Multiple sequence alignment - TraesCS4D01G185400

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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 TraesCS4D01G185400 chr4D 100.000 2393 0 0 1 2393 323355965 323353573 0.000000e+00 4420.0
1 TraesCS4D01G185400 chr4B 91.853 1964 80 39 1 1939 403625802 403623894 0.000000e+00 2667.0
2 TraesCS4D01G185400 chr4B 91.959 485 25 4 1923 2393 403623804 403623320 0.000000e+00 667.0
3 TraesCS4D01G185400 chr4B 96.591 88 2 1 1650 1736 413498544 413498631 6.890000e-31 145.0
4 TraesCS4D01G185400 chr4B 88.571 70 8 0 565 634 664947736 664947805 4.240000e-13 86.1
5 TraesCS4D01G185400 chr4B 88.571 70 8 0 565 634 664978525 664978594 4.240000e-13 86.1
6 TraesCS4D01G185400 chr4B 88.571 70 8 0 565 634 665007136 665007205 4.240000e-13 86.1
7 TraesCS4D01G185400 chr4B 88.571 70 8 0 565 634 665117180 665117249 4.240000e-13 86.1
8 TraesCS4D01G185400 chr4A 92.269 1591 81 19 838 2393 148757558 148759141 0.000000e+00 2218.0
9 TraesCS4D01G185400 chr4A 91.696 855 45 19 3 838 148756516 148757363 0.000000e+00 1162.0
10 TraesCS4D01G185400 chr2A 81.783 258 36 10 1150 1403 15270128 15270378 3.120000e-49 206.0
11 TraesCS4D01G185400 chr2D 81.395 258 37 11 1150 1403 13228795 13229045 1.450000e-47 200.0
12 TraesCS4D01G185400 chr2B 81.008 258 38 10 1150 1403 23878245 23878495 6.750000e-46 195.0
13 TraesCS4D01G185400 chr3B 77.848 316 42 14 276 568 633132660 633132350 1.140000e-38 171.0
14 TraesCS4D01G185400 chr3B 92.000 100 6 2 1659 1757 5587343 5587441 3.210000e-29 139.0
15 TraesCS4D01G185400 chr3B 92.079 101 4 3 1649 1747 16445108 16445206 3.210000e-29 139.0
16 TraesCS4D01G185400 chr5A 86.275 153 19 2 272 422 709417368 709417216 5.290000e-37 165.0
17 TraesCS4D01G185400 chr5A 85.714 91 12 1 274 364 19486569 19486480 7.040000e-16 95.3
18 TraesCS4D01G185400 chr1B 86.275 153 19 2 272 422 590505623 590505471 5.290000e-37 165.0
19 TraesCS4D01G185400 chr1B 80.392 153 23 7 279 429 584313902 584314049 2.510000e-20 110.0
20 TraesCS4D01G185400 chr6D 95.699 93 3 1 1654 1746 17887724 17887815 5.330000e-32 148.0
21 TraesCS4D01G185400 chr6A 96.629 89 3 0 1658 1746 18580792 18580880 5.330000e-32 148.0
22 TraesCS4D01G185400 chr6B 93.137 102 4 3 1646 1746 32019320 32019419 1.920000e-31 147.0
23 TraesCS4D01G185400 chr3A 94.624 93 4 1 1656 1748 25368086 25367995 2.480000e-30 143.0
24 TraesCS4D01G185400 chr5D 83.594 128 16 5 276 399 56917252 56917378 5.410000e-22 115.0
