Multiple sequence alignment - TraesCS1A01G135800

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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 TraesCS1A01G135800 chr1A 100.000 3044 0 0 1 3044 212019086 212016043 0.000000e+00 5622.0
1 TraesCS1A01G135800 chr1A 95.890 146 5 1 2819 2964 211992187 211992043 5.070000e-58 235.0
2 TraesCS1A01G135800 chr1A 100.000 37 0 0 2752 2788 300007539 300007575 5.450000e-08 69.4
3 TraesCS1A01G135800 chr1D 90.944 2363 140 42 36 2381 190480178 190482483 0.000000e+00 3110.0
4 TraesCS1A01G135800 chr1D 85.426 446 40 14 2334 2757 58568135 58567693 1.000000e-119 440.0
5 TraesCS1A01G135800 chr1D 95.918 147 6 0 2818 2964 486174495 486174641 3.920000e-59 239.0
6 TraesCS1A01G135800 chr1D 94.915 59 3 0 2285 2343 93124875 93124817 3.230000e-15 93.5
7 TraesCS1A01G135800 chr1B 97.681 690 15 1 1639 2328 263980660 263981348 0.000000e+00 1184.0
8 TraesCS1A01G135800 chr1B 90.144 903 49 28 34 916 263947936 263948818 0.000000e+00 1138.0
9 TraesCS1A01G135800 chr1B 95.766 685 25 3 904 1586 263979257 263979939 0.000000e+00 1101.0
10 TraesCS1A01G135800 chr1B 91.751 594 28 4 1625 2218 263980089 263980661 0.000000e+00 806.0
11 TraesCS1A01G135800 chr1B 93.147 394 25 2 2428 2819 263981351 263981744 7.320000e-161 577.0
12 TraesCS1A01G135800 chr1B 97.619 84 2 0 2961 3044 212121774 212121691 8.800000e-31 145.0
13 TraesCS1A01G135800 chr1B 100.000 33 0 0 1581 1613 263980059 263980091 9.110000e-06 62.1
14 TraesCS1A01G135800 chr6D 88.152 422 32 8 2343 2748 316101946 316102365 1.270000e-133 486.0
15 TraesCS1A01G135800 chr3D 85.811 444 45 11 2339 2768 384530323 384530762 3.580000e-124 455.0
16 TraesCS1A01G135800 chr3D 95.455 88 2 2 2957 3044 99746864 99746779 4.090000e-29 139.0
17 TraesCS1A01G135800 chr3D 93.548 62 3 1 2282 2343 42630679 42630739 1.160000e-14 91.6
18 TraesCS1A01G135800 chr3D 90.769 65 6 0 2278 2342 429605707 429605771 1.500000e-13 87.9
19 TraesCS1A01G135800 chr3D 97.561 41 1 0 2754 2794 516197306 516197266 1.510000e-08 71.3
20 TraesCS1A01G135800 chr4D 88.594 377 31 9 2391 2761 215458106 215457736 5.990000e-122 448.0
21 TraesCS1A01G135800 chr4A 89.011 364 33 6 2391 2751 395025884 395026243 7.740000e-121 444.0
22 TraesCS1A01G135800 chr4A 88.798 366 35 4 2397 2759 685789085 685789447 7.740000e-121 444.0
23 TraesCS1A01G135800 chr4A 85.116 430 54 7 2337 2758 596787815 596787388 6.030000e-117 431.0
24 TraesCS1A01G135800 chr4A 95.890 146 6 0 2819 2964 29613516 29613371 1.410000e-58 237.0
25 TraesCS1A01G135800 chr4A 93.197 147 9 1 2819 2964 729274184 729274038 6.610000e-52 215.0
26 TraesCS1A01G135800 chr4A 91.892 148 10 2 2813 2958 729276318 729276171 3.980000e-49 206.0
27 TraesCS1A01G135800 chr4A 98.765 81 1 0 2964 3044 65426621 65426541 8.800000e-31 145.0
28 TraesCS1A01G135800 chr4A 93.617 47 1 2 2752 2797 19508053 19508098 5.450000e-08 69.4
29 TraesCS1A01G135800 chr3A 85.432 405 46 11 2353 2750 710836371 710835973 2.830000e-110 409.0
30 TraesCS1A01G135800 chr5B 95.890 146 6 0 2819 2964 712900170 712900315 1.410000e-58 237.0
31 TraesCS1A01G135800 chr5B 95.205 146 7 0 2819 2964 712897168 712897313 6.560000e-57 231.0
32 TraesCS1A01G135800 chr5B 90.385 52 5 0 272 323 136018677 136018626 5.450000e-08 69.4
33 TraesCS1A01G135800 chr6A 95.205 146 7 0 2819 2964 27518687 27518542 6.560000e-57 231.0
34 TraesCS1A01G135800 chr6A 92.188 64 4 1 2281 2343 610518787 610518850 4.180000e-14 89.8
35 TraesCS1A01G135800 chr6A 91.667 48 2 2 2753 2799 569482730 569482684 7.040000e-07 65.8
36 TraesCS1A01G135800 chr2B 93.836 146 9 0 2819 2964 326257306 326257161 1.420000e-53 220.0
37 TraesCS1A01G135800 chr6B 97.561 82 2 0 2961 3042 154597599 154597518 1.140000e-29 141.0
38 TraesCS1A01G135800 chr6B 97.561 82 2 0 2961 3042 414342235 414342154 1.140000e-29 141.0
39 TraesCS1A01G135800 chr2D 96.429 84 3 0 2961 3044 334861079 334861162 4.090000e-29 139.0
40 TraesCS1A01G135800 chr2D 93.478 46 1 2 2754 2798 616924498 616924454 1.960000e-07 67.6
41 TraesCS1A01G135800 chr5A 96.386 83 3 0 2962 3044 601169203 601169121 1.470000e-28 137.0
42 TraesCS1A01G135800 chr5A 95.082 61 3 0 2283 2343 406022928 406022988 2.500000e-16 97.1
43 TraesCS1A01G135800 chr5A 90.385 52 5 0 272 323 135154603 135154552 5.450000e-08 69.4
