Multiple sequence alignment - TraesCS6B01G030800

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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 TraesCS6B01G030800 chr6B 100.000 3456 0 0 1 3456 18300906 18297451 0.000000e+00 6383.0
1 TraesCS6B01G030800 chr6B 93.802 2049 96 16 491 2508 18150172 18148124 0.000000e+00 3051.0
2 TraesCS6B01G030800 chr6B 91.057 369 19 6 2622 2984 18148125 18147765 1.440000e-133 486.0
3 TraesCS6B01G030800 chr6B 83.629 507 43 14 1 478 18150651 18150156 1.140000e-119 440.0
4 TraesCS6B01G030800 chr6D 92.499 2493 145 18 973 3456 9908038 9905579 0.000000e+00 3530.0
5 TraesCS6B01G030800 chr6D 93.333 45 3 0 3105 3149 159234482 159234526 2.230000e-07 67.6
6 TraesCS6B01G030800 chrUn 89.996 2579 154 34 1 2508 71218455 71221000 0.000000e+00 3238.0
7 TraesCS6B01G030800 chrUn 93.381 1390 80 6 1129 2508 321359139 321360526 0.000000e+00 2047.0
8 TraesCS6B01G030800 chrUn 88.342 995 103 9 1512 2500 71181591 71182578 0.000000e+00 1182.0
9 TraesCS6B01G030800 chrUn 89.332 928 63 15 497 1388 71265948 71265021 0.000000e+00 1133.0
10 TraesCS6B01G030800 chrUn 88.389 844 73 9 2622 3456 71263983 71263156 0.000000e+00 992.0
11 TraesCS6B01G030800 chrUn 96.082 485 19 0 1441 1925 71265024 71264540 0.000000e+00 791.0
12 TraesCS6B01G030800 chrUn 92.157 561 41 1 1951 2508 71264542 71263982 0.000000e+00 789.0
13 TraesCS6B01G030800 chrUn 82.340 889 102 31 754 1612 71180729 71181592 0.000000e+00 721.0
14 TraesCS6B01G030800 chrUn 88.683 486 41 8 2622 3098 71220999 71221479 6.430000e-162 580.0
15 TraesCS6B01G030800 chrUn 88.683 486 41 8 2622 3098 321360525 321361005 6.430000e-162 580.0
16 TraesCS6B01G030800 chrUn 88.084 428 20 8 19 419 423403553 423403976 2.410000e-131 479.0
17 TraesCS6B01G030800 chrUn 80.131 458 78 11 987 1439 172238050 172237601 2.570000e-86 329.0
18 TraesCS6B01G030800 chrUn 80.000 440 58 11 999 1422 423403753 423403328 7.250000e-77 298.0
19 TraesCS6B01G030800 chrUn 90.789 76 7 0 125 200 71184025 71183950 6.100000e-18 102.0
20 TraesCS6B01G030800 chr6A 86.743 1305 145 20 1085 2376 11434090 11432801 0.000000e+00 1426.0
21 TraesCS6B01G030800 chr6A 81.004 458 74 11 987 1439 11116375 11115926 5.490000e-93 351.0
22 TraesCS6B01G030800 chr6A 91.139 79 7 0 122 200 11116287 11116365 1.310000e-19 108.0
23 TraesCS6B01G030800 chr5D 79.885 348 54 15 3011 3350 539865372 539865033 1.240000e-59 241.0
