Multiple sequence alignment - TraesCS2D01G393500

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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 TraesCS2D01G393500 chr2D 100.000 4069 0 0 1 4069 503435440 503439508 0.000000e+00 7515.0
1 TraesCS2D01G393500 chr2B 92.432 3726 115 59 408 4069 591911961 591915583 0.000000e+00 5164.0
2 TraesCS2D01G393500 chr2B 88.889 63 3 1 359 417 591895089 591895151 1.570000e-09 75.0
3 TraesCS2D01G393500 chr2A 92.780 3504 126 53 420 3866 649483467 649486900 0.000000e+00 4951.0
4 TraesCS2D01G393500 chr2A 91.004 478 23 4 418 891 649477880 649478341 9.600000e-176 627.0
5 TraesCS2D01G393500 chr2A 84.135 208 29 4 82 287 649477110 649477315 8.920000e-47 198.0
6 TraesCS2D01G393500 chr2A 86.316 95 10 3 3923 4015 37307857 37307764 2.590000e-17 100.0
7 TraesCS2D01G393500 chr2A 95.161 62 2 1 370 430 649483048 649483109 3.350000e-16 97.1
8 TraesCS2D01G393500 chr2A 88.462 78 3 2 359 430 649477451 649477528 5.600000e-14 89.8
9 TraesCS2D01G393500 chr6B 85.584 1207 151 19 1325 2525 479396242 479397431 0.000000e+00 1243.0
10 TraesCS2D01G393500 chr6A 85.188 1195 153 15 1325 2513 480806548 480805372 0.000000e+00 1205.0
11 TraesCS2D01G393500 chr6D 85.105 1195 154 15 1325 2513 341079429 341078253 0.000000e+00 1199.0
12 TraesCS2D01G393500 chr1D 78.956 1169 207 29 1336 2495 269515939 269514801 0.000000e+00 760.0
13 TraesCS2D01G393500 chr1D 86.170 94 12 1 3923 4015 451041936 451041843 2.590000e-17 100.0
14 TraesCS2D01G393500 chr1D 85.263 95 13 1 3922 4015 84709103 84709009 3.350000e-16 97.1
15 TraesCS2D01G393500 chr1A 78.956 1169 207 29 1336 2495 333498735 333499873 0.000000e+00 760.0
16 TraesCS2D01G393500 chr4D 79.364 1037 177 31 1326 2345 497697186 497698202 0.000000e+00 695.0
17 TraesCS2D01G393500 chr4B 79.143 1050 176 36 1316 2345 639011490 639010464 0.000000e+00 686.0
18 TraesCS2D01G393500 chr3A 76.242 463 74 24 1887 2340 598410425 598410860 3.190000e-51 213.0
19 TraesCS2D01G393500 chr3A 88.889 90 9 1 3922 4010 461956711 461956800 4.300000e-20 110.0
20 TraesCS2D01G393500 chr3A 88.764 89 9 1 3923 4010 561060022 561059934 1.550000e-19 108.0
21 TraesCS2D01G393500 chr3A 87.368 95 9 3 3923 4015 496058810 496058903 5.560000e-19 106.0
22 TraesCS2D01G393500 chr5D 89.412 85 9 0 3926 4010 308459668 308459584 1.550000e-19 108.0
23 TraesCS2D01G393500 chr4A 86.316 95 10 3 3923 4015 693284097 693284190 2.590000e-17 100.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G393500 chr2D 503435440 503439508 4068 False 7515.000000 7515 100.0000 1 4069 1 chr2D.!!$F1 4068
1 TraesCS2D01G393500 chr2B 591911961 591915583 3622 False 5164.000000 5164 92.4320 408 4069 1 chr2B.!!$F2 3661
2 TraesCS2D01G393500 chr2A 649483048 649486900 3852 False 2524.050000 4951 93.9705 370 3866 2 chr2A.!!$F2 3496
3 TraesCS2D01G393500 chr2A 649477110 649478341 1231 False 304.933333 627 87.8670 82 891 3 chr2A.!!$F1 809
4 TraesCS2D01G393500 chr6B 479396242 479397431 1189 False 1243.000000 1243 85.5840 1325 2525 1 chr6B.!!$F1 1200
5 TraesCS2D01G393500 chr6A 480805372 480806548 1176 True 1205.000000 1205 85.1880 1325 2513 1 chr6A.!!$R1 1188
6 TraesCS2D01G393500 chr6D 341078253 341079429 1176 True 1199.000000 1199 85.1050 1325 2513 1 chr6D.!!$R1 1188
7 TraesCS2D01G393500 chr1D 269514801 269515939 1138 True 760.000000 760 78.9560 1336 2495 1 chr1D.!!$R2 1159
8 TraesCS2D01G393500 chr1A 333498735 333499873 1138 False 760.000000 760 78.9560 1336 2495 1 chr1A.!!$F1 1159
9 TraesCS2D01G393500 chr4D 497697186 497698202 1016 False 695.000000 695 79.3640 1326 2345 1 chr4D.!!$F1 1019
10 TraesCS2D01G393500 chr4B 639010464 639011490 1026 True 686.000000 686 79.1430 1316 2345 1 chr4B.!!$R1 1029

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
20 21 0.102481 AGACACTTCAGCGAACACGT 59.898 50.0 0.0 0.0 0.00 4.49 F
199 200 0.106708 TGATGGTTATGCGGAGGAGC 59.893 55.0 0.0 0.0 37.71 4.70 F
374 445 0.372334 CGATAGCGTTTTTGGGTCCG 59.628 55.0 0.0 0.0 0.00 4.79 F
1701 2174 0.460722 TCAACAAGTTCGACCACCGA 59.539 50.0 0.0 0.0 46.94 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 2174 2.125178 GCCGATGTAGTAGGGCTGT 58.875 57.895 0.00 0.00 42.29 4.40 R
