Multiple sequence alignment - TraesCS5D01G541900

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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 TraesCS5D01G541900 chr5D 100.000 4156 0 0 1 4156 552682725 552686880 0.000000e+00 7675.0
1 TraesCS5D01G541900 chr5D 85.135 1258 163 17 992 2242 552728997 552730237 0.000000e+00 1266.0
2 TraesCS5D01G541900 chr5D 86.789 545 61 11 2600 3140 552730714 552731251 7.690000e-167 597.0
3 TraesCS5D01G541900 chr5D 75.207 1206 241 42 980 2153 542411225 542410046 6.160000e-143 518.0
4 TraesCS5D01G541900 chr5D 74.841 1256 248 48 954 2170 552407643 552408869 1.330000e-139 507.0
5 TraesCS5D01G541900 chr5D 75.503 1143 218 41 1029 2147 552129691 552128587 1.720000e-138 503.0
6 TraesCS5D01G541900 chr5D 91.440 257 22 0 999 1255 551409722 551409466 1.840000e-93 353.0
7 TraesCS5D01G541900 chr5D 86.517 267 26 7 2339 2602 552730299 552730558 6.800000e-73 285.0
8 TraesCS5D01G541900 chr5D 84.158 303 28 8 680 970 551410286 551409992 4.090000e-70 276.0
9 TraesCS5D01G541900 chr5D 100.000 31 0 0 45 75 546223653 546223683 1.610000e-04 58.4
10 TraesCS5D01G541900 chr5D 100.000 31 0 0 45 75 546228291 546228321 1.610000e-04 58.4
11 TraesCS5D01G541900 chr5D 100.000 31 0 0 45 75 546229453 546229483 1.610000e-04 58.4
12 TraesCS5D01G541900 chr5B 92.280 4197 216 54 10 4155 697870119 697865980 0.000000e+00 5856.0
13 TraesCS5D01G541900 chr5B 85.235 1253 162 16 995 2241 697832242 697831007 0.000000e+00 1267.0
14 TraesCS5D01G541900 chr5B 77.986 1599 276 51 588 2151 699282960 699281403 0.000000e+00 933.0
15 TraesCS5D01G541900 chr5B 79.337 1297 203 35 871 2144 703805009 703803755 0.000000e+00 850.0
16 TraesCS5D01G541900 chr5B 87.734 481 50 8 2603 3079 697830521 697830046 1.690000e-153 553.0
17 TraesCS5D01G541900 chr5B 73.841 1208 226 59 1008 2161 697819176 697820347 8.370000e-107 398.0
18 TraesCS5D01G541900 chr5B 89.744 312 26 3 3816 4123 697865369 697865060 1.080000e-105 394.0
19 TraesCS5D01G541900 chr5B 87.423 326 29 4 871 1196 699616410 699616097 8.490000e-97 364.0
20 TraesCS5D01G541900 chr5B 77.329 569 110 15 2514 3071 698261627 698261067 6.700000e-83 318.0
21 TraesCS5D01G541900 chr5B 77.396 553 105 18 2517 3061 699790222 699789682 1.120000e-80 311.0
22 TraesCS5D01G541900 chr5B 77.451 510 90 18 2603 3089 697809281 697809788 8.800000e-72 281.0
23 TraesCS5D01G541900 chr5B 85.768 267 30 5 2339 2602 697830944 697830683 4.090000e-70 276.0
24 TraesCS5D01G541900 chr5B 84.058 207 27 6 1968 2170 703893834 703893630 1.180000e-45 195.0
25 TraesCS5D01G541900 chr5B 100.000 33 0 0 43 75 670789651 670789619 1.250000e-05 62.1
