Multiple sequence alignment - TraesCS5D01G023500

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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 TraesCS5D01G023500 chr5D 100.000 6217 0 0 1 6217 18188076 18194292 0.000000e+00 11481.0
1 TraesCS5D01G023500 chr5D 97.619 126 1 1 5672 5797 294640358 294640235 1.360000e-51 215.0
2 TraesCS5D01G023500 chr5D 90.476 126 4 3 5672 5797 358548761 358548644 6.450000e-35 159.0
3 TraesCS5D01G023500 chr5A 92.188 4903 243 55 848 5673 11965122 11969961 0.000000e+00 6804.0
4 TraesCS5D01G023500 chr5A 84.371 883 105 23 4496 5352 12041003 12041878 0.000000e+00 835.0
5 TraesCS5D01G023500 chr5A 85.457 777 99 11 4802 5571 12027074 12027843 0.000000e+00 797.0
6 TraesCS5D01G023500 chr5A 89.810 422 23 11 5796 6198 11969960 11970380 1.990000e-144 523.0
7 TraesCS5D01G023500 chr5A 87.150 428 48 4 4372 4796 12134226 12134649 4.360000e-131 479.0
8 TraesCS5D01G023500 chr5A 81.431 587 81 18 4761 5331 12033710 12034284 7.350000e-124 455.0
9 TraesCS5D01G023500 chr5A 80.143 559 79 18 4818 5354 12134704 12135252 7.560000e-104 388.0
10 TraesCS5D01G023500 chr5A 87.692 195 21 3 4126 4318 12132468 12132661 2.260000e-54 224.0
11 TraesCS5D01G023500 chr5A 95.745 47 2 0 6069 6115 11970196 11970242 6.680000e-10 76.8
12 TraesCS5D01G023500 chr5A 95.652 46 2 0 2395 2440 11976793 11976838 2.400000e-09 75.0
13 TraesCS5D01G023500 chr5B 91.097 2415 159 23 2958 5325 13723897 13726302 0.000000e+00 3217.0
14 TraesCS5D01G023500 chr5B 93.101 1638 74 10 1404 3023 13722281 13723897 0.000000e+00 2362.0
15 TraesCS5D01G023500 chr5B 91.419 606 30 11 808 1403 13721602 13722195 0.000000e+00 811.0
16 TraesCS5D01G023500 chr5B 91.071 336 21 5 4613 4939 13726859 13727194 4.420000e-121 446.0
17 TraesCS5D01G023500 chr5B 93.651 126 3 1 5672 5797 312761938 312761818 3.830000e-42 183.0
18 TraesCS5D01G023500 chr5B 91.603 131 7 1 5672 5802 680823753 680823627 1.780000e-40 178.0
19 TraesCS5D01G023500 chr5B 90.654 107 10 0 1584 1690 13722308 13722414 6.500000e-30 143.0
20 TraesCS5D01G023500 chr5B 96.970 66 1 1 4468 4533 13726805 13726869 6.590000e-20 110.0
21 TraesCS5D01G023500 chr5B 82.796 93 11 4 5085 5176 13727252 13727340 1.860000e-10 78.7
22 TraesCS5D01G023500 chr1B 90.700 828 35 10 1 801 637603679 637604491 0.000000e+00 1064.0
23 TraesCS5D01G023500 chr1B 94.531 128 7 0 5672 5799 136627014 136627141 1.370000e-46 198.0
24 TraesCS5D01G023500 chr1B 90.476 126 8 2 5672 5797 240488033 240487912 4.990000e-36 163.0
25 TraesCS5D01G023500 chr3B 95.149 639 18 3 1 638 104367644 104367018 0.000000e+00 996.0
26 TraesCS5D01G023500 chr3B 93.571 140 4 4 681 815 104367022 104366883 2.940000e-48 204.0
27 TraesCS5D01G023500 chr3B 91.270 126 11 0 5672 5797 190161045 190160920 8.290000e-39 172.0
28 TraesCS5D01G023500 chr7D 94.262 488 15 5 22 508 105827458 105827933 0.000000e+00 734.0
29 TraesCS5D01G023500 chr7A 93.060 317 7 5 1 315 623424897 623424594 3.420000e-122 449.0
30 TraesCS5D01G023500 chr7A 97.196 214 4 2 346 558 623424595 623424383 1.650000e-95 361.0
31 TraesCS5D01G023500 chr7A 88.261 230 19 2 572 801 623325308 623325087 1.030000e-67 268.0
32 TraesCS5D01G023500 chr2A 87.375 301 24 7 508 801 4011712 4011419 3.590000e-87 333.0
33 TraesCS5D01G023500 chr2A 96.875 128 3 1 5671 5797 1954658 1954531 4.880000e-51 213.0
34 TraesCS5D01G023500 chr2A 96.875 128 3 1 5671 5797 2084599 2084472 4.880000e-51 213.0
35 TraesCS5D01G023500 chr4A 80.734 109 11 8 5218 5324 643935160 643935060 6.680000e-10 76.8
36 TraesCS5D01G023500 chr4A 80.734 109 11 8 5218 5324 643954079 643953979 6.680000e-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 TraesCS5D01G023500 chr5D 18188076 18194292 6216 False 11481.000000 11481 100.000000 1 6217 1 chr5D.!!$F1 6216
1 TraesCS5D01G023500 chr5A 11965122 11970380 5258 False 2467.933333 6804 92.581000 848 6198 3 chr5A.!!$F5 5350
2 TraesCS5D01G023500 chr5A 12041003 12041878 875 False 835.000000 835 84.371000 4496 5352 1 chr5A.!!$F4 856
3 TraesCS5D01G023500 chr5A 12027074 12027843 769 False 797.000000 797 85.457000 4802 5571 1 chr5A.!!$F2 769
4 TraesCS5D01G023500 chr5A 12033710 12034284 574 False 455.000000 455 81.431000 4761 5331 1 chr5A.!!$F3 570
