Multiple sequence alignment - TraesCS1B01G225700

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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 TraesCS1B01G225700 chr1B 100.000 3475 0 0 1 3475 405527198 405523724 0.000000e+00 6418.0
1 TraesCS1B01G225700 chr1B 79.942 344 58 5 1846 2179 406037241 406037583 3.470000e-60 243.0
2 TraesCS1B01G225700 chr1B 87.342 79 10 0 1246 1324 405673634 405673556 1.330000e-14 91.6
3 TraesCS1B01G225700 chr1D 91.709 2581 115 50 169 2704 300327770 300325244 0.000000e+00 3489.0
4 TraesCS1B01G225700 chr1D 93.380 710 40 7 2769 3475 300325246 300324541 0.000000e+00 1044.0
5 TraesCS1B01G225700 chr1D 78.488 344 63 5 1846 2179 300859829 300860171 7.550000e-52 215.0
6 TraesCS1B01G225700 chr1A 89.109 1414 75 33 169 1527 374691636 374690247 0.000000e+00 1685.0
7 TraesCS1B01G225700 chr1A 91.753 1152 55 16 1584 2704 374690241 374689099 0.000000e+00 1565.0
8 TraesCS1B01G225700 chr1A 89.733 711 57 9 2769 3475 374689101 374688403 0.000000e+00 894.0
9 TraesCS1B01G225700 chr1A 79.651 344 59 5 1846 2179 375468980 375469322 1.610000e-58 237.0
10 TraesCS1B01G225700 chr1A 94.286 70 4 0 2702 2771 108743 108812 1.320000e-19 108.0
11 TraesCS1B01G225700 chr1A 94.286 70 4 0 2702 2771 125799 125868 1.320000e-19 108.0
12 TraesCS1B01G225700 chr1A 94.286 70 4 0 2702 2771 256337 256406 1.320000e-19 108.0
13 TraesCS1B01G225700 chr6D 79.365 504 88 11 1684 2173 15551133 15550632 1.190000e-89 340.0
14 TraesCS1B01G225700 chr6D 79.477 497 86 11 1684 2166 15586351 15585857 4.300000e-89 339.0
15 TraesCS1B01G225700 chr6D 78.571 504 94 10 1683 2173 15640543 15641045 1.560000e-83 320.0
16 TraesCS1B01G225700 chr6A 79.477 497 86 11 1684 2166 16338203 16338697 4.300000e-89 339.0
17 TraesCS1B01G225700 chrUn 78.926 503 83 15 1684 2166 319197530 319197031 1.560000e-83 320.0
18 TraesCS1B01G225700 chrUn 85.507 207 28 2 1684 1889 441168988 441168783 7.550000e-52 215.0
19 TraesCS1B01G225700 chrUn 94.286 70 4 0 2702 2771 199901481 199901550 1.320000e-19 108.0
20 TraesCS1B01G225700 chrUn 94.286 70 4 0 2702 2771 363990723 363990654 1.320000e-19 108.0
21 TraesCS1B01G225700 chrUn 94.286 70 4 0 2702 2771 370056175 370056244 1.320000e-19 108.0
22 TraesCS1B01G225700 chrUn 94.286 70 4 0 2702 2771 382940337 382940268 1.320000e-19 108.0
23 TraesCS1B01G225700 chr6B 78.427 496 93 9 1684 2166 27485728 27485234 9.370000e-81 311.0
24 TraesCS1B01G225700 chr6B 78.226 496 94 10 1684 2166 27532318 27531824 4.360000e-79 305.0
25 TraesCS1B01G225700 chr6B 78.024 496 95 9 1684 2166 27419528 27419034 2.030000e-77 300.0
26 TraesCS1B01G225700 chr6B 77.996 509 88 17 1683 2173 27669232 27669734 7.290000e-77 298.0
27 TraesCS1B01G225700 chr4B 77.134 328 63 10 75 396 561516393 561516714 2.760000e-41 180.0
28 TraesCS1B01G225700 chr3D 90.517 116 9 2 1414 1528 391736 391622 6.010000e-33 152.0
29 TraesCS1B01G225700 chr3D 87.826 115 14 0 1417 1531 357384 357270 6.050000e-28 135.0
30 TraesCS1B01G225700 chr3D 83.333 114 18 1 1414 1527 598476610 598476722 1.710000e-18 104.0
31 TraesCS1B01G225700 chr3B 88.793 116 11 2 1414 1528 5802830 5802716 1.300000e-29 141.0
32 TraesCS1B01G225700 chr5D 94.286 70 4 0 2702 2771 18873120 18873189 1.320000e-19 108.0
33 TraesCS1B01G225700 chr5D 94.286 70 4 0 2702 2771 18889080 18889149 1.320000e-19 108.0
34 TraesCS1B01G225700 chr2A 82.203 118 19 2 1408 1524 706207812 706207928 2.210000e-17 100.0


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 TraesCS1B01G225700 chr1B 405523724 405527198 3474 True 6418.000000 6418 100.000000 1 3475 1 chr1B.!!$R1 3474
1 TraesCS1B01G225700 chr1D 300324541 300327770 3229 True 2266.500000 3489 92.544500 169 3475 2 chr1D.!!$R1 3306
2 TraesCS1B01G225700 chr1A 374688403 374691636 3233 True 1381.333333 1685 90.198333 169 3475 3 chr1A.!!$R1 3306
3 TraesCS1B01G225700 chr6D 15550632 15551133 501 True 340.000000 340 79.365000 1684 2173 1 chr6D.!!$R1 489
4 TraesCS1B01G225700 chr6D 15640543 15641045 502 False 320.000000 320 78.571000 1683 2173 1 chr6D.!!$F1 490
5 TraesCS1B01G225700 chr6B 27669232 27669734 502 False 298.000000 298 77.996000 1683 2173 1 chr6B.!!$F1 490

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
876 912 0.177836 CCCATGTGAGCATACGACCA 59.822 55.0 0.0 0.0 33.30 4.02 F
1343 1396 0.463654 GCCTGCCGTGTGGATTCATA 60.464 55.0 0.0 0.0 37.49 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 2350 0.389391 ATGATTTCGATCGGCCGAGT 59.611 50.0 33.87 20.92 39.90 4.18 R
3144 3259 0.833409 AGAACGTACCCCCTCCGTTT 60.833 55.0 0.00 0.00 44.04 3.60 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 4.244802 GAGTCCTCGCGAGCTCGG 62.245 72.222 35.10 24.78 40.23 4.63
19 20 4.838486 GTCCTCGCGAGCTCGGTG 62.838 72.222 35.10 23.75 40.23 4.94
22 23 4.544689 CTCGCGAGCTCGGTGGAG 62.545 72.222 35.10 20.63 43.46 3.86
24 25 4.544689 CGCGAGCTCGGTGGAGAG 62.545 72.222 35.10 7.44 43.27 3.20
25 26 3.134792 GCGAGCTCGGTGGAGAGA 61.135 66.667 35.10 0.00 43.27 3.10
26 27 2.795297 CGAGCTCGGTGGAGAGAC 59.205 66.667 28.40 0.00 43.27 3.36
27 28 2.795297 GAGCTCGGTGGAGAGACG 59.205 66.667 0.00 0.00 43.27 4.18
