Multiple sequence alignment - TraesCS3D01G209500

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 TraesCS3D01G209500 chr3D 100.000 2078 0 0 941 3018 277066108 277068185 0.000000e+00 3838.0
1 TraesCS3D01G209500 chr3D 100.000 585 0 0 1 585 277065168 277065752 0.000000e+00 1081.0
2 TraesCS3D01G209500 chr3D 95.000 40 2 0 77 116 487229996 487230035 2.510000e-06 63.9
3 TraesCS3D01G209500 chr3D 95.000 40 2 0 77 116 576529650 576529611 2.510000e-06 63.9
4 TraesCS3D01G209500 chr3B 98.308 1123 17 2 942 2064 373286080 373284960 0.000000e+00 1967.0
5 TraesCS3D01G209500 chr3B 95.929 958 31 4 2060 3016 373282864 373281914 0.000000e+00 1546.0
6 TraesCS3D01G209500 chr3B 90.772 596 13 21 2 585 373286658 373286093 0.000000e+00 758.0
7 TraesCS3D01G209500 chr3B 94.007 267 12 3 275 537 325768202 325767936 4.690000e-108 401.0
8 TraesCS3D01G209500 chr3A 95.164 1096 42 6 943 2027 362591896 362590801 0.000000e+00 1720.0
9 TraesCS3D01G209500 chr3A 87.822 969 79 10 2075 3018 362590605 362589651 0.000000e+00 1099.0
10 TraesCS3D01G209500 chr3A 95.041 242 10 1 342 581 362592130 362591889 2.200000e-101 379.0
11 TraesCS3D01G209500 chr3A 81.757 296 39 8 2730 3012 719298208 719297915 1.810000e-57 233.0
12 TraesCS3D01G209500 chr3A 100.000 43 0 0 2022 2064 362590720 362590678 2.490000e-11 80.5
13 TraesCS3D01G209500 chr2D 89.735 302 31 0 1546 1847 363974675 363974374 1.310000e-103 387.0
14 TraesCS3D01G209500 chr2D 95.506 89 4 0 1365 1453 363974890 363974802 3.140000e-30 143.0
15 TraesCS3D01G209500 chr2D 92.308 39 3 0 78 116 93591352 93591314 4.200000e-04 56.5
16 TraesCS3D01G209500 chr2B 90.203 296 29 0 1552 1847 432133596 432133301 1.310000e-103 387.0
17 TraesCS3D01G209500 chr2B 95.506 89 4 0 1365 1453 432133817 432133729 3.140000e-30 143.0
18 TraesCS3D01G209500 chr2A 89.527 296 31 0 1552 1847 489960494 489960199 2.840000e-100 375.0
19 TraesCS3D01G209500 chr2A 94.382 89 5 0 1365 1453 489960715 489960627 1.460000e-28 137.0
20 TraesCS3D01G209500 chr5D 87.541 305 35 2 1546 1847 356901531 356901835 1.720000e-92 350.0
21 TraesCS3D01G209500 chr5D 84.615 286 30 8 2736 3009 391294438 391294721 3.830000e-69 272.0
22 TraesCS3D01G209500 chr5D 96.629 89 3 0 1359 1447 356901298 356901386 6.740000e-32 148.0
23 TraesCS3D01G209500 chr5A 86.885 305 37 2 1546 1847 458214121 458214425 3.730000e-89 339.0
24 TraesCS3D01G209500 chr5A 82.517 286 38 5 2736 3009 494460264 494460549 1.080000e-59 241.0
25 TraesCS3D01G209500 chr5A 97.590 83 2 0 1365 1447 458213895 458213977 3.140000e-30 143.0
26 TraesCS3D01G209500 chr5B 86.262 313 40 2 1546 1855 421668937 421669249 1.340000e-88 337.0
27 TraesCS3D01G209500 chr5B 96.629 89 3 0 1359 1447 421668705 421668793 6.740000e-32 148.0
