Multiple sequence alignment - TraesCS6B01G431700

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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 TraesCS6B01G431700 chr6B 100.000 2330 0 0 1 2330 700955293 700952964 0.000000e+00 4303.0
1 TraesCS6B01G431700 chr6B 93.435 914 35 8 713 1625 701057272 701056383 0.000000e+00 1332.0
2 TraesCS6B01G431700 chr6B 95.531 358 14 2 366 721 701057664 701057307 2.600000e-159 571.0
3 TraesCS6B01G431700 chr6B 90.934 364 25 3 4 365 701058484 701058127 1.250000e-132 483.0
4 TraesCS6B01G431700 chr6B 80.645 620 84 24 718 1335 700610044 700609459 4.570000e-122 448.0
5 TraesCS6B01G431700 chr6B 85.845 219 22 4 508 721 700682665 700682451 8.380000e-55 224.0
6 TraesCS6B01G431700 chr6B 78.731 268 38 9 1 251 695902318 695902053 6.660000e-36 161.0
7 TraesCS6B01G431700 chr6B 95.455 88 3 1 1634 1721 701050130 701050044 3.120000e-29 139.0
8 TraesCS6B01G431700 chr6B 92.405 79 4 2 1717 1793 700972415 700972337 6.810000e-21 111.0
9 TraesCS6B01G431700 chr6D 92.969 896 50 6 722 1614 460304959 460304074 0.000000e+00 1293.0
10 TraesCS6B01G431700 chr6D 89.606 279 26 3 897 1173 460290197 460289920 3.680000e-93 351.0
11 TraesCS6B01G431700 chr6D 85.417 192 19 6 1610 1793 460302831 460302641 8.500000e-45 191.0
12 TraesCS6B01G431700 chr6D 86.577 149 16 4 1 146 262302844 262302991 6.660000e-36 161.0
13 TraesCS6B01G431700 chr6D 78.210 257 43 9 1 248 422932260 422932512 4.010000e-33 152.0
14 TraesCS6B01G431700 chr6D 82.857 105 15 3 150 252 388158157 388158054 8.870000e-15 91.6
15 TraesCS6B01G431700 chr6A 94.690 678 30 1 721 1398 606318314 606317643 0.000000e+00 1048.0
16 TraesCS6B01G431700 chr6A 89.275 662 50 8 958 1601 606237279 606236621 0.000000e+00 809.0
17 TraesCS6B01G431700 chr6A 88.235 357 20 5 366 721 606244180 606243845 7.750000e-110 407.0
18 TraesCS6B01G431700 chr6A 90.698 258 16 4 713 969 606243806 606243556 1.030000e-88 337.0
19 TraesCS6B01G431700 chr6A 85.382 301 38 6 1 298 606244514 606244217 8.090000e-80 307.0
20 TraesCS6B01G431700 chr6A 89.954 219 16 4 1398 1614 606313470 606313256 6.340000e-71 278.0
21 TraesCS6B01G431700 chr6A 88.235 204 18 2 520 721 606131757 606131558 2.990000e-59 239.0
22 TraesCS6B01G431700 chr6A 88.482 191 15 5 1608 1793 606311981 606311793 8.380000e-55 224.0
23 TraesCS6B01G431700 chr6A 94.048 84 5 0 1606 1689 606236558 606236475 6.760000e-26 128.0
24 TraesCS6B01G431700 chr2B 92.585 499 34 3 1824 2319 708794934 708795432 0.000000e+00 713.0
