Multiple sequence alignment - TraesCS3D01G455800

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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 TraesCS3D01G455800 chr3D 100.000 4264 0 0 1 4264 561893669 561889406 0.000000e+00 7875
1 TraesCS3D01G455800 chr3D 91.112 1654 91 17 667 2305 561764035 561762423 0.000000e+00 2189
2 TraesCS3D01G455800 chr3D 93.117 1235 59 11 2911 4138 561748629 561747414 0.000000e+00 1786
3 TraesCS3D01G455800 chr3D 89.601 1077 92 11 1227 2297 561749714 561748652 0.000000e+00 1351
4 TraesCS3D01G455800 chr3D 94.961 635 27 4 3360 3992 561761926 561761295 0.000000e+00 990
5 TraesCS3D01G455800 chr3D 91.917 433 35 0 2928 3360 561762424 561761992 1.310000e-169 606
6 TraesCS3D01G455800 chr3D 88.918 379 36 4 854 1231 561750134 561749761 3.000000e-126 462
7 TraesCS3D01G455800 chr3D 90.598 234 16 2 448 675 134019304 134019537 5.360000e-79 305
8 TraesCS3D01G455800 chr3D 95.385 130 6 0 4135 4264 561761093 561760964 1.550000e-49 207
9 TraesCS3D01G455800 chr3D 90.909 143 9 2 3994 4133 561761266 561761125 5.630000e-44 189
10 TraesCS3D01G455800 chr3A 92.103 1950 116 23 854 2782 697474346 697472414 0.000000e+00 2713
11 TraesCS3D01G455800 chr3A 93.589 1123 30 11 2922 4015 697472219 697471110 0.000000e+00 1637
12 TraesCS3D01G455800 chr3A 90.231 1126 95 9 1174 2297 697493029 697491917 0.000000e+00 1456
13 TraesCS3D01G455800 chr3A 94.266 593 21 2 3360 3950 697491377 697490796 0.000000e+00 894
14 TraesCS3D01G455800 chr3A 90.708 452 40 2 2911 3360 697491894 697491443 6.100000e-168 601
15 TraesCS3D01G455800 chr3A 96.124 258 7 2 882 1139 697493282 697493028 6.590000e-113 418
16 TraesCS3D01G455800 chr3A 96.923 130 4 0 4135 4264 697471063 697470934 7.180000e-53 219
17 TraesCS3D01G455800 chr3A 90.000 130 8 1 4135 4264 697480685 697480561 3.410000e-36 163
18 TraesCS3D01G455800 chr3B 92.078 1641 90 18 667 2305 749093083 749091481 0.000000e+00 2274
19 TraesCS3D01G455800 chr3B 90.103 970 75 7 1329 2297 749148408 749147459 0.000000e+00 1240
20 TraesCS3D01G455800 chr3B 92.248 774 49 6 1330 2101 749313596 749312832 0.000000e+00 1086
21 TraesCS3D01G455800 chr3B 85.864 955 58 27 3359 4255 749146917 749145982 0.000000e+00 944
22 TraesCS3D01G455800 chr3B 96.128 439 11 1 2928 3360 749091482 749091044 0.000000e+00 712
23 TraesCS3D01G455800 chr3B 92.936 453 29 3 2911 3361 749312074 749311623 0.000000e+00 656
24 TraesCS3D01G455800 chr3B 93.237 414 24 3 3360 3772 749311558 749311148 1.310000e-169 606
25 TraesCS3D01G455800 chr3B 91.898 432 28 5 757 1187 749149040 749148615 7.890000e-167 597
26 TraesCS3D01G455800 chr3B 87.103 535 30 17 3360 3889 749090851 749090351 1.720000e-158 569
