Multiple sequence alignment - TraesCS3D01G240500

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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 TraesCS3D01G240500 chr3D 100.000 2832 0 0 1 2832 332805443 332802612 0.000000e+00 5230.0
1 TraesCS3D01G240500 chr3A 92.151 2255 83 31 622 2832 450304741 450302537 0.000000e+00 3097.0
2 TraesCS3D01G240500 chr3A 90.738 637 43 9 1 624 450311738 450311105 0.000000e+00 835.0
3 TraesCS3D01G240500 chr3B 91.731 1294 80 17 916 2198 431990306 431989029 0.000000e+00 1772.0
4 TraesCS3D01G240500 chr3B 90.840 524 33 5 1 512 431992637 431992117 0.000000e+00 688.0
5 TraesCS3D01G240500 chr3B 87.701 374 24 9 2479 2832 431988208 431987837 1.570000e-112 416.0
6 TraesCS3D01G240500 chr3B 84.116 447 29 13 504 920 431991929 431991495 7.350000e-106 394.0
7 TraesCS3D01G240500 chr3B 91.078 269 14 4 2195 2462 431988764 431988505 3.470000e-94 355.0
8 TraesCS3D01G240500 chr1B 86.066 122 8 6 1390 1511 659997734 659997846 3.830000e-24 122.0
9 TraesCS3D01G240500 chr1B 80.315 127 18 4 1388 1514 659975303 659975422 3.890000e-14 89.8


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 TraesCS3D01G240500 chr3D 332802612 332805443 2831 True 5230 5230 100.0000 1 2832 1 chr3D.!!$R1 2831
1 TraesCS3D01G240500 chr3A 450302537 450304741 2204 True 3097 3097 92.1510 622 2832 1 chr3A.!!$R1 2210
2 TraesCS3D01G240500 chr3A 450311105 450311738 633 True 835 835 90.7380 1 624 1 chr3A.!!$R2 623
3 TraesCS3D01G240500 chr3B 431987837 431992637 4800 True 725 1772 89.0932 1 2832 5 chr3B.!!$R1 2831

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
642 852 0.343726 AGGAGCCCTAAACCCTAGCT 59.656 55.0 0.0 0.0 36.25 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 3982 1.068402 TGCTTTGGCGACATCAATGTG 60.068 47.619 0.0 0.0 42.32 3.21 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
46 47 6.633500 TGTCAGGTAGTTTCAAAATCCTTG 57.367 37.500 0.00 0.00 0.00 3.61
86 87 1.897802 CAGTACCACGGACTTAGGGTT 59.102 52.381 0.00 0.00 34.88 4.11
194 195 5.529581 AACACCCAAACTGAATGGTAAAG 57.470 39.130 0.00 0.00 36.14 1.85
197 198 5.068591 ACACCCAAACTGAATGGTAAAGAAC 59.931 40.000 0.00 0.00 36.14 3.01
231 232 2.694628 AGTTGCCAATGTGCTTCTTTCA 59.305 40.909 0.00 0.00 0.00 2.69
258 271 3.425122 CATGCATACCTCATGGCCA 57.575 52.632 8.56 8.56 38.06 5.36
295 308 2.902608 AGTGTGAACCCTAGTCCATGA 58.097 47.619 0.00 0.00 0.00 3.07
344 357 0.839946 ACCGGATCATCCTCCCAAAG 59.160 55.000 9.46 0.00 33.30 2.77
364 377 3.044894 AGGAAGTCCTCTCCATCATTCC 58.955 50.000 0.00 0.00 44.77 3.01
379 392 3.548770 TCATTCCCATGCAGATCAAGAC 58.451 45.455 0.00 0.00 0.00 3.01
398 411 2.863137 GACGCTTGATCAGATCTTCCAC 59.137 50.000 11.83 0.00 0.00 4.02
