Multiple sequence alignment - TraesCS2B01G352400

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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 TraesCS2B01G352400 chr2B 100.000 3572 0 0 1 3572 503455047 503451476 0.000000e+00 6597.0
1 TraesCS2B01G352400 chr2B 97.917 48 1 0 2633 2680 503452367 503452320 2.290000e-12 84.2
2 TraesCS2B01G352400 chr2B 97.917 48 1 0 2681 2728 503452415 503452368 2.290000e-12 84.2
3 TraesCS2B01G352400 chr2A 97.404 2696 66 3 880 3572 562507896 562510590 0.000000e+00 4588.0
4 TraesCS2B01G352400 chr2A 98.178 878 15 1 1 878 673067787 673068663 0.000000e+00 1531.0
5 TraesCS2B01G352400 chr2A 97.917 48 1 0 2681 2728 562509649 562509696 2.290000e-12 84.2
6 TraesCS2B01G352400 chr2D 97.472 2690 60 5 885 3572 426435058 426432375 0.000000e+00 4584.0
7 TraesCS2B01G352400 chr2D 82.857 175 23 4 2240 2414 1819547 1819714 2.220000e-32 150.0
8 TraesCS2B01G352400 chr2D 100.000 48 0 0 2633 2680 426433262 426433215 4.910000e-14 89.8
9 TraesCS2B01G352400 chr2D 97.917 48 1 0 2681 2728 426433310 426433263 2.290000e-12 84.2
10 TraesCS2B01G352400 chr7B 98.409 880 14 0 1 880 73188202 73189081 0.000000e+00 1548.0
11 TraesCS2B01G352400 chr7B 97.725 879 20 0 1 879 399933161 399932283 0.000000e+00 1513.0
12 TraesCS2B01G352400 chr3A 98.180 879 16 0 1 879 479459291 479458413 0.000000e+00 1535.0
13 TraesCS2B01G352400 chr3A 94.438 881 48 1 1 880 674740564 674741444 0.000000e+00 1354.0
14 TraesCS2B01G352400 chr1B 98.288 876 15 0 2 877 594048782 594049657 0.000000e+00 1535.0
15 TraesCS2B01G352400 chr4A 94.205 880 51 0 1 880 598606744 598607623 0.000000e+00 1343.0
16 TraesCS2B01G352400 chr4A 94.091 880 52 0 1 880 31615386 31614507 0.000000e+00 1338.0
17 TraesCS2B01G352400 chr4A 81.170 393 62 6 1384 1766 603468903 603469293 4.480000e-79 305.0
18 TraesCS2B01G352400 chr4A 80.916 393 63 5 1384 1766 603390111 603389721 2.080000e-77 300.0
19 TraesCS2B01G352400 chr6B 93.970 879 53 0 1 879 118969589 118968711 0.000000e+00 1330.0
20 TraesCS2B01G352400 chrUn 79.437 710 112 25 1960 2654 43078989 43079679 4.170000e-129 472.0
21 TraesCS2B01G352400 chr3B 81.176 595 100 8 1960 2548 825290313 825290901 5.400000e-128 468.0
22 TraesCS2B01G352400 chr3B 79.267 709 114 23 1960 2654 825499950 825499261 6.980000e-127 464.0
23 TraesCS2B01G352400 chr3B 83.188 458 73 4 1960 2413 823976843 823977300 1.980000e-112 416.0
24 TraesCS2B01G352400 chr3B 84.010 394 61 2 1367 1759 825289858 825290250 9.360000e-101 377.0
