Multiple sequence alignment - TraesCS4A01G040100

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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 TraesCS4A01G040100 chr4A 100.000 2822 0 0 1 2822 32715859 32713038 0.000000e+00 5212.0
1 TraesCS4A01G040100 chr4A 89.066 942 79 12 1897 2822 423435215 423434282 0.000000e+00 1147.0
2 TraesCS4A01G040100 chr4A 85.745 470 57 6 289 754 591292759 591293222 3.270000e-134 488.0
3 TraesCS4A01G040100 chr4A 85.532 470 58 6 289 754 591674029 591674492 1.520000e-132 483.0
4 TraesCS4A01G040100 chr4A 85.350 471 59 7 289 755 591346525 591346989 1.970000e-131 479.0
5 TraesCS4A01G040100 chr4D 91.702 952 69 7 901 1843 431674128 431673178 0.000000e+00 1312.0
6 TraesCS4A01G040100 chr4D 91.474 950 73 6 901 1843 431555001 431554053 0.000000e+00 1299.0
7 TraesCS4A01G040100 chr4D 91.149 949 76 8 901 1843 431722331 431721385 0.000000e+00 1280.0
8 TraesCS4A01G040100 chr4D 89.990 959 74 9 901 1843 431620766 431619814 0.000000e+00 1219.0
9 TraesCS4A01G040100 chr4D 90.421 689 48 11 1897 2574 397690021 397689340 0.000000e+00 891.0
10 TraesCS4A01G040100 chr4D 80.845 1065 163 21 783 1827 10828993 10830036 0.000000e+00 798.0
11 TraesCS4A01G040100 chr4D 93.290 462 30 1 146 607 431556638 431556178 0.000000e+00 680.0
12 TraesCS4A01G040100 chr4D 93.074 462 32 0 146 607 431735304 431734843 0.000000e+00 676.0
13 TraesCS4A01G040100 chr4D 91.991 462 36 1 146 607 431622403 431621943 0.000000e+00 647.0
14 TraesCS4A01G040100 chr4D 92.446 278 17 4 597 871 431674402 431674126 7.330000e-106 394.0
15 TraesCS4A01G040100 chr4D 92.086 278 18 4 597 871 431621040 431620764 3.410000e-104 388.0
16 TraesCS4A01G040100 chr4D 91.053 190 13 4 685 871 431722517 431722329 1.300000e-63 254.0
17 TraesCS4A01G040100 chr4B 90.909 946 70 8 1890 2822 465050050 465050992 0.000000e+00 1256.0
18 TraesCS4A01G040100 chr4B 80.228 1052 174 23 752 1795 21158446 21157421 0.000000e+00 760.0
19 TraesCS4A01G040100 chr4B 94.872 39 2 0 1843 1881 465049832 465049870 8.440000e-06 62.1
20 TraesCS4A01G040100 chr7D 88.641 942 83 14 1897 2822 135344756 135343823 0.000000e+00 1125.0
21 TraesCS4A01G040100 chr7D 88.658 723 57 13 1890 2596 88477410 88478123 0.000000e+00 857.0
22 TraesCS4A01G040100 chrUn 88.614 931 93 9 901 1828 256114758 256115678 0.000000e+00 1120.0
23 TraesCS4A01G040100 chrUn 88.614 931 93 9 901 1828 390478579 390479499 0.000000e+00 1120.0
24 TraesCS4A01G040100 chrUn 91.621 728 47 6 146 870 256114043 256114759 0.000000e+00 994.0
25 TraesCS4A01G040100 chrUn 91.883 308 17 4 2522 2822 273931102 273930796 9.350000e-115 424.0
26 TraesCS4A01G040100 chrUn 91.883 308 17 4 2522 2822 295227222 295227528 9.350000e-115 424.0
27 TraesCS4A01G040100 chrUn 90.060 332 21 4 541 870 390478259 390478580 1.210000e-113 420.0
28 TraesCS4A01G040100 chrUn 91.558 308 18 4 2522 2822 293175879 293175573 4.350000e-113 418.0
29 TraesCS4A01G040100 chr5B 88.685 928 92 9 904 1828 660880245 660879328 0.000000e+00 1120.0
30 TraesCS4A01G040100 chr5B 88.254 928 96 7 904 1828 660926194 660925277 0.000000e+00 1098.0
31 TraesCS4A01G040100 chr5B 91.621 728 47 6 146 870 660880963 660880247 0.000000e+00 994.0
32 TraesCS4A01G040100 chr5B 91.621 728 47 6 146 870 660926912 660926196 0.000000e+00 994.0
33 TraesCS4A01G040100 chr5D 87.513 945 88 19 1890 2822 517562928 517562002 0.000000e+00 1064.0
34 TraesCS4A01G040100 chr7A 88.811 715 63 11 2119 2819 23159799 23160510 0.000000e+00 861.0
35 TraesCS4A01G040100 chr3D 88.676 627 56 8 1890 2504 575671465 575670842 0.000000e+00 750.0
36 TraesCS4A01G040100 chr6D 87.660 624 60 14 1890 2501 59178414 59179032 0.000000e+00 710.0
37 TraesCS4A01G040100 chr1D 87.540 626 55 16 1890 2501 475483207 475483823 0.000000e+00 702.0
38 TraesCS4A01G040100 chr2D 88.631 431 37 6 1891 2316 24551105 24551528 5.390000e-142 514.0
39 TraesCS4A01G040100 chr2D 87.980 391 43 4 2431 2819 24551562 24551950 2.560000e-125 459.0
40 TraesCS4A01G040100 chr7B 83.772 228 31 5 1894 2116 555317143 555317369 7.920000e-51 211.0


