Multiple sequence alignment - TraesCS7D01G120000

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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 TraesCS7D01G120000 chr7D 100.000 5384 0 0 1 5384 74453710 74459093 0.000000e+00 9943.0
1 TraesCS7D01G120000 chr2D 95.785 5386 202 11 1 5382 15451912 15446548 0.000000e+00 8665.0
2 TraesCS7D01G120000 chr3D 95.638 5387 193 11 1 5384 31029436 31024089 0.000000e+00 8608.0
3 TraesCS7D01G120000 chr3D 96.664 4377 137 8 1 4374 31054673 31050303 0.000000e+00 7265.0
4 TraesCS7D01G120000 chr3D 96.342 2679 86 7 1 2676 31005064 31002395 0.000000e+00 4394.0
5 TraesCS7D01G120000 chr3D 95.140 2037 69 4 3348 5384 31002398 31000392 0.000000e+00 3186.0
6 TraesCS7D01G120000 chr3D 95.802 667 27 1 4719 5384 31050312 31049646 0.000000e+00 1075.0
7 TraesCS7D01G120000 chr2B 94.371 2878 146 5 2507 5384 797812472 797809611 0.000000e+00 4403.0
8 TraesCS7D01G120000 chr2B 95.067 1196 53 6 3 1193 797772249 797771055 0.000000e+00 1877.0
9 TraesCS7D01G120000 chr2B 94.897 1117 52 5 3 1115 797813578 797812463 0.000000e+00 1742.0
10 TraesCS7D01G120000 chr2B 93.384 1058 54 4 4331 5384 797771042 797769997 0.000000e+00 1552.0
11 TraesCS7D01G120000 chr5D 95.706 1374 44 4 3 1374 542245904 542247264 0.000000e+00 2196.0
12 TraesCS7D01G120000 chr5D 96.094 640 23 2 3 641 542211605 542212243 0.000000e+00 1042.0
13 TraesCS7D01G120000 chr1A 84.965 858 105 15 211 1063 535734198 535733360 0.000000e+00 848.0
14 TraesCS7D01G120000 chr1A 76.596 517 80 27 4051 4530 535733240 535732728 4.160000e-61 246.0
15 TraesCS7D01G120000 chr7B 84.973 732 88 17 1 718 623570754 623570031 0.000000e+00 723.0
16 TraesCS7D01G120000 chr7B 90.426 376 36 0 2223 2598 623568037 623567662 3.750000e-136 496.0
17 TraesCS7D01G120000 chr7B 83.784 370 51 5 1198 1561 623569951 623569585 5.160000e-90 342.0
18 TraesCS7D01G120000 chr7B 94.915 59 3 0 797 855 623570007 623569949 5.740000e-15 93.5
19 TraesCS7D01G120000 chrUn 96.798 406 12 1 3910 4315 478256681 478257085 0.000000e+00 676.0
20 TraesCS7D01G120000 chr6A 83.938 386 55 3 1198 1578 18537188 18536805 3.960000e-96 363.0
21 TraesCS7D01G120000 chr4A 82.410 415 64 5 1169 1578 515454758 515455168 2.390000e-93 353.0
22 TraesCS7D01G120000 chr6B 74.298 961 163 48 4132 5039 715199352 715200281 4.020000e-86 329.0
23 TraesCS7D01G120000 chr2A 91.667 120 10 0 4267 4386 46345678 46345559 3.340000e-37 167.0


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 TraesCS7D01G120000 chr7D 74453710 74459093 5383 False 9943.000 9943 100.0000 1 5384 1 chr7D.!!$F1 5383
1 TraesCS7D01G120000 chr2D 15446548 15451912 5364 True 8665.000 8665 95.7850 1 5382 1 chr2D.!!$R1 5381
2 TraesCS7D01G120000 chr3D 31024089 31029436 5347 True 8608.000 8608 95.6380 1 5384 1 chr3D.!!$R1 5383
3 TraesCS7D01G120000 chr3D 31049646 31054673 5027 True 4170.000 7265 96.2330 1 5384 2 chr3D.!!$R3 5383
4 TraesCS7D01G120000 chr3D 31000392 31005064 4672 True 3790.000 4394 95.7410 1 5384 2 chr3D.!!$R2 5383
5 TraesCS7D01G120000 chr2B 797809611 797813578 3967 True 3072.500 4403 94.6340 3 5384 2 chr2B.!!$R2 5381
6 TraesCS7D01G120000 chr2B 797769997 797772249 2252 True 1714.500 1877 94.2255 3 5384 2 chr2B.!!$R1 5381
