Multiple sequence alignment - TraesCS7B01G167800

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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 TraesCS7B01G167800 chr7B 100.000 3085 0 0 1 3085 234015050 234011966 0 5698
1 TraesCS7B01G167800 chr7D 93.852 3139 79 44 1 3085 255785726 255782648 0 4623
2 TraesCS7B01G167800 chr7A 90.502 3127 110 78 33 3085 275547623 275544610 0 3956


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 TraesCS7B01G167800 chr7B 234011966 234015050 3084 True 5698 5698 100.000 1 3085 1 chr7B.!!$R1 3084
1 TraesCS7B01G167800 chr7D 255782648 255785726 3078 True 4623 4623 93.852 1 3085 1 chr7D.!!$R1 3084
2 TraesCS7B01G167800 chr7A 275544610 275547623 3013 True 3956 3956 90.502 33 3085 1 chr7A.!!$R1 3052

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
878 913 0.245813 CACAGCTGCTAGCACAGAGA 59.754 55.0 14.93 0.0 45.56 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2367 0.036388 GTGGATTTGGGAGTCGCTGA 60.036 55.0 8.82 0.0 0.0 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.625790 GCCACATTTCTGTAAACACCCA 59.374 45.455 0.00 0.00 33.14 4.51
29 30 3.552068 GCCACATTTCTGTAAACACCCAC 60.552 47.826 0.00 0.00 33.14 4.61
30 31 3.304391 CCACATTTCTGTAAACACCCACG 60.304 47.826 0.00 0.00 33.14 4.94
31 32 3.314080 CACATTTCTGTAAACACCCACGT 59.686 43.478 0.00 0.00 33.14 4.49
68 69 4.509970 CACGTACACTCCAAGATTCACAAA 59.490 41.667 0.00 0.00 0.00 2.83
122 127 3.866651 AGCATGCATATACCGATCCTTC 58.133 45.455 21.98 0.00 0.00 3.46
124 129 2.363788 TGCATATACCGATCCTTCGC 57.636 50.000 0.00 0.00 44.12 4.70
451 465 4.379243 CACCTCAACCGCTCGGCT 62.379 66.667 8.41 0.00 39.32 5.52
505 522 2.997315 CTCCTGTCCGGTCCTGCA 60.997 66.667 0.00 0.00 0.00 4.41
517 534 4.015406 CCTGCACACCCAGCCGTA 62.015 66.667 0.00 0.00 0.00 4.02
519 536 4.673298 TGCACACCCAGCCGTACG 62.673 66.667 8.69 8.69 0.00 3.67
520 537 4.675029 GCACACCCAGCCGTACGT 62.675 66.667 15.21 0.00 0.00 3.57
522 539 4.047059 ACACCCAGCCGTACGTCG 62.047 66.667 15.21 0.29 39.52 5.12
523 540 3.740397 CACCCAGCCGTACGTCGA 61.740 66.667 15.21 0.00 42.86 4.20
524 541 2.753043 ACCCAGCCGTACGTCGAT 60.753 61.111 15.21 0.00 42.86 3.59
525 542 2.278596 CCCAGCCGTACGTCGATG 60.279 66.667 15.21 8.61 42.86 3.84
526 543 2.954868 CCAGCCGTACGTCGATGC 60.955 66.667 15.21 9.91 42.86 3.91
529 546 3.252484 GCCGTACGTCGATGCCAC 61.252 66.667 15.21 2.18 42.86 5.01
533 550 0.248498 CGTACGTCGATGCCACTGAT 60.248 55.000 7.22 0.00 42.86 2.90
552 570 4.326826 TGATCTGATCACAGGGTGAAAAC 58.673 43.478 16.06 0.00 45.96 2.43
553 571 3.140325 TCTGATCACAGGGTGAAAACC 57.860 47.619 2.87 0.00 45.96 3.27
554 572 2.711009 TCTGATCACAGGGTGAAAACCT 59.289 45.455 2.87 0.00 45.96 3.50
622 645 4.713824 ATGTGCAATTGACAGATCTTGG 57.286 40.909 10.34 0.00 0.00 3.61
