Multiple sequence alignment - TraesCS4B01G169300

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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 TraesCS4B01G169300 chr4B 100.000 2255 0 0 1 2255 369781731 369779477 0.000000e+00 4165
1 TraesCS4B01G169300 chr6B 95.411 2288 72 4 1 2255 578015622 578017909 0.000000e+00 3613
2 TraesCS4B01G169300 chr3B 95.089 1120 23 3 1168 2255 52856941 52855822 0.000000e+00 1735
3 TraesCS4B01G169300 chr2B 88.905 1352 104 29 1 1341 516098538 516099854 0.000000e+00 1624
4 TraesCS4B01G169300 chr2B 93.886 965 26 4 1323 2255 198522504 198521541 0.000000e+00 1424
5 TraesCS4B01G169300 chr2B 88.700 823 57 18 1464 2254 516099883 516100701 0.000000e+00 972
6 TraesCS4B01G169300 chr2B 88.333 360 24 6 1912 2254 706400174 706400532 1.250000e-112 416
7 TraesCS4B01G169300 chr2B 96.907 194 6 0 1 194 198531457 198531264 2.160000e-85 326
8 TraesCS4B01G169300 chr2B 86.826 167 16 4 2090 2255 592573145 592573306 4.950000e-42 182
9 TraesCS4B01G169300 chr7A 90.649 909 59 10 1 897 219381478 219380584 0.000000e+00 1184
10 TraesCS4B01G169300 chr7A 89.065 695 64 7 1447 2138 219379954 219379269 0.000000e+00 852
11 TraesCS4B01G169300 chr7A 88.408 578 57 7 833 1403 219380537 219379963 0.000000e+00 688
12 TraesCS4B01G169300 chr3A 89.468 883 59 11 1 860 323384560 323385431 0.000000e+00 1085
13 TraesCS4B01G169300 chr3A 88.688 884 64 14 1376 2254 486211499 486210647 0.000000e+00 1046
14 TraesCS4B01G169300 chr3A 91.483 634 49 4 1504 2135 323385929 323386559 0.000000e+00 867
15 TraesCS4B01G169300 chr3A 90.850 459 34 5 887 1341 486211948 486211494 1.920000e-170 608
16 TraesCS4B01G169300 chr3A 92.987 385 27 0 963 1347 323385491 323385875 1.510000e-156 562
17 TraesCS4B01G169300 chr3A 92.216 167 10 2 694 859 486212088 486211924 1.350000e-57 233
18 TraesCS4B01G169300 chr3D 89.354 883 60 8 1 860 75768346 75767475 0.000000e+00 1079
19 TraesCS4B01G169300 chr3D 92.147 382 20 4 967 1347 75767411 75767039 4.260000e-147 531
20 TraesCS4B01G169300 chr1A 94.684 696 35 2 1 695 330763503 330762809 0.000000e+00 1079
21 TraesCS4B01G169300 chr1A 89.015 883 63 12 1 860 41320738 41319867 0.000000e+00 1062
22 TraesCS4B01G169300 chr1A 88.788 883 65 12 1 860 41411586 41412457 0.000000e+00 1051
23 TraesCS4B01G169300 chr1A 92.922 664 42 3 1464 2125 330762179 330761519 0.000000e+00 961
24 TraesCS4B01G169300 chr1A 90.810 457 35 4 887 1341 330762659 330762208 2.480000e-169 604
25 TraesCS4B01G169300 chr1A 89.461 427 39 4 963 1384 41319806 41319381 3.300000e-148 534
26 TraesCS4B01G169300 chr1A 91.688 385 32 0 963 1347 41412518 41412902 3.300000e-148 534
27 TraesCS4B01G169300 chr2D 89.241 883 59 9 1 860 348077516 348076647 0.000000e+00 1072
28 TraesCS4B01G169300 chr4A 89.975 798 55 14 1 796 527577780 527577006 0.000000e+00 1007
29 TraesCS4B01G169300 chr4A 91.066 638 49 4 1504 2139 527576372 527575741 0.000000e+00 856
30 TraesCS4B01G169300 chr4A 90.867 427 33 4 963 1384 527576828 527576403 3.250000e-158 568
31 TraesCS4B01G169300 chr4A 85.965 171 14 6 2090 2255 527575719 527575554 8.280000e-40 174
32 TraesCS4B01G169300 chr5D 92.517 147 11 0 2108 2254 240171140 240171286 6.310000e-51 211
33 TraesCS4B01G169300 chr1B 86.826 167 16 4 2090 2255 188444441 188444602 4.950000e-42 182


