Multiple sequence alignment - TraesCS6D01G406800

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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 TraesCS6D01G406800 chr6D 100.000 8169 0 0 1 8169 472947072 472938904 0.000000e+00 15086.0
1 TraesCS6D01G406800 chr6D 87.605 1791 193 14 1864 3643 472966974 472965202 0.000000e+00 2050.0
2 TraesCS6D01G406800 chr6D 90.483 1345 124 3 5783 7126 472963319 472961978 0.000000e+00 1772.0
3 TraesCS6D01G406800 chr6D 93.519 1188 77 0 2258 3445 472941207 472940020 0.000000e+00 1768.0
4 TraesCS6D01G406800 chr6D 93.519 1188 77 0 5866 7053 472944815 472943628 0.000000e+00 1768.0
5 TraesCS6D01G406800 chr6D 91.077 1188 106 0 5866 7053 472966583 472965396 0.000000e+00 1607.0
6 TraesCS6D01G406800 chr6D 90.360 1193 115 0 2258 3450 472963236 472962044 0.000000e+00 1567.0
7 TraesCS6D01G406800 chr6D 85.563 568 61 19 4848 5405 472964063 472963507 7.110000e-160 575.0
8 TraesCS6D01G406800 chr6D 82.085 681 67 17 298 932 472968523 472967852 1.560000e-146 531.0
9 TraesCS6D01G406800 chr6D 91.935 310 22 3 4385 4694 472964705 472964399 1.630000e-116 431.0
10 TraesCS6D01G406800 chr6D 85.203 419 46 9 988 1400 472967837 472967429 4.560000e-112 416.0
11 TraesCS6D01G406800 chr6D 81.368 424 52 14 1 424 472949128 472948732 3.680000e-83 320.0
12 TraesCS6D01G406800 chr6D 87.361 269 21 6 4001 4261 472965033 472964770 6.200000e-76 296.0
13 TraesCS6D01G406800 chr6D 87.970 266 13 9 1 259 472969057 472968804 6.200000e-76 296.0
14 TraesCS6D01G406800 chr6D 78.353 425 65 11 4 427 472970475 472970077 4.900000e-62 250.0
15 TraesCS6D01G406800 chr6D 90.964 166 14 1 5403 5567 68652263 68652428 1.070000e-53 222.0
16 TraesCS6D01G406800 chr6D 82.288 271 28 11 1700 1956 472967095 472966831 4.960000e-52 217.0
17 TraesCS6D01G406800 chr6A 94.930 2229 106 6 5866 8090 616880323 616882548 0.000000e+00 3483.0
18 TraesCS6D01G406800 chr6A 87.783 1588 158 11 1869 3450 616861455 616863012 0.000000e+00 1825.0
19 TraesCS6D01G406800 chr6A 93.215 1238 84 0 2208 3445 616880273 616881510 0.000000e+00 1821.0
20 TraesCS6D01G406800 chr6A 90.808 1262 115 1 5866 7126 616861820 616863081 0.000000e+00 1687.0
21 TraesCS6D01G406800 chr6A 91.422 443 25 10 1010 1448 616878971 616879404 5.460000e-166 595.0
22 TraesCS6D01G406800 chr6A 83.659 410 42 7 988 1380 616860565 616860966 6.030000e-96 363.0
23 TraesCS6D01G406800 chr6A 86.716 271 12 10 1 259 616859287 616859545 6.240000e-71 279.0
24 TraesCS6D01G406800 chr6A 84.564 298 20 10 474 770 616875902 616876174 1.040000e-68 272.0
25 TraesCS6D01G406800 chr6A 90.608 181 5 8 770 939 616878764 616878943 6.380000e-56 230.0
