Multiple sequence alignment - TraesCS2D01G167400

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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 TraesCS2D01G167400 chr2D 100.000 3944 0 0 1 3944 111232277 111236220 0.000000e+00 7284.0
1 TraesCS2D01G167400 chr2D 78.992 119 23 1 443 559 586150739 586150621 3.270000e-11 80.5
2 TraesCS2D01G167400 chr2A 95.666 3138 109 8 823 3944 109595319 109598445 0.000000e+00 5016.0
3 TraesCS2D01G167400 chr2A 92.090 670 46 4 1 666 109592790 109593456 0.000000e+00 937.0
4 TraesCS2D01G167400 chr2A 95.376 173 7 1 659 831 109594039 109594210 1.400000e-69 274.0
5 TraesCS2D01G167400 chr2B 94.940 2767 106 10 925 3684 161018618 161021357 0.000000e+00 4303.0
6 TraesCS2D01G167400 chr2B 90.777 206 12 3 3740 3944 161021470 161021669 6.500000e-68 268.0
7 TraesCS2D01G167400 chr2B 84.279 229 26 7 158 383 161017388 161017609 8.580000e-52 215.0
8 TraesCS2D01G167400 chr2B 100.000 35 0 0 3711 3745 161021360 161021394 9.150000e-07 65.8
9 TraesCS2D01G167400 chr5B 85.000 180 27 0 422 601 580735766 580735587 2.420000e-42 183.0
10 TraesCS2D01G167400 chr1D 83.889 180 29 0 422 601 467930111 467929932 5.240000e-39 172.0
11 TraesCS2D01G167400 chr1A 83.889 180 29 0 422 601 49354547 49354368 5.240000e-39 172.0
12 TraesCS2D01G167400 chr3B 84.091 176 27 1 422 596 401817166 401816991 6.780000e-38 169.0
13 TraesCS2D01G167400 chr5A 81.910 199 35 1 404 601 663324438 663324636 2.440000e-37 167.0
14 TraesCS2D01G167400 chr4D 82.540 189 33 0 413 601 459568727 459568915 2.440000e-37 167.0
15 TraesCS2D01G167400 chr4A 82.540 189 32 1 413 601 317070313 317070500 8.770000e-37 165.0
16 TraesCS2D01G167400 chr1B 82.778 180 31 0 422 601 378855442 378855263 1.130000e-35 161.0
17 TraesCS2D01G167400 chr6B 96.875 32 1 0 600 631 716310586 716310555 2.000000e-03 54.7
18 TraesCS2D01G167400 chr5D 96.875 32 1 0 600 631 434349270 434349239 2.000000e-03 54.7


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 TraesCS2D01G167400 chr2D 111232277 111236220 3943 False 7284.000000 7284 100.000000 1 3944 1 chr2D.!!$F1 3943
1 TraesCS2D01G167400 chr2A 109592790 109598445 5655 False 2075.666667 5016 94.377333 1 3944 3 chr2A.!!$F1 3943
2 TraesCS2D01G167400 chr2B 161017388 161021669 4281 False 1212.950000 4303 92.499000 158 3944 4 chr2B.!!$F1 3786

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
914 3123 0.029700 CACACCGTCACTACACACGA 59.970 55.000 0.0 0.0 38.32 4.35 F
916 3125 0.386858 CACCGTCACTACACACGAGG 60.387 60.000 0.0 0.0 38.32 4.63 F
919 3143 1.080025 GTCACTACACACGAGGCCC 60.080 63.158 0.0 0.0 0.00 5.80 F
2368 4592 1.133637 TGTTAAGGGCTTGCAAGGTCA 60.134 47.619 27.1 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 4681 2.026641 CTCCCGGAACAGGAATACGTA 58.973 52.381 0.73 0.0 31.49 3.57 R