25 TraesCS4D01G185400 chr5D 100.000 30 0 0 422 451 56917438 56917467 3.320000e-04 56.5
26 TraesCS4D01G185400 chr1A 74.919 307 48 18 271 558 94109031 94109327 1.940000e-21 113.0
27 TraesCS4D01G185400 chr7D 90.769 65 4 2 571 634 575037291 575037354 4.240000e-13 86.1
28 TraesCS4D01G185400 chr7B 90.625 64 6 0 571 634 557195234 557195171 4.240000e-13 86.1
29 TraesCS4D01G185400 chrUn 89.552 67 6 1 571 637 51188562 51188497 1.520000e-12 84.2


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 TraesCS4D01G185400 chr4D 323353573 323355965 2392 True 4420 4420 100.0000 1 2393 1 chr4D.!!$R1 2392
1 TraesCS4D01G185400 chr4B 403623320 403625802 2482 True 1667 2667 91.9060 1 2393 2 chr4B.!!$R1 2392
2 TraesCS4D01G185400 chr4A 148756516 148759141 2625 False 1690 2218 91.9825 3 2393 2 chr4A.!!$F1 2390

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
978 1195 0.400594 AAACCTTCTCTTCCACCCCG 59.599 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2355 0.179032 TCTGAAAACCTCGGCTGCAA 60.179 50.0 0.5 0.0 0.0 4.08 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
54 55 2.159043 AGTGAGAGTGTGGTGTGAACTG 60.159 50.000 0.00 0.00 0.00 3.16
157 169 1.528076 TGCCTGGCTCTGCGAAAAA 60.528 52.632 21.03 0.00 0.00 1.94
163 175 0.881118 GGCTCTGCGAAAAATGACCA 59.119 50.000 0.00 0.00 0.00 4.02
170 182 3.971150 TGCGAAAAATGACCAATTCGTT 58.029 36.364 8.32 0.00 44.67 3.85
183 195 4.457949 ACCAATTCGTTCATTCCCACTTAC 59.542 41.667 0.00 0.00 0.00 2.34
948 1165 1.376812 GTACCCCAAACGGCCAGAG 60.377 63.158 2.24 0.00 0.00 3.35
949 1166 1.536907 TACCCCAAACGGCCAGAGA 60.537 57.895 2.24 0.00 0.00 3.10
950 1167 0.912487 TACCCCAAACGGCCAGAGAT 60.912 55.000 2.24 0.00 0.00 2.75
977 1194 2.239400 CAAAACCTTCTCTTCCACCCC 58.761 52.381 0.00 0.00 0.00 4.95
978 1195 0.400594 AAACCTTCTCTTCCACCCCG 59.599 55.000 0.00 0.00 0.00 5.73
1040 1257 2.183409 CCTTCATGGCCACCTTTCG 58.817 57.895 8.16 0.00 0.00 3.46
1401 1618 3.181967 GACAGCTAGCCGTGCGTG 61.182 66.667 8.68 2.86 35.28 5.34
1439 1656 3.140141 CCATTGCCGGCCGTCATT 61.140 61.111 26.77 11.63 0.00 2.57
1440 1657 2.408835 CATTGCCGGCCGTCATTC 59.591 61.111 26.77 7.98 0.00 2.67
1441 1658 3.202001 ATTGCCGGCCGTCATTCG 61.202 61.111 26.77 8.60 39.52 3.34
1442 1659 3.673956 ATTGCCGGCCGTCATTCGA 62.674 57.895 26.77 1.66 42.86 3.71
1480 1711 0.899717 ATTGGCATCTTGGGCGTGTT 60.900 50.000 0.00 0.00 35.84 3.32
1506 1737 7.680442 AGTTTGGTTTGTTGCTTTATTTTGT 57.320 28.000 0.00 0.00 0.00 2.83