25 TraesCS6B01G431700 chr2B 89.544 526 43 9 1801 2319 197575773 197576293 0.000000e+00 656.0
26 TraesCS6B01G431700 chr1A 89.847 522 41 10 1806 2319 507952862 507952345 0.000000e+00 660.0
27 TraesCS6B01G431700 chr5A 90.079 504 41 7 1823 2319 59031271 59031772 0.000000e+00 645.0
28 TraesCS6B01G431700 chr3B 89.804 510 41 8 1816 2319 192019423 192019927 0.000000e+00 643.0
29 TraesCS6B01G431700 chr3B 81.429 140 23 2 1010 1146 18484768 18484907 6.810000e-21 111.0
30 TraesCS6B01G431700 chr7A 89.484 504 44 8 1822 2319 450373502 450373002 1.520000e-176 628.0
31 TraesCS6B01G431700 chr7A 84.340 530 50 18 1800 2319 665147872 665147366 2.690000e-134 488.0
32 TraesCS6B01G431700 chr4B 86.933 551 46 15 1784 2319 414262368 414261829 1.540000e-166 595.0
33 TraesCS6B01G431700 chr2A 82.261 513 72 11 1816 2319 736065894 736065392 2.140000e-115 425.0
34 TraesCS6B01G431700 chr2A 100.000 32 0 0 227 258 44794725 44794694 2.500000e-05 60.2
35 TraesCS6B01G431700 chr7D 86.667 150 18 2 1 148 32922662 32922811 5.150000e-37 165.0
36 TraesCS6B01G431700 chr7D 79.008 262 40 9 1 248 431374193 431374453 5.150000e-37 165.0
37 TraesCS6B01G431700 chr4D 78.947 266 38 10 1 250 493762753 493763016 5.150000e-37 165.0
38 TraesCS6B01G431700 chrUn 86.093 151 17 4 1 148 35210234 35210383 2.400000e-35 159.0
39 TraesCS6B01G431700 chr5D 81.026 195 24 8 1 182 363191605 363191799 2.410000e-30 143.0
40 TraesCS6B01G431700 chr5D 75.940 266 44 16 1 251 523317416 523317676 4.070000e-23 119.0
41 TraesCS6B01G431700 chr7B 76.953 256 51 8 1 251 634260057 634260309 3.120000e-29 139.0
42 TraesCS6B01G431700 chr7B 96.970 33 1 0 221 253 636724912 636724944 3.230000e-04 56.5
43 TraesCS6B01G431700 chr3D 81.429 140 23 2 1010 1146 12835839 12835978 6.810000e-21 111.0
44 TraesCS6B01G431700 chr3D 81.429 140 23 2 1010 1146 12848608 12848747 6.810000e-21 111.0
45 TraesCS6B01G431700 chr3D 80.165 121 21 3 148 267 85216743 85216625 1.150000e-13 87.9
46 TraesCS6B01G431700 chr3D 92.500 40 3 0 144 183 188415097 188415136 8.990000e-05 58.4
47 TraesCS6B01G431700 chr3A 79.832 119 19 5 147 263 102227673 102227558 5.340000e-12 82.4
48 TraesCS6B01G431700 chr2D 78.992 119 20 5 1 116 318626195 318626079 2.480000e-10 76.8
49 TraesCS6B01G431700 chr4A 100.000 32 0 0 152 183 86324562 86324531 2.500000e-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 TraesCS6B01G431700 chr6B 700952964 700955293 2329 True 4303.000000 4303 100.0000 1 2330 1 chr6B.!!$R4 2329
