Multiple sequence alignment - TraesCS2B01G221000

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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 TraesCS2B01G221000 chr2B 100.000 2443 0 0 1 2443 211156393 211158835 0.000000e+00 4512.0
1 TraesCS2B01G221000 chr2B 85.366 123 15 2 723 845 387627582 387627463 9.170000e-25 124.0
2 TraesCS2B01G221000 chr2B 88.421 95 11 0 2349 2443 30331926 30331832 5.520000e-22 115.0
3 TraesCS2B01G221000 chr2B 92.000 75 6 0 2124 2198 39147840 39147914 3.320000e-19 106.0
4 TraesCS2B01G221000 chr2A 91.471 2263 119 32 209 2443 429130211 429127995 0.000000e+00 3042.0
5 TraesCS2B01G221000 chr2A 91.165 249 18 3 209 455 17725227 17725473 3.890000e-88 335.0
6 TraesCS2B01G221000 chr3B 95.108 1063 52 0 1381 2443 62382772 62383834 0.000000e+00 1676.0
7 TraesCS2B01G221000 chr3B 92.407 619 42 4 451 1068 62359331 62359945 0.000000e+00 878.0
8 TraesCS2B01G221000 chr3B 92.481 266 20 0 1064 1329 62382507 62382772 4.930000e-102 381.0
9 TraesCS2B01G221000 chr3B 88.509 322 17 5 370 672 379303836 379304156 2.970000e-99 372.0
10 TraesCS2B01G221000 chr3B 82.121 330 38 8 1496 1824 563319566 563319257 1.860000e-66 263.0
11 TraesCS2B01G221000 chr3B 91.489 188 15 1 1103 1290 9188913 9188727 8.670000e-65 257.0
12 TraesCS2B01G221000 chr3B 79.843 382 50 13 1423 1796 804231784 804231422 1.120000e-63 254.0
13 TraesCS2B01G221000 chr3B 79.461 297 37 13 1524 1819 154797253 154796980 3.210000e-44 189.0
14 TraesCS2B01G221000 chr3B 84.967 153 17 5 698 848 804232033 804231885 1.510000e-32 150.0
15 TraesCS2B01G221000 chr1B 93.611 1080 57 3 1364 2443 348054767 348055834 0.000000e+00 1602.0
16 TraesCS2B01G221000 chr1B 87.959 1171 64 31 210 1339 348049052 348050186 0.000000e+00 1310.0
17 TraesCS2B01G221000 chr1B 83.893 149 13 5 680 826 8768387 8768248 5.480000e-27 132.0
18 TraesCS2B01G221000 chr1B 87.500 80 5 4 1864 1942 481721317 481721392 1.200000e-13 87.9
19 TraesCS2B01G221000 chr1D 90.062 483 27 12 209 672 107100008 107100488 7.470000e-170 606.0
20 TraesCS2B01G221000 chr1D 78.796 382 47 16 1443 1819 489450585 489450233 2.440000e-55 226.0
21 TraesCS2B01G221000 chr1D 85.549 173 18 5 1861 2031 30151942 30152109 8.980000e-40 174.0
22 TraesCS2B01G221000 chr1D 82.941 170 13 11 682 848 66241849 66241693 3.280000e-29 139.0
23 TraesCS2B01G221000 chr1A 90.287 453 34 5 1868 2316 48876850 48876404 3.500000e-163 584.0
24 TraesCS2B01G221000 chr1A 94.488 127 7 0 2317 2443 48876377 48876251 1.920000e-46 196.0
25 TraesCS2B01G221000 chr3A 90.022 451 38 3 1868 2314 33952486 33952039 5.860000e-161 577.0
26 TraesCS2B01G221000 chr3A 89.245 437 28 7 209 626 557945234 557944798 1.660000e-146 529.0
27 TraesCS2B01G221000 chr3A 90.361 249 21 3 208 455 576568773 576568527 8.430000e-85 324.0
28 TraesCS2B01G221000 chr3A 90.361 249 20 3 209 455 701236575 701236329 8.430000e-85 324.0
29 TraesCS2B01G221000 chr3A 93.701 127 8 0 2317 2443 33951870 33951744 8.920000e-45 191.0
30 TraesCS2B01G221000 chr5A 91.165 249 18 3 209 455 606263243 606262997 3.890000e-88 335.0
31 TraesCS2B01G221000 chr3D 91.393 244 16 5 209 450 445871704 445871464 1.810000e-86 329.0
32 TraesCS2B01G221000 chr3D 91.753 194 15 1 1101 1294 7288320 7288128 4.000000e-68 268.0
33 TraesCS2B01G221000 chr3D 80.858 303 36 11 1520 1821 104120454 104120173 4.090000e-53 219.0
34 TraesCS2B01G221000 chr6B 88.727 275 13 5 370 626 16450803 16451077 1.090000e-83 320.0
35 TraesCS2B01G221000 chr6B 79.641 167 12 10 1146 1294 597998441 597998279 1.550000e-17 100.0
36 TraesCS2B01G221000 chr4D 89.960 249 22 3 209 455 322297083 322296836 3.920000e-83 318.0
37 TraesCS2B01G221000 chr4D 93.000 200 11 3 475 672 433625632 433625830 3.070000e-74 289.0
38 TraesCS2B01G221000 chr7A 91.139 237 16 5 220 455 570294876 570294644 1.410000e-82 316.0
39 TraesCS2B01G221000 chr4B 92.000 200 11 4 475 672 620268184 620267988 2.390000e-70 276.0
40 TraesCS2B01G221000 chr4B 88.750 80 6 3 1864 1942 278519299 278519222 7.190000e-16 95.3
41 TraesCS2B01G221000 chr4B 85.897 78 4 2 2239 2316 642739275 642739345 2.600000e-10 76.8
42 TraesCS2B01G221000 chr7B 79.896 383 48 15 1423 1796 421703266 421703628 1.120000e-63 254.0
