Multiple sequence alignment - TraesCS1D01G086700

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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 TraesCS1D01G086700 chr1D 100.000 4560 0 0 1 4560 71283224 71287783 0.000000e+00 8421
1 TraesCS1D01G086700 chr1D 96.880 609 19 0 3952 4560 182580738 182581346 0.000000e+00 1020
2 TraesCS1D01G086700 chr1D 99.371 159 0 1 785 943 254486053 254485896 2.080000e-73 287
3 TraesCS1D01G086700 chr1D 93.684 190 7 5 3115 3300 270329452 270329640 3.470000e-71 279
4 TraesCS1D01G086700 chr1D 94.505 182 6 4 3115 3293 201260226 201260406 1.250000e-70 278
5 TraesCS1D01G086700 chr1D 94.054 185 7 4 3115 3296 250661968 250661785 1.250000e-70 278
6 TraesCS1D01G086700 chr1A 98.392 2176 34 1 943 3117 71692013 71694188 0.000000e+00 3823
7 TraesCS1D01G086700 chr1A 97.212 789 17 2 1 785 71691226 71692013 0.000000e+00 1330
8 TraesCS1D01G086700 chr1A 93.448 641 21 6 3329 3954 71694292 71694926 0.000000e+00 931
9 TraesCS1D01G086700 chr1A 92.206 603 34 2 3956 4558 546519079 546519668 0.000000e+00 841
10 TraesCS1D01G086700 chr1B 96.954 2134 56 4 943 3070 112750695 112752825 0.000000e+00 3572
11 TraesCS1D01G086700 chr1B 96.582 790 18 5 1 785 112749910 112750695 0.000000e+00 1301
12 TraesCS1D01G086700 chr1B 92.809 598 19 6 3282 3862 112752905 112753495 0.000000e+00 845
13 TraesCS1D01G086700 chr1B 98.742 159 2 0 785 943 633725399 633725241 2.690000e-72 283
14 TraesCS1D01G086700 chr1B 95.455 66 2 1 3890 3954 112753565 112753630 2.240000e-18 104
15 TraesCS1D01G086700 chr2D 98.020 606 12 0 3955 4560 639485012 639484407 0.000000e+00 1053
16 TraesCS1D01G086700 chr2D 96.370 606 22 0 3955 4560 345251459 345252064 0.000000e+00 998
17 TraesCS1D01G086700 chr5D 97.364 607 16 0 3954 4560 42206481 42207087 0.000000e+00 1033
18 TraesCS1D01G086700 chr5D 100.000 158 0 0 785 942 483799225 483799382 4.460000e-75 292
19 TraesCS1D01G086700 chr5D 99.371 159 0 1 785 943 6215094 6215251 2.080000e-73 287
20 TraesCS1D01G086700 chr5D 89.362 94 10 0 958 1051 69506221 69506128 8.010000e-23 119
21 TraesCS1D01G086700 chr7D 97.351 604 16 0 3955 4558 127375811 127376414 0.000000e+00 1027
22 TraesCS1D01G086700 chr7D 96.865 606 15 1 3955 4560 58131751 58131150 0.000000e+00 1011
23 TraesCS1D01G086700 chr2A 91.494 435 33 2 3954 4385 32113533 32113966 3.040000e-166 595
24 TraesCS1D01G086700 chr2A 96.610 59 2 0 4500 4558 32113979 32114037 1.040000e-16 99
25 TraesCS1D01G086700 chr3B 100.000 159 0 0 785 943 10275080 10274922 1.240000e-75 294
26 TraesCS1D01G086700 chr3B 99.371 159 0 1 785 943 201502906 201502749 2.080000e-73 287
27 TraesCS1D01G086700 chr3B 99.371 159 0 1 785 943 460162621 460162778 2.080000e-73 287
28 TraesCS1D01G086700 chrUn 99.371 159 0 1 785 943 443552936 443553093 2.080000e-73 287
29 TraesCS1D01G086700 chr6D 99.371 159 0 1 785 943 431394803 431394960 2.080000e-73 287
30 TraesCS1D01G086700 chr5A 93.684 190 7 5 3115 3300 349787348 349787536 3.470000e-71 279
31 TraesCS1D01G086700 chr4A 93.684 190 7 5 3115 3300 384371894 384371706 3.470000e-71 279
32 TraesCS1D01G086700 chr4A 89.313 131 12 2 997 1127 398502463 398502335 3.650000e-36 163
33 TraesCS1D01G086700 chr3D 93.684 190 7 5 3115 3300 298137227 298137415 3.470000e-71 279
34 TraesCS1D01G086700 chr3D 93.684 190 7 5 3115 3300 467257997 467257809 3.470000e-71 279
35 TraesCS1D01G086700 chr3A 94.536 183 7 3 3114 3294 264047749 264047568 3.470000e-71 279
36 TraesCS1D01G086700 chr4D 94.054 185 7 4 3115 3296 452926303 452926120 1.250000e-70 278
37 TraesCS1D01G086700 chr7B 91.549 142 11 1 987 1128 179758187 179758327 1.290000e-45 195


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 TraesCS1D01G086700 chr1D 71283224 71287783 4559 False 8421.0 8421 100.000000 1 4560 1 chr1D.!!$F1 4559
1 TraesCS1D01G086700 chr1D 182580738 182581346 608 False 1020.0 1020 96.880000 3952 4560 1 chr1D.!!$F2 608
2 TraesCS1D01G086700 chr1A 71691226 71694926 3700 False 2028.0 3823 96.350667 1 3954 3 chr1A.!!$F2 3953
3 TraesCS1D01G086700 chr1A 546519079 546519668 589 False 841.0 841 92.206000 3956 4558 1 chr1A.!!$F1 602
