Multiple sequence alignment - TraesCS5B01G052200

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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 TraesCS5B01G052200 chr5B 100.000 2529 0 0 1434 3962 57492191 57489663 0.000000e+00 4671.0
1 TraesCS5B01G052200 chr5B 100.000 1010 0 0 1 1010 57493624 57492615 0.000000e+00 1866.0
2 TraesCS5B01G052200 chr5D 95.442 2545 95 13 1434 3962 54934972 54937511 0.000000e+00 4037.0
3 TraesCS5B01G052200 chr5D 95.414 2442 95 12 1534 3962 54689343 54686906 0.000000e+00 3873.0
4 TraesCS5B01G052200 chr5D 84.697 379 34 7 441 799 54693678 54693304 1.350000e-94 357.0
5 TraesCS5B01G052200 chr5D 90.086 232 16 3 211 441 54708907 54708682 1.080000e-75 294.0
6 TraesCS5B01G052200 chr5D 90.187 214 14 4 1 214 54710057 54709851 5.040000e-69 272.0
7 TraesCS5B01G052200 chr5D 91.351 185 12 2 826 1010 54934780 54934960 2.360000e-62 250.0
8 TraesCS5B01G052200 chr5A 95.565 1601 55 6 1579 3165 42681197 42679599 0.000000e+00 2549.0
9 TraesCS5B01G052200 chr5A 92.716 1263 40 19 2710 3962 42676567 42675347 0.000000e+00 1775.0
10 TraesCS5B01G052200 chr5A 92.497 813 41 9 3156 3962 42678369 42677571 0.000000e+00 1146.0
11 TraesCS5B01G052200 chr5A 92.895 746 37 5 211 956 42693461 42692732 0.000000e+00 1070.0
12 TraesCS5B01G052200 chr5A 94.145 649 27 6 211 859 43252257 43251620 0.000000e+00 977.0
13 TraesCS5B01G052200 chr5A 79.618 942 144 30 1488 2412 42626536 42625626 2.010000e-177 632.0
14 TraesCS5B01G052200 chr5A 92.019 213 8 6 2 214 43252576 43252373 1.390000e-74 291.0
15 TraesCS5B01G052200 chr5A 92.353 170 5 5 1 170 42695339 42695178 6.620000e-58 235.0
16 TraesCS5B01G052200 chr1A 86.515 482 46 15 324 800 536363849 536364316 2.730000e-141 512.0
17 TraesCS5B01G052200 chr1D 83.034 501 48 18 324 800 442153872 442153385 1.700000e-113 420.0
18 TraesCS5B01G052200 chr2D 74.054 925 189 37 1502 2400 35231124 35230225 8.210000e-87 331.0
19 TraesCS5B01G052200 chr3B 82.152 409 50 6 323 710 258169503 258169909 2.950000e-86 329.0
20 TraesCS5B01G052200 chr3B 73.089 628 129 29 1786 2403 13865012 13864415 1.880000e-43 187.0
21 TraesCS5B01G052200 chr3B 77.869 122 14 10 3682 3802 47202976 47203085 3.310000e-06 63.9
22 TraesCS5B01G052200 chr2B 81.446 415 47 11 361 747 707600737 707600325 2.970000e-81 313.0
23 TraesCS5B01G052200 chr2B 94.444 36 0 2 3282 3316 177076749 177076715 2.000000e-03 54.7
24 TraesCS5B01G052200 chr7D 76.800 500 77 17 323 799 611883943 611884426 1.100000e-60 244.0
25 TraesCS5B01G052200 chr7B 77.747 364 66 15 442 800 619133255 619132902 4.010000e-50 209.0
26 TraesCS5B01G052200 chr7B 83.482 224 32 5 325 547 619144809 619144590 1.870000e-48 204.0
27 TraesCS5B01G052200 chr3D 73.428 636 134 28 1775 2403 4472127 4471520 5.190000e-49 206.0
28 TraesCS5B01G052200 chr3D 75.467 375 79 10 1773 2136 27672219 27671847 1.890000e-38 171.0
29 TraesCS5B01G052200 chrUn 73.228 635 138 22 1775 2403 32315455 32314847 6.710000e-48 202.0
30 TraesCS5B01G052200 chrUn 74.254 536 113 20 1466 1990 307248283 307247762 6.710000e-48 202.0