28 TraesCS3D01G209500 chr6D 85.034 294 31 5 2732 3012 15397274 15396981 1.370000e-73 287.0
29 TraesCS3D01G209500 chr1B 84.407 295 32 7 2731 3012 598846449 598846156 8.240000e-71 278.0
30 TraesCS3D01G209500 chr1B 91.667 48 4 0 2521 2568 611321797 611321750 1.940000e-07 67.6
31 TraesCS3D01G209500 chr1B 100.000 28 0 0 81 108 43452230 43452203 5.000000e-03 52.8
32 TraesCS3D01G209500 chr7B 85.714 266 27 6 2754 3009 511962767 511963031 1.380000e-68 270.0
33 TraesCS3D01G209500 chr4D 84.028 288 34 4 2734 3009 6922952 6923239 1.780000e-67 267.0
34 TraesCS3D01G209500 chr6B 86.154 65 9 0 2521 2585 79842758 79842822 1.500000e-08 71.3
35 TraesCS3D01G209500 chr7A 75.781 128 29 2 2521 2647 403292297 403292171 2.510000e-06 63.9


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 TraesCS3D01G209500 chr3D 277065168 277068185 3017 False 2459.500000 3838 100.00000 1 3018 2 chr3D.!!$F2 3017
1 TraesCS3D01G209500 chr3B 373281914 373286658 4744 True 1423.666667 1967 95.00300 2 3016 3 chr3B.!!$R2 3014
2 TraesCS3D01G209500 chr3A 362589651 362592130 2479 True 819.625000 1720 94.50675 342 3018 4 chr3A.!!$R2 2676
3 TraesCS3D01G209500 chr2D 363974374 363974890 516 True 265.000000 387 92.62050 1365 1847 2 chr2D.!!$R2 482
4 TraesCS3D01G209500 chr2B 432133301 432133817 516 True 265.000000 387 92.85450 1365 1847 2 chr2B.!!$R1 482
5 TraesCS3D01G209500 chr2A 489960199 489960715 516 True 256.000000 375 91.95450 1365 1847 2 chr2A.!!$R1 482
6 TraesCS3D01G209500 chr5D 356901298 356901835 537 False 249.000000 350 92.08500 1359 1847 2 chr5D.!!$F2 488
7 TraesCS3D01G209500 chr5A 458213895 458214425 530 False 241.000000 339 92.23750 1365 1847 2 chr5A.!!$F2 482
8 TraesCS3D01G209500 chr5B 421668705 421669249 544 False 242.500000 337 91.44550 1359 1855 2 chr5B.!!$F1 496

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
981 994 1.512926 GCGTCAGCTCCTTTTCTTCA 58.487 50.0 0.00 0.00 41.01 3.02 F
1528 1620 0.365859 GAGCGAACGTTGAACGATCC 59.634 55.0 25.62 15.01 46.05 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2059 1.168714 CCCTTTTCCCAAGCGAGAAG 58.831 55.000 0.0 0.0 0.0 2.85 R
2668 4973 1.630369 AGCAAATAGTGTCCCAGCAGA 59.370 47.619 0.0 0.0 0.0 4.26 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
66 67 5.854010 GGAACCTATCCCCTTGAAAATTC 57.146 43.478 0.00 0.00 43.00 2.17
121 124 7.750229 ATTTCAATATGTACTGCATGTAGGG 57.250 36.000 15.65 0.00 38.47 3.53
122 125 6.493189 TTCAATATGTACTGCATGTAGGGA 57.507 37.500 15.65 0.00 38.47 4.20
123 126 6.101650 TCAATATGTACTGCATGTAGGGAG 57.898 41.667 15.65 0.00 38.47 4.30
124 127 5.602561 TCAATATGTACTGCATGTAGGGAGT 59.397 40.000 15.65 0.00 42.45 3.85
125 128 6.780522 TCAATATGTACTGCATGTAGGGAGTA 59.219 38.462 15.65 3.66 40.20 2.59
126 129 7.454694 TCAATATGTACTGCATGTAGGGAGTAT 59.545 37.037 15.65 5.68 42.48 2.12
