Multiple sequence alignment - TraesCS1D01G150600

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 TraesCS1D01G150600 chr1D 100.000 4760 0 0 1 4760 208412370 208407611 0.000000e+00 8791.0
1 TraesCS1D01G150600 chr1D 96.368 1900 48 7 2032 3913 227653418 227655314 0.000000e+00 3107.0
2 TraesCS1D01G150600 chr1D 91.760 716 35 7 843 1552 227652181 227652878 0.000000e+00 974.0
3 TraesCS1D01G150600 chr1D 89.985 689 38 10 160 836 227650824 227651493 0.000000e+00 861.0
4 TraesCS1D01G150600 chr1D 90.030 662 63 2 3250 3908 477789530 477788869 0.000000e+00 854.0
5 TraesCS1D01G150600 chr1D 91.927 545 42 2 2666 3208 477790072 477789528 0.000000e+00 761.0
6 TraesCS1D01G150600 chr1D 84.701 804 65 19 1835 2626 477791035 477790278 0.000000e+00 750.0
7 TraesCS1D01G150600 chr1D 97.214 359 10 0 1677 2035 227652902 227653260 4.070000e-170 608.0
8 TraesCS1D01G150600 chr1D 83.596 445 46 15 760 1185 477792243 477791807 4.470000e-105 392.0
9 TraesCS1D01G150600 chr1D 98.068 207 3 1 3910 4115 227655416 227655622 4.530000e-95 359.0
10 TraesCS1D01G150600 chr1D 83.166 398 57 9 2707 3098 223163464 223163857 5.860000e-94 355.0
11 TraesCS1D01G150600 chr1D 84.348 345 54 0 2754 3098 226944382 226944726 5.900000e-89 339.0
12 TraesCS1D01G150600 chr1D 81.726 394 70 2 2707 3098 261723871 261724264 1.280000e-85 327.0
13 TraesCS1D01G150600 chr1D 90.960 177 10 3 1 174 227650458 227650631 2.860000e-57 233.0
14 TraesCS1D01G150600 chr1D 93.578 109 7 0 1682 1790 477791138 477791030 3.810000e-36 163.0
15 TraesCS1D01G150600 chr1D 89.147 129 11 1 1176 1301 477791786 477791658 1.770000e-34 158.0
16 TraesCS1D01G150600 chr1D 78.537 205 38 6 1830 2033 457811693 457811892 3.870000e-26 130.0
17 TraesCS1D01G150600 chr1D 78.537 205 38 6 1830 2033 457812205 457812404 3.870000e-26 130.0
18 TraesCS1D01G150600 chr1D 100.000 29 0 0 1362 1390 477791602 477791574 2.000000e-03 54.7
19 TraesCS1D01G150600 chr1B 97.099 4791 84 21 1 4760 327346075 327350841 0.000000e+00 8026.0
20 TraesCS1D01G150600 chr1B 89.857 1469 123 12 2666 4111 665244982 665243517 0.000000e+00 1864.0
21 TraesCS1D01G150600 chr1B 84.340 811 62 20 1835 2626 665246283 665245519 0.000000e+00 734.0
22 TraesCS1D01G150600 chr1B 77.669 1124 111 70 325 1390 665247655 665246614 1.500000e-154 556.0
23 TraesCS1D01G150600 chr1B 82.609 391 66 2 2710 3098 327228843 327229233 1.270000e-90 344.0
24 TraesCS1D01G150600 chr1A 95.587 1949 52 9 2138 4065 294514588 294516523 0.000000e+00 3092.0
25 TraesCS1D01G150600 chr1A 91.667 1860 70 25 312 2141 294512662 294514466 0.000000e+00 2497.0
26 TraesCS1D01G150600 chr1A 86.842 988 110 13 3133 4110 574271927 574270950 0.000000e+00 1086.0
