Multiple sequence alignment - TraesCS5D01G187300

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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 TraesCS5D01G187300 chr5D 100.000 2778 0 0 1 2778 289356145 289353368 0.000000e+00 5131.0
1 TraesCS5D01G187300 chr5D 96.959 1907 45 5 783 2676 289421183 289419277 0.000000e+00 3188.0
2 TraesCS5D01G187300 chr5D 91.304 46 2 1 322 365 289421326 289421281 8.310000e-06 62.1
3 TraesCS5D01G187300 chr5D 90.909 44 2 1 324 365 289727374 289727331 1.070000e-04 58.4
4 TraesCS5D01G187300 chr6A 93.364 1974 84 18 727 2676 107264267 107266217 0.000000e+00 2876.0
5 TraesCS5D01G187300 chr6A 100.000 32 0 0 374 405 107264075 107264106 2.990000e-05 60.2
6 TraesCS5D01G187300 chr1B 94.892 1801 62 15 857 2647 426496961 426495181 0.000000e+00 2789.0
7 TraesCS5D01G187300 chr1B 97.677 1033 18 1 1746 2778 133123277 133122251 0.000000e+00 1770.0
8 TraesCS5D01G187300 chr1B 97.870 986 20 1 1746 2731 133110648 133109664 0.000000e+00 1703.0
9 TraesCS5D01G187300 chr1B 97.465 986 23 2 1746 2731 426481238 426480255 0.000000e+00 1681.0
10 TraesCS5D01G187300 chr1B 92.582 1065 51 14 653 1700 133124328 133123275 0.000000e+00 1504.0
11 TraesCS5D01G187300 chr1B 87.006 962 56 31 772 1700 426482161 426481236 0.000000e+00 1020.0
12 TraesCS5D01G187300 chr1B 91.699 518 25 6 4 513 133124979 133124472 0.000000e+00 702.0
13 TraesCS5D01G187300 chr1B 90.722 97 4 2 559 655 133124470 133124379 1.040000e-24 124.0
14 TraesCS5D01G187300 chr1B 100.000 42 0 0 1752 1793 398962809 398962850 8.250000e-11 78.7
15 TraesCS5D01G187300 chr1B 100.000 33 0 0 2699 2731 426495180 426495148 8.310000e-06 62.1
16 TraesCS5D01G187300 chr7A 93.999 1833 67 11 766 2588 627232617 627230818 0.000000e+00 2736.0
17 TraesCS5D01G187300 chr7A 94.008 1769 78 13 784 2539 628645452 628647205 0.000000e+00 2654.0
18 TraesCS5D01G187300 chr7A 98.776 980 12 0 1799 2778 628384988 628384009 0.000000e+00 1744.0
19 TraesCS5D01G187300 chr7A 95.859 990 29 5 772 1750 627008772 627007784 0.000000e+00 1591.0
20 TraesCS5D01G187300 chr7A 92.330 1043 49 10 729 1750 628386018 628384986 0.000000e+00 1454.0
21 TraesCS5D01G187300 chr7A 92.929 99 3 3 373 468 627234228 627234131 1.040000e-29 141.0
22 TraesCS5D01G187300 chr7A 95.062 81 1 2 1 78 627234449 627234369 1.040000e-24 124.0
23 TraesCS5D01G187300 chr7A 91.304 46 2 1 322 365 627008896 627008851 8.310000e-06 62.1
24 TraesCS5D01G187300 chr7A 97.222 36 1 0 494 529 627234156 627234121 8.310000e-06 62.1
25 TraesCS5D01G187300 chr7A 100.000 28 0 0 653 680 628386049 628386022 5.000000e-03 52.8
26 TraesCS5D01G187300 chr7B 98.053 1027 12 1 1752 2778 589736202 589737220 0.000000e+00 1779.0
27 TraesCS5D01G187300 chr7B 90.918 1068 63 18 653 1700 588878435 588877382 0.000000e+00 1404.0
