Multiple sequence alignment - TraesCS5A01G212200

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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 TraesCS5A01G212200 chr5A 100.000 2651 0 0 1 2651 427585681 427583031 0.000000e+00 4896
1 TraesCS5A01G212200 chr5B 84.938 1766 123 48 702 2381 382315270 382316978 0.000000e+00 1655
2 TraesCS5A01G212200 chr5D 96.447 591 21 0 1046 1636 328924406 328924996 0.000000e+00 976
3 TraesCS5A01G212200 chr5D 93.086 405 20 6 615 1012 328924005 328924408 1.060000e-163 586
4 TraesCS5A01G212200 chr5D 93.871 310 16 3 1 309 328921119 328921426 5.170000e-127 464
5 TraesCS5A01G212200 chr5D 96.629 267 9 0 2385 2651 124784893 124784627 6.730000e-121 444
6 TraesCS5A01G212200 chr3D 97.753 267 6 0 2385 2651 164369759 164370025 6.690000e-126 460
7 TraesCS5A01G212200 chr3D 97.004 267 8 0 2385 2651 463073636 463073902 1.450000e-122 449
8 TraesCS5A01G212200 chr3D 96.654 269 8 1 2383 2651 151099283 151099016 1.870000e-121 446
9 TraesCS5A01G212200 chr3D 79.644 393 48 14 1692 2054 573616573 573616183 1.220000e-63 254
10 TraesCS5A01G212200 chr3D 78.734 395 54 12 1689 2055 61053110 61052718 1.230000e-58 237
11 TraesCS5A01G212200 chr4D 97.004 267 8 0 2385 2651 306189922 306189656 1.450000e-122 449
12 TraesCS5A01G212200 chr4D 96.981 265 8 0 2387 2651 75836748 75836484 1.870000e-121 446
13 TraesCS5A01G212200 chr7D 96.981 265 8 0 2387 2651 145950165 145949901 1.870000e-121 446
14 TraesCS5A01G212200 chr7D 83.120 391 33 10 1693 2055 66707521 66707906 2.540000e-85 326
15 TraesCS5A01G212200 chr7D 78.485 330 37 9 1706 2004 41432119 41431793 4.510000e-43 185
16 TraesCS5A01G212200 chr4B 96.629 267 9 0 2385 2651 391621428 391621162 6.730000e-121 444
17 TraesCS5A01G212200 chr4B 84.783 184 19 4 1887 2064 671775942 671775762 2.710000e-40 176
18 TraesCS5A01G212200 chr4A 96.629 267 9 0 2385 2651 114573802 114573536 6.730000e-121 444
19 TraesCS5A01G212200 chr4A 80.916 393 42 13 1689 2056 647562975 647563359 2.010000e-71 279
20 TraesCS5A01G212200 chr2A 81.481 378 37 9 1706 2055 757931959 757931587 2.010000e-71 279
21 TraesCS5A01G212200 chr2A 81.657 338 28 20 1706 2014 32335698 32335366 1.580000e-62 250
22 TraesCS5A01G212200 chr2B 80.250 400 41 19 1689 2055 729774510 729774116 1.560000e-67 267
23 TraesCS5A01G212200 chr2B 89.071 183 14 4 1706 1885 209380076 209379897 3.430000e-54 222
24 TraesCS5A01G212200 chr6A 80.645 372 43 7 1711 2057 549433969 549433602 7.280000e-66 261
25 TraesCS5A01G212200 chr2D 87.671 219 26 1 2162 2380 353354402 353354619 1.220000e-63 254
26 TraesCS5A01G212200 chr2D 90.816 98 9 0 2283 2380 353861894 353861991 5.950000e-27 132
27 TraesCS5A01G212200 chr1B 80.533 375 35 19 1713 2055 14545868 14546236 1.220000e-63 254
28 TraesCS5A01G212200 chr1B 76.503 366 47 10 1712 2044 629794335 629794694 2.110000e-36 163
29 TraesCS5A01G212200 chr6B 78.412 403 47 16 1689 2058 576267142 576267537 2.660000e-55 226
30 TraesCS5A01G212200 chr3B 78.684 380 48 10 1703 2055 55108194 55108567 3.430000e-54 222
31 TraesCS5A01G212200 chr3B 90.244 164 16 0 2171 2334 671014498 671014335 5.750000e-52 215
32 TraesCS5A01G212200 chr3B 80.882 136 20 4 1882 2016 716298939 716298809 4.670000e-18 102
33 TraesCS5A01G212200 chr7B 85.644 202 24 4 1689 1886 119887937 119888137 9.620000e-50 207
34 TraesCS5A01G212200 chr7B 91.667 108 9 0 2171 2278 141002608 141002501 1.640000e-32 150


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 TraesCS5A01G212200 chr5A 427583031 427585681 2650 True 4896.000000 4896 100.000 1 2651 1 chr5A.!!$R1 2650
1 TraesCS5A01G212200 chr5B 382315270 382316978 1708 False 1655.000000 1655 84.938 702 2381 1 chr5B.!!$F1 1679
2 TraesCS5A01G212200 chr5D 328921119 328924996 3877 False 675.333333 976 94.468 1 1636 3 chr5D.!!$F1 1635

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
605 2908 0.178973 TCGACAGACTTGGTCTCCCA 60.179 55.0 0.0 0.0 41.37 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 4774 0.034337 TAGTCAACGGGTCTGCCAAC 59.966 55.0 0.0 0.0 36.17 3.77 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
26 27 7.505585 TGTTCCTAGTCATCATCCAAAAACTTT 59.494 33.333 0.00 0.00 0.00 2.66
129 130 6.154203 TCATCGCAATAATAAAAATGCCCA 57.846 33.333 0.00 0.00 35.41 5.36
133 134 5.304101 TCGCAATAATAAAAATGCCCATCCT 59.696 36.000 0.00 0.00 35.41 3.24
137 138 8.938906 GCAATAATAAAAATGCCCATCCTATTG 58.061 33.333 0.00 0.00 32.73 1.90
177 178 6.389906 ACATGCTCTTGTAAATAAAACTGCC 58.610 36.000 0.00 0.00 0.00 4.85
181 182 6.036470 GCTCTTGTAAATAAAACTGCCATCC 58.964 40.000 0.00 0.00 0.00 3.51
322 666 9.248291 CCATATTCTTATAACACAAAATGCCAC 57.752 33.333 0.00 0.00 0.00 5.01
330 674 2.890945 ACACAAAATGCCACCCTCTTAC 59.109 45.455 0.00 0.00 0.00 2.34
353 698 5.888161 ACAATAAAATGCCACCCTCTTCTAG 59.112 40.000 0.00 0.00 0.00 2.43
406 751 9.631257 AAGAAAACAGGATTTTTGGATGAATTT 57.369 25.926 0.00 0.00 0.00 1.82
438 785 4.314740 AAGCTTCAAAATGCCAACGTTA 57.685 36.364 0.00 0.00 0.00 3.18
439 786 3.638484 AGCTTCAAAATGCCAACGTTAC 58.362 40.909 0.00 0.00 0.00 2.50
484 831 3.953542 ATGTTAACAATCCCCTCTCCC 57.046 47.619 13.23 0.00 0.00 4.30
490 837 3.739080 AATCCCCTCTCCCGCCCAT 62.739 63.158 0.00 0.00 0.00 4.00
492 839 4.195334 CCCCTCTCCCGCCCATTG 62.195 72.222 0.00 0.00 0.00 2.82
537 884 1.961394 GAGTTCAAAACCTCCCCCAAC 59.039 52.381 0.00 0.00 0.00 3.77
596 2899 1.272490 TCGCCAAGAATCGACAGACTT 59.728 47.619 0.00 0.00 0.00 3.01
