Multiple sequence alignment - TraesCS6A01G207800

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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 TraesCS6A01G207800 chr6A 100.000 3194 0 0 1 3194 371328825 371332018 0.000000e+00 5899.0
1 TraesCS6A01G207800 chr6A 95.172 145 7 0 2517 2661 371331193 371331337 2.480000e-56 230.0
2 TraesCS6A01G207800 chr6A 95.172 145 7 0 2369 2513 371331341 371331485 2.480000e-56 230.0
3 TraesCS6A01G207800 chr6D 93.164 1887 105 10 1 1884 263964118 263962253 0.000000e+00 2748.0
4 TraesCS6A01G207800 chr6D 91.769 571 36 3 2582 3151 263956690 263956130 0.000000e+00 784.0
5 TraesCS6A01G207800 chr6D 93.130 393 13 5 1883 2270 263957074 263956691 5.980000e-157 564.0
6 TraesCS6A01G207800 chr6D 94.521 73 4 0 2439 2511 263956685 263956613 2.600000e-21 113.0
7 TraesCS6A01G207800 chr6B 89.401 1953 141 33 1 1929 405061222 405059312 0.000000e+00 2399.0
8 TraesCS6A01G207800 chr6B 91.585 511 41 2 2643 3151 405057312 405056802 0.000000e+00 704.0
9 TraesCS6A01G207800 chr6B 87.500 184 11 6 1981 2157 405059311 405059133 5.400000e-48 202.0
10 TraesCS6A01G207800 chr3D 92.357 157 10 2 2272 2426 87925996 87926152 4.150000e-54 222.0
11 TraesCS6A01G207800 chr3D 88.827 179 19 1 2277 2454 91710769 91710947 5.360000e-53 219.0
12 TraesCS6A01G207800 chr4B 92.810 153 9 2 2275 2426 532435002 532435153 1.490000e-53 220.0
13 TraesCS6A01G207800 chr4B 95.522 67 3 0 2517 2583 532435096 532435162 1.210000e-19 108.0
14 TraesCS6A01G207800 chr2D 90.798 163 15 0 2275 2437 296364209 296364047 5.360000e-53 219.0
15 TraesCS6A01G207800 chr2D 92.647 68 5 0 2517 2584 483261089 483261156 7.290000e-17 99.0
16 TraesCS6A01G207800 chr2B 90.798 163 15 0 2275 2437 366017519 366017681 5.360000e-53 219.0
17 TraesCS6A01G207800 chr2A 92.157 153 11 1 2275 2426 758586577 758586729 6.940000e-52 215.0
18 TraesCS6A01G207800 chr4D 89.759 166 16 1 2275 2439 87570615 87570450 8.980000e-51 211.0
19 TraesCS6A01G207800 chr5D 88.506 174 19 1 2273 2445 150835566 150835739 3.230000e-50 209.0
20 TraesCS6A01G207800 chr5D 95.522 67 3 0 2517 2583 244634334 244634400 1.210000e-19 108.0
21 TraesCS6A01G207800 chrUn 86.316 190 19 5 2259 2442 382102462 382102274 1.940000e-47 200.0
22 TraesCS6A01G207800 chr1A 98.413 63 1 0 996 1058 285504124 285504186 9.370000e-21 111.0
23 TraesCS6A01G207800 chr5A 95.522 67 3 0 2517 2583 320214339 320214405 1.210000e-19 108.0
24 TraesCS6A01G207800 chr5B 93.056 72 5 0 2517 2588 702740123 702740194 4.360000e-19 106.0
25 TraesCS6A01G207800 chr3B 92.857 70 5 0 2517 2586 713288959 713289028 5.640000e-18 102.0
26 TraesCS6A01G207800 chr1D 96.721 61 2 0 2517 2577 9267298 9267358 5.640000e-18 102.0
27 TraesCS6A01G207800 chr7D 89.474 76 8 0 2517 2592 565296568 565296493 2.620000e-16 97.1


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 TraesCS6A01G207800 chr6A 371328825 371332018 3193 False 2119.666667 5899 96.781333 1 3194 3 chr6A.!!$F1 3193
1 TraesCS6A01G207800 chr6D 263962253 263964118 1865 True 2748.000000 2748 93.164000 1 1884 1 chr6D.!!$R1 1883
2 TraesCS6A01G207800 chr6D 263956130 263957074 944 True 487.000000 784 93.140000 1883 3151 3 chr6D.!!$R2 1268
3 TraesCS6A01G207800 chr6B 405056802 405061222 4420 True 1101.666667 2399 89.495333 1 3151 3 chr6B.!!$R1 3150

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
577 580 0.108992 GTGTAGGAATCACGTCCGCA 60.109 55.0 0.0 0.0 43.03 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2500 3104 0.249073 ATATGTCCGAGTGCGAGCAC 60.249 55.0 19.45 19.45 46.5 4.4 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
169 171 0.393944 ATCTACGGAGGCACGTCTGA 60.394 55.000 10.45 10.59 45.08 3.27
174 176 1.812922 GGAGGCACGTCTGATGCTG 60.813 63.158 3.53 0.42 42.93 4.41
232 235 4.045469 GGAGGAGCCGACCCTTAA 57.955 61.111 0.00 0.00 33.36 1.85
252 255 3.083997 GTGGAGGTCGATGGCCCT 61.084 66.667 0.00 0.00 0.00 5.19
261 264 2.865598 CGATGGCCCTGAGAGCGAT 61.866 63.158 0.00 0.00 0.00 4.58
281 284 0.618458 GGCTATGACACCAAGGTCCA 59.382 55.000 0.00 0.00 36.97 4.02
334 337 2.165641 ACTTCGGCATCGTCAACATCTA 59.834 45.455 0.00 0.00 37.69 1.98
430 433 1.254570 GTGCTTAAATAGACGCGACCG 59.745 52.381 15.93 0.00 41.14 4.79
464 467 2.148446 AAGCTGGCTTCAATATGGCA 57.852 45.000 1.60 0.00 37.22 4.92
480 483 1.078848 GCACACCAGCTGGAGTAGG 60.079 63.158 39.19 25.06 36.88 3.18
513 516 1.347221 CGTCGACATTAAAGCGGCC 59.653 57.895 17.16 0.00 0.00 6.13
