Multiple sequence alignment - TraesCS7B01G104900

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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 TraesCS7B01G104900 chr7B 100.000 1850 0 0 1 1850 121052510 121054359 0.000000e+00 3417.0
1 TraesCS7B01G104900 chr7B 88.540 1754 119 44 137 1850 121241682 121243393 0.000000e+00 2050.0
2 TraesCS7B01G104900 chr7B 88.299 1752 125 38 137 1850 121319925 121321634 0.000000e+00 2026.0
3 TraesCS7B01G104900 chr7B 96.334 982 25 5 869 1850 121115422 121116392 0.000000e+00 1604.0
4 TraesCS7B01G104900 chr7B 96.236 983 25 6 869 1850 121166748 121167719 0.000000e+00 1600.0
5 TraesCS7B01G104900 chr7B 88.527 1168 94 22 537 1692 121495581 121496720 0.000000e+00 1378.0
6 TraesCS7B01G104900 chr7B 94.602 778 31 2 1 770 121113136 121113910 0.000000e+00 1194.0
7 TraesCS7B01G104900 chr7B 94.602 778 31 2 1 770 121164492 121165266 0.000000e+00 1194.0
8 TraesCS7B01G104900 chr7B 96.785 622 19 1 1229 1850 121386488 121387108 0.000000e+00 1037.0
9 TraesCS7B01G104900 chr7B 100.000 377 0 0 2149 2525 121054658 121055034 0.000000e+00 697.0
10 TraesCS7B01G104900 chr7B 90.741 378 30 4 2149 2524 121387474 121387848 1.350000e-137 499.0
11 TraesCS7B01G104900 chr7B 90.463 367 32 3 2160 2524 121321915 121322280 4.890000e-132 481.0
12 TraesCS7B01G104900 chr7B 89.125 377 36 5 2151 2524 121243748 121244122 4.920000e-127 464.0
13 TraesCS7B01G104900 chr7B 87.831 378 29 8 2149 2524 121116456 121116818 6.450000e-116 427.0
14 TraesCS7B01G104900 chr7B 87.831 378 29 8 2149 2524 121167783 121168145 6.450000e-116 427.0
15 TraesCS7B01G104900 chr7B 76.923 559 88 24 137 668 121385579 121386123 1.910000e-71 279.0
16 TraesCS7B01G104900 chr7B 83.258 221 17 11 667 880 121386282 121386489 4.290000e-43 185.0
17 TraesCS7B01G104900 chr7B 78.764 259 31 16 315 550 121494520 121494777 4.350000e-33 152.0
18 TraesCS7B01G104900 chr7D 90.845 1715 103 22 3 1684 160486685 160488378 0.000000e+00 2248.0
19 TraesCS7B01G104900 chr7D 89.080 1163 82 22 537 1684 160533702 160534834 0.000000e+00 1402.0
20 TraesCS7B01G104900 chr7D 88.714 381 37 6 2149 2524 160488628 160489007 6.360000e-126 460.0
21 TraesCS7B01G104900 chr7D 89.344 122 4 2 1709 1821 160488371 160488492 7.280000e-31 145.0
22 TraesCS7B01G104900 chr7D 100.000 28 0 0 1821 1848 160488522 160488549 5.000000e-03 52.8
23 TraesCS7B01G104900 chr7A 91.691 1348 67 14 349 1671 161279223 161280550 0.000000e+00 1827.0
24 TraesCS7B01G104900 chr7A 88.879 1178 79 27 537 1692 161650173 161651320 0.000000e+00 1402.0
25 TraesCS7B01G104900 chr7A 89.337 347 32 3 1 345 161274587 161274930 4.990000e-117 431.0
26 TraesCS7B01G104900 chr7A 95.349 43 2 0 93 135 161648344 161648386 4.510000e-08 69.4
27 TraesCS7B01G104900 chr3D 92.857 42 2 1 415 456 3979283 3979243 2.710000e-05 60.2


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 TraesCS7B01G104900 chr7B 121052510 121055034 2524 False 2057.000000 3417 100.000000 1 2525 2 chr7B.!!$F1 2524
