Multiple sequence alignment - TraesCS4A01G438100

Loading Multiple Alignment...

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 TraesCS4A01G438100 chr4A 100.000 3188 0 0 1 3188 707673809 707676996 0.000000e+00 5888
1 TraesCS4A01G438100 chr4A 98.935 3193 18 3 1 3188 707701279 707704460 0.000000e+00 5694
2 TraesCS4A01G438100 chr4A 91.166 1630 124 15 971 2592 707487548 707489165 0.000000e+00 2194
3 TraesCS4A01G438100 chr4A 90.859 1630 134 12 971 2592 706089818 706088196 0.000000e+00 2170
4 TraesCS4A01G438100 chr4A 90.325 1633 139 14 971 2592 705953842 705952218 0.000000e+00 2122
5 TraesCS4A01G438100 chr4A 81.473 1317 211 22 996 2281 707305506 707304192 0.000000e+00 1050
6 TraesCS4A01G438100 chr4A 83.030 1043 160 10 1377 2419 707260630 707259605 0.000000e+00 929
7 TraesCS4A01G438100 chr7D 91.166 1664 132 10 975 2636 24021262 24019612 0.000000e+00 2244
8 TraesCS4A01G438100 chr7D 90.024 1664 141 15 975 2632 24118827 24117183 0.000000e+00 2130
9 TraesCS4A01G438100 chr7D 82.987 1252 197 11 954 2192 24326392 24327640 0.000000e+00 1118
10 TraesCS4A01G438100 chr7D 96.154 130 5 0 3059 3188 23688422 23688293 2.490000e-51 213
11 TraesCS4A01G438100 chr7D 94.340 106 6 0 3059 3164 23687352 23687247 2.540000e-36 163
12 TraesCS4A01G438100 chrUn 90.853 1629 135 11 971 2592 220049480 220047859 0.000000e+00 2170
13 TraesCS4A01G438100 chr4B 97.458 236 4 1 2825 3058 424705615 424705850 4.950000e-108 401
14 TraesCS4A01G438100 chr4B 87.805 164 16 4 2601 2764 652405288 652405129 4.200000e-44 189
15 TraesCS4A01G438100 chr7B 95.473 243 10 1 2825 3067 631064766 631065007 1.390000e-103 387
16 TraesCS4A01G438100 chr7B 93.644 236 13 2 2822 3056 611973813 611974047 5.060000e-93 351
17 TraesCS4A01G438100 chr5B 95.726 234 10 0 2825 3058 10517066 10516833 8.350000e-101 377
18 TraesCS4A01G438100 chr1B 94.468 235 13 0 2825 3059 309165306 309165540 2.340000e-96 363
19 TraesCS4A01G438100 chr5A 89.744 234 23 1 2825 3058 702630685 702630917 6.690000e-77 298
20 TraesCS4A01G438100 chr5A 88.085 235 27 1 2825 3059 378284957 378285190 8.710000e-71 278
21 TraesCS4A01G438100 chr2B 89.744 234 23 1 2825 3058 693311136 693311368 6.690000e-77 298
22 TraesCS4A01G438100 chr1A 94.074 135 7 1 2634 2767 481650971 481651105 1.500000e-48 204
23 TraesCS4A01G438100 chr6A 91.667 144 10 2 2634 2776 41255572 41255430 6.980000e-47 198
24 TraesCS4A01G438100 chr3B 90.196 153 10 4 2626 2776 315453497 315453348 9.020000e-46 195
25 TraesCS4A01G438100 chr2D 91.034 145 11 1 2634 2776 108668711 108668567 9.020000e-46 195
26 TraesCS4A01G438100 chr1D 89.542 153 12 3 2626 2776 455413840 455413990 1.170000e-44 191
27 TraesCS4A01G438100 chr7A 88.961 154 16 1 2631 2783 574117376 574117223 4.200000e-44 189
28 TraesCS4A01G438100 chr6B 87.500 168 12 9 2603 2764 444559076 444559240 5.430000e-43 185


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 TraesCS4A01G438100 chr4A 707673809 707676996 3187 False 5888 5888 100.000 1 3188 1 chr4A.!!$F2 3187
1 TraesCS4A01G438100 chr4A 707701279 707704460 3181 False 5694 5694 98.935 1 3188 1 chr4A.!!$F3 3187
2 TraesCS4A01G438100 chr4A 707487548 707489165 1617 False 2194 2194 91.166 971 2592 1 chr4A.!!$F1 1621
3 TraesCS4A01G438100 chr4A 706088196 706089818 1622 True 2170 2170 90.859 971 2592 1 chr4A.!!$R2 1621
4 TraesCS4A01G438100 chr4A 705952218 705953842 1624 True 2122 2122 90.325 971 2592 1 chr4A.!!$R1 1621
5 TraesCS4A01G438100 chr4A 707304192 707305506 1314 True 1050 1050 81.473 996 2281 1 chr4A.!!$R4 1285
6 TraesCS4A01G438100 chr4A 707259605 707260630 1025 True 929 929 83.030 1377 2419 1 chr4A.!!$R3 1042
7 TraesCS4A01G438100 chr7D 24019612 24021262 1650 True 2244 2244 91.166 975 2636 1 chr7D.!!$R1 1661
8 TraesCS4A01G438100 chr7D 24117183 24118827 1644 True 2130 2130 90.024 975 2632 1 chr7D.!!$R2 1657
9 TraesCS4A01G438100 chr7D 24326392 24327640 1248 False 1118 1118 82.987 954 2192 1 chr7D.!!$F1 1238
10 TraesCS4A01G438100 chrUn 220047859 220049480 1621 True 2170 2170 90.853 971 2592 1 chrUn.!!$R1 1621

