Multiple sequence alignment - TraesCS5B01G139400

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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 TraesCS5B01G139400 chr5B 100.000 4626 0 0 1 4626 263214319 263218944 0.000000e+00 8543
1 TraesCS5B01G139400 chr5B 84.211 342 42 11 4003 4339 679350068 679349734 5.770000e-84 322
2 TraesCS5B01G139400 chr5B 95.918 98 4 0 4154 4251 428958999 428958902 4.790000e-35 159
3 TraesCS5B01G139400 chr5A 93.477 4231 188 34 1 4157 313305780 313309996 0.000000e+00 6204
4 TraesCS5B01G139400 chr5A 91.509 212 16 2 4416 4626 313310123 313310333 1.630000e-74 291
5 TraesCS5B01G139400 chr5A 89.032 155 14 3 4003 4157 682941061 682940910 6.110000e-44 189
6 TraesCS5B01G139400 chr5A 87.662 154 18 1 4003 4156 589296696 589296848 1.320000e-40 178
7 TraesCS5B01G139400 chr5A 95.960 99 4 0 4154 4252 568267653 568267751 1.330000e-35 161
8 TraesCS5B01G139400 chr5A 86.131 137 16 3 4250 4385 313309994 313310128 1.340000e-30 145
9 TraesCS5B01G139400 chr5D 93.687 3279 169 15 820 4069 240510382 240507113 0.000000e+00 4874
10 TraesCS5B01G139400 chr5D 92.612 758 18 14 1 729 240511279 240510531 0.000000e+00 1055
11 TraesCS5B01G139400 chr5D 91.220 205 15 3 4424 4626 240506929 240506726 4.560000e-70 276
12 TraesCS5B01G139400 chr5D 88.387 155 16 1 4003 4157 4030138 4029986 7.900000e-43 185
13 TraesCS5B01G139400 chr5D 96.000 100 4 0 4153 4252 507553715 507553616 3.700000e-36 163
14 TraesCS5B01G139400 chr5D 86.567 134 17 1 4250 4383 240507066 240506934 3.730000e-31 147
15 TraesCS5B01G139400 chr2A 85.789 190 21 6 4423 4606 771680671 771680860 3.650000e-46 196
16 TraesCS5B01G139400 chr2A 83.951 162 21 4 3998 4157 691635797 691635955 2.880000e-32 150
17 TraesCS5B01G139400 chr2D 84.158 202 27 5 4424 4620 645934700 645934901 1.700000e-44 191
18 TraesCS5B01G139400 chr2D 83.871 155 21 4 4003 4157 515539849 515539999 1.340000e-30 145
19 TraesCS5B01G139400 chr7B 87.879 165 15 4 3995 4157 384201309 384201148 6.110000e-44 189
20 TraesCS5B01G139400 chr2B 82.381 210 31 6 4423 4626 789615538 789615329 1.320000e-40 178
21 TraesCS5B01G139400 chr6B 96.078 102 4 0 4154 4255 475446850 475446749 2.860000e-37 167
22 TraesCS5B01G139400 chr1D 96.000 100 4 0 4155 4254 275529297 275529198 3.700000e-36 163
23 TraesCS5B01G139400 chr1D 88.235 85 9 1 4250 4334 89134846 89134929 2.950000e-17 100
24 TraesCS5B01G139400 chr6A 93.519 108 5 2 4147 4253 11165048 11165154 4.790000e-35 159
25 TraesCS5B01G139400 chr1B 94.231 104 4 1 4152 4255 149273644 149273745 1.720000e-34 158
26 TraesCS5B01G139400 chr7D 91.667 108 7 2 4154 4260 41596644 41596538 1.040000e-31 148
27 TraesCS5B01G139400 chr6D 83.562 146 22 2 4003 4148 22113315 22113458 8.070000e-28 135


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 TraesCS5B01G139400 chr5B 263214319 263218944 4625 False 8543.000000 8543 100.000000 1 4626 1 chr5B.!!$F1 4625
1 TraesCS5B01G139400 chr5A 313305780 313310333 4553 False 2213.333333 6204 90.372333 1 4626 3 chr5A.!!$F3 4625
2 TraesCS5B01G139400 chr5D 240506726 240511279 4553 True 1588.000000 4874 91.021500 1 4626 4 chr5D.!!$R3 4625

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
592 628 0.179163 GCTGGTTTGCTATTGTCCGC 60.179 55.0 0.00 0.0 0.00 5.54 F
1087 1237 0.175760 TCTGCACGCCAAGAGGATAC 59.824 55.0 0.00 0.0 36.89 2.24 F
1309 1459 0.884514 TGCAGAAGGAGACTCTGACG 59.115 55.0 1.74 0.0 42.68 4.35 F
2157 2310 0.890683 CCATTTCCACACCAAGAGGC 59.109 55.0 0.00 0.0 39.06 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 2466 0.107116 AGTACGAGCGAGGAGTCCAT 60.107 55.0 12.86 0.00 0.00 3.41 R
2965 3118 0.322322 ATAACGCCGGGTCACTCAAA 59.678 50.0 2.18 0.00 0.00 2.69 R
2995 3148 1.116308 CTTCAATGGCATGCATCCCA 58.884 50.0 21.36 12.88 35.21 4.37 R
3991 4171 0.953003 CGGAGGTAGCAGTAGTAGCC 59.047 60.0 0.00 0.00 0.00 3.93 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
67 82 8.946085 CATTGTACTACCAAGCATAAAGAGAAA 58.054 33.333 0.00 0.00 0.00 2.52
71 86 3.701664 ACCAAGCATAAAGAGAAAGGGG 58.298 45.455 0.00 0.00 0.00 4.79
330 357 0.329596 AAGCAAGGGATCCAGACACC 59.670 55.000 15.23 0.00 0.00 4.16
