Multiple sequence alignment - TraesCS3B01G527200

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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 TraesCS3B01G527200 chr3B 100.000 3611 0 0 1 3611 769297419 769301029 0.000000e+00 6669
1 TraesCS3B01G527200 chr3B 97.144 3186 74 7 427 3611 770346162 770349331 0.000000e+00 5363
2 TraesCS3B01G527200 chr3B 86.024 1753 231 8 916 2663 769404854 769403111 0.000000e+00 1868
3 TraesCS3B01G527200 chr3B 76.761 1618 300 57 811 2400 770282218 770280649 0.000000e+00 835
4 TraesCS3B01G527200 chr3B 77.119 1416 277 32 995 2400 769267903 769266525 0.000000e+00 776
5 TraesCS3B01G527200 chr3B 76.561 1489 295 36 926 2400 770404280 770402832 0.000000e+00 767
6 TraesCS3B01G527200 chr3B 81.126 959 161 16 992 1938 769995122 769994172 0.000000e+00 750
7 TraesCS3B01G527200 chr3B 75.377 1722 332 41 690 2400 769907178 769905538 0.000000e+00 747
8 TraesCS3B01G527200 chr3B 75.968 1498 300 43 920 2400 769488819 769487365 0.000000e+00 717
9 TraesCS3B01G527200 chr3B 80.668 838 158 4 992 1827 770097541 770096706 0.000000e+00 647
10 TraesCS3B01G527200 chr3B 87.879 396 47 1 1983 2378 769002065 769001671 7.060000e-127 464
11 TraesCS3B01G527200 chr3B 87.500 392 43 3 2968 3359 769248485 769248100 7.110000e-122 448
12 TraesCS3B01G527200 chr3B 86.553 409 44 6 2956 3359 769305484 769305082 1.190000e-119 440
13 TraesCS3B01G527200 chr3B 86.064 409 46 6 2956 3359 770353783 770353381 2.580000e-116 429
14 TraesCS3B01G527200 chr3B 98.238 227 4 0 1 227 770342755 770342981 7.260000e-107 398
15 TraesCS3B01G527200 chr3B 93.274 223 4 3 222 433 770343059 770343281 5.820000e-83 318
16 TraesCS3B01G527200 chr3B 94.330 194 10 1 3363 3555 763223976 763224169 2.730000e-76 296
17 TraesCS3B01G527200 chr3B 89.167 240 23 3 2956 3194 769418224 769417987 2.730000e-76 296
18 TraesCS3B01G527200 chr3B 87.065 201 14 7 485 683 769907531 769907341 2.180000e-52 217
19 TraesCS3B01G527200 chr3B 83.886 211 18 6 3158 3359 770310196 770309993 1.710000e-43 187
20 TraesCS3B01G527200 chrUn 86.735 392 46 3 2968 3359 298658322 298657937 7.160000e-117 431
21 TraesCS3B01G527200 chrUn 86.735 392 46 3 2968 3359 311035274 311035659 7.160000e-117 431
22 TraesCS3B01G527200 chrUn 86.735 392 46 3 2968 3359 311053079 311052694 7.160000e-117 431
23 TraesCS3B01G527200 chrUn 86.735 392 46 3 2968 3359 344523874 344524259 7.160000e-117 431
24 TraesCS3B01G527200 chrUn 100.000 59 0 0 3553 3611 65418024 65417966 3.810000e-20 110
25 TraesCS3B01G527200 chrUn 100.000 59 0 0 3553 3611 96359591 96359649 3.810000e-20 110
26 TraesCS3B01G527200 chrUn 100.000 59 0 0 3553 3611 404037375 404037433 3.810000e-20 110
27 TraesCS3B01G527200 chr7B 96.392 194 7 0 3362 3555 638415089 638414896 1.620000e-83 320
28 TraesCS3B01G527200 chr1B 95.385 195 8 1 3362 3555 13047977 13048171 3.500000e-80 309
29 TraesCS3B01G527200 chr1D 94.872 195 10 0 3361 3555 418390418 418390224 4.530000e-79 305
30 TraesCS3B01G527200 chr7D 94.819 193 10 0 3363 3555 630764952 630764760 5.860000e-78 302
