Multiple sequence alignment - TraesCS4B01G212100

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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 TraesCS4B01G212100 chr4B 100.000 2126 0 0 595 2720 450469529 450471654 0.000000e+00 3927
1 TraesCS4B01G212100 chr4B 100.000 273 0 0 1 273 450468935 450469207 3.130000e-139 505
2 TraesCS4B01G212100 chr4D 96.986 1825 50 4 896 2720 365853329 365855148 0.000000e+00 3061
3 TraesCS4B01G212100 chr4D 96.959 296 7 2 595 889 365852744 365853038 1.880000e-136 496
4 TraesCS4B01G212100 chr4D 97.398 269 7 0 1 269 365852427 365852695 2.470000e-125 459
5 TraesCS4B01G212100 chr4A 93.898 295 15 1 595 889 99018334 99018043 2.490000e-120 442
6 TraesCS4B01G212100 chr4A 88.581 289 13 1 1 269 99018671 99018383 1.560000e-87 333
7 TraesCS4B01G212100 chr3B 75.460 326 64 13 2191 2508 9112087 9111770 7.850000e-31 145


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 TraesCS4B01G212100 chr4B 450468935 450471654 2719 False 2216.000000 3927 100.000000 1 2720 2 chr4B.!!$F1 2719
1 TraesCS4B01G212100 chr4D 365852427 365855148 2721 False 1338.666667 3061 97.114333 1 2720 3 chr4D.!!$F1 2719
2 TraesCS4B01G212100 chr4A 99018043 99018671 628 True 387.500000 442 91.239500 1 889 2 chr4A.!!$R1 888

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
885 907 0.79325 GCGAGCTCAGTTCCTCAAAC 59.207 55.0 15.4 0.0 38.21 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2909 1.678101 GAGGAACAGCAAACAAGCACT 59.322 47.619 0.0 0.0 36.85 4.4 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
98 119 1.421646 AGGCTACCAACTTCAAGCAGT 59.578 47.619 0.00 0.00 36.68 4.40
100 121 3.072476 AGGCTACCAACTTCAAGCAGTAA 59.928 43.478 0.00 0.00 36.68 2.24
194 215 2.627515 AGTGCTCAAAACTCTCAGCA 57.372 45.000 0.00 0.00 39.58 4.41
269 290 4.026052 GTCACATCAGGAAAAATCCCCAT 58.974 43.478 0.00 0.00 0.00 4.00
270 291 4.467438 GTCACATCAGGAAAAATCCCCATT 59.533 41.667 0.00 0.00 0.00 3.16
643 664 9.638176 ATTATTGATGGAGCAAGAGAAAACTAT 57.362 29.630 0.00 0.00 0.00 2.12
646 667 6.715280 TGATGGAGCAAGAGAAAACTATTCT 58.285 36.000 0.00 0.00 0.00 2.40
765 787 2.846206 TCTGTTCAGGGCTCACCAATAT 59.154 45.455 0.00 0.00 43.89 1.28
885 907 0.793250 GCGAGCTCAGTTCCTCAAAC 59.207 55.000 15.40 0.00 38.21 2.93
889 911 1.494721 AGCTCAGTTCCTCAAACCCAA 59.505 47.619 0.00 0.00 38.76 4.12
890 912 2.091885 AGCTCAGTTCCTCAAACCCAAA 60.092 45.455 0.00 0.00 38.76 3.28
891 913 2.893489 GCTCAGTTCCTCAAACCCAAAT 59.107 45.455 0.00 0.00 38.76 2.32
