Multiple sequence alignment - TraesCS6B01G088600

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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 TraesCS6B01G088600 chr6B 100.000 3125 0 0 1 3125 64317689 64320813 0.000000e+00 5771.0
1 TraesCS6B01G088600 chr6B 78.051 1180 223 27 955 2117 35596603 35595443 0.000000e+00 712.0
2 TraesCS6B01G088600 chrUn 94.054 3162 137 12 1 3125 103103261 103106408 0.000000e+00 4750.0
3 TraesCS6B01G088600 chrUn 88.037 535 33 9 2512 3046 103124120 103124623 3.450000e-169 604.0
4 TraesCS6B01G088600 chrUn 86.139 101 10 2 2640 2740 81701235 81701331 4.260000e-19 106.0
5 TraesCS6B01G088600 chr6A 93.815 3169 136 14 1 3125 35109480 35112632 0.000000e+00 4711.0
6 TraesCS6B01G088600 chr6A 78.753 1139 212 23 990 2117 20864094 20862975 0.000000e+00 736.0
7 TraesCS6B01G088600 chr6A 89.286 56 5 1 2772 2826 64083932 64083987 5.590000e-08 69.4
8 TraesCS6B01G088600 chr6A 87.500 56 7 0 2774 2829 414876325 414876270 7.230000e-07 65.8
9 TraesCS6B01G088600 chr6A 82.090 67 8 4 2845 2909 374411183 374411119 2.000000e-03 54.7
10 TraesCS6B01G088600 chr1A 78.908 1190 221 17 935 2117 130890487 130891653 0.000000e+00 780.0
11 TraesCS6B01G088600 chr1A 85.897 78 7 3 2779 2855 30125307 30125381 2.580000e-11 80.5
12 TraesCS6B01G088600 chr1A 91.071 56 5 0 647 702 519631377 519631322 3.340000e-10 76.8
13 TraesCS6B01G088600 chr1B 78.326 1135 226 17 990 2117 180549960 180551081 0.000000e+00 715.0
14 TraesCS6B01G088600 chr1B 90.741 54 5 0 2776 2829 151123131 151123078 4.320000e-09 73.1
15 TraesCS6B01G088600 chr1B 89.286 56 3 3 2773 2827 684089024 684089077 2.010000e-07 67.6
16 TraesCS6B01G088600 chr5B 83.408 223 29 7 213 430 603647398 603647617 1.900000e-47 200.0
17 TraesCS6B01G088600 chr1D 79.661 295 47 11 935 1223 118812541 118812828 1.900000e-47 200.0
18 TraesCS6B01G088600 chr7B 78.889 180 36 2 2879 3057 99296065 99296243 1.520000e-23 121.0
19 TraesCS6B01G088600 chr7B 84.762 105 10 4 2638 2741 727421807 727421708 1.980000e-17 100.0
20 TraesCS6B01G088600 chr7B 77.931 145 28 4 2883 3025 59675096 59675238 1.540000e-13 87.9
21 TraesCS6B01G088600 chr2B 87.000 100 9 2 2639 2738 679036081 679036176 3.300000e-20 110.0
22 TraesCS6B01G088600 chr2B 79.310 145 28 2 2929 3072 439941910 439942053 1.980000e-17 100.0
23 TraesCS6B01G088600 chr2B 79.054 148 28 3 2879 3025 762512790 762512935 7.130000e-17 99.0
24 TraesCS6B01G088600 chr4A 87.500 96 8 3 2647 2742 121501233 121501324 1.190000e-19 108.0
