Multiple sequence alignment - TraesCS5B01G343900

Loading Multiple Alignment...

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 TraesCS5B01G343900 chr5B 100.000 2342 0 0 1 2342 527254115 527256456 0.000000e+00 4325.0
1 TraesCS5B01G343900 chr5B 91.205 614 52 2 1730 2342 527491054 527490442 0.000000e+00 833.0
2 TraesCS5B01G343900 chr5B 84.588 571 43 21 674 1202 527247838 527248405 2.060000e-145 525.0
3 TraesCS5B01G343900 chr5B 80.792 682 88 29 748 1401 527492249 527491583 5.810000e-136 494.0
4 TraesCS5B01G343900 chr5B 93.750 48 2 1 464 510 527247681 527247728 1.160000e-08 71.3
5 TraesCS5B01G343900 chr5D 91.427 1423 82 17 3 1401 434479309 434480715 0.000000e+00 1916.0
6 TraesCS5B01G343900 chr5D 91.923 941 76 0 1402 2342 434480761 434481701 0.000000e+00 1317.0
7 TraesCS5B01G343900 chr5D 89.773 264 27 0 1728 1991 434599365 434599102 2.880000e-89 339.0
8 TraesCS5B01G343900 chr5D 80.702 456 68 12 845 1295 434666660 434667100 1.040000e-88 337.0
9 TraesCS5B01G343900 chr5D 95.745 47 2 0 464 510 434596408 434596362 2.500000e-10 76.8
10 TraesCS5B01G343900 chr5A 92.781 748 54 0 1595 2342 548504585 548505332 0.000000e+00 1083.0
11 TraesCS5B01G343900 chr5A 85.376 971 84 29 674 1600 548503572 548504528 0.000000e+00 953.0
12 TraesCS5B01G343900 chr5A 94.118 51 3 0 464 514 548503427 548503477 6.940000e-11 78.7
13 TraesCS5B01G343900 chr6B 94.118 51 3 0 464 514 123414688 123414738 6.940000e-11 78.7
14 TraesCS5B01G343900 chr6B 95.745 47 2 0 468 514 123203571 123203617 2.500000e-10 76.8
15 TraesCS5B01G343900 chr6A 95.745 47 2 0 468 514 66811471 66811517 2.500000e-10 76.8
16 TraesCS5B01G343900 chr6A 92.683 41 2 1 740 779 483061788 483061748 9.040000e-05 58.4
17 TraesCS5B01G343900 chr4B 92.683 41 2 1 740 779 508607993 508607953 9.040000e-05 58.4
18 TraesCS5B01G343900 chr3D 79.381 97 9 8 694 779 536960143 536960239 9.040000e-05 58.4


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 TraesCS5B01G343900 chr5B 527254115 527256456 2341 False 4325.00 4325 100.000000 1 2342 1 chr5B.!!$F1 2341
1 TraesCS5B01G343900 chr5B 527490442 527492249 1807 True 663.50 833 85.998500 748 2342 2 chr5B.!!$R1 1594
2 TraesCS5B01G343900 chr5B 527247681 527248405 724 False 298.15 525 89.169000 464 1202 2 chr5B.!!$F2 738
3 TraesCS5B01G343900 chr5D 434479309 434481701 2392 False 1616.50 1916 91.675000 3 2342 2 chr5D.!!$F2 2339
4 TraesCS5B01G343900 chr5D 434596362 434599365 3003 True 207.90 339 92.759000 464 1991 2 chr5D.!!$R1 1527
5 TraesCS5B01G343900 chr5A 548503427 548505332 1905 False 704.90 1083 90.758333 464 2342 3 chr5A.!!$F1 1878

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