44 TraesCS1A01G135800 chr7B 95.294 85 4 0 2960 3044 660479803 660479887 5.290000e-28 135.0
45 TraesCS1A01G135800 chr7B 96.341 82 3 0 2963 3044 713349464 713349383 5.290000e-28 135.0
46 TraesCS1A01G135800 chr7B 95.556 45 0 2 2748 2790 72767306 72767262 1.510000e-08 71.3
47 TraesCS1A01G135800 chr5D 95.000 60 3 0 2283 2342 457514315 457514374 8.980000e-16 95.3
48 TraesCS1A01G135800 chr3B 94.915 59 3 0 2285 2343 265853271 265853329 3.230000e-15 93.5
49 TraesCS1A01G135800 chr7D 93.333 60 4 0 2284 2343 441864033 441864092 4.180000e-14 89.8
50 TraesCS1A01G135800 chr7D 95.349 43 1 1 2753 2795 18555050 18555009 1.960000e-07 67.6
51 TraesCS1A01G135800 chr4B 93.333 60 4 0 2284 2343 417133586 417133645 4.180000e-14 89.8
52 TraesCS1A01G135800 chr2A 95.455 44 2 0 2752 2795 421915103 421915146 1.510000e-08 71.3


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 TraesCS1A01G135800 chr1A 212016043 212019086 3043 True 5622.00 5622 100.0000 1 3044 1 chr1A.!!$R2 3043
1 TraesCS1A01G135800 chr1D 190480178 190482483 2305 False 3110.00 3110 90.9440 36 2381 1 chr1D.!!$F1 2345
2 TraesCS1A01G135800 chr1B 263947936 263948818 882 False 1138.00 1138 90.1440 34 916 1 chr1B.!!$F1 882
3 TraesCS1A01G135800 chr1B 263979257 263981744 2487 False 746.02 1184 95.6690 904 2819 5 chr1B.!!$F2 1915
4 TraesCS1A01G135800 chr4A 729274038 729276318 2280 True 210.50 215 92.5445 2813 2964 2 chr4A.!!$R4 151
5 TraesCS1A01G135800 chr5B 712897168 712900315 3147 False 234.00 237 95.5475 2819 2964 2 chr5B.!!$F1 145

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
254 278 0.036952 AGTCGTCAATGGAGTGCCTG 60.037 55.0 0.0 0.0 34.31 4.85 F
1458 1507 0.179156 GCACCATGAAATCCGCAGTG 60.179 55.0 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1801 0.318441 ATGTGAGTCTGTCCCACACG 59.682 55.0 0.0 0.0 42.65 4.49 R
2482 3218 0.793861 TACAGGTCGCATTTCAACGC 59.206 50.0 0.0 0.0 0.00 4.84 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
28 29 2.413453 GAGTGTTCGATCTTGGAAGTGC 59.587 50.000 0.00 0.00 0.00 4.40
29 30 1.126846 GTGTTCGATCTTGGAAGTGCG 59.873 52.381 0.00 0.00 0.00 5.34
30 31 1.000394 TGTTCGATCTTGGAAGTGCGA 60.000 47.619 0.00 0.00 33.51 5.10
31 32 1.656095 GTTCGATCTTGGAAGTGCGAG 59.344 52.381 0.00 0.00 35.47 5.03
32 33 0.458543 TCGATCTTGGAAGTGCGAGC 60.459 55.000 0.00 0.00 32.37 5.03
50 51 1.446792 CAGCGCTCACCACGATCTT 60.447 57.895 7.13 0.00 0.00 2.40
186 191 0.971959 GGGTGGCTGGATCAAATGCA 60.972 55.000 0.00 0.00 0.00 3.96
200 205 5.534207 TCAAATGCAAACCATCAGTTTCT 57.466 34.783 0.00 0.00 45.85 2.52
201 206 5.291178 TCAAATGCAAACCATCAGTTTCTG 58.709 37.500 0.00 0.00 45.85 3.02
212 236 3.070476 TCAGTTTCTGTGCCATGCATA 57.930 42.857 0.00 0.00 41.91 3.14
214 238 2.488937 CAGTTTCTGTGCCATGCATACA 59.511 45.455 0.00 0.00 41.91 2.29
227 251 2.821546 TGCATACATGAACCGAGTAGC 58.178 47.619 0.00 0.00 0.00 3.58
228 252 2.430694 TGCATACATGAACCGAGTAGCT 59.569 45.455 0.00 0.00 0.00 3.32
229 253 3.634910 TGCATACATGAACCGAGTAGCTA 59.365 43.478 0.00 0.00 0.00 3.32
230 254 4.230657 GCATACATGAACCGAGTAGCTAG 58.769 47.826 0.00 0.00 0.00 3.42
231 255 4.023107 GCATACATGAACCGAGTAGCTAGA 60.023 45.833 0.00 0.00 0.00 2.43
232 256 5.694816 CATACATGAACCGAGTAGCTAGAG 58.305 45.833 0.00 0.00 0.00 2.43
233 257 3.887352 ACATGAACCGAGTAGCTAGAGA 58.113 45.455 0.00 0.00 0.00 3.10
234 258 3.880490 ACATGAACCGAGTAGCTAGAGAG 59.120 47.826 0.00 0.00 0.00 3.20
235 259 3.908643 TGAACCGAGTAGCTAGAGAGA 57.091 47.619 0.00 0.00 0.00 3.10
236 260 3.799366 TGAACCGAGTAGCTAGAGAGAG 58.201 50.000 0.00 0.00 0.00 3.20
237 261 3.198200 TGAACCGAGTAGCTAGAGAGAGT 59.802 47.826 0.00 0.00 0.00 3.24
238 262 3.464111 ACCGAGTAGCTAGAGAGAGTC 57.536 52.381 0.00 0.00 0.00 3.36
239 263 2.223876 ACCGAGTAGCTAGAGAGAGTCG 60.224 54.545 0.00 0.00 0.00 4.18
240 264 2.223876 CCGAGTAGCTAGAGAGAGTCGT 60.224 54.545 8.03 0.00 0.00 4.34
241 265 3.047796 CGAGTAGCTAGAGAGAGTCGTC 58.952 54.545 0.00 0.00 0.00 4.20
242 266 3.489568 CGAGTAGCTAGAGAGAGTCGTCA 60.490 52.174 0.00 0.00 0.00 4.35
243 267 4.435425 GAGTAGCTAGAGAGAGTCGTCAA 58.565 47.826 0.00 0.00 0.00 3.18
244 268 5.031066 AGTAGCTAGAGAGAGTCGTCAAT 57.969 43.478 0.00 0.00 0.00 2.57
245 269 4.814234 AGTAGCTAGAGAGAGTCGTCAATG 59.186 45.833 0.00 0.00 0.00 2.82
