Multiple sequence alignment - TraesCS2A01G237100

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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 TraesCS2A01G237100 chr2A 100.000 6804 0 0 1 6804 306686897 306680094 0.000000e+00 12565
1 TraesCS2A01G237100 chr2A 99.144 6312 35 3 1 6296 69254118 69260426 0.000000e+00 11339
2 TraesCS2A01G237100 chr2A 83.841 755 82 11 1815 2554 26027741 26028470 0.000000e+00 682
3 TraesCS2A01G237100 chr2A 90.989 455 36 4 219 671 43440380 43440831 5.830000e-170 608
4 TraesCS2A01G237100 chr2A 81.235 421 60 10 5442 5851 347871778 347872190 8.510000e-84 322
5 TraesCS2A01G237100 chr2A 89.266 177 17 2 655 829 43440845 43441021 3.190000e-53 220
6 TraesCS2A01G237100 chr5A 99.587 6296 22 2 1 6296 403895922 403902213 0.000000e+00 11479
7 TraesCS2A01G237100 chr5A 91.372 452 34 4 222 671 119062180 119061732 1.250000e-171 614
8 TraesCS2A01G237100 chr5A 86.667 225 27 2 2279 2501 688125413 688125636 5.270000e-61 246
9 TraesCS2A01G237100 chr5A 91.111 135 9 3 4676 4808 482027212 482027345 5.420000e-41 180
10 TraesCS2A01G237100 chr5A 78.922 204 24 8 698 883 425488914 425488712 3.330000e-23 121
11 TraesCS2A01G237100 chr3A 99.473 3228 17 0 1 3228 405844995 405841768 0.000000e+00 5867
12 TraesCS2A01G237100 chr3A 99.386 3092 14 4 3224 6312 405833217 405830128 0.000000e+00 5600
13 TraesCS2A01G237100 chr3A 85.520 808 88 16 70 860 95901320 95900525 0.000000e+00 817
14 TraesCS2A01G237100 chr3A 87.536 698 68 12 1058 1746 414406856 414406169 0.000000e+00 789
15 TraesCS2A01G237100 chr3A 84.479 451 52 5 1949 2393 644202672 644203110 4.880000e-116 429
16 TraesCS2A01G237100 chr3A 84.711 242 16 15 5628 5860 455227976 455227747 8.880000e-54 222
17 TraesCS2A01G237100 chr3A 90.370 135 9 4 4676 4808 672876261 672876393 2.520000e-39 174
18 TraesCS2A01G237100 chr3A 92.593 108 8 0 4049 4156 42045565 42045458 9.140000e-34 156
19 TraesCS2A01G237100 chr3B 96.767 3310 61 7 2556 5855 561700417 561703690 0.000000e+00 5478
20 TraesCS2A01G237100 chr3B 97.926 2555 49 3 1 2554 561697707 561700258 0.000000e+00 4421
21 TraesCS2A01G237100 chr3B 88.903 2334 160 36 3579 5855 793141591 793143882 0.000000e+00 2784
22 TraesCS2A01G237100 chr3B 80.952 903 132 26 4938 5812 412402880 412401990 0.000000e+00 678
23 TraesCS2A01G237100 chr3B 85.597 243 13 15 5628 5860 449164742 449164512 1.140000e-57 235
24 TraesCS2A01G237100 chr3B 89.431 123 8 3 3232 3350 774716298 774716419 4.250000e-32 150
25 TraesCS2A01G237100 chr6A 97.144 2556 64 5 1 2554 602826803 602829351 0.000000e+00 4307
26 TraesCS2A01G237100 chr6A 96.913 1879 52 3 2556 4431 602829510 602831385 0.000000e+00 3144
27 TraesCS2A01G237100 chr6A 86.074 833 86 16 70 884 383585152 383584332 0.000000e+00 869
28 TraesCS2A01G237100 chr6A 85.954 833 87 16 70 884 46572504 46571684 0.000000e+00 863
29 TraesCS2A01G237100 chrUn 99.568 1622 7 0 3635 5256 384178460 384180081 0.000000e+00 2957
