Multiple sequence alignment - TraesCS5A01G438900

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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 TraesCS5A01G438900 chr5A 100.000 2711 0 0 1 2711 620399300 620402010 0.000000e+00 5007
1 TraesCS5A01G438900 chr5A 93.750 144 9 0 2001 2144 649807650 649807793 1.630000e-52 217
2 TraesCS5A01G438900 chr5D 94.282 1644 77 12 72 1712 496546925 496548554 0.000000e+00 2499
3 TraesCS5A01G438900 chr5D 88.527 584 37 6 2143 2705 496548867 496549441 0.000000e+00 680
4 TraesCS5A01G438900 chr5D 91.986 287 9 3 1722 2004 496548594 496548870 9.100000e-105 390
5 TraesCS5A01G438900 chr5B 91.621 1456 74 20 561 2004 614982653 614984072 0.000000e+00 1969
6 TraesCS5A01G438900 chr5B 86.017 472 38 13 2143 2587 614984069 614984539 5.250000e-132 481
7 TraesCS5A01G438900 chr5B 81.842 380 29 18 1 377 614979220 614979562 1.590000e-72 283
8 TraesCS5A01G438900 chr5B 91.623 191 12 3 381 570 614979603 614979790 7.450000e-66 261
9 TraesCS5A01G438900 chr3B 99.320 147 1 0 2002 2148 175103398 175103544 1.600000e-67 267
10 TraesCS5A01G438900 chr3B 90.000 120 12 0 2592 2711 452679625 452679744 3.610000e-34 156
11 TraesCS5A01G438900 chr3B 87.097 124 16 0 2588 2711 184957803 184957926 1.010000e-29 141
12 TraesCS5A01G438900 chr7D 95.172 145 7 0 2002 2146 601783230 601783374 2.100000e-56 230
13 TraesCS5A01G438900 chr7D 89.916 119 12 0 2588 2706 415942041 415942159 1.300000e-33 154
14 TraesCS5A01G438900 chr7B 94.483 145 8 0 2001 2145 36499139 36498995 9.770000e-55 224
15 TraesCS5A01G438900 chr7B 92.361 144 8 2 2004 2146 722246232 722246373 4.580000e-48 202
16 TraesCS5A01G438900 chr6D 93.750 144 9 0 2001 2144 316230089 316230232 1.630000e-52 217
17 TraesCS5A01G438900 chr2B 93.750 144 9 0 2001 2144 521973703 521973846 1.630000e-52 217
18 TraesCS5A01G438900 chr7A 92.667 150 10 1 2000 2149 19970151 19970003 5.880000e-52 215
19 TraesCS5A01G438900 chr3A 91.156 147 13 0 2000 2146 691502636 691502782 1.650000e-47 200
20 TraesCS5A01G438900 chr1B 88.800 125 13 1 2588 2711 679290753 679290629 4.680000e-33 152
21 TraesCS5A01G438900 chr4A 88.333 120 14 0 2592 2711 630894946 630894827 7.820000e-31 145
22 TraesCS5A01G438900 chr1A 87.200 125 15 1 2588 2711 584529985 584530109 1.010000e-29 141
23 TraesCS5A01G438900 chr6B 86.992 123 16 0 2588 2710 720005793 720005671 3.640000e-29 139
24 TraesCS5A01G438900 chr2D 88.034 117 14 0 2595 2711 66864506 66864390 3.640000e-29 139


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 TraesCS5A01G438900 chr5A 620399300 620402010 2710 False 5007.000000 5007 100.000000 1 2711 1 chr5A.!!$F1 2710
1 TraesCS5A01G438900 chr5D 496546925 496549441 2516 False 1189.666667 2499 91.598333 72 2705 3 chr5D.!!$F1 2633
2 TraesCS5A01G438900 chr5B 614979220 614984539 5319 False 748.500000 1969 87.775750 1 2587 4 chr5B.!!$F1 2586

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
359 371 0.108329 AATAGTGAACGGCGGGAGTG 60.108 55.0 13.24 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 5045 0.10852 CGGCGGAGTTGTAGGCTAAA 60.109 55.0 0.0 0.0 0.0 1.85 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
36 37 2.356667 GGCCCTTCCCCTGTTCAG 59.643 66.667 0.00 0.00 0.00 3.02
37 38 2.231380 GGCCCTTCCCCTGTTCAGA 61.231 63.158 0.00 0.00 0.00 3.27
70 71 4.722220 CCATGTGGATCCTAATCACACAT 58.278 43.478 14.23 9.45 45.07 3.21
79 80 5.854010 TCCTAATCACACATAGACCTGAC 57.146 43.478 0.00 0.00 0.00 3.51
103 112 3.382865 TGTACTTACGGTGGTTGTACACA 59.617 43.478 0.00 0.00 43.08 3.72
104 113 3.102052 ACTTACGGTGGTTGTACACAG 57.898 47.619 0.00 0.00 43.08 3.66
106 115 3.636300 ACTTACGGTGGTTGTACACAGTA 59.364 43.478 0.00 5.47 45.57 2.74
107 116 2.514205 ACGGTGGTTGTACACAGTAC 57.486 50.000 0.00 0.51 45.57 2.73
108 117 1.755959 ACGGTGGTTGTACACAGTACA 59.244 47.619 5.94 5.94 45.57 2.90
109 118 2.129607 CGGTGGTTGTACACAGTACAC 58.870 52.381 9.33 0.65 43.08 2.90
123 132 4.500837 CACAGTACACTCTTGATGCGATAC 59.499 45.833 0.00 0.00 0.00 2.24
221 233 3.388676 TGACTTTTACTCCCTCCGTTTCA 59.611 43.478 0.00 0.00 0.00 2.69
