Multiple sequence alignment - TraesCS5B01G312600

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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 TraesCS5B01G312600 chr5B 100.000 2699 0 0 1 2699 494025365 494028063 0.000000e+00 4985.0
1 TraesCS5B01G312600 chr5B 84.683 914 109 20 748 1646 494032998 494033895 0.000000e+00 883.0
2 TraesCS5B01G312600 chr5B 88.995 627 66 3 2075 2699 229696416 229697041 0.000000e+00 773.0
3 TraesCS5B01G312600 chr5B 85.714 651 87 3 863 1510 494295929 494296576 0.000000e+00 682.0
4 TraesCS5B01G312600 chr5B 84.914 643 79 10 863 1490 494044798 494045437 3.790000e-178 634.0
5 TraesCS5B01G312600 chr5A 91.124 1690 96 23 161 1821 523565731 523567395 0.000000e+00 2241.0
6 TraesCS5B01G312600 chr5A 85.198 885 113 11 818 1691 523587311 523588188 0.000000e+00 893.0
7 TraesCS5B01G312600 chr5A 79.758 909 123 31 869 1768 523608839 523609695 1.070000e-168 603.0
8 TraesCS5B01G312600 chr5A 91.613 155 9 2 1864 2014 523567664 523567818 7.570000e-51 211.0
9 TraesCS5B01G312600 chr5D 90.749 1708 71 33 195 1876 411741802 411743448 0.000000e+00 2198.0
10 TraesCS5B01G312600 chr5D 87.618 848 92 7 818 1656 411784824 411785667 0.000000e+00 972.0
11 TraesCS5B01G312600 chr5D 80.084 949 121 36 834 1766 411789938 411790834 0.000000e+00 643.0
12 TraesCS5B01G312600 chr5D 90.476 63 2 3 1867 1928 411743467 411743526 2.230000e-11 80.5
13 TraesCS5B01G312600 chr5D 94.595 37 2 0 160 196 411741685 411741721 1.040000e-04 58.4
14 TraesCS5B01G312600 chr3A 96.480 625 22 0 2075 2699 747744276 747744900 0.000000e+00 1033.0
15 TraesCS5B01G312600 chr6B 93.760 625 39 0 2075 2699 102096968 102096344 0.000000e+00 939.0
16 TraesCS5B01G312600 chr2D 87.520 625 78 0 2075 2699 630989942 630990566 0.000000e+00 723.0
17 TraesCS5B01G312600 chr1D 81.833 622 106 5 2081 2697 337206207 337205588 1.430000e-142 516.0
18 TraesCS5B01G312600 chr6A 81.235 421 71 7 1157 1573 601005630 601006046 1.550000e-87 333.0
19 TraesCS5B01G312600 chr2B 76.206 622 145 3 2075 2695 743562657 743563276 2.590000e-85 326.0
20 TraesCS5B01G312600 chr1A 73.635 531 127 13 2086 2610 259077104 259076581 2.740000e-45 193.0
21 TraesCS5B01G312600 chr1A 75.745 235 55 2 2462 2695 585613582 585613815 1.700000e-22 117.0
22 TraesCS5B01G312600 chr7A 100.000 29 0 0 2075 2103 241746116 241746088 1.000000e-03 54.7


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 TraesCS5B01G312600 chr5B 494025365 494028063 2698 False 4985.000000 4985 100.0000 1 2699 1 chr5B.!!$F2 2698
1 TraesCS5B01G312600 chr5B 494032998 494033895 897 False 883.000000 883 84.6830 748 1646 1 chr5B.!!$F3 898
2 TraesCS5B01G312600 chr5B 229696416 229697041 625 False 773.000000 773 88.9950 2075 2699 1 chr5B.!!$F1 624
3 TraesCS5B01G312600 chr5B 494295929 494296576 647 False 682.000000 682 85.7140 863 1510 1 chr5B.!!$F5 647
4 TraesCS5B01G312600 chr5B 494044798 494045437 639 False 634.000000 634 84.9140 863 1490 1 chr5B.!!$F4 627
5 TraesCS5B01G312600 chr5A 523565731 523567818 2087 False 1226.000000 2241 91.3685 161 2014 2 chr5A.!!$F3 1853
6 TraesCS5B01G312600 chr5A 523587311 523588188 877 False 893.000000 893 85.1980 818 1691 1 chr5A.!!$F1 873
7 TraesCS5B01G312600 chr5A 523608839 523609695 856 False 603.000000 603 79.7580 869 1768 1 chr5A.!!$F2 899
8 TraesCS5B01G312600 chr5D 411784824 411785667 843 False 972.000000 972 87.6180 818 1656 1 chr5D.!!$F1 838
9 TraesCS5B01G312600 chr5D 411741685 411743526 1841 False 778.966667 2198 91.9400 160 1928 3 chr5D.!!$F3 1768
10 TraesCS5B01G312600 chr5D 411789938 411790834 896 False 643.000000 643 80.0840 834 1766 1 chr5D.!!$F2 932
11 TraesCS5B01G312600 chr3A 747744276 747744900 624 False 1033.000000 1033 96.4800 2075 2699 1 chr3A.!!$F1 624
12 TraesCS5B01G312600 chr6B 102096344 102096968 624 True 939.000000 939 93.7600 2075 2699 1 chr6B.!!$R1 624
13 TraesCS5B01G312600 chr2D 630989942 630990566 624 False 723.000000 723 87.5200 2075 2699 1 chr2D.!!$F1 624
14 TraesCS5B01G312600 chr1D 337205588 337206207 619 True 516.000000 516 81.8330 2081 2697 1 chr1D.!!$R1 616
15 TraesCS5B01G312600 chr2B 743562657 743563276 619 False 326.000000 326 76.2060 2075 2695 1 chr2B.!!$F1 620

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
87 88 0.174845 ATACATGGTCGTGTGGTCGG 59.825 55.0 6.12 0.0 33.62 4.79 F
96 97 0.245539 CGTGTGGTCGGGTGTCTATT 59.754 55.0 0.00 0.0 0.00 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1792 0.038251 CACGGCTAAGCTCACACTCA 60.038 55.0 0.0 0.0 0.0 3.41 R
2031 2437 0.178068 TGCTCCAACGGCCTTCTATC 59.822 55.0 0.0 0.0 0.0 2.08 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
17 18 2.203001 CTGTCACACGTGTGGGCA 60.203 61.111 39.88 34.29 45.65 5.36
18 19 2.203001 TGTCACACGTGTGGGCAG 60.203 61.111 39.88 20.74 45.65 4.85
19 20 2.203015 GTCACACGTGTGGGCAGT 60.203 61.111 39.88 7.83 45.65 4.40
