Multiple sequence alignment - TraesCS5B01G036100

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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 TraesCS5B01G036100 chr5B 100.000 3402 0 0 1 3402 39545447 39542046 0.000000e+00 6283.0
1 TraesCS5B01G036100 chr5B 96.695 2209 69 4 1 2207 39743223 39741017 0.000000e+00 3672.0
2 TraesCS5B01G036100 chr5B 96.439 674 22 2 2206 2879 39740782 39740111 0.000000e+00 1110.0
3 TraesCS5B01G036100 chr5B 93.630 675 35 5 2206 2878 713054550 713053882 0.000000e+00 1002.0
4 TraesCS5B01G036100 chr5B 96.349 493 18 0 2910 3402 656155413 656154921 0.000000e+00 811.0
5 TraesCS5B01G036100 chr5B 96.349 493 17 1 2910 3402 692132578 692133069 0.000000e+00 809.0
6 TraesCS5B01G036100 chr5B 93.194 191 13 0 2922 3112 668521634 668521824 7.190000e-72 281.0
7 TraesCS5B01G036100 chr7D 93.778 675 34 5 2206 2878 382021023 382020355 0.000000e+00 1007.0
8 TraesCS5B01G036100 chr7D 86.525 282 23 5 510 779 630180543 630180821 2.570000e-76 296.0
9 TraesCS5B01G036100 chr7D 73.548 465 105 13 1471 1926 629450433 629449978 9.770000e-36 161.0
10 TraesCS5B01G036100 chr5A 93.630 675 35 5 2206 2878 300040243 300040911 0.000000e+00 1002.0
11 TraesCS5B01G036100 chr1B 93.630 675 35 5 2206 2878 461443926 461444594 0.000000e+00 1002.0
12 TraesCS5B01G036100 chr7B 93.481 675 36 5 2206 2878 743121673 743121005 0.000000e+00 996.0
13 TraesCS5B01G036100 chr7B 96.349 493 18 0 2910 3402 17245642 17245150 0.000000e+00 811.0
14 TraesCS5B01G036100 chr7A 93.481 675 36 5 2206 2878 120934186 120933518 0.000000e+00 996.0
15 TraesCS5B01G036100 chr7A 94.366 497 16 3 2915 3402 715400189 715399696 0.000000e+00 752.0
16 TraesCS5B01G036100 chr7A 93.725 494 22 2 2915 3402 715320088 715319598 0.000000e+00 732.0
17 TraesCS5B01G036100 chr7A 84.556 777 65 25 27 774 731435901 731435151 0.000000e+00 719.0
18 TraesCS5B01G036100 chr7A 83.684 809 73 36 1 776 576404612 576403830 0.000000e+00 708.0
19 TraesCS5B01G036100 chr4D 93.481 675 36 5 2206 2878 123359293 123359961 0.000000e+00 996.0
20 TraesCS5B01G036100 chr4D 87.421 787 69 18 1 774 428622108 428621339 0.000000e+00 878.0
21 TraesCS5B01G036100 chr4D 85.507 69 6 2 870 938 18691380 18691444 6.090000e-08 69.4
22 TraesCS5B01G036100 chr3D 93.481 675 36 5 2206 2878 202603598 202604266 0.000000e+00 996.0
23 TraesCS5B01G036100 chr5D 88.679 795 51 14 1 771 391328990 391329769 0.000000e+00 933.0
24 TraesCS5B01G036100 chr5D 85.340 573 38 16 227 774 305761636 305762187 4.960000e-153 551.0
25 TraesCS5B01G036100 chr5D 74.702 672 156 10 1460 2127 524250253 524250914 1.540000e-73 287.0
26 TraesCS5B01G036100 chr5D 84.615 273 29 6 510 774 305736455 305736188 3.370000e-65 259.0
