Multiple sequence alignment - TraesCS6B01G126600

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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 TraesCS6B01G126600 chr6B 100.000 4280 0 0 1 4280 121962254 121957975 0.000000e+00 7904
1 TraesCS6B01G126600 chr6B 96.147 3919 135 9 1 3919 122188792 122184890 0.000000e+00 6386
2 TraesCS6B01G126600 chr6B 85.704 1378 155 18 2170 3521 121432688 121431327 0.000000e+00 1415
3 TraesCS6B01G126600 chr6B 87.179 273 28 6 3577 3846 121431221 121430953 1.930000e-78 303
4 TraesCS6B01G126600 chr6D 93.533 4098 207 23 1 4070 49180617 49184684 0.000000e+00 6047
5 TraesCS6B01G126600 chr6D 90.016 1853 162 10 2015 3846 50604941 50606791 0.000000e+00 2375
6 TraesCS6B01G126600 chr6D 81.224 2125 298 55 1503 3561 430846269 430844180 0.000000e+00 1620
7 TraesCS6B01G126600 chr6D 86.257 1368 159 18 2170 3510 50179795 50181160 0.000000e+00 1458
8 TraesCS6B01G126600 chr6D 88.533 1029 112 6 1 1027 50602669 50603693 0.000000e+00 1242
9 TraesCS6B01G126600 chr6D 85.947 861 99 8 1081 1920 50604069 50604928 0.000000e+00 900
10 TraesCS6B01G126600 chr6D 90.826 218 18 2 4063 4280 49185684 49185899 1.510000e-74 291
11 TraesCS6B01G126600 chr6D 90.909 198 15 3 4084 4280 49184474 49184669 3.280000e-66 263
12 TraesCS6B01G126600 chr7A 85.300 3313 361 55 576 3843 591022665 591025896 0.000000e+00 3304
13 TraesCS6B01G126600 chr7A 81.782 505 67 13 3084 3569 551541816 551541318 2.400000e-107 399
14 TraesCS6B01G126600 chr7A 80.102 392 65 9 322 707 616446179 616445795 3.260000e-71 279
15 TraesCS6B01G126600 chrUn 89.482 1854 170 11 2015 3846 277361152 277363002 0.000000e+00 2320
16 TraesCS6B01G126600 chrUn 89.640 888 89 2 1 888 71748736 71749620 0.000000e+00 1127
17 TraesCS6B01G126600 chrUn 84.171 1055 141 7 890 1919 373934200 373933147 0.000000e+00 1000
18 TraesCS6B01G126600 chrUn 91.559 699 54 3 2015 2708 373933137 373932439 0.000000e+00 959
19 TraesCS6B01G126600 chrUn 89.698 398 40 1 1369 1765 478961346 478960949 1.370000e-139 507
20 TraesCS6B01G126600 chr6A 89.428 1854 171 11 2015 3846 64679792 64677942 0.000000e+00 2314
21 TraesCS6B01G126600 chr6A 86.818 1942 224 14 1 1919 64681734 64679802 0.000000e+00 2139
22 TraesCS6B01G126600 chr6A 81.628 2052 267 51 1516 3495 577723981 577721968 0.000000e+00 1600
23 TraesCS6B01G126600 chr7B 81.633 2058 279 58 1549 3560 517933887 517931883 0.000000e+00 1615
24 TraesCS6B01G126600 chr7B 82.446 1014 130 24 1549 2535 509737169 509736177 0.000000e+00 843
25 TraesCS6B01G126600 chr7B 81.541 688 100 22 1 682 517936261 517935595 3.760000e-150 542
