Multiple sequence alignment - TraesCS2D01G589700

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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 TraesCS2D01G589700 chr2D 100.000 2669 0 0 1 2669 645957537 645960205 0.000000e+00 4929.0
1 TraesCS2D01G589700 chr2D 94.872 39 1 1 1 39 556232654 556232617 2.870000e-05 60.2
2 TraesCS2D01G589700 chr2A 96.648 1790 51 7 881 2669 771772319 771774100 0.000000e+00 2964.0
3 TraesCS2D01G589700 chr2A 89.405 1680 142 22 512 2176 773583570 773581912 0.000000e+00 2084.0
4 TraesCS2D01G589700 chr2A 87.841 1686 142 28 512 2176 773563970 773562327 0.000000e+00 1919.0
5 TraesCS2D01G589700 chr2A 96.980 563 15 2 321 883 771765610 771766170 0.000000e+00 944.0
6 TraesCS2D01G589700 chr2A 88.779 303 9 7 44 322 771765281 771765582 5.470000e-92 348.0
7 TraesCS2D01G589700 chr2A 100.000 41 0 0 1 41 771765219 771765259 2.850000e-10 76.8
8 TraesCS2D01G589700 chr2A 74.847 163 25 10 47 200 738852126 738852281 2.870000e-05 60.2
9 TraesCS2D01G589700 chr2B 87.708 2221 211 31 494 2669 789565153 789562950 0.000000e+00 2532.0
10 TraesCS2D01G589700 chr2B 81.000 1300 209 26 512 1786 789561524 789560238 0.000000e+00 998.0
11 TraesCS2D01G589700 chr2B 80.952 210 27 7 2327 2525 152750323 152750116 1.280000e-33 154.0
12 TraesCS2D01G589700 chr2B 89.831 118 11 1 327 443 87831168 87831051 1.660000e-32 150.0
13 TraesCS2D01G589700 chr1A 80.808 297 48 7 2375 2666 592982032 592982324 9.620000e-55 224.0
14 TraesCS2D01G589700 chr4D 77.811 338 55 13 2317 2639 93088328 93088660 9.750000e-45 191.0
15 TraesCS2D01G589700 chr7B 77.899 276 54 7 2368 2640 132971700 132971971 5.910000e-37 165.0
16 TraesCS2D01G589700 chr1B 83.799 179 24 5 327 503 477844686 477844861 5.910000e-37 165.0
17 TraesCS2D01G589700 chr6D 89.831 118 11 1 327 443 436889724 436889607 1.660000e-32 150.0
18 TraesCS2D01G589700 chr4B 91.111 45 4 0 2 46 386985063 386985019 7.980000e-06 62.1
19 TraesCS2D01G589700 chr5A 94.595 37 2 0 2 38 556442752 556442716 1.030000e-04 58.4
20 TraesCS2D01G589700 chr3A 100.000 31 0 0 2 32 1397777 1397747 1.030000e-04 58.4
21 TraesCS2D01G589700 chr1D 100.000 31 0 0 2 32 106512909 106512939 1.030000e-04 58.4
22 TraesCS2D01G589700 chr1D 83.333 60 10 0 138 197 256203597 256203656 3.710000e-04 56.5
23 TraesCS2D01G589700 chr6A 96.875 32 1 0 1 32 560642066 560642097 1.000000e-03 54.7
24 TraesCS2D01G589700 chr5D 100.000 28 0 0 2 29 65857275 65857302 5.000000e-03 52.8
25 TraesCS2D01G589700 chr4A 96.875 32 0 1 2 33 165063063 165063093 5.000000e-03 52.8


