Multiple sequence alignment - TraesCS5A01G158200

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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 TraesCS5A01G158200 chr5A 100.000 1879 0 0 1 1879 338257986 338256108 0.000000e+00 3470
1 TraesCS5A01G158200 chr5A 100.000 1278 0 0 2298 3575 338255689 338254412 0.000000e+00 2361
2 TraesCS5A01G158200 chr5A 91.292 356 23 4 1 353 338292015 338291665 2.500000e-131 479
3 TraesCS5A01G158200 chr2A 92.151 1032 65 6 2551 3575 611801901 611800879 0.000000e+00 1443
4 TraesCS5A01G158200 chr2A 82.370 1384 215 19 495 1867 566615239 566613874 0.000000e+00 1177
5 TraesCS5A01G158200 chr7A 87.250 1200 142 7 674 1872 438999414 438998225 0.000000e+00 1358
6 TraesCS5A01G158200 chr7A 81.621 1382 219 20 495 1867 540194637 540195992 0.000000e+00 1112
7 TraesCS5A01G158200 chr7A 80.925 1384 239 18 497 1866 374512681 374511309 0.000000e+00 1070
8 TraesCS5A01G158200 chr7A 82.381 210 35 2 1 209 671448179 671448387 7.880000e-42 182
9 TraesCS5A01G158200 chr3A 83.502 1382 204 18 495 1865 140031229 140029861 0.000000e+00 1267
10 TraesCS5A01G158200 chr3A 84.909 1206 171 8 2378 3572 393839469 393840674 0.000000e+00 1208
11 TraesCS5A01G158200 chr3A 82.549 1381 223 13 494 1867 393837913 393839282 0.000000e+00 1199
12 TraesCS5A01G158200 chr5B 83.176 1379 213 15 495 1867 118604494 118605859 0.000000e+00 1243
13 TraesCS5A01G158200 chr5B 96.865 319 9 1 1 319 287755075 287755392 1.890000e-147 532
14 TraesCS5A01G158200 chr5B 91.292 356 23 4 1 353 287432337 287432687 2.500000e-131 479
15 TraesCS5A01G158200 chr5B 93.923 181 9 1 315 493 287756070 287756250 4.550000e-69 272
16 TraesCS5A01G158200 chr5B 84.977 213 24 7 1 211 286866122 286866328 3.620000e-50 209
17 TraesCS5A01G158200 chr7D 83.067 1376 219 9 497 1867 520383582 520382216 0.000000e+00 1238
18 TraesCS5A01G158200 chr4D 86.667 1095 119 15 2488 3575 14423036 14421962 0.000000e+00 1188
19 TraesCS5A01G158200 chr2D 86.445 1055 130 6 818 1867 68909498 68910544 0.000000e+00 1144
20 TraesCS5A01G158200 chr3B 81.739 1380 229 15 495 1867 680760890 680762253 0.000000e+00 1131
21 TraesCS5A01G158200 chr3B 82.550 1106 170 14 2480 3575 808669349 808668257 0.000000e+00 952
22 TraesCS5A01G158200 chr1D 86.465 1027 129 7 856 1877 483398682 483399703 0.000000e+00 1118
23 TraesCS5A01G158200 chr6A 82.897 1222 189 9 2362 3572 355949479 355948267 0.000000e+00 1081