440 453 1.674057 CGCCACTTCCTCCACTCTT 59.326 57.895 0.00 0.00 0.00 2.85
496 509 3.419759 CCAAAACCTCGTCGGCCG 61.420 66.667 22.12 22.12 35.61 6.13
544 753 1.141019 GGATCAACACGAGCCGCTA 59.859 57.895 0.00 0.00 41.22 4.26
547 756 0.747255 ATCAACACGAGCCGCTAGAT 59.253 50.000 7.57 0.00 0.00 1.98
551 760 3.967335 ACGAGCCGCTAGATCCGC 61.967 66.667 7.57 0.00 0.00 5.54
606 815 4.477780 GACCTGAGTAGACAAAACTCTCG 58.522 47.826 4.99 0.00 43.13 4.04
626 836 2.475466 CGTAGCCGCCGTTAGAGGA 61.475 63.158 0.00 0.00 0.00 3.71
642 852 0.343726 AGGAGCCCTAAACCCTAGCT 59.656 55.000 0.00 0.00 36.25 3.32
662 872 0.392706 TGAGCGCTCACTCTTTTGGA 59.607 50.000 35.30 9.45 37.58 3.53
703 913 4.089361 CCCCATTTAGCTCCTTTTTGTCT 58.911 43.478 0.00 0.00 0.00 3.41
749 962 0.979665 TCTAGCCTGAGCAGCAACTT 59.020 50.000 0.00 0.00 43.56 2.66
750 963 1.349026 TCTAGCCTGAGCAGCAACTTT 59.651 47.619 0.00 0.00 43.56 2.66
751 964 2.567169 TCTAGCCTGAGCAGCAACTTTA 59.433 45.455 0.00 0.00 43.56 1.85
752 965 1.528129 AGCCTGAGCAGCAACTTTAC 58.472 50.000 0.00 0.00 43.56 2.01
794 1017 4.914420 CGCAAACCAAACGCGCCA 62.914 61.111 5.73 0.00 42.79 5.69
796 1019 2.354539 CAAACCAAACGCGCCAGG 60.355 61.111 5.73 8.05 0.00 4.45
798 1021 2.419739 AAACCAAACGCGCCAGGTT 61.420 52.632 19.87 19.87 45.73 3.50
801 1024 2.252260 CAAACGCGCCAGGTTCAG 59.748 61.111 5.73 0.00 0.00 3.02
958 2390 0.758123 CCCAGCCAAGCAAAAGGAAA 59.242 50.000 0.00 0.00 0.00 3.13
1043 2477 1.504912 CCATGGAGGACAGAGACCAT 58.495 55.000 5.56 0.00 42.83 3.55
1067 2501 0.108424 CCGCTGAGAACCTTCCTGAG 60.108 60.000 0.00 0.00 0.00 3.35
1117 2551 0.392729 GAGGGAGACGAAGACGGAGA 60.393 60.000 0.00 0.00 44.46 3.71
1147 2581 3.064324 CCCCGTCCTACCGTTCGT 61.064 66.667 0.00 0.00 0.00 3.85
1311 2745 1.671901 GAGGCAGAGGGACGAAGAGG 61.672 65.000 0.00 0.00 0.00 3.69
1315 2749 1.380650 AGAGGGACGAAGAGGGCTC 60.381 63.158 0.00 0.00 0.00 4.70
1418 2852 4.087892 TGCCGGAAGAGCAGCTCC 62.088 66.667 19.40 3.78 34.69 4.70
1493 2927 1.667830 CAGCGACGGCAAGGAGAAA 60.668 57.895 0.00 0.00 43.41 2.52
1550 2984 4.029809 GGGGACGTGGTGGAAGGG 62.030 72.222 0.00 0.00 0.00 3.95
1551 2985 4.029809 GGGACGTGGTGGAAGGGG 62.030 72.222 0.00 0.00 0.00 4.79
1620 3057 3.922171 ATTACAGCAAAGGAGGAGGAG 57.078 47.619 0.00 0.00 0.00 3.69
1621 3058 1.573108 TACAGCAAAGGAGGAGGAGG 58.427 55.000 0.00 0.00 0.00 4.30
1622 3059 0.474660 ACAGCAAAGGAGGAGGAGGT 60.475 55.000 0.00 0.00 0.00 3.85
1623 3060 0.035630 CAGCAAAGGAGGAGGAGGTG 60.036 60.000 0.00 0.00 0.00 4.00
1800 3237 7.919690 TCTGCTTTTGTGTGCATAATAGTATC 58.080 34.615 0.00 0.00 38.59 2.24
1902 3345 3.708563 AAAAACCACACCATCTCAACG 57.291 42.857 0.00 0.00 0.00 4.10
