Multiple sequence alignment - TraesCS3B01G560600

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 TraesCS3B01G560600 chr3B 100.000 2956 0 0 1 2956 794594395 794591440 0.000000e+00 5459
1 TraesCS3B01G560600 chr3B 95.419 2423 68 13 227 2635 794841177 794838784 0.000000e+00 3819
2 TraesCS3B01G560600 chr3B 87.614 985 102 14 1311 2293 794544101 794543135 0.000000e+00 1125
3 TraesCS3B01G560600 chr3B 89.292 551 54 5 706 1256 794544764 794544219 0.000000e+00 686
4 TraesCS3B01G560600 chr3B 93.717 191 12 0 44 234 794841519 794841329 1.340000e-73 287
5 TraesCS3B01G560600 chr3D 94.003 1434 62 9 1223 2636 592576653 592578082 0.000000e+00 2150
6 TraesCS3B01G560600 chr3D 94.253 957 46 8 279 1231 592575242 592576193 0.000000e+00 1454
7 TraesCS3B01G560600 chr3D 86.152 1372 144 23 1242 2604 592608366 592609700 0.000000e+00 1439
8 TraesCS3B01G560600 chr3D 90.520 538 43 5 719 1256 592607784 592608313 0.000000e+00 704
9 TraesCS3B01G560600 chr3D 91.290 310 21 4 2631 2937 592581436 592581742 4.560000e-113 418
10 TraesCS3B01G560600 chr3D 88.584 219 19 6 21 237 592575028 592575242 8.130000e-66 261
11 TraesCS3B01G560600 chr3A 93.440 1433 67 10 1223 2635 724023062 724021637 0.000000e+00 2100
12 TraesCS3B01G560600 chr3A 88.208 1289 125 14 1317 2596 723661413 723660143 0.000000e+00 1513
13 TraesCS3B01G560600 chr3A 89.609 972 50 26 44 1012 724024202 724023279 0.000000e+00 1188
14 TraesCS3B01G560600 chr3A 89.088 559 53 8 698 1256 723662085 723661535 0.000000e+00 688
15 TraesCS3B01G560600 chr3A 91.586 309 21 4 2631 2937 724018250 724017945 3.520000e-114 422


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 TraesCS3B01G560600 chr3B 794591440 794594395 2955 True 5459.000000 5459 100.0000 1 2956 1 chr3B.!!$R1 2955
1 TraesCS3B01G560600 chr3B 794838784 794841519 2735 True 2053.000000 3819 94.5680 44 2635 2 chr3B.!!$R3 2591
2 TraesCS3B01G560600 chr3B 794543135 794544764 1629 True 905.500000 1125 88.4530 706 2293 2 chr3B.!!$R2 1587
3 TraesCS3B01G560600 chr3D 592607784 592609700 1916 False 1071.500000 1439 88.3360 719 2604 2 chr3D.!!$F2 1885
4 TraesCS3B01G560600 chr3D 592575028 592581742 6714 False 1070.750000 2150 92.0325 21 2937 4 chr3D.!!$F1 2916
5 TraesCS3B01G560600 chr3A 724017945 724024202 6257 True 1236.666667 2100 91.5450 44 2937 3 chr3A.!!$R2 2893
6 TraesCS3B01G560600 chr3A 723660143 723662085 1942 True 1100.500000 1513 88.6480 698 2596 2 chr3A.!!$R1 1898

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
