Multiple sequence alignment - TraesCS7A01G125000

Loading Multiple Alignment...

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 TraesCS7A01G125000 chr7A 100.000 2837 0 0 1 2837 80556836 80559672 0.000000e+00 5240.0
1 TraesCS7A01G125000 chr5D 95.618 2510 102 6 305 2811 306249542 306247038 0.000000e+00 4019.0
2 TraesCS7A01G125000 chr5D 97.500 40 1 0 2798 2837 306247024 306246985 5.070000e-08 69.4
3 TraesCS7A01G125000 chr6A 93.855 2555 109 13 304 2837 535298196 535295669 0.000000e+00 3805.0
4 TraesCS7A01G125000 chr7D 93.864 2412 120 10 305 2702 135508445 135506048 0.000000e+00 3609.0
5 TraesCS7A01G125000 chr7D 95.112 2271 101 6 305 2571 71619920 71617656 0.000000e+00 3570.0
6 TraesCS7A01G125000 chr7D 90.718 1853 164 7 942 2789 370972586 370970737 0.000000e+00 2462.0
7 TraesCS7A01G125000 chr7D 82.710 642 79 13 308 948 209094827 209094217 2.490000e-150 542.0
8 TraesCS7A01G125000 chr7D 82.683 641 80 12 308 947 370973276 370972666 8.940000e-150 540.0
9 TraesCS7A01G125000 chr7D 95.098 102 5 0 1 102 484086046 484086147 8.130000e-36 161.0
10 TraesCS7A01G125000 chr3B 90.160 2124 182 18 305 2425 672250070 672252169 0.000000e+00 2739.0
11 TraesCS7A01G125000 chr3B 82.229 332 24 12 1 308 751162795 751162475 1.300000e-63 254.0
12 TraesCS7A01G125000 chr1B 89.854 2129 177 15 684 2803 52804274 52806372 0.000000e+00 2699.0
13 TraesCS7A01G125000 chr1B 95.098 102 5 0 1 102 121524722 121524621 8.130000e-36 161.0
14 TraesCS7A01G125000 chr1D 90.618 1812 140 14 291 2099 267989775 267991559 0.000000e+00 2377.0
15 TraesCS7A01G125000 chr1D 87.536 1749 203 9 1063 2807 18167308 18169045 0.000000e+00 2008.0
16 TraesCS7A01G125000 chr6B 91.389 1591 128 8 305 1892 431424144 431422560 0.000000e+00 2170.0
17 TraesCS7A01G125000 chr5A 86.998 1792 229 4 999 2788 638078379 638080168 0.000000e+00 2015.0
18 TraesCS7A01G125000 chr3A 86.551 1792 237 4 999 2788 716983108 716984897 0.000000e+00 1971.0
19 TraesCS7A01G125000 chr5B 86.257 1710 226 9 1098 2803 562284858 562283154 0.000000e+00 1847.0
20 TraesCS7A01G125000 chr5B 95.098 102 5 0 1 102 596312610 596312711 8.130000e-36 161.0
21 TraesCS7A01G125000 chr5B 94.118 102 6 0 1 102 535040576 535040475 3.780000e-34 156.0
22 TraesCS7A01G125000 chr7B 91.351 1029 80 8 306 1332 54922218 54923239 0.000000e+00 1399.0
23 TraesCS7A01G125000 chr7B 77.670 309 31 9 1 282 23706442 23706739 1.360000e-33 154.0
24 TraesCS7A01G125000 chr3D 83.636 330 23 7 1 303 559785110 559785435 5.980000e-72 281.0
25 TraesCS7A01G125000 chrUn 95.098 102 5 0 1 102 47709498 47709599 8.130000e-36 161.0
26 TraesCS7A01G125000 chrUn 84.874 119 18 0 102 220 263500959 263501077 1.380000e-23 121.0
27 TraesCS7A01G125000 chr2B 95.098 102 5 0 1 102 41601365 41601264 8.130000e-36 161.0
28 TraesCS7A01G125000 chr2A 95.098 102 5 0 1 102 21312650 21312549 8.130000e-36 161.0
29 TraesCS7A01G125000 chr2A 95.098 102 5 0 1 102 21357398 21357297 8.130000e-36 161.0
30 TraesCS7A01G125000 chr1A 95.098 102 5 0 1 102 569760089 569760190 8.130000e-36 161.0
31 TraesCS7A01G125000 chr4B 77.670 309 32 10 1 282 58965719 58966017 1.360000e-33 154.0
32 TraesCS7A01G125000 chr4B 77.097 310 33 11 1 282 661367733 661368032 8.190000e-31 145.0


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 TraesCS7A01G125000 chr7A 80556836 80559672 2836 False 5240.0 5240 100.0000 1 2837 1 chr7A.!!$F1 2836
1 TraesCS7A01G125000 chr5D 306246985 306249542 2557 True 2044.2 4019 96.5590 305 2837 2 chr5D.!!$R1 2532
2 TraesCS7A01G125000 chr6A 535295669 535298196 2527 True 3805.0 3805 93.8550 304 2837 1 chr6A.!!$R1 2533
3 TraesCS7A01G125000 chr7D 135506048 135508445 2397 True 3609.0 3609 93.8640 305 2702 1 chr7D.!!$R2 2397
4 TraesCS7A01G125000 chr7D 71617656 71619920 2264 True 3570.0 3570 95.1120 305 2571 1 chr7D.!!$R1 2266
5 TraesCS7A01G125000 chr7D 370970737 370973276 2539 True 1501.0 2462 86.7005 308 2789 2 chr7D.!!$R4 2481
6 TraesCS7A01G125000 chr7D 209094217 209094827 610 True 542.0 542 82.7100 308 948 1 chr7D.!!$R3 640
7 TraesCS7A01G125000 chr3B 672250070 672252169 2099 False 2739.0 2739 90.1600 305 2425 1 chr3B.!!$F1 2120
