Multiple sequence alignment - TraesCS1D01G022300

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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 TraesCS1D01G022300 chr1D 100.000 3894 0 0 1 3894 9439832 9443725 0.000000e+00 7191
1 TraesCS1D01G022300 chr1D 100.000 303 0 0 4180 4482 9444011 9444313 1.090000e-155 560
2 TraesCS1D01G022300 chr1A 94.724 2028 96 6 1876 3894 10749736 10751761 0.000000e+00 3142
3 TraesCS1D01G022300 chr1A 91.498 1435 92 17 485 1897 10748298 10749724 0.000000e+00 1947
4 TraesCS1D01G022300 chr1A 92.638 163 10 1 4182 4342 10752251 10752413 2.700000e-57 233
5 TraesCS1D01G022300 chr1A 92.308 143 10 1 4340 4482 10797328 10797469 7.600000e-48 202
6 TraesCS1D01G022300 chr1A 85.222 203 20 7 196 394 10720181 10720377 2.730000e-47 200
7 TraesCS1D01G022300 chr1A 90.667 75 5 1 4229 4301 10752166 10752240 1.030000e-16 99
8 TraesCS1D01G022300 chr1B 97.106 1624 44 3 1876 3498 12786110 12787731 0.000000e+00 2736
9 TraesCS1D01G022300 chr1B 93.605 1423 77 11 485 1897 12784681 12786099 0.000000e+00 2111
10 TraesCS1D01G022300 chr1B 92.997 714 46 3 485 1198 13020908 13021617 0.000000e+00 1038
11 TraesCS1D01G022300 chr1B 91.748 715 49 6 485 1198 13569370 13570075 0.000000e+00 985
12 TraesCS1D01G022300 chr1B 88.531 715 50 10 485 1198 12353811 12353128 0.000000e+00 837
13 TraesCS1D01G022300 chr1B 97.555 409 8 2 3488 3894 12789913 12790321 0.000000e+00 699
14 TraesCS1D01G022300 chr1B 93.510 339 21 1 1251 1588 12353117 12352779 1.860000e-138 503
15 TraesCS1D01G022300 chr1B 93.510 339 21 1 1251 1588 13021628 13021966 1.860000e-138 503
16 TraesCS1D01G022300 chr1B 92.920 339 23 1 1251 1588 13570086 13570424 4.030000e-135 492
17 TraesCS1D01G022300 chr1B 88.441 372 29 7 127 488 12784216 12784583 1.910000e-118 436
18 TraesCS1D01G022300 chr1B 83.967 368 40 6 139 488 13020450 13020816 7.180000e-88 335
19 TraesCS1D01G022300 chr1B 87.708 301 12 8 4180 4480 12790671 12790946 1.200000e-85 327
20 TraesCS1D01G022300 chr1B 94.286 105 6 0 1 105 12784125 12784229 1.290000e-35 161
21 TraesCS1D01G022300 chr1B 93.069 101 7 0 1 101 13568821 13568921 1.000000e-31 148
22 TraesCS1D01G022300 chr5D 78.968 252 45 8 2131 2378 352280425 352280672 9.970000e-37 165
23 TraesCS1D01G022300 chr3D 78.390 236 45 5 2141 2373 504013428 504013196 1.000000e-31 148
24 TraesCS1D01G022300 chr7D 75.524 286 47 17 2128 2407 613323326 613323594 7.880000e-23 119
25 TraesCS1D01G022300 chr7D 75.265 283 47 18 2128 2407 613327571 613327833 3.660000e-21 113
26 TraesCS1D01G022300 chr7D 74.444 270 49 14 2141 2407 613135333 613135081 1.030000e-16 99
27 TraesCS1D01G022300 chr3B 77.523 218 35 10 2131 2345 665446926 665446720 7.880000e-23 119