388 416 1.073923 TCCTTCCTTGCTTTGGTCTCC 59.926 52.381 0.00 0.00 0.00 3.71
453 484 3.514362 CTGCATGCATCTGCGCCA 61.514 61.111 22.97 0.00 45.30 5.69
489 520 0.749818 TTGGTTCTTGCTGTTCGCCA 60.750 50.000 0.00 0.00 38.05 5.69
589 625 2.584791 CGTTGCTGGTTTGCTATTGTC 58.415 47.619 0.00 0.00 0.00 3.18
592 628 0.179163 GCTGGTTTGCTATTGTCCGC 60.179 55.000 0.00 0.00 0.00 5.54
636 672 6.294397 GCTGTGATGAATCTTTGTTTCCTTCT 60.294 38.462 0.00 0.00 0.00 2.85
662 698 3.515602 AATTTCTGCCAGTCTGTTCCT 57.484 42.857 0.00 0.00 0.00 3.36
668 704 1.239347 GCCAGTCTGTTCCTCAAACC 58.761 55.000 0.00 0.00 37.03 3.27
758 794 7.684529 AGAAGTCATCTGGTTAATGAAGAACT 58.315 34.615 0.00 0.00 36.88 3.01
759 795 7.605691 AGAAGTCATCTGGTTAATGAAGAACTG 59.394 37.037 0.00 0.00 36.88 3.16
760 796 6.176183 AGTCATCTGGTTAATGAAGAACTGG 58.824 40.000 0.00 0.00 35.04 4.00
763 799 4.651778 TCTGGTTAATGAAGAACTGGGTG 58.348 43.478 0.00 0.00 0.00 4.61
764 800 4.104102 TCTGGTTAATGAAGAACTGGGTGT 59.896 41.667 0.00 0.00 0.00 4.16
765 801 4.394729 TGGTTAATGAAGAACTGGGTGTC 58.605 43.478 0.00 0.00 0.00 3.67
766 802 4.104102 TGGTTAATGAAGAACTGGGTGTCT 59.896 41.667 0.00 0.00 0.00 3.41
767 803 4.455877 GGTTAATGAAGAACTGGGTGTCTG 59.544 45.833 0.00 0.00 0.00 3.51
768 804 2.191128 ATGAAGAACTGGGTGTCTGC 57.809 50.000 0.00 0.00 0.00 4.26
769 805 1.131638 TGAAGAACTGGGTGTCTGCT 58.868 50.000 0.00 0.00 0.00 4.24
770 806 1.070758 TGAAGAACTGGGTGTCTGCTC 59.929 52.381 0.00 0.00 0.00 4.26
779 835 2.622942 TGGGTGTCTGCTCAAATTTGTC 59.377 45.455 17.47 11.20 0.00 3.18
840 990 7.380333 TCAACGTTCATTGTTAGTGTACTAGTG 59.620 37.037 5.39 0.00 0.00 2.74
862 1012 6.258727 AGTGTACAGAGTGTTCTTCAACAATG 59.741 38.462 0.00 0.00 44.32 2.82
890 1040 3.801050 CACCGCATCAGAAACAGATAGAG 59.199 47.826 0.00 0.00 0.00 2.43
931 1081 3.881220 TCATGAGCTCAATTCATCTGCA 58.119 40.909 22.50 0.40 33.14 4.41
954 1104 9.559732 TGCACATGCTTTATAATCACTAGTATT 57.440 29.630 5.31 0.00 42.66 1.89
955 1105 9.817365 GCACATGCTTTATAATCACTAGTATTG 57.183 33.333 0.00 0.00 38.21 1.90
1051 1201 7.423844 TTTAAGCAGATGACTAAGGATCTCA 57.576 36.000 0.00 0.00 0.00 3.27
1053 1203 4.545678 AGCAGATGACTAAGGATCTCAGT 58.454 43.478 0.00 0.00 0.00 3.41
1057 1207 6.183360 GCAGATGACTAAGGATCTCAGTACAA 60.183 42.308 0.00 0.00 0.00 2.41
1083 1233 2.671177 CGTTCTGCACGCCAAGAGG 61.671 63.158 0.00 0.00 43.37 3.69
1087 1237 0.175760 TCTGCACGCCAAGAGGATAC 59.824 55.000 0.00 0.00 36.89 2.24
1116 1266 2.923655 CTCTTTCGCAGTCGCTTATCAA 59.076 45.455 0.00 0.00 35.30 2.57
1146 1296 4.219944 TGTGATTATCCTATGGTACTCGGC 59.780 45.833 0.00 0.00 0.00 5.54
1155 1305 2.499685 GTACTCGGCGCTGGGATT 59.500 61.111 26.16 3.17 0.00 3.01
1182 1332 5.614324 TGCTGCTACTACATAGGATTTGT 57.386 39.130 0.00 0.00 29.68 2.83
1218 1368 4.349365 CTTTCCTAGTGTCTTCCTCTCCT 58.651 47.826 0.00 0.00 0.00 3.69
1308 1458 1.892474 ACTGCAGAAGGAGACTCTGAC 59.108 52.381 23.35 0.00 42.68 3.51
1309 1459 0.884514 TGCAGAAGGAGACTCTGACG 59.115 55.000 1.74 0.00 42.68 4.35
1321 1471 4.551388 AGACTCTGACGATCAACAAACTC 58.449 43.478 0.00 0.00 0.00 3.01
1322 1472 4.038042 AGACTCTGACGATCAACAAACTCA 59.962 41.667 0.00 0.00 0.00 3.41
1391 1541 5.944599 AGGTTGAGAGTGTTACTATCGAGAA 59.055 40.000 0.00 0.00 39.19 2.87
1393 1543 7.774157 AGGTTGAGAGTGTTACTATCGAGAATA 59.226 37.037 0.00 0.00 39.19 1.75
1404 1554 6.716934 ACTATCGAGAATAGCTTGGAGAAA 57.283 37.500 0.00 0.00 41.04 2.52
1454 1604 2.105806 GAGAGAGCCCCGGCCAATAG 62.106 65.000 2.24 0.00 43.17 1.73
1492 1642 4.634004 ACTGTGAAGAAACAAATGTCACGA 59.366 37.500 0.00 0.00 41.18 4.35
1613 1763 4.199432 AGTCTGATCTGCGAGAATTTGT 57.801 40.909 0.00 0.00 0.00 2.83
1652 1802 5.906113 AGAGGTGACTATGAAGTACACAG 57.094 43.478 0.00 0.00 44.43 3.66
1746 1896 8.149647 GGTTCTGAATCTGATCTTACTGATGAT 58.850 37.037 0.00 0.00 35.14 2.45
1773 1923 2.405559 TCTCCTGATGCATCCATGACT 58.594 47.619 23.67 0.00 0.00 3.41
1949 2102 3.902881 TGAAGATGAAGGAGAGGAAGC 57.097 47.619 0.00 0.00 0.00 3.86
1967 2120 3.191078 AGCGGAGAAAGATGATGGAAG 57.809 47.619 0.00 0.00 0.00 3.46
2157 2310 0.890683 CCATTTCCACACCAAGAGGC 59.109 55.000 0.00 0.00 39.06 4.70