597 2900 1.391485 CGCCAAGAATCGACAGACTTG 59.609 52.381 12.55 12.55 39.24 3.16
602 2905 3.859411 AGAATCGACAGACTTGGTCTC 57.141 47.619 0.00 0.00 41.37 3.36
604 2907 1.187087 ATCGACAGACTTGGTCTCCC 58.813 55.000 0.00 0.00 41.37 4.30
605 2908 0.178973 TCGACAGACTTGGTCTCCCA 60.179 55.000 0.00 0.00 41.37 4.37
606 2909 0.244994 CGACAGACTTGGTCTCCCAG 59.755 60.000 0.00 0.00 41.37 4.45
607 2910 0.610687 GACAGACTTGGTCTCCCAGG 59.389 60.000 0.00 0.00 41.37 4.45
608 2911 0.838122 ACAGACTTGGTCTCCCAGGG 60.838 60.000 0.00 0.00 41.37 4.45
609 2912 0.545309 CAGACTTGGTCTCCCAGGGA 60.545 60.000 8.35 8.35 41.37 4.20
610 2913 0.193574 AGACTTGGTCTCCCAGGGAA 59.806 55.000 10.32 0.00 38.71 3.97
611 2914 0.325272 GACTTGGTCTCCCAGGGAAC 59.675 60.000 10.32 10.62 42.02 3.62
612 2915 0.401395 ACTTGGTCTCCCAGGGAACA 60.401 55.000 10.32 6.37 42.02 3.18
613 2916 0.326264 CTTGGTCTCCCAGGGAACAG 59.674 60.000 10.32 0.00 43.15 3.16
614 2917 0.401395 TTGGTCTCCCAGGGAACAGT 60.401 55.000 10.32 0.00 43.15 3.55
615 2918 0.836400 TGGTCTCCCAGGGAACAGTC 60.836 60.000 10.32 0.00 35.17 3.51
616 2919 1.592223 GTCTCCCAGGGAACAGTCG 59.408 63.158 10.32 0.00 0.00 4.18
617 2920 2.266055 CTCCCAGGGAACAGTCGC 59.734 66.667 10.32 0.00 36.97 5.19
618 2921 3.316573 CTCCCAGGGAACAGTCGCC 62.317 68.421 10.32 0.00 37.42 5.54
619 2922 3.636231 CCCAGGGAACAGTCGCCA 61.636 66.667 0.00 0.00 37.42 5.69
620 2923 2.046892 CCAGGGAACAGTCGCCAG 60.047 66.667 0.00 0.00 37.42 4.85
621 2924 2.583441 CCAGGGAACAGTCGCCAGA 61.583 63.158 0.00 0.00 37.42 3.86
622 2925 1.599047 CAGGGAACAGTCGCCAGAT 59.401 57.895 0.00 0.00 37.42 2.90
623 2926 0.824109 CAGGGAACAGTCGCCAGATA 59.176 55.000 0.00 0.00 37.42 1.98
624 2927 1.207089 CAGGGAACAGTCGCCAGATAA 59.793 52.381 0.00 0.00 37.42 1.75
625 2928 1.207329 AGGGAACAGTCGCCAGATAAC 59.793 52.381 0.00 0.00 37.42 1.89
626 2929 1.066430 GGGAACAGTCGCCAGATAACA 60.066 52.381 0.00 0.00 0.00 2.41
627 2930 2.420129 GGGAACAGTCGCCAGATAACAT 60.420 50.000 0.00 0.00 0.00 2.71
628 2931 3.270877 GGAACAGTCGCCAGATAACATT 58.729 45.455 0.00 0.00 0.00 2.71
629 2932 3.689649 GGAACAGTCGCCAGATAACATTT 59.310 43.478 0.00 0.00 0.00 2.32
630 2933 4.201822 GGAACAGTCGCCAGATAACATTTC 60.202 45.833 0.00 0.00 0.00 2.17
631 2934 3.270877 ACAGTCGCCAGATAACATTTCC 58.729 45.455 0.00 0.00 0.00 3.13
686 2990 7.530861 GCGAATTTGCTATAGTTATGCTAACAC 59.469 37.037 10.62 0.00 32.72 3.32
729 3036 3.120321 TCACAACAGATTGCTAACCGT 57.880 42.857 0.00 0.00 39.66 4.83
782 3089 2.410730 GGATCGTGTCCGTTACAGTTTG 59.589 50.000 0.00 0.00 39.29 2.93
835 3142 0.236187 TGCGGCAAACGTATTCACAC 59.764 50.000 0.00 0.00 46.52 3.82
910 3217 0.252197 AACCCAAGCGCTACCTAAGG 59.748 55.000 12.05 8.07 0.00 2.69
964 3271 3.072211 TGCGACGAACTCTCTTCTTCTA 58.928 45.455 0.00 0.00 0.00 2.10
993 3300 3.016031 AGCACACATCAAAGAACACACA 58.984 40.909 0.00 0.00 0.00 3.72
1017 3324 1.668337 GCGATGATGATCAGGGACGAG 60.668 57.143 15.55 0.77 0.00 4.18
1030 3337 4.194720 ACGAGACTGCGGCCGATC 62.195 66.667 33.48 22.35 35.12 3.69
1031 3338 3.893763 CGAGACTGCGGCCGATCT 61.894 66.667 33.48 26.82 0.00 2.75
1032 3339 2.279120 GAGACTGCGGCCGATCTG 60.279 66.667 33.48 18.46 0.00 2.90
1033 3340 2.755876 AGACTGCGGCCGATCTGA 60.756 61.111 33.48 5.10 0.00 3.27
1034 3341 2.081425 GAGACTGCGGCCGATCTGAT 62.081 60.000 33.48 9.41 0.00 2.90
1035 3342 1.663074 GACTGCGGCCGATCTGATC 60.663 63.158 33.48 12.85 0.00 2.92
1116 3423 1.226974 CAGGCTATCGTCGGTGGTG 60.227 63.158 0.00 0.00 0.00 4.17
1194 3501 0.681175 GGGCGTATACCCGTTACCAT 59.319 55.000 0.00 0.00 40.98 3.55
1542 3849 1.608717 CCCTCTTCCCCACTGACTCG 61.609 65.000 0.00 0.00 0.00 4.18
1602 3909 3.775654 GGCCTGGGAGGAGTCACG 61.776 72.222 0.00 0.00 37.67 4.35
1636 3943 4.383552 GGGAGCATCTAGTCAACAACAGAT 60.384 45.833 0.00 0.00 33.73 2.90
1638 3945 4.764172 AGCATCTAGTCAACAACAGATCC 58.236 43.478 0.00 0.00 0.00 3.36
1640 3947 5.658634 AGCATCTAGTCAACAACAGATCCTA 59.341 40.000 0.00 0.00 0.00 2.94
1641 3948 5.751028 GCATCTAGTCAACAACAGATCCTAC 59.249 44.000 0.00 0.00 0.00 3.18
1643 3950 6.516739 TCTAGTCAACAACAGATCCTACAG 57.483 41.667 0.00 0.00 0.00 2.74
1644 3951 6.010850 TCTAGTCAACAACAGATCCTACAGT 58.989 40.000 0.00 0.00 0.00 3.55
1645 3952 7.173032 TCTAGTCAACAACAGATCCTACAGTA 58.827 38.462 0.00 0.00 0.00 2.74
1646 3953 6.026947 AGTCAACAACAGATCCTACAGTAC 57.973 41.667 0.00 0.00 0.00 2.73
1648 3955 5.047235 GTCAACAACAGATCCTACAGTACCT 60.047 44.000 0.00 0.00 0.00 3.08
1708 4075 3.157087 ACATGGAGCTCGGTTTTGAAAT 58.843 40.909 7.83 0.00 0.00 2.17
1709 4076 4.331968 ACATGGAGCTCGGTTTTGAAATA 58.668 39.130 7.83 0.00 0.00 1.40
1787 4156 2.810274 CAGATTCCATGGAGGCATAACG 59.190 50.000 15.53 0.00 37.29 3.18
1794 4163 1.356624 GGAGGCATAACGCACATGC 59.643 57.895 7.69 7.69 46.50 4.06
1808 4177 4.551056 GCACATGCGTGTAAATTTTCAG 57.449 40.909 12.10 0.00 45.50 3.02
1816 4185 4.450757 GCGTGTAAATTTTCAGGGCAAAAT 59.549 37.500 16.11 0.00 37.53 1.82
1818 4187 6.312672 GCGTGTAAATTTTCAGGGCAAAATAT 59.687 34.615 16.11 0.00 35.35 1.28
1819 4188 7.673776 GCGTGTAAATTTTCAGGGCAAAATATG 60.674 37.037 16.11 0.00 35.35 1.78
1823 4192 9.213799 GTAAATTTTCAGGGCAAAATATGTTGA 57.786 29.630 9.96 0.00 35.35 3.18
1835 4204 6.650390 GCAAAATATGTTGAAATGAGGGTTGT 59.350 34.615 9.96 0.00 0.00 3.32
1895 4287 8.135529 TGATACTATTCATTCTTGTACAGGTCG 58.864 37.037 4.75 0.00 0.00 4.79
1905 4297 2.839975 TGTACAGGTCGCATTTCAACA 58.160 42.857 0.00 0.00 0.00 3.33
