Multiple sequence alignment - TraesCS1A01G181800

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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 TraesCS1A01G181800 chr1A 100.000 2370 0 0 1 2370 328126624 328124255 0.000000e+00 4377.0
1 TraesCS1A01G181800 chr2A 95.488 1374 54 3 995 2367 452290412 452291778 0.000000e+00 2187.0
2 TraesCS1A01G181800 chr2A 93.851 992 51 1 1 992 452289399 452290380 0.000000e+00 1485.0
3 TraesCS1A01G181800 chr2A 85.714 343 39 3 650 992 314032899 314032567 1.040000e-93 353.0
4 TraesCS1A01G181800 chr2A 89.238 223 23 1 1799 2020 698228310 698228532 6.450000e-71 278.0
5 TraesCS1A01G181800 chr7D 91.553 1030 84 3 993 2020 251602027 251600999 0.000000e+00 1417.0
6 TraesCS1A01G181800 chr7D 89.416 548 51 4 1 541 526124822 526124275 0.000000e+00 684.0
7 TraesCS1A01G181800 chr7D 89.338 544 52 4 1 538 71113885 71114428 0.000000e+00 678.0
8 TraesCS1A01G181800 chr7D 88.746 311 23 4 684 992 251602357 251602057 1.030000e-98 370.0
9 TraesCS1A01G181800 chr5B 87.282 1030 128 3 993 2020 155846094 155847122 0.000000e+00 1173.0
10 TraesCS1A01G181800 chr2D 87.251 855 56 15 644 1475 593808313 593809137 0.000000e+00 926.0
11 TraesCS1A01G181800 chr2D 87.330 734 83 6 1 724 570388493 570387760 0.000000e+00 832.0
12 TraesCS1A01G181800 chr2D 87.023 393 47 3 329 718 500759870 500760261 7.780000e-120 440.0
13 TraesCS1A01G181800 chr2D 86.735 392 43 4 993 1384 349783969 349783587 6.050000e-116 427.0
14 TraesCS1A01G181800 chr2D 84.046 351 44 5 644 992 221966127 221965787 6.320000e-86 327.0
15 TraesCS1A01G181800 chr2D 86.294 197 24 1 1208 1401 429520367 429520171 6.640000e-51 211.0
16 TraesCS1A01G181800 chr4B 86.420 729 85 11 1 719 114981202 114981926 0.000000e+00 785.0
17 TraesCS1A01G181800 chr4B 87.805 123 15 0 1426 1548 161087084 161086962 6.830000e-31 145.0
18 TraesCS1A01G181800 chr4A 86.096 712 95 4 2 711 174267009 174266300 0.000000e+00 763.0
19 TraesCS1A01G181800 chr6D 90.976 543 46 3 1 541 273334236 273333695 0.000000e+00 728.0
20 TraesCS1A01G181800 chr5D 90.074 544 48 4 1 538 227974229 227974772 0.000000e+00 701.0
21 TraesCS1A01G181800 chr5D 86.429 140 18 1 2107 2245 143014860 143014999 4.080000e-33 152.0
22 TraesCS1A01G181800 chr1B 88.752 569 50 3 1805 2370 564637679 564637122 0.000000e+00 684.0
23 TraesCS1A01G181800 chr1B 85.397 315 45 1 1069 1382 378042748 378043062 2.270000e-85 326.0
24 TraesCS1A01G181800 chr5A 84.923 650 89 7 1 642 561029416 561028768 0.000000e+00 649.0
25 TraesCS1A01G181800 chr3D 87.206 383 45 2 1022 1401 178801799 178801418 1.300000e-117 433.0
