Multiple sequence alignment - TraesCS4A01G452200

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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 TraesCS4A01G452200 chr4A 100.000 5642 0 0 1 5642 717289165 717283524 0.000000e+00 10419.0
1 TraesCS4A01G452200 chr4A 93.750 3472 158 18 1525 4979 717803039 717806468 0.000000e+00 5155.0
2 TraesCS4A01G452200 chr4A 96.664 3028 84 6 1498 4510 717752195 717755220 0.000000e+00 5016.0
3 TraesCS4A01G452200 chr4A 97.148 2945 65 8 2048 4977 717225661 717222721 0.000000e+00 4955.0
4 TraesCS4A01G452200 chr4A 95.183 3031 124 12 1498 4510 717261313 717258287 0.000000e+00 4769.0
5 TraesCS4A01G452200 chr4A 93.769 1348 78 3 5 1348 717264580 717263235 0.000000e+00 2019.0
6 TraesCS4A01G452200 chr4A 92.704 1357 85 7 1 1348 717799640 717800991 0.000000e+00 1945.0
7 TraesCS4A01G452200 chr4A 95.450 1121 45 5 232 1348 717237358 717236240 0.000000e+00 1783.0
8 TraesCS4A01G452200 chr4A 98.588 708 10 0 1345 2052 717234903 717234196 0.000000e+00 1253.0
9 TraesCS4A01G452200 chr4A 95.553 742 33 0 1 742 717748643 717749384 0.000000e+00 1188.0
10 TraesCS4A01G452200 chr4A 98.799 666 5 1 4980 5642 717222503 717221838 0.000000e+00 1182.0
11 TraesCS4A01G452200 chr4A 94.895 666 24 3 4980 5642 717806628 717807286 0.000000e+00 1033.0
12 TraesCS4A01G452200 chr4A 94.745 666 13 4 4980 5642 717257661 717257015 0.000000e+00 1016.0
13 TraesCS4A01G452200 chr4A 97.041 507 15 0 842 1348 717749777 717750283 0.000000e+00 854.0
14 TraesCS4A01G452200 chr4A 98.721 391 5 0 5252 5642 717756095 717756485 0.000000e+00 695.0
15 TraesCS4A01G452200 chr4A 90.591 457 28 4 4522 4976 717258301 717257858 4.870000e-165 592.0
16 TraesCS4A01G452200 chr4A 96.029 277 8 1 4980 5253 717755769 717756045 1.120000e-121 448.0
17 TraesCS4A01G452200 chr4A 98.394 249 4 0 4522 4770 717755206 717755454 6.710000e-119 438.0
18 TraesCS4A01G452200 chr4A 95.455 154 7 0 1345 1498 717751608 717751761 4.370000e-61 246.0
19 TraesCS4A01G452200 chr4A 94.156 154 9 0 1345 1498 717261898 717261745 9.450000e-58 235.0
20 TraesCS4A01G452200 chr4A 93.506 154 10 0 1345 1498 717802325 717802478 4.400000e-56 230.0
21 TraesCS4A01G452200 chr4A 97.222 36 1 0 887 922 717749899 717749934 1.700000e-05 62.1
22 TraesCS4A01G452200 chr4A 94.444 36 2 0 887 922 717236623 717236588 7.900000e-04 56.5
23 TraesCS4A01G452200 chr7D 93.598 3499 175 23 1498 4976 17121093 17124562 0.000000e+00 5175.0
24 TraesCS4A01G452200 chr7D 95.050 3030 127 13 1498 4510 16761522 16758499 0.000000e+00 4743.0
25 TraesCS4A01G452200 chr7D 93.421 1368 65 12 4 1348 16764807 16763442 0.000000e+00 2004.0
26 TraesCS4A01G452200 chr7D 93.297 1298 69 8 1498 2779 16994530 16995825 0.000000e+00 1899.0
27 TraesCS4A01G452200 chr7D 93.016 673 30 5 4980 5642 16996246 16996911 0.000000e+00 966.0
28 TraesCS4A01G452200 chr7D 93.482 629 22 6 4980 5596 16757863 16757242 0.000000e+00 917.0