25 TraesCS6B01G088600 chr4A 85.714 56 7 1 2848 2903 650372413 650372467 1.210000e-04 58.4
26 TraesCS6B01G088600 chr5D 84.762 105 12 2 2639 2743 6918891 6918991 5.510000e-18 102.0
27 TraesCS6B01G088600 chr4D 85.294 102 11 3 2639 2740 31821999 31822096 5.510000e-18 102.0
28 TraesCS6B01G088600 chr4D 80.833 120 22 1 2939 3058 186503477 186503359 3.320000e-15 93.5
29 TraesCS6B01G088600 chr4D 80.583 103 20 0 2939 3041 239855968 239855866 2.580000e-11 80.5
30 TraesCS6B01G088600 chr7D 75.120 209 37 10 2845 3040 633232538 633232332 2.000000e-12 84.2
31 TraesCS6B01G088600 chr3A 97.727 44 1 0 2784 2827 378815126 378815083 3.340000e-10 76.8
32 TraesCS6B01G088600 chr2D 100.000 29 0 0 2842 2870 625187567 625187595 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 TraesCS6B01G088600 chr6B 64317689 64320813 3124 False 5771 5771 100.000 1 3125 1 chr6B.!!$F1 3124
1 TraesCS6B01G088600 chr6B 35595443 35596603 1160 True 712 712 78.051 955 2117 1 chr6B.!!$R1 1162
2 TraesCS6B01G088600 chrUn 103103261 103106408 3147 False 4750 4750 94.054 1 3125 1 chrUn.!!$F2 3124
3 TraesCS6B01G088600 chrUn 103124120 103124623 503 False 604 604 88.037 2512 3046 1 chrUn.!!$F3 534
4 TraesCS6B01G088600 chr6A 35109480 35112632 3152 False 4711 4711 93.815 1 3125 1 chr6A.!!$F1 3124
5 TraesCS6B01G088600 chr6A 20862975 20864094 1119 True 736 736 78.753 990 2117 1 chr6A.!!$R1 1127
6 TraesCS6B01G088600 chr1A 130890487 130891653 1166 False 780 780 78.908 935 2117 1 chr1A.!!$F2 1182
7 TraesCS6B01G088600 chr1B 180549960 180551081 1121 False 715 715 78.326 990 2117 1 chr1B.!!$F1 1127

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
593 609 0.258774 GCTTGGGGAGAAGGGCATTA 59.741 55.0 0.0 0.0 0.00 1.90 F
1536 1566 0.252057 TCAACTCCATCAGGACCCGA 60.252 55.0 0.0 0.0 39.61 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1693 0.593263 GGCCAACGTACGGATACTCG 60.593 60.000 21.06 0.53 0.0 4.18 R
2451 2506 2.069273 CAAAGCTCGAACGAAGGACAT 58.931 47.619 0.00 0.00 0.0 3.06 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
29 30 7.981789 CAGTTATGATTTGTGCTTCCTCTACTA 59.018 37.037 0.00 0.00 0.00 1.82
54 55 7.366847 AGGTTGTAGTATGATAGATGTGCTT 57.633 36.000 0.00 0.00 0.00 3.91
56 57 7.069950 AGGTTGTAGTATGATAGATGTGCTTCA 59.930 37.037 0.00 0.00 0.00 3.02
117 118 8.823220 AGCTAGGTTTTATTTGTGTTATCCAT 57.177 30.769 0.00 0.00 0.00 3.41
189 190 2.632028 TGTAGTTGCTTTACGTACCCCA 59.368 45.455 0.00 0.00 0.00 4.96
247 250 5.094812 TCAATCGCTTCATGTAATTTGTGC 58.905 37.500 0.00 0.00 0.00 4.57
