Multiple sequence alignment - TraesCS6D01G091400

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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 TraesCS6D01G091400 chr6D 100.000 3302 0 0 1 3302 57170274 57173575 0.000000e+00 6098
1 TraesCS6D01G091400 chr6D 88.115 2339 207 30 988 3300 57158826 57161119 0.000000e+00 2713
2 TraesCS6D01G091400 chr6D 81.162 637 105 13 991 1619 57215899 57216528 6.360000e-137 497
3 TraesCS6D01G091400 chr6D 79.968 629 102 19 988 1605 57514181 57514796 3.020000e-120 442
4 TraesCS6D01G091400 chr6D 78.701 662 121 16 1666 2313 57514833 57515488 1.100000e-114 424
5 TraesCS6D01G091400 chr6D 79.355 465 94 2 1887 2350 57483294 57483757 3.180000e-85 326
6 TraesCS6D01G091400 chr6D 84.138 145 14 5 848 983 57158439 57158583 7.430000e-27 132
7 TraesCS6D01G091400 chr6A 94.209 2884 119 19 458 3302 71948100 71950974 0.000000e+00 4357
8 TraesCS6D01G091400 chr6A 88.093 2486 227 27 848 3302 71924549 71926996 0.000000e+00 2887
9 TraesCS6D01G091400 chr6A 76.907 1455 291 35 991 2421 72429422 72430855 0.000000e+00 784
10 TraesCS6D01G091400 chr6A 92.060 466 35 1 1 466 71933412 71933875 0.000000e+00 654
11 TraesCS6D01G091400 chr6B 96.942 2420 66 4 887 3302 129237043 129239458 0.000000e+00 4052
12 TraesCS6D01G091400 chr6B 93.936 2523 121 15 258 2767 128015799 128018302 0.000000e+00 3783
13 TraesCS6D01G091400 chr6B 95.896 536 20 1 2769 3302 128018562 128019097 0.000000e+00 867
14 TraesCS6D01G091400 chr6B 77.930 1459 269 39 991 2421 129268682 129270115 0.000000e+00 861
15 TraesCS6D01G091400 chr6B 77.397 1429 268 45 988 2386 129447014 129448417 0.000000e+00 798
16 TraesCS6D01G091400 chr6B 88.103 580 56 3 258 824 129236424 129237003 0.000000e+00 676
17 TraesCS6D01G091400 chr6B 77.778 630 115 18 995 1607 129679489 129680110 6.730000e-97 364
18 TraesCS6D01G091400 chr6B 79.953 424 79 6 1889 2309 129680413 129680833 1.150000e-79 307
19 TraesCS6D01G091400 chr2D 88.327 257 29 1 1 256 593228775 593229031 1.150000e-79 307
20 TraesCS6D01G091400 chr2A 87.984 258 27 4 1 256 728026338 728026593 5.350000e-78 302
21 TraesCS6D01G091400 chr2A 79.018 224 35 8 34 255 764006238 764006451 3.430000e-30 143
22 TraesCS6D01G091400 chr2B 88.235 255 21 4 3 256 719501137 719501383 2.490000e-76 296
23 TraesCS6D01G091400 chr7D 86.260 262 33 3 1 259 180213488 180213227 6.980000e-72 281
24 TraesCS6D01G091400 chr3B 83.206 262 41 3 1 259 591360984 591360723 1.530000e-58 237
25 TraesCS6D01G091400 chr7A 82.963 270 35 7 1 259 184578041 184577772 1.980000e-57 233
26 TraesCS6D01G091400 chr4D 83.806 247 37 3 16 259 464400393 464400639 7.130000e-57 231


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 TraesCS6D01G091400 chr6D 57170274 57173575 3301 False 6098.0 6098 100.0000 1 3302 1 chr6D.!!$F1 3301
1 TraesCS6D01G091400 chr6D 57158439 57161119 2680 False 1422.5 2713 86.1265 848 3300 2 chr6D.!!$F4 2452
2 TraesCS6D01G091400 chr6D 57215899 57216528 629 False 497.0 497 81.1620 991 1619 1 chr6D.!!$F2 628
3 TraesCS6D01G091400 chr6D 57514181 57515488 1307 False 433.0 442 79.3345 988 2313 2 chr6D.!!$F5 1325
4 TraesCS6D01G091400 chr6A 71948100 71950974 2874 False 4357.0 4357 94.2090 458 3302 1 chr6A.!!$F3 2844
5 TraesCS6D01G091400 chr6A 71924549 71926996 2447 False 2887.0 2887 88.0930 848 3302 1 chr6A.!!$F1 2454
6 TraesCS6D01G091400 chr6A 72429422 72430855 1433 False 784.0 784 76.9070 991 2421 1 chr6A.!!$F4 1430
7 TraesCS6D01G091400 chr6B 129236424 129239458 3034 False 2364.0 4052 92.5225 258 3302 2 chr6B.!!$F4 3044
8 TraesCS6D01G091400 chr6B 128015799 128019097 3298 False 2325.0 3783 94.9160 258 3302 2 chr6B.!!$F3 3044
9 TraesCS6D01G091400 chr6B 129268682 129270115 1433 False 861.0 861 77.9300 991 2421 1 chr6B.!!$F1 1430
10 TraesCS6D01G091400 chr6B 129447014 129448417 1403 False 798.0 798 77.3970 988 2386 1 chr6B.!!$F2 1398
11 TraesCS6D01G091400 chr6B 129679489 129680833 1344 False 335.5 364 78.8655 995 2309 2 chr6B.!!$F5 1314

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
92 93 0.033090 CCTAACGCCGTTATCCCTCC 59.967 60.0 10.5 0.0 0.0 4.30 F
249 250 0.035056 CCACCCCATCTCCTTGTGTC 60.035 60.0 0.0 0.0 0.0 3.67 F
252 253 0.324943 CCCCATCTCCTTGTGTCGTT 59.675 55.0 0.0 0.0 0.0 3.85 F
554 568 0.378257 CTCTCTGCTCTCACTCGCTC 59.622 60.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1746 1.135344 GTACTCTTCCTGGACAGCGAC 60.135 57.143 0.00 0.0 0.00 5.19 R
1539 1863 2.572290 GCGGTTAGCTTGGAACCATAT 58.428 47.619 15.52 0.0 45.70 1.78 R
