Multiple sequence alignment - TraesCS7B01G294600

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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 TraesCS7B01G294600 chr7B 100.000 2201 0 0 1 2201 531613062 531610862 0.000000e+00 4065.0
1 TraesCS7B01G294600 chr7B 95.000 40 2 0 1790 1829 699845452 699845413 1.820000e-06 63.9
2 TraesCS7B01G294600 chr7A 93.168 1698 55 18 1 1667 569405014 569403347 0.000000e+00 2436.0
3 TraesCS7B01G294600 chr7A 87.222 360 31 3 1842 2201 569403014 569402670 1.580000e-106 396.0
4 TraesCS7B01G294600 chr7A 89.375 160 13 2 1670 1828 569403219 569403063 4.790000e-47 198.0
5 TraesCS7B01G294600 chr7D 92.405 1343 33 30 1 1306 501901267 501899957 0.000000e+00 1851.0
6 TraesCS7B01G294600 chr7D 92.124 419 16 11 916 1333 501842051 501842453 1.900000e-160 575.0
7 TraesCS7B01G294600 chr7D 90.608 362 29 3 1842 2201 501899530 501899172 1.980000e-130 475.0
8 TraesCS7B01G294600 chr7D 85.808 458 17 19 1340 1793 501899957 501899544 2.010000e-120 442.0
9 TraesCS7B01G294600 chr5B 95.238 42 2 0 1787 1828 372109465 372109506 1.410000e-07 67.6
10 TraesCS7B01G294600 chr1D 88.136 59 3 4 1773 1828 349792839 349792782 1.410000e-07 67.6
11 TraesCS7B01G294600 chr3A 93.182 44 3 0 1785 1828 416192343 416192300 5.070000e-07 65.8
12 TraesCS7B01G294600 chr5D 95.000 40 2 0 1789 1828 475308086 475308125 1.820000e-06 63.9
13 TraesCS7B01G294600 chrUn 94.872 39 2 0 1790 1828 93831751 93831713 6.560000e-06 62.1
14 TraesCS7B01G294600 chr6D 94.872 39 2 0 1790 1828 89352172 89352210 6.560000e-06 62.1
15 TraesCS7B01G294600 chr2B 92.683 41 3 0 1787 1827 706831378 706831418 2.360000e-05 60.2


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 TraesCS7B01G294600 chr7B 531610862 531613062 2200 True 4065.000000 4065 100.000000 1 2201 1 chr7B.!!$R1 2200
1 TraesCS7B01G294600 chr7A 569402670 569405014 2344 True 1010.000000 2436 89.921667 1 2201 3 chr7A.!!$R1 2200
2 TraesCS7B01G294600 chr7D 501899172 501901267 2095 True 922.666667 1851 89.607000 1 2201 3 chr7D.!!$R1 2200

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
554 573 1.369091 CTTCAAATCCAGCGACCCGG 61.369 60.0 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
1830 2013 1.306148 TACATGTAGCTCCCTCGACG 58.694 55.0 0.08 0.0 0.0 5.12 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
26 27 9.520515 AGTCAACAGAATAAGACAATAACCAAT 57.479 29.630 0.00 0.00 33.56 3.16
81 82 1.534729 GACCCGCAAAGAAAGGTCAT 58.465 50.000 3.21 0.00 46.61 3.06
279 296 1.475930 GGAGCTAGGCCAAATCCTGAC 60.476 57.143 5.01 0.00 37.01 3.51
432 449 8.469200 TGAATTACATCATCATCCCAGAAAAAC 58.531 33.333 0.00 0.00 0.00 2.43
433 450 7.959658 ATTACATCATCATCCCAGAAAAACA 57.040 32.000 0.00 0.00 0.00 2.83