5 TraesCS5D01G023500 chr5A 12132468 12135252 2784 False 363.666667 479 84.995000 4126 5354 3 chr5A.!!$F6 1228
6 TraesCS5D01G023500 chr5B 13721602 13727340 5738 False 1023.957143 3217 91.015429 808 5325 7 chr5B.!!$F1 4517
7 TraesCS5D01G023500 chr1B 637603679 637604491 812 False 1064.000000 1064 90.700000 1 801 1 chr1B.!!$F2 800
8 TraesCS5D01G023500 chr3B 104366883 104367644 761 True 600.000000 996 94.360000 1 815 2 chr3B.!!$R2 814
9 TraesCS5D01G023500 chr7A 623424383 623424897 514 True 405.000000 449 95.128000 1 558 2 chr7A.!!$R2 557

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
214 219 0.326264 AGCACTAGCCAGAACCAAGG 59.674 55.000 0.00 0.00 43.56 3.61 F
675 706 1.141881 CGTCAAGAGATGGGGGTCG 59.858 63.158 0.00 0.00 0.00 4.79 F
676 707 1.153349 GTCAAGAGATGGGGGTCGC 60.153 63.158 0.00 0.00 0.00 5.19 F
991 1028 1.227438 ACTTGACGTTGGGTCCACG 60.227 57.895 0.38 0.38 45.46 4.94 F
1478 1615 1.490574 AGTCATCTGGCTACAGGGAC 58.509 55.000 10.40 10.40 44.99 4.46 F
3309 3541 0.518636 CCTGTTCAATGCACTCCGTG 59.481 55.000 0.00 0.00 36.51 4.94 F
3700 3935 0.823356 AGCTCTTTTTCCGCCTTGCA 60.823 50.000 0.00 0.00 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 1326 1.257743 CTGACCCTTCCACTTCGAGA 58.742 55.000 0.00 0.0 0.00 4.04 R
1855 1995 1.680735 CCACAAACTGTTTAGCTGCCA 59.319 47.619 5.31 0.0 0.00 4.92 R
2315 2459 2.844122 AAGAACGACACAAACTTGCC 57.156 45.000 0.00 0.0 0.00 4.52 R
2540 2684 7.290014 TGGATAATAATCACTAGAAGCCACAGA 59.710 37.037 0.00 0.0 33.41 3.41 R
3370 3605 2.597578 AACCCTTTAGCCATTTCGGT 57.402 45.000 0.00 0.0 36.97 4.69 R
4429 6229 0.523072 AAGTTTGCATGGCACTAGCG 59.477 50.000 0.00 0.0 43.41 4.26 R
5421 7313 1.194547 CGTGTTCACGAGGTTTGATGG 59.805 52.381 18.64 0.0 34.64 3.51 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
120 125 7.206981 TCAAAATGAATGACAGAGAAAGGAC 57.793 36.000 0.00 0.00 0.00 3.85
121 126 6.207417 TCAAAATGAATGACAGAGAAAGGACC 59.793 38.462 0.00 0.00 0.00 4.46
122 127 4.916041 ATGAATGACAGAGAAAGGACCA 57.084 40.909 0.00 0.00 0.00 4.02
123 128 4.277515 TGAATGACAGAGAAAGGACCAG 57.722 45.455 0.00 0.00 0.00 4.00
124 129 3.903714 TGAATGACAGAGAAAGGACCAGA 59.096 43.478 0.00 0.00 0.00 3.86
125 130 4.020751 TGAATGACAGAGAAAGGACCAGAG 60.021 45.833 0.00 0.00 0.00 3.35
126 131 2.964209 TGACAGAGAAAGGACCAGAGT 58.036 47.619 0.00 0.00 0.00 3.24
155 160 9.155975 AGAACACAAAATCAGATACATGAGTAC 57.844 33.333 0.00 0.00 31.96 2.73
157 162 6.535150 ACACAAAATCAGATACATGAGTACGG 59.465 38.462 0.00 0.00 31.96 4.02
210 215 4.459337 ACAAATTAAGCACTAGCCAGAACC 59.541 41.667 0.00 0.00 43.56 3.62
211 216 4.301072 AATTAAGCACTAGCCAGAACCA 57.699 40.909 0.00 0.00 43.56 3.67
212 217 3.780804 TTAAGCACTAGCCAGAACCAA 57.219 42.857 0.00 0.00 43.56 3.67
213 218 2.191128 AAGCACTAGCCAGAACCAAG 57.809 50.000 0.00 0.00 43.56 3.61
214 219 0.326264 AGCACTAGCCAGAACCAAGG 59.674 55.000 0.00 0.00 43.56 3.61
225 230 1.856265 GAACCAAGGCAAGGCAGACG 61.856 60.000 0.00 0.00 0.00 4.18
602 608 4.719369 ACGCGGAGGCAGAACGAC 62.719 66.667 12.47 0.00 39.92 4.34
629 635 2.028337 GCGAGGAGAATCGAGGGC 59.972 66.667 0.00 0.00 45.56 5.19
639 645 3.408853 TCGAGGGCGAGGAGAGGA 61.409 66.667 0.00 0.00 42.51 3.71
672 703 2.190578 GGCGTCAAGAGATGGGGG 59.809 66.667 0.00 0.00 0.00 5.40
673 704 2.670148 GGCGTCAAGAGATGGGGGT 61.670 63.158 0.00 0.00 0.00 4.95
674 705 1.153349 GCGTCAAGAGATGGGGGTC 60.153 63.158 0.00 0.00 0.00 4.46
675 706 1.141881 CGTCAAGAGATGGGGGTCG 59.858 63.158 0.00 0.00 0.00 4.79
676 707 1.153349 GTCAAGAGATGGGGGTCGC 60.153 63.158 0.00 0.00 0.00 5.19
677 708 2.202932 CAAGAGATGGGGGTCGCG 60.203 66.667 0.00 0.00 0.00 5.87
678 709 4.162690 AAGAGATGGGGGTCGCGC 62.163 66.667 0.00 0.00 0.00 6.86
731 762 3.976793 TCGATCTGTTATGTACCCGTC 57.023 47.619 0.00 0.00 0.00 4.79
801 834 2.915738 CGGTTACTCGCTCTTGTAGT 57.084 50.000 0.00 0.00 0.00 2.73
802 835 2.516923 CGGTTACTCGCTCTTGTAGTG 58.483 52.381 0.00 0.00 37.03 2.74
803 836 2.095364 CGGTTACTCGCTCTTGTAGTGT 60.095 50.000 0.00 0.00 37.01 3.55
804 837 3.611057 CGGTTACTCGCTCTTGTAGTGTT 60.611 47.826 0.00 0.00 37.01 3.32
805 838 4.304939 GGTTACTCGCTCTTGTAGTGTTT 58.695 43.478 0.00 0.00 37.01 2.83
806 839 5.464168 GGTTACTCGCTCTTGTAGTGTTTA 58.536 41.667 0.00 0.00 37.01 2.01
816 849 7.010023 GCTCTTGTAGTGTTTAATTGTCTTCG 58.990 38.462 0.00 0.00 0.00 3.79
