Multiple sequence alignment - TraesCS5D01G295700

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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 TraesCS5D01G295700 chr5D 100.000 2938 0 0 746 3683 393619846 393616909 0.000000e+00 5426.0
1 TraesCS5D01G295700 chr5D 90.785 1910 120 17 1038 2946 393739221 393737367 0.000000e+00 2501.0
2 TraesCS5D01G295700 chr5D 100.000 486 0 0 1 486 393620591 393620106 0.000000e+00 898.0
3 TraesCS5D01G295700 chr5D 85.482 861 107 16 2823 3676 393737014 393736165 0.000000e+00 881.0
4 TraesCS5D01G295700 chr5D 84.026 313 32 13 1 304 393740761 393740458 6.020000e-73 285.0
5 TraesCS5D01G295700 chr5B 96.754 2249 61 5 746 2991 473520546 473518307 0.000000e+00 3738.0
6 TraesCS5D01G295700 chr5B 90.589 1902 133 23 1046 2946 473610438 473608582 0.000000e+00 2479.0
7 TraesCS5D01G295700 chr5B 86.909 1543 182 13 1139 2671 700945311 700946843 0.000000e+00 1712.0
8 TraesCS5D01G295700 chr5B 87.146 1517 178 12 1157 2671 701003445 701001944 0.000000e+00 1705.0
9 TraesCS5D01G295700 chr5B 96.708 486 16 0 1 486 473521024 473520539 0.000000e+00 809.0
10 TraesCS5D01G295700 chr5B 85.026 768 98 14 2827 3586 473608252 473607494 0.000000e+00 765.0
11 TraesCS5D01G295700 chr5B 90.927 507 25 9 1 486 473602789 473602283 0.000000e+00 662.0
12 TraesCS5D01G295700 chr5B 86.125 591 70 10 3098 3683 473518297 473517714 8.680000e-176 627.0
13 TraesCS5D01G295700 chr5B 86.709 316 28 6 1 304 473624378 473624065 4.560000e-89 339.0
14 TraesCS5D01G295700 chr5B 93.478 138 9 0 746 883 473602284 473602147 4.820000e-49 206.0
15 TraesCS5D01G295700 chr5A 96.205 2240 62 8 746 2974 495397822 495395595 0.000000e+00 3644.0
16 TraesCS5D01G295700 chr5A 89.730 1850 137 19 1038 2886 663336572 663338369 0.000000e+00 2314.0
17 TraesCS5D01G295700 chr5A 89.213 1854 143 20 1038 2890 495728892 495727095 0.000000e+00 2263.0
18 TraesCS5D01G295700 chr5A 88.653 1789 152 14 1038 2826 495819926 495818189 0.000000e+00 2132.0
19 TraesCS5D01G295700 chr5A 92.400 500 35 3 2964 3461 495395423 495394925 0.000000e+00 710.0
20 TraesCS5D01G295700 chr5A 95.577 407 16 2 1 405 495398251 495397845 0.000000e+00 651.0
21 TraesCS5D01G295700 chr5A 85.582 541 61 10 3102 3634 495578969 495578438 5.380000e-153 551.0
22 TraesCS5D01G295700 chr5A 90.358 363 27 6 2595 2955 495585157 495584801 1.550000e-128 470.0
23 TraesCS5D01G295700 chr5A 94.850 233 8 3 3455 3683 495381548 495381316 9.720000e-96 361.0
24 TraesCS5D01G295700 chr5A 84.713 314 24 7 1 299 495730443 495730139 3.600000e-75 292.0
25 TraesCS5D01G295700 chr5A 83.072 319 31 8 1 304 495821237 495820927 6.060000e-68 268.0
26 TraesCS5D01G295700 chr5A 90.217 184 12 3 2707 2890 495586880 495586703 6.150000e-58 235.0