26 TraesCS6D01G406800 chr6A 88.542 192 11 5 1700 1880 616861326 616861517 1.070000e-53 222.0
27 TraesCS6D01G406800 chr6A 80.000 315 46 11 305 602 616859618 616859932 4.960000e-52 217.0
28 TraesCS6D01G406800 chr6A 84.173 139 7 3 121 259 616875087 616875210 4.000000e-23 121.0
29 TraesCS6D01G406800 chr6A 85.542 83 11 1 5781 5863 88774950 88774869 1.460000e-12 86.1
30 TraesCS6D01G406800 chr6A 93.103 58 1 2 799 853 616859952 616860009 1.890000e-11 82.4
31 TraesCS6D01G406800 chr6A 87.324 71 6 1 7841 7908 616882198 616882268 2.440000e-10 78.7
32 TraesCS6D01G406800 chr6B 89.990 2048 187 9 5657 7697 718313677 718311641 0.000000e+00 2630.0
33 TraesCS6D01G406800 chr6B 91.662 1895 127 7 1816 3695 718317807 718315929 0.000000e+00 2595.0
34 TraesCS6D01G406800 chr6B 87.442 1736 190 12 1919 3643 718334642 718332924 0.000000e+00 1973.0
35 TraesCS6D01G406800 chr6B 88.100 1563 179 7 5561 7120 718328951 718327393 0.000000e+00 1849.0
36 TraesCS6D01G406800 chr6B 93.676 1186 75 0 5866 7051 718317366 718316181 0.000000e+00 1775.0
37 TraesCS6D01G406800 chr6B 91.450 1193 102 0 2258 3450 718313476 718312284 0.000000e+00 1639.0
38 TraesCS6D01G406800 chr6B 90.809 1186 109 0 5868 7053 718334303 718333118 0.000000e+00 1587.0
39 TraesCS6D01G406800 chr6B 89.271 1193 128 0 2258 3450 718328648 718327456 0.000000e+00 1495.0
40 TraesCS6D01G406800 chr6B 86.484 947 108 14 4471 5405 718314868 718313930 0.000000e+00 1022.0
41 TraesCS6D01G406800 chr6B 87.172 647 36 20 675 1286 718319033 718318399 0.000000e+00 691.0
42 TraesCS6D01G406800 chr6B 84.144 555 71 15 4862 5405 718329496 718328948 9.400000e-144 521.0
43 TraesCS6D01G406800 chr6B 84.363 518 56 5 1503 2020 718318197 718317705 1.230000e-132 484.0
44 TraesCS6D01G406800 chr6B 80.296 675 76 23 298 932 718336027 718335370 2.690000e-124 457.0
45 TraesCS6D01G406800 chr6B 88.630 387 16 6 276 638 718319592 718319210 5.820000e-121 446.0
46 TraesCS6D01G406800 chr6B 94.239 243 13 1 3750 3991 514883688 514883446 3.600000e-98 370.0
47 TraesCS6D01G406800 chr6B 93.827 243 14 1 3755 3996 129021371 129021613 1.680000e-96 364.0
48 TraesCS6D01G406800 chr6B 83.171 410 38 16 1052 1449 718335312 718334922 6.070000e-91 346.0
49 TraesCS6D01G406800 chr6B 96.429 196 4 2 84 276 718320024 718319829 3.680000e-83 320.0
50 TraesCS6D01G406800 chr6B 91.549 213 18 0 1237 1449 718318410 718318198 2.230000e-75 294.0
51 TraesCS6D01G406800 chr6B 85.232 237 17 4 15 244 718336903 718336678 2.290000e-55 228.0
52 TraesCS6D01G406800 chr6B 84.862 218 32 1 4471 4687 718330127 718329910 1.380000e-52 219.0