2170 2552 6.859715 CTTGACCTCAAGCGAAAAATAATG 57.140 37.500 2.13 0.0 45.59 1.90 R
2533 2920 3.281727 TGTAAATGGCCCTCAGACATC 57.718 47.619 0.00 0.0 0.00 3.06 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 4.094684 CGTCATGGCGTTCCTCTC 57.905 61.111 12.53 0.00 0.00 3.20
18 19 1.519455 CGTCATGGCGTTCCTCTCC 60.519 63.158 12.53 0.00 0.00 3.71
19 20 1.519455 GTCATGGCGTTCCTCTCCG 60.519 63.158 0.00 0.00 0.00 4.63
20 21 1.982395 TCATGGCGTTCCTCTCCGT 60.982 57.895 0.00 0.00 0.00 4.69
21 22 1.811266 CATGGCGTTCCTCTCCGTG 60.811 63.158 0.00 0.00 32.60 4.94
22 23 2.283529 ATGGCGTTCCTCTCCGTGT 61.284 57.895 0.00 0.00 0.00 4.49
23 24 2.126031 GGCGTTCCTCTCCGTGTC 60.126 66.667 0.00 0.00 0.00 3.67
24 25 2.126031 GCGTTCCTCTCCGTGTCC 60.126 66.667 0.00 0.00 0.00 4.02
25 26 2.178521 CGTTCCTCTCCGTGTCCG 59.821 66.667 0.00 0.00 0.00 4.79
35 36 4.195308 CGTGTCCGGGTTATGGTG 57.805 61.111 0.00 0.00 0.00 4.17
36 37 1.592743 CGTGTCCGGGTTATGGTGA 59.407 57.895 0.00 0.00 0.00 4.02
37 38 0.037139 CGTGTCCGGGTTATGGTGAA 60.037 55.000 0.00 0.00 0.00 3.18
38 39 1.608542 CGTGTCCGGGTTATGGTGAAA 60.609 52.381 0.00 0.00 0.00 2.69
39 40 2.506444 GTGTCCGGGTTATGGTGAAAA 58.494 47.619 0.00 0.00 0.00 2.29
40 41 2.227149 GTGTCCGGGTTATGGTGAAAAC 59.773 50.000 0.00 0.00 0.00 2.43
41 42 1.814394 GTCCGGGTTATGGTGAAAACC 59.186 52.381 0.00 0.00 43.70 3.27
42 43 1.706305 TCCGGGTTATGGTGAAAACCT 59.294 47.619 0.00 0.00 43.87 3.50
43 44 2.089201 CCGGGTTATGGTGAAAACCTC 58.911 52.381 0.00 0.00 43.87 3.85
44 45 2.290705 CCGGGTTATGGTGAAAACCTCT 60.291 50.000 0.00 0.00 43.87 3.69
45 46 3.054948 CCGGGTTATGGTGAAAACCTCTA 60.055 47.826 0.00 0.00 43.87 2.43
46 47 4.384868 CCGGGTTATGGTGAAAACCTCTAT 60.385 45.833 0.00 0.00 43.87 1.98
47 48 4.814771 CGGGTTATGGTGAAAACCTCTATC 59.185 45.833 4.40 0.00 43.87 2.08
48 49 5.396436 CGGGTTATGGTGAAAACCTCTATCT 60.396 44.000 4.40 0.00 43.87 1.98
49 50 6.183360 CGGGTTATGGTGAAAACCTCTATCTA 60.183 42.308 4.40 0.00 43.87 1.98
50 51 7.472945 CGGGTTATGGTGAAAACCTCTATCTAT 60.473 40.741 4.40 0.00 43.87 1.98
51 52 8.218488 GGGTTATGGTGAAAACCTCTATCTATT 58.782 37.037 4.40 0.00 43.87 1.73
52 53 9.057089 GGTTATGGTGAAAACCTCTATCTATTG 57.943 37.037 0.00 0.00 41.63 1.90
53 54 9.614792 GTTATGGTGAAAACCTCTATCTATTGT 57.385 33.333 0.00 0.00 0.00 2.71
56 57 8.603898 TGGTGAAAACCTCTATCTATTGTAGA 57.396 34.615 0.00 0.00 39.50 2.59
57 58 8.475639 TGGTGAAAACCTCTATCTATTGTAGAC 58.524 37.037 0.00 0.00 37.69 2.59
58 59 8.697292 GGTGAAAACCTCTATCTATTGTAGACT 58.303 37.037 0.00 0.00 37.69 3.24
59 60 9.738832 GTGAAAACCTCTATCTATTGTAGACTC 57.261 37.037 0.00 0.00 37.69 3.36
60 61 8.622157 TGAAAACCTCTATCTATTGTAGACTCG 58.378 37.037 0.00 0.00 37.69 4.18
61 62 7.513371 AAACCTCTATCTATTGTAGACTCGG 57.487 40.000 0.00 0.00 37.69 4.63
62 63 5.005094 ACCTCTATCTATTGTAGACTCGGC 58.995 45.833 0.00 0.00 37.69 5.54
63 64 5.004448 CCTCTATCTATTGTAGACTCGGCA 58.996 45.833 0.00 0.00 37.69 5.69
64 65 5.473846 CCTCTATCTATTGTAGACTCGGCAA 59.526 44.000 0.00 0.00 37.69 4.52
65 66 6.315091 TCTATCTATTGTAGACTCGGCAAC 57.685 41.667 0.00 0.00 37.69 4.17
66 67 5.826208 TCTATCTATTGTAGACTCGGCAACA 59.174 40.000 0.00 0.00 37.69 3.33
67 68 4.794278 TCTATTGTAGACTCGGCAACAA 57.206 40.909 0.00 0.00 36.37 2.83
68 69 4.491676 TCTATTGTAGACTCGGCAACAAC 58.508 43.478 0.00 0.00 34.89 3.32
69 70 1.493772 TTGTAGACTCGGCAACAACG 58.506 50.000 0.00 0.00 0.00 4.10
70 71 0.669619 TGTAGACTCGGCAACAACGA 59.330 50.000 0.00 0.00 38.79 3.85
71 72 1.058404 GTAGACTCGGCAACAACGAC 58.942 55.000 0.00 0.00 36.25 4.34
72 73 0.386352 TAGACTCGGCAACAACGACG 60.386 55.000 0.00 0.00 36.25 5.12
73 74 3.277742 GACTCGGCAACAACGACGC 62.278 63.158 0.00 0.00 36.25 5.19
74 75 4.072088 CTCGGCAACAACGACGCC 62.072 66.667 0.00 0.00 42.64 5.68
75 76 4.595538 TCGGCAACAACGACGCCT 62.596 61.111 0.00 0.00 43.95 5.52
76 77 2.735478 CGGCAACAACGACGCCTA 60.735 61.111 0.00 0.00 43.95 3.93
77 78 2.311701 CGGCAACAACGACGCCTAA 61.312 57.895 0.00 0.00 43.95 2.69
78 79 1.205820 GGCAACAACGACGCCTAAC 59.794 57.895 0.00 0.00 42.78 2.34
88 89 3.621520 CGCCTAACGCCGTTATCC 58.378 61.111 10.50 3.81 33.16 2.59
89 90 1.952635 CGCCTAACGCCGTTATCCC 60.953 63.158 10.50 1.39 33.16 3.85
90 91 1.444672 GCCTAACGCCGTTATCCCT 59.555 57.895 10.50 0.00 0.00 4.20
91 92 0.599466 GCCTAACGCCGTTATCCCTC 60.599 60.000 10.50 0.00 0.00 4.30
92 93 0.033090 CCTAACGCCGTTATCCCTCC 59.967 60.000 10.50 0.00 0.00 4.30
93 94 1.038280 CTAACGCCGTTATCCCTCCT 58.962 55.000 10.50 0.00 0.00 3.69
94 95 0.748450 TAACGCCGTTATCCCTCCTG 59.252 55.000 5.43 0.00 0.00 3.86
