Multiple sequence alignment - TraesCS7B01G163500

Loading Multiple Alignment...

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 TraesCS7B01G163500 chr7B 100.000 3078 0 0 1 3078 225506521 225509598 0.000000e+00 5685.0
1 TraesCS7B01G163500 chr7B 98.905 2284 17 3 797 3078 225390294 225392571 0.000000e+00 4072.0
2 TraesCS7B01G163500 chr7B 95.367 777 33 3 1 776 225389202 225389976 0.000000e+00 1232.0
3 TraesCS7B01G163500 chr7B 99.383 162 0 1 2629 2790 225391971 225392131 3.000000e-75 292.0
4 TraesCS7B01G163500 chr7B 99.375 160 0 1 2629 2788 225508992 225509150 3.880000e-74 289.0
5 TraesCS7B01G163500 chr7B 99.375 160 0 1 2472 2630 225509149 225509308 3.880000e-74 289.0
6 TraesCS7B01G163500 chr7B 98.125 160 2 1 2472 2630 225392128 225392287 8.410000e-71 278.0
7 TraesCS7B01G163500 chr7B 97.826 46 1 0 2484 2529 225391926 225391971 2.540000e-11 80.5
8 TraesCS7B01G163500 chr7B 97.826 46 1 0 2641 2686 225391926 225391971 2.540000e-11 80.5
9 TraesCS7B01G163500 chr7B 95.652 46 2 0 2427 2472 225391983 225392028 1.180000e-09 75.0
10 TraesCS7B01G163500 chr7B 95.652 46 2 0 2427 2472 225392140 225392185 1.180000e-09 75.0
11 TraesCS7B01G163500 chr7B 95.652 46 2 0 2427 2472 225509004 225509049 1.180000e-09 75.0
12 TraesCS7B01G163500 chr7B 95.652 46 2 0 2427 2472 225509161 225509206 1.180000e-09 75.0
13 TraesCS7B01G163500 chr7A 95.419 1768 64 10 599 2361 265926363 265928118 0.000000e+00 2800.0
14 TraesCS7B01G163500 chr7A 93.991 1581 43 20 801 2374 265501840 265503375 0.000000e+00 2346.0
15 TraesCS7B01G163500 chr7A 86.858 487 25 12 2629 3078 265928300 265928784 2.740000e-140 508.0
16 TraesCS7B01G163500 chr7A 94.340 265 7 2 2369 2630 265503453 265503712 1.720000e-107 399.0
17 TraesCS7B01G163500 chr7A 85.475 358 45 3 1 358 265925960 265926310 1.740000e-97 366.0
18 TraesCS7B01G163500 chr7A 88.168 262 12 7 2629 2876 265503556 265503812 8.350000e-76 294.0
19 TraesCS7B01G163500 chr7A 96.319 163 4 2 2469 2630 265928297 265928458 1.820000e-67 267.0
20 TraesCS7B01G163500 chr7A 88.356 146 8 4 2940 3078 265503817 265503960 1.900000e-37 167.0
21 TraesCS7B01G163500 chr7D 95.489 1574 54 4 802 2374 248466224 248467781 0.000000e+00 2497.0
22 TraesCS7B01G163500 chr7D 95.200 1375 46 10 802 2176 247883884 247885238 0.000000e+00 2156.0
23 TraesCS7B01G163500 chr7D 91.943 211 16 1 358 567 527466959 527466749 8.350000e-76 294.0
24 TraesCS7B01G163500 chr7D 92.188 192 9 4 2383 2568 247885934 247886125 1.820000e-67 267.0
25 TraesCS7B01G163500 chr7D 93.605 172 5 4 2205 2374 247885672 247885839 5.090000e-63 252.0
26 TraesCS7B01G163500 chr7D 93.130 131 9 0 2948 3078 248469491 248469621 3.130000e-45 193.0
27 TraesCS7B01G163500 chr7D 94.262 122 3 2 2469 2586 248468077 248468198 1.890000e-42 183.0
28 TraesCS7B01G163500 chr7D 94.958 119 3 2 2629 2744 248468080 248468198 1.890000e-42 183.0
