Multiple sequence alignment - TraesCS4A01G465500

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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 TraesCS4A01G465500 chr4A 100.000 3197 0 0 1 3197 729058863 729055667 0.000000e+00 5904
1 TraesCS4A01G465500 chr4A 96.827 1828 46 7 1377 3197 731061951 731063773 0.000000e+00 3044
2 TraesCS4A01G465500 chr4A 93.504 1170 76 0 1033 2202 731097687 731098856 0.000000e+00 1740
3 TraesCS4A01G465500 chr4A 88.636 1144 118 3 1068 2202 729827552 729828692 0.000000e+00 1382
4 TraesCS4A01G465500 chr4A 88.127 1137 120 7 1077 2202 728645366 728644234 0.000000e+00 1338
5 TraesCS4A01G465500 chr4A 81.706 1137 173 15 1083 2200 728353005 728351885 0.000000e+00 915
6 TraesCS4A01G465500 chr4A 84.375 672 76 15 2273 2937 731098880 731099529 1.620000e-177 632
7 TraesCS4A01G465500 chr4A 82.550 745 93 18 2202 2937 728644187 728643471 3.500000e-174 621
8 TraesCS4A01G465500 chr4A 99.190 247 1 1 2951 3197 729071877 729071632 8.140000e-121 444
9 TraesCS4A01G465500 chrUn 100.000 1322 0 0 1 1322 308002573 308003894 0.000000e+00 2442
10 TraesCS4A01G465500 chr7D 92.403 1132 80 1 1077 2202 10151024 10149893 0.000000e+00 1609
11 TraesCS4A01G465500 chr7D 79.261 1191 203 25 1033 2198 10087841 10086670 0.000000e+00 791
12 TraesCS4A01G465500 chr7D 77.391 1234 212 30 998 2200 109144722 109143525 0.000000e+00 671
13 TraesCS4A01G465500 chr7D 82.777 749 94 22 2202 2945 10149853 10149135 1.250000e-178 636
14 TraesCS4A01G465500 chr7D 89.113 248 25 2 2946 3192 593709648 593709894 1.110000e-79 307
15 TraesCS4A01G465500 chr7D 86.624 157 15 5 130 282 72769408 72769562 5.480000e-38 169
16 TraesCS4A01G465500 chr4B 81.380 1246 192 23 982 2198 654201923 654203157 0.000000e+00 979
17 TraesCS4A01G465500 chr5A 80.990 1252 204 17 968 2198 691820974 691822212 0.000000e+00 963
18 TraesCS4A01G465500 chr4D 81.124 1245 197 23 982 2198 507352260 507351026 0.000000e+00 963
19 TraesCS4A01G465500 chr4D 89.960 249 21 3 2945 3192 422930814 422930569 5.150000e-83 318
20 TraesCS4A01G465500 chr7A 78.715 1198 211 26 1033 2203 9669847 9668667 0.000000e+00 760
21 TraesCS4A01G465500 chr7A 78.873 1136 176 29 1085 2197 10269759 10270853 0.000000e+00 710
22 TraesCS4A01G465500 chr7A 78.277 801 135 19 1427 2200 114413995 114413207 2.230000e-131 479
23 TraesCS4A01G465500 chr7B 77.660 1231 205 33 998 2196 68160703 68159511 0.000000e+00 686
24 TraesCS4A01G465500 chr7B 77.579 1231 206 28 998 2196 68223652 68222460 0.000000e+00 680
25 TraesCS4A01G465500 chr7B 90.588 255 22 2 2945 3197 55051621 55051875 1.420000e-88 337
26 TraesCS4A01G465500 chr2D 91.633 251 18 3 2944 3192 5123906 5123657 8.490000e-91 344
27 TraesCS4A01G465500 chr1A 90.945 254 21 2 2946 3197 333497544 333497291 1.100000e-89 340
28 TraesCS4A01G465500 chr6B 90.000 250 21 2 2944 3192 24857312 24857066 1.430000e-83 320
29 TraesCS4A01G465500 chr6B 89.041 146 13 2 129 271 518676545 518676400 9.110000e-41 178
30 TraesCS4A01G465500 chr5D 89.558 249 23 2 2945 3192 547431689 547431935 2.390000e-81 313
31 TraesCS4A01G465500 chr1B 91.946 149 7 4 127 271 363447981 363448128 1.500000e-48 204
32 TraesCS4A01G465500 chr3D 90.604 149 10 3 127 271 23683583 23683435 9.050000e-46 195
33 TraesCS4A01G465500 chr3D 87.342 158 16 3 134 289 123489122 123488967 9.110000e-41 178
34 TraesCS4A01G465500 chr6D 90.278 144 11 2 131 271 311244737 311244594 5.450000e-43 185
35 TraesCS4A01G465500 chr6A 89.189 148 13 2 127 271 263561 263708 7.040000e-42 182
36 TraesCS4A01G465500 chr6A 79.920 249 38 10 127 366 190691499 190691254 4.240000e-39 172


