Multiple sequence alignment - TraesCS1D01G238500

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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 TraesCS1D01G238500 chr1D 100.000 6582 0 0 1 6582 328080745 328074164 0.000000e+00 12155.0
1 TraesCS1D01G238500 chr1D 96.581 117 2 1 3993 4109 328076636 328076522 6.740000e-45 193.0
2 TraesCS1D01G238500 chr1D 96.581 117 2 1 4110 4224 328076753 328076637 6.740000e-45 193.0
3 TraesCS1D01G238500 chr1D 93.333 45 1 2 2798 2840 81740712 81740668 1.530000e-06 65.8
4 TraesCS1D01G238500 chr1D 91.304 46 2 2 2801 2845 95795126 95795082 1.980000e-05 62.1
5 TraesCS1D01G238500 chr1D 89.796 49 2 3 2800 2846 100460897 100460850 7.130000e-05 60.2
6 TraesCS1D01G238500 chr1B 94.698 4866 177 38 5 4826 442173658 442168830 0.000000e+00 7481.0
7 TraesCS1D01G238500 chr1B 95.233 965 40 5 4825 5786 442168695 442167734 0.000000e+00 1522.0
8 TraesCS1D01G238500 chr1B 89.723 253 19 4 6015 6266 442164425 442164179 3.830000e-82 316.0
9 TraesCS1D01G238500 chr1B 96.429 112 2 1 4110 4219 442169669 442169558 4.050000e-42 183.0
10 TraesCS1D01G238500 chr1B 93.162 117 6 1 3993 4109 442169552 442169438 3.160000e-38 171.0
11 TraesCS1D01G238500 chr1B 91.667 84 5 1 5942 6023 442166447 442166364 1.500000e-21 115.0
12 TraesCS1D01G238500 chr1A 93.813 3459 155 31 308 3735 407320949 407317519 0.000000e+00 5147.0
13 TraesCS1D01G238500 chr1A 94.625 1079 33 5 3756 4826 407317539 407316478 0.000000e+00 1648.0
14 TraesCS1D01G238500 chr1A 92.909 959 39 14 4825 5759 407316343 407315390 0.000000e+00 1367.0
15 TraesCS1D01G238500 chr1A 89.503 543 51 5 5 545 407321495 407320957 0.000000e+00 682.0
16 TraesCS1D01G238500 chr1A 88.168 262 22 7 6325 6582 407310503 407310247 2.980000e-78 303.0
17 TraesCS1D01G238500 chr1A 92.000 150 12 0 6011 6160 407312704 407312555 1.860000e-50 211.0
18 TraesCS1D01G238500 chr1A 95.726 117 3 1 4110 4224 407317302 407317186 3.130000e-43 187.0
19 TraesCS1D01G238500 chr1A 96.154 78 1 1 3993 4070 407317185 407317110 6.930000e-25 126.0
20 TraesCS1D01G238500 chr1A 93.023 43 1 2 2795 2836 576530328 576530369 1.980000e-05 62.1
21 TraesCS1D01G238500 chr5D 91.667 72 5 1 5848 5918 541998922 541998993 1.510000e-16 99.0
22 TraesCS1D01G238500 chr2B 95.349 43 1 1 2795 2836 484930294 484930252 4.260000e-07 67.6
23 TraesCS1D01G238500 chr4D 86.441 59 1 6 2795 2851 93828240 93828187 2.560000e-04 58.4
24 TraesCS1D01G238500 chr6A 90.909 44 1 3 2795 2836 131446723 131446681 1.000000e-03 56.5


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 TraesCS1D01G238500 chr1D 328074164 328080745 6581 True 12155.000 12155 100.00000 1 6582 1 chr1D.!!$R4 6581
1 TraesCS1D01G238500 chr1B 442164179 442173658 9479 True 2358.500 7481 92.83025 5 6266 4 chr1B.!!$R1 6261
2 TraesCS1D01G238500 chr1A 407310247 407321495 11248 True 1208.875 5147 92.86225 5 6582 8 chr1A.!!$R1 6577

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
850 1100 0.036875 AGAGAAGAACCTTTGCCCCG 59.963 55.000 0.00 0.0 0.00 5.73 F
851 1101 1.587043 GAGAAGAACCTTTGCCCCGC 61.587 60.000 0.00 0.0 0.00 6.13 F
1759 2050 2.113860 TTGCTGCTATGGGAGTTGAC 57.886 50.000 0.00 0.0 33.26 3.18 F
2332 2623 2.286872 CCTGCAAGCTGGATTCTAGTG 58.713 52.381 12.06 0.0 37.23 2.74 F
4116 4420 0.978667 TCCTATGGCGCCCACAGTAA 60.979 55.000 26.77 2.6 35.80 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 2191 2.287728 TGCAGATGACAACAATGTGCAC 60.288 45.455 10.75 10.75 40.74 4.57 R
2804 3105 5.221165 CCGTCCCAAAATAAGTGTCAACTTT 60.221 40.000 0.00 0.00 44.47 2.66 R
3251 3554 1.398390 GCACTCCCTGAAAATGCGTAG 59.602 52.381 0.00 0.00 0.00 3.51 R
4185 4489 0.325933 TGCTCAAGGGAGATGTGGTG 59.674 55.000 0.00 0.00 44.26 4.17 R
5811 8902 0.032117 TCGGGACCACATGATCTCCT 60.032 55.000 0.00 0.00 0.00 3.69 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
63 64 6.494059 AGTAGGCTTCAAATTAAGGTGGATT 58.506 36.000 0.00 0.00 0.00 3.01
116 117 2.158475 TCAGTTCATCACCTTTTGCCCT 60.158 45.455 0.00 0.00 0.00 5.19
169 172 1.524621 CGGGCACAATGGCTCTAGG 60.525 63.158 2.17 0.00 43.20 3.02
182 185 2.706190 GGCTCTAGGGGCTCAAGAATTA 59.294 50.000 9.36 0.00 0.00 1.40
183 186 3.495276 GGCTCTAGGGGCTCAAGAATTAC 60.495 52.174 9.36 0.00 0.00 1.89
193 196 3.369576 GCTCAAGAATTACGGGAGAAGGT 60.370 47.826 0.00 0.00 0.00 3.50
246 249 3.614616 CGAAGAAGAGCACAATACTCACC 59.385 47.826 0.00 0.00 36.58 4.02
247 250 4.619394 CGAAGAAGAGCACAATACTCACCT 60.619 45.833 0.00 0.00 36.58 4.00