226 227 0.039618 GGGCCACATTTCCTTCTGGA 59.96 55.0 4.39 0.0 41.36 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1437 0.976641 TGAACGCCCTCATGACTTCT 59.023 50.0 0.0 0.0 0.0 2.85 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
28 29 8.462016 ACAGCAACCTCAGTAAATATTGATTTC 58.538 33.333 0.00 0.00 36.62 2.17
57 58 5.473039 AGTTTTGTTTAATGATGCAGAGGC 58.527 37.500 0.00 0.00 41.68 4.70
75 76 0.653636 GCACGTTTGTTTCGTCAGGA 59.346 50.000 0.00 0.00 39.55 3.86
77 78 2.476519 GCACGTTTGTTTCGTCAGGAAA 60.477 45.455 0.00 0.00 42.23 3.13
123 124 4.093703 TGTTTCGTGTCACTGTTTGGTTAG 59.906 41.667 0.65 0.00 0.00 2.34
131 132 6.046593 TGTCACTGTTTGGTTAGACACTTAG 58.953 40.000 0.00 0.00 31.72 2.18
132 133 6.127281 TGTCACTGTTTGGTTAGACACTTAGA 60.127 38.462 0.00 0.00 31.72 2.10
133 134 6.200475 GTCACTGTTTGGTTAGACACTTAGAC 59.800 42.308 0.00 0.00 0.00 2.59
134 135 6.097839 TCACTGTTTGGTTAGACACTTAGACT 59.902 38.462 0.00 0.00 0.00 3.24
135 136 6.761714 CACTGTTTGGTTAGACACTTAGACTT 59.238 38.462 0.00 0.00 0.00 3.01
136 137 6.761714 ACTGTTTGGTTAGACACTTAGACTTG 59.238 38.462 0.00 0.00 0.00 3.16
216 217 4.210331 GTCTAAGAATGATGGGCCACATT 58.790 43.478 24.70 24.70 40.72 2.71
218 219 4.889409 TCTAAGAATGATGGGCCACATTTC 59.111 41.667 25.01 19.67 40.72 2.17
219 220 2.391678 AGAATGATGGGCCACATTTCC 58.608 47.619 25.01 17.35 40.72 3.13
221 222 2.555732 ATGATGGGCCACATTTCCTT 57.444 45.000 9.28 0.00 40.72 3.36
222 223 1.851304 TGATGGGCCACATTTCCTTC 58.149 50.000 9.28 0.00 40.72 3.46
224 225 1.753073 GATGGGCCACATTTCCTTCTG 59.247 52.381 9.28 0.00 40.72 3.02
225 226 0.251742 TGGGCCACATTTCCTTCTGG 60.252 55.000 0.00 0.00 0.00 3.86
226 227 0.039618 GGGCCACATTTCCTTCTGGA 59.960 55.000 4.39 0.00 41.36 3.86
227 228 1.177401 GGCCACATTTCCTTCTGGAC 58.823 55.000 0.00 0.00 43.06 4.02
466 473 5.902613 TTTGTGATGGGAATGAAGTCATC 57.097 39.130 0.00 0.00 35.10 2.92
533 540 9.155785 CTATATAGGACTTCTTTTAAGGGACCA 57.844 37.037 1.40 0.00 0.00 4.02
537 544 5.012871 AGGACTTCTTTTAAGGGACCACTAC 59.987 44.000 0.00 0.00 0.00 2.73
582 589 6.865834 TGATATTACCAAGCACCCAAAAAT 57.134 33.333 0.00 0.00 0.00 1.82
583 590 7.962995 TGATATTACCAAGCACCCAAAAATA 57.037 32.000 0.00 0.00 0.00 1.40
584 591 8.367660 TGATATTACCAAGCACCCAAAAATAA 57.632 30.769 0.00 0.00 0.00 1.40
585 592 8.986991 TGATATTACCAAGCACCCAAAAATAAT 58.013 29.630 0.00 0.00 0.00 1.28
622 629 5.242171 TCTCATTGCACAATCACAAACAGAT 59.758 36.000 0.00 0.00 0.00 2.90
624 631 4.915158 TTGCACAATCACAAACAGATCA 57.085 36.364 0.00 0.00 0.00 2.92
625 632 5.456548 TTGCACAATCACAAACAGATCAT 57.543 34.783 0.00 0.00 0.00 2.45
656 664 1.031571 CACATGGTCCCCACATTCCG 61.032 60.000 0.00 0.00 35.80 4.30
671 679 6.147821 CCCACATTCCGTTATATGCTTCTTAG 59.852 42.308 0.00 0.00 0.00 2.18
