Multiple sequence alignment - TraesCS1D01G315600

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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 TraesCS1D01G315600 chr1D 100.000 6418 0 0 1 6418 410737992 410744409 0.000000e+00 11852.0
1 TraesCS1D01G315600 chr1D 94.030 134 8 0 6180 6313 158110375 158110242 3.030000e-48 204.0
2 TraesCS1D01G315600 chr1A 92.461 6155 263 83 32 6072 506997583 507003650 0.000000e+00 8610.0
3 TraesCS1D01G315600 chr1A 86.408 103 5 4 6311 6405 507003728 507003829 3.170000e-18 104.0
4 TraesCS1D01G315600 chr1B 91.378 6182 304 80 150 6180 553553032 553559135 0.000000e+00 8251.0
5 TraesCS1D01G315600 chr7D 88.999 1518 109 25 4366 5853 370516628 370518117 0.000000e+00 1825.0
6 TraesCS1D01G315600 chr7D 94.776 134 5 2 6180 6313 80042197 80042066 2.350000e-49 207.0
7 TraesCS1D01G315600 chr4B 84.507 355 31 10 1031 1382 8269944 8269611 4.800000e-86 329.0
8 TraesCS1D01G315600 chr4B 85.570 298 22 8 1088 1382 8121753 8121474 6.290000e-75 292.0
9 TraesCS1D01G315600 chr4B 87.356 261 20 4 866 1116 613179468 613179725 2.930000e-73 287.0
10 TraesCS1D01G315600 chr4B 86.973 261 18 6 866 1116 601913091 601913345 4.900000e-71 279.0
11 TraesCS1D01G315600 chr4B 84.211 285 24 8 1101 1382 8216758 8216492 2.300000e-64 257.0
12 TraesCS1D01G315600 chr4B 83.860 285 25 8 1101 1382 8252088 8251822 1.070000e-62 252.0
13 TraesCS1D01G315600 chr4B 83.509 285 26 10 1101 1382 8225221 8224955 4.970000e-61 246.0
14 TraesCS1D01G315600 chr4B 83.509 285 26 8 1101 1382 8243172 8242906 4.970000e-61 246.0
15 TraesCS1D01G315600 chr7A 84.375 320 34 7 3039 3350 49508998 49509309 3.760000e-77 300.0
16 TraesCS1D01G315600 chrUn 88.123 261 15 7 866 1116 49052742 49052488 4.870000e-76 296.0
17 TraesCS1D01G315600 chrUn 87.739 261 16 6 866 1116 49108228 49107974 2.260000e-74 291.0
18 TraesCS1D01G315600 chrUn 83.509 285 26 9 1101 1382 295769520 295769786 4.970000e-61 246.0
19 TraesCS1D01G315600 chr6A 88.123 261 15 5 866 1116 558130485 558130739 4.870000e-76 296.0
20 TraesCS1D01G315600 chr3B 87.739 261 16 6 866 1116 673562882 673562628 2.260000e-74 291.0
21 TraesCS1D01G315600 chr5D 86.022 279 20 11 855 1122 102639769 102639499 1.360000e-71 281.0
22 TraesCS1D01G315600 chr5A 84.333 300 26 7 1083 1379 442582805 442583086 2.280000e-69 274.0
23 TraesCS1D01G315600 chr2A 81.868 364 31 17 1026 1382 31354095 31354430 2.280000e-69 274.0
24 TraesCS1D01G315600 chr6D 94.656 131 7 0 6180 6310 78510794 78510664 3.030000e-48 204.0
25 TraesCS1D01G315600 chr6D 94.656 131 7 0 6180 6310 267059850 267059980 3.030000e-48 204.0
26 TraesCS1D01G315600 chr6B 94.656 131 7 0 6180 6310 713761911 713762041 3.030000e-48 204.0
27 TraesCS1D01G315600 chr3D 94.697 132 6 1 6180 6310 598116970 598116839 3.030000e-48 204.0
28 TraesCS1D01G315600 chr3D 93.893 131 8 0 6180 6310 105130749 105130879 1.410000e-46 198.0
29 TraesCS1D01G315600 chr3D 93.893 131 8 0 6180 6310 105132208 105132338 1.410000e-46 198.0
30 TraesCS1D01G315600 chr3D 93.893 131 8 0 6180 6310 272911676 272911806 1.410000e-46 198.0
31 TraesCS1D01G315600 chr3D 85.897 78 8 1 2794 2871 595276376 595276302 5.330000e-11 80.5
32 TraesCS1D01G315600 chr3D 81.915 94 13 3 2777 2868 595711164 595711255 6.900000e-10 76.8


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 TraesCS1D01G315600 chr1D 410737992 410744409 6417 False 11852 11852 100.0000 1 6418 1 chr1D.!!$F1 6417
1 TraesCS1D01G315600 chr1A 506997583 507003829 6246 False 4357 8610 89.4345 32 6405 2 chr1A.!!$F1 6373
2 TraesCS1D01G315600 chr1B 553553032 553559135 6103 False 8251 8251 91.3780 150 6180 1 chr1B.!!$F1 6030
3 TraesCS1D01G315600 chr7D 370516628 370518117 1489 False 1825 1825 88.9990 4366 5853 1 chr7D.!!$F1 1487

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
19 20 0.178961 GACAGAAAACCAGGGGGCTT 60.179 55.000 0.00 0.0 37.9 4.35 F
606 637 0.179012 GACCCCAAAAACCTCACCGA 60.179 55.000 0.00 0.0 0.0 4.69 F
1728 1821 0.454600 TTCGTATCCTGGCTCGTGTC 59.545 55.000 0.00 0.0 0.0 3.67 F
2595 2705 0.473886 ACCCCTCTGTTGCTGTAGGT 60.474 55.000 0.00 0.0 0.0 3.08 F
2979 3104 1.200020 GCCACTGTGTGTTCCATAAGC 59.800 52.381 7.08 0.0 0.0 3.09 F
4183 4318 1.744522 GGACGGACTAGTTCTCCTGAC 59.255 57.143 10.75 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 1589 0.178935 GAGAGGAGGAGGAGATGGGG 60.179 65.000 0.00 0.00 0.00 4.96 R
2085 2190 0.466124 ATTCAGAAGGTCGGGCTAGC 59.534 55.000 6.04 6.04 0.00 3.42 R
2873 2989 0.531200 GACTACAGGAGACAACGGGG 59.469 60.000 0.00 0.00 0.00 5.73 R
4315 4450 1.204146 TAGTCTTGGCAGGGGATGAC 58.796 55.000 0.00 0.00 37.50 3.06 R
4396 4531 2.345244 CGCAGTGGAGAAGTGGCT 59.655 61.111 0.00 0.00 0.00 4.75 R
5811 6007 0.524862 TGGGTTCGAGTTAGACGAGC 59.475 55.000 0.00 0.00 40.72 5.03 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
17 18 4.097218 GACAGAAAACCAGGGGGC 57.903 61.111 0.00 0.00 37.90 5.80
18 19 1.460699 GACAGAAAACCAGGGGGCT 59.539 57.895 0.00 0.00 37.90 5.19
19 20 0.178961 GACAGAAAACCAGGGGGCTT 60.179 55.000 0.00 0.00 37.90 4.35
20 21 0.264657 ACAGAAAACCAGGGGGCTTT 59.735 50.000 0.00 0.00 35.20 3.51
21 22 1.343985 ACAGAAAACCAGGGGGCTTTT 60.344 47.619 0.00 0.00 32.69 2.27
22 23 1.344438 CAGAAAACCAGGGGGCTTTTC 59.656 52.381 5.27 5.27 40.55 2.29
23 24 1.062505 AGAAAACCAGGGGGCTTTTCA 60.063 47.619 13.04 0.00 41.50 2.69