43 TraesCS2B01G221000 chr7B 83.007 153 19 5 694 845 421703016 421703162 5.480000e-27 132.0
44 TraesCS2B01G221000 chr4A 79.284 391 51 8 1423 1805 657088533 657088165 1.880000e-61 246.0
45 TraesCS2B01G221000 chr2D 80.451 266 42 9 1421 1677 593134351 593134087 6.890000e-46 195.0
46 TraesCS2B01G221000 chr5B 85.366 123 15 2 723 845 55032667 55032786 9.170000e-25 124.0
47 TraesCS2B01G221000 chr7D 77.686 242 21 14 2228 2443 499625150 499624916 1.530000e-22 117.0
48 TraesCS2B01G221000 chrUn 87.342 79 7 3 1864 1942 197235910 197235985 1.200000e-13 87.9


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 TraesCS2B01G221000 chr2B 211156393 211158835 2442 False 4512.0 4512 100.0000 1 2443 1 chr2B.!!$F2 2442
1 TraesCS2B01G221000 chr2A 429127995 429130211 2216 True 3042.0 3042 91.4710 209 2443 1 chr2A.!!$R1 2234
2 TraesCS2B01G221000 chr3B 62382507 62383834 1327 False 1028.5 1676 93.7945 1064 2443 2 chr3B.!!$F3 1379
3 TraesCS2B01G221000 chr3B 62359331 62359945 614 False 878.0 878 92.4070 451 1068 1 chr3B.!!$F1 617
4 TraesCS2B01G221000 chr3B 804231422 804232033 611 True 202.0 254 82.4050 698 1796 2 chr3B.!!$R4 1098
5 TraesCS2B01G221000 chr1B 348054767 348055834 1067 False 1602.0 1602 93.6110 1364 2443 1 chr1B.!!$F2 1079
6 TraesCS2B01G221000 chr1B 348049052 348050186 1134 False 1310.0 1310 87.9590 210 1339 1 chr1B.!!$F1 1129
7 TraesCS2B01G221000 chr1A 48876251 48876850 599 True 390.0 584 92.3875 1868 2443 2 chr1A.!!$R1 575
8 TraesCS2B01G221000 chr3A 33951744 33952486 742 True 384.0 577 91.8615 1868 2443 2 chr3A.!!$R4 575

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
196 197 0.032952 TCTGAACGACGGGTTTGAGG 59.967 55.0 0.0 0.0 39.5 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1706 0.039618 AAGATTGCACGGTGGGGAAT 59.96 50.0 10.6 0.0 0.0 3.01 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
34 35 4.701956 CAGGATGTGCGTATTTTCCTTT 57.298 40.909 0.26 0.00 34.59 3.11
35 36 4.662145 CAGGATGTGCGTATTTTCCTTTC 58.338 43.478 0.26 0.00 34.59 2.62
36 37 4.396166 CAGGATGTGCGTATTTTCCTTTCT 59.604 41.667 0.26 0.00 34.59 2.52
37 38 5.010282 AGGATGTGCGTATTTTCCTTTCTT 58.990 37.500 0.00 0.00 32.94 2.52
38 39 6.093495 CAGGATGTGCGTATTTTCCTTTCTTA 59.907 38.462 0.26 0.00 34.59 2.10
39 40 6.657541 AGGATGTGCGTATTTTCCTTTCTTAA 59.342 34.615 0.00 0.00 32.94 1.85
40 41 7.339466 AGGATGTGCGTATTTTCCTTTCTTAAT 59.661 33.333 0.00 0.00 32.94 1.40
41 42 7.432252 GGATGTGCGTATTTTCCTTTCTTAATG 59.568 37.037 0.00 0.00 0.00 1.90
42 43 7.441890 TGTGCGTATTTTCCTTTCTTAATGA 57.558 32.000 0.00 0.00 0.00 2.57
43 44 7.877003 TGTGCGTATTTTCCTTTCTTAATGAA 58.123 30.769 0.00 0.00 0.00 2.57
44 45 8.353684 TGTGCGTATTTTCCTTTCTTAATGAAA 58.646 29.630 0.00 0.00 41.85 2.69
45 46 9.187455 GTGCGTATTTTCCTTTCTTAATGAAAA 57.813 29.630 0.00 0.00 43.25 2.29
46 47 9.921637 TGCGTATTTTCCTTTCTTAATGAAAAT 57.078 25.926 12.13 12.13 44.06 1.82
53 54 9.691362 TTTCCTTTCTTAATGAAAATGTAGTGC 57.309 29.630 0.00 0.00 43.25 4.40
54 55 8.635765 TCCTTTCTTAATGAAAATGTAGTGCT 57.364 30.769 0.00 0.00 43.25 4.40
55 56 8.730680 TCCTTTCTTAATGAAAATGTAGTGCTC 58.269 33.333 0.00 0.00 43.25 4.26
56 57 7.693951 CCTTTCTTAATGAAAATGTAGTGCTCG 59.306 37.037 0.00 0.00 43.25 5.03
57 58 7.667043 TTCTTAATGAAAATGTAGTGCTCGT 57.333 32.000 0.00 0.00 0.00 4.18
58 59 7.060600 TCTTAATGAAAATGTAGTGCTCGTG 57.939 36.000 0.00 0.00 0.00 4.35
59 60 6.649141 TCTTAATGAAAATGTAGTGCTCGTGT 59.351 34.615 0.00 0.00 0.00 4.49
60 61 4.928661 ATGAAAATGTAGTGCTCGTGTC 57.071 40.909 0.00 0.00 0.00 3.67
61 62 3.723260 TGAAAATGTAGTGCTCGTGTCA 58.277 40.909 0.00 0.00 0.00 3.58
62 63 4.123506 TGAAAATGTAGTGCTCGTGTCAA 58.876 39.130 0.00 0.00 0.00 3.18
63 64 4.754618 TGAAAATGTAGTGCTCGTGTCAAT 59.245 37.500 0.00 0.00 0.00 2.57
64 65 5.238432 TGAAAATGTAGTGCTCGTGTCAATT 59.762 36.000 0.00 0.00 0.00 2.32
65 66 4.668576 AATGTAGTGCTCGTGTCAATTG 57.331 40.909 0.00 0.00 0.00 2.32
66 67 1.798223 TGTAGTGCTCGTGTCAATTGC 59.202 47.619 0.00 0.00 0.00 3.56
67 68 2.069273 GTAGTGCTCGTGTCAATTGCT 58.931 47.619 0.00 0.00 0.00 3.91
68 69 1.597742 AGTGCTCGTGTCAATTGCTT 58.402 45.000 0.00 0.00 0.00 3.91
69 70 2.766313 AGTGCTCGTGTCAATTGCTTA 58.234 42.857 0.00 0.00 0.00 3.09
