Multiple sequence alignment - TraesCS1A01G166700

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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 TraesCS1A01G166700 chr1A 100.000 2232 0 0 561 2792 299540153 299542384 0.000000e+00 4122.0
1 TraesCS1A01G166700 chr1A 95.440 614 28 0 561 1174 97423713 97423100 0.000000e+00 979.0
2 TraesCS1A01G166700 chr1A 100.000 226 0 0 1 226 299539593 299539818 4.300000e-113 418.0
3 TraesCS1A01G166700 chr1A 95.197 229 8 1 1 226 97423955 97423727 2.640000e-95 359.0
4 TraesCS1A01G166700 chr1A 96.396 111 4 0 2682 2792 97423109 97422999 1.710000e-42 183.0
5 TraesCS1A01G166700 chr1A 96.703 91 3 0 1 91 97421473 97421563 4.820000e-33 152.0
6 TraesCS1A01G166700 chr1A 95.604 91 4 0 1 91 299543899 299543809 2.240000e-31 147.0
7 TraesCS1A01G166700 chr2A 98.082 2190 40 2 603 2792 102023725 102021538 0.000000e+00 3810.0
8 TraesCS1A01G166700 chr2A 96.491 228 5 2 1 226 102024315 102024089 9.440000e-100 374.0
9 TraesCS1A01G166700 chr2A 96.774 62 1 1 561 621 102023735 102023674 4.920000e-18 102.0
10 TraesCS1A01G166700 chr1D 96.751 1693 54 1 585 2277 50967458 50969149 0.000000e+00 2820.0
11 TraesCS1A01G166700 chr1D 96.286 1050 39 0 1158 2207 51002253 51003302 0.000000e+00 1724.0
12 TraesCS1A01G166700 chr1D 94.850 602 30 1 561 1162 51000313 51000913 0.000000e+00 939.0
13 TraesCS1A01G166700 chr1D 98.635 293 4 0 2500 2792 50969151 50969443 1.150000e-143 520.0
14 TraesCS1A01G166700 chr1D 96.903 226 4 3 1 226 50966979 50967201 2.630000e-100 375.0
15 TraesCS1A01G166700 chr1D 95.794 214 8 1 3 216 51000099 51000311 7.400000e-91 344.0
16 TraesCS1A01G166700 chr1D 98.901 91 1 0 1 91 50970972 50970882 2.230000e-36 163.0
17 TraesCS1A01G166700 chr1D 94.231 52 3 0 570 621 50967476 50967527 2.310000e-11 80.5
18 TraesCS1A01G166700 chr3B 93.638 1336 79 4 835 2165 448751272 448752606 0.000000e+00 1991.0
19 TraesCS1A01G166700 chr3B 87.591 137 11 2 627 763 448751135 448751265 1.340000e-33 154.0
20 TraesCS1A01G166700 chr3B 95.556 90 1 2 4 91 448752943 448752855 1.040000e-29 141.0
21 TraesCS1A01G166700 chr3B 100.000 29 0 0 594 622 448751135 448751163 1.000000e-03 54.7
22 TraesCS1A01G166700 chr7A 81.991 211 13 12 27 226 533036357 533036553 3.720000e-34 156.0
23 TraesCS1A01G166700 chr7A 94.253 87 4 1 1 87 533037397 533037312 6.270000e-27 132.0
24 TraesCS1A01G166700 chr6D 71.074 363 92 12 2240 2593 452314711 452314353 2.980000e-10 76.8
25 TraesCS1A01G166700 chr5B 93.617 47 3 0 2555 2601 260237153 260237107 1.390000e-08 71.3
26 TraesCS1A01G166700 chr2B 93.617 47 3 0 2543 2589 697521724 697521770 1.390000e-08 71.3
27 TraesCS1A01G166700 chr2B 70.811 370 93 14 2240 2599 801009564 801009200 1.390000e-08 71.3
28 TraesCS1A01G166700 chr7D 91.489 47 4 0 2543 2589 552506640 552506686 6.460000e-07 65.8


