Multiple sequence alignment - TraesCS2D01G250900

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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 TraesCS2D01G250900 chr2D 100.000 3104 0 0 1 3104 299553333 299550230 0.000000e+00 5733.0
1 TraesCS2D01G250900 chr2D 83.607 671 87 10 1773 2421 47215295 47214626 2.650000e-170 608.0
2 TraesCS2D01G250900 chr2B 95.817 2582 67 18 405 2973 371563778 371561225 0.000000e+00 4132.0
3 TraesCS2D01G250900 chr2B 89.175 388 13 14 39 409 371564474 371564099 1.010000e-124 457.0
4 TraesCS2D01G250900 chr2B 91.781 73 4 1 2973 3043 371561201 371561129 1.970000e-17 100.0
5 TraesCS2D01G250900 chr2A 96.244 1970 56 8 468 2428 374722446 374720486 0.000000e+00 3212.0
6 TraesCS2D01G250900 chr2A 92.991 642 18 9 2490 3104 374718311 374717670 0.000000e+00 911.0
7 TraesCS2D01G250900 chr2A 86.505 289 23 13 202 481 374722744 374722463 1.400000e-78 303.0
8 TraesCS2D01G250900 chr2A 82.486 177 13 10 39 212 374723147 374722986 4.170000e-29 139.0
9 TraesCS2D01G250900 chr2A 97.674 43 1 0 2456 2498 374719717 374719675 1.190000e-09 75.0
10 TraesCS2D01G250900 chr2A 97.561 41 1 0 2419 2459 374720013 374719973 1.540000e-08 71.3
11 TraesCS2D01G250900 chr6A 83.153 647 86 11 1770 2395 92405923 92406567 1.250000e-158 569.0
12 TraesCS2D01G250900 chr3B 81.384 607 82 18 1826 2415 462053547 462054139 1.690000e-127 466.0
13 TraesCS2D01G250900 chr5A 76.932 841 172 18 1263 2092 25864187 25865016 2.820000e-125 459.0
14 TraesCS2D01G250900 chr5B 76.941 850 165 26 1263 2092 27486608 27487446 3.650000e-124 455.0
15 TraesCS2D01G250900 chr5D 76.694 841 174 18 1263 2092 36743377 36744206 6.110000e-122 448.0
16 TraesCS2D01G250900 chr5D 92.500 40 3 0 1 40 194285439 194285400 1.200000e-04 58.4
17 TraesCS2D01G250900 chr3D 87.352 253 29 3 1946 2196 255524323 255524072 1.410000e-73 287.0
18 TraesCS2D01G250900 chr4A 85.185 162 20 3 2035 2193 444153287 444153447 2.480000e-36 163.0
19 TraesCS2D01G250900 chr1B 89.474 95 9 1 2047 2141 573330793 573330700 5.440000e-23 119.0
20 TraesCS2D01G250900 chr1A 93.103 58 4 0 1845 1902 520161342 520161285 5.520000e-13 86.1
21 TraesCS2D01G250900 chr4B 92.500 40 3 0 1 40 600498736 600498697 1.200000e-04 58.4


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 TraesCS2D01G250900 chr2D 299550230 299553333 3103 True 5733.000000 5733 100.000000 1 3104 1 chr2D.!!$R2 3103
1 TraesCS2D01G250900 chr2D 47214626 47215295 669 True 608.000000 608 83.607000 1773 2421 1 chr2D.!!$R1 648
2 TraesCS2D01G250900 chr2B 371561129 371564474 3345 True 1563.000000 4132 92.257667 39 3043 3 chr2B.!!$R1 3004
3 TraesCS2D01G250900 chr2A 374717670 374723147 5477 True 785.216667 3212 92.243500 39 3104 6 chr2A.!!$R1 3065
4 TraesCS2D01G250900 chr6A 92405923 92406567 644 False 569.000000 569 83.153000 1770 2395 1 chr6A.!!$F1 625
5 TraesCS2D01G250900 chr3B 462053547 462054139 592 False 466.000000 466 81.384000 1826 2415 1 chr3B.!!$F1 589
6 TraesCS2D01G250900 chr5A 25864187 25865016 829 False 459.000000 459 76.932000 1263 2092 1 chr5A.!!$F1 829
7 TraesCS2D01G250900 chr5B 27486608 27487446 838 False 455.000000 455 76.941000 1263 2092 1 chr5B.!!$F1 829
8 TraesCS2D01G250900 chr5D 36743377 36744206 829 False 448.000000 448 76.694000 1263 2092 1 chr5D.!!$F1 829

