Multiple sequence alignment - TraesCS6B01G149100

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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 TraesCS6B01G149100 chr6B 100.000 3154 0 0 1 3154 149875715 149878868 0.000000e+00 5825.0
1 TraesCS6B01G149100 chr6B 71.215 1070 236 45 879 1918 87999734 87998707 1.480000e-48 204.0
2 TraesCS6B01G149100 chr6A 93.396 3195 163 22 1 3154 92574964 92578151 0.000000e+00 4687.0
3 TraesCS6B01G149100 chr6D 94.199 2741 144 10 427 3154 77171996 77174734 0.000000e+00 4167.0
4 TraesCS6B01G149100 chr6D 93.182 440 18 6 1 430 77171530 77171967 1.230000e-178 636.0
5 TraesCS6B01G149100 chr6D 89.855 69 7 0 970 1038 37659996 37659928 4.330000e-14 89.8


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 TraesCS6B01G149100 chr6B 149875715 149878868 3153 False 5825.0 5825 100.0000 1 3154 1 chr6B.!!$F1 3153
1 TraesCS6B01G149100 chr6B 87998707 87999734 1027 True 204.0 204 71.2150 879 1918 1 chr6B.!!$R1 1039
2 TraesCS6B01G149100 chr6A 92574964 92578151 3187 False 4687.0 4687 93.3960 1 3154 1 chr6A.!!$F1 3153
3 TraesCS6B01G149100 chr6D 77171530 77174734 3204 False 2401.5 4167 93.6905 1 3154 2 chr6D.!!$F1 3153

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
351 357 0.246635 AAGTACGTGCGCTGATTCCT 59.753 50.0 9.73 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 2430 0.249322 ACCACCATAGTCATACGCGC 60.249 55.0 5.73 0.0 0.0 6.86 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
21 22 3.370276 GGCGTCGATTTCCTCTAGTAAC 58.630 50.000 0.00 0.00 0.00 2.50
58 59 5.432157 CGCAATTTAAGACGATGATGTACC 58.568 41.667 0.00 0.00 0.00 3.34
87 92 3.935203 ACACACTTCGCAGAGATATTTGG 59.065 43.478 0.00 0.00 38.43 3.28
199 204 4.543590 ATCTGTTCTCACCGAATCAGTT 57.456 40.909 0.00 0.00 34.85 3.16
200 205 5.661056 ATCTGTTCTCACCGAATCAGTTA 57.339 39.130 0.00 0.00 34.85 2.24
234 239 3.821421 TCCTTCCTAATTTCGAGCCTC 57.179 47.619 0.00 0.00 0.00 4.70
282 288 2.280628 CTATGTCCTTTCCTGAACCGC 58.719 52.381 0.00 0.00 0.00 5.68
350 356 1.076332 AAAGTACGTGCGCTGATTCC 58.924 50.000 9.73 0.00 0.00 3.01
351 357 0.246635 AAGTACGTGCGCTGATTCCT 59.753 50.000 9.73 0.00 0.00 3.36
353 359 0.457853 GTACGTGCGCTGATTCCTGA 60.458 55.000 9.73 0.00 0.00 3.86
380 386 0.787787 GCAGTGCATGAACGAACGTA 59.212 50.000 11.09 0.00 0.00 3.57
381 387 1.193650 GCAGTGCATGAACGAACGTAA 59.806 47.619 11.09 0.00 0.00 3.18
