Multiple sequence alignment - TraesCS3A01G191700

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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 TraesCS3A01G191700 chr3A 100.000 4016 0 0 1 4016 244481510 244485525 0.000000e+00 7417.0
1 TraesCS3A01G191700 chr3A 90.698 86 8 0 2578 2663 113364139 113364054 9.120000e-22 115.0
2 TraesCS3A01G191700 chr3A 90.698 86 8 0 2578 2663 714035512 714035427 9.120000e-22 115.0
3 TraesCS3A01G191700 chr3A 100.000 33 0 0 3357 3389 244484830 244484862 1.210000e-05 62.1
4 TraesCS3A01G191700 chr3A 100.000 33 0 0 3321 3353 244484866 244484898 1.210000e-05 62.1
5 TraesCS3A01G191700 chr3B 94.516 3355 114 29 43 3353 264162706 264166034 0.000000e+00 5112.0
6 TraesCS3A01G191700 chr3B 94.713 662 31 3 3357 4016 264166003 264166662 0.000000e+00 1026.0
7 TraesCS3A01G191700 chr3D 93.885 1848 60 26 1 1818 185331561 185333385 0.000000e+00 2737.0
8 TraesCS3A01G191700 chr3D 91.282 1170 66 23 2662 3815 185334301 185335450 0.000000e+00 1563.0
9 TraesCS3A01G191700 chr3D 96.741 767 20 4 1815 2580 185333540 185334302 0.000000e+00 1273.0
10 TraesCS3A01G191700 chr3D 92.169 166 13 0 3851 4016 185336735 185336900 6.710000e-58 235.0
11 TraesCS3A01G191700 chr7A 90.588 85 8 0 2579 2663 133087786 133087702 3.280000e-21 113.0
12 TraesCS3A01G191700 chr7A 87.097 93 12 0 2571 2663 63332370 63332462 5.490000e-19 106.0
13 TraesCS3A01G191700 chr4A 90.698 86 7 1 2578 2663 211051205 211051121 3.280000e-21 113.0
14 TraesCS3A01G191700 chr4A 86.869 99 8 4 2579 2677 150668651 150668558 5.490000e-19 106.0
15 TraesCS3A01G191700 chr4B 89.535 86 9 0 2578 2663 26837429 26837344 4.240000e-20 110.0
16 TraesCS3A01G191700 chr1B 88.043 92 11 0 2572 2663 483877731 483877822 4.240000e-20 110.0
17 TraesCS3A01G191700 chr2B 84.615 78 10 2 3935 4011 453643359 453643283 4.300000e-10 76.8


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 TraesCS3A01G191700 chr3A 244481510 244485525 4015 False 2513.733333 7417 100.00000 1 4016 3 chr3A.!!$F1 4015
1 TraesCS3A01G191700 chr3B 264162706 264166662 3956 False 3069.000000 5112 94.61450 43 4016 2 chr3B.!!$F1 3973
2 TraesCS3A01G191700 chr3D 185331561 185336900 5339 False 1452.000000 2737 93.51925 1 4016 4 chr3D.!!$F1 4015

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
796 837 0.036765 GTGAGATGGGCGTGTGGTTA 60.037 55.0 0.0 0.0 0.00 2.85 F
797 838 0.249120 TGAGATGGGCGTGTGGTTAG 59.751 55.0 0.0 0.0 0.00 2.34 F
1257 1298 0.463833 TCGACGAGATGGAGCAGCTA 60.464 55.0 0.0 0.0 26.98 3.32 F
1371 1412 0.536460 GCAACCCCGAGTTCAAGGAA 60.536 55.0 0.0 0.0 36.18 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 2718 0.322975 TGAGCAGCTCTCCAGAAACC 59.677 55.000 23.15 0.00 41.18 3.27 R
