Multiple sequence alignment - TraesCS5B01G468700

Loading Multiple Alignment...

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 TraesCS5B01G468700 chr5B 100.000 3233 0 0 1 3233 642143359 642140127 0.000000e+00 5971.0
1 TraesCS5B01G468700 chr5B 95.125 2072 65 14 526 2578 642306152 642308206 0.000000e+00 3234.0
2 TraesCS5B01G468700 chr5B 82.731 1135 185 9 1088 2218 642281913 642283040 0.000000e+00 1000.0
3 TraesCS5B01G468700 chr5B 82.637 455 44 13 120 542 642305685 642306136 1.420000e-98 370.0
4 TraesCS5B01G468700 chr5B 94.488 127 6 1 1 126 642305516 642305642 9.150000e-46 195.0
5 TraesCS5B01G468700 chr5B 91.071 112 7 3 232 341 491603884 491603994 7.230000e-32 148.0
6 TraesCS5B01G468700 chr5B 92.157 51 4 0 136 186 137049669 137049719 4.470000e-09 73.1
7 TraesCS5B01G468700 chr5D 90.594 2456 145 33 120 2520 510960325 510957901 0.000000e+00 3177.0
8 TraesCS5B01G468700 chr5D 82.582 1131 186 9 1091 2217 510966695 510965572 0.000000e+00 987.0
9 TraesCS5B01G468700 chr5D 94.006 634 34 3 2602 3233 241110408 241111039 0.000000e+00 957.0
10 TraesCS5B01G468700 chr5D 93.671 632 36 3 2604 3233 205118172 205117543 0.000000e+00 942.0
11 TraesCS5B01G468700 chr5D 80.252 238 28 12 124 343 526752736 526752500 9.280000e-36 161.0
12 TraesCS5B01G468700 chr5A 90.570 2439 153 24 126 2520 639294223 639291818 0.000000e+00 3158.0
13 TraesCS5B01G468700 chr5A 82.099 1134 192 9 1088 2217 639301543 639300417 0.000000e+00 959.0
14 TraesCS5B01G468700 chr5A 80.357 560 93 11 1652 2209 639281107 639281651 3.000000e-110 409.0
15 TraesCS5B01G468700 chr5A 78.448 116 20 4 4 114 478863729 478863844 1.610000e-08 71.3
16 TraesCS5B01G468700 chr4A 94.173 635 35 2 2600 3233 648753571 648754204 0.000000e+00 966.0
17 TraesCS5B01G468700 chr4A 79.730 222 25 12 139 343 483958503 483958721 3.360000e-30 143.0
18 TraesCS5B01G468700 chr3B 93.691 634 38 2 2600 3233 263781512 263780881 0.000000e+00 948.0
19 TraesCS5B01G468700 chr7D 93.553 636 35 4 2602 3233 150754858 150755491 0.000000e+00 942.0
20 TraesCS5B01G468700 chr7D 87.654 81 7 3 1 79 604530108 604530187 1.240000e-14 91.6
21 TraesCS5B01G468700 chr6B 93.168 644 37 3 2593 3233 348693910 348693271 0.000000e+00 939.0
22 TraesCS5B01G468700 chr1A 93.386 635 38 3 2602 3233 574917975 574917342 0.000000e+00 937.0
23 TraesCS5B01G468700 chr1B 93.250 637 39 3 2600 3233 538198639 538199274 0.000000e+00 935.0
24 TraesCS5B01G468700 chr1B 79.821 223 27 10 125 332 495956499 495956280 2.600000e-31 147.0
25 TraesCS5B01G468700 chr7B 92.736 647 45 2 2587 3233 584258652 584258008 0.000000e+00 933.0
26 TraesCS5B01G468700 chr7B 80.579 242 28 9 120 343 52367715 52367475 5.550000e-38 169.0
27 TraesCS5B01G468700 chr7B 78.261 115 20 4 1 112 730184316 730184204 5.790000e-08 69.4
28 TraesCS5B01G468700 chr1D 73.442 738 180 16 1249 1978 47883150 47882421 2.470000e-66 263.0
