Multiple sequence alignment - TraesCS7B01G476500

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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 TraesCS7B01G476500 chr7B 100.000 2083 0 0 1 2083 732584267 732586349 0.000000e+00 3847.0
1 TraesCS7B01G476500 chr7B 100.000 687 0 0 2385 3071 732586651 732587337 0.000000e+00 1269.0
2 TraesCS7B01G476500 chr7B 93.883 752 31 9 1 751 732426465 732425728 0.000000e+00 1120.0
3 TraesCS7B01G476500 chr7B 78.645 679 131 12 2395 3066 497229496 497228825 3.640000e-119 438.0
4 TraesCS7B01G476500 chr7B 79.592 98 18 2 1985 2081 89889977 89889881 5.490000e-08 69.4
5 TraesCS7B01G476500 chr4B 93.288 1326 84 4 760 2083 581950081 581948759 0.000000e+00 1951.0
6 TraesCS7B01G476500 chr4B 92.431 687 52 0 2385 3071 581948728 581948042 0.000000e+00 981.0
7 TraesCS7B01G476500 chr2B 90.806 1327 96 10 757 2083 792978874 792980174 0.000000e+00 1751.0
8 TraesCS7B01G476500 chr2B 90.356 1151 109 1 914 2064 7587325 7586177 0.000000e+00 1509.0
9 TraesCS7B01G476500 chr2B 90.063 1117 109 1 914 2030 705362316 705363430 0.000000e+00 1447.0
10 TraesCS7B01G476500 chr2B 90.102 687 68 0 2385 3071 705363676 705364362 0.000000e+00 893.0
11 TraesCS7B01G476500 chr2B 88.840 681 72 1 2395 3071 7585939 7585259 0.000000e+00 833.0
12 TraesCS7B01G476500 chr2B 86.047 129 18 0 760 888 705362188 705362316 4.130000e-29 139.0
13 TraesCS7B01G476500 chr2D 90.288 1318 121 5 763 2079 442010924 442009613 0.000000e+00 1718.0
14 TraesCS7B01G476500 chr2D 91.557 687 58 0 2385 3071 442009578 442008892 0.000000e+00 948.0
15 TraesCS7B01G476500 chr2D 83.209 268 36 8 1 266 423339914 423340174 1.420000e-58 237.0
16 TraesCS7B01G476500 chr7D 84.644 1335 179 19 754 2076 123384805 123386125 0.000000e+00 1306.0
17 TraesCS7B01G476500 chr7D 86.684 766 71 12 1 751 629628762 629629511 0.000000e+00 821.0
18 TraesCS7B01G476500 chr7D 88.253 681 78 2 2385 3064 123386160 123386839 0.000000e+00 813.0
19 TraesCS7B01G476500 chr7D 83.209 268 37 6 4 270 154202070 154201810 3.960000e-59 239.0
20 TraesCS7B01G476500 chr6B 94.024 820 48 1 1264 2083 94011390 94010572 0.000000e+00 1242.0
21 TraesCS7B01G476500 chr6B 95.342 687 32 0 2385 3071 94010550 94009864 0.000000e+00 1092.0
22 TraesCS7B01G476500 chr4D 80.543 1326 237 15 760 2074 9066204 9064889 0.000000e+00 1000.0
23 TraesCS7B01G476500 chr1A 85.756 681 94 3 2385 3064 562248263 562247585 0.000000e+00 717.0
24 TraesCS7B01G476500 chr1A 79.900 602 115 5 2387 2985 510527720 510528318 1.310000e-118 436.0
25 TraesCS7B01G476500 chr1A 75.344 945 210 21 762 1694 510526371 510527304 1.690000e-117 433.0
26 TraesCS7B01G476500 chr1A 73.585 954 216 30 760 1694 12026915 12025979 1.760000e-87 333.0
27 TraesCS7B01G476500 chr3D 77.494 1173 242 16 919 2080 378781572 378780411 0.000000e+00 684.0