2634 2851 3.186409 CGCCGTCCCATAATACAAGAATG 59.814 47.826 0.00 0.00 0.00 2.67 R
2635 2852 3.399330 CGCCGTCCCATAATACAAGAAT 58.601 45.455 0.00 0.00 0.00 2.40 R
3370 3587 3.230134 ACCTAACAAACATGCCATGTGT 58.770 40.909 11.79 2.08 44.07 3.72 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
40 41 0.179225 CTATGTGGTGCAAACGACGC 60.179 55.000 0.00 0.00 0.00 5.19
132 133 8.303156 ACATTTATTTTTCGACCATGTCAATGA 58.697 29.630 0.00 0.00 35.67 2.57
189 191 4.218200 CCGCTATTGATAATTCATGGCCAA 59.782 41.667 10.96 0.00 0.00 4.52
299 301 5.293324 TCGCATACATTCACGAGCTAAAAAT 59.707 36.000 0.00 0.00 0.00 1.82
335 337 3.316588 TGTCCATAAAAGAAACTTGCGCA 59.683 39.130 5.66 5.66 0.00 6.09
344 346 1.222115 AAACTTGCGCACCTCTCGTC 61.222 55.000 11.12 0.00 0.00 4.20
357 359 3.564225 ACCTCTCGTCCATTTGTTTTCAC 59.436 43.478 0.00 0.00 0.00 3.18
412 414 6.997222 AGCTTCGTATATTCAAACGTTAACC 58.003 36.000 0.00 0.00 39.99 2.85
444 446 5.640357 TCGTGGTTCGATAGCAACTAAAAAT 59.360 36.000 0.00 0.00 44.01 1.82
569 574 7.719483 ACAAGAAATTGATTGCATATACCCAG 58.281 34.615 0.00 0.00 0.00 4.45
586 591 2.504367 CCAGTCGGTTTTCACCTCAAT 58.496 47.619 0.00 0.00 41.64 2.57
593 598 2.094026 GGTTTTCACCTCAATCCATGGC 60.094 50.000 6.96 0.00 40.44 4.40
604 609 4.774124 TCAATCCATGGCTAGAAAGTCAG 58.226 43.478 6.96 0.00 41.60 3.51
691 701 8.356657 TCTCCTTTGTGTGTAAATAAACAATGG 58.643 33.333 11.17 11.17 43.76 3.16
692 702 6.926272 TCCTTTGTGTGTAAATAAACAATGGC 59.074 34.615 12.13 0.00 42.87 4.40
721 734 7.100458 ACTCTGAAACAACAATAAGCAAAGT 57.900 32.000 0.00 0.00 0.00 2.66
723 736 8.129211 ACTCTGAAACAACAATAAGCAAAGTAC 58.871 33.333 0.00 0.00 0.00 2.73
740 753 2.171003 GTACAAGGGCCTTGCAAGAAT 58.829 47.619 39.34 24.34 44.43 2.40
747 760 2.428530 GGGCCTTGCAAGAATAAGAAGG 59.571 50.000 28.05 9.54 36.95 3.46
748 761 3.356290 GGCCTTGCAAGAATAAGAAGGA 58.644 45.455 28.05 0.00 36.09 3.36
796 837 0.036765 GTGAGATGGGCGTGTGGTTA 60.037 55.000 0.00 0.00 0.00 2.85
797 838 0.249120 TGAGATGGGCGTGTGGTTAG 59.751 55.000 0.00 0.00 0.00 2.34
875 916 2.125310 CCGCCTTATCGCACCACA 60.125 61.111 0.00 0.00 0.00 4.17
876 917 2.461110 CCGCCTTATCGCACCACAC 61.461 63.158 0.00 0.00 0.00 3.82
938 979 3.318886 CTCTGCTCTGCTGCATATACAG 58.681 50.000 1.31 9.07 42.48 2.74
1257 1298 0.463833 TCGACGAGATGGAGCAGCTA 60.464 55.000 0.00 0.00 26.98 3.32
1371 1412 0.536460 GCAACCCCGAGTTCAAGGAA 60.536 55.000 0.00 0.00 36.18 3.36
1374 1415 1.128188 ACCCCGAGTTCAAGGAAGCT 61.128 55.000 0.00 0.00 0.00 3.74
1501 1542 1.145803 GCTCAAGGTTCGTGTACCAC 58.854 55.000 0.00 0.00 40.82 4.16
1502 1543 1.270147 GCTCAAGGTTCGTGTACCACT 60.270 52.381 0.00 0.00 40.82 4.00
