.74 2.59
2047 7236 5.333798 CGTAGCTCGGATGAAAAAGTTTTCA 60.334 40.000 18.70 18.70 45.94 2.69
2062 7251 8.770438 AAAAGTTTTCAACATCAAAGTTGCTA 57.230 26.923 0.00 0.00 46.44 3.49
2068 7257 6.691754 TCAACATCAAAGTTGCTAAGAACA 57.308 33.333 2.14 0.00 46.44 3.18
2077 7266 1.415374 TGCTAAGAACAACGAGACGC 58.585 50.000 0.00 0.00 0.00 5.19
2081 7270 2.440539 AAGAACAACGAGACGCATCT 57.559 45.000 0.00 0.00 38.15 2.90
2112 7301 1.652012 CGTTTGTCCGCCACACATT 59.348 52.632 0.00 0.00 33.41 2.71
2131 7320 1.100510 TCCTAGCATAGCGAACACGT 58.899 50.000 0.00 0.00 37.37 4.49
2141 7331 1.069668 AGCGAACACGTAACTTTCCCT 59.930 47.619 0.00 0.00 0.00 4.20
2155 7346 4.547671 ACTTTCCCTCTCCGATTCATCTA 58.452 43.478 0.00 0.00 0.00 1.98
2230 7422 1.404035 GGTTTCACCCCATATTGCGTC 59.596 52.381 0.00 0.00 30.04 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 2938 5.176958 GCTTATAACTTTGATATGCCGTCGT 59.823 40.000 0.00 0.00 0.00 4.34
406 3111 4.811555 TCCGAAAACTGAACATCACAAG 57.188 40.909 0.00 0.00 0.00 3.16
452 3157 2.806244 GTGCCATATCGTCCACATAACC 59.194 50.000 0.00 0.00 0.00 2.85
491 3196 1.276138 TCCAGCTGATCGTTGTCATGT 59.724 47.619 17.39 0.00 0.00 3.21
523 3228 2.185350 CTCTGATGCGCCGAACCT 59.815 61.111 4.18 0.00 0.00 3.50
863 3568 2.511373 CGTTGCATGAGCGGGCTA 60.511 61.111 0.00 0.00 46.23 3.93
1026 4419 4.925646 GTGTGGCAATTTTTCCAGAGATTC 59.074 41.667 0.00 0.00 32.15 2.52
1042 4435 2.564771 CACTGAAAGAGAAGTGTGGCA 58.435 47.619 0.00 0.00 39.17 4.92
1051 4444 0.108585 GGTGCCACCACTGAAAGAGA 59.891 55.000 9.55 0.00 41.75 3.10
1059 4452 1.774856 AGAAGTAAAGGTGCCACCACT 59.225 47.619 17.80 8.14 41.95 4.00
1134 4527 1.507141 CCGAAACGTTGGCTGCTCTT 61.507 55.000 0.00 0.00 0.00 2.85
1167 4560 2.083774 GCCAGTGTGCAAGCATACTTA 58.916 47.619 19.73 0.00 44.09 2.24
1176 4569 1.965930 GATGACCGCCAGTGTGCAA 60.966 57.895 0.00 0.00 0.00 4.08
1186 4579 0.802607 GTCCAACTCTCGATGACCGC 60.803 60.000 0.00 0.00 38.37 5.68
1193 4586 1.157585 CGAGTCAGTCCAACTCTCGA 58.842 55.000 10.87 0.00 41.97 4.04
1266 6424 4.112634 ACCTGGGAGCTTTTATTCAACA 57.887 40.909 0.00 0.00 0.00 3.33
1339 6497 1.691215 GCAGAGTAGCAGCAACGAGC 61.691 60.000 0.00 0.00 46.19 5.03
1341 6499 0.318441 AAGCAGAGTAGCAGCAACGA 59.682 50.000 0.00 0.00 36.85 3.85
1367 6525 4.722361 ACTTGGTAGCAGTAGAAGTAGC 57.278 45.455 0.73 0.00 0.00 3.58
1376 6534 1.338200 GCAGCAGTACTTGGTAGCAGT 60.338 52.381 0.00 0.00 35.30 4.40
1554 6739 1.834822 GGCCTCGCCCAGTAGAGAT 60.835 63.158 0.00 0.00 44.06 2.75
1636 6822 5.063186 GGAAAGGTTAGCGCTAAACTAACTC 59.937 44.000 39.91 32.75 45.70 3.01
1739 6925 1.678970 GGTGGGACCCAATGTGAGC 60.679 63.158 16.98 0.00 34.18 4.26
1742 6928 3.061848 GCGGTGGGACCCAATGTG 61.062 66.667 16.98 6.49 34.18 3.21
1825 7011 4.634004 CCTTATCCAAATGAACAGTACGCA 59.366 41.667 0.00 0.00 0.00 5.24
1826 7012 4.495844 GCCTTATCCAAATGAACAGTACGC 60.496 45.833 0.00 0.00 0.00 4.42
1827 7013 4.876107 AGCCTTATCCAAATGAACAGTACG 59.124 41.667 0.00 0.00 0.00 3.67
2047 7236 5.971202 CGTTGTTCTTAGCAACTTTGATGTT 59.029 36.000 5.33 0.00 42.73 2.71
2052 7241 5.198274 GTCTCGTTGTTCTTAGCAACTTTG 58.802 41.667 5.33 0.00 42.73 2.77
2062 7251 2.061773 CAGATGCGTCTCGTTGTTCTT 58.938 47.619 5.16 0.00 30.42 2.52
2068 7257 1.268589 CGTATCCAGATGCGTCTCGTT 60.269 52.381 5.16 0.00 41.04 3.85
2077 7266 0.179084 ACGGGTTGCGTATCCAGATG 60.179 55.000 7.67 0.00 0.00 2.90
2081 7270 0.250381 ACAAACGGGTTGCGTATCCA 60.250 50.000 5.52 0.00 41.31 3.41
2112 7301 1.100510 ACGTGTTCGCTATGCTAGGA 58.899 50.000 0.00 0.00 41.18 2.94
2131 7320 4.962995 AGATGAATCGGAGAGGGAAAGTTA 59.037 41.667 0.00 0.00 43.63 2.24
2141 7331 5.529791 GTTTTCGGATAGATGAATCGGAGA 58.470 41.667 0.00 0.00 45.75 3.71
2230 7422 1.513158 CGGTGCTAGAGGTGACCTG 59.487 63.158 9.89 0.00 31.76 4.00


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

AutoCloner maintained by Alex Coulton.