278 281 1.002868 GGCTGGTGCACACTCTGAT 60.003 57.895 20.43 0.00 41.91 2.90
286 289 0.615331 GCACACTCTGATGGAAGGGA 59.385 55.000 0.00 0.00 0.00 4.20
290 293 0.842635 ACTCTGATGGAAGGGATGGC 59.157 55.000 0.00 0.00 0.00 4.40
291 294 1.138568 CTCTGATGGAAGGGATGGCT 58.861 55.000 0.00 0.00 0.00 4.75
296 299 1.144503 GATGGAAGGGATGGCTCACAT 59.855 52.381 0.00 0.00 44.18 3.21
301 304 1.496060 AGGGATGGCTCACATAACGA 58.504 50.000 0.00 0.00 40.72 3.85
303 306 1.209128 GGATGGCTCACATAACGACG 58.791 55.000 0.00 0.00 40.72 5.12
427 672 6.920569 TGAAGAGAACCTAAGTGTTTGAAC 57.079 37.500 0.00 0.00 0.00 3.18
435 680 6.937436 ACCTAAGTGTTTGAACGAGAAAAT 57.063 33.333 0.00 0.00 0.00 1.82
439 684 4.204012 AGTGTTTGAACGAGAAAATGGGA 58.796 39.130 0.00 0.00 0.00 4.37
474 719 9.533831 TGGAGCTTGAGATATGATAACACTATA 57.466 33.333 0.00 0.00 0.00 1.31
515 760 5.538813 ACAACCTCTATATCCGTATGAAGCA 59.461 40.000 0.00 0.00 0.00 3.91
527 772 4.270084 CCGTATGAAGCACGTTTCATATGT 59.730 41.667 25.95 9.09 46.24 2.29
534 779 7.860613 TGAAGCACGTTTCATATGTATTATGG 58.139 34.615 1.90 0.00 38.61 2.74
537 782 5.617609 CACGTTTCATATGTATTATGGCGG 58.382 41.667 1.90 0.00 38.61 6.13
614 860 0.893270 CACCCCTCATTTTGCGGTCA 60.893 55.000 0.00 0.00 0.00 4.02
615 861 0.609131 ACCCCTCATTTTGCGGTCAG 60.609 55.000 0.00 0.00 0.00 3.51
616 862 0.609131 CCCCTCATTTTGCGGTCAGT 60.609 55.000 0.00 0.00 0.00 3.41
619 865 2.086869 CCTCATTTTGCGGTCAGTGAT 58.913 47.619 0.00 0.00 0.00 3.06
620 866 2.489329 CCTCATTTTGCGGTCAGTGATT 59.511 45.455 0.00 0.00 0.00 2.57
722 971 2.411904 GATGAGAGGCTAATCCGCTTG 58.588 52.381 0.00 0.00 45.54 4.01
819 1069 1.296056 GCGAGCGCAGAAGGGTTTTA 61.296 55.000 11.47 0.00 41.49 1.52
850 1100 0.036875 AGAGAAGAACCTTTGCCCCG 59.963 55.000 0.00 0.00 0.00 5.73
851 1101 1.587043 GAGAAGAACCTTTGCCCCGC 61.587 60.000 0.00 0.00 0.00 6.13
852 1102 2.600470 AAGAACCTTTGCCCCGCC 60.600 61.111 0.00 0.00 0.00 6.13
956 1221 2.272797 CCTCTCCCGTCTCCGACT 59.727 66.667 0.00 0.00 35.63 4.18
1097 1382 3.748083 CCCCCACTCATGTATTCATCTG 58.252 50.000 0.00 0.00 31.15 2.90
1183 1468 3.603770 GTGCAGTGTTTTATGCGCTTAAG 59.396 43.478 9.73 0.00 46.72 1.85
1191 1476 6.020201 GTGTTTTATGCGCTTAAGTTGTTTGT 60.020 34.615 9.73 0.00 0.00 2.83
1302 1592 2.511218 TCTCTTAGCATCCAATTGGCCT 59.489 45.455 20.33 16.51 34.44 5.19
1304 1594 3.817647 CTCTTAGCATCCAATTGGCCTAC 59.182 47.826 20.33 8.86 34.44 3.18
1315 1605 9.601217 CATCCAATTGGCCTACTAGTATAATAC 57.399 37.037 20.33 0.00 34.44 1.89
1369 1659 5.009110 TCACCGTTTTGATGTGCTATTTTGA 59.991 36.000 0.00 0.00 0.00 2.69
1377 1667 8.746922 TTTGATGTGCTATTTTGATTCTGTTC 57.253 30.769 0.00 0.00 0.00 3.18
1536 1827 7.193377 TGCAGTATTTATATGCTGTGTCATG 57.807 36.000 11.64 0.00 43.83 3.07
1759 2050 2.113860 TTGCTGCTATGGGAGTTGAC 57.886 50.000 0.00 0.00 33.26 3.18
1768 2059 4.322801 GCTATGGGAGTTGACACTAGTGTT 60.323 45.833 28.49 13.66 45.05 3.32
2332 2623 2.286872 CCTGCAAGCTGGATTCTAGTG 58.713 52.381 12.06 0.00 37.23 2.74
2522 2813 4.771903 TCTTGTGTACAACCTAAAGCACA 58.228 39.130 0.00 0.00 35.43 4.57
2527 2818 5.703592 TGTGTACAACCTAAAGCACATAAGG 59.296 40.000 0.00 0.00 32.79 2.69
2772 3073 4.447389 AGCTTGTTGTTGTTGTTGTTGTTC 59.553 37.500 0.00 0.00 0.00 3.18
3296 3599 6.899771 CCGTTTGTGTTAATAGTCAATCATCG 59.100 38.462 0.00 0.00 0.00 3.84
3297 3600 6.408039 CGTTTGTGTTAATAGTCAATCATCGC 59.592 38.462 0.00 0.00 0.00 4.58
3671 3974 2.348411 AGTAGCTGTTGGTGTGCTTT 57.652 45.000 0.00 0.00 38.15 3.51
3711 4014 1.354705 GAGTAGCAAGGGAGGGGTTTT 59.645 52.381 0.00 0.00 0.00 2.43
3739 4042 5.061179 TCCTAGTAACACAAGGTCTTTTGC 58.939 41.667 0.00 0.00 0.00 3.68
3740 4043 4.819630 CCTAGTAACACAAGGTCTTTTGCA 59.180 41.667 0.00 0.00 0.00 4.08
3789 4093 5.221601 ACACCATGTCTACCAGATCATCATC 60.222 44.000 0.00 0.00 0.00 2.92
4116 4420 0.978667 TCCTATGGCGCCCACAGTAA 60.979 55.000 26.77 2.60 35.80 2.24
4185 4489 2.232696 GTCTCTCAGTTCTTCCAGGGTC 59.767 54.545 0.00 0.00 0.00 4.46
4215 4519 2.379907 TCCCTTGAGCATTTCCTTTCCT 59.620 45.455 0.00 0.00 0.00 3.36
4276 4580 8.364894 GTTTCCAAAGTCCCAATAAGTTGTAAT 58.635 33.333 0.00 0.00 33.36 1.89
4315 4619 0.548682 ATCTCCTGGCACTTGACCCT 60.549 55.000 0.00 0.00 0.00 4.34
4320 4624 0.976641 CTGGCACTTGACCCTGTCTA 59.023 55.000 0.00 0.00 33.15 2.59
4392 4698 8.517878 ACAGTGAATAATTTCTCAGTTTCCATG 58.482 33.333 0.00 0.00 32.78 3.66
4409 4715 2.094442 CCATGCAAATCACATCACTGCA 60.094 45.455 0.00 0.00 46.20 4.41
