Multiple sequence alignment - TraesCS1D01G030800

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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 TraesCS1D01G030800 chr1D 100.000 4106 0 0 1 4106 12032963 12028858 0.000000e+00 7583.0
1 TraesCS1D01G030800 chr1D 98.901 3822 23 2 1 3803 12163325 12159504 0.000000e+00 6807.0
2 TraesCS1D01G030800 chr1D 85.013 3096 332 62 271 3264 12057735 12054670 0.000000e+00 3025.0
3 TraesCS1D01G030800 chr1D 89.452 2228 214 12 887 3096 12222823 12220599 0.000000e+00 2793.0
4 TraesCS1D01G030800 chr1D 88.233 2269 236 17 887 3131 12149768 12147507 0.000000e+00 2682.0
5 TraesCS1D01G030800 chr1D 88.414 2011 192 13 1156 3135 12006857 12004857 0.000000e+00 2385.0
6 TraesCS1D01G030800 chr1D 86.798 2030 214 25 1151 3131 12052938 12050914 0.000000e+00 2215.0
7 TraesCS1D01G030800 chr1D 87.393 1404 147 12 1760 3133 12020006 12018603 0.000000e+00 1585.0
8 TraesCS1D01G030800 chr1D 87.615 759 55 16 1 733 12223768 12223023 0.000000e+00 845.0
9 TraesCS1D01G030800 chr1D 81.561 602 74 23 311 887 11972650 11972061 2.890000e-126 462.0
10 TraesCS1D01G030800 chr1D 81.754 570 72 22 24 572 12008141 12007583 8.100000e-122 448.0
11 TraesCS1D01G030800 chr1D 83.168 505 42 12 352 823 12150361 12149867 4.910000e-114 422.0
12 TraesCS1D01G030800 chr1D 79.606 559 63 25 352 887 12021504 12020974 1.820000e-93 353.0
13 TraesCS1D01G030800 chr1D 79.418 481 55 18 276 735 12013119 12012662 2.400000e-77 300.0
14 TraesCS1D01G030800 chr1D 80.412 291 21 16 3575 3845 12218648 12218374 5.420000e-44 189.0
15 TraesCS1D01G030800 chr1D 80.620 258 32 6 3773 4021 12017958 12017710 2.520000e-42 183.0
16 TraesCS1D01G030800 chr1D 77.903 267 37 17 3754 4010 12226657 12226403 3.310000e-31 147.0
17 TraesCS1D01G030800 chr1D 82.486 177 15 7 3575 3739 12147222 12147050 1.540000e-29 141.0
18 TraesCS1D01G030800 chr1D 79.736 227 17 18 3817 4021 12311211 12310992 1.990000e-28 137.0
19 TraesCS1D01G030800 chr1D 81.818 176 19 8 3684 3858 12041554 12041391 7.160000e-28 135.0
20 TraesCS1D01G030800 chr1D 87.387 111 13 1 777 887 12012664 12012555 4.310000e-25 126.0
21 TraesCS1D01G030800 chr1D 96.296 54 2 0 3953 4006 12218318 12218265 5.650000e-14 89.8
22 TraesCS1D01G030800 chr1D 93.220 59 4 0 3963 4021 12009802 12009744 2.030000e-13 87.9
23 TraesCS1D01G030800 chr1D 86.957 69 8 1 819 887 12222968 12222901 4.400000e-10 76.8
24 TraesCS1D01G030800 chr1D 85.246 61 4 4 3653 3712 12214501 12214445 1.590000e-04 58.4
25 TraesCS1D01G030800 chr1A 91.838 2573 161 25 887 3418 14077472 14074908 0.000000e+00 3542.0