434 451 7.959658 TTACATCATCATCCCAGAAAAACAT 57.040 32.000 0.00 0.00 0.00 2.71
436 453 7.248743 ACATCATCATCCCAGAAAAACATTT 57.751 32.000 0.00 0.00 0.00 2.32
516 535 2.682856 AGCATTTCGCCACAATTATCGT 59.317 40.909 0.00 0.00 44.04 3.73
554 573 1.369091 CTTCAAATCCAGCGACCCGG 61.369 60.000 0.00 0.00 0.00 5.73
697 720 2.955660 AGAATCGATCCTCCTCAGTGTC 59.044 50.000 0.00 0.00 0.00 3.67
853 879 3.841255 GGACTCTCCCTCCCCTATAAATG 59.159 52.174 0.00 0.00 0.00 2.32
1306 1360 2.223572 GCTTGGTTAATCGGCCATTGAG 60.224 50.000 2.24 0.00 34.37 3.02
1316 1370 2.238646 TCGGCCATTGAGTTGTTATCCT 59.761 45.455 2.24 0.00 0.00 3.24
1329 1383 3.866651 TGTTATCCTGCTGCTCTCTTTC 58.133 45.455 0.00 0.00 0.00 2.62
1430 1484 4.518211 CCATAAATAAGAGCAAGGCTGGAG 59.482 45.833 0.00 0.00 39.88 3.86
1431 1485 2.725221 AATAAGAGCAAGGCTGGAGG 57.275 50.000 0.00 0.00 39.88 4.30
1432 1486 0.842635 ATAAGAGCAAGGCTGGAGGG 59.157 55.000 0.00 0.00 39.88 4.30
1433 1487 0.252696 TAAGAGCAAGGCTGGAGGGA 60.253 55.000 0.00 0.00 39.88 4.20
1450 1504 2.370189 AGGGAGGCATGAGCTTATGTAC 59.630 50.000 18.68 12.42 41.70 2.90
1456 1510 3.621268 GGCATGAGCTTATGTACGTGAAA 59.379 43.478 18.68 0.00 41.70 2.69
1513 1567 2.893489 AGAAATTGGTCTTTCAGGTGCC 59.107 45.455 0.00 0.00 37.55 5.01
1537 1591 9.196552 GCCATATACTTAATTTTCTGATTTGCC 57.803 33.333 0.00 0.00 0.00 4.52
1594 1652 4.310769 AGTCGATCAAAGCATATGCCTAC 58.689 43.478 23.96 9.56 43.38 3.18
1595 1653 4.058124 GTCGATCAAAGCATATGCCTACA 58.942 43.478 23.96 6.77 43.38 2.74
1596 1654 4.151335 GTCGATCAAAGCATATGCCTACAG 59.849 45.833 23.96 10.05 43.38 2.74
1597 1655 4.060900 CGATCAAAGCATATGCCTACAGT 58.939 43.478 23.96 6.45 43.38 3.55
1598 1656 4.512944 CGATCAAAGCATATGCCTACAGTT 59.487 41.667 23.96 7.91 43.38 3.16
1599 1657 5.559608 CGATCAAAGCATATGCCTACAGTTG 60.560 44.000 23.96 16.70 43.38 3.16
1602 1660 2.292267 AGCATATGCCTACAGTTGCAC 58.708 47.619 23.96 0.00 40.88 4.57
1693 1876 9.845740 ATACATAAGATGTGCAACCACTTAATA 57.154 29.630 2.33 0.00 44.60 0.98
1694 1877 8.574251 ACATAAGATGTGCAACCACTTAATAA 57.426 30.769 0.00 0.00 43.01 1.40
1695 1878 9.189156 ACATAAGATGTGCAACCACTTAATAAT 57.811 29.630 0.00 0.00 43.01 1.28
1700 1883 5.694816 TGTGCAACCACTTAATAATTGACG 58.305 37.500 0.00 0.00 42.54 4.35
1779 1962 9.599322 CATTCAAGTAAAAACAGACACTCATAC 57.401 33.333 0.00 0.00 0.00 2.39
1780 1963 8.725405 TTCAAGTAAAAACAGACACTCATACA 57.275 30.769 0.00 0.00 0.00 2.29
1795 1978 7.786030 ACACTCATACATTGCTATGTACTCTT 58.214 34.615 20.77 4.96 46.91 2.85
1799 1982 6.923508 TCATACATTGCTATGTACTCTTTCCG 59.076 38.462 20.77 5.29 46.91 4.30
1809 1992 5.018539 TGTACTCTTTCCGTCCCATAATG 57.981 43.478 0.00 0.00 0.00 1.90
1820 2003 3.869246 CGTCCCATAATGTAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
