Multiple sequence alignment - TraesCS6B01G147700

Loading Multiple Alignment...

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 TraesCS6B01G147700 chr6B 100.000 2920 0 0 1 2920 148824817 148827736 0.000000e+00 5393.0
1 TraesCS6B01G147700 chr3D 95.918 2303 66 11 630 2920 575925847 575923561 0.000000e+00 3707.0
2 TraesCS6B01G147700 chr3D 96.815 628 18 2 7 634 575928482 575927857 0.000000e+00 1048.0
3 TraesCS6B01G147700 chr1D 93.443 854 44 7 128 977 826644 827489 0.000000e+00 1256.0
4 TraesCS6B01G147700 chr1D 87.209 688 60 10 617 1304 906473 907132 0.000000e+00 758.0
5 TraesCS6B01G147700 chr1D 80.345 580 66 22 20 593 905851 906388 2.110000e-106 396.0
6 TraesCS6B01G147700 chr1D 94.495 109 5 1 1 108 822584 822692 1.800000e-37 167.0
7 TraesCS6B01G147700 chr4D 90.402 771 50 11 1311 2059 416064821 416065589 0.000000e+00 992.0
8 TraesCS6B01G147700 chr4A 90.143 771 52 10 1311 2059 47747620 47746852 0.000000e+00 981.0
9 TraesCS6B01G147700 chr4B 88.265 784 53 21 1311 2059 512761501 512762280 0.000000e+00 902.0
10 TraesCS6B01G147700 chr1B 88.235 697 52 10 617 1305 3657374 3658048 0.000000e+00 806.0
11 TraesCS6B01G147700 chr1B 81.324 589 67 19 20 602 3656748 3657299 3.450000e-119 438.0
12 TraesCS6B01G147700 chr1B 92.500 80 6 0 1311 1390 470713184 470713105 6.610000e-22 115.0
13 TraesCS6B01G147700 chr1A 87.826 690 54 9 617 1304 2541285 2540624 0.000000e+00 782.0
14 TraesCS6B01G147700 chr1A 83.090 479 48 16 126 597 2541804 2541352 3.500000e-109 405.0
15 TraesCS6B01G147700 chr5D 91.314 449 33 5 2146 2590 549810732 549810286 2.490000e-170 608.0
16 TraesCS6B01G147700 chr5D 80.833 120 16 6 2740 2853 435470820 435470702 1.440000e-13 87.9
17 TraesCS6B01G147700 chr3A 90.402 448 39 3 2146 2590 156128592 156128146 1.170000e-163 586.0
18 TraesCS6B01G147700 chr2B 93.729 303 19 0 1311 1613 631346682 631346380 3.430000e-124 455.0
19 TraesCS6B01G147700 chr2D 90.120 334 26 3 2255 2587 44703105 44703432 7.480000e-116 427.0
20 TraesCS6B01G147700 chr7A 84.942 259 29 9 2234 2483 214856056 214855799 1.340000e-63 254.0
21 TraesCS6B01G147700 chr7A 92.157 102 5 2 2144 2243 214856189 214856089 1.090000e-29 141.0
22 TraesCS6B01G147700 chr7B 85.039 254 26 9 2234 2477 166773105 166773356 6.250000e-62 248.0
23 TraesCS6B01G147700 chr7B 98.611 72 0 1 2167 2237 166772995 166773066 3.050000e-25 126.0
24 TraesCS6B01G147700 chr2A 88.718 195 16 4 2591 2783 6243344 6243534 1.750000e-57 233.0
25 TraesCS6B01G147700 chr2A 87.179 195 19 4 2591 2783 6112218 6112028 1.760000e-52 217.0
26 TraesCS6B01G147700 chr2A 86.667 195 20 4 2591 2783 6163919 6163729 8.200000e-51 211.0
27 TraesCS6B01G147700 chr5A 87.701 187 19 2 2591 2777 415197815 415197633 6.340000e-52 215.0
28 TraesCS6B01G147700 chr7D 98.611 72 0 1 2167 2237 203043492 203043563 3.050000e-25 126.0
29 TraesCS6B01G147700 chr7D 92.958 71 3 2 2404 2473 203044691 203044760 5.150000e-18 102.0
30 TraesCS6B01G147700 chr6A 92.500 80 6 0 1311 1390 12143544 12143465 6.610000e-22 115.0
31 TraesCS6B01G147700 chr3B 93.421 76 5 0 1312 1387 806132077 806132152 2.380000e-21 113.0


