Multiple sequence alignment - TraesCS5D01G234800

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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 TraesCS5D01G234800 chr5D 100.000 3193 0 0 1 3193 342714137 342710945 0.000000e+00 5897.0
1 TraesCS5D01G234800 chr5D 90.370 135 13 0 1000 1134 238557792 238557658 9.100000e-41 178.0
2 TraesCS5D01G234800 chr5D 91.753 97 8 0 1501 1597 238557411 238557315 5.560000e-28 135.0
3 TraesCS5D01G234800 chr5A 93.170 3192 127 42 1 3134 443743844 443740686 0.000000e+00 4602.0
4 TraesCS5D01G234800 chr5A 90.370 135 13 0 1000 1134 316085020 316085154 9.100000e-41 178.0
5 TraesCS5D01G234800 chr5A 89.216 102 11 0 1496 1597 316085398 316085499 9.300000e-26 128.0
6 TraesCS5D01G234800 chr5A 98.276 58 1 0 3136 3193 443738974 443738917 5.640000e-18 102.0
7 TraesCS5D01G234800 chr5B 93.296 2834 95 41 353 3134 402752328 402749538 0.000000e+00 4093.0
8 TraesCS5D01G234800 chr5B 94.068 354 21 0 2 355 402759307 402758954 3.620000e-149 538.0
9 TraesCS5D01G234800 chr5B 89.630 135 14 0 1000 1134 266501406 266501540 4.230000e-39 172.0
10 TraesCS5D01G234800 chr5B 90.000 100 10 0 1498 1597 266501783 266501882 2.580000e-26 130.0
11 TraesCS5D01G234800 chr5B 86.905 84 11 0 1497 1580 704916514 704916597 9.430000e-16 95.3
12 TraesCS5D01G234800 chr5B 89.231 65 0 1 3136 3193 402749495 402749431 1.230000e-09 75.0
13 TraesCS5D01G234800 chr2D 93.478 138 9 0 1248 1385 108313296 108313433 4.180000e-49 206.0
14 TraesCS5D01G234800 chr2B 93.478 138 9 0 1248 1385 158146584 158146721 4.180000e-49 206.0
15 TraesCS5D01G234800 chr2A 93.478 138 9 0 1248 1385 104450622 104450759 4.180000e-49 206.0
16 TraesCS5D01G234800 chr2A 77.419 155 34 1 988 1141 572487844 572487690 1.220000e-14 91.6
17 TraesCS5D01G234800 chr4D 91.057 123 11 0 1001 1123 107710734 107710612 1.970000e-37 167.0
18 TraesCS5D01G234800 chr4D 93.407 91 4 2 1501 1590 107710356 107710267 2.000000e-27 134.0
19 TraesCS5D01G234800 chr4B 91.057 123 11 0 1001 1123 168984879 168985001 1.970000e-37 167.0
20 TraesCS5D01G234800 chr4B 91.489 94 6 2 1498 1590 168985244 168985336 9.300000e-26 128.0
21 TraesCS5D01G234800 chr4A 91.057 123 11 0 1001 1123 468603250 468603372 1.970000e-37 167.0
22 TraesCS5D01G234800 chr4A 91.489 94 6 2 1498 1590 468603626 468603718 9.300000e-26 128.0


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 TraesCS5D01G234800 chr5D 342710945 342714137 3192 True 5897 5897 100.0000 1 3193 1 chr5D.!!$R1 3192
1 TraesCS5D01G234800 chr5A 443738917 443743844 4927 True 2352 4602 95.7230 1 3193 2 chr5A.!!$R1 3192
2 TraesCS5D01G234800 chr5B 402749431 402752328 2897 True 2084 4093 91.2635 353 3193 2 chr5B.!!$R2 2840

