Multiple sequence alignment - TraesCS1D01G096700

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 TraesCS1D01G096700 chr1D 100.000 3149 0 0 1 3149 83056430 83053282 0.000000e+00 5816
1 TraesCS1D01G096700 chr7A 94.766 2904 115 21 249 3149 247703654 247700785 0.000000e+00 4486
2 TraesCS1D01G096700 chr7A 96.457 254 9 0 1 254 247723596 247723343 1.350000e-113 420
3 TraesCS1D01G096700 chr5A 96.207 2610 91 7 1 2606 190545595 190548200 0.000000e+00 4265
4 TraesCS1D01G096700 chr5A 94.184 533 26 4 2616 3146 190548711 190549240 0.000000e+00 808
5 TraesCS1D01G096700 chr5A 89.370 254 23 2 2592 2843 190548143 190548394 1.820000e-82 316
6 TraesCS1D01G096700 chr5A 83.902 205 25 3 2692 2892 190548131 190548331 4.150000e-44 189
7 TraesCS1D01G096700 chr5A 88.079 151 16 1 2743 2893 190548728 190548876 8.970000e-41 178
8 TraesCS1D01G096700 chr6B 94.109 2682 125 13 1 2664 120534832 120532166 0.000000e+00 4047
9 TraesCS1D01G096700 chr6B 90.158 1453 128 8 1163 2612 296847929 296849369 0.000000e+00 1877
10 TraesCS1D01G096700 chr6B 92.544 684 48 3 266 947 296846359 296847041 0.000000e+00 977
11 TraesCS1D01G096700 chr6B 91.592 333 23 5 2820 3149 120532188 120531858 3.700000e-124 455
12 TraesCS1D01G096700 chr6B 84.245 457 45 15 2695 3149 513263977 513264408 1.350000e-113 420
13 TraesCS1D01G096700 chr6B 93.061 245 17 0 34 278 296846102 296846346 2.990000e-95 359
14 TraesCS1D01G096700 chr6B 88.559 236 27 0 933 1168 296847136 296847371 1.430000e-73 287
15 TraesCS1D01G096700 chr4B 95.299 1957 86 2 185 2135 32575922 32573966 0.000000e+00 3099
16 TraesCS1D01G096700 chr4B 91.667 336 23 4 2817 3149 32570549 32570216 7.960000e-126 460
17 TraesCS1D01G096700 chr4B 91.369 336 24 4 2817 3149 32568514 32568181 3.700000e-124 455
18 TraesCS1D01G096700 chr4B 96.721 183 6 0 1 183 32576945 32576763 3.950000e-79 305
19 TraesCS1D01G096700 chr5B 95.866 1911 77 2 1 1909 697756951 697758861 0.000000e+00 3090
20 TraesCS1D01G096700 chr1B 93.797 1467 80 7 1317 2779 82550344 82548885 0.000000e+00 2194
21 TraesCS1D01G096700 chr1B 95.296 1233 57 1 1 1232 82551979 82550747 0.000000e+00 1954
22 TraesCS1D01G096700 chr1B 84.417 1354 158 27 1450 2774 117798516 117799845 0.000000e+00 1282
23 TraesCS1D01G096700 chr1B 84.417 1354 158 25 1450 2774 117830945 117832274 0.000000e+00 1282
24 TraesCS1D01G096700 chr1B 84.285 1349 157 24 1456 2774 118417536 118416213 0.000000e+00 1266
25 TraesCS1D01G096700 chr2A 87.832 1167 138 3 1456 2622 297541944 297540782 0.000000e+00 1365
26 TraesCS1D01G096700 chr1A 85.837 1278 165 15 1334 2606 84819232 84820498 0.000000e+00 1343
27 TraesCS1D01G096700 chr4A 87.414 1168 140 5 1456 2622 618794691 618793530 0.000000e+00 1336
28 TraesCS1D01G096700 chr4A 86.686 338 34 6 2817 3149 610971845 610972176 6.420000e-97 364
29 TraesCS1D01G096700 chr2B 81.090 1724 236 41 1456 3149 156047757 156046094 0.000000e+00 1295
30 TraesCS1D01G096700 chrUn 82.430 535 56 16 2616 3149 55650540 55650043 1.730000e-117 433
