Multiple sequence alignment - TraesCS5A01G470200

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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 TraesCS5A01G470200 chr5A 100.000 3971 0 0 1 3971 647028608 647032578 0.000000e+00 7334
1 TraesCS5A01G470200 chr5A 97.097 1929 50 5 1002 2927 534933738 534935663 0.000000e+00 3247
2 TraesCS5A01G470200 chr6D 96.553 2640 86 3 1332 3971 57921519 57924153 0.000000e+00 4366
3 TraesCS5A01G470200 chr6D 96.509 487 17 0 3485 3971 153923549 153923063 0.000000e+00 806
4 TraesCS5A01G470200 chr6D 92.269 401 21 8 974 1364 458964846 458965246 9.640000e-156 560
5 TraesCS5A01G470200 chr6D 94.278 367 16 3 1002 1364 369918077 369917712 1.250000e-154 556
6 TraesCS5A01G470200 chr3B 96.703 2002 64 2 1002 3003 39816714 39818713 0.000000e+00 3330
7 TraesCS5A01G470200 chr3B 96.404 2002 68 4 1002 3003 173888708 173890705 0.000000e+00 3295
8 TraesCS5A01G470200 chr6B 97.023 1948 57 1 1002 2949 625641239 625639293 0.000000e+00 3275
9 TraesCS5A01G470200 chr6B 94.344 442 20 4 1002 1443 215728546 215728110 0.000000e+00 673
10 TraesCS5A01G470200 chr7A 96.648 1969 57 1 1002 2970 211292248 211294207 0.000000e+00 3262
11 TraesCS5A01G470200 chr7A 92.689 383 21 6 974 1352 120880347 120880726 2.700000e-151 545
12 TraesCS5A01G470200 chr2B 97.036 1923 55 2 1002 2923 357718695 357716774 0.000000e+00 3234
13 TraesCS5A01G470200 chr2B 96.310 1924 66 3 1002 2923 357344469 357342549 0.000000e+00 3155
14 TraesCS5A01G470200 chr2B 95.146 515 23 2 1002 1515 357306958 357307471 0.000000e+00 811
15 TraesCS5A01G470200 chr2B 98.305 118 1 1 3400 3516 504772520 504772637 5.200000e-49 206
16 TraesCS5A01G470200 chr2B 98.291 117 2 0 3400 3516 512356094 512355978 5.200000e-49 206
17 TraesCS5A01G470200 chrUn 98.359 1645 27 0 1332 2976 221548123 221546479 0.000000e+00 2889
18 TraesCS5A01G470200 chrUn 97.587 1119 23 1 2853 3971 296251935 296250821 0.000000e+00 1914
19 TraesCS5A01G470200 chrUn 96.425 1007 35 1 1 1007 100880154 100881159 0.000000e+00 1659
20 TraesCS5A01G470200 chrUn 96.920 487 15 0 3485 3971 229491371 229491857 0.000000e+00 817
21 TraesCS5A01G470200 chrUn 95.368 367 13 2 1002 1364 186191486 186191120 7.400000e-162 580
22 TraesCS5A01G470200 chrUn 95.095 367 14 2 1002 1364 221548488 221548122 3.440000e-160 575
23 TraesCS5A01G470200 chr3A 97.548 1672 41 0 1332 3003 51916454 51918125 0.000000e+00 2861
24 TraesCS5A01G470200 chr3A 96.326 1007 36 1 1 1007 538080761 538079756 0.000000e+00 1653
25 TraesCS5A01G470200 chr2D 96.962 1119 30 1 2853 3971 322922554 322921440 0.000000e+00 1875
