Multiple sequence alignment - TraesCS7B01G445100

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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 TraesCS7B01G445100 chr7B 100.000 2276 0 0 1 2276 709109489 709111764 0.000000e+00 4204
1 TraesCS7B01G445100 chr7B 92.260 1279 88 5 1 1277 26210379 26209110 0.000000e+00 1803
2 TraesCS7B01G445100 chr7B 96.822 409 13 0 1274 1682 726743087 726742679 0.000000e+00 684
3 TraesCS7B01G445100 chr7B 96.059 406 16 0 1277 1682 746620020 746619615 0.000000e+00 662
4 TraesCS7B01G445100 chr7B 94.249 313 16 2 1277 1587 140265791 140265479 5.690000e-131 477
5 TraesCS7B01G445100 chr3A 92.874 1277 84 1 1 1277 440509558 440510827 0.000000e+00 1847
6 TraesCS7B01G445100 chr3A 90.323 155 14 1 2122 2276 403396626 403396473 3.830000e-48 202
7 TraesCS7B01G445100 chr5B 92.476 1276 87 2 4 1277 543261370 543260102 0.000000e+00 1816
8 TraesCS7B01G445100 chr5B 99.012 405 4 0 1278 1682 399036887 399037291 0.000000e+00 726
9 TraesCS7B01G445100 chr5B 95.833 408 16 1 1275 1682 708964545 708964951 0.000000e+00 658
10 TraesCS7B01G445100 chr6B 92.103 1279 90 5 1 1277 583194308 583193039 0.000000e+00 1792
11 TraesCS7B01G445100 chr6B 91.862 1278 96 4 1 1277 16962020 16960750 0.000000e+00 1777
12 TraesCS7B01G445100 chr6B 84.651 215 31 2 1687 1900 1163021 1162808 1.770000e-51 213
13 TraesCS7B01G445100 chr1B 92.013 1277 94 2 1 1277 487940112 487941380 0.000000e+00 1786
14 TraesCS7B01G445100 chr1B 97.831 415 9 0 1268 1682 564361353 564360939 0.000000e+00 717
15 TraesCS7B01G445100 chr1B 83.117 231 35 3 1687 1916 55975963 55975736 8.240000e-50 207
16 TraesCS7B01G445100 chr1B 83.117 231 35 3 1687 1916 55997537 55997310 8.240000e-50 207
17 TraesCS7B01G445100 chr5D 85.377 1272 176 4 7 1277 300148864 300147602 0.000000e+00 1310
18 TraesCS7B01G445100 chr5D 84.694 1274 180 8 7 1277 300324794 300323533 0.000000e+00 1258
19 TraesCS7B01G445100 chr5D 85.646 209 30 0 1687 1895 230488123 230487915 1.060000e-53 220
20 TraesCS7B01G445100 chr4D 84.235 1275 187 9 7 1277 59513412 59512148 0.000000e+00 1229
21 TraesCS7B01G445100 chr4B 99.492 590 3 0 1687 2276 617144678 617145267 0.000000e+00 1074
22 TraesCS7B01G445100 chr4B 81.016 1280 215 18 4 1277 480843951 480842694 0.000000e+00 992
23 TraesCS7B01G445100 chr6D 83.906 1019 157 1 5 1023 54048380 54049391 0.000000e+00 966
24 TraesCS7B01G445100 chr2B 98.280 407 4 2 1278 1682 460548635 460548230 0.000000e+00 710
25 TraesCS7B01G445100 chr2B 95.802 405 16 1 1278 1682 571156359 571156762 0.000000e+00 652
