Multiple sequence alignment - TraesCS2B01G232600

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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 TraesCS2B01G232600 chr2B 100.000 2552 0 0 1 2552 230282585 230285136 0.000000e+00 4713.0
1 TraesCS2B01G232600 chr2D 92.083 2501 88 43 5 2433 167706789 167704327 0.000000e+00 3421.0
2 TraesCS2B01G232600 chr2D 90.164 122 6 1 2431 2552 167703022 167702907 1.220000e-33 154.0
3 TraesCS2B01G232600 chr2A 88.424 2125 84 64 5 2047 182889132 182891176 0.000000e+00 2412.0
4 TraesCS2B01G232600 chr2A 90.613 522 32 7 2044 2552 182891449 182891966 0.000000e+00 676.0
5 TraesCS2B01G232600 chr7A 96.875 32 1 0 1448 1479 538298262 538298231 1.000000e-03 54.7


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 TraesCS2B01G232600 chr2B 230282585 230285136 2551 False 4713.0 4713 100.0000 1 2552 1 chr2B.!!$F1 2551
1 TraesCS2B01G232600 chr2D 167702907 167706789 3882 True 1787.5 3421 91.1235 5 2552 2 chr2D.!!$R1 2547
2 TraesCS2B01G232600 chr2A 182889132 182891966 2834 False 1544.0 2412 89.5185 5 2552 2 chr2A.!!$F1 2547

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
902 956 0.445043 GAATAAAACCGGAAGCGCGT 59.555 50.0 9.46 0.0 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2436 0.540454 TCTCCAGATCCAAGCAGCAG 59.46 55.0 0.0 0.0 0.0 4.24 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
44 49 1.815421 CCATGGCCTGTAGACGTGC 60.815 63.158 3.32 0.00 0.00 5.34
151 156 4.741781 CCGCGGCGCAAACAAGAG 62.742 66.667 32.61 12.47 0.00 2.85
152 157 3.711842 CGCGGCGCAAACAAGAGA 61.712 61.111 32.61 0.00 0.00 3.10
196 203 2.057137 TAACATGCAGGGAAGATGCC 57.943 50.000 2.31 0.00 43.18 4.40
202 209 2.906458 AGGGAAGATGCCTGCGAG 59.094 61.111 0.00 0.00 36.59 5.03
203 210 2.203126 GGGAAGATGCCTGCGAGG 60.203 66.667 0.00 0.00 38.80 4.63
389 403 2.126189 CCCGTTTCGTCTCGTCCC 60.126 66.667 0.00 0.00 0.00 4.46
627 650 1.741770 CGGACGCTCCTTTTCCTGG 60.742 63.158 0.00 0.00 33.30 4.45
641 680 0.757935 TCCTGGCCGTGGTAGATACC 60.758 60.000 13.43 1.86 46.62 2.73
719 758 2.166664 ACATTAGTCGCTGAAGAGGGTC 59.833 50.000 0.00 0.00 33.81 4.46
901 955 0.725117 AGAATAAAACCGGAAGCGCG 59.275 50.000 9.46 0.00 0.00 6.86
902 956 0.445043 GAATAAAACCGGAAGCGCGT 59.555 50.000 9.46 0.00 0.00 6.01
903 957 0.445043 AATAAAACCGGAAGCGCGTC 59.555 50.000 15.40 15.40 0.00 5.19
