Multiple sequence alignment - TraesCS1A01G413100

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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 TraesCS1A01G413100 chr1A 100.000 3144 0 0 1 3144 573205138 573208281 0.000000e+00 5806.0
1 TraesCS1A01G413100 chr1D 95.777 2131 65 16 180 2298 477164878 477166995 0.000000e+00 3413.0
2 TraesCS1A01G413100 chr1D 96.257 855 27 2 2295 3144 477167075 477167929 0.000000e+00 1397.0
3 TraesCS1A01G413100 chr1D 89.943 1054 101 4 1102 2153 416356355 416355305 0.000000e+00 1354.0
4 TraesCS1A01G413100 chr1D 99.422 173 1 0 1 173 477164550 477164722 6.550000e-82 315.0
5 TraesCS1A01G413100 chr1B 95.707 1887 59 15 1263 3144 664761899 664763768 0.000000e+00 3016.0
6 TraesCS1A01G413100 chr1B 92.547 805 38 11 306 1102 664761071 664761861 0.000000e+00 1134.0
7 TraesCS1A01G413100 chr6B 88.889 1035 113 2 1105 2139 52683064 52682032 0.000000e+00 1273.0
8 TraesCS1A01G413100 chr6B 79.778 1172 214 11 991 2145 52568252 52567087 0.000000e+00 830.0
9 TraesCS1A01G413100 chr6B 79.694 1177 212 15 988 2145 16428994 16430162 0.000000e+00 824.0
10 TraesCS1A01G413100 chr6B 77.026 1419 275 40 1102 2492 15225613 15224218 0.000000e+00 767.0
11 TraesCS1A01G413100 chr6B 78.063 1053 224 7 1105 2154 53062388 53061340 0.000000e+00 658.0
12 TraesCS1A01G413100 chr6B 92.283 311 21 1 2191 2498 55723277 55722967 3.720000e-119 438.0
13 TraesCS1A01G413100 chr6B 92.754 138 10 0 2593 2730 55722606 55722469 1.910000e-47 200.0
14 TraesCS1A01G413100 chr6B 88.393 112 7 4 2540 2650 15383667 15383561 2.540000e-26 130.0
15 TraesCS1A01G413100 chr6D 80.110 1448 239 26 1102 2526 8858304 8859725 0.000000e+00 1033.0
16 TraesCS1A01G413100 chr6D 79.531 1451 235 35 1102 2529 8480334 8478923 0.000000e+00 977.0
17 TraesCS1A01G413100 chr6D 82.578 993 161 11 1157 2144 34017623 34018608 0.000000e+00 865.0
18 TraesCS1A01G413100 chr6D 79.900 1199 222 16 956 2145 8899484 8900672 0.000000e+00 861.0
19 TraesCS1A01G413100 chr6D 80.636 346 50 10 2763 3100 8571407 8571071 5.210000e-63 252.0
20 TraesCS1A01G413100 chr6D 87.111 225 23 5 2527 2749 8571674 8571454 1.870000e-62 250.0
21 TraesCS1A01G413100 chr6D 87.500 224 18 7 2527 2746 8859886 8860103 1.870000e-62 250.0
22 TraesCS1A01G413100 chr6D 87.054 224 19 7 2527 2746 8478766 8478549 8.710000e-61 244.0
23 TraesCS1A01G413100 chr6D 86.222 225 25 4 2527 2746 34003041 34003264 4.050000e-59 239.0
24 TraesCS1A01G413100 chr6D 88.525 183 9 6 1 171 8921721 8921903 8.830000e-51 211.0
25 TraesCS1A01G413100 chr6D 87.356 174 14 2 2261 2433 8572072 8571906 3.200000e-45 193.0
26 TraesCS1A01G413100 chr6D 86.395 147 12 5 2869 3012 8860227 8860368 1.510000e-33 154.0
27 TraesCS1A01G413100 chr6D 89.720 107 10 1 180 285 33884132 33884238 5.470000e-28 135.0
28 TraesCS1A01G413100 chr6D 92.857 56 3 1 103 158 8574597 8574543 2.600000e-11 80.5
