Multiple sequence alignment - TraesCS4D01G333700

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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 TraesCS4D01G333700 chr4D 100.000 3240 0 0 1 3240 490989967 490993206 0.000000e+00 5984
1 TraesCS4D01G333700 chr4D 94.231 312 16 2 1 311 325428892 325428582 2.920000e-130 475
2 TraesCS4D01G333700 chr4D 82.526 475 35 16 312 756 45005984 45005528 1.100000e-99 374
3 TraesCS4D01G333700 chr4D 79.042 501 50 22 315 785 46140434 46139959 3.160000e-75 292
4 TraesCS4D01G333700 chr5A 95.670 2748 77 14 516 3240 160774244 160776972 0.000000e+00 4377
5 TraesCS4D01G333700 chr5A 89.604 202 9 5 311 500 584100321 584100120 2.500000e-61 246
6 TraesCS4D01G333700 chr5A 80.508 354 41 9 312 644 611694152 611694498 2.500000e-61 246
7 TraesCS4D01G333700 chr5A 89.552 201 9 3 312 500 160773584 160773784 8.980000e-61 244
8 TraesCS4D01G333700 chr7D 92.052 843 39 15 915 1736 102968614 102969449 0.000000e+00 1160
9 TraesCS4D01G333700 chr7D 91.987 312 24 1 1 311 104789049 104788738 1.380000e-118 436
10 TraesCS4D01G333700 chr7D 78.788 198 32 8 312 500 119902325 119902521 1.220000e-24 124
11 TraesCS4D01G333700 chr7B 92.233 824 45 8 926 1736 61557517 61558334 0.000000e+00 1149
12 TraesCS4D01G333700 chr7B 88.216 611 35 13 311 894 62675802 62676402 0.000000e+00 695
13 TraesCS4D01G333700 chr7A 91.294 850 37 18 913 1736 107847177 107848015 0.000000e+00 1125
14 TraesCS4D01G333700 chr7A 82.017 595 87 11 2179 2767 381463683 381463103 3.760000e-134 488
15 TraesCS4D01G333700 chr7A 78.697 568 71 24 2186 2739 21893764 21894295 1.860000e-87 333
16 TraesCS4D01G333700 chr7A 80.511 313 47 10 2933 3240 381463026 381462723 9.040000e-56 228
17 TraesCS4D01G333700 chr7A 84.091 132 8 7 772 893 10912952 10912824 7.350000e-22 115
18 TraesCS4D01G333700 chr7A 100.000 40 0 0 3201 3240 134477006 134477045 1.250000e-09 75
19 TraesCS4D01G333700 chr3D 98.571 560 8 0 2681 3240 125792497 125793056 0.000000e+00 990
20 TraesCS4D01G333700 chr3D 94.872 312 14 2 1 311 111863917 111863607 1.350000e-133 486
21 TraesCS4D01G333700 chrUn 92.384 604 24 7 312 894 101497966 101498568 0.000000e+00 841
22 TraesCS4D01G333700 chrUn 87.805 615 42 7 312 894 279889545 279890158 0.000000e+00 689
23 TraesCS4D01G333700 chrUn 88.421 570 31 11 312 846 12652937 12653506 0.000000e+00 654
24 TraesCS4D01G333700 chrUn 87.109 543 37 10 310 826 348340723 348340188 4.660000e-163 584
25 TraesCS4D01G333700 chrUn 86.740 543 39 12 310 826 371131694 371131159 1.010000e-159 573
26 TraesCS4D01G333700 chrUn 86.740 543 39 10 310 826 469113822 469113287 1.010000e-159 573
27 TraesCS4D01G333700 chrUn 83.934 361 25 7 312 640 288550053 288550412 6.750000e-82 315
28 TraesCS4D01G333700 chrUn 83.934 361 25 7 312 640 288556054 288556413 6.750000e-82 315
29 TraesCS4D01G333700 chrUn 83.934 361 25 7 312 640 311956548 311956189 6.750000e-82 315
30 TraesCS4D01G333700 chr6B 98.886 449 5 0 2791 3239 139136599 139136151 0.000000e+00 802
31 TraesCS4D01G333700 chr6B 89.180 610 36 12 312 894 585476543 585477149 0.000000e+00 734
32 TraesCS4D01G333700 chr3A 89.627 617 30 8 312 894 28578042 28577426 0.000000e+00 754
33 TraesCS4D01G333700 chr3A 86.911 191 20 3 312 500 555389631 555389818 3.280000e-50 209
34 TraesCS4D01G333700 chr4A 88.052 611 40 10 310 894 714703480 714704083 0.000000e+00 693
35 TraesCS4D01G333700 chr4A 91.667 324 19 4 572 894 714663919 714664235 2.970000e-120 442
36 TraesCS4D01G333700 chr4A 82.988 482 39 14 311 751 226046005 226046484 2.340000e-106 396
37 TraesCS4D01G333700 chr4B 87.869 610 45 14 312 894 430671030 430671637 0.000000e+00 689
38 TraesCS4D01G333700 chr4B 81.926 592 87 12 2183 2767 531476324 531476902 1.750000e-132 483
39 TraesCS4D01G333700 chr4B 75.693 1082 151 50 1743 2767 561515366 561514340 3.840000e-119 438
40 TraesCS4D01G333700 chr4B 83.036 336 27 9 313 622 547413768 547413437 8.850000e-71 278
41 TraesCS4D01G333700 chr4B 83.673 196 24 6 3017 3209 531477015 531477205 9.240000e-41 178
42 TraesCS4D01G333700 chr4B 87.023 131 15 2 2921 3051 561514275 561514147 2.600000e-31 147
43 TraesCS4D01G333700 chr1B 79.217 1073 157 40 2188 3240 136823635 136822609 0.000000e+00 686
44 TraesCS4D01G333700 chr6A 88.177 609 24 10 312 894 10664055 10663469 0.000000e+00 682
45 TraesCS4D01G333700 chr6A 100.000 40 0 0 3201 3240 10662380 10662341 1.250000e-09 75
46 TraesCS4D01G333700 chr1A 86.971 614 28 17 312 894 20539166 20539758 0.000000e+00 643
47 TraesCS4D01G333700 chr1A 86.020 608 36 11 312 893 43992173 43992757 9.940000e-170 606
48 TraesCS4D01G333700 chr1A 82.887 485 38 16 311 751 26281389 26280906 8.430000e-106 394
49 TraesCS4D01G333700 chr1A 82.249 338 33 8 312 622 378971902 378972239 1.920000e-67 267
50 TraesCS4D01G333700 chr1A 81.269 331 35 8 312 615 378939391 378939721 3.230000e-60 243
51 TraesCS4D01G333700 chr1A 100.000 40 0 0 3201 3240 43993849 43993888 1.250000e-09 75
52 TraesCS4D01G333700 chr5D 95.192 312 13 2 1 311 394411662 394411352 2.900000e-135 492
53 TraesCS4D01G333700 chr5D 92.258 310 23 1 1 309 471740734 471741043 3.840000e-119 438
54 TraesCS4D01G333700 chr5D 91.935 310 24 1 1 309 471589031 471589340 1.790000e-117 433
55 TraesCS4D01G333700 chr6D 94.231 312 16 2 1 311 455793163 455792853 2.920000e-130 475
56 TraesCS4D01G333700 chr6D 90.580 138 6 6 594 729 234436515 234436647 3.320000e-40 176
57 TraesCS4D01G333700 chr2D 91.987 312 24 1 1 311 349496531 349496842 1.380000e-118 436
58 TraesCS4D01G333700 chr2D 80.730 493 58 27 312 785 622710762 622711236 1.850000e-92 350
