Multiple sequence alignment - TraesCS4B01G183500

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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 TraesCS4B01G183500 chr4B 100.000 3566 0 0 1 3566 402951021 402947456 0.000000e+00 6586.0
1 TraesCS4B01G183500 chr4B 100.000 1392 0 0 3896 5287 402947126 402945735 0.000000e+00 2571.0
2 TraesCS4B01G183500 chr4B 92.079 1679 130 3 1882 3559 402874707 402873031 0.000000e+00 2361.0
3 TraesCS4B01G183500 chr4B 91.959 1679 133 2 1882 3559 402864615 402862938 0.000000e+00 2351.0
4 TraesCS4B01G183500 chr4B 92.035 1356 107 1 1882 3237 402871378 402870024 0.000000e+00 1905.0
5 TraesCS4B01G183500 chr4B 91.962 1356 108 1 1882 3237 402861284 402859930 0.000000e+00 1899.0
6 TraesCS4B01G183500 chr4B 96.555 987 33 1 3896 4881 402872948 402871962 0.000000e+00 1633.0
7 TraesCS4B01G183500 chr4B 96.552 986 33 1 3896 4880 402862854 402861869 0.000000e+00 1631.0
8 TraesCS4B01G183500 chr4B 89.988 869 80 7 4019 4882 402791974 402791108 0.000000e+00 1116.0
9 TraesCS4B01G183500 chr4B 94.074 405 24 0 4880 5284 184243110 184243514 2.710000e-172 616.0
10 TraesCS4B01G183500 chr4B 90.692 419 18 12 3149 3559 402820615 402820210 6.020000e-149 538.0
11 TraesCS4B01G183500 chr4B 93.388 121 8 0 3896 4016 402820127 402820007 4.210000e-41 180.0
12 TraesCS4B01G183500 chr4B 84.375 128 17 2 3287 3414 402859933 402859809 7.190000e-24 122.0
13 TraesCS4B01G183500 chr4B 84.375 128 17 2 3287 3414 402870027 402869903 7.190000e-24 122.0
14 TraesCS4B01G183500 chr4B 91.667 48 2 2 3486 3531 382203222 382203269 1.230000e-06 65.8
15 TraesCS4B01G183500 chr4B 84.722 72 2 3 3407 3476 402859783 402859719 4.420000e-06 63.9
16 TraesCS4B01G183500 chr4B 84.507 71 2 3 3408 3476 402869876 402869813 1.590000e-05 62.1
17 TraesCS4B01G183500 chr7B 96.209 3561 84 8 1 3559 113045784 113042273 0.000000e+00 5781.0
18 TraesCS4B01G183500 chr7B 96.985 1393 40 2 3896 5287 113041973 113040582 0.000000e+00 2338.0
19 TraesCS4B01G183500 chr7B 90.768 1679 152 3 1882 3559 112914605 112912929 0.000000e+00 2239.0
20 TraesCS4B01G183500 chr7B 89.577 1679 165 6 1882 3559 112911284 112909615 0.000000e+00 2122.0
21 TraesCS4B01G183500 chr7B 94.630 987 50 2 3896 4881 112909526 112908542 0.000000e+00 1526.0
22 TraesCS4B01G183500 chr7B 94.231 988 48 4 3896 4881 112912847 112911867 0.000000e+00 1500.0
23 TraesCS4B01G183500 chr7B 94.005 417 24 1 4872 5287 606597060 606597476 9.660000e-177 630.0
24 TraesCS4B01G183500 chr7B 91.111 45 2 2 3434 3476 112906439 112906395 5.720000e-05 60.2
25 TraesCS4B01G183500 chr7D 91.352 3018 203 25 403 3414 150838734 150835769 0.000000e+00 4074.0
26 TraesCS4B01G183500 chr7D 89.062 256 26 1 6 261 150838989 150838736 3.070000e-82 316.0
