Multiple sequence alignment - TraesCS3D01G208300

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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 TraesCS3D01G208300 chr3D 100.000 5183 0 0 1 5183 275129919 275124737 0.000000e+00 9572.0
1 TraesCS3D01G208300 chr3D 98.736 4351 43 3 834 5183 274496371 274500710 0.000000e+00 7720.0
2 TraesCS3D01G208300 chr3D 98.029 3146 41 4 1 3126 274494271 274491127 0.000000e+00 5446.0
3 TraesCS3D01G208300 chr3D 96.524 374 11 2 4812 5183 274391203 274391576 7.370000e-173 617.0
4 TraesCS3D01G208300 chr3D 95.989 374 13 2 4812 5183 274603077 274603450 1.600000e-169 606.0
5 TraesCS3D01G208300 chr3D 80.328 305 38 12 360 642 499961911 499962215 1.460000e-50 211.0
6 TraesCS3D01G208300 chr3D 82.627 236 30 8 348 572 512698134 512698369 1.140000e-46 198.0
7 TraesCS3D01G208300 chr3A 94.962 1191 33 4 1818 2981 365353950 365355140 0.000000e+00 1842.0
8 TraesCS3D01G208300 chr3A 96.912 1004 30 1 816 1818 365352906 365353909 0.000000e+00 1681.0
9 TraesCS3D01G208300 chr3A 93.465 811 26 1 3031 3841 365355468 365356251 0.000000e+00 1179.0
10 TraesCS3D01G208300 chr3A 95.789 665 23 3 3971 4634 365356252 365356912 0.000000e+00 1068.0
11 TraesCS3D01G208300 chr3A 96.341 82 3 0 3015 3096 365355134 365355215 9.050000e-28 135.0
12 TraesCS3D01G208300 chr3B 96.414 1004 35 1 816 1818 367240847 367241850 0.000000e+00 1653.0
13 TraesCS3D01G208300 chr3B 93.675 838 25 2 3092 3929 367243369 367244178 0.000000e+00 1229.0
14 TraesCS3D01G208300 chr3B 91.047 793 21 4 2178 2947 367242316 367243081 0.000000e+00 1026.0
15 TraesCS3D01G208300 chr3B 96.588 469 10 4 3928 4396 367244224 367244686 0.000000e+00 773.0
16 TraesCS3D01G208300 chr3B 95.368 367 10 4 1818 2181 367241888 367242250 1.250000e-160 577.0
17 TraesCS3D01G208300 chr3B 86.344 227 18 4 4589 4815 367244687 367244900 8.680000e-58 235.0
18 TraesCS3D01G208300 chr3B 80.162 247 36 10 363 597 32021628 32021383 6.900000e-39 172.0
19 TraesCS3D01G208300 chr3B 90.698 86 8 0 686 771 367240744 367240829 1.180000e-21 115.0
20 TraesCS3D01G208300 chr7A 94.706 340 16 2 4818 5156 375993171 375993509 1.280000e-145 527.0
21 TraesCS3D01G208300 chr7A 91.736 363 24 5 4815 5176 468239311 468238954 2.790000e-137 499.0
22 TraesCS3D01G208300 chr7A 84.375 96 15 0 4720 4815 113950632 113950727 1.540000e-15 95.3
23 TraesCS3D01G208300 chr7A 82.857 105 18 0 4711 4815 114087636 114087740 1.540000e-15 95.3
24 TraesCS3D01G208300 chr4B 91.644 371 24 7 4817 5183 169892911 169893278 1.670000e-139 507.0
25 TraesCS3D01G208300 chr4B 80.952 105 20 0 4711 4815 547597801 547597697 3.330000e-12 84.2
26 TraesCS3D01G208300 chr6A 91.200 375 26 7 4812 5183 130066891 130066521 2.150000e-138 503.0
27 TraesCS3D01G208300 chr6A 80.617 227 32 9 433 649 234088257 234088033 1.150000e-36 165.0