2504 4728 7.290948 TCTTCATGCCCTTCTTTCTCATAGATA 59.709 37.037 0.00 0.0 0.00 1.98 R
2848 5072 7.658525 TCTCTCTCTCAGCTATCTTTGAAAT 57.341 36.000 0.00 0.0 0.00 2.17 R
3707 5937 2.405559 AGGGGGATACTAAGGTTTCCG 58.594 52.381 0.00 0.0 42.13 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
29 30 3.136763 CTCTTGTGTGTGTCATTGCTCT 58.863 45.455 0.00 0.00 0.00 4.09
45 46 9.144747 GTCATTGCTCTATACCACATACAATAG 57.855 37.037 0.00 0.00 0.00 1.73
81 82 1.144057 GATAGCCGTGGACTGGGTG 59.856 63.158 0.00 0.00 37.84 4.61
82 83 1.305802 ATAGCCGTGGACTGGGTGA 60.306 57.895 0.00 0.00 37.84 4.02
106 107 1.628340 CCATTGAGGTGACCACTACCA 59.372 52.381 3.63 0.00 40.74 3.25
159 160 3.066760 GGGTTCTGTGTGGTTTGAGAAAG 59.933 47.826 0.00 0.00 0.00 2.62
165 166 4.136796 TGTGTGGTTTGAGAAAGGATGAG 58.863 43.478 0.00 0.00 0.00 2.90
250 253 4.283722 GGTGAAGTCTACCAGGAAAGAGAA 59.716 45.833 0.00 0.00 38.12 2.87
252 255 5.929415 GTGAAGTCTACCAGGAAAGAGAAAG 59.071 44.000 0.00 0.00 0.00 2.62
255 258 6.749036 AGTCTACCAGGAAAGAGAAAGAAA 57.251 37.500 0.00 0.00 0.00 2.52
256 259 6.526526 AGTCTACCAGGAAAGAGAAAGAAAC 58.473 40.000 0.00 0.00 0.00 2.78
257 260 6.327887 AGTCTACCAGGAAAGAGAAAGAAACT 59.672 38.462 0.00 0.00 0.00 2.66
258 261 6.993308 GTCTACCAGGAAAGAGAAAGAAACTT 59.007 38.462 0.00 0.00 0.00 2.66
259 262 8.148999 GTCTACCAGGAAAGAGAAAGAAACTTA 58.851 37.037 0.00 0.00 0.00 2.24
261 264 6.901300 ACCAGGAAAGAGAAAGAAACTTAGT 58.099 36.000 0.00 0.00 0.00 2.24
263 266 6.992715 CCAGGAAAGAGAAAGAAACTTAGTGA 59.007 38.462 0.00 0.00 0.00 3.41
303 306 2.543238 GGGTAACAGGCGAGAGATAACG 60.543 54.545 0.00 0.00 39.74 3.18
375 378 0.694771 TGGCAGCACTGAGGAGAAAT 59.305 50.000 0.81 0.00 0.00 2.17
401 406 6.034044 CAGAGTTGAAGAAAGTATACGCAGAC 59.966 42.308 0.00 0.00 0.00 3.51
438 444 2.124151 CCCTGCCCCTATGTGCAC 60.124 66.667 10.75 10.75 33.17 4.57
439 445 2.676608 CCTGCCCCTATGTGCACA 59.323 61.111 24.08 24.08 33.17 4.57
445 451 1.408683 GCCCCTATGTGCACATCTGAA 60.409 52.381 34.54 17.10 37.76 3.02
458 464 3.923354 TCTGAAAGACTGAGCTGGC 57.077 52.632 0.00 0.00 38.67 4.85
485 491 7.713734 ATCATCTTGAGATTGACAAAACCAT 57.286 32.000 0.00 0.00 31.21 3.55
490 496 8.272545 TCTTGAGATTGACAAAACCATCATAG 57.727 34.615 0.00 0.00 0.00 2.23
491 497 8.102676 TCTTGAGATTGACAAAACCATCATAGA 58.897 33.333 0.00 0.00 0.00 1.98
498 504 3.270027 CAAAACCATCATAGACGCCTCA 58.730 45.455 0.00 0.00 0.00 3.86
503 509 3.508012 ACCATCATAGACGCCTCATAGTC 59.492 47.826 0.00 0.00 37.63 2.59
507 513 1.215244 TAGACGCCTCATAGTCGACG 58.785 55.000 10.46 0.00 41.86 5.12
508 514 1.009900 GACGCCTCATAGTCGACGG 60.010 63.158 10.46 5.97 0.00 4.79
524 530 3.618652 GGGAACGTCTCCTCTCCC 58.381 66.667 5.02 5.02 44.68 4.30
526 532 1.324005 GGGAACGTCTCCTCTCCCTG 61.324 65.000 12.62 0.00 43.74 4.45
