Multiple sequence alignment - TraesCS3A01G018600

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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 TraesCS3A01G018600 chr3A 100.000 2915 0 0 1 2915 11527190 11530104 0.000000e+00 5384.0
1 TraesCS3A01G018600 chr3A 72.748 2242 448 102 412 2586 10961230 10963375 3.810000e-169 604.0
2 TraesCS3A01G018600 chr3A 100.000 179 0 0 3269 3447 11530458 11530636 7.130000e-87 331.0
3 TraesCS3A01G018600 chr3A 74.048 578 125 20 955 1525 11536420 11536979 2.690000e-51 213.0
4 TraesCS3A01G018600 chr3A 88.372 86 9 1 3336 3421 10875680 10875764 6.090000e-18 102.0
5 TraesCS3A01G018600 chr3A 93.333 60 4 0 3362 3421 10989429 10989488 4.740000e-14 89.8
6 TraesCS3A01G018600 chrUn 93.485 2686 155 12 227 2909 290168403 290171071 0.000000e+00 3973.0
7 TraesCS3A01G018600 chrUn 73.005 1278 275 49 412 1658 35303424 35302186 5.400000e-103 385.0
8 TraesCS3A01G018600 chrUn 73.005 1278 275 49 412 1658 229353264 229352026 5.400000e-103 385.0
9 TraesCS3A01G018600 chrUn 92.614 176 11 1 3269 3444 272236785 272236958 5.710000e-63 252.0
10 TraesCS3A01G018600 chrUn 82.456 114 17 3 3336 3447 35300834 35300722 2.830000e-16 97.1
11 TraesCS3A01G018600 chrUn 82.456 114 17 3 3336 3447 229350674 229350562 2.830000e-16 97.1
12 TraesCS3A01G018600 chrUn 77.500 160 28 6 1409 1564 43589288 43589133 4.740000e-14 89.8
13 TraesCS3A01G018600 chrUn 77.500 160 28 6 1409 1564 327179158 327179003 4.740000e-14 89.8
14 TraesCS3A01G018600 chrUn 77.500 160 28 6 1409 1564 366321140 366321295 4.740000e-14 89.8
15 TraesCS3A01G018600 chr3D 85.320 2282 266 41 654 2915 4843929 4846161 0.000000e+00 2294.0
16 TraesCS3A01G018600 chr3D 72.470 1522 340 60 466 1941 4649190 4650678 1.910000e-112 416.0
17 TraesCS3A01G018600 chr3D 72.479 1170 253 46 405 1553 5041814 5042935 2.580000e-81 313.0
18 TraesCS3A01G018600 chr3D 74.828 580 120 17 955 1525 5052497 5053059 4.450000e-59 239.0
19 TraesCS3A01G018600 chr3D 94.340 106 5 1 3339 3444 4846393 4846497 9.900000e-36 161.0
20 TraesCS3A01G018600 chr1B 95.000 220 4 1 1 220 280697595 280697807 4.260000e-89 339.0
21 TraesCS3A01G018600 chr2B 72.209 1263 282 49 405 1633 57791184 57789957 1.190000e-84 324.0
22 TraesCS3A01G018600 chr2B 73.094 918 196 33 402 1289 58086942 58086046 2.620000e-71 279.0
23 TraesCS3A01G018600 chr2B 74.847 652 134 21 385 1021 58298470 58297834 5.670000e-68 268.0
24 TraesCS3A01G018600 chr2D 72.200 1223 264 55 400 1582 35035155 35033969 4.320000e-79 305.0
25 TraesCS3A01G018600 chr2D 71.984 1235 279 41 385 1582 35231189 35229985 5.590000e-78 302.0
26 TraesCS3A01G018600 chr2A 74.099 749 158 24 407 1133 38348450 38347716 3.390000e-70 276.0
27 TraesCS3A01G018600 chr2A 74.099 749 158 24 407 1133 38590242 38590976 3.390000e-70 276.0
28 TraesCS3A01G018600 chr2A 71.801 1188 264 52 442 1582 38341645 38340482 4.380000e-69 272.0
29 TraesCS3A01G018600 chr4D 73.560 764 162 26 915 1653 67334162 67333414 4.410000e-64 255.0
30 TraesCS3A01G018600 chr4B 74.265 680 138 23 915 1572 99436239 99436903 5.710000e-63 252.0


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 TraesCS3A01G018600 chr3A 11527190 11530636 3446 False 2857.50 5384 100.0000 1 3447 2 chr3A.!!$F5 3446
1 TraesCS3A01G018600 chr3A 10961230 10963375 2145 False 604.00 604 72.7480 412 2586 1 chr3A.!!$F2 2174
2 TraesCS3A01G018600 chr3A 11536420 11536979 559 False 213.00 213 74.0480 955 1525 1 chr3A.!!$F4 570
3 TraesCS3A01G018600 chrUn 290168403 290171071 2668 False 3973.00 3973 93.4850 227 2909 1 chrUn.!!$F2 2682
4 TraesCS3A01G018600 chrUn 35300722 35303424 2702 True 241.05 385 77.7305 412 3447 2 chrUn.!!$R3 3035
5 TraesCS3A01G018600 chrUn 229350562 229353264 2702 True 241.05 385 77.7305 412 3447 2 chrUn.!!$R4 3035
6 TraesCS3A01G018600 chr3D 4843929 4846497 2568 False 1227.50 2294 89.8300 654 3444 2 chr3D.!!$F4 2790
7 TraesCS3A01G018600 chr3D 4649190 4650678 1488 False 416.00 416 72.4700 466 1941 1 chr3D.!!$F1 1475
8 TraesCS3A01G018600 chr3D 5041814 5042935 1121 False 313.00 313 72.4790 405 1553 1 chr3D.!!$F2 1148
9 TraesCS3A01G018600 chr3D 5052497 5053059 562 False 239.00 239 74.8280 955 1525 1 chr3D.!!$F3 570
10 TraesCS3A01G018600 chr2B 57789957 57791184 1227 True 324.00 324 72.2090 405 1633 1 chr2B.!!$R1 1228
11 TraesCS3A01G018600 chr2B 58086046 58086942 896 True 279.00 279 73.0940 402 1289 1 chr2B.!!$R2 887
12 TraesCS3A01G018600 chr2B 58297834 58298470 636 True 268.00 268 74.8470 385 1021 1 chr2B.!!$R3 636
13 TraesCS3A01G018600 chr2D 35033969 35035155 1186 True 305.00 305 72.2000 400 1582 1 chr2D.!!$R1 1182
14 TraesCS3A01G018600 chr2D 35229985 35231189 1204 True 302.00 302 71.9840 385 1582 1 chr2D.!!$R2 1197
15 TraesCS3A01G018600 chr2A 38347716 38348450 734 True 276.00 276 74.0990 407 1133 1 chr2A.!!$R2 726
16 TraesCS3A01G018600 chr2A 38590242 38590976 734 False 276.00 276 74.0990 407 1133 1 chr2A.!!$F1 726
17 TraesCS3A01G018600 chr2A 38340482 38341645 1163 True 272.00 272 71.8010 442 1582 1 chr2A.!!$R1 1140
18 TraesCS3A01G018600 chr4D 67333414 67334162 748 True 255.00 255 73.5600 915 1653 1 chr4D.!!$R1 738
19 TraesCS3A01G018600 chr4B 99436239 99436903 664 False 252.00 252 74.2650 915 1572 1 chr4B.!!$F1 657

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
126 127 0.037975 TAACTTTCTGACCGGACGGC 60.038 55.000 9.46 4.51 39.32 5.68 F
