Multiple sequence alignment - TraesCS6D01G116800

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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 TraesCS6D01G116800 chr6D 100.000 3113 0 0 1 3113 83047897 83044785 0.000000e+00 5749.0
1 TraesCS6D01G116800 chr6D 86.022 2089 273 17 1033 3110 83540604 83542684 0.000000e+00 2222.0
2 TraesCS6D01G116800 chr6D 86.235 2056 268 13 1064 3110 83124697 83122648 0.000000e+00 2215.0
3 TraesCS6D01G116800 chr6D 85.806 2029 263 18 1091 3111 83057865 83055854 0.000000e+00 2128.0
4 TraesCS6D01G116800 chr6D 86.598 291 35 4 54 341 312060007 312059718 5.010000e-83 318.0
5 TraesCS6D01G116800 chr6B 96.703 3063 83 10 1 3056 158077781 158074730 0.000000e+00 5081.0
6 TraesCS6D01G116800 chr6B 86.346 2058 262 17 1064 3110 158149766 158147717 0.000000e+00 2226.0
7 TraesCS6D01G116800 chr6B 85.817 2087 281 13 1033 3110 159402072 159404152 0.000000e+00 2200.0
8 TraesCS6D01G116800 chr6B 84.868 152 21 1 681 832 158077251 158077102 5.380000e-33 152.0
9 TraesCS6D01G116800 chr6B 96.203 79 3 0 3035 3113 158074730 158074652 2.520000e-26 130.0
10 TraesCS6D01G116800 chr6A 85.584 2088 284 15 1033 3110 100760978 100763058 0.000000e+00 2172.0
11 TraesCS6D01G116800 chr6A 85.805 2057 276 14 1064 3110 100185055 100183005 0.000000e+00 2167.0
12 TraesCS6D01G116800 chr6A 85.714 2037 272 17 1085 3110 100803091 100805119 0.000000e+00 2132.0
13 TraesCS6D01G116800 chr6A 94.582 443 19 4 1 440 100073888 100073448 0.000000e+00 680.0
14 TraesCS6D01G116800 chr6A 90.431 418 33 5 417 830 100357840 100357426 7.590000e-151 544.0
15 TraesCS6D01G116800 chr6A 85.172 290 39 4 56 341 516158049 516157760 8.440000e-76 294.0
16 TraesCS6D01G116800 chr6A 85.542 83 6 5 327 405 221545354 221545434 7.160000e-12 82.4
17 TraesCS6D01G116800 chr2D 88.316 291 30 3 54 341 262454925 262455214 2.300000e-91 346.0
18 TraesCS6D01G116800 chr2A 88.153 287 31 3 56 339 746760771 746761057 3.850000e-89 339.0
19 TraesCS6D01G116800 chr1D 87.333 300 28 7 53 343 429494428 429494726 4.970000e-88 335.0
20 TraesCS6D01G116800 chr1D 90.541 74 5 2 339 410 110052535 110052462 2.560000e-16 97.1
21 TraesCS6D01G116800 chr1A 86.957 299 34 4 47 341 507544051 507544348 6.430000e-87 331.0
22 TraesCS6D01G116800 chr1A 89.041 73 6 2 339 410 114061059 114060988 4.280000e-14 89.8
23 TraesCS6D01G116800 chr5B 86.007 293 36 3 54 341 615371701 615371409 3.020000e-80 309.0
24 TraesCS6D01G116800 chr4A 90.769 65 4 2 339 401 590111610 590111546 5.530000e-13 86.1
25 TraesCS6D01G116800 chr4A 88.571 70 6 2 328 395 605730233 605730302 1.990000e-12 84.2
26 TraesCS6D01G116800 chr3B 91.935 62 3 2 339 398 680423361 680423300 5.530000e-13 86.1