31 TraesCS5B01G052200 chrUn 71.969 635 146 23 1775 2403 35963582 35962974 1.470000e-34 158.0
32 TraesCS5B01G052200 chrUn 80.870 115 22 0 2248 2362 43589487 43589373 1.520000e-14 91.6
33 TraesCS5B01G052200 chrUn 80.870 115 22 0 2248 2362 327179357 327179243 1.520000e-14 91.6
34 TraesCS5B01G052200 chrUn 80.870 115 22 0 2248 2362 366320941 366321055 1.520000e-14 91.6
35 TraesCS5B01G052200 chr4A 74.560 511 84 23 323 800 733667115 733666618 8.750000e-42 182.0
36 TraesCS5B01G052200 chr7A 97.619 42 1 0 320 361 648659176 648659217 5.490000e-09 73.1


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 TraesCS5B01G052200 chr5B 57489663 57493624 3961 True 3268.500000 4671 100.000000 1 3962 2 chr5B.!!$R1 3961
1 TraesCS5B01G052200 chr5D 54934780 54937511 2731 False 2143.500000 4037 93.396500 826 3962 2 chr5D.!!$F1 3136
2 TraesCS5B01G052200 chr5D 54686906 54693678 6772 True 2115.000000 3873 90.055500 441 3962 2 chr5D.!!$R1 3521
3 TraesCS5B01G052200 chr5D 54708682 54710057 1375 True 283.000000 294 90.136500 1 441 2 chr5D.!!$R2 440
4 TraesCS5B01G052200 chr5A 42675347 42681197 5850 True 1823.333333 2549 93.592667 1579 3962 3 chr5A.!!$R2 2383
5 TraesCS5B01G052200 chr5A 42692732 42695339 2607 True 652.500000 1070 92.624000 1 956 2 chr5A.!!$R3 955
6 TraesCS5B01G052200 chr5A 43251620 43252576 956 True 634.000000 977 93.082000 2 859 2 chr5A.!!$R4 857
7 TraesCS5B01G052200 chr5A 42625626 42626536 910 True 632.000000 632 79.618000 1488 2412 1 chr5A.!!$R1 924
8 TraesCS5B01G052200 chr2D 35230225 35231124 899 True 331.000000 331 74.054000 1502 2400 1 chr2D.!!$R1 898
9 TraesCS5B01G052200 chr3D 4471520 4472127 607 True 206.000000 206 73.428000 1775 2403 1 chr3D.!!$R1 628
10 TraesCS5B01G052200 chrUn 32314847 32315455 608 True 202.000000 202 73.228000 1775 2403 1 chrUn.!!$R1 628
11 TraesCS5B01G052200 chrUn 307247762 307248283 521 True 202.000000 202 74.254000 1466 1990 1 chrUn.!!$R4 524

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
407 2915 0.963962 CACCTTTTGCTGCATCACCT 59.036 50.0 1.84 0.0 0.00 4.00 F
1004 7299 1.127567 TCCACACTCCCAAGTCCCAG 61.128 60.0 0.00 0.0 31.71 4.45 F
1997 8301 1.755179 CCTTGGTATCCTTGTGCAGG 58.245 55.0 0.00 0.0 45.64 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 8301 1.067495 GCGAGGGGTCTATAGTCATGC 60.067 57.143 0.0 0.0 0.00 4.06 R
2708 9045 2.680339 GGCTTAGATTGCCTGTGACTTC 59.320 50.000 0.0 0.0 46.38 3.01 R
3408 13246 1.522806 ACGTTCGGCTTCACTGCAA 60.523 52.632 0.0 0.0 34.04 4.08 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
52 53 2.726832 GGTAGGCACCGATCTACATC 57.273 55.000 0.00 0.00 38.00 3.06
182 1741 7.336931 AGCAACGGTGTGATTAGAATTAATCTT 59.663 33.333 0.66 0.00 43.62 2.40
183 1742 7.968405 GCAACGGTGTGATTAGAATTAATCTTT 59.032 33.333 0.66 0.00 43.62 2.52
185 1744 9.840427 AACGGTGTGATTAGAATTAATCTTTTG 57.160 29.630 8.31 0.13 43.62 2.44
292 2799 5.791336 TGATGGATGTAGTGATACTGACC 57.209 43.478 0.00 0.00 0.00 4.02