1 TraesCS6B01G431700 chr6B 701056383 701058484 2101 True 795.333333 1332 93.3000 4 1625 3 chr6B.!!$R7 1621
2 TraesCS6B01G431700 chr6B 700609459 700610044 585 True 448.000000 448 80.6450 718 1335 1 chr6B.!!$R2 617
3 TraesCS6B01G431700 chr6D 460302641 460304959 2318 True 742.000000 1293 89.1930 722 1793 2 chr6D.!!$R3 1071
4 TraesCS6B01G431700 chr6A 606317643 606318314 671 True 1048.000000 1048 94.6900 721 1398 1 chr6A.!!$R2 677
5 TraesCS6B01G431700 chr6A 606236475 606237279 804 True 468.500000 809 91.6615 958 1689 2 chr6A.!!$R3 731
6 TraesCS6B01G431700 chr6A 606243556 606244514 958 True 350.333333 407 88.1050 1 969 3 chr6A.!!$R4 968
7 TraesCS6B01G431700 chr6A 606311793 606313470 1677 True 251.000000 278 89.2180 1398 1793 2 chr6A.!!$R5 395
8 TraesCS6B01G431700 chr2B 197575773 197576293 520 False 656.000000 656 89.5440 1801 2319 1 chr2B.!!$F1 518
9 TraesCS6B01G431700 chr1A 507952345 507952862 517 True 660.000000 660 89.8470 1806 2319 1 chr1A.!!$R1 513
10 TraesCS6B01G431700 chr5A 59031271 59031772 501 False 645.000000 645 90.0790 1823 2319 1 chr5A.!!$F1 496
11 TraesCS6B01G431700 chr3B 192019423 192019927 504 False 643.000000 643 89.8040 1816 2319 1 chr3B.!!$F2 503
12 TraesCS6B01G431700 chr7A 450373002 450373502 500 True 628.000000 628 89.4840 1822 2319 1 chr7A.!!$R1 497
13 TraesCS6B01G431700 chr7A 665147366 665147872 506 True 488.000000 488 84.3400 1800 2319 1 chr7A.!!$R2 519
14 TraesCS6B01G431700 chr4B 414261829 414262368 539 True 595.000000 595 86.9330 1784 2319 1 chr4B.!!$R1 535
15 TraesCS6B01G431700 chr2A 736065392 736065894 502 True 425.000000 425 82.2610 1816 2319 1 chr2A.!!$R2 503

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
66 68 0.555769 AAGGGTTTTGAGTGGGCAGA 59.444 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 3579 0.969894 ACGGCTCCATGGCTAGTATC 59.03 55.0 6.96 0.0 39.32 2.24 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
36 37 0.839946 AAATGGGGAGGATGGAGTCG 59.160 55.000 0.00 0.00 0.00 4.18
43 45 3.148279 GGATGGAGTCGCGGGTCT 61.148 66.667 6.13 2.24 0.00 3.85
66 68 0.555769 AAGGGTTTTGAGTGGGCAGA 59.444 50.000 0.00 0.00 0.00 4.26
73 75 2.055689 TTGAGTGGGCAGAGGGTGTG 62.056 60.000 0.00 0.00 0.00 3.82
111 113 2.031682 CGTTTCTGAACTCCTGCAAAGG 60.032 50.000 0.00 0.00 33.51 3.11
135 137 6.427242 GGTCCCTAACTTTTGTCTCTAGTTTG 59.573 42.308 0.00 0.00 34.26 2.93
136 138 5.995897 TCCCTAACTTTTGTCTCTAGTTTGC 59.004 40.000 0.00 0.00 34.26 3.68
