Multiple sequence alignment - TraesCS1B01G036100

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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 TraesCS1B01G036100 chr1B 100.000 2252 0 0 1 2252 17287221 17289472 0.000000e+00 4159.0
1 TraesCS1B01G036100 chr1B 96.174 1359 36 7 1 1357 16669437 16668093 0.000000e+00 2207.0
2 TraesCS1B01G036100 chr1B 88.957 978 55 15 533 1479 16506983 16506028 0.000000e+00 1158.0
3 TraesCS1B01G036100 chr1B 93.074 693 36 3 787 1479 17331642 17330962 0.000000e+00 1003.0
4 TraesCS1B01G036100 chr1B 86.032 945 106 17 533 1466 16659007 16658078 0.000000e+00 990.0
5 TraesCS1B01G036100 chr1B 91.429 595 44 4 1493 2081 16820898 16820305 0.000000e+00 809.0
6 TraesCS1B01G036100 chr1B 89.228 492 36 9 1 485 16503491 16503010 1.150000e-167 599.0
7 TraesCS1B01G036100 chr1B 88.438 493 41 10 1 485 16659474 16658990 4.170000e-162 580.0
8 TraesCS1B01G036100 chr1B 88.391 491 46 8 1 485 17332738 17332253 4.170000e-162 580.0
9 TraesCS1B01G036100 chr1B 85.192 574 69 11 1558 2122 17330625 17330059 1.940000e-160 575.0
10 TraesCS1B01G036100 chr1D 91.339 1732 122 18 533 2252 11206793 11205078 0.000000e+00 2342.0
11 TraesCS1B01G036100 chr1D 88.763 970 60 15 533 1479 11136574 11135631 0.000000e+00 1142.0
12 TraesCS1B01G036100 chr1D 87.779 941 93 14 533 1466 11012724 11011799 0.000000e+00 1081.0
13 TraesCS1B01G036100 chr1D 87.779 941 92 15 533 1466 11050521 11049597 0.000000e+00 1079.0
14 TraesCS1B01G036100 chr1D 87.673 941 94 14 533 1466 11098058 11097133 0.000000e+00 1075.0
15 TraesCS1B01G036100 chr1D 87.248 941 99 13 533 1466 11132508 11131582 0.000000e+00 1053.0
16 TraesCS1B01G036100 chr1D 92.073 492 29 6 1 485 11098529 11098041 0.000000e+00 684.0
17 TraesCS1B01G036100 chr1D 91.870 492 30 6 1 485 11013195 11012707 0.000000e+00 678.0
18 TraesCS1B01G036100 chr1D 91.870 492 30 6 1 485 11050992 11050504 0.000000e+00 678.0
19 TraesCS1B01G036100 chr1D 81.461 712 96 27 1560 2252 11049375 11048681 3.270000e-153 551.0
20 TraesCS1B01G036100 chr1D 81.320 712 97 27 1560 2252 11096911 11096217 1.520000e-151 545.0
21 TraesCS1B01G036100 chr1D 81.180 712 98 27 1560 2252 11011577 11010883 7.080000e-150 540.0
22 TraesCS1B01G036100 chr1D 80.309 711 106 23 1560 2252 11131359 11130665 7.180000e-140 507.0
23 TraesCS1B01G036100 chr1A 88.056 921 88 9 533 1446 22626725 22627630 0.000000e+00 1072.0
24 TraesCS1B01G036100 chr1A 92.354 497 25 9 1 487 22626252 22626745 0.000000e+00 695.0
25 TraesCS1B01G036100 chr1A 89.095 486 40 11 6 485 13294309 13293831 1.930000e-165 592.0
