Multiple sequence alignment - TraesCS7B01G383600

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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 TraesCS7B01G383600 chr7B 100.000 3281 0 0 1 3281 649246363 649249643 0.000000e+00 6059
1 TraesCS7B01G383600 chr7B 97.986 1589 27 3 589 2176 649277845 649279429 0.000000e+00 2752
2 TraesCS7B01G383600 chr7B 97.243 653 17 1 2166 2817 649280150 649280802 0.000000e+00 1105
3 TraesCS7B01G383600 chr7B 91.823 587 40 5 1 581 649123077 649123661 0.000000e+00 811
4 TraesCS7B01G383600 chr7B 91.482 587 42 5 1 581 649275648 649276232 0.000000e+00 800
5 TraesCS7B01G383600 chr7B 79.742 543 98 8 44 579 649448918 649449455 1.850000e-102 383
6 TraesCS7B01G383600 chr7B 79.091 550 101 10 44 586 649458483 649459025 1.860000e-97 366
7 TraesCS7B01G383600 chr7D 95.559 2702 99 12 589 3281 581417472 581420161 0.000000e+00 4305
8 TraesCS7B01G383600 chr7D 91.222 1481 94 20 1783 3249 562629498 562628040 0.000000e+00 1982
9 TraesCS7B01G383600 chr7D 95.156 991 38 6 809 1797 562631740 562630758 0.000000e+00 1555
10 TraesCS7B01G383600 chr7D 95.036 967 45 1 589 1555 581662155 581663118 0.000000e+00 1517
11 TraesCS7B01G383600 chr7D 77.580 2132 327 83 987 3049 581289615 581291664 0.000000e+00 1149
12 TraesCS7B01G383600 chr7D 92.833 586 37 2 1 581 581659769 581660354 0.000000e+00 845
13 TraesCS7B01G383600 chr7D 92.675 587 36 3 1 581 581415315 581415900 0.000000e+00 839
14 TraesCS7B01G383600 chr7D 90.614 586 50 2 1 581 581625341 581625926 0.000000e+00 773
15 TraesCS7B01G383600 chr7D 94.129 511 25 2 589 1099 581627661 581628166 0.000000e+00 773
16 TraesCS7B01G383600 chr7D 91.000 200 12 2 589 784 562632318 562632121 6.980000e-67 265
17 TraesCS7B01G383600 chr7A 95.136 2652 118 10 589 3236 673304865 673307509 0.000000e+00 4172
18 TraesCS7B01G383600 chr7A 92.869 2454 140 19 809 3249 648274394 648271963 0.000000e+00 3530
19 TraesCS7B01G383600 chr7A 92.665 2454 145 19 809 3249 648304835 648302404 0.000000e+00 3502
20 TraesCS7B01G383600 chr7A 93.905 1690 90 8 809 2493 648215992 648214311 0.000000e+00 2538
21 TraesCS7B01G383600 chr7A 91.546 757 49 9 2525 3280 648214312 648213570 0.000000e+00 1029
22 TraesCS7B01G383600 chr7A 88.725 204 15 4 589 784 648275073 648274870 3.270000e-60 243
23 TraesCS7B01G383600 chr7A 89.000 200 15 4 589 781 648216674 648216475 1.180000e-59 241
24 TraesCS7B01G383600 chr7A 89.344 122 12 1 3128 3249 648271952 648271832 5.670000e-33 152
25 TraesCS7B01G383600 chrUn 96.082 2246 79 7 1040 3280 347063539 347061298 0.000000e+00 3651
26 TraesCS7B01G383600 chrUn 90.116 344 27 4 243 581 469729987 469730328 1.080000e-119 440
27 TraesCS7B01G383600 chrUn 79.742 543 98 8 44 579 286626311 286626848 1.850000e-102 383


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 TraesCS7B01G383600 chr7B 649246363 649249643 3280 False 6059.000000 6059 100.000000 1 3281 1 chr7B.!!$F2 3280