59 TraesCS4D01G333700 chr2D 90.000 100 9 1 2976 3075 638458771 638458673 9.440000e-26 128
60 TraesCS4D01G333700 chr1D 91.987 312 24 1 1 311 78929891 78930202 1.380000e-118 436
61 TraesCS4D01G333700 chr1D 97.449 196 5 0 3045 3240 260419890 260419695 5.180000e-88 335
62 TraesCS4D01G333700 chr5B 97.710 131 3 0 2618 2748 167816671 167816801 3.250000e-55 226
63 TraesCS4D01G333700 chr2B 91.603 131 9 2 765 894 50223423 50223552 2.570000e-41 180


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 TraesCS4D01G333700 chr4D 490989967 490993206 3239 False 5984.0 5984 100.0000 1 3240 1 chr4D.!!$F1 3239
1 TraesCS4D01G333700 chr5A 160773584 160776972 3388 False 2310.5 4377 92.6110 312 3240 2 chr5A.!!$F2 2928
2 TraesCS4D01G333700 chr7D 102968614 102969449 835 False 1160.0 1160 92.0520 915 1736 1 chr7D.!!$F1 821
3 TraesCS4D01G333700 chr7B 61557517 61558334 817 False 1149.0 1149 92.2330 926 1736 1 chr7B.!!$F1 810
4 TraesCS4D01G333700 chr7B 62675802 62676402 600 False 695.0 695 88.2160 311 894 1 chr7B.!!$F2 583
5 TraesCS4D01G333700 chr7A 107847177 107848015 838 False 1125.0 1125 91.2940 913 1736 1 chr7A.!!$F2 823
6 TraesCS4D01G333700 chr7A 381462723 381463683 960 True 358.0 488 81.2640 2179 3240 2 chr7A.!!$R2 1061
7 TraesCS4D01G333700 chr7A 21893764 21894295 531 False 333.0 333 78.6970 2186 2739 1 chr7A.!!$F1 553
8 TraesCS4D01G333700 chr3D 125792497 125793056 559 False 990.0 990 98.5710 2681 3240 1 chr3D.!!$F1 559
9 TraesCS4D01G333700 chrUn 101497966 101498568 602 False 841.0 841 92.3840 312 894 1 chrUn.!!$F2 582
10 TraesCS4D01G333700 chrUn 279889545 279890158 613 False 689.0 689 87.8050 312 894 1 chrUn.!!$F3 582
11 TraesCS4D01G333700 chrUn 12652937 12653506 569 False 654.0 654 88.4210 312 846 1 chrUn.!!$F1 534
12 TraesCS4D01G333700 chrUn 348340188 348340723 535 True 584.0 584 87.1090 310 826 1 chrUn.!!$R2 516
13 TraesCS4D01G333700 chrUn 371131159 371131694 535 True 573.0 573 86.7400 310 826 1 chrUn.!!$R3 516
14 TraesCS4D01G333700 chrUn 469113287 469113822 535 True 573.0 573 86.7400 310 826 1 chrUn.!!$R4 516
15 TraesCS4D01G333700 chr6B 585476543 585477149 606 False 734.0 734 89.1800 312 894 1 chr6B.!!$F1 582
16 TraesCS4D01G333700 chr3A 28577426 28578042 616 True 754.0 754 89.6270 312 894 1 chr3A.!!$R1 582
17 TraesCS4D01G333700 chr4A 714703480 714704083 603 False 693.0 693 88.0520 310 894 1 chr4A.!!$F3 584
18 TraesCS4D01G333700 chr4B 430671030 430671637 607 False 689.0 689 87.8690 312 894 1 chr4B.!!$F1 582
19 TraesCS4D01G333700 chr4B 531476324 531477205 881 False 330.5 483 82.7995 2183 3209 2 chr4B.!!$F2 1026
20 TraesCS4D01G333700 chr4B 561514147 561515366 1219 True 292.5 438 81.3580 1743 3051 2 chr4B.!!$R2 1308
21 TraesCS4D01G333700 chr1B 136822609 136823635 1026 True 686.0 686 79.2170 2188 3240 1 chr1B.!!$R1 1052
22 TraesCS4D01G333700 chr6A 10662341 10664055 1714 True 378.5 682 94.0885 312 3240 2 chr6A.!!$R1 2928
23 TraesCS4D01G333700 chr1A 20539166 20539758 592 False 643.0 643 86.9710 312 894 1 chr1A.!!$F1 582
24 TraesCS4D01G333700 chr1A 43992173 43993888 1715 False 340.5 606 93.0100 312 3240 2 chr1A.!!$F4 2928

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
239 240 0.037590 CCCCAGGTCAAATCGGTGAA 59.962 55.000 0.00 0.00 0.00 3.18 F
301 302 1.008309 GCGCTCAGGGACGTCTATC 60.008 63.158 16.46 5.79 0.00 2.08 F
303 304 1.158484 CGCTCAGGGACGTCTATCGA 61.158 60.000 16.46 6.44 42.86 3.59 F
304 305 1.240256 GCTCAGGGACGTCTATCGAT 58.760 55.000 16.46 2.16 42.86 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1710 1.343176 ACAGAGGCTAGGGTTAGGGTC 60.343 57.143 0.00 0.0 0.00 4.46 R
2136 2909 3.972133 TGAAAGATCAATGGTGCCATCT 58.028 40.909 3.96 0.0 35.31 2.90 R
2137 2910 4.931661 ATGAAAGATCAATGGTGCCATC 57.068 40.909 3.96 0.0 39.49 3.51 R
2794 3679 5.953183 TGCTGCCAATACTCAATTAACTTG 58.047 37.500 0.00 0.0 36.09 3.16 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
20 21 2.586648 AGAAACAACCAGGGACCATC 57.413 50.000 0.00 0.00 0.00 3.51
21 22 1.075536 AGAAACAACCAGGGACCATCC 59.924 52.381 0.00 0.00 35.23 3.51
22 23 0.856982 AAACAACCAGGGACCATCCA 59.143 50.000 0.00 0.00 38.64 3.41
23 24 0.405585 AACAACCAGGGACCATCCAG 59.594 55.000 0.00 0.00 38.64 3.86
24 25 1.379044 CAACCAGGGACCATCCAGC 60.379 63.158 0.00 0.00 38.64 4.85
25 26 2.616458 AACCAGGGACCATCCAGCC 61.616 63.158 0.00 0.00 38.64 4.85
26 27 2.693864 CCAGGGACCATCCAGCCT 60.694 66.667 0.00 0.00 38.64 4.58
27 28 2.593978 CAGGGACCATCCAGCCTG 59.406 66.667 0.00 0.00 38.64 4.85
28 29 2.693864 AGGGACCATCCAGCCTGG 60.694 66.667 3.69 3.69 38.64 4.45
36 37 2.364973 TCCAGCCTGGACCGCATA 60.365 61.111 10.05 0.00 42.67 3.14
37 38 2.203070 CCAGCCTGGACCGCATAC 60.203 66.667 4.15 0.00 40.96 2.39
38 39 2.735772 CCAGCCTGGACCGCATACT 61.736 63.158 4.15 0.00 40.96 2.12
39 40 1.221840 CAGCCTGGACCGCATACTT 59.778 57.895 0.00 0.00 0.00 2.24
40 41 1.091771 CAGCCTGGACCGCATACTTG 61.092 60.000 0.00 0.00 0.00 3.16
41 42 1.220749 GCCTGGACCGCATACTTGA 59.779 57.895 0.00 0.00 0.00 3.02
42 43 1.090052 GCCTGGACCGCATACTTGAC 61.090 60.000 0.00 0.00 0.00 3.18
43 44 0.462047 CCTGGACCGCATACTTGACC 60.462 60.000 0.00 0.00 0.00 4.02
44 45 0.806102 CTGGACCGCATACTTGACCG 60.806 60.000 0.00 0.00 0.00 4.79
45 46 2.171725 GGACCGCATACTTGACCGC 61.172 63.158 0.00 0.00 0.00 5.68
46 47 2.125269 ACCGCATACTTGACCGCC 60.125 61.111 0.00 0.00 0.00 6.13
47 48 2.895372 CCGCATACTTGACCGCCC 60.895 66.667 0.00 0.00 0.00 6.13
48 49 3.261951 CGCATACTTGACCGCCCG 61.262 66.667 0.00 0.00 0.00 6.13