7 TraesCS7D01G120000 chr5D 542245904 542247264 1360 False 2196.000 2196 95.7060 3 1374 1 chr5D.!!$F2 1371
8 TraesCS7D01G120000 chr5D 542211605 542212243 638 False 1042.000 1042 96.0940 3 641 1 chr5D.!!$F1 638
9 TraesCS7D01G120000 chr1A 535732728 535734198 1470 True 547.000 848 80.7805 211 4530 2 chr1A.!!$R1 4319
10 TraesCS7D01G120000 chr7B 623567662 623570754 3092 True 413.625 723 88.5245 1 2598 4 chr7B.!!$R1 2597
11 TraesCS7D01G120000 chr6B 715199352 715200281 929 False 329.000 329 74.2980 4132 5039 1 chr6B.!!$F1 907

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
372 386 0.675083 CAACAAGCTGCCCACAATCA 59.325 50.000 0.00 0.0 0.00 2.57 F
547 562 2.812358 TCAGCAAACTAAGCGTCAGA 57.188 45.000 0.00 0.0 37.01 3.27 F
1614 2460 3.061965 CACATGATATTCGTGCGTTGTCA 59.938 43.478 0.00 0.0 36.89 3.58 F
1740 2587 4.273318 AGAGGGCATCATTAAACAGGTTC 58.727 43.478 0.58 0.0 0.00 3.62 F
2780 3699 0.764890 GGTAGGGCCATGCATCACTA 59.235 55.000 8.02 0.0 37.17 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1367 1.299976 GGTGGGGACTTACTGCTGG 59.700 63.158 0.00 0.0 0.00 4.85 R
2432 3351 1.202290 GCCATCATTTCGCCACGATTT 60.202 47.619 0.00 0.0 35.23 2.17 R
2763 3682 1.506025 TGTAGTGATGCATGGCCCTA 58.494 50.000 2.46 0.0 0.00 3.53 R
3150 4069 2.798680 CTCCGTGGTCTATCTGTTTCG 58.201 52.381 0.00 0.0 0.00 3.46 R
4413 5362 1.988834 GCCCCTAACAACATTCGCCG 61.989 60.000 0.00 0.0 0.00 6.46 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
266 278 1.751924 GTGTTTGTTGGGTAACAGCCA 59.248 47.619 0.00 0.00 46.63 4.75
372 386 0.675083 CAACAAGCTGCCCACAATCA 59.325 50.000 0.00 0.00 0.00 2.57
388 402 5.124457 CCACAATCATTGAAGAGGACGAAAT 59.876 40.000 3.79 0.00 0.00 2.17
469 484 4.576873 TCTGTTATTTCGCAGTTTGACCAA 59.423 37.500 0.00 0.00 34.57 3.67
547 562 2.812358 TCAGCAAACTAAGCGTCAGA 57.188 45.000 0.00 0.00 37.01 3.27
655 670 3.871594 GTGATGTTGAGAAGGTATTCGGG 59.128 47.826 0.00 0.00 40.58 5.14
1350 1367 9.586435 AAAACGGAGATTTCATTTATGGAATTC 57.414 29.630 0.00 0.00 36.16 2.17
1614 2460 3.061965 CACATGATATTCGTGCGTTGTCA 59.938 43.478 0.00 0.00 36.89 3.58
1740 2587 4.273318 AGAGGGCATCATTAAACAGGTTC 58.727 43.478 0.58 0.00 0.00 3.62
1851 2698 5.244402 TCTGGGTTGACGATTGTAAGTAGAA 59.756 40.000 0.00 0.00 0.00 2.10
1970 2817 7.576403 TGTTAGCATGCATCCCATATGTATAT 58.424 34.615 21.98 0.00 31.47 0.86
2432 3351 4.587891 TCAAGGTGTTACATCATCATGCA 58.412 39.130 0.00 0.00 32.57 3.96
2780 3699 0.764890 GGTAGGGCCATGCATCACTA 59.235 55.000 8.02 0.00 37.17 2.74
2797 3716 4.201657 TCACTACATTGGCCAATCATGAG 58.798 43.478 28.42 21.89 0.00 2.90
2865 3784 4.398358 AGAATCACATGCAGAGAAATGGTG 59.602 41.667 0.00 0.00 0.00 4.17
3150 4069 4.602340 TTAGCCTTATGATTCGGAGACC 57.398 45.455 0.00 0.00 34.32 3.85
3164 4083 3.439895 GGAGACCGAAACAGATAGACC 57.560 52.381 0.00 0.00 0.00 3.85
3517 4437 6.016024 TGGAATATGAGCAAGCATACCATTTC 60.016 38.462 0.00 0.00 33.88 2.17
3778 4698 8.421249 AACATATTTTGAATCTTGGGACTTCA 57.579 30.769 0.00 0.00 0.00 3.02
3866 4786 2.839486 TCTCATGGTTTCTCTTGCGT 57.161 45.000 0.00 0.00 0.00 5.24
3907 4827 4.732672 AATCCCTTCGTCAGTAAGTACC 57.267 45.455 0.00 0.00 0.00 3.34