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 TraesCS4A01G040100 chr4A 32713038 32715859 2821 True 5212.000000 5212 100.000000 1 2822 1 chr4A.!!$R1 2821
1 TraesCS4A01G040100 chr4A 423434282 423435215 933 True 1147.000000 1147 89.066000 1897 2822 1 chr4A.!!$R2 925
2 TraesCS4A01G040100 chr4D 431554053 431556638 2585 True 989.500000 1299 92.382000 146 1843 2 chr4D.!!$R3 1697
3 TraesCS4A01G040100 chr4D 397689340 397690021 681 True 891.000000 891 90.421000 1897 2574 1 chr4D.!!$R1 677
4 TraesCS4A01G040100 chr4D 431673178 431674402 1224 True 853.000000 1312 92.074000 597 1843 2 chr4D.!!$R5 1246
5 TraesCS4A01G040100 chr4D 10828993 10830036 1043 False 798.000000 798 80.845000 783 1827 1 chr4D.!!$F1 1044
6 TraesCS4A01G040100 chr4D 431721385 431722517 1132 True 767.000000 1280 91.101000 685 1843 2 chr4D.!!$R6 1158
7 TraesCS4A01G040100 chr4D 431619814 431622403 2589 True 751.333333 1219 91.355667 146 1843 3 chr4D.!!$R4 1697
8 TraesCS4A01G040100 chr4B 21157421 21158446 1025 True 760.000000 760 80.228000 752 1795 1 chr4B.!!$R1 1043
9 TraesCS4A01G040100 chr4B 465049832 465050992 1160 False 659.050000 1256 92.890500 1843 2822 2 chr4B.!!$F1 979
10 TraesCS4A01G040100 chr7D 135343823 135344756 933 True 1125.000000 1125 88.641000 1897 2822 1 chr7D.!!$R1 925
11 TraesCS4A01G040100 chr7D 88477410 88478123 713 False 857.000000 857 88.658000 1890 2596 1 chr7D.!!$F1 706
12 TraesCS4A01G040100 chrUn 256114043 256115678 1635 False 1057.000000 1120 90.117500 146 1828 2 chrUn.!!$F2 1682
13 TraesCS4A01G040100 chrUn 390478259 390479499 1240 False 770.000000 1120 89.337000 541 1828 2 chrUn.!!$F3 1287
14 TraesCS4A01G040100 chr5B 660879328 660880963 1635 True 1057.000000 1120 90.153000 146 1828 2 chr5B.!!$R1 1682
15 TraesCS4A01G040100 chr5B 660925277 660926912 1635 True 1046.000000 1098 89.937500 146 1828 2 chr5B.!!$R2 1682
16 TraesCS4A01G040100 chr5D 517562002 517562928 926 True 1064.000000 1064 87.513000 1890 2822 1 chr5D.!!$R1 932
17 TraesCS4A01G040100 chr7A 23159799 23160510 711 False 861.000000 861 88.811000 2119 2819 1 chr7A.!!$F1 700
18 TraesCS4A01G040100 chr3D 575670842 575671465 623 True 750.000000 750 88.676000 1890 2504 1 chr3D.!!$R1 614
19 TraesCS4A01G040100 chr6D 59178414 59179032 618 False 710.000000 710 87.660000 1890 2501 1 chr6D.!!$F1 611
20 TraesCS4A01G040100 chr1D 475483207 475483823 616 False 702.000000 702 87.540000 1890 2501 1 chr1D.!!$F1 611
21 TraesCS4A01G040100 chr2D 24551105 24551950 845 False 486.500000 514 88.305500 1891 2819 2 chr2D.!!$F1 928

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
29 30 0.036875 ACTCACCTAGGCAAACCAGC 59.963 55.0 9.3 0.0 39.06 4.85 F
883 1816 0.106708 GGGCATGGTAATCTCTGCGA 59.893 55.0 0.0 0.0 35.47 5.10 F
898 1831 0.970427 TGCGAGCCTCTCACCATACA 60.970 55.0 0.0 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 2498 0.680061 AAGACGGTGGACTTGTCCTC 59.320 55.0 19.11 15.48 33.09 3.71 R
1688 2634 0.727398 GATCTTTTCCGTGGGCTTCG 59.273 55.0 0.00 0.00 0.00 3.79 R
2529 3693 2.038033 TCGTAGGGAGGAAGTTGTTTGG 59.962 50.0 0.00 0.00 0.00 3.28 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
27 28 3.306472 AAAACTCACCTAGGCAAACCA 57.694 42.857 9.30 0.00 39.06 3.67
28 29 2.568623 AACTCACCTAGGCAAACCAG 57.431 50.000 9.30 0.00 39.06 4.00
29 30 0.036875 ACTCACCTAGGCAAACCAGC 59.963 55.000 9.30 0.00 39.06 4.85
30 31 1.003839 TCACCTAGGCAAACCAGCG 60.004 57.895 9.30 0.00 39.06 5.18
31 32 1.003839 CACCTAGGCAAACCAGCGA 60.004 57.895 9.30 0.00 39.06 4.93
32 33 0.605319 CACCTAGGCAAACCAGCGAA 60.605 55.000 9.30 0.00 39.06 4.70
33 34 0.605589 ACCTAGGCAAACCAGCGAAC 60.606 55.000 9.30 0.00 39.06 3.95
34 35 0.605319 CCTAGGCAAACCAGCGAACA 60.605 55.000 0.00 0.00 39.06 3.18
35 36 1.453155 CTAGGCAAACCAGCGAACAT 58.547 50.000 0.00 0.00 39.06 2.71
36 37 1.812571 CTAGGCAAACCAGCGAACATT 59.187 47.619 0.00 0.00 39.06 2.71
37 38 1.039856 AGGCAAACCAGCGAACATTT 58.960 45.000 0.00 0.00 39.06 2.32
38 39 1.139163 GGCAAACCAGCGAACATTTG 58.861 50.000 0.00 0.00 35.57 2.32
40 41 1.850377 CAAACCAGCGAACATTTGCA 58.150 45.000 6.61 0.00 40.10 4.08
41 42 2.200067 CAAACCAGCGAACATTTGCAA 58.800 42.857 6.61 0.00 40.10 4.08