95 96 1.968050 AACGCCGTTATCCCTCCTGG 61.968 60.000 0.00 0.00 0.00 4.45
105 106 2.672996 CCTCCTGGGGCGTTGTTG 60.673 66.667 0.00 0.00 0.00 3.33
106 107 2.113139 CTCCTGGGGCGTTGTTGT 59.887 61.111 0.00 0.00 0.00 3.32
107 108 2.203280 TCCTGGGGCGTTGTTGTG 60.203 61.111 0.00 0.00 0.00 3.33
108 109 3.294493 CCTGGGGCGTTGTTGTGG 61.294 66.667 0.00 0.00 0.00 4.17
109 110 2.203280 CTGGGGCGTTGTTGTGGA 60.203 61.111 0.00 0.00 0.00 4.02
110 111 2.203280 TGGGGCGTTGTTGTGGAG 60.203 61.111 0.00 0.00 0.00 3.86
111 112 3.670377 GGGGCGTTGTTGTGGAGC 61.670 66.667 0.00 0.00 0.00 4.70
112 113 2.594592 GGGCGTTGTTGTGGAGCT 60.595 61.111 0.00 0.00 0.00 4.09
113 114 2.193536 GGGCGTTGTTGTGGAGCTT 61.194 57.895 0.00 0.00 0.00 3.74
114 115 0.887387 GGGCGTTGTTGTGGAGCTTA 60.887 55.000 0.00 0.00 0.00 3.09
115 116 0.517316 GGCGTTGTTGTGGAGCTTAG 59.483 55.000 0.00 0.00 0.00 2.18
116 117 0.517316 GCGTTGTTGTGGAGCTTAGG 59.483 55.000 0.00 0.00 0.00 2.69
117 118 1.878953 CGTTGTTGTGGAGCTTAGGT 58.121 50.000 0.00 0.00 0.00 3.08
118 119 1.531149 CGTTGTTGTGGAGCTTAGGTG 59.469 52.381 0.00 0.00 0.00 4.00
119 120 2.572290 GTTGTTGTGGAGCTTAGGTGT 58.428 47.619 0.00 0.00 0.00 4.16
120 121 2.949644 GTTGTTGTGGAGCTTAGGTGTT 59.050 45.455 0.00 0.00 0.00 3.32
121 122 4.131596 GTTGTTGTGGAGCTTAGGTGTTA 58.868 43.478 0.00 0.00 0.00 2.41
122 123 4.634012 TGTTGTGGAGCTTAGGTGTTAT 57.366 40.909 0.00 0.00 0.00 1.89
123 124 5.748670 TGTTGTGGAGCTTAGGTGTTATA 57.251 39.130 0.00 0.00 0.00 0.98
124 125 5.730550 TGTTGTGGAGCTTAGGTGTTATAG 58.269 41.667 0.00 0.00 0.00 1.31
125 126 5.116882 GTTGTGGAGCTTAGGTGTTATAGG 58.883 45.833 0.00 0.00 0.00 2.57
126 127 3.709653 TGTGGAGCTTAGGTGTTATAGGG 59.290 47.826 0.00 0.00 0.00 3.53
127 128 2.704065 TGGAGCTTAGGTGTTATAGGGC 59.296 50.000 0.00 0.00 0.00 5.19
128 129 2.973406 GGAGCTTAGGTGTTATAGGGCT 59.027 50.000 0.00 0.00 0.00 5.19
129 130 3.391626 GGAGCTTAGGTGTTATAGGGCTT 59.608 47.826 0.00 0.00 0.00 4.35
130 131 4.591924 GGAGCTTAGGTGTTATAGGGCTTA 59.408 45.833 0.00 0.00 0.00 3.09
131 132 5.279556 GGAGCTTAGGTGTTATAGGGCTTAG 60.280 48.000 0.00 0.00 0.00 2.18
132 133 4.040584 AGCTTAGGTGTTATAGGGCTTAGC 59.959 45.833 0.00 0.00 0.00 3.09
133 134 4.202326 GCTTAGGTGTTATAGGGCTTAGCA 60.202 45.833 6.53 0.00 0.00 3.49
134 135 5.513267 GCTTAGGTGTTATAGGGCTTAGCAT 60.513 44.000 6.53 0.00 0.00 3.79
135 136 4.357918 AGGTGTTATAGGGCTTAGCATG 57.642 45.455 6.53 0.00 0.00 4.06
136 137 3.073062 AGGTGTTATAGGGCTTAGCATGG 59.927 47.826 6.53 0.00 0.00 3.66
137 138 3.181443 GGTGTTATAGGGCTTAGCATGGT 60.181 47.826 6.53 1.62 0.00 3.55
138 139 3.815401 GTGTTATAGGGCTTAGCATGGTG 59.185 47.826 7.89 0.00 0.00 4.17
139 140 3.458118 TGTTATAGGGCTTAGCATGGTGT 59.542 43.478 7.89 0.00 0.00 4.16
140 141 4.080015 TGTTATAGGGCTTAGCATGGTGTT 60.080 41.667 7.89 0.00 0.00 3.32
141 142 2.418368 TAGGGCTTAGCATGGTGTTG 57.582 50.000 7.89 0.00 0.00 3.33
142 143 0.967380 AGGGCTTAGCATGGTGTTGC 60.967 55.000 7.89 8.68 43.09 4.17
151 152 3.641437 GCATGGTGTTGCTTTAGTTCA 57.359 42.857 0.00 0.00 39.57 3.18
152 153 4.178545 GCATGGTGTTGCTTTAGTTCAT 57.821 40.909 0.00 0.00 39.57 2.57
153 154 4.168760 GCATGGTGTTGCTTTAGTTCATC 58.831 43.478 0.00 0.00 39.57 2.92
154 155 4.082571 GCATGGTGTTGCTTTAGTTCATCT 60.083 41.667 0.00 0.00 39.57 2.90
155 156 5.565439 GCATGGTGTTGCTTTAGTTCATCTT 60.565 40.000 0.00 0.00 39.57 2.40
156 157 5.437289 TGGTGTTGCTTTAGTTCATCTTG 57.563 39.130 0.00 0.00 0.00 3.02
157 158 4.887071 TGGTGTTGCTTTAGTTCATCTTGT 59.113 37.500 0.00 0.00 0.00 3.16
158 159 6.058833 TGGTGTTGCTTTAGTTCATCTTGTA 58.941 36.000 0.00 0.00 0.00 2.41
159 160 6.017440 TGGTGTTGCTTTAGTTCATCTTGTAC 60.017 38.462 0.00 0.00 0.00 2.90
160 161 6.204882 GGTGTTGCTTTAGTTCATCTTGTACT 59.795 38.462 0.00 0.00 32.68 2.73
161 162 7.255139 GGTGTTGCTTTAGTTCATCTTGTACTT 60.255 37.037 0.00 0.00 30.57 2.24
162 163 8.129211 GTGTTGCTTTAGTTCATCTTGTACTTT 58.871 33.333 0.00 0.00 30.57 2.66
163 164 9.332502 TGTTGCTTTAGTTCATCTTGTACTTTA 57.667 29.630 0.00 0.00 30.57 1.85
173 174 9.556030 GTTCATCTTGTACTTTATTTTGGTAGC 57.444 33.333 0.00 0.00 0.00 3.58
174 175 8.856153 TCATCTTGTACTTTATTTTGGTAGCA 57.144 30.769 0.00 0.00 0.00 3.49
175 176 9.461312 TCATCTTGTACTTTATTTTGGTAGCAT 57.539 29.630 0.00 0.00 0.00 3.79
178 179 9.953565 TCTTGTACTTTATTTTGGTAGCATAGT 57.046 29.630 0.00 0.00 0.00 2.12
180 181 8.415192 TGTACTTTATTTTGGTAGCATAGTCG 57.585 34.615 0.00 0.00 0.00 4.18
181 182 6.359480 ACTTTATTTTGGTAGCATAGTCGC 57.641 37.500 0.00 0.00 0.00 5.19
182 183 5.006358 ACTTTATTTTGGTAGCATAGTCGCG 59.994 40.000 0.00 0.00 36.85 5.87
