Multiple sequence alignment - TraesCS4B01G169400

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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 TraesCS4B01G169400 chr4B 100.000 2393 0 0 1 2393 369878327 369880719 0.000000e+00 4420
1 TraesCS4B01G169400 chr4B 93.256 1468 95 2 1 1465 62158038 62156572 0.000000e+00 2159
2 TraesCS4B01G169400 chr4B 96.233 929 34 1 1466 2393 369894127 369895055 0.000000e+00 1520
3 TraesCS4B01G169400 chr4B 95.151 928 45 0 1466 2393 397337115 397336188 0.000000e+00 1465
4 TraesCS4B01G169400 chr7B 94.762 1470 69 5 1 1465 468442831 468441365 0.000000e+00 2281
5 TraesCS4B01G169400 chr7B 93.324 1468 93 4 1 1465 444367268 444365803 0.000000e+00 2163
6 TraesCS4B01G169400 chr7B 95.479 929 40 2 1466 2393 408573429 408572502 0.000000e+00 1482
7 TraesCS4B01G169400 chr1B 94.795 1460 72 3 1 1458 84172753 84171296 0.000000e+00 2272
8 TraesCS4B01G169400 chr1B 94.037 1459 86 1 1 1459 619517416 619518873 0.000000e+00 2211
9 TraesCS4B01G169400 chr1B 93.908 1461 84 3 2 1459 65160168 65161626 0.000000e+00 2200
10 TraesCS4B01G169400 chr1B 95.054 930 46 0 1464 2393 390643314 390642385 0.000000e+00 1463
11 TraesCS4B01G169400 chr2B 93.188 1468 96 2 1 1465 107976850 107975384 0.000000e+00 2154
12 TraesCS4B01G169400 chr2B 95.479 929 41 1 1466 2393 380854672 380855600 0.000000e+00 1482
13 TraesCS4B01G169400 chr2B 95.366 928 43 0 1466 2393 139181679 139180752 0.000000e+00 1476
14 TraesCS4B01G169400 chr2B 95.151 928 45 0 1466 2393 340385305 340386232 0.000000e+00 1465
15 TraesCS4B01G169400 chr3B 92.413 1463 107 1 1 1459 748301064 748302526 0.000000e+00 2084
16 TraesCS4B01G169400 chr3B 93.583 1309 79 3 1 1305 219315026 219316333 0.000000e+00 1947
17 TraesCS4B01G169400 chr3B 95.587 929 39 2 1466 2393 308438833 308437906 0.000000e+00 1487
18 TraesCS4B01G169400 chr3B 86.692 263 32 3 1198 1458 106112901 106113162 3.010000e-74 289
19 TraesCS4B01G169400 chr6B 95.156 929 43 2 1466 2393 58936858 58937785 0.000000e+00 1465


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 TraesCS4B01G169400 chr4B 369878327 369880719 2392 False 4420 4420 100.000 1 2393 1 chr4B.!!$F1 2392
1 TraesCS4B01G169400 chr4B 62156572 62158038 1466 True 2159 2159 93.256 1 1465 1 chr4B.!!$R1 1464
2 TraesCS4B01G169400 chr4B 369894127 369895055 928 False 1520 1520 96.233 1466 2393 1 chr4B.!!$F2 927
3 TraesCS4B01G169400 chr4B 397336188 397337115 927 True 1465 1465 95.151 1466 2393 1 chr4B.!!$R2 927
4 TraesCS4B01G169400 chr7B 468441365 468442831 1466 True 2281 2281 94.762 1 1465 1 chr7B.!!$R3 1464
5 TraesCS4B01G169400 chr7B 444365803 444367268 1465 True 2163 2163 93.324 1 1465 1 chr7B.!!$R2 1464
6 TraesCS4B01G169400 chr7B 408572502 408573429 927 True 1482 1482 95.479 1466 2393 1 chr7B.!!$R1 927
7 TraesCS4B01G169400 chr1B 84171296 84172753 1457 True 2272 2272 94.795 1 1458 1 chr1B.!!$R1 1457
8 TraesCS4B01G169400 chr1B 619517416 619518873 1457 False 2211 2211 94.037 1 1459 1 chr1B.!!$F2 1458
9 TraesCS4B01G169400 chr1B 65160168 65161626 1458 False 2200 2200 93.908 2 1459 1 chr1B.!!$F1 1457
10 TraesCS4B01G169400 chr1B 390642385 390643314 929 True 1463 1463 95.054 1464 2393 1 chr1B.!!$R2 929
11 TraesCS4B01G169400 chr2B 107975384 107976850 1466 True 2154 2154 93.188 1 1465 1 chr2B.!!$R1 1464
12 TraesCS4B01G169400 chr2B 380854672 380855600 928 False 1482 1482 95.479 1466 2393 1 chr2B.!!$F2 927
13 TraesCS4B01G169400 chr2B 139180752 139181679 927 True 1476 1476 95.366 1466 2393 1 chr2B.!!$R2 927
14 TraesCS4B01G169400 chr2B 340385305 340386232 927 False 1465 1465 95.151 1466 2393 1 chr2B.!!$F1 927
15 TraesCS4B01G169400 chr3B 748301064 748302526 1462 False 2084 2084 92.413 1 1459 1 chr3B.!!$F3 1458
16 TraesCS4B01G169400 chr3B 219315026 219316333 1307 False 1947 1947 93.583 1 1305 1 chr3B.!!$F2 1304
17 TraesCS4B01G169400 chr3B 308437906 308438833 927 True 1487 1487 95.587 1466 2393 1 chr3B.!!$R1 927
18 TraesCS4B01G169400 chr6B 58936858 58937785 927 False 1465 1465 95.156 1466 2393 1 chr6B.!!$F1 927