27 TraesCS3D01G455800 chr3B 89.451 455 43 3 2911 3360 749147436 749146982 1.720000e-158 569
28 TraesCS3D01G455800 chr3B 86.717 527 45 14 3759 4264 749309974 749309452 2.880000e-156 562
29 TraesCS3D01G455800 chr3B 83.390 584 46 14 670 1228 749314217 749313660 1.070000e-135 494
30 TraesCS3D01G455800 chr3B 79.681 689 89 35 2098 2749 749312750 749312076 2.340000e-122 449
31 TraesCS3D01G455800 chr3B 87.668 373 33 9 667 1031 749099071 749098704 5.100000e-114 422
32 TraesCS3D01G455800 chr3B 81.651 436 27 28 3879 4264 749078556 749078124 3.200000e-81 313
33 TraesCS3D01G455800 chr3B 86.620 284 35 1 3048 3331 749098708 749098428 1.150000e-80 311
34 TraesCS3D01G455800 chr3B 94.186 172 9 1 2742 2912 26256310 26256481 1.180000e-65 261
35 TraesCS3D01G455800 chr3B 93.605 172 10 1 2742 2912 26067010 26067181 5.470000e-64 255
36 TraesCS3D01G455800 chr3B 93.023 172 11 1 2742 2912 26409407 26409578 2.550000e-62 250
37 TraesCS3D01G455800 chr3B 89.941 169 12 1 3415 3578 749098061 749097893 3.340000e-51 213
38 TraesCS3D01G455800 chr2D 95.514 691 9 9 1 671 432072787 432073475 0.000000e+00 1085
39 TraesCS3D01G455800 chr6D 95.356 689 12 2 1 669 59072637 59071949 0.000000e+00 1077
40 TraesCS3D01G455800 chr6D 94.186 688 18 3 1 667 460235132 460235818 0.000000e+00 1029
41 TraesCS3D01G455800 chr6D 87.262 683 55 16 17 671 178836890 178836212 0.000000e+00 750
42 TraesCS3D01G455800 chr6D 95.092 163 8 0 2747 2909 93213739 93213901 1.520000e-64 257
43 TraesCS3D01G455800 chr6D 93.182 176 10 2 2747 2922 96521509 96521336 1.520000e-64 257
44 TraesCS3D01G455800 chr4D 94.606 686 18 10 1 667 359859056 359859741 0.000000e+00 1044
45 TraesCS3D01G455800 chr7D 94.477 688 17 8 1 667 394396838 394397525 0.000000e+00 1040
46 TraesCS3D01G455800 chr7D 93.595 687 22 9 1 666 192556165 192555480 0.000000e+00 1005
47 TraesCS3D01G455800 chr7D 93.450 687 23 9 1 666 43550906 43551591 0.000000e+00 1000
48 TraesCS3D01G455800 chr5D 93.886 687 20 9 1 666 563689860 563690545 0.000000e+00 1016
49 TraesCS3D01G455800 chr5D 93.860 684 20 9 1 663 394540458 394541140 0.000000e+00 1011
50 TraesCS3D01G455800 chr1D 92.140 687 20 11 1 666 400134558 400135231 0.000000e+00 939
51 TraesCS3D01G455800 chr1B 94.086 186 8 2 2724 2909 149248947 149249129 3.250000e-71 279
52 TraesCS3D01G455800 chr1B 92.045 176 13 1 2736 2911 414090857 414091031 3.290000e-61 246
53 TraesCS3D01G455800 chr7B 95.732 164 6 1 2746 2909 394828648 394828486 3.270000e-66 263
54 TraesCS3D01G455800 chr6B 94.186 172 9 1 2739 2909 408626270 408626099 1.180000e-65 261


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 TraesCS3D01G455800 chr3D 561889406 561893669 4263 True 7875.000000 7875 100.000000 1 4264 1 chr3D.!!$R1 4263