246 270 2.948979 AGCTAGAGAGAGTCGTCAATGG 59.051 50.000 0.00 0.00 0.00 3.16
247 271 2.946329 GCTAGAGAGAGTCGTCAATGGA 59.054 50.000 0.00 0.00 0.00 3.41
248 272 3.003275 GCTAGAGAGAGTCGTCAATGGAG 59.997 52.174 0.00 0.00 0.00 3.86
249 273 3.080300 AGAGAGAGTCGTCAATGGAGT 57.920 47.619 0.00 0.00 0.00 3.85
250 274 2.752354 AGAGAGAGTCGTCAATGGAGTG 59.248 50.000 0.00 0.00 0.00 3.51
251 275 1.203523 AGAGAGTCGTCAATGGAGTGC 59.796 52.381 0.00 0.00 0.00 4.40
252 276 0.247736 AGAGTCGTCAATGGAGTGCC 59.752 55.000 0.00 0.00 0.00 5.01
253 277 0.247736 GAGTCGTCAATGGAGTGCCT 59.752 55.000 0.00 0.00 34.31 4.75
254 278 0.036952 AGTCGTCAATGGAGTGCCTG 60.037 55.000 0.00 0.00 34.31 4.85
255 279 1.375908 TCGTCAATGGAGTGCCTGC 60.376 57.895 0.00 0.00 34.31 4.85
256 280 2.401766 CGTCAATGGAGTGCCTGCC 61.402 63.158 0.00 0.00 34.31 4.85
257 281 1.303561 GTCAATGGAGTGCCTGCCA 60.304 57.895 0.00 0.00 38.78 4.92
258 282 0.682209 GTCAATGGAGTGCCTGCCAT 60.682 55.000 0.00 0.00 46.49 4.40
259 283 0.681887 TCAATGGAGTGCCTGCCATG 60.682 55.000 0.00 0.00 43.85 3.66
260 284 2.056223 AATGGAGTGCCTGCCATGC 61.056 57.895 0.00 0.00 43.85 4.06
605 632 1.003355 CCGGTGTTGGTGCTGATCT 60.003 57.895 0.00 0.00 0.00 2.75
606 633 1.021390 CCGGTGTTGGTGCTGATCTC 61.021 60.000 0.00 0.00 0.00 2.75
607 634 0.036952 CGGTGTTGGTGCTGATCTCT 60.037 55.000 0.00 0.00 0.00 3.10
608 635 1.446907 GGTGTTGGTGCTGATCTCTG 58.553 55.000 0.00 0.00 0.00 3.35
609 636 1.002430 GGTGTTGGTGCTGATCTCTGA 59.998 52.381 0.00 0.00 0.00 3.27
610 637 2.355513 GGTGTTGGTGCTGATCTCTGAT 60.356 50.000 0.00 0.00 0.00 2.90
611 638 2.935201 GTGTTGGTGCTGATCTCTGATC 59.065 50.000 0.00 0.98 0.00 2.92
612 639 2.568509 TGTTGGTGCTGATCTCTGATCA 59.431 45.455 9.50 9.50 0.00 2.92
628 655 1.001293 GATCAGCTCACTCACACCACA 59.999 52.381 0.00 0.00 0.00 4.17
630 657 1.068083 AGCTCACTCACACCACACG 59.932 57.895 0.00 0.00 0.00 4.49
634 674 1.110518 TCACTCACACCACACGCCTA 61.111 55.000 0.00 0.00 0.00 3.93
636 676 1.374252 CTCACACCACACGCCTACC 60.374 63.158 0.00 0.00 0.00 3.18
701 741 8.722394 CGCATTGTAGTTATAGATAGAGAGACA 58.278 37.037 0.00 0.00 0.00 3.41
774 814 6.773976 TGAGACTCCAAATTCACAAGTTTT 57.226 33.333 0.00 0.00 0.00 2.43
778 818 3.802866 TCCAAATTCACAAGTTTTGGCC 58.197 40.909 0.00 0.00 45.79 5.36
794 834 0.963355 GGCCACCTCGGTTAATGCAA 60.963 55.000 0.00 0.00 36.97 4.08
813 853 4.201666 TGCAATTTTGTTGTTTCGTCAAGC 60.202 37.500 0.00 0.00 0.00 4.01
850 890 2.410262 CGTGTGAGCATTGTCTTCGTTC 60.410 50.000 0.00 0.00 0.00 3.95
937 985 1.079543 CTGGGTTGTCTGAGCCGAG 60.080 63.158 0.00 0.00 40.06 4.63
1176 1225 5.871524 TGATTGATCTCGTCTCTTTCCTTTG 59.128 40.000 0.00 0.00 0.00 2.77
1273 1322 1.152440 CCCTCCCGCTCCTCTATGT 60.152 63.158 0.00 0.00 0.00 2.29
1297 1346 1.010419 CGCTTGTTGAATGCTTGGGC 61.010 55.000 0.00 0.00 39.26 5.36
1324 1373 0.676782 CCTCTGGTGGTTTTAGCCGG 60.677 60.000 0.00 0.00 0.00 6.13
1328 1377 3.106054 TCTGGTGGTTTTAGCCGGTATA 58.894 45.455 1.90 0.00 0.00 1.47
1329 1378 3.712733 TCTGGTGGTTTTAGCCGGTATAT 59.287 43.478 1.90 0.00 0.00 0.86
1330 1379 4.164604 TCTGGTGGTTTTAGCCGGTATATT 59.835 41.667 1.90 0.00 0.00 1.28
1331 1380 4.200874 TGGTGGTTTTAGCCGGTATATTG 58.799 43.478 1.90 0.00 0.00 1.90
1424 1473 1.996070 AAGGGGGCCGATTTCCTAGC 61.996 60.000 0.00 0.00 0.00 3.42
1458 1507 0.179156 GCACCATGAAATCCGCAGTG 60.179 55.000 0.00 0.00 0.00 3.66
1550 1601 9.657419 AGAATTTGACTGTTTGATGAAGTTTTT 57.343 25.926 0.00 0.00 0.00 1.94
1553 1604 8.464770 TTTGACTGTTTGATGAAGTTTTTGAG 57.535 30.769 0.00 0.00 0.00 3.02
1688 1865 6.681777 AGGAGAAAATGATTAAAGTGCACAC 58.318 36.000 21.04 3.64 0.00 3.82
1689 1866 6.265196 AGGAGAAAATGATTAAAGTGCACACA 59.735 34.615 21.04 9.17 0.00 3.72
1722 1901 7.581213 AACAACCAACTGATTTGATGTTCTA 57.419 32.000 2.52 0.00 39.15 2.10
1727 1906 7.138736 ACCAACTGATTTGATGTTCTAAAACG 58.861 34.615 0.00 0.00 37.39 3.60
1739 1918 8.895737 TGATGTTCTAAAACGGGGATATTTTAC 58.104 33.333 0.00 0.00 38.28 2.01
2023 2759 2.134789 ATCAGGACATGAAACCAGCC 57.865 50.000 0.00 0.00 42.53 4.85
2154 2890 4.593597 TTCTTGTCGCCGTAAATCATTC 57.406 40.909 0.00 0.00 0.00 2.67
2235 2971 6.281848 TGCTCTTAGCCGTAATTTATTTCG 57.718 37.500 0.00 0.00 41.51 3.46
2268 3004 3.056536 TCTCTTTGCTGCTGTACCTGTAG 60.057 47.826 0.00 0.00 0.00 2.74
2293 3029 1.934410 ACCTTGCGTACTACTCCCTT 58.066 50.000 0.00 0.00 0.00 3.95