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
111 112 0.665835 GAGTCAGTCGCCATCGAGAT 59.334 55.0 0.0 0.0 46.46 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1784 1.696063 TAGTATTTCCTCGACCCCCG 58.304 55.0 0.0 0.0 40.25 5.73 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
111 112 0.665835 GAGTCAGTCGCCATCGAGAT 59.334 55.000 0.00 0.00 46.46 2.75
144 145 6.868864 CGGTAATGATCGAGATCCTTGTATTT 59.131 38.462 10.24 0.00 37.02 1.40
145 146 7.148738 CGGTAATGATCGAGATCCTTGTATTTG 60.149 40.741 10.24 0.00 37.02 2.32
216 217 3.664537 GCACTTCCGTTTGATCTCGTTTC 60.665 47.826 0.00 0.00 0.00 2.78
240 241 5.598769 GTTACAGCCATAACGAACTATCCT 58.401 41.667 0.00 0.00 0.00 3.24
326 336 7.113965 GCACGAATCTTAGCATAAAATCAATGG 59.886 37.037 0.00 0.00 0.00 3.16
341 351 8.773033 AAAATCAATGGCATAGGACTTAGATT 57.227 30.769 0.00 0.00 0.00 2.40
452 462 8.024285 AGTTCTTAGTCTCTAGTCATTGAAACG 58.976 37.037 0.00 0.00 0.00 3.60
462 472 3.502211 AGTCATTGAAACGGTTGGTGATC 59.498 43.478 0.00 0.00 0.00 2.92
630 640 5.874831 TGCAATTATTTTCGTAAGCGTGAT 58.125 33.333 0.00 0.00 39.49 3.06
669 679 6.294361 AGTGTACATAGACCAAAGTATGCA 57.706 37.500 0.00 0.00 30.91 3.96
732 742 6.183360 GCTGAGAGAGATAGCTTGTTTTTCTG 60.183 42.308 0.00 0.00 34.70 3.02
914 924 2.103601 AGGTTGCTTCTTTGCTGCAATT 59.896 40.909 16.77 0.00 46.25 2.32
954 964 5.356751 AGAATTAAACACACAGCAACTGACA 59.643 36.000 0.78 0.00 35.18 3.58
982 992 3.814504 AGTTGATTGGACTGGGTGAAT 57.185 42.857 0.00 0.00 0.00 2.57
983 993 3.424703 AGTTGATTGGACTGGGTGAATG 58.575 45.455 0.00 0.00 0.00 2.67
1012 1022 3.047115 ACTCCTGGCATGAGAATGAGAT 58.953 45.455 23.95 0.00 33.95 2.75
1040 1050 2.102578 GTGCCAGGCCATCACTTATTT 58.897 47.619 9.64 0.00 0.00 1.40
1150 1162 1.959282 GCATGGGGAAGAATCATGTCC 59.041 52.381 0.00 0.00 40.07 4.02
1165 1177 4.468713 TCATGTCCCTTCAAATCACAACA 58.531 39.130 0.00 0.00 0.00 3.33
1200 1212 2.106684 GTGGAAGGAACTGAAAGACCCT 59.893 50.000 0.00 0.00 40.86 4.34
1424 1436 3.111853 CCATCTTATGGCTAGCGTCAA 57.888 47.619 9.00 1.03 44.70 3.18
1459 1471 1.821332 GGAGCAAATCTGGAGGGCG 60.821 63.158 0.00 0.00 0.00 6.13
1460 1472 1.821332 GAGCAAATCTGGAGGGCGG 60.821 63.158 0.00 0.00 0.00 6.13
1593 1605 9.436957 GGAGTTTGATATTTACAGAGAAAGTCA 57.563 33.333 0.00 0.00 0.00 3.41
1712 1724 3.067106 GAGGAACATGAAGCGTGAAGAA 58.933 45.455 0.00 0.00 0.00 2.52
1715 1727 5.245531 AGGAACATGAAGCGTGAAGAATTA 58.754 37.500 0.00 0.00 0.00 1.40
1772 1784 6.089954 GTCATAGGAAACACCGTACTGTTAAC 59.910 42.308 0.00 0.00 44.74 2.01
2132 2146 2.289756 GGCTGCTCCCTAGGCTATAAAC 60.290 54.545 2.05 0.00 37.70 2.01
2169 2184 1.197430 ACTAGCTGGTTGGCTGCTCT 61.197 55.000 0.00 0.00 43.01 4.09
2212 2227 3.334910 TTGAGAGCATCCCATCCTCTA 57.665 47.619 0.00 0.00 36.16 2.43