24 TraesCS6B01G030800 chr2B 84.746 118 15 3 2507 2623 638269743 638269628 7.840000e-22 115.0
25 TraesCS6B01G030800 chr2B 89.583 48 4 1 2546 2592 709170624 709170671 3.720000e-05 60.2
26 TraesCS6B01G030800 chr3D 81.707 82 15 0 3066 3147 107439669 107439588 6.190000e-08 69.4
27 TraesCS6B01G030800 chr2A 92.157 51 0 2 261 310 646556592 646556545 6.190000e-08 69.4
28 TraesCS6B01G030800 chr7D 90.000 50 5 0 237 286 622195900 622195949 8.010000e-07 65.8
29 TraesCS6B01G030800 chr5A 76.000 125 26 4 3051 3172 14990142 14990265 1.040000e-05 62.1
30 TraesCS6B01G030800 chr1B 91.111 45 3 1 2549 2592 657665627 657665671 3.720000e-05 60.2
31 TraesCS6B01G030800 chr4B 87.500 48 5 1 2546 2592 511368077 511368030 2.000000e-03 54.7


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 TraesCS6B01G030800 chr6B 18297451 18300906 3455 True 6383.000000 6383 100.0000 1 3456 1 chr6B.!!$R1 3455
1 TraesCS6B01G030800 chr6B 18147765 18150651 2886 True 1325.666667 3051 89.4960 1 2984 3 chr6B.!!$R2 2983
2 TraesCS6B01G030800 chr6D 9905579 9908038 2459 True 3530.000000 3530 92.4990 973 3456 1 chr6D.!!$R1 2483
3 TraesCS6B01G030800 chrUn 71218455 71221479 3024 False 1909.000000 3238 89.3395 1 3098 2 chrUn.!!$F3 3097
4 TraesCS6B01G030800 chrUn 321359139 321361005 1866 False 1313.500000 2047 91.0320 1129 3098 2 chrUn.!!$F4 1969
5 TraesCS6B01G030800 chrUn 71180729 71182578 1849 False 951.500000 1182 85.3410 754 2500 2 chrUn.!!$F2 1746
6 TraesCS6B01G030800 chrUn 71263156 71265948 2792 True 926.250000 1133 91.4900 497 3456 4 chrUn.!!$R4 2959
7 TraesCS6B01G030800 chr6A 11432801 11434090 1289 True 1426.000000 1426 86.7430 1085 2376 1 chr6A.!!$R2 1291


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
222 245 0.252239 TTGCTCTGCTCTCCCCTACA 60.252 55.0 0.0 0.0 0.0 2.74 F
1320 1454 0.036671 TCGTGGCTCAGTCTCGTCTA 60.037 55.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2393 0.321671 ACCCGTCTGTGGATGTCTTG 59.678 55.0 0.0 0.0 0.0 3.02 R
2908 3202 0.700564 TCAGCAAGCTTCCTCCCATT 59.299 50.0 0.0 0.0 0.0 3.16 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
93 94 1.255667 TAGAAGTGGACGAGTGGGGC 61.256 60.000 0.00 0.00 0.00 5.80
220 243 0.689080 CCTTGCTCTGCTCTCCCCTA 60.689 60.000 0.00 0.00 0.00 3.53
222 245 0.252239 TTGCTCTGCTCTCCCCTACA 60.252 55.000 0.00 0.00 0.00 2.74
311 334 7.665080 AAAATTGTCTCGCTAAATAAATCGC 57.335 32.000 0.00 0.00 0.00 4.58
