Multiple sequence alignment - TraesCS7B01G420900

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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 TraesCS7B01G420900 chr7B 100.000 5868 0 0 1 5868 690093354 690099221 0.000000e+00 10837
1 TraesCS7B01G420900 chr7B 97.619 4536 78 12 1336 5868 690080898 690085406 0.000000e+00 7751
2 TraesCS7B01G420900 chr7B 96.624 3792 97 14 1997 5786 690031465 690035227 0.000000e+00 6264
3 TraesCS7B01G420900 chr7B 98.346 2358 36 3 1 2356 690118814 690121170 0.000000e+00 4135
4 TraesCS7B01G420900 chr7B 87.989 3372 302 35 889 4229 690199574 690202873 0.000000e+00 3888
5 TraesCS7B01G420900 chr7B 77.810 3434 566 118 931 4266 677961317 677964652 0.000000e+00 1940
6 TraesCS7B01G420900 chr7B 96.688 1087 31 1 881 1962 690030110 690031196 0.000000e+00 1803
7 TraesCS7B01G420900 chr7B 95.490 909 13 12 4961 5868 690080713 690079832 0.000000e+00 1426
8 TraesCS7B01G420900 chr7B 86.682 1284 144 13 4255 5522 690202870 690204142 0.000000e+00 1399
9 TraesCS7B01G420900 chr7B 95.221 272 10 2 1 272 426886654 426886386 1.510000e-115 427
10 TraesCS7B01G420900 chr7B 88.957 326 23 6 323 648 690198835 690199147 1.980000e-104 390
11 TraesCS7B01G420900 chr7B 89.695 262 24 3 387 646 690029638 690029898 1.220000e-86 331
12 TraesCS7B01G420900 chr7B 84.052 232 22 8 5561 5786 690204129 690204351 5.960000e-50 209
13 TraesCS7B01G420900 chr7B 100.000 86 0 0 5783 5868 64022441 64022526 6.090000e-35 159
14 TraesCS7B01G420900 chr7B 97.802 91 2 0 5778 5868 551216099 551216189 2.190000e-34 158
15 TraesCS7B01G420900 chr7B 100.000 85 0 0 5784 5868 627975673 627975757 2.190000e-34 158
16 TraesCS7B01G420900 chr7D 89.091 4629 435 34 674 5257 606010513 606015116 0.000000e+00 5686
17 TraesCS7B01G420900 chr7D 89.172 4119 392 28 1180 5257 606107122 606111227 0.000000e+00 5086
18 TraesCS7B01G420900 chr7D 91.116 3377 277 17 2158 5522 606182717 606186082 0.000000e+00 4553
19 TraesCS7B01G420900 chr7D 88.772 3527 283 33 727 4221 606301555 606305000 0.000000e+00 4215
20 TraesCS7B01G420900 chr7D 89.685 3170 290 18 2117 5257 605957465 605960626 0.000000e+00 4008
21 TraesCS7B01G420900 chr7D 92.450 1245 79 8 881 2125 605947279 605948508 0.000000e+00 1764
22 TraesCS7B01G420900 chr7D 93.058 994 60 4 1180 2169 606181448 606182436 0.000000e+00 1445
23 TraesCS7B01G420900 chr7D 86.994 1284 145 15 4255 5522 606305004 606306281 0.000000e+00 1426
24 TraesCS7B01G420900 chr7D 89.267 382 40 1 272 653 606180253 606180633 1.480000e-130 477
25 TraesCS7B01G420900 chr7D 95.133 226 10 1 5561 5786 606186069 606186293 7.230000e-94 355
26 TraesCS7B01G420900 chr7D 85.714 231 18 7 5561 5786 606306268 606306488 4.570000e-56 230
27 TraesCS7B01G420900 chr7D 83.471 242 23 8 658 884 605947013 605947252 5.960000e-50 209
28 TraesCS7B01G420900 chr7D 84.906 212 16 5 5579 5786 605963973 605964172 3.590000e-47 200
