Multiple sequence alignment - TraesCS2D01G532500

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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 TraesCS2D01G532500 chr2D 100.000 4043 0 0 1 4043 617759376 617763418 0.000000e+00 7467.0
1 TraesCS2D01G532500 chr2D 94.201 2535 147 0 1068 3602 617634173 617636707 0.000000e+00 3868.0
2 TraesCS2D01G532500 chr2D 95.295 2019 93 2 1068 3084 617887641 617889659 0.000000e+00 3201.0
3 TraesCS2D01G532500 chr2D 94.355 2055 114 2 1068 3120 617539173 617541227 0.000000e+00 3151.0
4 TraesCS2D01G532500 chr2D 93.059 2017 138 2 1068 3082 617909446 617907430 0.000000e+00 2948.0
5 TraesCS2D01G532500 chr2D 92.719 2019 143 3 1068 3084 617546788 617548804 0.000000e+00 2911.0
6 TraesCS2D01G532500 chr2D 89.415 1077 79 22 1 1069 617886555 617887604 0.000000e+00 1325.0
7 TraesCS2D01G532500 chr2D 94.253 696 12 5 396 1069 617633447 617634136 0.000000e+00 1038.0
8 TraesCS2D01G532500 chr2D 85.185 513 41 13 578 1069 617909981 617909483 1.010000e-135 494.0
9 TraesCS2D01G532500 chr2D 89.114 395 30 7 3660 4043 617636897 617637289 2.830000e-131 479.0
10 TraesCS2D01G532500 chr2D 82.574 505 62 6 578 1069 617730709 617731200 4.830000e-114 422.0
11 TraesCS2D01G532500 chr2D 82.192 511 52 21 561 1069 617546278 617546751 1.750000e-108 403.0
12 TraesCS2D01G532500 chr2D 86.405 331 29 7 3205 3520 617413661 617413332 8.320000e-92 348.0
13 TraesCS2D01G532500 chr2D 87.204 211 26 1 2834 3043 617414017 617413807 5.220000e-59 239.0
14 TraesCS2D01G532500 chr2D 87.349 166 12 4 3847 4011 617902203 617902046 8.930000e-42 182.0
15 TraesCS2D01G532500 chr2D 77.528 267 33 16 3741 3981 617413295 617413030 7.050000e-28 135.0
16 TraesCS2D01G532500 chr2B 92.647 2992 174 17 1068 4043 753793146 753796107 0.000000e+00 4265.0
17 TraesCS2D01G532500 chr2B 91.049 2536 224 3 1068 3602 753930967 753928434 0.000000e+00 3422.0
18 TraesCS2D01G532500 chr2B 92.290 2140 155 4 1229 3366 753786113 753788244 0.000000e+00 3029.0
19 TraesCS2D01G532500 chr2B 92.542 1314 83 5 2733 4043 753935066 753933765 0.000000e+00 1869.0
20 TraesCS2D01G532500 chr2B 89.027 401 37 6 3639 4035 753928428 753928031 1.310000e-134 490.0
21 TraesCS2D01G532500 chr2B 88.000 350 30 3 720 1069 753792772 753793109 1.750000e-108 403.0
22 TraesCS2D01G532500 chr2B 92.655 177 11 2 3869 4043 753788234 753788410 1.870000e-63 254.0
23 TraesCS2D01G532500 chr2A 94.025 2544 150 2 1068 3610 746620725 746623267 0.000000e+00 3855.0
24 TraesCS2D01G532500 chr2A 93.366 2020 131 3 1068 3084 748437887 748439906 0.000000e+00 2985.0
25 TraesCS2D01G532500 chr2A 93.160 1038 62 3 2526 3562 748209749 748210778 0.000000e+00 1515.0