183 184 2.373540 TTTTGGTAGCATAGTCGCGT 57.626 45.000 5.77 0.00 36.85 6.01
184 185 1.635844 TTTGGTAGCATAGTCGCGTG 58.364 50.000 5.77 0.00 36.85 5.34
185 186 0.804544 TTGGTAGCATAGTCGCGTGC 60.805 55.000 11.10 11.10 41.57 5.34
186 187 2.293627 GGTAGCATAGTCGCGTGCG 61.294 63.158 12.91 8.14 45.69 5.34
187 188 1.585521 GTAGCATAGTCGCGTGCGT 60.586 57.895 14.47 5.48 45.69 5.24
188 189 1.138036 TAGCATAGTCGCGTGCGTT 59.862 52.632 14.47 6.69 45.69 4.84
189 190 0.864377 TAGCATAGTCGCGTGCGTTC 60.864 55.000 14.47 8.83 45.69 3.95
190 191 2.158959 GCATAGTCGCGTGCGTTCT 61.159 57.895 14.47 15.07 40.74 3.01
191 192 1.625870 CATAGTCGCGTGCGTTCTG 59.374 57.895 14.47 4.59 40.74 3.02
192 193 2.158959 ATAGTCGCGTGCGTTCTGC 61.159 57.895 14.47 1.47 46.70 4.26
201 202 2.506217 GCGTTCTGCGTGATCCGA 60.506 61.111 7.64 0.00 43.66 4.55
202 203 1.878522 GCGTTCTGCGTGATCCGAT 60.879 57.895 7.64 0.00 43.66 4.18
203 204 1.812214 GCGTTCTGCGTGATCCGATC 61.812 60.000 7.64 1.01 43.66 3.69
204 205 0.525455 CGTTCTGCGTGATCCGATCA 60.525 55.000 7.00 7.00 39.56 2.92
205 206 1.858091 GTTCTGCGTGATCCGATCAT 58.142 50.000 14.15 0.00 42.04 2.45
206 207 1.789464 GTTCTGCGTGATCCGATCATC 59.211 52.381 14.15 9.79 42.04 2.92
207 208 1.322442 TCTGCGTGATCCGATCATCT 58.678 50.000 14.15 0.00 42.04 2.90
208 209 1.683385 TCTGCGTGATCCGATCATCTT 59.317 47.619 14.15 0.00 42.04 2.40
209 210 1.791204 CTGCGTGATCCGATCATCTTG 59.209 52.381 14.15 6.47 42.04 3.02
210 211 1.143305 GCGTGATCCGATCATCTTGG 58.857 55.000 14.15 3.82 42.04 3.61
211 212 1.788258 CGTGATCCGATCATCTTGGG 58.212 55.000 14.15 0.00 42.04 4.12
212 213 1.341209 CGTGATCCGATCATCTTGGGA 59.659 52.381 14.15 0.00 42.04 4.37
213 214 2.028658 CGTGATCCGATCATCTTGGGAT 60.029 50.000 14.15 0.00 42.04 3.85
219 220 1.805869 GATCATCTTGGGATCGGCAG 58.194 55.000 0.00 0.00 32.62 4.85
220 221 1.071385 GATCATCTTGGGATCGGCAGT 59.929 52.381 0.00 0.00 32.62 4.40
221 222 0.178767 TCATCTTGGGATCGGCAGTG 59.821 55.000 0.00 0.00 0.00 3.66
222 223 0.107508 CATCTTGGGATCGGCAGTGT 60.108 55.000 0.00 0.00 0.00 3.55
223 224 0.620556 ATCTTGGGATCGGCAGTGTT 59.379 50.000 0.00 0.00 0.00 3.32
224 225 0.400213 TCTTGGGATCGGCAGTGTTT 59.600 50.000 0.00 0.00 0.00 2.83
225 226 0.523072 CTTGGGATCGGCAGTGTTTG 59.477 55.000 0.00 0.00 0.00 2.93
226 227 0.109532 TTGGGATCGGCAGTGTTTGA 59.890 50.000 0.00 0.00 0.00 2.69
227 228 0.109532 TGGGATCGGCAGTGTTTGAA 59.890 50.000 0.00 0.00 0.00 2.69
228 229 0.804989 GGGATCGGCAGTGTTTGAAG 59.195 55.000 0.00 0.00 0.00 3.02
229 230 0.804989 GGATCGGCAGTGTTTGAAGG 59.195 55.000 0.00 0.00 0.00 3.46
230 231 0.169009 GATCGGCAGTGTTTGAAGGC 59.831 55.000 0.00 0.00 0.00 4.35
231 232 1.244019 ATCGGCAGTGTTTGAAGGCC 61.244 55.000 0.00 0.00 41.20 5.19
232 233 2.192861 CGGCAGTGTTTGAAGGCCA 61.193 57.895 5.01 0.00 44.82 5.36
233 234 1.363807 GGCAGTGTTTGAAGGCCAC 59.636 57.895 5.01 0.00 44.01 5.01
234 235 1.363807 GCAGTGTTTGAAGGCCACC 59.636 57.895 5.01 0.00 0.00 4.61
235 236 2.041153 CAGTGTTTGAAGGCCACCC 58.959 57.895 5.01 0.00 0.00 4.61
236 237 1.152546 AGTGTTTGAAGGCCACCCC 60.153 57.895 5.01 0.00 0.00 4.95
237 238 1.456705 GTGTTTGAAGGCCACCCCA 60.457 57.895 5.01 0.00 35.39 4.96
238 239 0.831711 GTGTTTGAAGGCCACCCCAT 60.832 55.000 5.01 0.00 35.39 4.00
239 240 0.541764 TGTTTGAAGGCCACCCCATC 60.542 55.000 5.01 0.00 35.39 3.51
240 241 0.251787 GTTTGAAGGCCACCCCATCT 60.252 55.000 5.01 0.00 32.50 2.90
241 242 0.039618 TTTGAAGGCCACCCCATCTC 59.960 55.000 5.01 0.00 32.50 2.75
242 243 1.863155 TTGAAGGCCACCCCATCTCC 61.863 60.000 5.01 0.00 32.50 3.71
243 244 2.003548 GAAGGCCACCCCATCTCCT 61.004 63.158 5.01 0.00 35.39 3.69
244 245 1.544917 AAGGCCACCCCATCTCCTT 60.545 57.895 5.01 0.00 35.39 3.36
245 246 1.867595 AAGGCCACCCCATCTCCTTG 61.868 60.000 5.01 0.00 35.95 3.61
246 247 2.616458 GGCCACCCCATCTCCTTGT 61.616 63.158 0.00 0.00 0.00 3.16
247 248 1.379044 GCCACCCCATCTCCTTGTG 60.379 63.158 0.00 0.00 0.00 3.33
248 249 2.078452 CCACCCCATCTCCTTGTGT 58.922 57.895 0.00 0.00 0.00 3.72
249 250 0.035056 CCACCCCATCTCCTTGTGTC 60.035 60.000 0.00 0.00 0.00 3.67
250 251 0.391661 CACCCCATCTCCTTGTGTCG 60.392 60.000 0.00 0.00 0.00 4.35
251 252 0.836400 ACCCCATCTCCTTGTGTCGT 60.836 55.000 0.00 0.00 0.00 4.34
252 253 0.324943 CCCCATCTCCTTGTGTCGTT 59.675 55.000 0.00 0.00 0.00 3.85
253 254 1.676014 CCCCATCTCCTTGTGTCGTTC 60.676 57.143 0.00 0.00 0.00 3.95
254 255 1.350193 CCATCTCCTTGTGTCGTTCG 58.650 55.000 0.00 0.00 0.00 3.95
255 256 1.350193 CATCTCCTTGTGTCGTTCGG 58.650 55.000 0.00 0.00 0.00 4.30