70 71 3.138304 AGTGCTCGTGTCAATTGCTTAA 58.862 40.909 0.00 0.00 0.00 1.85
71 72 3.563808 AGTGCTCGTGTCAATTGCTTAAA 59.436 39.130 0.00 0.00 0.00 1.52
72 73 4.036262 AGTGCTCGTGTCAATTGCTTAAAA 59.964 37.500 0.00 0.00 0.00 1.52
73 74 4.737765 GTGCTCGTGTCAATTGCTTAAAAA 59.262 37.500 0.00 0.00 0.00 1.94
95 96 6.833342 AAAAGAATCAACAACTTCATGTGC 57.167 33.333 0.00 0.00 32.81 4.57
96 97 5.518848 AAGAATCAACAACTTCATGTGCA 57.481 34.783 0.00 0.00 32.81 4.57
97 98 5.717078 AGAATCAACAACTTCATGTGCAT 57.283 34.783 0.00 0.00 32.81 3.96
98 99 6.092955 AGAATCAACAACTTCATGTGCATT 57.907 33.333 0.00 0.00 32.81 3.56
99 100 6.518493 AGAATCAACAACTTCATGTGCATTT 58.482 32.000 0.00 0.00 32.81 2.32
100 101 6.987992 AGAATCAACAACTTCATGTGCATTTT 59.012 30.769 0.00 0.00 32.81 1.82
101 102 7.496591 AGAATCAACAACTTCATGTGCATTTTT 59.503 29.630 0.00 0.00 32.81 1.94
102 103 6.347270 TCAACAACTTCATGTGCATTTTTG 57.653 33.333 0.00 0.00 32.81 2.44
103 104 4.799419 ACAACTTCATGTGCATTTTTGC 57.201 36.364 0.00 0.00 30.82 3.68
104 105 4.444536 ACAACTTCATGTGCATTTTTGCT 58.555 34.783 0.00 0.00 35.49 3.91
105 106 5.599732 ACAACTTCATGTGCATTTTTGCTA 58.400 33.333 0.00 0.00 35.49 3.49
106 107 5.463061 ACAACTTCATGTGCATTTTTGCTAC 59.537 36.000 0.00 0.00 35.49 3.58
107 108 4.229096 ACTTCATGTGCATTTTTGCTACG 58.771 39.130 0.00 0.00 35.49 3.51
108 109 4.023279 ACTTCATGTGCATTTTTGCTACGA 60.023 37.500 0.00 0.00 35.49 3.43
109 110 4.700268 TCATGTGCATTTTTGCTACGAT 57.300 36.364 0.00 0.00 35.49 3.73
110 111 5.058149 TCATGTGCATTTTTGCTACGATT 57.942 34.783 0.00 0.00 35.49 3.34
111 112 5.468592 TCATGTGCATTTTTGCTACGATTT 58.531 33.333 0.00 0.00 35.49 2.17
112 113 5.345472 TCATGTGCATTTTTGCTACGATTTG 59.655 36.000 0.00 0.00 35.49 2.32
113 114 4.864633 TGTGCATTTTTGCTACGATTTGA 58.135 34.783 0.00 0.00 35.49 2.69
114 115 5.284864 TGTGCATTTTTGCTACGATTTGAA 58.715 33.333 0.00 0.00 35.49 2.69
115 116 5.401972 TGTGCATTTTTGCTACGATTTGAAG 59.598 36.000 0.00 0.00 35.49 3.02
116 117 5.402270 GTGCATTTTTGCTACGATTTGAAGT 59.598 36.000 0.00 0.00 35.49 3.01
117 118 5.982516 TGCATTTTTGCTACGATTTGAAGTT 59.017 32.000 0.00 0.00 35.49 2.66
118 119 6.143758 TGCATTTTTGCTACGATTTGAAGTTC 59.856 34.615 0.00 0.00 35.49 3.01
119 120 6.143758 GCATTTTTGCTACGATTTGAAGTTCA 59.856 34.615 0.08 0.08 0.00 3.18
120 121 7.148755 GCATTTTTGCTACGATTTGAAGTTCAT 60.149 33.333 6.36 0.00 0.00 2.57
121 122 9.340695 CATTTTTGCTACGATTTGAAGTTCATA 57.659 29.630 6.36 1.98 0.00 2.15
122 123 8.948853 TTTTTGCTACGATTTGAAGTTCATAG 57.051 30.769 6.36 6.27 0.00 2.23
123 124 7.667043 TTTGCTACGATTTGAAGTTCATAGT 57.333 32.000 6.36 7.23 0.00 2.12
124 125 6.647212 TGCTACGATTTGAAGTTCATAGTG 57.353 37.500 6.36 1.65 0.00 2.74
125 126 6.163476 TGCTACGATTTGAAGTTCATAGTGT 58.837 36.000 6.36 7.31 0.00 3.55
126 127 6.649141 TGCTACGATTTGAAGTTCATAGTGTT 59.351 34.615 6.36 0.00 0.00 3.32
127 128 6.955963 GCTACGATTTGAAGTTCATAGTGTTG 59.044 38.462 6.36 7.00 0.00 3.33
128 129 5.689819 ACGATTTGAAGTTCATAGTGTTGC 58.310 37.500 6.36 0.00 0.00 4.17
129 130 5.470098 ACGATTTGAAGTTCATAGTGTTGCT 59.530 36.000 6.36 0.00 0.00 3.91
130 131 6.017933 CGATTTGAAGTTCATAGTGTTGCTC 58.982 40.000 6.36 0.00 0.00 4.26
131 132 5.689383 TTTGAAGTTCATAGTGTTGCTCC 57.311 39.130 6.36 0.00 0.00 4.70
132 133 4.623932 TGAAGTTCATAGTGTTGCTCCT 57.376 40.909 0.08 0.00 0.00 3.69
133 134 4.973168 TGAAGTTCATAGTGTTGCTCCTT 58.027 39.130 0.08 0.00 0.00 3.36
134 135 4.756642 TGAAGTTCATAGTGTTGCTCCTTG 59.243 41.667 0.08 0.00 0.00 3.61
135 136 4.357918 AGTTCATAGTGTTGCTCCTTGT 57.642 40.909 0.00 0.00 0.00 3.16
136 137 4.067896 AGTTCATAGTGTTGCTCCTTGTG 58.932 43.478 0.00 0.00 0.00 3.33
137 138 4.065088 GTTCATAGTGTTGCTCCTTGTGA 58.935 43.478 0.00 0.00 0.00 3.58
138 139 4.558226 TCATAGTGTTGCTCCTTGTGAT 57.442 40.909 0.00 0.00 0.00 3.06
139 140 4.256110 TCATAGTGTTGCTCCTTGTGATG 58.744 43.478 0.00 0.00 0.00 3.07
140 141 2.936919 AGTGTTGCTCCTTGTGATGA 57.063 45.000 0.00 0.00 0.00 2.92
141 142 2.775890 AGTGTTGCTCCTTGTGATGAG 58.224 47.619 0.00 0.00 0.00 2.90
142 143 2.369860 AGTGTTGCTCCTTGTGATGAGA 59.630 45.455 0.00 0.00 0.00 3.27
143 144 3.008813 AGTGTTGCTCCTTGTGATGAGAT 59.991 43.478 0.00 0.00 0.00 2.75