26 TraesCS2D01G532500 chr2A 97.477 436 11 0 634 1069 748437415 748437850 0.000000e+00 745.0
27 TraesCS2D01G532500 chr2A 89.184 527 39 4 3086 3610 748452801 748452291 3.410000e-180 641.0
28 TraesCS2D01G532500 chr2A 92.118 406 32 0 3087 3492 748464677 748464272 1.260000e-159 573.0
29 TraesCS2D01G532500 chr2A 90.617 373 28 5 3642 4011 748452299 748451931 4.700000e-134 488.0
30 TraesCS2D01G532500 chr2A 90.107 374 29 7 3642 4011 746623259 746623628 2.830000e-131 479.0
31 TraesCS2D01G532500 chr2A 88.205 390 28 6 3670 4043 748210784 748211171 2.220000e-122 449.0
32 TraesCS2D01G532500 chr2A 84.521 407 32 14 3642 4043 748464204 748463824 1.370000e-99 374.0
33 TraesCS2D01G532500 chr2A 86.517 356 27 2 714 1069 746620354 746620688 4.940000e-99 372.0
34 TraesCS2D01G532500 chr2A 93.145 248 15 2 823 1069 748285195 748285441 2.970000e-96 363.0
35 TraesCS2D01G532500 chr2A 88.929 280 31 0 790 1069 748204038 748204317 2.990000e-91 346.0
36 TraesCS2D01G532500 chr2A 83.436 326 40 13 3328 3645 748287786 748288105 1.420000e-74 291.0
37 TraesCS2D01G532500 chr2A 86.792 265 8 6 396 638 748436154 748436413 1.850000e-68 270.0
38 TraesCS2D01G532500 chr2A 80.906 309 38 16 3514 3819 747677664 747677374 1.460000e-54 224.0
39 TraesCS2D01G532500 chr2A 94.872 78 4 0 3533 3610 748464273 748464196 5.490000e-24 122.0
40 TraesCS2D01G532500 chr2A 94.828 58 3 0 3986 4043 748222548 748222605 1.550000e-14 91.6
41 TraesCS2D01G532500 chr7D 85.172 290 37 6 3 292 184996682 184996965 3.950000e-75 292.0
42 TraesCS2D01G532500 chr7B 84.192 291 40 5 3 292 154817886 154818171 1.110000e-70 278.0
43 TraesCS2D01G532500 chr5B 81.661 289 43 10 3 291 101827630 101827352 8.740000e-57 231.0
44 TraesCS2D01G532500 chr5A 81.081 296 41 10 3 291 88671834 88671547 5.260000e-54 222.0
45 TraesCS2D01G532500 chr5A 82.960 223 34 4 3 222 78326584 78326805 8.860000e-47 198.0
46 TraesCS2D01G532500 chr5D 80.068 296 45 9 3 291 94346781 94346493 1.470000e-49 207.0
47 TraesCS2D01G532500 chr1B 81.481 243 37 6 37 279 342978532 342978298 4.120000e-45 193.0
48 TraesCS2D01G532500 chr7A 81.250 224 39 3 3 224 285438373 285438595 1.150000e-40 178.0


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 TraesCS2D01G532500 chr2D 617759376 617763418 4042 False 7467.000000 7467 100.000000 1 4043 1 chr2D.!!$F3 4042
1 TraesCS2D01G532500 chr2D 617539173 617541227 2054 False 3151.000000 3151 94.355000 1068 3120 1 chr2D.!!$F1 2052
2 TraesCS2D01G532500 chr2D 617886555 617889659 3104 False 2263.000000 3201 92.355000 1 3084 2 chr2D.!!$F6 3083
3 TraesCS2D01G532500 chr2D 617633447 617637289 3842 False 1795.000000 3868 92.522667 396 4043 3 chr2D.!!$F5 3647