875 910 1.636570 CTGCACAGCTGCTAGCACAG 61.637 60.000 20.88 14.47 45.56 3.66
876 911 1.375140 GCACAGCTGCTAGCACAGA 60.375 57.895 14.93 0.00 45.56 3.41
877 912 1.360194 GCACAGCTGCTAGCACAGAG 61.360 60.000 14.93 5.20 45.56 3.35
878 913 0.245813 CACAGCTGCTAGCACAGAGA 59.754 55.000 14.93 0.00 45.56 3.10
879 914 0.531657 ACAGCTGCTAGCACAGAGAG 59.468 55.000 14.93 3.95 45.56 3.20
880 915 0.816373 CAGCTGCTAGCACAGAGAGA 59.184 55.000 14.93 0.00 45.56 3.10
881 916 1.105457 AGCTGCTAGCACAGAGAGAG 58.895 55.000 14.93 2.31 45.56 3.20
882 917 1.102154 GCTGCTAGCACAGAGAGAGA 58.898 55.000 14.93 0.00 41.89 3.10
883 918 1.066002 GCTGCTAGCACAGAGAGAGAG 59.934 57.143 14.93 0.68 41.89 3.20
884 919 2.642427 CTGCTAGCACAGAGAGAGAGA 58.358 52.381 14.93 0.00 40.25 3.10
885 920 2.615447 CTGCTAGCACAGAGAGAGAGAG 59.385 54.545 14.93 0.00 40.25 3.20
886 921 2.238395 TGCTAGCACAGAGAGAGAGAGA 59.762 50.000 14.93 0.00 0.00 3.10
887 922 2.874701 GCTAGCACAGAGAGAGAGAGAG 59.125 54.545 10.63 0.00 0.00 3.20
888 923 3.432186 GCTAGCACAGAGAGAGAGAGAGA 60.432 52.174 10.63 0.00 0.00 3.10
889 924 3.272574 AGCACAGAGAGAGAGAGAGAG 57.727 52.381 0.00 0.00 0.00 3.20
890 925 2.840038 AGCACAGAGAGAGAGAGAGAGA 59.160 50.000 0.00 0.00 0.00 3.10
891 926 3.118482 AGCACAGAGAGAGAGAGAGAGAG 60.118 52.174 0.00 0.00 0.00 3.20
1011 1053 4.619140 GCCAAGATGATGCGCGGC 62.619 66.667 8.83 2.32 0.00 6.53
1311 1353 1.218316 GTACAAGGACAGGGAGCGG 59.782 63.158 0.00 0.00 0.00 5.52
1420 1462 1.901948 ATCGAGGAGCGCCGGAATA 60.902 57.895 5.05 0.00 40.61 1.75
1553 1599 1.893808 CATGGATAGCCGGCGCTTT 60.894 57.895 23.20 5.85 45.55 3.51
1591 1642 2.281761 AGTTGACTTGGCTGGCGG 60.282 61.111 0.00 0.00 0.00 6.13
1592 1643 2.594592 GTTGACTTGGCTGGCGGT 60.595 61.111 0.00 0.00 0.00 5.68
1594 1645 3.842925 TTGACTTGGCTGGCGGTCC 62.843 63.158 18.72 0.00 0.00 4.46
1816 1870 3.691498 CCAAGACGACCAAGAAAAACAC 58.309 45.455 0.00 0.00 0.00 3.32
1826 1880 3.243401 CCAAGAAAAACACTACACCTGCC 60.243 47.826 0.00 0.00 0.00 4.85
2101 2155 3.961414 GAGGTTTGGACGGGCCCA 61.961 66.667 24.92 0.00 34.97 5.36
2137 2204 2.875080 GTGTACACGTTCATTGGCTC 57.125 50.000 10.84 0.00 0.00 4.70
2138 2205 1.126113 GTGTACACGTTCATTGGCTCG 59.874 52.381 10.84 0.00 0.00 5.03
2139 2206 0.719465 GTACACGTTCATTGGCTCGG 59.281 55.000 0.00 0.00 0.00 4.63
2140 2207 1.017177 TACACGTTCATTGGCTCGGC 61.017 55.000 0.00 0.00 0.00 5.54
2186 2253 2.872245 CGTCAACTGTCACATTGTTCCT 59.128 45.455 0.00 0.00 0.00 3.36
2189 2256 5.650543 GTCAACTGTCACATTGTTCCTTTT 58.349 37.500 0.00 0.00 0.00 2.27
2191 2258 6.253512 GTCAACTGTCACATTGTTCCTTTTTC 59.746 38.462 0.00 0.00 0.00 2.29
2192 2259 5.262588 ACTGTCACATTGTTCCTTTTTCC 57.737 39.130 0.00 0.00 0.00 3.13
