Multiple sequence alignment - TraesCS4A01G305500

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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 TraesCS4A01G305500 chr4A 100.000 3368 0 0 1 3368 600914370 600911003 0.000000e+00 6220
1 TraesCS4A01G305500 chr4A 84.811 1771 250 17 651 2413 601016850 601015091 0.000000e+00 1762
2 TraesCS4A01G305500 chr4A 83.891 1763 264 17 661 2413 600975487 600973735 0.000000e+00 1664
3 TraesCS4A01G305500 chr4A 81.546 1772 300 15 651 2413 600930814 600929061 0.000000e+00 1435
4 TraesCS4A01G305500 chr4A 83.723 1026 157 8 651 1673 601008117 601007099 0.000000e+00 961
5 TraesCS4A01G305500 chr4A 85.814 719 100 2 1695 2413 601007046 601006330 0.000000e+00 761
6 TraesCS4A01G305500 chr4A 81.667 660 104 15 2 654 601008835 601008186 1.780000e-147 532
7 TraesCS4A01G305500 chr4B 95.331 2870 130 2 1 2869 4718610 4721476 0.000000e+00 4554
8 TraesCS4A01G305500 chr4B 83.552 2444 355 28 1 2411 4998540 4996111 0.000000e+00 2242
9 TraesCS4A01G305500 chr4B 83.634 1772 272 14 651 2413 5196817 5195055 0.000000e+00 1650
10 TraesCS4A01G305500 chr4B 82.589 1792 270 32 651 2413 5015718 5013940 0.000000e+00 1543
11 TraesCS4A01G305500 chr4B 82.969 1098 165 10 1278 2369 5245911 5244830 0.000000e+00 972
12 TraesCS4A01G305500 chr4B 83.444 1051 163 9 1369 2413 5080432 5079387 0.000000e+00 966
13 TraesCS4A01G305500 chr4B 83.053 655 106 3 651 1304 5081116 5080466 1.040000e-164 590
14 TraesCS4A01G305500 chr4B 81.818 682 92 19 1 654 5016464 5015787 8.220000e-151 544
15 TraesCS4A01G305500 chr4B 81.850 573 98 6 661 1230 5178321 5177752 8.450000e-131 477
16 TraesCS4A01G305500 chr4B 91.579 95 8 0 2 96 5179079 5178985 7.580000e-27 132
17 TraesCS4A01G305500 chr4B 88.506 87 9 1 2420 2506 5013892 5013807 1.650000e-18 104
18 TraesCS4A01G305500 chr4B 92.308 52 4 0 1194 1245 5245956 5245905 1.300000e-09 75
19 TraesCS4A01G305500 chr4D 93.629 2731 128 13 661 3368 3840751 3838044 0.000000e+00 4037
20 TraesCS4A01G305500 chr4D 83.343 1777 252 29 651 2396 3693111 3694874 0.000000e+00 1602
21 TraesCS4A01G305500 chr4D 80.152 660 125 4 1 654 3692383 3693042 3.910000e-134 488
22 TraesCS4A01G305500 chr1D 89.256 121 13 0 3248 3368 493737867 493737987 5.820000e-33 152


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 TraesCS4A01G305500 chr4A 600911003 600914370 3367 True 6220.000000 6220 100.000000 1 3368 1 chr4A.!!$R1 3367