2187 2340 2.577563 TGATCCTTCAAATGCCTCAGGA 59.422 45.455 0.00 0.00 38.04 3.86
2235 2388 3.072184 AGATACCTGATTCAGCACCATCC 59.928 47.826 8.23 0.00 0.00 3.51
2313 2466 6.183360 ACCATAACAGTCAATTGCAAGAAACA 60.183 34.615 4.94 0.00 0.00 2.83
2393 2546 3.543884 GGCACTCCGTTAATCCACA 57.456 52.632 0.00 0.00 0.00 4.17
2426 2579 4.083271 CCTCAAATCGGAGAAAGGTGAAAC 60.083 45.833 0.00 0.00 43.58 2.78
2496 2649 2.381911 CAAGGGAATGATGGGAGGTTG 58.618 52.381 0.00 0.00 0.00 3.77
2716 2869 8.253113 CAGGTAAATTTGTTATGGCTTTCAGAT 58.747 33.333 0.00 0.00 0.00 2.90
2843 2996 5.895636 AAATAATTCCGAGCAACATGTCA 57.104 34.783 0.00 0.00 0.00 3.58
2847 3000 2.009108 CCGAGCAACATGTCATCGG 58.991 57.895 23.54 23.54 45.95 4.18
2861 3014 1.412343 TCATCGGAGCGAATTCCATCA 59.588 47.619 0.00 0.00 39.99 3.07
2965 3118 7.173907 CCTTTGACAGTTACACTTGAAGATGAT 59.826 37.037 0.00 0.00 0.00 2.45
2967 3120 8.450578 TTGACAGTTACACTTGAAGATGATTT 57.549 30.769 0.00 0.00 0.00 2.17
2995 3148 0.675522 CGGCGTTATGTCCAAACCCT 60.676 55.000 0.00 0.00 0.00 4.34
3085 3238 1.220529 CACTGACATGTGACGCTTGT 58.779 50.000 1.15 7.21 40.12 3.16
3094 3247 2.284190 TGTGACGCTTGTGATGTTGAA 58.716 42.857 0.00 0.00 0.00 2.69
3097 3250 1.601903 GACGCTTGTGATGTTGAACCA 59.398 47.619 0.00 0.00 0.00 3.67
3246 3399 3.118112 AGGCTCCATGTTATTGAGGTGAG 60.118 47.826 0.00 0.00 0.00 3.51
3301 3454 2.234661 ACTCGAAGATGTGCAGGATCAA 59.765 45.455 8.09 0.00 33.89 2.57
3393 3546 1.251527 ACAGAGCCCGTCGAAGATGT 61.252 55.000 0.00 0.00 43.09 3.06
3428 3581 1.839994 AGCAGTTAAGCTCTGGCCATA 59.160 47.619 5.51 0.00 42.18 2.74
3435 3588 0.995024 AGCTCTGGCCATAACAAGGT 59.005 50.000 5.51 1.82 39.73 3.50
3445 3598 3.378427 GCCATAACAAGGTGAAGATGTCC 59.622 47.826 0.00 0.00 0.00 4.02
3570 3723 4.691216 CAGTGGTTCTAAAGTAACTGAGCC 59.309 45.833 0.00 0.00 37.76 4.70
3583 3736 1.101331 CTGAGCCCAAAGATTCAGCC 58.899 55.000 0.00 0.00 31.68 4.85
3623 3778 1.754234 GTTGAAGGGCGGCATGGAT 60.754 57.895 12.47 0.00 0.00 3.41
3634 3789 2.417107 GCGGCATGGATGATGTTTGAAA 60.417 45.455 0.00 0.00 34.14 2.69
3640 3795 5.220586 GCATGGATGATGTTTGAAATTGCAG 60.221 40.000 0.00 0.00 34.14 4.41
3666 3821 2.756207 CAACACATGATCCAGGCATTGA 59.244 45.455 0.00 0.00 0.00 2.57
3675 3830 0.835941 CCAGGCATTGAGCTACTCCT 59.164 55.000 0.00 0.00 44.79 3.69
3678 3833 0.833287 GGCATTGAGCTACTCCTGGA 59.167 55.000 0.00 0.00 44.79 3.86
3691 3846 1.627834 CTCCTGGAGCTCTGGAAAGTT 59.372 52.381 22.59 0.00 41.94 2.66
3735 3890 8.691661 AGAAACTGAAGCTAAGTTCCATTAAA 57.308 30.769 13.50 0.00 36.87 1.52
3749 3904 5.467035 TCCATTAAACAAGGGCTCAAAAG 57.533 39.130 0.00 0.00 0.00 2.27
3767 3922 3.676091 GCACTACGCGCTCATTTTT 57.324 47.368 5.73 0.00 0.00 1.94
3822 3978 9.455847 GAATTATGAATGGCTATGTTCTCAAAC 57.544 33.333 0.00 0.00 35.85 2.93
3826 3982 5.240623 TGAATGGCTATGTTCTCAAACGTTT 59.759 36.000 7.96 7.96 38.28 3.60
3827 3983 4.481930 TGGCTATGTTCTCAAACGTTTG 57.518 40.909 30.63 30.63 38.28 2.93
3836 3993 4.712122 TCTCAAACGTTTGCCTTTCTTT 57.288 36.364 31.42 0.00 38.05 2.52
3845 4002 8.936070 AACGTTTGCCTTTCTTTATTTTTAGT 57.064 26.923 0.00 0.00 0.00 2.24
3846 4003 8.347729 ACGTTTGCCTTTCTTTATTTTTAGTG 57.652 30.769 0.00 0.00 0.00 2.74
3900 4062 7.510549 TCCCTCTGTACTTCAAAGAAAAATG 57.489 36.000 0.00 0.00 0.00 2.32
3903 4065 7.201821 CCCTCTGTACTTCAAAGAAAAATGTGT 60.202 37.037 0.00 0.00 0.00 3.72
3916 4078 0.035630 AATGTGTCAGGAGCTCTGCC 60.036 55.000 14.64 0.00 43.06 4.85
3928 4090 1.070445 CTCTGCCGATTAGCCCTGG 59.930 63.158 0.00 0.00 0.00 4.45
3931 4093 2.592861 GCCGATTAGCCCTGGCAG 60.593 66.667 11.38 7.75 46.76 4.85
3937 4099 2.224281 CGATTAGCCCTGGCAGTATCAA 60.224 50.000 14.43 2.65 44.88 2.57
3961 4123 6.838382 ACTTCAAAGCCTACTAAAAGGAAGA 58.162 36.000 0.00 0.00 39.15 2.87
3969 4131 8.794335 AGCCTACTAAAAGGAAGAATTTACTG 57.206 34.615 0.00 0.00 39.15 2.74
3971 4133 7.067129 GCCTACTAAAAGGAAGAATTTACTGGG 59.933 40.741 0.00 0.00 39.15 4.45
3991 4171 4.158764 TGGGGTAATCAAAATGCTTAACGG 59.841 41.667 0.00 0.00 0.00 4.44
4001 4184 2.953466 TGCTTAACGGGCTACTACTG 57.047 50.000 0.00 0.00 0.00 2.74
4019 4202 0.834687 TGCTACCTCCGTCCTGGTTT 60.835 55.000 0.00 0.00 39.52 3.27