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
635 695 0.179000 ATCACCAGATTCACTCGGCC 59.821 55.0 0.00 0.0 0.00 6.13 F
1397 1485 0.389391 ACCGGTGATGATAGCTTCCG 59.611 55.0 6.12 0.0 38.05 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 1938 1.341156 GCATCCAGCCCTCCAGTAGT 61.341 60.0 0.0 0.0 37.23 2.73 R
2222 2310 1.982612 TGTTCTTGCTCTCGTCGATG 58.017 50.0 0.0 0.0 0.00 3.84 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
98 99 3.448686 AGGTAGAATCATGAAAGTCGCG 58.551 45.455 0.00 0.00 0.00 5.87
102 103 5.006746 GGTAGAATCATGAAAGTCGCGAAAT 59.993 40.000 12.06 0.00 0.00 2.17
103 104 4.901814 AGAATCATGAAAGTCGCGAAATG 58.098 39.130 12.06 10.30 0.00 2.32
120 121 6.303022 CGCGAAATGCATATAATGTGTTTAGG 59.697 38.462 0.00 0.00 46.97 2.69
209 246 9.419297 CATGAGCCATTAGATTAAAATTGGATG 57.581 33.333 0.00 0.00 0.00 3.51
210 247 7.954835 TGAGCCATTAGATTAAAATTGGATGG 58.045 34.615 0.00 0.00 36.69 3.51
211 248 7.015487 TGAGCCATTAGATTAAAATTGGATGGG 59.985 37.037 0.00 0.00 34.73 4.00
212 249 5.934043 GCCATTAGATTAAAATTGGATGGGC 59.066 40.000 0.00 0.00 34.73 5.36
213 250 6.158598 CCATTAGATTAAAATTGGATGGGCG 58.841 40.000 0.00 0.00 31.43 6.13
214 251 6.015519 CCATTAGATTAAAATTGGATGGGCGA 60.016 38.462 0.00 0.00 31.43 5.54
215 252 7.309990 CCATTAGATTAAAATTGGATGGGCGAT 60.310 37.037 0.00 0.00 31.43 4.58
216 253 7.595819 TTAGATTAAAATTGGATGGGCGATT 57.404 32.000 0.00 0.00 0.00 3.34
217 254 6.089249 AGATTAAAATTGGATGGGCGATTC 57.911 37.500 0.00 0.00 0.00 2.52
218 255 5.598005 AGATTAAAATTGGATGGGCGATTCA 59.402 36.000 0.00 0.00 0.00 2.57
219 256 3.806625 AAAATTGGATGGGCGATTCAG 57.193 42.857 0.00 0.00 0.00 3.02
220 257 2.734755 AATTGGATGGGCGATTCAGA 57.265 45.000 0.00 0.00 0.00 3.27
221 258 2.965671 ATTGGATGGGCGATTCAGAT 57.034 45.000 0.00 0.00 0.00 2.90
222 259 2.734755 TTGGATGGGCGATTCAGATT 57.265 45.000 0.00 0.00 0.00 2.40
223 260 2.734755 TGGATGGGCGATTCAGATTT 57.265 45.000 0.00 0.00 0.00 2.17
224 261 3.017048 TGGATGGGCGATTCAGATTTT 57.983 42.857 0.00 0.00 0.00 1.82
225 262 3.364549 TGGATGGGCGATTCAGATTTTT 58.635 40.909 0.00 0.00 0.00 1.94
284 321 4.764050 TTTCGCATCCCTTAACCAGATA 57.236 40.909 0.00 0.00 0.00 1.98
285 322 3.746045 TCGCATCCCTTAACCAGATAC 57.254 47.619 0.00 0.00 0.00 2.24
305 342 1.001487 CGCTGCACCACAATTTTCTGA 60.001 47.619 0.00 0.00 0.00 3.27
313 350 6.094464 TGCACCACAATTTTCTGATCATCTAG 59.906 38.462 0.00 0.00 0.00 2.43
315 352 6.825213 CACCACAATTTTCTGATCATCTAGGA 59.175 38.462 0.00 0.00 0.00 2.94
335 376 5.434408 AGGAAACTTTTTACTCCTCGTGTT 58.566 37.500 0.00 0.00 37.44 3.32
562 622 9.912634 CCACATTTTCAAGTGTACTCATTTATT 57.087 29.630 0.00 0.00 33.99 1.40