1917 4309 7.255104 GGTCGCATTTCAACATATTTCATCCTA 60.255 37.037 0.00 0.00 0.00 2.94
1961 4353 7.598493 ACATAACATCCTTGTTTATTTGCACAC 59.402 33.333 0.00 0.00 43.57 3.82
1962 4354 5.528043 ACATCCTTGTTTATTTGCACACA 57.472 34.783 0.00 0.00 29.55 3.72
1963 4355 5.911752 ACATCCTTGTTTATTTGCACACAA 58.088 33.333 0.00 0.00 29.55 3.33
1964 4356 6.344500 ACATCCTTGTTTATTTGCACACAAA 58.656 32.000 0.00 0.00 40.72 2.83
2010 4402 9.986833 CCGAAAGTTTGAATTTTGAATTTTTCT 57.013 25.926 0.00 0.00 0.00 2.52
2048 4440 3.479269 GCCGAGAGCCAAACGTCG 61.479 66.667 0.00 0.00 34.35 5.12
2063 4455 5.163723 CCAAACGTCGGTTCTCACTACTATA 60.164 44.000 0.00 0.00 34.62 1.31
2070 4462 5.948162 TCGGTTCTCACTACTATACCAACTT 59.052 40.000 0.00 0.00 0.00 2.66
2113 4505 9.279904 CGAATGCGTACCAAATTTTTATAGAAA 57.720 29.630 0.00 0.00 0.00 2.52
2117 4509 9.221933 TGCGTACCAAATTTTTATAGAAAGAGA 57.778 29.630 0.00 0.00 0.00 3.10
2118 4510 9.704098 GCGTACCAAATTTTTATAGAAAGAGAG 57.296 33.333 0.00 0.00 0.00 3.20
2169 4561 1.660575 CGAACAACGAGCGTCACCT 60.661 57.895 0.00 0.00 45.77 4.00
2174 4566 1.300697 AACGAGCGTCACCTTCCAC 60.301 57.895 0.00 0.00 0.00 4.02
2191 4583 0.527565 CACCCTTGATGCCGAAAAGG 59.472 55.000 0.00 0.00 44.97 3.11
2203 4595 1.271163 CCGAAAAGGAGGTGGCAAGTA 60.271 52.381 0.00 0.00 45.00 2.24
2204 4596 2.076863 CGAAAAGGAGGTGGCAAGTAG 58.923 52.381 0.00 0.00 0.00 2.57
2209 4601 0.464554 GGAGGTGGCAAGTAGATGGC 60.465 60.000 0.00 0.00 45.44 4.40
2221 4613 1.476891 GTAGATGGCGAGACTTGGTCA 59.523 52.381 0.52 0.00 34.60 4.02
2238 4630 0.690762 TCAGTCCACTAAAGCCACCC 59.309 55.000 0.00 0.00 0.00 4.61
2240 4632 0.984995 AGTCCACTAAAGCCACCCTC 59.015 55.000 0.00 0.00 0.00 4.30
2248 4640 0.402121 AAAGCCACCCTCTTGGACTC 59.598 55.000 0.00 0.00 39.24 3.36
2278 4670 0.179145 ACGTACATAGCGCCACTGAC 60.179 55.000 2.29 0.00 0.00 3.51
2297 4689 1.275291 ACGATCACCTTGGACAACGAT 59.725 47.619 0.00 0.00 0.00 3.73
2322 4714 1.623811 ACCGGAAGTAGAGCAACATGT 59.376 47.619 9.46 0.00 0.00 3.21
2352 4744 1.270968 CGTGTCATCAAGCGCGATC 59.729 57.895 12.10 0.00 40.54 3.69
2359 4751 1.971505 ATCAAGCGCGATCCTCCCAA 61.972 55.000 12.10 0.00 0.00 4.12
2371 4763 2.584236 TCCTCCCAATAGAGTAGCGAC 58.416 52.381 0.00 0.00 31.53 5.19
2375 4767 3.544684 TCCCAATAGAGTAGCGACGTTA 58.455 45.455 0.00 0.00 0.00 3.18
2381 4773 3.484334 AGAGTAGCGACGTTAAGAACC 57.516 47.619 0.00 0.00 0.00 3.62
2382 4774 2.159599 AGAGTAGCGACGTTAAGAACCG 60.160 50.000 0.00 0.00 0.00 4.44
2383 4775 1.537202 AGTAGCGACGTTAAGAACCGT 59.463 47.619 0.00 0.00 40.54 4.83
2384 4776 2.030805 AGTAGCGACGTTAAGAACCGTT 60.031 45.455 0.00 0.00 37.44 4.44
2385 4777 1.134226 AGCGACGTTAAGAACCGTTG 58.866 50.000 0.00 0.00 40.58 4.10
2386 4778 0.162294 GCGACGTTAAGAACCGTTGG 59.838 55.000 0.00 0.00 38.58 3.77
2387 4779 0.162294 CGACGTTAAGAACCGTTGGC 59.838 55.000 0.00 0.00 37.44 4.52
2388 4780 1.219646 GACGTTAAGAACCGTTGGCA 58.780 50.000 0.00 0.00 37.44 4.92
2389 4781 1.193874 GACGTTAAGAACCGTTGGCAG 59.806 52.381 0.00 0.00 37.44 4.85
2390 4782 1.202557 ACGTTAAGAACCGTTGGCAGA 60.203 47.619 0.00 0.00 32.50 4.26
2391 4783 1.193874 CGTTAAGAACCGTTGGCAGAC 59.806 52.381 0.00 0.00 0.00 3.51
2392 4784 1.534163 GTTAAGAACCGTTGGCAGACC 59.466 52.381 0.00 0.00 0.00 3.85
2393 4785 0.035739 TAAGAACCGTTGGCAGACCC 59.964 55.000 0.00 0.00 33.59 4.46
2394 4786 3.047877 GAACCGTTGGCAGACCCG 61.048 66.667 0.00 0.00 35.87 5.28
2395 4787 3.819877 GAACCGTTGGCAGACCCGT 62.820 63.158 0.00 0.00 35.87 5.28
2396 4788 3.409605 AACCGTTGGCAGACCCGTT 62.410 57.895 0.00 0.00 35.87 4.44
2397 4789 3.353836 CCGTTGGCAGACCCGTTG 61.354 66.667 0.00 0.00 35.87 4.10
2398 4790 2.280524 CGTTGGCAGACCCGTTGA 60.281 61.111 0.00 0.00 35.87 3.18
2399 4791 2.604174 CGTTGGCAGACCCGTTGAC 61.604 63.158 0.00 0.00 35.87 3.18
2400 4792 1.227853 GTTGGCAGACCCGTTGACT 60.228 57.895 0.00 0.00 35.87 3.41
2401 4793 0.034337 GTTGGCAGACCCGTTGACTA 59.966 55.000 0.00 0.00 35.87 2.59
2402 4794 0.759959 TTGGCAGACCCGTTGACTAA 59.240 50.000 0.00 0.00 35.87 2.24
2403 4795 0.981183 TGGCAGACCCGTTGACTAAT 59.019 50.000 0.00 0.00 35.87 1.73
2404 4796 1.066430 TGGCAGACCCGTTGACTAATC 60.066 52.381 0.00 0.00 35.87 1.75
2405 4797 1.653151 GCAGACCCGTTGACTAATCC 58.347 55.000 0.00 0.00 0.00 3.01
2406 4798 1.207329 GCAGACCCGTTGACTAATCCT 59.793 52.381 0.00 0.00 0.00 3.24
2407 4799 2.738964 GCAGACCCGTTGACTAATCCTC 60.739 54.545 0.00 0.00 0.00 3.71
2408 4800 2.761208 CAGACCCGTTGACTAATCCTCT 59.239 50.000 0.00 0.00 0.00 3.69
2409 4801 3.195825 CAGACCCGTTGACTAATCCTCTT 59.804 47.826 0.00 0.00 0.00 2.85
2410 4802 3.447944 AGACCCGTTGACTAATCCTCTTC 59.552 47.826 0.00 0.00 0.00 2.87
2411 4803 2.500504 ACCCGTTGACTAATCCTCTTCC 59.499 50.000 0.00 0.00 0.00 3.46
2412 4804 2.500098 CCCGTTGACTAATCCTCTTCCA 59.500 50.000 0.00 0.00 0.00 3.53
2413 4805 3.522553 CCGTTGACTAATCCTCTTCCAC 58.477 50.000 0.00 0.00 0.00 4.02
2414 4806 3.179830 CGTTGACTAATCCTCTTCCACG 58.820 50.000 0.00 0.00 0.00 4.94
2415 4807 3.119602 CGTTGACTAATCCTCTTCCACGA 60.120 47.826 0.00 0.00 0.00 4.35
2416 4808 4.425520 GTTGACTAATCCTCTTCCACGAG 58.574 47.826 0.00 0.00 0.00 4.18
2417 4809 2.427453 TGACTAATCCTCTTCCACGAGC 59.573 50.000 0.00 0.00 0.00 5.03
2418 4810 2.427453 GACTAATCCTCTTCCACGAGCA 59.573 50.000 0.00 0.00 0.00 4.26
2419 4811 2.832129 ACTAATCCTCTTCCACGAGCAA 59.168 45.455 0.00 0.00 0.00 3.91
2420 4812 2.859165 AATCCTCTTCCACGAGCAAA 57.141 45.000 0.00 0.00 0.00 3.68