1503 1544 2.805657 GCTCAAGGTTCGTGTACCACTT 60.806 50.000 0.00 0.00 40.82 3.16
1543 1584 1.472082 CTTGCATGTGGGCATTTCGTA 59.528 47.619 0.00 0.00 44.48 3.43
1660 1702 2.203070 GGCACGCTGGGTATGGAG 60.203 66.667 0.00 0.00 0.00 3.86
1672 1714 2.355716 GGGTATGGAGTACTTGCTTGCA 60.356 50.000 0.00 0.00 33.64 4.08
1800 1852 7.259290 AGTTTAAGCTTCAACTCAATTTCGA 57.741 32.000 18.24 0.00 0.00 3.71
2008 2224 3.678056 AAGTTCATCTTCTACGCCACA 57.322 42.857 0.00 0.00 0.00 4.17
2062 2278 1.951209 TCACCATCTTCAGGCACCTA 58.049 50.000 0.00 0.00 0.00 3.08
2119 2335 3.635373 TCAAGTACTTCGAGAACTGGTGT 59.365 43.478 4.77 0.00 0.00 4.16
2501 2718 4.944962 TCATTGAGTGTTTTATCAGGCG 57.055 40.909 0.00 0.00 0.00 5.52
2590 2807 6.007703 AGCATTATACTCTACTCCCTCTGTC 58.992 44.000 0.00 0.00 0.00 3.51
2605 2822 7.572861 ACTCCCTCTGTCCCATAATATAAAAGT 59.427 37.037 0.00 0.00 0.00 2.66
2655 2872 4.134563 ACATTCTTGTATTATGGGACGGC 58.865 43.478 0.00 0.00 33.16 5.68
3026 3243 7.897575 AGCTTGTCTACTGAATTTGTAGAAG 57.102 36.000 17.90 14.84 45.14 2.85
3039 3256 8.992349 TGAATTTGTAGAAGAAGGATCCATCTA 58.008 33.333 19.49 14.39 0.00 1.98
3078 3295 4.700692 ACATAATCATGCATCATGCTCCTC 59.299 41.667 11.84 0.00 45.31 3.71
3349 3566 4.437772 TGTATCACACATGGCATGTTTG 57.562 40.909 31.25 31.25 42.70 2.93
3350 3567 3.825585 TGTATCACACATGGCATGTTTGT 59.174 39.130 33.61 25.39 42.70 2.83
3351 3568 4.280425 TGTATCACACATGGCATGTTTGTT 59.720 37.500 33.61 29.29 42.70 2.83
3352 3569 5.474876 TGTATCACACATGGCATGTTTGTTA 59.525 36.000 33.61 28.47 42.70 2.41
3353 3570 4.926140 TCACACATGGCATGTTTGTTAA 57.074 36.364 33.61 19.76 42.70 2.01
3354 3571 4.869215 TCACACATGGCATGTTTGTTAAG 58.131 39.130 33.61 22.46 42.70 1.85
3355 3572 4.340666 TCACACATGGCATGTTTGTTAAGT 59.659 37.500 33.61 23.00 42.70 2.24
3356 3573 5.532779 TCACACATGGCATGTTTGTTAAGTA 59.467 36.000 33.61 18.59 42.70 2.24
3357 3574 6.208402 TCACACATGGCATGTTTGTTAAGTAT 59.792 34.615 33.61 9.31 42.70 2.12
3358 3575 7.391833 TCACACATGGCATGTTTGTTAAGTATA 59.608 33.333 33.61 17.43 42.70 1.47
3359 3576 8.190122 CACACATGGCATGTTTGTTAAGTATAT 58.810 33.333 29.61 5.31 42.70 0.86
3360 3577 8.190122 ACACATGGCATGTTTGTTAAGTATATG 58.810 33.333 29.57 15.40 42.70 1.78
3361 3578 8.190122 CACATGGCATGTTTGTTAAGTATATGT 58.810 33.333 29.57 1.24 42.70 2.29
3362 3579 8.748412 ACATGGCATGTTTGTTAAGTATATGTT 58.252 29.630 26.78 0.00 41.63 2.71
3413 3630 3.801050 TCAACAACGGCATTGACATTTTG 59.199 39.130 0.00 0.00 41.23 2.44
3432 3649 8.247562 ACATTTTGTTACCGTAAATGTATGCAT 58.752 29.630 3.79 3.79 45.55 3.96
3608 3848 6.686630 TCTTTTTATGCCACGATGTCATTTT 58.313 32.000 0.00 0.00 0.00 1.82
3623 3863 5.825532 TGTCATTTTCCTACATGGATGGAA 58.174 37.500 10.84 10.84 45.68 3.53