28 29 2.752238 AGCTCGGTGGAGAGACGG 60.752 66.667 0.00 0.00 43.27 4.79
29 30 4.500116 GCTCGGTGGAGAGACGGC 62.500 72.222 0.00 0.00 43.27 5.68
30 31 4.180946 CTCGGTGGAGAGACGGCG 62.181 72.222 4.80 4.80 43.27 6.46
34 35 4.803426 GTGGAGAGACGGCGCCAG 62.803 72.222 28.98 21.29 0.00 4.85
45 46 3.838795 GCGCCAGCGACGTACTTG 61.839 66.667 17.53 0.00 42.83 3.16
46 47 2.430244 CGCCAGCGACGTACTTGT 60.430 61.111 6.06 0.00 42.83 3.16
47 48 2.019951 CGCCAGCGACGTACTTGTT 61.020 57.895 6.06 0.00 42.83 2.83
48 49 1.491563 GCCAGCGACGTACTTGTTG 59.508 57.895 0.00 0.00 0.00 3.33
49 50 0.942410 GCCAGCGACGTACTTGTTGA 60.942 55.000 0.00 0.00 0.00 3.18
50 51 1.710013 CCAGCGACGTACTTGTTGAT 58.290 50.000 0.00 0.00 0.00 2.57
51 52 1.390123 CCAGCGACGTACTTGTTGATG 59.610 52.381 0.00 0.78 38.96 3.07
52 53 2.058798 CAGCGACGTACTTGTTGATGT 58.941 47.619 0.00 0.00 35.43 3.06
53 54 2.090658 CAGCGACGTACTTGTTGATGTC 59.909 50.000 0.00 0.00 35.43 3.06
55 56 1.057285 CGACGTACTTGTTGATGTCGC 59.943 52.381 3.96 0.00 41.95 5.19
56 57 2.055838 GACGTACTTGTTGATGTCGCA 58.944 47.619 0.00 0.00 0.00 5.10
57 58 2.058798 ACGTACTTGTTGATGTCGCAG 58.941 47.619 0.00 0.00 0.00 5.18
58 59 2.287970 ACGTACTTGTTGATGTCGCAGA 60.288 45.455 0.00 0.00 0.00 4.26
69 70 3.066190 TCGCAGACGGTGTAGGGG 61.066 66.667 0.00 0.00 40.63 4.79
70 71 4.143333 CGCAGACGGTGTAGGGGG 62.143 72.222 0.00 0.00 34.97 5.40
71 72 2.682494 GCAGACGGTGTAGGGGGA 60.682 66.667 0.00 0.00 0.00 4.81
72 73 2.722201 GCAGACGGTGTAGGGGGAG 61.722 68.421 0.00 0.00 0.00 4.30
73 74 2.058595 CAGACGGTGTAGGGGGAGG 61.059 68.421 0.00 0.00 0.00 4.30
74 75 2.243888 AGACGGTGTAGGGGGAGGA 61.244 63.158 0.00 0.00 0.00 3.71
75 76 1.757340 GACGGTGTAGGGGGAGGAG 60.757 68.421 0.00 0.00 0.00 3.69
76 77 2.444140 CGGTGTAGGGGGAGGAGG 60.444 72.222 0.00 0.00 0.00 4.30
77 78 3.005148 CGGTGTAGGGGGAGGAGGA 62.005 68.421 0.00 0.00 0.00 3.71
78 79 1.075151 GGTGTAGGGGGAGGAGGAG 60.075 68.421 0.00 0.00 0.00 3.69
79 80 1.591280 GGTGTAGGGGGAGGAGGAGA 61.591 65.000 0.00 0.00 0.00 3.71
80 81 0.397394 GTGTAGGGGGAGGAGGAGAC 60.397 65.000 0.00 0.00 0.00 3.36
81 82 1.152715 GTAGGGGGAGGAGGAGACG 60.153 68.421 0.00 0.00 0.00 4.18
82 83 1.308481 TAGGGGGAGGAGGAGACGA 60.308 63.158 0.00 0.00 0.00 4.20
83 84 1.643475 TAGGGGGAGGAGGAGACGAC 61.643 65.000 0.00 0.00 0.00 4.34
84 85 2.829458 GGGGAGGAGGAGACGACG 60.829 72.222 0.00 0.00 0.00 5.12
85 86 2.829458 GGGAGGAGGAGACGACGG 60.829 72.222 0.00 0.00 0.00 4.79
86 87 2.829458 GGAGGAGGAGACGACGGG 60.829 72.222 0.00 0.00 0.00 5.28
87 88 2.271497 GAGGAGGAGACGACGGGA 59.729 66.667 0.00 0.00 0.00 5.14
88 89 1.378250 GAGGAGGAGACGACGGGAA 60.378 63.158 0.00 0.00 0.00 3.97
89 90 1.378124 GAGGAGGAGACGACGGGAAG 61.378 65.000 0.00 0.00 0.00 3.46
90 91 2.416432 GGAGGAGACGACGGGAAGG 61.416 68.421 0.00 0.00 0.00 3.46
91 92 1.378250 GAGGAGACGACGGGAAGGA 60.378 63.158 0.00 0.00 0.00 3.36
92 93 1.378124 GAGGAGACGACGGGAAGGAG 61.378 65.000 0.00 0.00 0.00 3.69
93 94 2.416432 GGAGACGACGGGAAGGAGG 61.416 68.421 0.00 0.00 0.00 4.30
94 95 2.362632 AGACGACGGGAAGGAGGG 60.363 66.667 0.00 0.00 0.00 4.30
95 96 3.459063 GACGACGGGAAGGAGGGG 61.459 72.222 0.00 0.00 0.00 4.79
96 97 3.951769 GACGACGGGAAGGAGGGGA 62.952 68.421 0.00 0.00 0.00 4.81
97 98 2.444140 CGACGGGAAGGAGGGGAT 60.444 66.667 0.00 0.00 0.00 3.85
98 99 2.797278 CGACGGGAAGGAGGGGATG 61.797 68.421 0.00 0.00 0.00 3.51
99 100 2.366972 ACGGGAAGGAGGGGATGG 60.367 66.667 0.00 0.00 0.00 3.51
100 101 3.878667 CGGGAAGGAGGGGATGGC 61.879 72.222 0.00 0.00 0.00 4.40
101 102 3.878667 GGGAAGGAGGGGATGGCG 61.879 72.222 0.00 0.00 0.00 5.69
102 103 2.768344 GGAAGGAGGGGATGGCGA 60.768 66.667 0.00 0.00 0.00 5.54
103 104 2.150051 GGAAGGAGGGGATGGCGAT 61.150 63.158 0.00 0.00 0.00 4.58
104 105 1.072159 GAAGGAGGGGATGGCGATG 59.928 63.158 0.00 0.00 0.00 3.84
105 106 2.403132 GAAGGAGGGGATGGCGATGG 62.403 65.000 0.00 0.00 0.00 3.51
106 107 2.849162 GGAGGGGATGGCGATGGA 60.849 66.667 0.00 0.00 0.00 3.41
107 108 2.427753 GAGGGGATGGCGATGGAC 59.572 66.667 0.00 0.00 0.00 4.02
108 109 3.521529 GAGGGGATGGCGATGGACG 62.522 68.421 0.00 0.00 45.66 4.79
117 118 2.584418 CGATGGACGCTGAGGCTG 60.584 66.667 0.00 0.00 36.09 4.85
118 119 2.894387 GATGGACGCTGAGGCTGC 60.894 66.667 0.00 0.00 36.09 5.25
119 120 3.382803 GATGGACGCTGAGGCTGCT 62.383 63.158 0.00 0.00 36.09 4.24
120 121 3.677284 ATGGACGCTGAGGCTGCTG 62.677 63.158 0.00 0.00 36.09 4.41
122 123 4.756458 GACGCTGAGGCTGCTGCT 62.756 66.667 15.64 1.41 39.59 4.24
138 139 4.200283 CTGCGGCGGAGAGGAGTC 62.200 72.222 24.84 0.00 0.00 3.36
141 142 3.578272 CGGCGGAGAGGAGTCGAG 61.578 72.222 0.00 0.00 37.72 4.04
142 143 2.124653 GGCGGAGAGGAGTCGAGA 60.125 66.667 0.00 0.00 0.00 4.04
143 144 2.184167 GGCGGAGAGGAGTCGAGAG 61.184 68.421 0.00 0.00 0.00 3.20
144 145 1.450669 GCGGAGAGGAGTCGAGAGT 60.451 63.158 0.00 0.00 0.00 3.24
145 146 0.179078 GCGGAGAGGAGTCGAGAGTA 60.179 60.000 0.00 0.00 0.00 2.59
146 147 1.860676 CGGAGAGGAGTCGAGAGTAG 58.139 60.000 0.00 0.00 0.00 2.57
147 148 1.409790 CGGAGAGGAGTCGAGAGTAGA 59.590 57.143 0.00 0.00 0.00 2.59
148 149 2.800629 CGGAGAGGAGTCGAGAGTAGAC 60.801 59.091 0.00 0.00 38.81 2.59
149 150 2.466846 GAGAGGAGTCGAGAGTAGACG 58.533 57.143 0.00 0.00 42.97 4.18