53 TraesCS6D01G406800 chr6B 92.617 149 10 1 1 149 718339294 718339147 6.420000e-51 213.0
54 TraesCS6D01G406800 chr6B 90.184 163 13 3 5404 5564 281335142 281335303 8.310000e-50 209.0
55 TraesCS6D01G406800 chr6B 90.604 149 14 0 1503 1651 718334921 718334773 1.800000e-46 198.0
56 TraesCS6D01G406800 chr6B 94.340 106 6 0 4323 4428 718315404 718315299 6.560000e-36 163.0
57 TraesCS6D01G406800 chr6B 95.960 99 4 0 4004 4102 718315865 718315767 2.360000e-35 161.0
58 TraesCS6D01G406800 chr6B 87.591 137 16 1 4088 4223 718331943 718331807 3.050000e-34 158.0
59 TraesCS6D01G406800 chr6B 92.391 92 7 0 1 92 718320805 718320714 1.850000e-26 132.0
60 TraesCS6D01G406800 chr6B 93.182 88 6 0 650 737 718318883 718318796 6.650000e-26 130.0
61 TraesCS6D01G406800 chr6B 82.353 153 19 7 4716 4864 718329745 718329597 8.610000e-25 126.0
62 TraesCS6D01G406800 chr6B 92.683 82 2 3 653 733 718319115 718319037 1.860000e-21 115.0
63 TraesCS6D01G406800 chr6B 86.000 100 10 4 782 881 718335682 718335587 4.030000e-18 104.0
64 TraesCS6D01G406800 chr5D 82.965 634 68 26 295 898 546337000 546337623 3.360000e-148 536.0
65 TraesCS6D01G406800 chr5D 85.225 467 52 7 988 1449 546337643 546338097 1.610000e-126 464.0
66 TraesCS6D01G406800 chr5D 86.508 252 16 6 1 245 546331974 546332214 2.260000e-65 261.0
67 TraesCS6D01G406800 chr5D 94.000 150 9 0 1 150 546313868 546314017 2.290000e-55 228.0
68 TraesCS6D01G406800 chr5D 88.000 100 8 4 782 881 546337353 546337448 1.860000e-21 115.0
69 TraesCS6D01G406800 chr5D 86.667 75 9 1 5781 5855 138470300 138470373 1.890000e-11 82.4
70 TraesCS6D01G406800 chr5D 95.000 40 2 0 4261 4300 340529837 340529876 6.840000e-06 63.9
71 TraesCS6D01G406800 chr2B 95.259 232 10 1 3761 3991 612565234 612565465 4.660000e-97 366.0
72 TraesCS6D01G406800 chr2B 89.222 167 2 3 3846 3996 45311806 45311972 2.330000e-45 195.0
73 TraesCS6D01G406800 chr2B 97.561 41 1 0 4265 4305 212932978 212932938 4.090000e-08 71.3
74 TraesCS6D01G406800 chr4B 93.827 243 14 1 3750 3991 259199858 259199616 1.680000e-96 364.0
75 TraesCS6D01G406800 chr4B 89.881 168 14 3 5404 5570 532435002 532435167 6.420000e-51 213.0
76 TraesCS6D01G406800 chr4B 83.516 91 15 0 1500 1590 73743579 73743669 1.460000e-12 86.1
77 TraesCS6D01G406800 chr4B 88.406 69 7 1 5781 5849 483510261 483510328 1.890000e-11 82.4
78 TraesCS6D01G406800 chr4B 79.464 112 19 3 1503 1610 451367327 451367216 8.790000e-10 76.8
79 TraesCS6D01G406800 chr4B 90.000 50 3 2 4254 4302 572211416 572211464 6.840000e-06 63.9
80 TraesCS6D01G406800 chr3D 93.173 249 16 1 3754 4001 540286878 540286630 1.680000e-96 364.0
81 TraesCS6D01G406800 chr3D 86.420 81 9 2 5772 5852 482599329 482599407 4.060000e-13 87.9
