Multiple sequence alignment - TraesCS2B01G489000

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 TraesCS2B01G489000 chr2B 100.000 2366 0 0 1 2366 686448733 686451098 0.000000e+00 4370.0
1 TraesCS2B01G489000 chr2B 92.669 2387 97 24 6 2364 685604590 685606926 0.000000e+00 3367.0
2 TraesCS2B01G489000 chr2B 86.927 1308 86 47 461 1729 685762681 685763942 0.000000e+00 1389.0
3 TraesCS2B01G489000 chr2B 83.838 1188 124 38 658 1824 686342799 686343939 0.000000e+00 1068.0
4 TraesCS2B01G489000 chr2B 90.160 752 59 12 719 1462 685279771 685280515 0.000000e+00 965.0
5 TraesCS2B01G489000 chr2B 86.331 417 47 8 959 1367 685502825 685503239 1.670000e-121 446.0
6 TraesCS2B01G489000 chr2B 86.091 417 48 8 959 1367 685518107 685518521 7.760000e-120 440.0
7 TraesCS2B01G489000 chr2B 89.143 350 36 2 1025 1373 686808284 686808632 3.610000e-118 435.0
8 TraesCS2B01G489000 chr2B 90.706 269 17 7 1462 1729 685280596 685280857 3.740000e-93 351.0
9 TraesCS2B01G489000 chr2B 91.129 248 11 4 380 617 686291831 686292077 2.270000e-85 326.0
10 TraesCS2B01G489000 chr2B 87.055 309 12 13 323 613 685277587 685277885 8.160000e-85 324.0
11 TraesCS2B01G489000 chr2B 90.726 248 12 4 380 617 686290726 686290972 1.060000e-83 320.0
12 TraesCS2B01G489000 chr2B 90.404 198 16 3 103 299 685762436 685762631 8.390000e-65 257.0
13 TraesCS2B01G489000 chr2B 88.701 177 18 2 16 191 685277364 685277539 5.120000e-52 215.0
14 TraesCS2B01G489000 chr2B 88.172 93 10 1 108 199 686291593 686291685 2.490000e-20 110.0
15 TraesCS2B01G489000 chr2B 94.737 38 1 1 349 385 686290681 686290718 9.130000e-05 58.4
16 TraesCS2B01G489000 chr2B 100.000 31 0 0 349 379 686291786 686291816 9.130000e-05 58.4
17 TraesCS2B01G489000 chr2A 90.929 1367 53 17 464 1804 711020738 711022059 0.000000e+00 1772.0
18 TraesCS2B01G489000 chr2A 93.313 658 23 9 6 645 710961734 710962388 0.000000e+00 952.0
19 TraesCS2B01G489000 chr2A 86.047 387 52 2 983 1368 711033134 711033519 4.700000e-112 414.0
20 TraesCS2B01G489000 chr2A 83.032 442 46 8 1932 2362 711022058 711022481 7.980000e-100 374.0
21 TraesCS2B01G489000 chr2A 84.463 354 38 14 643 987 710963699 710964044 1.360000e-87 333.0
22 TraesCS2B01G489000 chr2A 84.644 267 27 5 1906 2158 710965124 710965390 1.090000e-63 254.0
23 TraesCS2B01G489000 chr2A 88.485 165 17 2 27 190 711020389 711020552 5.160000e-47 198.0
24 TraesCS2B01G489000 chr2A 85.124 121 1 7 323 426 711020621 711020741 8.940000e-20 108.0
25 TraesCS2B01G489000 chr2A 90.541 74 3 2 1759 1832 710964044 710964113 6.960000e-16 95.3
26 TraesCS2B01G489000 chr5B 87.356 174 13 7 2166 2339 255649145 255649309 8.630000e-45 191.0
27 TraesCS2B01G489000 chr5B 91.837 98 8 0 2169 2266 294126224 294126127 1.140000e-28 137.0
28 TraesCS2B01G489000 chr5D 84.343 198 21 8 2169 2366 386179092 386178905 4.020000e-43 185.0
29 TraesCS2B01G489000 chr5D 88.660 97 11 0 2170 2266 260105515 260105611 4.130000e-23 119.0
30 TraesCS2B01G489000 chr6A 83.158 190 25 5 2175 2364 145992202 145992020 1.450000e-37 167.0
31 TraesCS2B01G489000 chr3D 83.799 179 18 4 2175 2353 580980391 580980224 2.430000e-35 159.0
32 TraesCS2B01G489000 chr5A 88.710 124 13 1 2167 2290 309271863 309271985 1.460000e-32 150.0
33 TraesCS2B01G489000 chr5A 89.796 98 9 1 2169 2266 346133603 346133507 8.880000e-25 124.0