26 TraesCS5A01G470200 chr2D 96.226 1007 37 1 1 1007 336249814 336250819 0.000000e+00 1648
27 TraesCS5A01G470200 chr2D 96.894 483 15 0 3485 3967 382488741 382489223 0.000000e+00 809
28 TraesCS5A01G470200 chr2D 96.099 487 17 1 3487 3971 39575797 39575311 0.000000e+00 793
29 TraesCS5A01G470200 chr2D 91.980 399 24 6 974 1364 200914127 200914525 1.610000e-153 553
30 TraesCS5A01G470200 chr1D 96.524 1007 34 1 1 1007 426831865 426830860 0.000000e+00 1664
31 TraesCS5A01G470200 chr6A 96.600 1000 33 1 8 1007 563295926 563296924 0.000000e+00 1657
32 TraesCS5A01G470200 chr7D 96.326 1007 32 2 1 1007 614315406 614316407 0.000000e+00 1650
33 TraesCS5A01G470200 chr7D 96.226 1007 37 1 1 1007 419319922 419320927 0.000000e+00 1648
34 TraesCS5A01G470200 chr1A 96.226 1007 37 1 1 1007 98656486 98657491 0.000000e+00 1648
35 TraesCS5A01G470200 chr1A 96.226 1007 37 1 1 1007 172092037 172091032 0.000000e+00 1648
36 TraesCS5A01G470200 chr4D 97.175 885 20 2 3087 3971 123443427 123442548 0.000000e+00 1491
37 TraesCS5A01G470200 chr5D 96.715 487 16 0 3485 3971 324471035 324470549 0.000000e+00 811
38 TraesCS5A01G470200 chr5D 92.167 383 23 6 974 1352 413024359 413024738 5.840000e-148 534
39 TraesCS5A01G470200 chr7B 92.500 400 21 7 974 1364 743005960 743006359 7.450000e-157 564
40 TraesCS5A01G470200 chr7B 95.699 186 6 2 3031 3216 489408368 489408185 8.340000e-77 298
41 TraesCS5A01G470200 chr4B 94.293 368 16 3 1002 1364 209271380 209271013 3.470000e-155 558


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 TraesCS5A01G470200 chr5A 647028608 647032578 3970 False 7334 7334 100.000 1 3971 1 chr5A.!!$F2 3970
1 TraesCS5A01G470200 chr5A 534933738 534935663 1925 False 3247 3247 97.097 1002 2927 1 chr5A.!!$F1 1925
2 TraesCS5A01G470200 chr6D 57921519 57924153 2634 False 4366 4366 96.553 1332 3971 1 chr6D.!!$F1 2639
3 TraesCS5A01G470200 chr3B 39816714 39818713 1999 False 3330 3330 96.703 1002 3003 1 chr3B.!!$F1 2001
4 TraesCS5A01G470200 chr3B 173888708 173890705 1997 False 3295 3295 96.404 1002 3003 1 chr3B.!!$F2 2001
5 TraesCS5A01G470200 chr6B 625639293 625641239 1946 True 3275 3275 97.023 1002 2949 1 chr6B.!!$R2 1947
6 TraesCS5A01G470200 chr7A 211292248 211294207 1959 False 3262 3262 96.648 1002 2970 1 chr7A.!!$F2 1968
7 TraesCS5A01G470200 chr2B 357716774 357718695 1921 True 3234 3234 97.036 1002 2923 1 chr2B.!!$R2 1921
8 TraesCS5A01G470200 chr2B 357342549 357344469 1920 True 3155 3155 96.310 1002 2923 1 chr2B.!!$R1 1921
9 TraesCS5A01G470200 chr2B 357306958 357307471 513 False 811 811 95.146 1002 1515 1 chr2B.!!$F1 513