42 43 2.801679 CAAACCAGCGAACATTTGCAAT 59.198 40.909 0.00 0.00 40.10 3.56
43 44 2.068837 ACCAGCGAACATTTGCAATG 57.931 45.000 0.00 3.61 40.10 2.82
44 45 1.340889 ACCAGCGAACATTTGCAATGT 59.659 42.857 0.00 4.30 40.10 2.71
45 46 1.722464 CCAGCGAACATTTGCAATGTG 59.278 47.619 13.05 11.55 40.10 3.21
46 47 1.125384 CAGCGAACATTTGCAATGTGC 59.875 47.619 13.05 10.96 45.29 4.57
47 48 1.000060 AGCGAACATTTGCAATGTGCT 60.000 42.857 13.05 14.13 45.31 4.40
48 49 1.125384 GCGAACATTTGCAATGTGCTG 59.875 47.619 13.05 9.66 45.31 4.41
49 50 1.722464 CGAACATTTGCAATGTGCTGG 59.278 47.619 13.05 0.92 45.31 4.85
50 51 1.461897 GAACATTTGCAATGTGCTGGC 59.538 47.619 13.05 0.00 45.31 4.85
51 52 0.682852 ACATTTGCAATGTGCTGGCT 59.317 45.000 0.00 0.00 45.31 4.75
52 53 1.075542 CATTTGCAATGTGCTGGCTG 58.924 50.000 0.00 0.00 45.31 4.85
53 54 0.682852 ATTTGCAATGTGCTGGCTGT 59.317 45.000 0.00 0.00 45.31 4.40
54 55 0.249531 TTTGCAATGTGCTGGCTGTG 60.250 50.000 0.00 0.00 45.31 3.66
55 56 2.431942 GCAATGTGCTGGCTGTGC 60.432 61.111 0.00 0.00 40.96 4.57
56 57 3.044280 CAATGTGCTGGCTGTGCA 58.956 55.556 0.00 0.00 38.19 4.57
57 58 1.589630 CAATGTGCTGGCTGTGCAT 59.410 52.632 0.00 1.45 42.69 3.96
58 59 0.457853 CAATGTGCTGGCTGTGCATC 60.458 55.000 0.00 0.00 42.69 3.91
59 60 1.929806 AATGTGCTGGCTGTGCATCG 61.930 55.000 0.00 0.00 42.69 3.84
60 61 3.807538 GTGCTGGCTGTGCATCGG 61.808 66.667 0.00 0.00 42.69 4.18
67 68 3.506096 CTGTGCATCGGCCAGCTG 61.506 66.667 6.78 6.78 40.13 4.24
80 81 0.672342 CCAGCTGGCATCATTTAGGC 59.328 55.000 22.33 0.00 0.00 3.93
81 82 0.309922 CAGCTGGCATCATTTAGGCG 59.690 55.000 5.57 0.00 35.10 5.52
82 83 0.181114 AGCTGGCATCATTTAGGCGA 59.819 50.000 0.00 0.00 35.10 5.54
83 84 1.024271 GCTGGCATCATTTAGGCGAA 58.976 50.000 0.00 0.00 35.10 4.70
84 85 1.268743 GCTGGCATCATTTAGGCGAAC 60.269 52.381 0.00 0.00 35.10 3.95
85 86 1.334869 CTGGCATCATTTAGGCGAACC 59.665 52.381 0.00 0.00 35.10 3.62
86 87 0.668535 GGCATCATTTAGGCGAACCC 59.331 55.000 0.00 0.00 35.10 4.11
87 88 1.388547 GCATCATTTAGGCGAACCCA 58.611 50.000 0.00 0.00 36.11 4.51
88 89 1.748493 GCATCATTTAGGCGAACCCAA 59.252 47.619 0.00 0.00 36.11 4.12
89 90 2.479560 GCATCATTTAGGCGAACCCAAC 60.480 50.000 0.00 0.00 36.11 3.77
90 91 1.444836 TCATTTAGGCGAACCCAACG 58.555 50.000 0.00 0.00 36.11 4.10
91 92 0.450184 CATTTAGGCGAACCCAACGG 59.550 55.000 0.00 0.00 36.11 4.44
92 93 0.325602 ATTTAGGCGAACCCAACGGA 59.674 50.000 0.00 0.00 36.11 4.69
93 94 0.603439 TTTAGGCGAACCCAACGGAC 60.603 55.000 0.00 0.00 36.11 4.79
94 95 1.756408 TTAGGCGAACCCAACGGACA 61.756 55.000 0.00 0.00 36.11 4.02
95 96 1.756408 TAGGCGAACCCAACGGACAA 61.756 55.000 0.00 0.00 36.11 3.18
96 97 1.969589 GGCGAACCCAACGGACAAT 60.970 57.895 0.00 0.00 0.00 2.71
97 98 1.209127 GCGAACCCAACGGACAATG 59.791 57.895 0.00 0.00 0.00 2.82
98 99 1.231958 GCGAACCCAACGGACAATGA 61.232 55.000 0.00 0.00 0.00 2.57
99 100 0.515564 CGAACCCAACGGACAATGAC 59.484 55.000 0.00 0.00 0.00 3.06
100 101 0.515564 GAACCCAACGGACAATGACG 59.484 55.000 0.00 0.00 0.00 4.35
101 102 1.512156 AACCCAACGGACAATGACGC 61.512 55.000 2.56 0.00 0.00 5.19
102 103 1.963855 CCCAACGGACAATGACGCA 60.964 57.895 2.56 0.00 0.00 5.24
103 104 1.305219 CCCAACGGACAATGACGCAT 61.305 55.000 2.56 0.00 0.00 4.73
104 105 0.179192 CCAACGGACAATGACGCATG 60.179 55.000 2.56 0.00 0.00 4.06
105 106 0.179192 CAACGGACAATGACGCATGG 60.179 55.000 0.00 0.00 0.00 3.66
106 107 1.305219 AACGGACAATGACGCATGGG 61.305 55.000 8.44 8.44 0.00 4.00
107 108 1.449423 CGGACAATGACGCATGGGA 60.449 57.895 17.76 0.00 0.00 4.37
108 109 1.024046 CGGACAATGACGCATGGGAA 61.024 55.000 17.76 4.56 0.00 3.97
109 110 1.392589 GGACAATGACGCATGGGAAT 58.607 50.000 17.76 6.82 0.00 3.01
110 111 1.066002 GGACAATGACGCATGGGAATG 59.934 52.381 17.76 11.16 0.00 2.67
111 112 2.016318 GACAATGACGCATGGGAATGA 58.984 47.619 17.76 0.00 0.00 2.57
112 113 1.745087 ACAATGACGCATGGGAATGAC 59.255 47.619 17.76 3.25 0.00 3.06
113 114 1.066002 CAATGACGCATGGGAATGACC 59.934 52.381 17.76 0.00 38.08 4.02
114 115 0.815213 ATGACGCATGGGAATGACCG 60.815 55.000 17.76 0.00 40.11 4.79
115 116 2.124736 ACGCATGGGAATGACCGG 60.125 61.111 17.76 0.00 40.11 5.28
