Multiple sequence alignment - TraesCS1A01G371700

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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 TraesCS1A01G371700 chr1A 100.000 4586 0 0 1 4586 548569093 548564508 0.000000e+00 8469.0
1 TraesCS1A01G371700 chr1D 94.706 3287 123 23 1309 4583 454232312 454229065 0.000000e+00 5059.0
2 TraesCS1A01G371700 chr1D 94.829 1315 54 9 1 1311 454233735 454232431 0.000000e+00 2039.0
3 TraesCS1A01G371700 chr1B 93.813 1697 90 10 2344 4038 624733709 624732026 0.000000e+00 2538.0
4 TraesCS1A01G371700 chr1B 93.365 1055 54 11 1309 2351 624734779 624733729 0.000000e+00 1546.0
5 TraesCS1A01G371700 chr1B 91.929 508 16 7 793 1281 624735413 624734912 0.000000e+00 688.0
6 TraesCS1A01G371700 chr1B 90.336 476 38 8 4094 4567 624732014 624731545 6.520000e-173 617.0
7 TraesCS1A01G371700 chr1B 83.594 384 41 11 1 368 624736166 624735789 1.580000e-89 340.0
8 TraesCS1A01G371700 chr5B 91.111 135 6 2 1146 1275 149454486 149454619 1.310000e-40 178.0
9 TraesCS1A01G371700 chr3D 96.970 33 1 0 525 557 508389196 508389164 6.410000e-04 56.5


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 TraesCS1A01G371700 chr1A 548564508 548569093 4585 True 8469.0 8469 100.0000 1 4586 1 chr1A.!!$R1 4585
1 TraesCS1A01G371700 chr1D 454229065 454233735 4670 True 3549.0 5059 94.7675 1 4583 2 chr1D.!!$R1 4582
2 TraesCS1A01G371700 chr1B 624731545 624736166 4621 True 1145.8 2538 90.6074 1 4567 5 chr1B.!!$R1 4566

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
88 89 0.682852 TCGACGGGTTGAGTTGGATT 59.317 50.000 0.0 0.0 0.00 3.01 F
1332 1595 0.738389 AACCTTGTTTGTGGAGCACG 59.262 50.000 0.0 0.0 37.14 5.34 F
1460 1725 0.748005 TCGCTAAATCCAAGCCCTGC 60.748 55.000 0.0 0.0 36.60 4.85 F
1463 1728 1.750193 CTAAATCCAAGCCCTGCGAA 58.250 50.000 0.0 0.0 0.00 4.70 F
3386 3700 2.158475 ACAAAATGAGAAGTCCTGCCCA 60.158 45.455 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1711 0.038166 TCTTCGCAGGGCTTGGATTT 59.962 50.000 0.00 0.0 0.0 2.17 R
2239 2517 5.128008 ACTTAGTAGCTCCAAAGGATCAGTC 59.872 44.000 0.00 0.0 0.0 3.51 R
2901 3215 6.662234 ACTGCTTAAGGTGTATATATCCGCTA 59.338 38.462 4.29 0.0 0.0 4.26 R
3549 3863 2.158623 ACCATTTGTCTTGCCTCTGTCA 60.159 45.455 0.00 0.0 0.0 3.58 R
4264 4581 0.608640 AACTCGTTGGCCTCCTACAG 59.391 55.000 3.32 0.0 0.0 2.74 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
69 70 7.944729 AGATAGAAACTTAAATGTGGTGCAT 57.055 32.000 0.00 0.00 40.03 3.96