139 143 3.139077 ACTTTTGTCTCTAGTTTGCGGG 58.861 45.455 0.00 0.00 0.00 6.13
175 180 1.876714 CGATACAGGTCCGCGTTGG 60.877 63.158 4.92 0.00 40.09 3.77
183 188 2.033448 TCCGCGTTGGATGGCTTT 59.967 55.556 4.92 0.00 43.74 3.51
346 351 9.647918 ACTCTCTAATATGGAATCAACAGACTA 57.352 33.333 0.00 0.00 0.00 2.59
462 930 4.006319 TGAACATGTTATCGATGCCACAA 58.994 39.130 11.95 0.00 0.00 3.33
514 984 2.791383 TGGCATATACAAATTGGCGC 57.209 45.000 0.00 0.00 38.65 6.53
546 1016 6.783708 TGACCTTTTATTTGACCAACTGTT 57.216 33.333 0.00 0.00 0.00 3.16
576 1046 6.980978 CCTGTCAATGTACACCTAGATTACTG 59.019 42.308 0.00 0.00 0.00 2.74
604 1074 1.066587 GTCTCGATCTTGCCCTCGG 59.933 63.158 0.00 0.00 35.64 4.63
667 1137 2.821969 GTTGGATTGCAACACTCCATCT 59.178 45.455 18.56 0.00 41.59 2.90
693 1163 6.602410 TTTTGGCAATATGAGATCCAACAA 57.398 33.333 0.00 0.00 36.63 2.83
921 1438 3.873952 GGAGCTTTTATCGCTGAATCACT 59.126 43.478 0.00 0.00 37.96 3.41
1170 1687 2.402305 CTGATCAGCGTCAATAGCTCC 58.598 52.381 10.38 0.00 44.06 4.70
1336 1854 5.125900 TCGGACGTAATCTGGTAAATCTGAA 59.874 40.000 0.00 0.00 34.03 3.02
1445 1963 8.186163 CAGTGTGAAGTTCGTAATGGTACTATA 58.814 37.037 0.00 0.00 0.00 1.31
1446 1964 8.742777 AGTGTGAAGTTCGTAATGGTACTATAA 58.257 33.333 0.00 0.00 0.00 0.98
1447 1965 9.525409 GTGTGAAGTTCGTAATGGTACTATAAT 57.475 33.333 0.00 0.00 0.00 1.28
1508 2043 4.997395 GTGCTTCCTTCTGTGAGTTTGATA 59.003 41.667 0.00 0.00 0.00 2.15
1590 2127 5.920193 AGCTTAAATAATGAAGGCAGCAA 57.080 34.783 0.00 0.00 0.00 3.91
1602 2139 3.160679 AGGCAGCAATCCTACAACTTT 57.839 42.857 0.00 0.00 30.79 2.66
1603 2140 3.084786 AGGCAGCAATCCTACAACTTTC 58.915 45.455 0.00 0.00 30.79 2.62
1693 3514 1.000955 GGCCTAGATATGTGGACCGTG 59.999 57.143 0.00 0.00 0.00 4.94
1726 3547 4.683832 AGTTCTACATGTGTCGCCTTATC 58.316 43.478 9.11 0.00 0.00 1.75
1728 3549 2.946990 TCTACATGTGTCGCCTTATCGA 59.053 45.455 9.11 0.00 35.95 3.59
1731 3552 2.930040 ACATGTGTCGCCTTATCGAAAG 59.070 45.455 0.00 0.00 40.43 2.62
1732 3553 2.736144 TGTGTCGCCTTATCGAAAGT 57.264 45.000 0.00 0.00 40.43 2.66
1879 3706 9.609950 CGTTCGTCATTAAAATTACCCTTTAAA 57.390 29.630 0.00 0.00 33.26 1.52
1964 3792 3.626028 ATCAACGCCTCTTTTGTTGTC 57.374 42.857 4.48 0.00 42.65 3.18
1971 3802 5.548406 ACGCCTCTTTTGTTGTCTTATAGT 58.452 37.500 0.00 0.00 0.00 2.12
1989 3820 1.153647 TGGCGCAACGAGTAGATGG 60.154 57.895 10.83 0.00 0.00 3.51
1990 3821 1.883084 GGCGCAACGAGTAGATGGG 60.883 63.158 10.83 0.00 38.35 4.00
2021 3852 1.127567 AGCAGTAGAGTGGTTGGCCA 61.128 55.000 0.00 0.00 43.73 5.36