24 TraesCS5A01G158200 chr6A 82.401 1108 178 10 2476 3575 241928152 241929250 0.000000e+00 950
25 TraesCS5A01G158200 chr1A 82.585 1114 174 16 2472 3572 68367857 68368963 0.000000e+00 965
26 TraesCS5A01G158200 chr1A 82.671 1108 173 10 2475 3572 278959573 278958475 0.000000e+00 965
27 TraesCS5A01G158200 chr1A 82.363 1117 167 20 2471 3572 99973990 99975091 0.000000e+00 944
28 TraesCS5A01G158200 chr5D 98.792 331 4 0 1 331 254851513 254851183 1.110000e-164 590
29 TraesCS5A01G158200 chr5D 90.449 356 26 4 1 353 255080666 255080316 2.510000e-126 462
30 TraesCS5A01G158200 chr5D 97.006 167 3 1 329 493 254849215 254849049 2.720000e-71 279
31 TraesCS5A01G158200 chr4B 85.446 213 23 7 1 211 43217045 43217251 7.770000e-52 215
32 TraesCS5A01G158200 chr7B 83.938 193 29 2 1 192 646046134 646046325 2.190000e-42 183


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 TraesCS5A01G158200 chr5A 338254412 338257986 3574 True 2915.5 3470 100.000 1 3575 2 chr5A.!!$R2 3574
1 TraesCS5A01G158200 chr2A 611800879 611801901 1022 True 1443.0 1443 92.151 2551 3575 1 chr2A.!!$R2 1024
2 TraesCS5A01G158200 chr2A 566613874 566615239 1365 True 1177.0 1177 82.370 495 1867 1 chr2A.!!$R1 1372
3 TraesCS5A01G158200 chr7A 438998225 438999414 1189 True 1358.0 1358 87.250 674 1872 1 chr7A.!!$R2 1198
4 TraesCS5A01G158200 chr7A 540194637 540195992 1355 False 1112.0 1112 81.621 495 1867 1 chr7A.!!$F1 1372
5 TraesCS5A01G158200 chr7A 374511309 374512681 1372 True 1070.0 1070 80.925 497 1866 1 chr7A.!!$R1 1369
6 TraesCS5A01G158200 chr3A 140029861 140031229 1368 True 1267.0 1267 83.502 495 1865 1 chr3A.!!$R1 1370
7 TraesCS5A01G158200 chr3A 393837913 393840674 2761 False 1203.5 1208 83.729 494 3572 2 chr3A.!!$F1 3078
8 TraesCS5A01G158200 chr5B 118604494 118605859 1365 False 1243.0 1243 83.176 495 1867 1 chr5B.!!$F1 1372
9 TraesCS5A01G158200 chr5B 287755075 287756250 1175 False 402.0 532 95.394 1 493 2 chr5B.!!$F4 492
10 TraesCS5A01G158200 chr7D 520382216 520383582 1366 True 1238.0 1238 83.067 497 1867 1 chr7D.!!$R1 1370
11 TraesCS5A01G158200 chr4D 14421962 14423036 1074 True 1188.0 1188 86.667 2488 3575 1 chr4D.!!$R1 1087
12 TraesCS5A01G158200 chr2D 68909498 68910544 1046 False 1144.0 1144 86.445 818 1867 1 chr2D.!!$F1 1049
13 TraesCS5A01G158200 chr3B 680760890 680762253 1363 False 1131.0 1131 81.739 495 1867 1 chr3B.!!$F1 1372
