Multiple sequence alignment - TraesCS7D01G292100

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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 TraesCS7D01G292100 chr7D 100.000 2243 0 0 1 2243 354526578 354528820 0.000000e+00 4143.0
1 TraesCS7D01G292100 chr7D 95.508 1603 46 9 656 2242 195395440 195397032 0.000000e+00 2538.0
2 TraesCS7D01G292100 chr7D 93.884 932 19 8 619 1549 346185167 346184273 0.000000e+00 1371.0
3 TraesCS7D01G292100 chr7D 96.369 661 19 3 1586 2242 346184266 346183607 0.000000e+00 1083.0
4 TraesCS7D01G292100 chr7D 90.210 715 42 14 841 1534 588678986 588678279 0.000000e+00 907.0
5 TraesCS7D01G292100 chr7D 86.310 672 73 13 2 658 366849320 366849987 0.000000e+00 713.0
6 TraesCS7D01G292100 chr7D 87.786 131 7 3 1413 1534 588841162 588841292 6.460000e-31 145.0
7 TraesCS7D01G292100 chr4B 91.300 1023 67 7 648 1667 141079891 141080894 0.000000e+00 1376.0
8 TraesCS7D01G292100 chr4B 92.759 580 33 7 1667 2242 141080926 141081500 0.000000e+00 830.0
9 TraesCS7D01G292100 chr4B 93.077 390 22 4 1856 2242 621660522 621660909 1.160000e-157 566.0
10 TraesCS7D01G292100 chr4B 83.065 620 85 12 6 609 198950481 198949866 1.510000e-151 545.0
11 TraesCS7D01G292100 chr4B 91.538 390 28 4 1856 2242 315214466 315214853 1.180000e-147 532.0
12 TraesCS7D01G292100 chr4B 81.313 594 88 16 6 583 425093905 425093319 5.640000e-126 460.0
13 TraesCS7D01G292100 chr4B 83.059 425 59 6 6 417 467637213 467636789 7.560000e-100 374.0
14 TraesCS7D01G292100 chr7B 92.780 928 60 5 744 1667 253264604 253263680 0.000000e+00 1336.0
15 TraesCS7D01G292100 chr7B 90.234 727 40 13 838 1534 663107679 663108404 0.000000e+00 920.0
16 TraesCS7D01G292100 chr7B 93.610 579 27 8 1669 2242 253263646 253263073 0.000000e+00 856.0
17 TraesCS7D01G292100 chr2B 91.712 929 70 5 743 1667 311334420 311335345 0.000000e+00 1282.0
18 TraesCS7D01G292100 chr2B 90.878 581 40 8 1667 2242 311335377 311335949 0.000000e+00 767.0
19 TraesCS7D01G292100 chr2B 92.327 391 23 6 1856 2242 519069650 519070037 1.170000e-152 549.0
20 TraesCS7D01G292100 chr2B 81.716 536 76 18 109 629 364266875 364266347 5.720000e-116 427.0
21 TraesCS7D01G292100 chr2B 100.000 41 0 0 802 842 220962970 220963010 2.390000e-10 76.8
22 TraesCS7D01G292100 chr7A 87.024 709 49 19 851 1523 680406665 680407366 0.000000e+00 760.0
23 TraesCS7D01G292100 chr7A 93.750 160 5 5 644 803 291220239 291220085 3.720000e-58 235.0
24 TraesCS7D01G292100 chr7A 89.697 165 13 4 1664 1825 238547034 238547197 8.120000e-50 207.0
25 TraesCS7D01G292100 chr4A 87.244 635 66 10 9 632 368296727 368296097 0.000000e+00 710.0
26 TraesCS7D01G292100 chr4A 89.732 224 6 4 619 842 462308917 462309123 1.020000e-68 270.0