25 TraesCS2B01G352400 chr3B 77.049 366 84 0 1385 1750 823651179 823651544 1.000000e-50 211.0
26 TraesCS2B01G352400 chr3B 75.862 377 91 0 1384 1760 823655894 823656270 3.640000e-45 193.0
27 TraesCS2B01G352400 chr3B 74.545 440 103 7 1327 1760 823699225 823699661 2.190000e-42 183.0
28 TraesCS2B01G352400 chr4B 81.250 592 96 6 2063 2653 1767396 1766819 6.980000e-127 464.0
29 TraesCS2B01G352400 chr4B 80.867 392 65 4 1384 1766 1767928 1767538 2.080000e-77 300.0
30 TraesCS2B01G352400 chr4D 73.633 622 133 21 2048 2652 1333552 1332945 1.000000e-50 211.0
31 TraesCS2B01G352400 chr4D 73.089 628 123 31 2055 2652 1338012 1337401 7.880000e-42 182.0
32 TraesCS2B01G352400 chr5B 72.952 647 122 36 1121 1737 619190909 619191532 3.670000e-40 176.0
33 TraesCS2B01G352400 chr5B 84.884 86 11 2 1193 1277 619106962 619107046 6.350000e-13 86.1


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 TraesCS2B01G352400 chr2B 503451476 503455047 3571 True 2255.133333 6597 98.611333 1 3572 3 chr2B.!!$R1 3571
1 TraesCS2B01G352400 chr2A 562507896 562510590 2694 False 2336.100000 4588 97.660500 880 3572 2 chr2A.!!$F2 2692
2 TraesCS2B01G352400 chr2A 673067787 673068663 876 False 1531.000000 1531 98.178000 1 878 1 chr2A.!!$F1 877
3 TraesCS2B01G352400 chr2D 426432375 426435058 2683 True 1586.000000 4584 98.463000 885 3572 3 chr2D.!!$R1 2687
4 TraesCS2B01G352400 chr7B 73188202 73189081 879 False 1548.000000 1548 98.409000 1 880 1 chr7B.!!$F1 879
5 TraesCS2B01G352400 chr7B 399932283 399933161 878 True 1513.000000 1513 97.725000 1 879 1 chr7B.!!$R1 878
6 TraesCS2B01G352400 chr3A 479458413 479459291 878 True 1535.000000 1535 98.180000 1 879 1 chr3A.!!$R1 878
7 TraesCS2B01G352400 chr3A 674740564 674741444 880 False 1354.000000 1354 94.438000 1 880 1 chr3A.!!$F1 879
8 TraesCS2B01G352400 chr1B 594048782 594049657 875 False 1535.000000 1535 98.288000 2 877 1 chr1B.!!$F1 875
9 TraesCS2B01G352400 chr4A 598606744 598607623 879 False 1343.000000 1343 94.205000 1 880 1 chr4A.!!$F1 879
10 TraesCS2B01G352400 chr4A 31614507 31615386 879 True 1338.000000 1338 94.091000 1 880 1 chr4A.!!$R1 879
11 TraesCS2B01G352400 chr6B 118968711 118969589 878 True 1330.000000 1330 93.970000 1 879 1 chr6B.!!$R1 878
12 TraesCS2B01G352400 chrUn 43078989 43079679 690 False 472.000000 472 79.437000 1960 2654 1 chrUn.!!$F1 694
13 TraesCS2B01G352400 chr3B 825499261 825499950 689 True 464.000000 464 79.267000 1960 2654 1 chr3B.!!$R1 694
14 TraesCS2B01G352400 chr3B 825289858 825290901 1043 False 422.500000 468 82.593000 1367 2548 2 chr3B.!!$F5 1181