27 TraesCS5B01G036100 chr2D 87.913 786 63 13 1 774 81395284 81394519 0.000000e+00 896.0
28 TraesCS5B01G036100 chr2D 86.786 280 22 5 510 777 573453103 573453379 7.140000e-77 298.0
29 TraesCS5B01G036100 chr2D 85.357 280 27 5 507 774 81417915 81418192 9.300000e-71 278.0
30 TraesCS5B01G036100 chr4B 87.802 787 51 12 1 774 187439886 187439132 0.000000e+00 880.0
31 TraesCS5B01G036100 chr4B 96.552 493 17 0 2910 3402 670755722 670755230 0.000000e+00 817.0
32 TraesCS5B01G036100 chr3B 94.539 531 27 1 2874 3402 17809385 17809915 0.000000e+00 819.0
33 TraesCS5B01G036100 chr6A 96.552 493 17 0 2910 3402 617139886 617139394 0.000000e+00 817.0
34 TraesCS5B01G036100 chr6A 83.787 808 76 38 1 774 71101338 71102124 0.000000e+00 715.0
35 TraesCS5B01G036100 chr6B 96.349 493 18 0 2910 3402 13444872 13445364 0.000000e+00 811.0
36 TraesCS5B01G036100 chr2B 96.349 493 18 0 2910 3402 716541401 716541893 0.000000e+00 811.0
37 TraesCS5B01G036100 chr2B 94.264 523 26 2 2880 3402 159093546 159093028 0.000000e+00 797.0
38 TraesCS5B01G036100 chr3A 86.010 772 62 23 1 754 22037431 22038174 0.000000e+00 785.0
39 TraesCS5B01G036100 chr3A 94.617 483 20 4 2922 3402 736157018 736157496 0.000000e+00 743.0
40 TraesCS5B01G036100 chr3A 94.748 476 22 1 2927 3402 17132031 17131559 0.000000e+00 737.0
41 TraesCS5B01G036100 chr4A 84.988 806 63 34 1 774 616787911 616788690 0.000000e+00 765.0
42 TraesCS5B01G036100 chr4A 95.668 277 12 0 2917 3193 645886077 645886353 2.410000e-121 446.0
43 TraesCS5B01G036100 chr1A 100.000 44 0 0 2879 2922 292137201 292137158 7.820000e-12 82.4


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 TraesCS5B01G036100 chr5B 39542046 39545447 3401 True 6283 6283 100.000 1 3402 1 chr5B.!!$R1 3401
1 TraesCS5B01G036100 chr5B 39740111 39743223 3112 True 2391 3672 96.567 1 2879 2 chr5B.!!$R4 2878
2 TraesCS5B01G036100 chr5B 713053882 713054550 668 True 1002 1002 93.630 2206 2878 1 chr5B.!!$R3 672
3 TraesCS5B01G036100 chr7D 382020355 382021023 668 True 1007 1007 93.778 2206 2878 1 chr7D.!!$R1 672
4 TraesCS5B01G036100 chr5A 300040243 300040911 668 False 1002 1002 93.630 2206 2878 1 chr5A.!!$F1 672
5 TraesCS5B01G036100 chr1B 461443926 461444594 668 False 1002 1002 93.630 2206 2878 1 chr1B.!!$F1 672
6 TraesCS5B01G036100 chr7B 743121005 743121673 668 True 996 996 93.481 2206 2878 1 chr7B.!!$R2 672
7 TraesCS5B01G036100 chr7A 120933518 120934186 668 True 996 996 93.481 2206 2878 1 chr7A.!!$R1 672
8 TraesCS5B01G036100 chr7A 731435151 731435901 750 True 719 719 84.556 27 774 1 chr7A.!!$R5 747
9 TraesCS5B01G036100 chr7A 576403830 576404612 782 True 708 708 83.684 1 776 1 chr7A.!!$R2 775
10 TraesCS5B01G036100 chr4D 123359293 123359961 668 False 996 996 93.481 2206 2878 1 chr4D.!!$F2 672