1959 3405 2.355756 TCTCTGTTTGCTTGCACACTTC 59.644 45.455 12.21 0.00 0.00 3.01
2041 3487 4.009370 GGTAGGATAGAACTGCCCATTC 57.991 50.000 0.00 0.00 35.02 2.67
2205 3926 8.290663 ACTGTGACGTTGTACTAATAGTTTTC 57.709 34.615 0.00 0.00 0.00 2.29
2237 3958 3.845775 CGTACAAAACAATTCATGCCTCG 59.154 43.478 0.00 0.00 0.00 4.63
2246 3968 4.943705 ACAATTCATGCCTCGTTGTCTTAT 59.056 37.500 0.00 0.00 0.00 1.73
2257 3979 3.000727 CGTTGTCTTATTGGTCCTCCAC 58.999 50.000 0.00 0.00 44.22 4.02
2258 3980 3.306780 CGTTGTCTTATTGGTCCTCCACT 60.307 47.826 0.00 0.00 44.22 4.00
2259 3981 4.254492 GTTGTCTTATTGGTCCTCCACTC 58.746 47.826 0.00 0.00 44.22 3.51
2260 3982 2.838202 TGTCTTATTGGTCCTCCACTCC 59.162 50.000 0.00 0.00 44.22 3.85
2261 3983 2.838202 GTCTTATTGGTCCTCCACTCCA 59.162 50.000 0.00 0.00 44.22 3.86
2262 3984 2.838202 TCTTATTGGTCCTCCACTCCAC 59.162 50.000 0.00 0.00 44.22 4.02
2323 4045 8.704234 GTCAGTACAGAGACTGTTCTATTTTTG 58.296 37.037 9.63 0.00 42.59 2.44
2326 4048 6.305693 ACAGAGACTGTTCTATTTTTGTGC 57.694 37.500 0.00 0.00 42.59 4.57
2333 4055 6.273071 ACTGTTCTATTTTTGTGCTTGGAAC 58.727 36.000 0.00 0.00 34.35 3.62
2394 4116 8.959058 CGTAGAGTACAATATACTTTTGCAGAG 58.041 37.037 0.00 0.00 0.00 3.35
2408 4130 1.942657 TGCAGAGCAGTCAAACAGTTC 59.057 47.619 0.00 0.00 33.32 3.01
2409 4131 1.942657 GCAGAGCAGTCAAACAGTTCA 59.057 47.619 0.00 0.00 0.00 3.18
2410 4132 2.551459 GCAGAGCAGTCAAACAGTTCAT 59.449 45.455 0.00 0.00 0.00 2.57
2411 4133 3.608707 GCAGAGCAGTCAAACAGTTCATG 60.609 47.826 0.00 0.00 0.00 3.07
2437 4163 6.385843 TCGCATGTATACAAAATTGCAAACT 58.614 32.000 22.48 0.00 30.79 2.66
2438 4164 6.865726 TCGCATGTATACAAAATTGCAAACTT 59.134 30.769 22.48 0.00 30.79 2.66
2442 4168 7.938563 TGTATACAAAATTGCAAACTTGGAC 57.061 32.000 21.31 16.90 0.00 4.02
2517 4523 6.183360 GGGCTCTTACGATAAGCAAGAATTTT 60.183 38.462 0.00 0.00 37.78 1.82
2573 4579 4.046938 TCTCCGTAGTGAGATGAATTGC 57.953 45.455 0.00 0.00 36.48 3.56
2598 4604 4.607293 TGTATATGTGTCCTCCAGATGC 57.393 45.455 0.00 0.00 0.00 3.91
2703 4709 2.359107 TTGGAGCTCGCCTGCTTG 60.359 61.111 7.83 0.00 44.17 4.01
2706 4712 2.511145 GAGCTCGCCTGCTTGGAG 60.511 66.667 0.00 0.00 44.17 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 5.496556 AGTTGAATATGATGGGTTCACGAA 58.503 37.500 0.00 0.00 37.11 3.85
140 141 1.154225 CACCGCGATGTTGAAAGGC 60.154 57.895 8.23 0.00 0.00 4.35
194 195 6.500684 TGGCAACTGATCAAAGATAAGTTC 57.499 37.500 6.75 3.62 37.61 3.01
197 198 6.750501 CACATTGGCAACTGATCAAAGATAAG 59.249 38.462 0.00 0.00 37.61 1.73
213 214 2.034939 CAGTGAAAGAAGCACATTGGCA 59.965 45.455 0.00 0.00 38.70 4.92
231 232 2.779430 TGAGGTATGCATGGAATCCAGT 59.221 45.455 10.16 0.00 36.75 4.00
