Multiple sequence alignment - TraesCS2B01G207500

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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 TraesCS2B01G207500 chr2B 100.000 2407 0 0 1 2407 188152658 188150252 0.000000e+00 4446.0
1 TraesCS2B01G207500 chr2B 98.692 2141 18 4 1 2131 188263269 188261129 0.000000e+00 3790.0
2 TraesCS2B01G207500 chr2B 100.000 1794 0 0 2676 4469 188149983 188148190 0.000000e+00 3314.0
3 TraesCS2B01G207500 chr2B 96.536 1790 26 9 2703 4469 188256231 188254455 0.000000e+00 2929.0
4 TraesCS2B01G207500 chr2B 97.355 1210 28 3 438 1646 188024091 188022885 0.000000e+00 2054.0
5 TraesCS2B01G207500 chr2B 98.433 766 7 1 1647 2407 188022823 188022058 0.000000e+00 1343.0
6 TraesCS2B01G207500 chr2B 97.903 620 11 2 3087 3704 188021294 188020675 0.000000e+00 1072.0
7 TraesCS2B01G207500 chr2B 95.287 488 18 3 1 484 188024470 188023984 0.000000e+00 769.0
8 TraesCS2B01G207500 chr2B 91.803 427 25 5 4052 4469 629027494 629027919 1.790000e-163 586.0
9 TraesCS2B01G207500 chr2B 100.000 284 0 0 2124 2407 188260943 188260660 3.960000e-145 525.0
10 TraesCS2B01G207500 chr2B 97.537 203 2 2 2898 3097 188021642 188021440 1.190000e-90 344.0
11 TraesCS2B01G207500 chr2B 89.071 183 17 2 631 812 188152462 188152642 1.620000e-54 224.0
12 TraesCS2B01G207500 chr2B 88.043 184 18 2 631 812 188024273 188024454 9.740000e-52 215.0
13 TraesCS2B01G207500 chr2B 88.043 184 18 2 631 812 188263072 188263253 9.740000e-52 215.0
14 TraesCS2B01G207500 chr2B 100.000 34 0 0 2679 2712 188260421 188260388 3.730000e-06 63.9
15 TraesCS2B01G207500 chr2B 94.595 37 0 2 3147 3182 758534096 758534061 6.240000e-04 56.5
16 TraesCS2B01G207500 chr4D 89.208 732 75 4 918 1646 86312941 86313671 0.000000e+00 911.0
17 TraesCS2B01G207500 chr4D 88.813 733 77 4 918 1646 86531777 86532508 0.000000e+00 894.0
18 TraesCS2B01G207500 chr4D 92.272 427 24 2 4052 4469 502781400 502780974 8.270000e-167 597.0
19 TraesCS2B01G207500 chr4D 87.765 425 51 1 1223 1646 5369287 5369711 3.100000e-136 496.0
20 TraesCS2B01G207500 chr4D 87.647 340 38 3 2732 3068 86533448 86533786 4.190000e-105 392.0
21 TraesCS2B01G207500 chr4D 94.595 37 0 2 3145 3181 402528827 402528861 6.240000e-04 56.5
22 TraesCS2B01G207500 chr4D 100.000 28 0 0 3145 3172 337933263 337933290 8.000000e-03 52.8
23 TraesCS2B01G207500 chr4A 89.208 732 75 4 918 1646 509225028 509224298 0.000000e+00 911.0
24 TraesCS2B01G207500 chr4A 86.037 752 77 14 1667 2400 598453798 598454539 0.000000e+00 782.0
25 TraesCS2B01G207500 chr4A 83.026 760 98 15 1664 2400 509224213 509223462 0.000000e+00 660.0
26 TraesCS2B01G207500 chr4A 81.992 783 112 13 1639 2400 508838363 508837589 4.880000e-179 638.0
27 TraesCS2B01G207500 chr4A 91.022 323 27 2 918 1239 508847832 508847511 6.870000e-118 435.0
