Multiple sequence alignment - TraesCS4A01G368000

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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 TraesCS4A01G368000 chr4A 100.000 3111 0 0 1 3111 640937834 640934724 0.000000e+00 5746.0
1 TraesCS4A01G368000 chr2A 97.084 2846 71 4 276 3111 688774574 688777417 0.000000e+00 4785.0
2 TraesCS4A01G368000 chr2A 93.268 2867 111 36 278 3111 84021467 84024284 0.000000e+00 4150.0
3 TraesCS4A01G368000 chr6D 93.967 2851 117 32 277 3111 472510962 472513773 0.000000e+00 4261.0
4 TraesCS4A01G368000 chr7D 93.583 2852 130 31 277 3111 245402432 245399617 0.000000e+00 4204.0
5 TraesCS4A01G368000 chr7D 93.018 2850 134 32 279 3111 10896028 10893227 0.000000e+00 4100.0
6 TraesCS4A01G368000 chr7D 94.632 1751 72 15 1371 3111 608523830 608522092 0.000000e+00 2693.0
7 TraesCS4A01G368000 chr5D 93.583 2852 129 32 277 3111 565815801 565818615 0.000000e+00 4204.0
8 TraesCS4A01G368000 chr5D 92.364 275 12 3 1 274 531460261 531460527 1.750000e-102 383.0
9 TraesCS4A01G368000 chr5D 93.293 164 5 1 117 274 531473182 531473345 1.440000e-58 237.0
10 TraesCS4A01G368000 chr5D 91.071 56 5 0 117 172 531468885 531468940 3.330000e-10 76.8
11 TraesCS4A01G368000 chr3D 93.577 2849 127 29 278 3110 574856805 574853997 0.000000e+00 4196.0
12 TraesCS4A01G368000 chr3D 93.096 2868 134 36 272 3111 42349624 42352455 0.000000e+00 4141.0
13 TraesCS4A01G368000 chr3D 93.700 2746 108 32 278 2998 359622499 359625204 0.000000e+00 4052.0
14 TraesCS4A01G368000 chr3D 93.227 2746 124 30 278 2998 85226134 85228842 0.000000e+00 3984.0
15 TraesCS4A01G368000 chr5A 98.223 2364 38 4 595 2957 700612173 700614533 0.000000e+00 4130.0
16 TraesCS4A01G368000 chr1D 93.100 2855 141 31 272 3111 6491902 6489089 0.000000e+00 4130.0
17 TraesCS4A01G368000 chr1D 93.511 2743 121 28 278 2998 475528296 475525589 0.000000e+00 4026.0
18 TraesCS4A01G368000 chr1D 90.972 2758 164 42 270 2997 110904260 110901558 0.000000e+00 3635.0
19 TraesCS4A01G368000 chr4D 93.486 2748 110 39 278 2997 428529859 428532565 0.000000e+00 4019.0
20 TraesCS4A01G368000 chr6A 95.907 1759 61 9 1360 3111 608439921 608438167 0.000000e+00 2839.0
21 TraesCS4A01G368000 chr6A 95.907 1759 61 9 1360 3111 608466207 608464453 0.000000e+00 2839.0
22 TraesCS4A01G368000 chr6A 94.667 1275 57 8 1730 2998 584382527 584381258 0.000000e+00 1967.0
23 TraesCS4A01G368000 chr3B 97.743 1462 29 3 1467 2927 766033480 766034938 0.000000e+00 2514.0
24 TraesCS4A01G368000 chr3B 96.245 932 34 1 278 1209 766032546 766033476 0.000000e+00 1526.0
25 TraesCS4A01G368000 chr5B 90.769 195 13 1 76 270 670792508 670792697 3.980000e-64 255.0


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 TraesCS4A01G368000 chr4A 640934724 640937834 3110 True 5746 5746 100.000 1 3111 1 chr4A.!!$R1 3110
1 TraesCS4A01G368000 chr2A 688774574 688777417 2843 False 4785 4785 97.084 276 3111 1 chr2A.!!$F2 2835
2 TraesCS4A01G368000 chr2A 84021467 84024284 2817 False 4150 4150 93.268 278 3111 1 chr2A.!!$F1 2833
3 TraesCS4A01G368000 chr6D 472510962 472513773 2811 False 4261 4261 93.967 277 3111 1 chr6D.!!$F1 2834
4 TraesCS4A01G368000 chr7D 245399617 245402432 2815 True 4204 4204 93.583 277 3111 1 chr7D.!!$R2 2834
5 TraesCS4A01G368000 chr7D 10893227 10896028 2801 True 4100 4100 93.018 279 3111 1 chr7D.!!$R1 2832
6 TraesCS4A01G368000 chr7D 608522092 608523830 1738 True 2693 2693 94.632 1371 3111 1 chr7D.!!$R3 1740
7 TraesCS4A01G368000 chr5D 565815801 565818615 2814 False 4204 4204 93.583 277 3111 1 chr5D.!!$F4 2834
8 TraesCS4A01G368000 chr3D 574853997 574856805 2808 True 4196 4196 93.577 278 3110 1 chr3D.!!$R1 2832
9 TraesCS4A01G368000 chr3D 42349624 42352455 2831 False 4141 4141 93.096 272 3111 1 chr3D.!!$F1 2839
10 TraesCS4A01G368000 chr3D 359622499 359625204 2705 False 4052 4052 93.700 278 2998 1 chr3D.!!$F3 2720
11 TraesCS4A01G368000 chr3D 85226134 85228842 2708 False 3984 3984 93.227 278 2998 1 chr3D.!!$F2 2720
12 TraesCS4A01G368000 chr5A 700612173 700614533 2360 False 4130 4130 98.223 595 2957 1 chr5A.!!$F1 2362
13 TraesCS4A01G368000 chr1D 6489089 6491902 2813 True 4130 4130 93.100 272 3111 1 chr1D.!!$R1 2839
14 TraesCS4A01G368000 chr1D 475525589 475528296 2707 True 4026 4026 93.511 278 2998 1 chr1D.!!$R3 2720
15 TraesCS4A01G368000 chr1D 110901558 110904260 2702 True 3635 3635 90.972 270 2997 1 chr1D.!!$R2 2727
16 TraesCS4A01G368000 chr4D 428529859 428532565 2706 False 4019 4019 93.486 278 2997 1 chr4D.!!$F1 2719
17 TraesCS4A01G368000 chr6A 608438167 608439921 1754 True 2839 2839 95.907 1360 3111 1 chr6A.!!$R2 1751
18 TraesCS4A01G368000 chr6A 608464453 608466207 1754 True 2839 2839 95.907 1360 3111 1 chr6A.!!$R3 1751
