Multiple sequence alignment - TraesCS5B01G208200

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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 TraesCS5B01G208200 chr5B 100.000 4217 0 0 1 4217 377697587 377701803 0.000000e+00 7788.0
1 TraesCS5B01G208200 chr5B 85.964 2572 261 63 1001 3522 377843634 377846155 0.000000e+00 2658.0
2 TraesCS5B01G208200 chr5B 83.645 642 66 24 1001 1608 378510565 378511201 6.120000e-158 568.0
3 TraesCS5B01G208200 chr5B 86.837 509 52 10 1112 1608 377978340 377978845 4.760000e-154 555.0
4 TraesCS5B01G208200 chr5B 86.154 520 50 13 1112 1609 378068455 378068974 3.710000e-150 542.0
5 TraesCS5B01G208200 chr5B 93.567 171 10 1 532 702 102630143 102629974 1.950000e-63 254.0
6 TraesCS5B01G208200 chr5B 84.979 233 30 5 1815 2045 378069267 378069496 9.120000e-57 231.0
7 TraesCS5B01G208200 chr5B 81.673 251 42 4 1815 2064 377979110 377979357 5.530000e-49 206.0
8 TraesCS5B01G208200 chr5B 94.792 96 3 2 3547 3641 290895025 290894931 9.450000e-32 148.0
9 TraesCS5B01G208200 chr5D 94.492 2778 99 20 704 3470 325422428 325425162 0.000000e+00 4233.0
10 TraesCS5B01G208200 chr5D 94.020 602 18 5 3631 4217 325425506 325426104 0.000000e+00 896.0
11 TraesCS5B01G208200 chr5D 86.320 519 49 15 1112 1608 326118243 326118761 2.870000e-151 545.0
12 TraesCS5B01G208200 chr5D 86.200 500 53 12 1112 1609 325663796 325664281 1.040000e-145 527.0
13 TraesCS5B01G208200 chr5D 85.714 504 60 9 1112 1609 325646957 325647454 4.830000e-144 521.0
14 TraesCS5B01G208200 chr5D 88.400 250 26 2 1815 2064 326119080 326119326 8.860000e-77 298.0
15 TraesCS5B01G208200 chr5D 86.667 195 19 5 3961 4154 325374577 325374765 4.270000e-50 209.0
16 TraesCS5B01G208200 chr5D 98.824 85 1 0 3467 3551 325425425 325425509 7.300000e-33 152.0
17 TraesCS5B01G208200 chr5D 95.402 87 4 0 3546 3632 21789113 21789199 5.690000e-29 139.0
18 TraesCS5B01G208200 chr5D 88.393 112 7 4 3524 3633 337703218 337703325 3.420000e-26 130.0
19 TraesCS5B01G208200 chr5A 92.286 1750 108 7 1828 3551 423681159 423682907 0.000000e+00 2459.0
20 TraesCS5B01G208200 chr5A 84.031 2605 265 77 1001 3535 423744978 423747501 0.000000e+00 2366.0
21 TraesCS5B01G208200 chr5A 93.123 1047 47 12 704 1725 423680107 423681153 0.000000e+00 1511.0
22 TraesCS5B01G208200 chr5A 87.525 505 49 12 1112 1608 430508317 430507819 4.730000e-159 571.0
23 TraesCS5B01G208200 chr5A 83.798 574 68 20 3631 4199 423682904 423683457 4.830000e-144 521.0
24 TraesCS5B01G208200 chr5A 85.772 492 50 11 1121 1609 430958477 430958003 1.750000e-138 503.0
25 TraesCS5B01G208200 chr5A 93.985 133 7 1 4023 4154 423664071 423664203 2.570000e-47 200.0
26 TraesCS5B01G208200 chr5A 87.302 63 6 2 2003 2064 666933475 666933414 2.100000e-08 71.3
27 TraesCS5B01G208200 chr2B 93.384 529 35 0 1 529 374217763 374217235 0.000000e+00 784.0
28 TraesCS5B01G208200 chr2B 92.030 527 42 0 1 527 94345870 94345344 0.000000e+00 741.0
29 TraesCS5B01G208200 chr2B 85.938 192 21 5 519 707 797329985 797329797 2.570000e-47 200.0
30 TraesCS5B01G208200 chr7B 92.453 530 39 1 1 529 284959235 284958706 0.000000e+00 756.0