4410 4716 3.580731 CATGCAAATCACATCACTGCAA 58.419 40.909 0.00 0.00 45.37 4.08
4415 4721 4.746115 GCAAATCACATCACTGCAAAAGAA 59.254 37.500 0.00 0.00 33.19 2.52
4424 4730 8.950961 CACATCACTGCAAAAGAAATAATATCG 58.049 33.333 0.00 0.00 0.00 2.92
4448 4754 3.408634 AGGTGTAAGTTTGGAATCACCG 58.591 45.455 0.00 0.00 46.50 4.94
4511 4817 1.821136 CCCAACCAATTCAGAAGCTCC 59.179 52.381 0.00 0.00 0.00 4.70
4513 4819 1.821136 CAACCAATTCAGAAGCTCCCC 59.179 52.381 0.00 0.00 0.00 4.81
4568 4874 5.914898 ACAGGCAATTAATACTTTGGGAC 57.085 39.130 0.00 0.00 0.00 4.46
4610 4922 3.803368 GCAAGGCACCAACATTTTAGCTT 60.803 43.478 0.00 0.00 0.00 3.74
4816 5129 2.490270 ATCCAGTGGCAGGGCTTGTC 62.490 60.000 3.51 0.00 0.00 3.18
4826 5139 2.045536 GGCTTGTCCCTGAGGCTG 60.046 66.667 0.00 0.00 35.73 4.85
4827 5140 2.749441 GCTTGTCCCTGAGGCTGC 60.749 66.667 0.00 0.00 0.00 5.25
4828 5141 2.752358 CTTGTCCCTGAGGCTGCA 59.248 61.111 0.50 0.00 0.00 4.41
4829 5142 1.376942 CTTGTCCCTGAGGCTGCAG 60.377 63.158 10.11 10.11 35.66 4.41
4830 5143 2.121992 CTTGTCCCTGAGGCTGCAGT 62.122 60.000 16.64 0.00 34.06 4.40
4881 5331 2.875672 GCTATTGTTGGCCTGTCTGACA 60.876 50.000 10.50 10.50 0.00 3.58
4943 5393 8.466798 GTCCATTTATGTTGGCATTTAACTAGT 58.533 33.333 0.00 0.00 36.58 2.57
5101 5558 8.107399 AGTTCAAACAAGTAACTAATAAGGGC 57.893 34.615 0.00 0.00 31.84 5.19
5282 5740 3.102052 CAGTTGTTGCAAAGCCAAGAT 57.898 42.857 0.00 0.00 0.00 2.40
5448 5907 1.297664 GCCTGCTGCTAATCAGAGTG 58.702 55.000 0.00 0.00 45.72 3.51
5503 5963 2.344203 CGAGTCCACCGGAGCTCTT 61.344 63.158 9.46 0.00 32.07 2.85
5585 6045 1.280457 ATCCGAACTTTCCTGAGCCT 58.720 50.000 0.00 0.00 0.00 4.58
5615 6075 7.865706 AAAGTTTTCAGTACTGTTCTGATGT 57.134 32.000 21.99 1.18 40.83 3.06
5640 6114 9.543018 GTAGTTTTTCTATTGCTATGTTGTGTC 57.457 33.333 0.00 0.00 0.00 3.67
5664 6138 5.391310 CGAGGACGAAAGCTTAGTGTACTAA 60.391 44.000 11.59 4.57 42.66 2.24
5727 6201 9.331282 GGAGTCACATTCAGCTAATTTATTACT 57.669 33.333 0.00 0.00 0.00 2.24
5778 6252 2.097825 GCATTTCAAGTGCCCTGAGAT 58.902 47.619 0.00 0.00 36.61 2.75
5779 6253 2.494870 GCATTTCAAGTGCCCTGAGATT 59.505 45.455 0.00 0.00 36.61 2.40
5786 6260 1.554160 AGTGCCCTGAGATTGAGACTG 59.446 52.381 0.00 0.00 0.00 3.51
5787 6261 1.552337 GTGCCCTGAGATTGAGACTGA 59.448 52.381 0.00 0.00 0.00 3.41
5791 6507 3.678529 GCCCTGAGATTGAGACTGACTTC 60.679 52.174 0.00 0.00 0.00 3.01
5794 6510 4.142182 CCTGAGATTGAGACTGACTTCCTC 60.142 50.000 0.00 0.00 0.00 3.71
5796 6512 2.757868 AGATTGAGACTGACTTCCTCCG 59.242 50.000 0.00 0.00 0.00 4.63
5798 8889 2.516227 TGAGACTGACTTCCTCCGAT 57.484 50.000 0.00 0.00 0.00 4.18
5799 8890 2.095461 TGAGACTGACTTCCTCCGATG 58.905 52.381 0.00 0.00 0.00 3.84
5813 8904 3.334583 TCCGATGAAAGGAGTGAAAGG 57.665 47.619 0.00 0.00 33.19 3.11
5815 8906 3.055819 TCCGATGAAAGGAGTGAAAGGAG 60.056 47.826 0.00 0.00 33.19 3.69
5817 8908 4.383552 CCGATGAAAGGAGTGAAAGGAGAT 60.384 45.833 0.00 0.00 0.00 2.75
5819 8910 5.625426 CGATGAAAGGAGTGAAAGGAGATCA 60.625 44.000 0.00 0.00 0.00 2.92
5824 8915 3.199508 AGGAGTGAAAGGAGATCATGTGG 59.800 47.826 0.00 0.00 0.00 4.17
5827 8918 3.054802 AGTGAAAGGAGATCATGTGGTCC 60.055 47.826 0.00 0.00 0.00 4.46
5828 8919 2.239654 TGAAAGGAGATCATGTGGTCCC 59.760 50.000 0.00 0.00 0.00 4.46
5829 8920 0.833287 AAGGAGATCATGTGGTCCCG 59.167 55.000 0.00 0.00 0.00 5.14
5846 9801 0.608640 CCGACACCTAGCAGGAGTTT 59.391 55.000 8.91 0.00 39.34 2.66
5848 9803 2.338500 CGACACCTAGCAGGAGTTTTC 58.662 52.381 8.91 0.00 39.34 2.29
5849 9804 2.288825 CGACACCTAGCAGGAGTTTTCA 60.289 50.000 8.91 0.00 39.34 2.69
5851 9806 2.079925 CACCTAGCAGGAGTTTTCAGC 58.920 52.381 8.91 0.00 37.67 4.26
5852 9807 1.981495 ACCTAGCAGGAGTTTTCAGCT 59.019 47.619 8.91 0.00 37.67 4.24
5853 9808 2.373502 ACCTAGCAGGAGTTTTCAGCTT 59.626 45.455 8.91 0.00 37.67 3.74
5854 9809 2.746362 CCTAGCAGGAGTTTTCAGCTTG 59.254 50.000 0.00 0.00 37.67 4.01
5856 9811 2.225467 AGCAGGAGTTTTCAGCTTGTC 58.775 47.619 0.00 0.00 33.97 3.18
5857 9812 1.949525 GCAGGAGTTTTCAGCTTGTCA 59.050 47.619 0.00 0.00 0.00 3.58
5870 9906 4.083164 TCAGCTTGTCAATGCATAACACTG 60.083 41.667 17.81 17.81 0.00 3.66
5895 9931 3.512516 GCAGACGGCTGGATTGGC 61.513 66.667 22.33 0.00 42.53 4.52
5896 9932 2.825836 CAGACGGCTGGATTGGCC 60.826 66.667 11.57 0.00 45.57 5.36
5901 9937 4.778143 GGCTGGATTGGCCGTCGT 62.778 66.667 0.00 0.00 40.19 4.34
5902 9938 2.746277 GCTGGATTGGCCGTCGTT 60.746 61.111 0.00 0.00 40.66 3.85
5903 9939 2.750888 GCTGGATTGGCCGTCGTTC 61.751 63.158 0.00 0.00 40.66 3.95