558 564 9.233232 ACATCGCCGAAAATCTTAAAATAAATC 57.767 29.630 0.00 0.00 0.00 2.17
561 567 8.410141 TCGCCGAAAATCTTAAAATAAATCCAT 58.590 29.630 0.00 0.00 0.00 3.41
580 586 5.610398 TCCATAAATAAAGCGAGCATCAGA 58.390 37.500 0.00 0.00 33.17 3.27
585 591 9.882996 CATAAATAAAGCGAGCATCAGAATTTA 57.117 29.630 0.00 0.00 33.17 1.40
588 594 8.620533 AATAAAGCGAGCATCAGAATTTAAAC 57.379 30.769 0.00 0.00 33.17 2.01
598 604 7.341256 AGCATCAGAATTTAAACCATGATGAGT 59.659 33.333 26.73 17.00 44.22 3.41
605 611 7.781324 ATTTAAACCATGATGAGTTGTCCTT 57.219 32.000 0.00 0.00 0.00 3.36
623 629 5.046591 TGTCCTTCTAACTATCCAACCACAG 60.047 44.000 0.00 0.00 0.00 3.66
633 639 6.180472 ACTATCCAACCACAGATTAGTTTGG 58.820 40.000 0.00 0.00 32.93 3.28
635 641 2.825532 CCAACCACAGATTAGTTTGGGG 59.174 50.000 0.00 0.00 43.69 4.96
705 1301 3.955551 GGTTGAAACTTTGAGTGGGGTAA 59.044 43.478 0.00 0.00 0.00 2.85
749 1345 2.468670 GCATCCATTGCGCCGTACA 61.469 57.895 4.18 0.00 42.54 2.90
850 3059 1.095228 ACATTGCATTCCCGGCGTAG 61.095 55.000 6.01 0.00 0.00 3.51
882 3091 2.805353 CGTTCCGTGTCTGCTCCG 60.805 66.667 0.00 0.00 0.00 4.63
896 3105 0.884704 GCTCCGTTGAAACCAGAGCA 60.885 55.000 20.04 0.00 44.71 4.26
901 3110 0.307760 GTTGAAACCAGAGCACACCG 59.692 55.000 0.00 0.00 0.00 4.94
907 3116 0.826256 ACCAGAGCACACCGTCACTA 60.826 55.000 0.00 0.00 0.00 2.74
909 3118 0.313987 CAGAGCACACCGTCACTACA 59.686 55.000 0.00 0.00 0.00 2.74
910 3119 0.314302 AGAGCACACCGTCACTACAC 59.686 55.000 0.00 0.00 0.00 2.90
911 3120 0.031585 GAGCACACCGTCACTACACA 59.968 55.000 0.00 0.00 0.00 3.72
912 3121 0.249322 AGCACACCGTCACTACACAC 60.249 55.000 0.00 0.00 0.00 3.82
913 3122 1.545614 GCACACCGTCACTACACACG 61.546 60.000 0.00 0.00 35.72 4.49
914 3123 0.029700 CACACCGTCACTACACACGA 59.970 55.000 0.00 0.00 38.32 4.35
916 3125 0.386858 CACCGTCACTACACACGAGG 60.387 60.000 0.00 0.00 38.32 4.63
919 3143 1.080025 GTCACTACACACGAGGCCC 60.080 63.158 0.00 0.00 0.00 5.80
923 3147 3.000819 TACACACGAGGCCCAGGG 61.001 66.667 0.00 0.00 0.00 4.45
982 3206 2.046604 GTTCGCTACCCCCGCTTT 60.047 61.111 0.00 0.00 0.00 3.51
983 3207 2.104859 GTTCGCTACCCCCGCTTTC 61.105 63.158 0.00 0.00 0.00 2.62
1656 3880 3.931468 GCAGCAGCTTGATCGATATGTAT 59.069 43.478 0.00 0.00 37.91 2.29
1659 3883 3.241900 GCAGCTTGATCGATATGTATGCG 60.242 47.826 0.00 0.00 0.00 4.73
1843 4067 2.011222 CTCGTACTTTCTCGAGCCTCT 58.989 52.381 7.81 0.00 44.82 3.69
1870 4094 1.666888 CCTGTGGAAATGTTGCTTCGC 60.667 52.381 0.00 0.00 0.00 4.70
2368 4592 1.133637 TGTTAAGGGCTTGCAAGGTCA 60.134 47.619 27.10 0.00 0.00 4.02
2848 5072 4.338682 ACTGCCACACGGTAACAAAATTTA 59.661 37.500 0.00 0.00 35.54 1.40
2919 5143 7.394016 GTTTCCACCATTTTAAGGATGGAAAT 58.606 34.615 16.27 2.70 46.07 2.17