4020 4203 1.188863 GCTACCTCCGTCCTGGTTTA 58.811 55.000 0.00 0.00 39.52 2.01
4030 4213 3.181468 CCGTCCTGGTTTATTAGTCCCTC 60.181 52.174 0.00 0.00 0.00 4.30
4035 4218 4.227527 CCTGGTTTATTAGTCCCTCCTTGT 59.772 45.833 0.00 0.00 0.00 3.16
4043 4226 6.652205 ATTAGTCCCTCCTTGTATTTTGGA 57.348 37.500 0.00 0.00 0.00 3.53
4113 4296 8.751302 ACACCAAAAATAATATCACCGAAAAC 57.249 30.769 0.00 0.00 0.00 2.43
4134 4317 7.938140 AAACCTCTTTCGAATATGAATCCAA 57.062 32.000 0.00 0.00 0.00 3.53
4139 4322 7.859377 CCTCTTTCGAATATGAATCCAACAATG 59.141 37.037 0.00 0.00 0.00 2.82
4154 4337 7.106439 TCCAACAATGTAAGTTTTGTGACAT 57.894 32.000 0.00 0.00 36.26 3.06
4155 4338 8.226819 TCCAACAATGTAAGTTTTGTGACATA 57.773 30.769 0.00 0.00 36.26 2.29
4156 4339 8.132362 TCCAACAATGTAAGTTTTGTGACATAC 58.868 33.333 0.00 0.00 36.26 2.39
4157 4340 8.134895 CCAACAATGTAAGTTTTGTGACATACT 58.865 33.333 0.00 0.00 36.26 2.12
4158 4341 9.169468 CAACAATGTAAGTTTTGTGACATACTC 57.831 33.333 2.04 0.00 36.26 2.59
4159 4342 7.871853 ACAATGTAAGTTTTGTGACATACTCC 58.128 34.615 2.04 0.00 34.87 3.85
4160 4343 7.040686 ACAATGTAAGTTTTGTGACATACTCCC 60.041 37.037 2.04 0.00 34.87 4.30
4161 4344 6.182507 TGTAAGTTTTGTGACATACTCCCT 57.817 37.500 2.04 0.00 0.00 4.20
4162 4345 6.228258 TGTAAGTTTTGTGACATACTCCCTC 58.772 40.000 2.04 0.00 0.00 4.30
4163 4346 5.568620 AAGTTTTGTGACATACTCCCTCT 57.431 39.130 2.04 0.00 0.00 3.69
4164 4347 4.899502 AGTTTTGTGACATACTCCCTCTG 58.100 43.478 0.00 0.00 0.00 3.35
4165 4348 4.348168 AGTTTTGTGACATACTCCCTCTGT 59.652 41.667 0.00 0.00 0.00 3.41
4166 4349 4.537135 TTTGTGACATACTCCCTCTGTC 57.463 45.455 0.00 0.00 39.74 3.51
4167 4350 3.458044 TGTGACATACTCCCTCTGTCT 57.542 47.619 3.86 0.00 39.94 3.41
4168 4351 3.357203 TGTGACATACTCCCTCTGTCTC 58.643 50.000 3.86 1.25 39.94 3.36
4169 4352 3.245264 TGTGACATACTCCCTCTGTCTCA 60.245 47.826 3.86 3.61 39.63 3.27
4170 4353 3.764434 GTGACATACTCCCTCTGTCTCAA 59.236 47.826 3.86 0.00 39.94 3.02
4171 4354 4.220821 GTGACATACTCCCTCTGTCTCAAA 59.779 45.833 3.86 0.00 39.94 2.69
4172 4355 4.838423 TGACATACTCCCTCTGTCTCAAAA 59.162 41.667 3.86 0.00 39.94 2.44
4173 4356 5.485353 TGACATACTCCCTCTGTCTCAAAAT 59.515 40.000 3.86 0.00 39.94 1.82
4174 4357 6.667848 TGACATACTCCCTCTGTCTCAAAATA 59.332 38.462 3.86 0.00 39.94 1.40
4175 4358 7.180229 TGACATACTCCCTCTGTCTCAAAATAA 59.820 37.037 3.86 0.00 39.94 1.40
4176 4359 7.560368 ACATACTCCCTCTGTCTCAAAATAAG 58.440 38.462 0.00 0.00 0.00 1.73
4177 4360 7.181125 ACATACTCCCTCTGTCTCAAAATAAGT 59.819 37.037 0.00 0.00 0.00 2.24
4178 4361 5.799213 ACTCCCTCTGTCTCAAAATAAGTG 58.201 41.667 0.00 0.00 0.00 3.16
4179 4362 5.544176 ACTCCCTCTGTCTCAAAATAAGTGA 59.456 40.000 0.00 0.00 0.00 3.41
4180 4363 5.794894 TCCCTCTGTCTCAAAATAAGTGAC 58.205 41.667 0.00 0.00 0.00 3.67
4181 4364 5.544176 TCCCTCTGTCTCAAAATAAGTGACT 59.456 40.000 0.00 0.00 32.38 3.41
4182 4365 5.872070 CCCTCTGTCTCAAAATAAGTGACTC 59.128 44.000 0.00 0.00 32.38 3.36
4183 4366 6.459066 CCTCTGTCTCAAAATAAGTGACTCA 58.541 40.000 0.00 0.00 32.38 3.41
4184 4367 6.931281 CCTCTGTCTCAAAATAAGTGACTCAA 59.069 38.462 0.00 0.00 32.38 3.02
4185 4368 7.117523 CCTCTGTCTCAAAATAAGTGACTCAAG 59.882 40.741 0.00 0.00 32.38 3.02
4186 4369 7.500992 TCTGTCTCAAAATAAGTGACTCAAGT 58.499 34.615 0.00 0.00 32.38 3.16
4187 4370 7.987458 TCTGTCTCAAAATAAGTGACTCAAGTT 59.013 33.333 0.00 0.00 32.38 2.66
4188 4371 8.506168 TGTCTCAAAATAAGTGACTCAAGTTT 57.494 30.769 0.00 0.00 32.38 2.66
4189 4372 8.397906 TGTCTCAAAATAAGTGACTCAAGTTTG 58.602 33.333 11.98 11.98 32.38 2.93
4190 4373 8.398665 GTCTCAAAATAAGTGACTCAAGTTTGT 58.601 33.333 15.56 0.00 0.00 2.83
4191 4374 9.607988 TCTCAAAATAAGTGACTCAAGTTTGTA 57.392 29.630 15.56 7.24 0.00 2.41
4226 4409 9.310716 AGTACAAAGTTAGTACAAACTTGAGTC 57.689 33.333 2.97 0.00 46.40 3.36
4227 4410 9.090692 GTACAAAGTTAGTACAAACTTGAGTCA 57.909 33.333 2.97 0.00 46.40 3.41
4228 4411 7.971455 ACAAAGTTAGTACAAACTTGAGTCAC 58.029 34.615 2.97 0.00 46.40 3.67
4229 4412 7.822822 ACAAAGTTAGTACAAACTTGAGTCACT 59.177 33.333 2.97 0.00 46.40 3.41
4230 4413 8.665685 CAAAGTTAGTACAAACTTGAGTCACTT 58.334 33.333 2.97 0.00 46.40 3.16