20 21 1.817941 GTCACACGTGTGGGCAGTT 60.818 57.895 39.88 7.04 45.65 3.16
21 22 1.078072 TCACACGTGTGGGCAGTTT 60.078 52.632 39.88 6.26 45.65 2.66
22 23 0.178301 TCACACGTGTGGGCAGTTTA 59.822 50.000 39.88 21.09 45.65 2.01
23 24 1.202710 TCACACGTGTGGGCAGTTTAT 60.203 47.619 39.88 4.93 45.65 1.40
24 25 1.606668 CACACGTGTGGGCAGTTTATT 59.393 47.619 35.65 0.33 42.10 1.40
25 26 1.606668 ACACGTGTGGGCAGTTTATTG 59.393 47.619 22.71 0.00 34.19 1.90
26 27 1.606668 CACGTGTGGGCAGTTTATTGT 59.393 47.619 7.58 0.00 0.00 2.71
27 28 2.034053 CACGTGTGGGCAGTTTATTGTT 59.966 45.455 7.58 0.00 0.00 2.83
28 29 2.292292 ACGTGTGGGCAGTTTATTGTTC 59.708 45.455 0.00 0.00 0.00 3.18
29 30 2.664424 CGTGTGGGCAGTTTATTGTTCG 60.664 50.000 0.00 0.00 0.00 3.95
30 31 1.268352 TGTGGGCAGTTTATTGTTCGC 59.732 47.619 0.00 0.00 0.00 4.70
31 32 0.885196 TGGGCAGTTTATTGTTCGCC 59.115 50.000 0.00 0.00 38.85 5.54
32 33 3.713936 GGCAGTTTATTGTTCGCCC 57.286 52.632 0.00 0.00 33.31 6.13
33 34 0.179174 GGCAGTTTATTGTTCGCCCG 60.179 55.000 0.00 0.00 33.31 6.13
34 35 0.796870 GCAGTTTATTGTTCGCCCGC 60.797 55.000 0.00 0.00 0.00 6.13
35 36 0.519519 CAGTTTATTGTTCGCCCGCA 59.480 50.000 0.00 0.00 0.00 5.69
36 37 0.519961 AGTTTATTGTTCGCCCGCAC 59.480 50.000 0.00 0.00 0.00 5.34
37 38 0.238817 GTTTATTGTTCGCCCGCACA 59.761 50.000 0.00 0.00 0.00 4.57
38 39 0.519519 TTTATTGTTCGCCCGCACAG 59.480 50.000 0.00 0.00 0.00 3.66
39 40 0.320858 TTATTGTTCGCCCGCACAGA 60.321 50.000 0.00 0.00 0.00 3.41
40 41 0.320858 TATTGTTCGCCCGCACAGAA 60.321 50.000 0.00 0.00 0.00 3.02
41 42 1.169661 ATTGTTCGCCCGCACAGAAA 61.170 50.000 0.00 0.00 0.00 2.52
42 43 2.054140 TTGTTCGCCCGCACAGAAAC 62.054 55.000 0.00 0.00 0.00 2.78
43 44 3.342627 TTCGCCCGCACAGAAACG 61.343 61.111 0.00 0.00 0.00 3.60
44 45 4.595538 TCGCCCGCACAGAAACGT 62.596 61.111 0.00 0.00 0.00 3.99
45 46 4.368808 CGCCCGCACAGAAACGTG 62.369 66.667 0.00 0.00 40.00 4.49
46 47 3.276846 GCCCGCACAGAAACGTGT 61.277 61.111 0.00 0.00 39.19 4.49
50 51 2.331451 GCACAGAAACGTGTGGGC 59.669 61.111 4.48 4.48 46.73 5.36
51 52 2.186826 GCACAGAAACGTGTGGGCT 61.187 57.895 11.71 0.00 44.02 5.19
52 53 1.648720 CACAGAAACGTGTGGGCTG 59.351 57.895 0.00 0.00 43.56 4.85
53 54 2.186826 ACAGAAACGTGTGGGCTGC 61.187 57.895 0.00 0.00 0.00 5.25
54 55 2.594592 AGAAACGTGTGGGCTGCC 60.595 61.111 11.05 11.05 0.00 4.85
55 56 2.594592 GAAACGTGTGGGCTGCCT 60.595 61.111 19.68 0.00 0.00 4.75
56 57 2.906897 AAACGTGTGGGCTGCCTG 60.907 61.111 19.68 6.28 0.00 4.85
57 58 3.714487 AAACGTGTGGGCTGCCTGT 62.714 57.895 19.68 6.91 0.00 4.00
58 59 3.714487 AACGTGTGGGCTGCCTGTT 62.714 57.895 19.68 12.32 0.00 3.16
59 60 3.663176 CGTGTGGGCTGCCTGTTG 61.663 66.667 19.68 1.37 0.00 3.33
60 61 2.519302 GTGTGGGCTGCCTGTTGT 60.519 61.111 19.68 0.00 0.00 3.32
61 62 2.519063 TGTGGGCTGCCTGTTGTG 60.519 61.111 19.68 0.00 0.00 3.33
62 63 3.982241 GTGGGCTGCCTGTTGTGC 61.982 66.667 19.68 0.00 0.00 4.57
63 64 4.519612 TGGGCTGCCTGTTGTGCA 62.520 61.111 19.68 2.78 37.17 4.57
64 65 2.993264 GGGCTGCCTGTTGTGCAT 60.993 61.111 19.68 0.00 38.22 3.96
65 66 2.260434 GGCTGCCTGTTGTGCATG 59.740 61.111 12.43 0.00 38.22 4.06
66 67 2.431942 GCTGCCTGTTGTGCATGC 60.432 61.111 11.82 11.82 38.22 4.06
67 68 2.260434 CTGCCTGTTGTGCATGCC 59.740 61.111 16.68 7.25 37.84 4.40
68 69 2.521224 TGCCTGTTGTGCATGCCA 60.521 55.556 16.68 10.08 37.84 4.92
69 70 1.884075 CTGCCTGTTGTGCATGCCAT 61.884 55.000 16.68 0.00 37.84 4.40
70 71 0.611340 TGCCTGTTGTGCATGCCATA 60.611 50.000 16.68 0.00 37.84 2.74
71 72 0.179129 GCCTGTTGTGCATGCCATAC 60.179 55.000 16.68 7.52 33.44 2.39
72 73 1.175654 CCTGTTGTGCATGCCATACA 58.824 50.000 16.68 10.43 0.00 2.29
73 74 1.752498 CCTGTTGTGCATGCCATACAT 59.248 47.619 16.68 0.00 40.66 2.29
84 85 3.853104 CCATACATGGTCGTGTGGT 57.147 52.632 6.12 0.00 41.77 4.16
85 86 1.651987 CCATACATGGTCGTGTGGTC 58.348 55.000 6.12 0.00 41.77 4.02
86 87 1.277326 CATACATGGTCGTGTGGTCG 58.723 55.000 6.12 0.00 33.62 4.79
87 88 0.174845 ATACATGGTCGTGTGGTCGG 59.825 55.000 6.12 0.00 33.62 4.79
88 89 1.879737 TACATGGTCGTGTGGTCGGG 61.880 60.000 6.12 0.00 33.62 5.14
89 90 2.920912 ATGGTCGTGTGGTCGGGT 60.921 61.111 0.00 0.00 0.00 5.28
90 91 3.234630 ATGGTCGTGTGGTCGGGTG 62.235 63.158 0.00 0.00 0.00 4.61
91 92 3.920196 GGTCGTGTGGTCGGGTGT 61.920 66.667 0.00 0.00 0.00 4.16
92 93 2.355481 GTCGTGTGGTCGGGTGTC 60.355 66.667 0.00 0.00 0.00 3.67
93 94 2.520020 TCGTGTGGTCGGGTGTCT 60.520 61.111 0.00 0.00 0.00 3.41
94 95 1.228215 TCGTGTGGTCGGGTGTCTA 60.228 57.895 0.00 0.00 0.00 2.59
95 96 0.609957 TCGTGTGGTCGGGTGTCTAT 60.610 55.000 0.00 0.00 0.00 1.98
96 97 0.245539 CGTGTGGTCGGGTGTCTATT 59.754 55.000 0.00 0.00 0.00 1.73
97 98 1.473677 CGTGTGGTCGGGTGTCTATTA 59.526 52.381 0.00 0.00 0.00 0.98
98 99 2.100252 CGTGTGGTCGGGTGTCTATTAT 59.900 50.000 0.00 0.00 0.00 1.28
99 100 3.454375 GTGTGGTCGGGTGTCTATTATG 58.546 50.000 0.00 0.00 0.00 1.90
