Multiple sequence alignment - TraesCS2B01G128400

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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 TraesCS2B01G128400 chr2B 100.000 8192 0 0 1 8192 96091792 96083601 0.000000e+00 15128.0
1 TraesCS2B01G128400 chr2B 83.677 1550 221 20 5670 7192 96238099 96236555 0.000000e+00 1432.0
2 TraesCS2B01G128400 chr2B 82.486 1553 229 32 5670 7192 96103491 96101952 0.000000e+00 1321.0
3 TraesCS2B01G128400 chr2B 88.592 561 57 4 2614 3174 96240553 96240000 0.000000e+00 675.0
4 TraesCS2B01G128400 chr2B 86.715 557 66 5 2610 3165 96108976 96108427 5.430000e-171 612.0
5 TraesCS2B01G128400 chr2B 85.658 509 63 6 970 1475 96242323 96241822 2.030000e-145 527.0
6 TraesCS2B01G128400 chr2B 87.871 404 43 2 970 1370 96242915 96242515 3.460000e-128 470.0
7 TraesCS2B01G128400 chr2B 82.111 559 66 19 936 1475 96110953 96110410 1.620000e-121 448.0
8 TraesCS2B01G128400 chr2B 81.071 280 50 3 1596 1875 195058403 195058127 3.850000e-53 220.0
9 TraesCS2B01G128400 chr2B 85.965 171 20 4 1696 1865 569019704 569019537 6.530000e-41 180.0
10 TraesCS2B01G128400 chr2B 90.625 128 10 1 1587 1714 610016466 610016341 1.410000e-37 169.0
11 TraesCS2B01G128400 chr2B 92.308 104 6 2 2353 2455 96089338 96089440 6.630000e-31 147.0
12 TraesCS2B01G128400 chr2B 88.393 112 7 4 2354 2459 248157801 248157912 6.670000e-26 130.0
13 TraesCS2B01G128400 chr2B 95.161 62 3 0 1813 1874 75846406 75846345 1.880000e-16 99.0
14 TraesCS2B01G128400 chr2D 92.857 2142 133 10 5260 7392 61317247 61315117 0.000000e+00 3090.0
15 TraesCS2B01G128400 chr2D 86.455 1639 139 37 1 1599 61320888 61319293 0.000000e+00 1720.0
16 TraesCS2B01G128400 chr2D 82.936 1553 233 25 5666 7192 61342091 61340545 0.000000e+00 1371.0
17 TraesCS2B01G128400 chr2D 95.244 757 29 6 2453 3204 61318814 61318060 0.000000e+00 1192.0
18 TraesCS2B01G128400 chr2D 89.362 611 59 3 3492 4098 61317852 61317244 0.000000e+00 763.0
19 TraesCS2B01G128400 chr2D 88.730 559 56 6 2613 3171 61347123 61346572 0.000000e+00 676.0
20 TraesCS2B01G128400 chr2D 90.437 481 39 5 1874 2352 61319295 61318820 1.940000e-175 627.0
21 TraesCS2B01G128400 chr2D 84.937 478 61 7 977 1450 61348916 61348446 2.680000e-129 473.0
22 TraesCS2B01G128400 chr2D 90.987 233 15 2 3230 3462 61318063 61317837 7.990000e-80 309.0
23 TraesCS2B01G128400 chr2D 81.071 280 50 3 1596 1875 136606710 136606434 3.850000e-53 220.0
24 TraesCS2B01G128400 chr2D 89.815 108 5 1 2354 2455 154110675 154110782 5.160000e-27 134.0
25 TraesCS2B01G128400 chr2A 92.733 1844 99 11 5554 7391 61810145 61808331 0.000000e+00 2630.0
26 TraesCS2B01G128400 chr2A 87.374 1584 165 19 3643 5201 61815527 61813954 0.000000e+00 1784.0
27 TraesCS2B01G128400 chr2A 86.496 1644 138 32 1 1599 61820077 61818473 0.000000e+00 1729.0
28 TraesCS2B01G128400 chr2A 96.086 792 31 0 2453 3244 61817989 61817198 0.000000e+00 1291.0
29 TraesCS2B01G128400 chr2A 85.784 823 108 7 6395 7212 61959138 61958320 0.000000e+00 863.0