8 TraesCS7A01G125000 chr1B 52804274 52806372 2098 False 2699.0 2699 89.8540 684 2803 1 chr1B.!!$F1 2119
9 TraesCS7A01G125000 chr1D 267989775 267991559 1784 False 2377.0 2377 90.6180 291 2099 1 chr1D.!!$F2 1808
10 TraesCS7A01G125000 chr1D 18167308 18169045 1737 False 2008.0 2008 87.5360 1063 2807 1 chr1D.!!$F1 1744
11 TraesCS7A01G125000 chr6B 431422560 431424144 1584 True 2170.0 2170 91.3890 305 1892 1 chr6B.!!$R1 1587
12 TraesCS7A01G125000 chr5A 638078379 638080168 1789 False 2015.0 2015 86.9980 999 2788 1 chr5A.!!$F1 1789
13 TraesCS7A01G125000 chr3A 716983108 716984897 1789 False 1971.0 1971 86.5510 999 2788 1 chr3A.!!$F1 1789
14 TraesCS7A01G125000 chr5B 562283154 562284858 1704 True 1847.0 1847 86.2570 1098 2803 1 chr5B.!!$R2 1705
15 TraesCS7A01G125000 chr7B 54922218 54923239 1021 False 1399.0 1399 91.3510 306 1332 1 chr7B.!!$F2 1026

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
127 128 0.040958 CAACTTCCGCTGCTTCACAC 60.041 55.0 0.0 0.0 0.0 3.82 F
714 718 0.321387 GGTGGTCTTCGTTTCCTCCC 60.321 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1814 1.532868 GCGCCACATAATCAGGATCAC 59.467 52.381 0.0 0.0 0.0 3.06 R
2662 2795 0.473694 TTCTCCACCAGAGCCCAAGA 60.474 55.000 0.0 0.0 42.9 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.740290 ATACCCGTCTTCCGATGATATTT 57.260 39.130 0.00 0.00 39.56 1.40
24 25 4.417426 ACCCGTCTTCCGATGATATTTT 57.583 40.909 0.00 0.00 39.56 1.82
25 26 4.377897 ACCCGTCTTCCGATGATATTTTC 58.622 43.478 0.00 0.00 39.56 2.29
26 27 4.141801 ACCCGTCTTCCGATGATATTTTCA 60.142 41.667 0.00 0.00 39.56 2.69
27 28 4.814234 CCCGTCTTCCGATGATATTTTCAA 59.186 41.667 0.00 0.00 38.03 2.69
28 29 5.277345 CCCGTCTTCCGATGATATTTTCAAC 60.277 44.000 0.00 0.00 38.03 3.18
29 30 5.423717 CGTCTTCCGATGATATTTTCAACG 58.576 41.667 0.89 0.89 46.67 4.10
30 31 5.005394 CGTCTTCCGATGATATTTTCAACGT 59.995 40.000 6.16 0.00 45.95 3.99
31 32 6.455113 CGTCTTCCGATGATATTTTCAACGTT 60.455 38.462 0.00 0.00 45.95 3.99
32 33 6.682863 GTCTTCCGATGATATTTTCAACGTTG 59.317 38.462 22.35 22.35 45.95 4.10
33 34 6.370442 TCTTCCGATGATATTTTCAACGTTGT 59.630 34.615 26.47 11.02 45.95 3.32
34 35 6.489127 TCCGATGATATTTTCAACGTTGTT 57.511 33.333 26.47 13.13 45.95 2.83
35 36 6.904498 TCCGATGATATTTTCAACGTTGTTT 58.096 32.000 26.47 12.81 45.95 2.83
36 37 8.030744 TCCGATGATATTTTCAACGTTGTTTA 57.969 30.769 26.47 13.57 45.95 2.01
37 38 7.958567 TCCGATGATATTTTCAACGTTGTTTAC 59.041 33.333 26.47 13.30 45.95 2.01
38 39 7.746916 CCGATGATATTTTCAACGTTGTTTACA 59.253 33.333 26.47 17.55 45.95 2.41
39 40 9.108449 CGATGATATTTTCAACGTTGTTTACAA 57.892 29.630 26.47 11.38 43.38 2.41
42 43 9.952188 TGATATTTTCAACGTTGTTTACAATGA 57.048 25.926 26.47 2.24 43.62 2.57
47 48 7.824100 TTCAACGTTGTTTACAATGATTACG 57.176 32.000 26.47 10.44 43.62 3.18
48 49 7.175073 TCAACGTTGTTTACAATGATTACGA 57.825 32.000 26.47 0.00 43.62 3.43
49 50 7.285069 TCAACGTTGTTTACAATGATTACGAG 58.715 34.615 26.47 7.32 43.62 4.18
50 51 5.614760 ACGTTGTTTACAATGATTACGAGC 58.385 37.500 18.83 0.00 43.62 5.03
51 52 5.177881 ACGTTGTTTACAATGATTACGAGCA 59.822 36.000 18.83 0.00 43.62 4.26
52 53 6.128391 ACGTTGTTTACAATGATTACGAGCAT 60.128 34.615 18.83 0.00 43.62 3.79
53 54 6.192682 CGTTGTTTACAATGATTACGAGCATG 59.807 38.462 8.76 0.00 43.62 4.06
54 55 5.568482 TGTTTACAATGATTACGAGCATGC 58.432 37.500 10.51 10.51 31.05 4.06
55 56 5.123027 TGTTTACAATGATTACGAGCATGCA 59.877 36.000 21.98 0.00 31.05 3.96
56 57 3.957671 ACAATGATTACGAGCATGCAG 57.042 42.857 21.98 15.84 31.05 4.41
57 58 3.534554 ACAATGATTACGAGCATGCAGA 58.465 40.909 21.98 0.44 31.05 4.26
58 59 3.310774 ACAATGATTACGAGCATGCAGAC 59.689 43.478 21.98 9.84 31.05 3.51
59 60 2.671130 TGATTACGAGCATGCAGACA 57.329 45.000 21.98 7.01 0.00 3.41
60 61 3.183793 TGATTACGAGCATGCAGACAT 57.816 42.857 21.98 10.38 36.79 3.06
61 62 3.534554 TGATTACGAGCATGCAGACATT 58.465 40.909 21.98 0.00 32.87 2.71
62 63 3.310501 TGATTACGAGCATGCAGACATTG 59.689 43.478 21.98 4.95 32.87 2.82
63 64 1.655484 TACGAGCATGCAGACATTGG 58.345 50.000 21.98 1.30 32.87 3.16
