Multiple sequence alignment - TraesCS2D01G359300

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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 TraesCS2D01G359300 chr2D 100.000 1899 0 0 1 1899 461088276 461090174 0.000000e+00 3507
1 TraesCS2D01G359300 chr2D 95.701 1512 44 10 1 1511 76977321 76978812 0.000000e+00 2412
2 TraesCS2D01G359300 chr2D 100.000 99 0 0 2301 2399 461090576 461090674 1.460000e-42 183
3 TraesCS2D01G359300 chrUn 96.294 1889 50 11 13 1894 30041007 30039132 0.000000e+00 3083
4 TraesCS2D01G359300 chrUn 90.152 1909 133 28 8 1896 84448906 84447033 0.000000e+00 2433
5 TraesCS2D01G359300 chrUn 90.909 99 7 2 2302 2399 84447154 84447057 5.380000e-27 132
6 TraesCS2D01G359300 chrUn 90.000 100 8 2 2301 2399 84447000 84446902 6.960000e-26 128
7 TraesCS2D01G359300 chrUn 89.000 100 10 1 2301 2399 30039290 30039191 3.240000e-24 122
8 TraesCS2D01G359300 chr6D 94.690 1902 65 26 5 1893 450843321 450845199 0.000000e+00 2920
9 TraesCS2D01G359300 chr6D 96.540 867 24 4 13 875 100536095 100535231 0.000000e+00 1430
10 TraesCS2D01G359300 chr6D 91.753 97 7 1 2301 2396 450845500 450845596 1.500000e-27 134
11 TraesCS2D01G359300 chr6D 89.691 97 9 1 2301 2396 450845040 450845136 3.240000e-24 122
12 TraesCS2D01G359300 chr5A 91.636 1913 116 25 5 1896 579246972 579248861 0.000000e+00 2606
13 TraesCS2D01G359300 chr1D 97.698 1303 27 3 585 1886 80294758 80293458 0.000000e+00 2237
14 TraesCS2D01G359300 chr1D 94.000 100 5 1 2301 2399 80293177 80293078 1.490000e-32 150
15 TraesCS2D01G359300 chr1D 90.909 99 8 1 2301 2399 80293607 80293510 5.380000e-27 132
16 TraesCS2D01G359300 chr2A 96.160 1250 45 3 647 1895 757910030 757911277 0.000000e+00 2039
17 TraesCS2D01G359300 chr2A 94.452 757 37 3 5 758 45103404 45104158 0.000000e+00 1160
18 TraesCS2D01G359300 chr7A 96.166 1252 39 5 647 1896 77498382 77499626 0.000000e+00 2037
19 TraesCS2D01G359300 chr7A 95.604 1251 51 4 647 1896 559187530 559188777 0.000000e+00 2002
20 TraesCS2D01G359300 chr7A 93.955 761 33 5 5 758 77497696 77498450 0.000000e+00 1138
21 TraesCS2D01G359300 chr7A 91.919 99 7 1 2301 2399 559188733 559188830 1.160000e-28 137
22 TraesCS2D01G359300 chr7A 90.722 97 7 2 2301 2396 77499942 77500037 6.960000e-26 128
23 TraesCS2D01G359300 chr3A 95.774 1254 51 2 647 1899 412385914 412384662 0.000000e+00 2021
24 TraesCS2D01G359300 chr3A 94.716 757 32 6 5 758 412386597 412385846 0.000000e+00 1170
25 TraesCS2D01G359300 chr5B 92.773 844 42 8 1 839 291497415 291496586 0.000000e+00 1203