28 TraesCS1D01G022300 chr2B 77.907 172 28 7 2212 2378 493559844 493559678 1.030000e-16 99


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 TraesCS1D01G022300 chr1D 9439832 9444313 4481 False 3875.500000 7191 100.000000 1 4482 2 chr1D.!!$F1 4481
1 TraesCS1D01G022300 chr1A 10748298 10752413 4115 False 1355.250000 3142 92.381750 485 4342 4 chr1A.!!$F3 3857
2 TraesCS1D01G022300 chr1B 12784125 12790946 6821 False 1078.333333 2736 93.116833 1 4480 6 chr1B.!!$F1 4479
3 TraesCS1D01G022300 chr1B 12352779 12353811 1032 True 670.000000 837 91.020500 485 1588 2 chr1B.!!$R1 1103
4 TraesCS1D01G022300 chr1B 13020450 13021966 1516 False 625.333333 1038 90.158000 139 1588 3 chr1B.!!$F2 1449
5 TraesCS1D01G022300 chr1B 13568821 13570424 1603 False 541.666667 985 92.579000 1 1588 3 chr1B.!!$F3 1587

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
323 334 0.109458 TCTCAATCTAACACGCGCGT 60.109 50.0 32.73 32.73 0.00 6.01 F
713 841 0.539438 TTGCTGGATTTCAGGGCGTT 60.539 50.0 0.00 0.00 43.54 4.84 F
1248 1382 0.445043 GGGACGGCGATAACAAACAC 59.555 55.0 16.62 0.00 0.00 3.32 F
1500 1644 0.817654 CGACATACCTCAGCTCACCA 59.182 55.0 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1298 0.037326 CAGAAGTAGGTGCCGCAGAA 60.037 55.000 0.00 0.0 0.00 3.02 R
2399 2584 0.172578 TCTCCGTGGTGATTGCTACG 59.827 55.000 0.00 0.0 41.85 3.51 R
3007 3193 1.139095 GACGAAGGAGGTAGCACCG 59.861 63.158 2.59 0.0 44.90 4.94 R
3504 5883 7.331026 TCACAGAGTGATACTAAATTTGGGAG 58.669 38.462 6.50 0.0 37.67 4.30 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
94 95 5.772825 TGCAAAGAGACTGCATAAAACTT 57.227 34.783 0.00 0.00 44.67 2.66
95 96 6.147864 TGCAAAGAGACTGCATAAAACTTT 57.852 33.333 0.00 0.00 44.67 2.66
96 97 5.978919 TGCAAAGAGACTGCATAAAACTTTG 59.021 36.000 19.42 19.42 44.67 2.77
97 98 6.183360 TGCAAAGAGACTGCATAAAACTTTGA 60.183 34.615 23.95 13.69 44.67 2.69
98 99 6.865205 GCAAAGAGACTGCATAAAACTTTGAT 59.135 34.615 23.95 0.00 42.57 2.57
99 100 7.148853 GCAAAGAGACTGCATAAAACTTTGATG 60.149 37.037 23.95 0.00 42.57 3.07
100 101 5.947443 AGAGACTGCATAAAACTTTGATGC 58.053 37.500 14.85 14.85 45.02 3.91
101 102 5.709164 AGAGACTGCATAAAACTTTGATGCT 59.291 36.000 20.27 5.59 45.04 3.79
102 103 5.947443 AGACTGCATAAAACTTTGATGCTC 58.053 37.500 20.27 12.71 45.04 4.26
103 104 5.709164 AGACTGCATAAAACTTTGATGCTCT 59.291 36.000 20.27 14.31 45.04 4.09
104 105 6.881065 AGACTGCATAAAACTTTGATGCTCTA 59.119 34.615 20.27 4.43 45.04 2.43
105 106 7.555554 AGACTGCATAAAACTTTGATGCTCTAT 59.444 33.333 20.27 7.18 45.04 1.98
106 107 7.701445 ACTGCATAAAACTTTGATGCTCTATC 58.299 34.615 20.27 0.00 45.04 2.08
107 108 7.031226 TGCATAAAACTTTGATGCTCTATCC 57.969 36.000 20.27 0.00 45.04 2.59