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 TraesCS4A01G465500 chr4A 729055667 729058863 3196 True 5904.0 5904 100.0000 1 3197 1 chr4A.!!$R2 3196
1 TraesCS4A01G465500 chr4A 731061951 731063773 1822 False 3044.0 3044 96.8270 1377 3197 1 chr4A.!!$F2 1820
2 TraesCS4A01G465500 chr4A 729827552 729828692 1140 False 1382.0 1382 88.6360 1068 2202 1 chr4A.!!$F1 1134
3 TraesCS4A01G465500 chr4A 731097687 731099529 1842 False 1186.0 1740 88.9395 1033 2937 2 chr4A.!!$F3 1904
4 TraesCS4A01G465500 chr4A 728643471 728645366 1895 True 979.5 1338 85.3385 1077 2937 2 chr4A.!!$R4 1860
5 TraesCS4A01G465500 chr4A 728351885 728353005 1120 True 915.0 915 81.7060 1083 2200 1 chr4A.!!$R1 1117
6 TraesCS4A01G465500 chrUn 308002573 308003894 1321 False 2442.0 2442 100.0000 1 1322 1 chrUn.!!$F1 1321
7 TraesCS4A01G465500 chr7D 10149135 10151024 1889 True 1122.5 1609 87.5900 1077 2945 2 chr7D.!!$R3 1868
8 TraesCS4A01G465500 chr7D 10086670 10087841 1171 True 791.0 791 79.2610 1033 2198 1 chr7D.!!$R1 1165
9 TraesCS4A01G465500 chr7D 109143525 109144722 1197 True 671.0 671 77.3910 998 2200 1 chr7D.!!$R2 1202
10 TraesCS4A01G465500 chr4B 654201923 654203157 1234 False 979.0 979 81.3800 982 2198 1 chr4B.!!$F1 1216
11 TraesCS4A01G465500 chr5A 691820974 691822212 1238 False 963.0 963 80.9900 968 2198 1 chr5A.!!$F1 1230
12 TraesCS4A01G465500 chr4D 507351026 507352260 1234 True 963.0 963 81.1240 982 2198 1 chr4D.!!$R2 1216
13 TraesCS4A01G465500 chr7A 9668667 9669847 1180 True 760.0 760 78.7150 1033 2203 1 chr7A.!!$R1 1170
14 TraesCS4A01G465500 chr7A 10269759 10270853 1094 False 710.0 710 78.8730 1085 2197 1 chr7A.!!$F1 1112
15 TraesCS4A01G465500 chr7A 114413207 114413995 788 True 479.0 479 78.2770 1427 2200 1 chr7A.!!$R2 773
16 TraesCS4A01G465500 chr7B 68159511 68160703 1192 True 686.0 686 77.6600 998 2196 1 chr7B.!!$R1 1198
17 TraesCS4A01G465500 chr7B 68222460 68223652 1192 True 680.0 680 77.5790 998 2196 1 chr7B.!!$R2 1198

