Multiple sequence alignment - TraesCS2A01G074600

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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 TraesCS2A01G074600 chr2A 100.000 2303 0 0 1 2303 32927260 32929562 0.000000e+00 4253.0
1 TraesCS2A01G074600 chr2A 98.364 978 12 4 1328 2303 32887490 32888465 0.000000e+00 1714.0
2 TraesCS2A01G074600 chr2A 89.640 1332 121 8 1 1328 746629880 746631198 0.000000e+00 1679.0
3 TraesCS2A01G074600 chr2A 76.667 570 95 20 1717 2275 32864560 32865102 4.840000e-72 281.0
4 TraesCS2A01G074600 chr2A 73.265 490 90 20 1717 2193 32551773 32552234 8.580000e-30 141.0
5 TraesCS2A01G074600 chr2A 86.047 86 12 0 1328 1413 32864454 32864539 2.440000e-15 93.5
6 TraesCS2A01G074600 chr4A 93.034 1335 76 9 1 1332 728106005 728104685 0.000000e+00 1934.0
7 TraesCS2A01G074600 chr7B 90.930 1334 116 4 1 1331 734689278 734690609 0.000000e+00 1788.0
8 TraesCS2A01G074600 chr7B 75.448 1340 301 25 3 1328 469484204 469482879 5.400000e-176 627.0
9 TraesCS2A01G074600 chr1B 86.142 1335 179 4 1 1332 677137114 677135783 0.000000e+00 1435.0
10 TraesCS2A01G074600 chr6A 83.873 1327 212 2 2 1327 378077728 378079053 0.000000e+00 1264.0
11 TraesCS2A01G074600 chr6A 92.045 264 17 3 1449 1709 19987767 19988029 3.610000e-98 368.0
12 TraesCS2A01G074600 chr6A 91.729 266 18 4 1449 1710 260523859 260524124 1.300000e-97 366.0
13 TraesCS2A01G074600 chr6A 90.775 271 22 2 1449 1716 105506698 105506428 2.180000e-95 359.0
14 TraesCS2A01G074600 chr6A 78.431 102 19 3 580 679 444702739 444702639 1.910000e-06 63.9
15 TraesCS2A01G074600 chr5A 97.719 570 11 2 760 1329 654172768 654172201 0.000000e+00 979.0
16 TraesCS2A01G074600 chr5A 78.024 1174 242 14 161 1326 387391492 387390327 0.000000e+00 725.0
17 TraesCS2A01G074600 chr5A 92.395 263 17 3 1449 1709 514606684 514606945 2.790000e-99 372.0
18 TraesCS2A01G074600 chr2D 95.025 603 22 2 1709 2303 30654192 30654794 0.000000e+00 941.0
19 TraesCS2A01G074600 chr2D 90.614 277 22 4 1449 1721 56650909 56651185 4.680000e-97 364.0
20 TraesCS2A01G074600 chr2D 76.644 578 97 27 1717 2283 30619700 30620250 3.740000e-73 285.0
21 TraesCS2A01G074600 chr2D 96.721 122 3 1 1327 1448 30654070 30654190 3.880000e-48 202.0
22 TraesCS2A01G074600 chr2D 85.556 90 13 0 1328 1417 30619594 30619683 6.770000e-16 95.3
23 TraesCS2A01G074600 chr6D 77.212 1356 274 32 1 1338 422296959 422298297 0.000000e+00 760.0
24 TraesCS2A01G074600 chr5B 78.328 1172 239 15 161 1325 482490194 482491357 0.000000e+00 743.0
25 TraesCS2A01G074600 chr2B 86.235 603 54 9 1708 2299 43798131 43798715 5.400000e-176 627.0
26 TraesCS2A01G074600 chr2B 74.875 601 110 23 1717 2303 50412211 50412784 3.830000e-58 235.0