360 361 0.667184 CAACGCCCAACCAAATCTGC 60.667 55.000 0.00 0.00 0.00 4.26 F
1003 1060 1.377725 GGCATCTGGGGCGATATGG 60.378 63.158 0.00 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1195 1278 0.842030 ACACCATCCTCTGCCTGGAA 60.842 55.0 0.00 0.0 37.13 3.53 R
1943 2110 2.592102 AACAATCACATGCAGGAGGT 57.408 45.0 4.84 0.0 0.00 3.85 R
2562 2773 0.683828 CATGCTACCCACATTGGCCA 60.684 55.0 0.00 0.0 35.79 5.36 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
25 26 5.713025 ACCGTTCATTCAAAGATTCATTGG 58.287 37.500 2.11 0.00 0.00 3.16
26 27 5.104374 CCGTTCATTCAAAGATTCATTGGG 58.896 41.667 2.11 0.00 0.00 4.12
27 28 5.105797 CCGTTCATTCAAAGATTCATTGGGA 60.106 40.000 2.11 0.00 0.00 4.37
28 29 6.389091 CGTTCATTCAAAGATTCATTGGGAA 58.611 36.000 2.11 2.32 40.46 3.97
29 30 6.308766 CGTTCATTCAAAGATTCATTGGGAAC 59.691 38.462 16.09 16.09 38.60 3.62
30 31 6.914654 TCATTCAAAGATTCATTGGGAACA 57.085 33.333 2.11 0.00 38.60 3.18
31 32 6.927416 TCATTCAAAGATTCATTGGGAACAG 58.073 36.000 2.11 0.00 44.54 3.16
32 33 6.494491 TCATTCAAAGATTCATTGGGAACAGT 59.506 34.615 2.11 0.00 44.54 3.55
33 34 7.669304 TCATTCAAAGATTCATTGGGAACAGTA 59.331 33.333 2.11 0.00 44.54 2.74
34 35 7.831691 TTCAAAGATTCATTGGGAACAGTAA 57.168 32.000 2.11 0.00 44.54 2.24
35 36 7.452880 TCAAAGATTCATTGGGAACAGTAAG 57.547 36.000 2.11 0.00 44.54 2.34
36 37 7.004086 TCAAAGATTCATTGGGAACAGTAAGT 58.996 34.615 2.11 0.00 44.54 2.24
37 38 8.160765 TCAAAGATTCATTGGGAACAGTAAGTA 58.839 33.333 2.11 0.00 44.54 2.24
38 39 8.960591 CAAAGATTCATTGGGAACAGTAAGTAT 58.039 33.333 0.00 0.00 44.54 2.12
39 40 9.533831 AAAGATTCATTGGGAACAGTAAGTATT 57.466 29.630 0.00 0.00 44.54 1.89
68 69 9.745880 TTTTATAGCGTTTCTTCTATACTCAGG 57.254 33.333 0.00 0.00 30.10 3.86
69 70 8.687292 TTATAGCGTTTCTTCTATACTCAGGA 57.313 34.615 0.00 0.00 30.10 3.86
70 71 5.251601 AGCGTTTCTTCTATACTCAGGAC 57.748 43.478 0.00 0.00 0.00 3.85
71 72 4.705507 AGCGTTTCTTCTATACTCAGGACA 59.294 41.667 0.00 0.00 0.00 4.02
72 73 5.185249 AGCGTTTCTTCTATACTCAGGACAA 59.815 40.000 0.00 0.00 0.00 3.18
73 74 5.288952 GCGTTTCTTCTATACTCAGGACAAC 59.711 44.000 0.00 0.00 0.00 3.32
74 75 5.805994 CGTTTCTTCTATACTCAGGACAACC 59.194 44.000 0.00 0.00 0.00 3.77
76 77 7.387643 GTTTCTTCTATACTCAGGACAACCTT 58.612 38.462 0.00 0.00 45.36 3.50
77 78 7.554959 TTCTTCTATACTCAGGACAACCTTT 57.445 36.000 0.00 0.00 45.36 3.11
78 79 8.660295 TTCTTCTATACTCAGGACAACCTTTA 57.340 34.615 0.00 0.00 45.36 1.85
79 80 8.064336 TCTTCTATACTCAGGACAACCTTTAC 57.936 38.462 0.00 0.00 45.36 2.01
80 81 6.786967 TCTATACTCAGGACAACCTTTACC 57.213 41.667 0.00 0.00 45.36 2.85
81 82 2.833631 ACTCAGGACAACCTTTACCG 57.166 50.000 0.00 0.00 45.36 4.02
82 83 2.322658 ACTCAGGACAACCTTTACCGA 58.677 47.619 0.00 0.00 45.36 4.69
83 84 2.701951 ACTCAGGACAACCTTTACCGAA 59.298 45.455 0.00 0.00 45.36 4.30
84 85 3.244112 ACTCAGGACAACCTTTACCGAAG 60.244 47.826 0.00 0.00 45.36 3.79
85 86 2.967201 TCAGGACAACCTTTACCGAAGA 59.033 45.455 0.00 0.00 45.36 2.87
86 87 3.388676 TCAGGACAACCTTTACCGAAGAA 59.611 43.478 0.00 0.00 45.36 2.52
87 88 4.131596 CAGGACAACCTTTACCGAAGAAA 58.868 43.478 0.00 0.00 45.36 2.52
88 89 4.577283 CAGGACAACCTTTACCGAAGAAAA 59.423 41.667 0.00 0.00 45.36 2.29
89 90 5.240844 CAGGACAACCTTTACCGAAGAAAAT 59.759 40.000 0.00 0.00 45.36 1.82
90 91 6.428771 CAGGACAACCTTTACCGAAGAAAATA 59.571 38.462 0.00 0.00 45.36 1.40
91 92 6.653740 AGGACAACCTTTACCGAAGAAAATAG 59.346 38.462 0.00 0.00 45.36 1.73
92 93 6.652062 GGACAACCTTTACCGAAGAAAATAGA 59.348 38.462 0.00 0.00 37.57 1.98
93 94 7.336176 GGACAACCTTTACCGAAGAAAATAGAT 59.664 37.037 0.00 0.00 37.57 1.98
94 95 8.040716 ACAACCTTTACCGAAGAAAATAGATG 57.959 34.615 0.00 0.00 37.57 2.90
95 96 7.881232 ACAACCTTTACCGAAGAAAATAGATGA 59.119 33.333 0.00 0.00 37.57 2.92
96 97 7.845066 ACCTTTACCGAAGAAAATAGATGAC 57.155 36.000 0.00 0.00 37.57 3.06
97 98 7.621796 ACCTTTACCGAAGAAAATAGATGACT 58.378 34.615 0.00 0.00 37.57 3.41
98 99 8.101419 ACCTTTACCGAAGAAAATAGATGACTT 58.899 33.333 0.00 0.00 37.57 3.01
99 100 8.947115 CCTTTACCGAAGAAAATAGATGACTTT 58.053 33.333 0.00 0.00 37.57 2.66
100 101 9.760660 CTTTACCGAAGAAAATAGATGACTTTG 57.239 33.333 0.00 0.00 37.57 2.77
101 102 6.183309 ACCGAAGAAAATAGATGACTTTGC 57.817 37.500 0.00 0.00 0.00 3.68
102 103 5.123979 ACCGAAGAAAATAGATGACTTTGCC 59.876 40.000 0.00 0.00 0.00 4.52
103 104 5.123820 CCGAAGAAAATAGATGACTTTGCCA 59.876 40.000 0.00 0.00 0.00 4.92
104 105 6.349280 CCGAAGAAAATAGATGACTTTGCCAA 60.349 38.462 0.00 0.00 0.00 4.52
105 106 6.744537 CGAAGAAAATAGATGACTTTGCCAAG 59.255 38.462 0.00 0.00 35.92 3.61
106 107 7.530426 AAGAAAATAGATGACTTTGCCAAGT 57.470 32.000 2.23 2.23 46.64 3.16
107 108 7.530426 AGAAAATAGATGACTTTGCCAAGTT 57.470 32.000 4.46 0.00 43.79 2.66
108 109 8.635765 AGAAAATAGATGACTTTGCCAAGTTA 57.364 30.769 4.46 0.78 43.79 2.24
109 110 9.077885 AGAAAATAGATGACTTTGCCAAGTTAA 57.922 29.630 4.46 0.00 43.79 2.01
110 111 9.129209 GAAAATAGATGACTTTGCCAAGTTAAC 57.871 33.333 4.46 0.00 43.79 2.01
111 112 8.409358 AAATAGATGACTTTGCCAAGTTAACT 57.591 30.769 4.46 1.12 43.79 2.24
112 113 8.409358 AATAGATGACTTTGCCAAGTTAACTT 57.591 30.769 15.22 15.22 43.79 2.66
113 114 6.715347 AGATGACTTTGCCAAGTTAACTTT 57.285 33.333 18.25 2.07 43.79 2.66
114 115 6.739112 AGATGACTTTGCCAAGTTAACTTTC 58.261 36.000 18.25 13.08 43.79 2.62
115 116 6.547510 AGATGACTTTGCCAAGTTAACTTTCT 59.452 34.615 18.25 11.27 43.79 2.52
