Multiple sequence alignment - TraesCS7B01G163300

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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 TraesCS7B01G163300 chr7B 100.000 2284 0 0 795 3078 225390294 225392577 0.000000e+00 4218.0
1 TraesCS7B01G163300 chr7B 98.908 2290 17 3 795 3078 225507317 225509604 0.000000e+00 4084.0
2 TraesCS7B01G163300 chr7B 100.000 477 0 0 1 477 225389500 225389976 0.000000e+00 881.0
3 TraesCS7B01G163300 chr7B 94.363 479 24 3 1 477 225506819 225507296 0.000000e+00 732.0
4 TraesCS7B01G163300 chr7B 99.383 162 0 1 2472 2632 225509149 225509310 3.000000e-75 292.0
5 TraesCS7B01G163300 chr7B 90.411 219 18 3 61 276 541957422 541957640 5.020000e-73 285.0
6 TraesCS7B01G163300 chr7B 98.148 162 2 1 2629 2790 225391971 225392131 6.500000e-72 281.0
7 TraesCS7B01G163300 chr7B 98.148 162 2 1 2472 2632 225392128 225392289 6.500000e-72 281.0
8 TraesCS7B01G163300 chr7B 98.125 160 2 1 2629 2788 225508992 225509150 8.410000e-71 278.0
9 TraesCS7B01G163300 chr7B 97.826 46 1 0 2484 2529 225391926 225391971 2.540000e-11 80.5
10 TraesCS7B01G163300 chr7B 97.826 46 1 0 2641 2686 225391926 225391971 2.540000e-11 80.5
11 TraesCS7B01G163300 chr7B 97.826 46 1 0 2427 2472 225391983 225392028 2.540000e-11 80.5
12 TraesCS7B01G163300 chr7B 97.826 46 1 0 2427 2472 225392140 225392185 2.540000e-11 80.5
13 TraesCS7B01G163300 chr7B 97.826 46 1 0 2427 2472 225509004 225509049 2.540000e-11 80.5
14 TraesCS7B01G163300 chr7B 97.826 46 1 0 2427 2472 225509161 225509206 2.540000e-11 80.5
15 TraesCS7B01G163300 chr7A 97.070 1570 38 4 795 2361 265926554 265928118 0.000000e+00 2638.0
16 TraesCS7B01G163300 chr7A 93.932 1582 44 19 799 2374 265501840 265503375 0.000000e+00 2342.0
17 TraesCS7B01G163300 chr7A 86.613 493 21 9 2629 3078 265928300 265928790 1.270000e-138 503.0
18 TraesCS7B01G163300 chr7A 95.094 265 5 2 2369 2630 265503453 265503712 7.940000e-111 411.0
19 TraesCS7B01G163300 chr7A 87.023 262 9 9 2629 2870 265503556 265503812 3.910000e-69 272.0
20 TraesCS7B01G163300 chr7A 96.364 165 4 2 2469 2632 265928297 265928460 1.410000e-68 270.0
21 TraesCS7B01G163300 chr7A 88.816 152 8 5 2934 3078 265503817 265503966 8.770000e-41 178.0
22 TraesCS7B01G163300 chr7D 95.365 1575 56 4 800 2374 248466224 248467781 0.000000e+00 2488.0
23 TraesCS7B01G163300 chr7D 95.062 1377 46 12 800 2176 247883884 247885238 0.000000e+00 2146.0
24 TraesCS7B01G163300 chr7D 93.229 192 7 4 2383 2568 247885934 247886125 8.410000e-71 278.0
25 TraesCS7B01G163300 chr7D 93.605 172 5 4 2205 2374 247885672 247885839 5.090000e-63 252.0
26 TraesCS7B01G163300 chr7D 81.270 315 21 9 2791 3078 247889829 247890132 1.440000e-53 220.0
27 TraesCS7B01G163300 chr7D 94.161 137 8 0 2942 3078 248469491 248469627 3.110000e-50 209.0
28 TraesCS7B01G163300 chr7D 94.262 122 3 2 2469 2586 248468077 248468198 1.890000e-42 183.0