82 TraesCS6D01G406800 chr1B 93.827 243 14 1 3750 3991 559902966 559902724 1.680000e-96 364.0
83 TraesCS6D01G406800 chr1B 90.310 258 9 3 3750 3991 118592819 118592562 2.840000e-84 324.0
84 TraesCS6D01G406800 chr1B 81.818 88 16 0 1503 1590 417618239 417618152 3.160000e-09 75.0
85 TraesCS6D01G406800 chr1B 88.136 59 6 1 7647 7705 661492366 661492309 1.470000e-07 69.4
86 TraesCS6D01G406800 chr1B 97.297 37 1 0 4266 4302 6393625 6393661 6.840000e-06 63.9
87 TraesCS6D01G406800 chr1B 97.059 34 1 0 4265 4298 236998325 236998292 3.180000e-04 58.4
88 TraesCS6D01G406800 chr2D 93.004 243 16 1 3755 3996 610630010 610629768 3.630000e-93 353.0
89 TraesCS6D01G406800 chr2D 88.757 169 18 1 5397 5564 336511302 336511134 1.070000e-48 206.0
90 TraesCS6D01G406800 chr7B 92.593 243 17 1 3750 3991 177083188 177083430 1.690000e-91 348.0
91 TraesCS6D01G406800 chr7B 91.358 162 13 1 5404 5564 176002831 176002992 3.840000e-53 220.0
92 TraesCS6D01G406800 chr7B 87.850 107 13 0 315 421 392852996 392853102 8.610000e-25 126.0
93 TraesCS6D01G406800 chr7B 84.270 89 12 2 1503 1589 662290599 662290511 1.460000e-12 86.1
94 TraesCS6D01G406800 chr4D 90.798 163 14 1 5404 5565 468362108 468362270 4.960000e-52 217.0
95 TraesCS6D01G406800 chr5B 90.741 162 14 1 5404 5564 358271831 358271992 1.790000e-51 215.0
96 TraesCS6D01G406800 chr5B 89.759 166 15 2 5404 5567 607838390 607838555 2.310000e-50 211.0
97 TraesCS6D01G406800 chr5B 86.486 74 10 0 1500 1573 597639201 597639274 1.890000e-11 82.4
98 TraesCS6D01G406800 chr1D 89.820 167 13 4 5404 5566 477229282 477229448 2.310000e-50 211.0
99 TraesCS6D01G406800 chr1D 83.636 110 18 0 315 424 224371559 224371450 4.030000e-18 104.0
100 TraesCS6D01G406800 chr1D 100.000 30 0 0 1390 1419 427697906 427697935 1.000000e-03 56.5
101 TraesCS6D01G406800 chr5A 77.872 235 49 2 1782 2016 664260982 664261213 8.550000e-30 143.0
102 TraesCS6D01G406800 chr5A 88.000 75 8 1 5781 5855 184231622 184231549 4.060000e-13 87.9
103 TraesCS6D01G406800 chr5A 91.111 45 3 1 4265 4309 44896996 44896953 8.850000e-05 60.2
104 TraesCS6D01G406800 chr4A 82.192 146 25 1 1505 1650 666643254 666643398 3.100000e-24 124.0
105 TraesCS6D01G406800 chrUn 83.654 104 16 1 310 413 322729784 322729886 6.750000e-16 97.1
106 TraesCS6D01G406800 chr7A 83.654 104 16 1 310 413 37344717 37344819 6.750000e-16 97.1
107 TraesCS6D01G406800 chr3B 83.168 101 14 3 315 413 787664110 787664011 1.130000e-13 89.8
108 TraesCS6D01G406800 chr3B 94.737 38 2 0 4265 4302 436546325 436546288 8.850000e-05 60.2
109 TraesCS6D01G406800 chr2A 88.732 71 8 0 5781 5851 141506388 141506318 4.060000e-13 87.9