100 101 2.159014 TGTGGTCGGGTGTCTATTATGC 60.159 50.000 0.00 0.00 0.00 3.14
101 102 1.414919 TGGTCGGGTGTCTATTATGCC 59.585 52.381 0.00 0.00 0.00 4.40
102 103 1.414919 GGTCGGGTGTCTATTATGCCA 59.585 52.381 0.00 0.00 0.00 4.92
103 104 2.480845 GTCGGGTGTCTATTATGCCAC 58.519 52.381 0.00 0.00 0.00 5.01
104 105 2.112190 TCGGGTGTCTATTATGCCACA 58.888 47.619 0.00 0.00 0.00 4.17
105 106 2.502130 TCGGGTGTCTATTATGCCACAA 59.498 45.455 0.00 0.00 0.00 3.33
106 107 2.872245 CGGGTGTCTATTATGCCACAAG 59.128 50.000 0.00 0.00 0.00 3.16
107 108 3.681594 CGGGTGTCTATTATGCCACAAGT 60.682 47.826 0.00 0.00 0.00 3.16
108 109 3.627577 GGGTGTCTATTATGCCACAAGTG 59.372 47.826 0.00 0.00 0.00 3.16
109 110 4.261801 GGTGTCTATTATGCCACAAGTGT 58.738 43.478 0.00 0.00 0.00 3.55
110 111 4.094887 GGTGTCTATTATGCCACAAGTGTG 59.905 45.833 4.38 4.38 45.23 3.82
123 124 4.316205 ACAAGTGTGACAGTTATCGACA 57.684 40.909 5.19 0.00 0.00 4.35
124 125 4.883083 ACAAGTGTGACAGTTATCGACAT 58.117 39.130 5.19 0.00 0.00 3.06
125 126 4.923871 ACAAGTGTGACAGTTATCGACATC 59.076 41.667 5.19 0.00 0.00 3.06
126 127 4.111375 AGTGTGACAGTTATCGACATCC 57.889 45.455 0.00 0.00 0.00 3.51
127 128 3.509967 AGTGTGACAGTTATCGACATCCA 59.490 43.478 0.00 0.00 0.00 3.41
128 129 4.160439 AGTGTGACAGTTATCGACATCCAT 59.840 41.667 0.00 0.00 0.00 3.41
129 130 5.359860 AGTGTGACAGTTATCGACATCCATA 59.640 40.000 0.00 0.00 0.00 2.74
130 131 6.040247 GTGTGACAGTTATCGACATCCATAA 58.960 40.000 0.00 0.00 0.00 1.90
131 132 6.533723 GTGTGACAGTTATCGACATCCATAAA 59.466 38.462 0.00 0.00 0.00 1.40
132 133 7.064134 GTGTGACAGTTATCGACATCCATAAAA 59.936 37.037 0.00 0.00 0.00 1.52
133 134 7.604545 TGTGACAGTTATCGACATCCATAAAAA 59.395 33.333 0.00 0.00 0.00 1.94
134 135 8.612619 GTGACAGTTATCGACATCCATAAAAAT 58.387 33.333 0.00 0.00 0.00 1.82
135 136 9.173021 TGACAGTTATCGACATCCATAAAAATT 57.827 29.630 0.00 0.00 0.00 1.82
143 144 8.669946 TCGACATCCATAAAAATTACTATGCA 57.330 30.769 0.00 0.00 0.00 3.96
144 145 8.556194 TCGACATCCATAAAAATTACTATGCAC 58.444 33.333 0.00 0.00 0.00 4.57
145 146 8.559536 CGACATCCATAAAAATTACTATGCACT 58.440 33.333 0.00 0.00 0.00 4.40
146 147 9.884465 GACATCCATAAAAATTACTATGCACTC 57.116 33.333 0.00 0.00 0.00 3.51
147 148 8.559536 ACATCCATAAAAATTACTATGCACTCG 58.440 33.333 0.00 0.00 0.00 4.18
148 149 8.559536 CATCCATAAAAATTACTATGCACTCGT 58.440 33.333 0.00 0.00 0.00 4.18
149 150 9.772973 ATCCATAAAAATTACTATGCACTCGTA 57.227 29.630 0.00 0.00 0.00 3.43
150 151 9.037737 TCCATAAAAATTACTATGCACTCGTAC 57.962 33.333 0.00 0.00 0.00 3.67
151 152 9.042008 CCATAAAAATTACTATGCACTCGTACT 57.958 33.333 0.00 0.00 0.00 2.73
155 156 8.853469 AAAATTACTATGCACTCGTACTAGTC 57.147 34.615 0.00 0.00 0.00 2.59
156 157 7.563888 AATTACTATGCACTCGTACTAGTCA 57.436 36.000 0.00 0.39 0.00 3.41
157 158 6.600246 TTACTATGCACTCGTACTAGTCAG 57.400 41.667 0.00 0.00 0.00 3.51
158 159 2.853731 ATGCACTCGTACTAGTCAGC 57.146 50.000 0.00 0.31 0.00 4.26
265 349 4.394712 GGTGTGGAGCCCGACTGG 62.395 72.222 0.00 0.00 37.09 4.00
303 387 2.437359 GTGCGGCAGCCTCTTCAT 60.437 61.111 10.54 0.00 44.33 2.57
334 418 2.922335 GCCCGTTCAAAATGACTGCTTC 60.922 50.000 0.00 0.00 0.00 3.86
351 435 4.873768 GCTTCCTCAGCTAACAAAGATC 57.126 45.455 0.00 0.00 46.27 2.75
352 436 4.512484 GCTTCCTCAGCTAACAAAGATCT 58.488 43.478 0.00 0.00 46.27 2.75
498 584 3.244665 TGTCTCTGTTGAAGTCATGGCAT 60.245 43.478 0.00 0.00 0.00 4.40
538 624 2.668212 TGGAACCCTTCGCAAGCG 60.668 61.111 8.36 8.36 41.35 4.68
560 646 4.499865 CGGTCTCAACCAATCGAGTATCAT 60.500 45.833 0.00 0.00 46.86 2.45
562 648 6.513180 GGTCTCAACCAATCGAGTATCATTA 58.487 40.000 0.00 0.00 45.68 1.90
589 675 5.248870 TCTTTTTCTTTGAAGGTGCAGAC 57.751 39.130 0.00 0.00 0.00 3.51
610 696 7.324616 GCAGACTATCAGTTTTGATTTTGTCAC 59.675 37.037 14.30 7.38 41.24 3.67
616 702 6.847400 TCAGTTTTGATTTTGTCACTTTCGA 58.153 32.000 0.00 0.00 36.32 3.71
631 717 4.686554 CACTTTCGAGTTCCTCTTTACAGG 59.313 45.833 0.00 0.00 34.40 4.00
637 723 5.422331 TCGAGTTCCTCTTTACAGGATGAAT 59.578 40.000 0.00 0.00 42.49 2.57
638 724 5.521735 CGAGTTCCTCTTTACAGGATGAATG 59.478 44.000 0.00 0.00 42.49 2.67
639 725 6.627087 AGTTCCTCTTTACAGGATGAATGA 57.373 37.500 0.00 0.00 42.49 2.57
640 726 7.020827 AGTTCCTCTTTACAGGATGAATGAA 57.979 36.000 0.00 0.00 42.49 2.57
641 727 7.461749 AGTTCCTCTTTACAGGATGAATGAAA 58.538 34.615 0.00 0.00 42.49 2.69
642 728 7.391833 AGTTCCTCTTTACAGGATGAATGAAAC 59.608 37.037 0.00 0.00 42.49 2.78
645 731 6.404074 CCTCTTTACAGGATGAATGAAACTGC 60.404 42.308 0.00 0.00 39.69 4.40
646 732 6.003326 TCTTTACAGGATGAATGAAACTGCA 58.997 36.000 0.00 0.00 39.69 4.41
647 733 6.660521 TCTTTACAGGATGAATGAAACTGCAT 59.339 34.615 0.00 0.00 39.69 3.96
648 734 4.713824 ACAGGATGAATGAAACTGCATG 57.286 40.909 0.00 0.00 39.69 4.06
649 735 4.084287 ACAGGATGAATGAAACTGCATGT 58.916 39.130 0.00 0.00 39.69 3.21
650 736 5.255687 ACAGGATGAATGAAACTGCATGTA 58.744 37.500 0.00 0.00 39.69 2.29