116 117 5.890334 TGACTTTGCCAAGTTAACTTTCTG 58.110 37.500 18.25 8.37 43.79 3.02
117 118 5.650266 TGACTTTGCCAAGTTAACTTTCTGA 59.350 36.000 18.25 2.99 43.79 3.27
118 119 5.891451 ACTTTGCCAAGTTAACTTTCTGAC 58.109 37.500 18.25 1.72 40.66 3.51
119 120 4.911514 TTGCCAAGTTAACTTTCTGACC 57.088 40.909 18.25 4.29 33.11 4.02
120 121 2.875933 TGCCAAGTTAACTTTCTGACCG 59.124 45.455 18.25 5.47 33.11 4.79
121 122 2.225727 GCCAAGTTAACTTTCTGACCGG 59.774 50.000 18.25 14.71 33.11 5.28
122 123 3.735591 CCAAGTTAACTTTCTGACCGGA 58.264 45.455 18.25 0.00 33.11 5.14
123 124 3.497262 CCAAGTTAACTTTCTGACCGGAC 59.503 47.826 18.25 1.07 33.11 4.79
124 125 3.022607 AGTTAACTTTCTGACCGGACG 57.977 47.619 9.46 0.00 0.00 4.79
125 126 2.064014 GTTAACTTTCTGACCGGACGG 58.936 52.381 9.46 7.67 42.03 4.79
126 127 0.037975 TAACTTTCTGACCGGACGGC 60.038 55.000 9.46 4.51 39.32 5.68
127 128 2.809601 CTTTCTGACCGGACGGCG 60.810 66.667 9.46 4.80 39.32 6.46
128 129 4.367023 TTTCTGACCGGACGGCGG 62.367 66.667 9.46 8.93 39.32 6.13
140 141 3.195002 CGGCGGACGCATCACAAT 61.195 61.111 18.95 0.00 44.11 2.71
141 142 1.880796 CGGCGGACGCATCACAATA 60.881 57.895 18.95 0.00 44.11 1.90
142 143 1.221466 CGGCGGACGCATCACAATAT 61.221 55.000 18.95 0.00 44.11 1.28
143 144 0.944386 GGCGGACGCATCACAATATT 59.056 50.000 18.95 0.00 44.11 1.28
144 145 1.334059 GGCGGACGCATCACAATATTG 60.334 52.381 18.95 14.01 44.11 1.90
145 146 1.330521 GCGGACGCATCACAATATTGT 59.669 47.619 15.47 15.47 40.77 2.71
146 147 2.223249 GCGGACGCATCACAATATTGTT 60.223 45.455 18.50 3.07 39.20 2.83
147 148 3.353524 CGGACGCATCACAATATTGTTG 58.646 45.455 18.50 15.73 39.91 3.33
148 149 3.108144 GGACGCATCACAATATTGTTGC 58.892 45.455 25.47 25.47 39.91 4.17
149 150 3.427368 GGACGCATCACAATATTGTTGCA 60.427 43.478 30.45 16.10 42.23 4.08
150 151 3.500982 ACGCATCACAATATTGTTGCAC 58.499 40.909 30.45 17.02 42.23 4.57
151 152 2.853594 CGCATCACAATATTGTTGCACC 59.146 45.455 30.45 15.09 42.23 5.01
152 153 2.853594 GCATCACAATATTGTTGCACCG 59.146 45.455 28.34 14.74 41.90 4.94
153 154 3.673052 GCATCACAATATTGTTGCACCGT 60.673 43.478 28.34 3.38 41.90 4.83
154 155 4.484236 CATCACAATATTGTTGCACCGTT 58.516 39.130 18.50 0.00 39.91 4.44
155 156 4.576216 TCACAATATTGTTGCACCGTTT 57.424 36.364 18.50 0.00 39.91 3.60
156 157 4.541779 TCACAATATTGTTGCACCGTTTC 58.458 39.130 18.50 0.00 39.91 2.78
157 158 4.277174 TCACAATATTGTTGCACCGTTTCT 59.723 37.500 18.50 0.00 39.91 2.52
158 159 4.981674 CACAATATTGTTGCACCGTTTCTT 59.018 37.500 18.50 0.00 39.91 2.52
159 160 5.461737 CACAATATTGTTGCACCGTTTCTTT 59.538 36.000 18.50 0.00 39.91 2.52
160 161 5.461737 ACAATATTGTTGCACCGTTTCTTTG 59.538 36.000 15.47 0.00 38.47 2.77
161 162 3.791973 ATTGTTGCACCGTTTCTTTGA 57.208 38.095 0.00 0.00 0.00 2.69
162 163 3.791973 TTGTTGCACCGTTTCTTTGAT 57.208 38.095 0.00 0.00 0.00 2.57
163 164 4.902443 TTGTTGCACCGTTTCTTTGATA 57.098 36.364 0.00 0.00 0.00 2.15
164 165 4.902443 TGTTGCACCGTTTCTTTGATAA 57.098 36.364 0.00 0.00 0.00 1.75
165 166 5.446143 TGTTGCACCGTTTCTTTGATAAT 57.554 34.783 0.00 0.00 0.00 1.28
166 167 5.837437 TGTTGCACCGTTTCTTTGATAATT 58.163 33.333 0.00 0.00 0.00 1.40
167 168 5.689514 TGTTGCACCGTTTCTTTGATAATTG 59.310 36.000 0.00 0.00 0.00 2.32
168 169 5.446143 TGCACCGTTTCTTTGATAATTGT 57.554 34.783 0.00 0.00 0.00 2.71
169 170 5.837437 TGCACCGTTTCTTTGATAATTGTT 58.163 33.333 0.00 0.00 0.00 2.83
170 171 5.689514 TGCACCGTTTCTTTGATAATTGTTG 59.310 36.000 0.00 0.00 0.00 3.33
171 172 5.388371 GCACCGTTTCTTTGATAATTGTTGC 60.388 40.000 0.00 0.00 0.00 4.17
172 173 5.920273 CACCGTTTCTTTGATAATTGTTGCT 59.080 36.000 0.00 0.00 0.00 3.91
173 174 5.920273 ACCGTTTCTTTGATAATTGTTGCTG 59.080 36.000 0.00 0.00 0.00 4.41
174 175 5.164061 CCGTTTCTTTGATAATTGTTGCTGC 60.164 40.000 0.00 0.00 0.00 5.25
175 176 5.630680 CGTTTCTTTGATAATTGTTGCTGCT 59.369 36.000 0.00 0.00 0.00 4.24
176 177 6.144402 CGTTTCTTTGATAATTGTTGCTGCTT 59.856 34.615 0.00 0.00 0.00 3.91
177 178 7.504818 GTTTCTTTGATAATTGTTGCTGCTTC 58.495 34.615 0.00 0.00 0.00 3.86
178 179 6.579666 TCTTTGATAATTGTTGCTGCTTCT 57.420 33.333 0.00 0.00 0.00 2.85
179 180 6.985117 TCTTTGATAATTGTTGCTGCTTCTT 58.015 32.000 0.00 0.00 0.00 2.52
180 181 7.086376 TCTTTGATAATTGTTGCTGCTTCTTC 58.914 34.615 0.00 0.00 0.00 2.87
181 182 5.963176 TGATAATTGTTGCTGCTTCTTCA 57.037 34.783 0.00 0.00 0.00 3.02
182 183 6.519679 TGATAATTGTTGCTGCTTCTTCAT 57.480 33.333 0.00 0.00 0.00 2.57
183 184 6.927416 TGATAATTGTTGCTGCTTCTTCATT 58.073 32.000 0.00 0.00 0.00 2.57
184 185 7.031372 TGATAATTGTTGCTGCTTCTTCATTC 58.969 34.615 0.00 0.00 0.00 2.67
185 186 2.975410 TGTTGCTGCTTCTTCATTCG 57.025 45.000 0.00 0.00 0.00 3.34
186 187 1.069022 TGTTGCTGCTTCTTCATTCGC 60.069 47.619 0.00 0.00 0.00 4.70
187 188 1.198637 GTTGCTGCTTCTTCATTCGCT 59.801 47.619 0.00 0.00 0.00 4.93
188 189 1.527034 TGCTGCTTCTTCATTCGCTT 58.473 45.000 0.00 0.00 0.00 4.68
189 190 1.881973 TGCTGCTTCTTCATTCGCTTT 59.118 42.857 0.00 0.00 0.00 3.51
190 191 3.073678 TGCTGCTTCTTCATTCGCTTTA 58.926 40.909 0.00 0.00 0.00 1.85
191 192 3.501828 TGCTGCTTCTTCATTCGCTTTAA 59.498 39.130 0.00 0.00 0.00 1.52
192 193 4.023279 TGCTGCTTCTTCATTCGCTTTAAA 60.023 37.500 0.00 0.00 0.00 1.52
193 194 4.322009 GCTGCTTCTTCATTCGCTTTAAAC 59.678 41.667 0.00 0.00 0.00 2.01
194 195 5.431420 TGCTTCTTCATTCGCTTTAAACA 57.569 34.783 0.00 0.00 0.00 2.83
