Multiple sequence alignment - TraesCS1B01G153900

Loading Multiple Alignment...

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 TraesCS1B01G153900 chr1B 100.000 2303 0 0 1 2303 253826132 253823830 0.000000e+00 4253
1 TraesCS1B01G153900 chr1B 96.035 681 24 3 1 680 578102933 578103611 0.000000e+00 1105
2 TraesCS1B01G153900 chr1D 94.937 2311 84 11 1 2291 235548247 235545950 0.000000e+00 3589
3 TraesCS1B01G153900 chr5D 94.894 1880 64 19 427 2289 462907619 462909483 0.000000e+00 2911
4 TraesCS1B01G153900 chr5D 95.714 420 15 3 1 419 462906871 462907288 0.000000e+00 673
5 TraesCS1B01G153900 chr7A 93.427 1856 87 15 457 2290 439030854 439032696 0.000000e+00 2719
6 TraesCS1B01G153900 chr7A 92.364 1362 65 18 653 1987 639884930 639883581 0.000000e+00 1903
7 TraesCS1B01G153900 chr2B 92.617 1639 82 19 674 2290 13184003 13185624 0.000000e+00 2320
8 TraesCS1B01G153900 chr3D 94.485 1505 52 18 449 1936 143483574 143482084 0.000000e+00 2290
9 TraesCS1B01G153900 chr3D 86.464 362 38 6 449 802 43022603 43022245 9.980000e-104 387
10 TraesCS1B01G153900 chr7D 93.573 1447 52 15 864 2290 635929327 635927902 0.000000e+00 2119
11 TraesCS1B01G153900 chr7D 96.774 682 19 3 4 683 635930006 635929326 0.000000e+00 1134
12 TraesCS1B01G153900 chr2A 93.301 1448 67 16 861 2290 441110111 441111546 0.000000e+00 2109
13 TraesCS1B01G153900 chr2A 95.888 681 26 2 1 680 441109433 441110112 0.000000e+00 1101
14 TraesCS1B01G153900 chr5B 92.956 1448 67 19 861 2290 89745418 89746848 0.000000e+00 2076
15 TraesCS1B01G153900 chr5B 94.726 493 23 3 1 492 89742448 89742938 0.000000e+00 763
16 TraesCS1B01G153900 chr5B 97.906 191 4 0 490 680 89745229 89745419 4.740000e-87 331
17 TraesCS1B01G153900 chr4A 92.664 1445 70 13 864 2289 281593802 281592375 0.000000e+00 2049
18 TraesCS1B01G153900 chr7B 92.028 1016 42 19 1297 2290 634824607 634825605 0.000000e+00 1391
19 TraesCS1B01G153900 chr7B 96.763 278 8 1 449 725 634824331 634824608 1.610000e-126 462
20 TraesCS1B01G153900 chr6D 96.125 800 30 1 449 1247 298140118 298139319 0.000000e+00 1304
21 TraesCS1B01G153900 chr6B 94.000 150 9 0 1 150 1494942 1494793 6.400000e-56 228


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 TraesCS1B01G153900 chr1B 253823830 253826132 2302 True 4253.000000 4253 100.0000 1 2303 1 chr1B.!!$R1 2302
1 TraesCS1B01G153900 chr1B 578102933 578103611 678 False 1105.000000 1105 96.0350 1 680 1 chr1B.!!$F1 679
2 TraesCS1B01G153900 chr1D 235545950 235548247 2297 True 3589.000000 3589 94.9370 1 2291 1 chr1D.!!$R1 2290