150 151 2.099592 GAGAGGAGTCGAGAGTAGACGA 59.900 54.545 0.00 0.00 42.97 4.20
153 154 4.950996 GTCGAGAGTAGACGACGC 57.049 61.111 0.00 0.00 46.39 5.19
154 155 1.347907 GTCGAGAGTAGACGACGCC 59.652 63.158 0.00 0.00 46.39 5.68
155 156 2.163390 TCGAGAGTAGACGACGCCG 61.163 63.158 0.00 0.00 42.50 6.46
156 157 2.708255 GAGAGTAGACGACGCCGG 59.292 66.667 0.00 0.00 40.78 6.13
157 158 2.046507 AGAGTAGACGACGCCGGT 60.047 61.111 1.90 0.00 40.78 5.28
158 159 2.099831 GAGTAGACGACGCCGGTG 59.900 66.667 14.93 14.93 40.78 4.94
159 160 3.392595 GAGTAGACGACGCCGGTGG 62.393 68.421 21.14 6.53 40.78 4.61
170 171 4.135153 CCGGTGGCGTGGAGAGAG 62.135 72.222 0.00 0.00 0.00 3.20
171 172 4.135153 CGGTGGCGTGGAGAGAGG 62.135 72.222 0.00 0.00 0.00 3.69
172 173 4.459089 GGTGGCGTGGAGAGAGGC 62.459 72.222 0.00 0.00 0.00 4.70
173 174 3.695606 GTGGCGTGGAGAGAGGCA 61.696 66.667 0.00 0.00 38.13 4.75
174 175 3.385384 TGGCGTGGAGAGAGGCAG 61.385 66.667 0.00 0.00 35.49 4.85
175 176 4.828925 GGCGTGGAGAGAGGCAGC 62.829 72.222 0.00 0.00 0.00 5.25
176 177 4.074526 GCGTGGAGAGAGGCAGCA 62.075 66.667 0.00 0.00 0.00 4.41
177 178 2.183811 CGTGGAGAGAGGCAGCAG 59.816 66.667 0.00 0.00 0.00 4.24
198 199 1.868498 CCGCTAACACTTCGGTTTCAA 59.132 47.619 0.00 0.00 38.47 2.69
199 200 2.288458 CCGCTAACACTTCGGTTTCAAA 59.712 45.455 0.00 0.00 38.47 2.69
200 201 3.242804 CCGCTAACACTTCGGTTTCAAAA 60.243 43.478 0.00 0.00 38.47 2.44
201 202 4.344448 CGCTAACACTTCGGTTTCAAAAA 58.656 39.130 0.00 0.00 32.29 1.94
234 237 2.028876 TCGATTACTCGGCTGATTGGA 58.971 47.619 0.00 0.00 45.10 3.53
253 256 1.344763 GATAAGGTGAGACGGGGATGG 59.655 57.143 0.00 0.00 0.00 3.51
265 269 1.002888 CGGGGATGGAGATGGATGAAG 59.997 57.143 0.00 0.00 0.00 3.02
276 280 4.564799 AGATGGATGAAGAGAATGAGGGA 58.435 43.478 0.00 0.00 0.00 4.20
312 316 3.055602 GTGAAGTGGGGTTACGTCCTATT 60.056 47.826 0.00 0.00 0.00 1.73
321 325 3.498397 GGTTACGTCCTATTCGTCGGATA 59.502 47.826 0.00 0.00 41.72 2.59
353 357 6.367695 AGACGATCAAAAACGACATATGACAA 59.632 34.615 10.38 0.00 0.00 3.18
372 376 5.876460 TGACAAGTACATCATCATCACCAAG 59.124 40.000 0.00 0.00 0.00 3.61
407 411 9.976776 TTATAGGAGTAGAGAAGAGAAAGTGAA 57.023 33.333 0.00 0.00 0.00 3.18
428 440 1.179152 TTGAGACGGGCTATCGTTGA 58.821 50.000 0.00 0.00 43.96 3.18
505 524 3.181540 CGATGCGACGATGAATTATCACC 60.182 47.826 0.00 0.00 38.69 4.02
521 540 1.140852 TCACCCTAGAAATGCCGGATG 59.859 52.381 5.05 0.00 0.00 3.51
623 653 1.477685 ATGGTGGGTCGTTCGTTCCT 61.478 55.000 8.30 0.00 0.00 3.36
683 713 3.717400 TCTCAGCTAATCCACATCGAC 57.283 47.619 0.00 0.00 0.00 4.20
876 912 0.177836 CCCATGTGAGCATACGACCA 59.822 55.000 0.00 0.00 33.30 4.02
882 918 0.817654 TGAGCATACGACCAGTGAGG 59.182 55.000 0.00 0.00 45.67 3.86
883 919 0.528684 GAGCATACGACCAGTGAGGC 60.529 60.000 0.00 0.00 43.14 4.70
884 920 1.218047 GCATACGACCAGTGAGGCA 59.782 57.895 0.00 0.00 43.14 4.75
885 921 1.084370 GCATACGACCAGTGAGGCAC 61.084 60.000 0.00 0.00 43.14 5.01
886 922 0.802222 CATACGACCAGTGAGGCACG 60.802 60.000 0.00 0.00 43.14 5.34
887 923 2.558554 ATACGACCAGTGAGGCACGC 62.559 60.000 0.00 0.00 43.14 5.34
888 924 4.662961 CGACCAGTGAGGCACGCA 62.663 66.667 0.00 0.00 43.14 5.24
912 948 3.075005 GCCACAGCTCCTCCGGTA 61.075 66.667 0.00 0.00 35.50 4.02
941 977 3.940640 CCGTTGCCGATGCCGATG 61.941 66.667 0.00 0.00 38.22 3.84
943 979 2.513666 GTTGCCGATGCCGATGGA 60.514 61.111 0.00 0.00 38.22 3.41
944 980 1.893808 GTTGCCGATGCCGATGGAT 60.894 57.895 0.00 0.00 38.22 3.41
945 981 1.893335 TTGCCGATGCCGATGGATG 60.893 57.895 0.00 0.00 38.22 3.51
947 983 2.427320 CCGATGCCGATGGATGGT 59.573 61.111 0.00 0.00 38.22 3.55
1152 1204 0.898320 GCTACTCTCTGTCAAGGCCA 59.102 55.000 5.01 0.00 0.00 5.36
1339 1392 2.672996 GTGCCTGCCGTGTGGATT 60.673 61.111 0.00 0.00 37.49 3.01
1343 1396 0.463654 GCCTGCCGTGTGGATTCATA 60.464 55.000 0.00 0.00 37.49 2.15
1379 1439 5.638596 TGCTCTCTGTTCTAATGTCGTTA 57.361 39.130 0.00 0.00 0.00 3.18
1451 1511 2.025418 GCACGTGAACCAGTACCCG 61.025 63.158 22.23 0.00 0.00 5.28
1475 1535 2.284625 TCCATGACCTCCTGCGGT 60.285 61.111 0.00 0.00 40.80 5.68
1592 1656 6.035843 CGGACCTTGGTGAAAATTGAATATG 58.964 40.000 0.00 0.00 0.00 1.78
1593 1657 6.127758 CGGACCTTGGTGAAAATTGAATATGA 60.128 38.462 0.00 0.00 0.00 2.15
1604 1668 8.738106 TGAAAATTGAATATGATACACTGCACA 58.262 29.630 0.00 0.00 0.00 4.57
1624 1688 4.991056 CACAACACACAGTTATCAGCTAGT 59.009 41.667 0.00 0.00 38.74 2.57
1625 1689 6.156519 CACAACACACAGTTATCAGCTAGTA 58.843 40.000 0.00 0.00 38.74 1.82
1626 1690 6.089551 CACAACACACAGTTATCAGCTAGTAC 59.910 42.308 0.00 0.00 38.74 2.73
1627 1691 5.326200 ACACACAGTTATCAGCTAGTACC 57.674 43.478 0.00 0.00 0.00 3.34
1628 1692 4.770531 ACACACAGTTATCAGCTAGTACCA 59.229 41.667 0.00 0.00 0.00 3.25
1643 1707 2.438021 AGTACCACAGTGTGTTGACCAT 59.562 45.455 21.48 0.00 0.00 3.55
1646 1710 2.146342 CCACAGTGTGTTGACCATCTC 58.854 52.381 21.48 0.00 0.00 2.75
1651 1715 1.461127 GTGTGTTGACCATCTCGCTTC 59.539 52.381 0.00 0.00 0.00 3.86
1672 1736 1.128692 GTGCTTTCAGATACGGTGCAC 59.871 52.381 8.80 8.80 41.53 4.57
1673 1737 1.270571 TGCTTTCAGATACGGTGCACA 60.271 47.619 20.43 0.00 0.00 4.57
1694 1758 1.218047 CGACAAATCCTGCTCCGGA 59.782 57.895 2.93 2.93 37.50 5.14