4 TraesCS1D01G086700 chr1B 112749910 112753630 3720 False 1455.5 3572 95.450000 1 3954 4 chr1B.!!$F1 3953
5 TraesCS1D01G086700 chr2D 639484407 639485012 605 True 1053.0 1053 98.020000 3955 4560 1 chr2D.!!$R1 605
6 TraesCS1D01G086700 chr2D 345251459 345252064 605 False 998.0 998 96.370000 3955 4560 1 chr2D.!!$F1 605
7 TraesCS1D01G086700 chr5D 42206481 42207087 606 False 1033.0 1033 97.364000 3954 4560 1 chr5D.!!$F2 606
8 TraesCS1D01G086700 chr7D 127375811 127376414 603 False 1027.0 1027 97.351000 3955 4558 1 chr7D.!!$F1 603
9 TraesCS1D01G086700 chr7D 58131150 58131751 601 True 1011.0 1011 96.865000 3955 4560 1 chr7D.!!$R1 605
10 TraesCS1D01G086700 chr2A 32113533 32114037 504 False 347.0 595 94.052000 3954 4558 2 chr2A.!!$F1 604

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
787 793 1.013596 TGTGTTGCCACTTCTGAACG 58.986 50.000 0.00 0.00 42.34 3.95 F
788 794 1.295792 GTGTTGCCACTTCTGAACGA 58.704 50.000 0.00 0.00 38.61 3.85 F
1693 1699 0.107312 ATGCTCGCTCAAGAGGCATT 60.107 50.000 6.51 0.00 38.63 3.56 F
2117 2129 1.672881 ACAACACACTTTGAGCTGCTC 59.327 47.619 22.38 22.38 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 1699 0.250553 CCACCAAAGCCCTAACGTCA 60.251 55.000 0.0 0.0 0.00 4.35 R
2761 2773 1.355381 ACCTCCAATGCCTGTGATCAA 59.645 47.619 0.0 0.0 0.00 2.57 R
2938 2950 0.246635 CAGGGACAACGACGATTCCT 59.753 55.000 0.0 0.0 0.00 3.36 R
3765 3837 2.231478 AGGTATTCCGCCACAGATATCG 59.769 50.000 0.0 0.0 39.05 2.92 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
125 126 2.426522 CTGGCATTTCCTGAAAGACGA 58.573 47.619 0.00 0.00 35.98 4.20
419 425 6.072175 GGTATGTGAATTTTGTACCTGCAGAA 60.072 38.462 17.39 0.00 33.63 3.02
434 440 7.112452 ACCTGCAGAATTTAAAGTTTGTTCT 57.888 32.000 17.39 2.31 0.00 3.01
598 604 8.996651 AAACTTAGTATGGGAGGATATTTTGG 57.003 34.615 0.00 0.00 0.00 3.28
599 605 7.707467 ACTTAGTATGGGAGGATATTTTGGT 57.293 36.000 0.00 0.00 0.00 3.67
784 790 1.667236 CTGTGTGTTGCCACTTCTGA 58.333 50.000 0.00 0.00 42.34 3.27
785 791 2.016318 CTGTGTGTTGCCACTTCTGAA 58.984 47.619 0.00 0.00 42.34 3.02
786 792 1.742831 TGTGTGTTGCCACTTCTGAAC 59.257 47.619 0.00 0.00 42.34 3.18
787 793 1.013596 TGTGTTGCCACTTCTGAACG 58.986 50.000 0.00 0.00 42.34 3.95
788 794 1.295792 GTGTTGCCACTTCTGAACGA 58.704 50.000 0.00 0.00 38.61 3.85
789 795 1.668751 GTGTTGCCACTTCTGAACGAA 59.331 47.619 0.00 0.00 38.61 3.85
790 796 2.290641 GTGTTGCCACTTCTGAACGAAT 59.709 45.455 0.00 0.00 38.61 3.34
791 797 2.948979 TGTTGCCACTTCTGAACGAATT 59.051 40.909 0.00 0.00 0.00 2.17
792 798 4.024387 GTGTTGCCACTTCTGAACGAATTA 60.024 41.667 0.00 0.00 38.61 1.40
793 799 4.024387 TGTTGCCACTTCTGAACGAATTAC 60.024 41.667 0.00 0.00 0.00 1.89
794 800 4.002906 TGCCACTTCTGAACGAATTACT 57.997 40.909 0.00 0.00 0.00 2.24
795 801 5.142061 TGCCACTTCTGAACGAATTACTA 57.858 39.130 0.00 0.00 0.00 1.82
796 802 5.168569 TGCCACTTCTGAACGAATTACTAG 58.831 41.667 0.00 0.00 0.00 2.57
797 803 5.169295 GCCACTTCTGAACGAATTACTAGT 58.831 41.667 0.00 0.00 0.00 2.57
798 804 5.638234 GCCACTTCTGAACGAATTACTAGTT 59.362 40.000 0.00 0.00 0.00 2.24
799 805 6.183360 GCCACTTCTGAACGAATTACTAGTTC 60.183 42.308 0.00 0.00 43.12 3.01
800 806 6.310711 CCACTTCTGAACGAATTACTAGTTCC 59.689 42.308 0.00 0.00 42.40 3.62
801 807 6.310711 CACTTCTGAACGAATTACTAGTTCCC 59.689 42.308 0.00 0.00 42.40 3.97
802 808 5.988310 TCTGAACGAATTACTAGTTCCCA 57.012 39.130 0.00 0.00 42.40 4.37
803 809 6.349243 TCTGAACGAATTACTAGTTCCCAA 57.651 37.500 0.00 0.00 42.40 4.12
804 810 6.161381 TCTGAACGAATTACTAGTTCCCAAC 58.839 40.000 0.00 0.00 42.40 3.77
805 811 5.240121 TGAACGAATTACTAGTTCCCAACC 58.760 41.667 0.00 0.00 42.40 3.77
806 812 4.895668 ACGAATTACTAGTTCCCAACCA 57.104 40.909 0.00 0.00 0.00 3.67
807 813 4.572909 ACGAATTACTAGTTCCCAACCAC 58.427 43.478 0.00 0.00 0.00 4.16
808 814 3.615496 CGAATTACTAGTTCCCAACCACG 59.385 47.826 0.00 0.00 0.00 4.94
809 815 3.622166 ATTACTAGTTCCCAACCACGG 57.378 47.619 0.00 0.00 0.00 4.94
823 829 2.854522 CACGGGTGGAGTGAAATCC 58.145 57.895 0.00 0.00 41.83 3.01
908 914 6.596309 GAAGAATTCCTGAACCCAAGAATT 57.404 37.500 0.65 0.00 42.82 2.17
912 918 6.745794 AATTCCTGAACCCAAGAATTCAAA 57.254 33.333 8.44 0.00 38.43 2.69
