Multiple sequence alignment - TraesCS4D01G079000

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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 TraesCS4D01G079000 chr4D 100.000 3810 0 0 1 3810 52778328 52782137 0.000000e+00 7036.0
1 TraesCS4D01G079000 chr4B 95.665 3391 118 14 12 3390 77663419 77666792 0.000000e+00 5421.0
2 TraesCS4D01G079000 chr4B 93.953 430 20 4 3386 3810 77733531 77733959 0.000000e+00 645.0
3 TraesCS4D01G079000 chr4B 87.778 450 34 10 2564 2998 646252405 646251962 1.220000e-139 507.0
4 TraesCS4D01G079000 chr4B 87.500 352 33 3 2994 3334 646248944 646248593 2.760000e-106 396.0
5 TraesCS4D01G079000 chr4B 94.000 50 2 1 2563 2612 259097412 259097364 1.470000e-09 75.0
6 TraesCS4D01G079000 chr4A 94.836 2905 104 21 930 3810 544032816 544029934 0.000000e+00 4492.0
7 TraesCS4D01G079000 chr4A 95.112 941 40 4 12 947 544033768 544032829 0.000000e+00 1478.0
8 TraesCS4D01G079000 chr4A 88.688 442 30 9 2573 2998 645259487 645259050 4.360000e-144 521.0
9 TraesCS4D01G079000 chr4A 86.313 358 38 3 2994 3340 645257556 645257199 2.780000e-101 379.0
10 TraesCS4D01G079000 chr6A 89.387 424 33 10 2573 2993 63094399 63093985 1.210000e-144 523.0
11 TraesCS4D01G079000 chr6A 92.308 52 2 2 2562 2612 586365753 586365803 5.280000e-09 73.1
12 TraesCS4D01G079000 chrUn 88.837 430 34 12 2573 2998 282890591 282891010 2.030000e-142 516.0
13 TraesCS4D01G079000 chrUn 88.837 430 34 12 2573 2998 295720950 295720531 2.030000e-142 516.0
14 TraesCS4D01G079000 chrUn 88.837 430 34 12 2573 2998 311088032 311088451 2.030000e-142 516.0
15 TraesCS4D01G079000 chrUn 83.333 210 17 9 2993 3191 320011858 320012060 1.090000e-40 178.0
16 TraesCS4D01G079000 chrUn 83.333 210 17 9 2993 3191 322841635 322841837 1.090000e-40 178.0
17 TraesCS4D01G079000 chrUn 83.333 210 17 9 2993 3191 346199874 346199672 1.090000e-40 178.0
18 TraesCS4D01G079000 chrUn 83.333 210 17 9 2993 3191 367263293 367263091 1.090000e-40 178.0
19 TraesCS4D01G079000 chr2B 88.435 441 31 9 2574 2998 799588896 799589332 7.300000e-142 514.0
20 TraesCS4D01G079000 chr2B 88.525 366 29 5 2984 3338 799590756 799591119 7.560000e-117 431.0
21 TraesCS4D01G079000 chr3B 86.406 434 35 12 2572 2988 20066124 20066550 1.610000e-123 453.0
22 TraesCS4D01G079000 chr7A 84.685 444 42 14 2573 2998 484716062 484715627 1.640000e-113 420.0
23 TraesCS4D01G079000 chr6B 87.123 365 29 10 2573 2933 243238499 243238149 7.670000e-107 398.0
24 TraesCS4D01G079000 chr6B 89.865 148 15 0 3191 3338 94723291 94723144 1.400000e-44 191.0
25 TraesCS4D01G079000 chr6B 77.285 361 48 20 2993 3341 477190615 477190277 8.410000e-42 182.0
