Multiple sequence alignment - TraesCS1B01G058500

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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 TraesCS1B01G058500 chr1B 100.000 2438 0 0 1 2438 40854586 40852149 0.000000e+00 4503
1 TraesCS1B01G058500 chr1B 87.198 414 20 14 1878 2291 40702885 40702505 8.000000e-120 440
2 TraesCS1B01G058500 chr1B 91.473 129 11 0 2288 2416 40700498 40700370 6.930000e-41 178
3 TraesCS1B01G058500 chr1B 87.288 118 8 6 1762 1878 642772607 642772496 7.080000e-26 128
4 TraesCS1B01G058500 chr6D 95.922 1888 63 9 1 1878 321115220 321117103 0.000000e+00 3048
5 TraesCS1B01G058500 chr1A 95.003 1881 89 5 1 1878 487768957 487770835 0.000000e+00 2948
6 TraesCS1B01G058500 chr1A 84.725 1892 259 23 1 1878 347624342 347626217 0.000000e+00 1866
7 TraesCS1B01G058500 chr1A 95.733 539 23 0 1878 2416 26590402 26589864 0.000000e+00 869
8 TraesCS1B01G058500 chr4B 90.122 1883 166 12 1 1878 642377834 642375967 0.000000e+00 2429
9 TraesCS1B01G058500 chr2D 87.507 1769 201 17 1 1758 610359089 610360848 0.000000e+00 2025
10 TraesCS1B01G058500 chr2D 86.408 103 7 6 1780 1878 610360904 610361003 3.320000e-19 106
11 TraesCS1B01G058500 chr1D 88.806 1599 173 5 1 1599 252296805 252298397 0.000000e+00 1956
12 TraesCS1B01G058500 chr1D 92.421 541 28 8 1878 2416 25464040 25463511 0.000000e+00 760
13 TraesCS1B01G058500 chr1D 91.159 328 17 4 1878 2205 25416818 25416503 3.720000e-118 435
14 TraesCS1B01G058500 chr1D 93.607 219 12 1 2200 2416 25411413 25411195 2.340000e-85 326
15 TraesCS1B01G058500 chr6B 85.989 1770 230 10 1 1760 617784100 617782339 0.000000e+00 1879
16 TraesCS1B01G058500 chr2A 84.733 1893 257 24 1 1878 146945604 146943729 0.000000e+00 1866
17 TraesCS1B01G058500 chr5B 84.972 1271 182 7 494 1760 357163716 357162451 0.000000e+00 1280
18 TraesCS1B01G058500 chr7B 81.858 226 30 9 1550 1773 606554084 606553868 1.930000e-41 180
19 TraesCS1B01G058500 chr7B 87.395 119 7 6 1765 1878 606553842 606553727 1.970000e-26 130
20 TraesCS1B01G058500 chr7B 90.110 91 3 5 1789 1878 720476585 720476500 1.980000e-21 113
21 TraesCS1B01G058500 chr3A 74.359 312 78 2 65 375 721978677 721978367 5.470000e-27 132


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 TraesCS1B01G058500 chr1B 40852149 40854586 2437 True 4503.0 4503 100.0000 1 2438 1 chr1B.!!$R1 2437
1 TraesCS1B01G058500 chr1B 40700370 40702885 2515 True 309.0 440 89.3355 1878 2416 2 chr1B.!!$R3 538
2 TraesCS1B01G058500 chr6D 321115220 321117103 1883 False 3048.0 3048 95.9220 1 1878 1 chr6D.!!$F1 1877
3 TraesCS1B01G058500 chr1A 487768957 487770835 1878 False 2948.0 2948 95.0030 1 1878 1 chr1A.!!$F2 1877
4 TraesCS1B01G058500 chr1A 347624342 347626217 1875 False 1866.0 1866 84.7250 1 1878 1 chr1A.!!$F1 1877
5 TraesCS1B01G058500 chr1A 26589864 26590402 538 True 869.0 869 95.7330 1878 2416 1 chr1A.!!$R1 538
6 TraesCS1B01G058500 chr4B 642375967 642377834 1867 True 2429.0 2429 90.1220 1 1878 1 chr4B.!!$R1 1877
7 TraesCS1B01G058500 chr2D 610359089 610361003 1914 False 1065.5 2025 86.9575 1 1878 2 chr2D.!!$F1 1877
