Multiple sequence alignment - TraesCS3D01G158800

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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 TraesCS3D01G158800 chr3D 100.000 3303 0 0 1 3303 127656598 127653296 0.000000e+00 6100
1 TraesCS3D01G158800 chr3A 92.241 2539 113 39 1 2479 138287021 138284507 0.000000e+00 3520
2 TraesCS3D01G158800 chr3A 88.098 731 42 23 2555 3250 138284368 138283648 0.000000e+00 826
3 TraesCS3D01G158800 chr3A 95.238 63 3 0 2475 2537 138284482 138284420 2.100000e-17 100
4 TraesCS3D01G158800 chr3B 91.155 2510 118 46 1 2479 181678534 181676098 0.000000e+00 3310
5 TraesCS3D01G158800 chr3B 94.040 604 23 7 2534 3134 181675988 181675395 0.000000e+00 904
6 TraesCS3D01G158800 chr3B 100.000 60 0 0 2475 2534 181676073 181676014 9.690000e-21 111


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 TraesCS3D01G158800 chr3D 127653296 127656598 3302 True 6100.000000 6100 100.000 1 3303 1 chr3D.!!$R1 3302
1 TraesCS3D01G158800 chr3A 138283648 138287021 3373 True 1482.000000 3520 91.859 1 3250 3 chr3A.!!$R1 3249
2 TraesCS3D01G158800 chr3B 181675395 181678534 3139 True 1441.666667 3310 95.065 1 3134 3 chr3B.!!$R1 3133

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
975 1038 0.251832 GGAGTGAGGGAGTGGAGTGA 60.252 60.0 0.0 0.0 0.0 3.41 F
977 1040 0.485099 AGTGAGGGAGTGGAGTGAGT 59.515 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2264 1.007387 CGGGTTGCAAGAAAGCACC 60.007 57.895 0.0 0.0 45.61 5.01 R
2731 2883 1.153745 CCTTTCTCCGTCCTGCTCG 60.154 63.158 0.0 0.0 0.00 5.03 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
98 99 1.335496 CGCGGGTTCTTTCAAGGAAAA 59.665 47.619 0.00 0.00 30.84 2.29
239 241 1.216710 CTCGTCTGACAGAAGCCCC 59.783 63.158 12.95 0.00 0.00 5.80
240 242 1.228894 TCGTCTGACAGAAGCCCCT 60.229 57.895 12.95 0.00 0.00 4.79
241 243 1.216710 CGTCTGACAGAAGCCCCTC 59.783 63.158 6.76 0.00 0.00 4.30
242 244 1.216710 GTCTGACAGAAGCCCCTCG 59.783 63.158 6.76 0.00 0.00 4.63
243 245 2.125350 CTGACAGAAGCCCCTCGC 60.125 66.667 0.00 0.00 37.98 5.03
261 263 1.855360 CGCTGCTCTCGACTTTTATCC 59.145 52.381 0.00 0.00 0.00 2.59
273 275 6.749139 TCGACTTTTATCCGATCAGATTCAT 58.251 36.000 0.00 0.00 0.00 2.57
503 538 9.909644 TCGATTAGATAAAGCTAGATTTACCAC 57.090 33.333 15.04 9.85 0.00 4.16
513 548 1.977594 GATTTACCACCCGCAGCACG 61.978 60.000 0.00 0.00 43.15 5.34
547 585 2.049063 AGCGAGGACACGAAGCAC 60.049 61.111 0.00 0.00 35.09 4.40
552 590 1.670087 CGAGGACACGAAGCACTTCAT 60.670 52.381 10.78 0.00 39.46 2.57
584 622 1.237285 GCAGCCAAAGTCCACGTCAT 61.237 55.000 0.00 0.00 0.00 3.06
588 626 1.069227 GCCAAAGTCCACGTCATTCAC 60.069 52.381 0.00 0.00 0.00 3.18
653 691 4.394920 TCTGGTCACTCACAGTTTCAAAAC 59.605 41.667 0.00 0.00 39.17 2.43
708 746 2.682136 TGGTTCGATCCTGGCGGA 60.682 61.111 13.55 0.00 45.16 5.54
889 940 0.252467 ACCTTGTCCTCCTCCTCCTG 60.252 60.000 0.00 0.00 0.00 3.86