383 389 1.459592 AGTGCATGAACGAACGTAAGC 59.540 47.619 0.00 3.74 45.62 3.09
384 390 0.436913 TGCATGAACGAACGTAAGCG 59.563 50.000 0.00 0.00 45.62 4.68
386 392 1.323534 GCATGAACGAACGTAAGCGAT 59.676 47.619 11.54 0.71 45.62 4.58
425 437 5.186021 CCTTTGCCAAGTCTAGTCTAGAGAA 59.814 44.000 9.97 0.00 35.04 2.87
474 521 2.798976 TTCATGCAGGTTGAAGCAAC 57.201 45.000 0.00 1.82 44.88 4.17
479 526 3.762407 TGCAGGTTGAAGCAACTACTA 57.238 42.857 9.80 0.00 43.14 1.82
483 530 4.799586 GCAGGTTGAAGCAACTACTACTCA 60.800 45.833 9.80 0.00 43.14 3.41
497 544 1.351430 TACTCAACGATGCACGCTGC 61.351 55.000 8.31 3.44 46.94 5.25
525 576 8.975663 TGGCGCTAGAACATATATATACTACT 57.024 34.615 7.64 0.00 0.00 2.57
541 592 4.382345 ACTACTGTAAACGAGTATGCCC 57.618 45.455 0.00 0.00 0.00 5.36
542 593 3.765511 ACTACTGTAAACGAGTATGCCCA 59.234 43.478 0.00 0.00 0.00 5.36
543 594 3.906720 ACTGTAAACGAGTATGCCCAT 57.093 42.857 0.00 0.00 0.00 4.00
544 595 3.531538 ACTGTAAACGAGTATGCCCATG 58.468 45.455 0.00 0.00 0.00 3.66
545 596 2.285083 TGTAAACGAGTATGCCCATGC 58.715 47.619 0.00 0.00 38.26 4.06
612 668 1.317431 ACCGGATCGATCGTTGGACA 61.317 55.000 26.97 0.00 0.00 4.02
745 801 3.531059 TCCATCCTGAAAAGGAGAGGAA 58.469 45.455 13.48 2.20 40.71 3.36
924 980 3.128068 TGGCTCTATATATACGGCGTGTG 59.872 47.826 24.86 3.53 0.00 3.82
968 1024 6.390721 GCTTATAGCAGATGATACTCGGAAA 58.609 40.000 0.00 0.00 41.89 3.13
981 1037 2.983592 GGAAACGGCCACCACCAG 60.984 66.667 2.24 0.00 0.00 4.00
1095 1166 3.003763 GGAGACCACTCGGGCCTT 61.004 66.667 0.84 0.00 44.30 4.35
1099 1170 2.847234 ACCACTCGGGCCTTGTCA 60.847 61.111 0.84 0.00 42.05 3.58
1145 1216 0.814010 GGTGTTGAGCTTGACGGTGT 60.814 55.000 0.00 0.00 0.00 4.16
1155 1226 3.071479 GCTTGACGGTGTTCAGGAAATA 58.929 45.455 0.00 0.00 0.00 1.40
1157 1228 4.023536 GCTTGACGGTGTTCAGGAAATAAA 60.024 41.667 0.00 0.00 0.00 1.40
1204 1275 1.210931 CAGTCCTCGTCGGCGTTTA 59.789 57.895 10.18 0.00 39.49 2.01
1268 1339 0.859232 CTGCGCAACGAAGTAAGTGT 59.141 50.000 13.05 0.00 45.00 3.55
1323 1394 5.065090 CAGATCCATACTTTGCGTTTGATGA 59.935 40.000 0.00 0.00 0.00 2.92
1328 1399 7.416817 TCCATACTTTGCGTTTGATGATTATG 58.583 34.615 0.00 0.00 0.00 1.90
1398 1470 0.813210 CTTTGGAGGAGGAGATGCGC 60.813 60.000 0.00 0.00 0.00 6.09
1499 1571 1.978455 AACTGGGGCGTGAACTGTGA 61.978 55.000 0.00 0.00 0.00 3.58
1810 1891 4.467084 CGCCGGTGGTGGTGCTAT 62.467 66.667 7.26 0.00 31.81 2.97
1918 1999 4.266502 GCATCTACATCAACTTCTCGTGAC 59.733 45.833 0.00 0.00 0.00 3.67