27 TraesCS1D01G150600 chr1A 91.460 644 37 3 4119 4760 249063273 249063900 0.000000e+00 869.0
28 TraesCS1D01G150600 chr1A 84.826 804 64 20 1835 2626 574273357 574272600 0.000000e+00 756.0
29 TraesCS1D01G150600 chr1A 91.405 477 39 2 2666 3140 574272515 574272039 0.000000e+00 652.0
30 TraesCS1D01G150600 chr1A 82.305 616 66 24 760 1352 574274337 574273742 1.190000e-135 494.0
31 TraesCS1D01G150600 chr1A 82.864 391 65 2 2710 3098 294040638 294041028 2.730000e-92 350.0
32 TraesCS1D01G150600 chr1A 81.395 344 64 0 2759 3102 550299399 550299742 1.010000e-71 281.0
33 TraesCS1D01G150600 chr1A 81.595 326 60 0 2777 3102 550136618 550136293 2.180000e-68 270.0
34 TraesCS1D01G150600 chr1A 80.636 346 67 0 2757 3102 550218062 550218407 7.850000e-68 268.0
35 TraesCS1D01G150600 chr1A 82.110 218 28 6 158 366 294512463 294512678 4.900000e-40 176.0
36 TraesCS1D01G150600 chr4D 95.016 642 14 3 4119 4760 214679987 214679364 0.000000e+00 992.0
37 TraesCS1D01G150600 chr3D 94.565 644 17 3 4119 4760 612007365 612006738 0.000000e+00 979.0
38 TraesCS1D01G150600 chr3D 92.391 644 31 3 4119 4760 577965657 577966284 0.000000e+00 902.0
39 TraesCS1D01G150600 chr7D 94.410 644 17 4 4119 4760 530942965 530942339 0.000000e+00 972.0
40 TraesCS1D01G150600 chr7D 83.168 404 61 7 2749 3150 90409577 90409975 3.500000e-96 363.0
41 TraesCS1D01G150600 chr7D 83.929 168 21 4 1835 1997 90408585 90408751 6.380000e-34 156.0
42 TraesCS1D01G150600 chr4B 93.944 644 19 5 4119 4760 65980930 65980305 0.000000e+00 955.0
43 TraesCS1D01G150600 chr4B 100.000 42 0 0 1637 1678 273429729 273429688 1.420000e-10 78.7
44 TraesCS1D01G150600 chr4B 94.231 52 1 2 1637 1687 483504878 483504928 1.420000e-10 78.7
45 TraesCS1D01G150600 chr6B 92.857 644 28 3 4119 4760 16388951 16388324 0.000000e+00 918.0
46 TraesCS1D01G150600 chr5D 91.460 644 37 4 4119 4760 562695648 562696275 0.000000e+00 869.0
47 TraesCS1D01G150600 chr7B 83.960 399 59 5 2753 3150 41285508 41285902 1.250000e-100 377.0
48 TraesCS1D01G150600 chr4A 100.000 43 0 0 1637 1679 455277528 455277570 3.950000e-11 80.5
49 TraesCS1D01G150600 chr2A 95.745 47 2 0 1637 1683 385679781 385679735 5.110000e-10 76.8
50 TraesCS1D01G150600 chr7A 95.652 46 2 0 1636 1681 438993281 438993236 1.840000e-09 75.0
51 TraesCS1D01G150600 chrUn 92.157 51 3 1 1637 1686 5996372 5996422 2.380000e-08 71.3
52 TraesCS1D01G150600 chr3A 89.286 56 5 1 1628 1682 606010362 606010417 8.550000e-08 69.4


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 TraesCS1D01G150600 chr1D 208407611 208412370 4759 True 8791.000000 8791 100.000000 1 4760 1 chr1D.!!$R1 4759
