Multiple sequence alignment - TraesCS3A01G460000

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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 TraesCS3A01G460000 chr3A 100.000 4178 0 0 1 4178 696333958 696329781 0.000000e+00 7716.0
1 TraesCS3A01G460000 chr3A 99.002 3306 26 4 1 3302 629086005 629089307 0.000000e+00 5915.0
2 TraesCS3A01G460000 chr3A 97.819 871 18 1 3309 4178 629090188 629091058 0.000000e+00 1502.0
3 TraesCS3A01G460000 chr3A 84.665 1076 145 16 987 2055 629056478 629057540 0.000000e+00 1055.0
4 TraesCS3A01G460000 chr3A 80.597 1072 163 21 993 2055 696478032 696476997 0.000000e+00 785.0
5 TraesCS3A01G460000 chr3A 83.554 529 70 15 2702 3218 629057931 629058454 2.920000e-131 479.0
6 TraesCS3A01G460000 chr3A 97.080 274 7 1 2390 2662 741483460 741483187 1.060000e-125 460.0
7 TraesCS3A01G460000 chr3A 97.080 274 7 1 2390 2662 741557380 741557107 1.060000e-125 460.0
8 TraesCS3A01G460000 chr3A 97.753 267 4 2 2387 2653 517388342 517388078 3.810000e-125 459.0
9 TraesCS3A01G460000 chr3A 96.715 274 8 1 2390 2662 741414254 741413981 4.920000e-124 455.0
10 TraesCS3A01G460000 chr3A 96.715 274 8 1 2390 2662 741465355 741465082 4.920000e-124 455.0
11 TraesCS3A01G460000 chr3A 96.350 274 9 1 2390 2662 741576328 741576055 2.290000e-122 449.0
12 TraesCS3A01G460000 chr3A 90.000 200 20 0 2166 2365 696343618 696343419 4.140000e-65 259.0
13 TraesCS3A01G460000 chr3A 86.385 213 22 5 2159 2370 696476926 696476720 4.200000e-55 226.0
14 TraesCS3A01G460000 chr3A 95.161 62 3 0 4117 4178 544922922 544922983 9.560000e-17 99.0
15 TraesCS3A01G460000 chr3B 91.771 2394 158 17 1 2368 744420874 744418494 0.000000e+00 3293.0
16 TraesCS3A01G460000 chr3B 91.747 2399 153 22 1 2368 747492022 747494406 0.000000e+00 3291.0
17 TraesCS3A01G460000 chr3B 85.489 1392 154 26 984 2367 745203414 745202063 0.000000e+00 1408.0
18 TraesCS3A01G460000 chr3B 84.576 1355 162 31 1027 2367 745474836 745473515 0.000000e+00 1301.0
19 TraesCS3A01G460000 chr3B 86.318 1089 141 6 945 2030 744590532 744591615 0.000000e+00 1179.0
20 TraesCS3A01G460000 chr3B 86.318 1089 141 6 945 2030 746856426 746855343 0.000000e+00 1179.0
21 TraesCS3A01G460000 chr3B 83.418 1182 163 23 902 2055 744513020 744511844 0.000000e+00 1066.0
22 TraesCS3A01G460000 chr3B 84.154 1117 143 26 982 2082 747093704 747094802 0.000000e+00 1051.0
23 TraesCS3A01G460000 chr3B 94.521 657 27 4 2650 3302 747494455 747495106 0.000000e+00 1005.0
24 TraesCS3A01G460000 chr3B 94.181 653 32 2 2650 3302 744418445 744417799 0.000000e+00 990.0
25 TraesCS3A01G460000 chr3B 84.676 509 71 5 2680 3185 744511373 744510869 6.240000e-138 501.0
26 TraesCS3A01G460000 chr3B 83.457 538 71 16 2702 3228 744545226 744544696 6.280000e-133 484.0
27 TraesCS3A01G460000 chr3B 90.521 211 15 2 3327 3536 744417164 744416958 1.480000e-69 274.0
28 TraesCS3A01G460000 chr3B 88.732 213 19 4 2158 2367 744339657 744339447 5.360000e-64 255.0