30 TraesCS2A01G237100 chrUn 90.431 209 18 2 1550 1756 76352938 76353146 2.420000e-69 274
31 TraesCS2A01G237100 chrUn 90.431 209 18 2 1550 1756 233823630 233823838 2.420000e-69 274
32 TraesCS2A01G237100 chr5B 97.959 441 9 0 5856 6296 678454812 678455252 0.000000e+00 765
33 TraesCS2A01G237100 chr5B 81.707 902 126 22 4938 5812 350710553 350709664 0.000000e+00 715
34 TraesCS2A01G237100 chr5B 90.769 455 35 5 219 671 697071500 697071949 9.760000e-168 601
35 TraesCS2A01G237100 chr5B 91.156 441 36 2 5856 6296 27381443 27381880 4.540000e-166 595
36 TraesCS2A01G237100 chr5B 87.451 255 26 6 2556 2805 672541152 672540899 8.630000e-74 289
37 TraesCS2A01G237100 chr5B 82.779 331 40 7 5531 5853 415054874 415055195 5.200000e-71 279
38 TraesCS2A01G237100 chr5B 86.404 228 24 6 3130 3350 533416995 533417222 6.820000e-60 243
39 TraesCS2A01G237100 chr5B 80.342 351 41 16 3701 4028 347127649 347127994 2.450000e-59 241
40 TraesCS2A01G237100 chr5B 89.894 188 17 2 3360 3545 505361014 505361201 2.450000e-59 241
41 TraesCS2A01G237100 chr7B 86.434 715 73 12 1058 1756 659831912 659832618 0.000000e+00 761
42 TraesCS2A01G237100 chr7B 81.953 471 70 10 4938 5399 524611207 524611671 1.070000e-102 385
43 TraesCS2A01G237100 chr7B 85.597 243 13 15 5628 5860 353328535 353328765 1.140000e-57 235
44 TraesCS2A01G237100 chr6B 93.439 442 25 3 5856 6297 176215908 176215471 0.000000e+00 652
45 TraesCS2A01G237100 chr6B 93.439 442 25 3 5856 6297 176240690 176240253 0.000000e+00 652
46 TraesCS2A01G237100 chr6B 92.760 442 28 3 5856 6297 176154602 176154165 2.680000e-178 636
47 TraesCS2A01G237100 chr6B 92.760 442 28 3 5856 6297 176178572 176178135 2.680000e-178 636
48 TraesCS2A01G237100 chr6B 91.455 433 31 6 455 884 49382308 49381879 2.110000e-164 590
49 TraesCS2A01G237100 chr6B 87.795 254 27 4 2556 2805 599819473 599819726 1.860000e-75 294
50 TraesCS2A01G237100 chr6B 84.052 232 26 5 5628 5852 536849880 536849653 5.350000e-51 213
51 TraesCS2A01G237100 chr2B 90.929 452 38 3 222 671 161446244 161445794 7.550000e-169 604
52 TraesCS2A01G237100 chr2B 91.503 306 25 1 6296 6601 272460651 272460955 2.930000e-113 420
53 TraesCS2A01G237100 chr2B 95.495 222 10 0 6583 6804 272460969 272461190 8.390000e-94 355
54 TraesCS2A01G237100 chr2B 87.795 254 27 4 2556 2805 183534428 183534175 1.860000e-75 294
55 TraesCS2A01G237100 chr7A 84.494 445 42 8 1955 2393 374542690 374542267 1.370000e-111 414
56 TraesCS2A01G237100 chr7A 93.443 122 7 1 4676 4796 731392157 731392036 5.420000e-41 180
57 TraesCS2A01G237100 chr7A 89.431 123 9 2 3232 3350 121783571 121783693 1.180000e-32 152
58 TraesCS2A01G237100 chr4A 88.379 327 38 0 4045 4371 222106844 222107170 1.780000e-105 394
59 TraesCS2A01G237100 chr4A 84.848 99 13 2 6702 6798 433634050 433633952 1.560000e-16 99
60 TraesCS2A01G237100 chr4A 95.238 63 2 1 1014 1075 693877369 693877307 1.560000e-16 99
