Multiple sequence alignment - TraesCS1D01G202900

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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 TraesCS1D01G202900 chr1D 100.000 4337 0 0 1 4337 286386215 286390551 0.000000e+00 8010.0
1 TraesCS1D01G202900 chr1D 98.993 4071 33 3 273 4337 400972652 400968584 0.000000e+00 7284.0
2 TraesCS1D01G202900 chr1D 94.684 1204 57 3 2633 3835 328859967 328858770 0.000000e+00 1862.0
3 TraesCS1D01G202900 chr1D 98.606 287 3 1 1 287 400972955 400972670 1.390000e-139 507.0
4 TraesCS1D01G202900 chr1D 87.129 101 11 2 2078 2178 298927504 298927602 3.540000e-21 113.0
5 TraesCS1D01G202900 chr6D 90.112 1163 55 24 588 1726 79602539 79603665 0.000000e+00 1456.0
6 TraesCS1D01G202900 chr6D 86.885 183 18 5 3888 4066 429780302 429780122 2.650000e-47 200.0
7 TraesCS1D01G202900 chr6D 95.556 90 4 0 1715 1804 79610718 79610807 1.260000e-30 145.0
8 TraesCS1D01G202900 chr6D 88.119 101 10 2 2078 2178 434785377 434785475 7.620000e-23 119.0
9 TraesCS1D01G202900 chr1B 93.314 703 33 7 2633 3335 589512787 589513475 0.000000e+00 1026.0
10 TraesCS1D01G202900 chr7D 97.461 512 5 3 3832 4337 188349916 188350425 0.000000e+00 867.0
11 TraesCS1D01G202900 chr7D 83.855 415 50 5 2218 2631 189911956 189911558 3.170000e-101 379.0
12 TraesCS1D01G202900 chr7D 82.938 422 58 3 2218 2639 579794764 579794357 6.850000e-98 368.0
13 TraesCS1D01G202900 chr7D 87.097 279 33 1 2362 2640 399013177 399013452 3.260000e-81 313.0
14 TraesCS1D01G202900 chr7D 86.139 101 12 2 2078 2178 400419507 400419409 1.650000e-19 108.0
15 TraesCS1D01G202900 chr2D 83.614 415 56 6 2218 2631 429080453 429080856 3.170000e-101 379.0
16 TraesCS1D01G202900 chr2D 87.556 225 25 3 1203 1426 543165168 543165390 1.550000e-64 257.0
17 TraesCS1D01G202900 chr2D 87.624 202 19 3 3046 3246 42695497 42695693 3.370000e-56 230.0
18 TraesCS1D01G202900 chr2D 89.109 101 9 1 2078 2178 389696454 389696356 1.640000e-24 124.0
19 TraesCS1D01G202900 chr2D 88.119 101 10 2 2078 2178 22813992 22813894 7.620000e-23 119.0
20 TraesCS1D01G202900 chr4D 83.920 398 50 3 2234 2631 7875879 7875496 6.850000e-98 368.0
21 TraesCS1D01G202900 chr1A 89.286 252 24 3 2633 2882 592765184 592765434 3.260000e-81 313.0
22 TraesCS1D01G202900 chr1A 89.189 222 22 2 1206 1426 513426089 513425869 4.270000e-70 276.0
23 TraesCS1D01G202900 chr5A 85.430 302 38 3 2336 2637 614928140 614927845 4.210000e-80 309.0
24 TraesCS1D01G202900 chr5A 85.430 302 38 3 2336 2637 614962055 614961760 4.210000e-80 309.0
25 TraesCS1D01G202900 chr5A 85.149 303 37 3 2336 2634 614795024 614794726 1.960000e-78 303.0
26 TraesCS1D01G202900 chr5A 85.477 241 33 2 1187 1426 545636335 545636574 2.590000e-62 250.0
27 TraesCS1D01G202900 chr5A 86.667 180 23 1 3907 4085 669627481 669627302 9.510000e-47 198.0
28 TraesCS1D01G202900 chr3A 88.845 251 26 2 2633 2882 658733537 658733288 1.520000e-79 307.0
29 TraesCS1D01G202900 chr3A 85.256 156 22 1 3247 3401 644667358 644667203 4.490000e-35 159.0
30 TraesCS1D01G202900 chr3A 84.146 164 20 3 3246 3403 644623285 644623122 2.090000e-33 154.0
31 TraesCS1D01G202900 chr3A 100.000 29 0 0 4253 4281 144473376 144473404 2.000000e-03 54.7
32 TraesCS1D01G202900 chr2A 88.492 252 22 4 2633 2882 777401734 777401980 9.120000e-77 298.0
33 TraesCS1D01G202900 chr5B 88.085 235 27 1 1193 1426 519150360 519150594 1.190000e-70 278.0
34 TraesCS1D01G202900 chr5B 81.707 328 49 5 835 1159 311077199 311077518 3.330000e-66 263.0
35 TraesCS1D01G202900 chr3D 82.019 317 46 8 3247 3553 505779486 505779171 4.300000e-65 259.0
36 TraesCS1D01G202900 chr3D 86.099 223 27 4 1206 1426 455711818 455711598 2.020000e-58 237.0
37 TraesCS1D01G202900 chr3D 85.586 222 30 2 1206 1426 455701900 455701680 9.380000e-57 231.0
38 TraesCS1D01G202900 chr3D 83.333 168 22 5 3247 3408 505795195 505795028 2.700000e-32 150.0
39 TraesCS1D01G202900 chr3D 83.333 162 15 8 3255 3405 505999062 505998902 5.850000e-29 139.0
40 TraesCS1D01G202900 chr5D 85.950 242 33 1 1186 1426 429908116 429908357 1.550000e-64 257.0
41 TraesCS1D01G202900 chr4B 89.189 185 19 1 3902 4085 666605059 666605243 3.370000e-56 230.0
42 TraesCS1D01G202900 chr6B 88.649 185 20 1 3902 4085 92433650 92433834 1.570000e-54 224.0
43 TraesCS1D01G202900 chr7B 88.889 180 19 1 3907 4085 634288583 634288762 2.030000e-53 220.0
44 TraesCS1D01G202900 chr6A 87.778 180 21 1 3907 4085 572982320 572982141 4.390000e-50 209.0
45 TraesCS1D01G202900 chr6A 87.222 180 22 1 3907 4085 562709264 562709085 2.040000e-48 204.0
46 TraesCS1D01G202900 chr7A 82.800 250 25 9 2633 2882 39494154 39494385 1.580000e-49 207.0
47 TraesCS1D01G202900 chr3B 83.832 167 18 5 3247 3405 667709193 667709028 2.700000e-32 150.0
48 TraesCS1D01G202900 chr3B 83.871 155 19 1 3247 3395 667681142 667680988 4.520000e-30 143.0