1865 1929 2.991540 GTGCCCTGCAACTTCCCC 60.992 66.667 0.00 0.00 41.47 4.81
1996 2072 2.656069 CCAAGTCGGGGTCGTGGAT 61.656 63.158 0.00 0.00 33.51 3.41
1998 2074 2.656069 AAGTCGGGGTCGTGGATGG 61.656 63.158 0.00 0.00 37.69 3.51
2109 2185 1.898574 AAGAAGCTGGTGGCCAACG 60.899 57.895 17.89 12.35 43.05 4.10
2180 2266 0.965866 AGTTCAGCTGATCCGACCGA 60.966 55.000 19.04 0.00 0.00 4.69
2239 2333 4.486503 CTCTGGCCCCTCTGCTGC 62.487 72.222 0.00 0.00 0.00 5.25
2245 2339 3.854669 CCCCTCTGCTGCCTACGG 61.855 72.222 0.00 0.00 0.00 4.02
2253 2350 2.698274 TCTGCTGCCTACGGATTAATCA 59.302 45.455 17.07 0.00 0.00 2.57
2316 2414 1.078143 GCGTGGGATCAAGGAGCTT 60.078 57.895 0.00 0.00 0.00 3.74
2453 2560 5.211973 ACCATACATGAGATGACACTACCT 58.788 41.667 0.00 0.00 0.00 3.08
2599 2710 5.654497 CTTTGCCATTTCATTAGGGAGAAC 58.346 41.667 0.00 0.00 0.00 3.01
2610 2723 6.228258 TCATTAGGGAGAACAAAGTGTGTAC 58.772 40.000 0.00 0.00 40.60 2.90
2704 2817 1.886655 CGGCTTTGACCTAAAGGGCTT 60.887 52.381 2.95 0.00 45.91 4.35
2705 2818 1.546029 GGCTTTGACCTAAAGGGCTTG 59.454 52.381 2.95 0.00 45.91 4.01
2707 2820 2.229062 GCTTTGACCTAAAGGGCTTGTC 59.771 50.000 2.95 0.00 45.91 3.18
2708 2821 3.756117 CTTTGACCTAAAGGGCTTGTCT 58.244 45.455 2.95 0.00 45.91 3.41
2709 2822 3.418684 TTGACCTAAAGGGCTTGTCTC 57.581 47.619 2.95 0.00 45.91 3.36
2710 2823 2.334977 TGACCTAAAGGGCTTGTCTCA 58.665 47.619 2.95 0.00 45.91 3.27
2711 2824 2.708861 TGACCTAAAGGGCTTGTCTCAA 59.291 45.455 2.95 0.00 45.91 3.02
2712 2825 3.137544 TGACCTAAAGGGCTTGTCTCAAA 59.862 43.478 2.95 0.00 45.91 2.69
2713 2826 3.753797 GACCTAAAGGGCTTGTCTCAAAG 59.246 47.826 0.20 0.00 41.12 2.77
2714 2827 3.394606 ACCTAAAGGGCTTGTCTCAAAGA 59.605 43.478 0.20 0.00 40.27 2.52
2715 2828 4.043435 ACCTAAAGGGCTTGTCTCAAAGAT 59.957 41.667 0.20 0.00 40.27 2.40
2716 2829 5.012893 CCTAAAGGGCTTGTCTCAAAGATT 58.987 41.667 0.00 0.00 0.00 2.40
2717 2830 6.180472 CCTAAAGGGCTTGTCTCAAAGATTA 58.820 40.000 0.00 0.00 0.00 1.75
2718 2831 6.659242 CCTAAAGGGCTTGTCTCAAAGATTAA 59.341 38.462 0.00 0.00 0.00 1.40
2719 2832 6.581171 AAAGGGCTTGTCTCAAAGATTAAG 57.419 37.500 0.00 0.00 0.00 1.85
2720 2833 4.013050 AGGGCTTGTCTCAAAGATTAAGC 58.987 43.478 15.05 15.05 41.95 3.09
2723 2836 5.573337 GCTTGTCTCAAAGATTAAGCCAT 57.427 39.130 13.51 0.00 39.37 4.40
2724 2837 5.338365 GCTTGTCTCAAAGATTAAGCCATG 58.662 41.667 13.51 0.00 39.37 3.66
2725 2838 4.970662 TGTCTCAAAGATTAAGCCATGC 57.029 40.909 0.00 0.00 0.00 4.06
2726 2839 4.334552 TGTCTCAAAGATTAAGCCATGCA 58.665 39.130 0.00 0.00 0.00 3.96
2727 2840 4.951715 TGTCTCAAAGATTAAGCCATGCAT 59.048 37.500 0.00 0.00 0.00 3.96
2728 2841 5.163591 TGTCTCAAAGATTAAGCCATGCATG 60.164 40.000 20.19 20.19 0.00 4.06
2729 2842 4.951715 TCTCAAAGATTAAGCCATGCATGT 59.048 37.500 24.58 9.62 0.00 3.21
2730 2843 5.001237 TCAAAGATTAAGCCATGCATGTG 57.999 39.130 24.58 16.68 0.00 3.21
2731 2844 3.447918 AAGATTAAGCCATGCATGTGC 57.552 42.857 24.58 24.41 42.50 4.57
2744 2857 3.574284 GCATGTGCAAGTATGAACCAA 57.426 42.857 10.13 0.00 41.59 3.67
2745 2858 4.114058 GCATGTGCAAGTATGAACCAAT 57.886 40.909 10.13 0.00 41.59 3.16
2746 2859 4.497300 GCATGTGCAAGTATGAACCAATT 58.503 39.130 10.13 0.00 41.59 2.32
2747 2860 4.931002 GCATGTGCAAGTATGAACCAATTT 59.069 37.500 10.13 0.00 41.59 1.82
2748 2861 5.163933 GCATGTGCAAGTATGAACCAATTTG 60.164 40.000 10.13 0.00 41.59 2.32
2749 2862 5.781210 TGTGCAAGTATGAACCAATTTGA 57.219 34.783 0.00 0.00 33.74 2.69
2750 2863 6.154203 TGTGCAAGTATGAACCAATTTGAA 57.846 33.333 0.00 0.00 33.74 2.69
2751 2864 5.982516 TGTGCAAGTATGAACCAATTTGAAC 59.017 36.000 0.00 0.00 33.74 3.18
2752 2865 6.183360 TGTGCAAGTATGAACCAATTTGAACT 60.183 34.615 0.00 0.00 33.74 3.01
2753 2866 7.013750 TGTGCAAGTATGAACCAATTTGAACTA 59.986 33.333 0.00 0.00 33.74 2.24
2754 2867 7.865385 GTGCAAGTATGAACCAATTTGAACTAA 59.135 33.333 0.00 0.00 0.00 2.24
2755 2868 7.865385 TGCAAGTATGAACCAATTTGAACTAAC 59.135 33.333 0.00 0.00 0.00 2.34
2756 2869 7.865385 GCAAGTATGAACCAATTTGAACTAACA 59.135 33.333 0.00 0.00 0.00 2.41
2757 2870 9.743057 CAAGTATGAACCAATTTGAACTAACAA 57.257 29.630 0.00 0.00 0.00 2.83
2759 2872 9.744468 AGTATGAACCAATTTGAACTAACAAAC 57.256 29.630 0.00 0.00 41.49 2.93
2760 2873 9.744468 GTATGAACCAATTTGAACTAACAAACT 57.256 29.630 0.00 0.00 41.49 2.66
2761 2874 8.647143 ATGAACCAATTTGAACTAACAAACTG 57.353 30.769 0.00 0.00 41.49 3.16
2762 2875 7.607250 TGAACCAATTTGAACTAACAAACTGT 58.393 30.769 0.00 0.00 41.49 3.55
2763 2876 7.543868 TGAACCAATTTGAACTAACAAACTGTG 59.456 33.333 0.00 0.00 41.49 3.66
2764 2877 7.164230 ACCAATTTGAACTAACAAACTGTGA 57.836 32.000 0.00 0.00 41.49 3.58
2765 2878 7.607250 ACCAATTTGAACTAACAAACTGTGAA 58.393 30.769 0.00 0.00 41.49 3.18
2766 2879 8.257306 ACCAATTTGAACTAACAAACTGTGAAT 58.743 29.630 0.00 0.00 41.49 2.57
2767 2880 9.743057 CCAATTTGAACTAACAAACTGTGAATA 57.257 29.630 0.00 0.00 41.49 1.75
2769 2882 9.463443 AATTTGAACTAACAAACTGTGAATAGC 57.537 29.630 0.00 0.00 41.49 2.97
2770 2883 7.801716 TTGAACTAACAAACTGTGAATAGCT 57.198 32.000 0.00 0.00 0.00 3.32
2771 2884 7.189693 TGAACTAACAAACTGTGAATAGCTG 57.810 36.000 0.00 0.00 0.00 4.24