26 TraesCS7B01G445100 chr2B 82.158 241 38 4 1684 1921 66032888 66033126 3.830000e-48 202
27 TraesCS7B01G445100 chr6A 93.949 314 17 2 1276 1587 602356386 602356073 7.360000e-130 473
28 TraesCS7B01G445100 chr6A 96.396 111 4 0 1572 1682 602355956 602355846 1.390000e-42 183
29 TraesCS7B01G445100 chr2A 84.958 359 48 3 1687 2045 30221813 30221461 2.150000e-95 359
30 TraesCS7B01G445100 chr2A 85.714 133 18 1 2144 2276 30220811 30220680 3.050000e-29 139
31 TraesCS7B01G445100 chr3D 85.714 210 30 0 1686 1895 135860179 135859970 2.940000e-54 222
32 TraesCS7B01G445100 chr3D 85.238 210 31 0 1686 1895 18400451 18400242 1.370000e-52 217
33 TraesCS7B01G445100 chr5A 98.131 107 2 0 1576 1682 706324321 706324215 1.070000e-43 187


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 TraesCS7B01G445100 chr7B 709109489 709111764 2275 False 4204 4204 100.0000 1 2276 1 chr7B.!!$F1 2275
1 TraesCS7B01G445100 chr7B 26209110 26210379 1269 True 1803 1803 92.2600 1 1277 1 chr7B.!!$R1 1276
2 TraesCS7B01G445100 chr3A 440509558 440510827 1269 False 1847 1847 92.8740 1 1277 1 chr3A.!!$F1 1276
3 TraesCS7B01G445100 chr5B 543260102 543261370 1268 True 1816 1816 92.4760 4 1277 1 chr5B.!!$R1 1273
4 TraesCS7B01G445100 chr6B 583193039 583194308 1269 True 1792 1792 92.1030 1 1277 1 chr6B.!!$R3 1276
5 TraesCS7B01G445100 chr6B 16960750 16962020 1270 True 1777 1777 91.8620 1 1277 1 chr6B.!!$R2 1276
6 TraesCS7B01G445100 chr1B 487940112 487941380 1268 False 1786 1786 92.0130 1 1277 1 chr1B.!!$F1 1276
7 TraesCS7B01G445100 chr5D 300147602 300148864 1262 True 1310 1310 85.3770 7 1277 1 chr5D.!!$R2 1270
8 TraesCS7B01G445100 chr5D 300323533 300324794 1261 True 1258 1258 84.6940 7 1277 1 chr5D.!!$R3 1270
9 TraesCS7B01G445100 chr4D 59512148 59513412 1264 True 1229 1229 84.2350 7 1277 1 chr4D.!!$R1 1270
10 TraesCS7B01G445100 chr4B 617144678 617145267 589 False 1074 1074 99.4920 1687 2276 1 chr4B.!!$F1 589
11 TraesCS7B01G445100 chr4B 480842694 480843951 1257 True 992 992 81.0160 4 1277 1 chr4B.!!$R1 1273
12 TraesCS7B01G445100 chr6D 54048380 54049391 1011 False 966 966 83.9060 5 1023 1 chr6D.!!$F1 1018
13 TraesCS7B01G445100 chr6A 602355846 602356386 540 True 328 473 95.1725 1276 1682 2 chr6A.!!$R1 406
14 TraesCS7B01G445100 chr2A 30220680 30221813 1133 True 249 359 85.3360 1687 2276 2 chr2A.!!$R1 589

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
