Multiple sequence alignment - TraesCS5D01G410300

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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 TraesCS5D01G410300 chr5D 100.000 2750 0 0 1 2750 473487632 473484883 0.000000e+00 5079.0
1 TraesCS5D01G410300 chr5D 95.556 45 2 0 1046 1090 90687338 90687294 3.800000e-09 73.1
2 TraesCS5D01G410300 chr5B 93.091 1954 86 23 1 1933 580741141 580739216 0.000000e+00 2815.0
3 TraesCS5D01G410300 chr5B 92.173 626 33 7 1937 2548 580739159 580738536 0.000000e+00 870.0
4 TraesCS5D01G410300 chr5B 94.771 153 8 0 2596 2748 580738521 580738369 3.540000e-59 239.0
5 TraesCS5D01G410300 chr5A 89.357 1898 90 39 206 2030 593242695 593240837 0.000000e+00 2283.0
6 TraesCS5D01G410300 chr5A 91.967 722 47 4 2028 2748 593240709 593239998 0.000000e+00 1002.0
7 TraesCS5D01G410300 chr5A 90.233 215 13 4 1 211 593243087 593242877 9.700000e-70 274.0
8 TraesCS5D01G410300 chr4D 85.124 121 14 4 2299 2419 363594863 363594747 1.340000e-23 121.0
9 TraesCS5D01G410300 chr2A 84.685 111 14 3 2311 2420 419462445 419462553 1.040000e-19 108.0
10 TraesCS5D01G410300 chr6D 81.679 131 20 4 2291 2420 330194575 330194702 3.750000e-19 106.0
11 TraesCS5D01G410300 chr6D 100.000 29 0 0 959 987 412753317 412753289 1.000000e-03 54.7
12 TraesCS5D01G410300 chr4A 82.031 128 20 3 2293 2420 342456873 342456997 3.750000e-19 106.0
13 TraesCS5D01G410300 chr4B 83.193 119 15 5 2298 2415 322769701 322769815 1.350000e-18 104.0
14 TraesCS5D01G410300 chr7B 80.916 131 24 1 2291 2420 363237725 363237595 4.850000e-18 102.0
15 TraesCS5D01G410300 chr3A 81.395 129 21 3 2293 2420 522186757 522186883 4.850000e-18 102.0


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 TraesCS5D01G410300 chr5D 473484883 473487632 2749 True 5079.000000 5079 100.000 1 2750 1 chr5D.!!$R2 2749
1 TraesCS5D01G410300 chr5B 580738369 580741141 2772 True 1308.000000 2815 93.345 1 2748 3 chr5B.!!$R1 2747
2 TraesCS5D01G410300 chr5A 593239998 593243087 3089 True 1186.333333 2283 90.519 1 2748 3 chr5A.!!$R1 2747

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
792 1018 0.179073 CCAGTGCCCGATTCTCGATT 60.179 55.0 0.0 0.0 43.74 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2258 0.099436 CCAACCATGCTTAGCTTCGC 59.901 55.0 5.6 0.0 0.0 4.7 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
52 57 2.158711 AGATCCATGATCGCACAACCAT 60.159 45.455 0.00 0.00 43.17 3.55
55 60 1.603802 CCATGATCGCACAACCATACC 59.396 52.381 0.00 0.00 0.00 2.73
