Multiple sequence alignment - TraesCS4B01G183000

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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 TraesCS4B01G183000 chr4B 100.000 3360 0 0 1 3360 402739672 402736313 0.000000e+00 6205.0
1 TraesCS4B01G183000 chr4B 71.747 1076 203 79 1306 2336 402763389 402762370 3.400000e-50 209.0
2 TraesCS4B01G183000 chr4B 88.333 60 7 0 1000 1059 62871467 62871526 4.650000e-09 73.1
3 TraesCS4B01G183000 chr7B 96.997 3363 70 11 1 3360 112299118 112295784 0.000000e+00 5622.0
4 TraesCS4B01G183000 chr7B 94.189 1153 43 13 1298 2433 112113987 112112842 0.000000e+00 1736.0
5 TraesCS4B01G183000 chr7B 94.539 586 32 0 1549 2134 727232958 727232373 0.000000e+00 905.0
6 TraesCS4B01G183000 chr7B 84.985 686 55 28 549 1203 112114667 112113999 0.000000e+00 652.0
7 TraesCS4B01G183000 chr7B 72.155 1081 201 81 1301 2336 112338819 112337794 1.560000e-58 237.0
8 TraesCS4B01G183000 chr7B 87.047 193 12 2 327 518 112127446 112127266 4.390000e-49 206.0
9 TraesCS4B01G183000 chr7B 86.000 150 21 0 3210 3359 749123570 749123719 9.650000e-36 161.0
10 TraesCS4B01G183000 chr7B 88.800 125 14 0 2552 2676 112108746 112108622 1.610000e-33 154.0
11 TraesCS4B01G183000 chr7B 94.253 87 5 0 410 496 112124768 112124682 2.100000e-27 134.0
12 TraesCS4B01G183000 chr7D 90.669 1704 100 19 993 2676 149849946 149848282 0.000000e+00 2211.0
13 TraesCS4B01G183000 chr7D 87.019 416 39 9 369 777 149850532 149850125 3.950000e-124 455.0
14 TraesCS4B01G183000 chr7D 93.401 197 12 1 31 226 72944486 72944290 1.180000e-74 291.0
15 TraesCS4B01G183000 chr7D 87.417 151 19 0 3209 3359 233069043 233069193 1.240000e-39 174.0
16 TraesCS4B01G183000 chr7D 97.436 39 0 1 877 914 149850032 149849994 7.780000e-07 65.8
17 TraesCS4B01G183000 chr7A 90.950 1326 75 25 1287 2596 150329527 150328231 0.000000e+00 1742.0
18 TraesCS4B01G183000 chr7A 87.067 433 23 12 369 777 150330396 150329973 3.060000e-125 459.0
19 TraesCS4B01G183000 chr7A 86.455 347 24 13 880 1203 150329877 150329531 3.190000e-95 359.0
20 TraesCS4B01G183000 chr7A 89.683 126 13 0 3234 3359 20989633 20989508 9.650000e-36 161.0
21 TraesCS4B01G183000 chr7A 91.860 86 4 2 260 343 150330480 150330396 2.120000e-22 117.0
22 TraesCS4B01G183000 chr5D 82.922 486 75 6 2726 3211 344989130 344989607 6.660000e-117 431.0
23 TraesCS4B01G183000 chr5D 85.135 148 21 1 3213 3359 155619884 155619737 2.090000e-32 150.0
24 TraesCS4B01G183000 chr3D 82.136 487 83 4 2726 3211 25185989 25185506 6.710000e-112 414.0
25 TraesCS4B01G183000 chr2A 82.627 472 76 6 2726 3194 16843595 16843127 2.410000e-111 412.0