26 TraesCS4D01G079000 chr6B 88.514 148 17 0 3191 3338 94849119 94848972 3.020000e-41 180.0
27 TraesCS4D01G079000 chr7D 84.826 402 33 7 2569 2954 634437362 634436973 2.780000e-101 379.0
28 TraesCS4D01G079000 chr7D 74.586 724 160 18 1102 1807 153405152 153404435 2.880000e-76 296.0
29 TraesCS4D01G079000 chr3A 86.014 143 11 5 3197 3339 730427311 730427178 1.100000e-30 145.0


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 TraesCS4D01G079000 chr4D 52778328 52782137 3809 False 7036.0 7036 100.0000 1 3810 1 chr4D.!!$F1 3809
1 TraesCS4D01G079000 chr4B 77663419 77666792 3373 False 5421.0 5421 95.6650 12 3390 1 chr4B.!!$F1 3378
2 TraesCS4D01G079000 chr4B 646248593 646252405 3812 True 451.5 507 87.6390 2564 3334 2 chr4B.!!$R2 770
3 TraesCS4D01G079000 chr4A 544029934 544033768 3834 True 2985.0 4492 94.9740 12 3810 2 chr4A.!!$R1 3798
4 TraesCS4D01G079000 chr4A 645257199 645259487 2288 True 450.0 521 87.5005 2573 3340 2 chr4A.!!$R2 767
5 TraesCS4D01G079000 chr2B 799588896 799591119 2223 False 472.5 514 88.4800 2574 3338 2 chr2B.!!$F1 764
6 TraesCS4D01G079000 chr7D 153404435 153405152 717 True 296.0 296 74.5860 1102 1807 1 chr7D.!!$R1 705

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
886 893 0.035343 AGTCCGACTCCATCTCGACA 60.035 55.0 0.00 0.0 32.65 4.35 F
1100 1141 0.391597 AGAGAGCGACCGGACAAAAA 59.608 50.0 9.46 0.0 0.00 1.94 F
1246 1287 0.909610 TCCTCCCGAACTCATTGGCT 60.910 55.0 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2349 2402 2.795329 TCCCCTGCTCAAATTTCTGTC 58.205 47.619 0.0 0.0 0.0 3.51 R
2350 2403 2.978156 TCCCCTGCTCAAATTTCTGT 57.022 45.000 0.0 0.0 0.0 3.41 R
3242 6388 1.808411 CCACATCAGCAACGTACCTT 58.192 50.000 0.0 0.0 0.0 3.50 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
26 27 2.614057 GCAAGCGCAAGATACCTTACAT 59.386 45.455 11.47 0.00 43.02 2.29
138 143 0.249398 AGTGGGTATGTCCGAGCAAC 59.751 55.000 0.00 0.00 37.00 4.17
213 219 0.163788 CAACCAGCAAACTACGAGCG 59.836 55.000 0.00 0.00 0.00 5.03
221 227 1.996898 CAAACTACGAGCGGCATTACA 59.003 47.619 1.45 0.00 0.00 2.41
228 234 2.159156 ACGAGCGGCATTACACTAATGA 60.159 45.455 1.45 0.00 46.52 2.57
251 257 5.185454 AGCATTTCATCGAACATAAGGTGA 58.815 37.500 0.00 0.00 0.00 4.02
267 273 0.036388 GTGAGCGAAGAACATCCCCA 60.036 55.000 0.00 0.00 0.00 4.96
311 318 1.594862 GATCCTGCATGCGTACTCAAC 59.405 52.381 14.09 0.00 0.00 3.18
314 321 1.535028 CCTGCATGCGTACTCAACAAA 59.465 47.619 14.09 0.00 0.00 2.83
377 384 1.153229 GATTGGGAGTACGGTGCCC 60.153 63.158 8.17 8.17 42.38 5.36
808 815 4.202535 TGGTTTTTCTTCCCCCTAGACTTC 60.203 45.833 0.00 0.00 0.00 3.01
882 889 2.022240 GCCCAGTCCGACTCCATCTC 62.022 65.000 0.00 0.00 0.00 2.75
