Multiple sequence alignment - TraesCS3B01G081200

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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 TraesCS3B01G081200 chr3B 100.000 3778 0 0 1 3778 51224120 51227897 0.000000e+00 6977.0
1 TraesCS3B01G081200 chr3B 95.075 1990 59 21 1823 3778 51945065 51947049 0.000000e+00 3096.0
2 TraesCS3B01G081200 chr3B 90.798 815 41 14 851 1664 51944287 51945068 0.000000e+00 1059.0
3 TraesCS3B01G081200 chr3B 92.848 741 30 5 3051 3778 52435355 52436085 0.000000e+00 1053.0
4 TraesCS3B01G081200 chr3B 83.628 849 81 28 2481 3284 51731278 51732113 0.000000e+00 745.0
5 TraesCS3B01G081200 chr3B 86.252 691 48 18 1967 2614 52431189 52431875 0.000000e+00 706.0
6 TraesCS3B01G081200 chr3B 85.285 666 51 21 3147 3778 52779034 52778382 0.000000e+00 643.0
7 TraesCS3B01G081200 chr3B 91.991 462 20 6 2610 3059 52434716 52435172 1.910000e-177 632.0
8 TraesCS3B01G081200 chr3B 83.986 587 70 20 1086 1664 496063058 496063628 3.320000e-150 542.0
9 TraesCS3B01G081200 chr3B 86.335 322 22 10 1962 2265 496063795 496064112 7.820000e-87 331.0
10 TraesCS3B01G081200 chr3B 86.869 297 15 15 2726 3008 52787076 52786790 1.020000e-80 311.0
11 TraesCS3B01G081200 chr3B 83.668 349 28 13 1324 1664 52430678 52431005 6.130000e-78 302.0
12 TraesCS3B01G081200 chr3B 86.063 287 19 13 980 1265 52430403 52430669 4.770000e-74 289.0
13 TraesCS3B01G081200 chr3B 90.909 55 5 0 2394 2448 52788645 52788591 1.460000e-09 75.0
14 TraesCS3B01G081200 chr3A 90.388 1238 61 22 851 2073 40913257 40914451 0.000000e+00 1574.0
15 TraesCS3B01G081200 chr3A 92.133 1055 46 7 2488 3527 40915053 40916085 0.000000e+00 1454.0
16 TraesCS3B01G081200 chr3A 81.550 645 71 27 2629 3242 41602366 41602993 4.390000e-134 488.0
17 TraesCS3B01G081200 chr3A 89.655 261 20 4 2680 2940 41627884 41628137 3.640000e-85 326.0
18 TraesCS3B01G081200 chr3A 84.211 304 22 5 3004 3284 41628232 41628532 4.810000e-69 272.0
19 TraesCS3B01G081200 chr3A 87.755 245 6 6 2272 2492 40914650 40914894 8.050000e-67 265.0
20 TraesCS3B01G081200 chr3A 96.203 158 5 1 2110 2267 40914448 40914604 1.350000e-64 257.0
21 TraesCS3B01G081200 chr2B 98.474 852 12 1 1 851 77777114 77776263 0.000000e+00 1500.0
22 TraesCS3B01G081200 chr2B 97.914 863 15 3 1 861 178454507 178453646 0.000000e+00 1491.0
23 TraesCS3B01G081200 chr2B 97.887 852 17 1 1 851 33732074 33732925 0.000000e+00 1472.0
24 TraesCS3B01G081200 chr5B 98.242 853 14 1 1 852 670709046 670709898 0.000000e+00 1491.0
25 TraesCS3B01G081200 chr5B 89.024 164 16 2 1668 1830 155279500 155279338 6.400000e-48 202.0