545 548 1.137825 CGGTCTTCTCGCTCTGACC 59.862 63.158 0.00 0.00 43.86 4.02
547 550 1.306642 GGTCTTCTCGCTCTGACCGA 61.307 60.000 0.00 0.00 39.39 4.69
576 579 2.662150 GTGTAGGAATCACGTCCGC 58.338 57.895 0.00 0.00 43.03 5.54
577 580 0.108992 GTGTAGGAATCACGTCCGCA 60.109 55.000 0.00 0.00 43.03 5.69
635 638 2.125832 CGCGCGGAGAGGGTTTTA 60.126 61.111 24.84 0.00 35.25 1.52
671 674 3.289834 AGGCGTGTACGTGTCGGT 61.290 61.111 0.00 0.00 42.22 4.69
695 698 1.135315 CAACGCCATCAAAGCTCCG 59.865 57.895 0.00 0.00 0.00 4.63
726 729 2.877786 TGTCTTGCTTGCAGAATTTCGA 59.122 40.909 0.00 0.00 0.00 3.71
742 746 2.828874 TCGAAAAACCAAACACGTCC 57.171 45.000 0.00 0.00 0.00 4.79
782 786 1.446099 TCGGATGACTTGCAGCGTC 60.446 57.895 10.33 10.33 32.46 5.19
783 787 2.456119 CGGATGACTTGCAGCGTCC 61.456 63.158 13.57 12.85 36.95 4.79
790 794 2.741985 TTGCAGCGTCCGGACATG 60.742 61.111 32.80 28.67 0.00 3.21
792 796 2.742372 GCAGCGTCCGGACATGTT 60.742 61.111 32.80 13.89 0.00 2.71
806 810 2.073816 ACATGTTGGTCCGAACGATTC 58.926 47.619 0.00 0.00 0.00 2.52
818 822 2.166007 GAACGATTCGCGGACATTTTG 58.834 47.619 6.13 0.00 46.49 2.44
819 823 1.434555 ACGATTCGCGGACATTTTGA 58.565 45.000 6.13 0.00 46.49 2.69
820 824 1.393539 ACGATTCGCGGACATTTTGAG 59.606 47.619 6.13 0.00 46.49 3.02
821 825 1.267532 CGATTCGCGGACATTTTGAGG 60.268 52.381 6.13 0.00 36.03 3.86
822 826 1.064060 GATTCGCGGACATTTTGAGGG 59.936 52.381 6.13 0.00 0.00 4.30
823 827 0.250553 TTCGCGGACATTTTGAGGGT 60.251 50.000 6.13 0.00 0.00 4.34
824 828 0.609151 TCGCGGACATTTTGAGGGTA 59.391 50.000 6.13 0.00 0.00 3.69
825 829 0.725117 CGCGGACATTTTGAGGGTAC 59.275 55.000 0.00 0.00 0.00 3.34
826 830 1.816074 GCGGACATTTTGAGGGTACA 58.184 50.000 0.00 0.00 0.00 2.90
829 833 3.343617 CGGACATTTTGAGGGTACATGT 58.656 45.455 2.69 2.69 0.00 3.21
830 834 3.756434 CGGACATTTTGAGGGTACATGTT 59.244 43.478 2.30 0.00 0.00 2.71
832 836 5.588648 CGGACATTTTGAGGGTACATGTTAT 59.411 40.000 2.30 0.00 0.00 1.89
834 838 7.042051 CGGACATTTTGAGGGTACATGTTATAG 60.042 40.741 2.30 0.00 0.00 1.31
876 880 2.882876 CGGGTAGACACGTCAGGG 59.117 66.667 0.00 0.00 38.11 4.45
900 904 2.707257 GGTCCCCGTATAGATTTTCCCA 59.293 50.000 0.00 0.00 0.00 4.37
929 933 3.678056 AACGCTTCCTCTACATGTTCA 57.322 42.857 2.30 0.00 0.00 3.18
980 984 2.723334 TAAGCACCAACCCCCTCCCT 62.723 60.000 0.00 0.00 0.00 4.20
1137 1141 0.917533 AGATCATCAGCAAGGCCACT 59.082 50.000 5.01 0.00 0.00 4.00
1161 1165 1.274728 CATAGCCCCAAGATCTCCTCG 59.725 57.143 0.00 0.00 0.00 4.63
1281 1285 5.769484 TCTACATGTACAGGTTAGCTAGC 57.231 43.478 19.42 6.62 0.00 3.42
1282 1286 5.446860 TCTACATGTACAGGTTAGCTAGCT 58.553 41.667 23.12 23.12 34.10 3.32
1283 1287 6.598503 TCTACATGTACAGGTTAGCTAGCTA 58.401 40.000 20.67 20.67 32.12 3.32
1284 1288 5.776173 ACATGTACAGGTTAGCTAGCTAG 57.224 43.478 23.03 16.84 32.12 3.42
1285 1289 5.446860 ACATGTACAGGTTAGCTAGCTAGA 58.553 41.667 25.15 12.45 32.12 2.43
1318 1322 2.559440 CTGCATCAAGAAGCTACCTCC 58.441 52.381 0.00 0.00 0.00 4.30
1444 1452 1.022735 GGTGCAGGCAGATCTTCATG 58.977 55.000 2.49 2.49 0.00 3.07
1559 1567 0.094216 CTTCGCGTTCTGATGTGCTG 59.906 55.000 5.77 0.00 0.00 4.41
1642 1657 4.908730 GCAAGAAGAAAAGAAAAGAGAGCG 59.091 41.667 0.00 0.00 0.00 5.03
1663 1678 6.002082 AGCGGTTTAAAGAATGGAGTTAAGT 58.998 36.000 0.00 0.00 0.00 2.24
1664 1679 7.163441 AGCGGTTTAAAGAATGGAGTTAAGTA 58.837 34.615 0.00 0.00 0.00 2.24
1665 1680 7.118825 AGCGGTTTAAAGAATGGAGTTAAGTAC 59.881 37.037 0.00 0.00 0.00 2.73
1757 1772 1.697982 ACCTAACGGATAAGATGGCCC 59.302 52.381 0.00 0.00 0.00 5.80
1891 1916 4.027540 GCGCGAAGATCAACTAGAACTTAC 60.028 45.833 12.10 0.00 39.21 2.34
1892 1917 5.333513 CGCGAAGATCAACTAGAACTTACT 58.666 41.667 0.00 0.00 39.21 2.24
1893 1918 5.228220 CGCGAAGATCAACTAGAACTTACTG 59.772 44.000 0.00 0.00 39.21 2.74
2008 2033 2.507484 CTGTGGATGTGGTTGTGTGAT 58.493 47.619 0.00 0.00 0.00 3.06
2009 2034 3.673902 CTGTGGATGTGGTTGTGTGATA 58.326 45.455 0.00 0.00 0.00 2.15
2010 2035 3.407698 TGTGGATGTGGTTGTGTGATAC 58.592 45.455 0.00 0.00 0.00 2.24
2031 2056 3.198068 CGTACAAGGATGGAGTGATTGG 58.802 50.000 0.00 0.00 0.00 3.16
2035 2060 4.047166 ACAAGGATGGAGTGATTGGGATA 58.953 43.478 0.00 0.00 0.00 2.59
2036 2061 4.103785 ACAAGGATGGAGTGATTGGGATAG 59.896 45.833 0.00 0.00 0.00 2.08
2118 2149 2.622942 AGCCGGCATTAATTGGTGTATG 59.377 45.455 31.54 0.00 0.00 2.39
2128 2159 7.063308 GCATTAATTGGTGTATGTGGTTTGAAG 59.937 37.037 0.00 0.00 0.00 3.02