14 TraesCS5A01G158200 chr3B 808668257 808669349 1092 True 952.0 952 82.550 2480 3575 1 chr3B.!!$R1 1095
15 TraesCS5A01G158200 chr1D 483398682 483399703 1021 False 1118.0 1118 86.465 856 1877 1 chr1D.!!$F1 1021
16 TraesCS5A01G158200 chr6A 355948267 355949479 1212 True 1081.0 1081 82.897 2362 3572 1 chr6A.!!$R1 1210
17 TraesCS5A01G158200 chr6A 241928152 241929250 1098 False 950.0 950 82.401 2476 3575 1 chr6A.!!$F1 1099
18 TraesCS5A01G158200 chr1A 68367857 68368963 1106 False 965.0 965 82.585 2472 3572 1 chr1A.!!$F1 1100
19 TraesCS5A01G158200 chr1A 278958475 278959573 1098 True 965.0 965 82.671 2475 3572 1 chr1A.!!$R1 1097
20 TraesCS5A01G158200 chr1A 99973990 99975091 1101 False 944.0 944 82.363 2471 3572 1 chr1A.!!$F2 1101
21 TraesCS5A01G158200 chr5D 254849049 254851513 2464 True 434.5 590 97.899 1 493 2 chr5D.!!$R2 492

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
915 3577 1.510480 GCCACTCTCAGGTTGTGTGC 61.510 60.0 0.0 0.0 0.00 4.57 F
1551 4218 0.179124 GCTTCGACTTCCGCATCTCT 60.179 55.0 0.0 0.0 38.37 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 5002 0.309302 CGTGAGCATAGGAGGAGTCG 59.691 60.0 0.00 0.0 0.0 4.18 R
3119 5820 0.388778 TTCGTTCGGAGCGCATGTAA 60.389 50.0 11.47 0.0 0.0 2.41 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
197 198 3.697619 ACTTGGAACTAAGGTGTAGGC 57.302 47.619 3.29 0.00 31.94 3.93
332 2984 7.883833 ACATATGCAGCTATCATGATCTTCTTT 59.116 33.333 12.53 0.00 0.00 2.52
493 3147 7.664318 AGAGGTACCGTTTCATTCTGTAAAAAT 59.336 33.333 6.18 0.00 0.00 1.82
558 3214 2.672307 AGTCGTCGGTCGCCTTCT 60.672 61.111 0.00 0.00 39.67 2.85
562 3218 2.963371 GTCGGTCGCCTTCTCTGT 59.037 61.111 0.00 0.00 0.00 3.41
767 3429 2.982744 GCAAGAAGAAGCGTGGCCC 61.983 63.158 0.00 0.00 0.00 5.80
770 3432 3.435186 GAAGAAGCGTGGCCCTGC 61.435 66.667 8.19 8.19 0.00 4.85
882 3544 2.417719 GACCTCGTCAAGTGCTTCAAT 58.582 47.619 0.00 0.00 32.09 2.57
883 3545 2.413453 GACCTCGTCAAGTGCTTCAATC 59.587 50.000 0.00 0.00 32.09 2.67
909 3571 2.203788 TCCGGCCACTCTCAGGTT 60.204 61.111 2.24 0.00 0.00 3.50
911 3573 2.743718 CGGCCACTCTCAGGTTGT 59.256 61.111 2.24 0.00 0.00 3.32
912 3574 1.669115 CGGCCACTCTCAGGTTGTG 60.669 63.158 2.24 0.00 0.00 3.33
915 3577 1.510480 GCCACTCTCAGGTTGTGTGC 61.510 60.000 0.00 0.00 0.00 4.57
921 3583 3.572539 CAGGTTGTGTGCACGCGT 61.573 61.111 24.30 5.58 0.00 6.01
1071 3734 3.090532 GACATCCCCGCCCCTTCT 61.091 66.667 0.00 0.00 0.00 2.85
