Multiple sequence alignment - TraesCS1B01G160500

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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 TraesCS1B01G160500 chr1B 100.000 3470 0 0 1 3470 275552356 275555825 0.000000e+00 6408.0
1 TraesCS1B01G160500 chr1B 97.867 3281 46 7 1 3262 275357399 275360674 0.000000e+00 5650.0
2 TraesCS1B01G160500 chr1B 97.745 3281 50 7 1 3262 275457389 275460664 0.000000e+00 5627.0
3 TraesCS1B01G160500 chr1B 97.440 2383 51 6 889 3262 275671865 275674246 0.000000e+00 4054.0
4 TraesCS1B01G160500 chr1B 97.968 689 14 0 1 689 275670612 275671300 0.000000e+00 1195.0
5 TraesCS1B01G160500 chr1B 99.052 211 2 0 681 891 275671866 275671656 2.530000e-101 379.0
6 TraesCS1B01G160500 chr1B 94.286 210 10 2 3262 3470 275360632 275360840 1.550000e-83 320.0
7 TraesCS1B01G160500 chr1B 94.258 209 10 1 3262 3470 275674204 275674410 5.590000e-83 318.0
8 TraesCS1B01G160500 chr1B 93.301 209 12 1 3262 3470 275460622 275460828 1.210000e-79 307.0
9 TraesCS1B01G160500 chr1A 96.543 2893 71 12 1 2870 246130287 246127401 0.000000e+00 4761.0
10 TraesCS1B01G160500 chr1A 88.917 397 36 5 2868 3264 246127332 246126944 1.870000e-132 483.0
11 TraesCS1B01G160500 chr1A 92.381 210 15 1 3262 3470 246126988 246126779 7.280000e-77 298.0
12 TraesCS1B01G160500 chr2A 83.533 1585 207 28 969 2505 610176624 610178202 0.000000e+00 1432.0
13 TraesCS1B01G160500 chr2A 82.420 1587 203 31 969 2505 607512686 607514246 0.000000e+00 1315.0
14 TraesCS1B01G160500 chr2A 81.868 728 77 23 2 717 610175499 610176183 2.340000e-156 562.0
15 TraesCS1B01G160500 chr2A 80.597 134 26 0 1270 1403 138527691 138527558 1.700000e-18 104.0
16 TraesCS1B01G160500 chr2B 83.428 1587 206 29 969 2505 545152384 545153963 0.000000e+00 1421.0
17 TraesCS1B01G160500 chr2B 80.221 1355 203 39 1270 2576 186403262 186404599 0.000000e+00 957.0
18 TraesCS1B01G160500 chr2B 84.182 727 82 18 2 717 545151263 545151967 0.000000e+00 675.0
19 TraesCS1B01G160500 chr2B 80.899 712 113 11 5 712 185763678 185762986 1.100000e-149 540.0
20 TraesCS1B01G160500 chr2B 81.190 622 110 5 2 621 186402135 186402751 8.650000e-136 494.0
21 TraesCS1B01G160500 chr2D 82.975 1069 163 13 1441 2500 131642728 131641670 0.000000e+00 948.0
22 TraesCS1B01G160500 chr2D 80.451 133 26 0 1270 1402 131642938 131642806 6.130000e-18 102.0
23 TraesCS1B01G160500 chr2D 87.342 79 10 0 5 83 131643888 131643810 1.330000e-14 91.6
24 TraesCS1B01G160500 chr7A 89.189 74 4 4 3031 3104 562324660 562324591 4.770000e-14 89.8
25 TraesCS1B01G160500 chr5D 81.333 75 11 3 3063 3134 510908027 510907953 1.350000e-04 58.4