31 TraesCS1D01G096700 chr3A 83.193 476 54 13 2678 3149 144039928 144039475 2.260000e-111 412
32 TraesCS1D01G096700 chr6A 78.836 189 20 13 2592 2778 117624869 117624699 3.320000e-20 110


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 TraesCS1D01G096700 chr1D 83053282 83056430 3148 True 5816.00 5816 100.0000 1 3149 1 chr1D.!!$R1 3148
1 TraesCS1D01G096700 chr7A 247700785 247703654 2869 True 4486.00 4486 94.7660 249 3149 1 chr7A.!!$R1 2900
2 TraesCS1D01G096700 chr5A 190545595 190549240 3645 False 1151.20 4265 90.3484 1 3146 5 chr5A.!!$F1 3145
3 TraesCS1D01G096700 chr6B 120531858 120534832 2974 True 2251.00 4047 92.8505 1 3149 2 chr6B.!!$R1 3148
4 TraesCS1D01G096700 chr6B 296846102 296849369 3267 False 875.00 1877 91.0805 34 2612 4 chr6B.!!$F2 2578
5 TraesCS1D01G096700 chr4B 32568181 32576945 8764 True 1079.75 3099 93.7640 1 3149 4 chr4B.!!$R1 3148
6 TraesCS1D01G096700 chr5B 697756951 697758861 1910 False 3090.00 3090 95.8660 1 1909 1 chr5B.!!$F1 1908
7 TraesCS1D01G096700 chr1B 82548885 82551979 3094 True 2074.00 2194 94.5465 1 2779 2 chr1B.!!$R2 2778
8 TraesCS1D01G096700 chr1B 117798516 117799845 1329 False 1282.00 1282 84.4170 1450 2774 1 chr1B.!!$F1 1324
9 TraesCS1D01G096700 chr1B 117830945 117832274 1329 False 1282.00 1282 84.4170 1450 2774 1 chr1B.!!$F2 1324
10 TraesCS1D01G096700 chr1B 118416213 118417536 1323 True 1266.00 1266 84.2850 1456 2774 1 chr1B.!!$R1 1318
11 TraesCS1D01G096700 chr2A 297540782 297541944 1162 True 1365.00 1365 87.8320 1456 2622 1 chr2A.!!$R1 1166
12 TraesCS1D01G096700 chr1A 84819232 84820498 1266 False 1343.00 1343 85.8370 1334 2606 1 chr1A.!!$F1 1272
13 TraesCS1D01G096700 chr4A 618793530 618794691 1161 True 1336.00 1336 87.4140 1456 2622 1 chr4A.!!$R1 1166
14 TraesCS1D01G096700 chr2B 156046094 156047757 1663 True 1295.00 1295 81.0900 1456 3149 1 chr2B.!!$R1 1693

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
208 1048 0.606401 AAGCACCATGTTCCGACCAG 60.606 55.000 0.00 0.0 0.00 4.00 F
574 1442 5.995897 CCCTTGGCACTAATTATGTAGGTAC 59.004 44.000 0.00 0.0 0.00 3.34 F
1290 2837 2.544721 TCAAGCTCAGGTCTTGATCCT 58.455 47.619 1.72 0.0 43.34 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1030 2008 0.241213 CCGAGCTCGTGAAGTGAAGA 59.759 55.0 32.41 0.0 37.74 2.87 R
1656 3532 0.981183 TATCACCAACCGGAAGCACT 59.019 50.0 9.46 0.0 35.59 4.40 R
3055 10456 1.091537 AATGAATGTTACACGCCGGG 58.908 50.0 2.18 0.0 0.00 5.73 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
125 126 8.025445 GCATCTTTATCTGAAGAAAGCTTTTGA 58.975 33.333 14.05 7.55 38.98 2.69
208 1048 0.606401 AAGCACCATGTTCCGACCAG 60.606 55.000 0.00 0.00 0.00 4.00
574 1442 5.995897 CCCTTGGCACTAATTATGTAGGTAC 59.004 44.000 0.00 0.00 0.00 3.34
1030 2008 4.641396 TGTTGATTGTCCTTCTCGTGATT 58.359 39.130 0.00 0.00 0.00 2.57
1139 2118 6.098982 ACTCTAAACGAAGAGGATGATTCCAT 59.901 38.462 15.20 0.00 46.11 3.41
