Multiple sequence alignment - TraesCS1D01G362500

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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 TraesCS1D01G362500 chr1D 100.000 3557 0 0 1 3557 444847959 444844403 0.000000e+00 6569.0
1 TraesCS1D01G362500 chr1D 85.489 634 89 3 2739 3371 272536520 272535889 0.000000e+00 658.0
2 TraesCS1D01G362500 chr1B 92.462 2295 111 26 1306 3557 604835323 604833048 0.000000e+00 3223.0
3 TraesCS1D01G362500 chr1B 87.088 1092 67 28 203 1235 604836738 604835662 0.000000e+00 1168.0
4 TraesCS1D01G362500 chr1B 85.290 639 82 9 2736 3368 26425753 26425121 0.000000e+00 649.0
5 TraesCS1D01G362500 chr1B 95.000 40 0 2 3508 3547 604833047 604833010 1.070000e-05 62.1
6 TraesCS1D01G362500 chr1A 96.478 1221 26 8 1502 2713 540135309 540134097 0.000000e+00 2001.0
7 TraesCS1D01G362500 chr1A 90.566 1113 81 16 304 1403 540136495 540135394 0.000000e+00 1452.0
8 TraesCS1D01G362500 chr1A 88.136 177 19 2 3381 3557 540134104 540133930 3.600000e-50 209.0
9 TraesCS1D01G362500 chr2A 86.562 640 79 6 2735 3368 2742398 2741760 0.000000e+00 699.0
10 TraesCS1D01G362500 chr7D 86.321 636 77 6 2737 3368 58135737 58136366 0.000000e+00 684.0
11 TraesCS1D01G362500 chr7D 86.777 242 30 2 1774 2014 54438043 54437803 5.850000e-68 268.0
12 TraesCS1D01G362500 chr7A 85.647 641 83 6 2736 3368 510900606 510901245 0.000000e+00 665.0
13 TraesCS1D01G362500 chr7A 85.950 242 32 2 1774 2014 57979362 57979122 1.270000e-64 257.0
14 TraesCS1D01G362500 chr6A 85.312 640 88 4 2736 3371 608656639 608656002 0.000000e+00 656.0
15 TraesCS1D01G362500 chr3B 85.335 641 84 8 2736 3368 186089046 186089684 0.000000e+00 654.0
16 TraesCS1D01G362500 chr7B 85.156 640 86 8 2736 3369 533309934 533310570 0.000000e+00 647.0
17 TraesCS1D01G362500 chr4A 86.364 242 31 2 1774 2014 670146744 670146504 2.720000e-66 263.0
18 TraesCS1D01G362500 chr5A 87.059 85 11 0 1825 1909 437915006 437914922 2.920000e-16 97.1
19 TraesCS1D01G362500 chr5B 85.882 85 12 0 1825 1909 394745741 394745657 1.360000e-14 91.6
20 TraesCS1D01G362500 chr5D 84.706 85 13 0 1825 1909 336424557 336424473 6.330000e-13 86.1


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 TraesCS1D01G362500 chr1D 444844403 444847959 3556 True 6569.000000 6569 100.000000 1 3557 1 chr1D.!!$R2 3556
1 TraesCS1D01G362500 chr1D 272535889 272536520 631 True 658.000000 658 85.489000 2739 3371 1 chr1D.!!$R1 632
2 TraesCS1D01G362500 chr1B 604833010 604836738 3728 True 1484.366667 3223 91.516667 203 3557 3 chr1B.!!$R2 3354
3 TraesCS1D01G362500 chr1B 26425121 26425753 632 True 649.000000 649 85.290000 2736 3368 1 chr1B.!!$R1 632
4 TraesCS1D01G362500 chr1A 540133930 540136495 2565 True 1220.666667 2001 91.726667 304 3557 3 chr1A.!!$R1 3253
5 TraesCS1D01G362500 chr2A 2741760 2742398 638 True 699.000000 699 86.562000 2735 3368 1 chr2A.!!$R1 633
6 TraesCS1D01G362500 chr7D 58135737 58136366 629 False 684.000000 684 86.321000 2737 3368 1 chr7D.!!$F1 631
7 TraesCS1D01G362500 chr7A 510900606 510901245 639 False 665.000000 665 85.647000 2736 3368 1 chr7A.!!$F1 632
8 TraesCS1D01G362500 chr6A 608656002 608656639 637 True 656.000000 656 85.312000 2736 3371 1 chr6A.!!$R1 635
9 TraesCS1D01G362500 chr3B 186089046 186089684 638 False 654.000000 654 85.335000 2736 3368 1 chr3B.!!$F1 632
10 TraesCS1D01G362500 chr7B 533309934 533310570 636 False 647.000000 647 85.156000 2736 3369 1 chr7B.!!$F1 633

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
500 536 0.029834 GCCGCTATTTCGTCCTCGTA 59.970 55.0 0.00 0.0 38.33 3.43 F
1239 1309 0.037326 TTCAAAGATGAGCTCGCCGT 60.037 50.0 9.64 0.0 36.78 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 2094 2.022195 GATTGGAGACATGCATGTGCT 58.978 47.619 35.92 28.45 41.95 4.40 R
2999 3418 0.248296 GCGAGATCCGACAGAGACAC 60.248 60.000 7.64 0.00 41.76 3.67 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
19 20 3.047280 CACCTACGCGCTTGCCAA 61.047 61.111 5.73 0.00 34.11 4.52
20 21 3.047877 ACCTACGCGCTTGCCAAC 61.048 61.111 5.73 0.00 34.11 3.77
21 22 2.742372 CCTACGCGCTTGCCAACT 60.742 61.111 5.73 0.00 34.11 3.16
22 23 2.476051 CTACGCGCTTGCCAACTG 59.524 61.111 5.73 0.00 34.11 3.16
23 24 3.651480 CTACGCGCTTGCCAACTGC 62.651 63.158 5.73 0.00 41.77 4.40
29 30 3.594775 CTTGCCAACTGCGCCACA 61.595 61.111 4.18 0.00 45.60 4.17
30 31 3.136345 CTTGCCAACTGCGCCACAA 62.136 57.895 4.18 0.00 45.60 3.33
31 32 3.423162 TTGCCAACTGCGCCACAAC 62.423 57.895 4.18 0.00 45.60 3.32
32 33 4.645921 GCCAACTGCGCCACAACC 62.646 66.667 4.18 0.00 0.00 3.77
33 34 3.215568 CCAACTGCGCCACAACCA 61.216 61.111 4.18 0.00 0.00 3.67
34 35 2.563798 CCAACTGCGCCACAACCAT 61.564 57.895 4.18 0.00 0.00 3.55
35 36 1.372004 CAACTGCGCCACAACCATG 60.372 57.895 4.18 0.00 0.00 3.66
36 37 1.827789 AACTGCGCCACAACCATGT 60.828 52.632 4.18 0.00 41.61 3.21
37 38 1.391157 AACTGCGCCACAACCATGTT 61.391 50.000 4.18 0.00 37.82 2.71
38 39 1.363443 CTGCGCCACAACCATGTTT 59.637 52.632 4.18 0.00 37.82 2.83