2252 2329 8.684386 TCTCTTTCGAGTGTATATTGATCTCT 57.316 34.615 0.00 0.00 38.45 3.10
2256 2333 9.179552 CTTTCGAGTGTATATTGATCTCTTCAG 57.820 37.037 0.00 0.00 35.27 3.02
2271 2348 7.011105 ATCTCTTCAGAAAAAGGCAACAGCC 62.011 44.000 0.00 0.00 39.48 4.85
2288 2365 1.143684 AGCCCCAGCGATATGATTGTT 59.856 47.619 0.00 0.00 46.67 2.83
2290 2367 2.811873 GCCCCAGCGATATGATTGTTCT 60.812 50.000 0.00 0.00 0.00 3.01
2358 2440 0.107263 TATGCATGCATCGGGTGTGT 60.107 50.000 35.35 13.09 37.82 3.72
2391 2473 2.200373 AGTGGTGGCCTTATGTTGAC 57.800 50.000 3.32 0.00 0.00 3.18
2416 2499 1.319541 TCGGAATTTCCACGGCAAAA 58.680 45.000 15.58 0.00 35.91 2.44
2546 2637 3.338249 ACAAATGCTAGTAGCTGGTGTG 58.662 45.455 22.34 15.10 42.97 3.82
2560 2651 3.743521 CTGGTGTGTTGATTCAAGAGGA 58.256 45.455 0.00 0.00 0.00 3.71
2562 2653 4.136796 TGGTGTGTTGATTCAAGAGGAAG 58.863 43.478 0.00 0.00 39.30 3.46
2564 2655 4.453819 GGTGTGTTGATTCAAGAGGAAGAG 59.546 45.833 0.00 0.00 39.30 2.85
2572 2663 6.346896 TGATTCAAGAGGAAGAGTGATGATG 58.653 40.000 0.00 0.00 39.30 3.07
2573 2664 4.750021 TCAAGAGGAAGAGTGATGATGG 57.250 45.455 0.00 0.00 0.00 3.51
2574 2665 4.356436 TCAAGAGGAAGAGTGATGATGGA 58.644 43.478 0.00 0.00 0.00 3.41
2575 2666 4.405036 TCAAGAGGAAGAGTGATGATGGAG 59.595 45.833 0.00 0.00 0.00 3.86
2576 2667 4.262891 AGAGGAAGAGTGATGATGGAGA 57.737 45.455 0.00 0.00 0.00 3.71
2577 2668 4.818447 AGAGGAAGAGTGATGATGGAGAT 58.182 43.478 0.00 0.00 0.00 2.75
2578 2669 4.834496 AGAGGAAGAGTGATGATGGAGATC 59.166 45.833 0.00 0.00 0.00 2.75
2579 2670 4.554683 AGGAAGAGTGATGATGGAGATCA 58.445 43.478 0.00 0.00 42.92 2.92
2580 2671 4.589798 AGGAAGAGTGATGATGGAGATCAG 59.410 45.833 0.00 0.00 42.01 2.90
2581 2672 4.309099 GAAGAGTGATGATGGAGATCAGC 58.691 47.826 0.00 0.00 44.00 4.26
2700 2791 5.532406 TCTCTTCAAAAGGTTCCATTCACTG 59.468 40.000 0.00 0.00 0.00 3.66
2778 2872 1.203237 TCTTCACCTCTGGCTTCCTCT 60.203 52.381 0.00 0.00 0.00 3.69
2862 2962 4.365514 TCATTAGCTGTTGGGAACTCAA 57.634 40.909 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.625790 GGGTGTTTACAGAAATGTGGCA 59.374 45.455 0.00 0.00 0.00 4.92
68 69 6.263168 CACACCATTGTAAAGTCTTTTCTCCT 59.737 38.462 2.51 0.00 33.30 3.69
276 287 0.633378 TCCTCATCTGCTCCTCCTCA 59.367 55.000 0.00 0.00 0.00 3.86
402 416 0.227234 GTGCGTACGCTTGATCGATG 59.773 55.000 36.99 0.00 42.51 3.84
403 417 1.200474 CGTGCGTACGCTTGATCGAT 61.200 55.000 36.99 0.00 44.11 3.59
404 418 1.866059 CGTGCGTACGCTTGATCGA 60.866 57.895 36.99 15.67 44.11 3.59
405 419 2.608204 CGTGCGTACGCTTGATCG 59.392 61.111 36.99 26.88 44.11 3.69
422 436 4.090057 GAGGTGGCGCGTTTCTGC 62.090 66.667 8.43 0.00 0.00 4.26
505 522 4.047059 CGACGTACGGCTGGGTGT 62.047 66.667 20.72 0.00 38.46 4.16
515 532 1.065701 AGATCAGTGGCATCGACGTAC 59.934 52.381 0.00 0.00 0.00 3.67