28 TraesCS5D01G187300 chr7B 88.843 1201 55 37 559 1700 589919623 589920803 0.000000e+00 1402.0
29 TraesCS5D01G187300 chr7B 95.423 852 31 4 857 1700 589735342 589736193 0.000000e+00 1351.0
30 TraesCS5D01G187300 chr7B 93.070 938 37 8 773 1700 588823544 588822625 0.000000e+00 1347.0
31 TraesCS5D01G187300 chr7B 91.949 857 29 13 856 1700 589696242 589695414 0.000000e+00 1164.0
32 TraesCS5D01G187300 chr7B 88.568 831 76 15 937 1759 589700636 589699817 0.000000e+00 990.0
33 TraesCS5D01G187300 chr7B 93.134 568 19 7 4 563 588879000 588878445 0.000000e+00 815.0
34 TraesCS5D01G187300 chr7B 87.831 189 14 6 105 286 537825930 537825744 2.170000e-51 213.0
35 TraesCS5D01G187300 chr7B 95.489 133 3 1 384 513 589919489 589919621 2.800000e-50 209.0
36 TraesCS5D01G187300 chr7B 100.000 28 0 0 384 411 589934822 589934849 5.000000e-03 52.8
37 TraesCS5D01G187300 chr2B 90.788 901 47 8 756 1653 135512529 135513396 0.000000e+00 1171.0
38 TraesCS5D01G187300 chr2B 92.763 152 8 1 320 468 135512325 135512476 1.680000e-52 217.0
39 TraesCS5D01G187300 chr7D 88.444 900 81 14 856 1750 545650494 545651375 0.000000e+00 1064.0
40 TraesCS5D01G187300 chr7D 89.474 798 68 10 966 1759 545647170 545647955 0.000000e+00 994.0
41 TraesCS5D01G187300 chr7D 85.326 184 18 4 108 282 509580053 509579870 6.110000e-42 182.0
42 TraesCS5D01G187300 chr7D 84.043 94 10 5 191 282 509599095 509599005 4.930000e-13 86.1
43 TraesCS5D01G187300 chr2D 96.923 65 1 1 2653 2717 85249074 85249011 1.050000e-19 108.0
44 TraesCS5D01G187300 chr4A 96.429 56 1 1 2653 2708 349804633 349804579 1.060000e-14 91.6


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 TraesCS5D01G187300 chr5D 289353368 289356145 2777 True 5131.000 5131 100.000000 1 2778 1 chr5D.!!$R1 2777
1 TraesCS5D01G187300 chr5D 289419277 289421326 2049 True 1625.050 3188 94.131500 322 2676 2 chr5D.!!$R3 2354
2 TraesCS5D01G187300 chr6A 107264075 107266217 2142 False 1468.100 2876 96.682000 374 2676 2 chr6A.!!$F1 2302
3 TraesCS5D01G187300 chr1B 133109664 133110648 984 True 1703.000 1703 97.870000 1746 2731 1 chr1B.!!$R1 985
4 TraesCS5D01G187300 chr1B 426495148 426496961 1813 True 1425.550 2789 97.446000 857 2731 2 chr1B.!!$R4 1874
5 TraesCS5D01G187300 chr1B 426480255 426482161 1906 True 1350.500 1681 92.235500 772 2731 2 chr1B.!!$R3 1959
6 TraesCS5D01G187300 chr1B 133122251 133124979 2728 True 1025.000 1770 93.170000 4 2778 4 chr1B.!!$R2 2774
7 TraesCS5D01G187300 chr7A 628645452 628647205 1753 False 2654.000 2654 94.008000 784 2539 1 chr7A.!!$F1 1755
8 TraesCS5D01G187300 chr7A 628384009 628386049 2040 True 1083.600 1744 97.035333 653 2778 3 chr7A.!!$R3 2125
9 TraesCS5D01G187300 chr7A 627007784 627008896 1112 True 826.550 1591 93.581500 322 1750 2 chr7A.!!$R1 1428
10 TraesCS5D01G187300 chr7A 627230818 627234449 3631 True 765.775 2736 94.803000 1 2588 4 chr7A.!!$R2 2587