49 50 2.125269 GCATACTTGACCGCCCGT 60.125 61.111 0.00 0.00 0.00 5.28
50 51 2.461110 GCATACTTGACCGCCCGTG 61.461 63.158 0.00 0.00 0.00 4.94
51 52 2.125269 ATACTTGACCGCCCGTGC 60.125 61.111 0.00 0.00 0.00 5.34
52 53 3.675619 ATACTTGACCGCCCGTGCC 62.676 63.158 0.00 0.00 0.00 5.01
57 58 3.845259 GACCGCCCGTGCCAGATA 61.845 66.667 0.00 0.00 0.00 1.98
58 59 4.157120 ACCGCCCGTGCCAGATAC 62.157 66.667 0.00 0.00 0.00 2.24
59 60 4.155733 CCGCCCGTGCCAGATACA 62.156 66.667 0.00 0.00 0.00 2.29
60 61 2.108976 CGCCCGTGCCAGATACAT 59.891 61.111 0.00 0.00 0.00 2.29
61 62 2.246739 CGCCCGTGCCAGATACATG 61.247 63.158 0.00 0.00 0.00 3.21
62 63 1.893808 GCCCGTGCCAGATACATGG 60.894 63.158 0.00 0.00 42.79 3.66
68 69 4.907457 CCAGATACATGGCACCCC 57.093 61.111 0.00 0.00 32.48 4.95
70 71 0.179009 CCAGATACATGGCACCCCAG 60.179 60.000 0.00 0.00 46.24 4.45
71 72 0.839277 CAGATACATGGCACCCCAGA 59.161 55.000 0.00 0.00 46.24 3.86
72 73 0.839946 AGATACATGGCACCCCAGAC 59.160 55.000 0.00 0.00 46.24 3.51
73 74 0.546122 GATACATGGCACCCCAGACA 59.454 55.000 0.00 0.00 46.24 3.41
74 75 0.998928 ATACATGGCACCCCAGACAA 59.001 50.000 0.00 0.00 46.24 3.18
75 76 0.327924 TACATGGCACCCCAGACAAG 59.672 55.000 0.00 0.00 46.24 3.16
76 77 2.036256 ATGGCACCCCAGACAAGC 59.964 61.111 0.00 0.00 46.24 4.01
77 78 3.590466 ATGGCACCCCAGACAAGCC 62.590 63.158 0.00 0.00 46.24 4.35
78 79 4.284550 GGCACCCCAGACAAGCCA 62.285 66.667 0.00 0.00 44.59 4.75
79 80 2.674380 GCACCCCAGACAAGCCAG 60.674 66.667 0.00 0.00 0.00 4.85
80 81 2.674380 CACCCCAGACAAGCCAGC 60.674 66.667 0.00 0.00 0.00 4.85
81 82 3.971702 ACCCCAGACAAGCCAGCC 61.972 66.667 0.00 0.00 0.00 4.85
82 83 3.970410 CCCCAGACAAGCCAGCCA 61.970 66.667 0.00 0.00 0.00 4.75
83 84 2.115910 CCCAGACAAGCCAGCCAA 59.884 61.111 0.00 0.00 0.00 4.52
84 85 2.270986 CCCAGACAAGCCAGCCAAC 61.271 63.158 0.00 0.00 0.00 3.77
85 86 2.270986 CCAGACAAGCCAGCCAACC 61.271 63.158 0.00 0.00 0.00 3.77
86 87 1.529010 CAGACAAGCCAGCCAACCA 60.529 57.895 0.00 0.00 0.00 3.67
87 88 0.896940 CAGACAAGCCAGCCAACCAT 60.897 55.000 0.00 0.00 0.00 3.55
88 89 0.698238 AGACAAGCCAGCCAACCATA 59.302 50.000 0.00 0.00 0.00 2.74
89 90 0.811281 GACAAGCCAGCCAACCATAC 59.189 55.000 0.00 0.00 0.00 2.39
90 91 0.611896 ACAAGCCAGCCAACCATACC 60.612 55.000 0.00 0.00 0.00 2.73
91 92 0.611618 CAAGCCAGCCAACCATACCA 60.612 55.000 0.00 0.00 0.00 3.25
92 93 0.114168 AAGCCAGCCAACCATACCAA 59.886 50.000 0.00 0.00 0.00 3.67
93 94 0.611896 AGCCAGCCAACCATACCAAC 60.612 55.000 0.00 0.00 0.00 3.77
94 95 0.897863 GCCAGCCAACCATACCAACA 60.898 55.000 0.00 0.00 0.00 3.33
95 96 1.176527 CCAGCCAACCATACCAACAG 58.823 55.000 0.00 0.00 0.00 3.16
96 97 1.271871 CCAGCCAACCATACCAACAGA 60.272 52.381 0.00 0.00 0.00 3.41
97 98 2.086869 CAGCCAACCATACCAACAGAG 58.913 52.381 0.00 0.00 0.00 3.35
98 99 1.985159 AGCCAACCATACCAACAGAGA 59.015 47.619 0.00 0.00 0.00 3.10
99 100 2.578021 AGCCAACCATACCAACAGAGAT 59.422 45.455 0.00 0.00 0.00 2.75
100 101 3.010584 AGCCAACCATACCAACAGAGATT 59.989 43.478 0.00 0.00 0.00 2.40
101 102 3.129287 GCCAACCATACCAACAGAGATTG 59.871 47.826 0.00 0.00 0.00 2.67
102 103 3.129287 CCAACCATACCAACAGAGATTGC 59.871 47.826 0.00 0.00 0.00 3.56
103 104 4.012374 CAACCATACCAACAGAGATTGCT 58.988 43.478 0.00 0.00 0.00 3.91
104 105 3.614092 ACCATACCAACAGAGATTGCTG 58.386 45.455 0.00 0.00 41.63 4.41
105 106 2.947652 CCATACCAACAGAGATTGCTGG 59.052 50.000 0.00 0.00 46.46 4.85
106 107 2.787473 TACCAACAGAGATTGCTGGG 57.213 50.000 0.00 0.00 45.53 4.45
107 108 0.773644 ACCAACAGAGATTGCTGGGT 59.226 50.000 0.00 0.00 45.53 4.51
108 109 1.145738 ACCAACAGAGATTGCTGGGTT 59.854 47.619 0.00 0.00 45.53 4.11
109 110 2.242043 CCAACAGAGATTGCTGGGTTT 58.758 47.619 0.00 0.00 39.02 3.27
110 111 2.629617 CCAACAGAGATTGCTGGGTTTT 59.370 45.455 0.00 0.00 39.02 2.43
111 112 3.070015 CCAACAGAGATTGCTGGGTTTTT 59.930 43.478 0.00 0.00 39.02 1.94
112 113 4.280677 CCAACAGAGATTGCTGGGTTTTTA 59.719 41.667 0.00 0.00 39.02 1.52
113 114 5.221422 CCAACAGAGATTGCTGGGTTTTTAA 60.221 40.000 0.00 0.00 39.02 1.52
114 115 6.279882 CAACAGAGATTGCTGGGTTTTTAAA 58.720 36.000 0.00 0.00 40.20 1.52
115 116 5.842907 ACAGAGATTGCTGGGTTTTTAAAC 58.157 37.500 0.00 0.00 40.20 2.01
116 117 5.362430 ACAGAGATTGCTGGGTTTTTAAACA 59.638 36.000 7.57 0.00 40.20 2.83
117 118 6.041979 ACAGAGATTGCTGGGTTTTTAAACAT 59.958 34.615 7.57 0.00 40.20 2.71
118 119 6.366877 CAGAGATTGCTGGGTTTTTAAACATG 59.633 38.462 7.57 0.00 40.63 3.21
119 120 6.041979 AGAGATTGCTGGGTTTTTAAACATGT 59.958 34.615 7.57 0.00 40.63 3.21
120 121 6.223120 AGATTGCTGGGTTTTTAAACATGTC 58.777 36.000 0.00 0.00 40.63 3.06
121 122 3.971150 TGCTGGGTTTTTAAACATGTCG 58.029 40.909 0.00 0.00 40.63 4.35
122 123 3.243569 TGCTGGGTTTTTAAACATGTCGG 60.244 43.478 0.00 0.00 40.63 4.79
123 124 3.313690 CTGGGTTTTTAAACATGTCGGC 58.686 45.455 0.00 0.00 40.63 5.54
124 125 2.693591 TGGGTTTTTAAACATGTCGGCA 59.306 40.909 0.00 0.00 40.63 5.69
125 126 3.132289 TGGGTTTTTAAACATGTCGGCAA 59.868 39.130 0.00 0.00 40.63 4.52
126 127 3.738791 GGGTTTTTAAACATGTCGGCAAG 59.261 43.478 0.00 0.00 40.63 4.01
127 128 4.364860 GGTTTTTAAACATGTCGGCAAGT 58.635 39.130 0.00 0.00 40.63 3.16
128 129 4.806775 GGTTTTTAAACATGTCGGCAAGTT 59.193 37.500 4.54 4.54 40.63 2.66
129 130 5.978322 GGTTTTTAAACATGTCGGCAAGTTA 59.022 36.000 11.41 0.00 40.63 2.24
130 131 6.476053 GGTTTTTAAACATGTCGGCAAGTTAA 59.524 34.615 11.41 5.18 40.63 2.01
131 132 7.010275 GGTTTTTAAACATGTCGGCAAGTTAAA 59.990 33.333 11.41 10.66 40.63 1.52
132 133 7.452630 TTTTAAACATGTCGGCAAGTTAAAC 57.547 32.000 11.41 0.00 35.76 2.01