1823 2006 6.027749 GTCCCATAATGTAAGAGCGTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
1824 2007 5.941058 TCCCATAATGTAAGAGCGTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
1825 2008 6.027749 CCCATAATGTAAGAGCGTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
1826 2009 6.348950 CCCATAATGTAAGAGCGTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
1827 2010 6.523201 CCATAATGTAAGAGCGTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
1830 2013 3.558418 TGTAAGAGCGTTTTTGACACCTC 59.442 43.478 0.00 0.00 0.00 3.85
1831 2014 1.217882 AGAGCGTTTTTGACACCTCG 58.782 50.000 0.00 0.00 33.71 4.63
1832 2015 0.935196 GAGCGTTTTTGACACCTCGT 59.065 50.000 0.00 0.00 0.00 4.18
1833 2016 0.935196 AGCGTTTTTGACACCTCGTC 59.065 50.000 0.00 0.00 45.61 4.20
1844 2027 3.423179 CCTCGTCGAGGGAGCTAC 58.577 66.667 30.23 0.00 45.43 3.58
1852 2071 3.501062 CGTCGAGGGAGCTACATGTATAA 59.499 47.826 5.91 0.00 0.00 0.98
1857 2076 6.774170 TCGAGGGAGCTACATGTATAAAGTTA 59.226 38.462 5.91 0.00 0.00 2.24
1859 2078 7.255520 CGAGGGAGCTACATGTATAAAGTTACT 60.256 40.741 5.91 0.00 0.00 2.24
1869 2088 9.817809 ACATGTATAAAGTTACTGTGATGGTAG 57.182 33.333 0.00 0.00 0.00 3.18
1905 2124 2.549349 GGTTAGTGGAGAAGCCGTGAAA 60.549 50.000 0.00 0.00 40.66 2.69
1930 2149 0.907486 TGAGCAGGAGCAAGCTACAT 59.093 50.000 7.10 0.00 45.49 2.29
1942 2161 3.064545 GCAAGCTACATGCCTAGTGAAAG 59.935 47.826 0.00 0.00 44.23 2.62
1951 2170 6.735130 ACATGCCTAGTGAAAGTTTTACAAC 58.265 36.000 12.51 0.00 0.00 3.32
1993 2212 7.564660 TGGATAAAAATCATGTGAATAAGCCCT 59.435 33.333 0.00 0.00 0.00 5.19
2004 2223 5.189180 GTGAATAAGCCCTGAAACTGAGAT 58.811 41.667 0.00 0.00 0.00 2.75
2023 2242 5.882557 TGAGATTAGCAACTTCCTGATTTCC 59.117 40.000 0.00 0.00 0.00 3.13
2049 2268 8.061268 CACTTTATTTGTTTGTGTTGTTATGGC 58.939 33.333 0.00 0.00 0.00 4.40
2052 2271 3.444703 TGTTTGTGTTGTTATGGCACC 57.555 42.857 0.00 0.00 32.62 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.050227 CACTTGGTTGTTGCATGGTTAATTG 60.050 40.000 0.00 0.00 0.00 2.32
24 25 5.055812 CACTTGGTTGTTGCATGGTTAATT 58.944 37.500 0.00 0.00 0.00 1.40
26 27 3.181471 CCACTTGGTTGTTGCATGGTTAA 60.181 43.478 0.00 0.00 0.00 2.01
27 28 2.363680 CCACTTGGTTGTTGCATGGTTA 59.636 45.455 0.00 0.00 0.00 2.85
28 29 1.138661 CCACTTGGTTGTTGCATGGTT 59.861 47.619 0.00 0.00 0.00 3.67
29 30 0.752054 CCACTTGGTTGTTGCATGGT 59.248 50.000 0.00 0.00 0.00 3.55
30 31 3.591979 CCACTTGGTTGTTGCATGG 57.408 52.632 0.00 0.00 0.00 3.66
81 82 3.870538 ATAAGATGCATTGGAGCTCCA 57.129 42.857 32.00 32.00 45.94 3.86
310 327 6.148811 CACTAATACGTTTGGTCATTTCAGGT 59.851 38.462 0.00 0.00 0.00 4.00
452 471 7.913821 CCATCGTTTTAAGGTAGAAAAATAGCC 59.086 37.037 0.00 0.00 0.00 3.93
554 573 3.241067 ACAATCAGCAAATGCATGGAC 57.759 42.857 0.00 0.00 45.16 4.02