288 300 7.910162 CGGACTGGAATAAATGAATAAACACAG 59.090 37.037 0.00 0.00 0.00 3.66
313 325 9.577110 AGTAAAACGTGTCTATATTCATTCGAA 57.423 29.630 0.00 0.00 35.05 3.71
314 326 9.615779 GTAAAACGTGTCTATATTCATTCGAAC 57.384 33.333 0.00 0.00 32.81 3.95
359 371 0.108329 AATAGTGAACGGCGGGAGTG 60.108 55.000 13.24 0.00 0.00 3.51
368 380 1.006832 CGGCGGGAGTGTTAATCAAG 58.993 55.000 0.00 0.00 0.00 3.02
519 569 1.599542 GTGCGATAGGAAGATGCCAAC 59.400 52.381 0.00 0.00 39.13 3.77
536 586 0.110486 AACCGGACAGCCAAGTCAAT 59.890 50.000 9.46 0.00 40.29 2.57
557 607 3.390135 TCAACTAACCAAGAGCAACGAG 58.610 45.455 0.00 0.00 0.00 4.18
564 614 2.162681 CCAAGAGCAACGAGGGAAAAT 58.837 47.619 0.00 0.00 0.00 1.82
585 3507 9.457436 GAAAATTAGTGTTTCCCAGACCTAATA 57.543 33.333 0.00 0.00 0.00 0.98
588 3510 4.781934 AGTGTTTCCCAGACCTAATATGC 58.218 43.478 0.00 0.00 0.00 3.14
598 3520 5.221803 CCAGACCTAATATGCTCATTCCAGT 60.222 44.000 0.00 0.00 0.00 4.00
623 3545 4.009002 TCAATCATTGATCAACCGCTCAA 58.991 39.130 11.07 0.00 34.08 3.02
628 3550 4.095334 TCATTGATCAACCGCTCAAATGAG 59.905 41.667 11.07 6.05 44.75 2.90
639 3561 4.676924 CCGCTCAAATGAGACAAGAAAAAC 59.323 41.667 14.43 0.00 44.74 2.43
650 3572 5.063880 AGACAAGAAAAACGGACTTGCTAT 58.936 37.500 0.00 0.00 42.93 2.97
657 3579 7.159372 AGAAAAACGGACTTGCTATAGAGAAA 58.841 34.615 3.21 0.00 0.00 2.52
658 3580 7.660208 AGAAAAACGGACTTGCTATAGAGAAAA 59.340 33.333 3.21 0.00 0.00 2.29
659 3581 6.969828 AAACGGACTTGCTATAGAGAAAAG 57.030 37.500 3.21 3.95 0.00 2.27
684 3606 9.284968 AGAATATTGCTTGTAACCGCTAATTAT 57.715 29.630 0.00 0.00 0.00 1.28
694 3616 8.373048 TGTAACCGCTAATTATAGGACAAATG 57.627 34.615 11.86 0.00 0.00 2.32
763 3686 1.916000 GCAACTAACGCTAGGTACGTG 59.084 52.381 0.00 0.00 44.30 4.49
796 3720 3.294079 ACGACCTAACGTTGGTTGG 57.706 52.632 26.88 20.59 44.14 3.77
837 3761 2.915463 CTCGTTTGACTACATCCACGAC 59.085 50.000 0.00 0.00 33.25 4.34
918 3843 5.366768 TGGACTAATTGAGGCTACTAGCAAT 59.633 40.000 10.27 0.00 44.75 3.56
922 3847 5.841957 AATTGAGGCTACTAGCAATTTGG 57.158 39.130 10.27 0.00 44.75 3.28
975 3900 5.936956 ACCATCTTGACTTCAATCAGTTCTC 59.063 40.000 0.00 0.00 35.02 2.87
976 3901 6.171921 CCATCTTGACTTCAATCAGTTCTCT 58.828 40.000 0.00 0.00 35.02 3.10
1019 3944 3.957535 GCCTTGCGATGGCGATGG 61.958 66.667 0.00 0.00 44.10 3.51
1021 3946 4.303603 CTTGCGATGGCGATGGCG 62.304 66.667 10.84 0.00 44.10 5.69
1044 3969 1.964373 GTCGAAAGGCCGCCTGAAA 60.964 57.895 14.19 0.00 32.13 2.69
1271 4196 2.639286 GAGCCTGGTTTGTGCGTG 59.361 61.111 0.00 0.00 0.00 5.34
1272 4197 2.906897 AGCCTGGTTTGTGCGTGG 60.907 61.111 0.00 0.00 0.00 4.94
1274 4199 3.977244 CCTGGTTTGTGCGTGGGC 61.977 66.667 0.00 0.00 40.52 5.36
1394 4319 2.979676 CAGCGGCAAGTGCTCCAA 60.980 61.111 1.45 0.00 41.72 3.53
1494 4419 0.532573 ACATGTCCTACTGCTCACCG 59.467 55.000 0.00 0.00 0.00 4.94
1495 4420 0.807667 CATGTCCTACTGCTCACCGC 60.808 60.000 0.00 0.00 39.77 5.68
1496 4421 2.202623 GTCCTACTGCTCACCGCG 60.203 66.667 0.00 0.00 43.27 6.46
1634 4568 2.806745 CGGAGCTGGTGAAGAACTTGAA 60.807 50.000 0.00 0.00 0.00 2.69
1712 4646 1.250154 TGCCACCACAAGCATTAGCC 61.250 55.000 0.00 0.00 43.56 3.93
1715 4649 1.614051 CCACCACAAGCATTAGCCAGA 60.614 52.381 0.00 0.00 43.56 3.86
1716 4650 1.741706 CACCACAAGCATTAGCCAGAG 59.258 52.381 0.00 0.00 43.56 3.35
1718 4652 2.571653 ACCACAAGCATTAGCCAGAGTA 59.428 45.455 0.00 0.00 43.56 2.59
1788 4752 2.862541 TCCAATTGTGCAGCTGTTAGT 58.137 42.857 16.64 0.00 0.00 2.24
1795 4759 1.264288 GTGCAGCTGTTAGTTGGTCAC 59.736 52.381 16.64 7.54 0.00 3.67
1832 4800 3.767673 TCTACGTTATGAAGGGAGCAACT 59.232 43.478 0.00 0.00 0.00 3.16
1877 4845 3.311322 TGCATTAATTTCCGCCGTTCTAG 59.689 43.478 0.00 0.00 0.00 2.43
1878 4846 3.311596 GCATTAATTTCCGCCGTTCTAGT 59.688 43.478 0.00 0.00 0.00 2.57
1879 4847 4.508861 GCATTAATTTCCGCCGTTCTAGTA 59.491 41.667 0.00 0.00 0.00 1.82
1934 4902 3.895232 ACTGTCGCATATGTTTCTCCT 57.105 42.857 4.29 0.00 0.00 3.69
1942 4910 7.126398 GTCGCATATGTTTCTCCTATGAAAAC 58.874 38.462 4.29 0.00 37.63 2.43
1949 4917 3.498927 TCTCCTATGAAAACCGACGAC 57.501 47.619 0.00 0.00 0.00 4.34
1981 4949 3.259902 GACTCCAGCCTACGGTTAAAAG 58.740 50.000 0.00 0.00 0.00 2.27