892 914 3.321968 GCTCAGTTCCTCAAACCCAAATT 59.678 43.478 0.00 0.00 38.76 1.82
893 915 4.202253 GCTCAGTTCCTCAAACCCAAATTT 60.202 41.667 0.00 0.00 38.76 1.82
946 1252 1.279496 TCTAATGGCTCAGGTGCAGT 58.721 50.000 0.00 0.00 34.04 4.40
1013 1319 4.768448 TGTGAATGGAATGAGAGCAACAAT 59.232 37.500 0.00 0.00 0.00 2.71
1029 1335 9.120538 AGAGCAACAATTAAGTTTCTGTTAAGA 57.879 29.630 0.00 0.00 31.00 2.10
1146 1452 4.387862 GGTACACAAAGACATACAACTCCG 59.612 45.833 0.00 0.00 0.00 4.63
1172 1478 0.249996 AAACAGCCAGGTGCAATTGC 60.250 50.000 23.69 23.69 44.83 3.56
1177 1483 1.383456 GCCAGGTGCAATTGCGGATA 61.383 55.000 24.58 4.95 45.83 2.59
1244 1550 1.903860 ACCTGGTAAGTGTTGGCGATA 59.096 47.619 0.00 0.00 0.00 2.92
1266 1572 1.256812 GGGACAGTTGGTTTCATGGG 58.743 55.000 0.00 0.00 0.00 4.00
1424 1730 4.066490 CAAATTTCTTTGCAGGCCATGAA 58.934 39.130 5.01 0.00 35.69 2.57
1526 1832 6.698766 AGCAATTCAACATTTCTGAACTTGAC 59.301 34.615 6.54 0.00 35.70 3.18
1582 1888 8.314021 TGAAAGATAAATCTAGAGCTGTGACAA 58.686 33.333 0.00 0.00 35.76 3.18
1599 1905 1.494721 ACAATAGCAGGTGGGGGTATG 59.505 52.381 0.00 0.00 0.00 2.39
1603 1909 2.052104 GCAGGTGGGGGTATGTTGC 61.052 63.158 0.00 0.00 0.00 4.17
1623 1929 0.912486 GGTCTGGTGCTTATGTCCCT 59.088 55.000 0.00 0.00 0.00 4.20
1624 1930 2.116238 GGTCTGGTGCTTATGTCCCTA 58.884 52.381 0.00 0.00 0.00 3.53
1625 1931 2.158943 GGTCTGGTGCTTATGTCCCTAC 60.159 54.545 0.00 0.00 0.00 3.18
1626 1932 2.766828 GTCTGGTGCTTATGTCCCTACT 59.233 50.000 0.00 0.00 0.00 2.57
1641 1947 8.980481 ATGTCCCTACTACTAAATTCCAAATG 57.020 34.615 0.00 0.00 0.00 2.32
1784 2090 7.450014 TGAAGAAGAATGGGCAACAAATTACTA 59.550 33.333 0.00 0.00 39.74 1.82
1935 2241 1.349026 ACATGTCACCCTCCTGAAGTG 59.651 52.381 0.00 0.00 0.00 3.16
1960 2266 3.514706 ACAATTAATTGCACAGCATCCCA 59.485 39.130 24.82 0.00 41.38 4.37
2166 2472 6.372937 GCCCTTATGCTTCTCCAGTTATTATC 59.627 42.308 0.00 0.00 0.00 1.75
2176 2482 9.765795 CTTCTCCAGTTATTATCGTTCCTAAAT 57.234 33.333 0.00 0.00 0.00 1.40
2204 2510 1.312815 ACTTGGAGACTTTGCACTGC 58.687 50.000 0.00 0.00 0.00 4.40
2207 2513 2.057137 TGGAGACTTTGCACTGCTTT 57.943 45.000 1.98 0.00 0.00 3.51
2254 2560 9.853177 CTATCAAGGACAAATTTCCTATACCTT 57.147 33.333 0.00 0.00 46.06 3.50
2281 2587 3.491766 AGGACCTCCTGGATGAACTAA 57.508 47.619 5.95 0.00 46.55 2.24
2300 2606 8.203485 TGAACTAAATGGAGCAAAGTTTTTCAT 58.797 29.630 0.00 0.00 30.83 2.57
2354 2660 7.230108 TCAAATTAGGATGAATGAGGAAGATGC 59.770 37.037 0.00 0.00 0.00 3.91