675 698 3.370104 ACACTGAGGAGGATCGATTCTT 58.630 45.455 7.87 0.00 34.37 2.52
688 711 2.900546 AGGGTGAAACTAGACACTGAGG 59.099 50.000 0.00 0.00 37.22 3.86
697 720 0.034896 ACGGTGCAGGGTGAAACTAG 59.965 55.000 0.00 0.00 36.74 2.57
764 790 4.477975 CGACGGACGGCAGAGACC 62.478 72.222 0.00 0.00 38.46 3.85
793 819 4.980805 TCTGAACCGCACCGCACC 62.981 66.667 0.00 0.00 0.00 5.01
794 820 3.414700 CTCTGAACCGCACCGCAC 61.415 66.667 0.00 0.00 0.00 5.34
795 821 4.680237 CCTCTGAACCGCACCGCA 62.680 66.667 0.00 0.00 0.00 5.69
796 822 3.876589 TTCCTCTGAACCGCACCGC 62.877 63.158 0.00 0.00 0.00 5.68
808 834 0.041238 TGGACGGACAGGATTCCTCT 59.959 55.000 0.98 0.00 32.88 3.69
1137 1191 0.543410 TGAACTCCGTGGCCTTCCTA 60.543 55.000 3.32 0.00 0.00 2.94
1179 1233 0.394080 AGGTAGCCTCGACGTAGCTT 60.394 55.000 17.06 0.44 38.06 3.74
1306 1360 3.258971 AGAGAGCAGCAGGATAACAAC 57.741 47.619 0.00 0.00 0.00 3.32
1316 1370 4.085733 AGAACTAGAGAAAGAGAGCAGCA 58.914 43.478 0.00 0.00 0.00 4.41
1423 1477 3.092511 TCATGCCTCCCTCCAGCC 61.093 66.667 0.00 0.00 0.00 4.85
1430 1484 2.772287 GTACATAAGCTCATGCCTCCC 58.228 52.381 0.00 0.00 40.80 4.30
1431 1485 2.224066 ACGTACATAAGCTCATGCCTCC 60.224 50.000 0.00 0.00 40.80 4.30
1432 1486 2.797156 CACGTACATAAGCTCATGCCTC 59.203 50.000 0.00 0.00 40.80 4.70
1433 1487 2.430694 TCACGTACATAAGCTCATGCCT 59.569 45.455 0.00 0.00 40.80 4.75
1450 1504 7.875041 AGACCAATATCTCTCCATATTTTCACG 59.125 37.037 0.00 0.00 28.11 4.35
1456 1510 9.347240 CAACAAAGACCAATATCTCTCCATATT 57.653 33.333 0.00 0.00 30.33 1.28
1580 1634 3.129287 GTGCAACTGTAGGCATATGCTTT 59.871 43.478 26.12 17.07 42.75 3.51
1596 1654 8.869764 ATCAAACTCTGATGTGCAAGTGCAAC 62.870 42.308 7.71 3.47 44.97 4.17
1597 1655 6.951225 ATCAAACTCTGATGTGCAAGTGCAA 61.951 40.000 7.71 0.00 44.97 4.08
1598 1656 5.523085 ATCAAACTCTGATGTGCAAGTGCA 61.523 41.667 0.82 0.82 45.39 4.57
1599 1657 2.291465 TCAAACTCTGATGTGCAAGTGC 59.709 45.455 0.00 0.00 42.50 4.40
1611 1669 3.503748 GGGGAGTTGTTCATCAAACTCTG 59.496 47.826 13.50 0.00 38.76 3.35
1693 1876 7.936584 TGTTTTTCTTCATCTAACCGTCAATT 58.063 30.769 0.00 0.00 0.00 2.32
1694 1877 7.504924 TGTTTTTCTTCATCTAACCGTCAAT 57.495 32.000 0.00 0.00 0.00 2.57
1695 1878 6.928979 TGTTTTTCTTCATCTAACCGTCAA 57.071 33.333 0.00 0.00 0.00 3.18
1700 1883 8.194769 TGGAAGTTTGTTTTTCTTCATCTAACC 58.805 33.333 0.00 0.00 39.19 2.85
1711 1894 7.169813 GTCAATGATCCTGGAAGTTTGTTTTTC 59.830 37.037 0.00 0.00 0.00 2.29
1779 1962 4.508124 GGACGGAAAGAGTACATAGCAATG 59.492 45.833 0.00 0.00 39.17 2.82
1780 1963 4.443034 GGGACGGAAAGAGTACATAGCAAT 60.443 45.833 0.00 0.00 0.00 3.56
1795 1978 3.491964 CGCTCTTACATTATGGGACGGAA 60.492 47.826 0.00 0.00 0.00 4.30
1799 1982 5.813080 AAAACGCTCTTACATTATGGGAC 57.187 39.130 0.00 0.00 0.00 4.46