1 TraesCS4A01G305500 chr4A 601015091 601016850 1759 True 1762.000000 1762 84.811000 651 2413 1 chr4A.!!$R4 1762
2 TraesCS4A01G305500 chr4A 600973735 600975487 1752 True 1664.000000 1664 83.891000 661 2413 1 chr4A.!!$R3 1752
3 TraesCS4A01G305500 chr4A 600929061 600930814 1753 True 1435.000000 1435 81.546000 651 2413 1 chr4A.!!$R2 1762
4 TraesCS4A01G305500 chr4A 601006330 601008835 2505 True 751.333333 961 83.734667 2 2413 3 chr4A.!!$R5 2411
5 TraesCS4A01G305500 chr4B 4718610 4721476 2866 False 4554.000000 4554 95.331000 1 2869 1 chr4B.!!$F1 2868
6 TraesCS4A01G305500 chr4B 4996111 4998540 2429 True 2242.000000 2242 83.552000 1 2411 1 chr4B.!!$R1 2410
7 TraesCS4A01G305500 chr4B 5195055 5196817 1762 True 1650.000000 1650 83.634000 651 2413 1 chr4B.!!$R2 1762
8 TraesCS4A01G305500 chr4B 5079387 5081116 1729 True 778.000000 966 83.248500 651 2413 2 chr4B.!!$R4 1762
9 TraesCS4A01G305500 chr4B 5013807 5016464 2657 True 730.333333 1543 84.304333 1 2506 3 chr4B.!!$R3 2505
10 TraesCS4A01G305500 chr4B 5244830 5245956 1126 True 523.500000 972 87.638500 1194 2369 2 chr4B.!!$R6 1175
11 TraesCS4A01G305500 chr4B 5177752 5179079 1327 True 304.500000 477 86.714500 2 1230 2 chr4B.!!$R5 1228
12 TraesCS4A01G305500 chr4D 3838044 3840751 2707 True 4037.000000 4037 93.629000 661 3368 1 chr4D.!!$R1 2707
13 TraesCS4A01G305500 chr4D 3692383 3694874 2491 False 1045.000000 1602 81.747500 1 2396 2 chr4D.!!$F1 2395

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
212 297 1.898902 TGGGTTCACATGGTTAACGG 58.101 50.0 0.00 0.0 0.00 4.44 F
1063 1223 2.435805 GCCATCAGTATTGGTCTGGAGA 59.564 50.0 6.59 0.0 36.57 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 1689 4.326826 ACATGTTTGATCTCACCGTCAAT 58.673 39.13 0.0 0.0 34.6 2.57 R
2970 3230 0.875059 GGACTACTGTTGCAAGCACC 59.125 55.00 0.0 0.0 0.0 5.01 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
64 65 4.811557 CCCAACTCGGTAATCTCTCAAATC 59.188 45.833 0.00 0.00 0.00 2.17
112 197 7.279313 GGGATTATTACAATGTTCTGTACACGT 59.721 37.037 0.00 0.00 40.19 4.49
117 202 3.558418 ACAATGTTCTGTACACGTTGGAC 59.442 43.478 16.76 3.76 42.95 4.02
120 205 2.223876 TGTTCTGTACACGTTGGACCTC 60.224 50.000 0.00 0.00 27.33 3.85
121 206 1.991121 TCTGTACACGTTGGACCTCT 58.009 50.000 0.00 0.00 27.33 3.69
164 249 5.119898 CACTGTTGAGCTATCTTGACTTGAC 59.880 44.000 0.00 0.00 0.00 3.18
