Multiple sequence alignment - TraesCS6A01G382300

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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 TraesCS6A01G382300 chr6A 100.000 3619 0 0 1 3619 601399515 601395897 0.000000e+00 6684.0
1 TraesCS6A01G382300 chr6A 91.864 1770 110 13 686 2434 601967700 601969456 0.000000e+00 2440.0
2 TraesCS6A01G382300 chr6D 93.558 2701 130 12 1 2667 455087390 455084700 0.000000e+00 3984.0
3 TraesCS6A01G382300 chr6D 89.345 1802 110 24 686 2423 455311343 455313126 0.000000e+00 2189.0
4 TraesCS6A01G382300 chr6D 82.609 253 24 9 2665 2916 409577947 409578180 4.740000e-49 206.0
5 TraesCS6A01G382300 chr6D 91.935 62 4 1 2531 2592 455313406 455313466 6.440000e-13 86.1
6 TraesCS6A01G382300 chr6B 90.474 2698 160 36 1 2647 691862705 691865356 0.000000e+00 3469.0
7 TraesCS6A01G382300 chr6B 90.390 2695 166 36 1 2647 692195947 692193298 0.000000e+00 3456.0
8 TraesCS6A01G382300 chr6B 91.970 1706 103 18 724 2423 692488864 692490541 0.000000e+00 2361.0
9 TraesCS6A01G382300 chr6B 90.698 43 4 0 2430 2472 691865238 691865280 1.400000e-04 58.4
10 TraesCS6A01G382300 chr6B 92.500 40 3 0 2433 2472 692193413 692193374 1.400000e-04 58.4
11 TraesCS6A01G382300 chr7A 94.555 955 39 4 2665 3619 549410516 549411457 0.000000e+00 1463.0
12 TraesCS6A01G382300 chr7A 88.276 145 17 0 3475 3619 705593616 705593472 1.340000e-39 174.0
13 TraesCS6A01G382300 chr3A 93.396 954 36 8 2666 3619 652108082 652109008 0.000000e+00 1387.0
14 TraesCS6A01G382300 chr3A 96.721 61 2 0 3350 3410 28479213 28479273 6.390000e-18 102.0
15 TraesCS6A01G382300 chr3A 96.721 61 2 0 3350 3410 34260152 34260212 6.390000e-18 102.0
16 TraesCS6A01G382300 chr1B 93.925 428 12 4 2667 3094 42306906 42307319 5.100000e-178 634.0
17 TraesCS6A01G382300 chr2B 91.841 429 19 6 2666 3094 69373901 69374313 5.210000e-163 584.0
18 TraesCS6A01G382300 chr2B 86.744 347 26 8 2669 3011 411512998 411513328 5.710000e-98 368.0
19 TraesCS6A01G382300 chr2B 86.705 346 20 7 2672 3011 254696441 254696116 9.550000e-96 361.0
20 TraesCS6A01G382300 chr2B 92.969 128 9 0 2997 3124 411513345 411513472 1.720000e-43 187.0
21 TraesCS6A01G382300 chr2B 90.000 130 5 2 2997 3126 254696099 254695978 1.040000e-35 161.0
22 TraesCS6A01G382300 chrUn 93.299 388 26 0 1809 2196 480245409 480245796 1.130000e-159 573.0
23 TraesCS6A01G382300 chr5B 94.410 322 4 4 2773 3094 480411292 480410985 1.950000e-132 483.0
24 TraesCS6A01G382300 chr3B 84.308 325 8 5 2770 3094 826145296 826145577 9.900000e-71 278.0
25 TraesCS6A01G382300 chr3B 93.023 172 12 0 3124 3295 635231102 635230931 6.000000e-63 252.0
26 TraesCS6A01G382300 chr3B 81.641 256 25 10 2667 2919 519050918 519050682 3.690000e-45 193.0