516 533 1.065551 CAGATCAGTGGCATCGACGTA 59.934 52.381 0.00 0.00 0.00 3.57
517 534 0.179127 CAGATCAGTGGCATCGACGT 60.179 55.000 0.00 0.00 0.00 4.34
519 536 2.223900 TGATCAGATCAGTGGCATCGAC 60.224 50.000 9.21 0.00 33.59 4.20
520 537 2.034124 TGATCAGATCAGTGGCATCGA 58.966 47.619 9.21 0.00 33.59 3.59
522 539 3.132160 CTGTGATCAGATCAGTGGCATC 58.868 50.000 13.78 0.90 43.76 3.91
523 540 2.158798 CCTGTGATCAGATCAGTGGCAT 60.159 50.000 13.78 0.00 43.76 4.40
524 541 1.208776 CCTGTGATCAGATCAGTGGCA 59.791 52.381 13.78 7.24 43.76 4.92
525 542 1.474677 CCCTGTGATCAGATCAGTGGC 60.475 57.143 13.78 2.71 43.76 5.01
526 543 1.836166 ACCCTGTGATCAGATCAGTGG 59.164 52.381 13.78 16.66 43.76 4.00
529 546 3.900966 TTCACCCTGTGATCAGATCAG 57.099 47.619 13.78 4.69 42.40 2.90
533 550 2.711009 AGGTTTTCACCCTGTGATCAGA 59.289 45.455 0.00 0.00 45.63 3.27
555 573 1.384222 CCTGAAATTACGGCCAGGCC 61.384 60.000 22.33 22.33 46.75 5.19
556 574 2.106844 CCTGAAATTACGGCCAGGC 58.893 57.895 1.26 1.26 39.59 4.85
622 645 1.032114 GTGGGGGCTCTACACAATGC 61.032 60.000 0.00 0.00 35.30 3.56
875 910 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
876 911 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
877 912 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
878 913 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
879 914 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
880 915 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
881 916 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
882 917 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
883 918 3.827008 TGCTCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
884 919 3.244009 CGATGCTCTCTCTCTCTCTCTCT 60.244 52.174 0.00 0.00 0.00 3.10
885 920 3.062763 CGATGCTCTCTCTCTCTCTCTC 58.937 54.545 0.00 0.00 0.00 3.20
886 921 2.224378 CCGATGCTCTCTCTCTCTCTCT 60.224 54.545 0.00 0.00 0.00 3.10
887 922 2.146342 CCGATGCTCTCTCTCTCTCTC 58.854 57.143 0.00 0.00 0.00 3.20
888 923 1.490490 ACCGATGCTCTCTCTCTCTCT 59.510 52.381 0.00 0.00 0.00 3.10
889 924 1.967319 ACCGATGCTCTCTCTCTCTC 58.033 55.000 0.00 0.00 0.00 3.20
890 925 2.810400 GCTACCGATGCTCTCTCTCTCT 60.810 54.545 0.00 0.00 0.00 3.10
891 926 1.535462 GCTACCGATGCTCTCTCTCTC 59.465 57.143 0.00 0.00 0.00 3.20
1011 1053 2.203126 GCGGGCCTCTGATCCTTG 60.203 66.667 0.84 0.00 0.00 3.61
1158 1200 3.309436 CTTGACGCGGATGGTGGGA 62.309 63.158 12.47 0.00 0.00 4.37
1311 1353 3.827752 AGGAAGGCCTTGGAGTCC 58.172 61.111 26.25 18.13 43.90 3.85
1816 1870 3.118454 CCGTTGCGGCAGGTGTAG 61.118 66.667 1.67 0.00 41.17 2.74
1963 2017 0.815734 CAGGTCGAACGTATCCCAGT 59.184 55.000 0.00 0.00 0.00 4.00
2135 2202 2.420890 GAGATGAGGCTGGCCGAG 59.579 66.667 5.93 0.00 41.95 4.63