64 65 0.321919 ACGAGCATGCAGACATTGGT 60.322 50.000 21.98 2.02 32.87 3.67
65 66 0.098200 CGAGCATGCAGACATTGGTG 59.902 55.000 21.98 0.00 32.87 4.17
66 67 1.456296 GAGCATGCAGACATTGGTGA 58.544 50.000 21.98 0.00 32.87 4.02
67 68 2.022195 GAGCATGCAGACATTGGTGAT 58.978 47.619 21.98 0.00 32.87 3.06
68 69 2.022195 AGCATGCAGACATTGGTGATC 58.978 47.619 21.98 0.00 32.87 2.92
69 70 1.746787 GCATGCAGACATTGGTGATCA 59.253 47.619 14.21 0.00 32.87 2.92
70 71 2.164827 GCATGCAGACATTGGTGATCAA 59.835 45.455 14.21 0.00 40.01 2.57
71 72 3.766151 CATGCAGACATTGGTGATCAAC 58.234 45.455 2.98 2.98 38.31 3.18
72 73 3.428452 CATGCAGACATTGGTGATCAACC 60.428 47.826 8.62 7.78 41.52 3.77
73 74 6.726249 CATGCAGACATTGGTGATCAACCG 62.726 50.000 8.62 0.00 43.16 4.44
97 98 3.912157 TCGATCGCGATAAACGGC 58.088 55.556 23.76 7.41 42.51 5.68
98 99 2.007114 TCGATCGCGATAAACGGCG 61.007 57.895 23.76 19.55 42.51 6.46
119 120 4.139420 CGCGAGCAACTTCCGCTG 62.139 66.667 0.00 0.00 45.91 5.18
120 121 4.451652 GCGAGCAACTTCCGCTGC 62.452 66.667 0.00 0.00 44.83 5.25
123 124 3.660621 AGCAACTTCCGCTGCTTC 58.339 55.556 0.00 0.00 46.71 3.86
124 125 1.227943 AGCAACTTCCGCTGCTTCA 60.228 52.632 0.00 0.00 46.71 3.02
125 126 1.081840 GCAACTTCCGCTGCTTCAC 60.082 57.895 0.00 0.00 35.62 3.18
126 127 1.785041 GCAACTTCCGCTGCTTCACA 61.785 55.000 0.00 0.00 35.62 3.58
127 128 0.040958 CAACTTCCGCTGCTTCACAC 60.041 55.000 0.00 0.00 0.00 3.82
128 129 1.498865 AACTTCCGCTGCTTCACACG 61.499 55.000 0.00 0.00 0.00 4.49
129 130 3.300667 CTTCCGCTGCTTCACACGC 62.301 63.158 0.00 0.00 0.00 5.34
134 135 4.126390 CTGCTTCACACGCGCGAG 62.126 66.667 39.36 32.08 0.00 5.03
135 136 4.639171 TGCTTCACACGCGCGAGA 62.639 61.111 39.36 26.52 0.00 4.04
136 137 3.832171 GCTTCACACGCGCGAGAG 61.832 66.667 39.36 27.50 0.00 3.20
137 138 3.175240 CTTCACACGCGCGAGAGG 61.175 66.667 39.36 25.08 34.13 3.69
138 139 3.610791 CTTCACACGCGCGAGAGGA 62.611 63.158 39.36 26.56 34.13 3.71
139 140 3.202216 TTCACACGCGCGAGAGGAA 62.202 57.895 39.36 30.12 34.13 3.36
140 141 3.470567 CACACGCGCGAGAGGAAC 61.471 66.667 39.36 0.00 34.13 3.62
141 142 4.719369 ACACGCGCGAGAGGAACC 62.719 66.667 39.36 0.00 34.13 3.62
145 146 3.818787 GCGCGAGAGGAACCGGTA 61.819 66.667 12.10 0.00 0.00 4.02
146 147 2.408022 CGCGAGAGGAACCGGTAG 59.592 66.667 8.00 0.00 0.00 3.18
147 148 2.104530 GCGAGAGGAACCGGTAGC 59.895 66.667 8.00 2.49 0.00 3.58
148 149 2.416432 GCGAGAGGAACCGGTAGCT 61.416 63.158 8.00 2.30 0.00 3.32
149 150 1.433879 CGAGAGGAACCGGTAGCTG 59.566 63.158 8.00 0.00 0.00 4.24
150 151 1.030488 CGAGAGGAACCGGTAGCTGA 61.030 60.000 8.00 0.00 0.00 4.26
151 152 0.456628 GAGAGGAACCGGTAGCTGAC 59.543 60.000 8.00 0.00 0.00 3.51
152 153 1.139095 GAGGAACCGGTAGCTGACG 59.861 63.158 8.00 0.00 0.00 4.35
153 154 2.508663 GGAACCGGTAGCTGACGC 60.509 66.667 8.00 0.00 0.00 5.19
154 155 2.879462 GAACCGGTAGCTGACGCG 60.879 66.667 8.00 3.53 42.32 6.01
173 174 3.133464 CCGAGGGCACGTACGGTA 61.133 66.667 21.06 0.00 40.42 4.02
174 175 2.100991 CGAGGGCACGTACGGTAC 59.899 66.667 21.06 8.25 0.00 3.34
187 188 2.202892 GGTACGCCTGGTAGCAGC 60.203 66.667 16.62 10.78 46.44 5.25
214 215 4.681978 GCTCGTCCTGGTGGCGTT 62.682 66.667 0.00 0.00 35.47 4.84
215 216 2.738521 CTCGTCCTGGTGGCGTTG 60.739 66.667 0.00 0.00 35.47 4.10
216 217 3.515316 CTCGTCCTGGTGGCGTTGT 62.515 63.158 0.00 0.00 35.47 3.32
217 218 2.590575 CGTCCTGGTGGCGTTGTT 60.591 61.111 0.00 0.00 0.00 2.83
218 219 2.604174 CGTCCTGGTGGCGTTGTTC 61.604 63.158 0.00 0.00 0.00 3.18
219 220 2.112297 TCCTGGTGGCGTTGTTCC 59.888 61.111 0.00 0.00 0.00 3.62
220 221 2.203280 CCTGGTGGCGTTGTTCCA 60.203 61.111 0.00 0.00 0.00 3.53
221 222 1.603455 CCTGGTGGCGTTGTTCCAT 60.603 57.895 0.00 0.00 35.81 3.41
222 223 1.586154 CCTGGTGGCGTTGTTCCATC 61.586 60.000 0.00 0.00 35.81 3.51
223 224 0.888736 CTGGTGGCGTTGTTCCATCA 60.889 55.000 0.00 0.00 42.07 3.07
224 225 0.888736 TGGTGGCGTTGTTCCATCAG 60.889 55.000 0.00 0.00 39.63 2.90
225 226 1.586154 GGTGGCGTTGTTCCATCAGG 61.586 60.000 0.00 0.00 34.86 3.86
226 227 0.605319 GTGGCGTTGTTCCATCAGGA 60.605 55.000 0.00 0.00 43.93 3.86