26 TraesCS6B01G126600 chr7B 89.944 179 17 1 4084 4262 691252139 691251962 3.330000e-56 230
27 TraesCS6B01G126600 chr7B 85.915 213 16 4 3848 4049 691252162 691251953 9.320000e-52 215
28 TraesCS6B01G126600 chr7D 81.374 1718 238 46 1887 3560 489302131 489300452 0.000000e+00 1325
29 TraesCS6B01G126600 chr7D 80.601 366 61 7 346 709 535508463 535508820 1.520000e-69 274
30 TraesCS6B01G126600 chr7D 85.600 250 20 5 3846 4082 559781229 559781475 9.190000e-62 248
31 TraesCS6B01G126600 chr7D 89.394 198 18 3 4084 4280 559781253 559781448 3.310000e-61 246
32 TraesCS6B01G126600 chr7D 90.857 175 15 1 4084 4258 612800646 612800473 2.570000e-57 233
33 TraesCS6B01G126600 chr7D 88.601 193 12 4 3855 4037 612800663 612800471 4.310000e-55 226
34 TraesCS6B01G126600 chr7D 89.385 179 18 1 4084 4262 589000651 589000474 1.550000e-54 224
35 TraesCS6B01G126600 chr7D 85.915 213 16 7 3848 4049 589000674 589000465 9.320000e-52 215
36 TraesCS6B01G126600 chr7D 85.437 206 17 6 3855 4049 589985331 589985128 7.260000e-48 202
37 TraesCS6B01G126600 chr4A 83.371 439 49 16 3855 4275 271050158 271050590 6.710000e-103 385
38 TraesCS6B01G126600 chr4A 85.657 251 20 9 3845 4082 271050374 271050621 2.560000e-62 250
39 TraesCS6B01G126600 chr1D 85.124 242 20 8 3855 4082 3847479 3847718 2.570000e-57 233
40 TraesCS6B01G126600 chr1D 87.629 194 20 4 4084 4275 3847496 3847687 5.570000e-54 222
41 TraesCS6B01G126600 chr1D 86.932 176 20 2 4101 4275 3855690 3855863 1.210000e-45 195
42 TraesCS6B01G126600 chr5A 83.750 160 13 5 3700 3846 531402536 531402695 5.770000e-29 139
43 TraesCS6B01G126600 chr2B 81.250 128 23 1 3572 3698 142297550 142297677 7.570000e-18 102


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 TraesCS6B01G126600 chr6B 121957975 121962254 4279 True 7904.000000 7904 100.000000 1 4280 1 chr6B.!!$R1 4279
1 TraesCS6B01G126600 chr6B 122184890 122188792 3902 True 6386.000000 6386 96.147000 1 3919 1 chr6B.!!$R2 3918
2 TraesCS6B01G126600 chr6B 121430953 121432688 1735 True 859.000000 1415 86.441500 2170 3846 2 chr6B.!!$R3 1676
3 TraesCS6B01G126600 chr6D 49180617 49185899 5282 False 2200.333333 6047 91.756000 1 4280 3 chr6D.!!$F2 4279
4 TraesCS6B01G126600 chr6D 430844180 430846269 2089 True 1620.000000 1620 81.224000 1503 3561 1 chr6D.!!$R1 2058
5 TraesCS6B01G126600 chr6D 50602669 50606791 4122 False 1505.666667 2375 88.165333 1 3846 3 chr6D.!!$F3 3845
6 TraesCS6B01G126600 chr6D 50179795 50181160 1365 False 1458.000000 1458 86.257000 2170 3510 1 chr6D.!!$F1 1340