195 196 6.012658 TGCTTCTTCATTCGCTTTAAACAT 57.987 33.333 0.00 0.00 0.00 2.71
196 197 6.446318 TGCTTCTTCATTCGCTTTAAACATT 58.554 32.000 0.00 0.00 0.00 2.71
197 198 7.589395 TGCTTCTTCATTCGCTTTAAACATTA 58.411 30.769 0.00 0.00 0.00 1.90
198 199 7.750458 TGCTTCTTCATTCGCTTTAAACATTAG 59.250 33.333 0.00 0.00 0.00 1.73
199 200 7.750903 GCTTCTTCATTCGCTTTAAACATTAGT 59.249 33.333 0.00 0.00 0.00 2.24
205 206 9.820229 TCATTCGCTTTAAACATTAGTAAACTG 57.180 29.630 0.00 0.00 0.00 3.16
206 207 9.607285 CATTCGCTTTAAACATTAGTAAACTGT 57.393 29.630 0.00 0.00 0.00 3.55
207 208 9.821662 ATTCGCTTTAAACATTAGTAAACTGTC 57.178 29.630 0.00 0.00 0.00 3.51
208 209 7.503991 TCGCTTTAAACATTAGTAAACTGTCG 58.496 34.615 0.00 0.00 0.00 4.35
209 210 7.169645 TCGCTTTAAACATTAGTAAACTGTCGT 59.830 33.333 0.00 0.00 0.00 4.34
210 211 7.473411 CGCTTTAAACATTAGTAAACTGTCGTC 59.527 37.037 0.00 0.00 0.00 4.20
211 212 8.277713 GCTTTAAACATTAGTAAACTGTCGTCA 58.722 33.333 0.00 0.00 0.00 4.35
212 213 9.793245 CTTTAAACATTAGTAAACTGTCGTCAG 57.207 33.333 8.17 8.17 46.18 3.51
213 214 5.840940 AACATTAGTAAACTGTCGTCAGC 57.159 39.130 9.67 0.00 44.77 4.26
214 215 4.878439 ACATTAGTAAACTGTCGTCAGCA 58.122 39.130 9.67 0.00 44.77 4.41
215 216 5.294356 ACATTAGTAAACTGTCGTCAGCAA 58.706 37.500 9.67 0.00 44.77 3.91
216 217 5.756347 ACATTAGTAAACTGTCGTCAGCAAA 59.244 36.000 9.67 0.00 44.77 3.68
217 218 5.646467 TTAGTAAACTGTCGTCAGCAAAC 57.354 39.130 9.67 5.37 44.77 2.93
218 219 3.527533 AGTAAACTGTCGTCAGCAAACA 58.472 40.909 9.67 0.00 44.77 2.83
219 220 3.936453 AGTAAACTGTCGTCAGCAAACAA 59.064 39.130 9.67 0.00 44.77 2.83
220 221 3.840890 AAACTGTCGTCAGCAAACAAA 57.159 38.095 9.67 0.00 44.77 2.83
221 222 3.405170 AACTGTCGTCAGCAAACAAAG 57.595 42.857 9.67 0.00 44.77 2.77
222 223 2.627945 ACTGTCGTCAGCAAACAAAGA 58.372 42.857 9.67 0.00 44.77 2.52
223 224 3.006940 ACTGTCGTCAGCAAACAAAGAA 58.993 40.909 9.67 0.00 44.77 2.52
224 225 3.438781 ACTGTCGTCAGCAAACAAAGAAA 59.561 39.130 9.67 0.00 44.77 2.52
225 226 4.014847 TGTCGTCAGCAAACAAAGAAAG 57.985 40.909 0.00 0.00 0.00 2.62
226 227 3.687212 TGTCGTCAGCAAACAAAGAAAGA 59.313 39.130 0.00 0.00 0.00 2.52
227 228 4.155099 TGTCGTCAGCAAACAAAGAAAGAA 59.845 37.500 0.00 0.00 0.00 2.52
228 229 5.092781 GTCGTCAGCAAACAAAGAAAGAAA 58.907 37.500 0.00 0.00 0.00 2.52
229 230 5.228012 GTCGTCAGCAAACAAAGAAAGAAAG 59.772 40.000 0.00 0.00 0.00 2.62
230 231 4.500477 CGTCAGCAAACAAAGAAAGAAAGG 59.500 41.667 0.00 0.00 0.00 3.11
231 232 5.410924 GTCAGCAAACAAAGAAAGAAAGGT 58.589 37.500 0.00 0.00 0.00 3.50
238 239 5.188327 ACAAAGAAAGAAAGGTTAGCAGC 57.812 39.130 0.00 0.00 0.00 5.25
249 250 2.375509 AGGTTAGCAGCCCAGTAAAGTT 59.624 45.455 0.00 0.00 0.00 2.66
273 274 1.866853 CGGCCCAGCAAAAAGGAGAC 61.867 60.000 0.00 0.00 0.00 3.36
276 277 1.172180 CCCAGCAAAAAGGAGACGCA 61.172 55.000 0.00 0.00 0.00 5.24
289 290 3.376234 AGGAGACGCATCATGACAATTTG 59.624 43.478 0.00 0.00 0.00 2.32
298 299 4.827304 TCATGACAATTTGAACTTGCGA 57.173 36.364 2.79 0.00 0.00 5.10
325 326 2.492484 CAACCCTAGTACGTCTTCTGCT 59.508 50.000 0.00 0.00 0.00 4.24
333 334 0.885196 ACGTCTTCTGCTCAGACTCC 59.115 55.000 0.00 0.00 38.89 3.85
347 348 4.547367 CTCCCGATCCCCAACGCC 62.547 72.222 0.00 0.00 0.00 5.68
350 351 4.418328 CCGATCCCCAACGCCCAA 62.418 66.667 0.00 0.00 0.00 4.12
351 352 3.131478 CGATCCCCAACGCCCAAC 61.131 66.667 0.00 0.00 0.00 3.77
360 361 0.667184 CAACGCCCAACCAAATCTGC 60.667 55.000 0.00 0.00 0.00 4.26
396 400 4.179579 GCCGAAATGACCAGCCGC 62.180 66.667 0.00 0.00 0.00 6.53
397 401 3.508840 CCGAAATGACCAGCCGCC 61.509 66.667 0.00 0.00 0.00 6.13
398 402 2.745884 CGAAATGACCAGCCGCCA 60.746 61.111 0.00 0.00 0.00 5.69
693 720 4.148825 CGCCTCTCCCTTGGACGG 62.149 72.222 0.00 0.00 0.00 4.79
869 911 4.077184 CAACGGGGCGGTGCTCTA 62.077 66.667 0.00 0.00 37.86 2.43
945 999 2.234414 GGTGGTATTGGTGTCCGAACTA 59.766 50.000 0.00 0.00 0.00 2.24
1002 1059 4.308526 GGCATCTGGGGCGATATG 57.691 61.111 0.00 0.00 0.00 1.78
1003 1060 1.377725 GGCATCTGGGGCGATATGG 60.378 63.158 0.00 0.00 0.00 2.74
1176 1253 5.120830 GCCTCGCTGTATGAATAATAGGTTG 59.879 44.000 0.00 0.00 0.00 3.77
1195 1278 4.455877 GGTTGATCGACCACTTTCAGATTT 59.544 41.667 25.05 0.00 39.57 2.17
1254 1347 5.643379 TGTCTTGCCATAACCTTCAAATC 57.357 39.130 0.00 0.00 0.00 2.17
1604 1733 5.231265 TGGATACGATCGCTCACATATAC 57.769 43.478 16.60 5.75 42.51 1.47
1715 1851 7.759607 AGATGGACCAACTTATAGCCATATTT 58.240 34.615 0.00 0.00 36.34 1.40
1716 1852 7.667219 AGATGGACCAACTTATAGCCATATTTG 59.333 37.037 0.00 0.00 36.34 2.32
1818 1971 2.675844 TGTCACGTGTTTGAAACCTCAG 59.324 45.455 16.51 0.00 31.69 3.35
1914 2078 5.252969 TCCATTCAATACATGCTTTCTGC 57.747 39.130 0.00 0.00 43.25 4.26
2015 2182 6.558771 TTCTTGTATCGGCATCCATTTATG 57.441 37.500 0.00 0.00 0.00 1.90
2021 2188 8.402798 TGTATCGGCATCCATTTATGTAAAAT 57.597 30.769 0.00 0.00 0.00 1.82
2027 2194 9.180678 CGGCATCCATTTATGTAAAATAGAAAC 57.819 33.333 0.00 0.00 0.00 2.78
2084 2251 8.518702 AGTTTGTTGTTTTGGCATAATTTTGTT 58.481 25.926 0.00 0.00 0.00 2.83
2118 2289 9.035607 ACGATGAATGAGTTTACATGAGTATTC 57.964 33.333 0.00 0.87 0.00 1.75
2128 2305 8.860088 AGTTTACATGAGTATTCTTGCCTTTTT 58.140 29.630 0.00 0.00 33.08 1.94
2361 2556 5.584649 CACGTGCCTTCTCTTATCCATTTTA 59.415 40.000 0.82 0.00 0.00 1.52
2412 2616 7.711339 ACTTCTTATGCTTATAGGCACAACTAC 59.289 37.037 12.22 0.00 45.36 2.73