4231 4414 9.880157 AAAGTTAGTACAAACTTGAGTCACTTA 57.120 29.630 2.97 0.00 46.40 2.24
4237 4420 8.621286 AGTACAAACTTGAGTCACTTATTTTGG 58.379 33.333 9.57 0.00 29.00 3.28
4238 4421 6.805713 ACAAACTTGAGTCACTTATTTTGGG 58.194 36.000 9.57 0.00 0.00 4.12
4239 4422 6.605594 ACAAACTTGAGTCACTTATTTTGGGA 59.394 34.615 9.57 0.00 0.00 4.37
4240 4423 6.635030 AACTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 0.00 4.46
4241 4424 4.755123 ACTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
4242 4425 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
4243 4426 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
4244 4427 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
4245 4428 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4246 4429 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4247 4430 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4248 4431 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4255 4438 1.611474 GGGACGGAGGGAGTACAACC 61.611 65.000 0.00 0.00 0.00 3.77
4262 4445 5.957132 ACGGAGGGAGTACAACCTATATTA 58.043 41.667 8.20 0.00 37.18 0.98
4292 4475 6.071391 AGTCAAATCTACGGCCAAAATTTGAT 60.071 34.615 23.95 15.44 43.93 2.57
4293 4476 6.034898 GTCAAATCTACGGCCAAAATTTGATG 59.965 38.462 23.95 7.04 43.93 3.07
4299 4482 3.003171 ACGGCCAAAATTTGATGCAAAAC 59.997 39.130 7.37 0.00 36.90 2.43
4302 4485 4.201990 GGCCAAAATTTGATGCAAAACACA 60.202 37.500 7.37 0.00 36.90 3.72
4317 4500 5.994668 GCAAAACACAAAGGGGATCAATAAA 59.005 36.000 0.00 0.00 0.00 1.40
4320 4503 5.010708 ACACAAAGGGGATCAATAAACCT 57.989 39.130 0.00 0.00 0.00 3.50
4349 4532 6.515200 CGGAGGTAGTACATCTGATCGAAAAT 60.515 42.308 17.04 0.00 37.46 1.82
4350 4533 7.308408 CGGAGGTAGTACATCTGATCGAAAATA 60.308 40.741 17.04 0.00 37.46 1.40
4351 4534 8.358148 GGAGGTAGTACATCTGATCGAAAATAA 58.642 37.037 14.16 0.00 0.00 1.40
4352 4535 9.745880 GAGGTAGTACATCTGATCGAAAATAAA 57.254 33.333 7.70 0.00 0.00 1.40
4355 4538 9.798885 GTAGTACATCTGATCGAAAATAAATGC 57.201 33.333 0.00 0.00 0.00 3.56
4356 4539 7.865707 AGTACATCTGATCGAAAATAAATGCC 58.134 34.615 0.00 0.00 0.00 4.40
4357 4540 5.751680 ACATCTGATCGAAAATAAATGCCG 58.248 37.500 0.00 0.00 0.00 5.69
4372 4556 1.003851 TGCCGTAGAATTTGTAGCGC 58.996 50.000 0.00 0.00 0.00 5.92
4385 4569 5.798015 TTTGTAGCGCCGAAACATTATTA 57.202 34.783 2.29 0.00 0.00 0.98
4386 4570 5.994887 TTGTAGCGCCGAAACATTATTAT 57.005 34.783 2.29 0.00 0.00 1.28
4391 4575 9.205719 TGTAGCGCCGAAACATTATTATTATTA 57.794 29.630 2.29 0.00 0.00 0.98
4477 4662 6.219417 TCCTTTTTGCACAAAAGATTCTCA 57.781 33.333 23.82 7.81 40.83 3.27
4481 4666 8.066000 CCTTTTTGCACAAAAGATTCTCATTTC 58.934 33.333 23.82 0.00 40.83 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 82 8.325787 ACTTTGTCTTTTGTTTTTATTTCCCCT 58.674 29.630 0.00 0.00 0.00 4.79
95 110 1.342496 CAATGCTAGGAGATCTCGGCA 59.658 52.381 26.76 26.76 38.19 5.69
330 357 0.909623 TAGGGAGGCTCCTTTTTCCG 59.090 55.000 31.39 0.00 38.30 4.30
388 416 3.678072 TGGATCGAACAAGTAAAGAAGCG 59.322 43.478 0.00 0.00 0.00 4.68
453 484 2.567615 ACCAAAATCTCCTAGCGTCACT 59.432 45.455 0.00 0.00 0.00 3.41
589 625 2.740714 GGCGTAGTGCTTTCAGCGG 61.741 63.158 0.00 0.00 46.26 5.52
592 628 1.594862 GCATAGGCGTAGTGCTTTCAG 59.405 52.381 11.23 0.00 45.43 3.02
636 672 4.460263 ACAGACTGGCAGAAATTACACAA 58.540 39.130 23.66 0.00 0.00 3.33
662 698 4.879598 GAGTAGAAGAAACTCCGGTTTGA 58.120 43.478 0.00 0.00 44.58 2.69
758 794 2.622942 GACAAATTTGAGCAGACACCCA 59.377 45.455 24.64 0.00 0.00 4.51
759 795 2.350772 CGACAAATTTGAGCAGACACCC 60.351 50.000 24.64 0.54 0.00 4.61
760 796 2.918131 GCGACAAATTTGAGCAGACACC 60.918 50.000 24.64 0.87 36.19 4.16
763 799 1.401539 GGGCGACAAATTTGAGCAGAC 60.402 52.381 29.36 20.51 37.20 3.51
764 800 0.881118 GGGCGACAAATTTGAGCAGA 59.119 50.000 29.36 0.00 37.20 4.26
765 801 0.597568 TGGGCGACAAATTTGAGCAG 59.402 50.000 29.36 17.74 37.20 4.24
766 802 0.597568 CTGGGCGACAAATTTGAGCA 59.402 50.000 29.36 17.50 37.20 4.26
767 803 0.598065 ACTGGGCGACAAATTTGAGC 59.402 50.000 24.64 24.55 35.72 4.26
768 804 2.293122 TGAACTGGGCGACAAATTTGAG 59.707 45.455 24.64 17.34 0.00 3.02
769 805 2.302260 TGAACTGGGCGACAAATTTGA 58.698 42.857 24.64 0.00 0.00 2.69