2000 4968 4.510038 AAGCAACCAACATGTCAAGATC 57.490 40.909 0.00 0.00 0.00 2.75
2001 4969 3.759581 AGCAACCAACATGTCAAGATCT 58.240 40.909 0.00 0.00 0.00 2.75
2002 4970 4.910195 AGCAACCAACATGTCAAGATCTA 58.090 39.130 0.00 0.00 0.00 1.98
2003 4971 5.316167 AGCAACCAACATGTCAAGATCTAA 58.684 37.500 0.00 0.00 0.00 2.10
2004 4972 5.413833 AGCAACCAACATGTCAAGATCTAAG 59.586 40.000 0.00 0.00 0.00 2.18
2005 4973 5.392380 GCAACCAACATGTCAAGATCTAAGG 60.392 44.000 0.00 0.00 0.00 2.69
2006 4974 4.265073 ACCAACATGTCAAGATCTAAGGC 58.735 43.478 0.00 0.00 0.00 4.35
2007 4975 3.629398 CCAACATGTCAAGATCTAAGGCC 59.371 47.826 0.00 0.00 0.00 5.19
2008 4976 3.567478 ACATGTCAAGATCTAAGGCCC 57.433 47.619 0.00 0.00 0.00 5.80
2009 4977 3.118531 ACATGTCAAGATCTAAGGCCCT 58.881 45.455 0.00 0.00 0.00 5.19
2010 4978 3.118112 ACATGTCAAGATCTAAGGCCCTG 60.118 47.826 0.00 0.00 0.00 4.45
2011 4979 2.551270 TGTCAAGATCTAAGGCCCTGT 58.449 47.619 0.00 0.00 0.00 4.00
2012 4980 2.912956 TGTCAAGATCTAAGGCCCTGTT 59.087 45.455 0.00 0.00 0.00 3.16
2013 4981 3.055094 TGTCAAGATCTAAGGCCCTGTTC 60.055 47.826 0.00 0.00 0.00 3.18
2014 4982 2.168521 TCAAGATCTAAGGCCCTGTTCG 59.831 50.000 0.00 0.00 0.00 3.95
2015 4983 1.123928 AGATCTAAGGCCCTGTTCGG 58.876 55.000 0.00 0.00 0.00 4.30
2016 4984 1.120530 GATCTAAGGCCCTGTTCGGA 58.879 55.000 0.00 0.00 33.16 4.55
2017 4985 1.694696 GATCTAAGGCCCTGTTCGGAT 59.305 52.381 0.00 0.00 33.16 4.18
2018 4986 2.464796 TCTAAGGCCCTGTTCGGATA 57.535 50.000 0.00 0.00 33.16 2.59
2019 4987 2.972348 TCTAAGGCCCTGTTCGGATAT 58.028 47.619 0.00 0.00 33.16 1.63
2020 4988 2.897969 TCTAAGGCCCTGTTCGGATATC 59.102 50.000 0.00 0.00 33.16 1.63
2021 4989 0.765510 AAGGCCCTGTTCGGATATCC 59.234 55.000 12.14 12.14 33.16 2.59
2022 4990 0.399949 AGGCCCTGTTCGGATATCCA 60.400 55.000 21.70 6.20 35.14 3.41
2023 4991 0.250338 GGCCCTGTTCGGATATCCAC 60.250 60.000 21.70 13.22 35.14 4.02
2024 4992 0.250338 GCCCTGTTCGGATATCCACC 60.250 60.000 21.70 8.72 35.14 4.61
2025 4993 1.128200 CCCTGTTCGGATATCCACCA 58.872 55.000 21.70 12.60 35.14 4.17
2026 4994 1.070758 CCCTGTTCGGATATCCACCAG 59.929 57.143 21.70 19.94 35.14 4.00
2027 4995 2.039418 CCTGTTCGGATATCCACCAGA 58.961 52.381 23.90 11.81 35.14 3.86
2028 4996 2.634940 CCTGTTCGGATATCCACCAGAT 59.365 50.000 23.90 0.00 35.12 2.90
2029 4997 3.306364 CCTGTTCGGATATCCACCAGATC 60.306 52.174 23.90 13.07 33.41 2.75
2030 4998 2.632996 TGTTCGGATATCCACCAGATCC 59.367 50.000 21.70 5.39 36.33 3.36
2033 5001 2.751166 GGATATCCACCAGATCCGTG 57.249 55.000 17.34 3.97 36.33 4.94
2041 5009 3.819564 CACCAGATCCGTGGAATTAGA 57.180 47.619 7.95 0.00 40.44 2.10
2042 5010 4.137116 CACCAGATCCGTGGAATTAGAA 57.863 45.455 7.95 0.00 40.44 2.10
2043 5011 4.122776 CACCAGATCCGTGGAATTAGAAG 58.877 47.826 7.95 0.00 40.44 2.85
2044 5012 4.030913 ACCAGATCCGTGGAATTAGAAGA 58.969 43.478 7.95 0.00 40.44 2.87
2045 5013 4.100189 ACCAGATCCGTGGAATTAGAAGAG 59.900 45.833 7.95 0.00 40.44 2.85
2046 5014 4.100189 CCAGATCCGTGGAATTAGAAGAGT 59.900 45.833 0.00 0.00 40.44 3.24
2047 5015 5.395768 CCAGATCCGTGGAATTAGAAGAGTT 60.396 44.000 0.00 0.00 40.44 3.01
2048 5016 5.521735 CAGATCCGTGGAATTAGAAGAGTTG 59.478 44.000 0.00 0.00 0.00 3.16
2049 5017 4.884668 TCCGTGGAATTAGAAGAGTTGT 57.115 40.909 0.00 0.00 0.00 3.32
2050 5018 4.566004 TCCGTGGAATTAGAAGAGTTGTG 58.434 43.478 0.00 0.00 0.00 3.33
2051 5019 3.684788 CCGTGGAATTAGAAGAGTTGTGG 59.315 47.826 0.00 0.00 0.00 4.17
2052 5020 4.562757 CCGTGGAATTAGAAGAGTTGTGGA 60.563 45.833 0.00 0.00 0.00 4.02
2053 5021 4.627467 CGTGGAATTAGAAGAGTTGTGGAG 59.373 45.833 0.00 0.00 0.00 3.86
2054 5022 4.393371 GTGGAATTAGAAGAGTTGTGGAGC 59.607 45.833 0.00 0.00 0.00 4.70
2055 5023 4.041567 TGGAATTAGAAGAGTTGTGGAGCA 59.958 41.667 0.00 0.00 0.00 4.26
2056 5024 4.393371 GGAATTAGAAGAGTTGTGGAGCAC 59.607 45.833 0.00 0.00 34.56 4.40
2057 5025 3.402628 TTAGAAGAGTTGTGGAGCACC 57.597 47.619 0.00 0.00 32.73 5.01
2058 5026 1.428869 AGAAGAGTTGTGGAGCACCT 58.571 50.000 0.71 0.00 37.04 4.00
2059 5027 2.609747 AGAAGAGTTGTGGAGCACCTA 58.390 47.619 0.71 0.00 37.04 3.08