247 409 0.319986 TTAGTGGCATGTTGCGTCGA 60.320 50.0 0.0 0.0 46.21 4.20 F
1554 2257 0.668535 GGTGTTTCTGTGGTCAAGGC 59.331 55.0 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 2591 0.698818 AACCCTTGGTGGAGATGGTC 59.301 55.0 0.00 0.0 35.34 4.02 R
2691 6873 0.102300 GTTGCAACAACAGGGGTGAC 59.898 55.0 24.52 0.0 0.00 3.67 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
75 76 9.885934 AAAACAAAAACAAAACCATAACAGAAC 57.114 25.926 0.00 0.00 0.00 3.01
115 116 5.163478 GCAGCAAAATCAGTGAATAGGGAAT 60.163 40.000 0.00 0.00 0.00 3.01
131 132 1.472878 GGAATCAACGAGAAAAGGCCC 59.527 52.381 0.00 0.00 0.00 5.80
132 133 2.159382 GAATCAACGAGAAAAGGCCCA 58.841 47.619 0.00 0.00 0.00 5.36
247 409 0.319986 TTAGTGGCATGTTGCGTCGA 60.320 50.000 0.00 0.00 46.21 4.20
248 410 0.735978 TAGTGGCATGTTGCGTCGAG 60.736 55.000 0.00 0.00 46.21 4.04
249 411 3.422303 TGGCATGTTGCGTCGAGC 61.422 61.111 0.00 0.00 46.21 5.03
389 552 3.428862 GGCACATTTAAAGGTGATTCCCG 60.429 47.826 31.11 8.27 42.86 5.14
456 619 7.048629 TCTGCAATTTATTTTCACAGTTGGA 57.951 32.000 0.00 0.00 0.00 3.53
629 792 2.618709 GCATTATGCTTGGTGACTACCC 59.381 50.000 10.27 0.00 42.59 3.69
1170 1335 3.144657 TGCTGTTCACACCATCATTCT 57.855 42.857 0.00 0.00 0.00 2.40
1304 2007 9.372369 AGTGTAAGTGATCATCTAAAAAGCTAC 57.628 33.333 0.00 0.00 0.00 3.58
1554 2257 0.668535 GGTGTTTCTGTGGTCAAGGC 59.331 55.000 0.00 0.00 0.00 4.35
1555 2258 1.388547 GTGTTTCTGTGGTCAAGGCA 58.611 50.000 0.00 0.00 0.00 4.75
1556 2259 1.956477 GTGTTTCTGTGGTCAAGGCAT 59.044 47.619 0.00 0.00 0.00 4.40
1825 2528 6.462500 AGGATGATGATACAGATTGCAGTAC 58.538 40.000 0.00 0.00 0.00 2.73
1984 2687 9.143631 GAAAGCTGTTATGAATAATTTGCTTGT 57.856 29.630 14.72 9.17 36.29 3.16
2011 2714 9.550406 ACCATAGCAAATGAATTGGAATAAATG 57.450 29.630 0.89 0.00 39.54 2.32
2230 2942 5.190677 TCGATGTATAATAGAGGCGATGGA 58.809 41.667 0.00 0.00 0.00 3.41
2388 3110 6.102663 CCTTGTCCAACACAATTTTTACACA 58.897 36.000 0.00 0.00 44.32 3.72
2407 3129 5.488341 ACACACACAATGGGAAGAGTATAC 58.512 41.667 0.00 0.00 34.14 1.47
2419 3141 8.375493 TGGGAAGAGTATACAACTACAAAGAT 57.625 34.615 5.50 0.00 39.07 2.40
2498 3222 2.541178 CCCACGAGTTCTATGCGTCTAC 60.541 54.545 0.00 0.00 35.90 2.59
2611 3349 5.125900 CACCAAAGTTCAAGATCCATATGCA 59.874 40.000 0.00 0.00 0.00 3.96
2658 6840 6.558394 TGGTCAATCCTGGATCATATCAACTA 59.442 38.462 10.14 0.00 37.07 2.24
2694 6876 8.966069 TGATACATTACCGGATATTTTTGTCA 57.034 30.769 9.46 0.00 0.00 3.58
2696 6878 6.445357 ACATTACCGGATATTTTTGTCACC 57.555 37.500 9.46 0.00 0.00 4.02