211 296 2.030628 GGTTGGGTTCACATGGTTAACG 60.031 50.000 0.00 0.00 0.00 3.18
212 297 1.898902 TGGGTTCACATGGTTAACGG 58.101 50.000 0.00 0.00 0.00 4.44
398 483 2.896443 GGAGCTTCACCTCTCCCG 59.104 66.667 0.00 0.00 42.30 5.14
811 971 8.600668 TGAAAATGGATATTGAACCAAATTGGA 58.399 29.630 20.25 0.00 40.96 3.53
957 1117 7.773489 TGATGTTATTCCTGATTGGTTTTGA 57.227 32.000 0.00 0.00 37.07 2.69
1063 1223 2.435805 GCCATCAGTATTGGTCTGGAGA 59.564 50.000 6.59 0.00 36.57 3.71
1064 1224 3.494048 GCCATCAGTATTGGTCTGGAGAG 60.494 52.174 6.59 0.00 36.57 3.20
1556 1721 3.748048 AGATCAAACATGTTCAGTGGTCG 59.252 43.478 12.39 0.00 0.00 4.79
1747 1953 3.938963 AGGCCAAACACGTGATTATACTG 59.061 43.478 25.01 4.94 0.00 2.74
1774 1980 3.607775 CGTCTTCAGCCAAGTTGTGAATG 60.608 47.826 8.80 5.06 33.27 2.67
2311 2518 6.216801 AGCTGTATGACGAGGTTTATGTAA 57.783 37.500 0.00 0.00 0.00 2.41
2448 2697 7.655521 ACTATATGTACTAGTTTCTGGTGCA 57.344 36.000 0.00 6.52 40.90 4.57
2541 2798 4.974645 TCTGGTCTGATTGTAAACCACT 57.025 40.909 0.00 0.00 36.88 4.00
2543 2800 3.659786 TGGTCTGATTGTAAACCACTCG 58.340 45.455 0.00 0.00 36.88 4.18
2549 2806 6.978659 GTCTGATTGTAAACCACTCGATCATA 59.021 38.462 0.00 0.00 0.00 2.15
2554 2811 9.477484 GATTGTAAACCACTCGATCATATAACT 57.523 33.333 0.00 0.00 0.00 2.24
2556 2813 9.740239 TTGTAAACCACTCGATCATATAACTAC 57.260 33.333 0.00 0.00 0.00 2.73
2891 3151 0.868406 GGAAGTGTGCTCTTCAACCG 59.132 55.000 13.66 0.00 43.72 4.44
2970 3230 3.371102 TGTCAAGAAACTGGAGAGTCG 57.629 47.619 0.00 0.00 0.00 4.18
3009 3269 3.380004 TCCCAAGCAAAGTAAGTTGTGTG 59.620 43.478 0.00 0.00 0.00 3.82
3027 3287 3.260632 GTGTGGCATGGGGTTTATTTCTT 59.739 43.478 0.00 0.00 0.00 2.52
3033 3293 5.872617 GGCATGGGGTTTATTTCTTGTTTAC 59.127 40.000 0.00 0.00 0.00 2.01
3036 3296 5.383476 TGGGGTTTATTTCTTGTTTACGGA 58.617 37.500 0.00 0.00 0.00 4.69
3059 3319 4.910195 TGACGAGGACACTACTAGGTTAA 58.090 43.478 0.00 0.00 0.00 2.01
3135 3395 9.189723 GTAATTTACTGTATGATAAGGTCGGAC 57.810 37.037 0.00 0.00 0.00 4.79
3146 3406 0.456221 AGGTCGGACGTAATCTGCTG 59.544 55.000 0.75 0.00 33.15 4.41
3158 3418 5.750547 ACGTAATCTGCTGTGTGATAATCTG 59.249 40.000 0.00 0.00 0.00 2.90
3161 3421 5.611128 ATCTGCTGTGTGATAATCTGTCT 57.389 39.130 0.00 0.00 0.00 3.41
3162 3422 6.721704 ATCTGCTGTGTGATAATCTGTCTA 57.278 37.500 0.00 0.00 0.00 2.59
3163 3423 6.530019 TCTGCTGTGTGATAATCTGTCTAA 57.470 37.500 0.00 0.00 0.00 2.10
3164 3424 6.567959 TCTGCTGTGTGATAATCTGTCTAAG 58.432 40.000 0.00 0.00 0.00 2.18