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 TraesCS2B01G489000 chr2B 686448733 686451098 2365 False 4370.000 4370 100.00000 1 2366 1 chr2B.!!$F5 2365
1 TraesCS2B01G489000 chr2B 685604590 685606926 2336 False 3367.000 3367 92.66900 6 2364 1 chr2B.!!$F3 2358
2 TraesCS2B01G489000 chr2B 686342799 686343939 1140 False 1068.000 1068 83.83800 658 1824 1 chr2B.!!$F4 1166
3 TraesCS2B01G489000 chr2B 685762436 685763942 1506 False 823.000 1389 88.66550 103 1729 2 chr2B.!!$F8 1626
4 TraesCS2B01G489000 chr2B 685277364 685280857 3493 False 463.750 965 89.15550 16 1729 4 chr2B.!!$F7 1713
5 TraesCS2B01G489000 chr2A 711020389 711022481 2092 False 613.000 1772 86.89250 27 2362 4 chr2A.!!$F3 2335
6 TraesCS2B01G489000 chr2A 710961734 710965390 3656 False 408.575 952 88.24025 6 2158 4 chr2A.!!$F2 2152

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
73 74 0.537188 CATACTCGGGTGGCACTCTT 59.463 55.0 16.74 2.04 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 5122 1.237285 AAAGCCTACAAGTGCAGCCG 61.237 55.0 0.0 0.0 0.0 5.52 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
73 74 0.537188 CATACTCGGGTGGCACTCTT 59.463 55.000 16.74 2.04 0.00 2.85
98 99 1.683011 CCAATCCTCTTTGGCCACGAT 60.683 52.381 3.88 0.00 39.76 3.73
99 100 2.421388 CCAATCCTCTTTGGCCACGATA 60.421 50.000 3.88 0.00 39.76 2.92
251 256 4.071961 TGGGTCGTGGAATGAATCTATG 57.928 45.455 0.00 0.00 30.74 2.23
1434 4666 5.243954 TGTCAGTTAGTGAGCTTGATGTACT 59.756 40.000 0.00 0.00 35.13 2.73
1542 4862 3.567478 AACAGAGTTTCAGGTTCTGCT 57.433 42.857 0.94 0.00 41.52 4.24
1544 4864 2.435805 ACAGAGTTTCAGGTTCTGCTCA 59.564 45.455 0.94 0.00 41.52 4.26
1605 4925 2.681848 TGCCTTGTTACGAACGGAAAAA 59.318 40.909 0.00 0.00 0.00 1.94
1629 4949 3.548668 CGTCTATTGCATTTTGGCACATG 59.451 43.478 0.00 0.00 44.86 3.21
1702 5027 1.520787 CAGTACCGTCCGGGCAATC 60.521 63.158 6.96 0.00 40.62 2.67
1713 5038 2.978010 GGCAATCCATACGCCCGG 60.978 66.667 0.00 0.00 40.07 5.73
1797 5122 2.825836 CCTGCCCGTCATCTTGGC 60.826 66.667 0.00 0.00 45.56 4.52
1864 6069 0.474184 ATGATCCCCGCCTTTCGATT 59.526 50.000 0.00 0.00 41.67 3.34
1910 6115 9.077885 AGTGTTGTAATCTGTTTTTCCATGTAT 57.922 29.630 0.00 0.00 0.00 2.29
1956 6222 1.806542 TCTTCATTTCCTTCACTGCGC 59.193 47.619 0.00 0.00 0.00 6.09
1978 6244 3.820590 CACCGGTCTGTTTGTGCA 58.179 55.556 2.59 0.00 0.00 4.57
1980 6246 1.518325 CACCGGTCTGTTTGTGCATA 58.482 50.000 2.59 0.00 0.00 3.14
2055 6321 8.081633 ACATGTGAAATTGTTAGTAATGTGGTG 58.918 33.333 0.00 0.00 0.00 4.17
2151 6431 4.141158 ACAGAGAGGGGAACAAAGTTCATT 60.141 41.667 11.51 0.00 0.00 2.57
2195 6475 2.088674 CTAATCTAGCCGCCGCCACT 62.089 60.000 0.00 0.00 34.57 4.00
2264 6544 3.114390 CTGGTCCCCTCTCCCTCT 58.886 66.667 0.00 0.00 0.00 3.69
2270 6550 1.149782 TCCCCTCTCCCTCTGACTGT 61.150 60.000 0.00 0.00 0.00 3.55
2291 6571 4.804420 TCCAGCGGCAGGAGGGAT 62.804 66.667 10.36 0.00 0.00 3.85
2292 6572 4.247380 CCAGCGGCAGGAGGGATC 62.247 72.222 5.33 0.00 0.00 3.36
2298 6578 2.123251 GCAGGAGGGATCGGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
