Multiple sequence alignment - TraesCS2D01G528600

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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 TraesCS2D01G528600 chr2D 100.000 2343 0 0 1 2343 616456448 616454106 0.000000e+00 4327.0
1 TraesCS2D01G528600 chr6B 93.072 2064 129 8 1 2055 104120886 104122944 0.000000e+00 3007.0
2 TraesCS2D01G528600 chr6B 94.743 875 36 8 1 870 420842867 420843736 0.000000e+00 1352.0
3 TraesCS2D01G528600 chr6B 92.593 729 41 5 1227 1943 57588739 57589466 0.000000e+00 1035.0
4 TraesCS2D01G528600 chr6B 95.294 595 24 2 1748 2341 420844276 420844867 0.000000e+00 941.0
5 TraesCS2D01G528600 chr6B 92.061 592 41 4 281 870 57587218 57587805 0.000000e+00 828.0
6 TraesCS2D01G528600 chr6B 93.902 492 24 1 862 1347 420843792 420844283 0.000000e+00 737.0
7 TraesCS2D01G528600 chr6B 93.075 361 21 1 869 1225 633534372 633534732 2.060000e-145 525.0
8 TraesCS2D01G528600 chr6B 94.301 193 9 2 2049 2239 104122902 104123094 6.330000e-76 294.0
9 TraesCS2D01G528600 chr6B 91.597 119 10 0 2054 2172 168775585 168775467 5.180000e-37 165.0
10 TraesCS2D01G528600 chr2A 95.161 1488 66 1 862 2343 95024061 95025548 0.000000e+00 2344.0
11 TraesCS2D01G528600 chr2A 92.603 730 38 7 1227 1943 388471854 388472580 0.000000e+00 1035.0
12 TraesCS2D01G528600 chr2A 92.318 729 41 6 1227 1943 92974972 92974247 0.000000e+00 1022.0
13 TraesCS2D01G528600 chr2A 92.386 591 39 4 282 870 388470334 388470920 0.000000e+00 837.0
14 TraesCS2D01G528600 chr2A 92.088 594 41 4 279 870 395716844 395716255 0.000000e+00 832.0
15 TraesCS2D01G528600 chr2A 91.892 592 42 4 281 870 92976493 92975906 0.000000e+00 822.0
16 TraesCS2D01G528600 chr2A 94.956 456 20 3 1 453 95023190 95023645 0.000000e+00 712.0
17 TraesCS2D01G528600 chr2A 89.000 200 20 2 3 200 388470097 388470296 1.800000e-61 246.0
18 TraesCS2D01G528600 chr1A 92.730 729 40 5 1227 1943 458921655 458920928 0.000000e+00 1040.0
19 TraesCS2D01G528600 chr1A 92.061 592 41 4 281 870 458923176 458922589 0.000000e+00 828.0
20 TraesCS2D01G528600 chr1A 91.081 370 27 4 862 1225 458922533 458922164 1.620000e-136 496.0
21 TraesCS2D01G528600 chrUn 92.318 729 43 5 1227 1943 315701377 315702104 0.000000e+00 1024.0
22 TraesCS2D01G528600 chrUn 92.061 592 41 4 281 870 41816252 41816839 0.000000e+00 828.0
23 TraesCS2D01G528600 chr3A 87.827 879 64 21 3 870 35851101 35851947 0.000000e+00 990.0
24 TraesCS2D01G528600 chr3A 91.513 707 44 6 1251 1943 35852875 35853579 0.000000e+00 959.0
25 TraesCS2D01G528600 chr3A 100.000 32 0 0 2141 2172 235369731 235369700 2.510000e-05 60.2
