Multiple sequence alignment - TraesCS7A01G215600

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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 TraesCS7A01G215600 chr7A 100.000 2411 0 0 1 2411 181998816 182001226 0.000000e+00 4453
1 TraesCS7A01G215600 chr7A 90.309 970 64 14 753 1693 14303373 14302405 0.000000e+00 1243
2 TraesCS7A01G215600 chr7A 95.244 757 36 0 1 757 131343369 131342613 0.000000e+00 1199
3 TraesCS7A01G215600 chr7A 90.694 720 60 7 1694 2411 379115779 379115065 0.000000e+00 952
4 TraesCS7A01G215600 chr5A 91.684 974 54 9 750 1696 446425176 446426149 0.000000e+00 1325
5 TraesCS7A01G215600 chr5A 95.497 755 34 0 1 755 542934690 542933936 0.000000e+00 1206
6 TraesCS7A01G215600 chr5A 95.491 754 33 1 1 754 676116036 676116788 0.000000e+00 1203
7 TraesCS7A01G215600 chr5A 95.278 720 30 4 1692 2410 422927508 422928224 0.000000e+00 1138
8 TraesCS7A01G215600 chr5A 93.629 722 41 5 1692 2411 215015540 215016258 0.000000e+00 1074
9 TraesCS7A01G215600 chr2A 91.237 970 55 12 755 1696 588429514 588428547 0.000000e+00 1293
10 TraesCS7A01G215600 chr2A 93.841 828 46 3 753 1576 740095765 740094939 0.000000e+00 1242
11 TraesCS7A01G215600 chr2A 93.607 829 47 4 753 1576 640296334 640295507 0.000000e+00 1232
12 TraesCS7A01G215600 chr2A 95.745 752 30 2 1 752 168628698 168629447 0.000000e+00 1210
13 TraesCS7A01G215600 chr2A 92.361 720 52 3 1692 2411 253288561 253287845 0.000000e+00 1022
14 TraesCS7A01G215600 chr2A 90.180 723 64 7 1692 2411 348576249 348575531 0.000000e+00 935
15 TraesCS7A01G215600 chr3A 90.995 955 73 7 753 1695 743517592 743518545 0.000000e+00 1275
16 TraesCS7A01G215600 chr3A 90.825 970 61 12 750 1693 717900186 717901153 0.000000e+00 1273
17 TraesCS7A01G215600 chr3A 94.053 824 46 2 753 1573 23344373 23343550 0.000000e+00 1247
18 TraesCS7A01G215600 chr3A 93.841 828 43 4 750 1570 721253326 721254152 0.000000e+00 1240
19 TraesCS7A01G215600 chr3A 95.612 752 33 0 1 752 448651158 448651909 0.000000e+00 1206
20 TraesCS7A01G215600 chr6A 95.878 752 31 0 1 752 87399413 87400164 0.000000e+00 1218
21 TraesCS7A01G215600 chr6A 95.600 750 33 0 1 750 560659763 560660512 0.000000e+00 1203
22 TraesCS7A01G215600 chr6A 95.479 752 34 0 1 752 460567303 460568054 0.000000e+00 1201
23 TraesCS7A01G215600 chr1A 95.883 753 28 3 1 752 76437433 76438183 0.000000e+00 1216
24 TraesCS7A01G215600 chr1A 90.859 722 61 5 1692 2411 439993021 439992303 0.000000e+00 963
25 TraesCS7A01G215600 chr4A 94.028 720 40 3 1693 2411 88078284 88079001 0.000000e+00 1088
26 TraesCS7A01G215600 chr4A 93.056 720 46 4 1692 2411 21297368 21298083 0.000000e+00 1050
27 TraesCS7A01G215600 chr4A 92.936 722 47 4 1692 2411 72655057 72654338 0.000000e+00 1048
28 TraesCS7A01G215600 chr4A 90.909 121 11 0 1575 1695 621133512 621133392 1.920000e-36 163