28 TraesCS2B01G207500 chr4A 85.784 408 52 6 1242 1646 508838828 508838424 1.150000e-115 427.0
29 TraesCS2B01G207500 chr4A 88.235 340 36 3 2732 3068 509223375 509223037 1.940000e-108 403.0
30 TraesCS2B01G207500 chr4A 87.316 339 39 3 2733 3068 508837501 508837164 7.010000e-103 385.0
31 TraesCS2B01G207500 chr4B 89.306 720 73 4 930 1646 123920422 123921140 0.000000e+00 900.0
32 TraesCS2B01G207500 chr4B 88.022 743 70 9 1673 2400 9463243 9463981 0.000000e+00 861.0
33 TraesCS2B01G207500 chr4B 83.333 756 96 14 1664 2397 123921225 123921972 0.000000e+00 671.0
34 TraesCS2B01G207500 chr4B 88.810 420 46 1 1228 1646 9462730 9463149 8.570000e-142 514.0
35 TraesCS2B01G207500 chr4B 87.941 340 37 3 2732 3068 123922061 123922399 9.010000e-107 398.0
36 TraesCS2B01G207500 chr4B 79.386 456 70 15 20 469 399951329 399951766 2.610000e-77 300.0
37 TraesCS2B01G207500 chrUn 100.000 411 0 0 3010 3420 477603397 477602987 0.000000e+00 760.0
38 TraesCS2B01G207500 chr7B 90.927 518 34 6 17 530 251034114 251034622 0.000000e+00 684.0
39 TraesCS2B01G207500 chr7B 93.680 269 15 2 546 814 251035100 251035366 6.960000e-108 401.0
40 TraesCS2B01G207500 chr7B 86.878 221 23 6 17 234 80854601 80854818 4.470000e-60 243.0
41 TraesCS2B01G207500 chr7B 88.462 182 15 4 631 812 251034289 251034114 9.740000e-52 215.0
42 TraesCS2B01G207500 chr7D 88.738 515 49 7 15 526 385843374 385843882 4.910000e-174 621.0
43 TraesCS2B01G207500 chr7D 92.453 424 23 2 4055 4469 604462477 604462054 8.270000e-167 597.0
44 TraesCS2B01G207500 chr7D 83.333 198 26 7 618 812 449380632 449380825 4.590000e-40 176.0
45 TraesCS2B01G207500 chr6B 88.346 532 42 3 17 545 308568373 308567859 4.910000e-174 621.0
46 TraesCS2B01G207500 chr6B 93.893 262 16 0 551 812 308567581 308567320 3.240000e-106 396.0
47 TraesCS2B01G207500 chr3B 82.034 757 106 13 1666 2399 793103261 793102512 6.350000e-173 617.0
48 TraesCS2B01G207500 chr3B 83.070 697 95 11 959 1644 793104034 793103350 2.950000e-171 612.0
49 TraesCS2B01G207500 chr3B 86.532 297 32 5 3168 3462 793099936 793099646 2.010000e-83 320.0
50 TraesCS2B01G207500 chr3B 86.458 96 10 2 3506 3598 793099550 793099455 7.910000e-18 102.0
51 TraesCS2B01G207500 chr3B 100.000 29 0 0 4024 4052 147897106 147897134 2.000000e-03 54.7
52 TraesCS2B01G207500 chr3D 92.272 427 24 2 4052 4469 579166181 579165755 8.270000e-167 597.0
53 TraesCS2B01G207500 chr3D 82.482 685 99 10 1663 2329 591343659 591344340 8.330000e-162 580.0
54 TraesCS2B01G207500 chr3D 83.628 452 58 11 17 463 213205876 213205436 1.160000e-110 411.0
55 TraesCS2B01G207500 chr3D 87.859 313 32 4 3168 3475 591344963 591345274 3.290000e-96 363.0
56 TraesCS2B01G207500 chr3D 85.460 337 41 4 2699 3027 591344608 591344944 1.190000e-90 344.0