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
447 448 1.961277 GAGCGGCATGAATACCCGG 60.961 63.158 10.18 0.0 42.17 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2727 2781 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.0 0.0 0.0 33.42 3.16 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
92 93 2.434336 AGGGATGCAGCTCGTTGTATTA 59.566 45.455 0.22 0.00 0.00 0.98
275 276 3.368531 GCAGGTAGATATTCGTCCCATCC 60.369 52.174 0.00 0.00 0.00 3.51
294 295 3.265791 TCCGTCTAGTAAACGTCTCTCC 58.734 50.000 0.00 0.00 38.44 3.71
297 298 3.369147 CGTCTAGTAAACGTCTCTCCGAA 59.631 47.826 0.00 0.00 35.47 4.30
447 448 1.961277 GAGCGGCATGAATACCCGG 60.961 63.158 10.18 0.00 42.17 5.73
930 931 9.251440 AGGGGTTAATTTAGTTAAATCCTTGAC 57.749 33.333 0.00 0.00 35.32 3.18
931 932 9.251440 GGGGTTAATTTAGTTAAATCCTTGACT 57.749 33.333 0.00 0.00 35.00 3.41
2834 2888 1.985473 TGGCTGCCATTATGGACATC 58.015 50.000 19.30 8.01 40.96 3.06
2935 2989 2.159226 AGATCGGCTGGCGTATTATAGC 60.159 50.000 23.07 5.70 35.49 2.97
3013 3067 5.376854 AACTTGTGCCACTTGATTGTATC 57.623 39.130 0.00 0.00 0.00 2.24
3036 3090 8.697507 ATCCCTATCACACTGGAATAAAAATC 57.302 34.615 0.00 0.00 0.00 2.17
3130 3189 1.339097 AGAGCACAACCGGAGTAGTT 58.661 50.000 9.46 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
275 276 2.926200 TCGGAGAGACGTTTACTAGACG 59.074 50.000 0.00 0.00 45.46 4.18
294 295 2.222624 GTTCGCGTCTGTTCAATTTCG 58.777 47.619 5.77 0.00 0.00 3.46
297 298 1.263217 GGTGTTCGCGTCTGTTCAATT 59.737 47.619 5.77 0.00 0.00 2.32
406 407 1.153086 GTGGCCGCTCTGGATTGAT 60.153 57.895 9.68 0.00 42.00 2.57
928 929 5.463724 CGGGTTCTTTCATCAGCTTATAGTC 59.536 44.000 0.00 0.00 0.00 2.59
929 930 5.360591 CGGGTTCTTTCATCAGCTTATAGT 58.639 41.667 0.00 0.00 0.00 2.12
930 931 4.752101 CCGGGTTCTTTCATCAGCTTATAG 59.248 45.833 0.00 0.00 0.00 1.31
931 932 4.703897 CCGGGTTCTTTCATCAGCTTATA 58.296 43.478 0.00 0.00 0.00 0.98
932 933 3.545703 CCGGGTTCTTTCATCAGCTTAT 58.454 45.455 0.00 0.00 0.00 1.73
933 934 2.939640 GCCGGGTTCTTTCATCAGCTTA 60.940 50.000 2.18 0.00 0.00 3.09
934 935 1.826385 CCGGGTTCTTTCATCAGCTT 58.174 50.000 0.00 0.00 0.00 3.74
935 936 0.678048 GCCGGGTTCTTTCATCAGCT 60.678 55.000 2.18 0.00 0.00 4.24
936 937 0.678048 AGCCGGGTTCTTTCATCAGC 60.678 55.000 0.00 0.00 0.00 4.26
937 938 1.826385 AAGCCGGGTTCTTTCATCAG 58.174 50.000 14.44 0.00 0.00 2.90
938 939 2.286365 AAAGCCGGGTTCTTTCATCA 57.714 45.000 21.02 0.00 0.00 3.07
2727 2781 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
2796 2850 6.406177 GCAGCCAAGATTCCAGAAATATCAAA 60.406 38.462 0.00 0.00 0.00 2.69
2935 2989 2.159282 AGCAGTTGTATTCTCCGTACGG 60.159 50.000 28.66 28.66 0.00 4.02
3013 3067 7.062957 AGGATTTTTATTCCAGTGTGATAGGG 58.937 38.462 0.00 0.00 35.59 3.53
3058 3117 6.311445 CACTGTCACTGTAGCCTATTAGTTTG 59.689 42.308 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.