886 893 0.035343 AGTCCGACTCCATCTCGACA 60.035 55.000 0.00 0.00 32.65 4.35
907 918 1.071071 TCCTCCACGACAACGGAAAAT 59.929 47.619 0.00 0.00 44.46 1.82
1009 1050 4.275936 GCTTAGCAACTTTCCAACAGAAGA 59.724 41.667 0.00 0.00 35.40 2.87
1010 1051 5.221048 GCTTAGCAACTTTCCAACAGAAGAA 60.221 40.000 0.00 0.00 35.40 2.52
1011 1052 4.907879 AGCAACTTTCCAACAGAAGAAG 57.092 40.909 0.00 0.00 35.40 2.85
1021 1062 2.945008 CAACAGAAGAAGCCTGACAACA 59.055 45.455 0.00 0.00 35.69 3.33
1044 1085 7.066781 ACATTTTCCCTCAAAGAAAGAACCTA 58.933 34.615 0.00 0.00 34.84 3.08
1081 1122 2.184322 GGTCGAGCGATGGAGCAA 59.816 61.111 10.05 0.00 40.15 3.91
1100 1141 0.391597 AGAGAGCGACCGGACAAAAA 59.608 50.000 9.46 0.00 0.00 1.94
1246 1287 0.909610 TCCTCCCGAACTCATTGGCT 60.910 55.000 0.00 0.00 0.00 4.75
1280 1321 4.619760 TCAACTTCAACGAGCTAACGTATG 59.380 41.667 0.39 3.11 45.83 2.39
1635 1688 1.207791 CCTACTTCATGGACCCTGCT 58.792 55.000 0.00 0.00 0.00 4.24
1658 1711 1.616865 TCTTCTCGTCGTTGAATGGGT 59.383 47.619 0.00 0.00 0.00 4.51
2126 2179 4.348020 TGATAGGGACCTCAAGTTACCT 57.652 45.455 0.00 0.00 38.97 3.08
2128 2181 5.098663 TGATAGGGACCTCAAGTTACCTTT 58.901 41.667 0.00 0.00 37.35 3.11
2217 2270 3.416277 CATTACGATGAAACCAACGCAG 58.584 45.455 0.00 0.00 35.16 5.18
2620 2682 3.120199 GCGGAAATTATGTATCAGCGCAT 60.120 43.478 11.47 0.00 0.00 4.73
2623 2685 5.445939 CGGAAATTATGTATCAGCGCATACC 60.446 44.000 11.47 0.00 0.00 2.73
2745 2817 1.418334 AGATGCTGGCCGAAGAGTAT 58.582 50.000 0.00 0.00 0.00 2.12
3229 6375 4.460263 TGGCTTTACCATATGCGAGAAAT 58.540 39.130 0.00 0.00 46.36 2.17
3242 6388 9.639601 CATATGCGAGAAATATTTAGTACTGGA 57.360 33.333 5.39 0.00 0.00 3.86
3286 6432 6.712095 GCAGGAATGATGATGTGGATAACTTA 59.288 38.462 0.00 0.00 0.00 2.24
3326 6476 9.805204 ATAGGATAGTGGGGATGAACTATTTAT 57.195 33.333 0.00 0.00 39.22 1.40
3444 6594 8.842358 TCTTACTCAATCTGACCGTTTATTTT 57.158 30.769 0.00 0.00 0.00 1.82
3590 6740 3.812053 GTGCATCCAATCTACATGAGACC 59.188 47.826 0.00 0.00 36.87 3.85
3679 6829 2.421739 GGTATCCACCGCTCGCAT 59.578 61.111 0.00 0.00 34.36 4.73
3680 6830 1.956170 GGTATCCACCGCTCGCATG 60.956 63.158 0.00 0.00 34.36 4.06
3682 6832 0.810031 GTATCCACCGCTCGCATGTT 60.810 55.000 0.00 0.00 0.00 2.71
3683 6833 0.529773 TATCCACCGCTCGCATGTTC 60.530 55.000 0.00 0.00 0.00 3.18
3684 6834 2.520465 ATCCACCGCTCGCATGTTCA 62.520 55.000 0.00 0.00 0.00 3.18
3722 6872 1.459450 TCTTCAAGCAAATACCCGCC 58.541 50.000 0.00 0.00 0.00 6.13
3723 6873 1.004277 TCTTCAAGCAAATACCCGCCT 59.996 47.619 0.00 0.00 0.00 5.52
3724 6874 1.401905 CTTCAAGCAAATACCCGCCTC 59.598 52.381 0.00 0.00 0.00 4.70
3727 6877 2.886730 AAGCAAATACCCGCCTCCCG 62.887 60.000 0.00 0.00 0.00 5.14