2421 4813 2.859165 ATCCTCTTCCACGAGCAAAA 57.141 45.000 0.00 0.00 0.00 2.44
2422 4814 1.878953 TCCTCTTCCACGAGCAAAAC 58.121 50.000 0.00 0.00 0.00 2.43
2423 4815 1.140052 TCCTCTTCCACGAGCAAAACA 59.860 47.619 0.00 0.00 0.00 2.83
2424 4816 2.154462 CCTCTTCCACGAGCAAAACAT 58.846 47.619 0.00 0.00 0.00 2.71
2425 4817 2.095567 CCTCTTCCACGAGCAAAACATG 60.096 50.000 0.00 0.00 0.00 3.21
2426 4818 2.807967 CTCTTCCACGAGCAAAACATGA 59.192 45.455 0.00 0.00 0.00 3.07
2427 4819 3.411446 TCTTCCACGAGCAAAACATGAT 58.589 40.909 0.00 0.00 0.00 2.45
2428 4820 3.436704 TCTTCCACGAGCAAAACATGATC 59.563 43.478 0.00 0.00 41.11 2.92
2429 4821 2.777094 TCCACGAGCAAAACATGATCA 58.223 42.857 0.00 0.00 44.81 2.92
2430 4822 2.743664 TCCACGAGCAAAACATGATCAG 59.256 45.455 0.00 0.00 44.81 2.90
2431 4823 2.512885 CACGAGCAAAACATGATCAGC 58.487 47.619 0.00 0.00 44.81 4.26
2432 4824 2.095617 CACGAGCAAAACATGATCAGCA 60.096 45.455 0.00 0.00 44.81 4.41
2433 4825 2.095567 ACGAGCAAAACATGATCAGCAC 60.096 45.455 0.00 0.00 44.81 4.40
2434 4826 2.730090 CGAGCAAAACATGATCAGCACC 60.730 50.000 0.00 0.00 44.81 5.01
2435 4827 2.229543 GAGCAAAACATGATCAGCACCA 59.770 45.455 0.00 0.00 43.99 4.17
2436 4828 2.629137 AGCAAAACATGATCAGCACCAA 59.371 40.909 0.00 0.00 0.00 3.67
2437 4829 2.991190 GCAAAACATGATCAGCACCAAG 59.009 45.455 0.00 0.00 0.00 3.61
2438 4830 3.305539 GCAAAACATGATCAGCACCAAGA 60.306 43.478 0.00 0.00 0.00 3.02
2439 4831 4.232221 CAAAACATGATCAGCACCAAGAC 58.768 43.478 0.00 0.00 0.00 3.01
2440 4832 3.430042 AACATGATCAGCACCAAGACT 57.570 42.857 0.00 0.00 0.00 3.24
2441 4833 2.983229 ACATGATCAGCACCAAGACTC 58.017 47.619 0.00 0.00 0.00 3.36
2442 4834 2.286872 CATGATCAGCACCAAGACTCC 58.713 52.381 0.09 0.00 0.00 3.85
2443 4835 1.351076 TGATCAGCACCAAGACTCCA 58.649 50.000 0.00 0.00 0.00 3.86
2444 4836 1.911357 TGATCAGCACCAAGACTCCAT 59.089 47.619 0.00 0.00 0.00 3.41
2445 4837 2.286872 GATCAGCACCAAGACTCCATG 58.713 52.381 0.00 0.00 0.00 3.66
2446 4838 0.325933 TCAGCACCAAGACTCCATGG 59.674 55.000 4.97 4.97 42.60 3.66
2447 4839 0.679002 CAGCACCAAGACTCCATGGG 60.679 60.000 13.02 5.22 41.17 4.00
2448 4840 1.136329 AGCACCAAGACTCCATGGGT 61.136 55.000 13.02 8.85 41.17 4.51
2449 4841 3.254629 CACCAAGACTCCATGGGTG 57.745 57.895 13.02 6.27 42.57 4.61
2450 4842 0.401738 CACCAAGACTCCATGGGTGT 59.598 55.000 13.02 11.47 43.08 4.16
2451 4843 1.149101 ACCAAGACTCCATGGGTGTT 58.851 50.000 13.02 10.64 41.17 3.32
2452 4844 2.039746 CACCAAGACTCCATGGGTGTTA 59.960 50.000 13.02 0.00 43.08 2.41
2453 4845 2.919602 ACCAAGACTCCATGGGTGTTAT 59.080 45.455 13.02 3.18 41.17 1.89
2454 4846 4.080582 CACCAAGACTCCATGGGTGTTATA 60.081 45.833 13.02 0.00 43.08 0.98
2455 4847 4.538490 ACCAAGACTCCATGGGTGTTATAA 59.462 41.667 13.02 0.00 41.17 0.98
2456 4848 5.193728 ACCAAGACTCCATGGGTGTTATAAT 59.806 40.000 13.02 0.00 41.17 1.28
2457 4849 5.765182 CCAAGACTCCATGGGTGTTATAATC 59.235 44.000 13.02 0.00 32.87 1.75
2458 4850 6.356556 CAAGACTCCATGGGTGTTATAATCA 58.643 40.000 13.02 0.00 28.96 2.57
2459 4851 6.770286 AGACTCCATGGGTGTTATAATCAT 57.230 37.500 13.02 0.00 28.96 2.45
2460 4852 7.154191 AGACTCCATGGGTGTTATAATCATT 57.846 36.000 13.02 0.00 28.96 2.57
2461 4853 8.275187 AGACTCCATGGGTGTTATAATCATTA 57.725 34.615 13.02 0.00 28.96 1.90
2462 4854 8.894592 AGACTCCATGGGTGTTATAATCATTAT 58.105 33.333 13.02 0.00 28.96 1.28
2494 4886 9.979578 AATCTAGATTATTGACTCTAGTGCAAG 57.020 33.333 16.50 0.00 41.08 4.01
2495 4887 8.526667 TCTAGATTATTGACTCTAGTGCAAGT 57.473 34.615 0.00 0.00 41.08 3.16
2496 4888 8.409371 TCTAGATTATTGACTCTAGTGCAAGTG 58.591 37.037 0.00 0.00 41.08 3.16
2497 4889 6.344500 AGATTATTGACTCTAGTGCAAGTGG 58.656 40.000 0.00 0.00 0.00 4.00
2498 4890 2.839486 TTGACTCTAGTGCAAGTGGG 57.161 50.000 0.00 0.00 0.00 4.61
2499 4891 2.009681 TGACTCTAGTGCAAGTGGGA 57.990 50.000 0.00 0.00 0.00 4.37
2500 4892 1.895798 TGACTCTAGTGCAAGTGGGAG 59.104 52.381 0.00 0.00 0.00 4.30
2501 4893 2.171840 GACTCTAGTGCAAGTGGGAGA 58.828 52.381 0.00 0.00 0.00 3.71
2502 4894 1.896465 ACTCTAGTGCAAGTGGGAGAC 59.104 52.381 0.00 0.00 0.00 3.36
2517 4909 2.879026 GGGAGACCGAAAGAAATATGCC 59.121 50.000 0.00 0.00 43.64 4.40
2518 4910 2.879026 GGAGACCGAAAGAAATATGCCC 59.121 50.000 0.00 0.00 0.00 5.36
2519 4911 3.433740 GGAGACCGAAAGAAATATGCCCT 60.434 47.826 0.00 0.00 0.00 5.19
2520 4912 4.202326 GGAGACCGAAAGAAATATGCCCTA 60.202 45.833 0.00 0.00 0.00 3.53
2521 4913 4.962155 AGACCGAAAGAAATATGCCCTAG 58.038 43.478 0.00 0.00 0.00 3.02
2522 4914 4.654262 AGACCGAAAGAAATATGCCCTAGA 59.346 41.667 0.00 0.00 0.00 2.43
2523 4915 4.962155 ACCGAAAGAAATATGCCCTAGAG 58.038 43.478 0.00 0.00 0.00 2.43
2524 4916 4.202367 ACCGAAAGAAATATGCCCTAGAGG 60.202 45.833 0.00 0.00 39.47 3.69
2602 4994 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
2603 4995 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
2604 4996 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
2605 4997 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
2606 4998 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
2607 4999 7.107542 TGCTAGAATTGTATTAACCGGAAACT 58.892 34.615 9.46 0.00 0.00 2.66
2608 5000 7.608761 TGCTAGAATTGTATTAACCGGAAACTT 59.391 33.333 9.46 0.00 0.00 2.66
2609 5001 7.908601 GCTAGAATTGTATTAACCGGAAACTTG 59.091 37.037 9.46 0.00 0.00 3.16
2610 5002 7.989416 AGAATTGTATTAACCGGAAACTTGA 57.011 32.000 9.46 0.00 0.00 3.02
2611 5003 8.575649 AGAATTGTATTAACCGGAAACTTGAT 57.424 30.769 9.46 0.00 0.00 2.57