116 117 3.585990 CGCATGGGAATGACCGGC 61.586 66.667 0.00 0.00 40.11 6.13
117 118 2.440065 GCATGGGAATGACCGGCA 60.440 61.111 0.00 0.00 40.11 5.69
118 119 2.484062 GCATGGGAATGACCGGCAG 61.484 63.158 0.00 0.00 40.11 4.85
119 120 1.077501 CATGGGAATGACCGGCAGT 60.078 57.895 0.00 0.00 40.11 4.40
120 121 1.077501 ATGGGAATGACCGGCAGTG 60.078 57.895 0.00 0.00 40.11 3.66
121 122 2.438434 GGGAATGACCGGCAGTGG 60.438 66.667 0.00 0.00 40.11 4.00
123 124 1.303317 GGAATGACCGGCAGTGGTT 60.303 57.895 0.00 0.00 44.01 3.67
124 125 1.305930 GGAATGACCGGCAGTGGTTC 61.306 60.000 0.00 1.54 44.01 3.62
125 126 1.303317 AATGACCGGCAGTGGTTCC 60.303 57.895 0.00 0.00 44.01 3.62
126 127 2.764637 AATGACCGGCAGTGGTTCCC 62.765 60.000 0.00 0.00 44.01 3.97
127 128 3.637273 GACCGGCAGTGGTTCCCT 61.637 66.667 0.00 0.00 44.01 4.20
128 129 2.203877 ACCGGCAGTGGTTCCCTA 60.204 61.111 0.00 0.00 39.99 3.53
129 130 2.240162 GACCGGCAGTGGTTCCCTAG 62.240 65.000 0.00 0.00 44.01 3.02
130 131 2.125106 CGGCAGTGGTTCCCTAGC 60.125 66.667 0.00 0.00 0.00 3.42
131 132 2.954684 CGGCAGTGGTTCCCTAGCA 61.955 63.158 0.00 0.00 0.00 3.49
132 133 1.609783 GGCAGTGGTTCCCTAGCAT 59.390 57.895 0.00 0.00 36.50 3.79
133 134 0.749454 GGCAGTGGTTCCCTAGCATG 60.749 60.000 0.00 0.00 36.50 4.06
134 135 0.749454 GCAGTGGTTCCCTAGCATGG 60.749 60.000 0.00 0.00 36.50 3.66
135 136 0.620556 CAGTGGTTCCCTAGCATGGT 59.379 55.000 1.62 1.62 36.50 3.55
136 137 0.912486 AGTGGTTCCCTAGCATGGTC 59.088 55.000 0.00 0.00 36.50 4.02
137 138 0.618458 GTGGTTCCCTAGCATGGTCA 59.382 55.000 0.00 0.00 36.50 4.02
138 139 0.911769 TGGTTCCCTAGCATGGTCAG 59.088 55.000 0.00 0.00 0.00 3.51
139 140 1.204146 GGTTCCCTAGCATGGTCAGA 58.796 55.000 0.00 0.00 0.00 3.27
140 141 1.771255 GGTTCCCTAGCATGGTCAGAT 59.229 52.381 0.00 0.00 0.00 2.90
141 142 2.486191 GGTTCCCTAGCATGGTCAGATG 60.486 54.545 0.00 0.00 0.00 2.90
142 143 2.171448 GTTCCCTAGCATGGTCAGATGT 59.829 50.000 0.00 0.00 0.00 3.06
143 144 1.764723 TCCCTAGCATGGTCAGATGTG 59.235 52.381 0.00 0.00 0.00 3.21
144 145 1.590932 CCTAGCATGGTCAGATGTGC 58.409 55.000 0.00 0.00 37.84 4.57
184 185 6.774170 TGATTTTATCCTGACAATGCAGCTAT 59.226 34.615 0.00 0.00 34.56 2.97
227 228 8.299570 ACACAAATTTCCTAATTCAGTAGCTTG 58.700 33.333 0.00 0.00 32.85 4.01
229 230 9.515226 ACAAATTTCCTAATTCAGTAGCTTGTA 57.485 29.630 0.00 0.00 32.85 2.41
258 259 4.687901 AAACAAGGGTTGAAAGGATTGG 57.312 40.909 0.00 0.00 37.30 3.16
310 311 4.783227 AGGAGATCTTACTAAAGGCCACAA 59.217 41.667 5.01 0.00 33.22 3.33
325 326 5.264395 AGGCCACAACTCAAGCTATAATTT 58.736 37.500 5.01 0.00 0.00 1.82
326 327 6.423182 AGGCCACAACTCAAGCTATAATTTA 58.577 36.000 5.01 0.00 0.00 1.40
330 331 8.889717 GCCACAACTCAAGCTATAATTTAGTTA 58.110 33.333 0.00 0.00 0.00 2.24
334 335 9.109393 CAACTCAAGCTATAATTTAGTTAGCCA 57.891 33.333 5.73 0.00 39.29 4.75
346 347 3.618690 AGTTAGCCATCTCTGTGTTCC 57.381 47.619 0.00 0.00 0.00 3.62
347 348 2.906389 AGTTAGCCATCTCTGTGTTCCA 59.094 45.455 0.00 0.00 0.00 3.53
352 353 4.922206 AGCCATCTCTGTGTTCCATTTAA 58.078 39.130 0.00 0.00 0.00 1.52
488 490 4.112331 AGTGAGGGAGGTAAAGGCTTTAT 58.888 43.478 21.59 7.84 0.00 1.40
581 583 9.535878 TTGTTATGTCCAAGAATTTTAAACACC 57.464 29.630 0.00 0.00 0.00 4.16
582 584 8.696374 TGTTATGTCCAAGAATTTTAAACACCA 58.304 29.630 0.00 0.00 0.00 4.17
583 585 9.535878 GTTATGTCCAAGAATTTTAAACACCAA 57.464 29.630 0.00 0.00 0.00 3.67
584 586 9.757227 TTATGTCCAAGAATTTTAAACACCAAG 57.243 29.630 0.00 0.00 0.00 3.61
585 587 7.176589 TGTCCAAGAATTTTAAACACCAAGT 57.823 32.000 0.00 0.00 0.00 3.16
586 588 8.294954 TGTCCAAGAATTTTAAACACCAAGTA 57.705 30.769 0.00 0.00 0.00 2.24
587 589 8.192110 TGTCCAAGAATTTTAAACACCAAGTAC 58.808 33.333 0.00 0.00 0.00 2.73
588 590 8.410912 GTCCAAGAATTTTAAACACCAAGTACT 58.589 33.333 0.00 0.00 0.00 2.73
589 591 9.629878 TCCAAGAATTTTAAACACCAAGTACTA 57.370 29.630 0.00 0.00 0.00 1.82
630 1555 7.622081 TGATCTGTTACAATCTACCCCTAAGAA 59.378 37.037 0.00 0.00 0.00 2.52
635 1560 5.695424 ACAATCTACCCCTAAGAAAGGTC 57.305 43.478 0.00 0.00 44.90 3.85
643 1568 4.294970 ACCCCTAAGAAAGGTCCATCATTT 59.705 41.667 0.00 0.00 44.90 2.32