110 TraesCS6D01G406800 chr2A 97.297 37 1 0 4265 4301 83760589 83760625 6.840000e-06 63.9
111 TraesCS6D01G406800 chr7D 77.333 150 25 6 1503 1650 80321485 80321627 6.800000e-11 80.5
112 TraesCS6D01G406800 chr3A 92.857 42 1 2 4261 4302 477150745 477150706 8.850000e-05 60.2


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 TraesCS6D01G406800 chr6D 472938904 472947072 8168 True 15086.000000 15086 100.000000 1 8169 1 chr6D.!!$R1 8168
1 TraesCS6D01G406800 chr6D 472940020 472949128 9108 True 1285.333333 1768 89.468667 1 7053 3 chr6D.!!$R2 7052
2 TraesCS6D01G406800 chr6D 472961978 472970475 8497 True 834.000000 2050 86.690250 1 7126 12 chr6D.!!$R3 7125
3 TraesCS6D01G406800 chr6A 616875087 616882548 7461 False 942.957143 3483 89.462286 121 8090 7 chr6A.!!$F2 7969
4 TraesCS6D01G406800 chr6A 616859287 616863081 3794 False 667.914286 1825 87.230143 1 7126 7 chr6A.!!$F1 7125
5 TraesCS6D01G406800 chr6B 718311641 718320805 9164 True 839.800000 2630 91.330733 1 7697 15 chr6B.!!$R2 7696
6 TraesCS6D01G406800 chr6B 718327393 718339294 11901 True 676.714286 1973 86.606571 1 7120 14 chr6B.!!$R3 7119
7 TraesCS6D01G406800 chr5D 546337000 546338097 1097 False 371.666667 536 85.396667 295 1449 3 chr5D.!!$F5 1154

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
7128 24647 3.67998 GCGATGCGGTCTATATGAAACAT 59.32 43.478 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
7960 25488 7.022979 CACAAGAATTTCAAATATGCGTCAGA 58.977 34.615 0.0 0.0 0.0 3.27 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
7128 24647 3.679980 GCGATGCGGTCTATATGAAACAT 59.320 43.478 0.00 0.00 0.00 2.71
7164 24683 3.702330 TCGCATCGTACGATCTCAATTT 58.298 40.909 27.24 2.57 33.96 1.82
7241 24760 5.643348 TCAAGGTACATATGCAGAAAGTGTG 59.357 40.000 1.58 0.00 0.00 3.82
7306 24825 9.394767 TGCTACTGAATATTCTTGAAAATGCTA 57.605 29.630 16.24 0.00 0.00 3.49
7355 24874 6.702329 ACTAATTCTGAAAGTGATCGGTCTT 58.298 36.000 0.00 0.00 33.76 3.01
7388 24908 7.724305 ACTCAAACTATTTCTAAAGCGTTCA 57.276 32.000 0.00 0.00 0.00 3.18
7406 24926 4.853196 CGTTCATAATGTTTTGCAGTCTGG 59.147 41.667 1.14 0.00 0.00 3.86
7442 24963 6.334102 TGTTTTACAAATACCCCACACATC 57.666 37.500 0.00 0.00 0.00 3.06
7562 25083 7.103641 ACAACATCTCGACCTAATACAAACAT 58.896 34.615 0.00 0.00 0.00 2.71
7659 25184 2.583739 CATAGCTTCGAGAGAGATGCG 58.416 52.381 0.00 0.00 43.43 4.73
7678 25203 2.688958 GCGACTAGTGAACCTATGGTCT 59.311 50.000 0.00 0.00 33.12 3.85
7812 25339 6.655078 AAAAGAAGTAGCCATGATGTTTGT 57.345 33.333 0.00 0.00 0.00 2.83
7824 25352 7.015195 AGCCATGATGTTTGTACCTAAAAGTTT 59.985 33.333 0.00 0.00 0.00 2.66