3 TraesCS1B01G153900 chr5D 462906871 462909483 2612 False 1792.000000 2911 95.3040 1 2289 2 chr5D.!!$F1 2288
4 TraesCS1B01G153900 chr7A 439030854 439032696 1842 False 2719.000000 2719 93.4270 457 2290 1 chr7A.!!$F1 1833
5 TraesCS1B01G153900 chr7A 639883581 639884930 1349 True 1903.000000 1903 92.3640 653 1987 1 chr7A.!!$R1 1334
6 TraesCS1B01G153900 chr2B 13184003 13185624 1621 False 2320.000000 2320 92.6170 674 2290 1 chr2B.!!$F1 1616
7 TraesCS1B01G153900 chr3D 143482084 143483574 1490 True 2290.000000 2290 94.4850 449 1936 1 chr3D.!!$R2 1487
8 TraesCS1B01G153900 chr7D 635927902 635930006 2104 True 1626.500000 2119 95.1735 4 2290 2 chr7D.!!$R1 2286
9 TraesCS1B01G153900 chr2A 441109433 441111546 2113 False 1605.000000 2109 94.5945 1 2290 2 chr2A.!!$F1 2289
10 TraesCS1B01G153900 chr5B 89742448 89746848 4400 False 1056.666667 2076 95.1960 1 2290 3 chr5B.!!$F1 2289
11 TraesCS1B01G153900 chr4A 281592375 281593802 1427 True 2049.000000 2049 92.6640 864 2289 1 chr4A.!!$R1 1425
12 TraesCS1B01G153900 chr7B 634824331 634825605 1274 False 926.500000 1391 94.3955 449 2290 2 chr7B.!!$F1 1841
13 TraesCS1B01G153900 chr6D 298139319 298140118 799 True 1304.000000 1304 96.1250 449 1247 1 chr6D.!!$R1 798

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
405 407 1.334054 GTGAGCTTTGCGCAGATTTG 58.666 50.0 11.31 1.4 39.27 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 4300 0.109086 CTTGTCAGCGTCGATCACCT 60.109 55.0 0.0 0.0 0.0 4.0 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
46 47 2.426024 TCTCCTGTAATCCCGAGTTTCG 59.574 50.000 0.00 0.00 40.07 3.46
168 170 6.478512 TTAAATTCCTTTGAAGTGGTGCTT 57.521 33.333 0.00 0.00 40.76 3.91
232 234 6.044520 TCCTAATGCTCTAGTAGAAGAGGCTA 59.955 42.308 0.64 0.00 42.79 3.93
246 248 1.377333 GGCTACTGAAGGGCACACC 60.377 63.158 0.00 0.00 40.67 4.16
291 293 3.743521 ACAAGAAGCATGTGCAAGTCTA 58.256 40.909 7.83 0.00 45.16 2.59
405 407 1.334054 GTGAGCTTTGCGCAGATTTG 58.666 50.000 11.31 1.40 39.27 2.32
577 3198 5.581126 TTCCATGTTAATCAGAATGTGGC 57.419 39.130 0.00 0.00 37.40 5.01
898 3520 7.532209 CGAAGAAGCAGAAAATGAAGAAGTAAC 59.468 37.037 0.00 0.00 0.00 2.50
916 3538 9.574516 AGAAGTAACTTGTCTAACCATTTGATT 57.425 29.630 0.00 0.00 0.00 2.57
948 3570 6.348540 GGTTTGCTTGACTCTAATTGTGTAGG 60.349 42.308 0.00 0.00 0.00 3.18
1137 3761 5.467063 ACATCTGGACGAGAAGAAAAAGAAC 59.533 40.000 0.00 0.00 33.12 3.01
1210 3834 6.783708 AGGTTAAATTTGGTGAAGTTGTCA 57.216 33.333 0.00 0.00 0.00 3.58