4186 5107 7.757097 AAGTATGCTGATTTAGTAGTCGTTG 57.243 36.000 0.00 0.00 0.00 4.10
4188 5109 7.544622 AGTATGCTGATTTAGTAGTCGTTGAA 58.455 34.615 0.00 0.00 0.00 2.69
4413 5362 4.352039 TCGAGTCTCGAATGAATGTAAGC 58.648 43.478 22.33 0.00 46.90 3.09
4619 5579 7.379059 TGGTATGAATGTCAAGATATGGACT 57.621 36.000 0.00 0.00 35.11 3.85
4786 5806 2.224744 ACATCACAATGTACCTGGCACA 60.225 45.455 1.48 1.48 44.38 4.57
5043 6068 4.506802 GGATGGAAGGGATGTGGGTTATAC 60.507 50.000 0.00 0.00 0.00 1.47
5106 6131 5.047802 AGAAGAATTTCCGATGTTGCAACAT 60.048 36.000 38.35 38.35 41.93 2.71
5255 6280 7.172532 GGAAATATAGTCAACGGACATGCATAA 59.827 37.037 0.00 0.00 46.80 1.90
5297 6322 5.012664 TCACATACCACACACAGAAGGTTAT 59.987 40.000 0.00 0.00 35.62 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 112 1.362224 CATCCCCGGATCCCAGTATT 58.638 55.000 0.73 0.00 31.62 1.89
372 386 5.395768 CCCTGTCTATTTCGTCCTCTTCAAT 60.396 44.000 0.00 0.00 0.00 2.57
388 402 0.473755 TATACCCGTCGCCCTGTCTA 59.526 55.000 0.00 0.00 0.00 2.59
547 562 2.975489 CCCTAGAAGCCAGACCATATGT 59.025 50.000 1.24 0.00 0.00 2.29
930 945 1.348036 ACTTATCCAAGCTATCCGGGC 59.652 52.381 0.00 0.00 34.94 6.13
1350 1367 1.299976 GGTGGGGACTTACTGCTGG 59.700 63.158 0.00 0.00 0.00 4.85
1614 2460 5.880901 TCAATTAAAAAGGACTGGCTCTCT 58.119 37.500 0.00 0.00 0.00 3.10
1740 2587 9.991388 CCCATAAAATTTTGCATTCATAACTTG 57.009 29.630 13.76 0.00 0.00 3.16
1851 2698 2.660490 CGATTTCGTGGCATTGTTGTT 58.340 42.857 0.00 0.00 34.11 2.83
1970 2817 8.911918 ACTTATTAGTTTTACACATGACCACA 57.088 30.769 0.00 0.00 0.00 4.17
2432 3351 1.202290 GCCATCATTTCGCCACGATTT 60.202 47.619 0.00 0.00 35.23 2.17
2646 3565 4.315803 CGTAAACCTTGTGTCCTTCTCAT 58.684 43.478 0.00 0.00 0.00 2.90
2763 3682 1.506025 TGTAGTGATGCATGGCCCTA 58.494 50.000 2.46 0.00 0.00 3.53
2780 3699 3.972133 TCTTCTCATGATTGGCCAATGT 58.028 40.909 35.31 20.15 0.00 2.71
2865 3784 3.059884 TGCAAGAGAACGTTGATGTCTC 58.940 45.455 5.00 5.72 0.00 3.36
3150 4069 2.798680 CTCCGTGGTCTATCTGTTTCG 58.201 52.381 0.00 0.00 0.00 3.46
3517 4437 8.446273 ACTCAACTTATCATTCGAACATGAAAG 58.554 33.333 0.00 10.14 36.74 2.62
3565 4485 6.360681 GGAAACATAATCTGCATCGCAATTAC 59.639 38.462 0.00 0.00 38.41 1.89
4025 4945 6.664515 TGAATCACTGAAAATTCAACGGTAC 58.335 36.000 0.00 0.00 38.57 3.34
4188 5109 9.178758 GTGATGTCCTATTCTATCTTTTTGGTT 57.821 33.333 0.00 0.00 0.00 3.67
4248 5197 5.722263 TGATTGCGGAAACATGATCAAAAT 58.278 33.333 0.00 0.00 0.00 1.82
4392 5341 3.178618 CGCTTACATTCATTCGAGACTCG 59.821 47.826 18.91 18.91 42.10 4.18
4413 5362 1.988834 GCCCCTAACAACATTCGCCG 61.989 60.000 0.00 0.00 0.00 6.46
4602 5562 4.080129 ACTGGCAGTCCATATCTTGACATT 60.080 41.667 15.88 0.00 42.51 2.71
4786 5806 0.395586 TCGCAAGGCAAGCCCAATAT 60.396 50.000 7.62 0.00 36.58 1.28
4899 5924 6.822442 TCTTCTTGTACCTTGTACATGACAA 58.178 36.000 17.45 11.60 46.03 3.18
5014 6039 4.292041 CCCACATCCCTTCCATCCATATTA 59.708 45.833 0.00 0.00 0.00 0.98
5043 6068 6.428771 TGCATATGATATGTTCATCACTGGTG 59.571 38.462 13.48 0.00 44.13 4.17
5255 6280 3.646162 TGTGACTATGTGACCTTTCCACT 59.354 43.478 0.00 0.00 35.66 4.00
5297 6322 4.168101 AGAACTCATGAACCTGGAACCTA 58.832 43.478 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.