Multiple sequence alignment - TraesCS5B01G466500

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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 TraesCS5B01G466500 chr5B 100.000 2318 0 0 1 2318 640492730 640490413 0.000000e+00 4281.0
1 TraesCS5B01G466500 chr5B 81.604 212 23 8 667 875 655901516 655901318 6.630000e-36 161.0
2 TraesCS5B01G466500 chr5D 95.624 1394 57 4 925 2316 509651671 509650280 0.000000e+00 2233.0
3 TraesCS5B01G466500 chr5D 83.088 1496 188 39 861 2316 520580666 520579196 0.000000e+00 1301.0
4 TraesCS5B01G466500 chr5D 93.821 615 23 7 257 869 509652283 509651682 0.000000e+00 911.0
5 TraesCS5B01G466500 chr5D 92.996 257 15 3 1 255 509653084 509652829 2.810000e-99 372.0
6 TraesCS5B01G466500 chr5D 88.163 245 26 3 13 255 440361896 440362139 2.910000e-74 289.0
7 TraesCS5B01G466500 chr5D 80.980 347 59 7 970 1312 520421890 520421547 3.800000e-68 268.0
8 TraesCS5B01G466500 chr5D 83.951 162 15 3 714 875 520580830 520580680 6.680000e-31 145.0
9 TraesCS5B01G466500 chr5A 81.812 1490 186 38 869 2316 648771066 648769620 0.000000e+00 1171.0
10 TraesCS5B01G466500 chr5A 89.453 256 20 5 3 255 533345453 533345704 1.340000e-82 316.0
11 TraesCS5B01G466500 chr1D 83.258 890 119 18 1438 2313 440581280 440582153 0.000000e+00 791.0
12 TraesCS5B01G466500 chr1D 81.371 875 132 22 1444 2306 440570731 440571586 0.000000e+00 684.0
13 TraesCS5B01G466500 chr1D 80.158 887 146 25 1438 2313 440565865 440566732 9.030000e-179 636.0
14 TraesCS5B01G466500 chr1D 79.450 691 114 19 1633 2313 440575806 440576478 4.510000e-127 464.0
15 TraesCS5B01G466500 chr1A 83.032 884 125 21 1444 2316 537367910 537367041 0.000000e+00 778.0
16 TraesCS5B01G466500 chr1B 81.158 881 133 27 1444 2311 597930650 597931510 0.000000e+00 676.0
17 TraesCS5B01G466500 chr1B 80.159 882 143 23 1446 2313 598074885 598075748 4.200000e-177 630.0
18 TraesCS5B01G466500 chr1B 79.727 878 146 23 1444 2313 597935522 597936375 7.080000e-170 606.0
19 TraesCS5B01G466500 chr1B 79.682 881 144 25 1444 2310 597979066 597979925 9.160000e-169 603.0
20 TraesCS5B01G466500 chr1B 78.555 886 154 28 1441 2313 597953489 597954351 3.370000e-153 551.0
21 TraesCS5B01G466500 chr1B 81.541 688 101 18 1449 2126 598080431 598081102 5.630000e-151 544.0
22 TraesCS5B01G466500 chr6B 89.796 245 22 3 13 255 688597500 688597257 6.220000e-81 311.0
23 TraesCS5B01G466500 chr2B 88.327 257 26 4 2 255 729803445 729803190 2.890000e-79 305.0
24 TraesCS5B01G466500 chr4D 89.300 243 25 1 14 255 16717324 16717082 1.040000e-78 303.0
25 TraesCS5B01G466500 chr7D 87.938 257 27 3 3 255 618495430 618495174 1.350000e-77 300.0
26 TraesCS5B01G466500 chr7A 87.891 256 26 5 4 255 20953758 20954012 1.740000e-76 296.0
27 TraesCS5B01G466500 chr7A 91.589 107 9 0 769 875 28209343 28209237 5.160000e-32 148.0
28 TraesCS5B01G466500 chr2D 86.822 258 28 5 3 255 24220975 24221231 1.360000e-72 283.0