2448 2656 3.879892 GGAGCTGAAATGTTAGGATGACC 59.120 47.826 0.00 0.00 0.00 4.02
2465 2673 2.076100 GACCGTCTGATTTGATGTGCA 58.924 47.619 0.00 0.00 0.00 4.57
2493 2701 4.220602 GGCTGAAATGGTTCAACAGGTAAT 59.779 41.667 0.00 0.00 43.18 1.89
2502 2710 9.533831 AATGGTTCAACAGGTAATAAGATCTTT 57.466 29.630 14.36 0.00 0.00 2.52
2503 2711 8.561738 TGGTTCAACAGGTAATAAGATCTTTC 57.438 34.615 14.36 2.56 0.00 2.62
2591 2802 0.740737 GGGTAGCATGCACCATCAAC 59.259 55.000 28.69 14.90 37.84 3.18
2600 2811 0.035056 GCACCATCAACCTACTGCCT 60.035 55.000 0.00 0.00 0.00 4.75
2730 2942 6.457392 GCAAATGATCCATATACTGTATGCCG 60.457 42.308 10.51 0.00 0.00 5.69
2734 2946 6.163476 TGATCCATATACTGTATGCCGAAAC 58.837 40.000 10.51 3.34 0.00 2.78
2742 2954 0.539986 GTATGCCGAAACTCCTCCCA 59.460 55.000 0.00 0.00 0.00 4.37
2746 2958 0.462759 GCCGAAACTCCTCCCATGAG 60.463 60.000 0.00 0.00 38.42 2.90
2832 3044 2.814269 ACATCGGTCTCATCATTCACG 58.186 47.619 0.00 0.00 0.00 4.35
2859 3071 4.332268 CCCACCAAACAAATTTGTGTGAAG 59.668 41.667 33.66 25.44 46.92 3.02
2883 3095 4.243007 ACTGATGGCTTTACTTTGTTGC 57.757 40.909 0.00 0.00 0.00 4.17
2911 3123 6.322931 TGGTATTCTCAGGAGATATAGCCAA 58.677 40.000 17.70 7.05 37.29 4.52
3303 3515 5.810587 GTCCATACACTGTGTTACATAGGTG 59.189 44.000 19.73 12.26 0.00 4.00
3309 3521 3.760151 ACTGTGTTACATAGGTGCGTCTA 59.240 43.478 13.39 0.00 0.00 2.59
3319 3531 7.016361 ACATAGGTGCGTCTATTTGATTTTC 57.984 36.000 0.00 0.00 0.00 2.29
3325 3537 7.552687 AGGTGCGTCTATTTGATTTTCTATTCA 59.447 33.333 0.00 0.00 0.00 2.57
3326 3538 8.345565 GGTGCGTCTATTTGATTTTCTATTCAT 58.654 33.333 0.00 0.00 0.00 2.57
3327 3539 9.722056 GTGCGTCTATTTGATTTTCTATTCATT 57.278 29.630 0.00 0.00 0.00 2.57
3357 3634 7.012989 AGTGGGTTACTAACAAATGAACACTTC 59.987 37.037 1.40 0.00 38.04 3.01
3395 3672 2.760387 GAAAGGGCTGCTGCAGTTGC 62.760 60.000 28.50 18.57 41.91 4.17
3406 3683 2.487934 CTGCAGTTGCTAGTTGTCACT 58.512 47.619 5.25 0.00 42.66 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.127758 CCCAATGAATCTTTGAATGAACGGTA 60.128 38.462 10.03 0.00 0.00 4.02
3 4 5.104374 CCCAATGAATCTTTGAATGAACGG 58.896 41.667 10.03 0.00 0.00 4.44
4 5 5.953183 TCCCAATGAATCTTTGAATGAACG 58.047 37.500 10.03 0.00 0.00 3.95
5 6 7.153985 TGTTCCCAATGAATCTTTGAATGAAC 58.846 34.615 19.36 19.36 34.90 3.18
6 7 7.015487 ACTGTTCCCAATGAATCTTTGAATGAA 59.985 33.333 10.03 7.19 34.90 2.57
7 8 6.494491 ACTGTTCCCAATGAATCTTTGAATGA 59.506 34.615 10.03 2.22 34.90 2.57
8 9 6.694447 ACTGTTCCCAATGAATCTTTGAATG 58.306 36.000 10.03 0.17 34.90 2.67
9 10 6.923199 ACTGTTCCCAATGAATCTTTGAAT 57.077 33.333 10.03 0.00 34.90 2.57
10 11 7.505585 ACTTACTGTTCCCAATGAATCTTTGAA 59.494 33.333 10.03 0.00 34.90 2.69
11 12 7.004086 ACTTACTGTTCCCAATGAATCTTTGA 58.996 34.615 10.03 0.00 34.90 2.69
12 13 7.219484 ACTTACTGTTCCCAATGAATCTTTG 57.781 36.000 2.28 2.28 34.90 2.77
13 14 9.533831 AATACTTACTGTTCCCAATGAATCTTT 57.466 29.630 0.00 0.00 34.90 2.52
42 43 9.745880 CCTGAGTATAGAAGAAACGCTATAAAA 57.254 33.333 0.00 0.00 32.93 1.52
43 44 9.128404 TCCTGAGTATAGAAGAAACGCTATAAA 57.872 33.333 0.00 0.00 32.93 1.40
44 45 8.566260 GTCCTGAGTATAGAAGAAACGCTATAA 58.434 37.037 0.00 0.00 32.93 0.98
45 46 7.718314 TGTCCTGAGTATAGAAGAAACGCTATA 59.282 37.037 0.00 0.00 0.00 1.31
46 47 6.546403 TGTCCTGAGTATAGAAGAAACGCTAT 59.454 38.462 0.00 0.00 0.00 2.97
47 48 5.884232 TGTCCTGAGTATAGAAGAAACGCTA 59.116 40.000 0.00 0.00 0.00 4.26
48 49 4.705507 TGTCCTGAGTATAGAAGAAACGCT 59.294 41.667 0.00 0.00 0.00 5.07
49 50 4.995124 TGTCCTGAGTATAGAAGAAACGC 58.005 43.478 0.00 0.00 0.00 4.84
50 51 5.805994 GGTTGTCCTGAGTATAGAAGAAACG 59.194 44.000 0.00 0.00 0.00 3.60
51 52 6.937392 AGGTTGTCCTGAGTATAGAAGAAAC 58.063 40.000 0.00 0.00 43.33 2.78
52 53 7.554959 AAGGTTGTCCTGAGTATAGAAGAAA 57.445 36.000 0.00 0.00 44.35 2.52
53 54 7.554959 AAAGGTTGTCCTGAGTATAGAAGAA 57.445 36.000 0.00 0.00 44.35 2.52
54 55 7.123847 GGTAAAGGTTGTCCTGAGTATAGAAGA 59.876 40.741 0.00 0.00 44.35 2.87
55 56 7.266400 GGTAAAGGTTGTCCTGAGTATAGAAG 58.734 42.308 0.00 0.00 44.35 2.85
56 57 6.127535 CGGTAAAGGTTGTCCTGAGTATAGAA 60.128 42.308 0.00 0.00 44.35 2.10
57 58 5.359009 CGGTAAAGGTTGTCCTGAGTATAGA 59.641 44.000 0.00 0.00 44.35 1.98
58 59 5.359009 TCGGTAAAGGTTGTCCTGAGTATAG 59.641 44.000 0.00 0.00 44.35 1.31
59 60 5.263599 TCGGTAAAGGTTGTCCTGAGTATA 58.736 41.667 0.00 0.00 44.35 1.47
60 61 4.091549 TCGGTAAAGGTTGTCCTGAGTAT 58.908 43.478 0.00 0.00 44.35 2.12
61 62 3.499338 TCGGTAAAGGTTGTCCTGAGTA 58.501 45.455 0.00 0.00 44.35 2.59
62 63 2.322658 TCGGTAAAGGTTGTCCTGAGT 58.677 47.619 0.00 0.00 44.35 3.41
63 64 3.006537 TCTTCGGTAAAGGTTGTCCTGAG 59.993 47.826 0.00 0.00 44.35 3.35
64 65 2.967201 TCTTCGGTAAAGGTTGTCCTGA 59.033 45.455 0.00 0.00 44.35 3.86
65 66 3.396260 TCTTCGGTAAAGGTTGTCCTG 57.604 47.619 0.00 0.00 44.35 3.86
67 68 5.700722 ATTTTCTTCGGTAAAGGTTGTCC 57.299 39.130 0.00 0.00 35.54 4.02
68 69 7.662604 TCTATTTTCTTCGGTAAAGGTTGTC 57.337 36.000 0.00 0.00 35.54 3.18
69 70 7.881232 TCATCTATTTTCTTCGGTAAAGGTTGT 59.119 33.333 0.00 0.00 35.54 3.32
70 71 8.175716 GTCATCTATTTTCTTCGGTAAAGGTTG 58.824 37.037 0.00 0.00 35.54 3.77
71 72 8.101419 AGTCATCTATTTTCTTCGGTAAAGGTT 58.899 33.333 0.00 0.00 35.54 3.50
72 73 7.621796 AGTCATCTATTTTCTTCGGTAAAGGT 58.378 34.615 0.00 0.00 35.54 3.50
73 74 8.494016 AAGTCATCTATTTTCTTCGGTAAAGG 57.506 34.615 0.00 0.00 35.54 3.11
