Multiple sequence alignment - TraesCS7D01G258200

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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 TraesCS7D01G258200 chr7D 100.000 5144 0 0 1 5144 234125679 234130822 0.000000e+00 9500
1 TraesCS7D01G258200 chr7B 98.015 4231 63 6 917 5141 205714786 205719001 0.000000e+00 7328
2 TraesCS7D01G258200 chr7B 86.653 944 109 5 1 930 205642402 205643342 0.000000e+00 1029
3 TraesCS7D01G258200 chr7A 95.541 1256 47 5 860 2111 247062617 247063867 0.000000e+00 2001
4 TraesCS7D01G258200 chr7A 89.921 1141 67 23 4042 5144 247065930 247067060 0.000000e+00 1426
5 TraesCS7D01G258200 chr7A 89.819 992 64 16 3093 4064 247064750 247065724 0.000000e+00 1238
6 TraesCS7D01G258200 chr7A 91.657 887 68 5 2131 3014 247063848 247064731 0.000000e+00 1223
7 TraesCS7D01G258200 chr7A 89.054 539 38 7 1 538 247061371 247061889 0.000000e+00 649
8 TraesCS7D01G258200 chr7A 84.615 338 47 3 513 847 247061907 247062242 1.070000e-86 331
9 TraesCS7D01G258200 chr7A 84.672 274 37 3 1692 1960 247063358 247063631 8.490000e-68 268
10 TraesCS7D01G258200 chr7A 78.095 210 38 6 1 206 657747543 657747338 5.410000e-25 126
11 TraesCS7D01G258200 chr1B 79.172 725 116 19 1 695 629454519 629455238 2.170000e-128 470
12 TraesCS7D01G258200 chrUn 79.522 669 120 15 101 756 340093135 340092471 1.310000e-125 460
13 TraesCS7D01G258200 chr4B 76.265 889 155 27 1 855 83308589 83307723 6.160000e-114 422
14 TraesCS7D01G258200 chr4B 79.861 144 22 7 623 763 557568842 557568981 1.180000e-16 99
15 TraesCS7D01G258200 chr3D 85.387 349 43 8 998 1342 162411100 162410756 6.340000e-94 355
16 TraesCS7D01G258200 chr3D 79.661 354 71 1 994 1346 162183864 162183511 2.380000e-63 254
17 TraesCS7D01G258200 chr4D 78.821 543 99 10 13 543 56726655 56726117 8.190000e-93 351
18 TraesCS7D01G258200 chr4D 85.252 278 37 4 1 276 34718714 34718439 3.030000e-72 283
19 TraesCS7D01G258200 chr4D 82.530 166 28 1 275 439 485044691 485044856 1.490000e-30 145
20 TraesCS7D01G258200 chr4A 76.636 642 135 12 127 756 657312639 657313277 1.770000e-89 340
21 TraesCS7D01G258200 chr4A 76.480 625 131 15 127 739 657372334 657372954 4.970000e-85 326
22 TraesCS7D01G258200 chr5B 82.114 369 54 9 2653 3014 611281524 611281161 6.470000e-79 305
23 TraesCS7D01G258200 chr5D 83.281 317 44 8 2653 2965 494756296 494755985 3.030000e-72 283
24 TraesCS7D01G258200 chr3B 80.112 357 62 8 994 1345 239255434 239255082 1.840000e-64 257
25 TraesCS7D01G258200 chr3B 78.058 278 52 5 266 543 618765010 618764742 3.190000e-37 167
26 TraesCS7D01G258200 chr3B 78.049 205 32 10 559 755 721864930 721864731 3.250000e-22 117
27 TraesCS7D01G258200 chr3A 80.000 355 66 5 995 1346 192857441 192857089 1.840000e-64 257


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 TraesCS7D01G258200 chr7D 234125679 234130822 5143 False 9500.000000 9500 100.000000 1 5144 1 chr7D.!!$F1 5143
1 TraesCS7D01G258200 chr7B 205714786 205719001 4215 False 7328.000000 7328 98.015000 917 5141 1 chr7B.!!$F2 4224