2548 3021 4.216257 GGCCATTTGTACAGTATATGCTGG 59.784 45.833 22.64 6.45 40.59 4.85 R
2678 3157 2.093869 ACGCAATTACCAGTGGATACGT 60.094 45.455 18.40 13.13 42.51 3.57 R
3335 3851 0.179936 CTCCTCCTGTTGCCATCTCC 59.820 60.000 0.00 0.00 0.00 3.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.504384 CAGACACTTCAGCGAACACG 59.496 55.000 0.00 0.00 0.00 4.49
20 21 0.102481 AGACACTTCAGCGAACACGT 59.898 50.000 0.00 0.00 0.00 4.49
21 22 1.335810 AGACACTTCAGCGAACACGTA 59.664 47.619 0.00 0.00 0.00 3.57
22 23 2.121786 GACACTTCAGCGAACACGTAA 58.878 47.619 0.00 0.00 0.00 3.18
23 24 2.536803 GACACTTCAGCGAACACGTAAA 59.463 45.455 0.00 0.00 0.00 2.01
24 25 2.538449 ACACTTCAGCGAACACGTAAAG 59.462 45.455 0.00 0.00 0.00 1.85
25 26 1.525619 ACTTCAGCGAACACGTAAAGC 59.474 47.619 0.00 0.00 0.00 3.51
35 36 3.945436 CGTAAAGCGTGAGGTGCA 58.055 55.556 0.00 0.00 43.76 4.57
36 37 2.230892 CGTAAAGCGTGAGGTGCAA 58.769 52.632 0.00 0.00 43.76 4.08
37 38 0.584396 CGTAAAGCGTGAGGTGCAAA 59.416 50.000 0.00 0.00 43.76 3.68
38 39 1.196808 CGTAAAGCGTGAGGTGCAAAT 59.803 47.619 0.00 0.00 43.76 2.32
39 40 2.413796 CGTAAAGCGTGAGGTGCAAATA 59.586 45.455 0.00 0.00 43.76 1.40
40 41 3.483574 CGTAAAGCGTGAGGTGCAAATAG 60.484 47.826 0.00 0.00 43.76 1.73
41 42 1.453155 AAGCGTGAGGTGCAAATAGG 58.547 50.000 0.00 0.00 43.76 2.57
42 43 0.613260 AGCGTGAGGTGCAAATAGGA 59.387 50.000 0.00 0.00 42.35 2.94
43 44 1.009829 GCGTGAGGTGCAAATAGGAG 58.990 55.000 0.00 0.00 0.00 3.69
44 45 1.676014 GCGTGAGGTGCAAATAGGAGT 60.676 52.381 0.00 0.00 0.00 3.85
45 46 2.002586 CGTGAGGTGCAAATAGGAGTG 58.997 52.381 0.00 0.00 0.00 3.51
46 47 2.612972 CGTGAGGTGCAAATAGGAGTGT 60.613 50.000 0.00 0.00 0.00 3.55
47 48 3.412386 GTGAGGTGCAAATAGGAGTGTT 58.588 45.455 0.00 0.00 0.00 3.32
48 49 4.575885 GTGAGGTGCAAATAGGAGTGTTA 58.424 43.478 0.00 0.00 0.00 2.41
49 50 5.001232 GTGAGGTGCAAATAGGAGTGTTAA 58.999 41.667 0.00 0.00 0.00 2.01
50 51 5.001232 TGAGGTGCAAATAGGAGTGTTAAC 58.999 41.667 0.00 0.00 0.00 2.01
51 52 4.332828 AGGTGCAAATAGGAGTGTTAACC 58.667 43.478 2.48 0.00 0.00 2.85
52 53 3.126343 GGTGCAAATAGGAGTGTTAACCG 59.874 47.826 2.48 0.00 0.00 4.44
53 54 3.126343 GTGCAAATAGGAGTGTTAACCGG 59.874 47.826 0.00 0.00 0.00 5.28
54 55 3.008157 TGCAAATAGGAGTGTTAACCGGA 59.992 43.478 9.46 0.00 0.00 5.14
55 56 3.621715 GCAAATAGGAGTGTTAACCGGAG 59.378 47.826 9.46 0.00 0.00 4.63
56 57 3.538634 AATAGGAGTGTTAACCGGAGC 57.461 47.619 9.46 0.00 0.00 4.70
57 58 0.813184 TAGGAGTGTTAACCGGAGCG 59.187 55.000 9.46 0.00 0.00 5.03
77 78 3.681835 GTCTGGTGGCGACGACCT 61.682 66.667 10.62 0.00 34.05 3.85
78 79 2.915659 TCTGGTGGCGACGACCTT 60.916 61.111 10.62 0.00 34.05 3.50
79 80 2.738521 CTGGTGGCGACGACCTTG 60.739 66.667 10.62 1.62 34.05 3.61
80 81 3.515316 CTGGTGGCGACGACCTTGT 62.515 63.158 10.62 0.00 34.05 3.16
84 85 4.047059 GGCGACGACCTTGTCCGA 62.047 66.667 0.00 0.00 35.40 4.55
149 150 1.229177 GCCTTGGGTTGGGAATGGT 60.229 57.895 0.00 0.00 0.00 3.55
171 172 0.179137 CGGAGCACAGATAGCGACAA 60.179 55.000 0.00 0.00 37.01 3.18
176 177 3.403038 AGCACAGATAGCGACAAAAGTT 58.597 40.909 0.00 0.00 37.01 2.66
188 189 3.495377 CGACAAAAGTTCGGTGATGGTTA 59.505 43.478 0.00 0.00 32.66 2.85
196 197 0.880278 CGGTGATGGTTATGCGGAGG 60.880 60.000 0.00 0.00 0.00 4.30
199 200 0.106708 TGATGGTTATGCGGAGGAGC 59.893 55.000 0.00 0.00 37.71 4.70
207 208 2.125512 GCGGAGGAGCACGAACAT 60.126 61.111 0.00 0.00 37.05 2.71
214 215 3.181475 GGAGGAGCACGAACATAGATGAA 60.181 47.826 0.00 0.00 0.00 2.57
221 222 5.809562 AGCACGAACATAGATGAAAAGAGAG 59.190 40.000 0.00 0.00 0.00 3.20
222 223 5.578727 GCACGAACATAGATGAAAAGAGAGT 59.421 40.000 0.00 0.00 0.00 3.24
227 228 7.489435 CGAACATAGATGAAAAGAGAGTTGCTA 59.511 37.037 0.00 0.00 0.00 3.49
242 243 2.764128 CTAGAGCAAGGCGGGGGA 60.764 66.667 0.00 0.00 0.00 4.81
243 244 2.764128 TAGAGCAAGGCGGGGGAG 60.764 66.667 0.00 0.00 0.00 4.30
253 254 2.603473 CGGGGGAGGCGGATATGA 60.603 66.667 0.00 0.00 0.00 2.15
255 256 2.665603 GGGGAGGCGGATATGAGC 59.334 66.667 0.00 0.00 0.00 4.26