15 TraesCS2B01G352400 chr4B 1766819 1767928 1109 True 382.000000 464 81.058500 1384 2653 2 chr4B.!!$R1 1269

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
469 470 3.439476 GCAATCTGCAGAAGTTCAGATGT 59.561 43.478 22.5 0.0 46.11 3.06 F
1100 1101 1.152881 GCCTAGCCACCATTCCCAG 60.153 63.158 0.0 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 1807 0.109039 GAAGACTGAGTGAGGGACGC 60.109 60.0 0.0 0.0 0.00 5.19 R
2717 2744 0.471617 ACTGCCAGTTCTTCAGTGCT 59.528 50.0 0.0 0.0 39.36 4.40 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
117 118 5.327732 AGGATTTGGTCAATCATCTTGTGT 58.672 37.500 0.00 0.00 43.04 3.72
469 470 3.439476 GCAATCTGCAGAAGTTCAGATGT 59.561 43.478 22.50 0.00 46.11 3.06
623 624 4.803098 TTGCAAGAAGGTAGTAGACTCC 57.197 45.455 0.00 0.00 0.00 3.85
662 663 5.491070 GCATCTCCATATGGTGCTATTGTA 58.509 41.667 22.41 5.37 33.45 2.41
671 672 8.579006 CCATATGGTGCTATTGTACATGAAATT 58.421 33.333 14.09 0.00 0.00 1.82
1100 1101 1.152881 GCCTAGCCACCATTCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
1623 1624 2.808206 GGCCATCCTCGATCCCGTT 61.808 63.158 0.00 0.00 37.05 4.44
1797 1807 0.842635 AGCCAGAGATGCCTTTAGGG 59.157 55.000 0.00 0.00 35.18 3.53
1906 1916 3.444742 TCCAATTGCTACAATGAAGGCTG 59.555 43.478 0.00 0.00 0.00 4.85
1968 1978 1.076265 TGGATCTGTCGGACCGGAT 60.076 57.895 15.25 9.00 0.00 4.18
2106 2122 0.319083 TGGTGTTCTGCGACGGTAAT 59.681 50.000 0.00 0.00 0.00 1.89
2112 2128 3.129813 TGTTCTGCGACGGTAATCTGTAT 59.870 43.478 0.00 0.00 32.75 2.29
2244 2260 4.758251 TGCTGGGATGCCGTGACG 62.758 66.667 0.00 0.00 0.00 4.35
2289 2305 0.693622 TTGGGAGGAACAATGCGGTA 59.306 50.000 0.00 0.00 0.00 4.02
2331 2347 2.026262 TCCAGGACTGAAGGGTAATTGC 60.026 50.000 0.00 0.00 0.00 3.56
2337 2353 4.189231 GACTGAAGGGTAATTGCGTGTAT 58.811 43.478 0.00 0.00 0.00 2.29
2506 2529 5.569059 GTGAATAACTGCAACATAAGTGCAC 59.431 40.000 9.40 9.40 34.61 4.57
2717 2744 5.183921 AGCAAGAGCCTCTCATATGGAGAA 61.184 45.833 17.78 0.00 45.56 2.87
2838 2867 7.288158 GGTTTGTACTCTAGTCCCTATCATCTT 59.712 40.741 0.00 0.00 0.00 2.40
2862 2891 7.575414 TTTGTGTGTTTATGTCCTGTAATGT 57.425 32.000 0.00 0.00 0.00 2.71
2939 2968 7.067981 AGAGGAGGATTTTCAGATATTTGCAAC 59.932 37.037 0.00 0.00 0.00 4.17
2973 3002 4.633565 TGTTTAATCGCTGTATGCATGACA 59.366 37.500 10.16 8.91 43.06 3.58
3157 3186 3.058293 ACACAACAGGCACGAAATACATG 60.058 43.478 0.00 0.00 0.00 3.21
3218 3247 4.019501 AGTGCTTCTCCAGTCAAAGATCAT 60.020 41.667 0.00 0.00 0.00 2.45
3294 3323 1.159713 TGCAGCGACCTCACAACTTG 61.160 55.000 0.00 0.00 0.00 3.16