29 TraesCS5B01G468700 chr1D 80.000 115 22 1 1 114 476447218 476447332 2.070000e-12 84.2
30 TraesCS5B01G468700 chr2B 81.328 241 28 8 120 343 363772648 363772888 2.560000e-41 180.0
31 TraesCS5B01G468700 chr2A 80.247 243 31 11 124 349 526100772 526100530 2.000000e-37 167.0
32 TraesCS5B01G468700 chr2A 88.496 113 12 1 3 114 716237408 716237520 5.630000e-28 135.0
33 TraesCS5B01G468700 chr2A 83.607 122 15 4 1 121 476217993 476217876 3.410000e-20 110.0
34 TraesCS5B01G468700 chr2A 94.643 56 2 1 68 122 30629775 30629720 5.750000e-13 86.1
35 TraesCS5B01G468700 chr2D 80.663 181 23 12 124 297 580621830 580622005 2.620000e-26 130.0
36 TraesCS5B01G468700 chr3A 83.784 111 17 1 1 110 13002165 13002275 1.590000e-18 104.0
37 TraesCS5B01G468700 chr6D 75.814 215 33 11 120 316 365598878 365599091 1.240000e-14 91.6
38 TraesCS5B01G468700 chr6D 85.542 83 10 2 1 82 29982018 29981937 5.750000e-13 86.1


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 TraesCS5B01G468700 chr5B 642140127 642143359 3232 True 5971.000000 5971 100.000 1 3233 1 chr5B.!!$R1 3232
1 TraesCS5B01G468700 chr5B 642305516 642308206 2690 False 1266.333333 3234 90.750 1 2578 3 chr5B.!!$F4 2577
2 TraesCS5B01G468700 chr5B 642281913 642283040 1127 False 1000.000000 1000 82.731 1088 2218 1 chr5B.!!$F3 1130
3 TraesCS5B01G468700 chr5D 510957901 510960325 2424 True 3177.000000 3177 90.594 120 2520 1 chr5D.!!$R2 2400
4 TraesCS5B01G468700 chr5D 510965572 510966695 1123 True 987.000000 987 82.582 1091 2217 1 chr5D.!!$R3 1126
5 TraesCS5B01G468700 chr5D 241110408 241111039 631 False 957.000000 957 94.006 2602 3233 1 chr5D.!!$F1 631
6 TraesCS5B01G468700 chr5D 205117543 205118172 629 True 942.000000 942 93.671 2604 3233 1 chr5D.!!$R1 629
7 TraesCS5B01G468700 chr5A 639291818 639294223 2405 True 3158.000000 3158 90.570 126 2520 1 chr5A.!!$R1 2394
8 TraesCS5B01G468700 chr5A 639300417 639301543 1126 True 959.000000 959 82.099 1088 2217 1 chr5A.!!$R2 1129
9 TraesCS5B01G468700 chr5A 639281107 639281651 544 False 409.000000 409 80.357 1652 2209 1 chr5A.!!$F2 557
10 TraesCS5B01G468700 chr4A 648753571 648754204 633 False 966.000000 966 94.173 2600 3233 1 chr4A.!!$F2 633
11 TraesCS5B01G468700 chr3B 263780881 263781512 631 True 948.000000 948 93.691 2600 3233 1 chr3B.!!$R1 633
12 TraesCS5B01G468700 chr7D 150754858 150755491 633 False 942.000000 942 93.553 2602 3233 1 chr7D.!!$F1 631
13 TraesCS5B01G468700 chr6B 348693271 348693910 639 True 939.000000 939 93.168 2593 3233 1 chr6B.!!$R1 640
14 TraesCS5B01G468700 chr1A 574917342 574917975 633 True 937.000000 937 93.386 2602 3233 1 chr1A.!!$R1 631
15 TraesCS5B01G468700 chr1B 538198639 538199274 635 False 935.000000 935 93.250 2600 3233 1 chr1B.!!$F1 633
16 TraesCS5B01G468700 chr7B 584258008 584258652 644 True 933.000000 933 92.736 2587 3233 1 chr7B.!!$R2 646