2959 5183 3.360867 TGGTGATTGAACAACAGTTGGT 58.639 40.909 17.76 11.37 32.24 3.67
3471 5701 9.753674 TGAAAAGGATGATACTTTAGGAAATGT 57.246 29.630 2.53 0.00 37.18 2.71
3684 5914 7.790782 AAAATAATGTTGGGAGTAATGTGGT 57.209 32.000 0.00 0.00 0.00 4.16
3703 5933 6.115446 TGTGGTCCTGAAGCAAGATTAATAG 58.885 40.000 0.00 0.00 37.07 1.73
3707 5937 6.425417 GGTCCTGAAGCAAGATTAATAGCTAC 59.575 42.308 0.00 4.87 36.07 3.58
3709 5939 5.406780 CCTGAAGCAAGATTAATAGCTACGG 59.593 44.000 0.00 7.11 36.07 4.02
3783 6094 6.095440 ACCTGTTGCCTCATTTACATTGTATC 59.905 38.462 0.00 0.00 0.00 2.24
3843 6156 6.376581 AGAGTGATCATCCTGGAACAAATTTC 59.623 38.462 0.00 0.00 38.70 2.17
3861 6174 6.741992 AATTTCGCAGAATACAATGTCTCA 57.258 33.333 0.00 0.00 45.90 3.27
3881 6194 7.492669 TGTCTCATATGCTTTTTACTACTGCTC 59.507 37.037 0.00 0.00 0.00 4.26
3884 6197 2.695359 TGCTTTTTACTACTGCTCGGG 58.305 47.619 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.645535 AGCAATGACACACACAAGAGTAT 58.354 39.130 0.00 0.0 0.00 2.12
29 30 7.797062 TGAGGCAAACTATTGTATGTGGTATA 58.203 34.615 0.00 0.0 38.85 1.47
45 46 4.622740 GCTATCAACAACAATGAGGCAAAC 59.377 41.667 0.00 0.0 33.00 2.93
91 92 0.037232 GCAGTGGTAGTGGTCACCTC 60.037 60.000 0.00 0.0 36.96 3.85
106 107 1.536662 ACCGAGAAAGGAGGGCAGT 60.537 57.895 0.00 0.0 34.73 4.40
250 253 2.441750 TGTGCCCCTCACTAAGTTTCTT 59.558 45.455 0.00 0.0 45.81 2.52
252 255 2.561478 TGTGCCCCTCACTAAGTTTC 57.439 50.000 0.00 0.0 45.81 2.78
255 258 1.729586 TCTTGTGCCCCTCACTAAGT 58.270 50.000 0.00 0.0 45.81 2.24
256 259 2.859165 TTCTTGTGCCCCTCACTAAG 57.141 50.000 0.00 0.0 45.81 2.18
257 260 2.224769 CCTTTCTTGTGCCCCTCACTAA 60.225 50.000 0.00 0.0 45.81 2.24
258 261 1.351017 CCTTTCTTGTGCCCCTCACTA 59.649 52.381 0.00 0.0 45.81 2.74
259 262 0.111253 CCTTTCTTGTGCCCCTCACT 59.889 55.000 0.00 0.0 45.81 3.41
261 264 1.065410 TCCCTTTCTTGTGCCCCTCA 61.065 55.000 0.00 0.0 0.00 3.86
263 266 1.770324 CTCCCTTTCTTGTGCCCCT 59.230 57.895 0.00 0.0 0.00 4.79
310 313 4.758674 CACATTGACTCAATTGACCAGAGT 59.241 41.667 3.38 0.0 44.71 3.24
360 363 3.172339 ACTCTGATTTCTCCTCAGTGCT 58.828 45.455 0.71 0.0 40.79 4.40
375 378 6.020971 TGCGTATACTTTCTTCAACTCTGA 57.979 37.500 0.56 0.0 0.00 3.27
401 406 3.116300 GGGATGCGCGTATATATGAGTG 58.884 50.000 10.42 0.0 0.00 3.51
438 444 2.008329 GCCAGCTCAGTCTTTCAGATG 58.992 52.381 0.00 0.0 0.00 2.90
439 445 1.627329 TGCCAGCTCAGTCTTTCAGAT 59.373 47.619 0.00 0.0 0.00 2.90
445 451 3.647113 AGATGATATGCCAGCTCAGTCTT 59.353 43.478 0.00 0.0 0.00 3.01
457 463 7.646922 GGTTTTGTCAATCTCAAGATGATATGC 59.353 37.037 0.00 0.0 34.49 3.14
458 464 8.680001 TGGTTTTGTCAATCTCAAGATGATATG 58.320 33.333 0.00 0.0 34.49 1.78
558 564 5.929697 TCTGATGCTCGCTTTATTTATGG 57.070 39.130 0.00 0.0 0.00 2.74
569 575 4.355543 TGGTTTAAATTCTGATGCTCGC 57.644 40.909 0.00 0.0 0.00 5.03