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 TraesCS6B01G147700 chr6B 148824817 148827736 2919 False 5393.0 5393 100.0000 1 2920 1 chr6B.!!$F1 2919
1 TraesCS6B01G147700 chr3D 575923561 575928482 4921 True 2377.5 3707 96.3665 7 2920 2 chr3D.!!$R1 2913
2 TraesCS6B01G147700 chr1D 822584 827489 4905 False 711.5 1256 93.9690 1 977 2 chr1D.!!$F1 976
3 TraesCS6B01G147700 chr1D 905851 907132 1281 False 577.0 758 83.7770 20 1304 2 chr1D.!!$F2 1284
4 TraesCS6B01G147700 chr4D 416064821 416065589 768 False 992.0 992 90.4020 1311 2059 1 chr4D.!!$F1 748
5 TraesCS6B01G147700 chr4A 47746852 47747620 768 True 981.0 981 90.1430 1311 2059 1 chr4A.!!$R1 748
6 TraesCS6B01G147700 chr4B 512761501 512762280 779 False 902.0 902 88.2650 1311 2059 1 chr4B.!!$F1 748
7 TraesCS6B01G147700 chr1B 3656748 3658048 1300 False 622.0 806 84.7795 20 1305 2 chr1B.!!$F1 1285
8 TraesCS6B01G147700 chr1A 2540624 2541804 1180 True 593.5 782 85.4580 126 1304 2 chr1A.!!$R1 1178