3380 3409 3.196207 ATGCCCTGTTGCTCCGTGT 62.196 57.895 0.00 0.00 0.00 4.49
3501 3530 3.329889 TGCTGGCCTTCCGGTGAT 61.330 61.111 3.32 0.00 40.99 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 5.366768 CCTTGGGATGTTCTTCCACTCTATA 59.633 44.000 6.98 0.00 37.53 1.31
469 470 2.362077 GCAGAAGCTCCCAAAAACAGAA 59.638 45.455 0.00 0.00 37.91 3.02
623 624 0.539051 ATGCGTCCTCCTTCTTCAGG 59.461 55.000 0.00 0.00 45.64 3.86
880 881 0.531532 CACCTGCCGGATCTCACATC 60.532 60.000 5.05 0.00 0.00 3.06
881 882 1.267574 ACACCTGCCGGATCTCACAT 61.268 55.000 5.05 0.00 0.00 3.21
986 987 0.960364 GGGCATCTTTCGGACAAGCA 60.960 55.000 0.00 0.00 0.00 3.91
1797 1807 0.109039 GAAGACTGAGTGAGGGACGC 60.109 60.000 0.00 0.00 0.00 5.19
1804 1814 3.244887 TCTTCCCTGAAGACTGAGTGA 57.755 47.619 2.50 0.00 42.78 3.41
1906 1916 0.610232 AACACATCTGGGCAGAAGGC 60.610 55.000 0.00 0.00 41.36 4.35
1916 1926 5.674525 TCCTAAGAGGCATAAACACATCTG 58.325 41.667 0.00 0.00 34.61 2.90
1968 1978 0.676466 CTGTGGCCGGTGCATTTAGA 60.676 55.000 1.90 0.00 40.13 2.10
2106 2122 5.104402 TGCATTCCTCCAGATTTGATACAGA 60.104 40.000 0.00 0.00 0.00 3.41
2112 2128 2.756760 GCTTGCATTCCTCCAGATTTGA 59.243 45.455 0.00 0.00 0.00 2.69
2244 2260 1.677637 CCGAGTAGCCTCCCAAGTCC 61.678 65.000 0.00 0.00 33.93 3.85
2289 2305 4.993584 GGAACATCTTCAGCATACATCGAT 59.006 41.667 0.00 0.00 0.00 3.59
2331 2347 1.954146 CCCGCCGATCCAATACACG 60.954 63.158 0.00 0.00 0.00 4.49
2506 2529 4.092968 CCGGGTCTGATAAACTTTTCTTCG 59.907 45.833 0.00 0.00 0.00 3.79
2717 2744 0.471617 ACTGCCAGTTCTTCAGTGCT 59.528 50.000 0.00 0.00 39.36 4.40
2838 2867 7.575414 ACATTACAGGACATAAACACACAAA 57.425 32.000 0.00 0.00 0.00 2.83
2916 2945 7.105241 AGTTGCAAATATCTGAAAATCCTCC 57.895 36.000 0.00 0.00 0.00 4.30
2939 2968 5.920273 ACAGCGATTAAACAACAATTCCAAG 59.080 36.000 0.00 0.00 0.00 3.61
2973 3002 4.576463 ACAAAACGAGCTTCAGAAGAACAT 59.424 37.500 14.86 0.00 0.00 2.71
3157 3186 4.499183 CTGAGTTCAGACCATCTGTTACC 58.501 47.826 2.97 2.36 46.59 2.85
3182 3211 3.994392 GAGAAGCACTTCGGTTTGTGATA 59.006 43.478 4.81 0.00 43.97 2.15
3192 3221 2.154854 TTGACTGGAGAAGCACTTCG 57.845 50.000 4.81 0.00 43.97 3.79
3218 3247 5.661312 ACCACCATACTCTGAAGTTGCTATA 59.339 40.000 0.00 0.00 36.92 1.31
3294 3323 0.034059 CCAGAGGCCGGACATGTATC 59.966 60.000 11.69 0.00 0.00 2.24
3380 3409 3.727258 CGACCCCAGCATTCCCCA 61.727 66.667 0.00 0.00 0.00 4.96
3501 3530 1.198713 GGTCATTCTCCTGGAGCTGA 58.801 55.000 19.08 19.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.