29 TraesCS3A01G460000 chr3B 84.211 247 35 4 3835 4078 523575480 523575235 1.940000e-58 237.0
30 TraesCS3A01G460000 chr3D 94.434 1545 66 10 831 2368 560235285 560233754 0.000000e+00 2359.0
31 TraesCS3A01G460000 chr3D 95.666 623 23 3 2650 3271 560233706 560233087 0.000000e+00 998.0
32 TraesCS3A01G460000 chr3D 79.274 854 115 38 12 851 560236145 560235340 1.320000e-149 540.0
33 TraesCS3A01G460000 chr3D 83.708 534 72 13 2705 3228 560285223 560284695 1.350000e-134 490.0
34 TraesCS3A01G460000 chr3D 81.319 455 51 17 1622 2055 560286133 560285692 5.170000e-89 339.0
35 TraesCS3A01G460000 chr3D 87.190 242 23 3 2126 2367 560784652 560784419 6.880000e-68 268.0
36 TraesCS3A01G460000 chr3D 83.275 287 39 8 3829 4110 565442434 565442716 5.360000e-64 255.0
37 TraesCS3A01G460000 chr3D 83.036 112 9 5 3328 3429 560231971 560231860 4.450000e-15 93.5
38 TraesCS3A01G460000 chrUn 96.934 424 10 1 2748 3171 476666784 476666364 0.000000e+00 708.0
39 TraesCS3A01G460000 chr7A 98.106 264 5 0 2390 2653 506291320 506291583 1.060000e-125 460.0
40 TraesCS3A01G460000 chr7A 83.453 278 39 7 3833 4108 214257595 214257323 6.930000e-63 252.0
41 TraesCS3A01G460000 chr6A 95.668 277 10 2 2393 2667 510256823 510256547 1.070000e-120 444.0
42 TraesCS3A01G460000 chr6A 84.436 257 38 2 3833 4087 415045515 415045259 6.930000e-63 252.0
43 TraesCS3A01G460000 chr6A 95.000 60 3 0 4119 4178 183622734 183622793 1.240000e-15 95.3
44 TraesCS3A01G460000 chr6D 84.116 277 39 5 3833 4105 346449036 346449311 3.200000e-66 263.0
45 TraesCS3A01G460000 chr6D 75.568 176 39 4 3643 3817 427761238 427761066 2.680000e-12 84.2
46 TraesCS3A01G460000 chr6D 81.319 91 17 0 3668 3758 418647838 418647748 1.610000e-09 75.0
47 TraesCS3A01G460000 chr4D 82.686 283 41 8 3832 4108 438516479 438516759 1.160000e-60 244.0
48 TraesCS3A01G460000 chr2D 83.936 249 35 5 3834 4079 372822347 372822101 2.510000e-57 233.0
49 TraesCS3A01G460000 chr2D 89.024 164 13 3 3117 3278 292665789 292665629 9.160000e-47 198.0
50 TraesCS3A01G460000 chr4B 81.206 282 44 9 3832 4108 542549534 542549811 7.030000e-53 219.0
51 TraesCS3A01G460000 chr1D 84.000 175 12 9 3321 3494 385624072 385624231 2.010000e-33 154.0
52 TraesCS3A01G460000 chr1B 83.429 175 13 9 3321 3494 517909141 517909300 9.360000e-32 148.0
53 TraesCS3A01G460000 chr1B 75.540 139 27 5 3650 3784 269210680 269210545 1.250000e-05 62.1
54 TraesCS3A01G460000 chr1A 81.977 172 15 11 3324 3494 485345252 485345408 9.420000e-27 132.0
55 TraesCS3A01G460000 chr5B 80.420 143 25 3 3642 3783 225547450 225547310 5.710000e-19 106.0
56 TraesCS3A01G460000 chr5D 96.667 60 2 0 4119 4178 367308597 367308656 2.660000e-17 100.0
57 TraesCS3A01G460000 chr2A 96.667 60 2 0 4119 4178 211140317 211140376 2.660000e-17 100.0
58 TraesCS3A01G460000 chr5A 98.148 54 1 0 4125 4178 350941079 350941026 1.240000e-15 95.3
59 TraesCS3A01G460000 chr5A 96.491 57 2 0 4122 4178 458387225 458387169 1.240000e-15 95.3