30 TraesCS2B01G128400 chr2A 93.210 486 28 3 1874 2354 61818475 61817990 0.000000e+00 710.0
31 TraesCS2B01G128400 chr2A 89.680 562 51 4 2613 3174 61963070 61962516 0.000000e+00 710.0
32 TraesCS2B01G128400 chr2A 80.780 692 114 10 5666 6341 61959911 61959223 2.620000e-144 523.0
33 TraesCS2B01G128400 chr2A 83.408 446 54 9 930 1360 61971995 61971555 5.960000e-106 396.0
34 TraesCS2B01G128400 chr2A 93.970 199 7 1 3264 3462 61816930 61816737 6.220000e-76 296.0
35 TraesCS2B01G128400 chr2A 93.860 114 7 0 1595 1708 107385616 107385729 1.090000e-38 172.0
36 TraesCS2B01G128400 chr2A 89.474 114 6 1 2347 2454 45119659 45119772 1.110000e-28 139.0
37 TraesCS2B01G128400 chr2A 96.667 60 2 0 1821 1880 691479849 691479790 5.230000e-17 100.0
38 TraesCS2B01G128400 chr2A 87.342 79 10 0 1797 1875 745051908 745051830 3.150000e-14 91.6
39 TraesCS2B01G128400 chr3D 82.633 547 60 24 7675 8192 573812603 573813143 1.250000e-122 451.0
40 TraesCS2B01G128400 chr3D 83.056 301 36 12 7897 8189 484120788 484121081 8.160000e-65 259.0
41 TraesCS2B01G128400 chr3D 81.203 133 22 3 107 238 553310971 553310841 4.040000e-18 104.0
42 TraesCS2B01G128400 chr5B 83.838 495 57 19 7705 8189 480740923 480741404 4.510000e-122 449.0
43 TraesCS2B01G128400 chr5B 87.000 300 30 7 7897 8192 503741353 503741059 6.130000e-86 329.0
44 TraesCS2B01G128400 chr5B 91.176 136 9 3 1693 1826 224621532 224621398 1.820000e-41 182.0
45 TraesCS2B01G128400 chr5B 89.189 111 6 1 2354 2458 336136505 336136395 5.160000e-27 134.0
46 TraesCS2B01G128400 chr6D 81.238 517 80 14 7683 8192 61469574 61469068 1.280000e-107 401.0
47 TraesCS2B01G128400 chr6D 83.893 298 40 6 7899 8192 152248329 152248622 2.250000e-70 278.0
48 TraesCS2B01G128400 chr6D 81.145 297 39 16 7897 8188 20161660 20161376 1.070000e-53 222.0
49 TraesCS2B01G128400 chr6D 82.377 244 31 11 7903 8141 82086998 82087234 1.390000e-47 202.0
50 TraesCS2B01G128400 chr6D 78.333 300 49 15 7902 8189 19631346 19631641 6.530000e-41 180.0
51 TraesCS2B01G128400 chr6D 92.437 119 9 0 1596 1714 75669368 75669250 3.930000e-38 171.0
52 TraesCS2B01G128400 chr6D 76.623 308 54 14 7897 8189 453767905 453767601 3.960000e-33 154.0
53 TraesCS2B01G128400 chr6D 97.143 35 1 0 8066 8100 5106315 5106349 8.880000e-05 60.2
54 TraesCS2B01G128400 chr6D 100.000 28 0 0 8031 8058 354063984 354063957 1.500000e-02 52.8
55 TraesCS2B01G128400 chr6A 82.812 448 52 19 7755 8192 414258868 414259300 2.160000e-100 377.0
56 TraesCS2B01G128400 chr6A 93.651 126 7 1 1699 1823 14481065 14480940 3.900000e-43 187.0
57 TraesCS2B01G128400 chr6A 92.523 107 7 1 2354 2459 577701416 577701310 1.420000e-32 152.0
58 TraesCS2B01G128400 chr6A 92.857 42 3 0 108 149 607937325 607937366 2.470000e-05 62.1
59 TraesCS2B01G128400 chr6A 94.872 39 1 1 107 144 33253886 33253924 8.880000e-05 60.2
60 TraesCS2B01G128400 chr5D 82.766 441 51 19 7768 8192 8971498 8971067 3.610000e-98 370.0