2355 2661 5.635278 TTAGGATGAATGAGGAAGATGCA 57.365 39.130 0.00 0.00 0.00 3.96
2375 2681 3.678529 GCACCCAAAACTGCTTTCAGAAA 60.679 43.478 0.00 0.00 42.95 2.52
2420 2726 3.096092 TGGTTATGCCCTTTGGATTGTC 58.904 45.455 0.00 0.00 36.04 3.18
2497 2803 9.855021 ACTTGAGGAAATTTATATTGGTTTTCG 57.145 29.630 0.00 0.00 0.00 3.46
2512 2818 6.435430 TGGTTTTCGTTGATGATATCTTGG 57.565 37.500 3.98 0.00 0.00 3.61
2522 2828 7.254898 CGTTGATGATATCTTGGTGTTTAGCAT 60.255 37.037 3.98 0.00 33.73 3.79
2559 2865 7.549147 ACACTTAGAACACTTGGGAATAGTA 57.451 36.000 0.00 0.00 0.00 1.82
2603 2909 7.424803 CATCAGTTGTCAGTTAAAATGTCCAA 58.575 34.615 0.00 0.00 0.00 3.53
2632 2938 4.202461 TGTTTGCTGTTCCTCAGGTAGATT 60.202 41.667 0.00 0.00 43.78 2.40
2663 2969 1.901591 ATCATAAATGAGCAGCGGGG 58.098 50.000 0.00 0.00 40.64 5.73
2672 2978 3.365265 GCAGCGGGGTTTCCACAG 61.365 66.667 0.00 0.00 34.36 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 119 4.394920 GGAAATCACCTTTGTCATCGCTTA 59.605 41.667 0.00 0.00 0.00 3.09
100 121 2.749621 GGAAATCACCTTTGTCATCGCT 59.250 45.455 0.00 0.00 0.00 4.93
194 215 2.563013 GATGTGGATGGGGCTGCTGT 62.563 60.000 0.00 0.00 0.00 4.40
248 269 3.824001 TGGGGATTTTTCCTGATGTGA 57.176 42.857 0.00 0.00 0.00 3.58
646 667 2.095461 TGCCTGTTAACAGTGCAAACA 58.905 42.857 31.93 19.46 42.68 2.83
722 744 7.181125 ACAGAGGGTCTATCTTGAAATTGTAGT 59.819 37.037 0.00 0.00 0.00 2.73
765 787 1.471119 CTAGTAGTCCTTGTGGGCGA 58.529 55.000 0.00 0.00 44.16 5.54
970 1276 7.022055 TCACATAACACTTTACAAACCACAG 57.978 36.000 0.00 0.00 0.00 3.66
1013 1319 7.709613 GTCTCAGTGGTCTTAACAGAAACTTAA 59.290 37.037 0.00 0.00 29.44 1.85
1029 1335 3.933861 AAAGTTTCAGGTCTCAGTGGT 57.066 42.857 0.00 0.00 0.00 4.16
1107 1413 4.645136 TGTGTACCAGATGTCAGAGGATAC 59.355 45.833 0.00 0.00 0.00 2.24
1146 1452 5.828299 TTGCACCTGGCTGTTTATAATAC 57.172 39.130 0.00 0.00 45.15 1.89
1172 1478 0.179084 TGCTTCGGCTCCTTTATCCG 60.179 55.000 0.00 0.00 44.16 4.18
1177 1483 0.465460 TGTGTTGCTTCGGCTCCTTT 60.465 50.000 0.00 0.00 42.37 3.11
1244 1550 2.528564 CATGAAACCAACTGTCCCCAT 58.471 47.619 0.00 0.00 0.00 4.00
1424 1730 0.758734 TGTGCTTACTCTGGCAGTGT 59.241 50.000 23.79 23.79 39.22 3.55
1526 1832 4.202000 TGCAGTTTGTGGTCAGTGTAAATG 60.202 41.667 0.00 0.00 0.00 2.32
1582 1888 1.494721 CAACATACCCCCACCTGCTAT 59.505 52.381 0.00 0.00 0.00 2.97
1599 1905 0.447801 CATAAGCACCAGACCGCAAC 59.552 55.000 0.00 0.00 0.00 4.17
1603 1909 0.462047 GGGACATAAGCACCAGACCG 60.462 60.000 0.00 0.00 0.00 4.79