913 919 6.745794 ATTCCTGAACCCAAGAATTCAAAA 57.254 33.333 8.44 0.00 31.26 2.44
914 920 6.745794 TTCCTGAACCCAAGAATTCAAAAT 57.254 33.333 8.44 0.00 34.52 1.82
915 921 6.100404 TCCTGAACCCAAGAATTCAAAATG 57.900 37.500 8.44 1.26 34.52 2.32
916 922 5.837979 TCCTGAACCCAAGAATTCAAAATGA 59.162 36.000 8.44 0.00 34.52 2.57
917 923 5.928264 CCTGAACCCAAGAATTCAAAATGAC 59.072 40.000 8.44 0.00 34.52 3.06
918 924 6.462768 CCTGAACCCAAGAATTCAAAATGACA 60.463 38.462 8.44 0.13 34.52 3.58
919 925 6.882656 TGAACCCAAGAATTCAAAATGACAA 58.117 32.000 8.44 0.00 31.95 3.18
920 926 6.985645 TGAACCCAAGAATTCAAAATGACAAG 59.014 34.615 8.44 0.00 31.95 3.16
921 927 6.484364 ACCCAAGAATTCAAAATGACAAGT 57.516 33.333 8.44 0.00 0.00 3.16
922 928 6.888105 ACCCAAGAATTCAAAATGACAAGTT 58.112 32.000 8.44 0.00 0.00 2.66
923 929 6.986231 ACCCAAGAATTCAAAATGACAAGTTC 59.014 34.615 8.44 0.00 0.00 3.01
924 930 6.424812 CCCAAGAATTCAAAATGACAAGTTCC 59.575 38.462 8.44 0.00 0.00 3.62
925 931 7.212274 CCAAGAATTCAAAATGACAAGTTCCT 58.788 34.615 8.44 0.00 0.00 3.36
926 932 7.383300 CCAAGAATTCAAAATGACAAGTTCCTC 59.617 37.037 8.44 0.00 0.00 3.71
927 933 7.830099 AGAATTCAAAATGACAAGTTCCTCT 57.170 32.000 8.44 0.00 0.00 3.69
928 934 8.242729 AGAATTCAAAATGACAAGTTCCTCTT 57.757 30.769 8.44 0.00 36.75 2.85
929 935 8.699130 AGAATTCAAAATGACAAGTTCCTCTTT 58.301 29.630 8.44 0.00 33.63 2.52
930 936 9.965824 GAATTCAAAATGACAAGTTCCTCTTTA 57.034 29.630 0.00 0.00 33.63 1.85
931 937 9.750125 AATTCAAAATGACAAGTTCCTCTTTAC 57.250 29.630 0.00 0.00 33.63 2.01
932 938 7.272037 TCAAAATGACAAGTTCCTCTTTACC 57.728 36.000 0.00 0.00 33.63 2.85
933 939 6.264518 TCAAAATGACAAGTTCCTCTTTACCC 59.735 38.462 0.00 0.00 33.63 3.69
934 940 4.993705 ATGACAAGTTCCTCTTTACCCA 57.006 40.909 0.00 0.00 33.63 4.51
935 941 4.351874 TGACAAGTTCCTCTTTACCCAG 57.648 45.455 0.00 0.00 33.63 4.45
936 942 3.971305 TGACAAGTTCCTCTTTACCCAGA 59.029 43.478 0.00 0.00 33.63 3.86
937 943 4.410883 TGACAAGTTCCTCTTTACCCAGAA 59.589 41.667 0.00 0.00 33.63 3.02
938 944 5.104277 TGACAAGTTCCTCTTTACCCAGAAA 60.104 40.000 0.00 0.00 33.63 2.52
939 945 5.762279 ACAAGTTCCTCTTTACCCAGAAAA 58.238 37.500 0.00 0.00 33.63 2.29
940 946 6.192044 ACAAGTTCCTCTTTACCCAGAAAAA 58.808 36.000 0.00 0.00 33.63 1.94
1179 1185 6.088016 TGGAATCTTGGATTGACTTTGTTG 57.912 37.500 0.00 0.00 0.00 3.33
1693 1699 0.107312 ATGCTCGCTCAAGAGGCATT 60.107 50.000 6.51 0.00 38.63 3.56
1768 1774 9.449719 GTTTATACTCATCTTTTTCCTTCTGGA 57.550 33.333 0.00 0.00 41.36 3.86
1930 1937 6.587608 GCTTGGGCTGCAATATGTATAAAATC 59.412 38.462 0.50 0.00 35.22 2.17
2066 2078 2.147150 GGTCTTGTTCTTCTGGCTGAC 58.853 52.381 0.00 0.00 0.00 3.51
2117 2129 1.672881 ACAACACACTTTGAGCTGCTC 59.327 47.619 22.38 22.38 0.00 4.26
2137 2149 4.263911 GCTCAATTCTATTGCTTTCGTTGC 59.736 41.667 0.00 0.00 0.00 4.17
2152 2164 2.803386 TCGTTGCGTGTAACATTCATGT 59.197 40.909 1.92 0.00 44.20 3.21
2646 2658 5.303165 TCATATGCTTCATACAAGGCAGAG 58.697 41.667 0.00 0.00 38.11 3.35
2655 2667 4.471025 TCATACAAGGCAGAGAAAGATGGA 59.529 41.667 0.00 0.00 0.00 3.41
2761 2773 6.642540 GCTAAAATTTGTTACTGCTGCTTTCT 59.357 34.615 0.00 0.00 0.00 2.52
2780 2792 2.022195 CTTGATCACAGGCATTGGAGG 58.978 52.381 0.00 0.00 0.00 4.30
2938 2950 1.535896 CTTCGTCTCCTTGAGTCGACA 59.464 52.381 19.50 0.00 45.85 4.35
3044 3056 6.216801 TGTAGTCGCTGATACTATTGGTTT 57.783 37.500 0.00 0.00 32.34 3.27
3096 3108 6.285224 CCACCAGGTAACAATCATATCGTTA 58.715 40.000 0.00 0.00 41.41 3.18
3131 3144 7.745620 AAACAATCATATATTCCCTCCGTTC 57.254 36.000 0.00 0.00 0.00 3.95
3132 3145 5.805728 ACAATCATATATTCCCTCCGTTCC 58.194 41.667 0.00 0.00 0.00 3.62
3133 3146 5.548056 ACAATCATATATTCCCTCCGTTCCT 59.452 40.000 0.00 0.00 0.00 3.36
3134 3147 6.729100 ACAATCATATATTCCCTCCGTTCCTA 59.271 38.462 0.00 0.00 0.00 2.94
3135 3148 7.236847 ACAATCATATATTCCCTCCGTTCCTAA 59.763 37.037 0.00 0.00 0.00 2.69
3136 3149 7.808279 ATCATATATTCCCTCCGTTCCTAAA 57.192 36.000 0.00 0.00 0.00 1.85
3137 3150 7.808279 TCATATATTCCCTCCGTTCCTAAAT 57.192 36.000 0.00 0.00 0.00 1.40
3138 3151 8.904648 TCATATATTCCCTCCGTTCCTAAATA 57.095 34.615 0.00 0.00 0.00 1.40
3139 3152 9.502035 TCATATATTCCCTCCGTTCCTAAATAT 57.498 33.333 0.00 0.00 0.00 1.28