61 TraesCS2A01G237100 chr6D 83.886 422 48 11 5442 5854 425060481 425060891 1.070000e-102 385
62 TraesCS2A01G237100 chr2D 86.716 271 33 2 2279 2547 117801407 117801676 1.430000e-76 298
63 TraesCS2A01G237100 chr7D 88.940 217 21 2 6583 6799 415748690 415748903 1.460000e-66 265
64 TraesCS2A01G237100 chr3D 86.000 250 31 4 2560 2805 550355777 550356026 1.460000e-66 265
65 TraesCS2A01G237100 chr4B 84.322 236 24 7 5628 5854 305510803 305510572 1.150000e-52 219
66 TraesCS2A01G237100 chr4B 86.500 200 23 2 2355 2554 241184998 241185193 4.130000e-52 217
67 TraesCS2A01G237100 chr1B 90.361 166 15 1 3379 3543 562727229 562727064 4.130000e-52 217
68 TraesCS2A01G237100 chr1B 88.710 124 9 3 3232 3350 562727811 562727688 5.500000e-31 147


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 TraesCS2A01G237100 chr2A 306680094 306686897 6803 True 12565.0 12565 100.0000 1 6804 1 chr2A.!!$R1 6803
1 TraesCS2A01G237100 chr2A 69254118 69260426 6308 False 11339.0 11339 99.1440 1 6296 1 chr2A.!!$F2 6295
2 TraesCS2A01G237100 chr2A 26027741 26028470 729 False 682.0 682 83.8410 1815 2554 1 chr2A.!!$F1 739
3 TraesCS2A01G237100 chr2A 43440380 43441021 641 False 414.0 608 90.1275 219 829 2 chr2A.!!$F4 610
4 TraesCS2A01G237100 chr5A 403895922 403902213 6291 False 11479.0 11479 99.5870 1 6296 1 chr5A.!!$F1 6295
5 TraesCS2A01G237100 chr3A 405841768 405844995 3227 True 5867.0 5867 99.4730 1 3228 1 chr3A.!!$R4 3227
6 TraesCS2A01G237100 chr3A 405830128 405833217 3089 True 5600.0 5600 99.3860 3224 6312 1 chr3A.!!$R3 3088
7 TraesCS2A01G237100 chr3A 95900525 95901320 795 True 817.0 817 85.5200 70 860 1 chr3A.!!$R2 790
8 TraesCS2A01G237100 chr3A 414406169 414406856 687 True 789.0 789 87.5360 1058 1746 1 chr3A.!!$R5 688
9 TraesCS2A01G237100 chr3B 561697707 561703690 5983 False 4949.5 5478 97.3465 1 5855 2 chr3B.!!$F3 5854
10 TraesCS2A01G237100 chr3B 793141591 793143882 2291 False 2784.0 2784 88.9030 3579 5855 1 chr3B.!!$F2 2276
11 TraesCS2A01G237100 chr3B 412401990 412402880 890 True 678.0 678 80.9520 4938 5812 1 chr3B.!!$R1 874
12 TraesCS2A01G237100 chr6A 602826803 602831385 4582 False 3725.5 4307 97.0285 1 4431 2 chr6A.!!$F1 4430
13 TraesCS2A01G237100 chr6A 383584332 383585152 820 True 869.0 869 86.0740 70 884 1 chr6A.!!$R2 814
14 TraesCS2A01G237100 chr6A 46571684 46572504 820 True 863.0 863 85.9540 70 884 1 chr6A.!!$R1 814
15 TraesCS2A01G237100 chrUn 384178460 384180081 1621 False 2957.0 2957 99.5680 3635 5256 1 chrUn.!!$F3 1621
16 TraesCS2A01G237100 chr5B 350709664 350710553 889 True 715.0 715 81.7070 4938 5812 1 chr5B.!!$R1 874
17 TraesCS2A01G237100 chr7B 659831912 659832618 706 False 761.0 761 86.4340 1058 1756 1 chr7B.!!$F3 698
18 TraesCS2A01G237100 chr2B 272460651 272461190 539 False 387.5 420 93.4990 6296 6804 2 chr2B.!!$F1 508

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