909 960 4.847255 CGAAAGGCAAAAGCCTCG 57.153 55.556 9.77 6.62 39.63 4.63
975 1038 0.251832 GGAGTGAGGGAGTGGAGTGA 60.252 60.000 0.00 0.00 0.00 3.41
977 1040 0.485099 AGTGAGGGAGTGGAGTGAGT 59.515 55.000 0.00 0.00 0.00 3.41
978 1041 0.605589 GTGAGGGAGTGGAGTGAGTG 59.394 60.000 0.00 0.00 0.00 3.51
986 1049 1.979155 TGGAGTGAGTGAGCTCGGG 60.979 63.158 9.64 0.00 44.48 5.14
1548 1611 3.774702 GAGGACGCGCCGTTTGTC 61.775 66.667 5.73 2.30 41.37 3.18
2156 2219 1.562672 CCCACTCATTTCCGTCCCCT 61.563 60.000 0.00 0.00 0.00 4.79
2193 2262 5.386060 TCAGGTCGATAGGTGATAACATCT 58.614 41.667 0.00 0.00 40.84 2.90
2195 2264 4.456222 AGGTCGATAGGTGATAACATCTCG 59.544 45.833 0.00 0.00 38.53 4.04
2196 2265 4.379603 GGTCGATAGGTGATAACATCTCGG 60.380 50.000 3.19 0.00 38.53 4.63
2205 2274 4.631813 GTGATAACATCTCGGTGCTTTCTT 59.368 41.667 0.00 0.00 0.00 2.52
2206 2275 4.631377 TGATAACATCTCGGTGCTTTCTTG 59.369 41.667 0.00 0.00 0.00 3.02
2214 2286 1.661509 GTGCTTTCTTGCAACCCGC 60.662 57.895 0.00 0.00 45.12 6.13
2420 2495 4.836825 AGTATCATGATGCCGGATTAAGG 58.163 43.478 18.72 0.00 0.00 2.69
2451 2538 4.429108 GCGCTCTCTTCTCTTGTCTTAAT 58.571 43.478 0.00 0.00 0.00 1.40
2623 2775 1.895280 GCTGAACAGCGAGAGTGCAC 61.895 60.000 9.40 9.40 45.29 4.57
2730 2882 2.452505 GAATTCGGGGAAAACCATGGA 58.547 47.619 21.47 0.00 42.91 3.41
2731 2883 1.847328 ATTCGGGGAAAACCATGGAC 58.153 50.000 21.47 6.60 42.91 4.02
2732 2884 0.606944 TTCGGGGAAAACCATGGACG 60.607 55.000 21.47 10.64 42.91 4.79
2813 2966 2.358247 GCCCGAGCTTTGTTCCGA 60.358 61.111 0.00 0.00 35.50 4.55
3127 3304 2.203070 CCGCGGCTGGCTATCTTT 60.203 61.111 14.67 0.00 40.44 2.52
3134 3327 0.938008 GCTGGCTATCTTTACGTGGC 59.062 55.000 0.00 0.00 0.00 5.01
3258 3455 3.006672 CTGGTCACCAGTTCACCAC 57.993 57.895 16.65 0.00 45.82 4.16
3259 3456 0.469917 CTGGTCACCAGTTCACCACT 59.530 55.000 16.65 0.00 45.82 4.00
3260 3457 0.468226 TGGTCACCAGTTCACCACTC 59.532 55.000 0.00 0.00 35.16 3.51
3261 3458 0.600255 GGTCACCAGTTCACCACTCG 60.600 60.000 0.00 0.00 30.92 4.18
3262 3459 1.069090 TCACCAGTTCACCACTCGC 59.931 57.895 0.00 0.00 30.92 5.03
3263 3460 1.069765 CACCAGTTCACCACTCGCT 59.930 57.895 0.00 0.00 30.92 4.93
3264 3461 0.946221 CACCAGTTCACCACTCGCTC 60.946 60.000 0.00 0.00 30.92 5.03
3265 3462 1.734477 CCAGTTCACCACTCGCTCG 60.734 63.158 0.00 0.00 30.92 5.03
3266 3463 1.007271 CAGTTCACCACTCGCTCGT 60.007 57.895 0.00 0.00 30.92 4.18
3267 3464 1.007271 AGTTCACCACTCGCTCGTG 60.007 57.895 0.00 0.00 34.71 4.35
3268 3465 2.355837 TTCACCACTCGCTCGTGC 60.356 61.111 0.00 0.00 33.60 5.34
3269 3466 3.145422 TTCACCACTCGCTCGTGCA 62.145 57.895 10.43 0.00 39.64 4.57
3270 3467 2.433145 CACCACTCGCTCGTGCAT 60.433 61.111 10.43 0.00 39.64 3.96
3271 3468 2.433145 ACCACTCGCTCGTGCATG 60.433 61.111 10.43 0.00 39.64 4.06
3272 3469 3.857854 CCACTCGCTCGTGCATGC 61.858 66.667 11.82 11.82 39.64 4.06
