Multiple sequence alignment - TraesCS5A01G006500

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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 TraesCS5A01G006500 chr5A 100.000 5500 0 0 1 5500 3768560 3774059 0.000000e+00 10157
1 TraesCS5A01G006500 chr5A 98.602 5507 68 6 1 5500 3723389 3728893 0.000000e+00 9734
2 TraesCS5A01G006500 chr5A 98.732 3313 31 7 2189 5500 3758145 3761447 0.000000e+00 5875
3 TraesCS5A01G006500 chr5A 98.192 2434 37 3 415 2842 3711264 3713696 0.000000e+00 4244
4 TraesCS5A01G006500 chr5A 98.838 2066 22 2 2871 4935 3798938 3801002 0.000000e+00 3681
5 TraesCS5A01G006500 chr5A 98.719 1796 22 1 3705 5500 3714076 3715870 0.000000e+00 3188
6 TraesCS5A01G006500 chr5A 98.617 1591 21 1 543 2133 3756094 3757683 0.000000e+00 2815
7 TraesCS5A01G006500 chr5A 98.298 1469 24 1 1405 2873 3783090 3784557 0.000000e+00 2573
8 TraesCS5A01G006500 chr5A 96.951 820 15 5 1 814 3781855 3782670 0.000000e+00 1367
9 TraesCS5A01G006500 chr5A 99.406 505 3 0 1 505 3755594 3756098 0.000000e+00 917
10 TraesCS5A01G006500 chr5A 95.789 380 12 1 912 1287 3782707 3783086 1.310000e-170 610
11 TraesCS5A01G006500 chr5A 91.603 131 9 1 449 577 30516708 30516838 4.380000e-41 180
12 TraesCS5A01G006500 chr5B 93.736 2634 108 29 1915 4529 6667354 6669949 0.000000e+00 3897
13 TraesCS5A01G006500 chr5B 88.235 1751 141 27 2979 4679 24628406 24626671 0.000000e+00 2032
14 TraesCS5A01G006500 chr5B 91.311 1358 76 20 3182 4529 24390866 24392191 0.000000e+00 1816
15 TraesCS5A01G006500 chr5B 90.387 1394 95 20 2138 3495 30941682 30940292 0.000000e+00 1796
16 TraesCS5A01G006500 chr5B 90.174 1089 76 16 2138 3196 31017526 31016439 0.000000e+00 1389
17 TraesCS5A01G006500 chr5B 80.698 974 131 31 3958 4910 30837210 30836273 0.000000e+00 704
18 TraesCS5A01G006500 chr5B 83.923 678 56 14 738 1376 6665950 6666613 2.840000e-167 599
19 TraesCS5A01G006500 chr5B 89.710 379 28 4 910 1281 30942052 30941678 1.790000e-129 473
20 TraesCS5A01G006500 chr5B 89.683 378 30 2 910 1281 31017896 31017522 1.790000e-129 473
21 TraesCS5A01G006500 chr5B 84.110 472 41 11 1480 1922 6666848 6667314 5.090000e-115 425
22 TraesCS5A01G006500 chr5B 81.295 417 64 12 2148 2558 24676734 24676326 5.310000e-85 326
23 TraesCS5A01G006500 chr5B 91.176 204 16 2 4731 4934 24392785 24392986 5.430000e-70 276
24 TraesCS5A01G006500 chr5B 90.854 164 15 0 4571 4734 6669950 6670113 2.580000e-53 220
25 TraesCS5A01G006500 chr5B 90.854 164 15 0 4571 4734 24392192 24392355 2.580000e-53 220
26 TraesCS5A01G006500 chr5B 91.720 157 12 1 4731 4887 6671265 6671420 3.340000e-52 217
27 TraesCS5A01G006500 chr5B 85.128 195 14 7 4761 4943 30921877 30921686 9.410000e-43 185
28 TraesCS5A01G006500 chr5B 85.217 115 16 1 1480 1593 13911324 13911210 3.480000e-22 117
29 TraesCS5A01G006500 chr5B 85.217 115 16 1 1480 1593 13917944 13917830 3.480000e-22 117
30 TraesCS5A01G006500 chr3B 93.719 2595 109 31 1951 4533 62668818 62671370 0.000000e+00 3840
31 TraesCS5A01G006500 chr3B 84.915 590 44 21 912 1481 62667492 62668056 6.220000e-154 555