27 TraesCS2A01G074600 chr2B 91.870 123 10 0 1328 1450 43798010 43798132 3.040000e-39 172.0
28 TraesCS2A01G074600 chr2B 86.047 86 12 0 1328 1413 50412105 50412190 2.440000e-15 93.5
29 TraesCS2A01G074600 chr1A 91.791 268 16 5 1446 1709 228831422 228831687 3.610000e-98 368.0
30 TraesCS2A01G074600 chr1A 91.760 267 18 4 1448 1712 482341700 482341964 3.610000e-98 368.0
31 TraesCS2A01G074600 chr7A 91.144 271 20 3 1446 1712 401821837 401822107 4.680000e-97 364.0


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 TraesCS2A01G074600 chr2A 32927260 32929562 2302 False 4253.0 4253 100.0000 1 2303 1 chr2A.!!$F3 2302
1 TraesCS2A01G074600 chr2A 32887490 32888465 975 False 1714.0 1714 98.3640 1328 2303 1 chr2A.!!$F2 975
2 TraesCS2A01G074600 chr2A 746629880 746631198 1318 False 1679.0 1679 89.6400 1 1328 1 chr2A.!!$F4 1327
3 TraesCS2A01G074600 chr4A 728104685 728106005 1320 True 1934.0 1934 93.0340 1 1332 1 chr4A.!!$R1 1331
4 TraesCS2A01G074600 chr7B 734689278 734690609 1331 False 1788.0 1788 90.9300 1 1331 1 chr7B.!!$F1 1330
5 TraesCS2A01G074600 chr7B 469482879 469484204 1325 True 627.0 627 75.4480 3 1328 1 chr7B.!!$R1 1325
6 TraesCS2A01G074600 chr1B 677135783 677137114 1331 True 1435.0 1435 86.1420 1 1332 1 chr1B.!!$R1 1331
7 TraesCS2A01G074600 chr6A 378077728 378079053 1325 False 1264.0 1264 83.8730 2 1327 1 chr6A.!!$F3 1325
8 TraesCS2A01G074600 chr5A 654172201 654172768 567 True 979.0 979 97.7190 760 1329 1 chr5A.!!$R2 569
9 TraesCS2A01G074600 chr5A 387390327 387391492 1165 True 725.0 725 78.0240 161 1326 1 chr5A.!!$R1 1165
10 TraesCS2A01G074600 chr2D 30654070 30654794 724 False 571.5 941 95.8730 1327 2303 2 chr2D.!!$F3 976
11 TraesCS2A01G074600 chr6D 422296959 422298297 1338 False 760.0 760 77.2120 1 1338 1 chr6D.!!$F1 1337
12 TraesCS2A01G074600 chr5B 482490194 482491357 1163 False 743.0 743 78.3280 161 1325 1 chr5B.!!$F1 1164
13 TraesCS2A01G074600 chr2B 43798010 43798715 705 False 399.5 627 89.0525 1328 2299 2 chr2B.!!$F1 971

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
713 715 1.00461 CACGCATGATAAAGCCAGTCG 60.005 52.381 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1887 5.049828 TCATCGTCAGGTGTTATATTGCAG 58.95 41.667 0.0 0.0 0.0 4.41 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
30 31 1.272554 GGAACGACCCTTGGATCCCT 61.273 60.000 9.90 0.00 0.00 4.20
47 48 2.175499 TCCCTGGCCTTATTTCCATGAG 59.825 50.000 3.32 0.00 0.00 2.90
156 157 2.279659 GCATGCAAATTTCATTCCGTCG 59.720 45.455 14.21 0.00 0.00 5.12
157 158 3.757184 CATGCAAATTTCATTCCGTCGA 58.243 40.909 0.00 0.00 0.00 4.20
