Multiple sequence alignment - TraesCS7A01G034400

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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 TraesCS7A01G034400 chr7A 100.000 4617 0 0 556 5172 15035480 15040096 0.000000e+00 8527.0
1 TraesCS7A01G034400 chr7A 100.000 231 0 0 1 231 15034925 15035155 1.330000e-115 427.0
2 TraesCS7A01G034400 chr7A 75.314 636 135 17 1062 1680 716233138 716233768 8.480000e-73 285.0
3 TraesCS7A01G034400 chr7A 71.207 1160 281 42 2723 3854 19019286 19018152 5.170000e-60 243.0
4 TraesCS7A01G034400 chr7D 95.850 4458 115 23 734 5172 16219886 16224292 0.000000e+00 7143.0
5 TraesCS7A01G034400 chr7D 97.653 213 5 0 1 213 16219251 16219463 2.940000e-97 366.0
6 TraesCS7A01G034400 chr7D 73.022 834 176 36 2722 3534 20262467 20261662 1.110000e-61 248.0
7 TraesCS7A01G034400 chr7D 91.617 167 14 0 2347 2513 26459441 26459607 1.120000e-56 231.0
8 TraesCS7A01G034400 chr7D 95.833 144 3 1 556 696 16219750 16219893 4.030000e-56 230.0
9 TraesCS7A01G034400 chr7D 100.000 50 0 0 5117 5166 26459700 26459749 5.510000e-15 93.5
10 TraesCS7A01G034400 chr4A 95.360 4332 161 8 863 5172 718855044 718859357 0.000000e+00 6850.0
11 TraesCS7A01G034400 chr4A 79.956 1811 312 33 3018 4802 714339552 714341337 0.000000e+00 1286.0
12 TraesCS7A01G034400 chr4A 79.247 930 148 29 963 1872 714330249 714331153 1.590000e-169 606.0
13 TraesCS7A01G034400 chr4A 97.059 34 1 0 3949 3982 718852330 718852297 2.010000e-04 58.4
14 TraesCS7A01G034400 chr3D 96.298 2080 63 3 3094 5172 585379338 585377272 0.000000e+00 3402.0
15 TraesCS7A01G034400 chr3D 81.154 1231 209 20 3590 4802 23615676 23616901 0.000000e+00 966.0
16 TraesCS7A01G034400 chr3D 80.308 843 146 14 2700 3526 23614822 23615660 2.050000e-173 619.0
17 TraesCS7A01G034400 chr3D 78.303 931 154 31 963 1872 23612419 23613322 1.630000e-154 556.0
18 TraesCS7A01G034400 chr3A 88.919 1092 115 6 2677 3765 7498607 7497519 0.000000e+00 1341.0
19 TraesCS7A01G034400 chr3A 84.551 1081 153 8 3758 4826 7487592 7486514 0.000000e+00 1059.0
20 TraesCS7A01G034400 chr3A 87.686 471 50 5 951 1413 7500154 7499684 4.560000e-150 542.0
21 TraesCS7A01G034400 chr3A 98.361 61 1 0 698 758 735655385 735655325 1.970000e-19 108.0
22 TraesCS7A01G034400 chr7B 76.471 799 156 24 1000 1785 740995114 740994335 6.240000e-109 405.0
23 TraesCS7A01G034400 chr7B 75.900 639 123 23 1062 1680 719097422 719096795 1.090000e-76 298.0
24 TraesCS7A01G034400 chr7B 74.026 770 163 26 1033 1785 717167611 717166862 3.940000e-71 279.0
25 TraesCS7A01G034400 chr7B 80.645 155 26 4 2719 2871 717154752 717154600 3.270000e-22 117.0
26 TraesCS7A01G034400 chr7B 80.645 155 26 4 2719 2871 717230224 717230072 3.270000e-22 117.0
27 TraesCS7A01G034400 chr7B 89.888 89 7 2 672 758 539323481 539323393 4.230000e-21 113.0
28 TraesCS7A01G034400 chr7B 87.755 98 8 2 670 767 409921305 409921398 1.520000e-20 111.0