1260 3884 3.648545 AGGTGCCTTCTCTACTCAAAACT 59.351 43.478 0.00 0.00 0.00 2.66
1355 3982 7.561021 TTCAGTGCTTGTATGTTTGTCTTAA 57.439 32.000 0.00 0.00 0.00 1.85
1392 4019 7.942894 TCTGATCTCTGCCAATATGAATTTGAT 59.057 33.333 0.00 0.00 0.00 2.57
1399 4026 6.944096 TGCCAATATGAATTTGATTGTTGGA 58.056 32.000 13.18 1.76 37.61 3.53
1428 4056 9.743057 TTGTTGTTACCAAATAGATCACTTTTG 57.257 29.630 0.00 2.01 30.94 2.44
1450 4078 8.862325 TTTGAGCCATTTAGAAATGAGAAGTA 57.138 30.769 15.09 0.00 46.72 2.24
1494 4127 6.531503 TTGGTGTACAGGATTTGACAAAAA 57.468 33.333 4.41 0.00 0.00 1.94
1570 4209 6.208204 ACATTGAGCTTTCTTATTCTTGCAGT 59.792 34.615 0.00 0.00 0.00 4.40
1641 4280 3.128068 ACAAGTTTTCACTTTCCCGACAC 59.872 43.478 0.00 0.00 40.66 3.67
1652 4291 4.189188 CCGACACGGGCGTAGAGG 62.189 72.222 2.00 0.00 44.15 3.69
1653 4292 3.437795 CGACACGGGCGTAGAGGT 61.438 66.667 0.00 0.00 0.00 3.85
1654 4293 2.181021 GACACGGGCGTAGAGGTG 59.819 66.667 0.00 0.00 36.50 4.00
1655 4294 2.282674 ACACGGGCGTAGAGGTGA 60.283 61.111 0.00 0.00 34.59 4.02
1656 4295 1.664321 GACACGGGCGTAGAGGTGAT 61.664 60.000 0.00 0.00 34.59 3.06
1657 4296 1.065928 CACGGGCGTAGAGGTGATC 59.934 63.158 0.00 0.00 32.23 2.92
1658 4297 2.331805 CGGGCGTAGAGGTGATCG 59.668 66.667 0.00 0.00 0.00 3.69
1659 4298 2.184830 CGGGCGTAGAGGTGATCGA 61.185 63.158 0.00 0.00 0.00 3.59
1660 4299 1.359475 GGGCGTAGAGGTGATCGAC 59.641 63.158 0.00 0.00 0.00 4.20
1661 4300 1.381928 GGGCGTAGAGGTGATCGACA 61.382 60.000 0.00 0.00 33.46 4.35
1712 4351 1.864862 CGCTGTGCTCTTCAACCAG 59.135 57.895 0.00 0.00 0.00 4.00
1714 4353 1.312815 GCTGTGCTCTTCAACCAGTT 58.687 50.000 0.00 0.00 0.00 3.16
1808 4447 2.990479 GCCGATGTGGAGGACCTT 59.010 61.111 0.00 0.00 42.00 3.50
1870 4509 2.672478 CGTCTGAACTCCTAGCCTTGTG 60.672 54.545 0.00 0.00 0.00 3.33
1905 4544 2.105993 AGGTGGTCTGTTTAGGTTGGTC 59.894 50.000 0.00 0.00 0.00 4.02
1906 4545 2.158726 GGTGGTCTGTTTAGGTTGGTCA 60.159 50.000 0.00 0.00 0.00 4.02
1959 4617 6.238621 GGTTGTGTGTGTCTGATGTTAAATGA 60.239 38.462 0.00 0.00 0.00 2.57
1962 4620 7.416817 TGTGTGTGTCTGATGTTAAATGAAAG 58.583 34.615 0.00 0.00 0.00 2.62
2086 4757 0.818040 GCGTGGGTCAAAAGTGAGGT 60.818 55.000 0.00 0.00 33.27 3.85
2291 4972 7.128234 TGGTAGTGTTTTTCCTAGTAGTGTT 57.872 36.000 0.00 0.00 0.00 3.32
2292 4973 8.248904 TGGTAGTGTTTTTCCTAGTAGTGTTA 57.751 34.615 0.00 0.00 0.00 2.41
2293 4974 8.143835 TGGTAGTGTTTTTCCTAGTAGTGTTAC 58.856 37.037 0.00 0.00 0.00 2.50
2294 4975 8.363390 GGTAGTGTTTTTCCTAGTAGTGTTACT 58.637 37.037 0.00 0.00 42.66 2.24