24 25 1.344438 GAAAACCAGGGGGCTTTTCAG 59.656 52.381 7.74 0.00 40.29 3.02
25 26 0.560688 AAACCAGGGGGCTTTTCAGA 59.439 50.000 0.00 0.00 37.90 3.27
26 27 0.560688 AACCAGGGGGCTTTTCAGAA 59.439 50.000 0.00 0.00 37.90 3.02
27 28 0.786435 ACCAGGGGGCTTTTCAGAAT 59.214 50.000 0.00 0.00 37.90 2.40
28 29 1.272704 ACCAGGGGGCTTTTCAGAATC 60.273 52.381 0.00 0.00 37.90 2.52
29 30 1.006400 CCAGGGGGCTTTTCAGAATCT 59.994 52.381 0.00 0.00 0.00 2.40
30 31 2.097825 CAGGGGGCTTTTCAGAATCTG 58.902 52.381 3.38 3.38 0.00 2.90
70 72 2.553770 CGACGCACGCATGGAAAA 59.446 55.556 0.00 0.00 34.51 2.29
99 101 2.674796 GAGGCTCACTCGGTTGTATT 57.325 50.000 10.25 0.00 36.29 1.89
100 102 2.271800 GAGGCTCACTCGGTTGTATTG 58.728 52.381 10.25 0.00 36.29 1.90
101 103 1.623811 AGGCTCACTCGGTTGTATTGT 59.376 47.619 0.00 0.00 0.00 2.71
147 149 0.601057 TCGATCGAAGCACTGGTGAA 59.399 50.000 16.99 0.00 0.00 3.18
159 161 3.810373 CACTGGTGAACACGAATTTAGC 58.190 45.455 0.00 0.00 0.00 3.09
171 173 2.478539 CGAATTTAGCTTCCCTTGCAGC 60.479 50.000 0.00 0.00 36.16 5.25
193 195 6.039493 CAGCAAATCAGAAGAGAAATATGGCT 59.961 38.462 0.00 0.00 0.00 4.75
211 213 5.105567 TGGCTTCTAAATACGGGAAATCA 57.894 39.130 0.00 0.00 0.00 2.57
228 230 5.296780 GGAAATCACGGAGAGAAATGCATTA 59.703 40.000 13.39 0.00 0.00 1.90
268 270 4.034510 GTGATAACATTTCAAGCGAGGAGG 59.965 45.833 0.00 0.00 0.00 4.30
269 271 2.568623 AACATTTCAAGCGAGGAGGT 57.431 45.000 0.00 0.00 0.00 3.85
286 288 3.193479 GGAGGTTTTTGCTGATAACCCAG 59.807 47.826 0.00 0.00 41.77 4.45
291 293 2.902343 GCTGATAACCCAGGCCGC 60.902 66.667 0.00 0.00 34.82 6.53
362 372 7.883391 TTCTTCTCTTCCAATACTAGATCGT 57.117 36.000 0.00 0.00 0.00 3.73
381 391 3.073678 CGTCAATCACTTGGATGGAACA 58.926 45.455 0.00 0.00 37.70 3.18
402 412 2.345124 AGGCGAATAGTCCTCGTACT 57.655 50.000 0.00 0.00 38.57 2.73
403 413 2.220313 AGGCGAATAGTCCTCGTACTC 58.780 52.381 0.00 0.00 38.57 2.59
404 414 1.070041 GGCGAATAGTCCTCGTACTCG 60.070 57.143 0.00 0.00 38.57 4.18
405 415 1.596727 GCGAATAGTCCTCGTACTCGT 59.403 52.381 0.00 0.00 38.57 4.18
406 416 2.797156 GCGAATAGTCCTCGTACTCGTA 59.203 50.000 0.00 0.00 38.57 3.43
439 449 0.232303 GCCGAAGAACACAACTCACG 59.768 55.000 0.00 0.00 0.00 4.35
467 477 0.666274 TTAGTCAACGCAGCCGAGTG 60.666 55.000 0.00 0.00 38.29 3.51
606 637 0.179012 GACCCCAAAAACCTCACCGA 60.179 55.000 0.00 0.00 0.00 4.69
683 717 5.577945 TCTTTATTTTTCCTACCGTACGCAG 59.422 40.000 10.49 8.89 0.00 5.18
685 719 0.968405 TTTTCCTACCGTACGCAGGT 59.032 50.000 24.85 14.95 45.28 4.00
705 739 6.410038 CAGGTCGCAAGTTAAAATTTTGTTG 58.590 36.000 13.76 13.83 39.48 3.33
765 815 2.335011 GCGCACCAACCCAAAGTC 59.665 61.111 0.30 0.00 0.00 3.01
1333 1409 3.917760 GATGCGGGGGAGGACGAG 61.918 72.222 0.00 0.00 0.00 4.18
1343 1425 1.820481 GAGGACGAGGACGAGGAGG 60.820 68.421 0.00 0.00 42.66 4.30
1426 1508 3.735029 GAGGACGCCGACGACAGT 61.735 66.667 0.00 0.00 43.93 3.55
1716 1809 0.989890 GTGGTGTCGTGCTTCGTATC 59.010 55.000 2.39 0.00 40.80 2.24
1725 1818 1.320344 TGCTTCGTATCCTGGCTCGT 61.320 55.000 0.00 0.00 0.00 4.18
1728 1821 0.454600 TTCGTATCCTGGCTCGTGTC 59.545 55.000 0.00 0.00 0.00 3.67
1942 2047 2.124736 GCCGCATACCCAAGCTGA 60.125 61.111 0.00 0.00 0.00 4.26
2006 2111 2.096980 CGTCGTGGTTCAGCTATCTACA 59.903 50.000 0.00 0.00 0.00 2.74
2012 2117 3.706594 TGGTTCAGCTATCTACAGGAAGG 59.293 47.826 0.00 0.00 0.00 3.46
2085 2190 3.437795 CCCGGCTCTTTGCTGCTG 61.438 66.667 0.00 0.00 46.34 4.41
2092 2197 1.375098 CTCTTTGCTGCTGCTAGCCC 61.375 60.000 13.29 3.74 41.51 5.19
2109 2214 1.811941 GCCCGACCTTCTGAATGATCC 60.812 57.143 0.00 0.00 0.00 3.36
2268 2378 3.408634 TCCCGTGGATTTTCTCAGTTTC 58.591 45.455 0.00 0.00 0.00 2.78
2384 2494 1.270839 TGCTTCTACTGTTGCTGTCCC 60.271 52.381 0.00 0.00 0.00 4.46
2510 2620 6.535963 TCAGCTGTCTCTATGAATCTTTCA 57.464 37.500 14.67 0.00 45.01 2.69
2531 2641 2.683968 TCGGTACTGAAATGCACAGAC 58.316 47.619 9.59 4.04 38.55 3.51
2595 2705 0.473886 ACCCCTCTGTTGCTGTAGGT 60.474 55.000 0.00 0.00 0.00 3.08
2638 2748 7.882791 TCAGGAAAGCATTTTGTTCACTAGATA 59.117 33.333 0.00 0.00 39.27 1.98
2639 2749 8.680903 CAGGAAAGCATTTTGTTCACTAGATAT 58.319 33.333 0.00 0.00 39.27 1.63
2640 2750 9.905713 AGGAAAGCATTTTGTTCACTAGATATA 57.094 29.630 0.00 0.00 39.27 0.86
2745 2861 7.589958 TTTTGTTGACCACCTATTGTATGTT 57.410 32.000 0.00 0.00 0.00 2.71
2767 2883 8.012957 TGTTGTTTGGATTTTATTGGTACTGT 57.987 30.769 0.00 0.00 0.00 3.55
2804 2920 7.599621 CAGCTGGTAAATTGAATCAAATCAACA 59.400 33.333 5.57 0.00 41.78 3.33
2805 2921 8.149647 AGCTGGTAAATTGAATCAAATCAACAA 58.850 29.630 0.00 0.00 41.78 2.83
2850 2966 3.358111 TTCCAGTGTTCAAGTTGTCCA 57.642 42.857 2.11 0.00 0.00 4.02
2873 2989 5.405935 AAGGTGCTAATGGTTCCATTTTC 57.594 39.130 20.02 13.17 37.73 2.29
2882 2998 1.271379 GGTTCCATTTTCCCCGTTGTC 59.729 52.381 0.00 0.00 0.00 3.18
2979 3104 1.200020 GCCACTGTGTGTTCCATAAGC 59.800 52.381 7.08 0.00 0.00 3.09
3024 3149 5.118286 GCCAATTGGTAATGGAAGATTTGG 58.882 41.667 25.19 0.00 39.12 3.28
3222 3352 4.621068 TGACAGCATTGCTTGTAATAGC 57.379 40.909 8.83 0.00 36.40 2.97
3228 3358 5.967674 CAGCATTGCTTGTAATAGCTGTAAC 59.032 40.000 8.83 0.00 41.76 2.50
3238 3368 5.815740 TGTAATAGCTGTAACTAAAGCAGGC 59.184 40.000 0.00 0.00 42.06 4.85
3246 3376 4.394920 TGTAACTAAAGCAGGCTAATGTGC 59.605 41.667 0.00 0.00 40.17 4.57
3271 3401 9.282247 GCTCTGTACATCTTTTTGTGATTATTG 57.718 33.333 0.00 0.00 0.00 1.90