26 TraesCS5D01G541900 chr4A 91.564 4208 246 54 4 4156 615458342 615454189 0.000000e+00 5703.0
27 TraesCS5D01G541900 chr4A 84.692 2195 229 45 1 2138 616699811 616701955 0.000000e+00 2093.0
28 TraesCS5D01G541900 chr4A 81.761 1590 175 48 2603 4121 615374354 615372809 0.000000e+00 1223.0
29 TraesCS5D01G541900 chr4A 82.326 1324 169 41 960 2236 615376144 615374839 0.000000e+00 1088.0
30 TraesCS5D01G541900 chr4A 91.750 703 48 6 1 696 616687941 616688640 0.000000e+00 968.0
31 TraesCS5D01G541900 chr4A 86.071 280 21 11 2326 2602 615374781 615374517 6.800000e-73 285.0
32 TraesCS5D01G541900 chr4A 97.059 34 1 0 45 78 622941795 622941762 1.610000e-04 58.4
33 TraesCS5D01G541900 chr2D 76.910 1178 215 41 999 2143 651431730 651432883 2.120000e-172 616.0
34 TraesCS5D01G541900 chr2B 76.510 1192 213 42 999 2151 781149700 781150863 4.630000e-164 588.0
35 TraesCS5D01G541900 chr2B 93.617 47 2 1 144 190 788143120 788143075 7.460000e-08 69.4
36 TraesCS5D01G541900 chr6B 79.694 458 81 9 2641 3089 41434192 41433738 1.860000e-83 320.0
37 TraesCS5D01G541900 chr3D 76.562 192 38 4 218 408 488953505 488953320 9.510000e-17 99.0
38 TraesCS5D01G541900 chr1B 84.848 99 12 3 320 417 665030703 665030607 3.420000e-16 97.1


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 TraesCS5D01G541900 chr5D 552682725 552686880 4155 False 7675.000000 7675 100.000000 1 4156 1 chr5D.!!$F3 4155
1 TraesCS5D01G541900 chr5D 552728997 552731251 2254 False 716.000000 1266 86.147000 992 3140 3 chr5D.!!$F5 2148
2 TraesCS5D01G541900 chr5D 542410046 542411225 1179 True 518.000000 518 75.207000 980 2153 1 chr5D.!!$R1 1173
3 TraesCS5D01G541900 chr5D 552407643 552408869 1226 False 507.000000 507 74.841000 954 2170 1 chr5D.!!$F2 1216
4 TraesCS5D01G541900 chr5D 552128587 552129691 1104 True 503.000000 503 75.503000 1029 2147 1 chr5D.!!$R2 1118
5 TraesCS5D01G541900 chr5D 551409466 551410286 820 True 314.500000 353 87.799000 680 1255 2 chr5D.!!$R3 575
6 TraesCS5D01G541900 chr5B 697865060 697870119 5059 True 3125.000000 5856 91.012000 10 4155 2 chr5B.!!$R9 4145
7 TraesCS5D01G541900 chr5B 699281403 699282960 1557 True 933.000000 933 77.986000 588 2151 1 chr5B.!!$R3 1563
8 TraesCS5D01G541900 chr5B 703803755 703805009 1254 True 850.000000 850 79.337000 871 2144 1 chr5B.!!$R6 1273
9 TraesCS5D01G541900 chr5B 697830046 697832242 2196 True 698.666667 1267 86.245667 995 3079 3 chr5B.!!$R8 2084
10 TraesCS5D01G541900 chr5B 697819176 697820347 1171 False 398.000000 398 73.841000 1008 2161 1 chr5B.!!$F2 1153
11 TraesCS5D01G541900 chr5B 698261067 698261627 560 True 318.000000 318 77.329000 2514 3071 1 chr5B.!!$R2 557
