Multiple sequence alignment - TraesCS4A01G194800

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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 TraesCS4A01G194800 chr4A 100.000 3350 0 0 1 3350 476978044 476981393 0.000000e+00 6187
1 TraesCS4A01G194800 chr4B 94.580 2657 80 21 325 2942 141429626 141426995 0.000000e+00 4050
2 TraesCS4A01G194800 chr4B 90.974 421 29 6 2938 3350 141426755 141426336 2.920000e-155 558
3 TraesCS4A01G194800 chr4B 86.624 314 33 5 19 324 141430002 141429690 4.140000e-89 339
4 TraesCS4A01G194800 chr4D 94.726 2522 80 13 325 2836 99163371 99160893 0.000000e+00 3871
5 TraesCS4A01G194800 chr4D 91.541 331 20 3 1 324 99163759 99163430 1.830000e-122 449
6 TraesCS4A01G194800 chr4D 93.802 242 12 3 3111 3350 99160569 99160329 8.840000e-96 361
7 TraesCS4A01G194800 chr4D 89.431 246 16 3 2877 3112 99160896 99160651 5.430000e-78 302
8 TraesCS4A01G194800 chr5D 85.403 1329 184 8 1007 2328 231352563 231351238 0.000000e+00 1371
9 TraesCS4A01G194800 chr5A 81.867 1671 249 38 677 2328 325931515 325933150 0.000000e+00 1358
10 TraesCS4A01G194800 chr5B 84.621 1320 178 12 1007 2319 275033524 275034825 0.000000e+00 1290


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 TraesCS4A01G194800 chr4A 476978044 476981393 3349 False 6187.00 6187 100.000 1 3350 1 chr4A.!!$F1 3349
1 TraesCS4A01G194800 chr4B 141426336 141430002 3666 True 1649.00 4050 90.726 19 3350 3 chr4B.!!$R1 3331
2 TraesCS4A01G194800 chr4D 99160329 99163759 3430 True 1245.75 3871 92.375 1 3350 4 chr4D.!!$R1 3349
3 TraesCS4A01G194800 chr5D 231351238 231352563 1325 True 1371.00 1371 85.403 1007 2328 1 chr5D.!!$R1 1321
4 TraesCS4A01G194800 chr5A 325931515 325933150 1635 False 1358.00 1358 81.867 677 2328 1 chr5A.!!$F1 1651
5 TraesCS4A01G194800 chr5B 275033524 275034825 1301 False 1290.00 1290 84.621 1007 2319 1 chr5B.!!$F1 1312

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
341 412 0.108756 GTACCACCGAGTTGCTCCTC 60.109 60.000 0.00 0.0 0.0 3.71 F
519 621 0.821711 AAACCACCGACCACCATGTG 60.822 55.000 0.00 0.0 0.0 3.21 F
2015 2121 1.270518 CCTGTCTGGCCTATTCATCCG 60.271 57.143 3.32 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 1975 0.798776 GAGGAGCATTTGTGGTGACG 59.201 55.000 0.00 0.00 0.00 4.35 R
2097 2203 1.137872 CTTACCCTGAGATTCAGCGCT 59.862 52.381 2.64 2.64 42.98 5.92 R
