Multiple sequence alignment - TraesCS2B01G374500

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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 TraesCS2B01G374500 chr2B 100.000 2593 0 0 1 2593 534407653 534410245 0 4789
1 TraesCS2B01G374500 chr2B 95.781 1043 42 2 3 1043 594144743 594143701 0 1681
2 TraesCS2B01G374500 chr7D 95.903 1562 56 4 1040 2593 85019937 85021498 0 2523
3 TraesCS2B01G374500 chr7B 95.772 1561 58 4 1040 2593 442358260 442359819 0 2510
4 TraesCS2B01G374500 chr7B 95.138 1049 46 4 1 1045 384454160 384455207 0 1650
5 TraesCS2B01G374500 chr7B 95.043 1049 48 3 1 1045 438761861 438760813 0 1646
6 TraesCS2B01G374500 chr3D 95.761 1557 61 3 1040 2591 515672626 515674182 0 2505
7 TraesCS2B01G374500 chr3B 95.501 1556 67 3 1040 2593 618438102 618436548 0 2483
8 TraesCS2B01G374500 chr5D 95.335 1565 62 5 1040 2593 544615843 544617407 0 2475
9 TraesCS2B01G374500 chr1B 95.308 1556 71 2 1040 2593 570458071 570456516 0 2468
10 TraesCS2B01G374500 chr1B 95.320 1047 44 4 1 1045 179452732 179453775 0 1657
11 TraesCS2B01G374500 chr6D 95.244 1556 72 2 1040 2593 347439290 347437735 0 2462
12 TraesCS2B01G374500 chr6A 95.244 1556 71 3 1040 2593 53152496 53154050 0 2460
13 TraesCS2B01G374500 chr4A 95.067 1561 68 5 1040 2592 138428683 138427124 0 2447
14 TraesCS2B01G374500 chr5B 95.690 1044 41 3 1 1041 114528678 114527636 0 1676
15 TraesCS2B01G374500 chr5B 95.211 1044 47 3 1 1041 226688705 226687662 0 1648
16 TraesCS2B01G374500 chr5B 95.134 1048 46 4 1 1045 301851006 301852051 0 1648
17 TraesCS2B01G374500 chr4B 95.224 1047 45 4 1 1043 386156571 386155526 0 1652
18 TraesCS2B01G374500 chr4B 95.220 1046 45 4 1 1044 187217702 187216660 0 1650


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 TraesCS2B01G374500 chr2B 534407653 534410245 2592 False 4789 4789 100.000 1 2593 1 chr2B.!!$F1 2592
1 TraesCS2B01G374500 chr2B 594143701 594144743 1042 True 1681 1681 95.781 3 1043 1 chr2B.!!$R1 1040
2 TraesCS2B01G374500 chr7D 85019937 85021498 1561 False 2523 2523 95.903 1040 2593 1 chr7D.!!$F1 1553
3 TraesCS2B01G374500 chr7B 442358260 442359819 1559 False 2510 2510 95.772 1040 2593 1 chr7B.!!$F2 1553
4 TraesCS2B01G374500 chr7B 384454160 384455207 1047 False 1650 1650 95.138 1 1045 1 chr7B.!!$F1 1044
5 TraesCS2B01G374500 chr7B 438760813 438761861 1048 True 1646 1646 95.043 1 1045 1 chr7B.!!$R1 1044
6 TraesCS2B01G374500 chr3D 515672626 515674182 1556 False 2505 2505 95.761 1040 2591 1 chr3D.!!$F1 1551
7 TraesCS2B01G374500 chr3B 618436548 618438102 1554 True 2483 2483 95.501 1040 2593 1 chr3B.!!$R1 1553
8 TraesCS2B01G374500 chr5D 544615843 544617407 1564 False 2475 2475 95.335 1040 2593 1 chr5D.!!$F1 1553
9 TraesCS2B01G374500 chr1B 570456516 570458071 1555 True 2468 2468 95.308 1040 2593 1 chr1B.!!$R1 1553
10 TraesCS2B01G374500 chr1B 179452732 179453775 1043 False 1657 1657 95.320 1 1045 1 chr1B.!!$F1 1044
11 TraesCS2B01G374500 chr6D 347437735 347439290 1555 True 2462 2462 95.244 1040 2593 1 chr6D.!!$R1 1553
12 TraesCS2B01G374500 chr6A 53152496 53154050 1554 False 2460 2460 95.244 1040 2593 1 chr6A.!!$F1 1553
13 TraesCS2B01G374500 chr4A 138427124 138428683 1559 True 2447 2447 95.067 1040 2592 1 chr4A.!!$R1 1552
14 TraesCS2B01G374500 chr5B 114527636 114528678 1042 True 1676 1676 95.690 1 1041 1 chr5B.!!$R1 1040
15 TraesCS2B01G374500 chr5B 226687662 226688705 1043 True 1648 1648 95.211 1 1041 1 chr5B.!!$R2 1040
16 TraesCS2B01G374500 chr5B 301851006 301852051 1045 False 1648 1648 95.134 1 1045 1 chr5B.!!$F1 1044
17 TraesCS2B01G374500 chr4B 386155526 386156571 1045 True 1652 1652 95.224 1 1043 1 chr4B.!!$R2 1042
18 TraesCS2B01G374500 chr4B 187216660 187217702 1042 True 1650 1650 95.220 1 1044 1 chr4B.!!$R1 1043