29 TraesCS1A01G413100 chr6D 93.333 45 3 0 3100 3144 8478197 8478153 2.020000e-07 67.6
30 TraesCS1A01G413100 chr6D 93.333 45 3 0 3100 3144 34003705 34003749 2.020000e-07 67.6
31 TraesCS1A01G413100 chr3D 79.019 1182 218 18 993 2152 33330499 33329326 0.000000e+00 782.0
32 TraesCS1A01G413100 chr3D 79.558 181 34 3 452 630 606368537 606368358 3.290000e-25 126.0
33 TraesCS1A01G413100 chrUn 84.615 416 46 6 1941 2345 477783064 477782656 6.320000e-107 398.0
34 TraesCS1A01G413100 chr2B 90.045 221 20 2 438 658 89506047 89506265 5.130000e-73 285.0
35 TraesCS1A01G413100 chr6A 93.333 165 11 0 2980 3144 9501609 9501773 8.710000e-61 244.0
36 TraesCS1A01G413100 chr3B 82.659 173 23 6 457 626 7238294 7238462 2.530000e-31 147.0
37 TraesCS1A01G413100 chr3B 78.286 175 35 3 454 627 815388142 815388314 3.320000e-20 110.0
38 TraesCS1A01G413100 chr5B 89.286 112 6 3 2540 2650 556788348 556788242 5.470000e-28 135.0
39 TraesCS1A01G413100 chr3A 80.124 161 28 4 470 627 737674271 737674430 1.980000e-22 117.0
40 TraesCS1A01G413100 chr4D 76.796 181 34 7 452 630 420511899 420511725 9.280000e-16 95.3
41 TraesCS1A01G413100 chr4B 75.706 177 37 6 452 627 517750642 517750813 2.010000e-12 84.2


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 TraesCS1A01G413100 chr1A 573205138 573208281 3143 False 5806.000000 5806 100.000000 1 3144 1 chr1A.!!$F1 3143
1 TraesCS1A01G413100 chr1D 477164550 477167929 3379 False 1708.333333 3413 97.152000 1 3144 3 chr1D.!!$F1 3143
2 TraesCS1A01G413100 chr1D 416355305 416356355 1050 True 1354.000000 1354 89.943000 1102 2153 1 chr1D.!!$R1 1051
3 TraesCS1A01G413100 chr1B 664761071 664763768 2697 False 2075.000000 3016 94.127000 306 3144 2 chr1B.!!$F1 2838
4 TraesCS1A01G413100 chr6B 52682032 52683064 1032 True 1273.000000 1273 88.889000 1105 2139 1 chr6B.!!$R4 1034
5 TraesCS1A01G413100 chr6B 52567087 52568252 1165 True 830.000000 830 79.778000 991 2145 1 chr6B.!!$R3 1154
6 TraesCS1A01G413100 chr6B 16428994 16430162 1168 False 824.000000 824 79.694000 988 2145 1 chr6B.!!$F1 1157
7 TraesCS1A01G413100 chr6B 15224218 15225613 1395 True 767.000000 767 77.026000 1102 2492 1 chr6B.!!$R1 1390
8 TraesCS1A01G413100 chr6B 53061340 53062388 1048 True 658.000000 658 78.063000 1105 2154 1 chr6B.!!$R5 1049
9 TraesCS1A01G413100 chr6B 55722469 55723277 808 True 319.000000 438 92.518500 2191 2730 2 chr6B.!!$R6 539
10 TraesCS1A01G413100 chr6D 34017623 34018608 985 False 865.000000 865 82.578000 1157 2144 1 chr6D.!!$F4 987
11 TraesCS1A01G413100 chr6D 8899484 8900672 1188 False 861.000000 861 79.900000 956 2145 1 chr6D.!!$F1 1189
12 TraesCS1A01G413100 chr6D 8858304 8860368 2064 False 479.000000 1033 84.668333 1102 3012 3 chr6D.!!$F5 1910
13 TraesCS1A01G413100 chr6D 8478153 8480334 2181 True 429.533333 977 86.639333 1102 3144 3 chr6D.!!$R1 2042