72 73 4.759693 AGAAACTTAAATGTGGTGCATCGA 59.240 37.500 0.00 0.00 36.67 3.59
88 89 0.682852 TCGACGGGTTGAGTTGGATT 59.317 50.000 0.00 0.00 0.00 3.01
102 113 1.717194 TGGATTAAAGACGTGTCGCC 58.283 50.000 0.00 0.00 34.09 5.54
114 125 1.858091 GTGTCGCCATGGTCTCTATG 58.142 55.000 14.67 0.00 0.00 2.23
246 261 6.607019 AGTTAGAGAGGTAGTAGAATCCAGG 58.393 44.000 0.00 0.00 0.00 4.45
369 386 1.342819 CCGATTAGAGGAGGCCTTCTG 59.657 57.143 21.72 1.88 31.76 3.02
438 460 3.138304 CGAGGTGAGTTTGGATGAACAA 58.862 45.455 0.00 0.00 31.94 2.83
1075 1134 2.125229 TCTCCTCGTCCTCGTCCG 60.125 66.667 0.00 0.00 38.33 4.79
1286 1428 8.166422 GCATTAGGCAATAACCATAGTAACTT 57.834 34.615 0.00 0.00 43.97 2.66
1322 1585 3.025322 TGTCACCATGGAACCTTGTTT 57.975 42.857 21.47 0.00 0.00 2.83
1332 1595 0.738389 AACCTTGTTTGTGGAGCACG 59.262 50.000 0.00 0.00 37.14 5.34
1365 1629 8.598075 GGAAAATCATGATGCATTTTGTTCTAC 58.402 33.333 9.46 0.00 33.31 2.59
1375 1639 5.871524 TGCATTTTGTTCTACTTTGTTTGCA 59.128 32.000 0.00 0.00 33.28 4.08
1405 1669 4.476846 TCATACCCTTCTGCCAGGAATTAA 59.523 41.667 0.00 0.00 35.71 1.40
1413 1677 3.826157 TCTGCCAGGAATTAACCACAAAG 59.174 43.478 0.00 0.00 0.00 2.77
1446 1711 5.654603 TTTGTGAGAATCCTACTTCGCTA 57.345 39.130 0.00 0.00 0.00 4.26
1460 1725 0.748005 TCGCTAAATCCAAGCCCTGC 60.748 55.000 0.00 0.00 36.60 4.85
1463 1728 1.750193 CTAAATCCAAGCCCTGCGAA 58.250 50.000 0.00 0.00 0.00 4.70
1488 1753 8.266392 AGATTTTCTTTTCTCATACTGAGCTG 57.734 34.615 0.00 0.00 43.95 4.24
1505 1770 3.500343 AGCTGGCAGTTGATTTAAACCT 58.500 40.909 17.16 0.00 0.00 3.50
1572 1837 5.512232 CCTGAACTGAAGCTAGGAAAGTTCT 60.512 44.000 19.20 0.00 44.48 3.01
1590 1855 9.994432 GAAAGTTCTCCATGTGTTCTAATAATG 57.006 33.333 0.00 0.00 0.00 1.90
1705 1974 5.652014 CAGTTCTTCCCATGGTGCTAATAAA 59.348 40.000 11.73 0.00 0.00 1.40
1706 1975 6.152661 CAGTTCTTCCCATGGTGCTAATAAAA 59.847 38.462 11.73 0.00 0.00 1.52
1707 1976 6.723977 AGTTCTTCCCATGGTGCTAATAAAAA 59.276 34.615 11.73 0.00 0.00 1.94
1798 2067 4.410099 TGCTGGTTTTGGAGATGATTTCT 58.590 39.130 0.00 0.00 37.41 2.52
1822 2091 7.831690 TCTGTTACAAACATATTCCTAATGGCA 59.168 33.333 0.00 0.00 41.26 4.92
1824 2093 7.613801 TGTTACAAACATATTCCTAATGGCAGT 59.386 33.333 0.00 0.00 36.25 4.40
1934 2203 7.545615 GGTTTGTTTCATGATAAACTCCATTCC 59.454 37.037 20.57 9.32 39.57 3.01
1957 2229 7.290061 TCCTTTCTGATATGTAATCTTTGGGG 58.710 38.462 0.00 0.00 0.00 4.96
1971 2243 3.636300 TCTTTGGGGTGTCAAATGTGAAG 59.364 43.478 0.00 0.00 36.24 3.02