2295 4976 9.755804 GTAGTGTTTTTCCTAGTAGTGTTACTT 57.244 33.333 0.00 0.00 40.55 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 5.734720 TCAGAAGTTCAGAACCATATGACC 58.265 41.667 9.85 0.0 0.00 4.02
91 92 3.603965 ACCAACATCCACCCAGTTTAA 57.396 42.857 0.00 0.0 0.00 1.52
93 94 2.038659 CAACCAACATCCACCCAGTTT 58.961 47.619 0.00 0.0 0.00 2.66
246 248 2.677875 GCAGCCCCCTGTTCTTGG 60.678 66.667 0.00 0.0 41.26 3.61
259 261 0.520847 GCTTCTTGTTCTGGAGCAGC 59.479 55.000 0.00 0.0 0.00 5.25
291 293 7.511268 TGGTAATTACCTTGTTTGTCTACACT 58.489 34.615 30.09 0.0 46.58 3.55
898 3520 7.596248 CCAAGACAAATCAAATGGTTAGACAAG 59.404 37.037 0.00 0.0 0.00 3.16
916 3538 3.620488 AGAGTCAAGCAAACCAAGACAA 58.380 40.909 0.00 0.0 0.00 3.18
948 3570 6.372103 TGGATCCAAATGAATTGATGCAAAAC 59.628 34.615 13.46 0.0 41.85 2.43
1042 3666 7.509546 AGTGAATGTGGAAGTTCTCTTAGAAA 58.490 34.615 2.25 0.0 35.75 2.52
1137 3761 1.021390 CGACCTTACCAGCCTTGCAG 61.021 60.000 0.00 0.0 0.00 4.41
1210 3834 5.185828 GGAATGATAACTTTGGTGGAGCTTT 59.814 40.000 0.00 0.0 0.00 3.51
1355 3982 5.131642 TGGCAGAGATCAGACCATAAGAATT 59.868 40.000 0.00 0.0 0.00 2.17
1428 4056 7.984617 AGTCTACTTCTCATTTCTAAATGGCTC 59.015 37.037 13.89 0.0 44.51 4.70
1450 4078 9.965824 CACCAAATTAACATTTACAAGAAGTCT 57.034 29.630 0.00 0.0 30.90 3.24
1467 4095 7.825331 TTGTCAAATCCTGTACACCAAATTA 57.175 32.000 0.00 0.0 0.00 1.40
1641 4280 2.184830 TCGATCACCTCTACGCCCG 61.185 63.158 0.00 0.0 0.00 6.13
1651 4290 0.738975 TCGATCACCTGTCGATCACC 59.261 55.000 0.00 0.0 42.57 4.02
1656 4295 2.038837 AGCGTCGATCACCTGTCGA 61.039 57.895 0.00 0.0 44.93 4.20
1657 4296 1.869574 CAGCGTCGATCACCTGTCG 60.870 63.158 0.00 0.0 40.30 4.35
1658 4297 0.798771 GTCAGCGTCGATCACCTGTC 60.799 60.000 0.00 0.0 0.00 3.51
1659 4298 1.213013 GTCAGCGTCGATCACCTGT 59.787 57.895 0.00 0.0 0.00 4.00
1660 4299 0.388520 TTGTCAGCGTCGATCACCTG 60.389 55.000 0.00 0.0 0.00 4.00
1661 4300 0.109086 CTTGTCAGCGTCGATCACCT 60.109 55.000 0.00 0.0 0.00 4.00
1833 4472 2.202690 CGCCGCTGGACACGAATA 60.203 61.111 0.00 0.0 0.00 1.75
1870 4509 4.764823 CAGACCACCTCTCTAGATGTATCC 59.235 50.000 0.00 0.0 0.00 2.59
1959 4617 4.070716 CTCACAGAACCATCTCAAGCTTT 58.929 43.478 0.00 0.0 32.03 3.51
1962 4620 3.051081 ACTCACAGAACCATCTCAAGC 57.949 47.619 0.00 0.0 32.03 4.01
2154 4825 6.366877 CCACGCTACAGCTAAAAAGTTAGTAA 59.633 38.462 0.00 0.0 39.23 2.24


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

AutoCloner maintained by Alex Coulton.