108 109 6.138761 GCATAAAACTTTGATGCTCTATCCG 58.861 40.000 14.54 0.00 42.19 4.18
109 110 4.622701 AAAACTTTGATGCTCTATCCGC 57.377 40.909 0.00 0.00 34.77 5.54
110 111 2.988010 ACTTTGATGCTCTATCCGCA 57.012 45.000 0.00 0.00 42.25 5.69
111 112 3.266510 ACTTTGATGCTCTATCCGCAA 57.733 42.857 0.00 0.00 41.26 4.85
112 113 3.609853 ACTTTGATGCTCTATCCGCAAA 58.390 40.909 0.00 0.00 41.26 3.68
113 114 4.009675 ACTTTGATGCTCTATCCGCAAAA 58.990 39.130 0.00 0.00 41.26 2.44
114 115 4.458989 ACTTTGATGCTCTATCCGCAAAAA 59.541 37.500 0.00 0.00 41.26 1.94
146 147 9.521503 AAAAAGACTTTGATGCTCTAAAACTTC 57.478 29.630 0.06 0.00 0.00 3.01
188 189 0.394488 TCAAACAACAGTCCCCGCAA 60.394 50.000 0.00 0.00 0.00 4.85
220 221 4.485163 GTTCAAACAACAGAACTGCAACT 58.515 39.130 1.46 0.00 40.63 3.16
309 310 4.029520 CCCCATCTCTCTCTTTCTCTCAA 58.970 47.826 0.00 0.00 0.00 3.02
323 334 0.109458 TCTCAATCTAACACGCGCGT 60.109 50.000 32.73 32.73 0.00 6.01
357 382 2.588596 TCACACACACCTGCGCAG 60.589 61.111 30.52 30.52 0.00 5.18
424 449 7.573710 ACTATACCCAAAAGAAGTGCATATGA 58.426 34.615 6.97 0.00 0.00 2.15
426 451 5.587388 ACCCAAAAGAAGTGCATATGATG 57.413 39.130 6.97 0.00 0.00 3.07
438 463 7.683437 AGTGCATATGATGATTAATGACTGG 57.317 36.000 6.97 0.00 0.00 4.00
452 477 0.741326 GACTGGTCGCTCTATGCAGA 59.259 55.000 0.00 0.00 43.06 4.26
468 493 2.432146 TGCAGATAAGGCTTCTCACGAT 59.568 45.455 14.18 0.00 0.00 3.73
548 674 7.198390 AGTATGATATGTGCATTCAAACAAGC 58.802 34.615 0.00 0.00 0.00 4.01
655 783 3.319405 AGTCGTCGATCCATAGCAAAGAT 59.681 43.478 0.00 0.00 0.00 2.40
713 841 0.539438 TTGCTGGATTTCAGGGCGTT 60.539 50.000 0.00 0.00 43.54 4.84
745 873 8.815912 TCTGCTAAGCATACATTCTCCATATTA 58.184 33.333 0.00 0.00 38.13 0.98
748 876 9.442047 GCTAAGCATACATTCTCCATATTAAGT 57.558 33.333 0.00 0.00 0.00 2.24
822 956 8.858003 ATGTAGTAGCACGTCAATATATATGC 57.142 34.615 0.00 0.00 0.00 3.14
884 1018 6.514048 GCAAGTGAAAAAGTAGAAGCAGTGAT 60.514 38.462 0.00 0.00 0.00 3.06
984 1118 9.093970 CGTTAGTTATAGTTCATCACCAATCAA 57.906 33.333 0.00 0.00 0.00 2.57
1164 1298 2.348998 CTTGCCTCCGCTGACCTT 59.651 61.111 0.00 0.00 35.36 3.50
1246 1380 0.674269 TGGGGACGGCGATAACAAAC 60.674 55.000 16.62 0.00 0.00 2.93
1248 1382 0.445043 GGGACGGCGATAACAAACAC 59.555 55.000 16.62 0.00 0.00 3.32
1500 1644 0.817654 CGACATACCTCAGCTCACCA 59.182 55.000 0.00 0.00 0.00 4.17
1661 1805 4.360951 AATTTTGTCCGTCCCTAAGTGA 57.639 40.909 0.00 0.00 0.00 3.41
1678 1822 7.513091 CCCTAAGTGAAACCCTTATCTATACCT 59.487 40.741 0.00 0.00 37.80 3.08
1684 1828 8.218488 GTGAAACCCTTATCTATACCTTCCAAT 58.782 37.037 0.00 0.00 0.00 3.16
1752 1901 5.751243 TTCCCTTTTTCGTTTCTCTCAAG 57.249 39.130 0.00 0.00 0.00 3.02
1762 1911 3.121194 CGTTTCTCTCAAGAGTGAAAGCG 60.121 47.826 21.07 20.86 45.64 4.68