26 TraesCS1B01G036100 chr1A 89.457 313 22 2 1167 1479 13284089 13283788 3.510000e-103 385.0
27 TraesCS1B01G036100 chrUn 86.996 892 97 10 533 1421 159315 158440 0.000000e+00 987.0
28 TraesCS1B01G036100 chrUn 80.872 711 102 24 1560 2252 158198 157504 1.530000e-146 529.0
29 TraesCS1B01G036100 chrUn 84.929 491 60 9 1641 2122 336669820 336669335 3.360000e-133 484.0
30 TraesCS1B01G036100 chrUn 89.457 313 22 2 1167 1479 381976550 381976249 3.510000e-103 385.0
31 TraesCS1B01G036100 chrUn 90.132 304 19 2 1167 1470 478190079 478190371 3.510000e-103 385.0
32 TraesCS1B01G036100 chrUn 90.272 257 21 1 533 789 466589627 466589375 1.290000e-87 333.0
33 TraesCS1B01G036100 chr3A 88.462 78 5 3 459 534 731259297 731259372 8.570000e-15 91.6
34 TraesCS1B01G036100 chr7A 98.039 51 1 0 482 532 80969543 80969593 3.080000e-14 89.8
35 TraesCS1B01G036100 chr7A 98.039 51 1 0 484 534 594870090 594870040 3.080000e-14 89.8
36 TraesCS1B01G036100 chr6A 98.000 50 1 0 484 533 35325238 35325189 1.110000e-13 87.9
37 TraesCS1B01G036100 chr7D 86.667 75 8 2 459 533 563309886 563309958 5.160000e-12 82.4
38 TraesCS1B01G036100 chr5B 86.842 76 7 3 459 533 436250739 436250812 5.160000e-12 82.4
39 TraesCS1B01G036100 chr4A 94.000 50 3 0 484 533 429542437 429542388 2.400000e-10 76.8
40 TraesCS1B01G036100 chr6B 85.333 75 7 3 459 532 62647699 62647770 8.630000e-10 75.0


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 TraesCS1B01G036100 chr1B 17287221 17289472 2251 False 4159.000000 4159 100.000000 1 2252 1 chr1B.!!$F1 2251
1 TraesCS1B01G036100 chr1B 16668093 16669437 1344 True 2207.000000 2207 96.174000 1 1357 1 chr1B.!!$R1 1356
2 TraesCS1B01G036100 chr1B 16503010 16506983 3973 True 878.500000 1158 89.092500 1 1479 2 chr1B.!!$R3 1478
3 TraesCS1B01G036100 chr1B 16820305 16820898 593 True 809.000000 809 91.429000 1493 2081 1 chr1B.!!$R2 588
4 TraesCS1B01G036100 chr1B 16658078 16659474 1396 True 785.000000 990 87.235000 1 1466 2 chr1B.!!$R4 1465
5 TraesCS1B01G036100 chr1B 17330059 17332738 2679 True 719.333333 1003 88.885667 1 2122 3 chr1B.!!$R5 2121
6 TraesCS1B01G036100 chr1D 11205078 11206793 1715 True 2342.000000 2342 91.339000 533 2252 1 chr1D.!!$R1 1719
7 TraesCS1B01G036100 chr1D 11130665 11136574 5909 True 900.666667 1142 85.440000 533 2252 3 chr1D.!!$R5 1719
8 TraesCS1B01G036100 chr1D 11048681 11050992 2311 True 769.333333 1079 87.036667 1 2252 3 chr1D.!!$R3 2251
9 TraesCS1B01G036100 chr1D 11096217 11098529 2312 True 768.000000 1075 87.022000 1 2252 3 chr1D.!!$R4 2251