26 TraesCS1D01G030800 chr1A 85.777 2496 270 43 887 3307 14051508 14049023 0.000000e+00 2564.0
27 TraesCS1D01G030800 chr1A 87.055 1406 152 9 1760 3135 14070507 14069102 0.000000e+00 1561.0
28 TraesCS1D01G030800 chr1A 86.183 854 105 7 887 1729 14071359 14070508 0.000000e+00 911.0
29 TraesCS1D01G030800 chr1A 87.124 598 46 20 165 736 14078240 14077648 0.000000e+00 649.0
30 TraesCS1D01G030800 chr1A 78.524 908 88 47 34 890 14052475 14051624 7.930000e-137 497.0
31 TraesCS1D01G030800 chr1A 77.255 787 96 46 145 890 14056362 14055618 6.440000e-103 385.0
32 TraesCS1D01G030800 chr1A 78.358 670 70 30 113 736 14066284 14065644 8.390000e-97 364.0
33 TraesCS1D01G030800 chr1A 90.000 270 23 2 887 1152 14065424 14065155 3.040000e-91 346.0
34 TraesCS1D01G030800 chr1A 78.610 374 45 26 318 666 14133236 14132873 8.940000e-52 215.0
35 TraesCS1D01G030800 chr1A 80.534 262 25 14 3772 4021 14068504 14068257 1.170000e-40 178.0
36 TraesCS1D01G030800 chr1A 89.189 111 11 1 777 887 14065647 14065538 1.990000e-28 137.0
37 TraesCS1D01G030800 chr1A 88.889 54 3 2 3368 3418 14062897 14062844 3.430000e-06 63.9
38 TraesCS1D01G030800 chr1A 81.250 80 9 5 3652 3731 14082124 14082051 4.430000e-05 60.2
39 TraesCS1D01G030800 chr1B 92.101 1899 106 22 1456 3321 17770397 17768510 0.000000e+00 2636.0
40 TraesCS1D01G030800 chr1B 86.168 2205 232 35 1153 3297 17745739 17743548 0.000000e+00 2314.0
41 TraesCS1D01G030800 chr1B 94.884 1036 42 5 387 1411 17771429 17770394 0.000000e+00 1609.0
42 TraesCS1D01G030800 chr1B 86.082 855 107 4 887 1729 17759742 17758888 0.000000e+00 909.0
43 TraesCS1D01G030800 chr1B 82.801 564 59 16 352 887 17746711 17746158 1.730000e-128 470.0
44 TraesCS1D01G030800 chr1B 79.563 504 60 30 322 793 17783680 17783188 1.840000e-83 320.0
45 TraesCS1D01G030800 chr1B 86.147 231 27 3 354 584 17761794 17761569 1.140000e-60 244.0
46 TraesCS1D01G030800 chr1B 90.643 171 12 1 2 168 17771600 17771430 1.490000e-54 224.0
47 TraesCS1D01G030800 chr1B 81.509 265 28 13 3785 4035 17742904 17742647 9.000000e-47 198.0
48 TraesCS1D01G030800 chr1B 80.077 261 31 13 3776 4021 17780086 17779832 1.520000e-39 174.0
49 TraesCS1D01G030800 chr1B 90.625 128 11 1 760 887 17759943 17759817 7.060000e-38 169.0
50 TraesCS1D01G030800 chr1B 86.164 159 16 2 3564 3716 17768070 17767912 2.540000e-37 167.0
51 TraesCS1D01G030800 chr1B 87.200 125 14 1 3295 3417 17768377 17768253 1.540000e-29 141.0
52 TraesCS1D01G030800 chr1B 85.185 135 13 3 120 247 17748906 17748772 9.260000e-27 132.0
