Multiple sequence alignment - TraesCS4B01G336500

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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 TraesCS4B01G336500 chr4B 100.000 3199 0 0 1 3199 628708014 628711212 0.000000e+00 5908.0
1 TraesCS4B01G336500 chr4D 91.462 1546 91 23 754 2287 489750361 489751877 0.000000e+00 2085.0
2 TraesCS4B01G336500 chr4D 85.344 771 75 18 1 762 489749495 489750236 0.000000e+00 763.0
3 TraesCS4B01G336500 chr5A 89.877 1136 56 25 721 1812 671197422 671198542 0.000000e+00 1406.0
4 TraesCS4B01G336500 chr5A 90.661 514 29 8 1804 2298 671198660 671199173 0.000000e+00 665.0
5 TraesCS4B01G336500 chr5A 80.796 427 38 15 187 598 671196973 671197370 8.680000e-76 294.0
6 TraesCS4B01G336500 chr5A 92.021 188 15 0 1 188 671196750 671196937 6.800000e-67 265.0
7 TraesCS4B01G336500 chr5A 74.464 560 120 17 1632 2172 591673683 591674238 1.490000e-53 220.0
8 TraesCS4B01G336500 chr2B 93.037 675 43 4 2506 3179 628927341 628926670 0.000000e+00 983.0
9 TraesCS4B01G336500 chr2B 92.171 677 47 6 2506 3179 777685613 777684940 0.000000e+00 952.0
10 TraesCS4B01G336500 chr2B 91.840 674 50 5 2507 3179 395268249 395267580 0.000000e+00 935.0
11 TraesCS4B01G336500 chr2B 80.742 997 157 26 1209 2179 248690413 248691400 0.000000e+00 745.0
12 TraesCS4B01G336500 chr2B 79.065 449 75 13 1668 2105 232923606 232923166 1.120000e-74 291.0
13 TraesCS4B01G336500 chr2B 93.023 129 9 0 2378 2506 421077402 421077274 4.210000e-44 189.0
14 TraesCS4B01G336500 chr2B 92.366 131 10 0 2374 2504 401145799 401145929 1.520000e-43 187.0
15 TraesCS4B01G336500 chr5B 92.889 675 44 4 2506 3179 704956876 704957547 0.000000e+00 977.0
16 TraesCS4B01G336500 chr5B 75.350 572 123 17 1632 2191 578815550 578816115 3.170000e-65 259.0
17 TraesCS4B01G336500 chr5B 73.759 564 119 22 1632 2172 579003542 579004099 9.050000e-46 195.0
18 TraesCS4B01G336500 chr5B 92.308 130 9 1 2378 2506 680837525 680837396 1.960000e-42 183.0
19 TraesCS4B01G336500 chr7B 92.582 674 47 3 2507 3179 187574059 187574730 0.000000e+00 965.0
20 TraesCS4B01G336500 chr7B 92.330 678 49 3 2503 3179 11710149 11710824 0.000000e+00 961.0
21 TraesCS4B01G336500 chr7B 91.840 674 52 3 2507 3179 122719665 122720336 0.000000e+00 937.0
22 TraesCS4B01G336500 chr7D 92.308 676 48 4 2506 3179 550213360 550212687 0.000000e+00 957.0
23 TraesCS4B01G336500 chr7A 91.568 676 54 3 2505 3179 275967918 275967245 0.000000e+00 929.0
24 TraesCS4B01G336500 chr2A 77.155 928 169 24 1210 2105 187203529 187204445 1.710000e-137 499.0
25 TraesCS4B01G336500 chr2A 75.000 876 182 27 1246 2108 187320122 187319271 1.400000e-98 370.0
26 TraesCS4B01G336500 chr2D 80.357 448 70 13 1668 2105 164278869 164279308 1.110000e-84 324.0
27 TraesCS4B01G336500 chr2D 93.798 129 8 0 2378 2506 575827300 575827172 9.050000e-46 195.0
28 TraesCS4B01G336500 chr5D 75.478 575 117 22 1632 2191 472399537 472400102 3.170000e-65 259.0
29 TraesCS4B01G336500 chr3B 93.023 129 9 0 2378 2506 109920983 109920855 4.210000e-44 189.0
30 TraesCS4B01G336500 chr1B 93.023 129 9 0 2378 2506 475286479 475286607 4.210000e-44 189.0
31 TraesCS4B01G336500 chr6B 92.248 129 10 0 2378 2506 678533155 678533027 1.960000e-42 183.0
32 TraesCS4B01G336500 chr6B 92.248 129 10 0 2378 2506 720755302 720755174 1.960000e-42 183.0
33 TraesCS4B01G336500 chr1D 92.248 129 10 0 2378 2506 1816321 1816193 1.960000e-42 183.0
34 TraesCS4B01G336500 chr6A 96.875 32 1 0 2300 2331 38443719 38443750 2.000000e-03 54.7


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 TraesCS4B01G336500 chr4B 628708014 628711212 3198 False 5908.0 5908 100.00000 1 3199 1 chr4B.!!$F1 3198
1 TraesCS4B01G336500 chr4D 489749495 489751877 2382 False 1424.0 2085 88.40300 1 2287 2 chr4D.!!$F1 2286
2 TraesCS4B01G336500 chr5A 671196750 671199173 2423 False 657.5 1406 88.33875 1 2298 4 chr5A.!!$F2 2297
3 TraesCS4B01G336500 chr5A 591673683 591674238 555 False 220.0 220 74.46400 1632 2172 1 chr5A.!!$F1 540
4 TraesCS4B01G336500 chr2B 628926670 628927341 671 True 983.0 983 93.03700 2506 3179 1 chr2B.!!$R4 673
5 TraesCS4B01G336500 chr2B 777684940 777685613 673 True 952.0 952 92.17100 2506 3179 1 chr2B.!!$R5 673
6 TraesCS4B01G336500 chr2B 395267580 395268249 669 True 935.0 935 91.84000 2507 3179 1 chr2B.!!$R2 672
7 TraesCS4B01G336500 chr2B 248690413 248691400 987 False 745.0 745 80.74200 1209 2179 1 chr2B.!!$F1 970
8 TraesCS4B01G336500 chr5B 704956876 704957547 671 False 977.0 977 92.88900 2506 3179 1 chr5B.!!$F3 673
9 TraesCS4B01G336500 chr5B 578815550 578816115 565 False 259.0 259 75.35000 1632 2191 1 chr5B.!!$F1 559
10 TraesCS4B01G336500 chr7B 187574059 187574730 671 False 965.0 965 92.58200 2507 3179 1 chr7B.!!$F3 672
11 TraesCS4B01G336500 chr7B 11710149 11710824 675 False 961.0 961 92.33000 2503 3179 1 chr7B.!!$F1 676
12 TraesCS4B01G336500 chr7B 122719665 122720336 671 False 937.0 937 91.84000 2507 3179 1 chr7B.!!$F2 672
13 TraesCS4B01G336500 chr7D 550212687 550213360 673 True 957.0 957 92.30800 2506 3179 1 chr7D.!!$R1 673
14 TraesCS4B01G336500 chr7A 275967245 275967918 673 True 929.0 929 91.56800 2505 3179 1 chr7A.!!$R1 674
