Multiple sequence alignment - TraesCS1A01G227800

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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 TraesCS1A01G227800 chr1A 100.000 3453 0 0 1 3453 398860267 398856815 0.000000e+00 6377.0
1 TraesCS1A01G227800 chr1A 98.562 1599 17 5 1351 2947 398892040 398890446 0.000000e+00 2820.0
2 TraesCS1A01G227800 chr1A 96.366 1376 28 5 1 1355 398893796 398892422 0.000000e+00 2244.0
3 TraesCS1A01G227800 chr1A 91.150 791 43 8 1 786 32823400 32822632 0.000000e+00 1048.0
4 TraesCS1A01G227800 chr1A 92.020 589 27 2 782 1350 32801453 32800865 0.000000e+00 809.0
5 TraesCS1A01G227800 chr1A 98.759 403 4 1 3051 3453 398847767 398847366 0.000000e+00 715.0
6 TraesCS1A01G227800 chr1A 86.212 631 66 10 1844 2465 14635017 14634399 0.000000e+00 664.0
7 TraesCS1A01G227800 chr1A 100.000 66 0 0 3986 4051 398856282 398856217 5.500000e-24 122.0
8 TraesCS1A01G227800 chr3A 96.855 1558 40 6 1351 2908 469873493 469875041 0.000000e+00 2597.0
9 TraesCS1A01G227800 chr3A 97.543 407 7 2 3048 3453 255581954 255582358 0.000000e+00 693.0
10 TraesCS1A01G227800 chr3A 80.696 575 56 23 1480 2026 683350599 683350052 2.930000e-106 396.0
11 TraesCS1A01G227800 chr3A 95.851 241 6 2 2678 2915 469875040 469875279 1.770000e-103 387.0
12 TraesCS1A01G227800 chr3A 91.892 37 3 0 225 261 414646635 414646599 7.000000e-03 52.8
13 TraesCS1A01G227800 chr5A 96.092 1177 36 10 1351 2525 536126705 536127873 0.000000e+00 1910.0
14 TraesCS1A01G227800 chr5A 97.767 403 8 1 3048 3449 683223644 683224046 0.000000e+00 693.0
15 TraesCS1A01G227800 chr5A 94.278 367 17 4 2549 2915 536127858 536128220 3.540000e-155 558.0
16 TraesCS1A01G227800 chr1D 90.501 1158 74 10 225 1351 323117232 323116080 0.000000e+00 1496.0
17 TraesCS1A01G227800 chr1D 89.374 1167 93 10 225 1362 322759784 322758620 0.000000e+00 1439.0
18 TraesCS1A01G227800 chr1D 87.580 1248 95 17 137 1351 322784589 322783369 0.000000e+00 1391.0
19 TraesCS1A01G227800 chr1D 88.658 1155 102 17 225 1351 322997262 322996109 0.000000e+00 1380.0
20 TraesCS1A01G227800 chr1D 90.757 1017 66 7 361 1351 323499881 323498867 0.000000e+00 1332.0
21 TraesCS1A01G227800 chr1D 88.493 1095 94 10 284 1351 322910567 322909478 0.000000e+00 1295.0
22 TraesCS1A01G227800 chr1D 82.831 862 68 20 133 984 322928653 322927862 0.000000e+00 699.0
23 TraesCS1A01G227800 chr1D 92.800 375 24 2 980 1351 322927002 322926628 1.280000e-149 540.0
24 TraesCS1A01G227800 chr1D 96.324 136 5 0 1 136 246668535 246668670 1.470000e-54 224.0
25 TraesCS1A01G227800 chr1D 95.714 140 5 1 2921 3059 322926558 322926419 1.470000e-54 224.0
26 TraesCS1A01G227800 chr1D 95.652 138 6 0 1 138 237228321 237228458 5.270000e-54 222.0
27 TraesCS1A01G227800 chr1D 95.000 140 6 1 2921 3059 322758562 322758423 6.820000e-53 219.0
28 TraesCS1A01G227800 chr1D 95.000 140 6 1 2921 3059 322996040 322995901 6.820000e-53 219.0
29 TraesCS1A01G227800 chr1D 94.286 140 7 1 2921 3059 322909409 322909270 3.170000e-51 213.0
30 TraesCS1A01G227800 chr1D 94.286 140 7 1 2921 3059 323116011 323115872 3.170000e-51 213.0