53 TraesCS1D01G030800 chr1B 84.375 128 13 7 120 240 17747000 17746873 7.210000e-23 119.0
54 TraesCS1D01G030800 chr1B 94.118 51 3 0 3406 3456 158428383 158428433 1.220000e-10 78.7
55 TraesCS1D01G030800 chr1B 94.118 51 3 0 3406 3456 320683900 320683850 1.220000e-10 78.7
56 TraesCS1D01G030800 chr1B 91.071 56 5 0 3664 3719 17780146 17780091 4.400000e-10 76.8
57 TraesCS1D01G030800 chr1B 92.000 50 4 0 3368 3417 17784410 17784361 2.050000e-08 71.3
58 TraesCS1D01G030800 chr6B 97.917 48 1 0 3412 3459 595956698 595956745 2.630000e-12 84.2
59 TraesCS1D01G030800 chr6A 97.917 48 1 0 3412 3459 142784314 142784267 2.630000e-12 84.2
60 TraesCS1D01G030800 chr6A 96.000 50 1 1 3411 3459 63593650 63593699 3.400000e-11 80.5
61 TraesCS1D01G030800 chr7B 94.118 51 3 0 3406 3456 223985049 223985099 1.220000e-10 78.7
62 TraesCS1D01G030800 chr5B 94.118 51 3 0 3406 3456 270549971 270550021 1.220000e-10 78.7
63 TraesCS1D01G030800 chr4B 94.118 51 3 0 3406 3456 415824556 415824606 1.220000e-10 78.7


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 TraesCS1D01G030800 chr1D 12028858 12032963 4105 True 7583.000000 7583 100.000000 1 4106 1 chr1D.!!$R2 4105
1 TraesCS1D01G030800 chr1D 12159504 12163325 3821 True 6807.000000 6807 98.901000 1 3803 1 chr1D.!!$R4 3802
2 TraesCS1D01G030800 chr1D 12050914 12057735 6821 True 2620.000000 3025 85.905500 271 3264 2 chr1D.!!$R8 2993
3 TraesCS1D01G030800 chr1D 12147050 12150361 3311 True 1081.666667 2682 84.629000 352 3739 3 chr1D.!!$R9 3387
4 TraesCS1D01G030800 chr1D 12017710 12021504 3794 True 707.000000 1585 82.539667 352 4021 3 chr1D.!!$R7 3669
5 TraesCS1D01G030800 chr1D 12004857 12013119 8262 True 669.380000 2385 86.038600 24 4021 5 chr1D.!!$R6 3997
6 TraesCS1D01G030800 chr1D 12214445 12226657 12212 True 599.857143 2793 86.268714 1 4010 7 chr1D.!!$R10 4009
7 TraesCS1D01G030800 chr1D 11972061 11972650 589 True 462.000000 462 81.561000 311 887 1 chr1D.!!$R1 576
8 TraesCS1D01G030800 chr1A 14049023 14056362 7339 True 1148.666667 2564 80.518667 34 3307 3 chr1A.!!$R2 3273
9 TraesCS1D01G030800 chr1A 14062844 14082124 19280 True 781.210000 3542 86.042000 113 4021 10 chr1A.!!$R3 3908
10 TraesCS1D01G030800 chr1B 17767912 17771600 3688 True 955.400000 2636 90.198400 2 3716 5 chr1B.!!$R4 3714
11 TraesCS1D01G030800 chr1B 17742647 17748906 6259 True 646.600000 2314 84.007600 120 4035 5 chr1B.!!$R2 3915
12 TraesCS1D01G030800 chr1B 17758888 17761794 2906 True 440.666667 909 87.618000 354 1729 3 chr1B.!!$R3 1375