607 667 1.400846 CTGAAGCAGCAAGGCACTATG 59.599 52.381 0.00 0.00 38.49 2.23
635 695 0.179000 ATCACCAGATTCACTCGGCC 59.821 55.000 0.00 0.00 0.00 6.13
1161 1249 1.299541 GGCAACGATCGTTCATGGAT 58.700 50.000 29.64 5.45 36.00 3.41
1162 1250 1.261619 GGCAACGATCGTTCATGGATC 59.738 52.381 29.64 12.48 36.00 3.36
1167 1255 2.071688 GATCGTTCATGGATCGGGAG 57.928 55.000 0.00 0.00 31.85 4.30
1168 1256 1.341531 GATCGTTCATGGATCGGGAGT 59.658 52.381 0.00 0.00 31.85 3.85
1210 1298 4.508226 TGCAGGTGAACTGGAATTGGAATA 60.508 41.667 0.00 0.00 45.18 1.75
1212 1300 6.780457 CAGGTGAACTGGAATTGGAATAAT 57.220 37.500 0.00 0.00 43.70 1.28
1213 1301 7.174107 CAGGTGAACTGGAATTGGAATAATT 57.826 36.000 0.00 0.00 43.70 1.40
1214 1302 7.037438 CAGGTGAACTGGAATTGGAATAATTG 58.963 38.462 0.00 0.00 43.70 2.32
1215 1303 6.155049 AGGTGAACTGGAATTGGAATAATTGG 59.845 38.462 0.00 0.00 0.00 3.16
1216 1304 6.154363 GGTGAACTGGAATTGGAATAATTGGA 59.846 38.462 0.00 0.00 0.00 3.53
1217 1305 7.310361 GGTGAACTGGAATTGGAATAATTGGAA 60.310 37.037 0.00 0.00 0.00 3.53
1218 1306 8.260114 GTGAACTGGAATTGGAATAATTGGAAT 58.740 33.333 0.00 0.00 0.00 3.01
1219 1307 8.824783 TGAACTGGAATTGGAATAATTGGAATT 58.175 29.630 0.00 0.00 0.00 2.17
1242 1330 4.486125 ACAAGCTTTGTTGATTTTGGGT 57.514 36.364 0.00 0.00 42.22 4.51
1243 1331 4.190772 ACAAGCTTTGTTGATTTTGGGTG 58.809 39.130 0.00 0.00 42.22 4.61
1244 1332 4.190772 CAAGCTTTGTTGATTTTGGGTGT 58.809 39.130 0.00 0.00 0.00 4.16
1246 1334 4.441792 AGCTTTGTTGATTTTGGGTGTTC 58.558 39.130 0.00 0.00 0.00 3.18
1330 1418 2.187599 ATCAAGCGCGGCAACTTCAC 62.188 55.000 8.83 0.00 0.00 3.18
1340 1428 0.534203 GCAACTTCACCGACCAGGAA 60.534 55.000 0.00 0.00 45.00 3.36
1397 1485 0.389391 ACCGGTGATGATAGCTTCCG 59.611 55.000 6.12 0.00 38.05 4.30
1659 1747 4.595538 GTGTCGGTGGTGGCGTCA 62.596 66.667 0.00 0.00 0.00 4.35
2222 2310 1.698714 CGCGTACCAACCGGGAATTC 61.699 60.000 6.32 0.00 40.27 2.17
2229 2317 0.650512 CAACCGGGAATTCATCGACG 59.349 55.000 18.04 9.42 0.00 5.12
2313 2406 3.887311 GCCGGGGGCTATAGTTCT 58.113 61.111 2.18 0.00 46.69 3.01
2314 2407 1.371558 GCCGGGGGCTATAGTTCTG 59.628 63.158 2.18 0.00 46.69 3.02
2315 2408 1.119574 GCCGGGGGCTATAGTTCTGA 61.120 60.000 2.18 0.00 46.69 3.27
2316 2409 1.645710 CCGGGGGCTATAGTTCTGAT 58.354 55.000 0.84 0.00 0.00 2.90
2317 2410 1.978580 CCGGGGGCTATAGTTCTGATT 59.021 52.381 0.84 0.00 0.00 2.57
2346 2439 2.365617 GGTGATTTAGATCGAGCTGGGA 59.634 50.000 14.67 0.00 34.91 4.37
2350 2443 1.693627 TTAGATCGAGCTGGGAGTCC 58.306 55.000 14.67 0.00 0.00 3.85
2351 2444 0.535328 TAGATCGAGCTGGGAGTCCG 60.535 60.000 14.67 0.00 35.24 4.79
2588 2683 8.896744 TCTCATCGAGCTGAAATAAATCATTTT 58.103 29.630 0.00 0.00 36.96 1.82
