Multiple sequence alignment - TraesCS3D01G370300

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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 TraesCS3D01G370300 chr3D 100.000 3203 0 0 1 3203 484095258 484092056 0.000000e+00 5915.0
1 TraesCS3D01G370300 chr3D 96.226 53 1 1 2163 2215 484093054 484093003 5.690000e-13 86.1
2 TraesCS3D01G370300 chr3D 96.226 53 1 1 2205 2256 484093096 484093044 5.690000e-13 86.1
3 TraesCS3D01G370300 chr3B 96.052 2229 62 10 1 2215 646708949 646706733 0.000000e+00 3605.0
4 TraesCS3D01G370300 chr3B 95.726 1006 36 4 2205 3203 646706784 646705779 0.000000e+00 1613.0
5 TraesCS3D01G370300 chr3A 94.930 2229 73 11 1 2215 626669395 626667193 0.000000e+00 3454.0
6 TraesCS3D01G370300 chr3A 94.831 1006 43 5 2205 3203 626667244 626666241 0.000000e+00 1561.0
7 TraesCS3D01G370300 chr7A 80.857 700 121 10 1480 2172 127903398 127904091 3.640000e-149 538.0
8 TraesCS3D01G370300 chr7B 79.710 690 124 14 1483 2162 88870345 88871028 4.800000e-133 484.0
9 TraesCS3D01G370300 chr7B 86.111 72 9 1 2868 2938 13309074 13309145 3.430000e-10 76.8
10 TraesCS3D01G370300 chr7B 86.111 72 9 1 2868 2938 16155934 16155863 3.430000e-10 76.8
11 TraesCS3D01G370300 chr7D 82.595 316 47 7 2889 3200 561516700 561517011 4.070000e-69 272.0
12 TraesCS3D01G370300 chr4A 82.906 117 14 4 2965 3079 732843665 732843777 2.030000e-17 100.0


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 TraesCS3D01G370300 chr3D 484092056 484095258 3202 True 2029.066667 5915 97.4840 1 3203 3 chr3D.!!$R1 3202
1 TraesCS3D01G370300 chr3B 646705779 646708949 3170 True 2609.000000 3605 95.8890 1 3203 2 chr3B.!!$R1 3202
2 TraesCS3D01G370300 chr3A 626666241 626669395 3154 True 2507.500000 3454 94.8805 1 3203 2 chr3A.!!$R1 3202
3 TraesCS3D01G370300 chr7A 127903398 127904091 693 False 538.000000 538 80.8570 1480 2172 1 chr7A.!!$F1 692
4 TraesCS3D01G370300 chr7B 88870345 88871028 683 False 484.000000 484 79.7100 1483 2162 1 chr7B.!!$F2 679

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
590 606 0.674895 GATCCAACCAGCTCGCTGTT 60.675 55.0 16.82 8.96 42.15 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2505 2538 0.250553 AAACGGCGATTGTCAAGGGA 60.251 50.0 16.62 0.0 0.0 4.2 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
28 29 9.709495 AACATTGCAAGTTGTATAATCACAAAT 57.291 25.926 4.94 0.00 39.98 2.32