29 TraesCS7B01G163500 chr7D 77.620 353 29 13 2762 3077 247889786 247890125 5.280000e-38 169.0
30 TraesCS7B01G163500 chr7D 93.204 103 2 4 2629 2726 247886023 247886125 2.470000e-31 147.0
31 TraesCS7B01G163500 chr7D 97.826 46 1 0 2484 2529 247885978 247886023 2.540000e-11 80.5
32 TraesCS7B01G163500 chr7D 97.826 46 1 0 2641 2686 247885978 247886023 2.540000e-11 80.5
33 TraesCS7B01G163500 chrUn 100.000 417 0 0 937 1353 477095380 477094964 0.000000e+00 771.0
34 TraesCS7B01G163500 chrUn 79.050 358 65 9 4 358 1932212 1931862 1.430000e-58 237.0
35 TraesCS7B01G163500 chr3D 92.453 212 15 1 359 569 484804115 484803904 4.990000e-78 302.0
36 TraesCS7B01G163500 chr3D 91.667 216 17 1 359 573 70280644 70280429 6.450000e-77 298.0
37 TraesCS7B01G163500 chr3D 91.549 213 17 1 359 570 136563256 136563044 3.000000e-75 292.0
38 TraesCS7B01G163500 chr3D 80.000 150 29 1 202 351 600831086 600831234 3.240000e-20 110.0
39 TraesCS7B01G163500 chr6D 92.381 210 12 3 360 567 61170596 61170389 2.320000e-76 296.0
40 TraesCS7B01G163500 chr6A 91.981 212 14 3 359 568 558457705 558457495 8.350000e-76 294.0
41 TraesCS7B01G163500 chr6A 91.981 212 14 3 359 568 558461025 558460815 8.350000e-76 294.0
42 TraesCS7B01G163500 chr6A 100.000 28 0 0 2943 2970 12895049 12895022 6.000000e-03 52.8
43 TraesCS7B01G163500 chr1D 91.905 210 16 1 359 567 18864558 18864767 3.000000e-75 292.0
44 TraesCS7B01G163500 chr1D 100.000 28 0 0 2945 2972 462087984 462088011 6.000000e-03 52.8
45 TraesCS7B01G163500 chr2B 76.986 365 72 10 1 359 799587916 799588274 6.730000e-47 198.0
46 TraesCS7B01G163500 chr5B 83.333 138 23 0 210 347 214143354 214143217 8.960000e-26 128.0
47 TraesCS7B01G163500 chr2A 80.769 156 28 2 190 344 144894846 144895000 1.500000e-23 121.0
48 TraesCS7B01G163500 chr3B 73.352 364 73 18 1 357 761957696 761958042 2.510000e-21 113.0
49 TraesCS7B01G163500 chr5D 79.355 155 31 1 206 359 291901933 291901779 1.170000e-19 108.0


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 TraesCS7B01G163500 chr7B 225506521 225509598 3077 False 1282.600000 5685 98.010800 1 3078 5 chr7B.!!$F2 3077
1 TraesCS7B01G163500 chr7B 225389202 225392571 3369 False 773.125000 4072 97.342000 1 3078 8 chr7B.!!$F1 3077
2 TraesCS7B01G163500 chr7A 265925960 265928784 2824 False 985.250000 2800 91.017750 1 3078 4 chr7A.!!$F2 3077
3 TraesCS7B01G163500 chr7A 265501840 265503960 2120 False 801.500000 2346 91.213750 801 3078 4 chr7A.!!$F1 2277
4 TraesCS7B01G163500 chr7D 248466224 248469621 3397 False 764.000000 2497 94.459750 802 3078 4 chr7D.!!$F2 2276
5 TraesCS7B01G163500 chr7D 247883884 247890125 6241 False 450.285714 2156 92.495571 802 3077 7 chr7D.!!$F1 2275
6 TraesCS7B01G163500 chr6A 558457495 558461025 3530 True 294.000000 294 91.981000 359 568 2 chr6A.!!$R2 209

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
