Multiple sequence alignment - TraesCS1A01G076000

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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 TraesCS1A01G076000 chr1A 100.000 6721 0 0 1 6721 58908703 58901983 0.000000e+00 12412
1 TraesCS1A01G076000 chr1A 94.958 119 6 0 4860 4978 148610440 148610322 3.200000e-43 187
2 TraesCS1A01G076000 chr1D 97.690 3290 66 4 1573 4862 60223618 60220339 0.000000e+00 5646
3 TraesCS1A01G076000 chr1D 95.388 1713 62 8 4970 6678 60220337 60218638 0.000000e+00 2710
4 TraesCS1A01G076000 chr1D 95.325 1583 49 8 1 1574 60225308 60223742 0.000000e+00 2490
5 TraesCS1A01G076000 chr1B 96.577 3418 83 10 1447 4862 96588741 96592126 0.000000e+00 5633
6 TraesCS1A01G076000 chr1B 94.859 1634 62 10 5000 6620 96592129 96593753 0.000000e+00 2532
7 TraesCS1A01G076000 chr1B 93.239 1479 60 15 1 1463 96587273 96588727 0.000000e+00 2141
8 TraesCS1A01G076000 chr6D 97.391 115 3 0 4860 4974 230814465 230814351 5.320000e-46 196
9 TraesCS1A01G076000 chr5B 95.868 121 3 2 4852 4970 622393563 622393443 1.910000e-45 195
10 TraesCS1A01G076000 chr2A 95.833 120 5 0 4860 4979 202041437 202041556 1.910000e-45 195
11 TraesCS1A01G076000 chr2D 93.182 132 6 2 4848 4977 542514659 542514789 2.470000e-44 191
12 TraesCS1A01G076000 chr6A 95.726 117 5 0 4855 4971 579148206 579148322 8.900000e-44 189
13 TraesCS1A01G076000 chr7A 96.396 111 4 0 4858 4968 176989583 176989473 4.140000e-42 183
14 TraesCS1A01G076000 chr5A 93.548 124 7 1 4854 4977 606350667 606350789 4.140000e-42 183
15 TraesCS1A01G076000 chr3A 93.333 120 6 2 4861 4979 552620374 552620492 6.930000e-40 176


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 TraesCS1A01G076000 chr1A 58901983 58908703 6720 True 12412.000000 12412 100.000000 1 6721 1 chr1A.!!$R1 6720
1 TraesCS1A01G076000 chr1D 60218638 60225308 6670 True 3615.333333 5646 96.134333 1 6678 3 chr1D.!!$R1 6677
2 TraesCS1A01G076000 chr1B 96587273 96593753 6480 False 3435.333333 5633 94.891667 1 6620 3 chr1B.!!$F1 6619

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
953 974 1.448985 TATCTGCCCAAAACGCTGAC 58.551 50.0 0.00 0.00 37.07 3.51 F
1080 1101 1.514678 CGCTGCTGGTGCACCTTTTA 61.515 55.0 34.75 15.31 45.31 1.52 F
2087 2267 0.318699 CGACAACTCGTGCAAGAGGA 60.319 55.0 29.26 6.26 42.31 3.71 F
3696 3876 1.032014 TGGGAACTGCAAAGCTCAAC 58.968 50.0 0.00 0.00 0.00 3.18 F
4922 5104 0.829333 ACAATGTGCAAAACAGCCCA 59.171 45.0 0.00 0.00 43.64 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2082 3.327757 ACTGTATCTTCTCAAAGCCACCA 59.672 43.478 0.00 0.0 32.18 4.17 R
2370 2550 4.941263 GGCAAGACATCTGTGGTGTAATAA 59.059 41.667 0.00 0.0 0.00 1.40 R
4036 4218 1.623811 TGGAGTAGAAGTCCAACCTGC 59.376 52.381 0.88 0.0 44.34 4.85 R
5559 5741 0.535335 GTAGACACGATTGCCAGGGA 59.465 55.000 0.00 0.0 0.00 4.20 R
6697 6896 0.107017 CCCTCATGTTACAGCCCAGG 60.107 60.000 0.00 0.0 0.00 4.45 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
71 72 8.591072 AGAACCAATTCATCAATTCAACAATCT 58.409 29.630 0.00 0.00 37.29 2.40
144 148 7.907389 TCTTTGATCTCCTAAGAAAAGCACTA 58.093 34.615 0.00 0.00 34.53 2.74
174 178 4.214310 TCGGCAACATCATTGGGAATATT 58.786 39.130 0.00 0.00 0.00 1.28
179 183 5.754890 GCAACATCATTGGGAATATTGAACC 59.245 40.000 0.00 0.00 0.00 3.62
182 186 7.493499 ACATCATTGGGAATATTGAACCAAA 57.507 32.000 15.72 2.84 45.18 3.28
185 189 5.424895 TCATTGGGAATATTGAACCAAAGGG 59.575 40.000 15.72 10.65 45.18 3.95
186 190 4.683766 TGGGAATATTGAACCAAAGGGA 57.316 40.909 0.00 0.00 38.05 4.20
225 229 5.997384 TGATGAATCGGATGAGAGATCAT 57.003 39.130 0.00 1.31 35.03 2.45
367 379 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
368 380 4.501229 GCAGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
369 381 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
370 382 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
371 383 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
372 384 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
373 385 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
374 386 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
375 387 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
