Multiple sequence alignment - TraesCS7D01G469500

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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 TraesCS7D01G469500 chr7D 100.000 2402 0 0 1 2402 582651787 582649386 0.000000e+00 4436
1 TraesCS7D01G469500 chr7D 97.961 2403 29 4 1 2402 582546313 582543930 0.000000e+00 4148
2 TraesCS7D01G469500 chr7D 89.255 1182 89 16 483 1640 582748408 582747241 0.000000e+00 1445
3 TraesCS7D01G469500 chr7D 88.352 352 39 2 216 566 582745421 582745071 2.850000e-114 422
4 TraesCS7D01G469500 chr7D 88.509 322 20 7 436 740 582662729 582662408 8.110000e-100 374
5 TraesCS7D01G469500 chr7D 87.888 322 22 7 436 740 582557554 582557233 1.760000e-96 363
6 TraesCS7D01G469500 chr7D 86.634 202 26 1 237 437 582756226 582756025 3.110000e-54 222
7 TraesCS7D01G469500 chr7B 92.003 1488 93 15 441 1910 650456189 650454710 0.000000e+00 2065
8 TraesCS7D01G469500 chr7B 91.550 1503 87 15 441 1910 650409449 650407954 0.000000e+00 2036
9 TraesCS7D01G469500 chr7B 91.423 1504 88 16 441 1910 650362466 650360970 0.000000e+00 2025
10 TraesCS7D01G469500 chr7B 91.270 1512 83 19 441 1910 650295275 650293771 0.000000e+00 2015
11 TraesCS7D01G469500 chr7B 91.090 1504 93 16 441 1910 650318194 650316698 0.000000e+00 1997
12 TraesCS7D01G469500 chr7B 90.622 1173 68 19 441 1578 650301422 650300257 0.000000e+00 1519
13 TraesCS7D01G469500 chr7B 94.758 496 22 3 1908 2402 650284449 650283957 0.000000e+00 769
14 TraesCS7D01G469500 chr7B 94.512 492 23 3 1912 2402 650351958 650351470 0.000000e+00 756
15 TraesCS7D01G469500 chr7B 93.952 496 26 3 1908 2402 650307505 650307013 0.000000e+00 747
16 TraesCS7D01G469500 chr7B 92.771 498 30 4 1908 2402 650382432 650381938 0.000000e+00 715
17 TraesCS7D01G469500 chr7B 92.771 498 30 4 1908 2402 650430107 650429613 0.000000e+00 715
18 TraesCS7D01G469500 chr7B 95.131 267 11 1 1912 2178 650398468 650398204 1.030000e-113 420
19 TraesCS7D01G469500 chr7A 89.101 1679 130 31 3 1639 674738788 674737121 0.000000e+00 2037
20 TraesCS7D01G469500 chr7A 90.512 1328 105 13 323 1639 674753172 674751855 0.000000e+00 1735
21 TraesCS7D01G469500 chr7A 85.880 1636 156 42 210 1798 674506947 674505340 0.000000e+00 1672
22 TraesCS7D01G469500 chr7A 88.818 626 45 12 214 821 674523203 674522585 0.000000e+00 745
23 TraesCS7D01G469500 chr7A 88.291 632 48 13 210 823 674527476 674526853 0.000000e+00 734
24 TraesCS7D01G469500 chr7A 84.615 338 21 15 3 310 674759087 674758751 8.340000e-80 307
25 TraesCS7D01G469500 chr7A 82.951 305 26 11 1787 2084 674503453 674503168 3.960000e-63 252
26 TraesCS7D01G469500 chr7A 85.345 232 15 5 2186 2400 674503160 674502931 3.110000e-54 222