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 TraesCS2D01G359300 chr2D 461088276 461090674 2398 False 1845.000000 3507 100.000000 1 2399 2 chr2D.!!$F2 2398
1 TraesCS2D01G359300 chr2D 76977321 76978812 1491 False 2412.000000 2412 95.701000 1 1511 1 chr2D.!!$F1 1510
2 TraesCS2D01G359300 chrUn 30039132 30041007 1875 True 1602.500000 3083 92.647000 13 2399 2 chrUn.!!$R1 2386
3 TraesCS2D01G359300 chrUn 84446902 84448906 2004 True 897.666667 2433 90.353667 8 2399 3 chrUn.!!$R2 2391
4 TraesCS2D01G359300 chr6D 100535231 100536095 864 True 1430.000000 1430 96.540000 13 875 1 chr6D.!!$R1 862
5 TraesCS2D01G359300 chr6D 450843321 450845596 2275 False 1058.666667 2920 92.044667 5 2396 3 chr6D.!!$F1 2391
6 TraesCS2D01G359300 chr5A 579246972 579248861 1889 False 2606.000000 2606 91.636000 5 1896 1 chr5A.!!$F1 1891
7 TraesCS2D01G359300 chr1D 80293078 80294758 1680 True 839.666667 2237 94.202333 585 2399 3 chr1D.!!$R1 1814
8 TraesCS2D01G359300 chr2A 757910030 757911277 1247 False 2039.000000 2039 96.160000 647 1895 1 chr2A.!!$F2 1248
9 TraesCS2D01G359300 chr2A 45103404 45104158 754 False 1160.000000 1160 94.452000 5 758 1 chr2A.!!$F1 753
10 TraesCS2D01G359300 chr7A 77497696 77500037 2341 False 1101.000000 2037 93.614333 5 2396 3 chr7A.!!$F1 2391
11 TraesCS2D01G359300 chr7A 559187530 559188830 1300 False 1069.500000 2002 93.761500 647 2399 2 chr7A.!!$F2 1752
12 TraesCS2D01G359300 chr3A 412384662 412386597 1935 True 1595.500000 2021 95.245000 5 1899 2 chr3A.!!$R1 1894
13 TraesCS2D01G359300 chr5B 291496586 291497415 829 True 1203.000000 1203 92.773000 1 839 1 chr5B.!!$R1 838