5904 9940 2.046700 TGGATTGGCCGTCGTTCC 60.047 61.111 0.00 0.00 40.66 3.62
5905 9941 2.267961 GGATTGGCCGTCGTTCCT 59.732 61.111 0.00 0.00 0.00 3.36
5906 9942 1.376812 GGATTGGCCGTCGTTCCTT 60.377 57.895 0.00 0.00 0.00 3.36
5907 9943 0.958876 GGATTGGCCGTCGTTCCTTT 60.959 55.000 0.00 0.00 0.00 3.11
5908 9944 0.168128 GATTGGCCGTCGTTCCTTTG 59.832 55.000 0.00 0.00 0.00 2.77
5909 9945 0.536460 ATTGGCCGTCGTTCCTTTGT 60.536 50.000 0.00 0.00 0.00 2.83
5910 9946 1.161563 TTGGCCGTCGTTCCTTTGTC 61.162 55.000 0.00 0.00 0.00 3.18
5911 9947 2.664436 GGCCGTCGTTCCTTTGTCG 61.664 63.158 0.00 0.00 0.00 4.35
5912 9948 1.952635 GCCGTCGTTCCTTTGTCGT 60.953 57.895 0.00 0.00 0.00 4.34
5913 9949 1.850640 CCGTCGTTCCTTTGTCGTG 59.149 57.895 0.00 0.00 0.00 4.35
5914 9950 1.200839 CGTCGTTCCTTTGTCGTGC 59.799 57.895 0.00 0.00 0.00 5.34
5915 9951 1.484227 CGTCGTTCCTTTGTCGTGCA 61.484 55.000 0.00 0.00 0.00 4.57
5916 9952 0.232303 GTCGTTCCTTTGTCGTGCAG 59.768 55.000 0.00 0.00 0.00 4.41
5917 9953 0.878523 TCGTTCCTTTGTCGTGCAGG 60.879 55.000 0.00 0.00 0.00 4.85
5918 9954 1.282875 GTTCCTTTGTCGTGCAGGC 59.717 57.895 0.35 0.00 0.00 4.85
5919 9955 2.250939 TTCCTTTGTCGTGCAGGCG 61.251 57.895 0.35 0.00 0.00 5.52
5920 9956 2.933878 TTCCTTTGTCGTGCAGGCGT 62.934 55.000 0.35 0.00 0.00 5.68
5921 9957 2.542907 CCTTTGTCGTGCAGGCGTT 61.543 57.895 0.35 0.00 0.00 4.84
5922 9958 1.355210 CTTTGTCGTGCAGGCGTTT 59.645 52.632 0.35 0.00 0.00 3.60
5923 9959 0.248458 CTTTGTCGTGCAGGCGTTTT 60.248 50.000 0.35 0.00 0.00 2.43
5924 9960 0.171455 TTTGTCGTGCAGGCGTTTTT 59.829 45.000 0.35 0.00 0.00 1.94
5925 9961 0.524392 TTGTCGTGCAGGCGTTTTTG 60.524 50.000 0.35 0.00 0.00 2.44
5926 9962 1.063488 GTCGTGCAGGCGTTTTTGT 59.937 52.632 0.35 0.00 0.00 2.83
5927 9963 0.928451 GTCGTGCAGGCGTTTTTGTC 60.928 55.000 0.35 0.00 0.00 3.18
5928 9964 1.657181 CGTGCAGGCGTTTTTGTCC 60.657 57.895 0.00 0.00 0.00 4.02
5929 9965 1.657181 GTGCAGGCGTTTTTGTCCG 60.657 57.895 0.00 0.00 0.00 4.79
5936 9972 3.314339 CGTTTTTGTCCGCACAACA 57.686 47.368 0.00 0.00 42.46 3.33
5937 9973 1.187715 CGTTTTTGTCCGCACAACAG 58.812 50.000 0.00 0.00 42.46 3.16
5938 9974 1.466697 CGTTTTTGTCCGCACAACAGT 60.467 47.619 0.00 0.00 42.46 3.55
5939 9975 2.601804 GTTTTTGTCCGCACAACAGTT 58.398 42.857 0.00 0.00 42.46 3.16
5940 9976 2.553079 TTTTGTCCGCACAACAGTTC 57.447 45.000 0.00 0.00 42.46 3.01
5978 10014 0.396811 CGGGACTCCTTGGTGAAAGT 59.603 55.000 0.00 0.00 33.66 2.66
5986 10022 1.806542 CCTTGGTGAAAGTCGTGGATG 59.193 52.381 0.00 0.00 33.66 3.51
5987 10023 2.549992 CCTTGGTGAAAGTCGTGGATGA 60.550 50.000 0.00 0.00 33.66 2.92
5998 10036 2.677836 GTCGTGGATGATAAAAGCAGCA 59.322 45.455 0.00 0.00 0.00 4.41
6004 10042 4.766373 TGGATGATAAAAGCAGCAGAAACA 59.234 37.500 0.00 0.00 0.00 2.83
6023 10061 0.541764 AAGCTGGGGAATCGGCAAAA 60.542 50.000 0.00 0.00 41.26 2.44
6024 10062 0.324645 AGCTGGGGAATCGGCAAAAT 60.325 50.000 0.00 0.00 41.26 1.82
6025 10063 0.103026 GCTGGGGAATCGGCAAAATC 59.897 55.000 0.00 0.00 38.79 2.17
6031 12016 0.027586 GAATCGGCAAAATCGTCGGG 59.972 55.000 0.00 0.00 33.97 5.14
6071 12056 1.198637 GCAGCACGAATCTGCTTTTCT 59.801 47.619 16.61 0.00 45.64 2.52
6142 12127 2.775032 TTACCTTGTCGCTGGTCGGC 62.775 60.000 0.00 0.00 44.40 5.54
6190 13951 1.606903 ACGCCCGGTTGACAATTTTA 58.393 45.000 0.00 0.00 0.00 1.52
6222 13983 4.041740 TCGTATCCGATCTTGGTCAAAG 57.958 45.455 0.00 0.00 38.40 2.77
6223 13984 2.540101 CGTATCCGATCTTGGTCAAAGC 59.460 50.000 0.00 0.00 34.04 3.51
6231 14024 0.239347 CTTGGTCAAAGCGGCAGAAG 59.761 55.000 1.45 0.00 0.00 2.85
6251 14044 5.889853 AGAAGGCATGCAGATCTTGAAATTA 59.110 36.000 21.36 0.00 0.00 1.40
6266 14059 6.584563 TCTTGAAATTAACCGCAGTAATTTGC 59.415 34.615 11.60 0.00 40.67 3.68
6279 14072 3.549873 AGTAATTTGCACAACGTGTTTGC 59.450 39.130 8.88 8.88 39.01 3.68
6283 14076 0.179150 TGCACAACGTGTTTGCTTCC 60.179 50.000 15.05 0.00 39.01 3.46
6286 14079 1.355210 CAACGTGTTTGCTTCCGCT 59.645 52.632 0.00 0.00 36.97 5.52
6297 14090 0.461339 GCTTCCGCTCGGGTAATCAA 60.461 55.000 8.59 0.00 37.00 2.57
6298 14091 1.810412 GCTTCCGCTCGGGTAATCAAT 60.810 52.381 8.59 0.00 37.00 2.57
6299 14092 2.135933 CTTCCGCTCGGGTAATCAATC 58.864 52.381 8.59 0.00 37.00 2.67
6300 14093 0.031585 TCCGCTCGGGTAATCAATCG 59.968 55.000 8.59 0.00 37.00 3.34
6308 14101 2.607635 CGGGTAATCAATCGTGTTGAGG 59.392 50.000 10.69 0.00 0.00 3.86
6317 14110 2.526304 TCGTGTTGAGGTTCTCTTGG 57.474 50.000 0.00 0.00 0.00 3.61