2060 5028 2.972713 AGAAGAGTTGTGGAGCACCTAA 59.027 45.455 0.71 0.00 37.04 2.69
2061 5029 3.584848 AGAAGAGTTGTGGAGCACCTAAT 59.415 43.478 0.71 0.00 37.04 1.73
2062 5030 4.042187 AGAAGAGTTGTGGAGCACCTAATT 59.958 41.667 0.71 0.00 37.04 1.40
2063 5031 4.373156 AGAGTTGTGGAGCACCTAATTT 57.627 40.909 0.71 0.00 37.04 1.82
2064 5032 4.074970 AGAGTTGTGGAGCACCTAATTTG 58.925 43.478 0.71 0.00 37.04 2.32
2065 5033 2.558359 AGTTGTGGAGCACCTAATTTGC 59.442 45.455 0.71 0.00 40.52 3.68
2066 5034 2.284754 TGTGGAGCACCTAATTTGCA 57.715 45.000 0.71 0.00 42.83 4.08
2067 5035 2.161855 TGTGGAGCACCTAATTTGCAG 58.838 47.619 0.71 0.00 42.83 4.41
2068 5036 1.135286 GTGGAGCACCTAATTTGCAGC 60.135 52.381 0.71 0.00 42.83 5.25
2069 5037 1.272092 TGGAGCACCTAATTTGCAGCT 60.272 47.619 0.71 4.09 42.83 4.24
2070 5038 1.403323 GGAGCACCTAATTTGCAGCTC 59.597 52.381 17.15 17.15 45.65 4.09
2071 5039 1.403323 GAGCACCTAATTTGCAGCTCC 59.597 52.381 15.60 0.00 42.83 4.70
2072 5040 1.176527 GCACCTAATTTGCAGCTCCA 58.823 50.000 0.00 0.00 39.93 3.86
2073 5041 1.133790 GCACCTAATTTGCAGCTCCAG 59.866 52.381 0.00 0.00 39.93 3.86
2074 5042 2.440409 CACCTAATTTGCAGCTCCAGT 58.560 47.619 0.00 0.00 0.00 4.00
2075 5043 3.609853 CACCTAATTTGCAGCTCCAGTA 58.390 45.455 0.00 0.00 0.00 2.74
2076 5044 4.202441 CACCTAATTTGCAGCTCCAGTAT 58.798 43.478 0.00 0.00 0.00 2.12
2077 5045 4.641989 CACCTAATTTGCAGCTCCAGTATT 59.358 41.667 0.00 0.00 0.00 1.89
2078 5046 5.126061 CACCTAATTTGCAGCTCCAGTATTT 59.874 40.000 0.00 0.00 0.00 1.40
2079 5047 5.716703 ACCTAATTTGCAGCTCCAGTATTTT 59.283 36.000 0.00 0.00 0.00 1.82
2080 5048 6.889722 ACCTAATTTGCAGCTCCAGTATTTTA 59.110 34.615 0.00 0.00 0.00 1.52
2081 5049 7.067494 ACCTAATTTGCAGCTCCAGTATTTTAG 59.933 37.037 0.00 0.00 0.00 1.85
2082 5050 4.701956 TTTGCAGCTCCAGTATTTTAGC 57.298 40.909 0.00 0.00 35.16 3.09
2083 5051 2.643551 TGCAGCTCCAGTATTTTAGCC 58.356 47.619 0.00 0.00 35.54 3.93
2084 5052 2.239654 TGCAGCTCCAGTATTTTAGCCT 59.760 45.455 0.00 0.00 35.54 4.58
2085 5053 3.454447 TGCAGCTCCAGTATTTTAGCCTA 59.546 43.478 0.00 0.00 35.54 3.93
2086 5054 3.810386 GCAGCTCCAGTATTTTAGCCTAC 59.190 47.826 0.00 0.00 35.54 3.18
2087 5055 4.683400 GCAGCTCCAGTATTTTAGCCTACA 60.683 45.833 0.00 0.00 35.54 2.74
2088 5056 5.428253 CAGCTCCAGTATTTTAGCCTACAA 58.572 41.667 0.00 0.00 35.54 2.41
2089 5057 5.294552 CAGCTCCAGTATTTTAGCCTACAAC 59.705 44.000 0.00 0.00 35.54 3.32
2090 5058 5.189934 AGCTCCAGTATTTTAGCCTACAACT 59.810 40.000 0.00 0.00 35.54 3.16
2091 5059 5.524281 GCTCCAGTATTTTAGCCTACAACTC 59.476 44.000 0.00 0.00 0.00 3.01
2092 5060 5.985911 TCCAGTATTTTAGCCTACAACTCC 58.014 41.667 0.00 0.00 0.00 3.85
2093 5061 4.809426 CCAGTATTTTAGCCTACAACTCCG 59.191 45.833 0.00 0.00 0.00 4.63
2094 5062 4.270325 CAGTATTTTAGCCTACAACTCCGC 59.730 45.833 0.00 0.00 0.00 5.54
2095 5063 2.103537 TTTTAGCCTACAACTCCGCC 57.896 50.000 0.00 0.00 0.00 6.13
2096 5064 0.108520 TTTAGCCTACAACTCCGCCG 60.109 55.000 0.00 0.00 0.00 6.46
2097 5065 1.952102 TTAGCCTACAACTCCGCCGG 61.952 60.000 0.00 0.00 0.00 6.13
2099 5067 3.771160 CCTACAACTCCGCCGGCT 61.771 66.667 26.68 6.03 0.00 5.52
2100 5068 2.202756 CTACAACTCCGCCGGCTC 60.203 66.667 26.68 0.00 0.00 4.70
2101 5069 3.718210 CTACAACTCCGCCGGCTCC 62.718 68.421 26.68 0.00 0.00 4.70
2120 5088 3.522731 CGGAGCCGAGTCTGGGAG 61.523 72.222 4.84 0.00 42.83 4.30
2121 5089 3.844090 GGAGCCGAGTCTGGGAGC 61.844 72.222 4.84 0.00 0.00 4.70
2122 5090 4.200283 GAGCCGAGTCTGGGAGCG 62.200 72.222 4.84 0.00 0.00 5.03
2125 5093 3.522731 CCGAGTCTGGGAGCGGAG 61.523 72.222 0.00 0.00 46.29 4.63
2126 5094 3.522731 CGAGTCTGGGAGCGGAGG 61.523 72.222 0.00 0.00 0.00 4.30
2127 5095 3.151022 GAGTCTGGGAGCGGAGGG 61.151 72.222 0.00 0.00 0.00 4.30
2128 5096 3.663815 GAGTCTGGGAGCGGAGGGA 62.664 68.421 0.00 0.00 0.00 4.20
2129 5097 3.462678 GTCTGGGAGCGGAGGGAC 61.463 72.222 0.00 0.00 0.00 4.46
2141 5109 2.606826 AGGGACTCCGAACACCCC 60.607 66.667 0.00 0.00 42.97 4.95
2174 5142 1.073763 TGGTTTCTGGTCCTGGTCATG 59.926 52.381 0.00 0.00 0.00 3.07
2215 5183 2.206750 CGGTCCAACAAAGAGACGAAA 58.793 47.619 0.00 0.00 0.00 3.46
2223 5191 5.008217 CCAACAAAGAGACGAAATTGTGGTA 59.992 40.000 0.00 0.00 36.23 3.25