27 TraesCS6D01G116800 chr7D 88.571 70 5 3 340 407 21789147 21789215 7.160000e-12 82.4


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 TraesCS6D01G116800 chr6D 83044785 83047897 3112 True 5749.000000 5749 100.000000 1 3113 1 chr6D.!!$R1 3112
1 TraesCS6D01G116800 chr6D 83540604 83542684 2080 False 2222.000000 2222 86.022000 1033 3110 1 chr6D.!!$F1 2077
2 TraesCS6D01G116800 chr6D 83122648 83124697 2049 True 2215.000000 2215 86.235000 1064 3110 1 chr6D.!!$R3 2046
3 TraesCS6D01G116800 chr6D 83055854 83057865 2011 True 2128.000000 2128 85.806000 1091 3111 1 chr6D.!!$R2 2020
4 TraesCS6D01G116800 chr6B 158147717 158149766 2049 True 2226.000000 2226 86.346000 1064 3110 1 chr6B.!!$R1 2046
5 TraesCS6D01G116800 chr6B 159402072 159404152 2080 False 2200.000000 2200 85.817000 1033 3110 1 chr6B.!!$F1 2077
6 TraesCS6D01G116800 chr6B 158074652 158077781 3129 True 1787.666667 5081 92.591333 1 3113 3 chr6B.!!$R2 3112
7 TraesCS6D01G116800 chr6A 100760978 100763058 2080 False 2172.000000 2172 85.584000 1033 3110 1 chr6A.!!$F1 2077
8 TraesCS6D01G116800 chr6A 100183005 100185055 2050 True 2167.000000 2167 85.805000 1064 3110 1 chr6A.!!$R2 2046
9 TraesCS6D01G116800 chr6A 100803091 100805119 2028 False 2132.000000 2132 85.714000 1085 3110 1 chr6A.!!$F2 2025

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
22 23 1.596603 TGTGCAATGACCACTCACTG 58.403 50.0 0.00 0.0 34.38 3.66 F
1311 1317 0.324943 GCAACCTCACTGGCCTCTTA 59.675 55.0 3.32 0.0 40.22 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 1902 0.609957 TGGTCCAAATGCAGCTCCTG 60.61 55.0 0.0 0.0 34.12 3.86 R
2299 2308 0.179702 GCTGTCATCCTCTGGCATGA 59.82 55.0 0.0 0.0 39.17 3.07 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
22 23 1.596603 TGTGCAATGACCACTCACTG 58.403 50.000 0.00 0.00 34.38 3.66
24 25 2.632643 GCAATGACCACTCACTGCA 58.367 52.632 0.00 0.00 46.75 4.41
99 100 5.766670 CCAACTGATGGCTATATGATGTTGT 59.233 40.000 0.00 0.00 43.80 3.32
141 142 5.012768 ACCTTATAGCCGGCAAGTACAATAT 59.987 40.000 31.54 16.90 0.00 1.28
236 237 3.129871 GCTACAGCTGGCTCTTATTCTG 58.870 50.000 19.93 0.00 38.21 3.02
274 275 3.657727 CTCTCTCCTATTCTCTCCCCTCT 59.342 52.174 0.00 0.00 0.00 3.69
281 282 5.136220 TCCTATTCTCTCCCCTCTATGTCAA 59.864 44.000 0.00 0.00 0.00 3.18
342 345 9.534565 CATAAGCTTATTGTACTTGCTCTAAGA 57.465 33.333 16.46 0.00 39.76 2.10
487 493 3.396260 TTCAGTAAGAACCCTTCACGG 57.604 47.619 0.00 0.00 33.94 4.94
543 549 2.672961 TCGACCCTGACATTGATGAC 57.327 50.000 0.00 0.00 0.00 3.06
545 551 2.094026 TCGACCCTGACATTGATGACAG 60.094 50.000 13.92 13.92 45.63 3.51