1936 2017 3.749609 GTGACGCAAGGGTGTAATAGTTT 59.250 43.478 0.00 0.00 46.39 2.66
1953 2034 2.693074 AGTTTTTGGAACGCATGAACCT 59.307 40.909 0.00 0.00 0.00 3.50
1973 2054 2.191375 CGGTGCCAGGCATCAGAT 59.809 61.111 24.97 0.00 40.05 2.90
2132 2213 4.603946 GGGGATGCTACCGCGACC 62.604 72.222 8.23 0.00 39.65 4.79
2213 2294 8.732746 TTCTTCTTAAGCTATTGTACCATTCC 57.267 34.615 0.00 0.00 0.00 3.01
2268 2349 1.935925 GCGTTTGCGGTGAGTTACA 59.064 52.632 0.00 0.00 38.78 2.41
2303 2384 2.998097 CGGTGGGTGATGGTGGAT 59.002 61.111 0.00 0.00 0.00 3.41
2320 2402 5.166398 GGTGGATATAGTGTATACGGTTGC 58.834 45.833 0.00 0.00 0.00 4.17
2340 2422 4.631131 TGCGTGGAAATATTCGAGATGAT 58.369 39.130 0.00 0.00 0.00 2.45
2348 2430 9.440773 TGGAAATATTCGAGATGATAAAGATGG 57.559 33.333 0.00 0.00 0.00 3.51
2350 2432 7.531280 AATATTCGAGATGATAAAGATGGCG 57.469 36.000 0.00 0.00 0.00 5.69
2443 2526 2.001269 GGAGTGGGTGGGTGGCTAT 61.001 63.158 0.00 0.00 0.00 2.97
2466 2549 4.146564 GGTTAGGTTTTAGCAAGGAACCA 58.853 43.478 12.00 0.00 44.10 3.67
2523 2606 8.112822 TCCACAAAGATTGGTTGGATTTATAGA 58.887 33.333 0.00 0.00 32.68 1.98
2637 2720 1.141053 AGAGAAGGTTCGCCACAAAGT 59.859 47.619 0.00 0.00 40.60 2.66
2652 2735 1.538512 CAAAGTGGCACATGTGAGGAG 59.461 52.381 29.80 2.54 44.52 3.69
2658 2741 0.826715 GCACATGTGAGGAGAGGCTA 59.173 55.000 29.80 0.00 0.00 3.93
2718 2801 8.027524 AGCAGATAGGAACTGATTTTAGATCA 57.972 34.615 0.00 0.00 41.52 2.92
2805 2888 7.230108 CCATCAACAAGATACAAGGATATGCTT 59.770 37.037 3.24 3.24 34.43 3.91
2813 2896 6.784969 AGATACAAGGATATGCTTGAGTACCT 59.215 38.462 35.10 22.14 34.88 3.08
2863 2946 1.617850 GCCTCTCACATGATCCGATCT 59.382 52.381 9.78 0.00 0.00 2.75
2867 2950 2.631545 TCTCACATGATCCGATCTGCAT 59.368 45.455 9.78 0.00 0.00 3.96
2895 2978 1.073548 GTACCCGTTGGCCAGGAAA 59.926 57.895 16.13 1.36 33.59 3.13
2904 2987 0.539986 TGGCCAGGAAACTCGATACC 59.460 55.000 0.00 0.00 40.21 2.73
2938 3021 1.365633 CCTAGAAGGCCTAGCTGCG 59.634 63.158 5.16 2.87 42.79 5.18
2969 3052 1.228063 CGATCCATCAAGGGCCCAG 60.228 63.158 27.56 16.94 38.24 4.45
3000 3083 0.109179 GCATGATCTTGGCGTGCAAA 60.109 50.000 10.35 0.00 45.25 3.68
3053 3136 4.320023 GGCCCTATAAAAGCTTAGCTCTC 58.680 47.826 7.36 0.00 38.25 3.20
3072 3155 2.820787 CTCGTCCCCTCTATAAAGCGAT 59.179 50.000 0.00 0.00 0.00 4.58
3110 3193 2.423947 GGGCCTCTGTTCCATGATTCAT 60.424 50.000 0.84 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 7.855904 GTCTTAAATTGCGGGATACAAATACAG 59.144 37.037 0.00 0.00 39.74 2.74