1 TraesCS7B01G383600 chr7B 649275648 649280802 5154 False 1552.333333 2752 95.570333 1 2817 3 chr7B.!!$F5 2816
2 TraesCS7B01G383600 chr7B 649123077 649123661 584 False 811.000000 811 91.823000 1 581 1 chr7B.!!$F1 580
3 TraesCS7B01G383600 chr7B 649448918 649449455 537 False 383.000000 383 79.742000 44 579 1 chr7B.!!$F3 535
4 TraesCS7B01G383600 chr7B 649458483 649459025 542 False 366.000000 366 79.091000 44 586 1 chr7B.!!$F4 542
5 TraesCS7B01G383600 chr7D 581415315 581420161 4846 False 2572.000000 4305 94.117000 1 3281 2 chr7D.!!$F2 3280
6 TraesCS7B01G383600 chr7D 562628040 562632318 4278 True 1267.333333 1982 92.459333 589 3249 3 chr7D.!!$R1 2660
7 TraesCS7B01G383600 chr7D 581659769 581663118 3349 False 1181.000000 1517 93.934500 1 1555 2 chr7D.!!$F4 1554
8 TraesCS7B01G383600 chr7D 581289615 581291664 2049 False 1149.000000 1149 77.580000 987 3049 1 chr7D.!!$F1 2062
9 TraesCS7B01G383600 chr7D 581625341 581628166 2825 False 773.000000 773 92.371500 1 1099 2 chr7D.!!$F3 1098
10 TraesCS7B01G383600 chr7A 673304865 673307509 2644 False 4172.000000 4172 95.136000 589 3236 1 chr7A.!!$F1 2647
11 TraesCS7B01G383600 chr7A 648302404 648304835 2431 True 3502.000000 3502 92.665000 809 3249 1 chr7A.!!$R1 2440
12 TraesCS7B01G383600 chr7A 648271832 648275073 3241 True 1308.333333 3530 90.312667 589 3249 3 chr7A.!!$R3 2660
13 TraesCS7B01G383600 chr7A 648213570 648216674 3104 True 1269.333333 2538 91.483667 589 3280 3 chr7A.!!$R2 2691
14 TraesCS7B01G383600 chrUn 347061298 347063539 2241 True 3651.000000 3651 96.082000 1040 3280 1 chrUn.!!$R1 2240
15 TraesCS7B01G383600 chrUn 286626311 286626848 537 False 383.000000 383 79.742000 44 579 1 chrUn.!!$F1 535

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
63 64 0.614294 TTTGGGTTTCGATCCGGCTA 59.386 50.000 0.0 0.0 0.00 3.93 F
273 275 1.202842 CCCCTGGTAAAAGTTCACCGT 60.203 52.381 0.0 0.0 37.66 4.83 F
340 343 1.837439 TGGTATCCCTGGTAAGCTGTG 59.163 52.381 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 5461 0.893727 TGTCGGCAGCTAGACACAGA 60.894 55.000 16.66 0.0 41.81 3.41 R
2069 5697 5.426509 TCCTCCTCAATGTCTACATCATGTT 59.573 40.000 0.00 0.0 35.10 2.71 R
2414 6854 3.009363 TGAGAGAAATCAGCCACAATGGA 59.991 43.478 0.00 0.0 40.96 3.41 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
42 43 2.216046 CTGACAATGTGTGAGCACTGT 58.784 47.619 0.00 0.00 45.44 3.55
63 64 0.614294 TTTGGGTTTCGATCCGGCTA 59.386 50.000 0.00 0.00 0.00 3.93
117 118 5.836821 GGAGGATGTCCATTTTAACTTCC 57.163 43.478 1.30 0.00 46.10 3.46
148 149 1.278127 AGTGGAAGTGTATTCACCGGG 59.722 52.381 6.32 0.00 44.83 5.73
181 183 8.218423 AGATGGGTTTAAAAGGAAATTGGATT 57.782 30.769 0.00 0.00 0.00 3.01
245 247 2.554636 CCTCAACGGCTGCTTGCAA 61.555 57.895 0.00 0.00 45.15 4.08
255 257 1.667212 GCTGCTTGCAATTTTATGCCC 59.333 47.619 0.00 0.00 45.83 5.36
260 262 1.949799 TGCAATTTTATGCCCCTGGT 58.050 45.000 0.00 0.00 45.83 4.00
273 275 1.202842 CCCCTGGTAAAAGTTCACCGT 60.203 52.381 0.00 0.00 37.66 4.83
