Multiple sequence alignment - TraesCS4D01G256600

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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 TraesCS4D01G256600 chr4D 100.000 3470 0 0 1 3470 426266278 426262809 0 6408
1 TraesCS4D01G256600 chr6D 97.023 3426 79 14 56 3470 249264292 249267705 0 5740
2 TraesCS4D01G256600 chr1D 96.462 3477 103 10 3 3470 285939050 285942515 0 5722
3 TraesCS4D01G256600 chr7D 96.725 3420 87 9 56 3470 387292997 387296396 0 5672
4 TraesCS4D01G256600 chr3A 95.115 3480 145 14 1 3470 204342959 204339495 0 5461
5 TraesCS4D01G256600 chr3A 94.911 3478 150 11 1 3470 204308730 204305272 0 5417
6 TraesCS4D01G256600 chr3A 94.473 3492 151 19 1 3470 665589538 665593009 0 5341
7 TraesCS4D01G256600 chr3A 94.022 3496 168 30 1 3470 174072939 174069459 0 5260
8 TraesCS4D01G256600 chr3A 93.971 3500 153 22 1 3470 240521753 240518282 0 5241
9 TraesCS4D01G256600 chr3D 96.785 3235 95 6 3 3233 254419840 254416611 0 5389
10 TraesCS4D01G256600 chr7A 94.578 3486 145 26 1 3470 421609606 421613063 0 5350
11 TraesCS4D01G256600 chr6A 94.015 3492 167 26 1 3470 118303832 118307303 0 5252
12 TraesCS4D01G256600 chr2A 93.614 3492 151 20 1 3470 442321796 442325237 0 5147


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 TraesCS4D01G256600 chr4D 426262809 426266278 3469 True 6408 6408 100.000 1 3470 1 chr4D.!!$R1 3469
1 TraesCS4D01G256600 chr6D 249264292 249267705 3413 False 5740 5740 97.023 56 3470 1 chr6D.!!$F1 3414
2 TraesCS4D01G256600 chr1D 285939050 285942515 3465 False 5722 5722 96.462 3 3470 1 chr1D.!!$F1 3467
3 TraesCS4D01G256600 chr7D 387292997 387296396 3399 False 5672 5672 96.725 56 3470 1 chr7D.!!$F1 3414
4 TraesCS4D01G256600 chr3A 204339495 204342959 3464 True 5461 5461 95.115 1 3470 1 chr3A.!!$R3 3469
5 TraesCS4D01G256600 chr3A 204305272 204308730 3458 True 5417 5417 94.911 1 3470 1 chr3A.!!$R2 3469
6 TraesCS4D01G256600 chr3A 665589538 665593009 3471 False 5341 5341 94.473 1 3470 1 chr3A.!!$F1 3469
7 TraesCS4D01G256600 chr3A 174069459 174072939 3480 True 5260 5260 94.022 1 3470 1 chr3A.!!$R1 3469
8 TraesCS4D01G256600 chr3A 240518282 240521753 3471 True 5241 5241 93.971 1 3470 1 chr3A.!!$R4 3469
9 TraesCS4D01G256600 chr3D 254416611 254419840 3229 True 5389 5389 96.785 3 3233 1 chr3D.!!$R1 3230
10 TraesCS4D01G256600 chr7A 421609606 421613063 3457 False 5350 5350 94.578 1 3470 1 chr7A.!!$F1 3469
11 TraesCS4D01G256600 chr6A 118303832 118307303 3471 False 5252 5252 94.015 1 3470 1 chr6A.!!$F1 3469
12 TraesCS4D01G256600 chr2A 442321796 442325237 3441 False 5147 5147 93.614 1 3470 1 chr2A.!!$F1 3469