7 TraesCS6B01G126600 chr7A 591022665 591025896 3231 False 3304.000000 3304 85.300000 576 3843 1 chr7A.!!$F1 3267
8 TraesCS6B01G126600 chrUn 277361152 277363002 1850 False 2320.000000 2320 89.482000 2015 3846 1 chrUn.!!$F2 1831
9 TraesCS6B01G126600 chrUn 71748736 71749620 884 False 1127.000000 1127 89.640000 1 888 1 chrUn.!!$F1 887
10 TraesCS6B01G126600 chrUn 373932439 373934200 1761 True 979.500000 1000 87.865000 890 2708 2 chrUn.!!$R2 1818
11 TraesCS6B01G126600 chr6A 64677942 64681734 3792 True 2226.500000 2314 88.123000 1 3846 2 chr6A.!!$R2 3845
12 TraesCS6B01G126600 chr6A 577721968 577723981 2013 True 1600.000000 1600 81.628000 1516 3495 1 chr6A.!!$R1 1979
13 TraesCS6B01G126600 chr7B 517931883 517936261 4378 True 1078.500000 1615 81.587000 1 3560 2 chr7B.!!$R2 3559
14 TraesCS6B01G126600 chr7B 509736177 509737169 992 True 843.000000 843 82.446000 1549 2535 1 chr7B.!!$R1 986
15 TraesCS6B01G126600 chr7D 489300452 489302131 1679 True 1325.000000 1325 81.374000 1887 3560 1 chr7D.!!$R1 1673

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
503 849 0.106116 ATCTGGACGGGAGGAGTACC 60.106 60.000 0.0 0.00 0.00 3.34 F
688 1392 1.136984 CGGAGAGTGTACGGCAGTC 59.863 63.158 0.0 8.47 45.57 3.51 F
1168 2197 1.218047 CGCGGAGGATGACAAAGGA 59.782 57.895 0.0 0.00 0.00 3.36 F
2390 3677 1.229690 TGGGGTAAGTGGGCTGCTA 60.230 57.895 0.0 0.00 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 3039 1.132881 AGAAATTTGGCCCTTCCCACA 60.133 47.619 0.00 0.0 33.82 4.17 R
2580 3867 0.823356 AGGTTCATGTGCCACGCTTT 60.823 50.000 10.09 0.0 0.00 3.51 R
2927 4214 0.401356 TGGGCAAGTGCAGATTCAGA 59.599 50.000 5.52 0.0 44.36 3.27 R
3674 5060 2.346766 TGCCAGAGCTTGAAGTGAAA 57.653 45.000 0.00 0.0 40.80 2.69 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
204 210 7.410120 ACTTTCCTTTTCACTGAGAACAATT 57.590 32.000 0.00 0.00 35.56 2.32
280 287 9.699410 ATTTATGAGAAGATATTGGTCCAACAA 57.301 29.630 6.41 0.00 34.41 2.83
485 831 6.154877 TGGTTGGATGAATCTGTGCAATAAAT 59.845 34.615 0.00 0.00 0.00 1.40
503 849 0.106116 ATCTGGACGGGAGGAGTACC 60.106 60.000 0.00 0.00 0.00 3.34
540 886 4.770531 AGTCATACTACAGGTGTGCAGTAA 59.229 41.667 0.00 0.00 37.05 2.24
688 1392 1.136984 CGGAGAGTGTACGGCAGTC 59.863 63.158 0.00 8.47 45.57 3.51
766 1470 5.275067 TGTTTGCTTGCCTACAAAGAAAT 57.725 34.783 0.00 0.00 36.50 2.17
907 1614 2.253452 CTTCCACAAGCAGCGCAC 59.747 61.111 11.47 0.00 0.00 5.34
908 1615 2.515757 TTCCACAAGCAGCGCACA 60.516 55.556 11.47 0.00 0.00 4.57
911 1618 3.282157 CACAAGCAGCGCACACCT 61.282 61.111 11.47 0.00 0.00 4.00
979 1686 2.957006 GTCCATCGCGTATATAGGGGAT 59.043 50.000 22.34 22.34 42.11 3.85