3165 3425 6.153510 TCTGCTGTGTGATAATCTGTCTAAGT 59.846 38.462 0.00 0.00 0.00 2.24
3171 3431 8.753133 TGTGTGATAATCTGTCTAAGTGATTCT 58.247 33.333 0.00 0.00 33.24 2.40
3192 3452 3.916761 TGATTTCACTGCAAAATGAGGC 58.083 40.909 0.00 0.00 0.00 4.70
3217 3487 2.426738 TGACCTTGCTTCTGTTGGTTTG 59.573 45.455 0.00 0.00 0.00 2.93
3232 3502 5.529060 TGTTGGTTTGCTTTGTTTGAAGTTT 59.471 32.000 0.00 0.00 0.00 2.66
3243 3513 5.461032 TGTTTGAAGTTTGTTGTCAGGTT 57.539 34.783 0.00 0.00 0.00 3.50
3301 3571 4.335315 GCACCAACGGAATCATGAATAAGA 59.665 41.667 0.00 0.00 0.00 2.10
3304 3574 7.255104 GCACCAACGGAATCATGAATAAGATAA 60.255 37.037 0.00 0.00 0.00 1.75
3341 3611 6.959639 TTCAGCTCTTTTATGTTGGTTTCT 57.040 33.333 0.00 0.00 0.00 2.52
3343 3613 7.672983 TCAGCTCTTTTATGTTGGTTTCTAG 57.327 36.000 0.00 0.00 0.00 2.43
3346 3616 5.183140 GCTCTTTTATGTTGGTTTCTAGGCA 59.817 40.000 0.00 0.00 0.00 4.75
3364 3634 8.225603 TCTAGGCATTCCTGTTTTGAAATATC 57.774 34.615 0.00 0.00 44.08 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 7.397221 TCCCCACTAATATCAAGATATTGCAG 58.603 38.462 20.23 14.57 42.26 4.41
101 153 2.295349 GAGAGGTCCAACGTGTACAGAA 59.705 50.000 0.00 0.00 0.00 3.02
112 197 2.054021 TGACAACCATGAGAGGTCCAA 58.946 47.619 0.00 0.00 42.25 3.53
117 202 3.623906 AGATGTGACAACCATGAGAGG 57.376 47.619 0.00 0.00 0.00 3.69
120 205 5.522824 CAGTGATAGATGTGACAACCATGAG 59.477 44.000 0.00 0.00 0.00 2.90
121 206 5.046376 ACAGTGATAGATGTGACAACCATGA 60.046 40.000 0.00 0.00 0.00 3.07
191 276 2.030628 CCGTTAACCATGTGAACCCAAC 60.031 50.000 0.00 0.00 0.00 3.77
211 296 4.075682 AGCACTTTTAGAGAAGAAAGCCC 58.924 43.478 0.00 0.00 36.56 5.19
212 297 5.615764 CGAAGCACTTTTAGAGAAGAAAGCC 60.616 44.000 0.00 0.00 36.56 4.35
263 348 8.621532 ATTTGATTTTGAAGTAGCAGACACTA 57.378 30.769 0.00 0.00 0.00 2.74
398 483 0.250901 AGGTCCATGCCACTCACAAC 60.251 55.000 0.00 0.00 0.00 3.32
811 971 5.176592 GTGCTTTAGTCTAAACGGAGGAAT 58.823 41.667 0.65 0.00 0.00 3.01
957 1117 3.565307 TGAAGCTTGGGAAAATGTCACT 58.435 40.909 2.10 0.00 0.00 3.41
1063 1223 9.268282 TGGAACTAGACCTGTAAGATTATTTCT 57.732 33.333 0.00 0.00 34.07 2.52
1064 1224 9.315525 GTGGAACTAGACCTGTAAGATTATTTC 57.684 37.037 0.00 0.00 34.07 2.17
1359 1524 5.120519 GTCTAGACTATACATCCGAGAACCG 59.879 48.000 15.91 0.00 38.18 4.44
1464 1629 8.830915 TTGGCAATATTCCAAAGAACCTATTA 57.169 30.769 13.64 0.00 40.35 0.98