27 TraesCS6A01G382300 chr3D 92.982 171 12 0 3125 3295 476564150 476563980 2.160000e-62 250.0
28 TraesCS6A01G382300 chr3D 80.952 252 31 5 2666 2916 306088143 306088378 2.220000e-42 183.0
29 TraesCS6A01G382300 chr1A 80.556 252 28 8 2672 2919 561649893 561649659 1.340000e-39 174.0
30 TraesCS6A01G382300 chr4D 98.611 72 1 0 3350 3421 5812902 5812831 1.050000e-25 128.0
31 TraesCS6A01G382300 chr4D 91.954 87 5 2 3493 3578 5812521 5812436 1.760000e-23 121.0
32 TraesCS6A01G382300 chr4B 98.611 72 1 0 3350 3421 10517749 10517678 1.050000e-25 128.0
33 TraesCS6A01G382300 chr4B 95.833 72 3 0 3350 3421 10532627 10532556 2.280000e-22 117.0
34 TraesCS6A01G382300 chr4B 88.372 86 10 0 3493 3578 10517368 10517283 1.780000e-18 104.0
35 TraesCS6A01G382300 chr4A 93.023 86 6 0 3493 3578 597725616 597725701 3.790000e-25 126.0
36 TraesCS6A01G382300 chr4A 97.222 72 2 0 3350 3421 597725235 597725306 4.910000e-24 122.0
37 TraesCS6A01G382300 chr5D 82.166 157 16 8 2861 3006 43072688 43072843 1.360000e-24 124.0
38 TraesCS6A01G382300 chr5A 95.238 63 1 1 3350 3410 637620404 637620466 8.270000e-17 99.0


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 TraesCS6A01G382300 chr6A 601395897 601399515 3618 True 6684.00 6684 100.000 1 3619 1 chr6A.!!$R1 3618
1 TraesCS6A01G382300 chr6A 601967700 601969456 1756 False 2440.00 2440 91.864 686 2434 1 chr6A.!!$F1 1748
2 TraesCS6A01G382300 chr6D 455084700 455087390 2690 True 3984.00 3984 93.558 1 2667 1 chr6D.!!$R1 2666
3 TraesCS6A01G382300 chr6D 455311343 455313466 2123 False 1137.55 2189 90.640 686 2592 2 chr6D.!!$F2 1906
4 TraesCS6A01G382300 chr6B 692488864 692490541 1677 False 2361.00 2361 91.970 724 2423 1 chr6B.!!$F1 1699
5 TraesCS6A01G382300 chr6B 691862705 691865356 2651 False 1763.70 3469 90.586 1 2647 2 chr6B.!!$F2 2646
6 TraesCS6A01G382300 chr6B 692193298 692195947 2649 True 1757.20 3456 91.445 1 2647 2 chr6B.!!$R1 2646
7 TraesCS6A01G382300 chr7A 549410516 549411457 941 False 1463.00 1463 94.555 2665 3619 1 chr7A.!!$F1 954
8 TraesCS6A01G382300 chr3A 652108082 652109008 926 False 1387.00 1387 93.396 2666 3619 1 chr3A.!!$F3 953

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
976 1081 0.101579 TCTCTTGTGAACACGCGTGA 59.898 50.0 42.94 20.79 0.00 4.35 F
1647 1794 0.252284 ACTGTCTCTGGATTCCCCGT 60.252 55.0 0.00 0.00 37.93 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2289 1.134699 CACTCGCATAGCCTTCTTGGA 60.135 52.381 0.0 0.0 38.35 3.53 R
3330 3658 1.306997 TTCCTCCTCCTCCGCCAAT 60.307 57.895 0.0 0.0 0.00 3.16 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
66 67 6.149142 ACACAAATGCACATTTTGAAACTGTT 59.851 30.769 16.18 0.00 38.84 3.16
67 68 6.466413 CACAAATGCACATTTTGAAACTGTTG 59.534 34.615 16.18 0.00 38.84 3.33