256 257 0.389948 ATCTCCTTGTGTCGTTCGGC 60.390 55.000 0.00 0.00 0.00 5.54
310 311 2.286067 CGATGCGAAAATCTCCTCTTGC 60.286 50.000 0.00 0.00 0.00 4.01
311 312 1.453155 TGCGAAAATCTCCTCTTGCC 58.547 50.000 0.00 0.00 0.00 4.52
422 423 2.780094 CGCTCCTCGCCTCAGATGT 61.780 63.158 0.00 0.00 34.21 3.06
471 472 2.434185 GGAGTGCGCCGTGATTGA 60.434 61.111 4.18 0.00 0.00 2.57
476 477 2.434185 GCGCCGTGATTGACTCCA 60.434 61.111 0.00 0.00 0.00 3.86
502 503 2.123854 TCCGAGATGGTAGGCGCT 60.124 61.111 7.64 0.00 39.52 5.92
554 568 0.378257 CTCTCTGCTCTCACTCGCTC 59.622 60.000 0.00 0.00 0.00 5.03
560 574 2.673341 TCTCACTCGCTCGCAGGT 60.673 61.111 0.00 0.00 0.00 4.00
584 598 2.159517 ACGAATGAAAATGAGAAGCGGC 60.160 45.455 0.00 0.00 0.00 6.53
673 695 2.624838 AGAAAAAGTGTGATGTGGCTGG 59.375 45.455 0.00 0.00 0.00 4.85
801 823 4.203076 ATACAGCGACCGCCGTCC 62.203 66.667 11.03 0.00 43.17 4.79
837 879 3.350612 CCGGCCGCAAACGAAGAA 61.351 61.111 22.85 0.00 43.93 2.52
1138 1438 2.756283 CCGACCGCTCCTTCCTCT 60.756 66.667 0.00 0.00 0.00 3.69
1438 1746 4.918129 CGCCCATACCGACGGACG 62.918 72.222 23.38 10.03 42.18 4.79
1529 1853 8.370940 AGATGATATGTCGTTCAAGGTGATATT 58.629 33.333 0.00 0.00 0.00 1.28
1539 1863 6.929049 CGTTCAAGGTGATATTCTTAGCCATA 59.071 38.462 0.00 0.00 0.00 2.74
1631 1955 0.887387 TGGAGTTTGTTAGGCGTGCC 60.887 55.000 1.67 1.67 0.00 5.01
1997 2379 1.882912 ACGACTCAGCAAAGCAATGA 58.117 45.000 0.00 0.00 0.00 2.57
2033 2415 6.801539 TGAATGGCGGATGAAGAATATTAC 57.198 37.500 0.00 0.00 0.00 1.89
2170 2552 2.771943 TCCAGGACTGATTGGGATGTAC 59.228 50.000 0.00 0.00 35.13 2.90
2342 2725 6.071784 TGTTTTATGATCATTGTGCTCTGCTT 60.072 34.615 14.65 0.00 0.00 3.91
2346 2729 0.251033 TCATTGTGCTCTGCTTGCCT 60.251 50.000 0.00 0.00 0.00 4.75
2347 2730 1.003464 TCATTGTGCTCTGCTTGCCTA 59.997 47.619 0.00 0.00 0.00 3.93
2348 2731 1.814394 CATTGTGCTCTGCTTGCCTAA 59.186 47.619 0.00 0.00 0.00 2.69
2533 2920 6.201425 AGTTTGCATAACATTTGCTTCAGTTG 59.799 34.615 12.28 0.00 40.77 3.16
2558 2946 4.660303 TGTCTGAGGGCCATTTACATCTAT 59.340 41.667 6.18 0.00 0.00 1.98
2565 2953 5.134339 AGGGCCATTTACATCTATGGAAAGA 59.866 40.000 6.18 0.00 43.31 2.52
2755 3144 3.130693 CGCCTTTCTAGTTAGTAGGCACT 59.869 47.826 22.52 1.52 44.61 4.40
3086 3737 1.310904 AGGTTTTCGGCGCAGTTTTA 58.689 45.000 10.83 0.00 0.00 1.52
3097 3748 3.072211 GCGCAGTTTTACCTAGAAACCT 58.928 45.455 0.30 0.00 37.64 3.50
3167 3818 4.348486 TGGAACAAAAAGCTGCCCATATA 58.652 39.130 0.00 0.00 31.92 0.86
3289 3941 4.036027 GCACATGAATAAGAGTCCACATGG 59.964 45.833 0.00 0.00 39.20 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.519455 GGAGAGGAACGCCATGACG 60.519 63.158 0.00 0.00 38.35 4.35
1 2 1.519455 CGGAGAGGAACGCCATGAC 60.519 63.158 0.00 0.00 38.38 3.06
2 3 1.982395 ACGGAGAGGAACGCCATGA 60.982 57.895 0.00 0.00 38.38 3.07
3 4 1.811266 CACGGAGAGGAACGCCATG 60.811 63.158 0.00 0.00 38.38 3.66
4 5 2.227089 GACACGGAGAGGAACGCCAT 62.227 60.000 0.00 0.00 38.38 4.40
5 6 2.915659 ACACGGAGAGGAACGCCA 60.916 61.111 0.00 0.00 38.38 5.69
6 7 2.126031 GACACGGAGAGGAACGCC 60.126 66.667 0.00 0.00 35.10 5.68
7 8 2.126031 GGACACGGAGAGGAACGC 60.126 66.667 0.00 0.00 0.00 4.84
8 9 2.178521 CGGACACGGAGAGGAACG 59.821 66.667 0.00 0.00 36.18 3.95
18 19 0.037139 TTCACCATAACCCGGACACG 60.037 55.000 0.73 0.00 40.55 4.49
19 20 2.188062 TTTCACCATAACCCGGACAC 57.812 50.000 0.73 0.00 0.00 3.67
20 21 2.506444 GTTTTCACCATAACCCGGACA 58.494 47.619 0.73 0.00 0.00 4.02
21 22 1.814394 GGTTTTCACCATAACCCGGAC 59.186 52.381 0.73 0.00 43.61 4.79
22 23 2.203470 GGTTTTCACCATAACCCGGA 57.797 50.000 0.73 0.00 43.61 5.14
31 32 8.475639 GTCTACAATAGATAGAGGTTTTCACCA 58.524 37.037 0.00 0.00 40.45 4.17
32 33 8.697292 AGTCTACAATAGATAGAGGTTTTCACC 58.303 37.037 0.00 0.00 39.21 4.02
33 34 9.738832 GAGTCTACAATAGATAGAGGTTTTCAC 57.261 37.037 0.00 0.00 37.13 3.18
34 35 8.622157 CGAGTCTACAATAGATAGAGGTTTTCA 58.378 37.037 0.00 0.00 37.13 2.69
35 36 8.077386 CCGAGTCTACAATAGATAGAGGTTTTC 58.923 40.741 0.00 0.00 37.13 2.29
36 37 7.470286 GCCGAGTCTACAATAGATAGAGGTTTT 60.470 40.741 0.00 0.00 37.13 2.43
37 38 6.016108 GCCGAGTCTACAATAGATAGAGGTTT 60.016 42.308 0.00 0.00 37.13 3.27
38 39 5.474189 GCCGAGTCTACAATAGATAGAGGTT 59.526 44.000 0.00 0.00 37.13 3.50
39 40 5.005094 GCCGAGTCTACAATAGATAGAGGT 58.995 45.833 0.00 0.00 37.13 3.85
40 41 5.004448 TGCCGAGTCTACAATAGATAGAGG 58.996 45.833 0.00 0.00 37.13 3.69
41 42 6.017026 TGTTGCCGAGTCTACAATAGATAGAG 60.017 42.308 0.00 0.00 37.13 2.43
42 43 5.826208 TGTTGCCGAGTCTACAATAGATAGA 59.174 40.000 0.00 0.00 37.13 1.98