144 145 3.126514 GTGTTGCTCCTTGTGATGAGATG 59.873 47.826 0.00 0.00 0.00 2.90
145 146 3.008266 TGTTGCTCCTTGTGATGAGATGA 59.992 43.478 0.00 0.00 0.00 2.92
146 147 4.197750 GTTGCTCCTTGTGATGAGATGAT 58.802 43.478 0.00 0.00 0.00 2.45
147 148 5.104817 TGTTGCTCCTTGTGATGAGATGATA 60.105 40.000 0.00 0.00 0.00 2.15
148 149 5.619132 TGCTCCTTGTGATGAGATGATAA 57.381 39.130 0.00 0.00 0.00 1.75
149 150 5.993055 TGCTCCTTGTGATGAGATGATAAA 58.007 37.500 0.00 0.00 0.00 1.40
150 151 6.598503 TGCTCCTTGTGATGAGATGATAAAT 58.401 36.000 0.00 0.00 0.00 1.40
151 152 7.738847 TGCTCCTTGTGATGAGATGATAAATA 58.261 34.615 0.00 0.00 0.00 1.40
152 153 8.212995 TGCTCCTTGTGATGAGATGATAAATAA 58.787 33.333 0.00 0.00 0.00 1.40
153 154 9.228949 GCTCCTTGTGATGAGATGATAAATAAT 57.771 33.333 0.00 0.00 0.00 1.28
184 185 8.883731 AGAATATAAGGAAATTGTGTCTGAACG 58.116 33.333 0.00 0.00 0.00 3.95
185 186 8.786826 AATATAAGGAAATTGTGTCTGAACGA 57.213 30.769 0.00 0.00 0.00 3.85
186 187 4.813296 AAGGAAATTGTGTCTGAACGAC 57.187 40.909 0.00 0.00 43.14 4.34
187 188 2.800544 AGGAAATTGTGTCTGAACGACG 59.199 45.455 0.00 0.00 45.87 5.12
188 189 2.096417 GGAAATTGTGTCTGAACGACGG 60.096 50.000 0.00 0.00 45.87 4.79
189 190 1.508632 AATTGTGTCTGAACGACGGG 58.491 50.000 0.00 0.00 45.87 5.28
190 191 0.391597 ATTGTGTCTGAACGACGGGT 59.608 50.000 0.00 0.00 45.87 5.28
191 192 0.176219 TTGTGTCTGAACGACGGGTT 59.824 50.000 0.00 0.00 45.87 4.11
192 193 0.176219 TGTGTCTGAACGACGGGTTT 59.824 50.000 0.00 0.00 45.87 3.27
193 194 0.580104 GTGTCTGAACGACGGGTTTG 59.420 55.000 0.00 0.00 45.87 2.93
194 195 0.460722 TGTCTGAACGACGGGTTTGA 59.539 50.000 0.00 0.00 45.87 2.69
195 196 1.137513 GTCTGAACGACGGGTTTGAG 58.862 55.000 0.00 0.00 39.50 3.02
196 197 0.032952 TCTGAACGACGGGTTTGAGG 59.967 55.000 0.00 0.00 39.50 3.86
197 198 0.032952 CTGAACGACGGGTTTGAGGA 59.967 55.000 0.00 0.00 39.50 3.71
198 199 0.249573 TGAACGACGGGTTTGAGGAC 60.250 55.000 0.00 0.00 39.50 3.85
199 200 0.947660 GAACGACGGGTTTGAGGACC 60.948 60.000 0.00 0.00 39.50 4.46
200 201 1.688269 AACGACGGGTTTGAGGACCA 61.688 55.000 0.00 0.00 41.65 4.02
201 202 1.070105 CGACGGGTTTGAGGACCAA 59.930 57.895 0.00 0.00 41.65 3.67
202 203 0.949105 CGACGGGTTTGAGGACCAAG 60.949 60.000 0.00 0.00 41.65 3.61
203 204 0.108019 GACGGGTTTGAGGACCAAGT 59.892 55.000 0.00 0.00 41.65 3.16
204 205 1.345415 GACGGGTTTGAGGACCAAGTA 59.655 52.381 0.00 0.00 41.65 2.24
205 206 1.982958 ACGGGTTTGAGGACCAAGTAT 59.017 47.619 0.00 0.00 41.65 2.12
206 207 2.290071 ACGGGTTTGAGGACCAAGTATG 60.290 50.000 0.00 0.00 41.65 2.39
207 208 2.092323 GGGTTTGAGGACCAAGTATGC 58.908 52.381 0.00 0.00 41.65 3.14
208 209 2.554344 GGGTTTGAGGACCAAGTATGCA 60.554 50.000 0.00 0.00 41.65 3.96
209 210 3.356290 GGTTTGAGGACCAAGTATGCAT 58.644 45.455 3.79 3.79 39.57 3.96
210 211 3.378427 GGTTTGAGGACCAAGTATGCATC 59.622 47.826 0.19 0.00 39.57 3.91
211 212 4.265073 GTTTGAGGACCAAGTATGCATCT 58.735 43.478 0.19 0.00 35.94 2.90
212 213 3.827008 TGAGGACCAAGTATGCATCTC 57.173 47.619 0.19 1.25 0.00 2.75
213 214 3.378512 TGAGGACCAAGTATGCATCTCT 58.621 45.455 0.19 0.00 0.00 3.10
214 215 4.546674 TGAGGACCAAGTATGCATCTCTA 58.453 43.478 0.19 0.00 0.00 2.43
215 216 5.150715 TGAGGACCAAGTATGCATCTCTAT 58.849 41.667 0.19 0.00 0.00 1.98
216 217 5.604231 TGAGGACCAAGTATGCATCTCTATT 59.396 40.000 0.19 0.00 0.00 1.73
217 218 6.100279 TGAGGACCAAGTATGCATCTCTATTT 59.900 38.462 0.19 0.00 0.00 1.40
218 219 6.904626 AGGACCAAGTATGCATCTCTATTTT 58.095 36.000 0.19 0.00 0.00 1.82
257 258 3.071892 TGAATAGTCCCACCACTTTCGTT 59.928 43.478 0.00 0.00 0.00 3.85
260 261 1.064979 AGTCCCACCACTTTCGTTTGT 60.065 47.619 0.00 0.00 0.00 2.83
291 309 1.202722 TCTGGTTTTCTTCGTCCCACC 60.203 52.381 0.00 0.00 0.00 4.61
362 380 4.542735 GCAATACCCAACGTATTTATGGC 58.457 43.478 0.00 0.00 43.77 4.40
403 422 4.000988 CACGTATGGTAAGGCTGAAACTT 58.999 43.478 0.00 0.00 0.00 2.66
410 429 8.957466 GTATGGTAAGGCTGAAACTTAGAAATT 58.043 33.333 0.00 0.00 31.57 1.82
551 588 0.251608 ACCCATTTTTCCCACCTCCG 60.252 55.000 0.00 0.00 0.00 4.63
576 616 4.724074 TTGGCAAGTGATGATTCAATCC 57.276 40.909 0.00 0.00 32.48 3.01
654 694 9.739276 TCCTTATTATCCACATTACCATTCATC 57.261 33.333 0.00 0.00 0.00 2.92
655 695 9.519191 CCTTATTATCCACATTACCATTCATCA 57.481 33.333 0.00 0.00 0.00 3.07