2237 2252 5.241506 AGGACTTTGAGCGAAAATCATCAAA 59.758 36.000 0.00 0.00 38.85 2.69
2334 2350 3.375922 TCCGACACTTGTTTCCTTTGAAC 59.624 43.478 0.00 0.00 0.00 3.18
2368 2384 1.447314 GACGGTTAGGCGTCAAGGG 60.447 63.158 0.00 0.00 35.46 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.318441 CTTCTCTGACGTGCCCTTCA 59.682 55.000 0.00 0.00 0.00 3.02
61 62 5.273944 GTTCACTTTCATCTTTTGCTTCGT 58.726 37.500 0.00 0.00 0.00 3.85
111 112 5.357314 GATCTCGATCATTACCGGAGGATTA 59.643 44.000 9.46 0.00 44.02 1.75
144 145 1.941682 TGGGAAGGAGGGAGTATACCA 59.058 52.381 0.00 0.00 0.00 3.25
145 146 2.789323 TGGGAAGGAGGGAGTATACC 57.211 55.000 0.00 0.00 0.00 2.73
240 241 4.475747 ACCCATCTCCCTTCGGTAAAATAA 59.524 41.667 0.00 0.00 0.00 1.40
326 336 9.971922 ATTTTATTGCAAATCTAAGTCCTATGC 57.028 29.630 1.71 0.00 0.00 3.14
341 351 8.050778 AGACGATAACCTTGATTTTATTGCAA 57.949 30.769 0.00 0.00 0.00 4.08
443 453 2.850321 CGATCACCAACCGTTTCAATG 58.150 47.619 0.00 0.00 0.00 2.82
452 462 2.052782 ATTAAGGGCGATCACCAACC 57.947 50.000 1.44 0.00 0.00 3.77
462 472 2.166254 AGACCATGCAAAATTAAGGGCG 59.834 45.455 0.00 0.00 0.00 6.13
630 640 6.164417 TGTACACTACTAAAGTTTCAGGCA 57.836 37.500 0.00 0.00 35.76 4.75
712 722 6.648725 AGACACAGAAAAACAAGCTATCTCTC 59.351 38.462 0.00 0.00 0.00 3.20
732 742 4.275936 GGCCATATAATGAACACCAGACAC 59.724 45.833 0.00 0.00 0.00 3.67
954 964 5.195940 CCCAGTCCAATCAACTTGATGTAT 58.804 41.667 4.99 0.00 37.15 2.29
983 993 1.552337 TCATGCCAGGAGTCTTGAGAC 59.448 52.381 3.36 2.93 45.08 3.36
1040 1050 3.384789 GGCATCCCGCTCTGTATCATATA 59.615 47.826 0.00 0.00 41.91 0.86
1055 1065 7.122799 GTCTCCCATTAATTATAAAGGCATCCC 59.877 40.741 0.00 0.00 30.18 3.85
1150 1162 7.432869 TCCAAAGTATTGTTGTGATTTGAAGG 58.567 34.615 0.00 0.00 34.60 3.46
1165 1177 5.319043 TCCTTCCACAACTCCAAAGTATT 57.681 39.130 0.00 0.00 33.48 1.89
1200 1212 9.796120 CCTTTCAAAGTTACTTTTGTGTCATTA 57.204 29.630 7.71 0.00 38.77 1.90
1424 1436 6.418057 TTGCTCCACCATTTACAAATTTCT 57.582 33.333 0.00 0.00 0.00 2.52
1459 1471 4.310769 CACTAGATGCACTTACATAGGCC 58.689 47.826 0.00 0.00 0.00 5.19
1715 1727 9.679661 AAAGGGAAAATGAAACTACAAAAACAT 57.320 25.926 0.00 0.00 0.00 2.71
1772 1784 1.696063 TAGTATTTCCTCGACCCCCG 58.304 55.000 0.00 0.00 40.25 5.73
1912 1925 5.013495 TCAGAACAAATTCCTCAGAGACCAT 59.987 40.000 0.00 0.00 35.18 3.55
2169 2184 3.735237 GACAAGTGTCAGTTCCTCTCA 57.265 47.619 6.57 0.00 44.18 3.27
2212 2227 4.761739 TGATGATTTTCGCTCAAAGTCCTT 59.238 37.500 0.10 0.00 31.19 3.36
2237 2252 2.703536 GTTGGGTTTGGGTTTTCCTCAT 59.296 45.455 0.00 0.00 40.46 2.90
2368 2384 3.767902 ATTCCTCTTGGATGCTCTAGC 57.232 47.619 0.00 0.00 42.81 3.42


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

AutoCloner maintained by Alex Coulton.