Multiple sequence alignment - TraesCS7B01G308900

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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 TraesCS7B01G308900 chr7B 100.000 2465 0 0 1 2465 552707060 552704596 0.000000e+00 4553.0
1 TraesCS7B01G308900 chr7B 98.540 2465 32 3 1 2465 552754046 552751586 0.000000e+00 4349.0
2 TraesCS7B01G308900 chr7B 91.682 1599 124 4 875 2465 192802627 192801030 0.000000e+00 2207.0
3 TraesCS7B01G308900 chr7B 78.674 1599 323 16 874 2462 621915986 621914396 0.000000e+00 1048.0
4 TraesCS7B01G308900 chr7B 80.022 926 164 18 879 1793 120456424 120457339 0.000000e+00 665.0
5 TraesCS7B01G308900 chr7B 86.758 219 19 5 244 461 570103180 570102971 4.100000e-58 235.0
6 TraesCS7B01G308900 chr5B 89.470 1605 152 11 874 2465 348580248 348578648 0.000000e+00 2012.0
7 TraesCS7B01G308900 chr5B 92.982 171 12 0 286 456 230774810 230774980 1.460000e-62 250.0
8 TraesCS7B01G308900 chr6B 91.560 1327 106 5 874 2197 151413898 151412575 0.000000e+00 1825.0
9 TraesCS7B01G308900 chr6B 86.528 1581 202 9 891 2464 87507254 87505678 0.000000e+00 1729.0
10 TraesCS7B01G308900 chr6B 77.100 1476 319 17 1000 2464 573746775 573745308 0.000000e+00 835.0
11 TraesCS7B01G308900 chr6B 92.308 273 21 0 2193 2465 151390000 151389728 2.970000e-104 388.0
12 TraesCS7B01G308900 chr4A 87.749 1306 148 5 876 2177 676919844 676918547 0.000000e+00 1515.0
13 TraesCS7B01G308900 chr4A 85.430 151 9 9 244 390 683443735 683443594 7.100000e-31 145.0
14 TraesCS7B01G308900 chr2B 94.935 928 43 3 1273 2196 534688099 534689026 0.000000e+00 1450.0
15 TraesCS7B01G308900 chr5A 90.314 1084 98 6 1385 2465 71136084 71137163 0.000000e+00 1413.0
16 TraesCS7B01G308900 chr1D 80.500 1600 292 20 876 2464 442404185 442402595 0.000000e+00 1208.0
17 TraesCS7B01G308900 chr1D 87.736 212 16 3 248 459 487509604 487509403 3.170000e-59 239.0
18 TraesCS7B01G308900 chr6A 77.136 1299 269 24 876 2159 511532056 511533341 0.000000e+00 728.0
19 TraesCS7B01G308900 chr3B 89.714 350 36 0 1823 2172 766176280 766175931 4.840000e-122 448.0
20 TraesCS7B01G308900 chr3B 93.143 175 11 1 286 459 228425032 228424858 3.150000e-64 255.0
21 TraesCS7B01G308900 chr7A 89.049 347 19 9 455 783 595281121 595280776 1.760000e-111 412.0
22 TraesCS7B01G308900 chr7A 92.683 246 16 2 1 244 595281353 595281108 1.080000e-93 353.0
23 TraesCS7B01G308900 chr7A 86.111 216 20 4 246 460 701288500 701288294 8.870000e-55 224.0
24 TraesCS7B01G308900 chr7D 88.252 349 18 13 455 783 519406751 519406406 1.780000e-106 396.0
25 TraesCS7B01G308900 chr7D 89.205 176 17 2 286 461 230926749 230926922 4.130000e-53 219.0
26 TraesCS7B01G308900 chr4D 88.991 218 15 3 244 461 393953964 393953756 6.760000e-66 261.0
27 TraesCS7B01G308900 chr4D 97.778 45 1 0 803 847 5235995 5236039 7.310000e-11 78.7
28 TraesCS7B01G308900 chr3D 86.449 214 19 4 249 461 336826170 336825966 2.470000e-55 226.0
29 TraesCS7B01G308900 chr1A 85.973 221 20 4 242 461 10585706 10585496 2.470000e-55 226.0
30 TraesCS7B01G308900 chr1B 85.388 219 20 5 245 461 160502164 160501956 1.480000e-52 217.0
31 TraesCS7B01G308900 chr4B 100.000 32 0 0 816 847 9388701 9388670 2.650000e-05 60.2