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
238 244 4.537135 ATCTGTACACACCTCAACGAAT 57.463 40.909 0.00 0.00 0.00 3.34 F
1018 1040 1.550130 GATGGTGGAGGAACCGTCCA 61.550 60.000 4.46 4.46 46.49 4.02 F
2242 2289 0.174845 CGACTCCTTGGCCGATGTTA 59.825 55.000 0.00 0.00 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1201 1.145819 GAGCCTGCTCATCACCTCC 59.854 63.158 14.07 0.0 42.31 4.30 R
2268 2315 1.762370 TCCATCTTCTTCATGCCGCTA 59.238 47.619 0.00 0.0 0.00 4.26 R
3156 3230 6.456501 ACTTGCCTTACAGACTAAGTTGTAG 58.543 40.000 0.00 0.0 31.95 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
80 84 9.646427 ACAAGTTCAACTACTAAAATGCAAAAA 57.354 25.926 0.00 0.00 0.00 1.94
238 244 4.537135 ATCTGTACACACCTCAACGAAT 57.463 40.909 0.00 0.00 0.00 3.34
700 714 6.785337 TTAGCAGGTCATAAGTACAGCTTA 57.215 37.500 0.00 0.00 43.13 3.09
1018 1040 1.550130 GATGGTGGAGGAACCGTCCA 61.550 60.000 4.46 4.46 46.49 4.02
1130 1152 2.203788 AGGGGTTGAGCTCCACGA 60.204 61.111 12.15 0.00 41.40 4.35
1175 1197 1.672356 CCAGCGAACCAGACAAGGG 60.672 63.158 0.00 0.00 0.00 3.95
1179 1201 1.738099 CGAACCAGACAAGGGCGAG 60.738 63.158 0.00 0.00 34.01 5.03
1385 1407 8.534333 TTGTTCATTCATCTGTTGTACTAGTC 57.466 34.615 0.00 0.00 0.00 2.59
1386 1408 7.896811 TGTTCATTCATCTGTTGTACTAGTCT 58.103 34.615 0.00 0.00 0.00 3.24
1486 1510 6.864560 CATGTTTCTCAACTTACATGCATG 57.135 37.500 25.09 25.09 40.73 4.06
1946 1989 8.219868 TGGACAACATTCATCCATGACTTATAT 58.780 33.333 0.00 0.00 37.60 0.86
2188 2231 4.500205 CCAACAACTTCATTGACATGCAGT 60.500 41.667 0.00 0.00 38.40 4.40
2242 2289 0.174845 CGACTCCTTGGCCGATGTTA 59.825 55.000 0.00 0.00 0.00 2.41
2268 2315 2.289444 CGGCGTAATCCACCCATTCTAT 60.289 50.000 0.00 0.00 0.00 1.98
2485 2538 3.317430 GGGATGAAGATGCATGAAAGTCC 59.683 47.826 2.46 6.20 0.00 3.85
2576 2629 6.018994 CGTTATGTTGAACCAGCTACCTTATC 60.019 42.308 0.00 0.00 0.00 1.75
2909 2978 1.968493 ACTAAGTTTCAGCCGAGGACA 59.032 47.619 0.00 0.00 0.00 4.02
2910 2979 2.367567 ACTAAGTTTCAGCCGAGGACAA 59.632 45.455 0.00 0.00 0.00 3.18
2911 2980 1.594331 AAGTTTCAGCCGAGGACAAC 58.406 50.000 0.00 0.00 0.00 3.32
2912 2981 0.468226 AGTTTCAGCCGAGGACAACA 59.532 50.000 0.00 0.00 0.00 3.33
2913 2982 1.072331 AGTTTCAGCCGAGGACAACAT 59.928 47.619 0.00 0.00 0.00 2.71
2914 2983 1.880027 GTTTCAGCCGAGGACAACATT 59.120 47.619 0.00 0.00 0.00 2.71
2915 2984 1.808411 TTCAGCCGAGGACAACATTC 58.192 50.000 0.00 0.00 0.00 2.67
2916 2985 0.684535 TCAGCCGAGGACAACATTCA 59.315 50.000 0.00 0.00 0.00 2.57
