Multiple sequence alignment - TraesCS7A01G284400

Loading Multiple Alignment...

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 TraesCS7A01G284400 chr7A 100.000 3396 0 0 1 3396 321637833 321634438 0.000000e+00 6272
1 TraesCS7A01G284400 chr7A 88.112 143 14 2 2317 2459 282333433 282333572 2.100000e-37 167
2 TraesCS7A01G284400 chr7A 83.036 112 16 1 2344 2455 425836846 425836738 7.760000e-17 99
3 TraesCS7A01G284400 chr4B 93.052 1468 52 17 1955 3396 16787988 16789431 0.000000e+00 2100
4 TraesCS7A01G284400 chr4B 96.549 1072 24 4 910 1969 16786875 16787945 0.000000e+00 1762
5 TraesCS7A01G284400 chr4B 96.017 929 32 5 1 926 16783319 16784245 0.000000e+00 1506
6 TraesCS7A01G284400 chr3B 92.916 1468 54 18 1955 3396 555549811 555548368 0.000000e+00 2089
7 TraesCS7A01G284400 chr3B 96.549 1072 24 4 910 1969 555550924 555549854 0.000000e+00 1762
8 TraesCS7A01G284400 chr3B 96.108 925 32 4 1 923 555554233 555553311 0.000000e+00 1506
9 TraesCS7A01G284400 chr3B 90.398 427 29 6 3 428 254463136 254463551 4.950000e-153 551
10 TraesCS7A01G284400 chr3D 89.135 1491 77 22 1955 3396 16449903 16451357 0.000000e+00 1777
11 TraesCS7A01G284400 chr3D 97.109 588 16 1 1383 1969 16449271 16449858 0.000000e+00 990
12 TraesCS7A01G284400 chr3D 93.511 524 29 5 405 926 16446522 16447042 0.000000e+00 774
13 TraesCS7A01G284400 chr3D 96.341 410 14 1 1 409 16432538 16432947 0.000000e+00 673
14 TraesCS7A01G284400 chr4A 92.834 1214 50 15 2209 3396 729644473 729643271 0.000000e+00 1725
15 TraesCS7A01G284400 chr4A 96.555 929 27 5 1 926 729648352 729647426 0.000000e+00 1533
16 TraesCS7A01G284400 chr4A 96.087 460 13 2 910 1365 729644925 729644467 0.000000e+00 745
17 TraesCS7A01G284400 chr4A 88.722 133 12 2 2317 2449 575685871 575686000 3.510000e-35 159
18 TraesCS7A01G284400 chr7D 95.802 1072 29 6 910 1969 446551446 446550379 0.000000e+00 1716
19 TraesCS7A01G284400 chr7D 90.356 954 41 9 1955 2862 446550334 446549386 0.000000e+00 1205
20 TraesCS7A01G284400 chr7D 93.504 508 31 1 2891 3396 446549385 446548878 0.000000e+00 754
21 TraesCS7A01G284400 chr7D 91.171 521 42 4 1 520 469636687 469636170 0.000000e+00 704
22 TraesCS7A01G284400 chr7D 89.223 399 30 4 519 916 469636245 469635859 1.420000e-133 486
23 TraesCS7A01G284400 chr2A 94.963 1072 38 6 910 1969 46336423 46337490 0.000000e+00 1666
24 TraesCS7A01G284400 chr2A 94.409 930 47 5 1 926 46333022 46333950 0.000000e+00 1424
25 TraesCS7A01G284400 chr2A 90.832 938 48 14 1955 2862 46337535 46338464 0.000000e+00 1221