840 873 1.905215 AGCTGTGATGTAGAGCCTGTT 59.095 47.619 0.00 0.00 46.35 3.16
851 885 8.049117 TGATGTAGAGCCTGTTATCTGAAAATT 58.951 33.333 0.00 0.00 0.00 1.82
991 1028 1.227438 ACTTGACGTTGGGTCCACG 60.227 57.895 0.38 0.38 45.46 4.94
1001 1038 2.207924 GGGTCCACGAGTCCAGTGT 61.208 63.158 0.00 0.00 37.88 3.55
1027 1066 3.056393 ACCGAACAAATATCTCCACGTCA 60.056 43.478 0.00 0.00 0.00 4.35
1478 1615 1.490574 AGTCATCTGGCTACAGGGAC 58.509 55.000 10.40 10.40 44.99 4.46
1518 1655 6.926272 GGGATAGAACTGCTCTGTAAATGTAG 59.074 42.308 0.00 0.00 35.41 2.74
1580 1717 3.933332 GACACATGGCTAGTTTCTGGTAC 59.067 47.826 0.00 0.00 0.00 3.34
1635 1772 3.928754 AGTCATCTGGCTACAGGGATAA 58.071 45.455 0.00 0.00 44.99 1.75
1651 1788 4.603610 AGGGATAAAGTAGGAATCATGGGG 59.396 45.833 0.00 0.00 0.00 4.96
1659 1796 3.637821 AGGAATCATGGGGTAGAGCTA 57.362 47.619 0.00 0.00 0.00 3.32
1742 1879 4.259810 CGTATCTTGTTACTGTGATTGCGG 60.260 45.833 0.00 0.00 0.00 5.69
1764 1901 6.031003 GCGGTATTACATCGATTTAAAATGCG 59.969 38.462 8.02 0.00 0.00 4.73
1781 1918 4.717233 ATGCGCCATGTTTCATTCTTTA 57.283 36.364 4.18 0.00 0.00 1.85
1786 1923 4.266029 CGCCATGTTTCATTCTTTATGCAC 59.734 41.667 0.00 0.00 34.06 4.57
1801 1941 7.630026 TCTTTATGCACATACTAGCAATTTCG 58.370 34.615 0.00 0.00 44.88 3.46
1917 2057 5.221843 TGGCTGTATTCCAGTACTGACTTTT 60.222 40.000 24.68 6.71 43.55 2.27
1940 2080 6.091718 TGCTATTATCGTGCCATGTAGTAA 57.908 37.500 0.00 0.00 0.00 2.24
1972 2115 3.054878 GTTGTTACCTGACGTGTACTGG 58.945 50.000 0.00 0.00 0.00 4.00
2130 2274 2.934553 GCTTTACGCCCTTACCAAGTAG 59.065 50.000 0.00 0.00 0.00 2.57
2131 2275 3.618263 GCTTTACGCCCTTACCAAGTAGT 60.618 47.826 0.00 0.00 0.00 2.73
2132 2276 4.381932 GCTTTACGCCCTTACCAAGTAGTA 60.382 45.833 0.00 0.00 0.00 1.82
2229 2373 1.747355 AGACAATGTGGCAGCATTAGC 59.253 47.619 12.68 9.10 37.00 3.09
2315 2459 8.915654 GTTTAACACAATAGAAATCTTGCAAGG 58.084 33.333 25.73 9.10 0.00 3.61
2540 2684 9.942526 ATATTTCCCTCTTCTATTTGTTCCATT 57.057 29.630 0.00 0.00 0.00 3.16
2566 2717 7.290014 TCTGTGGCTTCTAGTGATTATTATCCA 59.710 37.037 0.00 0.00 0.00 3.41
2610 2767 3.441572 ACTAGGCTGCATGTGAATTTGTC 59.558 43.478 0.50 0.00 0.00 3.18
2738 2896 4.068599 CCTCTGTTTCTTCTCCCAACTTC 58.931 47.826 0.00 0.00 0.00 3.01
2795 2953 9.787435 TTTATTTCTCCTGTACAACATAACTGT 57.213 29.630 0.00 0.00 37.12 3.55
3015 3247 6.317857 CAACCATTCTTTAGCAGCTTTACTC 58.682 40.000 0.00 0.00 0.00 2.59
3026 3258 8.539770 TTAGCAGCTTTACTCTATGCATTATC 57.460 34.615 3.54 0.00 39.34 1.75
3086 3318 7.766283 TGATCATAGGCTACTATCTTGATTCG 58.234 38.462 15.26 0.00 37.82 3.34
3087 3319 5.955488 TCATAGGCTACTATCTTGATTCGC 58.045 41.667 0.00 0.00 37.82 4.70
3122 3354 5.702865 CAAATGTGATTCACCTCGTTTCAT 58.297 37.500 14.05 0.00 32.73 2.57
3167 3399 6.713450 CAGTCAATATCATCATTGTCATGGGA 59.287 38.462 0.00 0.00 37.23 4.37
3208 3440 1.145571 AGGAAGGTGGGTAGCAAACA 58.854 50.000 0.00 0.00 0.00 2.83
3219 3451 6.546034 GGTGGGTAGCAAACAGATATTTACAT 59.454 38.462 0.00 0.00 0.00 2.29
3237 3469 2.708861 ACATGTTACAACTGGGACTCCA 59.291 45.455 0.00 0.00 41.58 3.86
3246 3478 2.284995 GGGACTCCAGGAGGCACT 60.285 66.667 24.89 0.00 38.25 4.40
3306 3538 5.183904 ACTTATTTCCTGTTCAATGCACTCC 59.816 40.000 0.00 0.00 0.00 3.85
3309 3541 0.518636 CCTGTTCAATGCACTCCGTG 59.481 55.000 0.00 0.00 36.51 4.94
3318 3550 4.277174 TCAATGCACTCCGTGTTATGTTTT 59.723 37.500 0.00 0.00 35.75 2.43
3373 3608 4.692155 AGTTTAATTTTACACCCGAGACCG 59.308 41.667 0.00 0.00 0.00 4.79
3473 3708 8.718102 TTACACATCAGACTAAAAGGCTAATC 57.282 34.615 0.00 0.00 26.27 1.75
3506 3741 6.652481 TCTTCTCATAGTTGAAAGCTTTGGAG 59.348 38.462 18.30 10.94 0.00 3.86
3700 3935 0.823356 AGCTCTTTTTCCGCCTTGCA 60.823 50.000 0.00 0.00 0.00 4.08
3706 3941 3.807071 TCTTTTTCCGCCTTGCAAAATTC 59.193 39.130 0.00 0.00 0.00 2.17
3734 3981 8.693504 GTCATTGGATAAATAAATTGCATCGTG 58.306 33.333 0.00 0.00 0.00 4.35
3742 3989 1.167851 AATTGCATCGTGTGTGAGGG 58.832 50.000 0.00 0.00 0.00 4.30
3769 4016 7.452880 TTGCTGTTATATGCAATAAGGGATC 57.547 36.000 0.00 0.00 43.17 3.36
3830 4077 5.260424 TCTTACCCATTCAGCATGCTTTAA 58.740 37.500 19.98 15.92 34.76 1.52
3905 4152 6.127897 GCAGTTATTGTCTCTTTTATGTGCCT 60.128 38.462 0.00 0.00 0.00 4.75
3939 4193 6.333416 TCTATGAATGACTCTTTCCTTGACG 58.667 40.000 2.97 0.00 0.00 4.35