10 TraesCS5A01G470200 chrUn 296250821 296251935 1114 True 1914 1914 97.587 2853 3971 1 chrUn.!!$R2 1118
11 TraesCS5A01G470200 chrUn 221546479 221548488 2009 True 1732 2889 96.727 1002 2976 2 chrUn.!!$R3 1974
12 TraesCS5A01G470200 chrUn 100880154 100881159 1005 False 1659 1659 96.425 1 1007 1 chrUn.!!$F1 1006
13 TraesCS5A01G470200 chr3A 51916454 51918125 1671 False 2861 2861 97.548 1332 3003 1 chr3A.!!$F1 1671
14 TraesCS5A01G470200 chr3A 538079756 538080761 1005 True 1653 1653 96.326 1 1007 1 chr3A.!!$R1 1006
15 TraesCS5A01G470200 chr2D 322921440 322922554 1114 True 1875 1875 96.962 2853 3971 1 chr2D.!!$R2 1118
16 TraesCS5A01G470200 chr2D 336249814 336250819 1005 False 1648 1648 96.226 1 1007 1 chr2D.!!$F2 1006
17 TraesCS5A01G470200 chr1D 426830860 426831865 1005 True 1664 1664 96.524 1 1007 1 chr1D.!!$R1 1006
18 TraesCS5A01G470200 chr6A 563295926 563296924 998 False 1657 1657 96.600 8 1007 1 chr6A.!!$F1 999
19 TraesCS5A01G470200 chr7D 614315406 614316407 1001 False 1650 1650 96.326 1 1007 1 chr7D.!!$F2 1006
20 TraesCS5A01G470200 chr7D 419319922 419320927 1005 False 1648 1648 96.226 1 1007 1 chr7D.!!$F1 1006
21 TraesCS5A01G470200 chr1A 98656486 98657491 1005 False 1648 1648 96.226 1 1007 1 chr1A.!!$F1 1006
22 TraesCS5A01G470200 chr1A 172091032 172092037 1005 True 1648 1648 96.226 1 1007 1 chr1A.!!$R1 1006
23 TraesCS5A01G470200 chr4D 123442548 123443427 879 True 1491 1491 97.175 3087 3971 1 chr4D.!!$R1 884

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
232 233 0.249955 TATCGGGTCGGGTTTTGGAC 59.750 55.000 0.0 0.0 0.0 4.02 F
1194 1195 0.398318 GCCTGGAAGTGGAACAGAGT 59.602 55.000 0.0 0.0 41.8 3.24 F
1234 1235 1.544093 CCAAGAGCAAGGCAAGTCTCA 60.544 52.381 0.0 0.0 0.0 3.27 F
1941 1980 2.092968 TGGACCTGGAATGACTATGCAC 60.093 50.000 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1249 0.605083 ACAAGTCGAGAGCATGCTCA 59.395 50.000 40.91 23.68 44.99 4.26 R
2737 2780 0.531974 GCATTCCATCCGGCGTAAGA 60.532 55.000 6.01 0.00 43.02 2.10 R
2786 2829 2.413837 AGAAACGACGAATCCCAACTG 58.586 47.619 0.00 0.00 0.00 3.16 R
3516 3559 0.105039 GCCCACTCTTCTATCCCACG 59.895 60.000 0.00 0.00 0.00 4.94 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
232 233 0.249955 TATCGGGTCGGGTTTTGGAC 59.750 55.000 0.00 0.00 0.00 4.02
311 312 0.531974 GCTGGAGGAAACACGTGTCA 60.532 55.000 23.61 13.29 0.00 3.58
420 421 4.499024 ATTCCTGTGAAAAGGCTGGCCT 62.499 50.000 8.50 8.50 39.25 5.19
421 422 5.167066 ATTCCTGTGAAAAGGCTGGCCTA 62.167 47.826 14.95 0.00 38.21 3.93
648 649 6.240002 CCATATGAGGCCCTATGTAACTCTTT 60.240 42.308 3.65 0.00 0.00 2.52