770 806 2.791383 TGAACTGGGCGACAAATTTG 57.209 45.000 16.67 16.67 0.00 2.32
779 835 1.207089 TCCTACAAGATGAACTGGGCG 59.793 52.381 0.00 0.00 0.00 6.13
840 990 5.049405 CCCATTGTTGAAGAACACTCTGTAC 60.049 44.000 0.00 0.00 41.92 2.90
862 1012 1.031571 TTTCTGATGCGGTGATGCCC 61.032 55.000 0.00 0.00 0.00 5.36
890 1040 7.147312 TCATGATCCTGTGAAAATGTTTGTTC 58.853 34.615 0.00 0.00 0.00 3.18
954 1104 6.505344 AGATCATTAGCCTGGGTATAATTCCA 59.495 38.462 6.42 0.00 0.00 3.53
955 1105 6.825721 CAGATCATTAGCCTGGGTATAATTCC 59.174 42.308 6.42 0.00 0.00 3.01
1083 1233 3.198068 TGCGAAAGAGGAATGCAGTATC 58.802 45.455 0.00 0.00 0.00 2.24
1116 1266 9.386122 AGTACCATAGGATAATCACAAGAAGAT 57.614 33.333 0.00 0.00 0.00 2.40
1146 1296 1.010419 GCAGCAACAAAATCCCAGCG 61.010 55.000 0.00 0.00 0.00 5.18
1155 1305 5.414789 TCCTATGTAGTAGCAGCAACAAA 57.585 39.130 0.00 0.00 0.00 2.83
1182 1332 3.191888 AGGAAAGCAAGTAGAGGAGGA 57.808 47.619 0.00 0.00 0.00 3.71
1218 1368 0.606604 GTCCGGTTAACAGCAGGAGA 59.393 55.000 8.10 0.00 0.00 3.71
1273 1423 0.466124 GCAGTCACTGAGGGGGTATC 59.534 60.000 9.70 0.00 32.44 2.24
1308 1458 2.076863 GGGGACTGAGTTTGTTGATCG 58.923 52.381 0.00 0.00 0.00 3.69
1309 1459 2.076863 CGGGGACTGAGTTTGTTGATC 58.923 52.381 0.00 0.00 36.31 2.92
1321 1471 0.109723 TTTTTGGACTCCGGGGACTG 59.890 55.000 9.33 0.00 0.00 3.51
1322 1472 1.073098 ATTTTTGGACTCCGGGGACT 58.927 50.000 9.33 0.00 0.00 3.85
1391 1541 4.013050 GCCAGTTCTTTTCTCCAAGCTAT 58.987 43.478 0.00 0.00 0.00 2.97
1393 1543 2.234143 GCCAGTTCTTTTCTCCAAGCT 58.766 47.619 0.00 0.00 0.00 3.74
1404 1554 0.250640 CTCCTGCACTGCCAGTTCTT 60.251 55.000 0.00 0.00 0.00 2.52
1454 1604 0.518636 ACAGTGATTGTCATGCGTGC 59.481 50.000 0.00 0.00 33.87 5.34
1492 1642 0.253044 ACAGTATCAGCCGCCACAAT 59.747 50.000 0.00 0.00 0.00 2.71
1500 1650 2.315925 TGCTAAGCACAGTATCAGCC 57.684 50.000 0.00 0.00 31.71 4.85
1549 1699 4.934797 ATCCTTCTCTTCCCACAATGAA 57.065 40.909 0.00 0.00 0.00 2.57
1613 1763 4.397103 CACCTCTTTCATTATTGCTGCTCA 59.603 41.667 0.00 0.00 0.00 4.26
1652 1802 5.310720 GGGTTCACCAAACTGATAATGAC 57.689 43.478 0.00 0.00 39.85 3.06
1746 1896 4.033009 TGGATGCATCAGGAGAAGAACTA 58.967 43.478 27.25 0.00 0.00 2.24
1949 2102 4.128925 TCACTTCCATCATCTTTCTCCG 57.871 45.455 0.00 0.00 0.00 4.63
1967 2120 4.155709 TCCTATGACATCCTCCTGATCAC 58.844 47.826 0.00 0.00 0.00 3.06
2157 2310 5.455392 GCATTTGAAGGATCATATGGTTCG 58.545 41.667 2.13 0.00 42.12 3.95
2187 2340 3.198853 GCAACTCTATCACTTCCCCTTCT 59.801 47.826 0.00 0.00 0.00 2.85
2255 2408 5.488919 TGGTCAGAAGGAAGATCAAATAGGT 59.511 40.000 0.00 0.00 0.00 3.08
2313 2466 0.107116 AGTACGAGCGAGGAGTCCAT 60.107 55.000 12.86 0.00 0.00 3.41
2391 2544 0.322816 ATTTGAGGCCACTGCGATGT 60.323 50.000 5.01 0.00 38.85 3.06
2392 2545 0.379669 GATTTGAGGCCACTGCGATG 59.620 55.000 5.01 0.00 38.85 3.84
2393 2546 1.091771 CGATTTGAGGCCACTGCGAT 61.092 55.000 5.01 0.00 38.85 4.58
2426 2579 0.622665 AAGGGCATCTTCTCCACTGG 59.377 55.000 0.00 0.00 0.00 4.00
2496 2649 2.288666 TGTGCTTCCTGTGAACAAGAC 58.711 47.619 0.00 0.00 0.00 3.01
2685 2838 5.957774 AGCCATAACAAATTTACCTGGATGT 59.042 36.000 0.00 0.00 0.00 3.06
2843 2996 2.620251 TTGATGGAATTCGCTCCGAT 57.380 45.000 0.00 0.00 38.44 4.18
2847 3000 4.889832 ACTTCATTGATGGAATTCGCTC 57.110 40.909 0.00 0.00 0.00 5.03
2861 3014 7.064728 GCTCCTGAATAACGAGTTAACTTCATT 59.935 37.037 10.02 7.29 29.21 2.57
2913 3066 1.674817 CCATAACGGGCTCTGAAACGT 60.675 52.381 0.00 0.00 41.88 3.99
2965 3118 0.322322 ATAACGCCGGGTCACTCAAA 59.678 50.000 2.18 0.00 0.00 2.69
2967 3120 1.216977 CATAACGCCGGGTCACTCA 59.783 57.895 2.18 0.00 0.00 3.41
2995 3148 1.116308 CTTCAATGGCATGCATCCCA 58.884 50.000 21.36 12.88 35.21 4.37
3041 3194 7.651304 TGCTTCGTGATTGATTTGTACAAATTT 59.349 29.630 29.47 19.26 40.77 1.82
3094 3247 6.174720 TCACTTGACTTATCTTGAACTGGT 57.825 37.500 0.00 0.00 0.00 4.00
3097 3250 7.172361 GCTTCTTCACTTGACTTATCTTGAACT 59.828 37.037 0.00 0.00 0.00 3.01
3106 3259 6.205464 CAGGAAATGCTTCTTCACTTGACTTA 59.795 38.462 0.00 0.00 0.00 2.24
3246 3399 3.374678 CCTTTTCATCTCTTCAGCTGAGC 59.625 47.826 17.43 0.00 0.00 4.26