1 TraesCS7B01G104900 chr7B 121241682 121244122 2440 False 1257.000000 2050 88.832500 137 2524 2 chr7B.!!$F4 2387
2 TraesCS7B01G104900 chr7B 121319925 121322280 2355 False 1253.500000 2026 89.381000 137 2524 2 chr7B.!!$F5 2387
3 TraesCS7B01G104900 chr7B 121113136 121116818 3682 False 1075.000000 1604 92.922333 1 2524 3 chr7B.!!$F2 2523
4 TraesCS7B01G104900 chr7B 121164492 121168145 3653 False 1073.666667 1600 92.889667 1 2524 3 chr7B.!!$F3 2523
5 TraesCS7B01G104900 chr7B 121494520 121496720 2200 False 765.000000 1378 83.645500 315 1692 2 chr7B.!!$F7 1377
6 TraesCS7B01G104900 chr7B 121385579 121387848 2269 False 500.000000 1037 86.926750 137 2524 4 chr7B.!!$F6 2387
7 TraesCS7B01G104900 chr7D 160533702 160534834 1132 False 1402.000000 1402 89.080000 537 1684 1 chr7D.!!$F1 1147
8 TraesCS7B01G104900 chr7D 160486685 160489007 2322 False 726.450000 2248 92.225750 3 2524 4 chr7D.!!$F2 2521
9 TraesCS7B01G104900 chr7A 161279223 161280550 1327 False 1827.000000 1827 91.691000 349 1671 1 chr7A.!!$F2 1322
10 TraesCS7B01G104900 chr7A 161648344 161651320 2976 False 735.700000 1402 92.114000 93 1692 2 chr7A.!!$F3 1599

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
553 2538 0.251165 ATAAGCCGCAACCACCAACT 60.251 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 6012 0.04087 TTGGCGTAATGTTGCACACG 60.041 50.0 0.0 0.0 37.45 4.49 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
260 290 8.996024 TTTTCATGAGAACAGATGATTACGTA 57.004 30.769 0.00 0.00 32.39 3.57
324 358 6.146673 AGTTCCGTACAACAAATAGCTTACAC 59.853 38.462 0.00 0.00 0.00 2.90
553 2538 0.251165 ATAAGCCGCAACCACCAACT 60.251 50.000 0.00 0.00 0.00 3.16
581 2566 0.526662 ACAGTAGGCAGTAGCGACAC 59.473 55.000 0.00 0.00 43.41 3.67
714 2869 6.727394 ACTGCCCAAACAAATAGACCTAATA 58.273 36.000 0.00 0.00 0.00 0.98
788 2958 5.988092 TGGAAATAAAACGAAACTGTACCG 58.012 37.500 0.00 1.11 0.00 4.02
1445 5046 1.910580 AACCGGGGCGTCTTCATCAT 61.911 55.000 6.32 0.00 0.00 2.45
1482 5083 2.251371 GGCAACTTCAACGGCGAC 59.749 61.111 16.62 0.00 0.00 5.19
1527 5128 0.822164 ACGCCGAAGCCAAGTAGTAT 59.178 50.000 0.00 0.00 34.57 2.12
1557 5162 7.295930 GTGTGAATGTGATCATACATGCATAG 58.704 38.462 9.57 0.00 45.72 2.23
1561 5170 5.294734 TGTGATCATACATGCATAGGTGT 57.705 39.130 0.00 0.00 0.00 4.16
1579 5202 3.488384 GGTGTGTGTGTTTATGTGTGTGG 60.488 47.826 0.00 0.00 0.00 4.17
1687 5310 0.319555 TCTGTGGAGCGTGTAAGTGC 60.320 55.000 0.00 0.00 0.00 4.40
2237 5971 9.582431 CAAAGGTATAACGAAGACAAAGATCTA 57.418 33.333 0.00 0.00 0.00 1.98
2276 6012 2.399916 AGCAGAGAAATGGCACTCTC 57.600 50.000 16.88 16.88 40.85 3.20
2280 6016 1.620819 AGAGAAATGGCACTCTCGTGT 59.379 47.619 17.97 3.74 42.46 4.49
2281 6017 1.728971 GAGAAATGGCACTCTCGTGTG 59.271 52.381 11.46 0.00 43.16 3.82
2328 6065 7.151308 ACAATGAAACAACAGAAAGACACAAA 58.849 30.769 0.00 0.00 0.00 2.83
2333 6070 6.407475 AACAACAGAAAGACACAAATTTGC 57.593 33.333 18.12 2.19 0.00 3.68
2336 6073 6.036300 ACAACAGAAAGACACAAATTTGCATG 59.964 34.615 18.12 12.07 0.00 4.06
2433 6172 3.191162 GTGTGCTTGATAGTTTGGCATGA 59.809 43.478 0.00 0.00 35.37 3.07