2612 5004 9.675464 AGAATTGTATTAACCGGAAACTTGATA 57.325 29.630 9.46 0.00 0.00 2.15
2613 5005 9.712359 GAATTGTATTAACCGGAAACTTGATAC 57.288 33.333 9.46 9.36 0.00 2.24
2614 5006 8.795842 ATTGTATTAACCGGAAACTTGATACA 57.204 30.769 9.46 11.96 30.33 2.29
2615 5007 8.795842 TTGTATTAACCGGAAACTTGATACAT 57.204 30.769 9.46 0.00 31.55 2.29
2616 5008 8.203937 TGTATTAACCGGAAACTTGATACATG 57.796 34.615 9.46 0.00 28.53 3.21
2617 5009 7.825270 TGTATTAACCGGAAACTTGATACATGT 59.175 33.333 9.46 2.69 28.53 3.21
2618 5010 6.489127 TTAACCGGAAACTTGATACATGTG 57.511 37.500 9.46 0.00 0.00 3.21
2619 5011 4.015872 ACCGGAAACTTGATACATGTGT 57.984 40.909 9.46 0.10 0.00 3.72
2620 5012 3.751175 ACCGGAAACTTGATACATGTGTG 59.249 43.478 9.46 0.00 0.00 3.82
2621 5013 3.126858 CCGGAAACTTGATACATGTGTGG 59.873 47.826 9.11 0.00 0.00 4.17
2622 5014 4.000325 CGGAAACTTGATACATGTGTGGA 59.000 43.478 9.11 0.00 0.00 4.02
2623 5015 4.635765 CGGAAACTTGATACATGTGTGGAT 59.364 41.667 9.11 0.00 0.00 3.41
2624 5016 5.815222 CGGAAACTTGATACATGTGTGGATA 59.185 40.000 9.11 0.00 0.00 2.59
2625 5017 6.238103 CGGAAACTTGATACATGTGTGGATAC 60.238 42.308 9.11 0.00 0.00 2.24
2641 5033 5.155278 TGGATACATAGACAAAACACCGT 57.845 39.130 0.00 0.00 46.17 4.83
2642 5034 4.932799 TGGATACATAGACAAAACACCGTG 59.067 41.667 0.00 0.00 46.17 4.94
2643 5035 4.933400 GGATACATAGACAAAACACCGTGT 59.067 41.667 0.00 0.00 0.00 4.49
2644 5036 5.063060 GGATACATAGACAAAACACCGTGTC 59.937 44.000 4.23 0.00 43.70 3.67
2645 5037 3.135994 ACATAGACAAAACACCGTGTCC 58.864 45.455 4.23 0.00 44.30 4.02
2646 5038 2.243602 TAGACAAAACACCGTGTCCC 57.756 50.000 4.23 0.00 44.30 4.46
2647 5039 0.544697 AGACAAAACACCGTGTCCCT 59.455 50.000 4.23 0.00 44.30 4.20
2648 5040 1.764134 AGACAAAACACCGTGTCCCTA 59.236 47.619 4.23 0.00 44.30 3.53
2649 5041 2.140717 GACAAAACACCGTGTCCCTAG 58.859 52.381 4.23 0.00 38.57 3.02
2650 5042 1.487558 ACAAAACACCGTGTCCCTAGT 59.512 47.619 4.23 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.146010 ACTTCCACTTTTCTTTTGCACAA 57.854 34.783 0.00 0.00 0.00 3.33
108 109 6.014327 AGGATGGGCATTTTTATTATTGCGAT 60.014 34.615 0.00 0.00 35.95 4.58
152 153 7.175816 TGGCAGTTTTATTTACAAGAGCATGTA 59.824 33.333 0.00 0.00 34.75 2.29
322 666 4.099419 GGGTGGCATTTTATTGTAAGAGGG 59.901 45.833 0.00 0.00 0.00 4.30
330 674 5.888161 ACTAGAAGAGGGTGGCATTTTATTG 59.112 40.000 0.00 0.00 0.00 1.90
353 698 4.061596 ACTTTCTCACAGAGCAGCTTTAC 58.938 43.478 0.00 0.00 0.00 2.01
450 797 9.139174 GGATTGTTAACATTCATGGTAAAACTG 57.861 33.333 24.42 0.00 41.21 3.16
458 805 5.203528 AGAGGGGATTGTTAACATTCATGG 58.796 41.667 24.42 0.00 0.00 3.66
490 837 2.503382 GCGAGGGGTTTTTGGCCAA 61.503 57.895 16.05 16.05 0.00 4.52
492 839 2.434658 CTTGCGAGGGGTTTTTGGCC 62.435 60.000 0.00 0.00 0.00 5.36
523 870 1.152631 CCACGTTGGGGGAGGTTTT 60.153 57.895 0.00 0.00 32.67 2.43
566 2863 0.865769 TTCTTGGCGAACGCTTCTTC 59.134 50.000 18.14 2.64 41.60 2.87
569 2872 0.247301 CGATTCTTGGCGAACGCTTC 60.247 55.000 18.14 4.03 41.60 3.86
573 2876 0.366871 CTGTCGATTCTTGGCGAACG 59.633 55.000 0.00 0.00 38.36 3.95
598 2901 1.592223 CGACTGTTCCCTGGGAGAC 59.408 63.158 16.38 16.43 31.21 3.36
599 2902 2.283529 GCGACTGTTCCCTGGGAGA 61.284 63.158 16.38 5.95 31.21 3.71
600 2903 2.266055 GCGACTGTTCCCTGGGAG 59.734 66.667 16.38 7.24 31.21 4.30
602 2905 3.612247 CTGGCGACTGTTCCCTGGG 62.612 68.421 6.33 6.33 0.00 4.45
604 2907 0.824109 TATCTGGCGACTGTTCCCTG 59.176 55.000 0.00 0.38 0.00 4.45
605 2908 1.207329 GTTATCTGGCGACTGTTCCCT 59.793 52.381 0.00 0.00 0.00 4.20
606 2909 1.066430 TGTTATCTGGCGACTGTTCCC 60.066 52.381 0.00 0.00 0.00 3.97
607 2910 2.380084 TGTTATCTGGCGACTGTTCC 57.620 50.000 0.00 0.00 0.00 3.62
608 2911 4.201822 GGAAATGTTATCTGGCGACTGTTC 60.202 45.833 0.00 0.00 0.00 3.18
609 2912 3.689649 GGAAATGTTATCTGGCGACTGTT 59.310 43.478 0.00 0.00 0.00 3.16
610 2913 3.270877 GGAAATGTTATCTGGCGACTGT 58.729 45.455 0.00 0.00 0.00 3.55
611 2914 3.270027 TGGAAATGTTATCTGGCGACTG 58.730 45.455 0.00 0.00 0.00 3.51
612 2915 3.627395 TGGAAATGTTATCTGGCGACT 57.373 42.857 0.00 0.00 0.00 4.18
613 2916 4.695217 TTTGGAAATGTTATCTGGCGAC 57.305 40.909 0.00 0.00 0.00 5.19
614 2917 5.713792 TTTTTGGAAATGTTATCTGGCGA 57.286 34.783 0.00 0.00 0.00 5.54
678 2982 8.458052 CAAACCTGAATTGTATATGTGTTAGCA 58.542 33.333 0.00 0.00 0.00 3.49
686 2990 7.692291 GTGAACGTCAAACCTGAATTGTATATG 59.308 37.037 0.00 0.00 31.88 1.78
700 3007 3.482110 GCAATCTGTTGTGAACGTCAAAC 59.518 43.478 0.00 0.00 37.65 2.93
729 3036 1.266446 TCGTAACAATCGTGGTCGTGA 59.734 47.619 0.00 0.00 38.33 4.35
782 3089 2.155279 GGCAAGGAGAGGACAAAGTTC 58.845 52.381 0.00 0.00 0.00 3.01
835 3142 2.278857 CGGAGATCTCAACCGGCG 60.279 66.667 23.85 12.96 42.48 6.46
874 3181 0.645868 GTTGAATACGTCGAGCTGGC 59.354 55.000 0.00 0.00 0.00 4.85
922 3229 4.549458 CAGTCGTTTCCAAGCATGATTTT 58.451 39.130 0.00 0.00 0.00 1.82
923 3230 3.612479 GCAGTCGTTTCCAAGCATGATTT 60.612 43.478 0.00 0.00 0.00 2.17
964 3271 3.953612 TCTTTGATGTGTGCTTCACCTTT 59.046 39.130 9.37 0.00 45.61 3.11
984 3291 0.969149 TCATCGCCTCTGTGTGTTCT 59.031 50.000 0.00 0.00 0.00 3.01
988 3295 2.133553 GATCATCATCGCCTCTGTGTG 58.866 52.381 0.00 0.00 0.00 3.82
993 3300 0.975135 CCCTGATCATCATCGCCTCT 59.025 55.000 0.00 0.00 0.00 3.69
1017 3324 1.663074 GATCAGATCGGCCGCAGTC 60.663 63.158 23.51 18.05 0.00 3.51
1177 3484 1.606224 CCCATGGTAACGGGTATACGC 60.606 57.143 11.73 9.80 37.70 4.42
