Multiple sequence alignment - TraesCS1B01G209000

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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 TraesCS1B01G209000 chr1B 100.000 2407 0 0 1 2407 378832704 378835110 0.000000e+00 4446
1 TraesCS1B01G209000 chr1D 93.614 2114 84 23 303 2404 279098548 279100622 0.000000e+00 3109
2 TraesCS1B01G209000 chr1D 88.797 241 10 6 1 241 279098294 279098517 1.820000e-71 279
3 TraesCS1B01G209000 chr1A 92.653 1470 62 22 1 1460 351344278 351345711 0.000000e+00 2074
4 TraesCS1B01G209000 chr1A 91.346 624 33 7 1462 2080 351345751 351346358 0.000000e+00 833
5 TraesCS1B01G209000 chr1A 96.649 388 11 2 2021 2407 351346354 351346740 0.000000e+00 643


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 TraesCS1B01G209000 chr1B 378832704 378835110 2406 False 4446.000000 4446 100.000000 1 2407 1 chr1B.!!$F1 2406
1 TraesCS1B01G209000 chr1D 279098294 279100622 2328 False 1694.000000 3109 91.205500 1 2404 2 chr1D.!!$F1 2403
2 TraesCS1B01G209000 chr1A 351344278 351346740 2462 False 1183.333333 2074 93.549333 1 2407 3 chr1A.!!$F1 2406

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
301 316 0.032017 ATCTCAGTTCCTAGCGGGGT 60.032 55.0 0.0 0.0 35.33 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1761 0.109723 TCCAGTTCAAACCCCTTCCG 59.89 55.0 0.0 0.0 0.0 4.3 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
70 71 3.668447 CAGAATGCAACTACAGGTGACT 58.332 45.455 0.00 0.0 46.44 3.41
113 128 0.112995 AGCACAGCCTGGATGGAAAA 59.887 50.000 17.33 0.0 38.35 2.29
122 137 5.242393 CAGCCTGGATGGAAAACCTATAATG 59.758 44.000 3.47 0.0 38.35 1.90
146 161 3.845781 AGCAGTTCCTTGTCTTCTTGA 57.154 42.857 0.00 0.0 0.00 3.02
147 162 3.737850 AGCAGTTCCTTGTCTTCTTGAG 58.262 45.455 0.00 0.0 0.00 3.02
216 231 2.886523 CACCTGAGAAGAACATGCCAAA 59.113 45.455 0.00 0.0 0.00 3.28
224 239 2.247358 AGAACATGCCAAACCGGAAAT 58.753 42.857 9.46 0.0 36.56 2.17
225 240 2.231235 AGAACATGCCAAACCGGAAATC 59.769 45.455 9.46 0.0 36.56 2.17
228 243 2.366916 ACATGCCAAACCGGAAATCAAA 59.633 40.909 9.46 0.0 36.56 2.69
229 244 2.517650 TGCCAAACCGGAAATCAAAC 57.482 45.000 9.46 0.0 36.56 2.93
230 245 1.069358 TGCCAAACCGGAAATCAAACC 59.931 47.619 9.46 0.0 36.56 3.27
231 246 1.343142 GCCAAACCGGAAATCAAACCT 59.657 47.619 9.46 0.0 36.56 3.50