28 TraesCS7B01G476500 chr7A 80.580 793 149 3 919 1710 29992600 29991812 9.420000e-170 606.0
29 TraesCS7B01G476500 chr7A 87.126 334 26 4 435 751 725652204 725652537 2.250000e-96 363.0
30 TraesCS7B01G476500 chr7A 85.019 267 35 4 1 266 735766797 735767059 1.820000e-67 267.0
31 TraesCS7B01G476500 chr5D 78.388 819 165 10 1269 2080 89362869 89362056 3.510000e-144 521.0
32 TraesCS7B01G476500 chr1D 75.053 946 216 16 760 1694 476594079 476595015 3.660000e-114 422.0
33 TraesCS7B01G476500 chr1D 85.227 264 34 4 4 266 483359242 483358983 1.820000e-67 267.0
34 TraesCS7B01G476500 chrUn 85.019 267 35 4 1 266 305830790 305831052 1.820000e-67 267.0
35 TraesCS7B01G476500 chrUn 85.019 267 35 4 1 266 327651757 327652019 1.820000e-67 267.0
36 TraesCS7B01G476500 chr5A 83.582 268 37 6 1 266 105413453 105413715 8.510000e-61 244.0
37 TraesCS7B01G476500 chr2A 84.677 248 33 4 20 266 450537364 450537121 3.060000e-60 243.0
38 TraesCS7B01G476500 chr1B 70.955 513 122 21 1583 2080 31657654 31658154 2.520000e-16 97.1


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 TraesCS7B01G476500 chr7B 732584267 732587337 3070 False 2558.000000 3847 100.000000 1 3071 2 chr7B.!!$F1 3070
1 TraesCS7B01G476500 chr7B 732425728 732426465 737 True 1120.000000 1120 93.883000 1 751 1 chr7B.!!$R3 750
2 TraesCS7B01G476500 chr7B 497228825 497229496 671 True 438.000000 438 78.645000 2395 3066 1 chr7B.!!$R2 671
3 TraesCS7B01G476500 chr4B 581948042 581950081 2039 True 1466.000000 1951 92.859500 760 3071 2 chr4B.!!$R1 2311
4 TraesCS7B01G476500 chr2B 792978874 792980174 1300 False 1751.000000 1751 90.806000 757 2083 1 chr2B.!!$F1 1326
5 TraesCS7B01G476500 chr2B 7585259 7587325 2066 True 1171.000000 1509 89.598000 914 3071 2 chr2B.!!$R1 2157
6 TraesCS7B01G476500 chr2B 705362188 705364362 2174 False 826.333333 1447 88.737333 760 3071 3 chr2B.!!$F2 2311
7 TraesCS7B01G476500 chr2D 442008892 442010924 2032 True 1333.000000 1718 90.922500 763 3071 2 chr2D.!!$R1 2308
8 TraesCS7B01G476500 chr7D 123384805 123386839 2034 False 1059.500000 1306 86.448500 754 3064 2 chr7D.!!$F2 2310
9 TraesCS7B01G476500 chr7D 629628762 629629511 749 False 821.000000 821 86.684000 1 751 1 chr7D.!!$F1 750
10 TraesCS7B01G476500 chr6B 94009864 94011390 1526 True 1167.000000 1242 94.683000 1264 3071 2 chr6B.!!$R1 1807
11 TraesCS7B01G476500 chr4D 9064889 9066204 1315 True 1000.000000 1000 80.543000 760 2074 1 chr4D.!!$R1 1314
12 TraesCS7B01G476500 chr1A 562247585 562248263 678 True 717.000000 717 85.756000 2385 3064 1 chr1A.!!$R2 679
13 TraesCS7B01G476500 chr1A 510526371 510528318 1947 False 434.500000 436 77.622000 762 2985 2 chr1A.!!$F1 2223
14 TraesCS7B01G476500 chr1A 12025979 12026915 936 True 333.000000 333 73.585000 760 1694 1 chr1A.!!$R1 934
15 TraesCS7B01G476500 chr3D 378780411 378781572 1161 True 684.000000 684 77.494000 919 2080 1 chr3D.!!$R1 1161