259 260 0.389166 GGAGGCGGATATGAGCGAAG 60.389 60.000 0.00 0.00 0.00 3.79
262 263 0.946221 GGCGGATATGAGCGAAGTGG 60.946 60.000 0.00 0.00 0.00 4.00
274 275 1.448013 GAAGTGGCGCAGACCCTAC 60.448 63.158 10.83 0.00 25.51 3.18
293 294 4.447365 GGTCAGTCCGACGTAACG 57.553 61.111 0.00 0.00 46.42 3.18
304 305 2.256158 CGTAACGGACACGCCTGA 59.744 61.111 0.00 0.00 46.04 3.86
310 311 2.512515 GGACACGCCTGAGCATCC 60.513 66.667 0.00 0.00 39.83 3.51
311 312 2.581354 GACACGCCTGAGCATCCT 59.419 61.111 0.00 0.00 39.83 3.24
315 316 2.035961 GACACGCCTGAGCATCCTTATA 59.964 50.000 0.00 0.00 39.83 0.98
317 318 3.257393 CACGCCTGAGCATCCTTATATC 58.743 50.000 0.00 0.00 39.83 1.63
319 320 2.234661 CGCCTGAGCATCCTTATATCCA 59.765 50.000 0.00 0.00 39.83 3.41
325 326 5.411493 TGAGCATCCTTATATCCACCCTAA 58.589 41.667 0.00 0.00 0.00 2.69
326 327 5.485353 TGAGCATCCTTATATCCACCCTAAG 59.515 44.000 0.00 0.00 0.00 2.18
329 330 6.440965 AGCATCCTTATATCCACCCTAAGTAC 59.559 42.308 0.00 0.00 0.00 2.73
330 331 6.627508 GCATCCTTATATCCACCCTAAGTACG 60.628 46.154 0.00 0.00 0.00 3.67
333 334 1.708341 TATCCACCCTAAGTACGGGC 58.292 55.000 4.34 0.00 46.04 6.13
334 335 1.052694 ATCCACCCTAAGTACGGGCC 61.053 60.000 4.34 0.00 46.04 5.80
336 337 2.037847 ACCCTAAGTACGGGCCGT 59.962 61.111 35.91 35.91 46.04 5.68
337 338 2.353610 ACCCTAAGTACGGGCCGTG 61.354 63.158 39.80 23.80 46.04 4.94
343 344 2.057137 AAGTACGGGCCGTGTATAGA 57.943 50.000 39.80 17.87 41.39 1.98
344 345 2.057137 AGTACGGGCCGTGTATAGAA 57.943 50.000 39.80 17.05 41.39 2.10
349 350 1.263217 CGGGCCGTGTATAGAAAATGC 59.737 52.381 19.97 0.00 0.00 3.56
350 351 1.263217 GGGCCGTGTATAGAAAATGCG 59.737 52.381 0.00 0.00 0.00 4.73
351 352 2.206750 GGCCGTGTATAGAAAATGCGA 58.793 47.619 0.00 0.00 0.00 5.10
352 353 2.610374 GGCCGTGTATAGAAAATGCGAA 59.390 45.455 0.00 0.00 0.00 4.70
353 354 3.303132 GGCCGTGTATAGAAAATGCGAAG 60.303 47.826 0.00 0.00 0.00 3.79
374 445 0.372334 CGATAGCGTTTTTGGGTCCG 59.628 55.000 0.00 0.00 0.00 4.79
428 868 7.201410 CGTTTGACGCTCTAACACAAATATAGT 60.201 37.037 0.00 0.00 32.90 2.12
472 912 1.004080 CTGCATATCTCCAGCCCGG 60.004 63.158 0.00 0.00 0.00 5.73
547 988 5.026038 TCCCACGTTTCTGTAAAGAGAAA 57.974 39.130 0.00 0.00 39.20 2.52
604 1045 2.976589 GCAGCACCTTGCCATAAAATT 58.023 42.857 0.00 0.00 46.52 1.82
699 1145 2.691526 ACTTGATTAGCGACGGGACATA 59.308 45.455 0.00 0.00 0.00 2.29
836 1299 2.928757 CAAGCGAAGAGAGTGAGATTGG 59.071 50.000 0.00 0.00 0.00 3.16
837 1300 1.480137 AGCGAAGAGAGTGAGATTGGG 59.520 52.381 0.00 0.00 0.00 4.12
838 1301 1.478510 GCGAAGAGAGTGAGATTGGGA 59.521 52.381 0.00 0.00 0.00 4.37
839 1302 2.737039 GCGAAGAGAGTGAGATTGGGAC 60.737 54.545 0.00 0.00 0.00 4.46
840 1303 2.478709 CGAAGAGAGTGAGATTGGGACG 60.479 54.545 0.00 0.00 0.00 4.79
841 1304 2.516227 AGAGAGTGAGATTGGGACGA 57.484 50.000 0.00 0.00 0.00 4.20
842 1305 2.374184 AGAGAGTGAGATTGGGACGAG 58.626 52.381 0.00 0.00 0.00 4.18
843 1306 1.407258 GAGAGTGAGATTGGGACGAGG 59.593 57.143 0.00 0.00 0.00 4.63
844 1307 1.006043 AGAGTGAGATTGGGACGAGGA 59.994 52.381 0.00 0.00 0.00 3.71
845 1308 1.825474 GAGTGAGATTGGGACGAGGAA 59.175 52.381 0.00 0.00 0.00 3.36
846 1309 1.827969 AGTGAGATTGGGACGAGGAAG 59.172 52.381 0.00 0.00 0.00 3.46
961 1424 2.426522 CCAAATCTCACTCGCCAGAAA 58.573 47.619 0.00 0.00 0.00 2.52
968 1431 0.951040 CACTCGCCAGAAACCCACTC 60.951 60.000 0.00 0.00 0.00 3.51
1074 1547 3.521796 GCGCCAGGAATGAAGGGC 61.522 66.667 0.00 0.00 42.98 5.19
1080 1553 4.796495 GGAATGAAGGGCGGCGGT 62.796 66.667 9.78 0.00 0.00 5.68
1701 2174 0.460722 TCAACAAGTTCGACCACCGA 59.539 50.000 0.00 0.00 46.94 4.69
2548 3021 6.719829 TCCTTCCCTTAACTCAATTCCTTTTC 59.280 38.462 0.00 0.00 0.00 2.29
2560 3033 7.284034 ACTCAATTCCTTTTCCAGCATATACTG 59.716 37.037 0.00 0.00 37.42 2.74
2575 3054 5.068460 GCATATACTGTACAAATGGCCCAAA 59.932 40.000 0.00 0.00 0.00 3.28
2669 3148 9.218440 AGTTAAAAATTCCAGCAATGGTATTTG 57.782 29.630 11.20 0.00 38.41 2.32
2670 3149 8.998377 GTTAAAAATTCCAGCAATGGTATTTGT 58.002 29.630 11.20 9.08 38.41 2.83
2678 3157 5.652014 CCAGCAATGGTATTTGTAGGAGAAA 59.348 40.000 0.00 0.00 0.00 2.52
2736 3215 5.163683 TGACTACCTGAGCGAATGTTAGTAC 60.164 44.000 0.00 0.00 0.00 2.73