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 TraesCS2D01G589700 chr2D 645957537 645960205 2668 False 4929.000000 4929 100.000 1 2669 1 chr2D.!!$F1 2668
1 TraesCS2D01G589700 chr2A 771772319 771774100 1781 False 2964.000000 2964 96.648 881 2669 1 chr2A.!!$F2 1788
2 TraesCS2D01G589700 chr2A 773581912 773583570 1658 True 2084.000000 2084 89.405 512 2176 1 chr2A.!!$R2 1664
3 TraesCS2D01G589700 chr2A 773562327 773563970 1643 True 1919.000000 1919 87.841 512 2176 1 chr2A.!!$R1 1664
4 TraesCS2D01G589700 chr2A 771765219 771766170 951 False 456.266667 944 95.253 1 883 3 chr2A.!!$F3 882
5 TraesCS2D01G589700 chr2B 789560238 789565153 4915 True 1765.000000 2532 84.354 494 2669 2 chr2B.!!$R3 2175

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
151 199 1.065928 CTATCTCGCTCGCCCGTTT 59.934 57.895 0.0 0.0 0.0 3.60 F
1093 1191 1.300697 ACCCACGTCTCGCTTGTTC 60.301 57.895 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1328 1431 0.327924 TGTTCACGATTGGCTCCCAT 59.672 50.000 0.00 0.00 31.53 4.00 R
2208 2333 1.071814 GTGTTGTAGGGCCGACCAA 59.928 57.895 14.52 7.82 43.89 3.67 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
148 196 4.708968 GCCTATCTCGCTCGCCCG 62.709 72.222 0.00 0.00 0.00 6.13
151 199 1.065928 CTATCTCGCTCGCCCGTTT 59.934 57.895 0.00 0.00 0.00 3.60
218 266 1.401905 CCTTCTGGAGCGCAATTAACC 59.598 52.381 11.47 3.47 34.57 2.85
498 576 5.522641 AGCAAACCAATCAATCTCCCTAAT 58.477 37.500 0.00 0.00 0.00 1.73
639 718 6.874134 GTGCTTTCTACAATTCTACTTCCTCA 59.126 38.462 0.00 0.00 0.00 3.86
744 832 2.369860 AGATGCTGGCATTTAGATCGGA 59.630 45.455 9.52 0.00 36.70 4.55
752 841 4.897076 TGGCATTTAGATCGGAGGTAGTAA 59.103 41.667 0.00 0.00 0.00 2.24
754 843 5.010820 GGCATTTAGATCGGAGGTAGTAACT 59.989 44.000 0.00 0.00 0.00 2.24
1023 1121 7.341769 GTCATAAATGCCCTATTAATGCCCATA 59.658 37.037 0.00 0.00 0.00 2.74
1093 1191 1.300697 ACCCACGTCTCGCTTGTTC 60.301 57.895 0.00 0.00 0.00 3.18
1130 1229 2.158667 TGAAGTTCACCAAAGTCCCTCC 60.159 50.000 0.08 0.00 0.00 4.30
1137 1236 2.107552 CACCAAAGTCCCTCCTAAACCA 59.892 50.000 0.00 0.00 0.00 3.67
1227 1326 2.777536 AGGACAACCAGCATCCTCA 58.222 52.632 0.00 0.00 38.55 3.86
1328 1431 2.092323 CACACGACAGTAGAGGATGGA 58.908 52.381 0.00 0.00 0.00 3.41
1463 1566 1.336755 GGCCGACAAAAACATGTGTCT 59.663 47.619 0.00 0.00 41.65 3.41
1740 1843 2.614057 GCAACTTGATTACGATGAGGGG 59.386 50.000 0.00 0.00 0.00 4.79
1754 1857 4.142469 CGATGAGGGGAAACAAATGTAACC 60.142 45.833 0.00 0.00 0.00 2.85