1182 3489 1.909228 CTGCCCATGGTAACGGGTA 59.091 57.895 11.73 0.00 45.07 3.69
1456 3763 2.279069 ATATCCCGAGCCGCTCCAG 61.279 63.158 14.85 6.40 0.00 3.86
1542 3849 2.033424 GGCGAATCTTGTATTCTTGGCC 59.967 50.000 0.00 0.00 0.00 5.36
1590 3897 0.461961 CTGATTCCGTGACTCCTCCC 59.538 60.000 0.00 0.00 0.00 4.30
1602 3909 0.536915 GATGCTCCCTGGCTGATTCC 60.537 60.000 0.00 0.00 0.00 3.01
1636 3943 8.342327 ACTACTCCTATTTAGGTACTGTAGGA 57.658 38.462 19.59 0.00 42.12 2.94
1638 3945 9.624373 TCAACTACTCCTATTTAGGTACTGTAG 57.376 37.037 16.96 16.96 44.02 2.74
1691 4032 5.560966 TGAATATTTCAAAACCGAGCTCC 57.439 39.130 8.47 0.00 36.59 4.70
1772 4141 0.747644 TGTGCGTTATGCCTCCATGG 60.748 55.000 4.97 4.97 45.60 3.66
1794 4163 7.330700 ACATATTTTGCCCTGAAAATTTACACG 59.669 33.333 0.00 0.00 36.94 4.49
1799 4168 8.688747 TTCAACATATTTTGCCCTGAAAATTT 57.311 26.923 0.00 0.00 36.94 1.82
1808 4177 5.118286 CCCTCATTTCAACATATTTTGCCC 58.882 41.667 0.00 0.00 0.00 5.36
1816 4185 4.148079 TGCACAACCCTCATTTCAACATA 58.852 39.130 0.00 0.00 0.00 2.29
1818 4187 2.382882 TGCACAACCCTCATTTCAACA 58.617 42.857 0.00 0.00 0.00 3.33
1819 4188 3.451141 TTGCACAACCCTCATTTCAAC 57.549 42.857 0.00 0.00 0.00 3.18
1846 4215 9.768662 ATCATGTGTTAAAAAGCTTCAGATTTT 57.231 25.926 0.00 0.00 44.36 1.82
1882 4251 3.394674 TGAAATGCGACCTGTACAAGA 57.605 42.857 0.00 0.00 0.00 3.02
1889 4281 5.639757 TGAAATATGTTGAAATGCGACCTG 58.360 37.500 0.00 0.00 0.00 4.00
1975 4367 9.387123 CAAAATTCAAACTTTCGGTTTCAAAAA 57.613 25.926 0.00 0.00 45.26 1.94
1976 4368 8.774586 TCAAAATTCAAACTTTCGGTTTCAAAA 58.225 25.926 0.00 0.00 45.26 2.44
1977 4369 8.311650 TCAAAATTCAAACTTTCGGTTTCAAA 57.688 26.923 0.00 0.00 45.26 2.69
1978 4370 7.891183 TCAAAATTCAAACTTTCGGTTTCAA 57.109 28.000 0.00 0.00 45.26 2.69
1979 4371 7.891183 TTCAAAATTCAAACTTTCGGTTTCA 57.109 28.000 0.00 0.00 45.26 2.69
1980 4372 9.767684 AAATTCAAAATTCAAACTTTCGGTTTC 57.232 25.926 0.00 0.00 45.26 2.78
1983 4375 9.767684 GAAAAATTCAAAATTCAAACTTTCGGT 57.232 25.926 0.00 0.00 0.00 4.69
1984 4376 9.986833 AGAAAAATTCAAAATTCAAACTTTCGG 57.013 25.926 0.00 0.00 0.00 4.30
2010 4402 4.466015 GGCCTCCATGGAATGTTCTTTTTA 59.534 41.667 17.00 0.00 44.81 1.52
2016 4408 0.107214 TCGGCCTCCATGGAATGTTC 60.107 55.000 17.00 3.08 44.81 3.18
2017 4409 0.107017 CTCGGCCTCCATGGAATGTT 60.107 55.000 17.00 0.00 44.81 2.71
2018 4410 0.982852 TCTCGGCCTCCATGGAATGT 60.983 55.000 17.00 0.00 44.81 2.71
2020 4412 2.049627 GCTCTCGGCCTCCATGGAAT 62.050 60.000 17.00 0.00 38.35 3.01
2021 4413 2.735772 GCTCTCGGCCTCCATGGAA 61.736 63.158 17.00 0.00 38.35 3.53
2045 4437 5.356470 AGTTGGTATAGTAGTGAGAACCGAC 59.644 44.000 0.00 0.00 40.33 4.79
2048 4440 8.843885 AAAAAGTTGGTATAGTAGTGAGAACC 57.156 34.615 0.00 0.00 0.00 3.62
2076 4468 3.307829 CGCATTCGTGTACTCTCGT 57.692 52.632 0.00 0.00 33.21 4.18
2113 4505 9.620259 AGTCTTTTTGTACTTGAAATTCTCTCT 57.380 29.630 0.00 0.00 0.00 3.10
2126 4518 9.925268 CGTAACAAATTGTAGTCTTTTTGTACT 57.075 29.630 0.00 0.00 40.39 2.73
2127 4519 9.919348 TCGTAACAAATTGTAGTCTTTTTGTAC 57.081 29.630 0.00 0.00 40.39 2.90
2129 4521 9.281075 GTTCGTAACAAATTGTAGTCTTTTTGT 57.719 29.630 0.00 0.00 42.40 2.83
2130 4522 9.279904 TGTTCGTAACAAATTGTAGTCTTTTTG 57.720 29.630 0.00 0.00 38.72 2.44
2150 4542 1.947642 GGTGACGCTCGTTGTTCGT 60.948 57.895 0.00 0.00 40.80 3.85
2169 4561 0.111446 TTTCGGCATCAAGGGTGGAA 59.889 50.000 0.00 0.00 0.00 3.53
2174 4566 1.098050 CTCCTTTTCGGCATCAAGGG 58.902 55.000 5.91 0.00 38.13 3.95
2191 4583 0.811616 CGCCATCTACTTGCCACCTC 60.812 60.000 0.00 0.00 0.00 3.85
2203 4595 0.534412 CTGACCAAGTCTCGCCATCT 59.466 55.000 0.00 0.00 33.15 2.90
2204 4596 0.247736 ACTGACCAAGTCTCGCCATC 59.752 55.000 0.00 0.00 31.64 3.51
2221 4613 0.984995 GAGGGTGGCTTTAGTGGACT 59.015 55.000 0.00 0.00 0.00 3.85
2226 4618 1.351350 GTCCAAGAGGGTGGCTTTAGT 59.649 52.381 0.00 0.00 38.68 2.24
2248 4640 2.720561 TATGTACGTCATCGCCGGCG 62.721 60.000 42.13 42.13 41.18 6.46
2278 4670 1.660607 CATCGTTGTCCAAGGTGATCG 59.339 52.381 0.29 0.00 0.00 3.69
2297 4689 0.898326 TGCTCTACTTCCGGTGCTCA 60.898 55.000 0.00 0.00 0.00 4.26
2322 4714 1.272490 GATGACACGGTCTTGAGGTCA 59.728 52.381 0.00 0.00 42.07 4.02
2352 4744 1.267261 CGTCGCTACTCTATTGGGAGG 59.733 57.143 0.00 0.00 37.63 4.30
2359 4751 4.260538 CGGTTCTTAACGTCGCTACTCTAT 60.261 45.833 0.00 0.00 0.00 1.98
2371 4763 1.193874 GTCTGCCAACGGTTCTTAACG 59.806 52.381 0.00 0.00 0.00 3.18
2375 4767 1.228154 GGGTCTGCCAACGGTTCTT 60.228 57.895 0.00 0.00 36.17 2.52
2381 4773 2.280524 TCAACGGGTCTGCCAACG 60.281 61.111 0.00 0.00 36.17 4.10
2382 4774 0.034337 TAGTCAACGGGTCTGCCAAC 59.966 55.000 0.00 0.00 36.17 3.77
2383 4775 0.759959 TTAGTCAACGGGTCTGCCAA 59.240 50.000 0.00 0.00 36.17 4.52
2384 4776 0.981183 ATTAGTCAACGGGTCTGCCA 59.019 50.000 0.00 0.00 36.17 4.92
2385 4777 1.653151 GATTAGTCAACGGGTCTGCC 58.347 55.000 0.00 0.00 0.00 4.85
2386 4778 1.207329 AGGATTAGTCAACGGGTCTGC 59.793 52.381 0.00 0.00 0.00 4.26
2387 4779 2.761208 AGAGGATTAGTCAACGGGTCTG 59.239 50.000 0.00 0.00 0.00 3.51
2388 4780 3.103080 AGAGGATTAGTCAACGGGTCT 57.897 47.619 0.00 0.00 0.00 3.85
2389 4781 3.430513 GGAAGAGGATTAGTCAACGGGTC 60.431 52.174 0.00 0.00 0.00 4.46
2390 4782 2.500504 GGAAGAGGATTAGTCAACGGGT 59.499 50.000 0.00 0.00 0.00 5.28
2391 4783 2.500098 TGGAAGAGGATTAGTCAACGGG 59.500 50.000 0.00 0.00 0.00 5.28
2392 4784 3.522553 GTGGAAGAGGATTAGTCAACGG 58.477 50.000 0.00 0.00 0.00 4.44