61 TraesCS2B01G128400 chr5D 89.492 295 26 5 7897 8189 116426063 116426354 1.300000e-97 368.0
62 TraesCS2B01G128400 chr5D 82.759 290 38 11 7904 8186 456684357 456684641 1.770000e-61 248.0
63 TraesCS2B01G128400 chr5D 80.851 282 44 8 1596 1874 525083055 525082781 6.440000e-51 213.0
64 TraesCS2B01G128400 chr5D 89.623 106 8 2 2350 2454 548469401 548469298 1.860000e-26 132.0
65 TraesCS2B01G128400 chr5D 82.400 125 19 1 96 220 384351114 384350993 1.120000e-18 106.0
66 TraesCS2B01G128400 chr6B 83.704 405 49 15 7794 8192 624675338 624674945 4.670000e-97 366.0
67 TraesCS2B01G128400 chr6B 86.182 275 31 7 7921 8192 641416472 641416742 2.890000e-74 291.0
68 TraesCS2B01G128400 chr1A 85.174 344 35 15 7859 8192 141428681 141429018 1.020000e-88 339.0
69 TraesCS2B01G128400 chr1A 82.500 280 38 11 7903 8177 331927395 331927668 1.370000e-57 235.0
70 TraesCS2B01G128400 chr1A 77.108 415 68 22 7792 8188 319339154 319339559 1.790000e-51 215.0
71 TraesCS2B01G128400 chr3A 80.493 446 48 18 7783 8192 606722276 606721834 1.030000e-78 305.0
72 TraesCS2B01G128400 chr3A 92.683 123 9 0 1592 1714 197996830 197996708 2.350000e-40 178.0
73 TraesCS2B01G128400 chr7D 83.882 304 31 17 7897 8192 593967665 593967958 2.910000e-69 274.0
74 TraesCS2B01G128400 chr7D 83.696 92 15 0 108 199 232420625 232420716 4.070000e-13 87.9
75 TraesCS2B01G128400 chr4D 84.502 271 32 10 7921 8187 84606931 84606667 8.160000e-65 259.0
76 TraesCS2B01G128400 chr4D 83.333 270 38 7 7923 8190 84605162 84604898 8.210000e-60 243.0
77 TraesCS2B01G128400 chr4D 79.300 343 46 22 7814 8140 3755764 3756097 4.980000e-52 217.0
78 TraesCS2B01G128400 chr4D 83.568 213 25 9 7981 8189 399190573 399190779 3.020000e-44 191.0
79 TraesCS2B01G128400 chr4D 90.654 107 4 1 2354 2454 261757904 261758010 3.990000e-28 137.0
80 TraesCS2B01G128400 chr4D 100.000 29 0 0 4170 4198 294086422 294086394 4.000000e-03 54.7
81 TraesCS2B01G128400 chr1D 81.145 297 44 11 7903 8192 3112847 3112556 2.300000e-55 228.0
82 TraesCS2B01G128400 chr1D 79.805 307 52 10 7889 8189 25698923 25699225 1.790000e-51 215.0
83 TraesCS2B01G128400 chr4B 95.000 120 6 0 1704 1823 467274871 467274990 1.090000e-43 189.0
84 TraesCS2B01G128400 chr4B 94.309 123 6 1 1701 1823 165306630 165306509 3.900000e-43 187.0
85 TraesCS2B01G128400 chr3B 92.308 130 8 2 1695 1823 616185403 616185275 5.050000e-42 183.0
86 TraesCS2B01G128400 chr3B 97.030 101 2 1 2354 2454 547122973 547122874 1.410000e-37 169.0
87 TraesCS2B01G128400 chr3B 96.970 33 1 0 7675 7707 15073433 15073465 1.000000e-03 56.5
88 TraesCS2B01G128400 chr7B 94.690 113 6 0 1596 1708 588875583 588875695 8.450000e-40 176.0
89 TraesCS2B01G128400 chr7B 77.703 148 26 5 87 230 381600612 381600756 5.270000e-12 84.2
90 TraesCS2B01G128400 chr1B 93.913 115 7 0 1594 1708 526522627 526522741 3.040000e-39 174.0
91 TraesCS2B01G128400 chrUn 79.104 201 30 10 7903 8092 50416862 50416663 2.400000e-25 128.0
92 TraesCS2B01G128400 chrUn 91.549 71 2 4 1821 1888 34148289 34148358 2.430000e-15 95.3