27 TraesCS4B01G183500 chr7D 94.030 134 8 0 268 401 580887678 580887545 2.500000e-48 204.0
28 TraesCS4B01G183500 chr7A 92.896 2407 150 8 1079 3476 150445305 150442911 0.000000e+00 3478.0
29 TraesCS4B01G183500 chr7A 83.855 991 149 11 3896 4880 150442711 150441726 0.000000e+00 933.0
30 TraesCS4B01G183500 chr7A 79.580 333 37 17 641 971 150446641 150446338 5.370000e-50 209.0
31 TraesCS4B01G183500 chr7A 93.431 137 9 0 265 401 437074371 437074507 2.500000e-48 204.0
32 TraesCS4B01G183500 chr7A 94.340 53 3 0 990 1042 150445358 150445306 1.220000e-11 82.4
33 TraesCS4B01G183500 chr1B 94.349 407 23 0 4881 5287 492237638 492238044 4.500000e-175 625.0
34 TraesCS4B01G183500 chr1B 89.655 58 3 3 3484 3538 397991868 397991925 2.640000e-08 71.3
35 TraesCS4B01G183500 chr5B 94.335 406 23 0 4882 5287 108546933 108546528 1.620000e-174 623.0
36 TraesCS4B01G183500 chr5B 94.103 407 23 1 4882 5287 465831483 465831077 7.520000e-173 617.0
37 TraesCS4B01G183500 chr5B 92.199 141 10 1 261 400 659822567 659822707 1.160000e-46 198.0
38 TraesCS4B01G183500 chr5B 92.086 139 11 0 263 401 646377960 646377822 4.180000e-46 196.0
39 TraesCS4B01G183500 chr6B 93.873 408 25 0 4880 5287 704502608 704502201 2.710000e-172 616.0
40 TraesCS4B01G183500 chr2B 93.888 409 24 1 4880 5287 227917164 227916756 2.710000e-172 616.0
41 TraesCS4B01G183500 chr4A 92.857 420 28 2 4869 5287 665530638 665531056 4.530000e-170 608.0
42 TraesCS4B01G183500 chr4A 93.333 135 9 0 267 401 603722679 603722545 3.230000e-47 200.0
43 TraesCS4B01G183500 chr3B 93.478 138 8 1 265 402 779368889 779369025 2.500000e-48 204.0
44 TraesCS4B01G183500 chr2A 92.361 144 9 2 258 401 98897407 98897548 2.500000e-48 204.0
45 TraesCS4B01G183500 chr2D 92.199 141 11 0 261 401 126951509 126951649 3.230000e-47 200.0
46 TraesCS4B01G183500 chr6A 95.349 43 1 1 3487 3529 493105762 493105721 3.420000e-07 67.6
47 TraesCS4B01G183500 chr1D 93.023 43 2 1 3487 3529 131005759 131005800 1.590000e-05 62.1


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 TraesCS4B01G183500 chr4B 402945735 402951021 5286 True 4578.50 6586 100.00000 1 5287 2 chr4B.!!$R5 5286
1 TraesCS4B01G183500 chr4B 402869813 402874707 4894 True 1216.62 2361 89.91020 1882 4881 5 chr4B.!!$R4 2999
2 TraesCS4B01G183500 chr4B 402859719 402864615 4896 True 1213.38 2351 89.91400 1882 4880 5 chr4B.!!$R3 2998
3 TraesCS4B01G183500 chr4B 402791108 402791974 866 True 1116.00 1116 89.98800 4019 4882 1 chr4B.!!$R1 863
4 TraesCS4B01G183500 chr4B 402820007 402820615 608 True 359.00 538 92.04000 3149 4016 2 chr4B.!!$R2 867
5 TraesCS4B01G183500 chr7B 113040582 113045784 5202 True 4059.50 5781 96.59700 1 5287 2 chr7B.!!$R2 5286