26 TraesCS3B01G081200 chr6A 98.122 852 15 1 1 851 592442140 592441289 0.000000e+00 1483.0
27 TraesCS3B01G081200 chr4B 98.120 851 16 0 1 851 508523339 508524189 0.000000e+00 1483.0
28 TraesCS3B01G081200 chr2A 98.122 852 15 1 1 851 519548186 519549037 0.000000e+00 1483.0
29 TraesCS3B01G081200 chr7B 98.000 850 16 1 1 849 593908380 593909229 0.000000e+00 1474.0
30 TraesCS3B01G081200 chr7B 97.998 849 17 0 1 849 593910073 593910921 0.000000e+00 1474.0
31 TraesCS3B01G081200 chr3D 84.666 1213 75 39 1823 2940 29968148 29969344 0.000000e+00 1107.0
32 TraesCS3B01G081200 chr3D 86.675 818 52 29 851 1664 29967387 29968151 0.000000e+00 854.0
33 TraesCS3B01G081200 chr3D 88.235 289 31 2 3394 3682 30063790 30064075 3.610000e-90 342.0
34 TraesCS3B01G081200 chr3D 89.313 262 19 6 2680 2940 30063090 30063343 1.690000e-83 320.0
35 TraesCS3B01G081200 chr3D 91.912 136 7 1 3153 3284 30063491 30063626 1.790000e-43 187.0
36 TraesCS3B01G081200 chr4A 90.000 60 4 2 1426 1484 410040607 410040665 4.050000e-10 76.8


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 TraesCS3B01G081200 chr3B 51224120 51227897 3777 False 6977.0 6977 100.00000 1 3778 1 chr3B.!!$F1 3777
1 TraesCS3B01G081200 chr3B 51944287 51947049 2762 False 2077.5 3096 92.93650 851 3778 2 chr3B.!!$F3 2927
2 TraesCS3B01G081200 chr3B 51731278 51732113 835 False 745.0 745 83.62800 2481 3284 1 chr3B.!!$F2 803
3 TraesCS3B01G081200 chr3B 52778382 52779034 652 True 643.0 643 85.28500 3147 3778 1 chr3B.!!$R1 631
4 TraesCS3B01G081200 chr3B 52430403 52436085 5682 False 596.4 1053 88.16440 980 3778 5 chr3B.!!$F4 2798
5 TraesCS3B01G081200 chr3B 496063058 496064112 1054 False 436.5 542 85.16050 1086 2265 2 chr3B.!!$F5 1179
6 TraesCS3B01G081200 chr3A 40913257 40916085 2828 False 887.5 1574 91.61975 851 3527 4 chr3A.!!$F2 2676
7 TraesCS3B01G081200 chr3A 41602366 41602993 627 False 488.0 488 81.55000 2629 3242 1 chr3A.!!$F1 613
8 TraesCS3B01G081200 chr3A 41627884 41628532 648 False 299.0 326 86.93300 2680 3284 2 chr3A.!!$F3 604
9 TraesCS3B01G081200 chr2B 77776263 77777114 851 True 1500.0 1500 98.47400 1 851 1 chr2B.!!$R1 850
10 TraesCS3B01G081200 chr2B 178453646 178454507 861 True 1491.0 1491 97.91400 1 861 1 chr2B.!!$R2 860
11 TraesCS3B01G081200 chr2B 33732074 33732925 851 False 1472.0 1472 97.88700 1 851 1 chr2B.!!$F1 850
12 TraesCS3B01G081200 chr5B 670709046 670709898 852 False 1491.0 1491 98.24200 1 852 1 chr5B.!!$F1 851
13 TraesCS3B01G081200 chr6A 592441289 592442140 851 True 1483.0 1483 98.12200 1 851 1 chr6A.!!$R1 850