2697 6879 5.358725 ACATTACCGGATATTTTTGTCACCC 59.641 40.000 9.46 0.00 0.00 4.61
2700 6882 2.687935 CCGGATATTTTTGTCACCCCTG 59.312 50.000 0.00 0.00 0.00 4.45
2701 6883 3.352648 CGGATATTTTTGTCACCCCTGT 58.647 45.455 0.00 0.00 0.00 4.00
2702 6884 3.761752 CGGATATTTTTGTCACCCCTGTT 59.238 43.478 0.00 0.00 0.00 3.16
2707 6889 0.820871 TTTGTCACCCCTGTTGTTGC 59.179 50.000 0.00 0.00 0.00 4.17
2708 6890 0.323816 TTGTCACCCCTGTTGTTGCA 60.324 50.000 0.00 0.00 0.00 4.08
2710 6892 0.102300 GTCACCCCTGTTGTTGCAAC 59.898 55.000 22.83 22.83 0.00 4.17
2715 6897 0.453793 CCCTGTTGTTGCAACGAACA 59.546 50.000 29.07 29.07 33.96 3.18
2794 6976 5.301551 TGCAAAGTCATCTTACCAACACATT 59.698 36.000 0.00 0.00 33.09 2.71
2809 6991 5.125900 CCAACACATTGATGCCTCTCATTTA 59.874 40.000 0.00 0.00 38.15 1.40
2828 7010 8.836268 TCATTTAAAATCAGCTGCTTGAATTT 57.164 26.923 9.47 6.67 35.16 1.82
2832 7014 9.709495 TTTAAAATCAGCTGCTTGAATTTATGT 57.291 25.926 9.47 0.00 34.29 2.29
2836 7018 4.100529 CAGCTGCTTGAATTTATGTTCGG 58.899 43.478 0.00 0.00 0.00 4.30
2845 7027 6.582677 TGAATTTATGTTCGGTTGGTTCAT 57.417 33.333 0.00 0.00 0.00 2.57
2918 7100 8.919145 TGGGTTCATTTGTTATTAGTTCTTGTT 58.081 29.630 0.00 0.00 0.00 2.83
2937 7119 7.258441 TCTTGTTAGTATGCTAGCAACTACTG 58.742 38.462 29.12 17.85 41.37 2.74
2938 7120 6.769134 TGTTAGTATGCTAGCAACTACTGA 57.231 37.500 29.12 22.55 35.86 3.41
2939 7121 7.348080 TGTTAGTATGCTAGCAACTACTGAT 57.652 36.000 29.12 13.17 35.86 2.90
2940 7122 8.459911 TGTTAGTATGCTAGCAACTACTGATA 57.540 34.615 29.12 21.00 35.86 2.15
2941 7123 8.909923 TGTTAGTATGCTAGCAACTACTGATAA 58.090 33.333 29.12 18.47 35.86 1.75
2942 7124 9.915629 GTTAGTATGCTAGCAACTACTGATAAT 57.084 33.333 29.12 15.35 0.00 1.28
2943 7125 9.914131 TTAGTATGCTAGCAACTACTGATAATG 57.086 33.333 29.12 0.00 0.00 1.90
2944 7126 7.382110 AGTATGCTAGCAACTACTGATAATGG 58.618 38.462 23.84 0.00 0.00 3.16
2945 7127 5.614324 TGCTAGCAACTACTGATAATGGT 57.386 39.130 16.84 0.00 0.00 3.55
2946 7128 5.601662 TGCTAGCAACTACTGATAATGGTC 58.398 41.667 16.84 0.00 0.00 4.02
2947 7129 4.681942 GCTAGCAACTACTGATAATGGTCG 59.318 45.833 10.63 0.00 0.00 4.79
2948 7130 5.507482 GCTAGCAACTACTGATAATGGTCGA 60.507 44.000 10.63 0.00 0.00 4.20
2949 7131 5.339008 AGCAACTACTGATAATGGTCGAA 57.661 39.130 0.00 0.00 0.00 3.71
2950 7132 5.918608 AGCAACTACTGATAATGGTCGAAT 58.081 37.500 0.00 0.00 0.00 3.34
2951 7133 5.755375 AGCAACTACTGATAATGGTCGAATG 59.245 40.000 0.00 0.00 0.00 2.67
2952 7134 5.559035 GCAACTACTGATAATGGTCGAATGC 60.559 44.000 0.00 0.00 0.00 3.56