2737 3216 4.948621 ACTACCTGAGCGAATGTTAGTACT 59.051 41.667 0.00 0.00 0.00 2.73
2738 3217 6.118170 ACTACCTGAGCGAATGTTAGTACTA 58.882 40.000 0.00 0.00 0.00 1.82
2741 3220 6.118170 ACCTGAGCGAATGTTAGTACTACTA 58.882 40.000 0.91 0.00 0.00 1.82
2742 3221 6.260493 ACCTGAGCGAATGTTAGTACTACTAG 59.740 42.308 0.91 0.00 31.47 2.57
2743 3222 6.260493 CCTGAGCGAATGTTAGTACTACTAGT 59.740 42.308 0.91 0.00 31.47 2.57
2744 3223 7.440556 CCTGAGCGAATGTTAGTACTACTAGTA 59.559 40.741 0.91 1.89 31.47 1.82
2745 3224 8.899427 TGAGCGAATGTTAGTACTACTAGTAT 57.101 34.615 0.91 0.00 32.65 2.12
2746 3225 9.987272 TGAGCGAATGTTAGTACTACTAGTATA 57.013 33.333 0.91 0.00 32.65 1.47
2805 3288 7.767261 ACATTACTTATATTGCTTTTGGCGAA 58.233 30.769 0.00 0.00 45.43 4.70
2837 3323 3.391955 TGATGTATGGCTCACATGGATGA 59.608 43.478 8.88 0.00 40.82 2.92
3012 3500 9.309516 GAACACTGTAGGACGATTCAATATTTA 57.690 33.333 0.00 0.00 0.00 1.40
3102 3593 1.064783 GCGTACCTACTACCGTGCC 59.935 63.158 0.00 0.00 0.00 5.01
3160 3662 0.606673 GAAGCTTTGGCCGGACTTCT 60.607 55.000 9.82 0.00 39.73 2.85
3163 3665 1.912371 GCTTTGGCCGGACTTCTTCG 61.912 60.000 9.82 0.00 0.00 3.79
3164 3671 1.912371 CTTTGGCCGGACTTCTTCGC 61.912 60.000 9.82 0.00 0.00 4.70
3167 3674 3.119096 GCCGGACTTCTTCGCCAC 61.119 66.667 5.05 0.00 0.00 5.01
3171 3678 1.588082 GGACTTCTTCGCCACCGTA 59.412 57.895 0.00 0.00 35.54 4.02
3172 3679 0.175073 GGACTTCTTCGCCACCGTAT 59.825 55.000 0.00 0.00 35.54 3.06
3196 3704 1.898574 CTGCCCCCACAGTGTTGAC 60.899 63.158 0.00 0.00 32.78 3.18
3241 3757 1.202770 AGGTTCGCTGTGCTAAAAGGT 60.203 47.619 0.00 0.00 0.00 3.50
3245 3761 0.238289 CGCTGTGCTAAAAGGTGTGG 59.762 55.000 0.00 0.00 0.00 4.17
3246 3762 1.318576 GCTGTGCTAAAAGGTGTGGT 58.681 50.000 0.00 0.00 0.00 4.16
3248 3764 1.001378 CTGTGCTAAAAGGTGTGGTGC 60.001 52.381 0.00 0.00 0.00 5.01
3249 3765 1.318576 GTGCTAAAAGGTGTGGTGCT 58.681 50.000 0.00 0.00 0.00 4.40
3250 3766 1.001378 GTGCTAAAAGGTGTGGTGCTG 60.001 52.381 0.00 0.00 0.00 4.41
3252 3768 1.001378 GCTAAAAGGTGTGGTGCTGTG 60.001 52.381 0.00 0.00 0.00 3.66
3253 3769 2.297701 CTAAAAGGTGTGGTGCTGTGT 58.702 47.619 0.00 0.00 0.00 3.72
3254 3770 0.817013 AAAAGGTGTGGTGCTGTGTG 59.183 50.000 0.00 0.00 0.00 3.82
3255 3771 0.323360 AAAGGTGTGGTGCTGTGTGT 60.323 50.000 0.00 0.00 0.00 3.72
3256 3772 0.323360 AAGGTGTGGTGCTGTGTGTT 60.323 50.000 0.00 0.00 0.00 3.32
3257 3773 1.031571 AGGTGTGGTGCTGTGTGTTG 61.032 55.000 0.00 0.00 0.00 3.33
3258 3774 1.312371 GGTGTGGTGCTGTGTGTTGT 61.312 55.000 0.00 0.00 0.00 3.32
3259 3775 0.179166 GTGTGGTGCTGTGTGTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
3260 3776 1.311651 TGTGGTGCTGTGTGTTGTGG 61.312 55.000 0.00 0.00 0.00 4.17
3261 3777 1.752310 TGGTGCTGTGTGTTGTGGG 60.752 57.895 0.00 0.00 0.00 4.61
3262 3778 2.489275 GGTGCTGTGTGTTGTGGGG 61.489 63.158 0.00 0.00 0.00 4.96
3293 3809 0.540597 ACTTGGGGAAAGCTTGGCTC 60.541 55.000 0.00 0.00 38.25 4.70
3323 3839 1.304282 GGCAAGATCCAGGCCTTCA 59.696 57.895 0.00 0.00 44.32 3.02
3334 3850 3.365265 GCCTTCAGCCAACACGGG 61.365 66.667 0.00 0.00 34.35 5.28
3335 3851 2.672996 CCTTCAGCCAACACGGGG 60.673 66.667 0.00 0.00 34.06 5.73
3337 3853 3.172106 TTCAGCCAACACGGGGGA 61.172 61.111 0.00 0.00 34.06 4.81
3339 3855 3.636231 CAGCCAACACGGGGGAGA 61.636 66.667 0.00 0.00 34.06 3.71
3340 3856 2.610859 AGCCAACACGGGGGAGAT 60.611 61.111 0.00 0.00 34.06 2.75
3342 3858 2.272146 CCAACACGGGGGAGATGG 59.728 66.667 0.00 0.00 0.00 3.51
3370 3900 1.227556 GAGCACGGTTCTGGTGTGT 60.228 57.895 0.00 0.00 37.70 3.72
3397 3927 2.258755 GTGTTTGTGTGTGAAACTGGC 58.741 47.619 0.00 0.00 38.04 4.85
3398 3928 1.203523 TGTTTGTGTGTGAAACTGGCC 59.796 47.619 0.00 0.00 38.04 5.36
3399 3929 1.203523 GTTTGTGTGTGAAACTGGCCA 59.796 47.619 4.71 4.71 38.04 5.36
3401 3931 1.550327 TGTGTGTGAAACTGGCCAAA 58.450 45.000 7.01 0.00 38.04 3.28
3481 4014 1.735376 GAGGCAATAGCTCGTCCGGA 61.735 60.000 0.00 0.00 41.70 5.14
3538 4076 2.537143 ACAGGGACGACCAAATCTACT 58.463 47.619 6.20 0.00 43.89 2.57
3564 4102 2.069273 CATCCGCCCGAGACATAATTC 58.931 52.381 0.00 0.00 0.00 2.17