12 TraesCS5D01G541900 chr5B 699789682 699790222 540 True 311.000000 311 77.396000 2517 3061 1 chr5B.!!$R5 544
13 TraesCS5D01G541900 chr5B 697809281 697809788 507 False 281.000000 281 77.451000 2603 3089 1 chr5B.!!$F1 486
14 TraesCS5D01G541900 chr4A 615454189 615458342 4153 True 5703.000000 5703 91.564000 4 4156 1 chr4A.!!$R1 4152
15 TraesCS5D01G541900 chr4A 616699811 616701955 2144 False 2093.000000 2093 84.692000 1 2138 1 chr4A.!!$F2 2137
16 TraesCS5D01G541900 chr4A 616687941 616688640 699 False 968.000000 968 91.750000 1 696 1 chr4A.!!$F1 695
17 TraesCS5D01G541900 chr4A 615372809 615376144 3335 True 865.333333 1223 83.386000 960 4121 3 chr4A.!!$R3 3161
18 TraesCS5D01G541900 chr2D 651431730 651432883 1153 False 616.000000 616 76.910000 999 2143 1 chr2D.!!$F1 1144
19 TraesCS5D01G541900 chr2B 781149700 781150863 1163 False 588.000000 588 76.510000 999 2151 1 chr2B.!!$F1 1152

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
782 823 0.755079 ATCTCATCGGCTAGCAGCAA 59.245 50.000 18.24 0.0 44.75 3.91 F
949 1016 2.583593 GCATCTCAGCGGTCGGTC 60.584 66.667 0.00 0.0 0.00 4.79 F
1890 2312 2.907892 AGGAGTTCCAGGAATCTGTCA 58.092 47.619 4.80 0.0 39.31 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 2963 1.068753 CCTCCTATGCTGCTCACCG 59.931 63.158 0.0 0.0 0.00 4.94 R
2546 3048 6.153851 TGGATGAATTTGCATGAACTGAATCT 59.846 34.615 0.0 0.0 0.00 2.40 R
3686 4462 0.161870 GTGCACGTCGAAAGAGAAGC 59.838 55.000 0.0 0.0 43.49 3.86 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
216 237 1.141449 CTCTCTCTGCCGCTTCAGG 59.859 63.158 0.00 0.00 34.91 3.86
278 307 5.594317 CGGGCTAGTAGTTTAGGTTAGGTTA 59.406 44.000 0.00 0.00 0.00 2.85
299 328 7.123247 AGGTTATTTTTAGTCCTCGTAGCTGTA 59.877 37.037 0.00 0.00 0.00 2.74
449 480 2.225727 CGAGGTTAGGGTTTCTTGTTGC 59.774 50.000 0.00 0.00 0.00 4.17
460 492 3.578089 CTTGTTGCACGTGCGCGAT 62.578 57.895 33.22 7.87 45.83 4.58
525 557 5.487488 ACTTCACATAGGAGTATTTGGGTGA 59.513 40.000 0.00 0.00 32.73 4.02
554 586 8.463930 TGAAAATTCACCTACTGAAAAGTGAT 57.536 30.769 0.00 0.00 42.37 3.06
557 589 8.567285 AAATTCACCTACTGAAAAGTGATAGG 57.433 34.615 0.00 0.00 42.37 2.57
558 590 5.086104 TCACCTACTGAAAAGTGATAGGC 57.914 43.478 0.00 0.00 36.63 3.93
559 591 4.530553 TCACCTACTGAAAAGTGATAGGCA 59.469 41.667 0.00 0.00 36.63 4.75
560 592 5.189736 TCACCTACTGAAAAGTGATAGGCAT 59.810 40.000 0.00 0.00 36.63 4.40
607 641 7.687941 CAAACTATATTTGGAAGGTGACTGT 57.312 36.000 0.00 0.00 42.68 3.55
684 725 1.824329 TCGATCCCCACTCTCGAGC 60.824 63.158 7.81 0.00 36.57 5.03