26 TraesCS1A01G181800 chr3D 86.464 362 48 1 364 724 284194640 284194279 1.710000e-106 396.0
27 TraesCS1A01G181800 chr3D 85.634 355 50 1 364 717 224372207 224371853 2.880000e-99 372.0
28 TraesCS1A01G181800 chr3D 87.273 275 25 3 715 989 69781414 69781678 2.960000e-79 305.0
29 TraesCS1A01G181800 chr3D 92.810 153 8 3 780 930 178801952 178801801 3.970000e-53 219.0
30 TraesCS1A01G181800 chr6A 91.786 280 23 0 1177 1456 588633407 588633686 7.940000e-105 390.0
31 TraesCS1A01G181800 chr6A 87.153 288 26 3 644 930 588633005 588633282 1.370000e-82 316.0
32 TraesCS1A01G181800 chr7A 86.313 358 46 3 364 719 225172019 225171663 1.030000e-103 387.0
33 TraesCS1A01G181800 chr6B 83.122 237 17 7 1080 1316 567083608 567083395 6.680000e-46 195.0
34 TraesCS1A01G181800 chr3A 88.889 144 16 0 1875 2018 414029679 414029536 6.730000e-41 178.0
35 TraesCS1A01G181800 chr4D 90.833 120 9 2 1286 1405 179718752 179718869 2.440000e-35 159.0
36 TraesCS1A01G181800 chr1D 100.000 28 0 0 1774 1801 255127426 255127399 4.000000e-03 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 TraesCS1A01G181800 chr1A 328124255 328126624 2369 True 4377.0 4377 100.0000 1 2370 1 chr1A.!!$R1 2369
1 TraesCS1A01G181800 chr2A 452289399 452291778 2379 False 1836.0 2187 94.6695 1 2367 2 chr2A.!!$F2 2366
2 TraesCS1A01G181800 chr7D 251600999 251602357 1358 True 893.5 1417 90.1495 684 2020 2 chr7D.!!$R2 1336
3 TraesCS1A01G181800 chr7D 526124275 526124822 547 True 684.0 684 89.4160 1 541 1 chr7D.!!$R1 540
4 TraesCS1A01G181800 chr7D 71113885 71114428 543 False 678.0 678 89.3380 1 538 1 chr7D.!!$F1 537
5 TraesCS1A01G181800 chr5B 155846094 155847122 1028 False 1173.0 1173 87.2820 993 2020 1 chr5B.!!$F1 1027
6 TraesCS1A01G181800 chr2D 593808313 593809137 824 False 926.0 926 87.2510 644 1475 1 chr2D.!!$F2 831
7 TraesCS1A01G181800 chr2D 570387760 570388493 733 True 832.0 832 87.3300 1 724 1 chr2D.!!$R4 723
8 TraesCS1A01G181800 chr4B 114981202 114981926 724 False 785.0 785 86.4200 1 719 1 chr4B.!!$F1 718
9 TraesCS1A01G181800 chr4A 174266300 174267009 709 True 763.0 763 86.0960 2 711 1 chr4A.!!$R1 709
10 TraesCS1A01G181800 chr6D 273333695 273334236 541 True 728.0 728 90.9760 1 541 1 chr6D.!!$R1 540
11 TraesCS1A01G181800 chr5D 227974229 227974772 543 False 701.0 701 90.0740 1 538 1 chr5D.!!$F2 537
12 TraesCS1A01G181800 chr1B 564637122 564637679 557 True 684.0 684 88.7520 1805 2370 1 chr1B.!!$R1 565
13 TraesCS1A01G181800 chr5A 561028768 561029416 648 True 649.0 649 84.9230 1 642 1 chr5A.!!$R1 641
14 TraesCS1A01G181800 chr3D 178801418 178801952 534 True 326.0 433 90.0080 780 1401 2 chr3D.!!$R3 621