3301 3454 3.139850 GTGCTCTGAGCTATGATGCATT 58.860 45.455 28.04 0.00 42.97 3.56
3417 3570 1.098050 CACCTTGTTATGGCCAGAGC 58.902 55.000 13.05 9.99 38.76 4.09
3428 3581 3.138283 TCTTGGGACATCTTCACCTTGTT 59.862 43.478 0.00 0.00 39.30 2.83
3435 3588 4.566278 CCTCAACATCTTGGGACATCTTCA 60.566 45.833 0.00 0.00 39.30 3.02
3445 3598 1.004044 AGCTCCACCTCAACATCTTGG 59.996 52.381 0.00 0.00 0.00 3.61
3530 3683 3.367292 CCACTGCCAAATGTGTCATAACC 60.367 47.826 0.00 0.00 32.76 2.85
3570 3723 1.740025 GAGTTCCGGCTGAATCTTTGG 59.260 52.381 0.00 0.00 34.90 3.28
3583 3736 3.372206 CAGCAACAGATTTAGGAGTTCCG 59.628 47.826 0.00 0.00 42.08 4.30
3623 3778 3.808726 GCAACCTGCAATTTCAAACATCA 59.191 39.130 0.00 0.00 44.26 3.07
3640 3795 1.203052 CCTGGATCATGTGTTGCAACC 59.797 52.381 26.14 17.38 0.00 3.77
3675 3830 3.576078 TTGAAACTTTCCAGAGCTCCA 57.424 42.857 10.93 0.00 0.00 3.86
3678 3833 5.320277 AGCTATTTGAAACTTTCCAGAGCT 58.680 37.500 11.56 11.56 33.91 4.09
3735 3890 2.230660 GTAGTGCTTTTGAGCCCTTGT 58.769 47.619 0.00 0.00 0.00 3.16
3786 3942 7.427989 AGCCATTCATAATTCAAATCCAGTT 57.572 32.000 0.00 0.00 0.00 3.16
3822 3978 8.568732 TCACTAAAAATAAAGAAAGGCAAACG 57.431 30.769 0.00 0.00 0.00 3.60
3864 4021 7.839705 TGAAGTACAGAGGGATATAGTTCAACT 59.160 37.037 0.00 0.00 35.21 3.16
3877 4039 7.141363 CACATTTTTCTTTGAAGTACAGAGGG 58.859 38.462 0.00 0.00 32.49 4.30
3879 4041 8.397906 TGACACATTTTTCTTTGAAGTACAGAG 58.602 33.333 0.00 0.00 32.83 3.35
3903 4065 1.035923 CTAATCGGCAGAGCTCCTGA 58.964 55.000 10.93 7.05 45.78 3.86
3916 4078 1.344438 TGATACTGCCAGGGCTAATCG 59.656 52.381 12.19 0.00 42.51 3.34
3928 4090 4.938226 AGTAGGCTTTGAAGTTGATACTGC 59.062 41.667 0.00 0.00 34.01 4.40
3931 4093 8.451748 CCTTTTAGTAGGCTTTGAAGTTGATAC 58.548 37.037 0.00 0.00 0.00 2.24
3937 4099 6.838382 TCTTCCTTTTAGTAGGCTTTGAAGT 58.162 36.000 0.00 0.00 35.15 3.01
3961 4123 7.494922 AGCATTTTGATTACCCCAGTAAATT 57.505 32.000 0.00 0.00 41.68 1.82
3969 4131 4.440940 CCCGTTAAGCATTTTGATTACCCC 60.441 45.833 0.00 0.00 26.81 4.95
3971 4133 4.109766 GCCCGTTAAGCATTTTGATTACC 58.890 43.478 0.00 0.00 26.81 2.85
3991 4171 0.953003 CGGAGGTAGCAGTAGTAGCC 59.047 60.000 0.00 0.00 0.00 3.93
4001 4184 1.188863 TAAACCAGGACGGAGGTAGC 58.811 55.000 0.00 0.00 37.07 3.58
4019 4202 7.758820 TCCAAAATACAAGGAGGGACTAATA 57.241 36.000 0.00 0.00 41.55 0.98
4020 4203 6.652205 TCCAAAATACAAGGAGGGACTAAT 57.348 37.500 0.00 0.00 41.55 1.73
4030 4213 8.720562 GGTCAAAATTTGATCCAAAATACAAGG 58.279 33.333 11.87 0.00 42.47 3.61
4113 4296 6.925610 TGTTGGATTCATATTCGAAAGAGG 57.074 37.500 0.00 0.00 43.69 3.69
4128 4311 7.551585 TGTCACAAAACTTACATTGTTGGATT 58.448 30.769 0.00 0.00 37.66 3.01
4134 4317 7.040686 GGGAGTATGTCACAAAACTTACATTGT 60.041 37.037 0.00 0.00 40.24 2.71
4139 4322 6.369065 CAGAGGGAGTATGTCACAAAACTTAC 59.631 42.308 0.00 0.00 32.66 2.34
4154 4337 6.724441 TCACTTATTTTGAGACAGAGGGAGTA 59.276 38.462 0.00 0.00 0.00 2.59
4155 4338 5.544176 TCACTTATTTTGAGACAGAGGGAGT 59.456 40.000 0.00 0.00 0.00 3.85
4156 4339 5.872070 GTCACTTATTTTGAGACAGAGGGAG 59.128 44.000 0.00 0.00 0.00 4.30
4157 4340 5.544176 AGTCACTTATTTTGAGACAGAGGGA 59.456 40.000 0.00 0.00 0.00 4.20
4158 4341 5.799213 AGTCACTTATTTTGAGACAGAGGG 58.201 41.667 0.00 0.00 0.00 4.30
4159 4342 6.459066 TGAGTCACTTATTTTGAGACAGAGG 58.541 40.000 0.00 0.00 0.00 3.69
4160 4343 7.655328 ACTTGAGTCACTTATTTTGAGACAGAG 59.345 37.037 0.00 0.00 0.00 3.35
4161 4344 7.500992 ACTTGAGTCACTTATTTTGAGACAGA 58.499 34.615 0.00 0.00 0.00 3.41
4162 4345 7.721286 ACTTGAGTCACTTATTTTGAGACAG 57.279 36.000 0.00 0.00 0.00 3.51
4163 4346 8.397906 CAAACTTGAGTCACTTATTTTGAGACA 58.602 33.333 0.00 0.00 0.00 3.41
4164 4347 8.398665 ACAAACTTGAGTCACTTATTTTGAGAC 58.601 33.333 11.12 0.00 0.00 3.36
4165 4348 8.506168 ACAAACTTGAGTCACTTATTTTGAGA 57.494 30.769 11.12 0.00 0.00 3.27
4200 4383 9.310716 GACTCAAGTTTGTACTAACTTTGTACT 57.689 33.333 26.14 11.72 43.85 2.73
4201 4384 9.090692 TGACTCAAGTTTGTACTAACTTTGTAC 57.909 33.333 26.14 19.04 43.85 2.90
4202 4385 9.090692 GTGACTCAAGTTTGTACTAACTTTGTA 57.909 33.333 26.14 16.32 43.85 2.41
4203 4386 7.822822 AGTGACTCAAGTTTGTACTAACTTTGT 59.177 33.333 26.14 25.01 43.85 2.83