904 958 1.363885 ATAAAACCGGAAGCGCGTCC 61.364 55.000 29.68 29.68 0.00 4.79
905 959 2.438951 TAAAACCGGAAGCGCGTCCT 62.439 55.000 34.17 20.72 35.31 3.85
942 996 5.493133 TGCTTGTCGCTTTAAAAAGAGAA 57.507 34.783 9.95 2.56 44.42 2.87
981 1040 1.269723 GTGGCTTGGCTTTAACCACTC 59.730 52.381 3.28 0.00 45.86 3.51
1000 1062 0.326927 CCACTCCTCCCGCCTTAAAA 59.673 55.000 0.00 0.00 0.00 1.52
1232 1294 3.024356 TCCTCCTCCTCCTCCGCT 61.024 66.667 0.00 0.00 0.00 5.52
1314 1391 4.379243 AGCGTGTTCCTGGAGCCG 62.379 66.667 8.14 11.61 0.00 5.52
1558 1638 0.394352 GAGGTGCCGGTGATGGATTT 60.394 55.000 1.90 0.00 0.00 2.17
1559 1639 0.916086 AGGTGCCGGTGATGGATTTA 59.084 50.000 1.90 0.00 0.00 1.40
1584 1664 0.607217 ACATTCCGACCGGTTTTCCC 60.607 55.000 9.42 0.00 36.42 3.97
1585 1665 1.001764 ATTCCGACCGGTTTTCCCC 60.002 57.895 9.42 0.00 36.42 4.81
1586 1666 2.488771 ATTCCGACCGGTTTTCCCCC 62.489 60.000 9.42 0.00 36.42 5.40
1587 1667 3.643554 CCGACCGGTTTTCCCCCT 61.644 66.667 9.42 0.00 36.42 4.79
1588 1668 2.433004 CGACCGGTTTTCCCCCTT 59.567 61.111 9.42 0.00 36.42 3.95
1589 1669 1.228337 CGACCGGTTTTCCCCCTTT 60.228 57.895 9.42 0.00 36.42 3.11
1590 1670 1.520600 CGACCGGTTTTCCCCCTTTG 61.521 60.000 9.42 0.00 36.42 2.77
1591 1671 1.812686 GACCGGTTTTCCCCCTTTGC 61.813 60.000 9.42 0.00 36.42 3.68
1708 1796 2.615447 CTGCAATGTACATAGGCTGGTG 59.385 50.000 24.44 13.26 0.00 4.17
1718 1806 0.114364 TAGGCTGGTGACTGGTGAGA 59.886 55.000 0.00 0.00 31.35 3.27
1719 1807 1.004440 GGCTGGTGACTGGTGAGAC 60.004 63.158 0.00 0.00 0.00 3.36
1723 1811 1.179174 TGGTGACTGGTGAGACGAGG 61.179 60.000 0.00 0.00 0.00 4.63
1823 1918 8.856103 ACTACTAGTTTTTGTGCCATGTTAATT 58.144 29.630 0.00 0.00 0.00 1.40
1903 2003 8.973378 CAAGCATCTTAGCTAGTGTTTACTATC 58.027 37.037 0.00 0.00 45.89 2.08
1942 2042 3.113322 GTCCGCTTTTTGTTCTTGTTCC 58.887 45.455 0.00 0.00 0.00 3.62
1945 2045 3.035942 CGCTTTTTGTTCTTGTTCCGAG 58.964 45.455 0.00 0.00 0.00 4.63
1949 2049 4.893424 TTTTGTTCTTGTTCCGAGAAGG 57.107 40.909 0.00 0.00 34.90 3.46
2005 2106 7.617528 GCGTTTTACTATATTCGAGTGCAGATC 60.618 40.741 0.00 0.00 0.00 2.75
2048 2429 4.920340 CGATAGCTTGGTGATACACTGATC 59.080 45.833 0.00 0.00 34.40 2.92
2049 2430 5.278709 CGATAGCTTGGTGATACACTGATCT 60.279 44.000 0.00 0.00 34.40 2.75
2050 2431 6.072452 CGATAGCTTGGTGATACACTGATCTA 60.072 42.308 0.00 0.00 34.40 1.98