26 TraesCS2D01G528600 chr5B 87.713 879 65 21 3 870 480308900 480308054 0.000000e+00 985.0
27 TraesCS2D01G528600 chr5B 92.391 368 24 3 862 1225 237818307 237817940 2.670000e-144 521.0
28 TraesCS2D01G528600 chr5B 94.839 155 8 0 2189 2343 237812552 237812398 2.330000e-60 243.0
29 TraesCS2D01G528600 chr5B 95.489 133 6 0 1923 2055 237812820 237812688 1.820000e-51 213.0
30 TraesCS2D01G528600 chr5B 91.089 101 9 0 1955 2055 257027028 257026928 1.130000e-28 137.0
31 TraesCS2D01G528600 chr5B 83.333 138 5 2 2054 2191 237812723 237812604 6.840000e-21 111.0
32 TraesCS2D01G528600 chr7B 87.643 874 69 15 3 870 520117528 520118368 0.000000e+00 979.0
33 TraesCS2D01G528600 chr7B 91.489 705 46 6 1251 1943 520119296 520119998 0.000000e+00 957.0
34 TraesCS2D01G528600 chr3B 87.486 879 67 21 3 870 532210747 532209901 0.000000e+00 974.0
35 TraesCS2D01G528600 chr6A 93.352 361 20 1 869 1225 563376099 563376459 4.430000e-147 531.0
36 TraesCS2D01G528600 chr6D 93.075 361 21 1 869 1225 420392223 420392583 2.060000e-145 525.0
37 TraesCS2D01G528600 chr2B 82.673 606 74 17 1 596 94194864 94194280 2.080000e-140 508.0
38 TraesCS2D01G528600 chr1B 91.304 368 28 3 862 1225 646747341 646747708 1.250000e-137 499.0
39 TraesCS2D01G528600 chr1B 94.194 155 9 0 2189 2343 646749135 646749289 1.080000e-58 237.0
40 TraesCS2D01G528600 chr1B 94.483 145 4 3 2049 2191 646748940 646749082 1.090000e-53 220.0
41 TraesCS2D01G528600 chr1B 91.525 118 10 0 2054 2171 47213508 47213391 1.860000e-36 163.0
42 TraesCS2D01G528600 chr7A 92.903 155 11 0 2189 2343 393331929 393331775 2.340000e-55 226.0
43 TraesCS2D01G528600 chr7A 92.903 155 11 0 2189 2343 401559147 401558993 2.340000e-55 226.0
44 TraesCS2D01G528600 chr7A 89.855 138 12 1 2054 2191 393332117 393331982 2.390000e-40 176.0
45 TraesCS2D01G528600 chr7A 89.855 138 12 1 2054 2191 401559335 401559200 2.390000e-40 176.0


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 TraesCS2D01G528600 chr2D 616454106 616456448 2342 True 4327.000000 4327 100.000000 1 2343 1 chr2D.!!$R1 2342
1 TraesCS2D01G528600 chr6B 104120886 104123094 2208 False 1650.500000 3007 93.686500 1 2239 2 chr6B.!!$F3 2238
2 TraesCS2D01G528600 chr6B 420842867 420844867 2000 False 1010.000000 1352 94.646333 1 2341 3 chr6B.!!$F4 2340
3 TraesCS2D01G528600 chr6B 57587218 57589466 2248 False 931.500000 1035 92.327000 281 1943 2 chr6B.!!$F2 1662
4 TraesCS2D01G528600 chr2A 95023190 95025548 2358 False 1528.000000 2344 95.058500 1 2343 2 chr2A.!!$F1 2342
5 TraesCS2D01G528600 chr2A 92974247 92976493 2246 True 922.000000 1022 92.105000 281 1943 2 chr2A.!!$R2 1662