3667 3907 3.017581 GCCCCAGGGGTGTCTCAT 61.018 66.667 27.04 0.00 46.51 2.90
3669 3909 1.609783 CCCCAGGGGTGTCTCATTC 59.390 63.158 18.09 0.00 38.25 2.67
3857 4166 1.076995 ACCCATAAAAGCCGAGGCC 60.077 57.895 10.95 0.00 43.17 5.19
3899 5406 6.296026 ACAACAACAAAACCATAGAGCTCTA 58.704 36.000 25.23 25.23 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 191 1.949525 GGCCATGATGCGACAAGTATT 59.050 47.619 0.00 0.00 0.00 1.89
309 311 6.073819 GCGCAAGTTTCTTTTATGGACAAATT 60.074 34.615 0.30 0.00 41.68 1.82
328 330 2.811317 GGACGAGAGGTGCGCAAG 60.811 66.667 14.00 1.89 43.44 4.01
335 337 3.564225 GTGAAAACAAATGGACGAGAGGT 59.436 43.478 0.00 0.00 0.00 3.85
344 346 7.918562 CGGGGTAATATAAGTGAAAACAAATGG 59.081 37.037 0.00 0.00 0.00 3.16
357 359 5.717078 TGTAGTCAGCGGGGTAATATAAG 57.283 43.478 0.00 0.00 0.00 1.73
412 414 2.738521 CGAACCACGAGGCACCTG 60.739 66.667 0.00 0.00 45.77 4.00
515 520 0.810031 GGATGGACATTCCCGTGACG 60.810 60.000 0.00 0.00 35.03 4.35
565 570 0.107831 TGAGGTGAAAACCGACTGGG 59.892 55.000 0.00 0.00 40.75 4.45
569 574 2.500229 TGGATTGAGGTGAAAACCGAC 58.500 47.619 0.00 0.00 34.28 4.79
586 591 5.441718 AATTCTGACTTTCTAGCCATGGA 57.558 39.130 18.40 0.00 0.00 3.41
604 609 9.463443 AAGAACAAAGCAACATGTACTAAATTC 57.537 29.630 0.00 5.06 0.00 2.17
691 701 3.502191 TTGTTGTTTCAGAGTTGGTGC 57.498 42.857 0.00 0.00 0.00 5.01
692 702 5.687285 GCTTATTGTTGTTTCAGAGTTGGTG 59.313 40.000 0.00 0.00 0.00 4.17
721 734 2.603075 ATTCTTGCAAGGCCCTTGTA 57.397 45.000 25.73 17.74 42.77 2.41
723 736 3.091545 TCTTATTCTTGCAAGGCCCTTG 58.908 45.455 25.73 19.47 43.57 3.61
796 837 1.065854 GTGTACAGCAGGCCAATCTCT 60.066 52.381 5.01 0.00 0.00 3.10
797 838 1.339055 TGTGTACAGCAGGCCAATCTC 60.339 52.381 5.01 0.00 0.00 2.75
875 916 4.551671 AGCTGACATGTAAGAGATAGGGT 58.448 43.478 14.96 0.00 0.00 4.34
876 917 4.832266 AGAGCTGACATGTAAGAGATAGGG 59.168 45.833 14.96 0.00 0.00 3.53
938 979 4.516195 GGAACGGAGAGGGAGCGC 62.516 72.222 0.00 0.00 0.00 5.92
1257 1298 3.181510 GCTTGTTAATCTCGGCGTTGAAT 60.182 43.478 6.85 2.64 0.00 2.57
1371 1412 2.348620 TGCATCTTGTCGGCAGCT 59.651 55.556 0.57 0.00 32.95 4.24
1374 1415 2.046023 CCCTGCATCTTGTCGGCA 60.046 61.111 0.00 0.00 35.96 5.69
1501 1542 6.029346 AGAGCAGAGAAGAAGAAGAAGAAG 57.971 41.667 0.00 0.00 0.00 2.85
1502 1543 6.222389 CAAGAGCAGAGAAGAAGAAGAAGAA 58.778 40.000 0.00 0.00 0.00 2.52
1503 1544 5.782047 CAAGAGCAGAGAAGAAGAAGAAGA 58.218 41.667 0.00 0.00 0.00 2.87
1543 1584 2.851102 ACACCCACCAGCTGCTCT 60.851 61.111 8.66 0.00 0.00 4.09
1659 1701 4.938226 GGAATAAGAGTGCAAGCAAGTACT 59.062 41.667 0.00 0.00 37.15 2.73
1660 1702 4.095036 GGGAATAAGAGTGCAAGCAAGTAC 59.905 45.833 0.00 0.00 0.00 2.73