1 TraesCS3D01G455800 chr3D 561747414 561750134 2720 True 1199.666667 1786 90.545333 854 4138 3 chr3D.!!$R2 3284
2 TraesCS3D01G455800 chr3D 561760964 561764035 3071 True 836.200000 2189 92.856800 667 4264 5 chr3D.!!$R3 3597
3 TraesCS3D01G455800 chr3A 697470934 697474346 3412 True 1523.000000 2713 94.205000 854 4264 3 chr3A.!!$R2 3410
4 TraesCS3D01G455800 chr3A 697490796 697493282 2486 True 842.250000 1456 92.832250 882 3950 4 chr3A.!!$R3 3068
5 TraesCS3D01G455800 chr3B 749090351 749093083 2732 True 1185.000000 2274 91.769667 667 3889 3 chr3B.!!$R2 3222
6 TraesCS3D01G455800 chr3B 749145982 749149040 3058 True 837.500000 1240 89.329000 757 4255 4 chr3B.!!$R4 3498
7 TraesCS3D01G455800 chr3B 749309452 749314217 4765 True 642.166667 1086 88.034833 670 4264 6 chr3B.!!$R5 3594
8 TraesCS3D01G455800 chr3B 749097893 749099071 1178 True 315.333333 422 88.076333 667 3578 3 chr3B.!!$R3 2911
9 TraesCS3D01G455800 chr2D 432072787 432073475 688 False 1085.000000 1085 95.514000 1 671 1 chr2D.!!$F1 670
10 TraesCS3D01G455800 chr6D 59071949 59072637 688 True 1077.000000 1077 95.356000 1 669 1 chr6D.!!$R1 668
11 TraesCS3D01G455800 chr6D 460235132 460235818 686 False 1029.000000 1029 94.186000 1 667 1 chr6D.!!$F2 666
12 TraesCS3D01G455800 chr6D 178836212 178836890 678 True 750.000000 750 87.262000 17 671 1 chr6D.!!$R3 654
13 TraesCS3D01G455800 chr4D 359859056 359859741 685 False 1044.000000 1044 94.606000 1 667 1 chr4D.!!$F1 666
14 TraesCS3D01G455800 chr7D 394396838 394397525 687 False 1040.000000 1040 94.477000 1 667 1 chr7D.!!$F2 666
15 TraesCS3D01G455800 chr7D 192555480 192556165 685 True 1005.000000 1005 93.595000 1 666 1 chr7D.!!$R1 665
16 TraesCS3D01G455800 chr7D 43550906 43551591 685 False 1000.000000 1000 93.450000 1 666 1 chr7D.!!$F1 665
17 TraesCS3D01G455800 chr5D 563689860 563690545 685 False 1016.000000 1016 93.886000 1 666 1 chr5D.!!$F2 665
18 TraesCS3D01G455800 chr5D 394540458 394541140 682 False 1011.000000 1011 93.860000 1 663 1 chr5D.!!$F1 662
19 TraesCS3D01G455800 chr1D 400134558 400135231 673 False 939.000000 939 92.140000 1 666 1 chr1D.!!$F1 665

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
262 263 0.479378 GGGGATCGGAGGAGAGTACT 59.521 60.0 0.0 0.0 0.0 2.73 F
1519 1745 0.400213 TCTGGATGGAAGGCGTTTGT 59.600 50.0 0.0 0.0 0.0 2.83 F
2761 3112 1.031235 GCTACTACTCCCTCCGTTCC 58.969 60.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1980 0.326522 TCCCCTGCCTTGAGCTATCA 60.327 55.000 0.00 0.0 44.23 2.15 R
3089 3562 0.931702 TCTTAACACAACACCGCACG 59.068 50.000 0.00 0.0 0.00 5.34 R
4067 6347 1.942657 CATGAATCACCATCGTGGACC 59.057 52.381 10.46 0.0 40.96 4.46 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