74 75 9.760660 CAAAGTCATCTATTTTCTTCGGTAAAG 57.239 33.333 0.00 0.00 36.22 1.85
75 76 8.234546 GCAAAGTCATCTATTTTCTTCGGTAAA 58.765 33.333 0.00 0.00 0.00 2.01
76 77 7.148306 GGCAAAGTCATCTATTTTCTTCGGTAA 60.148 37.037 0.00 0.00 0.00 2.85
77 78 6.315393 GGCAAAGTCATCTATTTTCTTCGGTA 59.685 38.462 0.00 0.00 0.00 4.02
78 79 5.123979 GGCAAAGTCATCTATTTTCTTCGGT 59.876 40.000 0.00 0.00 0.00 4.69
79 80 5.123820 TGGCAAAGTCATCTATTTTCTTCGG 59.876 40.000 0.00 0.00 0.00 4.30
80 81 6.182039 TGGCAAAGTCATCTATTTTCTTCG 57.818 37.500 0.00 0.00 0.00 3.79
81 82 7.597386 ACTTGGCAAAGTCATCTATTTTCTTC 58.403 34.615 0.00 0.00 43.34 2.87
82 83 7.530426 ACTTGGCAAAGTCATCTATTTTCTT 57.470 32.000 0.00 0.00 43.34 2.52
83 84 7.530426 AACTTGGCAAAGTCATCTATTTTCT 57.470 32.000 7.02 0.00 46.15 2.52
84 85 9.129209 GTTAACTTGGCAAAGTCATCTATTTTC 57.871 33.333 7.02 0.00 46.15 2.29
85 86 8.860088 AGTTAACTTGGCAAAGTCATCTATTTT 58.140 29.630 7.02 0.00 46.15 1.82
86 87 8.409358 AGTTAACTTGGCAAAGTCATCTATTT 57.591 30.769 7.02 0.00 46.15 1.40
87 88 8.409358 AAGTTAACTTGGCAAAGTCATCTATT 57.591 30.769 19.94 0.00 46.15 1.73
88 89 8.409358 AAAGTTAACTTGGCAAAGTCATCTAT 57.591 30.769 21.22 0.00 46.15 1.98
89 90 7.719633 AGAAAGTTAACTTGGCAAAGTCATCTA 59.280 33.333 21.22 0.00 46.15 1.98
90 91 6.547510 AGAAAGTTAACTTGGCAAAGTCATCT 59.452 34.615 21.22 12.66 46.15 2.90
91 92 6.638468 CAGAAAGTTAACTTGGCAAAGTCATC 59.362 38.462 21.22 10.72 46.15 2.92
92 93 6.321181 TCAGAAAGTTAACTTGGCAAAGTCAT 59.679 34.615 21.22 1.65 46.15 3.06
93 94 5.650266 TCAGAAAGTTAACTTGGCAAAGTCA 59.350 36.000 21.22 0.00 46.15 3.41
94 95 5.971792 GTCAGAAAGTTAACTTGGCAAAGTC 59.028 40.000 21.22 12.72 46.15 3.01
96 97 5.281727 GGTCAGAAAGTTAACTTGGCAAAG 58.718 41.667 21.22 0.00 39.49 2.77
97 98 4.201970 CGGTCAGAAAGTTAACTTGGCAAA 60.202 41.667 21.22 4.40 36.12 3.68
98 99 3.314080 CGGTCAGAAAGTTAACTTGGCAA 59.686 43.478 21.22 0.00 36.12 4.52
99 100 2.875933 CGGTCAGAAAGTTAACTTGGCA 59.124 45.455 21.22 3.82 36.12 4.92
100 101 2.225727 CCGGTCAGAAAGTTAACTTGGC 59.774 50.000 21.22 15.70 36.12 4.52
101 102 3.497262 GTCCGGTCAGAAAGTTAACTTGG 59.503 47.826 21.22 15.31 36.12 3.61
102 103 3.183775 CGTCCGGTCAGAAAGTTAACTTG 59.816 47.826 21.22 10.29 36.12 3.16
103 104 3.387397 CGTCCGGTCAGAAAGTTAACTT 58.613 45.455 15.22 15.22 37.91 2.66
104 105 2.288640 CCGTCCGGTCAGAAAGTTAACT 60.289 50.000 1.12 1.12 0.00 2.24
105 106 2.064014 CCGTCCGGTCAGAAAGTTAAC 58.936 52.381 0.00 0.00 0.00 2.01
106 107 1.606224 GCCGTCCGGTCAGAAAGTTAA 60.606 52.381 7.66 0.00 37.65 2.01
107 108 0.037975 GCCGTCCGGTCAGAAAGTTA 60.038 55.000 7.66 0.00 37.65 2.24
108 109 1.301479 GCCGTCCGGTCAGAAAGTT 60.301 57.895 7.66 0.00 37.65 2.66
109 110 2.342648 GCCGTCCGGTCAGAAAGT 59.657 61.111 7.66 0.00 37.65 2.66
110 111 2.809601 CGCCGTCCGGTCAGAAAG 60.810 66.667 7.66 0.00 37.65 2.62
122 123 2.566057 TATTGTGATGCGTCCGCCGT 62.566 55.000 9.43 0.00 41.09 5.68
123 124 1.221466 ATATTGTGATGCGTCCGCCG 61.221 55.000 9.43 0.00 41.09 6.46
124 125 0.944386 AATATTGTGATGCGTCCGCC 59.056 50.000 9.43 0.00 41.09 6.13
125 126 1.330521 ACAATATTGTGATGCGTCCGC 59.669 47.619 20.19 4.42 40.49 5.54
126 127 3.353524 CAACAATATTGTGATGCGTCCG 58.646 45.455 21.46 0.00 41.31 4.79
127 128 3.108144 GCAACAATATTGTGATGCGTCC 58.892 45.455 22.79 5.19 41.31 4.79
128 129 3.543494 GTGCAACAATATTGTGATGCGTC 59.457 43.478 27.70 21.96 44.01 5.19
129 130 3.500982 GTGCAACAATATTGTGATGCGT 58.499 40.909 27.70 10.46 44.01 5.24
130 131 2.853594 GGTGCAACAATATTGTGATGCG 59.146 45.455 27.70 14.99 44.01 4.73
131 132 2.853594 CGGTGCAACAATATTGTGATGC 59.146 45.455 27.31 27.31 42.37 3.91
132 133 4.095410 ACGGTGCAACAATATTGTGATG 57.905 40.909 21.46 17.07 41.31 3.07
133 134 4.782019 AACGGTGCAACAATATTGTGAT 57.218 36.364 21.46 4.38 41.31 3.06
134 135 4.277174 AGAAACGGTGCAACAATATTGTGA 59.723 37.500 21.46 6.50 41.31 3.58
135 136 4.545610 AGAAACGGTGCAACAATATTGTG 58.454 39.130 21.46 15.57 41.31 3.33
136 137 4.846779 AGAAACGGTGCAACAATATTGT 57.153 36.364 15.47 15.47 44.72 2.71
137 138 5.689514 TCAAAGAAACGGTGCAACAATATTG 59.310 36.000 14.01 14.01 39.98 1.90
138 139 5.837437 TCAAAGAAACGGTGCAACAATATT 58.163 33.333 0.98 0.00 39.98 1.28
139 140 5.446143 TCAAAGAAACGGTGCAACAATAT 57.554 34.783 0.98 0.00 39.98 1.28
140 141 4.902443 TCAAAGAAACGGTGCAACAATA 57.098 36.364 0.98 0.00 39.98 1.90
141 142 3.791973 TCAAAGAAACGGTGCAACAAT 57.208 38.095 0.98 0.00 39.98 2.71
142 143 3.791973 ATCAAAGAAACGGTGCAACAA 57.208 38.095 0.98 0.00 39.98 2.83
143 144 4.902443 TTATCAAAGAAACGGTGCAACA 57.098 36.364 0.98 0.00 39.98 3.33
144 145 5.689961 ACAATTATCAAAGAAACGGTGCAAC 59.310 36.000 0.00 0.00 0.00 4.17
145 146 5.837437 ACAATTATCAAAGAAACGGTGCAA 58.163 33.333 0.00 0.00 0.00 4.08
146 147 5.446143 ACAATTATCAAAGAAACGGTGCA 57.554 34.783 0.00 0.00 0.00 4.57
147 148 5.388371 GCAACAATTATCAAAGAAACGGTGC 60.388 40.000 0.00 0.00 0.00 5.01
148 149 5.920273 AGCAACAATTATCAAAGAAACGGTG 59.080 36.000 0.00 0.00 0.00 4.94
149 150 5.920273 CAGCAACAATTATCAAAGAAACGGT 59.080 36.000 0.00 0.00 0.00 4.83
150 151 5.164061 GCAGCAACAATTATCAAAGAAACGG 60.164 40.000 0.00 0.00 0.00 4.44
151 152 5.630680 AGCAGCAACAATTATCAAAGAAACG 59.369 36.000 0.00 0.00 0.00 3.60
152 153 7.383300 AGAAGCAGCAACAATTATCAAAGAAAC 59.617 33.333 0.00 0.00 0.00 2.78
153 154 7.436118 AGAAGCAGCAACAATTATCAAAGAAA 58.564 30.769 0.00 0.00 0.00 2.52
154 155 6.985117 AGAAGCAGCAACAATTATCAAAGAA 58.015 32.000 0.00 0.00 0.00 2.52