127 130 7.798710 ATATGTACTGCATGTAGGGAGTATT 57.201 36.000 15.65 0.00 42.48 1.89
128 131 5.531122 TGTACTGCATGTAGGGAGTATTC 57.469 43.478 15.65 0.00 42.48 1.75
132 135 4.655649 ACTGCATGTAGGGAGTATTCATGA 59.344 41.667 15.65 0.00 37.72 3.07
182 185 1.537202 GTTTTCAGACTTGAGCGGCAT 59.463 47.619 1.45 0.00 34.15 4.40
310 313 4.383948 CCGTGAACCGAAAAGACTACTAAC 59.616 45.833 0.00 0.00 39.56 2.34
312 315 5.632347 CGTGAACCGAAAAGACTACTAACAT 59.368 40.000 0.00 0.00 39.56 2.71
571 584 6.651225 GGACATCCTTACCATACAGAATTAGC 59.349 42.308 0.00 0.00 0.00 3.09
981 994 1.512926 GCGTCAGCTCCTTTTCTTCA 58.487 50.000 0.00 0.00 41.01 3.02
1083 1103 0.948623 CACCACGCTTCATCGGTTGA 60.949 55.000 0.00 0.00 0.00 3.18
1528 1620 0.365859 GAGCGAACGTTGAACGATCC 59.634 55.000 25.62 15.01 46.05 3.36
1591 1683 1.704628 TGAACCCCAAGATGAGCAAGA 59.295 47.619 0.00 0.00 0.00 3.02
1937 2032 6.613755 TTGATATGTCTTCATGCATCACAG 57.386 37.500 0.00 0.00 32.27 3.66
2233 4538 7.500559 CCAGCTCTTATGTTTAATCTTTAGCCT 59.499 37.037 0.00 0.00 0.00 4.58
2242 4547 9.643693 ATGTTTAATCTTTAGCCTTGATGTTTG 57.356 29.630 0.00 0.00 0.00 2.93
2336 4641 7.556733 AACAATTGTTCTACAGTTTCGGTTA 57.443 32.000 18.13 0.00 31.64 2.85
2337 4642 7.556733 ACAATTGTTCTACAGTTTCGGTTAA 57.443 32.000 4.92 0.00 0.00 2.01
2338 4643 7.987649 ACAATTGTTCTACAGTTTCGGTTAAA 58.012 30.769 4.92 0.00 0.00 1.52
2339 4644 8.460428 ACAATTGTTCTACAGTTTCGGTTAAAA 58.540 29.630 4.92 0.00 0.00 1.52
2647 4952 2.952310 GCACACTCAAGAAACCTCCTTT 59.048 45.455 0.00 0.00 0.00 3.11
2668 4973 2.113243 GACTGCCCCTTTGTCCTCGT 62.113 60.000 0.00 0.00 0.00 4.18
2716 5021 3.575256 AGAAACAATGGCATCTCTTTGCA 59.425 39.130 0.00 0.00 44.59 4.08
2807 5116 3.296709 GACCAGCGGACACGGATGT 62.297 63.158 1.50 0.00 43.71 3.06
2832 5141 3.499737 CGACATCCAACGCTGCCC 61.500 66.667 0.00 0.00 0.00 5.36
2849 5158 1.202290 GCCCGCATACATTTCAACCAG 60.202 52.381 0.00 0.00 0.00 4.00
3016 5326 2.940994 TTTCATCAACGGGTCTTCCA 57.059 45.000 0.00 0.00 34.36 3.53
3017 5327 2.178912 TTCATCAACGGGTCTTCCAC 57.821 50.000 0.00 0.00 34.36 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.795329 CCACAAAGCCAGGAGTGTTAT 58.205 47.619 0.00 0.00 0.00 1.89
32 33 1.342672 TAGGTTCCCCCGCCTGAATC 61.343 60.000 0.00 0.00 38.74 2.52
101 104 5.858381 ACTCCCTACATGCAGTACATATTG 58.142 41.667 0.00 0.00 36.64 1.90
102 105 7.798710 ATACTCCCTACATGCAGTACATATT 57.201 36.000 0.00 0.00 36.64 1.28
103 106 7.454694 TGAATACTCCCTACATGCAGTACATAT 59.545 37.037 0.00 0.00 36.64 1.78
104 107 6.780522 TGAATACTCCCTACATGCAGTACATA 59.219 38.462 0.00 0.00 36.64 2.29
105 108 5.602561 TGAATACTCCCTACATGCAGTACAT 59.397 40.000 0.00 0.00 40.66 2.29
106 109 4.959839 TGAATACTCCCTACATGCAGTACA 59.040 41.667 0.00 0.00 0.00 2.90