3273 3470 3.857854 CACTCGCTCGTGCATGCC 61.858 66.667 16.68 5.63 39.64 4.40
3274 3471 4.377708 ACTCGCTCGTGCATGCCA 62.378 61.111 16.68 0.00 39.64 4.92
3275 3472 2.893895 CTCGCTCGTGCATGCCAT 60.894 61.111 16.68 0.00 39.64 4.40
3276 3473 2.879070 CTCGCTCGTGCATGCCATC 61.879 63.158 16.68 4.90 39.64 3.51
3277 3474 2.893895 CGCTCGTGCATGCCATCT 60.894 61.111 16.68 0.00 39.64 2.90
3278 3475 2.879070 CGCTCGTGCATGCCATCTC 61.879 63.158 16.68 0.63 39.64 2.75
3279 3476 1.523258 GCTCGTGCATGCCATCTCT 60.523 57.895 16.68 0.00 39.41 3.10
3280 3477 1.094073 GCTCGTGCATGCCATCTCTT 61.094 55.000 16.68 0.00 39.41 2.85
3281 3478 0.656259 CTCGTGCATGCCATCTCTTG 59.344 55.000 16.68 0.00 0.00 3.02
3289 3486 2.892425 CCATCTCTTGGCCGCGAC 60.892 66.667 8.23 0.00 39.09 5.19
3290 3487 3.257561 CATCTCTTGGCCGCGACG 61.258 66.667 8.23 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 5.287226 GCAATCATGATGTTCCTTCAATCC 58.713 41.667 9.46 0.00 0.00 3.01
239 241 2.264109 TAAAAGTCGAGAGCAGCGAG 57.736 50.000 0.00 0.00 38.59 5.03
240 242 2.479730 GGATAAAAGTCGAGAGCAGCGA 60.480 50.000 0.00 0.00 35.08 4.93
241 243 1.855360 GGATAAAAGTCGAGAGCAGCG 59.145 52.381 0.00 0.00 0.00 5.18
242 244 1.855360 CGGATAAAAGTCGAGAGCAGC 59.145 52.381 0.00 0.00 0.00 5.25
243 245 3.422417 TCGGATAAAAGTCGAGAGCAG 57.578 47.619 0.00 0.00 0.00 4.24
244 246 3.380320 TGATCGGATAAAAGTCGAGAGCA 59.620 43.478 0.00 0.00 36.34 4.26
245 247 3.966154 TGATCGGATAAAAGTCGAGAGC 58.034 45.455 0.00 0.00 36.34 4.09
246 248 5.425577 TCTGATCGGATAAAAGTCGAGAG 57.574 43.478 0.00 0.00 36.34 3.20
247 249 6.039382 TGAATCTGATCGGATAAAAGTCGAGA 59.961 38.462 17.46 0.00 36.34 4.04
248 250 6.209361 TGAATCTGATCGGATAAAAGTCGAG 58.791 40.000 17.46 0.00 36.34 4.04
261 263 4.212636 TGCATGCTACAATGAATCTGATCG 59.787 41.667 20.33 0.00 0.00 3.69
273 275 2.635714 CACAGGAGATGCATGCTACAA 58.364 47.619 20.33 0.00 0.00 2.41
353 374 5.994668 GCTTCTTCTTCTTCCTCAGAGAAAA 59.005 40.000 0.00 0.00 33.10 2.29
547 585 0.524816 GCACATGCTCGGCAATGAAG 60.525 55.000 13.81 8.21 43.62 3.02
552 590 3.740397 GCTGCACATGCTCGGCAA 61.740 61.111 12.23 0.00 43.62 4.52
653 691 7.412891 GCCACCGGATTTCTTTGAATTTATTTG 60.413 37.037 9.46 0.00 0.00 2.32
865 916 0.836400 GGAGGAGGACAAGGTGGTGA 60.836 60.000 0.00 0.00 0.00 4.02
899 950 0.166814 CTCTTTCGGCGAGGCTTTTG 59.833 55.000 10.46 0.00 0.00 2.44
909 960 6.669278 ACTCAAATAAAAAGACTCTTTCGGC 58.331 36.000 4.46 0.00 0.00 5.54
986 1049 0.615331 TTCCATCACACCCAGAGAGC 59.385 55.000 0.00 0.00 0.00 4.09
1221 1284 1.258676 AGTTGAACTCGACCCTCTCC 58.741 55.000 0.00 0.00 0.00 3.71
1304 1367 0.389166 GCCGTTCTCAGTCTCACTGG 60.389 60.000 3.86 0.00 45.94 4.00
1484 1547 1.754234 GTCTTGGGCGCCATGGAAT 60.754 57.895 30.85 0.00 31.53 3.01
1489 1552 2.746277 GTTCGTCTTGGGCGCCAT 60.746 61.111 30.85 0.00 31.53 4.40
1509 1572 1.702957 ACCCGGAACTTGATCAGGAAA 59.297 47.619 12.40 0.00 36.87 3.13