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 TraesCS1D01G202900 chr1D 286386215 286390551 4336 False 8010.0 8010 100.0000 1 4337 1 chr1D.!!$F1 4336
1 TraesCS1D01G202900 chr1D 400968584 400972955 4371 True 3895.5 7284 98.7995 1 4337 2 chr1D.!!$R2 4336
2 TraesCS1D01G202900 chr1D 328858770 328859967 1197 True 1862.0 1862 94.6840 2633 3835 1 chr1D.!!$R1 1202
3 TraesCS1D01G202900 chr6D 79602539 79603665 1126 False 1456.0 1456 90.1120 588 1726 1 chr6D.!!$F1 1138
4 TraesCS1D01G202900 chr1B 589512787 589513475 688 False 1026.0 1026 93.3140 2633 3335 1 chr1B.!!$F1 702
5 TraesCS1D01G202900 chr7D 188349916 188350425 509 False 867.0 867 97.4610 3832 4337 1 chr7D.!!$F1 505

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
72 73 0.759346 AATCGCTGGTAGGTCATCCC 59.241 55.000 0.00 0.0 0.00 3.85 F
506 539 1.262417 GCTATCTAGGGAGGTGGCTC 58.738 60.000 0.00 0.0 37.32 4.70 F
1384 1422 3.310774 CAGGTGCTGACAATCTAATTCCG 59.689 47.826 0.00 0.0 32.44 4.30 F
2229 2285 4.635765 AGCGCTGATTGTTTGTATGTGTAT 59.364 37.500 10.39 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1807 4.034394 GCAAGAAGCAATGTCACGATATCA 59.966 41.667 3.12 0.0 44.79 2.15 R
2276 2332 0.108396 TAGTGCAACAAGAGGCAGCA 59.892 50.000 0.00 0.0 41.35 4.41 R
2319 2375 3.380637 GGTCGACTACTCTGCCTTTGATA 59.619 47.826 16.46 0.0 0.00 2.15 R
4145 4214 1.665679 CATACGTCACCACCATGAAGC 59.334 52.381 0.00 0.0 32.00 3.86 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
72 73 0.759346 AATCGCTGGTAGGTCATCCC 59.241 55.000 0.00 0.00 0.00 3.85
83 84 2.682136 TCATCCCTCGCACCGGAA 60.682 61.111 9.46 0.00 0.00 4.30
284 317 2.486918 CTATTGTCGATGAGCATGGCA 58.513 47.619 0.00 0.00 0.00 4.92
331 364 1.487976 GACATCCAGGCAGATGAAGGA 59.512 52.381 20.35 1.86 45.43 3.36
354 387 1.884464 CGGCATGGATCTGGTGACG 60.884 63.158 6.43 6.43 38.10 4.35
506 539 1.262417 GCTATCTAGGGAGGTGGCTC 58.738 60.000 0.00 0.00 37.32 4.70
1384 1422 3.310774 CAGGTGCTGACAATCTAATTCCG 59.689 47.826 0.00 0.00 32.44 4.30
1751 1807 7.875327 AGGTTTAGTGTACAATGTTTCTTGT 57.125 32.000 5.98 0.00 41.95 3.16
2229 2285 4.635765 AGCGCTGATTGTTTGTATGTGTAT 59.364 37.500 10.39 0.00 0.00 2.29
2271 2327 7.188468 ACCGAACGTCTAGAACTATCTAATC 57.812 40.000 0.00 0.00 37.70 1.75
2274 2330 8.434661 CCGAACGTCTAGAACTATCTAATCTAC 58.565 40.741 0.00 0.00 37.70 2.59
2517 2573 6.967199 GGTTTTAGATATGCTGCAGTTTGTAC 59.033 38.462 16.64 3.40 0.00 2.90
2630 2686 1.438651 TACTAAGCAGCCAAACGCAG 58.561 50.000 0.00 0.00 41.38 5.18
3216 3278 2.415512 GGTTTGCTACTGAGTTTAGCGG 59.584 50.000 3.21 0.00 44.27 5.52
3217 3279 3.064931 GTTTGCTACTGAGTTTAGCGGT 58.935 45.455 3.21 0.00 44.27 5.68