29 TraesCS7A01G034400 chr6D 73.024 1227 272 48 2727 3931 440644823 440646012 1.360000e-100 377.0
30 TraesCS7A01G034400 chr5D 73.070 1166 253 49 2726 3856 35963030 35961891 1.770000e-94 357.0
31 TraesCS7A01G034400 chr2B 72.422 1222 286 44 2722 3913 778469051 778467851 4.960000e-90 342.0
32 TraesCS7A01G034400 chr2B 93.506 77 3 2 698 772 710270962 710271038 4.230000e-21 113.0
33 TraesCS7A01G034400 chr2A 74.123 827 192 18 2722 3531 778586802 778587623 6.460000e-84 322.0
34 TraesCS7A01G034400 chr5B 72.685 1069 250 34 2809 3856 26875581 26874534 8.360000e-83 318.0
35 TraesCS7A01G034400 chr5B 95.775 71 2 1 698 768 456281551 456281620 4.230000e-21 113.0
36 TraesCS7A01G034400 chrUn 72.147 1174 267 46 2722 3856 23407667 23408819 5.030000e-80 309.0
37 TraesCS7A01G034400 chr1B 89.011 91 6 1 667 757 9694711 9694797 5.480000e-20 110.0
38 TraesCS7A01G034400 chr1B 88.764 89 9 1 673 761 15235319 15235406 1.970000e-19 108.0
39 TraesCS7A01G034400 chr4B 89.535 86 6 1 673 758 41535814 41535732 7.080000e-19 106.0
40 TraesCS7A01G034400 chr6B 87.778 90 7 1 672 761 199745285 199745200 9.160000e-18 102.0


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 TraesCS7A01G034400 chr7A 15034925 15040096 5171 False 4477.000000 8527 100.000000 1 5172 2 chr7A.!!$F2 5171
1 TraesCS7A01G034400 chr7A 716233138 716233768 630 False 285.000000 285 75.314000 1062 1680 1 chr7A.!!$F1 618
2 TraesCS7A01G034400 chr7A 19018152 19019286 1134 True 243.000000 243 71.207000 2723 3854 1 chr7A.!!$R1 1131
3 TraesCS7A01G034400 chr7D 16219251 16224292 5041 False 2579.666667 7143 96.445333 1 5172 3 chr7D.!!$F1 5171
4 TraesCS7A01G034400 chr7D 20261662 20262467 805 True 248.000000 248 73.022000 2722 3534 1 chr7D.!!$R1 812
5 TraesCS7A01G034400 chr4A 718855044 718859357 4313 False 6850.000000 6850 95.360000 863 5172 1 chr4A.!!$F3 4309
6 TraesCS7A01G034400 chr4A 714339552 714341337 1785 False 1286.000000 1286 79.956000 3018 4802 1 chr4A.!!$F2 1784
7 TraesCS7A01G034400 chr4A 714330249 714331153 904 False 606.000000 606 79.247000 963 1872 1 chr4A.!!$F1 909
8 TraesCS7A01G034400 chr3D 585377272 585379338 2066 True 3402.000000 3402 96.298000 3094 5172 1 chr3D.!!$R1 2078
9 TraesCS7A01G034400 chr3D 23612419 23616901 4482 False 713.666667 966 79.921667 963 4802 3 chr3D.!!$F1 3839
10 TraesCS7A01G034400 chr3A 7486514 7487592 1078 True 1059.000000 1059 84.551000 3758 4826 1 chr3A.!!$R1 1068
11 TraesCS7A01G034400 chr3A 7497519 7500154 2635 True 941.500000 1341 88.302500 951 3765 2 chr3A.!!$R3 2814
12 TraesCS7A01G034400 chr7B 740994335 740995114 779 True 405.000000 405 76.471000 1000 1785 1 chr7B.!!$R6 785
13 TraesCS7A01G034400 chr7B 719096795 719097422 627 True 298.000000 298 75.900000 1062 1680 1 chr7B.!!$R5 618
14 TraesCS7A01G034400 chr7B 717166862 717167611 749 True 279.000000 279 74.026000 1033 1785 1 chr7B.!!$R3 752
