Multiple sequence alignment - TraesCS7A01G296700

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 TraesCS7A01G296700 chr7A 100.000 2438 0 0 1 2438 396167361 396164924 0.000000e+00 4503
1 TraesCS7A01G296700 chr7A 86.636 1100 113 22 1357 2438 400450362 400449279 0.000000e+00 1186
2 TraesCS7A01G296700 chr2A 92.481 2447 141 21 1 2438 267980610 267983022 0.000000e+00 3459
3 TraesCS7A01G296700 chr2A 85.191 2458 297 45 1 2438 679108478 679106068 0.000000e+00 2460
4 TraesCS7A01G296700 chr2A 86.093 1244 163 8 1 1241 100908403 100907167 0.000000e+00 1330
5 TraesCS7A01G296700 chr5B 90.458 2316 199 14 1 2304 316555838 316553533 0.000000e+00 3033
6 TraesCS7A01G296700 chr2B 90.047 2321 184 22 1 2304 550642955 550640665 0.000000e+00 2963
7 TraesCS7A01G296700 chr2B 87.150 2319 263 21 1 2308 281422365 281420071 0.000000e+00 2599
8 TraesCS7A01G296700 chr2B 88.711 2126 207 23 3 2106 298275992 298278106 0.000000e+00 2566
9 TraesCS7A01G296700 chr2B 86.128 2314 273 25 1 2305 388226117 388228391 0.000000e+00 2451
10 TraesCS7A01G296700 chr2B 85.252 2319 268 48 1 2296 724014213 724011946 0.000000e+00 2320
11 TraesCS7A01G296700 chr2B 86.136 2034 233 31 1 2024 426924134 426926128 0.000000e+00 2148
12 TraesCS7A01G296700 chr2B 87.056 1182 138 9 1 1170 279189394 279188216 0.000000e+00 1321
13 TraesCS7A01G296700 chr2B 91.781 219 17 1 2220 2438 465449102 465448885 1.100000e-78 303
14 TraesCS7A01G296700 chr3B 89.733 2318 182 29 1 2304 409840460 409838185 0.000000e+00 2911
15 TraesCS7A01G296700 chr3B 90.909 99 8 1 2341 2438 361556015 361556113 5.470000e-27 132
16 TraesCS7A01G296700 chrUn 88.932 2322 230 17 1 2304 59444581 59442269 0.000000e+00 2839
17 TraesCS7A01G296700 chrUn 87.465 2473 265 26 1 2438 79020032 79017570 0.000000e+00 2808
18 TraesCS7A01G296700 chr6B 88.749 2311 236 19 1 2296 144614295 144616596 0.000000e+00 2806
19 TraesCS7A01G296700 chr6B 85.472 2244 274 30 72 2304 371840573 371842775 0.000000e+00 2290
20 TraesCS7A01G296700 chr7B 88.579 2329 228 22 1 2304 476087856 476085541 0.000000e+00 2793
21 TraesCS7A01G296700 chr7B 93.548 93 5 1 2347 2438 242317189 242317281 1.180000e-28 137
22 TraesCS7A01G296700 chr7B 90.909 99 8 1 2341 2438 550722694 550722596 5.470000e-27 132
23 TraesCS7A01G296700 chr7B 90.909 99 8 1 2341 2438 594474915 594474817 5.470000e-27 132
24 TraesCS7A01G296700 chr7B 90.909 99 8 1 2341 2438 594479302 594479204 5.470000e-27 132
25 TraesCS7A01G296700 chr1B 87.077 2453 268 27 1 2438 200995229 200997647 0.000000e+00 2728
26 TraesCS7A01G296700 chr2D 87.015 1186 123 22 1269 2438 290209893 290208723 0.000000e+00 1308


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 TraesCS7A01G296700 chr7A 396164924 396167361 2437 True 4503 4503 100.000 1 2438 1 chr7A.!!$R1 2437