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 TraesCS4B01G169300 chr4B 369779477 369781731 2254 True 4165.000000 4165 100.000000 1 2255 1 chr4B.!!$R1 2254
1 TraesCS4B01G169300 chr6B 578015622 578017909 2287 False 3613.000000 3613 95.411000 1 2255 1 chr6B.!!$F1 2254
2 TraesCS4B01G169300 chr3B 52855822 52856941 1119 True 1735.000000 1735 95.089000 1168 2255 1 chr3B.!!$R1 1087
3 TraesCS4B01G169300 chr2B 198521541 198522504 963 True 1424.000000 1424 93.886000 1323 2255 1 chr2B.!!$R1 932
4 TraesCS4B01G169300 chr2B 516098538 516100701 2163 False 1298.000000 1624 88.802500 1 2254 2 chr2B.!!$F3 2253
5 TraesCS4B01G169300 chr7A 219379269 219381478 2209 True 908.000000 1184 89.374000 1 2138 3 chr7A.!!$R1 2137
6 TraesCS4B01G169300 chr3A 323384560 323386559 1999 False 838.000000 1085 91.312667 1 2135 3 chr3A.!!$F1 2134
7 TraesCS4B01G169300 chr3A 486210647 486212088 1441 True 629.000000 1046 90.584667 694 2254 3 chr3A.!!$R1 1560
8 TraesCS4B01G169300 chr3D 75767039 75768346 1307 True 805.000000 1079 90.750500 1 1347 2 chr3D.!!$R1 1346
9 TraesCS4B01G169300 chr1A 330761519 330763503 1984 True 881.333333 1079 92.805333 1 2125 3 chr1A.!!$R2 2124
10 TraesCS4B01G169300 chr1A 41319381 41320738 1357 True 798.000000 1062 89.238000 1 1384 2 chr1A.!!$R1 1383
11 TraesCS4B01G169300 chr1A 41411586 41412902 1316 False 792.500000 1051 90.238000 1 1347 2 chr1A.!!$F1 1346
12 TraesCS4B01G169300 chr2D 348076647 348077516 869 True 1072.000000 1072 89.241000 1 860 1 chr2D.!!$R1 859
13 TraesCS4B01G169300 chr4A 527575554 527577780 2226 True 651.250000 1007 89.468250 1 2255 4 chr4A.!!$R1 2254