3278 3408 8.450964 ACATCTTTTTGTGATTATTGACTACCG 58.549 33.333 0.00 0.00 0.00 4.02
3288 3418 7.277981 GTGATTATTGACTACCGATGTTGAAGT 59.722 37.037 0.00 0.00 0.00 3.01
3360 3490 2.012673 GGACTGTCCACATCATCAAGC 58.987 52.381 21.70 0.00 36.28 4.01
3780 3910 9.277783 GCTTTATATCCAGACATTGACAAGTAT 57.722 33.333 0.00 0.00 0.00 2.12
3820 3950 3.788227 ATTTCTCCAGTTGCCACACTA 57.212 42.857 0.00 0.00 0.00 2.74
3871 4001 2.554370 TTGTTGTAGTACCTGCCACC 57.446 50.000 0.00 0.00 0.00 4.61
3908 4038 3.994392 TGATACGTCAGGAACTTGCTTTC 59.006 43.478 0.00 0.00 34.60 2.62
3949 4079 6.145338 TCGCAACAAAAAGGTTGGTTTATA 57.855 33.333 7.99 0.00 46.36 0.98
4183 4318 1.744522 GGACGGACTAGTTCTCCTGAC 59.255 57.143 10.75 0.00 0.00 3.51
4327 4462 4.489771 CCACGGTCATCCCCTGCC 62.490 72.222 0.00 0.00 0.00 4.85
4396 4531 3.116746 TGGGAGGTGCCAGAGATATCTTA 60.117 47.826 6.70 0.00 38.95 2.10
4534 4670 2.225091 TGCCAAGTTGGTGGATCATCTT 60.225 45.455 22.85 0.00 41.65 2.40
4628 4767 7.871853 TCCTGTTGCAAAAATAAGTAGAGTTC 58.128 34.615 0.00 0.00 0.00 3.01
4741 4880 2.159503 TGGTGTGTTTTGTAGTGTTGCG 60.160 45.455 0.00 0.00 0.00 4.85
4775 4914 2.019249 ACATCAGCACATGCACATACC 58.981 47.619 6.64 0.00 45.16 2.73
4779 4918 0.394762 AGCACATGCACATACCTGGG 60.395 55.000 6.64 0.00 45.16 4.45
4908 5049 1.203052 CCGCTTGATGGACAAAGCATT 59.797 47.619 8.01 0.00 38.08 3.56
5012 5167 5.586643 TGCTGTTTGTAATGTGACACAACTA 59.413 36.000 13.23 4.57 34.52 2.24
5014 5169 7.442666 TGCTGTTTGTAATGTGACACAACTATA 59.557 33.333 13.23 3.14 34.52 1.31
5058 5213 0.460459 GCGAAGACTCTGCTTACCCC 60.460 60.000 0.00 0.00 0.00 4.95
5101 5260 1.739562 GCTCTTCAGCTGTCACGGG 60.740 63.158 14.67 1.83 43.09 5.28
5180 5339 3.865929 AAGACACCAGCGCAGACGG 62.866 63.158 11.47 6.93 40.57 4.79
5241 5400 3.679980 TCAAGGAAGAGAATTCGCTTTCG 59.320 43.478 22.92 11.23 36.53 3.46
5362 5521 6.461640 TCAGCATCCTAATGATCTGTATGTG 58.538 40.000 0.00 0.00 34.61 3.21
5411 5570 2.061773 CTGTACTCCGTGAAAGCACAG 58.938 52.381 0.00 0.00 45.41 3.66
5451 5614 2.903357 GCACCAGCCAGCTAGCTA 59.097 61.111 18.86 0.00 42.61 3.32
5452 5615 1.221840 GCACCAGCCAGCTAGCTAA 59.778 57.895 18.86 0.00 42.61 3.09
5453 5616 1.092345 GCACCAGCCAGCTAGCTAAC 61.092 60.000 18.86 12.52 42.61 2.34
5454 5617 0.539051 CACCAGCCAGCTAGCTAACT 59.461 55.000 18.86 14.77 42.61 2.24
5498 5673 0.247736 GGATGGATCGCCGCTAATCT 59.752 55.000 3.49 0.00 36.79 2.40
5499 5674 1.338200 GGATGGATCGCCGCTAATCTT 60.338 52.381 3.49 0.00 36.79 2.40
5550 5725 7.746034 GCCGTGAAAACATGTACATATATCATG 59.254 37.037 8.32 14.35 42.86 3.07
5666 5846 5.187967 AGTGGTTCATTGGTTGGTTAAAACA 59.812 36.000 0.00 0.00 32.06 2.83
5670 5850 7.928706 TGGTTCATTGGTTGGTTAAAACATAAG 59.071 33.333 0.00 0.00 34.73 1.73
5671 5851 7.095397 GGTTCATTGGTTGGTTAAAACATAAGC 60.095 37.037 0.00 0.84 34.73 3.09
5694 5877 3.081329 GACTAGTGGTAGTCGGATTGC 57.919 52.381 0.00 0.00 44.50 3.56
5725 5910 7.759433 CAGTGTAAAACAGGTCAGACAAAATTT 59.241 33.333 2.17 1.46 0.00 1.82
5726 5911 8.962679 AGTGTAAAACAGGTCAGACAAAATTTA 58.037 29.630 2.17 0.55 0.00 1.40
5787 5983 2.100216 GTATTTGGTGGCGCTGCG 59.900 61.111 19.17 19.17 0.00 5.18
5811 6007 1.401905 GCAGCGGTAATTCTTCTTGGG 59.598 52.381 0.00 0.00 0.00 4.12
5857 6065 2.165030 GGAGTGAATGTGAATTGGCCAG 59.835 50.000 5.11 0.00 0.00 4.85
5906 6115 1.302993 GCCAATACACACCCACGGT 60.303 57.895 0.00 0.00 35.62 4.83
5924 6140 3.429141 CGCACAGAAGCCAGCCTG 61.429 66.667 0.00 0.00 36.53 4.85
6054 6276 3.071479 TGGTCATAAAGTTGTCTTCGCC 58.929 45.455 0.00 0.00 32.90 5.54
6076 6298 2.589442 GTCGTTGTTGACCGCCCA 60.589 61.111 0.00 0.00 32.61 5.36
6077 6299 2.181521 GTCGTTGTTGACCGCCCAA 61.182 57.895 0.00 0.00 32.61 4.12
6078 6300 1.890041 TCGTTGTTGACCGCCCAAG 60.890 57.895 0.00 0.00 0.00 3.61
6079 6301 1.890041 CGTTGTTGACCGCCCAAGA 60.890 57.895 0.00 0.00 0.00 3.02
6173 6395 4.208686 GCTAGCTCGTGACGGGGG 62.209 72.222 7.10 0.00 0.00 5.40
6182 6404 4.000620 TGACGGGGGTCCAGGCTA 62.001 66.667 0.00 0.00 0.00 3.93
6183 6405 3.468140 GACGGGGGTCCAGGCTAC 61.468 72.222 0.00 0.00 0.00 3.58
6187 6409 4.791069 GGGGTCCAGGCTACGGGA 62.791 72.222 0.00 0.00 38.72 5.14
6188 6410 3.155167 GGGTCCAGGCTACGGGAG 61.155 72.222 0.00 0.00 41.78 4.30
6201 6423 4.043037 CTACGGGAGCACCTAAGTTTAG 57.957 50.000 0.00 0.00 36.97 1.85
6212 6434 4.553330 CCTAAGTTTAGGTGCTTCCAGA 57.447 45.455 9.36 0.00 44.26 3.86
6213 6435 4.508662 CCTAAGTTTAGGTGCTTCCAGAG 58.491 47.826 9.36 0.00 44.26 3.35
6214 6436 5.158618 CCTAAGTTTAGGTGCTTCCAGAGC 61.159 50.000 9.36 0.00 45.18 4.09
6215 6437 7.318278 CCTAAGTTTAGGTGCTTCCAGAGCT 62.318 48.000 9.36 0.00 45.19 4.09
6216 6438 8.703522 CCTAAGTTTAGGTGCTTCCAGAGCTT 62.704 46.154 9.36 5.40 45.19 3.74
6222 6444 4.511636 CTTCCAGAGCTTCTCGGC 57.488 61.111 0.00 0.00 35.36 5.54
6223 6445 1.153469 CTTCCAGAGCTTCTCGGCC 60.153 63.158 0.00 0.00 35.36 6.13
6224 6446 1.892819 CTTCCAGAGCTTCTCGGCCA 61.893 60.000 2.24 0.00 35.36 5.36
6225 6447 1.267574 TTCCAGAGCTTCTCGGCCAT 61.268 55.000 2.24 0.00 35.36 4.40
6226 6448 1.222936 CCAGAGCTTCTCGGCCATT 59.777 57.895 2.24 0.00 35.36 3.16
6227 6449 1.094073 CCAGAGCTTCTCGGCCATTG 61.094 60.000 2.24 0.00 35.36 2.82
6228 6450 1.094073 CAGAGCTTCTCGGCCATTGG 61.094 60.000 2.24 0.00 35.36 3.16
6229 6451 1.221840 GAGCTTCTCGGCCATTGGA 59.778 57.895 6.95 0.00 0.00 3.53