27 TraesCS5D01G295700 chr5A 85.366 82 9 3 3111 3191 671523231 671523152 8.480000e-12 82.4
28 TraesCS5D01G295700 chr5A 97.778 45 1 0 3639 3683 495578403 495578359 1.100000e-10 78.7
29 TraesCS5D01G295700 chr4A 87.434 1512 176 8 1157 2664 620950969 620952470 0.000000e+00 1727.0
30 TraesCS5D01G295700 chr7B 87.848 1292 151 4 1368 2657 559561840 559563127 0.000000e+00 1511.0
31 TraesCS5D01G295700 chr1A 97.368 38 1 0 2978 3015 254184642 254184679 8.540000e-07 65.8


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 TraesCS5D01G295700 chr5D 393616909 393620591 3682 True 3162.000000 5426 100.000000 1 3683 2 chr5D.!!$R1 3682
1 TraesCS5D01G295700 chr5D 393736165 393740761 4596 True 1222.333333 2501 86.764333 1 3676 3 chr5D.!!$R2 3675
2 TraesCS5D01G295700 chr5B 473517714 473521024 3310 True 1724.666667 3738 93.195667 1 3683 3 chr5B.!!$R3 3682
3 TraesCS5D01G295700 chr5B 700945311 700946843 1532 False 1712.000000 1712 86.909000 1139 2671 1 chr5B.!!$F1 1532
4 TraesCS5D01G295700 chr5B 701001944 701003445 1501 True 1705.000000 1705 87.146000 1157 2671 1 chr5B.!!$R2 1514
5 TraesCS5D01G295700 chr5B 473607494 473610438 2944 True 1622.000000 2479 87.807500 1046 3586 2 chr5B.!!$R5 2540
6 TraesCS5D01G295700 chr5B 473602147 473602789 642 True 434.000000 662 92.202500 1 883 2 chr5B.!!$R4 882
7 TraesCS5D01G295700 chr5A 663336572 663338369 1797 False 2314.000000 2314 89.730000 1038 2886 1 chr5A.!!$F1 1848
8 TraesCS5D01G295700 chr5A 495394925 495398251 3326 True 1668.333333 3644 94.727333 1 3461 3 chr5A.!!$R3 3460
9 TraesCS5D01G295700 chr5A 495727095 495730443 3348 True 1277.500000 2263 86.963000 1 2890 2 chr5A.!!$R6 2889
10 TraesCS5D01G295700 chr5A 495818189 495821237 3048 True 1200.000000 2132 85.862500 1 2826 2 chr5A.!!$R7 2825
11 TraesCS5D01G295700 chr5A 495584801 495586880 2079 True 352.500000 470 90.287500 2595 2955 2 chr5A.!!$R5 360
12 TraesCS5D01G295700 chr5A 495578359 495578969 610 True 314.850000 551 91.680000 3102 3683 2 chr5A.!!$R4 581
13 TraesCS5D01G295700 chr4A 620950969 620952470 1501 False 1727.000000 1727 87.434000 1157 2664 1 chr4A.!!$F1 1507
14 TraesCS5D01G295700 chr7B 559561840 559563127 1287 False 1511.000000 1511 87.848000 1368 2657 1 chr7B.!!$F1 1289

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
452 489 0.419459 ATGGGAAGAGGGAGTGACCT 59.581 55.000 0.00 0.0 45.57 3.85 F
461 498 1.142748 GGAGTGACCTGCGGATCTG 59.857 63.158 0.00 0.0 35.41 2.90 F
1076 2291 3.807538 CCGACGACCGTCCACGAT 61.808 66.667 15.74 0.0 41.76 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 2812 3.386237 GCCTGTCGACCTGCTCCT 61.386 66.667 14.12 0.0 0.00 3.69 R
1638 2858 3.909258 CTCGTCCAACGACACCGGG 62.909 68.421 6.32 0.0 46.73 5.73 R