15 TraesCS7A01G034400 chr6D 440644823 440646012 1189 False 377.000000 377 73.024000 2727 3931 1 chr6D.!!$F1 1204
16 TraesCS7A01G034400 chr5D 35961891 35963030 1139 True 357.000000 357 73.070000 2726 3856 1 chr5D.!!$R1 1130
17 TraesCS7A01G034400 chr2B 778467851 778469051 1200 True 342.000000 342 72.422000 2722 3913 1 chr2B.!!$R1 1191
18 TraesCS7A01G034400 chr2A 778586802 778587623 821 False 322.000000 322 74.123000 2722 3531 1 chr2A.!!$F1 809
19 TraesCS7A01G034400 chr5B 26874534 26875581 1047 True 318.000000 318 72.685000 2809 3856 1 chr5B.!!$R1 1047
20 TraesCS7A01G034400 chrUn 23407667 23408819 1152 False 309.000000 309 72.147000 2722 3856 1 chrUn.!!$F1 1134

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
699 703 0.099791 CGGGCCGAAAATATTTGCGT 59.900 50.000 24.41 0.0 37.51 5.24 F
1836 1886 1.064946 GGATGTCGAGGAGCTGACG 59.935 63.158 0.00 0.0 37.94 4.35 F
2524 3825 1.068055 CATCTTTGCAGACCAGTTGCC 60.068 52.381 0.00 0.0 40.81 4.52 F
2525 3826 1.165907 TCTTTGCAGACCAGTTGCCG 61.166 55.000 0.00 0.0 40.81 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2307 0.537188 CGGTGAGGATGTAGCCAGTT 59.463 55.000 0.00 0.00 0.00 3.16 R
3313 4642 0.610174 TGAAGTAGGCCTCTGCAGTG 59.390 55.000 9.68 11.58 40.13 3.66 R
3694 5047 3.474798 TCCAGATCAAGTACCCTCAGT 57.525 47.619 0.00 0.00 0.00 3.41 R
4370 5735 3.866816 AGATGCTATTCAGGATGGGAGA 58.133 45.455 0.00 0.00 32.14 3.71 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
78 79 5.880332 GCACAGACCTAAAGGATTTGATACA 59.120 40.000 2.23 0.00 39.63 2.29
88 89 6.894339 AAGGATTTGATACACTTCCGTTTT 57.106 33.333 0.00 0.00 0.00 2.43
136 137 1.018148 CCGTTTTATATGCACGCCCA 58.982 50.000 0.00 0.00 32.43 5.36
158 159 1.804151 CGTCATTTGGGGTATATGCCG 59.196 52.381 3.53 0.00 0.00 5.69
179 180 3.930848 CGTCATAGTGGTTAAAGTGGACC 59.069 47.826 0.00 0.00 36.45 4.46
219 220 9.556030 AAGAAAATCGCAAGTTATAAACTAAGC 57.444 29.630 6.94 6.94 41.91 3.09
220 221 8.726988 AGAAAATCGCAAGTTATAAACTAAGCA 58.273 29.630 13.86 5.51 41.91 3.91
221 222 9.337091 GAAAATCGCAAGTTATAAACTAAGCAA 57.663 29.630 13.86 1.05 41.91 3.91
222 223 8.669394 AAATCGCAAGTTATAAACTAAGCAAC 57.331 30.769 13.86 0.00 41.91 4.17
223 224 6.788684 TCGCAAGTTATAAACTAAGCAACA 57.211 33.333 13.86 0.33 41.91 3.33
224 225 6.595794 TCGCAAGTTATAAACTAAGCAACAC 58.404 36.000 13.86 0.00 41.91 3.32
225 226 5.793457 CGCAAGTTATAAACTAAGCAACACC 59.207 40.000 13.86 0.00 41.91 4.16
226 227 6.348213 CGCAAGTTATAAACTAAGCAACACCT 60.348 38.462 13.86 0.00 41.91 4.00
227 228 7.368059 GCAAGTTATAAACTAAGCAACACCTT 58.632 34.615 10.48 0.00 41.91 3.50
228 229 7.326063 GCAAGTTATAAACTAAGCAACACCTTG 59.674 37.037 10.48 0.00 41.91 3.61
229 230 8.564574 CAAGTTATAAACTAAGCAACACCTTGA 58.435 33.333 0.00 0.00 41.91 3.02
230 231 8.685838 AGTTATAAACTAAGCAACACCTTGAA 57.314 30.769 0.00 0.00 40.69 2.69