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 TraesCS1B01G160500 chr1B 275552356 275555825 3469 False 6408.000000 6408 100.000000 1 3470 1 chr1B.!!$F1 3469
1 TraesCS1B01G160500 chr1B 275357399 275360840 3441 False 2985.000000 5650 96.076500 1 3470 2 chr1B.!!$F2 3469
2 TraesCS1B01G160500 chr1B 275457389 275460828 3439 False 2967.000000 5627 95.523000 1 3470 2 chr1B.!!$F3 3469
3 TraesCS1B01G160500 chr1B 275670612 275674410 3798 False 1855.666667 4054 96.555333 1 3470 3 chr1B.!!$F4 3469
4 TraesCS1B01G160500 chr1A 246126779 246130287 3508 True 1847.333333 4761 92.613667 1 3470 3 chr1A.!!$R1 3469
5 TraesCS1B01G160500 chr2A 607512686 607514246 1560 False 1315.000000 1315 82.420000 969 2505 1 chr2A.!!$F1 1536
6 TraesCS1B01G160500 chr2A 610175499 610178202 2703 False 997.000000 1432 82.700500 2 2505 2 chr2A.!!$F2 2503
7 TraesCS1B01G160500 chr2B 545151263 545153963 2700 False 1048.000000 1421 83.805000 2 2505 2 chr2B.!!$F2 2503
8 TraesCS1B01G160500 chr2B 186402135 186404599 2464 False 725.500000 957 80.705500 2 2576 2 chr2B.!!$F1 2574
9 TraesCS1B01G160500 chr2B 185762986 185763678 692 True 540.000000 540 80.899000 5 712 1 chr2B.!!$R1 707
10 TraesCS1B01G160500 chr2D 131641670 131643888 2218 True 380.533333 948 83.589333 5 2500 3 chr2D.!!$R1 2495

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
640 651 0.683973 GATGACCGATCAGATGGGCT 59.316 55.000 11.31 0.0 38.57 5.19 F
1230 1825 4.153330 GCGGTAGGGGAGGAGGGA 62.153 72.222 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 2533 0.677288 TCGAAGTCAACGTGGTCCAT 59.323 50.000 0.0 0.0 0.0 3.41 R
3166 3927 3.680196 GCAGCTCGGTTCCTCTAAGAAAT 60.680 47.826 0.0 0.0 0.0 2.17 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
108 109 1.657556 GCGCAAAGCCTTGGTTACA 59.342 52.632 0.30 0.00 40.81 2.41
276 280 4.335647 CAGTTGCCCGAGCCCTGT 62.336 66.667 0.00 0.00 38.69 4.00
414 418 6.147581 CCAATTCAGTCATATATTGCAGCAC 58.852 40.000 0.00 0.00 0.00 4.40
640 651 0.683973 GATGACCGATCAGATGGGCT 59.316 55.000 11.31 0.00 38.57 5.19
1230 1825 4.153330 GCGGTAGGGGAGGAGGGA 62.153 72.222 0.00 0.00 0.00 4.20
1997 2663 4.649674 AGGTTTAGATACCGCTCTCATCAA 59.350 41.667 0.00 0.00 43.21 2.57
2625 3297 3.797039 TCTGTGTCCACTTCAACTTCTG 58.203 45.455 0.00 0.00 0.00 3.02
2738 3410 2.028203 TGGTCTGCATCGTCAAATCTCA 60.028 45.455 0.00 0.00 0.00 3.27
2874 3622 4.962362 GGAATAAATTTCCAGGGTCATGGT 59.038 41.667 0.00 0.00 41.43 3.55
3011 3769 2.932083 CTGTCGTGCGTGTCACTGC 61.932 63.158 11.34 11.34 43.46 4.40
3113 3871 4.038042 TGGGATCTGACAAAGTAGCTATCG 59.962 45.833 0.00 0.00 0.00 2.92