2990 3357 0.829333 TGCAAATTGTTGGCACCACT 59.171 45.000 0.00 0.00 35.10 4.00 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
79 80 1.092345 GGGCGAATCACTGGAGAAGC 61.092 60.000 0.00 0.00 0.00 3.86
94 95 2.420372 GAGAAGCAATTCTTTCCCGTCC 59.580 50.000 0.00 0.00 34.56 4.79
201 203 1.915228 CGGTTGGATGGATCTGGGT 59.085 57.895 0.00 0.00 0.00 4.51
244 250 7.012799 GCTCTTAGTTTTAGGATTGGAGGAATG 59.987 40.741 0.00 0.00 0.00 2.67
247 253 3.312736 TTTAGGATTGGAGGAATGGCC 57.687 47.619 0.00 0.00 0.00 5.36
249 255 1.529244 GGATTGGAGGAATGGCCCG 60.529 63.158 0.00 0.00 37.37 6.13
250 256 1.529244 GATTGGAGGAATGGCCCGG 60.529 63.158 0.00 0.00 37.37 5.73
264 270 0.171231 GCCCGGTTCTCTGCAAAATC 59.829 55.000 0.00 0.00 0.00 2.17
269 275 3.243367 CCGGTTCTCTGCAAAATCAAACA 60.243 43.478 0.00 0.00 0.00 2.83
271 277 4.383649 CGGTTCTCTGCAAAATCAAACATG 59.616 41.667 0.00 0.00 0.00 3.21
286 294 4.190772 CAAACATGTTTGGCCACTTTTCT 58.809 39.130 34.07 4.26 44.47 2.52
288 296 4.058721 ACATGTTTGGCCACTTTTCTTC 57.941 40.909 3.88 0.00 0.00 2.87
303 311 7.306167 CCACTTTTCTTCATGAATTTGTTGACG 60.306 37.037 8.96 0.00 34.24 4.35
319 327 4.445052 TGTTGACGGTGTTATGTTTCTACG 59.555 41.667 0.00 0.00 0.00 3.51
328 399 6.035327 GGTGTTATGTTTCTACGATGTACCAC 59.965 42.308 0.00 0.00 0.00 4.16
338 409 1.641577 GATGTACCACCGAGTTGCTC 58.358 55.000 0.00 0.00 0.00 4.26
341 412 0.108756 GTACCACCGAGTTGCTCCTC 60.109 60.000 0.00 0.00 0.00 3.71
365 436 3.274288 CCCTGACTTTTCTGCATACCTC 58.726 50.000 0.00 0.00 0.00 3.85
407 478 1.270550 GCACAAGTATGCAGCCTTGTT 59.729 47.619 23.77 11.78 46.82 2.83
408 479 2.923605 GCACAAGTATGCAGCCTTGTTG 60.924 50.000 23.77 19.91 46.82 3.33
423 499 7.814587 GCAGCCTTGTTGATTCTAAAGTAAAAT 59.185 33.333 0.00 0.00 0.00 1.82
469 571 1.871039 TGCTGTTTCTAGTTTGCCGTC 59.129 47.619 0.00 0.00 0.00 4.79
489 591 4.562394 CGTCTGCACAGAACAAATGTTTTT 59.438 37.500 1.05 0.00 39.48 1.94
519 621 0.821711 AAACCACCGACCACCATGTG 60.822 55.000 0.00 0.00 0.00 3.21
528 630 1.454479 CCACCATGTGCCTGATCCC 60.454 63.158 0.00 0.00 31.34 3.85
605 707 6.166279 TCTTCTGTATGCTCCAGTTGTTAAG 58.834 40.000 0.00 0.00 0.00 1.85
786 888 2.229792 AGAAGAAATTTCACCTGCGCA 58.770 42.857 19.99 10.98 0.00 6.09
891 993 2.139917 CCATCTAGACTCCGTCGAGAG 58.860 57.143 11.41 8.60 44.65 3.20
915 1017 6.426328 AGAAAGACATGAGAGTGTTGTTCATC 59.574 38.462 0.00 0.00 32.22 2.92
