Multiple sequence alignment - TraesCS2D01G008800

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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 TraesCS2D01G008800 chr2D 100.000 7102 0 0 1 7102 4712225 4705124 0.000000e+00 13116.0
1 TraesCS2D01G008800 chr2D 98.687 5940 59 6 1 5933 4673831 4667904 0.000000e+00 10525.0
2 TraesCS2D01G008800 chr2D 99.446 5057 27 1 2047 7102 4689905 4684849 0.000000e+00 9182.0
3 TraesCS2D01G008800 chr2D 99.356 2020 12 1 1 2020 4692061 4690043 0.000000e+00 3657.0
4 TraesCS2D01G008800 chr2D 98.211 559 8 2 6544 7102 4667910 4667354 0.000000e+00 976.0
5 TraesCS2D01G008800 chr2D 78.748 1374 255 29 2199 3557 2695861 2694510 0.000000e+00 885.0
6 TraesCS2D01G008800 chr2D 78.571 756 145 13 2203 2949 3449730 3450477 4.190000e-132 483.0
7 TraesCS2D01G008800 chr2D 100.000 169 0 0 7561 7729 4704665 4704497 5.820000e-81 313.0
8 TraesCS2D01G008800 chr2D 84.790 309 44 1 6229 6537 2693369 2693064 2.710000e-79 307.0
9 TraesCS2D01G008800 chr2D 98.204 167 3 0 7561 7727 4667033 4666867 7.590000e-75 292.0
10 TraesCS2D01G008800 chr2D 90.517 116 11 0 2834 2949 2101293 2101408 3.740000e-33 154.0
11 TraesCS2D01G008800 chr2B 93.329 5202 250 36 1863 7035 6407832 6412965 0.000000e+00 7594.0
12 TraesCS2D01G008800 chr2B 95.101 2776 83 17 1863 4634 6378665 6381391 0.000000e+00 4324.0
13 TraesCS2D01G008800 chr2B 91.744 3028 199 20 4085 7088 6424081 6427081 0.000000e+00 4159.0
14 TraesCS2D01G008800 chr2B 95.259 2236 93 8 4877 7102 6381385 6383617 0.000000e+00 3530.0
15 TraesCS2D01G008800 chr2B 80.798 1453 198 49 1 1398 6404785 6406211 0.000000e+00 1062.0
16 TraesCS2D01G008800 chr2B 84.168 979 108 29 445 1398 6376088 6377044 0.000000e+00 905.0
17 TraesCS2D01G008800 chr2B 77.153 1370 279 30 2200 3552 31060158 31061510 0.000000e+00 765.0
18 TraesCS2D01G008800 chr2B 86.008 243 25 8 3805 4042 31064162 31064400 1.290000e-62 252.0
19 TraesCS2D01G008800 chr2B 97.619 42 1 0 402 443 6405164 6405205 1.080000e-08 73.1
20 TraesCS2D01G008800 chr2B 100.000 28 0 0 339 366 448921597 448921624 1.400000e-02 52.8
21 TraesCS2D01G008800 chr2B 100.000 28 0 0 724 751 741973516 741973489 1.400000e-02 52.8
22 TraesCS2D01G008800 chrUn 100.000 414 0 0 6150 6563 477374847 477375260 0.000000e+00 765.0
23 TraesCS2D01G008800 chr4D 95.882 170 6 1 7561 7729 307847430 307847599 2.750000e-69 274.0
24 TraesCS2D01G008800 chr7A 94.675 169 9 0 7561 7729 349155392 349155560 5.950000e-66 263.0
25 TraesCS2D01G008800 chr7A 92.941 170 10 2 7561 7729 593937103 593936935 5.990000e-61 246.0
26 TraesCS2D01G008800 chr3D 94.083 169 9 1 7561 7729 311187451 311187618 9.950000e-64 255.0
27 TraesCS2D01G008800 chr3A 93.491 169 9 2 7561 7729 336923538 336923704 4.630000e-62 250.0
28 TraesCS2D01G008800 chr3A 92.941 170 11 1 7561 7729 447566181 447566350 5.990000e-61 246.0
29 TraesCS2D01G008800 chr4A 92.941 170 11 1 7561 7729 556505881 556505712 5.990000e-61 246.0
30 TraesCS2D01G008800 chr1A 92.941 170 9 3 7561 7729 205222419 205222252 2.150000e-60 244.0
31 TraesCS2D01G008800 chr2A 86.986 146 16 3 3048 3191 1978591 1978735 2.230000e-35 161.0
32 TraesCS2D01G008800 chr2A 86.986 146 16 3 3048 3191 2016611 2016755 2.230000e-35 161.0
33 TraesCS2D01G008800 chr2A 86.986 146 16 3 3048 3191 2053589 2053733 2.230000e-35 161.0
34 TraesCS2D01G008800 chr2A 97.222 36 1 0 2914 2949 1978461 1978496 2.330000e-05 62.1
35 TraesCS2D01G008800 chr2A 97.222 36 1 0 2914 2949 2016481 2016516 2.330000e-05 62.1
36 TraesCS2D01G008800 chr1D 73.230 452 104 12 3 438 361132943 361133393 1.740000e-31 148.0
37 TraesCS2D01G008800 chr7D 92.308 39 3 0 2081 2119 30936837 30936875 1.000000e-03 56.5
38 TraesCS2D01G008800 chr1B 90.476 42 4 0 811 852 307010625 307010584 1.000000e-03 56.5
39 TraesCS2D01G008800 chr5B 100.000 28 0 0 724 751 421834380 421834353 1.400000e-02 52.8