2240 5209 4.283978 TGTGGTATCTTTCTTTCCGGTACA 59.716 41.667 0.00 0.00 0.00 2.90
2323 5310 2.419297 CCGAAGTAGATGAGCAGGCTTT 60.419 50.000 0.00 0.00 0.00 3.51
2351 5338 2.874849 ACGCAACAAACCAAAGTTCAG 58.125 42.857 0.00 0.00 34.19 3.02
2354 5341 3.186909 GCAACAAACCAAAGTTCAGTCC 58.813 45.455 0.00 0.00 34.19 3.85
2367 5354 3.894427 AGTTCAGTCCATATGCTCGAGAT 59.106 43.478 18.75 9.48 0.00 2.75
2402 5389 4.815308 AGATTAGCAGCATCACAATCAGAC 59.185 41.667 0.00 0.00 0.00 3.51
2444 5431 4.764823 GGGTGACATTACCTGAAATTGTCA 59.235 41.667 0.24 0.24 40.66 3.58
2451 5438 6.538742 ACATTACCTGAAATTGTCATACCTCG 59.461 38.462 0.00 0.00 35.07 4.63
2488 5477 2.290896 TGGCCTTCTTTATGTCACCCTG 60.291 50.000 3.32 0.00 0.00 4.45
2506 5495 3.820467 CCCTGCATTACAACAAGAGAACA 59.180 43.478 0.00 0.00 0.00 3.18
2548 5545 2.045045 GTGCATGGGCTGGCTACA 60.045 61.111 0.00 0.00 41.91 2.74
2590 5588 2.656002 AGCCAGACTAGCAGATTCGTA 58.344 47.619 0.00 0.00 0.00 3.43
2604 5602 3.381908 AGATTCGTATGGAGGTGTGTCTC 59.618 47.826 0.00 0.00 0.00 3.36
2605 5603 2.509166 TCGTATGGAGGTGTGTCTCT 57.491 50.000 0.00 0.00 34.39 3.10
2616 5614 1.813178 GTGTGTCTCTGTCGGATCTCA 59.187 52.381 0.00 0.00 0.00 3.27
2626 5624 2.959030 TGTCGGATCTCACAGGATTAGG 59.041 50.000 0.00 0.00 0.00 2.69
2633 5631 0.535335 TCACAGGATTAGGTCGGTGC 59.465 55.000 0.00 0.00 34.59 5.01
2639 5637 0.824759 GATTAGGTCGGTGCTGGTCT 59.175 55.000 0.00 0.00 0.00 3.85
2646 5644 2.358737 GGTGCTGGTCTTCGGTGG 60.359 66.667 0.00 0.00 0.00 4.61
2671 5669 1.730612 GTTTGGATCCGGTCTTCGTTC 59.269 52.381 7.39 0.00 37.11 3.95
2676 5674 0.450983 ATCCGGTCTTCGTTCGTCTC 59.549 55.000 0.00 0.00 37.11 3.36
2679 5677 1.154073 GGTCTTCGTTCGTCTCCGG 60.154 63.158 0.00 0.00 33.95 5.14
2680 5678 1.800713 GTCTTCGTTCGTCTCCGGC 60.801 63.158 0.00 0.00 33.95 6.13
2683 5681 3.277211 TTCGTTCGTCTCCGGCTGG 62.277 63.158 4.71 4.71 33.95 4.85
2692 5690 4.218856 TCCGGCTGGGAGTTTACA 57.781 55.556 12.87 0.00 40.94 2.41
2694 5692 1.078426 CCGGCTGGGAGTTTACAGG 60.078 63.158 2.57 0.00 38.47 4.00
2705 5703 4.700692 GGGAGTTTACAGGTTTGATCCTTC 59.299 45.833 0.00 0.00 35.37 3.46
2706 5704 4.700692 GGAGTTTACAGGTTTGATCCTTCC 59.299 45.833 0.00 0.00 35.37 3.46
2707 5705 4.324267 AGTTTACAGGTTTGATCCTTCCG 58.676 43.478 0.00 0.00 35.37 4.30
2708 5706 4.041198 AGTTTACAGGTTTGATCCTTCCGA 59.959 41.667 0.00 0.00 35.37 4.55
2709 5707 4.837093 TTACAGGTTTGATCCTTCCGAT 57.163 40.909 0.00 0.00 35.37 4.18
2710 5708 3.268023 ACAGGTTTGATCCTTCCGATC 57.732 47.619 0.00 0.00 46.70 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.500375 GGATCCACATGGCTAGCATTTTTC 60.500 45.833 18.24 0.00 34.44 2.29
37 38 3.385755 GGATCCACATGGCTAGCATTTTT 59.614 43.478 18.24 0.00 34.44 1.94
70 71 3.002791 CCGTAAGTACACGTCAGGTCTA 58.997 50.000 5.19 0.00 40.31 2.59
79 80 2.138596 ACAACCACCGTAAGTACACG 57.861 50.000 0.00 0.00 41.59 4.49
103 112 6.542735 TCTTAGTATCGCATCAAGAGTGTACT 59.457 38.462 0.00 0.00 0.00 2.73
104 113 6.726230 TCTTAGTATCGCATCAAGAGTGTAC 58.274 40.000 0.00 0.00 0.00 2.90
105 114 6.513556 GCTCTTAGTATCGCATCAAGAGTGTA 60.514 42.308 10.39 0.00 42.63 2.90
106 115 5.734786 GCTCTTAGTATCGCATCAAGAGTGT 60.735 44.000 10.39 0.00 42.63 3.55
107 116 4.679197 GCTCTTAGTATCGCATCAAGAGTG 59.321 45.833 10.39 0.00 42.63 3.51
108 117 4.339530 TGCTCTTAGTATCGCATCAAGAGT 59.660 41.667 10.39 0.00 42.63 3.24
109 118 4.864633 TGCTCTTAGTATCGCATCAAGAG 58.135 43.478 5.49 5.49 43.23 2.85
252 264 1.557099 TTCCAGTCCGTATGCAGTCT 58.443 50.000 0.00 0.00 0.00 3.24
288 300 9.615779 GTTCGAATGAATATAGACACGTTTTAC 57.384 33.333 0.00 0.00 36.29 2.01
295 307 5.526115 TCCGGTTCGAATGAATATAGACAC 58.474 41.667 0.00 0.00 36.29 3.67
519 569 0.321564 TGATTGACTTGGCTGTCCGG 60.322 55.000 0.00 0.00 36.21 5.14
536 586 3.390135 CTCGTTGCTCTTGGTTAGTTGA 58.610 45.455 0.00 0.00 0.00 3.18
564 614 6.157994 AGCATATTAGGTCTGGGAAACACTAA 59.842 38.462 0.00 0.00 0.00 2.24
585 3507 4.338012 TGATTGAACACTGGAATGAGCAT 58.662 39.130 0.00 0.00 0.00 3.79
588 3510 6.505044 TCAATGATTGAACACTGGAATGAG 57.495 37.500 5.21 0.00 36.59 2.90
598 3520 3.758023 AGCGGTTGATCAATGATTGAACA 59.242 39.130 12.36 12.82 43.95 3.18