6 TraesCS4B01G183500 chr7B 112906395 112914605 8210 True 1489.44 2239 92.06340 1882 4881 5 chr7B.!!$R1 2999
7 TraesCS4B01G183500 chr7D 150835769 150838989 3220 True 2195.00 4074 90.20700 6 3414 2 chr7D.!!$R2 3408
8 TraesCS4B01G183500 chr7A 150441726 150446641 4915 True 1175.60 3478 87.66775 641 4880 4 chr7A.!!$R1 4239

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
978 993 0.802607 GAGTTGAGGCGCCGACTTAG 60.803 60.0 26.32 0.00 0.00 2.18 F
1520 2496 0.526211 CAGTTCGATCCTGACCACGA 59.474 55.0 6.75 0.00 31.38 4.35 F
2816 3792 0.317103 CTGAGATACGCGAGGTTCGG 60.317 60.0 15.93 6.49 40.84 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 3417 0.531974 GAGACACCGGTGCAGTTTCA 60.532 55.0 34.26 0.0 0.0 2.69 R
3133 4109 0.600255 AGCACCTCAAAGTCGTTCCG 60.600 55.0 0.00 0.0 0.0 4.30 R
4416 5428 0.036732 TCAACGGGCAGCAGATCTTT 59.963 50.0 0.00 0.0 0.0 2.52 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
146 147 7.187824 TCTGTGTTTAGATAAAGCTCCATCT 57.812 36.000 13.03 13.03 35.67 2.90
290 291 3.708563 TTTTGCGGGAAAGACTTTCAG 57.291 42.857 25.38 19.60 41.43 3.02
292 293 1.878953 TGCGGGAAAGACTTTCAGTC 58.121 50.000 25.38 14.92 45.38 3.51
381 382 1.274167 CCACCTAGCCACGACTACAAA 59.726 52.381 0.00 0.00 0.00 2.83
645 653 8.988060 AGGAAAAACCAGAAGGAAAATAAAGAA 58.012 29.630 0.00 0.00 42.04 2.52
779 787 2.749600 TGCATATCTGGCCCAACAAAT 58.250 42.857 0.00 0.00 0.00 2.32
977 992 1.214589 GAGTTGAGGCGCCGACTTA 59.785 57.895 26.32 13.56 0.00 2.24
978 993 0.802607 GAGTTGAGGCGCCGACTTAG 60.803 60.000 26.32 0.00 0.00 2.18
979 994 1.810030 GTTGAGGCGCCGACTTAGG 60.810 63.158 23.20 0.00 0.00 2.69
980 995 1.980232 TTGAGGCGCCGACTTAGGA 60.980 57.895 23.20 0.00 0.00 2.94
981 996 1.945354 TTGAGGCGCCGACTTAGGAG 61.945 60.000 23.20 0.00 0.00 3.69
1509 2485 2.579201 CGCCACCTCCAGTTCGAT 59.421 61.111 0.00 0.00 0.00 3.59
1512 2488 1.617947 GCCACCTCCAGTTCGATCCT 61.618 60.000 0.00 0.00 0.00 3.24
1520 2496 0.526211 CAGTTCGATCCTGACCACGA 59.474 55.000 6.75 0.00 31.38 4.35
2082 3058 4.980805 GTCCAGGCGTGGCACGAA 62.981 66.667 40.94 18.12 46.05 3.85
2157 3133 1.313091 CCGTCAGGACTGTCGATCCA 61.313 60.000 17.92 0.00 42.92 3.41
2223 3199 0.527817 CCAAGATGTACGAGGACCGC 60.528 60.000 0.00 0.00 43.32 5.68
2408 3384 3.120979 CTATCGAGCCCACGACGCA 62.121 63.158 0.00 0.00 44.84 5.24
2482 3458 1.964448 CTGTGGCTCGTGTACCTGA 59.036 57.895 0.00 0.00 0.00 3.86
2523 3499 3.753434 CTCGAGTCCACCTGCGCT 61.753 66.667 9.73 0.00 0.00 5.92
2589 3565 3.066190 CTGGACCACGCGACCCTA 61.066 66.667 15.93 0.00 0.00 3.53
2707 3683 0.679505 CCTGACCAAGTTCGTCCAGA 59.320 55.000 0.00 0.00 0.00 3.86
2799 3775 0.391263 GGAAGAAGGCCGTGTACCTG 60.391 60.000 0.00 0.00 37.67 4.00
2816 3792 0.317103 CTGAGATACGCGAGGTTCGG 60.317 60.000 15.93 6.49 40.84 4.30