75 80 4.139038 ACCCGGGCATGTAATTTATGTAC 58.861 43.478 24.08 0.00 0.00 2.90
76 81 4.138290 CCCGGGCATGTAATTTATGTACA 58.862 43.478 8.08 0.00 35.98 2.90
107 113 1.066358 CCCGTTCCTTACTCAACCTCC 60.066 57.143 0.00 0.00 0.00 4.30
119 125 3.175714 AACCTCCGGTCCTGTCCCT 62.176 63.158 0.00 0.00 33.12 4.20
162 170 2.359107 CGCAAGAGCAAGGCCAGA 60.359 61.111 5.01 0.00 42.27 3.86
164 172 2.698763 GCAAGAGCAAGGCCAGAGC 61.699 63.158 5.01 5.62 41.58 4.09
174 182 2.489275 GGCCAGAGCGAGAGAGAGG 61.489 68.421 0.00 0.00 41.24 3.69
320 527 1.383386 GTCCCCTCCCCCTTCTCTC 60.383 68.421 0.00 0.00 0.00 3.20
323 530 0.253394 CCCCTCCCCCTTCTCTCTTT 60.253 60.000 0.00 0.00 0.00 2.52
324 531 1.675007 CCCTCCCCCTTCTCTCTTTT 58.325 55.000 0.00 0.00 0.00 2.27
325 532 1.562008 CCCTCCCCCTTCTCTCTTTTC 59.438 57.143 0.00 0.00 0.00 2.29
326 533 1.562008 CCTCCCCCTTCTCTCTTTTCC 59.438 57.143 0.00 0.00 0.00 3.13
327 534 2.556766 CTCCCCCTTCTCTCTTTTCCT 58.443 52.381 0.00 0.00 0.00 3.36
356 573 3.591527 TCTTCTTCAGAGAGGAGGAGAGT 59.408 47.826 0.00 0.00 33.53 3.24
485 702 1.905894 GAAGAGAAGAGGAACAGGGCT 59.094 52.381 0.00 0.00 0.00 5.19
486 703 1.567357 AGAGAAGAGGAACAGGGCTC 58.433 55.000 0.00 0.00 0.00 4.70
555 774 8.681806 TCACTTCTCTGACATCTAGTAATTGAG 58.318 37.037 0.00 0.00 0.00 3.02
567 786 9.829507 CATCTAGTAATTGAGAGGTGAGAAATT 57.170 33.333 0.00 0.00 0.00 1.82
726 951 3.384146 GCAGAGAGATTCTCCTGTCATGA 59.616 47.826 22.39 0.00 44.42 3.07
746 971 2.640316 ACACTGTTGTTCTTCCCCTC 57.360 50.000 0.00 0.00 28.43 4.30
747 972 2.127708 ACACTGTTGTTCTTCCCCTCT 58.872 47.619 0.00 0.00 28.43 3.69
748 973 2.509964 ACACTGTTGTTCTTCCCCTCTT 59.490 45.455 0.00 0.00 28.43 2.85
751 976 4.036852 CACTGTTGTTCTTCCCCTCTTTTC 59.963 45.833 0.00 0.00 0.00 2.29
752 977 3.562182 TGTTGTTCTTCCCCTCTTTTCC 58.438 45.455 0.00 0.00 0.00 3.13
756 982 3.722101 TGTTCTTCCCCTCTTTTCCTTCT 59.278 43.478 0.00 0.00 0.00 2.85
760 986 5.777449 TCTTCCCCTCTTTTCCTTCTTTTT 58.223 37.500 0.00 0.00 0.00 1.94
763 989 4.170053 TCCCCTCTTTTCCTTCTTTTTCCT 59.830 41.667 0.00 0.00 0.00 3.36
771 997 4.899352 TCCTTCTTTTTCCTCCTCTGAG 57.101 45.455 0.00 0.00 38.42 3.35
774 1000 4.564613 CCTTCTTTTTCCTCCTCTGAGTCC 60.565 50.000 3.66 0.00 36.86 3.85
792 1018 0.179073 CCAGTGCCCGATTCTCGATT 60.179 55.000 0.00 0.00 43.74 3.34
896 1122 2.797156 CTGTATGGCAAGATACAGCGTC 59.203 50.000 12.37 0.00 45.42 5.19
912 1138 3.361053 CAGCGTCGTGTAGTTAGAAACAG 59.639 47.826 0.00 0.00 0.00 3.16