31 TraesCS1A01G227800 chr1D 94.737 133 7 0 2921 3053 322783300 322783168 1.480000e-49 207.0
32 TraesCS1A01G227800 chr1D 93.571 140 8 1 2921 3059 323498798 323498659 1.480000e-49 207.0
33 TraesCS1A01G227800 chr1D 91.509 106 9 0 225 330 323499958 323499853 3.260000e-31 147.0
34 TraesCS1A01G227800 chr1D 92.135 89 7 0 137 225 322997329 322997241 4.250000e-25 126.0
35 TraesCS1A01G227800 chr1D 91.111 90 7 1 137 225 323500026 323499937 1.980000e-23 121.0
36 TraesCS1A01G227800 chr1D 90.909 88 7 1 137 223 323117300 323117213 2.560000e-22 117.0
37 TraesCS1A01G227800 chr3B 84.558 1470 150 38 1485 2915 367472939 367474370 0.000000e+00 1386.0
38 TraesCS1A01G227800 chr3B 83.511 1407 162 39 1542 2915 134266939 134268308 0.000000e+00 1249.0
39 TraesCS1A01G227800 chr3B 82.374 1129 143 36 1482 2580 79939309 79940411 0.000000e+00 931.0
40 TraesCS1A01G227800 chr7A 82.661 1240 160 40 1485 2693 719721144 719722359 0.000000e+00 1048.0
41 TraesCS1A01G227800 chr7A 92.105 152 10 2 1 151 218024162 218024312 3.170000e-51 213.0
42 TraesCS1A01G227800 chr7A 100.000 46 0 0 4006 4051 629054326 629054371 7.210000e-13 86.1
43 TraesCS1A01G227800 chrUn 82.337 1087 124 38 1844 2920 82183635 82184663 0.000000e+00 881.0
44 TraesCS1A01G227800 chrUn 98.015 403 7 1 3051 3453 170739590 170739189 0.000000e+00 699.0
45 TraesCS1A01G227800 chrUn 97.270 403 9 2 3051 3453 427670368 427669968 0.000000e+00 682.0
46 TraesCS1A01G227800 chrUn 100.000 46 0 0 4006 4051 385339135 385339180 7.210000e-13 86.1
47 TraesCS1A01G227800 chrUn 95.833 48 0 1 4006 4051 170734546 170734499 4.340000e-10 76.8
48 TraesCS1A01G227800 chrUn 100.000 37 0 0 4015 4051 248394235 248394199 7.270000e-08 69.4
49 TraesCS1A01G227800 chr3D 85.230 738 82 17 2185 2915 48534858 48535575 0.000000e+00 734.0
50 TraesCS1A01G227800 chr3D 95.620 137 5 1 1 137 139861267 139861402 6.820000e-53 219.0
51 TraesCS1A01G227800 chr6B 79.908 1085 134 44 1603 2618 569934226 569933157 0.000000e+00 719.0
52 TraesCS1A01G227800 chr2B 98.492 398 5 1 3057 3453 791900945 791900548 0.000000e+00 701.0
53 TraesCS1A01G227800 chr2B 81.146 541 67 6 613 1131 744190526 744189999 6.310000e-108 401.0
54 TraesCS1A01G227800 chr2B 81.538 455 52 17 1603 2026 479257873 479258326 3.000000e-91 346.0
55 TraesCS1A01G227800 chr2B 100.000 66 0 0 3986 4051 512132533 512132598 5.500000e-24 122.0
56 TraesCS1A01G227800 chr2B 100.000 30 0 0 4022 4051 791891225 791891196 5.660000e-04 56.5
57 TraesCS1A01G227800 chr7B 98.481 395 5 1 3060 3453 324005213 324005607 0.000000e+00 695.0
58 TraesCS1A01G227800 chr7B 80.586 273 42 10 3035 3302 121029872 121030138 2.470000e-47 200.0
59 TraesCS1A01G227800 chr5B 98.232 396 6 1 3058 3453 408043612 408043218 0.000000e+00 691.0
60 TraesCS1A01G227800 chr5B 97.750 400 9 0 3048 3447 448394287 448394686 0.000000e+00 689.0
61 TraesCS1A01G227800 chr5B 100.000 66 0 0 3986 4051 408042902 408042837 5.500000e-24 122.0
62 TraesCS1A01G227800 chr5B 100.000 66 0 0 3986 4051 557993876 557993811 5.500000e-24 122.0
