Multiple sequence alignment - TraesCS2B01G061200

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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 TraesCS2B01G061200 chr2B 100.000 2339 0 0 1 2339 29218215 29220553 0.000000e+00 4320.0
1 TraesCS2B01G061200 chr2B 89.442 1326 97 9 1 1317 29263085 29264376 0.000000e+00 1633.0
2 TraesCS2B01G061200 chr2B 89.216 1326 100 9 1 1317 29318322 29319613 0.000000e+00 1616.0
3 TraesCS2B01G061200 chr2B 89.073 1327 100 8 1 1317 29349441 29350732 0.000000e+00 1605.0
4 TraesCS2B01G061200 chr2B 81.742 1309 170 28 306 1566 29549480 29550767 0.000000e+00 1029.0
5 TraesCS2B01G061200 chr2B 84.530 362 25 9 1317 1659 29319644 29319993 1.730000e-86 329.0
6 TraesCS2B01G061200 chr2B 83.978 362 27 9 1317 1659 29264407 29264756 3.750000e-83 318.0
7 TraesCS2B01G061200 chr2B 83.978 362 27 9 1317 1659 29350763 29351112 3.750000e-83 318.0
8 TraesCS2B01G061200 chr2B 86.777 242 28 4 3 240 29549211 29549452 1.380000e-67 267.0
9 TraesCS2B01G061200 chr2B 100.000 30 0 0 258 287 29218444 29218473 3.250000e-04 56.5
10 TraesCS2B01G061200 chr2B 100.000 30 0 0 230 259 29218472 29218501 3.250000e-04 56.5
11 TraesCS2B01G061200 chr2D 93.096 1318 61 4 1 1317 17775271 17773983 0.000000e+00 1903.0
12 TraesCS2B01G061200 chr2D 84.645 1029 137 15 299 1317 17612635 17611618 0.000000e+00 1005.0
13 TraesCS2B01G061200 chr2D 84.548 1029 138 15 299 1317 17640006 17638989 0.000000e+00 1000.0
14 TraesCS2B01G061200 chr2D 92.619 691 47 4 1649 2339 8429136 8429822 0.000000e+00 990.0
15 TraesCS2B01G061200 chr2D 97.576 165 4 0 1317 1481 17773952 17773788 1.370000e-72 283.0
16 TraesCS2B01G061200 chr2D 85.950 242 30 3 3 240 17612897 17612656 2.980000e-64 255.0
17 TraesCS2B01G061200 chr2D 85.656 244 31 3 1 240 17640270 17640027 1.070000e-63 254.0
18 TraesCS2B01G061200 chr2D 90.452 199 5 4 1475 1660 17772466 17772269 1.390000e-62 250.0
19 TraesCS2B01G061200 chr7B 97.654 682 15 1 1658 2339 697430932 697431612 0.000000e+00 1170.0
20 TraesCS2B01G061200 chr7B 93.109 682 43 3 1658 2339 145972362 145971685 0.000000e+00 996.0
21 TraesCS2B01G061200 chr7B 94.872 312 16 0 1006 1317 745128183 745128494 2.700000e-134 488.0
22 TraesCS2B01G061200 chr7B 91.292 356 11 6 1317 1660 745128526 745128873 3.520000e-128 468.0
23 TraesCS2B01G061200 chr3B 97.788 678 12 3 1662 2339 99674149 99673475 0.000000e+00 1166.0
24 TraesCS2B01G061200 chr3B 97.198 678 18 1 1662 2339 669764137 669763461 0.000000e+00 1146.0
25 TraesCS2B01G061200 chr6B 97.345 678 17 1 1662 2339 131733689 131733013 0.000000e+00 1151.0
26 TraesCS2B01G061200 chr1B 96.798 687 20 2 1653 2339 667961116 667960432 0.000000e+00 1146.0
27 TraesCS2B01G061200 chr1B 91.854 356 13 6 1317 1660 651061315 651060964 1.260000e-132 483.0
28 TraesCS2B01G061200 chr1B 94.551 312 17 0 1006 1317 651061658 651061347 1.260000e-132 483.0