623 3545 5.733373 GCAAGTCCGTTTTTCTTGTCTCATT 60.733 40.000 0.00 0.00 40.14 2.57
628 3550 3.692791 AGCAAGTCCGTTTTTCTTGTC 57.307 42.857 0.00 0.00 40.14 3.18
639 3561 9.482627 AATATTCTTTTCTCTATAGCAAGTCCG 57.517 33.333 0.00 0.00 0.00 4.79
650 3572 8.879759 CGGTTACAAGCAATATTCTTTTCTCTA 58.120 33.333 0.00 0.00 0.00 2.43
657 3579 6.995511 TTAGCGGTTACAAGCAATATTCTT 57.004 33.333 0.00 0.00 35.48 2.52
658 3580 7.568199 AATTAGCGGTTACAAGCAATATTCT 57.432 32.000 0.00 0.00 35.48 2.40
675 3597 6.929049 TCACTCCATTTGTCCTATAATTAGCG 59.071 38.462 0.00 0.00 0.00 4.26
684 3606 7.685481 TGTTAATTCTCACTCCATTTGTCCTA 58.315 34.615 0.00 0.00 0.00 2.94
716 3638 3.119459 TCGCTCACTTCACCTCTCATTAC 60.119 47.826 0.00 0.00 0.00 1.89
796 3720 0.393537 CCTGTGATTGGAGGGAGCAC 60.394 60.000 0.00 0.00 0.00 4.40
837 3761 1.890876 TTGTGACAAGGGGATGTTCG 58.109 50.000 0.00 0.00 32.57 3.95
887 3811 4.353777 AGCCTCAATTAGTCCACTACTCA 58.646 43.478 0.00 0.00 39.80 3.41
918 3843 1.478654 GGTTCTCTGGCTTGGACCAAA 60.479 52.381 8.59 0.00 39.86 3.28
922 3847 1.981256 TTTGGTTCTCTGGCTTGGAC 58.019 50.000 0.00 0.00 0.00 4.02
1021 3946 3.179939 GCGGCCTTTCGACTCGTC 61.180 66.667 0.00 0.00 0.00 4.20
1023 3948 4.436998 AGGCGGCCTTTCGACTCG 62.437 66.667 17.69 0.00 46.93 4.18
1271 4196 4.785453 CCCGCCTTGTCAGAGCCC 62.785 72.222 0.00 0.00 0.00 5.19
1272 4197 3.553095 AACCCGCCTTGTCAGAGCC 62.553 63.158 0.00 0.00 0.00 4.70
1274 4199 1.738099 CGAACCCGCCTTGTCAGAG 60.738 63.158 0.00 0.00 0.00 3.35
1469 4394 2.025155 AGCAGTAGGACATGTACTCGG 58.975 52.381 15.66 8.42 0.00 4.63
1510 4435 3.558411 GCCATCGCAGACGCTGAC 61.558 66.667 10.46 2.34 42.51 3.51
1820 4788 1.594331 ACGAACAAGTTGCTCCCTTC 58.406 50.000 1.81 0.00 0.00 3.46
1832 4800 0.808125 AACAGCAGCACAACGAACAA 59.192 45.000 0.00 0.00 0.00 2.83
1877 4845 5.593010 AGAGAGCGGTAGTCAATCAAATAC 58.407 41.667 0.00 0.00 0.00 1.89
1878 4846 5.221263 GGAGAGAGCGGTAGTCAATCAAATA 60.221 44.000 0.00 0.00 0.00 1.40
1879 4847 4.442192 GGAGAGAGCGGTAGTCAATCAAAT 60.442 45.833 0.00 0.00 0.00 2.32
1934 4902 1.733389 GCCTCGTCGTCGGTTTTCATA 60.733 52.381 1.55 0.00 37.69 2.15
1949 4917 1.153939 CTGGAGTCAACGAGCCTCG 60.154 63.158 13.52 13.52 46.93 4.63
1981 4949 5.392380 CCTTAGATCTTGACATGTTGGTTGC 60.392 44.000 0.00 0.00 0.00 4.17
2000 4968 2.028020 GGATATCCGAACAGGGCCTTAG 60.028 54.545 1.32 0.00 41.52 2.18
2001 4969 1.975680 GGATATCCGAACAGGGCCTTA 59.024 52.381 1.32 0.00 41.52 2.69
2002 4970 0.765510 GGATATCCGAACAGGGCCTT 59.234 55.000 1.32 0.00 41.52 4.35
2003 4971 0.399949 TGGATATCCGAACAGGGCCT 60.400 55.000 17.04 0.00 41.52 5.19
2004 4972 0.250338 GTGGATATCCGAACAGGGCC 60.250 60.000 17.04 0.00 41.52 5.80
2005 4973 0.250338 GGTGGATATCCGAACAGGGC 60.250 60.000 17.04 0.15 41.52 5.19
2006 4974 1.070758 CTGGTGGATATCCGAACAGGG 59.929 57.143 22.08 7.36 41.52 4.45
2007 4975 2.039418 TCTGGTGGATATCCGAACAGG 58.961 52.381 26.00 14.04 39.43 4.00
2008 4976 3.306364 GGATCTGGTGGATATCCGAACAG 60.306 52.174 23.09 23.09 39.43 3.16
2009 4977 2.632996 GGATCTGGTGGATATCCGAACA 59.367 50.000 17.04 13.21 39.43 3.18
2010 4978 3.320673 GGATCTGGTGGATATCCGAAC 57.679 52.381 17.04 10.20 39.43 3.95
2014 4982 2.751166 CACGGATCTGGTGGATATCC 57.249 55.000 15.39 15.39 36.59 2.59
2021 4989 3.819564 TCTAATTCCACGGATCTGGTG 57.180 47.619 6.47 8.33 32.50 4.17
2022 4990 4.030913 TCTTCTAATTCCACGGATCTGGT 58.969 43.478 6.47 0.00 32.50 4.00
2023 4991 4.100189 ACTCTTCTAATTCCACGGATCTGG 59.900 45.833 6.47 0.00 0.00 3.86
2024 4992 5.269505 ACTCTTCTAATTCCACGGATCTG 57.730 43.478 0.00 0.00 0.00 2.90
2025 4993 5.187967 ACAACTCTTCTAATTCCACGGATCT 59.812 40.000 0.00 0.00 0.00 2.75
2026 4994 5.292101 CACAACTCTTCTAATTCCACGGATC 59.708 44.000 0.00 0.00 0.00 3.36
2027 4995 5.178797 CACAACTCTTCTAATTCCACGGAT 58.821 41.667 0.00 0.00 0.00 4.18
2028 4996 4.562757 CCACAACTCTTCTAATTCCACGGA 60.563 45.833 0.00 0.00 0.00 4.69
2029 4997 3.684788 CCACAACTCTTCTAATTCCACGG 59.315 47.826 0.00 0.00 0.00 4.94
2030 4998 4.566004 TCCACAACTCTTCTAATTCCACG 58.434 43.478 0.00 0.00 0.00 4.94
2031 4999 4.393371 GCTCCACAACTCTTCTAATTCCAC 59.607 45.833 0.00 0.00 0.00 4.02