63 TraesCS1A01G227800 chr5B 100.000 46 0 0 4006 4051 558002244 558002199 7.210000e-13 86.1
64 TraesCS1A01G227800 chr4A 88.851 296 27 4 1555 1849 702701882 702702172 3.850000e-95 359.0
65 TraesCS1A01G227800 chr4A 85.666 293 33 6 2632 2915 702702213 702702505 2.370000e-77 300.0
66 TraesCS1A01G227800 chr4B 86.333 300 31 7 2632 2922 623399714 623400012 6.530000e-83 318.0
67 TraesCS1A01G227800 chr6A 95.652 138 6 0 1 138 209081775 209081912 5.270000e-54 222.0
68 TraesCS1A01G227800 chr5D 95.652 138 6 0 1 138 304948328 304948465 5.270000e-54 222.0
69 TraesCS1A01G227800 chr7D 95.620 137 6 0 2 138 500289672 500289536 1.900000e-53 220.0
70 TraesCS1A01G227800 chr2A 77.473 182 34 6 3037 3216 453714785 453714961 7.160000e-18 102.0
71 TraesCS1A01G227800 chr2A 83.750 80 9 4 3035 3113 98839696 98839620 5.620000e-09 73.1


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 TraesCS1A01G227800 chr1A 398856217 398860267 4050 True 3249.500000 6377 100.000000 1 4051 2 chr1A.!!$R5 4050
1 TraesCS1A01G227800 chr1A 398890446 398893796 3350 True 2532.000000 2820 97.464000 1 2947 2 chr1A.!!$R6 2946
2 TraesCS1A01G227800 chr1A 32822632 32823400 768 True 1048.000000 1048 91.150000 1 786 1 chr1A.!!$R3 785
3 TraesCS1A01G227800 chr1A 32800865 32801453 588 True 809.000000 809 92.020000 782 1350 1 chr1A.!!$R2 568
4 TraesCS1A01G227800 chr1A 14634399 14635017 618 True 664.000000 664 86.212000 1844 2465 1 chr1A.!!$R1 621
5 TraesCS1A01G227800 chr3A 469873493 469875279 1786 False 1492.000000 2597 96.353000 1351 2915 2 chr3A.!!$F2 1564
6 TraesCS1A01G227800 chr3A 683350052 683350599 547 True 396.000000 396 80.696000 1480 2026 1 chr3A.!!$R2 546
7 TraesCS1A01G227800 chr5A 536126705 536128220 1515 False 1234.000000 1910 95.185000 1351 2915 2 chr5A.!!$F2 1564
8 TraesCS1A01G227800 chr1D 322758423 322759784 1361 True 829.000000 1439 92.187000 225 3059 2 chr1D.!!$R1 2834
9 TraesCS1A01G227800 chr1D 322783168 322784589 1421 True 799.000000 1391 91.158500 137 3053 2 chr1D.!!$R2 2916
10 TraesCS1A01G227800 chr1D 322909270 322910567 1297 True 754.000000 1295 91.389500 284 3059 2 chr1D.!!$R3 2775
11 TraesCS1A01G227800 chr1D 323115872 323117300 1428 True 608.666667 1496 91.898667 137 3059 3 chr1D.!!$R6 2922
12 TraesCS1A01G227800 chr1D 322995901 322997329 1428 True 575.000000 1380 91.931000 137 3059 3 chr1D.!!$R5 2922
13 TraesCS1A01G227800 chr1D 322926419 322928653 2234 True 487.666667 699 90.448333 133 3059 3 chr1D.!!$R4 2926
14 TraesCS1A01G227800 chr1D 323498659 323500026 1367 True 451.750000 1332 91.737000 137 3059 4 chr1D.!!$R7 2922
15 TraesCS1A01G227800 chr3B 367472939 367474370 1431 False 1386.000000 1386 84.558000 1485 2915 1 chr3B.!!$F3 1430
16 TraesCS1A01G227800 chr3B 134266939 134268308 1369 False 1249.000000 1249 83.511000 1542 2915 1 chr3B.!!$F2 1373
17 TraesCS1A01G227800 chr3B 79939309 79940411 1102 False 931.000000 931 82.374000 1482 2580 1 chr3B.!!$F1 1098
18 TraesCS1A01G227800 chr7A 719721144 719722359 1215 False 1048.000000 1048 82.661000 1485 2693 1 chr7A.!!$F3 1208