1623 1929 7.891183 TCTTTGCCCATTTGGAATTTAGTAGTA 59.109 33.333 0.00 0.00 37.39 1.82
1624 1930 6.723977 TCTTTGCCCATTTGGAATTTAGTAGT 59.276 34.615 0.00 0.00 37.39 2.73
1625 1931 7.169158 TCTTTGCCCATTTGGAATTTAGTAG 57.831 36.000 0.00 0.00 37.39 2.57
1626 1932 7.015682 TGTTCTTTGCCCATTTGGAATTTAGTA 59.984 33.333 0.00 0.00 37.39 1.82
1677 1983 3.569701 CCATGTCATACCCTGGTAAATGC 59.430 47.826 0.00 0.00 33.99 3.56
1678 1984 4.792068 ACCATGTCATACCCTGGTAAATG 58.208 43.478 0.00 0.00 40.16 2.32
1736 2042 3.577848 ACAAGGATTTGCTTGTTGCCATA 59.422 39.130 11.16 0.00 40.43 2.74
1740 2046 3.096489 TCACAAGGATTTGCTTGTTGC 57.904 42.857 13.88 0.00 41.26 4.17
1757 2063 4.320608 TTTGTTGCCCATTCTTCTTCAC 57.679 40.909 0.00 0.00 0.00 3.18
1784 2090 3.507622 GCAAAGGAGTTACAAGCAGGAAT 59.492 43.478 0.00 0.00 0.00 3.01
1935 2241 4.567959 GGATGCTGTGCAATTAATTGTTCC 59.432 41.667 25.15 16.36 43.62 3.62
1960 2266 3.132824 CCCTCAGGTTCTGCAAAAACTTT 59.867 43.478 10.48 0.00 0.00 2.66
2176 2482 4.383118 GCAAAGTCTCCAAGTAGCATCCTA 60.383 45.833 0.00 0.00 0.00 2.94
2178 2484 2.680339 GCAAAGTCTCCAAGTAGCATCC 59.320 50.000 0.00 0.00 0.00 3.51
2247 2553 5.366768 CAGGAGGTCCTCAATGAAAGGTATA 59.633 44.000 20.72 0.00 46.65 1.47
2254 2560 2.342406 TCCAGGAGGTCCTCAATGAA 57.658 50.000 20.72 0.00 46.65 2.57
2281 2587 8.829612 CACTTTTATGAAAAACTTTGCTCCATT 58.170 29.630 0.00 0.00 31.37 3.16
2300 2606 9.561069 GATAGCCTGATCTTAAATCCACTTTTA 57.439 33.333 0.00 0.00 0.00 1.52
2305 2611 7.164122 TGATGATAGCCTGATCTTAAATCCAC 58.836 38.462 0.00 0.00 0.00 4.02
2354 2660 3.799281 TTCTGAAAGCAGTTTTGGGTG 57.201 42.857 0.00 0.00 42.84 4.61
2355 2661 4.020662 TGTTTTCTGAAAGCAGTTTTGGGT 60.021 37.500 14.50 0.00 42.84 4.51
2375 2681 6.875195 CAGATATTCAAAATGGCCAAAGTGTT 59.125 34.615 10.96 0.00 0.00 3.32
2429 2735 2.703416 TCAGTGCCTGAAATGTGCTAG 58.297 47.619 2.78 0.00 37.57 3.42
2497 2803 7.320443 TGCTAAACACCAAGATATCATCAAC 57.680 36.000 5.32 0.00 0.00 3.18
2512 2818 6.426937 TGTTCTTCCAGACTTATGCTAAACAC 59.573 38.462 0.00 0.00 0.00 3.32
2522 2828 7.069578 AGTGTTCTAAGTGTTCTTCCAGACTTA 59.930 37.037 0.00 0.00 35.36 2.24
2603 2909 1.678101 GAGGAACAGCAAACAAGCACT 59.322 47.619 0.00 0.00 36.85 4.40
2632 2938 9.234827 CTGCTCATTTATGATATGACCCAAATA 57.765 33.333 0.00 0.00 36.02 1.40
2663 2969 2.930826 TTCTCAGGGTCTGTGGAAAC 57.069 50.000 0.00 0.00 32.61 2.78
2672 2978 3.244249 ACTGCACTTACTTTCTCAGGGTC 60.244 47.826 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.