31 TraesCS3B01G527200 chr7D 94.330 194 10 1 3363 3555 74721525 74721718 2.730000e-76 296
32 TraesCS3B01G527200 chr2B 93.564 202 11 2 3356 3555 525788417 525788216 2.110000e-77 300
33 TraesCS3B01G527200 chr5B 92.574 202 15 0 3354 3555 678086368 678086569 1.270000e-74 291
34 TraesCS3B01G527200 chr6D 100.000 59 0 0 3553 3611 358103605 358103663 3.810000e-20 110
35 TraesCS3B01G527200 chr6D 100.000 59 0 0 3553 3611 455394352 455394294 3.810000e-20 110
36 TraesCS3B01G527200 chr6D 100.000 59 0 0 3553 3611 465537333 465537275 3.810000e-20 110
37 TraesCS3B01G527200 chr4D 100.000 59 0 0 3553 3611 71407426 71407368 3.810000e-20 110
38 TraesCS3B01G527200 chr2A 98.413 63 0 1 3550 3611 771284359 771284297 3.810000e-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 TraesCS3B01G527200 chr3B 769297419 769301029 3610 False 6669.000000 6669 100.000000 1 3611 1 chr3B.!!$F2 3610
1 TraesCS3B01G527200 chr3B 770342755 770349331 6576 False 2026.333333 5363 96.218667 1 3611 3 chr3B.!!$F3 3610
2 TraesCS3B01G527200 chr3B 769403111 769404854 1743 True 1868.000000 1868 86.024000 916 2663 1 chr3B.!!$R5 1747
3 TraesCS3B01G527200 chr3B 770280649 770282218 1569 True 835.000000 835 76.761000 811 2400 1 chr3B.!!$R10 1589
4 TraesCS3B01G527200 chr3B 769266525 769267903 1378 True 776.000000 776 77.119000 995 2400 1 chr3B.!!$R3 1405
5 TraesCS3B01G527200 chr3B 770402832 770404280 1448 True 767.000000 767 76.561000 926 2400 1 chr3B.!!$R13 1474
6 TraesCS3B01G527200 chr3B 769994172 769995122 950 True 750.000000 750 81.126000 992 1938 1 chr3B.!!$R8 946
7 TraesCS3B01G527200 chr3B 769487365 769488819 1454 True 717.000000 717 75.968000 920 2400 1 chr3B.!!$R7 1480
8 TraesCS3B01G527200 chr3B 770096706 770097541 835 True 647.000000 647 80.668000 992 1827 1 chr3B.!!$R9 835
9 TraesCS3B01G527200 chr3B 769905538 769907531 1993 True 482.000000 747 81.221000 485 2400 2 chr3B.!!$R14 1915

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
324 410 0.107017 CCACAATTCCTCAGCCGGAT 60.107 55.000 5.05 0.00 32.02 4.18 F
625 3606 1.929836 CGATAGAGTTCAGCTGGCAAC 59.070 52.381 15.13 11.98 39.76 4.17 F
2380 5572 1.042003 AAACCATGGCAGTGCACACA 61.042 50.000 21.04 15.11 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 4974 0.324943 AATCTTGCGTGGGTAGCTGT 59.675 50.000 0.00 0.0 35.28 4.40 R
2430 5622 0.320160 GTTTCCTACCTCGCCGTGTT 60.320 55.000 0.00 0.0 0.00 3.32 R
3502 6694 1.000896 CCAAAGGGGCCAGACGAAT 60.001 57.895 4.39 0.0 0.00 3.34 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
138 139 3.070015 TGCAGATCTCTGATAAATGGCGA 59.930 43.478 11.34 0.00 46.59 5.54
204 205 4.246458 CCTGTTACTTTCTAGTGGTGCTC 58.754 47.826 0.00 0.00 35.78 4.26
227 228 5.303845 TCGGATCAGTAGCTCACTAGTACTA 59.696 44.000 1.89 1.89 34.98 1.82
304 390 5.319140 TGCGCACTTATCTACTAAACAGA 57.681 39.130 5.66 0.00 0.00 3.41
324 410 0.107017 CCACAATTCCTCAGCCGGAT 60.107 55.000 5.05 0.00 32.02 4.18
404 499 8.696410 TCTCCAATTTCTTTGTGTAAAAACAC 57.304 30.769 1.73 1.73 40.78 3.32