4 TraesCS2D01G532500 chr2D 617907430 617909981 2551 True 1721.000000 2948 89.122000 578 3082 2 chr2D.!!$R3 2504
5 TraesCS2D01G532500 chr2D 617546278 617548804 2526 False 1657.000000 2911 87.455500 561 3084 2 chr2D.!!$F4 2523
6 TraesCS2D01G532500 chr2D 617413030 617414017 987 True 240.666667 348 83.712333 2834 3981 3 chr2D.!!$R2 1147
7 TraesCS2D01G532500 chr2B 753792772 753796107 3335 False 2334.000000 4265 90.323500 720 4043 2 chr2B.!!$F2 3323
8 TraesCS2D01G532500 chr2B 753928031 753935066 7035 True 1927.000000 3422 90.872667 1068 4043 3 chr2B.!!$R1 2975
9 TraesCS2D01G532500 chr2B 753786113 753788410 2297 False 1641.500000 3029 92.472500 1229 4043 2 chr2B.!!$F1 2814
10 TraesCS2D01G532500 chr2A 746620354 746623628 3274 False 1568.666667 3855 90.216333 714 4011 3 chr2A.!!$F3 3297
11 TraesCS2D01G532500 chr2A 748436154 748439906 3752 False 1333.333333 2985 92.545000 396 3084 3 chr2A.!!$F6 2688
12 TraesCS2D01G532500 chr2A 748209749 748211171 1422 False 982.000000 1515 90.682500 2526 4043 2 chr2A.!!$F4 1517
13 TraesCS2D01G532500 chr2A 748451931 748452801 870 True 564.500000 641 89.900500 3086 4011 2 chr2A.!!$R2 925
14 TraesCS2D01G532500 chr2A 748463824 748464677 853 True 356.333333 573 90.503667 3087 4043 3 chr2A.!!$R3 956
15 TraesCS2D01G532500 chr2A 748285195 748288105 2910 False 327.000000 363 88.290500 823 3645 2 chr2A.!!$F5 2822

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
383 407 1.500396 GACAAAATCCACGCCCGTC 59.500 57.895 0.00 0.0 0.00 4.79 F
507 534 2.214920 GGACCACCGGAGTTCCTGT 61.215 63.158 9.46 0.0 33.52 4.00 F
2387 5421 4.104738 TCTTTTCAGGGAAATGTCACTCCT 59.895 41.667 0.00 0.0 34.22 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2943 5977 8.167392 TCCCCTGAGAAGAGAGATACTATTAAG 58.833 40.741 0.00 0.00 29.65 1.85 R
2992 6026 2.740447 GGTACTTTACCGGAAGCAACTG 59.260 50.000 9.46 0.00 39.39 3.16 R
3269 6490 0.731417 CGCCTTCTTGCTGGATGAAG 59.269 55.000 15.03 15.03 36.18 3.02 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
21 22 2.124983 GCGCCTGAGCATGAAGGA 60.125 61.111 12.35 0.00 39.83 3.36
39 40 3.454375 AGGAGTGACAACGTTTGTACAG 58.546 45.455 0.00 0.00 45.52 2.74
84 85 5.058149 TGCGTTATTGAGCAATTCACATT 57.942 34.783 0.52 0.00 40.78 2.71
119 120 4.038282 TGATTTGATTGAGCATATGTGGGC 59.962 41.667 4.29 0.00 0.00 5.36
165 166 5.712152 ATCGGCTCTTTTCTTTGAAATGT 57.288 34.783 0.00 0.00 0.00 2.71
172 173 8.490355 GGCTCTTTTCTTTGAAATGTATTTGTG 58.510 33.333 0.00 0.00 0.00 3.33
278 280 7.111247 TGAATTATGGGAAGTTTAGGCAATG 57.889 36.000 0.00 0.00 0.00 2.82
294 296 5.113502 GGCAATGCCTTTGATATGTACTC 57.886 43.478 18.47 0.00 46.69 2.59
296 298 4.823989 GCAATGCCTTTGATATGTACTCCT 59.176 41.667 0.00 0.00 37.53 3.69