666 667 8.921670 CCGGGAGTTAAAATTTTGATGTTTAAG 58.078 33.333 13.76 0.00 29.73 1.85
681 685 8.112016 TGATGTTTAAGAGATATACTCCCTCG 57.888 38.462 0.00 0.00 45.96 4.63
696 700 1.336755 CCCTCGGGCCGAAAATATTTG 59.663 52.381 30.59 15.08 34.74 2.32
699 703 0.099791 CGGGCCGAAAATATTTGCGT 59.900 50.000 24.41 0.00 37.51 5.24
700 704 1.835121 GGGCCGAAAATATTTGCGTC 58.165 50.000 23.69 13.72 37.51 5.19
701 705 1.404035 GGGCCGAAAATATTTGCGTCT 59.596 47.619 23.69 0.00 37.51 4.18
702 706 2.614983 GGGCCGAAAATATTTGCGTCTA 59.385 45.455 23.69 0.00 37.51 2.59
703 707 3.303791 GGGCCGAAAATATTTGCGTCTAG 60.304 47.826 23.69 11.77 37.51 2.43
704 708 3.558418 GGCCGAAAATATTTGCGTCTAGA 59.442 43.478 23.69 0.00 37.51 2.43
705 709 4.213482 GGCCGAAAATATTTGCGTCTAGAT 59.787 41.667 23.69 0.00 37.51 1.98
706 710 5.407387 GGCCGAAAATATTTGCGTCTAGATA 59.593 40.000 23.69 0.00 37.51 1.98
707 711 6.297353 GCCGAAAATATTTGCGTCTAGATAC 58.703 40.000 23.69 3.11 37.51 2.24
708 712 6.073980 GCCGAAAATATTTGCGTCTAGATACA 60.074 38.462 23.69 0.00 37.51 2.29
709 713 7.360101 GCCGAAAATATTTGCGTCTAGATACAT 60.360 37.037 23.69 0.00 37.51 2.29
710 714 8.162880 CCGAAAATATTTGCGTCTAGATACATC 58.837 37.037 23.69 2.96 37.51 3.06
711 715 8.162880 CGAAAATATTTGCGTCTAGATACATCC 58.837 37.037 18.77 0.00 34.53 3.51
712 716 9.209175 GAAAATATTTGCGTCTAGATACATCCT 57.791 33.333 0.39 0.00 0.00 3.24
713 717 8.764524 AAATATTTGCGTCTAGATACATCCTC 57.235 34.615 0.00 0.00 0.00 3.71
714 718 7.710676 ATATTTGCGTCTAGATACATCCTCT 57.289 36.000 0.00 0.00 0.00 3.69
715 719 5.854010 TTTGCGTCTAGATACATCCTCTT 57.146 39.130 0.00 0.00 0.00 2.85
716 720 5.854010 TTGCGTCTAGATACATCCTCTTT 57.146 39.130 0.00 0.00 0.00 2.52
717 721 5.854010 TGCGTCTAGATACATCCTCTTTT 57.146 39.130 0.00 0.00 0.00 2.27
718 722 6.954487 TGCGTCTAGATACATCCTCTTTTA 57.046 37.500 0.00 0.00 0.00 1.52
719 723 7.526142 TGCGTCTAGATACATCCTCTTTTAT 57.474 36.000 0.00 0.00 0.00 1.40
720 724 7.594714 TGCGTCTAGATACATCCTCTTTTATC 58.405 38.462 0.00 0.00 0.00 1.75
721 725 7.030768 GCGTCTAGATACATCCTCTTTTATCC 58.969 42.308 0.00 0.00 0.00 2.59
722 726 7.309255 GCGTCTAGATACATCCTCTTTTATCCA 60.309 40.741 0.00 0.00 0.00 3.41
723 727 8.744652 CGTCTAGATACATCCTCTTTTATCCAT 58.255 37.037 0.00 0.00 0.00 3.41
731 735 8.827832 ACATCCTCTTTTATCCATTTTGATGA 57.172 30.769 0.00 0.00 32.39 2.92
732 736 8.689972 ACATCCTCTTTTATCCATTTTGATGAC 58.310 33.333 0.00 0.00 32.39 3.06
733 737 8.689061 CATCCTCTTTTATCCATTTTGATGACA 58.311 33.333 0.00 0.00 0.00 3.58
734 738 8.648698 TCCTCTTTTATCCATTTTGATGACAA 57.351 30.769 0.00 0.00 0.00 3.18
735 739 8.742777 TCCTCTTTTATCCATTTTGATGACAAG 58.257 33.333 0.00 0.00 37.32 3.16
736 740 8.526147 CCTCTTTTATCCATTTTGATGACAAGT 58.474 33.333 0.00 0.00 37.32 3.16
743 747 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
744 748 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
745 749 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