227 228 0.605319 TGGCGTTGTTCCATCAGGAC 60.605 55.000 0.00 0.00 45.73 3.85
228 229 0.321653 GGCGTTGTTCCATCAGGACT 60.322 55.000 0.00 0.00 45.73 3.85
229 230 1.066430 GGCGTTGTTCCATCAGGACTA 60.066 52.381 0.00 0.00 45.73 2.59
230 231 2.271800 GCGTTGTTCCATCAGGACTAG 58.728 52.381 0.00 0.00 45.73 2.57
231 232 2.094182 GCGTTGTTCCATCAGGACTAGA 60.094 50.000 0.00 0.00 45.73 2.43
232 233 3.616560 GCGTTGTTCCATCAGGACTAGAA 60.617 47.826 0.00 0.00 45.73 2.10
233 234 4.566004 CGTTGTTCCATCAGGACTAGAAA 58.434 43.478 0.00 0.00 45.73 2.52
234 235 4.389077 CGTTGTTCCATCAGGACTAGAAAC 59.611 45.833 0.00 0.00 45.73 2.78
235 236 5.305585 GTTGTTCCATCAGGACTAGAAACA 58.694 41.667 0.00 0.00 45.73 2.83
236 237 5.762179 TGTTCCATCAGGACTAGAAACAT 57.238 39.130 0.00 0.00 45.73 2.71
237 238 5.491070 TGTTCCATCAGGACTAGAAACATG 58.509 41.667 0.00 0.00 45.73 3.21
238 239 4.142609 TCCATCAGGACTAGAAACATGC 57.857 45.455 0.00 0.00 39.61 4.06
239 240 3.118261 TCCATCAGGACTAGAAACATGCC 60.118 47.826 0.00 0.00 39.61 4.40
240 241 3.370846 CCATCAGGACTAGAAACATGCCA 60.371 47.826 0.00 0.00 36.89 4.92
241 242 3.334583 TCAGGACTAGAAACATGCCAC 57.665 47.619 0.00 0.00 0.00 5.01
242 243 2.027192 TCAGGACTAGAAACATGCCACC 60.027 50.000 0.00 0.00 0.00 4.61
243 244 1.282157 AGGACTAGAAACATGCCACCC 59.718 52.381 0.00 0.00 0.00 4.61
244 245 1.682087 GGACTAGAAACATGCCACCCC 60.682 57.143 0.00 0.00 0.00 4.95
245 246 1.004277 GACTAGAAACATGCCACCCCA 59.996 52.381 0.00 0.00 0.00 4.96
246 247 1.004745 ACTAGAAACATGCCACCCCAG 59.995 52.381 0.00 0.00 0.00 4.45
247 248 0.323360 TAGAAACATGCCACCCCAGC 60.323 55.000 0.00 0.00 0.00 4.85
248 249 1.607467 GAAACATGCCACCCCAGCT 60.607 57.895 0.00 0.00 0.00 4.24
249 250 1.152269 AAACATGCCACCCCAGCTT 60.152 52.632 0.00 0.00 0.00 3.74
250 251 1.474332 AAACATGCCACCCCAGCTTG 61.474 55.000 0.00 0.00 40.27 4.01
251 252 2.283388 CATGCCACCCCAGCTTGT 60.283 61.111 0.00 0.00 32.38 3.16
252 253 2.283388 ATGCCACCCCAGCTTGTG 60.283 61.111 0.00 0.00 0.00 3.33
258 259 4.748144 CCCCAGCTTGTGGCCCTC 62.748 72.222 0.00 0.00 46.45 4.30
260 261 4.020617 CCAGCTTGTGGCCCTCGA 62.021 66.667 0.00 0.00 40.39 4.04
261 262 2.435586 CAGCTTGTGGCCCTCGAG 60.436 66.667 5.13 5.13 43.05 4.04
262 263 3.710722 AGCTTGTGGCCCTCGAGG 61.711 66.667 25.36 25.36 43.05 4.63
285 286 4.087892 CACCGACCAGCCCAGGAG 62.088 72.222 0.00 0.00 0.00 3.69
288 289 4.020617 CGACCAGCCCAGGAGCAA 62.021 66.667 3.08 0.00 34.23 3.91
289 290 2.436109 GACCAGCCCAGGAGCAAA 59.564 61.111 3.08 0.00 34.23 3.68
290 291 1.228552 GACCAGCCCAGGAGCAAAA 60.229 57.895 3.08 0.00 34.23 2.44
291 292 0.827507 GACCAGCCCAGGAGCAAAAA 60.828 55.000 3.08 0.00 34.23 1.94
292 293 0.829182 ACCAGCCCAGGAGCAAAAAG 60.829 55.000 3.08 0.00 34.23 2.27
293 294 1.291272 CAGCCCAGGAGCAAAAAGC 59.709 57.895 3.08 0.00 46.19 3.51
339 340 6.056884 TGTTTTAAACCCTGAACTCATACGT 58.943 36.000 5.32 0.00 0.00 3.57
345 346 2.352421 CCCTGAACTCATACGTGTCGTT 60.352 50.000 0.00 0.00 41.54 3.85
404 405 2.024273 ACCCTCAACTCTCTAATCCCGA 60.024 50.000 0.00 0.00 0.00 5.14
434 435 0.734889 CCTTGCAGGCGTATCCAAAG 59.265 55.000 0.00 0.00 37.29 2.77
453 455 1.575447 GGGAGGAAGGCTGGGATTGT 61.575 60.000 0.00 0.00 0.00 2.71
568 572 2.301738 CGCCCCTTCCCCTTCTCTT 61.302 63.158 0.00 0.00 0.00 2.85
714 718 0.321387 GGTGGTCTTCGTTTCCTCCC 60.321 60.000 0.00 0.00 0.00 4.30
724 728 0.527565 GTTTCCTCCCGCGTGTAGTA 59.472 55.000 4.92 0.00 0.00 1.82
860 866 9.285770 GATGGATTGTAGGTTTAATCGTTTTTC 57.714 33.333 0.00 0.00 34.83 2.29
977 1070 6.972328 GTGAACCGATTGCATATATGTGTTTT 59.028 34.615 14.14 0.00 0.00 2.43
982 1075 8.128582 ACCGATTGCATATATGTGTTTTTGTAG 58.871 33.333 14.14 0.00 0.00 2.74
1054 1150 4.111577 TCACTATGGAGGGGAGTTCATTT 58.888 43.478 0.00 0.00 0.00 2.32
1083 1179 4.210331 GGCCATCTCTTGATTATGTTGGT 58.790 43.478 0.00 0.00 0.00 3.67
1130 1226 3.177228 AGAGGGATAAGTTGTCACTGCT 58.823 45.455 9.38 3.91 31.60 4.24
1390 1488 7.950512 TGAGTTGAATGACATGGTAAACAATT 58.049 30.769 0.00 0.00 0.00 2.32
1547 1675 4.039852 TGTTACTGAAGTGATACACAGCCA 59.960 41.667 4.75 0.00 36.74 4.75
1668 1797 2.789917 GCTGCAGAGCATGGTTCG 59.210 61.111 20.43 0.00 45.46 3.95