2874 4130 3.195825 ACTTTACTCAGAAGACCCGATGG 59.804 47.826 0.00 0.0 37.80 3.51 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
149 150 4.082125 ACAAGTCATTGACCTGGATTTCC 58.918 43.478 17.45 0.00 38.83 3.13
187 188 9.681062 TTCCAAAGGGATCTAAAATAACAGTAG 57.319 33.333 0.00 0.00 44.48 2.57
329 347 5.833082 TCTGACCTGAAATATAAGTCGCTC 58.167 41.667 0.00 0.00 0.00 5.03
383 401 2.997584 CGGGGAGAGGGAGAGGACA 61.998 68.421 0.00 0.00 0.00 4.02
452 489 0.419459 ATGGGAAGAGGGAGTGACCT 59.581 55.000 0.00 0.00 45.57 3.85
461 498 1.142748 GGAGTGACCTGCGGATCTG 59.857 63.158 0.00 0.00 35.41 2.90
769 816 7.111247 GAGAGAGAGATGAGAAAATCTGGAA 57.889 40.000 0.00 0.00 37.03 3.53
778 825 4.230272 TGAGAAAATCTGGAATGGATGGGA 59.770 41.667 0.00 0.00 0.00 4.37
840 887 9.352784 CGAGGATAGTTTTGCAAAATGATTTTA 57.647 29.630 26.24 12.75 0.00 1.52
934 982 6.322201 AGCATGGGGTATAAGAAATTGTTCAG 59.678 38.462 0.00 0.00 36.09 3.02
1008 1057 7.214467 TCTTACAGGAATTTCAATGTTGGAC 57.786 36.000 10.58 0.00 0.00 4.02
1076 2291 3.807538 CCGACGACCGTCCACGAT 61.808 66.667 15.74 0.00 41.76 3.73
2560 3804 0.038892 GTTGTACGGCTTCGAGTGGA 60.039 55.000 0.00 0.00 37.63 4.02
2729 3983 6.482524 AGCTCTGGTAGTGGTATATATCGAA 58.517 40.000 0.00 0.00 0.00 3.71
2874 4130 4.558860 GCACAAATTTGCTCCGAGTTTATC 59.441 41.667 18.12 0.00 39.59 1.75
2925 4181 9.645128 AAATGTAATGGGACTATGATTGATTCA 57.355 29.630 0.00 0.00 39.12 2.57
2926 4182 8.859236 ATGTAATGGGACTATGATTGATTCAG 57.141 34.615 0.00 0.00 37.89 3.02
3155 5069 6.928520 ACTAAATTTTTCATCCTTCAGCCAG 58.071 36.000 0.00 0.00 0.00 4.85
3174 5088 7.814107 TCAGCCAGCTAAATTTGTCATAAAAAG 59.186 33.333 0.00 0.00 0.00 2.27
3386 5300 3.945981 AAATGATCAGCATGCACACAA 57.054 38.095 21.98 2.37 37.28 3.33
3486 5401 3.730761 GTTGTGCTCAGGCTGCCG 61.731 66.667 13.96 8.60 39.59 5.69
3579 5501 1.298014 GGGTGAAGAGCAGAGGGTG 59.702 63.158 0.00 0.00 0.00 4.61
3609 5531 4.608170 ATTCCAGGCCCTCTTTCAAATA 57.392 40.909 0.00 0.00 0.00 1.40
3624 5546 9.736023 CTCTTTCAAATAAGTACAAAGTTTGCT 57.264 29.630 15.59 2.81 31.64 3.91
3648 5600 0.601057 CGAATTTCAAAAGGCCGGGT 59.399 50.000 2.18 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 150 5.806654 TCCCTTTGGAAAGATGGAAAAAG 57.193 39.130 0.47 0.00 37.86 2.27
187 188 6.385649 TTTGAAGACACCTAAATGTTGTCC 57.614 37.500 0.00 0.00 31.24 4.02
207 208 6.738200 CGTAATATGCCATCGCTCTTAATTTG 59.262 38.462 0.00 0.00 35.36 2.32
329 347 1.787155 CGCTGGTCGGAAAATATCTCG 59.213 52.381 0.00 0.00 33.78 4.04
383 401 0.036010 CTTTCCATGTCCCTGTCGCT 60.036 55.000 0.00 0.00 0.00 4.93
434 471 0.545309 CAGGTCACTCCCTCTTCCCA 60.545 60.000 0.00 0.00 36.75 4.37
452 489 0.548510 TCTCTCTCTCCAGATCCGCA 59.451 55.000 0.00 0.00 0.00 5.69
461 498 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