580 586 7.781324 AGGACAACTCATCATGGTTTAAATT 57.219 32.000 0.00 0.0 0.00 1.82
585 591 4.990526 AGAAGGACAACTCATCATGGTTT 58.009 39.130 0.00 0.0 0.00 3.27
588 594 5.738909 AGTTAGAAGGACAACTCATCATGG 58.261 41.667 0.00 0.0 28.88 3.66
598 604 5.308497 TGTGGTTGGATAGTTAGAAGGACAA 59.692 40.000 0.00 0.0 0.00 3.18
605 611 7.973048 ACTAATCTGTGGTTGGATAGTTAGA 57.027 36.000 0.00 0.0 0.00 2.10
623 629 4.948341 ACAAAACCACCCCAAACTAATC 57.052 40.909 0.00 0.0 0.00 1.75
633 639 4.504165 CCCCTCAAAATTACAAAACCACCC 60.504 45.833 0.00 0.0 0.00 4.61
635 641 4.637276 CCCCCTCAAAATTACAAAACCAC 58.363 43.478 0.00 0.0 0.00 4.16
705 1301 0.179084 CGTGTTGGGAGCGTCCATAT 60.179 55.000 2.00 0.0 38.64 1.78
833 3042 0.107410 TTCTACGCCGGGAATGCAAT 60.107 50.000 2.18 0.0 0.00 3.56
850 3059 0.818938 GAACGGGTCTCTCCTCCTTC 59.181 60.000 0.00 0.0 36.25 3.46
882 3091 0.307760 CGGTGTGCTCTGGTTTCAAC 59.692 55.000 0.00 0.0 0.00 3.18
896 3105 0.309922 CTCGTGTGTAGTGACGGTGT 59.690 55.000 0.00 0.0 36.23 4.16
901 3110 1.080025 GGGCCTCGTGTGTAGTGAC 60.080 63.158 0.84 0.0 0.00 3.67
964 3188 3.945304 AAAGCGGGGGTAGCGAACG 62.945 63.158 0.00 0.0 40.04 3.95
971 3195 0.545787 TGAGAAGGAAAGCGGGGGTA 60.546 55.000 0.00 0.0 0.00 3.69
972 3196 1.846124 TGAGAAGGAAAGCGGGGGT 60.846 57.895 0.00 0.0 0.00 4.95
1659 3883 1.429463 AATCCGTTCGAGTGCAGTTC 58.571 50.000 0.00 0.0 0.00 3.01
1843 4067 2.890311 CAACATTTCCACAGGCAGGTAA 59.110 45.455 0.00 0.0 0.00 2.85
2368 4592 6.380095 TTCAGCTAACACGGTATTTTTGTT 57.620 33.333 0.00 0.0 37.27 2.83
2457 4681 2.026641 CTCCCGGAACAGGAATACGTA 58.973 52.381 0.73 0.0 31.49 3.57
2504 4728 7.290948 TCTTCATGCCCTTCTTTCTCATAGATA 59.709 37.037 0.00 0.0 0.00 1.98
2848 5072 7.658525 TCTCTCTCTCAGCTATCTTTGAAAT 57.341 36.000 0.00 0.0 0.00 2.17
2919 5143 2.159310 CCAAAAGTCACCGCAAGAACAA 60.159 45.455 0.00 0.0 43.02 2.83
3243 5468 8.475639 AGTACACCTGAATACGTCAAAATAGAT 58.524 33.333 0.00 0.0 35.22 1.98
3247 5472 7.609056 ACTAGTACACCTGAATACGTCAAAAT 58.391 34.615 0.00 0.0 35.22 1.82
3684 5914 6.216569 CGTAGCTATTAATCTTGCTTCAGGA 58.783 40.000 13.31 0.0 37.02 3.86
3703 5933 3.244009 GGGGATACTAAGGTTTCCGTAGC 60.244 52.174 8.26 0.0 42.13 3.58
3707 5937 2.405559 AGGGGGATACTAAGGTTTCCG 58.594 52.381 0.00 0.0 42.13 4.30
3709 5939 4.226620 TGTCAAGGGGGATACTAAGGTTTC 59.773 45.833 0.00 0.0 0.00 2.78
3765 6076 5.106555 CCATCCGATACAATGTAAATGAGGC 60.107 44.000 0.00 0.0 0.00 4.70
3818 6130 4.916041 TTTGTTCCAGGATGATCACTCT 57.084 40.909 0.00 0.0 39.69 3.24
3843 6156 5.407691 AGCATATGAGACATTGTATTCTGCG 59.592 40.000 6.97 0.0 0.00 5.18
3861 6174 5.057149 CCCGAGCAGTAGTAAAAAGCATAT 58.943 41.667 0.00 0.0 0.00 1.78


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

AutoCloner maintained by Alex Coulton.