2772 2885 5.613358 ACTAACAAACTGTGAATAGCTGC 57.387 39.130 0.00 0.00 0.00 5.25
2795 2909 5.917447 GCTTTTTCTTGATGTTGGAGAAGAC 59.083 40.000 0.00 0.00 31.67 3.01
2801 2915 6.298361 TCTTGATGTTGGAGAAGACAATTGA 58.702 36.000 13.59 0.00 0.00 2.57
2835 2949 7.825331 TCAAGATATGACGAAAGATCCTAGT 57.175 36.000 0.00 0.00 31.50 2.57
2840 2954 9.303116 AGATATGACGAAAGATCCTAGTATTGT 57.697 33.333 0.00 0.00 0.00 2.71
2978 3093 2.093869 CGAGAAAGGGGGTCGACATTAA 60.094 50.000 18.91 0.00 35.70 1.40
3001 3116 2.101917 GCCATCCAACCCAATCATTCAG 59.898 50.000 0.00 0.00 0.00 3.02
3028 3143 1.472552 CCAAATCCGCACCGAGTATCA 60.473 52.381 0.00 0.00 33.17 2.15
3110 3225 7.772166 TGACACATCCAAGTTATACTACTCTG 58.228 38.462 0.00 0.00 0.00 3.35
3154 3269 3.449737 TCTTACACTATGAAACGGAGGGG 59.550 47.826 0.00 0.00 0.00 4.79
3175 3290 3.450578 GGTACGTTCTATCAAATCCGCA 58.549 45.455 0.00 0.00 0.00 5.69
3332 3448 6.456584 GCGGATATTCAGCTGATATTGTGATG 60.457 42.308 19.04 3.78 34.72 3.07
3431 3548 1.126488 TCTCTGATCTGCCCATCCAC 58.874 55.000 0.00 0.00 0.00 4.02
3465 3582 3.303593 GCATAATCATCACGAGCACCAAG 60.304 47.826 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.544689 CTCCACCGAGCTCGCGAG 62.545 72.222 31.37 31.37 38.18 5.03
7 8 4.544689 CTCTCCACCGAGCTCGCG 62.545 72.222 30.49 23.97 35.94 5.87
8 9 3.134792 TCTCTCCACCGAGCTCGC 61.135 66.667 30.49 0.00 35.94 5.03
9 10 2.795297 GTCTCTCCACCGAGCTCG 59.205 66.667 29.06 29.06 35.94 5.03
10 11 2.766400 CCGTCTCTCCACCGAGCTC 61.766 68.421 2.73 2.73 35.94 4.09
11 12 2.752238 CCGTCTCTCCACCGAGCT 60.752 66.667 0.00 0.00 35.94 4.09
12 13 4.500116 GCCGTCTCTCCACCGAGC 62.500 72.222 0.00 0.00 35.94 5.03
13 14 4.180946 CGCCGTCTCTCCACCGAG 62.181 72.222 0.00 0.00 37.48 4.63
17 18 4.803426 CTGGCGCCGTCTCTCCAC 62.803 72.222 23.90 0.00 0.00 4.02
28 29 3.838795 CAAGTACGTCGCTGGCGC 61.839 66.667 10.28 0.00 39.59 6.53
29 30 2.019951 AACAAGTACGTCGCTGGCG 61.020 57.895 8.80 8.80 41.35 5.69
30 31 0.942410 TCAACAAGTACGTCGCTGGC 60.942 55.000 0.00 0.00 0.00 4.85
31 32 1.390123 CATCAACAAGTACGTCGCTGG 59.610 52.381 0.00 0.00 0.00 4.85
32 33 2.058798 ACATCAACAAGTACGTCGCTG 58.941 47.619 0.00 0.00 0.00 5.18
33 34 2.325761 GACATCAACAAGTACGTCGCT 58.674 47.619 0.00 0.00 0.00 4.93
34 35 1.057285 CGACATCAACAAGTACGTCGC 59.943 52.381 0.00 0.00 39.62 5.19
35 36 1.057285 GCGACATCAACAAGTACGTCG 59.943 52.381 10.16 10.16 46.59 5.12
36 37 2.055838 TGCGACATCAACAAGTACGTC 58.944 47.619 0.00 0.00 0.00 4.34
37 38 2.058798 CTGCGACATCAACAAGTACGT 58.941 47.619 0.00 0.00 0.00 3.57
38 39 2.090658 GTCTGCGACATCAACAAGTACG 59.909 50.000 4.20 0.00 32.09 3.67
39 40 2.090658 CGTCTGCGACATCAACAAGTAC 59.909 50.000 8.91 0.00 41.33 2.73
40 41 2.324860 CGTCTGCGACATCAACAAGTA 58.675 47.619 8.91 0.00 41.33 2.24
41 42 1.139989 CGTCTGCGACATCAACAAGT 58.860 50.000 8.91 0.00 41.33 3.16
42 43 0.439985 CCGTCTGCGACATCAACAAG 59.560 55.000 8.91 0.00 41.33 3.16
43 44 0.249699 ACCGTCTGCGACATCAACAA 60.250 50.000 8.91 0.00 41.33 2.83
44 45 0.943835 CACCGTCTGCGACATCAACA 60.944 55.000 8.91 0.00 41.33 3.33
45 46 0.944311 ACACCGTCTGCGACATCAAC 60.944 55.000 8.91 0.00 41.33 3.18
46 47 0.599060 TACACCGTCTGCGACATCAA 59.401 50.000 8.91 0.00 41.33 2.57
47 48 0.170339 CTACACCGTCTGCGACATCA 59.830 55.000 8.91 0.00 41.33 3.07
48 49 0.525668 CCTACACCGTCTGCGACATC 60.526 60.000 8.91 0.00 41.33 3.06
49 50 1.511305 CCTACACCGTCTGCGACAT 59.489 57.895 8.91 0.00 41.33 3.06
50 51 2.632544 CCCTACACCGTCTGCGACA 61.633 63.158 8.91 0.00 41.33 4.35
51 52 2.181021 CCCTACACCGTCTGCGAC 59.819 66.667 0.00 0.00 41.33 5.19
52 53 3.066190 CCCCTACACCGTCTGCGA 61.066 66.667 0.00 0.00 41.33 5.10
53 54 4.143333 CCCCCTACACCGTCTGCG 62.143 72.222 0.00 0.00 37.95 5.18
54 55 2.682494 TCCCCCTACACCGTCTGC 60.682 66.667 0.00 0.00 0.00 4.26
55 56 2.058595 CCTCCCCCTACACCGTCTG 61.059 68.421 0.00 0.00 0.00 3.51
56 57 2.226149 CTCCTCCCCCTACACCGTCT 62.226 65.000 0.00 0.00 0.00 4.18
57 58 1.757340 CTCCTCCCCCTACACCGTC 60.757 68.421 0.00 0.00 0.00 4.79
58 59 2.363361 CTCCTCCCCCTACACCGT 59.637 66.667 0.00 0.00 0.00 4.83
59 60 2.444140 CCTCCTCCCCCTACACCG 60.444 72.222 0.00 0.00 0.00 4.94
60 61 1.075151 CTCCTCCTCCCCCTACACC 60.075 68.421 0.00 0.00 0.00 4.16
61 62 0.397394 GTCTCCTCCTCCCCCTACAC 60.397 65.000 0.00 0.00 0.00 2.90
62 63 1.934459 CGTCTCCTCCTCCCCCTACA 61.934 65.000 0.00 0.00 0.00 2.74
63 64 1.152715 CGTCTCCTCCTCCCCCTAC 60.153 68.421 0.00 0.00 0.00 3.18
64 65 1.308481 TCGTCTCCTCCTCCCCCTA 60.308 63.158 0.00 0.00 0.00 3.53
65 66 2.617538 TCGTCTCCTCCTCCCCCT 60.618 66.667 0.00 0.00 0.00 4.79
66 67 2.442458 GTCGTCTCCTCCTCCCCC 60.442 72.222 0.00 0.00 0.00 5.40
67 68 2.829458 CGTCGTCTCCTCCTCCCC 60.829 72.222 0.00 0.00 0.00 4.81
68 69 2.829458 CCGTCGTCTCCTCCTCCC 60.829 72.222 0.00 0.00 0.00 4.30
69 70 2.829458 CCCGTCGTCTCCTCCTCC 60.829 72.222 0.00 0.00 0.00 4.30
70 71 1.378124 CTTCCCGTCGTCTCCTCCTC 61.378 65.000 0.00 0.00 0.00 3.71
71 72 1.378778 CTTCCCGTCGTCTCCTCCT 60.379 63.158 0.00 0.00 0.00 3.69
72 73 2.416432 CCTTCCCGTCGTCTCCTCC 61.416 68.421 0.00 0.00 0.00 4.30
73 74 1.378124 CTCCTTCCCGTCGTCTCCTC 61.378 65.000 0.00 0.00 0.00 3.71
74 75 1.378778 CTCCTTCCCGTCGTCTCCT 60.379 63.158 0.00 0.00 0.00 3.69