696 702 6.149308 ACTCAAATTGACGCTAACATCAATGA 59.851 34.615 0.00 0.00 43.21 2.57
704 710 4.883585 ACGCTAACATCAATGATGGAATGT 59.116 37.500 24.99 14.22 43.60 2.71
816 822 4.097741 GCATATGCAACTCACCAATACCAA 59.902 41.667 22.84 0.00 41.59 3.67
842 848 2.448961 TCCTTGACCCATTCCCTCAAAA 59.551 45.455 0.00 0.00 0.00 2.44
874 880 7.566760 AATCCTTGACCCAAATTTTGTTTTC 57.433 32.000 8.26 2.56 0.00 2.29
892 898 3.918294 TTCATCATGATGACCAGAGCA 57.082 42.857 33.02 17.09 46.49 4.26
953 959 4.826274 AACTAGTGCTTTATCTGGCAGA 57.174 40.909 21.19 21.19 39.22 4.26
1020 1026 1.244019 TGCAGCTACTCAGTCGCTCA 61.244 55.000 0.00 0.51 32.27 4.26
1048 1054 6.296026 TGGAATAGATTTCCCATACCTTTCG 58.704 40.000 2.11 0.00 37.79 3.46
1050 1056 6.427242 GGAATAGATTTCCCATACCTTTCGTC 59.573 42.308 0.00 0.00 32.48 4.20
1058 1064 2.419667 CATACCTTTCGTCGGTTTGGT 58.580 47.619 0.00 0.00 35.98 3.67
1173 1179 3.626924 GGTGGCCTCACGGTGTCT 61.627 66.667 3.32 0.00 44.50 3.41
1311 1317 0.324943 GCAACCTCACTGGCCTCTTA 59.675 55.000 3.32 0.00 40.22 2.10
1482 1488 5.171339 AGGTACTGAACATCTCAAGCAAT 57.829 39.130 0.00 0.00 37.18 3.56
1745 1752 6.748333 TCCAGATGAGCTTTTCAATGTTAG 57.252 37.500 0.00 0.00 39.77 2.34
1889 1897 6.775142 CCAGAGTCTATAGGTGATCTGAAGAA 59.225 42.308 18.16 0.00 37.03 2.52
1894 1902 7.930865 AGTCTATAGGTGATCTGAAGAAATTGC 59.069 37.037 0.00 0.00 0.00 3.56
2205 2214 6.766944 CCTCTCATTCTTATCACTTGCTCATT 59.233 38.462 0.00 0.00 0.00 2.57
2299 2308 3.350833 GGTTCAACTTCCTGCATGAGAT 58.649 45.455 0.00 0.00 0.00 2.75
2352 2361 3.055819 TGAGAATCTCCAGGTTCTTTCCG 60.056 47.826 7.91 0.00 34.97 4.30
2435 2444 5.334802 GGGGATGCTATTTTTGCAAAACAAC 60.335 40.000 23.79 15.82 44.01 3.32
2461 2470 7.147724 CCAACTAACTGGATCAATACCTGACTA 60.148 40.741 0.00 0.00 38.96 2.59
2528 2537 1.064685 AGCCTTACAGGGGAAATTCCG 60.065 52.381 5.87 0.00 37.43 4.30
2721 2730 3.293311 TCGGTCAGTTAAAAGGACTCG 57.707 47.619 0.00 0.00 0.00 4.18
2811 2820 2.359214 CTGCAGGTGCTCGACTTATCTA 59.641 50.000 5.57 0.00 42.66 1.98
2849 2858 4.399303 GGTGTAATTCCAGCTGCACTAAAT 59.601 41.667 8.66 0.00 0.00 1.40
2903 2912 4.844655 TCTAATAATGACCTAGAAGGCCCC 59.155 45.833 0.00 0.00 39.63 5.80
2981 2990 4.385825 TCAAAACTGTGTGGTCCTATGAC 58.614 43.478 0.00 0.00 40.98 3.06
3014 3023 3.385469 CTCAGCAGGAGCAGGTCA 58.615 61.111 1.20 0.00 45.49 4.02
3022 3031 3.071580 GGAGCAGGTCAAATCTCCG 57.928 57.895 1.20 0.00 36.18 4.63
3093 3126 1.607148 GGTGTTTTCTTTGGAGTCGGG 59.393 52.381 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.892474 CAGGAGGGAGTAGCTATCTGC 59.108 57.143 0.00 1.55 43.29 4.26
24 25 4.417518 AGTTACAGGAGGGAGTAGCTATCT 59.582 45.833 0.00 0.00 31.31 1.98