3143 3156 5.703730 TCCCTCCGTTCCTAAATATTTGT 57.296 39.130 11.05 0.00 0.00 2.83
3144 3157 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3145 3158 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3148 3161 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3150 3163 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3151 3164 9.947433 TCCGTTCCTAAATATTTGTCTTTCTAA 57.053 29.630 11.05 0.00 0.00 2.10
3166 3179 9.965824 TTGTCTTTCTAAGAATTTCAAATGGAC 57.034 29.630 0.00 0.00 39.67 4.02
3167 3180 9.354673 TGTCTTTCTAAGAATTTCAAATGGACT 57.645 29.630 0.00 0.00 39.67 3.85
3183 3196 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
3184 3197 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
3185 3198 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
3186 3199 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
3187 3200 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
3188 3201 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
3189 3202 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
3190 3203 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
3191 3204 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
3192 3205 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
3194 3207 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
3223 3236 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3224 3237 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3225 3238 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3226 3239 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3227 3240 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3228 3241 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3229 3242 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3230 3243 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3231 3244 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3232 3245 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3233 3246 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3234 3247 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3235 3248 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3236 3249 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3237 3250 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3238 3251 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3239 3252 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3240 3253 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
3241 3254 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3242 3255 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3243 3256 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
3244 3257 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
3245 3258 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
3246 3259 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
3247 3260 7.604549 TCCGTATGTAGTCACTTGTTGAAATA 58.395 34.615 0.00 0.00 35.39 1.40
3248 3261 8.255206 TCCGTATGTAGTCACTTGTTGAAATAT 58.745 33.333 0.00 0.00 35.39 1.28
3249 3262 8.540492 CCGTATGTAGTCACTTGTTGAAATATC 58.460 37.037 0.00 0.00 35.39 1.63
3250 3263 8.259872 CGTATGTAGTCACTTGTTGAAATATCG 58.740 37.037 0.00 0.00 35.39 2.92
3251 3264 9.297586 GTATGTAGTCACTTGTTGAAATATCGA 57.702 33.333 0.00 0.00 35.39 3.59
3252 3265 7.812309 TGTAGTCACTTGTTGAAATATCGAG 57.188 36.000 0.00 0.00 35.39 4.04
3253 3266 7.599171 TGTAGTCACTTGTTGAAATATCGAGA 58.401 34.615 0.00 0.00 35.39 4.04
3254 3267 8.085909 TGTAGTCACTTGTTGAAATATCGAGAA 58.914 33.333 0.00 0.00 35.39 2.87
3255 3268 7.962964 AGTCACTTGTTGAAATATCGAGAAA 57.037 32.000 0.00 0.00 35.39 2.52
3256 3269 8.023050 AGTCACTTGTTGAAATATCGAGAAAG 57.977 34.615 0.00 0.00 35.39 2.62
3257 3270 7.872993 AGTCACTTGTTGAAATATCGAGAAAGA 59.127 33.333 0.00 0.00 35.39 2.52
3258 3271 7.952637 GTCACTTGTTGAAATATCGAGAAAGAC 59.047 37.037 0.00 0.00 35.39 3.01
3259 3272 7.655732 TCACTTGTTGAAATATCGAGAAAGACA 59.344 33.333 0.00 0.00 0.00 3.41
3260 3273 8.282592 CACTTGTTGAAATATCGAGAAAGACAA 58.717 33.333 0.00 0.00 0.00 3.18
3261 3274 8.836413 ACTTGTTGAAATATCGAGAAAGACAAA 58.164 29.630 0.00 0.00 0.00 2.83