1809 1992 3.362693 CGAGGTGTCAAAAACGCTCTTAC 60.363 47.826 0.00 0.00 38.49 2.34
1830 2013 1.306148 TACATGTAGCTCCCTCGACG 58.694 55.000 0.08 0.00 0.00 5.12
1831 2014 5.009811 ACTTTATACATGTAGCTCCCTCGAC 59.990 44.000 11.91 0.00 0.00 4.20
1832 2015 5.138276 ACTTTATACATGTAGCTCCCTCGA 58.862 41.667 11.91 0.00 0.00 4.04
1833 2016 5.455056 ACTTTATACATGTAGCTCCCTCG 57.545 43.478 11.91 0.00 0.00 4.63
1835 2018 7.344871 ACAGTAACTTTATACATGTAGCTCCCT 59.655 37.037 11.91 0.00 0.00 4.20
1836 2019 7.438459 CACAGTAACTTTATACATGTAGCTCCC 59.562 40.741 11.91 0.00 0.00 4.30
1838 2021 9.751542 ATCACAGTAACTTTATACATGTAGCTC 57.248 33.333 11.91 0.00 0.00 4.09
1839 2022 9.534565 CATCACAGTAACTTTATACATGTAGCT 57.465 33.333 11.91 0.00 0.00 3.32
1840 2023 8.765219 CCATCACAGTAACTTTATACATGTAGC 58.235 37.037 11.91 0.00 0.00 3.58
1841 2024 9.817809 ACCATCACAGTAACTTTATACATGTAG 57.182 33.333 11.91 1.58 0.00 2.74
1843 2026 9.817809 CTACCATCACAGTAACTTTATACATGT 57.182 33.333 2.69 2.69 0.00 3.21
1844 2027 9.261180 CCTACCATCACAGTAACTTTATACATG 57.739 37.037 0.00 0.00 0.00 3.21
1852 2071 6.041069 GCTCTATCCTACCATCACAGTAACTT 59.959 42.308 0.00 0.00 0.00 2.66
1857 2076 3.235200 GGCTCTATCCTACCATCACAGT 58.765 50.000 0.00 0.00 0.00 3.55
1859 2078 3.328535 TGGCTCTATCCTACCATCACA 57.671 47.619 0.00 0.00 0.00 3.58
1869 2088 4.020128 CCACTAACCCTATTGGCTCTATCC 60.020 50.000 0.00 0.00 37.83 2.59
1893 2112 3.437049 GCTCAAGTATTTTCACGGCTTCT 59.563 43.478 0.00 0.00 0.00 2.85
1905 2124 2.026449 AGCTTGCTCCTGCTCAAGTATT 60.026 45.455 0.00 0.00 41.15 1.89
1930 2149 4.581409 GGGTTGTAAAACTTTCACTAGGCA 59.419 41.667 0.00 0.00 30.93 4.75
1942 2161 2.215196 TCTGAGTGCGGGTTGTAAAAC 58.785 47.619 0.00 0.00 0.00 2.43
1951 2170 2.620251 TCCAAATATCTGAGTGCGGG 57.380 50.000 0.00 0.00 0.00 6.13
1993 2212 5.702670 CAGGAAGTTGCTAATCTCAGTTTCA 59.297 40.000 0.00 0.00 0.00 2.69
2004 2223 4.985538 AGTGGAAATCAGGAAGTTGCTAA 58.014 39.130 0.00 0.00 0.00 3.09
2023 2242 8.061268 GCCATAACAACACAAACAAATAAAGTG 58.939 33.333 0.00 0.00 36.34 3.16
2129 2348 4.245845 TGTAGTGTCGCAGATTGTGTTA 57.754 40.909 0.00 0.00 40.67 2.41
2130 2349 3.106242 TGTAGTGTCGCAGATTGTGTT 57.894 42.857 0.00 0.00 40.67 3.32
2131 2350 2.812358 TGTAGTGTCGCAGATTGTGT 57.188 45.000 0.00 0.00 40.67 3.72
2132 2351 2.995939 ACATGTAGTGTCGCAGATTGTG 59.004 45.455 0.00 0.00 40.67 3.33
2133 2352 3.319137 ACATGTAGTGTCGCAGATTGT 57.681 42.857 0.00 0.00 40.67 2.71
2134 2353 4.672409 TCTACATGTAGTGTCGCAGATTG 58.328 43.478 27.83 3.54 42.29 2.67
2136 2355 5.300539 AGAATCTACATGTAGTGTCGCAGAT 59.699 40.000 27.83 13.83 42.29 2.90
2142 2362 8.932945 TTGATCAAGAATCTACATGTAGTGTC 57.067 34.615 27.83 24.08 35.96 3.67


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

AutoCloner maintained by Alex Coulton.