4204 4387 8.197988 AGTGACTCAAGTTTGTACTAACTTTG 57.802 34.615 26.14 22.84 43.85 2.77
4205 4388 8.788325 AAGTGACTCAAGTTTGTACTAACTTT 57.212 30.769 26.14 15.97 43.85 2.66
4211 4394 8.621286 CCAAAATAAGTGACTCAAGTTTGTACT 58.379 33.333 15.07 0.00 35.68 2.73
4212 4395 7.860872 CCCAAAATAAGTGACTCAAGTTTGTAC 59.139 37.037 15.07 0.00 0.00 2.90
4213 4396 7.776030 TCCCAAAATAAGTGACTCAAGTTTGTA 59.224 33.333 15.07 5.29 0.00 2.41
4214 4397 6.605594 TCCCAAAATAAGTGACTCAAGTTTGT 59.394 34.615 15.07 0.00 0.00 2.83
4215 4398 6.918022 GTCCCAAAATAAGTGACTCAAGTTTG 59.082 38.462 11.50 11.50 0.00 2.93
4216 4399 6.238648 CGTCCCAAAATAAGTGACTCAAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
4217 4400 5.238650 CGTCCCAAAATAAGTGACTCAAGTT 59.761 40.000 0.00 0.00 0.00 2.66
4218 4401 4.755123 CGTCCCAAAATAAGTGACTCAAGT 59.245 41.667 0.00 0.00 0.00 3.16
4219 4402 4.154195 CCGTCCCAAAATAAGTGACTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
4220 4403 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4221 4404 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
4222 4405 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
4223 4406 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
4224 4407 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
4225 4408 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
4226 4409 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4227 4410 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4228 4411 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4229 4412 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4230 4413 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4231 4414 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
4232 4415 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
4233 4416 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
4234 4417 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
4235 4418 0.901580 GTTGTACTCCCTCCGTCCCA 60.902 60.000 0.00 0.00 0.00 4.37
4236 4419 1.611474 GGTTGTACTCCCTCCGTCCC 61.611 65.000 0.00 0.00 0.00 4.46
4237 4420 0.614134 AGGTTGTACTCCCTCCGTCC 60.614 60.000 0.00 0.00 0.00 4.79
4238 4421 2.134789 TAGGTTGTACTCCCTCCGTC 57.865 55.000 7.11 0.00 32.08 4.79
4239 4422 2.842645 ATAGGTTGTACTCCCTCCGT 57.157 50.000 7.11 0.00 32.08 4.69
4240 4423 6.436532 ACATAATATAGGTTGTACTCCCTCCG 59.563 42.308 7.11 0.00 32.08 4.63
4241 4424 7.793948 ACATAATATAGGTTGTACTCCCTCC 57.206 40.000 7.11 0.00 32.08 4.30
4243 4426 9.893975 ACTAACATAATATAGGTTGTACTCCCT 57.106 33.333 8.63 8.63 34.24 4.20
4262 4445 4.481368 TGGCCGTAGATTTGACTAACAT 57.519 40.909 0.00 0.00 0.00 2.71
4280 4463 4.918037 TGTGTTTTGCATCAAATTTTGGC 58.082 34.783 9.18 6.39 33.19 4.52
4292 4475 2.392662 TGATCCCCTTTGTGTTTTGCA 58.607 42.857 0.00 0.00 0.00 4.08
4293 4476 3.467374 TTGATCCCCTTTGTGTTTTGC 57.533 42.857 0.00 0.00 0.00 3.68
4299 4482 6.318900 GTCTAGGTTTATTGATCCCCTTTGTG 59.681 42.308 0.00 0.00 0.00 3.33
4302 4485 5.397559 CCGTCTAGGTTTATTGATCCCCTTT 60.398 44.000 0.00 0.00 34.51 3.11
4320 4503 5.549347 GATCAGATGTACTACCTCCGTCTA 58.451 45.833 0.00 0.00 0.00 2.59
4349 4532 4.260456 GCGCTACAAATTCTACGGCATTTA 60.260 41.667 0.00 0.00 0.00 1.40
4350 4533 3.486875 GCGCTACAAATTCTACGGCATTT 60.487 43.478 0.00 0.00 0.00 2.32
4351 4534 2.031683 GCGCTACAAATTCTACGGCATT 59.968 45.455 0.00 0.00 0.00 3.56
4352 4535 1.597663 GCGCTACAAATTCTACGGCAT 59.402 47.619 0.00 0.00 0.00 4.40
4353 4536 1.003851 GCGCTACAAATTCTACGGCA 58.996 50.000 0.00 0.00 0.00 5.69
4354 4537 0.303796 GGCGCTACAAATTCTACGGC 59.696 55.000 7.64 0.00 38.88 5.68
4355 4538 0.575390 CGGCGCTACAAATTCTACGG 59.425 55.000 7.64 0.00 0.00 4.02
4356 4539 1.552226 TCGGCGCTACAAATTCTACG 58.448 50.000 7.64 0.00 0.00 3.51
4357 4540 3.123959 TGTTTCGGCGCTACAAATTCTAC 59.876 43.478 7.64 0.00 0.00 2.59
4454 4639 6.219417 TGAGAATCTTTTGTGCAAAAAGGA 57.781 33.333 15.75 15.75 39.49 3.36
4477 4662 4.586001 GCACATTGATAGACATGGGGAAAT 59.414 41.667 0.00 0.00 0.00 2.17
4481 4666 3.219176 AGCACATTGATAGACATGGGG 57.781 47.619 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.