2835 3811 4.516195 GAGGACTTCGGCCTCGCC 62.516 72.222 0.00 0.00 46.75 5.54
2858 3834 4.590487 CGCCATGAAGGTGTACGT 57.410 55.556 0.00 0.00 43.15 3.57
2865 3841 1.288127 GAAGGTGTACGTGGACGCT 59.712 57.895 0.00 0.00 44.43 5.07
3133 4109 0.955919 CCCTGAGTTCTGGAAACGGC 60.956 60.000 6.62 0.00 37.15 5.68
3255 4231 2.815308 GGTGAGATCCGCACCGAT 59.185 61.111 16.80 0.00 43.57 4.18
3984 4987 2.029964 GGTTTGGCGTCGAGGTCA 59.970 61.111 8.58 8.58 0.00 4.02
4394 5406 0.181587 ATCCGTTGGTGTTGGTGACA 59.818 50.000 0.00 0.00 39.83 3.58
4407 5419 3.507162 TGGTGACAATTGGAGTCATGT 57.493 42.857 10.83 0.00 46.52 3.21
4416 5428 3.500448 TTGGAGTCATGTTTGGTGCTA 57.500 42.857 0.00 0.00 0.00 3.49
4586 8924 1.873863 CTAGGCGCGGTATCATCGA 59.126 57.895 8.83 0.00 0.00 3.59
4642 8980 4.237724 CAAAGCTCAGATACGACACAAGA 58.762 43.478 0.00 0.00 0.00 3.02
4840 9179 1.001706 CGGAGTCGAAGATCGCCATAA 60.002 52.381 0.00 0.00 40.67 1.90
4991 9777 3.118261 ACGTACCCTCGTAGACCATAAGA 60.118 47.826 0.00 0.00 42.35 2.10
4998 10099 3.628008 TCGTAGACCATAAGAGGAAGCA 58.372 45.455 0.00 0.00 0.00 3.91
5027 10128 1.402968 ACGCGGTTGATGTAGTCGTAT 59.597 47.619 12.47 0.00 0.00 3.06
5043 10311 0.804933 GTATGTCTTCACGGCCCGAC 60.805 60.000 11.71 0.00 0.00 4.79
5065 10333 0.602638 ATCAAGCACCGAAAGCACGA 60.603 50.000 0.00 0.00 35.09 4.35
5109 10377 0.171231 CAGCTCGATGACGTTCCTCA 59.829 55.000 0.00 0.00 40.69 3.86
5122 10390 2.611971 CGTTCCTCAAACTCCGATCCAA 60.612 50.000 0.00 0.00 35.59 3.53
5134 10535 0.100682 CGATCCAACCGAGTGTCGAT 59.899 55.000 0.00 0.00 43.74 3.59
5212 10613 1.281899 CTTCGCCTAAGCACTGCTAC 58.718 55.000 3.33 0.00 38.25 3.58
5222 10737 6.621613 CCTAAGCACTGCTACGATATTATCA 58.378 40.000 3.33 0.00 38.25 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 1.616725 GGATGGATCAAGGCCAACACA 60.617 52.381 5.01 0.00 39.21 3.72
354 355 0.389391 CGTGGCTAGGTGGTCTATGG 59.611 60.000 0.00 0.00 0.00 2.74
381 382 0.600255 CCTTCGGTTCGCTTCAGTGT 60.600 55.000 0.00 0.00 0.00 3.55
645 653 7.565029 CCCATAGTCCCTGATTTTTATCCTTTT 59.435 37.037 0.00 0.00 0.00 2.27
839 847 1.071857 ACGAAGTGGGTTCTTCTTCCC 59.928 52.381 0.00 0.00 42.51 3.97
977 992 3.502356 ACCGACTCTTTCTTCTTCTCCT 58.498 45.455 0.00 0.00 0.00 3.69
978 993 3.256136 TGACCGACTCTTTCTTCTTCTCC 59.744 47.826 0.00 0.00 0.00 3.71
979 994 4.506886 TGACCGACTCTTTCTTCTTCTC 57.493 45.455 0.00 0.00 0.00 2.87
980 995 4.322349 CCATGACCGACTCTTTCTTCTTCT 60.322 45.833 0.00 0.00 0.00 2.85
981 996 3.929610 CCATGACCGACTCTTTCTTCTTC 59.070 47.826 0.00 0.00 0.00 2.87
1509 2485 0.041238 AATCCTCCTCGTGGTCAGGA 59.959 55.000 14.37 14.37 39.69 3.86
1512 2488 1.639722 TGAAATCCTCCTCGTGGTCA 58.360 50.000 2.99 0.00 34.23 4.02
1520 2496 1.141858 GGAAGGCGATGAAATCCTCCT 59.858 52.381 0.00 0.00 42.44 3.69