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
456 474 0.324943 GAGGTTCCTTGCCTGTGCTA 59.675 55.0 0.0 0.0 36.29 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 3107 0.251341 AAATGAGTCCAGGGTGCCAC 60.251 55.0 0.0 0.0 0.0 5.01 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
367 385 2.031682 CCGATTTCGAGGGCAATGATTC 60.032 50.000 0.67 0.0 43.02 2.52
456 474 0.324943 GAGGTTCCTTGCCTGTGCTA 59.675 55.000 0.00 0.0 36.29 3.49
649 673 2.555325 CAGAGTGTTGTGGCATGTTCAT 59.445 45.455 0.00 0.0 0.00 2.57
945 1025 9.856488 TTGCTGTTTAACACTGTAATTTAACAA 57.144 25.926 0.00 0.0 0.00 2.83
1405 1485 5.277876 GCAATCTTAGATGAATGAGCCACAG 60.278 44.000 0.00 0.0 0.00 3.66
1478 1558 6.187727 AGTTATGTAATGGTCCTGTATGGG 57.812 41.667 0.00 0.0 36.20 4.00
1612 1782 0.324943 GGTCATGTATGGATCCCCCG 59.675 60.000 9.90 0.0 37.93 5.73
1803 2015 3.200165 GGCACCCTAGACTCATTTAGGTT 59.800 47.826 0.00 0.0 35.66 3.50
2320 3121 3.626924 GTCGTGGCACCCTGGACT 61.627 66.667 12.86 0.0 0.00 3.85
2321 3122 3.311110 TCGTGGCACCCTGGACTC 61.311 66.667 12.86 0.0 0.00 3.36
2322 3123 3.625897 CGTGGCACCCTGGACTCA 61.626 66.667 12.86 0.0 0.00 3.41
2323 3124 2.959484 CGTGGCACCCTGGACTCAT 61.959 63.158 12.86 0.0 0.00 2.90
2324 3125 1.380302 GTGGCACCCTGGACTCATT 59.620 57.895 6.29 0.0 0.00 2.57
2325 3126 0.251341 GTGGCACCCTGGACTCATTT 60.251 55.000 6.29 0.0 0.00 2.32
2326 3127 1.004277 GTGGCACCCTGGACTCATTTA 59.996 52.381 6.29 0.0 0.00 1.40
2327 3128 1.281867 TGGCACCCTGGACTCATTTAG 59.718 52.381 0.00 0.0 0.00 1.85
2328 3129 1.408822 GGCACCCTGGACTCATTTAGG 60.409 57.143 0.00 0.0 0.00 2.69
2329 3130 1.282157 GCACCCTGGACTCATTTAGGT 59.718 52.381 0.00 0.0 0.00 3.08
2330 3131 2.941415 GCACCCTGGACTCATTTAGGTG 60.941 54.545 0.00 0.0 44.85 4.00
2331 3132 1.916181 ACCCTGGACTCATTTAGGTGG 59.084 52.381 0.00 0.0 0.00 4.61
2332 3133 1.916181 CCCTGGACTCATTTAGGTGGT 59.084 52.381 0.00 0.0 0.00 4.16
2333 3134 2.308866 CCCTGGACTCATTTAGGTGGTT 59.691 50.000 0.00 0.0 0.00 3.67
2334 3135 3.347216 CCTGGACTCATTTAGGTGGTTG 58.653 50.000 0.00 0.0 0.00 3.77
2335 3136 3.244911 CCTGGACTCATTTAGGTGGTTGT 60.245 47.826 0.00 0.0 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 133 1.352352 CTCACTCCAGGAAACCATGGT 59.648 52.381 13.00 13.0 37.84 3.55
350 368 3.071874 ACAGAATCATTGCCCTCGAAA 57.928 42.857 0.00 0.0 0.00 3.46
456 474 6.435277 AGCAGAAATTTGACACATACCTTCAT 59.565 34.615 0.00 0.0 0.00 2.57
945 1025 6.435292 ACTAGTCCACAGTTTTTACCATCT 57.565 37.500 0.00 0.0 0.00 2.90
1077 1157 5.101628 GTCAGTTTGTGAACAGCAAATGAA 58.898 37.500 0.98 0.0 38.00 2.57
1405 1485 3.454812 ACTCCATGACCATTACTACCCAC 59.545 47.826 0.00 0.0 0.00 4.61
2303 3104 3.591254 GAGTCCAGGGTGCCACGAC 62.591 68.421 0.00 0.0 0.00 4.34
2304 3105 3.311110 GAGTCCAGGGTGCCACGA 61.311 66.667 0.00 0.0 0.00 4.35
2305 3106 2.469465 AATGAGTCCAGGGTGCCACG 62.469 60.000 0.00 0.0 0.00 4.94
2306 3107 0.251341 AAATGAGTCCAGGGTGCCAC 60.251 55.000 0.00 0.0 0.00 5.01
2307 3108 1.281867 CTAAATGAGTCCAGGGTGCCA 59.718 52.381 0.00 0.0 0.00 4.92
2308 3109 1.408822 CCTAAATGAGTCCAGGGTGCC 60.409 57.143 0.00 0.0 0.00 5.01
2309 3110 1.282157 ACCTAAATGAGTCCAGGGTGC 59.718 52.381 0.00 0.0 32.12 5.01
2310 3111 2.356125 CCACCTAAATGAGTCCAGGGTG 60.356 54.545 0.00 0.0 41.40 4.61
2311 3112 1.916181 CCACCTAAATGAGTCCAGGGT 59.084 52.381 0.00 0.0 32.12 4.34
2312 3113 1.916181 ACCACCTAAATGAGTCCAGGG 59.084 52.381 0.00 0.0 32.12 4.45
2313 3114 3.244911 ACAACCACCTAAATGAGTCCAGG 60.245 47.826 0.00 0.0 0.00 4.45
2314 3115 4.021102 ACAACCACCTAAATGAGTCCAG 57.979 45.455 0.00 0.0 0.00 3.86
2315 3116 4.447138 AACAACCACCTAAATGAGTCCA 57.553 40.909 0.00 0.0 0.00 4.02
2316 3117 4.083484 CGAAACAACCACCTAAATGAGTCC 60.083 45.833 0.00 0.0 0.00 3.85
2317 3118 4.753107 TCGAAACAACCACCTAAATGAGTC 59.247 41.667 0.00 0.0 0.00 3.36
2318 3119 4.514066 GTCGAAACAACCACCTAAATGAGT 59.486 41.667 0.00 0.0 0.00 3.41
2319 3120 4.377022 CGTCGAAACAACCACCTAAATGAG 60.377 45.833 0.00 0.0 0.00 2.90
2320 3121 3.495377 CGTCGAAACAACCACCTAAATGA 59.505 43.478 0.00 0.0 0.00 2.57
2321 3122 3.249080 ACGTCGAAACAACCACCTAAATG 59.751 43.478 0.00 0.0 0.00 2.32
2322 3123 3.469739 ACGTCGAAACAACCACCTAAAT 58.530 40.909 0.00 0.0 0.00 1.40
2323 3124 2.865551 GACGTCGAAACAACCACCTAAA 59.134 45.455 0.00 0.0 0.00 1.85
2324 3125 2.472816 GACGTCGAAACAACCACCTAA 58.527 47.619 0.00 0.0 0.00 2.69
2325 3126 1.600164 CGACGTCGAAACAACCACCTA 60.600 52.381 33.35 0.0 43.02 3.08
2326 3127 0.872881 CGACGTCGAAACAACCACCT 60.873 55.000 33.35 0.0 43.02 4.00
2327 3128 0.871163 TCGACGTCGAAACAACCACC 60.871 55.000 36.25 0.0 46.30 4.61
2328 3129 2.580661 TCGACGTCGAAACAACCAC 58.419 52.632 36.25 0.0 46.30 4.16


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

AutoCloner maintained by Alex Coulton.