19 TraesCS4A01G368000 chr6A 584381258 584382527 1269 True 1967 1967 94.667 1730 2998 1 chr6A.!!$R1 1268
20 TraesCS4A01G368000 chr3B 766032546 766034938 2392 False 2020 2514 96.994 278 2927 2 chr3B.!!$F1 2649

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
263 264 0.036306 GGTGTCTCCATCCGTGGTTT 59.964 55.000 0.0 0.0 46.16 3.27 F
264 265 1.276989 GGTGTCTCCATCCGTGGTTTA 59.723 52.381 0.0 0.0 46.16 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1544 0.03254 CTGAAACCCAACCTGCTTGC 59.967 55.000 0.0 0.0 0.0 4.01 R
2295 2436 7.54040 TCAAATACAGGCAAAACATTCATTACG 59.460 33.333 0.0 0.0 0.0 3.18 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
23 24 4.177026 AGCAAGCAAGAAGATGTAGTACG 58.823 43.478 0.00 0.00 0.00 3.67
24 25 3.242123 GCAAGCAAGAAGATGTAGTACGC 60.242 47.826 0.00 0.00 0.00 4.42
25 26 2.798680 AGCAAGAAGATGTAGTACGCG 58.201 47.619 3.53 3.53 0.00 6.01
26 27 2.163815 AGCAAGAAGATGTAGTACGCGT 59.836 45.455 19.17 19.17 0.00 6.01
27 28 2.279136 GCAAGAAGATGTAGTACGCGTG 59.721 50.000 24.59 0.00 0.00 5.34
28 29 3.499048 CAAGAAGATGTAGTACGCGTGT 58.501 45.455 24.59 11.88 0.00 4.49
29 30 3.132629 AGAAGATGTAGTACGCGTGTG 57.867 47.619 24.59 0.00 0.00 3.82
30 31 2.745821 AGAAGATGTAGTACGCGTGTGA 59.254 45.455 24.59 2.93 0.00 3.58
31 32 2.539346 AGATGTAGTACGCGTGTGAC 57.461 50.000 24.59 16.47 0.00 3.67
32 33 1.131883 AGATGTAGTACGCGTGTGACC 59.868 52.381 24.59 6.41 0.00 4.02
33 34 1.131883 GATGTAGTACGCGTGTGACCT 59.868 52.381 24.59 11.76 0.00 3.85
34 35 0.518636 TGTAGTACGCGTGTGACCTC 59.481 55.000 24.59 8.67 0.00 3.85
35 36 0.179179 GTAGTACGCGTGTGACCTCC 60.179 60.000 24.59 0.00 0.00 4.30
36 37 0.606130 TAGTACGCGTGTGACCTCCA 60.606 55.000 24.59 0.00 0.00 3.86
37 38 1.443872 GTACGCGTGTGACCTCCAG 60.444 63.158 24.59 0.00 0.00 3.86
38 39 1.900016 TACGCGTGTGACCTCCAGT 60.900 57.895 24.59 0.00 0.00 4.00
39 40 0.606130 TACGCGTGTGACCTCCAGTA 60.606 55.000 24.59 0.00 0.00 2.74
40 41 1.154016 CGCGTGTGACCTCCAGTAG 60.154 63.158 0.00 0.00 0.00 2.57
41 42 1.583495 CGCGTGTGACCTCCAGTAGA 61.583 60.000 0.00 0.00 0.00 2.59
42 43 0.601558 GCGTGTGACCTCCAGTAGAA 59.398 55.000 0.00 0.00 0.00 2.10
43 44 1.669211 GCGTGTGACCTCCAGTAGAAC 60.669 57.143 0.00 0.00 0.00 3.01
44 45 1.067776 CGTGTGACCTCCAGTAGAACC 60.068 57.143 0.00 0.00 0.00 3.62
45 46 2.249139 GTGTGACCTCCAGTAGAACCT 58.751 52.381 0.00 0.00 0.00 3.50
46 47 2.231721 GTGTGACCTCCAGTAGAACCTC 59.768 54.545 0.00 0.00 0.00 3.85
47 48 1.826096 GTGACCTCCAGTAGAACCTCC 59.174 57.143 0.00 0.00 0.00 4.30
48 49 1.273098 TGACCTCCAGTAGAACCTCCC 60.273 57.143 0.00 0.00 0.00 4.30
49 50 1.007359 GACCTCCAGTAGAACCTCCCT 59.993 57.143 0.00 0.00 0.00 4.20
50 51 2.244252 GACCTCCAGTAGAACCTCCCTA 59.756 54.545 0.00 0.00 0.00 3.53
51 52 2.245287 ACCTCCAGTAGAACCTCCCTAG 59.755 54.545 0.00 0.00 0.00 3.02
52 53 2.312390 CTCCAGTAGAACCTCCCTAGC 58.688 57.143 0.00 0.00 0.00 3.42
53 54 1.033574 CCAGTAGAACCTCCCTAGCG 58.966 60.000 0.00 0.00 0.00 4.26
54 55 1.033574 CAGTAGAACCTCCCTAGCGG 58.966 60.000 0.00 0.00 0.00 5.52
55 56 0.756070 AGTAGAACCTCCCTAGCGGC 60.756 60.000 0.00 0.00 0.00 6.53
56 57 1.041447 GTAGAACCTCCCTAGCGGCA 61.041 60.000 1.45 0.00 0.00 5.69
57 58 0.755698 TAGAACCTCCCTAGCGGCAG 60.756 60.000 1.45 0.00 0.00 4.85
58 59 2.038975 AACCTCCCTAGCGGCAGA 59.961 61.111 1.45 0.00 0.00 4.26
59 60 1.612442 AACCTCCCTAGCGGCAGAA 60.612 57.895 1.45 0.00 0.00 3.02
60 61 1.900545 AACCTCCCTAGCGGCAGAAC 61.901 60.000 1.45 0.00 0.00 3.01
61 62 2.501610 CTCCCTAGCGGCAGAACC 59.498 66.667 1.45 0.00 0.00 3.62
86 87 1.967319 AAAAGAGTGCTTCCTTCGCA 58.033 45.000 0.00 0.00 31.82 5.10
91 92 4.361253 TGCTTCCTTCGCACTGTC 57.639 55.556 0.00 0.00 31.40 3.51
92 93 1.748403 TGCTTCCTTCGCACTGTCT 59.252 52.632 0.00 0.00 31.40 3.41
93 94 0.319900 TGCTTCCTTCGCACTGTCTC 60.320 55.000 0.00 0.00 31.40 3.36
94 95 0.037790 GCTTCCTTCGCACTGTCTCT 60.038 55.000 0.00 0.00 0.00 3.10
95 96 1.989430 CTTCCTTCGCACTGTCTCTC 58.011 55.000 0.00 0.00 0.00 3.20
96 97 1.543802 CTTCCTTCGCACTGTCTCTCT 59.456 52.381 0.00 0.00 0.00 3.10
97 98 0.884514 TCCTTCGCACTGTCTCTCTG 59.115 55.000 0.00 0.00 0.00 3.35
98 99 0.735632 CCTTCGCACTGTCTCTCTGC 60.736 60.000 0.00 0.00 0.00 4.26
99 100 0.243365 CTTCGCACTGTCTCTCTGCT 59.757 55.000 0.00 0.00 0.00 4.24
100 101 0.676184 TTCGCACTGTCTCTCTGCTT 59.324 50.000 0.00 0.00 0.00 3.91
101 102 0.038801 TCGCACTGTCTCTCTGCTTG 60.039 55.000 0.00 0.00 0.00 4.01
102 103 0.319383 CGCACTGTCTCTCTGCTTGT 60.319 55.000 0.00 0.00 0.00 3.16
103 104 1.427435 GCACTGTCTCTCTGCTTGTC 58.573 55.000 0.00 0.00 0.00 3.18
104 105 1.000731 GCACTGTCTCTCTGCTTGTCT 59.999 52.381 0.00 0.00 0.00 3.41
105 106 2.926159 GCACTGTCTCTCTGCTTGTCTC 60.926 54.545 0.00 0.00 0.00 3.36