1092 1198 3.576550 GGAAAGGAACATTTGGCAAGGTA 59.423 43.478 0.00 0.00 0.00 3.08
1755 1861 4.978099 TCCAGAAGCTCTTGTTCAAGATT 58.022 39.130 14.37 8.07 0.00 2.40
1833 1939 2.228480 CCGGAAAGGTCCAAGGGGA 61.228 63.158 0.00 0.00 45.26 4.81
1869 1975 3.586100 GAGAGAACTCCCAGTGAGAAC 57.414 52.381 0.00 0.00 44.42 3.01
2015 2121 1.270518 CCTGTCTGGCCTATTCATCCG 60.271 57.143 3.32 0.00 0.00 4.18
2097 2203 3.181511 CGAAGCTGGAATATGTTGCGAAA 60.182 43.478 0.00 0.00 0.00 3.46
2334 2444 1.741770 GCACGGAGATGACCACCAC 60.742 63.158 0.00 0.00 0.00 4.16
2395 2505 0.034198 TGGTTCTGCGAATTCGTCCA 59.966 50.000 27.24 22.06 42.22 4.02
2482 2592 2.479566 TGAGGTGAGGCATTCTGTTC 57.520 50.000 0.00 0.00 0.00 3.18
2504 2614 3.250762 CGAGGCATTGTTGAGAAGTTGAA 59.749 43.478 0.00 0.00 0.00 2.69
2573 2683 5.948162 ACTGTCCTGTCATAATGCTCATTTT 59.052 36.000 0.00 0.00 32.50 1.82
2655 2765 8.849490 CCATAAACACATTTCTCAAAACATACG 58.151 33.333 0.00 0.00 0.00 3.06
2658 2768 5.675970 ACACATTTCTCAAAACATACGACG 58.324 37.500 0.00 0.00 0.00 5.12
2678 2793 3.000041 CGTATTAGCCAGCACTTGAACA 59.000 45.455 0.00 0.00 0.00 3.18
2707 2822 4.460382 TGATTTGCCATCTCTGGAAGAAAC 59.540 41.667 0.00 0.00 46.34 2.78
2854 2972 8.378115 TGAATATGTCCCATGGAAATTTCTTT 57.622 30.769 15.22 3.17 31.20 2.52
2898 3016 1.795768 TTAACAGAGGTTGCTCAGCG 58.204 50.000 0.00 0.00 37.88 5.18
2980 3347 5.977489 TTCAGTCTGATCCGAAAAGTAGA 57.023 39.130 2.68 0.00 0.00 2.59
2983 3350 6.755206 TCAGTCTGATCCGAAAAGTAGAAAA 58.245 36.000 0.00 0.00 0.00 2.29
2984 3351 7.386851 TCAGTCTGATCCGAAAAGTAGAAAAT 58.613 34.615 0.00 0.00 0.00 1.82
2985 3352 7.545965 TCAGTCTGATCCGAAAAGTAGAAAATC 59.454 37.037 0.00 0.00 0.00 2.17
2989 3356 7.659799 TCTGATCCGAAAAGTAGAAAATCAACA 59.340 33.333 0.00 0.00 0.00 3.33
2990 3357 8.160521 TGATCCGAAAAGTAGAAAATCAACAA 57.839 30.769 0.00 0.00 0.00 2.83
2993 3360 7.414436 TCCGAAAAGTAGAAAATCAACAAGTG 58.586 34.615 0.00 0.00 0.00 3.16
2994 3361 6.636850 CCGAAAAGTAGAAAATCAACAAGTGG 59.363 38.462 0.00 0.00 0.00 4.00
3047 3419 6.334989 TCACCGAGAAAGCGAAATAATAGAA 58.665 36.000 0.00 0.00 0.00 2.10
3154 3610 0.461548 TGCTGGCAGGTTCGATCTAG 59.538 55.000 17.64 0.00 0.00 2.43
3316 3774 7.795047 TGAGCTAACCAATCATAGATTTCTCA 58.205 34.615 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 3.609853 TCTGATGGACGGGAAAGAATTG 58.390 45.455 0.00 0.00 0.00 2.32