699 740 1.880340 GAGCGCTCCAATCCACTCG 60.880 63.158 27.22 0.00 0.00 4.18
758 799 2.084546 GCCACCAAATCGAAGCTAACT 58.915 47.619 0.00 0.00 0.00 2.24
782 823 0.755079 ATCTCATCGGCTAGCAGCAA 59.245 50.000 18.24 0.00 44.75 3.91
949 1016 2.583593 GCATCTCAGCGGTCGGTC 60.584 66.667 0.00 0.00 0.00 4.79
1890 2312 2.907892 AGGAGTTCCAGGAATCTGTCA 58.092 47.619 4.80 0.00 39.31 3.58
1935 2357 5.631929 CAGCCAAACGGTAAAGTTAATTTCC 59.368 40.000 0.00 0.00 33.41 3.13
2829 3538 4.378774 CATCGAAGGATCTGAAGCATCTT 58.621 43.478 0.00 0.00 0.00 2.40
3079 3791 8.806146 AGATAATAATTTGTTGATGGGTATGGC 58.194 33.333 0.00 0.00 0.00 4.40
3102 3814 8.799367 TGGCCAAGAAATGATAATAATCTCATG 58.201 33.333 0.61 0.00 32.56 3.07
3279 4017 5.850557 TTTGTGAGGCATTCTCTTTTCAA 57.149 34.783 0.00 0.00 42.86 2.69
3314 4061 6.206787 TGGGATAGTAGAAAATGGTACCAGA 58.793 40.000 21.41 0.00 0.00 3.86
3395 4157 2.196749 ACAGCTCGTTTGATGATAGCG 58.803 47.619 0.00 0.00 38.23 4.26
3438 4200 5.894393 TGGTGTTCCATTTTCCTTCTTGTTA 59.106 36.000 0.00 0.00 39.03 2.41
3568 4330 2.292103 TGCAACCACAAGCTTTTGTC 57.708 45.000 11.49 4.53 31.86 3.18
3685 4461 3.119280 CCCTGTTTGAACCGAAGTTTTGT 60.119 43.478 0.00 0.00 35.94 2.83
3686 4462 3.857093 CCTGTTTGAACCGAAGTTTTGTG 59.143 43.478 0.00 0.00 35.94 3.33
3755 4531 4.442375 TCGTTGTTTCCACATTTGTGTT 57.558 36.364 9.66 0.00 44.21 3.32
3964 4741 6.742718 CCGTGTCTGATTAAGCTGTTAATTTG 59.257 38.462 0.00 0.00 38.70 2.32
3973 4754 9.103861 GATTAAGCTGTTAATTTGCTAGAGTCT 57.896 33.333 0.00 0.00 38.70 3.24
3984 4765 1.821753 GCTAGAGTCTTGACTGAGCCA 59.178 52.381 17.07 0.00 0.00 4.75
4021 4802 8.336080 CAGATGCGGATGATTATAAAGATCATG 58.664 37.037 0.00 0.00 42.63 3.07
4061 4842 0.671472 TCTGTGAGACAAGCATGCCG 60.671 55.000 15.66 8.79 0.00 5.69
4076 4857 2.335316 TGCCGACTGGTACTTGTTTT 57.665 45.000 0.00 0.00 37.67 2.43
4138 4920 6.370442 TCCATGAATTTAGTGTGGACTTTACG 59.630 38.462 0.00 0.00 34.23 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.719144 GTGCCGACGAAAACCCCG 61.719 66.667 0.00 0.00 0.00 5.73
197 218 1.141449 CTGAAGCGGCAGAGAGAGG 59.859 63.158 1.45 0.00 38.14 3.69
198 219 1.141449 CCTGAAGCGGCAGAGAGAG 59.859 63.158 1.45 0.00 38.14 3.20
242 271 2.579684 CTAGCCCGAGTGAAGCCACC 62.580 65.000 0.00 0.00 44.22 4.61
246 275 1.104630 ACTACTAGCCCGAGTGAAGC 58.895 55.000 0.00 0.00 0.00 3.86
278 307 5.349809 GCTACAGCTACGAGGACTAAAAAT 58.650 41.667 0.00 0.00 38.21 1.82
449 480 4.799473 CTTGCCATCGCGCACGTG 62.799 66.667 12.28 12.28 38.83 4.49
460 492 8.637986 AGATCAAATTAACACTAAAACTTGCCA 58.362 29.630 0.00 0.00 0.00 4.92
495 527 9.667107 CCAAATACTCCTATGTGAAGTTTTAGA 57.333 33.333 0.00 0.00 0.00 2.10