26 TraesCS7A01G284400 chr2A 80.351 1140 141 54 2317 3395 375041088 375042205 0.000000e+00 787
27 TraesCS7A01G284400 chr2A 93.504 508 31 1 2891 3396 46338465 46338972 0.000000e+00 754
28 TraesCS7A01G284400 chr2A 82.775 836 91 22 1155 1969 632588080 632587277 0.000000e+00 697
29 TraesCS7A01G284400 chr2A 91.709 398 33 0 519 916 594379107 594378710 1.380000e-153 553
30 TraesCS7A01G284400 chr2A 91.589 214 17 1 910 1123 631856231 631856443 9.220000e-76 294
31 TraesCS7A01G284400 chr6B 96.204 685 16 6 1 676 247038169 247037486 0.000000e+00 1112
32 TraesCS7A01G284400 chr6B 96.462 537 14 2 910 1442 247035639 247035104 0.000000e+00 881
33 TraesCS7A01G284400 chr5A 95.738 657 24 2 260 915 606397519 606396866 0.000000e+00 1055
34 TraesCS7A01G284400 chr2D 83.967 1104 112 32 912 1969 486391405 486392489 0.000000e+00 998
35 TraesCS7A01G284400 chr2D 85.008 647 75 8 1158 1787 487933467 487932826 3.700000e-179 638
36 TraesCS7A01G284400 chr2D 84.000 150 15 7 1823 1969 487932818 487932675 5.910000e-28 135
37 TraesCS7A01G284400 chr6A 84.043 846 108 18 2546 3375 25067676 25068510 0.000000e+00 789
38 TraesCS7A01G284400 chr1D 80.000 1130 153 46 2317 3395 339095559 339094452 0.000000e+00 767
39 TraesCS7A01G284400 chrUn 91.985 524 33 6 1452 1969 195337988 195338508 0.000000e+00 726
40 TraesCS7A01G284400 chrUn 96.209 422 15 1 159 579 476762514 476762935 0.000000e+00 689
41 TraesCS7A01G284400 chrUn 92.237 438 29 2 1452 1886 40175628 40175193 1.730000e-172 616
42 TraesCS7A01G284400 chrUn 91.971 411 25 6 910 1317 40176034 40175629 1.370000e-158 569
43 TraesCS7A01G284400 chrUn 92.231 399 26 4 910 1308 195337582 195337975 8.230000e-156 560
44 TraesCS7A01G284400 chrUn 86.104 403 23 12 1960 2336 40170330 40169935 1.470000e-108 403
45 TraesCS7A01G284400 chrUn 86.104 403 23 12 1960 2336 422925746 422926141 1.470000e-108 403
46 TraesCS7A01G284400 chrUn 89.535 258 15 8 2084 2336 431172399 431172649 1.970000e-82 316
47 TraesCS7A01G284400 chrUn 86.486 259 11 5 1959 2193 195338557 195338815 2.600000e-66 263
48 TraesCS7A01G284400 chr3A 90.787 521 44 4 1 520 640036085 640035568 0.000000e+00 693
49 TraesCS7A01G284400 chr3A 89.447 398 35 2 519 916 640035643 640035253 2.350000e-136 496
50 TraesCS7A01G284400 chr2B 90.265 226 19 3 910 1134 572313330 572313107 3.310000e-75 292
51 TraesCS7A01G284400 chr2B 85.217 230 18 6 1960 2188 571347779 571347993 4.410000e-54 222


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 TraesCS7A01G284400 chr7A 321634438 321637833 3395 True 6272.000000 6272 100.000000 1 3396 1 chr7A.!!$R1 3395