99 100 5.894298 AAGGTTGGCTACAGATGATATGA 57.106 39.130 0.80 0.00 0.00 2.15
103 104 5.280215 GGCTATAAGGTTGGCTACAGATGAT 60.280 44.000 0.80 0.00 0.00 2.45
110 111 1.876837 GCCGGCTATAAGGTTGGCTAC 60.877 57.143 22.15 0.00 39.38 3.58
213 214 2.611225 ATAAGAGCCAGCTGTAGCAC 57.389 50.000 13.81 8.57 45.16 4.40
236 237 0.753848 AGAGAAGAGGAGCCGGCTAC 60.754 60.000 32.56 32.56 0.00 3.58
311 314 9.314321 GAGCAAGTACAATAAGCTTATGTAAGA 57.686 33.333 19.53 1.77 35.36 2.10
342 345 4.618920 ACCTCATGGACTCTAAAAACGT 57.381 40.909 0.00 0.00 37.04 3.99
487 493 1.677217 GGACAAGAGCATGTGGAGGTC 60.677 57.143 0.00 0.00 32.57 3.85
696 702 9.528489 ACTACCAGTTTTACAATTACATTCCAT 57.472 29.630 0.00 0.00 0.00 3.41
803 809 6.316390 GTCAAGGATTAGTTGGTATTGGTGAG 59.684 42.308 0.00 0.00 0.00 3.51
816 822 3.459969 GAGGGAATGGGTCAAGGATTAGT 59.540 47.826 0.00 0.00 0.00 2.24
874 880 3.470645 TCTGCTCTGGTCATCATGATG 57.529 47.619 26.79 26.79 40.09 3.07
892 898 4.956700 TCTGGTCTCCGTTTCATTAGATCT 59.043 41.667 0.00 0.00 0.00 2.75
942 948 3.439857 AAGCTTTGGTCTGCCAGATAA 57.560 42.857 0.00 0.00 46.91 1.75
953 959 1.425448 ACCAGAGGCTTAAGCTTTGGT 59.575 47.619 29.02 29.02 40.89 3.67
1020 1026 5.373854 AGGTATGGGAAATCTATTCCAGCTT 59.626 40.000 9.27 0.00 40.32 3.74
1048 1054 3.749609 AGTAGCACAATAACCAAACCGAC 59.250 43.478 0.00 0.00 0.00 4.79
1050 1056 3.119990 CCAGTAGCACAATAACCAAACCG 60.120 47.826 0.00 0.00 0.00 4.44
1058 1064 4.323485 CCAAGGAGACCAGTAGCACAATAA 60.323 45.833 0.00 0.00 0.00 1.40
1191 1197 3.010027 TGATCCCTTTCCATGTGCAGTAA 59.990 43.478 0.00 0.00 0.00 2.24
1193 1199 1.355381 TGATCCCTTTCCATGTGCAGT 59.645 47.619 0.00 0.00 0.00 4.40
1311 1317 2.029073 CGCGACAGGTTGAGGTGT 59.971 61.111 0.00 0.00 0.00 4.16
1894 1902 0.609957 TGGTCCAAATGCAGCTCCTG 60.610 55.000 0.00 0.00 34.12 3.86
2205 2214 7.877612 TGTTCTTGTGATATTTGTAAGAGAGCA 59.122 33.333 0.00 0.00 0.00 4.26
2299 2308 0.179702 GCTGTCATCCTCTGGCATGA 59.820 55.000 0.00 0.00 39.17 3.07
2386 2395 2.029838 AGCGAGCTTTGATAACCAGG 57.970 50.000 0.00 0.00 0.00 4.45
2435 2444 5.817816 GTCAGGTATTGATCCAGTTAGTTGG 59.182 44.000 0.00 0.00 38.29 3.77
2528 2537 2.225467 GGCATCTCCATTAAGGCACTC 58.775 52.381 0.00 0.00 37.29 3.51
2721 2730 4.404507 TTGAGCTTAAATTGAGTGCGAC 57.595 40.909 0.00 0.00 0.00 5.19
2849 2858 8.210946 TCAAACTCAGAAAGGAAGTTCAGATTA 58.789 33.333 5.01 0.00 0.00 1.75
2918 2927 1.502190 GGAAACGTGCTAAGCTGCC 59.498 57.895 0.00 0.00 0.00 4.85
3014 3023 6.059484 TGTTTTCTGTAGGAAACGGAGATTT 58.941 36.000 10.36 0.00 44.36 2.17
3022 3031 6.920569 TCTGAACTGTTTTCTGTAGGAAAC 57.079 37.500 8.53 8.53 42.80 2.78


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

AutoCloner maintained by Alex Coulton.