Multiple sequence alignment - TraesCS1A01G272800

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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 TraesCS1A01G272800 chr1A 100.000 2225 0 0 1 2225 466342241 466340017 0.000000e+00 4109.0
1 TraesCS1A01G272800 chr1D 92.093 1543 43 16 1 1484 366095819 366094297 0.000000e+00 2100.0
2 TraesCS1A01G272800 chr1D 95.513 1315 24 6 1 1284 367154245 367152935 0.000000e+00 2069.0
3 TraesCS1A01G272800 chr1D 91.150 452 17 3 1484 1912 366094099 366093648 1.900000e-165 592.0
4 TraesCS1A01G272800 chr1D 90.708 452 19 3 1484 1912 367152503 367152052 4.120000e-162 580.0
5 TraesCS1A01G272800 chr1D 95.873 315 11 2 1912 2225 366093614 366093301 1.970000e-140 508.0
6 TraesCS1A01G272800 chr1D 95.833 312 12 1 1914 2225 367152017 367151707 9.170000e-139 503.0
7 TraesCS1A01G272800 chr1D 92.118 203 9 1 1282 1484 367152897 367152702 1.680000e-71 279.0
8 TraesCS1A01G272800 chr1D 95.413 109 5 0 1376 1484 367152655 367152547 8.170000e-40 174.0
9 TraesCS1A01G272800 chr1D 92.661 109 7 1 1376 1484 366094250 366094143 2.960000e-34 156.0
10 TraesCS1A01G272800 chr1D 97.222 36 1 0 243 278 366095646 366095611 6.630000e-06 62.1
11 TraesCS1A01G272800 chr1D 97.222 36 1 0 243 278 367154072 367154037 6.630000e-06 62.1
12 TraesCS1A01G272800 chr1B 95.847 313 13 0 1912 2224 491402416 491402104 7.090000e-140 507.0
13 TraesCS1A01G272800 chr1B 93.226 310 21 0 1603 1912 491402759 491402450 7.240000e-125 457.0
14 TraesCS1A01G272800 chr1B 96.154 52 2 0 1560 1611 491402823 491402772 3.940000e-13 86.1
15 TraesCS1A01G272800 chr6A 82.379 454 23 25 1484 1912 428621713 428622134 2.120000e-90 342.0
16 TraesCS1A01G272800 chr6A 96.429 168 6 0 1912 2079 428622168 428622335 6.050000e-71 278.0
17 TraesCS1A01G272800 chr6A 94.675 169 8 1 2054 2221 428681508 428681340 6.090000e-66 261.0
18 TraesCS1A01G272800 chr6A 93.197 147 10 0 2079 2225 428663041 428663187 1.340000e-52 217.0
19 TraesCS1A01G272800 chr6A 97.297 111 3 0 1370 1480 428621555 428621665 2.920000e-44 189.0
20 TraesCS1A01G272800 chr6A 100.000 68 0 0 2003 2070 428681590 428681523 2.320000e-25 126.0


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 TraesCS1A01G272800 chr1A 466340017 466342241 2224 True 4109.000000 4109 100.000000 1 2225 1 chr1A.!!$R1 2224
1 TraesCS1A01G272800 chr1D 366093301 366095819 2518 True 683.620000 2100 93.799800 1 2225 5 chr1D.!!$R1 2224
2 TraesCS1A01G272800 chr1D 367151707 367154245 2538 True 611.183333 2069 94.467833 1 2225 6 chr1D.!!$R2 2224
3 TraesCS1A01G272800 chr1B 491402104 491402823 719 True 350.033333 507 95.075667 1560 2224 3 chr1B.!!$R1 664
4 TraesCS1A01G272800 chr6A 428621555 428622335 780 False 269.666667 342 92.035000 1370 2079 3 chr6A.!!$F2 709