407 2915 0.963962 CACCTTTTGCTGCATCACCT 59.036 50.000 1.84 0.00 0.00 4.00
580 3107 8.715191 TGCAAACATTTTTCTAAAACTGTGAT 57.285 26.923 10.69 3.05 39.76 3.06
714 3243 8.744923 CGATCATTTTTCGAAATGCATGATTAA 58.255 29.630 25.99 12.54 39.39 1.40
859 7110 1.283793 CAAAGCCCAGACGCACTTG 59.716 57.895 0.00 0.00 0.00 3.16
897 7192 2.239201 GTAACAAATCGAGCGGTTTGC 58.761 47.619 23.75 8.32 46.98 3.68
957 7252 7.049799 TGGAGTAAAAGAAATCCAACCTTTG 57.950 36.000 0.00 0.00 38.86 2.77
976 7271 1.750399 CCCCACTCCATTGCCTTCG 60.750 63.158 0.00 0.00 0.00 3.79
1004 7299 1.127567 TCCACACTCCCAAGTCCCAG 61.128 60.000 0.00 0.00 31.71 4.45
1486 7781 3.842923 CTCGCCGATGGAGCCTGT 61.843 66.667 0.00 0.00 0.00 4.00
1997 8301 1.755179 CCTTGGTATCCTTGTGCAGG 58.245 55.000 0.00 0.00 45.64 4.85
2124 8445 1.871039 GCTCACTCGTTGGTAAAGCAA 59.129 47.619 0.00 0.00 31.62 3.91
2227 8558 2.210116 CCCGTTACAGATGATTTCCCG 58.790 52.381 0.00 0.00 0.00 5.14
2569 8906 5.418840 GCAATCCAAGAGTATTCCTGGAAAA 59.581 40.000 14.03 0.00 44.92 2.29
2689 9026 8.863049 GTTATGTTTCATAAATGGTTGCTCAAG 58.137 33.333 4.15 0.00 0.00 3.02
2708 9045 8.020861 GCTCAAGCATCTTAATTCTATCTCTG 57.979 38.462 0.00 0.00 41.59 3.35
2718 9055 8.690884 TCTTAATTCTATCTCTGAAGTCACAGG 58.309 37.037 0.00 0.00 38.31 4.00
2722 9059 3.996921 ATCTCTGAAGTCACAGGCAAT 57.003 42.857 0.00 0.00 38.31 3.56
2723 9060 3.325293 TCTCTGAAGTCACAGGCAATC 57.675 47.619 0.00 0.00 38.31 2.67
2806 9143 8.635765 TTTTCCTTATGTTCTCATTAGCTGTT 57.364 30.769 0.00 0.00 35.70 3.16
2992 12824 6.494491 CCTTAAATGATATTCCTGCCATTCCA 59.506 38.462 0.00 0.00 0.00 3.53
3026 12858 8.032451 GGGCTTATTATGTTTTGCTAAGACAAA 58.968 33.333 0.00 0.00 37.74 2.83
3207 13040 7.341030 TCTTCATCAAAGCCTCATCTTAATGA 58.659 34.615 0.00 0.00 35.89 2.57
3408 13246 9.754382 CTTGCATTGCATAAAAATATCTACCTT 57.246 29.630 12.95 0.00 38.76 3.50
3504 13342 4.824537 TGCAGCACTTACCTAATTTTGTCA 59.175 37.500 0.00 0.00 0.00 3.58
3557 13400 2.032634 GCGGCAGATTTGGACGTCA 61.033 57.895 18.91 0.27 0.00 4.35
3648 13491 5.451520 GCATTTCTTGGCTCTAATCATGCTT 60.452 40.000 0.00 0.00 33.29 3.91
3817 13661 5.031066 TGGCTAAGTGTACTGTTTTCTGT 57.969 39.130 0.00 0.00 36.09 3.41
3905 13750 4.689071 TCTTTCGCTCAAGTAGTGTTTCA 58.311 39.130 0.00 0.00 37.01 2.69
3906 13751 4.745125 TCTTTCGCTCAAGTAGTGTTTCAG 59.255 41.667 0.00 0.00 37.01 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 1.371758 CAGCTGCTACACGTCACGT 60.372 57.895 0.00 0.00 42.36 4.49
57 58 2.720758 GCAGCTGCTACACGTCACG 61.721 63.158 31.33 0.00 38.21 4.35
58 59 2.720758 CGCAGCTGCTACACGTCAC 61.721 63.158 34.22 3.85 39.32 3.67
59 60 2.430751 CGCAGCTGCTACACGTCA 60.431 61.111 34.22 0.00 39.32 4.35
60 61 2.430921 ACGCAGCTGCTACACGTC 60.431 61.111 34.22 5.37 39.32 4.34
134 135 5.462729 GCTCTGCATCGATATCCATGAATAG 59.537 44.000 13.79 6.87 0.00 1.73
138 139 2.564062 TGCTCTGCATCGATATCCATGA 59.436 45.455 13.79 0.00 31.71 3.07
149 150 0.950555 TCACACCGTTGCTCTGCATC 60.951 55.000 0.00 0.00 38.76 3.91
182 1741 5.701224 ACCTGATTACCCTTTGAAGTCAAA 58.299 37.500 6.33 6.33 42.90 2.69
