Multiple sequence alignment - TraesCS4A01G438200

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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 TraesCS4A01G438200 chr4A 100.000 3188 0 0 1 3188 707701268 707704455 0.000000e+00 5888
1 TraesCS4A01G438200 chr4A 98.937 3199 18 3 1 3188 707673798 707676991 0.000000e+00 5705
2 TraesCS4A01G438200 chr4A 90.982 1630 127 15 971 2592 707487548 707489165 0.000000e+00 2178
3 TraesCS4A01G438200 chr4A 90.798 1630 135 12 971 2592 706089818 706088196 0.000000e+00 2165
4 TraesCS4A01G438200 chr4A 90.263 1633 140 14 971 2592 705953842 705952218 0.000000e+00 2117
5 TraesCS4A01G438200 chr4A 81.473 1317 211 22 996 2281 707305506 707304192 0.000000e+00 1050
6 TraesCS4A01G438200 chr4A 82.934 1043 161 10 1377 2419 707260630 707259605 0.000000e+00 924
7 TraesCS4A01G438200 chr7D 90.986 1664 135 10 975 2636 24021262 24019612 0.000000e+00 2228
8 TraesCS4A01G438200 chr7D 89.844 1664 144 15 975 2632 24118827 24117183 0.000000e+00 2113
9 TraesCS4A01G438200 chr7D 82.827 1252 199 11 954 2192 24326392 24327640 0.000000e+00 1107
10 TraesCS4A01G438200 chr7D 96.774 124 4 0 3065 3188 23688421 23688298 1.160000e-49 207
11 TraesCS4A01G438200 chr7D 95.238 105 5 0 3065 3169 23687351 23687247 1.970000e-37 167
12 TraesCS4A01G438200 chrUn 90.792 1629 136 11 971 2592 220049480 220047859 0.000000e+00 2165
13 TraesCS4A01G438200 chr4B 96.610 236 6 1 2825 3058 424705615 424705850 1.070000e-104 390
14 TraesCS4A01G438200 chr4B 87.195 164 17 4 2601 2764 652405288 652405129 1.950000e-42 183
15 TraesCS4A01G438200 chr5B 94.650 243 13 0 2825 3067 10517066 10516824 8.350000e-101 377
16 TraesCS4A01G438200 chr5B 87.952 166 16 4 2637 2800 42698139 42697976 3.250000e-45 193
17 TraesCS4A01G438200 chr7B 94.628 242 12 1 2825 3066 631064766 631065006 1.080000e-99 374
18 TraesCS4A01G438200 chr7B 92.797 236 15 2 2822 3056 611973813 611974047 1.100000e-89 340
19 TraesCS4A01G438200 chr7B 94.074 135 8 0 2637 2771 723351985 723351851 4.170000e-49 206
20 TraesCS4A01G438200 chr7B 94.030 134 8 0 2638 2771 723178509 723178376 1.500000e-48 204
21 TraesCS4A01G438200 chr1B 93.644 236 14 1 2825 3060 309165306 309165540 5.060000e-93 351
22 TraesCS4A01G438200 chr1B 95.349 129 6 0 2637 2765 172000111 172000239 4.170000e-49 206
23 TraesCS4A01G438200 chr2B 89.362 235 24 1 2825 3059 693311136 693311369 8.650000e-76 294
24 TraesCS4A01G438200 chr2B 91.489 141 12 0 2634 2774 378986164 378986024 9.020000e-46 195
25 TraesCS4A01G438200 chr5A 88.889 234 25 1 2825 3058 702630685 702630917 1.450000e-73 287
26 TraesCS4A01G438200 chr5A 87.607 234 28 1 2825 3058 378284957 378285189 1.460000e-68 270
27 TraesCS4A01G438200 chr1A 93.333 135 8 1 2634 2767 481650971 481651105 6.980000e-47 198
28 TraesCS4A01G438200 chr3B 89.474 152 13 3 2637 2786 182379302 182379452 4.200000e-44 189