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
439 448 3.434299 GCTGCAATTTCAACTCCATTTGG 59.566 43.478 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 2033 1.003718 GGTGCTACTTGCCGGAGTT 60.004 57.895 5.05 0.0 42.0 3.01 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
170 171 8.472007 TCAAACATAAACCAAGTCAAGGTAAT 57.528 30.769 0.00 0.00 38.76 1.89
410 419 3.803778 CCTTTGCAAATGTCACCAAACTC 59.196 43.478 13.23 0.00 0.00 3.01
439 448 3.434299 GCTGCAATTTCAACTCCATTTGG 59.566 43.478 0.00 0.00 0.00 3.28
669 678 4.223953 TCTCTACAGTGGAAAACAGACCT 58.776 43.478 0.00 0.00 0.00 3.85
701 710 7.743104 ACTAAATCTGAATAGAACACTTTGCG 58.257 34.615 7.58 0.00 36.32 4.85
1064 1109 2.757508 CGAGGGAGAGGAGCAGCA 60.758 66.667 0.00 0.00 0.00 4.41
1121 1175 2.048127 GCTCGTGTCCGCCTTCTT 60.048 61.111 0.00 0.00 0.00 2.52
1185 1239 1.593787 CGAGAGAGGAGGCAAGCAA 59.406 57.895 0.00 0.00 0.00 3.91
1318 1417 2.813754 CGAGAAGGTTTCCATGCTGAAA 59.186 45.455 0.00 0.00 32.02 2.69
1362 1461 5.165652 AGACCCATATGTCATGGACCTATT 58.834 41.667 4.83 0.00 41.64 1.73
1363 1462 5.249393 AGACCCATATGTCATGGACCTATTC 59.751 44.000 4.83 0.00 41.64 1.75
1364 1463 4.913355 ACCCATATGTCATGGACCTATTCA 59.087 41.667 4.83 0.00 41.64 2.57
1365 1464 5.372363 ACCCATATGTCATGGACCTATTCAA 59.628 40.000 4.83 0.00 41.64 2.69
1366 1465 5.707298 CCCATATGTCATGGACCTATTCAAC 59.293 44.000 4.83 0.00 41.64 3.18
1367 1466 5.707298 CCATATGTCATGGACCTATTCAACC 59.293 44.000 1.24 0.00 41.64 3.77
1368 1467 4.860802 ATGTCATGGACCTATTCAACCA 57.139 40.909 0.00 0.00 36.83 3.67
1379 1478 4.766891 ACCTATTCAACCATCAACCAAGTG 59.233 41.667 0.00 0.00 0.00 3.16
1480 1735 0.250166 AACGAGGTTGGTTTCGGGAG 60.250 55.000 0.00 0.00 40.93 4.30
1495 1794 1.064060 CGGGAGGCAATTCAATTCGTC 59.936 52.381 0.00 0.00 0.00 4.20
1500 1799 5.940470 GGGAGGCAATTCAATTCGTCTATAT 59.060 40.000 0.00 0.00 0.00 0.86
1692 2033 0.318699 GCATCGTCGGTAGCATGCTA 60.319 55.000 23.52 23.52 38.89 3.49
1764 2106 2.202703 GAACGCGGACGGTAGCAT 60.203 61.111 12.47 0.00 41.26 3.79
1789 2131 2.758089 CCGCTGATGGAAGCACTGC 61.758 63.158 0.00 0.00 43.73 4.40
1862 2209 8.288208 GTCAGGATATAGACTAATTCGAAACGA 58.712 37.037 0.00 0.00 0.00 3.85
1918 2300 0.947180 CGGTATATGGGGCGGTTTCG 60.947 60.000 0.00 0.00 39.81 3.46
2114 2496 4.759693 ACAACGCTTGGAAATATTGACAGA 59.240 37.500 0.00 0.00 34.12 3.41
2128 2510 3.186702 TGACAGACGTTCATTGGTTCA 57.813 42.857 0.00 0.00 0.00 3.18
2213 2596 5.066968 TGATTTTGAAAATTAGTCCGGGC 57.933 39.130 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 2.028476 GCAAGGTACCCCCAATTTTCAC 60.028 50.000 8.74 0.00 34.66 3.18