2340 6620 3.390639 TCCGTAGTTAGGGTTTGGTTTCA 59.609 43.478 0.00 0.00 33.18 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.064003 TGTGGCCATGTGAGGTACTT 58.936 50.000 9.72 0.00 41.55 2.24
1 2 1.065199 CATGTGGCCATGTGAGGTACT 60.065 52.381 9.72 0.00 42.92 2.73
3 4 3.880040 CATGTGGCCATGTGAGGTA 57.120 52.632 9.72 0.00 42.92 3.08
4 5 4.749323 CATGTGGCCATGTGAGGT 57.251 55.556 9.72 0.00 42.92 3.85
84 85 4.035208 GGTTTATGTATCGTGGCCAAAGAG 59.965 45.833 7.24 0.00 0.00 2.85
251 256 7.815068 TCTTTTTGTGATGCTACTAGTCTCTTC 59.185 37.037 0.00 1.21 0.00 2.87
1434 4666 4.196193 CGGATAACAGGTGGAAGCAAATA 58.804 43.478 0.00 0.00 36.26 1.40
1544 4864 4.370049 CATCTCACATCGATCAGAAAGCT 58.630 43.478 0.00 0.00 0.00 3.74
1605 4925 3.443329 TGTGCCAAAATGCAATAGACGAT 59.557 39.130 0.00 0.00 44.11 3.73
1629 4949 4.398319 TGATTTCTGAGAGGGGAACAAAC 58.602 43.478 0.00 0.00 0.00 2.93
1750 5075 1.296392 CCACAGCATCGTCTTCCCA 59.704 57.895 0.00 0.00 0.00 4.37
1790 5115 2.034687 AAGTGCAGCCGCCAAGAT 59.965 55.556 0.00 0.00 37.32 2.40
1797 5122 1.237285 AAAGCCTACAAGTGCAGCCG 61.237 55.000 0.00 0.00 0.00 5.52
1885 6090 9.128107 CATACATGGAAAAACAGATTACAACAC 57.872 33.333 0.00 0.00 0.00 3.32
1901 6106 4.584874 CACAGGGTACAACATACATGGAA 58.415 43.478 0.00 0.00 0.00 3.53
1910 6115 2.663520 CGCGCACAGGGTACAACA 60.664 61.111 8.75 0.00 0.00 3.33
1956 6222 1.464608 CACAAACAGACCGGTGCATAG 59.535 52.381 14.63 0.00 0.00 2.23
1978 6244 3.554960 CCGTTGTCCATCGATCCACATAT 60.555 47.826 0.00 0.00 0.00 1.78
1980 6246 1.473257 CCGTTGTCCATCGATCCACAT 60.473 52.381 0.00 0.00 0.00 3.21
2101 6372 8.578308 TCCGGTGTATTTTTGTTCGTATATAG 57.422 34.615 0.00 0.00 0.00 1.31
2103 6374 7.846644 TTCCGGTGTATTTTTGTTCGTATAT 57.153 32.000 0.00 0.00 0.00 0.86
2113 6384 4.760204 CCTCTCTGTTTCCGGTGTATTTTT 59.240 41.667 0.00 0.00 0.00 1.94
2151 6431 8.221944 AGGGGAAAACGATTTATACATATCCAA 58.778 33.333 0.00 0.00 0.00 3.53
2158 6438 9.991906 CTAGATTAGGGGAAAACGATTTATACA 57.008 33.333 0.00 0.00 0.00 2.29
2163 6443 5.131067 GGCTAGATTAGGGGAAAACGATTT 58.869 41.667 0.00 0.00 0.00 2.17
2180 6460 4.451150 CAAGTGGCGGCGGCTAGA 62.451 66.667 33.21 11.79 39.81 2.43
2195 6475 1.614241 GCCTCCCTAGTCGCCTTCAA 61.614 60.000 0.00 0.00 0.00 2.69
2227 6507 2.184830 CCTCGCCGGTGTAGATCGA 61.185 63.158 16.01 6.40 0.00 3.59
2264 6544 2.031012 CCGCTGGAGCAACAGTCA 59.969 61.111 9.07 0.00 42.21 3.41
2270 6550 4.399395 CTCCTGCCGCTGGAGCAA 62.399 66.667 27.53 4.58 41.35 3.91
2288 6568 2.524640 GGGTCCCTCCTCCGATCC 60.525 72.222 0.00 0.00 36.25 3.36
2289 6569 2.524640 GGGGTCCCTCCTCCGATC 60.525 72.222 8.15 0.00 36.25 3.69
2290 6570 2.271493 AATGGGGTCCCTCCTCCGAT 62.271 60.000 8.15 0.00 35.35 4.18
2291 6571 2.486410 AAATGGGGTCCCTCCTCCGA 62.486 60.000 8.15 0.00 35.35 4.55
2292 6572 1.984288 GAAATGGGGTCCCTCCTCCG 61.984 65.000 8.15 0.00 35.35 4.63
2298 6578 2.001269 CGGAGGAAATGGGGTCCCT 61.001 63.158 8.15 0.00 35.59 4.20


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

AutoCloner maintained by Alex Coulton.