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
173 175 0.397941 TGCTGTCACTGGGAAAGGAG 59.602 55.000 0.0 0.0 30.87 3.69 F
1053 1070 1.548719 ACGTATCAGGCAGCAACACTA 59.451 47.619 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1109 1126 0.035439 GCGGATCAAAGGTCTCCCAA 60.035 55.0 0.0 0.0 0.0 4.12 R
2219 2240 0.673985 GCCCACTCCAACCTTTTGTC 59.326 55.0 0.0 0.0 0.0 3.18 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
173 175 0.397941 TGCTGTCACTGGGAAAGGAG 59.602 55.000 0.00 0.00 30.87 3.69
432 434 4.080299 AGAGGGGGAGAACATTGTATTGAC 60.080 45.833 0.00 0.00 0.00 3.18
626 628 1.971481 AAGGTTACGGTGGTGGAAAC 58.029 50.000 0.00 0.00 0.00 2.78
692 694 7.039853 GGCTTATATAGGAGGAAGAAGTACGTT 60.040 40.741 0.00 0.00 0.00 3.99
851 865 3.619233 CGAAGGTTTCATTCCGTTTGT 57.381 42.857 0.00 0.00 0.00 2.83
940 956 1.678101 CCGGTTAGTAGGTTAGTCCCG 59.322 57.143 0.00 0.00 36.75 5.14
1032 1049 8.342634 CAATCGGAAATTTTAGATACGTTGGAT 58.657 33.333 0.00 0.00 0.00 3.41
1053 1070 1.548719 ACGTATCAGGCAGCAACACTA 59.451 47.619 0.00 0.00 0.00 2.74
1109 1126 1.269102 CCAGAGAGTTGTTCGTCGTGT 60.269 52.381 0.00 0.00 0.00 4.49
1229 1246 6.183360 GCTCTGTGGATGCTTAGAATGAAAAT 60.183 38.462 0.00 0.00 0.00 1.82
1237 1254 6.832520 TGCTTAGAATGAAAATAGCACCAA 57.167 33.333 0.00 0.00 34.05 3.67
1273 1290 3.333219 CCTTCAGGAGCAGGGGCA 61.333 66.667 0.00 0.00 44.61 5.36
1326 1343 0.178953 AGCAAGTGGCCATGTTCCTT 60.179 50.000 9.72 3.78 46.50 3.36
1416 1434 3.507411 TCTAGGTACTTCAAGCAGGTGT 58.493 45.455 0.00 0.00 41.75 4.16
1443 1461 1.208293 CTGTTGGGGAGCTTAGAGGAC 59.792 57.143 0.00 0.00 0.00 3.85
1576 1594 8.791675 TGATATGCTTGTATTGTTCAAGTTCAA 58.208 29.630 7.35 0.00 42.67 2.69
1621 1639 1.570803 TTTCAGGATTGCATTGGGGG 58.429 50.000 0.00 0.00 0.00 5.40
1676 1694 1.836166 AGGTCACAGTCTGCAGCATAT 59.164 47.619 9.47 0.00 0.00 1.78
1741 1761 5.296780 TGTTGACTTTGATCTGAAGTTCACC 59.703 40.000 13.75 8.41 37.46 4.02
1863 1884 1.419012 CCTTGGAGATGCTGGCTATGA 59.581 52.381 0.00 0.00 0.00 2.15
1867 1888 1.811359 GGAGATGCTGGCTATGAATGC 59.189 52.381 0.00 0.00 0.00 3.56
1968 1989 4.761227 TGCACATGAGCTGTTTAATCTCAA 59.239 37.500 16.24 0.00 39.88 3.02
2219 2240 1.522668 TGACAATGACGCTTGGAAGG 58.477 50.000 0.00 0.00 0.00 3.46
2241 2262 1.693606 CAAAAGGTTGGAGTGGGCAAT 59.306 47.619 0.00 0.00 0.00 3.56
2307 2328 1.209640 GAAGAAGCAGCAGCAGCAC 59.790 57.895 12.92 5.77 45.49 4.40