39 40 0.940519 CTGCGCCACAACCATGTTTG 60.941 55.000 4.18 0.81 37.82 2.93
40 41 1.067250 GCGCCACAACCATGTTTGT 59.933 52.632 2.30 2.30 40.46 2.83
41 42 0.529555 GCGCCACAACCATGTTTGTT 60.530 50.000 5.81 0.00 37.62 2.83
42 43 1.207390 CGCCACAACCATGTTTGTTG 58.793 50.000 5.81 8.65 46.60 3.33
51 52 6.659361 CAACCATGTTTGTTGTTTGATCAA 57.341 33.333 3.38 3.38 38.58 2.57
52 53 6.707711 CAACCATGTTTGTTGTTTGATCAAG 58.292 36.000 8.41 0.00 38.58 3.02
53 54 4.810491 ACCATGTTTGTTGTTTGATCAAGC 59.190 37.500 14.76 14.76 0.00 4.01
54 55 4.809958 CCATGTTTGTTGTTTGATCAAGCA 59.190 37.500 19.66 19.66 36.91 3.91
55 56 5.467399 CCATGTTTGTTGTTTGATCAAGCAT 59.533 36.000 23.33 6.20 41.21 3.79
56 57 6.645827 CCATGTTTGTTGTTTGATCAAGCATA 59.354 34.615 23.33 13.95 39.57 3.14
57 58 7.359431 CCATGTTTGTTGTTTGATCAAGCATAC 60.359 37.037 23.33 21.44 39.57 2.39
58 59 6.804677 TGTTTGTTGTTTGATCAAGCATACT 58.195 32.000 23.33 0.00 31.74 2.12
59 60 7.935520 TGTTTGTTGTTTGATCAAGCATACTA 58.064 30.769 23.33 17.06 31.74 1.82
60 61 8.409371 TGTTTGTTGTTTGATCAAGCATACTAA 58.591 29.630 23.33 20.53 31.74 2.24
61 62 8.690840 GTTTGTTGTTTGATCAAGCATACTAAC 58.309 33.333 26.03 26.03 31.74 2.34
62 63 6.908825 TGTTGTTTGATCAAGCATACTAACC 58.091 36.000 23.33 8.23 31.74 2.85
63 64 6.488344 TGTTGTTTGATCAAGCATACTAACCA 59.512 34.615 23.33 5.51 31.74 3.67
64 65 7.013750 TGTTGTTTGATCAAGCATACTAACCAA 59.986 33.333 23.33 4.84 31.74 3.67
65 66 7.517614 TGTTTGATCAAGCATACTAACCAAA 57.482 32.000 19.66 0.00 0.00 3.28
66 67 7.946207 TGTTTGATCAAGCATACTAACCAAAA 58.054 30.769 19.66 0.00 0.00 2.44
67 68 8.417106 TGTTTGATCAAGCATACTAACCAAAAA 58.583 29.630 19.66 0.00 0.00 1.94
68 69 8.915654 GTTTGATCAAGCATACTAACCAAAAAG 58.084 33.333 16.49 0.00 0.00 2.27
69 70 7.759489 TGATCAAGCATACTAACCAAAAAGT 57.241 32.000 0.00 0.00 0.00 2.66
70 71 7.816640 TGATCAAGCATACTAACCAAAAAGTC 58.183 34.615 0.00 0.00 0.00 3.01
71 72 7.665559 TGATCAAGCATACTAACCAAAAAGTCT 59.334 33.333 0.00 0.00 0.00 3.24
72 73 7.817418 TCAAGCATACTAACCAAAAAGTCTT 57.183 32.000 0.00 0.00 0.00 3.01
73 74 8.911918 TCAAGCATACTAACCAAAAAGTCTTA 57.088 30.769 0.00 0.00 0.00 2.10
74 75 9.515226 TCAAGCATACTAACCAAAAAGTCTTAT 57.485 29.630 0.00 0.00 0.00 1.73
77 78 8.665685 AGCATACTAACCAAAAAGTCTTATTCG 58.334 33.333 0.00 0.00 0.00 3.34
78 79 8.662141 GCATACTAACCAAAAAGTCTTATTCGA 58.338 33.333 0.00 0.00 0.00 3.71
82 83 8.936864 ACTAACCAAAAAGTCTTATTCGAGATG 58.063 33.333 0.00 0.00 0.00 2.90
83 84 7.745620 AACCAAAAAGTCTTATTCGAGATGT 57.254 32.000 0.00 0.00 0.00 3.06
84 85 7.365840 ACCAAAAAGTCTTATTCGAGATGTC 57.634 36.000 0.00 0.00 0.00 3.06
85 86 6.371825 ACCAAAAAGTCTTATTCGAGATGTCC 59.628 38.462 0.00 0.00 0.00 4.02
86 87 6.595716 CCAAAAAGTCTTATTCGAGATGTCCT 59.404 38.462 0.00 0.00 0.00 3.85
87 88 7.764443 CCAAAAAGTCTTATTCGAGATGTCCTA 59.236 37.037 0.00 0.00 0.00 2.94
88 89 8.596380 CAAAAAGTCTTATTCGAGATGTCCTAC 58.404 37.037 0.00 0.00 0.00 3.18
89 90 7.648039 AAAGTCTTATTCGAGATGTCCTACT 57.352 36.000 0.00 0.00 0.00 2.57
90 91 6.870971 AGTCTTATTCGAGATGTCCTACTC 57.129 41.667 0.00 0.00 0.00 2.59
91 92 5.766174 AGTCTTATTCGAGATGTCCTACTCC 59.234 44.000 0.00 0.00 0.00 3.85
92 93 5.766174 GTCTTATTCGAGATGTCCTACTCCT 59.234 44.000 0.00 0.00 0.00 3.69
93 94 5.765677 TCTTATTCGAGATGTCCTACTCCTG 59.234 44.000 0.00 0.00 0.00 3.86
94 95 1.681538 TCGAGATGTCCTACTCCTGC 58.318 55.000 0.00 0.00 0.00 4.85
95 96 0.671251 CGAGATGTCCTACTCCTGCC 59.329 60.000 0.00 0.00 0.00 4.85
96 97 1.781786 GAGATGTCCTACTCCTGCCA 58.218 55.000 0.00 0.00 0.00 4.92
97 98 2.111384 GAGATGTCCTACTCCTGCCAA 58.889 52.381 0.00 0.00 0.00 4.52
98 99 2.501723 GAGATGTCCTACTCCTGCCAAA 59.498 50.000 0.00 0.00 0.00 3.28
99 100 2.912956 AGATGTCCTACTCCTGCCAAAA 59.087 45.455 0.00 0.00 0.00 2.44
100 101 2.561478 TGTCCTACTCCTGCCAAAAC 57.439 50.000 0.00 0.00 0.00 2.43
101 102 1.771854 TGTCCTACTCCTGCCAAAACA 59.228 47.619 0.00 0.00 0.00 2.83
102 103 2.375174 TGTCCTACTCCTGCCAAAACAT 59.625 45.455 0.00 0.00 0.00 2.71
103 104 3.010420 GTCCTACTCCTGCCAAAACATC 58.990 50.000 0.00 0.00 0.00 3.06
104 105 2.642311 TCCTACTCCTGCCAAAACATCA 59.358 45.455 0.00 0.00 0.00 3.07
105 106 3.266772 TCCTACTCCTGCCAAAACATCAT 59.733 43.478 0.00 0.00 0.00 2.45
106 107 3.629398 CCTACTCCTGCCAAAACATCATC 59.371 47.826 0.00 0.00 0.00 2.92
107 108 2.086869 ACTCCTGCCAAAACATCATCG 58.913 47.619 0.00 0.00 0.00 3.84
108 109 0.810648 TCCTGCCAAAACATCATCGC 59.189 50.000 0.00 0.00 0.00 4.58
109 110 0.527113 CCTGCCAAAACATCATCGCA 59.473 50.000 0.00 0.00 0.00 5.10
110 111 1.067706 CCTGCCAAAACATCATCGCAA 60.068 47.619 0.00 0.00 0.00 4.85
111 112 2.609984 CCTGCCAAAACATCATCGCAAA 60.610 45.455 0.00 0.00 0.00 3.68
112 113 2.402305 TGCCAAAACATCATCGCAAAC 58.598 42.857 0.00 0.00 0.00 2.93
113 114 1.726248 GCCAAAACATCATCGCAAACC 59.274 47.619 0.00 0.00 0.00 3.27
114 115 2.865670 GCCAAAACATCATCGCAAACCA 60.866 45.455 0.00 0.00 0.00 3.67
115 116 3.587923 CCAAAACATCATCGCAAACCAT 58.412 40.909 0.00 0.00 0.00 3.55