258 271 5.648247 TCACACTAGTAAGGGGTTTAGTCT 58.352 41.667 0.00 0.00 0.00 3.24
344 357 2.105649 GGGAATGATGGAGAGGACTTCC 59.894 54.545 0.00 0.00 0.00 3.46
362 375 0.462581 GCGTCTTGATCTGCATGGGA 60.463 55.000 0.00 0.00 0.00 4.37
364 377 1.063616 CAAGCGTCTTGATCTGCATGG 59.936 52.381 12.43 0.00 0.00 3.66
379 392 1.857217 CGTGGAAGATCTGATCAAGCG 59.143 52.381 19.12 11.58 0.00 4.68
398 411 1.463444 GGAAACATGAGTCGGGAAACG 59.537 52.381 0.00 0.00 46.11 3.60
440 453 6.662865 TTTCCAATTTAGTTCAGGCAATGA 57.337 33.333 0.00 0.00 35.62 2.57
496 509 1.226717 CACGCTTCTACCTCGCCTC 60.227 63.158 0.00 0.00 0.00 4.70
501 514 4.816990 GCCTCACGCTTCTACCTC 57.183 61.111 0.00 0.00 0.00 3.85
544 753 1.528776 GTCTACCTCCGGCGGATCT 60.529 63.158 31.23 19.25 0.00 2.75
547 756 4.100084 TCGTCTACCTCCGGCGGA 62.100 66.667 29.14 29.14 0.00 5.54
551 760 0.662085 GCTAACTCGTCTACCTCCGG 59.338 60.000 0.00 0.00 0.00 5.14
562 771 2.441532 TCCCCTCCGGCTAACTCG 60.442 66.667 0.00 0.00 0.00 4.18
566 775 2.042230 GGTCTCCCCTCCGGCTAA 60.042 66.667 0.00 0.00 0.00 3.09
582 791 3.256136 AGAGTTTTGTCTACTCAGGTCGG 59.744 47.826 0.00 0.00 43.52 4.79
606 815 1.298190 CTCTAACGGCGGCTACGTC 60.298 63.158 13.24 0.00 44.83 4.34
626 836 1.840635 CTCAAGCTAGGGTTTAGGGCT 59.159 52.381 0.00 0.00 34.52 5.19
642 852 1.202639 TCCAAAAGAGTGAGCGCTCAA 60.203 47.619 39.63 22.05 41.85 3.02
655 865 1.068954 GGAGCGCTCAGTTTCCAAAAG 60.069 52.381 36.27 0.00 0.00 2.27
662 872 1.518903 GCCAAAGGAGCGCTCAGTTT 61.519 55.000 36.27 29.40 0.00 2.66
749 962 0.179105 AACGTGTCAGTGCGTGGTAA 60.179 50.000 0.00 0.00 41.42 2.85
750 963 0.179105 AAACGTGTCAGTGCGTGGTA 60.179 50.000 0.00 0.00 41.42 3.25
751 964 1.426041 GAAACGTGTCAGTGCGTGGT 61.426 55.000 0.00 0.00 41.42 4.16
752 965 1.151777 AGAAACGTGTCAGTGCGTGG 61.152 55.000 8.78 0.00 41.42 4.94
794 1017 1.004440 GAGCTGAACGCCTGAACCT 60.004 57.895 0.00 0.00 40.39 3.50
796 1019 3.567473 GGAGCTGAACGCCTGAAC 58.433 61.111 0.00 0.00 40.39 3.18
801 1024 2.656069 TACCCAGGAGCTGAACGCC 61.656 63.158 0.00 0.00 40.39 5.68
804 1027 1.066787 GTCAGTACCCAGGAGCTGAAC 60.067 57.143 13.50 7.36 39.33 3.18
958 2390 2.584835 TGCCTTTATGTGTGGCTTCT 57.415 45.000 0.00 0.00 46.23 2.85
979 2411 6.092807 GGGTTGAAGGATAGATATTTGATCGC 59.907 42.308 0.00 0.00 0.00 4.58
1067 2501 1.805945 GACGATGCGGTGTGGAGAC 60.806 63.158 0.00 0.00 0.00 3.36
1117 2551 4.016706 CGGGGAAGGTGAAGCCGT 62.017 66.667 0.00 0.00 43.70 5.68
1159 2593 2.263540 GGTACACGGGCACGATGT 59.736 61.111 19.19 18.46 44.60 3.06
1618 3055 2.726351 CCGCTTCCTCCTCCACCTC 61.726 68.421 0.00 0.00 0.00 3.85
1619 3056 2.685380 CCGCTTCCTCCTCCACCT 60.685 66.667 0.00 0.00 0.00 4.00
1620 3057 4.475135 GCCGCTTCCTCCTCCACC 62.475 72.222 0.00 0.00 0.00 4.61