155 156 6.579666 AGAAGCAGCAACAATTATCAAAGA 57.420 33.333 0.00 0.00 0.00 2.52
156 157 6.864685 TGAAGAAGCAGCAACAATTATCAAAG 59.135 34.615 0.00 0.00 0.00 2.77
157 158 6.747125 TGAAGAAGCAGCAACAATTATCAAA 58.253 32.000 0.00 0.00 0.00 2.69
158 159 6.330004 TGAAGAAGCAGCAACAATTATCAA 57.670 33.333 0.00 0.00 0.00 2.57
159 160 5.963176 TGAAGAAGCAGCAACAATTATCA 57.037 34.783 0.00 0.00 0.00 2.15
160 161 6.195983 CGAATGAAGAAGCAGCAACAATTATC 59.804 38.462 0.00 0.00 0.00 1.75
161 162 6.032094 CGAATGAAGAAGCAGCAACAATTAT 58.968 36.000 0.00 0.00 0.00 1.28
162 163 5.393124 CGAATGAAGAAGCAGCAACAATTA 58.607 37.500 0.00 0.00 0.00 1.40
163 164 4.232221 CGAATGAAGAAGCAGCAACAATT 58.768 39.130 0.00 0.00 0.00 2.32
164 165 3.829948 CGAATGAAGAAGCAGCAACAAT 58.170 40.909 0.00 0.00 0.00 2.71
165 166 2.605338 GCGAATGAAGAAGCAGCAACAA 60.605 45.455 0.00 0.00 0.00 2.83
166 167 1.069022 GCGAATGAAGAAGCAGCAACA 60.069 47.619 0.00 0.00 0.00 3.33
167 168 1.198637 AGCGAATGAAGAAGCAGCAAC 59.801 47.619 0.00 0.00 0.00 4.17
168 169 1.527034 AGCGAATGAAGAAGCAGCAA 58.473 45.000 0.00 0.00 0.00 3.91
169 170 1.527034 AAGCGAATGAAGAAGCAGCA 58.473 45.000 0.00 0.00 0.00 4.41
170 171 2.626088 AAAGCGAATGAAGAAGCAGC 57.374 45.000 0.00 0.00 0.00 5.25
171 172 5.451908 TGTTTAAAGCGAATGAAGAAGCAG 58.548 37.500 0.00 0.00 0.00 4.24
172 173 5.431420 TGTTTAAAGCGAATGAAGAAGCA 57.569 34.783 0.00 0.00 0.00 3.91
173 174 6.934561 AATGTTTAAAGCGAATGAAGAAGC 57.065 33.333 0.00 0.00 0.00 3.86
179 180 9.820229 CAGTTTACTAATGTTTAAAGCGAATGA 57.180 29.630 0.00 0.00 0.00 2.57
180 181 9.607285 ACAGTTTACTAATGTTTAAAGCGAATG 57.393 29.630 0.00 0.00 0.00 2.67
181 182 9.821662 GACAGTTTACTAATGTTTAAAGCGAAT 57.178 29.630 0.00 0.00 0.00 3.34
182 183 8.005466 CGACAGTTTACTAATGTTTAAAGCGAA 58.995 33.333 0.00 0.00 0.00 4.70
183 184 7.169645 ACGACAGTTTACTAATGTTTAAAGCGA 59.830 33.333 0.00 0.00 0.00 4.93
184 185 7.285788 ACGACAGTTTACTAATGTTTAAAGCG 58.714 34.615 0.00 0.00 0.00 4.68
185 186 8.277713 TGACGACAGTTTACTAATGTTTAAAGC 58.722 33.333 0.00 0.00 0.00 3.51
186 187 9.793245 CTGACGACAGTTTACTAATGTTTAAAG 57.207 33.333 6.73 0.00 39.11 1.85
187 188 8.277713 GCTGACGACAGTTTACTAATGTTTAAA 58.722 33.333 16.02 0.00 45.04 1.52
188 189 7.438757 TGCTGACGACAGTTTACTAATGTTTAA 59.561 33.333 16.02 0.00 45.04 1.52
189 190 6.924612 TGCTGACGACAGTTTACTAATGTTTA 59.075 34.615 16.02 0.00 45.04 2.01
190 191 5.756347 TGCTGACGACAGTTTACTAATGTTT 59.244 36.000 16.02 0.00 45.04 2.83
191 192 5.294356 TGCTGACGACAGTTTACTAATGTT 58.706 37.500 16.02 0.00 45.04 2.71
192 193 4.878439 TGCTGACGACAGTTTACTAATGT 58.122 39.130 16.02 0.00 45.04 2.71
193 194 5.839262 TTGCTGACGACAGTTTACTAATG 57.161 39.130 16.02 0.00 45.04 1.90
194 195 5.756347 TGTTTGCTGACGACAGTTTACTAAT 59.244 36.000 16.02 0.00 45.04 1.73
195 196 5.110598 TGTTTGCTGACGACAGTTTACTAA 58.889 37.500 16.02 0.78 45.04 2.24
196 197 4.684877 TGTTTGCTGACGACAGTTTACTA 58.315 39.130 16.02 0.00 45.04 1.82
197 198 3.527533 TGTTTGCTGACGACAGTTTACT 58.472 40.909 16.02 0.00 45.04 2.24
198 199 3.936902 TGTTTGCTGACGACAGTTTAC 57.063 42.857 16.02 11.26 45.04 2.01
199 200 4.632251 TCTTTGTTTGCTGACGACAGTTTA 59.368 37.500 16.02 1.22 45.04 2.01
200 201 3.438781 TCTTTGTTTGCTGACGACAGTTT 59.561 39.130 16.02 0.00 45.04 2.66
201 202 3.006940 TCTTTGTTTGCTGACGACAGTT 58.993 40.909 16.02 0.00 45.04 3.16
202 203 2.627945 TCTTTGTTTGCTGACGACAGT 58.372 42.857 16.02 0.00 45.04 3.55
203 204 3.673746 TTCTTTGTTTGCTGACGACAG 57.326 42.857 10.66 10.66 45.91 3.51
204 205 3.687212 TCTTTCTTTGTTTGCTGACGACA 59.313 39.130 0.00 0.00 0.00 4.35
205 206 4.273005 TCTTTCTTTGTTTGCTGACGAC 57.727 40.909 0.00 0.00 0.00 4.34
206 207 4.955925 TTCTTTCTTTGTTTGCTGACGA 57.044 36.364 0.00 0.00 0.00 4.20
207 208 4.500477 CCTTTCTTTCTTTGTTTGCTGACG 59.500 41.667 0.00 0.00 0.00 4.35
208 209 5.410924 ACCTTTCTTTCTTTGTTTGCTGAC 58.589 37.500 0.00 0.00 0.00 3.51
209 210 5.659440 ACCTTTCTTTCTTTGTTTGCTGA 57.341 34.783 0.00 0.00 0.00 4.26
210 211 6.019559 GCTAACCTTTCTTTCTTTGTTTGCTG 60.020 38.462 0.00 0.00 33.68 4.41
211 212 6.042777 GCTAACCTTTCTTTCTTTGTTTGCT 58.957 36.000 0.00 0.00 33.68 3.91
212 213 5.810074 TGCTAACCTTTCTTTCTTTGTTTGC 59.190 36.000 0.00 0.00 35.84 3.68
213 214 6.019559 GCTGCTAACCTTTCTTTCTTTGTTTG 60.020 38.462 0.00 0.00 0.00 2.93
214 215 6.042777 GCTGCTAACCTTTCTTTCTTTGTTT 58.957 36.000 0.00 0.00 0.00 2.83
215 216 5.451937 GGCTGCTAACCTTTCTTTCTTTGTT 60.452 40.000 0.00 0.00 0.00 2.83
216 217 4.038042 GGCTGCTAACCTTTCTTTCTTTGT 59.962 41.667 0.00 0.00 0.00 2.83
217 218 4.550422 GGCTGCTAACCTTTCTTTCTTTG 58.450 43.478 0.00 0.00 0.00 2.77
218 219 3.574396 GGGCTGCTAACCTTTCTTTCTTT 59.426 43.478 0.00 0.00 0.00 2.52
219 220 3.157881 GGGCTGCTAACCTTTCTTTCTT 58.842 45.455 0.00 0.00 0.00 2.52
220 221 2.108250 TGGGCTGCTAACCTTTCTTTCT 59.892 45.455 0.00 0.00 0.00 2.52
221 222 2.489722 CTGGGCTGCTAACCTTTCTTTC 59.510 50.000 0.00 0.00 0.00 2.62
222 223 2.158460 ACTGGGCTGCTAACCTTTCTTT 60.158 45.455 0.00 0.00 0.00 2.52
223 224 1.425448 ACTGGGCTGCTAACCTTTCTT 59.575 47.619 0.00 0.00 0.00 2.52
224 225 1.068121 ACTGGGCTGCTAACCTTTCT 58.932 50.000 0.00 0.00 0.00 2.52
225 226 2.781681 TACTGGGCTGCTAACCTTTC 57.218 50.000 0.00 0.00 0.00 2.62
226 227 3.181433 ACTTTACTGGGCTGCTAACCTTT 60.181 43.478 0.00 0.00 0.00 3.11
227 228 2.375509 ACTTTACTGGGCTGCTAACCTT 59.624 45.455 0.00 0.00 0.00 3.50