390 402 2.757917 AGAGAGAGCGCCCCACTC 60.758 66.667 2.29 10.23 0.00 3.51
555 567 5.337330 CGTTCCCCTCCATCTATATTGTACC 60.337 48.000 0.00 0.00 0.00 3.34
686 707 4.814294 GGTTCGATCGCGTGGGCT 62.814 66.667 11.09 0.00 38.98 5.19
953 974 1.448985 TATCTGCCCAAAACGCTGAC 58.551 50.000 0.00 0.00 37.07 3.51
1080 1101 1.514678 CGCTGCTGGTGCACCTTTTA 61.515 55.000 34.75 15.31 45.31 1.52
1170 1191 8.188799 TCGGTAAGTCATGAGTATTACTTTCAG 58.811 37.037 18.03 8.35 33.83 3.02
1410 1435 8.819015 GTTTGTAACTTCTATTCCTAGCTTAGC 58.181 37.037 0.00 0.00 0.00 3.09
1469 1524 8.383175 ACCTACCTTTTTCAGACATTGAATAGA 58.617 33.333 0.00 0.00 44.90 1.98
1548 1603 1.675641 CCTCCCCTGTTTTCTGGCG 60.676 63.158 0.00 0.00 37.55 5.69
1571 1626 5.625886 CGACATTGTAATCACCACTCCCTAA 60.626 44.000 0.00 0.00 0.00 2.69
1682 1862 5.007528 TGCTTTGCTTTATTTGGAAGTTTGC 59.992 36.000 0.00 0.00 0.00 3.68
1961 2141 3.598019 AGTGCTAATTGCCATTTGTGG 57.402 42.857 0.00 0.00 42.00 4.17
2087 2267 0.318699 CGACAACTCGTGCAAGAGGA 60.319 55.000 29.26 6.26 42.31 3.71
2100 2280 2.679349 GCAAGAGGAATCAGGTCACCTC 60.679 54.545 0.00 0.00 46.28 3.85
2370 2550 5.663106 TCCTAAGAATACAGCCACTTCAGAT 59.337 40.000 0.00 0.00 0.00 2.90
2476 2656 1.196012 CTCCAGGTCCCACTAACTCC 58.804 60.000 0.00 0.00 0.00 3.85
2662 2842 3.438434 GGAAGGTGATGCTTTCTGTCTTC 59.562 47.826 0.00 0.00 34.12 2.87
2691 2871 5.372343 TTTGTACATGCTATGGATCACCT 57.628 39.130 0.00 0.00 37.04 4.00
2767 2947 3.058224 GTGGTTGCATTGACTGTAACTCC 60.058 47.826 4.06 0.00 46.24 3.85
2772 2952 3.008923 TGCATTGACTGTAACTCCCATCA 59.991 43.478 0.00 0.00 0.00 3.07
2826 3006 5.772825 AAGCTTCAATTTGCTAGTTGTCA 57.227 34.783 0.00 0.00 38.75 3.58
2827 3007 5.772825 AGCTTCAATTTGCTAGTTGTCAA 57.227 34.783 3.59 0.00 37.81 3.18
3008 3188 8.836268 AATCTGCTATTTTGATTTGCTTTTGA 57.164 26.923 0.00 0.00 0.00 2.69
3187 3367 2.226330 TGTGAAGGTTGGACGGATTTG 58.774 47.619 0.00 0.00 0.00 2.32
3435 3615 4.523943 TGCTTATCTGGCATTGAACTGTTT 59.476 37.500 0.00 0.00 34.56 2.83
3498 3678 9.950496 ATAGAAATATGTAATAGTGCTTCCAGG 57.050 33.333 0.00 0.00 34.04 4.45
3619 3799 2.697751 TGGTTGTCTTCCCCATGTTTTG 59.302 45.455 0.00 0.00 0.00 2.44
3651 3831 5.074115 TGGTGACCTTAGGTTGGTTTTATG 58.926 41.667 4.99 0.00 38.03 1.90
3696 3876 1.032014 TGGGAACTGCAAAGCTCAAC 58.968 50.000 0.00 0.00 0.00 3.18
3797 3979 2.809446 CATGGCATGCACATTCAGAAG 58.191 47.619 21.36 4.13 0.00 2.85
3825 4007 6.882610 AGAGAAACAAAATGTAGTCATGCA 57.117 33.333 0.00 0.00 34.19 3.96
3826 4008 7.458409 AGAGAAACAAAATGTAGTCATGCAT 57.542 32.000 0.00 0.00 34.19 3.96
3827 4009 7.889469 AGAGAAACAAAATGTAGTCATGCATT 58.111 30.769 0.00 0.00 42.72 3.56
3828 4010 7.811236 AGAGAAACAAAATGTAGTCATGCATTG 59.189 33.333 0.00 0.00 40.38 2.82
3829 4011 6.366877 AGAAACAAAATGTAGTCATGCATTGC 59.633 34.615 0.00 0.46 40.38 3.56
3989 4171 7.354257 GTTTGCTTATTACCGTGTTTAACTCA 58.646 34.615 0.00 0.00 0.00 3.41
4036 4218 9.769093 GCTTATGGTGTAAACTATTTGTACTTG 57.231 33.333 0.00 0.00 0.00 3.16
4546 4728 6.629515 CGGACTACTCAAGTTTGATTATGGGA 60.630 42.308 0.00 0.00 39.07 4.37
4853 5035 4.471386 AGCTTAATGTCAGGATGTAGGTGT 59.529 41.667 0.00 0.00 37.40 4.16
4862 5044 7.948357 TGTCAGGATGTAGGTGTATAACATAC 58.052 38.462 0.00 0.00 44.52 2.39
4863 5045 7.783119 TGTCAGGATGTAGGTGTATAACATACT 59.217 37.037 2.52 0.00 43.97 2.12
4864 5046 8.298140 GTCAGGATGTAGGTGTATAACATACTC 58.702 40.741 0.00 0.00 41.78 2.59
4865 5047 7.450634 TCAGGATGTAGGTGTATAACATACTCC 59.549 40.741 8.65 8.65 41.78 3.85
4867 5049 6.724905 GGATGTAGGTGTATAACATACTCCCT 59.275 42.308 11.81 11.23 44.56 4.20
4868 5050 7.093858 GGATGTAGGTGTATAACATACTCCCTC 60.094 44.444 11.81 7.61 44.56 4.30
4869 5051 6.919158 TGTAGGTGTATAACATACTCCCTCT 58.081 40.000 11.81 0.62 44.56 3.69
4870 5052 6.776116 TGTAGGTGTATAACATACTCCCTCTG 59.224 42.308 11.81 0.00 44.56 3.35
4871 5053 5.778542 AGGTGTATAACATACTCCCTCTGT 58.221 41.667 11.81 0.00 33.00 3.41
4872 5054 6.203072 AGGTGTATAACATACTCCCTCTGTT 58.797 40.000 11.81 0.00 37.00 3.16
4873 5055 6.324254 AGGTGTATAACATACTCCCTCTGTTC 59.676 42.308 11.81 0.00 35.00 3.18
4874 5056 6.097839 GGTGTATAACATACTCCCTCTGTTCA 59.902 42.308 6.26 0.00 35.00 3.18
4875 5057 6.979238 GTGTATAACATACTCCCTCTGTTCAC 59.021 42.308 0.00 0.00 35.00 3.18