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 TraesCS7B01G308900 chr7B 552704596 552707060 2464 True 4553.0 4553 100.000 1 2465 1 chr7B.!!$R2 2464
1 TraesCS7B01G308900 chr7B 552751586 552754046 2460 True 4349.0 4349 98.540 1 2465 1 chr7B.!!$R3 2464
2 TraesCS7B01G308900 chr7B 192801030 192802627 1597 True 2207.0 2207 91.682 875 2465 1 chr7B.!!$R1 1590
3 TraesCS7B01G308900 chr7B 621914396 621915986 1590 True 1048.0 1048 78.674 874 2462 1 chr7B.!!$R5 1588
4 TraesCS7B01G308900 chr7B 120456424 120457339 915 False 665.0 665 80.022 879 1793 1 chr7B.!!$F1 914
5 TraesCS7B01G308900 chr5B 348578648 348580248 1600 True 2012.0 2012 89.470 874 2465 1 chr5B.!!$R1 1591
6 TraesCS7B01G308900 chr6B 151412575 151413898 1323 True 1825.0 1825 91.560 874 2197 1 chr6B.!!$R3 1323
7 TraesCS7B01G308900 chr6B 87505678 87507254 1576 True 1729.0 1729 86.528 891 2464 1 chr6B.!!$R1 1573
8 TraesCS7B01G308900 chr6B 573745308 573746775 1467 True 835.0 835 77.100 1000 2464 1 chr6B.!!$R4 1464
9 TraesCS7B01G308900 chr4A 676918547 676919844 1297 True 1515.0 1515 87.749 876 2177 1 chr4A.!!$R1 1301
10 TraesCS7B01G308900 chr2B 534688099 534689026 927 False 1450.0 1450 94.935 1273 2196 1 chr2B.!!$F1 923
11 TraesCS7B01G308900 chr5A 71136084 71137163 1079 False 1413.0 1413 90.314 1385 2465 1 chr5A.!!$F1 1080
12 TraesCS7B01G308900 chr1D 442402595 442404185 1590 True 1208.0 1208 80.500 876 2464 1 chr1D.!!$R1 1588
13 TraesCS7B01G308900 chr6A 511532056 511533341 1285 False 728.0 728 77.136 876 2159 1 chr6A.!!$F1 1283
14 TraesCS7B01G308900 chr7A 595280776 595281353 577 True 382.5 412 90.866 1 783 2 chr7A.!!$R2 782

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
216 217 1.493022 TGGTTCAAGCCACTACCAACT 59.507 47.619 0.0 0.0 37.71 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 2089 2.273557 TCGCTTTCGGGTTATTAGCAC 58.726 47.619 0.0 0.0 36.13 4.4 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
216 217 1.493022 TGGTTCAAGCCACTACCAACT 59.507 47.619 0.00 0.0 37.71 3.16
275 276 4.751767 AACTGGGCAAAAGATTTGTCAA 57.248 36.364 9.36 0.0 0.00 3.18
407 408 4.215109 AGGCACCATAGTTTTGAAACACT 58.785 39.130 9.08 0.0 41.30 3.55
958 961 3.282021 CCACCCATACCTCAACTTGATG 58.718 50.000 0.00 0.0 0.00 3.07
1087 1091 1.555075 TGGAGGATTTCTTCGACCAGG 59.445 52.381 0.00 0.0 0.00 4.45
1101 1105 4.264253 TCGACCAGGTAGATCTAAACGAA 58.736 43.478 3.40 0.0 0.00 3.85
1276 1320 2.281276 GGTTTCGTCCGGTTGGCT 60.281 61.111 0.00 0.0 34.14 4.75
1972 2070 7.202011 GGAAGAGGCTAAATATGGACAACTCTA 60.202 40.741 0.00 0.0 32.93 2.43
1991 2089 9.247126 CAACTCTAGTGATGATGTTCTGAATAG 57.753 37.037 0.00 0.0 0.00 1.73
2155 2253 1.306141 TCCCATGAGGAAGACCGCT 60.306 57.895 0.00 0.0 43.78 5.52
2442 2555 4.265904 TCGATGTTAGTGTGGTTGATGT 57.734 40.909 0.00 0.0 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 6.985188 TCTAGACCATTGAACTTTGCATAC 57.015 37.500 0.00 0.0 0.00 2.39
149 150 8.622157 TCGTAAACAATTATTTTGACCTGTGAA 58.378 29.630 0.00 0.0 0.00 3.18
164 165 4.919168 TGAAGTCGATCGTCGTAAACAATT 59.081 37.500 15.94 0.0 41.35 2.32
216 217 0.033405 TGTGTTTTGGGGGTTTCGGA 60.033 50.000 0.00 0.0 0.00 4.55
325 326 4.152938 AGAGTAACGTTTTGTAATTCGGCC 59.847 41.667 5.91 0.0 0.00 6.13
407 408 5.010617 GGGGTTCTTGTTGCTAGAATCAAAA 59.989 40.000 0.00 0.0 35.00 2.44
630 631 7.588497 TCACTGACTCATTGTACTAGCATAT 57.412 36.000 0.00 0.0 0.00 1.78
738 739 6.335471 TGTGCTTGTTTCAGATCATTTGAT 57.665 33.333 0.00 0.0 37.51 2.57
853 854 5.577554 GGAAACACGGATCTACTCTTTTCTC 59.422 44.000 0.00 0.0 0.00 2.87
958 961 4.292178 CGGCCAGAGAGATCGCCC 62.292 72.222 2.24 0.0 38.19 6.13
1087 1091 8.967552 TTGAACTCTTCTTCGTTTAGATCTAC 57.032 34.615 0.67 0.0 0.00 2.59
1101 1105 5.752036 TCTCCACATCATTGAACTCTTCT 57.248 39.130 0.00 0.0 0.00 2.85
1972 2070 5.987098 AGCACTATTCAGAACATCATCACT 58.013 37.500 0.00 0.0 0.00 3.41
1991 2089 2.273557 TCGCTTTCGGGTTATTAGCAC 58.726 47.619 0.00 0.0 36.13 4.40
2155 2253 6.356556 CAGAATAGGGTATTCATTGTGTCCA 58.643 40.000 8.90 0.0 45.41 4.02
2442 2555 1.597854 CAAGACGTGCCTGAGCCAA 60.598 57.895 0.00 0.0 38.69 4.52


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

AutoCloner maintained by Alex Coulton.