2381 3117 4.115199 GGCCTCCATGGAAGCCGT 62.115 66.667 33.49 0.00 41.23 5.68
2382 3118 2.044946 GCCTCCATGGAAGCCGTT 60.045 61.111 22.79 0.00 38.35 4.44
2383 3119 2.115291 GCCTCCATGGAAGCCGTTC 61.115 63.158 22.79 0.00 38.35 3.95
2384 3120 1.604378 CCTCCATGGAAGCCGTTCT 59.396 57.895 17.00 0.00 38.35 3.01
2385 3121 0.035056 CCTCCATGGAAGCCGTTCTT 60.035 55.000 17.00 0.00 38.35 2.52
2386 3122 1.614317 CCTCCATGGAAGCCGTTCTTT 60.614 52.381 17.00 0.00 38.35 2.52
2387 3123 2.162681 CTCCATGGAAGCCGTTCTTTT 58.837 47.619 17.00 0.00 34.56 2.27
2388 3124 2.558359 CTCCATGGAAGCCGTTCTTTTT 59.442 45.455 17.00 0.00 34.56 1.94
2467 3203 5.405571 GGATATGAGGCGTATGTGTGTAAAG 59.594 44.000 0.00 0.00 0.00 1.85
2474 3210 4.378046 GGCGTATGTGTGTAAAGTTTCAGG 60.378 45.833 0.00 0.00 0.00 3.86
2537 3273 7.729124 AATTCATGGTCTTGAAGGATGAATT 57.271 32.000 21.64 21.64 43.76 2.17
2547 3283 9.330063 GTCTTGAAGGATGAATTGTATCATGTA 57.670 33.333 0.00 0.00 40.08 2.29
2593 3329 0.825425 TGCACCGCCCTCATTTCAAA 60.825 50.000 0.00 0.00 0.00 2.69
2603 3339 5.619086 CGCCCTCATTTCAAAGTATTTCGTT 60.619 40.000 0.00 0.00 35.03 3.85
2653 3389 9.368674 CTATGCCTTCATCTATCTCTGTATTTG 57.631 37.037 0.00 0.00 34.22 2.32
2758 3496 6.292150 TCCAAAAGCAATTTCCGGTAAAAAT 58.708 32.000 0.00 0.00 0.00 1.82
2778 3516 7.687941 AAAATGCTCTTATATTATGGGACGG 57.312 36.000 0.00 0.00 0.00 4.79
2795 3533 3.197116 GGACGGAGGGAGTAAATCAGAAA 59.803 47.826 0.00 0.00 0.00 2.52
2809 3547 6.759497 AAATCAGAAAAACCCTAGAATCCG 57.241 37.500 0.00 0.00 0.00 4.18
2826 3564 3.159353 TCCGGATGTCAATGTTAGACG 57.841 47.619 0.00 0.00 38.83 4.18
2881 7755 1.213013 CAGAGCTGGTCGTACGCTT 59.787 57.895 11.24 0.00 33.47 4.68
2964 7839 5.881777 TCGATCTAGGATCGATTGTTAGG 57.118 43.478 23.02 0.00 44.42 2.69
2965 7840 4.156190 TCGATCTAGGATCGATTGTTAGGC 59.844 45.833 23.02 0.00 44.42 3.93
2966 7841 4.675671 CGATCTAGGATCGATTGTTAGGCC 60.676 50.000 20.77 0.00 43.59 5.19
2967 7842 2.897969 TCTAGGATCGATTGTTAGGCCC 59.102 50.000 0.00 0.00 0.00 5.80
2968 7843 1.807814 AGGATCGATTGTTAGGCCCT 58.192 50.000 0.00 0.00 0.00 5.19
2969 7844 1.694696 AGGATCGATTGTTAGGCCCTC 59.305 52.381 0.00 0.00 0.00 4.30
2970 7845 1.694696 GGATCGATTGTTAGGCCCTCT 59.305 52.381 0.00 0.00 0.00 3.69
2971 7846 2.104963 GGATCGATTGTTAGGCCCTCTT 59.895 50.000 0.00 0.00 0.00 2.85
2972 7847 3.433740 GGATCGATTGTTAGGCCCTCTTT 60.434 47.826 0.00 0.00 0.00 2.52
2973 7848 2.985896 TCGATTGTTAGGCCCTCTTTG 58.014 47.619 0.00 0.00 0.00 2.77
2974 7849 2.569853 TCGATTGTTAGGCCCTCTTTGA 59.430 45.455 0.00 0.00 0.00 2.69
2975 7850 3.199946 TCGATTGTTAGGCCCTCTTTGAT 59.800 43.478 0.00 0.00 0.00 2.57
2976 7851 3.947834 CGATTGTTAGGCCCTCTTTGATT 59.052 43.478 0.00 0.00 0.00 2.57
2977 7852 4.399303 CGATTGTTAGGCCCTCTTTGATTT 59.601 41.667 0.00 0.00 0.00 2.17
2978 7853 5.654497 GATTGTTAGGCCCTCTTTGATTTG 58.346 41.667 0.00 0.00 0.00 2.32
2979 7854 2.825532 TGTTAGGCCCTCTTTGATTTGC 59.174 45.455 0.00 0.00 0.00 3.68
2980 7855 2.825532 GTTAGGCCCTCTTTGATTTGCA 59.174 45.455 0.00 0.00 0.00 4.08
2981 7856 1.553706 AGGCCCTCTTTGATTTGCAG 58.446 50.000 0.00 0.00 0.00 4.41
2982 7857 0.533951 GGCCCTCTTTGATTTGCAGG 59.466 55.000 0.00 0.00 0.00 4.85
2983 7858 1.549203 GCCCTCTTTGATTTGCAGGA 58.451 50.000 0.00 0.00 0.00 3.86
2984 7859 2.105766 GCCCTCTTTGATTTGCAGGAT 58.894 47.619 0.00 0.00 0.00 3.24
2985 7860 2.498885 GCCCTCTTTGATTTGCAGGATT 59.501 45.455 0.00 0.00 0.00 3.01
2986 7861 3.055602 GCCCTCTTTGATTTGCAGGATTT 60.056 43.478 0.00 0.00 0.00 2.17
2987 7862 4.564199 GCCCTCTTTGATTTGCAGGATTTT 60.564 41.667 0.00 0.00 0.00 1.82
2988 7863 5.173664 CCCTCTTTGATTTGCAGGATTTTC 58.826 41.667 0.00 0.00 0.00 2.29
2989 7864 5.279607 CCCTCTTTGATTTGCAGGATTTTCA 60.280 40.000 0.00 0.00 0.00 2.69
2990 7865 6.225318 CCTCTTTGATTTGCAGGATTTTCAA 58.775 36.000 0.00 0.00 0.00 2.69
2991 7866 6.707161 CCTCTTTGATTTGCAGGATTTTCAAA 59.293 34.615 0.00 0.00 34.68 2.69
2992 7867 7.227116 CCTCTTTGATTTGCAGGATTTTCAAAA 59.773 33.333 0.00 0.00 33.97 2.44
2993 7868 7.918643 TCTTTGATTTGCAGGATTTTCAAAAC 58.081 30.769 0.00 0.00 33.97 2.43
2994 7869 7.551974 TCTTTGATTTGCAGGATTTTCAAAACA 59.448 29.630 0.00 0.00 33.97 2.83
2995 7870 6.601741 TGATTTGCAGGATTTTCAAAACAC 57.398 33.333 0.00 0.00 34.00 3.32