746 750 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
804 808 7.068839 GGTCTGGAGAGAGAGTATGTAATTGAA 59.931 40.741 0.00 0.00 0.00 2.69
826 830 1.371595 TTTTATGGCCGGCGAGTAAC 58.628 50.000 22.54 5.65 0.00 2.50
829 833 1.605971 TATGGCCGGCGAGTAACACA 61.606 55.000 22.54 10.56 0.00 3.72
844 848 2.936919 ACACAAGGATGCAGACTGAA 57.063 45.000 6.65 0.00 0.00 3.02
850 854 3.098774 AGGATGCAGACTGAAGAGAGA 57.901 47.619 6.65 0.00 0.00 3.10
851 855 3.025978 AGGATGCAGACTGAAGAGAGAG 58.974 50.000 6.65 0.00 0.00 3.20
852 856 2.760092 GGATGCAGACTGAAGAGAGAGT 59.240 50.000 6.65 0.00 0.00 3.24
853 857 3.181487 GGATGCAGACTGAAGAGAGAGTC 60.181 52.174 6.65 0.00 39.18 3.36
991 1002 2.040178 ACATAGTAGCGGAAAGGGAGG 58.960 52.381 0.00 0.00 0.00 4.30
1125 1139 3.803082 CTGGCCACCATGAACGCG 61.803 66.667 0.00 3.53 30.82 6.01
1266 1283 3.296709 AATCAAGCGCCGTCCGAGT 62.297 57.895 2.29 0.00 40.02 4.18
1567 1617 4.350816 TGGAGAAGGAAAAGGATGACAAGA 59.649 41.667 0.00 0.00 0.00 3.02
1682 1732 2.022129 CGCAAGTGTCCGTGTCTCC 61.022 63.158 0.00 0.00 0.00 3.71
1824 1874 5.066505 GGGTAACATTGACAGAATGGATGTC 59.933 44.000 0.00 0.00 42.83 3.06
1836 1886 1.064946 GGATGTCGAGGAGCTGACG 59.935 63.158 0.00 0.00 37.94 4.35
2038 2186 6.775142 TCTTGATCTAAGTAGGATGACTGAGG 59.225 42.308 0.00 0.00 37.65 3.86
2090 2238 6.957920 TTCTGATGGTTTGTGAATTCAGAA 57.042 33.333 13.63 13.63 43.91 3.02
2155 2303 4.374843 GCACTGGCATCAACAATATCAA 57.625 40.909 0.00 0.00 40.72 2.57
2156 2304 4.746729 GCACTGGCATCAACAATATCAAA 58.253 39.130 0.00 0.00 40.72 2.69
2157 2305 5.353938 GCACTGGCATCAACAATATCAAAT 58.646 37.500 0.00 0.00 40.72 2.32
2158 2306 6.506147 GCACTGGCATCAACAATATCAAATA 58.494 36.000 0.00 0.00 40.72 1.40
2159 2307 6.979817 GCACTGGCATCAACAATATCAAATAA 59.020 34.615 0.00 0.00 40.72 1.40
2160 2308 7.492020 GCACTGGCATCAACAATATCAAATAAA 59.508 33.333 0.00 0.00 40.72 1.40
2161 2309 8.810427 CACTGGCATCAACAATATCAAATAAAC 58.190 33.333 0.00 0.00 0.00 2.01
2162 2310 8.752187 ACTGGCATCAACAATATCAAATAAACT 58.248 29.630 0.00 0.00 0.00 2.66
2163 2311 8.929827 TGGCATCAACAATATCAAATAAACTG 57.070 30.769 0.00 0.00 0.00 3.16
2264 2412 9.802039 AAGGTTTGACCAAGTTACAGAATAATA 57.198 29.630 0.00 0.00 41.95 0.98
2285 2531 6.964807 ATACCAGCATCAGCAATATCAAAA 57.035 33.333 0.00 0.00 45.49 2.44
2287 2533 5.657474 ACCAGCATCAGCAATATCAAAAAG 58.343 37.500 0.00 0.00 45.49 2.27
2299 2545 9.998106 AGCAATATCAAAAAGATACGGTATACT 57.002 29.630 0.00 0.00 41.81 2.12
2523 3824 2.342910 CATCTTTGCAGACCAGTTGC 57.657 50.000 0.00 0.00 41.86 4.17
2524 3825 1.068055 CATCTTTGCAGACCAGTTGCC 60.068 52.381 0.00 0.00 40.81 4.52
2525 3826 1.165907 TCTTTGCAGACCAGTTGCCG 61.166 55.000 0.00 0.00 40.81 5.69
2526 3827 2.737932 CTTTGCAGACCAGTTGCCGC 62.738 60.000 0.00 0.00 40.81 6.53
2527 3828 3.772853 TTGCAGACCAGTTGCCGCT 62.773 57.895 0.00 0.00 40.81 5.52