31 TraesCS5B01G208200 chr7B 92.075 530 39 3 1 529 194597118 194596591 0.000000e+00 743.0
32 TraesCS5B01G208200 chr3D 91.871 529 43 0 1 529 28272520 28273048 0.000000e+00 739.0
33 TraesCS5B01G208200 chr3D 93.293 164 11 0 540 703 459077268 459077431 4.210000e-60 243.0
34 TraesCS5B01G208200 chr3D 91.279 172 15 0 535 706 6667270 6667441 7.050000e-58 235.0
35 TraesCS5B01G208200 chr3D 95.556 90 3 1 3545 3634 296034413 296034501 4.400000e-30 143.0
36 TraesCS5B01G208200 chr3D 93.750 96 5 1 3548 3642 505557393 505557298 4.400000e-30 143.0
37 TraesCS5B01G208200 chr6B 91.698 530 43 1 1 529 21938517 21937988 0.000000e+00 734.0
38 TraesCS5B01G208200 chr6B 91.682 529 44 0 1 529 714185330 714184802 0.000000e+00 734.0
39 TraesCS5B01G208200 chr6B 92.941 170 10 2 537 705 314547152 314546984 3.260000e-61 246.0
40 TraesCS5B01G208200 chr6B 92.398 171 12 1 537 706 119526975 119526805 4.210000e-60 243.0
41 TraesCS5B01G208200 chr6B 92.073 164 13 0 541 704 98892445 98892608 9.120000e-57 231.0
42 TraesCS5B01G208200 chr6B 87.097 186 19 5 524 705 656279215 656279399 5.530000e-49 206.0
43 TraesCS5B01G208200 chr6B 96.774 93 3 0 3547 3639 68002400 68002308 5.650000e-34 156.0
44 TraesCS5B01G208200 chr6B 92.929 99 6 1 3537 3635 38004042 38003945 4.400000e-30 143.0
45 TraesCS5B01G208200 chr3B 91.682 529 43 1 1 529 242480663 242480136 0.000000e+00 732.0
46 TraesCS5B01G208200 chr3B 85.484 186 23 3 522 704 456554366 456554182 1.550000e-44 191.0
47 TraesCS5B01G208200 chr3B 96.809 94 3 0 3542 3635 748777085 748777178 1.570000e-34 158.0
48 TraesCS5B01G208200 chr1B 91.493 529 45 0 1 529 645415369 645415897 0.000000e+00 728.0
49 TraesCS5B01G208200 chr1B 86.857 175 23 0 528 702 687090925 687091099 3.330000e-46 196.0
50 TraesCS5B01G208200 chr1B 85.915 142 20 0 1461 1602 121404862 121405003 7.300000e-33 152.0
51 TraesCS5B01G208200 chr1B 95.604 91 4 0 3545 3635 234252677 234252587 3.400000e-31 147.0
52 TraesCS5B01G208200 chr1B 93.684 95 6 0 3542 3636 28500414 28500508 4.400000e-30 143.0
53 TraesCS5B01G208200 chrUn 93.976 166 10 0 537 702 141680742 141680907 7.000000e-63 252.0
54 TraesCS5B01G208200 chrUn 94.444 90 5 0 3544 3633 244923808 244923897 5.690000e-29 139.0
55 TraesCS5B01G208200 chrUn 94.444 90 5 0 3544 3633 287095696 287095785 5.690000e-29 139.0
56 TraesCS5B01G208200 chrUn 93.407 91 6 0 3548 3638 371558133 371558043 7.350000e-28 135.0
57 TraesCS5B01G208200 chrUn 93.407 91 6 0 3548 3638 371616940 371616850 7.350000e-28 135.0
58 TraesCS5B01G208200 chrUn 92.473 93 7 0 3542 3634 27475949 27476041 2.650000e-27 134.0
59 TraesCS5B01G208200 chrUn 93.333 90 6 0 3545 3634 55723609 55723698 2.650000e-27 134.0
60 TraesCS5B01G208200 chrUn 88.596 114 7 5 3527 3639 335557631 335557739 2.650000e-27 134.0
61 TraesCS5B01G208200 chrUn 93.258 89 6 0 3544 3632 2693318 2693230 9.510000e-27 132.0
62 TraesCS5B01G208200 chrUn 94.118 85 5 0 3548 3632 13209427 13209343 3.420000e-26 130.0
63 TraesCS5B01G208200 chrUn 93.182 88 6 0 3548 3635 16901709 16901622 3.420000e-26 130.0
64 TraesCS5B01G208200 chrUn 87.302 63 6 2 2003 2064 30412927 30412866 2.100000e-08 71.3