26 TraesCS4B01G183000 chr2A 84.127 63 10 0 1000 1062 53332096 53332034 1.010000e-05 62.1
27 TraesCS4B01G183000 chr2B 81.930 487 79 9 2729 3211 1803485 1803004 1.450000e-108 403.0
28 TraesCS4B01G183000 chr2B 92.929 198 13 1 31 227 722461867 722461670 1.530000e-73 287.0
29 TraesCS4B01G183000 chr4D 81.595 489 85 5 2728 3213 54280955 54280469 1.880000e-107 399.0
30 TraesCS4B01G183000 chr1A 81.670 491 80 9 2726 3211 230130492 230130007 1.880000e-107 399.0
31 TraesCS4B01G183000 chr1D 82.533 458 67 9 2732 3182 25718295 25717844 1.130000e-104 390.0
32 TraesCS4B01G183000 chr1D 85.897 156 18 4 3205 3359 439741268 439741420 2.680000e-36 163.0
33 TraesCS4B01G183000 chr6B 80.612 490 82 11 2726 3211 662145202 662144722 1.900000e-97 366.0
34 TraesCS4B01G183000 chr6B 84.667 150 23 0 3210 3359 151419631 151419780 2.090000e-32 150.0
35 TraesCS4B01G183000 chr6B 88.333 60 7 0 1000 1059 663786049 663785990 4.650000e-09 73.1
36 TraesCS4B01G183000 chr6B 85.938 64 9 0 1000 1063 45729772 45729835 6.020000e-08 69.4
37 TraesCS4B01G183000 chr6D 93.434 198 12 1 31 227 424820756 424820953 3.280000e-75 292.0
38 TraesCS4B01G183000 chr6D 92.929 198 13 1 31 227 91818584 91818387 1.530000e-73 287.0
39 TraesCS4B01G183000 chr6D 92.929 198 13 1 31 227 221858782 221858979 1.530000e-73 287.0
40 TraesCS4B01G183000 chrUn 92.929 198 13 1 31 227 86973358 86973555 1.530000e-73 287.0
41 TraesCS4B01G183000 chrUn 92.929 198 13 1 31 227 87001479 87001282 1.530000e-73 287.0
42 TraesCS4B01G183000 chrUn 92.929 198 13 1 31 227 273672125 273672322 1.530000e-73 287.0
43 TraesCS4B01G183000 chr2D 92.241 116 9 0 3244 3359 621745785 621745670 7.460000e-37 165.0
44 TraesCS4B01G183000 chr2D 84.932 146 22 0 3214 3359 69492288 69492143 7.510000e-32 148.0


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 TraesCS4B01G183000 chr4B 402736313 402739672 3359 True 6205.00 6205 100.000 1 3360 1 chr4B.!!$R1 3359
1 TraesCS4B01G183000 chr4B 402762370 402763389 1019 True 209.00 209 71.747 1306 2336 1 chr4B.!!$R2 1030
2 TraesCS4B01G183000 chr7B 112295784 112299118 3334 True 5622.00 5622 96.997 1 3360 1 chr7B.!!$R2 3359
3 TraesCS4B01G183000 chr7B 112112842 112114667 1825 True 1194.00 1736 89.587 549 2433 2 chr7B.!!$R5 1884
4 TraesCS4B01G183000 chr7B 727232373 727232958 585 True 905.00 905 94.539 1549 2134 1 chr7B.!!$R4 585
5 TraesCS4B01G183000 chr7B 112337794 112338819 1025 True 237.00 237 72.155 1301 2336 1 chr7B.!!$R3 1035
6 TraesCS4B01G183000 chr7D 149848282 149850532 2250 True 910.60 2211 91.708 369 2676 3 chr7D.!!$R2 2307