27 TraesCS7D01G469500 chrUn 94.883 469 17 1 1449 1910 388900209 388900677 0.000000e+00 726
28 TraesCS7D01G469500 chrUn 94.883 469 17 1 1449 1910 388901873 388902341 0.000000e+00 726
29 TraesCS7D01G469500 chrUn 92.771 498 30 4 1908 2402 377681250 377681744 0.000000e+00 715


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 TraesCS7D01G469500 chr7D 582649386 582651787 2401 True 4436.000000 4436 100.000000 1 2402 1 chr7D.!!$R3 2401
1 TraesCS7D01G469500 chr7D 582543930 582546313 2383 True 4148.000000 4148 97.961000 1 2402 1 chr7D.!!$R1 2401
2 TraesCS7D01G469500 chr7D 582745071 582748408 3337 True 933.500000 1445 88.803500 216 1640 2 chr7D.!!$R6 1424
3 TraesCS7D01G469500 chr7B 650454710 650456189 1479 True 2065.000000 2065 92.003000 441 1910 1 chr7B.!!$R12 1469
4 TraesCS7D01G469500 chr7B 650407954 650409449 1495 True 2036.000000 2036 91.550000 441 1910 1 chr7B.!!$R10 1469
5 TraesCS7D01G469500 chr7B 650360970 650362466 1496 True 2025.000000 2025 91.423000 441 1910 1 chr7B.!!$R7 1469
6 TraesCS7D01G469500 chr7B 650293771 650295275 1504 True 2015.000000 2015 91.270000 441 1910 1 chr7B.!!$R2 1469
7 TraesCS7D01G469500 chr7B 650316698 650318194 1496 True 1997.000000 1997 91.090000 441 1910 1 chr7B.!!$R5 1469
8 TraesCS7D01G469500 chr7B 650300257 650301422 1165 True 1519.000000 1519 90.622000 441 1578 1 chr7B.!!$R3 1137
9 TraesCS7D01G469500 chr7A 674737121 674738788 1667 True 2037.000000 2037 89.101000 3 1639 1 chr7A.!!$R1 1636
10 TraesCS7D01G469500 chr7A 674751855 674753172 1317 True 1735.000000 1735 90.512000 323 1639 1 chr7A.!!$R2 1316
11 TraesCS7D01G469500 chr7A 674522585 674527476 4891 True 739.500000 745 88.554500 210 823 2 chr7A.!!$R5 613
12 TraesCS7D01G469500 chr7A 674502931 674506947 4016 True 715.333333 1672 84.725333 210 2400 3 chr7A.!!$R4 2190
13 TraesCS7D01G469500 chrUn 388900209 388902341 2132 False 726.000000 726 94.883000 1449 1910 2 chrUn.!!$F2 461

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
957 5294 0.179 ACCATCCCGAGCTAGCAAAG 59.821 55.0 18.83 7.31 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 9571 3.61004 TTGAAGCTGACATATCACGGT 57.39 42.857 0.0 0.0 0.0 4.83 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
91 97 1.203287 CACATCTTCCTCTCTCGTGCA 59.797 52.381 0.00 0.00 0.00 4.57
293 325 4.796231 CCCCGCTTGTCCTCGTCG 62.796 72.222 0.00 0.00 0.00 5.12
504 538 6.640092 GCCAGTATAATAAACCAGAGTACGAC 59.360 42.308 0.00 0.00 0.00 4.34
585 4890 1.066787 TGATGATCACGGTTACGCCAA 60.067 47.619 0.00 0.00 46.04 4.52
945 5282 2.325484 ACAACCCAAGAAAACCATCCC 58.675 47.619 0.00 0.00 0.00 3.85