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
2411 29812 2.024655 TCACAGGTATAGACGTTCCCCT 60.025 50.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3934 39534 1.202166 GCGTAGGAGAAGGAAGACGAC 60.202 57.143 0.0 0.0 32.2 4.34 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
2411 29812 2.024655 TCACAGGTATAGACGTTCCCCT 60.025 50.000 0.00 0.00 0.00 4.79
2561 29962 5.977635 TGATGATCTTAACATTGACGAGGT 58.022 37.500 0.00 0.00 0.00 3.85
3138 35972 0.920664 GTTTTTCAAGTGCACACGCC 59.079 50.000 21.04 0.00 37.32 5.68
3189 36048 3.191371 GGGTCTAAATTGCTGAACACCAG 59.809 47.826 0.00 0.00 45.67 4.00
3798 38432 1.955080 CTAGTTCCCTAGGGCACTACG 59.045 57.143 30.06 22.49 39.86 3.51
3805 38439 2.169769 CCCTAGGGCACTACGAAATCAA 59.830 50.000 16.90 0.00 0.00 2.57
3858 38492 1.996187 GGAGGGAGGGACCTTGGAC 60.996 68.421 0.00 0.00 42.10 4.02
3862 38496 1.685820 GGAGGGACCTTGGACTTGG 59.314 63.158 0.00 0.00 35.41 3.61
3869 38503 2.045926 CTTGGACTTGGAGGCGGG 60.046 66.667 0.00 0.00 0.00 6.13
3924 39524 2.504996 CCAAGGAGCTCCAAGAGAAGAT 59.495 50.000 33.90 7.59 38.89 2.40
3933 39533 1.490574 CAAGAGAAGATCCCCTCCGT 58.509 55.000 7.99 0.00 0.00 4.69
3934 39534 1.137872 CAAGAGAAGATCCCCTCCGTG 59.862 57.143 7.99 4.42 0.00 4.94
4039 39648 2.922162 TCCAAGAGGAGAGATGGGC 58.078 57.895 0.00 0.00 39.61 5.36
4040 39649 0.043183 TCCAAGAGGAGAGATGGGCA 59.957 55.000 0.00 0.00 39.61 5.36
4041 39650 1.138568 CCAAGAGGAGAGATGGGCAT 58.861 55.000 0.00 0.00 36.89 4.40
4042 39651 1.072015 CCAAGAGGAGAGATGGGCATC 59.928 57.143 0.00 0.00 36.89 3.91
4043 39652 3.291925 CCAAGAGGAGAGATGGGCATCT 61.292 54.545 0.00 0.00 43.72 2.90
4044 39653 4.775406 CCAAGAGGAGAGATGGGCATCTT 61.775 52.174 0.00 0.00 42.16 2.40
4045 39654 6.218368 CCAAGAGGAGAGATGGGCATCTTT 62.218 50.000 0.00 0.00 42.16 2.52
4046 39655 7.625699 CCAAGAGGAGAGATGGGCATCTTTT 62.626 48.000 0.00 0.00 42.16 2.27
4052 39661 1.287146 AGATGGGCATCTTTTCAGCCT 59.713 47.619 0.00 0.00 45.31 4.58
4053 39662 2.511218 AGATGGGCATCTTTTCAGCCTA 59.489 45.455 0.00 0.00 45.31 3.93
4056 39665 1.017387 GGCATCTTTTCAGCCTACGG 58.983 55.000 0.00 0.00 44.92 4.02
4057 39666 1.406887 GGCATCTTTTCAGCCTACGGA 60.407 52.381 0.00 0.00 44.92 4.69
4058 39667 1.936547 GCATCTTTTCAGCCTACGGAG 59.063 52.381 0.00 0.00 0.00 4.63
4062 39671 3.162666 TCTTTTCAGCCTACGGAGAGAA 58.837 45.455 0.00 0.00 0.00 2.87
4063 39672 3.769844 TCTTTTCAGCCTACGGAGAGAAT 59.230 43.478 0.00 0.00 0.00 2.40
4064 39673 4.223032 TCTTTTCAGCCTACGGAGAGAATT 59.777 41.667 0.00 0.00 0.00 2.17