181 182 8.531146 CAAAAGTTCCCCAAATCTAATACATGT 58.469 33.333 2.69 2.69 0.00 3.21
262 263 0.479378 GGGGATCGGAGGAGAGTACT 59.521 60.000 0.00 0.00 0.00 2.73
672 698 0.665835 TGTCAAATTTGCCGCGTCTT 59.334 45.000 13.54 0.00 0.00 3.01
695 721 4.637489 CGGAGAGGCGCTGGATCG 62.637 72.222 7.64 2.80 0.00 3.69
715 742 5.293319 TCGTCTATACTTGCCTAGTCTCT 57.707 43.478 0.00 0.00 38.33 3.10
716 743 5.057819 TCGTCTATACTTGCCTAGTCTCTG 58.942 45.833 0.00 0.00 38.33 3.35
743 770 4.261572 CGTTTGGCTTTCTCCATTCTTCAA 60.262 41.667 0.00 0.00 35.77 2.69
790 845 5.641636 TCTCTCTCTGAATCTCCGATAATCG 59.358 44.000 0.00 0.00 40.07 3.34
815 870 4.774726 TGGTATGCTTCAACTCTTCTCTCT 59.225 41.667 0.00 0.00 0.00 3.10
874 930 2.633481 AGCTCTCGTTTTACCTTCACCT 59.367 45.455 0.00 0.00 0.00 4.00
883 939 5.560183 CGTTTTACCTTCACCTTGTTAGCTG 60.560 44.000 0.00 0.00 0.00 4.24
938 1002 5.823209 AACTTTTAGTTGGTACTTTGCGT 57.177 34.783 0.00 0.00 37.00 5.24
939 1003 5.413969 ACTTTTAGTTGGTACTTTGCGTC 57.586 39.130 0.00 0.00 35.78 5.19
940 1004 5.121105 ACTTTTAGTTGGTACTTTGCGTCT 58.879 37.500 0.00 0.00 35.78 4.18
941 1005 5.587443 ACTTTTAGTTGGTACTTTGCGTCTT 59.413 36.000 0.00 0.00 35.78 3.01
942 1006 6.094464 ACTTTTAGTTGGTACTTTGCGTCTTT 59.906 34.615 0.00 0.00 35.78 2.52
943 1007 3.963383 AGTTGGTACTTTGCGTCTTTG 57.037 42.857 0.00 0.00 0.00 2.77
944 1008 2.032924 AGTTGGTACTTTGCGTCTTTGC 59.967 45.455 0.00 0.00 0.00 3.68
1130 1203 6.078202 TGAGAGAATGGTAAGCTATCTTCG 57.922 41.667 0.00 0.00 33.85 3.79
1194 1350 3.558505 CTGGATTGTGTTCTTGCTTTCG 58.441 45.455 0.00 0.00 0.00 3.46
1248 1470 4.574674 ATTTGGTCAGATCTGGCAACTA 57.425 40.909 27.64 11.82 36.81 2.24
1456 1682 1.518325 TCACGCCATGGTTACACTTG 58.482 50.000 14.67 0.00 0.00 3.16
1479 1705 7.615582 TGTGATGTTCAGATTACCAAGAATC 57.384 36.000 0.00 0.00 36.28 2.52
1493 1719 6.441088 ACCAAGAATCTGGAGAAACTAGTT 57.559 37.500 1.12 1.12 38.96 2.24
1519 1745 0.400213 TCTGGATGGAAGGCGTTTGT 59.600 50.000 0.00 0.00 0.00 2.83
1554 1780 1.772453 TGAGAACGGGGGACTTTCTTT 59.228 47.619 0.00 0.00 34.23 2.52
1648 1874 3.983344 GCGTGCAATCTCAAGAAAAATGT 59.017 39.130 0.00 0.00 0.00 2.71
1716 1942 3.192001 CACTTGTCACAATCTTCCCATGG 59.808 47.826 4.14 4.14 0.00 3.66
1754 1980 4.081476 GGAAGACAAATTAGGCCAAGCAAT 60.081 41.667 5.01 0.00 0.00 3.56
1785 2011 1.233019 GCAGGGGAATGACATCATCG 58.767 55.000 0.00 0.00 35.10 3.84
1788 2014 3.306989 GCAGGGGAATGACATCATCGATA 60.307 47.826 0.00 0.00 35.10 2.92
2172 2484 3.133014 GCCGGCTGCTATCTCTGA 58.867 61.111 22.15 0.00 36.87 3.27
2380 2710 4.925646 CAGAAACTTTTATGCTTGCTTCCC 59.074 41.667 0.00 0.00 0.00 3.97
2386 2716 2.238847 TATGCTTGCTTCCCGTCGCT 62.239 55.000 0.00 0.00 0.00 4.93
2451 2790 1.746220 GGTGGTGTTTGTTGTAGTGCA 59.254 47.619 0.00 0.00 0.00 4.57