43 44 6.073327 TGTTGCCGAGTCTACAATAGATAG 57.927 41.667 0.00 0.00 37.13 2.08
44 45 6.270815 GTTGTTGCCGAGTCTACAATAGATA 58.729 40.000 0.00 0.00 37.13 1.98
45 46 5.109903 GTTGTTGCCGAGTCTACAATAGAT 58.890 41.667 0.00 0.00 37.13 1.98
46 47 4.491676 GTTGTTGCCGAGTCTACAATAGA 58.508 43.478 0.00 0.00 35.07 1.98
47 48 3.303495 CGTTGTTGCCGAGTCTACAATAG 59.697 47.826 0.00 0.00 35.07 1.73
48 49 3.057386 TCGTTGTTGCCGAGTCTACAATA 60.057 43.478 0.00 0.00 35.07 1.90
49 50 2.066262 CGTTGTTGCCGAGTCTACAAT 58.934 47.619 0.00 0.00 35.07 2.71
50 51 1.067364 TCGTTGTTGCCGAGTCTACAA 59.933 47.619 0.00 0.00 31.32 2.41
51 52 0.669619 TCGTTGTTGCCGAGTCTACA 59.330 50.000 0.00 0.00 0.00 2.74
52 53 1.058404 GTCGTTGTTGCCGAGTCTAC 58.942 55.000 0.00 0.00 34.56 2.59
53 54 0.386352 CGTCGTTGTTGCCGAGTCTA 60.386 55.000 0.00 0.00 34.56 2.59
54 55 1.660575 CGTCGTTGTTGCCGAGTCT 60.661 57.895 0.00 0.00 34.56 3.24
55 56 2.844146 CGTCGTTGTTGCCGAGTC 59.156 61.111 0.00 0.00 34.56 3.36
56 57 3.335534 GCGTCGTTGTTGCCGAGT 61.336 61.111 0.00 0.00 34.56 4.18
57 58 4.072088 GGCGTCGTTGTTGCCGAG 62.072 66.667 0.00 0.00 39.30 4.63
61 62 1.154727 CGTTAGGCGTCGTTGTTGC 60.155 57.895 0.00 0.00 35.54 4.17
62 63 1.154727 GCGTTAGGCGTCGTTGTTG 60.155 57.895 0.00 0.00 43.66 3.33
63 64 2.312436 GGCGTTAGGCGTCGTTGTT 61.312 57.895 0.00 0.00 44.92 2.83
64 65 2.735857 GGCGTTAGGCGTCGTTGT 60.736 61.111 0.00 0.00 44.92 3.32
72 73 0.599466 GAGGGATAACGGCGTTAGGC 60.599 60.000 32.39 25.95 42.51 3.93
73 74 0.033090 GGAGGGATAACGGCGTTAGG 59.967 60.000 32.39 0.00 31.29 2.69
74 75 1.038280 AGGAGGGATAACGGCGTTAG 58.962 55.000 32.39 0.00 31.29 2.34
75 76 0.748450 CAGGAGGGATAACGGCGTTA 59.252 55.000 31.66 31.66 32.36 3.18
76 77 1.520666 CAGGAGGGATAACGGCGTT 59.479 57.895 29.36 29.36 0.00 4.84
77 78 2.432300 CCAGGAGGGATAACGGCGT 61.432 63.158 6.77 6.77 40.01 5.68
78 79 2.421739 CCAGGAGGGATAACGGCG 59.578 66.667 4.80 4.80 40.01 6.46
88 89 2.672996 CAACAACGCCCCAGGAGG 60.673 66.667 0.00 0.00 0.00 4.30
89 90 2.113139 ACAACAACGCCCCAGGAG 59.887 61.111 0.00 0.00 0.00 3.69
90 91 2.203280 CACAACAACGCCCCAGGA 60.203 61.111 0.00 0.00 0.00 3.86
91 92 3.294493 CCACAACAACGCCCCAGG 61.294 66.667 0.00 0.00 0.00 4.45
92 93 2.203280 TCCACAACAACGCCCCAG 60.203 61.111 0.00 0.00 0.00 4.45
93 94 2.203280 CTCCACAACAACGCCCCA 60.203 61.111 0.00 0.00 0.00 4.96
94 95 3.670377 GCTCCACAACAACGCCCC 61.670 66.667 0.00 0.00 0.00 5.80
95 96 0.887387 TAAGCTCCACAACAACGCCC 60.887 55.000 0.00 0.00 0.00 6.13
96 97 0.517316 CTAAGCTCCACAACAACGCC 59.483 55.000 0.00 0.00 0.00 5.68
97 98 0.517316 CCTAAGCTCCACAACAACGC 59.483 55.000 0.00 0.00 0.00 4.84
98 99 1.531149 CACCTAAGCTCCACAACAACG 59.469 52.381 0.00 0.00 0.00 4.10
99 100 2.572290 ACACCTAAGCTCCACAACAAC 58.428 47.619 0.00 0.00 0.00 3.32
100 101 3.290948 AACACCTAAGCTCCACAACAA 57.709 42.857 0.00 0.00 0.00 2.83
101 102 4.634012 ATAACACCTAAGCTCCACAACA 57.366 40.909 0.00 0.00 0.00 3.33
102 103 5.116882 CCTATAACACCTAAGCTCCACAAC 58.883 45.833 0.00 0.00 0.00 3.32
103 104 4.163458 CCCTATAACACCTAAGCTCCACAA 59.837 45.833 0.00 0.00 0.00 3.33
104 105 3.709653 CCCTATAACACCTAAGCTCCACA 59.290 47.826 0.00 0.00 0.00 4.17
105 106 3.494573 GCCCTATAACACCTAAGCTCCAC 60.495 52.174 0.00 0.00 0.00 4.02
106 107 2.704065 GCCCTATAACACCTAAGCTCCA 59.296 50.000 0.00 0.00 0.00 3.86
107 108 2.973406 AGCCCTATAACACCTAAGCTCC 59.027 50.000 0.00 0.00 0.00 4.70
108 109 4.691326 AAGCCCTATAACACCTAAGCTC 57.309 45.455 0.00 0.00 0.00 4.09
109 110 4.040584 GCTAAGCCCTATAACACCTAAGCT 59.959 45.833 0.00 0.00 0.00 3.74
110 111 4.202326 TGCTAAGCCCTATAACACCTAAGC 60.202 45.833 0.00 0.00 0.00 3.09
111 112 5.546621 TGCTAAGCCCTATAACACCTAAG 57.453 43.478 0.00 0.00 0.00 2.18
112 113 5.221843 CCATGCTAAGCCCTATAACACCTAA 60.222 44.000 0.00 0.00 0.00 2.69
113 114 4.286032 CCATGCTAAGCCCTATAACACCTA 59.714 45.833 0.00 0.00 0.00 3.08
114 115 3.073062 CCATGCTAAGCCCTATAACACCT 59.927 47.826 0.00 0.00 0.00 4.00
115 116 3.181443 ACCATGCTAAGCCCTATAACACC 60.181 47.826 0.00 0.00 0.00 4.16
116 117 3.815401 CACCATGCTAAGCCCTATAACAC 59.185 47.826 0.00 0.00 0.00 3.32
117 118 3.458118 ACACCATGCTAAGCCCTATAACA 59.542 43.478 0.00 0.00 0.00 2.41
118 119 4.086706 ACACCATGCTAAGCCCTATAAC 57.913 45.455 0.00 0.00 0.00 1.89
119 120 4.460263 CAACACCATGCTAAGCCCTATAA 58.540 43.478 0.00 0.00 0.00 0.98
120 121 3.747388 GCAACACCATGCTAAGCCCTATA 60.747 47.826 0.00 0.00 43.06 1.31
121 122 2.936202 CAACACCATGCTAAGCCCTAT 58.064 47.619 0.00 0.00 0.00 2.57
122 123 1.681780 GCAACACCATGCTAAGCCCTA 60.682 52.381 0.00 0.00 43.06 3.53