8 TraesCS1B01G058500 chr1D 252296805 252298397 1592 False 1956.0 1956 88.8060 1 1599 1 chr1D.!!$F1 1598
9 TraesCS1B01G058500 chr1D 25463511 25464040 529 True 760.0 760 92.4210 1878 2416 1 chr1D.!!$R3 538
10 TraesCS1B01G058500 chr6B 617782339 617784100 1761 True 1879.0 1879 85.9890 1 1760 1 chr6B.!!$R1 1759
11 TraesCS1B01G058500 chr2A 146943729 146945604 1875 True 1866.0 1866 84.7330 1 1878 1 chr2A.!!$R1 1877
12 TraesCS1B01G058500 chr5B 357162451 357163716 1265 True 1280.0 1280 84.9720 494 1760 1 chr5B.!!$R1 1266

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
557 560 2.623418 TTCTGGCAAGGAGTCCTCTA 57.377 50.0 13.43 0.0 30.89 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2378 4459 0.107654 GCTAGGCACTACCCTGGTTG 60.108 60.0 0.0 0.0 41.75 3.77 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
249 250 9.817809 GTTTACCTTCTTTCCTTCTTCAAATTT 57.182 29.630 0.00 0.00 0.00 1.82
281 283 5.088739 GGCACTTGATTTGATTAACACTCG 58.911 41.667 0.00 0.00 0.00 4.18
557 560 2.623418 TTCTGGCAAGGAGTCCTCTA 57.377 50.000 13.43 0.00 30.89 2.43
601 604 4.429505 TGGCTATAGATGGCAAGTAGGAT 58.570 43.478 3.21 0.00 37.05 3.24
701 704 4.990257 ACTATTTGTGATCAGCATTGTGC 58.010 39.130 0.00 0.00 45.46 4.57
772 775 7.741554 AGAAGGACCTTTACTGATAAGATGT 57.258 36.000 8.49 0.00 0.00 3.06
1114 1120 3.473625 AGTTGTGCGGTAGCTAAAAACT 58.526 40.909 0.00 0.00 45.42 2.66
1247 1253 3.685550 GCTTGTATACTGTGGGGCATCTT 60.686 47.826 4.17 0.00 0.00 2.40
1385 1391 0.253044 CCCCAGATCGAGGCTTTTGA 59.747 55.000 2.03 0.00 0.00 2.69
1451 1457 0.911769 GGGTGACACATCTGGATCCA 59.088 55.000 15.27 15.27 0.00 3.41
1803 1867 6.663565 TGCAAAACTGAACTTTTGTTTTTCC 58.336 32.000 0.00 0.00 43.66 3.13
1807 1871 9.729023 CAAAACTGAACTTTTGTTTTTCCTTTT 57.271 25.926 0.00 0.00 43.66 2.27
1816 1880 9.549078 ACTTTTGTTTTTCCTTTTTGTGAACTA 57.451 25.926 0.00 0.00 0.00 2.24
1949 2020 0.399091 TGGCCTGCCTAGCTCACTAT 60.399 55.000 9.97 0.00 36.94 2.12
2121 2192 4.566545 TGGTTGTTGCATTGAACTACAG 57.433 40.909 0.00 0.00 34.47 2.74
2132 2203 6.321945 TGCATTGAACTACAGCCAATATGATT 59.678 34.615 0.00 0.00 0.00 2.57
2141 2212 3.133362 CAGCCAATATGATTGTGCCCTTT 59.867 43.478 8.23 0.00 0.00 3.11
2168 2239 3.115390 TCTTATAAGGAGCAACAGCCCT 58.885 45.455 12.54 0.00 32.52 5.19
2228 2299 4.681744 TCAACATGAACTTTGGCAAAGAC 58.318 39.130 38.62 29.96 41.02 3.01
2229 2300 4.159321 TCAACATGAACTTTGGCAAAGACA 59.841 37.500 38.62 33.28 41.02 3.41
2230 2301 4.942761 ACATGAACTTTGGCAAAGACAT 57.057 36.364 38.62 33.75 41.02 3.06
2271 2342 5.048083 TGTCTTTGCTAATGGATGTGAAACC 60.048 40.000 0.00 0.00 34.36 3.27
2309 4390 1.808411 AGTAGTGCACATTTCGGGTG 58.192 50.000 21.04 0.00 39.25 4.61
2378 4459 2.083774 TGACCGCTGATGTCCAAATTC 58.916 47.619 0.00 0.00 31.60 2.17
2380 4461 2.487762 GACCGCTGATGTCCAAATTCAA 59.512 45.455 0.00 0.00 0.00 2.69
2416 4497 3.447918 GCCTGTTGCTACCTTATCGTA 57.552 47.619 0.00 0.00 36.87 3.43
2417 4498 3.991367 GCCTGTTGCTACCTTATCGTAT 58.009 45.455 0.00 0.00 36.87 3.06
2418 4499 4.377897 GCCTGTTGCTACCTTATCGTATT 58.622 43.478 0.00 0.00 36.87 1.89
2419 4500 4.211374 GCCTGTTGCTACCTTATCGTATTG 59.789 45.833 0.00 0.00 36.87 1.90