3262 3275 9.831737 CTTGTTGAAATATCGAGAAAGACAAAT 57.168 29.630 0.00 0.00 0.00 2.32
3273 3286 8.181487 TCGAGAAAGACAAATATTTAGGAACG 57.819 34.615 0.00 1.20 0.00 3.95
3274 3287 7.277098 TCGAGAAAGACAAATATTTAGGAACGG 59.723 37.037 0.00 0.00 0.00 4.44
3275 3288 7.277098 CGAGAAAGACAAATATTTAGGAACGGA 59.723 37.037 0.00 0.00 0.00 4.69
3276 3289 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3277 3290 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3278 3291 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3279 3292 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3280 3293 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3289 3302 3.398292 AGGAACGGAGGGAGTAGATATGA 59.602 47.826 0.00 0.00 0.00 2.15
3311 3324 2.423577 ACTAACATGCCCGAACTGAAC 58.576 47.619 0.00 0.00 0.00 3.18
3314 3327 0.396435 ACATGCCCGAACTGAACTGA 59.604 50.000 0.00 0.00 0.00 3.41
3315 3328 1.202758 ACATGCCCGAACTGAACTGAA 60.203 47.619 0.00 0.00 0.00 3.02
3316 3329 1.879380 CATGCCCGAACTGAACTGAAA 59.121 47.619 0.00 0.00 0.00 2.69
3317 3330 1.305201 TGCCCGAACTGAACTGAAAC 58.695 50.000 0.00 0.00 0.00 2.78
3319 3332 1.578583 CCCGAACTGAACTGAAACGT 58.421 50.000 0.00 0.00 0.00 3.99
3320 3333 1.937899 CCCGAACTGAACTGAAACGTT 59.062 47.619 0.00 0.00 0.00 3.99
3321 3334 2.353579 CCCGAACTGAACTGAAACGTTT 59.646 45.455 14.57 14.57 0.00 3.60
3322 3335 3.556775 CCCGAACTGAACTGAAACGTTTA 59.443 43.478 14.65 1.97 0.00 2.01
3323 3336 4.318546 CCCGAACTGAACTGAAACGTTTAG 60.319 45.833 14.65 13.49 36.78 1.85
3324 3337 4.269363 CCGAACTGAACTGAAACGTTTAGT 59.731 41.667 14.65 14.10 43.06 2.24
3325 3338 5.421203 CGAACTGAACTGAAACGTTTAGTC 58.579 41.667 14.65 9.29 41.19 2.59
3326 3339 5.555818 CGAACTGAACTGAAACGTTTAGTCC 60.556 44.000 14.65 6.71 41.19 3.85
3406 3462 4.042435 TCCCTTCCAGTGTTTTTACCCTAG 59.958 45.833 0.00 0.00 0.00 3.02
3739 3809 2.818130 GGCAAATTGGCAACTGAGAA 57.182 45.000 14.91 0.00 43.14 2.87
3744 3814 5.008911 GGCAAATTGGCAACTGAGAATTTTT 59.991 36.000 14.91 0.39 43.14 1.94
3745 3815 6.204495 GGCAAATTGGCAACTGAGAATTTTTA 59.796 34.615 14.91 0.00 43.14 1.52
3765 3837 8.880878 TTTTTATTTCCACCTTTAGTTTGCTC 57.119 30.769 0.00 0.00 0.00 4.26
3805 3877 2.393764 CTTCGCGTTCTTGGCAATTTT 58.606 42.857 5.77 0.00 0.00 1.82
3957 4072 3.774702 GCGTGGTTTCTCGGCGAC 61.775 66.667 4.99 0.00 0.00 5.19
4022 4137 3.074369 TTCGATCCGCTGGAGGCA 61.074 61.111 3.76 0.00 41.91 4.75
4050 4165 1.403116 CCCGCTGTATTGTACGTGACA 60.403 52.381 0.00 0.00 35.78 3.58
4423 4541 1.375396 CCAATCGTGCCTTGTCCGA 60.375 57.895 0.00 0.00 34.79 4.55
4450 4568 0.677288 CAGGAACGTGGTGACCTACA 59.323 55.000 2.11 0.00 0.00 2.74
4506 4624 1.909700 ACAAGTGCCGGAATCACAAT 58.090 45.000 5.05 0.00 36.93 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
419 425 7.955918 AGAATCCAGCAGAACAAACTTTAAAT 58.044 30.769 0.00 0.00 0.00 1.40
434 440 6.398095 CGATATACCATGTAAGAATCCAGCA 58.602 40.000 0.00 0.00 0.00 4.41
598 604 3.014623 GCACTTGGTTAAGGGTATCCAC 58.985 50.000 0.00 0.00 39.59 4.02
599 605 2.916934 AGCACTTGGTTAAGGGTATCCA 59.083 45.455 0.00 0.00 39.59 3.41
784 790 4.999311 GTGGTTGGGAACTAGTAATTCGTT 59.001 41.667 0.00 0.00 0.00 3.85
785 791 4.572909 GTGGTTGGGAACTAGTAATTCGT 58.427 43.478 0.00 0.00 0.00 3.85
786 792 3.615496 CGTGGTTGGGAACTAGTAATTCG 59.385 47.826 0.00 0.00 0.00 3.34
787 793 3.937079 CCGTGGTTGGGAACTAGTAATTC 59.063 47.826 0.00 0.00 0.00 2.17
788 794 3.946606 CCGTGGTTGGGAACTAGTAATT 58.053 45.455 0.00 0.00 0.00 1.40
789 795 3.622166 CCGTGGTTGGGAACTAGTAAT 57.378 47.619 0.00 0.00 0.00 1.89
805 811 0.036164 TGGATTTCACTCCACCCGTG 59.964 55.000 0.00 0.00 40.43 4.94
806 812 0.768622 TTGGATTTCACTCCACCCGT 59.231 50.000 0.00 0.00 44.97 5.28
807 813 1.165270 GTTGGATTTCACTCCACCCG 58.835 55.000 0.00 0.00 44.97 5.28
808 814 2.286365 TGTTGGATTTCACTCCACCC 57.714 50.000 0.00 0.00 44.97 4.61
809 815 4.664150 TTTTGTTGGATTTCACTCCACC 57.336 40.909 0.00 0.00 44.97 4.61
877 883 9.768215 TTGGGTTCAGGAATTCTTCTATAATTT 57.232 29.630 5.23 0.00 0.00 1.82
878 884 9.413734 CTTGGGTTCAGGAATTCTTCTATAATT 57.586 33.333 5.23 0.00 0.00 1.40
879 885 8.781951 TCTTGGGTTCAGGAATTCTTCTATAAT 58.218 33.333 5.23 0.00 0.00 1.28