29 TraesCS2B01G061200 chr3A 94.041 688 29 5 1659 2339 340280732 340281414 0.000000e+00 1033.0
30 TraesCS2B01G061200 chr3D 92.533 683 48 3 1658 2339 512982848 512983528 0.000000e+00 976.0
31 TraesCS2B01G061200 chr2A 93.934 610 31 4 258 864 19054675 19054069 0.000000e+00 917.0
32 TraesCS2B01G061200 chr2A 94.694 490 26 0 828 1317 19054071 19053582 0.000000e+00 761.0
33 TraesCS2B01G061200 chr2A 92.157 357 11 4 1317 1660 19053551 19053199 2.700000e-134 488.0
34 TraesCS2B01G061200 chr2A 94.531 256 12 2 1 254 19054906 19054651 6.060000e-106 394.0
35 TraesCS2B01G061200 chr2A 86.008 243 29 4 3 240 19035108 19034866 2.980000e-64 255.0
36 TraesCS2B01G061200 chr4B 91.450 269 11 2 1382 1640 662549027 662548761 2.210000e-95 359.0


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 TraesCS2B01G061200 chr2B 29218215 29220553 2338 False 1477.666667 4320 100.0000 1 2339 3 chr2B.!!$F1 2338
1 TraesCS2B01G061200 chr2B 29263085 29264756 1671 False 975.500000 1633 86.7100 1 1659 2 chr2B.!!$F2 1658
2 TraesCS2B01G061200 chr2B 29318322 29319993 1671 False 972.500000 1616 86.8730 1 1659 2 chr2B.!!$F3 1658
3 TraesCS2B01G061200 chr2B 29349441 29351112 1671 False 961.500000 1605 86.5255 1 1659 2 chr2B.!!$F4 1658
4 TraesCS2B01G061200 chr2B 29549211 29550767 1556 False 648.000000 1029 84.2595 3 1566 2 chr2B.!!$F5 1563
5 TraesCS2B01G061200 chr2D 8429136 8429822 686 False 990.000000 990 92.6190 1649 2339 1 chr2D.!!$F1 690
6 TraesCS2B01G061200 chr2D 17772269 17775271 3002 True 812.000000 1903 93.7080 1 1660 3 chr2D.!!$R3 1659
7 TraesCS2B01G061200 chr2D 17611618 17612897 1279 True 630.000000 1005 85.2975 3 1317 2 chr2D.!!$R1 1314
8 TraesCS2B01G061200 chr2D 17638989 17640270 1281 True 627.000000 1000 85.1020 1 1317 2 chr2D.!!$R2 1316
9 TraesCS2B01G061200 chr7B 697430932 697431612 680 False 1170.000000 1170 97.6540 1658 2339 1 chr7B.!!$F1 681
10 TraesCS2B01G061200 chr7B 145971685 145972362 677 True 996.000000 996 93.1090 1658 2339 1 chr7B.!!$R1 681
11 TraesCS2B01G061200 chr7B 745128183 745128873 690 False 478.000000 488 93.0820 1006 1660 2 chr7B.!!$F2 654
12 TraesCS2B01G061200 chr3B 99673475 99674149 674 True 1166.000000 1166 97.7880 1662 2339 1 chr3B.!!$R1 677
13 TraesCS2B01G061200 chr3B 669763461 669764137 676 True 1146.000000 1146 97.1980 1662 2339 1 chr3B.!!$R2 677
14 TraesCS2B01G061200 chr6B 131733013 131733689 676 True 1151.000000 1151 97.3450 1662 2339 1 chr6B.!!$R1 677
15 TraesCS2B01G061200 chr1B 667960432 667961116 684 True 1146.000000 1146 96.7980 1653 2339 1 chr1B.!!$R1 686
16 TraesCS2B01G061200 chr1B 651060964 651061658 694 True 483.000000 483 93.2025 1006 1660 2 chr1B.!!$R2 654
17 TraesCS2B01G061200 chr3A 340280732 340281414 682 False 1033.000000 1033 94.0410 1659 2339 1 chr3A.!!$F1 680