4073 4328 5.048434 GGAGAGAAGATTTCAAGGTTTGGTG 60.048 44.000 0.00 0.00 0.00 4.17
4083 4338 8.880878 ATTTCAAGGTTTGGTGTAATGTTTAC 57.119 30.769 0.00 0.00 0.00 2.01
4183 4450 3.696051 GGCACTGTGTTCATGGTAATGAT 59.304 43.478 9.86 0.00 42.41 2.45
4200 4467 8.325787 TGGTAATGATATCCAGTAAACACTGTT 58.674 33.333 0.00 0.00 36.06 3.16
4265 4533 1.531578 GCCCTGAGAGAACGTCAAAAC 59.468 52.381 0.00 0.00 0.00 2.43
4417 6217 9.362539 CTAATTAGAGCAATTGCATTCTTGTTT 57.637 29.630 30.89 19.13 45.16 2.83
4418 6218 7.823149 ATTAGAGCAATTGCATTCTTGTTTC 57.177 32.000 30.89 16.33 45.16 2.78
4421 6221 6.618811 AGAGCAATTGCATTCTTGTTTCTAG 58.381 36.000 30.89 0.00 45.16 2.43
4425 6225 8.025445 AGCAATTGCATTCTTGTTTCTAGTTAG 58.975 33.333 30.89 0.00 45.16 2.34
4429 6229 5.106555 TGCATTCTTGTTTCTAGTTAGCAGC 60.107 40.000 0.00 0.00 0.00 5.25
4439 6239 1.447838 GTTAGCAGCGCTAGTGCCA 60.448 57.895 24.25 0.00 42.34 4.92
4441 6241 0.811219 TTAGCAGCGCTAGTGCCATG 60.811 55.000 24.25 17.58 42.34 3.66
4560 6360 9.073475 ACATTAACACAGCATCTAAAAGGTTAA 57.927 29.630 0.00 0.00 34.97 2.01
4568 6368 9.780186 ACAGCATCTAAAAGGTTAATACTATCC 57.220 33.333 0.00 0.00 0.00 2.59
4642 6447 0.716108 CAATCACGACTCAGTTCCGC 59.284 55.000 0.00 0.00 0.00 5.54
4694 6500 3.584834 CGAATATGTGGGATGCGATGTA 58.415 45.455 0.00 0.00 0.00 2.29
4957 6805 3.100671 ACTTAGCAAGAGGTGGTCCTAG 58.899 50.000 3.37 0.00 45.24 3.02
5075 6933 2.742589 AGCTAGCAAAACGAGGCTTTAC 59.257 45.455 18.83 0.00 41.41 2.01
5114 6972 4.154195 CGGCAGAAAGTTACAATAAGCACT 59.846 41.667 0.00 0.00 0.00 4.40
5185 7043 7.773864 TTGAACATTTGTACTGTTACTCGAA 57.226 32.000 0.00 0.00 36.98 3.71
5262 7151 5.696270 CCTTACTTATTGCATCACGATAGCA 59.304 40.000 0.00 0.00 42.67 3.49
5421 7313 4.718961 AGGCATTGGGAAGTATACATCAC 58.281 43.478 10.09 6.91 0.00 3.06
5432 7324 6.483640 GGAAGTATACATCACCATCAAACCTC 59.516 42.308 10.09 0.00 0.00 3.85
5456 7349 1.389555 ACACGAGACTGATATGGCGA 58.610 50.000 0.00 0.00 0.00 5.54
5530 7423 1.271934 CAGTATGAGATGAGGCTCCCG 59.728 57.143 12.86 0.00 39.69 5.14
5559 7452 2.767505 GGCGACCTTCTTTCTTTGAGA 58.232 47.619 0.00 0.00 0.00 3.27
5584 7477 8.674263 ACTGAAACTTCATCATCCATTCTATC 57.326 34.615 0.00 0.00 36.46 2.08
5594 7487 4.347876 TCATCCATTCTATCCGGTTGTGAT 59.652 41.667 0.00 0.00 0.00 3.06
5631 7524 9.522804 CTAGGACTTGTACATATTGAAGAAGAC 57.477 37.037 0.00 0.00 0.00 3.01
5683 7675 1.068250 GCATGCTACTCCCTCCGTC 59.932 63.158 11.37 0.00 0.00 4.79
5686 7678 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
5687 7679 1.457831 GCTACTCCCTCCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
5694 7686 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5696 7688 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5697 7689 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
5698 7690 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
5699 7691 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
5701 7693 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
5703 7695 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
5704 7696 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
5705 7697 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
5706 7698 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
5707 7699 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
5708 7700 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
5709 7701 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
5710 7702 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
5724 8151 0.810016 GACACTACACTCCCTCCGTC 59.190 60.000 0.00 0.00 0.00 4.79
5725 8152 0.611340 ACACTACACTCCCTCCGTCC 60.611 60.000 0.00 0.00 0.00 4.79
5727 8154 1.000019 CTACACTCCCTCCGTCCCA 60.000 63.158 0.00 0.00 0.00 4.37
5728 8155 0.397254 CTACACTCCCTCCGTCCCAT 60.397 60.000 0.00 0.00 0.00 4.00
5732 8159 2.090943 ACACTCCCTCCGTCCCATAATA 60.091 50.000 0.00 0.00 0.00 0.98
5737 8164 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5738 8165 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
5740 8245 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
5747 8252 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
5748 8253 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
5749 8254 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