11 TraesCS5B01G036100 chr4D 428621339 428622108 769 True 878 878 87.421 1 774 1 chr4D.!!$R1 773
12 TraesCS5B01G036100 chr3D 202603598 202604266 668 False 996 996 93.481 2206 2878 1 chr3D.!!$F1 672
13 TraesCS5B01G036100 chr5D 391328990 391329769 779 False 933 933 88.679 1 771 1 chr5D.!!$F2 770
14 TraesCS5B01G036100 chr5D 305761636 305762187 551 False 551 551 85.340 227 774 1 chr5D.!!$F1 547
15 TraesCS5B01G036100 chr5D 524250253 524250914 661 False 287 287 74.702 1460 2127 1 chr5D.!!$F3 667
16 TraesCS5B01G036100 chr2D 81394519 81395284 765 True 896 896 87.913 1 774 1 chr2D.!!$R1 773
17 TraesCS5B01G036100 chr4B 187439132 187439886 754 True 880 880 87.802 1 774 1 chr4B.!!$R1 773
18 TraesCS5B01G036100 chr3B 17809385 17809915 530 False 819 819 94.539 2874 3402 1 chr3B.!!$F1 528
19 TraesCS5B01G036100 chr6A 71101338 71102124 786 False 715 715 83.787 1 774 1 chr6A.!!$F1 773
20 TraesCS5B01G036100 chr2B 159093028 159093546 518 True 797 797 94.264 2880 3402 1 chr2B.!!$R1 522
21 TraesCS5B01G036100 chr3A 22037431 22038174 743 False 785 785 86.010 1 754 1 chr3A.!!$F1 753
22 TraesCS5B01G036100 chr4A 616787911 616788690 779 False 765 765 84.988 1 774 1 chr4A.!!$F1 773

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
853 930 0.106015 GGGTTGGCATGCCCTTAGAT 60.106 55.0 33.44 0.0 41.63 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2667 2982 0.958876 CAGCTGCAGCCTTGATCACA 60.959 55.0 34.39 0.0 43.38 3.58 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
96 101 1.693606 CCTTCAAATGCCACAAACCCT 59.306 47.619 0.00 0.00 0.00 4.34
181 186 3.130516 TGGATCTATCACCGTGTCAAGAC 59.869 47.826 0.00 0.00 0.00 3.01
335 342 3.937814 ACAAAATACTCCATCTGCACGA 58.062 40.909 0.00 0.00 0.00 4.35
346 353 3.253230 CATCTGCACGATGTTGTACTCA 58.747 45.455 14.42 0.00 43.66 3.41
392 429 2.594303 CGTTGCTGTTGGGCCAGA 60.594 61.111 6.23 0.00 34.23 3.86
492 540 1.612199 GGAGAGGAGTGAGTGAGACGT 60.612 57.143 0.00 0.00 0.00 4.34
574 637 1.146358 GGCACTAACATCCGCGAGTC 61.146 60.000 8.23 0.00 0.00 3.36
787 864 2.068834 ATACTCGTGTAGGGAGGGTG 57.931 55.000 3.50 0.00 35.82 4.61
824 901 2.137528 TGATATTCGGCCGGGAGCA 61.138 57.895 27.83 16.77 46.50 4.26
849 926 3.910784 CTGGGGTTGGCATGCCCTT 62.911 63.158 33.44 0.00 44.25 3.95
853 930 0.106015 GGGTTGGCATGCCCTTAGAT 60.106 55.000 33.44 0.00 41.63 1.98
862 939 4.217118 GGCATGCCCTTAGATTTGATACTG 59.783 45.833 27.24 0.00 0.00 2.74
863 940 4.217118 GCATGCCCTTAGATTTGATACTGG 59.783 45.833 6.36 0.00 0.00 4.00
1009 1088 8.861033 TGTACCGTACAACAAGCTATAAATAG 57.139 34.615 8.99 0.00 35.38 1.73
1088 1167 3.903714 AGCCCAATAATTAGGAAATGGCC 59.096 43.478 0.00 0.00 32.26 5.36
1134 1213 2.042259 TTGCAGCTCTCATTGGCGG 61.042 57.895 0.00 0.00 0.00 6.13