29 TraesCS4A01G452200 chr7D 89.398 698 63 6 6 693 17117261 17117957 0.000000e+00 869.0
30 TraesCS4A01G452200 chr7D 96.264 455 15 2 4522 4976 16758513 16758061 0.000000e+00 745.0
31 TraesCS4A01G452200 chr7D 94.412 340 18 1 1010 1348 16992270 16992609 6.480000e-144 521.0
32 TraesCS4A01G452200 chr7D 93.235 340 20 2 1010 1348 17118833 17119170 1.090000e-136 497.0
33 TraesCS4A01G452200 chr7D 95.076 264 11 2 4713 4976 16995822 16996083 1.130000e-111 414.0
34 TraesCS4A01G452200 chr7D 93.506 154 10 0 1345 1498 16762106 16761953 4.400000e-56 230.0
35 TraesCS4A01G452200 chr7A 93.598 3374 173 21 1498 4849 16314059 16317411 0.000000e+00 4994.0
36 TraesCS4A01G452200 chr7A 93.470 3032 166 15 1498 4510 16426154 16429172 0.000000e+00 4473.0
37 TraesCS4A01G452200 chr7A 91.084 2445 164 25 2449 4870 15822539 15820126 0.000000e+00 3258.0
38 TraesCS4A01G452200 chr7A 91.816 1845 116 11 2976 4813 15793428 15791612 0.000000e+00 2538.0
39 TraesCS4A01G452200 chr7A 92.425 1571 91 14 1498 3041 16380964 16382533 0.000000e+00 2217.0
40 TraesCS4A01G452200 chr7A 94.003 667 34 4 4980 5642 16429776 16430440 0.000000e+00 1005.0
41 TraesCS4A01G452200 chr7A 92.342 666 41 7 4980 5642 16394098 16394756 0.000000e+00 939.0
42 TraesCS4A01G452200 chr7A 90.950 674 48 5 4980 5642 15819830 15819159 0.000000e+00 894.0
43 TraesCS4A01G452200 chr7A 90.173 692 60 4 5 692 15837579 15836892 0.000000e+00 894.0
44 TraesCS4A01G452200 chr7A 89.625 694 66 3 5 693 16310193 16310885 0.000000e+00 878.0
45 TraesCS4A01G452200 chr7A 89.481 694 68 2 4 693 16422543 16423235 0.000000e+00 872.0
46 TraesCS4A01G452200 chr7A 95.423 437 17 1 4522 4958 16429158 16429591 0.000000e+00 693.0
47 TraesCS4A01G452200 chr7A 91.868 455 21 1 4522 4976 16393465 16393903 6.210000e-174 621.0
48 TraesCS4A01G452200 chr7A 95.550 382 17 0 5261 5642 16322918 16323299 3.740000e-171 612.0
49 TraesCS4A01G452200 chr7A 95.550 382 17 0 5261 5642 16435054 16435435 3.740000e-171 612.0
50 TraesCS4A01G452200 chr7A 93.805 339 21 0 1010 1348 16423900 16424238 1.400000e-140 510.0
51 TraesCS4A01G452200 chr7A 93.510 339 17 2 1010 1348 16378726 16379059 3.040000e-137 499.0
52 TraesCS4A01G452200 chr7A 91.065 291 16 3 4980 5267 16317626 16317909 8.870000e-103 385.0
53 TraesCS4A01G452200 chr7B 93.097 2144 111 11 2841 4979 655811491 655813602 0.000000e+00 3105.0
54 TraesCS4A01G452200 chr7B 89.899 693 65 4 5 693 655706486 655707177 0.000000e+00 887.0
55 TraesCS4A01G452200 chr7B 90.347 663 49 6 4989 5642 655813810 655814466 0.000000e+00 856.0
56 TraesCS4A01G452200 chr7B 86.641 262 23 8 690 951 655805227 655805476 4.300000e-71 279.0
57 TraesCS4A01G452200 chr7B 83.398 259 27 11 690 946 655750110 655750354 5.690000e-55 226.0
58 TraesCS4A01G452200 chr7B 97.059 34 1 0 695 728 655707575 655707608 2.200000e-04 58.4