880 886 8.158025 TCTTGGGTTCAGGAATTCTTCTATAA 57.842 34.615 5.23 0.00 0.00 0.98
881 887 7.749377 TCTTGGGTTCAGGAATTCTTCTATA 57.251 36.000 5.23 0.00 0.00 1.31
882 888 6.642733 TCTTGGGTTCAGGAATTCTTCTAT 57.357 37.500 5.23 0.00 0.00 1.98
883 889 6.448369 TTCTTGGGTTCAGGAATTCTTCTA 57.552 37.500 5.23 0.00 34.64 2.10
884 890 5.324832 TTCTTGGGTTCAGGAATTCTTCT 57.675 39.130 5.23 0.00 34.64 2.85
891 897 6.326064 TCATTTTGAATTCTTGGGTTCAGGAA 59.674 34.615 7.05 0.00 42.00 3.36
892 898 5.837979 TCATTTTGAATTCTTGGGTTCAGGA 59.162 36.000 7.05 0.00 35.91 3.86
893 899 5.928264 GTCATTTTGAATTCTTGGGTTCAGG 59.072 40.000 7.05 0.00 35.91 3.86
894 900 6.514947 TGTCATTTTGAATTCTTGGGTTCAG 58.485 36.000 7.05 0.00 35.91 3.02
895 901 6.477053 TGTCATTTTGAATTCTTGGGTTCA 57.523 33.333 7.05 0.00 32.86 3.18
896 902 6.986231 ACTTGTCATTTTGAATTCTTGGGTTC 59.014 34.615 7.05 0.00 0.00 3.62
897 903 6.888105 ACTTGTCATTTTGAATTCTTGGGTT 58.112 32.000 7.05 0.00 0.00 4.11
898 904 6.484364 ACTTGTCATTTTGAATTCTTGGGT 57.516 33.333 7.05 0.00 0.00 4.51
899 905 6.424812 GGAACTTGTCATTTTGAATTCTTGGG 59.575 38.462 7.05 0.00 0.00 4.12
900 906 7.212274 AGGAACTTGTCATTTTGAATTCTTGG 58.788 34.615 7.05 0.00 27.25 3.61
901 907 8.139989 AGAGGAACTTGTCATTTTGAATTCTTG 58.860 33.333 7.05 0.06 41.55 3.02
902 908 8.242729 AGAGGAACTTGTCATTTTGAATTCTT 57.757 30.769 7.05 0.00 41.55 2.52
903 909 7.830099 AGAGGAACTTGTCATTTTGAATTCT 57.170 32.000 7.05 0.00 41.55 2.40
904 910 8.877808 AAAGAGGAACTTGTCATTTTGAATTC 57.122 30.769 0.00 0.00 41.55 2.17
905 911 9.750125 GTAAAGAGGAACTTGTCATTTTGAATT 57.250 29.630 0.00 0.00 41.55 2.17
906 912 8.360390 GGTAAAGAGGAACTTGTCATTTTGAAT 58.640 33.333 0.00 0.00 41.55 2.57
907 913 7.201875 GGGTAAAGAGGAACTTGTCATTTTGAA 60.202 37.037 0.00 0.00 41.55 2.69
908 914 6.264518 GGGTAAAGAGGAACTTGTCATTTTGA 59.735 38.462 0.00 0.00 41.55 2.69
909 915 6.040391 TGGGTAAAGAGGAACTTGTCATTTTG 59.960 38.462 0.00 0.00 41.55 2.44
910 916 6.133356 TGGGTAAAGAGGAACTTGTCATTTT 58.867 36.000 0.00 0.00 41.55 1.82
911 917 5.701224 TGGGTAAAGAGGAACTTGTCATTT 58.299 37.500 0.00 0.00 41.55 2.32
912 918 5.073144 TCTGGGTAAAGAGGAACTTGTCATT 59.927 40.000 0.00 0.00 41.55 2.57
913 919 4.597507 TCTGGGTAAAGAGGAACTTGTCAT 59.402 41.667 0.00 0.00 41.55 3.06
914 920 3.971305 TCTGGGTAAAGAGGAACTTGTCA 59.029 43.478 0.00 0.00 41.55 3.58
915 921 4.618920 TCTGGGTAAAGAGGAACTTGTC 57.381 45.455 0.00 0.00 41.55 3.18
916 922 5.382664 TTTCTGGGTAAAGAGGAACTTGT 57.617 39.130 0.00 0.00 41.55 3.16
917 923 6.709018 TTTTTCTGGGTAAAGAGGAACTTG 57.291 37.500 0.00 0.00 41.55 3.16
1179 1185 9.910267 TTTTATACCCTAGGAGAATGGTAAAAC 57.090 33.333 11.48 0.00 36.95 2.43
1693 1699 0.250553 CCACCAAAGCCCTAACGTCA 60.251 55.000 0.00 0.00 0.00 4.35
2066 2078 2.700897 AGAACCATTATCCCTCACCTCG 59.299 50.000 0.00 0.00 0.00 4.63
2117 2129 4.029418 CACGCAACGAAAGCAATAGAATTG 59.971 41.667 0.00 0.00 0.00 2.32
2646 2658 3.629398 ACGATGCAAGGATTCCATCTTTC 59.371 43.478 5.29 0.00 34.63 2.62
2655 2667 2.205074 CGAGCTAACGATGCAAGGATT 58.795 47.619 0.00 0.00 35.09 3.01
2690 2702 5.396884 GGGGTATGAGATATAGAACCATGGC 60.397 48.000 13.04 0.00 0.00 4.40
2735 2747 5.452078 AGCAGCAGTAACAAATTTTAGCA 57.548 34.783 0.00 0.00 0.00 3.49
2761 2773 1.355381 ACCTCCAATGCCTGTGATCAA 59.645 47.619 0.00 0.00 0.00 2.57
2780 2792 4.518970 TCCCTCAAGTTTACTGAATGCAAC 59.481 41.667 0.00 0.00 0.00 4.17
2938 2950 0.246635 CAGGGACAACGACGATTCCT 59.753 55.000 0.00 0.00 0.00 3.36
3059 3071 6.493802 TGTTACCTGGTGGTTAAAATAATGCA 59.506 34.615 10.23 0.00 46.05 3.96
3073 3085 7.655732 TGATAACGATATGATTGTTACCTGGTG 59.344 37.037 10.23 0.00 40.81 4.17
3122 3135 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3123 3136 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3124 3137 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3145 3158 9.581289 TGGTAGTCCATTTGAAATTCTTAGAAA 57.419 29.630 0.00 0.00 39.03 2.52
3148 3161 8.335532 TGTGGTAGTCCATTTGAAATTCTTAG 57.664 34.615 0.00 0.00 46.20 2.18
3150 3163 7.781324 ATGTGGTAGTCCATTTGAAATTCTT 57.219 32.000 0.00 0.00 46.20 2.52
3151 3164 7.065803 CGTATGTGGTAGTCCATTTGAAATTCT 59.934 37.037 0.00 0.00 46.20 2.40
3152 3165 7.186804 CGTATGTGGTAGTCCATTTGAAATTC 58.813 38.462 0.00 0.00 46.20 2.17