1621 3058 4.821589 CGCCGCTTCCTCCTCCAC 62.822 72.222 0.00 0.00 0.00 4.02
1721 3158 1.343465 ACGCATTAGAACGGGGGATAG 59.657 52.381 0.00 0.00 0.00 2.08
1800 3237 6.982141 TCTAATAACACTACCAAGGTTATGCG 59.018 38.462 0.00 0.00 37.67 4.73
1861 3304 7.475137 TTTTACATTTACCTTAGCCAAGCAT 57.525 32.000 0.00 0.00 0.00 3.79
1902 3345 6.650120 AGTCTATCCTTCTCCGATCTCTATC 58.350 44.000 0.00 0.00 0.00 2.08
1921 3364 9.706691 CAAACAGAGAACCTACAAAATAGTCTA 57.293 33.333 0.00 0.00 0.00 2.59
1922 3365 7.173390 GCAAACAGAGAACCTACAAAATAGTCT 59.827 37.037 0.00 0.00 0.00 3.24
1923 3366 7.173390 AGCAAACAGAGAACCTACAAAATAGTC 59.827 37.037 0.00 0.00 0.00 2.59
2041 3487 8.338259 CAAAATTCTCTCCCGTACAATCATTAG 58.662 37.037 0.00 0.00 0.00 1.73
2257 3979 1.452110 TTGGCGACATCAATGTGGAG 58.548 50.000 9.04 0.00 41.95 3.86
2258 3980 1.811965 CTTTGGCGACATCAATGTGGA 59.188 47.619 9.04 0.00 41.95 4.02
2259 3981 1.733389 GCTTTGGCGACATCAATGTGG 60.733 52.381 0.00 0.35 41.95 4.17
2260 3982 1.068402 TGCTTTGGCGACATCAATGTG 60.068 47.619 0.00 0.00 42.32 3.21
2261 3983 1.246649 TGCTTTGGCGACATCAATGT 58.753 45.000 0.00 0.00 42.32 2.71
2262 3984 2.350899 TTGCTTTGGCGACATCAATG 57.649 45.000 0.00 0.00 42.32 2.82
2387 4109 2.042686 ACTGTTTGACTGCTCTGCAA 57.957 45.000 0.00 0.00 38.41 4.08
2394 4116 2.663879 CGAGCATGAACTGTTTGACTGC 60.664 50.000 0.00 2.41 0.00 4.40
2409 4131 4.977963 GCAATTTTGTATACATGCGAGCAT 59.022 37.500 12.14 4.52 37.08 3.79
2410 4132 4.142513 TGCAATTTTGTATACATGCGAGCA 60.143 37.500 19.19 16.94 36.62 4.26
2411 4133 4.350346 TGCAATTTTGTATACATGCGAGC 58.650 39.130 19.19 15.11 36.62 5.03
2437 4163 4.808414 AATCGACAGAATCAGAGTCCAA 57.192 40.909 0.00 0.00 0.00 3.53
2438 4164 7.767250 ATATAATCGACAGAATCAGAGTCCA 57.233 36.000 0.00 0.00 0.00 4.02
2472 4320 5.832060 AGCCCACTACAATATACTCGTACTT 59.168 40.000 0.00 0.00 0.00 2.24
2474 4322 5.472820 AGAGCCCACTACAATATACTCGTAC 59.527 44.000 0.00 0.00 0.00 3.67
2475 4323 5.628130 AGAGCCCACTACAATATACTCGTA 58.372 41.667 0.00 0.00 0.00 3.43
2476 4324 4.471548 AGAGCCCACTACAATATACTCGT 58.528 43.478 0.00 0.00 0.00 4.18
2477 4325 5.455056 AAGAGCCCACTACAATATACTCG 57.545 43.478 0.00 0.00 0.00 4.18
2517 4523 2.421388 GGCAACTGGGTATACATCAGCA 60.421 50.000 19.18 0.00 32.19 4.41
2562 4568 9.390795 GACACATATACAAATGCAATTCATCTC 57.609 33.333 0.00 0.00 33.67 2.75
2573 4579 6.072838 GCATCTGGAGGACACATATACAAATG 60.073 42.308 0.00 0.00 0.00 2.32
2598 4604 4.624882 GCATAATTGTAGATGCTCTCTCCG 59.375 45.833 4.05 0.00 44.15 4.63
2673 4679 4.065789 CGAGCTCCAAGGAGTAAAGTTTT 58.934 43.478 16.94 0.00 43.70 2.43


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

AutoCloner maintained by Alex Coulton.