1 TraesCS7A01G296700 chr7A 400449279 400450362 1083 True 1186 1186 86.636 1357 2438 1 chr7A.!!$R2 1081
2 TraesCS7A01G296700 chr2A 267980610 267983022 2412 False 3459 3459 92.481 1 2438 1 chr2A.!!$F1 2437
3 TraesCS7A01G296700 chr2A 679106068 679108478 2410 True 2460 2460 85.191 1 2438 1 chr2A.!!$R2 2437
4 TraesCS7A01G296700 chr2A 100907167 100908403 1236 True 1330 1330 86.093 1 1241 1 chr2A.!!$R1 1240
5 TraesCS7A01G296700 chr5B 316553533 316555838 2305 True 3033 3033 90.458 1 2304 1 chr5B.!!$R1 2303
6 TraesCS7A01G296700 chr2B 550640665 550642955 2290 True 2963 2963 90.047 1 2304 1 chr2B.!!$R4 2303
7 TraesCS7A01G296700 chr2B 281420071 281422365 2294 True 2599 2599 87.150 1 2308 1 chr2B.!!$R2 2307
8 TraesCS7A01G296700 chr2B 298275992 298278106 2114 False 2566 2566 88.711 3 2106 1 chr2B.!!$F1 2103
9 TraesCS7A01G296700 chr2B 388226117 388228391 2274 False 2451 2451 86.128 1 2305 1 chr2B.!!$F2 2304
10 TraesCS7A01G296700 chr2B 724011946 724014213 2267 True 2320 2320 85.252 1 2296 1 chr2B.!!$R5 2295
11 TraesCS7A01G296700 chr2B 426924134 426926128 1994 False 2148 2148 86.136 1 2024 1 chr2B.!!$F3 2023
12 TraesCS7A01G296700 chr2B 279188216 279189394 1178 True 1321 1321 87.056 1 1170 1 chr2B.!!$R1 1169
13 TraesCS7A01G296700 chr3B 409838185 409840460 2275 True 2911 2911 89.733 1 2304 1 chr3B.!!$R1 2303
14 TraesCS7A01G296700 chrUn 59442269 59444581 2312 True 2839 2839 88.932 1 2304 1 chrUn.!!$R1 2303
15 TraesCS7A01G296700 chrUn 79017570 79020032 2462 True 2808 2808 87.465 1 2438 1 chrUn.!!$R2 2437
16 TraesCS7A01G296700 chr6B 144614295 144616596 2301 False 2806 2806 88.749 1 2296 1 chr6B.!!$F1 2295
17 TraesCS7A01G296700 chr6B 371840573 371842775 2202 False 2290 2290 85.472 72 2304 1 chr6B.!!$F2 2232
18 TraesCS7A01G296700 chr7B 476085541 476087856 2315 True 2793 2793 88.579 1 2304 1 chr7B.!!$R1 2303
19 TraesCS7A01G296700 chr1B 200995229 200997647 2418 False 2728 2728 87.077 1 2438 1 chr1B.!!$F1 2437
20 TraesCS7A01G296700 chr2D 290208723 290209893 1170 True 1308 1308 87.015 1269 2438 1 chr2D.!!$R1 1169

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
187 188 2.263077 GTCAGCGTGGTTACTCTCATG 58.737 52.381 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2156 0.037447 TTCACATGCCACCGATCCAA 59.963 50.0 0.0 0.0 0.0 3.53 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
98 99 7.080353 AGGCCTAGTTCTTATGGTCCTTATTA 58.920 38.462 1.29 0.00 0.00 0.98
137 138 5.689835 TGTTGCTCCTACATGCCATATTTA 58.310 37.500 0.00 0.00 0.00 1.40
187 188 2.263077 GTCAGCGTGGTTACTCTCATG 58.737 52.381 0.00 0.00 0.00 3.07
225 226 3.842925 GAGCTTCGCCCCACAACCA 62.843 63.158 0.00 0.00 0.00 3.67
313 314 4.256920 CAACCCTGAGATCTCATCGTTTT 58.743 43.478 25.30 11.58 39.13 2.43
389 390 3.732212 CACCACAACAGTCTCATTCAGA 58.268 45.455 0.00 0.00 0.00 3.27