6 TraesCS2D01G528600 chr2A 395716255 395716844 589 True 832.000000 832 92.088000 279 870 1 chr2A.!!$R1 591
7 TraesCS2D01G528600 chr2A 388470097 388472580 2483 False 706.000000 1035 91.329667 3 1943 3 chr2A.!!$F2 1940
8 TraesCS2D01G528600 chr1A 458920928 458923176 2248 True 788.000000 1040 91.957333 281 1943 3 chr1A.!!$R1 1662
9 TraesCS2D01G528600 chrUn 315701377 315702104 727 False 1024.000000 1024 92.318000 1227 1943 1 chrUn.!!$F2 716
10 TraesCS2D01G528600 chrUn 41816252 41816839 587 False 828.000000 828 92.061000 281 870 1 chrUn.!!$F1 589
11 TraesCS2D01G528600 chr3A 35851101 35853579 2478 False 974.500000 990 89.670000 3 1943 2 chr3A.!!$F1 1940
12 TraesCS2D01G528600 chr5B 480308054 480308900 846 True 985.000000 985 87.713000 3 870 1 chr5B.!!$R3 867
13 TraesCS2D01G528600 chr7B 520117528 520119998 2470 False 968.000000 979 89.566000 3 1943 2 chr7B.!!$F1 1940
14 TraesCS2D01G528600 chr3B 532209901 532210747 846 True 974.000000 974 87.486000 3 870 1 chr3B.!!$R1 867
15 TraesCS2D01G528600 chr2B 94194280 94194864 584 True 508.000000 508 82.673000 1 596 1 chr2B.!!$R1 595
16 TraesCS2D01G528600 chr1B 646747341 646749289 1948 False 318.666667 499 93.327000 862 2343 3 chr1B.!!$F1 1481

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
45 48 0.035439 CCATGGCTAGGGTTTCGTGT 60.035 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2679 0.179067 CATGGAATTGCATGTGGGGC 60.179 55.0 26.66 0.0 0.0 5.8 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
43 46 1.607612 CCCATGGCTAGGGTTTCGT 59.392 57.895 6.09 0.00 41.61 3.85
45 48 0.035439 CCATGGCTAGGGTTTCGTGT 60.035 55.000 0.00 0.00 0.00 4.49
123 131 0.183014 CCCTAGCTACCCTCTCGTCA 59.817 60.000 0.00 0.00 0.00 4.35
464 499 1.202770 CGAAACTCTTCAAGGGTGGGT 60.203 52.381 0.00 0.00 0.00 4.51
522 557 2.688507 CTTGCTCTCCATGTGTACGTT 58.311 47.619 0.00 0.00 0.00 3.99
566 601 1.686355 TGGTTCTTCCAATGTGCGTT 58.314 45.000 0.00 0.00 44.12 4.84
760 796 3.216800 TGGGTTGATTAGCTGATGCATC 58.783 45.455 20.14 20.14 42.74 3.91
763 799 3.252701 GGTTGATTAGCTGATGCATCTGG 59.747 47.826 28.32 20.74 42.74 3.86
792 828 8.883731 CGTATAAATGGATAATTGAGATGGGTC 58.116 37.037 0.00 0.00 0.00 4.46
807 843 7.752638 TGAGATGGGTCTGATTTATTCATGAT 58.247 34.615 0.00 0.00 33.97 2.45
1062 1166 6.265577 CAAGTTTGGGTTCTACAAGTTCTTG 58.734 40.000 10.50 10.50 32.60 3.02
1489 2119 1.781786 TTTTGTTGGGCTGCCAACTA 58.218 45.000 22.05 15.62 46.99 2.24
1530 2161 9.433317 GATTATGTTATTGTTCCGTACACAATG 57.567 33.333 16.36 0.00 43.31 2.82
1541 2172 3.057876 CCGTACACAATGCCTTGCTAAAA 60.058 43.478 1.19 0.00 35.69 1.52