913 1139 3.251729 AGCGTCGTGTAGTTAGAAACAGA 59.748 43.478 0.00 0.00 0.00 3.41
962 1188 4.776322 CCATGCAGGTCCGGCGAA 62.776 66.667 9.30 0.00 0.00 4.70
1074 1300 1.589113 GCTCAAGCACGAGGAGACT 59.411 57.895 4.75 0.00 42.62 3.24
1098 1324 5.667539 TCAGGCAGCAGGTATATAAGATC 57.332 43.478 0.00 0.00 0.00 2.75
1117 1343 9.896645 ATAAGATCAGAATTCAGAAGCTACAAA 57.103 29.630 8.44 0.00 0.00 2.83
1178 1404 4.320202 GCCTCATGATTTGTGTACGTTGTT 60.320 41.667 0.00 0.00 0.00 2.83
1313 1539 3.740397 CGCCGAGTACGACCACCA 61.740 66.667 0.00 0.00 42.66 4.17
1353 1579 2.882876 GCGTCCTCCTACGAGCAA 59.117 61.111 0.00 0.00 45.68 3.91
1855 2113 5.308825 AGTACTGCTATGTTTCTGTGCTTT 58.691 37.500 0.00 0.00 0.00 3.51
1882 2140 6.287525 GCTTAGTCTTGGATCAAGCTAATCT 58.712 40.000 16.66 8.35 40.84 2.40
1910 2170 7.528481 AATAATTAACATGTCGTTGAGCGTA 57.472 32.000 0.00 0.00 38.63 4.42
1933 2193 1.348036 GTAGGAGCCACTTTCCACAGT 59.652 52.381 0.00 0.00 37.18 3.55
1935 2195 2.054799 AGGAGCCACTTTCCACAGTTA 58.945 47.619 0.00 0.00 37.18 2.24
1941 2254 3.304726 GCCACTTTCCACAGTTAGCTTTC 60.305 47.826 0.00 0.00 0.00 2.62
1945 2258 2.859165 TCCACAGTTAGCTTTCCAGG 57.141 50.000 0.00 0.00 0.00 4.45
1946 2259 1.168714 CCACAGTTAGCTTTCCAGGC 58.831 55.000 0.00 0.00 0.00 4.85
1981 2297 1.342074 TGGCTCTCAGTGCAAGTAGT 58.658 50.000 0.29 0.00 0.00 2.73
2043 2489 6.208599 TCTGTTATTTTAAGGGGCAGTCTTTG 59.791 38.462 0.00 0.00 0.00 2.77
2085 2531 7.228706 TCACAAGAACTAAGAACAGAATTTCCC 59.771 37.037 0.00 0.00 0.00 3.97
2252 2699 2.050144 TGGATGCCAGAGGTAATCTCC 58.950 52.381 0.00 0.00 43.44 3.71
2326 2774 1.790123 CGCGACGAAATTGAACATGGG 60.790 52.381 0.00 0.00 0.00 4.00
2327 2775 1.199097 GCGACGAAATTGAACATGGGT 59.801 47.619 0.00 0.00 0.00 4.51
2423 2878 6.150396 ACTATATTCATATAGAGGTGCCGC 57.850 41.667 17.31 0.00 43.02 6.53
2448 2903 2.417243 CCAATGCATTTCTCGTTTCCCC 60.417 50.000 9.83 0.00 0.00 4.81
2548 3006 6.785488 TCTTAGTTGTGCATGTAACTCTTG 57.215 37.500 14.61 8.54 38.11 3.02
2557 3015 1.078637 GTAACTCTTGGGGGTCCGC 60.079 63.158 0.00 0.00 35.24 5.54
2601 3059 1.808945 GGTTTGAGAGAGTGCCATGTG 59.191 52.381 0.00 0.00 0.00 3.21
2633 3091 1.799916 CGTCATGTGTCGCGTGCTA 60.800 57.895 5.77 0.00 34.19 3.49
2694 3152 4.250464 ACGCGTTTTCAGGATTTAGATGA 58.750 39.130 5.58 0.00 0.00 2.92
2748 3206 7.926018 TGTTTTTCTTAGGCTTTGGAGATTTTC 59.074 33.333 0.00 0.00 0.00 2.29
2749 3207 7.839680 TTTTCTTAGGCTTTGGAGATTTTCT 57.160 32.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.198807 TCATGGATCTGCTGATAGAGAATTAA 57.801 34.615 6.02 0.00 32.19 1.40