2953 7135 4.632153 ACTACTGATAATGGTCGAATGCC 58.368 43.478 0.00 0.00 0.00 4.40
2954 7136 3.558931 ACTGATAATGGTCGAATGCCA 57.441 42.857 0.00 0.00 40.68 4.92
2955 7137 3.470709 ACTGATAATGGTCGAATGCCAG 58.529 45.455 0.00 0.00 39.65 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.077674 GGTTTTGTTTTTGTTTTTGTTTTCAGT 57.922 25.926 0.00 0.00 0.00 3.41
40 41 9.076596 TGGTTTTGTTTTTGTTTTTGTTTTCAG 57.923 25.926 0.00 0.00 0.00 3.02
41 42 8.980143 TGGTTTTGTTTTTGTTTTTGTTTTCA 57.020 23.077 0.00 0.00 0.00 2.69
47 48 9.884465 TCTGTTATGGTTTTGTTTTTGTTTTTG 57.116 25.926 0.00 0.00 0.00 2.44
51 52 8.499967 GTGTTCTGTTATGGTTTTGTTTTTGTT 58.500 29.630 0.00 0.00 0.00 2.83
53 54 7.118390 TGGTGTTCTGTTATGGTTTTGTTTTTG 59.882 33.333 0.00 0.00 0.00 2.44
75 76 2.195922 GCTGCAACTTTTCTGTTGGTG 58.804 47.619 9.04 0.00 45.19 4.17
115 116 1.679153 GTTTGGGCCTTTTCTCGTTGA 59.321 47.619 4.53 0.00 0.00 3.18
131 132 1.398960 CGGCTTTTCTCGCTCAGTTTG 60.399 52.381 0.00 0.00 0.00 2.93
132 133 0.868406 CGGCTTTTCTCGCTCAGTTT 59.132 50.000 0.00 0.00 0.00 2.66
247 409 0.107116 AGAGATGGTAGTCCGACGCT 60.107 55.000 0.00 0.00 36.30 5.07
248 410 0.308376 GAGAGATGGTAGTCCGACGC 59.692 60.000 0.00 0.00 36.30 5.19
249 411 1.868498 GAGAGAGATGGTAGTCCGACG 59.132 57.143 0.00 0.00 36.30 5.12
250 412 2.614983 GTGAGAGAGATGGTAGTCCGAC 59.385 54.545 0.00 0.00 36.30 4.79
251 413 2.238898 TGTGAGAGAGATGGTAGTCCGA 59.761 50.000 0.00 0.00 36.30 4.55
252 414 2.356382 GTGTGAGAGAGATGGTAGTCCG 59.644 54.545 0.00 0.00 36.30 4.79
253 415 3.129638 GTGTGTGAGAGAGATGGTAGTCC 59.870 52.174 0.00 0.00 0.00 3.85
254 416 3.759086 TGTGTGTGAGAGAGATGGTAGTC 59.241 47.826 0.00 0.00 0.00 2.59
607 770 3.545703 GGTAGTCACCAAGCATAATGCT 58.454 45.455 0.00 0.00 45.67 3.79
620 783 3.055385 TCACCAAGCATAAGGGTAGTCAC 60.055 47.826 0.00 0.00 32.55 3.67
622 785 3.197983 AGTCACCAAGCATAAGGGTAGTC 59.802 47.826 0.00 0.00 32.55 2.59
623 786 3.182152 AGTCACCAAGCATAAGGGTAGT 58.818 45.455 0.00 0.00 32.55 2.73
626 789 2.238898 GGTAGTCACCAAGCATAAGGGT 59.761 50.000 0.00 0.00 45.04 4.34
935 1100 3.043418 GCTTAGTAAGGGGTGGTATGGA 58.957 50.000 11.84 0.00 0.00 3.41
944 1109 3.134574 TGTGTTGTGCTTAGTAAGGGG 57.865 47.619 11.84 0.00 0.00 4.79
1170 1335 3.323774 ACCTGGATTACTCGATGGGTA 57.676 47.619 0.00 0.00 0.00 3.69
1554 2257 9.559958 CACAATTGTATGATGATGATGATGATG 57.440 33.333 11.53 0.00 0.00 3.07
1555 2258 9.515226 TCACAATTGTATGATGATGATGATGAT 57.485 29.630 11.53 0.00 0.00 2.45