76 77 5.975693 TTTTGAAACTGTTGAACCAGTCT 57.024 34.783 0.00 0.00 44.74 3.24
77 78 7.122055 ACATTTTGAAACTGTTGAACCAGTCTA 59.878 33.333 0.00 0.00 44.74 2.59
78 79 7.639113 TTTTGAAACTGTTGAACCAGTCTAT 57.361 32.000 0.00 0.00 44.74 1.98
79 80 7.639113 TTTGAAACTGTTGAACCAGTCTATT 57.361 32.000 0.00 0.00 44.74 1.73
80 81 8.740123 TTTGAAACTGTTGAACCAGTCTATTA 57.260 30.769 0.00 0.00 44.74 0.98
111 112 4.142609 TGTGCAACTGGCCAAAATAAAA 57.857 36.364 7.01 0.00 43.89 1.52
311 314 7.444299 AGAATGGTTGCATAGTTTCAAAACAT 58.556 30.769 8.23 0.00 41.30 2.71
368 371 7.014115 GTCGATGCTATGCTCATAAGATTTTG 58.986 38.462 0.00 0.00 0.00 2.44
476 510 8.884124 TGATTTCCCTAGAAAAATCAATCAGT 57.116 30.769 20.86 0.00 44.60 3.41
721 760 3.395639 CAGTGGCTAAACTTCAACGGTA 58.604 45.455 0.00 0.00 0.00 4.02
942 1040 3.756434 CCCGTTTTACTGTGTCATTCCAT 59.244 43.478 0.00 0.00 0.00 3.41
976 1081 0.101579 TCTCTTGTGAACACGCGTGA 59.898 50.000 42.94 20.79 0.00 4.35
992 1097 0.321996 GTGAACTTCTTCGCCTCCCT 59.678 55.000 0.00 0.00 31.62 4.20
1078 1216 0.390472 CTTCTTCCGCTCTCCACCAC 60.390 60.000 0.00 0.00 0.00 4.16
1099 1237 2.332063 TCCATTTCCCGAGCAATCTC 57.668 50.000 0.00 0.00 35.99 2.75
1120 1258 1.135373 TCGCGACCTAGCTTCTTCTTG 60.135 52.381 3.71 0.00 34.40 3.02
1457 1595 0.962489 CTATCGTCGAAGAGGGCCAT 59.038 55.000 6.18 0.00 43.36 4.40
1503 1641 3.082579 GCGCTCCGGGAGATCAAGT 62.083 63.158 27.95 0.00 0.00 3.16
1509 1647 1.123077 CCGGGAGATCAAGTCCATCA 58.877 55.000 0.00 0.00 35.57 3.07
1634 1781 5.703130 GGCAGAAGATTTGTTAGAACTGTCT 59.297 40.000 0.00 0.00 37.95 3.41
1647 1794 0.252284 ACTGTCTCTGGATTCCCCGT 60.252 55.000 0.00 0.00 37.93 5.28
1832 1979 1.078848 GCTCAAGGCGATGGTGTCT 60.079 57.895 0.00 0.00 0.00 3.41
1865 2012 2.202797 CGTCTCATGGCGGTGAGG 60.203 66.667 16.55 3.84 44.51 3.86
1914 2061 2.123208 TGTCCGACAGGGTGTCCA 60.123 61.111 0.00 0.00 44.20 4.02
2159 2306 0.901827 TGTCCAAGAAGGCTATGCGA 59.098 50.000 0.00 0.00 37.29 5.10
2165 2312 0.461961 AGAAGGCTATGCGAGTGTCC 59.538 55.000 0.00 0.00 0.00 4.02
2540 2863 1.486726 AGTTAATTGGGAGGAGGAGCG 59.513 52.381 0.00 0.00 0.00 5.03
2659 2986 1.459450 TTTAAGGGCATCTCCAACGC 58.541 50.000 0.00 0.00 36.21 4.84
2761 3089 1.062488 AGTCAGGCACCCAAGACCTT 61.062 55.000 0.00 0.00 33.37 3.50
2781 3109 5.712917 ACCTTATTTTTAGCCGGATTTGACA 59.287 36.000 5.05 0.00 0.00 3.58
2819 3147 3.252284 CACCCCACACCCAGCTCT 61.252 66.667 0.00 0.00 0.00 4.09
2821 3149 2.930019 CCCCACACCCAGCTCTCA 60.930 66.667 0.00 0.00 0.00 3.27
3173 3501 1.535462 CTCCTTCACGTTCGGCAATTT 59.465 47.619 0.00 0.00 0.00 1.82
3514 3842 1.154016 CGAAGTCGAGTGCGGACAT 60.154 57.895 13.14 0.00 43.02 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.756272 AGTGTGCAATGATTATTGTGTTATGTG 59.244 33.333 11.44 0.00 44.41 3.21