1162 1241 1.800805 CCAATGACACTCAAGAGCGT 58.199 50.000 0.00 0.00 0.00 5.07
1220 1299 2.268920 GGGAAGATGCTGTCGCCA 59.731 61.111 0.00 0.00 34.43 5.69
1347 1426 2.203938 AAGGGAAGGACGGCCTGA 60.204 61.111 12.91 0.00 46.28 3.86
1349 1428 1.627297 AAGGGAAGGACGGCCTGATC 61.627 60.000 12.91 5.18 46.28 2.92
1350 1429 2.367202 GGGAAGGACGGCCTGATCA 61.367 63.158 12.91 0.00 46.28 2.92
1425 1504 2.764128 CTTCCCTAGGCCCGCTCA 60.764 66.667 2.05 0.00 0.00 4.26
1481 1560 2.680312 ATCATCTCAAGGACACGGTG 57.320 50.000 6.58 6.58 0.00 4.94
1541 1620 0.460284 CGCTGTTCGATTACCAGGCT 60.460 55.000 0.00 0.00 41.67 4.58
1664 1743 1.682982 CCGTCAGTACACTTGTCGAC 58.317 55.000 9.11 9.11 0.00 4.20
1763 1842 1.599047 CCACGTCATCTCCCAAGCT 59.401 57.895 0.00 0.00 0.00 3.74
1842 1921 0.533755 GGACGCCATCCTCATGAAGG 60.534 60.000 0.00 0.68 45.22 3.46
1944 2023 3.281395 TCGTCGTGGACTGCGTCA 61.281 61.111 10.14 0.00 33.68 4.35
1989 2068 1.067846 CCGAGGTGAAGACGATGTTCA 60.068 52.381 0.00 0.00 0.00 3.18
2168 2247 1.230324 GTGCTTTCGAGCTTCCTTGT 58.770 50.000 0.00 0.00 35.49 3.16
2185 2264 5.054477 TCCTTGTTTTCTCTCGATCGTTTT 58.946 37.500 15.94 0.00 0.00 2.43
2233 2548 0.404040 TAAGGCAGAACCCAGGGTTG 59.596 55.000 30.03 17.36 46.95 3.77
2253 2568 5.067805 GGTTGTAGCCCATTTCCATTTCTAG 59.932 44.000 0.00 0.00 0.00 2.43
2327 2642 5.237344 CAGTTGCTAGCCATATGTTTAGGAC 59.763 44.000 13.29 1.07 0.00 3.85
2667 2982 5.126545 AGCATGCATGTATCAGAACAACAAT 59.873 36.000 26.79 0.00 32.02 2.71
2717 3032 3.326880 AGGACTAACGACACAAGGGAAAT 59.673 43.478 0.00 0.00 0.00 2.17
2747 3062 3.406595 CTGAAGGCCACCGATCCCC 62.407 68.421 5.01 0.00 0.00 4.81
2810 3127 0.606673 GGGGCACTTCACTTGTCCTC 60.607 60.000 0.00 0.00 38.90 3.71
3068 3385 4.162690 GCCTCGTACCTGGCCCAG 62.163 72.222 2.91 2.91 43.11 4.45
3176 3493 1.612463 GCCTATATATACCCCCTCGCG 59.388 57.143 0.00 0.00 0.00 5.87
3183 3500 0.106318 ATACCCCCTCGCGTAAGAGT 60.106 55.000 5.77 2.37 43.02 3.24
3270 3589 2.485426 CTCCTATGCACACAAGGTGTTG 59.515 50.000 0.00 0.00 45.08 3.33
3311 3630 5.866633 CACACTACTTAAGCTTTCTCCTCTG 59.133 44.000 3.20 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.470098 AGAGCAAACAATAGTCGTGTTCATT 59.530 36.000 0.00 0.00 38.24 2.57
96 101 1.228245 GCACAGGCAAAGACCAGGA 60.228 57.895 0.00 0.00 40.72 3.86
181 186 0.598065 GGGTTGGTACTGCAGCAAAG 59.402 55.000 15.27 0.00 45.74 2.77
335 342 5.127194 ACGAGTACATGGATGAGTACAACAT 59.873 40.000 0.00 5.48 42.26 2.71
346 353 3.490933 CCAACGATGACGAGTACATGGAT 60.491 47.826 0.00 0.00 42.66 3.41
492 540 0.394488 CCGGCTCACTCACTCCTCTA 60.394 60.000 0.00 0.00 0.00 2.43
617 692 3.597255 AGCTAGTTTAACCGCTTTCCTC 58.403 45.455 4.08 0.00 0.00 3.71