228 229 1.985895 ACTTTACTGGGCTGCTAACCT 59.014 47.619 0.00 0.00 0.00 3.50
229 230 2.491675 ACTTTACTGGGCTGCTAACC 57.508 50.000 0.00 0.00 0.00 2.85
230 231 3.057526 CCAAACTTTACTGGGCTGCTAAC 60.058 47.826 0.00 0.00 0.00 2.34
231 232 3.153919 CCAAACTTTACTGGGCTGCTAA 58.846 45.455 0.00 0.00 0.00 3.09
238 239 0.879090 GCCGTCCAAACTTTACTGGG 59.121 55.000 0.00 0.00 33.19 4.45
249 250 1.743321 CTTTTTGCTGGGCCGTCCAA 61.743 55.000 0.00 0.00 46.51 3.53
265 266 2.768253 TGTCATGATGCGTCTCCTTT 57.232 45.000 7.58 0.00 0.00 3.11
273 274 4.201551 GCAAGTTCAAATTGTCATGATGCG 60.202 41.667 0.00 0.00 0.00 4.73
276 277 5.375417 TCGCAAGTTCAAATTGTCATGAT 57.625 34.783 0.00 0.00 39.48 2.45
289 290 1.235281 GGTTGTCCCCTCGCAAGTTC 61.235 60.000 0.00 0.00 39.48 3.01
325 326 0.976073 GTTGGGGATCGGGAGTCTGA 60.976 60.000 0.00 0.00 0.00 3.27
333 334 4.418328 TTGGGCGTTGGGGATCGG 62.418 66.667 0.00 0.00 0.00 4.18
347 348 0.963962 ACAGCTGCAGATTTGGTTGG 59.036 50.000 20.43 0.00 0.00 3.77
350 351 1.072806 TCTCACAGCTGCAGATTTGGT 59.927 47.619 20.43 2.03 0.00 3.67
351 352 1.738350 CTCTCACAGCTGCAGATTTGG 59.262 52.381 20.43 8.98 0.00 3.28
375 376 3.864686 CTGGTCATTTCGGCGCGG 61.865 66.667 8.83 8.94 0.00 6.46
376 377 4.520846 GCTGGTCATTTCGGCGCG 62.521 66.667 0.00 0.00 0.00 6.86
693 720 2.260088 TATGCCGGGGGTTGCTGTAC 62.260 60.000 2.18 0.00 0.00 2.90
813 855 3.078837 GTTGAACTTGGGCGGAATAGAA 58.921 45.455 0.00 0.00 0.00 2.10
963 1020 2.547218 GGTCTCCGAGCAGTAAACACAA 60.547 50.000 0.00 0.00 0.00 3.33
1002 1059 3.402628 TTTGTAGCCTCTGTTGAGACC 57.597 47.619 0.00 0.00 42.73 3.85
1003 1060 5.725362 AGTATTTGTAGCCTCTGTTGAGAC 58.275 41.667 0.00 0.00 42.73 3.36
1176 1253 4.695455 TGGAAAATCTGAAAGTGGTCGATC 59.305 41.667 0.00 0.00 33.76 3.69
1195 1278 0.842030 ACACCATCCTCTGCCTGGAA 60.842 55.000 0.00 0.00 37.13 3.53
1254 1347 3.555966 ACAGTCCACCTTTCTTTTCCAG 58.444 45.455 0.00 0.00 0.00 3.86
1588 1717 5.802451 AGCAATAAGTATATGTGAGCGATCG 59.198 40.000 11.69 11.69 0.00 3.69
1687 1823 6.763715 TGGCTATAAGTTGGTCCATCTAAT 57.236 37.500 2.77 0.00 0.00 1.73
1748 1884 7.715249 TGATTTGGTATTTTCGAGGATAGAAGG 59.285 37.037 0.00 0.00 29.57 3.46
1943 2110 2.592102 AACAATCACATGCAGGAGGT 57.408 45.000 4.84 0.00 0.00 3.85
2027 2194 9.825972 CAACAAAAAGTGACACTAGGTATTATG 57.174 33.333 8.91 3.08 0.00 1.90
2084 2251 5.375417 AAACTCATTCATCGTCATGCAAA 57.625 34.783 0.00 0.00 0.00 3.68
2246 2430 9.448438 TTGTGAGCAATAGATGTGTTATAAGTT 57.552 29.630 0.00 0.00 0.00 2.66
2361 2556 6.042143 CAGGCAATAAATTCGGCAATAAAGT 58.958 36.000 0.00 0.00 0.00 2.66
2370 2565 5.567138 AAGAAGTCAGGCAATAAATTCGG 57.433 39.130 0.00 0.00 0.00 4.30
2412 2616 3.603532 TCAGCTCCATTTTCAGCAGTAG 58.396 45.455 0.00 0.00 38.18 2.57
2465 2673 3.390639 TGTTGAACCATTTCAGCCCATTT 59.609 39.130 0.00 0.00 42.79 2.32
2493 2701 9.524106 TTCGCAAACTATATTCGAAAGATCTTA 57.476 29.630 8.75 0.00 41.60 2.10
2502 2710 7.310072 TCCAAATTTCGCAAACTATATTCGA 57.690 32.000 0.00 0.00 0.00 3.71
2503 2711 8.560576 AATCCAAATTTCGCAAACTATATTCG 57.439 30.769 0.00 0.00 0.00 3.34
2545 2754 9.330063 ACATTGGCCACAAGATATATAATATCG 57.670 33.333 3.88 0.00 40.49 2.92
2548 2757 7.833682 CCCACATTGGCCACAAGATATATAATA 59.166 37.037 3.88 0.00 40.49 0.98
2549 2758 6.664816 CCCACATTGGCCACAAGATATATAAT 59.335 38.462 3.88 0.00 40.49 1.28
2550 2759 6.009589 CCCACATTGGCCACAAGATATATAA 58.990 40.000 3.88 0.00 40.49 0.98
2551 2760 5.074377 ACCCACATTGGCCACAAGATATATA 59.926 40.000 3.88 0.00 40.49 0.86
2560 2771 1.304052 GCTACCCACATTGGCCACA 60.304 57.895 3.88 0.00 35.79 4.17
2562 2773 0.683828 CATGCTACCCACATTGGCCA 60.684 55.000 0.00 0.00 35.79 5.36
2600 2811 4.836175 TGTATGAATCCCTATAGCCGAACA 59.164 41.667 0.00 0.00 0.00 3.18
2717 2929 4.280174 GGAGGAGTTTCGGCATACAGTATA 59.720 45.833 0.00 0.00 0.00 1.47
2721 2933 1.473434 GGGAGGAGTTTCGGCATACAG 60.473 57.143 0.00 0.00 0.00 2.74
2734 2946 2.089980 CAAGCAAACTCATGGGAGGAG 58.910 52.381 0.00 0.00 45.81 3.69
2811 3023 3.380320 ACGTGAATGATGAGACCGATGTA 59.620 43.478 0.00 0.00 0.00 2.29
2817 3029 1.473434 GGGGACGTGAATGATGAGACC 60.473 57.143 0.00 0.00 0.00 3.85
2832 3044 2.171659 ACAAATTTGTTTGGTGGGGGAC 59.828 45.455 18.13 0.00 38.47 4.46
2859 3071 5.175673 GCAACAAAGTAAAGCCATCAGTTTC 59.824 40.000 0.00 0.00 0.00 2.78
2883 3095 7.271511 GCTATATCTCCTGAGAATACCAATGG 58.728 42.308 0.00 0.00 41.36 3.16
3271 3483 3.391296 ACACAGTGTATGGACAAGAGGTT 59.609 43.478 3.69 0.00 37.31 3.50
3303 3515 9.935682 TGAATGAATAGAAAATCAAATAGACGC 57.064 29.630 0.00 0.00 0.00 5.19
3325 3537 9.747898 TTCATTTGTTAGTAACCCACTATGAAT 57.252 29.630 10.51 0.00 39.51 2.57
3326 3538 9.005777 GTTCATTTGTTAGTAACCCACTATGAA 57.994 33.333 10.51 13.13 39.51 2.57
3327 3539 8.158132 TGTTCATTTGTTAGTAACCCACTATGA 58.842 33.333 10.51 8.82 39.51 2.15
3331 3543 6.362248 AGTGTTCATTTGTTAGTAACCCACT 58.638 36.000 10.51 7.83 41.62 4.00
3332 3544 6.628919 AGTGTTCATTTGTTAGTAACCCAC 57.371 37.500 10.51 6.04 0.00 4.61
3333 3545 6.017770 CGAAGTGTTCATTTGTTAGTAACCCA 60.018 38.462 10.51 0.00 0.00 4.51
3357 3634 2.846193 TCTTCACCTGGAGAAAAACCG 58.154 47.619 7.94 0.00 0.00 4.44
3395 3672 3.182572 GCGACAAACTCAGTGACAACTAG 59.817 47.826 0.00 0.00 33.79 2.57
3406 3683 5.181056 ACATTAATGTGATGCGACAAACTCA 59.819 36.000 20.19 0.00 40.03 3.41


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

AutoCloner maintained by Alex Coulton.