2481 2820 6.514063 AGTAGAAGTTGGTTGTAGTCTTGTC 58.486 40.000 0.00 0.00 0.00 3.18
2483 2822 5.930135 AGAAGTTGGTTGTAGTCTTGTCAT 58.070 37.500 0.00 0.00 0.00 3.06
2641 2991 5.239525 GGTGTCAAATTAGAGGTGATATGCC 59.760 44.000 0.00 0.00 0.00 4.40
2761 3112 1.031235 GCTACTACTCCCTCCGTTCC 58.969 60.000 0.00 0.00 0.00 3.62
2762 3113 1.409942 GCTACTACTCCCTCCGTTCCT 60.410 57.143 0.00 0.00 0.00 3.36
2763 3114 2.158696 GCTACTACTCCCTCCGTTCCTA 60.159 54.545 0.00 0.00 0.00 2.94
2764 3115 3.686691 GCTACTACTCCCTCCGTTCCTAA 60.687 52.174 0.00 0.00 0.00 2.69
2765 3116 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2774 3125 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2778 3129 7.174426 CCTCCGTTCCTAAATGTAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
2789 3140 7.674471 ATGTAAGTCTTTTTAGAGCTTCCAC 57.326 36.000 0.00 0.00 0.00 4.02
2790 3141 6.827727 TGTAAGTCTTTTTAGAGCTTCCACT 58.172 36.000 0.00 0.00 0.00 4.00
2794 3145 7.246171 AGTCTTTTTAGAGCTTCCACTATGA 57.754 36.000 0.00 0.00 0.00 2.15
2795 3146 7.680730 AGTCTTTTTAGAGCTTCCACTATGAA 58.319 34.615 0.00 0.00 0.00 2.57
2798 3149 8.812972 TCTTTTTAGAGCTTCCACTATGAACTA 58.187 33.333 0.00 0.00 0.00 2.24
2799 3150 8.773404 TTTTTAGAGCTTCCACTATGAACTAC 57.227 34.615 0.00 0.00 0.00 2.73
2800 3151 7.476540 TTTAGAGCTTCCACTATGAACTACA 57.523 36.000 0.00 0.00 0.00 2.74
2802 3153 8.762481 TTAGAGCTTCCACTATGAACTACATA 57.238 34.615 0.00 0.00 40.07 2.29
2803 3154 7.045126 AGAGCTTCCACTATGAACTACATAC 57.955 40.000 0.00 0.00 40.07 2.39
2804 3155 5.833082 AGCTTCCACTATGAACTACATACG 58.167 41.667 0.00 0.00 40.07 3.06
2805 3156 4.982916 GCTTCCACTATGAACTACATACGG 59.017 45.833 0.00 0.00 40.07 4.02
2806 3157 5.221185 GCTTCCACTATGAACTACATACGGA 60.221 44.000 0.00 0.00 40.07 4.69
2807 3158 6.387041 TTCCACTATGAACTACATACGGAG 57.613 41.667 0.00 0.00 38.29 4.63
2808 3159 5.687780 TCCACTATGAACTACATACGGAGA 58.312 41.667 0.00 0.00 40.07 3.71
2809 3160 6.124340 TCCACTATGAACTACATACGGAGAA 58.876 40.000 0.00 0.00 40.07 2.87
2810 3161 6.604396 TCCACTATGAACTACATACGGAGAAA 59.396 38.462 0.00 0.00 40.07 2.52
2811 3162 7.123098 TCCACTATGAACTACATACGGAGAAAA 59.877 37.037 0.00 0.00 40.07 2.29
2812 3163 7.762615 CCACTATGAACTACATACGGAGAAAAA 59.237 37.037 0.00 0.00 40.07 1.94
2813 3164 9.314321 CACTATGAACTACATACGGAGAAAAAT 57.686 33.333 0.00 0.00 40.07 1.82
2814 3165 9.314321 ACTATGAACTACATACGGAGAAAAATG 57.686 33.333 0.00 0.00 40.07 2.32
2815 3166 9.529325 CTATGAACTACATACGGAGAAAAATGA 57.471 33.333 0.00 0.00 40.07 2.57
2816 3167 7.827819 TGAACTACATACGGAGAAAAATGAG 57.172 36.000 0.00 0.00 0.00 2.90
2817 3168 7.383687 TGAACTACATACGGAGAAAAATGAGT 58.616 34.615 0.00 0.00 0.00 3.41