15 TraesCS4B01G336500 chr2A 187203529 187204445 916 False 499.0 499 77.15500 1210 2105 1 chr2A.!!$F1 895
16 TraesCS4B01G336500 chr2A 187319271 187320122 851 True 370.0 370 75.00000 1246 2108 1 chr2A.!!$R1 862
17 TraesCS4B01G336500 chr5D 472399537 472400102 565 False 259.0 259 75.47800 1632 2191 1 chr5D.!!$F1 559

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
724 786 0.034337 CGGAAGTCCCAAAACGGAGA 59.966 55.0 0.0 0.0 36.56 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2830 0.109458 TAACGCTCGTCGCAGTGATT 60.109 50.0 10.76 5.77 43.23 2.57 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
18 19 2.829384 GGGGAGTGGTCTTGTGCCA 61.829 63.158 0.00 0.00 0.00 4.92
43 44 4.573900 AGACACGAGCATTTCTCTCATTT 58.426 39.130 0.00 0.00 39.70 2.32
49 50 6.805271 CACGAGCATTTCTCTCATTTCAAATT 59.195 34.615 0.00 0.00 39.70 1.82
54 55 7.813148 AGCATTTCTCTCATTTCAAATTGTCTG 59.187 33.333 0.00 0.00 0.00 3.51
98 107 2.427506 CTATGGCCTTTCTATTCGGGC 58.572 52.381 3.32 0.00 43.42 6.13
101 110 1.448119 GGCCTTTCTATTCGGGCTGC 61.448 60.000 0.00 0.00 43.62 5.25
141 150 2.375174 ACCAGCACTCCTTAATGGAACA 59.625 45.455 0.00 0.00 45.63 3.18
156 165 2.229792 GGAACACTTCAAGCACCATGA 58.770 47.619 0.00 0.00 0.00 3.07
183 192 5.243507 TGGTGTCAATATGCACAAGTTGAAT 59.756 36.000 10.54 3.02 37.35 2.57
210 256 2.097036 CTTGATCATGCCTCAAAGCCA 58.903 47.619 0.00 0.00 32.53 4.75
213 259 3.101437 TGATCATGCCTCAAAGCCAAAT 58.899 40.909 0.00 0.00 0.00 2.32
214 260 4.279982 TGATCATGCCTCAAAGCCAAATA 58.720 39.130 0.00 0.00 0.00 1.40
243 289 3.443681 CGGCATTTGAAGAATAGGTGGTT 59.556 43.478 0.00 0.00 0.00 3.67
254 300 5.491982 AGAATAGGTGGTTAGCACTTTCAG 58.508 41.667 14.31 0.00 0.00 3.02
258 304 3.067833 GGTGGTTAGCACTTTCAGTCTC 58.932 50.000 14.31 0.00 0.00 3.36
283 329 2.228545 TGCAAAGTGGGCATAATCCA 57.771 45.000 0.00 0.00 36.11 3.41
297 343 5.810074 GGCATAATCCACAATTTGTACAACC 59.190 40.000 8.07 0.00 0.00 3.77
298 344 5.514914 GCATAATCCACAATTTGTACAACCG 59.485 40.000 8.07 2.18 0.00 4.44
327 373 2.702592 TCTTTCGGCGGTCCAAATAT 57.297 45.000 7.21 0.00 0.00 1.28
360 406 4.646945 TGGACAACCAAGCAAAATTACTCA 59.353 37.500 0.00 0.00 43.91 3.41
404 462 1.347707 ACACGGTGGAACTCATGACAT 59.652 47.619 13.48 0.00 36.74 3.06
407 465 4.404394 ACACGGTGGAACTCATGACATATA 59.596 41.667 13.48 0.00 36.74 0.86
438 500 6.238759 GCTTTGAGGAATTGTGTCTTGTAAGT 60.239 38.462 0.00 0.00 0.00 2.24
444 506 6.497259 AGGAATTGTGTCTTGTAAGTAGAGGA 59.503 38.462 0.00 0.00 0.00 3.71
448 510 3.190953 GTGTCTTGTAAGTAGAGGACGCT 59.809 47.826 4.63 0.00 34.64 5.07
455 517 4.634883 TGTAAGTAGAGGACGCTGAGTAAG 59.365 45.833 0.00 0.00 0.00 2.34
456 518 3.630892 AGTAGAGGACGCTGAGTAAGA 57.369 47.619 0.00 0.00 0.00 2.10
493 555 3.808618 GCTTCCAAGTGATGTTGTCCTCT 60.809 47.826 0.00 0.00 0.00 3.69
502 564 3.006430 TGATGTTGTCCTCTGCGTCTTTA 59.994 43.478 0.00 0.00 0.00 1.85
512 574 1.026182 TGCGTCTTTATGCAGCTGGG 61.026 55.000 17.12 0.00 42.73 4.45
528 590 0.183492 TGGGCATCACCTAGGATTGC 59.817 55.000 17.98 19.34 39.10 3.56
565 627 5.598416 TCTCACGAATGTGGTAGAATGAT 57.402 39.130 0.00 0.00 46.42 2.45
570 632 6.823182 TCACGAATGTGGTAGAATGATCAATT 59.177 34.615 0.00 0.00 46.42 2.32
572 634 7.985295 CACGAATGTGGTAGAATGATCAATTCG 60.985 40.741 22.31 22.31 44.37 3.34
619 681 1.956636 GCACAATCCTTCATGGCCTCA 60.957 52.381 3.32 0.00 35.26 3.86
634 696 0.901580 CCTCATGCACCTTGCCCTTT 60.902 55.000 0.00 0.00 44.23 3.11
652 714 3.526534 CTTTTTCCTAGAAGAGGCCTCG 58.473 50.000 26.95 12.24 46.25 4.63
657 719 2.158784 TCCTAGAAGAGGCCTCGTAGAC 60.159 54.545 28.17 19.15 46.25 2.59
677 739 2.194271 CGAGCGGAGAAATGTCCTTAC 58.806 52.381 0.00 0.00 34.00 2.34
678 740 2.194271 GAGCGGAGAAATGTCCTTACG 58.806 52.381 0.00 0.00 34.00 3.18
679 741 0.651031 GCGGAGAAATGTCCTTACGC 59.349 55.000 0.00 0.00 38.94 4.42
680 742 1.287425 CGGAGAAATGTCCTTACGCC 58.713 55.000 0.00 0.00 34.00 5.68
683 745 0.743345 AGAAATGTCCTTACGCCGGC 60.743 55.000 19.07 19.07 0.00 6.13
697 759 4.506255 CGGCCCCCATTGACCCTC 62.506 72.222 0.00 0.00 0.00 4.30
700 762 3.809013 CCCCCATTGACCCTCCGG 61.809 72.222 0.00 0.00 0.00 5.14
719 781 2.951458 CGCCGGAAGTCCCAAAAC 59.049 61.111 5.05 0.00 34.14 2.43
724 786 0.034337 CGGAAGTCCCAAAACGGAGA 59.966 55.000 0.00 0.00 36.56 3.71
726 788 1.346722 GGAAGTCCCAAAACGGAGAGA 59.653 52.381 0.00 0.00 36.56 3.10
806 1008 3.521937 CCCCTGGTTTTGAGATACCACTA 59.478 47.826 0.00 0.00 39.44 2.74
829 1039 4.759693 ACAACTTGGATGAAGCATCGTTAA 59.240 37.500 0.00 0.00 41.35 2.01
830 1040 5.415701 ACAACTTGGATGAAGCATCGTTAAT 59.584 36.000 0.00 0.00 41.35 1.40
831 1041 6.071952 ACAACTTGGATGAAGCATCGTTAATT 60.072 34.615 0.00 0.00 41.35 1.40
832 1042 7.120579 ACAACTTGGATGAAGCATCGTTAATTA 59.879 33.333 0.00 0.00 41.35 1.40
871 1081 8.905660 ACAGAACGAGACTGTATAGTACATAT 57.094 34.615 10.77 0.00 45.10 1.78
872 1082 9.993454 ACAGAACGAGACTGTATAGTACATATA 57.007 33.333 10.77 0.00 45.10 0.86
875 1085 9.705471 GAACGAGACTGTATAGTACATATATGC 57.295 37.037 12.79 0.00 37.25 3.14
876 1086 7.907194 ACGAGACTGTATAGTACATATATGCG 58.093 38.462 12.79 5.52 37.25 4.73