722 733 4.577693 AGCATACTGTATTGTCCAAGCATG 59.422 41.667 0.00 0.00 0.00 4.06
880 923 6.319141 ACCTAAACTGCATTGTTCTCTTTC 57.681 37.500 0.00 0.00 0.00 2.62
885 928 6.959639 AACTGCATTGTTCTCTTTCCTTTA 57.040 33.333 0.00 0.00 0.00 1.85
928 999 1.470098 GCTTAGCACCACCATCACTTG 59.530 52.381 0.00 0.00 0.00 3.16
1024 1105 3.748568 GGTTAGTGCCAAGAGACTTTCTG 59.251 47.826 0.00 0.00 35.91 3.02
1026 1107 3.399440 AGTGCCAAGAGACTTTCTGAG 57.601 47.619 0.00 0.00 35.91 3.35
1027 1108 2.968574 AGTGCCAAGAGACTTTCTGAGA 59.031 45.455 0.00 0.00 35.91 3.27
1028 1109 3.582208 AGTGCCAAGAGACTTTCTGAGAT 59.418 43.478 0.00 0.00 35.91 2.75
1035 1116 4.032310 AGAGACTTTCTGAGATGATGGCT 58.968 43.478 0.00 0.00 33.93 4.75
1082 1163 0.906756 CAGAGGAAGAGGCTCACCCA 60.907 60.000 18.26 0.00 36.11 4.51
1165 1246 1.620822 GATGAAGGGCCACTGTGTTT 58.379 50.000 6.18 0.00 0.00 2.83
1268 1349 1.479389 CCAGGAGGAGTTTGGCTTTGT 60.479 52.381 0.00 0.00 36.89 2.83
1289 1370 2.105128 CGGCGATGACAGGAGGAC 59.895 66.667 0.00 0.00 0.00 3.85
1339 1420 0.107508 ATACGCCATGTGCTTGCTCT 60.108 50.000 4.92 0.00 38.05 4.09
1356 1437 2.942804 CTCTAGAGAGATGCCTCCACA 58.057 52.381 15.05 0.00 44.74 4.17
1391 1472 2.867333 TTCATGAGCTCCGTCGCGAC 62.867 60.000 28.96 28.96 34.40 5.19
1463 1595 5.880332 TGTTTGTTAGCTTCTGAAGAACAGT 59.120 36.000 21.06 2.38 45.86 3.55
1468 1600 1.716581 GCTTCTGAAGAACAGTCGACG 59.283 52.381 21.06 7.86 45.86 5.12
1492 1627 1.522580 CTAGCTTTCGCCCTGCTCC 60.523 63.158 0.00 0.00 38.15 4.70
1506 1641 0.874390 TGCTCCGTTTCTTGCATGAC 59.126 50.000 1.02 0.00 0.00 3.06
1590 1728 4.739716 CAGCATGGTGAACTTTGTAACAAC 59.260 41.667 20.20 0.00 0.00 3.32
1648 1848 8.122472 TCTATTCTGTCTCTGATTTGTGTGTA 57.878 34.615 0.00 0.00 0.00 2.90
1772 2129 4.688413 GCGAAGAAGACTCTGATGAAAGTT 59.312 41.667 0.00 0.00 30.03 2.66
1813 2170 1.275291 TCCAGTCCGTCATCCAAACTC 59.725 52.381 0.00 0.00 0.00 3.01
1887 2244 2.584608 CGGTCCCTCGCTTTCCAT 59.415 61.111 0.00 0.00 0.00 3.41
1945 2302 1.008995 CGGGTGGTTCTTTGTTGCG 60.009 57.895 0.00 0.00 0.00 4.85
1987 2344 1.214062 GTCAGGCACTCCAGAGTCG 59.786 63.158 0.00 0.00 40.20 4.18
2031 2388 2.306805 TGAGGTGTCTGATTTGGATGCT 59.693 45.455 0.00 0.00 0.00 3.79
2051 3241 1.777878 TGGAAAAACCAGCTAGACCCA 59.222 47.619 0.00 0.00 44.64 4.51
2080 3270 1.771255 AGCTGGAGTGAGACAAGGTTT 59.229 47.619 0.00 0.00 0.00 3.27
2092 4734 0.538057 CAAGGTTTGGCAGAGCTCCA 60.538 55.000 10.93 0.00 0.00 3.86
2243 5044 7.521099 GCAAGTTTCTCAAATTGATCAGAGACA 60.521 37.037 10.94 3.77 36.90 3.41
2328 5129 3.502356 GAACAAATGGGGGTAACTGGAA 58.498 45.455 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.711277 TCAATATTTACTGAGGTTGCTGTCT 58.289 36.000 0.00 0.00 0.00 3.41