340 343 1.837439 TGGTATCCCTGGTAAGCTGTG 59.163 52.381 0.00 0.00 0.00 3.66
354 357 5.221362 GGTAAGCTGTGTGGTGGTTTTATTT 60.221 40.000 0.00 0.00 0.00 1.40
361 364 3.181471 TGTGGTGGTTTTATTTGGCAGTG 60.181 43.478 0.00 0.00 0.00 3.66
405 408 8.275015 TGCGAATTTTAAGAAAGATCACCATA 57.725 30.769 0.00 0.00 0.00 2.74
449 452 7.994425 AGTCTATGTTCTCGATGACTATGAT 57.006 36.000 0.00 0.00 33.67 2.45
476 479 6.585322 GCAAAGAATGGATATTGAAGCATAGC 59.415 38.462 0.00 0.00 0.00 2.97
494 497 6.018425 AGCATAGCGTTGAAACTTCAGATATG 60.018 38.462 10.37 10.37 38.61 1.78
504 507 6.149973 TGAAACTTCAGATATGTTTGGAGCAG 59.850 38.462 0.00 0.00 36.03 4.24
551 559 5.982890 ATTCATTCAGTTGATTCCCGTTT 57.017 34.783 0.00 0.00 0.00 3.60
581 589 5.447144 CGATTCATCCGCAATGTAACTTGAA 60.447 40.000 0.00 0.00 36.68 2.69
582 590 4.944962 TCATCCGCAATGTAACTTGAAG 57.055 40.909 0.00 0.00 36.68 3.02
583 591 3.126858 TCATCCGCAATGTAACTTGAAGC 59.873 43.478 0.00 0.00 36.68 3.86
585 593 3.146066 TCCGCAATGTAACTTGAAGCTT 58.854 40.909 0.00 0.00 0.00 3.74
586 594 3.058293 TCCGCAATGTAACTTGAAGCTTG 60.058 43.478 2.10 0.00 0.00 4.01
672 2519 8.156820 CCATCTCCCTACATGAAATAACACATA 58.843 37.037 0.00 0.00 0.00 2.29
745 2600 2.719531 TCATACAGAGGAGAGAGCGT 57.280 50.000 0.00 0.00 0.00 5.07
1242 3566 3.471244 GATACTCTCGCGCGTGCCT 62.471 63.158 30.98 16.82 38.08 4.75
1533 3863 2.355009 AAGCGCCGTTACGTCGTT 60.355 55.556 10.30 0.00 34.88 3.85
1839 5461 4.188462 TCGCCGAAATCAATCACAATACT 58.812 39.130 0.00 0.00 0.00 2.12
2414 6854 1.348064 TGGTGAGATTCGTTCTGGGT 58.652 50.000 0.00 0.00 33.74 4.51
2528 7101 4.081420 ACACCAGAGGATGTGATACACTTC 60.081 45.833 0.00 0.00 37.66 3.01
2548 7123 4.729227 TCGGCTGATTACATTGTCACTA 57.271 40.909 0.00 0.00 0.00 2.74
2581 7161 9.282247 GTGCTATTTACTTGTCTGATTCAAATG 57.718 33.333 0.00 0.00 0.00 2.32
2717 7298 4.810191 AGAAAACTAGGAAGTCATCGCT 57.190 40.909 0.00 0.00 33.75 4.93
2756 8645 7.481275 TTTTGTTCACGTAGGTAGGTTTAAG 57.519 36.000 0.00 0.00 0.00 1.85
2806 8695 2.079925 GCACTTCCCATGTCAGTCTTC 58.920 52.381 0.00 0.00 0.00 2.87
2837 8727 1.208052 CCACATACACTCCAGTCCAGG 59.792 57.143 0.00 0.00 0.00 4.45
2892 8783 1.098129 TTACTGCTGTGGCGTTTGCA 61.098 50.000 6.48 0.00 45.35 4.08
2895 8786 0.179181 CTGCTGTGGCGTTTGCATAG 60.179 55.000 0.00 0.00 45.35 2.23
2999 8890 4.812626 TGGAAAACTAGGACTTCGAACAAC 59.187 41.667 0.00 0.00 0.00 3.32
3043 8934 9.173021 TCTTATGCAAATTTAGCAGCTTAGTAA 57.827 29.630 16.58 10.32 46.36 2.24
3096 9001 1.306911 TGGAGTGCCCTGATGCCTA 60.307 57.895 0.00 0.00 35.38 3.93
3120 9025 6.290605 ACATGCTTTTAAGTTTGGAGCAATT 58.709 32.000 9.74 0.39 45.31 2.32
3208 9113 1.969208 TGTGAATTGCAATCCAGCCAA 59.031 42.857 13.38 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.748493 GAAACCCAAACACAGTGCTCA 59.252 47.619 0.00 0.00 0.00 4.26
42 43 1.238625 GCCGGATCGAAACCCAAACA 61.239 55.000 5.05 0.00 0.00 2.83
63 64 2.573462 ACACATAGAAGTGGGCAGACAT 59.427 45.455 0.00 0.00 43.72 3.06
117 118 1.672356 CTTCCACTCCGGCAAGGTG 60.672 63.158 0.00 3.09 41.99 4.00