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 TraesCS2D01G008800 chr2D 4704497 4712225 7728 True 6714.500000 13116 100.000000 1 7729 2 chr2D.!!$R4 7728
1 TraesCS2D01G008800 chr2D 4684849 4692061 7212 True 6419.500000 9182 99.401000 1 7102 2 chr2D.!!$R3 7101
2 TraesCS2D01G008800 chr2D 4666867 4673831 6964 True 3931.000000 10525 98.367333 1 7727 3 chr2D.!!$R2 7726
3 TraesCS2D01G008800 chr2D 2693064 2695861 2797 True 596.000000 885 81.769000 2199 6537 2 chr2D.!!$R1 4338
4 TraesCS2D01G008800 chr2D 3449730 3450477 747 False 483.000000 483 78.571000 2203 2949 1 chr2D.!!$F2 746
5 TraesCS2D01G008800 chr2B 6424081 6427081 3000 False 4159.000000 4159 91.744000 4085 7088 1 chr2B.!!$F1 3003
6 TraesCS2D01G008800 chr2B 6376088 6383617 7529 False 2919.666667 4324 91.509333 445 7102 3 chr2B.!!$F3 6657
7 TraesCS2D01G008800 chr2B 6404785 6412965 8180 False 2909.700000 7594 90.582000 1 7035 3 chr2B.!!$F4 7034
8 TraesCS2D01G008800 chr2B 31060158 31064400 4242 False 508.500000 765 81.580500 2200 4042 2 chr2B.!!$F5 1842