495 497 0.03438 AGTGCATTGCTCTCATGCCT 60.034 50.0 10.49 0.0 40.34 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1539 0.661187 ATTTTCGCAGCAACGCACAG 60.661 50.0 0.0 0.0 0.0 3.66 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
110 111 4.147653 CGTCGGGAATTAATACGTGATGTC 59.852 45.833 0.00 0.00 0.00 3.06
115 116 6.256975 CGGGAATTAATACGTGATGTCTTTGA 59.743 38.462 0.00 0.00 0.00 2.69
118 119 8.612619 GGAATTAATACGTGATGTCTTTGATGT 58.387 33.333 0.00 0.00 0.00 3.06
119 120 9.425893 GAATTAATACGTGATGTCTTTGATGTG 57.574 33.333 0.00 0.00 0.00 3.21
137 138 3.017323 CCTGACGCGGATGCAATC 58.983 61.111 12.47 0.00 44.55 2.67
305 307 4.262635 GGATCCTCACAGACTGAAGAACAA 60.263 45.833 10.08 0.00 0.00 2.83
341 343 0.318441 GGAAGCTCAAGGTTTTGCCC 59.682 55.000 0.00 0.00 38.26 5.36
380 382 1.303317 GAGGGTTGTCCGTGGCATT 60.303 57.895 0.00 0.00 41.52 3.56
430 432 4.122046 CGCCATATCAAACTCATCAGTCA 58.878 43.478 0.00 0.00 29.93 3.41
473 475 3.693578 TGGATGAAGATTTAATGCACGCA 59.306 39.130 0.00 0.00 0.00 5.24
492 494 3.946308 CACTAGTGCATTGCTCTCATG 57.054 47.619 15.93 11.76 34.22 3.07
493 495 2.031807 CACTAGTGCATTGCTCTCATGC 59.968 50.000 15.93 0.00 41.35 4.06
494 496 1.602851 CTAGTGCATTGCTCTCATGCC 59.397 52.381 15.93 0.00 40.34 4.40
495 497 0.034380 AGTGCATTGCTCTCATGCCT 60.034 50.000 10.49 0.00 40.34 4.75
496 498 0.381089 GTGCATTGCTCTCATGCCTC 59.619 55.000 10.49 0.00 40.34 4.70
497 499 0.034863 TGCATTGCTCTCATGCCTCA 60.035 50.000 10.49 0.00 40.34 3.86
538 540 3.810941 ACAAGCCTTCGTTTTGTTCGATA 59.189 39.130 0.00 0.00 37.18 2.92
540 542 5.640357 ACAAGCCTTCGTTTTGTTCGATATA 59.360 36.000 0.00 0.00 37.18 0.86
628 630 4.494091 TTGGAAAGGTCTCAGATGATCC 57.506 45.455 0.00 0.00 0.00 3.36
629 631 3.729108 TGGAAAGGTCTCAGATGATCCT 58.271 45.455 0.00 2.23 32.45 3.24
640 642 5.244851 TCTCAGATGATCCTAGTTATGTGGC 59.755 44.000 0.00 0.00 0.00 5.01
683 685 9.941325 AAATAGAGTTACTCATGATGATGATCC 57.059 33.333 15.23 0.00 37.97 3.36
727 731 0.389757 GAGGATACGGGAGGACTTGC 59.610 60.000 0.00 0.00 46.39 4.01
729 733 1.446366 GATACGGGAGGACTTGCCC 59.554 63.158 0.00 0.00 41.11 5.36
730 734 2.041206 GATACGGGAGGACTTGCCCC 62.041 65.000 0.00 0.00 41.50 5.80
755 759 4.895889 ACTCGATATTCCTCTTCCACATGA 59.104 41.667 0.00 0.00 0.00 3.07
757 761 5.787380 TCGATATTCCTCTTCCACATGATG 58.213 41.667 0.00 0.00 0.00 3.07
939 943 1.828595 TCGGATCCGTTCATTGGAGAA 59.171 47.619 32.15 6.86 39.30 2.87
980 984 3.585862 GAGTCATCTTTGCGAACCTACA 58.414 45.455 0.00 0.00 0.00 2.74
1286 1292 8.299570 TGCCTTTGTTGAATAAAGAGAGAATTC 58.700 33.333 14.80 0.00 37.33 2.17