148 149 5.773176 TCCTTTTAAACCCATCTTCTGGTTC 59.227 40.000 0.00 0.00 43.94 3.62
181 183 6.677913 GCAGGAAGCTTAATTCTTTTGTACA 58.322 36.000 0.00 0.00 41.15 2.90
220 222 0.884704 GCAGCCGTTGAGGAAGACAA 60.885 55.000 0.00 0.00 45.00 3.18
245 247 5.782845 TGAACTTTTACCAGGGGCATAAAAT 59.217 36.000 0.00 0.00 29.82 1.82
255 257 4.642445 AAAACGGTGAACTTTTACCAGG 57.358 40.909 4.02 0.00 36.76 4.45
260 262 9.202273 ACACGTATATAAAACGGTGAACTTTTA 57.798 29.630 13.55 0.00 44.48 1.52
340 343 3.068873 TCACTGCCAAATAAAACCACCAC 59.931 43.478 0.00 0.00 0.00 4.16
361 364 2.804212 GCATAATGCAAATGGCCCTGTC 60.804 50.000 0.00 0.00 44.26 3.51
405 408 4.333690 ACTACTAGTCGAACCACATCACT 58.666 43.478 0.00 0.00 0.00 3.41
449 452 7.828508 ATGCTTCAATATCCATTCTTTGCTA 57.171 32.000 0.00 0.00 0.00 3.49
476 479 6.898041 TCCAAACATATCTGAAGTTTCAACG 58.102 36.000 0.00 0.00 36.64 4.10
494 497 3.983344 CAGTAACATTTGCTGCTCCAAAC 59.017 43.478 0.00 0.00 37.51 2.93
504 507 7.364522 TGTAGTCAGAATCAGTAACATTTGC 57.635 36.000 0.00 0.00 0.00 3.68
581 589 4.012374 CCTTCCACAACATATGACAAGCT 58.988 43.478 10.38 0.00 0.00 3.74
582 590 3.428045 GCCTTCCACAACATATGACAAGC 60.428 47.826 10.38 0.00 0.00 4.01
583 591 3.181507 CGCCTTCCACAACATATGACAAG 60.182 47.826 10.38 2.13 0.00 3.16
585 593 2.355197 CGCCTTCCACAACATATGACA 58.645 47.619 10.38 0.00 0.00 3.58
586 594 1.064060 GCGCCTTCCACAACATATGAC 59.936 52.381 10.38 0.00 0.00 3.06
623 2470 3.761897 AGTTGTGCTGGCCTAATTAACA 58.238 40.909 3.32 0.00 0.00 2.41
745 2600 1.507140 AATATCTCCCTGGGCGACAA 58.493 50.000 7.74 0.00 0.00 3.18
1547 3877 1.003580 GCAACTCAGTCCATTCCTCCA 59.996 52.381 0.00 0.00 0.00 3.86
1839 5461 0.893727 TGTCGGCAGCTAGACACAGA 60.894 55.000 16.66 0.00 41.81 3.41
2069 5697 5.426509 TCCTCCTCAATGTCTACATCATGTT 59.573 40.000 0.00 0.00 35.10 2.71
2414 6854 3.009363 TGAGAGAAATCAGCCACAATGGA 59.991 43.478 0.00 0.00 40.96 3.41
2528 7101 4.433615 AGTAGTGACAATGTAATCAGCCG 58.566 43.478 0.00 0.00 0.00 5.52
2548 7123 6.770785 TCAGACAAGTAAATAGCACCAAAAGT 59.229 34.615 0.00 0.00 0.00 2.66
2717 7298 6.090088 CGTGAACAAAATCCACAAAGACAAAA 59.910 34.615 0.00 0.00 0.00 2.44
2756 8645 3.725010 CGACATCGCTTGCTTTAAACTCC 60.725 47.826 0.00 0.00 0.00 3.85
2806 8695 5.306937 TGGAGTGTATGTGGACCATTATAGG 59.693 44.000 0.00 0.00 34.86 2.57
2861 8752 4.759693 CCACAGCAGTAAGTTGAATTACCA 59.240 41.667 0.00 0.00 36.49 3.25
2967 8858 6.465439 AGTCCTAGTTTTCCAAAGGTTTTG 57.535 37.500 0.00 0.00 0.00 2.44
2999 8890 2.350522 AGAACAGGTAAGATTGCAGCG 58.649 47.619 0.00 0.00 0.00 5.18
3049 8940 1.740025 GAGGACGAAATTCAAGCAGGG 59.260 52.381 0.00 0.00 0.00 4.45
3096 9001 4.935352 TGCTCCAAACTTAAAAGCATGT 57.065 36.364 0.00 0.00 38.01 3.21
3120 9025 1.303236 CCCCGCAGAATGAACCACA 60.303 57.895 0.00 0.00 39.69 4.17
3208 9113 0.813184 CAGCATGACGCAATTCCCTT 59.187 50.000 0.00 0.00 46.13 3.95


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

AutoCloner maintained by Alex Coulton.