1098 2127 2.001361 CTTCGGCGAGGTACCATCGT 62.001 60.000 24.83 3.68 42.13 3.73
1156 2185 3.220999 TTCCCACAGTGACGCGGAG 62.221 63.158 12.47 0.00 0.00 4.63
1168 2197 1.218047 CGCGGAGGATGACAAAGGA 59.782 57.895 0.00 0.00 0.00 3.36
1342 2392 3.649981 AGTATGGTGGATGAGAAGGATGG 59.350 47.826 0.00 0.00 0.00 3.51
1382 2432 1.669760 CAAGTCCTTTGCCGCCGTA 60.670 57.895 0.00 0.00 0.00 4.02
1474 2524 6.403855 GCCTTTTAGCGGTTGATTGTTGTATA 60.404 38.462 0.00 0.00 0.00 1.47
1668 2893 5.413309 TTTTCCAATTGTCTGTTGTGGTT 57.587 34.783 4.43 0.00 0.00 3.67
1813 3039 4.741928 AGTCAAAAGGGGTGGTAAATCT 57.258 40.909 0.00 0.00 0.00 2.40
1916 3142 8.784043 GTGTGTGTAAGGATTGTTCTAGATTTT 58.216 33.333 0.00 0.00 0.00 1.82
2252 3518 4.099419 GGGAGAAATTTGTGAGTGTTGGTT 59.901 41.667 0.00 0.00 0.00 3.67
2390 3677 1.229690 TGGGGTAAGTGGGCTGCTA 60.230 57.895 0.00 0.00 0.00 3.49
2580 3867 3.650647 CTCCTAAAGCACCCAAGCA 57.349 52.632 0.00 0.00 36.85 3.91
2838 4125 5.667626 ACACCAAGACTCCAGATATACCATT 59.332 40.000 0.00 0.00 0.00 3.16
2868 4155 4.018506 TCCCATTTCTACCATTGCTGAAGA 60.019 41.667 0.00 0.00 0.00 2.87
2976 4266 0.317160 TACAACTCAGTGGTGCCTCG 59.683 55.000 0.00 0.00 36.69 4.63
3123 4413 2.685897 ACCTCTAGAGCTTCGATGACAC 59.314 50.000 14.73 0.00 0.00 3.67
3508 4825 6.075099 CGTTAATTTGTGCACTTGATCGTTTT 60.075 34.615 19.41 1.94 0.00 2.43
3829 5215 3.421394 ACTCATGAGTTGGGGGATCTA 57.579 47.619 22.89 0.00 38.83 1.98
3857 5243 8.435187 TCCATTTCAGTGCATCTATCTATTCTT 58.565 33.333 0.00 0.00 0.00 2.52
4102 6507 9.573166 TCATTAGGTATTTGATGGGTTAATCAG 57.427 33.333 0.00 0.00 37.83 2.90
4107 6512 9.320295 AGGTATTTGATGGGTTAATCAGAAAAA 57.680 29.630 0.00 0.00 37.83 1.94
4133 6538 9.477484 AGATAAATACGCTAGAAATTACCACAG 57.523 33.333 0.00 0.00 0.00 3.66
4240 6645 7.147312 CACCATTGCCATTACAATTATAGTGG 58.853 38.462 1.03 1.03 38.19 4.00
4241 6646 7.014134 CACCATTGCCATTACAATTATAGTGGA 59.986 37.037 9.33 0.00 38.19 4.02
4266 6671 9.599322 GAGAAAATCATACTAAAACACACACAG 57.401 33.333 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.744238 TCACGTTCTTGATCTGACCAA 57.256 42.857 0.00 0.00 0.00 3.67
485 831 1.305623 GGTACTCCTCCCGTCCAGA 59.694 63.158 0.00 0.00 0.00 3.86
766 1470 7.915293 ATGGATGAATGTACGTTTCACTTTA 57.085 32.000 11.85 2.65 36.02 1.85
908 1615 2.029073 CCACACGTCAGCGAAGGT 59.971 61.111 0.00 0.00 42.00 3.50
911 1618 2.028484 GTCCCACACGTCAGCGAA 59.972 61.111 0.00 0.00 42.00 4.70
979 1686 2.780924 AAGTGGGGGTGAGGCCAA 60.781 61.111 5.01 0.00 39.65 4.52
1098 2127 1.221566 CTCCACCGCACATGATGGA 59.778 57.895 0.00 3.63 38.94 3.41
1156 2185 3.209410 CATAGTGCCTCCTTTGTCATCC 58.791 50.000 0.00 0.00 0.00 3.51