2655 2750 6.202379 CACTGATCATATGCAGTTAAGTGGAG 59.798 42.308 12.19 0.00 42.33 3.86
2706 2801 6.864685 TGTTTTCAAGATCAGATGCATCAAAC 59.135 34.615 27.81 22.51 0.00 2.93
2708 2803 4.506758 TCAAGATCAGATGCATCAAACGA 58.493 39.130 27.81 17.74 0.00 3.85
2729 2824 7.437793 ACGAACCTGTTATCGGAAATTTTAA 57.562 32.000 0.00 0.00 43.11 1.52
2820 2940 0.106268 TGCAAAGCCAAGTCCCTCAA 60.106 50.000 0.00 0.00 0.00 3.02
2821 2941 1.039856 GCAAAGCCAAGTCCCTCAAA 58.960 50.000 0.00 0.00 0.00 2.69
2822 2942 1.412343 GCAAAGCCAAGTCCCTCAAAA 59.588 47.619 0.00 0.00 0.00 2.44
2823 2943 2.037641 GCAAAGCCAAGTCCCTCAAAAT 59.962 45.455 0.00 0.00 0.00 1.82
2829 2950 6.686484 AGCCAAGTCCCTCAAAATAAAAAT 57.314 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 7.359595 TCCTAAACACATTATATGCATTTCGC 58.640 34.615 3.54 0.00 42.89 4.70
102 103 8.664798 GCGATATTCCTAAACACATTATATGCA 58.335 33.333 0.00 0.00 0.00 3.96
103 104 8.664798 TGCGATATTCCTAAACACATTATATGC 58.335 33.333 0.00 0.00 0.00 3.14
222 259 9.865321 ACTATACGAGTTAGTAGAATGCAAAAA 57.135 29.630 0.00 0.00 33.13 1.94
247 284 8.448615 GGGATGCGAAATATATACCTACAAAAC 58.551 37.037 0.00 0.00 0.00 2.43
271 308 1.134521 TGCAGCGTATCTGGTTAAGGG 60.135 52.381 0.00 0.00 43.06 3.95
284 321 1.032014 AGAAAATTGTGGTGCAGCGT 58.968 45.000 11.91 0.00 0.00 5.07
285 322 1.001487 TCAGAAAATTGTGGTGCAGCG 60.001 47.619 11.91 0.00 0.00 5.18
305 342 7.982354 CGAGGAGTAAAAAGTTTCCTAGATGAT 59.018 37.037 0.00 0.00 40.07 2.45
313 350 5.295045 TGAACACGAGGAGTAAAAAGTTTCC 59.705 40.000 0.00 0.00 0.00 3.13
315 352 5.644636 TGTGAACACGAGGAGTAAAAAGTTT 59.355 36.000 0.00 0.00 0.00 2.66
335 376 6.476380 GCAGTCAAAACATCATTTTTCTGTGA 59.524 34.615 11.90 0.00 0.00 3.58
562 622 4.703379 ATCTGCCATTTTTGTTTCCCAA 57.297 36.364 0.00 0.00 0.00 4.12
563 623 5.104982 GGATATCTGCCATTTTTGTTTCCCA 60.105 40.000 2.05 0.00 0.00 4.37
607 667 1.478105 GAATCTGGTGATGGGTTTGGC 59.522 52.381 0.00 0.00 32.44 4.52
635 695 4.260212 CCGTCAGCAGAATTATTGTAACCG 60.260 45.833 0.00 0.00 0.00 4.44
680 741 2.142292 AAATGAGAAGGGGGCGCAGT 62.142 55.000 10.83 0.00 0.00 4.40
1125 1199 2.662527 CCGTGCGTACCGGTGTTT 60.663 61.111 19.93 0.00 40.59 2.83
1222 1310 4.190772 ACACCCAAAATCAACAAAGCTTG 58.809 39.130 0.00 0.00 0.00 4.01
1238 1326 3.177884 AGCCCTGCAGAACACCCA 61.178 61.111 17.39 0.00 0.00 4.51
1242 1330 1.676635 GCATCAGCCCTGCAGAACA 60.677 57.895 17.39 0.00 39.46 3.18
1243 1331 2.758089 CGCATCAGCCCTGCAGAAC 61.758 63.158 17.39 6.56 39.64 3.01
1244 1332 2.437180 CGCATCAGCCCTGCAGAA 60.437 61.111 17.39 0.00 39.64 3.02
1246 1334 4.790962 ACCGCATCAGCCCTGCAG 62.791 66.667 6.78 6.78 39.64 4.41
1330 1418 0.174617 GAGCTTCTCTTCCTGGTCGG 59.825 60.000 0.00 0.00 0.00 4.79
