Multiple sequence alignment - TraesCS6A01G056900

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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 TraesCS6A01G056900 chr6A 100.000 3680 0 0 1 3680 29882381 29878702 0.000000e+00 6796.0
1 TraesCS6A01G056900 chr6D 97.604 3715 50 8 1 3680 27976813 27980523 0.000000e+00 6331.0
2 TraesCS6A01G056900 chr6D 88.274 2746 271 22 963 3680 28299944 28297222 0.000000e+00 3240.0
3 TraesCS6A01G056900 chr6B 87.824 2743 286 22 963 3680 52354874 52352155 0.000000e+00 3171.0
4 TraesCS6A01G056900 chr6B 88.344 2059 217 12 1642 3680 51756305 51758360 0.000000e+00 2451.0
5 TraesCS6A01G056900 chr6B 87.640 2047 237 12 1642 3680 52179360 52177322 0.000000e+00 2364.0
6 TraesCS6A01G056900 chr6B 87.665 2043 230 16 1650 3678 51946169 51948203 0.000000e+00 2357.0
7 TraesCS6A01G056900 chr6B 87.894 1999 225 10 1689 3680 51919439 51921427 0.000000e+00 2335.0
8 TraesCS6A01G056900 chr6B 86.551 1725 221 10 1689 3406 52229712 52227992 0.000000e+00 1890.0
9 TraesCS6A01G056900 chr6B 81.461 1095 139 40 604 1656 52180457 52179385 0.000000e+00 839.0
10 TraesCS6A01G056900 chr6B 80.488 1107 137 41 598 1656 51755205 51756280 0.000000e+00 774.0
11 TraesCS6A01G056900 chr6B 79.443 1114 135 38 598 1655 52230785 52229710 0.000000e+00 702.0
12 TraesCS6A01G056900 chr6B 85.630 682 74 9 971 1652 51918781 51919438 0.000000e+00 695.0
13 TraesCS6A01G056900 chr6B 81.211 809 118 24 852 1638 51945322 51946118 4.040000e-174 621.0
14 TraesCS6A01G056900 chr6B 84.574 188 20 3 1 180 539959620 539959806 1.050000e-40 178.0
15 TraesCS6A01G056900 chr6B 88.235 102 10 2 798 898 51918577 51918677 1.790000e-23 121.0
16 TraesCS6A01G056900 chr6B 82.645 121 17 3 227 343 152711768 152711888 1.810000e-18 104.0
17 TraesCS6A01G056900 chrUn 88.120 1995 221 12 1698 3678 272919320 272917328 0.000000e+00 2357.0
18 TraesCS6A01G056900 chrUn 80.947 824 123 24 855 1656 272920206 272919395 4.040000e-174 621.0
19 TraesCS6A01G056900 chr4D 72.542 2014 485 54 1704 3680 1708225 1706243 8.800000e-166 593.0
20 TraesCS6A01G056900 chr2A 88.235 187 14 3 1 179 633689498 633689684 2.230000e-52 217.0
21 TraesCS6A01G056900 chr2A 87.692 130 16 0 7 136 662347858 662347729 6.370000e-33 152.0
22 TraesCS6A01G056900 chr4B 84.173 139 13 4 50 180 512922559 512922422 3.860000e-25 126.0
23 TraesCS6A01G056900 chr7B 97.222 36 0 1 430 465 609923634 609923668 3.970000e-05 60.2


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 TraesCS6A01G056900 chr6A 29878702 29882381 3679 True 6796.000000 6796 100.0000 1 3680 1 chr6A.!!$R1 3679
1 TraesCS6A01G056900 chr6D 27976813 27980523 3710 False 6331.000000 6331 97.6040 1 3680 1 chr6D.!!$F1 3679
2 TraesCS6A01G056900 chr6D 28297222 28299944 2722 True 3240.000000 3240 88.2740 963 3680 1 chr6D.!!$R1 2717
3 TraesCS6A01G056900 chr6B 52352155 52354874 2719 True 3171.000000 3171 87.8240 963 3680 1 chr6B.!!$R1 2717
4 TraesCS6A01G056900 chr6B 51755205 51758360 3155 False 1612.500000 2451 84.4160 598 3680 2 chr6B.!!$F3 3082
5 TraesCS6A01G056900 chr6B 52177322 52180457 3135 True 1601.500000 2364 84.5505 604 3680 2 chr6B.!!$R2 3076
6 TraesCS6A01G056900 chr6B 51945322 51948203 2881 False 1489.000000 2357 84.4380 852 3678 2 chr6B.!!$F5 2826
7 TraesCS6A01G056900 chr6B 52227992 52230785 2793 True 1296.000000 1890 82.9970 598 3406 2 chr6B.!!$R3 2808
8 TraesCS6A01G056900 chr6B 51918577 51921427 2850 False 1050.333333 2335 87.2530 798 3680 3 chr6B.!!$F4 2882
9 TraesCS6A01G056900 chrUn 272917328 272920206 2878 True 1489.000000 2357 84.5335 855 3678 2 chrUn.!!$R1 2823
10 TraesCS6A01G056900 chr4D 1706243 1708225 1982 True 593.000000 593 72.5420 1704 3680 1 chr4D.!!$R1 1976