3768 4306 2.826725 CCCGATTCCATCCTAGTCCTAC 59.173 54.545 0.00 0.00 0.00 3.18
3868 4407 9.258826 CTACAGTGTCAATCGTATACTAGTAGT 57.741 37.037 8.85 8.14 0.00 2.73
3871 4410 9.258826 CAGTGTCAATCGTATACTAGTAGTAGT 57.741 37.037 15.08 14.57 42.49 2.73
3874 4413 9.416794 TGTCAATCGTATACTAGTAGTAGTAGC 57.583 37.037 19.63 14.39 43.55 3.58
3875 4414 8.582930 GTCAATCGTATACTAGTAGTAGTAGCG 58.417 40.741 24.10 24.10 43.55 4.26
3876 4415 8.515414 TCAATCGTATACTAGTAGTAGTAGCGA 58.485 37.037 29.13 29.13 45.99 4.93
3924 4463 2.889045 GTTTAGGGTCTGTTTGGTTCCC 59.111 50.000 0.00 0.00 38.50 3.97
3927 4466 0.185175 GGGTCTGTTTGGTTCCCACT 59.815 55.000 0.00 0.00 38.15 4.00
3928 4467 1.605753 GGTCTGTTTGGTTCCCACTC 58.394 55.000 0.00 0.00 30.78 3.51
3929 4468 1.133915 GGTCTGTTTGGTTCCCACTCA 60.134 52.381 0.00 0.00 30.78 3.41
3930 4469 2.650322 GTCTGTTTGGTTCCCACTCAA 58.350 47.619 0.00 0.00 30.78 3.02
3931 4470 2.357952 GTCTGTTTGGTTCCCACTCAAC 59.642 50.000 0.00 0.00 30.78 3.18
3932 4471 1.681264 CTGTTTGGTTCCCACTCAACC 59.319 52.381 0.00 0.00 43.35 3.77
3933 4472 1.286553 TGTTTGGTTCCCACTCAACCT 59.713 47.619 3.39 0.00 43.43 3.50
3934 4473 2.510382 TGTTTGGTTCCCACTCAACCTA 59.490 45.455 3.39 0.00 43.43 3.08
3935 4474 2.882761 GTTTGGTTCCCACTCAACCTAC 59.117 50.000 3.39 0.00 43.43 3.18
3936 4475 1.061546 TGGTTCCCACTCAACCTACC 58.938 55.000 3.39 0.00 43.43 3.18
3937 4476 1.061546 GGTTCCCACTCAACCTACCA 58.938 55.000 0.00 0.00 40.33 3.25
3953 4492 1.732683 CCAAAACATTGGTCGCGCC 60.733 57.895 0.00 6.97 37.32 6.53
3962 4501 1.741401 TGGTCGCGCCAAATCTCTG 60.741 57.895 17.94 0.00 45.94 3.35
4029 4570 5.465390 GTCCTTTGTTAAATCTTTGGCCAAC 59.535 40.000 20.35 5.16 0.00 3.77
4032 4573 2.635427 TGTTAAATCTTTGGCCAACCCC 59.365 45.455 20.35 0.99 33.59 4.95
4033 4574 2.903784 GTTAAATCTTTGGCCAACCCCT 59.096 45.455 20.35 4.55 33.59 4.79
4034 4575 4.090819 GTTAAATCTTTGGCCAACCCCTA 58.909 43.478 20.35 1.32 33.59 3.53
4042 4583 3.327404 CCAACCCCTAGGCGGTGT 61.327 66.667 19.26 9.39 36.11 4.16
4047 4588 1.052694 ACCCCTAGGCGGTGTAATCC 61.053 60.000 18.20 0.00 36.11 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.504384 CGTGTTCGCTGAAGTGTCTG 59.496 55.000 0.00 0.00 0.00 3.51
1 2 0.102481 ACGTGTTCGCTGAAGTGTCT 59.898 50.000 0.00 0.00 41.18 3.41
2 3 1.762419 TACGTGTTCGCTGAAGTGTC 58.238 50.000 0.00 0.00 41.18 3.67
3 4 2.212869 TTACGTGTTCGCTGAAGTGT 57.787 45.000 0.00 0.00 41.18 3.55
4 5 2.659291 GCTTTACGTGTTCGCTGAAGTG 60.659 50.000 0.00 0.00 41.18 3.16
5 6 1.525619 GCTTTACGTGTTCGCTGAAGT 59.474 47.619 0.00 0.00 41.18 3.01
6 7 1.460267 CGCTTTACGTGTTCGCTGAAG 60.460 52.381 0.00 0.00 41.18 3.02
7 8 0.505231 CGCTTTACGTGTTCGCTGAA 59.495 50.000 0.00 0.00 41.18 3.02
8 9 2.138355 CGCTTTACGTGTTCGCTGA 58.862 52.632 0.00 0.00 41.18 4.26
9 10 4.698496 CGCTTTACGTGTTCGCTG 57.302 55.556 0.00 0.00 41.18 5.18
19 20 2.989422 ATTTGCACCTCACGCTTTAC 57.011 45.000 0.00 0.00 0.00 2.01
20 21 3.006940 CCTATTTGCACCTCACGCTTTA 58.993 45.455 0.00 0.00 0.00 1.85
21 22 1.812571 CCTATTTGCACCTCACGCTTT 59.187 47.619 0.00 0.00 0.00 3.51
22 23 1.003118 TCCTATTTGCACCTCACGCTT 59.997 47.619 0.00 0.00 0.00 4.68
23 24 0.613260 TCCTATTTGCACCTCACGCT 59.387 50.000 0.00 0.00 0.00 5.07
24 25 1.009829 CTCCTATTTGCACCTCACGC 58.990 55.000 0.00 0.00 0.00 5.34
25 26 2.002586 CACTCCTATTTGCACCTCACG 58.997 52.381 0.00 0.00 0.00 4.35
26 27 3.059352 ACACTCCTATTTGCACCTCAC 57.941 47.619 0.00 0.00 0.00 3.51
27 28 3.788227 AACACTCCTATTTGCACCTCA 57.212 42.857 0.00 0.00 0.00 3.86
28 29 4.395231 GGTTAACACTCCTATTTGCACCTC 59.605 45.833 8.10 0.00 0.00 3.85
29 30 4.332828 GGTTAACACTCCTATTTGCACCT 58.667 43.478 8.10 0.00 0.00 4.00
30 31 3.126343 CGGTTAACACTCCTATTTGCACC 59.874 47.826 8.10 0.00 0.00 5.01
31 32 3.126343 CCGGTTAACACTCCTATTTGCAC 59.874 47.826 8.10 0.00 0.00 4.57
32 33 3.008157 TCCGGTTAACACTCCTATTTGCA 59.992 43.478 8.10 0.00 0.00 4.08
33 34 3.602483 TCCGGTTAACACTCCTATTTGC 58.398 45.455 8.10 0.00 0.00 3.68
34 35 3.621715 GCTCCGGTTAACACTCCTATTTG 59.378 47.826 8.10 0.00 0.00 2.32
35 36 3.677976 CGCTCCGGTTAACACTCCTATTT 60.678 47.826 8.10 0.00 0.00 1.40
36 37 2.159142 CGCTCCGGTTAACACTCCTATT 60.159 50.000 8.10 0.00 0.00 1.73