4876 5058 6.895756 TGTATAACATACTCCCTCTGTTCACT 59.104 38.462 0.00 0.00 35.00 3.41
4877 5059 6.875972 ATAACATACTCCCTCTGTTCACTT 57.124 37.500 0.00 0.00 35.00 3.16
4878 5060 5.568620 AACATACTCCCTCTGTTCACTTT 57.431 39.130 0.00 0.00 0.00 2.66
4879 5061 5.568620 ACATACTCCCTCTGTTCACTTTT 57.431 39.130 0.00 0.00 0.00 2.27
4880 5062 6.681729 ACATACTCCCTCTGTTCACTTTTA 57.318 37.500 0.00 0.00 0.00 1.52
4881 5063 7.259088 ACATACTCCCTCTGTTCACTTTTAT 57.741 36.000 0.00 0.00 0.00 1.40
4882 5064 8.375493 ACATACTCCCTCTGTTCACTTTTATA 57.625 34.615 0.00 0.00 0.00 0.98
4883 5065 8.822805 ACATACTCCCTCTGTTCACTTTTATAA 58.177 33.333 0.00 0.00 0.00 0.98
4884 5066 9.319143 CATACTCCCTCTGTTCACTTTTATAAG 57.681 37.037 0.00 0.00 37.40 1.73
4885 5067 7.554959 ACTCCCTCTGTTCACTTTTATAAGA 57.445 36.000 0.00 0.00 35.30 2.10
4886 5068 7.387643 ACTCCCTCTGTTCACTTTTATAAGAC 58.612 38.462 0.00 0.00 35.30 3.01
4887 5069 6.708285 TCCCTCTGTTCACTTTTATAAGACC 58.292 40.000 0.00 0.00 35.30 3.85
4888 5070 6.500751 TCCCTCTGTTCACTTTTATAAGACCT 59.499 38.462 0.00 0.00 35.30 3.85
4889 5071 7.017254 TCCCTCTGTTCACTTTTATAAGACCTT 59.983 37.037 0.00 0.00 35.30 3.50
4890 5072 7.119846 CCCTCTGTTCACTTTTATAAGACCTTG 59.880 40.741 0.00 0.00 35.30 3.61
4891 5073 7.878127 CCTCTGTTCACTTTTATAAGACCTTGA 59.122 37.037 0.00 0.00 35.30 3.02
4892 5074 9.273016 CTCTGTTCACTTTTATAAGACCTTGAA 57.727 33.333 0.00 0.00 35.30 2.69
4893 5075 9.273016 TCTGTTCACTTTTATAAGACCTTGAAG 57.727 33.333 0.00 0.00 35.30 3.02
4894 5076 9.273016 CTGTTCACTTTTATAAGACCTTGAAGA 57.727 33.333 0.00 0.00 35.30 2.87
4895 5077 9.793259 TGTTCACTTTTATAAGACCTTGAAGAT 57.207 29.630 0.00 0.00 35.30 2.40
4908 5090 8.503458 AGACCTTGAAGATATTTCAGACAATG 57.497 34.615 0.00 0.00 0.00 2.82
4909 5091 8.105829 AGACCTTGAAGATATTTCAGACAATGT 58.894 33.333 0.00 0.00 0.00 2.71
4910 5092 8.048534 ACCTTGAAGATATTTCAGACAATGTG 57.951 34.615 0.00 0.00 0.00 3.21
4911 5093 6.971184 CCTTGAAGATATTTCAGACAATGTGC 59.029 38.462 0.00 0.00 0.00 4.57
4912 5094 7.362315 CCTTGAAGATATTTCAGACAATGTGCA 60.362 37.037 0.00 0.00 0.00 4.57
4913 5095 7.451501 TGAAGATATTTCAGACAATGTGCAA 57.548 32.000 0.00 0.00 0.00 4.08
4914 5096 7.884257 TGAAGATATTTCAGACAATGTGCAAA 58.116 30.769 0.00 0.00 0.00 3.68
4915 5097 8.358895 TGAAGATATTTCAGACAATGTGCAAAA 58.641 29.630 0.00 0.00 0.00 2.44
4916 5098 8.524870 AAGATATTTCAGACAATGTGCAAAAC 57.475 30.769 0.00 0.00 0.00 2.43
4917 5099 7.660112 AGATATTTCAGACAATGTGCAAAACA 58.340 30.769 0.00 0.00 44.79 2.83
4918 5100 7.811236 AGATATTTCAGACAATGTGCAAAACAG 59.189 33.333 0.00 0.00 43.64 3.16
4919 5101 3.082698 TCAGACAATGTGCAAAACAGC 57.917 42.857 0.00 0.00 43.64 4.40
4920 5102 2.129607 CAGACAATGTGCAAAACAGCC 58.870 47.619 0.00 0.00 43.64 4.85
4921 5103 1.069049 AGACAATGTGCAAAACAGCCC 59.931 47.619 0.00 0.00 43.64 5.19
4922 5104 0.829333 ACAATGTGCAAAACAGCCCA 59.171 45.000 0.00 0.00 43.64 5.36
4923 5105 1.417145 ACAATGTGCAAAACAGCCCAT 59.583 42.857 0.00 0.00 43.64 4.00
4924 5106 2.158784 ACAATGTGCAAAACAGCCCATT 60.159 40.909 0.00 0.00 43.64 3.16
4925 5107 2.879646 CAATGTGCAAAACAGCCCATTT 59.120 40.909 0.00 0.00 43.64 2.32
4926 5108 2.706339 TGTGCAAAACAGCCCATTTT 57.294 40.000 0.00 0.00 33.78 1.82
4927 5109 2.286872 TGTGCAAAACAGCCCATTTTG 58.713 42.857 11.43 11.43 45.68 2.44
4928 5110 2.093288 TGTGCAAAACAGCCCATTTTGA 60.093 40.909 17.34 4.68 45.75 2.69
4929 5111 2.545106 GTGCAAAACAGCCCATTTTGAG 59.455 45.455 17.34 0.00 45.75 3.02
4930 5112 2.170187 TGCAAAACAGCCCATTTTGAGT 59.830 40.909 17.34 0.00 45.75 3.41
4931 5113 3.205338 GCAAAACAGCCCATTTTGAGTT 58.795 40.909 17.34 0.00 45.75 3.01
4932 5114 3.002553 GCAAAACAGCCCATTTTGAGTTG 59.997 43.478 17.34 4.12 45.75 3.16
4933 5115 4.190772 CAAAACAGCCCATTTTGAGTTGT 58.809 39.130 10.61 0.00 45.75 3.32
4934 5116 3.733443 AACAGCCCATTTTGAGTTGTC 57.267 42.857 0.00 0.00 0.00 3.18
4935 5117 2.949447 ACAGCCCATTTTGAGTTGTCT 58.051 42.857 0.00 0.00 0.00 3.41
4936 5118 2.624838 ACAGCCCATTTTGAGTTGTCTG 59.375 45.455 0.00 0.00 0.00 3.51
4937 5119 2.886523 CAGCCCATTTTGAGTTGTCTGA 59.113 45.455 0.00 0.00 0.00 3.27
4938 5120 3.318839 CAGCCCATTTTGAGTTGTCTGAA 59.681 43.478 0.00 0.00 0.00 3.02