307 322 6.389830 TTGAGTTTGCACACATAGTTGAAT 57.610 33.333 5.67 0.00 0.00 2.57
371 386 8.160765 TCTTCATGTTTCTTACTATTTGTGGGA 58.839 33.333 0.00 0.00 0.00 4.37
499 515 5.861727 TGTACTACTTTTCAGGGGACTTTC 58.138 41.667 0.00 0.00 40.21 2.62
570 586 2.505819 GGTAGATTCCAGAAGCTTGGGA 59.494 50.000 2.10 8.16 38.17 4.37
571 587 3.432890 GGTAGATTCCAGAAGCTTGGGAG 60.433 52.174 2.10 0.00 38.17 4.30
572 588 2.555664 AGATTCCAGAAGCTTGGGAGA 58.444 47.619 2.10 2.76 38.81 3.71
573 589 2.915604 AGATTCCAGAAGCTTGGGAGAA 59.084 45.455 2.10 1.77 38.81 2.87
574 590 2.867109 TTCCAGAAGCTTGGGAGAAG 57.133 50.000 2.10 0.00 38.81 2.85
575 591 0.326264 TCCAGAAGCTTGGGAGAAGC 59.674 55.000 2.10 0.00 43.31 3.86
580 596 4.009015 GCTTGGGAGAAGCTTGGG 57.991 61.111 2.10 0.00 40.01 4.12
593 609 0.258774 GCTTGGGGAGAAGGGCATTA 59.741 55.000 0.00 0.00 0.00 1.90
598 614 2.091885 TGGGGAGAAGGGCATTATTGTC 60.092 50.000 0.00 0.00 0.00 3.18
599 615 2.175715 GGGGAGAAGGGCATTATTGTCT 59.824 50.000 0.00 0.00 0.00 3.41
600 616 3.481453 GGGAGAAGGGCATTATTGTCTC 58.519 50.000 0.00 0.00 0.00 3.36
601 617 3.137360 GGGAGAAGGGCATTATTGTCTCT 59.863 47.826 0.00 0.00 33.56 3.10
607 623 5.441718 AGGGCATTATTGTCTCTTCTTCA 57.558 39.130 0.00 0.00 0.00 3.02
608 624 6.011122 AGGGCATTATTGTCTCTTCTTCAT 57.989 37.500 0.00 0.00 0.00 2.57
629 645 6.124340 TCATATGGAAGTGTTGATTCAGCAT 58.876 36.000 6.48 0.00 0.00 3.79
635 651 5.125097 GGAAGTGTTGATTCAGCATCAGATT 59.875 40.000 6.48 0.00 43.15 2.40
645 661 7.919091 TGATTCAGCATCAGATTAATCTTTTGC 59.081 33.333 27.19 27.19 40.15 3.68
741 757 9.483916 TGCGTGTATGCATTTAATAGTACTAAT 57.516 29.630 3.54 0.51 40.62 1.73
742 758 9.741168 GCGTGTATGCATTTAATAGTACTAATG 57.259 33.333 3.54 9.01 34.15 1.90
981 1005 2.562296 AGGTCCACCATTACCAGACAT 58.438 47.619 0.00 0.00 38.30 3.06
1059 1084 1.134367 GCGCTGACCACTACTATGTCA 59.866 52.381 0.00 0.00 37.45 3.58
1063 1088 2.683362 CTGACCACTACTATGTCAGCGA 59.317 50.000 6.01 0.00 46.50 4.93
1092 1117 4.506271 GCCATGGACATCACAGATAAGGAT 60.506 45.833 18.40 0.00 0.00 3.24
1103 1128 0.674534 GATAAGGATCTGGCGTCGGT 59.325 55.000 0.00 0.00 0.00 4.69
1120 1145 2.847234 TGGAGTCCTTGTGGGCGT 60.847 61.111 11.33 0.00 44.16 5.68
1188 1214 2.329379 GACAAGACTCGACGCTTCAAT 58.671 47.619 0.00 0.00 0.00 2.57
1236 1262 2.878406 CCACGAGTTCAACCAACAAGAT 59.122 45.455 0.00 0.00 37.48 2.40
1352 1378 4.838152 GAAGCGCCGGCATCAGGA 62.838 66.667 28.98 0.00 43.41 3.86
1536 1566 0.252057 TCAACTCCATCAGGACCCGA 60.252 55.000 0.00 0.00 39.61 5.14
1655 1686 0.756442 CACCATGGGGGCATCGAAAT 60.756 55.000 18.09 0.00 42.05 2.17