651 737 5.124457 ACAGGATGAATGAAACTGCATGTAC 59.876 40.000 0.00 0.00 39.69 2.90
700 789 9.502145 TCAGTCGCATAAAATTGTTTCATAATC 57.498 29.630 0.00 0.00 0.00 1.75
702 791 7.643764 AGTCGCATAAAATTGTTTCATAATCGG 59.356 33.333 0.00 0.00 0.00 4.18
746 847 2.080654 AGCTACAGAGTCATCTCCCC 57.919 55.000 0.00 0.00 41.26 4.81
787 895 5.390991 GCAAAGGGAAAAATCTACAGAGTCG 60.391 44.000 0.00 0.00 0.00 4.18
891 1013 1.735559 GTTGTCCCAGTACGCGTCC 60.736 63.158 18.63 3.38 0.00 4.79
1118 1240 2.143419 CGCTAGATGGGGCCTCCTT 61.143 63.158 0.00 0.00 36.20 3.36
1269 1412 1.961277 CGCGAAGTTGAGGCACCTT 60.961 57.895 0.00 0.00 0.00 3.50
1272 1415 0.886490 CGAAGTTGAGGCACCTTGCT 60.886 55.000 0.00 0.00 44.28 3.91
1646 1792 3.341823 CTTGGTGCTTGAGCTTAGTGAT 58.658 45.455 4.44 0.00 42.66 3.06
1731 1888 0.321919 CATCTGTGGAGTGTGTGGGG 60.322 60.000 0.00 0.00 0.00 4.96
1746 1903 4.470664 TGTGTGGGGACGTATTTATAGGTT 59.529 41.667 0.00 0.00 32.14 3.50
1757 1915 6.646240 ACGTATTTATAGGTTTGTGTCGTGTT 59.354 34.615 0.00 0.00 0.00 3.32
1759 1917 5.676532 TTTATAGGTTTGTGTCGTGTTGG 57.323 39.130 0.00 0.00 0.00 3.77
1760 1918 2.983907 TAGGTTTGTGTCGTGTTGGA 57.016 45.000 0.00 0.00 0.00 3.53
1761 1919 1.663695 AGGTTTGTGTCGTGTTGGAG 58.336 50.000 0.00 0.00 0.00 3.86
1762 1920 0.028902 GGTTTGTGTCGTGTTGGAGC 59.971 55.000 0.00 0.00 0.00 4.70
1769 1945 1.134521 TGTCGTGTTGGAGCTTGAACT 60.135 47.619 9.47 0.00 0.00 3.01
1798 1975 0.243907 CAGCAGCTGGTAGTACGTGT 59.756 55.000 19.71 0.00 0.00 4.49
1821 2194 7.169476 GTGTCCCTTATTCTAGTCGATTTAAGC 59.831 40.741 0.00 0.00 0.00 3.09
1832 2205 3.071479 TCGATTTAAGCGCCTTTTGTCT 58.929 40.909 2.29 0.00 0.00 3.41
1835 2208 4.546570 GATTTAAGCGCCTTTTGTCTTGT 58.453 39.130 2.29 0.00 0.00 3.16
1843 2217 3.364366 CGCCTTTTGTCTTGTGACTCATC 60.364 47.826 0.00 0.00 43.29 2.92
1861 2235 4.492160 TGAGATCGACGCGTGGCC 62.492 66.667 20.70 11.07 0.00 5.36
1862 2236 4.194720 GAGATCGACGCGTGGCCT 62.195 66.667 20.70 16.13 0.00 5.19
1900 2302 2.433868 AAGACAGCTTGCAGCATTTG 57.566 45.000 0.00 0.00 45.56 2.32
1965 2371 3.148279 GCTCCACCGACCGGATCT 61.148 66.667 16.07 0.00 38.96 2.75
1993 2399 2.607892 GGCCCAGCGACGCATATTC 61.608 63.158 23.70 6.59 0.00 1.75
2000 2406 2.668457 CAGCGACGCATATTCCCTTATC 59.332 50.000 23.70 0.00 0.00 1.75
2005 2411 5.475719 CGACGCATATTCCCTTATCCTTTA 58.524 41.667 0.00 0.00 0.00 1.85
2014 2420 4.506758 TCCCTTATCCTTTACGGTTTTCG 58.493 43.478 0.00 0.00 45.88 3.46
2015 2421 3.624410 CCCTTATCCTTTACGGTTTTCGG 59.376 47.826 0.00 0.00 44.45 4.30
2016 2422 4.506758 CCTTATCCTTTACGGTTTTCGGA 58.493 43.478 0.00 0.00 44.45 4.55
2017 2423 4.937015 CCTTATCCTTTACGGTTTTCGGAA 59.063 41.667 0.00 0.00 44.45 4.30
2018 2424 5.064325 CCTTATCCTTTACGGTTTTCGGAAG 59.936 44.000 0.00 0.00 43.32 3.46
2019 2425 3.473923 TCCTTTACGGTTTTCGGAAGT 57.526 42.857 0.00 0.00 43.32 3.01
2020 2426 3.807553 TCCTTTACGGTTTTCGGAAGTT 58.192 40.909 0.00 0.00 43.32 2.66
2021 2427 4.954875 TCCTTTACGGTTTTCGGAAGTTA 58.045 39.130 0.00 0.00 43.32 2.24
2022 2428 5.550290 TCCTTTACGGTTTTCGGAAGTTAT 58.450 37.500 0.00 0.00 43.32 1.89
2023 2429 5.409214 TCCTTTACGGTTTTCGGAAGTTATG 59.591 40.000 0.00 0.00 43.32 1.90
2024 2430 5.409214 CCTTTACGGTTTTCGGAAGTTATGA 59.591 40.000 0.00 0.00 43.32 2.15
2025 2431 6.073112 CCTTTACGGTTTTCGGAAGTTATGAA 60.073 38.462 0.00 0.00 43.32 2.57
2026 2432 4.737353 ACGGTTTTCGGAAGTTATGAAC 57.263 40.909 0.00 0.00 44.45 3.18
2027 2433 4.128643 ACGGTTTTCGGAAGTTATGAACA 58.871 39.130 3.88 0.00 44.45 3.18
2028 2434 4.024641 ACGGTTTTCGGAAGTTATGAACAC 60.025 41.667 3.88 0.00 44.45 3.32
2029 2435 4.212636 CGGTTTTCGGAAGTTATGAACACT 59.787 41.667 3.88 0.00 34.75 3.55
2030 2436 5.614013 CGGTTTTCGGAAGTTATGAACACTC 60.614 44.000 3.88 0.00 34.75 3.51
2031 2437 5.371629 GTTTTCGGAAGTTATGAACACTCG 58.628 41.667 0.00 0.00 0.00 4.18
2032 2438 4.508461 TTCGGAAGTTATGAACACTCGA 57.492 40.909 0.00 0.00 0.00 4.04
2033 2439 4.713824 TCGGAAGTTATGAACACTCGAT 57.286 40.909 0.00 0.00 0.00 3.59
2034 2440 5.823209 TCGGAAGTTATGAACACTCGATA 57.177 39.130 0.00 0.00 0.00 2.92
2035 2441 5.817988 TCGGAAGTTATGAACACTCGATAG 58.182 41.667 0.00 0.00 0.00 2.08
2047 2453 2.890612 TCGATAGAAGGCCGTTGGA 58.109 52.632 0.00 0.00 46.15 3.53
2048 2454 0.744874 TCGATAGAAGGCCGTTGGAG 59.255 55.000 0.00 0.00 46.15 3.86
2049 2455 0.876342 CGATAGAAGGCCGTTGGAGC 60.876 60.000 0.00 0.00 39.76 4.70
2050 2456 0.178068 GATAGAAGGCCGTTGGAGCA 59.822 55.000 0.00 0.00 0.00 4.26
2051 2457 0.839946 ATAGAAGGCCGTTGGAGCAT 59.160 50.000 0.00 0.00 0.00 3.79
2052 2458 0.618458 TAGAAGGCCGTTGGAGCATT 59.382 50.000 0.00 0.00 36.86 3.56
2053 2459 0.251341 AGAAGGCCGTTGGAGCATTT 60.251 50.000 0.00 0.00 33.80 2.32
2054 2460 0.603065 GAAGGCCGTTGGAGCATTTT 59.397 50.000 0.00 0.00 33.80 1.82
2055 2461 0.318120 AAGGCCGTTGGAGCATTTTG 59.682 50.000 0.00 0.00 28.09 2.44