770 771 8.698210 AGTGTATCACTTTATACCCATTAACGA 58.302 33.333 0.00 0.00 42.59 3.85
881 882 0.681175 ACTTACGGCCCGTTACTGTT 59.319 50.000 16.82 0.00 41.54 3.16
1046 1047 3.558931 TCTGGACCATATTCACGCAAT 57.441 42.857 0.00 0.00 0.00 3.56
1047 1048 3.466836 TCTGGACCATATTCACGCAATC 58.533 45.455 0.00 0.00 0.00 2.67
1138 1139 2.034558 CGAAATGCTGTTTCCCACAACT 59.965 45.455 8.80 0.00 33.87 3.16
1194 1195 0.398318 GCCTGGAAGTGGAACAGAGT 59.602 55.000 0.00 0.00 41.80 3.24
1234 1235 1.544093 CCAAGAGCAAGGCAAGTCTCA 60.544 52.381 0.00 0.00 0.00 3.27
1241 1242 2.620585 GCAAGGCAAGTCTCAAAAGAGT 59.379 45.455 0.00 0.00 36.72 3.24
1301 1302 7.934665 GGAGGATCTTAGAAGGGAATTAGAAAC 59.065 40.741 0.00 0.00 33.73 2.78
1533 1572 2.738938 GGAATTAGCCCGACCCGGT 61.739 63.158 0.00 0.00 46.80 5.28
1941 1980 2.092968 TGGACCTGGAATGACTATGCAC 60.093 50.000 0.00 0.00 0.00 4.57
2037 2076 6.183360 CGGGGGCAATTACAATGTTATTAACT 60.183 38.462 7.99 0.00 0.00 2.24
2152 2193 7.013220 AGAGGTGTATATTCTCATTCTGCCTA 58.987 38.462 0.00 0.00 0.00 3.93
2284 2325 7.573710 AGTTTGGGCTCATCATATGTTTACTA 58.426 34.615 1.90 0.00 0.00 1.82
2458 2500 4.105697 TCTTTTTGTTCACCATAGGAGGGT 59.894 41.667 0.00 0.00 39.88 4.34
2459 2501 3.713826 TTTGTTCACCATAGGAGGGTC 57.286 47.619 0.00 0.00 36.19 4.46
2557 2599 6.465751 CCATTATGTACTTTCTATGGGAGCCA 60.466 42.308 0.00 0.00 38.19 4.75
2629 2671 6.126883 TGGTCGGACATATCCTGAAACTTTAT 60.127 38.462 10.76 0.00 43.73 1.40
2737 2780 4.999950 GTCGCATTCCAGATTATCCAGATT 59.000 41.667 0.00 0.00 0.00 2.40
2786 2829 6.145696 AGCAGTTTCGTTTCTTATATATCCGC 59.854 38.462 0.00 0.00 0.00 5.54
2867 2910 5.011635 ACCAAAAATATGCGGAAAGTCCTTT 59.988 36.000 0.00 0.00 33.30 3.11
2940 2983 4.335416 TGGCCTTTCATACTTTTGGAGAG 58.665 43.478 3.32 0.00 0.00 3.20
3274 3317 4.318121 CGTAGGCAATAAACTCGAAGATGC 60.318 45.833 0.00 0.00 33.89 3.91
3275 3318 3.609853 AGGCAATAAACTCGAAGATGCA 58.390 40.909 0.00 0.00 33.89 3.96
3276 3319 4.202441 AGGCAATAAACTCGAAGATGCAT 58.798 39.130 0.00 0.00 33.89 3.96
3277 3320 5.368145 AGGCAATAAACTCGAAGATGCATA 58.632 37.500 0.00 0.00 33.89 3.14
3694 3737 2.159156 ACTCGTCATAAATAGCGGCACA 60.159 45.455 1.45 0.00 0.00 4.57
3734 3777 5.850557 TGTTTCCTTTTCTTGCTTCATGA 57.149 34.783 0.00 0.00 0.00 3.07
3750 3793 5.240183 GCTTCATGACACATGCCTATTGTAT 59.760 40.000 0.00 0.00 0.00 2.29
3763 3806 7.859026 TGCCTATTGTATAACATACCTACCA 57.141 36.000 0.00 0.00 0.00 3.25
3937 3980 7.772332 ACTAGAAATGAATCGGTGTCATAAC 57.228 36.000 0.00 0.00 34.60 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 7.507277 AGCACAGGTATGACTATCTTGATTCTA 59.493 37.037 0.00 0.00 0.00 2.10