1556 2259 8.911918 TCACAATTGTATGATGATGATGATGA 57.088 30.769 11.53 0.00 0.00 2.92
1657 2360 8.340757 TCCATGGGGTAACTTTTCAATAGTTAT 58.659 33.333 13.02 0.00 39.51 1.89
1697 2400 9.744468 AATGTCCAGTCAAAAATAAGTAAACAC 57.256 29.630 0.00 0.00 0.00 3.32
1825 2528 4.582656 TGTTTCCAGTATTTCCACTTGTGG 59.417 41.667 13.24 13.24 0.00 4.17
1888 2591 0.698818 AACCCTTGGTGGAGATGGTC 59.301 55.000 0.00 0.00 35.34 4.02
2217 2929 5.440610 AGAAAATTTGTCCATCGCCTCTAT 58.559 37.500 0.00 0.00 0.00 1.98
2388 3110 6.374417 AGTTGTATACTCTTCCCATTGTGT 57.626 37.500 4.17 0.00 28.23 3.72
2407 3129 3.926616 ACCGTCTCCATCTTTGTAGTTG 58.073 45.455 0.00 0.00 0.00 3.16
2419 3141 2.297698 TTTGTCTCCTACCGTCTCCA 57.702 50.000 0.00 0.00 0.00 3.86
2498 3222 6.592798 AAAATTGCAGACAATGTTCAAGTG 57.407 33.333 0.00 0.00 45.90 3.16
2611 3349 4.746115 CAGTTTGTGTAGCATGCAATTTGT 59.254 37.500 21.98 0.00 27.52 2.83
2676 6858 4.018233 AGGGGTGACAAAAATATCCGGTAA 60.018 41.667 0.00 0.00 0.00 2.85
2681 6863 4.526650 ACAACAGGGGTGACAAAAATATCC 59.473 41.667 0.00 0.00 0.00 2.59
2685 6867 3.681313 GCAACAACAGGGGTGACAAAAAT 60.681 43.478 0.00 0.00 0.00 1.82
2691 6873 0.102300 GTTGCAACAACAGGGGTGAC 59.898 55.000 24.52 0.00 0.00 3.67
2694 6876 0.681564 TTCGTTGCAACAACAGGGGT 60.682 50.000 28.01 0.00 0.00 4.95
2696 6878 0.453793 TGTTCGTTGCAACAACAGGG 59.546 50.000 28.22 15.21 33.21 4.45
2697 6879 1.826327 CTGTTCGTTGCAACAACAGG 58.174 50.000 36.16 27.03 40.38 4.00
2700 6882 0.179150 TGCCTGTTCGTTGCAACAAC 60.179 50.000 28.01 26.33 35.83 3.32
2701 6883 0.743688 ATGCCTGTTCGTTGCAACAA 59.256 45.000 28.01 17.96 38.69 2.83
2702 6884 1.598882 TATGCCTGTTCGTTGCAACA 58.401 45.000 28.01 13.24 38.69 3.33
2745 6927 5.590259 AGCATTGACCAATATAGTGTGTTCC 59.410 40.000 0.00 0.00 0.00 3.62
2794 6976 5.889853 AGCTGATTTTAAATGAGAGGCATCA 59.110 36.000 8.27 0.00 35.78 3.07
2809 6991 7.062605 CGAACATAAATTCAAGCAGCTGATTTT 59.937 33.333 20.43 11.27 34.75 1.82
2828 7010 6.228616 TCAGATATGAACCAACCGAACATA 57.771 37.500 0.00 0.00 0.00 2.29
2832 7014 8.746052 AAATATTCAGATATGAACCAACCGAA 57.254 30.769 4.61 0.00 0.00 4.30
2836 7018 9.736023 GGTGAAAATATTCAGATATGAACCAAC 57.264 33.333 4.61 0.00 45.88 3.77
2845 7027 8.494433 ACCTGCTTAGGTGAAAATATTCAGATA 58.506 33.333 0.00 0.00 45.88 1.98
2918 7100 8.523658 CCATTATCAGTAGTTGCTAGCATACTA 58.476 37.037 23.94 23.96 0.00 1.82
2924 7106 4.681942 CGACCATTATCAGTAGTTGCTAGC 59.318 45.833 8.10 8.10 0.00 3.42
2925 7107 6.073327 TCGACCATTATCAGTAGTTGCTAG 57.927 41.667 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.