1698 1729 2.827190 CATGAGCATGGCCGCTGT 60.827 61.111 10.14 0.00 44.01 4.40
1774 1811 3.443045 CGCCCAATGAGGTGGCAC 61.443 66.667 9.70 9.70 45.63 5.01
1830 1867 2.544480 CACTCGATGCTAACTCGACA 57.456 50.000 0.00 0.00 40.01 4.35
2107 2155 3.855689 AAAGGAAAGGCGTGAATGATG 57.144 42.857 0.00 0.00 0.00 3.07
2255 2307 5.725338 AGGTAGGATGATGCATGTCTATGAT 59.275 40.000 2.46 0.00 36.36 2.45
2400 2452 3.091545 TGCCATGATTGGAGGAGAAAAC 58.908 45.455 0.00 0.00 46.92 2.43
2403 2455 4.592942 CCATGATTGGAGGAGAAAACTGA 58.407 43.478 0.00 0.00 46.92 3.41
2412 2464 5.425217 TGGAGGAGAAAACTGACATATAGCA 59.575 40.000 0.00 0.00 0.00 3.49
2414 2466 6.299805 AGGAGAAAACTGACATATAGCACA 57.700 37.500 0.00 0.00 0.00 4.57
2758 2838 6.637254 CGGAGTACAACATATGCTAGTACAAG 59.363 42.308 23.51 15.14 37.96 3.16
3046 3127 8.884726 TCAAATTATGACCGAAAATACGATGAA 58.115 29.630 0.00 0.00 31.50 2.57
3072 3153 8.808092 AGACTAATAAACTCATATGGAGGTAGC 58.192 37.037 2.13 0.00 44.90 3.58
3082 3163 8.908786 CTCATATGGAGGTAGCAAAATTTAGA 57.091 34.615 2.13 0.00 40.13 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.163237 ACAACCTTAGTAGAGGAAGCACAAA 60.163 40.000 0.00 0.00 39.25 2.83
29 30 7.366847 AGCACATCTATCATACTACAACCTT 57.633 36.000 0.00 0.00 0.00 3.50
54 55 6.533730 AGAGTAAACTGGTCATGATTTGTGA 58.466 36.000 0.00 0.00 0.00 3.58
56 57 7.907389 TCTAGAGTAAACTGGTCATGATTTGT 58.093 34.615 0.00 0.00 0.00 2.83
133 134 9.971922 CAGAAATGAAAAGTAGGACTGAAAAAT 57.028 29.630 0.00 0.00 0.00 1.82
247 250 5.163992 ACTCGATAACTGCATTACACAAACG 60.164 40.000 0.00 0.00 0.00 3.60
307 322 3.734463 TCGAAACATGTAGCCTCAACAA 58.266 40.909 0.00 0.00 0.00 2.83
434 449 6.698380 AGGAAAACTAGCGAATAAAGAGACA 58.302 36.000 0.00 0.00 0.00 3.41
499 515 1.792949 GCTACAACTCACGTGGAACAG 59.207 52.381 17.00 8.13 41.80 3.16
570 586 1.857638 GCCCTTCTCCCCAAGCTTCT 61.858 60.000 0.00 0.00 0.00 2.85
571 587 1.379176 GCCCTTCTCCCCAAGCTTC 60.379 63.158 0.00 0.00 0.00 3.86
572 588 1.513087 ATGCCCTTCTCCCCAAGCTT 61.513 55.000 0.00 0.00 0.00 3.74
573 589 1.513087 AATGCCCTTCTCCCCAAGCT 61.513 55.000 0.00 0.00 0.00 3.74
574 590 0.258774 TAATGCCCTTCTCCCCAAGC 59.741 55.000 0.00 0.00 0.00 4.01
575 591 2.961062 CAATAATGCCCTTCTCCCCAAG 59.039 50.000 0.00 0.00 0.00 3.61
576 592 2.314549 ACAATAATGCCCTTCTCCCCAA 59.685 45.455 0.00 0.00 0.00 4.12
577 593 1.929494 ACAATAATGCCCTTCTCCCCA 59.071 47.619 0.00 0.00 0.00 4.96
578 594 2.175715 AGACAATAATGCCCTTCTCCCC 59.824 50.000 0.00 0.00 0.00 4.81
579 595 3.137360 AGAGACAATAATGCCCTTCTCCC 59.863 47.826 0.00 0.00 29.56 4.30