29 TraesCS5B01G466500 chr6D 94.872 39 1 1 360 397 8101576 8101538 2.490000e-05 60.2
30 TraesCS5B01G466500 chr6D 100.000 28 0 0 370 397 8101411 8101384 4.000000e-03 52.8


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 TraesCS5B01G466500 chr5B 640490413 640492730 2317 True 4281 4281 100.0000 1 2318 1 chr5B.!!$R1 2317
1 TraesCS5B01G466500 chr5D 509650280 509653084 2804 True 1172 2233 94.1470 1 2316 3 chr5D.!!$R2 2315
2 TraesCS5B01G466500 chr5D 520579196 520580830 1634 True 723 1301 83.5195 714 2316 2 chr5D.!!$R3 1602
3 TraesCS5B01G466500 chr5A 648769620 648771066 1446 True 1171 1171 81.8120 869 2316 1 chr5A.!!$R1 1447
4 TraesCS5B01G466500 chr1D 440581280 440582153 873 False 791 791 83.2580 1438 2313 1 chr1D.!!$F2 875
5 TraesCS5B01G466500 chr1D 440565865 440571586 5721 False 660 684 80.7645 1438 2313 2 chr1D.!!$F3 875
6 TraesCS5B01G466500 chr1D 440575806 440576478 672 False 464 464 79.4500 1633 2313 1 chr1D.!!$F1 680
7 TraesCS5B01G466500 chr1A 537367041 537367910 869 True 778 778 83.0320 1444 2316 1 chr1A.!!$R1 872
8 TraesCS5B01G466500 chr1B 597930650 597931510 860 False 676 676 81.1580 1444 2311 1 chr1B.!!$F1 867
9 TraesCS5B01G466500 chr1B 598074885 598075748 863 False 630 630 80.1590 1446 2313 1 chr1B.!!$F5 867
10 TraesCS5B01G466500 chr1B 597935522 597936375 853 False 606 606 79.7270 1444 2313 1 chr1B.!!$F2 869
11 TraesCS5B01G466500 chr1B 597979066 597979925 859 False 603 603 79.6820 1444 2310 1 chr1B.!!$F4 866
12 TraesCS5B01G466500 chr1B 597953489 597954351 862 False 551 551 78.5550 1441 2313 1 chr1B.!!$F3 872
13 TraesCS5B01G466500 chr1B 598080431 598081102 671 False 544 544 81.5410 1449 2126 1 chr1B.!!$F6 677

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
887 1465 0.250858 CGATGGCATGCATCCCCTAA 60.251 55.0 21.36 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 2311 5.215252 TCACTGTTTCGAAGAATTCCTCT 57.785 39.13 0.65 0.0 43.81 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
72 75 1.669115 CACCTGTGCCTGAACTCCG 60.669 63.158 0.00 0.00 0.00 4.63
79 82 2.903547 GCCTGAACTCCGCGCAAAA 61.904 57.895 8.75 0.00 0.00 2.44
101 104 3.392769 TTTGTGAACTTTGGACGTTCG 57.607 42.857 0.00 0.00 42.73 3.95
160 163 6.638468 GTCTGAGAAACTTTTGAAAATCGCAT 59.362 34.615 0.00 0.00 0.00 4.73
168 171 5.809562 ACTTTTGAAAATCGCATTGTTCACA 59.190 32.000 0.00 0.00 30.00 3.58
172 175 4.517075 TGAAAATCGCATTGTTCACACCTA 59.483 37.500 0.00 0.00 0.00 3.08
178 181 5.218885 TCGCATTGTTCACACCTAATTTTG 58.781 37.500 0.00 0.00 0.00 2.44
203 206 2.662006 TTTGTCATGAGCTCCTCGAG 57.338 50.000 12.15 5.13 32.35 4.04
248 251 2.029844 GGAGTTCACGCACAGGAGC 61.030 63.158 0.00 0.00 0.00 4.70
318 865 7.017056 ACATGGATTTTAAAAGGGTTCATGGAA 59.983 33.333 18.87 0.00 35.25 3.53
320 867 8.671987 TGGATTTTAAAAGGGTTCATGGAATA 57.328 30.769 6.79 0.00 0.00 1.75