2 TraesCS7D01G258200 chr7B 205642402 205643342 940 False 1029.000000 1029 86.653000 1 930 1 chr7B.!!$F1 929
3 TraesCS7D01G258200 chr7A 247061371 247067060 5689 False 1019.428571 2001 89.325571 1 5144 7 chr7A.!!$F1 5143
4 TraesCS7D01G258200 chr1B 629454519 629455238 719 False 470.000000 470 79.172000 1 695 1 chr1B.!!$F1 694
5 TraesCS7D01G258200 chrUn 340092471 340093135 664 True 460.000000 460 79.522000 101 756 1 chrUn.!!$R1 655
6 TraesCS7D01G258200 chr4B 83307723 83308589 866 True 422.000000 422 76.265000 1 855 1 chr4B.!!$R1 854
7 TraesCS7D01G258200 chr4D 56726117 56726655 538 True 351.000000 351 78.821000 13 543 1 chr4D.!!$R2 530
8 TraesCS7D01G258200 chr4A 657312639 657313277 638 False 340.000000 340 76.636000 127 756 1 chr4A.!!$F1 629
9 TraesCS7D01G258200 chr4A 657372334 657372954 620 False 326.000000 326 76.480000 127 739 1 chr4A.!!$F2 612

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
234 251 1.062047 GACATGCGCGACGACTCTA 59.938 57.895 12.10 0.00 0.0 2.43 F
1455 1913 0.548510 GGAAGATGGTGGGGAAGAGG 59.451 60.000 0.00 0.00 0.0 3.69 F
2145 2612 0.178921 AGGAGAAGAGTGAGGTGGCA 60.179 55.000 0.00 0.00 0.0 4.92 F
3279 3753 0.105862 ATAATGGCCATGCAGCACCT 60.106 50.000 21.63 2.82 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 2144 0.107993 CCTCTTTCCGCTCATCTGCA 60.108 55.000 0.00 0.0 0.00 4.41 R
3269 3743 0.034670 GAAAGGAGGAGGTGCTGCAT 60.035 55.000 5.27 0.0 0.00 3.96 R
3330 3807 0.526954 CAAATGCGGGATTCTGCTGC 60.527 55.000 6.33 0.0 45.25 5.25 R
4995 5755 2.658285 TGATTGATGGATTGTCAGCCC 58.342 47.619 0.00 0.0 0.00 5.19 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
30 31 2.047655 TCGGGTTGCATGTCGGAC 60.048 61.111 0.00 0.00 0.00 4.79
170 186 1.821216 GAGCAATTCCCGGAGAAACA 58.179 50.000 0.73 0.00 38.21 2.83
234 251 1.062047 GACATGCGCGACGACTCTA 59.938 57.895 12.10 0.00 0.00 2.43
264 281 2.660802 GGGGAAAAGCCGACGAGA 59.339 61.111 0.00 0.00 37.63 4.04
344 362 1.205655 CTGGCGATGTTCTCCTCTTCA 59.794 52.381 0.00 0.00 0.00 3.02
351 369 3.490439 TGTTCTCCTCTTCATGTGCAA 57.510 42.857 0.00 0.00 0.00 4.08
354 372 1.618343 TCTCCTCTTCATGTGCAACGA 59.382 47.619 0.00 0.00 42.39 3.85
359 377 1.078709 CTTCATGTGCAACGACGGAT 58.921 50.000 0.00 0.00 42.39 4.18
434 452 2.345244 CTCTTGGCCGACTGCACT 59.655 61.111 0.00 0.00 43.89 4.40
602 698 5.080337 AGATTTTTGGGAAAGAGAGGGAAC 58.920 41.667 0.00 0.00 0.00 3.62
705 801 4.882427 TGACACAAACGAGGTCCAAATTTA 59.118 37.500 0.00 0.00 0.00 1.40
739 835 2.976840 GCATGGCGGACGAAAAGCA 61.977 57.895 0.00 0.00 0.00 3.91
756 852 1.421485 CAGACGCTCATCCGTTTGC 59.579 57.895 0.00 0.00 42.24 3.68
791 887 1.722464 CGCGTTGGATCGACTTTTGTA 59.278 47.619 0.00 0.00 0.00 2.41
804 900 7.481275 TCGACTTTTGTATTCGTTTTAACCT 57.519 32.000 0.00 0.00 0.00 3.50
817 913 7.966246 TCGTTTTAACCTAAATAGACAAGCA 57.034 32.000 0.00 0.00 0.00 3.91
820 916 8.234546 CGTTTTAACCTAAATAGACAAGCACAT 58.765 33.333 0.00 0.00 0.00 3.21