1290 2837 2.544721 TCAAGCTCAGGTCTTGATCCT 58.455 47.619 1.72 0.00 43.34 3.24
1561 3437 5.139727 CCATTACCAAGCCAATTCTGGATA 58.860 41.667 0.00 0.00 41.80 2.59
1624 3500 7.967908 AGATACCCCTACATTAACTGATTCTG 58.032 38.462 0.00 0.00 0.00 3.02
1656 3532 2.559698 TTTTCCAGGCAGTTCGATCA 57.440 45.000 0.00 0.00 0.00 2.92
1860 3736 0.825410 CCTCAGCAGCAGAGATGTCT 59.175 55.000 16.17 0.00 35.09 3.41
2018 3894 0.172803 GAAGCCAAGAAGCTGCATGG 59.827 55.000 11.94 11.94 44.11 3.66
2076 3952 3.193782 ACTGGAGGCTCTTAAAGGGAAT 58.806 45.455 15.23 0.00 0.00 3.01
2150 6936 1.202698 GCACTCCAAGTCCAACTGAGT 60.203 52.381 0.00 0.00 33.39 3.41
2765 7606 3.454812 GCCCCAGTTTATACTCTTGAGGA 59.545 47.826 2.55 0.00 30.26 3.71
2788 7629 9.696572 AGGATATGGAGTATATACGTACACATT 57.303 33.333 7.23 0.00 37.61 2.71
2865 10155 2.682155 TTTTTGTGTGCCCCAGTTTC 57.318 45.000 0.00 0.00 0.00 2.78
2926 10327 1.846782 CACTCACGCATAGTAACGCTC 59.153 52.381 0.00 0.00 0.00 5.03
2999 10400 1.763968 TCCTATATGCGCCGCTAGAT 58.236 50.000 11.67 3.32 0.00 1.98
3137 10538 1.529438 CTCCTTTTAACGCGCTTGTCA 59.471 47.619 5.73 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 2.951642 GCATAGCCAGTTGCATAGGAAA 59.048 45.455 3.98 0.00 44.83 3.13
208 1048 1.977009 CCGGGGAAAAGACCTTGGC 60.977 63.158 0.00 0.00 0.00 4.52
574 1442 0.676151 GGTCCAAGCCAGAGAAGCAG 60.676 60.000 0.00 0.00 0.00 4.24
813 1682 3.949754 TGATATGCAAAAGCCTTCTCCTG 59.050 43.478 0.00 0.00 0.00 3.86
1030 2008 0.241213 CCGAGCTCGTGAAGTGAAGA 59.759 55.000 32.41 0.00 37.74 2.87
1139 2118 4.054369 AGGTCCATCCAATCTAATGGGAA 58.946 43.478 1.80 0.00 42.31 3.97
1326 3186 1.083489 TTAAAACATCAGCGCTCGGG 58.917 50.000 7.13 1.25 0.00 5.14
1624 3500 2.412089 CCTGGAAAATCTCACGACGTTC 59.588 50.000 0.00 0.00 0.00 3.95
1656 3532 0.981183 TATCACCAACCGGAAGCACT 59.019 50.000 9.46 0.00 35.59 4.40
1860 3736 1.881973 GCATGTTTCTCCAGCACAGAA 59.118 47.619 0.00 0.00 0.00 3.02
2076 3952 4.991056 GCTTCATTCTCCAGCGTTGATATA 59.009 41.667 0.00 0.00 0.00 0.86
2635 7468 6.126883 CCACACCCTTATGAGTATAAACTGGA 60.127 42.308 0.00 0.00 35.56 3.86
2649 7482 4.312487 ACATATACACCCCACACCCTTAT 58.688 43.478 0.00 0.00 0.00 1.73
2739 7572 3.214696 AGAGTATAAACTGGGGCATGC 57.785 47.619 9.90 9.90 35.56 4.06
2740 7573 4.780815 TCAAGAGTATAAACTGGGGCATG 58.219 43.478 0.00 0.00 35.56 4.06
2741 7574 4.141390 CCTCAAGAGTATAAACTGGGGCAT 60.141 45.833 0.00 0.00 35.56 4.40
2805 10005 5.351465 ACGAGTATAAACTGTGATGCAAAGG 59.649 40.000 0.00 0.00 35.56 3.11
2865 10155 9.398538 GTATATACTCCATACCCTCAAGAGTAG 57.601 40.741 5.58 0.00 41.82 2.57
2906 10307 1.846782 GAGCGTTACTATGCGTGAGTG 59.153 52.381 0.00 0.00 41.30 3.51
2912 10313 2.203800 TCCTTGAGCGTTACTATGCG 57.796 50.000 0.00 0.00 41.30 4.73
2926 10327 3.481112 CGGTAAACGGGAAATTCCTTG 57.519 47.619 12.28 7.55 36.57 3.61
2999 10400 6.096001 GTCCCTACATCGTAAAGGAAGTCTAA 59.904 42.308 0.00 0.00 31.64 2.10
3055 10456 1.091537 AATGAATGTTACACGCCGGG 58.908 50.000 2.18 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.