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 TraesCS1A01G166700 chr1A 299539593 299542384 2791 False 2270.000000 4122 100.000000 1 2792 2 chr1A.!!$F2 2791
1 TraesCS1A01G166700 chr1A 97422999 97423955 956 True 507.000000 979 95.677667 1 2792 3 chr1A.!!$R2 2791
2 TraesCS1A01G166700 chr2A 102021538 102024315 2777 True 1428.666667 3810 97.115667 1 2792 3 chr2A.!!$R1 2791
3 TraesCS1A01G166700 chr1D 51000099 51003302 3203 False 1002.333333 1724 95.643333 3 2207 3 chr1D.!!$F2 2204
4 TraesCS1A01G166700 chr1D 50966979 50969443 2464 False 948.875000 2820 96.630000 1 2792 4 chr1D.!!$F1 2791
5 TraesCS1A01G166700 chr3B 448751135 448752606 1471 False 733.233333 1991 93.743000 594 2165 3 chr3B.!!$F1 1571

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
129 130 1.544825 CGAGCACCCCCTTTCTCTCA 61.545 60.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 3445 2.065899 TGTGCACTTTGCCCTTACTT 57.934 45.0 19.41 0.0 44.23 2.24 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
129 130 1.544825 CGAGCACCCCCTTTCTCTCA 61.545 60.000 0.00 0.00 0.00 3.27
158 162 2.045047 TCTCTCTCAGATTTCCCCACCT 59.955 50.000 0.00 0.00 0.00 4.00
624 900 3.299190 GCCCCGATCTCTCCCGAG 61.299 72.222 0.00 0.00 38.67 4.63
625 901 2.598985 CCCCGATCTCTCCCGAGG 60.599 72.222 0.00 0.00 37.86 4.63
626 902 2.516405 CCCGATCTCTCCCGAGGA 59.484 66.667 0.00 0.00 37.86 3.71
851 1127 2.649034 GACGCGAGGTTGAGGACA 59.351 61.111 15.93 0.00 0.00 4.02
1022 1303 4.508551 TGGATCCAGCAGATTGTATTGT 57.491 40.909 11.44 0.00 34.42 2.71
1143 1424 6.128336 CCTTGAGCTTACAGAGAATTCAACAG 60.128 42.308 8.44 1.24 0.00 3.16
1457 3082 2.362077 GTGACTTTGTGCCACCAGATTT 59.638 45.455 0.00 0.00 0.00 2.17
1470 3095 4.581824 CCACCAGATTTTTCATCGGATGAT 59.418 41.667 20.53 6.52 39.39 2.45
1605 3230 6.189859 ACCTGAAGGCAATTATGAAGATGAA 58.810 36.000 0.00 0.00 39.32 2.57
1614 3239 7.201145 GCAATTATGAAGATGAATCAAGTGCT 58.799 34.615 0.00 0.00 0.00 4.40
1789 3414 6.206634 TCGTTATGCACTGAAGGAAAGAAAAT 59.793 34.615 0.00 0.00 0.00 1.82
1820 3445 7.079451 AGTTCTTAAAAGATGAGGGAGTCAA 57.921 36.000 0.00 0.00 39.19 3.18
1915 3540 6.170506 AGTTGGCAGATTACTTCATTTACGA 58.829 36.000 0.00 0.00 0.00 3.43
1966 3591 8.577048 AGATAGTGCACTAGTTACAAGTAGAA 57.423 34.615 29.05 5.71 35.85 2.10
1969 3594 5.539193 AGTGCACTAGTTACAAGTAGAAGGT 59.461 40.000 20.16 0.00 35.85 3.50
2036 3661 6.211184 TGGTCAATCCAGCAATTAAAGTCAAT 59.789 34.615 0.00 0.00 41.93 2.57
2137 3762 1.334243 CGGCTAAAGAGGGAGAGTACG 59.666 57.143 0.00 0.00 0.00 3.67