658 698 4.860802 TCCACATTACCATTCATCACCT 57.139 40.909 0.00 0.00 0.00 4.00
659 699 5.966853 TCCACATTACCATTCATCACCTA 57.033 39.130 0.00 0.00 0.00 3.08
663 703 7.339212 TCCACATTACCATTCATCACCTAAAAG 59.661 37.037 0.00 0.00 0.00 2.27
746 788 2.439701 TGCTAGCGCTACCCTCGT 60.440 61.111 14.45 0.00 36.97 4.18
749 791 2.894565 CTAGCGCTACCCTCGTCCG 61.895 68.421 14.45 0.00 0.00 4.79
826 871 1.002069 ATCCAATGCCAAGGAGGACA 58.998 50.000 0.00 0.00 41.22 4.02
849 894 2.034179 CCGTCATACGATCCAGCTACAA 59.966 50.000 0.15 0.00 46.05 2.41
854 899 1.141881 CGATCCAGCTACAACCGCT 59.858 57.895 0.00 0.00 38.49 5.52
902 973 5.396213 CCAAAAGAGGCTCTTCTACATAGCT 60.396 44.000 28.69 8.28 35.27 3.32
916 987 2.502947 ACATAGCTGAGGTGAAGATGCA 59.497 45.455 0.00 0.00 0.00 3.96
918 989 1.818642 AGCTGAGGTGAAGATGCAAC 58.181 50.000 0.00 0.00 0.00 4.17
1014 1085 2.029288 CACCATGCGCTTCGTCTGT 61.029 57.895 9.73 0.00 0.00 3.41
1106 1184 1.506718 CGCTGCTCTTCTCGGTACA 59.493 57.895 0.00 0.00 0.00 2.90
1132 1210 0.540830 AGGTGCAGTTCCTCGTCTCT 60.541 55.000 0.00 0.00 0.00 3.10
1136 1214 0.598562 GCAGTTCCTCGTCTCTGACA 59.401 55.000 0.00 0.00 32.09 3.58
1154 1232 5.045651 TCTGACATGTAGATGTGGTTGGATT 60.046 40.000 10.71 0.00 43.22 3.01
1193 1271 3.511934 TCTTCAAGAGCCTCTCCAACTAC 59.488 47.826 0.00 0.00 0.00 2.73
1194 1272 1.819288 TCAAGAGCCTCTCCAACTACG 59.181 52.381 0.00 0.00 0.00 3.51
1195 1273 1.819288 CAAGAGCCTCTCCAACTACGA 59.181 52.381 0.00 0.00 0.00 3.43
1196 1274 1.757682 AGAGCCTCTCCAACTACGAG 58.242 55.000 0.00 0.00 0.00 4.18
1197 1275 0.101579 GAGCCTCTCCAACTACGAGC 59.898 60.000 0.00 0.00 0.00 5.03
1198 1276 0.323908 AGCCTCTCCAACTACGAGCT 60.324 55.000 0.00 0.00 0.00 4.09
1199 1277 0.101579 GCCTCTCCAACTACGAGCTC 59.898 60.000 2.73 2.73 0.00 4.09
1200 1278 1.464734 CCTCTCCAACTACGAGCTCA 58.535 55.000 15.40 0.00 0.00 4.26
1201 1279 2.028130 CCTCTCCAACTACGAGCTCAT 58.972 52.381 15.40 0.00 0.00 2.90
1310 1397 4.072088 GTGGCACCGTTCGCGAAG 62.072 66.667 24.13 14.38 44.71 3.79
1323 1410 2.972505 CGAAGCTGGCCAACACGT 60.973 61.111 7.01 0.00 0.00 4.49
1324 1411 2.639286 GAAGCTGGCCAACACGTG 59.361 61.111 15.48 15.48 0.00 4.49
1325 1412 3.542629 GAAGCTGGCCAACACGTGC 62.543 63.158 17.22 5.42 0.00 5.34
1326 1413 4.873810 AGCTGGCCAACACGTGCA 62.874 61.111 17.22 3.87 0.00 4.57
1327 1414 3.898509 GCTGGCCAACACGTGCAA 61.899 61.111 17.22 0.00 0.00 4.08
1328 1415 2.026014 CTGGCCAACACGTGCAAC 59.974 61.111 17.22 2.43 0.00 4.17
1418 1505 0.179100 CGTGCACGAGAGGATCCAAT 60.179 55.000 34.93 0.55 43.02 3.16
1427 1514 2.113986 GGATCCAATGCCCCTCCG 59.886 66.667 6.95 0.00 0.00 4.63
1553 1648 3.378112 CGGCAGAGGCAATTTTTCATAGA 59.622 43.478 0.00 0.00 43.71 1.98
1574 1669 2.578021 ACCAAGGTAAGCATCCATGTCT 59.422 45.455 0.00 0.00 0.00 3.41
1579 1674 3.713248 AGGTAAGCATCCATGTCTGATGA 59.287 43.478 12.88 0.00 41.72 2.92
1611 1706 0.251297 CTGGTTCCATGGGCACTTCA 60.251 55.000 13.02 3.24 0.00 3.02
1650 1745 3.848272 TCGTTGATTTGGAAAGATGGC 57.152 42.857 0.00 0.00 0.00 4.40
1796 1894 5.187772 ACAATACTTATGTGTGGAGAGCTCA 59.812 40.000 17.77 0.00 0.00 4.26
1802 1900 2.210013 TGTGGAGAGCTCAGGCGTT 61.210 57.895 17.77 0.00 44.37 4.84
1818 1916 2.115910 TTGGCAGCTGTGGGGAAG 59.884 61.111 16.64 0.00 0.00 3.46
1914 2012 6.299023 CTGATTAGCAGTTTAACACACACA 57.701 37.500 0.00 0.00 39.85 3.72
1915 2013 6.685527 TGATTAGCAGTTTAACACACACAA 57.314 33.333 0.00 0.00 0.00 3.33
2069 2167 6.775142 TCACCTTTTGTCTCATCAAATTACCA 59.225 34.615 0.00 0.00 37.20 3.25
2150 2252 3.492337 TGAAACCTTTCATGGTGTACCC 58.508 45.455 0.00 0.00 41.88 3.69
2315 2585 7.414436 TGTTTACACCAAGATTTTTCTTCTCG 58.586 34.615 0.00 0.00 0.00 4.04
2394 2664 5.970317 TGATGTGCTCATGATTGTTCTTT 57.030 34.783 5.89 0.00 34.06 2.52
2406 2676 7.449395 TCATGATTGTTCTTTCTTGGACAGAAT 59.551 33.333 0.00 0.00 41.42 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.049828 CGCACATCCTGTCATGTATAAAGA 58.950 41.667 0.00 0.00 35.10 2.52
1 2 4.811024 ACGCACATCCTGTCATGTATAAAG 59.189 41.667 0.00 0.00 35.10 1.85
2 3 4.765273 ACGCACATCCTGTCATGTATAAA 58.235 39.130 0.00 0.00 35.10 1.40
4 5 5.722021 ATACGCACATCCTGTCATGTATA 57.278 39.130 0.00 0.00 35.10 1.47