6230 6452 0.179034 GAGCTTCTCGGCCATTGGAT 60.179 55.000 6.95 0.00 0.00 3.41
6231 6453 0.179034 AGCTTCTCGGCCATTGGATC 60.179 55.000 6.95 0.00 0.00 3.36
6232 6454 0.179034 GCTTCTCGGCCATTGGATCT 60.179 55.000 6.95 0.00 0.00 2.75
6233 6455 1.590932 CTTCTCGGCCATTGGATCTG 58.409 55.000 6.95 0.00 0.00 2.90
6234 6456 1.139654 CTTCTCGGCCATTGGATCTGA 59.860 52.381 6.95 0.00 0.00 3.27
6235 6457 1.203237 TCTCGGCCATTGGATCTGAA 58.797 50.000 6.95 0.00 0.00 3.02
6236 6458 1.559219 TCTCGGCCATTGGATCTGAAA 59.441 47.619 6.95 0.00 0.00 2.69
6237 6459 2.173356 TCTCGGCCATTGGATCTGAAAT 59.827 45.455 6.95 0.00 0.00 2.17
6238 6460 2.551459 CTCGGCCATTGGATCTGAAATC 59.449 50.000 6.95 0.00 0.00 2.17
6239 6461 1.610522 CGGCCATTGGATCTGAAATCC 59.389 52.381 6.95 0.00 38.66 3.01
6240 6462 2.669781 GGCCATTGGATCTGAAATCCA 58.330 47.619 6.95 2.63 45.71 3.41
6246 6468 2.985896 TGGATCTGAAATCCAACGGTC 58.014 47.619 4.30 0.00 44.54 4.79
6247 6469 2.304470 TGGATCTGAAATCCAACGGTCA 59.696 45.455 4.30 0.00 44.54 4.02
6248 6470 3.054434 TGGATCTGAAATCCAACGGTCAT 60.054 43.478 4.30 0.00 44.54 3.06
6249 6471 3.947834 GGATCTGAAATCCAACGGTCATT 59.052 43.478 0.00 0.00 38.09 2.57
6250 6472 4.399303 GGATCTGAAATCCAACGGTCATTT 59.601 41.667 0.00 0.00 38.09 2.32
6251 6473 5.588648 GGATCTGAAATCCAACGGTCATTTA 59.411 40.000 0.00 0.00 38.09 1.40
6252 6474 5.873179 TCTGAAATCCAACGGTCATTTAC 57.127 39.130 0.00 0.00 0.00 2.01
6253 6475 5.309638 TCTGAAATCCAACGGTCATTTACA 58.690 37.500 0.00 0.00 0.00 2.41
6254 6476 5.411361 TCTGAAATCCAACGGTCATTTACAG 59.589 40.000 0.00 0.00 0.00 2.74
6255 6477 5.309638 TGAAATCCAACGGTCATTTACAGA 58.690 37.500 0.00 0.00 0.00 3.41
6256 6478 5.943416 TGAAATCCAACGGTCATTTACAGAT 59.057 36.000 0.00 0.00 0.00 2.90
6257 6479 5.818136 AATCCAACGGTCATTTACAGATG 57.182 39.130 0.00 0.00 0.00 2.90
6258 6480 3.006940 TCCAACGGTCATTTACAGATGC 58.993 45.455 0.00 0.00 0.00 3.91
6259 6481 2.223021 CCAACGGTCATTTACAGATGCG 60.223 50.000 0.00 0.00 0.00 4.73
6260 6482 1.006832 ACGGTCATTTACAGATGCGC 58.993 50.000 0.00 0.00 0.00 6.09
6261 6483 1.290203 CGGTCATTTACAGATGCGCT 58.710 50.000 9.73 0.00 0.00 5.92
6269 6491 4.147449 CAGATGCGCTGGACCCGA 62.147 66.667 9.73 0.00 41.07 5.14
6270 6492 3.157252 AGATGCGCTGGACCCGAT 61.157 61.111 9.73 0.00 0.00 4.18
6271 6493 2.203070 GATGCGCTGGACCCGATT 60.203 61.111 9.73 0.00 0.00 3.34
6272 6494 1.819632 GATGCGCTGGACCCGATTT 60.820 57.895 9.73 0.00 0.00 2.17
6273 6495 2.051804 GATGCGCTGGACCCGATTTG 62.052 60.000 9.73 0.00 0.00 2.32
6274 6496 4.179579 GCGCTGGACCCGATTTGC 62.180 66.667 0.00 0.00 0.00 3.68
6275 6497 2.745884 CGCTGGACCCGATTTGCA 60.746 61.111 0.00 0.00 0.00 4.08
6276 6498 2.331893 CGCTGGACCCGATTTGCAA 61.332 57.895 0.00 0.00 0.00 4.08
6277 6499 1.656818 CGCTGGACCCGATTTGCAAT 61.657 55.000 0.00 0.00 0.00 3.56
6278 6500 1.388547 GCTGGACCCGATTTGCAATA 58.611 50.000 0.00 0.00 0.00 1.90
6279 6501 1.065551 GCTGGACCCGATTTGCAATAC 59.934 52.381 0.00 0.00 0.00 1.89
6280 6502 1.676006 CTGGACCCGATTTGCAATACC 59.324 52.381 0.00 0.00 0.00 2.73
6281 6503 1.004862 TGGACCCGATTTGCAATACCA 59.995 47.619 0.00 0.08 0.00 3.25
6282 6504 2.096248 GGACCCGATTTGCAATACCAA 58.904 47.619 0.00 0.00 0.00 3.67
6283 6505 2.494073 GGACCCGATTTGCAATACCAAA 59.506 45.455 0.00 0.00 38.87 3.28
6284 6506 3.132111 GGACCCGATTTGCAATACCAAAT 59.868 43.478 0.00 0.22 45.37 2.32
6285 6507 4.382577 GGACCCGATTTGCAATACCAAATT 60.383 41.667 0.00 0.00 43.41 1.82
6286 6508 5.159273 ACCCGATTTGCAATACCAAATTT 57.841 34.783 0.00 0.00 43.41 1.82
6287 6509 5.175127 ACCCGATTTGCAATACCAAATTTC 58.825 37.500 0.00 0.00 43.41 2.17
6288 6510 5.046663 ACCCGATTTGCAATACCAAATTTCT 60.047 36.000 0.00 0.00 43.41 2.52
6289 6511 5.291614 CCCGATTTGCAATACCAAATTTCTG 59.708 40.000 0.00 0.00 43.41 3.02
6290 6512 6.098679 CCGATTTGCAATACCAAATTTCTGA 58.901 36.000 0.00 0.00 43.41 3.27
6291 6513 6.589523 CCGATTTGCAATACCAAATTTCTGAA 59.410 34.615 0.00 0.00 43.41 3.02
6292 6514 7.201461 CCGATTTGCAATACCAAATTTCTGAAG 60.201 37.037 0.00 0.00 43.41 3.02
6293 6515 7.201461 CGATTTGCAATACCAAATTTCTGAAGG 60.201 37.037 0.00 0.00 43.41 3.46
6294 6516 6.418057 TTGCAATACCAAATTTCTGAAGGT 57.582 33.333 0.00 4.70 36.40 3.50
6295 6517 5.782047 TGCAATACCAAATTTCTGAAGGTG 58.218 37.500 8.78 1.05 33.91 4.00
6296 6518 4.627035 GCAATACCAAATTTCTGAAGGTGC 59.373 41.667 8.78 1.92 33.91 5.01
6297 6519 5.567423 GCAATACCAAATTTCTGAAGGTGCT 60.567 40.000 8.78 0.00 33.91 4.40
6298 6520 6.458210 CAATACCAAATTTCTGAAGGTGCTT 58.542 36.000 8.78 1.65 33.91 3.91
6299 6521 6.670695 ATACCAAATTTCTGAAGGTGCTTT 57.329 33.333 8.78 0.00 33.91 3.51
6300 6522 4.948847 ACCAAATTTCTGAAGGTGCTTTC 58.051 39.130 0.00 0.00 0.00 2.62
6301 6523 4.651045 ACCAAATTTCTGAAGGTGCTTTCT 59.349 37.500 0.00 0.00 0.00 2.52
6302 6524 4.986659 CCAAATTTCTGAAGGTGCTTTCTG 59.013 41.667 0.00 0.00 0.00 3.02
6303 6525 5.221303 CCAAATTTCTGAAGGTGCTTTCTGA 60.221 40.000 0.00 0.85 34.51 3.27
6304 6526 6.275335 CAAATTTCTGAAGGTGCTTTCTGAA 58.725 36.000 10.59 10.59 40.77 3.02
6305 6527 6.661304 AATTTCTGAAGGTGCTTTCTGAAT 57.339 33.333 13.78 2.40 41.51 2.57
6306 6528 7.765695 AATTTCTGAAGGTGCTTTCTGAATA 57.234 32.000 13.78 8.14 41.51 1.75
6307 6529 7.765695 ATTTCTGAAGGTGCTTTCTGAATAA 57.234 32.000 13.78 4.73 41.51 1.40
6308 6530 7.581213 TTTCTGAAGGTGCTTTCTGAATAAA 57.419 32.000 13.78 1.88 41.51 1.40
6309 6531 7.581213 TTCTGAAGGTGCTTTCTGAATAAAA 57.419 32.000 10.59 0.00 38.95 1.52