29 TraesCS7A01G215600 chr6D 93.939 132 6 2 1575 1705 462800363 462800233 5.260000e-47 198
30 TraesCS7A01G215600 chr4D 94.262 122 7 0 1572 1693 439874903 439875024 1.140000e-43 187


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 TraesCS7A01G215600 chr7A 181998816 182001226 2410 False 4453 4453 100.000 1 2411 1 chr7A.!!$F1 2410
1 TraesCS7A01G215600 chr7A 14302405 14303373 968 True 1243 1243 90.309 753 1693 1 chr7A.!!$R1 940
2 TraesCS7A01G215600 chr7A 131342613 131343369 756 True 1199 1199 95.244 1 757 1 chr7A.!!$R2 756
3 TraesCS7A01G215600 chr7A 379115065 379115779 714 True 952 952 90.694 1694 2411 1 chr7A.!!$R3 717
4 TraesCS7A01G215600 chr5A 446425176 446426149 973 False 1325 1325 91.684 750 1696 1 chr5A.!!$F3 946
5 TraesCS7A01G215600 chr5A 542933936 542934690 754 True 1206 1206 95.497 1 755 1 chr5A.!!$R1 754
6 TraesCS7A01G215600 chr5A 676116036 676116788 752 False 1203 1203 95.491 1 754 1 chr5A.!!$F4 753
7 TraesCS7A01G215600 chr5A 422927508 422928224 716 False 1138 1138 95.278 1692 2410 1 chr5A.!!$F2 718
8 TraesCS7A01G215600 chr5A 215015540 215016258 718 False 1074 1074 93.629 1692 2411 1 chr5A.!!$F1 719
9 TraesCS7A01G215600 chr2A 588428547 588429514 967 True 1293 1293 91.237 755 1696 1 chr2A.!!$R3 941
10 TraesCS7A01G215600 chr2A 740094939 740095765 826 True 1242 1242 93.841 753 1576 1 chr2A.!!$R5 823
11 TraesCS7A01G215600 chr2A 640295507 640296334 827 True 1232 1232 93.607 753 1576 1 chr2A.!!$R4 823
12 TraesCS7A01G215600 chr2A 168628698 168629447 749 False 1210 1210 95.745 1 752 1 chr2A.!!$F1 751
13 TraesCS7A01G215600 chr2A 253287845 253288561 716 True 1022 1022 92.361 1692 2411 1 chr2A.!!$R1 719
14 TraesCS7A01G215600 chr2A 348575531 348576249 718 True 935 935 90.180 1692 2411 1 chr2A.!!$R2 719
15 TraesCS7A01G215600 chr3A 743517592 743518545 953 False 1275 1275 90.995 753 1695 1 chr3A.!!$F4 942
16 TraesCS7A01G215600 chr3A 717900186 717901153 967 False 1273 1273 90.825 750 1693 1 chr3A.!!$F2 943
17 TraesCS7A01G215600 chr3A 23343550 23344373 823 True 1247 1247 94.053 753 1573 1 chr3A.!!$R1 820
18 TraesCS7A01G215600 chr3A 721253326 721254152 826 False 1240 1240 93.841 750 1570 1 chr3A.!!$F3 820
19 TraesCS7A01G215600 chr3A 448651158 448651909 751 False 1206 1206 95.612 1 752 1 chr3A.!!$F1 751
20 TraesCS7A01G215600 chr6A 87399413 87400164 751 False 1218 1218 95.878 1 752 1 chr6A.!!$F1 751
21 TraesCS7A01G215600 chr6A 560659763 560660512 749 False 1203 1203 95.600 1 750 1 chr6A.!!$F3 749
22 TraesCS7A01G215600 chr6A 460567303 460568054 751 False 1201 1201 95.479 1 752 1 chr6A.!!$F2 751
23 TraesCS7A01G215600 chr1A 76437433 76438183 750 False 1216 1216 95.883 1 752 1 chr1A.!!$F1 751
24 TraesCS7A01G215600 chr1A 439992303 439993021 718 True 963 963 90.859 1692 2411 1 chr1A.!!$R1 719