14 TraesCS1A01G413100 chr3D 33329326 33330499 1173 True 782.000000 782 79.019000 993 2152 1 chr3D.!!$R1 1159

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
378 529 1.198759 ACGGGGCTGGCTTTTCTAGA 61.199 55.000 0.0 0.0 0.0 2.43 F
407 558 1.211457 GCTGAGGATGACAACAGGGAT 59.789 52.381 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1863 1.028330 CAGACACGGCATGCCTGAAT 61.028 55.0 33.07 16.53 0.00 2.57 R
2330 2606 1.878211 TGGACATGCCAGGTCTCATA 58.122 50.0 9.58 0.00 43.33 2.15 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
34 35 9.838339 CTAGGTGTGAAAATATCTTTATCAGGT 57.162 33.333 0.00 0.0 0.00 4.00
210 361 5.061179 GTCTGTGAAGCCCTTAGTTGTAAA 58.939 41.667 0.00 0.0 0.00 2.01
239 390 3.305608 GGCAGAGCAAAGCATTTTGTAGT 60.306 43.478 0.99 0.0 44.41 2.73
242 393 5.284079 CAGAGCAAAGCATTTTGTAGTTGT 58.716 37.500 0.99 0.0 44.41 3.32
283 434 8.948631 TGATTTACCTATGTGCTAAAGAAGAG 57.051 34.615 0.00 0.0 0.00 2.85
284 435 7.987458 TGATTTACCTATGTGCTAAAGAAGAGG 59.013 37.037 0.00 0.0 0.00 3.69
285 436 7.490657 TTTACCTATGTGCTAAAGAAGAGGA 57.509 36.000 0.00 0.0 0.00 3.71
286 437 5.606348 ACCTATGTGCTAAAGAAGAGGAG 57.394 43.478 0.00 0.0 0.00 3.69
287 438 5.273208 ACCTATGTGCTAAAGAAGAGGAGA 58.727 41.667 0.00 0.0 0.00 3.71
288 439 5.902431 ACCTATGTGCTAAAGAAGAGGAGAT 59.098 40.000 0.00 0.0 0.00 2.75
378 529 1.198759 ACGGGGCTGGCTTTTCTAGA 61.199 55.000 0.00 0.0 0.00 2.43
407 558 1.211457 GCTGAGGATGACAACAGGGAT 59.789 52.381 0.00 0.0 0.00 3.85
494 646 7.548075 CCTTGTACTCCACGTATAAGATTTGTT 59.452 37.037 9.30 0.0 45.11 2.83
909 1064 3.108289 CTCACACGCTGACGCTGG 61.108 66.667 0.00 0.0 45.53 4.85
922 1077 4.329545 GCTGGTGGGCTCGTGGAA 62.330 66.667 0.00 0.0 0.00 3.53
1057 1221 1.889530 CTCGTTTCCCTCCGCCTCTT 61.890 60.000 0.00 0.0 0.00 2.85
1264 1443 4.056125 CCAGCTCTGACGTCGCCA 62.056 66.667 11.62 0.0 0.00 5.69
1471 1650 2.227194 GTTCCATCGACAACACCCTTT 58.773 47.619 0.00 0.0 0.00 3.11
1472 1651 2.621526 GTTCCATCGACAACACCCTTTT 59.378 45.455 0.00 0.0 0.00 2.27
1862 2041 2.023673 AGAGCAGATCAGAGTTCCTCG 58.976 52.381 0.00 0.0 35.36 4.63
2148 2327 5.578005 AGATTCAGATTTGCATGAACCAG 57.422 39.130 2.68 0.0 38.19 4.00
2534 3129 1.630369 TGAAAGGACCAGGATGACCAG 59.370 52.381 0.00 0.0 39.69 4.00
2538 3133 1.203364 AGGACCAGGATGACCAGAGTT 60.203 52.381 0.00 0.0 39.69 3.01
2609 3205 5.468540 TGCTCTAGTTCTTGTTAGCTGAA 57.531 39.130 0.00 0.0 0.00 3.02
2650 3246 4.521639 TCTGCAGCATCTTTGTTTGAAGAT 59.478 37.500 9.47 0.0 44.94 2.40
2754 3350 3.789756 CGTACTGGCTGATACTTTGTACG 59.210 47.826 0.00 0.0 43.10 3.67
2799 3429 3.995048 GCCTACCAGTACAGTCTTTGTTC 59.005 47.826 0.00 0.0 41.29 3.18
2900 3531 7.725818 TTATTTTGCATGTGATGAAAAGCAA 57.274 28.000 0.00 0.0 38.92 3.91
3052 3685 1.238439 TGCAAGAAAGGAAAGCTCGG 58.762 50.000 0.00 0.0 0.00 4.63