2968 3037 9.726438 AGTTAGAAATTTACTGAGTACTGCAAT 57.274 29.630 0.00 0.00 0.00 3.56
3053 3123 2.678836 TGGTACACTTGAACAAACGGTG 59.321 45.455 0.00 0.00 0.00 4.94
3156 3230 9.204570 ACAGTAATAGTACAACTGAAATGTCAC 57.795 33.333 18.63 0.00 42.59 3.67
3236 3311 3.200165 ACCACAGCCTAGAAAATAGGTCC 59.800 47.826 3.05 0.00 37.06 4.46
3237 3312 3.433740 CCACAGCCTAGAAAATAGGTCCC 60.434 52.174 3.05 0.00 37.06 4.46
3238 3313 2.778270 ACAGCCTAGAAAATAGGTCCCC 59.222 50.000 3.05 0.00 37.06 4.81
3239 3314 2.106684 CAGCCTAGAAAATAGGTCCCCC 59.893 54.545 3.05 0.00 37.06 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 55 8.165239 TGCATTTTAGTAGTTGAACTTGTCAT 57.835 30.769 1.97 0.0 35.70 3.06
238 244 9.261180 GATTGAGATTATTTTACGACCAGATCA 57.739 33.333 0.00 0.0 0.00 2.92
700 714 1.672881 GCTGCACTGACTTGTCTTGTT 59.327 47.619 0.00 0.0 0.00 2.83
1018 1040 0.107066 TCGCCATGATGATGCTTGGT 60.107 50.000 0.00 0.0 35.96 3.67
1130 1152 2.499289 ACGATCTCCAGCATCTCTTTGT 59.501 45.455 0.00 0.0 0.00 2.83
1175 1197 1.227205 CTGCTCATCACCTCCTCGC 60.227 63.158 0.00 0.0 0.00 5.03
1179 1201 1.145819 GAGCCTGCTCATCACCTCC 59.854 63.158 14.07 0.0 42.31 4.30
1360 1382 8.367911 AGACTAGTACAACAGATGAATGAACAA 58.632 33.333 0.00 0.0 0.00 2.83
1486 1510 2.910688 TCCACTCCACAGTTTCAGAC 57.089 50.000 0.00 0.0 0.00 3.51
1968 2011 8.424918 TGCCTTTTGGTTTTGAAAGTGATAATA 58.575 29.630 0.00 0.0 42.99 0.98
2242 2289 2.125269 GTGGATTACGCCGCCTGT 60.125 61.111 0.00 0.0 32.25 4.00
2268 2315 1.762370 TCCATCTTCTTCATGCCGCTA 59.238 47.619 0.00 0.0 0.00 4.26
2576 2629 4.578516 TGTTCAAACCCTGACACACATAAG 59.421 41.667 0.00 0.0 32.21 1.73
2909 2978 5.348724 CACGATGCTGTTAGTAGTGAATGTT 59.651 40.000 0.00 0.0 0.00 2.71
2910 2979 4.864806 CACGATGCTGTTAGTAGTGAATGT 59.135 41.667 0.00 0.0 0.00 2.71
2911 2980 4.259970 GCACGATGCTGTTAGTAGTGAATG 60.260 45.833 0.00 0.0 40.96 2.67
2912 2981 3.865745 GCACGATGCTGTTAGTAGTGAAT 59.134 43.478 0.00 0.0 40.96 2.57
2913 2982 3.250744 GCACGATGCTGTTAGTAGTGAA 58.749 45.455 0.00 0.0 40.96 3.18
2914 2983 2.876091 GCACGATGCTGTTAGTAGTGA 58.124 47.619 0.00 0.0 40.96 3.41
2968 3037 6.959639 ACTGATTGTTCTTTGCTTTTCCTA 57.040 33.333 0.00 0.0 0.00 2.94
3022 3091 5.105106 TGTTCAAGTGTACCAGAACTCTCAA 60.105 40.000 14.26 0.0 40.62 3.02
3156 3230 6.456501 ACTTGCCTTACAGACTAAGTTGTAG 58.543 40.000 0.00 0.0 31.95 2.74
3308 3394 9.997482 TTGTTTGAACTTCTTGAATTGTAGTAC 57.003 29.630 0.00 0.0 0.00 2.73


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

AutoCloner maintained by Alex Coulton.