6319 14112 1.541233 CGTGTTGAGGTTCTCTTGGCT 60.541 52.381 0.00 0.00 0.00 4.75
6321 14114 1.768275 TGTTGAGGTTCTCTTGGCTCA 59.232 47.619 0.00 0.00 0.00 4.26
6323 14116 3.214328 GTTGAGGTTCTCTTGGCTCAAA 58.786 45.455 0.00 0.00 33.48 2.69
6422 14301 3.895656 ACTTCCAAAGCTACTTTTTCCCC 59.104 43.478 0.00 0.00 30.60 4.81
6434 14313 7.993758 AGCTACTTTTTCCCCTTTCAGATATAC 59.006 37.037 0.00 0.00 0.00 1.47
6446 14325 9.743057 CCCTTTCAGATATACATATTCGATCTC 57.257 37.037 0.00 0.00 0.00 2.75
6458 14337 8.783833 ACATATTCGATCTCATTTATTCCTGG 57.216 34.615 0.00 0.00 0.00 4.45
6459 14338 8.597167 ACATATTCGATCTCATTTATTCCTGGA 58.403 33.333 0.00 0.00 0.00 3.86
6460 14339 9.610705 CATATTCGATCTCATTTATTCCTGGAT 57.389 33.333 0.00 0.00 0.00 3.41
6476 14355 3.346631 GATTGCTGCAACCGCCTGG 62.347 63.158 18.51 0.00 42.84 4.45
6478 14357 4.577677 TGCTGCAACCGCCTGGAA 62.578 61.111 0.00 0.00 39.21 3.53
6479 14358 3.741476 GCTGCAACCGCCTGGAAG 61.741 66.667 0.00 0.00 39.21 3.46
6480 14359 2.032528 CTGCAACCGCCTGGAAGA 59.967 61.111 0.00 0.00 39.21 2.87
6481 14360 1.377725 CTGCAACCGCCTGGAAGAT 60.378 57.895 0.00 0.00 39.21 2.40
6493 14372 0.820226 TGGAAGATGTCAGGAGAGCG 59.180 55.000 0.00 0.00 0.00 5.03
6510 14389 6.491745 AGGAGAGCGACTCAAGAATATATTCA 59.508 38.462 24.00 6.10 46.54 2.57
6533 14412 3.057734 AGAACACAAACTAGCTACGTGC 58.942 45.455 0.00 0.00 43.29 5.34
6543 14422 1.654743 GCTACGTGCTCGATCGTCC 60.655 63.158 15.94 7.86 40.70 4.79
6544 14423 1.367782 CTACGTGCTCGATCGTCCG 60.368 63.158 15.94 14.52 40.70 4.79
6571 14450 1.553690 GCCCTGCCTCTCACACCTTA 61.554 60.000 0.00 0.00 0.00 2.69
6572 14451 1.207791 CCCTGCCTCTCACACCTTAT 58.792 55.000 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.849294 AGTTGGAGCACCTTCTCTTC 57.151 50.000 0.71 0.00 37.04 2.87
1 2 4.103311 ACTTAAGTTGGAGCACCTTCTCTT 59.897 41.667 1.12 3.85 37.04 2.85
2 3 3.648545 ACTTAAGTTGGAGCACCTTCTCT 59.351 43.478 1.12 0.00 37.04 3.10
3 4 3.997681 GACTTAAGTTGGAGCACCTTCTC 59.002 47.826 10.02 0.00 37.04 2.87
9 10 4.258702 TCTCTGACTTAAGTTGGAGCAC 57.741 45.455 22.85 7.34 31.72 4.40
63 64 2.310779 AGGCGGGCATCTCTTATCTA 57.689 50.000 3.78 0.00 0.00 1.98
88 89 3.252974 AGGTGATGAACTGATTCCGAC 57.747 47.619 0.00 0.00 33.49 4.79
89 90 3.981071 AAGGTGATGAACTGATTCCGA 57.019 42.857 0.00 0.00 33.49 4.55
91 92 4.488879 GCAAAAGGTGATGAACTGATTCC 58.511 43.478 0.00 0.00 33.49 3.01
133 135 2.146342 CCGGATACATCATGCTGAACC 58.854 52.381 3.02 3.01 0.00 3.62
142 144 1.476652 CCATTGTGCCCGGATACATCA 60.477 52.381 0.73 0.00 0.00 3.07
169 172 1.485066 TCTCCCGTAATTCTTGAGCCC 59.515 52.381 0.00 0.00 0.00 5.19
182 185 0.395311 TATCTCGCACCTTCTCCCGT 60.395 55.000 0.00 0.00 0.00 5.28
183 186 0.962489 ATATCTCGCACCTTCTCCCG 59.038 55.000 0.00 0.00 0.00 5.14
193 196 6.094048 TCTCGAATGTATGATGATATCTCGCA 59.906 38.462 3.98 0.04 0.00 5.10
246 249 4.150454 AGCCCCTCCTCCTCCGAG 62.150 72.222 0.00 0.00 35.72 4.63
247 250 4.465446 CAGCCCCTCCTCCTCCGA 62.465 72.222 0.00 0.00 0.00 4.55
262 265 0.322648 TCCATCAGAGTGTGCACCAG 59.677 55.000 15.69 0.00 0.00 4.00
278 281 1.891933 TATGTGAGCCATCCCTTCCA 58.108 50.000 0.00 0.00 34.86 3.53
286 289 1.640428 CACGTCGTTATGTGAGCCAT 58.360 50.000 0.00 0.00 44.09 4.40
290 293 1.719246 CACACCACGTCGTTATGTGAG 59.281 52.381 24.71 14.39 44.09 3.51
291 294 1.337387 TCACACCACGTCGTTATGTGA 59.663 47.619 26.38 26.38 45.51 3.58
296 299 2.136728 CCAAATCACACCACGTCGTTA 58.863 47.619 0.00 0.00 0.00 3.18
301 304 1.879380 CATGTCCAAATCACACCACGT 59.121 47.619 0.00 0.00 0.00 4.49
303 306 2.095768 CGACATGTCCAAATCACACCAC 60.096 50.000 20.03 0.00 0.00 4.16
406 651 5.667466 TCGTTCAAACACTTAGGTTCTCTT 58.333 37.500 0.00 0.00 0.00 2.85
413 658 6.142817 CCATTTTCTCGTTCAAACACTTAGG 58.857 40.000 0.00 0.00 0.00 2.69
498 743 5.918576 TGAAACGTGCTTCATACGGATATAG 59.081 40.000 0.00 0.00 45.24 1.31
515 760 5.302360 ACCGCCATAATACATATGAAACGT 58.698 37.500 10.38 0.00 43.52 3.99
527 772 3.127589 CACATTGACGACCGCCATAATA 58.872 45.455 0.00 0.00 0.00 0.98
534 779 2.047655 TCCCACATTGACGACCGC 60.048 61.111 0.00 0.00 0.00 5.68
537 782 1.714794 CAGAGTCCCACATTGACGAC 58.285 55.000 0.00 0.00 37.80 4.34
722 971 3.064987 CTGCCTGATGCCTTGCTGC 62.065 63.158 0.00 0.00 40.16 5.25
819 1069 2.301583 GTTCTTCTCTTCTGCAGGGAGT 59.698 50.000 25.45 0.00 31.61 3.85
827 1077 2.816672 GGGCAAAGGTTCTTCTCTTCTG 59.183 50.000 0.00 0.00 0.00 3.02
1024 1309 2.075338 GAGCTCAAGAAAGTCTGGCAG 58.925 52.381 9.40 8.58 0.00 4.85