2051 2432 5.269505 AGCTTGGTGATACACTGATCTAC 57.730 43.478 0.00 0.00 34.40 2.59
2052 2433 4.959210 AGCTTGGTGATACACTGATCTACT 59.041 41.667 0.00 0.00 34.40 2.57
2053 2434 6.129874 AGCTTGGTGATACACTGATCTACTA 58.870 40.000 0.00 0.00 34.40 1.82
2054 2435 6.264292 AGCTTGGTGATACACTGATCTACTAG 59.736 42.308 0.00 0.00 34.40 2.57
2055 2436 6.392625 TTGGTGATACACTGATCTACTAGC 57.607 41.667 0.00 0.00 34.40 3.42
2056 2437 5.696030 TGGTGATACACTGATCTACTAGCT 58.304 41.667 0.00 0.00 34.40 3.32
2117 2503 1.270412 TGTGTAAAGATCGTGCCGGTT 60.270 47.619 1.90 0.00 0.00 4.44
2130 2516 1.454111 CCGGTTGTTGGTGGTTGGA 60.454 57.895 0.00 0.00 0.00 3.53
2149 2535 3.617284 GGAATGGATCCGTTAAGTTGGT 58.383 45.455 19.38 0.00 38.79 3.67
2197 2583 2.164624 ACGAGAACATACTCCTGCTGTC 59.835 50.000 0.00 0.00 33.83 3.51
2198 2584 2.425312 CGAGAACATACTCCTGCTGTCT 59.575 50.000 0.00 0.00 33.83 3.41
2199 2585 3.733380 CGAGAACATACTCCTGCTGTCTG 60.733 52.174 0.00 0.00 33.83 3.51
2200 2586 3.169099 AGAACATACTCCTGCTGTCTGT 58.831 45.455 0.00 0.00 0.00 3.41
2201 2587 3.056250 AGAACATACTCCTGCTGTCTGTG 60.056 47.826 0.00 0.00 0.00 3.66
2203 2589 0.539051 ATACTCCTGCTGTCTGTGCC 59.461 55.000 0.00 0.00 0.00 5.01
2204 2590 0.831711 TACTCCTGCTGTCTGTGCCA 60.832 55.000 0.00 0.00 0.00 4.92
2205 2591 1.298993 CTCCTGCTGTCTGTGCCAT 59.701 57.895 0.00 0.00 0.00 4.40
2206 2592 1.002990 TCCTGCTGTCTGTGCCATG 60.003 57.895 0.00 0.00 0.00 3.66
2250 2636 0.897401 AGGCTGCTTTGCTTCCCTTC 60.897 55.000 0.00 0.00 0.00 3.46
2252 2638 0.675633 GCTGCTTTGCTTCCCTTCAA 59.324 50.000 0.00 0.00 0.00 2.69
2367 2761 6.934645 CAGTTGAGTTGGTACTTTTCTATGGA 59.065 38.462 0.00 0.00 33.84 3.41
2372 2766 7.770433 TGAGTTGGTACTTTTCTATGGATGATG 59.230 37.037 0.00 0.00 33.84 3.07
2374 2768 5.376625 TGGTACTTTTCTATGGATGATGGC 58.623 41.667 0.00 0.00 0.00 4.40
2468 4169 1.336148 CGGCAGCAAAAGATCAAGCAA 60.336 47.619 0.00 0.00 0.00 3.91
2544 4245 3.872603 CGATGGGGATTCCGGCCA 61.873 66.667 2.24 0.00 38.76 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.339055 ACTCGCTGTACCTGTACGGTA 60.339 52.381 15.64 11.12 46.73 4.02
5 6 0.098376 GACTCGCTGTACCTGTACGG 59.902 60.000 11.16 11.16 43.50 4.02
7 8 0.455005 GGGACTCGCTGTACCTGTAC 59.545 60.000 0.45 0.45 46.37 2.90
8 9 2.877975 GGGACTCGCTGTACCTGTA 58.122 57.895 2.86 0.00 46.37 2.74
9 10 3.696084 GGGACTCGCTGTACCTGT 58.304 61.111 2.86 0.00 46.37 4.00