6368 6598 1.093159 CCAGCTCAAGTCCAATCAGC 58.907 55.000 0.00 0.00 0.00 4.26
6371 6601 0.450983 GCTCAAGTCCAATCAGCAGC 59.549 55.000 0.00 0.00 0.00 5.25
6397 6627 0.758123 ATGCTTCTCTAGGCCTGCTC 59.242 55.000 17.99 0.00 0.00 4.26
6399 6629 1.671901 GCTTCTCTAGGCCTGCTCGT 61.672 60.000 17.99 0.00 0.00 4.18
6401 6631 1.038130 TTCTCTAGGCCTGCTCGTCC 61.038 60.000 17.99 0.00 0.00 4.79
6402 6632 1.454847 CTCTAGGCCTGCTCGTCCT 60.455 63.158 17.99 0.00 0.00 3.85
6403 6633 0.179015 CTCTAGGCCTGCTCGTCCTA 60.179 60.000 17.99 0.00 0.00 2.94
6404 6634 0.179015 TCTAGGCCTGCTCGTCCTAG 60.179 60.000 17.99 0.35 46.76 3.02
6405 6635 1.152735 TAGGCCTGCTCGTCCTAGG 60.153 63.158 17.99 0.82 34.67 3.02
6406 6636 2.642183 TAGGCCTGCTCGTCCTAGGG 62.642 65.000 17.99 0.00 32.15 3.53
6407 6637 2.760385 GCCTGCTCGTCCTAGGGT 60.760 66.667 9.46 0.00 32.15 4.34
6408 6638 1.455217 GCCTGCTCGTCCTAGGGTA 60.455 63.158 9.46 0.00 32.15 3.69
6409 6639 1.457009 GCCTGCTCGTCCTAGGGTAG 61.457 65.000 9.46 5.29 32.15 3.18
6411 6641 0.824182 CTGCTCGTCCTAGGGTAGGG 60.824 65.000 9.46 1.59 46.24 3.53
6412 6642 1.284111 TGCTCGTCCTAGGGTAGGGA 61.284 60.000 9.46 0.00 46.24 4.20
6413 6643 0.106318 GCTCGTCCTAGGGTAGGGAA 60.106 60.000 9.46 0.00 46.24 3.97
6414 6644 1.984066 CTCGTCCTAGGGTAGGGAAG 58.016 60.000 9.46 0.00 46.24 3.46
6415 6645 1.493871 CTCGTCCTAGGGTAGGGAAGA 59.506 57.143 9.46 0.00 46.24 2.87
6416 6646 1.925255 TCGTCCTAGGGTAGGGAAGAA 59.075 52.381 9.46 0.00 46.24 2.52
6417 6647 2.312741 TCGTCCTAGGGTAGGGAAGAAA 59.687 50.000 9.46 0.00 46.24 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.178961 AAGCCCCCTGGTTTTCTGTC 60.179 55.000 0.00 0.00 29.58 3.51
1 2 0.264657 AAAGCCCCCTGGTTTTCTGT 59.735 50.000 0.00 0.00 40.66 3.41
2 3 3.147826 AAAGCCCCCTGGTTTTCTG 57.852 52.632 0.00 0.00 40.66 3.02
6 7 0.560688 TCTGAAAAGCCCCCTGGTTT 59.439 50.000 0.00 0.00 46.22 3.27
7 8 0.560688 TTCTGAAAAGCCCCCTGGTT 59.439 50.000 0.00 0.00 35.85 3.67
8 9 0.786435 ATTCTGAAAAGCCCCCTGGT 59.214 50.000 0.00 0.00 0.00 4.00
9 10 1.006400 AGATTCTGAAAAGCCCCCTGG 59.994 52.381 0.00 0.00 0.00 4.45
10 11 2.097825 CAGATTCTGAAAAGCCCCCTG 58.902 52.381 8.00 0.00 32.44 4.45
11 12 1.618074 GCAGATTCTGAAAAGCCCCCT 60.618 52.381 17.87 0.00 32.44 4.79
12 13 0.820226 GCAGATTCTGAAAAGCCCCC 59.180 55.000 17.87 0.00 32.44 5.40
13 14 0.820226 GGCAGATTCTGAAAAGCCCC 59.180 55.000 17.87 3.37 36.17 5.80
14 15 1.549203 TGGCAGATTCTGAAAAGCCC 58.451 50.000 17.87 8.15 41.33 5.19
15 16 2.737679 GCATGGCAGATTCTGAAAAGCC 60.738 50.000 17.87 18.43 42.32 4.35
16 17 2.094390 TGCATGGCAGATTCTGAAAAGC 60.094 45.455 17.87 14.34 33.32 3.51
17 18 3.861276 TGCATGGCAGATTCTGAAAAG 57.139 42.857 17.87 5.25 33.32 2.27
29 30 5.111293 CGTGATATATATGTCTGCATGGCA 58.889 41.667 10.42 0.00 36.58 4.92
30 31 4.025396 GCGTGATATATATGTCTGCATGGC 60.025 45.833 16.55 6.74 36.58 4.40
41 42 2.437626 CGTGCGTCGCGTGATATATAT 58.562 47.619 13.38 0.00 32.40 0.86
70 72 0.104304 AGTGAGCCTCGTGTCGTTTT 59.896 50.000 0.00 0.00 0.00 2.43
73 75 2.955402 GAGTGAGCCTCGTGTCGT 59.045 61.111 0.00 0.00 0.00 4.34
93 95 7.221450 GTTGTATATCCAGGCCTACAATACAA 58.779 38.462 24.30 24.30 36.70 2.41
97 99 4.042934 GGGTTGTATATCCAGGCCTACAAT 59.957 45.833 17.30 8.91 36.70 2.71
98 100 3.393278 GGGTTGTATATCCAGGCCTACAA 59.607 47.826 3.98 8.93 33.07 2.41
99 101 2.976882 GGGTTGTATATCCAGGCCTACA 59.023 50.000 3.98 1.22 0.00 2.74
100 102 2.305052 GGGGTTGTATATCCAGGCCTAC 59.695 54.545 3.98 0.00 0.00 3.18
101 103 2.627933 GGGGTTGTATATCCAGGCCTA 58.372 52.381 3.98 0.00 0.00 3.93
142 144 3.119955 GGGAAGCTAAATTCGTGTTCACC 60.120 47.826 0.00 0.00 0.00 4.02
143 145 3.751698 AGGGAAGCTAAATTCGTGTTCAC 59.248 43.478 0.00 0.00 0.00 3.18
147 149 2.488153 GCAAGGGAAGCTAAATTCGTGT 59.512 45.455 0.00 0.00 0.00 4.49
159 161 2.165167 TCTGATTTGCTGCAAGGGAAG 58.835 47.619 15.39 11.57 0.00 3.46
171 173 8.223177 AGAAGCCATATTTCTCTTCTGATTTG 57.777 34.615 2.93 0.00 42.38 2.32
193 195 5.127519 TCTCCGTGATTTCCCGTATTTAGAA 59.872 40.000 0.00 0.00 0.00 2.10
211 213 3.520290 TCGTAATGCATTTCTCTCCGT 57.480 42.857 18.75 0.00 0.00 4.69
228 230 7.489160 TGTTATCACTAGAGTGCAATTATCGT 58.511 34.615 4.72 0.00 45.25 3.73
268 270 2.353704 GGCCTGGGTTATCAGCAAAAAC 60.354 50.000 0.00 0.00 33.64 2.43
269 271 1.899142 GGCCTGGGTTATCAGCAAAAA 59.101 47.619 0.00 0.00 33.64 1.94
300 302 4.732672 AAACTAAGGATACAGTCGTCCC 57.267 45.455 2.02 0.00 41.41 4.46
304 306 7.378995 CCTTCGATTAAACTAAGGATACAGTCG 59.621 40.741 9.66 0.00 40.85 4.18
338 348 7.556635 TGACGATCTAGTATTGGAAGAGAAGAA 59.443 37.037 0.00 0.00 0.00 2.52
339 349 7.054751 TGACGATCTAGTATTGGAAGAGAAGA 58.945 38.462 0.00 0.00 0.00 2.87
362 372 4.523943 CCTTTGTTCCATCCAAGTGATTGA 59.476 41.667 0.00 0.00 0.00 2.57
381 391 3.022406 AGTACGAGGACTATTCGCCTTT 58.978 45.455 0.00 0.00 41.57 3.11
402 412 2.689785 CGTGTGGCTACGGGTACGA 61.690 63.158 5.06 0.00 44.60 3.43
404 414 2.507769 GCGTGTGGCTACGGGTAC 60.508 66.667 14.65 0.00 43.87 3.34
405 415 3.762247 GGCGTGTGGCTACGGGTA 61.762 66.667 14.65 0.00 43.87 3.69
439 449 0.316196 GCGTTGACTAATGCATCGGC 60.316 55.000 0.00 0.00 45.91 5.54
467 477 0.034186 TGGTGATGATTGGGAGTGGC 60.034 55.000 0.00 0.00 0.00 5.01
683 717 5.194657 GCAACAAAATTTTAACTTGCGACC 58.805 37.500 17.54 2.11 0.00 4.79
1054 1118 2.063378 CAGCCTCCTCCTCCTGGTC 61.063 68.421 0.00 0.00 34.23 4.02