1382 2432 1.284313 CTTGGGAGAGGGAGCTCTTT 58.716 55.000 14.64 1.52 35.26 2.52
1449 2499 2.986479 CAACAATCAACCGCTAAAAGGC 59.014 45.455 0.00 0.00 0.00 4.35
1474 2524 4.728772 TGAACCAATCACACAATCTCCTT 58.271 39.130 0.00 0.00 31.50 3.36
1653 2877 2.430332 CCAACCAACCACAACAGACAAT 59.570 45.455 0.00 0.00 0.00 2.71
1668 2893 2.691011 GTCAAAAACAGCCTACCAACCA 59.309 45.455 0.00 0.00 0.00 3.67
1774 3000 7.938140 TTTGACTAAATGCTAAGCTTATGGT 57.062 32.000 6.64 0.00 0.00 3.55
1813 3039 1.132881 AGAAATTTGGCCCTTCCCACA 60.133 47.619 0.00 0.00 33.82 4.17
2037 3268 7.770897 GTCCTGATAAACAAGACCTCATGTTAT 59.229 37.037 0.00 0.00 36.86 1.89
2252 3518 9.685276 TTAAGATCAATTTCAATGCTAAGAGGA 57.315 29.630 0.00 0.00 0.00 3.71
2390 3677 4.021916 CCCTTGCTTGGATCTCTGATTTT 58.978 43.478 0.00 0.00 0.00 1.82
2580 3867 0.823356 AGGTTCATGTGCCACGCTTT 60.823 50.000 10.09 0.00 0.00 3.51
2838 4125 4.524802 ATGGTAGAAATGGGAGCAATGA 57.475 40.909 0.00 0.00 0.00 2.57
2927 4214 0.401356 TGGGCAAGTGCAGATTCAGA 59.599 50.000 5.52 0.00 44.36 3.27
2976 4266 5.580691 TCGACATCATTGTTCTCCATAACAC 59.419 40.000 0.00 0.00 39.02 3.32
3417 4730 6.421405 ACGACGACATAAAAGGTTACAAAAC 58.579 36.000 0.00 0.00 34.66 2.43
3508 4825 7.648039 TTAAACAGGCAGAACTAAAGGAAAA 57.352 32.000 0.00 0.00 0.00 2.29
3674 5060 2.346766 TGCCAGAGCTTGAAGTGAAA 57.653 45.000 0.00 0.00 40.80 2.69
3712 5098 9.926158 ATGATCACACATCTAGTATCAAAGATC 57.074 33.333 0.00 0.00 29.93 2.75
3829 5215 9.228949 GAATAGATAGATGCACTGAAATGGAAT 57.771 33.333 0.00 0.00 0.00 3.01
3932 5318 7.837863 AGTCTCTTAAAATGAACGACTGGATA 58.162 34.615 0.00 0.00 0.00 2.59
3935 5321 6.787085 AAGTCTCTTAAAATGAACGACTGG 57.213 37.500 0.00 0.00 31.35 4.00
4107 6512 9.477484 CTGTGGTAATTTCTAGCGTATTTATCT 57.523 33.333 0.00 0.00 0.00 1.98
4128 6533 7.047891 TGGCTAGATGTTTCTATTTACTGTGG 58.952 38.462 0.00 0.00 33.98 4.17
4211 6616 9.241919 CTATAATTGTAATGGCAATGGTGGATA 57.758 33.333 0.00 0.00 38.87 2.59
4212 6617 6.999705 ATAATTGTAATGGCAATGGTGGAT 57.000 33.333 0.00 0.00 38.87 3.41
4213 6618 7.014134 CACTATAATTGTAATGGCAATGGTGGA 59.986 37.037 0.00 0.00 38.87 4.02
4215 6620 7.014134 TCCACTATAATTGTAATGGCAATGGTG 59.986 37.037 4.94 0.00 38.87 4.17
4216 6621 7.066142 TCCACTATAATTGTAATGGCAATGGT 58.934 34.615 4.94 0.00 38.87 3.55
4217 6622 7.448161 TCTCCACTATAATTGTAATGGCAATGG 59.552 37.037 4.94 0.00 38.87 3.16
4240 6645 9.599322 CTGTGTGTGTTTTAGTATGATTTTCTC 57.401 33.333 0.00 0.00 0.00 2.87
4241 6646 9.337396 TCTGTGTGTGTTTTAGTATGATTTTCT 57.663 29.630 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.