1312 1318 8.729756 CCTTATTTGGCCCTTTCTTAAATTTTG 58.270 33.333 0.00 0.00 0.00 2.44
1313 1319 9.283768 CTTATTTGGCCCTTTCTTAAATTTTGT 57.716 29.630 0.00 0.00 0.00 2.83
1335 1341 3.500448 TCCCTTTTTGGCCCAAAATTC 57.500 42.857 21.65 0.00 41.89 2.17
1338 1344 3.411446 CCTTTTTGGCCCAAAATTCTCC 58.589 45.455 21.65 0.00 41.89 3.71
1339 1345 3.072915 CCTTTTTGGCCCAAAATTCTCCT 59.927 43.478 21.65 0.00 41.89 3.69
1372 1378 8.170553 CCTTTTTGACACTCAAACTTCATTTTG 58.829 33.333 0.00 0.00 45.03 2.44
1376 1382 6.329496 TGACACTCAAACTTCATTTTGTTCC 58.671 36.000 0.00 0.00 37.66 3.62
1431 1437 6.839820 AACGGTGTTAAGTCTGAACTAAAG 57.160 37.500 1.66 0.00 33.48 1.85
1533 1539 7.556275 TGGTGTTGAATAAACTAGATGATTCCC 59.444 37.037 7.45 3.02 39.70 3.97
1536 1542 8.328758 TGTTGAATAAACTAGATGATTCCCTGT 58.671 33.333 7.45 0.00 39.70 4.00
1542 1548 1.742761 AGATGATTCCCTGTGCGTTG 58.257 50.000 0.00 0.00 0.00 4.10
1559 1565 4.074272 GCGTTGCTGCGAAAATTTTTATG 58.926 39.130 4.63 0.03 0.00 1.90
1561 1567 5.297314 CGTTGCTGCGAAAATTTTTATGAC 58.703 37.500 4.63 0.00 0.00 3.06
1566 1572 5.569823 GCTGCGAAAATTTTTATGACGGTAA 59.430 36.000 4.63 0.00 0.00 2.85
1614 1754 9.764363 CTTATGTATAGCAATCAGGTTTGTAGA 57.236 33.333 0.00 0.00 0.00 2.59
1682 1822 9.236006 TCCATTAGATACGTACCTAGGTTAATC 57.764 37.037 22.11 16.57 0.00 1.75
1683 1823 9.240734 CCATTAGATACGTACCTAGGTTAATCT 57.759 37.037 22.11 21.85 0.00 2.40
1757 1897 6.627276 CACAACAAACTGTACACAGAATAACG 59.373 38.462 16.05 3.38 46.59 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 1.133253 CGCGTCAGGCACATCAAAG 59.867 57.895 0.00 0.00 43.84 2.77
115 116 2.512286 CATCCGCGTCAGGCACAT 60.512 61.111 4.92 0.00 43.84 3.21
118 119 3.974835 ATTGCATCCGCGTCAGGCA 62.975 57.895 10.20 10.20 43.84 4.75
119 120 3.173390 GATTGCATCCGCGTCAGGC 62.173 63.158 4.92 5.03 42.97 4.85
134 135 3.646162 TGCGTAGTGGGATATTCAGGATT 59.354 43.478 0.00 0.00 0.00 3.01
137 138 2.628178 TCTGCGTAGTGGGATATTCAGG 59.372 50.000 0.00 0.00 0.00 3.86
167 168 2.419159 GGCCCAAGCAAGAAAATCATCC 60.419 50.000 0.00 0.00 42.56 3.51
231 232 4.576463 ACGCTCTTTTTGATTCACAAGAGT 59.424 37.500 23.55 11.85 39.77 3.24
305 307 3.535561 CTTCCATAGCGACTTCCACATT 58.464 45.455 0.00 0.00 0.00 2.71
341 343 1.464608 CACCAGAATACACGCACCTTG 59.535 52.381 0.00 0.00 0.00 3.61
380 382 2.507058 CAAGGTGGATTCATCAGGGAGA 59.493 50.000 0.00 0.00 0.00 3.71
430 432 4.155099 CCATTGCATGACAAACATTGCATT 59.845 37.500 0.00 0.00 42.86 3.56
473 475 2.286872 GCATGAGAGCAATGCACTAGT 58.713 47.619 8.35 0.00 40.72 2.57