405 406 8.394040 TCTCATTCAGATCCTACTCATATACCA 58.606 37.037 0.00 0.00 0.00 3.25
411 412 8.615705 TCAGATCCTACTCATATACCACAGTAT 58.384 37.037 0.00 0.00 42.05 2.12
613 645 8.929487 AGGTTATACTAGAGGAAATGAAGAAGG 58.071 37.037 0.00 0.00 0.00 3.46
758 790 4.098960 GGTTCCAATACCGTCACATCTAGA 59.901 45.833 0.00 0.00 0.00 2.43
762 794 5.009710 TCCAATACCGTCACATCTAGATGAC 59.990 44.000 34.16 23.74 41.20 3.06
784 816 3.341823 CAAGATAGCAAGTGCCTTGAGT 58.658 45.455 16.28 7.10 43.42 3.41
789 821 2.772287 AGCAAGTGCCTTGAGTAAGAC 58.228 47.619 16.28 0.62 43.42 3.01
846 881 5.946942 AGGAACAAGATGATCAAGAGCTA 57.053 39.130 0.00 0.00 0.00 3.32
847 882 6.497624 AGGAACAAGATGATCAAGAGCTAT 57.502 37.500 0.00 0.00 0.00 2.97
976 1011 2.391616 ACATGAGCGTGATGTGTCAT 57.608 45.000 0.00 0.00 36.60 3.06
1118 1153 8.848474 ATATACACTGTTAATGGCATTACTCC 57.152 34.615 19.11 10.76 0.00 3.85
1247 1282 4.210331 AGTGTTGACCTTGCTGATTTCTT 58.790 39.130 0.00 0.00 0.00 2.52
1307 1343 8.992073 TGTAATTGGATATTCGATTGATGACTG 58.008 33.333 6.73 0.00 0.00 3.51
1446 1482 2.060383 TGGATCCTGAGCACGGAGG 61.060 63.158 14.23 0.00 33.29 4.30
1473 1510 3.195683 GCAATGGGCGCACACATA 58.804 55.556 18.24 0.00 0.00 2.29
1474 1511 1.735360 GCAATGGGCGCACACATAT 59.265 52.632 18.24 0.00 0.00 1.78
1484 1521 2.477825 CGCACACATATGGAAGAGAGG 58.522 52.381 7.80 0.00 0.00 3.69
1531 1574 0.391661 GGAGAGGAGTCGCAATGCAA 60.392 55.000 5.91 0.00 0.00 4.08
1552 1596 5.672503 CAAGAGGATGTGAGATGATCAAGT 58.327 41.667 0.00 0.00 40.43 3.16
1554 1598 4.101274 AGAGGATGTGAGATGATCAAGTGG 59.899 45.833 0.00 0.00 40.43 4.00
1557 1601 4.521146 GATGTGAGATGATCAAGTGGGTT 58.479 43.478 0.00 0.00 40.43 4.11
1570 1618 5.245531 TCAAGTGGGTTCTACATGATCAAC 58.754 41.667 0.00 0.00 0.00 3.18
1591 1639 0.606401 CCCGGTGAGCTGTTTCATGT 60.606 55.000 0.00 0.00 0.00 3.21
1685 1742 7.630242 TCTTAAATGATGTCCCACTGAATTC 57.370 36.000 0.00 0.00 0.00 2.17
1691 1750 8.599624 AATGATGTCCCACTGAATTCTATTTT 57.400 30.769 7.05 0.00 0.00 1.82
1740 1800 3.308438 ACTGATTGTTGAATGCCTTGC 57.692 42.857 0.00 0.00 0.00 4.01
1944 2004 7.837689 TCACTTTACCACTATGGACTAGTATGT 59.162 37.037 0.84 0.00 40.96 2.29
2083 2156 5.841237 ACCTATAGTAGCATGTCATGTTCCT 59.159 40.000 14.26 7.28 0.00 3.36
2163 2245 7.915293 TGTAATTGTCAAACCAGGTGTATAG 57.085 36.000 0.00 0.00 0.00 1.31
2258 2354 5.009710 GGTGTATACCATGTTCTCGAGATCA 59.990 44.000 24.40 24.40 46.71 2.92
2410 2522 9.285770 CACAATCATCATTTGAACTAGTTGATG 57.714 33.333 21.08 21.08 43.10 3.07
2425 2537 9.846248 AACTAGTTGATGTTCTTTTATCATTGC 57.154 29.630 7.48 0.00 33.68 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.339929 TCGCTGCCGAGCTAAATCATA 59.660 47.619 0.00 0.00 43.77 2.15
137 138 3.308401 GGTGAATGGCCCTAAAATCCAT 58.692 45.455 0.00 0.00 42.01 3.41
145 146 3.804329 GGCGGGTGAATGGCCCTA 61.804 66.667 0.00 0.00 43.92 3.53