878 1088 8.270111 CGAGACTGTATAGTACATATATGCGAG 58.730 40.741 12.79 0.69 37.25 5.03
879 1089 7.921787 AGACTGTATAGTACATATATGCGAGC 58.078 38.462 12.79 1.10 37.25 5.03
920 1133 1.345410 AACACAACAAGCAAACACGC 58.655 45.000 0.00 0.00 0.00 5.34
934 1147 2.873170 ACACGCACGTATTTGTCATG 57.127 45.000 0.00 0.00 0.00 3.07
938 1151 2.669434 ACGCACGTATTTGTCATGTACC 59.331 45.455 0.00 0.00 0.00 3.34
946 1159 5.872617 CGTATTTGTCATGTACCCTTGAGAA 59.127 40.000 0.00 0.00 0.00 2.87
954 1167 2.972713 TGTACCCTTGAGAAAGAGCAGT 59.027 45.455 0.00 0.00 0.00 4.40
960 1196 4.262635 CCCTTGAGAAAGAGCAGTAACAGA 60.263 45.833 0.00 0.00 0.00 3.41
1517 1770 4.410400 CTGAAGCACCCCGACCCC 62.410 72.222 0.00 0.00 0.00 4.95
1529 1782 0.616679 CCGACCCCTTCAAGGACCTA 60.617 60.000 4.43 0.00 37.67 3.08
1700 1980 2.029666 CGGAGGATGATGGCGGAC 59.970 66.667 0.00 0.00 0.00 4.79
1817 2223 0.976073 ACCTGTACGCCACCAGCTAT 60.976 55.000 0.00 0.00 40.39 2.97
1943 2360 3.681835 GACGTCGTCTGCCTGGGT 61.682 66.667 18.09 0.00 0.00 4.51
2048 2477 3.055819 GTGACATGCTCTTCTCCTTGGTA 60.056 47.826 0.00 0.00 0.00 3.25
2195 2638 1.409064 CGTTACAGCTATCCTGGAGCA 59.591 52.381 10.18 0.00 46.14 4.26
2233 2676 1.736282 CCACGCTGTGTGCATCGTA 60.736 57.895 15.61 0.00 44.25 3.43
2237 2680 1.128507 ACGCTGTGTGCATCGTAAATG 59.871 47.619 0.00 0.00 44.24 2.32
2244 2687 5.182487 TGTGTGCATCGTAAATGTATTCCT 58.818 37.500 0.00 0.00 0.00 3.36
2245 2688 6.342111 TGTGTGCATCGTAAATGTATTCCTA 58.658 36.000 0.00 0.00 0.00 2.94
2275 2737 7.579589 TTTGTGCTACATTTACATTGCATTC 57.420 32.000 0.00 0.00 32.98 2.67
2280 2742 6.536941 TGCTACATTTACATTGCATTCTCGTA 59.463 34.615 0.00 0.00 0.00 3.43
2298 2760 2.287368 CGTATACGCACTCCACATGCTA 60.287 50.000 13.08 0.00 41.10 3.49
2299 2761 3.611766 CGTATACGCACTCCACATGCTAT 60.612 47.826 13.08 0.00 41.10 2.97
2300 2762 2.223537 TACGCACTCCACATGCTATG 57.776 50.000 0.00 0.00 41.10 2.23
2301 2763 1.091771 ACGCACTCCACATGCTATGC 61.092 55.000 0.00 0.00 41.10 3.14
2302 2764 0.812811 CGCACTCCACATGCTATGCT 60.813 55.000 0.00 0.00 41.10 3.79
2303 2765 1.538849 CGCACTCCACATGCTATGCTA 60.539 52.381 0.00 0.00 41.10 3.49
2304 2766 2.564771 GCACTCCACATGCTATGCTAA 58.435 47.619 0.00 0.00 40.08 3.09
2305 2767 2.547211 GCACTCCACATGCTATGCTAAG 59.453 50.000 0.00 0.00 40.08 2.18
2306 2768 3.136763 CACTCCACATGCTATGCTAAGG 58.863 50.000 0.00 0.00 0.00 2.69
2307 2769 2.105477 ACTCCACATGCTATGCTAAGGG 59.895 50.000 0.00 0.00 0.00 3.95
2308 2770 1.202806 TCCACATGCTATGCTAAGGGC 60.203 52.381 0.00 0.00 42.22 5.19
2320 2782 3.611766 GCTAAGGGCAACTCTAACTGA 57.388 47.619 0.00 0.00 41.35 3.41
2321 2783 4.143986 GCTAAGGGCAACTCTAACTGAT 57.856 45.455 0.00 0.00 41.35 2.90
2322 2784 4.123506 GCTAAGGGCAACTCTAACTGATC 58.876 47.826 0.00 0.00 41.35 2.92
2323 2785 3.636153 AAGGGCAACTCTAACTGATCC 57.364 47.619 0.00 0.00 0.00 3.36
2324 2786 1.840635 AGGGCAACTCTAACTGATCCC 59.159 52.381 0.00 0.00 0.00 3.85
2325 2787 1.134068 GGGCAACTCTAACTGATCCCC 60.134 57.143 0.00 0.00 0.00 4.81
2326 2788 1.840635 GGCAACTCTAACTGATCCCCT 59.159 52.381 0.00 0.00 0.00 4.79
2327 2789 2.158885 GGCAACTCTAACTGATCCCCTC 60.159 54.545 0.00 0.00 0.00 4.30
2328 2790 2.769095 GCAACTCTAACTGATCCCCTCT 59.231 50.000 0.00 0.00 0.00 3.69
2329 2791 3.961408 GCAACTCTAACTGATCCCCTCTA 59.039 47.826 0.00 0.00 0.00 2.43
2330 2792 4.038642 GCAACTCTAACTGATCCCCTCTAG 59.961 50.000 0.00 0.00 0.00 2.43
2331 2793 5.450453 CAACTCTAACTGATCCCCTCTAGA 58.550 45.833 0.00 0.00 0.00 2.43
2332 2794 5.735733 ACTCTAACTGATCCCCTCTAGAA 57.264 43.478 0.00 0.00 0.00 2.10
2333 2795 5.451354 ACTCTAACTGATCCCCTCTAGAAC 58.549 45.833 0.00 0.00 0.00 3.01
2334 2796 4.805744 TCTAACTGATCCCCTCTAGAACC 58.194 47.826 0.00 0.00 0.00 3.62
2335 2797 3.491766 AACTGATCCCCTCTAGAACCA 57.508 47.619 0.00 0.00 0.00 3.67
2336 2798 3.715648 ACTGATCCCCTCTAGAACCAT 57.284 47.619 0.00 0.00 0.00 3.55
2337 2799 3.582164 ACTGATCCCCTCTAGAACCATC 58.418 50.000 0.00 0.00 0.00 3.51
2338 2800 3.051803 ACTGATCCCCTCTAGAACCATCA 60.052 47.826 0.00 0.00 0.00 3.07
2339 2801 4.166539 CTGATCCCCTCTAGAACCATCAT 58.833 47.826 0.00 0.00 0.00 2.45
2340 2802 5.162826 ACTGATCCCCTCTAGAACCATCATA 60.163 44.000 0.00 0.00 0.00 2.15
2341 2803 5.336945 TGATCCCCTCTAGAACCATCATAG 58.663 45.833 0.00 0.00 0.00 2.23
2342 2804 3.511477 TCCCCTCTAGAACCATCATAGC 58.489 50.000 0.00 0.00 0.00 2.97
2343 2805 3.116746 TCCCCTCTAGAACCATCATAGCA 60.117 47.826 0.00 0.00 0.00 3.49
2344 2806 3.260380 CCCCTCTAGAACCATCATAGCAG 59.740 52.174 0.00 0.00 0.00 4.24
2345 2807 3.306641 CCCTCTAGAACCATCATAGCAGC 60.307 52.174 0.00 0.00 0.00 5.25
2346 2808 3.306641 CCTCTAGAACCATCATAGCAGCC 60.307 52.174 0.00 0.00 0.00 4.85
2347 2809 3.308401 TCTAGAACCATCATAGCAGCCA 58.692 45.455 0.00 0.00 0.00 4.75
2348 2810 2.338577 AGAACCATCATAGCAGCCAC 57.661 50.000 0.00 0.00 0.00 5.01
2349 2811 0.940126 GAACCATCATAGCAGCCACG 59.060 55.000 0.00 0.00 0.00 4.94
2350 2812 0.541392 AACCATCATAGCAGCCACGA 59.459 50.000 0.00 0.00 0.00 4.35
2351 2813 0.541392 ACCATCATAGCAGCCACGAA 59.459 50.000 0.00 0.00 0.00 3.85
2352 2814 1.065491 ACCATCATAGCAGCCACGAAA 60.065 47.619 0.00 0.00 0.00 3.46