116 117 3.368539 CCAAAACATCATCGCAAACCATG 59.631 43.478 0.00 0.00 0.00 3.66
117 118 3.940209 AAACATCATCGCAAACCATGT 57.060 38.095 0.00 0.00 0.00 3.21
118 119 2.925578 ACATCATCGCAAACCATGTG 57.074 45.000 0.00 0.00 41.04 3.21
119 120 2.161855 ACATCATCGCAAACCATGTGT 58.838 42.857 0.00 0.00 40.52 3.72
120 121 2.557924 ACATCATCGCAAACCATGTGTT 59.442 40.909 0.00 0.00 40.52 3.32
122 123 3.281341 TCATCGCAAACCATGTGTTTC 57.719 42.857 8.73 5.05 45.35 2.78
123 124 2.030363 TCATCGCAAACCATGTGTTTCC 60.030 45.455 8.73 1.33 45.35 3.13
124 125 1.393603 TCGCAAACCATGTGTTTCCA 58.606 45.000 8.73 0.00 45.35 3.53
125 126 1.066303 TCGCAAACCATGTGTTTCCAC 59.934 47.619 8.73 0.00 45.35 4.02
126 127 1.066908 CGCAAACCATGTGTTTCCACT 59.933 47.619 8.73 0.00 45.35 4.00
127 128 2.292016 CGCAAACCATGTGTTTCCACTA 59.708 45.455 8.73 0.00 45.35 2.74
128 129 3.243234 CGCAAACCATGTGTTTCCACTAA 60.243 43.478 8.73 0.00 45.35 2.24
129 130 4.558496 CGCAAACCATGTGTTTCCACTAAT 60.558 41.667 8.73 0.00 45.35 1.73
130 131 4.685628 GCAAACCATGTGTTTCCACTAATG 59.314 41.667 8.73 0.34 45.35 1.90
131 132 4.519540 AACCATGTGTTTCCACTAATGC 57.480 40.909 0.00 0.00 42.34 3.56
132 133 2.487762 ACCATGTGTTTCCACTAATGCG 59.512 45.455 0.00 0.00 42.34 4.73
133 134 2.487762 CCATGTGTTTCCACTAATGCGT 59.512 45.455 0.00 0.00 42.34 5.24
134 135 3.687212 CCATGTGTTTCCACTAATGCGTA 59.313 43.478 0.00 0.00 42.34 4.42
135 136 4.436852 CCATGTGTTTCCACTAATGCGTAC 60.437 45.833 0.00 0.00 42.34 3.67
136 137 3.729966 TGTGTTTCCACTAATGCGTACA 58.270 40.909 0.00 0.00 42.34 2.90
137 138 3.743911 TGTGTTTCCACTAATGCGTACAG 59.256 43.478 0.00 0.00 42.34 2.74
138 139 3.744426 GTGTTTCCACTAATGCGTACAGT 59.256 43.478 0.00 0.00 38.61 3.55
139 140 4.925054 GTGTTTCCACTAATGCGTACAGTA 59.075 41.667 0.00 0.00 38.61 2.74
159 160 5.551233 AGTAGTACTGAAGATTTTGCTGCA 58.449 37.500 5.39 0.00 0.00 4.41
160 161 5.641209 AGTAGTACTGAAGATTTTGCTGCAG 59.359 40.000 10.11 10.11 45.43 4.41
164 165 4.233123 CTGAAGATTTTGCTGCAGTTCA 57.767 40.909 16.64 13.67 36.89 3.18
165 166 4.806330 CTGAAGATTTTGCTGCAGTTCAT 58.194 39.130 16.64 2.51 36.89 2.57
166 167 5.204409 TGAAGATTTTGCTGCAGTTCATT 57.796 34.783 16.64 1.61 0.00 2.57
167 168 4.986034 TGAAGATTTTGCTGCAGTTCATTG 59.014 37.500 16.64 0.00 0.00 2.82
168 169 3.323243 AGATTTTGCTGCAGTTCATTGC 58.677 40.909 16.64 0.00 44.33 3.56
184 185 3.695606 GCGGTCAGCTGACTCCCA 61.696 66.667 38.17 6.63 44.20 4.37
185 186 3.059982 CGGTCAGCTGACTCCCAA 58.940 61.111 38.17 5.84 44.20 4.12
186 187 1.599047 CGGTCAGCTGACTCCCAAT 59.401 57.895 38.17 0.00 44.20 3.16
187 188 0.742281 CGGTCAGCTGACTCCCAATG 60.742 60.000 38.17 19.40 44.20 2.82
188 189 0.393537 GGTCAGCTGACTCCCAATGG 60.394 60.000 38.17 0.00 44.20 3.16
189 190 1.028868 GTCAGCTGACTCCCAATGGC 61.029 60.000 34.54 8.64 41.65 4.40
190 191 1.001764 CAGCTGACTCCCAATGGCA 60.002 57.895 8.42 0.00 0.00 4.92
191 192 0.395311 CAGCTGACTCCCAATGGCAT 60.395 55.000 8.42 0.00 0.00 4.40
192 193 0.106819 AGCTGACTCCCAATGGCATC 60.107 55.000 0.00 0.00 0.00 3.91
193 194 1.442526 GCTGACTCCCAATGGCATCG 61.443 60.000 0.00 0.00 0.00 3.84
194 195 0.178767 CTGACTCCCAATGGCATCGA 59.821 55.000 0.00 0.00 0.00 3.59
195 196 0.617935 TGACTCCCAATGGCATCGAA 59.382 50.000 0.00 0.00 0.00 3.71
196 197 1.303309 GACTCCCAATGGCATCGAAG 58.697 55.000 0.00 0.00 0.00 3.79
197 198 0.749454 ACTCCCAATGGCATCGAAGC 60.749 55.000 3.54 3.54 0.00 3.86
205 206 2.202797 GCATCGAAGCCGCTCTGA 60.203 61.111 0.00 0.00 35.37 3.27
209 210 1.395045 ATCGAAGCCGCTCTGATGGA 61.395 55.000 6.53 0.00 35.37 3.41
211 212 1.519719 GAAGCCGCTCTGATGGACT 59.480 57.895 0.00 0.00 0.00 3.85
220 221 0.541998 TCTGATGGACTGGACGGTGT 60.542 55.000 0.00 0.00 0.00 4.16
287 297 3.144285 GGTCCCTGTCACCGTCAA 58.856 61.111 0.00 0.00 0.00 3.18
365 400 2.755650 TGTTGAGAAGCCGAGAGTTTC 58.244 47.619 0.00 0.00 0.00 2.78
370 405 0.034896 GAAGCCGAGAGTTTCCACCA 59.965 55.000 0.00 0.00 0.00 4.17
392 427 3.006537 AGAAAGAAAACGAGGGATCGTCA 59.993 43.478 3.51 0.00 46.41 4.35
434 470 0.530744 GACATGTCACCTACTCCGCA 59.469 55.000 21.07 0.00 0.00 5.69
500 536 0.029834 GCCGCTATTTCGTCCTCGTA 59.970 55.000 0.00 0.00 38.33 3.43
511 547 1.094650 GTCCTCGTACTCTCGTCCCC 61.095 65.000 0.00 0.00 0.00 4.81
516 552 1.511768 GTACTCTCGTCCCCAGCAC 59.488 63.158 0.00 0.00 0.00 4.40
602 659 0.387878 GACATATGCTCTCCGCTCCG 60.388 60.000 1.58 0.00 40.11 4.63
780 847 1.742761 ACCATCAATCGCCTTGTCTG 58.257 50.000 0.00 0.00 36.20 3.51
835 902 2.863153 CGCCAGCATATAAGCGCC 59.137 61.111 2.29 0.00 42.31 6.53
883 950 1.662438 CTCGTCTCCTCACCTGGCTC 61.662 65.000 0.00 0.00 0.00 4.70
884 951 2.716017 CGTCTCCTCACCTGGCTCC 61.716 68.421 0.00 0.00 0.00 4.70
885 952 1.305718 GTCTCCTCACCTGGCTCCT 60.306 63.158 0.00 0.00 0.00 3.69
897 964 1.739562 GGCTCCTCTCACACAAGCG 60.740 63.158 0.00 0.00 33.77 4.68
906 973 1.226632 CACACAAGCGCAACTGCAA 60.227 52.632 11.47 0.00 42.21 4.08
961 1028 3.259064 GTTTCCTTGGTTCGATCGATCA 58.741 45.455 24.40 17.03 0.00 2.92