37 38 1.407979 CGCTCCGGTTAACACTCCTAT 59.592 52.381 8.10 0.00 0.00 2.57
38 39 0.813184 CGCTCCGGTTAACACTCCTA 59.187 55.000 8.10 0.00 0.00 2.94
39 40 1.590147 CGCTCCGGTTAACACTCCT 59.410 57.895 8.10 0.00 0.00 3.69
40 41 1.447314 CCGCTCCGGTTAACACTCC 60.447 63.158 8.10 0.00 42.73 3.85
41 42 4.180496 CCGCTCCGGTTAACACTC 57.820 61.111 8.10 0.00 42.73 3.51
60 61 3.222354 AAGGTCGTCGCCACCAGAC 62.222 63.158 5.95 0.00 36.23 3.51
61 62 2.915659 AAGGTCGTCGCCACCAGA 60.916 61.111 5.95 0.00 36.23 3.86
62 63 2.738521 CAAGGTCGTCGCCACCAG 60.739 66.667 5.95 0.00 36.23 4.00
63 64 3.509137 GACAAGGTCGTCGCCACCA 62.509 63.158 5.95 0.00 36.23 4.17
64 65 2.737376 GACAAGGTCGTCGCCACC 60.737 66.667 8.15 2.13 0.00 4.61
65 66 2.737376 GGACAAGGTCGTCGCCAC 60.737 66.667 8.15 0.00 36.73 5.01
66 67 4.351938 CGGACAAGGTCGTCGCCA 62.352 66.667 8.15 0.00 36.73 5.69
67 68 3.352338 ATCGGACAAGGTCGTCGCC 62.352 63.158 0.00 0.00 36.73 5.54
68 69 2.158959 CATCGGACAAGGTCGTCGC 61.159 63.158 0.00 0.00 36.73 5.19
69 70 1.516386 CCATCGGACAAGGTCGTCG 60.516 63.158 0.00 0.00 36.73 5.12
70 71 1.810030 GCCATCGGACAAGGTCGTC 60.810 63.158 0.00 0.00 32.65 4.20
71 72 2.264794 GCCATCGGACAAGGTCGT 59.735 61.111 0.00 0.00 32.65 4.34
72 73 2.885644 CGCCATCGGACAAGGTCG 60.886 66.667 0.00 0.00 32.65 4.79
149 150 2.501128 GCTATCTGTGCTCCGCCA 59.499 61.111 0.00 0.00 0.00 5.69
160 161 2.993899 CACCGAACTTTTGTCGCTATCT 59.006 45.455 0.00 0.00 0.00 1.98
171 172 2.418628 CGCATAACCATCACCGAACTTT 59.581 45.455 0.00 0.00 0.00 2.66
176 177 0.104120 CTCCGCATAACCATCACCGA 59.896 55.000 0.00 0.00 0.00 4.69
188 189 2.125512 GTTCGTGCTCCTCCGCAT 60.126 61.111 0.00 0.00 42.62 4.73
196 197 5.807520 TCTCTTTTCATCTATGTTCGTGCTC 59.192 40.000 0.00 0.00 0.00 4.26
199 200 7.451429 CAACTCTCTTTTCATCTATGTTCGTG 58.549 38.462 0.00 0.00 0.00 4.35
203 204 8.535335 TCTAGCAACTCTCTTTTCATCTATGTT 58.465 33.333 0.00 0.00 0.00 2.71
204 205 8.072321 TCTAGCAACTCTCTTTTCATCTATGT 57.928 34.615 0.00 0.00 0.00 2.29
207 208 6.568869 GCTCTAGCAACTCTCTTTTCATCTA 58.431 40.000 0.00 0.00 41.59 1.98
236 237 2.603473 TCATATCCGCCTCCCCCG 60.603 66.667 0.00 0.00 0.00 5.73
240 241 0.389166 CTTCGCTCATATCCGCCTCC 60.389 60.000 0.00 0.00 0.00 4.30
242 243 0.032678 CACTTCGCTCATATCCGCCT 59.967 55.000 0.00 0.00 0.00 5.52
243 244 0.946221 CCACTTCGCTCATATCCGCC 60.946 60.000 0.00 0.00 0.00 6.13
255 256 3.001902 TAGGGTCTGCGCCACTTCG 62.002 63.158 4.18 0.00 0.00 3.79
259 260 4.814294 CGGTAGGGTCTGCGCCAC 62.814 72.222 4.18 0.46 0.00 5.01
287 288 1.800315 CTCAGGCGTGTCCGTTACG 60.800 63.158 6.26 0.00 43.93 3.18
288 289 2.092882 GCTCAGGCGTGTCCGTTAC 61.093 63.158 6.26 0.00 40.77 2.50
289 290 1.884075 ATGCTCAGGCGTGTCCGTTA 61.884 55.000 6.26 0.00 42.25 3.18
290 291 3.240134 ATGCTCAGGCGTGTCCGTT 62.240 57.895 6.26 0.00 42.25 4.44
291 292 3.649277 GATGCTCAGGCGTGTCCGT 62.649 63.158 6.26 0.21 42.25 4.69
292 293 2.887568 GATGCTCAGGCGTGTCCG 60.888 66.667 6.26 0.00 42.25 4.79
293 294 2.512515 GGATGCTCAGGCGTGTCC 60.513 66.667 6.26 2.16 42.25 4.02
294 295 0.175760 TAAGGATGCTCAGGCGTGTC 59.824 55.000 6.26 0.71 42.25 3.67
297 298 2.234908 GGATATAAGGATGCTCAGGCGT 59.765 50.000 0.00 0.00 42.25 5.68
300 301 3.054802 GGGTGGATATAAGGATGCTCAGG 60.055 52.174 0.00 0.00 0.00 3.86
304 305 5.415961 ACTTAGGGTGGATATAAGGATGCT 58.584 41.667 0.00 0.00 32.05 3.79
310 311 5.656213 CCCGTACTTAGGGTGGATATAAG 57.344 47.826 0.00 0.00 43.89 1.73
325 326 2.057137 TTCTATACACGGCCCGTACT 57.943 50.000 9.25 0.00 38.32 2.73
326 327 2.869233 TTTCTATACACGGCCCGTAC 57.131 50.000 9.25 0.00 38.32 3.67
329 330 1.263217 GCATTTTCTATACACGGCCCG 59.737 52.381 0.00 0.00 0.00 6.13
330 331 1.263217 CGCATTTTCTATACACGGCCC 59.737 52.381 0.00 0.00 0.00 5.80
333 334 3.303132 GGCTTCGCATTTTCTATACACGG 60.303 47.826 0.00 0.00 0.00 4.94
334 335 3.601586 CGGCTTCGCATTTTCTATACACG 60.602 47.826 0.00 0.00 0.00 4.49
336 337 3.787785 TCGGCTTCGCATTTTCTATACA 58.212 40.909 0.00 0.00 0.00 2.29
337 338 4.992381 ATCGGCTTCGCATTTTCTATAC 57.008 40.909 0.00 0.00 0.00 1.47
343 344 0.304705 CGCTATCGGCTTCGCATTTT 59.695 50.000 0.00 0.00 39.13 1.82