1 TraesCS1D01G150600 chr1D 227650458 227655622 5164 False 1023.666667 3107 94.059167 1 4115 6 chr1D.!!$F4 4114
2 TraesCS1D01G150600 chr1D 477788869 477792243 3374 True 447.528571 854 90.425571 760 3908 7 chr1D.!!$R2 3148
3 TraesCS1D01G150600 chr1B 327346075 327350841 4766 False 8026.000000 8026 97.099000 1 4760 1 chr1B.!!$F2 4759
4 TraesCS1D01G150600 chr1B 665243517 665247655 4138 True 1051.333333 1864 83.955333 325 4111 3 chr1B.!!$R1 3786
5 TraesCS1D01G150600 chr1A 294512463 294516523 4060 False 1921.666667 3092 89.788000 158 4065 3 chr1A.!!$F5 3907
6 TraesCS1D01G150600 chr1A 249063273 249063900 627 False 869.000000 869 91.460000 4119 4760 1 chr1A.!!$F1 641
7 TraesCS1D01G150600 chr1A 574270950 574274337 3387 True 747.000000 1086 86.344500 760 4110 4 chr1A.!!$R2 3350
8 TraesCS1D01G150600 chr4D 214679364 214679987 623 True 992.000000 992 95.016000 4119 4760 1 chr4D.!!$R1 641
9 TraesCS1D01G150600 chr3D 612006738 612007365 627 True 979.000000 979 94.565000 4119 4760 1 chr3D.!!$R1 641
10 TraesCS1D01G150600 chr3D 577965657 577966284 627 False 902.000000 902 92.391000 4119 4760 1 chr3D.!!$F1 641
11 TraesCS1D01G150600 chr7D 530942339 530942965 626 True 972.000000 972 94.410000 4119 4760 1 chr7D.!!$R1 641
12 TraesCS1D01G150600 chr7D 90408585 90409975 1390 False 259.500000 363 83.548500 1835 3150 2 chr7D.!!$F1 1315
13 TraesCS1D01G150600 chr4B 65980305 65980930 625 True 955.000000 955 93.944000 4119 4760 1 chr4B.!!$R1 641
14 TraesCS1D01G150600 chr6B 16388324 16388951 627 True 918.000000 918 92.857000 4119 4760 1 chr6B.!!$R1 641
15 TraesCS1D01G150600 chr5D 562695648 562696275 627 False 869.000000 869 91.460000 4119 4760 1 chr5D.!!$F1 641

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
254 464 0.179040 TCTTTCCTTTGTCCGCCGTT 60.179 50.000 0.0 0.0 0.00 4.44 F
288 498 1.075600 CCAGGAGGAGGAGGAGGAC 60.076 68.421 0.0 0.0 36.89 3.85 F
1308 2385 1.151450 CTCTTGTGCCCCTGTGGTT 59.849 57.895 0.0 0.0 36.04 3.67 F
1833 3196 1.473434 CCTTTCCCTGGACTCGTATGC 60.473 57.143 0.0 0.0 0.00 3.14 F
3242 5854 0.107456 CTCCCGTGCTCTATGCCAAT 59.893 55.000 0.0 0.0 42.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 3289 2.296190 TGTCTCAAGTAGCGCTGAGAAA 59.704 45.455 23.70 18.02 38.87 2.52 R
2176 3839 5.119931 AGAAGCATGATTAGCGAGAGTAG 57.880 43.478 0.00 0.00 37.01 2.57 R
3214 5826 3.083122 AGAGCACGGGAGAAGTACTTA 57.917 47.619 8.42 0.00 0.00 2.24 R
3625 6253 2.644299 TGAACCTGAAGTGATGGTGGAT 59.356 45.455 0.00 0.00 33.89 3.41 R
4156 6900 2.123589 TCTTTTCCTGACACCCACTGA 58.876 47.619 0.00 0.00 0.00 3.41 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