29 TraesCS7B01G420900 chr7D 81.897 232 26 11 649 875 606180836 606181056 1.300000e-41 182
30 TraesCS7B01G420900 chr7D 81.897 232 25 11 649 875 606106510 606106729 4.670000e-41 180
31 TraesCS7B01G420900 chr7D 90.909 132 11 1 5247 5378 605963763 605963893 6.040000e-40 176
32 TraesCS7B01G420900 chr7D 89.474 114 12 0 649 762 606180660 606180773 1.700000e-30 145
33 TraesCS7B01G420900 chr7D 95.833 72 3 0 582 653 606106319 606106390 3.720000e-22 117
34 TraesCS7B01G420900 chr7A 90.068 4390 367 28 881 5247 697823513 697827856 0.000000e+00 5627
35 TraesCS7B01G420900 chr7A 90.627 3862 325 20 881 4731 697878160 697881995 0.000000e+00 5092
36 TraesCS7B01G420900 chr7A 90.633 3715 309 20 881 4581 697975718 697979407 0.000000e+00 4896
37 TraesCS7B01G420900 chr7A 88.235 306 32 4 349 652 697975122 697975425 4.320000e-96 363
38 TraesCS7B01G420900 chr7A 89.130 276 27 2 5247 5522 698141040 698141312 2.030000e-89 340
39 TraesCS7B01G420900 chr7A 89.571 163 16 1 349 511 698131586 698131747 7.710000e-49 206
40 TraesCS7B01G420900 chr7A 87.671 146 14 2 742 884 697823342 697823486 3.640000e-37 167
41 TraesCS7B01G420900 chr7A 87.671 146 14 2 742 884 697877989 697878133 3.640000e-37 167
42 TraesCS7B01G420900 chrUn 100.000 411 0 0 617 1027 477661752 477662162 0.000000e+00 760
43 TraesCS7B01G420900 chrUn 98.864 88 0 1 5782 5868 264233234 264233147 7.870000e-34 156
44 TraesCS7B01G420900 chr3B 95.956 272 10 1 1 271 794380946 794381217 1.940000e-119 440
45 TraesCS7B01G420900 chr2B 95.817 263 10 1 6 267 705041554 705041292 1.950000e-114 424
46 TraesCS7B01G420900 chr2B 95.094 265 12 1 4 267 675209892 675210156 3.270000e-112 416
47 TraesCS7B01G420900 chr2B 93.069 101 5 2 5769 5868 188165066 188165165 4.740000e-31 147
48 TraesCS7B01G420900 chr4A 94.776 268 12 2 1 267 403379532 403379798 3.270000e-112 416
49 TraesCS7B01G420900 chr6B 94.737 266 13 1 3 267 536639674 536639409 4.230000e-111 412
50 TraesCS7B01G420900 chr6B 94.717 265 13 1 4 267 115025748 115025484 1.520000e-110 411
51 TraesCS7B01G420900 chr5D 94.737 266 11 3 4 267 13982444 13982180 1.520000e-110 411
52 TraesCS7B01G420900 chr1B 96.939 98 0 3 5773 5868 602225797 602225701 1.690000e-35 161
53 TraesCS7B01G420900 chr4B 98.851 87 1 0 5782 5868 648744801 648744715 7.870000e-34 156


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 TraesCS7B01G420900 chr7B 690093354 690099221 5867 False 10837.000000 10837 100.000000 1 5868 1 chr7B.!!$F6 5867
1 TraesCS7B01G420900 chr7B 690080898 690085406 4508 False 7751.000000 7751 97.619000 1336 5868 1 chr7B.!!$F5 4532
2 TraesCS7B01G420900 chr7B 690118814 690121170 2356 False 4135.000000 4135 98.346000 1 2356 1 chr7B.!!$F7 2355
3 TraesCS7B01G420900 chr7B 690029638 690035227 5589 False 2799.333333 6264 94.335667 387 5786 3 chr7B.!!$F8 5399