996 1063 2.107366 GGAGAGAGGGAAGAAGAGGTG 58.893 57.143 0.00 0.00 0.00 4.00
998 1065 1.199615 GAGAGGGAAGAAGAGGTGGG 58.800 60.000 0.00 0.00 0.00 4.61
999 1066 0.494095 AGAGGGAAGAAGAGGTGGGT 59.506 55.000 0.00 0.00 0.00 4.51
1194 1264 2.284405 TCCAGGTTCCGGGGAGTC 60.284 66.667 0.00 0.00 0.00 3.36
1202 1272 2.363795 CCGGGGAGTCAGCAGGTA 60.364 66.667 0.00 0.00 0.00 3.08
1203 1273 1.987855 CCGGGGAGTCAGCAGGTAA 60.988 63.158 0.00 0.00 0.00 2.85
1210 1280 1.801178 GAGTCAGCAGGTAAAGTGTGC 59.199 52.381 0.00 0.00 37.48 4.57
1219 1289 5.643777 AGCAGGTAAAGTGTGCTTACTTATG 59.356 40.000 6.60 5.62 45.31 1.90
1229 1299 7.810658 AGTGTGCTTACTTATGTTCAAAGATG 58.189 34.615 0.00 0.00 0.00 2.90
1235 1305 7.525688 TTACTTATGTTCAAAGATGAGCTCG 57.474 36.000 9.64 0.00 37.64 5.03
1236 1306 4.331168 ACTTATGTTCAAAGATGAGCTCGC 59.669 41.667 9.64 3.59 37.64 5.03
1237 1307 1.442769 TGTTCAAAGATGAGCTCGCC 58.557 50.000 9.64 2.98 37.64 5.54
1238 1308 0.371645 GTTCAAAGATGAGCTCGCCG 59.628 55.000 9.64 0.00 36.78 6.46
1239 1309 0.037326 TTCAAAGATGAGCTCGCCGT 60.037 50.000 9.64 0.00 36.78 5.68
1240 1310 0.737367 TCAAAGATGAGCTCGCCGTG 60.737 55.000 9.64 7.27 0.00 4.94
1242 1312 0.320771 AAAGATGAGCTCGCCGTGTT 60.321 50.000 9.64 0.00 0.00 3.32
1243 1313 0.737715 AAGATGAGCTCGCCGTGTTC 60.738 55.000 9.64 0.00 0.00 3.18
1244 1314 1.446099 GATGAGCTCGCCGTGTTCA 60.446 57.895 9.64 8.09 0.00 3.18
1245 1315 0.807667 GATGAGCTCGCCGTGTTCAT 60.808 55.000 16.45 16.45 0.00 2.57
1246 1316 0.807667 ATGAGCTCGCCGTGTTCATC 60.808 55.000 11.82 0.00 0.00 2.92
1247 1317 1.446099 GAGCTCGCCGTGTTCATCA 60.446 57.895 0.00 0.00 0.00 3.07
1248 1318 1.005037 AGCTCGCCGTGTTCATCAA 60.005 52.632 0.00 0.00 0.00 2.57
1249 1319 0.602638 AGCTCGCCGTGTTCATCAAA 60.603 50.000 0.00 0.00 0.00 2.69
1250 1320 0.237235 GCTCGCCGTGTTCATCAAAA 59.763 50.000 0.00 0.00 0.00 2.44
1260 1330 5.806502 CCGTGTTCATCAAAATTGCATATGT 59.193 36.000 4.29 0.00 0.00 2.29
1261 1331 6.020440 CCGTGTTCATCAAAATTGCATATGTC 60.020 38.462 4.29 0.00 0.00 3.06
1262 1332 6.020440 CGTGTTCATCAAAATTGCATATGTCC 60.020 38.462 4.29 0.00 0.00 4.02
1263 1333 6.256321 GTGTTCATCAAAATTGCATATGTCCC 59.744 38.462 4.29 0.00 0.00 4.46
1264 1334 5.185668 TCATCAAAATTGCATATGTCCCG 57.814 39.130 4.29 0.00 0.00 5.14
1265 1335 4.886489 TCATCAAAATTGCATATGTCCCGA 59.114 37.500 4.29 0.00 0.00 5.14
1267 1337 5.185668 TCAAAATTGCATATGTCCCGATG 57.814 39.130 4.29 0.00 0.00 3.84
1271 1341 0.473755 TGCATATGTCCCGATGCCTT 59.526 50.000 4.29 0.00 46.45 4.35
1272 1342 0.877071 GCATATGTCCCGATGCCTTG 59.123 55.000 4.29 0.00 42.18 3.61
1279 1624 1.303236 CCCGATGCCTTGGTGTGAA 60.303 57.895 0.00 0.00 0.00 3.18
1286 1631 1.244816 GCCTTGGTGTGAAGGTAACC 58.755 55.000 0.00 0.00 44.04 2.85
1287 1632 1.477923 GCCTTGGTGTGAAGGTAACCA 60.478 52.381 0.00 0.00 44.04 3.67
1293 1638 4.798882 TGGTGTGAAGGTAACCAATTCTT 58.201 39.130 0.00 0.00 40.97 2.52
1294 1639 4.825085 TGGTGTGAAGGTAACCAATTCTTC 59.175 41.667 0.00 0.00 40.97 2.87
1295 1640 4.217767 GGTGTGAAGGTAACCAATTCTTCC 59.782 45.833 0.00 0.00 35.91 3.46
1298 1643 5.476599 TGTGAAGGTAACCAATTCTTCCATG 59.523 40.000 0.00 0.00 35.91 3.66
1303 1648 4.956075 GGTAACCAATTCTTCCATGGATGT 59.044 41.667 23.12 6.28 37.66 3.06
1304 1649 5.163519 GGTAACCAATTCTTCCATGGATGTG 60.164 44.000 23.12 15.63 37.66 3.21
1405 1750 1.294138 GGCAAGCAGGGTACGTACA 59.706 57.895 26.02 0.00 0.00 2.90
1406 1751 0.320946 GGCAAGCAGGGTACGTACAA 60.321 55.000 26.02 0.00 0.00 2.41
1416 1761 4.021916 AGGGTACGTACAATACTCTGCTT 58.978 43.478 26.02 0.17 31.90 3.91
1431 1776 2.023223 GCTTTGTTGCCATGCCACG 61.023 57.895 0.00 0.00 0.00 4.94
1446 1818 3.183754 TGCCACGATAGAAATGTACACG 58.816 45.455 0.00 0.00 41.38 4.49
1447 1819 2.034001 GCCACGATAGAAATGTACACGC 60.034 50.000 0.00 0.00 41.38 5.34
1472 1863 4.202245 AGCTGATTAACGCTGGAAAGTA 57.798 40.909 0.00 0.00 34.69 2.24
1476 1867 5.232414 GCTGATTAACGCTGGAAAGTAGTAG 59.768 44.000 0.00 0.00 0.00 2.57
1477 1868 6.276832 TGATTAACGCTGGAAAGTAGTAGT 57.723 37.500 0.00 0.00 0.00 2.73
1478 1869 6.097356 TGATTAACGCTGGAAAGTAGTAGTG 58.903 40.000 0.00 0.00 0.00 2.74
1479 1870 5.710513 TTAACGCTGGAAAGTAGTAGTGA 57.289 39.130 0.00 0.00 0.00 3.41
1480 1871 3.572604 ACGCTGGAAAGTAGTAGTGAC 57.427 47.619 0.00 0.00 0.00 3.67
1481 1872 2.889045 ACGCTGGAAAGTAGTAGTGACA 59.111 45.455 0.00 0.00 0.00 3.58
1482 1873 3.243336 CGCTGGAAAGTAGTAGTGACAC 58.757 50.000 0.00 0.00 0.00 3.67
1483 1874 3.305131 CGCTGGAAAGTAGTAGTGACACA 60.305 47.826 8.59 0.00 0.00 3.72
1484 1875 4.238514 GCTGGAAAGTAGTAGTGACACAG 58.761 47.826 8.59 0.00 0.00 3.66
1485 1876 4.022242 GCTGGAAAGTAGTAGTGACACAGA 60.022 45.833 8.59 0.00 0.00 3.41
1703 2094 4.658063 CACATGTTAACTCCAAACCCCTA 58.342 43.478 7.22 0.00 0.00 3.53
1704 2095 4.700213 CACATGTTAACTCCAAACCCCTAG 59.300 45.833 7.22 0.00 0.00 3.02
1707 2098 3.079578 GTTAACTCCAAACCCCTAGCAC 58.920 50.000 0.00 0.00 0.00 4.40