2056 2462 0.827507 AGGCCGTTGGAGCATTTTGT 60.828 50.000 0.00 0.00 0.00 2.83
2057 2463 0.885196 GGCCGTTGGAGCATTTTGTA 59.115 50.000 0.00 0.00 0.00 2.41
2058 2464 1.271102 GGCCGTTGGAGCATTTTGTAA 59.729 47.619 0.00 0.00 0.00 2.41
2059 2465 2.288518 GGCCGTTGGAGCATTTTGTAAA 60.289 45.455 0.00 0.00 0.00 2.01
2060 2466 3.584834 GCCGTTGGAGCATTTTGTAAAT 58.415 40.909 0.00 0.00 0.00 1.40
2061 2467 3.367630 GCCGTTGGAGCATTTTGTAAATG 59.632 43.478 7.58 7.58 0.00 2.32
2062 2468 3.925913 CCGTTGGAGCATTTTGTAAATGG 59.074 43.478 12.53 0.00 0.00 3.16
2063 2469 4.321601 CCGTTGGAGCATTTTGTAAATGGA 60.322 41.667 12.53 0.00 0.00 3.41
2064 2470 4.858692 CGTTGGAGCATTTTGTAAATGGAG 59.141 41.667 12.53 0.00 0.00 3.86
2065 2471 4.454728 TGGAGCATTTTGTAAATGGAGC 57.545 40.909 12.53 0.97 0.00 4.70
2066 2472 3.831333 TGGAGCATTTTGTAAATGGAGCA 59.169 39.130 12.53 0.00 0.00 4.26
2067 2473 4.467082 TGGAGCATTTTGTAAATGGAGCAT 59.533 37.500 12.53 0.00 0.00 3.79
2068 2474 5.046448 TGGAGCATTTTGTAAATGGAGCATT 60.046 36.000 12.53 0.00 35.39 3.56
2069 2475 5.876460 GGAGCATTTTGTAAATGGAGCATTT 59.124 36.000 12.53 0.00 44.74 2.32
2070 2476 6.372381 GGAGCATTTTGTAAATGGAGCATTTT 59.628 34.615 12.53 0.00 40.60 1.82
2071 2477 7.368480 AGCATTTTGTAAATGGAGCATTTTC 57.632 32.000 12.53 0.00 40.60 2.29
2072 2478 6.091169 AGCATTTTGTAAATGGAGCATTTTCG 59.909 34.615 12.53 0.00 40.60 3.46
2073 2479 6.672836 GCATTTTGTAAATGGAGCATTTTCGG 60.673 38.462 12.53 0.00 40.60 4.30
2204 2610 0.961019 GCAATGGTTGGAGCTGACAA 59.039 50.000 0.00 0.00 0.00 3.18
2310 2719 7.390823 GGAAAGAGATCCTTCTTAAGTCTGTT 58.609 38.462 1.63 0.00 36.42 3.16
2445 2854 6.057533 CAGGAGAATGCATTGGTATACTTGA 58.942 40.000 18.59 0.00 0.00 3.02
2518 2927 8.034313 TCTATACTCCTTTAATCTGGCAATGT 57.966 34.615 0.00 0.00 0.00 2.71
2520 2929 9.778741 CTATACTCCTTTAATCTGGCAATGTTA 57.221 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.234821 ATAAACTGCCCACACGTGTG 58.765 50.000 36.13 36.13 45.23 3.82
6 7 1.606668 ACAATAAACTGCCCACACGTG 59.393 47.619 15.48 15.48 0.00 4.49
7 8 1.975660 ACAATAAACTGCCCACACGT 58.024 45.000 0.00 0.00 0.00 4.49
8 9 2.664424 CGAACAATAAACTGCCCACACG 60.664 50.000 0.00 0.00 0.00 4.49
9 10 2.920647 GCGAACAATAAACTGCCCACAC 60.921 50.000 0.00 0.00 0.00 3.82
10 11 1.268352 GCGAACAATAAACTGCCCACA 59.732 47.619 0.00 0.00 0.00 4.17
11 12 1.402325 GGCGAACAATAAACTGCCCAC 60.402 52.381 0.00 0.00 36.51 4.61
12 13 0.885196 GGCGAACAATAAACTGCCCA 59.115 50.000 0.00 0.00 36.51 5.36
13 14 3.713936 GGCGAACAATAAACTGCCC 57.286 52.632 0.00 0.00 36.51 5.36
14 15 0.179174 CGGGCGAACAATAAACTGCC 60.179 55.000 0.00 0.00 41.72 4.85
15 16 0.796870 GCGGGCGAACAATAAACTGC 60.797 55.000 0.00 0.00 0.00 4.40
16 17 0.519519 TGCGGGCGAACAATAAACTG 59.480 50.000 0.00 0.00 0.00 3.16
17 18 0.519961 GTGCGGGCGAACAATAAACT 59.480 50.000 0.00 0.00 0.00 2.66
18 19 0.238817 TGTGCGGGCGAACAATAAAC 59.761 50.000 0.00 0.00 29.25 2.01
19 20 0.519519 CTGTGCGGGCGAACAATAAA 59.480 50.000 0.00 0.00 32.51 1.40
20 21 0.320858 TCTGTGCGGGCGAACAATAA 60.321 50.000 0.00 0.00 32.51 1.40
21 22 0.320858 TTCTGTGCGGGCGAACAATA 60.321 50.000 0.00 0.00 32.51 1.90
22 23 1.169661 TTTCTGTGCGGGCGAACAAT 61.170 50.000 0.00 0.00 32.51 2.71
23 24 1.820056 TTTCTGTGCGGGCGAACAA 60.820 52.632 0.00 0.00 32.51 2.83
24 25 2.203084 TTTCTGTGCGGGCGAACA 60.203 55.556 0.00 0.00 31.89 3.18
25 26 2.251371 GTTTCTGTGCGGGCGAAC 59.749 61.111 0.00 0.00 0.00 3.95
26 27 3.342627 CGTTTCTGTGCGGGCGAA 61.343 61.111 0.00 0.00 0.00 4.70
27 28 4.595538 ACGTTTCTGTGCGGGCGA 62.596 61.111 0.00 0.00 0.00 5.54
28 29 4.368808 CACGTTTCTGTGCGGGCG 62.369 66.667 0.00 0.00 32.31 6.13
29 30 3.276846 ACACGTTTCTGTGCGGGC 61.277 61.111 0.00 0.00 43.74 6.13
30 31 2.631428 CACACGTTTCTGTGCGGG 59.369 61.111 0.00 0.00 43.74 6.13
31 32 2.631428 CCACACGTTTCTGTGCGG 59.369 61.111 0.00 0.00 43.74 5.69
32 33 2.631428 CCCACACGTTTCTGTGCG 59.369 61.111 0.00 0.00 43.74 5.34
33 34 2.186826 AGCCCACACGTTTCTGTGC 61.187 57.895 0.00 0.00 43.74 4.57
34 35 1.648720 CAGCCCACACGTTTCTGTG 59.351 57.895 0.00 0.00 45.41 3.66
35 36 2.186826 GCAGCCCACACGTTTCTGT 61.187 57.895 0.00 0.00 0.00 3.41
36 37 2.639286 GCAGCCCACACGTTTCTG 59.361 61.111 0.00 0.00 0.00 3.02
37 38 2.594592 GGCAGCCCACACGTTTCT 60.595 61.111 0.00 0.00 0.00 2.52
38 39 2.594592 AGGCAGCCCACACGTTTC 60.595 61.111 8.22 0.00 0.00 2.78
39 40 2.906897 CAGGCAGCCCACACGTTT 60.907 61.111 8.22 0.00 0.00 3.60
40 41 3.714487 AACAGGCAGCCCACACGTT 62.714 57.895 8.22 1.24 0.00 3.99
41 42 4.189580 AACAGGCAGCCCACACGT 62.190 61.111 8.22 0.00 0.00 4.49
42 43 3.663176 CAACAGGCAGCCCACACG 61.663 66.667 8.22 0.00 0.00 4.49
43 44 2.519302 ACAACAGGCAGCCCACAC 60.519 61.111 8.22 0.00 0.00 3.82
44 45 2.519063 CACAACAGGCAGCCCACA 60.519 61.111 8.22 0.00 0.00 4.17
45 46 3.982241 GCACAACAGGCAGCCCAC 61.982 66.667 8.22 0.00 0.00 4.61