28 TraesCS3D01G208300 chr7D 92.837 349 19 6 4812 5156 343092982 343093328 7.750000e-138 501.0
29 TraesCS3D01G208300 chr7D 97.143 35 1 0 1007 1041 540411927 540411893 5.600000e-05 60.2
30 TraesCS3D01G208300 chr6D 92.733 344 19 5 4816 5156 221870468 221870808 4.660000e-135 492.0
31 TraesCS3D01G208300 chr5D 85.345 232 24 7 348 573 354716740 354716967 1.120000e-56 231.0
32 TraesCS3D01G208300 chr5D 81.933 238 24 13 351 573 459489637 459489404 3.190000e-42 183.0
33 TraesCS3D01G208300 chr5D 81.092 238 35 8 348 583 68460642 68460871 1.150000e-41 182.0
34 TraesCS3D01G208300 chr2D 83.784 222 25 8 360 576 158100860 158100645 3.170000e-47 200.0
35 TraesCS3D01G208300 chr2D 83.036 112 15 3 269 380 460619070 460619177 1.190000e-16 99.0
36 TraesCS3D01G208300 chr2B 78.505 321 47 12 348 649 212926321 212926638 1.900000e-44 191.0
37 TraesCS3D01G208300 chr2B 81.416 226 35 6 433 652 585716497 585716273 1.480000e-40 178.0
38 TraesCS3D01G208300 chr2A 77.987 318 48 15 348 650 607867778 607868088 4.120000e-41 180.0
39 TraesCS3D01G208300 chr5B 81.116 233 35 7 359 582 697235965 697235733 1.480000e-40 178.0
40 TraesCS3D01G208300 chr5B 81.304 230 26 14 433 649 508594780 508594555 2.480000e-38 171.0
41 TraesCS3D01G208300 chr4D 80.263 228 33 12 436 656 390860581 390860359 1.490000e-35 161.0
42 TraesCS3D01G208300 chr1B 79.730 222 40 5 433 649 580528803 580528582 6.950000e-34 156.0
43 TraesCS3D01G208300 chr1B 79.464 224 39 4 433 649 670530645 670530422 8.990000e-33 152.0
44 TraesCS3D01G208300 chr1B 80.952 105 18 2 4711 4815 582151915 582152017 1.200000e-11 82.4
45 TraesCS3D01G208300 chr1B 90.000 60 6 0 4756 4815 440729596 440729537 1.550000e-10 78.7
46 TraesCS3D01G208300 chr7B 85.567 97 13 1 4720 4815 412870864 412870768 3.300000e-17 100.0
47 TraesCS3D01G208300 chr1A 80.769 104 20 0 4712 4815 410515249 410515352 1.200000e-11 82.4
48 TraesCS3D01G208300 chr1A 94.444 36 2 0 1006 1041 525011939 525011974 7.250000e-04 56.5
49 TraesCS3D01G208300 chr1A 94.444 36 2 0 1006 1041 544362867 544362832 7.250000e-04 56.5
50 TraesCS3D01G208300 chr1A 94.444 36 2 0 1006 1041 569481241 569481206 7.250000e-04 56.5
51 TraesCS3D01G208300 chrUn 94.444 36 2 0 1006 1041 271843104 271843069 7.250000e-04 56.5


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 TraesCS3D01G208300 chr3D 275124737 275129919 5182 True 9572.000000 9572 100.000000 1 5183 1 chr3D.!!$R2 5182
1 TraesCS3D01G208300 chr3D 274496371 274500710 4339 False 7720.000000 7720 98.736000 834 5183 1 chr3D.!!$F2 4349
2 TraesCS3D01G208300 chr3D 274491127 274494271 3144 True 5446.000000 5446 98.029000 1 3126 1 chr3D.!!$R1 3125
3 TraesCS3D01G208300 chr3A 365352906 365356912 4006 False 1181.000000 1842 95.493800 816 4634 5 chr3A.!!$F1 3818
4 TraesCS3D01G208300 chr3B 367240744 367244900 4156 False 801.142857 1653 92.876286 686 4815 7 chr3B.!!$F1 4129