344 345 0.810031 ACGCTATCGGCTTCGCATTT 60.810 50.000 0.00 0.00 40.69 2.32
349 350 1.529010 CCAAAAACGCTATCGGCTTCG 60.529 52.381 0.00 0.00 40.69 3.79
350 351 1.202143 CCCAAAAACGCTATCGGCTTC 60.202 52.381 0.00 0.00 40.69 3.86
351 352 0.808755 CCCAAAAACGCTATCGGCTT 59.191 50.000 0.00 0.00 40.69 4.35
352 353 0.322187 ACCCAAAAACGCTATCGGCT 60.322 50.000 0.00 0.00 40.69 5.52
353 354 0.098200 GACCCAAAAACGCTATCGGC 59.902 55.000 0.00 0.00 40.69 5.54
355 356 0.372334 CGGACCCAAAAACGCTATCG 59.628 55.000 0.00 0.00 42.43 2.92
357 358 0.037160 ACCGGACCCAAAAACGCTAT 59.963 50.000 9.46 0.00 0.00 2.97
385 456 2.487532 CGATCCGGACGGGCTACTT 61.488 63.158 6.12 0.00 34.94 2.24
472 912 4.389077 CCGCCGGAATAGTTGATTAGATTC 59.611 45.833 5.05 0.00 0.00 2.52
504 944 4.925646 GGAGGTTCTTCAATTGATTTGCAC 59.074 41.667 9.40 3.78 35.16 4.57
547 988 1.229428 CTTGCTGTGATGACGTTGGT 58.771 50.000 0.00 0.00 0.00 3.67
551 992 3.925379 TGATTACTTGCTGTGATGACGT 58.075 40.909 0.00 0.00 0.00 4.34
836 1299 1.546961 TCTGGTTCTCTTCCTCGTCC 58.453 55.000 0.00 0.00 0.00 4.79
837 1300 2.672760 GCTTCTGGTTCTCTTCCTCGTC 60.673 54.545 0.00 0.00 0.00 4.20
838 1301 1.273886 GCTTCTGGTTCTCTTCCTCGT 59.726 52.381 0.00 0.00 0.00 4.18
839 1302 1.273606 TGCTTCTGGTTCTCTTCCTCG 59.726 52.381 0.00 0.00 0.00 4.63
840 1303 2.564947 TCTGCTTCTGGTTCTCTTCCTC 59.435 50.000 0.00 0.00 0.00 3.71
841 1304 2.566724 CTCTGCTTCTGGTTCTCTTCCT 59.433 50.000 0.00 0.00 0.00 3.36
842 1305 2.934801 GCTCTGCTTCTGGTTCTCTTCC 60.935 54.545 0.00 0.00 0.00 3.46
843 1306 2.289320 TGCTCTGCTTCTGGTTCTCTTC 60.289 50.000 0.00 0.00 0.00 2.87
844 1307 1.696336 TGCTCTGCTTCTGGTTCTCTT 59.304 47.619 0.00 0.00 0.00 2.85
845 1308 1.346062 TGCTCTGCTTCTGGTTCTCT 58.654 50.000 0.00 0.00 0.00 3.10
846 1309 1.803555 GTTGCTCTGCTTCTGGTTCTC 59.196 52.381 0.00 0.00 0.00 2.87
961 1424 1.382695 CTGGTATCGGGGAGTGGGT 60.383 63.158 0.00 0.00 0.00 4.51
1106 1579 2.683933 GGAGGAAGGAGCCGGTGA 60.684 66.667 1.90 0.00 0.00 4.02
1701 2174 2.125178 GCCGATGTAGTAGGGCTGT 58.875 57.895 0.00 0.00 42.29 4.40
2548 3021 4.216257 GGCCATTTGTACAGTATATGCTGG 59.784 45.833 22.64 6.45 40.59 4.85
2560 3033 4.464069 TTAGCATTTGGGCCATTTGTAC 57.536 40.909 7.26 0.00 0.00 2.90
2666 3145 5.475719 CAGTGGATACGTTTCTCCTACAAA 58.524 41.667 5.97 0.00 42.51 2.83
2667 3146 4.081862 CCAGTGGATACGTTTCTCCTACAA 60.082 45.833 1.68 0.00 42.51 2.41
2668 3147 3.446161 CCAGTGGATACGTTTCTCCTACA 59.554 47.826 1.68 0.00 42.51 2.74
2669 3148 3.446516 ACCAGTGGATACGTTTCTCCTAC 59.553 47.826 18.40 6.14 42.51 3.18
2670 3149 3.705051 ACCAGTGGATACGTTTCTCCTA 58.295 45.455 18.40 0.00 42.51 2.94
2671 3150 2.537143 ACCAGTGGATACGTTTCTCCT 58.463 47.619 18.40 0.00 42.51 3.69
2678 3157 2.093869 ACGCAATTACCAGTGGATACGT 60.094 45.455 18.40 13.13 42.51 3.57
2796 3279 6.276847 ACATCAGTAAACAAATTCGCCAAAA 58.723 32.000 0.00 0.00 0.00 2.44
2805 3288 6.658816 TGTGAGCCATACATCAGTAAACAAAT 59.341 34.615 0.00 0.00 33.13 2.32
2837 3323 3.362399 CTCCTCGGCGACTGCACAT 62.362 63.158 4.99 0.00 45.35 3.21
3012 3500 8.945057 GCAAGAATACAAGAAGAGAGAGAAAAT 58.055 33.333 0.00 0.00 0.00 1.82
3017 3505 5.811613 CCAGCAAGAATACAAGAAGAGAGAG 59.188 44.000 0.00 0.00 0.00 3.20
3189 3696 2.308039 GCCACGTCTCCGTCAACAC 61.308 63.158 0.00 0.00 46.28 3.32
3190 3697 2.028484 GCCACGTCTCCGTCAACA 59.972 61.111 0.00 0.00 46.28 3.33
3241 3757 1.311651 CCACAACACACAGCACCACA 61.312 55.000 0.00 0.00 0.00 4.17
3245 3761 3.119193 CCCCACAACACACAGCAC 58.881 61.111 0.00 0.00 0.00 4.40
3246 3762 2.832661 GCCCCACAACACACAGCA 60.833 61.111 0.00 0.00 0.00 4.41
3248 3764 2.195567 CCAGCCCCACAACACACAG 61.196 63.158 0.00 0.00 0.00 3.66
3249 3765 2.123939 CCAGCCCCACAACACACA 60.124 61.111 0.00 0.00 0.00 3.72
3250 3766 2.713531 ATCCCAGCCCCACAACACAC 62.714 60.000 0.00 0.00 0.00 3.82
3252 3768 0.831711 AAATCCCAGCCCCACAACAC 60.832 55.000 0.00 0.00 0.00 3.32
3253 3769 0.831288 CAAATCCCAGCCCCACAACA 60.831 55.000 0.00 0.00 0.00 3.33
3254 3770 1.543944 CCAAATCCCAGCCCCACAAC 61.544 60.000 0.00 0.00 0.00 3.32
3255 3771 1.229145 CCAAATCCCAGCCCCACAA 60.229 57.895 0.00 0.00 0.00 3.33