2528 3829 3.730761 GCAGACCAGTTGCCGCTG 61.731 66.667 0.00 0.00 35.54 5.18
2617 3918 7.776618 TCAGAGAAAACTCTCACCACTAATA 57.223 36.000 5.03 0.00 39.12 0.98
2790 4091 4.521256 GTGGGCTACAATACACTCCAAAAA 59.479 41.667 0.00 0.00 0.00 1.94
2800 4101 4.551702 ACACTCCAAAAAGCCAAAAACT 57.448 36.364 0.00 0.00 0.00 2.66
2937 4247 5.359194 AAGAAGTTGTTTGTGAGGAGAGA 57.641 39.130 0.00 0.00 0.00 3.10
3313 4642 1.763968 GGGGGCTTACTTTGATGGAC 58.236 55.000 0.00 0.00 0.00 4.02
3694 5047 7.663827 TCGATCAACTAGGAAAGTTCAAACTA 58.336 34.615 0.00 0.00 45.64 2.24
3823 5176 4.033009 TCAGTCTCATGCCTCCAGAAATA 58.967 43.478 0.00 0.00 0.00 1.40
3994 5347 2.067766 TCAAAAATGAAGGCATTGCGC 58.932 42.857 0.00 0.00 43.71 6.09
4002 5355 4.166011 GGCATTGCGCGAGGTGAC 62.166 66.667 12.10 1.96 43.84 3.67
4169 5528 1.079819 CTTCGGTGGCTCGATGTGT 60.080 57.895 4.59 0.00 39.03 3.72
4370 5735 5.061721 ACCATTTGAGGTCCTTTGTAAGT 57.938 39.130 0.00 0.00 37.28 2.24
4532 5897 3.903714 TGAGGAAGACTCCATGACAAAGA 59.096 43.478 0.00 0.00 46.01 2.52
4701 6076 2.745884 CGCGGCAGGTCCAATCAA 60.746 61.111 0.00 0.00 34.01 2.57
4719 6094 6.707161 CCAATCAATTTCCATTCACAGTTGTT 59.293 34.615 0.00 0.00 0.00 2.83
4767 6145 0.376852 TGTTCTTTGTGCACGTGAGC 59.623 50.000 22.23 11.33 0.00 4.26
4769 6147 1.864711 GTTCTTTGTGCACGTGAGCTA 59.135 47.619 22.23 4.75 34.99 3.32
4816 6197 6.472163 CGTTTTTGTTATCTTTGTCAAGCTGT 59.528 34.615 0.00 0.00 0.00 4.40
4817 6198 7.009174 CGTTTTTGTTATCTTTGTCAAGCTGTT 59.991 33.333 0.00 0.00 0.00 3.16
4818 6199 7.754069 TTTTGTTATCTTTGTCAAGCTGTTG 57.246 32.000 0.00 0.00 34.67 3.33
4924 6318 4.674101 CGTTGTTTCTGAATGTGGTGTTGT 60.674 41.667 0.00 0.00 0.00 3.32
5011 6405 2.374184 TGTAGCAAGTTTTGTGTGCCT 58.626 42.857 0.00 0.00 39.13 4.75
5029 6423 7.013942 TGTGTGCCTTAGTATACATTCGAGTAT 59.986 37.037 5.50 3.20 38.24 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 3.686016 GGCATATACCCCAAATGACGAT 58.314 45.455 0.00 0.00 0.00 3.73
158 159 3.930848 CGGTCCACTTTAACCACTATGAC 59.069 47.826 0.00 0.00 35.13 3.06
179 180 6.171006 GCGATTTTCTTAAACAATCAATGCG 58.829 36.000 0.00 0.00 0.00 4.73
666 667 1.476477 GGCCCGAGGGAGTATATCTC 58.524 60.000 13.28 0.00 42.07 2.75
681 685 1.404035 AGACGCAAATATTTTCGGCCC 59.596 47.619 20.26 10.71 35.40 5.80
696 700 7.030768 GGATAAAAGAGGATGTATCTAGACGC 58.969 42.308 0.00 0.00 0.00 5.19
705 709 9.919416 TCATCAAAATGGATAAAAGAGGATGTA 57.081 29.630 0.00 0.00 33.42 2.29
706 710 8.689972 GTCATCAAAATGGATAAAAGAGGATGT 58.310 33.333 0.00 0.00 33.42 3.06
707 711 8.689061 TGTCATCAAAATGGATAAAAGAGGATG 58.311 33.333 0.00 0.00 33.42 3.51
708 712 8.827832 TGTCATCAAAATGGATAAAAGAGGAT 57.172 30.769 0.00 0.00 33.42 3.24
709 713 8.648698 TTGTCATCAAAATGGATAAAAGAGGA 57.351 30.769 0.00 0.00 33.42 3.71
710 714 8.526147 ACTTGTCATCAAAATGGATAAAAGAGG 58.474 33.333 0.00 0.00 33.42 3.69
717 721 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