232 247 2.224185 GCCAAACCGGAAATCAAACCTT 60.224 45.455 9.46 0.0 36.56 3.50
234 249 4.501743 GCCAAACCGGAAATCAAACCTTAA 60.502 41.667 9.46 0.0 36.56 1.85
235 250 5.602628 CCAAACCGGAAATCAAACCTTAAA 58.397 37.500 9.46 0.0 36.56 1.52
236 251 6.227522 CCAAACCGGAAATCAAACCTTAAAT 58.772 36.000 9.46 0.0 36.56 1.40
237 252 6.708502 CCAAACCGGAAATCAAACCTTAAATT 59.291 34.615 9.46 0.0 36.56 1.82
238 253 7.095397 CCAAACCGGAAATCAAACCTTAAATTC 60.095 37.037 9.46 0.0 36.56 2.17
239 254 6.911250 ACCGGAAATCAAACCTTAAATTCT 57.089 33.333 9.46 0.0 0.00 2.40
240 255 7.297936 ACCGGAAATCAAACCTTAAATTCTT 57.702 32.000 9.46 0.0 0.00 2.52
241 256 8.411991 ACCGGAAATCAAACCTTAAATTCTTA 57.588 30.769 9.46 0.0 0.00 2.10
242 257 9.031537 ACCGGAAATCAAACCTTAAATTCTTAT 57.968 29.630 9.46 0.0 0.00 1.73
243 258 9.301153 CCGGAAATCAAACCTTAAATTCTTATG 57.699 33.333 0.00 0.0 0.00 1.90
244 259 8.807581 CGGAAATCAAACCTTAAATTCTTATGC 58.192 33.333 0.00 0.0 0.00 3.14
245 260 9.651913 GGAAATCAAACCTTAAATTCTTATGCA 57.348 29.630 0.00 0.0 0.00 3.96
265 280 7.658525 ATGCATTTTGTATCCCATTCTTGTA 57.341 32.000 0.00 0.0 0.00 2.41
277 292 8.603242 ATCCCATTCTTGTAATCGTATTACAC 57.397 34.615 15.46 0.0 34.93 2.90
288 303 7.704899 TGTAATCGTATTACACCACAATCTCAG 59.295 37.037 13.14 0.0 30.68 3.35
297 312 2.093973 ACCACAATCTCAGTTCCTAGCG 60.094 50.000 0.00 0.0 0.00 4.26
301 316 0.032017 ATCTCAGTTCCTAGCGGGGT 60.032 55.000 0.00 0.0 35.33 4.95
315 330 4.081322 AGCGGGGTACAATAAACCATAG 57.919 45.455 0.00 0.0 38.87 2.23
336 351 7.012421 CCATAGTCAACCTTAAACTCTTATGCC 59.988 40.741 0.00 0.0 0.00 4.40
373 388 4.697352 AGTGAGATTTATGGTGTTGCTGTC 59.303 41.667 0.00 0.0 0.00 3.51
379 394 0.670162 ATGGTGTTGCTGTCTGTTGC 59.330 50.000 0.00 0.0 0.00 4.17
801 819 6.042777 CAGACTCAACAGCGAATTATAGGAA 58.957 40.000 0.00 0.0 0.00 3.36
863 881 0.739112 GGCTGCTACTGCACTCTGTC 60.739 60.000 0.00 0.0 45.31 3.51
864 882 0.246086 GCTGCTACTGCACTCTGTCT 59.754 55.000 0.00 0.0 45.31 3.41
869 890 3.057245 TGCTACTGCACTCTGTCTGTAAG 60.057 47.826 0.00 0.0 45.31 2.34
1314 1339 0.179062 CCCGAATCCTTCTCTGCCTG 60.179 60.000 0.00 0.0 0.00 4.85
1368 1394 3.990959 ATGGTTTGGTTGTTTGGTGTT 57.009 38.095 0.00 0.0 0.00 3.32
1391 1417 0.111253 CAGAGCCCAAGAAGGTGGTT 59.889 55.000 0.00 0.0 36.90 3.67
1408 1434 1.465794 GTTGAGGTCGAGGAGTAGCT 58.534 55.000 0.00 0.0 0.00 3.32