4939 5121 3.960102 AGCCCATTTTGAGTTGTCTGAAA 59.040 39.130 0.00 0.00 0.00 2.69
4940 5122 4.051237 GCCCATTTTGAGTTGTCTGAAAC 58.949 43.478 0.00 0.00 0.00 2.78
4941 5123 4.290155 CCCATTTTGAGTTGTCTGAAACG 58.710 43.478 0.00 0.00 35.13 3.60
4942 5124 4.036262 CCCATTTTGAGTTGTCTGAAACGA 59.964 41.667 0.00 0.00 35.13 3.85
4943 5125 4.970003 CCATTTTGAGTTGTCTGAAACGAC 59.030 41.667 0.00 0.00 41.93 4.34
4954 5136 6.102006 TGTCTGAAACGACTTACAAAAGTG 57.898 37.500 0.00 0.00 46.09 3.16
4955 5137 5.870433 TGTCTGAAACGACTTACAAAAGTGA 59.130 36.000 0.00 0.00 46.09 3.41
4956 5138 6.369340 TGTCTGAAACGACTTACAAAAGTGAA 59.631 34.615 0.00 0.00 46.09 3.18
4957 5139 6.681599 GTCTGAAACGACTTACAAAAGTGAAC 59.318 38.462 0.00 0.00 46.09 3.18
4958 5140 5.552807 TGAAACGACTTACAAAAGTGAACG 58.447 37.500 0.00 0.00 46.09 3.95
4959 5141 4.525411 AACGACTTACAAAAGTGAACGG 57.475 40.909 0.00 0.00 46.09 4.44
4960 5142 3.784338 ACGACTTACAAAAGTGAACGGA 58.216 40.909 0.00 0.00 46.09 4.69
4961 5143 3.800506 ACGACTTACAAAAGTGAACGGAG 59.199 43.478 0.00 0.00 46.09 4.63
4962 5144 3.183775 CGACTTACAAAAGTGAACGGAGG 59.816 47.826 0.00 0.00 46.09 4.30
4963 5145 3.473625 ACTTACAAAAGTGAACGGAGGG 58.526 45.455 0.00 0.00 44.40 4.30
4964 5146 3.135167 ACTTACAAAAGTGAACGGAGGGA 59.865 43.478 0.00 0.00 44.40 4.20
4965 5147 2.256117 ACAAAAGTGAACGGAGGGAG 57.744 50.000 0.00 0.00 0.00 4.30
4966 5148 1.489230 ACAAAAGTGAACGGAGGGAGT 59.511 47.619 0.00 0.00 0.00 3.85
4967 5149 2.701951 ACAAAAGTGAACGGAGGGAGTA 59.298 45.455 0.00 0.00 0.00 2.59
4968 5150 3.064931 CAAAAGTGAACGGAGGGAGTAC 58.935 50.000 0.00 0.00 0.00 2.73
4999 5181 2.420022 CGCCAAGCAAAAGCTATGTACT 59.580 45.455 0.00 0.00 0.00 2.73
5000 5182 3.621268 CGCCAAGCAAAAGCTATGTACTA 59.379 43.478 0.00 0.00 0.00 1.82
5001 5183 4.260375 CGCCAAGCAAAAGCTATGTACTAG 60.260 45.833 0.00 0.00 0.00 2.57
5181 5363 3.628032 GGCCACTTGAGAATTTAGTAGCC 59.372 47.826 0.00 0.00 38.99 3.93
5192 5374 8.225416 TGAGAATTTAGTAGCCTATCTAGGTGA 58.775 37.037 5.21 0.00 45.42 4.02
5207 5389 5.559770 TCTAGGTGATGTTCAAAAGCATCA 58.440 37.500 3.45 3.45 46.16 3.07
5444 5626 1.340889 GCATCTTTTCTTGCACACCCA 59.659 47.619 0.00 0.00 38.72 4.51
5559 5741 0.107017 CCCTGATTGGATGGTTCGCT 60.107 55.000 0.00 0.00 38.35 4.93
5762 5944 1.089920 CCCATTATGCGCTATGAGGC 58.910 55.000 9.73 0.00 0.00 4.70
5766 5948 0.472044 TTATGCGCTATGAGGCCCAA 59.528 50.000 9.73 0.00 0.00 4.12
5823 6005 3.620374 AGCAAGATCAGCGTACATTTCAG 59.380 43.478 0.00 0.00 37.01 3.02
5874 6056 2.224597 ACACTGACACATCATGGAAGCA 60.225 45.455 0.00 0.00 33.22 3.91
5915 6097 0.109597 GTTGACCTTGGATGCTTGCG 60.110 55.000 0.00 0.00 0.00 4.85
6048 6230 9.168451 TGTTTCTGTAGAAATGTCTAACAACAA 57.832 29.630 9.98 0.00 44.69 2.83
6049 6231 9.651718 GTTTCTGTAGAAATGTCTAACAACAAG 57.348 33.333 9.98 0.00 44.69 3.16
6050 6232 9.607988 TTTCTGTAGAAATGTCTAACAACAAGA 57.392 29.630 3.05 0.00 38.11 3.02
6095 6277 1.656095 CGAGCTTGGTTTCTAAGAGCG 59.344 52.381 0.00 0.00 38.34 5.03
6129 6311 8.982723 AGGACTTCTATTTTGCTCTATAACTGA 58.017 33.333 0.00 0.00 0.00 3.41
6144 6326 7.512130 TCTATAACTGATGGATCTTGCATTGT 58.488 34.615 0.00 0.00 0.00 2.71
6172 6354 2.165641 TGTAGTTGGCGGATACACTCAG 59.834 50.000 0.00 0.00 0.00 3.35
6180 6362 2.288702 GCGGATACACTCAGCTCATGAT 60.289 50.000 0.00 0.00 41.31 2.45
6252 6437 9.155053 GTACTTTATAAATTCTGCGTTATGTGC 57.845 33.333 0.00 0.00 0.00 4.57
6269 6454 2.719774 GCGCTTGTTTTGGCATCGC 61.720 57.895 0.00 0.00 35.13 4.58
6270 6455 1.371512 CGCTTGTTTTGGCATCGCA 60.372 52.632 0.00 0.00 0.00 5.10
6277 6462 1.531739 TTTTGGCATCGCAAGGGACC 61.532 55.000 0.00 0.00 38.47 4.46
6278 6463 3.936772 TTGGCATCGCAAGGGACCC 62.937 63.158 0.59 0.59 38.47 4.46
6354 6539 2.030540 TGCGGTACTTATATCGGCTCAC 60.031 50.000 0.00 0.00 35.33 3.51
6403 6588 5.750067 ACATCAAAACAATGTTGCAAGAGTC 59.250 36.000 0.00 0.00 33.62 3.36
6404 6589 5.321959 TCAAAACAATGTTGCAAGAGTCA 57.678 34.783 0.00 0.00 0.00 3.41
6425 6620 7.653647 AGTCAACTTTTACATTTCCGCAATAA 58.346 30.769 0.00 0.00 0.00 1.40
6539 6734 3.730215 TGTTATGCTTTCCAAGGCCTA 57.270 42.857 5.16 0.00 0.00 3.93
6635 6834 0.696501 GGCTCCAGGGTACTTTTGGA 59.303 55.000 11.30 11.30 38.62 3.53
6659 6858 8.709646 GGATACATAATGTTAGAACAACCGATC 58.290 37.037 0.00 0.00 43.03 3.69