1524 1689 4.326826 ACATGTTTGATCTCACCGTCAAT 58.673 39.130 0.00 0.00 34.60 2.57
1556 1721 4.398358 GGCAAGTAAGGTTCTTGGGAATAC 59.602 45.833 7.58 0.00 41.50 1.89
2311 2518 1.408453 GCCCGAGTTATAGCCACCCT 61.408 60.000 0.00 0.00 0.00 4.34
2516 2773 6.605594 AGTGGTTTACAATCAGACCAGAAAAA 59.394 34.615 0.00 0.00 42.42 1.94
2541 2798 7.883311 TCCATCTGTCTGTAGTTATATGATCGA 59.117 37.037 0.00 0.00 0.00 3.59
2543 2800 9.800433 CATCCATCTGTCTGTAGTTATATGATC 57.200 37.037 0.00 0.00 0.00 2.92
2549 2806 8.708378 TCAAATCATCCATCTGTCTGTAGTTAT 58.292 33.333 0.00 0.00 0.00 1.89
2554 2811 6.994496 GGATTCAAATCATCCATCTGTCTGTA 59.006 38.462 5.19 0.00 40.21 2.74
2556 2813 6.017026 CAGGATTCAAATCATCCATCTGTCTG 60.017 42.308 5.19 0.00 42.63 3.51
2869 3129 2.210116 GTTGAAGAGCACACTTCCGAA 58.790 47.619 13.05 2.98 43.67 4.30
2891 3151 2.301346 CCCAAGGATATCTGCAACCAC 58.699 52.381 2.05 0.00 0.00 4.16
2970 3230 0.875059 GGACTACTGTTGCAAGCACC 59.125 55.000 0.00 0.00 0.00 5.01
3009 3269 4.551702 AACAAGAAATAAACCCCATGCC 57.448 40.909 0.00 0.00 0.00 4.40
3027 3287 1.887854 TGTCCTCGTCATCCGTAAACA 59.112 47.619 0.00 0.00 37.94 2.83
3033 3293 1.380524 AGTAGTGTCCTCGTCATCCG 58.619 55.000 0.00 0.00 38.13 4.18
3036 3296 3.648507 ACCTAGTAGTGTCCTCGTCAT 57.351 47.619 0.00 0.00 0.00 3.06
3059 3319 5.633182 AGAATTAAAATCGCGTTGCACAATT 59.367 32.000 5.77 6.53 0.00 2.32
3132 3392 2.363788 TCACACAGCAGATTACGTCC 57.636 50.000 0.00 0.00 0.00 4.79
3135 3395 5.750547 ACAGATTATCACACAGCAGATTACG 59.249 40.000 0.00 0.00 0.00 3.18
3146 3406 9.029243 CAGAATCACTTAGACAGATTATCACAC 57.971 37.037 0.00 0.00 32.51 3.82
3164 3424 6.864685 TCATTTTGCAGTGAAATCAGAATCAC 59.135 34.615 10.41 10.41 44.92 3.06
3165 3425 6.983984 TCATTTTGCAGTGAAATCAGAATCA 58.016 32.000 0.00 0.00 0.00 2.57
3171 3431 3.306225 GGCCTCATTTTGCAGTGAAATCA 60.306 43.478 0.00 0.00 0.00 2.57
3192 3452 2.029649 CCAACAGAAGCAAGGTCAATGG 60.030 50.000 0.00 0.00 0.00 3.16
3217 3487 5.163963 CCTGACAACAAACTTCAAACAAAGC 60.164 40.000 0.00 0.00 0.00 3.51
3232 3502 5.698741 AGATATCCATGAACCTGACAACA 57.301 39.130 0.00 0.00 0.00 3.33
3243 3513 7.235399 TCAAATACAGGCACTAGATATCCATGA 59.765 37.037 0.00 0.00 36.02 3.07
3315 3585 8.515414 AGAAACCAACATAAAAGAGCTGAATAC 58.485 33.333 0.00 0.00 0.00 1.89
3341 3611 8.593945 AAGATATTTCAAAACAGGAATGCCTA 57.406 30.769 0.00 0.00 44.80 3.93


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

AutoCloner maintained by Alex Coulton.