1 TraesCS7A01G284400 chr4B 16783319 16789431 6112 False 1789.333333 2100 95.206000 1 3396 3 chr4B.!!$F1 3395
2 TraesCS7A01G284400 chr3B 555548368 555554233 5865 True 1785.666667 2089 95.191000 1 3396 3 chr3B.!!$R1 3395
3 TraesCS7A01G284400 chr3D 16446522 16451357 4835 False 1180.333333 1777 93.251667 405 3396 3 chr3D.!!$F2 2991
4 TraesCS7A01G284400 chr4A 729643271 729648352 5081 True 1334.333333 1725 95.158667 1 3396 3 chr4A.!!$R1 3395
5 TraesCS7A01G284400 chr7D 446548878 446551446 2568 True 1225.000000 1716 93.220667 910 3396 3 chr7D.!!$R1 2486
6 TraesCS7A01G284400 chr7D 469635859 469636687 828 True 595.000000 704 90.197000 1 916 2 chr7D.!!$R2 915
7 TraesCS7A01G284400 chr2A 46333022 46338972 5950 False 1266.250000 1666 93.427000 1 3396 4 chr2A.!!$F3 3395
8 TraesCS7A01G284400 chr2A 375041088 375042205 1117 False 787.000000 787 80.351000 2317 3395 1 chr2A.!!$F1 1078
9 TraesCS7A01G284400 chr2A 632587277 632588080 803 True 697.000000 697 82.775000 1155 1969 1 chr2A.!!$R2 814
10 TraesCS7A01G284400 chr6B 247035104 247038169 3065 True 996.500000 1112 96.333000 1 1442 2 chr6B.!!$R1 1441
11 TraesCS7A01G284400 chr5A 606396866 606397519 653 True 1055.000000 1055 95.738000 260 915 1 chr5A.!!$R1 655
12 TraesCS7A01G284400 chr2D 486391405 486392489 1084 False 998.000000 998 83.967000 912 1969 1 chr2D.!!$F1 1057
13 TraesCS7A01G284400 chr2D 487932675 487933467 792 True 386.500000 638 84.504000 1158 1969 2 chr2D.!!$R1 811
14 TraesCS7A01G284400 chr6A 25067676 25068510 834 False 789.000000 789 84.043000 2546 3375 1 chr6A.!!$F1 829
15 TraesCS7A01G284400 chr1D 339094452 339095559 1107 True 767.000000 767 80.000000 2317 3395 1 chr1D.!!$R1 1078
16 TraesCS7A01G284400 chrUn 40175193 40176034 841 True 592.500000 616 92.104000 910 1886 2 chrUn.!!$R2 976
17 TraesCS7A01G284400 chrUn 195337582 195338815 1233 False 516.333333 726 90.234000 910 2193 3 chrUn.!!$F4 1283
18 TraesCS7A01G284400 chr3A 640035253 640036085 832 True 594.500000 693 90.117000 1 916 2 chr3A.!!$R1 915

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
239 248 0.831711 TGTCCTGTAGCAGAGCCACA 60.832 55.0 0.00 0.00 32.44 4.17 F
1049 4297 0.990282 AGCATACTGCCCTGGGATGT 60.990 55.0 19.27 16.02 46.52 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1221 4512 0.108186 TCGTACTGCTGCTTGATGGG 60.108 55.000 0.0 0.0 0.00 4.00 R
2719 6223 1.069596 CTTGGCCCAAACACAAGCC 59.930 57.895 0.0 0.0 45.96 4.35 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