75 76 2.416432 CCTCCTTCCCGTCGTCTCC 61.416 68.421 0.00 0.00 0.00 3.71
76 77 2.416432 CCCTCCTTCCCGTCGTCTC 61.416 68.421 0.00 0.00 0.00 3.36
77 78 2.362632 CCCTCCTTCCCGTCGTCT 60.363 66.667 0.00 0.00 0.00 4.18
78 79 3.459063 CCCCTCCTTCCCGTCGTC 61.459 72.222 0.00 0.00 0.00 4.20
79 80 3.312989 ATCCCCTCCTTCCCGTCGT 62.313 63.158 0.00 0.00 0.00 4.34
80 81 2.444140 ATCCCCTCCTTCCCGTCG 60.444 66.667 0.00 0.00 0.00 5.12
81 82 2.444256 CCATCCCCTCCTTCCCGTC 61.444 68.421 0.00 0.00 0.00 4.79
82 83 2.366972 CCATCCCCTCCTTCCCGT 60.367 66.667 0.00 0.00 0.00 5.28
83 84 3.878667 GCCATCCCCTCCTTCCCG 61.879 72.222 0.00 0.00 0.00 5.14
84 85 3.878667 CGCCATCCCCTCCTTCCC 61.879 72.222 0.00 0.00 0.00 3.97
85 86 2.150051 ATCGCCATCCCCTCCTTCC 61.150 63.158 0.00 0.00 0.00 3.46
86 87 1.072159 CATCGCCATCCCCTCCTTC 59.928 63.158 0.00 0.00 0.00 3.46
87 88 2.455565 CCATCGCCATCCCCTCCTT 61.456 63.158 0.00 0.00 0.00 3.36
88 89 2.851102 CCATCGCCATCCCCTCCT 60.851 66.667 0.00 0.00 0.00 3.69
89 90 2.849162 TCCATCGCCATCCCCTCC 60.849 66.667 0.00 0.00 0.00 4.30
90 91 2.427753 GTCCATCGCCATCCCCTC 59.572 66.667 0.00 0.00 0.00 4.30
91 92 3.550431 CGTCCATCGCCATCCCCT 61.550 66.667 0.00 0.00 0.00 4.79
100 101 2.584418 CAGCCTCAGCGTCCATCG 60.584 66.667 0.00 0.00 46.67 3.84
101 102 2.894387 GCAGCCTCAGCGTCCATC 60.894 66.667 0.00 0.00 46.67 3.51
102 103 3.397439 AGCAGCCTCAGCGTCCAT 61.397 61.111 0.00 0.00 46.67 3.41
103 104 4.383861 CAGCAGCCTCAGCGTCCA 62.384 66.667 0.00 0.00 46.67 4.02
105 106 4.756458 AGCAGCAGCCTCAGCGTC 62.756 66.667 0.00 0.00 46.67 5.19
121 122 4.200283 GACTCCTCTCCGCCGCAG 62.200 72.222 0.00 0.00 0.00 5.18
124 125 3.578272 CTCGACTCCTCTCCGCCG 61.578 72.222 0.00 0.00 0.00 6.46
125 126 2.124653 TCTCGACTCCTCTCCGCC 60.125 66.667 0.00 0.00 0.00 6.13
126 127 0.179078 TACTCTCGACTCCTCTCCGC 60.179 60.000 0.00 0.00 0.00 5.54
127 128 1.409790 TCTACTCTCGACTCCTCTCCG 59.590 57.143 0.00 0.00 0.00 4.63
128 129 2.800629 CGTCTACTCTCGACTCCTCTCC 60.801 59.091 0.00 0.00 0.00 3.71
129 130 2.099592 TCGTCTACTCTCGACTCCTCTC 59.900 54.545 0.00 0.00 0.00 3.20
130 131 2.101783 TCGTCTACTCTCGACTCCTCT 58.898 52.381 0.00 0.00 0.00 3.69
131 132 2.582728 TCGTCTACTCTCGACTCCTC 57.417 55.000 0.00 0.00 0.00 3.71
137 138 2.163390 CGGCGTCGTCTACTCTCGA 61.163 63.158 0.00 0.00 0.00 4.04
138 139 2.320383 CGGCGTCGTCTACTCTCG 59.680 66.667 0.00 0.00 0.00 4.04
139 140 2.105466 ACCGGCGTCGTCTACTCTC 61.105 63.158 9.28 0.00 33.95 3.20
140 141 2.046507 ACCGGCGTCGTCTACTCT 60.047 61.111 9.28 0.00 33.95 3.24
141 142 2.099831 CACCGGCGTCGTCTACTC 59.900 66.667 9.28 0.00 33.95 2.59
142 143 3.437795 CCACCGGCGTCGTCTACT 61.438 66.667 9.28 0.00 33.95 2.57
153 154 4.135153 CTCTCTCCACGCCACCGG 62.135 72.222 0.00 0.00 39.22 5.28
154 155 4.135153 CCTCTCTCCACGCCACCG 62.135 72.222 0.00 0.00 41.14 4.94
155 156 4.459089 GCCTCTCTCCACGCCACC 62.459 72.222 0.00 0.00 0.00 4.61
156 157 3.655810 CTGCCTCTCTCCACGCCAC 62.656 68.421 0.00 0.00 0.00 5.01
157 158 3.385384 CTGCCTCTCTCCACGCCA 61.385 66.667 0.00 0.00 0.00 5.69
158 159 4.828925 GCTGCCTCTCTCCACGCC 62.829 72.222 0.00 0.00 0.00 5.68
159 160 4.074526 TGCTGCCTCTCTCCACGC 62.075 66.667 0.00 0.00 0.00 5.34
160 161 2.183811 CTGCTGCCTCTCTCCACG 59.816 66.667 0.00 0.00 0.00 4.94
161 162 2.125188 GCTGCTGCCTCTCTCCAC 60.125 66.667 3.85 0.00 0.00 4.02
174 175 2.740714 CCGAAGTGTTAGCGGCTGC 61.741 63.158 13.86 10.33 38.46 5.25
175 176 3.474806 CCGAAGTGTTAGCGGCTG 58.525 61.111 13.86 0.00 38.46 4.85
199 200 9.769093 CCGAGTAATCGATCTGTTTAAAATTTT 57.231 29.630 15.13 8.75 34.64 1.82
200 201 7.908601 GCCGAGTAATCGATCTGTTTAAAATTT 59.091 33.333 15.13 0.00 34.64 1.82
201 202 7.280205 AGCCGAGTAATCGATCTGTTTAAAATT 59.720 33.333 15.13 0.00 34.64 1.82
202 203 6.761714 AGCCGAGTAATCGATCTGTTTAAAAT 59.238 34.615 15.13 0.00 34.64 1.82
207 208 3.130516 TCAGCCGAGTAATCGATCTGTTT 59.869 43.478 23.51 0.00 36.10 2.83
208 209 2.688446 TCAGCCGAGTAATCGATCTGTT 59.312 45.455 23.51 3.30 36.10 3.16
211 214 3.305676 CCAATCAGCCGAGTAATCGATCT 60.306 47.826 15.13 7.77 34.64 2.75
220 223 2.119495 ACCTTATCCAATCAGCCGAGT 58.881 47.619 0.00 0.00 0.00 4.18
223 226 2.103094 TCTCACCTTATCCAATCAGCCG 59.897 50.000 0.00 0.00 0.00 5.52
234 237 1.062428 TCCATCCCCGTCTCACCTTAT 60.062 52.381 0.00 0.00 0.00 1.73
253 256 4.592351 TCCCTCATTCTCTTCATCCATCTC 59.408 45.833 0.00 0.00 0.00 2.75
265 269 4.789012 TGCAAACAAATCCCTCATTCTC 57.211 40.909 0.00 0.00 0.00 2.87
333 337 8.317891 TGTACTTGTCATATGTCGTTTTTGAT 57.682 30.769 1.90 0.00 0.00 2.57
353 357 5.426689 ACACTTGGTGATGATGATGTACT 57.573 39.130 4.62 0.00 36.96 2.73
389 393 8.921670 GTCTCAAATTCACTTTCTCTTCTCTAC 58.078 37.037 0.00 0.00 0.00 2.59
403 407 2.540101 CGATAGCCCGTCTCAAATTCAC 59.460 50.000 0.00 0.00 0.00 3.18
407 411 2.167693 TCAACGATAGCCCGTCTCAAAT 59.832 45.455 0.00 0.00 42.54 2.32
428 440 3.663025 GCAACAACAAAATATGGGCACT 58.337 40.909 0.00 0.00 0.00 4.40
505 524 0.249868 TCGCATCCGGCATTTCTAGG 60.250 55.000 0.00 0.00 45.17 3.02
521 540 2.175878 ACTATGGAGGCAATCATCGC 57.824 50.000 0.00 0.00 0.00 4.58
612 638 1.574134 GAAACCACAGGAACGAACGA 58.426 50.000 0.14 0.00 0.00 3.85
613 639 0.584876 GGAAACCACAGGAACGAACG 59.415 55.000 0.00 0.00 0.00 3.95