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 TraesCS4A01G452200 chr4A 717283524 717289165 5641 True 10419.000000 10419 100.000000 1 5642 1 chr4A.!!$R1 5641
1 TraesCS4A01G452200 chr4A 717221838 717225661 3823 True 3068.500000 4955 97.973500 2048 5642 2 chr4A.!!$R2 3594
2 TraesCS4A01G452200 chr4A 717799640 717807286 7646 False 2090.750000 5155 93.713750 1 5642 4 chr4A.!!$F2 5641
3 TraesCS4A01G452200 chr4A 717257015 717264580 7565 True 1726.200000 4769 93.688800 5 5642 5 chr4A.!!$R4 5637
4 TraesCS4A01G452200 chr4A 717748643 717756485 7842 False 1118.387500 5016 96.884875 1 5642 8 chr4A.!!$F1 5641
5 TraesCS4A01G452200 chr4A 717234196 717237358 3162 True 1030.833333 1783 96.160667 232 2052 3 chr4A.!!$R3 1820
6 TraesCS4A01G452200 chr7D 17117261 17124562 7301 False 2180.333333 5175 92.077000 6 4976 3 chr7D.!!$F2 4970
7 TraesCS4A01G452200 chr7D 16757242 16764807 7565 True 1727.800000 4743 94.344600 4 5596 5 chr7D.!!$R1 5592
8 TraesCS4A01G452200 chr7D 16992270 16996911 4641 False 950.000000 1899 93.950250 1010 5642 4 chr7D.!!$F1 4632
9 TraesCS4A01G452200 chr7A 15791612 15793428 1816 True 2538.000000 2538 91.816000 2976 4813 1 chr7A.!!$R1 1837
10 TraesCS4A01G452200 chr7A 16310193 16317909 7716 False 2085.666667 4994 91.429333 5 5267 3 chr7A.!!$F3 5262
11 TraesCS4A01G452200 chr7A 15819159 15822539 3380 True 2076.000000 3258 91.017000 2449 5642 2 chr7A.!!$R3 3193
12 TraesCS4A01G452200 chr7A 16422543 16430440 7897 False 1510.600000 4473 93.236400 4 5642 5 chr7A.!!$F6 5638
13 TraesCS4A01G452200 chr7A 16378726 16382533 3807 False 1358.000000 2217 92.967500 1010 3041 2 chr7A.!!$F4 2031
14 TraesCS4A01G452200 chr7A 15836892 15837579 687 True 894.000000 894 90.173000 5 692 1 chr7A.!!$R2 687
15 TraesCS4A01G452200 chr7A 16393465 16394756 1291 False 780.000000 939 92.105000 4522 5642 2 chr7A.!!$F5 1120
16 TraesCS4A01G452200 chr7B 655811491 655814466 2975 False 1980.500000 3105 91.722000 2841 5642 2 chr7B.!!$F4 2801
17 TraesCS4A01G452200 chr7B 655706486 655707608 1122 False 472.700000 887 93.479000 5 728 2 chr7B.!!$F3 723

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
865 1972 0.249699 TGATGCGTTGAGACAACCGT 60.250 50.000 8.67 4.07 0.00 4.83 F
1098 2205 0.179100 CACGACTGGCATCGGAGAAT 60.179 55.000 18.63 0.87 46.56 2.40 F
2059 5074 1.145571 TTCCTGGCTTACCCTTGTGT 58.854 50.000 0.00 0.00 33.59 3.72 F
2685 5716 1.140852 CATCTTCCTTGGCCCGTCATA 59.859 52.381 0.00 0.00 0.00 2.15 F
4093 7138 0.319405 CTTGGTCGTAACGGGGAAGT 59.681 55.000 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 5340 0.494551 TCCAGTAGGAGGTGGGGAAA 59.505 55.000 0.00 0.00 39.61 3.13 R
2493 5514 1.455786 CGCAAACACGTGAACTCCTAG 59.544 52.381 25.01 4.02 0.00 3.02 R
3913 6957 0.404040 AATGACCCGGCCTTTGAAGA 59.596 50.000 0.00 0.00 0.00 2.87 R
4292 7337 0.606401 ACTCCTCATGTTGGTTGCCG 60.606 55.000 7.23 0.00 0.00 5.69 R