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 TraesCS4A01G438200 chr4A 707701268 707704455 3187 False 5888 5888 100.000 1 3188 1 chr4A.!!$F3 3187
1 TraesCS4A01G438200 chr4A 707673798 707676991 3193 False 5705 5705 98.937 1 3188 1 chr4A.!!$F2 3187
2 TraesCS4A01G438200 chr4A 707487548 707489165 1617 False 2178 2178 90.982 971 2592 1 chr4A.!!$F1 1621
3 TraesCS4A01G438200 chr4A 706088196 706089818 1622 True 2165 2165 90.798 971 2592 1 chr4A.!!$R2 1621
4 TraesCS4A01G438200 chr4A 705952218 705953842 1624 True 2117 2117 90.263 971 2592 1 chr4A.!!$R1 1621
5 TraesCS4A01G438200 chr4A 707304192 707305506 1314 True 1050 1050 81.473 996 2281 1 chr4A.!!$R4 1285
6 TraesCS4A01G438200 chr4A 707259605 707260630 1025 True 924 924 82.934 1377 2419 1 chr4A.!!$R3 1042
7 TraesCS4A01G438200 chr7D 24019612 24021262 1650 True 2228 2228 90.986 975 2636 1 chr7D.!!$R1 1661
8 TraesCS4A01G438200 chr7D 24117183 24118827 1644 True 2113 2113 89.844 975 2632 1 chr7D.!!$R2 1657
9 TraesCS4A01G438200 chr7D 24326392 24327640 1248 False 1107 1107 82.827 954 2192 1 chr7D.!!$F1 1238
10 TraesCS4A01G438200 chrUn 220047859 220049480 1621 True 2165 2165 90.792 971 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
458 459 1.227556 GAGCGGCATGAATACCCGT 60.228 57.895 1.45 0.0 43.7 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2727 2792 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.0 0.0 39.63 2.57 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
103 104 1.599542 GGGATGCAGCTCGTTGTATTC 59.400 52.381 0.22 0.00 0.00 1.75
286 287 3.258372 GCAGGTAGATATTCGTCCCATCA 59.742 47.826 0.00 0.00 0.00 3.07
305 306 5.354513 CCATCAGTCTAGTAAACGTCTCTCA 59.645 44.000 0.00 0.00 0.00 3.27
308 309 5.638657 TCAGTCTAGTAAACGTCTCTCAGAC 59.361 44.000 10.08 10.08 41.71 3.51
458 459 1.227556 GAGCGGCATGAATACCCGT 60.228 57.895 1.45 0.00 43.70 5.28
1133 1149 2.040606 GCCCCAGGGAGACTACCA 59.959 66.667 7.25 0.00 37.50 3.25
1501 1517 4.069232 AGCTCAACGGCTGCGCTA 62.069 61.111 9.73 0.00 44.34 4.26
2834 2899 3.138098 TCTTGGCTGCCATTATGGACATA 59.862 43.478 24.03 1.85 40.96 2.29
2935 3000 3.090037 AGATCGGCTGGCGTATTATAGT 58.910 45.455 23.07 0.00 0.00 2.12
3013 3078 4.771590 ACTTGTGCCACTTGATTGTATG 57.228 40.909 0.00 0.00 0.00 2.39
3036 3101 8.995027 ATGCCTATCACACTGGAATAAAAATA 57.005 30.769 0.00 0.00 0.00 1.40
3135 3200 0.603569 AGAGCACAACCGGAGTAGTG 59.396 55.000 9.46 12.07 35.19 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 306 1.792949 GTTCGCGTCTGTTCAATGTCT 59.207 47.619 5.77 0.00 0.00 3.41
308 309 1.398451 GGTGTTCGCGTCTGTTCAATG 60.398 52.381 5.77 0.00 0.00 2.82
417 418 2.109126 GTGGCCGCTCTGGATTGAC 61.109 63.158 9.68 0.00 42.00 3.18
1133 1149 0.723981 GACGCGGAAGTAGTAGTCGT 59.276 55.000 12.47 0.00 0.00 4.34
2727 2792 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
2796 2861 6.501781 CAGCCAAGATTCCAGAAATATCAAC 58.498 40.000 0.00 0.00 0.00 3.18
2935 3000 2.751259 AGCAGTTGTATTCTCCGTACGA 59.249 45.455 18.76 1.79 0.00 3.43
3013 3078 8.451908 AGTATTTTTATTCCAGTGTGATAGGC 57.548 34.615 0.00 0.00 0.00 3.93
3062 3127 7.387948 CACTGTCACTGTAGCCTATTAGTTTTT 59.612 37.037 0.00 0.00 0.00 1.94
3063 3128 6.874134 CACTGTCACTGTAGCCTATTAGTTTT 59.126 38.462 0.00 0.00 0.00 2.43
3135 3200 9.429359 CTCACTATATTGGGACATATGAAGAAC 57.571 37.037 10.38 0.00 39.30 3.01


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

AutoCloner maintained by Alex Coulton.