187 190 2.834549 CCAGTCTAGGTTGTCCATCTGT 59.165 50.000 0.0 0.00 35.89 3.41 F
409 418 4.806247 GGATATTCAGGAGTTGAGAACACG 59.194 45.833 0.0 0.00 37.07 4.49 F
1543 1610 7.541162 CAAATGACTTTGATGCCAGAAATAGA 58.459 34.615 0.0 0.00 43.71 1.98 F
3147 3385 4.051167 CCCCATCCCAGCAGCACA 62.051 66.667 0.0 0.00 0.00 4.57 F
3366 3608 3.396685 ACTGGCCAGTTCTAGAGAGAT 57.603 47.619 33.2 5.31 38.83 2.75 F
5224 5543 5.431765 AGAACCCACATGATTGATACTGAC 58.568 41.667 0.0 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1610 8.268878 AGAGCATAGTATTTTCATTACCTCCT 57.731 34.615 0.0 0.0 0.00 3.69 R
3147 3385 2.990479 GAAGACACCGGCTCCCAT 59.010 61.111 0.0 0.0 0.00 4.00 R
3366 3608 7.126061 TCTCTTTCTCTCTCTCTCTCTCTCTA 58.874 42.308 0.0 0.0 0.00 2.43 R
5224 5543 5.973651 ACTGCTGATAACACATTACATCG 57.026 39.130 0.0 0.0 0.00 3.84 R
5241 5561 9.399797 TCACATTCAAAATTGAGATATACTGCT 57.600 29.630 0.0 0.0 38.61 4.24 R
6617 6994 1.000171 GGCAAAAGCTCCTCACCTTTG 60.000 52.381 0.0 0.0 32.06 2.77 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
187 190 2.834549 CCAGTCTAGGTTGTCCATCTGT 59.165 50.000 0.00 0.00 35.89 3.41
409 418 4.806247 GGATATTCAGGAGTTGAGAACACG 59.194 45.833 0.00 0.00 37.07 4.49
1543 1610 7.541162 CAAATGACTTTGATGCCAGAAATAGA 58.459 34.615 0.00 0.00 43.71 1.98
3147 3385 4.051167 CCCCATCCCAGCAGCACA 62.051 66.667 0.00 0.00 0.00 4.57
3366 3608 3.396685 ACTGGCCAGTTCTAGAGAGAT 57.603 47.619 33.20 5.31 38.83 2.75
4470 4778 8.771920 ATCTTATTCAGATGTTGTAAACGACA 57.228 30.769 5.67 5.67 41.25 4.35
5224 5543 5.431765 AGAACCCACATGATTGATACTGAC 58.568 41.667 0.00 0.00 0.00 3.51
5241 5561 8.410141 TGATACTGACGATGTAATGTGTTATCA 58.590 33.333 0.00 0.00 0.00 2.15
6308 6654 7.556635 CCGGGTCATCTAGTATGACTATATGAA 59.443 40.741 23.06 0.91 42.25 2.57
6310 6656 8.908903 GGGTCATCTAGTATGACTATATGAAGG 58.091 40.741 23.06 0.00 42.25 3.46
6391 6737 4.003648 ACCGAAGAAGATTAAAGGCACAG 58.996 43.478 0.00 0.00 0.00 3.66
6392 6738 4.253685 CCGAAGAAGATTAAAGGCACAGA 58.746 43.478 0.00 0.00 0.00 3.41
6401 6747 6.174049 AGATTAAAGGCACAGACTTCTTACC 58.826 40.000 0.00 0.00 26.61 2.85
6406 6752 3.003480 GGCACAGACTTCTTACCATCAC 58.997 50.000 0.00 0.00 0.00 3.06
6420 6766 6.837048 TCTTACCATCACTGCTACCACTATTA 59.163 38.462 0.00 0.00 0.00 0.98
6432 6778 5.221048 GCTACCACTATTATTGTTTGGCCAG 60.221 44.000 5.11 0.00 0.00 4.85
6446 6792 3.845781 TGGCCAGACAGATTATTCCTC 57.154 47.619 0.00 0.00 0.00 3.71
6474 6820 8.565416 CAGCATCTAACATGATGTGAACAATAT 58.435 33.333 0.00 0.00 44.02 1.28
6511 6857 8.401709 ACAAGACAGAAATCTTCTTCAAAAGAC 58.598 33.333 5.46 0.00 38.06 3.01
6536 6882 9.448438 ACTATGTTTATAAGCAACACATTCAGA 57.552 29.630 6.08 0.00 36.97 3.27
6556 6902 8.684386 TTCAGACCATGTTTACAATTACTTGA 57.316 30.769 0.00 0.00 36.20 3.02
6579 6925 3.323691 TGTTGGAGCTGTCTTTGCTACTA 59.676 43.478 0.00 0.00 41.70 1.82
6594 6971 3.783642 TGCTACTACCCTCTCTCTCTCTT 59.216 47.826 0.00 0.00 0.00 2.85