1515 1746 7.475771 TGTTGCTTTATTTTGTTTGGCTTAG 57.524 32.000 0.00 0.00 0.00 2.18
1595 1826 7.904558 TTAGGAGTTCTGAGTGTGATATCAT 57.095 36.000 9.02 0.00 0.00 2.45
1610 1841 9.440773 GTGTGATATCATATTATCAAGGCAAGA 57.559 33.333 9.02 0.00 39.61 3.02
1617 1848 2.988010 TATCAAGGCAAGATGCGAGT 57.012 45.000 2.43 0.00 46.21 4.18
1618 1849 1.376543 ATCAAGGCAAGATGCGAGTG 58.623 50.000 0.00 0.00 46.21 3.51
1620 1851 0.445436 CAAGGCAAGATGCGAGTGAC 59.555 55.000 0.00 0.00 46.21 3.67
1625 1856 1.730501 CAAGATGCGAGTGACCATGT 58.269 50.000 0.00 0.00 0.00 3.21
1632 1863 5.755375 AGATGCGAGTGACCATGTTAATTAG 59.245 40.000 0.00 0.00 0.00 1.73
1633 1864 4.827692 TGCGAGTGACCATGTTAATTAGT 58.172 39.130 0.00 0.00 0.00 2.24
1635 1866 4.494199 GCGAGTGACCATGTTAATTAGTGC 60.494 45.833 0.00 0.00 0.00 4.40
1636 1867 4.034048 CGAGTGACCATGTTAATTAGTGCC 59.966 45.833 0.00 0.00 0.00 5.01
1641 1872 4.270008 ACCATGTTAATTAGTGCCCACTC 58.730 43.478 3.88 0.00 42.54 3.51
1642 1873 4.263727 ACCATGTTAATTAGTGCCCACTCA 60.264 41.667 3.88 0.00 42.54 3.41
1644 1875 5.393027 CCATGTTAATTAGTGCCCACTCAAC 60.393 44.000 3.88 6.28 42.54 3.18
1647 1878 6.717289 TGTTAATTAGTGCCCACTCAACTAT 58.283 36.000 3.88 0.00 42.54 2.12
1648 1879 7.853299 TGTTAATTAGTGCCCACTCAACTATA 58.147 34.615 3.88 0.00 42.54 1.31
1649 1880 8.491134 TGTTAATTAGTGCCCACTCAACTATAT 58.509 33.333 3.88 0.00 42.54 0.86
1650 1881 9.991906 GTTAATTAGTGCCCACTCAACTATATA 57.008 33.333 3.88 0.00 42.54 0.86
1733 1965 5.279506 GGATCGAAACCTGGCTCTGATATTA 60.280 44.000 0.00 0.00 0.00 0.98
1825 2077 3.909776 CAGCATGCTCTTTCAGAAACA 57.090 42.857 19.68 0.00 0.00 2.83
1853 2106 4.820716 AGGGTCATATGACGTACTGTACTC 59.179 45.833 25.65 10.43 45.65 2.59
1856 2109 6.360844 GTCATATGACGTACTGTACTCAGT 57.639 41.667 19.63 6.55 44.52 3.41
1874 2127 3.619483 TCAGTAACTGGTTGTGACGTTTG 59.381 43.478 0.00 0.00 35.16 2.93
1918 2171 4.959631 TTCAGTTCGCTACAAACTTACG 57.040 40.909 0.00 0.00 34.79 3.18
1973 2332 6.959361 AGAAGCCAGCATAAAAATACATACG 58.041 36.000 0.00 0.00 0.00 3.06
1996 2355 5.522460 CGGACAAAAACATCTATACCGACAT 59.478 40.000 0.00 0.00 40.16 3.06
2015 2374 0.179032 TTGCAGCCGAGGTTTTCAGA 60.179 50.000 0.00 0.00 0.00 3.27
2016 2375 0.179032 TGCAGCCGAGGTTTTCAGAA 60.179 50.000 0.00 0.00 0.00 3.02
2057 2416 3.619929 ACCGACAAAAACATCTATACCGC 59.380 43.478 0.00 0.00 0.00 5.68
2178 2537 2.487762 CAGGTTATTGCACGGTGTTCAT 59.512 45.455 10.24 2.44 0.00 2.57
2230 2590 1.412079 AAAATGCTGAACCCACTGCA 58.588 45.000 0.00 0.00 45.48 4.41