25 TraesCS7A01G215600 chr4A 88078284 88079001 717 False 1088 1088 94.028 1693 2411 1 chr4A.!!$F2 718
26 TraesCS7A01G215600 chr4A 21297368 21298083 715 False 1050 1050 93.056 1692 2411 1 chr4A.!!$F1 719
27 TraesCS7A01G215600 chr4A 72654338 72655057 719 True 1048 1048 92.936 1692 2411 1 chr4A.!!$R1 719

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
706 709 1.153449 CCATCCGCCTTAGACGCAA 60.153 57.895 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2210 1.001503 CAGAGAGCACCTCCCCTCT 59.998 63.158 2.95 0.0 42.97 3.69 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
33 34 1.202687 TGTGTGGAGCTGGTTGAAGAG 60.203 52.381 0.00 0.00 0.00 2.85
46 47 3.302935 GGTTGAAGAGAAACGGTTCGAAC 60.303 47.826 20.14 20.14 38.90 3.95
166 168 1.855295 TTGCAGGGTCGGACACTATA 58.145 50.000 13.46 1.98 25.53 1.31
364 366 9.958180 TTGGACTATGAAGATACAAGATTGAAA 57.042 29.630 0.00 0.00 0.00 2.69
417 419 1.296715 CGTGGAAGGCAAGCTAGGT 59.703 57.895 0.00 0.00 0.00 3.08
475 477 3.329814 CCTTGTGTAACCCTAACCCTCTT 59.670 47.826 0.00 0.00 34.36 2.85
561 564 3.375699 CTTCTAGGGTTTAGCCTCTCCA 58.624 50.000 3.32 0.00 37.43 3.86
638 641 2.354103 GGACGTAGGGTTTTACCTCCAC 60.354 54.545 0.00 0.00 42.09 4.02
642 645 2.670019 AGGGTTTTACCTCCACCAAC 57.330 50.000 0.00 0.00 38.64 3.77
673 676 2.370849 ACCTGGGTAAAACATCGTGTCT 59.629 45.455 0.00 0.00 0.00 3.41
706 709 1.153449 CCATCCGCCTTAGACGCAA 60.153 57.895 0.00 0.00 0.00 4.85
1074 1079 4.059459 CGTCTTCGCACGGCACAC 62.059 66.667 0.00 0.00 36.07 3.82
1143 1148 4.451150 GACGAGCGGGTCATGGCA 62.451 66.667 8.06 0.00 36.91 4.92
1255 1260 4.309950 GGTTGGACAGGCGTCGGT 62.310 66.667 0.00 0.00 43.61 4.69
1307 1312 4.532126 TGTAGTTGAGAATGGTGGTGAGAT 59.468 41.667 0.00 0.00 0.00 2.75
1412 1420 1.005569 TGACGATGACTGGGAGTAGGT 59.994 52.381 0.00 0.00 0.00 3.08
1573 1589 3.404707 GCGCGCTGCATTTTTGCA 61.405 55.556 26.67 0.23 45.45 4.08
1576 1592 2.466788 CGCTGCATTTTTGCACGC 59.533 55.556 0.00 4.77 40.23 5.34
1578 1594 1.489824 GCTGCATTTTTGCACGCTG 59.510 52.632 12.14 0.00 40.23 5.18
1579 1595 1.489824 CTGCATTTTTGCACGCTGC 59.510 52.632 0.00 3.44 45.29 5.25
1591 1632 3.829975 CGCTGCATTTTTGCGCGG 61.830 61.111 20.79 5.51 45.83 6.46
1647 1688 4.811761 GATGGGCGCGCGACAAAC 62.812 66.667 39.18 23.54 0.00 2.93
1696 1737 3.549794 GCCTGTTGGAGATGCTCTAATT 58.450 45.455 0.00 0.00 33.81 1.40
2064 2111 7.069986 ACCTAGAAAGTCCTAATGCAGATCTA 58.930 38.462 0.00 0.00 0.00 1.98
2105 2152 2.971901 TACAGCCATAGATCCTCCGA 57.028 50.000 0.00 0.00 0.00 4.55
2125 2172 2.292292 GAGGAAAGTTGCTGCCGTTTTA 59.708 45.455 0.00 0.00 0.00 1.52
2163 2210 2.195567 GCAGCAGCCAAGGTTGACA 61.196 57.895 7.16 0.00 33.58 3.58
2189 2236 1.761784 GAGGTGCTCTCTGATGGTGAT 59.238 52.381 1.28 0.00 39.38 3.06
2237 2284 2.425668 GAGAGGAGGAAGACGAAGAAGG 59.574 54.545 0.00 0.00 0.00 3.46