106 107 1.892474 ACTGTCTCTCTGCTTGTCTCC 59.108 52.381 0.00 0.00 0.00 3.71
107 108 1.891811 CTGTCTCTCTGCTTGTCTCCA 59.108 52.381 0.00 0.00 0.00 3.86
108 109 1.615883 TGTCTCTCTGCTTGTCTCCAC 59.384 52.381 0.00 0.00 0.00 4.02
109 110 1.067213 GTCTCTCTGCTTGTCTCCACC 60.067 57.143 0.00 0.00 0.00 4.61
110 111 0.108898 CTCTCTGCTTGTCTCCACCG 60.109 60.000 0.00 0.00 0.00 4.94
111 112 0.539669 TCTCTGCTTGTCTCCACCGA 60.540 55.000 0.00 0.00 0.00 4.69
112 113 0.534412 CTCTGCTTGTCTCCACCGAT 59.466 55.000 0.00 0.00 0.00 4.18
113 114 0.247460 TCTGCTTGTCTCCACCGATG 59.753 55.000 0.00 0.00 0.00 3.84
114 115 0.036952 CTGCTTGTCTCCACCGATGT 60.037 55.000 0.00 0.00 0.00 3.06
115 116 0.396435 TGCTTGTCTCCACCGATGTT 59.604 50.000 0.00 0.00 0.00 2.71
116 117 1.621317 TGCTTGTCTCCACCGATGTTA 59.379 47.619 0.00 0.00 0.00 2.41
117 118 2.236146 TGCTTGTCTCCACCGATGTTAT 59.764 45.455 0.00 0.00 0.00 1.89
118 119 2.609459 GCTTGTCTCCACCGATGTTATG 59.391 50.000 0.00 0.00 0.00 1.90
119 120 3.861840 CTTGTCTCCACCGATGTTATGT 58.138 45.455 0.00 0.00 0.00 2.29
120 121 4.679639 GCTTGTCTCCACCGATGTTATGTA 60.680 45.833 0.00 0.00 0.00 2.29
121 122 5.408880 TTGTCTCCACCGATGTTATGTAA 57.591 39.130 0.00 0.00 0.00 2.41
122 123 4.751060 TGTCTCCACCGATGTTATGTAAC 58.249 43.478 0.00 0.00 36.74 2.50
123 124 3.795101 GTCTCCACCGATGTTATGTAACG 59.205 47.826 0.00 0.00 39.00 3.18
124 125 2.538449 CTCCACCGATGTTATGTAACGC 59.462 50.000 0.00 0.00 39.00 4.84
125 126 2.094130 TCCACCGATGTTATGTAACGCA 60.094 45.455 0.00 0.00 39.00 5.24
126 127 2.869801 CCACCGATGTTATGTAACGCAT 59.130 45.455 0.00 0.00 39.00 4.73
127 128 4.052608 CCACCGATGTTATGTAACGCATA 58.947 43.478 0.00 0.00 39.00 3.14
128 129 4.084745 CCACCGATGTTATGTAACGCATAC 60.085 45.833 0.00 0.00 39.57 2.39
129 130 4.053295 ACCGATGTTATGTAACGCATACC 58.947 43.478 0.00 0.00 39.57 2.73
130 131 4.052608 CCGATGTTATGTAACGCATACCA 58.947 43.478 0.00 0.00 39.57 3.25
131 132 4.084745 CCGATGTTATGTAACGCATACCAC 60.085 45.833 0.00 0.00 39.57 4.16
132 133 4.504826 CGATGTTATGTAACGCATACCACA 59.495 41.667 0.00 0.00 39.57 4.17
133 134 5.555631 CGATGTTATGTAACGCATACCACAC 60.556 44.000 0.00 0.00 39.57 3.82
134 135 4.566987 TGTTATGTAACGCATACCACACA 58.433 39.130 0.00 0.00 39.57 3.72
135 136 4.389382 TGTTATGTAACGCATACCACACAC 59.611 41.667 0.00 0.00 39.57 3.82
136 137 1.420378 TGTAACGCATACCACACACG 58.580 50.000 0.00 0.00 33.27 4.49
137 138 1.269673 TGTAACGCATACCACACACGT 60.270 47.619 0.00 0.00 38.88 4.49
138 139 1.125384 GTAACGCATACCACACACGTG 59.875 52.381 15.48 15.48 43.21 4.49
139 140 0.531090 AACGCATACCACACACGTGT 60.531 50.000 17.22 17.22 46.17 4.49
140 141 0.942410 ACGCATACCACACACGTGTC 60.942 55.000 20.49 3.78 42.83 3.67
141 142 1.623081 CGCATACCACACACGTGTCC 61.623 60.000 20.49 0.00 42.83 4.02
142 143 0.601576 GCATACCACACACGTGTCCA 60.602 55.000 20.49 2.33 42.83 4.02
143 144 1.144969 CATACCACACACGTGTCCAC 58.855 55.000 20.49 0.00 42.83 4.02
153 154 4.634133 GTGTCCACGTCGACGGCA 62.634 66.667 37.89 26.81 44.95 5.69
154 155 4.337060 TGTCCACGTCGACGGCAG 62.337 66.667 37.89 26.66 44.95 4.85
155 156 4.338539 GTCCACGTCGACGGCAGT 62.339 66.667 37.89 17.63 44.95 4.40
156 157 3.598715 TCCACGTCGACGGCAGTT 61.599 61.111 37.89 17.23 44.95 3.16
157 158 2.256158 CCACGTCGACGGCAGTTA 59.744 61.111 37.89 0.00 44.95 2.24
158 159 1.372004 CCACGTCGACGGCAGTTAA 60.372 57.895 37.89 0.00 44.95 2.01
159 160 1.611592 CCACGTCGACGGCAGTTAAC 61.612 60.000 37.89 0.00 44.95 2.01
160 161 0.935831 CACGTCGACGGCAGTTAACA 60.936 55.000 37.89 0.00 44.95 2.41
161 162 0.038892 ACGTCGACGGCAGTTAACAT 60.039 50.000 37.89 13.44 44.95 2.71
162 163 0.638746 CGTCGACGGCAGTTAACATC 59.361 55.000 29.70 0.00 35.37 3.06
163 164 0.638746 GTCGACGGCAGTTAACATCG 59.361 55.000 8.61 10.51 0.00 3.84
164 165 1.074319 TCGACGGCAGTTAACATCGC 61.074 55.000 8.61 7.22 0.00 4.58
165 166 1.076533 CGACGGCAGTTAACATCGCT 61.077 55.000 8.61 0.41 0.00 4.93
166 167 0.370273 GACGGCAGTTAACATCGCTG 59.630 55.000 17.19 17.19 36.79 5.18
167 168 0.037697 ACGGCAGTTAACATCGCTGA 60.038 50.000 22.72 0.00 34.76 4.26
168 169 1.075542 CGGCAGTTAACATCGCTGAA 58.924 50.000 14.87 0.00 32.30 3.02
169 170 1.463056 CGGCAGTTAACATCGCTGAAA 59.537 47.619 14.87 0.00 32.30 2.69
170 171 2.095853 CGGCAGTTAACATCGCTGAAAT 59.904 45.455 14.87 0.00 32.30 2.17
171 172 3.308595 CGGCAGTTAACATCGCTGAAATA 59.691 43.478 14.87 0.00 32.30 1.40
172 173 4.024893 CGGCAGTTAACATCGCTGAAATAT 60.025 41.667 14.87 0.00 32.30 1.28
173 174 5.504010 CGGCAGTTAACATCGCTGAAATATT 60.504 40.000 14.87 0.00 32.30 1.28
174 175 6.265577 GGCAGTTAACATCGCTGAAATATTT 58.734 36.000 8.61 0.00 32.39 1.40
175 176 6.751888 GGCAGTTAACATCGCTGAAATATTTT 59.248 34.615 8.61 0.00 32.39 1.82
176 177 7.253750 GGCAGTTAACATCGCTGAAATATTTTG 60.254 37.037 8.61 0.00 32.39 2.44
