Multiple sequence alignment - TraesCS7B01G248900

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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 TraesCS7B01G248900 chr7B 100.000 2404 0 0 1 2404 459588413 459586010 0.000000e+00 4440
1 TraesCS7B01G248900 chr7B 92.135 534 42 0 1871 2404 207168488 207169021 0.000000e+00 754
2 TraesCS7B01G248900 chr6A 96.758 1820 58 1 1 1820 74542050 74543868 0.000000e+00 3033
3 TraesCS7B01G248900 chr6A 95.175 1285 61 1 550 1833 602833708 602834992 0.000000e+00 2028
4 TraesCS7B01G248900 chr4D 95.901 1659 61 2 162 1820 451883451 451881800 0.000000e+00 2680
5 TraesCS7B01G248900 chr2B 95.678 1666 70 1 159 1822 638286678 638288343 0.000000e+00 2676
6 TraesCS7B01G248900 chr2B 94.913 688 32 2 158 845 39117544 39118228 0.000000e+00 1074
7 TraesCS7B01G248900 chr2B 92.135 534 42 0 1871 2404 232503313 232502780 0.000000e+00 754
8 TraesCS7B01G248900 chr5B 95.310 1663 75 2 160 1820 547904887 547906548 0.000000e+00 2636
9 TraesCS7B01G248900 chr3B 95.072 1664 80 1 159 1820 629799281 629800944 0.000000e+00 2617
10 TraesCS7B01G248900 chr3B 91.948 534 43 0 1871 2404 99434067 99433534 0.000000e+00 749
11 TraesCS7B01G248900 chr3B 91.948 534 43 0 1871 2404 187252302 187252835 0.000000e+00 749
12 TraesCS7B01G248900 chr2D 95.024 1668 69 9 159 1821 344567689 344569347 0.000000e+00 2608
13 TraesCS7B01G248900 chr1B 94.781 1667 85 1 159 1823 109348891 109347225 0.000000e+00 2595
14 TraesCS7B01G248900 chr1B 92.509 534 40 0 1871 2404 390198525 390197992 0.000000e+00 765
15 TraesCS7B01G248900 chr1B 92.322 534 40 1 1871 2404 150172724 150172192 0.000000e+00 758
16 TraesCS7B01G248900 chr1B 91.745 533 44 0 1871 2403 266771766 266772298 0.000000e+00 741
17 TraesCS7B01G248900 chrUn 94.595 1665 79 4 158 1820 49945085 49946740 0.000000e+00 2566
18 TraesCS7B01G248900 chr6B 94.195 534 31 0 1871 2404 456294774 456295307 0.000000e+00 815
19 TraesCS7B01G248900 chr6B 91.760 534 44 0 1871 2404 245144270 245143737 0.000000e+00 743
20 TraesCS7B01G248900 chr6D 91.250 160 13 1 1 159 407182475 407182316 1.450000e-52 217
21 TraesCS7B01G248900 chr3D 86.076 158 15 2 3 159 601861940 601861789 1.910000e-36 163
22 TraesCS7B01G248900 chr4A 93.478 92 5 1 69 159 181642641 181642550 4.170000e-28 135


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 TraesCS7B01G248900 chr7B 459586010 459588413 2403 True 4440 4440 100.000 1 2404 1 chr7B.!!$R1 2403
1 TraesCS7B01G248900 chr7B 207168488 207169021 533 False 754 754 92.135 1871 2404 1 chr7B.!!$F1 533
2 TraesCS7B01G248900 chr6A 74542050 74543868 1818 False 3033 3033 96.758 1 1820 1 chr6A.!!$F1 1819
3 TraesCS7B01G248900 chr6A 602833708 602834992 1284 False 2028 2028 95.175 550 1833 1 chr6A.!!$F2 1283
4 TraesCS7B01G248900 chr4D 451881800 451883451 1651 True 2680 2680 95.901 162 1820 1 chr4D.!!$R1 1658