2213 2543 5.310451 TGTTGGACCGTAAGCTTTTCTAAT 58.690 37.500 3.20 0.00 0.00 1.73
2257 2861 2.647299 TCCCTCTTTCTATTGGGCAACA 59.353 45.455 0.00 0.00 39.49 3.33
2258 2862 3.075283 TCCCTCTTTCTATTGGGCAACAA 59.925 43.478 0.00 0.00 44.54 2.83
2272 2876 8.588290 ATTGGGCAACAAAAATAGTATGTCTA 57.412 30.769 0.00 0.00 43.46 2.59
2275 2879 9.688091 TGGGCAACAAAAATAGTATGTCTATTA 57.312 29.630 5.74 0.00 42.61 0.98
2276 2880 9.946165 GGGCAACAAAAATAGTATGTCTATTAC 57.054 33.333 5.74 0.00 42.61 1.89
2285 2889 8.937207 AATAGTATGTCTATTACTCCCTTCGT 57.063 34.615 4.04 0.00 44.58 3.85
2286 2890 8.937207 ATAGTATGTCTATTACTCCCTTCGTT 57.063 34.615 0.00 0.00 36.05 3.85
2287 2891 7.274603 AGTATGTCTATTACTCCCTTCGTTC 57.725 40.000 0.00 0.00 0.00 3.95
2288 2892 4.996788 TGTCTATTACTCCCTTCGTTCC 57.003 45.455 0.00 0.00 0.00 3.62
2289 2893 4.607239 TGTCTATTACTCCCTTCGTTCCT 58.393 43.478 0.00 0.00 0.00 3.36
2290 2894 5.759059 TGTCTATTACTCCCTTCGTTCCTA 58.241 41.667 0.00 0.00 0.00 2.94
2291 2895 6.189859 TGTCTATTACTCCCTTCGTTCCTAA 58.810 40.000 0.00 0.00 0.00 2.69
2292 2896 6.664816 TGTCTATTACTCCCTTCGTTCCTAAA 59.335 38.462 0.00 0.00 0.00 1.85
2293 2897 7.343833 TGTCTATTACTCCCTTCGTTCCTAAAT 59.656 37.037 0.00 0.00 0.00 1.40
2294 2898 8.854117 GTCTATTACTCCCTTCGTTCCTAAATA 58.146 37.037 0.00 0.00 0.00 1.40
2295 2899 9.597681 TCTATTACTCCCTTCGTTCCTAAATAT 57.402 33.333 0.00 0.00 0.00 1.28
2299 2903 7.672122 ACTCCCTTCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2300 2904 7.724287 ACTCCCTTCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2301 2905 7.564292 ACTCCCTTCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2302 2906 8.315220 TCCCTTCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
2303 2907 8.765517 TCCCTTCGTTCCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
2304 2908 9.392259 CCCTTCGTTCCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
2334 2938 9.924650 GATTTTAATATGGACTACATACGGAGT 57.075 33.333 0.00 0.00 44.41 3.85
2352 2956 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
2353 2957 7.556844 ACGGAGTAAAATGAGTGAATCTACAT 58.443 34.615 0.00 0.00 41.94 2.29
2354 2958 8.041323 ACGGAGTAAAATGAGTGAATCTACATT 58.959 33.333 0.00 0.00 41.94 2.71
2355 2959 8.883731 CGGAGTAAAATGAGTGAATCTACATTT 58.116 33.333 0.00 0.00 42.25 2.32
2379 2983 9.772973 TTTTAAACTATGTCTATATGCATCCGT 57.227 29.630 0.19 0.00 0.00 4.69
2383 2987 8.526667 AACTATGTCTATATGCATCCGTATCT 57.473 34.615 0.19 0.00 0.00 1.98
2384 2988 9.628500 AACTATGTCTATATGCATCCGTATCTA 57.372 33.333 0.19 0.00 0.00 1.98
2385 2989 9.278978 ACTATGTCTATATGCATCCGTATCTAG 57.721 37.037 0.19 1.51 0.00 2.43
2386 2990 9.278978 CTATGTCTATATGCATCCGTATCTAGT 57.721 37.037 0.19 0.00 0.00 2.57
2387 2991 7.555306 TGTCTATATGCATCCGTATCTAGTC 57.445 40.000 0.19 0.00 0.00 2.59
2388 2992 6.542735 TGTCTATATGCATCCGTATCTAGTCC 59.457 42.308 0.19 0.00 0.00 3.85
2389 2993 6.542735 GTCTATATGCATCCGTATCTAGTCCA 59.457 42.308 0.19 0.00 0.00 4.02
2390 2994 7.229707 GTCTATATGCATCCGTATCTAGTCCAT 59.770 40.741 0.19 0.00 0.00 3.41
2391 2995 8.437575 TCTATATGCATCCGTATCTAGTCCATA 58.562 37.037 0.19 0.00 0.00 2.74
2392 2996 9.237187 CTATATGCATCCGTATCTAGTCCATAT 57.763 37.037 0.19 0.00 0.00 1.78
2393 2997 6.798427 ATGCATCCGTATCTAGTCCATATT 57.202 37.500 0.00 0.00 0.00 1.28
2394 2998 5.965922 TGCATCCGTATCTAGTCCATATTG 58.034 41.667 0.00 0.00 0.00 1.90
2395 2999 5.714806 TGCATCCGTATCTAGTCCATATTGA 59.285 40.000 0.00 0.00 0.00 2.57
2396 3000 6.210584 TGCATCCGTATCTAGTCCATATTGAA 59.789 38.462 0.00 0.00 0.00 2.69
2397 3001 7.097192 GCATCCGTATCTAGTCCATATTGAAA 58.903 38.462 0.00 0.00 0.00 2.69
2398 3002 7.766278 GCATCCGTATCTAGTCCATATTGAAAT 59.234 37.037 0.00 0.00 0.00 2.17
2481 3085 7.280205 AGAGAAACAACAAGTTCGAAACACTAT 59.720 33.333 0.00 0.00 40.26 2.12
2489 3093 6.710744 ACAAGTTCGAAACACTATCAGGAAAT 59.289 34.615 0.00 0.00 0.00 2.17
2499 3103 9.715121 AAACACTATCAGGAAATACGTTCTAAA 57.285 29.630 0.00 0.00 36.40 1.85
2500 3104 8.928270 ACACTATCAGGAAATACGTTCTAAAG 57.072 34.615 0.00 0.00 36.40 1.85
2501 3105 8.529476 ACACTATCAGGAAATACGTTCTAAAGT 58.471 33.333 0.00 0.00 36.40 2.66
2502 3106 8.808529 CACTATCAGGAAATACGTTCTAAAGTG 58.191 37.037 0.00 0.00 36.40 3.16
2503 3107 6.663944 ATCAGGAAATACGTTCTAAAGTGC 57.336 37.500 0.00 0.00 36.40 4.40
2504 3108 5.790593 TCAGGAAATACGTTCTAAAGTGCT 58.209 37.500 0.00 0.00 36.40 4.40