1974 2246 2.955660 TGGGGTGTCAAATGTGAAGTTC 59.044 45.455 0.00 0.00 34.87 3.01
1975 2247 3.222603 GGGGTGTCAAATGTGAAGTTCT 58.777 45.455 4.17 0.00 34.87 3.01
2480 2786 5.639139 AGTGATCACTCTCTGCCAGATATA 58.361 41.667 22.89 0.00 36.92 0.86
3167 3481 7.058525 AGATTCTTGTCATGATATGAAAGGCA 58.941 34.615 19.82 2.98 41.69 4.75
3386 3700 2.158475 ACAAAATGAGAAGTCCTGCCCA 60.158 45.455 0.00 0.00 0.00 5.36
3548 3862 2.143925 GACACAGCAGGACACTAAACC 58.856 52.381 0.00 0.00 0.00 3.27
3549 3863 1.768870 ACACAGCAGGACACTAAACCT 59.231 47.619 0.00 0.00 36.92 3.50
3638 3952 5.047802 CCTTTGAAATGTGTTGTAGCCATCT 60.048 40.000 0.00 0.00 0.00 2.90
3660 3974 3.316029 TGTTCAATTTGCAGTCTGTGGAG 59.684 43.478 0.93 0.00 0.00 3.86
3717 4031 3.402628 TTGAGGGAGAACAGTTAGCAC 57.597 47.619 0.00 0.00 0.00 4.40
3719 4033 1.903183 GAGGGAGAACAGTTAGCACCT 59.097 52.381 0.00 0.00 0.00 4.00
3881 4195 5.946377 ACCTAATCCTGAGGCTAAAGTTTTG 59.054 40.000 0.00 0.00 37.63 2.44
4000 4314 4.463539 TGGTAGATTAGCGTAGGTCAACAA 59.536 41.667 0.00 0.00 40.68 2.83
4078 4392 7.301054 CACAACCAGAATTTGTAAGATCTGAC 58.699 38.462 2.87 2.87 41.38 3.51
4135 4450 3.007723 TGGTAACCGCAATGTACCTAACA 59.992 43.478 0.00 0.00 43.86 2.41
4158 4473 5.843019 TCAGGTTTTCCCTCTGAAATACT 57.157 39.130 0.00 0.00 43.86 2.12
4159 4474 6.945636 TCAGGTTTTCCCTCTGAAATACTA 57.054 37.500 0.00 0.00 43.86 1.82
4160 4475 6.708285 TCAGGTTTTCCCTCTGAAATACTAC 58.292 40.000 0.00 0.00 43.86 2.73
4211 4528 9.727627 GAATTCCTTGTATCATCTGTCATTTTC 57.272 33.333 0.00 0.00 0.00 2.29
4212 4529 8.812513 ATTCCTTGTATCATCTGTCATTTTCA 57.187 30.769 0.00 0.00 0.00 2.69
4215 4532 6.421377 TTGTATCATCTGTCATTTTCACCG 57.579 37.500 0.00 0.00 0.00 4.94
4218 4535 5.964958 ATCATCTGTCATTTTCACCGTTT 57.035 34.783 0.00 0.00 0.00 3.60
4226 4543 5.236695 TGTCATTTTCACCGTTTCGATTACA 59.763 36.000 0.00 0.00 0.00 2.41
4227 4544 6.137415 GTCATTTTCACCGTTTCGATTACAA 58.863 36.000 0.00 0.00 0.00 2.41
4231 4548 9.119329 CATTTTCACCGTTTCGATTACAAATAA 57.881 29.630 0.00 0.00 0.00 1.40
4254 4571 0.543749 GCTATGGGCACTCTGGTCTT 59.456 55.000 0.00 0.00 41.35 3.01
4264 4581 5.297029 GGGCACTCTGGTCTTTATATGTTTC 59.703 44.000 0.00 0.00 0.00 2.78
4422 4739 8.537016 GGTATATGCCATAGAAGTTATACCACA 58.463 37.037 4.76 0.00 40.22 4.17
4441 4758 7.039313 ACCACAGAAAACCTCTTTCAAATAC 57.961 36.000 0.52 0.00 29.07 1.89