2072 3903 4.861196 TCGATCCCCAATTTCCACAATTA 58.139 39.130 0.00 0.00 0.00 1.40
2075 3906 6.040391 TCGATCCCCAATTTCCACAATTATTC 59.960 38.462 0.00 0.00 0.00 1.75
2109 3950 2.440796 CATGTTCATGGGCCGGCT 60.441 61.111 28.56 2.77 0.00 5.52
2116 3957 3.410628 ATGGGCCGGCTCATGTGA 61.411 61.111 40.47 14.45 35.52 3.58
2319 4171 8.578308 TCATACAAAGTTTGCAGATTCAAAAG 57.422 30.769 15.59 0.00 37.65 2.27
2320 4172 7.652909 TCATACAAAGTTTGCAGATTCAAAAGG 59.347 33.333 15.59 0.00 37.65 3.11
2321 4173 5.733676 ACAAAGTTTGCAGATTCAAAAGGT 58.266 33.333 15.59 0.00 37.65 3.50
2322 4174 6.172630 ACAAAGTTTGCAGATTCAAAAGGTT 58.827 32.000 15.59 0.00 37.65 3.50
2323 4175 6.654582 ACAAAGTTTGCAGATTCAAAAGGTTT 59.345 30.769 15.59 0.00 37.65 3.27
2324 4176 6.667007 AAGTTTGCAGATTCAAAAGGTTTG 57.333 33.333 0.00 0.00 37.65 2.93
2325 4177 4.571984 AGTTTGCAGATTCAAAAGGTTTGC 59.428 37.500 0.00 0.00 37.65 3.68
2326 4178 3.815856 TGCAGATTCAAAAGGTTTGCA 57.184 38.095 0.00 0.00 37.70 4.08
2327 4179 4.134379 TGCAGATTCAAAAGGTTTGCAA 57.866 36.364 0.00 0.00 37.17 4.08
2328 4180 4.511527 TGCAGATTCAAAAGGTTTGCAAA 58.488 34.783 8.05 8.05 37.17 3.68
2329 4181 4.940046 TGCAGATTCAAAAGGTTTGCAAAA 59.060 33.333 14.67 0.00 37.17 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.708593 AAAACCCTTCCCAGACCCGC 62.709 60.000 0.00 0.00 0.00 6.13
43 45 0.187361 CCCACTCAAAACCCTTCCCA 59.813 55.000 0.00 0.00 0.00 4.37
66 68 2.233305 ACGTAGGAATCTCACACCCT 57.767 50.000 0.00 0.00 0.00 4.34
93 95 2.487265 GGACCTTTGCAGGAGTTCAGAA 60.487 50.000 0.00 0.00 44.19 3.02
98 100 1.742308 TAGGGACCTTTGCAGGAGTT 58.258 50.000 0.00 0.00 44.19 3.01
111 113 6.073167 GCAAACTAGAGACAAAAGTTAGGGAC 60.073 42.308 0.00 0.00 33.24 4.46
139 143 3.202706 GTCTGCGGGGCGATTTCC 61.203 66.667 0.00 0.00 0.00 3.13
175 180 1.092345 GTCCAGCCTCGAAAGCCATC 61.092 60.000 3.59 0.00 0.00 3.51
209 214 1.133823 ACCCACAAACTGACAGCATCA 60.134 47.619 1.25 0.00 35.45 3.07
317 322 6.749139 TGTTGATTCCATATTAGAGAGTCCG 58.251 40.000 0.00 0.00 0.00 4.79
319 324 8.637986 AGTCTGTTGATTCCATATTAGAGAGTC 58.362 37.037 0.00 0.00 0.00 3.36
346 351 5.488341 AGTTTCAAGACTGCCACGTATTAT 58.512 37.500 0.00 0.00 0.00 1.28
462 930 2.552315 CCACATGTTTCGTAGTTGGCTT 59.448 45.455 0.00 0.00 0.00 4.35
514 984 5.016173 TCAAATAAAAGGTCATCCAGGTGG 58.984 41.667 0.00 0.00 35.89 4.61
546 1016 6.833041 TCTAGGTGTACATTGACAGGAAAAA 58.167 36.000 0.00 0.00 0.00 1.94
604 1074 5.971895 ATTGCACAACAAACAAAGATGAC 57.028 34.783 0.00 0.00 42.86 3.06