836 932 1.608590 CACATATCAAATGGGTCGGCC 59.391 52.381 0.00 0.00 0.00 6.13
855 951 1.270625 CCCGTTGGAGTTGCTGTAAGA 60.271 52.381 0.00 0.00 34.07 2.10
856 952 2.069273 CCGTTGGAGTTGCTGTAAGAG 58.931 52.381 0.00 0.00 34.07 2.85
857 953 2.288825 CCGTTGGAGTTGCTGTAAGAGA 60.289 50.000 0.00 0.00 34.07 3.10
879 1337 9.886132 AGAGAACTAAACTCACTTTACAAAGAA 57.114 29.630 8.65 0.00 36.27 2.52
890 1348 6.943718 TCACTTTACAAAGAATAACCCCGAAT 59.056 34.615 8.65 0.00 39.31 3.34
1455 1913 0.548510 GGAAGATGGTGGGGAAGAGG 59.451 60.000 0.00 0.00 0.00 3.69
1456 1914 0.548510 GAAGATGGTGGGGAAGAGGG 59.451 60.000 0.00 0.00 0.00 4.30
1457 1915 1.575447 AAGATGGTGGGGAAGAGGGC 61.575 60.000 0.00 0.00 0.00 5.19
1680 2144 0.551131 AGCCCCCTGAACTGGAGAAT 60.551 55.000 0.00 0.00 0.00 2.40
1884 2348 1.194781 AGAAAGAGGAGAAGGCCGCA 61.195 55.000 0.00 0.00 0.00 5.69
2107 2574 0.633921 TCTTGAGGAGGAGGAGGAGG 59.366 60.000 0.00 0.00 0.00 4.30
2145 2612 0.178921 AGGAGAAGAGTGAGGTGGCA 60.179 55.000 0.00 0.00 0.00 4.92
2253 2720 6.849085 AAAGAGATGACAGATACTGAGTGT 57.151 37.500 5.76 0.00 35.18 3.55
2254 2721 5.833406 AGAGATGACAGATACTGAGTGTG 57.167 43.478 5.76 0.00 35.18 3.82
2334 2801 4.762251 GGAAAGATGGAAGCAGTTAACAGT 59.238 41.667 8.61 0.00 0.00 3.55
2586 3053 4.404073 GTCAGGAATGATGGTCAGTCTACT 59.596 45.833 7.25 0.00 40.88 2.57
2790 3257 5.520288 CCATGCGGTGACATATTATACTAGC 59.480 44.000 0.00 0.00 0.00 3.42
2825 3292 7.486232 GCTAAAGCATTAAAATGGAACTCTGTC 59.514 37.037 4.93 0.00 41.59 3.51
2859 3326 5.355596 CATCCTGTAGGTTCACTTCTGATC 58.644 45.833 0.00 0.00 36.34 2.92
2869 3336 8.006298 AGGTTCACTTCTGATCAGATTACTAG 57.994 38.462 25.64 20.44 37.29 2.57
3269 3743 5.628797 TCTTGTGATGTCTATAATGGCCA 57.371 39.130 8.56 8.56 0.00 5.36
3279 3753 0.105862 ATAATGGCCATGCAGCACCT 60.106 50.000 21.63 2.82 0.00 4.00
3280 3754 0.752743 TAATGGCCATGCAGCACCTC 60.753 55.000 21.63 0.00 0.00 3.85
3281 3755 4.746309 TGGCCATGCAGCACCTCC 62.746 66.667 0.00 0.00 0.00 4.30
3354 3831 2.518949 CAGAATCCCGCATTTGTTTCG 58.481 47.619 0.00 0.00 0.00 3.46
3408 3889 4.855388 CGCATATTTGCCTTATGATGCTTC 59.145 41.667 2.35 0.00 46.57 3.86
3676 4161 7.766278 TCCTGAGAAAAGAATGTGCTATTAGTC 59.234 37.037 0.00 0.00 0.00 2.59
3771 4256 6.550938 TCTTGTAGTCTTGATCATGGACAT 57.449 37.500 22.68 14.19 32.98 3.06
3968 4464 2.574006 ATGCTGACATGTTCTGTGGT 57.426 45.000 0.00 0.00 38.54 4.16
3973 4469 1.488393 TGACATGTTCTGTGGTCCACA 59.512 47.619 23.38 23.38 42.45 4.17
4582 5312 4.396166 GCTTATACTCATGTGGCAGTTTGT 59.604 41.667 0.00 0.00 0.00 2.83
4995 5755 6.622549 AGTTTCTTTCTACCATAGTCTGTCG 58.377 40.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.742372 GACATGCAACCCGACGCT 60.742 61.111 0.00 0.00 0.00 5.07
170 186 1.065418 CATCCCTACCCGCAAACTTCT 60.065 52.381 0.00 0.00 0.00 2.85
344 362 1.651987 CCTTATCCGTCGTTGCACAT 58.348 50.000 0.00 0.00 0.00 3.21
351 369 2.406401 CGTCGCCTTATCCGTCGT 59.594 61.111 0.00 0.00 33.81 4.34