718 722 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
719 723 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
720 724 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
721 725 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
722 726 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
723 727 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
724 728 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
725 729 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
726 730 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
727 731 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
728 732 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
729 733 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
730 734 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
731 735 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
732 736 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
733 737 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
734 738 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
735 739 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
736 740 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
737 741 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
738 742 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
739 743 0.466922 GATACTCCCTCCGTCCGGAA 60.467 60.000 5.23 0.00 44.66 4.30
740 744 1.150081 GATACTCCCTCCGTCCGGA 59.850 63.158 0.00 0.00 42.90 5.14
741 745 1.150992 AGATACTCCCTCCGTCCGG 59.849 63.158 0.00 0.00 0.00 5.14
742 746 0.179026 TCAGATACTCCCTCCGTCCG 60.179 60.000 0.00 0.00 0.00 4.79
743 747 2.068834 TTCAGATACTCCCTCCGTCC 57.931 55.000 0.00 0.00 0.00 4.79
744 748 3.637229 TGATTTCAGATACTCCCTCCGTC 59.363 47.826 0.00 0.00 0.00 4.79
745 749 3.643237 TGATTTCAGATACTCCCTCCGT 58.357 45.455 0.00 0.00 0.00 4.69
746 750 4.881019 ATGATTTCAGATACTCCCTCCG 57.119 45.455 0.00 0.00 0.00 4.63
804 808 1.470051 ACTCGCCGGCCATAAAAATT 58.530 45.000 23.46 0.00 0.00 1.82
826 830 3.001414 CTCTTCAGTCTGCATCCTTGTG 58.999 50.000 0.00 0.00 0.00 3.33
829 833 3.439154 TCTCTCTTCAGTCTGCATCCTT 58.561 45.455 0.00 0.00 0.00 3.36
991 1002 1.092345 GTGCGCTCCATTCTTCCTCC 61.092 60.000 9.73 0.00 0.00 4.30
1125 1139 2.512515 GACTGCATGCGGAGGACC 60.513 66.667 32.80 11.80 34.24 4.46
1836 1886 1.905922 GCTGTTCCTTGAGCGTGCTC 61.906 60.000 14.81 14.81 43.01 4.26
2069 2217 5.049474 TCGTTCTGAATTCACAAACCATCAG 60.049 40.000 17.29 0.00 36.50 2.90
2090 2238 2.101249 TCGTGGGTTTGTTAGTTCTCGT 59.899 45.455 0.00 0.00 0.00 4.18
2146 2294 8.850156 GGATGTAGCCAGTTTATTTGATATTGT 58.150 33.333 0.00 0.00 0.00 2.71
2147 2295 9.071276 AGGATGTAGCCAGTTTATTTGATATTG 57.929 33.333 0.00 0.00 0.00 1.90
2148 2296 9.289782 GAGGATGTAGCCAGTTTATTTGATATT 57.710 33.333 0.00 0.00 0.00 1.28
2149 2297 8.439971 TGAGGATGTAGCCAGTTTATTTGATAT 58.560 33.333 0.00 0.00 0.00 1.63