5750 8255 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
5758 8263 4.982916 AGAGCGTTTTTGACACTAGTGTAG 59.017 41.667 27.98 13.76 45.05 2.74
5772 8277 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
5773 8278 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
5774 8279 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
5775 8280 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
5777 8282 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
5779 8284 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
5783 8288 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
5784 8289 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
5785 8290 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
5786 8291 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
5787 8292 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
5788 8293 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
5789 8294 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
5790 8295 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
5791 8296 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
5792 8297 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
5793 8298 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
5794 8299 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
5795 8300 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
5848 8353 7.237055 GGGGTATCCAAGTTATAAGAGTATGGT 59.763 40.741 0.00 0.00 35.00 3.55
5885 8390 0.324943 TAAGAAGAGTGTGCTGGCCC 59.675 55.000 0.00 0.00 0.00 5.80
6029 8534 0.739813 CTGCGGTTTTACTCCCCTCG 60.740 60.000 0.00 0.00 0.00 4.63
6038 8543 2.307496 TACTCCCCTCGTACACCAAA 57.693 50.000 0.00 0.00 0.00 3.28
6039 8544 1.652947 ACTCCCCTCGTACACCAAAT 58.347 50.000 0.00 0.00 0.00 2.32
6041 8546 2.290071 ACTCCCCTCGTACACCAAATTG 60.290 50.000 0.00 0.00 0.00 2.32
6043 8548 2.081462 CCCCTCGTACACCAAATTGTC 58.919 52.381 0.00 0.00 0.00 3.18
6044 8549 1.730064 CCCTCGTACACCAAATTGTCG 59.270 52.381 0.00 0.00 0.00 4.35
6045 8550 2.409975 CCTCGTACACCAAATTGTCGT 58.590 47.619 0.00 0.00 0.00 4.34
6047 8552 3.120786 CCTCGTACACCAAATTGTCGTTC 60.121 47.826 0.00 0.00 0.00 3.95
6048 8553 3.455327 TCGTACACCAAATTGTCGTTCA 58.545 40.909 0.00 0.00 0.00 3.18
6049 8554 3.245754 TCGTACACCAAATTGTCGTTCAC 59.754 43.478 0.00 0.00 0.00 3.18
6050 8555 3.001431 CGTACACCAAATTGTCGTTCACA 59.999 43.478 0.00 0.00 0.00 3.58
6051 8556 3.691049 ACACCAAATTGTCGTTCACAG 57.309 42.857 0.00 0.00 35.97 3.66
6053 8558 4.193090 ACACCAAATTGTCGTTCACAGTA 58.807 39.130 0.00 0.00 35.97 2.74
6054 8559 4.034742 ACACCAAATTGTCGTTCACAGTAC 59.965 41.667 0.00 0.00 35.97 2.73
6056 8561 3.491639 CCAAATTGTCGTTCACAGTACGA 59.508 43.478 0.00 0.00 44.88 3.43
6066 8590 4.031314 CGTTCACAGTACGAACCATACATG 59.969 45.833 6.56 0.00 41.33 3.21
6071 8595 2.500098 AGTACGAACCATACATGCCACT 59.500 45.455 0.00 0.00 0.00 4.00
6080 8604 9.594478 CGAACCATACATGCCACTAATATATAA 57.406 33.333 0.00 0.00 0.00 0.98
6134 8658 8.356657 TGGTATCGATTTTCTTGACACATTTTT 58.643 29.630 1.71 0.00 0.00 1.94
6171 8695 1.532868 CTCTCCAAGCCAAAAGACACG 59.467 52.381 0.00 0.00 0.00 4.49
6178 8702 1.071699 AGCCAAAAGACACGGAGCTAA 59.928 47.619 0.00 0.00 0.00 3.09
6189 8713 5.080969 ACACGGAGCTAAGCTTTTACATA 57.919 39.130 3.20 0.00 39.88 2.29
6198 8722 9.712305 GAGCTAAGCTTTTACATAGATTCCATA 57.288 33.333 3.20 0.00 39.88 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.573166 CTATGATTTTGTATTACCTGGATGGAA 57.427 33.333 0.00 0.00 39.71 3.53
120 125 4.136796 TGATTTTGTGTTCTGGACTCTGG 58.863 43.478 0.00 0.00 0.00 3.86
121 126 5.059161 TCTGATTTTGTGTTCTGGACTCTG 58.941 41.667 0.00 0.00 0.00 3.35
122 127 5.296151 TCTGATTTTGTGTTCTGGACTCT 57.704 39.130 0.00 0.00 0.00 3.24
123 128 6.650807 TGTATCTGATTTTGTGTTCTGGACTC 59.349 38.462 0.00 0.00 0.00 3.36
124 129 6.533730 TGTATCTGATTTTGTGTTCTGGACT 58.466 36.000 0.00 0.00 0.00 3.85
125 130 6.801539 TGTATCTGATTTTGTGTTCTGGAC 57.198 37.500 0.00 0.00 0.00 4.02
126 131 7.167535 TCATGTATCTGATTTTGTGTTCTGGA 58.832 34.615 0.00 0.00 0.00 3.86
155 160 1.205655 TCATGACTGAAGAAGCCTCCG 59.794 52.381 0.00 0.00 0.00 4.63
157 162 4.505922 CGTATTCATGACTGAAGAAGCCTC 59.494 45.833 0.00 0.00 44.32 4.70
210 215 1.165907 TGAACGTCTGCCTTGCCTTG 61.166 55.000 0.00 0.00 0.00 3.61