403 404 0.987081 ATGCTCCCATCTGTGCTCCT 60.987 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2630 4203 9.719355 GGTCTTATTCCAAAAATGTAACCAATT 57.281 29.63 0.0 0.0 0.0 2.32 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
217 218 1.459348 AGTTTTTGGTGGGCCAGGG 60.459 57.895 6.40 0.0 46.91 4.45
237 238 1.901464 GGTCAAAAGCGGGCTTGGA 60.901 57.895 6.69 5.4 36.26 3.53
269 270 1.144913 CTCCCACAAACCTCTCCCAAA 59.855 52.381 0.00 0.0 0.00 3.28
277 278 4.342092 ACAAACCTCTCCCAAATTTGTCTG 59.658 41.667 16.73 5.5 38.75 3.51
373 374 1.686325 GACAGGATCCGGCTTGCCTA 61.686 60.000 12.27 0.0 0.00 3.93
403 404 0.987081 ATGCTCCCATCTGTGCTCCT 60.987 55.000 0.00 0.0 0.00 3.69
431 432 2.156917 CCTACGGTTGTCTTTTTCCCC 58.843 52.381 0.00 0.0 0.00 4.81
446 447 9.085645 GTCTTTTTCCCCTTTTCCTTTCTAATA 57.914 33.333 0.00 0.0 0.00 0.98
513 515 6.777526 TTTTGTTCCAATTAAATCAAGCCG 57.222 33.333 0.00 0.0 0.00 5.52
649 964 6.267471 CCCTAAAAATATAGCTGGCCAAATGA 59.733 38.462 7.01 0.0 0.00 2.57
710 1025 1.439228 CGTCATGGAGAGGCACGAT 59.561 57.895 0.00 0.0 32.08 3.73
713 1028 1.409064 GTCATGGAGAGGCACGATACA 59.591 52.381 0.00 0.0 0.00 2.29
912 1533 2.765807 CGGCTGACATCCCTCCCT 60.766 66.667 0.00 0.0 0.00 4.20
2464 3803 0.531974 GCCTTGTGGACAGAACACGA 60.532 55.000 0.00 0.0 41.64 4.35
2851 8261 5.010012 GGGGTGAAGCATTTCCTAACATATG 59.990 44.000 0.00 0.0 32.09 1.78
2909 8351 8.019094 CAGCGAGCATTCAATATTTGATGAATA 58.981 33.333 10.54 0.0 42.72 1.75
2955 9402 8.246430 ACTTCCTCCGTTCATAATATAAGACA 57.754 34.615 0.00 0.0 0.00 3.41
2995 9481 7.232941 ACAGAGGTAGAACAAGTTACAGTACAT 59.767 37.037 0.00 0.0 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 4.050934 ACGCCGCACTCATGTCGA 62.051 61.111 0.00 0.00 0.00 4.20
217 218 3.670377 AAGCCCGCTTTTGACCGC 61.670 61.111 0.00 0.00 31.29 5.68
241 242 2.852075 TTTGTGGGAGTCCGGGCT 60.852 61.111 9.26 9.26 35.24 5.19
269 270 4.883083 TCTCTCGCAAACTACAGACAAAT 58.117 39.130 0.00 0.00 0.00 2.32
277 278 5.220491 GGATGTGATTTCTCTCGCAAACTAC 60.220 44.000 0.00 0.00 38.98 2.73
373 374 1.237458 GGGAGCATAGGGAGGGAGT 59.763 63.158 0.00 0.00 0.00 3.85
596 881 3.695060 TCAAGTCAGATCCGTAAGTCTCC 59.305 47.826 0.00 0.00 0.00 3.71
649 964 1.303317 CGGTTTGGTTAGCCAGGCT 60.303 57.895 20.63 20.63 46.91 4.58
794 1109 1.004918 CTGATATTCCGGGGGCGTC 60.005 63.158 0.00 0.00 0.00 5.19
835 1449 3.063588 CGGCTTTAGGGTTCTCGATTTTC 59.936 47.826 0.00 0.00 0.00 2.29
938 1559 1.644786 GCTTGGGTGGATTTCGTCGG 61.645 60.000 0.00 0.00 0.00 4.79
2630 4203 9.719355 GGTCTTATTCCAAAAATGTAACCAATT 57.281 29.630 0.00 0.00 0.00 2.32
2851 8261 7.439056 ACAAAATGTCATTTCAGGTTGTTCATC 59.561 33.333 11.19 0.00 29.84 2.92
2909 8351 6.123045 AGTAACAATTAACCTGCCTAGTGT 57.877 37.500 0.00 0.00 0.00 3.55
2955 9402 5.827797 TCTACCTCTGTTGAACTGCAAAAAT 59.172 36.000 0.00 0.00 38.44 1.82
2995 9481 7.437267 GCCACAGTTATCGCTATTTACTTAAGA 59.563 37.037 10.09 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.