223 224 4.033009 AGATGATATATGGGCATGGTCGA 58.967 43.478 0.00 0.00 0.00 4.20
246 247 6.535150 CGACAGAAAAAGCAGGAATCTATACA 59.465 38.462 0.00 0.00 0.00 2.29
493 495 1.134128 TGTGTCTTGCAGCTGAGGAAA 60.134 47.619 20.43 3.78 0.00 3.13
552 554 1.056660 ACTTTTGGAGAGAAGCCCGA 58.943 50.000 0.00 0.00 0.00 5.14
600 602 2.825205 CTGCATACGATGACATGGTCA 58.175 47.619 6.34 1.05 46.90 4.02
681 683 2.036958 TGTGGGCAATATGGACTTCG 57.963 50.000 0.00 0.00 0.00 3.79
712 714 2.279741 TCACGCATGATAAAGCCAGTC 58.720 47.619 0.00 0.00 0.00 3.51
713 715 1.004610 CACGCATGATAAAGCCAGTCG 60.005 52.381 0.00 0.00 0.00 4.18
720 722 1.416401 GATAAAGCCAGTCGGGATCCA 59.584 52.381 15.23 0.00 40.01 3.41
737 740 4.499183 GATCCAGTCCAGTCACTAAAGTG 58.501 47.826 3.64 3.64 46.91 3.16
738 741 3.305720 TCCAGTCCAGTCACTAAAGTGT 58.694 45.455 9.81 0.00 45.76 3.55
744 747 5.186021 AGTCCAGTCACTAAAGTGTATCAGG 59.814 44.000 9.81 8.29 45.76 3.86
1457 1464 6.783482 GGTTTCCATATACTTCTACTCCCTCT 59.217 42.308 0.00 0.00 0.00 3.69
1478 1485 5.428253 TCTGTTCCTTGATATTAGGTGCAC 58.572 41.667 8.80 8.80 34.29 4.57
1533 1540 1.873698 ATTACGTTGCACCACTCGTT 58.126 45.000 0.00 0.00 37.66 3.85
1619 1626 8.321353 TCATGTCAATTAGTCAGGTGTAATCTT 58.679 33.333 0.00 0.00 0.00 2.40
1642 1650 7.390162 TCTTGCCAAAACTTGTGAAATTTTCTT 59.610 29.630 10.33 0.00 0.00 2.52
1878 1887 9.646427 AATGAGTATCTCAAAGAGTACAAGAAC 57.354 33.333 3.58 0.00 44.04 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.852449 AGGTCTCATGGAAATAAGGCCA 59.148 45.455 5.01 0.00 35.93 5.36
174 175 4.445162 CCAAACCGCCTCAAGGGTATATTA 60.445 45.833 0.00 0.00 34.85 0.98
223 224 7.398024 ACTGTATAGATTCCTGCTTTTTCTGT 58.602 34.615 0.00 0.00 0.00 3.41
493 495 8.137437 GCACTTTATCAAAGCATGGTACATATT 58.863 33.333 0.00 0.00 42.69 1.28
528 530 3.384668 GGCTTCTCTCCAAAAGTTTTGC 58.615 45.455 20.74 8.35 0.00 3.68
552 554 0.814010 GCTTCACGTCCAACCACTGT 60.814 55.000 0.00 0.00 0.00 3.55
681 683 7.322222 GCTTTATCATGCGTGATATTGTTTCTC 59.678 37.037 25.47 8.74 44.53 2.87
702 704 0.830648 CTGGATCCCGACTGGCTTTA 59.169 55.000 9.90 0.00 0.00 1.85
737 740 0.463654 TGCCAACGCATCCCTGATAC 60.464 55.000 0.00 0.00 41.12 2.24
738 741 0.179048 CTGCCAACGCATCCCTGATA 60.179 55.000 0.00 0.00 46.11 2.15
744 747 1.709147 CTAGCACTGCCAACGCATCC 61.709 60.000 0.00 0.00 46.11 3.51
1457 1464 5.045942 TCTGTGCACCTAATATCAAGGAACA 60.046 40.000 15.69 9.81 37.57 3.18
1619 1626 7.446001 AAAGAAAATTTCACAAGTTTTGGCA 57.554 28.000 8.55 0.00 30.39 4.92
1642 1650 5.627367 CGGAAATTAAAGAACGCATGTGAAA 59.373 36.000 14.43 0.00 0.00 2.69
1878 1887 5.049828 TCATCGTCAGGTGTTATATTGCAG 58.950 41.667 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.