5 6 2.988010 ACGCACATCCTGTCATGTAT 57.012 45.000 0.00 0.00 35.10 2.29
6 7 4.400529 AATACGCACATCCTGTCATGTA 57.599 40.909 0.00 0.00 35.10 2.29
7 8 2.988010 ATACGCACATCCTGTCATGT 57.012 45.000 0.00 0.00 37.49 3.21
8 9 4.496341 GGAAAATACGCACATCCTGTCATG 60.496 45.833 0.00 0.00 0.00 3.07
9 10 3.627577 GGAAAATACGCACATCCTGTCAT 59.372 43.478 0.00 0.00 0.00 3.06
10 11 3.006940 GGAAAATACGCACATCCTGTCA 58.993 45.455 0.00 0.00 0.00 3.58
11 12 3.270877 AGGAAAATACGCACATCCTGTC 58.729 45.455 0.00 0.00 39.03 3.51
12 13 3.350219 AGGAAAATACGCACATCCTGT 57.650 42.857 0.00 0.00 39.03 4.00
13 14 4.396166 AGAAAGGAAAATACGCACATCCTG 59.604 41.667 0.00 0.00 40.33 3.86
14 15 4.589908 AGAAAGGAAAATACGCACATCCT 58.410 39.130 0.00 0.00 42.22 3.24
15 16 4.965119 AGAAAGGAAAATACGCACATCC 57.035 40.909 0.00 0.00 0.00 3.51
16 17 8.181573 TCATTAAGAAAGGAAAATACGCACATC 58.818 33.333 0.00 0.00 0.00 3.06
17 18 8.050778 TCATTAAGAAAGGAAAATACGCACAT 57.949 30.769 0.00 0.00 0.00 3.21
18 19 7.441890 TCATTAAGAAAGGAAAATACGCACA 57.558 32.000 0.00 0.00 0.00 4.57
19 20 8.736751 TTTCATTAAGAAAGGAAAATACGCAC 57.263 30.769 0.00 0.00 41.11 5.34
27 28 9.691362 GCACTACATTTTCATTAAGAAAGGAAA 57.309 29.630 0.00 0.00 46.24 3.13
28 29 9.077885 AGCACTACATTTTCATTAAGAAAGGAA 57.922 29.630 0.00 0.00 46.24 3.36
29 30 8.635765 AGCACTACATTTTCATTAAGAAAGGA 57.364 30.769 0.00 0.00 46.24 3.36
30 31 7.693951 CGAGCACTACATTTTCATTAAGAAAGG 59.306 37.037 0.00 0.00 46.24 3.11
31 32 8.230486 ACGAGCACTACATTTTCATTAAGAAAG 58.770 33.333 0.00 0.00 46.24 2.62
32 33 8.015087 CACGAGCACTACATTTTCATTAAGAAA 58.985 33.333 0.00 0.00 44.21 2.52
33 34 7.172532 ACACGAGCACTACATTTTCATTAAGAA 59.827 33.333 0.00 0.00 0.00 2.52
34 35 6.649141 ACACGAGCACTACATTTTCATTAAGA 59.351 34.615 0.00 0.00 0.00 2.10
35 36 6.831769 ACACGAGCACTACATTTTCATTAAG 58.168 36.000 0.00 0.00 0.00 1.85
36 37 6.425417 TGACACGAGCACTACATTTTCATTAA 59.575 34.615 0.00 0.00 0.00 1.40
37 38 5.929415 TGACACGAGCACTACATTTTCATTA 59.071 36.000 0.00 0.00 0.00 1.90
38 39 4.754618 TGACACGAGCACTACATTTTCATT 59.245 37.500 0.00 0.00 0.00 2.57
39 40 4.314961 TGACACGAGCACTACATTTTCAT 58.685 39.130 0.00 0.00 0.00 2.57
40 41 3.723260 TGACACGAGCACTACATTTTCA 58.277 40.909 0.00 0.00 0.00 2.69
41 42 4.725556 TTGACACGAGCACTACATTTTC 57.274 40.909 0.00 0.00 0.00 2.29
42 43 5.451908 CAATTGACACGAGCACTACATTTT 58.548 37.500 0.00 0.00 0.00 1.82
43 44 4.613622 GCAATTGACACGAGCACTACATTT 60.614 41.667 10.34 0.00 0.00 2.32
44 45 3.120199 GCAATTGACACGAGCACTACATT 60.120 43.478 10.34 0.00 0.00 2.71
45 46 2.416547 GCAATTGACACGAGCACTACAT 59.583 45.455 10.34 0.00 0.00 2.29
46 47 1.798223 GCAATTGACACGAGCACTACA 59.202 47.619 10.34 0.00 0.00 2.74
47 48 2.069273 AGCAATTGACACGAGCACTAC 58.931 47.619 10.34 0.00 0.00 2.73
48 49 2.455674 AGCAATTGACACGAGCACTA 57.544 45.000 10.34 0.00 0.00 2.74
49 50 1.597742 AAGCAATTGACACGAGCACT 58.402 45.000 10.34 0.00 0.00 4.40
50 51 3.536158 TTAAGCAATTGACACGAGCAC 57.464 42.857 10.34 0.00 0.00 4.40
51 52 4.560136 TTTTAAGCAATTGACACGAGCA 57.440 36.364 10.34 0.00 0.00 4.26
71 72 6.817641 TGCACATGAAGTTGTTGATTCTTTTT 59.182 30.769 0.00 0.00 0.00 1.94
72 73 6.339730 TGCACATGAAGTTGTTGATTCTTTT 58.660 32.000 0.00 0.00 0.00 2.27
73 74 5.904941 TGCACATGAAGTTGTTGATTCTTT 58.095 33.333 0.00 0.00 0.00 2.52
74 75 5.518848 TGCACATGAAGTTGTTGATTCTT 57.481 34.783 0.00 0.00 0.00 2.52
75 76 5.717078 ATGCACATGAAGTTGTTGATTCT 57.283 34.783 0.00 0.00 0.00 2.40
76 77 6.774354 AAATGCACATGAAGTTGTTGATTC 57.226 33.333 0.00 0.00 0.00 2.52
77 78 7.411274 CAAAAATGCACATGAAGTTGTTGATT 58.589 30.769 0.00 0.00 0.00 2.57
78 79 6.512091 GCAAAAATGCACATGAAGTTGTTGAT 60.512 34.615 0.00 0.00 34.41 2.57
79 80 5.220624 GCAAAAATGCACATGAAGTTGTTGA 60.221 36.000 0.00 0.00 34.41 3.18
80 81 4.965158 GCAAAAATGCACATGAAGTTGTTG 59.035 37.500 0.00 1.99 34.41 3.33
81 82 4.877251 AGCAAAAATGCACATGAAGTTGTT 59.123 33.333 0.00 0.00 37.25 2.83
82 83 4.444536 AGCAAAAATGCACATGAAGTTGT 58.555 34.783 0.00 0.00 37.25 3.32
83 84 5.387649 CGTAGCAAAAATGCACATGAAGTTG 60.388 40.000 0.00 0.00 37.25 3.16
84 85 4.681025 CGTAGCAAAAATGCACATGAAGTT 59.319 37.500 0.00 0.00 37.25 2.66
85 86 4.023279 TCGTAGCAAAAATGCACATGAAGT 60.023 37.500 0.00 0.00 37.25 3.01