1682 1811 4.096984 GCATGGTTCGGATTCTGAAGATTT 59.903 41.667 8.20 0.00 0.00 2.17
1685 1814 5.428253 TGGTTCGGATTCTGAAGATTTAGG 58.572 41.667 8.20 0.00 0.00 2.69
1704 1833 2.146342 GGTGATCCTGATTATGTGGCG 58.854 52.381 0.00 0.00 0.00 5.69
1785 1914 7.232127 AGGAAATTCAAGAAGAAGATGAAAGCA 59.768 33.333 0.00 0.00 40.15 3.91
2130 2263 2.757099 CTGGTTGCCCCTGGATGC 60.757 66.667 0.00 0.00 0.00 3.91
2132 2265 1.925285 CTGGTTGCCCCTGGATGCTA 61.925 60.000 0.00 0.00 0.00 3.49
2156 2289 2.290260 TGGTGCCAAGACAAGTAGATGG 60.290 50.000 0.00 0.00 0.00 3.51
2175 2308 6.653989 AGATGGTCTAGGTTTCAGGTAATTG 58.346 40.000 0.00 0.00 0.00 2.32
2247 2380 7.475015 TGTTAGTGCTAAGATGATTGCAAATC 58.525 34.615 1.71 2.71 37.17 2.17
2248 2381 5.511234 AGTGCTAAGATGATTGCAAATCC 57.489 39.130 1.71 0.00 37.17 3.01
2249 2382 4.951715 AGTGCTAAGATGATTGCAAATCCA 59.048 37.500 1.71 2.35 37.17 3.41
2252 2385 6.200286 GTGCTAAGATGATTGCAAATCCAATG 59.800 38.462 1.71 0.00 35.67 2.82
2278 2411 6.543465 TGAACACATTATCCTAGCAAATCCAG 59.457 38.462 0.00 0.00 0.00 3.86
2297 2430 3.181477 CCAGTGTGGAAAATTGACAGCAA 60.181 43.478 0.00 0.00 40.96 3.91
2408 2541 4.036262 GTGTGGCATGAAAAGTGAGTACAA 59.964 41.667 0.00 0.00 0.00 2.41
2437 2570 6.047231 GTGTTTGACTACCAACTAGAACTGT 58.953 40.000 0.00 0.00 33.85 3.55
2471 2604 2.348411 GGCAGTACTGTGGCCATTAT 57.652 50.000 23.44 0.00 46.92 1.28
2488 2621 6.069963 GGCCATTATATTAGATCCCACAGAGT 60.070 42.308 0.00 0.00 0.00 3.24
2556 2689 6.976934 ATGAAGAAAGGTTTTAAAGCAGGA 57.023 33.333 9.59 0.00 0.00 3.86
2599 2732 1.786937 TGGCTGCTTTTTCAAGGGAA 58.213 45.000 0.00 0.00 0.00 3.97
2623 2756 5.539955 ACTTATCAAGGTGAATTGTTGGCTT 59.460 36.000 0.00 0.00 0.00 4.35
2662 2795 5.590259 GCAAATAATCAGATGTACCCAGTGT 59.410 40.000 0.00 0.00 0.00 3.55
2731 2864 8.296713 GGTTTATTGCTCTGTTAATCAAAGACA 58.703 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.845758 AAATATCATCGGAAGACGGGTATA 57.154 37.500 0.00 0.00 46.97 1.47
2 3 5.069383 TGAAAATATCATCGGAAGACGGGTA 59.931 40.000 0.00 0.00 46.97 3.69
3 4 4.141801 TGAAAATATCATCGGAAGACGGGT 60.142 41.667 0.00 0.00 46.97 5.28
5 6 5.556382 CGTTGAAAATATCATCGGAAGACGG 60.556 44.000 1.97 0.00 46.97 4.79
6 7 5.423717 CGTTGAAAATATCATCGGAAGACG 58.576 41.667 1.97 0.00 46.97 4.18
16 17 9.952188 TCATTGTAAACAACGTTGAAAATATCA 57.048 25.926 33.66 18.14 38.86 2.15
21 22 8.734933 CGTAATCATTGTAAACAACGTTGAAAA 58.265 29.630 33.66 18.59 38.86 2.29
22 23 8.121086 TCGTAATCATTGTAAACAACGTTGAAA 58.879 29.630 33.66 18.28 38.86 2.69
23 24 7.628235 TCGTAATCATTGTAAACAACGTTGAA 58.372 30.769 33.66 17.57 38.86 2.69
24 25 7.175073 TCGTAATCATTGTAAACAACGTTGA 57.825 32.000 33.66 11.45 38.86 3.18
25 26 6.031003 GCTCGTAATCATTGTAAACAACGTTG 59.969 38.462 26.20 26.20 38.86 4.10
26 27 6.075280 GCTCGTAATCATTGTAAACAACGTT 58.925 36.000 0.00 0.00 38.86 3.99
27 28 5.177881 TGCTCGTAATCATTGTAAACAACGT 59.822 36.000 0.00 0.00 38.86 3.99
28 29 5.613812 TGCTCGTAATCATTGTAAACAACG 58.386 37.500 0.00 0.00 38.86 4.10
29 30 6.021468 GCATGCTCGTAATCATTGTAAACAAC 60.021 38.462 11.37 0.00 38.86 3.32
30 31 6.027131 GCATGCTCGTAATCATTGTAAACAA 58.973 36.000 11.37 0.00 40.51 2.83
31 32 5.123027 TGCATGCTCGTAATCATTGTAAACA 59.877 36.000 20.33 0.00 0.00 2.83
32 33 5.568482 TGCATGCTCGTAATCATTGTAAAC 58.432 37.500 20.33 0.00 0.00 2.01
33 34 5.584251 TCTGCATGCTCGTAATCATTGTAAA 59.416 36.000 20.33 0.00 0.00 2.01
34 35 5.006649 GTCTGCATGCTCGTAATCATTGTAA 59.993 40.000 20.33 0.00 0.00 2.41
35 36 4.507756 GTCTGCATGCTCGTAATCATTGTA 59.492 41.667 20.33 0.00 0.00 2.41
36 37 3.310774 GTCTGCATGCTCGTAATCATTGT 59.689 43.478 20.33 0.00 0.00 2.71
37 38 3.310501 TGTCTGCATGCTCGTAATCATTG 59.689 43.478 20.33 0.00 0.00 2.82
38 39 3.534554 TGTCTGCATGCTCGTAATCATT 58.465 40.909 20.33 0.00 0.00 2.57
39 40 3.183793 TGTCTGCATGCTCGTAATCAT 57.816 42.857 20.33 0.00 0.00 2.45
40 41 2.671130 TGTCTGCATGCTCGTAATCA 57.329 45.000 20.33 5.81 0.00 2.57
41 42 3.303593 CCAATGTCTGCATGCTCGTAATC 60.304 47.826 20.33 3.29 35.15 1.75
42 43 2.615447 CCAATGTCTGCATGCTCGTAAT 59.385 45.455 20.33 3.53 35.15 1.89