2818 3169 7.330946 TGAACTACATACGGAGAAAAATGAGTG 59.669 37.037 0.00 0.00 0.00 3.51
2819 3170 6.931838 ACTACATACGGAGAAAAATGAGTGA 58.068 36.000 0.00 0.00 0.00 3.41
2820 3171 7.383687 ACTACATACGGAGAAAAATGAGTGAA 58.616 34.615 0.00 0.00 0.00 3.18
2821 3172 8.041323 ACTACATACGGAGAAAAATGAGTGAAT 58.959 33.333 0.00 0.00 0.00 2.57
2822 3173 7.308782 ACATACGGAGAAAAATGAGTGAATC 57.691 36.000 0.00 0.00 0.00 2.52
2823 3174 7.106239 ACATACGGAGAAAAATGAGTGAATCT 58.894 34.615 0.00 0.00 0.00 2.40
2824 3175 8.258007 ACATACGGAGAAAAATGAGTGAATCTA 58.742 33.333 0.00 0.00 0.00 1.98
2825 3176 6.969828 ACGGAGAAAAATGAGTGAATCTAC 57.030 37.500 0.00 0.00 0.00 2.59
2826 3177 6.464222 ACGGAGAAAAATGAGTGAATCTACA 58.536 36.000 0.00 0.00 0.00 2.74
2827 3178 6.369065 ACGGAGAAAAATGAGTGAATCTACAC 59.631 38.462 0.00 0.00 40.60 2.90
2918 3272 5.303845 GGAACGGAGGGAGTATACTACAAAT 59.696 44.000 17.06 2.04 0.00 2.32
2919 3273 5.786264 ACGGAGGGAGTATACTACAAATG 57.214 43.478 17.06 6.31 0.00 2.32
2920 3274 5.452255 ACGGAGGGAGTATACTACAAATGA 58.548 41.667 17.06 0.00 0.00 2.57
2933 3393 6.791867 ACTACAAATGATAGTAGCTGGACA 57.208 37.500 0.00 0.00 41.01 4.02
3089 3562 0.251341 ACCATGGCAAGAAGTGGGAC 60.251 55.000 13.04 0.00 36.05 4.46
3466 4457 6.601613 TCAAGAAACAGAAGTAGCAAAAGGAA 59.398 34.615 0.00 0.00 0.00 3.36
3648 4645 4.665833 TGAACTGTAATGTCGGATAGGG 57.334 45.455 0.00 0.00 0.00 3.53
3699 4739 3.512496 TGTACTGTGGGTTATGTCAGGA 58.488 45.455 0.00 0.00 32.92 3.86
4067 6347 4.994852 TCCCTGTCTGTTTCATTTACTTCG 59.005 41.667 0.00 0.00 0.00 3.79
4074 6354 3.495377 TGTTTCATTTACTTCGGTCCACG 59.505 43.478 0.00 0.00 46.11 4.94
4133 6413 6.708676 CCTTTGTCAGCAAGAAAAATTTCAC 58.291 36.000 8.47 0.00 39.61 3.18
4157 6467 5.363101 TGATCAGAACTGAATCATAGTGGC 58.637 41.667 8.59 0.00 43.58 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 233 3.007398 CCTCCGATCCCCTTCTTTCTATG 59.993 52.174 0.00 0.00 0.00 2.23
262 263 5.414789 TCTTCACCAATCCATCGTAGAAA 57.585 39.130 0.00 0.00 43.58 2.52
672 698 2.676822 AGCGCCTCTCCGACTTCA 60.677 61.111 2.29 0.00 0.00 3.02
695 721 5.823570 TCACAGAGACTAGGCAAGTATAGAC 59.176 44.000 0.00 0.00 39.07 2.59
715 742 1.305201 GGAGAAAGCCAAACGTCACA 58.695 50.000 0.00 0.00 0.00 3.58
716 743 1.305201 TGGAGAAAGCCAAACGTCAC 58.695 50.000 0.00 0.00 34.31 3.67
743 770 1.619332 GAGGGAGACTGGAGAACGTTT 59.381 52.381 0.46 0.00 0.00 3.60
790 845 3.604582 AGAAGAGTTGAAGCATACCAGC 58.395 45.455 0.00 0.00 0.00 4.85
815 870 3.369892 GCTTGCAGTATTTCAGAGGGAGA 60.370 47.826 0.00 0.00 0.00 3.71
874 930 7.466746 AAATAGAGGAAATTGCAGCTAACAA 57.533 32.000 4.01 4.01 0.00 2.83
883 939 7.257722 TCATTTCGGAAAATAGAGGAAATTGC 58.742 34.615 7.33 0.00 35.72 3.56
1130 1203 3.160872 GCTAGAACAGAGCCCAACC 57.839 57.895 0.00 0.00 33.60 3.77