6647 7024 1.885871 GCTTTTGCCCCTGCTACAG 59.114 57.895 0.00 0.00 40.15 2.74
6718 7095 9.471702 AGTGATCTGATCTCCAATAATGTTTTT 57.528 29.630 17.82 0.00 0.00 1.94
6755 7132 9.399797 AGTGCAGATAAATGTCATCAAAGATAA 57.600 29.630 0.00 0.00 0.00 1.75
6775 7152 2.040178 ACCAGGGATCGATCCTACAAC 58.960 52.381 36.72 23.09 46.35 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 190 1.475403 GGAGGAAGATGACTCGGACA 58.525 55.000 0.00 0.00 34.58 4.02
409 418 6.128227 TGCCATTACGAACACCTACAAAATAC 60.128 38.462 0.00 0.00 0.00 1.89
1543 1610 8.268878 AGAGCATAGTATTTTCATTACCTCCT 57.731 34.615 0.00 0.00 0.00 3.69
3147 3385 2.990479 GAAGACACCGGCTCCCAT 59.010 61.111 0.00 0.00 0.00 4.00
3366 3608 7.126061 TCTCTTTCTCTCTCTCTCTCTCTCTA 58.874 42.308 0.00 0.00 0.00 2.43
4470 4778 6.992063 ATCGACAAAAAGCATCTAGTTGAT 57.008 33.333 4.94 0.00 35.40 2.57
5224 5543 5.973651 ACTGCTGATAACACATTACATCG 57.026 39.130 0.00 0.00 0.00 3.84
5241 5561 9.399797 TCACATTCAAAATTGAGATATACTGCT 57.600 29.630 0.00 0.00 38.61 4.24
6308 6654 6.484288 TGTTGTTGACCTTGAATCATATCCT 58.516 36.000 0.00 0.00 0.00 3.24
6310 6656 7.253422 CCTTGTTGTTGACCTTGAATCATATC 58.747 38.462 0.00 0.00 0.00 1.63
6312 6658 5.048083 GCCTTGTTGTTGACCTTGAATCATA 60.048 40.000 0.00 0.00 0.00 2.15
6323 6669 2.888834 AACATGGCCTTGTTGTTGAC 57.111 45.000 30.33 0.00 38.37 3.18
6391 6737 4.081642 TGGTAGCAGTGATGGTAAGAAGTC 60.082 45.833 0.00 0.00 0.00 3.01
6392 6738 3.838317 TGGTAGCAGTGATGGTAAGAAGT 59.162 43.478 0.00 0.00 0.00 3.01
6401 6747 7.792374 AACAATAATAGTGGTAGCAGTGATG 57.208 36.000 12.54 6.54 0.00 3.07
6406 6752 5.221048 GGCCAAACAATAATAGTGGTAGCAG 60.221 44.000 0.00 0.00 0.00 4.24
6420 6766 5.127682 GGAATAATCTGTCTGGCCAAACAAT 59.872 40.000 14.06 7.16 0.00 2.71
6432 6778 6.100404 AGATGCTGAGAGGAATAATCTGTC 57.900 41.667 0.00 0.00 0.00 3.51
6490 6836 9.566432 ACATAGTCTTTTGAAGAAGATTTCTGT 57.434 29.630 0.00 0.00 40.59 3.41
6511 6857 9.708222 GTCTGAATGTGTTGCTTATAAACATAG 57.292 33.333 1.20 0.00 39.57 2.23
6523 6869 3.648339 AACATGGTCTGAATGTGTTGC 57.352 42.857 0.00 0.00 38.27 4.17
6533 6879 8.514594 ACATCAAGTAATTGTAAACATGGTCTG 58.485 33.333 2.43 0.00 0.00 3.51
6536 6882 8.087750 CCAACATCAAGTAATTGTAAACATGGT 58.912 33.333 2.43 0.00 0.00 3.55
6556 6902 2.283145 AGCAAAGACAGCTCCAACAT 57.717 45.000 0.00 0.00 38.01 2.71
6579 6925 3.591527 TGAGAGAAAGAGAGAGAGAGGGT 59.408 47.826 0.00 0.00 0.00 4.34
6594 6971 5.222027 TGTTTGTACCATGGGATTGAGAGAA 60.222 40.000 18.09 0.00 0.00 2.87
6617 6994 1.000171 GGCAAAAGCTCCTCACCTTTG 60.000 52.381 0.00 0.00 32.06 2.77
6647 7024 5.614923 TCGAGCTAGTATATCTGCACTTC 57.385 43.478 0.00 0.00 0.00 3.01
6722 7099 9.176460 TGATGACATTTATCTGCACTTTATTCA 57.824 29.630 0.00 0.00 0.00 2.57
6775 7152 4.158209 TGTGTGGTTCAAATGCCATATGAG 59.842 41.667 3.65 0.00 37.09 2.90


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

AutoCloner maintained by Alex Coulton.