1419 1448 1.671901 GGAGTAGCTCTGCTTCCGCT 61.672 60.000 0.00 0.0 40.44 5.52
1469 1536 5.293569 GGTGCTTCTTGTTATTATGTACGCT 59.706 40.000 0.00 0.0 0.00 5.07
1516 1583 8.333908 TGCACATGATTTGTTTCAAATGTTTAC 58.666 29.630 11.60 0.0 36.00 2.01
1534 1602 9.447157 AATGTTTACCATTCCATTAACCAATTG 57.553 29.630 0.00 0.0 39.66 2.32
1539 1607 7.352079 ACCATTCCATTAACCAATTGAGATC 57.648 36.000 7.12 0.0 0.00 2.75
1576 1644 4.202253 ACATCGCCATGCTTAGATAGTTGA 60.202 41.667 0.00 0.0 32.57 3.18
1591 1659 5.663106 AGATAGTTGAGAGCTTGGGAATGTA 59.337 40.000 0.00 0.0 0.00 2.29
1639 1710 7.439655 GCACTGGTGAACATTTTTGGTTTATAA 59.560 33.333 4.79 0.0 0.00 0.98
1684 1755 3.565902 GGTTTTGTCCAAGAGTTGAGGAG 59.434 47.826 0.00 0.0 30.78 3.69
1685 1756 3.492102 TTTGTCCAAGAGTTGAGGAGG 57.508 47.619 0.00 0.0 30.78 4.30
1686 1757 2.398754 TGTCCAAGAGTTGAGGAGGA 57.601 50.000 0.00 0.0 30.78 3.71
1687 1758 2.689658 TGTCCAAGAGTTGAGGAGGAA 58.310 47.619 0.00 0.0 30.78 3.36
1688 1759 2.634940 TGTCCAAGAGTTGAGGAGGAAG 59.365 50.000 0.00 0.0 30.78 3.46
1689 1760 2.027653 GTCCAAGAGTTGAGGAGGAAGG 60.028 54.545 0.00 0.0 30.78 3.46
1690 1761 1.339535 CCAAGAGTTGAGGAGGAAGGC 60.340 57.143 0.00 0.0 0.00 4.35
1728 1799 1.963515 GAAGGGTGTTTGTCTTGGCAT 59.036 47.619 0.00 0.0 0.00 4.40
1814 1885 4.037803 ACAACAAATACTGCTTGTCATGCA 59.962 37.500 12.40 12.4 35.98 3.96
1864 1935 5.039645 TCCCAAAGAAATATCCCTCACTCT 58.960 41.667 0.00 0.0 0.00 3.24
1922 1993 2.666317 CAAACCTGGGTGAAAAGGAGT 58.334 47.619 0.00 0.0 37.01 3.85
1926 1997 4.302559 ACCTGGGTGAAAAGGAGTTATC 57.697 45.455 0.00 0.0 37.01 1.75
1929 2000 4.263506 CCTGGGTGAAAAGGAGTTATCTGT 60.264 45.833 0.00 0.0 35.40 3.41
1933 2004 6.940298 TGGGTGAAAAGGAGTTATCTGTTAAG 59.060 38.462 0.00 0.0 0.00 1.85
1982 2054 2.017782 CCTCGCTGCTAAGACTCACTA 58.982 52.381 0.00 0.0 0.00 2.74
2321 2448 3.072211 GGGTACTGACTAACAAAGGCAC 58.928 50.000 0.00 0.0 38.78 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.778741 TTTCCAAGTACATGCTAGGATATTTAG 57.221 33.333 0.00 0.00 0.00 1.85
56 57 4.692625 CCTGATTTCAGTCACCTGTAGTTG 59.307 45.833 6.81 0.00 42.27 3.16
58 59 3.904339 ACCTGATTTCAGTCACCTGTAGT 59.096 43.478 6.81 0.00 42.27 2.73
59 60 4.021104 TCACCTGATTTCAGTCACCTGTAG 60.021 45.833 6.81 0.00 42.27 2.74
60 61 3.901222 TCACCTGATTTCAGTCACCTGTA 59.099 43.478 6.81 0.00 42.27 2.74