177 178 7.273381 GCAGTTAACATCGCTGAAATATTTTGT 59.727 33.333 8.61 0.00 32.39 2.83
178 179 8.577939 CAGTTAACATCGCTGAAATATTTTGTG 58.422 33.333 8.61 5.87 32.39 3.33
179 180 8.296713 AGTTAACATCGCTGAAATATTTTGTGT 58.703 29.630 8.61 0.00 0.00 3.72
180 181 8.575454 GTTAACATCGCTGAAATATTTTGTGTC 58.425 33.333 1.43 0.00 0.00 3.67
181 182 5.323900 ACATCGCTGAAATATTTTGTGTCG 58.676 37.500 1.43 3.18 0.00 4.35
182 183 5.121611 ACATCGCTGAAATATTTTGTGTCGA 59.878 36.000 1.43 7.96 0.00 4.20
183 184 4.953269 TCGCTGAAATATTTTGTGTCGAC 58.047 39.130 9.11 9.11 0.00 4.20
184 185 3.773549 CGCTGAAATATTTTGTGTCGACG 59.226 43.478 11.62 0.00 0.00 5.12
185 186 4.665645 CGCTGAAATATTTTGTGTCGACGT 60.666 41.667 11.62 0.00 0.00 4.34
186 187 4.781528 GCTGAAATATTTTGTGTCGACGTC 59.218 41.667 11.62 5.18 0.00 4.34
187 188 4.936974 TGAAATATTTTGTGTCGACGTCG 58.063 39.130 31.30 31.30 41.45 5.12
196 197 2.959372 TCGACGTCGATGGCAGTT 59.041 55.556 34.97 0.00 44.22 3.16
197 198 2.173433 TCGACGTCGATGGCAGTTA 58.827 52.632 34.97 11.39 44.22 2.24
198 199 0.522626 TCGACGTCGATGGCAGTTAA 59.477 50.000 34.97 10.59 44.22 2.01
199 200 0.638746 CGACGTCGATGGCAGTTAAC 59.361 55.000 33.35 0.00 43.02 2.01
200 201 1.705256 GACGTCGATGGCAGTTAACA 58.295 50.000 5.34 0.00 0.00 2.41
201 202 1.389106 GACGTCGATGGCAGTTAACAC 59.611 52.381 5.34 0.00 0.00 3.32
202 203 1.000506 ACGTCGATGGCAGTTAACACT 59.999 47.619 9.90 0.00 0.00 3.55
212 213 3.253371 CAGTTAACACTGCTGAAACGG 57.747 47.619 8.61 0.00 44.16 4.44
213 214 2.612212 CAGTTAACACTGCTGAAACGGT 59.388 45.455 8.61 0.00 44.16 4.83
214 215 3.805422 CAGTTAACACTGCTGAAACGGTA 59.195 43.478 8.61 0.00 44.16 4.02
215 216 4.451096 CAGTTAACACTGCTGAAACGGTAT 59.549 41.667 8.61 0.00 44.16 2.73
216 217 5.049680 CAGTTAACACTGCTGAAACGGTATT 60.050 40.000 8.61 0.00 44.16 1.89
217 218 5.529800 AGTTAACACTGCTGAAACGGTATTT 59.470 36.000 8.61 0.00 0.00 1.40
218 219 4.911514 AACACTGCTGAAACGGTATTTT 57.088 36.364 0.00 0.00 0.00 1.82
219 220 4.911514 ACACTGCTGAAACGGTATTTTT 57.088 36.364 0.00 0.00 0.00 1.94
220 221 6.380095 AACACTGCTGAAACGGTATTTTTA 57.620 33.333 0.00 0.00 0.00 1.52
221 222 6.569179 ACACTGCTGAAACGGTATTTTTAT 57.431 33.333 0.00 0.00 0.00 1.40
222 223 6.977213 ACACTGCTGAAACGGTATTTTTATT 58.023 32.000 0.00 0.00 0.00 1.40
223 224 6.861055 ACACTGCTGAAACGGTATTTTTATTG 59.139 34.615 0.00 0.00 0.00 1.90
224 225 6.861055 CACTGCTGAAACGGTATTTTTATTGT 59.139 34.615 0.00 0.00 0.00 2.71
225 226 7.060633 CACTGCTGAAACGGTATTTTTATTGTC 59.939 37.037 0.00 0.00 0.00 3.18
226 227 6.971602 TGCTGAAACGGTATTTTTATTGTCA 58.028 32.000 0.00 0.00 0.00 3.58
227 228 6.858993 TGCTGAAACGGTATTTTTATTGTCAC 59.141 34.615 0.00 0.00 0.00 3.67
228 229 6.307077 GCTGAAACGGTATTTTTATTGTCACC 59.693 38.462 0.00 0.00 0.00 4.02
229 230 6.679843 TGAAACGGTATTTTTATTGTCACCC 58.320 36.000 0.00 0.00 0.00 4.61
230 231 6.490721 TGAAACGGTATTTTTATTGTCACCCT 59.509 34.615 0.00 0.00 0.00 4.34
231 232 6.505044 AACGGTATTTTTATTGTCACCCTC 57.495 37.500 0.00 0.00 0.00 4.30
232 233 5.562635 ACGGTATTTTTATTGTCACCCTCA 58.437 37.500 0.00 0.00 0.00 3.86
233 234 5.646360 ACGGTATTTTTATTGTCACCCTCAG 59.354 40.000 0.00 0.00 0.00 3.35
234 235 5.065988 CGGTATTTTTATTGTCACCCTCAGG 59.934 44.000 0.00 0.00 40.04 3.86
235 236 5.163550 GGTATTTTTATTGTCACCCTCAGGC 60.164 44.000 0.00 0.00 36.11 4.85
236 237 3.517296 TTTTATTGTCACCCTCAGGCA 57.483 42.857 0.00 0.00 36.11 4.75
237 238 3.517296 TTTATTGTCACCCTCAGGCAA 57.483 42.857 0.00 0.00 36.11 4.52
238 239 2.489938 TATTGTCACCCTCAGGCAAC 57.510 50.000 0.00 0.00 36.11 4.17
239 240 0.606401 ATTGTCACCCTCAGGCAACG 60.606 55.000 0.00 0.00 46.39 4.10
240 241 1.978455 TTGTCACCCTCAGGCAACGT 61.978 55.000 0.00 0.00 46.39 3.99
241 242 1.227853 GTCACCCTCAGGCAACGTT 60.228 57.895 0.00 0.00 46.39 3.99
242 243 1.227823 TCACCCTCAGGCAACGTTG 60.228 57.895 23.90 23.90 46.39 4.10
243 244 1.227823 CACCCTCAGGCAACGTTGA 60.228 57.895 31.62 10.08 46.39 3.18
244 245 1.071471 ACCCTCAGGCAACGTTGAG 59.929 57.895 31.62 19.09 46.39 3.02
246 247 4.779475 CTCAGGCAACGTTGAGGT 57.221 55.556 31.62 11.82 46.39 3.85
247 248 2.238353 CTCAGGCAACGTTGAGGTG 58.762 57.895 31.62 22.12 46.39 4.00
248 249 0.532862 CTCAGGCAACGTTGAGGTGT 60.533 55.000 31.62 7.42 40.44 4.16
249 250 0.531974 TCAGGCAACGTTGAGGTGTC 60.532 55.000 31.62 12.31 43.99 3.67
250 251 4.456806 GGCAACGTTGAGGTGTCT 57.543 55.556 31.62 0.00 39.55 3.41
251 252 2.235546 GGCAACGTTGAGGTGTCTC 58.764 57.895 31.62 10.84 39.55 3.36
252 253 1.228657 GGCAACGTTGAGGTGTCTCC 61.229 60.000 31.62 16.06 39.55 3.71
253 254 0.531974 GCAACGTTGAGGTGTCTCCA 60.532 55.000 31.62 0.00 40.44 3.86
254 255 1.878102 GCAACGTTGAGGTGTCTCCAT 60.878 52.381 31.62 0.00 40.44 3.41