312 335 4.789095 TTGTCTCGCTAAATAAATCGCC 57.211 40.909 0.00 0.00 0.00 5.54
315 338 5.779922 TGTCTCGCTAAATAAATCGCCTAT 58.220 37.500 0.00 0.00 0.00 2.57
344 367 6.513180 ACACACTAATAGCACGCTATAACAT 58.487 36.000 11.80 0.00 38.20 2.71
372 401 1.917872 AAAGCGTATTTCAAGGCCCA 58.082 45.000 0.00 0.00 0.00 5.36
387 417 0.657840 GCCCACGCTATTTGCTGTAG 59.342 55.000 0.00 0.00 40.11 2.74
388 418 1.299541 CCCACGCTATTTGCTGTAGG 58.700 55.000 0.00 0.00 40.11 3.18
540 596 6.204301 ACAAGCAATTATTGATGGAGAGATCG 59.796 38.462 9.36 0.00 0.00 3.69
545 601 0.385751 TTGATGGAGAGATCGCGTCC 59.614 55.000 5.77 5.78 0.00 4.79
563 619 0.609131 CCCGCTGTTTTCCCACTGAT 60.609 55.000 0.00 0.00 0.00 2.90
570 626 0.326927 TTTTCCCACTGATCGGTCCC 59.673 55.000 3.54 0.00 0.00 4.46
633 705 4.176752 GCCTCTAACAGGGCCCGG 62.177 72.222 21.67 21.67 43.70 5.73
649 721 0.749091 CCGGCAGAGAATCAATGGCA 60.749 55.000 10.77 0.00 35.91 4.92
673 745 3.741476 GCGCCTGCCTCCAAACAG 61.741 66.667 0.00 0.00 33.98 3.16
787 868 6.363357 GGGAAAGAAAACAACGAGATTTGATG 59.637 38.462 0.00 0.00 0.00 3.07
865 979 3.999046 AGAAGATATGCGATCACATGCA 58.001 40.909 6.48 0.84 46.51 3.96
970 1098 3.436496 CGGTAGTAGCTAGAGCAACAAC 58.564 50.000 4.01 0.00 45.16 3.32
985 1118 3.857093 GCAACAACGAGAAACAACAACAT 59.143 39.130 0.00 0.00 0.00 2.71
987 1120 5.171337 GCAACAACGAGAAACAACAACATAG 59.829 40.000 0.00 0.00 0.00 2.23
994 1127 5.220043 CGAGAAACAACAACATAGCTACTCG 60.220 44.000 0.00 1.49 36.85 4.18
996 1129 5.989777 AGAAACAACAACATAGCTACTCGTT 59.010 36.000 0.00 0.00 0.00 3.85
1041 1175 1.062488 AGGTGGTGGAGTCCTGCTTT 61.062 55.000 11.33 0.00 0.00 3.51
1156 1290 1.885163 CTACCGCCGACCAGAAACCT 61.885 60.000 0.00 0.00 0.00 3.50
1181 1315 1.709203 CGACGACTTCTTCAACGTGAG 59.291 52.381 0.00 0.00 39.04 3.51
1320 1454 0.036671 TCGTGGCTCAGTCTCGTCTA 60.037 55.000 0.00 0.00 0.00 2.59
1337 1471 3.865745 CGTCTAACCATGGATGACTTCAC 59.134 47.826 21.47 1.72 0.00 3.18
1496 1641 7.962918 CACCTACAATTAACAGAACTAACATGC 59.037 37.037 0.00 0.00 0.00 4.06
1667 1921 2.373169 ACATGGTCAGCTTTCTCCAGAA 59.627 45.455 0.00 0.00 33.33 3.02
1698 1952 1.694693 GGCTATGGTGAACCTCCCCTA 60.695 57.143 0.37 0.00 36.82 3.53
1783 2037 6.070251 CCATTTTTAGCCCCAAGATAAACCTT 60.070 38.462 0.00 0.00 0.00 3.50
1784 2038 7.125053 CCATTTTTAGCCCCAAGATAAACCTTA 59.875 37.037 0.00 0.00 0.00 2.69
1812 2066 3.231736 AGGGCCAGTCGTCAACGT 61.232 61.111 6.18 0.00 40.80 3.99