1056 1120 3.478274 GCAGCCTCCTCCTCCTGG 61.478 72.222 0.00 0.00 0.00 4.45
1057 1121 3.478274 GGCAGCCTCCTCCTCCTG 61.478 72.222 3.29 0.00 0.00 3.86
1208 1284 4.933064 GGAGATGAGTCGGCGGCG 62.933 72.222 27.15 27.15 0.00 6.46
1209 1285 4.593864 GGGAGATGAGTCGGCGGC 62.594 72.222 1.71 1.71 0.00 6.53
1210 1286 3.147595 TGGGAGATGAGTCGGCGG 61.148 66.667 7.21 0.00 0.00 6.13
1333 1409 4.200283 CGCTGCTCCTCCTCGTCC 62.200 72.222 0.00 0.00 0.00 4.79
1336 1418 3.423162 CTTCCGCTGCTCCTCCTCG 62.423 68.421 0.00 0.00 0.00 4.63
1426 1508 2.047560 TCGCTCTCCGACGACTGA 60.048 61.111 0.00 0.00 41.89 3.41
1502 1589 0.178935 GAGAGGAGGAGGAGATGGGG 60.179 65.000 0.00 0.00 0.00 4.96
1716 1809 2.336478 ACGAGAGACACGAGCCAGG 61.336 63.158 0.00 0.00 34.70 4.45
1823 1928 3.118261 TGCTACAGAAAGATCCCATGACC 60.118 47.826 0.00 0.00 0.00 4.02
1942 2047 2.838225 CTGGCGACTCCGGGGTAT 60.838 66.667 7.16 0.00 37.58 2.73
2012 2117 4.764308 AGAAGCAAGAGAAACAGGGAATTC 59.236 41.667 0.00 0.00 0.00 2.17
2085 2190 0.466124 ATTCAGAAGGTCGGGCTAGC 59.534 55.000 6.04 6.04 0.00 3.42
2092 2197 2.208431 GCAGGATCATTCAGAAGGTCG 58.792 52.381 0.00 0.00 0.00 4.79
2109 2214 1.091771 CACGGGTCTAAGCATGGCAG 61.092 60.000 0.00 0.00 0.00 4.85
2384 2494 1.744320 TATCGCAGTCATGGGGGTCG 61.744 60.000 0.00 0.00 39.74 4.79
2510 2620 3.262420 GTCTGTGCATTTCAGTACCGAT 58.738 45.455 3.05 0.00 34.86 4.18
2531 2641 4.505922 AGCGAGAAAAGATTCATAGAAGCG 59.494 41.667 0.00 0.00 38.06 4.68
2767 2883 8.862325 TCAATTTACCAGCTGAGAAATCTAAA 57.138 30.769 17.39 6.39 0.00 1.85
2804 2920 6.888632 ACTCATATTTGACAGGCAGAAGAATT 59.111 34.615 0.00 0.00 0.00 2.17
2805 2921 6.421485 ACTCATATTTGACAGGCAGAAGAAT 58.579 36.000 0.00 0.00 0.00 2.40
2850 2966 5.279960 GGAAAATGGAACCATTAGCACCTTT 60.280 40.000 17.73 7.99 44.86 3.11
2873 2989 0.531200 GACTACAGGAGACAACGGGG 59.469 60.000 0.00 0.00 0.00 5.73
2882 2998 1.924731 TCACAGTGGGACTACAGGAG 58.075 55.000 0.00 0.00 0.00 3.69
2954 3070 3.153369 TGGAACACACAGTGGCATTAT 57.847 42.857 5.31 0.00 37.94 1.28
2955 3071 2.647683 TGGAACACACAGTGGCATTA 57.352 45.000 5.31 0.00 37.94 1.90
3024 3149 5.593183 ACTAGTTTCGCTAACAAGAAAGC 57.407 39.130 0.00 0.00 39.30 3.51
3222 3352 5.447818 GCACATTAGCCTGCTTTAGTTACAG 60.448 44.000 0.00 0.00 0.00 2.74
3228 3358 3.311871 CAGAGCACATTAGCCTGCTTTAG 59.688 47.826 0.00 0.00 43.94 1.85
3238 3368 7.747799 CACAAAAAGATGTACAGAGCACATTAG 59.252 37.037 0.33 0.00 36.76 1.73
3271 3401 4.326548 GTGCTAACTTCAACATCGGTAGTC 59.673 45.833 0.00 0.00 0.00 2.59
3278 3408 6.845302 TGATGAATGTGCTAACTTCAACATC 58.155 36.000 0.00 0.00 33.03 3.06
3288 3418 4.761227 TGTGAGCTTTGATGAATGTGCTAA 59.239 37.500 0.00 0.00 0.00 3.09
3360 3490 8.948631 TTCTTGTATAAAACTCATCCTAGCTG 57.051 34.615 0.00 0.00 0.00 4.24
3577 3707 6.076981 CAATCAGGTTGGGCTATACATTTC 57.923 41.667 0.00 0.00 34.06 2.17
3780 3910 5.378230 AATTATGCATCACCTCTTCCTCA 57.622 39.130 0.19 0.00 0.00 3.86
3820 3950 7.770897 AGATAAACAAGAGTGACAAGACAACTT 59.229 33.333 0.00 0.00 36.73 2.66
3871 4001 6.933130 TGACGTATCAAGCAAATTAGAATCG 58.067 36.000 0.00 0.00 0.00 3.34
3908 4038 2.857618 CGAGTCTTCTCTTCTTCACCG 58.142 52.381 0.00 0.00 38.45 4.94
3949 4079 1.487976 CCACCAGACATAGACAGCCAT 59.512 52.381 0.00 0.00 0.00 4.40
4183 4318 1.894466 TCAATGTCAGTTGGGGCATTG 59.106 47.619 12.82 12.82 45.45 2.82
4315 4450 1.204146 TAGTCTTGGCAGGGGATGAC 58.796 55.000 0.00 0.00 37.50 3.06
4327 4462 5.220739 GCTATCAACACTGCCAATAGTCTTG 60.221 44.000 0.00 0.00 30.68 3.02
4396 4531 2.345244 CGCAGTGGAGAAGTGGCT 59.655 61.111 0.00 0.00 0.00 4.75
4534 4670 6.765512 TGGTATCAAATTCATCAGCATTACGA 59.234 34.615 0.00 0.00 0.00 3.43
4635 4774 8.954950 TGAATCTTCCAAAGCACAAATAAAAA 57.045 26.923 0.00 0.00 0.00 1.94
4741 4880 4.741676 GTGCTGATGTTTTATATTGCCTGC 59.258 41.667 0.00 0.00 0.00 4.85
4779 4918 3.084786 ACAAGATTTTGGCCTAGTGAGC 58.915 45.455 3.32 0.00 38.66 4.26
4780 4919 5.245531 TGTACAAGATTTTGGCCTAGTGAG 58.754 41.667 3.32 0.00 38.66 3.51
4781 4920 5.235850 TGTACAAGATTTTGGCCTAGTGA 57.764 39.130 3.32 0.00 38.66 3.41
4783 4922 4.459337 GCTTGTACAAGATTTTGGCCTAGT 59.541 41.667 34.43 0.00 40.79 2.57
4784 4923 4.458989 TGCTTGTACAAGATTTTGGCCTAG 59.541 41.667 34.43 8.71 40.79 3.02
4785 4924 4.402829 TGCTTGTACAAGATTTTGGCCTA 58.597 39.130 34.43 4.96 40.79 3.93
4786 4925 3.230134 TGCTTGTACAAGATTTTGGCCT 58.770 40.909 34.43 0.00 40.79 5.19
4788 4927 3.983344 CACTGCTTGTACAAGATTTTGGC 59.017 43.478 34.43 20.35 40.79 4.52
4790 4929 3.983344 GCCACTGCTTGTACAAGATTTTG 59.017 43.478 34.43 23.31 40.79 2.44
4791 4930 3.005791 GGCCACTGCTTGTACAAGATTTT 59.994 43.478 34.43 14.95 40.79 1.82
4792 4931 2.558359 GGCCACTGCTTGTACAAGATTT 59.442 45.455 34.43 16.58 40.79 2.17
4908 5049 6.729100 TGAGATAGGACTTTTCCAGTTTAGGA 59.271 38.462 0.00 0.00 45.72 2.94
5014 5169 7.386299 GCTTATTCATTTCGATCTATGTCCACT 59.614 37.037 0.00 0.00 0.00 4.00
5058 5213 0.575390 ACTGAAACGACGCAGAAACG 59.425 50.000 7.79 0.00 36.07 3.60
5101 5260 2.222227 ATTTCCACCTCTTGGGCTTC 57.778 50.000 0.00 0.00 46.92 3.86
5362 5521 3.053896 CGTTGGGAGGGAAACGGC 61.054 66.667 0.21 0.00 44.08 5.68
5411 5570 1.443828 GACTGTGCCTAGCTAGCCC 59.556 63.158 15.74 8.77 0.00 5.19
5451 5614 0.693049 ATTTGACGGCCAGGAGAGTT 59.307 50.000 2.24 0.00 0.00 3.01
5452 5615 0.693049 AATTTGACGGCCAGGAGAGT 59.307 50.000 2.24 0.00 0.00 3.24