46 47 3.813606 ATGCACAACAGGCAGCCCA 62.814 57.895 8.22 0.00 45.68 5.36
47 48 2.993264 ATGCACAACAGGCAGCCC 60.993 61.111 8.22 0.00 45.68 5.19
48 49 2.260434 CATGCACAACAGGCAGCC 59.740 61.111 1.84 1.84 45.68 4.85
53 54 1.175654 TGTATGGCATGCACAACAGG 58.824 50.000 21.36 0.00 0.00 4.00
67 68 1.277326 CGACCACACGACCATGTATG 58.723 55.000 0.00 0.00 35.09 2.39
68 69 0.174845 CCGACCACACGACCATGTAT 59.825 55.000 0.00 0.00 35.09 2.29
69 70 1.587568 CCGACCACACGACCATGTA 59.412 57.895 0.00 0.00 35.09 2.29
70 71 2.342279 CCGACCACACGACCATGT 59.658 61.111 0.00 0.00 35.09 3.21
71 72 2.434185 CCCGACCACACGACCATG 60.434 66.667 0.00 0.00 35.09 3.66
72 73 2.920912 ACCCGACCACACGACCAT 60.921 61.111 0.00 0.00 35.09 3.55
73 74 3.918977 CACCCGACCACACGACCA 61.919 66.667 0.00 0.00 35.09 4.02
74 75 3.853597 GACACCCGACCACACGACC 62.854 68.421 0.00 0.00 35.09 4.79
75 76 1.518056 TAGACACCCGACCACACGAC 61.518 60.000 0.00 0.00 35.09 4.34
76 77 0.609957 ATAGACACCCGACCACACGA 60.610 55.000 0.00 0.00 35.09 4.35
77 78 0.245539 AATAGACACCCGACCACACG 59.754 55.000 0.00 0.00 0.00 4.49
78 79 3.454375 CATAATAGACACCCGACCACAC 58.546 50.000 0.00 0.00 0.00 3.82
79 80 2.159014 GCATAATAGACACCCGACCACA 60.159 50.000 0.00 0.00 0.00 4.17
80 81 2.480845 GCATAATAGACACCCGACCAC 58.519 52.381 0.00 0.00 0.00 4.16
81 82 1.414919 GGCATAATAGACACCCGACCA 59.585 52.381 0.00 0.00 0.00 4.02
82 83 1.414919 TGGCATAATAGACACCCGACC 59.585 52.381 0.00 0.00 0.00 4.79
83 84 2.480845 GTGGCATAATAGACACCCGAC 58.519 52.381 0.00 0.00 41.79 4.79
84 85 2.902705 GTGGCATAATAGACACCCGA 57.097 50.000 0.00 0.00 41.79 5.14
89 90 5.159273 TCACACTTGTGGCATAATAGACA 57.841 39.130 9.46 0.00 45.65 3.41
100 101 3.428870 GTCGATAACTGTCACACTTGTGG 59.571 47.826 9.46 0.00 45.65 4.17
101 102 4.048504 TGTCGATAACTGTCACACTTGTG 58.951 43.478 2.75 2.75 46.91 3.33
102 103 4.316205 TGTCGATAACTGTCACACTTGT 57.684 40.909 0.00 0.00 0.00 3.16
103 104 4.327357 GGATGTCGATAACTGTCACACTTG 59.673 45.833 0.00 0.00 0.00 3.16
104 105 4.021456 TGGATGTCGATAACTGTCACACTT 60.021 41.667 0.00 0.00 0.00 3.16
105 106 3.509967 TGGATGTCGATAACTGTCACACT 59.490 43.478 0.00 0.00 0.00 3.55
106 107 3.845178 TGGATGTCGATAACTGTCACAC 58.155 45.455 0.00 0.00 0.00 3.82
107 108 4.736126 ATGGATGTCGATAACTGTCACA 57.264 40.909 0.00 0.00 0.00 3.58
108 109 7.534085 TTTTATGGATGTCGATAACTGTCAC 57.466 36.000 0.00 0.00 0.00 3.67
109 110 8.731275 ATTTTTATGGATGTCGATAACTGTCA 57.269 30.769 0.00 0.00 0.00 3.58
117 118 9.283768 TGCATAGTAATTTTTATGGATGTCGAT 57.716 29.630 0.00 0.00 0.00 3.59
118 119 8.556194 GTGCATAGTAATTTTTATGGATGTCGA 58.444 33.333 0.00 0.00 31.67 4.20
119 120 8.559536 AGTGCATAGTAATTTTTATGGATGTCG 58.440 33.333 0.00 0.00 31.67 4.35
120 121 9.884465 GAGTGCATAGTAATTTTTATGGATGTC 57.116 33.333 0.00 5.93 31.67 3.06
121 122 8.559536 CGAGTGCATAGTAATTTTTATGGATGT 58.440 33.333 0.00 1.90 31.67 3.06
122 123 8.559536 ACGAGTGCATAGTAATTTTTATGGATG 58.440 33.333 0.00 5.55 31.67 3.51
123 124 8.677148 ACGAGTGCATAGTAATTTTTATGGAT 57.323 30.769 0.00 1.11 31.67 3.41
124 125 9.037737 GTACGAGTGCATAGTAATTTTTATGGA 57.962 33.333 0.00 5.47 0.00 3.41
125 126 9.042008 AGTACGAGTGCATAGTAATTTTTATGG 57.958 33.333 0.00 0.00 0.00 2.74
129 130 9.298774 GACTAGTACGAGTGCATAGTAATTTTT 57.701 33.333 13.78 0.00 0.00 1.94
130 131 8.464404 TGACTAGTACGAGTGCATAGTAATTTT 58.536 33.333 13.78 0.00 0.00 1.82
131 132 7.993101 TGACTAGTACGAGTGCATAGTAATTT 58.007 34.615 13.78 0.00 0.00 1.82
132 133 7.563888 TGACTAGTACGAGTGCATAGTAATT 57.436 36.000 13.78 0.00 0.00 1.40
133 134 6.293516 GCTGACTAGTACGAGTGCATAGTAAT 60.294 42.308 13.78 0.00 0.00 1.89
134 135 5.007430 GCTGACTAGTACGAGTGCATAGTAA 59.993 44.000 13.78 0.00 0.00 2.24
135 136 4.510711 GCTGACTAGTACGAGTGCATAGTA 59.489 45.833 13.78 0.00 0.00 1.82
136 137 3.312973 GCTGACTAGTACGAGTGCATAGT 59.687 47.826 13.78 0.82 0.00 2.12
137 138 3.312697 TGCTGACTAGTACGAGTGCATAG 59.687 47.826 13.78 7.45 0.00 2.23
138 139 3.064958 GTGCTGACTAGTACGAGTGCATA 59.935 47.826 19.20 1.01 32.78 3.14
139 140 2.092323 TGCTGACTAGTACGAGTGCAT 58.908 47.619 13.78 0.00 0.00 3.96
140 141 1.199327 GTGCTGACTAGTACGAGTGCA 59.801 52.381 13.78 14.16 29.89 4.57
141 142 1.469308 AGTGCTGACTAGTACGAGTGC 59.531 52.381 13.78 11.78 43.37 4.40
142 143 3.933955 AGTAGTGCTGACTAGTACGAGTG 59.066 47.826 13.78 1.35 43.37 3.51
143 144 4.183101 GAGTAGTGCTGACTAGTACGAGT 58.817 47.826 8.51 8.51 43.37 4.18
144 145 4.033129 GTGAGTAGTGCTGACTAGTACGAG 59.967 50.000 0.00 0.91 43.37 4.18
145 146 3.931468 GTGAGTAGTGCTGACTAGTACGA 59.069 47.826 0.00 0.00 43.37 3.43
146 147 3.063725 GGTGAGTAGTGCTGACTAGTACG 59.936 52.174 0.00 0.00 43.37 3.67
147 148 4.008330 TGGTGAGTAGTGCTGACTAGTAC 58.992 47.826 0.00 0.00 38.29 2.73
148 149 4.296621 TGGTGAGTAGTGCTGACTAGTA 57.703 45.455 0.00 0.00 38.29 1.82
149 150 3.156288 TGGTGAGTAGTGCTGACTAGT 57.844 47.619 0.00 0.00 40.49 2.57