43 44 2.009051 CCAATGTCTGCATGCTCGTAA 58.991 47.619 20.33 1.03 35.15 3.18
44 45 1.066215 ACCAATGTCTGCATGCTCGTA 60.066 47.619 20.33 3.45 35.15 3.43
45 46 0.321919 ACCAATGTCTGCATGCTCGT 60.322 50.000 20.33 8.01 35.15 4.18
46 47 0.098200 CACCAATGTCTGCATGCTCG 59.902 55.000 20.33 10.19 35.15 5.03
47 48 1.456296 TCACCAATGTCTGCATGCTC 58.544 50.000 20.33 9.94 35.15 4.26
48 49 2.022195 GATCACCAATGTCTGCATGCT 58.978 47.619 20.33 0.00 35.15 3.79
49 50 1.746787 TGATCACCAATGTCTGCATGC 59.253 47.619 11.82 11.82 35.15 4.06
50 51 3.428452 GGTTGATCACCAATGTCTGCATG 60.428 47.826 0.00 0.00 46.42 4.06
51 52 2.756760 GGTTGATCACCAATGTCTGCAT 59.243 45.455 0.00 0.00 46.42 3.96
52 53 2.161855 GGTTGATCACCAATGTCTGCA 58.838 47.619 0.00 0.00 46.42 4.41
53 54 2.927553 GGTTGATCACCAATGTCTGC 57.072 50.000 0.00 0.00 46.42 4.26
62 63 0.458025 GACGTCTCCGGTTGATCACC 60.458 60.000 8.70 0.00 43.16 4.02
63 64 0.797249 CGACGTCTCCGGTTGATCAC 60.797 60.000 14.70 0.00 38.78 3.06
64 65 0.956902 TCGACGTCTCCGGTTGATCA 60.957 55.000 14.70 0.00 38.78 2.92
65 66 0.381089 ATCGACGTCTCCGGTTGATC 59.619 55.000 14.70 0.00 38.78 2.92
66 67 0.381089 GATCGACGTCTCCGGTTGAT 59.619 55.000 14.70 6.77 38.78 2.57
67 68 1.798735 GATCGACGTCTCCGGTTGA 59.201 57.895 14.70 1.51 38.78 3.18
68 69 1.582937 CGATCGACGTCTCCGGTTG 60.583 63.158 10.26 0.00 38.78 3.77
69 70 2.789917 CGATCGACGTCTCCGGTT 59.210 61.111 10.26 0.00 38.78 4.44
70 71 3.873883 GCGATCGACGTCTCCGGT 61.874 66.667 21.57 0.00 44.60 5.28
71 72 4.939915 CGCGATCGACGTCTCCGG 62.940 72.222 21.57 0.00 44.60 5.14
72 73 3.921722 TCGCGATCGACGTCTCCG 61.922 66.667 21.57 11.05 44.60 4.63
81 82 2.459904 CGCCGTTTATCGCGATCG 59.540 61.111 27.45 22.17 39.77 3.69
82 83 2.167918 GCGCCGTTTATCGCGATC 59.832 61.111 27.45 10.75 41.95 3.69
108 109 0.040958 GTGTGAAGCAGCGGAAGTTG 60.041 55.000 0.00 0.00 45.86 3.16
109 110 1.498865 CGTGTGAAGCAGCGGAAGTT 61.499 55.000 0.00 0.00 0.00 2.66
110 111 1.956170 CGTGTGAAGCAGCGGAAGT 60.956 57.895 0.00 0.00 0.00 3.01
111 112 2.856032 CGTGTGAAGCAGCGGAAG 59.144 61.111 0.00 0.00 0.00 3.46
112 113 3.345808 GCGTGTGAAGCAGCGGAA 61.346 61.111 0.00 0.00 34.19 4.30
117 118 4.126390 CTCGCGCGTGTGAAGCAG 62.126 66.667 30.98 13.33 33.42 4.24
118 119 4.639171 TCTCGCGCGTGTGAAGCA 62.639 61.111 30.98 7.17 33.42 3.91
119 120 3.832171 CTCTCGCGCGTGTGAAGC 61.832 66.667 30.98 0.00 33.42 3.86
120 121 3.175240 CCTCTCGCGCGTGTGAAG 61.175 66.667 30.98 19.37 33.42 3.02
121 122 3.202216 TTCCTCTCGCGCGTGTGAA 62.202 57.895 30.98 26.75 33.42 3.18
122 123 3.666253 TTCCTCTCGCGCGTGTGA 61.666 61.111 30.98 23.05 0.00 3.58
123 124 3.470567 GTTCCTCTCGCGCGTGTG 61.471 66.667 30.98 26.18 0.00 3.82
124 125 4.719369 GGTTCCTCTCGCGCGTGT 62.719 66.667 30.98 0.00 0.00 4.49
128 129 3.753070 CTACCGGTTCCTCTCGCGC 62.753 68.421 15.04 0.00 0.00 6.86
129 130 2.408022 CTACCGGTTCCTCTCGCG 59.592 66.667 15.04 0.00 0.00 5.87
130 131 2.104530 GCTACCGGTTCCTCTCGC 59.895 66.667 15.04 0.51 0.00 5.03
131 132 1.030488 TCAGCTACCGGTTCCTCTCG 61.030 60.000 15.04 0.00 0.00 4.04
132 133 0.456628 GTCAGCTACCGGTTCCTCTC 59.543 60.000 15.04 1.17 0.00 3.20
133 134 1.313812 CGTCAGCTACCGGTTCCTCT 61.314 60.000 15.04 1.62 0.00 3.69
134 135 1.139095 CGTCAGCTACCGGTTCCTC 59.861 63.158 15.04 0.00 0.00 3.71
135 136 3.003113 GCGTCAGCTACCGGTTCCT 62.003 63.158 15.04 6.65 41.01 3.36
136 137 2.508663 GCGTCAGCTACCGGTTCC 60.509 66.667 15.04 3.83 41.01 3.62
137 138 2.879462 CGCGTCAGCTACCGGTTC 60.879 66.667 15.04 5.24 42.32 3.62
156 157 3.133464 TACCGTACGTGCCCTCGG 61.133 66.667 15.21 7.33 46.98 4.63
157 158 2.100991 GTACCGTACGTGCCCTCG 59.899 66.667 15.21 0.00 0.00 4.63
158 159 2.100991 CGTACCGTACGTGCCCTC 59.899 66.667 20.61 0.00 46.41 4.30
166 167 1.064783 GCTACCAGGCGTACCGTAC 59.935 63.158 0.00 0.00 42.76 3.67
167 168 1.378382 TGCTACCAGGCGTACCGTA 60.378 57.895 0.00 0.00 42.76 4.02
168 169 2.677524 TGCTACCAGGCGTACCGT 60.678 61.111 0.00 0.00 42.76 4.83
169 170 2.104331 CTGCTACCAGGCGTACCG 59.896 66.667 0.00 0.00 42.76 4.02
170 171 2.202892 GCTGCTACCAGGCGTACC 60.203 66.667 0.00 0.00 39.54 3.34