62 63 3.407424 TCACCTGATTTCAGTCACCTG 57.593 47.619 6.81 0.00 42.27 4.00
63 64 4.383552 GCTATCACCTGATTTCAGTCACCT 60.384 45.833 6.81 0.00 42.27 4.00
64 65 3.873952 GCTATCACCTGATTTCAGTCACC 59.126 47.826 6.81 0.00 42.27 4.02
65 66 3.873952 GGCTATCACCTGATTTCAGTCAC 59.126 47.826 6.81 0.00 42.27 3.67
66 67 3.118261 GGGCTATCACCTGATTTCAGTCA 60.118 47.826 6.81 0.00 42.27 3.41
67 68 3.471680 GGGCTATCACCTGATTTCAGTC 58.528 50.000 6.81 0.00 42.27 3.51
68 69 2.173569 GGGGCTATCACCTGATTTCAGT 59.826 50.000 6.81 0.00 42.27 3.41
69 70 2.441001 AGGGGCTATCACCTGATTTCAG 59.559 50.000 0.39 0.39 43.40 3.02
70 71 2.492025 AGGGGCTATCACCTGATTTCA 58.508 47.619 0.00 0.00 35.30 2.69
71 72 3.008485 CCTAGGGGCTATCACCTGATTTC 59.992 52.174 0.00 0.00 37.72 2.17
72 73 2.982488 CCTAGGGGCTATCACCTGATTT 59.018 50.000 0.00 0.00 37.72 2.17
73 74 2.182312 TCCTAGGGGCTATCACCTGATT 59.818 50.000 9.46 0.00 37.72 2.57
74 75 1.795786 TCCTAGGGGCTATCACCTGAT 59.204 52.381 9.46 0.00 37.72 2.90
75 76 1.148027 CTCCTAGGGGCTATCACCTGA 59.852 57.143 9.46 0.00 37.72 3.86
76 77 1.638529 CTCCTAGGGGCTATCACCTG 58.361 60.000 9.46 0.00 37.72 4.00
113 128 4.235372 AGGAACTGCTAGGCATTATAGGT 58.765 43.478 0.00 0.00 38.13 3.08
122 137 2.027653 AGAAGACAAGGAACTGCTAGGC 60.028 50.000 0.00 0.00 40.86 3.93
216 231 6.911250 AGAATTTAAGGTTTGATTTCCGGT 57.089 33.333 0.00 0.00 0.00 5.28
234 249 9.768662 GAATGGGATACAAAATGCATAAGAATT 57.231 29.630 0.00 0.00 39.74 2.17
235 250 9.151177 AGAATGGGATACAAAATGCATAAGAAT 57.849 29.630 0.00 0.00 39.74 2.40
236 251 8.537728 AGAATGGGATACAAAATGCATAAGAA 57.462 30.769 0.00 0.00 39.74 2.52
237 252 8.415553 CAAGAATGGGATACAAAATGCATAAGA 58.584 33.333 0.00 0.00 39.74 2.10
238 253 8.199449 ACAAGAATGGGATACAAAATGCATAAG 58.801 33.333 0.00 0.00 39.74 1.73
239 254 8.076910 ACAAGAATGGGATACAAAATGCATAA 57.923 30.769 0.00 0.00 39.74 1.90
240 255 7.658525 ACAAGAATGGGATACAAAATGCATA 57.341 32.000 0.00 0.00 39.74 3.14
241 256 6.549433 ACAAGAATGGGATACAAAATGCAT 57.451 33.333 0.00 0.00 39.74 3.96
242 257 5.999205 ACAAGAATGGGATACAAAATGCA 57.001 34.783 0.00 0.00 39.74 3.96
243 258 7.379529 CGATTACAAGAATGGGATACAAAATGC 59.620 37.037 0.00 0.00 39.74 3.56
244 259 8.405531 ACGATTACAAGAATGGGATACAAAATG 58.594 33.333 0.00 0.00 39.74 2.32
245 260 8.519799 ACGATTACAAGAATGGGATACAAAAT 57.480 30.769 0.00 0.00 39.74 1.82