2032 5000 4.041567 TGCTCCACAACTCTTCTAATTCCA 59.958 41.667 0.00 0.00 0.00 3.53
2033 5001 4.393371 GTGCTCCACAACTCTTCTAATTCC 59.607 45.833 0.00 0.00 34.08 3.01
2034 5002 4.393371 GGTGCTCCACAACTCTTCTAATTC 59.607 45.833 0.00 0.00 35.86 2.17
2035 5003 4.042187 AGGTGCTCCACAACTCTTCTAATT 59.958 41.667 7.70 0.00 45.97 1.40
2036 5004 3.584848 AGGTGCTCCACAACTCTTCTAAT 59.415 43.478 7.70 0.00 45.97 1.73
2037 5005 2.972713 AGGTGCTCCACAACTCTTCTAA 59.027 45.455 7.70 0.00 45.97 2.10
2038 5006 2.609747 AGGTGCTCCACAACTCTTCTA 58.390 47.619 7.70 0.00 45.97 2.10
2039 5007 1.428869 AGGTGCTCCACAACTCTTCT 58.571 50.000 7.70 0.00 45.97 2.85
2040 5008 3.402628 TTAGGTGCTCCACAACTCTTC 57.597 47.619 7.70 0.00 45.97 2.87
2041 5009 4.373156 AATTAGGTGCTCCACAACTCTT 57.627 40.909 7.70 0.00 45.97 2.85
2042 5010 4.074970 CAAATTAGGTGCTCCACAACTCT 58.925 43.478 7.70 0.00 45.97 3.24
2043 5011 3.366374 GCAAATTAGGTGCTCCACAACTC 60.366 47.826 7.70 0.00 45.97 3.01
2045 5013 2.295909 TGCAAATTAGGTGCTCCACAAC 59.704 45.455 7.70 0.00 42.69 3.32
2046 5014 2.557924 CTGCAAATTAGGTGCTCCACAA 59.442 45.455 7.70 0.96 42.69 3.33
2047 5015 2.161855 CTGCAAATTAGGTGCTCCACA 58.838 47.619 7.70 0.00 42.69 4.17
2048 5016 1.135286 GCTGCAAATTAGGTGCTCCAC 60.135 52.381 7.70 0.00 42.69 4.02
2049 5017 1.176527 GCTGCAAATTAGGTGCTCCA 58.823 50.000 7.70 0.00 42.69 3.86
2050 5018 1.403323 GAGCTGCAAATTAGGTGCTCC 59.597 52.381 8.67 0.00 42.69 4.70
2051 5019 1.403323 GGAGCTGCAAATTAGGTGCTC 59.597 52.381 10.85 10.85 44.08 4.26
2052 5020 1.272092 TGGAGCTGCAAATTAGGTGCT 60.272 47.619 5.01 0.00 42.69 4.40
2053 5021 1.133790 CTGGAGCTGCAAATTAGGTGC 59.866 52.381 9.92 0.00 42.55 5.01
2054 5022 2.440409 ACTGGAGCTGCAAATTAGGTG 58.560 47.619 9.92 0.00 0.00 4.00
2055 5023 2.887151 ACTGGAGCTGCAAATTAGGT 57.113 45.000 9.92 0.00 0.00 3.08
2056 5024 5.841957 AAATACTGGAGCTGCAAATTAGG 57.158 39.130 9.92 0.00 0.00 2.69
2057 5025 6.914757 GCTAAAATACTGGAGCTGCAAATTAG 59.085 38.462 9.92 13.26 32.04 1.73
2058 5026 6.183360 GGCTAAAATACTGGAGCTGCAAATTA 60.183 38.462 9.92 1.27 35.23 1.40
2059 5027 5.394553 GGCTAAAATACTGGAGCTGCAAATT 60.395 40.000 9.92 9.36 35.23 1.82
2060 5028 4.098501 GGCTAAAATACTGGAGCTGCAAAT 59.901 41.667 9.92 3.00 35.23 2.32
2061 5029 3.443681 GGCTAAAATACTGGAGCTGCAAA 59.556 43.478 9.92 0.26 35.23 3.68
2062 5030 3.016736 GGCTAAAATACTGGAGCTGCAA 58.983 45.455 9.92 0.00 35.23 4.08
2063 5031 2.239654 AGGCTAAAATACTGGAGCTGCA 59.760 45.455 7.99 7.99 35.23 4.41
2064 5032 2.924421 AGGCTAAAATACTGGAGCTGC 58.076 47.619 0.00 0.00 35.23 5.25
2065 5033 5.023533 TGTAGGCTAAAATACTGGAGCTG 57.976 43.478 0.00 0.00 35.23 4.24
2066 5034 5.189934 AGTTGTAGGCTAAAATACTGGAGCT 59.810 40.000 0.00 0.00 35.23 4.09
2067 5035 5.429130 AGTTGTAGGCTAAAATACTGGAGC 58.571 41.667 0.00 0.00 0.00 4.70
2068 5036 6.049790 GGAGTTGTAGGCTAAAATACTGGAG 58.950 44.000 0.00 0.00 0.00 3.86
2069 5037 5.394883 CGGAGTTGTAGGCTAAAATACTGGA 60.395 44.000 0.00 0.00 0.00 3.86
2070 5038 4.809426 CGGAGTTGTAGGCTAAAATACTGG 59.191 45.833 0.00 0.00 0.00 4.00
2071 5039 4.270325 GCGGAGTTGTAGGCTAAAATACTG 59.730 45.833 0.00 4.70 0.00 2.74
2072 5040 4.439968 GCGGAGTTGTAGGCTAAAATACT 58.560 43.478 0.00 0.00 0.00 2.12
2073 5041 3.558829 GGCGGAGTTGTAGGCTAAAATAC 59.441 47.826 0.00 0.00 0.00 1.89
2074 5042 3.738899 CGGCGGAGTTGTAGGCTAAAATA 60.739 47.826 0.00 0.00 0.00 1.40
2075 5043 2.640184 GGCGGAGTTGTAGGCTAAAAT 58.360 47.619 0.00 0.00 0.00 1.82
2076 5044 1.673626 CGGCGGAGTTGTAGGCTAAAA 60.674 52.381 0.00 0.00 0.00 1.52
2077 5045 0.108520 CGGCGGAGTTGTAGGCTAAA 60.109 55.000 0.00 0.00 0.00 1.85
2078 5046 1.514087 CGGCGGAGTTGTAGGCTAA 59.486 57.895 0.00 0.00 0.00 3.09
2079 5047 2.420568 CCGGCGGAGTTGTAGGCTA 61.421 63.158 24.41 0.00 0.00 3.93
2080 5048 3.771160 CCGGCGGAGTTGTAGGCT 61.771 66.667 24.41 0.00 0.00 4.58
2082 5050 3.718210 GAGCCGGCGGAGTTGTAGG 62.718 68.421 33.44 0.00 0.00 3.18
2083 5051 2.202756 GAGCCGGCGGAGTTGTAG 60.203 66.667 33.44 0.00 0.00 2.74
2084 5052 3.766691 GGAGCCGGCGGAGTTGTA 61.767 66.667 33.44 0.00 0.00 2.41