2445 6184 2.113860 TGGCATGAGTTCTTACTGCC 57.886 50.000 0.00 4.95 39.96 4.85
2447 6186 1.405526 GGCATGAGTTCTTACTGCCGA 60.406 52.381 0.00 0.00 33.07 5.54
2459 6198 2.015736 ACTGCCGATTTGCTAGAGTG 57.984 50.000 0.00 0.00 0.00 3.51
2488 6227 7.110810 CCTATATTGCAGACATGAAGATCCAT 58.889 38.462 0.00 0.00 0.00 3.41
2500 6239 2.795231 AGATCCATATGGCGATTGGG 57.205 50.000 17.58 2.19 34.44 4.12
2524 6263 2.496070 TCATCTAGGCTGCGTAGTGTTT 59.504 45.455 23.84 9.20 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 60 6.144886 GTGACATTTGTATGCATGCATTATGG 59.855 38.462 36.23 22.26 37.82 2.74
106 116 0.320771 TTGTCGAGCTCCTTTGCCTC 60.321 55.000 8.47 0.00 0.00 4.70
107 117 0.321122 CTTGTCGAGCTCCTTTGCCT 60.321 55.000 8.47 0.00 0.00 4.75
108 118 2.166270 CTTGTCGAGCTCCTTTGCC 58.834 57.895 8.47 0.00 0.00 4.52
189 217 0.101399 AAGAGCGCGATGACGAAGAT 59.899 50.000 12.10 0.00 42.66 2.40
223 253 6.317140 TGTTCTCATGAAAATAGCCATGACTC 59.683 38.462 0.00 0.00 42.76 3.36
419 454 7.681939 TGAGTCAATAAAAGCGTCCTTTAAT 57.318 32.000 0.00 0.00 40.30 1.40
474 1617 9.597170 GTCATGCATAGATCACATGTCTATTAT 57.403 33.333 0.00 0.00 41.51 1.28
486 1629 5.916318 TGTGTGTATGTCATGCATAGATCA 58.084 37.500 6.89 0.00 40.42 2.92
631 2617 1.305930 GGGCGGCGAAGATGAAAACT 61.306 55.000 12.98 0.00 0.00 2.66
714 2869 0.756294 TCCATGCAATCCCGACGTAT 59.244 50.000 0.00 0.00 0.00 3.06
788 2958 3.461061 TCATGACTTGCTAGCTACATGC 58.539 45.455 24.37 5.85 43.29 4.06
819 2993 6.870439 GGGGAAAAGAATAATTAGATGCATGC 59.130 38.462 11.82 11.82 0.00 4.06
836 4343 1.135286 GCAAGAAGATGCGGGGAAAAG 60.135 52.381 0.00 0.00 36.45 2.27
1138 4739 1.577328 CTGTTGTCCCATGTCACCGC 61.577 60.000 0.00 0.00 0.00 5.68
1527 5128 5.715070 TGTATGATCACATTCACACGTACA 58.285 37.500 0.00 0.00 37.87 2.90
1557 5162 3.488384 CCACACACATAAACACACACACC 60.488 47.826 0.00 0.00 0.00 4.16
1561 5170 5.843673 AAATCCACACACATAAACACACA 57.156 34.783 0.00 0.00 0.00 3.72
1618 5241 3.541916 GTGCGCTTATTTACGTACGTACA 59.458 43.478 26.83 21.25 35.32 2.90
2237 5971 4.286032 TGCTAGTAACATGTTCAAGTCCCT 59.714 41.667 15.85 3.72 0.00 4.20
2276 6012 0.040870 TTGGCGTAATGTTGCACACG 60.041 50.000 0.00 0.00 37.45 4.49
2280 6016 0.878416 GGTCTTGGCGTAATGTTGCA 59.122 50.000 0.00 0.00 0.00 4.08
2281 6017 1.135689 CAGGTCTTGGCGTAATGTTGC 60.136 52.381 0.00 0.00 0.00 4.17
2284 6020 3.551259 CCAGGTCTTGGCGTAATGT 57.449 52.632 0.00 0.00 40.87 2.71
2303 6039 6.266168 TGTGTCTTTCTGTTGTTTCATTGT 57.734 33.333 0.00 0.00 0.00 2.71
2328 6065 8.477984 AATTTAAGTCATTAACGCATGCAAAT 57.522 26.923 19.57 11.01 30.58 2.32
2433 6172 3.059352 AGCAAATCGGCAGTAAGAACT 57.941 42.857 0.00 0.00 35.91 3.01
2463 6202 6.470278 TGGATCTTCATGTCTGCAATATAGG 58.530 40.000 0.00 0.00 0.00 2.57
2479 6218 3.012518 CCCAATCGCCATATGGATCTTC 58.987 50.000 26.47 6.09 36.27 2.87
2488 6227 1.774254 AGATGAACCCCAATCGCCATA 59.226 47.619 0.00 0.00 0.00 2.74
2500 6239 1.409427 ACTACGCAGCCTAGATGAACC 59.591 52.381 5.52 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.