693 1163 2.095263 GCATTGTTAAGACCACGCATGT 60.095 45.455 0.00 0.00 0.00 3.21
921 1438 1.026182 CCTTGCAAGTGCTCGCCATA 61.026 55.000 24.35 0.00 42.66 2.74
1234 1751 1.154016 CGGACGTGCTGATCTCGTT 60.154 57.895 5.27 0.00 43.85 3.85
1352 1870 4.534794 TGTACGCATGCACATTATTGAG 57.465 40.909 19.57 0.00 0.00 3.02
1415 1933 6.460781 ACCATTACGAACTTCACACTGATTA 58.539 36.000 0.00 0.00 0.00 1.75
1445 1963 7.657761 ACTGAGATCGTTTCAAACAGACTAATT 59.342 33.333 0.22 0.00 0.00 1.40
1446 1964 7.155328 ACTGAGATCGTTTCAAACAGACTAAT 58.845 34.615 0.22 0.00 0.00 1.73
1447 1965 6.513180 ACTGAGATCGTTTCAAACAGACTAA 58.487 36.000 0.22 0.00 0.00 2.24
1522 2057 6.770785 CGAATTGGGAGAATAAATACAAGGGA 59.229 38.462 0.00 0.00 0.00 4.20
1531 2067 6.317893 GGAAAGTAGCGAATTGGGAGAATAAA 59.682 38.462 0.00 0.00 0.00 1.40
1625 3446 3.606687 ACTGGTGTCTCGTTTTCTTGTT 58.393 40.909 0.00 0.00 0.00 2.83
1693 3514 6.040962 CACATGTAGAACTATGTGCATGTC 57.959 41.667 0.00 0.00 45.09 3.06
1751 3575 3.258372 CGGCTCCATGGCTAGTATCTTAA 59.742 47.826 6.96 0.00 39.32 1.85
1752 3576 2.826128 CGGCTCCATGGCTAGTATCTTA 59.174 50.000 6.96 0.00 39.32 2.10
1755 3579 0.969894 ACGGCTCCATGGCTAGTATC 59.030 55.000 6.96 0.00 39.32 2.24
1756 3580 1.893801 GTACGGCTCCATGGCTAGTAT 59.106 52.381 6.96 0.00 39.32 2.12
1813 3640 9.201127 GCCGTTTTATTAGTATAGGTAAAGAGG 57.799 37.037 0.00 0.00 0.00 3.69
1927 3754 6.074249 GGCGTTGATTTTTGTCCGAAAAATTA 60.074 34.615 7.28 2.05 39.23 1.40
1964 3792 1.922570 ACTCGTTGCGCCACTATAAG 58.077 50.000 10.16 4.66 0.00 1.73
1971 3802 1.153647 CCATCTACTCGTTGCGCCA 60.154 57.895 4.18 0.00 0.00 5.69
1989 3820 6.460399 CCACTCTACTGCTATTAGTTCTGTCC 60.460 46.154 0.00 0.00 32.19 4.02
1990 3821 6.095720 ACCACTCTACTGCTATTAGTTCTGTC 59.904 42.308 0.00 0.00 32.19 3.51
1998 3829 3.134081 GGCCAACCACTCTACTGCTATTA 59.866 47.826 0.00 0.00 35.26 0.98
2000 3831 1.486726 GGCCAACCACTCTACTGCTAT 59.513 52.381 0.00 0.00 35.26 2.97
2039 3870 2.297937 GGGATCGAACCCTGGTCTT 58.702 57.895 22.87 0.00 45.90 3.01
2072 3903 6.970484 ACATGCGTAAGAAAAGAAAGTGAAT 58.030 32.000 0.00 0.00 43.02 2.57
2075 3906 6.198687 TGAACATGCGTAAGAAAAGAAAGTG 58.801 36.000 0.00 0.00 43.02 3.16
2088 3920 1.817520 CGGCCCATGAACATGCGTA 60.818 57.895 9.03 0.00 37.49 4.42
2109 3950 0.615331 GAGTGAAGCCCCTCACATGA 59.385 55.000 0.00 0.00 46.81 3.07
2299 4151 6.667007 AACCTTTTGAATCTGCAAACTTTG 57.333 33.333 0.00 0.00 37.48 2.77


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

AutoCloner maintained by Alex Coulton.