454 3435 6.294010 CCGCAAGCATGATTCTAGTACTAGTA 60.294 42.308 25.58 18.71 34.84 1.82
535 3516 3.714798 TCCTAAGTGTCCAACTTCCAACT 59.285 43.478 0.00 0.00 46.60 3.16
536 3517 4.903049 TCCTAAGTGTCCAACTTCCAACTA 59.097 41.667 0.00 0.00 46.60 2.24
537 3518 5.011738 TCCTAAGTGTCCAACTTCCAACTAG 59.988 44.000 0.00 0.00 46.60 2.57
538 3519 3.127425 AGTGTCCAACTTCCAACTAGC 57.873 47.619 0.00 0.00 34.57 3.42
625 3606 1.929836 CGATAGAGTTCAGCTGGCAAC 59.070 52.381 15.13 11.98 39.76 4.17
1106 4274 3.181489 GGCAAATCAGATGAAGAAGCAGG 60.181 47.826 0.00 0.00 0.00 4.85
1600 4771 3.802948 ATCAGTTCTTCGGCGTAAGAT 57.197 42.857 17.88 6.17 43.02 2.40
1803 4974 4.769688 ACGCCATCATAAAAGAGATCACA 58.230 39.130 0.00 0.00 0.00 3.58
1827 4998 2.935238 GCTACCCACGCAAGATTTCTCA 60.935 50.000 0.00 0.00 43.62 3.27
2320 5512 6.464222 CCCAAGGCGATAACTCATCTTTATA 58.536 40.000 0.00 0.00 0.00 0.98
2380 5572 1.042003 AAACCATGGCAGTGCACACA 61.042 50.000 21.04 15.11 0.00 3.72
2407 5599 3.490933 CGTGGAGAAGACAAGAACACTCA 60.491 47.826 0.00 0.00 0.00 3.41
2416 5608 2.942376 ACAAGAACACTCAAACGATGCA 59.058 40.909 0.00 0.00 0.00 3.96
2474 5666 1.226603 GCACGAGTACTAGGGTGCG 60.227 63.158 22.53 12.47 45.13 5.34
2592 5784 3.655481 CGGAGCTTGTTTTCGGCT 58.345 55.556 0.00 0.00 39.16 5.52
2677 5869 4.876679 GCTTGTTGAAATCTACCCTAGACC 59.123 45.833 0.00 0.00 37.69 3.85
2683 5875 3.614568 AATCTACCCTAGACCGGTGAT 57.385 47.619 14.63 2.20 37.69 3.06
2687 5879 2.068834 ACCCTAGACCGGTGATGTAG 57.931 55.000 14.63 7.37 30.39 2.74
2696 5888 2.631062 ACCGGTGATGTAGTTGAGTCAA 59.369 45.455 6.12 0.08 0.00 3.18
2704 5896 6.360681 GTGATGTAGTTGAGTCAAATTTGTGC 59.639 38.462 17.47 11.70 0.00 4.57
2717 5909 2.700722 TTTGTGCCTTTTGTTTCCCC 57.299 45.000 0.00 0.00 0.00 4.81
2721 5913 2.312390 GTGCCTTTTGTTTCCCCTGTA 58.688 47.619 0.00 0.00 0.00 2.74
2722 5914 2.696187 GTGCCTTTTGTTTCCCCTGTAA 59.304 45.455 0.00 0.00 0.00 2.41
2724 5916 3.323403 TGCCTTTTGTTTCCCCTGTAATG 59.677 43.478 0.00 0.00 0.00 1.90
2733 5925 5.119694 GTTTCCCCTGTAATGAGATGTCTC 58.880 45.833 3.07 3.07 43.15 3.36
2739 5931 6.338146 CCCTGTAATGAGATGTCTCGTTTAA 58.662 40.000 19.34 9.71 46.79 1.52
2972 6164 5.437289 TGTTGCATCCAAATCGATATTCC 57.563 39.130 0.00 0.00 31.68 3.01
3344 6536 2.395988 TTTCTTGAGCAGAGCGGCCA 62.396 55.000 2.24 0.00 31.12 5.36
3413 6605 3.862642 GCCAGATAAGCCCATTAGTCTCG 60.863 52.174 0.00 0.00 0.00 4.04
3419 6611 1.207329 AGCCCATTAGTCTCGGTTCAC 59.793 52.381 0.00 0.00 0.00 3.18
3502 6694 1.996748 GTGGGGGTATTGGTCCCGA 60.997 63.158 0.00 0.00 45.46 5.14
3546 6738 3.396570 GGTGGGACGAACCGGGAT 61.397 66.667 6.32 0.00 40.11 3.85
3569 6761 0.680618 TGGGCAAACAAGCAGAATGG 59.319 50.000 0.00 0.00 35.86 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 188 2.799017 TCCGAGCACCACTAGAAAGTA 58.201 47.619 0.00 0.00 33.48 2.24
204 205 4.382291 AGTACTAGTGAGCTACTGATCCG 58.618 47.826 5.39 0.00 40.65 4.18
227 228 8.667592 ATTAAGAACTACTACCTCTGTTCCTT 57.332 34.615 0.00 0.00 39.45 3.36
304 390 1.002134 CCGGCTGAGGAATTGTGGT 60.002 57.895 0.00 0.00 0.00 4.16
324 410 2.095461 TGCTACAAAACTGGCACACAA 58.905 42.857 0.00 0.00 0.00 3.33