255 256 2.069273 CAACGTTGAGGTGTCTCCATC 58.931 52.381 23.90 0.00 39.23 3.51
256 257 0.608640 ACGTTGAGGTGTCTCCATCC 59.391 55.000 0.00 0.00 39.23 3.51
257 258 0.458543 CGTTGAGGTGTCTCCATCCG 60.459 60.000 0.00 0.00 39.23 4.18
258 259 0.608640 GTTGAGGTGTCTCCATCCGT 59.391 55.000 0.00 0.00 39.23 4.69
259 260 0.608130 TTGAGGTGTCTCCATCCGTG 59.392 55.000 0.00 0.00 39.23 4.94
261 262 1.229209 AGGTGTCTCCATCCGTGGT 60.229 57.895 0.00 0.00 46.16 4.16
262 263 0.836400 AGGTGTCTCCATCCGTGGTT 60.836 55.000 0.00 0.00 46.16 3.67
263 264 0.036306 GGTGTCTCCATCCGTGGTTT 59.964 55.000 0.00 0.00 46.16 3.27
264 265 1.276989 GGTGTCTCCATCCGTGGTTTA 59.723 52.381 0.00 0.00 46.16 2.01
265 266 2.093128 GGTGTCTCCATCCGTGGTTTAT 60.093 50.000 0.00 0.00 46.16 1.40
266 267 3.606687 GTGTCTCCATCCGTGGTTTATT 58.393 45.455 0.00 0.00 46.16 1.40
267 268 4.007659 GTGTCTCCATCCGTGGTTTATTT 58.992 43.478 0.00 0.00 46.16 1.40
268 269 4.094442 GTGTCTCCATCCGTGGTTTATTTC 59.906 45.833 0.00 0.00 46.16 2.17
269 270 4.019681 TGTCTCCATCCGTGGTTTATTTCT 60.020 41.667 0.00 0.00 46.16 2.52
270 271 5.188163 TGTCTCCATCCGTGGTTTATTTCTA 59.812 40.000 0.00 0.00 46.16 2.10
271 272 6.126883 TGTCTCCATCCGTGGTTTATTTCTAT 60.127 38.462 0.00 0.00 46.16 1.98
272 273 6.766467 GTCTCCATCCGTGGTTTATTTCTATT 59.234 38.462 0.00 0.00 46.16 1.73
273 274 7.282450 GTCTCCATCCGTGGTTTATTTCTATTT 59.718 37.037 0.00 0.00 46.16 1.40
274 275 7.832187 TCTCCATCCGTGGTTTATTTCTATTTT 59.168 33.333 0.00 0.00 46.16 1.82
427 428 3.483901 CGTTTTGAACCGTTTTCTGACGA 60.484 43.478 0.00 0.00 45.47 4.20
612 679 2.779755 TCTCTCTCTCGCTCTCACTT 57.220 50.000 0.00 0.00 0.00 3.16
687 754 4.802051 GCCGCCATGCCTTCCTGA 62.802 66.667 0.00 0.00 0.00 3.86
796 863 3.655384 AGGGTTAGGGTTCATCTAGGAC 58.345 50.000 0.00 0.00 0.00 3.85
946 1013 4.248058 GTTCTTGCTGGATTTGGGAAATG 58.752 43.478 0.00 0.00 0.00 2.32
1218 1306 5.885352 CCCACACATGTATTTACAAGGATGA 59.115 40.000 0.00 0.00 39.99 2.92
1219 1307 6.183360 CCCACACATGTATTTACAAGGATGAC 60.183 42.308 0.00 0.00 39.99 3.06
1220 1308 6.183360 CCACACATGTATTTACAAGGATGACC 60.183 42.308 0.00 0.00 39.99 4.02
1221 1309 6.374053 CACACATGTATTTACAAGGATGACCA 59.626 38.462 0.00 0.00 39.99 4.02
1222 1310 6.374333 ACACATGTATTTACAAGGATGACCAC 59.626 38.462 0.00 0.00 39.99 4.16
1223 1311 6.374053 CACATGTATTTACAAGGATGACCACA 59.626 38.462 0.00 0.00 39.99 4.17
1224 1312 6.374333 ACATGTATTTACAAGGATGACCACAC 59.626 38.462 0.00 0.00 39.99 3.82
1225 1313 5.870706 TGTATTTACAAGGATGACCACACA 58.129 37.500 0.00 0.00 38.94 3.72
1226 1314 6.299922 TGTATTTACAAGGATGACCACACAA 58.700 36.000 0.00 0.00 38.94 3.33
1227 1315 6.945435 TGTATTTACAAGGATGACCACACAAT 59.055 34.615 0.00 0.00 38.94 2.71
1228 1316 8.103935 TGTATTTACAAGGATGACCACACAATA 58.896 33.333 0.00 0.00 38.94 1.90
1229 1317 9.120538 GTATTTACAAGGATGACCACACAATAT 57.879 33.333 0.00 0.00 38.94 1.28
1230 1318 8.593945 ATTTACAAGGATGACCACACAATATT 57.406 30.769 0.00 0.00 38.94 1.28
1231 1319 9.693739 ATTTACAAGGATGACCACACAATATTA 57.306 29.630 0.00 0.00 38.94 0.98
1232 1320 9.693739 TTTACAAGGATGACCACACAATATTAT 57.306 29.630 0.00 0.00 38.94 1.28
1233 1321 7.572523 ACAAGGATGACCACACAATATTATG 57.427 36.000 0.00 0.00 38.94 1.90
1234 1322 7.118723 ACAAGGATGACCACACAATATTATGT 58.881 34.615 0.00 0.00 38.94 2.29
1235 1323 7.615365 ACAAGGATGACCACACAATATTATGTT 59.385 33.333 0.00 0.00 38.94 2.71
1236 1324 7.572523 AGGATGACCACACAATATTATGTTG 57.427 36.000 0.00 0.00 38.94 3.33
1245 1352 8.296000 CCACACAATATTATGTTGACAAGTTGA 58.704 33.333 10.54 0.00 0.00 3.18
1408 1544 8.654230 AGCATATATCTGTGAAAGTACTTGTG 57.346 34.615 9.34 0.00 0.00 3.33
2346 2487 7.380423 ACCTCTTATGCTATGTTATGGAGTT 57.620 36.000 0.00 0.00 0.00 3.01
2775 2940 1.962807 AGAGCTCAGGGAAGATCATCG 59.037 52.381 17.77 0.00 34.11 3.84
2875 3042 6.346477 TGATTGAGAGTTGTTGCTAGTAGT 57.654 37.500 0.00 0.00 0.00 2.73
3034 3210 5.551233 TGAATCTACCCAGAAGTCACAAAG 58.449 41.667 0.00 0.00 33.50 2.77
3040 3216 2.951642 CCCAGAAGTCACAAAGAAGCAA 59.048 45.455 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.627467 CGTACTACATCTTCTTGCTTGCTT 59.373 41.667 0.00 0.00 0.00 3.91
2 3 3.242123 GCGTACTACATCTTCTTGCTTGC 60.242 47.826 0.00 0.00 0.00 4.01
3 4 3.000674 CGCGTACTACATCTTCTTGCTTG 60.001 47.826 0.00 0.00 0.00 4.01
5 6 2.163815 ACGCGTACTACATCTTCTTGCT 59.836 45.455 11.67 0.00 0.00 3.91
6 7 2.279136 CACGCGTACTACATCTTCTTGC 59.721 50.000 13.44 0.00 0.00 4.01
7 8 3.300853 CACACGCGTACTACATCTTCTTG 59.699 47.826 13.44 0.00 0.00 3.02
8 9 3.189910 TCACACGCGTACTACATCTTCTT 59.810 43.478 13.44 0.00 0.00 2.52
9 10 2.745821 TCACACGCGTACTACATCTTCT 59.254 45.455 13.44 0.00 0.00 2.85
10 11 2.844804 GTCACACGCGTACTACATCTTC 59.155 50.000 13.44 0.00 0.00 2.87
11 12 2.415090 GGTCACACGCGTACTACATCTT 60.415 50.000 13.44 0.00 0.00 2.40