2353 2815 2.016318 CCATCATAGCAGCCACGAAAA 58.984 47.619 0.00 0.00 0.00 2.29
2354 2816 2.032550 CCATCATAGCAGCCACGAAAAG 59.967 50.000 0.00 0.00 0.00 2.27
2355 2817 2.760634 TCATAGCAGCCACGAAAAGA 57.239 45.000 0.00 0.00 0.00 2.52
2356 2818 3.052455 TCATAGCAGCCACGAAAAGAA 57.948 42.857 0.00 0.00 0.00 2.52
2357 2819 3.407698 TCATAGCAGCCACGAAAAGAAA 58.592 40.909 0.00 0.00 0.00 2.52
2358 2820 3.818210 TCATAGCAGCCACGAAAAGAAAA 59.182 39.130 0.00 0.00 0.00 2.29
2359 2821 4.277174 TCATAGCAGCCACGAAAAGAAAAA 59.723 37.500 0.00 0.00 0.00 1.94
2379 2841 3.455619 AAAATGACGAATCACTGCGAC 57.544 42.857 0.00 0.00 37.79 5.19
2380 2842 0.992072 AATGACGAATCACTGCGACG 59.008 50.000 0.00 0.00 37.79 5.12
2381 2843 0.170339 ATGACGAATCACTGCGACGA 59.830 50.000 0.00 0.00 37.79 4.20
2382 2844 0.454452 TGACGAATCACTGCGACGAG 60.454 55.000 0.00 0.00 0.00 4.18
2392 2854 3.360766 GCGACGAGCGTTAGTGTC 58.639 61.111 0.00 0.00 43.41 3.67
2393 2855 1.441515 GCGACGAGCGTTAGTGTCA 60.442 57.895 0.00 0.00 43.41 3.58
2394 2856 1.000233 GCGACGAGCGTTAGTGTCAA 61.000 55.000 0.00 0.00 43.41 3.18
2395 2857 0.975544 CGACGAGCGTTAGTGTCAAG 59.024 55.000 0.00 0.00 34.64 3.02
2396 2858 1.662309 CGACGAGCGTTAGTGTCAAGT 60.662 52.381 0.00 0.00 34.64 3.16
2397 2859 2.391879 GACGAGCGTTAGTGTCAAGTT 58.608 47.619 0.00 0.00 0.00 2.66
2398 2860 2.391879 ACGAGCGTTAGTGTCAAGTTC 58.608 47.619 0.00 0.00 0.00 3.01
2399 2861 2.223641 ACGAGCGTTAGTGTCAAGTTCA 60.224 45.455 0.00 0.00 0.00 3.18
2400 2862 2.405357 CGAGCGTTAGTGTCAAGTTCAG 59.595 50.000 0.00 0.00 0.00 3.02
2401 2863 3.639538 GAGCGTTAGTGTCAAGTTCAGA 58.360 45.455 0.00 0.00 0.00 3.27
2402 2864 3.643763 AGCGTTAGTGTCAAGTTCAGAG 58.356 45.455 0.00 0.00 0.00 3.35
2403 2865 2.731976 GCGTTAGTGTCAAGTTCAGAGG 59.268 50.000 0.00 0.00 0.00 3.69
2404 2866 3.799232 GCGTTAGTGTCAAGTTCAGAGGT 60.799 47.826 0.00 0.00 0.00 3.85
2405 2867 4.369182 CGTTAGTGTCAAGTTCAGAGGTT 58.631 43.478 0.00 0.00 0.00 3.50
2406 2868 4.809426 CGTTAGTGTCAAGTTCAGAGGTTT 59.191 41.667 0.00 0.00 0.00 3.27
2407 2869 5.050972 CGTTAGTGTCAAGTTCAGAGGTTTC 60.051 44.000 0.00 0.00 0.00 2.78
2408 2870 4.762289 AGTGTCAAGTTCAGAGGTTTCT 57.238 40.909 0.00 0.00 0.00 2.52
2409 2871 5.104259 AGTGTCAAGTTCAGAGGTTTCTT 57.896 39.130 0.00 0.00 0.00 2.52
2410 2872 5.119694 AGTGTCAAGTTCAGAGGTTTCTTC 58.880 41.667 0.00 0.00 0.00 2.87
2411 2873 4.025647 GTGTCAAGTTCAGAGGTTTCTTCG 60.026 45.833 0.00 0.00 0.00 3.79
2412 2874 3.495001 GTCAAGTTCAGAGGTTTCTTCGG 59.505 47.826 0.00 0.00 0.00 4.30
2413 2875 3.134081 TCAAGTTCAGAGGTTTCTTCGGT 59.866 43.478 0.00 0.00 0.00 4.69
2414 2876 3.388345 AGTTCAGAGGTTTCTTCGGTC 57.612 47.619 0.00 0.00 0.00 4.79
2415 2877 2.966516 AGTTCAGAGGTTTCTTCGGTCT 59.033 45.455 0.00 0.00 0.00 3.85
2416 2878 3.388350 AGTTCAGAGGTTTCTTCGGTCTT 59.612 43.478 0.00 0.00 0.00 3.01
2417 2879 3.386768 TCAGAGGTTTCTTCGGTCTTG 57.613 47.619 0.00 0.00 0.00 3.02
2418 2880 2.963101 TCAGAGGTTTCTTCGGTCTTGA 59.037 45.455 0.00 0.00 0.00 3.02
2419 2881 3.578716 TCAGAGGTTTCTTCGGTCTTGAT 59.421 43.478 0.00 0.00 0.00 2.57
2420 2882 4.040461 TCAGAGGTTTCTTCGGTCTTGATT 59.960 41.667 0.00 0.00 0.00 2.57
2421 2883 4.153117 CAGAGGTTTCTTCGGTCTTGATTG 59.847 45.833 0.00 0.00 0.00 2.67
2422 2884 4.065789 GAGGTTTCTTCGGTCTTGATTGT 58.934 43.478 0.00 0.00 0.00 2.71
2423 2885 5.011738 AGAGGTTTCTTCGGTCTTGATTGTA 59.988 40.000 0.00 0.00 0.00 2.41
2424 2886 5.617252 AGGTTTCTTCGGTCTTGATTGTAA 58.383 37.500 0.00 0.00 0.00 2.41
2425 2887 6.238648 AGGTTTCTTCGGTCTTGATTGTAAT 58.761 36.000 0.00 0.00 0.00 1.89
2426 2888 6.715264 AGGTTTCTTCGGTCTTGATTGTAATT 59.285 34.615 0.00 0.00 0.00 1.40
2427 2889 7.230712 AGGTTTCTTCGGTCTTGATTGTAATTT 59.769 33.333 0.00 0.00 0.00 1.82
2428 2890 7.865889 GGTTTCTTCGGTCTTGATTGTAATTTT 59.134 33.333 0.00 0.00 0.00 1.82
2429 2891 9.887406 GTTTCTTCGGTCTTGATTGTAATTTTA 57.113 29.630 0.00 0.00 0.00 1.52
2430 2892 9.887406 TTTCTTCGGTCTTGATTGTAATTTTAC 57.113 29.630 0.00 0.00 0.00 2.01
2431 2893 8.842358 TCTTCGGTCTTGATTGTAATTTTACT 57.158 30.769 2.45 0.00 34.77 2.24
2432 2894 9.280174 TCTTCGGTCTTGATTGTAATTTTACTT 57.720 29.630 2.45 0.00 34.77 2.24
2433 2895 9.543018 CTTCGGTCTTGATTGTAATTTTACTTC 57.457 33.333 2.45 1.11 34.77 3.01
2434 2896 8.842358 TCGGTCTTGATTGTAATTTTACTTCT 57.158 30.769 2.45 0.00 34.77 2.85
2435 2897 9.280174 TCGGTCTTGATTGTAATTTTACTTCTT 57.720 29.630 2.45 0.00 34.77 2.52
2436 2898 9.329913 CGGTCTTGATTGTAATTTTACTTCTTG 57.670 33.333 2.45 0.00 34.77 3.02
2437 2899 9.626045 GGTCTTGATTGTAATTTTACTTCTTGG 57.374 33.333 2.45 0.00 34.77 3.61
2438 2900 9.129209 GTCTTGATTGTAATTTTACTTCTTGGC 57.871 33.333 2.45 0.00 34.77 4.52
2439 2901 9.077885 TCTTGATTGTAATTTTACTTCTTGGCT 57.922 29.630 2.45 0.00 34.77 4.75
2442 2904 9.515226 TGATTGTAATTTTACTTCTTGGCTACT 57.485 29.630 2.45 0.00 34.77 2.57
2443 2905 9.774742 GATTGTAATTTTACTTCTTGGCTACTG 57.225 33.333 2.45 0.00 34.77 2.74
2444 2906 8.685838 TTGTAATTTTACTTCTTGGCTACTGT 57.314 30.769 2.45 0.00 34.77 3.55
2445 2907 8.685838 TGTAATTTTACTTCTTGGCTACTGTT 57.314 30.769 2.45 0.00 34.77 3.16
2446 2908 8.780249 TGTAATTTTACTTCTTGGCTACTGTTC 58.220 33.333 2.45 0.00 34.77 3.18