683 713 3.628942 TGATTTCGATTGAGATGGGCAAG 59.371 43.478 0.00 0.00 0.00 4.01
876 912 2.973899 CTAGGTGCGTGCCTCACT 59.026 61.111 3.23 0.00 39.94 3.41
886 922 4.767255 AGCTGTGGCGCTAGGTGC 62.767 66.667 7.64 5.87 44.37 5.01
887 923 2.510238 GAGCTGTGGCGCTAGGTG 60.510 66.667 7.64 0.00 41.08 4.00
888 924 3.775654 GGAGCTGTGGCGCTAGGT 61.776 66.667 7.64 9.37 41.08 3.08
889 925 3.438017 GAGGAGCTGTGGCGCTAGG 62.438 68.421 7.64 0.00 41.08 3.02
890 926 2.105930 GAGGAGCTGTGGCGCTAG 59.894 66.667 7.64 4.84 41.08 3.42
891 927 3.461773 GGAGGAGCTGTGGCGCTA 61.462 66.667 7.64 0.00 41.08 4.26
912 948 3.582120 CAACGGCCGTTGCACTGT 61.582 61.111 46.76 23.46 46.92 3.55
936 972 1.153168 GTCACCCACCATCCATCGG 60.153 63.158 0.00 0.00 0.00 4.18
937 973 1.521457 CGTCACCCACCATCCATCG 60.521 63.158 0.00 0.00 0.00 3.84
938 974 0.462047 GTCGTCACCCACCATCCATC 60.462 60.000 0.00 0.00 0.00 3.51
939 975 1.602237 GTCGTCACCCACCATCCAT 59.398 57.895 0.00 0.00 0.00 3.41
940 976 2.938086 CGTCGTCACCCACCATCCA 61.938 63.158 0.00 0.00 0.00 3.41
941 977 2.125673 CGTCGTCACCCACCATCC 60.126 66.667 0.00 0.00 0.00 3.51
943 979 4.388499 GGCGTCGTCACCCACCAT 62.388 66.667 0.00 0.00 0.00 3.55
1117 1169 0.106708 TAGCCCAGCCATCTTTAGCG 59.893 55.000 0.00 0.00 0.00 4.26
1307 1359 2.367344 GCACGTACCGTTGTCGTCC 61.367 63.158 0.00 0.00 38.32 4.79
1379 1439 3.253188 CACACCGATGAACCAAATTGAGT 59.747 43.478 0.00 0.00 0.00 3.41
1451 1511 1.484240 CAGGAGGTCATGGAGGAGAAC 59.516 57.143 0.00 0.00 0.00 3.01
1475 1535 0.404040 CCTTGAACAGGGGCTGGTTA 59.596 55.000 0.00 0.00 39.39 2.85
1550 1613 9.273016 CAAGGTCCGTAAATGATATTAACTGAT 57.727 33.333 0.00 0.00 0.00 2.90
1552 1615 7.497909 ACCAAGGTCCGTAAATGATATTAACTG 59.502 37.037 0.00 0.00 0.00 3.16
1553 1616 7.497909 CACCAAGGTCCGTAAATGATATTAACT 59.502 37.037 0.00 0.00 0.00 2.24
1554 1617 7.496591 TCACCAAGGTCCGTAAATGATATTAAC 59.503 37.037 0.00 0.00 0.00 2.01
1555 1618 7.566569 TCACCAAGGTCCGTAAATGATATTAA 58.433 34.615 0.00 0.00 0.00 1.40
1557 1620 5.996644 TCACCAAGGTCCGTAAATGATATT 58.003 37.500 0.00 0.00 0.00 1.28
1558 1621 5.623956 TCACCAAGGTCCGTAAATGATAT 57.376 39.130 0.00 0.00 0.00 1.63
1559 1622 5.423704 TTCACCAAGGTCCGTAAATGATA 57.576 39.130 0.00 0.00 0.00 2.15
1560 1623 3.992943 TCACCAAGGTCCGTAAATGAT 57.007 42.857 0.00 0.00 0.00 2.45
1561 1624 3.773418 TTCACCAAGGTCCGTAAATGA 57.227 42.857 0.00 0.00 0.00 2.57
1562 1625 4.839668 TTTTCACCAAGGTCCGTAAATG 57.160 40.909 0.00 0.00 0.00 2.32
1563 1626 5.536916 TCAATTTTCACCAAGGTCCGTAAAT 59.463 36.000 0.00 0.00 0.00 1.40
1564 1627 4.888239 TCAATTTTCACCAAGGTCCGTAAA 59.112 37.500 0.00 0.00 0.00 2.01
1565 1628 4.462133 TCAATTTTCACCAAGGTCCGTAA 58.538 39.130 0.00 0.00 0.00 3.18
1566 1629 4.088056 TCAATTTTCACCAAGGTCCGTA 57.912 40.909 0.00 0.00 0.00 4.02
1567 1630 2.938838 TCAATTTTCACCAAGGTCCGT 58.061 42.857 0.00 0.00 0.00 4.69
1568 1631 4.519540 ATTCAATTTTCACCAAGGTCCG 57.480 40.909 0.00 0.00 0.00 4.79
1592 1656 2.872245 ACTGTGTGTTGTGCAGTGTATC 59.128 45.455 0.00 0.00 41.33 2.24
1593 1657 2.917933 ACTGTGTGTTGTGCAGTGTAT 58.082 42.857 0.00 0.00 41.33 2.29
1604 1668 5.245301 TGGTACTAGCTGATAACTGTGTGTT 59.755 40.000 0.00 0.00 42.31 3.32
1624 1688 2.703536 AGATGGTCAACACACTGTGGTA 59.296 45.455 13.77 0.00 37.94 3.25
1625 1689 1.490490 AGATGGTCAACACACTGTGGT 59.510 47.619 13.77 3.72 37.94 4.16
1626 1690 2.146342 GAGATGGTCAACACACTGTGG 58.854 52.381 13.77 3.85 37.94 4.17
1627 1691 1.794701 CGAGATGGTCAACACACTGTG 59.205 52.381 7.68 7.68 39.75 3.66
1628 1692 1.873903 GCGAGATGGTCAACACACTGT 60.874 52.381 0.00 0.00 0.00 3.55
1651 1715 0.370273 GCACCGTATCTGAAAGCACG 59.630 55.000 0.00 0.00 40.35 5.34
1673 1737 1.078143 GGAGCAGGATTTGTCGCCT 60.078 57.895 0.00 0.00 33.99 5.52
1694 1758 3.381590 TGATCATCACCGTCTCGATCTTT 59.618 43.478 0.00 0.00 34.80 2.52
1865 1929 1.339055 TGGAAGTTGATCTTGAGGCCG 60.339 52.381 0.00 0.00 36.40 6.13
1901 1965 2.262292 GCCAGGTACACCGCGTTA 59.738 61.111 4.92 0.00 42.08 3.18
2109 2185 1.097547 CAGTTGGCCGGGATGACATC 61.098 60.000 2.18 6.91 0.00 3.06
2245 2339 1.986378 CGATCGGCCGAGTGATTAATC 59.014 52.381 33.87 21.19 0.00 1.75
2253 2350 0.389391 ATGATTTCGATCGGCCGAGT 59.611 50.000 33.87 20.92 39.90 4.18
2316 2414 0.900182 ACCAGACAGACGGCATCTCA 60.900 55.000 0.00 0.00 34.41 3.27
2453 2560 8.693120 TTATAACTTGGATTTGGTTACACACA 57.307 30.769 0.00 0.00 0.00 3.72
2599 2710 7.010183 CCCGTCTCTTTATATGTACACACTTTG 59.990 40.741 0.00 0.00 0.00 2.77
2610 2723 2.814280 ACGGCCCGTCTCTTTATATG 57.186 50.000 1.02 0.00 33.69 1.78
2659 2772 6.128254 GGAGCAAATCACCTTAGAGTTGTAAC 60.128 42.308 6.10 0.00 43.37 2.50
2704 2817 4.334552 TGCATGGCTTAATCTTTGAGACA 58.665 39.130 0.00 0.00 32.02 3.41
2705 2818 4.970662 TGCATGGCTTAATCTTTGAGAC 57.029 40.909 0.00 0.00 0.00 3.36
2707 2820 5.041287 CACATGCATGGCTTAATCTTTGAG 58.959 41.667 29.41 0.00 0.00 3.02
2708 2821 4.678574 GCACATGCATGGCTTAATCTTTGA 60.679 41.667 29.41 0.00 41.59 2.69
2709 2822 3.554324 GCACATGCATGGCTTAATCTTTG 59.446 43.478 29.41 15.45 41.59 2.77
2710 2823 3.788937 GCACATGCATGGCTTAATCTTT 58.211 40.909 29.41 2.39 41.59 2.52
2711 2824 3.447918 GCACATGCATGGCTTAATCTT 57.552 42.857 29.41 3.16 41.59 2.40