297 299 5.997746 GCAATGCCTTTGATATGTACTCCTA 59.002 40.000 0.00 0.00 37.53 2.94
298 300 6.073003 GCAATGCCTTTGATATGTACTCCTAC 60.073 42.308 0.00 0.00 37.53 3.18
301 303 5.829391 TGCCTTTGATATGTACTCCTACGTA 59.171 40.000 0.00 0.00 0.00 3.57
362 386 4.436998 CACTGACCCGAGCGGACC 62.437 72.222 11.05 2.17 37.50 4.46
383 407 1.500396 GACAAAATCCACGCCCGTC 59.500 57.895 0.00 0.00 0.00 4.79
384 408 2.235536 GACAAAATCCACGCCCGTCG 62.236 60.000 0.00 0.00 45.38 5.12
385 409 2.744709 AAAATCCACGCCCGTCGG 60.745 61.111 3.60 3.60 43.86 4.79
399 423 3.592814 TCGGCGCGATAGGTCCAG 61.593 66.667 12.10 0.00 0.00 3.86
403 427 2.851071 GCGCGATAGGTCCAGCTCT 61.851 63.158 12.10 0.00 0.00 4.09
507 534 2.214920 GGACCACCGGAGTTCCTGT 61.215 63.158 9.46 0.00 33.52 4.00
2386 5420 4.216472 GTCTTTTCAGGGAAATGTCACTCC 59.784 45.833 0.00 0.00 34.22 3.85
2387 5421 4.104738 TCTTTTCAGGGAAATGTCACTCCT 59.895 41.667 0.00 0.00 34.22 3.69
2992 6026 2.941064 GGGAAATTAAGGGAGCACGTAC 59.059 50.000 0.00 0.00 0.00 3.67
3182 6393 9.205719 CTGATCTGGAATGTTTAGATATCTGTG 57.794 37.037 15.79 0.00 31.67 3.66
3185 6396 8.311395 TCTGGAATGTTTAGATATCTGTGACT 57.689 34.615 15.79 0.00 0.00 3.41
3269 6490 1.334869 CCCAATCTCAGCGTTTATGCC 59.665 52.381 0.00 0.00 34.65 4.40
3275 6496 3.198068 TCTCAGCGTTTATGCCTTCATC 58.802 45.455 0.00 0.00 34.22 2.92
3366 6592 2.030371 TGGTTGATGCACTGCTTTTGA 58.970 42.857 1.98 0.00 0.00 2.69
3432 6666 5.772672 TCCAACTAAGCTATGATCTCTCTCC 59.227 44.000 0.00 0.00 0.00 3.71
3625 6888 0.909133 TCATGGGCTGCAGACTGGTA 60.909 55.000 21.42 4.06 0.00 3.25
3645 6908 5.238432 TGGTAAACAGTATTGAGCTGTGTTG 59.762 40.000 0.00 0.00 45.36 3.33
3721 7149 7.377398 TGTTATGTGCTAAGCATGTTTTGAAT 58.623 30.769 7.84 1.45 41.91 2.57
3731 7159 5.899299 AGCATGTTTTGAATATGAGAAGCC 58.101 37.500 0.00 0.00 32.37 4.35
3812 7242 8.726870 TCTCCGGTAAGAAATATTTACCTTTG 57.273 34.615 14.03 5.65 45.06 2.77
3845 7301 5.473066 TGACTGACTGACTGATCATGAAA 57.527 39.130 0.00 0.00 33.22 2.69
3851 7307 5.163281 ACTGACTGATCATGAAAAGAGCT 57.837 39.130 13.39 0.00 33.22 4.09
3905 7368 6.471976 TTCTCATCTCAGAAACATTTGTCG 57.528 37.500 0.00 0.00 29.01 4.35
4026 7500 2.628178 TCTGTATGGTCATGATCGGTCC 59.372 50.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.088340 CACTCCTTCATGCTCAGGCG 61.088 60.000 0.00 0.00 42.25 5.52
16 17 3.866910 TGTACAAACGTTGTCACTCCTTC 59.133 43.478 0.00 0.00 44.12 3.46
19 20 3.192466 ACTGTACAAACGTTGTCACTCC 58.808 45.455 0.00 0.00 44.12 3.85
21 22 4.247258 TGAACTGTACAAACGTTGTCACT 58.753 39.130 0.00 0.00 44.12 3.41
35 36 8.856153 TTCATGGTAAAATTAGCTGAACTGTA 57.144 30.769 0.00 0.00 30.75 2.74
39 40 7.253750 CGCATTTCATGGTAAAATTAGCTGAAC 60.254 37.037 0.00 0.00 32.99 3.18