1 2 6.985188 TCAATATTTACTGAGGTTGCTGTC 57.015 37.500 0.00 0.00 0.00 3.51
28 29 9.409312 TCTGCATCATTAAACAAAACTTACATG 57.591 29.630 0.00 0.00 0.00 3.21
57 58 3.392769 TTTCCTGACGAAACAAACGTG 57.607 42.857 0.00 0.00 43.97 4.49
60 61 3.067601 ACCCATTTCCTGACGAAACAAAC 59.932 43.478 0.00 0.00 43.21 2.93
75 76 3.864789 AGAGACACTGACAACCCATTT 57.135 42.857 0.00 0.00 0.00 2.32
98 99 3.119990 ACCAAACAGTGACACGAAACAAG 60.120 43.478 0.00 0.00 0.00 3.16
100 101 2.428491 ACCAAACAGTGACACGAAACA 58.572 42.857 0.00 0.00 0.00 2.83
123 124 7.907214 ATTGTTATGTCCAAGTCTAAGTGTC 57.093 36.000 0.00 0.00 0.00 3.67
131 132 7.672983 TCTTCTGAATTGTTATGTCCAAGTC 57.327 36.000 0.00 0.00 37.41 3.01
132 133 7.721399 AGTTCTTCTGAATTGTTATGTCCAAGT 59.279 33.333 0.00 0.00 34.40 3.16
133 134 8.103948 AGTTCTTCTGAATTGTTATGTCCAAG 57.896 34.615 0.00 0.00 34.40 3.61
134 135 9.739276 ATAGTTCTTCTGAATTGTTATGTCCAA 57.261 29.630 0.00 0.00 34.40 3.53
197 198 3.960102 GGAAATGTGGCCCATCATTCTTA 59.040 43.478 15.03 0.00 33.86 2.10
205 206 1.620524 CCAGAAGGAAATGTGGCCCAT 60.621 52.381 0.00 0.00 36.89 4.00
218 219 4.136796 TCAACAAGAACATGTCCAGAAGG 58.863 43.478 0.00 0.00 31.81 3.46
219 220 4.320057 GCTCAACAAGAACATGTCCAGAAG 60.320 45.833 0.00 0.00 31.81 2.85
221 222 3.141398 GCTCAACAAGAACATGTCCAGA 58.859 45.455 0.00 0.00 31.81 3.86
222 223 3.144506 AGCTCAACAAGAACATGTCCAG 58.855 45.455 0.00 0.00 31.81 3.86
224 225 4.276926 AGAAAGCTCAACAAGAACATGTCC 59.723 41.667 0.00 0.00 31.81 4.02
225 226 5.210715 CAGAAAGCTCAACAAGAACATGTC 58.789 41.667 0.00 0.00 31.81 3.06
226 227 4.498682 GCAGAAAGCTCAACAAGAACATGT 60.499 41.667 0.00 0.00 41.15 3.21
227 228 3.979495 GCAGAAAGCTCAACAAGAACATG 59.021 43.478 0.00 0.00 41.15 3.21
466 473 7.148000 TGGAGATATCTAGTCTGACAGTTGTTG 60.148 40.741 4.89 0.00 0.00 3.33
583 590 9.407380 TGTGCAATGAGATACCAACTAATTATT 57.593 29.630 0.00 0.00 0.00 1.40
584 591 8.978874 TGTGCAATGAGATACCAACTAATTAT 57.021 30.769 0.00 0.00 0.00 1.28
585 592 8.800370 TTGTGCAATGAGATACCAACTAATTA 57.200 30.769 0.00 0.00 0.00 1.40
622 629 5.164620 ACCATGTGTAGATTGTGTCATGA 57.835 39.130 0.00 0.00 35.98 3.07
624 631 4.517285 GGACCATGTGTAGATTGTGTCAT 58.483 43.478 0.00 0.00 0.00 3.06
625 632 3.307410 GGGACCATGTGTAGATTGTGTCA 60.307 47.826 0.00 0.00 0.00 3.58
656 664 5.823045 AGTGGCAACCTAAGAAGCATATAAC 59.177 40.000 0.00 0.00 0.00 1.89
671 679 2.293399 CTCACCTGTTTTAGTGGCAACC 59.707 50.000 0.00 0.00 34.67 3.77
722 733 2.710902 GGGGACGATGCTTTTGGGC 61.711 63.158 0.00 0.00 0.00 5.36
880 923 9.454859 GATGAATTTATAGGTGAGGGATAAAGG 57.545 37.037 0.00 0.00 30.69 3.11
885 928 6.274200 AGCTGATGAATTTATAGGTGAGGGAT 59.726 38.462 0.00 0.00 0.00 3.85