492 494 1.068055 CAGAACAACTTGGCATGAGGC 60.068 52.381 7.45 0.00 43.74 4.70
493 495 1.542915 CCAGAACAACTTGGCATGAGG 59.457 52.381 7.45 1.42 0.00 3.86
494 496 1.542915 CCCAGAACAACTTGGCATGAG 59.457 52.381 7.45 0.00 0.00 2.90
495 497 1.144708 TCCCAGAACAACTTGGCATGA 59.855 47.619 7.45 0.00 32.20 3.07
496 498 1.619654 TCCCAGAACAACTTGGCATG 58.380 50.000 0.00 0.00 32.20 4.06
497 499 1.963515 GTTCCCAGAACAACTTGGCAT 59.036 47.619 2.65 0.00 32.20 4.40
538 540 1.520787 GTAAGCGTGGCCTGCGTAT 60.521 57.895 18.53 11.66 37.44 3.06
540 542 4.308458 TGTAAGCGTGGCCTGCGT 62.308 61.111 18.53 15.71 37.44 5.24
683 685 6.564709 TGACAGATGAAAAAGGATCAAGTG 57.435 37.500 0.00 0.00 0.00 3.16
727 731 3.764972 GGAAGAGGAATATCGAGTAGGGG 59.235 52.174 0.00 0.00 0.00 4.79
729 733 4.827835 TGTGGAAGAGGAATATCGAGTAGG 59.172 45.833 0.00 0.00 0.00 3.18
730 734 6.207614 TCATGTGGAAGAGGAATATCGAGTAG 59.792 42.308 0.00 0.00 0.00 2.57
755 759 4.666253 AACCTGGCAGCACCGCAT 62.666 61.111 9.56 0.00 43.94 4.73
757 761 3.605664 AAAACCTGGCAGCACCGC 61.606 61.111 9.56 0.00 43.94 5.68
799 803 5.062683 CCGCATCGGTATTGATCTTGATAAG 59.937 44.000 0.00 0.00 42.73 1.73
939 943 0.813184 CATCTCGCAAAGCCATGGTT 59.187 50.000 14.67 3.81 0.00 3.67
972 976 7.240678 TCACATGTGAGAAACCATGTAGGTTC 61.241 42.308 24.56 0.00 46.68 3.62
980 984 5.830000 CATGATCACATGTGAGAAACCAT 57.170 39.130 30.63 22.71 46.01 3.55
1286 1292 8.729756 CAAAATTTAAGAAAGGGCCAAATAAGG 58.270 33.333 6.18 0.00 0.00 2.69
1312 1318 2.719531 TTTGGGCCAAAAAGGGAAAC 57.280 45.000 28.69 0.00 38.09 2.78
1313 1319 3.961484 ATTTTGGGCCAAAAAGGGAAA 57.039 38.095 39.28 21.51 44.68 3.13
1335 1341 4.889995 AGTGTCAAAAAGGGAAGAAAGGAG 59.110 41.667 0.00 0.00 0.00 3.69
1338 1344 5.835113 TGAGTGTCAAAAAGGGAAGAAAG 57.165 39.130 0.00 0.00 0.00 2.62
1339 1345 6.210584 AGTTTGAGTGTCAAAAAGGGAAGAAA 59.789 34.615 3.71 0.00 46.53 2.52
1372 1378 2.028385 ACGGAAGTGTCACATAGGGAAC 60.028 50.000 5.62 0.00 46.97 3.62
1431 1437 4.886496 ACACTAGGGGTAAAACAGTCTC 57.114 45.455 0.00 0.00 0.00 3.36
1533 1539 0.661187 ATTTTCGCAGCAACGCACAG 60.661 50.000 0.00 0.00 0.00 3.66
1536 1542 1.565305 AAAATTTTCGCAGCAACGCA 58.435 40.000 0.00 0.00 0.00 5.24
1542 1548 3.917985 ACCGTCATAAAAATTTTCGCAGC 59.082 39.130 3.41 0.00 0.00 5.25
1603 1743 8.954950 ATCAGACAAGATTATCTACAAACCTG 57.045 34.615 0.00 0.00 0.00 4.00
1614 1754 7.829706 AGATGCATGCATATCAGACAAGATTAT 59.170 33.333 32.27 5.62 36.70 1.28


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

AutoCloner maintained by Alex Coulton.