27 TraesCS7D01G292100 chr2D 84.835 666 80 15 6 656 241971462 241972121 0.000000e+00 651.0
28 TraesCS7D01G292100 chr2D 94.194 155 5 4 619 773 274709746 274709596 1.340000e-57 233.0
29 TraesCS7D01G292100 chr4D 96.345 383 12 2 1860 2242 35719764 35720144 1.460000e-176 628.0
30 TraesCS7D01G292100 chr4D 95.057 263 8 3 1627 1884 35659421 35659159 2.070000e-110 409.0
31 TraesCS7D01G292100 chr4D 95.038 262 8 3 1627 1884 35645040 35644780 7.460000e-110 407.0
32 TraesCS7D01G292100 chr4D 95.161 186 6 3 619 803 384430753 384430936 7.840000e-75 291.0
33 TraesCS7D01G292100 chr4D 90.576 191 6 1 619 797 310939832 310939642 2.230000e-60 243.0
34 TraesCS7D01G292100 chr4D 87.845 181 9 3 629 797 182406275 182406454 1.360000e-47 200.0
35 TraesCS7D01G292100 chr4D 87.293 181 10 2 619 787 153518893 153518714 6.320000e-46 195.0
36 TraesCS7D01G292100 chr4D 92.593 135 7 3 619 752 310809408 310809540 8.180000e-45 191.0
37 TraesCS7D01G292100 chr4D 88.095 168 7 2 642 797 384432245 384432411 1.060000e-43 187.0
38 TraesCS7D01G292100 chr6A 83.680 625 78 13 107 719 180867066 180866454 3.230000e-158 568.0
39 TraesCS7D01G292100 chr6A 83.360 619 87 9 6 610 180823034 180822418 1.950000e-155 558.0
40 TraesCS7D01G292100 chr6A 95.484 155 3 4 619 773 468509444 468509594 6.190000e-61 244.0
41 TraesCS7D01G292100 chr6A 95.833 144 4 2 620 761 385100617 385100760 4.820000e-57 231.0
42 TraesCS7D01G292100 chr3B 93.077 390 22 4 1856 2242 658959599 658959986 1.160000e-157 566.0
43 TraesCS7D01G292100 chr3B 80.861 627 94 16 6 612 370558267 370558887 9.380000e-129 470.0
44 TraesCS7D01G292100 chr3B 95.122 41 2 0 802 842 556457111 556457151 5.170000e-07 65.8
45 TraesCS7D01G292100 chr1B 92.051 390 25 5 1856 2242 30060643 30061029 5.450000e-151 544.0
46 TraesCS7D01G292100 chr1B 93.197 147 7 3 617 761 616926924 616926779 1.740000e-51 213.0
47 TraesCS7D01G292100 chr1B 87.805 164 13 5 1667 1823 280436035 280436198 3.800000e-43 185.0
48 TraesCS7D01G292100 chr1B 85.890 163 17 4 1667 1823 560819443 560819605 3.830000e-38 169.0
49 TraesCS7D01G292100 chr5B 86.900 458 48 8 7 453 160511868 160512324 9.250000e-139 503.0
50 TraesCS7D01G292100 chr5B 93.529 170 10 1 640 809 380597774 380597942 3.700000e-63 252.0
51 TraesCS7D01G292100 chr5B 86.829 205 15 7 1667 1859 308024021 308023817 3.750000e-53 219.0
52 TraesCS7D01G292100 chr5B 87.117 163 15 4 1667 1823 570010600 570010762 1.770000e-41 180.0
53 TraesCS7D01G292100 chr5B 87.121 132 13 4 1545 1674 308024175 308024046 1.800000e-31 147.0
54 TraesCS7D01G292100 chr5B 92.683 41 3 0 802 842 380598298 380598338 2.410000e-05 60.2
55 TraesCS7D01G292100 chr3A 81.869 535 80 10 6 526 297321571 297322102 3.420000e-118 435.0