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
708 1364 0.394899 CCTGCCTTGCCTTCCCTTAG 60.395 60.0 0.0 0.0 0.0 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 3921 0.755686 CTCAGGGGGTCTCAGCATAC 59.244 60.0 0.0 0.0 0.0 2.39 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
31 32 9.747898 TGAATTGAGCCCTATAAACTAAAAAGA 57.252 29.630 0.00 0.00 0.00 2.52
35 36 9.747898 TTGAGCCCTATAAACTAAAAAGAATGA 57.252 29.630 0.00 0.00 0.00 2.57
36 37 9.747898 TGAGCCCTATAAACTAAAAAGAATGAA 57.252 29.630 0.00 0.00 0.00 2.57
80 86 1.597027 CAGGCGGACACGAACCTTT 60.597 57.895 0.00 0.00 44.60 3.11
212 230 1.068434 GCTGCTGGCTAGTCCTAAGAG 59.932 57.143 0.00 0.00 38.06 2.85
213 231 1.686052 CTGCTGGCTAGTCCTAAGAGG 59.314 57.143 0.00 0.00 36.46 3.69
229 498 6.012245 TCCTAAGAGGATACGGATACCATACA 60.012 42.308 0.00 0.00 40.06 2.29
449 1060 3.998672 CACTACCACACCGCCCGT 61.999 66.667 0.00 0.00 0.00 5.28
466 1081 2.349722 CCCGTTTAACAAACCGCACTAC 60.350 50.000 0.00 0.00 38.14 2.73
687 1339 2.461110 CCCGTGGCGCACTTGATAC 61.461 63.158 10.83 0.00 31.34 2.24
706 1362 2.147433 CTCCTGCCTTGCCTTCCCTT 62.147 60.000 0.00 0.00 0.00 3.95
708 1364 0.394899 CCTGCCTTGCCTTCCCTTAG 60.395 60.000 0.00 0.00 0.00 2.18
732 1388 0.734889 ACTTGATATTGCTGCCACGC 59.265 50.000 0.00 0.00 0.00 5.34
1005 1661 2.494059 CCGGAATTAATCGCCATGACT 58.506 47.619 0.00 0.00 0.00 3.41
1569 2225 3.382832 CTCCACTCCTTCCCGCGT 61.383 66.667 4.92 0.00 0.00 6.01
2262 2941 4.153655 CAGCCCATAGATGATCGAAACATG 59.846 45.833 12.06 0.00 0.00 3.21
2306 2985 4.505191 CCCAAATTCATTTAAGATGCTGCG 59.495 41.667 0.00 0.00 0.00 5.18
2485 3921 3.369147 CAGAACTCAATAGTCAACAGCGG 59.631 47.826 0.00 0.00 33.75 5.52
2578 5386 6.717084 CCTTTTGACTAGTTTTCCCTTCAGAT 59.283 38.462 0.00 0.00 0.00 2.90
2657 5466 4.218417 TGGCTAAGAAACCTCATTTGCTTC 59.782 41.667 0.00 0.00 0.00 3.86
2756 5566 0.322008 CAGACTGGTGCTTTCCCTCC 60.322 60.000 0.00 0.00 0.00 4.30
2793 5603 6.517864 CGTTCTTCTCCTCCTGGTACTTTTAA 60.518 42.308 0.00 0.00 34.23 1.52
2848 5658 0.454600 CAGGTGTTGCATCTGATGGC 59.545 55.000 18.60 11.44 44.59 4.40
2926 5736 3.482436 TCTGTTGAAATGCGTAAAGGGT 58.518 40.909 0.00 0.00 0.00 4.34
2959 5769 2.033424 GGTGTTCTGTTCAGCTGAAACC 59.967 50.000 29.99 26.09 36.91 3.27
3096 5932 4.561735 TTTCTTTCGACAATGGGTTGAC 57.438 40.909 0.00 0.00 39.68 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.747898 TCTTTTTAGTTTATAGGGCTCAATTCA 57.252 29.630 0.00 0.00 0.00 2.57