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
326 328 0.459237 GACATGGACGTGCCTCTCAG 60.459 60.000 4.04 0.00 37.63 3.35 F
1241 1244 0.313043 CAAATCCAGCATCGATGGCC 59.687 55.000 26.00 10.98 39.19 5.36 F
2701 2856 1.130955 AATTGCTTTGTTTCTGCGCG 58.869 45.000 0.00 0.00 0.00 6.86 F
3547 4159 3.057526 GTGGGTTATCAAGGTCACTTTGC 60.058 47.826 0.00 0.00 33.81 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1285 1288 2.034179 CCTCGGAAAACTTGTTTGGACC 59.966 50.0 0.0 4.08 0.00 4.46 R
2730 2885 2.917713 TGCACTATTTTGGGGTCCAT 57.082 45.0 0.0 0.00 31.53 3.41 R
4174 4833 1.747709 CAAGGAATCCCTCAGTGCAG 58.252 55.0 0.0 0.00 43.48 4.41 R
4855 5519 1.064825 TCTTCACTTTCCCCACCTCC 58.935 55.0 0.0 0.00 0.00 4.30 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
63 64 1.069906 AGCGCGTCACTTGAATGTTTC 60.070 47.619 8.43 0.00 0.00 2.78
260 261 2.290134 GCCTCTAGGAAACGGGAAAACT 60.290 50.000 0.00 0.00 37.39 2.66
263 264 4.504340 CCTCTAGGAAACGGGAAAACTCAA 60.504 45.833 0.00 0.00 37.39 3.02
264 265 5.038651 TCTAGGAAACGGGAAAACTCAAA 57.961 39.130 0.00 0.00 0.00 2.69
265 266 5.438833 TCTAGGAAACGGGAAAACTCAAAA 58.561 37.500 0.00 0.00 0.00 2.44
266 267 5.887035 TCTAGGAAACGGGAAAACTCAAAAA 59.113 36.000 0.00 0.00 0.00 1.94
325 327 0.900182 AGACATGGACGTGCCTCTCA 60.900 55.000 4.04 0.00 37.63 3.27
326 328 0.459237 GACATGGACGTGCCTCTCAG 60.459 60.000 4.04 0.00 37.63 3.35
334 336 1.202486 ACGTGCCTCTCAGAAACGAAA 60.202 47.619 10.35 0.00 37.66 3.46
546 548 9.615295 GCACGGTTTAAGAGATAAAACATTTTA 57.385 29.630 0.00 0.00 40.57 1.52
854 856 4.167554 TGCGCTTTCGATTTTGGTTTAT 57.832 36.364 9.73 0.00 38.10 1.40
966 968 3.662247 GGAACGAGGAAGACTTTGAGA 57.338 47.619 0.00 0.00 0.00 3.27
1217 1220 1.188219 ACTGAAGCAGAAGGCCTCGA 61.188 55.000 5.23 0.00 46.50 4.04
1229 1232 1.839994 AGGCCTCGAAGATCAAATCCA 59.160 47.619 0.00 0.00 33.89 3.41
1241 1244 0.313043 CAAATCCAGCATCGATGGCC 59.687 55.000 26.00 10.98 39.19 5.36
1285 1288 8.251750 TCTTCTTTGTAACCAAACATATCTCG 57.748 34.615 0.00 0.00 35.67 4.04
1375 1378 4.789012 ACGATCGGGAAACTGTTTACTA 57.211 40.909 20.98 4.76 38.16 1.82
1514 1517 4.475135 GGAACCTCCAGCCGAGCC 62.475 72.222 0.00 0.00 37.27 4.70
1578 1581 4.079730 GGATCTTAACAATCTGAAGGGGGT 60.080 45.833 0.00 0.00 0.00 4.95
1653 1656 3.321039 TGGAGTCAGGAATGGCAGATAT 58.679 45.455 0.00 0.00 0.00 1.63
1933 2015 5.687285 GCCCAGATATTCTTTTAAATGCACG 59.313 40.000 0.00 0.00 0.00 5.34
2701 2856 1.130955 AATTGCTTTGTTTCTGCGCG 58.869 45.000 0.00 0.00 0.00 6.86
2730 2885 9.868277 ATTCATTTTTCCATCGCAAAGTATTTA 57.132 25.926 0.00 0.00 35.03 1.40
2759 2914 6.895204 ACCCCAAAATAGTGCATAGTTTATGT 59.105 34.615 0.00 0.00 38.43 2.29
3042 3654 8.243426 TGTATCTGTATGCTTTAAGCCTTTTTG 58.757 33.333 14.80 1.10 41.51 2.44