32 TraesCS5A01G006500 chr3B 87.252 353 26 3 1584 1922 62668408 62668755 8.640000e-103 385
33 TraesCS5A01G006500 chr3B 92.647 204 14 1 4731 4934 62671878 62672080 5.390000e-75 292
34 TraesCS5A01G006500 chr3B 87.805 164 20 0 4571 4734 62671367 62671530 5.620000e-45 193
35 TraesCS5A01G006500 chr5D 94.532 2414 88 23 2131 4532 5102526 5100145 0.000000e+00 3687
36 TraesCS5A01G006500 chr5D 82.455 1157 157 24 3797 4932 3928431 3927300 0.000000e+00 970
37 TraesCS5A01G006500 chr5D 87.201 586 38 14 910 1483 5103964 5103404 2.800000e-177 632
38 TraesCS5A01G006500 chr5D 83.721 559 43 22 1583 2102 5103071 5102522 8.280000e-133 484
39 TraesCS5A01G006500 chr5D 82.635 334 39 12 1583 1903 420927970 420927643 1.510000e-70 278
40 TraesCS5A01G006500 chr5D 90.244 164 16 0 4571 4734 5100147 5099984 1.200000e-51 215
41 TraesCS5A01G006500 chr5D 87.719 171 16 2 1915 2084 420927584 420927418 1.560000e-45 195
42 TraesCS5A01G006500 chr5D 91.150 113 9 1 4822 4934 5099496 5099385 9.540000e-33 152
43 TraesCS5A01G006500 chr5D 83.193 119 18 2 1476 1593 420928119 420928002 2.100000e-19 108
44 TraesCS5A01G006500 chr4A 82.816 1385 188 38 2120 3475 18681553 18682916 0.000000e+00 1194
45 TraesCS5A01G006500 chr4A 82.599 1385 190 39 2120 3475 18647740 18649102 0.000000e+00 1175
46 TraesCS5A01G006500 chr7A 97.168 565 15 1 4936 5500 693125076 693125639 0.000000e+00 953
47 TraesCS5A01G006500 chr7A 92.424 132 8 1 449 578 247073114 247073245 2.620000e-43 187
48 TraesCS5A01G006500 chr6B 90.783 575 43 3 4936 5500 707825063 707824489 0.000000e+00 760
49 TraesCS5A01G006500 chr6B 88.953 344 38 0 4936 5279 11157815 11158158 5.090000e-115 425
50 TraesCS5A01G006500 chrUn 90.261 575 47 1 4935 5500 47565914 47565340 0.000000e+00 743
51 TraesCS5A01G006500 chrUn 91.990 412 30 3 1 410 225680417 225680007 4.780000e-160 575
52 TraesCS5A01G006500 chrUn 91.241 411 34 2 1 410 287109134 287108725 4.810000e-155 558
53 TraesCS5A01G006500 chrUn 91.241 411 34 2 1 410 347579225 347578816 4.810000e-155 558
54 TraesCS5A01G006500 chrUn 90.998 411 35 2 1 410 269607692 269607283 2.240000e-153 553
55 TraesCS5A01G006500 chrUn 87.919 298 36 0 4935 5232 47692020 47692317 8.770000e-93 351
56 TraesCS5A01G006500 chr1B 91.041 413 33 3 1 410 8844731 8844320 6.220000e-154 555
57 TraesCS5A01G006500 chr1B 86.770 257 28 6 5218 5473 646044700 646044951 1.170000e-71 281
58 TraesCS5A01G006500 chr1A 90.954 409 35 2 3 410 507232028 507232435 2.900000e-152 549
59 TraesCS5A01G006500 chr1A 90.210 143 12 1 449 589 148617132 148617274 9.410000e-43 185
60 TraesCS5A01G006500 chr2A 82.842 373 58 5 4936 5306 1113289 1112921 4.110000e-86 329
61 TraesCS5A01G006500 chr2A 93.130 131 7 1 449 577 27650869 27650739 2.020000e-44 191
62 TraesCS5A01G006500 chr3A 80.805 323 48 9 1583 1896 327625703 327625386 1.980000e-59 241
63 TraesCS5A01G006500 chr3A 93.130 131 7 1 449 577 654391293 654391423 2.020000e-44 191
64 TraesCS5A01G006500 chr3A 84.615 104 14 2 1476 1578 327625852 327625750 9.750000e-18 102