1097 1382 0.327259 AAAAGAACGGGGTAGGGAGC 59.673 55.000 0.00 0.00 0.00 4.70
1315 1605 7.733402 ACCAAAATCACCTTCATTTTCAATG 57.267 32.000 0.00 0.00 32.25 2.82
1377 1667 4.843220 AGAGAACATGTTCAAGCCTTTG 57.157 40.909 33.92 0.00 41.84 2.77
1503 1794 9.229784 CAGCATATAAATACTGCAAAACTGAAG 57.770 33.333 0.00 0.00 38.37 3.02
1625 1916 8.177119 ACAGCCTTCAATAACAATAAACAGAA 57.823 30.769 0.00 0.00 0.00 3.02
1626 1917 7.446931 TGACAGCCTTCAATAACAATAAACAGA 59.553 33.333 0.00 0.00 0.00 3.41
1759 2050 6.758886 AGAACTTCTCAACTGAAACACTAGTG 59.241 38.462 21.44 21.44 0.00 2.74
1768 2059 4.769688 TCTTGCAGAACTTCTCAACTGAA 58.230 39.130 0.00 0.00 32.90 3.02
1900 2191 2.287728 TGCAGATGACAACAATGTGCAC 60.288 45.455 10.75 10.75 40.74 4.57
2332 2623 5.841957 ATGGTAAGATGATTGGAAACTGC 57.158 39.130 0.00 0.00 0.00 4.40
2423 2714 8.481314 AGACATGATACAGAAGAATAAGCTGAA 58.519 33.333 0.00 0.00 33.94 3.02
2522 2813 9.646522 ACATATCAGCAAAATAGGTTTCCTTAT 57.353 29.630 0.00 0.00 34.61 1.73
2804 3105 5.221165 CCGTCCCAAAATAAGTGTCAACTTT 60.221 40.000 0.00 0.00 44.47 2.66
3132 3433 8.561738 TTCATCTAAATGAAGGAACCAAGTAC 57.438 34.615 0.00 0.00 44.94 2.73
3251 3554 1.398390 GCACTCCCTGAAAATGCGTAG 59.602 52.381 0.00 0.00 0.00 3.51
3671 3974 9.151471 GCTACTCAGATACAACAGTCAATAAAA 57.849 33.333 0.00 0.00 0.00 1.52
3711 4014 9.856162 AAAAGACCTTGTGTTACTAGGATTAAA 57.144 29.630 14.73 0.00 42.55 1.52
3713 4016 7.389607 GCAAAAGACCTTGTGTTACTAGGATTA 59.610 37.037 14.73 0.00 42.55 1.75
4116 4420 3.560896 GCAGCAACAATGGAATGTTTGTT 59.439 39.130 0.00 0.00 44.59 2.83
4185 4489 0.325933 TGCTCAAGGGAGATGTGGTG 59.674 55.000 0.00 0.00 44.26 4.17
4276 4580 0.988063 TGTTGTGCTGGGGCTATACA 59.012 50.000 0.00 0.00 39.59 2.29
4315 4619 8.275758 GGAGGTACCATGATAGAGATATAGACA 58.724 40.741 15.94 0.00 38.79 3.41
4392 4698 4.300803 TCTTTTGCAGTGATGTGATTTGC 58.699 39.130 0.00 0.00 35.42 3.68
4424 4730 5.293569 CGGTGATTCCAAACTTACACCTATC 59.706 44.000 0.00 0.00 43.50 2.08
4448 4754 3.440522 GGTTGAATTGCTAGTCCCTGTTC 59.559 47.826 0.00 0.00 0.00 3.18
4530 4836 2.693069 CCTGTTTCCAGAGTGTGCTAG 58.307 52.381 0.00 0.00 41.50 3.42
4616 4928 2.177394 TTTGCGGATGCTGTCTAACA 57.823 45.000 0.00 0.00 43.34 2.41
4816 5129 2.816601 CTTGGACTGCAGCCTCAGGG 62.817 65.000 22.36 9.25 38.36 4.45
4826 5139 3.877508 ACACTAAAGACAACTTGGACTGC 59.122 43.478 0.00 0.00 36.39 4.40
4827 5140 5.360591 AGACACTAAAGACAACTTGGACTG 58.639 41.667 0.00 0.00 36.39 3.51
4828 5141 5.615925 AGACACTAAAGACAACTTGGACT 57.384 39.130 0.00 0.00 36.39 3.85
4829 5142 8.923683 GTTATAGACACTAAAGACAACTTGGAC 58.076 37.037 0.00 0.00 36.39 4.02
4830 5143 8.867097 AGTTATAGACACTAAAGACAACTTGGA 58.133 33.333 0.00 0.00 36.39 3.53
4881 5331 7.966204 CGTAAACATCCAAATAAATCGGAACTT 59.034 33.333 0.00 0.00 31.18 2.66
4943 5393 1.001120 TCCAGTGGGTGCTCGGATA 59.999 57.895 9.92 0.00 34.93 2.59
4945 5395 3.311110 GTCCAGTGGGTGCTCGGA 61.311 66.667 9.92 0.00 34.93 4.55
4946 5396 4.394712 GGTCCAGTGGGTGCTCGG 62.395 72.222 9.92 0.00 34.93 4.63
4987 5440 6.607735 AATGCTTCAAAAACAACCATCTTG 57.392 33.333 0.00 0.00 0.00 3.02
5146 5603 6.653740 GGCACCTATAAACACTAGACACTTTT 59.346 38.462 0.00 0.00 0.00 2.27
5320 5778 1.660614 CGCCGTAGCTCTACTTGATCG 60.661 57.143 0.00 0.00 36.60 3.69
5503 5963 2.604686 AAGAGCACCTCTGGCGGA 60.605 61.111 0.00 0.00 40.28 5.54
5615 6075 8.440059 CGACACAACATAGCAATAGAAAAACTA 58.560 33.333 0.00 0.00 35.42 2.24
5640 6114 2.349297 ACACTAAGCTTTCGTCCTCG 57.651 50.000 3.20 0.00 38.55 4.63
5697 6171 4.890158 TTAGCTGAATGTGACTCCAGAA 57.110 40.909 0.00 0.00 0.00 3.02
5778 6252 2.287977 TCGGAGGAAGTCAGTCTCAA 57.712 50.000 0.00 0.00 0.00 3.02
5779 6253 2.095461 CATCGGAGGAAGTCAGTCTCA 58.905 52.381 0.00 0.00 0.00 3.27
5786 6260 3.172229 CTCCTTTCATCGGAGGAAGTC 57.828 52.381 5.18 0.00 43.47 3.01
5794 6510 3.055819 TCTCCTTTCACTCCTTTCATCGG 60.056 47.826 0.00 0.00 0.00 4.18
5796 6512 5.738909 TGATCTCCTTTCACTCCTTTCATC 58.261 41.667 0.00 0.00 0.00 2.92
5798 8889 5.013495 ACATGATCTCCTTTCACTCCTTTCA 59.987 40.000 0.00 0.00 0.00 2.69
5799 8890 5.353678 CACATGATCTCCTTTCACTCCTTTC 59.646 44.000 0.00 0.00 0.00 2.62
5811 8902 0.032117 TCGGGACCACATGATCTCCT 60.032 55.000 0.00 0.00 0.00 3.69
5812 8903 0.105039 GTCGGGACCACATGATCTCC 59.895 60.000 0.00 0.00 0.00 3.71
5813 8904 0.824109 TGTCGGGACCACATGATCTC 59.176 55.000 0.00 0.00 0.00 2.75
5815 8906 0.462047 GGTGTCGGGACCACATGATC 60.462 60.000 0.00 0.00 35.88 2.92
5817 8908 0.251877 TAGGTGTCGGGACCACATGA 60.252 55.000 0.00 0.00 38.63 3.07