15 TraesCS1A01G181800 chr6A 588633005 588633686 681 False 353.0 390 89.4695 644 1456 2 chr6A.!!$F1 812

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
761 787 0.399833 TGTGATGTAGGCCTTGCACA 59.6 50.0 12.58 17.27 34.28 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1899 0.035317 CAGCCACTGTTACAGCCTCA 59.965 55.0 12.8 0.0 34.37 3.86 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
188 193 2.267006 CATCCAGTGCAGACGGCT 59.733 61.111 0.00 0.00 45.15 5.52
450 473 3.461773 CGGGAGAGTCGGGCACAT 61.462 66.667 0.00 0.00 0.00 3.21
573 597 1.500512 GGCTGCAACGTTTACACCGA 61.501 55.000 0.00 0.00 0.00 4.69
731 757 6.461927 CCTGGTATTTTCATTGGATGGACATG 60.462 42.308 0.00 0.00 0.00 3.21
752 778 4.930963 TGCAACAAAAAGTGTGATGTAGG 58.069 39.130 0.00 0.00 40.60 3.18
761 787 0.399833 TGTGATGTAGGCCTTGCACA 59.600 50.000 12.58 17.27 34.28 4.57
769 795 3.745803 GCCTTGCACAGCTGCTCC 61.746 66.667 15.27 2.49 44.57 4.70
770 796 2.033757 CCTTGCACAGCTGCTCCT 59.966 61.111 15.27 0.00 44.57 3.69
771 797 1.602888 CCTTGCACAGCTGCTCCTT 60.603 57.895 15.27 0.00 44.57 3.36
772 798 1.177256 CCTTGCACAGCTGCTCCTTT 61.177 55.000 15.27 0.00 44.57 3.11
773 799 0.672342 CTTGCACAGCTGCTCCTTTT 59.328 50.000 15.27 0.00 44.57 2.27
774 800 1.881973 CTTGCACAGCTGCTCCTTTTA 59.118 47.619 15.27 0.00 44.57 1.52
775 801 2.205022 TGCACAGCTGCTCCTTTTAT 57.795 45.000 15.27 0.00 44.57 1.40
776 802 2.517959 TGCACAGCTGCTCCTTTTATT 58.482 42.857 15.27 0.00 44.57 1.40
777 803 2.892852 TGCACAGCTGCTCCTTTTATTT 59.107 40.909 15.27 0.00 44.57 1.40
778 804 3.321682 TGCACAGCTGCTCCTTTTATTTT 59.678 39.130 15.27 0.00 44.57 1.82
930 956 1.866853 CTCCACAGCGAAAAAGGCCC 61.867 60.000 0.00 0.00 0.00 5.80
970 996 0.978146 ATCAGGTAGCCGGCTCAAGT 60.978 55.000 36.73 13.94 0.00 3.16
984 1010 0.401356 TCAAGTGGCTCAGATGGCAA 59.599 50.000 0.00 0.00 44.02 4.52
1318 1376 4.920112 CGTGGTGACCCGGCAACA 62.920 66.667 0.00 0.00 31.99 3.33
1570 1628 0.175760 GTAGACTGGCGGCTCAATGA 59.824 55.000 11.43 0.00 0.00 2.57
1633 1692 2.357034 GAGTCAACGGCGGCTCAA 60.357 61.111 13.24 0.00 0.00 3.02
1851 1911 1.174078 TCGGTCGTGAGGCTGTAACA 61.174 55.000 0.00 0.00 44.15 2.41
1941 2005 4.312443 GGATTGACTTTAACACGAGGACA 58.688 43.478 0.00 0.00 0.00 4.02
1945 2009 3.181469 TGACTTTAACACGAGGACAGCTT 60.181 43.478 0.00 0.00 0.00 3.74
1975 2039 0.324943 CAGAATTGACCCGGTGAGGT 59.675 55.000 0.00 0.00 45.12 3.85
2025 2089 0.921347 CGTCAATTAGAACTCGCGGG 59.079 55.000 3.27 3.27 0.00 6.13
2027 2091 0.535335 TCAATTAGAACTCGCGGGCT 59.465 50.000 5.51 0.00 0.00 5.19
2201 2265 5.257262 TGATTCCATTAATCCAACCGACAA 58.743 37.500 0.00 0.00 42.97 3.18
2284 2348 4.040829 TGGTTCATCATGAAGTGACTCAGT 59.959 41.667 0.00 0.00 40.28 3.41