171 172 2.582498 CGCTGCTACCAGGCGTAC 60.582 66.667 0.00 0.00 39.54 3.67
172 173 4.508128 GCGCTGCTACCAGGCGTA 62.508 66.667 0.00 0.00 39.28 4.42
197 198 4.681978 AACGCCACCAGGACGAGC 62.682 66.667 0.00 0.00 37.69 5.03
198 199 2.738521 CAACGCCACCAGGACGAG 60.739 66.667 0.00 0.00 37.69 4.18
199 200 2.981977 GAACAACGCCACCAGGACGA 62.982 60.000 0.00 0.00 37.69 4.20
200 201 2.590575 AACAACGCCACCAGGACG 60.591 61.111 0.00 0.00 39.35 4.79
201 202 2.258726 GGAACAACGCCACCAGGAC 61.259 63.158 0.00 0.00 36.89 3.85
202 203 2.112297 GGAACAACGCCACCAGGA 59.888 61.111 0.00 0.00 36.89 3.86
203 204 2.203280 TGGAACAACGCCACCAGG 60.203 61.111 0.00 0.00 31.92 4.45
214 215 5.491070 CATGTTTCTAGTCCTGATGGAACA 58.509 41.667 0.00 0.00 45.18 3.18
215 216 4.333926 GCATGTTTCTAGTCCTGATGGAAC 59.666 45.833 0.00 0.00 45.18 3.62
216 217 4.517285 GCATGTTTCTAGTCCTGATGGAA 58.483 43.478 0.00 0.00 45.18 3.53
217 218 3.118261 GGCATGTTTCTAGTCCTGATGGA 60.118 47.826 0.00 0.00 40.69 3.41
218 219 3.209410 GGCATGTTTCTAGTCCTGATGG 58.791 50.000 0.00 0.00 0.00 3.51
219 220 3.624861 GTGGCATGTTTCTAGTCCTGATG 59.375 47.826 0.00 0.00 0.00 3.07
220 221 3.370953 GGTGGCATGTTTCTAGTCCTGAT 60.371 47.826 0.00 0.00 0.00 2.90
221 222 2.027192 GGTGGCATGTTTCTAGTCCTGA 60.027 50.000 0.00 0.00 0.00 3.86
222 223 2.359900 GGTGGCATGTTTCTAGTCCTG 58.640 52.381 0.00 0.00 0.00 3.86
223 224 1.282157 GGGTGGCATGTTTCTAGTCCT 59.718 52.381 0.00 0.00 0.00 3.85
224 225 1.682087 GGGGTGGCATGTTTCTAGTCC 60.682 57.143 0.00 0.00 0.00 3.85
225 226 1.004277 TGGGGTGGCATGTTTCTAGTC 59.996 52.381 0.00 0.00 0.00 2.59
226 227 1.004745 CTGGGGTGGCATGTTTCTAGT 59.995 52.381 0.00 0.00 0.00 2.57
227 228 1.755179 CTGGGGTGGCATGTTTCTAG 58.245 55.000 0.00 0.00 0.00 2.43
228 229 0.323360 GCTGGGGTGGCATGTTTCTA 60.323 55.000 0.00 0.00 0.00 2.10
229 230 1.607467 GCTGGGGTGGCATGTTTCT 60.607 57.895 0.00 0.00 0.00 2.52
230 231 1.187567 AAGCTGGGGTGGCATGTTTC 61.188 55.000 0.00 0.00 0.00 2.78
231 232 1.152269 AAGCTGGGGTGGCATGTTT 60.152 52.632 0.00 0.00 0.00 2.83
232 233 1.909781 CAAGCTGGGGTGGCATGTT 60.910 57.895 0.00 0.00 0.00 2.71
233 234 2.283388 CAAGCTGGGGTGGCATGT 60.283 61.111 0.00 0.00 0.00 3.21
234 235 2.283388 ACAAGCTGGGGTGGCATG 60.283 61.111 0.00 0.00 35.01 4.06
235 236 2.283388 CACAAGCTGGGGTGGCAT 60.283 61.111 0.00 0.00 0.00 4.40
241 242 4.748144 GAGGGCCACAAGCTGGGG 62.748 72.222 6.18 0.00 46.01 4.96
243 244 3.965539 CTCGAGGGCCACAAGCTGG 62.966 68.421 6.18 0.00 44.08 4.85
244 245 2.435586 CTCGAGGGCCACAAGCTG 60.436 66.667 6.18 0.00 43.05 4.24
245 246 3.710722 CCTCGAGGGCCACAAGCT 61.711 66.667 24.62 0.00 43.05 3.74
268 269 4.087892 CTCCTGGGCTGGTCGGTG 62.088 72.222 0.00 0.00 0.00 4.94
271 272 3.551496 TTTGCTCCTGGGCTGGTCG 62.551 63.158 8.32 0.00 0.00 4.79
272 273 0.827507 TTTTTGCTCCTGGGCTGGTC 60.828 55.000 8.32 0.00 0.00 4.02
273 274 0.829182 CTTTTTGCTCCTGGGCTGGT 60.829 55.000 8.32 0.00 0.00 4.00
274 275 1.969862 CTTTTTGCTCCTGGGCTGG 59.030 57.895 8.32 0.00 0.00 4.85
275 276 1.291272 GCTTTTTGCTCCTGGGCTG 59.709 57.895 8.32 0.00 38.95 4.85
276 277 1.910276 GGCTTTTTGCTCCTGGGCT 60.910 57.895 8.32 0.00 42.39 5.19
277 278 0.611896 TAGGCTTTTTGCTCCTGGGC 60.612 55.000 0.00 0.00 42.39 5.36
278 279 2.027385 GATAGGCTTTTTGCTCCTGGG 58.973 52.381 0.00 0.00 42.39 4.45
279 280 2.027385 GGATAGGCTTTTTGCTCCTGG 58.973 52.381 0.00 0.00 42.39 4.45
280 281 2.424956 GTGGATAGGCTTTTTGCTCCTG 59.575 50.000 0.00 0.00 42.39 3.86
281 282 2.310052 AGTGGATAGGCTTTTTGCTCCT 59.690 45.455 0.00 0.00 42.39 3.69
282 283 2.424956 CAGTGGATAGGCTTTTTGCTCC 59.575 50.000 0.00 0.00 42.39 4.70
283 284 2.424956 CCAGTGGATAGGCTTTTTGCTC 59.575 50.000 1.68 0.00 42.39 4.26
284 285 2.450476 CCAGTGGATAGGCTTTTTGCT 58.550 47.619 1.68 0.00 42.39 3.91
285 286 1.478105 CCCAGTGGATAGGCTTTTTGC 59.522 52.381 11.95 0.00 41.94 3.68
286 287 2.102578 CCCCAGTGGATAGGCTTTTTG 58.897 52.381 11.95 0.00 35.39 2.44
287 288 1.007118 CCCCCAGTGGATAGGCTTTTT 59.993 52.381 11.95 0.00 35.39 1.94
288 289 0.631212 CCCCCAGTGGATAGGCTTTT 59.369 55.000 11.95 0.00 35.39 2.27
289 290 0.552615 ACCCCCAGTGGATAGGCTTT 60.553 55.000 11.95 0.00 35.39 3.51