2447 2909 6.819397 ATTTTACTTCTTGGCTACTGTTCC 57.181 37.500 0.00 0.00 0.00 3.62
2448 2910 5.562298 TTTACTTCTTGGCTACTGTTCCT 57.438 39.130 0.00 0.00 0.00 3.36
2449 2911 5.562298 TTACTTCTTGGCTACTGTTCCTT 57.438 39.130 0.00 0.00 0.00 3.36
2450 2912 4.439253 ACTTCTTGGCTACTGTTCCTTT 57.561 40.909 0.00 0.00 0.00 3.11
2451 2913 4.137543 ACTTCTTGGCTACTGTTCCTTTG 58.862 43.478 0.00 0.00 0.00 2.77
2452 2914 3.857157 TCTTGGCTACTGTTCCTTTGT 57.143 42.857 0.00 0.00 0.00 2.83
2453 2915 3.476552 TCTTGGCTACTGTTCCTTTGTG 58.523 45.455 0.00 0.00 0.00 3.33
2454 2916 1.604604 TGGCTACTGTTCCTTTGTGC 58.395 50.000 0.00 0.00 0.00 4.57
2455 2917 1.133945 TGGCTACTGTTCCTTTGTGCA 60.134 47.619 0.00 0.00 0.00 4.57
2456 2918 1.953686 GGCTACTGTTCCTTTGTGCAA 59.046 47.619 0.00 0.00 0.00 4.08
2457 2919 2.360801 GGCTACTGTTCCTTTGTGCAAA 59.639 45.455 0.00 0.00 0.00 3.68
2458 2920 3.550842 GGCTACTGTTCCTTTGTGCAAAG 60.551 47.826 15.53 15.53 45.47 2.77
2465 2927 3.389741 CTTTGTGCAAAGGCTAGCG 57.610 52.632 9.00 0.00 42.96 4.26
2466 2928 0.874390 CTTTGTGCAAAGGCTAGCGA 59.126 50.000 9.00 0.00 42.96 4.93
2467 2929 1.470098 CTTTGTGCAAAGGCTAGCGAT 59.530 47.619 9.00 0.00 42.96 4.58
2468 2930 1.533625 TTGTGCAAAGGCTAGCGATT 58.466 45.000 9.00 3.10 41.91 3.34
2469 2931 1.533625 TGTGCAAAGGCTAGCGATTT 58.466 45.000 9.00 9.57 41.91 2.17
2470 2932 1.199789 TGTGCAAAGGCTAGCGATTTG 59.800 47.619 27.24 27.24 41.91 2.32
2483 2945 3.273919 GCGATTTGCTGTCTTTTCAGT 57.726 42.857 0.00 0.00 41.73 3.41
2484 2946 3.632189 GCGATTTGCTGTCTTTTCAGTT 58.368 40.909 0.00 0.00 41.73 3.16
2485 2947 4.044426 GCGATTTGCTGTCTTTTCAGTTT 58.956 39.130 0.00 0.00 41.73 2.66
2486 2948 4.504097 GCGATTTGCTGTCTTTTCAGTTTT 59.496 37.500 0.00 0.00 41.73 2.43
2487 2949 5.685511 GCGATTTGCTGTCTTTTCAGTTTTA 59.314 36.000 0.00 0.00 41.73 1.52
2488 2950 6.345015 GCGATTTGCTGTCTTTTCAGTTTTAC 60.345 38.462 0.00 0.00 41.73 2.01
2489 2951 6.142320 CGATTTGCTGTCTTTTCAGTTTTACC 59.858 38.462 0.00 0.00 37.70 2.85
2490 2952 5.906113 TTGCTGTCTTTTCAGTTTTACCA 57.094 34.783 0.00 0.00 37.70 3.25
2491 2953 5.499139 TGCTGTCTTTTCAGTTTTACCAG 57.501 39.130 0.00 0.00 37.70 4.00
2492 2954 4.338118 TGCTGTCTTTTCAGTTTTACCAGG 59.662 41.667 0.00 0.00 37.70 4.45
2493 2955 4.338400 GCTGTCTTTTCAGTTTTACCAGGT 59.662 41.667 0.00 0.00 37.70 4.00
2494 2956 5.505819 GCTGTCTTTTCAGTTTTACCAGGTC 60.506 44.000 0.00 0.00 37.70 3.85
2495 2957 4.573201 TGTCTTTTCAGTTTTACCAGGTCG 59.427 41.667 0.00 0.00 0.00 4.79
2496 2958 4.024302 GTCTTTTCAGTTTTACCAGGTCGG 60.024 45.833 0.00 0.00 42.50 4.79
2632 3094 4.797275 GCAAAAGTAAAGGCAAGCTCACAT 60.797 41.667 0.00 0.00 0.00 3.21
2695 3157 5.116084 ACTGGCTGGCATAAGAAAGATAA 57.884 39.130 3.74 0.00 0.00 1.75
2735 3197 2.957402 ATTACATGACCGCCATCCAT 57.043 45.000 0.00 0.00 31.94 3.41
2736 3198 2.727123 TTACATGACCGCCATCCATT 57.273 45.000 0.00 0.00 31.94 3.16
2776 3238 0.969894 CTACCATCTCCCACCGGATC 59.030 60.000 9.46 0.00 37.60 3.36
2848 3310 2.845752 TACGGATCAACGCAGTGGCC 62.846 60.000 0.00 0.00 45.00 5.36
2924 3389 1.999648 TCTGCAGTTCCAAATTGCCT 58.000 45.000 14.67 0.00 42.75 4.75
2941 3406 5.828299 TTGCCTACAATAAAGCACATACC 57.172 39.130 0.00 0.00 34.37 2.73
3018 3483 5.351233 AATAACGTGCTGACAAAATTCGA 57.649 34.783 0.00 0.00 0.00 3.71
3111 3577 5.220854 GGTGTTTGATAGTTTCATCCCGATG 60.221 44.000 0.00 0.00 40.09 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.141398 GCTCACCTCACAGACAATTTGA 58.859 45.455 2.79 0.00 0.00 2.69
49 50 0.322648 CCATGCTCACCTCACAGACA 59.677 55.000 0.00 0.00 0.00 3.41
54 55 0.322975 ACTCACCATGCTCACCTCAC 59.677 55.000 0.00 0.00 0.00 3.51
98 107 1.854743 CGACATGTCCGACATTAGCAG 59.145 52.381 20.03 3.03 36.53 4.24
101 110 2.858344 GGTTCGACATGTCCGACATTAG 59.142 50.000 20.03 4.44 36.53 1.73
156 165 2.877097 TGTGCATATTGACACCACCT 57.123 45.000 0.00 0.00 35.90 4.00
183 192 2.510800 TGAGGCATGATCAAGGAATGGA 59.489 45.455 0.00 0.00 0.00 3.41
210 256 4.764823 TCTTCAAATGCCGGTTCACTATTT 59.235 37.500 1.90 0.00 0.00 1.40
213 259 3.410631 TCTTCAAATGCCGGTTCACTA 57.589 42.857 1.90 0.00 0.00 2.74
214 260 2.270352 TCTTCAAATGCCGGTTCACT 57.730 45.000 1.90 0.00 0.00 3.41
254 300 0.040958 CCACTTTGCAAGCACGAGAC 60.041 55.000 0.00 0.00 0.00 3.36
258 304 2.355009 GCCCACTTTGCAAGCACG 60.355 61.111 0.00 0.00 0.00 5.34
283 329 2.544903 GCCAAGCGGTTGTACAAATTGT 60.545 45.455 24.38 3.43 33.28 2.71
292 338 0.827507 AAGATTGGCCAAGCGGTTGT 60.828 50.000 26.95 7.38 33.28 3.32
297 343 1.137404 CCGAAAGATTGGCCAAGCG 59.863 57.895 26.95 20.47 0.00 4.68
327 373 3.057596 GCTTGGTTGTCCATCGAAAATCA 60.058 43.478 0.00 0.00 43.91 2.57
404 462 5.593909 CACAATTCCTCAAAGCCACCATATA 59.406 40.000 0.00 0.00 0.00 0.86
407 465 2.564062 CACAATTCCTCAAAGCCACCAT 59.436 45.455 0.00 0.00 0.00 3.55
438 500 2.641305 GGTCTTACTCAGCGTCCTCTA 58.359 52.381 0.00 0.00 0.00 2.43
444 506 2.093106 CTAGTGGGTCTTACTCAGCGT 58.907 52.381 0.00 0.00 0.00 5.07
448 510 1.272313 ACGGCTAGTGGGTCTTACTCA 60.272 52.381 0.00 0.00 0.00 3.41
455 517 4.752514 GCATACGGCTAGTGGGTC 57.247 61.111 0.00 0.00 40.25 4.46
493 555 1.026182 CCCAGCTGCATAAAGACGCA 61.026 55.000 8.66 0.00 36.52 5.24