56 TraesCS7D01G292100 chr5A 94.444 162 7 1 642 803 454103493 454103334 4.780000e-62 248.0
57 TraesCS7D01G292100 chr5D 93.452 168 7 3 1856 2020 427199018 427198852 1.720000e-61 246.0
58 TraesCS7D01G292100 chr3D 89.062 192 8 6 619 797 368369506 368369315 2.240000e-55 226.0
59 TraesCS7D01G292100 chr6B 89.444 180 16 2 619 796 83598804 83598626 8.060000e-55 224.0
60 TraesCS7D01G292100 chr1A 89.080 174 5 2 642 803 273196599 273196428 1.050000e-48 204.0
61 TraesCS7D01G292100 chr1A 88.304 171 8 1 645 803 230722862 230722692 6.320000e-46 195.0
62 TraesCS7D01G292100 chr1A 92.800 125 5 4 649 773 499323908 499323788 6.370000e-41 178.0
63 TraesCS7D01G292100 chr1A 79.641 167 21 10 1667 1828 251226440 251226282 8.470000e-20 108.0


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 TraesCS7D01G292100 chr7D 354526578 354528820 2242 False 4143.0 4143 100.0000 1 2243 1 chr7D.!!$F2 2242
1 TraesCS7D01G292100 chr7D 195395440 195397032 1592 False 2538.0 2538 95.5080 656 2242 1 chr7D.!!$F1 1586
2 TraesCS7D01G292100 chr7D 346183607 346185167 1560 True 1227.0 1371 95.1265 619 2242 2 chr7D.!!$R2 1623
3 TraesCS7D01G292100 chr7D 588678279 588678986 707 True 907.0 907 90.2100 841 1534 1 chr7D.!!$R1 693
4 TraesCS7D01G292100 chr7D 366849320 366849987 667 False 713.0 713 86.3100 2 658 1 chr7D.!!$F3 656
5 TraesCS7D01G292100 chr4B 141079891 141081500 1609 False 1103.0 1376 92.0295 648 2242 2 chr4B.!!$F3 1594
6 TraesCS7D01G292100 chr4B 198949866 198950481 615 True 545.0 545 83.0650 6 609 1 chr4B.!!$R1 603
7 TraesCS7D01G292100 chr4B 425093319 425093905 586 True 460.0 460 81.3130 6 583 1 chr4B.!!$R2 577
8 TraesCS7D01G292100 chr7B 253263073 253264604 1531 True 1096.0 1336 93.1950 744 2242 2 chr7B.!!$R1 1498
9 TraesCS7D01G292100 chr7B 663107679 663108404 725 False 920.0 920 90.2340 838 1534 1 chr7B.!!$F1 696
10 TraesCS7D01G292100 chr2B 311334420 311335949 1529 False 1024.5 1282 91.2950 743 2242 2 chr2B.!!$F3 1499
11 TraesCS7D01G292100 chr2B 364266347 364266875 528 True 427.0 427 81.7160 109 629 1 chr2B.!!$R1 520
12 TraesCS7D01G292100 chr7A 680406665 680407366 701 False 760.0 760 87.0240 851 1523 1 chr7A.!!$F2 672
13 TraesCS7D01G292100 chr4A 368296097 368296727 630 True 710.0 710 87.2440 9 632 1 chr4A.!!$R1 623
14 TraesCS7D01G292100 chr2D 241971462 241972121 659 False 651.0 651 84.8350 6 656 1 chr2D.!!$F1 650
15 TraesCS7D01G292100 chr4D 384430753 384432411 1658 False 239.0 291 91.6280 619 803 2 chr4D.!!$F4 184
16 TraesCS7D01G292100 chr6A 180866454 180867066 612 True 568.0 568 83.6800 107 719 1 chr6A.!!$R2 612
17 TraesCS7D01G292100 chr6A 180822418 180823034 616 True 558.0 558 83.3600 6 610 1 chr6A.!!$R1 604
18 TraesCS7D01G292100 chr3B 370558267 370558887 620 False 470.0 470 80.8610 6 612 1 chr3B.!!$F1 606