11 TraesCS5D01G187300 chr7B 589735342 589737220 1878 False 1565.000 1779 96.738000 857 2778 2 chr7B.!!$F2 1921
12 TraesCS5D01G187300 chr7B 588822625 588823544 919 True 1347.000 1347 93.070000 773 1700 1 chr7B.!!$R2 927
13 TraesCS5D01G187300 chr7B 588877382 588879000 1618 True 1109.500 1404 92.026000 4 1700 2 chr7B.!!$R3 1696
14 TraesCS5D01G187300 chr7B 589695414 589700636 5222 True 1077.000 1164 90.258500 856 1759 2 chr7B.!!$R4 903
15 TraesCS5D01G187300 chr7B 589919489 589920803 1314 False 805.500 1402 92.166000 384 1700 2 chr7B.!!$F3 1316
16 TraesCS5D01G187300 chr2B 135512325 135513396 1071 False 694.000 1171 91.775500 320 1653 2 chr2B.!!$F1 1333
17 TraesCS5D01G187300 chr7D 545647170 545651375 4205 False 1029.000 1064 88.959000 856 1759 2 chr7D.!!$F1 903

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
793 2244 1.141881 CCTGGGTCGACTCGGATTG 59.858 63.158 26.18 5.16 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 6163 1.302383 CCACGACGCCAATGCCTAAA 61.302 55.0 0.0 0.0 0.0 1.85 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
48 51 4.668636 ACTCTAGCCAGTTCTTAGTGACT 58.331 43.478 0.00 0.00 0.00 3.41
51 54 6.720288 ACTCTAGCCAGTTCTTAGTGACTTTA 59.280 38.462 0.00 0.00 0.00 1.85
53 56 4.570930 AGCCAGTTCTTAGTGACTTTAGC 58.429 43.478 0.00 0.00 0.00 3.09
55 58 4.802918 GCCAGTTCTTAGTGACTTTAGCCA 60.803 45.833 0.00 0.00 0.00 4.75
56 59 4.932200 CCAGTTCTTAGTGACTTTAGCCAG 59.068 45.833 0.00 0.00 0.00 4.85
57 60 4.932200 CAGTTCTTAGTGACTTTAGCCAGG 59.068 45.833 0.00 0.00 0.00 4.45
58 61 4.593634 AGTTCTTAGTGACTTTAGCCAGGT 59.406 41.667 0.00 0.00 0.00 4.00
59 62 5.071923 AGTTCTTAGTGACTTTAGCCAGGTT 59.928 40.000 0.00 0.00 0.00 3.50
60 63 5.562298 TCTTAGTGACTTTAGCCAGGTTT 57.438 39.130 0.00 0.00 0.00 3.27
61 64 5.305585 TCTTAGTGACTTTAGCCAGGTTTG 58.694 41.667 0.00 0.00 0.00 2.93
62 65 2.230660 AGTGACTTTAGCCAGGTTTGC 58.769 47.619 0.00 0.00 0.00 3.68
63 66 2.158608 AGTGACTTTAGCCAGGTTTGCT 60.159 45.455 0.00 0.00 42.81 3.91
100 114 8.677148 ACAGTTATTCGCATGTCCTTTTATAT 57.323 30.769 0.00 0.00 0.00 0.86
101 115 9.120538 ACAGTTATTCGCATGTCCTTTTATATT 57.879 29.630 0.00 0.00 0.00 1.28
174 188 8.302438 ACATTCAACTTGAGAAATGAGAAATCC 58.698 33.333 8.36 0.00 0.00 3.01
235 249 9.567776 CTCAGAGTTAAGATAAGGATCTGTAGA 57.432 37.037 0.00 0.00 41.87 2.59
537 570 1.340889 TGCAGGTCATTTGTGCTTTCC 59.659 47.619 0.00 0.00 38.09 3.13
643 676 8.416329 GGGATTTATGATTTGTGCTTTATGAGT 58.584 33.333 0.00 0.00 0.00 3.41
696 782 5.072040 GCTTTAGCCTTTATGCTTTGGAA 57.928 39.130 0.00 0.00 42.75 3.53
752 2197 5.734720 AGCAATTTGAATCCGAGTCTCTTA 58.265 37.500 0.00 0.00 0.00 2.10
793 2244 1.141881 CCTGGGTCGACTCGGATTG 59.858 63.158 26.18 5.16 0.00 2.67
1656 5512 1.066605 GCTCAAGCGATGCAAATCCAT 59.933 47.619 0.00 0.00 0.00 3.41