499 531 6.659242 CACCCAAATACTCCTATGTGAAGTTT 59.341 38.462 0.00 0.00 0.00 2.66
507 539 5.363868 TCACTCTCACCCAAATACTCCTATG 59.636 44.000 0.00 0.00 0.00 2.23
547 579 3.623060 CGTGTGCTAATGCCTATCACTTT 59.377 43.478 0.00 0.00 38.71 2.66
554 586 2.293677 CACTCGTGTGCTAATGCCTA 57.706 50.000 4.47 0.00 37.38 3.93
607 641 1.417517 TGCTGTGCTGGAGAAAGAAGA 59.582 47.619 0.00 0.00 0.00 2.87
684 725 1.298157 TTTGCGAGTGGATTGGAGCG 61.298 55.000 0.00 0.00 0.00 5.03
699 740 1.401905 GTCGGATTGGAGTGGATTTGC 59.598 52.381 0.00 0.00 0.00 3.68
758 799 1.895131 TGCTAGCCGATGAGATGCATA 59.105 47.619 13.29 0.00 37.34 3.14
881 948 3.838271 GGACGCGGCTCCTCATCA 61.838 66.667 13.91 0.00 0.00 3.07
943 1010 4.202451 ACCCTAGATAGAAGTAGGACCGAC 60.202 50.000 0.00 0.00 38.54 4.79
949 1016 6.818233 GGTTGAAACCCTAGATAGAAGTAGG 58.182 44.000 0.36 0.00 43.43 3.18
1044 1358 2.880879 GTGAGCGCGCTGATTCGA 60.881 61.111 41.82 11.95 0.00 3.71
1179 1493 1.671379 GCCTTGGAAGTGACCGACC 60.671 63.158 0.00 0.00 0.00 4.79
1890 2312 7.150640 GGCTGAAGAAATTGAGATTCAGTTTT 58.849 34.615 16.87 0.00 46.62 2.43
1935 2357 1.202020 CGGGTGATGTGTAAATGCACG 60.202 52.381 0.00 0.00 41.94 5.34
2181 2641 7.886629 AATGCTGAATATTCCAGTAACATGT 57.113 32.000 12.90 0.00 34.29 3.21
2323 2818 4.471386 ACAAGGTACTACAATCCAGCAGAT 59.529 41.667 0.00 0.00 38.49 2.90
2466 2963 1.068753 CCTCCTATGCTGCTCACCG 59.931 63.158 0.00 0.00 0.00 4.94
2546 3048 6.153851 TGGATGAATTTGCATGAACTGAATCT 59.846 34.615 0.00 0.00 0.00 2.40
2829 3538 6.882610 AACATCATCAGCAACTTCAAGTTA 57.117 33.333 1.43 0.00 36.03 2.24
3279 4017 8.934023 TTTTCTACTATCCCAAAGTCACATTT 57.066 30.769 0.00 0.00 0.00 2.32
3314 4061 9.988350 CTATCAGCGTATTTTACTGTTTTTCAT 57.012 29.630 0.00 0.00 33.12 2.57
3395 4157 3.578282 ACCATTTCCCAGACACCAAATTC 59.422 43.478 0.00 0.00 0.00 2.17
3568 4330 0.602106 TCGACCGTCGCTATAGGAGG 60.602 60.000 16.24 3.37 40.21 4.30
3685 4461 0.249280 TGCACGTCGAAAGAGAAGCA 60.249 50.000 0.00 0.00 43.49 3.91
3686 4462 0.161870 GTGCACGTCGAAAGAGAAGC 59.838 55.000 0.00 0.00 43.49 3.86
3796 4573 4.009370 AGAGAGCAACTTTCCTAACCAC 57.991 45.455 0.00 0.00 0.00 4.16
3802 4579 5.338789 GGAATAGGAAGAGAGCAACTTTCCT 60.339 44.000 19.56 19.56 42.63 3.36
3964 4741 1.821753 TGGCTCAGTCAAGACTCTAGC 59.178 52.381 18.85 18.85 42.42 3.42
3973 4754 2.936928 CTGTGCATGGCTCAGTCAA 58.063 52.632 11.06 0.00 42.75 3.18
4021 4802 1.506493 CCACACTGCAGTCTGTCTTC 58.494 55.000 18.64 0.00 0.00 2.87
4121 4903 6.476380 CACTGTAACGTAAAGTCCACACTAAA 59.524 38.462 0.00 0.00 30.14 1.85


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

AutoCloner maintained by Alex Coulton.