150 151 3.508012 ACTTGGTGAGTAGTGCTGACTAG 59.492 47.826 0.00 0.00 36.65 2.57
151 152 3.497332 ACTTGGTGAGTAGTGCTGACTA 58.503 45.455 0.00 0.00 36.65 2.59
152 153 2.320781 ACTTGGTGAGTAGTGCTGACT 58.679 47.619 0.00 0.00 36.65 3.41
153 154 2.821991 ACTTGGTGAGTAGTGCTGAC 57.178 50.000 0.00 0.00 36.65 3.51
347 431 8.156165 AGTTCTGAATCTTCTTGTCAAAGATCT 58.844 33.333 1.14 0.00 41.47 2.75
348 432 8.321650 AGTTCTGAATCTTCTTGTCAAAGATC 57.678 34.615 1.14 0.00 41.47 2.75
349 433 8.156165 AGAGTTCTGAATCTTCTTGTCAAAGAT 58.844 33.333 0.00 0.00 43.58 2.40
350 434 7.504403 AGAGTTCTGAATCTTCTTGTCAAAGA 58.496 34.615 0.00 0.00 40.76 2.52
351 435 7.656948 AGAGAGTTCTGAATCTTCTTGTCAAAG 59.343 37.037 0.00 0.00 30.72 2.77
352 436 7.504403 AGAGAGTTCTGAATCTTCTTGTCAAA 58.496 34.615 0.00 0.00 30.72 2.69
378 463 1.067142 TCCGTCTACAAGATGTGGTGC 60.067 52.381 0.00 0.00 30.33 5.01
451 536 2.024871 CGAGATCGACGAGGTGGC 59.975 66.667 3.01 0.00 43.02 5.01
452 537 3.809423 TCGAGATCGACGAGGTGG 58.191 61.111 12.46 0.00 44.22 4.61
477 563 2.771089 TGCCATGACTTCAACAGAGAC 58.229 47.619 0.00 0.00 0.00 3.36
498 584 8.167392 TCCAGAAAAAGGAAATATACCTTCACA 58.833 33.333 12.53 0.00 45.55 3.58
538 624 4.386867 TGATACTCGATTGGTTGAGACC 57.613 45.455 0.00 0.00 46.71 3.85
560 646 9.442047 TGCACCTTCAAAGAAAAAGAAAAATAA 57.558 25.926 0.00 0.00 0.00 1.40
562 648 7.823799 TCTGCACCTTCAAAGAAAAAGAAAAAT 59.176 29.630 0.00 0.00 0.00 1.82
589 675 8.895845 CGAAAGTGACAAAATCAAAACTGATAG 58.104 33.333 0.00 0.00 39.72 2.08
616 702 6.627087 TCATTCATCCTGTAAAGAGGAACT 57.373 37.500 0.00 0.00 45.53 3.01
631 717 6.036083 ACGTAGTACATGCAGTTTCATTCATC 59.964 38.462 0.38 0.00 41.94 2.92
637 723 5.585500 GAAACGTAGTACATGCAGTTTCA 57.415 39.130 18.25 0.00 45.00 2.69
638 724 5.389516 CCTGAAACGTAGTACATGCAGTTTC 60.390 44.000 17.14 17.14 45.00 2.78
639 725 4.451096 CCTGAAACGTAGTACATGCAGTTT 59.549 41.667 9.24 6.63 45.00 2.66
640 726 3.994392 CCTGAAACGTAGTACATGCAGTT 59.006 43.478 9.24 0.00 45.00 3.16
641 727 3.257375 TCCTGAAACGTAGTACATGCAGT 59.743 43.478 9.24 0.00 45.00 4.40
642 728 3.845178 TCCTGAAACGTAGTACATGCAG 58.155 45.455 0.38 2.93 45.00 4.41
645 731 4.081862 TCCCTTCCTGAAACGTAGTACATG 60.082 45.833 0.38 0.00 45.00 3.21
646 732 4.091549 TCCCTTCCTGAAACGTAGTACAT 58.908 43.478 0.38 0.00 45.00 2.29
647 733 3.499338 TCCCTTCCTGAAACGTAGTACA 58.501 45.455 0.38 0.00 45.00 2.90
648 734 4.219288 TCTTCCCTTCCTGAAACGTAGTAC 59.781 45.833 0.00 0.00 45.00 2.73
649 735 4.410099 TCTTCCCTTCCTGAAACGTAGTA 58.590 43.478 0.00 0.00 45.00 1.82
651 737 3.955650 TCTTCCCTTCCTGAAACGTAG 57.044 47.619 0.00 0.00 0.00 3.51
700 789 0.893270 TGTTTCCAATCCAGCACCCG 60.893 55.000 0.00 0.00 0.00 5.28
729 830 4.826274 TTTTGGGGAGATGACTCTGTAG 57.174 45.455 0.00 0.00 42.28 2.74
787 895 3.626670 CCCATCTGATTCTGCTCTGTTTC 59.373 47.826 0.00 0.00 0.00 2.78
891 1013 4.889856 TCGACGGCGGCCATCATG 62.890 66.667 20.71 4.43 38.28 3.07
1062 1184 2.126424 GAGTCCGACAGTGCCGAC 60.126 66.667 0.00 0.00 0.00 4.79
1514 1657 0.888619 GTCCTCGTCTGTGTCATCCA 59.111 55.000 0.00 0.00 0.00 3.41
1524 1667 3.336568 TCCTCCCCGTCCTCGTCT 61.337 66.667 0.00 0.00 35.01 4.18
1646 1792 0.038251 CACGGCTAAGCTCACACTCA 60.038 55.000 0.00 0.00 0.00 3.41
1731 1888 6.308766 ACACGACACAAACCTATAAATACGTC 59.691 38.462 0.00 0.00 0.00 4.34
1746 1903 1.013596 CAAGCTCCAACACGACACAA 58.986 50.000 0.00 0.00 0.00 3.33
1757 1915 1.229428 CAAAGCGAGTTCAAGCTCCA 58.771 50.000 0.00 0.00 43.78 3.86
1759 1917 1.195674 GTCCAAAGCGAGTTCAAGCTC 59.804 52.381 0.00 0.00 43.78 4.09
1760 1918 1.230324 GTCCAAAGCGAGTTCAAGCT 58.770 50.000 0.00 0.00 46.97 3.74
1761 1919 0.944386 TGTCCAAAGCGAGTTCAAGC 59.056 50.000 0.00 0.00 0.00 4.01
1762 1920 1.069636 GCTGTCCAAAGCGAGTTCAAG 60.070 52.381 0.00 0.00 32.56 3.02
1769 1945 1.962822 CAGCTGCTGTCCAAAGCGA 60.963 57.895 21.21 0.00 46.65 4.93
1798 1975 6.444633 CGCTTAAATCGACTAGAATAAGGGA 58.555 40.000 0.00 0.00 41.88 4.20
1832 2205 3.181506 CGTCGATCTCAGATGAGTCACAA 60.182 47.826 9.56 0.00 42.60 3.33
1835 2208 1.332065 GCGTCGATCTCAGATGAGTCA 59.668 52.381 9.56 0.00 42.60 3.41
1843 2217 2.951745 GCCACGCGTCGATCTCAG 60.952 66.667 9.86 0.00 0.00 3.35
1861 2235 3.469899 TTGCTTAACACGCTGCAATAG 57.530 42.857 0.00 0.00 39.98 1.73
1862 2236 3.500299 TCTTTGCTTAACACGCTGCAATA 59.500 39.130 0.00 0.00 43.53 1.90
1931 2336 1.032114 AGCCCAATTTACCGCTGCTC 61.032 55.000 0.00 0.00 0.00 4.26
1932 2337 1.000896 AGCCCAATTTACCGCTGCT 60.001 52.632 0.00 0.00 0.00 4.24
1983 2389 5.347907 CGTAAAGGATAAGGGAATATGCGTC 59.652 44.000 0.00 0.00 0.00 5.19
1993 2399 3.624410 CCGAAAACCGTAAAGGATAAGGG 59.376 47.826 0.00 0.00 45.00 3.95
2005 2411 4.024641 GTGTTCATAACTTCCGAAAACCGT 60.025 41.667 0.00 0.00 36.31 4.83
2014 2420 6.697892 CCTTCTATCGAGTGTTCATAACTTCC 59.302 42.308 0.00 0.00 0.00 3.46
2015 2421 6.199342 GCCTTCTATCGAGTGTTCATAACTTC 59.801 42.308 0.00 0.00 0.00 3.01