2996 7871 5.233902 TGATTTGCAGGATTTTCAAAACACG 59.766 36.000 0.00 0.00 34.00 4.49
2997 7872 3.090952 TGCAGGATTTTCAAAACACGG 57.909 42.857 0.00 0.00 0.00 4.94
2998 7873 2.223923 TGCAGGATTTTCAAAACACGGG 60.224 45.455 0.00 0.00 0.00 5.28
2999 7874 2.035321 GCAGGATTTTCAAAACACGGGA 59.965 45.455 0.00 0.00 0.00 5.14
3000 7875 3.491792 GCAGGATTTTCAAAACACGGGAA 60.492 43.478 0.00 0.00 0.00 3.97
3001 7876 4.799255 GCAGGATTTTCAAAACACGGGAAT 60.799 41.667 0.00 0.00 0.00 3.01
3002 7877 5.565834 GCAGGATTTTCAAAACACGGGAATA 60.566 40.000 0.00 0.00 0.00 1.75
3003 7878 6.092748 CAGGATTTTCAAAACACGGGAATAG 58.907 40.000 0.00 0.00 0.00 1.73
3004 7879 5.185056 AGGATTTTCAAAACACGGGAATAGG 59.815 40.000 0.00 0.00 0.00 2.57
3005 7880 4.857509 TTTTCAAAACACGGGAATAGGG 57.142 40.909 0.00 0.00 0.00 3.53
3006 7881 3.791953 TTCAAAACACGGGAATAGGGA 57.208 42.857 0.00 0.00 0.00 4.20
3007 7882 3.791953 TCAAAACACGGGAATAGGGAA 57.208 42.857 0.00 0.00 0.00 3.97
3008 7883 4.101645 TCAAAACACGGGAATAGGGAAA 57.898 40.909 0.00 0.00 0.00 3.13
3009 7884 4.471548 TCAAAACACGGGAATAGGGAAAA 58.528 39.130 0.00 0.00 0.00 2.29
3010 7885 5.081032 TCAAAACACGGGAATAGGGAAAAT 58.919 37.500 0.00 0.00 0.00 1.82
3011 7886 6.246919 TCAAAACACGGGAATAGGGAAAATA 58.753 36.000 0.00 0.00 0.00 1.40
3012 7887 6.151480 TCAAAACACGGGAATAGGGAAAATAC 59.849 38.462 0.00 0.00 0.00 1.89
3013 7888 4.847990 ACACGGGAATAGGGAAAATACA 57.152 40.909 0.00 0.00 0.00 2.29
3014 7889 5.382664 ACACGGGAATAGGGAAAATACAT 57.617 39.130 0.00 0.00 0.00 2.29
3015 7890 5.130350 ACACGGGAATAGGGAAAATACATG 58.870 41.667 0.00 0.00 0.00 3.21
3016 7891 5.104277 ACACGGGAATAGGGAAAATACATGA 60.104 40.000 0.00 0.00 0.00 3.07
3017 7892 6.003950 CACGGGAATAGGGAAAATACATGAT 58.996 40.000 0.00 0.00 0.00 2.45
3018 7893 6.490040 CACGGGAATAGGGAAAATACATGATT 59.510 38.462 0.00 0.00 0.00 2.57
3019 7894 7.014230 CACGGGAATAGGGAAAATACATGATTT 59.986 37.037 0.00 0.00 39.56 2.17
3020 7895 7.014230 ACGGGAATAGGGAAAATACATGATTTG 59.986 37.037 0.00 0.00 37.82 2.32
3021 7896 7.230510 CGGGAATAGGGAAAATACATGATTTGA 59.769 37.037 0.00 0.00 37.82 2.69
3022 7897 8.579863 GGGAATAGGGAAAATACATGATTTGAG 58.420 37.037 0.00 0.00 37.82 3.02
3023 7898 9.136323 GGAATAGGGAAAATACATGATTTGAGT 57.864 33.333 0.00 0.00 37.82 3.41
3024 7899 9.956720 GAATAGGGAAAATACATGATTTGAGTG 57.043 33.333 0.00 0.00 37.82 3.51
3025 7900 6.780457 AGGGAAAATACATGATTTGAGTGG 57.220 37.500 0.00 0.00 37.82 4.00
3026 7901 5.127682 AGGGAAAATACATGATTTGAGTGGC 59.872 40.000 0.00 0.00 37.82 5.01
3027 7902 5.105392 GGGAAAATACATGATTTGAGTGGCA 60.105 40.000 0.00 0.00 37.82 4.92
3028 7903 6.407299 GGGAAAATACATGATTTGAGTGGCAT 60.407 38.462 0.00 0.00 37.82 4.40
3029 7904 6.477688 GGAAAATACATGATTTGAGTGGCATG 59.522 38.462 0.00 0.00 42.75 4.06
3031 7906 5.762825 ATACATGATTTGAGTGGCATGTC 57.237 39.130 10.19 0.00 45.82 3.06
3032 7907 2.756760 ACATGATTTGAGTGGCATGTCC 59.243 45.455 0.00 0.00 45.82 4.02
3033 7908 2.583024 TGATTTGAGTGGCATGTCCA 57.417 45.000 4.93 4.93 44.18 4.02
3042 7917 1.838112 TGGCATGTCCACTTGAATCC 58.162 50.000 4.93 0.00 40.72 3.01
3043 7918 1.355381 TGGCATGTCCACTTGAATCCT 59.645 47.619 4.93 0.00 40.72 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.663602 CACTTCCAAGATCGAACACTCG 59.336 50.000 0.00 0.00 46.87 4.18
7 8 2.413453 GCACTTCCAAGATCGAACACTC 59.587 50.000 0.00 0.00 0.00 3.51
8 9 2.417719 GCACTTCCAAGATCGAACACT 58.582 47.619 0.00 0.00 0.00 3.55
9 10 1.126846 CGCACTTCCAAGATCGAACAC 59.873 52.381 0.00 0.00 0.00 3.32
10 11 1.000394 TCGCACTTCCAAGATCGAACA 60.000 47.619 0.00 0.00 33.35 3.18
11 12 1.656095 CTCGCACTTCCAAGATCGAAC 59.344 52.381 0.00 0.00 34.83 3.95
12 13 1.996292 CTCGCACTTCCAAGATCGAA 58.004 50.000 0.00 0.00 34.83 3.71
13 14 0.458543 GCTCGCACTTCCAAGATCGA 60.459 55.000 0.00 0.00 34.39 3.59
14 15 0.737367 TGCTCGCACTTCCAAGATCG 60.737 55.000 0.00 0.00 0.00 3.69
15 16 1.005340 CTGCTCGCACTTCCAAGATC 58.995 55.000 0.00 0.00 0.00 2.75
16 17 1.023513 GCTGCTCGCACTTCCAAGAT 61.024 55.000 0.00 0.00 38.92 2.40
17 18 1.669115 GCTGCTCGCACTTCCAAGA 60.669 57.895 0.00 0.00 38.92 3.02
18 19 2.866028 GCTGCTCGCACTTCCAAG 59.134 61.111 0.00 0.00 38.92 3.61
19 20 3.043713 CGCTGCTCGCACTTCCAA 61.044 61.111 0.00 0.00 39.08 3.53
30 31 3.997064 GATCGTGGTGAGCGCTGCT 62.997 63.158 18.48 2.68 43.88 4.24