6671 6870 0.181350 AACCGATCAATCTCCTGGGC 59.819 55.000 0.00 0.00 0.00 5.36
6678 6877 1.492176 TCAATCTCCTGGGCTGGAATC 59.508 52.381 0.00 0.00 35.43 2.52
6679 6878 1.493871 CAATCTCCTGGGCTGGAATCT 59.506 52.381 0.00 0.00 35.43 2.40
6680 6879 2.707791 CAATCTCCTGGGCTGGAATCTA 59.292 50.000 0.00 0.00 35.43 1.98
6681 6880 2.803285 TCTCCTGGGCTGGAATCTAT 57.197 50.000 0.00 0.00 35.43 1.98
6682 6881 3.923273 TCTCCTGGGCTGGAATCTATA 57.077 47.619 0.00 0.00 35.43 1.31
6683 6882 4.213531 TCTCCTGGGCTGGAATCTATAA 57.786 45.455 0.00 0.00 35.43 0.98
6684 6883 4.566837 TCTCCTGGGCTGGAATCTATAAA 58.433 43.478 0.00 0.00 35.43 1.40
6685 6884 4.975147 TCTCCTGGGCTGGAATCTATAAAA 59.025 41.667 0.00 0.00 35.43 1.52
6686 6885 5.431731 TCTCCTGGGCTGGAATCTATAAAAA 59.568 40.000 0.00 0.00 35.43 1.94
6708 6907 3.825908 AAAAATCCTCCTGGGCTGTAA 57.174 42.857 0.00 0.00 34.39 2.41
6709 6908 2.808906 AAATCCTCCTGGGCTGTAAC 57.191 50.000 0.00 0.00 34.39 2.50
6710 6909 1.668826 AATCCTCCTGGGCTGTAACA 58.331 50.000 0.00 0.00 34.39 2.41
6711 6910 1.898863 ATCCTCCTGGGCTGTAACAT 58.101 50.000 0.00 0.00 34.39 2.71
6712 6911 0.911769 TCCTCCTGGGCTGTAACATG 59.088 55.000 0.00 0.00 34.39 3.21
6713 6912 0.911769 CCTCCTGGGCTGTAACATGA 59.088 55.000 0.00 0.00 0.00 3.07
6714 6913 1.134280 CCTCCTGGGCTGTAACATGAG 60.134 57.143 0.00 0.00 31.68 2.90
6715 6914 0.911769 TCCTGGGCTGTAACATGAGG 59.088 55.000 0.00 0.00 0.00 3.86
6716 6915 0.107017 CCTGGGCTGTAACATGAGGG 60.107 60.000 0.00 0.00 0.00 4.30
6717 6916 0.107017 CTGGGCTGTAACATGAGGGG 60.107 60.000 0.00 0.00 0.00 4.79
6718 6917 1.227383 GGGCTGTAACATGAGGGGG 59.773 63.158 0.00 0.00 0.00 5.40
6719 6918 1.453928 GGCTGTAACATGAGGGGGC 60.454 63.158 0.00 0.00 0.00 5.80
6720 6919 1.609783 GCTGTAACATGAGGGGGCT 59.390 57.895 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.988287 TGGTTCTGTGTTATATGATCTGCA 58.012 37.500 0.00 0.00 0.00 4.41
30 31 9.112725 TGAATTGGTTCTGTGTTATATGATCTG 57.887 33.333 0.00 0.00 35.33 2.90
88 89 6.494491 ACAAGGGAGACAATTTGATTCATTCA 59.506 34.615 2.79 0.00 0.00 2.57
367 379 1.152963 GGGCGCTCTCTCTCTCTCT 60.153 63.158 7.64 0.00 0.00 3.10
368 380 2.193536 GGGGCGCTCTCTCTCTCTC 61.194 68.421 7.48 0.00 0.00 3.20
369 381 2.123897 GGGGCGCTCTCTCTCTCT 60.124 66.667 7.48 0.00 0.00 3.10
370 382 2.441164 TGGGGCGCTCTCTCTCTC 60.441 66.667 7.48 0.00 0.00 3.20
371 383 2.757917 GTGGGGCGCTCTCTCTCT 60.758 66.667 7.48 0.00 0.00 3.10
372 384 2.757917 AGTGGGGCGCTCTCTCTC 60.758 66.667 7.48 0.00 0.00 3.20
373 385 2.757917 GAGTGGGGCGCTCTCTCT 60.758 66.667 21.84 11.52 37.92 3.10
374 386 3.844090 GGAGTGGGGCGCTCTCTC 61.844 72.222 26.01 19.35 40.43 3.20
375 387 4.704103 TGGAGTGGGGCGCTCTCT 62.704 66.667 26.01 6.19 40.43 3.10
390 402 1.261238 GGAGTGGAGAGGTGGAGTGG 61.261 65.000 0.00 0.00 0.00 4.00
657 678 3.382832 CGAACCAGTCGCCTCCCT 61.383 66.667 0.00 0.00 44.14 4.20
730 751 2.364632 CTAATCAATCAACACCCGCCA 58.635 47.619 0.00 0.00 0.00 5.69
798 819 1.271054 GGGCAGATCTTATCGCATGGT 60.271 52.381 5.26 0.00 32.91 3.55
799 820 1.446907 GGGCAGATCTTATCGCATGG 58.553 55.000 5.26 0.00 32.91 3.66
800 821 1.271001 TGGGGCAGATCTTATCGCATG 60.271 52.381 5.26 0.00 32.91 4.06
875 896 0.883833 AACCAGAAATGCAAGGCTCG 59.116 50.000 0.00 0.00 0.00 5.03
953 974 2.358957 TCCTGCTGAACGGATTCAATG 58.641 47.619 0.00 0.00 44.28 2.82
1080 1101 2.166254 CCCGGCAGAATAATTTGCAAGT 59.834 45.455 0.00 0.00 42.02 3.16
1170 1191 5.353400 TCAGCATCTGAACTGTGAATTCATC 59.647 40.000 12.12 5.63 37.57 2.92
1214 1235 6.323739 AGCTCCAAAACAACTCTTTCCATAAA 59.676 34.615 0.00 0.00 0.00 1.40
1410 1435 8.487176 GTTTGCTGTTATAAACAAACTGAATGG 58.513 33.333 21.36 0.26 45.23 3.16
1438 1463 4.532834 TGTCTGAAAAAGGTAGGTTGCTT 58.467 39.130 0.00 0.00 0.00 3.91
1439 1464 4.164843 TGTCTGAAAAAGGTAGGTTGCT 57.835 40.909 0.00 0.00 0.00 3.91
1469 1524 9.840427 GTAAATAAAAGCATCAAGTATGTGTGT 57.160 29.630 0.00 0.00 37.93 3.72
1548 1603 4.222124 AGGGAGTGGTGATTACAATGTC 57.778 45.455 0.00 0.00 0.00 3.06
1682 1862 6.051074 TCTGCAGTAATTACAGATGATGTGG 58.949 40.000 17.65 4.13 43.80 4.17
1902 2082 3.327757 ACTGTATCTTCTCAAAGCCACCA 59.672 43.478 0.00 0.00 32.18 4.17
1961 2141 7.657354 TGTCATATTCCTACAGCATAATGACAC 59.343 37.037 9.96 0.00 39.45 3.67