222 229 0.890542 CCCGTATCCCGTATCCGTCA 60.891 60.000 0.00 0.00 33.66 4.35
228 235 1.639628 AGATCCTCCCGTATCCCGTAT 59.360 52.381 0.00 0.00 33.66 3.06
230 237 0.539901 CAGATCCTCCCGTATCCCGT 60.540 60.000 0.00 0.00 33.66 5.28
231 238 1.251527 CCAGATCCTCCCGTATCCCG 61.252 65.000 0.00 0.00 0.00 5.14
232 239 1.545706 GCCAGATCCTCCCGTATCCC 61.546 65.000 0.00 0.00 0.00 3.85
341 354 0.871722 CGACGGGCAGAGAGAGATAG 59.128 60.000 0.00 0.00 0.00 2.08
342 355 0.535328 CCGACGGGCAGAGAGAGATA 60.535 60.000 5.81 0.00 0.00 1.98
343 356 1.826054 CCGACGGGCAGAGAGAGAT 60.826 63.158 5.81 0.00 0.00 2.75
344 357 2.438614 CCGACGGGCAGAGAGAGA 60.439 66.667 5.81 0.00 0.00 3.10
389 403 0.666374 AACGGGAAGAAAAGGCAACG 59.334 50.000 0.00 0.00 46.39 4.10
641 680 2.290071 ACAGTACTGGGGAAATTGACCG 60.290 50.000 26.12 0.00 34.19 4.79
763 809 0.249573 GTTCGTCCGTTGTCCTCCAA 60.250 55.000 0.00 0.00 0.00 3.53
764 810 1.364901 GTTCGTCCGTTGTCCTCCA 59.635 57.895 0.00 0.00 0.00 3.86
803 851 6.543100 AGGACGGTAGAATGTTGTGTTAAAAA 59.457 34.615 0.00 0.00 0.00 1.94
851 904 3.253230 CAGCGAAATCAAAACCCCAATC 58.747 45.455 0.00 0.00 0.00 2.67
852 905 2.028203 CCAGCGAAATCAAAACCCCAAT 60.028 45.455 0.00 0.00 0.00 3.16
853 906 1.342819 CCAGCGAAATCAAAACCCCAA 59.657 47.619 0.00 0.00 0.00 4.12
855 908 0.389817 GCCAGCGAAATCAAAACCCC 60.390 55.000 0.00 0.00 0.00 4.95
901 955 0.386985 AAACGAGACGAGCGAAGGAC 60.387 55.000 0.00 0.00 0.00 3.85
902 956 0.386858 CAAACGAGACGAGCGAAGGA 60.387 55.000 0.00 0.00 0.00 3.36
903 957 1.945776 GCAAACGAGACGAGCGAAGG 61.946 60.000 0.00 0.00 0.00 3.46
904 958 1.004277 AGCAAACGAGACGAGCGAAG 61.004 55.000 0.00 0.00 0.00 3.79
905 959 0.596600 AAGCAAACGAGACGAGCGAA 60.597 50.000 0.00 0.00 0.00 4.70
981 1040 0.326927 TTTTAAGGCGGGAGGAGTGG 59.673 55.000 0.00 0.00 0.00 4.00
1000 1062 4.143266 AGGGGATGGGGAGGCCAT 62.143 66.667 5.01 0.00 0.00 4.40
1446 1523 3.015293 GCCGTCGTCGTAGTCGTCA 62.015 63.158 0.71 0.00 40.43 4.35
1479 1559 2.932855 TCTCGATCATCCCGTACTCT 57.067 50.000 0.00 0.00 0.00 3.24
1542 1622 1.021968 GGTAAATCCATCACCGGCAC 58.978 55.000 0.00 0.00 35.97 5.01
1558 1638 2.417257 CGGTCGGAATGTCGGGGTA 61.417 63.158 0.00 0.00 0.00 3.69
1559 1639 3.766691 CGGTCGGAATGTCGGGGT 61.767 66.667 0.00 0.00 0.00 4.95
1584 1664 0.954452 AACGCAAGAGAAGCAAAGGG 59.046 50.000 0.00 0.00 43.62 3.95