14 TraesCS3B01G081200 chr4B 508523339 508524189 850 False 1483.0 1483 98.12000 1 851 1 chr4B.!!$F1 850
15 TraesCS3B01G081200 chr2A 519548186 519549037 851 False 1483.0 1483 98.12200 1 851 1 chr2A.!!$F1 850
16 TraesCS3B01G081200 chr7B 593908380 593910921 2541 False 1474.0 1474 97.99900 1 849 2 chr7B.!!$F1 848
17 TraesCS3B01G081200 chr3D 29967387 29969344 1957 False 980.5 1107 85.67050 851 2940 2 chr3D.!!$F1 2089
18 TraesCS3B01G081200 chr3D 30063090 30064075 985 False 283.0 342 89.82000 2680 3682 3 chr3D.!!$F2 1002

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
518 521 3.547746 TGAAACGGTTCCTTAGCTTGTT 58.452 40.909 11.41 0.00 32.28 2.83 F
1148 1167 0.468400 GGGTATGTCCGAGCTCCTCT 60.468 60.000 8.47 0.00 37.00 3.69 F
1149 1168 0.671251 GGTATGTCCGAGCTCCTCTG 59.329 60.000 8.47 0.00 0.00 3.35 F
1683 1729 1.298638 GGCGCGCTTGGAATTGATC 60.299 57.895 32.29 5.31 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2011 0.824759 GGCGAAGTCAGAGGGTACAT 59.175 55.000 0.00 0.00 0.00 2.29 R
1962 2043 1.286248 GGGAGGGTAAGGCAGAAGAA 58.714 55.000 0.00 0.00 0.00 2.52 R
2019 2120 2.633657 GTCAGTTGGTGCAGCACG 59.366 61.111 20.03 10.39 34.83 5.34 R
3322 7385 0.250901 GGTGCTGGCTGGAAGAGAAA 60.251 55.000 0.00 0.00 34.07 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
153 154 8.813643 AAATGTGTAGTACTCAAGTAACTGTC 57.186 34.615 8.98 0.00 31.52 3.51
322 324 6.325545 TGGTGTAATAGTAGAATCGGATGGTT 59.674 38.462 0.00 0.00 0.00 3.67
518 521 3.547746 TGAAACGGTTCCTTAGCTTGTT 58.452 40.909 11.41 0.00 32.28 2.83
539 542 6.494842 TGTTCTAAGTGACTTTTTCATGTGC 58.505 36.000 1.97 0.00 36.32 4.57
583 586 5.938125 TGTGCATATGGAGAATCATGATGAG 59.062 40.000 9.46 0.00 36.25 2.90
585 588 6.430308 GTGCATATGGAGAATCATGATGAGTT 59.570 38.462 9.46 0.00 36.25 3.01
974 984 4.065281 CTCGAACCCCGGCGAGTT 62.065 66.667 17.83 12.13 46.43 3.01
1146 1165 0.757188 CAGGGTATGTCCGAGCTCCT 60.757 60.000 8.47 0.00 37.00 3.69
1148 1167 0.468400 GGGTATGTCCGAGCTCCTCT 60.468 60.000 8.47 0.00 37.00 3.69
1149 1168 0.671251 GGTATGTCCGAGCTCCTCTG 59.329 60.000 8.47 0.00 0.00 3.35
1150 1169 1.681538 GTATGTCCGAGCTCCTCTGA 58.318 55.000 8.47 0.00 0.00 3.27
1151 1170 2.235016 GTATGTCCGAGCTCCTCTGAT 58.765 52.381 8.47 0.00 0.00 2.90
1161 1180 1.739338 CTCCTCTGATTCCCCGTCCG 61.739 65.000 0.00 0.00 0.00 4.79
1294 1315 5.005394 GGTGTATCAAGCGTATTGTACTGTG 59.995 44.000 0.00 0.00 0.00 3.66
1301 1322 3.057104 AGCGTATTGTACTGTGCACTGTA 60.057 43.478 26.93 26.93 0.00 2.74
1470 1510 5.057149 GCTTCAGTTATGTGTATGGTAGGG 58.943 45.833 0.00 0.00 0.00 3.53