1132 3795 1.227853 TCGCCGGAGATGATCGAGA 60.228 57.895 5.05 0.00 0.00 4.04
1177 3840 1.229951 TCCTGGGATTGGCAGGTCT 60.230 57.895 0.00 0.00 37.38 3.85
1186 3849 2.827642 GGCAGGTCTCCATGCTGC 60.828 66.667 12.31 12.31 42.19 5.25
1212 3875 1.473278 GGTCAGATCTCGGTCGTCTTT 59.527 52.381 0.00 0.00 0.00 2.52
1270 3933 0.399233 AGACATCACCCTAGCCCTCC 60.399 60.000 0.00 0.00 0.00 4.30
1335 3998 3.681835 GTCGCGGTCCTGGACACT 61.682 66.667 26.94 0.00 33.68 3.55
1436 4100 2.213513 TGGTCGTGGTGGATGAGCA 61.214 57.895 0.00 0.00 44.18 4.26
1502 4169 1.482182 TGATTCATCCAGACTCCGTGG 59.518 52.381 0.00 0.00 36.28 4.94
1540 4207 2.207924 AACGACCAGGGCTTCGACT 61.208 57.895 5.00 0.00 38.63 4.18
1551 4218 0.179124 GCTTCGACTTCCGCATCTCT 60.179 55.000 0.00 0.00 38.37 3.10
1602 4269 0.249911 GCATCCCCGACGATAGCTTT 60.250 55.000 0.00 0.00 42.67 3.51
1700 4379 2.408022 GGAGGATGACGACGACGG 59.592 66.667 12.58 0.00 44.46 4.79
1716 4398 1.738099 CGGCTTCAAGGACAGTCCG 60.738 63.158 14.32 0.78 42.75 4.79
1796 4480 4.843331 GGATCCCCTGCCCCCTGA 62.843 72.222 0.00 0.00 0.00 3.86
1797 4481 2.451294 GATCCCCTGCCCCCTGAT 60.451 66.667 0.00 0.00 0.00 2.90
1800 4484 3.813724 CCCCTGCCCCCTGATGAC 61.814 72.222 0.00 0.00 0.00 3.06
1804 4488 2.284625 TGCCCCCTGATGACGACT 60.285 61.111 0.00 0.00 0.00 4.18
1877 4561 2.834968 CCCCGACCGTACTACCCC 60.835 72.222 0.00 0.00 0.00 4.95
1878 4562 2.834968 CCCGACCGTACTACCCCC 60.835 72.222 0.00 0.00 0.00 5.40
2324 5008 4.754667 GGTTGCGACCCCGACTCC 62.755 72.222 12.67 0.00 40.25 3.85
2325 5009 3.692406 GTTGCGACCCCGACTCCT 61.692 66.667 0.00 0.00 38.22 3.69
2326 5010 3.379445 TTGCGACCCCGACTCCTC 61.379 66.667 0.00 0.00 38.22 3.71
2329 5013 2.593978 CGACCCCGACTCCTCCTA 59.406 66.667 0.00 0.00 38.22 2.94
2335 5019 0.468214 CCCGACTCCTCCTATGCTCA 60.468 60.000 0.00 0.00 0.00 4.26
2339 5023 0.757188 ACTCCTCCTATGCTCACGGG 60.757 60.000 0.00 0.00 0.00 5.28
2341 5025 2.511452 CCTCCTATGCTCACGGGGG 61.511 68.421 0.00 0.00 30.78 5.40
2345 5029 3.757248 CTATGCTCACGGGGGTGGC 62.757 68.421 0.00 0.00 0.00 5.01
2384 5068 3.075641 GGTCTCCCCACCTCCGAC 61.076 72.222 0.00 0.00 33.08 4.79
2428 5115 3.732849 CCTCCCCTGGTTCCTGCC 61.733 72.222 0.00 0.00 0.00 4.85
2734 5425 3.132824 ACTTGTTCCTTTTCTGCTTTGGG 59.867 43.478 0.00 0.00 0.00 4.12
2905 5605 4.475444 CCCCTCCTACCTCGGGCA 62.475 72.222 0.00 0.00 36.62 5.36
3119 5820 2.586079 CGCCGCCAACTCATCGAT 60.586 61.111 0.00 0.00 0.00 3.59