211 216 0.886490 CTGAACGTCTGCCTTGCCTT 60.886 55.000 0.00 0.00 0.00 4.35
212 217 1.302033 CTGAACGTCTGCCTTGCCT 60.302 57.895 0.00 0.00 0.00 4.75
213 218 1.294659 CTCTGAACGTCTGCCTTGCC 61.295 60.000 0.00 0.00 0.00 4.52
214 219 0.319900 TCTCTGAACGTCTGCCTTGC 60.320 55.000 0.00 0.00 0.00 4.01
225 230 2.681848 CTGGCCATGAACATCTCTGAAC 59.318 50.000 5.51 0.00 0.00 3.18
661 692 4.162690 GCGCGACCCCCATCTCTT 62.163 66.667 12.10 0.00 0.00 2.85
762 793 1.265905 GCGATGTCCACGTTCCTTTTT 59.734 47.619 0.00 0.00 0.00 1.94
801 834 5.761234 ACAGCTAACCGAAGACAATTAAACA 59.239 36.000 0.00 0.00 0.00 2.83
802 835 6.073440 TCACAGCTAACCGAAGACAATTAAAC 60.073 38.462 0.00 0.00 0.00 2.01
803 836 5.992829 TCACAGCTAACCGAAGACAATTAAA 59.007 36.000 0.00 0.00 0.00 1.52
804 837 5.543714 TCACAGCTAACCGAAGACAATTAA 58.456 37.500 0.00 0.00 0.00 1.40
805 838 5.142061 TCACAGCTAACCGAAGACAATTA 57.858 39.130 0.00 0.00 0.00 1.40
806 839 4.002906 TCACAGCTAACCGAAGACAATT 57.997 40.909 0.00 0.00 0.00 2.32
816 849 2.432510 AGGCTCTACATCACAGCTAACC 59.567 50.000 0.00 0.00 33.38 2.85
876 910 7.864882 TGAAATGTGCTCAAATTTCGAATACAA 59.135 29.630 16.42 0.42 42.93 2.41
879 913 8.698854 GTTTGAAATGTGCTCAAATTTCGAATA 58.301 29.630 21.87 7.05 43.22 1.75
991 1028 1.521450 TTCGGTCGGACACTGGACTC 61.521 60.000 10.76 0.00 33.70 3.36
1001 1038 2.761767 TGGAGATATTTGTTCGGTCGGA 59.238 45.455 0.00 0.00 0.00 4.55
1027 1066 4.824515 AGGCGAGGCGAGCTACCT 62.825 66.667 7.50 7.50 41.41 3.08
1138 1186 3.706373 GCTGGAGGAGGCGTGGAA 61.706 66.667 0.00 0.00 0.00 3.53
1278 1326 1.257743 CTGACCCTTCCACTTCGAGA 58.742 55.000 0.00 0.00 0.00 4.04
1370 1420 2.568956 TGATACAGAAGCAGAGCAGGTT 59.431 45.455 0.00 0.00 0.00 3.50
1478 1615 5.752036 TCTATCCCATAATTCCTGCTCTG 57.248 43.478 0.00 0.00 0.00 3.35
1518 1655 5.612725 TGGGGATAATTCCTGCATTTTTC 57.387 39.130 0.00 0.00 42.20 2.29
1539 1676 5.991606 TGTGTCCAGAAACTAGTCTTCAATG 59.008 40.000 15.53 8.90 0.00 2.82
1543 1680 4.932200 CCATGTGTCCAGAAACTAGTCTTC 59.068 45.833 0.00 2.91 0.00 2.87
1597 1734 4.202245 TGACTAGATGGGTAACAGCAAC 57.798 45.455 0.00 0.00 38.15 4.17
1635 1772 3.648545 GCTCTACCCCATGATTCCTACTT 59.351 47.826 0.00 0.00 0.00 2.24
1651 1788 8.665643 TCTCTACATTTACAGAGTAGCTCTAC 57.334 38.462 0.00 0.00 38.99 2.59
1659 1796 6.820656 CCTGCATTTCTCTACATTTACAGAGT 59.179 38.462 0.00 0.00 39.48 3.24
1742 1879 6.853872 TGGCGCATTTTAAATCGATGTAATAC 59.146 34.615 10.83 0.00 0.00 1.89
1764 1901 5.170021 TGTGCATAAAGAATGAAACATGGC 58.830 37.500 0.00 0.00 37.86 4.40
1781 1918 3.627123 TGCGAAATTGCTAGTATGTGCAT 59.373 39.130 0.00 0.00 39.07 3.96
1786 1923 6.233430 AGCTAATGCGAAATTGCTAGTATG 57.767 37.500 0.00 0.00 45.42 2.39
1801 1941 4.818546 TCCTCAGCAGAATAAAGCTAATGC 59.181 41.667 0.00 0.00 39.50 3.56
1855 1995 1.680735 CCACAAACTGTTTAGCTGCCA 59.319 47.619 5.31 0.00 0.00 4.92
1917 2057 4.600692 ACTACATGGCACGATAATAGCA 57.399 40.909 0.00 0.00 0.00 3.49
1940 2080 6.316890 ACGTCAGGTAACAACAAACAAGTTAT 59.683 34.615 0.00 0.00 41.41 1.89
1972 2115 5.648092 AGCACAAAAGGGACATACAGATTAC 59.352 40.000 0.00 0.00 0.00 1.89
2113 2257 3.968265 AGTACTACTTGGTAAGGGCGTA 58.032 45.455 0.00 0.00 0.00 4.42
2167 2311 4.099881 ACTTAAATGTTGGCATGGCATAGG 59.900 41.667 23.96 14.17 35.15 2.57
2251 2395 7.227512 CAGGTTTGATTCTACAGAGAACAGTTT 59.772 37.037 0.00 0.00 44.50 2.66
2315 2459 2.844122 AAGAACGACACAAACTTGCC 57.156 45.000 0.00 0.00 0.00 4.52
2540 2684 7.290014 TGGATAATAATCACTAGAAGCCACAGA 59.710 37.037 0.00 0.00 33.41 3.41
2566 2717 9.449719 CTAGTCCAAACATGTTTATAAAGGAGT 57.550 33.333 26.02 26.02 31.98 3.85
2813 2979 8.650143 AAAATGTAATTAGTCAGGTCCACAAT 57.350 30.769 0.00 0.00 33.67 2.71
3026 3258 5.243981 CCAGGCTGGTGATATTTCTAGATG 58.756 45.833 25.74 0.00 31.35 2.90
3086 3318 7.531534 GTGAATCACATTTGCAAATTTTAGTGC 59.468 33.333 24.77 16.32 36.48 4.40
3087 3319 8.011106 GGTGAATCACATTTGCAAATTTTAGTG 58.989 33.333 24.09 24.09 35.86 2.74
3159 3391 9.442047 CAGAACTAAGGATAATATTCCCATGAC 57.558 37.037 0.00 0.00 36.35 3.06
3208 3440 8.548877 AGTCCCAGTTGTAACATGTAAATATCT 58.451 33.333 0.00 0.00 0.00 1.98
3237 3469 7.092399 GGGTATTATATAAATCCAGTGCCTCCT 60.092 40.741 16.09 0.00 0.00 3.69
3239 3471 7.862675 AGGGTATTATATAAATCCAGTGCCTC 58.137 38.462 16.09 2.50 0.00 4.70