4442 4759 6.605594 ACCACAGAAAACCTCTTTCAAATACA 59.394 34.615 0.52 0.00 29.07 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.682852 AATCCAACTCAACCCGTCGA 59.317 50.000 0.00 0.00 0.00 4.20
72 73 4.070009 GTCTTTAATCCAACTCAACCCGT 58.930 43.478 0.00 0.00 0.00 5.28
88 89 3.978666 AGACCATGGCGACACGTCTTTA 61.979 50.000 15.49 0.00 46.00 1.85
102 113 9.177608 TGGTTTTAAAGATTCATAGAGACCATG 57.822 33.333 0.00 0.00 0.00 3.66
114 125 9.549078 TGGTATGGTTTTTGGTTTTAAAGATTC 57.451 29.630 0.00 0.00 0.00 2.52
234 249 1.898863 ACATGGCCCTGGATTCTACT 58.101 50.000 13.03 0.00 0.00 2.57
284 301 7.111247 TGGCTCTGAATTCTTTTCTTTTTGA 57.889 32.000 7.05 0.00 0.00 2.69
369 386 1.819288 GGCCTCCTCTTTGCCTAAAAC 59.181 52.381 0.00 0.00 42.01 2.43
599 636 3.681897 AGCAGATGACATTCGTGAAAGAC 59.318 43.478 0.00 0.00 0.00 3.01
1271 1345 6.534079 GCAACGAGACAAGTTACTATGGTTAT 59.466 38.462 0.00 0.00 0.00 1.89
1286 1428 1.295792 GACAACCTTGCAACGAGACA 58.704 50.000 0.00 0.00 0.00 3.41
1322 1585 1.221566 CCATGATCCGTGCTCCACA 59.778 57.895 0.00 0.00 33.40 4.17
1375 1639 6.505344 TCCTGGCAGAAGGGTATGATTTATAT 59.495 38.462 17.94 0.00 37.96 0.86
1413 1677 9.833182 GTAGGATTCTCACAAAAGAAAATCTTC 57.167 33.333 0.00 0.00 38.69 2.87
1446 1711 0.038166 TCTTCGCAGGGCTTGGATTT 59.962 50.000 0.00 0.00 0.00 2.17
1488 1753 5.644977 AGCTAAGGTTTAAATCAACTGCC 57.355 39.130 0.43 0.00 0.00 4.85
1505 1770 7.661536 AACAGAATAGGAGTCACATAGCTAA 57.338 36.000 0.00 0.00 0.00 3.09
1572 1837 7.194112 TGACCTCATTATTAGAACACATGGA 57.806 36.000 0.00 0.00 0.00 3.41
1590 1855 4.943705 TGCAACTTCTATTTCCATGACCTC 59.056 41.667 0.00 0.00 0.00 3.85
1605 1870 7.281774 TCTCATTCTGAGGAAATATGCAACTTC 59.718 37.037 4.43 0.00 44.39 3.01
1705 1974 7.599998 GGCATTCTAGATTTCACACATGTTTTT 59.400 33.333 0.00 0.00 0.00 1.94
1706 1975 7.039504 AGGCATTCTAGATTTCACACATGTTTT 60.040 33.333 0.00 0.00 0.00 2.43
1707 1976 6.435277 AGGCATTCTAGATTTCACACATGTTT 59.565 34.615 0.00 0.00 0.00 2.83
1708 1977 5.948162 AGGCATTCTAGATTTCACACATGTT 59.052 36.000 0.00 0.00 0.00 2.71
1709 1978 5.503927 AGGCATTCTAGATTTCACACATGT 58.496 37.500 0.00 0.00 0.00 3.21
1710 1979 6.446781 AAGGCATTCTAGATTTCACACATG 57.553 37.500 0.00 0.00 0.00 3.21
1711 1980 7.611467 TGTAAAGGCATTCTAGATTTCACACAT 59.389 33.333 0.00 0.00 0.00 3.21
1798 2067 7.613801 ACTGCCATTAGGAATATGTTTGTAACA 59.386 33.333 0.00 0.00 41.16 2.41
1862 2131 1.000955 AGCTGTACAAGGTGGAAGTCG 59.999 52.381 0.00 0.00 34.56 4.18
1934 2203 7.557719 ACACCCCAAAGATTACATATCAGAAAG 59.442 37.037 0.00 0.00 0.00 2.62