31 32 3.558411 GATCGTGGTGAGCGCTGC 61.558 66.667 18.48 7.45 0.00 5.25
32 33 1.446792 AAGATCGTGGTGAGCGCTG 60.447 57.895 18.48 0.00 38.28 5.18
50 51 4.770362 TCGATCCCCTCACGGCCA 62.770 66.667 2.24 0.00 0.00 5.36
212 236 3.880490 CTCTCTAGCTACTCGGTTCATGT 59.120 47.826 0.00 0.00 0.00 3.21
214 238 4.141574 ACTCTCTCTAGCTACTCGGTTCAT 60.142 45.833 0.00 0.00 0.00 2.57
221 245 4.049546 TGACGACTCTCTCTAGCTACTC 57.950 50.000 0.00 0.00 0.00 2.59
222 246 4.475051 TTGACGACTCTCTCTAGCTACT 57.525 45.455 0.00 0.00 0.00 2.57
223 247 4.024387 CCATTGACGACTCTCTCTAGCTAC 60.024 50.000 0.00 0.00 0.00 3.58
225 249 2.948979 CCATTGACGACTCTCTCTAGCT 59.051 50.000 0.00 0.00 0.00 3.32
226 250 2.946329 TCCATTGACGACTCTCTCTAGC 59.054 50.000 0.00 0.00 0.00 3.42
227 251 4.035091 CACTCCATTGACGACTCTCTCTAG 59.965 50.000 0.00 0.00 0.00 2.43
228 252 3.942115 CACTCCATTGACGACTCTCTCTA 59.058 47.826 0.00 0.00 0.00 2.43
229 253 2.752354 CACTCCATTGACGACTCTCTCT 59.248 50.000 0.00 0.00 0.00 3.10
230 254 2.733858 GCACTCCATTGACGACTCTCTC 60.734 54.545 0.00 0.00 0.00 3.20
231 255 1.203523 GCACTCCATTGACGACTCTCT 59.796 52.381 0.00 0.00 0.00 3.10
232 256 1.634702 GCACTCCATTGACGACTCTC 58.365 55.000 0.00 0.00 0.00 3.20
233 257 0.247736 GGCACTCCATTGACGACTCT 59.752 55.000 0.00 0.00 0.00 3.24
234 258 0.247736 AGGCACTCCATTGACGACTC 59.752 55.000 0.00 0.00 33.74 3.36
235 259 0.036952 CAGGCACTCCATTGACGACT 60.037 55.000 0.00 0.00 34.60 4.18
236 260 1.639298 GCAGGCACTCCATTGACGAC 61.639 60.000 0.00 0.00 34.60 4.34
237 261 1.375908 GCAGGCACTCCATTGACGA 60.376 57.895 0.00 0.00 34.60 4.20
238 262 2.401766 GGCAGGCACTCCATTGACG 61.402 63.158 0.00 0.00 34.60 4.35
239 263 0.682209 ATGGCAGGCACTCCATTGAC 60.682 55.000 0.00 0.00 41.29 3.18
240 264 0.681887 CATGGCAGGCACTCCATTGA 60.682 55.000 0.00 0.00 41.83 2.57
241 265 1.813859 CATGGCAGGCACTCCATTG 59.186 57.895 0.00 0.00 41.83 2.82
242 266 2.056223 GCATGGCAGGCACTCCATT 61.056 57.895 20.53 0.00 41.83 3.16
243 267 2.441532 GCATGGCAGGCACTCCAT 60.442 61.111 20.53 0.22 43.54 3.41
244 268 1.924145 TATGCATGGCAGGCACTCCA 61.924 55.000 30.38 12.03 45.23 3.86
245 269 0.538977 ATATGCATGGCAGGCACTCC 60.539 55.000 30.38 0.00 45.23 3.85
246 270 1.808945 GTATATGCATGGCAGGCACTC 59.191 52.381 30.38 15.31 45.23 3.51
247 271 1.546323 GGTATATGCATGGCAGGCACT 60.546 52.381 30.38 21.13 45.23 4.40
248 272 0.883833 GGTATATGCATGGCAGGCAC 59.116 55.000 30.38 16.28 45.23 5.01
249 273 0.251297 GGGTATATGCATGGCAGGCA 60.251 55.000 29.92 29.92 43.65 4.75
250 274 0.251297 TGGGTATATGCATGGCAGGC 60.251 55.000 18.55 18.55 43.65 4.85
251 275 2.519771 ATGGGTATATGCATGGCAGG 57.480 50.000 10.16 0.00 43.65 4.85
252 276 3.282021 GGTATGGGTATATGCATGGCAG 58.718 50.000 10.16 0.00 43.65 4.85
253 277 2.355615 CGGTATGGGTATATGCATGGCA 60.356 50.000 10.16 0.00 44.86 4.92
254 278 2.093181 TCGGTATGGGTATATGCATGGC 60.093 50.000 10.16 0.00 0.00 4.40
255 279 3.432186 CCTCGGTATGGGTATATGCATGG 60.432 52.174 10.16 0.00 0.00 3.66
256 280 3.450817 TCCTCGGTATGGGTATATGCATG 59.549 47.826 10.16 0.00 0.00 4.06
257 281 3.719871 TCCTCGGTATGGGTATATGCAT 58.280 45.455 3.79 3.79 0.00 3.96
258 282 3.178412 TCCTCGGTATGGGTATATGCA 57.822 47.619 0.00 0.00 0.00 3.96
259 283 3.451178 ACATCCTCGGTATGGGTATATGC 59.549 47.826 0.00 0.00 0.00 3.14
260 284 4.202020 CGACATCCTCGGTATGGGTATATG 60.202 50.000 0.00 0.00 38.87 1.78
507 534 0.656259 CATTCTCATCGCCACAGCAG 59.344 55.000 0.00 0.00 39.83 4.24
515 542 2.602322 GCCGCCTCATTCTCATCGC 61.602 63.158 0.00 0.00 0.00 4.58
516 543 2.305853 CGCCGCCTCATTCTCATCG 61.306 63.158 0.00 0.00 0.00 3.84
605 632 1.547820 GGTGTGAGTGAGCTGATCAGA 59.452 52.381 27.04 2.29 39.07 3.27
606 633 1.274447 TGGTGTGAGTGAGCTGATCAG 59.726 52.381 18.84 18.84 39.07 2.90
607 634 1.001293 GTGGTGTGAGTGAGCTGATCA 59.999 52.381 0.00 0.00 34.79 2.92
608 635 1.001293 TGTGGTGTGAGTGAGCTGATC 59.999 52.381 0.00 0.00 0.00 2.92
609 636 1.051008 TGTGGTGTGAGTGAGCTGAT 58.949 50.000 0.00 0.00 0.00 2.90
610 637 0.104855 GTGTGGTGTGAGTGAGCTGA 59.895 55.000 0.00 0.00 0.00 4.26
611 638 1.217585 CGTGTGGTGTGAGTGAGCTG 61.218 60.000 0.00 0.00 0.00 4.24
612 639 1.068083 CGTGTGGTGTGAGTGAGCT 59.932 57.895 0.00 0.00 0.00 4.09
630 657 2.202810 GACAGAGCAGCGGTAGGC 60.203 66.667 0.00 0.00 44.05 3.93
634 674 3.069980 GATCGGACAGAGCAGCGGT 62.070 63.158 0.00 0.00 34.89 5.68