1711 2102 0.323360 TCCAAACCCCTAGCACATGC 60.323 55.000 0.00 0.00 42.49 4.06
1712 2103 0.611618 CCAAACCCCTAGCACATGCA 60.612 55.000 6.64 0.00 45.16 3.96
1716 2110 0.107017 ACCCCTAGCACATGCATGTC 60.107 55.000 29.23 21.85 45.16 3.06
1719 2113 1.590932 CCTAGCACATGCATGTCTCC 58.409 55.000 29.23 19.16 45.16 3.71
2280 2677 0.167470 CGACCATGTTCAAGCAGCTG 59.833 55.000 10.11 10.11 0.00 4.24
2400 2797 2.489938 TCTTCCATGGGGTTTCTTCG 57.510 50.000 13.02 0.00 34.93 3.79
2594 2998 1.474077 GTGTTGAGGGGCATGATGAAC 59.526 52.381 0.00 0.00 0.00 3.18
2662 3066 4.219288 ACAAGCTGATCAGGGTTTGATTTC 59.781 41.667 23.89 3.37 46.51 2.17
2754 3159 7.069331 ACAACATATCTCTTTCCTCCTCTACAG 59.931 40.741 0.00 0.00 0.00 2.74
2775 3183 1.729517 GAAAAGCTCTTCTCCACTCGC 59.270 52.381 0.00 0.00 0.00 5.03
2999 3418 4.394712 GGAGGGCGTGTGGAGGTG 62.395 72.222 0.00 0.00 0.00 4.00
3133 3552 5.965922 TCTATGACTTTCTTCAGCGATGAA 58.034 37.500 16.26 16.26 0.00 2.57
3203 3622 6.281405 ACTTTCCAACTGTCTACTACAACAG 58.719 40.000 1.17 1.17 46.61 3.16
3238 3658 1.128188 GGTAAGGGAGGGGCGATGAT 61.128 60.000 0.00 0.00 0.00 2.45
3240 3660 0.105194 TAAGGGAGGGGCGATGATGA 60.105 55.000 0.00 0.00 0.00 2.92
3242 3662 2.443394 GGGAGGGGCGATGATGACA 61.443 63.158 0.00 0.00 0.00 3.58
3294 3715 1.898154 GTCGCTAGGTGGTCCACAT 59.102 57.895 23.48 19.21 35.86 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.047280 TTGGCAAGCGCGTAGGTG 61.047 61.111 8.43 1.80 39.92 4.00
3 4 3.047877 GTTGGCAAGCGCGTAGGT 61.048 61.111 8.43 0.00 39.92 3.08
4 5 2.742372 AGTTGGCAAGCGCGTAGG 60.742 61.111 8.43 0.00 39.92 3.18
5 6 2.476051 CAGTTGGCAAGCGCGTAG 59.524 61.111 8.43 0.00 39.92 3.51
6 7 3.722295 GCAGTTGGCAAGCGCGTA 61.722 61.111 8.43 0.00 43.97 4.42
12 13 3.136345 TTGTGGCGCAGTTGGCAAG 62.136 57.895 10.83 0.00 46.76 4.01
13 14 3.143515 TTGTGGCGCAGTTGGCAA 61.144 55.556 10.83 0.00 46.76 4.52
14 15 3.898509 GTTGTGGCGCAGTTGGCA 61.899 61.111 10.83 0.00 45.17 4.92
15 16 4.645921 GGTTGTGGCGCAGTTGGC 62.646 66.667 10.83 0.00 39.90 4.52
16 17 2.563798 ATGGTTGTGGCGCAGTTGG 61.564 57.895 10.83 0.00 0.00 3.77
17 18 1.372004 CATGGTTGTGGCGCAGTTG 60.372 57.895 10.83 0.00 0.00 3.16
18 19 1.391157 AACATGGTTGTGGCGCAGTT 61.391 50.000 10.83 0.00 35.83 3.16
19 20 1.391157 AAACATGGTTGTGGCGCAGT 61.391 50.000 10.83 0.00 35.83 4.40
20 21 0.940519 CAAACATGGTTGTGGCGCAG 60.941 55.000 15.63 0.00 35.83 5.18
21 22 1.067084 CAAACATGGTTGTGGCGCA 59.933 52.632 15.63 0.00 35.83 6.09
22 23 0.529555 AACAAACATGGTTGTGGCGC 60.530 50.000 28.99 0.00 40.86 6.53
23 24 1.207390 CAACAAACATGGTTGTGGCG 58.793 50.000 28.99 16.67 40.86 5.69
29 30 5.294060 GCTTGATCAAACAACAAACATGGTT 59.706 36.000 9.88 0.00 0.00 3.67
30 31 4.810491 GCTTGATCAAACAACAAACATGGT 59.190 37.500 9.88 0.00 0.00 3.55
31 32 4.809958 TGCTTGATCAAACAACAAACATGG 59.190 37.500 9.07 0.00 0.00 3.66
32 33 5.970140 TGCTTGATCAAACAACAAACATG 57.030 34.783 9.07 0.00 0.00 3.21
33 34 7.436118 AGTATGCTTGATCAAACAACAAACAT 58.564 30.769 15.08 8.29 35.50 2.71
34 35 6.804677 AGTATGCTTGATCAAACAACAAACA 58.195 32.000 15.08 2.03 0.00 2.83
35 36 8.690840 GTTAGTATGCTTGATCAAACAACAAAC 58.309 33.333 15.08 12.54 0.00 2.93
36 37 7.865385 GGTTAGTATGCTTGATCAAACAACAAA 59.135 33.333 15.08 5.65 0.00 2.83
37 38 7.013750 TGGTTAGTATGCTTGATCAAACAACAA 59.986 33.333 15.08 0.22 0.00 2.83
38 39 6.488344 TGGTTAGTATGCTTGATCAAACAACA 59.512 34.615 15.08 8.73 0.00 3.33
39 40 6.908825 TGGTTAGTATGCTTGATCAAACAAC 58.091 36.000 15.08 13.46 0.00 3.32
40 41 7.517614 TTGGTTAGTATGCTTGATCAAACAA 57.482 32.000 15.08 0.30 0.00 2.83
41 42 7.517614 TTTGGTTAGTATGCTTGATCAAACA 57.482 32.000 13.61 13.61 0.00 2.83
42 43 8.810652 TTTTTGGTTAGTATGCTTGATCAAAC 57.189 30.769 9.88 5.69 0.00 2.93
43 44 8.637986 ACTTTTTGGTTAGTATGCTTGATCAAA 58.362 29.630 9.88 0.00 0.00 2.69
44 45 8.177119 ACTTTTTGGTTAGTATGCTTGATCAA 57.823 30.769 8.12 8.12 0.00 2.57
45 46 7.665559 AGACTTTTTGGTTAGTATGCTTGATCA 59.334 33.333 0.00 0.00 0.00 2.92
46 47 8.045176 AGACTTTTTGGTTAGTATGCTTGATC 57.955 34.615 0.00 0.00 0.00 2.92
47 48 8.409358 AAGACTTTTTGGTTAGTATGCTTGAT 57.591 30.769 0.00 0.00 0.00 2.57
48 49 7.817418 AAGACTTTTTGGTTAGTATGCTTGA 57.183 32.000 0.00 0.00 0.00 3.02
51 52 8.665685 CGAATAAGACTTTTTGGTTAGTATGCT 58.334 33.333 0.00 0.00 0.00 3.79
52 53 8.662141 TCGAATAAGACTTTTTGGTTAGTATGC 58.338 33.333 0.00 0.00 0.00 3.14
56 57 8.936864 CATCTCGAATAAGACTTTTTGGTTAGT 58.063 33.333 0.00 0.00 0.00 2.24
57 58 8.936864 ACATCTCGAATAAGACTTTTTGGTTAG 58.063 33.333 0.00 0.00 0.00 2.34
58 59 8.842358 ACATCTCGAATAAGACTTTTTGGTTA 57.158 30.769 0.00 0.00 0.00 2.85
59 60 7.094762 GGACATCTCGAATAAGACTTTTTGGTT 60.095 37.037 0.00 0.00 0.00 3.67
60 61 6.371825 GGACATCTCGAATAAGACTTTTTGGT 59.628 38.462 0.00 0.00 0.00 3.67
61 62 6.595716 AGGACATCTCGAATAAGACTTTTTGG 59.404 38.462 0.00 0.00 0.00 3.28
62 63 7.602517 AGGACATCTCGAATAAGACTTTTTG 57.397 36.000 0.00 0.00 0.00 2.44
63 64 8.532819 AGTAGGACATCTCGAATAAGACTTTTT 58.467 33.333 0.00 0.00 0.00 1.94