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
620 651 1.065564 ACAAGATCTGAAGCAGAGCCC 60.066 52.381 8.87 0.0 46.56 5.19 F
785 873 1.743958 CTAGCTGCTGATTGCTTTGCT 59.256 47.619 13.43 0.0 43.37 3.91 F
786 874 1.830279 AGCTGCTGATTGCTTTGCTA 58.170 45.000 0.00 0.0 43.37 3.49 F
2216 2540 1.339055 CGTCTTGGATGATGTGTGGGT 60.339 52.381 0.00 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 1711 1.040339 GCCTTGTTGGTGGGTGTCAA 61.040 55.000 0.0 0.00 38.35 3.18 R
2216 2540 7.690454 TTTTCCCACTCATCCTCTTGATATA 57.310 36.000 0.0 0.00 30.56 0.86 R
2621 2948 8.585018 GTTTTAGATGGAAAGGGAGAAAATCAA 58.415 33.333 0.0 0.00 0.00 2.57 R
3481 3826 5.729974 AGTTGACTTAGTTCGAAACCAAC 57.270 39.130 0.0 8.18 34.55 3.77 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
45 46 1.768870 CCATACCCCTTCCGTCTCAAT 59.231 52.381 0.00 0.00 0.00 2.57
153 163 2.456577 ACATCCATTTGGCCAACCTAC 58.543 47.619 20.35 0.00 36.63 3.18
166 176 4.055360 GCCAACCTACATTTGGTTTTGTC 58.945 43.478 3.20 0.00 44.54 3.18
335 347 3.325135 CCCCGAGATTCCTATGTAGCTTT 59.675 47.826 0.00 0.00 0.00 3.51
340 352 4.455606 AGATTCCTATGTAGCTTTGCCAC 58.544 43.478 0.00 0.00 0.00 5.01
477 508 7.560991 TCCATCATATGCATTTTTAGGACAGTT 59.439 33.333 3.54 0.00 0.00 3.16
510 541 7.607223 ACAAATAGCCATAAACATTGTTTGCAT 59.393 29.630 22.04 8.12 0.00 3.96
539 570 3.127533 GTTTCCGCGAGCATGCCT 61.128 61.111 15.66 1.01 0.00 4.75
620 651 1.065564 ACAAGATCTGAAGCAGAGCCC 60.066 52.381 8.87 0.00 46.56 5.19
784 872 1.798079 GCTAGCTGCTGATTGCTTTGC 60.798 52.381 13.43 0.00 43.37 3.68
785 873 1.743958 CTAGCTGCTGATTGCTTTGCT 59.256 47.619 13.43 0.00 43.37 3.91
786 874 1.830279 AGCTGCTGATTGCTTTGCTA 58.170 45.000 0.00 0.00 43.37 3.49
787 875 2.376109 AGCTGCTGATTGCTTTGCTAT 58.624 42.857 0.00 0.00 43.37 2.97
790 878 3.548415 GCTGCTGATTGCTTTGCTATCTC 60.548 47.826 13.16 7.35 40.37 2.75
798 886 4.916983 TGCTTTGCTATCTCTCTCTCTC 57.083 45.455 0.00 0.00 0.00 3.20
1318 1459 1.959226 GCCGGTGTGAACGATGTGT 60.959 57.895 1.90 0.00 0.00 3.72
2216 2540 1.339055 CGTCTTGGATGATGTGTGGGT 60.339 52.381 0.00 0.00 0.00 4.51
2545 2872 4.148838 TCAACTTACTTTGGACCATTGGG 58.851 43.478 7.78 0.00 41.29 4.12
2621 2948 1.888391 GCCAGCCCTCAAACTTAGCTT 60.888 52.381 0.00 0.00 0.00 3.74
2677 3004 8.200792 TGTTTGTATATTGTGCTTTGTTTCCTT 58.799 29.630 0.00 0.00 0.00 3.36
2838 3168 6.980397 TCAAGAAAGACAAAAGAAAAGATGGC 59.020 34.615 0.00 0.00 0.00 4.40
3157 3487 2.422127 GCTAAAGCCCTTCGCACAATTA 59.578 45.455 0.00 0.00 41.38 1.40