77 78 9.500785 TCAAATCATAGTGTAGTTGAATGTGAA 57.499 29.630 0.00 0.00 0.00 3.18
84 85 7.823799 TGCTCAATCAAATCATAGTGTAGTTGA 59.176 33.333 0.00 0.00 0.00 3.18
172 173 7.360361 ACGAGCCGGATGAAATTTAAATTATC 58.640 34.615 13.68 12.95 0.00 1.75
190 191 5.968387 AAAATCTCATAGTTTACGAGCCG 57.032 39.130 0.00 0.00 0.00 5.52
278 280 5.197682 ACGTAGGAGTACATATCAAAGGC 57.802 43.478 0.00 0.00 0.00 4.35
327 329 3.005898 CATCCAACGCGACCGATG 58.994 61.111 15.93 15.72 37.05 3.84
379 403 4.977126 GACCTATCGCGCCGACGG 62.977 72.222 10.29 10.29 39.18 4.79
380 404 4.977126 GGACCTATCGCGCCGACG 62.977 72.222 0.00 0.00 39.18 5.12
384 408 3.850095 GAGCTGGACCTATCGCGCC 62.850 68.421 0.00 0.00 0.00 6.53
385 409 2.355244 GAGCTGGACCTATCGCGC 60.355 66.667 0.00 0.00 0.00 6.86
386 410 1.284408 GAGAGCTGGACCTATCGCG 59.716 63.158 0.00 0.00 0.00 5.87
387 411 1.663173 GGAGAGCTGGACCTATCGC 59.337 63.158 0.00 0.00 0.00 4.58
388 412 0.468214 TGGGAGAGCTGGACCTATCG 60.468 60.000 0.00 0.00 0.00 2.92
391 415 0.033011 GAGTGGGAGAGCTGGACCTA 60.033 60.000 0.00 0.00 0.00 3.08
394 418 2.716017 CGGAGTGGGAGAGCTGGAC 61.716 68.421 0.00 0.00 0.00 4.02
507 534 0.685097 CGTTGGAGAGAAAGGGGACA 59.315 55.000 0.00 0.00 0.00 4.02
2943 5977 8.167392 TCCCCTGAGAAGAGAGATACTATTAAG 58.833 40.741 0.00 0.00 29.65 1.85
2992 6026 2.740447 GGTACTTTACCGGAAGCAACTG 59.260 50.000 9.46 0.00 39.39 3.16
3182 6393 9.440773 TGGATGCTGATAAATATGTAATGAGTC 57.559 33.333 0.00 0.00 0.00 3.36
3185 6396 9.797642 ACTTGGATGCTGATAAATATGTAATGA 57.202 29.630 0.00 0.00 0.00 2.57
3269 6490 0.731417 CGCCTTCTTGCTGGATGAAG 59.269 55.000 15.03 15.03 36.18 3.02
3275 6496 2.328099 GGTCACGCCTTCTTGCTGG 61.328 63.158 0.00 0.00 0.00 4.85
3432 6666 8.607459 CAACCTAGCTTTCTGTAACATTATGAG 58.393 37.037 0.00 0.00 0.00 2.90
3581 6830 3.625764 ACAACACACTTAACGCTTCACAT 59.374 39.130 0.00 0.00 0.00 3.21
3625 6888 4.881273 TGACAACACAGCTCAATACTGTTT 59.119 37.500 0.00 0.00 46.01 2.83
3645 6908 4.666237 GCAGCAACTGGATTTTAGATGAC 58.334 43.478 0.00 0.00 31.21 3.06
3731 7159 3.680196 GCAGTTCCTGGGAGTAGCTTAAG 60.680 52.174 0.00 0.00 31.21 1.85
3812 7242 8.932945 TCAGTCAGTCAGTCAATATAATGAAC 57.067 34.615 0.00 0.00 0.00 3.18
3819 7251 7.357429 TCATGATCAGTCAGTCAGTCAATAT 57.643 36.000 0.09 0.00 37.87 1.28
3845 7301 2.011046 GCGCTGATCCTTCAAGCTCTT 61.011 52.381 0.00 0.00 34.55 2.85
3851 7307 1.550524 AGTACAGCGCTGATCCTTCAA 59.449 47.619 42.03 14.12 0.00 2.69
3905 7368 1.812571 CAACACCCTAGAATGCACCAC 59.187 52.381 0.00 0.00 0.00 4.16
3982 7453 6.261603 AGAATATGTGTAATGTGTGCATCCAG 59.738 38.462 0.00 0.00 33.50 3.86


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

AutoCloner maintained by Alex Coulton.