60 TraesCS3A01G460000 chr4A 96.491 57 2 0 4122 4178 189424067 189424011 1.240000e-15 95.3
61 TraesCS3A01G460000 chr2B 76.744 172 36 3 3664 3832 485887042 485886872 4.450000e-15 93.5
62 TraesCS3A01G460000 chr7D 92.188 64 5 0 4115 4178 551348989 551348926 1.600000e-14 91.6


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 TraesCS3A01G460000 chr3A 696329781 696333958 4177 True 7716.000 7716 100.000000 1 4178 1 chr3A.!!$R2 4177
1 TraesCS3A01G460000 chr3A 629086005 629091058 5053 False 3708.500 5915 98.410500 1 4178 2 chr3A.!!$F3 4177
2 TraesCS3A01G460000 chr3A 629056478 629058454 1976 False 767.000 1055 84.109500 987 3218 2 chr3A.!!$F2 2231
3 TraesCS3A01G460000 chr3A 696476720 696478032 1312 True 505.500 785 83.491000 993 2370 2 chr3A.!!$R9 1377
4 TraesCS3A01G460000 chr3B 747492022 747495106 3084 False 2148.000 3291 93.134000 1 3302 2 chr3B.!!$F3 3301
5 TraesCS3A01G460000 chr3B 744416958 744420874 3916 True 1519.000 3293 92.157667 1 3536 3 chr3B.!!$R7 3535
6 TraesCS3A01G460000 chr3B 745202063 745203414 1351 True 1408.000 1408 85.489000 984 2367 1 chr3B.!!$R4 1383
7 TraesCS3A01G460000 chr3B 745473515 745474836 1321 True 1301.000 1301 84.576000 1027 2367 1 chr3B.!!$R5 1340
8 TraesCS3A01G460000 chr3B 744590532 744591615 1083 False 1179.000 1179 86.318000 945 2030 1 chr3B.!!$F1 1085
9 TraesCS3A01G460000 chr3B 746855343 746856426 1083 True 1179.000 1179 86.318000 945 2030 1 chr3B.!!$R6 1085
10 TraesCS3A01G460000 chr3B 747093704 747094802 1098 False 1051.000 1051 84.154000 982 2082 1 chr3B.!!$F2 1100
11 TraesCS3A01G460000 chr3B 744510869 744513020 2151 True 783.500 1066 84.047000 902 3185 2 chr3B.!!$R8 2283
12 TraesCS3A01G460000 chr3B 744544696 744545226 530 True 484.000 484 83.457000 2702 3228 1 chr3B.!!$R3 526
13 TraesCS3A01G460000 chr3D 560231860 560236145 4285 True 997.625 2359 88.102500 12 3429 4 chr3D.!!$R2 3417
14 TraesCS3A01G460000 chr3D 560284695 560286133 1438 True 414.500 490 82.513500 1622 3228 2 chr3D.!!$R3 1606

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
155 161 3.683802 AGGAGGCTGAGTTTCTTTGATG 58.316 45.455 0.00 0.0 0.0 3.07 F
2230 2579 1.305219 TTTGGCCATAGACGTGCAGC 61.305 55.000 6.09 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2369 2718 9.431887 AGTACTAAATCAAAGACGCTTATTTCA 57.568 29.63 0.0 0.0 0.0 2.69 R
4066 5694 0.454957 CCTTGGCGTTGATTCTTGCG 60.455 55.00 0.0 0.0 0.0 4.85 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
155 161 3.683802 AGGAGGCTGAGTTTCTTTGATG 58.316 45.455 0.00 0.00 0.00 3.07
457 469 5.254115 GGGATAAGTGAGCCACTAAGTTTT 58.746 41.667 8.07 0.00 44.62 2.43
778 796 8.494016 AGTTAGTATTGAGTATTTTCCACAGC 57.506 34.615 0.00 0.00 0.00 4.40
783 801 5.843673 TTGAGTATTTTCCACAGCAAACA 57.156 34.783 0.00 0.00 0.00 2.83
784 802 5.843673 TGAGTATTTTCCACAGCAAACAA 57.156 34.783 0.00 0.00 0.00 2.83
1135 1248 2.109126 GCGTACGAGTACCTCCCGT 61.109 63.158 21.65 0.00 39.94 5.28
1584 1715 3.545124 TTGGCCGATTGACCTGCGT 62.545 57.895 0.00 0.00 0.00 5.24