133 134 2.961522 ACATGTCGGCAAGTTAAACG 57.038 45.000 0.00 0.00 0.00 3.60
134 135 1.069500 ACATGTCGGCAAGTTAAACGC 60.069 47.619 0.00 0.00 0.00 4.84
135 136 0.519961 ATGTCGGCAAGTTAAACGCC 59.480 50.000 0.00 0.00 42.64 5.68
139 140 3.081741 GGCAAGTTAAACGCCGAAC 57.918 52.632 0.00 0.00 35.79 3.95
140 141 0.308376 GGCAAGTTAAACGCCGAACA 59.692 50.000 0.00 0.00 35.79 3.18
141 142 1.068816 GGCAAGTTAAACGCCGAACAT 60.069 47.619 0.00 0.00 35.79 2.71
142 143 2.160022 GGCAAGTTAAACGCCGAACATA 59.840 45.455 0.00 0.00 35.79 2.29
143 144 3.365164 GGCAAGTTAAACGCCGAACATAA 60.365 43.478 0.00 0.00 35.79 1.90
144 145 3.844099 GCAAGTTAAACGCCGAACATAAG 59.156 43.478 0.00 0.00 0.00 1.73
145 146 4.399978 CAAGTTAAACGCCGAACATAAGG 58.600 43.478 0.00 0.00 0.00 2.69
146 147 3.929094 AGTTAAACGCCGAACATAAGGA 58.071 40.909 0.00 0.00 0.00 3.36
147 148 4.317488 AGTTAAACGCCGAACATAAGGAA 58.683 39.130 0.00 0.00 0.00 3.36
148 149 4.756135 AGTTAAACGCCGAACATAAGGAAA 59.244 37.500 0.00 0.00 0.00 3.13
149 150 5.239087 AGTTAAACGCCGAACATAAGGAAAA 59.761 36.000 0.00 0.00 0.00 2.29
150 151 3.824414 AACGCCGAACATAAGGAAAAG 57.176 42.857 0.00 0.00 0.00 2.27
151 152 2.081462 ACGCCGAACATAAGGAAAAGG 58.919 47.619 0.00 0.00 0.00 3.11
152 153 1.400494 CGCCGAACATAAGGAAAAGGG 59.600 52.381 0.00 0.00 0.00 3.95
153 154 2.718563 GCCGAACATAAGGAAAAGGGA 58.281 47.619 0.00 0.00 0.00 4.20
154 155 3.288092 GCCGAACATAAGGAAAAGGGAT 58.712 45.455 0.00 0.00 0.00 3.85
155 156 3.315470 GCCGAACATAAGGAAAAGGGATC 59.685 47.826 0.00 0.00 0.00 3.36
156 157 4.523083 CCGAACATAAGGAAAAGGGATCA 58.477 43.478 0.00 0.00 0.00 2.92
157 158 4.335594 CCGAACATAAGGAAAAGGGATCAC 59.664 45.833 0.00 0.00 0.00 3.06
158 159 4.941263 CGAACATAAGGAAAAGGGATCACA 59.059 41.667 0.00 0.00 0.00 3.58
159 160 5.414454 CGAACATAAGGAAAAGGGATCACAA 59.586 40.000 0.00 0.00 0.00 3.33
160 161 6.072175 CGAACATAAGGAAAAGGGATCACAAA 60.072 38.462 0.00 0.00 0.00 2.83
161 162 6.840780 ACATAAGGAAAAGGGATCACAAAG 57.159 37.500 0.00 0.00 0.00 2.77
162 163 5.185828 ACATAAGGAAAAGGGATCACAAAGC 59.814 40.000 0.00 0.00 0.00 3.51
163 164 2.162681 AGGAAAAGGGATCACAAAGCG 58.837 47.619 0.00 0.00 0.00 4.68
164 165 2.159382 GGAAAAGGGATCACAAAGCGA 58.841 47.619 0.00 0.00 0.00 4.93
165 166 2.162408 GGAAAAGGGATCACAAAGCGAG 59.838 50.000 0.00 0.00 0.00 5.03
166 167 1.826385 AAAGGGATCACAAAGCGAGG 58.174 50.000 0.00 0.00 0.00 4.63
167 168 0.984230 AAGGGATCACAAAGCGAGGA 59.016 50.000 0.00 0.00 0.00 3.71
168 169 0.250513 AGGGATCACAAAGCGAGGAC 59.749 55.000 0.00 0.00 0.00 3.85
169 170 1.084370 GGGATCACAAAGCGAGGACG 61.084 60.000 0.00 0.00 42.93 4.79
170 171 0.108804 GGATCACAAAGCGAGGACGA 60.109 55.000 0.00 0.00 42.66 4.20
171 172 1.471676 GGATCACAAAGCGAGGACGAT 60.472 52.381 0.00 0.00 42.66 3.73
172 173 1.590238 GATCACAAAGCGAGGACGATG 59.410 52.381 0.00 0.00 42.66 3.84
173 174 0.601057 TCACAAAGCGAGGACGATGA 59.399 50.000 0.00 0.00 42.66 2.92
174 175 0.716108 CACAAAGCGAGGACGATGAC 59.284 55.000 0.00 0.00 42.66 3.06
175 176 0.732880 ACAAAGCGAGGACGATGACG 60.733 55.000 0.00 0.00 42.66 4.35
176 177 0.456142 CAAAGCGAGGACGATGACGA 60.456 55.000 0.00 0.00 42.66 4.20
177 178 0.179161 AAAGCGAGGACGATGACGAG 60.179 55.000 0.00 0.00 42.66 4.18
178 179 1.994507 AAGCGAGGACGATGACGAGG 61.995 60.000 0.00 0.00 42.66 4.63
179 180 2.470362 GCGAGGACGATGACGAGGA 61.470 63.158 0.00 0.00 42.66 3.71
180 181 1.644372 CGAGGACGATGACGAGGAG 59.356 63.158 0.00 0.00 42.66 3.69
181 182 1.357334 GAGGACGATGACGAGGAGC 59.643 63.158 0.00 0.00 42.66 4.70
182 183 2.065906 GAGGACGATGACGAGGAGCC 62.066 65.000 0.00 0.00 42.66 4.70
183 184 2.413765 GACGATGACGAGGAGCCC 59.586 66.667 0.00 0.00 42.66 5.19
184 185 3.140225 GACGATGACGAGGAGCCCC 62.140 68.421 0.00 0.00 42.66 5.80
185 186 4.271816 CGATGACGAGGAGCCCCG 62.272 72.222 0.00 0.00 42.66 5.73
186 187 3.917760 GATGACGAGGAGCCCCGG 61.918 72.222 0.00 0.00 37.58 5.73
192 193 4.785453 GAGGAGCCCCGGCAACTG 62.785 72.222 8.74 0.00 44.88 3.16
194 195 4.344865 GGAGCCCCGGCAACTGAA 62.345 66.667 8.74 0.00 44.88 3.02
195 196 3.056328 GAGCCCCGGCAACTGAAC 61.056 66.667 8.74 0.00 44.88 3.18
196 197 3.842925 GAGCCCCGGCAACTGAACA 62.843 63.158 8.74 0.00 44.88 3.18
197 198 3.670377 GCCCCGGCAACTGAACAC 61.670 66.667 0.00 0.00 41.49 3.32
198 199 2.203280 CCCCGGCAACTGAACACA 60.203 61.111 0.00 0.00 0.00 3.72
199 200 2.260869 CCCCGGCAACTGAACACAG 61.261 63.158 0.00 0.00 37.63 3.66
200 201 2.260869 CCCGGCAACTGAACACAGG 61.261 63.158 0.00 0.00 36.12 4.00
201 202 2.260869 CCGGCAACTGAACACAGGG 61.261 63.158 0.00 0.00 36.12 4.45
202 203 2.260869 CGGCAACTGAACACAGGGG 61.261 63.158 0.00 0.00 36.12 4.79
203 204 1.903404 GGCAACTGAACACAGGGGG 60.903 63.158 0.00 0.00 36.12 5.40
204 205 1.150536 GCAACTGAACACAGGGGGA 59.849 57.895 0.00 0.00 36.12 4.81
205 206 1.172812 GCAACTGAACACAGGGGGAC 61.173 60.000 0.00 0.00 36.12 4.46
206 207 0.182537 CAACTGAACACAGGGGGACA 59.817 55.000 0.00 0.00 36.12 4.02
207 208 0.474184 AACTGAACACAGGGGGACAG 59.526 55.000 0.00 0.00 36.12 3.51
208 209 0.399949 ACTGAACACAGGGGGACAGA 60.400 55.000 0.00 0.00 36.12 3.41
209 210 0.764890 CTGAACACAGGGGGACAGAA 59.235 55.000 0.00 0.00 0.00 3.02
210 211 0.764890 TGAACACAGGGGGACAGAAG 59.235 55.000 0.00 0.00 0.00 2.85
211 212 1.056660 GAACACAGGGGGACAGAAGA 58.943 55.000 0.00 0.00 0.00 2.87
212 213 1.420138 GAACACAGGGGGACAGAAGAA 59.580 52.381 0.00 0.00 0.00 2.52
213 214 1.059913 ACACAGGGGGACAGAAGAAG 58.940 55.000 0.00 0.00 0.00 2.85
214 215 1.059913 CACAGGGGGACAGAAGAAGT 58.940 55.000 0.00 0.00 0.00 3.01
215 216 1.002544 CACAGGGGGACAGAAGAAGTC 59.997 57.143 0.00 0.00 35.29 3.01