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
259 265 1.168714 GTCGCTTGCCTCCTGAAAAT 58.831 50.000 0.00 0.0 0.00 1.82 F
311 317 7.148120 CGGTCTCTAGGTGAAAACACTAATCTA 60.148 40.741 0.00 0.0 0.00 1.98 F
867 942 9.935241 AGTATCTATTACCGACTTAGTTATCGA 57.065 33.333 0.00 0.0 40.86 3.59 F
2967 4429 1.482182 TGTGAGCTCTGACACACACTT 59.518 47.619 16.19 0.0 41.19 3.16 F
3022 4484 4.668289 CACAGACACGCACATACTACATA 58.332 43.478 0.00 0.0 0.00 2.29 F
3780 5988 5.405935 ACTGTTACTCATGTCTATGCACA 57.594 39.130 0.00 0.0 34.21 4.57 F
5357 9430 4.858850 AGGCAATATGAACAATCTGGACA 58.141 39.130 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 3386 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.0 0.0 0.00 3.72 R
2045 3387 1.093972 ATGGTGTGTGTGTGTGTGTG 58.906 50.000 0.0 0.0 0.00 3.82 R
2967 4429 8.043113 AGTGTGATATGTCAAAGAAGATGCTTA 58.957 33.333 0.0 0.0 35.80 3.09 R
4418 8461 2.099756 GTCTATTGCCATTTGGTGAGCC 59.900 50.000 0.0 0.0 37.57 4.70 R
4566 8609 6.009589 TGGCAGTTTATTCCATTTTCTGAGA 58.990 36.000 0.0 0.0 0.00 3.27 R
5454 9527 5.407049 ACTCATGCCCATACCTAGTCTATT 58.593 41.667 0.0 0.0 0.00 1.73 R
6962 11060 4.944619 ATCAACATCGGATCTAGCTTCA 57.055 40.909 0.0 0.0 0.00 3.02 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
45 46 3.181488 GGTTAGCTTTCCGGTAGTCTCTC 60.181 52.174 0.00 0.77 0.00 3.20
179 185 1.553704 GTGACCGGGACAACTCCTATT 59.446 52.381 6.32 0.00 36.68 1.73
191 197 5.116882 ACAACTCCTATTGGCGAGTTTATC 58.883 41.667 2.52 0.00 44.90 1.75
194 200 4.406003 ACTCCTATTGGCGAGTTTATCAGT 59.594 41.667 0.00 0.00 35.84 3.41
259 265 1.168714 GTCGCTTGCCTCCTGAAAAT 58.831 50.000 0.00 0.00 0.00 1.82
311 317 7.148120 CGGTCTCTAGGTGAAAACACTAATCTA 60.148 40.741 0.00 0.00 0.00 1.98
867 942 9.935241 AGTATCTATTACCGACTTAGTTATCGA 57.065 33.333 0.00 0.00 40.86 3.59
2967 4429 1.482182 TGTGAGCTCTGACACACACTT 59.518 47.619 16.19 0.00 41.19 3.16
3022 4484 4.668289 CACAGACACGCACATACTACATA 58.332 43.478 0.00 0.00 0.00 2.29
3780 5988 5.405935 ACTGTTACTCATGTCTATGCACA 57.594 39.130 0.00 0.00 34.21 4.57
4159 8202 5.877012 ACTTCGCTTGAGAACATGTCATAAT 59.123 36.000 0.00 0.00 0.00 1.28
4827 8870 7.117956 GTGGTCCTTCAACATAAAACTCTAGAC 59.882 40.741 0.00 0.00 0.00 2.59
5357 9430 4.858850 AGGCAATATGAACAATCTGGACA 58.141 39.130 0.00 0.00 0.00 4.02
6148 10225 5.232414 GTCTGACATAGATTTAGCCGACAAC 59.768 44.000 2.24 0.00 37.83 3.32
6598 10679 5.546621 TCCGCCTAGTGCTTAATTAGATT 57.453 39.130 2.39 0.00 38.05 2.40
6962 11060 7.548075 CAGTACAACCCTCGTGTAAATATCTTT 59.452 37.037 0.00 0.00 33.40 2.52
7012 11110 2.157668 CAGGGACTTCGTTTGAACATCG 59.842 50.000 0.00 0.00 34.60 3.84
7609 11707 8.511604 TTTCCCAAACTTTCATTTTGCATTTA 57.488 26.923 0.00 0.00 33.37 1.40
7657 11755 1.208706 TCACAACACCCTGGAGTGAA 58.791 50.000 18.30 1.05 40.34 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 185 2.742053 GCTTTCACTGATAAACTCGCCA 59.258 45.455 0.00 0.00 0.00 5.69
191 197 4.107622 CCAGAAACACAAAGCTTTCACTG 58.892 43.478 9.23 11.50 0.00 3.66
194 200 2.479389 CGCCAGAAACACAAAGCTTTCA 60.479 45.455 9.23 0.00 0.00 2.69
259 265 1.866015 AGGGAAGATCCATGACGACA 58.134 50.000 0.00 0.00 38.64 4.35
311 317 0.031994 GCTGCCGTGTCCAAACAAAT 59.968 50.000 0.00 0.00 37.08 2.32
375 381 1.078426 CGGCCAAAGACACCTAGGG 60.078 63.158 14.81 4.64 0.00 3.53
2043 3385 1.002087 TGGTGTGTGTGTGTGTGTGTA 59.998 47.619 0.00 0.00 0.00 2.90
2044 3386 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
2045 3387 1.093972 ATGGTGTGTGTGTGTGTGTG 58.906 50.000 0.00 0.00 0.00 3.82
2967 4429 8.043113 AGTGTGATATGTCAAAGAAGATGCTTA 58.957 33.333 0.00 0.00 35.80 3.09
3780 5988 5.659440 ATTTTGACTGTTGTTGGAACTGT 57.341 34.783 0.00 0.00 35.48 3.55
4159 8202 4.097135 TGATCAAACTTTGCGACCTTCAAA 59.903 37.500 0.00 0.00 33.04 2.69
4418 8461 2.099756 GTCTATTGCCATTTGGTGAGCC 59.900 50.000 0.00 0.00 37.57 4.70
4566 8609 6.009589 TGGCAGTTTATTCCATTTTCTGAGA 58.990 36.000 0.00 0.00 0.00 3.27
5357 9430 9.326413 CCGTCTTCCATTATTCTAAGTTGTATT 57.674 33.333 0.00 0.00 0.00 1.89
5454 9527 5.407049 ACTCATGCCCATACCTAGTCTATT 58.593 41.667 0.00 0.00 0.00 1.73
6148 10225 3.340814 AGTTGATGCTGGGTCTAACTG 57.659 47.619 0.00 0.00 0.00 3.16
6598 10679 6.976636 TTCATGCTGAAATACATACGAACA 57.023 33.333 0.00 0.00 32.71 3.18
6962 11060 4.944619 ATCAACATCGGATCTAGCTTCA 57.055 40.909 0.00 0.00 0.00 3.02
7690 11788 8.267620 ACTTCAAATCTTTTCAAAACCCTTTG 57.732 30.769 0.00 0.00 42.88 2.77


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

AutoCloner maintained by Alex Coulton.