94 95 5.123502 GCTCATATATGCCCAAACTCTGATG 59.876 44.000 7.92 0.00 0.00 3.07
201 203 8.335532 ACTAAGAGCATAACAACTTGCAAATA 57.664 30.769 0.00 0.00 41.35 1.40
244 250 1.250840 ATTTTGCAGAGAACCGGGCC 61.251 55.000 6.32 0.00 0.00 5.80
247 253 3.243367 TGTTTGATTTTGCAGAGAACCGG 60.243 43.478 0.00 0.00 0.00 5.28
249 255 5.291971 ACATGTTTGATTTTGCAGAGAACC 58.708 37.500 0.00 0.00 0.00 3.62
250 256 6.833342 AACATGTTTGATTTTGCAGAGAAC 57.167 33.333 4.92 0.00 0.00 3.01
264 270 4.190772 AGAAAAGTGGCCAAACATGTTTG 58.809 39.130 34.51 34.51 46.93 2.93
269 275 4.344679 TCATGAAGAAAAGTGGCCAAACAT 59.655 37.500 7.24 1.77 0.00 2.71
271 277 4.320608 TCATGAAGAAAAGTGGCCAAAC 57.679 40.909 7.24 0.00 0.00 2.93
279 285 6.697019 CCGTCAACAAATTCATGAAGAAAAGT 59.303 34.615 14.54 5.30 40.22 2.66
280 286 6.697019 ACCGTCAACAAATTCATGAAGAAAAG 59.303 34.615 14.54 4.70 40.22 2.27
286 294 4.909696 ACACCGTCAACAAATTCATGAA 57.090 36.364 11.26 11.26 0.00 2.57
288 296 6.148948 ACATAACACCGTCAACAAATTCATG 58.851 36.000 0.00 0.00 0.00 3.07
303 311 6.035327 GTGGTACATCGTAGAAACATAACACC 59.965 42.308 0.00 0.00 44.52 4.16
319 327 1.641577 GAGCAACTCGGTGGTACATC 58.358 55.000 0.00 0.00 44.52 3.06
338 409 1.882623 GCAGAAAAGTCAGGGTTGAGG 59.117 52.381 0.00 0.00 32.98 3.86
341 412 3.191371 GGTATGCAGAAAAGTCAGGGTTG 59.809 47.826 0.00 0.00 0.00 3.77
345 416 3.937706 CAGAGGTATGCAGAAAAGTCAGG 59.062 47.826 0.00 0.00 0.00 3.86
365 436 5.181811 TGCATCCAGTTGAGAATGTAAACAG 59.818 40.000 0.00 0.00 0.00 3.16
427 503 8.869897 CAGCAGAAAACGTATCTGTAATTCTTA 58.130 33.333 24.11 0.00 44.88 2.10
451 527 2.096218 GCAGACGGCAAACTAGAAACAG 60.096 50.000 0.00 0.00 43.97 3.16
489 591 4.225492 TGGTCGGTGGTTTATATGAAGGAA 59.775 41.667 0.00 0.00 0.00 3.36
491 593 3.875134 GTGGTCGGTGGTTTATATGAAGG 59.125 47.826 0.00 0.00 0.00 3.46
492 594 3.875134 GGTGGTCGGTGGTTTATATGAAG 59.125 47.826 0.00 0.00 0.00 3.02
528 630 7.602517 ATCTTTAGAGGAAACAAATCTGACG 57.397 36.000 0.00 0.00 0.00 4.35
605 707 9.605955 GAAATAACAAAACATTTATTGGTTGGC 57.394 29.630 0.00 0.00 34.73 4.52
666 768 6.864342 AGAAATCTTCAGATTCTGCAATTGG 58.136 36.000 8.89 0.00 43.41 3.16
891 993 5.991328 TGAACAACACTCTCATGTCTTTC 57.009 39.130 0.00 0.00 30.55 2.62
915 1017 4.985538 AAGGTAGTCTTGATCCACTACG 57.014 45.455 15.37 0.00 44.09 3.51
1833 1939 1.072965 CTCTCCTTCACTGCAAGGGTT 59.927 52.381 2.34 0.00 43.07 4.11