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
1334 1368 0.466124 CTCCCTTACCTGCAGCCTAC 59.534 60.0 8.66 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2699 2850 0.682852 CACACTCCCAGGTTCCGTAA 59.317 55.0 0.0 0.0 0.0 3.18 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
1334 1368 0.466124 CTCCCTTACCTGCAGCCTAC 59.534 60.000 8.66 0.00 0.00 3.18
1351 1388 3.307480 GCCTACCAAGTACAAGGACATGT 60.307 47.826 0.00 0.00 37.32 3.21
1637 1692 1.001268 GAGCATCTACTCATCGCGGAA 60.001 52.381 6.13 0.00 36.65 4.30
1920 1991 2.233431 AGTTCCTGAGATGACACTCTGC 59.767 50.000 0.00 0.00 37.73 4.26
1985 2056 1.334869 CGCCAACATGGATAAGCTTCC 59.665 52.381 0.00 0.00 40.96 3.46
2007 2078 4.219507 CCGAGCATGACTAGGATGAAGTAT 59.780 45.833 9.59 0.00 43.58 2.12
2213 2343 4.799428 GCAGTAGTTTCTCGGCTAAAGTAG 59.201 45.833 0.00 0.00 0.00 2.57
2241 2371 4.418392 CATGTACTTTGGAATCTGCTTGC 58.582 43.478 0.00 0.00 0.00 4.01
2242 2372 2.819608 TGTACTTTGGAATCTGCTTGCC 59.180 45.455 0.00 0.00 0.00 4.52
2243 2373 1.999648 ACTTTGGAATCTGCTTGCCA 58.000 45.000 0.00 0.00 0.00 4.92
2244 2374 2.318908 ACTTTGGAATCTGCTTGCCAA 58.681 42.857 0.00 0.00 38.54 4.52
2245 2375 2.901839 ACTTTGGAATCTGCTTGCCAAT 59.098 40.909 0.00 0.00 39.87 3.16
2246 2376 4.088634 ACTTTGGAATCTGCTTGCCAATA 58.911 39.130 0.00 0.00 39.87 1.90
2247 2377 4.527816 ACTTTGGAATCTGCTTGCCAATAA 59.472 37.500 0.00 0.00 39.87 1.40
2248 2378 5.188359 ACTTTGGAATCTGCTTGCCAATAAT 59.812 36.000 0.00 0.00 39.87 1.28
2249 2379 5.680594 TTGGAATCTGCTTGCCAATAATT 57.319 34.783 0.00 0.00 35.61 1.40
2291 2428 5.406767 TGTTTGCTTGATTTGCATTTCAC 57.593 34.783 0.00 0.00 40.34 3.18
2380 2517 7.640675 GGTCTTATTTACCTAGCACTGGCGT 62.641 48.000 0.00 0.00 38.41 5.68
2453 2593 9.103861 GTAATCAGCCTTCTTATCCATAATAGC 57.896 37.037 0.00 0.00 0.00 2.97
2610 2751 4.967036 AGCTAATGAATTCAGTAGAGCCC 58.033 43.478 35.17 22.00 44.59 5.19
2659 2809 9.221933 ATTGCATCAATGTCAACAAAATATTGT 57.778 25.926 0.00 0.00 40.86 2.71
3007 3174 5.582269 TGATTAAGAAGAGTGAGAATTGCCG 59.418 40.000 0.00 0.00 0.00 5.69
3018 3185 3.128589 TGAGAATTGCCGGCTTAATTGAC 59.871 43.478 29.70 19.16 0.00 3.18
3031 3198 0.824182 AATTGACGGAAAACCGGGCA 60.824 50.000 6.32 7.78 37.53 5.36
3129 3296 2.872557 CTGCACAAGCCATGACGG 59.127 61.111 0.00 0.00 41.13 4.79
3164 3331 1.876263 GCCACACGCACAAACAACC 60.876 57.895 0.00 0.00 37.47 3.77
3169 3336 0.179187 CACGCACAAACAACCGACAA 60.179 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1375 1412 3.917760 GCCGCGGTAGAGGAGCAT 61.918 66.667 28.70 0.00 39.96 3.79
1637 1692 3.764466 CGCGACTCCAGGCTCCTT 61.764 66.667 0.00 0.00 0.00 3.36
1920 1991 2.877168 GCTATCACAATCCTTGAGGCAG 59.123 50.000 0.00 0.00 34.44 4.85
1945 2016 2.936498 CGGTATGCTTCAGGACGAATTT 59.064 45.455 0.00 0.00 31.69 1.82
1985 2056 3.724508 ACTTCATCCTAGTCATGCTCG 57.275 47.619 0.00 0.00 0.00 5.03
2007 2078 4.288366 TCTGGATGAATGTCAACCACCTTA 59.712 41.667 3.33 0.00 43.21 2.69
2213 2343 5.619981 GCAGATTCCAAAGTACATGGACAAC 60.620 44.000 17.29 12.23 46.37 3.32
2380 2517 7.564793 ACTAATACATGTCCAGATTAACAGCA 58.435 34.615 0.00 0.00 0.00 4.41
2610 2751 4.682778 TCCCCGTTATTAACAGATCCAG 57.317 45.455 7.31 0.00 0.00 3.86
2659 2809 5.738783 GCAGGAAATGTTTGGTCAAAGCTTA 60.739 40.000 0.00 0.00 0.00 3.09
2699 2850 0.682852 CACACTCCCAGGTTCCGTAA 59.317 55.000 0.00 0.00 0.00 3.18
2959 3126 4.692228 TGAAAATGACAAGTCTTTTGCCC 58.308 39.130 12.85 7.77 37.14 5.36
3031 3198 3.018149 TGGCTAAGTTGTGTCGGTTTTT 58.982 40.909 0.00 0.00 0.00 1.94
3075 3242 2.220586 TTCCATGTCGGTGGCCAGA 61.221 57.895 5.11 0.00 39.19 3.86
3112 3279 2.872557 CCGTCATGGCTTGTGCAG 59.127 61.111 0.00 0.00 41.91 4.41
3139 3306 2.669569 GTGCGTGTGGCCATCTGT 60.670 61.111 9.72 0.00 42.61 3.41
3169 3336 1.925068 GCTCGTCGTCAAAGTCGAAGT 60.925 52.381 0.00 0.00 39.01 3.01


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

AutoCloner maintained by Alex Coulton.