946 5283 1.272212 CAACCCAAGAAAACCATCCCG 59.728 52.381 0.00 0.00 0.00 5.14
947 5284 0.774908 ACCCAAGAAAACCATCCCGA 59.225 50.000 0.00 0.00 0.00 5.14
948 5285 1.271926 ACCCAAGAAAACCATCCCGAG 60.272 52.381 0.00 0.00 0.00 4.63
949 5286 0.811281 CCAAGAAAACCATCCCGAGC 59.189 55.000 0.00 0.00 0.00 5.03
950 5287 1.614317 CCAAGAAAACCATCCCGAGCT 60.614 52.381 0.00 0.00 0.00 4.09
951 5288 2.355716 CCAAGAAAACCATCCCGAGCTA 60.356 50.000 0.00 0.00 0.00 3.32
952 5289 2.939103 CAAGAAAACCATCCCGAGCTAG 59.061 50.000 0.00 0.00 0.00 3.42
953 5290 1.134371 AGAAAACCATCCCGAGCTAGC 60.134 52.381 6.62 6.62 0.00 3.42
954 5291 0.618458 AAAACCATCCCGAGCTAGCA 59.382 50.000 18.83 0.00 0.00 3.49
955 5292 0.618458 AAACCATCCCGAGCTAGCAA 59.382 50.000 18.83 0.00 0.00 3.91
956 5293 0.618458 AACCATCCCGAGCTAGCAAA 59.382 50.000 18.83 0.00 0.00 3.68
957 5294 0.179000 ACCATCCCGAGCTAGCAAAG 59.821 55.000 18.83 7.31 0.00 2.77
1180 5537 4.560743 TGAAGCTGGGCGTGTGCA 62.561 61.111 0.00 0.00 45.35 4.57
1402 5759 0.393537 CTTCACCTGCCCCATCTGAC 60.394 60.000 0.00 0.00 0.00 3.51
1966 8279 7.450014 TGCCACCTTTTATCTTGATTTGTTAGA 59.550 33.333 0.00 0.00 0.00 2.10
2363 9571 8.138712 AGTTTGTTCAACTTGTGTTAACTTGAA 58.861 29.630 13.14 13.14 43.89 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 97 2.609921 GGAGGGGGAGGAACCGTT 60.610 66.667 0.00 0.00 40.11 4.44
293 325 3.008049 AGGGTTATGTGAGAGGTGACAAC 59.992 47.826 0.00 0.00 0.00 3.32
504 538 8.707938 TTGATTCCATGCGTCTATTATATCTG 57.292 34.615 0.00 0.00 0.00 2.90
585 4890 1.517257 GCATGACAGCGCTACGAGT 60.517 57.895 10.99 2.89 0.00 4.18
946 5283 2.679349 AGCTTGTAGGCTTTGCTAGCTC 60.679 50.000 17.23 2.43 44.40 4.09
956 5293 0.984230 TGTGGCTAAGCTTGTAGGCT 59.016 50.000 19.95 0.00 44.78 4.58
957 5294 1.066143 TCTGTGGCTAAGCTTGTAGGC 60.066 52.381 9.86 12.52 44.75 3.93
958 5295 2.622436 GTCTGTGGCTAAGCTTGTAGG 58.378 52.381 9.86 0.00 0.00 3.18
959 5296 2.028112 TGGTCTGTGGCTAAGCTTGTAG 60.028 50.000 9.86 0.00 0.00 2.74
960 5297 1.974957 TGGTCTGTGGCTAAGCTTGTA 59.025 47.619 9.86 0.00 0.00 2.41
961 5298 0.764890 TGGTCTGTGGCTAAGCTTGT 59.235 50.000 9.86 0.00 0.00 3.16
1068 5425 3.161450 GGCGGGCAGTAGGATCCA 61.161 66.667 15.82 0.00 0.00 3.41
1180 5537 2.029073 CAGGTTCAGCACGTCGGT 59.971 61.111 0.00 0.00 0.00 4.69
1183 5540 0.880278 TTCAGCAGGTTCAGCACGTC 60.880 55.000 0.00 0.00 0.00 4.34
1212 5569 3.220999 CTCGTTCTCCGGCACACCA 62.221 63.158 0.00 0.00 37.11 4.17
1402 5759 1.134128 TCATCGATGGTGTTGGATGGG 60.134 52.381 24.61 0.00 37.47 4.00
2202 8683 7.039082 TCACAACTAGCTGCCATATATATCACA 60.039 37.037 0.00 0.00 0.00 3.58
2363 9571 3.610040 TTGAAGCTGACATATCACGGT 57.390 42.857 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.