2016 2422 6.043411 GCCTTCTATCGAGTGTTCATAACTT 58.957 40.000 0.00 0.00 0.00 2.66
2017 2423 5.452077 GGCCTTCTATCGAGTGTTCATAACT 60.452 44.000 0.00 0.00 0.00 2.24
2018 2424 4.745620 GGCCTTCTATCGAGTGTTCATAAC 59.254 45.833 0.00 0.00 0.00 1.89
2019 2425 4.499188 CGGCCTTCTATCGAGTGTTCATAA 60.499 45.833 0.00 0.00 0.00 1.90
2020 2426 3.004419 CGGCCTTCTATCGAGTGTTCATA 59.996 47.826 0.00 0.00 0.00 2.15
2021 2427 2.223829 CGGCCTTCTATCGAGTGTTCAT 60.224 50.000 0.00 0.00 0.00 2.57
2022 2428 1.134367 CGGCCTTCTATCGAGTGTTCA 59.866 52.381 0.00 0.00 0.00 3.18
2023 2429 1.134560 ACGGCCTTCTATCGAGTGTTC 59.865 52.381 0.00 0.00 0.00 3.18
2024 2430 1.183549 ACGGCCTTCTATCGAGTGTT 58.816 50.000 0.00 0.00 0.00 3.32
2025 2431 1.135083 CAACGGCCTTCTATCGAGTGT 60.135 52.381 0.00 0.00 0.00 3.55
2026 2432 1.560923 CAACGGCCTTCTATCGAGTG 58.439 55.000 0.00 0.00 0.00 3.51
2027 2433 0.460311 CCAACGGCCTTCTATCGAGT 59.540 55.000 0.00 0.00 0.00 4.18
2028 2434 0.744874 TCCAACGGCCTTCTATCGAG 59.255 55.000 0.00 0.00 0.00 4.04
2029 2435 0.744874 CTCCAACGGCCTTCTATCGA 59.255 55.000 0.00 0.00 0.00 3.59
2030 2436 0.876342 GCTCCAACGGCCTTCTATCG 60.876 60.000 0.00 0.00 0.00 2.92
2031 2437 0.178068 TGCTCCAACGGCCTTCTATC 59.822 55.000 0.00 0.00 0.00 2.08
2032 2438 0.839946 ATGCTCCAACGGCCTTCTAT 59.160 50.000 0.00 0.00 0.00 1.98
2033 2439 0.618458 AATGCTCCAACGGCCTTCTA 59.382 50.000 0.00 0.00 0.00 2.10
2034 2440 0.251341 AAATGCTCCAACGGCCTTCT 60.251 50.000 0.00 0.00 0.00 2.85
2035 2441 0.603065 AAAATGCTCCAACGGCCTTC 59.397 50.000 0.00 0.00 0.00 3.46
2036 2442 0.318120 CAAAATGCTCCAACGGCCTT 59.682 50.000 0.00 0.00 0.00 4.35
2037 2443 0.827507 ACAAAATGCTCCAACGGCCT 60.828 50.000 0.00 0.00 0.00 5.19
2038 2444 0.885196 TACAAAATGCTCCAACGGCC 59.115 50.000 0.00 0.00 0.00 6.13
2039 2445 2.715737 TTACAAAATGCTCCAACGGC 57.284 45.000 0.00 0.00 0.00 5.68
2040 2446 3.925913 CCATTTACAAAATGCTCCAACGG 59.074 43.478 6.82 0.00 0.00 4.44
2041 2447 4.804108 TCCATTTACAAAATGCTCCAACG 58.196 39.130 6.82 0.00 0.00 4.10
2042 2448 4.627035 GCTCCATTTACAAAATGCTCCAAC 59.373 41.667 6.82 0.00 0.00 3.77
2043 2449 4.282957 TGCTCCATTTACAAAATGCTCCAA 59.717 37.500 6.82 0.00 0.00 3.53
2044 2450 3.831333 TGCTCCATTTACAAAATGCTCCA 59.169 39.130 6.82 1.59 0.00 3.86
2045 2451 4.454728 TGCTCCATTTACAAAATGCTCC 57.545 40.909 6.82 0.00 0.00 4.70
2046 2452 6.973229 AAATGCTCCATTTACAAAATGCTC 57.027 33.333 6.82 0.40 41.50 4.26
2047 2453 6.091169 CGAAAATGCTCCATTTACAAAATGCT 59.909 34.615 6.82 0.00 42.32 3.79
2048 2454 6.242829 CGAAAATGCTCCATTTACAAAATGC 58.757 36.000 6.82 0.00 42.32 3.56
2049 2455 6.589523 TCCGAAAATGCTCCATTTACAAAATG 59.410 34.615 3.86 5.56 42.32 2.32
2050 2456 6.696411 TCCGAAAATGCTCCATTTACAAAAT 58.304 32.000 3.86 0.00 42.32 1.82
2051 2457 6.090483 TCCGAAAATGCTCCATTTACAAAA 57.910 33.333 3.86 0.00 42.32 2.44
2052 2458 5.713792 TCCGAAAATGCTCCATTTACAAA 57.286 34.783 3.86 0.00 42.32 2.83
2053 2459 5.242838 ACTTCCGAAAATGCTCCATTTACAA 59.757 36.000 3.86 0.00 42.32 2.41
2054 2460 4.764823 ACTTCCGAAAATGCTCCATTTACA 59.235 37.500 3.86 0.00 42.32 2.41
2055 2461 5.106317 TGACTTCCGAAAATGCTCCATTTAC 60.106 40.000 3.86 0.00 42.32 2.01
2056 2462 5.007034 TGACTTCCGAAAATGCTCCATTTA 58.993 37.500 3.86 0.00 42.32 1.40
2057 2463 3.826157 TGACTTCCGAAAATGCTCCATTT 59.174 39.130 0.00 0.00 44.62 2.32
2058 2464 3.420893 TGACTTCCGAAAATGCTCCATT 58.579 40.909 0.00 0.00 35.39 3.16
2059 2465 3.071874 TGACTTCCGAAAATGCTCCAT 57.928 42.857 0.00 0.00 0.00 3.41
2060 2466 2.559698 TGACTTCCGAAAATGCTCCA 57.440 45.000 0.00 0.00 0.00 3.86
2061 2467 2.814336 ACTTGACTTCCGAAAATGCTCC 59.186 45.455 0.00 0.00 0.00 4.70
2062 2468 5.803020 ATACTTGACTTCCGAAAATGCTC 57.197 39.130 0.00 0.00 0.00 4.26
2063 2469 6.575162 AAATACTTGACTTCCGAAAATGCT 57.425 33.333 0.00 0.00 0.00 3.79
2064 2470 7.084486 AGAAAATACTTGACTTCCGAAAATGC 58.916 34.615 0.00 0.00 0.00 3.56
2065 2471 9.463443 AAAGAAAATACTTGACTTCCGAAAATG 57.537 29.630 0.00 0.00 0.00 2.32
2068 2474 8.287503 GCTAAAGAAAATACTTGACTTCCGAAA 58.712 33.333 0.00 0.00 0.00 3.46
2069 2475 7.094933 GGCTAAAGAAAATACTTGACTTCCGAA 60.095 37.037 0.00 0.00 0.00 4.30
2070 2476 6.370718 GGCTAAAGAAAATACTTGACTTCCGA 59.629 38.462 0.00 0.00 0.00 4.55
2071 2477 6.403309 GGGCTAAAGAAAATACTTGACTTCCG 60.403 42.308 0.00 0.00 0.00 4.30
2072 2478 6.659668 AGGGCTAAAGAAAATACTTGACTTCC 59.340 38.462 0.00 0.00 0.00 3.46
2073 2479 7.689446 AGGGCTAAAGAAAATACTTGACTTC 57.311 36.000 0.00 0.00 0.00 3.01
2176 2582 3.624777 CTCCAACCATTGCAGGTAATCT 58.375 45.455 0.00 0.00 42.25 2.40
2229 2638 4.680171 AAGCCGTTCTTTAATCCTTTCG 57.320 40.909 0.00 0.00 0.00 3.46
2310 2719 0.036164 ACACCGGAATAGCTTGTGCA 59.964 50.000 9.46 0.00 42.74 4.57
2445 2854 3.706594 TCTTCGGATAGCAGAGTTTCCAT 59.293 43.478 0.00 0.00 0.00 3.41
2545 2954 3.738282 GCACATAACGACTCTGGATCATC 59.262 47.826 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.