3132 3890 8.044908 AGCTATCGTGAAACTTCCCTTAAAATA 58.955 33.333 0.00 0.00 31.75 1.40
3166 3927 6.267471 TCCTGTAAAACTAGTAGTTCGGGAAA 59.733 38.462 20.68 6.77 37.47 3.13
3222 3983 6.252599 ACTTCAATAGATGCCCTGTTCATA 57.747 37.500 0.00 0.00 0.00 2.15
3223 3984 6.662755 ACTTCAATAGATGCCCTGTTCATAA 58.337 36.000 0.00 0.00 0.00 1.90
3224 3985 7.118723 ACTTCAATAGATGCCCTGTTCATAAA 58.881 34.615 0.00 0.00 0.00 1.40
3225 3986 7.615365 ACTTCAATAGATGCCCTGTTCATAAAA 59.385 33.333 0.00 0.00 0.00 1.52
3226 3987 7.953005 TCAATAGATGCCCTGTTCATAAAAA 57.047 32.000 0.00 0.00 0.00 1.94
3249 4010 7.454260 AAAGCTACATTTAGAGGAAGTTTGG 57.546 36.000 0.00 0.00 0.00 3.28
3250 4011 5.501156 AGCTACATTTAGAGGAAGTTTGGG 58.499 41.667 0.00 0.00 0.00 4.12
3251 4012 4.096532 GCTACATTTAGAGGAAGTTTGGGC 59.903 45.833 0.00 0.00 0.00 5.36
3252 4013 4.112634 ACATTTAGAGGAAGTTTGGGCA 57.887 40.909 0.00 0.00 0.00 5.36
3253 4014 4.479158 ACATTTAGAGGAAGTTTGGGCAA 58.521 39.130 0.00 0.00 0.00 4.52
3254 4015 4.898861 ACATTTAGAGGAAGTTTGGGCAAA 59.101 37.500 0.00 0.00 0.00 3.68
3255 4016 5.365314 ACATTTAGAGGAAGTTTGGGCAAAA 59.635 36.000 0.00 0.00 31.33 2.44
3256 4017 5.941555 TTTAGAGGAAGTTTGGGCAAAAA 57.058 34.783 0.00 0.00 31.33 1.94
3257 4018 3.819564 AGAGGAAGTTTGGGCAAAAAC 57.180 42.857 6.87 6.87 39.80 2.43
3258 4019 3.103742 AGAGGAAGTTTGGGCAAAAACA 58.896 40.909 14.88 0.00 41.56 2.83
3259 4020 3.517500 AGAGGAAGTTTGGGCAAAAACAA 59.482 39.130 14.88 0.00 41.56 2.83
3260 4021 4.019771 AGAGGAAGTTTGGGCAAAAACAAA 60.020 37.500 14.88 0.65 41.56 2.83
3360 4122 4.096190 AGGATCCTATAAACTCGACCGA 57.904 45.455 14.27 0.00 0.00 4.69
3361 4123 3.819902 AGGATCCTATAAACTCGACCGAC 59.180 47.826 14.27 0.00 0.00 4.79
3454 4218 2.044053 CCATGCATTCCCCCACGT 60.044 61.111 0.00 0.00 0.00 4.49
3465 4229 4.657824 CCCACGTCGTCACCGCTT 62.658 66.667 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 1.160329 GCACTGTGCGTTTGACCTCT 61.160 55.000 17.93 0.00 31.71 3.69
276 280 2.370349 GAGTCGATCTCCTTCTGGTCA 58.630 52.381 0.00 0.00 37.22 4.02
414 418 2.741985 TCACACAAGGCATCCGCG 60.742 61.111 0.00 0.00 39.92 6.46
640 651 0.407528 TGGGTGCTGGATTTGCCTTA 59.592 50.000 0.00 0.00 37.63 2.69
1230 1825 0.334676 CTGTCACCTCCTCCTCCTCT 59.665 60.000 0.00 0.00 0.00 3.69
1867 2533 0.677288 TCGAAGTCAACGTGGTCCAT 59.323 50.000 0.00 0.00 0.00 3.41
1997 2663 1.333619 CTACCGTGCAAAAGCAGTTGT 59.666 47.619 0.00 0.00 0.00 3.32
2738 3410 3.857157 TTGTTGGAGTTGCTCTAACCT 57.143 42.857 18.17 0.00 46.56 3.50
2786 3458 8.585471 AGATACATGATTTGTTGGAGATGTTT 57.415 30.769 0.00 0.00 39.87 2.83