71 72 6.159293 AGTACTTGTATATGCATGGATGACG 58.841 40.000 10.16 0.00 0.00 4.35
254 464 0.179040 TCTTTCCTTTGTCCGCCGTT 60.179 50.000 0.00 0.00 0.00 4.44
288 498 1.075600 CCAGGAGGAGGAGGAGGAC 60.076 68.421 0.00 0.00 36.89 3.85
522 810 2.900273 CTTCGATCTGCCCCCGAA 59.100 61.111 0.00 0.00 39.58 4.30
618 911 3.131223 TCTCTATCTTTTCACCTGCCTCG 59.869 47.826 0.00 0.00 0.00 4.63
645 939 1.530323 AAGAACAAACGATTCCCGGG 58.470 50.000 16.85 16.85 43.93 5.73
844 1834 3.355378 TGTCCTCGGCAAATTGATTGAT 58.645 40.909 0.00 0.00 41.85 2.57
845 1835 3.763360 TGTCCTCGGCAAATTGATTGATT 59.237 39.130 0.00 0.00 41.85 2.57
846 1836 4.107622 GTCCTCGGCAAATTGATTGATTG 58.892 43.478 0.00 0.00 41.85 2.67
847 1837 4.015764 TCCTCGGCAAATTGATTGATTGA 58.984 39.130 0.00 0.00 41.85 2.57
932 1935 5.591643 TTTCGTCAAGATTTGCACTACTC 57.408 39.130 0.00 0.00 0.00 2.59
1034 2051 5.395324 CCGGGAGTACATGTATGTCTTCTTT 60.395 44.000 9.18 0.00 41.97 2.52
1040 2058 7.680730 AGTACATGTATGTCTTCTTTGTCCTT 58.319 34.615 9.18 0.00 41.97 3.36
1060 2078 8.621286 TGTCCTTTTTCTAGTTGAAATTCAGAC 58.379 33.333 0.53 6.77 43.34 3.51
1062 2080 9.057089 TCCTTTTTCTAGTTGAAATTCAGACTC 57.943 33.333 11.89 0.00 43.34 3.36
1099 2117 5.421056 ACGGAAGACACATACCAATTAGAGA 59.579 40.000 0.00 0.00 0.00 3.10
1108 2126 7.831193 ACACATACCAATTAGAGAGCTCATTTT 59.169 33.333 17.77 0.00 0.00 1.82
1308 2385 1.151450 CTCTTGTGCCCCTGTGGTT 59.849 57.895 0.00 0.00 36.04 3.67
1401 2499 3.244875 TGGCTGATGACCAAACATACACT 60.245 43.478 0.00 0.00 33.12 3.55
1827 3190 2.375509 TCCTTTTCCTTTCCCTGGACTC 59.624 50.000 0.00 0.00 32.65 3.36
1833 3196 1.473434 CCTTTCCCTGGACTCGTATGC 60.473 57.143 0.00 0.00 0.00 3.14
1922 3289 7.364056 CCACATTTACAATGGAAGGTTCATGAT 60.364 37.037 0.00 0.00 35.33 2.45
3214 5826 4.454728 TTACTAATTTCGTAGTGGCCGT 57.545 40.909 0.00 0.00 35.85 5.68
3242 5854 0.107456 CTCCCGTGCTCTATGCCAAT 59.893 55.000 0.00 0.00 42.00 3.16
3583 6211 0.679321 ACGAGTCCGGGAAGGTAGTC 60.679 60.000 0.00 0.00 41.99 2.59
3625 6253 3.358118 AGACCAAAAGAACGGGAAACAA 58.642 40.909 0.00 0.00 0.00 2.83
4156 6900 7.067008 TGTTTCTTTTGTCCTTTTTCGAGATCT 59.933 33.333 0.00 0.00 0.00 2.75
4381 7125 0.525242 CACGTGGGCGCAAATATTGG 60.525 55.000 10.83 0.00 42.83 3.16
4382 7126 1.065600 CGTGGGCGCAAATATTGGG 59.934 57.895 10.83 3.09 45.41 4.12
4393 7137 5.219633 CGCAAATATTGGGCAATAAGTACC 58.780 41.667 11.55 0.00 36.90 3.34
4394 7138 5.009610 CGCAAATATTGGGCAATAAGTACCT 59.990 40.000 11.55 0.00 36.90 3.08
4395 7139 6.460953 CGCAAATATTGGGCAATAAGTACCTT 60.461 38.462 11.55 0.00 36.90 3.50
4396 7140 6.701400 GCAAATATTGGGCAATAAGTACCTTG 59.299 38.462 7.33 0.00 36.90 3.61