64 65 8.068892 AGTAGGACATCTCGAATAAGACTTTT 57.931 34.615 0.00 0.00 0.00 2.27
65 66 7.201839 GGAGTAGGACATCTCGAATAAGACTTT 60.202 40.741 0.00 0.00 0.00 2.66
66 67 6.263617 GGAGTAGGACATCTCGAATAAGACTT 59.736 42.308 0.00 0.00 0.00 3.01
67 68 5.766174 GGAGTAGGACATCTCGAATAAGACT 59.234 44.000 0.00 0.00 0.00 3.24
68 69 5.766174 AGGAGTAGGACATCTCGAATAAGAC 59.234 44.000 0.00 0.00 0.00 3.01
69 70 5.765677 CAGGAGTAGGACATCTCGAATAAGA 59.234 44.000 0.00 0.00 0.00 2.10
70 71 5.563867 GCAGGAGTAGGACATCTCGAATAAG 60.564 48.000 0.00 0.00 0.00 1.73
71 72 4.278669 GCAGGAGTAGGACATCTCGAATAA 59.721 45.833 0.00 0.00 0.00 1.40
72 73 3.821600 GCAGGAGTAGGACATCTCGAATA 59.178 47.826 0.00 0.00 0.00 1.75
73 74 2.625790 GCAGGAGTAGGACATCTCGAAT 59.374 50.000 0.00 0.00 0.00 3.34
74 75 2.025155 GCAGGAGTAGGACATCTCGAA 58.975 52.381 0.00 0.00 0.00 3.71
75 76 1.681538 GCAGGAGTAGGACATCTCGA 58.318 55.000 0.00 0.00 0.00 4.04
76 77 0.671251 GGCAGGAGTAGGACATCTCG 59.329 60.000 0.00 0.00 0.00 4.04
77 78 1.781786 TGGCAGGAGTAGGACATCTC 58.218 55.000 0.00 0.00 0.00 2.75
78 79 2.254152 TTGGCAGGAGTAGGACATCT 57.746 50.000 0.00 0.00 0.00 2.90
79 80 3.010420 GTTTTGGCAGGAGTAGGACATC 58.990 50.000 0.00 0.00 0.00 3.06
80 81 2.375174 TGTTTTGGCAGGAGTAGGACAT 59.625 45.455 0.00 0.00 0.00 3.06
81 82 1.771854 TGTTTTGGCAGGAGTAGGACA 59.228 47.619 0.00 0.00 0.00 4.02
82 83 2.561478 TGTTTTGGCAGGAGTAGGAC 57.439 50.000 0.00 0.00 0.00 3.85
83 84 2.642311 TGATGTTTTGGCAGGAGTAGGA 59.358 45.455 0.00 0.00 0.00 2.94
84 85 3.071874 TGATGTTTTGGCAGGAGTAGG 57.928 47.619 0.00 0.00 0.00 3.18
85 86 3.310774 CGATGATGTTTTGGCAGGAGTAG 59.689 47.826 0.00 0.00 0.00 2.57
86 87 3.270027 CGATGATGTTTTGGCAGGAGTA 58.730 45.455 0.00 0.00 0.00 2.59
87 88 2.086869 CGATGATGTTTTGGCAGGAGT 58.913 47.619 0.00 0.00 0.00 3.85
88 89 1.202222 GCGATGATGTTTTGGCAGGAG 60.202 52.381 0.00 0.00 0.00 3.69
89 90 0.810648 GCGATGATGTTTTGGCAGGA 59.189 50.000 0.00 0.00 0.00 3.86
90 91 0.527113 TGCGATGATGTTTTGGCAGG 59.473 50.000 0.00 0.00 0.00 4.85
91 92 2.350899 TTGCGATGATGTTTTGGCAG 57.649 45.000 0.00 0.00 0.00 4.85
92 93 2.402305 GTTTGCGATGATGTTTTGGCA 58.598 42.857 0.00 0.00 0.00 4.92
93 94 1.726248 GGTTTGCGATGATGTTTTGGC 59.274 47.619 0.00 0.00 0.00 4.52
94 95 3.023946 TGGTTTGCGATGATGTTTTGG 57.976 42.857 0.00 0.00 0.00 3.28
95 96 3.989167 ACATGGTTTGCGATGATGTTTTG 59.011 39.130 0.00 0.00 35.26 2.44
96 97 3.989167 CACATGGTTTGCGATGATGTTTT 59.011 39.130 0.00 0.00 35.26 2.43
97 98 3.005684 ACACATGGTTTGCGATGATGTTT 59.994 39.130 0.00 0.00 35.26 2.83
98 99 2.557924 ACACATGGTTTGCGATGATGTT 59.442 40.909 0.00 0.00 35.26 2.71
99 100 2.161855 ACACATGGTTTGCGATGATGT 58.838 42.857 0.00 0.00 35.26 3.06
100 101 2.925578 ACACATGGTTTGCGATGATG 57.074 45.000 0.00 0.00 35.26 3.07
117 118 3.997762 ACTGTACGCATTAGTGGAAACA 58.002 40.909 0.00 0.00 38.70 2.83
118 119 5.166398 ACTACTGTACGCATTAGTGGAAAC 58.834 41.667 1.42 0.00 38.91 2.78
119 120 5.395682 ACTACTGTACGCATTAGTGGAAA 57.604 39.130 1.42 0.00 38.91 3.13
120 121 5.883661 GTACTACTGTACGCATTAGTGGAA 58.116 41.667 7.56 0.00 40.06 3.53
121 122 5.490139 GTACTACTGTACGCATTAGTGGA 57.510 43.478 7.56 0.00 40.06 4.02
132 133 7.412020 GCAGCAAAATCTTCAGTACTACTGTAC 60.412 40.741 14.63 1.99 46.03 2.90
133 134 6.590292 GCAGCAAAATCTTCAGTACTACTGTA 59.410 38.462 14.63 5.85 46.03 2.74
134 135 5.409826 GCAGCAAAATCTTCAGTACTACTGT 59.590 40.000 14.63 0.00 46.03 3.55
136 137 5.551233 TGCAGCAAAATCTTCAGTACTACT 58.449 37.500 0.00 0.00 0.00 2.57
137 138 5.409826 ACTGCAGCAAAATCTTCAGTACTAC 59.590 40.000 15.27 0.00 38.46 2.73
138 139 5.551233 ACTGCAGCAAAATCTTCAGTACTA 58.449 37.500 15.27 0.00 38.46 1.82
139 140 4.392940 ACTGCAGCAAAATCTTCAGTACT 58.607 39.130 15.27 0.00 38.46 2.73
140 141 4.756084 ACTGCAGCAAAATCTTCAGTAC 57.244 40.909 15.27 0.00 38.46 2.73
141 142 4.821260 TGAACTGCAGCAAAATCTTCAGTA 59.179 37.500 15.27 0.00 39.11 2.74
142 143 3.633525 TGAACTGCAGCAAAATCTTCAGT 59.366 39.130 15.27 0.00 41.17 3.41
143 144 4.233123 TGAACTGCAGCAAAATCTTCAG 57.767 40.909 15.27 0.00 34.29 3.02
144 145 4.859304 ATGAACTGCAGCAAAATCTTCA 57.141 36.364 15.27 14.43 0.00 3.02
145 146 4.143179 GCAATGAACTGCAGCAAAATCTTC 60.143 41.667 15.27 8.80 42.17 2.87
146 147 3.744426 GCAATGAACTGCAGCAAAATCTT 59.256 39.130 15.27 0.00 42.17 2.40
147 148 3.323243 GCAATGAACTGCAGCAAAATCT 58.677 40.909 15.27 0.00 42.17 2.40
148 149 2.091588 CGCAATGAACTGCAGCAAAATC 59.908 45.455 15.27 5.41 42.77 2.17
149 150 2.063266 CGCAATGAACTGCAGCAAAAT 58.937 42.857 15.27 0.00 42.77 1.82
150 151 1.489574 CGCAATGAACTGCAGCAAAA 58.510 45.000 15.27 0.00 42.77 2.44
151 152 0.318869 CCGCAATGAACTGCAGCAAA 60.319 50.000 15.27 0.00 42.77 3.68
152 153 1.286570 CCGCAATGAACTGCAGCAA 59.713 52.632 15.27 0.00 42.77 3.91
153 154 1.855213 GACCGCAATGAACTGCAGCA 61.855 55.000 15.27 4.85 42.77 4.41
154 155 1.154150 GACCGCAATGAACTGCAGC 60.154 57.895 15.27 0.00 42.77 5.25
155 156 0.167470 CTGACCGCAATGAACTGCAG 59.833 55.000 13.48 13.48 42.77 4.41