354 372 4.564116 CGCCGTCGCCTTATCCGT 62.564 66.667 0.00 0.00 0.00 4.69
661 757 1.947642 GCGGACACGAAACAGACGT 60.948 57.895 0.00 0.00 44.60 4.34
739 835 2.094659 CGCAAACGGATGAGCGTCT 61.095 57.895 0.00 0.00 44.67 4.18
756 852 4.479121 GCGCGTTACTTGCCGACG 62.479 66.667 8.43 0.00 39.61 5.12
763 859 1.680105 CGATCCAACGCGCGTTACTT 61.680 55.000 43.29 30.25 36.46 2.24
764 860 2.156446 CGATCCAACGCGCGTTACT 61.156 57.895 43.29 30.45 36.46 2.24
791 887 9.005777 TGCTTGTCTATTTAGGTTAAAACGAAT 57.994 29.630 0.00 0.00 0.00 3.34
804 900 8.849168 CCCATTTGATATGTGCTTGTCTATTTA 58.151 33.333 0.00 0.00 0.00 1.40
817 913 1.981256 GGCCGACCCATTTGATATGT 58.019 50.000 0.00 0.00 0.00 2.29
836 932 2.069273 CTCTTACAGCAACTCCAACGG 58.931 52.381 0.00 0.00 0.00 4.44
890 1348 2.304761 AGGTATTTTTGCGAGACCCAGA 59.695 45.455 0.00 0.00 0.00 3.86
895 1353 3.596214 TGAGGAGGTATTTTTGCGAGAC 58.404 45.455 0.00 0.00 0.00 3.36
1389 1847 2.583441 CGGCTTCTCCTCCACCACA 61.583 63.158 0.00 0.00 0.00 4.17
1680 2144 0.107993 CCTCTTTCCGCTCATCTGCA 60.108 55.000 0.00 0.00 0.00 4.41
1807 2271 1.480212 TTCTTCCTCTTCCTGCCGCA 61.480 55.000 0.00 0.00 0.00 5.69
2145 2612 0.622665 CCACTTCTTCATCCCCAGCT 59.377 55.000 0.00 0.00 0.00 4.24
2234 2701 5.718146 CAACACACTCAGTATCTGTCATCT 58.282 41.667 0.00 0.00 32.61 2.90
2254 2721 0.954452 CCCCTGTTGTCAGAAGCAAC 59.046 55.000 0.00 0.00 43.76 4.17
2269 2736 5.132816 CACCTTCATTTATCTCCTTACCCCT 59.867 44.000 0.00 0.00 0.00 4.79
2334 2801 4.168871 TCATCATCCTCTAACTCTCCTCCA 59.831 45.833 0.00 0.00 0.00 3.86
2790 3257 8.345565 CCATTTTAATGCTTTAGCCTACTACTG 58.654 37.037 0.00 0.00 41.18 2.74
2825 3292 4.395625 ACCTACAGGATGCATCATCAATG 58.604 43.478 27.25 18.02 42.13 2.82
3269 3743 0.034670 GAAAGGAGGAGGTGCTGCAT 60.035 55.000 5.27 0.00 0.00 3.96
3279 3753 6.363167 TTTGGATACTTTACGAAAGGAGGA 57.637 37.500 10.65 0.00 42.82 3.71
3280 3754 6.260271 GGATTTGGATACTTTACGAAAGGAGG 59.740 42.308 10.65 0.00 42.82 4.30
3281 3755 6.821665 TGGATTTGGATACTTTACGAAAGGAG 59.178 38.462 10.65 0.00 42.82 3.69
3328 3805 2.437180 TGCGGGATTCTGCTGCAG 60.437 61.111 23.31 23.31 45.26 4.41
3330 3807 0.526954 CAAATGCGGGATTCTGCTGC 60.527 55.000 6.33 0.00 45.25 5.25
3331 3808 0.813184 ACAAATGCGGGATTCTGCTG 59.187 50.000 6.33 0.00 45.25 4.41
3332 3809 1.549203 AACAAATGCGGGATTCTGCT 58.451 45.000 6.33 0.00 45.25 4.24
3333 3810 2.262211 GAAACAAATGCGGGATTCTGC 58.738 47.619 0.00 0.00 45.23 4.26
3334 3811 2.161410 TCGAAACAAATGCGGGATTCTG 59.839 45.455 0.00 0.00 0.00 3.02
3335 3812 2.432444 TCGAAACAAATGCGGGATTCT 58.568 42.857 0.00 0.00 0.00 2.40
3408 3889 5.518128 TGACAATGTTTTCATCCAACAAACG 59.482 36.000 0.00 0.00 39.94 3.60
3968 4464 2.647299 ACATCCAGTTAACCCATGTGGA 59.353 45.455 14.00 14.00 41.50 4.02
3973 4469 5.191727 TCATCAACATCCAGTTAACCCAT 57.808 39.130 0.88 0.00 38.74 4.00
4406 5131 6.014898 GCATTGAAACTTTGAACACAACAAC 58.985 36.000 0.00 0.00 0.00 3.32
4995 5755 2.658285 TGATTGATGGATTGTCAGCCC 58.342 47.619 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.