4 TraesCS7B01G420900 chr7B 677961317 677964652 3335 False 1940.000000 1940 77.810000 931 4266 1 chr7B.!!$F4 3335
5 TraesCS7B01G420900 chr7B 690198835 690204351 5516 False 1471.500000 3888 86.920000 323 5786 4 chr7B.!!$F9 5463
6 TraesCS7B01G420900 chr7B 690079832 690080713 881 True 1426.000000 1426 95.490000 4961 5868 1 chr7B.!!$R2 907
7 TraesCS7B01G420900 chr7D 606010513 606015116 4603 False 5686.000000 5686 89.091000 674 5257 1 chr7D.!!$F1 4583
8 TraesCS7B01G420900 chr7D 606301555 606306488 4933 False 1957.000000 4215 87.160000 727 5786 3 chr7D.!!$F6 5059
9 TraesCS7B01G420900 chr7D 606106319 606111227 4908 False 1794.333333 5086 88.967333 582 5257 3 chr7D.!!$F4 4675
10 TraesCS7B01G420900 chr7D 605957465 605964172 6707 False 1461.333333 4008 88.500000 2117 5786 3 chr7D.!!$F3 3669
11 TraesCS7B01G420900 chr7D 606180253 606186293 6040 False 1192.833333 4553 89.990833 272 5786 6 chr7D.!!$F5 5514
12 TraesCS7B01G420900 chr7D 605947013 605948508 1495 False 986.500000 1764 87.960500 658 2125 2 chr7D.!!$F2 1467
13 TraesCS7B01G420900 chr7A 697823342 697827856 4514 False 2897.000000 5627 88.869500 742 5247 2 chr7A.!!$F3 4505
14 TraesCS7B01G420900 chr7A 697877989 697881995 4006 False 2629.500000 5092 89.149000 742 4731 2 chr7A.!!$F4 3989
15 TraesCS7B01G420900 chr7A 697975122 697979407 4285 False 2629.500000 4896 89.434000 349 4581 2 chr7A.!!$F5 4232

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
260 261 1.485066 TGAGAATCTCCTTTACCCCGC 59.515 52.381 7.91 0.0 34.92 6.13 F
340 341 1.669440 GTGTGTGCGTTCCTAGGGA 59.331 57.895 9.46 0.0 0.00 4.20 F
1826 2468 4.870636 TCCAACCTAATTGCTCATCCATT 58.129 39.130 0.00 0.0 36.93 3.16 F
3234 4489 0.398696 TGGGGCGTGTGACTATTTGT 59.601 50.000 0.00 0.0 0.00 2.83 F
4419 5716 1.066858 ACAGCGACCCAATCACTACAG 60.067 52.381 0.00 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 3388 0.251916 CACCCACACCGGACACATAT 59.748 55.000 9.46 0.0 36.56 1.78 R
2351 3544 3.067180 ACTTTGTGTGATTGCAAGGACTG 59.933 43.478 4.94 0.0 0.00 3.51 R
3363 4618 1.072331 AGCTCCATCGTTGTTCTTGGT 59.928 47.619 0.00 0.0 0.00 3.67 R
4469 5766 0.107214 TCATTCCAACCGAGCCCATC 60.107 55.000 0.00 0.0 0.00 3.51 R
5526 10007 1.423541 AGTTAGGCACCACCATTCACA 59.576 47.619 0.00 0.0 43.14 3.58 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
199 200 3.367806 GGTTGTACTCGGGGTTAGACTTC 60.368 52.174 0.00 0.00 0.00 3.01
259 260 4.423625 AATGAGAATCTCCTTTACCCCG 57.576 45.455 7.91 0.00 34.92 5.73
260 261 1.485066 TGAGAATCTCCTTTACCCCGC 59.515 52.381 7.91 0.00 34.92 6.13
261 262 1.485066 GAGAATCTCCTTTACCCCGCA 59.515 52.381 0.00 0.00 0.00 5.69
263 264 2.307686 AGAATCTCCTTTACCCCGCAAA 59.692 45.455 0.00 0.00 0.00 3.68
289 290 4.707448 AGAAGGATGATGTGTCGTCTTAGT 59.293 41.667 0.00 0.00 39.77 2.24
296 297 3.136009 TGTGTCGTCTTAGTCTCTGGA 57.864 47.619 0.00 0.00 0.00 3.86