18 TraesCS2B01G061200 chr3D 512982848 512983528 680 False 976.000000 976 92.5330 1658 2339 1 chr3D.!!$F1 681
19 TraesCS2B01G061200 chr2A 19053199 19054906 1707 True 640.000000 917 93.8290 1 1660 4 chr2A.!!$R2 1659

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
234 241 0.465705 GCTCCAACATCGGGATCTCA 59.534 55.0 0.0 0.0 33.04 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 3647 1.153745 CCGGCTCCTCTTCTTCACG 60.154 63.158 0.0 0.0 0.0 4.35 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
58 62 8.423906 TCAAGTTATACCTTGAGTCTTTCTCT 57.576 34.615 8.52 0.00 44.39 3.10
157 162 7.201635 GCCATAATGTTTTCCCATGTTTGATTC 60.202 37.037 0.00 0.00 0.00 2.52
182 188 8.522003 TCAATGCATGTGTTCTATATTGTTGTT 58.478 29.630 0.00 0.00 0.00 2.83
234 241 0.465705 GCTCCAACATCGGGATCTCA 59.534 55.000 0.00 0.00 33.04 3.27
235 242 1.071385 GCTCCAACATCGGGATCTCAT 59.929 52.381 0.00 0.00 33.04 2.90
236 243 2.763933 CTCCAACATCGGGATCTCATG 58.236 52.381 0.00 0.00 33.04 3.07
237 244 2.366590 CTCCAACATCGGGATCTCATGA 59.633 50.000 10.75 0.00 33.04 3.07
238 245 2.974794 TCCAACATCGGGATCTCATGAT 59.025 45.455 10.75 0.00 35.26 2.45
239 246 3.392285 TCCAACATCGGGATCTCATGATT 59.608 43.478 10.75 0.00 32.19 2.57
240 247 4.592778 TCCAACATCGGGATCTCATGATTA 59.407 41.667 10.75 0.00 32.19 1.75
241 248 5.249163 TCCAACATCGGGATCTCATGATTAT 59.751 40.000 10.75 0.00 32.19 1.28
242 249 5.583854 CCAACATCGGGATCTCATGATTATC 59.416 44.000 10.75 2.72 32.19 1.75
243 250 6.168389 CAACATCGGGATCTCATGATTATCA 58.832 40.000 16.07 0.00 32.19 2.15
244 251 6.364568 ACATCGGGATCTCATGATTATCAA 57.635 37.500 16.07 5.58 32.19 2.57
245 252 6.772605 ACATCGGGATCTCATGATTATCAAA 58.227 36.000 16.07 5.32 32.19 2.69
246 253 7.226441 ACATCGGGATCTCATGATTATCAAAA 58.774 34.615 16.07 5.07 32.19 2.44
247 254 7.173907 ACATCGGGATCTCATGATTATCAAAAC 59.826 37.037 16.07 6.18 32.19 2.43
248 255 5.997746 TCGGGATCTCATGATTATCAAAACC 59.002 40.000 16.07 9.35 32.19 3.27
249 256 5.764686 CGGGATCTCATGATTATCAAAACCA 59.235 40.000 16.07 0.00 32.19 3.67
250 257 6.432162 CGGGATCTCATGATTATCAAAACCAT 59.568 38.462 16.07 0.00 32.19 3.55
251 258 7.574404 CGGGATCTCATGATTATCAAAACCATG 60.574 40.741 16.07 0.00 36.78 3.66
252 259 7.088905 GGATCTCATGATTATCAAAACCATGC 58.911 38.462 16.07 0.00 35.76 4.06
253 260 7.255695 GGATCTCATGATTATCAAAACCATGCA 60.256 37.037 16.07 0.00 35.76 3.96
254 261 7.407393 TCTCATGATTATCAAAACCATGCAA 57.593 32.000 0.00 0.00 35.76 4.08
255 262 8.014070 TCTCATGATTATCAAAACCATGCAAT 57.986 30.769 0.00 0.00 35.76 3.56
256 263 9.134055 TCTCATGATTATCAAAACCATGCAATA 57.866 29.630 0.00 0.00 35.76 1.90
257 264 9.752961 CTCATGATTATCAAAACCATGCAATAA 57.247 29.630 0.00 0.00 35.76 1.40
261 268 9.970395 TGATTATCAAAACCATGCAATAATCTC 57.030 29.630 17.78 2.90 37.16 2.75
282 289 7.407393 TCTCATGATTATCAAAACCATGCAA 57.593 32.000 0.00 0.00 35.76 4.08