1766 1915 6.510879 TTCTCTCAAGAGTGAAAGCGTATA 57.489 37.500 11.03 0.00 42.60 1.47
2091 2272 6.204882 GCCGCTTATATTTCTGGTTTACTGAT 59.795 38.462 0.00 0.00 0.00 2.90
2126 2307 2.158900 AGTAAACAGGATGATGCTCCCG 60.159 50.000 0.00 0.00 39.69 5.14
2159 2340 5.813080 ACGAAAAGGCAAAGACCATATAC 57.187 39.130 0.00 0.00 0.00 1.47
2169 2350 9.067986 AGGCAAAGACCATATACTTTAAATAGC 57.932 33.333 0.00 0.00 35.07 2.97
2238 2419 2.438434 CTTGGGGGTGCCGATGTC 60.438 66.667 0.00 0.00 0.00 3.06
2399 2584 0.882042 CGCAGGTGGCCATGATCTAC 60.882 60.000 9.72 0.00 40.31 2.59
2555 2740 3.686241 TGTCCAGCTTTGAATCAAGATCG 59.314 43.478 0.00 0.00 0.00 3.69
2795 2981 5.184864 ACCCATCTAAAATGACGCATTTTCA 59.815 36.000 24.06 16.49 46.82 2.69
2840 3026 5.870978 GGATGCAGTTTAATTGCTGATTGTT 59.129 36.000 13.27 0.00 42.02 2.83
3007 3193 1.883084 CTACCTCACGCAATCCGCC 60.883 63.158 0.00 0.00 41.76 6.13
3074 3260 0.969149 CCGCTATAGACCTGCCATGA 59.031 55.000 3.21 0.00 0.00 3.07
3370 3556 1.444933 TGAGGAACCATGGGAACTGT 58.555 50.000 18.09 0.00 0.00 3.55
3403 3589 1.668419 GGACCACATCGCTTTGCTAT 58.332 50.000 0.00 0.00 0.00 2.97
4343 6932 9.030452 ACTTTGCCACAAAAATATGGAGTTATA 57.970 29.630 0.00 0.00 38.34 0.98
4410 6999 0.109342 AGGAACCTGCACCTGAACAG 59.891 55.000 0.00 0.00 34.99 3.16
4480 7069 3.452466 GCATCTAAGATGCTCGAATGC 57.548 47.619 1.67 3.06 41.52 3.56
4481 7070 2.159867 GCATCTAAGATGCTCGAATGCG 60.160 50.000 1.67 0.00 41.52 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.913170 TGTTTGTTCCTTCTAGATGCATTTC 58.087 36.000 0.00 0.00 0.00 2.17
76 77 6.208204 AGCATCAAAGTTTTATGCAGTCTCTT 59.792 34.615 27.86 9.94 46.66 2.85
82 83 7.137426 GGATAGAGCATCAAAGTTTTATGCAG 58.863 38.462 27.86 0.51 46.66 4.41
87 88 5.182487 TGCGGATAGAGCATCAAAGTTTTA 58.818 37.500 0.00 0.00 40.01 1.52
89 90 3.609853 TGCGGATAGAGCATCAAAGTTT 58.390 40.909 0.00 0.00 40.01 2.66
91 92 2.988010 TGCGGATAGAGCATCAAAGT 57.012 45.000 0.00 0.00 40.01 2.66
92 93 4.621068 TTTTGCGGATAGAGCATCAAAG 57.379 40.909 0.00 0.00 44.74 2.77
120 121 9.521503 GAAGTTTTAGAGCATCAAAGTCTTTTT 57.478 29.630 0.00 0.00 37.82 1.94
121 122 7.857885 CGAAGTTTTAGAGCATCAAAGTCTTTT 59.142 33.333 0.00 0.00 37.82 2.27
122 123 7.226720 TCGAAGTTTTAGAGCATCAAAGTCTTT 59.773 33.333 0.00 0.00 37.82 2.52
123 124 6.706270 TCGAAGTTTTAGAGCATCAAAGTCTT 59.294 34.615 0.00 0.00 37.82 3.01
124 125 6.223852 TCGAAGTTTTAGAGCATCAAAGTCT 58.776 36.000 0.00 0.00 37.82 3.24
125 126 6.467723 TCGAAGTTTTAGAGCATCAAAGTC 57.532 37.500 0.00 0.00 37.82 3.01
197 198 3.502191 TGCAGTTCTGTTGTTTGAACC 57.498 42.857 0.00 0.00 42.32 3.62
254 255 8.397906 CACAACCAACTCGTGATGAAATATTAT 58.602 33.333 0.00 0.00 32.23 1.28