672 1597 4.549458 CCACAACATCATGTTTGGTCTTC 58.451 43.478 17.25 0.00 38.77 2.87
677 1602 4.665451 ACATCATGTTTGGTCTTCCATCA 58.335 39.130 0.00 0.00 43.91 3.07
720 1645 1.062044 GGATTGGTAGAGGGGAGAGGT 60.062 57.143 0.00 0.00 0.00 3.85
728 1653 2.520184 AGAGGGGAGAGGTTCCTATCT 58.480 52.381 12.31 0.00 45.98 1.98
737 1662 4.463070 AGAGGTTCCTATCTAGTTCGGAC 58.537 47.826 0.00 0.00 0.00 4.79
746 1671 1.281867 TCTAGTTCGGACGGGAAGGTA 59.718 52.381 0.00 0.00 0.00 3.08
765 1691 1.652947 AATACCCCACGAGGTCAACT 58.347 50.000 0.00 0.00 41.58 3.16
823 1750 6.382608 TGACGAGCTCATGAGTATAATTAGC 58.617 40.000 23.38 7.11 0.00 3.09
844 1777 3.348119 CTTGGCTAAAAAGGGAGAGGAC 58.652 50.000 0.00 0.00 0.00 3.85
868 1801 3.290710 GAGGAGATTGCTAATTTGGGCA 58.709 45.455 0.00 0.00 36.62 5.36
869 1802 3.893813 GAGGAGATTGCTAATTTGGGCAT 59.106 43.478 0.00 0.00 38.30 4.40
880 1813 5.278660 GCTAATTTGGGCATGGTAATCTCTG 60.279 44.000 0.00 0.00 0.00 3.35
882 1815 0.179048 TGGGCATGGTAATCTCTGCG 60.179 55.000 0.00 0.00 35.47 5.18
883 1816 0.106708 GGGCATGGTAATCTCTGCGA 59.893 55.000 0.00 0.00 35.47 5.10
894 1827 2.283173 TCTGCGAGCCTCTCACCA 60.283 61.111 0.00 0.00 0.00 4.17
898 1831 0.970427 TGCGAGCCTCTCACCATACA 60.970 55.000 0.00 0.00 0.00 2.29
954 1895 2.057922 ACCACACCACAATCTCTCCTT 58.942 47.619 0.00 0.00 0.00 3.36
958 1899 4.163078 CCACACCACAATCTCTCCTTCTAT 59.837 45.833 0.00 0.00 0.00 1.98
962 1905 6.613271 ACACCACAATCTCTCCTTCTATGTAT 59.387 38.462 0.00 0.00 0.00 2.29
989 1932 1.178276 ACCAACCAACGCAAGACAAA 58.822 45.000 0.00 0.00 43.62 2.83
1135 2078 1.303398 ACGACCGAGGAGCAGAAGA 60.303 57.895 0.00 0.00 0.00 2.87
1144 2087 3.740321 CGAGGAGCAGAAGATAATTGAGC 59.260 47.826 0.00 0.00 0.00 4.26
1155 2098 4.088634 AGATAATTGAGCAGGCCAACAAA 58.911 39.130 5.01 0.00 0.00 2.83
1410 2356 1.589993 CGAGTCGCTCCGCATCATT 60.590 57.895 0.00 0.00 0.00 2.57
1435 2381 1.918293 ATCCTTGAGGTCCACGCCA 60.918 57.895 0.00 0.00 36.34 5.69
1469 2415 2.245438 GAGGAAGTCAAGGGGGCGAG 62.245 65.000 0.00 0.00 0.00 5.03
1672 2618 3.089284 TCTGCCGTCAAGAAGATCTACA 58.911 45.455 0.00 0.00 0.00 2.74
1680 2626 5.348986 GTCAAGAAGATCTACACCGCATTA 58.651 41.667 0.00 0.00 0.00 1.90
1688 2634 0.460635 TACACCGCATTAGTTCCCGC 60.461 55.000 0.00 0.00 0.00 6.13
1729 2675 1.630244 CGTCTTTGAGAGCGCCCTTG 61.630 60.000 2.29 0.00 0.00 3.61
1730 2676 0.320771 GTCTTTGAGAGCGCCCTTGA 60.321 55.000 2.29 0.00 0.00 3.02
1731 2677 0.396435 TCTTTGAGAGCGCCCTTGAA 59.604 50.000 2.29 0.00 0.00 2.69
1877 2841 6.540438 ACATCCTATCAGTCGGACTTTAAA 57.460 37.500 8.18 0.00 30.90 1.52
1881 2845 6.161381 TCCTATCAGTCGGACTTTAAACAAC 58.839 40.000 8.18 0.00 0.00 3.32
1882 2846 5.929992 CCTATCAGTCGGACTTTAAACAACA 59.070 40.000 8.18 0.00 0.00 3.33
1887 2851 7.383687 TCAGTCGGACTTTAAACAACATATCT 58.616 34.615 8.18 0.00 0.00 1.98
1892 3027 8.095792 TCGGACTTTAAACAACATATCTGGTAA 58.904 33.333 0.00 0.00 0.00 2.85
1948 3083 4.714802 ACCATAGATGTGTGTAACCAGCTA 59.285 41.667 0.00 0.00 39.21 3.32
1953 3088 3.849563 TGTGTGTAACCAGCTAACCTT 57.150 42.857 0.00 0.00 34.36 3.50
1960 3095 5.414765 GTGTAACCAGCTAACCTTGCTTAAT 59.585 40.000 0.00 0.00 38.92 1.40
1964 3099 4.156008 ACCAGCTAACCTTGCTTAATTTCG 59.844 41.667 0.00 0.00 38.92 3.46
2283 3434 0.534412 CAACTTGGGCACAAACACCA 59.466 50.000 1.48 0.00 35.89 4.17
2392 3546 5.179368 CGAACCTGATAACTCACACACAAAT 59.821 40.000 0.00 0.00 0.00 2.32
2484 3647 5.163468 TGGTAATTTATACGCCACGAACCTA 60.163 40.000 0.00 0.00 0.00 3.08
2504 3668 8.472007 AACCTAATAACTCATGGACAAAAACA 57.528 30.769 0.00 0.00 0.00 2.83
2529 3693 8.548721 CAACATAAGTTATCGAGGGTATGTTTC 58.451 37.037 14.82 0.00 39.13 2.78
2574 3738 6.922247 TCAAAGTTATCACGGTGTTTGTAA 57.078 33.333 16.05 7.21 0.00 2.41
2577 3741 9.053840 TCAAAGTTATCACGGTGTTTGTAAATA 57.946 29.630 16.05 1.65 0.00 1.40
2673 3846 1.065053 CCCCGACCAATGTTACCATGA 60.065 52.381 0.00 0.00 0.00 3.07
2702 3875 8.677871 TTACGCATAAGTTATCACATATACGG 57.322 34.615 0.00 0.00 30.75 4.02
2706 3879 6.590292 GCATAAGTTATCACATATACGGTGCT 59.410 38.462 0.00 0.00 36.22 4.40
2707 3880 7.117812 GCATAAGTTATCACATATACGGTGCTT 59.882 37.037 0.00 3.23 36.22 3.91