454 3435 3.602205 AAAGGAGACAAGGAAAAGGCT 57.398 42.857 0.00 0.00 0.00 4.58
625 3606 1.949015 GCATCGCCATCGCTATCACG 61.949 60.000 0.00 0.00 35.26 4.35
889 4041 2.158475 AGCTGGCTATCTCACTCTAGCT 60.158 50.000 0.00 0.00 40.17 3.32
890 4042 2.238521 AGCTGGCTATCTCACTCTAGC 58.761 52.381 0.00 0.00 39.69 3.42
891 4043 3.005684 CCAAGCTGGCTATCTCACTCTAG 59.994 52.174 0.00 0.00 0.00 2.43
892 4044 2.961741 CCAAGCTGGCTATCTCACTCTA 59.038 50.000 0.00 0.00 0.00 2.43
1106 4274 0.469144 CTCTAGGCCACCTCCTCCTC 60.469 65.000 5.01 0.00 37.66 3.71
1577 4748 4.856664 TCTTACGCCGAAGAACTGATATC 58.143 43.478 0.00 0.00 32.46 1.63
1803 4974 0.324943 AATCTTGCGTGGGTAGCTGT 59.675 50.000 0.00 0.00 35.28 4.40
1827 4998 0.981183 TAACTTCTGTCGGCACCCAT 59.019 50.000 0.00 0.00 0.00 4.00
2320 5512 2.792878 AGTCGTAGCCTGAGTGTTAGT 58.207 47.619 0.00 0.00 0.00 2.24
2380 5572 1.344438 TCTTGTCTTCTCCACGCACAT 59.656 47.619 0.00 0.00 0.00 3.21
2416 5608 1.676916 CCGTGTTGATCTGATGCCACT 60.677 52.381 0.00 0.00 0.00 4.00
2430 5622 0.320160 GTTTCCTACCTCGCCGTGTT 60.320 55.000 0.00 0.00 0.00 3.32
2474 5666 4.888038 TGAATCTGCTGCATATGACAAC 57.112 40.909 6.97 0.49 0.00 3.32
2592 5784 2.355108 GCCTCAGTACTGCTCAATCCAA 60.355 50.000 18.45 0.00 0.00 3.53
2621 5813 6.622427 AATTAGGCCACTAACTTCTAGTGT 57.378 37.500 5.01 0.00 41.68 3.55
2626 5818 7.888546 ACATGTAAAATTAGGCCACTAACTTCT 59.111 33.333 5.01 0.00 41.68 2.85
2677 5869 5.862924 AATTTGACTCAACTACATCACCG 57.137 39.130 0.00 0.00 0.00 4.94
2683 5875 4.887071 AGGCACAAATTTGACTCAACTACA 59.113 37.500 24.64 0.00 0.00 2.74
2687 5879 5.351189 ACAAAAGGCACAAATTTGACTCAAC 59.649 36.000 24.64 8.23 37.46 3.18
2696 5888 3.201930 AGGGGAAACAAAAGGCACAAATT 59.798 39.130 0.00 0.00 0.00 1.82
2704 5896 5.076873 TCTCATTACAGGGGAAACAAAAGG 58.923 41.667 0.00 0.00 0.00 3.11
2717 5909 7.517417 GCCATTAAACGAGACATCTCATTACAG 60.517 40.741 9.49 3.71 43.00 2.74
2721 5913 5.295292 CAGCCATTAAACGAGACATCTCATT 59.705 40.000 9.49 6.05 43.00 2.57
2722 5914 4.813161 CAGCCATTAAACGAGACATCTCAT 59.187 41.667 9.49 0.00 43.00 2.90
2724 5916 3.557595 CCAGCCATTAAACGAGACATCTC 59.442 47.826 0.00 0.00 39.55 2.75
2733 5925 3.181487 CCAAAGGATCCAGCCATTAAACG 60.181 47.826 15.82 0.00 0.00 3.60
2739 5931 2.181975 CAAACCAAAGGATCCAGCCAT 58.818 47.619 15.82 0.00 0.00 4.40
3057 6249 3.814504 ACAGAATGGGTGTTGGAGAAT 57.185 42.857 0.00 0.00 43.62 2.40
3153 6345 8.140628 TGAAATCTCTAAATCTGCTAGCTGTAG 58.859 37.037 17.23 12.78 0.00 2.74
3292 6484 3.350219 TCTTGTTGTTCTCCTATGGCC 57.650 47.619 0.00 0.00 0.00 5.36
3447 6639 4.754667 GCCTCACGAACCGGGACC 62.755 72.222 6.32 0.00 32.99 4.46
3502 6694 1.000896 CCAAAGGGGCCAGACGAAT 60.001 57.895 4.39 0.00 0.00 3.34
3546 6738 1.702182 TCTGCTTGTTTGCCCATTGA 58.298 45.000 0.00 0.00 0.00 2.57
3569 6761 3.258123 AGGGCATGGACAACACATAAAAC 59.742 43.478 0.00 0.00 0.00 2.43
3583 6775 3.744940 ATTCCCACATATAGGGCATGG 57.255 47.619 7.42 0.00 46.36 3.66


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

AutoCloner maintained by Alex Coulton.