636 676 2.399511 ATCGATCGGACAGAGCAGCG 62.400 60.000 16.41 0.00 34.30 5.18
774 814 1.377987 GCATTAACCGAGGTGGCCA 60.378 57.895 0.00 0.00 43.94 5.36
778 818 4.555262 ACAAAATTGCATTAACCGAGGTG 58.445 39.130 0.00 0.00 0.00 4.00
850 890 4.640201 TCCATTCCAAGATTCCGCTAAAAG 59.360 41.667 0.00 0.00 0.00 2.27
1066 1115 3.790437 CAGGGGGCAGACGAGCAT 61.790 66.667 0.00 0.00 35.83 3.79
1125 1174 1.481363 GTAGTGTGGAAGTAGGAGGGC 59.519 57.143 0.00 0.00 0.00 5.19
1176 1225 3.665675 CTCGCAGTACCTGGTGGGC 62.666 68.421 10.23 9.21 39.10 5.36
1253 1302 2.091924 ATAGAGGAGCGGGAGGGGA 61.092 63.158 0.00 0.00 0.00 4.81
1273 1322 2.254951 CATTCAACAAGCGCGGCA 59.745 55.556 8.83 0.00 0.00 5.69
1310 1359 3.004002 GCAATATACCGGCTAAAACCACC 59.996 47.826 0.00 0.00 0.00 4.61
1312 1361 3.887352 TGCAATATACCGGCTAAAACCA 58.113 40.909 0.00 0.00 0.00 3.67
1424 1473 2.560504 TGGTGCCATTAAGTAGCGATG 58.439 47.619 0.00 0.00 0.00 3.84
1458 1507 4.161377 AGCTACTTCCTGAATTGAGTCTCC 59.839 45.833 0.00 0.00 0.00 3.71
1517 1566 9.166173 TCATCAAACAGTCAAATTCTCGATAAT 57.834 29.630 0.00 0.00 0.00 1.28
1625 1801 0.318441 ATGTGAGTCTGTCCCACACG 59.682 55.000 0.00 0.00 42.65 4.49
1688 1865 5.895636 TCAGTTGGTTGTTAGCCATTATG 57.104 39.130 0.00 0.00 35.71 1.90
1689 1866 7.178274 TCAAATCAGTTGGTTGTTAGCCATTAT 59.822 33.333 0.00 0.00 37.85 1.28
1722 1901 5.706833 AGTTGACGTAAAATATCCCCGTTTT 59.293 36.000 0.00 0.00 0.00 2.43
1727 1906 6.746745 TCAAAGTTGACGTAAAATATCCCC 57.253 37.500 0.00 0.00 31.01 4.81
1739 1918 9.166126 GTTTATCCTAAAAGTTCAAAGTTGACG 57.834 33.333 0.00 0.00 36.83 4.35
2023 2759 5.803552 GATTCAATCAGAGGAATCCCTAGG 58.196 45.833 0.06 0.06 44.53 3.02
2154 2890 7.582435 AATAGTCAGTACAAATCAACGTGAG 57.418 36.000 0.00 0.00 0.00 3.51
2235 2971 3.572584 CAGCAAAGAGAAACATGAAGCC 58.427 45.455 0.00 0.00 0.00 4.35
2268 3004 3.500014 GAGTAGTACGCAAGGTTCACTC 58.500 50.000 0.00 0.00 46.39 3.51
2336 3072 5.068591 AGCCAAAACACTATTCTCCGTTTTT 59.931 36.000 0.00 0.00 39.01 1.94
2337 3073 4.583073 AGCCAAAACACTATTCTCCGTTTT 59.417 37.500 0.00 0.00 41.05 2.43
2338 3074 4.142038 AGCCAAAACACTATTCTCCGTTT 58.858 39.130 0.00 0.00 33.15 3.60
2339 3075 3.751518 AGCCAAAACACTATTCTCCGTT 58.248 40.909 0.00 0.00 0.00 4.44
2340 3076 3.008049 AGAGCCAAAACACTATTCTCCGT 59.992 43.478 0.00 0.00 0.00 4.69
2341 3077 3.600388 AGAGCCAAAACACTATTCTCCG 58.400 45.455 0.00 0.00 0.00 4.63
2342 3078 3.619038 CGAGAGCCAAAACACTATTCTCC 59.381 47.826 0.00 0.00 0.00 3.71
2343 3079 3.619038 CCGAGAGCCAAAACACTATTCTC 59.381 47.826 0.00 0.00 0.00 2.87
2344 3080 3.600388 CCGAGAGCCAAAACACTATTCT 58.400 45.455 0.00 0.00 0.00 2.40
2345 3081 2.096013 GCCGAGAGCCAAAACACTATTC 59.904 50.000 0.00 0.00 34.35 1.75
2346 3082 2.084546 GCCGAGAGCCAAAACACTATT 58.915 47.619 0.00 0.00 34.35 1.73
2426 3162 9.396022 CCTCATATCCTTGTTTACTTGTACAAT 57.604 33.333 9.13 2.49 34.10 2.71
2436 3172 5.989168 CACATACGCCTCATATCCTTGTTTA 59.011 40.000 0.00 0.00 0.00 2.01
2447 3183 4.202245 ACTTTACACACATACGCCTCAT 57.798 40.909 0.00 0.00 0.00 2.90
2474 3210 3.001758 GTCGCATTTCAACGCATTTCATC 60.002 43.478 0.00 0.00 0.00 2.92
2482 3218 0.793861 TACAGGTCGCATTTCAACGC 59.206 50.000 0.00 0.00 0.00 4.84
2484 3220 3.889196 TTGTACAGGTCGCATTTCAAC 57.111 42.857 0.00 0.00 0.00 3.18
2579 3315 4.142687 ACGAAATACTTTGAAATGAGGGCG 60.143 41.667 0.00 0.00 0.00 6.13
2580 3316 5.310720 ACGAAATACTTTGAAATGAGGGC 57.689 39.130 0.00 0.00 0.00 5.19
2581 3317 7.023575 CAGAACGAAATACTTTGAAATGAGGG 58.976 38.462 0.00 0.00 0.00 4.30
2593 3329 9.659830 GTGTGTAAATTTTCAGAACGAAATACT 57.340 29.630 0.00 0.00 43.12 2.12
2712 3449 2.739996 CGAGCTCCATGGAGGCCTT 61.740 63.158 36.92 17.72 42.19 4.35
2714 3451 4.247380 CCGAGCTCCATGGAGGCC 62.247 72.222 36.92 23.97 42.19 5.19
2758 3496 4.466370 CCTCCGTCCCATAATATAAGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
2778 3516 5.571285 AGGGTTTTTCTGATTTACTCCCTC 58.429 41.667 0.00 0.00 38.37 4.30
2795 3533 3.112263 TGACATCCGGATTCTAGGGTTT 58.888 45.455 16.19 0.00 0.00 3.27
2809 3547 4.122776 AGCATCGTCTAACATTGACATCC 58.877 43.478 0.00 0.00 34.37 3.51
2826 3564 3.437049 GTCCAACAGTAGACCAAAGCATC 59.563 47.826 0.00 0.00 0.00 3.91
2926 7800 4.735369 AGATCGATGGGAAGATAGAGTGT 58.265 43.478 0.54 0.00 0.00 3.55