3728 6878 2.587889 CAAATACCCGCCTCCCGT 59.412 61.111 0.00 0.00 34.38 5.28
3732 6882 0.393402 AATACCCGCCTCCCGTTTTC 60.393 55.000 0.00 0.00 34.38 2.29
3795 6953 1.375523 CCACCTACGCACCAAGGAC 60.376 63.158 0.00 0.00 36.66 3.85
3798 6956 2.125673 CTACGCACCAAGGACCCG 60.126 66.667 0.00 0.00 0.00 5.28
3807 6965 1.176619 CCAAGGACCCGGAAAACCAC 61.177 60.000 0.73 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.006888 TGTAAGGTATCTTGCGCTTGC 58.993 47.619 9.73 0.00 38.25 4.01
6 7 5.050490 ACTATGTAAGGTATCTTGCGCTTG 58.950 41.667 9.73 0.65 38.25 4.01
8 9 4.556898 CGACTATGTAAGGTATCTTGCGCT 60.557 45.833 9.73 0.00 38.25 5.92
9 10 3.669122 CGACTATGTAAGGTATCTTGCGC 59.331 47.826 0.00 0.00 38.25 6.09
10 11 5.104562 TCGACTATGTAAGGTATCTTGCG 57.895 43.478 0.00 0.00 38.25 4.85
26 27 7.551617 TCTTGTGATCATAGTGTAGTTCGACTA 59.448 37.037 0.00 0.00 0.00 2.59
138 143 8.779354 ACTTAATTGTACTTCCTTAGCAGAAG 57.221 34.615 0.00 0.00 45.12 2.85
213 219 6.135290 TGAAATGCTCATTAGTGTAATGCC 57.865 37.500 2.34 0.00 43.97 4.40
221 227 6.932356 ATGTTCGATGAAATGCTCATTAGT 57.068 33.333 0.00 0.00 45.23 2.24
228 234 5.185454 TCACCTTATGTTCGATGAAATGCT 58.815 37.500 0.00 0.00 0.00 3.79
251 257 1.299976 GGTGGGGATGTTCTTCGCT 59.700 57.895 3.67 0.00 0.00 4.93
267 273 1.302832 CTTTGCGCTCCTTCCTGGT 60.303 57.895 9.73 0.00 37.07 4.00
305 311 4.401022 TGAGATTGCATCCTTTGTTGAGT 58.599 39.130 0.00 0.00 0.00 3.41
311 318 1.065102 CGGCTGAGATTGCATCCTTTG 59.935 52.381 0.00 0.00 0.00 2.77
314 321 1.147824 CCGGCTGAGATTGCATCCT 59.852 57.895 0.00 0.00 0.00 3.24
345 352 2.104111 TCCCAATCAAGGTATACCAGCG 59.896 50.000 23.87 11.26 38.89 5.18
882 889 1.071019 CGTTGTCGTGGAGGATGTCG 61.071 60.000 0.00 0.00 0.00 4.35
886 893 0.682852 TTTCCGTTGTCGTGGAGGAT 59.317 50.000 0.00 0.00 35.26 3.24
907 918 2.188469 GTCGGGGAGCCGCAATAA 59.812 61.111 4.41 0.00 0.00 1.40
1009 1050 2.893489 GAGGGAAAATGTTGTCAGGCTT 59.107 45.455 0.00 0.00 0.00 4.35
1010 1051 2.158475 TGAGGGAAAATGTTGTCAGGCT 60.158 45.455 0.00 0.00 0.00 4.58
1011 1052 2.238521 TGAGGGAAAATGTTGTCAGGC 58.761 47.619 0.00 0.00 0.00 4.85
1021 1062 7.255977 GCTTAGGTTCTTTCTTTGAGGGAAAAT 60.256 37.037 0.00 0.00 33.17 1.82
1081 1122 0.391597 TTTTTGTCCGGTCGCTCTCT 59.608 50.000 0.00 0.00 0.00 3.10
1167 1208 1.351707 CACGTCTTGCAAACGCACT 59.648 52.632 24.26 10.28 43.76 4.40
1246 1287 5.789521 TCGTTGAAGTTGATGAAGATACCA 58.210 37.500 0.00 0.00 0.00 3.25
1349 1399 0.247736 AGACCGTTGCAGTGATCCTC 59.752 55.000 0.00 0.00 0.00 3.71
1431 1481 4.522975 ATAGGCTTTGGGGCGGCC 62.523 66.667 22.00 22.00 45.89 6.13
1635 1688 2.609491 CCATTCAACGACGAGAAGACCA 60.609 50.000 0.00 0.00 0.00 4.02