2252 2612 5.502544 GCAGCATCTATTTCGTCCAAGTAAC 60.503 44.000 0.00 0.00 0.00 2.50
2261 2628 1.957186 TCCAAGTAACGCACGGTGC 60.957 57.895 22.78 22.78 40.69 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 84 1.065709 GGACGCTTCATAACTTCCCCA 60.066 52.381 0.00 0.00 0.00 4.96
128 140 0.618680 AGCCAGGCACTAGTGATCCA 60.619 55.000 27.08 0.00 36.02 3.41
134 146 2.985456 GCAGAGCCAGGCACTAGT 59.015 61.111 15.80 0.00 36.02 2.57
157 169 3.443681 GTGGGAATGAACGAATTGGTCAT 59.556 43.478 0.00 0.00 0.00 3.06
163 175 5.643777 CAGAGTAAGTGGGAATGAACGAATT 59.356 40.000 0.00 0.00 0.00 2.17
170 182 6.673583 TCTAGATCAGAGTAAGTGGGAATGA 58.326 40.000 0.00 0.00 0.00 2.57
183 195 5.105392 ACCTCAAAGCACTTCTAGATCAGAG 60.105 44.000 0.00 0.00 33.83 3.35
284 296 6.878389 ACAAAACATTTGTCAAAGTTCACCAT 59.122 30.769 4.03 0.00 0.00 3.55
423 439 8.712285 ATTTCAGCAGAAAATAACATTCATGG 57.288 30.769 8.45 0.00 46.06 3.66
729 747 1.735973 CCTACGTAAGGGCCGGTAC 59.264 63.158 1.90 9.63 42.32 3.34
837 857 6.605194 GGCAGATTTCCCTTCTAGAAGATTTT 59.395 38.462 30.17 12.88 40.79 1.82
948 1165 3.767711 AGAGAAGGTTTTGGTTGGGATC 58.232 45.455 0.00 0.00 0.00 3.36
949 1166 3.903530 AGAGAAGGTTTTGGTTGGGAT 57.096 42.857 0.00 0.00 0.00 3.85
950 1167 3.562182 GAAGAGAAGGTTTTGGTTGGGA 58.438 45.455 0.00 0.00 0.00 4.37
977 1194 4.724697 CGCACTTGGTTCGCAGCG 62.725 66.667 9.06 9.06 39.17 5.18
978 1195 2.770587 CTTCGCACTTGGTTCGCAGC 62.771 60.000 0.00 0.00 0.00 5.25
1040 1257 2.359975 CAACGGTTCTGGGAGCCC 60.360 66.667 0.00 0.00 28.75 5.19
1401 1618 4.400961 AAGACGGCAGGAGCAGGC 62.401 66.667 0.00 0.00 45.11 4.85
1402 1619 2.125350 GAAGACGGCAGGAGCAGG 60.125 66.667 0.00 0.00 44.61 4.85
1439 1656 1.446099 CCACGCAAGCTAAGCTCGA 60.446 57.895 9.12 0.00 38.25 4.04
1440 1657 3.084579 CCACGCAAGCTAAGCTCG 58.915 61.111 9.12 0.00 38.25 5.03
1441 1658 2.034879 TGCCACGCAAGCTAAGCTC 61.035 57.895 9.12 0.00 38.25 4.09
1442 1659 2.032528 TGCCACGCAAGCTAAGCT 59.967 55.556 9.12 0.00 42.56 3.74
1480 1711 9.220767 ACAAAATAAAGCAACAAACCAAACTTA 57.779 25.926 0.00 0.00 0.00 2.24
1504 1735 4.142687 GCTCGCTTTATTCTAAGCCAAACA 60.143 41.667 0.00 0.00 46.06 2.83
1506 1737 4.006989 TGCTCGCTTTATTCTAAGCCAAA 58.993 39.130 0.00 0.00 46.06 3.28
1515 1746 6.934561 AACAAATCTTTGCTCGCTTTATTC 57.065 33.333 2.63 0.00 41.79 1.75
1595 1826 4.751600 CACTCGCATCTTGCCTTGATAATA 59.248 41.667 0.00 0.00 41.12 0.98
1610 1841 5.294306 CACTAATTAACATGGTCACTCGCAT 59.706 40.000 0.00 0.00 0.00 4.73