5819 8910 1.614241 GCTAGGTGTCGGGACCACAT 61.614 60.000 6.55 0.00 38.63 3.21
5824 8915 1.668101 CTCCTGCTAGGTGTCGGGAC 61.668 65.000 0.00 0.00 36.53 4.46
5827 8918 0.608640 AAACTCCTGCTAGGTGTCGG 59.391 55.000 9.38 0.00 40.88 4.79
5828 8919 2.288825 TGAAAACTCCTGCTAGGTGTCG 60.289 50.000 9.38 0.00 40.88 4.35
5829 8920 3.330267 CTGAAAACTCCTGCTAGGTGTC 58.670 50.000 9.38 0.00 40.88 3.67
5846 9801 4.520111 AGTGTTATGCATTGACAAGCTGAA 59.480 37.500 3.54 0.00 0.00 3.02
5848 9803 4.083164 TCAGTGTTATGCATTGACAAGCTG 60.083 41.667 3.54 14.01 38.64 4.24
5849 9804 4.074259 TCAGTGTTATGCATTGACAAGCT 58.926 39.130 3.54 2.65 38.64 3.74
5851 9806 5.854866 CACTTCAGTGTTATGCATTGACAAG 59.145 40.000 3.54 7.51 42.37 3.16
5852 9807 5.530543 TCACTTCAGTGTTATGCATTGACAA 59.469 36.000 3.54 0.00 42.37 3.18
5853 9808 5.062528 TCACTTCAGTGTTATGCATTGACA 58.937 37.500 3.54 8.05 42.37 3.58
5854 9809 5.611796 TCACTTCAGTGTTATGCATTGAC 57.388 39.130 3.54 5.17 42.37 3.18
5856 9811 4.855388 GCTTCACTTCAGTGTTATGCATTG 59.145 41.667 3.54 0.00 45.76 2.82
5857 9812 4.520111 TGCTTCACTTCAGTGTTATGCATT 59.480 37.500 3.54 0.00 45.76 3.56
5893 9929 2.664436 CGACAAAGGAACGACGGCC 61.664 63.158 0.00 0.00 0.00 6.13
5894 9930 1.952635 ACGACAAAGGAACGACGGC 60.953 57.895 0.00 0.00 0.00 5.68
5895 9931 1.850640 CACGACAAAGGAACGACGG 59.149 57.895 0.00 0.00 0.00 4.79
5896 9932 1.200839 GCACGACAAAGGAACGACG 59.799 57.895 0.00 0.00 0.00 5.12
5897 9933 0.232303 CTGCACGACAAAGGAACGAC 59.768 55.000 0.00 0.00 0.00 4.34
5898 9934 0.878523 CCTGCACGACAAAGGAACGA 60.879 55.000 0.00 0.00 32.43 3.85
5899 9935 1.569493 CCTGCACGACAAAGGAACG 59.431 57.895 0.00 0.00 32.43 3.95
5900 9936 1.282875 GCCTGCACGACAAAGGAAC 59.717 57.895 0.00 0.00 32.43 3.62
5901 9937 2.250939 CGCCTGCACGACAAAGGAA 61.251 57.895 0.00 0.00 32.43 3.36
5902 9938 2.664851 CGCCTGCACGACAAAGGA 60.665 61.111 0.00 0.00 32.43 3.36
5903 9939 2.058829 AAACGCCTGCACGACAAAGG 62.059 55.000 3.48 0.00 36.70 3.11
5904 9940 0.248458 AAAACGCCTGCACGACAAAG 60.248 50.000 3.48 0.00 36.70 2.77
5905 9941 0.171455 AAAAACGCCTGCACGACAAA 59.829 45.000 3.48 0.00 36.70 2.83
5906 9942 0.524392 CAAAAACGCCTGCACGACAA 60.524 50.000 3.48 0.00 36.70 3.18
5907 9943 1.063327 CAAAAACGCCTGCACGACA 59.937 52.632 3.48 0.00 36.70 4.35
5908 9944 0.928451 GACAAAAACGCCTGCACGAC 60.928 55.000 3.48 0.00 36.70 4.34
5909 9945 1.353804 GACAAAAACGCCTGCACGA 59.646 52.632 3.48 0.00 36.70 4.35
5910 9946 1.657181 GGACAAAAACGCCTGCACG 60.657 57.895 0.00 0.00 39.50 5.34
5911 9947 1.657181 CGGACAAAAACGCCTGCAC 60.657 57.895 0.00 0.00 0.00 4.57
5912 9948 2.718731 CGGACAAAAACGCCTGCA 59.281 55.556 0.00 0.00 0.00 4.41
5918 9954 1.187715 CTGTTGTGCGGACAAAAACG 58.812 50.000 24.60 4.39 43.77 3.60
5919 9955 2.271821 ACTGTTGTGCGGACAAAAAC 57.728 45.000 24.60 13.56 43.77 2.43
5920 9956 2.416162 GGAACTGTTGTGCGGACAAAAA 60.416 45.455 24.60 14.38 43.77 1.94
5921 9957 1.133407 GGAACTGTTGTGCGGACAAAA 59.867 47.619 24.60 18.42 43.77 2.44
5922 9958 0.736053 GGAACTGTTGTGCGGACAAA 59.264 50.000 24.60 13.23 43.77 2.83
5923 9959 1.433053 CGGAACTGTTGTGCGGACAA 61.433 55.000 19.24 19.24 39.88 3.18
5924 9960 1.885388 CGGAACTGTTGTGCGGACA 60.885 57.895 5.33 5.33 0.00 4.02
5925 9961 1.433837 AACGGAACTGTTGTGCGGAC 61.434 55.000 0.00 0.00 33.68 4.79
5926 9962 0.745128 AAACGGAACTGTTGTGCGGA 60.745 50.000 0.00 0.00 33.68 5.54
5927 9963 0.099791 AAAACGGAACTGTTGTGCGG 59.900 50.000 0.00 0.00 33.68 5.69
5928 9964 1.187715 CAAAACGGAACTGTTGTGCG 58.812 50.000 0.00 0.00 30.81 5.34
5929 9965 2.450160 CTCAAAACGGAACTGTTGTGC 58.550 47.619 10.75 0.00 37.07 4.57
5930 9966 2.223479 CCCTCAAAACGGAACTGTTGTG 60.223 50.000 9.64 9.64 38.23 3.33
5931 9967 2.021457 CCCTCAAAACGGAACTGTTGT 58.979 47.619 0.00 0.00 31.10 3.32
5932 9968 1.269051 GCCCTCAAAACGGAACTGTTG 60.269 52.381 0.00 0.00 31.10 3.33
5933 9969 1.029681 GCCCTCAAAACGGAACTGTT 58.970 50.000 0.00 0.00 0.00 3.16
5934 9970 0.106918 TGCCCTCAAAACGGAACTGT 60.107 50.000 0.00 0.00 0.00 3.55
5935 9971 0.310854 GTGCCCTCAAAACGGAACTG 59.689 55.000 0.00 0.00 0.00 3.16
5936 9972 0.182775 AGTGCCCTCAAAACGGAACT 59.817 50.000 0.00 0.00 0.00 3.01
5937 9973 0.310854 CAGTGCCCTCAAAACGGAAC 59.689 55.000 0.00 0.00 0.00 3.62
5938 9974 1.452145 GCAGTGCCCTCAAAACGGAA 61.452 55.000 2.85 0.00 0.00 4.30
5939 9975 1.896660 GCAGTGCCCTCAAAACGGA 60.897 57.895 2.85 0.00 0.00 4.69
5940 9976 2.192861 TGCAGTGCCCTCAAAACGG 61.193 57.895 13.72 0.00 0.00 4.44