3547 4159 3.057526 GTGGGTTATCAAGGTCACTTTGC 60.058 47.826 0.00 0.00 33.81 3.68
3815 4427 5.698741 AGATCACCCAACTGTCATGATAA 57.301 39.130 0.00 0.00 30.23 1.75
4174 4833 8.529476 TCCTAGTAGTCCTGTATTTCAAGTTTC 58.471 37.037 0.00 0.00 0.00 2.78
4313 4976 3.827302 ACCATTTAATGTGGCCGTGTTTA 59.173 39.130 0.00 0.00 40.49 2.01
4316 4979 5.290643 CCATTTAATGTGGCCGTGTTTATTG 59.709 40.000 0.00 0.00 0.00 1.90
4317 4980 5.455056 TTTAATGTGGCCGTGTTTATTGT 57.545 34.783 0.00 0.00 0.00 2.71
4318 4981 5.455056 TTAATGTGGCCGTGTTTATTGTT 57.545 34.783 0.00 0.00 0.00 2.83
4471 5134 6.184789 AGGGTGAAAAGAAAGTTGAGTAACA 58.815 36.000 0.00 0.00 39.30 2.41
4786 5450 6.515272 AGCAAATAAATCAGTCCACGATTT 57.485 33.333 0.00 0.00 43.63 2.17
4855 5519 6.094603 CCTTAGATGGGATCTTTTCACACTTG 59.905 42.308 0.00 0.00 41.66 3.16
5063 5727 5.195940 CAAGAGAAGGCCTTGATAATCCAA 58.804 41.667 26.25 0.00 42.57 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 264 5.221422 TGCCTCTCGTGGAATGAAAATTTTT 60.221 36.000 4.63 0.00 0.00 1.94
264 265 4.280677 TGCCTCTCGTGGAATGAAAATTTT 59.719 37.500 2.28 2.28 0.00 1.82
265 266 3.826157 TGCCTCTCGTGGAATGAAAATTT 59.174 39.130 0.00 0.00 0.00 1.82
266 267 3.191371 GTGCCTCTCGTGGAATGAAAATT 59.809 43.478 0.00 0.00 0.00 1.82
267 268 2.749621 GTGCCTCTCGTGGAATGAAAAT 59.250 45.455 0.00 0.00 0.00 1.82
302 304 0.613292 AGGCACGTCCATGTCTCTCT 60.613 55.000 6.78 0.00 37.29 3.10
811 813 3.836365 TTGCATCGAACCCATAGATCA 57.164 42.857 0.00 0.00 0.00 2.92
854 856 1.542915 CGAGAGGAGAAACCGGTTACA 59.457 52.381 22.60 0.00 44.74 2.41
1217 1220 3.819337 CCATCGATGCTGGATTTGATCTT 59.181 43.478 20.25 0.00 35.70 2.40
1229 1232 3.933722 CTCGGGGCCATCGATGCT 61.934 66.667 20.25 0.00 36.01 3.79
1285 1288 2.034179 CCTCGGAAAACTTGTTTGGACC 59.966 50.000 0.00 4.08 0.00 4.46
1578 1581 3.181451 ACCAGCAGTGATTCTCTTCAACA 60.181 43.478 0.00 0.00 0.00 3.33
1653 1656 6.134535 AGAATAAGGAACATACCACCAACA 57.865 37.500 0.00 0.00 0.00 3.33
2701 2856 7.581011 ACTTTGCGATGGAAAAATGAATAAC 57.419 32.000 0.00 0.00 0.00 1.89
2730 2885 2.917713 TGCACTATTTTGGGGTCCAT 57.082 45.000 0.00 0.00 31.53 3.41
2759 2914 8.801299 TCAACATGATTTGAATTAAGCAACCTA 58.199 29.630 0.00 0.00 32.42 3.08
3410 4022 4.709886 GGAAAGTTATGGGTAGGCAAATGT 59.290 41.667 0.00 0.00 0.00 2.71
3547 4159 3.853831 TGCAAAGATACTGCCACAATG 57.146 42.857 0.00 0.00 39.13 2.82
3626 4238 7.045126 TGTTTTTCCGACATACAAGGATTTT 57.955 32.000 0.00 0.00 33.57 1.82
4174 4833 1.747709 CAAGGAATCCCTCAGTGCAG 58.252 55.000 0.00 0.00 43.48 4.41
4381 5044 6.594744 ACTGCTCATGAATTGTGTATATCCA 58.405 36.000 0.00 0.00 0.00 3.41
4786 5450 5.115480 GTTTTGGAGATTGTTGCCAGAAAA 58.885 37.500 0.00 0.00 32.47 2.29
4824 5488 7.010160 TGAAAAGATCCCATCTAAGGTTTTGT 58.990 34.615 0.00 0.00 39.08 2.83
4855 5519 1.064825 TCTTCACTTTCCCCACCTCC 58.935 55.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.