1961 5833 2.556622 GAGTCTCCATCTAGCTAGGCAC 59.443 54.545 20.58 8.33 0.00 5.01
2106 5978 3.944015 GGAAGCTCATGTACTGCAATTCT 59.056 43.478 0.00 0.00 0.00 2.40
2291 6163 7.486407 AATTAATCTTGGCTGACTTGGATTT 57.514 32.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 51 2.875296 ACATGAGCAAACCTGGCTAAA 58.125 42.857 0.00 0.00 42.78 1.85
51 54 1.342174 CAAACATGAGCAAACCTGGCT 59.658 47.619 0.00 0.00 46.07 4.75
53 56 1.001181 CCCAAACATGAGCAAACCTGG 59.999 52.381 0.00 0.00 0.00 4.45
55 58 2.365293 GTTCCCAAACATGAGCAAACCT 59.635 45.455 0.00 0.00 35.36 3.50
56 59 2.102252 TGTTCCCAAACATGAGCAAACC 59.898 45.455 0.00 0.00 40.45 3.27
57 60 3.181476 ACTGTTCCCAAACATGAGCAAAC 60.181 43.478 0.00 0.00 44.18 2.93
58 61 3.030291 ACTGTTCCCAAACATGAGCAAA 58.970 40.909 0.00 0.00 44.18 3.68
59 62 2.665165 ACTGTTCCCAAACATGAGCAA 58.335 42.857 0.00 0.00 44.18 3.91
60 63 2.363306 ACTGTTCCCAAACATGAGCA 57.637 45.000 0.00 0.00 44.18 4.26
61 64 5.391312 AATAACTGTTCCCAAACATGAGC 57.609 39.130 0.00 0.00 44.18 4.26
62 65 5.631026 CGAATAACTGTTCCCAAACATGAG 58.369 41.667 0.00 0.00 44.18 2.90
63 66 4.083003 GCGAATAACTGTTCCCAAACATGA 60.083 41.667 0.00 0.00 44.18 3.07
100 114 3.002246 GCAAACAGTCGTTCTCATGTCAA 59.998 43.478 0.00 0.00 32.91 3.18
101 115 2.543848 GCAAACAGTCGTTCTCATGTCA 59.456 45.455 0.00 0.00 32.91 3.58
174 188 4.985413 TGCTTGTCAAGTTGAAGTTTGAG 58.015 39.130 14.03 1.29 34.25 3.02
235 249 2.232756 TGTGTTCGTAGTGTGTGCAT 57.767 45.000 0.00 0.00 0.00 3.96
363 384 2.872370 GCATGGTGCATTCAGAACTTC 58.128 47.619 0.00 0.00 44.26 3.01
537 570 6.806751 TCTATTCTTGGATTGTAACTCCTCG 58.193 40.000 0.00 0.00 33.69 4.63
570 603 8.155510 TCTCCTTTCCCTTTCTAAAAAGAGTAC 58.844 37.037 0.00 0.00 43.90 2.73
586 619 7.608376 GCCAGTATATAAGAAATCTCCTTTCCC 59.392 40.741 0.00 0.00 43.66 3.97
588 621 9.213799 CTGCCAGTATATAAGAAATCTCCTTTC 57.786 37.037 0.00 0.00 43.07 2.62
589 622 8.160106 CCTGCCAGTATATAAGAAATCTCCTTT 58.840 37.037 0.00 0.00 0.00 3.11
696 782 5.009410 CCTGAGAGAAAGCACAAATGAGTTT 59.991 40.000 0.00 0.00 0.00 2.66
752 2197 1.339631 TGCATAGCTAAAACTGGCGGT 60.340 47.619 0.00 0.00 0.00 5.68
793 2244 1.273688 AACGCGCACTTTGGTTTTTC 58.726 45.000 5.73 0.00 0.00 2.29
1343 5199 1.093496 CATGCTCATCTGCGGCTTCA 61.093 55.000 0.00 0.00 35.36 3.02
1656 5512 4.147449 CACCCGAGCGCTCATCCA 62.147 66.667 34.69 0.00 0.00 3.41
1961 5833 6.635239 CGTACACATCTTAACAAGGTTTTTGG 59.365 38.462 0.00 0.00 0.00 3.28
2062 5934 6.426587 TCCTTTTTAGGCTCATCTGCTTTAT 58.573 36.000 0.00 0.00 0.00 1.40
2106 5978 1.520600 TTACGCTCTGTCTCGTGCCA 61.521 55.000 0.00 0.00 39.46 4.92
2291 6163 1.302383 CCACGACGCCAATGCCTAAA 61.302 55.000 0.00 0.00 0.00 1.85
2578 6450 6.771267 TGAAATCAGAGATGAATCCATTGGAG 59.229 38.462 11.78 0.00 34.05 3.86


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

AutoCloner maintained by Alex Coulton.