2506 3110 4.863131 AGGAAATACGTTCTAAAGTGCTCG 59.137 41.667 0.00 0.00 36.40 5.03
2507 3111 4.492085 GGAAATACGTTCTAAAGTGCTCGC 60.492 45.833 0.00 0.00 36.40 5.03
2508 3112 2.710220 TACGTTCTAAAGTGCTCGCA 57.290 45.000 0.00 0.00 0.00 5.10
2509 3113 1.137513 ACGTTCTAAAGTGCTCGCAC 58.862 50.000 13.86 13.86 46.50 5.34
2510 3114 8.028278 GAAATACGTTCTAAAGTGCTCGCACT 62.028 42.308 18.15 18.15 44.55 4.40
2517 3121 2.125912 GTGCTCGCACTCGGACAT 60.126 61.111 14.38 0.00 43.12 3.06
2518 3122 1.138883 GTGCTCGCACTCGGACATA 59.861 57.895 14.38 0.00 43.12 2.29
2519 3123 0.249073 GTGCTCGCACTCGGACATAT 60.249 55.000 14.38 0.00 43.12 1.78
2520 3124 1.001706 GTGCTCGCACTCGGACATATA 60.002 52.381 14.38 0.00 43.12 0.86
2521 3125 1.001706 TGCTCGCACTCGGACATATAC 60.002 52.381 0.00 0.00 36.13 1.47
2522 3126 1.001706 GCTCGCACTCGGACATATACA 60.002 52.381 0.00 0.00 36.13 2.29
2524 3128 3.493272 CTCGCACTCGGACATATACATC 58.507 50.000 0.00 0.00 36.13 3.06
2536 3140 7.261829 GGACATATACATCCGTATCTAGTCC 57.738 44.000 11.75 11.75 41.30 3.85
2537 3141 6.827251 GGACATATACATCCGTATCTAGTCCA 59.173 42.308 17.32 0.00 43.84 4.02
2538 3142 7.502895 GGACATATACATCCGTATCTAGTCCAT 59.497 40.741 17.32 0.00 43.84 3.41
2539 3143 9.557061 GACATATACATCCGTATCTAGTCCATA 57.443 37.037 0.00 0.00 39.17 2.74
2544 3148 7.776618 ACATCCGTATCTAGTCCATATTGAA 57.223 36.000 0.00 0.00 0.00 2.69
2545 3149 8.190326 ACATCCGTATCTAGTCCATATTGAAA 57.810 34.615 0.00 0.00 0.00 2.69
2546 3150 8.816894 ACATCCGTATCTAGTCCATATTGAAAT 58.183 33.333 0.00 0.00 0.00 2.17
2580 3184 9.819267 AAGACTTATATTTAGGAACGAAGGAAG 57.181 33.333 0.00 0.00 0.00 3.46
2581 3185 8.979534 AGACTTATATTTAGGAACGAAGGAAGT 58.020 33.333 0.00 0.00 0.00 3.01
2586 3190 8.943909 ATATTTAGGAACGAAGGAAGTACAAG 57.056 34.615 0.00 0.00 0.00 3.16
2587 3191 6.409524 TTTAGGAACGAAGGAAGTACAAGA 57.590 37.500 0.00 0.00 0.00 3.02
2588 3192 6.600882 TTAGGAACGAAGGAAGTACAAGAT 57.399 37.500 0.00 0.00 0.00 2.40
2589 3193 7.707624 TTAGGAACGAAGGAAGTACAAGATA 57.292 36.000 0.00 0.00 0.00 1.98
2590 3194 6.600882 AGGAACGAAGGAAGTACAAGATAA 57.399 37.500 0.00 0.00 0.00 1.75
2591 3195 7.001099 AGGAACGAAGGAAGTACAAGATAAA 57.999 36.000 0.00 0.00 0.00 1.40
2592 3196 7.097834 AGGAACGAAGGAAGTACAAGATAAAG 58.902 38.462 0.00 0.00 0.00 1.85
2593 3197 6.313164 GGAACGAAGGAAGTACAAGATAAAGG 59.687 42.308 0.00 0.00 0.00 3.11
2595 3199 6.766429 ACGAAGGAAGTACAAGATAAAGGTT 58.234 36.000 0.00 0.00 0.00 3.50
2596 3200 7.899973 ACGAAGGAAGTACAAGATAAAGGTTA 58.100 34.615 0.00 0.00 0.00 2.85
2597 3201 8.537858 ACGAAGGAAGTACAAGATAAAGGTTAT 58.462 33.333 0.00 0.00 0.00 1.89
2599 3203 9.668497 GAAGGAAGTACAAGATAAAGGTTATGT 57.332 33.333 0.00 0.00 0.00 2.29
2600 3204 9.449719 AAGGAAGTACAAGATAAAGGTTATGTG 57.550 33.333 0.00 0.00 0.00 3.21
2601 3205 8.822805 AGGAAGTACAAGATAAAGGTTATGTGA 58.177 33.333 0.00 0.00 0.00 3.58
2602 3206 9.444600 GGAAGTACAAGATAAAGGTTATGTGAA 57.555 33.333 0.00 0.00 0.00 3.18
2608 3212 9.793259 ACAAGATAAAGGTTATGTGAAAGAGAA 57.207 29.630 0.00 0.00 0.00 2.87
2611 3215 9.793259 AGATAAAGGTTATGTGAAAGAGAAACA 57.207 29.630 0.00 0.00 0.00 2.83
2614 3218 7.639113 AAGGTTATGTGAAAGAGAAACAACA 57.361 32.000 0.00 0.00 0.00 3.33
2616 3220 7.707104 AGGTTATGTGAAAGAGAAACAACAAG 58.293 34.615 0.00 0.00 0.00 3.16
2633 3237 6.795399 ACAACAAGTTTGAAACACTATCAGG 58.205 36.000 11.02 0.00 0.00 3.86
2635 3239 7.122055 ACAACAAGTTTGAAACACTATCAGGAA 59.878 33.333 11.02 0.00 0.00 3.36
2636 3240 7.639113 ACAAGTTTGAAACACTATCAGGAAA 57.361 32.000 11.02 0.00 0.00 3.13
2638 3242 7.122055 ACAAGTTTGAAACACTATCAGGAAACA 59.878 33.333 11.02 0.00 0.00 2.83
2639 3243 7.027778 AGTTTGAAACACTATCAGGAAACAC 57.972 36.000 11.02 0.00 0.00 3.32
2640 3244 5.666969 TTGAAACACTATCAGGAAACACG 57.333 39.130 0.00 0.00 0.00 4.49
2641 3245 4.699637 TGAAACACTATCAGGAAACACGT 58.300 39.130 0.00 0.00 0.00 4.49
2646 4192 6.092955 ACACTATCAGGAAACACGTTCTAA 57.907 37.500 0.00 0.00 36.40 2.10
2667 4213 1.067416 TGCTCGCACTCGAAACACT 59.933 52.632 0.00 0.00 44.98 3.55
2683 4229 1.004292 ACACTTGCTACGCGACAAAAC 60.004 47.619 15.93 0.00 0.00 2.43
2686 4232 1.508808 TTGCTACGCGACAAAACCCC 61.509 55.000 15.93 0.00 0.00 4.95
2701 4248 2.203070 CCCGCTACCACTGCCATC 60.203 66.667 0.00 0.00 0.00 3.51
2717 4264 2.426522 CCATCATTACAGGCGGTATGG 58.573 52.381 0.00 0.62 0.00 2.74
2774 4321 4.858850 ACCAAGCTCCATCAACATTATCA 58.141 39.130 0.00 0.00 0.00 2.15
2791 4338 2.906897 ACAAGCACCGCACCCAAG 60.907 61.111 0.00 0.00 0.00 3.61