5 TraesCS7B01G248900 chr2B 638286678 638288343 1665 False 2676 2676 95.678 159 1822 1 chr2B.!!$F2 1663
6 TraesCS7B01G248900 chr2B 39117544 39118228 684 False 1074 1074 94.913 158 845 1 chr2B.!!$F1 687
7 TraesCS7B01G248900 chr2B 232502780 232503313 533 True 754 754 92.135 1871 2404 1 chr2B.!!$R1 533
8 TraesCS7B01G248900 chr5B 547904887 547906548 1661 False 2636 2636 95.310 160 1820 1 chr5B.!!$F1 1660
9 TraesCS7B01G248900 chr3B 629799281 629800944 1663 False 2617 2617 95.072 159 1820 1 chr3B.!!$F2 1661
10 TraesCS7B01G248900 chr3B 99433534 99434067 533 True 749 749 91.948 1871 2404 1 chr3B.!!$R1 533
11 TraesCS7B01G248900 chr3B 187252302 187252835 533 False 749 749 91.948 1871 2404 1 chr3B.!!$F1 533
12 TraesCS7B01G248900 chr2D 344567689 344569347 1658 False 2608 2608 95.024 159 1821 1 chr2D.!!$F1 1662
13 TraesCS7B01G248900 chr1B 109347225 109348891 1666 True 2595 2595 94.781 159 1823 1 chr1B.!!$R1 1664
14 TraesCS7B01G248900 chr1B 390197992 390198525 533 True 765 765 92.509 1871 2404 1 chr1B.!!$R3 533
15 TraesCS7B01G248900 chr1B 150172192 150172724 532 True 758 758 92.322 1871 2404 1 chr1B.!!$R2 533
16 TraesCS7B01G248900 chr1B 266771766 266772298 532 False 741 741 91.745 1871 2403 1 chr1B.!!$F1 532
17 TraesCS7B01G248900 chrUn 49945085 49946740 1655 False 2566 2566 94.595 158 1820 1 chrUn.!!$F1 1662
18 TraesCS7B01G248900 chr6B 456294774 456295307 533 False 815 815 94.195 1871 2404 1 chr6B.!!$F1 533
19 TraesCS7B01G248900 chr6B 245143737 245144270 533 True 743 743 91.760 1871 2404 1 chr6B.!!$R1 533

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
294 295 1.004628 ACACAGCCAATGATACCAGCA 59.995 47.619 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2284 0.322456 TGGCAAGTATGAGGCGCTTT 60.322 50.0 7.64 0.0 0.0 3.51 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
252 253 7.914427 TCTATTACTTCTTTCCAGATGGCTA 57.086 36.000 0.00 0.00 34.44 3.93
294 295 1.004628 ACACAGCCAATGATACCAGCA 59.995 47.619 0.00 0.00 0.00 4.41
473 478 6.642733 TCTTTCAGGGTCCAATAGATCTTT 57.357 37.500 0.00 0.00 0.00 2.52
543 548 2.612972 GCACTGCTTACTACTTCCAGCA 60.613 50.000 0.00 0.00 39.98 4.41
545 550 3.620374 CACTGCTTACTACTTCCAGCATG 59.380 47.826 0.00 0.00 41.37 4.06
681 686 5.103000 CCTTACCTATTCAACACAGACGAG 58.897 45.833 0.00 0.00 0.00 4.18
845 850 2.219458 CATTCCATCAGCTCTCGCAAT 58.781 47.619 0.00 0.00 39.10 3.56
898 903 1.630369 ACATAGGTGAGCCTTGCAAGA 59.370 47.619 28.05 4.58 44.18 3.02
911 916 4.938226 GCCTTGCAAGAACTACTTAGATGT 59.062 41.667 28.05 0.00 37.03 3.06
984 994 2.073117 TTCGTGCACTGCGAAAGATA 57.927 45.000 16.19 0.00 43.98 1.98
1026 1036 6.053005 GCCTAATAACTACTATGTGTGCCAA 58.947 40.000 0.00 0.00 0.00 4.52
1210 1220 2.436646 GGATGCTCACCACGGTGG 60.437 66.667 25.21 25.21 45.43 4.61