3132 3794 1.065564 AGAGCTCATTGCCTCCTTGAC 60.066 52.381 17.77 0.0 44.23 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 5.911838 GCTTCACAGACTGAATTTTCTTCAC 59.088 40.000 10.08 0.00 38.26 3.18
174 175 5.009010 GGCTTCACAGACTGAATTTTCTTCA 59.991 40.000 10.08 0.00 38.26 3.02
175 176 5.456265 GGCTTCACAGACTGAATTTTCTTC 58.544 41.667 10.08 0.00 38.26 2.87
176 177 4.279420 GGGCTTCACAGACTGAATTTTCTT 59.721 41.667 10.08 0.00 38.26 2.52
177 178 3.823304 GGGCTTCACAGACTGAATTTTCT 59.177 43.478 10.08 0.00 38.26 2.52
178 179 3.823304 AGGGCTTCACAGACTGAATTTTC 59.177 43.478 10.08 0.00 38.26 2.29
210 361 1.271762 TGCTTTGCTCTGCCATCTCTT 60.272 47.619 0.00 0.00 0.00 2.85
283 434 0.602562 CTCGCTCCATCTCCATCTCC 59.397 60.000 0.00 0.00 0.00 3.71
284 435 0.038343 GCTCGCTCCATCTCCATCTC 60.038 60.000 0.00 0.00 0.00 2.75
285 436 0.758310 TGCTCGCTCCATCTCCATCT 60.758 55.000 0.00 0.00 0.00 2.90
286 437 0.321021 ATGCTCGCTCCATCTCCATC 59.679 55.000 0.00 0.00 0.00 3.51
287 438 0.035036 CATGCTCGCTCCATCTCCAT 59.965 55.000 0.00 0.00 0.00 3.41
288 439 1.444672 CATGCTCGCTCCATCTCCA 59.555 57.895 0.00 0.00 0.00 3.86
378 529 1.145598 CATCCTCAGCTCACGCCAT 59.854 57.895 0.00 0.00 36.60 4.40
392 543 4.757149 GCAACTATATCCCTGTTGTCATCC 59.243 45.833 0.00 0.00 41.93 3.51
407 558 0.248907 GAGCCGCTCGTGCAACTATA 60.249 55.000 4.23 0.00 39.64 1.31
588 741 7.799784 TCAGAAATATGTCATTACATGCATCG 58.200 34.615 0.00 0.00 45.99 3.84
645 798 8.102676 AGCCAACCTTTTTAATATTTGCTCAAT 58.897 29.630 0.00 0.00 0.00 2.57
665 818 8.630917 TGTCTACTCTGTATATAAGAAGCCAAC 58.369 37.037 0.00 0.00 0.00 3.77
909 1064 2.047179 GACCTTCCACGAGCCCAC 60.047 66.667 0.00 0.00 0.00 4.61
1057 1221 1.306997 GGTGGATCTGGGAGGTGGA 60.307 63.158 0.00 0.00 0.00 4.02
1471 1650 2.317609 GCCGCGCTTGAGAACTCAA 61.318 57.895 15.05 15.05 46.27 3.02
1472 1651 2.738521 GCCGCGCTTGAGAACTCA 60.739 61.111 5.56 0.00 37.91 3.41
1684 1863 1.028330 CAGACACGGCATGCCTGAAT 61.028 55.000 33.07 16.53 0.00 2.57
1862 2041 2.664081 CCAGCCCCACCTCAGAGAC 61.664 68.421 0.00 0.00 0.00 3.36
2330 2606 1.878211 TGGACATGCCAGGTCTCATA 58.122 50.000 9.58 0.00 43.33 2.15
2342 2618 4.134563 TGCTGAATGATGAGATGGACATG 58.865 43.478 0.00 0.00 0.00 3.21
2534 3129 2.143122 TCGGCAGTGATCAACAAACTC 58.857 47.619 0.00 0.00 0.00 3.01
2538 3133 0.684535 TCCTCGGCAGTGATCAACAA 59.315 50.000 0.00 0.00 0.00 2.83
2609 3205 8.308931 TGCTGCAGAAAGAAAGATGATTAATTT 58.691 29.630 20.43 0.00 0.00 1.82
2754 3350 7.227512 AGGCTGTATGCAGAAATTGTAATACTC 59.772 37.037 15.68 0.00 45.28 2.59
2838 3469 3.096092 AGGTCTTTCTCCTGTGCTCTAG 58.904 50.000 0.00 0.00 33.62 2.43
2900 3531 4.343231 TCTGTACAATGGCATCCAAATGT 58.657 39.130 0.00 3.51 39.66 2.71
2985 3616 7.551617 TCTCCTATTCTTAAAAGCTAAAACCGG 59.448 37.037 0.00 0.00 0.00 5.28
3052 3685 3.303406 ACAACACTTTCTACGACGTAGC 58.697 45.455 26.58 0.00 36.22 3.58


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

AutoCloner maintained by Alex Coulton.