3370 3605 2.597578 AACCCTTTAGCCATTTCGGT 57.402 45.000 0.00 0.00 36.97 4.69
3373 3608 4.082190 GGACAGAAACCCTTTAGCCATTTC 60.082 45.833 0.00 0.00 0.00 2.17
3454 3689 5.615925 ACCGATTAGCCTTTTAGTCTGAT 57.384 39.130 0.00 0.00 0.00 2.90
3455 3690 5.416271 AACCGATTAGCCTTTTAGTCTGA 57.584 39.130 0.00 0.00 0.00 3.27
3473 3708 7.905493 GCTTTCAACTATGAGAAGAATAAACCG 59.095 37.037 0.00 0.00 36.78 4.44
3706 3941 7.060979 CGATGCAATTTATTTATCCAATGACGG 59.939 37.037 0.00 0.00 0.00 4.79
3734 3981 1.975660 TAACAGCAAACCCCTCACAC 58.024 50.000 0.00 0.00 0.00 3.82
3795 4042 5.048083 TGAATGGGTAAGAACATGCAGAAAC 60.048 40.000 0.00 0.00 29.45 2.78
3905 4152 6.233434 AGAGTCATTCATAGAGCAAACACAA 58.767 36.000 0.00 0.00 0.00 3.33
4036 4291 5.028549 TCTTCTCTCCATTTCTGCCATAC 57.971 43.478 0.00 0.00 0.00 2.39
4109 4366 3.831911 GACATGGAAAACAATTCTCCCCA 59.168 43.478 0.00 0.00 0.00 4.96
4200 4467 3.795150 GCAGTGCGAAAAGAAATCCACAA 60.795 43.478 0.00 0.00 0.00 3.33
4265 4533 6.265422 ACCTCCTCTTTTCCAACAATGTTTAG 59.735 38.462 0.00 0.00 0.00 1.85
4417 6217 1.065701 GCACTAGCGCTGCTAACTAGA 59.934 52.381 22.90 0.00 40.82 2.43
4418 6218 1.482278 GCACTAGCGCTGCTAACTAG 58.518 55.000 22.90 10.14 40.82 2.57
4421 6221 0.811616 ATGGCACTAGCGCTGCTAAC 60.812 55.000 22.90 8.26 40.82 2.34
4425 6225 4.247612 GCATGGCACTAGCGCTGC 62.248 66.667 22.90 16.49 43.41 5.25
4429 6229 0.523072 AAGTTTGCATGGCACTAGCG 59.477 50.000 0.00 0.00 43.41 4.26
4560 6360 4.737855 ATGCTTAATCCGCGGATAGTAT 57.262 40.909 39.08 31.79 33.97 2.12
4568 6368 5.108254 GCAAGAAAATAATGCTTAATCCGCG 60.108 40.000 0.00 0.00 37.12 6.46
4642 6447 1.457303 GCAGCGTGGCTATTATCTTCG 59.543 52.381 0.00 0.00 36.40 3.79
4694 6500 2.226437 CGCTACAAGGATGCAGTTTTGT 59.774 45.455 14.39 14.39 37.51 2.83
4957 6805 5.941647 TCCAATGCCTAGTTTACAAAGGTAC 59.058 40.000 0.00 0.00 32.67 3.34
5075 6933 1.280746 CCGCAAGCTCGGCATTATG 59.719 57.895 10.51 0.00 43.18 1.90
5185 7043 4.002906 TGAAGGCATAGAACAAACTCGT 57.997 40.909 0.00 0.00 0.00 4.18
5198 7068 8.371571 TCAGTCAGATGTATATATGAAGGCAT 57.628 34.615 0.00 0.00 36.39 4.40
5262 7151 2.249743 ACAGGGAAGATCCAGATCCTCT 59.750 50.000 4.01 0.00 38.64 3.69
5421 7313 1.194547 CGTGTTCACGAGGTTTGATGG 59.805 52.381 18.64 0.00 34.64 3.51
5432 7324 3.108881 CCATATCAGTCTCGTGTTCACG 58.891 50.000 17.57 17.57 0.00 4.35
5543 7436 6.418946 AGTTTCAGTCTCAAAGAAAGAAGGT 58.581 36.000 0.00 0.00 32.48 3.50
5545 7438 7.978982 TGAAGTTTCAGTCTCAAAGAAAGAAG 58.021 34.615 0.00 0.00 32.48 2.85
5558 7451 6.998968 AGAATGGATGATGAAGTTTCAGTC 57.001 37.500 0.74 0.00 41.08 3.51
5559 7452 7.718753 GGATAGAATGGATGATGAAGTTTCAGT 59.281 37.037 0.74 0.00 41.08 3.41
5584 7477 2.504367 GGGGATATGAATCACAACCGG 58.496 52.381 0.00 0.00 37.25 5.28
5631 7524 6.329496 ACCCATGCAATTACGAATAAACAAG 58.671 36.000 0.00 0.00 0.00 3.16
5640 7535 2.942376 CTGCTAACCCATGCAATTACGA 59.058 45.455 0.00 0.00 38.81 3.43
5683 7675 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
5687 7679 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
5694 7686 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
5697 7689 2.032290 GGGAGTGTAGTGTCAAAAACGC 60.032 50.000 0.00 0.00 38.74 4.84
5698 7690 3.463944 AGGGAGTGTAGTGTCAAAAACG 58.536 45.455 0.00 0.00 0.00 3.60
5699 7691 3.813724 GGAGGGAGTGTAGTGTCAAAAAC 59.186 47.826 0.00 0.00 0.00 2.43
5701 7693 2.036733 CGGAGGGAGTGTAGTGTCAAAA 59.963 50.000 0.00 0.00 0.00 2.44
5703 7695 1.254026 CGGAGGGAGTGTAGTGTCAA 58.746 55.000 0.00 0.00 0.00 3.18
5704 7696 0.111832 ACGGAGGGAGTGTAGTGTCA 59.888 55.000 0.00 0.00 0.00 3.58
5705 7697 0.810016 GACGGAGGGAGTGTAGTGTC 59.190 60.000 0.00 0.00 0.00 3.67
5706 7698 0.611340 GGACGGAGGGAGTGTAGTGT 60.611 60.000 0.00 0.00 0.00 3.55
5707 7699 1.321074 GGGACGGAGGGAGTGTAGTG 61.321 65.000 0.00 0.00 0.00 2.74
5708 7700 1.000107 GGGACGGAGGGAGTGTAGT 60.000 63.158 0.00 0.00 0.00 2.73
5709 7701 0.397254 ATGGGACGGAGGGAGTGTAG 60.397 60.000 0.00 0.00 0.00 2.74
5710 7702 0.928505 TATGGGACGGAGGGAGTGTA 59.071 55.000 0.00 0.00 0.00 2.90
5711 7703 0.042131 TTATGGGACGGAGGGAGTGT 59.958 55.000 0.00 0.00 0.00 3.55
5712 7704 1.424638 ATTATGGGACGGAGGGAGTG 58.575 55.000 0.00 0.00 0.00 3.51
5724 8151 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
5725 8152 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