7 TraesCS4B01G183000 chr7A 150328231 150330480 2249 True 669.25 1742 89.083 260 2596 4 chr7A.!!$R2 2336

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
109 110 1.956477 GCAAGTCCTTCTTTTGCTCCA 59.044 47.619 1.51 0.0 42.84 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2517 6.697455 TGTAAGCAATACTCGATCAGTTGATC 59.303 38.462 11.27 11.27 40.07 2.92 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
17 18 2.897972 GTCCCACGAATACCCGCT 59.102 61.111 0.00 0.00 0.00 5.52
68 69 5.652891 TCGGTATCTTATCATAGGCCTTCTC 59.347 44.000 12.58 0.00 0.00 2.87
78 79 4.968719 TCATAGGCCTTCTCCAAGTCAATA 59.031 41.667 12.58 0.00 0.00 1.90
109 110 1.956477 GCAAGTCCTTCTTTTGCTCCA 59.044 47.619 1.51 0.00 42.84 3.86
189 190 5.528320 AGGCATGAAACAAACTGATTTTTGG 59.472 36.000 0.00 0.00 40.25 3.28
192 193 6.639212 CATGAAACAAACTGATTTTTGGTCG 58.361 36.000 0.00 0.00 40.25 4.79
212 213 5.389935 GGTCGTGCTTGTCATTCTTCTTAAG 60.390 44.000 0.00 0.00 0.00 1.85
1156 1249 2.553770 CCGCACGCGAAAATGTCA 59.446 55.556 15.93 0.00 42.83 3.58
1231 1328 2.279318 TGCGCGTCGTGTGGTTTA 60.279 55.556 8.43 0.00 0.00 2.01
2086 2226 1.622752 GGGGGAAAGGGAGGTGGAT 60.623 63.158 0.00 0.00 0.00 3.41
2396 2559 5.103000 ACTGATCGAGTATTGCTTACACAC 58.897 41.667 0.00 0.00 30.86 3.82
2439 2610 6.669125 AAAAGGGTGTCAATCAATCAATCA 57.331 33.333 0.00 0.00 0.00 2.57
2440 2611 6.669125 AAAGGGTGTCAATCAATCAATCAA 57.331 33.333 0.00 0.00 0.00 2.57
2441 2612 6.862469 AAGGGTGTCAATCAATCAATCAAT 57.138 33.333 0.00 0.00 0.00 2.57
2442 2613 6.461110 AGGGTGTCAATCAATCAATCAATC 57.539 37.500 0.00 0.00 0.00 2.67
2485 2656 0.112995 TGTACTACCTGGTCACCGGT 59.887 55.000 13.87 13.87 35.40 5.28
2553 2735 9.634021 ATCGGATAGTGCTCTTATCTTCATATA 57.366 33.333 0.00 0.00 0.00 0.86
2776 2958 1.948145 AGGTTCGTAGATCACCTAGCG 59.052 52.381 0.00 0.00 45.08 4.26
2823 3005 1.666553 GGCACACCGTCGTCATTGA 60.667 57.895 0.00 0.00 0.00 2.57
2825 3007 1.897398 GCACACCGTCGTCATTGACC 61.897 60.000 11.12 0.00 35.40 4.02
2826 3008 1.005394 ACACCGTCGTCATTGACCC 60.005 57.895 11.12 1.62 35.40 4.46
2827 3009 1.292223 CACCGTCGTCATTGACCCT 59.708 57.895 11.12 0.00 35.40 4.34
2828 3010 0.736325 CACCGTCGTCATTGACCCTC 60.736 60.000 11.12 1.65 35.40 4.30
2829 3011 1.153628 CCGTCGTCATTGACCCTCC 60.154 63.158 11.12 0.00 35.40 4.30
2830 3012 1.153628 CGTCGTCATTGACCCTCCC 60.154 63.158 11.12 0.00 35.40 4.30
2831 3013 1.605058 CGTCGTCATTGACCCTCCCT 61.605 60.000 11.12 0.00 35.40 4.20
2832 3014 0.613777 GTCGTCATTGACCCTCCCTT 59.386 55.000 11.12 0.00 32.61 3.95
2833 3015 1.829222 GTCGTCATTGACCCTCCCTTA 59.171 52.381 11.12 0.00 32.61 2.69
2834 3016 2.434702 GTCGTCATTGACCCTCCCTTAT 59.565 50.000 11.12 0.00 32.61 1.73