2420 4501 4.750098 CCTGTTGCTACCTTATCGTATTGG 59.250 45.833 0.00 0.00 0.00 3.16
2421 4502 4.124238 TGTTGCTACCTTATCGTATTGGC 58.876 43.478 0.00 0.00 0.00 4.52
2422 4503 4.141801 TGTTGCTACCTTATCGTATTGGCT 60.142 41.667 0.00 0.00 0.00 4.75
2423 4504 5.069383 TGTTGCTACCTTATCGTATTGGCTA 59.931 40.000 0.00 0.00 0.00 3.93
2424 4505 5.130292 TGCTACCTTATCGTATTGGCTAC 57.870 43.478 0.00 0.00 0.00 3.58
2425 4506 4.831155 TGCTACCTTATCGTATTGGCTACT 59.169 41.667 0.00 0.00 0.00 2.57
2426 4507 5.048224 TGCTACCTTATCGTATTGGCTACTC 60.048 44.000 0.00 0.00 0.00 2.59
2427 4508 4.868314 ACCTTATCGTATTGGCTACTCC 57.132 45.455 0.00 0.00 0.00 3.85
2428 4509 3.577415 ACCTTATCGTATTGGCTACTCCC 59.423 47.826 0.00 0.00 0.00 4.30
2429 4510 3.833070 CCTTATCGTATTGGCTACTCCCT 59.167 47.826 0.00 0.00 0.00 4.20
2430 4511 4.082136 CCTTATCGTATTGGCTACTCCCTC 60.082 50.000 0.00 0.00 0.00 4.30
2431 4512 1.700955 TCGTATTGGCTACTCCCTCC 58.299 55.000 0.00 0.00 0.00 4.30
2432 4513 0.680061 CGTATTGGCTACTCCCTCCC 59.320 60.000 0.00 0.00 0.00 4.30
2433 4514 1.758123 CGTATTGGCTACTCCCTCCCT 60.758 57.143 0.00 0.00 0.00 4.20
2434 4515 2.409570 GTATTGGCTACTCCCTCCCTT 58.590 52.381 0.00 0.00 0.00 3.95
2435 4516 1.512735 ATTGGCTACTCCCTCCCTTC 58.487 55.000 0.00 0.00 0.00 3.46
2436 4517 0.417841 TTGGCTACTCCCTCCCTTCT 59.582 55.000 0.00 0.00 0.00 2.85
2437 4518 0.325671 TGGCTACTCCCTCCCTTCTG 60.326 60.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 250 4.671831 TCAAATCAAGTGCCCATTTAGGA 58.328 39.130 0.00 0.00 41.22 2.94
419 421 5.181245 ACAATGTATCTTTTCACCCAGTTCG 59.819 40.000 0.00 0.00 0.00 3.95
624 627 2.140717 GTACCAAACCAGGTGTCTTCG 58.859 52.381 0.00 0.00 43.14 3.79
630 633 1.546998 GGGGAAGTACCAAACCAGGTG 60.547 57.143 0.00 0.00 43.14 4.00
701 704 5.047448 CCATCCCACACATCAGATAGAGTAG 60.047 48.000 0.00 0.00 0.00 2.57
772 775 2.658285 GATGCACATCCAGGAATCCAA 58.342 47.619 0.61 0.00 31.76 3.53
1114 1120 3.777106 AGCAGACACATCTTTCCAGAA 57.223 42.857 0.00 0.00 30.42 3.02
1247 1253 4.023279 ACACATGCGCATTTCTAGTTTTCA 60.023 37.500 22.81 0.00 0.00 2.69
1399 1405 1.000171 GAAGGGGTTTTTGAGCAGCTG 60.000 52.381 10.11 10.11 0.00 4.24
1579 1591 3.285290 TCTTCAAGGGGGAAGGTTCTA 57.715 47.619 3.37 0.00 43.52 2.10
2121 2192 3.385755 AGAAAGGGCACAATCATATTGGC 59.614 43.478 4.78 5.01 35.14 4.52
2132 2203 6.012858 TCCTTATAAGAAAGAGAAAGGGCACA 60.013 38.462 14.28 0.00 35.31 4.57
2141 2212 6.109359 GCTGTTGCTCCTTATAAGAAAGAGA 58.891 40.000 14.28 1.49 36.03 3.10
2168 2239 4.365514 TGAAGCAACCATCTTTACCTCA 57.634 40.909 0.00 0.00 0.00 3.86
2309 4390 0.250513 ACGATGCCTCCCAAACTCTC 59.749 55.000 0.00 0.00 0.00 3.20
2378 4459 0.107654 GCTAGGCACTACCCTGGTTG 60.108 60.000 0.00 0.00 41.75 3.77
2380 4461 1.689582 GGCTAGGCACTACCCTGGT 60.690 63.158 12.16 0.00 41.75 4.00
2416 4497 1.010170 AGAAGGGAGGGAGTAGCCAAT 59.990 52.381 0.00 0.00 38.95 3.16
2417 4498 0.417841 AGAAGGGAGGGAGTAGCCAA 59.582 55.000 0.00 0.00 38.95 4.52
2418 4499 0.325671 CAGAAGGGAGGGAGTAGCCA 60.326 60.000 0.00 0.00 38.95 4.75
2419 4500 2.522271 CAGAAGGGAGGGAGTAGCC 58.478 63.158 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.