29 34 1.003116 GTTGTGCGATCATGGATCTGC 60.003 52.381 12.68 12.68 36.96 4.26
52 57 4.440826 ACATAAATTACATGCCCGGGTA 57.559 40.909 24.63 20.49 0.00 3.69
55 60 5.759506 TTGTACATAAATTACATGCCCGG 57.240 39.130 0.00 0.00 29.60 5.73
75 80 2.600173 AACGGGCCACCCACATTG 60.600 61.111 4.39 0.00 45.83 2.82
76 81 2.282887 GAACGGGCCACCCACATT 60.283 61.111 4.39 0.00 45.83 2.71
107 113 2.232298 GAGCAGAAGGGACAGGACCG 62.232 65.000 0.00 0.00 0.00 4.79
162 170 0.916086 TTCTCTCCCTCTCTCTCGCT 59.084 55.000 0.00 0.00 0.00 4.93
164 172 3.275617 TCTTTCTCTCCCTCTCTCTCG 57.724 52.381 0.00 0.00 0.00 4.04
174 182 4.758165 CCGACTAGGAGTATCTTTCTCTCC 59.242 50.000 0.00 0.00 45.56 3.71
320 527 7.930865 TCTCTGAAGAAGAAAGAGAAGGAAAAG 59.069 37.037 0.00 0.00 42.60 2.27
323 530 6.014669 CCTCTCTGAAGAAGAAAGAGAAGGAA 60.015 42.308 3.46 0.00 44.33 3.36
324 531 5.480073 CCTCTCTGAAGAAGAAAGAGAAGGA 59.520 44.000 3.46 0.00 44.33 3.36
325 532 5.480073 TCCTCTCTGAAGAAGAAAGAGAAGG 59.520 44.000 3.46 6.95 44.33 3.46
326 533 6.350445 CCTCCTCTCTGAAGAAGAAAGAGAAG 60.350 46.154 3.46 0.00 44.33 2.85
327 534 5.480073 CCTCCTCTCTGAAGAAGAAAGAGAA 59.520 44.000 3.46 0.00 44.33 2.87
356 573 0.923358 GTCCCTCTCCCTCTCTCTCA 59.077 60.000 0.00 0.00 0.00 3.27
485 702 1.618837 GCTCCAACTACCACTCACTGA 59.381 52.381 0.00 0.00 0.00 3.41
486 703 1.620819 AGCTCCAACTACCACTCACTG 59.379 52.381 0.00 0.00 0.00 3.66
555 774 5.298026 GGGAAATGAGCTAATTTCTCACCTC 59.702 44.000 28.21 14.98 43.62 3.85
567 786 5.104735 GGAAAGAAGAGAGGGAAATGAGCTA 60.105 44.000 0.00 0.00 0.00 3.32
663 887 1.338020 GCAAGTCACAACCCAAAGGAG 59.662 52.381 0.00 0.00 36.73 3.69
745 970 6.064717 CAGAGGAGGAAAAAGAAGGAAAAGA 58.935 40.000 0.00 0.00 0.00 2.52
746 971 6.064717 TCAGAGGAGGAAAAAGAAGGAAAAG 58.935 40.000 0.00 0.00 0.00 2.27
747 972 6.013554 TCAGAGGAGGAAAAAGAAGGAAAA 57.986 37.500 0.00 0.00 0.00 2.29
748 973 5.132816 ACTCAGAGGAGGAAAAAGAAGGAAA 59.867 40.000 1.53 0.00 45.81 3.13
751 976 4.564613 GGACTCAGAGGAGGAAAAAGAAGG 60.565 50.000 1.53 0.00 45.81 3.46
752 977 4.040952 TGGACTCAGAGGAGGAAAAAGAAG 59.959 45.833 1.53 0.00 45.81 2.85
756 982 3.071602 CACTGGACTCAGAGGAGGAAAAA 59.928 47.826 1.53 0.00 45.81 1.94
760 986 0.613292 GCACTGGACTCAGAGGAGGA 60.613 60.000 1.53 0.00 45.81 3.71
763 989 1.610673 GGGCACTGGACTCAGAGGA 60.611 63.158 1.53 0.00 43.49 3.71
771 997 4.522971 GAGAATCGGGCACTGGAC 57.477 61.111 0.00 0.00 33.92 4.02