57 TraesCS2B01G207500 chr3D 100.000 31 0 0 3111 3141 149612019 149611989 1.740000e-04 58.4
58 TraesCS2B01G207500 chr5D 92.217 424 24 2 4055 4469 320663478 320663055 3.850000e-165 592.0
59 TraesCS2B01G207500 chr5D 81.768 362 50 10 1654 2009 450117113 450117464 5.660000e-74 289.0
60 TraesCS2B01G207500 chr5D 97.059 34 1 0 4019 4052 51512010 51511977 1.740000e-04 58.4
61 TraesCS2B01G207500 chr5D 100.000 29 0 0 4024 4052 350366580 350366608 2.000000e-03 54.7
62 TraesCS2B01G207500 chr2D 92.037 427 25 2 4052 4469 562565747 562566173 3.850000e-165 592.0
63 TraesCS2B01G207500 chr3A 91.803 427 25 5 4052 4469 509380893 509381318 1.790000e-163 586.0
64 TraesCS2B01G207500 chr3A 79.406 471 73 15 20 484 61559134 61558682 1.210000e-80 311.0
65 TraesCS2B01G207500 chr3A 94.161 137 8 0 3326 3462 721602982 721603118 4.530000e-50 209.0
66 TraesCS2B01G207500 chr3A 85.714 126 18 0 427 552 61558800 61558675 2.800000e-27 134.0
67 TraesCS2B01G207500 chr3A 100.000 30 0 0 4023 4052 509380822 509380851 6.240000e-04 56.5
68 TraesCS2B01G207500 chr3A 100.000 29 0 0 3113 3141 167915650 167915622 2.000000e-03 54.7
69 TraesCS2B01G207500 chr1D 91.803 427 26 2 4052 4469 377964319 377963893 1.790000e-163 586.0
70 TraesCS2B01G207500 chr1D 82.700 474 66 10 17 485 18775339 18774877 1.500000e-109 407.0
71 TraesCS2B01G207500 chr1D 81.913 481 65 11 17 485 495006435 495005965 1.950000e-103 387.0
72 TraesCS2B01G207500 chr1D 93.182 44 3 0 3038 3081 281400550 281400593 1.040000e-06 65.8
73 TraesCS2B01G207500 chr2A 87.838 222 22 5 16 234 527613693 527613912 5.740000e-64 255.0
74 TraesCS2B01G207500 chr5A 77.946 331 61 7 1679 2008 569436857 569437176 3.530000e-46 196.0
75 TraesCS2B01G207500 chr6D 82.353 153 17 3 3826 3968 70558892 70558740 1.690000e-24 124.0
76 TraesCS2B01G207500 chr6D 87.097 62 5 3 3031 3089 26404954 26404893 2.880000e-07 67.6
77 TraesCS2B01G207500 chr6D 100.000 28 0 0 3145 3172 4268759 4268786 8.000000e-03 52.8
78 TraesCS2B01G207500 chr7A 100.000 29 0 0 3145 3173 26026177 26026149 2.000000e-03 54.7


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 TraesCS2B01G207500 chr2B 188148190 188152658 4468 True 3880.000000 4446 100.000000 1 4469 2 chr2B.!!$R4 4468
1 TraesCS2B01G207500 chr2B 188254455 188256231 1776 True 2929.000000 2929 96.536000 2703 4469 1 chr2B.!!$R1 1766
2 TraesCS2B01G207500 chr2B 188260388 188263269 2881 True 1459.633333 3790 99.564000 1 2712 3 chr2B.!!$R5 2711
3 TraesCS2B01G207500 chr2B 188020675 188024470 3795 True 1116.400000 2054 97.303000 1 3704 5 chr2B.!!$R3 3703
4 TraesCS2B01G207500 chr4D 86312941 86313671 730 False 911.000000 911 89.208000 918 1646 1 chr4D.!!$F2 728
5 TraesCS2B01G207500 chr4D 86531777 86533786 2009 False 643.000000 894 88.230000 918 3068 2 chr4D.!!$F5 2150