216 217 1.132689 ACAGGGGGACAGAAGAAGTCT 60.133 52.381 0.00 0.00 36.88 3.24
217 218 1.552792 CAGGGGGACAGAAGAAGTCTC 59.447 57.143 0.00 0.00 32.70 3.36
220 221 0.906066 GGGACAGAAGAAGTCTCCCC 59.094 60.000 0.00 0.00 38.46 4.81
221 222 0.906066 GGACAGAAGAAGTCTCCCCC 59.094 60.000 0.00 0.00 32.70 5.40
236 237 3.087065 CCCCCAGGTCAAATCGGT 58.913 61.111 0.00 0.00 0.00 4.69
237 238 1.378514 CCCCCAGGTCAAATCGGTG 60.379 63.158 0.00 0.00 0.00 4.94
238 239 1.682849 CCCCAGGTCAAATCGGTGA 59.317 57.895 0.00 0.00 0.00 4.02
239 240 0.037590 CCCCAGGTCAAATCGGTGAA 59.962 55.000 0.00 0.00 0.00 3.18
240 241 1.340991 CCCCAGGTCAAATCGGTGAAT 60.341 52.381 0.00 0.00 0.00 2.57
241 242 2.092646 CCCCAGGTCAAATCGGTGAATA 60.093 50.000 0.00 0.00 0.00 1.75
242 243 3.435026 CCCCAGGTCAAATCGGTGAATAT 60.435 47.826 0.00 0.00 0.00 1.28
243 244 3.565482 CCCAGGTCAAATCGGTGAATATG 59.435 47.826 0.00 0.00 0.00 1.78
244 245 4.450976 CCAGGTCAAATCGGTGAATATGA 58.549 43.478 0.00 0.00 0.00 2.15
245 246 5.065914 CCAGGTCAAATCGGTGAATATGAT 58.934 41.667 0.00 0.00 0.00 2.45
246 247 6.230472 CCAGGTCAAATCGGTGAATATGATA 58.770 40.000 0.00 0.00 0.00 2.15
247 248 6.881065 CCAGGTCAAATCGGTGAATATGATAT 59.119 38.462 0.00 0.00 0.00 1.63
248 249 8.040727 CCAGGTCAAATCGGTGAATATGATATA 58.959 37.037 0.00 0.00 0.00 0.86
249 250 9.605275 CAGGTCAAATCGGTGAATATGATATAT 57.395 33.333 0.00 0.00 0.00 0.86
250 251 9.605275 AGGTCAAATCGGTGAATATGATATATG 57.395 33.333 0.00 0.00 0.00 1.78
251 252 8.338259 GGTCAAATCGGTGAATATGATATATGC 58.662 37.037 0.00 0.00 0.00 3.14
252 253 9.102757 GTCAAATCGGTGAATATGATATATGCT 57.897 33.333 0.00 0.00 0.00 3.79
256 257 9.534565 AATCGGTGAATATGATATATGCTACAC 57.465 33.333 0.00 0.00 0.00 2.90
257 258 8.062065 TCGGTGAATATGATATATGCTACACA 57.938 34.615 0.00 0.00 0.00 3.72
258 259 7.973944 TCGGTGAATATGATATATGCTACACAC 59.026 37.037 0.00 0.00 0.00 3.82
259 260 7.759433 CGGTGAATATGATATATGCTACACACA 59.241 37.037 0.00 0.00 0.00 3.72
260 261 9.605275 GGTGAATATGATATATGCTACACACAT 57.395 33.333 0.00 0.00 0.00 3.21
262 263 9.822185 TGAATATGATATATGCTACACACATCC 57.178 33.333 0.00 0.00 0.00 3.51
263 264 9.265901 GAATATGATATATGCTACACACATCCC 57.734 37.037 0.00 0.00 0.00 3.85
264 265 5.420725 TGATATATGCTACACACATCCCC 57.579 43.478 0.00 0.00 0.00 4.81
265 266 4.843516 TGATATATGCTACACACATCCCCA 59.156 41.667 0.00 0.00 0.00 4.96
266 267 5.309282 TGATATATGCTACACACATCCCCAA 59.691 40.000 0.00 0.00 0.00 4.12
267 268 2.425143 ATGCTACACACATCCCCAAG 57.575 50.000 0.00 0.00 0.00 3.61
268 269 1.357137 TGCTACACACATCCCCAAGA 58.643 50.000 0.00 0.00 0.00 3.02
269 270 1.278985 TGCTACACACATCCCCAAGAG 59.721 52.381 0.00 0.00 0.00 2.85
270 271 1.407437 GCTACACACATCCCCAAGAGG 60.407 57.143 0.00 0.00 0.00 3.69
280 281 3.267974 CCAAGAGGGAGCGCAAAC 58.732 61.111 11.47 0.00 40.01 2.93
281 282 2.680913 CCAAGAGGGAGCGCAAACG 61.681 63.158 11.47 0.00 40.01 3.60
299 300 3.506096 CGCGCTCAGGGACGTCTA 61.506 66.667 16.46 0.00 34.27 2.59
300 301 2.835705 CGCGCTCAGGGACGTCTAT 61.836 63.158 16.46 0.93 34.27 1.98
301 302 1.008309 GCGCTCAGGGACGTCTATC 60.008 63.158 16.46 5.79 0.00 2.08
302 303 1.280142 CGCTCAGGGACGTCTATCG 59.720 63.158 16.46 7.09 46.00 2.92
303 304 1.158484 CGCTCAGGGACGTCTATCGA 61.158 60.000 16.46 6.44 42.86 3.59
304 305 1.240256 GCTCAGGGACGTCTATCGAT 58.760 55.000 16.46 2.16 42.86 3.59
305 306 2.424557 GCTCAGGGACGTCTATCGATA 58.575 52.381 16.46 4.78 42.86 2.92
306 307 2.417239 GCTCAGGGACGTCTATCGATAG 59.583 54.545 23.87 23.87 42.86 2.08
965 1458 5.244755 CAACCCCCAAATCGATTTCAAATT 58.755 37.500 20.31 8.82 0.00 1.82
1165 1710 1.738350 TCTCCGAGTTCTCGTAAGCAG 59.262 52.381 18.59 8.16 37.18 4.24
1696 2359 7.269316 ACATTTAACCTGAAATTTTCGTTGGT 58.731 30.769 12.50 12.50 33.79 3.67
1796 2459 7.021196 CAGAAACATGATTTAAGGTGGTTACG 58.979 38.462 0.00 0.00 0.00 3.18
1806 2469 9.120422 GATTTAAGGTGGTTACGTAAAACATTG 57.880 33.333 22.49 0.00 37.07 2.82
1829 2492 6.194235 TGGACCAATGGCTTTAGTTATCAAT 58.806 36.000 0.00 0.00 0.00 2.57
2127 2900 9.308318 ACTGTTGTTCCACAATTTTTGTTATAC 57.692 29.630 0.00 0.00 43.23 1.47
2794 3679 5.508200 TTCTTTGTTACCATGTGTTGTCC 57.492 39.130 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.490902 GGATGGTCCCTGGTTGTTTCTT 60.491 50.000 0.00 0.00 0.00 2.52
1 2 1.075536 GGATGGTCCCTGGTTGTTTCT 59.924 52.381 0.00 0.00 0.00 2.52
2 3 1.203001 TGGATGGTCCCTGGTTGTTTC 60.203 52.381 0.00 0.00 35.03 2.78
3 4 0.856982 TGGATGGTCCCTGGTTGTTT 59.143 50.000 0.00 0.00 35.03 2.83
4 5 0.405585 CTGGATGGTCCCTGGTTGTT 59.594 55.000 0.00 0.00 35.03 2.83
5 6 2.078452 CTGGATGGTCCCTGGTTGT 58.922 57.895 0.00 0.00 35.03 3.32
6 7 1.379044 GCTGGATGGTCCCTGGTTG 60.379 63.158 0.00 0.00 35.03 3.77
7 8 2.616458 GGCTGGATGGTCCCTGGTT 61.616 63.158 0.00 0.00 35.03 3.67
8 9 3.017581 GGCTGGATGGTCCCTGGT 61.018 66.667 0.00 0.00 35.03 4.00
9 10 2.693864 AGGCTGGATGGTCCCTGG 60.694 66.667 0.00 0.00 35.03 4.45
10 11 2.593978 CAGGCTGGATGGTCCCTG 59.406 66.667 6.61 0.00 38.93 4.45
11 12 2.693864 CCAGGCTGGATGGTCCCT 60.694 66.667 29.96 0.00 40.96 4.20
12 13 2.692368 TCCAGGCTGGATGGTCCC 60.692 66.667 32.01 0.00 42.67 4.46
19 20 2.364973 TATGCGGTCCAGGCTGGA 60.365 61.111 32.01 32.01 45.98 3.86
20 21 2.203070 GTATGCGGTCCAGGCTGG 60.203 66.667 28.01 28.01 39.43 4.85
21 22 1.091771 CAAGTATGCGGTCCAGGCTG 61.092 60.000 7.75 7.75 0.00 4.85
22 23 1.221840 CAAGTATGCGGTCCAGGCT 59.778 57.895 0.00 0.00 0.00 4.58
23 24 1.090052 GTCAAGTATGCGGTCCAGGC 61.090 60.000 0.00 0.00 0.00 4.85
24 25 0.462047 GGTCAAGTATGCGGTCCAGG 60.462 60.000 0.00 0.00 0.00 4.45
25 26 0.806102 CGGTCAAGTATGCGGTCCAG 60.806 60.000 0.00 0.00 0.00 3.86