1658 1711 6.430925 CGCATGAATATTCTTTCCTCCCATTA 59.569 38.462 16.24 0.00 0.00 1.90
2098 2151 3.051940 TGAGGTCCCTATCATGCTTCT 57.948 47.619 0.00 0.00 0.00 2.85
2099 2152 3.135530 ACTTGAGGTCCCTATCATGCTTC 59.864 47.826 0.00 0.00 0.00 3.86
2100 2153 3.118531 ACTTGAGGTCCCTATCATGCTT 58.881 45.455 0.00 0.00 0.00 3.91
2126 2179 4.021544 GGACCATTGTTTAGACATGGCAAA 60.022 41.667 0.00 0.00 37.67 3.68
2128 2181 3.088532 GGACCATTGTTTAGACATGGCA 58.911 45.455 0.00 0.00 37.67 4.92
2217 2270 7.826744 AGAGTTCCATTCAAAATCCTCTTCTAC 59.173 37.037 0.00 0.00 0.00 2.59
2345 2398 3.512724 CCCTGCTCAAATTTCTGTCCAAT 59.487 43.478 0.00 0.00 0.00 3.16
2349 2402 2.795329 TCCCCTGCTCAAATTTCTGTC 58.205 47.619 0.00 0.00 0.00 3.51
2350 2403 2.978156 TCCCCTGCTCAAATTTCTGT 57.022 45.000 0.00 0.00 0.00 3.41
2607 2660 6.230472 TGAATTAAGGTATGCGCTGATACAT 58.770 36.000 16.87 9.19 31.38 2.29
3229 6375 6.153340 AGCAACGTACCTTCCAGTACTAAATA 59.847 38.462 0.00 0.00 40.42 1.40
3238 6384 2.002586 CATCAGCAACGTACCTTCCAG 58.997 52.381 0.00 0.00 0.00 3.86
3242 6388 1.808411 CCACATCAGCAACGTACCTT 58.192 50.000 0.00 0.00 0.00 3.50
3286 6432 8.432805 CCCACTATCCTATTTCTCTAAACATGT 58.567 37.037 0.00 0.00 0.00 3.21
3549 6699 3.119637 GCACGCCAATACCACTTGTATTT 60.120 43.478 0.00 0.00 45.78 1.40
3675 6825 0.179156 GCAGGGAATGTGAACATGCG 60.179 55.000 0.00 0.00 36.56 4.73
3676 6826 0.174162 GGCAGGGAATGTGAACATGC 59.826 55.000 0.00 0.00 36.56 4.06
3677 6827 0.819582 GGGCAGGGAATGTGAACATG 59.180 55.000 0.00 0.00 36.56 3.21
3678 6828 0.324645 GGGGCAGGGAATGTGAACAT 60.325 55.000 0.00 0.00 38.41 2.71
3679 6829 1.076549 GGGGCAGGGAATGTGAACA 59.923 57.895 0.00 0.00 0.00 3.18
3680 6830 0.541764 TTGGGGCAGGGAATGTGAAC 60.542 55.000 0.00 0.00 0.00 3.18
3682 6832 1.076549 GTTGGGGCAGGGAATGTGA 59.923 57.895 0.00 0.00 0.00 3.58
3683 6833 2.342650 CGTTGGGGCAGGGAATGTG 61.343 63.158 0.00 0.00 0.00 3.21
3684 6834 2.035626 CGTTGGGGCAGGGAATGT 59.964 61.111 0.00 0.00 0.00 2.71
3722 6872 6.509039 CGGTAATAAAGAATCGAAAACGGGAG 60.509 42.308 0.00 0.00 0.00 4.30
3723 6873 5.291614 CGGTAATAAAGAATCGAAAACGGGA 59.708 40.000 0.00 0.00 0.00 5.14
3724 6874 5.495502 CGGTAATAAAGAATCGAAAACGGG 58.504 41.667 0.00 0.00 0.00 5.28
3727 6877 8.732413 AAAACCGGTAATAAAGAATCGAAAAC 57.268 30.769 8.00 0.00 0.00 2.43
3728 6878 9.396938 GAAAAACCGGTAATAAAGAATCGAAAA 57.603 29.630 8.00 0.00 0.00 2.29
3732 6882 6.468000 GCAGAAAAACCGGTAATAAAGAATCG 59.532 38.462 8.00 0.00 0.00 3.34
3745 6895 3.866883 ACATTATGGCAGAAAAACCGG 57.133 42.857 0.00 0.00 0.00 5.28
3746 6896 4.082245 AGGAACATTATGGCAGAAAAACCG 60.082 41.667 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.