2393 4785 3.119602 TCGTGGAAGAGGATTAGTCAACG 60.120 47.826 0.00 0.00 0.00 4.10
2394 4786 4.425520 CTCGTGGAAGAGGATTAGTCAAC 58.574 47.826 0.00 0.00 34.74 3.18
2395 4787 3.119101 GCTCGTGGAAGAGGATTAGTCAA 60.119 47.826 0.00 0.00 38.63 3.18
2396 4788 2.427453 GCTCGTGGAAGAGGATTAGTCA 59.573 50.000 0.00 0.00 38.63 3.41
2397 4789 2.427453 TGCTCGTGGAAGAGGATTAGTC 59.573 50.000 0.00 0.00 38.63 2.59
2398 4790 2.457598 TGCTCGTGGAAGAGGATTAGT 58.542 47.619 0.00 0.00 38.63 2.24
2399 4791 3.526931 TTGCTCGTGGAAGAGGATTAG 57.473 47.619 0.00 0.00 38.37 1.73
2400 4792 3.973206 TTTGCTCGTGGAAGAGGATTA 57.027 42.857 0.00 0.00 38.37 1.75
2401 4793 2.814336 GTTTTGCTCGTGGAAGAGGATT 59.186 45.455 0.00 0.00 38.37 3.01
2402 4794 2.224523 TGTTTTGCTCGTGGAAGAGGAT 60.225 45.455 0.00 0.00 38.37 3.24
2403 4795 1.140052 TGTTTTGCTCGTGGAAGAGGA 59.860 47.619 0.00 0.00 38.63 3.71
2404 4796 1.593196 TGTTTTGCTCGTGGAAGAGG 58.407 50.000 0.00 0.00 38.63 3.69
2405 4797 2.807967 TCATGTTTTGCTCGTGGAAGAG 59.192 45.455 0.00 0.00 41.03 2.85
2406 4798 2.844946 TCATGTTTTGCTCGTGGAAGA 58.155 42.857 0.00 0.00 0.00 2.87
2407 4799 3.189080 TGATCATGTTTTGCTCGTGGAAG 59.811 43.478 0.00 0.00 0.00 3.46
2408 4800 3.145286 TGATCATGTTTTGCTCGTGGAA 58.855 40.909 0.00 0.00 0.00 3.53
2409 4801 2.743664 CTGATCATGTTTTGCTCGTGGA 59.256 45.455 0.00 0.00 0.00 4.02
2410 4802 2.730090 GCTGATCATGTTTTGCTCGTGG 60.730 50.000 0.00 0.00 0.00 4.94
2411 4803 2.095617 TGCTGATCATGTTTTGCTCGTG 60.096 45.455 0.00 0.00 0.00 4.35
2412 4804 2.095567 GTGCTGATCATGTTTTGCTCGT 60.096 45.455 0.00 0.00 0.00 4.18
2413 4805 2.512885 GTGCTGATCATGTTTTGCTCG 58.487 47.619 0.00 0.00 0.00 5.03
2414 4806 2.229543 TGGTGCTGATCATGTTTTGCTC 59.770 45.455 0.00 0.00 0.00 4.26
2415 4807 2.241160 TGGTGCTGATCATGTTTTGCT 58.759 42.857 0.00 0.00 0.00 3.91
2416 4808 2.728690 TGGTGCTGATCATGTTTTGC 57.271 45.000 0.00 0.00 0.00 3.68
2417 4809 4.022589 AGTCTTGGTGCTGATCATGTTTTG 60.023 41.667 0.00 0.00 0.00 2.44
2418 4810 4.147321 AGTCTTGGTGCTGATCATGTTTT 58.853 39.130 0.00 0.00 0.00 2.43
2419 4811 3.755378 GAGTCTTGGTGCTGATCATGTTT 59.245 43.478 0.00 0.00 0.00 2.83
2420 4812 3.341823 GAGTCTTGGTGCTGATCATGTT 58.658 45.455 0.00 0.00 0.00 2.71
2421 4813 2.355513 GGAGTCTTGGTGCTGATCATGT 60.356 50.000 0.00 0.00 0.00 3.21
2422 4814 2.286872 GGAGTCTTGGTGCTGATCATG 58.713 52.381 0.00 0.00 0.00 3.07
2423 4815 1.911357 TGGAGTCTTGGTGCTGATCAT 59.089 47.619 0.00 0.00 0.00 2.45
2424 4816 1.351076 TGGAGTCTTGGTGCTGATCA 58.649 50.000 0.00 0.00 0.00 2.92
2425 4817 2.286872 CATGGAGTCTTGGTGCTGATC 58.713 52.381 0.00 0.00 0.00 2.92
2426 4818 1.064906 CCATGGAGTCTTGGTGCTGAT 60.065 52.381 5.56 0.00 34.54 2.90
2427 4819 0.325933 CCATGGAGTCTTGGTGCTGA 59.674 55.000 5.56 0.00 34.54 4.26
2428 4820 0.679002 CCCATGGAGTCTTGGTGCTG 60.679 60.000 15.22 0.00 36.71 4.41
2429 4821 1.136329 ACCCATGGAGTCTTGGTGCT 61.136 55.000 15.22 0.00 36.71 4.40
2430 4822 0.962356 CACCCATGGAGTCTTGGTGC 60.962 60.000 15.22 0.00 36.71 5.01
2431 4823 0.401738 ACACCCATGGAGTCTTGGTG 59.598 55.000 15.22 13.20 36.71 4.17
2432 4824 1.149101 AACACCCATGGAGTCTTGGT 58.851 50.000 15.22 0.00 36.71 3.67
2433 4825 3.652057 ATAACACCCATGGAGTCTTGG 57.348 47.619 15.22 0.00 37.79 3.61
2434 4826 6.356556 TGATTATAACACCCATGGAGTCTTG 58.643 40.000 15.22 4.57 0.00 3.02
2435 4827 6.575244 TGATTATAACACCCATGGAGTCTT 57.425 37.500 15.22 6.23 0.00 3.01
2436 4828 6.770286 ATGATTATAACACCCATGGAGTCT 57.230 37.500 15.22 5.57 0.00 3.24
2468 4860 9.979578 CTTGCACTAGAGTCAATAATCTAGATT 57.020 33.333 21.28 21.28 45.21 2.40
2469 4861 9.142014 ACTTGCACTAGAGTCAATAATCTAGAT 57.858 33.333 14.71 0.00 45.21 1.98
2470 4862 8.409371 CACTTGCACTAGAGTCAATAATCTAGA 58.591 37.037 14.71 0.00 45.21 2.43
2471 4863 7.651304 CCACTTGCACTAGAGTCAATAATCTAG 59.349 40.741 8.00 8.00 46.90 2.43
2472 4864 7.417911 CCCACTTGCACTAGAGTCAATAATCTA 60.418 40.741 0.00 0.00 0.00 1.98
2473 4865 6.344500 CCACTTGCACTAGAGTCAATAATCT 58.656 40.000 0.00 0.00 0.00 2.40
2474 4866 5.525378 CCCACTTGCACTAGAGTCAATAATC 59.475 44.000 0.00 0.00 0.00 1.75
2475 4867 5.189736 TCCCACTTGCACTAGAGTCAATAAT 59.810 40.000 0.00 0.00 0.00 1.28
2476 4868 4.530553 TCCCACTTGCACTAGAGTCAATAA 59.469 41.667 0.00 0.00 0.00 1.40
2477 4869 4.093743 TCCCACTTGCACTAGAGTCAATA 58.906 43.478 0.00 0.00 0.00 1.90
2478 4870 2.906389 TCCCACTTGCACTAGAGTCAAT 59.094 45.455 0.00 0.00 0.00 2.57
2479 4871 2.300152 CTCCCACTTGCACTAGAGTCAA 59.700 50.000 0.00 0.00 0.00 3.18
2480 4872 1.895798 CTCCCACTTGCACTAGAGTCA 59.104 52.381 0.00 0.00 0.00 3.41
2481 4873 2.094442 GTCTCCCACTTGCACTAGAGTC 60.094 54.545 0.00 0.00 0.00 3.36
2482 4874 1.896465 GTCTCCCACTTGCACTAGAGT 59.104 52.381 0.00 0.00 0.00 3.24
2483 4875 1.205893 GGTCTCCCACTTGCACTAGAG 59.794 57.143 0.00 0.00 0.00 2.43
2484 4876 1.267121 GGTCTCCCACTTGCACTAGA 58.733 55.000 0.00 0.00 0.00 2.43
2485 4877 0.108615 CGGTCTCCCACTTGCACTAG 60.109 60.000 0.00 0.00 0.00 2.57
2486 4878 0.541063 TCGGTCTCCCACTTGCACTA 60.541 55.000 0.00 0.00 0.00 2.74
2487 4879 1.407656 TTCGGTCTCCCACTTGCACT 61.408 55.000 0.00 0.00 0.00 4.40
2488 4880 0.534203 TTTCGGTCTCCCACTTGCAC 60.534 55.000 0.00 0.00 0.00 4.57
2489 4881 0.250295 CTTTCGGTCTCCCACTTGCA 60.250 55.000 0.00 0.00 0.00 4.08
2490 4882 0.034896 TCTTTCGGTCTCCCACTTGC 59.965 55.000 0.00 0.00 0.00 4.01
2491 4883 2.543777 TTCTTTCGGTCTCCCACTTG 57.456 50.000 0.00 0.00 0.00 3.16
2492 4884 3.790089 ATTTCTTTCGGTCTCCCACTT 57.210 42.857 0.00 0.00 0.00 3.16