1528 1538 4.012374 ACAGTGCTGTGCATTTAGCTATT 58.988 39.130 17.61 4.90 45.94 1.73
1537 1547 7.452880 TGTGCATTTAGCTATTGATTATCCC 57.547 36.000 8.07 0.00 45.94 3.85
1679 1689 2.087646 GGTCCTTTCCTGCATGACTTC 58.912 52.381 0.00 0.00 0.00 3.01
1792 1802 1.917872 TGGCTTACATTCGGCCTTTT 58.082 45.000 0.00 0.00 45.45 2.27
1843 1853 9.725019 AGTGATGTTAACAATGAGTAGATTCAA 57.275 29.630 13.23 0.00 0.00 2.69
1844 1854 9.979270 GTGATGTTAACAATGAGTAGATTCAAG 57.021 33.333 13.23 0.00 0.00 3.02
1845 1855 8.668353 TGATGTTAACAATGAGTAGATTCAAGC 58.332 33.333 13.23 0.00 0.00 4.01
1846 1856 7.977789 TGTTAACAATGAGTAGATTCAAGCA 57.022 32.000 5.64 0.00 0.00 3.91
1847 1857 8.032952 TGTTAACAATGAGTAGATTCAAGCAG 57.967 34.615 5.64 0.00 0.00 4.24
1848 1858 7.661437 TGTTAACAATGAGTAGATTCAAGCAGT 59.339 33.333 5.64 0.00 0.00 4.40
1849 1859 6.492007 AACAATGAGTAGATTCAAGCAGTG 57.508 37.500 0.00 0.00 0.00 3.66
1850 1860 5.555017 ACAATGAGTAGATTCAAGCAGTGT 58.445 37.500 0.00 0.00 30.91 3.55
1851 1861 6.701340 ACAATGAGTAGATTCAAGCAGTGTA 58.299 36.000 0.00 0.00 33.56 2.90
1852 1862 7.334090 ACAATGAGTAGATTCAAGCAGTGTAT 58.666 34.615 0.00 0.00 33.56 2.29
1853 1863 8.478066 ACAATGAGTAGATTCAAGCAGTGTATA 58.522 33.333 0.00 0.00 33.56 1.47
1854 1864 9.486497 CAATGAGTAGATTCAAGCAGTGTATAT 57.514 33.333 0.00 0.00 0.00 0.86
1855 1865 9.703892 AATGAGTAGATTCAAGCAGTGTATATC 57.296 33.333 0.00 0.00 0.00 1.63
1856 1866 8.237811 TGAGTAGATTCAAGCAGTGTATATCA 57.762 34.615 0.00 0.00 0.00 2.15
1857 1867 8.138074 TGAGTAGATTCAAGCAGTGTATATCAC 58.862 37.037 0.00 0.00 46.46 3.06
1951 1961 1.493950 GGATGTCGCGCCTTGATCTG 61.494 60.000 0.00 0.00 0.00 2.90
1961 1971 2.040442 TTGATCTGGGCGGGGAGA 59.960 61.111 0.00 0.00 0.00 3.71
2025 2035 2.892425 GCATTCTGCGCGGCTACT 60.892 61.111 12.58 0.00 31.71 2.57
2061 2071 2.597455 TGGACTCGCTCCATCATCATA 58.403 47.619 0.00 0.00 44.99 2.15
2157 2167 1.078426 GTACACAGGGCGATTGGCT 60.078 57.895 6.45 0.00 42.94 4.75
2174 2184 2.027625 CTCCGAACAGGTTGGCGAC 61.028 63.158 0.00 0.00 41.99 5.19
2274 2284 0.037326 CACGCTGGTAGGCTTCTGAA 60.037 55.000 0.00 0.00 0.00 3.02
2286 2296 2.009774 GCTTCTGAAAAGCGCCTCATA 58.990 47.619 2.29 0.00 33.20 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.321625 TCATTAATCTCCCTAGGGGTAGGAT 59.678 44.000 28.19 20.56 44.74 3.24
82 83 3.340337 AGTTTCTCACGCAAAGAAAGC 57.660 42.857 7.48 4.49 41.94 3.51
181 182 6.984474 ACCGTGGTATTAGTTGTGATGATTAG 59.016 38.462 0.00 0.00 0.00 1.73
252 253 5.542635 TGTCTACCTCCTCATGTTTAACAGT 59.457 40.000 3.63 0.00 0.00 3.55
294 295 1.078656 ACCATGGGTAATTTGGCCACT 59.921 47.619 18.09 0.00 32.11 4.00
444 449 6.238648 TCTATTGGACCCTGAAAGAAGTTTC 58.761 40.000 0.00 0.00 42.27 2.78
569 574 5.106157 GCTTGTGTGTATTAGTGAAAGGCAT 60.106 40.000 0.00 0.00 0.00 4.40
681 686 0.391130 TGTGCTTCCGACATAGTGGC 60.391 55.000 0.00 0.00 0.00 5.01
898 903 6.098017 GGCGACTAAACACATCTAAGTAGTT 58.902 40.000 0.00 0.00 0.00 2.24