792 1018 2.813754 CAATTGGAGCTTTCGAAGTGGA 59.186 45.455 0.00 0.00 0.00 4.02
893 1119 4.557690 CCATCTGTTTCTAACTACACGACG 59.442 45.833 0.00 0.00 0.00 5.12
896 1122 4.563184 GCTCCATCTGTTTCTAACTACACG 59.437 45.833 0.00 0.00 0.00 4.49
960 1186 6.481644 TCTTGCTCTGTTTCTTCTTCTTCTTC 59.518 38.462 0.00 0.00 0.00 2.87
961 1187 6.352516 TCTTGCTCTGTTTCTTCTTCTTCTT 58.647 36.000 0.00 0.00 0.00 2.52
962 1188 5.923204 TCTTGCTCTGTTTCTTCTTCTTCT 58.077 37.500 0.00 0.00 0.00 2.85
1074 1300 5.887214 TCTTATATACCTGCTGCCTGAAA 57.113 39.130 0.00 0.00 0.00 2.69
1098 1324 8.749499 CAAAAAGTTTGTAGCTTCTGAATTCTG 58.251 33.333 7.05 6.50 0.00 3.02
1117 1343 1.140852 GGGGAGGCAAAAGCAAAAAGT 59.859 47.619 0.00 0.00 0.00 2.66
1178 1404 0.904649 ATGGAGATCGTGAACCTGCA 59.095 50.000 0.00 0.00 33.00 4.41
1641 1873 2.125106 GGCCTCCGCTTGTGGTAG 60.125 66.667 0.00 0.00 34.44 3.18
1746 1981 2.872732 CCATTCCATGGCTAGCTTCAT 58.127 47.619 15.72 7.69 44.70 2.57
1808 2066 3.838244 ACTACAGCTCAACAAACAGGA 57.162 42.857 0.00 0.00 0.00 3.86
1855 2113 3.866651 GCTTGATCCAAGACTAAGCTGA 58.133 45.455 10.55 0.00 43.42 4.26
1907 2167 3.195661 GGAAAGTGGCTCCTACATTACG 58.804 50.000 0.00 0.00 0.00 3.18
1910 2170 2.375174 TGTGGAAAGTGGCTCCTACATT 59.625 45.455 0.00 0.00 33.77 2.71
1933 2193 0.324943 AGCTTCGCCTGGAAAGCTAA 59.675 50.000 25.98 0.00 37.36 3.09
1935 2195 0.324943 TTAGCTTCGCCTGGAAAGCT 59.675 50.000 28.36 28.36 40.15 3.74
1941 2254 1.442526 CCATGCTTAGCTTCGCCTGG 61.443 60.000 13.83 13.83 36.00 4.45
1945 2258 0.099436 CCAACCATGCTTAGCTTCGC 59.901 55.000 5.60 0.00 0.00 4.70
1946 2259 0.099436 GCCAACCATGCTTAGCTTCG 59.901 55.000 5.60 0.00 0.00 3.79
1981 2297 8.233190 CACTCACAAAAGCAAACCAAAATTAAA 58.767 29.630 0.00 0.00 0.00 1.52
2043 2489 8.306761 AGTTCTTGTGAATTTGATTTCATACCC 58.693 33.333 0.00 0.00 37.88 3.69
2085 2531 2.947652 AGCCACAAATCCTCATTCGATG 59.052 45.455 0.00 0.00 0.00 3.84
2326 2774 1.374252 CTGGGTGCCGACTGTACAC 60.374 63.158 0.00 0.79 32.89 2.90
2327 2775 0.902984 ATCTGGGTGCCGACTGTACA 60.903 55.000 0.00 0.00 0.00 2.90
2421 2876 0.590732 GAGAAATGCATTGGAGCGCG 60.591 55.000 13.82 0.00 37.31 6.86
2423 2878 0.729116 ACGAGAAATGCATTGGAGCG 59.271 50.000 13.82 16.00 37.31 5.03
2548 3006 0.761702 TTAGGTGATAGCGGACCCCC 60.762 60.000 0.00 0.00 32.03 5.40
2557 3015 5.643777 CACAAAAGTGTCCCTTAGGTGATAG 59.356 44.000 0.00 0.00 38.58 2.08
2633 3091 6.603940 AACTACAATTCAGAGAGAGAAGCT 57.396 37.500 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.