301 302 3.127376 GTCGTCTTAGTCTCTGGAAGGTC 59.873 52.174 0.00 0.00 0.00 3.85
340 341 1.669440 GTGTGTGCGTTCCTAGGGA 59.331 57.895 9.46 0.00 0.00 4.20
1240 1865 5.393124 TGTTTCTCTGCGAATAATGCTTTG 58.607 37.500 0.00 0.00 0.00 2.77
1826 2468 4.870636 TCCAACCTAATTGCTCATCCATT 58.129 39.130 0.00 0.00 36.93 3.16
2036 2930 8.550710 TTTTTGATCAATTGATGTCCCAATTC 57.449 30.769 25.37 9.09 42.83 2.17
2375 3568 4.275936 AGTCCTTGCAATCACACAAAGTAC 59.724 41.667 0.00 0.00 0.00 2.73
2642 3856 2.815158 AGTCCCATTATTTTTGCCGGT 58.185 42.857 1.90 0.00 0.00 5.28
2720 3951 0.459899 CGCTGCCAGGTGTATGACTA 59.540 55.000 0.00 0.00 0.00 2.59
3033 4271 3.432890 GGAAAACATGTTTGCTTCCCCAA 60.433 43.478 25.20 0.00 34.35 4.12
3234 4489 0.398696 TGGGGCGTGTGACTATTTGT 59.601 50.000 0.00 0.00 0.00 2.83
3363 4618 1.208052 GATCACAGCTTGGGACTGCTA 59.792 52.381 0.00 0.00 38.79 3.49
3463 4739 1.640069 CATGGACAATCGAGCTGCG 59.360 57.895 0.00 0.00 42.69 5.18
3571 4850 8.875168 TGTTGTTACTTGGGATTTTCCATTAAT 58.125 29.630 0.00 0.00 38.64 1.40
3687 4967 8.698973 TTCATCTACAGGTTTATTTTCAACCA 57.301 30.769 4.70 0.00 45.55 3.67
3955 5252 6.126409 GTCCACCATTACTATTTCCCATGAA 58.874 40.000 0.00 0.00 0.00 2.57
4141 5438 1.302033 GTGTGTCCTCAGGTGGCAG 60.302 63.158 0.00 0.00 0.00 4.85
4419 5716 1.066858 ACAGCGACCCAATCACTACAG 60.067 52.381 0.00 0.00 0.00 2.74
4469 5766 3.184541 GCCATTCAACATAGCAAGCAAG 58.815 45.455 0.00 0.00 0.00 4.01
4684 5981 1.242076 ACAGTTGATCAGCAAGCACC 58.758 50.000 12.41 0.00 37.12 5.01
4928 6249 1.106351 TTTCGCATGTGTGTTGGGCT 61.106 50.000 6.09 0.00 0.00 5.19
5169 6501 4.319766 CCGAGACAACATTTCAAGGTGAAG 60.320 45.833 0.00 0.00 37.70 3.02
5392 9873 4.025396 CCAATTCTGATGTCGTGTGATAGC 60.025 45.833 0.00 0.00 0.00 2.97
5541 10022 2.611225 TTTTTGTGAATGGTGGTGCC 57.389 45.000 0.00 0.00 37.90 5.01
5542 10023 1.786937 TTTTGTGAATGGTGGTGCCT 58.213 45.000 0.00 0.00 38.35 4.75
5543 10024 2.666272 TTTGTGAATGGTGGTGCCTA 57.334 45.000 0.00 0.00 38.35 3.93
5544 10025 2.666272 TTGTGAATGGTGGTGCCTAA 57.334 45.000 0.00 0.00 38.35 2.69
5545 10026 1.904287 TGTGAATGGTGGTGCCTAAC 58.096 50.000 0.00 0.00 38.35 2.34
5546 10027 1.423541 TGTGAATGGTGGTGCCTAACT 59.576 47.619 0.00 0.00 38.35 2.24
5547 10028 2.158534 TGTGAATGGTGGTGCCTAACTT 60.159 45.455 0.00 0.00 38.35 2.66
5548 10029 2.890945 GTGAATGGTGGTGCCTAACTTT 59.109 45.455 0.00 0.00 38.35 2.66
5787 10275 6.923199 AAAATGACAATGGAAGGAATCACT 57.077 33.333 0.00 0.00 0.00 3.41
5855 10343 1.972795 TGGCCCGGTACTAATGGTATC 59.027 52.381 0.00 0.00 32.56 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 200 4.050553 CAGCCACAACCAAGTTTACAATG 58.949 43.478 0.00 0.00 0.00 2.82
263 264 4.899502 AGACGACACATCATCCTTCTTTT 58.100 39.130 0.00 0.00 0.00 2.27
289 290 2.587777 ACCTATGAGGACCTTCCAGAGA 59.412 50.000 6.43 0.00 39.61 3.10
296 297 5.070981 CACATCATACACCTATGAGGACCTT 59.929 44.000 8.87 0.00 41.71 3.50