5453 5616 1.089920 CAATTTGACGGCCAGGAGAG 58.910 55.000 2.24 0.00 0.00 3.20
5454 5617 0.690192 TCAATTTGACGGCCAGGAGA 59.310 50.000 2.24 0.00 0.00 3.71
5498 5673 3.387962 AGATCCTTCCTGCAGGTCATAA 58.612 45.455 31.58 17.64 35.15 1.90
5499 5674 3.051940 AGATCCTTCCTGCAGGTCATA 57.948 47.619 31.58 16.58 35.15 2.15
5630 5810 5.221441 CCAATGAACCACTCCACGAGATATA 60.221 44.000 0.00 0.00 33.32 0.86
5631 5811 4.443457 CCAATGAACCACTCCACGAGATAT 60.443 45.833 0.00 0.00 33.32 1.63
5637 5817 1.266718 CAACCAATGAACCACTCCACG 59.733 52.381 0.00 0.00 0.00 4.94
5666 5846 4.338682 CCGACTACCACTAGTCAAGCTTAT 59.661 45.833 0.00 0.00 46.69 1.73
5670 5850 2.089980 TCCGACTACCACTAGTCAAGC 58.910 52.381 8.28 0.00 46.69 4.01
5671 5851 4.673441 CAATCCGACTACCACTAGTCAAG 58.327 47.826 8.28 0.00 46.69 3.02
5689 5869 4.394795 CTGTTTTACACTGCTACGCAATC 58.605 43.478 0.00 0.00 38.41 2.67
5694 5877 3.386486 TGACCTGTTTTACACTGCTACG 58.614 45.455 0.00 0.00 0.00 3.51
5725 5910 9.670442 AGTATAGAATAAGGAATGAACCAGGTA 57.330 33.333 0.00 0.00 0.00 3.08
5726 5911 8.432805 CAGTATAGAATAAGGAATGAACCAGGT 58.567 37.037 0.00 0.00 0.00 4.00
5787 5983 1.672881 AGAAGAATTACCGCTGCATGC 59.327 47.619 11.82 11.82 38.57 4.06
5811 6007 0.524862 TGGGTTCGAGTTAGACGAGC 59.475 55.000 0.00 0.00 40.72 5.03
5857 6065 2.854805 GCTGTCAAAAGAACCAGAACGC 60.855 50.000 0.00 0.00 0.00 4.84
5895 6104 4.901123 TGTGCGACCGTGGGTGTG 62.901 66.667 0.00 0.00 35.25 3.82
5906 6115 3.630013 AGGCTGGCTTCTGTGCGA 61.630 61.111 0.00 0.00 0.00 5.10
5924 6140 3.712881 GACCGCACACCGCACTTC 61.713 66.667 0.00 0.00 42.60 3.01
6054 6276 3.946907 GGTCAACAACGACCGAGG 58.053 61.111 0.00 0.00 45.77 4.63
6072 6294 2.815647 CTCCGTTCGCTCTTGGGC 60.816 66.667 0.00 0.00 0.00 5.36
6074 6296 2.815647 GGCTCCGTTCGCTCTTGG 60.816 66.667 0.00 0.00 0.00 3.61
6075 6297 3.181967 CGGCTCCGTTCGCTCTTG 61.182 66.667 0.00 0.00 34.35 3.02
6076 6298 3.371063 TCGGCTCCGTTCGCTCTT 61.371 61.111 8.28 0.00 40.74 2.85
6077 6299 4.117661 GTCGGCTCCGTTCGCTCT 62.118 66.667 8.28 0.00 40.74 4.09
6110 6332 3.361977 GGGCTTTTCGCTTCGCCA 61.362 61.111 0.00 0.00 44.23 5.69
6128 6350 2.876645 CGTCAGCGACTCGAAGGC 60.877 66.667 1.63 0.00 41.33 4.35
6129 6351 2.876645 GCGTCAGCGACTCGAAGG 60.877 66.667 1.63 0.00 41.33 3.46
6151 6373 1.064296 CGTCACGAGCTAGCGGAAT 59.936 57.895 9.55 0.00 35.12 3.01
6180 6402 3.181478 CCTAAACTTAGGTGCTCCCGTAG 60.181 52.174 7.28 0.00 44.26 3.51
6182 6404 1.553704 CCTAAACTTAGGTGCTCCCGT 59.446 52.381 7.28 0.00 44.26 5.28
6183 6405 2.311124 CCTAAACTTAGGTGCTCCCG 57.689 55.000 7.28 0.00 44.26 5.14
6205 6427 1.153469 GGCCGAGAAGCTCTGGAAG 60.153 63.158 0.00 0.00 0.00 3.46
6206 6428 1.267574 ATGGCCGAGAAGCTCTGGAA 61.268 55.000 0.00 0.00 0.00 3.53
6207 6429 1.267574 AATGGCCGAGAAGCTCTGGA 61.268 55.000 0.00 0.00 0.00 3.86
6208 6430 1.094073 CAATGGCCGAGAAGCTCTGG 61.094 60.000 0.00 0.00 0.00 3.86
6209 6431 1.094073 CCAATGGCCGAGAAGCTCTG 61.094 60.000 0.00 0.00 0.00 3.35
6210 6432 1.222936 CCAATGGCCGAGAAGCTCT 59.777 57.895 0.00 0.00 0.00 4.09
6211 6433 0.179034 ATCCAATGGCCGAGAAGCTC 60.179 55.000 0.00 0.00 0.00 4.09
6212 6434 0.179034 GATCCAATGGCCGAGAAGCT 60.179 55.000 0.00 0.00 0.00 3.74
6213 6435 0.179034 AGATCCAATGGCCGAGAAGC 60.179 55.000 0.00 0.00 0.00 3.86
6214 6436 1.139654 TCAGATCCAATGGCCGAGAAG 59.860 52.381 0.00 0.00 0.00 2.85
6215 6437 1.203237 TCAGATCCAATGGCCGAGAA 58.797 50.000 0.00 0.00 0.00 2.87
6216 6438 1.203237 TTCAGATCCAATGGCCGAGA 58.797 50.000 0.00 0.00 0.00 4.04
6217 6439 2.042686 TTTCAGATCCAATGGCCGAG 57.957 50.000 0.00 0.00 0.00 4.63
6218 6440 2.575532 GATTTCAGATCCAATGGCCGA 58.424 47.619 0.00 0.00 0.00 5.54
6219 6441 1.610522 GGATTTCAGATCCAATGGCCG 59.389 52.381 0.00 0.00 38.09 6.13
6220 6442 2.669781 TGGATTTCAGATCCAATGGCC 58.330 47.619 5.31 0.00 44.54 5.36
6226 6448 2.304470 TGACCGTTGGATTTCAGATCCA 59.696 45.455 3.70 3.70 45.71 3.41
6227 6449 2.985896 TGACCGTTGGATTTCAGATCC 58.014 47.619 0.00 0.00 38.66 3.36
6228 6450 5.567138 AAATGACCGTTGGATTTCAGATC 57.433 39.130 0.00 0.00 0.00 2.75
6229 6451 5.943416 TGTAAATGACCGTTGGATTTCAGAT 59.057 36.000 0.00 0.00 0.00 2.90
6230 6452 5.309638 TGTAAATGACCGTTGGATTTCAGA 58.690 37.500 0.00 0.00 0.00 3.27
6231 6453 5.411361 TCTGTAAATGACCGTTGGATTTCAG 59.589 40.000 0.00 0.00 0.00 3.02
6232 6454 5.309638 TCTGTAAATGACCGTTGGATTTCA 58.690 37.500 0.00 0.00 0.00 2.69
6233 6455 5.873179 TCTGTAAATGACCGTTGGATTTC 57.127 39.130 0.00 0.00 0.00 2.17
6234 6456 5.393027 GCATCTGTAAATGACCGTTGGATTT 60.393 40.000 0.00 0.00 0.00 2.17
6235 6457 4.096382 GCATCTGTAAATGACCGTTGGATT 59.904 41.667 0.00 0.00 0.00 3.01
6236 6458 3.627577 GCATCTGTAAATGACCGTTGGAT 59.372 43.478 0.00 0.00 0.00 3.41
6237 6459 3.006940 GCATCTGTAAATGACCGTTGGA 58.993 45.455 0.00 0.00 0.00 3.53
6238 6460 2.223021 CGCATCTGTAAATGACCGTTGG 60.223 50.000 0.00 0.00 0.00 3.77
6239 6461 2.787723 GCGCATCTGTAAATGACCGTTG 60.788 50.000 0.30 0.00 0.00 4.10
6240 6462 1.396996 GCGCATCTGTAAATGACCGTT 59.603 47.619 0.30 0.00 0.00 4.44
6241 6463 1.006832 GCGCATCTGTAAATGACCGT 58.993 50.000 0.30 0.00 0.00 4.83
6242 6464 1.004610 CAGCGCATCTGTAAATGACCG 60.005 52.381 11.47 0.00 38.02 4.79
6243 6465 1.331756 CCAGCGCATCTGTAAATGACC 59.668 52.381 11.47 0.00 41.25 4.02
6244 6466 2.030946 GTCCAGCGCATCTGTAAATGAC 59.969 50.000 11.47 0.00 41.25 3.06
6245 6467 2.279741 GTCCAGCGCATCTGTAAATGA 58.720 47.619 11.47 0.00 41.25 2.57