2811 4358 1.079819 GCACACGAGCCAGCTCTAA 60.080 57.895 17.06 0.00 40.69 2.10
2864 4411 3.701040 ACAGTCCACTTTCTTGTGCAAAT 59.299 39.130 0.00 0.00 36.68 2.32
2876 4423 7.459795 TTCTTGTGCAAATATGTCCAATACA 57.540 32.000 0.00 0.00 43.86 2.29
2928 4475 3.340928 TCAAAGGATGAGCACATGTCAG 58.659 45.455 0.00 0.00 36.82 3.51
2983 4531 6.284459 TCCATAAAATCCAACAAACAACCAC 58.716 36.000 0.00 0.00 0.00 4.16
2999 4547 0.967662 CCACCAATGACAATGCCACA 59.032 50.000 0.00 0.00 0.00 4.17
3106 4654 8.263181 TGTGGAGTACAAGACAAGGAGTTTGT 62.263 42.308 0.00 0.00 43.85 2.83
3124 4672 1.680314 TGCATATTGGGCGCAACCA 60.680 52.632 19.39 10.13 42.05 3.67
3170 4718 4.454717 CGCAAAACGCCCCGTAGC 62.455 66.667 0.00 0.00 39.99 3.58
3171 4719 4.111016 GCAAAACGCCCCGTAGCC 62.111 66.667 0.00 0.00 39.99 3.93
3172 4720 2.670251 CAAAACGCCCCGTAGCCA 60.670 61.111 0.00 0.00 39.99 4.75
3173 4721 2.043980 CAAAACGCCCCGTAGCCAT 61.044 57.895 0.00 0.00 39.99 4.40
3174 4722 1.303806 AAAACGCCCCGTAGCCATT 60.304 52.632 0.00 0.00 39.99 3.16
3175 4723 0.896479 AAAACGCCCCGTAGCCATTT 60.896 50.000 0.00 0.00 39.99 2.32
3176 4724 0.896479 AAACGCCCCGTAGCCATTTT 60.896 50.000 0.00 0.00 39.99 1.82
3177 4725 0.035247 AACGCCCCGTAGCCATTTTA 60.035 50.000 0.00 0.00 39.99 1.52
3178 4726 0.745486 ACGCCCCGTAGCCATTTTAC 60.745 55.000 0.00 0.00 38.73 2.01
3179 4727 0.745128 CGCCCCGTAGCCATTTTACA 60.745 55.000 0.00 0.00 0.00 2.41
3180 4728 1.465794 GCCCCGTAGCCATTTTACAA 58.534 50.000 0.00 0.00 0.00 2.41
3181 4729 1.133598 GCCCCGTAGCCATTTTACAAC 59.866 52.381 0.00 0.00 0.00 3.32
3182 4730 2.438411 CCCCGTAGCCATTTTACAACA 58.562 47.619 0.00 0.00 0.00 3.33
3183 4731 2.820787 CCCCGTAGCCATTTTACAACAA 59.179 45.455 0.00 0.00 0.00 2.83
3184 4732 3.256136 CCCCGTAGCCATTTTACAACAAA 59.744 43.478 0.00 0.00 0.00 2.83
3185 4733 4.262079 CCCCGTAGCCATTTTACAACAAAA 60.262 41.667 0.00 0.00 0.00 2.44
3186 4734 5.290386 CCCGTAGCCATTTTACAACAAAAA 58.710 37.500 0.00 0.00 33.15 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.063649 GACAGAATCGGCGTCGCTA 59.936 57.895 18.11 6.21 36.13 4.26
36 37 1.300620 CCACCGCGTCAAGACAGAA 60.301 57.895 4.92 0.00 0.00 3.02
63 64 0.970937 TCAAGGAGGATTCGGCGTCT 60.971 55.000 6.85 0.33 0.00 4.18
72 73 3.077556 AGCCGCGTCAAGGAGGAT 61.078 61.111 4.92 0.00 0.00 3.24
169 171 4.521062 GGCGACGAGGAGCAGCAT 62.521 66.667 0.00 0.00 34.54 3.79
252 255 1.067669 GTGTCATAGCCATCGCTCTCA 59.932 52.381 0.00 0.00 43.95 3.27
261 264 0.618458 GGACCTTGGTGTCATAGCCA 59.382 55.000 0.00 0.00 36.97 4.75
266 269 0.326264 GCTCTGGACCTTGGTGTCAT 59.674 55.000 0.00 0.00 36.97 3.06
334 337 0.394488 TCCTCTCGGTCTTCGCTCAT 60.394 55.000 0.00 0.00 39.05 2.90
430 433 2.322830 GCTTCCCGTCCGTTTGTCC 61.323 63.158 0.00 0.00 0.00 4.02
459 462 1.200760 TACTCCAGCTGGTGTGCCAT 61.201 55.000 38.41 21.16 45.05 4.40
464 467 0.838122 AAGCCTACTCCAGCTGGTGT 60.838 55.000 35.42 35.42 43.53 4.16
472 475 1.137086 GCAATCGAGAAGCCTACTCCA 59.863 52.381 0.00 0.00 0.00 3.86
480 483 2.125106 ACGGGGCAATCGAGAAGC 60.125 61.111 0.00 0.00 0.00 3.86
494 497 1.347221 GCCGCTTTAATGTCGACGG 59.653 57.895 11.62 6.77 43.37 4.79
547 550 4.870426 GTGATTCCTACACGACATTGATGT 59.130 41.667 0.00 0.00 45.16 3.06
562 565 1.079819 CAGTGCGGACGTGATTCCT 60.080 57.895 0.00 0.00 32.88 3.36
566 569 1.374252 GTTCCAGTGCGGACGTGAT 60.374 57.895 0.00 0.00 46.36 3.06
576 579 1.669115 CGGTCAGCCTGTTCCAGTG 60.669 63.158 8.74 0.00 0.00 3.66
577 580 2.743718 CGGTCAGCCTGTTCCAGT 59.256 61.111 8.74 0.00 0.00 4.00
586 589 3.113745 CATTCATGCCGGTCAGCC 58.886 61.111 1.90 0.00 0.00 4.85
619 622 1.814169 CCTAAAACCCTCTCCGCGC 60.814 63.158 0.00 0.00 0.00 6.86
671 674 0.893270 CTTTGATGGCGTTGGGACCA 60.893 55.000 0.00 0.00 41.06 4.02
695 698 2.989166 GCAAGCAAGACACAAATTAGGC 59.011 45.455 0.00 0.00 0.00 3.93
726 729 4.037089 GGTCTATGGACGTGTTTGGTTTTT 59.963 41.667 2.84 0.00 42.97 1.94
761 765 1.690283 CGCTGCAAGTCATCCGACAG 61.690 60.000 0.00 0.00 45.23 3.51
762 766 1.737735 CGCTGCAAGTCATCCGACA 60.738 57.895 0.00 0.00 45.23 4.35
765 769 2.456119 GGACGCTGCAAGTCATCCG 61.456 63.158 19.54 3.57 40.20 4.18
801 805 1.267532 CCTCAAAATGTCCGCGAATCG 60.268 52.381 8.23 0.00 38.08 3.34
806 810 0.725117 GTACCCTCAAAATGTCCGCG 59.275 55.000 0.00 0.00 0.00 6.46
810 814 8.958119 TCTATAACATGTACCCTCAAAATGTC 57.042 34.615 0.00 0.00 31.29 3.06
818 822 5.246429 CCTCCCTTCTATAACATGTACCCTC 59.754 48.000 0.00 0.00 0.00 4.30