3233 3295 2.565834 AGCGGTTAACTCTCCTGCTTTA 59.434 45.455 5.42 0.00 32.86 1.85
3697 3760 6.531240 CACCAAACAATATGCATCCAAGTTAC 59.469 38.462 0.19 0.00 0.00 2.50
3699 3762 7.039082 ACCAAACAATATGCATCCAAGTTACTT 60.039 33.333 0.19 0.00 0.00 2.24
3777 3840 5.920193 TTTTGATCATTCATGTTCCCTCC 57.080 39.130 0.00 0.00 0.00 4.30
4118 4181 1.748122 GTGCCTGAGGTCATGGCTG 60.748 63.158 16.47 0.00 46.23 4.85
4145 4214 2.932614 CAGGAACCTCTTATTGAGCGTG 59.067 50.000 0.00 0.00 41.35 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 1.726853 AAAAGATCTTCCGGTGCGAG 58.273 50.000 8.78 0.00 0.00 5.03
331 364 2.191375 CAGATCCATGCCGCCACT 59.809 61.111 0.00 0.00 0.00 4.00
354 387 1.374758 CTCAAGCTCCGACACCACC 60.375 63.158 0.00 0.00 0.00 4.61
498 531 2.039624 ATCTGGTCCGAGCCACCT 59.960 61.111 0.00 0.00 34.66 4.00
506 539 1.068083 CCATGGTCGATCTGGTCCG 59.932 63.158 2.57 0.00 0.00 4.79
1384 1422 5.420739 TGTAATTTTAAGGGCCAGTTCCATC 59.579 40.000 6.18 0.00 0.00 3.51
1751 1807 4.034394 GCAAGAAGCAATGTCACGATATCA 59.966 41.667 3.12 0.00 44.79 2.15
2229 2285 1.961394 GGTCCTATCGGATAGTGCACA 59.039 52.381 21.04 5.47 42.43 4.57
2271 2327 1.131883 GCAACAAGAGGCAGCATGTAG 59.868 52.381 0.00 0.00 39.31 2.74
2274 2330 0.388134 GTGCAACAAGAGGCAGCATG 60.388 55.000 0.00 0.00 41.35 4.06
2276 2332 0.108396 TAGTGCAACAAGAGGCAGCA 59.892 50.000 0.00 0.00 41.35 4.41
2319 2375 3.380637 GGTCGACTACTCTGCCTTTGATA 59.619 47.826 16.46 0.00 0.00 2.15
2517 2573 6.236017 TGGCTTCGACAAATACTTTAGTTG 57.764 37.500 0.00 0.00 39.45 3.16
2583 2639 6.636454 TGGAGTTTTAGGAGAATACCATGT 57.364 37.500 0.00 0.00 0.00 3.21
2593 2649 9.010029 TGCTTAGTATTTTTGGAGTTTTAGGAG 57.990 33.333 0.00 0.00 0.00 3.69
2630 2686 8.884726 GTCCTATGGAATTCAGAAAACTAAGAC 58.115 37.037 7.93 0.00 31.38 3.01
2631 2687 7.764443 CGTCCTATGGAATTCAGAAAACTAAGA 59.236 37.037 7.93 0.00 31.38 2.10
3216 3278 5.148651 TGGAGTAAAGCAGGAGAGTTAAC 57.851 43.478 0.00 0.00 0.00 2.01
3217 3279 5.818678 TTGGAGTAAAGCAGGAGAGTTAA 57.181 39.130 0.00 0.00 0.00 2.01
3233 3295 3.775316 CCTGTAGAGGTAACCATTGGAGT 59.225 47.826 10.37 0.00 34.16 3.85
3697 3760 9.142014 TGGTTACATAATTCCCCATTATTGAAG 57.858 33.333 0.00 0.00 36.10 3.02
3699 3762 8.285891 ACTGGTTACATAATTCCCCATTATTGA 58.714 33.333 0.00 0.00 36.10 2.57
3777 3840 8.728088 AAAGTGTTGTTAATAAGCAAGATTCG 57.272 30.769 0.00 0.00 0.00 3.34
4118 4181 5.407407 TCAATAAGAGGTTCCTGACTCAC 57.593 43.478 0.00 0.00 36.20 3.51
4145 4214 1.665679 CATACGTCACCACCATGAAGC 59.334 52.381 0.00 0.00 32.00 3.86


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

AutoCloner maintained by Alex Coulton.