6 TraesCS2B01G207500 chr4A 598453798 598454539 741 False 782.000000 782 86.037000 1667 2400 1 chr4A.!!$F1 733
7 TraesCS2B01G207500 chr4A 509223037 509225028 1991 True 658.000000 911 86.823000 918 3068 3 chr4A.!!$R3 2150
8 TraesCS2B01G207500 chr4A 508837164 508838828 1664 True 483.333333 638 85.030667 1242 3068 3 chr4A.!!$R2 1826
9 TraesCS2B01G207500 chr4B 9462730 9463981 1251 False 687.500000 861 88.416000 1228 2400 2 chr4B.!!$F2 1172
10 TraesCS2B01G207500 chr4B 123920422 123922399 1977 False 656.333333 900 86.860000 930 3068 3 chr4B.!!$F3 2138
11 TraesCS2B01G207500 chr7B 251034114 251035366 1252 False 542.500000 684 92.303500 17 814 2 chr7B.!!$F2 797
12 TraesCS2B01G207500 chr7D 385843374 385843882 508 False 621.000000 621 88.738000 15 526 1 chr7D.!!$F1 511
13 TraesCS2B01G207500 chr6B 308567320 308568373 1053 True 508.500000 621 91.119500 17 812 2 chr6B.!!$R1 795
14 TraesCS2B01G207500 chr3B 793099455 793104034 4579 True 412.750000 617 84.523500 959 3598 4 chr3B.!!$R1 2639
15 TraesCS2B01G207500 chr3D 591343659 591345274 1615 False 429.000000 580 85.267000 1663 3475 3 chr3D.!!$F1 1812

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
791 1321 1.014352 CGAAGCCCGGTATTGAAAGG 58.986 55.000 0.0 0.0 33.91 3.11 F
2894 5923 3.646162 AGAGTGTAACATGTGGTGGAAGA 59.354 43.478 0.0 0.0 41.43 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2852 5879 1.376683 TGTTATCGGTGCTGTGCCC 60.377 57.895 0.0 0.0 0.00 5.36 R
4320 7595 1.067776 GTGGATCGTCAGTTCGTCCTT 60.068 52.381 0.0 0.0 34.61 3.36 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
93 94 5.124645 TCAAGATTGGCTTTGCAAAAATGT 58.875 33.333 13.84 6.15 33.60 2.71
104 105 3.485394 TGCAAAAATGTCACCTAGCTCA 58.515 40.909 0.00 0.00 0.00 4.26
498 817 1.227205 CCTCATCACTGCCGCTCTC 60.227 63.158 0.00 0.00 0.00 3.20
791 1321 1.014352 CGAAGCCCGGTATTGAAAGG 58.986 55.000 0.00 0.00 33.91 3.11
2894 5923 3.646162 AGAGTGTAACATGTGGTGGAAGA 59.354 43.478 0.00 0.00 41.43 2.87
3420 6620 3.299503 ACAAGTGGAAGGAGTTTGCATT 58.700 40.909 0.00 0.00 39.44 3.56
3864 7119 6.038825 TGTTGCTCAGAATTTTCCGAACTTAA 59.961 34.615 0.00 0.00 0.00 1.85
3952 7207 1.602851 GCTTATGTGCAGATGAGGCTG 59.397 52.381 16.07 0.00 38.91 4.85
4071 7342 4.401519 GGAAGGAAAAACAGGCCCTAATAC 59.598 45.833 0.00 0.00 0.00 1.89
4098 7369 3.518634 TGAAACTTGTTTGGTTGCCTC 57.481 42.857 3.27 0.00 0.00 4.70
4100 7371 1.119684 AACTTGTTTGGTTGCCTCCC 58.880 50.000 0.00 0.00 0.00 4.30
4102 7373 1.497286 ACTTGTTTGGTTGCCTCCCTA 59.503 47.619 0.00 0.00 0.00 3.53
4103 7374 2.162681 CTTGTTTGGTTGCCTCCCTAG 58.837 52.381 0.00 0.00 0.00 3.02
4104 7375 1.145571 TGTTTGGTTGCCTCCCTAGT 58.854 50.000 0.00 0.00 0.00 2.57
4105 7376 2.340731 TGTTTGGTTGCCTCCCTAGTA 58.659 47.619 0.00 0.00 0.00 1.82