4065 39674 4.553330 TTTCAGCCTACGGAGAGAATTT 57.447 40.909 0.00 0.00 0.00 1.82
4067 39676 4.650754 TCAGCCTACGGAGAGAATTTAC 57.349 45.455 0.00 0.00 0.00 2.01
4068 39677 4.279145 TCAGCCTACGGAGAGAATTTACT 58.721 43.478 0.00 0.00 0.00 2.24
4069 39678 4.710375 TCAGCCTACGGAGAGAATTTACTT 59.290 41.667 0.00 0.00 0.00 2.24
4070 39679 5.187186 TCAGCCTACGGAGAGAATTTACTTT 59.813 40.000 0.00 0.00 0.00 2.66
4071 39680 5.875359 CAGCCTACGGAGAGAATTTACTTTT 59.125 40.000 0.00 0.00 0.00 2.27
4101 39710 7.714703 AGACATACGGAGAGAATTTACTTACC 58.285 38.462 0.00 0.00 0.00 2.85
4102 39711 6.814043 ACATACGGAGAGAATTTACTTACCC 58.186 40.000 0.00 0.00 0.00 3.69
4105 39714 4.161754 ACGGAGAGAATTTACTTACCCTGG 59.838 45.833 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1983 17287 1.601759 AGCTTGTGCGCAGTGGATT 60.602 52.632 12.22 0.00 45.42 3.01
2411 29812 4.430388 AGGGGTGGAAACCTGACA 57.570 55.556 0.00 0.00 35.30 3.58
3138 35972 4.645762 TGAGAATCTAGTAGCTGCACAG 57.354 45.455 4.12 0.62 34.92 3.66
3189 36048 7.869937 TCATCTGACGAAAGAATATCCATCTTC 59.130 37.037 0.00 0.00 36.14 2.87
3458 36678 9.750882 CATATTCAGCATAATGATTGTAAGACG 57.249 33.333 0.00 0.00 0.00 4.18
3798 38432 1.734465 CTCTGTCGCCCTGTTGATTTC 59.266 52.381 0.00 0.00 0.00 2.17
3805 38439 2.920645 CGTGTCTCTGTCGCCCTGT 61.921 63.158 0.00 0.00 0.00 4.00
3924 39524 1.975407 GAAGACGACACGGAGGGGA 60.975 63.158 0.00 0.00 0.00 4.81
3933 39533 2.082231 CGTAGGAGAAGGAAGACGACA 58.918 52.381 0.00 0.00 32.20 4.35
3934 39534 1.202166 GCGTAGGAGAAGGAAGACGAC 60.202 57.143 0.00 0.00 32.20 4.34
4023 39632 2.048601 AGATGCCCATCTCTCCTCTTG 58.951 52.381 4.98 0.00 44.37 3.02
4025 39634 2.493099 AAGATGCCCATCTCTCCTCT 57.507 50.000 10.93 0.00 46.75 3.69
4035 39644 4.900643 CCGTAGGCTGAAAAGATGCCCA 62.901 54.545 0.00 0.00 46.14 5.36
4036 39645 2.349148 CCGTAGGCTGAAAAGATGCCC 61.349 57.143 0.00 0.00 46.14 5.36
4075 39684 8.844244 GGTAAGTAAATTCTCTCCGTATGTCTA 58.156 37.037 0.00 0.00 0.00 2.59
4077 39686 6.922407 GGGTAAGTAAATTCTCTCCGTATGTC 59.078 42.308 0.00 0.00 0.00 3.06
4078 39687 6.610425 AGGGTAAGTAAATTCTCTCCGTATGT 59.390 38.462 0.00 0.00 0.00 2.29
4079 39688 6.924060 CAGGGTAAGTAAATTCTCTCCGTATG 59.076 42.308 0.00 0.00 0.00 2.39
4080 39689 6.041751 CCAGGGTAAGTAAATTCTCTCCGTAT 59.958 42.308 0.00 0.00 0.00 3.06
4081 39690 5.361857 CCAGGGTAAGTAAATTCTCTCCGTA 59.638 44.000 0.00 0.00 0.00 4.02
4082 39691 4.161754 CCAGGGTAAGTAAATTCTCTCCGT 59.838 45.833 0.00 0.00 0.00 4.69
4083 39692 4.694339 CCAGGGTAAGTAAATTCTCTCCG 58.306 47.826 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.