183 1742 5.073144 AGACCTGATTACCCTTTGAAGTCAA 59.927 40.000 0.00 0.00 0.00 3.18
185 1744 5.167303 AGACCTGATTACCCTTTGAAGTC 57.833 43.478 0.00 0.00 0.00 3.01
194 1753 9.852091 CGTAAATAAGTATAGACCTGATTACCC 57.148 37.037 0.00 0.00 0.00 3.69
281 2788 2.991250 ACAATGCCAGGTCAGTATCAC 58.009 47.619 0.00 0.00 0.00 3.06
370 2878 2.621998 GGTGATCATGGCCATTGAAGAG 59.378 50.000 17.92 3.44 0.00 2.85
751 3280 8.876275 AACTGTTCGTGACTTACAAAATACTA 57.124 30.769 0.00 0.00 0.00 1.82
752 3281 7.781548 AACTGTTCGTGACTTACAAAATACT 57.218 32.000 0.00 0.00 0.00 2.12
753 3282 8.831000 AAAACTGTTCGTGACTTACAAAATAC 57.169 30.769 0.00 0.00 0.00 1.89
859 7110 0.738412 ACACGGGCTAATACACACGC 60.738 55.000 0.00 0.00 0.00 5.34
907 7202 4.787286 TGGTATTGGGCCGCCACG 62.787 66.667 12.58 0.00 0.00 4.94
957 7252 2.037847 AAGGCAATGGAGTGGGGC 59.962 61.111 0.00 0.00 0.00 5.80
976 7271 1.275291 TGGGAGTGTGGATCGAACTTC 59.725 52.381 0.00 0.00 0.00 3.01
991 7286 1.592223 GTCGTCTGGGACTTGGGAG 59.408 63.158 0.00 0.00 34.09 4.30
1997 8301 1.067495 GCGAGGGGTCTATAGTCATGC 60.067 57.143 0.00 0.00 0.00 4.06
2289 8620 2.882137 CACGTTTGGAAGTGTGGGTAAT 59.118 45.455 0.00 0.00 33.97 1.89
2569 8906 3.756933 TGGTAGGCACTTCTAAAACGT 57.243 42.857 0.00 0.00 41.75 3.99
2689 9026 8.977505 GTGACTTCAGAGATAGAATTAAGATGC 58.022 37.037 0.00 0.00 0.00 3.91
2708 9045 2.680339 GGCTTAGATTGCCTGTGACTTC 59.320 50.000 0.00 0.00 46.38 3.01
2718 9055 5.702349 ATTGCTGATTAGGCTTAGATTGC 57.298 39.130 0.00 0.00 0.00 3.56
2722 9059 6.273260 AGGGATAATTGCTGATTAGGCTTAGA 59.727 38.462 0.00 0.00 33.87 2.10
2723 9060 6.479884 AGGGATAATTGCTGATTAGGCTTAG 58.520 40.000 0.00 0.00 33.87 2.18
2992 12824 8.927411 AGCAAAACATAATAAGCCCAAGATATT 58.073 29.630 0.00 0.00 0.00 1.28
3026 12858 3.442273 TCTTTTGCGACCAAGTCAAAGTT 59.558 39.130 0.00 0.00 30.40 2.66
3207 13040 4.968259 TCATATGCAGGCGTATTAGGTTT 58.032 39.130 3.31 0.00 0.00 3.27
3320 13155 1.722034 TCCCATCATGGTCCTAGAGC 58.278 55.000 2.07 0.00 35.17 4.09
3325 13160 1.985622 TTCCTTCCCATCATGGTCCT 58.014 50.000 2.07 0.00 35.17 3.85
3408 13246 1.522806 ACGTTCGGCTTCACTGCAA 60.523 52.632 0.00 0.00 34.04 4.08
3517 13355 5.284079 GCGTGCAATGAAATTAATCAGGAT 58.716 37.500 0.00 0.00 32.46 3.24
3544 13382 2.228822 GCAACCAATGACGTCCAAATCT 59.771 45.455 14.12 0.00 0.00 2.40
3545 13383 2.595386 GCAACCAATGACGTCCAAATC 58.405 47.619 14.12 0.00 0.00 2.17
3662 13505 4.887071 ACAAAAGTGACTTCAGGTATGCAA 59.113 37.500 0.00 0.00 0.00 4.08
3672 13515 7.812309 AAACTTTAGCAACAAAAGTGACTTC 57.188 32.000 0.00 0.00 44.35 3.01
3737 13581 4.768448 TCATGTAAACTCGTCCCTAGTCAA 59.232 41.667 0.00 0.00 0.00 3.18
3787 13631 7.907214 AACAGTACACTTAGCCAATAAGAAG 57.093 36.000 0.00 0.00 43.17 2.85
3858 13703 5.971202 ACTCACTTTTGTAACTCGCATTTTG 59.029 36.000 0.00 0.00 0.00 2.44
3905 13750 4.968080 AGGAAAAGACAGATGGATAGCTCT 59.032 41.667 0.00 0.00 0.00 4.09
3906 13751 5.289083 AGGAAAAGACAGATGGATAGCTC 57.711 43.478 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.