4164 7439 3.704231 CTGCATTGGCCCTAGCGGT 62.704 63.158 0.00 0.00 41.24 5.68
4183 7458 2.486203 GGTACATGAACATGGCGTTTGA 59.514 45.455 17.25 0.00 42.91 2.69
4270 7545 1.596752 CTAGCACACCAACGCCACA 60.597 57.895 0.00 0.00 0.00 4.17
4282 7557 0.102120 ACGCCACAACACAACAATGG 59.898 50.000 0.00 0.00 0.00 3.16
4314 7589 7.678837 ACTGAGAGAAGATGATGAAGTTCTTT 58.321 34.615 4.17 0.00 30.11 2.52
4315 7590 8.811017 ACTGAGAGAAGATGATGAAGTTCTTTA 58.189 33.333 4.17 0.00 30.11 1.85
4317 7592 9.029368 TGAGAGAAGATGATGAAGTTCTTTAGA 57.971 33.333 4.17 0.00 30.11 2.10
4383 7658 1.831389 CTCCAAGCACGGTCAACACG 61.831 60.000 0.00 0.00 37.36 4.49
4436 7711 2.266627 GCTTGTTCTGCTGCCTGCT 61.267 57.895 0.00 0.00 43.37 4.24
4441 7716 1.082690 GTTCTGCTGCCTGCTTAGTC 58.917 55.000 0.00 0.00 43.37 2.59
4460 7735 7.363968 GCTTAGTCTTGAACCCTCTATAGTTGT 60.364 40.741 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.380444 GCAAATAGCCGATTTTCTCCACAA 60.380 41.667 0.00 0.00 35.45 3.33
93 94 1.269958 AGTGCACATGAGCTAGGTGA 58.730 50.000 21.04 0.00 43.52 4.02
104 105 3.119029 GGCATGGTAATCAAAGTGCACAT 60.119 43.478 21.04 3.48 34.45 3.21
399 404 4.318021 CAACTTGCAGCAGCGCGT 62.318 61.111 8.43 0.00 46.23 6.01
2852 5879 1.376683 TGTTATCGGTGCTGTGCCC 60.377 57.895 0.00 0.00 0.00 5.36
3420 6620 5.163405 GGTCATATACTCCAGTTCAGCTCAA 60.163 44.000 0.00 0.00 0.00 3.02
3864 7119 7.831193 AGGACAAATGAGACTTTGCATATAACT 59.169 33.333 0.00 0.00 39.26 2.24
3888 7143 3.733684 CGGAAACAACAAACTTGTGGAGG 60.734 47.826 3.95 0.00 41.31 4.30
3983 7238 7.634671 TGACGAATCTAACTATCCAGTTACA 57.365 36.000 0.00 0.00 43.33 2.41
3987 7242 6.096987 ACACATGACGAATCTAACTATCCAGT 59.903 38.462 0.00 0.00 36.19 4.00
4071 7342 4.173036 ACCAAACAAGTTTCATATGGCG 57.827 40.909 2.13 0.00 0.00 5.69
4164 7439 4.731720 CAATCAAACGCCATGTTCATGTA 58.268 39.130 11.13 0.00 40.84 2.29
4183 7458 1.948104 ACATGTACGCCGTATGCAAT 58.052 45.000 0.00 0.00 41.33 3.56
4270 7545 3.013921 AGTTCGTCACCATTGTTGTGTT 58.986 40.909 0.00 0.00 35.25 3.32
4282 7557 4.427096 TCATCTTCTCTCAGTTCGTCAC 57.573 45.455 0.00 0.00 0.00 3.67
4314 7589 5.008415 GGATCGTCAGTTCGTCCTTTATCTA 59.992 44.000 0.00 0.00 32.59 1.98
4315 7590 4.202030 GGATCGTCAGTTCGTCCTTTATCT 60.202 45.833 0.00 0.00 32.59 1.98
4317 7592 3.446161 TGGATCGTCAGTTCGTCCTTTAT 59.554 43.478 0.00 0.00 34.61 1.40
4319 7594 1.616865 TGGATCGTCAGTTCGTCCTTT 59.383 47.619 0.00 0.00 34.61 3.11
4320 7595 1.067776 GTGGATCGTCAGTTCGTCCTT 60.068 52.381 0.00 0.00 34.61 3.36
4383 7658 3.435186 GAAAGCACGGAGGCAGCC 61.435 66.667 1.84 1.84 35.83 4.85
4436 7711 8.311836 CAACAACTATAGAGGGTTCAAGACTAA 58.688 37.037 6.78 0.00 0.00 2.24
4441 7716 6.348540 GCAACAACAACTATAGAGGGTTCAAG 60.349 42.308 6.78 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.