512 574 0.183492 TGGGCAATCCTAGGTGATGC 59.817 55.000 20.64 20.64 36.20 3.91
528 590 1.134670 GTGAGATCGTCTCCCTTTGGG 60.135 57.143 11.01 0.00 42.73 4.12
572 634 2.752903 TCTCCAAAAATAAGCTTCCGGC 59.247 45.455 0.00 0.00 42.19 6.13
652 714 2.452105 GACATTTCTCCGCTCGTCTAC 58.548 52.381 0.00 0.00 0.00 2.59
657 719 2.194271 GTAAGGACATTTCTCCGCTCG 58.806 52.381 0.00 0.00 35.20 5.03
680 742 4.506255 GAGGGTCAATGGGGGCCG 62.506 72.222 0.00 0.00 0.00 6.13
702 764 2.951458 GTTTTGGGACTTCCGGCG 59.049 61.111 0.00 0.00 38.76 6.46
703 765 2.622962 CCGTTTTGGGACTTCCGGC 61.623 63.158 0.00 0.00 38.76 6.13
704 766 0.953960 CTCCGTTTTGGGACTTCCGG 60.954 60.000 0.00 0.00 38.76 5.14
705 767 0.034337 TCTCCGTTTTGGGACTTCCG 59.966 55.000 0.00 0.00 38.76 4.30
706 768 1.346722 TCTCTCCGTTTTGGGACTTCC 59.653 52.381 0.00 0.00 38.76 3.46
707 769 2.299297 TCTCTCTCCGTTTTGGGACTTC 59.701 50.000 0.00 0.00 38.76 3.01
708 770 2.300437 CTCTCTCTCCGTTTTGGGACTT 59.700 50.000 0.00 0.00 38.76 3.01
719 781 1.045350 TCAATGGGGCTCTCTCTCCG 61.045 60.000 0.00 0.00 0.00 4.63
724 786 2.431954 CATTGTCAATGGGGCTCTCT 57.568 50.000 16.53 0.00 35.23 3.10
749 811 3.842436 ACTTATTCTACCCTTCCACCGTT 59.158 43.478 0.00 0.00 0.00 4.44
806 1008 2.783135 ACGATGCTTCATCCAAGTTGT 58.217 42.857 1.45 0.00 37.57 3.32
829 1039 4.212143 TCTGTTGACATCAGCTGCTAAT 57.788 40.909 9.47 0.00 33.48 1.73
830 1040 3.683365 TCTGTTGACATCAGCTGCTAA 57.317 42.857 9.47 0.00 33.48 3.09
831 1041 3.329386 GTTCTGTTGACATCAGCTGCTA 58.671 45.455 9.47 0.00 33.48 3.49
832 1042 2.149578 GTTCTGTTGACATCAGCTGCT 58.850 47.619 9.47 0.00 33.48 4.24
875 1085 1.730902 CCATCCTATGCGTCGCTCG 60.731 63.158 19.50 6.40 43.12 5.03
876 1086 1.373497 CCCATCCTATGCGTCGCTC 60.373 63.158 19.50 0.00 0.00 5.03
878 1088 1.373497 CTCCCATCCTATGCGTCGC 60.373 63.158 11.10 11.10 0.00 5.19
879 1089 1.373497 GCTCCCATCCTATGCGTCG 60.373 63.158 0.00 0.00 0.00 5.12
920 1133 4.932799 TCAAGGGTACATGACAAATACGTG 59.067 41.667 0.00 0.00 0.00 4.49
934 1147 3.686916 ACTGCTCTTTCTCAAGGGTAC 57.313 47.619 0.00 0.00 32.27 3.34
938 1151 4.887748 TCTGTTACTGCTCTTTCTCAAGG 58.112 43.478 0.00 0.00 0.00 3.61
946 1159 6.459024 CGAACTAGCTATCTGTTACTGCTCTT 60.459 42.308 0.00 0.00 35.47 2.85
954 1167 6.856135 TTCGATCGAACTAGCTATCTGTTA 57.144 37.500 25.96 0.00 0.00 2.41
1067 1314 1.400990 CGTCGCTAAAGAACGGACGG 61.401 60.000 4.14 0.00 32.89 4.79
1144 1391 4.003788 AAGCACGACCCCACTCGG 62.004 66.667 0.00 0.00 38.02 4.63
1145 1392 2.738521 CAAGCACGACCCCACTCG 60.739 66.667 0.00 0.00 39.68 4.18
1146 1393 3.050275 GCAAGCACGACCCCACTC 61.050 66.667 0.00 0.00 0.00 3.51
1147 1394 3.832237 CTGCAAGCACGACCCCACT 62.832 63.158 0.00 0.00 0.00 4.00
1148 1395 3.357079 CTGCAAGCACGACCCCAC 61.357 66.667 0.00 0.00 0.00 4.61
1251 1503 0.613260 TAGGTGCCTTTGACGATGCT 59.387 50.000 0.00 0.00 0.00 3.79
1349 1602 1.680735 AGCACTTTGACAATGCGGAAA 59.319 42.857 7.86 0.00 44.25 3.13
1517 1770 1.757118 TCGAGCCATAGGTCCTTGAAG 59.243 52.381 0.00 0.00 37.19 3.02
1700 1980 3.732849 GGGAGGCTCACCCCCTTG 61.733 72.222 17.69 0.00 41.17 3.61
1817 2223 3.249189 AGGCCGGCCTTCAAGACA 61.249 61.111 42.84 0.00 45.70 3.41
1943 2360 3.849911 CTGCTGGAAGTAGTCGATGAAA 58.150 45.455 0.00 0.00 42.18 2.69
2048 2477 4.379243 CGCTCCTTGTCCGTGCCT 62.379 66.667 0.00 0.00 0.00 4.75
2066 2495 1.153289 CGAAGGCAGGAGATGTGGG 60.153 63.158 0.00 0.00 0.00 4.61
2173 2616 1.683917 CTCCAGGATAGCTGTAACGCT 59.316 52.381 0.00 0.00 43.83 5.07
2195 2638 2.634285 GGTAGGGAAGGGAGGGGTTTAT 60.634 54.545 0.00 0.00 0.00 1.40
2275 2737 2.385315 CATGTGGAGTGCGTATACGAG 58.615 52.381 28.66 1.12 43.02 4.18
2280 2742 2.759191 CATAGCATGTGGAGTGCGTAT 58.241 47.619 0.00 0.00 46.86 3.06
2283 2745 0.812811 AGCATAGCATGTGGAGTGCG 60.813 55.000 0.00 0.00 46.86 5.34
2300 2762 3.611766 TCAGTTAGAGTTGCCCTTAGC 57.388 47.619 0.00 0.00 44.14 3.09
2301 2763 4.443598 GGGATCAGTTAGAGTTGCCCTTAG 60.444 50.000 0.00 0.00 0.00 2.18
2302 2764 3.454812 GGGATCAGTTAGAGTTGCCCTTA 59.545 47.826 0.00 0.00 0.00 2.69
2303 2765 2.239907 GGGATCAGTTAGAGTTGCCCTT 59.760 50.000 0.00 0.00 0.00 3.95
2304 2766 1.840635 GGGATCAGTTAGAGTTGCCCT 59.159 52.381 0.00 0.00 0.00 5.19
2305 2767 1.134068 GGGGATCAGTTAGAGTTGCCC 60.134 57.143 0.00 0.00 0.00 5.36
2306 2768 1.840635 AGGGGATCAGTTAGAGTTGCC 59.159 52.381 0.00 0.00 0.00 4.52
2307 2769 2.769095 AGAGGGGATCAGTTAGAGTTGC 59.231 50.000 0.00 0.00 0.00 4.17
2308 2770 5.450453 TCTAGAGGGGATCAGTTAGAGTTG 58.550 45.833 0.00 0.00 0.00 3.16
2309 2771 5.735733 TCTAGAGGGGATCAGTTAGAGTT 57.264 43.478 0.00 0.00 0.00 3.01
2310 2772 5.451354 GTTCTAGAGGGGATCAGTTAGAGT 58.549 45.833 0.00 0.00 0.00 3.24
2311 2773 4.830600 GGTTCTAGAGGGGATCAGTTAGAG 59.169 50.000 0.00 0.00 0.00 2.43
2312 2774 4.232122 TGGTTCTAGAGGGGATCAGTTAGA 59.768 45.833 0.00 0.00 0.00 2.10
2313 2775 4.547671 TGGTTCTAGAGGGGATCAGTTAG 58.452 47.826 0.00 0.00 0.00 2.34
2314 2776 4.620086 TGGTTCTAGAGGGGATCAGTTA 57.380 45.455 0.00 0.00 0.00 2.24
2315 2777 3.491766 TGGTTCTAGAGGGGATCAGTT 57.508 47.619 0.00 0.00 0.00 3.16
2316 2778 3.051803 TGATGGTTCTAGAGGGGATCAGT 60.052 47.826 0.00 0.00 0.00 3.41