2835 3017 2.698797 TCGTCATTGACCCTCCCTTATC 59.301 50.000 11.12 0.00 0.00 1.75
2836 3018 2.545952 CGTCATTGACCCTCCCTTATCG 60.546 54.545 11.12 0.00 0.00 2.92
2837 3019 2.047061 TCATTGACCCTCCCTTATCGG 58.953 52.381 0.00 0.00 0.00 4.18
2838 3020 2.047061 CATTGACCCTCCCTTATCGGA 58.953 52.381 0.00 0.00 33.16 4.55
2851 3033 0.178984 TATCGGAGCCGGACATACCA 60.179 55.000 5.05 0.00 40.25 3.25
2900 3082 2.483714 CGTGCTAATGCCACATAGGACT 60.484 50.000 8.62 0.00 41.22 3.85
2915 3097 1.137086 AGGACTAGCGCACCATAACAG 59.863 52.381 11.47 0.00 0.00 3.16
2943 3125 4.504461 CACCGACGATGAAAAGAATCCTAG 59.496 45.833 0.00 0.00 0.00 3.02
2970 3152 1.825474 AGGATCCAACCTGTAGACACG 59.175 52.381 15.82 0.00 39.01 4.49
2972 3154 0.973632 ATCCAACCTGTAGACACGCA 59.026 50.000 0.00 0.00 0.00 5.24
3000 3182 0.102481 CGAACGAAGACCGGATCCAT 59.898 55.000 9.46 0.00 43.93 3.41
3001 3183 1.571919 GAACGAAGACCGGATCCATG 58.428 55.000 9.46 4.51 43.93 3.66
3133 3315 2.439507 GGAGGACCTTATTCCATCTGCA 59.560 50.000 0.00 0.00 38.25 4.41
3162 3344 3.181492 TGTCTCAAGCTCGCATCTTAGAG 60.181 47.826 0.00 0.00 37.54 2.43
3181 3363 1.493022 AGCAGGACACAAACCCTAACA 59.507 47.619 0.00 0.00 0.00 2.41
3184 3366 3.490249 GCAGGACACAAACCCTAACAAAC 60.490 47.826 0.00 0.00 0.00 2.93
3228 3411 1.315257 GCACGAAGGGGACATGCATT 61.315 55.000 0.00 0.00 36.30 3.56
3229 3412 2.016604 GCACGAAGGGGACATGCATTA 61.017 52.381 0.00 0.00 36.30 1.90
3236 3419 1.133976 GGGGACATGCATTAGCTGAGT 60.134 52.381 0.00 0.00 42.74 3.41
3345 3528 3.906649 CGCACGAGTCGATGCAGC 61.907 66.667 27.44 18.36 42.17 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.705337 GGAACGTCATGTGGCATCGG 61.705 60.000 0.00 0.00 0.00 4.18
68 69 8.192774 ACTTGCATATGATGTTTATTGACTTGG 58.807 33.333 6.97 0.00 0.00 3.61
78 79 7.472334 AAAGAAGGACTTGCATATGATGTTT 57.528 32.000 6.97 0.00 38.98 2.83
109 110 3.484407 GGCAACTTATGGAGAGATGCAT 58.516 45.455 0.00 0.00 35.90 3.96
189 190 5.591643 TTAAGAAGAATGACAAGCACGAC 57.408 39.130 0.00 0.00 0.00 4.34
192 193 4.398247 CGCTTAAGAAGAATGACAAGCAC 58.602 43.478 6.67 0.00 38.59 4.40
212 213 3.313526 AGATTATTGTCATTGAGCACCGC 59.686 43.478 0.00 0.00 0.00 5.68
874 944 0.967380 CTCATGGTGGGTGGCTTTCC 60.967 60.000 0.00 0.00 0.00 3.13
875 945 0.251341 ACTCATGGTGGGTGGCTTTC 60.251 55.000 0.00 0.00 23.94 2.62
2368 2517 6.697455 TGTAAGCAATACTCGATCAGTTGATC 59.303 38.462 11.27 11.27 40.07 2.92
2396 2559 2.917701 TTTTACACTCATGCATGCCG 57.082 45.000 22.25 16.64 0.00 5.69
2435 2606 9.826574 AGCATGCTATGTTTATTTTGATTGATT 57.173 25.926 21.21 0.00 0.00 2.57
2436 2607 9.826574 AAGCATGCTATGTTTATTTTGATTGAT 57.173 25.926 23.00 0.00 31.68 2.57