5027 8401 3.050089 TGGAGTTTTCTTGTACCTGGGA 58.950 45.455 0.00 0.00 0.00 4.37 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
145 149 0.321210 TCACCGTCATTGGCATCGTT 60.321 50.000 0.00 0.00 0.00 3.85
174 178 1.737838 ATCATCGGCAACAACGACAT 58.262 45.000 0.00 0.00 43.78 3.06
391 396 3.916392 GAGTCGCGGGTGTCTGGTG 62.916 68.421 6.13 0.00 0.00 4.17
444 456 6.238759 GGTTCACTATTTGTATGCAGGAATCC 60.239 42.308 0.00 0.00 0.00 3.01
477 489 2.758009 GCATGTTGCATGGTGTCTTTT 58.242 42.857 10.59 0.00 44.26 2.27
521 542 0.534203 ATTGACTCCGTGGCGTTTGT 60.534 50.000 0.00 0.00 0.00 2.83
750 1563 3.555966 CTCCTCTCCTCTCTTTCTCTCC 58.444 54.545 0.00 0.00 0.00 3.71
774 1603 3.522731 CCCGCTCCCTCTCTCGTG 61.523 72.222 0.00 0.00 0.00 4.35
811 1886 2.278206 CTCGACATCCACGCCGAG 60.278 66.667 0.00 0.00 41.71 4.63
812 1887 2.748647 TCGACATCCACGCCGAGA 60.749 61.111 0.00 0.00 0.00 4.04
865 1972 0.249699 TGATGCGTTGAGACAACCGT 60.250 50.000 8.67 4.07 0.00 4.83
990 2097 0.784495 TCTGGAGTCCTAGGTGTGGT 59.216 55.000 11.33 0.00 0.00 4.16
1098 2205 0.179100 CACGACTGGCATCGGAGAAT 60.179 55.000 18.63 0.87 46.56 2.40
1649 4655 3.866582 GGCGGCCTAGCATCCACT 61.867 66.667 12.87 0.00 39.27 4.00
2010 5025 1.676303 ATTTACCCAACACCGCCCG 60.676 57.895 0.00 0.00 0.00 6.13
2041 5056 5.711976 CACCAGGGATTGATCAACTTACTTT 59.288 40.000 11.07 0.00 0.00 2.66
2059 5074 1.145571 TTCCTGGCTTACCCTTGTGT 58.854 50.000 0.00 0.00 33.59 3.72
2068 5083 4.636206 GGCTTACCCTTGTGTCTATTCTTG 59.364 45.833 0.00 0.00 0.00 3.02
2173 5191 4.687215 TGCTGCTGCCGGACTCAC 62.687 66.667 5.05 0.00 38.71 3.51
2294 5314 4.393834 TGTACATACAAGCAGCTTTGGAA 58.606 39.130 4.38 0.00 32.40 3.53
2311 5331 1.798813 GGAATGATTGCCGGTATCGTC 59.201 52.381 1.90 8.20 33.95 4.20
2465 5486 3.254657 CACGTGGCTTTATTTCTTTGGGA 59.745 43.478 7.95 0.00 0.00 4.37
2493 5514 7.900782 AACCAAAGTCATGTACATGTACTAC 57.099 36.000 30.69 24.72 39.72 2.73
2534 5555 4.570772 GCGTCAAGCTTGAGTCCAAATATA 59.429 41.667 29.13 0.31 44.04 0.86
2578 5609 5.710099 GGTTAAGTCAATTTCCATGGTCTCA 59.290 40.000 12.58 0.00 0.00 3.27
2685 5716 1.140852 CATCTTCCTTGGCCCGTCATA 59.859 52.381 0.00 0.00 0.00 2.15
2693 5725 2.124445 GCCCGTCATAACCCCCAC 60.124 66.667 0.00 0.00 0.00 4.61
3341 6385 2.692368 ACCCCCATCTCCGTGCAT 60.692 61.111 0.00 0.00 0.00 3.96
3408 6452 5.300034 GGATTATTGCACTCCATCATTGTCA 59.700 40.000 0.00 0.00 0.00 3.58
3913 6957 5.184479 CACATTTGATCAAGGAGATGGTGTT 59.816 40.000 17.81 0.00 37.00 3.32
3978 7022 1.511850 CGTGCATTTGACACCTCAGA 58.488 50.000 0.00 0.00 34.45 3.27
4093 7138 0.319405 CTTGGTCGTAACGGGGAAGT 59.681 55.000 0.00 0.00 0.00 3.01
4181 7226 1.964373 GGCGTTCTTCTTGGGCGAA 60.964 57.895 0.00 0.00 0.00 4.70
4292 7337 7.035840 TCGAGTATTTTCATACCCAGTAGAC 57.964 40.000 0.00 0.00 36.63 2.59
4597 7681 5.067153 ACTTGTGCTACATGTTGCTGTTTTA 59.933 36.000 28.07 8.47 33.38 1.52