1617 1848 4.013728 GTGGGCACTAATTAACATGGTCA 58.986 43.478 0.00 0.00 0.00 4.02
1618 1849 4.270008 AGTGGGCACTAATTAACATGGTC 58.730 43.478 0.00 0.00 40.43 4.02
1620 1851 4.269183 TGAGTGGGCACTAATTAACATGG 58.731 43.478 0.00 0.00 42.66 3.66
1632 1863 4.058817 GTGCTATATAGTTGAGTGGGCAC 58.941 47.826 11.38 6.86 40.11 5.01
1633 1864 3.709141 TGTGCTATATAGTTGAGTGGGCA 59.291 43.478 11.38 0.00 0.00 5.36
1635 1866 5.276461 TGTGTGCTATATAGTTGAGTGGG 57.724 43.478 11.38 0.00 0.00 4.61
1636 1867 7.495606 TGATTTGTGTGCTATATAGTTGAGTGG 59.504 37.037 11.38 0.00 0.00 4.00
1641 1872 8.546244 CACTCTGATTTGTGTGCTATATAGTTG 58.454 37.037 11.38 0.00 0.00 3.16
1642 1873 7.712639 CCACTCTGATTTGTGTGCTATATAGTT 59.287 37.037 11.38 0.00 32.17 2.24
1644 1875 6.146837 GCCACTCTGATTTGTGTGCTATATAG 59.853 42.308 5.30 5.30 32.17 1.31
1647 1878 4.191544 GCCACTCTGATTTGTGTGCTATA 58.808 43.478 0.00 0.00 32.17 1.31
1648 1879 3.012518 GCCACTCTGATTTGTGTGCTAT 58.987 45.455 0.00 0.00 32.17 2.97
1649 1880 2.426522 GCCACTCTGATTTGTGTGCTA 58.573 47.619 0.00 0.00 32.17 3.49
1650 1881 1.242076 GCCACTCTGATTTGTGTGCT 58.758 50.000 0.00 0.00 32.17 4.40
1651 1882 0.110056 CGCCACTCTGATTTGTGTGC 60.110 55.000 0.00 0.00 32.17 4.57
1772 2018 9.095700 AGTAAAAGCAAAGGGGAAAAACATATA 57.904 29.630 0.00 0.00 0.00 0.86
1775 2021 6.247229 AGTAAAAGCAAAGGGGAAAAACAT 57.753 33.333 0.00 0.00 0.00 2.71
1825 2077 5.597182 ACAGTACGTCATATGACCCTACATT 59.403 40.000 26.33 14.48 41.86 2.71
1853 2106 3.242608 CCAAACGTCACAACCAGTTACTG 60.243 47.826 5.22 5.22 0.00 2.74
1856 2109 2.290464 CCCAAACGTCACAACCAGTTA 58.710 47.619 0.00 0.00 0.00 2.24
1874 2127 2.837532 ATGTTGCCATGTGAAAACCC 57.162 45.000 0.00 0.00 0.00 4.11
1973 2332 6.920569 ATGTCGGTATAGATGTTTTTGTCC 57.079 37.500 0.00 0.00 0.00 4.02
1996 2355 0.179032 TCTGAAAACCTCGGCTGCAA 60.179 50.000 0.50 0.00 0.00 4.08
2015 2374 6.018180 GTCGGTTTAGTGTTCAGTCTTTCATT 60.018 38.462 0.00 0.00 0.00 2.57
2016 2375 5.465724 GTCGGTTTAGTGTTCAGTCTTTCAT 59.534 40.000 0.00 0.00 0.00 2.57
2057 2416 2.194201 ACACCGTGGAATTACTTGGG 57.806 50.000 3.03 0.00 0.00 4.12
2178 2537 3.519510 CCCCTGTATCTTGGTTTCTCTGA 59.480 47.826 0.00 0.00 0.00 3.27
2230 2590 4.804139 CGTTACTTGGACGAAATAGATGCT 59.196 41.667 0.00 0.00 42.82 3.79
2272 2639 1.517257 CAGTCCTAAGCGGCGACTG 60.517 63.158 12.98 17.25 45.33 3.51
2355 2722 2.229792 GCCACCTGATGTTGTCAAGAA 58.770 47.619 0.00 0.00 36.14 2.52


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

AutoCloner maintained by Alex Coulton.