1562 2193 1.949847 ATGGACGTCCTCAGCGAAGG 61.950 60.000 33.39 1.24 37.81 3.46
1614 2245 6.547510 AGAAAGAACACAAGCCATAAGAAACT 59.452 34.615 0.00 0.00 0.00 2.66
1712 2343 6.302269 AGATATTGACATCAGAAATCCCCAC 58.698 40.000 0.00 0.00 0.00 4.61
1754 2385 9.906660 CTTAAATTGCAGGACAAGTTTACATAA 57.093 29.630 0.00 0.00 43.68 1.90
2043 2679 2.837498 TCCATGACAATGAGCATACCG 58.163 47.619 0.00 0.00 35.67 4.02
2210 2901 5.769662 CCTGTAGCCTATTGCCATGAATTTA 59.230 40.000 0.00 0.00 42.71 1.40
2220 2911 9.330063 CTATTGCCATGAATTTAGTCAGAGTTA 57.670 33.333 0.00 0.00 0.00 2.24
2231 2922 2.303311 AGTCAGAGTTAAGGAACTGGGC 59.697 50.000 0.00 0.00 46.23 5.36
2307 2998 1.344953 ATAGATGCCAGGCGGGACAA 61.345 55.000 8.22 0.00 40.01 3.18
2333 3024 3.722147 AGATGTGATGCCGATGTCTAAC 58.278 45.455 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 131 3.005539 AGTGCGAGGGTGCTCCAT 61.006 61.111 7.20 0.00 38.24 3.41
217 244 1.302949 GGTGTTGCTGCCCCAGATA 59.697 57.895 0.00 0.00 32.44 1.98
220 247 2.283388 ATGGTGTTGCTGCCCCAG 60.283 61.111 0.00 0.00 34.12 4.45
464 499 2.427453 CGATCTCGGGGAAAAGAGAAGA 59.573 50.000 0.00 0.00 45.31 2.87
522 557 1.908344 TGCAGGCAAATACAGCAAGA 58.092 45.000 0.00 0.00 31.42 3.02
566 601 3.942829 CCTGCAGGTGTATTTCTCAAGA 58.057 45.455 25.53 0.00 0.00 3.02
760 796 7.387673 TCTCAATTATCCATTTATACGCACCAG 59.612 37.037 0.00 0.00 0.00 4.00
763 799 8.177663 CCATCTCAATTATCCATTTATACGCAC 58.822 37.037 0.00 0.00 0.00 5.34
1019 1123 2.530151 AAGCCCCCTGAGCACTGA 60.530 61.111 0.00 0.00 0.00 3.41
1062 1166 5.538433 AGCCATATCTGAGTAGGTCTTCTTC 59.462 44.000 0.00 0.00 0.00 2.87
1213 1319 6.867293 AGCTAAAAACTTCGACGAGTAAATCT 59.133 34.615 0.00 0.00 0.00 2.40
1423 2043 5.721960 AGATGACATACTTAACAGTCTGGGT 59.278 40.000 4.53 0.65 32.53 4.51
1530 2161 2.084546 ACGTCCATCTTTTAGCAAGGC 58.915 47.619 0.00 0.00 0.00 4.35
1541 2172 0.965866 TTCGCTGAGGACGTCCATCT 60.966 55.000 35.00 16.29 38.89 2.90
1562 2193 1.745489 GGGTCACGGACATGGCTTC 60.745 63.158 0.00 0.00 33.68 3.86
1712 2343 7.080724 GCAATTTAAGTGTTCAAGGAAGAGAG 58.919 38.462 0.00 0.00 0.00 3.20
1985 2621 2.886523 CACATTGTGAACTGGACACCAT 59.113 45.455 11.45 0.00 37.45 3.55
2043 2679 0.179067 CATGGAATTGCATGTGGGGC 60.179 55.000 26.66 0.00 0.00 5.80
2210 2901 2.303311 GCCCAGTTCCTTAACTCTGACT 59.697 50.000 0.00 0.00 44.28 3.41
2220 2911 1.774217 TGTCCTGGCCCAGTTCCTT 60.774 57.895 10.47 0.00 0.00 3.36
2231 2922 1.279496 TCTCCCTTGATGTGTCCTGG 58.721 55.000 0.00 0.00 0.00 4.45
2307 2998 1.752358 ATCGGCATCACATCTCGCCT 61.752 55.000 0.00 0.00 42.59 5.52


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

AutoCloner maintained by Alex Coulton.