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
368 4303 0.400213 TGCCACTGTGGAAGTTAGGG 59.6 55.0 30.23 0.51 40.96 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 8339 0.462047 CTAAATCACGCGGGCTTCCT 60.462 55.0 12.47 0.0 0.0 3.36 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
124 125 5.178797 AGCACATTATATTCAGGATACCGC 58.821 41.667 0.00 0.00 37.17 5.68
368 4303 0.400213 TGCCACTGTGGAAGTTAGGG 59.600 55.000 30.23 0.51 40.96 3.53
472 4413 7.759489 ACAATAATCAAGTTGCCTTCTTGTA 57.241 32.000 14.46 1.30 41.78 2.41
626 4621 6.764877 ATACTGAAATCGTTTAGCATACCG 57.235 37.500 0.00 0.00 0.00 4.02
714 6723 6.645700 TCCGTCGGTTAAATGTGTAATTAC 57.354 37.500 11.88 8.75 0.00 1.89
1244 7271 2.196595 CCATTGGTTCCTCCTCACCTA 58.803 52.381 0.00 0.00 37.07 3.08
1435 7464 3.490439 TTGAGTCATGCCTCAGTTTGA 57.510 42.857 6.55 0.00 42.16 2.69
1440 7469 6.003326 TGAGTCATGCCTCAGTTTGAAATAA 58.997 36.000 1.46 0.00 36.57 1.40
1582 7637 7.792374 TGGTCATTGCAGTCTATTTTATCTC 57.208 36.000 0.00 0.00 0.00 2.75
1724 7779 4.860907 GTGACATGATGCTTCACATTTTCC 59.139 41.667 4.14 0.00 39.84 3.13
1771 7826 5.239306 TGAGCACTTACTCCATTCTTTTGTG 59.761 40.000 0.00 0.00 35.72 3.33
1885 7940 3.507233 CAGTATGACCAACATGGCAAAGT 59.493 43.478 0.00 0.00 42.67 2.66
1908 7963 7.425606 AGTTGTTATTCTTGTTCATGAACCAC 58.574 34.615 30.66 17.23 40.46 4.16
2126 8186 2.481952 CAGTAGCAACAGCAAGAAGGAC 59.518 50.000 0.00 0.00 0.00 3.85
2204 8264 7.208064 AGGTAAAGGGCATAGATTCAACTTA 57.792 36.000 0.00 0.00 0.00 2.24
2206 8266 7.054751 GGTAAAGGGCATAGATTCAACTTACT 58.945 38.462 0.00 0.00 0.00 2.24
2279 8339 1.123928 ACCGGCAATTTTCCACCAAA 58.876 45.000 0.00 0.00 0.00 3.28
2365 8425 9.338291 CATGTTAAATATTATGCAGCTTGCTAG 57.662 33.333 9.12 0.00 45.31 3.42
2382 8442 9.627395 AGCTTGCTAGTGTTATATATTTAGTCG 57.373 33.333 0.00 0.00 0.00 4.18
2408 8468 5.801350 ATATGATGTCTGTTTGGTCGTTG 57.199 39.130 0.00 0.00 0.00 4.10
2436 8496 3.876320 GCCTCAGATCCAAGAAATCTGTC 59.124 47.826 11.65 1.82 46.66 3.51
2437 8497 4.383989 GCCTCAGATCCAAGAAATCTGTCT 60.384 45.833 11.65 0.00 46.66 3.41
2438 8498 5.117584 CCTCAGATCCAAGAAATCTGTCTG 58.882 45.833 11.65 0.00 46.66 3.51
2439 8499 5.338219 CCTCAGATCCAAGAAATCTGTCTGT 60.338 44.000 11.65 0.00 46.66 3.41
2666 8726 9.928236 GTTTTCAAGAAGATAGATCATAACTGC 57.072 33.333 0.00 0.00 0.00 4.40
2721 8781 7.990886 TCTGTAGGTTTTATATTTCTGCGGATT 59.009 33.333 0.00 0.00 0.00 3.01
2733 8793 4.149511 TCTGCGGATTTATGTGATTGGA 57.850 40.909 0.00 0.00 0.00 3.53
2789 8849 3.873910 CCACTAATGGTCCTGTAACTGG 58.126 50.000 0.00 0.00 41.64 4.00
2815 8878 3.264947 CTGCTACACATTGCTGAGCTTA 58.735 45.455 5.83 0.00 34.19 3.09
2861 8924 5.497464 TCACATGAGTTTATGAGGGACAA 57.503 39.130 0.00 0.00 0.00 3.18
2879 8942 3.230134 ACAACCTTTGCCATGAAAGCTA 58.770 40.909 0.00 0.00 32.45 3.32
2905 8968 7.168219 ACGTATGCCCAAATGATACATAGAAT 58.832 34.615 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
463 4400 9.533253 AACAGAAAATGAAACAATACAAGAAGG 57.467 29.630 0.00 0.00 0.00 3.46
472 4413 6.817641 TGCAAGTCAACAGAAAATGAAACAAT 59.182 30.769 0.00 0.00 0.00 2.71
626 4621 2.754552 ACAGAGAGTGAGAGAGCATGAC 59.245 50.000 0.00 0.00 0.00 3.06
714 6723 9.334693 CATAGAAAACAAAAGCTAGCAGTAAAG 57.665 33.333 18.83 3.98 0.00 1.85
895 6906 1.543358 TGTGTGCAGTGCAAGTTGAAA 59.457 42.857 21.67 0.00 41.47 2.69
1297 7324 3.913370 ATAGAGTAGGTGAGGGCAGAT 57.087 47.619 0.00 0.00 0.00 2.90
1435 7464 5.104193 AGACCTCCATGATGCAGACTTATTT 60.104 40.000 0.00 0.00 0.00 1.40
1440 7469 1.876849 AGACCTCCATGATGCAGACT 58.123 50.000 0.00 0.00 0.00 3.24
1771 7826 5.145564 TCTCACCATAGTATTCAGTACCCC 58.854 45.833 0.00 0.00 33.58 4.95
1885 7940 7.340122 TGTGGTTCATGAACAAGAATAACAA 57.660 32.000 33.42 12.05 42.85 2.83
1908 7963 5.126061 ACATGCCACCTTCTTATAAAAGCTG 59.874 40.000 0.00 0.00 32.36 4.24
2021 8081 5.849510 TCAGATTACTTTCGACAGGAAACA 58.150 37.500 0.00 0.00 39.67 2.83
2102 8162 2.169832 TCTTGCTGTTGCTACTGGTC 57.830 50.000 7.24 0.00 40.48 4.02
2126 8186 2.699954 AGGTATCCTCGTTGTTGCTTG 58.300 47.619 0.00 0.00 0.00 4.01
2279 8339 0.462047 CTAAATCACGCGGGCTTCCT 60.462 55.000 12.47 0.00 0.00 3.36
2382 8442 5.523916 ACGACCAAACAGACATCATATAAGC 59.476 40.000 0.00 0.00 0.00 3.09
2395 8455 1.461127 GCTAGAGCAACGACCAAACAG 59.539 52.381 0.00 0.00 41.59 3.16
2408 8468 2.315176 TCTTGGATCTGAGGCTAGAGC 58.685 52.381 0.00 0.00 41.14 4.09
2480 8540 7.429920 GCATCGAAGTTGTTTGTTTGTTTACTA 59.570 33.333 0.00 0.00 0.00 1.82
2482 8542 6.034044 TGCATCGAAGTTGTTTGTTTGTTTAC 59.966 34.615 0.00 0.00 0.00 2.01
2713 8773 3.003689 GGTCCAATCACATAAATCCGCAG 59.996 47.826 0.00 0.00 0.00 5.18
2716 8776 6.936900 AGATAAGGTCCAATCACATAAATCCG 59.063 38.462 6.92 0.00 0.00 4.18
2721 8781 9.699410 AATCAAAGATAAGGTCCAATCACATAA 57.301 29.630 6.92 0.00 0.00 1.90
2771 8831 3.914426 AGCCAGTTACAGGACCATTAG 57.086 47.619 0.00 0.00 0.00 1.73
2777 8837 2.347731 GCAGTTAGCCAGTTACAGGAC 58.652 52.381 0.00 0.00 37.23 3.85
2778 8838 2.762535 GCAGTTAGCCAGTTACAGGA 57.237 50.000 0.00 0.00 37.23 3.86
2789 8849 3.002791 TCAGCAATGTGTAGCAGTTAGC 58.997 45.455 0.00 0.00 46.19 3.09
2815 8878 8.902806 TGATGAACTGAACTTTGATTACAGTTT 58.097 29.630 0.00 0.00 46.81 2.66
2861 8924 2.228822 CGTTAGCTTTCATGGCAAAGGT 59.771 45.455 13.94 13.94 44.38 3.50
2867 8930 2.287009 GGCATACGTTAGCTTTCATGGC 60.287 50.000 11.02 6.67 32.81 4.40
2871 8934 2.772077 TGGGCATACGTTAGCTTTCA 57.228 45.000 11.02 5.76 0.00 2.69
2879 8942 6.530120 TCTATGTATCATTTGGGCATACGTT 58.470 36.000 0.00 0.00 0.00 3.99


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

AutoCloner maintained by Alex Coulton.