10 TraesCS1B01G036100 chr1D 11010883 11013195 2312 True 766.333333 1081 86.943000 1 2252 3 chr1D.!!$R2 2251
11 TraesCS1B01G036100 chr1A 22626252 22627630 1378 False 883.500000 1072 90.205000 1 1446 2 chr1A.!!$F1 1445
12 TraesCS1B01G036100 chrUn 157504 159315 1811 True 758.000000 987 83.934000 533 2252 2 chrUn.!!$R4 1719

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
580 596 0.762418 TACGGGCATGTAATCCAGGG 59.238 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 6646 1.141053 GATGGAGGCCAACTTCGGTAT 59.859 52.381 5.01 0.0 36.95 2.73 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
284 297 8.990163 AGTACAAACTTGAAGGGAAAGAAATA 57.010 30.769 0.00 0.00 29.00 1.40
472 488 2.838804 AAAAAGGCTGGGCATGTGT 58.161 47.368 0.00 0.00 0.00 3.72
517 533 9.499585 CCTCGATATATCAATTGAATGAAATGC 57.500 33.333 13.09 0.00 32.06 3.56
565 581 1.937223 TGTTTTGTCTGCAGTGTACGG 59.063 47.619 14.67 0.00 0.00 4.02
566 582 1.263217 GTTTTGTCTGCAGTGTACGGG 59.737 52.381 14.67 0.00 0.00 5.28
567 583 0.882927 TTTGTCTGCAGTGTACGGGC 60.883 55.000 14.67 0.00 0.00 6.13
568 584 2.034048 TTGTCTGCAGTGTACGGGCA 62.034 55.000 14.67 5.89 35.96 5.36
580 596 0.762418 TACGGGCATGTAATCCAGGG 59.238 55.000 0.00 0.00 0.00 4.45
610 626 2.092049 TGCCAATCTTCCATGATGCTCT 60.092 45.455 0.00 0.00 0.00 4.09
635 651 5.759763 GTGCAAGATTTCATTCACCCTTTTT 59.240 36.000 0.00 0.00 0.00 1.94
673 690 6.471233 AAGGATCACTTTATCTGATGACGA 57.529 37.500 0.00 0.00 35.35 4.20
769 834 3.502920 CAAGGAGTACACTTCTAGCGTG 58.497 50.000 9.57 9.57 38.32 5.34
972 1426 7.188157 TGTGTTACAGTTTCGGTTATTTGTTC 58.812 34.615 0.00 0.00 0.00 3.18
978 1432 6.072673 ACAGTTTCGGTTATTTGTTCTGATCC 60.073 38.462 0.00 0.00 0.00 3.36
1020 1474 4.010349 GGATGAGTTCCGTGGAAAAGAAT 58.990 43.478 2.23 0.00 35.75 2.40
1120 1577 2.232208 GAGGCCAAGAAGGTGATTTTGG 59.768 50.000 5.01 0.00 42.30 3.28
1214 5729 1.214367 GTTCGCCTCTTTGTCGACAA 58.786 50.000 26.53 26.53 31.48 3.18
1286 5801 2.520039 CCTGCTGCTCGCGTACATG 61.520 63.158 5.77 0.00 43.27 3.21
1287 5802 1.807165 CTGCTGCTCGCGTACATGT 60.807 57.895 5.77 2.69 43.27 3.21
1288 5803 0.525455 CTGCTGCTCGCGTACATGTA 60.525 55.000 5.77 0.08 43.27 2.29
1289 5804 0.525455 TGCTGCTCGCGTACATGTAG 60.525 55.000 5.62 2.03 43.27 2.74
1532 6393 8.639761 ACACCCTATACTACATATGTTCAGTTC 58.360 37.037 14.77 0.00 0.00 3.01
1549 6410 8.383175 TGTTCAGTTCTATTTAGGAAACTCCAT 58.617 33.333 0.00 0.00 43.67 3.41
1607 6535 5.124936 GCCGTCAAAACCATAAAAGTAGGAT 59.875 40.000 0.00 0.00 0.00 3.24
1716 6646 5.866633 CCAGCGTTCCAAAAGCAAAAATATA 59.133 36.000 0.77 0.00 0.00 0.86