388 936 8.479313 AAGTTCCTGAATTTGAAAAAGTTCAC 57.521 30.769 0.00 0.00 43.52 3.18
523 1072 8.303156 ACAAAAGAAAAAGGAAACAAAAATGGG 58.697 29.630 0.00 0.00 0.00 4.00
527 1076 8.821686 AGAAAAAGGAAACAAAAATGGGAAAT 57.178 26.923 0.00 0.00 0.00 2.17
618 1167 5.339008 AGAACCAGAACAAAAACTTTCCC 57.661 39.130 0.00 0.00 0.00 3.97
730 1279 5.280011 CCTTCTACCTTAAGCACCAAAGAGA 60.280 44.000 0.00 0.00 0.00 3.10
755 1304 2.234414 GTGTGTACCTTATTCCGTCCCA 59.766 50.000 0.00 0.00 0.00 4.37
784 1333 1.012486 CGTGGTTAGGCCGAGAACAC 61.012 60.000 16.78 14.69 41.21 3.32
875 1424 5.010112 TCAACAATTAAAAAGGTCGATGGCA 59.990 36.000 0.00 0.00 0.00 4.92
879 1428 1.255882 AAAAAGGTCGATGGCATGCA 58.744 45.000 21.36 6.13 0.00 3.96
887 1465 0.250858 CGATGGCATGCATCCCCTAA 60.251 55.000 21.36 0.00 0.00 2.69
889 1467 2.356022 CGATGGCATGCATCCCCTAATA 60.356 50.000 21.36 0.00 0.00 0.98
899 1477 3.197983 GCATCCCCTAATACGCCTCTATT 59.802 47.826 0.00 0.00 0.00 1.73
905 1483 5.116882 CCCTAATACGCCTCTATTATTGGC 58.883 45.833 0.00 0.00 42.94 4.52
918 1496 7.141758 TCTATTATTGGCCTCTCAATTCACT 57.858 36.000 3.32 0.00 38.24 3.41
923 1501 1.003580 GGCCTCTCAATTCACTGGACA 59.996 52.381 0.00 0.00 0.00 4.02
966 1546 1.557269 CCAACTCCCCACTCCCAGAG 61.557 65.000 0.00 0.00 35.52 3.35
1169 1749 1.157870 AAACACGAGGTTGTGCTCCG 61.158 55.000 0.00 0.00 43.74 4.63
1221 1801 4.719369 GCAGCCGTCGACCGTTCT 62.719 66.667 10.58 0.00 33.66 3.01
1242 1822 1.122019 ACGGACAGCTCAGGGAGTTT 61.122 55.000 0.00 0.00 31.39 2.66
1245 1825 0.250467 GACAGCTCAGGGAGTTTGCA 60.250 55.000 0.00 0.00 31.39 4.08
1252 1832 1.464198 AGGGAGTTTGCAGGGAGGT 60.464 57.895 0.00 0.00 0.00 3.85
1298 1878 9.923143 CATCAAGTATATCGTGGAAAGGTATTA 57.077 33.333 0.00 0.00 0.00 0.98
1485 2069 2.944349 GGAGTCCCTACTGTAACTCTCG 59.056 54.545 14.47 0.00 38.52 4.04
1580 2166 4.597004 AGTCTTCTTGGACATTGCATCAT 58.403 39.130 0.00 0.00 38.57 2.45
1720 2311 4.402155 CCAAATACTCCAATAGCCAGCAAA 59.598 41.667 0.00 0.00 0.00 3.68
1725 2316 1.915489 TCCAATAGCCAGCAAAGAGGA 59.085 47.619 0.00 0.00 0.00 3.71
1732 2323 3.087781 AGCCAGCAAAGAGGAATTCTTC 58.912 45.455 9.47 9.47 45.41 2.87
1769 2361 4.384465 AGTATCTCCCTTTCCCTTCCATT 58.616 43.478 0.00 0.00 0.00 3.16
2306 7802 5.612725 ATCTTTCCTGAAGAGTCTCATCC 57.387 43.478 1.94 0.00 46.99 3.51
2316 7812 5.186021 TGAAGAGTCTCATCCTTCCACTTAC 59.814 44.000 1.94 0.00 36.41 2.34
2317 7813 4.027437 AGAGTCTCATCCTTCCACTTACC 58.973 47.826 1.94 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 75 4.027724 CCAAAGTTCACAAAATTTTGCGC 58.972 39.130 26.94 15.67 41.79 6.09
79 82 4.095185 TCGAACGTCCAAAGTTCACAAAAT 59.905 37.500 9.33 0.00 45.93 1.82
89 92 0.038159 AGCTCCTCGAACGTCCAAAG 60.038 55.000 0.00 0.00 0.00 2.77
101 104 2.629002 TTTTTGCCACGAGCTCCTC 58.371 52.632 8.47 0.00 44.23 3.71
120 123 1.895798 TCAGACATCCGCAGTTTCTCT 59.104 47.619 0.00 0.00 0.00 3.10
121 124 2.094494 TCTCAGACATCCGCAGTTTCTC 60.094 50.000 0.00 0.00 0.00 2.87