65 TraesCS5B01G208200 chr2D 93.902 164 10 0 540 703 87407526 87407363 9.050000e-62 248.0
66 TraesCS5B01G208200 chr2D 88.506 174 14 4 526 697 565312765 565312596 5.530000e-49 206.0
67 TraesCS5B01G208200 chr2D 93.617 94 6 0 3547 3640 572049125 572049218 1.580000e-29 141.0
68 TraesCS5B01G208200 chr4A 92.857 168 11 1 537 703 517406637 517406470 4.210000e-60 243.0
69 TraesCS5B01G208200 chr4A 87.931 116 11 3 3538 3653 34261960 34262072 2.650000e-27 134.0
70 TraesCS5B01G208200 chr4A 88.034 117 8 5 3527 3642 632934475 632934364 2.650000e-27 134.0
71 TraesCS5B01G208200 chr4D 89.831 177 15 3 528 703 23312045 23312219 1.530000e-54 224.0
72 TraesCS5B01G208200 chr4D 94.444 90 5 0 3544 3633 436376805 436376716 5.690000e-29 139.0
73 TraesCS5B01G208200 chr1A 87.912 182 21 1 522 702 139560037 139560218 3.300000e-51 213.0
74 TraesCS5B01G208200 chr1A 96.512 86 3 0 3548 3633 542440397 542440312 4.400000e-30 143.0
75 TraesCS5B01G208200 chr1A 93.548 93 6 0 3542 3634 498811738 498811646 5.690000e-29 139.0
76 TraesCS5B01G208200 chr1A 91.919 99 6 2 3544 3642 551465803 551465707 2.040000e-28 137.0
77 TraesCS5B01G208200 chr1A 77.253 233 49 3 1820 2052 50749026 50748798 2.650000e-27 134.0
78 TraesCS5B01G208200 chr1A 89.524 105 9 2 3541 3643 448911830 448911934 9.510000e-27 132.0
79 TraesCS5B01G208200 chr1A 87.719 114 8 5 3527 3639 555691336 555691444 1.230000e-25 128.0
80 TraesCS5B01G208200 chr3A 87.709 179 21 1 528 706 659527403 659527226 1.540000e-49 207.0
81 TraesCS5B01G208200 chr3A 91.429 105 7 2 3546 3648 709065498 709065602 4.400000e-30 143.0
82 TraesCS5B01G208200 chr7A 86.932 176 23 0 527 702 727851110 727851285 9.250000e-47 198.0
83 TraesCS5B01G208200 chr6A 84.868 152 21 2 1820 1971 57963272 57963123 7.300000e-33 152.0
84 TraesCS5B01G208200 chr6A 95.556 90 4 0 3548 3637 439517401 439517312 1.220000e-30 145.0
85 TraesCS5B01G208200 chr6A 94.505 91 5 0 3544 3634 7099612 7099702 1.580000e-29 141.0
86 TraesCS5B01G208200 chr6A 92.708 96 6 1 3548 3643 89971069 89971163 2.040000e-28 137.0
87 TraesCS5B01G208200 chr4B 97.701 87 2 0 3548 3634 248358333 248358247 2.630000e-32 150.0
88 TraesCS5B01G208200 chr2A 89.256 121 8 4 3547 3667 386732356 386732241 3.400000e-31 147.0
89 TraesCS5B01G208200 chr7D 90.826 109 8 2 3544 3650 53485498 53485606 1.220000e-30 145.0
90 TraesCS5B01G208200 chr7D 93.684 95 6 0 3544 3638 511659434 511659528 4.400000e-30 143.0
91 TraesCS5B01G208200 chr7D 86.066 122 14 3 3535 3653 37655966 37655845 1.230000e-25 128.0
92 TraesCS5B01G208200 chr6D 96.512 86 3 0 3547 3632 36675481 36675396 4.400000e-30 143.0
93 TraesCS5B01G208200 chr6D 94.565 92 4 1 3548 3638 157328025 157328116 1.580000e-29 141.0
94 TraesCS5B01G208200 chr6D 94.444 90 5 0 3545 3634 31474853 31474942 5.690000e-29 139.0
95 TraesCS5B01G208200 chr6D 92.784 97 6 1 3547 3642 206553954 206553858 5.690000e-29 139.0
96 TraesCS5B01G208200 chr6D 94.382 89 5 0 3547 3635 199144927 199144839 2.040000e-28 137.0
97 TraesCS5B01G208200 chr6D 94.382 89 5 0 3548 3636 380781868 380781780 2.040000e-28 137.0
98 TraesCS5B01G208200 chr6D 91.000 100 7 2 3541 3639 58042851 58042753 2.650000e-27 134.0