2724 2837 3.574284 TTGGTTCATACTTGCACATGC 57.426 42.857 0.00 0.00 42.50 4.06
2725 2838 6.157904 TCAAATTGGTTCATACTTGCACATG 58.842 36.000 0.00 0.00 0.00 3.21
2726 2839 6.343716 TCAAATTGGTTCATACTTGCACAT 57.656 33.333 0.00 0.00 0.00 3.21
2727 2840 5.781210 TCAAATTGGTTCATACTTGCACA 57.219 34.783 0.00 0.00 0.00 4.57
2728 2841 6.215845 AGTTCAAATTGGTTCATACTTGCAC 58.784 36.000 0.00 0.00 0.00 4.57
2729 2842 6.403866 AGTTCAAATTGGTTCATACTTGCA 57.596 33.333 0.00 0.00 0.00 4.08
2730 2843 7.865385 TGTTAGTTCAAATTGGTTCATACTTGC 59.135 33.333 0.00 0.00 0.00 4.01
2731 2844 9.743057 TTGTTAGTTCAAATTGGTTCATACTTG 57.257 29.630 0.00 0.00 0.00 3.16
2733 2846 9.744468 GTTTGTTAGTTCAAATTGGTTCATACT 57.256 29.630 0.00 0.00 39.09 2.12
2734 2847 9.744468 AGTTTGTTAGTTCAAATTGGTTCATAC 57.256 29.630 0.00 0.00 39.09 2.39
2735 2848 9.743057 CAGTTTGTTAGTTCAAATTGGTTCATA 57.257 29.630 0.00 0.00 39.57 2.15
2736 2849 8.257306 ACAGTTTGTTAGTTCAAATTGGTTCAT 58.743 29.630 15.15 0.00 43.93 2.57
2737 2850 7.543868 CACAGTTTGTTAGTTCAAATTGGTTCA 59.456 33.333 15.15 0.00 43.93 3.18
2738 2851 7.757624 TCACAGTTTGTTAGTTCAAATTGGTTC 59.242 33.333 15.15 0.00 43.93 3.62
2739 2852 7.607250 TCACAGTTTGTTAGTTCAAATTGGTT 58.393 30.769 15.15 0.00 43.93 3.67
2740 2853 7.164230 TCACAGTTTGTTAGTTCAAATTGGT 57.836 32.000 15.15 4.55 43.93 3.67
2741 2854 8.647143 ATTCACAGTTTGTTAGTTCAAATTGG 57.353 30.769 15.15 7.62 43.93 3.16
2743 2856 9.463443 GCTATTCACAGTTTGTTAGTTCAAATT 57.537 29.630 0.00 0.00 39.09 1.82
2744 2857 8.850156 AGCTATTCACAGTTTGTTAGTTCAAAT 58.150 29.630 0.00 0.00 39.09 2.32
2745 2858 8.128582 CAGCTATTCACAGTTTGTTAGTTCAAA 58.871 33.333 0.00 0.00 35.36 2.69
2746 2859 7.639039 CAGCTATTCACAGTTTGTTAGTTCAA 58.361 34.615 0.00 0.00 0.00 2.69
2747 2860 6.293407 GCAGCTATTCACAGTTTGTTAGTTCA 60.293 38.462 0.00 0.00 0.00 3.18
2748 2861 6.073003 AGCAGCTATTCACAGTTTGTTAGTTC 60.073 38.462 0.00 0.00 0.00 3.01
2749 2862 5.765182 AGCAGCTATTCACAGTTTGTTAGTT 59.235 36.000 0.00 0.00 0.00 2.24
2750 2863 5.308825 AGCAGCTATTCACAGTTTGTTAGT 58.691 37.500 0.00 0.00 0.00 2.24
2751 2864 5.869753 AGCAGCTATTCACAGTTTGTTAG 57.130 39.130 0.00 0.00 0.00 2.34
2752 2865 6.633500 AAAGCAGCTATTCACAGTTTGTTA 57.367 33.333 0.00 0.00 0.00 2.41
2753 2866 5.520376 AAAGCAGCTATTCACAGTTTGTT 57.480 34.783 0.00 0.00 0.00 2.83
2754 2867 5.520376 AAAAGCAGCTATTCACAGTTTGT 57.480 34.783 0.00 0.00 0.00 2.83
2755 2868 6.211515 AGAAAAAGCAGCTATTCACAGTTTG 58.788 36.000 18.40 0.00 0.00 2.93
2756 2869 6.396829 AGAAAAAGCAGCTATTCACAGTTT 57.603 33.333 18.40 2.01 0.00 2.66
2757 2870 6.039717 TCAAGAAAAAGCAGCTATTCACAGTT 59.960 34.615 18.40 5.79 0.00 3.16
2758 2871 5.532406 TCAAGAAAAAGCAGCTATTCACAGT 59.468 36.000 18.40 0.91 0.00 3.55
2759 2872 6.005583 TCAAGAAAAAGCAGCTATTCACAG 57.994 37.500 18.40 10.30 0.00 3.66
2760 2873 6.016024 ACATCAAGAAAAAGCAGCTATTCACA 60.016 34.615 18.40 6.37 0.00 3.58
2761 2874 6.385033 ACATCAAGAAAAAGCAGCTATTCAC 58.615 36.000 18.40 2.20 0.00 3.18
2762 2875 6.579666 ACATCAAGAAAAAGCAGCTATTCA 57.420 33.333 18.40 3.74 0.00 2.57
2763 2876 6.309737 CCAACATCAAGAAAAAGCAGCTATTC 59.690 38.462 11.32 11.32 0.00 1.75
2764 2877 6.015180 TCCAACATCAAGAAAAAGCAGCTATT 60.015 34.615 0.00 0.00 0.00 1.73
2765 2878 5.477984 TCCAACATCAAGAAAAAGCAGCTAT 59.522 36.000 0.00 0.00 0.00 2.97
2766 2879 4.826733 TCCAACATCAAGAAAAAGCAGCTA 59.173 37.500 0.00 0.00 0.00 3.32
2767 2880 3.638160 TCCAACATCAAGAAAAAGCAGCT 59.362 39.130 0.00 0.00 0.00 4.24
2768 2881 3.981211 TCCAACATCAAGAAAAAGCAGC 58.019 40.909 0.00 0.00 0.00 5.25
2769 2882 5.443185 TCTCCAACATCAAGAAAAAGCAG 57.557 39.130 0.00 0.00 0.00 4.24
2770 2883 5.593909 TCTTCTCCAACATCAAGAAAAAGCA 59.406 36.000 0.00 0.00 0.00 3.91
2771 2884 5.917447 GTCTTCTCCAACATCAAGAAAAAGC 59.083 40.000 0.00 0.00 0.00 3.51
2772 2885 7.031226 TGTCTTCTCCAACATCAAGAAAAAG 57.969 36.000 0.00 0.00 0.00 2.27
2795 2909 7.977293 TCATATCTTGACAAATGCCTTCAATTG 59.023 33.333 0.00 0.00 38.66 2.32
2835 2949 4.233789 GGCAATTTTGAACGAGCACAATA 58.766 39.130 0.00 0.00 0.00 1.90
2840 2954 2.360483 TCTTGGCAATTTTGAACGAGCA 59.640 40.909 0.00 0.00 0.00 4.26
2942 3057 1.666553 CTCGGCGCAACCACAACTA 60.667 57.895 10.83 0.00 39.03 2.24
2947 3062 2.556287 CTTTCTCGGCGCAACCAC 59.444 61.111 10.83 0.00 39.03 4.16
2978 3093 2.482414 ATGATTGGGTTGGATGGCAT 57.518 45.000 0.00 0.00 0.00 4.40
3001 3116 1.334960 CGGTGCGGATTTGGAATATGC 60.335 52.381 0.00 0.00 0.00 3.14
3028 3143 2.481952 GCTCACTCGCTCTTCAAATGTT 59.518 45.455 0.00 0.00 0.00 2.71
3057 3172 3.123620 GCAAGCACGAGAGCAGGG 61.124 66.667 0.00 0.00 36.85 4.45
3137 3252 0.909623 ACCCCCTCCGTTTCATAGTG 59.090 55.000 0.00 0.00 0.00 2.74
3144 3259 0.833409 AGAACGTACCCCCTCCGTTT 60.833 55.000 0.00 0.00 44.04 3.60
3154 3269 3.450578 TGCGGATTTGATAGAACGTACC 58.549 45.455 0.00 0.00 0.00 3.34
3224 3340 0.976641 TCGCTTGGAGTCCATGAGTT 59.023 50.000 25.32 0.00 32.23 3.01
3226 3342 1.579698 CATCGCTTGGAGTCCATGAG 58.420 55.000 25.32 22.09 31.53 2.90
3332 3448 6.365247 TGTTCTGAAAAGCTATCGTACTGTTC 59.635 38.462 0.00 0.00 31.83 3.18
3431 3548 8.337532 TCGTGATGATTATGCTGATACTTTTTG 58.662 33.333 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.