2100 2280 5.591877 AGCTGAATATACAAAAAGCAGGAGG 59.408 40.000 0.00 0.00 33.08 4.30
2370 2550 4.941263 GGCAAGACATCTGTGGTGTAATAA 59.059 41.667 0.00 0.00 0.00 1.40
2496 2676 7.818997 TCATACTCTAAATCCACGATGTACT 57.181 36.000 0.00 0.00 0.00 2.73
2662 2842 9.671279 TGATCCATAGCATGTACAAATATTAGG 57.329 33.333 0.00 0.00 0.00 2.69
2691 2871 9.658475 CAACTACAGATAATTCAAAACACGAAA 57.342 29.630 0.00 0.00 0.00 3.46
2980 3160 9.444600 AAAAGCAAATCAAAATAGCAGATTCAT 57.555 25.926 0.00 0.00 31.21 2.57
3435 3615 6.230472 ACTTTACTCAAGTATGTGCATCACA 58.770 36.000 1.88 1.88 44.56 3.58
3498 3678 2.748461 TTGCAAGCTACACACGAAAC 57.252 45.000 0.00 0.00 0.00 2.78
3619 3799 3.070590 ACCTAAGGTCACCAAGTGTACAC 59.929 47.826 18.56 18.56 34.79 2.90
3651 3831 6.141685 CGCAAAGGTTTAAACATGAAGTGTAC 59.858 38.462 19.57 0.00 41.14 2.90
3797 3979 9.604626 CATGACTACATTTTGTTTCTCTTCTTC 57.395 33.333 0.00 0.00 34.15 2.87
3825 4007 3.927476 AGGCCCCAAAGTATAATGCAAT 58.073 40.909 0.00 0.00 0.00 3.56
3826 4008 3.396685 AGGCCCCAAAGTATAATGCAA 57.603 42.857 0.00 0.00 0.00 4.08
3827 4009 3.052944 AGAAGGCCCCAAAGTATAATGCA 60.053 43.478 0.00 0.00 0.00 3.96
3828 4010 3.566351 AGAAGGCCCCAAAGTATAATGC 58.434 45.455 0.00 0.00 0.00 3.56
3829 4011 7.234355 AGATTAGAAGGCCCCAAAGTATAATG 58.766 38.462 0.00 0.00 0.00 1.90
4036 4218 1.623811 TGGAGTAGAAGTCCAACCTGC 59.376 52.381 0.88 0.00 44.34 4.85
4441 4623 1.014352 AATAATCAAGCGCGTCCCAC 58.986 50.000 8.43 0.00 0.00 4.61
4522 4704 6.539103 GTCCCATAATCAAACTTGAGTAGTCC 59.461 42.308 5.90 0.00 40.50 3.85
4546 4728 1.004628 GGGGTTTGGTATAACCGGTGT 59.995 52.381 8.52 2.17 46.93 4.16
4853 5035 7.973048 AAGTGAACAGAGGGAGTATGTTATA 57.027 36.000 0.00 0.00 40.76 0.98
4862 5044 6.819146 GGTCTTATAAAAGTGAACAGAGGGAG 59.181 42.308 0.00 0.00 34.13 4.30
4863 5045 6.500751 AGGTCTTATAAAAGTGAACAGAGGGA 59.499 38.462 0.00 0.00 34.13 4.20
4864 5046 6.712276 AGGTCTTATAAAAGTGAACAGAGGG 58.288 40.000 0.00 0.00 34.13 4.30
4865 5047 7.878127 TCAAGGTCTTATAAAAGTGAACAGAGG 59.122 37.037 0.00 0.00 34.13 3.69
4867 5049 9.273016 CTTCAAGGTCTTATAAAAGTGAACAGA 57.727 33.333 0.00 0.00 34.13 3.41
4868 5050 9.273016 TCTTCAAGGTCTTATAAAAGTGAACAG 57.727 33.333 0.00 0.00 34.13 3.16
4869 5051 9.793259 ATCTTCAAGGTCTTATAAAAGTGAACA 57.207 29.630 0.00 0.00 34.13 3.18
4882 5064 8.954350 CATTGTCTGAAATATCTTCAAGGTCTT 58.046 33.333 0.00 0.00 0.00 3.01
4883 5065 8.105829 ACATTGTCTGAAATATCTTCAAGGTCT 58.894 33.333 0.00 0.00 0.00 3.85
4884 5066 8.180267 CACATTGTCTGAAATATCTTCAAGGTC 58.820 37.037 0.00 0.00 30.13 3.85
4885 5067 7.362401 GCACATTGTCTGAAATATCTTCAAGGT 60.362 37.037 0.00 0.00 31.40 3.50
4886 5068 6.971184 GCACATTGTCTGAAATATCTTCAAGG 59.029 38.462 0.00 0.00 0.00 3.61
4887 5069 7.532571 TGCACATTGTCTGAAATATCTTCAAG 58.467 34.615 0.00 0.00 0.00 3.02
4888 5070 7.451501 TGCACATTGTCTGAAATATCTTCAA 57.548 32.000 0.00 0.00 0.00 2.69
4889 5071 7.451501 TTGCACATTGTCTGAAATATCTTCA 57.548 32.000 0.00 1.96 0.00 3.02
4890 5072 8.642020 GTTTTGCACATTGTCTGAAATATCTTC 58.358 33.333 0.00 0.00 0.00 2.87
4891 5073 8.143193 TGTTTTGCACATTGTCTGAAATATCTT 58.857 29.630 0.00 0.00 0.00 2.40
4892 5074 7.660112 TGTTTTGCACATTGTCTGAAATATCT 58.340 30.769 0.00 0.00 0.00 1.98
4893 5075 7.411157 GCTGTTTTGCACATTGTCTGAAATATC 60.411 37.037 0.00 0.00 33.76 1.63
4894 5076 6.366877 GCTGTTTTGCACATTGTCTGAAATAT 59.633 34.615 0.00 0.00 33.76 1.28
4895 5077 5.691305 GCTGTTTTGCACATTGTCTGAAATA 59.309 36.000 0.00 0.00 33.76 1.40
4896 5078 4.508861 GCTGTTTTGCACATTGTCTGAAAT 59.491 37.500 0.00 0.00 33.76 2.17
4897 5079 3.864583 GCTGTTTTGCACATTGTCTGAAA 59.135 39.130 0.00 0.00 33.76 2.69
4898 5080 3.446799 GCTGTTTTGCACATTGTCTGAA 58.553 40.909 0.00 0.00 33.76 3.02
4899 5081 2.223782 GGCTGTTTTGCACATTGTCTGA 60.224 45.455 0.00 0.00 33.76 3.27
4900 5082 2.129607 GGCTGTTTTGCACATTGTCTG 58.870 47.619 0.00 0.00 33.76 3.51
4901 5083 1.069049 GGGCTGTTTTGCACATTGTCT 59.931 47.619 0.00 0.00 36.18 3.41
4902 5084 1.202510 TGGGCTGTTTTGCACATTGTC 60.203 47.619 0.00 0.00 41.96 3.18
4903 5085 0.829333 TGGGCTGTTTTGCACATTGT 59.171 45.000 0.00 0.00 41.96 2.71
4904 5086 3.682766 TGGGCTGTTTTGCACATTG 57.317 47.368 0.00 0.00 41.96 2.82