580 596 4.429854 AGAGACAATAATGCCCTTCTCC 57.570 45.455 0.00 0.00 29.56 3.71
607 623 6.124340 TGATGCTGAATCAACACTTCCATAT 58.876 36.000 0.00 0.00 42.49 1.78
608 624 5.499313 TGATGCTGAATCAACACTTCCATA 58.501 37.500 0.00 0.00 42.49 2.74
828 844 9.541143 TGTTCGTGCTAATCTCATAATTAATGA 57.459 29.630 0.00 0.00 42.48 2.57
891 909 7.568349 TCTATAACAATGGTGAGCTCTCAAAT 58.432 34.615 16.19 6.35 41.85 2.32
892 910 6.946340 TCTATAACAATGGTGAGCTCTCAAA 58.054 36.000 16.19 4.09 41.85 2.69
981 1005 4.736168 GCCATTGTGTGTAGTTGCTTCAAA 60.736 41.667 0.00 0.00 0.00 2.69
1050 1075 0.303796 CGCTCGTCGCTGACATAGTA 59.696 55.000 8.91 0.00 36.13 1.82
1063 1088 2.202932 GATGTCCATGGCGCTCGT 60.203 61.111 6.96 0.00 0.00 4.18
1092 1117 3.371063 GACTCCACCGACGCCAGA 61.371 66.667 0.00 0.00 0.00 3.86
1103 1128 2.448582 AACGCCCACAAGGACTCCA 61.449 57.895 0.00 0.00 38.24 3.86
1120 1145 3.889227 GCACCAGCGCTCATACAA 58.111 55.556 7.13 0.00 0.00 2.41
1188 1214 1.872952 CGTGCATTCTCCTTGAACACA 59.127 47.619 0.00 0.00 37.52 3.72
1236 1262 0.035439 GGCTTAGCTTGTAGGGCACA 60.035 55.000 3.59 0.00 34.51 4.57
1536 1566 5.242434 TGCACAGATAATGACGTTAGGTTT 58.758 37.500 0.00 0.00 0.00 3.27
1624 1655 3.244911 CCCCCATGGTGGATAATGTACTC 60.245 52.174 7.64 0.00 40.96 2.59
1655 1686 1.606480 CGTACGGATACTCGGCCTCTA 60.606 57.143 7.57 0.00 0.00 2.43
1662 1693 0.593263 GGCCAACGTACGGATACTCG 60.593 60.000 21.06 0.53 0.00 4.18
1715 1746 2.659244 TGACGACGGTGTTTCGGC 60.659 61.111 0.00 0.00 45.27 5.54
1719 1750 0.941542 CAATGGTGACGACGGTGTTT 59.058 50.000 0.00 0.00 0.00 2.83
1774 1811 3.506096 CGCCACTGCCTGCATCAG 61.506 66.667 12.84 12.84 37.56 2.90
2107 2155 6.901887 CGCATTTGTTACACTATCTTCATGAC 59.098 38.462 0.00 0.00 0.00 3.06
2266 2318 9.919416 CCCATAATATTGTGGTCCATATAATCA 57.081 33.333 24.66 0.00 37.71 2.57
2274 2326 6.024563 ACATTCCCATAATATTGTGGTCCA 57.975 37.500 24.66 11.91 37.71 4.02
2280 2332 9.667607 TCCCATAAAACATTCCCATAATATTGT 57.332 29.630 0.00 0.00 0.00 2.71
2288 2340 2.958355 CGCTCCCATAAAACATTCCCAT 59.042 45.455 0.00 0.00 0.00 4.00
2451 2506 2.069273 CAAAGCTCGAACGAAGGACAT 58.931 47.619 0.00 0.00 0.00 3.06
2625 2705 9.485206 AACGAAAGAAGTATGTGTTAATACTGT 57.515 29.630 3.89 0.00 41.49 3.55
2645 2725 9.505995 GTTAAGACACTTATTTTTGGAACGAAA 57.494 29.630 0.00 0.00 0.00 3.46
3046 3127 8.808092 GCTACCTCCATATGAGTTTATTAGTCT 58.192 37.037 3.65 0.00 39.65 3.24
3063 3144 6.945435 TCACAATCTAAATTTTGCTACCTCCA 59.055 34.615 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.