123 124 0.967380 GCAACACCATGCTAAGCCCT 60.967 55.000 0.00 0.00 43.06 5.19
124 125 1.512694 GCAACACCATGCTAAGCCC 59.487 57.895 0.00 0.00 43.06 5.19
131 132 3.641437 TGAACTAAAGCAACACCATGC 57.359 42.857 0.00 0.00 46.78 4.06
132 133 5.633830 AGATGAACTAAAGCAACACCATG 57.366 39.130 0.00 0.00 0.00 3.66
133 134 5.536161 ACAAGATGAACTAAAGCAACACCAT 59.464 36.000 0.00 0.00 0.00 3.55
134 135 4.887071 ACAAGATGAACTAAAGCAACACCA 59.113 37.500 0.00 0.00 0.00 4.17
135 136 5.438761 ACAAGATGAACTAAAGCAACACC 57.561 39.130 0.00 0.00 0.00 4.16
136 137 7.190920 AGTACAAGATGAACTAAAGCAACAC 57.809 36.000 0.00 0.00 0.00 3.32
137 138 7.801716 AAGTACAAGATGAACTAAAGCAACA 57.198 32.000 0.00 0.00 0.00 3.33
147 148 9.556030 GCTACCAAAATAAAGTACAAGATGAAC 57.444 33.333 0.00 0.00 0.00 3.18
148 149 9.290988 TGCTACCAAAATAAAGTACAAGATGAA 57.709 29.630 0.00 0.00 0.00 2.57
149 150 8.856153 TGCTACCAAAATAAAGTACAAGATGA 57.144 30.769 0.00 0.00 0.00 2.92
152 153 9.953565 ACTATGCTACCAAAATAAAGTACAAGA 57.046 29.630 0.00 0.00 0.00 3.02
154 155 8.875803 CGACTATGCTACCAAAATAAAGTACAA 58.124 33.333 0.00 0.00 0.00 2.41
155 156 7.010738 GCGACTATGCTACCAAAATAAAGTACA 59.989 37.037 0.00 0.00 0.00 2.90
156 157 7.342942 GCGACTATGCTACCAAAATAAAGTAC 58.657 38.462 0.00 0.00 0.00 2.73
157 158 6.199531 CGCGACTATGCTACCAAAATAAAGTA 59.800 38.462 0.00 0.00 0.00 2.24
158 159 5.006358 CGCGACTATGCTACCAAAATAAAGT 59.994 40.000 0.00 0.00 0.00 2.66
159 160 5.006358 ACGCGACTATGCTACCAAAATAAAG 59.994 40.000 15.93 0.00 0.00 1.85
160 161 4.871557 ACGCGACTATGCTACCAAAATAAA 59.128 37.500 15.93 0.00 0.00 1.40
161 162 4.269123 CACGCGACTATGCTACCAAAATAA 59.731 41.667 15.93 0.00 0.00 1.40
162 163 3.799963 CACGCGACTATGCTACCAAAATA 59.200 43.478 15.93 0.00 0.00 1.40
163 164 2.607635 CACGCGACTATGCTACCAAAAT 59.392 45.455 15.93 0.00 0.00 1.82
164 165 1.996898 CACGCGACTATGCTACCAAAA 59.003 47.619 15.93 0.00 0.00 2.44
165 166 1.635844 CACGCGACTATGCTACCAAA 58.364 50.000 15.93 0.00 0.00 3.28
166 167 0.804544 GCACGCGACTATGCTACCAA 60.805 55.000 15.93 0.00 38.84 3.67
167 168 1.226859 GCACGCGACTATGCTACCA 60.227 57.895 15.93 0.00 38.84 3.25
168 169 2.293627 CGCACGCGACTATGCTACC 61.294 63.158 15.93 0.00 42.83 3.18
169 170 1.138047 AACGCACGCGACTATGCTAC 61.138 55.000 19.66 0.00 42.83 3.58
170 171 0.864377 GAACGCACGCGACTATGCTA 60.864 55.000 19.66 0.00 42.83 3.49
171 172 2.126071 AACGCACGCGACTATGCT 60.126 55.556 19.66 0.00 42.83 3.79
172 173 2.158959 AGAACGCACGCGACTATGC 61.159 57.895 19.66 11.86 42.83 3.14
173 174 1.625870 CAGAACGCACGCGACTATG 59.374 57.895 19.66 8.32 42.83 2.23
174 175 2.158959 GCAGAACGCACGCGACTAT 61.159 57.895 19.66 0.92 42.83 2.12
175 176 2.803670 GCAGAACGCACGCGACTA 60.804 61.111 19.66 0.00 42.83 2.59
186 187 1.789464 GATGATCGGATCACGCAGAAC 59.211 52.381 22.09 5.49 43.01 3.01
187 188 1.683385 AGATGATCGGATCACGCAGAA 59.317 47.619 22.09 0.00 43.01 3.02
188 189 1.322442 AGATGATCGGATCACGCAGA 58.678 50.000 22.09 0.00 43.01 4.26
189 190 1.791204 CAAGATGATCGGATCACGCAG 59.209 52.381 22.09 9.78 43.01 5.18
190 191 1.538849 CCAAGATGATCGGATCACGCA 60.539 52.381 22.09 1.11 43.01 5.24
191 192 1.143305 CCAAGATGATCGGATCACGC 58.857 55.000 22.09 16.55 43.01 5.34
192 193 1.341209 TCCCAAGATGATCGGATCACG 59.659 52.381 22.09 11.17 43.01 4.35
193 194 3.594134 GATCCCAAGATGATCGGATCAC 58.406 50.000 22.09 15.40 46.74 3.06
194 195 3.969287 GATCCCAAGATGATCGGATCA 57.031 47.619 21.92 21.92 46.74 2.92
200 201 1.071385 ACTGCCGATCCCAAGATGATC 59.929 52.381 0.00 0.00 36.18 2.92
201 202 1.135094 ACTGCCGATCCCAAGATGAT 58.865 50.000 0.00 0.00 30.90 2.45
202 203 0.178767 CACTGCCGATCCCAAGATGA 59.821 55.000 0.00 0.00 30.90 2.92
203 204 0.107508 ACACTGCCGATCCCAAGATG 60.108 55.000 0.00 0.00 30.90 2.90
204 205 0.620556 AACACTGCCGATCCCAAGAT 59.379 50.000 0.00 0.00 34.57 2.40
205 206 0.400213 AAACACTGCCGATCCCAAGA 59.600 50.000 0.00 0.00 0.00 3.02
206 207 0.523072 CAAACACTGCCGATCCCAAG 59.477 55.000 0.00 0.00 0.00 3.61
207 208 0.109532 TCAAACACTGCCGATCCCAA 59.890 50.000 0.00 0.00 0.00 4.12
208 209 0.109532 TTCAAACACTGCCGATCCCA 59.890 50.000 0.00 0.00 0.00 4.37
209 210 0.804989 CTTCAAACACTGCCGATCCC 59.195 55.000 0.00 0.00 0.00 3.85
210 211 0.804989 CCTTCAAACACTGCCGATCC 59.195 55.000 0.00 0.00 0.00 3.36
211 212 0.169009 GCCTTCAAACACTGCCGATC 59.831 55.000 0.00 0.00 0.00 3.69
212 213 1.244019 GGCCTTCAAACACTGCCGAT 61.244 55.000 0.00 0.00 31.55 4.18
213 214 1.896660 GGCCTTCAAACACTGCCGA 60.897 57.895 0.00 0.00 31.55 5.54