1957 2229 7.542130 ACTGAAAAAGAACTTCACATTTGACAC 59.458 33.333 0.00 0.00 0.00 3.67
2184 2462 9.393249 GCAGCATAATGTTCGCTAAATAATAAA 57.607 29.630 0.00 0.00 33.82 1.40
2239 2517 5.128008 ACTTAGTAGCTCCAAAGGATCAGTC 59.872 44.000 0.00 0.00 0.00 3.51
2310 2588 7.492352 TTAGAATGCTGAATGATCATGACTG 57.508 36.000 9.46 11.37 34.37 3.51
2901 3215 6.662234 ACTGCTTAAGGTGTATATATCCGCTA 59.338 38.462 4.29 0.00 0.00 4.26
3548 3862 2.486982 CCATTTGTCTTGCCTCTGTCAG 59.513 50.000 0.00 0.00 0.00 3.51
3549 3863 2.158623 ACCATTTGTCTTGCCTCTGTCA 60.159 45.455 0.00 0.00 0.00 3.58
3638 3952 3.286353 TCCACAGACTGCAAATTGAACA 58.714 40.909 1.25 0.00 0.00 3.18
3660 3974 0.821301 GGATCTAGCCCTTTGCCTGC 60.821 60.000 0.00 0.00 42.71 4.85
3679 3993 4.537015 CTCAAAAAGAAAAGGTGCTACCG 58.463 43.478 0.00 0.00 44.90 4.02
3717 4031 5.772169 ACTGATCTCCCTCAAAAAGAAAAGG 59.228 40.000 0.00 0.00 0.00 3.11
3719 4033 7.040409 GCTAACTGATCTCCCTCAAAAAGAAAA 60.040 37.037 0.00 0.00 0.00 2.29
3881 4195 8.389603 TGCAACTCTGAAAAATGAAATTCAAAC 58.610 29.630 0.00 0.00 33.67 2.93
3900 4214 4.578928 TCCTAGGTTTGAAACTTGCAACTC 59.421 41.667 9.08 0.00 0.00 3.01
3986 4300 3.067106 CACAAGATTGTTGACCTACGCT 58.933 45.455 0.00 0.00 39.91 5.07
4000 4314 1.985159 TGTAACCTGGAGCCACAAGAT 59.015 47.619 0.00 0.00 0.00 2.40
4042 4356 0.777631 CTGGTTGTGCGCGAAAATTG 59.222 50.000 12.10 0.00 0.00 2.32
4043 4357 0.665835 TCTGGTTGTGCGCGAAAATT 59.334 45.000 12.10 0.00 0.00 1.82
4050 4364 2.697431 TACAAATTCTGGTTGTGCGC 57.303 45.000 0.00 0.00 39.50 6.09
4100 4414 3.518590 CGGTTACCACCAGAGACAATAC 58.481 50.000 1.13 0.00 44.53 1.89
4211 4528 6.021782 GCATGTTATTTGTAATCGAAACGGTG 60.022 38.462 0.00 0.00 0.00 4.94
4212 4529 6.025280 GCATGTTATTTGTAATCGAAACGGT 58.975 36.000 0.00 0.00 0.00 4.83
4215 4532 9.169468 CCATAGCATGTTATTTGTAATCGAAAC 57.831 33.333 0.00 0.00 0.00 2.78
4218 4535 6.072728 GCCCATAGCATGTTATTTGTAATCGA 60.073 38.462 0.00 0.00 42.97 3.59
4254 4571 6.354130 GTTGGCCTCCTACAGAAACATATAA 58.646 40.000 3.32 0.00 0.00 0.98
4264 4581 0.608640 AACTCGTTGGCCTCCTACAG 59.391 55.000 3.32 0.00 0.00 2.74
4409 4726 7.981102 AAGAGGTTTTCTGTGGTATAACTTC 57.019 36.000 0.00 0.00 35.91 3.01
4422 4739 9.463443 CGAATTTGTATTTGAAAGAGGTTTTCT 57.537 29.630 1.88 0.00 37.93 2.52
4441 4758 8.320295 GCAACAACATTTATACCATCGAATTTG 58.680 33.333 0.00 0.00 0.00 2.32
4442 4759 8.031864 TGCAACAACATTTATACCATCGAATTT 58.968 29.630 0.00 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.