29 TraesCS7B01G163300 chr7D 93.277 119 5 2 2629 2744 248468080 248468198 4.080000e-39 172.0
30 TraesCS7B01G163300 chr7D 91.262 103 4 4 2629 2726 247886023 247886125 5.350000e-28 135.0
31 TraesCS7B01G163300 chr7D 88.542 96 2 3 2792 2878 248468689 248468784 1.170000e-19 108.0
32 TraesCS7B01G163300 chr7D 90.769 65 6 0 2879 2943 248468810 248468874 1.520000e-13 87.9
33 TraesCS7B01G163300 chr7D 97.826 46 1 0 2484 2529 247885978 247886023 2.540000e-11 80.5
34 TraesCS7B01G163300 chr7D 97.826 46 1 0 2641 2686 247885978 247886023 2.540000e-11 80.5
35 TraesCS7B01G163300 chr7D 92.857 42 3 0 2943 2984 248469453 248469494 9.220000e-06 62.1
36 TraesCS7B01G163300 chrUn 99.517 414 2 0 940 1353 477095377 477094964 0.000000e+00 754.0
37 TraesCS7B01G163300 chr6B 91.388 209 16 2 61 267 109608921 109608713 5.020000e-73 285.0
38 TraesCS7B01G163300 chr3D 91.429 210 15 3 61 267 70280644 70280435 5.020000e-73 285.0
39 TraesCS7B01G163300 chr3D 91.080 213 16 3 61 270 136563256 136563044 5.020000e-73 285.0
40 TraesCS7B01G163300 chr3D 82.243 107 16 3 331 435 547002067 547002172 4.230000e-14 89.8
41 TraesCS7B01G163300 chr3D 90.476 42 4 0 12 53 600831193 600831234 4.290000e-04 56.5
42 TraesCS7B01G163300 chr3B 91.388 209 16 2 61 267 262079825 262080033 5.020000e-73 285.0
43 TraesCS7B01G163300 chr1B 91.038 212 15 4 60 267 453708410 453708621 1.810000e-72 283.0
44 TraesCS7B01G163300 chr1B 91.080 213 14 4 60 267 453726080 453726292 1.810000e-72 283.0
45 TraesCS7B01G163300 chr1B 89.238 223 20 3 60 278 504951846 504951624 3.020000e-70 276.0
46 TraesCS7B01G163300 chr1B 79.545 132 26 1 334 464 17348114 17347983 3.270000e-15 93.5
47 TraesCS7B01G163300 chr1B 79.104 134 23 4 334 464 604657482 604657613 1.520000e-13 87.9
48 TraesCS7B01G163300 chr4D 81.250 144 24 3 322 464 327427454 327427595 2.510000e-21 113.0
49 TraesCS7B01G163300 chr2B 82.090 134 19 4 334 464 622642179 622642048 3.240000e-20 110.0
50 TraesCS7B01G163300 chr5B 81.061 132 24 1 334 464 67541805 67541674 1.510000e-18 104.0
51 TraesCS7B01G163300 chr5B 91.489 47 4 0 14 60 256368932 256368978 7.120000e-07 65.8
52 TraesCS7B01G163300 chr5B 97.222 36 1 0 14 49 214143252 214143217 9.220000e-06 62.1
53 TraesCS7B01G163300 chr4B 78.788 132 27 1 334 464 139563362 139563231 1.520000e-13 87.9
54 TraesCS7B01G163300 chr4B 100.000 28 0 0 2937 2964 14016262 14016235 6.000000e-03 52.8
55 TraesCS7B01G163300 chr3A 78.030 132 28 1 334 464 725837664 725837795 7.070000e-12 82.4
56 TraesCS7B01G163300 chr3A 90.476 42 3 1 2924 2964 419336097 419336138 2.000000e-03 54.7
57 TraesCS7B01G163300 chr5D 95.000 40 2 0 10 49 264076521 264076560 2.560000e-06 63.9
58 TraesCS7B01G163300 chr5A 94.872 39 2 0 16 54 596590013 596590051 9.220000e-06 62.1
59 TraesCS7B01G163300 chr6A 96.875 32 0 1 2937 2968 330052376 330052406 6.000000e-03 52.8