2317 2779 3.581101 TGATGGTTCTAGAGGGGATCAG 58.419 50.000 0.00 0.00 0.00 2.90
2318 2780 3.706389 TGATGGTTCTAGAGGGGATCA 57.294 47.619 0.00 0.00 0.00 2.92
2319 2781 4.161377 GCTATGATGGTTCTAGAGGGGATC 59.839 50.000 0.00 0.00 0.00 3.36
2320 2782 4.100373 GCTATGATGGTTCTAGAGGGGAT 58.900 47.826 0.00 0.00 0.00 3.85
2321 2783 3.116746 TGCTATGATGGTTCTAGAGGGGA 60.117 47.826 0.00 0.00 0.00 4.81
2322 2784 3.242867 TGCTATGATGGTTCTAGAGGGG 58.757 50.000 0.00 0.00 0.00 4.79
2323 2785 3.306641 GCTGCTATGATGGTTCTAGAGGG 60.307 52.174 0.00 0.00 0.00 4.30
2324 2786 3.306641 GGCTGCTATGATGGTTCTAGAGG 60.307 52.174 0.00 0.00 0.00 3.69
2325 2787 3.323115 TGGCTGCTATGATGGTTCTAGAG 59.677 47.826 0.00 0.00 0.00 2.43
2326 2788 3.070159 GTGGCTGCTATGATGGTTCTAGA 59.930 47.826 0.00 0.00 0.00 2.43
2327 2789 3.397482 GTGGCTGCTATGATGGTTCTAG 58.603 50.000 0.00 0.00 0.00 2.43
2328 2790 2.224042 CGTGGCTGCTATGATGGTTCTA 60.224 50.000 0.00 0.00 0.00 2.10
2329 2791 1.473965 CGTGGCTGCTATGATGGTTCT 60.474 52.381 0.00 0.00 0.00 3.01
2330 2792 0.940126 CGTGGCTGCTATGATGGTTC 59.060 55.000 0.00 0.00 0.00 3.62
2331 2793 0.541392 TCGTGGCTGCTATGATGGTT 59.459 50.000 3.59 0.00 0.00 3.67
2332 2794 0.541392 TTCGTGGCTGCTATGATGGT 59.459 50.000 8.79 0.00 0.00 3.55
2333 2795 1.667236 TTTCGTGGCTGCTATGATGG 58.333 50.000 8.79 0.00 0.00 3.51
2334 2796 2.938451 TCTTTTCGTGGCTGCTATGATG 59.062 45.455 8.79 3.48 0.00 3.07
2335 2797 3.266510 TCTTTTCGTGGCTGCTATGAT 57.733 42.857 8.79 0.00 0.00 2.45
2336 2798 2.760634 TCTTTTCGTGGCTGCTATGA 57.239 45.000 3.59 3.59 0.00 2.15
2337 2799 3.829886 TTTCTTTTCGTGGCTGCTATG 57.170 42.857 0.00 0.00 0.00 2.23
2338 2800 4.846779 TTTTTCTTTTCGTGGCTGCTAT 57.153 36.364 0.00 0.00 0.00 2.97
2358 2820 3.664276 CGTCGCAGTGATTCGTCATTTTT 60.664 43.478 0.00 0.00 0.00 1.94
2359 2821 2.159841 CGTCGCAGTGATTCGTCATTTT 60.160 45.455 0.00 0.00 0.00 1.82
2360 2822 1.390123 CGTCGCAGTGATTCGTCATTT 59.610 47.619 0.00 0.00 0.00 2.32
2361 2823 0.992072 CGTCGCAGTGATTCGTCATT 59.008 50.000 0.00 0.00 0.00 2.57
2362 2824 0.170339 TCGTCGCAGTGATTCGTCAT 59.830 50.000 0.00 0.00 0.00 3.06
2363 2825 0.454452 CTCGTCGCAGTGATTCGTCA 60.454 55.000 0.00 0.00 0.00 4.35
2364 2826 1.734359 GCTCGTCGCAGTGATTCGTC 61.734 60.000 0.00 0.00 38.92 4.20
2365 2827 1.801913 GCTCGTCGCAGTGATTCGT 60.802 57.895 0.00 0.00 38.92 3.85
2366 2828 2.839438 CGCTCGTCGCAGTGATTCG 61.839 63.158 0.00 0.00 39.08 3.34
2367 2829 1.344942 AACGCTCGTCGCAGTGATTC 61.345 55.000 10.76 0.00 43.23 2.52
2368 2830 0.109458 TAACGCTCGTCGCAGTGATT 60.109 50.000 10.76 5.77 43.23 2.57
2369 2831 0.523546 CTAACGCTCGTCGCAGTGAT 60.524 55.000 10.76 3.78 43.23 3.06
2370 2832 1.154282 CTAACGCTCGTCGCAGTGA 60.154 57.895 10.76 0.00 43.23 3.41
2371 2833 1.442184 ACTAACGCTCGTCGCAGTG 60.442 57.895 0.00 0.00 43.23 3.66
2372 2834 1.442184 CACTAACGCTCGTCGCAGT 60.442 57.895 0.00 0.00 43.23 4.40
2373 2835 1.396543 GACACTAACGCTCGTCGCAG 61.397 60.000 0.00 0.00 43.23 5.18
2374 2836 1.441515 GACACTAACGCTCGTCGCA 60.442 57.895 0.00 0.00 43.23 5.10
2375 2837 1.000233 TTGACACTAACGCTCGTCGC 61.000 55.000 0.00 0.00 43.23 5.19
2376 2838 0.975544 CTTGACACTAACGCTCGTCG 59.024 55.000 0.00 0.00 45.38 5.12
2377 2839 2.047679 ACTTGACACTAACGCTCGTC 57.952 50.000 0.00 0.00 0.00 4.20
2378 2840 2.223641 TGAACTTGACACTAACGCTCGT 60.224 45.455 0.00 0.00 0.00 4.18
2379 2841 2.390938 TGAACTTGACACTAACGCTCG 58.609 47.619 0.00 0.00 0.00 5.03
2380 2842 3.639538 TCTGAACTTGACACTAACGCTC 58.360 45.455 0.00 0.00 0.00 5.03
2381 2843 3.553096 CCTCTGAACTTGACACTAACGCT 60.553 47.826 0.00 0.00 0.00 5.07
2382 2844 2.731976 CCTCTGAACTTGACACTAACGC 59.268 50.000 0.00 0.00 0.00 4.84
2383 2845 3.978687 ACCTCTGAACTTGACACTAACG 58.021 45.455 0.00 0.00 0.00 3.18
2384 2846 6.049790 AGAAACCTCTGAACTTGACACTAAC 58.950 40.000 0.00 0.00 0.00 2.34
2385 2847 6.235231 AGAAACCTCTGAACTTGACACTAA 57.765 37.500 0.00 0.00 0.00 2.24
2386 2848 5.871396 AGAAACCTCTGAACTTGACACTA 57.129 39.130 0.00 0.00 0.00 2.74
2387 2849 4.762289 AGAAACCTCTGAACTTGACACT 57.238 40.909 0.00 0.00 0.00 3.55
2388 2850 4.025647 CGAAGAAACCTCTGAACTTGACAC 60.026 45.833 0.00 0.00 30.03 3.67
2389 2851 4.119862 CGAAGAAACCTCTGAACTTGACA 58.880 43.478 0.00 0.00 30.03 3.58
2390 2852 3.495001 CCGAAGAAACCTCTGAACTTGAC 59.505 47.826 0.00 0.00 30.03 3.18
2391 2853 3.134081 ACCGAAGAAACCTCTGAACTTGA 59.866 43.478 0.00 0.00 30.03 3.02
2392 2854 3.467803 ACCGAAGAAACCTCTGAACTTG 58.532 45.455 0.00 0.00 30.03 3.16
2393 2855 3.388350 AGACCGAAGAAACCTCTGAACTT 59.612 43.478 0.00 0.00 30.03 2.66
2394 2856 2.966516 AGACCGAAGAAACCTCTGAACT 59.033 45.455 0.00 0.00 30.03 3.01
2395 2857 3.388345 AGACCGAAGAAACCTCTGAAC 57.612 47.619 0.00 0.00 30.03 3.18
2396 2858 3.386726 TCAAGACCGAAGAAACCTCTGAA 59.613 43.478 0.00 0.00 30.03 3.02
2397 2859 2.963101 TCAAGACCGAAGAAACCTCTGA 59.037 45.455 0.00 0.00 30.03 3.27
2398 2860 3.386768 TCAAGACCGAAGAAACCTCTG 57.613 47.619 0.00 0.00 30.03 3.35
2399 2861 4.202367 ACAATCAAGACCGAAGAAACCTCT 60.202 41.667 0.00 0.00 0.00 3.69
2400 2862 4.065789 ACAATCAAGACCGAAGAAACCTC 58.934 43.478 0.00 0.00 0.00 3.85