187 188 1.267806 CATGCCATAACAATCGGGAGC 59.732 52.381 0.00 0.00 0.00 4.70
225 226 7.230510 TGTGAGTAATTGTTTTGGTATGAGCTT 59.769 33.333 0.00 0.00 0.00 3.74
313 314 3.648067 CCCTGCATTGGATAACTAGAGGA 59.352 47.826 0.00 0.00 0.00 3.71
389 390 7.836685 CCTGATACTGTGGTATATGAGTAGGAT 59.163 40.741 0.00 0.00 38.60 3.24
405 406 3.713003 TGGACACATCTCCTGATACTGT 58.287 45.455 0.00 0.00 0.00 3.55
411 412 2.502947 CTCCATTGGACACATCTCCTGA 59.497 50.000 0.00 0.00 0.00 3.86
613 645 2.777832 AGCTCATTCCCACTCTTGAC 57.222 50.000 0.00 0.00 0.00 3.18
669 701 5.500234 TGTGAAGAAATAGTATTGCCAGCT 58.500 37.500 0.00 0.00 0.00 4.24
758 790 2.240667 AGGCACTTGCTATCTTGGTCAT 59.759 45.455 0.38 0.00 41.70 3.06
784 816 8.595362 TCTTCTTCAATCTGAGGTATGTCTTA 57.405 34.615 0.00 0.00 0.00 2.10
789 821 7.986320 AGTTCATCTTCTTCAATCTGAGGTATG 59.014 37.037 0.00 0.00 0.00 2.39
846 881 7.890127 TCTTCAACTTGATCACTTGGGAATTAT 59.110 33.333 10.92 0.00 0.00 1.28
847 882 7.174946 GTCTTCAACTTGATCACTTGGGAATTA 59.825 37.037 10.92 0.00 0.00 1.40
976 1011 5.222027 TGTCATCAAGAGGATTGGGTAAACA 60.222 40.000 0.00 0.00 32.57 2.83
1065 1100 8.533657 TCATCATATCCAAGCAAATGAGTTTTT 58.466 29.630 0.00 0.00 32.25 1.94
1106 1141 3.979911 TCACAAATGGGAGTAATGCCAT 58.020 40.909 10.74 10.74 0.00 4.40
1118 1153 9.941664 GAAAGTAACTATGATCATCACAAATGG 57.058 33.333 12.53 0.00 0.00 3.16
1446 1482 1.372087 CGCCCATTGCTTCTCCTCAC 61.372 60.000 0.00 0.00 38.05 3.51
1473 1510 1.792115 CTCCAGCTCCTCTCTTCCAT 58.208 55.000 0.00 0.00 0.00 3.41
1474 1511 0.975040 GCTCCAGCTCCTCTCTTCCA 60.975 60.000 0.00 0.00 38.21 3.53
1484 1521 2.125391 TCGTGCATGCTCCAGCTC 60.125 61.111 20.33 0.14 42.66 4.09
1531 1574 4.101274 CCACTTGATCATCTCACATCCTCT 59.899 45.833 0.00 0.00 32.17 3.69
1552 1596 3.308117 GGGTGTTGATCATGTAGAACCCA 60.308 47.826 16.84 0.00 40.55 4.51
1554 1598 2.936498 CGGGTGTTGATCATGTAGAACC 59.064 50.000 0.00 0.00 0.00 3.62
1557 1601 2.093711 CACCGGGTGTTGATCATGTAGA 60.094 50.000 19.15 0.00 0.00 2.59
1570 1618 0.606401 ATGAAACAGCTCACCGGGTG 60.606 55.000 21.27 21.27 40.13 4.61
1591 1639 7.776291 ATGGATGATATATTCAGAATGGGGA 57.224 36.000 5.85 0.00 37.89 4.81
1691 1750 7.336427 TCATGTTCACATCAAGCACAATATGTA 59.664 33.333 0.00 0.00 33.61 2.29
1740 1800 4.268644 CGCATGGTGTAGATCACTAGTTTG 59.731 45.833 0.00 0.00 45.50 2.93
1944 2004 2.367567 GCTACCGATCCAGGGAACATAA 59.632 50.000 0.00 0.00 35.02 1.90
1990 2050 6.088824 GCATAAGAACAAACACAGGAATCAG 58.911 40.000 0.00 0.00 0.00 2.90
2055 2123 7.841282 ACATGACATGCTACTATAGGTAGTT 57.159 36.000 15.49 0.00 46.99 2.24
2083 2156 0.037447 TTCACATGCCACCGATCCAA 59.963 50.000 0.00 0.00 0.00 3.53
2163 2245 1.293924 CACCGATCCAGAGAACATGC 58.706 55.000 0.00 0.00 0.00 4.06
2258 2354 3.650942 TCTCACCAAAGGAACATACCACT 59.349 43.478 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.