1194 1350 5.048434 CAGAGGTTCCTCTTTTGTTTCCATC 60.048 44.000 17.59 0.00 41.02 3.51
1248 1470 5.268387 ACAGAGTAACATGAGAGGACAGAT 58.732 41.667 0.00 0.00 0.00 2.90
1456 1682 7.856145 AGATTCTTGGTAATCTGAACATCAC 57.144 36.000 0.00 0.00 43.09 3.06
1479 1705 6.593382 CCAGAATCAAGAACTAGTTTCTCCAG 59.407 42.308 10.02 3.54 44.41 3.86
1493 1719 2.420547 CGCCTTCCATCCAGAATCAAGA 60.421 50.000 0.00 0.00 0.00 3.02
1519 1745 3.071479 GTTCTCAAGTTATGGGCACGAA 58.929 45.455 0.00 0.00 0.00 3.85
1554 1780 4.009675 GAGTGGCCATCATACTTGAACAA 58.990 43.478 9.72 0.00 34.96 2.83
1648 1874 3.420893 CACCATTCTTTACCAGGAGCAA 58.579 45.455 0.00 0.00 0.00 3.91
1754 1980 0.326522 TCCCCTGCCTTGAGCTATCA 60.327 55.000 0.00 0.00 44.23 2.15
2386 2716 2.102070 AATACACGGACGCAAATCCA 57.898 45.000 0.00 0.00 38.87 3.41
2451 2790 7.670559 AGACTACAACCAACTTCTACTAGACAT 59.329 37.037 0.00 0.00 0.00 3.06
2481 2820 5.099575 GGCCGAAATAACCAAACACTTATG 58.900 41.667 0.00 0.00 0.00 1.90
2483 2822 4.400120 AGGCCGAAATAACCAAACACTTA 58.600 39.130 0.00 0.00 0.00 2.24
2551 2898 6.183360 GGACAAAATGCAAAGCTTGTGTTTTA 60.183 34.615 0.00 0.00 32.31 1.52
2557 2904 3.540314 TGGACAAAATGCAAAGCTTGT 57.460 38.095 0.00 0.00 34.78 3.16
2641 2991 6.195165 GGTTGCTATCTTAGAAAATTCAGCG 58.805 40.000 0.00 0.00 0.00 5.18
2734 3085 3.429135 GGAGGGAGTAGTAGCAAAGTTCG 60.429 52.174 0.00 0.00 0.00 3.95
2749 3100 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2750 3101 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2762 3113 9.787435 TGGAAGCTCTAAAAAGACTTACATTTA 57.213 29.630 0.00 0.00 0.00 1.40
2763 3114 8.568794 GTGGAAGCTCTAAAAAGACTTACATTT 58.431 33.333 0.00 0.00 33.93 2.32
2764 3115 7.939588 AGTGGAAGCTCTAAAAAGACTTACATT 59.060 33.333 0.00 0.00 33.93 2.71
2765 3116 7.454225 AGTGGAAGCTCTAAAAAGACTTACAT 58.546 34.615 0.00 0.00 33.93 2.29
2774 3125 8.372459 TGTAGTTCATAGTGGAAGCTCTAAAAA 58.628 33.333 0.00 0.00 0.00 1.94
2778 3129 7.041303 CGTATGTAGTTCATAGTGGAAGCTCTA 60.041 40.741 0.00 0.00 39.36 2.43
2782 3133 4.982916 CCGTATGTAGTTCATAGTGGAAGC 59.017 45.833 3.20 0.00 39.36 3.86
2783 3134 6.262496 TCTCCGTATGTAGTTCATAGTGGAAG 59.738 42.308 10.20 6.61 40.80 3.46
2784 3135 6.124340 TCTCCGTATGTAGTTCATAGTGGAA 58.876 40.000 10.20 0.00 40.80 3.53
2785 3136 5.687780 TCTCCGTATGTAGTTCATAGTGGA 58.312 41.667 9.16 9.16 39.94 4.02
2786 3137 6.387041 TTCTCCGTATGTAGTTCATAGTGG 57.613 41.667 2.99 2.99 39.36 4.00
2789 3140 9.529325 TCATTTTTCTCCGTATGTAGTTCATAG 57.471 33.333 0.00 0.00 39.36 2.23
2790 3141 9.529325 CTCATTTTTCTCCGTATGTAGTTCATA 57.471 33.333 0.00 0.00 37.91 2.15
2794 3145 7.383687 TCACTCATTTTTCTCCGTATGTAGTT 58.616 34.615 0.00 0.00 0.00 2.24
2795 3146 6.931838 TCACTCATTTTTCTCCGTATGTAGT 58.068 36.000 0.00 0.00 0.00 2.73