3275 5980 0.764752 GGGTGGCATCCTACTAGGCT 60.765 60.000 10.27 0.00 34.61 4.58
3355 6060 1.045911 AGGTCTTCGAGAGGGCCATC 61.046 60.000 10.05 10.05 0.00 3.51
3372 6077 3.996363 GCCATCAACTTCAAATGGGAAAC 59.004 43.478 3.04 0.00 40.29 2.78
3391 6096 2.550175 ACCATTGCTTTTTATGGGCCT 58.450 42.857 4.53 0.00 44.53 5.19
3435 6140 1.133407 CTTCCTCACTGAGCTCCGTAC 59.867 57.143 12.15 0.00 0.00 3.67
3476 6181 4.155733 CGGTGATAGTGGGCGGCA 62.156 66.667 12.47 0.00 0.00 5.69
3498 6203 5.975939 GCAATTTCAACCTCATTAGATCAGC 59.024 40.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 198 5.840243 TCATGTGGGCAATTCAGATAAAG 57.160 39.130 0.00 0.00 0.00 1.85
332 2984 7.142680 GTGTTTTAGCAGTGCCAATTAAGTAA 58.857 34.615 12.58 0.00 0.00 2.24
463 3117 4.152402 CAGAATGAAACGGTACCTCTGTTG 59.848 45.833 10.90 0.00 43.93 3.33
546 3202 2.687805 CGACAGAGAAGGCGACCGA 61.688 63.158 0.00 0.00 0.00 4.69
658 3320 4.382320 GTACCGGCGCACCTTGGA 62.382 66.667 10.83 0.00 0.00 3.53
661 3323 4.388499 CTGGTACCGGCGCACCTT 62.388 66.667 23.59 0.00 35.73 3.50
739 3401 2.674380 CTTCTTGCGCTTGCCCCT 60.674 61.111 9.73 0.00 38.03 4.79
767 3429 3.576356 CACCATTAGCCCGCGCAG 61.576 66.667 8.75 0.00 37.52 5.18
770 3432 3.576356 CAGCACCATTAGCCCGCG 61.576 66.667 0.00 0.00 0.00 6.46
774 3436 2.834968 GGGGCAGCACCATTAGCC 60.835 66.667 9.59 0.00 46.28 3.93
810 3472 4.933064 GTCGAGGCAGCCGGATCG 62.933 72.222 14.07 14.07 36.54 3.69
909 3571 4.214327 TGAGGACGCGTGCACACA 62.214 61.111 32.28 23.81 0.00 3.72
911 3573 3.911698 ACTGAGGACGCGTGCACA 61.912 61.111 32.28 29.32 0.00 4.57
912 3574 3.406361 CACTGAGGACGCGTGCAC 61.406 66.667 32.28 26.26 0.00 4.57
915 3577 3.108289 CAGCACTGAGGACGCGTG 61.108 66.667 20.70 3.63 0.00 5.34
921 3583 0.040351 AGAGGTAGCAGCACTGAGGA 59.960 55.000 0.81 0.00 0.00 3.71
990 3653 2.620585 CTCATACGTCATCAGCTCCTCA 59.379 50.000 0.00 0.00 0.00 3.86
1068 3731 1.221840 GGCCAAGAGCGATGGAGAA 59.778 57.895 0.00 0.00 45.17 2.87
1071 3734 2.954684 AACGGCCAAGAGCGATGGA 61.955 57.895 2.24 0.00 45.17 3.41
1132 3795 3.060866 GAGGTGGTTGAGCTCGGT 58.939 61.111 9.64 0.00 39.36 4.69
1186 3849 2.196925 CCGAGATCTGACCTCCCGG 61.197 68.421 0.00 0.32 0.00 5.73
1198 3861 1.473278 GTCTGGAAAGACGACCGAGAT 59.527 52.381 0.00 0.00 0.00 2.75
1270 3933 2.027745 AGATGTCCACCACTAGCTTGTG 60.028 50.000 19.75 19.75 37.66 3.33
1335 3998 0.603065 CGCCGATGAGGATCCATGTA 59.397 55.000 15.82 0.00 45.00 2.29
1452 4116 1.305381 CTTGACCCGGACCTCCTCT 60.305 63.158 0.73 0.00 0.00 3.69