3154 3167 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
3155 3168 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
3156 3169 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
3157 3170 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
3158 3171 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
3159 3172 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
3160 3173 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
3161 3174 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
3162 3175 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
3163 3176 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
3164 3177 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
3165 3178 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
3166 3179 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
3168 3181 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
3201 3214 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3202 3215 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3203 3216 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3204 3217 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3205 3218 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3206 3219 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3207 3220 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3208 3221 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3209 3222 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3210 3223 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3211 3224 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3212 3225 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3213 3226 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3214 3227 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
3215 3228 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
3216 3229 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3217 3230 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
3218 3231 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
3219 3232 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
3220 3233 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3221 3234 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
3222 3235 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
3223 3236 6.721571 ATTTCAACAAGTGACTACATACGG 57.278 37.500 0.00 0.00 35.39 4.02
3224 3237 8.259872 CGATATTTCAACAAGTGACTACATACG 58.740 37.037 0.00 0.00 35.39 3.06
3225 3238 9.297586 TCGATATTTCAACAAGTGACTACATAC 57.702 33.333 0.00 0.00 35.39 2.39
3226 3239 9.516314 CTCGATATTTCAACAAGTGACTACATA 57.484 33.333 0.00 0.00 35.39 2.29
3227 3240 8.251026 TCTCGATATTTCAACAAGTGACTACAT 58.749 33.333 0.00 0.00 35.39 2.29
3228 3241 7.599171 TCTCGATATTTCAACAAGTGACTACA 58.401 34.615 0.00 0.00 35.39 2.74
3229 3242 8.462143 TTCTCGATATTTCAACAAGTGACTAC 57.538 34.615 0.00 0.00 35.39 2.73
3230 3243 9.140286 CTTTCTCGATATTTCAACAAGTGACTA 57.860 33.333 0.00 0.00 35.39 2.59
3231 3244 7.872993 TCTTTCTCGATATTTCAACAAGTGACT 59.127 33.333 0.00 0.00 35.39 3.41
3232 3245 7.952637 GTCTTTCTCGATATTTCAACAAGTGAC 59.047 37.037 0.00 0.00 35.39 3.67
3233 3246 7.655732 TGTCTTTCTCGATATTTCAACAAGTGA 59.344 33.333 0.00 0.00 0.00 3.41
3234 3247 7.796838 TGTCTTTCTCGATATTTCAACAAGTG 58.203 34.615 0.00 0.00 0.00 3.16
3235 3248 7.962964 TGTCTTTCTCGATATTTCAACAAGT 57.037 32.000 0.00 0.00 0.00 3.16
3236 3249 9.831737 ATTTGTCTTTCTCGATATTTCAACAAG 57.168 29.630 0.00 0.00 0.00 3.16
3247 3260 8.818057 CGTTCCTAAATATTTGTCTTTCTCGAT 58.182 33.333 11.05 0.00 0.00 3.59
3248 3261 7.277098 CCGTTCCTAAATATTTGTCTTTCTCGA 59.723 37.037 11.05 0.00 0.00 4.04
3249 3262 7.277098 TCCGTTCCTAAATATTTGTCTTTCTCG 59.723 37.037 11.05 5.67 0.00 4.04
3250 3263 8.488651 TCCGTTCCTAAATATTTGTCTTTCTC 57.511 34.615 11.05 0.00 0.00 2.87