1820 2074 0.108520 AGTCGTCAACGTGGTTGTGT 60.109 50.000 8.21 0.00 43.23 3.72
1867 2121 1.069204 TCCACTCTCAAGCGCATATCC 59.931 52.381 11.47 0.00 0.00 2.59
2005 2287 2.191375 CGCATCATGAGGCCACCT 59.809 61.111 25.30 0.00 34.12 4.00
2013 2295 3.086600 GAGGCCACCTCTCCCAGG 61.087 72.222 5.01 0.00 46.41 4.45
2063 2345 3.335534 GTGTCGGCGACAAAGCGT 61.336 61.111 40.38 0.00 44.49 5.07
2115 2400 1.715585 CGCGGCGAATTCAAGACAT 59.284 52.632 19.16 0.00 0.00 3.06
2137 2422 1.728426 CAGACGGGTGAACGACGAC 60.728 63.158 0.00 0.00 37.61 4.34
2342 2627 1.896220 TGTTCACCTGATTGACAGCC 58.104 50.000 0.00 0.00 44.52 4.85
2414 2699 1.330521 TCAGTGAGTTGAAGCGTTTGC 59.669 47.619 0.00 0.00 43.24 3.68
2428 2713 2.092524 GCGTTTGCTGTATGCCAAATTG 59.907 45.455 0.00 0.00 42.00 2.32
2436 2721 4.749099 GCTGTATGCCAAATTGAACAACAA 59.251 37.500 0.00 0.00 38.11 2.83
2516 2804 5.724370 TGATTGTATCTTGTTACTCCCTCCA 59.276 40.000 0.00 0.00 0.00 3.86
2534 2822 4.430908 CTCCATCCGGACTTACTTGTTAC 58.569 47.826 6.12 0.00 35.91 2.50
2536 2824 4.283978 TCCATCCGGACTTACTTGTTACAA 59.716 41.667 6.12 0.00 35.91 2.41
2666 2954 2.810650 TCTTAAGCAGCTTACGCTAGC 58.189 47.619 14.80 4.06 46.99 3.42
2674 2962 3.305471 GCAGCTTACGCTAGCCTTATACT 60.305 47.826 9.66 0.00 46.99 2.12
2723 3011 4.439563 GCTTCAGAGTAGAGTAGTTGCTCC 60.440 50.000 0.00 0.00 36.20 4.70
2908 3202 9.837681 TTTGAATCCATCTACTATATACTGGGA 57.162 33.333 0.00 0.00 0.00 4.37
3008 3302 1.194781 ACGCAGGTCCAGATGTTCCT 61.195 55.000 0.00 0.00 0.00 3.36
3041 3336 9.550811 GAACAAGAAATCGTTTAAATAACCGAT 57.449 29.630 5.81 5.81 41.41 4.18
3146 3442 2.170397 TCGAGGAGCTCATGGCATAAAA 59.830 45.455 17.19 0.00 44.79 1.52
3149 3445 3.549794 AGGAGCTCATGGCATAAAAGAC 58.450 45.455 17.19 0.00 44.79 3.01
3191 3487 2.923020 AGTTTGAAAAAGCGCACTGTTG 59.077 40.909 11.47 0.00 0.00 3.33
3237 3533 2.730090 GCAAGCTCCATGAATGTCGTTG 60.730 50.000 0.00 0.00 0.00 4.10
3244 3540 2.754552 CCATGAATGTCGTTGACCCATT 59.245 45.455 0.00 0.00 0.00 3.16
3374 3680 3.172919 GCTTGAGCTCCGAACAGC 58.827 61.111 12.15 7.19 39.99 4.40
3380 3686 2.261671 GCTCCGAACAGCTCCGAA 59.738 61.111 1.70 0.00 36.38 4.30
3381 3687 1.374252 GCTCCGAACAGCTCCGAAA 60.374 57.895 1.70 0.00 36.38 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.203294 GACCAAACAGCCACGGGT 60.203 61.111 0.00 0.00 33.78 5.28
43 44 2.892334 CGGTGACCAAACAGCCACG 61.892 63.158 1.11 0.00 35.24 4.94
93 94 1.409064 TGCTAGTCCATGAAGGCTACG 59.591 52.381 0.00 0.00 37.29 3.51