17 TraesCS5B01G468700 chr1D 47882421 47883150 729 True 263.000000 263 73.442 1249 1978 1 chr1D.!!$R1 729

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
95 97 0.039617 GATCTGCTCGGATCTGGTCG 60.040 60.000 10.61 0.0 39.06 4.79 F
254 317 0.100861 GTGCTCTAGGTGGTCTACGC 59.899 60.000 0.00 0.0 0.00 4.42 F
1125 1277 1.370778 CGTCGACAACTACGGTGCA 60.371 57.895 17.16 0.0 35.51 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1781 2.271821 CGGGTGATGTGGATGCCA 59.728 61.111 0.0 0.0 0.0 4.92 R
2125 2277 1.256812 CCGCCTTCCATTTTCAGGTT 58.743 50.000 0.0 0.0 0.0 3.50 R
2571 2737 0.322456 CCCTCCTTGCGGTCAATGAA 60.322 55.000 0.0 0.0 0.0 2.57 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
47 48 1.338105 GGTGGCGCATCTAGCATCATA 60.338 52.381 10.83 0.00 46.13 2.15
48 49 1.998315 GTGGCGCATCTAGCATCATAG 59.002 52.381 10.83 0.00 46.13 2.23
49 50 1.620323 TGGCGCATCTAGCATCATAGT 59.380 47.619 10.83 0.00 46.13 2.12
50 51 1.998315 GGCGCATCTAGCATCATAGTG 59.002 52.381 10.83 0.00 46.13 2.74
51 52 2.353109 GGCGCATCTAGCATCATAGTGA 60.353 50.000 10.83 0.00 46.13 3.41
95 97 0.039617 GATCTGCTCGGATCTGGTCG 60.040 60.000 10.61 0.00 39.06 4.79
107 109 0.792640 TCTGGTCGTCGTTCGTCTAC 59.207 55.000 0.00 0.00 40.80 2.59
114 116 1.201661 CGTCGTTCGTCTACGTTCGTA 60.202 52.381 16.12 5.02 42.01 3.43
122 173 2.476686 CGTCTACGTTCGTATGGCTTCA 60.477 50.000 5.55 0.00 34.11 3.02
157 208 2.132352 GGGGCCTTAGGACGACGAT 61.132 63.158 0.69 0.00 0.00 3.73
160 211 1.406477 GGGCCTTAGGACGACGATTTT 60.406 52.381 0.69 0.00 0.00 1.82
172 223 4.679662 ACGACGATTTTCCGATTGTCTAT 58.320 39.130 0.00 0.00 37.99 1.98
220 272 3.998672 GAGGGACGTTGACGGGCA 61.999 66.667 8.52 0.00 44.95 5.36
254 317 0.100861 GTGCTCTAGGTGGTCTACGC 59.899 60.000 0.00 0.00 0.00 4.42
304 367 5.576774 TGATGTTCGTTGTACTGTCATGATC 59.423 40.000 0.00 0.00 0.00 2.92
322 386 7.009448 GTCATGATCGAAGATGAATAGATCAGC 59.991 40.741 10.42 0.00 46.98 4.26
332 396 6.841443 ATGAATAGATCAGCAGTTTTCTCG 57.159 37.500 0.00 0.00 42.53 4.04
333 397 5.111989 TGAATAGATCAGCAGTTTTCTCGG 58.888 41.667 0.00 0.00 33.04 4.63
446 533 3.899360 ACGATGGGACCTAATAAATCCGA 59.101 43.478 0.00 0.00 32.90 4.55
448 535 5.012768 ACGATGGGACCTAATAAATCCGAAT 59.987 40.000 0.00 0.00 32.90 3.34
660 788 4.237724 GTTTATCTCCTTTGTTGCCAAGC 58.762 43.478 0.00 0.00 0.00 4.01
793 927 4.757149 ACTCTTGCCAAGCTAACTAAACTG 59.243 41.667 0.00 0.00 0.00 3.16
917 1069 3.245193 ACTCCTACTCCTACGACCAAACT 60.245 47.826 0.00 0.00 0.00 2.66
977 1129 3.365364 CCAATCTTCACTCTTGCGTTTCC 60.365 47.826 0.00 0.00 0.00 3.13
978 1130 1.878953 TCTTCACTCTTGCGTTTCCC 58.121 50.000 0.00 0.00 0.00 3.97
1125 1277 1.370778 CGTCGACAACTACGGTGCA 60.371 57.895 17.16 0.00 35.51 4.57
1629 1781 3.256960 ACCAGCCCCAACACCGAT 61.257 61.111 0.00 0.00 0.00 4.18
2125 2277 5.128663 TCCGACATTGTCTTGGAGAATATCA 59.871 40.000 14.54 0.00 0.00 2.15
2169 2321 1.014352 GTGACACGGAAAGCACTTGT 58.986 50.000 0.00 0.00 0.00 3.16