2343 2379 2.903135 AGGAAGAAGAAGCAGTAGCAGT 59.097 45.455 0.00 0.00 45.49 4.40
2367 2412 4.531732 AGAAGCAGAAGAGGAAGATGAAGT 59.468 41.667 0.00 0.00 0.00 3.01
2376 2421 4.530161 AGAGGAAGATGAAGTAGCAACACT 59.470 41.667 0.00 0.00 0.00 3.55
2583 2628 2.792500 CACCTAATGCAATGCGGGA 58.208 52.632 11.79 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 175 1.243902 TTGGGTTCAATCTTGCGGTC 58.756 50.000 0.00 0.00 0.00 4.79
432 434 4.763793 TGGCTTCTTCTCTCTTTTTGGATG 59.236 41.667 0.00 0.00 0.00 3.51
626 628 1.067516 CAGGGAGCCAACAAAACACAG 59.932 52.381 0.00 0.00 0.00 3.66
801 814 4.513692 TGATTTTTGGAACGAACGTGATCT 59.486 37.500 0.00 0.00 0.00 2.75
851 865 7.277098 CGAAGAAAAGGAATATCAAACGGAGTA 59.723 37.037 0.00 0.00 45.00 2.59
1032 1049 1.548719 AGTGTTGCTGCCTGATACGTA 59.451 47.619 0.00 0.00 0.00 3.57
1053 1070 3.956199 CCCATGCCTGAATCACACTAATT 59.044 43.478 0.00 0.00 0.00 1.40
1109 1126 0.035439 GCGGATCAAAGGTCTCCCAA 60.035 55.000 0.00 0.00 0.00 4.12
1229 1246 2.170166 CAAGCCTGGAAATTGGTGCTA 58.830 47.619 0.00 0.00 0.00 3.49
1237 1254 1.339151 GGTCTCGACAAGCCTGGAAAT 60.339 52.381 0.00 0.00 0.00 2.17
1273 1290 6.179756 TGGTGTTGATGCTATCTTGTAACAT 58.820 36.000 0.00 0.00 0.00 2.71
1621 1639 5.694006 GCAGTGACATGAGTACCATCTATTC 59.306 44.000 0.00 0.00 31.94 1.75
1676 1694 1.078159 TGTGTAGTGCTTCCTCCCCTA 59.922 52.381 0.00 0.00 0.00 3.53
1741 1761 1.822613 CCAGCCAGCCAGCACATAG 60.823 63.158 0.00 0.00 34.23 2.23
1863 1884 2.203294 GAATACCCGGCCGGCATT 60.203 61.111 39.46 34.55 33.26 3.56
1867 1888 2.110420 GGAAGAATACCCGGCCGG 59.890 66.667 37.99 37.99 37.81 6.13
1941 1962 2.267174 AAACAGCTCATGTGCAGTCT 57.733 45.000 20.92 3.93 43.00 3.24
1968 1989 4.021016 CAGTTACTCTAAGGCTGGAGTGTT 60.021 45.833 24.39 12.44 42.83 3.32
2219 2240 0.673985 GCCCACTCCAACCTTTTGTC 59.326 55.000 0.00 0.00 0.00 3.18
2241 2262 2.161855 CTCTGTTAAGCCACATTGCCA 58.838 47.619 0.00 0.00 0.00 4.92
2307 2328 4.000331 TCTTCCTCTTCTTCTGTGCTTG 58.000 45.455 0.00 0.00 0.00 4.01
2343 2379 5.719085 ACTTCATCTTCCTCTTCTGCTTCTA 59.281 40.000 0.00 0.00 0.00 2.10
2367 2412 4.141711 GGGGATAGTTCATCAGTGTTGCTA 60.142 45.833 0.00 0.00 35.11 3.49
2376 2421 5.849475 TGGCTAAATAGGGGATAGTTCATCA 59.151 40.000 0.00 0.00 35.11 3.07


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

AutoCloner maintained by Alex Coulton.