2057 2162 6.486657 TCAGCCTAATATGTTCTTGCCAATAC 59.513 38.462 0.00 0.00 0.00 1.89
2128 2233 9.868277 TTTTGCCTCAATAAAAGGTACATATTG 57.132 29.630 0.00 4.69 38.02 1.90
2341 2467 6.101650 TGATGCATCTCCAACGTATCTATT 57.898 37.500 26.32 0.00 0.00 1.73
2549 2684 3.770388 ACTAAGGACCCTAGAAGCTTCAC 59.230 47.826 27.57 11.14 0.00 3.18
2588 2723 1.100510 CAAGCTAGGCACATGCACAT 58.899 50.000 6.15 0.00 44.36 3.21
2601 2736 3.434319 CACATGTGGTGCGGCCTC 61.434 66.667 18.51 0.00 41.36 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 136 4.281941 GCCACATCCTCTTTTCCTTTTTCT 59.718 41.667 0.00 0.00 0.00 2.52
108 139 2.899900 GGCCACATCCTCTTTTCCTTTT 59.100 45.455 0.00 0.00 0.00 2.27
112 143 1.467920 CAGGCCACATCCTCTTTTCC 58.532 55.000 5.01 0.00 33.25 3.13
113 144 0.813821 GCAGGCCACATCCTCTTTTC 59.186 55.000 5.01 0.00 33.25 2.29
148 196 4.206404 GGTTCAGCTTTCGTTTTGCTAAAC 59.794 41.667 12.94 12.94 40.19 2.01
151 199 2.292292 GGGTTCAGCTTTCGTTTTGCTA 59.708 45.455 0.00 0.00 35.05 3.49
358 436 8.843262 TGAAAATTGATATGCTACCAATCTCTG 58.157 33.333 0.00 0.00 30.93 3.35
384 462 3.446442 ACCTTCTGTGAGATTGGCAAT 57.554 42.857 13.54 13.54 0.00 3.56
744 832 7.719633 CCAAATATGGTGCATTAGTTACTACCT 59.280 37.037 3.35 0.00 42.18 3.08
752 841 6.720748 TGCATATCCAAATATGGTGCATTAGT 59.279 34.615 7.34 0.00 45.84 2.24
1093 1191 3.436243 ACTTCAGAGTGAGGGGTTCTAG 58.564 50.000 0.00 0.00 33.99 2.43
1130 1229 4.616835 GCTTGAGATGGCAAGTTGGTTTAG 60.617 45.833 4.75 0.00 45.41 1.85
1137 1236 2.574006 TGAGCTTGAGATGGCAAGTT 57.426 45.000 0.00 0.00 45.41 2.66
1288 1391 2.101783 GCCACAATTGATGTCCCATCA 58.898 47.619 13.59 2.88 41.46 3.07
1328 1431 0.327924 TGTTCACGATTGGCTCCCAT 59.672 50.000 0.00 0.00 31.53 4.00
1463 1566 0.894835 TGAGCTCGTAGTTCATGCCA 59.105 50.000 9.64 0.00 30.30 4.92
1605 1708 9.822185 AGGAACCAAATTATTGCTAATGAAATC 57.178 29.630 0.00 0.00 35.10 2.17
1754 1857 6.152932 AGACATTGCTGGCTTTATTTATGG 57.847 37.500 0.00 0.00 37.52 2.74
1765 1868 1.818642 AGAGTTGAGACATTGCTGGC 58.181 50.000 0.00 0.00 0.00 4.85
1851 1955 4.833478 ATAGCTTCAGGACTGTGTTCAT 57.167 40.909 0.00 0.00 0.00 2.57
2057 2162 6.115448 AGTAGAAAATATGAGGAATCCCCG 57.885 41.667 0.00 0.00 40.87 5.73
2208 2333 1.071814 GTGTTGTAGGGCCGACCAA 59.928 57.895 14.52 7.82 43.89 3.67
2469 2604 8.651389 TGTATTTGGACCTTCCTAGATATTGAG 58.349 37.037 0.00 0.00 37.46 3.02
2549 2684 1.899534 GGGTCCCCTCGATCTCTCG 60.900 68.421 0.00 0.00 46.41 4.04


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

AutoCloner maintained by Alex Coulton.