3256 3772 2.166346 TCCAAATCCCAGCCCCACA 61.166 57.895 0.00 0.00 0.00 4.17
3257 3773 1.682344 GTCCAAATCCCAGCCCCAC 60.682 63.158 0.00 0.00 0.00 4.61
3258 3774 1.442886 AAGTCCAAATCCCAGCCCCA 61.443 55.000 0.00 0.00 0.00 4.96
3259 3775 0.972471 CAAGTCCAAATCCCAGCCCC 60.972 60.000 0.00 0.00 0.00 5.80
3260 3776 0.972471 CCAAGTCCAAATCCCAGCCC 60.972 60.000 0.00 0.00 0.00 5.19
3261 3777 0.972471 CCCAAGTCCAAATCCCAGCC 60.972 60.000 0.00 0.00 0.00 4.85
3262 3778 0.972471 CCCCAAGTCCAAATCCCAGC 60.972 60.000 0.00 0.00 0.00 4.85
3301 3817 2.825836 GCCTGGATCTTGCCACCG 60.826 66.667 0.00 0.00 33.52 4.94
3319 3835 2.672996 CCCCCGTGTTGGCTGAAG 60.673 66.667 0.00 0.00 35.87 3.02
3323 3839 2.610859 ATCTCCCCCGTGTTGGCT 60.611 61.111 0.00 0.00 35.87 4.75
3332 3848 2.276309 CTCCTGTTGCCATCTCCCCC 62.276 65.000 0.00 0.00 0.00 5.40
3333 3849 1.225704 CTCCTGTTGCCATCTCCCC 59.774 63.158 0.00 0.00 0.00 4.81
3334 3850 1.225704 CCTCCTGTTGCCATCTCCC 59.774 63.158 0.00 0.00 0.00 4.30
3335 3851 0.179936 CTCCTCCTGTTGCCATCTCC 59.820 60.000 0.00 0.00 0.00 3.71
3337 3853 1.203441 TGCTCCTCCTGTTGCCATCT 61.203 55.000 0.00 0.00 0.00 2.90
3339 3855 1.001641 GTGCTCCTCCTGTTGCCAT 60.002 57.895 0.00 0.00 0.00 4.40
3340 3856 2.431683 GTGCTCCTCCTGTTGCCA 59.568 61.111 0.00 0.00 0.00 4.92
3342 3858 2.743928 CCGTGCTCCTCCTGTTGC 60.744 66.667 0.00 0.00 0.00 4.17
3370 3900 1.675972 ACACACAAACACACGCCCA 60.676 52.632 0.00 0.00 0.00 5.36
3397 3927 3.294102 GAAGTAAAAACCGACGCTTTGG 58.706 45.455 0.00 0.00 0.00 3.28
3398 3928 2.962191 CGAAGTAAAAACCGACGCTTTG 59.038 45.455 0.00 0.00 0.00 2.77
3399 3929 2.609002 ACGAAGTAAAAACCGACGCTTT 59.391 40.909 0.00 0.00 41.94 3.51
3401 3931 1.856802 ACGAAGTAAAAACCGACGCT 58.143 45.000 0.00 0.00 41.94 5.07
3466 3999 0.738975 TGTCTCCGGACGAGCTATTG 59.261 55.000 0.00 0.00 44.83 1.90
3467 4000 1.025812 CTGTCTCCGGACGAGCTATT 58.974 55.000 0.00 0.00 44.83 1.73
3469 4002 2.113433 GCTGTCTCCGGACGAGCTA 61.113 63.158 14.65 1.69 44.83 3.32
3473 4006 0.678684 TACATGCTGTCTCCGGACGA 60.679 55.000 0.00 0.00 44.83 4.20
3481 4014 2.105477 CAAGCCCCTATACATGCTGTCT 59.895 50.000 0.00 0.00 33.59 3.41
3564 4102 2.037641 TGAACACTCTCCACATCACCTG 59.962 50.000 0.00 0.00 0.00 4.00
3701 4239 1.026718 GGCATGTGACCTCCTTTCCG 61.027 60.000 0.00 0.00 0.00 4.30
3703 4241 1.541588 GTTGGCATGTGACCTCCTTTC 59.458 52.381 0.00 0.00 0.00 2.62
3768 4306 1.130613 CGCCTTTCGCTCTCGTTTG 59.869 57.895 0.00 0.00 36.96 2.93
3792 4330 6.260936 AGGAATGGCATAAAATACTCGAGTTG 59.739 38.462 25.44 15.58 0.00 3.16
3868 4407 7.466996 GCTCGATAAAAGGCTATATCGCTACTA 60.467 40.741 25.75 14.46 46.42 1.82
3871 4410 5.579718 GCTCGATAAAAGGCTATATCGCTA 58.420 41.667 25.75 15.43 46.42 4.26
3872 4411 4.425520 GCTCGATAAAAGGCTATATCGCT 58.574 43.478 25.75 0.00 46.42 4.93
3873 4412 3.240861 CGCTCGATAAAAGGCTATATCGC 59.759 47.826 25.75 17.08 46.42 4.58
3875 4414 4.496183 CGTCGCTCGATAAAAGGCTATATC 59.504 45.833 9.19 9.19 42.86 1.63
3876 4415 4.155462 TCGTCGCTCGATAAAAGGCTATAT 59.845 41.667 0.00 0.00 44.01 0.86
3877 4416 3.499537 TCGTCGCTCGATAAAAGGCTATA 59.500 43.478 0.00 0.00 44.01 1.31
3878 4417 2.292569 TCGTCGCTCGATAAAAGGCTAT 59.707 45.455 0.00 0.00 44.01 2.97
3880 4419 0.454600 TCGTCGCTCGATAAAAGGCT 59.545 50.000 0.00 0.00 44.01 4.58
3881 4420 2.953669 TCGTCGCTCGATAAAAGGC 58.046 52.632 0.00 0.00 44.01 4.35
3924 4463 4.870363 CCAATGTTTTGGTAGGTTGAGTG 58.130 43.478 0.00 0.00 46.27 3.51
3936 4475 3.841222 GGCGCGACCAATGTTTTG 58.159 55.556 12.10 0.00 38.86 2.44
3953 4492 4.274950 ACCAAACAACGTACCAGAGATTTG 59.725 41.667 0.00 0.00 0.00 2.32
3959 4498 3.345414 ACAAACCAAACAACGTACCAGA 58.655 40.909 0.00 0.00 0.00 3.86
3960 4499 3.768468 ACAAACCAAACAACGTACCAG 57.232 42.857 0.00 0.00 0.00 4.00
3962 4501 2.599527 GCAACAAACCAAACAACGTACC 59.400 45.455 0.00 0.00 0.00 3.34
4032 4573 0.314302 CGAGGGATTACACCGCCTAG 59.686 60.000 0.00 0.00 0.00 3.02
4033 4574 1.741327 GCGAGGGATTACACCGCCTA 61.741 60.000 0.00 0.00 39.97 3.93
4034 4575 3.090219 GCGAGGGATTACACCGCCT 62.090 63.158 0.00 0.00 39.97 5.52


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

AutoCloner maintained by Alex Coulton.