2769 3942 0.545787 TTAAACAGCTCCTCCCCGGA 60.546 55.000 0.73 0.00 40.30 5.14
2782 3955 3.073062 CCTCCCCGGATCAAAGTTATCAT 59.927 47.826 0.73 0.00 33.16 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.636764 CTGGTTTGCCTAGGTGAGTTTTT 59.363 43.478 11.31 0.00 35.27 1.94
7 8 3.222603 CTGGTTTGCCTAGGTGAGTTTT 58.777 45.455 11.31 0.00 35.27 2.43
8 9 2.863809 CTGGTTTGCCTAGGTGAGTTT 58.136 47.619 11.31 0.00 35.27 2.66
9 10 1.545651 GCTGGTTTGCCTAGGTGAGTT 60.546 52.381 11.31 0.00 35.27 3.01
10 11 0.036875 GCTGGTTTGCCTAGGTGAGT 59.963 55.000 11.31 0.00 35.27 3.41
11 12 1.021390 CGCTGGTTTGCCTAGGTGAG 61.021 60.000 11.31 0.00 35.27 3.51
12 13 1.003839 CGCTGGTTTGCCTAGGTGA 60.004 57.895 11.31 0.00 35.27 4.02
13 14 0.605319 TTCGCTGGTTTGCCTAGGTG 60.605 55.000 11.31 0.00 35.27 4.00
14 15 0.605589 GTTCGCTGGTTTGCCTAGGT 60.606 55.000 11.31 0.00 35.27 3.08
15 16 0.605319 TGTTCGCTGGTTTGCCTAGG 60.605 55.000 3.67 3.67 35.27 3.02
16 17 1.453155 ATGTTCGCTGGTTTGCCTAG 58.547 50.000 0.00 0.00 35.27 3.02
17 18 1.904287 AATGTTCGCTGGTTTGCCTA 58.096 45.000 0.00 0.00 35.27 3.93
18 19 1.039856 AAATGTTCGCTGGTTTGCCT 58.960 45.000 0.00 0.00 35.27 4.75
19 20 1.139163 CAAATGTTCGCTGGTTTGCC 58.861 50.000 0.00 0.00 0.00 4.52
20 21 0.508213 GCAAATGTTCGCTGGTTTGC 59.492 50.000 6.00 6.00 46.23 3.68
21 22 1.850377 TGCAAATGTTCGCTGGTTTG 58.150 45.000 0.00 0.00 35.30 2.93
22 23 2.593346 TTGCAAATGTTCGCTGGTTT 57.407 40.000 0.00 0.00 0.00 3.27
23 24 2.224018 ACATTGCAAATGTTCGCTGGTT 60.224 40.909 1.71 0.00 0.00 3.67
24 25 1.340889 ACATTGCAAATGTTCGCTGGT 59.659 42.857 1.71 0.00 0.00 4.00
25 26 1.722464 CACATTGCAAATGTTCGCTGG 59.278 47.619 1.71 0.00 0.00 4.85
26 27 1.125384 GCACATTGCAAATGTTCGCTG 59.875 47.619 1.71 0.00 44.26 5.18
27 28 1.421382 GCACATTGCAAATGTTCGCT 58.579 45.000 1.71 0.00 44.26 4.93
28 29 3.933118 GCACATTGCAAATGTTCGC 57.067 47.368 1.71 5.99 44.26 4.70
38 39 2.431942 GCACAGCCAGCACATTGC 60.432 61.111 0.00 0.00 45.46 3.56
39 40 0.457853 GATGCACAGCCAGCACATTG 60.458 55.000 0.00 0.00 45.95 2.82
40 41 1.888018 GATGCACAGCCAGCACATT 59.112 52.632 0.00 0.00 45.95 2.71
41 42 2.404186 CGATGCACAGCCAGCACAT 61.404 57.895 0.00 0.00 45.95 3.21
42 43 3.051479 CGATGCACAGCCAGCACA 61.051 61.111 0.00 0.00 45.95 4.57
43 44 3.807538 CCGATGCACAGCCAGCAC 61.808 66.667 0.00 0.00 45.95 4.40
50 51 3.506096 CAGCTGGCCGATGCACAG 61.506 66.667 5.57 0.00 40.13 3.66
61 62 0.672342 GCCTAAATGATGCCAGCTGG 59.328 55.000 29.34 29.34 38.53 4.85
62 63 0.309922 CGCCTAAATGATGCCAGCTG 59.690 55.000 6.78 6.78 0.00 4.24
63 64 0.181114 TCGCCTAAATGATGCCAGCT 59.819 50.000 0.00 0.00 0.00 4.24
64 65 1.024271 TTCGCCTAAATGATGCCAGC 58.976 50.000 0.00 0.00 0.00 4.85
65 66 1.334869 GGTTCGCCTAAATGATGCCAG 59.665 52.381 0.00 0.00 0.00 4.85
66 67 1.388547 GGTTCGCCTAAATGATGCCA 58.611 50.000 0.00 0.00 0.00 4.92
67 68 0.668535 GGGTTCGCCTAAATGATGCC 59.331 55.000 0.00 0.00 37.45 4.40
68 69 1.388547 TGGGTTCGCCTAAATGATGC 58.611 50.000 0.00 0.00 37.45 3.91
69 70 2.223249 CGTTGGGTTCGCCTAAATGATG 60.223 50.000 0.00 0.00 39.52 3.07
70 71 2.014128 CGTTGGGTTCGCCTAAATGAT 58.986 47.619 0.00 0.00 39.52 2.45
71 72 1.444836 CGTTGGGTTCGCCTAAATGA 58.555 50.000 0.00 0.00 39.52 2.57
72 73 0.450184 CCGTTGGGTTCGCCTAAATG 59.550 55.000 0.00 0.00 39.52 2.32
73 74 0.325602 TCCGTTGGGTTCGCCTAAAT 59.674 50.000 0.00 0.00 39.52 1.40
74 75 0.603439 GTCCGTTGGGTTCGCCTAAA 60.603 55.000 0.00 0.00 39.52 1.85
75 76 1.004679 GTCCGTTGGGTTCGCCTAA 60.005 57.895 0.00 0.00 35.23 2.69
76 77 1.756408 TTGTCCGTTGGGTTCGCCTA 61.756 55.000 0.00 0.00 37.45 3.93
77 78 2.406002 ATTGTCCGTTGGGTTCGCCT 62.406 55.000 0.00 0.00 37.45 5.52
78 79 1.969589 ATTGTCCGTTGGGTTCGCC 60.970 57.895 0.00 0.00 33.83 5.54
79 80 1.209127 CATTGTCCGTTGGGTTCGC 59.791 57.895 0.00 0.00 33.83 4.70
80 81 0.515564 GTCATTGTCCGTTGGGTTCG 59.484 55.000 0.00 0.00 33.83 3.95
81 82 0.515564 CGTCATTGTCCGTTGGGTTC 59.484 55.000 0.00 0.00 33.83 3.62
82 83 1.512156 GCGTCATTGTCCGTTGGGTT 61.512 55.000 0.00 0.00 33.83 4.11
83 84 1.964373 GCGTCATTGTCCGTTGGGT 60.964 57.895 0.00 0.00 33.83 4.51
84 85 1.305219 ATGCGTCATTGTCCGTTGGG 61.305 55.000 0.00 0.00 0.00 4.12