4908 5090 2.545106 CTCAAAATGGGCTGTTTTGCAC 59.455 45.455 17.18 0.00 43.04 4.57
4909 5091 2.170187 ACTCAAAATGGGCTGTTTTGCA 59.830 40.909 17.18 0.00 43.04 4.08
4910 5092 2.837498 ACTCAAAATGGGCTGTTTTGC 58.163 42.857 17.18 0.00 43.04 3.68
4911 5093 4.190772 ACAACTCAAAATGGGCTGTTTTG 58.809 39.130 16.38 16.38 44.10 2.44
4912 5094 4.162131 AGACAACTCAAAATGGGCTGTTTT 59.838 37.500 0.00 0.00 0.00 2.43
4913 5095 3.706086 AGACAACTCAAAATGGGCTGTTT 59.294 39.130 0.00 0.00 0.00 2.83
4914 5096 3.068590 CAGACAACTCAAAATGGGCTGTT 59.931 43.478 0.00 0.00 0.00 3.16
4915 5097 2.624838 CAGACAACTCAAAATGGGCTGT 59.375 45.455 0.00 0.00 0.00 4.40
4916 5098 2.886523 TCAGACAACTCAAAATGGGCTG 59.113 45.455 0.00 0.00 0.00 4.85
4917 5099 3.228188 TCAGACAACTCAAAATGGGCT 57.772 42.857 0.00 0.00 0.00 5.19
4918 5100 4.051237 GTTTCAGACAACTCAAAATGGGC 58.949 43.478 0.00 0.00 0.00 5.36
4919 5101 4.036262 TCGTTTCAGACAACTCAAAATGGG 59.964 41.667 0.00 0.00 0.00 4.00
4920 5102 4.970003 GTCGTTTCAGACAACTCAAAATGG 59.030 41.667 0.00 0.00 40.65 3.16
4921 5103 5.810525 AGTCGTTTCAGACAACTCAAAATG 58.189 37.500 0.00 0.00 43.24 2.32
4922 5104 6.436843 AAGTCGTTTCAGACAACTCAAAAT 57.563 33.333 0.00 0.00 43.24 1.82
4923 5105 5.873179 AAGTCGTTTCAGACAACTCAAAA 57.127 34.783 0.00 0.00 43.24 2.44
4924 5106 5.870433 TGTAAGTCGTTTCAGACAACTCAAA 59.130 36.000 0.00 0.00 43.24 2.69
4925 5107 5.412640 TGTAAGTCGTTTCAGACAACTCAA 58.587 37.500 0.00 0.00 43.24 3.02
4926 5108 5.001237 TGTAAGTCGTTTCAGACAACTCA 57.999 39.130 0.00 0.00 43.24 3.41
4927 5109 5.961395 TTGTAAGTCGTTTCAGACAACTC 57.039 39.130 0.00 0.00 43.24 3.01
4928 5110 6.370718 ACTTTTGTAAGTCGTTTCAGACAACT 59.629 34.615 0.00 0.00 40.60 3.16
4929 5111 6.464834 CACTTTTGTAAGTCGTTTCAGACAAC 59.535 38.462 0.00 0.00 42.67 3.32
4930 5112 6.369340 TCACTTTTGTAAGTCGTTTCAGACAA 59.631 34.615 0.00 0.00 42.67 3.18
4931 5113 5.870433 TCACTTTTGTAAGTCGTTTCAGACA 59.130 36.000 0.00 0.00 42.67 3.41
4932 5114 6.340537 TCACTTTTGTAAGTCGTTTCAGAC 57.659 37.500 0.00 0.00 42.67 3.51
4933 5115 6.454583 CGTTCACTTTTGTAAGTCGTTTCAGA 60.455 38.462 0.00 0.00 42.67 3.27
4934 5116 5.671140 CGTTCACTTTTGTAAGTCGTTTCAG 59.329 40.000 0.00 0.00 42.67 3.02
4935 5117 5.446206 CCGTTCACTTTTGTAAGTCGTTTCA 60.446 40.000 0.00 0.00 42.67 2.69
4936 5118 4.959757 CCGTTCACTTTTGTAAGTCGTTTC 59.040 41.667 0.00 0.00 42.67 2.78
4937 5119 4.630940 TCCGTTCACTTTTGTAAGTCGTTT 59.369 37.500 0.00 0.00 42.67 3.60
4938 5120 4.183101 TCCGTTCACTTTTGTAAGTCGTT 58.817 39.130 0.00 0.00 42.67 3.85
4939 5121 3.784338 TCCGTTCACTTTTGTAAGTCGT 58.216 40.909 0.00 0.00 42.67 4.34
4940 5122 3.183775 CCTCCGTTCACTTTTGTAAGTCG 59.816 47.826 0.00 0.00 42.67 4.18
4941 5123 3.497262 CCCTCCGTTCACTTTTGTAAGTC 59.503 47.826 0.00 0.00 42.67 3.01
4942 5124 3.135167 TCCCTCCGTTCACTTTTGTAAGT 59.865 43.478 0.00 0.00 45.40 2.24
4943 5125 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
4944 5126 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
4945 5127 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
4946 5128 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
4947 5129 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
4948 5130 2.970640 AGTACTCCCTCCGTTCACTTTT 59.029 45.455 0.00 0.00 0.00 2.27
4949 5131 2.606378 AGTACTCCCTCCGTTCACTTT 58.394 47.619 0.00 0.00 0.00 2.66
4950 5132 2.305858 AGTACTCCCTCCGTTCACTT 57.694 50.000 0.00 0.00 0.00 3.16
4951 5133 2.575279 TCTAGTACTCCCTCCGTTCACT 59.425 50.000 0.00 0.00 0.00 3.41
4952 5134 2.996631 TCTAGTACTCCCTCCGTTCAC 58.003 52.381 0.00 0.00 0.00 3.18
4953 5135 3.947612 ATCTAGTACTCCCTCCGTTCA 57.052 47.619 0.00 0.00 0.00 3.18
4954 5136 5.349809 CAAAATCTAGTACTCCCTCCGTTC 58.650 45.833 0.00 0.00 0.00 3.95
4955 5137 4.382793 GCAAAATCTAGTACTCCCTCCGTT 60.383 45.833 0.00 0.00 0.00 4.44
4956 5138 3.132467 GCAAAATCTAGTACTCCCTCCGT 59.868 47.826 0.00 0.00 0.00 4.69
4957 5139 3.718815 GCAAAATCTAGTACTCCCTCCG 58.281 50.000 0.00 0.00 0.00 4.63
4958 5140 3.718815 CGCAAAATCTAGTACTCCCTCC 58.281 50.000 0.00 0.00 0.00 4.30
4959 5141 3.124560 GCGCAAAATCTAGTACTCCCTC 58.875 50.000 0.30 0.00 0.00 4.30
4960 5142 2.158943 GGCGCAAAATCTAGTACTCCCT 60.159 50.000 10.83 0.00 0.00 4.20