2304 2368 2.885113 CAGGATGACGACGAGGCA 59.115 61.111 0.00 0.00 45.56 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 193 3.772387 TGGAGGCAAATTATCACCAACA 58.228 40.909 0.00 0.00 0.00 3.33
241 262 7.222872 AGCTATTTATTGAGTATGAGCAAGCT 58.777 34.615 0.00 0.00 0.00 3.74
242 263 7.172190 TGAGCTATTTATTGAGTATGAGCAAGC 59.828 37.037 0.00 0.00 0.00 4.01
445 468 3.241701 CACCGGTTTACAAATGATGTGC 58.758 45.455 2.97 0.00 43.77 4.57
450 473 0.875728 CCGCACCGGTTTACAAATGA 59.124 50.000 2.97 0.00 42.73 2.57
573 597 0.321671 CATGGACAGGAGGTTCGTGT 59.678 55.000 4.28 4.28 46.67 4.49
731 757 3.735746 GCCTACATCACACTTTTTGTTGC 59.264 43.478 0.00 0.00 35.67 4.17
761 787 7.295322 AGAAAAGAAAATAAAAGGAGCAGCT 57.705 32.000 0.00 0.00 0.00 4.24
774 800 9.921637 TTTGGCGTCATATAAAGAAAAGAAAAT 57.078 25.926 0.00 0.00 0.00 1.82
775 801 9.187455 GTTTGGCGTCATATAAAGAAAAGAAAA 57.813 29.630 0.00 0.00 0.00 2.29
776 802 8.573035 AGTTTGGCGTCATATAAAGAAAAGAAA 58.427 29.630 0.00 0.00 0.00 2.52
777 803 8.106247 AGTTTGGCGTCATATAAAGAAAAGAA 57.894 30.769 0.00 0.00 0.00 2.52
778 804 7.681939 AGTTTGGCGTCATATAAAGAAAAGA 57.318 32.000 0.00 0.00 0.00 2.52
944 970 1.261480 CCGGCTACCTGATGCTCTAT 58.739 55.000 0.00 0.00 0.00 1.98
970 996 0.035725 CTCTGTTGCCATCTGAGCCA 60.036 55.000 0.00 0.00 0.00 4.75
1124 1179 0.902531 CTGGGTCTCCTCCGCTTTAA 59.097 55.000 0.00 0.00 0.00 1.52
1151 1206 1.107538 TCGACCCGCTTGGATCCTAG 61.108 60.000 17.84 17.84 38.00 3.02
1318 1376 1.005630 GTTCACCACTGCTCGAGCT 60.006 57.895 35.27 16.24 42.66 4.09
1527 1585 3.134879 CCGCCCTCCGCTATTGTA 58.865 61.111 0.00 0.00 35.03 2.41
1557 1615 1.153107 CTCCATCATTGAGCCGCCA 60.153 57.895 0.00 0.00 0.00 5.69
1570 1628 3.005539 ACAGCTGCCCGTCTCCAT 61.006 61.111 15.27 0.00 0.00 3.41
1702 1762 1.165907 CCACGAGCTGCCACTTCAAA 61.166 55.000 0.00 0.00 0.00 2.69
1839 1899 0.035317 CAGCCACTGTTACAGCCTCA 59.965 55.000 12.80 0.00 34.37 3.86
1884 1948 2.442188 CGTACCGTTCCTGAAGCGC 61.442 63.158 0.00 0.00 0.00 5.92
1945 2009 2.079158 GTCAATTCTGCAGCAGCTACA 58.921 47.619 18.43 0.00 42.74 2.74
2201 2265 1.469940 CGTCTAGGCAAGCGAGATTGT 60.470 52.381 3.00 0.00 32.56 2.71
2260 2324 4.971939 TGAGTCACTTCATGATGAACCAA 58.028 39.130 15.03 2.61 40.28 3.67
2284 2348 1.725557 GCCTCGTCGTCATCCTGCTA 61.726 60.000 0.00 0.00 0.00 3.49
2304 2368 0.826715 TTCTTATCTCCGCTGCTGCT 59.173 50.000 14.03 0.00 36.97 4.24
2335 2399 1.292223 GTTGACTCGCCTGGCAGTA 59.708 57.895 20.29 2.16 0.00 2.74
2338 2402 4.680237 CCGTTGACTCGCCTGGCA 62.680 66.667 20.29 5.07 0.00 4.92


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

AutoCloner maintained by Alex Coulton.