5728 8155 9.865321 ACTAGTGTCAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 45.69 0.98
5732 8159 5.989777 ACACTAGTGTCAAAAACGCTCTTAT 59.010 36.000 22.95 0.00 45.69 1.73
5749 8254 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
5750 8255 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
5753 8258 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
5758 8263 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
5760 8265 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
5763 8268 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
5767 8272 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
5768 8273 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
5769 8274 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
5770 8275 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
5771 8276 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5772 8277 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5773 8278 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5774 8279 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5775 8280 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5777 8282 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
5779 8284 2.852714 TTTACTCCCTCCGTCCCATA 57.147 50.000 0.00 0.00 0.00 2.74
5781 8286 1.273381 TGATTTACTCCCTCCGTCCCA 60.273 52.381 0.00 0.00 0.00 4.37
5782 8287 1.492764 TGATTTACTCCCTCCGTCCC 58.507 55.000 0.00 0.00 0.00 4.46
5783 8288 4.629092 GTTATGATTTACTCCCTCCGTCC 58.371 47.826 0.00 0.00 0.00 4.79
5784 8289 4.202090 ACGTTATGATTTACTCCCTCCGTC 60.202 45.833 0.00 0.00 0.00 4.79
5785 8290 3.703052 ACGTTATGATTTACTCCCTCCGT 59.297 43.478 0.00 0.00 0.00 4.69
5786 8291 4.049186 CACGTTATGATTTACTCCCTCCG 58.951 47.826 0.00 0.00 0.00 4.63
5787 8292 3.808174 GCACGTTATGATTTACTCCCTCC 59.192 47.826 0.00 0.00 0.00 4.30
5788 8293 3.808174 GGCACGTTATGATTTACTCCCTC 59.192 47.826 0.00 0.00 0.00 4.30
5789 8294 3.454812 AGGCACGTTATGATTTACTCCCT 59.545 43.478 0.00 0.00 0.00 4.20
5790 8295 3.805207 AGGCACGTTATGATTTACTCCC 58.195 45.455 0.00 0.00 0.00 4.30
5791 8296 5.813080 AAAGGCACGTTATGATTTACTCC 57.187 39.130 0.00 0.00 0.00 3.85
5792 8297 7.225931 TGGATAAAGGCACGTTATGATTTACTC 59.774 37.037 0.00 0.00 42.61 2.59
5793 8298 7.051623 TGGATAAAGGCACGTTATGATTTACT 58.948 34.615 0.00 0.00 42.61 2.24
5794 8299 7.254227 TGGATAAAGGCACGTTATGATTTAC 57.746 36.000 0.00 0.00 42.61 2.01
5795 8300 7.867305 TTGGATAAAGGCACGTTATGATTTA 57.133 32.000 0.00 0.00 42.61 1.40
5857 8362 7.201767 GCCAGCACACTCTTCTTAAATATGATT 60.202 37.037 0.00 0.00 0.00 2.57
5858 8363 6.261826 GCCAGCACACTCTTCTTAAATATGAT 59.738 38.462 0.00 0.00 0.00 2.45
5919 8424 3.760151 ACAGACACATGCATAGCACAAAT 59.240 39.130 0.00 0.00 43.04 2.32
5923 8428 2.349590 TGACAGACACATGCATAGCAC 58.650 47.619 0.00 0.00 43.04 4.40
6011 8516 1.294138 CGAGGGGAGTAAAACCGCA 59.706 57.895 0.00 0.00 41.77 5.69
6029 8534 4.034742 ACTGTGAACGACAATTTGGTGTAC 59.965 41.667 0.78 0.00 32.80 2.90
6043 8548 3.567530 TGTATGGTTCGTACTGTGAACG 58.432 45.455 6.18 1.60 45.19 3.95
6044 8549 4.201685 GCATGTATGGTTCGTACTGTGAAC 60.202 45.833 0.00 4.15 43.87 3.18
6045 8550 3.930229 GCATGTATGGTTCGTACTGTGAA 59.070 43.478 0.00 0.00 0.00 3.18
6047 8552 2.607635 GGCATGTATGGTTCGTACTGTG 59.392 50.000 0.00 0.00 0.00 3.66
6048 8553 2.235155 TGGCATGTATGGTTCGTACTGT 59.765 45.455 0.00 0.00 0.00 3.55
6049 8554 2.607635 GTGGCATGTATGGTTCGTACTG 59.392 50.000 0.00 0.00 0.00 2.74
6050 8555 2.500098 AGTGGCATGTATGGTTCGTACT 59.500 45.455 0.00 0.00 0.00 2.73
6051 8556 2.901249 AGTGGCATGTATGGTTCGTAC 58.099 47.619 0.00 0.00 0.00 3.67
6053 8558 3.620427 TTAGTGGCATGTATGGTTCGT 57.380 42.857 0.00 0.00 0.00 3.85
6054 8559 9.594478 TTATATATTAGTGGCATGTATGGTTCG 57.406 33.333 0.00 0.00 0.00 3.95
6080 8604 7.951347 ATGAGAAGGAGCACTGAAAAATATT 57.049 32.000 0.00 0.00 0.00 1.28
6084 8608 7.500227 CCATATATGAGAAGGAGCACTGAAAAA 59.500 37.037 14.54 0.00 0.00 1.94
6090 8614 6.096141 CGATACCATATATGAGAAGGAGCACT 59.904 42.308 14.54 0.00 0.00 4.40
6134 8658 4.080582 TGGAGAGTGTGTTTGAGGAAAAGA 60.081 41.667 0.00 0.00 0.00 2.52
6171 8695 6.992715 TGGAATCTATGTAAAAGCTTAGCTCC 59.007 38.462 7.36 0.00 38.25 4.70


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

AutoCloner maintained by Alex Coulton.