156 157 1.855213 GCTGACCGCAATGAACTGCA 61.855 55.000 0.00 0.00 42.77 4.41
157 158 1.154150 GCTGACCGCAATGAACTGC 60.154 57.895 0.00 0.00 38.92 4.40
158 159 0.167470 CAGCTGACCGCAATGAACTG 59.833 55.000 8.42 0.00 42.61 3.16
159 160 0.035317 TCAGCTGACCGCAATGAACT 59.965 50.000 13.74 0.00 42.61 3.01
160 161 0.166814 GTCAGCTGACCGCAATGAAC 59.833 55.000 32.55 7.33 42.61 3.18
161 162 0.035317 AGTCAGCTGACCGCAATGAA 59.965 50.000 37.09 1.45 45.85 2.57
162 163 0.390340 GAGTCAGCTGACCGCAATGA 60.390 55.000 37.09 2.58 45.85 2.57
163 164 1.364626 GGAGTCAGCTGACCGCAATG 61.365 60.000 37.09 0.00 45.85 2.82
164 165 1.078848 GGAGTCAGCTGACCGCAAT 60.079 57.895 37.09 22.30 45.85 3.56
165 166 2.343758 GGAGTCAGCTGACCGCAA 59.656 61.111 37.09 4.69 45.85 4.85
166 167 3.695606 GGGAGTCAGCTGACCGCA 61.696 66.667 37.09 5.51 45.85 5.69
167 168 2.527951 ATTGGGAGTCAGCTGACCGC 62.528 60.000 37.09 32.40 45.85 5.68
168 169 0.742281 CATTGGGAGTCAGCTGACCG 60.742 60.000 37.09 16.76 45.85 4.79
169 170 0.393537 CCATTGGGAGTCAGCTGACC 60.394 60.000 37.09 28.19 45.85 4.02
170 171 1.028868 GCCATTGGGAGTCAGCTGAC 61.029 60.000 34.82 34.82 38.91 3.51
171 172 1.300963 GCCATTGGGAGTCAGCTGA 59.699 57.895 13.74 13.74 35.59 4.26
172 173 0.395311 ATGCCATTGGGAGTCAGCTG 60.395 55.000 7.63 7.63 35.59 4.24
173 174 0.106819 GATGCCATTGGGAGTCAGCT 60.107 55.000 4.53 0.00 35.59 4.24
174 175 1.442526 CGATGCCATTGGGAGTCAGC 61.443 60.000 4.53 0.00 35.59 4.26
175 176 0.178767 TCGATGCCATTGGGAGTCAG 59.821 55.000 4.53 0.00 35.59 3.51
176 177 0.617935 TTCGATGCCATTGGGAGTCA 59.382 50.000 4.53 0.00 35.59 3.41
177 178 1.303309 CTTCGATGCCATTGGGAGTC 58.697 55.000 4.53 1.22 35.59 3.36
178 179 0.749454 GCTTCGATGCCATTGGGAGT 60.749 55.000 12.05 0.00 35.59 3.85
179 180 2.028130 GCTTCGATGCCATTGGGAG 58.972 57.895 12.05 0.00 35.59 4.30
180 181 4.240881 GCTTCGATGCCATTGGGA 57.759 55.556 12.05 1.02 35.59 4.37
188 189 1.593750 ATCAGAGCGGCTTCGATGC 60.594 57.895 14.55 14.55 35.61 3.91
189 190 1.220169 CCATCAGAGCGGCTTCGATG 61.220 60.000 24.51 24.51 35.61 3.84
190 191 1.068753 CCATCAGAGCGGCTTCGAT 59.931 57.895 2.97 6.61 35.61 3.59
191 192 2.052104 TCCATCAGAGCGGCTTCGA 61.052 57.895 2.97 4.20 35.61 3.71
192 193 1.880340 GTCCATCAGAGCGGCTTCG 60.880 63.158 2.97 0.00 0.00 3.79
193 194 0.809241 CAGTCCATCAGAGCGGCTTC 60.809 60.000 2.97 0.00 0.00 3.86
194 195 1.220206 CAGTCCATCAGAGCGGCTT 59.780 57.895 2.97 0.00 0.00 4.35
195 196 2.729479 CCAGTCCATCAGAGCGGCT 61.729 63.158 0.00 0.00 0.00 5.52
196 197 2.202987 CCAGTCCATCAGAGCGGC 60.203 66.667 0.00 0.00 0.00 6.53
197 198 1.142748 GTCCAGTCCATCAGAGCGG 59.857 63.158 0.00 0.00 0.00 5.52
198 199 1.226802 CGTCCAGTCCATCAGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
199 200 1.142748 CCGTCCAGTCCATCAGAGC 59.857 63.158 0.00 0.00 0.00 4.09
200 201 0.174389 CACCGTCCAGTCCATCAGAG 59.826 60.000 0.00 0.00 0.00 3.35
201 202 0.541998 ACACCGTCCAGTCCATCAGA 60.542 55.000 0.00 0.00 0.00 3.27
205 206 1.371183 CACACACCGTCCAGTCCAT 59.629 57.895 0.00 0.00 0.00 3.41
209 210 3.475494 TGCCACACACCGTCCAGT 61.475 61.111 0.00 0.00 0.00 4.00
220 221 4.934942 CGTCCGTGTCGTGCCACA 62.935 66.667 0.00 0.00 34.98 4.17
365 400 1.880027 CCCTCGTTTTCTTTCTGGTGG 59.120 52.381 0.00 0.00 0.00 4.61
434 470 0.320247 CCTTGTCTCGTGCTCTGCTT 60.320 55.000 0.00 0.00 0.00 3.91
511 547 3.726517 CCGGACCAAAGCGTGCTG 61.727 66.667 0.00 0.00 0.00 4.41
563 620 2.494918 CGTGGCGAACTAGGGAGG 59.505 66.667 0.00 0.00 0.00 4.30
602 659 9.403110 CCTTGTTATATTATACAGTACGTGACC 57.597 37.037 0.00 0.00 0.00 4.02
727 794 2.460918 CGTCTGTCTTTACTATGCGGG 58.539 52.381 0.00 0.00 0.00 6.13
780 847 1.445518 GCAGCTAGGGAGGAGAAGC 59.554 63.158 0.00 0.00 35.16 3.86
883 950 0.882042 AGTTGCGCTTGTGTGAGAGG 60.882 55.000 9.73 0.00 0.00 3.69
884 951 0.234106 CAGTTGCGCTTGTGTGAGAG 59.766 55.000 9.73 0.00 0.00 3.20
885 952 1.775039 GCAGTTGCGCTTGTGTGAGA 61.775 55.000 9.73 0.00 0.00 3.27
906 973 2.742372 GAGGACGTGCGGCAATGT 60.742 61.111 3.23 6.53 0.00 2.71
914 981 4.849329 CGTAGGCCGAGGACGTGC 62.849 72.222 0.00 0.00 39.56 5.34
961 1028 4.323333 CCTCTCTCCAACAGATGTGAATGT 60.323 45.833 0.00 0.00 0.00 2.71
1188 1258 1.348036 ACACTTTACCTGCTGACTCCC 59.652 52.381 0.00 0.00 0.00 4.30
1194 1264 3.403038 AGTAAGCACACTTTACCTGCTG 58.597 45.455 0.00 0.00 40.43 4.41
1202 1272 8.220755 TCTTTGAACATAAGTAAGCACACTTT 57.779 30.769 8.09 0.00 39.45 2.66
1203 1273 7.801716 TCTTTGAACATAAGTAAGCACACTT 57.198 32.000 7.92 7.92 41.56 3.16
1210 1280 7.616673 CGAGCTCATCTTTGAACATAAGTAAG 58.383 38.462 15.40 0.00 0.00 2.34
1211 1281 6.036083 GCGAGCTCATCTTTGAACATAAGTAA 59.964 38.462 15.40 0.00 0.00 2.24
1219 1289 0.371645 CGGCGAGCTCATCTTTGAAC 59.628 55.000 15.40 0.00 0.00 3.18
1229 1299 1.014044 TTGATGAACACGGCGAGCTC 61.014 55.000 16.62 7.47 0.00 4.09
1235 1305 2.402305 TGCAATTTTGATGAACACGGC 58.598 42.857 0.00 0.00 0.00 5.68
1236 1306 5.806502 ACATATGCAATTTTGATGAACACGG 59.193 36.000 1.58 0.00 0.00 4.94