1340 1428 0.820871 GGTGGACGATGAGCTTCTCT 59.179 55.000 0.00 0.00 0.00 3.10
1397 1485 8.257830 AGACGGAAATTAAGAAAAGATGAGAC 57.742 34.615 0.00 0.00 0.00 3.36
1850 1938 1.341156 GCATCCAGCCCTCCAGTAGT 61.341 60.000 0.00 0.00 37.23 2.73
2222 2310 1.982612 TGTTCTTGCTCTCGTCGATG 58.017 50.000 0.00 0.00 0.00 3.84
2229 2317 8.972349 CCTTTCTTAAATTTTGTTCTTGCTCTC 58.028 33.333 0.00 0.00 0.00 3.20
2306 2399 6.978674 TCACCGAGGATTAATCAGAACTAT 57.021 37.500 17.07 0.00 0.00 2.12
2307 2400 6.978674 ATCACCGAGGATTAATCAGAACTA 57.021 37.500 17.07 0.00 0.00 2.24
2308 2401 5.878406 ATCACCGAGGATTAATCAGAACT 57.122 39.130 17.07 4.84 0.00 3.01
2309 2402 6.927294 AAATCACCGAGGATTAATCAGAAC 57.073 37.500 17.07 0.00 36.51 3.01
2310 2403 8.018537 TCTAAATCACCGAGGATTAATCAGAA 57.981 34.615 17.07 0.00 36.51 3.02
2311 2404 7.597288 TCTAAATCACCGAGGATTAATCAGA 57.403 36.000 17.07 4.07 36.51 3.27
2312 2405 7.274468 CGATCTAAATCACCGAGGATTAATCAG 59.726 40.741 17.07 7.64 36.51 2.90
2313 2406 7.039993 TCGATCTAAATCACCGAGGATTAATCA 60.040 37.037 17.07 0.00 36.51 2.57
2314 2407 7.313646 TCGATCTAAATCACCGAGGATTAATC 58.686 38.462 6.93 6.93 36.51 1.75
2315 2408 7.228314 TCGATCTAAATCACCGAGGATTAAT 57.772 36.000 0.00 0.00 36.51 1.40
2316 2409 6.644248 TCGATCTAAATCACCGAGGATTAA 57.356 37.500 0.00 0.00 36.51 1.40
2317 2410 5.335740 GCTCGATCTAAATCACCGAGGATTA 60.336 44.000 0.00 0.00 44.63 1.75
2346 2439 2.922740 TTAAGCAAACTGGACGGACT 57.077 45.000 0.00 0.00 0.00 3.85
2350 2443 3.806316 AACGATTAAGCAAACTGGACG 57.194 42.857 0.00 0.00 0.00 4.79
2351 2444 6.894828 TCTAAAACGATTAAGCAAACTGGAC 58.105 36.000 0.00 0.00 0.00 4.02
2564 2659 8.461222 ACAAAATGATTTATTTCAGCTCGATGA 58.539 29.630 0.00 0.00 38.01 2.92
2606 2701 9.301153 GTGTCAATCAAACTTGAAACAAATACT 57.699 29.630 0.00 0.00 41.23 2.12
2607 2702 9.301153 AGTGTCAATCAAACTTGAAACAAATAC 57.699 29.630 9.19 0.00 43.13 1.89
2678 2773 6.431852 TGATGCATCTGATCTTGAAAACAAGA 59.568 34.615 26.32 13.64 44.21 3.02
2679 2774 6.617879 TGATGCATCTGATCTTGAAAACAAG 58.382 36.000 26.32 0.00 0.00 3.16
2706 2801 8.905103 AATTAAAATTTCCGATAACAGGTTCG 57.095 30.769 0.00 0.00 35.19 3.95
2820 2940 7.658167 CCCAGTTTAACCCGAACATTTTTATTT 59.342 33.333 0.00 0.00 0.00 1.40
2821 2941 7.015389 TCCCAGTTTAACCCGAACATTTTTATT 59.985 33.333 0.00 0.00 0.00 1.40
2822 2942 6.494146 TCCCAGTTTAACCCGAACATTTTTAT 59.506 34.615 0.00 0.00 0.00 1.40
2823 2943 5.832060 TCCCAGTTTAACCCGAACATTTTTA 59.168 36.000 0.00 0.00 0.00 1.52
2829 2950 2.640826 AGATCCCAGTTTAACCCGAACA 59.359 45.455 0.00 0.00 0.00 3.18
3134 3255 7.908827 TGTCAAGTTAGCACCGAAAATATAA 57.091 32.000 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.