290 291 0.345502 TACCCCCAGTGGATAGGCTT 59.654 55.000 11.95 0.00 35.39 4.35
291 292 0.345502 TTACCCCCAGTGGATAGGCT 59.654 55.000 11.95 0.00 35.39 4.58
292 293 1.143073 CTTTACCCCCAGTGGATAGGC 59.857 57.143 11.95 0.00 35.39 3.93
293 294 2.438392 GACTTTACCCCCAGTGGATAGG 59.562 54.545 11.95 10.99 35.39 2.57
294 295 3.134804 CAGACTTTACCCCCAGTGGATAG 59.865 52.174 11.95 0.65 35.39 2.08
295 296 3.112263 CAGACTTTACCCCCAGTGGATA 58.888 50.000 11.95 0.00 35.39 2.59
296 297 1.916181 CAGACTTTACCCCCAGTGGAT 59.084 52.381 11.95 0.00 35.39 3.41
297 298 1.358152 CAGACTTTACCCCCAGTGGA 58.642 55.000 11.95 0.00 35.39 4.02
298 299 1.064825 ACAGACTTTACCCCCAGTGG 58.935 55.000 0.63 0.63 0.00 4.00
299 300 2.951229 AACAGACTTTACCCCCAGTG 57.049 50.000 0.00 0.00 0.00 3.66
300 301 3.965470 AAAACAGACTTTACCCCCAGT 57.035 42.857 0.00 0.00 0.00 4.00
301 302 5.010314 GGTTTAAAACAGACTTTACCCCCAG 59.990 44.000 0.00 0.00 0.00 4.45
302 303 4.894705 GGTTTAAAACAGACTTTACCCCCA 59.105 41.667 0.00 0.00 0.00 4.96
339 340 4.492611 GTTGGGGTTTAAAAACAACGACA 58.507 39.130 12.30 0.00 40.63 4.35
345 346 3.721021 TGGAGGTTGGGGTTTAAAAACA 58.279 40.909 7.80 0.00 40.63 2.83
404 405 1.868997 CTGCAAGGACGCAAACGAT 59.131 52.632 0.00 0.00 42.45 3.73
434 435 1.228510 CAATCCCAGCCTTCCTCCC 59.771 63.158 0.00 0.00 0.00 4.30
453 455 3.264193 ACCCACAATGATAGCTGACTCAA 59.736 43.478 0.00 0.00 0.00 3.02
568 572 3.876589 GAAGCTGGTGCGTCGGGAA 62.877 63.158 0.00 0.00 45.42 3.97
714 718 2.094545 ACCCTAAACCTTACTACACGCG 60.095 50.000 3.53 3.53 0.00 6.01
724 728 4.141779 CGCCACTATAGAACCCTAAACCTT 60.142 45.833 6.78 0.00 0.00 3.50
1054 1150 4.524802 AATCAAGAGATGGCCCAATACA 57.475 40.909 0.00 0.00 33.90 2.29
1083 1179 4.026052 TCTCTGACAATGCAGTATCTCCA 58.974 43.478 0.00 0.00 37.20 3.86
1130 1226 8.697292 GGTCTCCTAAAAATTCTCTAAGCTCTA 58.303 37.037 0.00 0.00 0.00 2.43
1390 1488 4.678256 ACATCTGGTTCTTCCTCACTAGA 58.322 43.478 0.00 0.00 35.26 2.43
1547 1675 7.572523 TCAACTCTGAAATTGTTCTTCACAT 57.427 32.000 2.36 0.00 34.43 3.21
1668 1797 6.709846 CAGGATCACCTAAATCTTCAGAATCC 59.290 42.308 0.00 0.00 45.94 3.01
1682 1811 3.006859 CGCCACATAATCAGGATCACCTA 59.993 47.826 0.00 0.00 45.94 3.08
1685 1814 1.532868 GCGCCACATAATCAGGATCAC 59.467 52.381 0.00 0.00 0.00 3.06
1987 2120 3.651803 TGCTTTTAAACACCATTCCCG 57.348 42.857 0.00 0.00 0.00 5.14
2130 2263 6.161855 TCTACTTGTCTTGGCACCATATAG 57.838 41.667 0.00 0.00 0.00 1.31
2132 2265 5.371526 CATCTACTTGTCTTGGCACCATAT 58.628 41.667 0.00 0.00 0.00 1.78
2156 2289 4.844884 AGGCAATTACCTGAAACCTAGAC 58.155 43.478 0.00 0.00 39.13 2.59
2175 2308 2.158842 ACTGGTGCTCATCTTCATAGGC 60.159 50.000 0.00 0.00 0.00 3.93
2235 2368 5.640357 GTGTTCACATTGGATTTGCAATCAT 59.360 36.000 0.00 0.00 0.00 2.45
2247 2380 5.589855 TGCTAGGATAATGTGTTCACATTGG 59.410 40.000 29.61 14.17 40.20 3.16
2248 2381 6.682423 TGCTAGGATAATGTGTTCACATTG 57.318 37.500 29.61 18.18 40.20 2.82
2249 2382 7.701539 TTTGCTAGGATAATGTGTTCACATT 57.298 32.000 26.69 26.69 42.34 2.71
2252 2385 6.318648 TGGATTTGCTAGGATAATGTGTTCAC 59.681 38.462 0.00 0.00 0.00 3.18
2278 2411 6.346838 GCTTTATTGCTGTCAATTTTCCACAC 60.347 38.462 3.37 0.00 42.51 3.82
2297 2430 3.754965 TCTTTGAGCACAGTGGCTTTAT 58.245 40.909 1.84 0.00 45.99 1.40
2408 2541 8.456471 GTTCTAGTTGGTAGTCAAACACTTTTT 58.544 33.333 0.00 0.00 37.08 1.94
2437 2570 2.416107 CTGCCAGGGTTGCTCCTCAA 62.416 60.000 0.00 0.00 34.31 3.02
2471 2604 4.962362 TCTGCAACTCTGTGGGATCTAATA 59.038 41.667 0.00 0.00 0.00 0.98
2488 2621 6.397272 ACTGTTGAAAAATGTTCTTCTGCAA 58.603 32.000 0.00 0.00 0.00 4.08
2526 2659 7.489435 GCTTTAAAACCTTTCTTCATAGCATCC 59.511 37.037 0.00 0.00 0.00 3.51
2599 2732 5.079643 AGCCAACAATTCACCTTGATAAGT 58.920 37.500 0.00 0.00 0.00 2.24
2603 2736 3.896888 TGAAGCCAACAATTCACCTTGAT 59.103 39.130 0.00 0.00 30.67 2.57
2662 2795 0.473694 TTCTCCACCAGAGCCCAAGA 60.474 55.000 0.00 0.00 42.90 3.02
2671 2804 7.011857 GCTATCATTAGTTTCTTTCTCCACCAG 59.988 40.741 0.00 0.00 0.00 4.00
2731 2864 6.204852 TGCTCCTTGGTCATTAATATCCAT 57.795 37.500 10.33 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.