1842 6780 6.337356 CACAATTACTGGAAACAACACCTTT 58.663 36.000 0.00 0.00 42.06 3.11
2059 9227 4.334481 TCGACTCAAAGTTTTCTCCCAAAC 59.666 41.667 0.00 0.00 36.97 2.93
2135 9303 9.208022 TCCGAGACAAAGCTATATTTGATATTG 57.792 33.333 6.22 0.00 41.71 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
321 334 5.810080 AGCTAAGAAGTTTGTACTCCACT 57.190 39.130 0.00 0.00 31.99 4.00
472 488 6.227522 TCGAGGTGATACAAACAAGAATCAA 58.772 36.000 0.00 0.00 30.60 2.57
539 555 4.675510 ACACTGCAGACAAAACAAGAATG 58.324 39.130 23.35 5.61 0.00 2.67
565 581 0.396974 TTGGCCCTGGATTACATGCC 60.397 55.000 0.00 0.00 43.53 4.40
566 582 1.035139 CTTGGCCCTGGATTACATGC 58.965 55.000 0.00 0.00 0.00 4.06
567 583 2.734755 TCTTGGCCCTGGATTACATG 57.265 50.000 0.00 0.00 0.00 3.21
568 584 4.812096 GCATATCTTGGCCCTGGATTACAT 60.812 45.833 0.00 0.00 0.00 2.29
595 611 2.034104 GCACAGAGCATCATGGAAGA 57.966 50.000 0.00 0.00 44.79 2.87
610 626 3.499338 AGGGTGAATGAAATCTTGCACA 58.501 40.909 9.03 0.00 0.00 4.57
635 651 4.278669 GTGATCCTTATCTACCTCGAGCAA 59.721 45.833 6.99 0.00 32.93 3.91
939 1391 5.124138 ACCGAAACTGTAACACAAAATCACA 59.876 36.000 0.00 0.00 0.00 3.58
972 1426 1.830279 TGCTTGCTTCCTTGGATCAG 58.170 50.000 0.00 0.00 0.00 2.90
978 1432 2.352421 CCTTGTGATGCTTGCTTCCTTG 60.352 50.000 6.13 0.00 0.00 3.61
1020 1474 2.284405 GTGTTCCCTCCCTCCGGA 60.284 66.667 2.93 2.93 36.45 5.14
1214 5729 1.331214 CTGGGCAATGGTGTTGAGTT 58.669 50.000 0.00 0.00 0.00 3.01
1286 5801 6.479990 TGATCAAGCTGCAATACATGTACTAC 59.520 38.462 7.96 0.81 0.00 2.73
1287 5802 6.581712 TGATCAAGCTGCAATACATGTACTA 58.418 36.000 7.96 0.00 0.00 1.82
1288 5803 5.430886 TGATCAAGCTGCAATACATGTACT 58.569 37.500 7.96 0.00 0.00 2.73
1289 5804 5.739752 TGATCAAGCTGCAATACATGTAC 57.260 39.130 7.96 0.00 0.00 2.90
1549 6410 3.446873 ACTGTGTTTTTCATGCCACTTCA 59.553 39.130 0.00 0.00 0.00 3.02
1607 6535 9.537852 TTGATCTCTAGTTTTACTAGGTGGTTA 57.462 33.333 12.53 0.00 46.25 2.85
1716 6646 1.141053 GATGGAGGCCAACTTCGGTAT 59.859 52.381 5.01 0.00 36.95 2.73
1812 6747 2.625790 GTTTCCAGTAATTGTGGCACCA 59.374 45.455 16.26 4.06 34.77 4.17
2059 9227 3.316029 TCATTGGACAGAAGTTGCAACAG 59.684 43.478 30.11 18.51 0.00 3.16
2135 9303 2.904011 TGTGTCGGTGTGTGTTTTTC 57.096 45.000 0.00 0.00 0.00 2.29
2191 9360 9.593134 GTCCTAACATGGATAATGATCAGATAC 57.407 37.037 0.09 0.00 38.72 2.24
2199 9368 9.739276 GGAAATATGTCCTAACATGGATAATGA 57.261 33.333 4.48 0.00 45.72 2.57


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

AutoCloner maintained by Alex Coulton.