2136 2203 3.531207 CGAGATGAGGCTGGCCGA 61.531 66.667 5.93 0.00 41.95 5.54
2137 2204 4.598894 CCGAGATGAGGCTGGCCG 62.599 72.222 5.93 0.00 41.95 6.13
2138 2205 3.453070 GACCGAGATGAGGCTGGCC 62.453 68.421 3.00 3.00 0.00 5.36
2139 2206 2.037620 ATGACCGAGATGAGGCTGGC 62.038 60.000 0.00 0.00 0.00 4.85
2140 2207 0.249784 CATGACCGAGATGAGGCTGG 60.250 60.000 0.00 0.00 0.00 4.85
2186 2253 5.075067 AGGAAAGAATGGAGAGAGGGAAAAA 59.925 40.000 0.00 0.00 0.00 1.94
2189 2256 3.808189 AGGAAAGAATGGAGAGAGGGAA 58.192 45.455 0.00 0.00 0.00 3.97
2191 2258 3.118075 GGAAGGAAAGAATGGAGAGAGGG 60.118 52.174 0.00 0.00 0.00 4.30
2192 2259 3.521126 TGGAAGGAAAGAATGGAGAGAGG 59.479 47.826 0.00 0.00 0.00 3.69
2271 2348 3.732212 TGAGAACAATCATATCGCTGGG 58.268 45.455 0.00 0.00 0.00 4.45
2276 2353 4.294232 AGTCGCTGAGAACAATCATATCG 58.706 43.478 0.00 0.00 0.00 2.92
2288 2365 0.537188 GGATTTGGGAGTCGCTGAGA 59.463 55.000 8.82 0.00 0.00 3.27
2290 2367 0.036388 GTGGATTTGGGAGTCGCTGA 60.036 55.000 8.82 0.00 0.00 4.26
2358 2440 2.035704 CCACCACTTATTTGCAGCACAA 59.964 45.455 0.00 0.00 36.13 3.33
2391 2473 1.127951 CCGTGGAAATTCCGAACTTCG 59.872 52.381 7.60 4.07 40.17 3.79
2536 2627 4.318332 CTCTTGAATCAACACACCAGCTA 58.682 43.478 0.00 0.00 0.00 3.32
2537 2628 3.144506 CTCTTGAATCAACACACCAGCT 58.855 45.455 0.00 0.00 0.00 4.24
2538 2629 2.227388 CCTCTTGAATCAACACACCAGC 59.773 50.000 0.00 0.00 0.00 4.85
2546 2637 6.169094 TCATCACTCTTCCTCTTGAATCAAC 58.831 40.000 0.00 0.00 31.06 3.18
2560 2651 3.243805 CGCTGATCTCCATCATCACTCTT 60.244 47.826 0.00 0.00 38.42 2.85
2562 2653 2.609984 CCGCTGATCTCCATCATCACTC 60.610 54.545 0.00 0.00 38.42 3.51
2564 2655 1.607509 CCCGCTGATCTCCATCATCAC 60.608 57.143 0.00 0.00 38.42 3.06
2572 2663 0.689623 ATCAATCCCCGCTGATCTCC 59.310 55.000 0.00 0.00 0.00 3.71
2573 2664 2.557920 AATCAATCCCCGCTGATCTC 57.442 50.000 0.00 0.00 30.97 2.75
2574 2665 4.647564 ATTAATCAATCCCCGCTGATCT 57.352 40.909 0.00 0.00 30.97 2.75
2575 2666 4.616835 GCAATTAATCAATCCCCGCTGATC 60.617 45.833 0.00 0.00 30.97 2.92
2576 2667 3.256631 GCAATTAATCAATCCCCGCTGAT 59.743 43.478 0.00 0.00 33.66 2.90
2577 2668 2.622942 GCAATTAATCAATCCCCGCTGA 59.377 45.455 0.00 0.00 0.00 4.26
2578 2669 2.361757 TGCAATTAATCAATCCCCGCTG 59.638 45.455 0.00 0.00 0.00 5.18
2579 2670 2.624838 CTGCAATTAATCAATCCCCGCT 59.375 45.455 0.00 0.00 0.00 5.52
2580 2671 2.288395 CCTGCAATTAATCAATCCCCGC 60.288 50.000 0.00 0.00 0.00 6.13
2581 2672 2.958355 ACCTGCAATTAATCAATCCCCG 59.042 45.455 0.00 0.00 0.00 5.73
2609 2700 2.079158 CGATTGGTCAATCAGTGCTGT 58.921 47.619 19.68 0.00 45.60 4.40
2778 2872 0.322456 CACCGCATGGAAGAAAGGGA 60.322 55.000 0.00 0.00 39.21 4.20


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

AutoCloner maintained by Alex Coulton.