103 104 3.323403 GCACTCCTCTTATGCTAGTCCAT 59.677 47.826 0.00 0.00 36.40 3.41
193 216 0.323178 AGCAGAGCAAGGTGAATGGG 60.323 55.000 0.00 0.00 0.00 4.00
248 271 3.921021 CGTGCTATTAGTGGTGCTATAGC 59.079 47.826 18.18 18.18 37.34 2.97
286 309 7.220108 GGCGATTTATTTAGCGAGACAATTTTT 59.780 33.333 0.00 0.00 0.00 1.94
287 310 6.691388 GGCGATTTATTTAGCGAGACAATTTT 59.309 34.615 0.00 0.00 0.00 1.82
288 311 6.038271 AGGCGATTTATTTAGCGAGACAATTT 59.962 34.615 0.00 0.00 0.00 1.82
311 334 6.089551 GCGTGCTATTAGTGTGTCATTATAGG 59.910 42.308 0.00 0.00 0.00 2.57
312 335 6.863645 AGCGTGCTATTAGTGTGTCATTATAG 59.136 38.462 0.00 0.00 0.00 1.31
315 338 5.006153 AGCGTGCTATTAGTGTGTCATTA 57.994 39.130 0.00 0.00 0.00 1.90
344 367 4.693538 TGAAATACGCTTTTAGCATGCA 57.306 36.364 21.98 2.77 42.58 3.96
545 601 0.804989 GATCAGTGGGAAAACAGCGG 59.195 55.000 0.00 0.00 0.00 5.52
577 633 1.154263 GAAGACAGACGGACGGACG 60.154 63.158 0.00 0.00 40.31 4.79
580 636 0.448593 GAGAGAAGACAGACGGACGG 59.551 60.000 0.00 0.00 0.00 4.79
581 637 0.448593 GGAGAGAAGACAGACGGACG 59.551 60.000 0.00 0.00 0.00 4.79
585 641 3.343617 AGAAGAGGAGAGAAGACAGACG 58.656 50.000 0.00 0.00 0.00 4.18
633 705 1.674962 GTCCTGCCATTGATTCTCTGC 59.325 52.381 0.00 0.00 0.00 4.26
673 745 5.068591 ACCCATTCAAGGAAACTAAACACAC 59.931 40.000 0.00 0.00 42.68 3.82
787 868 1.346395 TGGGGACATACATGGCGATAC 59.654 52.381 0.00 0.00 36.40 2.24
970 1098 5.220043 CGAGTAGCTATGTTGTTGTTTCTCG 60.220 44.000 0.00 2.18 35.07 4.04
985 1118 1.138266 GGCCATTCCAACGAGTAGCTA 59.862 52.381 0.00 0.00 34.01 3.32
987 1120 1.429148 CGGCCATTCCAACGAGTAGC 61.429 60.000 2.24 0.00 34.01 3.58
994 1127 3.508840 CTCGCCGGCCATTCCAAC 61.509 66.667 23.46 0.00 34.01 3.77
1156 1290 1.798234 TTGAAGAAGTCGTCGCCGGA 61.798 55.000 5.05 0.00 33.95 5.14
1174 1308 1.583054 GTCTTCAACCTGCTCACGTT 58.417 50.000 0.00 0.00 0.00 3.99
1181 1315 2.251642 AACGCCGTCTTCAACCTGC 61.252 57.895 0.00 0.00 0.00 4.85
1320 1454 1.628340 TCGGTGAAGTCATCCATGGTT 59.372 47.619 12.58 0.00 0.00 3.67
1337 1471 2.028420 TGATGATGGCTTGAAGTCGG 57.972 50.000 0.00 0.00 0.00 4.79
1618 1872 5.762179 AGAAGTGGAATACAACAGATCCA 57.238 39.130 0.00 0.00 39.57 3.41
1667 1921 4.524318 CATAGCCCGGTCGCCGTT 62.524 66.667 15.38 5.37 46.80 4.44
1820 2074 1.460255 CCTTGGCAAGGGTGAAGGA 59.540 57.895 34.03 0.00 45.27 3.36
1898 2152 4.415150 CCACAGGTGGGCGCTCAT 62.415 66.667 15.93 0.00 46.81 2.90