86 87 4.475028 TCGTAGCAAAAATGCACATGAAG 58.525 39.130 0.00 0.00 37.25 3.02
87 88 4.495911 TCGTAGCAAAAATGCACATGAA 57.504 36.364 0.00 0.00 37.25 2.57
88 89 4.700268 ATCGTAGCAAAAATGCACATGA 57.300 36.364 0.00 2.31 37.25 3.07
89 90 5.345472 TCAAATCGTAGCAAAAATGCACATG 59.655 36.000 3.41 0.00 37.25 3.21
90 91 5.468592 TCAAATCGTAGCAAAAATGCACAT 58.531 33.333 3.41 0.00 37.25 3.21
91 92 4.864633 TCAAATCGTAGCAAAAATGCACA 58.135 34.783 3.41 0.00 37.25 4.57
92 93 5.402270 ACTTCAAATCGTAGCAAAAATGCAC 59.598 36.000 3.41 0.00 37.25 4.57
93 94 5.527951 ACTTCAAATCGTAGCAAAAATGCA 58.472 33.333 3.41 0.00 37.25 3.96
94 95 6.143758 TGAACTTCAAATCGTAGCAAAAATGC 59.856 34.615 0.00 0.00 0.00 3.56
95 96 7.621832 TGAACTTCAAATCGTAGCAAAAATG 57.378 32.000 0.00 0.00 0.00 2.32
96 97 9.559958 CTATGAACTTCAAATCGTAGCAAAAAT 57.440 29.630 0.00 0.00 30.74 1.82
97 98 8.564574 ACTATGAACTTCAAATCGTAGCAAAAA 58.435 29.630 0.00 0.00 38.26 1.94
98 99 8.015087 CACTATGAACTTCAAATCGTAGCAAAA 58.985 33.333 0.00 0.00 38.26 2.44
99 100 7.172532 ACACTATGAACTTCAAATCGTAGCAAA 59.827 33.333 0.00 0.00 38.26 3.68
100 101 6.649141 ACACTATGAACTTCAAATCGTAGCAA 59.351 34.615 0.00 0.00 38.26 3.91
101 102 6.163476 ACACTATGAACTTCAAATCGTAGCA 58.837 36.000 0.00 0.00 38.26 3.49
102 103 6.648725 ACACTATGAACTTCAAATCGTAGC 57.351 37.500 0.00 0.00 38.26 3.58
103 104 6.955963 GCAACACTATGAACTTCAAATCGTAG 59.044 38.462 0.00 0.00 39.81 3.51
104 105 6.649141 AGCAACACTATGAACTTCAAATCGTA 59.351 34.615 0.00 0.00 0.00 3.43
105 106 5.470098 AGCAACACTATGAACTTCAAATCGT 59.530 36.000 0.00 0.00 0.00 3.73
106 107 5.931532 AGCAACACTATGAACTTCAAATCG 58.068 37.500 0.00 0.00 0.00 3.34
107 108 6.150140 AGGAGCAACACTATGAACTTCAAATC 59.850 38.462 0.00 0.00 0.00 2.17
108 109 6.006449 AGGAGCAACACTATGAACTTCAAAT 58.994 36.000 0.00 0.00 0.00 2.32
109 110 5.376625 AGGAGCAACACTATGAACTTCAAA 58.623 37.500 0.00 0.00 0.00 2.69
110 111 4.973168 AGGAGCAACACTATGAACTTCAA 58.027 39.130 0.00 0.00 0.00 2.69
111 112 4.623932 AGGAGCAACACTATGAACTTCA 57.376 40.909 0.00 0.00 0.00 3.02
112 113 4.757149 ACAAGGAGCAACACTATGAACTTC 59.243 41.667 0.00 0.00 0.00 3.01
113 114 4.516698 CACAAGGAGCAACACTATGAACTT 59.483 41.667 0.00 0.00 0.00 2.66
114 115 4.067896 CACAAGGAGCAACACTATGAACT 58.932 43.478 0.00 0.00 0.00 3.01
115 116 4.065088 TCACAAGGAGCAACACTATGAAC 58.935 43.478 0.00 0.00 0.00 3.18
116 117 4.350368 TCACAAGGAGCAACACTATGAA 57.650 40.909 0.00 0.00 0.00 2.57
117 118 4.020307 TCATCACAAGGAGCAACACTATGA 60.020 41.667 0.00 0.00 0.00 2.15
118 119 4.256110 TCATCACAAGGAGCAACACTATG 58.744 43.478 0.00 0.00 0.00 2.23
119 120 4.223700 TCTCATCACAAGGAGCAACACTAT 59.776 41.667 0.00 0.00 33.31 2.12
120 121 3.578282 TCTCATCACAAGGAGCAACACTA 59.422 43.478 0.00 0.00 33.31 2.74
121 122 2.369860 TCTCATCACAAGGAGCAACACT 59.630 45.455 0.00 0.00 33.31 3.55
122 123 2.771089 TCTCATCACAAGGAGCAACAC 58.229 47.619 0.00 0.00 33.31 3.32
123 124 3.008266 TCATCTCATCACAAGGAGCAACA 59.992 43.478 0.00 0.00 33.31 3.33
124 125 3.603532 TCATCTCATCACAAGGAGCAAC 58.396 45.455 0.00 0.00 33.31 4.17
125 126 3.986996 TCATCTCATCACAAGGAGCAA 57.013 42.857 0.00 0.00 33.31 3.91
126 127 5.619132 TTATCATCTCATCACAAGGAGCA 57.381 39.130 0.00 0.00 33.31 4.26
127 128 8.613060 TTATTTATCATCTCATCACAAGGAGC 57.387 34.615 0.00 0.00 33.31 4.70
158 159 8.883731 CGTTCAGACACAATTTCCTTATATTCT 58.116 33.333 0.00 0.00 0.00 2.40
159 160 8.879759 TCGTTCAGACACAATTTCCTTATATTC 58.120 33.333 0.00 0.00 0.00 1.75
160 161 8.786826 TCGTTCAGACACAATTTCCTTATATT 57.213 30.769 0.00 0.00 0.00 1.28
176 177 1.137513 CTCAAACCCGTCGTTCAGAC 58.862 55.000 0.00 0.00 46.16 3.51
177 178 0.032952 CCTCAAACCCGTCGTTCAGA 59.967 55.000 0.00 0.00 31.78 3.27
178 179 0.032952 TCCTCAAACCCGTCGTTCAG 59.967 55.000 0.00 0.00 31.78 3.02
179 180 0.249573 GTCCTCAAACCCGTCGTTCA 60.250 55.000 0.00 0.00 31.78 3.18
180 181 0.947660 GGTCCTCAAACCCGTCGTTC 60.948 60.000 0.00 0.00 31.78 3.95
181 182 1.070275 GGTCCTCAAACCCGTCGTT 59.930 57.895 0.00 0.00 35.70 3.85
182 183 1.688269 TTGGTCCTCAAACCCGTCGT 61.688 55.000 0.00 0.00 38.65 4.34
183 184 0.949105 CTTGGTCCTCAAACCCGTCG 60.949 60.000 0.00 0.00 38.65 5.12
184 185 0.108019 ACTTGGTCCTCAAACCCGTC 59.892 55.000 0.00 0.00 38.65 4.79