3481 3826 7.848223 AGGTTTGAAGTTGGAAAAGAAAATG 57.152 32.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 5.962433 GCAAATGGCTATATAGACTACCGA 58.038 41.667 16.65 0.00 40.25 4.69
89 90 3.420893 TGGGCATTGAAAATCTCGAAGT 58.579 40.909 0.00 0.00 0.00 3.01
90 91 4.418392 CTTGGGCATTGAAAATCTCGAAG 58.582 43.478 0.00 0.00 0.00 3.79
91 92 3.367292 GCTTGGGCATTGAAAATCTCGAA 60.367 43.478 0.00 0.00 38.54 3.71
93 94 2.533266 GCTTGGGCATTGAAAATCTCG 58.467 47.619 0.00 0.00 38.54 4.04
94 95 2.419159 GGGCTTGGGCATTGAAAATCTC 60.419 50.000 0.00 0.00 40.87 2.75
153 163 3.980646 TGACGAGGACAAAACCAAATG 57.019 42.857 0.00 0.00 0.00 2.32
166 176 1.021390 AGCTCCGCAAATTGACGAGG 61.021 55.000 10.41 2.13 0.00 4.63
335 347 1.758440 GAGGTCTGTGGACAGTGGCA 61.758 60.000 0.00 0.00 43.77 4.92
340 352 1.543429 GGGTTTGAGGTCTGTGGACAG 60.543 57.143 0.00 0.00 43.77 3.51
477 508 5.087323 TGTTTATGGCTATTTGTCCCCAAA 58.913 37.500 0.00 0.00 44.27 3.28
493 524 6.782298 TTGTCCATGCAAACAATGTTTATG 57.218 33.333 11.33 11.94 30.73 1.90
539 570 2.010670 CGTTTGAACAGTGTCCGCA 58.989 52.632 0.00 0.00 0.00 5.69
620 651 1.611491 TGGCGCCAAAGTAAAAGAAGG 59.389 47.619 30.74 0.00 0.00 3.46
662 697 7.920682 GCAATTACGGGATGAAGTGAAATAATT 59.079 33.333 0.00 0.00 0.00 1.40
784 872 3.329386 CGCAGGAGAGAGAGAGAGATAG 58.671 54.545 0.00 0.00 0.00 2.08
785 873 2.549992 GCGCAGGAGAGAGAGAGAGATA 60.550 54.545 0.30 0.00 0.00 1.98
786 874 1.815408 GCGCAGGAGAGAGAGAGAGAT 60.815 57.143 0.30 0.00 0.00 2.75
787 875 0.463654 GCGCAGGAGAGAGAGAGAGA 60.464 60.000 0.30 0.00 0.00 3.10
790 878 1.311651 TGTGCGCAGGAGAGAGAGAG 61.312 60.000 12.22 0.00 0.00 3.20
798 886 2.821366 GTGGGATGTGCGCAGGAG 60.821 66.667 12.22 0.00 40.43 3.69
1044 1180 4.954118 TCTGTGACCGGGGCCAGT 62.954 66.667 6.32 0.83 0.00 4.00
1059 1195 1.761784 CAGGACTCTAGCAAGCCATCT 59.238 52.381 0.00 0.00 0.00 2.90
1318 1459 1.314534 CGGATGCCTTGGATGCAACA 61.315 55.000 0.00 0.00 42.92 3.33
1507 1711 1.040339 GCCTTGTTGGTGGGTGTCAA 61.040 55.000 0.00 0.00 38.35 3.18
2216 2540 7.690454 TTTTCCCACTCATCCTCTTGATATA 57.310 36.000 0.00 0.00 30.56 0.86
2545 2872 9.780413 CCATTCTTTGCTTTCTAGTATTCTTTC 57.220 33.333 0.00 0.00 0.00 2.62
2621 2948 8.585018 GTTTTAGATGGAAAGGGAGAAAATCAA 58.415 33.333 0.00 0.00 0.00 2.57
2677 3004 9.261180 CTCCTTGCTATCAAATTCGTAATCTTA 57.739 33.333 0.00 0.00 0.00 2.10
3157 3487 8.916062 CATAGAGTATGATGCTCCAGATAGAAT 58.084 37.037 6.92 0.00 38.45 2.40
3481 3826 5.729974 AGTTGACTTAGTTCGAAACCAAC 57.270 39.130 0.00 8.18 34.55 3.77


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

AutoCloner maintained by Alex Coulton.