5978 10014 2.938451 CTGCTGCTTTTATCATCCACGA 59.062 45.455 0.00 0.00 0.00 4.35
5986 10022 4.802999 AGCTTGTTTCTGCTGCTTTTATC 58.197 39.130 0.00 0.00 38.21 1.75
5987 10023 4.861102 AGCTTGTTTCTGCTGCTTTTAT 57.139 36.364 0.00 0.00 38.21 1.40
5998 10036 1.614317 CCGATTCCCCAGCTTGTTTCT 60.614 52.381 0.00 0.00 0.00 2.52
6004 10042 0.541764 TTTTGCCGATTCCCCAGCTT 60.542 50.000 0.00 0.00 0.00 3.74
6023 10061 1.152525 AGGTATGGCTCCCGACGAT 60.153 57.895 0.00 0.00 0.00 3.73
6024 10062 1.826921 GAGGTATGGCTCCCGACGA 60.827 63.158 0.00 0.00 0.00 4.20
6025 10063 1.672854 TTGAGGTATGGCTCCCGACG 61.673 60.000 0.00 0.00 0.00 5.12
6071 12056 2.285718 CGTCGCCGTTGTGTTCTAAAAA 60.286 45.455 0.00 0.00 0.00 1.94
6114 12099 1.918609 GCGACAAGGTAAGATCGTGTC 59.081 52.381 0.00 0.00 39.21 3.67
6142 12127 3.871006 TGCTGATATTGCTACCACTTTCG 59.129 43.478 3.85 0.00 0.00 3.46
6215 13976 2.982744 GCCTTCTGCCGCTTTGACC 61.983 63.158 0.00 0.00 0.00 4.02
6218 13979 1.153901 CATGCCTTCTGCCGCTTTG 60.154 57.895 0.00 0.00 40.16 2.77
6219 13980 2.998279 GCATGCCTTCTGCCGCTTT 61.998 57.895 6.36 0.00 40.16 3.51
6222 13983 4.189188 CTGCATGCCTTCTGCCGC 62.189 66.667 16.68 0.00 38.89 6.53
6223 13984 1.783031 GATCTGCATGCCTTCTGCCG 61.783 60.000 16.68 0.00 38.89 5.69
6231 14024 5.045872 GGTTAATTTCAAGATCTGCATGCC 58.954 41.667 16.68 0.00 0.00 4.40
6251 14044 2.738135 GTTGTGCAAATTACTGCGGTT 58.262 42.857 1.99 0.00 45.74 4.44
6266 14059 2.853457 CGGAAGCAAACACGTTGTG 58.147 52.632 0.00 0.00 39.63 3.33
6279 14072 2.135933 GATTGATTACCCGAGCGGAAG 58.864 52.381 11.05 0.00 37.50 3.46
6283 14076 0.852777 CACGATTGATTACCCGAGCG 59.147 55.000 0.00 0.00 35.63 5.03
6286 14079 3.517602 CTCAACACGATTGATTACCCGA 58.482 45.455 7.21 0.00 0.00 5.14
6297 14090 2.872038 GCCAAGAGAACCTCAACACGAT 60.872 50.000 0.00 0.00 32.06 3.73
6298 14091 1.540363 GCCAAGAGAACCTCAACACGA 60.540 52.381 0.00 0.00 32.06 4.35
6299 14092 0.868406 GCCAAGAGAACCTCAACACG 59.132 55.000 0.00 0.00 32.06 4.49
6300 14093 2.147150 GAGCCAAGAGAACCTCAACAC 58.853 52.381 0.00 0.00 32.06 3.32
6308 14101 6.560253 TCTTTACATTTGAGCCAAGAGAAC 57.440 37.500 0.00 0.00 0.00 3.01
6317 14110 8.351495 TGTTGTTGATTTCTTTACATTTGAGC 57.649 30.769 0.00 0.00 0.00 4.26
6406 14285 5.454966 TCTGAAAGGGGAAAAAGTAGCTTT 58.545 37.500 0.00 0.00 34.94 3.51
6434 14313 9.610705 ATCCAGGAATAAATGAGATCGAATATG 57.389 33.333 0.00 0.00 0.00 1.78
6446 14325 4.659111 TGCAGCAATCCAGGAATAAATG 57.341 40.909 0.00 0.00 0.00 2.32
6454 14333 2.879907 CGGTTGCAGCAATCCAGG 59.120 61.111 11.96 0.00 0.00 4.45
6456 14335 3.372730 GGCGGTTGCAGCAATCCA 61.373 61.111 11.96 0.00 45.35 3.41
6457 14336 3.064324 AGGCGGTTGCAGCAATCC 61.064 61.111 11.96 13.11 45.35 3.01
6458 14337 2.180017 CAGGCGGTTGCAGCAATC 59.820 61.111 11.96 10.16 45.35 2.67
6459 14338 3.376078 CCAGGCGGTTGCAGCAAT 61.376 61.111 11.96 0.00 45.35 3.56
6460 14339 4.577677 TCCAGGCGGTTGCAGCAA 62.578 61.111 2.83 2.83 45.35 3.91
6476 14355 1.748493 AGTCGCTCTCCTGACATCTTC 59.252 52.381 0.00 0.00 37.58 2.87
6478 14357 1.340502 TGAGTCGCTCTCCTGACATCT 60.341 52.381 8.07 0.00 42.12 2.90
6479 14358 1.098869 TGAGTCGCTCTCCTGACATC 58.901 55.000 8.07 0.00 42.12 3.06
6480 14359 1.476085 CTTGAGTCGCTCTCCTGACAT 59.524 52.381 8.07 0.00 42.12 3.06
6481 14360 0.884514 CTTGAGTCGCTCTCCTGACA 59.115 55.000 8.07 0.00 42.12 3.58
6489 14368 8.581057 TCTTTGAATATATTCTTGAGTCGCTC 57.419 34.615 22.77 0.58 37.67 5.03
6510 14389 4.025145 GCACGTAGCTAGTTTGTGTTCTTT 60.025 41.667 13.63 0.00 41.15 2.52
6525 14404 1.654743 GGACGATCGAGCACGTAGC 60.655 63.158 24.34 0.00 42.74 3.58
6526 14405 1.367782 CGGACGATCGAGCACGTAG 60.368 63.158 24.34 8.38 42.74 3.51
6527 14406 2.705220 CGGACGATCGAGCACGTA 59.295 61.111 24.34 0.00 42.74 3.57
6528 14407 4.831307 GCGGACGATCGAGCACGT 62.831 66.667 24.34 13.23 45.32 4.49
6529 14408 4.829518 TGCGGACGATCGAGCACG 62.830 66.667 24.34 19.36 41.26 5.34
6533 14412 1.371022 CTCCATGCGGACGATCGAG 60.371 63.158 24.34 13.43 35.91 4.04
6534 14413 2.721859 CTCCATGCGGACGATCGA 59.278 61.111 24.34 0.00 35.91 3.59
6535 14414 2.355126 CCTCCATGCGGACGATCG 60.355 66.667 14.88 14.88 35.91 3.69
6536 14415 2.663188 GCCTCCATGCGGACGATC 60.663 66.667 3.67 0.00 35.91 3.69
6537 14416 4.241555 GGCCTCCATGCGGACGAT 62.242 66.667 0.00 0.00 35.91 3.73
6540 14419 4.864334 CAGGGCCTCCATGCGGAC 62.864 72.222 0.95 0.24 35.91 4.79


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

AutoCloner maintained by Alex Coulton.