118 131 4.314522 TCTTTTCTGACCCATGCCATTA 57.685 40.909 0.00 0.00 0.00 1.90
120 133 5.271598 TCTTTTCTGACCCATGCCATTATT 58.728 37.500 0.00 0.00 0.00 1.40
121 134 6.430864 TCTTTTCTGACCCATGCCATTATTA 58.569 36.000 0.00 0.00 0.00 0.98
122 135 7.068702 TCTTTTCTGACCCATGCCATTATTAT 58.931 34.615 0.00 0.00 0.00 1.28
123 136 7.564660 TCTTTTCTGACCCATGCCATTATTATT 59.435 33.333 0.00 0.00 0.00 1.40
124 137 8.774546 TTTTCTGACCCATGCCATTATTATTA 57.225 30.769 0.00 0.00 0.00 0.98
125 138 8.954834 TTTCTGACCCATGCCATTATTATTAT 57.045 30.769 0.00 0.00 0.00 1.28
126 139 8.954834 TTCTGACCCATGCCATTATTATTATT 57.045 30.769 0.00 0.00 0.00 1.40
438 452 1.154413 GCAATGGCGAGTTCACGTG 60.154 57.895 9.94 9.94 35.59 4.49
487 502 3.940209 TTTTCTTGATGCGGCAGATTT 57.060 38.095 9.25 0.00 0.00 2.17
500 515 7.575332 TGCGGCAGATTTTTAGTTTTTAATC 57.425 32.000 0.00 0.00 0.00 1.75
503 518 7.117092 GCGGCAGATTTTTAGTTTTTAATCCAA 59.883 33.333 0.00 0.00 0.00 3.53
589 605 1.078848 GATCCAACCAGCTCGCTGT 60.079 57.895 16.82 3.60 42.15 4.40
590 606 0.674895 GATCCAACCAGCTCGCTGTT 60.675 55.000 16.82 8.96 42.15 3.16
728 744 2.815647 CGCTTGCGAGTTCCTCCC 60.816 66.667 9.60 0.00 0.00 4.30
749 765 3.548587 CAGCGAATGTTTCTGTTCACTG 58.451 45.455 0.00 0.00 30.91 3.66
863 879 7.693132 AGATATCAGCTAAATTAATGCTCCCA 58.307 34.615 5.32 0.00 34.51 4.37
975 991 9.457110 CTACAGTATGCTCTAATTGAGTACTTG 57.543 37.037 0.00 0.00 44.41 3.16
998 1014 1.813786 AGACTCTGTACTCTTCGGTGC 59.186 52.381 0.00 0.00 0.00 5.01
1008 1024 0.107643 TCTTCGGTGCCATGTCAACA 59.892 50.000 0.00 0.00 0.00 3.33
1134 1150 4.181578 CTGGATGGACGGTAAGTTAGTTG 58.818 47.826 0.00 0.00 0.00 3.16
1149 1165 6.458232 AGTTAGTTGCTCGATGATTACTCT 57.542 37.500 0.00 0.00 0.00 3.24
1585 1602 1.202143 GCCAGTACAAAATGCGCCTAC 60.202 52.381 4.18 0.00 0.00 3.18
1683 1700 4.701956 AACCCGATGAAAGCACTAAATG 57.298 40.909 0.00 0.00 0.00 2.32
2038 2062 1.602311 GCCTGGGATACATTCTGCAG 58.398 55.000 7.63 7.63 39.74 4.41
2039 2063 1.133976 GCCTGGGATACATTCTGCAGT 60.134 52.381 14.67 0.00 39.74 4.40
2203 2229 4.422984 ACCTGGTGGTTGTACTATGTAGT 58.577 43.478 0.00 0.00 46.05 2.73
2204 2230 5.582953 ACCTGGTGGTTGTACTATGTAGTA 58.417 41.667 0.00 0.00 46.05 1.82
2205 2231 6.018469 ACCTGGTGGTTGTACTATGTAGTAA 58.982 40.000 0.00 0.00 46.05 2.24