16 TraesCS7B01G476500 chr7A 29991812 29992600 788 True 606.000000 606 80.580000 919 1710 1 chr7A.!!$R1 791
17 TraesCS7B01G476500 chr5D 89362056 89362869 813 True 521.000000 521 78.388000 1269 2080 1 chr5D.!!$R1 811
18 TraesCS7B01G476500 chr1D 476594079 476595015 936 False 422.000000 422 75.053000 760 1694 1 chr1D.!!$F1 934

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
618 634 2.159517 GCATTAGGTTTGACGCTCCAAG 60.160 50.0 0.0 0.0 0.00 3.61 F
1752 1788 0.861837 AGCAGTTTCAGCGTTCTTCG 59.138 50.0 0.0 0.0 43.12 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 1897 0.189574 TCCATGGCCAACCTTTTCCA 59.81 50.000 10.96 0.0 36.63 3.53 R
2747 2801 1.299976 GCCTCGTTGAAGTCCCCAT 59.70 57.895 0.00 0.0 0.00 4.00 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
49 50 4.810191 TGGTTTTTGTTGTAGTTTGCCT 57.190 36.364 0.00 0.00 0.00 4.75
95 99 6.715264 GGATTTTTCTTTCTTCCTCACCTACA 59.285 38.462 0.00 0.00 0.00 2.74
260 265 9.614792 TGAGCTAATAAAGTTCTCCTTTTATCC 57.385 33.333 0.00 0.00 40.55 2.59
269 274 9.987272 AAAGTTCTCCTTTTATCCAAAAAGATG 57.013 29.630 10.91 4.65 40.55 2.90
433 440 5.382303 CGCTCTCGTTATTTTTGTTCATGT 58.618 37.500 0.00 0.00 0.00 3.21
480 487 3.383761 CAGAATGACTGGCACCAAAAAC 58.616 45.455 0.00 0.00 42.39 2.43
618 634 2.159517 GCATTAGGTTTGACGCTCCAAG 60.160 50.000 0.00 0.00 0.00 3.61
638 654 9.152595 CTCCAAGTTTAATTTACAGGAGAGTAC 57.847 37.037 17.57 0.00 40.01 2.73
751 767 8.717717 ACATGGAGATAGAATGACAATCCTTAA 58.282 33.333 0.00 0.00 0.00 1.85
752 768 9.217278 CATGGAGATAGAATGACAATCCTTAAG 57.783 37.037 0.00 0.00 0.00 1.85
753 769 7.739825 TGGAGATAGAATGACAATCCTTAAGG 58.260 38.462 15.98 15.98 0.00 2.69
999 1026 4.670765 AGGCTTCAGATCTTGGTGATTTT 58.329 39.130 0.00 0.00 35.14 1.82
1038 1065 2.540515 GAAGATGCGGACTTCGATGAA 58.459 47.619 5.16 0.00 42.43 2.57
1169 1196 2.186826 GTGCTGCTTGGAACACGGT 61.187 57.895 0.00 0.00 39.29 4.83
1262 1295 2.484062 GCATGGTGGATCAAGGGCG 61.484 63.158 0.00 0.00 0.00 6.13
1316 1349 1.136305 ACCGTATGATGGGTTCACGAG 59.864 52.381 0.00 0.00 37.11 4.18
1431 1464 6.795144 TTGTTAAGGAACTCCGGTGATATA 57.205 37.500 11.17 0.00 38.49 0.86
1724 1760 1.419387 GGATGAGGCTGGTCATAGCTT 59.581 52.381 0.00 0.00 43.22 3.74
1749 1785 1.869767 CAGAAGCAGTTTCAGCGTTCT 59.130 47.619 0.00 0.00 38.31 3.01
1752 1788 0.861837 AGCAGTTTCAGCGTTCTTCG 59.138 50.000 0.00 0.00 43.12 3.79
1802 1838 4.715534 TGGACCCAGATTTAACTGACAA 57.284 40.909 0.00 0.00 39.94 3.18
1824 1860 1.828832 CGTCTAGTCCATCGAAGCAC 58.171 55.000 0.00 0.00 0.00 4.40
1889 1928 1.210478 GGCCATGGAGCTAGAAGTTGA 59.790 52.381 18.40 0.00 0.00 3.18
2747 2801 1.961394 GTCAGATCCGTGGCTGGTATA 59.039 52.381 0.00 0.00 33.05 1.47
2793 2847 4.037327 TGGCAACATGAACATTTTTCTCGA 59.963 37.500 0.00 0.00 46.17 4.04
2816 2870 2.719046 CGCAACGGTCTGAAAATCAAAC 59.281 45.455 0.00 0.00 0.00 2.93