1533 1596 3.774702 GAGACAAACGGCGCGTCC 61.775 66.667 17.60 7.39 39.99 4.79
1674 1737 1.004277 AGCATAACCTCCTTGGCGAAA 59.996 47.619 0.00 0.00 40.22 3.46
1872 1935 2.915659 ACGACGGGCTGTGGAAGA 60.916 61.111 15.80 0.00 0.00 2.87
1874 1937 4.351938 CGACGACGGGCTGTGGAA 62.352 66.667 15.80 0.00 35.72 3.53
2118 2181 1.534729 GGCTTGTGGTACCTTTGGAG 58.465 55.000 14.36 5.35 0.00 3.86
2182 2251 4.184629 AGAAAGCACCGAGATGTTATCAC 58.815 43.478 0.00 0.00 0.00 3.06
2193 2262 1.452145 GGGTTGCAAGAAAGCACCGA 61.452 55.000 0.00 0.00 45.61 4.69
2195 2264 1.007387 CGGGTTGCAAGAAAGCACC 60.007 57.895 0.00 0.00 45.61 5.01
2196 2265 1.661509 GCGGGTTGCAAGAAAGCAC 60.662 57.895 0.00 0.00 45.61 4.40
2420 2495 2.535688 GAAGAGAGCGCGCACGTTTC 62.536 60.000 35.10 27.71 42.83 2.78
2547 2691 7.330208 GTGAAGTTCAAATGAAATGCTAGCAAT 59.670 33.333 23.54 11.27 35.58 3.56
2616 2768 1.227556 AAGTCACACCCGTGCACTC 60.228 57.895 16.19 0.00 43.28 3.51
2623 2775 2.031191 GTGTTTACACAAGTCACACCCG 59.969 50.000 8.09 0.00 45.75 5.28
2730 2882 1.587054 CTTTCTCCGTCCTGCTCGT 59.413 57.895 0.00 0.00 0.00 4.18
2731 2883 1.153745 CCTTTCTCCGTCCTGCTCG 60.154 63.158 0.00 0.00 0.00 5.03
2732 2884 1.448717 GCCTTTCTCCGTCCTGCTC 60.449 63.158 0.00 0.00 0.00 4.26
2773 2925 4.166011 GTGCGTGCAGAATCGGCC 62.166 66.667 2.45 0.00 0.00 6.13
2908 3063 1.293498 GAGCGGACAGAAAGCCAGA 59.707 57.895 0.00 0.00 0.00 3.86
3127 3304 2.344500 CCGGGACAAAGCCACGTA 59.656 61.111 0.00 0.00 0.00 3.57
3250 3447 2.658707 GCACGAGCGAGTGGTGAAC 61.659 63.158 14.66 0.00 42.09 3.18
3251 3448 2.355837 GCACGAGCGAGTGGTGAA 60.356 61.111 14.66 0.00 42.09 3.18
3252 3449 2.931068 ATGCACGAGCGAGTGGTGA 61.931 57.895 14.66 0.00 46.23 4.02
3253 3450 2.433145 ATGCACGAGCGAGTGGTG 60.433 61.111 14.66 4.46 46.23 4.17
3254 3451 2.433145 CATGCACGAGCGAGTGGT 60.433 61.111 14.66 0.00 46.23 4.16
3255 3452 3.857854 GCATGCACGAGCGAGTGG 61.858 66.667 14.21 2.02 46.23 4.00
3256 3453 3.857854 GGCATGCACGAGCGAGTG 61.858 66.667 21.36 9.73 46.23 3.51
3257 3454 3.670637 ATGGCATGCACGAGCGAGT 62.671 57.895 21.36 0.00 46.23 4.18
3258 3455 2.879070 GATGGCATGCACGAGCGAG 61.879 63.158 21.36 0.00 46.23 5.03
3259 3456 2.891936 GATGGCATGCACGAGCGA 60.892 61.111 21.36 0.00 46.23 4.93
3260 3457 2.879070 GAGATGGCATGCACGAGCG 61.879 63.158 21.36 0.00 46.23 5.03
3261 3458 1.094073 AAGAGATGGCATGCACGAGC 61.094 55.000 21.36 5.34 42.57 5.03
3262 3459 0.656259 CAAGAGATGGCATGCACGAG 59.344 55.000 21.36 0.00 0.00 4.18
3263 3460 0.745486 CCAAGAGATGGCATGCACGA 60.745 55.000 21.36 2.52 43.80 4.35
3264 3461 1.725665 CCAAGAGATGGCATGCACG 59.274 57.895 21.36 0.00 43.80 5.34
3273 3470 3.257561 CGTCGCGGCCAAGAGATG 61.258 66.667 4.51 0.00 0.00 2.90
3274 3471 4.514577 CCGTCGCGGCCAAGAGAT 62.515 66.667 4.51 0.00 41.17 2.75


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

AutoCloner maintained by Alex Coulton.