2272 2428 4.015872 TGACAGGTTCTTGTTGTATCCC 57.984 45.455 0.00 0.00 0.00 3.85
2273 2429 3.650942 TGACAGGTTCTTGTTGTATCCCT 59.349 43.478 0.00 0.00 0.00 4.20
2274 2430 4.003648 GACAGGTTCTTGTTGTATCCCTG 58.996 47.826 0.00 0.00 42.84 4.45
2275 2431 3.394606 ACAGGTTCTTGTTGTATCCCTGT 59.605 43.478 0.00 0.00 44.70 4.00
2276 2432 4.595781 ACAGGTTCTTGTTGTATCCCTGTA 59.404 41.667 6.64 0.00 46.89 2.74
2277 2433 4.935808 CAGGTTCTTGTTGTATCCCTGTAC 59.064 45.833 0.00 0.00 34.63 2.90
2278 2434 4.595781 AGGTTCTTGTTGTATCCCTGTACA 59.404 41.667 0.00 0.00 32.99 2.90
2529 2695 7.757624 GTCAGAAAACAGGTGATTTGTTTGTAA 59.242 33.333 4.35 0.00 45.28 2.41
2571 2737 4.081972 AGACTATGAGAACGCACATGAACT 60.082 41.667 0.00 0.00 0.00 3.01
2578 2744 3.814842 AGAACGCACATGAACTTCATTGA 59.185 39.130 0.00 0.00 34.28 2.57
2579 2745 3.542712 ACGCACATGAACTTCATTGAC 57.457 42.857 0.00 0.00 34.28 3.18
2580 2746 2.226437 ACGCACATGAACTTCATTGACC 59.774 45.455 0.00 0.00 34.28 4.02
2581 2747 2.725759 CGCACATGAACTTCATTGACCG 60.726 50.000 0.00 0.25 34.28 4.79
2582 2748 2.855180 CACATGAACTTCATTGACCGC 58.145 47.619 0.00 0.00 34.28 5.68
2583 2749 2.226200 CACATGAACTTCATTGACCGCA 59.774 45.455 0.00 0.00 34.28 5.69
2584 2750 2.884012 ACATGAACTTCATTGACCGCAA 59.116 40.909 0.00 0.00 34.28 4.85
2585 2751 3.058016 ACATGAACTTCATTGACCGCAAG 60.058 43.478 0.00 0.00 34.28 4.01
2752 2922 2.041265 GGCTCTTCCTCCCTCCCA 59.959 66.667 0.00 0.00 0.00 4.37
2757 2927 2.284405 TTCCTCCCTCCCACGTCC 60.284 66.667 0.00 0.00 0.00 4.79
2813 2983 2.023318 CCGATCTAGAAGCGACGGT 58.977 57.895 16.98 0.00 36.38 4.83
2940 3110 2.766263 TGTCATCTGGCTTTAGATCGGT 59.234 45.455 0.00 0.00 35.28 4.69
2941 3111 3.958147 TGTCATCTGGCTTTAGATCGGTA 59.042 43.478 0.00 0.00 35.28 4.02
2944 3114 2.384828 TCTGGCTTTAGATCGGTAGCA 58.615 47.619 14.85 4.27 35.36 3.49
2945 3115 2.764010 TCTGGCTTTAGATCGGTAGCAA 59.236 45.455 14.85 5.85 35.36 3.91
3013 3183 1.304630 TGGCCGGTGTAGCTAGTGA 60.305 57.895 1.90 0.00 0.00 3.41
3094 3264 1.427753 TCCATCATCTAGTCCCGGCTA 59.572 52.381 0.00 0.00 0.00 3.93
3109 3279 1.139095 GCTACGAGTTGGGGAGACG 59.861 63.158 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.946201 CAGGATGGGGGCTAGGCG 61.946 72.222 10.58 0.00 0.00 5.52
47 48 0.179084 CACACCTCCACACGTTCACT 60.179 55.000 0.00 0.00 0.00 3.41
48 49 0.461339 ACACACCTCCACACGTTCAC 60.461 55.000 0.00 0.00 0.00 3.18
49 50 0.179094 GACACACCTCCACACGTTCA 60.179 55.000 0.00 0.00 0.00 3.18
50 51 0.104304 AGACACACCTCCACACGTTC 59.896 55.000 0.00 0.00 0.00 3.95
51 52 0.539986 AAGACACACCTCCACACGTT 59.460 50.000 0.00 0.00 0.00 3.99
95 97 2.487406 TACGAACGTAGACGAACGAC 57.513 50.000 22.89 0.00 45.68 4.34
107 109 0.999406 CACCTGAAGCCATACGAACG 59.001 55.000 0.00 0.00 0.00 3.95
114 116 2.749044 CAGCGCACCTGAAGCCAT 60.749 61.111 11.47 0.00 44.64 4.40
122 173 1.221840 CCATAGAACCAGCGCACCT 59.778 57.895 11.47 0.93 0.00 4.00