122 125 1.895798 TCTCAGACATCCGCAGTTTCT 59.104 47.619 0.00 0.00 0.00 2.52
123 126 2.370281 TCTCAGACATCCGCAGTTTC 57.630 50.000 0.00 0.00 0.00 2.78
126 129 1.620819 AGTTTCTCAGACATCCGCAGT 59.379 47.619 0.00 0.00 0.00 4.40
127 130 2.376808 AGTTTCTCAGACATCCGCAG 57.623 50.000 0.00 0.00 0.00 5.18
129 132 3.498397 TCAAAAGTTTCTCAGACATCCGC 59.502 43.478 0.00 0.00 0.00 5.54
130 133 5.673337 TTCAAAAGTTTCTCAGACATCCG 57.327 39.130 0.00 0.00 0.00 4.18
203 206 6.020984 GCAAAATTTTGTGAAGTTTGGACAC 58.979 36.000 27.13 6.29 40.24 3.67
248 251 4.764679 TCAAATCCGTGGAAACAAGATG 57.235 40.909 0.00 0.00 46.06 2.90
255 258 4.392921 TGCTTTTTCAAATCCGTGGAAA 57.607 36.364 0.00 0.00 0.00 3.13
292 839 6.500049 TCCATGAACCCTTTTAAAATCCATGT 59.500 34.615 0.09 0.00 0.00 3.21
371 919 6.704819 ACAATGCGTGAACTTTTTCAAATTC 58.295 32.000 0.00 0.00 43.52 2.17
388 936 1.850377 TTTCAAAGCCACACAATGCG 58.150 45.000 0.00 0.00 0.00 4.73
400 948 7.138692 TCAAACCCACAAACATTTTTCAAAG 57.861 32.000 0.00 0.00 0.00 2.77
601 1150 6.713792 TTTTTCGGGAAAGTTTTTGTTCTG 57.286 33.333 0.00 0.00 0.00 3.02
626 1175 2.593956 GGCCGGTTTCTCTCTGGGT 61.594 63.158 1.90 0.00 32.41 4.51
755 1304 0.536460 CCTAACCACGTGCCAACCTT 60.536 55.000 10.91 0.00 0.00 3.50
768 1317 0.458025 CTCGTGTTCTCGGCCTAACC 60.458 60.000 0.00 0.00 0.00 2.85
784 1333 2.450479 AAACCAAGGGCGGTCTCTCG 62.450 60.000 0.00 0.00 38.76 4.04
875 1424 1.279271 GAGGCGTATTAGGGGATGCAT 59.721 52.381 0.00 0.00 0.00 3.96
879 1428 6.099845 CCAATAATAGAGGCGTATTAGGGGAT 59.900 42.308 12.29 0.00 30.56 3.85
899 1477 3.523157 TCCAGTGAATTGAGAGGCCAATA 59.477 43.478 5.01 0.00 35.86 1.90
905 1483 3.007290 TCAGTGTCCAGTGAATTGAGAGG 59.993 47.826 2.36 0.00 37.79 3.69
918 1496 5.883115 TGAAAACAGTAATTGTCAGTGTCCA 59.117 36.000 0.00 0.00 39.73 4.02
923 1501 7.122055 TGGAAACTGAAAACAGTAATTGTCAGT 59.878 33.333 5.65 5.65 41.51 3.41
1169 1749 1.078143 AGGACAGCATCGCCCTTTC 60.078 57.895 0.00 0.00 0.00 2.62
1221 1801 1.979155 CTCCCTGAGCTGTCCGTCA 60.979 63.158 0.00 0.00 0.00 4.35
1242 1822 0.257328 TGACAAACAACCTCCCTGCA 59.743 50.000 0.00 0.00 0.00 4.41
1245 1825 0.179029 CGGTGACAAACAACCTCCCT 60.179 55.000 0.00 0.00 31.55 4.20
1252 1832 2.143122 GAGCTCATCGGTGACAAACAA 58.857 47.619 9.40 0.00 0.00 2.83
1485 2069 9.730420 GTACATGTCCCACAAATATTAATGAAC 57.270 33.333 0.00 0.00 0.00 3.18
1580 2166 3.089284 GGCCAAGCTAGCTTAAAGGAAA 58.911 45.455 28.87 0.00 34.50 3.13
1720 2311 5.215252 TCACTGTTTCGAAGAATTCCTCT 57.785 39.130 0.65 0.00 43.81 3.69
1725 2316 7.264373 ACTCAATTCACTGTTTCGAAGAATT 57.736 32.000 13.56 13.56 45.90 2.17
1732 2323 5.292101 GGGAGATACTCAATTCACTGTTTCG 59.708 44.000 0.00 0.00 31.08 3.46
2034 2633 8.618240 TCTGGAACTTATTGGAAATCTACCTA 57.382 34.615 0.00 0.00 0.00 3.08
2093 2693 5.507985 GCAAAGACACTTGGCAGTTCTATTT 60.508 40.000 6.06 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.