1585 1665 1.335324 CCAACGCAAGAGAAGCAAAGG 60.335 52.381 0.00 0.00 43.62 3.11
1586 1666 1.927710 GCCAACGCAAGAGAAGCAAAG 60.928 52.381 0.00 0.00 43.62 2.77
1587 1667 0.030638 GCCAACGCAAGAGAAGCAAA 59.969 50.000 0.00 0.00 43.62 3.68
1588 1668 0.819259 AGCCAACGCAAGAGAAGCAA 60.819 50.000 0.00 0.00 43.62 3.91
1589 1669 0.819259 AAGCCAACGCAAGAGAAGCA 60.819 50.000 0.00 0.00 43.62 3.91
1590 1670 0.312102 AAAGCCAACGCAAGAGAAGC 59.688 50.000 0.00 0.00 43.62 3.86
1591 1671 1.603802 TCAAAGCCAACGCAAGAGAAG 59.396 47.619 0.00 0.00 43.62 2.85
1637 1717 1.736645 ACTCGAATTCACACGCCGG 60.737 57.895 6.22 0.00 0.00 6.13
1708 1796 1.535833 TCTTCCTCGTCTCACCAGTC 58.464 55.000 0.00 0.00 0.00 3.51
1718 1806 2.290464 CTCACTCGGTATCTTCCTCGT 58.710 52.381 0.00 0.00 0.00 4.18
1719 1807 1.604755 CCTCACTCGGTATCTTCCTCG 59.395 57.143 0.00 0.00 0.00 4.63
1723 1811 2.223852 GCCTTCCTCACTCGGTATCTTC 60.224 54.545 0.00 0.00 0.00 2.87
1823 1918 5.071788 AGTTGATTCCTTGAGGTGACAAGTA 59.928 40.000 0.00 0.00 43.72 2.24
1903 2003 4.910456 GCGGACGATCTTGTAGTACTAATG 59.090 45.833 3.61 0.00 0.00 1.90
1909 2009 4.445452 AAAAGCGGACGATCTTGTAGTA 57.555 40.909 0.00 0.00 0.00 1.82
2005 2106 2.159841 CGTAACATGGAACTCAAGCACG 60.160 50.000 0.00 0.00 0.00 5.34
2017 2118 3.792401 TCACCAAGCTATCGTAACATGG 58.208 45.455 0.00 0.00 0.00 3.66
2054 2435 1.077930 TCCAGATCCAAGCAGCAGC 60.078 57.895 0.00 0.00 42.56 5.25
2055 2436 0.540454 TCTCCAGATCCAAGCAGCAG 59.460 55.000 0.00 0.00 0.00 4.24
2056 2437 0.986527 TTCTCCAGATCCAAGCAGCA 59.013 50.000 0.00 0.00 0.00 4.41
2117 2503 2.524306 GATCCATTCCAACCACCAACA 58.476 47.619 0.00 0.00 0.00 3.33
2130 2516 4.457949 GTGAACCAACTTAACGGATCCATT 59.542 41.667 13.41 5.19 0.00 3.16
2149 2535 4.679662 GGAGATCGACCTAATTTCGTGAA 58.320 43.478 0.00 0.00 37.73 3.18
2205 2591 9.225436 TGTCAGTATTAATTGAACATGCTTACA 57.775 29.630 0.00 0.00 0.00 2.41
2206 2592 9.708222 CTGTCAGTATTAATTGAACATGCTTAC 57.292 33.333 0.00 0.00 0.00 2.34
2367 2761 1.683943 CTCCGATTTGGTGCCATCAT 58.316 50.000 0.00 0.00 39.52 2.45
2374 2768 2.114670 ATGCGGCTCCGATTTGGTG 61.115 57.895 13.11 0.00 42.83 4.17
2486 4187 3.782244 GCTCTTGTGCGGCGTGAG 61.782 66.667 9.37 9.78 0.00 3.51
2533 4234 3.138128 CGGGTTTGGCCGGAATCC 61.138 66.667 5.05 10.26 39.69 3.01


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

AutoCloner maintained by Alex Coulton.