340 365 2.588596 CTGCGCAGGTGTGTGTGA 60.589 61.111 29.88 0.00 36.48 3.58
424 449 4.679373 AGAGCGACCAGTCATTAATCAT 57.321 40.909 0.00 0.00 0.00 2.45
426 451 4.387256 GCATAGAGCGACCAGTCATTAATC 59.613 45.833 0.00 0.00 0.00 1.75
663 791 2.886523 TCTTCTTTCTGGTGGCATTGTG 59.113 45.455 0.00 0.00 0.00 3.33
737 865 2.635915 CGTAGGGGGCACTTAATATGGA 59.364 50.000 0.00 0.00 0.00 3.41
745 873 1.991722 GGGTACGTAGGGGGCACTT 60.992 63.158 0.00 0.00 0.00 3.16
748 876 2.042639 GAGGGTACGTAGGGGGCA 60.043 66.667 0.00 0.00 0.00 5.36
822 956 4.156182 GTGTTGATCGATGCATGCATATG 58.844 43.478 32.27 25.79 36.70 1.78
902 1036 8.167081 GGCTTGAGCTAGCTACTTAATTAGCTT 61.167 40.741 26.51 13.22 46.39 3.74
984 1118 2.700897 CCCCATGGTTTCGATCTCTAGT 59.299 50.000 11.73 0.00 0.00 2.57
1164 1298 0.037326 CAGAAGTAGGTGCCGCAGAA 60.037 55.000 0.00 0.00 0.00 3.02
1227 1361 0.674269 GTTTGTTATCGCCGTCCCCA 60.674 55.000 0.00 0.00 0.00 4.96
1246 1380 4.935495 ACCACCGCTGCCACTGTG 62.935 66.667 0.00 0.00 0.00 3.66
1340 1475 1.683707 ACCAGCGAGCTGATCCTCA 60.684 57.895 24.93 0.00 46.30 3.86
1500 1644 0.410270 AGAAGACCGACCCCTTCTCT 59.590 55.000 0.00 0.00 43.95 3.10
1638 1782 5.867330 TCACTTAGGGACGGACAAAATTAA 58.133 37.500 0.00 0.00 0.00 1.40
1661 1805 8.373220 CGTATTGGAAGGTATAGATAAGGGTTT 58.627 37.037 0.00 0.00 0.00 3.27
1678 1822 8.335532 AGAAAGATTTCAATGACGTATTGGAA 57.664 30.769 7.97 11.43 45.83 3.53
1684 1828 8.523523 TTTCGTAGAAAGATTTCAATGACGTA 57.476 30.769 7.97 3.68 45.90 3.57
1752 1901 6.946229 TTTGAAGTCTATACGCTTTCACTC 57.054 37.500 0.00 0.00 0.00 3.51
1762 1911 8.999431 TGATGTGGAAAGTTTTGAAGTCTATAC 58.001 33.333 0.00 0.00 0.00 1.47
1766 1915 6.152661 TGTTGATGTGGAAAGTTTTGAAGTCT 59.847 34.615 0.00 0.00 0.00 3.24
1916 2097 8.485976 TTTAAACTTCTTGGGTCAACAAAATG 57.514 30.769 0.00 0.00 0.00 2.32
1917 2098 8.318412 ACTTTAAACTTCTTGGGTCAACAAAAT 58.682 29.630 0.00 0.00 0.00 1.82
2169 2350 9.673454 GTAAGAGTGTTTTTATAAGGGTTTGTG 57.327 33.333 0.00 0.00 0.00 3.33
2238 2419 2.892852 TGTTGGATGCAGGAGGAAAAAG 59.107 45.455 0.00 0.00 0.00 2.27
2399 2584 0.172578 TCTCCGTGGTGATTGCTACG 59.827 55.000 0.00 0.00 41.85 3.51
2576 2761 9.903682 ATCTCATTTTATATGTTTATGCTGCAC 57.096 29.630 3.57 0.00 0.00 4.57
2745 2931 5.124457 CACCTGCACTGCTATCTAAAACAAT 59.876 40.000 1.98 0.00 0.00 2.71
2750 2936 2.632377 GCACCTGCACTGCTATCTAAA 58.368 47.619 1.98 0.00 41.59 1.85
2840 3026 2.693591 CCCAACGAGCTTCCTGTAGATA 59.306 50.000 0.00 0.00 0.00 1.98
3007 3193 1.139095 GACGAAGGAGGTAGCACCG 59.861 63.158 2.59 0.00 44.90 4.94
3504 5883 7.331026 TCACAGAGTGATACTAAATTTGGGAG 58.669 38.462 6.50 0.00 37.67 4.30
4343 6932 6.136071 GCACTCGTAATATCAATTTTGCGAT 58.864 36.000 6.77 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.