1499 1539 7.119262 ACCCAATTATTCGACTTCTGTTTACTG 59.881 37.037 0.00 0.00 0.00 2.74
1527 1572 5.702065 TGCCAGTATTTTGGGTGTCTATA 57.298 39.130 0.00 0.00 38.72 1.31
1528 1573 5.433526 TGCCAGTATTTTGGGTGTCTATAC 58.566 41.667 0.00 0.00 38.72 1.47
1594 1640 1.828979 ATAACCGATGCCAAACCGTT 58.171 45.000 0.00 0.00 0.00 4.44
1661 1707 7.500892 TGTTGTACATGTATTTGTGGAACTTCT 59.499 33.333 9.18 0.00 38.04 2.85
1679 1725 1.376609 CTAAGGGCGCGCTTGGAATT 61.377 55.000 40.07 21.95 0.00 2.17
1683 1729 1.298638 GGCGCGCTTGGAATTGATC 60.299 57.895 32.29 5.31 0.00 2.92
1703 1749 7.450124 TGATCTATTTAGATACGGAGGTGTC 57.550 40.000 0.13 0.00 42.79 3.67
1808 1856 7.499895 ACAACTGTATCTAAAAGAAAAACGGGA 59.500 33.333 0.00 0.00 0.00 5.14
1878 1934 2.403252 AGCCACGTTGATTTAGGAGG 57.597 50.000 0.00 0.00 0.00 4.30
1934 2011 8.893563 AATTTTCCATATCCCACTTCTACAAA 57.106 30.769 0.00 0.00 0.00 2.83
1951 2029 3.926616 ACAAATGTACCCTCTGACTTCG 58.073 45.455 0.00 0.00 0.00 3.79
1962 2043 2.164865 CTGACTTCGCCTGTGCCTCT 62.165 60.000 0.00 0.00 0.00 3.69
2931 6163 8.023128 TGTAAGCTGTATTGCAAAATTCTCTTC 58.977 33.333 1.71 0.00 34.99 2.87
3102 6953 5.031066 TGGAAGTAGCTACTGTTGTTTGT 57.969 39.130 26.70 8.65 36.50 2.83
3320 7383 5.372343 TCATCATTAGCCTTCTTTGCCTA 57.628 39.130 0.00 0.00 0.00 3.93
3322 7385 6.367983 TCATCATTAGCCTTCTTTGCCTATT 58.632 36.000 0.00 0.00 0.00 1.73
3350 7413 2.914097 GCCAGCACCAAAGCCTGT 60.914 61.111 0.00 0.00 34.23 4.00
3408 7506 2.262915 CGCTGAGTTCGCCTCCTT 59.737 61.111 0.31 0.00 39.65 3.36
3522 7620 2.126189 CGTCGTTCCTTCCCCGTC 60.126 66.667 0.00 0.00 0.00 4.79
3745 7995 7.175119 TGAACGGTAATCTTCTATGAGATCGAT 59.825 37.037 0.00 0.00 35.37 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 7.818930 ACAAAAGCATTAATATGACAACTTGGG 59.181 33.333 0.00 0.00 33.37 4.12
352 355 5.411831 TGTCTTGACTGCATAGAATCAGT 57.588 39.130 2.35 0.00 45.32 3.41
518 521 5.053811 TCGCACATGAAAAAGTCACTTAGA 58.946 37.500 0.00 0.00 39.72 2.10
539 542 7.538981 GCACACATTTATGCAAGTATAATCG 57.461 36.000 0.00 0.00 41.65 3.34
879 882 8.678199 GGTGGTAAATAAGAGAAGGAATTTGAG 58.322 37.037 0.00 0.00 0.00 3.02
880 883 7.614192 GGGTGGTAAATAAGAGAAGGAATTTGA 59.386 37.037 0.00 0.00 0.00 2.69
881 884 7.147897 GGGGTGGTAAATAAGAGAAGGAATTTG 60.148 40.741 0.00 0.00 0.00 2.32
973 983 1.379977 ATCCCGACCTCTCGCTGAA 60.380 57.895 0.00 0.00 38.70 3.02
974 984 1.824329 GATCCCGACCTCTCGCTGA 60.824 63.158 0.00 0.00 38.70 4.26
1146 1165 3.467226 GGCGGACGGGGAATCAGA 61.467 66.667 0.00 0.00 0.00 3.27
1148 1167 3.467226 GAGGCGGACGGGGAATCA 61.467 66.667 0.00 0.00 0.00 2.57