99 TraesCS5B01G208200 chr1D 92.929 99 5 2 3548 3646 234329042 234329138 4.400000e-30 143.0
100 TraesCS5B01G208200 chr1D 95.455 88 4 0 3547 3634 85191512 85191599 1.580000e-29 141.0
101 TraesCS5B01G208200 chr1D 92.708 96 6 1 3548 3642 200825983 200826078 2.040000e-28 137.0
102 TraesCS5B01G208200 chr1D 88.785 107 10 2 3531 3636 253197637 253197532 3.420000e-26 130.0


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 TraesCS5B01G208200 chr5B 377697587 377701803 4216 False 7788.000000 7788 100.000000 1 4217 1 chr5B.!!$F1 4216
1 TraesCS5B01G208200 chr5B 377843634 377846155 2521 False 2658.000000 2658 85.964000 1001 3522 1 chr5B.!!$F2 2521
2 TraesCS5B01G208200 chr5B 378510565 378511201 636 False 568.000000 568 83.645000 1001 1608 1 chr5B.!!$F3 607
3 TraesCS5B01G208200 chr5B 378068455 378069496 1041 False 386.500000 542 85.566500 1112 2045 2 chr5B.!!$F5 933
4 TraesCS5B01G208200 chr5B 377978340 377979357 1017 False 380.500000 555 84.255000 1112 2064 2 chr5B.!!$F4 952
5 TraesCS5B01G208200 chr5D 325422428 325426104 3676 False 1760.333333 4233 95.778667 704 4217 3 chr5D.!!$F6 3513
6 TraesCS5B01G208200 chr5D 326118243 326119326 1083 False 421.500000 545 87.360000 1112 2064 2 chr5D.!!$F7 952
7 TraesCS5B01G208200 chr5A 423744978 423747501 2523 False 2366.000000 2366 84.031000 1001 3535 1 chr5A.!!$F2 2534
8 TraesCS5B01G208200 chr5A 423680107 423683457 3350 False 1497.000000 2459 89.735667 704 4199 3 chr5A.!!$F3 3495
9 TraesCS5B01G208200 chr2B 374217235 374217763 528 True 784.000000 784 93.384000 1 529 1 chr2B.!!$R2 528
10 TraesCS5B01G208200 chr2B 94345344 94345870 526 True 741.000000 741 92.030000 1 527 1 chr2B.!!$R1 526
11 TraesCS5B01G208200 chr7B 284958706 284959235 529 True 756.000000 756 92.453000 1 529 1 chr7B.!!$R2 528
12 TraesCS5B01G208200 chr7B 194596591 194597118 527 True 743.000000 743 92.075000 1 529 1 chr7B.!!$R1 528
13 TraesCS5B01G208200 chr3D 28272520 28273048 528 False 739.000000 739 91.871000 1 529 1 chr3D.!!$F2 528
14 TraesCS5B01G208200 chr6B 21937988 21938517 529 True 734.000000 734 91.698000 1 529 1 chr6B.!!$R1 528
15 TraesCS5B01G208200 chr6B 714184802 714185330 528 True 734.000000 734 91.682000 1 529 1 chr6B.!!$R6 528
16 TraesCS5B01G208200 chr3B 242480136 242480663 527 True 732.000000 732 91.682000 1 529 1 chr3B.!!$R1 528
17 TraesCS5B01G208200 chr1B 645415369 645415897 528 False 728.000000 728 91.493000 1 529 1 chr1B.!!$F3 528


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
522 525 0.608130 ACCACAGAGTGCGCAATCTA 59.392 50.0 36.48 0.0 33.56 1.98 F
752 756 0.877071 GCAACCACATCAGACACCAG 59.123 55.0 0.00 0.0 0.00 4.00 F
1697 1880 0.322008 CTGTTCTTGTCCCCTGCCTC 60.322 60.0 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1428 1.258720 TCGCAAGCATTTCATCGATCG 59.741 47.619 9.36 9.36 37.18 3.69 R
2698 2976 1.004394 TCGTCCTGAGAGTAGCTCCAA 59.996 52.381 0.00 0.00 43.26 3.53 R
3224 3503 2.238898 GCACACTTCCCCTACCATACTT 59.761 50.000 0.00 0.00 0.00 2.24 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)



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AutoCloner maintained by Alex Coulton.