2150 2298 7.715249 GTGAGGATGTAGCCAGTTTATTTGATA 59.285 37.037 0.00 0.00 0.00 2.15
2151 2299 6.543831 GTGAGGATGTAGCCAGTTTATTTGAT 59.456 38.462 0.00 0.00 0.00 2.57
2152 2300 5.880332 GTGAGGATGTAGCCAGTTTATTTGA 59.120 40.000 0.00 0.00 0.00 2.69
2153 2301 5.066505 GGTGAGGATGTAGCCAGTTTATTTG 59.933 44.000 0.00 0.00 0.00 2.32
2154 2302 5.193679 GGTGAGGATGTAGCCAGTTTATTT 58.806 41.667 0.00 0.00 0.00 1.40
2155 2303 4.683400 CGGTGAGGATGTAGCCAGTTTATT 60.683 45.833 0.00 0.00 0.00 1.40
2156 2304 3.181465 CGGTGAGGATGTAGCCAGTTTAT 60.181 47.826 0.00 0.00 0.00 1.40
2157 2305 2.167693 CGGTGAGGATGTAGCCAGTTTA 59.832 50.000 0.00 0.00 0.00 2.01
2158 2306 1.066143 CGGTGAGGATGTAGCCAGTTT 60.066 52.381 0.00 0.00 0.00 2.66
2159 2307 0.537188 CGGTGAGGATGTAGCCAGTT 59.463 55.000 0.00 0.00 0.00 3.16
2160 2308 1.330655 CCGGTGAGGATGTAGCCAGT 61.331 60.000 0.00 0.00 45.00 4.00
2161 2309 1.330655 ACCGGTGAGGATGTAGCCAG 61.331 60.000 6.12 0.00 45.00 4.85
2162 2310 1.305802 ACCGGTGAGGATGTAGCCA 60.306 57.895 6.12 0.00 45.00 4.75
2163 2311 1.327690 TGACCGGTGAGGATGTAGCC 61.328 60.000 14.63 0.00 45.00 3.93
2264 2412 5.419788 TCTTTTTGATATTGCTGATGCTGGT 59.580 36.000 0.00 0.00 40.48 4.00
2533 3834 2.340328 GGTTTTACCTGCCGGCCAG 61.340 63.158 26.77 20.47 41.41 4.85
2534 3835 2.282603 GGTTTTACCTGCCGGCCA 60.283 61.111 26.77 11.42 34.73 5.36
2545 3846 7.827236 CCACTGATGGTTATAAGACAGGTTTTA 59.173 37.037 0.00 0.00 41.64 1.52
2617 3918 9.173021 TCTGTTGACATCAATTTATACGGATTT 57.827 29.630 0.00 0.00 38.24 2.17
2790 4091 2.747446 CTGCCGTATGTAGTTTTTGGCT 59.253 45.455 1.76 0.00 41.51 4.75
2800 4101 3.751479 ATGATTCTGCTGCCGTATGTA 57.249 42.857 0.00 0.00 0.00 2.29
2890 4200 1.412710 TCTTCCAAGCTGAGTCGTTGT 59.587 47.619 0.00 0.00 0.00 3.32
2937 4247 3.076032 AGAAGTACTCTTGGGGCCAAATT 59.924 43.478 4.39 0.00 35.33 1.82
3313 4642 0.610174 TGAAGTAGGCCTCTGCAGTG 59.390 55.000 9.68 11.58 40.13 3.66
3694 5047 3.474798 TCCAGATCAAGTACCCTCAGT 57.525 47.619 0.00 0.00 0.00 3.41
4002 5355 7.224362 CCTCAACATTTCTAATGACTGCTCTAG 59.776 40.741 6.42 0.00 0.00 2.43
4169 5528 7.830099 TTCTATAGACATCATTCAGCTCTCA 57.170 36.000 0.67 0.00 0.00 3.27
4370 5735 3.866816 AGATGCTATTCAGGATGGGAGA 58.133 45.455 0.00 0.00 32.14 3.71
4532 5897 5.508153 CCGAAGTCCAATTCAGTATCTCGAT 60.508 44.000 0.00 0.00 0.00 3.59
4719 6094 4.017126 AGAGTGATCAACCGTATCTCACA 58.983 43.478 0.00 0.00 38.90 3.58
4767 6145 6.436843 AACAAACAAACCTGACAAGACTAG 57.563 37.500 0.00 0.00 0.00 2.57
4769 6147 4.142687 CGAACAAACAAACCTGACAAGACT 60.143 41.667 0.00 0.00 0.00 3.24
4872 6265 0.549469 ACCGGATAATTCACCCACCC 59.451 55.000 9.46 0.00 0.00 4.61
4876 6269 3.329814 AGGGATAACCGGATAATTCACCC 59.670 47.826 9.46 10.40 46.96 4.61
4924 6318 4.937620 GTCTATCATGCTGGACAAGAAACA 59.062 41.667 8.04 0.00 28.16 2.83


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

AutoCloner maintained by Alex Coulton.