58 59 1.204704 TCTGCGAAGTGTGTATCCCTG 59.795 52.381 0.00 0.00 0.00 4.45
130 135 4.268884 GCAAATCGGCCGATATAGATCTTC 59.731 45.833 39.08 17.33 33.97 2.87
170 175 3.253432 TCGGTGAGAACAGATATCCATCG 59.747 47.826 0.00 1.53 36.20 3.84
264 269 0.322546 GGCGGTTCAGGAAAGGACAT 60.323 55.000 0.00 0.00 0.00 3.06
310 316 6.488006 ACTTTTAATGTGCTGCTGGGATATAG 59.512 38.462 0.00 0.00 0.00 1.31
350 356 4.141883 GCACTGCATGCGTTTCAG 57.858 55.556 14.09 6.83 46.55 3.02
380 386 5.733676 AGGGAAATTGCATTTTTATCGCTT 58.266 33.333 7.92 0.00 31.47 4.68
381 387 5.343307 AGGGAAATTGCATTTTTATCGCT 57.657 34.783 7.92 6.64 31.47 4.93
425 437 6.350949 GGGGTGTGTATGCAAACTCAAATTAT 60.351 38.462 6.31 0.00 34.97 1.28
433 477 1.547675 CCTGGGGTGTGTATGCAAACT 60.548 52.381 3.98 0.00 33.40 2.66
438 482 1.064758 TGAATCCTGGGGTGTGTATGC 60.065 52.381 0.00 0.00 0.00 3.14
474 521 1.846782 GCGTGCATCGTTGAGTAGTAG 59.153 52.381 9.76 0.00 42.13 2.57
525 576 2.285083 GCATGGGCATACTCGTTTACA 58.715 47.619 0.00 0.00 40.72 2.41
543 594 2.297315 CCTAGATAGATGCCGAGTTGCA 59.703 50.000 0.00 0.00 46.94 4.08
544 595 2.297597 ACCTAGATAGATGCCGAGTTGC 59.702 50.000 0.00 0.00 0.00 4.17
545 596 4.592485 AACCTAGATAGATGCCGAGTTG 57.408 45.455 0.00 0.00 0.00 3.16
546 597 5.453480 GGAAAACCTAGATAGATGCCGAGTT 60.453 44.000 0.00 0.00 0.00 3.01
547 598 4.039366 GGAAAACCTAGATAGATGCCGAGT 59.961 45.833 0.00 0.00 0.00 4.18
612 668 1.609208 AATTGCTGGCTTCTGTTCGT 58.391 45.000 0.00 0.00 0.00 3.85
762 818 6.397272 AGTGAGAAGAGCAACTGAAGATTAG 58.603 40.000 0.00 0.00 0.00 1.73
924 980 1.583054 GTTGGTCGTCTATGGCCATC 58.417 55.000 24.80 7.24 0.00 3.51
933 989 1.475280 TGCTATAAGCGTTGGTCGTCT 59.525 47.619 0.00 0.00 46.26 4.18
1128 1199 1.295792 GAACACCGTCAAGCTCAACA 58.704 50.000 0.00 0.00 0.00 3.33
1131 1202 0.249868 CCTGAACACCGTCAAGCTCA 60.250 55.000 0.00 0.00 0.00 4.26
1145 1216 6.531503 TGTTGTTGGTGTTTATTTCCTGAA 57.468 33.333 0.00 0.00 0.00 3.02
1155 1226 1.178276 TCCGCTTGTTGTTGGTGTTT 58.822 45.000 0.00 0.00 0.00 2.83
1157 1228 0.738389 CTTCCGCTTGTTGTTGGTGT 59.262 50.000 0.00 0.00 0.00 4.16
1268 1339 0.617935 TGGTGGCGATTTGATCTGGA 59.382 50.000 0.00 0.00 0.00 3.86
1648 1720 0.679505 TCCTCACCTTCACCTTCACG 59.320 55.000 0.00 0.00 0.00 4.35
1720 1792 3.382832 CGGCGTCTCCACCTCCTT 61.383 66.667 0.00 0.00 34.01 3.36