12 13 1.131883 GGTCACACGCGTACTACATCT 59.868 52.381 13.44 0.00 0.00 2.90
13 14 1.131883 AGGTCACACGCGTACTACATC 59.868 52.381 13.44 0.00 0.00 3.06
14 15 1.131883 GAGGTCACACGCGTACTACAT 59.868 52.381 13.44 7.75 0.00 2.29
15 16 0.518636 GAGGTCACACGCGTACTACA 59.481 55.000 13.44 0.00 0.00 2.74
16 17 0.179179 GGAGGTCACACGCGTACTAC 60.179 60.000 13.44 10.06 0.00 2.73
17 18 0.606130 TGGAGGTCACACGCGTACTA 60.606 55.000 13.44 0.00 0.00 1.82
18 19 1.863662 CTGGAGGTCACACGCGTACT 61.864 60.000 13.44 5.27 0.00 2.73
19 20 1.443872 CTGGAGGTCACACGCGTAC 60.444 63.158 13.44 6.79 0.00 3.67
20 21 0.606130 TACTGGAGGTCACACGCGTA 60.606 55.000 13.44 0.00 0.00 4.42
21 22 1.863662 CTACTGGAGGTCACACGCGT 61.864 60.000 5.58 5.58 0.00 6.01
22 23 1.154016 CTACTGGAGGTCACACGCG 60.154 63.158 3.53 3.53 0.00 6.01
23 24 0.601558 TTCTACTGGAGGTCACACGC 59.398 55.000 0.00 0.00 0.00 5.34
24 25 1.067776 GGTTCTACTGGAGGTCACACG 60.068 57.143 0.00 0.00 0.00 4.49
25 26 2.231721 GAGGTTCTACTGGAGGTCACAC 59.768 54.545 0.00 0.00 0.00 3.82
26 27 2.526432 GAGGTTCTACTGGAGGTCACA 58.474 52.381 0.00 0.00 0.00 3.58
27 28 1.826096 GGAGGTTCTACTGGAGGTCAC 59.174 57.143 0.00 0.00 0.00 3.67
28 29 1.273098 GGGAGGTTCTACTGGAGGTCA 60.273 57.143 0.00 0.00 0.00 4.02
29 30 1.007359 AGGGAGGTTCTACTGGAGGTC 59.993 57.143 0.00 0.00 0.00 3.85
30 31 1.094269 AGGGAGGTTCTACTGGAGGT 58.906 55.000 0.00 0.00 0.00 3.85
31 32 2.952116 CTAGGGAGGTTCTACTGGAGG 58.048 57.143 0.00 0.00 0.00 4.30
32 33 2.312390 GCTAGGGAGGTTCTACTGGAG 58.688 57.143 0.00 0.00 0.00 3.86
33 34 1.409802 CGCTAGGGAGGTTCTACTGGA 60.410 57.143 0.00 0.00 0.00 3.86
34 35 1.033574 CGCTAGGGAGGTTCTACTGG 58.966 60.000 0.00 0.00 0.00 4.00
35 36 1.033574 CCGCTAGGGAGGTTCTACTG 58.966 60.000 8.65 0.00 38.47 2.74
36 37 0.756070 GCCGCTAGGGAGGTTCTACT 60.756 60.000 8.65 0.00 38.47 2.57
37 38 1.041447 TGCCGCTAGGGAGGTTCTAC 61.041 60.000 8.65 0.00 38.47 2.59
38 39 1.308666 TGCCGCTAGGGAGGTTCTA 59.691 57.895 8.65 0.00 38.47 2.10
39 40 2.038975 TGCCGCTAGGGAGGTTCT 59.961 61.111 8.65 0.00 38.47 3.01
66 67 2.297701 TGCGAAGGAAGCACTCTTTTT 58.702 42.857 0.00 0.00 40.01 1.94
67 68 1.967319 TGCGAAGGAAGCACTCTTTT 58.033 45.000 0.00 0.00 40.01 2.27
68 69 3.706055 TGCGAAGGAAGCACTCTTT 57.294 47.368 0.00 0.00 40.01 2.52
74 75 0.319900 GAGACAGTGCGAAGGAAGCA 60.320 55.000 0.00 0.00 42.99 3.91
75 76 0.037790 AGAGACAGTGCGAAGGAAGC 60.038 55.000 0.00 0.00 0.00 3.86
76 77 1.543802 AGAGAGACAGTGCGAAGGAAG 59.456 52.381 0.00 0.00 0.00 3.46
77 78 1.270826 CAGAGAGACAGTGCGAAGGAA 59.729 52.381 0.00 0.00 0.00 3.36
78 79 0.884514 CAGAGAGACAGTGCGAAGGA 59.115 55.000 0.00 0.00 0.00 3.36
79 80 0.735632 GCAGAGAGACAGTGCGAAGG 60.736 60.000 0.00 0.00 0.00 3.46
80 81 0.243365 AGCAGAGAGACAGTGCGAAG 59.757 55.000 0.00 0.00 42.26 3.79
81 82 0.676184 AAGCAGAGAGACAGTGCGAA 59.324 50.000 0.00 0.00 42.26 4.70
82 83 0.038801 CAAGCAGAGAGACAGTGCGA 60.039 55.000 0.00 0.00 42.26 5.10
83 84 0.319383 ACAAGCAGAGAGACAGTGCG 60.319 55.000 0.00 0.00 42.26 5.34
84 85 1.000731 AGACAAGCAGAGAGACAGTGC 59.999 52.381 0.00 0.00 37.48 4.40
85 86 2.352617 GGAGACAAGCAGAGAGACAGTG 60.353 54.545 0.00 0.00 0.00 3.66
86 87 1.892474 GGAGACAAGCAGAGAGACAGT 59.108 52.381 0.00 0.00 0.00 3.55
87 88 1.891811 TGGAGACAAGCAGAGAGACAG 59.108 52.381 0.00 0.00 37.44 3.51
88 89 1.615883 GTGGAGACAAGCAGAGAGACA 59.384 52.381 0.00 0.00 46.06 3.41
89 90 1.067213 GGTGGAGACAAGCAGAGAGAC 60.067 57.143 0.00 0.00 46.06 3.36
90 91 1.261480 GGTGGAGACAAGCAGAGAGA 58.739 55.000 0.00 0.00 46.06 3.10
91 92 0.108898 CGGTGGAGACAAGCAGAGAG 60.109 60.000 0.00 0.00 46.06 3.20
92 93 0.539669 TCGGTGGAGACAAGCAGAGA 60.540 55.000 0.00 0.00 46.06 3.10
93 94 0.534412 ATCGGTGGAGACAAGCAGAG 59.466 55.000 0.00 0.00 46.06 3.35
94 95 0.247460 CATCGGTGGAGACAAGCAGA 59.753 55.000 0.00 0.00 46.06 4.26
95 96 0.036952 ACATCGGTGGAGACAAGCAG 60.037 55.000 0.00 0.00 46.06 4.24
96 97 0.396435 AACATCGGTGGAGACAAGCA 59.604 50.000 0.00 0.00 46.06 3.91
97 98 2.380084 TAACATCGGTGGAGACAAGC 57.620 50.000 0.00 0.00 46.06 4.01
98 99 3.861840 ACATAACATCGGTGGAGACAAG 58.138 45.455 0.00 0.00 46.06 3.16
99 100 3.973206 ACATAACATCGGTGGAGACAA 57.027 42.857 0.00 0.00 46.06 3.18
100 101 4.675933 CGTTACATAACATCGGTGGAGACA 60.676 45.833 0.00 0.00 35.99 3.41
101 102 3.795101 CGTTACATAACATCGGTGGAGAC 59.205 47.826 0.00 0.00 35.99 3.36
102 103 3.735820 GCGTTACATAACATCGGTGGAGA 60.736 47.826 0.00 0.00 35.99 3.71
103 104 2.538449 GCGTTACATAACATCGGTGGAG 59.462 50.000 0.00 0.00 35.99 3.86
104 105 2.094130 TGCGTTACATAACATCGGTGGA 60.094 45.455 0.00 0.00 35.99 4.02
105 106 2.272678 TGCGTTACATAACATCGGTGG 58.727 47.619 0.00 0.00 35.99 4.61
106 107 4.084745 GGTATGCGTTACATAACATCGGTG 60.085 45.833 0.00 0.00 46.56 4.94