2841 2895 5.772521 CTTCTTTTCCGTGATTGTTTGGAT 58.227 37.500 0.00 0.00 0.00 3.41
2948 3002 0.390866 CTAGATAGGGCATGCGCTGG 60.391 60.000 38.79 22.08 39.59 4.85
3013 3067 3.055530 CCTTGCTACCTCATGTTCAGACT 60.056 47.826 0.00 0.00 0.00 3.24
3022 3076 3.096852 TCATGTTCAGACTATGTCCCGT 58.903 45.455 0.00 0.00 32.18 5.28
3025 3079 2.631062 TGTTCAGACTATGTCCCGTTGT 59.369 45.455 0.00 0.00 32.18 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.146010 ACAAAAACCATATCCGCACAAAT 57.854 34.783 0.00 0.00 0.00 2.32
49 50 3.186909 CAAAGCGATCAGATCCACGTTA 58.813 45.455 4.73 0.00 0.00 3.18
95 99 8.627403 CAAAATCATATGAGACCAAAGCTATGT 58.373 33.333 11.78 0.00 0.00 2.29
310 315 8.535592 CGAGATCACTACTAAATCAATTCACAC 58.464 37.037 0.00 0.00 0.00 3.82
388 394 3.099141 CCCCATCAGCCAATTAACACTT 58.901 45.455 0.00 0.00 0.00 3.16
433 440 4.935205 CCGTTCTCCAATCTAACATGTTGA 59.065 41.667 21.42 15.65 0.00 3.18
517 524 3.064900 AGAGTGGAGCCAGTCATTTTC 57.935 47.619 22.63 0.00 45.95 2.29
618 634 7.710044 GCTAGGGTACTCTCCTGTAAATTAAAC 59.290 40.741 0.00 0.00 35.92 2.01
773 789 1.454201 GAGACAAACCCTAGCCTTGC 58.546 55.000 0.00 0.00 0.00 4.01
999 1026 6.373005 TCTTCCAGATGGAGTTGTTTCATA 57.627 37.500 1.13 0.00 46.36 2.15
1038 1065 3.981071 TCGTCCTCTTCAATCACCAAT 57.019 42.857 0.00 0.00 0.00 3.16
1169 1196 1.118965 TCTGAACCTCACGGGCTTCA 61.119 55.000 0.00 0.00 39.10 3.02
1262 1295 4.070716 CACCATATTCCTGAAGAGCCATC 58.929 47.826 0.00 0.00 0.00 3.51
1431 1464 0.534412 CGTTCAGCCTCATCTCCAGT 59.466 55.000 0.00 0.00 0.00 4.00
1681 1714 2.738321 GCCTTATTTTGTTCGGGCCATG 60.738 50.000 4.39 0.00 34.19 3.66
1724 1760 2.341257 GCTGAAACTGCTTCTGATCGA 58.659 47.619 2.40 0.00 35.54 3.59
1749 1785 1.202722 ACTTCCTTTTCCTTCGCCGAA 60.203 47.619 0.00 0.00 0.00 4.30
1752 1788 0.881796 CCACTTCCTTTTCCTTCGCC 59.118 55.000 0.00 0.00 0.00 5.54
1802 1838 1.025812 CTTCGATGGACTAGACGCCT 58.974 55.000 0.00 0.00 0.00 5.52
1824 1860 2.029623 ACCTGCATACTACTGGTACCG 58.970 52.381 7.57 4.79 37.56 4.02
1858 1897 0.189574 TCCATGGCCAACCTTTTCCA 59.810 50.000 10.96 0.00 36.63 3.53
1889 1928 1.063266 TGGCCTTGTTTTGTTCCTCCT 60.063 47.619 3.32 0.00 0.00 3.69
1918 1968 1.239968 CCCTGAGTCAGCACCAAAGC 61.240 60.000 15.10 0.00 0.00 3.51
2673 2727 2.970639 CGATGACGGTGGTCCACT 59.029 61.111 21.40 2.38 42.73 4.00
2747 2801 1.299976 GCCTCGTTGAAGTCCCCAT 59.700 57.895 0.00 0.00 0.00 4.00
2793 2847 2.422597 TGATTTTCAGACCGTTGCGAT 58.577 42.857 0.00 0.00 0.00 4.58
2816 2870 2.969443 ACAATCACGGAAAAGAAGCG 57.031 45.000 0.00 0.00 0.00 4.68
2841 2895 3.306294 CCAAGTCCATGAGCTCGCATATA 60.306 47.826 9.64 0.00 0.00 0.86
3013 3067 3.199071 AGCCTAATCAACAACGGGACATA 59.801 43.478 0.00 0.00 0.00 2.29
3022 3076 3.825585 TCATGTGCAAGCCTAATCAACAA 59.174 39.130 0.00 0.00 0.00 2.83
3025 3079 3.018856 CCTCATGTGCAAGCCTAATCAA 58.981 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.