1149 1168 4.237207 GGAGGCGGACGGGGAATC 62.237 72.222 0.00 0.00 0.00 2.52
1150 1169 4.798682 AGGAGGCGGACGGGGAAT 62.799 66.667 0.00 0.00 0.00 3.01
1161 1180 1.753368 CTCGAATCAGGGGAGGAGGC 61.753 65.000 0.00 0.00 0.00 4.70
1188 1209 4.697756 CCGAAACAGGGCGCCTCA 62.698 66.667 28.56 0.00 0.00 3.86
1294 1315 4.260294 CGTCAGCTACTACTACTACAGTGC 60.260 50.000 0.00 0.00 38.24 4.40
1301 1322 2.708051 TGTGCGTCAGCTACTACTACT 58.292 47.619 0.00 0.00 45.42 2.57
1470 1510 4.156008 ACAGAAGTCGAATAATTGGGTTGC 59.844 41.667 0.00 0.00 0.00 4.17
1499 1539 6.546034 AGACACCCAAAATACTGGCATATAAC 59.454 38.462 0.00 0.00 34.88 1.89
1504 1544 3.456380 AGACACCCAAAATACTGGCAT 57.544 42.857 0.00 0.00 34.88 4.40
1505 1545 2.969821 AGACACCCAAAATACTGGCA 57.030 45.000 0.00 0.00 34.88 4.92
1594 1640 6.173339 CAGCCTAATTCTTGTTCTCAGGTTA 58.827 40.000 0.00 0.00 0.00 2.85
1661 1707 1.377987 AATTCCAAGCGCGCCCTTA 60.378 52.632 30.33 10.44 0.00 2.69
1679 1725 7.232188 AGACACCTCCGTATCTAAATAGATCA 58.768 38.462 6.22 0.00 41.85 2.92
1683 1729 6.487331 AGTGAGACACCTCCGTATCTAAATAG 59.513 42.308 0.00 0.00 38.66 1.73
1703 1749 4.497006 CGGTAAGATACGGGTGTAAGTGAG 60.497 50.000 0.00 0.00 33.44 3.51
1808 1856 3.165071 CTGTTTAGGCCCTGTTTGGATT 58.835 45.455 0.00 0.00 38.35 3.01
1934 2011 0.824759 GGCGAAGTCAGAGGGTACAT 59.175 55.000 0.00 0.00 0.00 2.29
1951 2029 1.304509 GCAGAAGAAGAGGCACAGGC 61.305 60.000 0.00 0.00 40.13 4.85
1962 2043 1.286248 GGGAGGGTAAGGCAGAAGAA 58.714 55.000 0.00 0.00 0.00 2.52
2019 2120 2.633657 GTCAGTTGGTGCAGCACG 59.366 61.111 20.03 10.39 34.83 5.34
2256 2382 5.480205 ACTTCGGACAAATCCTAGAACTTC 58.520 41.667 0.00 0.00 43.73 3.01
2931 6163 4.137543 GCACCAGTAATAAAGATCCCCAG 58.862 47.826 0.00 0.00 0.00 4.45
3298 7361 4.240881 AGGCAAAGAAGGCTAATGATGA 57.759 40.909 0.00 0.00 43.28 2.92
3315 7378 2.308570 TGGCTGGAAGAGAAAATAGGCA 59.691 45.455 0.00 0.00 38.21 4.75
3316 7379 2.948315 CTGGCTGGAAGAGAAAATAGGC 59.052 50.000 0.00 0.00 34.07 3.93
3320 7383 2.165998 GTGCTGGCTGGAAGAGAAAAT 58.834 47.619 0.00 0.00 34.07 1.82
3322 7385 0.250901 GGTGCTGGCTGGAAGAGAAA 60.251 55.000 0.00 0.00 34.07 2.52
3350 7413 8.478066 TCTGAAGCAAGAATTAGTAGCATAAGA 58.522 33.333 0.00 0.00 0.00 2.10
3528 7626 1.808945 CTTCAATCAGTGGTGACCAGC 59.191 52.381 3.58 0.00 34.75 4.85
3674 7918 7.976734 GCTTCTACACCTGCAGTATTATATAGG 59.023 40.741 13.81 0.00 0.00 2.57
3745 7995 8.515695 AAGAATCAGTTTGCTATGATGATCAA 57.484 30.769 0.00 0.00 36.31 2.57


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

AutoCloner maintained by Alex Coulton.