214 215 2.192861 TGGCCTTCAAACACTGCCG 61.193 57.895 3.32 0.00 45.12 5.69
215 216 1.363807 GTGGCCTTCAAACACTGCC 59.636 57.895 3.32 0.00 42.49 4.85
216 217 1.363807 GGTGGCCTTCAAACACTGC 59.636 57.895 3.32 0.00 35.53 4.40
217 218 1.463553 GGGGTGGCCTTCAAACACTG 61.464 60.000 3.32 0.00 35.53 3.66
218 219 1.152546 GGGGTGGCCTTCAAACACT 60.153 57.895 3.32 0.00 35.53 3.55
219 220 0.831711 ATGGGGTGGCCTTCAAACAC 60.832 55.000 3.32 0.00 0.00 3.32
220 221 0.541764 GATGGGGTGGCCTTCAAACA 60.542 55.000 3.32 0.00 0.00 2.83
221 222 0.251787 AGATGGGGTGGCCTTCAAAC 60.252 55.000 3.32 0.00 0.00 2.93
222 223 0.039618 GAGATGGGGTGGCCTTCAAA 59.960 55.000 3.32 0.00 0.00 2.69
223 224 1.691219 GAGATGGGGTGGCCTTCAA 59.309 57.895 3.32 0.00 0.00 2.69
224 225 2.308722 GGAGATGGGGTGGCCTTCA 61.309 63.158 3.32 0.00 0.00 3.02
225 226 1.575447 AAGGAGATGGGGTGGCCTTC 61.575 60.000 3.32 0.00 33.94 3.46
226 227 1.544917 AAGGAGATGGGGTGGCCTT 60.545 57.895 3.32 0.00 34.28 4.35
227 228 2.128226 AAGGAGATGGGGTGGCCT 59.872 61.111 3.32 0.00 0.00 5.19
228 229 2.276740 CAAGGAGATGGGGTGGCC 59.723 66.667 0.00 0.00 0.00 5.36
229 230 1.379044 CACAAGGAGATGGGGTGGC 60.379 63.158 0.00 0.00 0.00 5.01
230 231 0.035056 GACACAAGGAGATGGGGTGG 60.035 60.000 0.00 0.00 33.91 4.61
231 232 0.391661 CGACACAAGGAGATGGGGTG 60.392 60.000 0.00 0.00 35.66 4.61
232 233 0.836400 ACGACACAAGGAGATGGGGT 60.836 55.000 0.00 0.00 0.00 4.95
233 234 0.324943 AACGACACAAGGAGATGGGG 59.675 55.000 0.00 0.00 0.00 4.96
234 235 1.726853 GAACGACACAAGGAGATGGG 58.273 55.000 0.00 0.00 0.00 4.00
235 236 1.350193 CGAACGACACAAGGAGATGG 58.650 55.000 0.00 0.00 0.00 3.51
236 237 1.350193 CCGAACGACACAAGGAGATG 58.650 55.000 0.00 0.00 0.00 2.90
237 238 0.389948 GCCGAACGACACAAGGAGAT 60.390 55.000 0.00 0.00 0.00 2.75
238 239 1.006571 GCCGAACGACACAAGGAGA 60.007 57.895 0.00 0.00 0.00 3.71
239 240 2.027625 GGCCGAACGACACAAGGAG 61.028 63.158 0.00 0.00 0.00 3.69
240 241 2.029964 GGCCGAACGACACAAGGA 59.970 61.111 0.00 0.00 0.00 3.36
241 242 3.411351 CGGCCGAACGACACAAGG 61.411 66.667 24.07 0.00 35.47 3.61
242 243 4.072088 GCGGCCGAACGACACAAG 62.072 66.667 33.48 0.00 35.47 3.16
296 297 1.457346 CGCAGGCAAGAGGAGATTTT 58.543 50.000 0.00 0.00 0.00 1.82
492 493 4.063967 CCACGACAGCGCCTACCA 62.064 66.667 2.29 0.00 42.48 3.25
519 520 3.396911 GAGAGTGTGATCGCGCGGA 62.397 63.158 31.69 17.27 0.00 5.54
522 523 0.865218 CAGAGAGAGTGTGATCGCGC 60.865 60.000 11.91 11.91 0.00 6.86
528 529 2.158559 GTGAGAGCAGAGAGAGTGTGA 58.841 52.381 0.00 0.00 0.00 3.58
554 568 2.679355 TTTTCATTCGTTGACCTGCG 57.321 45.000 0.00 0.00 32.84 5.18
560 574 4.378356 CCGCTTCTCATTTTCATTCGTTGA 60.378 41.667 0.00 0.00 0.00 3.18
584 598 1.296715 CTTTCTCCACCACTCCCCG 59.703 63.158 0.00 0.00 0.00 5.73
597 619 3.243771 CGCAGGTATCGTATTCCCTTTCT 60.244 47.826 0.00 0.00 0.00 2.52
673 695 1.207329 ACGAATCTTAGTGCAGGGGAC 59.793 52.381 0.00 0.00 0.00 4.46
682 704 6.161855 TGGATCATTAGCACGAATCTTAGT 57.838 37.500 0.00 0.00 0.00 2.24
825 867 1.726853 ATCTCCCTTCTTCGTTTGCG 58.273 50.000 0.00 0.00 39.92 4.85
835 877 6.181206 AGGTTGCTAATTCTATCTCCCTTC 57.819 41.667 0.00 0.00 0.00 3.46
836 878 5.667626 TGAGGTTGCTAATTCTATCTCCCTT 59.332 40.000 0.00 0.00 0.00 3.95
837 879 5.071115 GTGAGGTTGCTAATTCTATCTCCCT 59.929 44.000 0.00 0.00 0.00 4.20
888 933 3.857052 TGTTCACGGAATTAAGCGAGAT 58.143 40.909 0.00 0.00 0.00 2.75
1438 1746 1.135344 GTACTCTTCCTGGACAGCGAC 60.135 57.143 0.00 0.00 0.00 5.19
1539 1863 2.572290 GCGGTTAGCTTGGAACCATAT 58.428 47.619 15.52 0.00 45.70 1.78
2170 2552 6.859715 CTTGACCTCAAGCGAAAAATAATG 57.140 37.500 2.13 0.00 45.59 1.90
2342 2725 8.839343 CACATCTACATGAACAATTATTAGGCA 58.161 33.333 0.00 0.00 33.72 4.75
2347 2730 9.740239 GCAATCACATCTACATGAACAATTATT 57.260 29.630 0.00 0.00 33.72 1.40
2348 2731 9.128404 AGCAATCACATCTACATGAACAATTAT 57.872 29.630 0.00 0.00 33.72 1.28
2533 2920 3.281727 TGTAAATGGCCCTCAGACATC 57.718 47.619 0.00 0.00 0.00 3.06
2558 2946 7.309920 GCAAAGGATAAATTAACGTCTTTCCA 58.690 34.615 0.00 0.00 0.00 3.53
2565 2953 9.101655 ACTAATACGCAAAGGATAAATTAACGT 57.898 29.630 0.00 0.00 35.21 3.99
2700 3089 9.224058 GTACGCACAAAAATTTAAACAAGAGTA 57.776 29.630 0.00 0.00 0.00 2.59
2755 3144 6.128486 ACTGATGTCATATTTGCATGGGTTA 58.872 36.000 0.00 0.00 0.00 2.85
3038 3687 5.385198 TGAATGGCTTCCAGAAGTTTAGTT 58.615 37.500 9.07 0.00 40.45 2.24
3040 3689 7.814264 ATATGAATGGCTTCCAGAAGTTTAG 57.186 36.000 9.07 0.00 40.45 1.85
3097 3748 8.565896 TTTATGAAAAGAGAATAGAGCTGCAA 57.434 30.769 1.02 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.