7830 25358 6.961576 TGTTTGTACCTAAAAGTTTCCATCG 58.038 36.000 0.00 0.00 0.00 3.84
7951 25479 6.830324 AGCAAAACCATTATTCATGCTCTAGA 59.170 34.615 0.00 0.00 38.16 2.43
7967 25495 7.005062 TGCTCTAGAAAAATAAATCTGACGC 57.995 36.000 0.00 0.00 0.00 5.19
7986 25514 6.676950 TGACGCATATTTGAAATTCTTGTGT 58.323 32.000 11.52 11.52 0.00 3.72
8100 25628 6.712179 AAAACCAAAATTTGCCATGATTGT 57.288 29.167 0.00 0.00 0.00 2.71
8101 25629 7.814264 AAAACCAAAATTTGCCATGATTGTA 57.186 28.000 0.00 0.00 0.00 2.41
8102 25630 7.437793 AAACCAAAATTTGCCATGATTGTAG 57.562 32.000 0.00 0.00 0.00 2.74
8103 25631 6.357579 ACCAAAATTTGCCATGATTGTAGA 57.642 33.333 0.00 0.00 0.00 2.59
8104 25632 6.767456 ACCAAAATTTGCCATGATTGTAGAA 58.233 32.000 0.00 0.00 0.00 2.10
8105 25633 7.396418 ACCAAAATTTGCCATGATTGTAGAAT 58.604 30.769 0.00 0.00 0.00 2.40
8106 25634 7.334921 ACCAAAATTTGCCATGATTGTAGAATG 59.665 33.333 0.00 0.00 0.00 2.67
8107 25635 7.334921 CCAAAATTTGCCATGATTGTAGAATGT 59.665 33.333 0.00 0.00 0.00 2.71
8108 25636 8.723311 CAAAATTTGCCATGATTGTAGAATGTT 58.277 29.630 0.00 0.00 0.00 2.71
8109 25637 8.851541 AAATTTGCCATGATTGTAGAATGTTT 57.148 26.923 0.00 0.00 0.00 2.83
8110 25638 9.941325 AAATTTGCCATGATTGTAGAATGTTTA 57.059 25.926 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7084 24603 4.379918 GCTTCTTGGTTGCATTAGGTCTTC 60.380 45.833 0.00 0.00 0.00 2.87
7128 24647 4.157649 CGATGCGAACAATTCATGAAACA 58.842 39.130 13.09 3.17 0.00 2.83
7241 24760 9.865484 GTTTGAGAACTTCTAGAATGTTTGTAC 57.135 33.333 5.44 1.98 32.91 2.90
7306 24825 9.800299 GTCACAAAAACGTTTTGAAATAGTTTT 57.200 25.926 25.83 14.09 40.17 2.43
7322 24841 9.736023 ATCACTTTCAGAATTAGTCACAAAAAC 57.264 29.630 0.00 0.00 0.00 2.43
7388 24908 6.594788 AATGTCCAGACTGCAAAACATTAT 57.405 33.333 15.92 1.91 36.02 1.28
7531 25052 3.314541 AGGTCGAGATGTTGTTGGTAC 57.685 47.619 0.00 0.00 0.00 3.34
7610 25131 2.541120 CCCTGCTGCTTAGATGCGC 61.541 63.158 0.00 0.00 35.36 6.09
7659 25184 4.339814 CAGGAGACCATAGGTTCACTAGTC 59.660 50.000 0.00 0.00 35.25 2.59
7678 25203 5.157770 AGTTATGGAGAATAGACCCAGGA 57.842 43.478 0.00 0.00 32.90 3.86
7736 25262 7.459795 TGTCATGCATGGTAAATCTAAAACA 57.540 32.000 25.97 14.83 0.00 2.83
7812 25339 4.563140 AGCCGATGGAAACTTTTAGGTA 57.437 40.909 0.00 0.00 0.00 3.08
7824 25352 5.280011 GGAAATCTAGGATTTAGCCGATGGA 60.280 44.000 5.63 0.00 0.00 3.41
7830 25358 4.460731 GCATGGGAAATCTAGGATTTAGCC 59.539 45.833 5.63 4.47 0.00 3.93
7886 25414 5.859205 AAAACATCATGGCTAATTCTCCC 57.141 39.130 0.00 0.00 0.00 4.30
7960 25488 7.022979 CACAAGAATTTCAAATATGCGTCAGA 58.977 34.615 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.