819 823 5.155905 CCTCCCTTCTATAACATGTACCCT 58.844 45.833 0.00 0.00 0.00 4.34
820 824 4.262938 GCCTCCCTTCTATAACATGTACCC 60.263 50.000 0.00 0.00 0.00 3.69
821 825 4.262938 GGCCTCCCTTCTATAACATGTACC 60.263 50.000 0.00 0.00 0.00 3.34
822 826 4.560919 CGGCCTCCCTTCTATAACATGTAC 60.561 50.000 0.00 0.00 0.00 2.90
823 827 3.576982 CGGCCTCCCTTCTATAACATGTA 59.423 47.826 0.00 0.00 0.00 2.29
824 828 2.368875 CGGCCTCCCTTCTATAACATGT 59.631 50.000 0.00 0.00 0.00 3.21
825 829 2.368875 ACGGCCTCCCTTCTATAACATG 59.631 50.000 0.00 0.00 0.00 3.21
826 830 2.690840 ACGGCCTCCCTTCTATAACAT 58.309 47.619 0.00 0.00 0.00 2.71
829 833 2.754465 TCAACGGCCTCCCTTCTATAA 58.246 47.619 0.00 0.00 0.00 0.98
830 834 2.464796 TCAACGGCCTCCCTTCTATA 57.535 50.000 0.00 0.00 0.00 1.31
832 836 1.278127 CTTTCAACGGCCTCCCTTCTA 59.722 52.381 0.00 0.00 0.00 2.10
834 838 0.036306 TCTTTCAACGGCCTCCCTTC 59.964 55.000 0.00 0.00 0.00 3.46
929 933 0.250295 AGTGTGTGTGCTGCGGTATT 60.250 50.000 0.00 0.00 0.00 1.89
980 984 4.150627 CGAGTGCGAGATCTTTTCTTTCAA 59.849 41.667 0.00 0.00 40.82 2.69
1137 1141 2.614259 GAGATCTTGGGGCTATGGAGA 58.386 52.381 0.00 0.00 0.00 3.71
1318 1322 6.975197 AGATCGGTTGTGCATCGATTATATAG 59.025 38.462 14.82 0.00 42.65 1.31
1548 1556 0.321919 GTTGGAGGCAGCACATCAGA 60.322 55.000 0.00 0.00 0.00 3.27
1559 1567 1.363807 GTTGCTTGGTGTTGGAGGC 59.636 57.895 0.00 0.00 0.00 4.70
1587 1602 2.995466 ACGTTACGTGCTAGCACTAA 57.005 45.000 37.42 29.82 44.16 2.24
1663 1678 2.090760 TGTCACATAACGGCGGTAGTA 58.909 47.619 11.54 0.00 0.00 1.82
1664 1679 0.889994 TGTCACATAACGGCGGTAGT 59.110 50.000 11.54 6.03 0.00 2.73
1665 1680 1.556564 CTGTCACATAACGGCGGTAG 58.443 55.000 11.54 5.35 0.00 3.18
1822 1839 8.544622 AGAGAGGAGAGACGTGATATGATAATA 58.455 37.037 0.00 0.00 0.00 0.98
1823 1840 7.402054 AGAGAGGAGAGACGTGATATGATAAT 58.598 38.462 0.00 0.00 0.00 1.28
1891 1916 5.922053 TCATCCTCTCACCATGATTAACAG 58.078 41.667 0.00 0.00 0.00 3.16
1892 1917 5.685861 GCTCATCCTCTCACCATGATTAACA 60.686 44.000 0.00 0.00 0.00 2.41
1893 1918 4.754114 GCTCATCCTCTCACCATGATTAAC 59.246 45.833 0.00 0.00 0.00 2.01
2008 2033 4.142026 CCAATCACTCCATCCTTGTACGTA 60.142 45.833 0.00 0.00 0.00 3.57
2009 2034 3.369471 CCAATCACTCCATCCTTGTACGT 60.369 47.826 0.00 0.00 0.00 3.57
2010 2035 3.198068 CCAATCACTCCATCCTTGTACG 58.802 50.000 0.00 0.00 0.00 3.67
2031 2056 4.125703 CAGGCATGTCAAACTCTCTATCC 58.874 47.826 0.00 0.00 0.00 2.59
2035 2060 1.612726 GCCAGGCATGTCAAACTCTCT 60.613 52.381 6.55 0.00 0.00 3.10
2036 2061 0.807496 GCCAGGCATGTCAAACTCTC 59.193 55.000 6.55 0.00 0.00 3.20
2118 2149 5.705609 TCTTATCCAAAGCTTCAAACCAC 57.294 39.130 0.00 0.00 0.00 4.16
2128 2159 7.575332 TTAACGCAAAATTCTTATCCAAAGC 57.425 32.000 0.00 0.00 0.00 3.51
2275 2879 7.564292 AGACTTATATTTAGGAACGAAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
2276 2880 7.953752 AGACTTATATTTAGGAACGAAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
2277 2881 7.909485 AGACTTATATTTAGGAACGAAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
2278 2882 8.959705 AAAGACTTATATTTAGGAACGAAGGG 57.040 34.615 0.00 0.00 0.00 3.95
2308 2912 9.924650 ACTCCGTATGTAGTCCATATTAAAATC 57.075 33.333 0.00 0.00 38.29 2.17
2314 2918 9.706691 CATTTTACTCCGTATGTAGTCCATATT 57.293 33.333 0.00 0.00 38.29 1.28
2315 2919 9.085645 TCATTTTACTCCGTATGTAGTCCATAT 57.914 33.333 0.00 0.00 38.29 1.78
2316 2920 8.467963 TCATTTTACTCCGTATGTAGTCCATA 57.532 34.615 0.00 0.00 34.86 2.74
2317 2921 7.069578 ACTCATTTTACTCCGTATGTAGTCCAT 59.930 37.037 0.00 0.00 37.58 3.41
2318 2922 6.379133 ACTCATTTTACTCCGTATGTAGTCCA 59.621 38.462 0.00 0.00 0.00 4.02
2319 2923 6.696148 CACTCATTTTACTCCGTATGTAGTCC 59.304 42.308 0.00 0.00 0.00 3.85
2320 2924 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2321 2925 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2322 2926 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2323 2927 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
2324 2928 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
2325 2929 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
2326 2930 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
2327 2931 8.058667 TGTAGATTCACTCATTTTACTCCGTA 57.941 34.615 0.00 0.00 0.00 4.02
2328 2932 6.931838 TGTAGATTCACTCATTTTACTCCGT 58.068 36.000 0.00 0.00 0.00 4.69
2329 2933 8.425577 AATGTAGATTCACTCATTTTACTCCG 57.574 34.615 0.00 0.00 0.00 4.63