928 999 5.241662 AGCTTGTACTTTCTGGATGAACTC 58.758 41.667 0.00 0.00 33.88 3.01
1024 1105 3.137533 GCCACTTCTTAGCCATCATCTC 58.862 50.000 0.00 0.00 0.00 2.75
1026 1107 2.877168 CTGCCACTTCTTAGCCATCATC 59.123 50.000 0.00 0.00 0.00 2.92
1027 1108 2.507058 TCTGCCACTTCTTAGCCATCAT 59.493 45.455 0.00 0.00 0.00 2.45
1028 1109 1.908619 TCTGCCACTTCTTAGCCATCA 59.091 47.619 0.00 0.00 0.00 3.07
1035 1116 3.938963 CCGCTATTTTCTGCCACTTCTTA 59.061 43.478 0.00 0.00 0.00 2.10
1165 1246 1.369692 CCCTGTCAGCGGTGTACAA 59.630 57.895 15.22 0.00 0.00 2.41
1213 1294 2.277969 CTCGCTGAAGATCAATGTGCT 58.722 47.619 0.00 0.00 0.00 4.40
1260 1341 3.323758 ATCGCCGCCTACAAAGCCA 62.324 57.895 0.00 0.00 0.00 4.75
1268 1349 2.441348 TCCTGTCATCGCCGCCTA 60.441 61.111 0.00 0.00 0.00 3.93
1289 1370 2.499205 CATTGCAGGGCAGCATGG 59.501 61.111 4.68 0.00 45.19 3.66
1339 1420 3.295093 CTTCTGTGGAGGCATCTCTCTA 58.705 50.000 0.00 0.00 39.86 2.43
1356 1437 0.976641 TGAACGCCCTCATGACTTCT 59.023 50.000 0.00 0.00 0.00 2.85
1463 1595 1.201998 CGAAAGCTAGCACTACGTCGA 60.202 52.381 18.83 0.00 0.00 4.20
1482 1617 2.358737 AAGAAACGGAGCAGGGCG 60.359 61.111 0.00 0.00 0.00 6.13
1492 1627 2.661504 TTCACGTCATGCAAGAAACG 57.338 45.000 10.66 10.66 40.77 3.60
1506 1641 4.391830 ACCACTTGCAACTGTATATTCACG 59.608 41.667 0.00 0.00 0.00 4.35
1556 1694 3.419943 TCACCATGCTGCAGATTGTAAA 58.580 40.909 20.43 0.00 0.00 2.01
1564 1702 1.338973 ACAAAGTTCACCATGCTGCAG 59.661 47.619 10.11 10.11 0.00 4.41
1590 1728 4.789481 GCTGTTGTATTGTGTGGTGTTCTG 60.789 45.833 0.00 0.00 0.00 3.02
1648 1848 2.479566 ACGGTGATGATTCAGCTTGT 57.520 45.000 3.27 0.00 46.01 3.16
1772 2129 7.398618 ACTGGATTCTAGTCTCAAGAAGATGAA 59.601 37.037 0.00 0.00 36.46 2.57
1813 2170 4.033587 CGGAAAATATGTGTACTCCAACCG 59.966 45.833 0.00 0.00 0.00 4.44
1821 2178 4.272748 GGGAGAAGCGGAAAATATGTGTAC 59.727 45.833 0.00 0.00 0.00 2.90
1867 2224 3.703127 GAAAGCGAGGGACCGGGT 61.703 66.667 6.32 0.00 0.00 5.28
1887 2244 1.813178 TGCACAAAAGTGGTGTTCGAA 59.187 42.857 0.00 0.00 38.51 3.71
1945 2302 1.202698 ACAAGACAAGACTGGGAGCAC 60.203 52.381 0.00 0.00 0.00 4.40
1987 2344 1.134965 CATCTCAAGGAGGTCACGGTC 60.135 57.143 0.00 0.00 0.00 4.79
2031 2388 1.777878 TGGGTCTAGCTGGTTTTTCCA 59.222 47.619 0.00 0.00 45.01 3.53
2042 3232 1.002134 TGCTTTGCCTGGGTCTAGC 60.002 57.895 0.00 0.00 0.00 3.42
2051 3241 1.602888 CACTCCAGCTGCTTTGCCT 60.603 57.895 8.66 0.00 0.00 4.75
2080 3270 1.078918 CGAACATGGAGCTCTGCCA 60.079 57.895 14.64 4.08 40.24 4.92
2092 4734 1.376543 CTCTGCCAGCAATCGAACAT 58.623 50.000 0.00 0.00 0.00 2.71
2243 5044 4.282496 ACTCTGACACGGGATCTTCTATT 58.718 43.478 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.