26 27 1.216977 CGGTCAAGTATGCGGTCCA 59.783 57.895 0.00 0.00 0.00 4.02
27 28 2.171725 GCGGTCAAGTATGCGGTCC 61.172 63.158 0.00 0.00 0.00 4.46
28 29 2.171725 GGCGGTCAAGTATGCGGTC 61.172 63.158 0.00 0.00 0.00 4.79
29 30 2.125269 GGCGGTCAAGTATGCGGT 60.125 61.111 0.00 0.00 0.00 5.68
30 31 2.895372 GGGCGGTCAAGTATGCGG 60.895 66.667 0.00 0.00 0.00 5.69
31 32 3.261951 CGGGCGGTCAAGTATGCG 61.262 66.667 0.00 0.00 0.00 4.73
32 33 2.125269 ACGGGCGGTCAAGTATGC 60.125 61.111 0.00 0.00 0.00 3.14
33 34 2.461110 GCACGGGCGGTCAAGTATG 61.461 63.158 0.00 0.00 0.00 2.39
34 35 2.125269 GCACGGGCGGTCAAGTAT 60.125 61.111 0.00 0.00 0.00 2.12
35 36 4.382320 GGCACGGGCGGTCAAGTA 62.382 66.667 2.17 0.00 42.47 2.24
40 41 3.845259 TATCTGGCACGGGCGGTC 61.845 66.667 2.17 0.00 42.47 4.79
41 42 4.157120 GTATCTGGCACGGGCGGT 62.157 66.667 2.17 0.00 42.47 5.68
42 43 3.460672 ATGTATCTGGCACGGGCGG 62.461 63.158 2.17 0.00 42.47 6.13
43 44 2.108976 ATGTATCTGGCACGGGCG 59.891 61.111 2.17 0.00 42.47 6.13
44 45 1.893808 CCATGTATCTGGCACGGGC 60.894 63.158 0.00 0.00 40.13 6.13
45 46 4.462394 CCATGTATCTGGCACGGG 57.538 61.111 0.00 0.00 33.92 5.28
51 52 0.179009 CTGGGGTGCCATGTATCTGG 60.179 60.000 0.00 0.00 39.45 3.86
52 53 0.839277 TCTGGGGTGCCATGTATCTG 59.161 55.000 0.00 0.00 0.00 2.90
53 54 0.839946 GTCTGGGGTGCCATGTATCT 59.160 55.000 0.00 0.00 0.00 1.98
54 55 0.546122 TGTCTGGGGTGCCATGTATC 59.454 55.000 0.00 0.00 0.00 2.24
55 56 0.998928 TTGTCTGGGGTGCCATGTAT 59.001 50.000 0.00 0.00 0.00 2.29
56 57 0.327924 CTTGTCTGGGGTGCCATGTA 59.672 55.000 0.00 0.00 0.00 2.29
57 58 1.075482 CTTGTCTGGGGTGCCATGT 59.925 57.895 0.00 0.00 0.00 3.21
58 59 2.345760 GCTTGTCTGGGGTGCCATG 61.346 63.158 0.00 0.00 0.00 3.66
59 60 2.036256 GCTTGTCTGGGGTGCCAT 59.964 61.111 0.00 0.00 0.00 4.40
60 61 4.284550 GGCTTGTCTGGGGTGCCA 62.285 66.667 0.00 0.00 42.79 4.92
61 62 4.284550 TGGCTTGTCTGGGGTGCC 62.285 66.667 0.00 0.00 43.49 5.01
62 63 2.674380 CTGGCTTGTCTGGGGTGC 60.674 66.667 0.00 0.00 0.00 5.01
63 64 2.674380 GCTGGCTTGTCTGGGGTG 60.674 66.667 0.00 0.00 0.00 4.61
64 65 3.971702 GGCTGGCTTGTCTGGGGT 61.972 66.667 0.00 0.00 0.00 4.95
65 66 3.512154 TTGGCTGGCTTGTCTGGGG 62.512 63.158 2.00 0.00 0.00 4.96
66 67 2.115910 TTGGCTGGCTTGTCTGGG 59.884 61.111 2.00 0.00 0.00 4.45
67 68 2.270986 GGTTGGCTGGCTTGTCTGG 61.271 63.158 2.00 0.00 0.00 3.86
68 69 0.896940 ATGGTTGGCTGGCTTGTCTG 60.897 55.000 2.00 0.00 0.00 3.51
69 70 0.698238 TATGGTTGGCTGGCTTGTCT 59.302 50.000 2.00 0.00 0.00 3.41
70 71 0.811281 GTATGGTTGGCTGGCTTGTC 59.189 55.000 2.00 0.00 0.00 3.18
71 72 0.611896 GGTATGGTTGGCTGGCTTGT 60.612 55.000 2.00 0.00 0.00 3.16
72 73 0.611618 TGGTATGGTTGGCTGGCTTG 60.612 55.000 2.00 0.00 0.00 4.01
73 74 0.114168 TTGGTATGGTTGGCTGGCTT 59.886 50.000 2.00 0.00 0.00 4.35
74 75 0.611896 GTTGGTATGGTTGGCTGGCT 60.612 55.000 2.00 0.00 0.00 4.75
75 76 0.897863 TGTTGGTATGGTTGGCTGGC 60.898 55.000 0.00 0.00 0.00 4.85
76 77 1.176527 CTGTTGGTATGGTTGGCTGG 58.823 55.000 0.00 0.00 0.00 4.85
77 78 2.086869 CTCTGTTGGTATGGTTGGCTG 58.913 52.381 0.00 0.00 0.00 4.85
78 79 1.985159 TCTCTGTTGGTATGGTTGGCT 59.015 47.619 0.00 0.00 0.00 4.75
79 80 2.489938 TCTCTGTTGGTATGGTTGGC 57.510 50.000 0.00 0.00 0.00 4.52
80 81 3.129287 GCAATCTCTGTTGGTATGGTTGG 59.871 47.826 0.00 0.00 0.00 3.77
81 82 4.012374 AGCAATCTCTGTTGGTATGGTTG 58.988 43.478 0.00 0.00 37.98 3.77
82 83 4.012374 CAGCAATCTCTGTTGGTATGGTT 58.988 43.478 0.00 0.00 37.69 3.67
83 84 3.614092 CAGCAATCTCTGTTGGTATGGT 58.386 45.455 0.00 0.00 37.69 3.55
90 91 4.326504 AAAAACCCAGCAATCTCTGTTG 57.673 40.909 0.00 0.00 36.09 3.33
91 92 6.127196 TGTTTAAAAACCCAGCAATCTCTGTT 60.127 34.615 3.27 0.00 38.11 3.16
92 93 5.362430 TGTTTAAAAACCCAGCAATCTCTGT 59.638 36.000 3.27 0.00 38.11 3.41
93 94 5.841810 TGTTTAAAAACCCAGCAATCTCTG 58.158 37.500 3.27 0.00 38.11 3.35
94 95 6.041979 ACATGTTTAAAAACCCAGCAATCTCT 59.958 34.615 0.00 0.00 38.11 3.10
95 96 6.223120 ACATGTTTAAAAACCCAGCAATCTC 58.777 36.000 0.00 0.00 38.11 2.75
96 97 6.173427 ACATGTTTAAAAACCCAGCAATCT 57.827 33.333 0.00 0.00 38.11 2.40
97 98 5.118510 CGACATGTTTAAAAACCCAGCAATC 59.881 40.000 0.00 0.00 38.11 2.67
98 99 4.987912 CGACATGTTTAAAAACCCAGCAAT 59.012 37.500 0.00 0.00 38.11 3.56
99 100 4.363999 CGACATGTTTAAAAACCCAGCAA 58.636 39.130 0.00 0.00 38.11 3.91
100 101 3.243569 CCGACATGTTTAAAAACCCAGCA 60.244 43.478 0.00 0.00 38.11 4.41
101 102 3.313690 CCGACATGTTTAAAAACCCAGC 58.686 45.455 0.00 0.00 38.11 4.85
102 103 3.243569 TGCCGACATGTTTAAAAACCCAG 60.244 43.478 0.00 0.00 38.11 4.45
103 104 2.693591 TGCCGACATGTTTAAAAACCCA 59.306 40.909 0.00 0.00 38.11 4.51
104 105 3.372660 TGCCGACATGTTTAAAAACCC 57.627 42.857 0.00 0.00 38.11 4.11
105 106 4.364860 ACTTGCCGACATGTTTAAAAACC 58.635 39.130 0.00 0.00 38.11 3.27
106 107 5.959652 AACTTGCCGACATGTTTAAAAAC 57.040 34.783 0.00 0.00 40.24 2.43
107 108 7.253684 CGTTTAACTTGCCGACATGTTTAAAAA 60.254 33.333 8.22 1.54 42.37 1.94
108 109 6.196724 CGTTTAACTTGCCGACATGTTTAAAA 59.803 34.615 8.22 2.17 42.37 1.52
109 110 5.681982 CGTTTAACTTGCCGACATGTTTAAA 59.318 36.000 8.22 2.62 42.37 1.52
110 111 5.206299 CGTTTAACTTGCCGACATGTTTAA 58.794 37.500 8.22 3.46 42.37 1.52
111 112 4.774586 CGTTTAACTTGCCGACATGTTTA 58.225 39.130 8.22 0.00 42.37 2.01
112 113 3.623863 CGTTTAACTTGCCGACATGTTT 58.376 40.909 8.22 0.00 42.37 2.83
113 114 2.603652 GCGTTTAACTTGCCGACATGTT 60.604 45.455 0.00 8.02 44.02 2.71
114 115 1.069500 GCGTTTAACTTGCCGACATGT 60.069 47.619 0.00 0.00 35.81 3.21
115 116 1.602191 GCGTTTAACTTGCCGACATG 58.398 50.000 0.00 0.00 0.00 3.21