6246 6468 1.331756 GGTCCAGCGCATCTGTAAATG 59.668 52.381 11.47 0.00 41.25 2.32
6247 6469 1.668419 GGTCCAGCGCATCTGTAAAT 58.332 50.000 11.47 0.00 41.25 1.40
6248 6470 0.392461 GGGTCCAGCGCATCTGTAAA 60.392 55.000 11.47 0.00 41.25 2.01
6249 6471 1.220749 GGGTCCAGCGCATCTGTAA 59.779 57.895 11.47 0.00 41.25 2.41
6250 6472 2.900273 GGGTCCAGCGCATCTGTA 59.100 61.111 11.47 0.00 41.25 2.74
6251 6473 4.457496 CGGGTCCAGCGCATCTGT 62.457 66.667 11.47 0.00 41.25 3.41
6252 6474 2.930385 AATCGGGTCCAGCGCATCTG 62.930 60.000 11.47 0.00 42.49 2.90
6253 6475 2.257409 AAATCGGGTCCAGCGCATCT 62.257 55.000 11.47 0.00 0.00 2.90
6254 6476 1.819632 AAATCGGGTCCAGCGCATC 60.820 57.895 11.47 0.00 0.00 3.91
6255 6477 2.114670 CAAATCGGGTCCAGCGCAT 61.115 57.895 11.47 0.00 0.00 4.73
6256 6478 2.745884 CAAATCGGGTCCAGCGCA 60.746 61.111 11.47 0.00 0.00 6.09
6257 6479 4.179579 GCAAATCGGGTCCAGCGC 62.180 66.667 0.00 0.00 0.00 5.92
6258 6480 1.656818 ATTGCAAATCGGGTCCAGCG 61.657 55.000 1.71 0.00 0.00 5.18
6259 6481 1.065551 GTATTGCAAATCGGGTCCAGC 59.934 52.381 1.71 0.00 0.00 4.85
6260 6482 1.676006 GGTATTGCAAATCGGGTCCAG 59.324 52.381 1.71 0.00 0.00 3.86
6261 6483 1.004862 TGGTATTGCAAATCGGGTCCA 59.995 47.619 1.71 2.09 0.00 4.02
6262 6484 1.757682 TGGTATTGCAAATCGGGTCC 58.242 50.000 1.71 0.00 0.00 4.46
6263 6485 3.859411 TTTGGTATTGCAAATCGGGTC 57.141 42.857 1.71 0.00 0.00 4.46
6264 6486 4.817318 AATTTGGTATTGCAAATCGGGT 57.183 36.364 1.71 0.00 31.42 5.28
6265 6487 5.291614 CAGAAATTTGGTATTGCAAATCGGG 59.708 40.000 1.71 0.00 31.42 5.14
6266 6488 6.098679 TCAGAAATTTGGTATTGCAAATCGG 58.901 36.000 1.71 0.00 31.42 4.18
6267 6489 7.201461 CCTTCAGAAATTTGGTATTGCAAATCG 60.201 37.037 1.71 0.00 31.42 3.34
6268 6490 7.603784 ACCTTCAGAAATTTGGTATTGCAAATC 59.396 33.333 1.71 0.00 31.42 2.17
6269 6491 7.388500 CACCTTCAGAAATTTGGTATTGCAAAT 59.612 33.333 1.71 0.00 32.98 2.32
6270 6492 6.705381 CACCTTCAGAAATTTGGTATTGCAAA 59.295 34.615 1.71 0.00 0.00 3.68
6271 6493 6.222389 CACCTTCAGAAATTTGGTATTGCAA 58.778 36.000 0.00 0.00 0.00 4.08
6272 6494 5.782047 CACCTTCAGAAATTTGGTATTGCA 58.218 37.500 0.00 0.00 0.00 4.08
6273 6495 4.627035 GCACCTTCAGAAATTTGGTATTGC 59.373 41.667 0.00 0.00 0.00 3.56
6274 6496 6.029346 AGCACCTTCAGAAATTTGGTATTG 57.971 37.500 0.00 0.00 0.00 1.90
6275 6497 6.670695 AAGCACCTTCAGAAATTTGGTATT 57.329 33.333 0.00 0.00 0.00 1.89
6276 6498 6.494835 AGAAAGCACCTTCAGAAATTTGGTAT 59.505 34.615 0.00 0.00 0.00 2.73
6277 6499 5.833131 AGAAAGCACCTTCAGAAATTTGGTA 59.167 36.000 0.00 0.00 0.00 3.25
6278 6500 4.651045 AGAAAGCACCTTCAGAAATTTGGT 59.349 37.500 0.00 0.00 0.00 3.67
6279 6501 4.986659 CAGAAAGCACCTTCAGAAATTTGG 59.013 41.667 0.00 0.00 0.00 3.28
6280 6502 5.835257 TCAGAAAGCACCTTCAGAAATTTG 58.165 37.500 0.00 0.00 0.00 2.32
6281 6503 6.469782 TTCAGAAAGCACCTTCAGAAATTT 57.530 33.333 0.00 0.00 30.56 1.82
6282 6504 6.661304 ATTCAGAAAGCACCTTCAGAAATT 57.339 33.333 5.55 0.00 35.34 1.82
6283 6505 7.765695 TTATTCAGAAAGCACCTTCAGAAAT 57.234 32.000 5.55 1.68 35.34 2.17
6284 6506 7.581213 TTTATTCAGAAAGCACCTTCAGAAA 57.419 32.000 5.55 0.00 35.34 2.52
6285 6507 7.425606 GTTTTATTCAGAAAGCACCTTCAGAA 58.574 34.615 4.37 4.37 35.91 3.02
6286 6508 6.016276 GGTTTTATTCAGAAAGCACCTTCAGA 60.016 38.462 0.00 0.00 35.27 3.27
6287 6509 6.152379 GGTTTTATTCAGAAAGCACCTTCAG 58.848 40.000 0.00 0.00 35.27 3.02
6288 6510 5.278266 CGGTTTTATTCAGAAAGCACCTTCA 60.278 40.000 0.00 0.00 34.96 3.02
6289 6511 5.154222 CGGTTTTATTCAGAAAGCACCTTC 58.846 41.667 0.00 0.00 34.96 3.46
6290 6512 4.022329 CCGGTTTTATTCAGAAAGCACCTT 60.022 41.667 0.00 0.00 34.96 3.50
6291 6513 3.506067 CCGGTTTTATTCAGAAAGCACCT 59.494 43.478 0.00 0.00 34.96 4.00
6292 6514 3.833442 CCGGTTTTATTCAGAAAGCACC 58.167 45.455 0.00 0.00 34.96 5.01
6293 6515 3.242518 GCCGGTTTTATTCAGAAAGCAC 58.757 45.455 1.90 0.00 34.96 4.40
6294 6516 2.230266 GGCCGGTTTTATTCAGAAAGCA 59.770 45.455 1.90 0.00 34.96 3.91
6295 6517 2.230266 TGGCCGGTTTTATTCAGAAAGC 59.770 45.455 1.90 0.00 0.00 3.51
6296 6518 4.234574 GTTGGCCGGTTTTATTCAGAAAG 58.765 43.478 1.90 0.00 0.00 2.62
6297 6519 3.006003 GGTTGGCCGGTTTTATTCAGAAA 59.994 43.478 1.90 0.00 0.00 2.52
6298 6520 2.559231 GGTTGGCCGGTTTTATTCAGAA 59.441 45.455 1.90 0.00 0.00 3.02
6299 6521 2.164338 GGTTGGCCGGTTTTATTCAGA 58.836 47.619 1.90 0.00 0.00 3.27
6300 6522 2.647529 GGTTGGCCGGTTTTATTCAG 57.352 50.000 1.90 0.00 0.00 3.02
6342 6564 4.335647 ACTTGAGCTGGGGGCACG 62.336 66.667 0.00 0.00 44.79 5.34
6344 6566 3.650950 GGACTTGAGCTGGGGGCA 61.651 66.667 0.00 0.00 44.79 5.36
6345 6567 2.505364 ATTGGACTTGAGCTGGGGGC 62.505 60.000 0.00 0.00 42.19 5.80
6346 6568 0.394899 GATTGGACTTGAGCTGGGGG 60.395 60.000 0.00 0.00 0.00 5.40
6347 6569 0.329261 TGATTGGACTTGAGCTGGGG 59.671 55.000 0.00 0.00 0.00 4.96
6351 6573 1.949547 GCTGCTGATTGGACTTGAGCT 60.950 52.381 0.00 0.00 0.00 4.09
6352 6574 0.450983 GCTGCTGATTGGACTTGAGC 59.549 55.000 0.00 0.00 0.00 4.26
6354 6576 1.527034 GTGCTGCTGATTGGACTTGA 58.473 50.000 0.00 0.00 0.00 3.02
6356 6578 0.035317 TCGTGCTGCTGATTGGACTT 59.965 50.000 0.00 0.00 0.00 3.01
6357 6579 0.035317 TTCGTGCTGCTGATTGGACT 59.965 50.000 0.00 0.00 0.00 3.85
6371 6601 2.468831 GCCTAGAGAAGCATCTTCGTG 58.531 52.381 0.00 0.00 35.54 4.35


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

AutoCloner maintained by Alex Coulton.