2005 2287 2.038975 AAGTAGCCGCCTGGGAGA 59.961 61.111 0.00 0.00 38.47 3.71
2013 2295 3.849953 CGTTGCCGAAGTAGCCGC 61.850 66.667 0.00 0.00 35.63 6.53
2032 2314 5.045215 TCGCCGACACTTAGGTTTATTATG 58.955 41.667 0.00 0.00 0.00 1.90
2063 2345 1.227234 CACGTGAGGCGATGGCATA 60.227 57.895 10.90 0.00 44.77 3.14
2108 2393 0.321671 ACCCGTCTGTGGATGTCTTG 59.678 55.000 0.00 0.00 0.00 3.02
2109 2394 0.321671 CACCCGTCTGTGGATGTCTT 59.678 55.000 0.00 0.00 32.50 3.01
2115 2400 1.829096 TCGTTCACCCGTCTGTGGA 60.829 57.895 0.00 0.00 36.87 4.02
2137 2422 1.278172 CGATCGCCGAATGCACTAGG 61.278 60.000 0.26 0.00 41.33 3.02
2298 2583 2.625823 CCGCGGTTTGGTTCAGCAT 61.626 57.895 19.50 0.00 0.00 3.79
2342 2627 1.676635 CACTGCCATCACCCTGTGG 60.677 63.158 0.00 0.00 38.55 4.17
2414 2699 5.984926 ACTTGTTGTTCAATTTGGCATACAG 59.015 36.000 0.00 0.00 35.35 2.74
2464 2752 3.126001 TCCATGACTCAAACACACCTC 57.874 47.619 0.00 0.00 0.00 3.85
2474 2762 4.677673 ATCATCGAACATCCATGACTCA 57.322 40.909 0.00 0.00 29.36 3.41
2606 2894 1.062886 CACCTACTCCCTCCATCCAGA 60.063 57.143 0.00 0.00 0.00 3.86
2608 2896 0.716591 ACACCTACTCCCTCCATCCA 59.283 55.000 0.00 0.00 0.00 3.41
2612 2900 2.112279 ACAAACACCTACTCCCTCCA 57.888 50.000 0.00 0.00 0.00 3.86
2636 2924 7.568433 CGTAAGCTGCTTAAGATTATTTCTCC 58.432 38.462 24.78 8.21 38.92 3.71
2674 2962 7.632861 TGAGACCAGAAGGATTGAATTCAATA 58.367 34.615 29.05 7.95 45.72 1.90
2723 3011 5.343058 CACTAAACAAAATCGTGCATTCCAG 59.657 40.000 0.00 0.00 0.00 3.86
2896 3190 5.104735 GCTTCCTCCCATTCCCAGTATATAG 60.105 48.000 0.00 0.00 0.00 1.31
2897 3191 4.783227 GCTTCCTCCCATTCCCAGTATATA 59.217 45.833 0.00 0.00 0.00 0.86
2898 3192 3.589288 GCTTCCTCCCATTCCCAGTATAT 59.411 47.826 0.00 0.00 0.00 0.86
2908 3202 0.700564 TCAGCAAGCTTCCTCCCATT 59.299 50.000 0.00 0.00 0.00 3.16
3008 3302 7.789273 TTAAACGATTTCTTGTTCACACCTA 57.211 32.000 0.00 0.00 0.00 3.08
3075 3371 3.004629 GGGCATAACGCATTTGATCATCA 59.995 43.478 0.00 0.00 45.17 3.07
3146 3442 1.202879 TCACAGGCCCGAAAATTGTCT 60.203 47.619 0.00 0.00 0.00 3.41
3149 3445 1.533625 TCTCACAGGCCCGAAAATTG 58.466 50.000 0.00 0.00 0.00 2.32
3191 3487 5.222631 CCAAAACAGACAAAATCAGCTACC 58.777 41.667 0.00 0.00 0.00 3.18
3237 3533 4.450757 GGTGTGTGCAAAAATTAATGGGTC 59.549 41.667 0.00 0.00 0.00 4.46
3244 3540 4.052159 CACCAGGTGTGTGCAAAAATTA 57.948 40.909 11.99 0.00 40.26 1.40



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

AutoCloner maintained by Alex Coulton.