1672 1714 8.017418 TGTTTTGTTTTGATGGGAATAAGAGT 57.983 30.769 0.00 0.00 0.00 3.24
1837 2053 8.409371 CAAATCATGCTGAGAACTAGAGTAGTA 58.591 37.037 0.00 0.00 38.26 1.82
1838 2054 7.093552 ACAAATCATGCTGAGAACTAGAGTAGT 60.094 37.037 0.00 0.00 41.73 2.73
1839 2055 7.222417 CACAAATCATGCTGAGAACTAGAGTAG 59.778 40.741 0.00 0.00 0.00 2.57
1840 2056 7.038048 CACAAATCATGCTGAGAACTAGAGTA 58.962 38.462 0.00 0.00 0.00 2.59
1841 2057 5.873712 CACAAATCATGCTGAGAACTAGAGT 59.126 40.000 0.00 0.00 0.00 3.24
1842 2058 5.873712 ACACAAATCATGCTGAGAACTAGAG 59.126 40.000 0.00 0.00 0.00 2.43
1843 2059 5.798132 ACACAAATCATGCTGAGAACTAGA 58.202 37.500 0.00 0.00 0.00 2.43
1844 2060 6.492007 AACACAAATCATGCTGAGAACTAG 57.508 37.500 0.00 0.00 0.00 2.57
1845 2061 8.565896 AATAACACAAATCATGCTGAGAACTA 57.434 30.769 0.00 0.00 0.00 2.24
1874 2090 3.910170 CACAGCACGAATCATGTTTCTTG 59.090 43.478 15.25 15.25 0.00 3.02
2062 2278 1.377612 GTACTCCGGGTTGGCCTTT 59.622 57.895 3.32 0.00 37.80 3.11
2119 2335 1.982395 ATGCCGGTTCTCGTCCTGA 60.982 57.895 1.90 0.00 37.11 3.86
2501 2718 0.322975 TGAGCAGCTCTCCAGAAACC 59.677 55.000 23.15 0.00 41.18 3.27
2634 2851 3.186409 CGCCGTCCCATAATACAAGAATG 59.814 47.826 0.00 0.00 0.00 2.67
2635 2852 3.399330 CGCCGTCCCATAATACAAGAAT 58.601 45.455 0.00 0.00 0.00 2.40
3026 3243 5.240013 AGAAAGGCATAGATGGATCCTTC 57.760 43.478 17.90 17.90 36.22 3.46
3039 3256 7.707624 TGATTATGTCTGAAAAGAAAGGCAT 57.292 32.000 0.00 0.00 41.47 4.40
3370 3587 3.230134 ACCTAACAAACATGCCATGTGT 58.770 40.909 11.79 2.08 44.07 3.72
3371 3588 3.255395 TGACCTAACAAACATGCCATGTG 59.745 43.478 11.79 2.23 44.07 3.21
3372 3589 4.261994 GTTGACCTAACAAACATGCCATGT 60.262 41.667 4.03 4.03 41.24 3.21
3373 3590 4.236935 GTTGACCTAACAAACATGCCATG 58.763 43.478 2.40 2.40 39.16 3.66
3374 3591 3.894427 TGTTGACCTAACAAACATGCCAT 59.106 39.130 0.00 0.00 45.86 4.40
3375 3592 3.291584 TGTTGACCTAACAAACATGCCA 58.708 40.909 0.00 0.00 45.86 4.92
3413 3630 8.850454 AATTTCATGCATACATTTACGGTAAC 57.150 30.769 0.00 0.00 32.87 2.50
3623 3863 7.264817 GACAGCGTCACAATGTTAACCACAT 62.265 44.000 2.48 0.00 38.98 3.21
3667 3907 1.275291 CGGCTTCTGGTAAGGTGAGAA 59.725 52.381 0.00 0.00 0.00 2.87
3669 3909 0.108138 CCGGCTTCTGGTAAGGTGAG 60.108 60.000 0.00 0.00 0.00 3.51
3741 3999 1.172812 GCCTTCCGGGACCATTATGC 61.173 60.000 0.00 0.00 37.23 3.14
3745 4003 1.000896 CAAGCCTTCCGGGACCATT 60.001 57.895 0.00 0.00 37.23 3.16
3796 4104 5.548406 TGTTCTAAGTTGGTTAAGAGGAGC 58.452 41.667 0.00 0.00 0.00 4.70
3899 5406 5.823045 GGTTACAAAGATCGAGGGATTGATT 59.177 40.000 9.21 0.00 31.51 2.57
3980 5487 4.469657 AGCAGAGTTTTACCCATGTTCAA 58.530 39.130 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.