232 233 1.292992 GCTGTTAACGGGTTATCGGG 58.707 55.000 16.13 1.67 0.00 5.14
311 312 2.508716 ACATCTGTCCCAATGATGAGCT 59.491 45.455 8.86 0.00 39.72 4.09
352 353 1.893137 TCGACATATCATAGGCGCCTT 59.107 47.619 37.74 20.00 0.00 4.35
770 771 1.377594 GCCCAACGGAATAACGGGT 60.378 57.895 0.00 0.00 39.27 5.28
881 882 2.300956 TGGCCCACAAGCAGAAAATA 57.699 45.000 0.00 0.00 0.00 1.40
1046 1047 4.600692 TGGAGAACAGTGAAAGAATCGA 57.399 40.909 0.00 0.00 0.00 3.59
1047 1048 4.377841 GCTTGGAGAACAGTGAAAGAATCG 60.378 45.833 0.00 0.00 0.00 3.34
1138 1139 2.066393 CCGCCTCAAGGAGATCCCA 61.066 63.158 0.00 0.00 37.14 4.37
1234 1235 4.436242 CATGCTCATGCTCAACTCTTTT 57.564 40.909 0.00 0.00 40.48 2.27
1248 1249 0.605083 ACAAGTCGAGAGCATGCTCA 59.395 50.000 40.91 23.68 44.99 4.26
1321 1325 8.901793 GCTGGAAGAGAAAAGAATCAGAATTAT 58.098 33.333 0.00 0.00 34.07 1.28
1533 1572 5.331906 TGATTCCCACCAAGAATTTGATCA 58.668 37.500 0.00 0.00 36.36 2.92
2284 2325 3.093717 CGTATCAACGTCTAAGCCCAT 57.906 47.619 0.00 0.00 44.21 4.00
2458 2500 5.248477 AGTTTGCTAGAACTATTCCAGTGGA 59.752 40.000 8.12 8.12 38.06 4.02
2459 2501 5.491982 AGTTTGCTAGAACTATTCCAGTGG 58.508 41.667 1.40 1.40 38.06 4.00
2668 2711 2.905415 TGCATGGGAAAGAAGGTCAT 57.095 45.000 0.00 0.00 0.00 3.06
2737 2780 0.531974 GCATTCCATCCGGCGTAAGA 60.532 55.000 6.01 0.00 43.02 2.10
2771 2814 6.428083 TCCCAACTGCGGATATATAAGAAA 57.572 37.500 0.00 0.00 0.00 2.52
2786 2829 2.413837 AGAAACGACGAATCCCAACTG 58.586 47.619 0.00 0.00 0.00 3.16
2867 2910 2.622942 GTTGGATTCTGTTCAACAGCCA 59.377 45.455 13.15 11.62 45.54 4.75
2918 2961 4.335416 CTCTCCAAAAGTATGAAAGGCCA 58.665 43.478 5.01 0.00 0.00 5.36
3066 3109 7.690256 TCCATAGCTTTTTCTTAACTTCCTCT 58.310 34.615 0.00 0.00 0.00 3.69
3236 3279 4.684877 TGCCTACGAATTTCGCATAGTTA 58.315 39.130 18.24 2.04 45.12 2.24
3245 3288 6.340537 TCGAGTTTATTGCCTACGAATTTC 57.659 37.500 0.00 0.00 0.00 2.17
3251 3294 4.318121 GCATCTTCGAGTTTATTGCCTACG 60.318 45.833 0.00 0.00 0.00 3.51
3313 3356 5.468072 CCGAGCTGATATCTTTAGCAAACAT 59.532 40.000 14.09 0.00 39.84 2.71
3516 3559 0.105039 GCCCACTCTTCTATCCCACG 59.895 60.000 0.00 0.00 0.00 4.94
3734 3777 7.745717 AGGTATGTTATACAATAGGCATGTGT 58.254 34.615 0.00 0.00 32.27 3.72
3750 3793 7.124750 GGTACTTTTCTCCTGGTAGGTATGTTA 59.875 40.741 0.00 0.00 36.53 2.41
3763 3806 5.367945 TCACAAACTGGTACTTTTCTCCT 57.632 39.130 0.00 0.00 0.00 3.69
3937 3980 2.533266 ACTACGGTTAGCGAAATTCGG 58.467 47.619 17.49 1.62 40.84 4.30


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

AutoCloner maintained by Alex Coulton.