1485 4152 1.191489 TGCCACGGAGTCTGGATGAA 61.191 55.000 3.50 0.00 41.61 2.57
1515 4182 0.035458 AGCCCTGGTCGTTGAAGAAG 59.965 55.000 0.00 0.00 0.00 2.85
1615 4283 4.804420 ATCGCCTCCCCCAGCAGA 62.804 66.667 0.00 0.00 0.00 4.26
1619 4287 4.181010 CACCATCGCCTCCCCCAG 62.181 72.222 0.00 0.00 0.00 4.45
1700 4379 1.301716 TGCGGACTGTCCTTGAAGC 60.302 57.895 23.49 18.55 33.30 3.86
1781 4464 2.780040 CATCAGGGGGCAGGGGAT 60.780 66.667 0.00 0.00 0.00 3.85
1789 4473 2.187946 GCAGTCGTCATCAGGGGG 59.812 66.667 0.00 0.00 0.00 5.40
2311 4995 2.980105 ATAGGAGGAGTCGGGGTCGC 62.980 65.000 0.00 0.00 36.13 5.19
2314 4998 1.457831 GCATAGGAGGAGTCGGGGT 60.458 63.158 0.00 0.00 0.00 4.95
2318 5002 0.309302 CGTGAGCATAGGAGGAGTCG 59.691 60.000 0.00 0.00 0.00 4.18
2319 5003 0.671251 CCGTGAGCATAGGAGGAGTC 59.329 60.000 0.00 0.00 0.00 3.36
2320 5004 0.757188 CCCGTGAGCATAGGAGGAGT 60.757 60.000 0.00 0.00 0.00 3.85
2322 5006 1.457643 CCCCGTGAGCATAGGAGGA 60.458 63.158 0.00 0.00 0.00 3.71
2323 5007 2.511452 CCCCCGTGAGCATAGGAGG 61.511 68.421 0.00 0.00 0.00 4.30
2324 5008 1.762460 ACCCCCGTGAGCATAGGAG 60.762 63.158 0.00 0.00 0.00 3.69
2325 5009 2.063979 CACCCCCGTGAGCATAGGA 61.064 63.158 0.00 0.00 43.14 2.94
2326 5010 2.505982 CACCCCCGTGAGCATAGG 59.494 66.667 0.00 0.00 43.14 2.57
2327 5011 2.505982 CCACCCCCGTGAGCATAG 59.494 66.667 0.00 0.00 43.14 2.23
2328 5012 3.792736 GCCACCCCCGTGAGCATA 61.793 66.667 0.00 0.00 43.14 3.14
2409 5093 2.204151 CAGGAACCAGGGGAGGGT 60.204 66.667 0.00 0.00 41.41 4.34
2412 5096 3.732849 GGGCAGGAACCAGGGGAG 61.733 72.222 0.00 0.00 0.00 4.30
3003 5703 3.268965 GACACGTGAGGCGCTCTGA 62.269 63.158 25.01 0.00 46.11 3.27
3119 5820 0.388778 TTCGTTCGGAGCGCATGTAA 60.389 50.000 11.47 0.00 0.00 2.41
3275 5980 4.415596 ACCTCAAATGTGGCATCCTTTAA 58.584 39.130 0.00 0.00 32.19 1.52
3289 5994 2.827921 GTCCATGCTTCCAACCTCAAAT 59.172 45.455 0.00 0.00 0.00 2.32
3372 6077 2.908916 CAGGCCCATAAAAAGCAATGG 58.091 47.619 0.00 0.00 42.02 3.16
3379 6084 0.968393 GGTCGGCAGGCCCATAAAAA 60.968 55.000 0.00 0.00 35.69 1.94
3380 6085 1.379309 GGTCGGCAGGCCCATAAAA 60.379 57.895 0.00 0.00 35.69 1.52
3435 6140 4.362476 GGGCGGCTGCAACCTTTG 62.362 66.667 21.31 0.00 45.35 2.77
3476 6181 7.114754 TCTGCTGATCTAATGAGGTTGAAATT 58.885 34.615 0.00 0.00 0.00 1.82
3498 6203 8.939929 TCACTAAATTATTGCTCTTGTCTTCTG 58.060 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.