19 TraesCS7D01G292100 chr3A 297321571 297322102 531 False 435.0 435 81.8690 6 526 1 chr3A.!!$F1 520

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
313 334 0.319641 GAGTCCGCGTCTCCTTTTGT 60.320 55.000 4.92 0.0 0.0 2.83 F
613 643 1.075374 ACCCATGTGTAGTTGTGGCAT 59.925 47.619 0.00 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1224 1343 0.253044 GCTAGTCCTGGACAATGGCA 59.747 55.0 27.48 5.54 34.6 4.92 R
1852 2387 0.395586 ATGGCATGCGTGTATGGGTT 60.396 50.0 12.44 0.00 0.0 4.11 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
39 40 6.811170 TCATAGCCGAAATGTTTGAAAATTCC 59.189 34.615 0.00 0.00 0.00 3.01
66 68 5.163683 CGCTTCTCAGACAATGGATGAAAAT 60.164 40.000 0.00 0.00 0.00 1.82
67 69 6.264088 GCTTCTCAGACAATGGATGAAAATC 58.736 40.000 0.00 0.00 0.00 2.17
175 182 5.938438 AAATGCATGGTAAACGCAAAAAT 57.062 30.435 0.00 0.00 39.48 1.82
190 198 8.419076 AACGCAAAAATTGGCTTAAATATAGG 57.581 30.769 0.00 0.00 0.00 2.57
194 202 9.987272 GCAAAAATTGGCTTAAATATAGGAGAT 57.013 29.630 0.00 0.00 0.00 2.75
221 232 6.547510 AGACCTGAAATGGGCTATAAAATCAC 59.452 38.462 0.00 0.00 45.24 3.06
229 240 4.972568 TGGGCTATAAAATCACACCTAGGA 59.027 41.667 17.98 0.00 0.00 2.94
243 254 9.997172 ATCACACCTAGGATATATCAGTGATTA 57.003 33.333 17.98 4.41 40.18 1.75
254 265 3.906720 TCAGTGATTACTTACCCTGGC 57.093 47.619 0.00 0.00 34.07 4.85
282 294 1.272490 TCGAGGCAGAACGATGAAGTT 59.728 47.619 0.00 0.00 36.99 2.66
293 306 3.841643 ACGATGAAGTTACCGACGATTT 58.158 40.909 0.00 0.00 0.00 2.17
313 334 0.319641 GAGTCCGCGTCTCCTTTTGT 60.320 55.000 4.92 0.00 0.00 2.83
496 520 9.796180 TTAAAATACCAACAAAGCCTACTTCTA 57.204 29.630 0.00 0.00 34.05 2.10
519 543 2.396157 CGCACCCTAAGGCCGAAAC 61.396 63.158 0.00 0.00 36.11 2.78
527 553 2.095919 CCTAAGGCCGAAACGTTTGAAG 60.096 50.000 20.10 9.35 0.00 3.02
613 643 1.075374 ACCCATGTGTAGTTGTGGCAT 59.925 47.619 0.00 0.00 0.00 4.40
990 1109 2.498941 GGAGGGATCATCGTCGGCA 61.499 63.158 0.00 0.00 0.00 5.69
1224 1343 2.435693 GCGCCTCATCACCTACCCT 61.436 63.158 0.00 0.00 0.00 4.34
1333 1459 9.086758 AGATTGATCCAAGAACTGAAGATTTTT 57.913 29.630 0.00 0.00 0.00 1.94
1375 1501 1.000938 CTGGAGATCGATCGATGTGCA 60.001 52.381 35.38 35.38 42.13 4.57
1393 1519 3.879180 ATCCCGGCCGGTTGCTTTT 62.879 57.895 40.52 15.30 40.92 2.27
1511 1657 3.165875 ACAGTCCTTCTTACTGCAGCTA 58.834 45.455 15.27 2.59 46.73 3.32
1852 2387 0.472352 AGGTGGGGAAGTGAACGGTA 60.472 55.000 0.00 0.00 0.00 4.02
1873 2408 0.818852 CCCATACACGCATGCCATCA 60.819 55.000 13.15 0.00 0.00 3.07
1933 2515 4.842574 TCTAGCATGCAAAACAGTGGATA 58.157 39.130 21.98 0.00 0.00 2.59
2194 2818 8.181573 AGTTAACATCATAATTTACAGCGGTTG 58.818 33.333 8.61 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.530857 GCTATGAGGTGCGGCCGT 62.531 66.667 28.70 6.29 43.70 5.68