2206 2232 6.497954 ACCTGGTGGTTGTACTATGTAGTAAA 59.502 38.462 0.00 0.00 46.05 2.01
2207 2233 7.181485 ACCTGGTGGTTGTACTATGTAGTAAAT 59.819 37.037 0.00 0.00 46.05 1.40
2208 2234 7.494625 CCTGGTGGTTGTACTATGTAGTAAATG 59.505 40.741 1.67 0.00 40.20 2.32
2209 2235 7.909518 TGGTGGTTGTACTATGTAGTAAATGT 58.090 34.615 1.67 0.00 40.20 2.71
2210 2236 8.377034 TGGTGGTTGTACTATGTAGTAAATGTT 58.623 33.333 1.67 0.00 40.20 2.71
2211 2237 9.223099 GGTGGTTGTACTATGTAGTAAATGTTT 57.777 33.333 1.67 0.00 40.20 2.83
2223 2249 8.734218 TGTAGTAAATGTTTTATTATGGCGGA 57.266 30.769 0.00 0.00 0.00 5.54
2224 2250 8.614346 TGTAGTAAATGTTTTATTATGGCGGAC 58.386 33.333 0.00 0.00 0.00 4.79
2225 2251 7.034685 AGTAAATGTTTTATTATGGCGGACC 57.965 36.000 0.00 0.00 0.00 4.46
2226 2252 6.831868 AGTAAATGTTTTATTATGGCGGACCT 59.168 34.615 0.00 0.00 36.63 3.85
2227 2253 5.514274 AATGTTTTATTATGGCGGACCTG 57.486 39.130 0.00 0.00 36.63 4.00
2228 2254 3.283751 TGTTTTATTATGGCGGACCTGG 58.716 45.455 0.00 0.00 36.63 4.45
2229 2255 3.284617 GTTTTATTATGGCGGACCTGGT 58.715 45.455 0.00 0.00 36.63 4.00
2230 2256 2.631160 TTATTATGGCGGACCTGGTG 57.369 50.000 2.82 0.00 36.63 4.17
2231 2257 0.762418 TATTATGGCGGACCTGGTGG 59.238 55.000 2.82 0.00 36.63 4.61
2346 2372 5.435686 TTGTTATGGCTCTCCTTGTATGT 57.564 39.130 0.00 0.00 0.00 2.29
2452 2479 4.568152 TTTACAGCAAGCAAAAGACTCC 57.432 40.909 0.00 0.00 0.00 3.85
2454 2481 1.133668 ACAGCAAGCAAAAGACTCCCT 60.134 47.619 0.00 0.00 0.00 4.20
2492 2525 5.011125 TCGTTTCTCTTTCACCATTCTCTCT 59.989 40.000 0.00 0.00 0.00 3.10
2505 2538 5.840693 ACCATTCTCTCTCCCATTTTGTTTT 59.159 36.000 0.00 0.00 0.00 2.43
2510 2543 4.814967 TCTCTCCCATTTTGTTTTCCCTT 58.185 39.130 0.00 0.00 0.00 3.95
2574 2607 1.826096 TGATGGCATGTGGTTTCCATG 59.174 47.619 3.81 0.00 39.25 3.66
2678 2711 1.229951 TCACTGCCCCTCCTTCCAT 60.230 57.895 0.00 0.00 0.00 3.41
2797 2830 7.420002 TGAAAGATGCATGCACTACAATATTC 58.580 34.615 25.37 18.64 0.00 1.75
2936 2969 0.753867 TTGGACCTTCACACGCTACA 59.246 50.000 0.00 0.00 0.00 2.74
2996 3029 8.375506 ACCTCTGATCATGAAAACAAACTACTA 58.624 33.333 0.00 0.00 0.00 1.82
3120 3153 6.313905 AGTTATAATGCGACTCTGGTCAAAAG 59.686 38.462 0.00 0.00 42.21 2.27
3134 3167 8.402798 TCTGGTCAAAAGAAACAAGCATAATA 57.597 30.769 0.00 0.00 0.00 0.98
3156 3189 1.972588 AGGGGGAAACTGCATCTAGT 58.027 50.000 0.00 0.00 0.00 2.57