2230 2579 1.305219 TTTGGCCATAGACGTGCAGC 61.305 55.000 6.09 0.00 0.00 5.25
2369 2718 9.125026 CATTGGCAATTTTAGAATACTAGTCCT 57.875 33.333 10.65 0.00 0.00 3.85
3302 3774 3.630312 GGTTGTTTGTGCCAAGAAGTCTA 59.370 43.478 0.00 0.00 0.00 2.59
3303 3775 4.097286 GGTTGTTTGTGCCAAGAAGTCTAA 59.903 41.667 0.00 0.00 0.00 2.10
3304 3776 5.393678 GGTTGTTTGTGCCAAGAAGTCTAAA 60.394 40.000 0.00 0.00 0.00 1.85
3566 5193 2.329379 CCAACTCTAACGTGCTGACTC 58.671 52.381 0.00 0.00 0.00 3.36
3662 5289 6.092259 AGCTGATACGTTTATTGGTTTCTCAC 59.908 38.462 0.00 0.00 0.00 3.51
3718 5345 2.238245 CTGAATGCGAGTTGTTCAGC 57.762 50.000 1.92 0.00 41.41 4.26
3728 5355 3.656559 GAGTTGTTCAGCCATGCATTTT 58.343 40.909 0.00 0.00 0.00 1.82
3819 5446 6.094325 TGAAAATCACACTTTTGGTCGTAACT 59.906 34.615 0.00 0.00 0.00 2.24
4026 5654 8.519526 TCAAACTAAGTCCAAATGCGATAAAAT 58.480 29.630 0.00 0.00 0.00 1.82
4144 5772 4.141287 TGTTGGGGAACACAGTATTTCAG 58.859 43.478 0.00 0.00 0.00 3.02
4150 5778 6.553100 TGGGGAACACAGTATTTCAGAAAAAT 59.447 34.615 0.00 0.00 0.00 1.82
4152 5780 7.598869 GGGGAACACAGTATTTCAGAAAAATTC 59.401 37.037 0.00 0.00 0.00 2.17
4174 5802 6.596309 TCCTATGATCACGCAAGATCTATT 57.404 37.500 14.33 4.86 43.76 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 161 1.079057 GGAGGCCCGACTCTTCAAC 60.079 63.158 0.00 0.00 37.63 3.18
457 469 1.939255 GGTTACCCGTGTCGTGAAAAA 59.061 47.619 0.00 0.00 0.00 1.94
2369 2718 9.431887 AGTACTAAATCAAAGACGCTTATTTCA 57.568 29.630 0.00 0.00 0.00 2.69
2627 3002 5.697633 ACTCGCTCCGTTTTTATTTAGTTCA 59.302 36.000 0.00 0.00 0.00 3.18
2637 3012 2.830104 AGTTGTACTCGCTCCGTTTTT 58.170 42.857 0.00 0.00 0.00 1.94
3232 3704 1.481871 ATGCCAAGAGAAATGCAGGG 58.518 50.000 0.00 0.00 37.12 4.45
3302 3774 2.032681 GCCTGAGTCCGCCACTTT 59.967 61.111 0.00 0.00 34.41 2.66
3303 3775 4.021925 GGCCTGAGTCCGCCACTT 62.022 66.667 12.35 0.00 45.01 3.16
3553 5180 1.733041 GCGCAGAGTCAGCACGTTA 60.733 57.895 0.30 0.00 0.00 3.18
3590 5217 1.510844 CAATGTTTACAGCCGGCCC 59.489 57.895 26.15 4.77 0.00 5.80
3662 5289 5.011586 TGATTATGCATATGTGGACCCATG 58.988 41.667 7.36 0.00 0.00 3.66
3728 5355 7.838884 TGCATAGTTCATCCAATTTCATCAAA 58.161 30.769 0.00 0.00 0.00 2.69
3819 5446 0.744057 CGTATCACATGGTGGCAGCA 60.744 55.000 22.88 22.88 33.87 4.41
4011 5639 6.970043 TCTCCGTAAAATTTTATCGCATTTGG 59.030 34.615 13.54 6.54 0.00 3.28
4056 5684 4.663889 CGTTGATTCTTGCGCCAAAAATTC 60.664 41.667 4.18 0.00 0.00 2.17
4066 5694 0.454957 CCTTGGCGTTGATTCTTGCG 60.455 55.000 0.00 0.00 0.00 4.85
4068 5696 0.527565 CCCCTTGGCGTTGATTCTTG 59.472 55.000 0.00 0.00 0.00 3.02
4144 5772 6.785191 TCTTGCGTGATCATAGGAATTTTTC 58.215 36.000 0.00 0.00 0.00 2.29
4150 5778 4.944619 AGATCTTGCGTGATCATAGGAA 57.055 40.909 17.28 3.31 43.76 3.36
4152 5780 8.404889 CTAAATAGATCTTGCGTGATCATAGG 57.595 38.462 17.28 0.00 43.76 2.57


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

AutoCloner maintained by Alex Coulton.