39 40 0.745845 CCATTGTCTGAGAAGCGGGG 60.746 60.000 0.00 0.00 0.00 5.73
96 98 0.251165 TGGGTGTTAGCAAAGGAGGC 60.251 55.000 0.00 0.00 0.00 4.70
167 174 8.134895 TCTCCTATATTTAAGCCAATTTTTGCG 58.865 33.333 0.00 0.00 0.00 4.85
175 182 7.514127 AGGTCTCATCTCCTATATTTAAGCCAA 59.486 37.037 0.00 0.00 31.66 4.52
190 198 2.172293 AGCCCATTTCAGGTCTCATCTC 59.828 50.000 0.00 0.00 0.00 2.75
194 202 5.708736 TTTATAGCCCATTTCAGGTCTCA 57.291 39.130 0.00 0.00 0.00 3.27
229 240 7.457852 TGCCAGGGTAAGTAATCACTGATATAT 59.542 37.037 0.00 0.00 34.36 0.86
236 247 4.650972 TTTGCCAGGGTAAGTAATCACT 57.349 40.909 0.00 0.00 36.19 3.41
243 254 3.892588 TCGAAATTTTTGCCAGGGTAAGT 59.107 39.130 0.00 0.00 0.00 2.24
250 261 2.030007 TCTGCCTCGAAATTTTTGCCAG 60.030 45.455 0.00 0.00 0.00 4.85
254 265 3.884169 TCGTTCTGCCTCGAAATTTTTG 58.116 40.909 0.00 0.00 33.13 2.44
282 294 0.179156 GCGGACTCAAATCGTCGGTA 60.179 55.000 0.00 0.00 35.10 4.02
293 306 0.319555 CAAAAGGAGACGCGGACTCA 60.320 55.000 27.23 0.00 36.26 3.41
313 334 7.712639 GCATCTCACAAGAAGGATCATAGTTTA 59.287 37.037 0.00 0.00 34.49 2.01
397 419 1.153489 CATGCTCTCACGACCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
417 439 5.970592 TCATGAAAATTGGTGTGTCAACAA 58.029 33.333 2.73 2.73 45.40 2.83
492 516 0.468226 CTTAGGGTGCGGCCATAGAA 59.532 55.000 2.24 0.00 39.65 2.10
493 517 1.407656 CCTTAGGGTGCGGCCATAGA 61.408 60.000 2.24 0.00 39.65 1.98
496 520 4.506255 GCCTTAGGGTGCGGCCAT 62.506 66.667 2.24 0.00 39.65 4.40
519 543 2.806244 AGACCGGAACAATCTTCAAACG 59.194 45.455 9.46 0.00 0.00 3.60
781 837 3.385384 CCTGCAGACCCGAGCTCA 61.385 66.667 17.39 0.00 0.00 4.26
857 946 1.637553 AGATGGATGGATATGTGGGCC 59.362 52.381 0.00 0.00 0.00 5.80
862 951 4.848660 AGCCTACAAGATGGATGGATATGT 59.151 41.667 0.00 0.00 0.00 2.29
1224 1343 0.253044 GCTAGTCCTGGACAATGGCA 59.747 55.000 27.48 5.54 34.60 4.92
1333 1459 3.885724 TGTTCGATCTGGCATCTAACA 57.114 42.857 4.60 4.60 33.29 2.41
1375 1501 3.879180 AAAAGCAACCGGCCGGGAT 62.879 57.895 44.99 31.75 46.50 3.85
1393 1519 4.812476 CAAGATCCGCGGGCACGA 62.812 66.667 27.83 5.39 44.60 4.35
1511 1657 6.291648 ACTGTATCGCATCATCTATCCATT 57.708 37.500 0.00 0.00 0.00 3.16
1852 2387 0.395586 ATGGCATGCGTGTATGGGTT 60.396 50.000 12.44 0.00 0.00 4.11
1873 2408 4.098349 ACTGAACAATGCACAAACACATCT 59.902 37.500 0.00 0.00 0.00 2.90
1995 2577 7.981225 CACATAAACCATTCATTTTCCCCTAAG 59.019 37.037 0.00 0.00 0.00 2.18
2051 2634 4.641396 TCATACCCTGTGACAACTGAAAG 58.359 43.478 0.00 0.00 42.29 2.62
2194 2818 9.028185 CCCGAACTAGTATACATTTGTAAAGTC 57.972 37.037 5.50 0.00 33.76 3.01


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

AutoCloner maintained by Alex Coulton.