2353 2957 9.772973 ACGGATGCATATAGACATAGTTTAAAA 57.227 29.630 0.00 0.00 0.00 1.52
2357 2961 8.972127 AGATACGGATGCATATAGACATAGTTT 58.028 33.333 0.00 0.00 0.00 2.66
2358 2962 8.526667 AGATACGGATGCATATAGACATAGTT 57.473 34.615 0.00 0.00 0.00 2.24
2359 2963 9.278978 CTAGATACGGATGCATATAGACATAGT 57.721 37.037 0.00 0.00 0.00 2.12
2360 2964 9.278978 ACTAGATACGGATGCATATAGACATAG 57.721 37.037 0.00 0.93 0.00 2.23
2361 2965 9.274206 GACTAGATACGGATGCATATAGACATA 57.726 37.037 0.00 0.00 0.00 2.29
2362 2966 7.229707 GGACTAGATACGGATGCATATAGACAT 59.770 40.741 0.00 0.00 0.00 3.06
2363 2967 6.542735 GGACTAGATACGGATGCATATAGACA 59.457 42.308 0.00 0.00 0.00 3.41
2364 2968 6.542735 TGGACTAGATACGGATGCATATAGAC 59.457 42.308 0.00 0.00 0.00 2.59
2365 2969 6.659824 TGGACTAGATACGGATGCATATAGA 58.340 40.000 0.00 0.00 0.00 1.98
2366 2970 6.944234 TGGACTAGATACGGATGCATATAG 57.056 41.667 0.00 0.00 0.00 1.31
2367 2971 9.588096 AATATGGACTAGATACGGATGCATATA 57.412 33.333 0.00 0.00 34.42 0.86
2368 2972 8.363390 CAATATGGACTAGATACGGATGCATAT 58.637 37.037 0.00 0.00 36.29 1.78
2369 2973 7.559897 TCAATATGGACTAGATACGGATGCATA 59.440 37.037 0.00 0.00 0.00 3.14
2370 2974 6.381133 TCAATATGGACTAGATACGGATGCAT 59.619 38.462 0.00 0.00 0.00 3.96
2371 2975 5.714806 TCAATATGGACTAGATACGGATGCA 59.285 40.000 0.00 0.00 0.00 3.96
2372 2976 6.208988 TCAATATGGACTAGATACGGATGC 57.791 41.667 0.00 0.00 0.00 3.91
2444 3048 8.050778 ACTTGTTGTTTCTCTTTCACATAACA 57.949 30.769 0.00 0.00 0.00 2.41
2447 3051 7.279090 TCGAACTTGTTGTTTCTCTTTCACATA 59.721 33.333 0.00 0.00 39.30 2.29
2481 3085 5.790593 AGCACTTTAGAACGTATTTCCTGA 58.209 37.500 0.00 0.00 34.32 3.86
2489 3093 2.322161 GTGCGAGCACTTTAGAACGTA 58.678 47.619 19.74 0.00 43.12 3.57
2500 3104 0.249073 ATATGTCCGAGTGCGAGCAC 60.249 55.000 19.45 19.45 46.50 4.40
2501 3105 1.001706 GTATATGTCCGAGTGCGAGCA 60.002 52.381 0.00 0.00 40.82 4.26
2502 3106 1.001706 TGTATATGTCCGAGTGCGAGC 60.002 52.381 0.00 0.00 40.82 5.03
2503 3107 3.493272 GATGTATATGTCCGAGTGCGAG 58.507 50.000 0.00 0.00 40.82 5.03
2504 3108 2.228103 GGATGTATATGTCCGAGTGCGA 59.772 50.000 0.00 0.00 40.82 5.10
2513 3117 7.860918 TGGACTAGATACGGATGTATATGTC 57.139 40.000 0.00 0.00 41.37 3.06
2518 3122 9.475620 TTCAATATGGACTAGATACGGATGTAT 57.524 33.333 0.00 0.00 43.97 2.29
2519 3123 8.873186 TTCAATATGGACTAGATACGGATGTA 57.127 34.615 0.00 0.00 34.45 2.29
2520 3124 7.776618 TTCAATATGGACTAGATACGGATGT 57.223 36.000 0.00 0.00 0.00 3.06
2561 3165 8.755977 TCTTGTACTTCCTTCGTTCCTAAATAT 58.244 33.333 0.00 0.00 0.00 1.28
2562 3166 8.125978 TCTTGTACTTCCTTCGTTCCTAAATA 57.874 34.615 0.00 0.00 0.00 1.40
2563 3167 7.001099 TCTTGTACTTCCTTCGTTCCTAAAT 57.999 36.000 0.00 0.00 0.00 1.40
2564 3168 6.409524 TCTTGTACTTCCTTCGTTCCTAAA 57.590 37.500 0.00 0.00 0.00 1.85
2565 3169 6.600882 ATCTTGTACTTCCTTCGTTCCTAA 57.399 37.500 0.00 0.00 0.00 2.69
2566 3170 7.707624 TTATCTTGTACTTCCTTCGTTCCTA 57.292 36.000 0.00 0.00 0.00 2.94
2567 3171 6.600882 TTATCTTGTACTTCCTTCGTTCCT 57.399 37.500 0.00 0.00 0.00 3.36
2568 3172 6.313164 CCTTTATCTTGTACTTCCTTCGTTCC 59.687 42.308 0.00 0.00 0.00 3.62
2569 3173 6.872547 ACCTTTATCTTGTACTTCCTTCGTTC 59.127 38.462 0.00 0.00 0.00 3.95
2570 3174 6.766429 ACCTTTATCTTGTACTTCCTTCGTT 58.234 36.000 0.00 0.00 0.00 3.85
2571 3175 6.356186 ACCTTTATCTTGTACTTCCTTCGT 57.644 37.500 0.00 0.00 0.00 3.85
2572 3176 8.818057 CATAACCTTTATCTTGTACTTCCTTCG 58.182 37.037 0.00 0.00 0.00 3.79
2573 3177 9.668497 ACATAACCTTTATCTTGTACTTCCTTC 57.332 33.333 0.00 0.00 0.00 3.46
2574 3178 9.449719 CACATAACCTTTATCTTGTACTTCCTT 57.550 33.333 0.00 0.00 0.00 3.36
2575 3179 8.822805 TCACATAACCTTTATCTTGTACTTCCT 58.177 33.333 0.00 0.00 0.00 3.36
2576 3180 9.444600 TTCACATAACCTTTATCTTGTACTTCC 57.555 33.333 0.00 0.00 0.00 3.46
2582 3186 9.793259 TTCTCTTTCACATAACCTTTATCTTGT 57.207 29.630 0.00 0.00 0.00 3.16
2585 3189 9.793259 TGTTTCTCTTTCACATAACCTTTATCT 57.207 29.630 0.00 0.00 0.00 1.98
2588 3192 9.179909 TGTTGTTTCTCTTTCACATAACCTTTA 57.820 29.630 0.00 0.00 0.00 1.85
2589 3193 8.062065 TGTTGTTTCTCTTTCACATAACCTTT 57.938 30.769 0.00 0.00 0.00 3.11
2590 3194 7.639113 TGTTGTTTCTCTTTCACATAACCTT 57.361 32.000 0.00 0.00 0.00 3.50
2591 3195 7.339466 ACTTGTTGTTTCTCTTTCACATAACCT 59.661 33.333 0.00 0.00 0.00 3.50
2592 3196 7.480810 ACTTGTTGTTTCTCTTTCACATAACC 58.519 34.615 0.00 0.00 0.00 2.85
2593 3197 8.911247 AACTTGTTGTTTCTCTTTCACATAAC 57.089 30.769 0.00 0.00 34.84 1.89