2493 4885 4.770795 CATATTTCTTTCGGTCTCCCACT 58.229 43.478 0.00 0.00 0.00 4.00
2494 4886 3.312697 GCATATTTCTTTCGGTCTCCCAC 59.687 47.826 0.00 0.00 0.00 4.61
2495 4887 3.541632 GCATATTTCTTTCGGTCTCCCA 58.458 45.455 0.00 0.00 0.00 4.37
2496 4888 2.879026 GGCATATTTCTTTCGGTCTCCC 59.121 50.000 0.00 0.00 0.00 4.30
2497 4889 2.879026 GGGCATATTTCTTTCGGTCTCC 59.121 50.000 0.00 0.00 0.00 3.71
2498 4890 3.809905 AGGGCATATTTCTTTCGGTCTC 58.190 45.455 0.00 0.00 0.00 3.36
2499 4891 3.933861 AGGGCATATTTCTTTCGGTCT 57.066 42.857 0.00 0.00 0.00 3.85
2500 4892 4.957296 TCTAGGGCATATTTCTTTCGGTC 58.043 43.478 0.00 0.00 0.00 4.79
2501 4893 4.202367 CCTCTAGGGCATATTTCTTTCGGT 60.202 45.833 0.00 0.00 0.00 4.69
2502 4894 4.319177 CCTCTAGGGCATATTTCTTTCGG 58.681 47.826 0.00 0.00 0.00 4.30
2576 4968 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
2577 4969 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
2578 4970 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
2579 4971 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
2580 4972 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
2581 4973 7.773690 AGTTTCCGGTTAATACAATTCTAGCAT 59.226 33.333 0.00 0.00 0.00 3.79
2582 4974 7.107542 AGTTTCCGGTTAATACAATTCTAGCA 58.892 34.615 0.00 0.00 0.00 3.49
2583 4975 7.549615 AGTTTCCGGTTAATACAATTCTAGC 57.450 36.000 0.00 0.00 0.00 3.42
2584 4976 9.158233 TCAAGTTTCCGGTTAATACAATTCTAG 57.842 33.333 0.00 0.00 0.00 2.43
2585 4977 9.675464 ATCAAGTTTCCGGTTAATACAATTCTA 57.325 29.630 0.00 0.00 0.00 2.10
2586 4978 7.989416 TCAAGTTTCCGGTTAATACAATTCT 57.011 32.000 0.00 0.00 0.00 2.40
2587 4979 9.712359 GTATCAAGTTTCCGGTTAATACAATTC 57.288 33.333 0.00 0.00 0.00 2.17
2588 4980 9.233649 TGTATCAAGTTTCCGGTTAATACAATT 57.766 29.630 0.00 0.00 0.00 2.32
2589 4981 8.795842 TGTATCAAGTTTCCGGTTAATACAAT 57.204 30.769 0.00 0.00 0.00 2.71
2590 4982 8.670135 CATGTATCAAGTTTCCGGTTAATACAA 58.330 33.333 0.00 0.00 33.52 2.41
2591 4983 7.825270 ACATGTATCAAGTTTCCGGTTAATACA 59.175 33.333 0.00 0.88 34.10 2.29
2592 4984 8.120465 CACATGTATCAAGTTTCCGGTTAATAC 58.880 37.037 0.00 0.00 0.00 1.89
2593 4985 7.825270 ACACATGTATCAAGTTTCCGGTTAATA 59.175 33.333 0.00 0.00 0.00 0.98
2594 4986 6.657541 ACACATGTATCAAGTTTCCGGTTAAT 59.342 34.615 0.00 0.00 0.00 1.40
2595 4987 5.998981 ACACATGTATCAAGTTTCCGGTTAA 59.001 36.000 0.00 0.00 0.00 2.01
2596 4988 5.410132 CACACATGTATCAAGTTTCCGGTTA 59.590 40.000 0.00 0.00 0.00 2.85
2597 4989 4.215399 CACACATGTATCAAGTTTCCGGTT 59.785 41.667 0.00 0.00 0.00 4.44
2598 4990 3.751175 CACACATGTATCAAGTTTCCGGT 59.249 43.478 0.00 0.00 0.00 5.28
2599 4991 3.126858 CCACACATGTATCAAGTTTCCGG 59.873 47.826 0.00 0.00 0.00 5.14
2600 4992 4.000325 TCCACACATGTATCAAGTTTCCG 59.000 43.478 0.00 0.00 0.00 4.30
2601 4993 6.597672 TGTATCCACACATGTATCAAGTTTCC 59.402 38.462 0.00 0.00 0.00 3.13
2602 4994 7.609760 TGTATCCACACATGTATCAAGTTTC 57.390 36.000 0.00 0.00 0.00 2.78
2603 4995 9.330063 CTATGTATCCACACATGTATCAAGTTT 57.670 33.333 0.00 0.00 39.46 2.66
2604 4996 8.704668 TCTATGTATCCACACATGTATCAAGTT 58.295 33.333 0.00 0.00 39.46 2.66
2605 4997 8.144478 GTCTATGTATCCACACATGTATCAAGT 58.856 37.037 0.00 0.00 39.46 3.16
2606 4998 8.143835 TGTCTATGTATCCACACATGTATCAAG 58.856 37.037 0.00 0.00 39.46 3.02
2607 4999 8.017418 TGTCTATGTATCCACACATGTATCAA 57.983 34.615 0.00 0.00 39.46 2.57
2608 5000 7.595819 TGTCTATGTATCCACACATGTATCA 57.404 36.000 0.00 0.00 39.46 2.15
2609 5001 8.887036 TTTGTCTATGTATCCACACATGTATC 57.113 34.615 0.00 0.00 39.46 2.24
2610 5002 9.109393 GTTTTGTCTATGTATCCACACATGTAT 57.891 33.333 0.00 0.00 39.46 2.29
2611 5003 8.097662 TGTTTTGTCTATGTATCCACACATGTA 58.902 33.333 0.00 0.00 39.46 2.29
2612 5004 6.939730 TGTTTTGTCTATGTATCCACACATGT 59.060 34.615 0.00 0.00 39.46 3.21
2613 5005 7.243487 GTGTTTTGTCTATGTATCCACACATG 58.757 38.462 0.00 0.00 39.46 3.21
2614 5006 6.374333 GGTGTTTTGTCTATGTATCCACACAT 59.626 38.462 0.00 0.00 41.88 3.21
2615 5007 5.703592 GGTGTTTTGTCTATGTATCCACACA 59.296 40.000 0.00 0.00 37.54 3.72
2616 5008 5.163893 CGGTGTTTTGTCTATGTATCCACAC 60.164 44.000 0.00 0.00 37.54 3.82
2617 5009 4.932799 CGGTGTTTTGTCTATGTATCCACA 59.067 41.667 0.00 0.00 39.52 4.17
2618 5010 4.933400 ACGGTGTTTTGTCTATGTATCCAC 59.067 41.667 0.00 0.00 0.00 4.02
2619 5011 4.932799 CACGGTGTTTTGTCTATGTATCCA 59.067 41.667 0.00 0.00 0.00 3.41
2620 5012 4.933400 ACACGGTGTTTTGTCTATGTATCC 59.067 41.667 8.21 0.00 0.00 2.59
2621 5013 5.063060 GGACACGGTGTTTTGTCTATGTATC 59.937 44.000 15.94 0.00 41.65 2.24
2622 5014 4.933400 GGACACGGTGTTTTGTCTATGTAT 59.067 41.667 15.94 0.00 41.65 2.29
2623 5015 4.309099 GGACACGGTGTTTTGTCTATGTA 58.691 43.478 15.94 0.00 41.65 2.29
2624 5016 3.135994 GGACACGGTGTTTTGTCTATGT 58.864 45.455 15.94 0.00 41.65 2.29
2625 5017 2.482721 GGGACACGGTGTTTTGTCTATG 59.517 50.000 15.94 0.00 41.65 2.23
2626 5018 2.370849 AGGGACACGGTGTTTTGTCTAT 59.629 45.455 15.94 0.00 41.65 1.98
2627 5019 1.764134 AGGGACACGGTGTTTTGTCTA 59.236 47.619 15.94 0.00 41.65 2.59
2628 5020 0.544697 AGGGACACGGTGTTTTGTCT 59.455 50.000 15.94 6.16 41.65 3.41
2629 5021 2.140717 CTAGGGACACGGTGTTTTGTC 58.859 52.381 15.94 1.68 41.28 3.18
2630 5022 1.487558 ACTAGGGACACGGTGTTTTGT 59.512 47.619 15.94 8.56 0.00 2.83
2631 5023 2.249844 ACTAGGGACACGGTGTTTTG 57.750 50.000 15.94 7.98 0.00 2.44


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

AutoCloner maintained by Alex Coulton.