9 10 9.747898 TCATTCTTTTTAGTTTATAGGGCTCAA 57.252 29.630 0.00 0.00 0.00 3.02
10 11 9.747898 TTCATTCTTTTTAGTTTATAGGGCTCA 57.252 29.630 0.00 0.00 0.00 4.26
12 13 9.755122 ACTTCATTCTTTTTAGTTTATAGGGCT 57.245 29.630 0.00 0.00 0.00 5.19
80 86 1.337703 GTGTGAAGCATGCAGAAACCA 59.662 47.619 21.98 5.59 0.00 3.67
212 230 6.827251 TGTCTATCTGTATGGTATCCGTATCC 59.173 42.308 0.00 0.00 0.00 2.59
213 231 7.336176 TGTGTCTATCTGTATGGTATCCGTATC 59.664 40.741 0.00 0.00 0.00 2.24
215 233 6.536447 TGTGTCTATCTGTATGGTATCCGTA 58.464 40.000 0.00 0.00 0.00 4.02
216 234 5.382616 TGTGTCTATCTGTATGGTATCCGT 58.617 41.667 0.00 0.00 0.00 4.69
288 566 1.952621 TCAGCAGGGTAGGTAAGCTT 58.047 50.000 3.48 3.48 32.35 3.74
449 1060 3.001127 GTGTCGTAGTGCGGTTTGTTAAA 59.999 43.478 0.00 0.00 41.72 1.52
466 1081 4.730042 CGATTTGCCAAGATAATTGTGTCG 59.270 41.667 0.00 0.00 0.00 4.35
598 1250 2.416107 CTGTGGCAGTGGGTGTGGAT 62.416 60.000 0.00 0.00 0.00 3.41
687 1339 2.044551 GGGAAGGCAAGGCAGGAG 60.045 66.667 0.00 0.00 0.00 3.69
706 1362 6.620678 GTGGCAGCAATATCAAGTTTTTCTA 58.379 36.000 0.00 0.00 0.00 2.10
708 1364 4.324402 CGTGGCAGCAATATCAAGTTTTTC 59.676 41.667 0.00 0.00 0.00 2.29
1176 1832 4.649705 TCCTCAACTCCCGCCCCA 62.650 66.667 0.00 0.00 0.00 4.96
2262 2941 3.989817 GGGAGTGAAATGACATTTGCAAC 59.010 43.478 18.00 12.50 31.47 4.17
2306 2985 6.870965 AGTATTCAGTGTTCTTCAGTCATGTC 59.129 38.462 0.00 0.00 0.00 3.06
2485 3921 0.755686 CTCAGGGGGTCTCAGCATAC 59.244 60.000 0.00 0.00 0.00 2.39
2578 5386 2.168496 ACAGCGAGCCAACTACTCTAA 58.832 47.619 0.00 0.00 31.71 2.10
2657 5466 2.952978 ACTCTAACGGATAGACCTGCAG 59.047 50.000 6.78 6.78 35.68 4.41
2766 5576 0.905337 ACCAGGAGGAGAAGAACGGG 60.905 60.000 0.00 0.00 38.69 5.28
2793 5603 4.102681 AGGTTGTTGCCACTTAAGTCTACT 59.897 41.667 4.77 0.00 0.00 2.57
2848 5658 0.914644 ACAGTGGATGGATGGACTGG 59.085 55.000 0.00 0.00 40.16 4.00
2926 5736 0.179004 AGAACACCGCCACAATCCAA 60.179 50.000 0.00 0.00 0.00 3.53
2959 5769 6.801862 CCTTGCTTATGTAAAGTTCCTTTTCG 59.198 38.462 0.00 0.00 35.21 3.46
3004 5840 4.483311 GTGCTAGTGCTACGAAAACTAGT 58.517 43.478 15.44 0.00 43.45 2.57
3006 5842 3.671433 CGGTGCTAGTGCTACGAAAACTA 60.671 47.826 0.00 0.00 39.81 2.24


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

AutoCloner maintained by Alex Coulton.