1815 2791 1.144936 GGTCATGGCCTCCTCGAAG 59.855 63.158 9.76 0.00 0.00 3.79
1977 2953 2.892425 CTCGCCATCGCCAAGTCC 60.892 66.667 0.00 0.00 35.26 3.85
2082 3058 1.299976 GTGGAAGATCTTGGCCCGT 59.700 57.895 14.00 0.00 0.00 5.28
2148 3124 2.184322 GCCTTCGCTGGATCGACA 59.816 61.111 0.00 0.00 38.30 4.35
2328 3304 1.997874 GGGATCCTGGTGCCTCAGT 60.998 63.158 12.58 0.00 33.14 3.41
2391 3367 3.135457 TGCGTCGTGGGCTCGATA 61.135 61.111 8.27 0.00 41.78 2.92
2441 3417 0.531974 GAGACACCGGTGCAGTTTCA 60.532 55.000 34.26 0.00 0.00 2.69
2482 3458 1.593196 CCGTGTGTTGTCATCAGGTT 58.407 50.000 0.00 0.00 0.00 3.50
2707 3683 3.710722 CCTGCTCTTCCCGTGCCT 61.711 66.667 0.00 0.00 0.00 4.75
2769 3745 3.302347 CTTCTTCCTCTGCGGCGGT 62.302 63.158 9.78 0.00 0.00 5.68
2776 3752 0.895530 TACACGGCCTTCTTCCTCTG 59.104 55.000 0.00 0.00 0.00 3.35
2799 3775 1.008767 CCCGAACCTCGCGTATCTC 60.009 63.158 5.77 0.00 38.82 2.75
3133 4109 0.600255 AGCACCTCAAAGTCGTTCCG 60.600 55.000 0.00 0.00 0.00 4.30
3190 4166 1.528824 CCGCCATGGTCCTCTTCAT 59.471 57.895 14.67 0.00 0.00 2.57
3522 4510 8.788325 AGTAAACAAACTCAAAACAGTACTCT 57.212 30.769 0.00 0.00 0.00 3.24
4102 5108 6.994221 ACTAGGAAATAACCCGACATATGAG 58.006 40.000 10.38 2.85 0.00 2.90
4111 5118 4.162888 ACACCCTTACTAGGAAATAACCCG 59.837 45.833 0.00 0.00 45.05 5.28
4394 5406 3.233507 AGCACCAAACATGACTCCAATT 58.766 40.909 0.00 0.00 0.00 2.32
4407 5419 2.489329 GCAGCAGATCTTTAGCACCAAA 59.511 45.455 6.33 0.00 0.00 3.28
4416 5428 0.036732 TCAACGGGCAGCAGATCTTT 59.963 50.000 0.00 0.00 0.00 2.52
4586 8924 3.685756 TCACTTCCGAAAACAAAAGACGT 59.314 39.130 0.00 0.00 0.00 4.34
4840 9179 1.211969 CAGGTTCGTCATCGACCGT 59.788 57.895 0.00 0.00 46.03 4.83
4909 9695 0.320421 TCTTGCCTGTGCGTAGGAAC 60.320 55.000 10.03 0.00 40.42 3.62
4922 9708 1.395635 TGCATCACCATGATCTTGCC 58.604 50.000 3.07 0.00 34.28 4.52
4986 9772 4.572389 CGTTGTGCTAATGCTTCCTCTTAT 59.428 41.667 0.00 0.00 40.48 1.73
4991 9777 0.804989 GCGTTGTGCTAATGCTTCCT 59.195 50.000 10.09 0.00 41.73 3.36
4998 10099 1.130373 CATCAACCGCGTTGTGCTAAT 59.870 47.619 16.97 4.76 43.23 1.73
5027 10128 3.998672 GGTCGGGCCGTGAAGACA 61.999 66.667 27.32 0.36 35.49 3.41
5043 10311 1.298157 TGCTTTCGGTGCTTGATCGG 61.298 55.000 0.00 0.00 0.00 4.18
5065 10333 0.249911 GTGCAAGAACTCGGAGGTGT 60.250 55.000 10.23 0.00 0.00 4.16
5109 10377 0.974383 ACTCGGTTGGATCGGAGTTT 59.026 50.000 0.00 0.00 42.45 2.66
5122 10390 0.322636 ACTCTCCATCGACACTCGGT 60.323 55.000 0.00 0.00 40.88 4.69
5134 10535 1.666011 GTGCTGACGGAACTCTCCA 59.334 57.895 0.00 0.00 42.58 3.86
5212 10613 7.261325 CACCATAGTCCTCCTTGATAATATCG 58.739 42.308 0.00 0.00 0.00 2.92
5222 10737 1.344496 CCCTCCACCATAGTCCTCCTT 60.344 57.143 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.