2798 3149 7.106239 AGATTCACTCATTTTTCTCCGTATGT 58.894 34.615 0.00 0.00 0.00 2.29
2799 3150 7.545362 AGATTCACTCATTTTTCTCCGTATG 57.455 36.000 0.00 0.00 0.00 2.39
2800 3151 8.258007 TGTAGATTCACTCATTTTTCTCCGTAT 58.742 33.333 0.00 0.00 0.00 3.06
2802 3153 6.369065 GTGTAGATTCACTCATTTTTCTCCGT 59.631 38.462 0.00 0.00 35.68 4.69
2803 3154 6.591834 AGTGTAGATTCACTCATTTTTCTCCG 59.408 38.462 0.00 0.00 44.07 4.63
2804 3155 7.913674 AGTGTAGATTCACTCATTTTTCTCC 57.086 36.000 0.00 0.00 44.07 3.71
2875 3226 7.818930 TCCGTTCCTAAATGTAAGTCGTTTTAT 59.181 33.333 0.00 0.00 36.72 1.40
2877 3228 5.990996 TCCGTTCCTAAATGTAAGTCGTTTT 59.009 36.000 0.00 0.00 36.72 2.43
2878 3229 5.540911 TCCGTTCCTAAATGTAAGTCGTTT 58.459 37.500 0.00 0.00 38.58 3.60
2881 3232 4.110482 CCTCCGTTCCTAAATGTAAGTCG 58.890 47.826 0.00 0.00 0.00 4.18
2883 3234 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2888 3239 4.957684 ATACTCCCTCCGTTCCTAAATG 57.042 45.455 0.00 0.00 0.00 2.32
2890 3241 5.134725 AGTATACTCCCTCCGTTCCTAAA 57.865 43.478 0.00 0.00 0.00 1.85
2891 3242 4.803329 AGTATACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
2892 3243 4.660303 TGTAGTATACTCCCTCCGTTCCTA 59.340 45.833 9.12 0.00 43.54 2.94
2893 3244 3.461085 TGTAGTATACTCCCTCCGTTCCT 59.539 47.826 9.12 0.00 43.54 3.36
2894 3245 3.825328 TGTAGTATACTCCCTCCGTTCC 58.175 50.000 9.12 0.00 43.54 3.62
2899 3250 8.653036 ACTATCATTTGTAGTATACTCCCTCC 57.347 38.462 9.12 0.00 43.54 4.30
2918 3272 7.004691 ACTATGTACATGTCCAGCTACTATCA 58.995 38.462 18.81 0.00 0.00 2.15
2919 3273 7.455641 ACTATGTACATGTCCAGCTACTATC 57.544 40.000 18.81 0.00 0.00 2.08
2920 3274 7.505923 TGAACTATGTACATGTCCAGCTACTAT 59.494 37.037 18.81 0.00 0.00 2.12
2933 3393 7.418337 TCATGGTGTAGTGAACTATGTACAT 57.582 36.000 13.93 13.93 37.65 2.29
3089 3562 0.931702 TCTTAACACAACACCGCACG 59.068 50.000 0.00 0.00 0.00 5.34
3466 4457 3.076032 ACTCTTCTGGCCTTACCCAAAAT 59.924 43.478 3.32 0.00 37.83 1.82
3648 4645 8.504005 ACGCAATAACCTCTAACATAATATTGC 58.496 33.333 14.39 14.39 45.14 3.56
3699 4739 5.643777 GCAACTGACCATAATGTAACTCTGT 59.356 40.000 0.00 0.00 0.00 3.41
4067 6347 1.942657 CATGAATCACCATCGTGGACC 59.057 52.381 10.46 0.00 40.96 4.46
4074 6354 5.593909 TGGTTAATGTCCATGAATCACCATC 59.406 40.000 0.00 0.00 0.00 3.51
4133 6413 5.466058 GCCACTATGATTCAGTTCTGATCAG 59.534 44.000 17.07 17.07 0.00 2.90
4157 6467 7.385205 CAGGGTATCTAATGAAGTTAATGTCCG 59.615 40.741 0.00 0.00 0.00 4.79
4189 6499 2.621668 CCATCCTCCCTTCTTTGTTCCC 60.622 54.545 0.00 0.00 0.00 3.97
4220 6530 5.887598 TGGCTTCACTAAAGTGCATCATATT 59.112 36.000 5.21 0.00 45.25 1.28


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

AutoCloner maintained by Alex Coulton.