85 86 0.179192 CATGCGTCATTGTCCGTTGG 60.179 55.000 0.00 0.00 0.00 3.77
86 87 0.179192 CCATGCGTCATTGTCCGTTG 60.179 55.000 0.00 0.00 0.00 4.10
87 88 1.305219 CCCATGCGTCATTGTCCGTT 61.305 55.000 0.00 0.00 0.00 4.44
88 89 1.745115 CCCATGCGTCATTGTCCGT 60.745 57.895 0.00 0.00 0.00 4.69
89 90 1.024046 TTCCCATGCGTCATTGTCCG 61.024 55.000 0.00 0.00 0.00 4.79
90 91 1.066002 CATTCCCATGCGTCATTGTCC 59.934 52.381 0.00 0.00 0.00 4.02
91 92 2.016318 TCATTCCCATGCGTCATTGTC 58.984 47.619 0.00 0.00 0.00 3.18
92 93 1.745087 GTCATTCCCATGCGTCATTGT 59.255 47.619 0.00 0.00 0.00 2.71
93 94 1.066002 GGTCATTCCCATGCGTCATTG 59.934 52.381 0.00 0.00 0.00 2.82
94 95 1.392589 GGTCATTCCCATGCGTCATT 58.607 50.000 0.00 0.00 0.00 2.57
95 96 0.815213 CGGTCATTCCCATGCGTCAT 60.815 55.000 0.00 0.00 0.00 3.06
96 97 1.449423 CGGTCATTCCCATGCGTCA 60.449 57.895 0.00 0.00 0.00 4.35
97 98 2.180204 CCGGTCATTCCCATGCGTC 61.180 63.158 0.00 0.00 0.00 5.19
98 99 2.124736 CCGGTCATTCCCATGCGT 60.125 61.111 0.00 0.00 0.00 5.24
99 100 3.585990 GCCGGTCATTCCCATGCG 61.586 66.667 1.90 0.00 0.00 4.73
100 101 2.440065 TGCCGGTCATTCCCATGC 60.440 61.111 1.90 0.00 0.00 4.06
101 102 1.077501 ACTGCCGGTCATTCCCATG 60.078 57.895 1.90 0.00 0.00 3.66
102 103 1.077501 CACTGCCGGTCATTCCCAT 60.078 57.895 1.90 0.00 0.00 4.00
103 104 2.350895 CACTGCCGGTCATTCCCA 59.649 61.111 1.90 0.00 0.00 4.37
104 105 2.438434 CCACTGCCGGTCATTCCC 60.438 66.667 1.90 0.00 0.00 3.97
105 106 1.303317 AACCACTGCCGGTCATTCC 60.303 57.895 1.90 0.00 38.76 3.01
106 107 1.305930 GGAACCACTGCCGGTCATTC 61.306 60.000 1.90 2.64 38.76 2.67
107 108 1.303317 GGAACCACTGCCGGTCATT 60.303 57.895 1.90 0.00 38.76 2.57
108 109 2.351276 GGAACCACTGCCGGTCAT 59.649 61.111 1.90 0.00 38.76 3.06
121 122 2.171448 ACATCTGACCATGCTAGGGAAC 59.829 50.000 0.00 0.00 0.00 3.62
122 123 2.171237 CACATCTGACCATGCTAGGGAA 59.829 50.000 0.00 0.00 0.00 3.97
123 124 1.764723 CACATCTGACCATGCTAGGGA 59.235 52.381 0.00 0.00 0.00 4.20
124 125 1.813092 GCACATCTGACCATGCTAGGG 60.813 57.143 0.00 0.00 35.16 3.53
125 126 1.590932 GCACATCTGACCATGCTAGG 58.409 55.000 0.00 0.00 35.16 3.02
126 127 1.140452 AGGCACATCTGACCATGCTAG 59.860 52.381 8.85 0.00 38.18 3.42
127 128 1.206878 AGGCACATCTGACCATGCTA 58.793 50.000 8.85 0.00 38.18 3.49
128 129 0.330604 AAGGCACATCTGACCATGCT 59.669 50.000 8.85 0.00 38.18 3.79
129 130 1.133790 GAAAGGCACATCTGACCATGC 59.866 52.381 1.99 1.99 37.35 4.06
130 131 2.719739 AGAAAGGCACATCTGACCATG 58.280 47.619 0.00 0.00 0.00 3.66
131 132 3.446442 AAGAAAGGCACATCTGACCAT 57.554 42.857 0.00 0.00 0.00 3.55
132 133 2.957402 AAGAAAGGCACATCTGACCA 57.043 45.000 0.00 0.00 0.00 4.02
133 134 4.943705 TCAATAAGAAAGGCACATCTGACC 59.056 41.667 0.00 0.00 0.00 4.02
134 135 5.163713 GGTCAATAAGAAAGGCACATCTGAC 60.164 44.000 0.00 0.00 0.00 3.51
135 136 4.943705 GGTCAATAAGAAAGGCACATCTGA 59.056 41.667 0.00 0.00 0.00 3.27
136 137 4.946157 AGGTCAATAAGAAAGGCACATCTG 59.054 41.667 0.00 0.00 0.00 2.90
137 138 4.946157 CAGGTCAATAAGAAAGGCACATCT 59.054 41.667 0.00 0.00 0.00 2.90
138 139 4.943705 TCAGGTCAATAAGAAAGGCACATC 59.056 41.667 0.00 0.00 0.00 3.06
139 140 4.922206 TCAGGTCAATAAGAAAGGCACAT 58.078 39.130 0.00 0.00 0.00 3.21
140 141 4.365514 TCAGGTCAATAAGAAAGGCACA 57.634 40.909 0.00 0.00 0.00 4.57
141 142 5.904362 AATCAGGTCAATAAGAAAGGCAC 57.096 39.130 0.00 0.00 0.00 5.01
142 143 6.916360 AAAATCAGGTCAATAAGAAAGGCA 57.084 33.333 0.00 0.00 0.00 4.75
143 144 8.138074 GGATAAAATCAGGTCAATAAGAAAGGC 58.862 37.037 0.00 0.00 0.00 4.35
144 145 9.413734 AGGATAAAATCAGGTCAATAAGAAAGG 57.586 33.333 0.00 0.00 0.00 3.11
243 244 3.496331 TCTCAACCAATCCTTTCAACCC 58.504 45.455 0.00 0.00 0.00 4.11
258 259 6.866480 TCCAATGGAATAATTGCTTCTCAAC 58.134 36.000 0.00 0.00 37.53 3.18
310 311 9.495572 GATGGCTAACTAAATTATAGCTTGAGT 57.504 33.333 0.00 0.00 41.35 3.41
325 326 4.093743 TGGAACACAGAGATGGCTAACTA 58.906 43.478 0.00 0.00 0.00 2.24
326 327 2.906389 TGGAACACAGAGATGGCTAACT 59.094 45.455 0.00 0.00 0.00 2.24
630 1555 2.365582 GCCACGTAAATGATGGACCTT 58.634 47.619 0.00 0.00 35.33 3.50
635 1560 1.458398 TGTGGCCACGTAAATGATGG 58.542 50.000 30.07 0.00 36.51 3.51