301 302 3.243873 ACGCACATCATACACCTATGAGG 60.244 47.826 1.78 1.78 43.77 3.86
340 341 3.732219 CACGTACACAAACATACACTCGT 59.268 43.478 0.00 0.00 0.00 4.18
1029 1586 1.168407 CCGCCGCATCTTCCATCATT 61.168 55.000 0.00 0.00 0.00 2.57
1240 1865 2.202222 GTCGTTGCTGCATCGCAC 60.202 61.111 24.00 18.78 40.09 5.34
1826 2468 1.215173 CCCCCACTAGCCATTTGATCA 59.785 52.381 0.00 0.00 0.00 2.92
1994 2654 8.620416 TGATCAAAAATACAATCGGTTCCTATG 58.380 33.333 0.00 0.00 0.00 2.23
2005 2899 9.603921 GGGACATCAATTGATCAAAAATACAAT 57.396 29.630 18.16 0.00 34.99 2.71
2036 2930 2.752354 TCCAGACGGCATGTTTTAATGG 59.248 45.455 0.00 0.00 0.00 3.16
2195 3388 0.251916 CACCCACACCGGACACATAT 59.748 55.000 9.46 0.00 36.56 1.78
2351 3544 3.067180 ACTTTGTGTGATTGCAAGGACTG 59.933 43.478 4.94 0.00 0.00 3.51
2375 3568 2.746269 CAAACAGGTGGTGCAATTCTG 58.254 47.619 0.00 0.00 0.00 3.02
2509 3709 5.705905 GTGGCACTCCTTTATATGGTATTCC 59.294 44.000 11.13 0.00 0.00 3.01
2709 3940 6.338146 TGAGCATGTTAAGTAGTCATACACC 58.662 40.000 0.00 0.00 34.07 4.16
2720 3951 6.128553 CGTGTAATGTTCTGAGCATGTTAAGT 60.129 38.462 7.79 0.00 0.00 2.24
3178 4432 6.500684 TCATCATAGCCTTCTTTTCACAAC 57.499 37.500 0.00 0.00 0.00 3.32
3234 4489 1.885887 GTTGGTATGCACTGGCTTCAA 59.114 47.619 0.00 0.00 41.91 2.69
3363 4618 1.072331 AGCTCCATCGTTGTTCTTGGT 59.928 47.619 0.00 0.00 0.00 3.67
3370 4646 4.683832 GTCAGTATTAGCTCCATCGTTGT 58.316 43.478 0.00 0.00 0.00 3.32
3420 4696 3.394606 ACTTTTGGCTTCTTCTGGGTAGA 59.605 43.478 0.00 0.00 0.00 2.59
3463 4739 8.182227 GGTTGATAGCTTCCATAAACTTTGTAC 58.818 37.037 0.00 0.00 0.00 2.90
3662 4942 8.698973 TGGTTGAAAATAAACCTGTAGATGAA 57.301 30.769 6.86 0.00 46.11 2.57
3955 5252 8.607441 AATAAACATGTATATGAGATGCACGT 57.393 30.769 6.45 0.00 37.73 4.49
4419 5716 2.103042 CGCTGAAGCCTGCCACTAC 61.103 63.158 0.00 0.00 37.91 2.73
4469 5766 0.107214 TCATTCCAACCGAGCCCATC 60.107 55.000 0.00 0.00 0.00 3.51
4684 5981 5.664457 TGATGCCATTCAGTTGACTACTAG 58.336 41.667 0.00 0.00 34.56 2.57
4813 6134 8.746052 TGAAATCCTACAACAAGAAAGAAAGA 57.254 30.769 0.00 0.00 0.00 2.52
4928 6249 4.339814 ACAAAGGAATGGCACGTTAAAAGA 59.660 37.500 0.00 0.00 0.00 2.52
5392 9873 7.012704 AGGATAATACATTAGTGCAAGCAACTG 59.987 37.037 0.00 0.00 0.00 3.16
5491 9972 5.451242 GGCACCACTGACTTTCACAATTAAA 60.451 40.000 0.00 0.00 0.00 1.52
5526 10007 1.423541 AGTTAGGCACCACCATTCACA 59.576 47.619 0.00 0.00 43.14 3.58
5527 10008 2.200373 AGTTAGGCACCACCATTCAC 57.800 50.000 0.00 0.00 43.14 3.18
5528 10009 2.969821 AAGTTAGGCACCACCATTCA 57.030 45.000 0.00 0.00 43.14 2.57
5529 10010 4.600692 AAAAAGTTAGGCACCACCATTC 57.399 40.909 0.00 0.00 43.14 2.67
5548 10029 2.114616 AGGCACCACCATTCACAAAAA 58.885 42.857 0.00 0.00 43.14 1.94
5787 10275 8.529476 GTCTCACATAAGGTCCTTTTTCTACTA 58.471 37.037 10.04 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.