2437 2608 9.089601 CAAGCATGCTATGTTTATTTTGATTGA 57.910 29.630 23.00 0.00 32.62 2.57
2485 2656 3.350909 CTTCGTCCACCATCCGCGA 62.351 63.158 8.23 0.00 0.00 5.87
2753 2935 2.526888 AGGTGATCTACGAACCTGGA 57.473 50.000 0.00 0.00 42.78 3.86
2757 2939 1.945394 TCGCTAGGTGATCTACGAACC 59.055 52.381 0.00 0.00 32.69 3.62
2776 2958 2.059541 GTTCCAGTGCTTGTAGTCGTC 58.940 52.381 0.00 0.00 0.00 4.20
2810 2992 1.590147 GAGGGTCAATGACGACGGT 59.410 57.895 7.35 0.00 36.73 4.83
2827 3009 1.831286 GTCCGGCTCCGATAAGGGA 60.831 63.158 10.28 0.00 42.83 4.20
2828 3010 1.472662 ATGTCCGGCTCCGATAAGGG 61.473 60.000 10.28 0.00 42.83 3.95
2829 3011 1.067776 GTATGTCCGGCTCCGATAAGG 60.068 57.143 10.28 0.00 42.83 2.69
2830 3012 1.067776 GGTATGTCCGGCTCCGATAAG 60.068 57.143 10.28 0.00 42.83 1.73
2831 3013 0.963962 GGTATGTCCGGCTCCGATAA 59.036 55.000 10.28 0.00 42.83 1.75
2832 3014 0.178984 TGGTATGTCCGGCTCCGATA 60.179 55.000 10.28 0.00 42.83 2.92
2833 3015 0.832135 ATGGTATGTCCGGCTCCGAT 60.832 55.000 10.28 0.00 42.83 4.18
2834 3016 1.456892 ATGGTATGTCCGGCTCCGA 60.457 57.895 10.28 0.00 42.83 4.55
2835 3017 1.300931 CATGGTATGTCCGGCTCCG 60.301 63.158 0.00 0.48 39.52 4.63
2836 3018 0.180406 AACATGGTATGTCCGGCTCC 59.820 55.000 0.00 0.00 44.07 4.70
2837 3019 1.299541 CAACATGGTATGTCCGGCTC 58.700 55.000 0.00 0.00 44.07 4.70
2838 3020 0.618458 ACAACATGGTATGTCCGGCT 59.382 50.000 0.00 0.00 44.07 5.52
2839 3021 2.210116 CTACAACATGGTATGTCCGGC 58.790 52.381 0.00 0.00 44.07 6.13
2840 3022 3.536956 ACTACAACATGGTATGTCCGG 57.463 47.619 0.00 0.00 44.07 5.14
2871 3053 1.076332 GGCATTAGCACGACGACTTT 58.924 50.000 0.00 0.00 44.61 2.66
2887 3069 1.326951 TGCGCTAGTCCTATGTGGCA 61.327 55.000 9.73 0.00 35.26 4.92
2900 3082 2.159028 TGTATGCTGTTATGGTGCGCTA 60.159 45.455 9.73 0.00 0.00 4.26
2915 3097 2.927477 TCTTTTCATCGTCGGTGTATGC 59.073 45.455 5.22 0.00 0.00 3.14
2943 3125 1.486726 ACAGGTTGGATCCTTCCGATC 59.513 52.381 14.23 0.00 45.89 3.69
2970 3152 1.591158 TCTTCGTTCGTCTGTGTTTGC 59.409 47.619 0.00 0.00 0.00 3.68
2972 3154 2.199236 GGTCTTCGTTCGTCTGTGTTT 58.801 47.619 0.00 0.00 0.00 2.83
3000 3182 2.920724 TTGTCTTCGGTGGATTCACA 57.079 45.000 6.44 0.00 45.32 3.58
3001 3183 3.670627 GCATTTGTCTTCGGTGGATTCAC 60.671 47.826 0.00 0.00 42.91 3.18
3061 3243 1.811266 CATCTTCGGAGGGTGTGCG 60.811 63.158 0.00 0.00 42.36 5.34
3162 3344 1.975660 TGTTAGGGTTTGTGTCCTGC 58.024 50.000 0.00 0.00 34.75 4.85
3228 3411 3.449227 CCGTCCCGCACTCAGCTA 61.449 66.667 0.00 0.00 42.61 3.32
3308 3491 3.706373 ACCGCTGCGTCATCCCTT 61.706 61.111 21.59 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.