1918 1999 4.216687 TCCAAAAACTATTACACCCTTGCG 59.783 41.667 0.00 0.00 0.00 4.85
1936 2017 0.313672 GCAGGTTCATGCGTTCCAAA 59.686 50.000 0.00 0.00 36.28 3.28
1959 2040 1.153309 CGTCATCTGATGCCTGGCA 60.153 57.895 25.65 25.65 44.86 4.92
1992 2073 0.378257 ATGCATGAATGTTCGGCGTC 59.622 50.000 6.85 2.07 34.19 5.19
2079 2160 9.931210 AAACGAAGTAGAAGAAAACATAACTTG 57.069 29.630 0.00 0.00 45.00 3.16
2108 2189 2.125961 GGTAGCATCCCCGTCGAGT 61.126 63.158 0.00 0.00 0.00 4.18
2142 2223 2.230660 ACTCATCCGCTCATATCGACA 58.769 47.619 0.00 0.00 0.00 4.35
2237 2318 1.396996 GCAAACGCTCGGATGTTGTAT 59.603 47.619 0.00 0.00 0.00 2.29
2241 2322 2.860293 CGCAAACGCTCGGATGTT 59.140 55.556 0.00 0.00 0.00 2.71
2268 2349 1.667191 GCTCTGATGCGGCGATCAT 60.667 57.895 12.98 5.16 31.88 2.45
2320 2402 8.520835 TCTTTATCATCTCGAATATTTCCACG 57.479 34.615 0.00 0.00 0.00 4.94
2340 2422 2.882927 AGTCATACGCGCCATCTTTA 57.117 45.000 5.73 0.00 0.00 1.85
2348 2430 0.249322 ACCACCATAGTCATACGCGC 60.249 55.000 5.73 0.00 0.00 6.86
2350 2432 3.317149 TCTGTACCACCATAGTCATACGC 59.683 47.826 0.00 0.00 0.00 4.42
2443 2526 4.146564 GGTTCCTTGCTAAAACCTAACCA 58.853 43.478 0.00 0.00 39.48 3.67
2466 2549 7.890127 TGGATCTAAATCTGGTCTGTTCATTTT 59.110 33.333 0.00 0.00 32.12 1.82
2523 2606 0.319813 GCCAGCCGAGCAATTTGTTT 60.320 50.000 0.00 0.00 0.00 2.83
2526 2609 1.289694 TTGCCAGCCGAGCAATTTG 59.710 52.632 1.81 0.00 44.95 2.32
2637 2720 1.985614 CCTCTCCTCACATGTGCCA 59.014 57.895 21.38 3.89 0.00 4.92
2652 2735 1.411651 CCCTAGCCCTGGTTAGCCTC 61.412 65.000 0.00 0.00 35.27 4.70
2658 2741 0.044244 TCTAAGCCCTAGCCCTGGTT 59.956 55.000 0.00 0.00 41.25 3.67
2805 2888 1.413082 CCCATAGGAGGCAGGTACTCA 60.413 57.143 0.00 0.00 36.70 3.41
2858 2941 1.135046 CCGTTAGAGCATGCAGATCG 58.865 55.000 21.98 16.26 37.82 3.69
2863 2946 0.177141 GGGTACCGTTAGAGCATGCA 59.823 55.000 21.98 0.00 40.86 3.96
2983 3066 0.527565 GGTTTGCACGCCAAGATCAT 59.472 50.000 0.00 0.00 34.34 2.45
3000 3083 1.080638 TTGCCAGGGGAACTATTGGT 58.919 50.000 0.00 0.00 33.21 3.67
3032 3115 3.991121 CGAGAGCTAAGCTTTTATAGGGC 59.009 47.826 3.20 0.00 39.88 5.19
3053 3136 2.927014 GCATCGCTTTATAGAGGGGACG 60.927 54.545 7.39 0.00 0.00 4.79
3072 3155 1.229359 CCTCGACCTACCCCTAGCA 59.771 63.158 0.00 0.00 0.00 3.49
3110 3193 8.920174 TGAAGATGATAAAAATCTACCGAGGTA 58.080 33.333 1.66 1.66 33.17 3.08


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

AutoCloner maintained by Alex Coulton.