107 108 4.053295 GGTATGCGTTACATAACATCGGT 58.947 43.478 2.88 0.00 46.56 4.69
108 109 4.640805 GGTATGCGTTACATAACATCGG 57.359 45.455 2.88 0.00 46.56 4.18
114 115 3.613299 CGTGTGTGGTATGCGTTACATAA 59.387 43.478 0.00 0.00 42.88 1.90
115 116 3.180613 CGTGTGTGGTATGCGTTACATA 58.819 45.455 0.00 0.00 40.38 2.29
116 117 1.996898 CGTGTGTGGTATGCGTTACAT 59.003 47.619 0.00 0.00 43.18 2.29
117 118 1.269673 ACGTGTGTGGTATGCGTTACA 60.270 47.619 0.00 0.00 31.99 2.41
118 119 1.125384 CACGTGTGTGGTATGCGTTAC 59.875 52.381 7.58 0.00 42.59 2.50
119 120 1.420378 CACGTGTGTGGTATGCGTTA 58.580 50.000 7.58 0.00 42.59 3.18
120 121 2.230892 CACGTGTGTGGTATGCGTT 58.769 52.632 7.58 0.00 42.59 4.84
121 122 3.945436 CACGTGTGTGGTATGCGT 58.055 55.556 7.58 0.00 42.59 5.24
136 137 4.634133 TGCCGTCGACGTGGACAC 62.634 66.667 33.49 19.24 36.73 3.67
137 138 4.337060 CTGCCGTCGACGTGGACA 62.337 66.667 33.49 23.71 36.73 4.02
138 139 2.462255 TAACTGCCGTCGACGTGGAC 62.462 60.000 33.49 19.53 37.74 4.02
139 140 1.794151 TTAACTGCCGTCGACGTGGA 61.794 55.000 33.49 24.37 37.74 4.02
140 141 1.372004 TTAACTGCCGTCGACGTGG 60.372 57.895 33.49 24.05 37.74 4.94
141 142 0.935831 TGTTAACTGCCGTCGACGTG 60.936 55.000 33.49 25.32 37.74 4.49
142 143 0.038892 ATGTTAACTGCCGTCGACGT 60.039 50.000 33.49 18.95 37.74 4.34
143 144 0.638746 GATGTTAACTGCCGTCGACG 59.361 55.000 30.33 30.33 39.44 5.12
144 145 0.638746 CGATGTTAACTGCCGTCGAC 59.361 55.000 5.18 5.18 41.42 4.20
145 146 1.074319 GCGATGTTAACTGCCGTCGA 61.074 55.000 7.22 0.00 41.42 4.20
146 147 1.076533 AGCGATGTTAACTGCCGTCG 61.077 55.000 7.22 9.62 41.73 5.12
147 148 0.370273 CAGCGATGTTAACTGCCGTC 59.630 55.000 7.22 4.72 0.00 4.79
148 149 0.037697 TCAGCGATGTTAACTGCCGT 60.038 50.000 7.22 0.00 0.00 5.68
149 150 1.075542 TTCAGCGATGTTAACTGCCG 58.924 50.000 7.22 8.54 0.00 5.69
150 151 3.764885 ATTTCAGCGATGTTAACTGCC 57.235 42.857 7.22 0.00 0.00 4.85
151 152 7.273381 ACAAAATATTTCAGCGATGTTAACTGC 59.727 33.333 7.22 8.38 0.00 4.40
152 153 8.577939 CACAAAATATTTCAGCGATGTTAACTG 58.422 33.333 7.22 0.00 0.00 3.16
153 154 8.296713 ACACAAAATATTTCAGCGATGTTAACT 58.703 29.630 7.22 0.00 0.00 2.24
154 155 8.447787 ACACAAAATATTTCAGCGATGTTAAC 57.552 30.769 0.00 0.00 0.00 2.01
155 156 7.480229 CGACACAAAATATTTCAGCGATGTTAA 59.520 33.333 0.00 0.00 0.00 2.01
156 157 6.958752 CGACACAAAATATTTCAGCGATGTTA 59.041 34.615 0.00 0.00 0.00 2.41
157 158 5.794945 CGACACAAAATATTTCAGCGATGTT 59.205 36.000 0.00 0.00 0.00 2.71
158 159 5.121611 TCGACACAAAATATTTCAGCGATGT 59.878 36.000 0.00 0.00 0.00 3.06
159 160 5.449113 GTCGACACAAAATATTTCAGCGATG 59.551 40.000 11.55 0.00 0.00 3.84
160 161 5.560148 GTCGACACAAAATATTTCAGCGAT 58.440 37.500 11.55 0.00 0.00 4.58
161 162 4.433674 CGTCGACACAAAATATTTCAGCGA 60.434 41.667 17.16 4.66 0.00 4.93
162 163 3.773549 CGTCGACACAAAATATTTCAGCG 59.226 43.478 17.16 2.49 0.00 5.18
163 164 4.708601 ACGTCGACACAAAATATTTCAGC 58.291 39.130 17.16 0.00 0.00 4.26
164 165 5.007039 CGACGTCGACACAAAATATTTCAG 58.993 41.667 33.35 0.32 43.02 3.02
165 166 4.680567 TCGACGTCGACACAAAATATTTCA 59.319 37.500 34.97 8.66 44.22 2.69
166 167 5.181235 TCGACGTCGACACAAAATATTTC 57.819 39.130 34.97 0.00 44.22 2.17
180 181 0.638746 GTTAACTGCCATCGACGTCG 59.361 55.000 31.30 31.30 41.45 5.12
181 182 1.389106 GTGTTAACTGCCATCGACGTC 59.611 52.381 5.18 5.18 0.00 4.34
182 183 1.000506 AGTGTTAACTGCCATCGACGT 59.999 47.619 7.22 0.00 34.48 4.34
183 184 1.390123 CAGTGTTAACTGCCATCGACG 59.610 52.381 7.22 0.00 46.98 5.12
193 194 2.914059 ACCGTTTCAGCAGTGTTAACT 58.086 42.857 7.22 0.00 36.98 2.24
194 195 5.352643 AATACCGTTTCAGCAGTGTTAAC 57.647 39.130 0.00 0.00 0.00 2.01
195 196 6.380095 AAAATACCGTTTCAGCAGTGTTAA 57.620 33.333 0.00 0.00 0.00 2.01
196 197 6.380095 AAAAATACCGTTTCAGCAGTGTTA 57.620 33.333 0.00 0.00 0.00 2.41
197 198 4.911514 AAAATACCGTTTCAGCAGTGTT 57.088 36.364 0.00 0.00 0.00 3.32
198 199 4.911514 AAAAATACCGTTTCAGCAGTGT 57.088 36.364 0.00 0.00 0.00 3.55
199 200 6.861055 ACAATAAAAATACCGTTTCAGCAGTG 59.139 34.615 0.00 0.00 0.00 3.66
200 201 6.977213 ACAATAAAAATACCGTTTCAGCAGT 58.023 32.000 0.00 0.00 0.00 4.40
201 202 7.060633 GTGACAATAAAAATACCGTTTCAGCAG 59.939 37.037 0.00 0.00 0.00 4.24
202 203 6.858993 GTGACAATAAAAATACCGTTTCAGCA 59.141 34.615 0.00 0.00 0.00 4.41
203 204 6.307077 GGTGACAATAAAAATACCGTTTCAGC 59.693 38.462 0.00 0.00 0.00 4.26
204 205 6.804783 GGGTGACAATAAAAATACCGTTTCAG 59.195 38.462 0.00 0.00 0.00 3.02
205 206 6.490721 AGGGTGACAATAAAAATACCGTTTCA 59.509 34.615 0.00 0.00 0.00 2.69
206 207 6.916440 AGGGTGACAATAAAAATACCGTTTC 58.084 36.000 0.00 0.00 0.00 2.78
207 208 6.490721 TGAGGGTGACAATAAAAATACCGTTT 59.509 34.615 0.00 0.00 0.00 3.60
208 209 6.005198 TGAGGGTGACAATAAAAATACCGTT 58.995 36.000 0.00 0.00 0.00 4.44