2964 7839 1.549203 TCCTGCAAATCAAAGAGGGC 58.451 50.000 0.00 0.00 0.00 5.19
2965 7840 4.813750 AAATCCTGCAAATCAAAGAGGG 57.186 40.909 0.00 0.00 0.00 4.30
2966 7841 5.786311 TGAAAATCCTGCAAATCAAAGAGG 58.214 37.500 0.00 0.00 0.00 3.69
2967 7842 7.718272 TTTGAAAATCCTGCAAATCAAAGAG 57.282 32.000 0.00 0.00 33.32 2.85
2968 7843 7.551974 TGTTTTGAAAATCCTGCAAATCAAAGA 59.448 29.630 0.00 0.00 37.86 2.52
2969 7844 7.641020 GTGTTTTGAAAATCCTGCAAATCAAAG 59.359 33.333 0.00 0.00 37.86 2.77
2970 7845 7.470900 GTGTTTTGAAAATCCTGCAAATCAAA 58.529 30.769 0.00 0.00 34.76 2.69
2971 7846 6.238049 CGTGTTTTGAAAATCCTGCAAATCAA 60.238 34.615 0.00 0.00 34.76 2.57
2972 7847 5.233902 CGTGTTTTGAAAATCCTGCAAATCA 59.766 36.000 0.00 0.00 32.27 2.57
2973 7848 5.333263 CCGTGTTTTGAAAATCCTGCAAATC 60.333 40.000 0.00 0.00 32.27 2.17
2974 7849 4.511082 CCGTGTTTTGAAAATCCTGCAAAT 59.489 37.500 0.00 0.00 32.27 2.32
2975 7850 3.868077 CCGTGTTTTGAAAATCCTGCAAA 59.132 39.130 0.00 0.00 0.00 3.68
2976 7851 3.452474 CCGTGTTTTGAAAATCCTGCAA 58.548 40.909 0.00 0.00 0.00 4.08
2977 7852 2.223923 CCCGTGTTTTGAAAATCCTGCA 60.224 45.455 0.00 0.00 0.00 4.41
2978 7853 2.035321 TCCCGTGTTTTGAAAATCCTGC 59.965 45.455 0.00 0.00 0.00 4.85
2979 7854 4.314740 TTCCCGTGTTTTGAAAATCCTG 57.685 40.909 0.00 0.00 0.00 3.86
2980 7855 5.185056 CCTATTCCCGTGTTTTGAAAATCCT 59.815 40.000 0.00 0.00 0.00 3.24
2981 7856 5.407502 CCTATTCCCGTGTTTTGAAAATCC 58.592 41.667 0.00 0.00 0.00 3.01
2982 7857 5.184287 TCCCTATTCCCGTGTTTTGAAAATC 59.816 40.000 0.00 0.00 0.00 2.17
2983 7858 5.081032 TCCCTATTCCCGTGTTTTGAAAAT 58.919 37.500 0.00 0.00 0.00 1.82
2984 7859 4.471548 TCCCTATTCCCGTGTTTTGAAAA 58.528 39.130 0.00 0.00 0.00 2.29
2985 7860 4.101645 TCCCTATTCCCGTGTTTTGAAA 57.898 40.909 0.00 0.00 0.00 2.69
2986 7861 3.791953 TCCCTATTCCCGTGTTTTGAA 57.208 42.857 0.00 0.00 0.00 2.69
2987 7862 3.791953 TTCCCTATTCCCGTGTTTTGA 57.208 42.857 0.00 0.00 0.00 2.69
2988 7863 4.857509 TTTTCCCTATTCCCGTGTTTTG 57.142 40.909 0.00 0.00 0.00 2.44
2989 7864 6.011481 TGTATTTTCCCTATTCCCGTGTTTT 58.989 36.000 0.00 0.00 0.00 2.43
2990 7865 5.572252 TGTATTTTCCCTATTCCCGTGTTT 58.428 37.500 0.00 0.00 0.00 2.83
2991 7866 5.182169 TGTATTTTCCCTATTCCCGTGTT 57.818 39.130 0.00 0.00 0.00 3.32
2992 7867 4.847990 TGTATTTTCCCTATTCCCGTGT 57.152 40.909 0.00 0.00 0.00 4.49
2993 7868 5.373222 TCATGTATTTTCCCTATTCCCGTG 58.627 41.667 0.00 0.00 0.00 4.94
2994 7869 5.640158 TCATGTATTTTCCCTATTCCCGT 57.360 39.130 0.00 0.00 0.00 5.28
2995 7870 7.230510 TCAAATCATGTATTTTCCCTATTCCCG 59.769 37.037 0.00 0.00 35.54 5.14
2996 7871 8.477419 TCAAATCATGTATTTTCCCTATTCCC 57.523 34.615 0.00 0.00 35.54 3.97
2997 7872 9.136323 ACTCAAATCATGTATTTTCCCTATTCC 57.864 33.333 0.00 0.00 35.54 3.01
2998 7873 9.956720 CACTCAAATCATGTATTTTCCCTATTC 57.043 33.333 0.00 0.00 35.54 1.75
2999 7874 8.917088 CCACTCAAATCATGTATTTTCCCTATT 58.083 33.333 0.00 0.00 35.54 1.73
3000 7875 7.014615 GCCACTCAAATCATGTATTTTCCCTAT 59.985 37.037 0.00 0.00 35.54 2.57
3001 7876 6.321181 GCCACTCAAATCATGTATTTTCCCTA 59.679 38.462 0.00 0.00 35.54 3.53
3002 7877 5.127682 GCCACTCAAATCATGTATTTTCCCT 59.872 40.000 0.00 0.00 35.54 4.20
3003 7878 5.105392 TGCCACTCAAATCATGTATTTTCCC 60.105 40.000 0.00 0.00 35.54 3.97
3004 7879 5.964758 TGCCACTCAAATCATGTATTTTCC 58.035 37.500 0.00 0.00 35.54 3.13
3005 7880 7.037438 ACATGCCACTCAAATCATGTATTTTC 58.963 34.615 5.07 0.00 45.17 2.29
3006 7881 6.938507 ACATGCCACTCAAATCATGTATTTT 58.061 32.000 5.07 0.00 45.17 1.82
3007 7882 6.406177 GGACATGCCACTCAAATCATGTATTT 60.406 38.462 6.68 0.00 46.45 1.40
3008 7883 5.068198 GGACATGCCACTCAAATCATGTATT 59.932 40.000 6.68 0.00 46.45 1.89
3009 7884 4.581824 GGACATGCCACTCAAATCATGTAT 59.418 41.667 6.68 0.00 46.45 2.29
3010 7885 3.947196 GGACATGCCACTCAAATCATGTA 59.053 43.478 6.68 0.00 46.45 2.29
3012 7887 2.756207 TGGACATGCCACTCAAATCATG 59.244 45.455 4.93 0.00 43.33 3.07
3013 7888 3.090210 TGGACATGCCACTCAAATCAT 57.910 42.857 4.93 0.00 43.33 2.45
3014 7889 2.583024 TGGACATGCCACTCAAATCA 57.417 45.000 4.93 0.00 43.33 2.57
3023 7898 1.355381 AGGATTCAAGTGGACATGCCA 59.645 47.619 4.93 4.93 46.96 4.92
3024 7899 2.134789 AGGATTCAAGTGGACATGCC 57.865 50.000 0.00 0.00 37.10 4.40


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

AutoCloner maintained by Alex Coulton.