19 TraesCS1A01G227800 chrUn 82183635 82184663 1028 False 881.000000 881 82.337000 1844 2920 1 chrUn.!!$F1 1076
20 TraesCS1A01G227800 chr3D 48534858 48535575 717 False 734.000000 734 85.230000 2185 2915 1 chr3D.!!$F1 730
21 TraesCS1A01G227800 chr6B 569933157 569934226 1069 True 719.000000 719 79.908000 1603 2618 1 chr6B.!!$R1 1015
22 TraesCS1A01G227800 chr2B 744189999 744190526 527 True 401.000000 401 81.146000 613 1131 1 chr2B.!!$R1 518
23 TraesCS1A01G227800 chr5B 408042837 408043612 775 True 406.500000 691 99.116000 3058 4051 2 chr5B.!!$R3 993
24 TraesCS1A01G227800 chr4A 702701882 702702505 623 False 329.500000 359 87.258500 1555 2915 2 chr4A.!!$F1 1360

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
21 22 3.519579 CTGCACAAAAACAACACCATGA 58.480 40.909 0.00 0.00 0.00 3.07 F
257 259 4.378774 TGTTTGTTCGGACCGATAGAAAA 58.621 39.130 19.12 12.63 35.23 2.29 F
1089 2000 0.607620 TGTCGTGTGATGCATCAGGA 59.392 50.000 29.38 22.06 37.51 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1069 1980 1.004595 CCTGATGCATCACACGACAG 58.995 55.000 25.42 13.4 32.5 3.51 R
1340 2262 3.215975 TGTGGTGGCTTGTACTTAAACC 58.784 45.455 0.00 0.0 0.0 3.27 R
3056 4759 2.341846 ATTATCCGGGCGTCACATTT 57.658 45.000 0.00 0.0 0.0 2.32 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 3.519579 CTGCACAAAAACAACACCATGA 58.480 40.909 0.00 0.00 0.00 3.07
170 172 4.596643 ACAAAATGGATGTTCATTTGGGGA 59.403 37.500 6.19 0.00 43.93 4.81
257 259 4.378774 TGTTTGTTCGGACCGATAGAAAA 58.621 39.130 19.12 12.63 35.23 2.29
532 563 5.692613 TTTTTATTCGGACCGACACATTT 57.307 34.783 18.12 0.12 34.89 2.32
1089 2000 0.607620 TGTCGTGTGATGCATCAGGA 59.392 50.000 29.38 22.06 37.51 3.86
1593 2913 7.425595 CGAACCATAGTTTATCTTCTTTTTCGC 59.574 37.037 0.00 0.00 35.94 4.70
2446 3878 4.034626 CGTGGACATTGTTTTGTAGACACA 59.965 41.667 0.00 0.00 32.67 3.72
3008 4711 0.613012 AAGATGGCAAGGGAAGTGGC 60.613 55.000 0.00 0.00 41.71 5.01
3056 4759 4.038282 TGCTCCAAACGTTTGTAGAGTAGA 59.962 41.667 30.66 20.66 36.45 2.59
3152 4855 3.607741 ACTCTCGATAGTTCAGAACCGA 58.392 45.455 9.85 10.67 37.40 4.69
3158 4861 4.921515 TCGATAGTTCAGAACCGAAACAAG 59.078 41.667 9.85 0.00 37.40 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 7.899973 TCCAACGTATCTACTTTTCCTAACTT 58.100 34.615 0.00 0.00 0.00 2.66
170 172 2.104281 AGAACACGTCTTAGGCCAACTT 59.896 45.455 5.01 0.00 29.66 2.66
411 439 7.735500 GTGTCAAACACGCTCTTATATTACAA 58.264 34.615 0.00 0.00 39.53 2.41
532 563 8.646356 CGTAACAAGATACACCGTGTATAAAAA 58.354 33.333 21.54 5.74 43.08 1.94
608 641 9.106070 ACGAAATTGATTACTAATACTCCCAAC 57.894 33.333 0.00 0.00 0.00 3.77
1069 1980 1.004595 CCTGATGCATCACACGACAG 58.995 55.000 25.42 13.40 32.50 3.51
1340 2262 3.215975 TGTGGTGGCTTGTACTTAAACC 58.784 45.455 0.00 0.00 0.00 3.27
2695 4150 6.046593 CGTTTGTAGAAGGCCTATATGTCAA 58.953 40.000 5.16 4.80 0.00 3.18
2915 4618 4.069312 TGGTTCCTGGTATCCACTAGAA 57.931 45.455 0.00 0.00 35.34 2.10
3056 4759 2.341846 ATTATCCGGGCGTCACATTT 57.658 45.000 0.00 0.00 0.00 2.32
3421 5124 0.470341 GATAAGGGAGTGAGGGGTGC 59.530 60.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.