246 261 7.931578 ACGATTACAAGAATGGGATACAAAA 57.068 32.000 0.00 0.00 39.74 2.44
247 262 9.621629 AATACGATTACAAGAATGGGATACAAA 57.378 29.630 0.00 0.00 39.74 2.83
249 264 9.701098 GTAATACGATTACAAGAATGGGATACA 57.299 33.333 10.81 0.00 39.74 2.29
250 265 9.701098 TGTAATACGATTACAAGAATGGGATAC 57.299 33.333 14.18 0.00 32.53 2.24
251 266 9.701098 GTGTAATACGATTACAAGAATGGGATA 57.299 33.333 16.68 0.00 36.74 2.59
252 267 7.660208 GGTGTAATACGATTACAAGAATGGGAT 59.340 37.037 16.68 0.00 36.74 3.85
253 268 6.987992 GGTGTAATACGATTACAAGAATGGGA 59.012 38.462 16.68 0.00 36.74 4.37
254 269 6.764085 TGGTGTAATACGATTACAAGAATGGG 59.236 38.462 16.68 0.00 36.74 4.00
255 270 7.279090 TGTGGTGTAATACGATTACAAGAATGG 59.721 37.037 16.68 0.00 36.74 3.16
256 271 8.192068 TGTGGTGTAATACGATTACAAGAATG 57.808 34.615 16.68 0.00 36.74 2.67
257 272 8.780846 TTGTGGTGTAATACGATTACAAGAAT 57.219 30.769 16.68 0.00 36.74 2.40
258 273 8.780846 ATTGTGGTGTAATACGATTACAAGAA 57.219 30.769 16.68 10.63 36.74 2.52
265 280 6.640518 ACTGAGATTGTGGTGTAATACGATT 58.359 36.000 0.00 0.00 0.00 3.34
277 292 2.544685 CGCTAGGAACTGAGATTGTGG 58.455 52.381 0.00 0.00 41.52 4.17
288 303 3.825143 TTATTGTACCCCGCTAGGAAC 57.175 47.619 0.00 0.00 41.02 3.62
297 312 5.591472 GGTTGACTATGGTTTATTGTACCCC 59.409 44.000 0.00 0.00 34.66 4.95
315 330 5.007682 TGGGCATAAGAGTTTAAGGTTGAC 58.992 41.667 0.00 0.00 0.00 3.18
373 388 1.377725 CCAGGCCAGGTAGCAACAG 60.378 63.158 5.01 0.00 0.00 3.16
379 394 1.379977 TCGTCTCCAGGCCAGGTAG 60.380 63.158 14.79 10.32 0.00 3.18
863 881 1.743772 CGGATGGCTTCCCACTTACAG 60.744 57.143 13.33 0.00 45.77 2.74
864 882 0.251916 CGGATGGCTTCCCACTTACA 59.748 55.000 13.33 0.00 45.77 2.41
884 905 1.036707 GAATGGGGGAGAGAGACGAG 58.963 60.000 0.00 0.00 0.00 4.18
982 1003 2.158559 CATCTCCGATCGTCTGATCCT 58.841 52.381 15.09 0.00 46.89 3.24
986 1007 1.025041 CACCATCTCCGATCGTCTGA 58.975 55.000 15.09 9.20 0.00 3.27
990 1014 2.413351 CGCACCATCTCCGATCGT 59.587 61.111 15.09 0.00 0.00 3.73
1020 1044 2.687805 CGGCCTCTCGTCGAACTCA 61.688 63.158 0.00 0.00 0.00 3.41
1251 1275 4.047125 CGGTGGTCCTTGCCCCAT 62.047 66.667 0.00 0.00 32.32 4.00
1314 1339 0.451783 CAAACGGAACCATAGCCTGC 59.548 55.000 0.00 0.00 0.00 4.85
1326 1351 1.021202 CAGCCAGTGAAACAAACGGA 58.979 50.000 0.00 0.00 41.43 4.69
1327 1352 1.021202 TCAGCCAGTGAAACAAACGG 58.979 50.000 0.00 0.00 41.43 4.44