911 916 0.931702 CACAACGTGGCGACTAAACA 59.068 50.000 0.00 0.00 0.00 2.83
984 994 1.252904 GCATGGTGGTGCTGTGGATT 61.253 55.000 0.00 0.00 41.82 3.01
1026 1036 5.417811 TGTGTTGCAAATGTTTCTGTCATT 58.582 33.333 0.00 0.00 37.14 2.57
1200 1210 2.825982 TGGAAGTCCACCGTGGTG 59.174 61.111 17.32 12.17 42.01 4.17
1210 1220 3.748568 GTCTCCAGTTGTGATTGGAAGTC 59.251 47.826 0.00 0.00 40.68 3.01
1528 1538 5.716979 AGCAGTCTAAGTAGGGGATAATCA 58.283 41.667 0.00 0.00 0.00 2.57
1537 1547 3.815962 TGCGATAGAGCAGTCTAAGTAGG 59.184 47.826 0.00 0.00 42.92 3.18
1679 1689 9.261180 AGTACATAAGATTGGAAATGATACACG 57.739 33.333 0.00 0.00 0.00 4.49
1823 1833 7.959651 CACTGCTTGAATCTACTCATTGTTAAC 59.040 37.037 0.00 0.00 0.00 2.01
1830 1840 8.864087 TGATATACACTGCTTGAATCTACTCAT 58.136 33.333 0.00 0.00 0.00 2.90
1831 1841 8.138074 GTGATATACACTGCTTGAATCTACTCA 58.862 37.037 0.00 0.00 45.13 3.41
1832 1842 8.514136 GTGATATACACTGCTTGAATCTACTC 57.486 38.462 0.00 0.00 45.13 2.59
1848 1858 6.019075 GTCGCAAAACTGCTATGTGATATACA 60.019 38.462 0.00 0.00 44.87 2.29
1849 1859 6.201044 AGTCGCAAAACTGCTATGTGATATAC 59.799 38.462 0.00 0.00 36.16 1.47
1850 1860 6.200854 CAGTCGCAAAACTGCTATGTGATATA 59.799 38.462 0.00 0.00 40.18 0.86
1851 1861 5.007039 CAGTCGCAAAACTGCTATGTGATAT 59.993 40.000 0.00 0.00 40.18 1.63
1852 1862 4.329801 CAGTCGCAAAACTGCTATGTGATA 59.670 41.667 0.00 0.00 40.18 2.15
1853 1863 3.125829 CAGTCGCAAAACTGCTATGTGAT 59.874 43.478 0.00 0.00 40.18 3.06
1854 1864 2.480037 CAGTCGCAAAACTGCTATGTGA 59.520 45.455 0.00 0.00 40.18 3.58
1855 1865 2.843077 CAGTCGCAAAACTGCTATGTG 58.157 47.619 0.00 0.00 40.18 3.21
1862 1872 6.524147 CTGTCAGTCACAGTCGCAAAACTG 62.524 50.000 8.82 8.82 46.81 3.16
1863 1873 1.933853 GTCAGTCACAGTCGCAAAACT 59.066 47.619 0.00 0.00 0.00 2.66
1864 1874 1.663643 TGTCAGTCACAGTCGCAAAAC 59.336 47.619 0.00 0.00 0.00 2.43
1865 1875 1.933181 CTGTCAGTCACAGTCGCAAAA 59.067 47.619 0.00 0.00 46.81 2.44
1866 1876 1.570813 CTGTCAGTCACAGTCGCAAA 58.429 50.000 0.00 0.00 46.81 3.68
1867 1877 3.272766 CTGTCAGTCACAGTCGCAA 57.727 52.632 0.00 0.00 46.81 4.85
1886 1896 3.139077 GGAAGAAAAGACAAAGAGCCGA 58.861 45.455 0.00 0.00 0.00 5.54
1935 1945 2.125552 CCAGATCAAGGCGCGACA 60.126 61.111 17.71 0.00 0.00 4.35
1951 1961 4.452733 CGACTTGTCTCCCCGCCC 62.453 72.222 0.00 0.00 0.00 6.13
1961 1971 2.338984 GGCCAGACGACGACTTGT 59.661 61.111 0.00 0.00 0.00 3.16
2025 2035 4.426112 CAGCAGCTCCTCGACGCA 62.426 66.667 0.00 0.00 0.00 5.24
2145 2155 3.399181 TTCGGAGCCAATCGCCCT 61.399 61.111 0.00 0.00 38.78 5.19
2157 2167 2.029964 GTCGCCAACCTGTTCGGA 59.970 61.111 3.63 0.00 36.31 4.55
2240 2250 1.589993 CGTGAGATGGATCGCGCTT 60.590 57.895 5.56 0.00 45.03 4.68
2274 2284 0.322456 TGGCAAGTATGAGGCGCTTT 60.322 50.000 7.64 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.