71 72 2.407340 TGCAAGGTACCCCCAATTTT 57.593 45.000 8.74 0.00 34.66 1.82
410 419 1.190763 GTTGAAATTGCAGCTGCGTTG 59.809 47.619 32.11 0.00 45.83 4.10
606 615 2.514803 AGCCTTGGGTTACATGACAAC 58.485 47.619 0.00 2.93 0.00 3.32
669 678 9.371136 GTGTTCTATTCAGATTTAGTCATGACA 57.629 33.333 27.02 10.87 0.00 3.58
701 710 8.037758 ACATCATATCAGTAAGGCAATAGCTAC 58.962 37.037 0.00 0.00 41.70 3.58
893 919 3.461773 CCCACGCGAGGTCCTGAT 61.462 66.667 21.30 0.00 0.00 2.90
1064 1109 3.660111 GTGTTTCTTGCCGCCGCT 61.660 61.111 0.00 0.00 35.36 5.52
1121 1175 2.609491 GCGGCATATTGTCCGTAGATGA 60.609 50.000 0.00 0.00 46.79 2.92
1185 1239 0.252467 CCACCACCTCCTCCTCTCTT 60.252 60.000 0.00 0.00 0.00 2.85
1213 1267 3.631046 CCTCCCTCATAGCCCCGC 61.631 72.222 0.00 0.00 0.00 6.13
1318 1417 5.705905 GTCTAAGAAAGTACAGTGCCCAAAT 59.294 40.000 0.00 0.00 0.00 2.32
1362 1461 1.496857 TCCCACTTGGTTGATGGTTGA 59.503 47.619 0.00 0.00 34.77 3.18
1363 1462 1.993956 TCCCACTTGGTTGATGGTTG 58.006 50.000 0.00 0.00 34.77 3.77
1364 1463 2.091333 ACTTCCCACTTGGTTGATGGTT 60.091 45.455 0.00 0.00 34.77 3.67
1365 1464 1.499007 ACTTCCCACTTGGTTGATGGT 59.501 47.619 0.00 0.00 34.77 3.55
1366 1465 1.888512 CACTTCCCACTTGGTTGATGG 59.111 52.381 0.00 0.00 34.77 3.51
1367 1466 1.888512 CCACTTCCCACTTGGTTGATG 59.111 52.381 0.00 0.00 34.77 3.07
1368 1467 1.203050 CCCACTTCCCACTTGGTTGAT 60.203 52.381 0.00 0.00 34.77 2.57
1480 1735 7.426929 AGTGATATAGACGAATTGAATTGCC 57.573 36.000 0.00 0.00 0.00 4.52
1495 1794 7.437748 CCTAGAAGGACCACAAAGTGATATAG 58.562 42.308 0.00 0.00 37.67 1.31
1500 1799 2.637872 CCCTAGAAGGACCACAAAGTGA 59.362 50.000 0.00 0.00 37.67 3.41
1692 2033 1.003718 GGTGCTACTTGCCGGAGTT 60.004 57.895 5.05 0.00 42.00 3.01
1764 2106 2.649245 CTTCCATCAGCGGCCATCGA 62.649 60.000 2.24 0.00 42.43 3.59
1789 2131 4.213564 ACATTCTACCAAGGAAGAGCAG 57.786 45.455 0.00 0.00 0.00 4.24
1793 2136 8.840200 ATTAGTCTACATTCTACCAAGGAAGA 57.160 34.615 0.00 0.00 0.00 2.87
1844 2191 6.096564 ACTCCCTTCGTTTCGAATTAGTCTAT 59.903 38.462 0.00 0.00 44.85 1.98
1862 2209 4.625963 AGAGCCTTATTCAGTACTCCCTT 58.374 43.478 0.00 0.00 0.00 3.95
1918 2300 5.977129 CGAATTGGAATGTTATTAACAGGGC 59.023 40.000 14.18 6.50 45.95 5.19
2114 2496 3.417069 TGGATCTGAACCAATGAACGT 57.583 42.857 3.93 0.00 34.25 3.99
2157 2540 5.933463 CCACTATTTAGGTTCCGTGTAACAA 59.067 40.000 0.00 0.00 35.74 2.83


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

AutoCloner maintained by Alex Coulton.