65 TraesCS5A01G006500 chr6A 93.130 131 7 1 449 577 559528665 559528795 2.020000e-44 191
66 TraesCS5A01G006500 chr2D 86.982 169 18 1 1915 2083 490826231 490826067 2.620000e-43 187
67 TraesCS5A01G006500 chr4D 84.167 120 16 3 1476 1593 247494642 247494760 4.500000e-21 113


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 TraesCS5A01G006500 chr5A 3768560 3774059 5499 False 10157.000000 10157 100.000000 1 5500 1 chr5A.!!$F2 5499
1 TraesCS5A01G006500 chr5A 3723389 3728893 5504 False 9734.000000 9734 98.602000 1 5500 1 chr5A.!!$F1 5499
2 TraesCS5A01G006500 chr5A 3711264 3715870 4606 False 3716.000000 4244 98.455500 415 5500 2 chr5A.!!$F5 5085
3 TraesCS5A01G006500 chr5A 3798938 3801002 2064 False 3681.000000 3681 98.838000 2871 4935 1 chr5A.!!$F3 2064
4 TraesCS5A01G006500 chr5A 3755594 3761447 5853 False 3202.333333 5875 98.918333 1 5500 3 chr5A.!!$F6 5499
5 TraesCS5A01G006500 chr5A 3781855 3784557 2702 False 1516.666667 2573 97.012667 1 2873 3 chr5A.!!$F7 2872
6 TraesCS5A01G006500 chr5B 24626671 24628406 1735 True 2032.000000 2032 88.235000 2979 4679 1 chr5B.!!$R3 1700
7 TraesCS5A01G006500 chr5B 30940292 30942052 1760 True 1134.500000 1796 90.048500 910 3495 2 chr5B.!!$R7 2585
8 TraesCS5A01G006500 chr5B 6665950 6671420 5470 False 1071.600000 3897 88.868600 738 4887 5 chr5B.!!$F1 4149
9 TraesCS5A01G006500 chr5B 31016439 31017896 1457 True 931.000000 1389 89.928500 910 3196 2 chr5B.!!$R8 2286
10 TraesCS5A01G006500 chr5B 24390866 24392986 2120 False 770.666667 1816 91.113667 3182 4934 3 chr5B.!!$F2 1752
11 TraesCS5A01G006500 chr5B 30836273 30837210 937 True 704.000000 704 80.698000 3958 4910 1 chr5B.!!$R5 952
12 TraesCS5A01G006500 chr3B 62667492 62672080 4588 False 1053.000000 3840 89.267600 912 4934 5 chr3B.!!$F1 4022
13 TraesCS5A01G006500 chr5D 5099385 5103964 4579 True 1034.000000 3687 89.369600 910 4934 5 chr5D.!!$R2 4024
14 TraesCS5A01G006500 chr5D 3927300 3928431 1131 True 970.000000 970 82.455000 3797 4932 1 chr5D.!!$R1 1135
15 TraesCS5A01G006500 chr4A 18681553 18682916 1363 False 1194.000000 1194 82.816000 2120 3475 1 chr4A.!!$F2 1355
16 TraesCS5A01G006500 chr4A 18647740 18649102 1362 False 1175.000000 1175 82.599000 2120 3475 1 chr4A.!!$F1 1355
17 TraesCS5A01G006500 chr7A 693125076 693125639 563 False 953.000000 953 97.168000 4936 5500 1 chr7A.!!$F2 564
18 TraesCS5A01G006500 chr6B 707824489 707825063 574 True 760.000000 760 90.783000 4936 5500 1 chr6B.!!$R1 564
19 TraesCS5A01G006500 chrUn 47565340 47565914 574 True 743.000000 743 90.261000 4935 5500 1 chrUn.!!$R1 565

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
629 675 1.129326 GTACGTACGCATGCATCCTC 58.871 55.000 19.57 2.07 0.00 3.71 F
1579 1910 1.745115 GCTAGCATGGCAACGTCCA 60.745 57.895 10.63 0.00 44.73 4.02 F
2173 2605 1.202348 CCCGCCCTGTGAAAATTTCTC 59.798 52.381 7.29 4.14 0.00 2.87 F
2975 3864 5.361857 CAGGGCAGAATATTTGAATCCAACT 59.638 40.000 0.00 0.00 30.88 3.16 F