3159 3192 2.026262 GGGGGAAACTGCATCTAGTTCA 60.026 50.000 0.00 0.00 39.86 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 249 4.956700 TCCAACAAAAGTTACCATGTTCCA 59.043 37.500 0.00 0.00 33.97 3.53
396 410 7.332430 TGCTTCATAAAAAGATGATGGCAAAAG 59.668 33.333 0.00 0.00 39.61 2.27
659 675 0.113190 CAGGCCTCCTTCCCAAAAGT 59.887 55.000 0.00 0.00 0.00 2.66
728 744 3.885484 AGTGAACAGAAACATTCGCTG 57.115 42.857 0.00 0.00 42.57 5.18
846 862 8.667076 AATCAAATTGGGAGCATTAATTTAGC 57.333 30.769 0.00 0.00 33.59 3.09
975 991 3.075884 ACCGAAGAGTACAGAGTCTGTC 58.924 50.000 28.70 19.12 41.21 3.51
998 1014 5.049886 CCATAGACATCGAATGTTGACATGG 60.050 44.000 0.00 3.68 45.03 3.66
1008 1024 9.342308 ACATTTTTCATACCATAGACATCGAAT 57.658 29.630 0.00 0.00 0.00 3.34
1134 1150 5.802956 GGTTATGCTAGAGTAATCATCGAGC 59.197 44.000 0.00 1.71 43.31 5.03
1149 1165 6.209192 CCATGCATTCCAAATAGGTTATGCTA 59.791 38.462 17.74 9.75 46.79 3.49
1532 1549 3.605461 CGCATTTCAAGTCATAGCATCCG 60.605 47.826 0.00 0.00 0.00 4.18
1585 1602 2.025793 TCTAGAGTGTCTCCTGGAGTGG 60.026 54.545 22.50 5.29 0.00 4.00
1690 1707 7.993758 ACCTCCTTAGATAAAAATTCTAGTGGC 59.006 37.037 0.00 0.00 0.00 5.01
1977 2001 1.473434 GGACTAGCACTCCCGGAATTG 60.473 57.143 0.73 0.00 0.00 2.32
2038 2062 7.572759 TCAACAAATCTAACATCTCGAACAAC 58.427 34.615 0.00 0.00 0.00 3.32
2039 2063 7.722795 TCAACAAATCTAACATCTCGAACAA 57.277 32.000 0.00 0.00 0.00 2.83
2172 2198 2.994699 CCACCAGGTCCGCCATAA 59.005 61.111 0.00 0.00 37.19 1.90
2200 2226 7.994334 AGGTCCGCCATAATAAAACATTTACTA 59.006 33.333 0.00 0.00 37.19 1.82
2201 2227 6.831868 AGGTCCGCCATAATAAAACATTTACT 59.168 34.615 0.00 0.00 37.19 2.24
2202 2228 6.915843 CAGGTCCGCCATAATAAAACATTTAC 59.084 38.462 0.00 0.00 37.19 2.01
2203 2229 6.039941 CCAGGTCCGCCATAATAAAACATTTA 59.960 38.462 0.00 0.00 37.19 1.40
2204 2230 5.163457 CCAGGTCCGCCATAATAAAACATTT 60.163 40.000 0.00 0.00 37.19 2.32
2205 2231 4.340950 CCAGGTCCGCCATAATAAAACATT 59.659 41.667 0.00 0.00 37.19 2.71
2206 2232 3.888930 CCAGGTCCGCCATAATAAAACAT 59.111 43.478 0.00 0.00 37.19 2.71
2207 2233 3.283751 CCAGGTCCGCCATAATAAAACA 58.716 45.455 0.00 0.00 37.19 2.83
2208 2234 3.066203 CACCAGGTCCGCCATAATAAAAC 59.934 47.826 0.00 0.00 37.19 2.43
2209 2235 3.283751 CACCAGGTCCGCCATAATAAAA 58.716 45.455 0.00 0.00 37.19 1.52
2210 2236 2.422235 CCACCAGGTCCGCCATAATAAA 60.422 50.000 0.00 0.00 37.19 1.40