107 110 5.531122 TGAATACTCCCTACATGCAGTAC 57.469 43.478 0.00 0.00 0.00 2.73
108 111 5.838521 TCATGAATACTCCCTACATGCAGTA 59.161 40.000 0.00 0.00 38.39 2.74
109 112 4.655649 TCATGAATACTCCCTACATGCAGT 59.344 41.667 0.00 0.00 38.39 4.40
110 113 5.219343 TCATGAATACTCCCTACATGCAG 57.781 43.478 0.00 0.00 38.39 4.41
111 114 5.628797 TTCATGAATACTCCCTACATGCA 57.371 39.130 3.38 0.00 38.39 3.96
112 115 5.413833 CCATTCATGAATACTCCCTACATGC 59.586 44.000 20.32 0.00 38.39 4.06
113 116 6.772605 TCCATTCATGAATACTCCCTACATG 58.227 40.000 20.32 5.55 39.40 3.21
114 117 6.013032 CCTCCATTCATGAATACTCCCTACAT 60.013 42.308 20.32 0.00 0.00 2.29
115 118 5.307976 CCTCCATTCATGAATACTCCCTACA 59.692 44.000 20.32 0.00 0.00 2.74
116 119 5.280215 CCCTCCATTCATGAATACTCCCTAC 60.280 48.000 20.32 0.00 0.00 3.18
117 120 4.846367 CCCTCCATTCATGAATACTCCCTA 59.154 45.833 20.32 1.47 0.00 3.53
118 121 3.654806 CCCTCCATTCATGAATACTCCCT 59.345 47.826 20.32 0.00 0.00 4.20
119 122 3.652869 TCCCTCCATTCATGAATACTCCC 59.347 47.826 20.32 0.00 0.00 4.30
120 123 4.349342 ACTCCCTCCATTCATGAATACTCC 59.651 45.833 20.32 0.00 0.00 3.85
121 124 5.559148 ACTCCCTCCATTCATGAATACTC 57.441 43.478 20.32 0.00 0.00 2.59
122 125 7.639062 AATACTCCCTCCATTCATGAATACT 57.361 36.000 20.32 0.00 0.00 2.12
123 126 9.793259 TTTAATACTCCCTCCATTCATGAATAC 57.207 33.333 20.32 0.00 0.00 1.89
128 131 9.102757 CGATATTTAATACTCCCTCCATTCATG 57.897 37.037 0.00 0.00 0.00 3.07
132 135 6.879458 GCACGATATTTAATACTCCCTCCATT 59.121 38.462 0.00 0.00 0.00 3.16
182 185 8.410141 CACTTTCCACATTTCCTTACTTTTACA 58.590 33.333 0.00 0.00 0.00 2.41
423 436 2.832643 TAACGATGGACCACTCCCTA 57.167 50.000 0.00 0.00 35.34 3.53
940 953 2.030805 GTCTTACTGTTTGGCTTGCTGG 60.031 50.000 0.00 0.00 0.00 4.85
1083 1103 3.260632 ACACAACTTTTGCCTTTGAACCT 59.739 39.130 0.00 0.00 0.00 3.50
1528 1620 1.300963 CACCCACCCACAGAGATGG 59.699 63.158 0.00 0.00 39.71 3.51
1563 1655 3.783362 CTTGGGGTTCACGGCCACA 62.783 63.158 2.24 0.00 37.69 4.17
1591 1683 4.388499 GTGCCCCGTCACCGTCAT 62.388 66.667 0.00 0.00 0.00 3.06
1961 2059 1.168714 CCCTTTTCCCAAGCGAGAAG 58.831 55.000 0.00 0.00 0.00 2.85
2068 4352 2.051703 GAAAAACGGCGCGCTTCA 60.052 55.556 32.29 0.00 0.00 3.02
2233 4538 3.025322 ACCAGTTCCACCAAACATCAA 57.975 42.857 0.00 0.00 0.00 2.57
2242 4547 6.093633 GTCTATCAACAAATACCAGTTCCACC 59.906 42.308 0.00 0.00 0.00 4.61
2345 4650 9.730705 TTGAAGAATCAATAGAGTTGATTGTCT 57.269 29.630 17.74 9.13 45.88 3.41
2351 4656 9.506018 TTGATGTTGAAGAATCAATAGAGTTGA 57.494 29.630 0.46 0.00 46.67 3.18
2668 4973 1.630369 AGCAAATAGTGTCCCAGCAGA 59.370 47.619 0.00 0.00 0.00 4.26
2807 5116 2.609299 TTGGATGTCGGCCTCCCA 60.609 61.111 8.97 0.00 0.00 4.37
2832 5141 2.917701 TGCTGGTTGAAATGTATGCG 57.082 45.000 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.