209 210 5.562635 TGAGGGTGACAATAAAAATACCGT 58.437 37.500 0.00 0.00 0.00 4.83
210 211 5.065988 CCTGAGGGTGACAATAAAAATACCG 59.934 44.000 0.00 0.00 0.00 4.02
211 212 5.163550 GCCTGAGGGTGACAATAAAAATACC 60.164 44.000 0.00 0.00 34.45 2.73
212 213 5.417580 TGCCTGAGGGTGACAATAAAAATAC 59.582 40.000 0.00 0.00 34.45 1.89
213 214 5.575157 TGCCTGAGGGTGACAATAAAAATA 58.425 37.500 0.00 0.00 34.45 1.40
214 215 4.415596 TGCCTGAGGGTGACAATAAAAAT 58.584 39.130 0.00 0.00 34.45 1.82
215 216 3.838565 TGCCTGAGGGTGACAATAAAAA 58.161 40.909 0.00 0.00 34.45 1.94
216 217 3.517296 TGCCTGAGGGTGACAATAAAA 57.483 42.857 0.00 0.00 34.45 1.52
217 218 3.153919 GTTGCCTGAGGGTGACAATAAA 58.846 45.455 0.00 0.00 34.45 1.40
218 219 2.790433 GTTGCCTGAGGGTGACAATAA 58.210 47.619 0.00 0.00 34.45 1.40
219 220 1.338674 CGTTGCCTGAGGGTGACAATA 60.339 52.381 0.00 0.00 34.45 1.90
220 221 0.606401 CGTTGCCTGAGGGTGACAAT 60.606 55.000 0.00 0.00 34.45 2.71
221 222 1.227823 CGTTGCCTGAGGGTGACAA 60.228 57.895 0.00 0.00 34.45 3.18
222 223 1.978455 AACGTTGCCTGAGGGTGACA 61.978 55.000 0.00 0.00 34.45 3.58
223 224 1.227853 AACGTTGCCTGAGGGTGAC 60.228 57.895 0.00 0.00 34.45 3.67
224 225 1.227823 CAACGTTGCCTGAGGGTGA 60.228 57.895 16.51 0.00 34.45 4.02
225 226 1.227823 TCAACGTTGCCTGAGGGTG 60.228 57.895 23.47 0.00 34.45 4.61
226 227 1.071471 CTCAACGTTGCCTGAGGGT 59.929 57.895 23.47 0.00 36.27 4.34
227 228 3.972227 CTCAACGTTGCCTGAGGG 58.028 61.111 23.47 0.00 36.27 4.30
229 230 0.532862 ACACCTCAACGTTGCCTGAG 60.533 55.000 23.47 15.09 39.06 3.35
230 231 0.531974 GACACCTCAACGTTGCCTGA 60.532 55.000 23.47 5.40 0.00 3.86
231 232 0.532862 AGACACCTCAACGTTGCCTG 60.533 55.000 23.47 18.11 0.00 4.85
232 233 0.249911 GAGACACCTCAACGTTGCCT 60.250 55.000 23.47 12.00 39.24 4.75
233 234 1.228657 GGAGACACCTCAACGTTGCC 61.229 60.000 23.47 12.04 41.20 4.52
234 235 0.531974 TGGAGACACCTCAACGTTGC 60.532 55.000 23.47 8.27 41.20 4.17
235 236 3.678921 TGGAGACACCTCAACGTTG 57.321 52.632 22.35 22.35 41.20 4.10
252 253 8.247562 TCCAAAAATAGAAATAAACCACGGATG 58.752 33.333 0.00 0.00 0.00 3.51
253 254 8.356000 TCCAAAAATAGAAATAAACCACGGAT 57.644 30.769 0.00 0.00 0.00 4.18
254 255 7.449086 ACTCCAAAAATAGAAATAAACCACGGA 59.551 33.333 0.00 0.00 0.00 4.69
255 256 7.599171 ACTCCAAAAATAGAAATAAACCACGG 58.401 34.615 0.00 0.00 0.00 4.94
476 487 0.454285 CGAGTAACGGCCGTTAACGA 60.454 55.000 42.18 29.95 41.51 3.85
612 679 2.830923 CAAAGAGCAGAGAGGAGAGGAA 59.169 50.000 0.00 0.00 0.00 3.36
687 754 1.068741 GAGCTCGTATCCCCGTCATTT 59.931 52.381 0.00 0.00 0.00 2.32
946 1013 4.572389 ACAACCAGACATAGATCGCAAATC 59.428 41.667 0.00 0.00 0.00 2.17
1218 1306 7.759489 ACTTGTCAACATAATATTGTGTGGT 57.241 32.000 17.35 1.54 32.63 4.16
1219 1307 8.296000 TCAACTTGTCAACATAATATTGTGTGG 58.704 33.333 17.35 14.78 32.63 4.17
1220 1308 9.844790 ATCAACTTGTCAACATAATATTGTGTG 57.155 29.630 17.35 11.84 32.63 3.82
1221 1309 9.844790 CATCAACTTGTCAACATAATATTGTGT 57.155 29.630 11.68 11.68 33.75 3.72
1222 1310 9.844790 ACATCAACTTGTCAACATAATATTGTG 57.155 29.630 10.37 10.37 0.00 3.33
1227 1315 9.500785 TCAGAACATCAACTTGTCAACATAATA 57.499 29.630 0.00 0.00 0.00 0.98
1228 1316 8.394971 TCAGAACATCAACTTGTCAACATAAT 57.605 30.769 0.00 0.00 0.00 1.28
1229 1317 7.800155 TCAGAACATCAACTTGTCAACATAA 57.200 32.000 0.00 0.00 0.00 1.90
1230 1318 7.255104 GGTTCAGAACATCAACTTGTCAACATA 60.255 37.037 15.36 0.00 0.00 2.29
1231 1319 6.460123 GGTTCAGAACATCAACTTGTCAACAT 60.460 38.462 15.36 0.00 0.00 2.71
1232 1320 5.163663 GGTTCAGAACATCAACTTGTCAACA 60.164 40.000 15.36 0.00 0.00 3.33
1233 1321 5.273944 GGTTCAGAACATCAACTTGTCAAC 58.726 41.667 15.36 0.00 0.00 3.18
1234 1322 4.338118 GGGTTCAGAACATCAACTTGTCAA 59.662 41.667 15.36 0.00 0.00 3.18
1235 1323 3.882888 GGGTTCAGAACATCAACTTGTCA 59.117 43.478 15.36 0.00 0.00 3.58
1236 1324 3.882888 TGGGTTCAGAACATCAACTTGTC 59.117 43.478 15.36 0.00 0.00 3.18
1245 1352 5.774690 ACAATATTGTGTGGGTTCAGAACAT 59.225 36.000 20.19 0.92 40.49 2.71
1408 1544 0.032540 CTGAAACCCAACCTGCTTGC 59.967 55.000 0.00 0.00 0.00 4.01
2295 2436 7.540400 TCAAATACAGGCAAAACATTCATTACG 59.460 33.333 0.00 0.00 0.00 3.18
2308 2449 5.125417 GCATAAGAGGTTCAAATACAGGCAA 59.875 40.000 0.00 0.00 0.00 4.52
2775 2940 4.115199 CTGTGCCCTAGCCCACCC 62.115 72.222 8.08 0.00 38.69 4.61
2794 2961 0.263765 AGGGTGGGGAGCGATTACTA 59.736 55.000 0.00 0.00 0.00 1.82
3003 3179 5.249393 ACTTCTGGGTAGATTCAGACAACAT 59.751 40.000 0.00 0.00 39.43 2.71
3034 3210 5.119125 GTGGTTGCATTATGAAACTTGCTTC 59.881 40.000 14.94 0.00 36.17 3.86
3040 3216 6.515272 CCTAAGTGGTTGCATTATGAAACT 57.485 37.500 14.94 0.00 36.17 2.66


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

AutoCloner maintained by Alex Coulton.