3518 4441 3.734463 TCTCGTTTGAACATGTGGCTAA 58.266 40.909 0.00 0.00 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2605 1.471684 AGGTTTGTAGTAGTCGAGCGG 59.528 52.381 0.00 0.0 0.00 5.52 R
2975 3864 0.250510 TGTGGTGCCGCTCAAACATA 60.251 50.000 3.31 0.0 0.00 2.29 R
3211 4105 3.093814 TCTCCACGCAGGTCAATAACTA 58.906 45.455 0.00 0.0 39.02 2.24 R
4301 5238 0.111446 TGGCCGGGATCAAGAAAACA 59.889 50.000 2.18 0.0 0.00 2.83 R
4844 7407 1.873591 ACAACTCAAAGTTAGCGCCAG 59.126 47.619 2.29 0.0 36.03 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
629 675 1.129326 GTACGTACGCATGCATCCTC 58.871 55.000 19.57 2.07 0.00 3.71
843 917 2.268076 ACCTTTGCCACCGCATGTC 61.268 57.895 0.00 0.00 46.67 3.06
1579 1910 1.745115 GCTAGCATGGCAACGTCCA 60.745 57.895 10.63 0.00 44.73 4.02
1759 2136 3.066064 GGCGCAATTAATGTACACCATCA 59.934 43.478 10.83 0.00 31.75 3.07
1814 2191 2.683933 CAGGCCCTACCGTCCACT 60.684 66.667 0.00 0.00 46.52 4.00
1827 2205 2.036733 CCGTCCACTTTACTGACTTCCA 59.963 50.000 0.00 0.00 0.00 3.53
1877 2255 2.288666 TGTGTTGTCCTTGAGTCTTGC 58.711 47.619 0.00 0.00 0.00 4.01
2173 2605 1.202348 CCCGCCCTGTGAAAATTTCTC 59.798 52.381 7.29 4.14 0.00 2.87
2975 3864 5.361857 CAGGGCAGAATATTTGAATCCAACT 59.638 40.000 0.00 0.00 30.88 3.16
3304 4198 6.146673 CCTTCTTCCATTTTGCTCAATTGTTC 59.853 38.462 5.13 0.00 0.00 3.18
3518 4441 3.734463 TCTCGTTTGAACATGTGGCTAA 58.266 40.909 0.00 0.00 0.00 3.09
4633 5589 6.559042 GCATTGTGCAATACATTCTTACAC 57.441 37.500 0.00 0.00 44.26 2.90
4844 7407 3.350833 AGAGATGCATGTCTGGGTTTTC 58.649 45.455 24.40 0.00 0.00 2.29
4942 7518 7.665559 AGTTTTCTTTCTGGATATGCACTACAA 59.334 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
534 538 8.219105 GTGCAATACACGTTTATATTAGGTAGC 58.781 37.037 0.00 0.00 40.07 3.58
1392 1504 1.221840 CCTTCCCCACACCAGATCG 59.778 63.158 0.00 0.00 0.00 3.69
1400 1512 1.856873 AAGCCATCCCTTCCCCACA 60.857 57.895 0.00 0.00 0.00 4.17
1814 2191 2.158871 ACGCCAAGTGGAAGTCAGTAAA 60.159 45.455 0.18 0.00 37.39 2.01
1827 2205 2.747686 CCACCCACTACGCCAAGT 59.252 61.111 0.00 0.00 0.00 3.16
1877 2255 4.499183 GTCAGAGACCTCTACAACAATGG 58.501 47.826 0.00 0.00 37.98 3.16
2173 2605 1.471684 AGGTTTGTAGTAGTCGAGCGG 59.528 52.381 0.00 0.00 0.00 5.52
2293 3131 7.502696 ACAAGGATACATATAAAAGTACCGCA 58.497 34.615 0.00 0.00 41.41 5.69
2975 3864 0.250510 TGTGGTGCCGCTCAAACATA 60.251 50.000 3.31 0.00 0.00 2.29
3211 4105 3.093814 TCTCCACGCAGGTCAATAACTA 58.906 45.455 0.00 0.00 39.02 2.24
3304 4198 7.148738 CGTACTGATATTTCTTCCATGAATCCG 60.149 40.741 0.00 0.00 0.00 4.18
4176 5110 9.274206 GGAAACTAAAACATTCTAGTCAAGACT 57.726 33.333 7.96 7.96 45.02 3.24
4196 5130 5.324409 TCCAACTGATAATTGCAGGAAACT 58.676 37.500 12.82 0.00 46.44 2.66
4301 5238 0.111446 TGGCCGGGATCAAGAAAACA 59.889 50.000 2.18 0.00 0.00 2.83
4501 5440 3.753294 AATAATCTGTAGACGGGGCTG 57.247 47.619 0.00 0.00 0.00 4.85
4844 7407 1.873591 ACAACTCAAAGTTAGCGCCAG 59.126 47.619 2.29 0.00 36.03 4.85
5114 7691 2.676342 CCGAGTGGCTTGTATAAACACC 59.324 50.000 0.00 0.00 34.61 4.16
5461 8056 4.756642 GCTGGATATACATTGTTGCTGCTA 59.243 41.667 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.