186 237 3.702048 CCCTCGCCGGAGTTGGAA 61.702 66.667 5.05 0.00 38.70 3.53
187 238 4.689549 TCCCTCGCCGGAGTTGGA 62.690 66.667 5.05 10.22 38.70 3.53
208 260 2.740826 CCGAATGCCCGTCAACGT 60.741 61.111 1.48 0.00 37.74 3.99
211 263 2.435938 GAGCCGAATGCCCGTCAA 60.436 61.111 0.00 0.00 42.71 3.18
220 272 0.108138 AGCACTAAAGCGAGCCGAAT 60.108 50.000 0.00 0.00 40.15 3.34
304 367 6.841443 AAACTGCTGATCTATTCATCTTCG 57.159 37.500 0.00 0.00 32.72 3.79
356 425 7.201565 GCCACAAAAAGTATAGAGATGTCTGAC 60.202 40.741 1.88 0.00 33.84 3.51
360 429 6.371548 TGTGCCACAAAAAGTATAGAGATGTC 59.628 38.462 0.00 0.00 0.00 3.06
432 519 6.099845 ACTCACTCCATTCGGATTTATTAGGT 59.900 38.462 0.00 0.00 41.79 3.08
448 535 8.584063 TGTTACATACAATAGTACTCACTCCA 57.416 34.615 0.00 0.00 33.07 3.86
660 788 2.985282 AGGTGTTGTGCATGGCCG 60.985 61.111 0.00 0.00 0.00 6.13
851 999 1.078143 AAGCCGATGGAGACCAAGC 60.078 57.895 0.00 0.00 36.95 4.01
896 1044 3.354467 AGTTTGGTCGTAGGAGTAGGAG 58.646 50.000 0.00 0.00 0.00 3.69
917 1069 1.302192 GCCTGGTTTGTAGCGTGGA 60.302 57.895 0.00 0.00 0.00 4.02
977 1129 2.027745 TGAAGCAGCTAGAGACAAAGGG 60.028 50.000 0.00 0.00 0.00 3.95
978 1130 2.999355 GTGAAGCAGCTAGAGACAAAGG 59.001 50.000 0.00 0.00 0.00 3.11
1083 1235 3.575687 TGAAGACATTCTGCTGAGTCTCA 59.424 43.478 13.54 1.78 40.22 3.27
1629 1781 2.271821 CGGGTGATGTGGATGCCA 59.728 61.111 0.00 0.00 0.00 4.92
2125 2277 1.256812 CCGCCTTCCATTTTCAGGTT 58.743 50.000 0.00 0.00 0.00 3.50
2157 2309 2.294233 TGCATTCTGACAAGTGCTTTCC 59.706 45.455 7.58 0.00 38.37 3.13
2169 2321 4.603989 TTCTTGCCATTTTGCATTCTGA 57.396 36.364 0.00 0.00 41.70 3.27
2319 2476 6.564709 ATGTATGCACAAGTATATGGCTTG 57.435 37.500 15.77 15.77 46.23 4.01
2529 2695 8.562892 CATAGTCTTCACTCTGTTTTGTTTCAT 58.437 33.333 0.00 0.00 33.62 2.57
2571 2737 0.322456 CCCTCCTTGCGGTCAATGAA 60.322 55.000 0.00 0.00 0.00 2.57
2578 2744 4.016706 CGGTTCCCTCCTTGCGGT 62.017 66.667 0.00 0.00 0.00 5.68
2581 2747 4.388499 TCGCGGTTCCCTCCTTGC 62.388 66.667 6.13 0.00 0.00 4.01
2582 2748 2.125512 CTCGCGGTTCCCTCCTTG 60.126 66.667 6.13 0.00 0.00 3.61
2583 2749 3.391382 CCTCGCGGTTCCCTCCTT 61.391 66.667 6.13 0.00 0.00 3.36
2768 2938 2.034066 CACGCATGTTGGGGTCCT 59.966 61.111 0.00 0.00 34.28 3.85
2940 3110 2.678934 AGGCCCTCGACGTTGCTA 60.679 61.111 0.00 0.00 0.00 3.49
2941 3111 4.379243 CAGGCCCTCGACGTTGCT 62.379 66.667 0.00 0.00 0.00 3.91
2944 3114 4.003788 CACCAGGCCCTCGACGTT 62.004 66.667 0.00 0.00 0.00 3.99
3013 3183 2.417379 CGACGAAGAAGATGACCACCAT 60.417 50.000 0.00 0.00 38.43 3.55
3094 3264 2.571216 CCACGTCTCCCCAACTCGT 61.571 63.158 0.00 0.00 35.12 4.18
3109 3279 1.066752 GGTTTTCACCGGCAACCAC 59.933 57.895 16.71 3.41 39.93 4.16
3152 3322 3.131577 TCATCAAGGTTACGGCGTAGAAT 59.868 43.478 20.01 6.98 0.00 2.40


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

AutoCloner maintained by Alex Coulton.