4817 7906 4.338964 ACAGAGACAATCAAATGCACACAA 59.661 37.500 0.00 0.00 0.00 3.33
4872 7961 1.661617 TGTTTGGTTGTCGAACACTCG 59.338 47.619 0.00 0.00 42.98 4.18
4899 7990 4.333926 TGCCTAATTTTTGTTGGTGCAAAC 59.666 37.500 0.00 0.00 37.98 2.93
5027 8401 3.555966 GCCTAGCCCATGTTATCAAGTT 58.444 45.455 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 149 2.689553 TGCCGATGATAGCAAAGTGA 57.310 45.000 0.00 0.00 35.69 3.41
174 178 4.462133 CGACCTCTCCTCTTTGTCCTATA 58.538 47.826 0.00 0.00 0.00 1.31
391 396 3.008049 ACACCAATGACCTTACCTCACTC 59.992 47.826 0.00 0.00 0.00 3.51
530 551 0.307760 GTGTTGGTCAGTTTGCTCGG 59.692 55.000 0.00 0.00 0.00 4.63
774 1603 1.302271 GGAAGGGGGAACGTGTGTC 60.302 63.158 0.00 0.00 0.00 3.67
865 1972 1.071699 GAAACACAGTAGGAGCCCACA 59.928 52.381 0.00 0.00 0.00 4.17
1022 2129 1.199327 CTCCATCGCCAATCATCATGC 59.801 52.381 0.00 0.00 0.00 4.06
1098 2205 2.875933 CGAAGTGGAGGCAACAACTAAA 59.124 45.455 0.00 0.00 41.41 1.85
2041 5056 0.690762 GACACAAGGGTAAGCCAGGA 59.309 55.000 0.00 0.00 36.17 3.86
2059 5074 4.973168 AGCACCACAAAGACAAGAATAGA 58.027 39.130 0.00 0.00 0.00 1.98
2068 5083 0.746659 AAGCCAAGCACCACAAAGAC 59.253 50.000 0.00 0.00 0.00 3.01
2294 5314 0.671796 TCGACGATACCGGCAATCAT 59.328 50.000 15.54 2.28 46.16 2.45
2311 5331 1.080025 GGTGGGGAAAGTCTCGTCG 60.080 63.158 0.00 0.00 0.00 5.12
2320 5340 0.494551 TCCAGTAGGAGGTGGGGAAA 59.505 55.000 0.00 0.00 39.61 3.13
2465 5486 8.154856 AGTACATGTACATGACTTTGGTTAGTT 58.845 33.333 36.36 15.47 41.20 2.24
2493 5514 1.455786 CGCAAACACGTGAACTCCTAG 59.544 52.381 25.01 4.02 0.00 3.02
2543 5564 9.178758 GGAAATTGACTTAACCTAGATCACATT 57.821 33.333 0.00 0.00 0.00 2.71
2578 5609 6.824958 AATATATATACTCGGCCAACCCAT 57.175 37.500 2.24 0.00 0.00 4.00
2693 5725 1.741770 GCGTAGAGGTTGCCCACAG 60.742 63.158 0.00 0.00 0.00 3.66
3164 6204 8.417273 TGGTACTGCTACAGCTATGATAATTA 57.583 34.615 2.44 0.00 42.66 1.40
3165 6205 7.303182 TGGTACTGCTACAGCTATGATAATT 57.697 36.000 2.44 0.00 42.66 1.40
3322 6364 3.399181 GCACGGAGATGGGGGTGA 61.399 66.667 0.00 0.00 32.23 4.02
3341 6385 3.315765 GGGTCCAAACATGACACGA 57.684 52.632 0.00 0.00 34.36 4.35
3536 6580 1.004080 GCCAGCTGAGCTTGTCTGA 60.004 57.895 17.39 0.00 36.40 3.27
3913 6957 0.404040 AATGACCCGGCCTTTGAAGA 59.596 50.000 0.00 0.00 0.00 2.87
3978 7022 7.615403 TCAAGTCTTAGTAGCTCAACATGAAT 58.385 34.615 0.00 0.00 0.00 2.57
4093 7138 5.305386 TCAGTTGAGAAGTCAATGGAGAAGA 59.695 40.000 0.00 0.00 44.58 2.87
4181 7226 1.589803 GTGGCTGTCCAGTACGTTTT 58.410 50.000 0.00 0.00 44.48 2.43
4292 7337 0.606401 ACTCCTCATGTTGGTTGCCG 60.606 55.000 7.23 0.00 0.00 5.69
4597 7681 5.254115 GGGAGTAATTAACAAGGTTCAGCT 58.746 41.667 0.00 0.00 0.00 4.24
4872 7961 4.306600 CACCAACAAAAATTAGGCAGACC 58.693 43.478 0.00 0.00 0.00 3.85
5027 8401 3.050089 TGGAGTTTTCTTGTACCTGGGA 58.950 45.455 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.