2211 2237 1.142060 CCACCAGGTCCGCCATAATAA 59.858 52.381 0.00 0.00 37.19 1.40
2212 2238 0.762418 CCACCAGGTCCGCCATAATA 59.238 55.000 0.00 0.00 37.19 0.98
2213 2239 1.531748 CCACCAGGTCCGCCATAAT 59.468 57.895 0.00 0.00 37.19 1.28
2214 2240 2.994699 CCACCAGGTCCGCCATAA 59.005 61.111 0.00 0.00 37.19 1.90
2221 2247 6.567432 ACTACATAGTACAACCACCAGGTCC 61.567 48.000 0.00 0.00 40.41 4.46
2222 2248 4.465305 ACTACATAGTACAACCACCAGGTC 59.535 45.833 0.00 0.00 40.41 3.85
2223 2249 4.422984 ACTACATAGTACAACCACCAGGT 58.577 43.478 0.00 0.00 42.14 4.00
2224 2250 6.534475 TTACTACATAGTACAACCACCAGG 57.466 41.667 0.00 0.00 38.43 4.45
2225 2251 6.534079 GCTTTACTACATAGTACAACCACCAG 59.466 42.308 0.00 0.00 38.43 4.00
2226 2252 6.211986 AGCTTTACTACATAGTACAACCACCA 59.788 38.462 0.00 0.00 38.43 4.17
2227 2253 6.637657 AGCTTTACTACATAGTACAACCACC 58.362 40.000 0.00 0.00 38.43 4.61
2228 2254 8.543862 AAAGCTTTACTACATAGTACAACCAC 57.456 34.615 10.72 0.00 38.43 4.16
2370 2396 5.006386 CCTTAGGTGGATGATTCTATTGCC 58.994 45.833 0.00 0.00 0.00 4.52
2407 2433 2.515290 CCATGGCAGCGCATGAGA 60.515 61.111 19.81 0.00 0.00 3.27
2411 2437 1.324740 AAATCACCATGGCAGCGCAT 61.325 50.000 13.04 0.00 0.00 4.73
2449 2476 2.029828 CGACGATTATTGAGGGAGGGAG 60.030 54.545 0.00 0.00 0.00 4.30
2450 2477 1.961394 CGACGATTATTGAGGGAGGGA 59.039 52.381 0.00 0.00 0.00 4.20
2451 2478 1.687123 ACGACGATTATTGAGGGAGGG 59.313 52.381 0.00 0.00 0.00 4.30
2452 2479 3.454371 AACGACGATTATTGAGGGAGG 57.546 47.619 0.00 0.00 0.00 4.30
2454 2481 4.401519 AGAGAAACGACGATTATTGAGGGA 59.598 41.667 0.00 0.00 0.00 4.20
2492 2525 4.033709 TGTCAAGGGAAAACAAAATGGGA 58.966 39.130 0.00 0.00 0.00 4.37
2505 2538 0.250553 AAACGGCGATTGTCAAGGGA 60.251 50.000 16.62 0.00 0.00 4.20
2510 2543 0.787787 CGAAGAAACGGCGATTGTCA 59.212 50.000 16.62 0.00 0.00 3.58
2574 2607 7.907214 TTGGAGAGAGAATTAGTTTGTAAGC 57.093 36.000 0.00 0.00 0.00 3.09
2678 2711 4.039245 ACAAGATCGAGAGTGAAGGTGAAA 59.961 41.667 0.00 0.00 0.00 2.69
2797 2830 3.120442 GGGTCGAAAAATAAGGTGACACG 60.120 47.826 0.00 0.00 0.00 4.49
2936 2969 0.763223 GGACGTGGGGAGTGGGATAT 60.763 60.000 0.00 0.00 0.00 1.63
3120 3153 5.445964 TCCCCCTTCTATTATGCTTGTTTC 58.554 41.667 0.00 0.00 0.00 2.78
3134 3167 1.376649 AGATGCAGTTTCCCCCTTCT 58.623 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.