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
294 300 1.179174 GCCAGGGTTTCTTCCACCAC 61.179 60.0 0.0 0.0 35.8 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2305 0.881796 TGCGACGAGTCTCTGACATT 59.118 50.0 0.0 0.0 34.6 2.71 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
94 95 4.593033 GGTCAGCCCATGATGCAT 57.407 55.556 0.00 0.00 40.92 3.96
133 134 5.723295 CGTTGGAAAGGAATGATGGATTTT 58.277 37.500 0.00 0.00 32.44 1.82
204 210 8.889717 GGATTTTGATCGTTTCCTAATTACTGA 58.110 33.333 0.00 0.00 0.00 3.41
294 300 1.179174 GCCAGGGTTTCTTCCACCAC 61.179 60.000 0.00 0.00 35.80 4.16
319 325 4.605183 AGGGCTACTCGCTATCATCTTAT 58.395 43.478 0.00 0.00 39.13 1.73
441 447 1.290203 CCGATGGAGAATTGTGGACG 58.710 55.000 0.00 0.00 0.00 4.79
474 480 1.203994 ACCCTTATCCGTCACAAGTCG 59.796 52.381 0.00 0.00 0.00 4.18
491 497 4.273148 AGTCGAAATTGTCCTAGCTTGT 57.727 40.909 0.00 0.00 0.00 3.16
685 691 1.314730 TCACGTGTGTAGAGCTCACA 58.685 50.000 17.77 14.91 42.41 3.58
841 921 5.620206 TGTTTGAGCTCCACTTCAATTCTA 58.380 37.500 12.15 0.00 0.00 2.10
940 1181 6.874134 GGTGCTTCACTTTAGACTTGAGATAA 59.126 38.462 0.00 0.00 34.40 1.75
987 1241 6.488683 TCCTTTTTGTTGTTCTGTACATAGGG 59.511 38.462 0.00 0.00 36.44 3.53
1005 1259 1.148723 GCTGATGGCTGAGATGGCT 59.851 57.895 0.00 0.00 38.06 4.75
1312 1571 4.033009 TGTCATATTGCTGGAGGAAGAGA 58.967 43.478 0.00 0.00 0.00 3.10
1347 1606 8.202137 GGTCATATCAAGGTTTGTACTAGCTTA 58.798 37.037 11.03 0.54 32.49 3.09
1356 1615 8.591114 AGGTTTGTACTAGCTTAGAGTTGATA 57.409 34.615 0.00 0.00 0.00 2.15
1497 1758 8.989980 GTAGCTATTTAACTAACCTTGCCATAG 58.010 37.037 0.00 0.00 0.00 2.23
1713 1978 7.773489 TCTGAATTTGTTGTTGATGGGAATA 57.227 32.000 0.00 0.00 0.00 1.75
1734 1999 1.835494 ACTTGGCTCGAGTGCTACTA 58.165 50.000 15.13 0.00 0.00 1.82
1940 2205 1.474077 CACCCAGAGCTTTACAATGCC 59.526 52.381 0.00 0.00 0.00 4.40
1992 2258 9.109246 AGGATGATCTATTGATTGTCTTGGATA 57.891 33.333 0.00 0.00 32.19 2.59
1993 2259 9.902684 GGATGATCTATTGATTGTCTTGGATAT 57.097 33.333 0.00 0.00 32.19 1.63
2038 2305 0.955428 GGAGCCACTCATTCGTGCAA 60.955 55.000 0.00 0.00 33.60 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.741927 GCAGCCATCACATTTTGGGC 60.742 55.000 0.00 0.00 44.92 5.36
94 95 0.600557 AACGCATCGGCCAAAATGAA 59.399 45.000 2.24 0.00 36.38 2.57
133 134 3.585289 TCACTAATACCTGCAGGGACAAA 59.415 43.478 35.42 15.93 40.27 2.83
204 210 6.360370 AGAGGTCATGTGTTGTGTTACTAT 57.640 37.500 0.00 0.00 0.00 2.12
251 257 2.203195 GCATAGCCCGCATCCACA 60.203 61.111 0.00 0.00 0.00 4.17
319 325 2.955660 GGGACACATTCACCAAACTCAA 59.044 45.455 0.00 0.00 0.00 3.02
391 397 0.178967 TGCAAATGCCCTCTCAACCA 60.179 50.000 2.46 0.00 41.18 3.67
441 447 0.690762 TAAGGGTGGTGAGGCTTGTC 59.309 55.000 0.00 0.00 0.00 3.18
474 480 4.503741 TGCAACAAGCTAGGACAATTTC 57.496 40.909 0.00 0.00 45.94 2.17
685 691 9.793259 ACGATAGAATTATTCATAACCCAACAT 57.207 29.630 7.74 0.00 41.38 2.71
892 1127 9.757227 CACCAACAGAATTAAAGAACCATAAAA 57.243 29.630 0.00 0.00 0.00 1.52
940 1181 7.452562 AGGAGCACCAACATAATCAAAATTTT 58.547 30.769 2.07 0.00 38.94 1.82
987 1241 1.148723 AGCCATCTCAGCCATCAGC 59.851 57.895 0.00 0.00 44.25 4.26
1005 1259 0.899253 CACCATGCCCACCATCAACA 60.899 55.000 0.00 0.00 29.71 3.33
1312 1571 4.371681 ACCTTGATATGACCCAGGTAGTT 58.628 43.478 0.00 0.00 0.00 2.24
1347 1606 5.730550 TGAAATAGCGTGGTTATCAACTCT 58.269 37.500 0.00 0.00 0.00 3.24
1356 1615 4.457603 TGCAAGTAATGAAATAGCGTGGTT 59.542 37.500 0.00 0.00 0.00 3.67
1497 1758 3.746045 TGGTCCTACAAGAAGTGTGAC 57.254 47.619 0.00 0.00 41.89 3.67
1713 1978 1.344763 AGTAGCACTCGAGCCAAGTTT 59.655 47.619 13.61 0.00 34.23 2.66
1734 1999 1.203441 TCTTCCCCATGAGCAGCAGT 61.203 55.000 0.00 0.00 0.00 4.40
1992 2258 2.485426 CTGTTGGCGTTCTCATTGACAT 59.515 45.455 0.00 0.00 0.00 3.06
1993 2259 1.872952 CTGTTGGCGTTCTCATTGACA 59.127 47.619 0.00 0.00 0.00 3.58
1994 2260 1.197721 CCTGTTGGCGTTCTCATTGAC 59.802 52.381 0.00 0.00 0.00 3.18
2038 2305 0.881796 TGCGACGAGTCTCTGACATT 59.118 50.000 0.00 0.00 34.60 2.71


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

AutoCloner maintained by Alex Coulton.