2787 3459 8.051535 AGAGATACATGATTTGTTGGAGATGTT 58.948 33.333 0.00 0.00 39.87 2.71
2842 3519 7.093068 ACCCTGGAAATTTATTCCATGTTTACC 60.093 37.037 10.13 0.00 46.47 2.85
2988 3746 4.221422 ACACGCACGACAGCCACT 62.221 61.111 0.00 0.00 0.00 4.00
2990 3748 4.214327 TGACACGCACGACAGCCA 62.214 61.111 0.00 0.00 0.00 4.75
3113 3871 9.764870 GTTCGTATATTTTAAGGGAAGTTTCAC 57.235 33.333 0.00 0.00 0.00 3.18
3154 3915 6.637657 TCCTCTAAGAAATTTCCCGAACTAC 58.362 40.000 14.61 0.00 0.00 2.73
3155 3916 6.862469 TCCTCTAAGAAATTTCCCGAACTA 57.138 37.500 14.61 0.00 0.00 2.24
3156 3917 5.757099 TCCTCTAAGAAATTTCCCGAACT 57.243 39.130 14.61 0.00 0.00 3.01
3166 3927 3.680196 GCAGCTCGGTTCCTCTAAGAAAT 60.680 47.826 0.00 0.00 0.00 2.17
3223 3984 8.360390 CCAAACTTCCTCTAAATGTAGCTTTTT 58.640 33.333 0.00 0.00 0.00 1.94
3224 3985 7.039714 CCCAAACTTCCTCTAAATGTAGCTTTT 60.040 37.037 0.00 0.00 0.00 2.27
3225 3986 6.434340 CCCAAACTTCCTCTAAATGTAGCTTT 59.566 38.462 0.00 0.00 0.00 3.51
3226 3987 5.946377 CCCAAACTTCCTCTAAATGTAGCTT 59.054 40.000 0.00 0.00 0.00 3.74
3227 3988 5.501156 CCCAAACTTCCTCTAAATGTAGCT 58.499 41.667 0.00 0.00 0.00 3.32
3228 3989 4.096532 GCCCAAACTTCCTCTAAATGTAGC 59.903 45.833 0.00 0.00 0.00 3.58
3229 3990 5.253330 TGCCCAAACTTCCTCTAAATGTAG 58.747 41.667 0.00 0.00 0.00 2.74
3230 3991 5.249780 TGCCCAAACTTCCTCTAAATGTA 57.750 39.130 0.00 0.00 0.00 2.29
3231 3992 4.112634 TGCCCAAACTTCCTCTAAATGT 57.887 40.909 0.00 0.00 0.00 2.71
3232 3993 5.467035 TTTGCCCAAACTTCCTCTAAATG 57.533 39.130 0.00 0.00 0.00 2.32
3233 3994 6.126911 TGTTTTTGCCCAAACTTCCTCTAAAT 60.127 34.615 8.77 0.00 37.51 1.40
3234 3995 5.187967 TGTTTTTGCCCAAACTTCCTCTAAA 59.812 36.000 8.77 0.00 37.51 1.85
3235 3996 4.712337 TGTTTTTGCCCAAACTTCCTCTAA 59.288 37.500 8.77 0.00 37.51 2.10
3236 3997 4.282496 TGTTTTTGCCCAAACTTCCTCTA 58.718 39.130 8.77 0.00 37.51 2.43
3237 3998 3.103742 TGTTTTTGCCCAAACTTCCTCT 58.896 40.909 8.77 0.00 37.51 3.69
3238 3999 3.535280 TGTTTTTGCCCAAACTTCCTC 57.465 42.857 8.77 0.00 37.51 3.71
3239 4000 3.990959 TTGTTTTTGCCCAAACTTCCT 57.009 38.095 8.77 0.00 37.51 3.36
3240 4001 3.753797 TGTTTGTTTTTGCCCAAACTTCC 59.246 39.130 14.18 0.00 46.61 3.46
3241 4002 5.559427 ATGTTTGTTTTTGCCCAAACTTC 57.441 34.783 14.18 2.04 46.61 3.01
3242 4003 7.454260 TTTATGTTTGTTTTTGCCCAAACTT 57.546 28.000 14.18 11.07 46.61 2.66
3243 4004 7.454260 TTTTATGTTTGTTTTTGCCCAAACT 57.546 28.000 14.18 5.22 46.61 2.66
3396 4159 1.176619 AGCCCACCAACGTTTTAGGC 61.177 55.000 16.69 16.69 39.25 3.93


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

AutoCloner maintained by Alex Coulton.