745 792 6.713762 TCCAGATTTTCTCATCTCTCTCTC 57.286 41.667 0.00 0.00 30.50 3.20
746 793 7.419287 CCATTCCAGATTTTCTCATCTCTCTCT 60.419 40.741 0.00 0.00 30.50 3.10
747 794 6.707161 CCATTCCAGATTTTCTCATCTCTCTC 59.293 42.308 0.00 0.00 30.50 3.20
748 795 6.386342 TCCATTCCAGATTTTCTCATCTCTCT 59.614 38.462 0.00 0.00 30.50 3.10
749 796 6.590068 TCCATTCCAGATTTTCTCATCTCTC 58.410 40.000 0.00 0.00 30.50 3.20
752 799 6.069331 CCATCCATTCCAGATTTTCTCATCT 58.931 40.000 0.00 0.00 33.44 2.90
753 800 5.243283 CCCATCCATTCCAGATTTTCTCATC 59.757 44.000 0.00 0.00 0.00 2.92
754 801 5.103387 TCCCATCCATTCCAGATTTTCTCAT 60.103 40.000 0.00 0.00 0.00 2.90
769 816 0.467384 CACTCGCTCTTCCCATCCAT 59.533 55.000 0.00 0.00 0.00 3.41
778 825 2.259818 CGCAGTCCACTCGCTCTT 59.740 61.111 0.00 0.00 0.00 2.85
840 887 6.208204 AGCTTTTCTACTGCAAATTCTGTCAT 59.792 34.615 0.00 0.00 0.00 3.06
883 930 9.812347 TGAATACTCCCTTCGTACCTAAATATA 57.188 33.333 0.00 0.00 0.00 0.86
884 931 8.716674 TGAATACTCCCTTCGTACCTAAATAT 57.283 34.615 0.00 0.00 0.00 1.28
886 933 6.462628 GCTGAATACTCCCTTCGTACCTAAAT 60.463 42.308 0.00 0.00 0.00 1.40
887 934 5.163478 GCTGAATACTCCCTTCGTACCTAAA 60.163 44.000 0.00 0.00 0.00 1.85
888 935 4.340381 GCTGAATACTCCCTTCGTACCTAA 59.660 45.833 0.00 0.00 0.00 2.69
934 982 9.516314 AAACACTAGAATTTGTTTTTCACTAGC 57.484 29.630 0.00 0.00 42.04 3.42
1008 1057 1.073125 TGGACACCATGTACCAGTTGG 59.927 52.381 0.00 0.00 42.17 3.77
1076 2291 4.056125 CGGACGAGGTGCTGCTGA 62.056 66.667 0.00 0.00 0.00 4.26
1592 2812 3.386237 GCCTGTCGACCTGCTCCT 61.386 66.667 14.12 0.00 0.00 3.69
1638 2858 3.909258 CTCGTCCAACGACACCGGG 62.909 68.421 6.32 0.00 46.73 5.73
2560 3804 3.801997 CATCCCCTCCGGCAGCTT 61.802 66.667 0.00 0.00 0.00 3.74
2874 4130 3.195825 ACTTTACTCAGAAGACCCGATGG 59.804 47.826 0.00 0.00 37.80 3.51
3045 4959 8.576442 CAACTAAACTTACCATCCTTCACAAAT 58.424 33.333 0.00 0.00 0.00 2.32
3127 5041 9.875691 GGCTGAAGGATGAAAAATTTAGTTTAT 57.124 29.630 0.00 0.00 0.00 1.40
3155 5069 9.176181 TCGAACACTTTTTATGACAAATTTAGC 57.824 29.630 0.00 0.00 0.00 3.09
3174 5088 2.352503 AAGCATGGCAAATCGAACAC 57.647 45.000 0.00 0.00 0.00 3.32
3236 5150 7.283807 TGCACAAAAGAATGCTGATAGTATCAT 59.716 33.333 13.22 0.00 42.55 2.45
3369 5283 3.945981 AAATTGTGTGCATGCTGATCA 57.054 38.095 20.33 9.96 0.00 2.92
3444 5359 5.914898 AGTGGATGCCTAAATGGTTAAAC 57.085 39.130 0.00 0.00 38.35 2.01
3511 5429 7.839680 AATATCCGAATCTAAAGGGCAATTT 57.160 32.000 0.00 0.00 0.00 1.82
3513 5431 7.839680 AAAATATCCGAATCTAAAGGGCAAT 57.160 32.000 0.00 0.00 0.00 3.56
3563 5485 1.609320 GGAACACCCTCTGCTCTTCAC 60.609 57.143 0.00 0.00 0.00 3.18
3579 5501 1.186200 GGGCCTGGAATTCTTGGAAC 58.814 55.000 17.32 10.63 0.00 3.62


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

AutoCloner maintained by Alex Coulton.