4610 7358 9.499369 AGTATCCCTCTCTATAATATTGTGCAT 57.501 33.333 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
254 464 2.758423 TCCTGGAGATCGAAACGAATGA 59.242 45.455 0.00 0.00 39.99 2.57
288 498 0.879090 GGACAAGTTAAACGCCCTGG 59.121 55.000 0.00 0.00 0.00 4.45
409 683 2.200955 GTGGGGATTCCTTCCTCTCTT 58.799 52.381 2.01 0.00 46.38 2.85
522 810 1.202940 GGAGAAAGACCTGGCTTGGTT 60.203 52.381 4.42 0.00 41.00 3.67
618 911 4.467735 GAATCGTTTGTTCTTTCCAGAGC 58.532 43.478 0.00 0.00 0.00 4.09
645 939 2.304221 AAACCCTAAAACCCTCTGCC 57.696 50.000 0.00 0.00 0.00 4.85
726 1021 5.758924 AGGTTCAGCTTTGTCGAAAATAAC 58.241 37.500 0.00 0.00 0.00 1.89
844 1834 5.613329 ACTTACCACTTGGACGTAAATCAA 58.387 37.500 1.14 0.00 38.94 2.57
845 1835 5.217978 ACTTACCACTTGGACGTAAATCA 57.782 39.130 1.14 0.00 38.94 2.57
846 1836 5.232463 TGACTTACCACTTGGACGTAAATC 58.768 41.667 1.14 0.00 38.94 2.17
847 1837 5.217978 TGACTTACCACTTGGACGTAAAT 57.782 39.130 1.14 0.00 38.94 1.40
1060 2078 8.141909 TGTGTCTTCCGTTTATAATATGGAGAG 58.858 37.037 7.96 8.61 32.50 3.20
1062 2080 8.833231 ATGTGTCTTCCGTTTATAATATGGAG 57.167 34.615 7.96 5.00 32.50 3.86
1064 2082 8.932791 GGTATGTGTCTTCCGTTTATAATATGG 58.067 37.037 0.00 0.00 0.00 2.74
1308 2385 3.492011 CGATCGATGATTGTTGCATGAGA 59.508 43.478 10.26 0.00 0.00 3.27
1547 2647 8.634444 CCCCCTATCTATGAGAATAGTTATTCG 58.366 40.741 6.30 0.00 45.10 3.34
1833 3196 3.872771 ACAAAGGCAGCAACTCAAAATTG 59.127 39.130 0.00 0.00 0.00 2.32
1922 3289 2.296190 TGTCTCAAGTAGCGCTGAGAAA 59.704 45.455 23.70 18.02 38.87 2.52
2176 3839 5.119931 AGAAGCATGATTAGCGAGAGTAG 57.880 43.478 0.00 0.00 37.01 2.57
3214 5826 3.083122 AGAGCACGGGAGAAGTACTTA 57.917 47.619 8.42 0.00 0.00 2.24
3583 6211 6.349777 GGTCTAGGATGGATAGAGTCAATTCG 60.350 46.154 0.00 0.00 30.04 3.34
3625 6253 2.644299 TGAACCTGAAGTGATGGTGGAT 59.356 45.455 0.00 0.00 33.89 3.41
4156 6900 2.123589 TCTTTTCCTGACACCCACTGA 58.876 47.619 0.00 0.00 0.00 3.41
4384 7128 7.092128 AGGTACTTATTGCCCAAGGTACTTATT 60.092 37.037 14.82 0.00 43.37 1.40
4385 7129 6.388983 AGGTACTTATTGCCCAAGGTACTTAT 59.611 38.462 14.82 0.00 43.37 1.73
4386 7130 5.727766 AGGTACTTATTGCCCAAGGTACTTA 59.272 40.000 14.82 0.00 43.37 2.24
4387 7131 4.538891 AGGTACTTATTGCCCAAGGTACTT 59.461 41.667 14.82 9.21 46.81 2.24
4388 7132 4.109320 AGGTACTTATTGCCCAAGGTACT 58.891 43.478 14.82 0.00 34.02 2.73
4389 7133 4.498894 AGGTACTTATTGCCCAAGGTAC 57.501 45.455 0.00 10.45 27.25 3.34
4610 7358 3.925379 TGCAACATAAGCTTCTCTTCGA 58.075 40.909 0.00 0.00 36.25 3.71


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

AutoCloner maintained by Alex Coulton.