1869 1975 0.798776 GAGGAGCATTTGTGGTGACG 59.201 55.000 0.00 0.00 0.00 4.35
2015 2121 2.094234 GTCTCCTTTCTGCACTCCTCTC 60.094 54.545 0.00 0.00 0.00 3.20
2097 2203 1.137872 CTTACCCTGAGATTCAGCGCT 59.862 52.381 2.64 2.64 42.98 5.92
2334 2444 3.265791 CAAAACCTACTCTAGCTGCTGG 58.734 50.000 13.43 9.98 0.00 4.85
2395 2505 2.039084 AGGATCGTTCCAGCTGAAAACT 59.961 45.455 17.39 4.47 45.30 2.66
2482 2592 2.807967 TCAACTTCTCAACAATGCCTCG 59.192 45.455 0.00 0.00 0.00 4.63
2550 2660 6.263344 CAAAATGAGCATTATGACAGGACAG 58.737 40.000 0.00 0.00 0.00 3.51
2573 2683 4.713814 TGGCATAGCATTTAATTTCACCCA 59.286 37.500 0.00 0.00 0.00 4.51
2655 2765 2.888594 TCAAGTGCTGGCTAATACGTC 58.111 47.619 0.00 0.00 0.00 4.34
2658 2768 5.567138 AATGTTCAAGTGCTGGCTAATAC 57.433 39.130 0.00 0.00 0.00 1.89
2678 2793 4.773674 TCCAGAGATGGCAAATCACAAAAT 59.226 37.500 0.00 0.00 0.00 1.82
2898 3016 5.356751 TGTGCATTGGTTATTGAGTATGACC 59.643 40.000 0.00 0.00 41.98 4.02
2980 3347 3.055530 TGTTGGCACCACTTGTTGATTTT 60.056 39.130 0.00 0.00 0.00 1.82
2983 3350 1.774110 TGTTGGCACCACTTGTTGAT 58.226 45.000 0.00 0.00 0.00 2.57
2984 3351 1.550327 TTGTTGGCACCACTTGTTGA 58.450 45.000 0.00 0.00 0.00 3.18
2985 3352 2.600470 ATTGTTGGCACCACTTGTTG 57.400 45.000 0.00 0.00 0.00 3.33
2989 3356 1.209019 TGCAAATTGTTGGCACCACTT 59.791 42.857 0.00 0.00 35.10 3.16
2990 3357 0.829333 TGCAAATTGTTGGCACCACT 59.171 45.000 0.00 0.00 35.10 4.00
2993 3360 1.340889 TCTCTGCAAATTGTTGGCACC 59.659 47.619 0.00 0.00 35.10 5.01
2994 3361 2.669364 CTCTCTGCAAATTGTTGGCAC 58.331 47.619 0.00 0.00 35.10 5.01
3116 3572 3.555956 AGCAAGTGAATTTATACGCTCGG 59.444 43.478 0.00 0.00 0.00 4.63
3118 3574 4.786609 GCCAGCAAGTGAATTTATACGCTC 60.787 45.833 0.00 0.00 0.00 5.03
3154 3610 6.876257 ACTCACAGTGGAGTTCAGATATTTTC 59.124 38.462 0.00 0.00 45.59 2.29
3201 3658 1.203376 TGTTGGACCTATCCCCTGTGA 60.203 52.381 0.00 0.00 45.59 3.58
3306 3764 6.755206 TCCTTCAACGACTTTGAGAAATCTA 58.245 36.000 0.00 0.00 45.22 1.98
3309 3767 7.979444 TTATCCTTCAACGACTTTGAGAAAT 57.021 32.000 0.00 0.00 45.22 2.17
3311 3769 6.990349 AGTTTATCCTTCAACGACTTTGAGAA 59.010 34.615 0.00 0.00 45.22 2.87
3313 3771 6.647067 AGAGTTTATCCTTCAACGACTTTGAG 59.353 38.462 0.00 0.00 45.22 3.02
3316 3774 7.803279 AAAGAGTTTATCCTTCAACGACTTT 57.197 32.000 0.00 0.00 33.70 2.66


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

AutoCloner maintained by Alex Coulton.