93 TraesCS2B01G128400 chrUn 91.549 71 2 4 1821 1888 282032595 282032664 2.430000e-15 95.3
94 TraesCS2B01G128400 chrUn 82.558 86 12 3 8110 8192 459803743 459803658 1.140000e-08 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 TraesCS2B01G128400 chr2B 96083601 96091792 8191 True 15128.000000 15128 100.000000 1 8192 1 chr2B.!!$R2 8191
1 TraesCS2B01G128400 chr2B 96101952 96103491 1539 True 1321.000000 1321 82.486000 5670 7192 1 chr2B.!!$R3 1522
2 TraesCS2B01G128400 chr2B 96236555 96242915 6360 True 776.000000 1432 86.449500 970 7192 4 chr2B.!!$R8 6222
3 TraesCS2B01G128400 chr2B 96108427 96110953 2526 True 530.000000 612 84.413000 936 3165 2 chr2B.!!$R7 2229
4 TraesCS2B01G128400 chr2D 61340545 61342091 1546 True 1371.000000 1371 82.936000 5666 7192 1 chr2D.!!$R1 1526
5 TraesCS2B01G128400 chr2D 61315117 61320888 5771 True 1283.500000 3090 90.890333 1 7392 6 chr2D.!!$R3 7391
6 TraesCS2B01G128400 chr2D 61346572 61348916 2344 True 574.500000 676 86.833500 977 3171 2 chr2D.!!$R4 2194
7 TraesCS2B01G128400 chr2A 61808331 61820077 11746 True 1406.666667 2630 91.644833 1 7391 6 chr2A.!!$R4 7390
8 TraesCS2B01G128400 chr2A 61958320 61963070 4750 True 698.666667 863 85.414667 2613 7212 3 chr2A.!!$R5 4599
9 TraesCS2B01G128400 chr3D 573812603 573813143 540 False 451.000000 451 82.633000 7675 8192 1 chr3D.!!$F2 517
10 TraesCS2B01G128400 chr6D 61469068 61469574 506 True 401.000000 401 81.238000 7683 8192 1 chr6D.!!$R2 509
11 TraesCS2B01G128400 chr4D 84604898 84606931 2033 True 251.000000 259 83.917500 7921 8190 2 chr4D.!!$R2 269

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
976 995 0.368907 GCGCTGGTATACACAACACG 59.631 55.0 0.00 6.11 0.00 4.49 F
1811 1962 0.030369 CTCCGACGAGTAATTCCGGG 59.970 60.0 0.00 0.00 40.48 5.73 F
3486 5068 0.033208 TGGAAATGGAGGCATGTCCC 60.033 55.0 0.00 0.00 38.02 4.46 F
4681 7439 0.179004 TTTCCCACCTCACGTGCATT 60.179 50.0 11.67 0.00 41.53 3.56 F
4683 7441 0.179004 TCCCACCTCACGTGCATTTT 60.179 50.0 11.67 0.00 41.53 1.82 F
5253 10892 0.180171 TGCGAGGGACCATACCATTG 59.820 55.0 0.00 0.00 0.00 2.82 F
5278 10917 0.744874 TGTAGCTTCCCGATTCCTCG 59.255 55.0 0.00 0.00 44.62 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2222 3091 0.761323 TTGGGTCCAAGTCGTCCTGA 60.761 55.000 0.00 0.0 0.00 3.86 R
3624 5287 0.036732 TGTAGCCTTCAACCTGCCTG 59.963 55.000 0.00 0.0 0.00 4.85 R
5234 9234 0.180171 CAATGGTATGGTCCCTCGCA 59.820 55.000 0.00 0.0 0.00 5.10 R
6011 13573 3.243975 CCTGATTTGTTTGCCTTGCTTCT 60.244 43.478 0.00 0.0 0.00 2.85 R
6657 14267 3.702792 AGCAGGTAGTACACAGATGAGT 58.297 45.455 2.06 0.0 0.00 3.41 R
7142 14758 0.243636 GGGTTTTGCCACATCGGAAG 59.756 55.000 0.00 0.0 39.65 3.46 R
7328 14944 5.123820 TGAATACAGTGGCAATTTAGTCAGC 59.876 40.000 7.10 0.0 0.00 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)


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

AutoCloner maintained by Alex Coulton.