2197 3822 1.348064 CCCTGGGACTACTTGTGTGA 58.652 55.000 7.01 0.00 0.00 3.58
2239 3864 3.222603 GAAGAACCAACATTCCACCACT 58.777 45.455 0.00 0.00 0.00 4.00
2348 3974 5.467035 AGAGCAGGAGAGATATTAAGTGC 57.533 43.478 0.00 0.00 0.00 4.40
2478 4104 2.814805 AAGTTGGAGATGGTGATGGG 57.185 50.000 0.00 0.00 0.00 4.00
2492 4118 5.594777 TGGTGATGGGTGGGTTATAATTTT 58.405 37.500 0.00 0.00 0.00 1.82
2519 4145 7.493320 TGATCAGCAAAAAGGAATATTGAATGC 59.507 33.333 0.00 0.00 0.00 3.56
2741 4367 0.250901 GACCCACAACACTGGAGCAT 60.251 55.000 0.00 0.00 32.30 3.79
2775 4401 5.048713 CAGGTTAGGAAGTTGTTGTGATTCC 60.049 44.000 0.00 0.00 41.29 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 5.243730 GGGAAATCTGAGAGAGAGATCGAAT 59.756 44.000 0.00 0.0 32.80 3.34
621 897 4.803426 GTGGCGCTGGTCTCCTCG 62.803 72.222 7.64 0.0 0.00 4.63
622 898 4.459089 GGTGGCGCTGGTCTCCTC 62.459 72.222 7.64 0.0 0.00 3.71
775 1051 3.242641 CGATACTTCACCGTCGAGATCAA 60.243 47.826 0.00 0.0 36.25 2.57
851 1127 6.483640 GGAATATTGCTCACCTAATTCTTCGT 59.516 38.462 0.00 0.0 0.00 3.85
1022 1303 4.502259 CCCCATTGAAATGAAAACGGACAA 60.502 41.667 4.58 0.0 38.70 3.18
1143 1424 5.049474 TGTGACATAATGCTCACTCAAACAC 60.049 40.000 3.56 0.0 38.12 3.32
1406 3031 4.811024 CGGAGCTGCTTTCTACATCAATTA 59.189 41.667 2.53 0.0 0.00 1.40
1470 3095 4.321718 GCTTAATAGCATCTGCCTCATCA 58.678 43.478 0.00 0.0 46.95 3.07
1605 3230 4.564782 TTCATCCTCTTCAGCACTTGAT 57.435 40.909 0.00 0.0 35.27 2.57
1614 3239 6.239148 CCTCGTCATAAGATTCATCCTCTTCA 60.239 42.308 0.00 0.0 34.81 3.02
1820 3445 2.065899 TGTGCACTTTGCCCTTACTT 57.934 45.000 19.41 0.0 44.23 2.24
1915 3540 4.081697 CCTTTTTGGACAAGTGTGTTCCTT 60.082 41.667 0.00 0.0 38.41 3.36
1966 3591 4.706962 ACTCTCAAACTTTTCTGCAAACCT 59.293 37.500 0.00 0.0 0.00 3.50
1969 3594 6.686630 TCAAACTCTCAAACTTTTCTGCAAA 58.313 32.000 0.00 0.0 0.00 3.68
2137 3762 3.320826 AGTTGGTAATCAAACACTTGGCC 59.679 43.478 0.00 0.0 37.08 5.36
2197 3822 4.410099 TCAAAATCTGGGTGAAGCTTGAT 58.590 39.130 2.10 0.0 0.00 2.57
2239 3864 5.599732 ACAAGCATCAAAGCACACATAAAA 58.400 33.333 0.00 0.0 36.85 1.52
2348 3974 3.270027 TGATTTGCATCTCTACCAACGG 58.730 45.455 0.00 0.0 0.00 4.44
2478 4104 8.770438 TTTGCTGATCAAAAATTATAACCCAC 57.230 30.769 0.00 0.0 41.36 4.61
2492 4118 9.373603 CATTCAATATTCCTTTTTGCTGATCAA 57.626 29.630 0.00 0.0 0.00 2.57
2519 4145 1.302832 GGAGCCCAGTGGTGAACAG 60.303 63.158 8.74 0.0 0.00 3.16
2741 4367 1.440618 TCCTAACCTGAACCAAGCCA 58.559 50.000 0.00 0.0 0.00 4.75


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

AutoCloner maintained by Alex Coulton.