3251 3264 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3252 3265 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3253 3266 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3254 3267 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3255 3268 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3256 3269 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3257 3270 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3258 3271 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3259 3272 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3260 3273 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
3261 3274 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
3262 3275 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
3263 3276 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3264 3277 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
3265 3278 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
3266 3279 4.600547 TCATATCTACTCCCTCCGTTCCTA 59.399 45.833 0.00 0.00 0.00 2.94
3267 3280 3.398292 TCATATCTACTCCCTCCGTTCCT 59.602 47.826 0.00 0.00 0.00 3.36
3268 3281 3.764218 TCATATCTACTCCCTCCGTTCC 58.236 50.000 0.00 0.00 0.00 3.62
3269 3282 5.302313 AGTTTCATATCTACTCCCTCCGTTC 59.698 44.000 0.00 0.00 0.00 3.95
3270 3283 5.209659 AGTTTCATATCTACTCCCTCCGTT 58.790 41.667 0.00 0.00 0.00 4.44
3271 3284 4.805744 AGTTTCATATCTACTCCCTCCGT 58.194 43.478 0.00 0.00 0.00 4.69
3272 3285 6.264744 TGTTAGTTTCATATCTACTCCCTCCG 59.735 42.308 0.00 0.00 0.00 4.63
3273 3286 7.598759 TGTTAGTTTCATATCTACTCCCTCC 57.401 40.000 0.00 0.00 0.00 4.30
3274 3287 7.600752 GCATGTTAGTTTCATATCTACTCCCTC 59.399 40.741 0.00 0.00 0.00 4.30
3275 3288 7.445945 GCATGTTAGTTTCATATCTACTCCCT 58.554 38.462 0.00 0.00 0.00 4.20
3276 3289 6.651225 GGCATGTTAGTTTCATATCTACTCCC 59.349 42.308 0.00 0.00 0.00 4.30
3277 3290 6.651225 GGGCATGTTAGTTTCATATCTACTCC 59.349 42.308 0.00 0.00 0.00 3.85
3278 3291 6.366332 CGGGCATGTTAGTTTCATATCTACTC 59.634 42.308 0.00 0.00 0.00 2.59
3279 3292 6.041637 TCGGGCATGTTAGTTTCATATCTACT 59.958 38.462 0.00 0.00 0.00 2.57
3280 3293 6.220930 TCGGGCATGTTAGTTTCATATCTAC 58.779 40.000 0.00 0.00 0.00 2.59
3289 3302 3.134574 TCAGTTCGGGCATGTTAGTTT 57.865 42.857 0.00 0.00 0.00 2.66
3311 3324 7.416154 TTCACTAATGGACTAAACGTTTCAG 57.584 36.000 18.42 14.87 0.00 3.02
3314 3327 6.261381 TGCTTTCACTAATGGACTAAACGTTT 59.739 34.615 18.90 18.90 0.00 3.60
3315 3328 5.761234 TGCTTTCACTAATGGACTAAACGTT 59.239 36.000 0.00 0.00 0.00 3.99
3316 3329 5.302360 TGCTTTCACTAATGGACTAAACGT 58.698 37.500 0.00 0.00 0.00 3.99
3317 3330 5.856126 TGCTTTCACTAATGGACTAAACG 57.144 39.130 0.00 0.00 0.00 3.60
3320 3333 8.902806 CCATAAATGCTTTCACTAATGGACTAA 58.097 33.333 0.00 0.00 0.00 2.24
3321 3334 8.271458 TCCATAAATGCTTTCACTAATGGACTA 58.729 33.333 0.00 0.00 30.46 2.59
3322 3335 7.067494 GTCCATAAATGCTTTCACTAATGGACT 59.933 37.037 19.06 0.00 46.31 3.85
3323 3336 7.196331 GTCCATAAATGCTTTCACTAATGGAC 58.804 38.462 13.58 13.58 44.68 4.02
3324 3337 7.118723 AGTCCATAAATGCTTTCACTAATGGA 58.881 34.615 0.00 0.00 32.71 3.41
3325 3338 7.284034 AGAGTCCATAAATGCTTTCACTAATGG 59.716 37.037 0.00 0.00 0.00 3.16
3326 3339 8.127327 CAGAGTCCATAAATGCTTTCACTAATG 58.873 37.037 0.00 0.00 0.00 1.90
3377 3433 5.847111 AAAAACACTGGAAGGGAAAGTAC 57.153 39.130 0.00 0.00 43.23 2.73
3406 3462 5.565439 GAGTATCAATGGCAATGTTATGGCC 60.565 44.000 1.93 0.00 41.13 5.36
3502 3558 3.369381 CGTGAAGCGGGAGATGATT 57.631 52.632 0.00 0.00 36.85 2.57
3739 3809 9.489084 GAGCAAACTAAAGGTGGAAATAAAAAT 57.511 29.630 0.00 0.00 0.00 1.82
3744 3814 5.553123 TCGAGCAAACTAAAGGTGGAAATA 58.447 37.500 0.00 0.00 0.00 1.40
3745 3815 4.394729 TCGAGCAAACTAAAGGTGGAAAT 58.605 39.130 0.00 0.00 0.00 2.17
3765 3837 2.231478 AGGTATTCCGCCACAGATATCG 59.769 50.000 0.00 0.00 39.05 2.92
3805 3877 2.346803 GCCTTGCTCGTCATACTTCAA 58.653 47.619 0.00 0.00 0.00 2.69
3847 3919 5.094387 CCTATACTCCCACCCATACAGATT 58.906 45.833 0.00 0.00 0.00 2.40
4050 4165 2.612972 CGCACATTAACTGTCCTCACCT 60.613 50.000 0.00 0.00 35.29 4.00
4110 4225 3.389925 AAACACCGTGAAATCCTCGTA 57.610 42.857 5.28 0.00 0.00 3.43
4298 4416 0.774491 TGGGGCCAGTCTAGGGTTTT 60.774 55.000 4.39 0.00 0.00 2.43
4423 4541 2.625823 CCACGTTCCTGCCGCAATT 61.626 57.895 0.00 0.00 0.00 2.32
4506 4624 5.534654 CCCAATCCAAGAAACTTGACTTACA 59.465 40.000 12.25 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.