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 TraesCS7B01G163300 chr7B 225389500 225392577 3077 False 747.875000 4218 98.450000 1 3078 8 chr7B.!!$F2 3077
1 TraesCS7B01G163300 chr7B 225506819 225509604 2785 False 924.500000 4084 97.738500 1 3078 6 chr7B.!!$F3 3077
2 TraesCS7B01G163300 chr7A 265926554 265928790 2236 False 1137.000000 2638 93.349000 795 3078 3 chr7A.!!$F2 2283
3 TraesCS7B01G163300 chr7A 265501840 265503966 2126 False 800.750000 2342 91.216250 799 3078 4 chr7A.!!$F1 2279
4 TraesCS7B01G163300 chr7D 248466224 248469627 3403 False 472.857143 2488 92.747571 800 3078 7 chr7D.!!$F2 2278
5 TraesCS7B01G163300 chr7D 247883884 247890132 6248 False 456.000000 2146 92.868571 800 3078 7 chr7D.!!$F1 2278

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
410 413 0.531532 CCATCATGGAGAGGCACGAC 60.532 60.000 0.0 0.0 40.96 4.34 F
413 416 1.807165 CATGGAGAGGCACGACACG 60.807 63.158 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1278 2.283604 TCCTGGTAGGCGCACTCA 60.284 61.111 10.83 0.3 34.61 3.41 R
2687 3358 9.442047 AATTAACAAAGTCTTCCTCTGATACAG 57.558 33.333 0.00 0.0 0.00 2.74 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
75 76 2.515523 CAGGATCCGGCTTGCCTG 60.516 66.667 5.98 14.40 41.62 4.85
83 84 4.039092 GGCTTGCCTGCTCCTCCA 62.039 66.667 4.11 0.00 0.00 3.86
104 106 1.992519 ATGCTCCCATCTGTGCTCCC 61.993 60.000 0.00 0.00 0.00 4.30
132 134 2.707257 TCCTACGGTTGTCTTTTTCCCT 59.293 45.455 0.00 0.00 0.00 4.20
147 149 9.477484 GTCTTTTTCCCTTTTTCCTTTCTAATC 57.523 33.333 0.00 0.00 0.00 1.75
162 164 6.503570 CCTTTCTAATCTAATCATCTCCCCCT 59.496 42.308 0.00 0.00 0.00 4.79
163 165 7.680310 CCTTTCTAATCTAATCATCTCCCCCTA 59.320 40.741 0.00 0.00 0.00 3.53
182 185 1.456518 AATTTAAGGGGGTGGGGCCA 61.457 55.000 4.39 0.00 39.65 5.36
198 201 2.179427 GGCCAGGCCTTATTTTGTTCT 58.821 47.619 24.99 0.00 46.69 3.01
272 275 2.927580 GCAAGTCTCGTCCGTCCCA 61.928 63.158 0.00 0.00 0.00 4.37
304 307 4.090642 GTCAGCACAATTACGAGAGACTTG 59.909 45.833 0.00 0.00 0.00 3.16
323 326 2.897436 TGCGGATCTGACTTGAAGATG 58.103 47.619 5.48 0.00 34.50 2.90
349 352 6.458210 CCTAAAAATATAGCTGGCCAAATGG 58.542 40.000 7.01 0.00 38.53 3.16
410 413 0.531532 CCATCATGGAGAGGCACGAC 60.532 60.000 0.00 0.00 40.96 4.34
413 416 1.807165 CATGGAGAGGCACGACACG 60.807 63.158 0.00 0.00 0.00 4.49
831 834 1.873165 GGATGCTTTTCACGCGGAA 59.127 52.632 12.47 8.60 0.00 4.30
2687 3358 2.287368 GGACACAACACGGTTGGATTTC 60.287 50.000 17.36 9.55 0.00 2.17
2928 7474 6.433093 CCACTAGGCAGGTTAATTGTTACTTT 59.567 38.462 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 0.990374 ATGGGAGCATATGGAGGAGC 59.010 55.000 4.56 0.0 0.00 4.70
80 81 1.072806 GCACAGATGGGAGCATATGGA 59.927 52.381 4.56 0.0 0.00 3.41
81 82 1.073444 AGCACAGATGGGAGCATATGG 59.927 52.381 4.56 0.0 0.00 2.74
83 84 1.350351 GGAGCACAGATGGGAGCATAT 59.650 52.381 0.00 0.0 0.00 1.78
162 164 0.637743 GGCCCCACCCCCTTAAATTA 59.362 55.000 0.00 0.0 0.00 1.40
163 165 1.394557 GGCCCCACCCCCTTAAATT 59.605 57.895 0.00 0.0 0.00 1.82
198 201 6.018588 CCCGCATACGTGACTTGATTTAATTA 60.019 38.462 0.00 0.0 37.70 1.40
252 255 2.126031 GACGGACGAGACTTGCCC 60.126 66.667 0.00 0.0 0.00 5.36
272 275 1.444119 ATTGTGCTGACCGCGTTGTT 61.444 50.000 4.92 0.0 43.27 2.83
296 299 1.846007 AGTCAGATCCGCAAGTCTCT 58.154 50.000 0.00 0.0 0.00 3.10
304 307 1.596727 GCATCTTCAAGTCAGATCCGC 59.403 52.381 0.00 0.0 0.00 5.54
323 326 3.496331 TGGCCAGCTATATTTTTAGGGC 58.504 45.455 0.00 0.0 40.27 5.19
349 352 1.745489 CGACTTGGTTAGCCAGGCC 60.745 63.158 8.22 0.0 46.91 5.19
393 396 0.176680 GTGTCGTGCCTCTCCATGAT 59.823 55.000 0.00 0.0 33.67 2.45
831 834 3.713826 TTAGGGTTCTCGATTTTGCCT 57.286 42.857 0.00 0.0 0.00 4.75
938 947 0.953960 GCTTGGGTGGATTTCGTCGT 60.954 55.000 0.00 0.0 0.00 4.34
1081 1090 4.222847 GGGGATGACGGCGGAGAC 62.223 72.222 13.24 0.0 0.00 3.36
1269 1278 2.283604 TCCTGGTAGGCGCACTCA 60.284 61.111 10.83 0.3 34.61 3.41
2687 3358 9.442047 AATTAACAAAGTCTTCCTCTGATACAG 57.558 33.333 0.00 0.0 0.00 2.74
2928 7474 9.590451 AAAAACGTCTTATATTATGAACGGAGA 57.410 29.630 0.00 0.0 0.00 3.71


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

AutoCloner maintained by Alex Coulton.