125 134 3.490761 GCACATACACAAGTTTGTTGGCT 60.491 43.478 0.00 0.00 39.91 4.75
156 165 2.640989 CACTCGTGGTCGTCGGAA 59.359 61.111 0.00 0.00 38.33 4.30
239 248 0.831711 TGTCCTGTAGCAGAGCCACA 60.832 55.000 0.00 0.00 32.44 4.17
345 355 3.451178 ACGCCTATTTCTGCTTCCTTCTA 59.549 43.478 0.00 0.00 0.00 2.10
431 441 6.154203 TGATGGCTTTTTGTGACATGTTTA 57.846 33.333 0.00 0.00 0.00 2.01
489 499 5.573337 AAAGAGCATGAGTTTTGATAGGC 57.427 39.130 0.00 0.00 0.00 3.93
492 502 4.880696 AGAGCATGAGTTTTGATAGGCTTC 59.119 41.667 0.00 0.00 0.00 3.86
693 851 6.843069 ATTTGTTTGGTTTGCTGTATTGTC 57.157 33.333 0.00 0.00 0.00 3.18
716 874 8.274322 TGTCATGACCATCAGAAATTACCTATT 58.726 33.333 22.85 0.00 0.00 1.73
750 908 9.695526 TTCGTACTGTTAAATTTAGTTCTAGCA 57.304 29.630 0.00 0.00 0.00 3.49
767 925 2.474112 AGCAACCCCGAGGAAGTAATA 58.526 47.619 0.00 0.00 36.73 0.98
775 933 5.605488 ACCCCGAGGAAGTAATATGTTGTAT 59.395 40.000 0.00 0.00 36.73 2.29
882 1042 7.784633 TTTTGGAAATTTTGATCAACACTCC 57.215 32.000 7.89 11.82 0.00 3.85
956 4204 3.441572 GCATGTGAAAGTGGCAGTATCTT 59.558 43.478 0.00 0.00 0.00 2.40
976 4224 4.462483 TCTTTTGAGGGATTAATGCCACAC 59.538 41.667 25.87 16.81 38.45 3.82
1049 4297 0.990282 AGCATACTGCCCTGGGATGT 60.990 55.000 19.27 16.02 46.52 3.06
1058 4306 1.834188 CCCTGGGATGTAAACACCAC 58.166 55.000 7.01 0.00 0.00 4.16
1221 4512 6.706270 TGAAACTCACAATCTACAGAAGGAAC 59.294 38.462 0.00 0.00 0.00 3.62
1371 4666 7.550597 TCTATCCTATGAAGTCAAGCATCAT 57.449 36.000 0.00 0.00 38.79 2.45
1378 4673 7.496920 CCTATGAAGTCAAGCATCATAAACAGA 59.503 37.037 0.00 0.00 37.34 3.41
1533 4877 8.044060 TCATGTGTTTTGTTTTGCCAAATTTA 57.956 26.923 0.00 0.00 34.50 1.40
1661 5012 1.862008 GCTTCTCGACAGCAGTATCGG 60.862 57.143 6.93 0.00 38.86 4.18
1679 5030 0.171231 GGTTTCATCGGGAAGCTTGC 59.829 55.000 9.87 9.87 36.97 4.01
2202 5646 3.255888 TGCTCGTGATTTGACTGTAGTCT 59.744 43.478 12.75 0.00 44.99 3.24
2455 5903 7.010367 GCATTTAAATTCAATCATCGCCTTTCA 59.990 33.333 0.00 0.00 0.00 2.69
2480 5956 7.223777 CACCTCTACTTTGAGCTAGCTATTTTC 59.776 40.741 19.38 5.51 33.02 2.29
2520 5996 8.459635 GCTACTAATTTTGAAGACCCCTAAAAG 58.540 37.037 0.00 0.00 0.00 2.27
2688 6192 6.787225 ACTCTACAAAATGTGCGTGTTTTTA 58.213 32.000 0.00 0.00 0.00 1.52
2719 6223 5.230942 AGAACCTACAATCAACACGAGAAG 58.769 41.667 0.00 0.00 0.00 2.85
2748 6299 0.400213 TGGGCCAAGTCCAAGTGTAG 59.600 55.000 2.13 0.00 32.75 2.74
2947 6502 8.141268 GTGGGTTCATCAAGTTTTTCTGAATTA 58.859 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 134 1.598962 GAGTGCAGCAACTCCAGCA 60.599 57.895 0.00 0.00 40.66 4.41