643 1568 1.271108 ACATGATGTTGTGGCCACGTA 60.271 47.619 30.07 18.31 0.00 3.57
672 1597 7.093640 CCAAATATATCCACCCTTGAATGATGG 60.094 40.741 0.00 0.00 0.00 3.51
677 1602 6.335311 TCCTCCAAATATATCCACCCTTGAAT 59.665 38.462 0.00 0.00 0.00 2.57
720 1645 2.173356 TCCCGTCCGAACTAGATAGGAA 59.827 50.000 3.38 0.00 34.17 3.36
728 1653 2.214376 TTACCTTCCCGTCCGAACTA 57.786 50.000 0.00 0.00 0.00 2.24
737 1662 0.105408 CGTGGGGTATTACCTTCCCG 59.895 60.000 12.54 8.21 42.20 5.14
746 1671 1.652947 AGTTGACCTCGTGGGGTATT 58.347 50.000 8.63 0.00 40.06 1.89
765 1691 9.826574 AACCAACAATTAGATCGCTAAATACTA 57.173 29.630 0.00 0.00 39.85 1.82
823 1750 3.244911 TGTCCTCTCCCTTTTTAGCCAAG 60.245 47.826 0.00 0.00 0.00 3.61
844 1777 3.887716 CCCAAATTAGCAATCTCCTCCTG 59.112 47.826 0.00 0.00 0.00 3.86
880 1813 0.249238 CTGTATGGTGAGAGGCTCGC 60.249 60.000 11.63 11.63 39.93 5.03
882 1815 2.697751 ACATCTGTATGGTGAGAGGCTC 59.302 50.000 6.34 6.34 37.43 4.70
883 1816 2.756907 ACATCTGTATGGTGAGAGGCT 58.243 47.619 0.00 0.00 37.43 4.58
954 1895 5.073428 TGGTTGGTTTGCACAATACATAGA 58.927 37.500 0.00 0.00 0.00 1.98
958 1899 3.735208 CGTTGGTTGGTTTGCACAATACA 60.735 43.478 0.00 0.00 0.00 2.29
962 1905 0.737715 GCGTTGGTTGGTTTGCACAA 60.738 50.000 0.00 0.00 0.00 3.33
989 1932 0.032952 CACTGCCATTGTTGCTGCTT 59.967 50.000 0.00 0.00 0.00 3.91
1060 2003 2.494918 GGCAGCGTACGAGATGGT 59.505 61.111 21.65 0.00 0.00 3.55
1135 2078 3.368739 GCTTTGTTGGCCTGCTCAATTAT 60.369 43.478 3.32 0.00 0.00 1.28
1179 2122 3.851128 GGAGGGACTACGGCTGCC 61.851 72.222 9.11 9.11 41.55 4.85
1296 2242 1.537135 GCGAAGATGACCCTAGTGCTC 60.537 57.143 0.00 0.00 0.00 4.26
1348 2294 4.798682 CTGGGCCTCCGGGGTAGT 62.799 72.222 4.53 0.00 35.76 2.73
1363 2309 1.471676 GGCCACGAAGGAGTCATACTG 60.472 57.143 0.00 0.00 41.22 2.74
1410 2356 1.300963 GACCTCAAGGATGCCAGCA 59.699 57.895 2.30 0.00 38.94 4.41
1413 2359 1.685224 GTGGACCTCAAGGATGCCA 59.315 57.895 2.30 4.69 38.94 4.92
1552 2498 0.680061 AAGACGGTGGACTTGTCCTC 59.320 55.000 19.11 15.48 33.09 3.71
1650 2596 3.701542 TGTAGATCTTCTTGACGGCAGAT 59.298 43.478 0.00 0.00 0.00 2.90
1672 2618 2.510691 CGCGGGAACTAATGCGGT 60.511 61.111 0.00 0.00 46.31 5.68
1680 2626 4.699522 GTGGGCTTCGCGGGAACT 62.700 66.667 11.32 0.00 0.00 3.01
1688 2634 0.727398 GATCTTTTCCGTGGGCTTCG 59.273 55.000 0.00 0.00 0.00 3.79
1697 2643 4.923871 TCTCAAAGACGAAGATCTTTTCCG 59.076 41.667 9.87 11.20 44.74 4.30
1729 2675 3.195698 GGCGCCGATGGTGTCTTC 61.196 66.667 12.58 0.00 34.64 2.87
1730 2676 3.329542 ATGGCGCCGATGGTGTCTT 62.330 57.895 23.90 0.00 38.79 3.01
1731 2677 3.785859 ATGGCGCCGATGGTGTCT 61.786 61.111 23.90 0.00 38.79 3.41
1877 2841 5.487488 TCCCACTTCTTACCAGATATGTTGT 59.513 40.000 0.00 0.00 0.00 3.32
1881 2845 5.508153 CGACTCCCACTTCTTACCAGATATG 60.508 48.000 0.00 0.00 0.00 1.78
1882 2846 4.585162 CGACTCCCACTTCTTACCAGATAT 59.415 45.833 0.00 0.00 0.00 1.63
1887 2851 2.297698 TCGACTCCCACTTCTTACCA 57.702 50.000 0.00 0.00 0.00 3.25
1892 3027 2.363297 GGGTTCGACTCCCACTTCT 58.637 57.895 17.12 0.00 44.05 2.85
1937 3072 3.502123 AAGCAAGGTTAGCTGGTTACA 57.498 42.857 0.00 0.00 42.53 2.41
2004 3140 4.142773 GGTTTATTTTTCTCATGGTCGCGA 60.143 41.667 3.71 3.71 0.00 5.87
2058 3194 9.430623 CAAAACAAAATATAGTACAAAAGGGGG 57.569 33.333 0.00 0.00 0.00 5.40
2059 3195 9.990360 ACAAAACAAAATATAGTACAAAAGGGG 57.010 29.630 0.00 0.00 0.00 4.79
2283 3434 6.833346 TTTTCCTGGGGTTAAATTTTCCTT 57.167 33.333 0.00 0.00 0.00 3.36
2392 3546 8.515695 TTTCTCTAGGTCAAGTTATCGTGATA 57.484 34.615 0.00 0.00 34.93 2.15
2504 3668 7.713942 GGAAACATACCCTCGATAACTTATGTT 59.286 37.037 10.11 10.11 40.28 2.71
2529 3693 2.038033 TCGTAGGGAGGAAGTTGTTTGG 59.962 50.000 0.00 0.00 0.00 3.28
2574 3738 4.634443 GCACCGTGGACTTGATAACTTATT 59.366 41.667 0.00 0.00 0.00 1.40
2577 3741 2.423577 GCACCGTGGACTTGATAACTT 58.576 47.619 0.00 0.00 0.00 2.66
2769 3942 5.345741 GCGCAAACAACATGATAACTTTGAT 59.654 36.000 0.30 0.00 0.00 2.57
2782 3955 3.251972 TGATAACTCATGCGCAAACAACA 59.748 39.130 17.11 4.97 0.00 3.33


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

AutoCloner maintained by Alex Coulton.