4961 5143 2.210961 GGCGCAAAATCTAGTACTCCC 58.789 52.381 10.83 0.00 0.00 4.30
4962 5144 2.901249 TGGCGCAAAATCTAGTACTCC 58.099 47.619 10.83 0.00 0.00 3.85
4963 5145 3.242446 GCTTGGCGCAAAATCTAGTACTC 60.242 47.826 10.83 0.00 38.92 2.59
4964 5146 2.678336 GCTTGGCGCAAAATCTAGTACT 59.322 45.455 10.83 0.00 38.92 2.73
4965 5147 3.052940 GCTTGGCGCAAAATCTAGTAC 57.947 47.619 10.83 0.00 38.92 2.73
5181 5363 7.496920 TGATGCTTTTGAACATCACCTAGATAG 59.503 37.037 1.71 0.00 45.79 2.08
5207 5389 6.209192 TCAGTGAACAATCTACATTGGCAAAT 59.791 34.615 3.01 0.00 43.47 2.32
5244 5426 4.849813 AAGGGAATCAGTCATCATGTGA 57.150 40.909 0.00 0.00 0.00 3.58
5295 5477 2.468777 CGCTGACATTTTCAAACAGTGC 59.531 45.455 0.00 0.00 32.21 4.40
5444 5626 3.460648 GCAAGAGCACTCCGGTAAT 57.539 52.632 0.00 0.00 41.58 1.89
5559 5741 0.535335 GTAGACACGATTGCCAGGGA 59.465 55.000 0.00 0.00 0.00 4.20
5762 5944 3.621715 GGTAGTTGCTCGACTAATTTGGG 59.378 47.826 0.00 0.00 34.15 4.12
5766 5948 3.195825 AGCTGGTAGTTGCTCGACTAATT 59.804 43.478 0.00 0.00 33.90 1.40
5823 6005 1.139853 CCCTCTGGCCAAGTAGATCAC 59.860 57.143 7.01 0.00 0.00 3.06
5850 6032 4.455533 GCTTCCATGATGTGTCAGTGTAAA 59.544 41.667 0.00 0.00 37.87 2.01
5874 6056 0.545171 CACTCCTGTCATGCCTGGAT 59.455 55.000 2.61 0.00 32.74 3.41
6048 6230 9.506018 CCAAAAATTTAATGTTTCCATCCTTCT 57.494 29.630 0.00 0.00 0.00 2.85
6049 6231 8.236586 GCCAAAAATTTAATGTTTCCATCCTTC 58.763 33.333 0.00 0.00 0.00 3.46
6050 6232 7.094848 CGCCAAAAATTTAATGTTTCCATCCTT 60.095 33.333 0.00 0.00 0.00 3.36
6066 6248 2.908688 AACCAAGCTCGCCAAAAATT 57.091 40.000 0.00 0.00 0.00 1.82
6095 6277 7.604545 AGAGCAAAATAGAAGTCCTTTACAGAC 59.395 37.037 0.00 0.00 34.31 3.51
6129 6311 2.811410 ACACCACAATGCAAGATCCAT 58.189 42.857 0.00 0.00 0.00 3.41
6144 6326 1.268066 TCCGCCAACTACATACACCA 58.732 50.000 0.00 0.00 0.00 4.17
6172 6354 5.064452 CAGAGTTTTCACCTGTATCATGAGC 59.936 44.000 0.09 0.00 0.00 4.26
6180 6362 2.224523 CCTGCCAGAGTTTTCACCTGTA 60.225 50.000 0.00 0.00 0.00 2.74
6252 6437 0.938637 TTGCGATGCCAAAACAAGCG 60.939 50.000 0.00 0.00 32.18 4.68
6269 6454 3.396685 TGATTTAATGGGGGTCCCTTG 57.603 47.619 8.15 0.00 45.70 3.61
6270 6455 4.015730 TGAATGATTTAATGGGGGTCCCTT 60.016 41.667 8.15 0.00 45.70 3.95
6318 6503 3.302365 ACCGCAAGAAAAATGATGGTG 57.698 42.857 0.00 0.00 43.02 4.17
6329 6514 3.319972 AGCCGATATAAGTACCGCAAGAA 59.680 43.478 0.00 0.00 43.02 2.52
6354 6539 3.255395 TCACATACACAACATGGGCAAAG 59.745 43.478 0.00 0.00 0.00 2.77
6403 6588 8.687824 AGATTATTGCGGAAATGTAAAAGTTG 57.312 30.769 0.00 0.00 0.00 3.16
6404 6589 9.783256 GTAGATTATTGCGGAAATGTAAAAGTT 57.217 29.630 0.00 0.00 0.00 2.66
6425 6620 3.379452 AGCTTGCTCCCAGTAAGTAGAT 58.621 45.455 3.71 0.00 39.65 1.98
6433 6628 1.577736 ACAGATAGCTTGCTCCCAGT 58.422 50.000 0.00 0.00 0.00 4.00
6539 6734 7.355101 TCTAGGACATACAGAGAGTAACCAAT 58.645 38.462 0.00 0.00 36.05 3.16
6635 6834 9.607988 TTGATCGGTTGTTCTAACATTATGTAT 57.392 29.630 0.00 0.00 38.95 2.29
6659 6858 1.493871 AGATTCCAGCCCAGGAGATTG 59.506 52.381 0.00 0.00 39.25 2.67
6688 6887 3.181423 TGTTACAGCCCAGGAGGATTTTT 60.181 43.478 0.00 0.00 38.24 1.94
6689 6888 2.378547 TGTTACAGCCCAGGAGGATTTT 59.621 45.455 0.00 0.00 38.24 1.82
6690 6889 1.992557 TGTTACAGCCCAGGAGGATTT 59.007 47.619 0.00 0.00 38.24 2.17
6691 6890 1.668826 TGTTACAGCCCAGGAGGATT 58.331 50.000 0.00 0.00 38.24 3.01
6692 6891 1.492176 CATGTTACAGCCCAGGAGGAT 59.508 52.381 0.00 0.00 38.24 3.24
6693 6892 0.911769 CATGTTACAGCCCAGGAGGA 59.088 55.000 0.00 0.00 38.24 3.71
6694 6893 0.911769 TCATGTTACAGCCCAGGAGG 59.088 55.000 0.00 0.00 39.47 4.30
6695 6894 1.134280 CCTCATGTTACAGCCCAGGAG 60.134 57.143 0.00 0.00 38.77 3.69
6696 6895 0.911769 CCTCATGTTACAGCCCAGGA 59.088 55.000 0.00 0.00 0.00 3.86
6697 6896 0.107017 CCCTCATGTTACAGCCCAGG 60.107 60.000 0.00 0.00 0.00 4.45
6698 6897 0.107017 CCCCTCATGTTACAGCCCAG 60.107 60.000 0.00 0.00 0.00 4.45
6699 6898 1.570857 CCCCCTCATGTTACAGCCCA 61.571 60.000 0.00 0.00 0.00 5.36
6700 6899 1.227383 CCCCCTCATGTTACAGCCC 59.773 63.158 0.00 0.00 0.00 5.19
6701 6900 1.453928 GCCCCCTCATGTTACAGCC 60.454 63.158 0.00 0.00 0.00 4.85
6702 6901 1.609783 AGCCCCCTCATGTTACAGC 59.390 57.895 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.