26 27 6.092092 GCATTTGTGTAGTGTGCAATGATTA 58.908 36.000 0.00 0.00 35.93 1.75
76 77 8.739039 GGCCAGTTGCACATCATAAATATAATA 58.261 33.333 0.00 0.00 43.89 0.98
77 78 7.233144 TGGCCAGTTGCACATCATAAATATAAT 59.767 33.333 0.00 0.00 43.89 1.28
78 79 6.548993 TGGCCAGTTGCACATCATAAATATAA 59.451 34.615 0.00 0.00 43.89 0.98
79 80 6.067350 TGGCCAGTTGCACATCATAAATATA 58.933 36.000 0.00 0.00 43.89 0.86
80 81 4.894705 TGGCCAGTTGCACATCATAAATAT 59.105 37.500 0.00 0.00 43.89 1.28
337 340 4.495911 TGAGCATAGCATCGACTAAGAG 57.504 45.455 0.00 0.00 0.00 2.85
368 371 4.376340 AAATTTTCACGGATCTCCATGC 57.624 40.909 0.00 0.00 35.14 4.06
411 445 6.054941 TGCACTTTCAAGTCTCAGTCAAATA 58.945 36.000 0.00 0.00 37.08 1.40
413 447 4.260985 TGCACTTTCAAGTCTCAGTCAAA 58.739 39.130 0.00 0.00 37.08 2.69
594 631 7.954835 TGGCCTGATCAAATGGATAAAATTAG 58.045 34.615 3.32 0.00 36.00 1.73
721 760 1.901464 GTGGGCATGAAACACCGGT 60.901 57.895 0.00 0.00 0.00 5.28
906 959 2.196229 CGGGTTGGGTTGGGTTCA 59.804 61.111 0.00 0.00 0.00 3.18
907 960 1.044231 AAACGGGTTGGGTTGGGTTC 61.044 55.000 0.00 0.00 0.00 3.62
942 1040 9.102757 GTTCACAAGAGATTAGAGATTATTGCA 57.897 33.333 0.00 0.00 0.00 4.08
976 1081 1.003233 GCAGGGAGGCGAAGAAGTT 60.003 57.895 0.00 0.00 0.00 2.66
992 1097 0.328592 TGCGTTTTATAGGGGTGGCA 59.671 50.000 0.00 0.00 0.00 4.92
1078 1216 2.551459 GAGATTGCTCGGGAAATGGATG 59.449 50.000 0.00 0.00 0.00 3.51
1099 1237 0.736053 AGAAGAAGCTAGGTCGCGAG 59.264 55.000 10.24 0.00 34.40 5.03
1120 1258 2.873649 GCCATAGCCTGCTGTAAGATCC 60.874 54.545 0.97 0.00 34.07 3.36
1467 1605 3.726144 GGCCAGCTCCTTCTGCCT 61.726 66.667 0.00 0.00 32.87 4.75
1503 1641 2.730733 GCTCTCGGCGATGATGGA 59.269 61.111 11.27 2.33 0.00 3.41
1581 1719 0.409092 ATGGTGGCATGGTTCCTGAA 59.591 50.000 0.00 0.00 0.00 3.02
1634 1781 2.056223 GGACGACGGGGAATCCAGA 61.056 63.158 0.09 0.00 34.36 3.86
1664 1811 3.137459 CTGAGCGCGTCCTCCTCT 61.137 66.667 8.43 0.00 0.00 3.69
1893 2040 2.343758 CACCCTGTCGGACACCAG 59.656 66.667 6.76 1.40 34.64 4.00
2142 2289 1.134699 CACTCGCATAGCCTTCTTGGA 60.135 52.381 0.00 0.00 38.35 3.53
2159 2306 2.147387 GGTGGTGGTCAGGGACACT 61.147 63.158 0.00 0.00 33.68 3.55
2165 2312 2.973899 CTCTCGGTGGTGGTCAGG 59.026 66.667 0.00 0.00 0.00 3.86
2641 2968 3.168773 GCGTTGGAGATGCCCTTAA 57.831 52.632 0.00 0.00 34.03 1.85
2659 2986 1.694150 TGGAGATGCCCTAAGAATCGG 59.306 52.381 0.00 0.00 34.97 4.18
2761 3089 7.607250 ACATTTGTCAAATCCGGCTAAAAATA 58.393 30.769 7.87 0.00 0.00 1.40
2781 3109 3.806422 GCGCCGGCCGTAACATTT 61.806 61.111 26.12 0.00 39.71 2.32
3330 3658 1.306997 TTCCTCCTCCTCCGCCAAT 60.307 57.895 0.00 0.00 0.00 3.16
3375 3703 3.064324 GCCAACGGAGCCAAGCAT 61.064 61.111 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.