116 117 0.519961 GGCGTTTAACTTGCCGACAT 59.480 50.000 0.00 0.00 39.30 3.06
117 118 1.943293 GGCGTTTAACTTGCCGACA 59.057 52.632 0.00 0.00 39.30 4.35
118 119 4.832767 GGCGTTTAACTTGCCGAC 57.167 55.556 0.00 0.00 39.30 4.79
121 122 0.308376 TGTTCGGCGTTTAACTTGCC 59.692 50.000 6.85 4.30 45.39 4.52
122 123 2.325509 ATGTTCGGCGTTTAACTTGC 57.674 45.000 6.85 0.00 0.00 4.01
123 124 4.152759 TCCTTATGTTCGGCGTTTAACTTG 59.847 41.667 6.85 0.00 0.00 3.16
124 125 4.317488 TCCTTATGTTCGGCGTTTAACTT 58.683 39.130 6.85 5.23 0.00 2.66
125 126 3.929094 TCCTTATGTTCGGCGTTTAACT 58.071 40.909 6.85 0.00 0.00 2.24
126 127 4.666928 TTCCTTATGTTCGGCGTTTAAC 57.333 40.909 6.85 4.75 0.00 2.01
127 128 5.335035 CCTTTTCCTTATGTTCGGCGTTTAA 60.335 40.000 6.85 0.45 0.00 1.52
128 129 4.154556 CCTTTTCCTTATGTTCGGCGTTTA 59.845 41.667 6.85 0.00 0.00 2.01
129 130 3.057806 CCTTTTCCTTATGTTCGGCGTTT 60.058 43.478 6.85 0.00 0.00 3.60
130 131 2.486592 CCTTTTCCTTATGTTCGGCGTT 59.513 45.455 6.85 0.00 0.00 4.84
131 132 2.081462 CCTTTTCCTTATGTTCGGCGT 58.919 47.619 6.85 0.00 0.00 5.68
132 133 1.400494 CCCTTTTCCTTATGTTCGGCG 59.600 52.381 0.00 0.00 0.00 6.46
133 134 2.718563 TCCCTTTTCCTTATGTTCGGC 58.281 47.619 0.00 0.00 0.00 5.54
134 135 4.335594 GTGATCCCTTTTCCTTATGTTCGG 59.664 45.833 0.00 0.00 0.00 4.30
135 136 4.941263 TGTGATCCCTTTTCCTTATGTTCG 59.059 41.667 0.00 0.00 0.00 3.95
136 137 6.834168 TTGTGATCCCTTTTCCTTATGTTC 57.166 37.500 0.00 0.00 0.00 3.18
137 138 6.295292 GCTTTGTGATCCCTTTTCCTTATGTT 60.295 38.462 0.00 0.00 0.00 2.71
138 139 5.185828 GCTTTGTGATCCCTTTTCCTTATGT 59.814 40.000 0.00 0.00 0.00 2.29
139 140 5.654497 GCTTTGTGATCCCTTTTCCTTATG 58.346 41.667 0.00 0.00 0.00 1.90
140 141 4.399303 CGCTTTGTGATCCCTTTTCCTTAT 59.601 41.667 0.00 0.00 0.00 1.73
141 142 3.756434 CGCTTTGTGATCCCTTTTCCTTA 59.244 43.478 0.00 0.00 0.00 2.69
142 143 2.558359 CGCTTTGTGATCCCTTTTCCTT 59.442 45.455 0.00 0.00 0.00 3.36
143 144 2.162681 CGCTTTGTGATCCCTTTTCCT 58.837 47.619 0.00 0.00 0.00 3.36
144 145 2.159382 TCGCTTTGTGATCCCTTTTCC 58.841 47.619 0.00 0.00 0.00 3.13
145 146 2.162408 CCTCGCTTTGTGATCCCTTTTC 59.838 50.000 0.00 0.00 0.00 2.29
146 147 2.162681 CCTCGCTTTGTGATCCCTTTT 58.837 47.619 0.00 0.00 0.00 2.27
147 148 1.351017 TCCTCGCTTTGTGATCCCTTT 59.649 47.619 0.00 0.00 0.00 3.11
148 149 0.984230 TCCTCGCTTTGTGATCCCTT 59.016 50.000 0.00 0.00 0.00 3.95
149 150 0.250513 GTCCTCGCTTTGTGATCCCT 59.749 55.000 0.00 0.00 0.00 4.20
150 151 1.084370 CGTCCTCGCTTTGTGATCCC 61.084 60.000 0.00 0.00 0.00 3.85
151 152 0.108804 TCGTCCTCGCTTTGTGATCC 60.109 55.000 0.00 0.00 36.96 3.36
152 153 1.590238 CATCGTCCTCGCTTTGTGATC 59.410 52.381 0.00 0.00 36.96 2.92
153 154 1.204704 TCATCGTCCTCGCTTTGTGAT 59.795 47.619 0.00 0.00 36.96 3.06
154 155 0.601057 TCATCGTCCTCGCTTTGTGA 59.399 50.000 0.00 0.00 36.96 3.58
155 156 0.716108 GTCATCGTCCTCGCTTTGTG 59.284 55.000 0.00 0.00 36.96 3.33
156 157 0.732880 CGTCATCGTCCTCGCTTTGT 60.733 55.000 0.00 0.00 36.96 2.83
157 158 0.456142 TCGTCATCGTCCTCGCTTTG 60.456 55.000 0.00 0.00 38.33 2.77
158 159 0.179161 CTCGTCATCGTCCTCGCTTT 60.179 55.000 0.00 0.00 38.33 3.51
159 160 1.429825 CTCGTCATCGTCCTCGCTT 59.570 57.895 0.00 0.00 38.33 4.68
160 161 2.473760 CCTCGTCATCGTCCTCGCT 61.474 63.158 0.00 0.00 38.33 4.93
161 162 2.024871 CCTCGTCATCGTCCTCGC 59.975 66.667 0.00 0.00 38.33 5.03
162 163 1.644372 CTCCTCGTCATCGTCCTCG 59.356 63.158 0.00 0.00 38.33 4.63
163 164 1.357334 GCTCCTCGTCATCGTCCTC 59.643 63.158 0.00 0.00 38.33 3.71
164 165 2.122167 GGCTCCTCGTCATCGTCCT 61.122 63.158 0.00 0.00 38.33 3.85
165 166 2.413765 GGCTCCTCGTCATCGTCC 59.586 66.667 0.00 0.00 38.33 4.79
166 167 2.413765 GGGCTCCTCGTCATCGTC 59.586 66.667 0.00 0.00 38.33 4.20
167 168 3.148279 GGGGCTCCTCGTCATCGT 61.148 66.667 0.00 0.00 38.33 3.73
168 169 4.271816 CGGGGCTCCTCGTCATCG 62.272 72.222 0.00 0.00 38.55 3.84
169 170 3.917760 CCGGGGCTCCTCGTCATC 61.918 72.222 0.00 0.00 0.00 2.92
175 176 4.785453 CAGTTGCCGGGGCTCCTC 62.785 72.222 11.55 0.00 42.51 3.71
177 178 4.344865 TTCAGTTGCCGGGGCTCC 62.345 66.667 11.55 0.00 42.51 4.70
178 179 3.056328 GTTCAGTTGCCGGGGCTC 61.056 66.667 11.55 4.46 42.51 4.70
179 180 3.884774 TGTTCAGTTGCCGGGGCT 61.885 61.111 11.55 0.00 42.51 5.19
180 181 3.670377 GTGTTCAGTTGCCGGGGC 61.670 66.667 2.18 1.86 42.35 5.80
181 182 2.203280 TGTGTTCAGTTGCCGGGG 60.203 61.111 2.18 0.00 0.00 5.73
182 183 2.260869 CCTGTGTTCAGTTGCCGGG 61.261 63.158 2.18 0.00 39.82 5.73
183 184 2.260869 CCCTGTGTTCAGTTGCCGG 61.261 63.158 0.00 0.00 39.82 6.13
184 185 2.260869 CCCCTGTGTTCAGTTGCCG 61.261 63.158 0.00 0.00 39.82 5.69
185 186 1.903404 CCCCCTGTGTTCAGTTGCC 60.903 63.158 0.00 0.00 39.82 4.52
186 187 1.150536 TCCCCCTGTGTTCAGTTGC 59.849 57.895 0.00 0.00 39.82 4.17
187 188 0.182537 TGTCCCCCTGTGTTCAGTTG 59.817 55.000 0.00 0.00 39.82 3.16
188 189 0.474184 CTGTCCCCCTGTGTTCAGTT 59.526 55.000 0.00 0.00 39.82 3.16
189 190 0.399949 TCTGTCCCCCTGTGTTCAGT 60.400 55.000 0.00 0.00 39.82 3.41
190 191 0.764890 TTCTGTCCCCCTGTGTTCAG 59.235 55.000 0.00 0.00 41.01 3.02
191 192 0.764890 CTTCTGTCCCCCTGTGTTCA 59.235 55.000 0.00 0.00 0.00 3.18
192 193 1.056660 TCTTCTGTCCCCCTGTGTTC 58.943 55.000 0.00 0.00 0.00 3.18
193 194 1.421646 CTTCTTCTGTCCCCCTGTGTT 59.578 52.381 0.00 0.00 0.00 3.32
194 195 1.059913 CTTCTTCTGTCCCCCTGTGT 58.940 55.000 0.00 0.00 0.00 3.72
195 196 1.002544 GACTTCTTCTGTCCCCCTGTG 59.997 57.143 0.00 0.00 0.00 3.66
196 197 1.132689 AGACTTCTTCTGTCCCCCTGT 60.133 52.381 0.00 0.00 35.21 4.00
197 198 1.552792 GAGACTTCTTCTGTCCCCCTG 59.447 57.143 0.00 0.00 33.22 4.45