1391 1417 0.913205 AGAGCTACTCCTCGACCTCA 59.087 55.000 0.00 0.00 36.95 3.86
1419 1448 1.198094 TCTCCATTCCAGGAACGGCA 61.198 55.000 9.68 0.00 37.20 5.69
1469 1536 4.438608 GCATTTCACCATAAACTGCATCGA 60.439 41.667 0.00 0.00 0.00 3.59
1516 1583 7.504911 AGAGATCTCAATTGGTTAATGGAATGG 59.495 37.037 24.39 0.00 0.00 3.16
1534 1602 2.303022 TGTGACCCCAAACAGAGATCTC 59.697 50.000 15.29 15.29 0.00 2.75
1539 1607 1.442769 CGATGTGACCCCAAACAGAG 58.557 55.000 0.00 0.00 0.00 3.35
1576 1644 5.767670 TCTACTACTACATTCCCAAGCTCT 58.232 41.667 0.00 0.00 0.00 4.09
1591 1659 6.649557 GTGCTAATGTTTGGTGTTCTACTACT 59.350 38.462 0.00 0.00 0.00 2.57
1639 1710 2.127651 TGTCCTAGTTCAAACCCCCT 57.872 50.000 0.00 0.00 0.00 4.79
1671 1742 1.674221 CGCCTTCCTCCTCAACTCTTG 60.674 57.143 0.00 0.00 0.00 3.02
1673 1744 1.261238 CCGCCTTCCTCCTCAACTCT 61.261 60.000 0.00 0.00 0.00 3.24
1684 1755 1.977009 CAAACCCCTTCCGCCTTCC 60.977 63.158 0.00 0.00 0.00 3.46
1685 1756 0.538746 TTCAAACCCCTTCCGCCTTC 60.539 55.000 0.00 0.00 0.00 3.46
1686 1757 0.826256 GTTCAAACCCCTTCCGCCTT 60.826 55.000 0.00 0.00 0.00 4.35
1687 1758 1.228459 GTTCAAACCCCTTCCGCCT 60.228 57.895 0.00 0.00 0.00 5.52
1688 1759 1.228459 AGTTCAAACCCCTTCCGCC 60.228 57.895 0.00 0.00 0.00 6.13
1689 1760 1.524008 CCAGTTCAAACCCCTTCCGC 61.524 60.000 0.00 0.00 0.00 5.54
1690 1761 0.109723 TCCAGTTCAAACCCCTTCCG 59.890 55.000 0.00 0.00 0.00 4.30
1728 1799 4.006989 ACAGTTTGCACACACAGTTAAGA 58.993 39.130 5.67 0.00 0.00 2.10
1814 1885 5.779529 TTAGGATTTAATACCGCTCGTCT 57.220 39.130 0.00 0.00 0.00 4.18
1821 1892 7.868906 TGGGAAGTTTTAGGATTTAATACCG 57.131 36.000 0.00 0.00 0.00 4.02
1864 1935 4.901197 TGAGTCAACTTAGTGGGCATTA 57.099 40.909 0.00 0.00 0.00 1.90
1922 1993 4.262463 CGATGCTAGCCCCTTAACAGATAA 60.262 45.833 13.29 0.00 0.00 1.75
1926 1997 1.139058 ACGATGCTAGCCCCTTAACAG 59.861 52.381 13.29 0.00 0.00 3.16
1929 2000 3.275999 GAAAACGATGCTAGCCCCTTAA 58.724 45.455 13.29 0.00 0.00 1.85
1933 2004 1.101635 GGGAAAACGATGCTAGCCCC 61.102 60.000 13.29 9.00 0.00 5.80
1982 2054 2.449137 AGAAATAGGCCAGCAGCAAT 57.551 45.000 5.01 0.00 46.50 3.56
2153 2280 9.592196 AGGTATGATGATGGCTAACAAAATTAT 57.408 29.630 0.00 0.00 0.00 1.28
2157 2284 8.995027 ATAAGGTATGATGATGGCTAACAAAA 57.005 30.769 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.