1237 1307 6.020440 GGACATATGCAATTTTGATGAACACG 60.020 38.462 1.58 0.00 0.00 4.49
1238 1308 6.256321 GGGACATATGCAATTTTGATGAACAC 59.744 38.462 1.58 0.00 0.00 3.32
1239 1309 6.339730 GGGACATATGCAATTTTGATGAACA 58.660 36.000 1.58 0.00 0.00 3.18
1240 1310 5.459762 CGGGACATATGCAATTTTGATGAAC 59.540 40.000 1.58 0.00 0.00 3.18
1242 1312 4.886489 TCGGGACATATGCAATTTTGATGA 59.114 37.500 1.58 0.00 0.00 2.92
1243 1313 5.185668 TCGGGACATATGCAATTTTGATG 57.814 39.130 1.58 0.00 0.00 3.07
1244 1314 5.775686 CATCGGGACATATGCAATTTTGAT 58.224 37.500 1.58 0.00 0.00 2.57
1245 1315 4.499526 GCATCGGGACATATGCAATTTTGA 60.500 41.667 1.58 0.00 43.93 2.69
1246 1316 3.737266 GCATCGGGACATATGCAATTTTG 59.263 43.478 1.58 0.00 43.93 2.44
1247 1317 3.243839 GGCATCGGGACATATGCAATTTT 60.244 43.478 1.58 0.00 45.57 1.82
1248 1318 2.297033 GGCATCGGGACATATGCAATTT 59.703 45.455 1.58 0.00 45.57 1.82
1249 1319 1.888512 GGCATCGGGACATATGCAATT 59.111 47.619 1.58 0.00 45.57 2.32
1250 1320 1.074405 AGGCATCGGGACATATGCAAT 59.926 47.619 1.58 0.00 45.57 3.56
1260 1330 1.773856 TTCACACCAAGGCATCGGGA 61.774 55.000 0.00 0.00 0.00 5.14
1261 1331 1.303236 TTCACACCAAGGCATCGGG 60.303 57.895 0.00 0.00 0.00 5.14
1262 1332 1.308069 CCTTCACACCAAGGCATCGG 61.308 60.000 0.00 0.00 36.72 4.18
1263 1333 0.606401 ACCTTCACACCAAGGCATCG 60.606 55.000 0.00 0.00 46.34 3.84
1264 1334 2.488153 GTTACCTTCACACCAAGGCATC 59.512 50.000 0.00 0.00 46.34 3.91
1265 1335 2.514803 GTTACCTTCACACCAAGGCAT 58.485 47.619 0.00 0.00 46.34 4.40
1267 1337 1.244816 GGTTACCTTCACACCAAGGC 58.755 55.000 0.00 0.00 46.34 4.35
1271 1341 4.447138 AGAATTGGTTACCTTCACACCA 57.553 40.909 2.07 0.00 38.89 4.17
1272 1342 4.217767 GGAAGAATTGGTTACCTTCACACC 59.782 45.833 2.07 1.31 37.38 4.16
1279 1624 4.946160 TCCATGGAAGAATTGGTTACCT 57.054 40.909 13.46 0.00 0.00 3.08
1286 1631 4.018490 TCCACACATCCATGGAAGAATTG 58.982 43.478 23.35 16.42 42.14 2.32
1287 1632 4.320546 TCCACACATCCATGGAAGAATT 57.679 40.909 23.35 0.88 42.14 2.17
1294 1639 1.029681 CTGCATCCACACATCCATGG 58.970 55.000 4.97 4.97 37.32 3.66
1295 1640 1.029681 CCTGCATCCACACATCCATG 58.970 55.000 0.00 0.00 0.00 3.66
1298 1643 0.754217 ATGCCTGCATCCACACATCC 60.754 55.000 0.00 0.00 29.42 3.51
1431 1776 4.747108 AGCTGATGCGTGTACATTTCTATC 59.253 41.667 0.00 0.69 45.42 2.08
1478 1869 9.977529 CTGTTGCAGATCAAACACTTCTGTGTC 62.978 44.444 2.18 0.00 44.22 3.67
1479 1870 8.326453 CTGTTGCAGATCAAACACTTCTGTGT 62.326 42.308 0.00 0.00 45.64 3.72
1480 1871 6.010807 CTGTTGCAGATCAAACACTTCTGTG 61.011 44.000 0.00 0.00 40.83 3.66
1481 1872 3.947196 TGTTGCAGATCAAACACTTCTGT 59.053 39.130 0.00 0.00 39.24 3.41
1482 1873 4.036027 ACTGTTGCAGATCAAACACTTCTG 59.964 41.667 2.91 0.00 39.87 3.02
1483 1874 4.036027 CACTGTTGCAGATCAAACACTTCT 59.964 41.667 2.91 0.00 36.26 2.85
1484 1875 4.201950 ACACTGTTGCAGATCAAACACTTC 60.202 41.667 2.91 0.00 36.26 3.01
1485 1876 3.696051 ACACTGTTGCAGATCAAACACTT 59.304 39.130 2.91 0.00 36.26 3.16
1490 1881 5.181811 CCAAGATACACTGTTGCAGATCAAA 59.818 40.000 2.91 0.00 36.26 2.69
1703 2094 2.022195 GATTGGAGACATGCATGTGCT 58.978 47.619 35.92 28.45 41.95 4.40
1704 2095 2.022195 AGATTGGAGACATGCATGTGC 58.978 47.619 35.92 25.16 41.95 4.57
1707 2098 3.139850 GAGGAGATTGGAGACATGCATG 58.860 50.000 25.09 25.09 42.32 4.06
1711 2102 4.098654 ACGTAAGAGGAGATTGGAGACATG 59.901 45.833 0.00 0.00 40.63 3.21
1712 2103 4.098654 CACGTAAGAGGAGATTGGAGACAT 59.901 45.833 0.00 0.00 40.63 3.06
1716 2110 2.166459 TGCACGTAAGAGGAGATTGGAG 59.834 50.000 0.00 0.00 43.62 3.86
1719 2113 2.093973 AGGTGCACGTAAGAGGAGATTG 60.094 50.000 10.95 0.00 43.62 2.67
2122 2516 2.060383 TCGTGGGAGGGAGCATGAG 61.060 63.158 0.00 0.00 0.00 2.90
2253 2650 3.653344 CTTGAACATGGTCGACTTGAGA 58.347 45.455 16.46 1.40 0.00 3.27
2280 2677 2.979649 GGGTCGTTCCTCTCCACC 59.020 66.667 0.30 0.00 36.25 4.61
2400 2797 4.681978 AAGAGGCCGCACACGTCC 62.682 66.667 9.88 0.00 37.67 4.79
2493 2890 2.710902 CGTCGGTGCCATCCTCTCA 61.711 63.158 0.00 0.00 0.00 3.27
2630 3034 6.426587 ACCCTGATCAGCTTGTTATTTACAT 58.573 36.000 17.76 0.00 36.44 2.29
2662 3066 3.705043 GCCTATGAAGATTGGCTTGTG 57.295 47.619 0.00 0.00 44.51 3.33
2720 3125 4.927267 AAGAGATATGTTGTGGGACCAA 57.073 40.909 0.00 0.00 0.00 3.67
2754 3159 2.342179 CGAGTGGAGAAGAGCTTTTCC 58.658 52.381 13.08 11.69 42.38 3.13
2850 3259 4.030216 AGAAGAGAACAGAATCCCTCCTC 58.970 47.826 0.00 0.00 0.00 3.71
2859 3268 6.884832 TGAACCTAACAAGAAGAGAACAGAA 58.115 36.000 0.00 0.00 0.00 3.02
2860 3270 6.479972 TGAACCTAACAAGAAGAGAACAGA 57.520 37.500 0.00 0.00 0.00 3.41
2999 3418 0.248296 GCGAGATCCGACAGAGACAC 60.248 60.000 7.64 0.00 41.76 3.67
3133 3552 1.293498 CGCACCAGAGTAGCAACCT 59.707 57.895 0.00 0.00 0.00 3.50
3249 3669 1.741770 GCACTGGAACGAGCCGAAT 60.742 57.895 1.50 0.00 0.00 3.34
3259 3679 2.333926 CGACGATTACAAGCACTGGAA 58.666 47.619 0.00 0.00 30.29 3.53
3465 3890 2.976882 TGGTTCAAGGGTAGCTGTAACT 59.023 45.455 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.