732 808 0.826062 ACATTAGGGGTTACCGTCCG 59.174 55.000 0.00 0.00 46.96 4.79
787 864 1.065418 CACTGACAATCTACCACCCCC 60.065 57.143 0.00 0.00 0.00 5.40
853 930 6.425721 CGGTTTTCTTACAGACCAGTATCAAA 59.574 38.462 0.00 0.00 32.41 2.69
862 939 4.025145 CACTTCACGGTTTTCTTACAGACC 60.025 45.833 0.00 0.00 0.00 3.85
863 940 4.025145 CCACTTCACGGTTTTCTTACAGAC 60.025 45.833 0.00 0.00 0.00 3.51
873 951 2.713863 TTGGTACCACTTCACGGTTT 57.286 45.000 16.04 0.00 37.99 3.27
880 958 5.425630 AGGATAACGAATTGGTACCACTTC 58.574 41.667 27.08 27.08 33.88 3.01
881 959 5.431179 AGGATAACGAATTGGTACCACTT 57.569 39.130 16.04 16.45 0.00 3.16
1009 1088 1.807142 GCAGTCTGCTTGTTAAGGGTC 59.193 52.381 17.89 0.00 40.96 4.46
1017 1096 3.557903 ATGCCGGCAGTCTGCTTGT 62.558 57.895 35.36 11.90 44.28 3.16
1088 1167 3.358076 GAAGGCCTCCCTGTCGTCG 62.358 68.421 5.23 0.00 41.90 5.12
1134 1213 1.594862 GAGTGTCATTGGCACGATAGC 59.405 52.381 15.25 1.46 41.36 2.97
1162 1241 4.746309 GCATGCCCAGCTCCACCA 62.746 66.667 6.36 0.00 0.00 4.17
1293 1372 0.108992 ACGATGTTGTACGACGCCAT 60.109 50.000 8.73 0.00 0.00 4.40
1334 1413 1.153349 GGTGATCAGGCCGTCCTTC 60.153 63.158 0.00 0.00 41.93 3.46
1425 1504 2.432510 GGATCTTGTCGTTCAGGAGGAT 59.567 50.000 0.00 0.00 35.68 3.24
1541 1620 1.674519 CCGTTGAATCGTGGATCCACA 60.675 52.381 37.42 26.52 46.47 4.17
1989 2068 4.701651 TGAGCATGAGAATATCCAGCTT 57.298 40.909 0.00 0.00 37.22 3.74
2168 2247 4.089493 CACGCTAAAACGATCGAGAGAAAA 59.911 41.667 24.34 0.00 39.33 2.29
2233 2548 6.299141 TGATCTAGAAATGGAAATGGGCTAC 58.701 40.000 0.00 0.00 0.00 3.58
2253 2568 9.952188 GGTAAAAAGCACTAGGAATTATTGATC 57.048 33.333 0.00 0.00 0.00 2.92
2274 2589 4.312443 CAGGAGTACGCAAGAAAGGTAAA 58.688 43.478 0.00 0.00 43.62 2.01
2667 2982 0.958876 CAGCTGCAGCCTTGATCACA 60.959 55.000 34.39 0.00 43.38 3.58
2717 3032 1.374947 CCTTCAGTTCCTGCCGGAA 59.625 57.895 5.05 5.36 46.90 4.30
2826 3143 5.717078 ATTGAAATCAGTTGTGCATGTCT 57.283 34.783 0.00 0.00 0.00 3.41
2913 3230 3.787394 TCCCGGTTCTGGACTGAC 58.213 61.111 0.00 0.00 36.72 3.51
2988 3305 2.617788 CCAGACGAAATGGGACCAATGA 60.618 50.000 0.00 0.00 33.94 2.57
2999 3316 3.146847 GACCAAAAGGTCCAGACGAAAT 58.853 45.455 3.27 0.00 33.21 2.17
3057 3374 2.237965 AATGGTGCTGGGCCAGGTA 61.238 57.895 33.43 12.31 39.65 3.08
3058 3375 3.593680 AATGGTGCTGGGCCAGGT 61.594 61.111 33.43 0.00 39.65 4.00
3068 3385 2.282887 AACCGGGACCAATGGTGC 60.283 61.111 15.99 15.99 43.47 5.01
3214 3533 2.285668 CAAGCCCTCTCCCCCTCA 60.286 66.667 0.00 0.00 0.00 3.86
3270 3589 2.595754 GGCTCGGGCATTCCATCC 60.596 66.667 10.74 0.00 40.87 3.51
3311 3630 2.394563 GCTTGGAGGTCGAGCTTGC 61.395 63.158 19.66 16.02 46.85 4.01


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

AutoCloner maintained by Alex Coulton.