2595 3199 8.735315 TCAAACTTGTTGTTTCTCTTTCACATA 58.265 29.630 0.00 0.00 46.11 2.29
2596 3200 7.601856 TCAAACTTGTTGTTTCTCTTTCACAT 58.398 30.769 0.00 0.00 46.11 3.21
2597 3201 6.976088 TCAAACTTGTTGTTTCTCTTTCACA 58.024 32.000 0.00 0.00 46.11 3.58
2599 3203 7.923344 TGTTTCAAACTTGTTGTTTCTCTTTCA 59.077 29.630 1.10 0.00 46.11 2.69
2600 3204 8.214472 GTGTTTCAAACTTGTTGTTTCTCTTTC 58.786 33.333 1.10 0.00 46.11 2.62
2601 3205 7.926018 AGTGTTTCAAACTTGTTGTTTCTCTTT 59.074 29.630 1.10 0.00 46.11 2.52
2602 3206 7.433680 AGTGTTTCAAACTTGTTGTTTCTCTT 58.566 30.769 1.10 0.00 46.11 2.85
2604 3208 8.911247 ATAGTGTTTCAAACTTGTTGTTTCTC 57.089 30.769 1.10 0.00 46.11 2.87
2605 3209 8.519526 TGATAGTGTTTCAAACTTGTTGTTTCT 58.480 29.630 1.10 0.00 46.11 2.52
2606 3210 8.682128 TGATAGTGTTTCAAACTTGTTGTTTC 57.318 30.769 1.10 0.00 46.11 2.78
2608 3212 7.122055 TCCTGATAGTGTTTCAAACTTGTTGTT 59.878 33.333 1.10 0.00 41.29 2.83
2609 3213 6.601613 TCCTGATAGTGTTTCAAACTTGTTGT 59.398 34.615 1.10 0.00 0.00 3.32
2610 3214 7.026631 TCCTGATAGTGTTTCAAACTTGTTG 57.973 36.000 1.10 0.00 0.00 3.33
2611 3215 7.639113 TTCCTGATAGTGTTTCAAACTTGTT 57.361 32.000 1.10 0.00 0.00 2.83
2612 3216 7.122055 TGTTTCCTGATAGTGTTTCAAACTTGT 59.878 33.333 1.10 0.00 0.00 3.16
2614 3218 7.480810 GTGTTTCCTGATAGTGTTTCAAACTT 58.519 34.615 1.10 0.00 0.00 2.66
2616 3220 5.907391 CGTGTTTCCTGATAGTGTTTCAAAC 59.093 40.000 0.00 0.00 0.00 2.93
2621 3225 5.365619 AGAACGTGTTTCCTGATAGTGTTT 58.634 37.500 0.00 0.00 34.32 2.83
2622 3226 4.957296 AGAACGTGTTTCCTGATAGTGTT 58.043 39.130 0.00 0.00 34.32 3.32
2623 3227 4.602340 AGAACGTGTTTCCTGATAGTGT 57.398 40.909 0.00 0.00 34.32 3.55
2625 3229 6.645415 CACTTTAGAACGTGTTTCCTGATAGT 59.355 38.462 0.00 0.00 34.32 2.12
2626 3230 6.401153 GCACTTTAGAACGTGTTTCCTGATAG 60.401 42.308 0.00 0.00 34.32 2.08
2627 3231 5.407387 GCACTTTAGAACGTGTTTCCTGATA 59.593 40.000 0.00 0.00 34.32 2.15
2628 3232 4.213482 GCACTTTAGAACGTGTTTCCTGAT 59.787 41.667 0.00 0.00 34.32 2.90
2629 3233 3.558418 GCACTTTAGAACGTGTTTCCTGA 59.442 43.478 0.00 0.00 34.32 3.86
2630 3234 3.560068 AGCACTTTAGAACGTGTTTCCTG 59.440 43.478 0.00 0.00 34.32 3.86
2631 3235 3.805207 AGCACTTTAGAACGTGTTTCCT 58.195 40.909 0.00 0.00 34.32 3.36
2632 3236 3.362693 CGAGCACTTTAGAACGTGTTTCC 60.363 47.826 0.00 0.00 34.32 3.13
2633 3237 3.784488 CGAGCACTTTAGAACGTGTTTC 58.216 45.455 0.00 0.00 33.78 2.78
2635 3239 1.525619 GCGAGCACTTTAGAACGTGTT 59.474 47.619 0.00 0.00 33.78 3.32
2636 3240 1.137513 GCGAGCACTTTAGAACGTGT 58.862 50.000 0.00 0.00 33.78 4.49
2638 3242 1.137513 GTGCGAGCACTTTAGAACGT 58.862 50.000 19.74 0.00 43.12 3.99
2639 3243 3.929095 GTGCGAGCACTTTAGAACG 57.071 52.632 19.74 0.00 43.12 3.95
2683 4229 3.757248 GATGGCAGTGGTAGCGGGG 62.757 68.421 0.00 0.00 0.00 5.73
2686 4232 1.867233 GTAATGATGGCAGTGGTAGCG 59.133 52.381 0.00 0.00 0.00 4.26
2701 4248 3.804036 TCTTTCCATACCGCCTGTAATG 58.196 45.455 0.00 0.00 31.94 1.90
2774 4321 2.906897 CTTGGGTGCGGTGCTTGT 60.907 61.111 0.00 0.00 0.00 3.16
2791 4338 2.492449 TAGAGCTGGCTCGTGTGCAC 62.492 60.000 10.75 10.75 46.90 4.57
2811 4358 4.593206 TGAAGTGGTTGTCATAGAAGGTCT 59.407 41.667 0.00 0.00 0.00 3.85
2864 4411 3.055021 TCGTTGCCCTTGTATTGGACATA 60.055 43.478 0.00 0.00 38.07 2.29
2876 4423 1.812571 CTATGCTTGTTCGTTGCCCTT 59.187 47.619 0.00 0.00 0.00 3.95
2928 4475 6.926826 CCAAACAAGGTTACTTTTTATCACCC 59.073 38.462 0.00 0.00 33.81 4.61
2983 4531 1.826096 TGGATGTGGCATTGTCATTGG 59.174 47.619 0.00 0.00 0.00 3.16
2999 4547 1.152963 GTTGCTATGCCCCGTGGAT 60.153 57.895 0.00 0.00 0.00 3.41
3106 4654 1.680314 TGGTTGCGCCCAATATGCA 60.680 52.632 4.18 0.00 36.72 3.96
3114 4662 0.679960 AATCTAAGGTGGTTGCGCCC 60.680 55.000 4.18 0.00 36.04 6.13
3154 4702 4.111016 GGCTACGGGGCGTTTTGC 62.111 66.667 0.00 0.00 41.54 3.68
3155 4703 1.591504 AATGGCTACGGGGCGTTTTG 61.592 55.000 5.99 0.00 45.62 2.44
3156 4704 1.303806 AATGGCTACGGGGCGTTTT 60.304 52.632 5.99 0.00 45.62 2.43
3157 4705 2.353573 AATGGCTACGGGGCGTTT 59.646 55.556 5.99 0.00 45.62 3.60
3159 4707 0.745486 GTAAAATGGCTACGGGGCGT 60.745 55.000 0.00 0.00 44.35 5.68
3160 4708 0.745128 TGTAAAATGGCTACGGGGCG 60.745 55.000 0.00 0.00 44.11 6.13
3161 4709 1.133598 GTTGTAAAATGGCTACGGGGC 59.866 52.381 0.00 0.00 41.27 5.80
3162 4710 2.438411 TGTTGTAAAATGGCTACGGGG 58.562 47.619 0.00 0.00 0.00 5.73
3163 4711 4.506886 TTTGTTGTAAAATGGCTACGGG 57.493 40.909 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.