2242 2289 1.834263 AGGAAGACGAAGAAGGGATGG 59.166 52.381 0.00 0.00 0.00 3.51
2257 2304 4.635473 AGGGATGGGAATGAGAAAGACTA 58.365 43.478 0.00 0.00 0.00 2.59
2349 2398 3.256558 GTTATCCAACTAAACGGACGCT 58.743 45.455 0.00 0.00 33.05 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.912366 GGTGATTGTTCGAACCGTTTC 58.088 47.619 24.78 15.58 0.00 2.78
46 47 2.484062 GGCCATGGCTCGGTGATTG 61.484 63.158 34.70 0.00 41.60 2.67
126 128 6.014242 TGCAAAATAAATTCCACATACCACCA 60.014 34.615 0.00 0.00 0.00 4.17
166 168 8.589338 ACATCACAGAAGAGTTTGAATACTAGT 58.411 33.333 0.00 0.00 0.00 2.57
417 419 6.620267 AGGAGGAGATATCCATATCCGTACTA 59.380 42.308 9.50 0.00 45.63 1.82
475 477 4.831155 CCCTCCGGTTTATATAGACACTGA 59.169 45.833 0.00 0.00 0.00 3.41
518 520 6.192970 AGCTAGCCTATGGTATGATTGTTT 57.807 37.500 12.13 0.00 0.00 2.83
561 564 5.186021 ACAAGAGTTGATCTACCACGAGATT 59.814 40.000 3.54 0.00 37.23 2.40
638 641 3.966543 AGGTTCGGGCCCTGTTGG 61.967 66.667 22.43 3.20 37.09 3.77
673 676 2.621070 GGATGGTAATAGGAGGCAGGA 58.379 52.381 0.00 0.00 0.00 3.86
833 838 3.709567 GGTAGCCCGACACTCCTT 58.290 61.111 0.00 0.00 0.00 3.36
874 879 0.106619 ATCTCCGAGTAGAACCGGCT 60.107 55.000 0.00 0.00 44.96 5.52
877 882 3.147629 ACCATATCTCCGAGTAGAACCG 58.852 50.000 0.00 0.00 0.00 4.44
1052 1057 4.717629 CCGTGCGAAGACGAGGCA 62.718 66.667 0.00 0.00 42.10 4.75
1097 1102 4.069232 CGAGGAGGCGGTTCTGCA 62.069 66.667 5.97 0.00 36.28 4.41
1143 1148 2.186826 GTGTTGTTGGCGCCACTCT 61.187 57.895 32.95 0.00 0.00 3.24
1232 1237 2.281484 GCCTGTCCAACCGCTCAA 60.281 61.111 0.00 0.00 0.00 3.02
1383 1388 2.223572 CCAGTCATCGTCATCGTCATCA 60.224 50.000 0.00 0.00 38.33 3.07
1412 1420 8.311836 AGATAAAAACTACTAGTGCAGCTACAA 58.688 33.333 5.39 0.00 0.00 2.41
1576 1592 2.431260 AGCCGCGCAAAAATGCAG 60.431 55.556 8.75 0.00 34.41 4.41
1578 1594 4.138109 GCAGCCGCGCAAAAATGC 62.138 61.111 8.75 6.25 0.00 3.56
1579 1595 2.431260 AGCAGCCGCGCAAAAATG 60.431 55.556 8.75 0.00 45.49 2.32
1671 1712 3.197790 CATCTCCAACAGGCGCCG 61.198 66.667 23.20 18.60 0.00 6.46
1672 1713 3.512516 GCATCTCCAACAGGCGCC 61.513 66.667 21.89 21.89 0.00 6.53
1696 1737 7.332557 TGCCGTCTTACTTTTCCTTATATGAA 58.667 34.615 0.00 0.00 0.00 2.57
2064 2111 2.175715 AGTGTTTCCCTTCTTGCTCCTT 59.824 45.455 0.00 0.00 0.00 3.36
2105 2152 1.111277 AAAACGGCAGCAACTTTCCT 58.889 45.000 0.00 0.00 0.00 3.36
2113 2160 1.164411 CAGTCCATAAAACGGCAGCA 58.836 50.000 0.00 0.00 0.00 4.41
2163 2210 1.001503 CAGAGAGCACCTCCCCTCT 59.998 63.158 2.95 0.00 42.97 3.69
2237 2284 4.745172 GCCTAGTCTTTCTCATTCCCATCC 60.745 50.000 0.00 0.00 0.00 3.51
2242 2289 2.205911 GCGCCTAGTCTTTCTCATTCC 58.794 52.381 0.00 0.00 0.00 3.01
2302 2349 7.067494 CCATTATTCAGGTCTTCCTCGATTTTT 59.933 37.037 0.00 0.00 43.07 1.94


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

AutoCloner maintained by Alex Coulton.