198 199 1.553651 GGAGACTTCTTCTGTCCCCCT 60.554 57.143 0.00 0.00 33.22 4.79
199 200 0.906066 GGAGACTTCTTCTGTCCCCC 59.094 60.000 0.00 0.00 33.22 5.40
200 201 0.906066 GGGAGACTTCTTCTGTCCCC 59.094 60.000 0.00 0.00 33.71 4.81
201 202 0.906066 GGGGAGACTTCTTCTGTCCC 59.094 60.000 0.00 0.00 37.57 4.46
202 203 0.906066 GGGGGAGACTTCTTCTGTCC 59.094 60.000 0.00 0.00 33.22 4.02
219 220 1.378514 CACCGATTTGACCTGGGGG 60.379 63.158 0.00 0.00 38.88 5.40
220 221 0.037590 TTCACCGATTTGACCTGGGG 59.962 55.000 0.00 0.00 0.00 4.96
221 222 2.128771 ATTCACCGATTTGACCTGGG 57.871 50.000 0.00 0.00 0.00 4.45
222 223 4.450976 TCATATTCACCGATTTGACCTGG 58.549 43.478 0.00 0.00 0.00 4.45
223 224 7.912056 ATATCATATTCACCGATTTGACCTG 57.088 36.000 0.00 0.00 0.00 4.00
224 225 9.605275 CATATATCATATTCACCGATTTGACCT 57.395 33.333 0.00 0.00 0.00 3.85
225 226 8.338259 GCATATATCATATTCACCGATTTGACC 58.662 37.037 0.00 0.00 0.00 4.02
226 227 9.102757 AGCATATATCATATTCACCGATTTGAC 57.897 33.333 0.00 0.00 0.00 3.18
230 231 9.534565 GTGTAGCATATATCATATTCACCGATT 57.465 33.333 0.00 0.00 0.00 3.34
231 232 8.695456 TGTGTAGCATATATCATATTCACCGAT 58.305 33.333 0.00 0.00 0.00 4.18
232 233 7.973944 GTGTGTAGCATATATCATATTCACCGA 59.026 37.037 0.00 0.00 0.00 4.69
233 234 7.759433 TGTGTGTAGCATATATCATATTCACCG 59.241 37.037 0.00 0.00 0.00 4.94
234 235 9.605275 ATGTGTGTAGCATATATCATATTCACC 57.395 33.333 0.00 0.00 0.00 4.02
236 237 9.822185 GGATGTGTGTAGCATATATCATATTCA 57.178 33.333 5.39 0.00 0.00 2.57
237 238 9.265901 GGGATGTGTGTAGCATATATCATATTC 57.734 37.037 5.39 0.00 0.00 1.75
238 239 8.213679 GGGGATGTGTGTAGCATATATCATATT 58.786 37.037 5.39 0.00 0.00 1.28
239 240 7.348011 TGGGGATGTGTGTAGCATATATCATAT 59.652 37.037 5.39 0.00 0.00 1.78
240 241 6.671779 TGGGGATGTGTGTAGCATATATCATA 59.328 38.462 5.39 0.00 0.00 2.15
241 242 5.488561 TGGGGATGTGTGTAGCATATATCAT 59.511 40.000 5.39 0.00 0.00 2.45
242 243 4.843516 TGGGGATGTGTGTAGCATATATCA 59.156 41.667 5.39 0.00 0.00 2.15
243 244 5.420725 TGGGGATGTGTGTAGCATATATC 57.579 43.478 0.00 0.00 0.00 1.63
244 245 5.547666 TCTTGGGGATGTGTGTAGCATATAT 59.452 40.000 0.00 0.00 0.00 0.86
245 246 4.904853 TCTTGGGGATGTGTGTAGCATATA 59.095 41.667 0.00 0.00 0.00 0.86
246 247 3.716353 TCTTGGGGATGTGTGTAGCATAT 59.284 43.478 0.00 0.00 0.00 1.78
247 248 3.111484 TCTTGGGGATGTGTGTAGCATA 58.889 45.455 0.00 0.00 0.00 3.14
248 249 1.915489 TCTTGGGGATGTGTGTAGCAT 59.085 47.619 0.00 0.00 0.00 3.79
249 250 1.278985 CTCTTGGGGATGTGTGTAGCA 59.721 52.381 0.00 0.00 0.00 3.49
250 251 1.407437 CCTCTTGGGGATGTGTGTAGC 60.407 57.143 0.00 0.00 0.00 3.58
251 252 2.698855 CCTCTTGGGGATGTGTGTAG 57.301 55.000 0.00 0.00 0.00 2.74
263 264 2.680913 CGTTTGCGCTCCCTCTTGG 61.681 63.158 9.73 0.00 0.00 3.61
264 265 2.863153 CGTTTGCGCTCCCTCTTG 59.137 61.111 9.73 0.00 0.00 3.02
282 283 2.718993 GATAGACGTCCCTGAGCGCG 62.719 65.000 13.01 0.00 0.00 6.86
283 284 1.008309 GATAGACGTCCCTGAGCGC 60.008 63.158 13.01 0.00 0.00 5.92
284 285 1.158484 TCGATAGACGTCCCTGAGCG 61.158 60.000 13.01 10.12 42.67 5.03
285 286 2.704108 TCGATAGACGTCCCTGAGC 58.296 57.895 13.01 0.00 42.67 4.26
295 296 9.939466 CCCTAGTAGTGGGCTCTATCGATAGAC 62.939 51.852 27.44 22.43 43.13 2.59
296 297 8.044613 CCCTAGTAGTGGGCTCTATCGATAGA 62.045 50.000 28.71 28.71 44.02 1.98
297 298 5.120399 CCTAGTAGTGGGCTCTATCGATAG 58.880 50.000 23.87 23.87 0.00 2.08
298 299 4.080469 CCCTAGTAGTGGGCTCTATCGATA 60.080 50.000 4.78 4.78 37.99 2.92
299 300 3.308545 CCCTAGTAGTGGGCTCTATCGAT 60.309 52.174 2.16 2.16 37.99 3.59
300 301 2.040012 CCCTAGTAGTGGGCTCTATCGA 59.960 54.545 0.00 0.00 37.99 3.59
301 302 2.040012 TCCCTAGTAGTGGGCTCTATCG 59.960 54.545 0.00 0.00 44.23 2.92
302 303 3.810721 TCCCTAGTAGTGGGCTCTATC 57.189 52.381 0.00 0.00 44.23 2.08
303 304 4.554553 TTTCCCTAGTAGTGGGCTCTAT 57.445 45.455 0.00 0.00 44.23 1.98
304 305 4.028825 GTTTTCCCTAGTAGTGGGCTCTA 58.971 47.826 0.00 0.00 44.23 2.43
305 306 2.838813 GTTTTCCCTAGTAGTGGGCTCT 59.161 50.000 0.00 0.00 44.23 4.09
306 307 2.093075 GGTTTTCCCTAGTAGTGGGCTC 60.093 54.545 0.00 0.00 44.23 4.70
307 308 1.914108 GGTTTTCCCTAGTAGTGGGCT 59.086 52.381 0.00 0.00 44.23 5.19
308 309 1.914108 AGGTTTTCCCTAGTAGTGGGC 59.086 52.381 0.00 0.00 43.87 5.36
746 1212 2.154074 GGAGGAGGTGGGGTGTTGT 61.154 63.158 0.00 0.00 0.00 3.32
1165 1710 1.343176 ACAGAGGCTAGGGTTAGGGTC 60.343 57.143 0.00 0.00 0.00 4.46
1696 2359 4.083537 GCACATTGTTAATGACGACAGGAA 60.084 41.667 8.41 0.00 41.46 3.36
1796 2459 4.535526 AGCCATTGGTCCAATGTTTTAC 57.464 40.909 32.99 20.50 46.69 2.01
1806 2469 6.715347 ATTGATAACTAAAGCCATTGGTCC 57.285 37.500 4.26 0.00 30.50 4.46
1835 2498 7.231317 ACATTTTTATCAGTTCAAGGAGAAGCA 59.769 33.333 0.00 0.00 36.78 3.91
2127 2900 6.106648 TCAATGGTGCCATCTATCTAGAAG 57.893 41.667 3.96 0.00 35.31 2.85
2130 2903 6.297080 AGATCAATGGTGCCATCTATCTAG 57.703 41.667 18.74 0.00 36.71 2.43
2131 2904 6.692849 AAGATCAATGGTGCCATCTATCTA 57.307 37.500 19.72 1.43 37.09 1.98
2133 2906 5.766670 TGAAAGATCAATGGTGCCATCTATC 59.233 40.000 3.96 10.04 35.31 2.08
2135 2908 5.114764 TGAAAGATCAATGGTGCCATCTA 57.885 39.130 3.96 0.00 35.31 1.98
2136 2909 3.972133 TGAAAGATCAATGGTGCCATCT 58.028 40.909 3.96 0.00 35.31 2.90
2137 2910 4.931661 ATGAAAGATCAATGGTGCCATC 57.068 40.909 3.96 0.00 39.49 3.51
2794 3679 5.953183 TGCTGCCAATACTCAATTAACTTG 58.047 37.500 0.00 0.00 36.09 3.16
2888 3774 7.649306 GCTGGATGCTTAAAAATATGTAACCTG 59.351 37.037 0.00 0.00 38.95 4.00


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

AutoCloner maintained by Alex Coulton.