2401 2863 4.086706 ACAATCAAGACCGAAGAAACCT 57.913 40.909 0.00 0.00 0.00 3.50
2402 2864 5.934935 TTACAATCAAGACCGAAGAAACC 57.065 39.130 0.00 0.00 0.00 3.27
2403 2865 8.797266 AAAATTACAATCAAGACCGAAGAAAC 57.203 30.769 0.00 0.00 0.00 2.78
2404 2866 9.887406 GTAAAATTACAATCAAGACCGAAGAAA 57.113 29.630 0.00 0.00 33.88 2.52
2405 2867 9.280174 AGTAAAATTACAATCAAGACCGAAGAA 57.720 29.630 6.13 0.00 36.12 2.52
2406 2868 8.842358 AGTAAAATTACAATCAAGACCGAAGA 57.158 30.769 6.13 0.00 36.12 2.87
2407 2869 9.543018 GAAGTAAAATTACAATCAAGACCGAAG 57.457 33.333 6.13 0.00 36.12 3.79
2408 2870 9.280174 AGAAGTAAAATTACAATCAAGACCGAA 57.720 29.630 6.13 0.00 36.12 4.30
2409 2871 8.842358 AGAAGTAAAATTACAATCAAGACCGA 57.158 30.769 6.13 0.00 36.12 4.69
2410 2872 9.329913 CAAGAAGTAAAATTACAATCAAGACCG 57.670 33.333 6.13 0.00 36.12 4.79
2411 2873 9.626045 CCAAGAAGTAAAATTACAATCAAGACC 57.374 33.333 6.13 0.00 36.12 3.85
2412 2874 9.129209 GCCAAGAAGTAAAATTACAATCAAGAC 57.871 33.333 6.13 0.00 36.12 3.01
2413 2875 9.077885 AGCCAAGAAGTAAAATTACAATCAAGA 57.922 29.630 6.13 0.00 36.12 3.02
2416 2878 9.515226 AGTAGCCAAGAAGTAAAATTACAATCA 57.485 29.630 6.13 0.00 36.12 2.57
2417 2879 9.774742 CAGTAGCCAAGAAGTAAAATTACAATC 57.225 33.333 6.13 4.17 36.12 2.67
2418 2880 9.297037 ACAGTAGCCAAGAAGTAAAATTACAAT 57.703 29.630 6.13 0.00 36.12 2.71
2419 2881 8.685838 ACAGTAGCCAAGAAGTAAAATTACAA 57.314 30.769 6.13 0.00 36.12 2.41
2420 2882 8.685838 AACAGTAGCCAAGAAGTAAAATTACA 57.314 30.769 6.13 0.00 36.12 2.41
2421 2883 8.235226 GGAACAGTAGCCAAGAAGTAAAATTAC 58.765 37.037 0.00 0.00 0.00 1.89
2422 2884 8.161425 AGGAACAGTAGCCAAGAAGTAAAATTA 58.839 33.333 0.00 0.00 0.00 1.40
2423 2885 7.004691 AGGAACAGTAGCCAAGAAGTAAAATT 58.995 34.615 0.00 0.00 0.00 1.82
2424 2886 6.543735 AGGAACAGTAGCCAAGAAGTAAAAT 58.456 36.000 0.00 0.00 0.00 1.82
2425 2887 5.937111 AGGAACAGTAGCCAAGAAGTAAAA 58.063 37.500 0.00 0.00 0.00 1.52
2426 2888 5.562298 AGGAACAGTAGCCAAGAAGTAAA 57.438 39.130 0.00 0.00 0.00 2.01
2427 2889 5.562298 AAGGAACAGTAGCCAAGAAGTAA 57.438 39.130 0.00 0.00 0.00 2.24
2428 2890 5.163237 ACAAAGGAACAGTAGCCAAGAAGTA 60.163 40.000 0.00 0.00 0.00 2.24
2429 2891 4.137543 CAAAGGAACAGTAGCCAAGAAGT 58.862 43.478 0.00 0.00 0.00 3.01
2430 2892 4.023707 CACAAAGGAACAGTAGCCAAGAAG 60.024 45.833 0.00 0.00 0.00 2.85
2431 2893 3.882888 CACAAAGGAACAGTAGCCAAGAA 59.117 43.478 0.00 0.00 0.00 2.52
2432 2894 3.476552 CACAAAGGAACAGTAGCCAAGA 58.523 45.455 0.00 0.00 0.00 3.02
2433 2895 2.030805 GCACAAAGGAACAGTAGCCAAG 60.031 50.000 0.00 0.00 0.00 3.61
2434 2896 1.953686 GCACAAAGGAACAGTAGCCAA 59.046 47.619 0.00 0.00 0.00 4.52
2435 2897 1.133945 TGCACAAAGGAACAGTAGCCA 60.134 47.619 0.00 0.00 0.00 4.75
2436 2898 1.604604 TGCACAAAGGAACAGTAGCC 58.395 50.000 0.00 0.00 0.00 3.93
2437 2899 3.632189 CTTTGCACAAAGGAACAGTAGC 58.368 45.455 14.08 0.00 42.96 3.58
2447 2909 0.874390 TCGCTAGCCTTTGCACAAAG 59.126 50.000 14.79 14.79 45.47 2.77
2448 2910 1.533625 ATCGCTAGCCTTTGCACAAA 58.466 45.000 9.66 0.00 41.13 2.83
2449 2911 1.533625 AATCGCTAGCCTTTGCACAA 58.466 45.000 9.66 0.00 41.13 3.33
2450 2912 1.199789 CAAATCGCTAGCCTTTGCACA 59.800 47.619 18.93 0.00 41.13 4.57
2451 2913 1.900237 CAAATCGCTAGCCTTTGCAC 58.100 50.000 18.93 0.00 41.13 4.57
2453 2915 2.949484 GCAAATCGCTAGCCTTTGC 58.051 52.632 30.70 30.70 45.32 3.68
2463 2925 3.273919 ACTGAAAAGACAGCAAATCGC 57.726 42.857 0.00 0.00 41.06 4.58
2464 2926 6.142320 GGTAAAACTGAAAAGACAGCAAATCG 59.858 38.462 0.00 0.00 41.06 3.34
2465 2927 6.978080 TGGTAAAACTGAAAAGACAGCAAATC 59.022 34.615 0.00 0.00 41.06 2.17
2466 2928 6.872920 TGGTAAAACTGAAAAGACAGCAAAT 58.127 32.000 0.00 0.00 41.06 2.32
2467 2929 6.274157 TGGTAAAACTGAAAAGACAGCAAA 57.726 33.333 0.00 0.00 41.06 3.68
2468 2930 5.163561 CCTGGTAAAACTGAAAAGACAGCAA 60.164 40.000 0.00 0.00 41.06 3.91
2469 2931 4.338118 CCTGGTAAAACTGAAAAGACAGCA 59.662 41.667 0.00 0.00 41.06 4.41
2470 2932 4.338400 ACCTGGTAAAACTGAAAAGACAGC 59.662 41.667 0.00 0.00 41.06 4.40
2471 2933 5.277345 CGACCTGGTAAAACTGAAAAGACAG 60.277 44.000 0.00 0.00 42.78 3.51
2472 2934 4.573201 CGACCTGGTAAAACTGAAAAGACA 59.427 41.667 0.00 0.00 0.00 3.41
2473 2935 4.024302 CCGACCTGGTAAAACTGAAAAGAC 60.024 45.833 0.00 0.00 0.00 3.01
2474 2936 4.131596 CCGACCTGGTAAAACTGAAAAGA 58.868 43.478 0.00 0.00 0.00 2.52
2475 2937 4.483476 CCGACCTGGTAAAACTGAAAAG 57.517 45.455 0.00 0.00 0.00 2.27
2735 3197 2.902705 CGGGATATCTTCAACCGGAA 57.097 50.000 9.46 0.00 40.79 4.30
2776 3238 1.659098 GAGCGTTTGGTTACTGGATCG 59.341 52.381 0.00 0.00 0.00 3.69
2808 3270 0.171455 GTGGTCGCTACTCACTCTGG 59.829 60.000 3.71 0.00 0.00 3.86
2924 3389 5.603596 CGTAGGGGTATGTGCTTTATTGTA 58.396 41.667 0.00 0.00 0.00 2.41
2941 3406 1.864435 GCTAGACACATTCGCGTAGGG 60.864 57.143 5.77 0.25 44.04 3.53
2978 3443 5.391097 CGTTATTTGGAACGTGGCTTATTGA 60.391 40.000 0.00 0.00 45.55 2.57
3018 3483 6.873605 GCAAATTGCCTTTAACATTACTCCTT 59.126 34.615 6.72 0.00 37.42 3.36
3111 3577 7.760340 CAGGATCTACTAGGTGTAGTTTTTGTC 59.240 40.741 0.00 0.00 46.50 3.18


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

AutoCloner maintained by Alex Coulton.