156 165 0.179073 GCATGAGCGTGGTGGTAGAT 60.179 55.000 0.00 0.00 0.00 1.98
239 248 2.978824 CTCCCACGGTCGGTCAAT 59.021 61.111 0.00 0.00 0.00 2.57
345 355 2.169352 CGTCCATCTCCCTTGTTCATCT 59.831 50.000 0.00 0.00 0.00 2.90
450 460 7.524294 TGCTCTTTTCAAATTTCAGTTTCAC 57.476 32.000 0.00 0.00 0.00 3.18
489 499 9.915629 AGTAAGCAACCGAAGAATATATAGAAG 57.084 33.333 0.00 0.00 0.00 2.85
750 908 4.226620 ACAACATATTACTTCCTCGGGGTT 59.773 41.667 0.00 0.00 0.00 4.11
767 925 3.954200 TCATGTGTCAGGCATACAACAT 58.046 40.909 0.00 0.00 28.55 2.71
775 933 3.421919 TTCTCAATCATGTGTCAGGCA 57.578 42.857 0.00 0.00 0.00 4.75
882 1042 8.980143 AAAAAGGTACATCATACATTTTTCCG 57.020 30.769 13.47 0.00 43.39 4.30
956 4204 2.752354 CGTGTGGCATTAATCCCTCAAA 59.248 45.455 1.73 0.00 0.00 2.69
1049 4297 2.409064 TCAGGAGGAGGTGGTGTTTA 57.591 50.000 0.00 0.00 0.00 2.01
1058 4306 4.081198 GCAGGTCATATATTCAGGAGGAGG 60.081 50.000 0.00 0.00 0.00 4.30
1127 4391 8.213679 ACAGAGCATAAATATTACACCTGATGT 58.786 33.333 0.00 0.00 46.06 3.06
1221 4512 0.108186 TCGTACTGCTGCTTGATGGG 60.108 55.000 0.00 0.00 0.00 4.00
1371 4666 1.144969 CGAAAGCAGCGGTCTGTTTA 58.855 50.000 0.00 0.00 41.89 2.01
1405 4743 5.633927 TCAACATCTCTTTGATTGATTGCG 58.366 37.500 0.00 0.00 32.05 4.85
1533 4877 5.694006 GCGAGAAGATACATTGTTAGCAGAT 59.306 40.000 0.00 0.00 0.00 2.90
1643 4994 1.460504 ACCGATACTGCTGTCGAGAA 58.539 50.000 0.00 0.00 40.11 2.87
1661 5012 0.171231 GGCAAGCTTCCCGATGAAAC 59.829 55.000 0.00 0.00 31.06 2.78
1679 5030 2.907458 AGGTCCCTCAAATCCAAAGG 57.093 50.000 0.00 0.00 0.00 3.11
2202 5646 4.809958 CACAACAATCATTGCCTTTCAACA 59.190 37.500 0.00 0.00 37.53 3.33
2455 5903 6.800072 AAATAGCTAGCTCAAAGTAGAGGT 57.200 37.500 23.26 0.00 46.97 3.85
2520 5996 6.539103 AGCGAACCCTTTGAAATTAGTAGATC 59.461 38.462 0.00 0.00 0.00 2.75
2533 6009 1.076332 CTCCGTTAGCGAACCCTTTG 58.924 55.000 0.00 0.00 41.33 2.77
2617 6119 6.494893 TCCGTTCCAGATCACAATAAAAAG 57.505 37.500 0.00 0.00 0.00 2.27
2663 6167 5.994887 AAACACGCACATTTTGTAGAGTA 57.005 34.783 0.00 0.00 0.00 2.59
2688 6192 7.700656 CGTGTTGATTGTAGGTTCTTTCTTTTT 59.299 33.333 0.00 0.00 0.00 1.94
2719 6223 1.069596 CTTGGCCCAAACACAAGCC 59.930 57.895 0.00 0.00 45.96 4.35
2748 6299 4.631813 TGTTGGTTGTTTGGTTTGCAATAC 59.368 37.500 0.00 1.43 0.00 1.89
2947 6502 7.389803 TGATGATATGATTTTTGGTGTTCGT 57.610 32.000 0.00 0.00 0.00 3.85
3218 6775 6.773976 TTATTTCTCTGGATGGCGATTTTT 57.226 33.333 0.00 0.00 0.00 1.94
3279 6840 7.236640 ACCCCAGTACCAACATGAATTAAAATT 59.763 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.