284 291 9.134055 TCTCATGATTATCAAAACCATGCAATA 57.866 29.630 0.00 0.00 35.76 1.90
396 404 6.653526 TTATGACCAATGGCCAGAATAATG 57.346 37.500 13.05 3.06 0.00 1.90
435 444 6.699642 ACCATGTGTTTTACTTAATTGTGTGC 59.300 34.615 0.00 0.00 0.00 4.57
527 538 5.643664 TGTCATTCTATGCAAATGCTTGAC 58.356 37.500 6.97 8.00 42.66 3.18
603 615 4.378774 TCCAACCAACATGCTTGAAATTG 58.621 39.130 6.60 0.90 0.00 2.32
1342 1433 3.004839 ACTCGATATCCGTGGATGAACTG 59.995 47.826 11.68 2.34 39.75 3.16
1363 1454 5.155509 TGATTATCAAGTTGGCGATTTCG 57.844 39.130 2.34 0.00 43.27 3.46
1725 3190 3.314553 CGAGACAACAAACGATAGGTGT 58.685 45.455 0.00 0.00 39.73 4.16
1940 3406 4.586235 ACGCTGCTGCCAAGGGTT 62.586 61.111 10.24 0.00 35.36 4.11
2068 3534 1.490910 GGATTTCTCCCGATCCCAACT 59.509 52.381 0.00 0.00 36.61 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 88 3.750371 TGCTGGCAAGTATGTAACACTT 58.250 40.909 0.00 0.00 36.68 3.16
157 162 8.692110 AACAACAATATAGAACACATGCATTG 57.308 30.769 0.00 1.69 0.00 2.82
235 242 9.970395 GAGATTATTGCATGGTTTTGATAATCA 57.030 29.630 18.66 0.00 38.22 2.57
236 243 9.970395 TGAGATTATTGCATGGTTTTGATAATC 57.030 29.630 12.49 12.49 37.02 1.75
238 245 9.752961 CATGAGATTATTGCATGGTTTTGATAA 57.247 29.630 0.00 0.00 36.61 1.75
239 246 9.134055 TCATGAGATTATTGCATGGTTTTGATA 57.866 29.630 0.00 0.00 39.76 2.15
240 247 8.014070 TCATGAGATTATTGCATGGTTTTGAT 57.986 30.769 0.00 0.00 39.76 2.57
241 248 7.407393 TCATGAGATTATTGCATGGTTTTGA 57.593 32.000 0.00 0.00 39.76 2.69
242 249 8.657074 AATCATGAGATTATTGCATGGTTTTG 57.343 30.769 0.09 0.00 39.58 2.44
256 263 8.014070 TGCATGGTTTTGATAATCATGAGATT 57.986 30.769 12.13 0.00 45.98 2.40
257 264 7.591421 TGCATGGTTTTGATAATCATGAGAT 57.409 32.000 12.13 0.00 37.87 2.75
258 265 7.407393 TTGCATGGTTTTGATAATCATGAGA 57.593 32.000 12.13 0.00 37.87 3.27
259 266 9.752961 TTATTGCATGGTTTTGATAATCATGAG 57.247 29.630 12.13 0.00 37.87 2.90
302 309 9.352784 TGCATGTATTAGTTTGTTTCTAATTGC 57.647 29.630 0.00 10.95 38.37 3.56
396 404 7.538303 AAACACATGGTGAATTTTCAAAGAC 57.462 32.000 2.98 0.00 39.21 3.01
471 480 6.180472 ACCTCAGGTGTTAGTGGAAATATTG 58.820 40.000 0.00 0.00 32.98 1.90
491 500 8.623903 TGCATAGAATGACAAATATTGAACCTC 58.376 33.333 0.00 0.00 0.00 3.85
712 727 7.009179 TGGTTAACCATGCATTAATTTGGAA 57.991 32.000 23.69 0.00 42.01 3.53
987 1046 0.035439 TCGCCATTTTCCCTCTGGAC 60.035 55.000 0.00 0.00 41.57 4.02
1048 1107 4.026744 TCCTCCAAGACATTGTAGGAGAG 58.973 47.826 23.65 16.85 44.23 3.20
1342 1433 5.198274 GTCGAAATCGCCAACTTGATAATC 58.802 41.667 0.00 0.00 39.60 1.75
1422 1513 1.768275 TGACACTCCAACACACCATCT 59.232 47.619 0.00 0.00 0.00 2.90
1582 3045 4.872124 GGGCTAAAATCATTTTCCTTGCTG 59.128 41.667 0.00 0.00 34.19 4.41
2068 3534 1.371183 CGGAGTGCCTGAGGTGAAA 59.629 57.895 0.00 0.00 0.00 2.69
2181 3647 1.153745 CCGGCTCCTCTTCTTCACG 60.154 63.158 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.