2103 5071 3.522731 CTCCCAGACTCGGCTCCG 61.523 72.222 1.14 1.14 41.35 4.63
2104 5072 3.844090 GCTCCCAGACTCGGCTCC 61.844 72.222 0.00 0.00 0.00 4.70
2105 5073 4.200283 CGCTCCCAGACTCGGCTC 62.200 72.222 0.00 0.00 0.00 4.70
2108 5076 3.522731 CTCCGCTCCCAGACTCGG 61.523 72.222 0.00 0.00 42.96 4.63
2109 5077 3.522731 CCTCCGCTCCCAGACTCG 61.523 72.222 0.00 0.00 0.00 4.18
2110 5078 3.151022 CCCTCCGCTCCCAGACTC 61.151 72.222 0.00 0.00 0.00 3.36
2111 5079 3.673597 TCCCTCCGCTCCCAGACT 61.674 66.667 0.00 0.00 0.00 3.24
2112 5080 3.462678 GTCCCTCCGCTCCCAGAC 61.463 72.222 0.00 0.00 0.00 3.51
2113 5081 3.663815 GAGTCCCTCCGCTCCCAGA 62.664 68.421 0.00 0.00 0.00 3.86
2114 5082 3.151022 GAGTCCCTCCGCTCCCAG 61.151 72.222 0.00 0.00 0.00 4.45
2115 5083 4.779733 GGAGTCCCTCCGCTCCCA 62.780 72.222 0.00 0.00 44.06 4.37
2122 5090 2.657066 GGGTGTTCGGAGTCCCTCC 61.657 68.421 2.80 0.00 46.44 4.30
2123 5091 2.657066 GGGGTGTTCGGAGTCCCTC 61.657 68.421 2.80 0.00 39.80 4.30
2124 5092 2.606826 GGGGTGTTCGGAGTCCCT 60.607 66.667 2.80 0.00 39.80 4.20
2125 5093 2.810488 TAGGGGGTGTTCGGAGTCCC 62.810 65.000 2.80 5.90 39.22 4.46
2126 5094 0.906282 TTAGGGGGTGTTCGGAGTCC 60.906 60.000 0.00 0.00 0.00 3.85
2127 5095 0.978907 TTTAGGGGGTGTTCGGAGTC 59.021 55.000 0.00 0.00 0.00 3.36
2128 5096 1.665137 ATTTAGGGGGTGTTCGGAGT 58.335 50.000 0.00 0.00 0.00 3.85
2129 5097 2.640184 GAATTTAGGGGGTGTTCGGAG 58.360 52.381 0.00 0.00 0.00 4.63
2130 5098 1.065998 CGAATTTAGGGGGTGTTCGGA 60.066 52.381 0.00 0.00 38.30 4.55
2131 5099 1.065998 TCGAATTTAGGGGGTGTTCGG 60.066 52.381 6.05 0.00 41.25 4.30
2132 5100 2.389962 TCGAATTTAGGGGGTGTTCG 57.610 50.000 0.00 0.00 42.00 3.95
2133 5101 4.142249 CCATTTCGAATTTAGGGGGTGTTC 60.142 45.833 0.00 0.00 0.00 3.18
2134 5102 3.767131 CCATTTCGAATTTAGGGGGTGTT 59.233 43.478 0.00 0.00 0.00 3.32
2135 5103 3.245479 ACCATTTCGAATTTAGGGGGTGT 60.245 43.478 0.00 0.00 0.00 4.16
2136 5104 3.361786 ACCATTTCGAATTTAGGGGGTG 58.638 45.455 0.00 0.00 0.00 4.61
2137 5105 3.750501 ACCATTTCGAATTTAGGGGGT 57.249 42.857 0.00 0.00 0.00 4.95
2138 5106 4.709886 AGAAACCATTTCGAATTTAGGGGG 59.290 41.667 0.00 0.00 44.29 5.40
2139 5107 5.394115 CCAGAAACCATTTCGAATTTAGGGG 60.394 44.000 0.00 0.00 44.29 4.79
2140 5108 5.185056 ACCAGAAACCATTTCGAATTTAGGG 59.815 40.000 0.00 0.00 44.29 3.53
2141 5109 6.267496 ACCAGAAACCATTTCGAATTTAGG 57.733 37.500 0.00 5.22 44.29 2.69
2174 5142 0.872388 GGACGTGAACACAATGGTCC 59.128 55.000 0.00 11.63 31.76 4.46
2215 5183 4.918588 ACCGGAAAGAAAGATACCACAAT 58.081 39.130 9.46 0.00 0.00 2.71
2223 5191 5.591067 TGTTGTTTGTACCGGAAAGAAAGAT 59.409 36.000 9.46 0.00 0.00 2.40
2351 5338 2.445565 TGCATCTCGAGCATATGGAC 57.554 50.000 7.81 0.00 37.02 4.02
2402 5389 6.421801 GTCACCCTGTTCTTTCAAATGAATTG 59.578 38.462 0.00 0.00 40.58 2.32
2444 5431 9.601217 GCCAACAATATATTATCTTCGAGGTAT 57.399 33.333 0.00 0.00 0.00 2.73
2463 5450 3.572255 GGTGACATAAAGAAGGCCAACAA 59.428 43.478 5.01 0.00 0.00 2.83
2488 5477 7.809331 TCATCAAATGTTCTCTTGTTGTAATGC 59.191 33.333 0.00 0.00 0.00 3.56
2506 5495 5.339200 CCTGGTAGTGGTAAGGTCATCAAAT 60.339 44.000 0.00 0.00 0.00 2.32
2590 5588 0.891373 CGACAGAGACACACCTCCAT 59.109 55.000 0.00 0.00 33.76 3.41
2604 5602 3.005261 CCTAATCCTGTGAGATCCGACAG 59.995 52.174 12.76 12.76 39.51 3.51
2605 5603 2.959030 CCTAATCCTGTGAGATCCGACA 59.041 50.000 0.00 0.00 0.00 4.35
2616 5614 0.537188 CAGCACCGACCTAATCCTGT 59.463 55.000 0.00 0.00 0.00 4.00
2626 5624 2.432628 CCGAAGACCAGCACCGAC 60.433 66.667 0.00 0.00 0.00 4.79
2633 5631 0.898320 ACAGATCCACCGAAGACCAG 59.102 55.000 0.00 0.00 0.00 4.00
2639 5637 2.985896 GATCCAAACAGATCCACCGAA 58.014 47.619 0.00 0.00 37.31 4.30
2646 5644 2.990066 AGACCGGATCCAAACAGATC 57.010 50.000 9.46 0.00 41.69 2.75
2676 5674 1.078426 CCTGTAAACTCCCAGCCGG 60.078 63.158 0.00 0.00 0.00 6.13
2679 5677 2.858745 TCAAACCTGTAAACTCCCAGC 58.141 47.619 0.00 0.00 0.00 4.85
2680 5678 4.010349 GGATCAAACCTGTAAACTCCCAG 58.990 47.826 0.00 0.00 0.00 4.45
2683 5681 4.700692 GGAAGGATCAAACCTGTAAACTCC 59.299 45.833 0.00 0.00 40.49 3.85


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

AutoCloner maintained by Alex Coulton.