185 186 1.426751 TACTTGGTCCTCAAACCCGT 58.573 50.000 0.00 0.00 38.65 5.28
186 187 2.356135 CATACTTGGTCCTCAAACCCG 58.644 52.381 0.00 0.00 38.65 5.28
187 188 2.092323 GCATACTTGGTCCTCAAACCC 58.908 52.381 0.00 0.00 38.65 4.11
188 189 2.790433 TGCATACTTGGTCCTCAAACC 58.210 47.619 0.00 0.00 39.94 3.27
189 190 4.265073 AGATGCATACTTGGTCCTCAAAC 58.735 43.478 0.00 0.00 34.56 2.93
190 191 4.225942 AGAGATGCATACTTGGTCCTCAAA 59.774 41.667 0.00 0.00 34.56 2.69
191 192 3.776969 AGAGATGCATACTTGGTCCTCAA 59.223 43.478 0.00 0.00 0.00 3.02
192 193 3.378512 AGAGATGCATACTTGGTCCTCA 58.621 45.455 0.00 0.00 0.00 3.86
193 194 5.736951 ATAGAGATGCATACTTGGTCCTC 57.263 43.478 0.00 0.00 0.00 3.71
194 195 6.506538 AAATAGAGATGCATACTTGGTCCT 57.493 37.500 0.00 0.00 0.00 3.85
195 196 7.573968 AAAAATAGAGATGCATACTTGGTCC 57.426 36.000 0.00 0.00 0.00 4.46
198 199 9.903682 CCATTAAAAATAGAGATGCATACTTGG 57.096 33.333 0.00 1.13 0.00 3.61
201 202 8.993121 CGTCCATTAAAAATAGAGATGCATACT 58.007 33.333 0.00 5.09 0.00 2.12
202 203 8.988934 TCGTCCATTAAAAATAGAGATGCATAC 58.011 33.333 0.00 0.00 0.00 2.39
203 204 9.208022 CTCGTCCATTAAAAATAGAGATGCATA 57.792 33.333 0.00 0.00 0.00 3.14
204 205 7.716998 ACTCGTCCATTAAAAATAGAGATGCAT 59.283 33.333 0.00 0.00 0.00 3.96
205 206 7.047891 ACTCGTCCATTAAAAATAGAGATGCA 58.952 34.615 0.00 0.00 0.00 3.96
206 207 7.484035 ACTCGTCCATTAAAAATAGAGATGC 57.516 36.000 7.36 0.00 0.00 3.91
207 208 8.338259 CCAACTCGTCCATTAAAAATAGAGATG 58.662 37.037 7.36 6.03 0.00 2.90
208 209 8.047310 ACCAACTCGTCCATTAAAAATAGAGAT 58.953 33.333 7.36 0.00 0.00 2.75
209 210 7.391620 ACCAACTCGTCCATTAAAAATAGAGA 58.608 34.615 7.36 0.00 0.00 3.10
210 211 7.611213 ACCAACTCGTCCATTAAAAATAGAG 57.389 36.000 0.00 0.00 0.00 2.43
211 212 7.662258 TCAACCAACTCGTCCATTAAAAATAGA 59.338 33.333 0.00 0.00 0.00 1.98
212 213 7.812648 TCAACCAACTCGTCCATTAAAAATAG 58.187 34.615 0.00 0.00 0.00 1.73
213 214 7.747155 TCAACCAACTCGTCCATTAAAAATA 57.253 32.000 0.00 0.00 0.00 1.40
214 215 6.642707 TCAACCAACTCGTCCATTAAAAAT 57.357 33.333 0.00 0.00 0.00 1.82
215 216 6.452494 TTCAACCAACTCGTCCATTAAAAA 57.548 33.333 0.00 0.00 0.00 1.94
216 217 6.642707 ATTCAACCAACTCGTCCATTAAAA 57.357 33.333 0.00 0.00 0.00 1.52
217 218 6.938030 ACTATTCAACCAACTCGTCCATTAAA 59.062 34.615 0.00 0.00 0.00 1.52
218 219 6.469410 ACTATTCAACCAACTCGTCCATTAA 58.531 36.000 0.00 0.00 0.00 1.40
283 301 4.016706 GTGGTGGGAGGTGGGACG 62.017 72.222 0.00 0.00 0.00 4.79
305 323 0.400594 AGAGGAAAACCGGTGGGAAG 59.599 55.000 8.52 0.00 36.97 3.46
306 324 0.848053 AAGAGGAAAACCGGTGGGAA 59.152 50.000 8.52 0.00 36.97 3.97
362 380 9.172820 CATACGTGGATTAATTGTGATTGATTG 57.827 33.333 0.00 0.00 0.00 2.67
443 462 6.539173 ACCATATTCGAAATTGCCATACCTA 58.461 36.000 0.00 0.00 0.00 3.08
551 588 4.724074 TGAATCATCACTTGCCAAATCC 57.276 40.909 0.00 0.00 0.00 3.01
576 616 1.912417 TTTGTGTGGGGGAATTACGG 58.088 50.000 0.00 0.00 0.00 4.02
653 693 3.055819 AGCGCTTCTCATCTTTTAGGTGA 60.056 43.478 2.64 0.00 0.00 4.02
654 694 3.265791 AGCGCTTCTCATCTTTTAGGTG 58.734 45.455 2.64 0.00 0.00 4.00
655 695 3.055819 TGAGCGCTTCTCATCTTTTAGGT 60.056 43.478 13.26 0.00 46.34 3.08
656 696 3.525537 TGAGCGCTTCTCATCTTTTAGG 58.474 45.455 13.26 0.00 46.34 2.69
678 719 2.026542 GGGGAAAATTAGACCAGGACGT 60.027 50.000 0.00 0.00 0.00 4.34
826 871 1.112113 AGCTGGATCGTATGACGGTT 58.888 50.000 0.00 0.00 42.81 4.44
854 899 3.147595 CTGGGACGAGGCCGATCA 61.148 66.667 0.00 0.00 39.50 2.92
902 973 0.321564 CCGGTTGCATCTTCACCTCA 60.322 55.000 3.15 0.00 0.00 3.86
916 987 3.168528 AGGGTGACTGTGCCGGTT 61.169 61.111 1.90 0.00 0.00 4.44
1014 1085 1.079681 GGACCGCACCGTGATGTTA 60.080 57.895 1.65 0.00 0.00 2.41
1132 1210 4.842531 ATCCAACCACATCTACATGTCA 57.157 40.909 0.00 0.00 41.69 3.58
1136 1214 3.290710 GCCAATCCAACCACATCTACAT 58.709 45.455 0.00 0.00 0.00 2.29
1195 1273 3.842923 CGGCGAGGTCCATGAGCT 61.843 66.667 0.00 0.00 43.43 4.09
1196 1274 4.148825 ACGGCGAGGTCCATGAGC 62.149 66.667 16.62 0.00 0.00 4.26
1197 1275 2.105128 GACGGCGAGGTCCATGAG 59.895 66.667 16.62 0.00 0.00 2.90
1198 1276 3.822192 CGACGGCGAGGTCCATGA 61.822 66.667 16.62 0.00 40.82 3.07
1199 1277 3.822192 TCGACGGCGAGGTCCATG 61.822 66.667 10.67 0.00 42.51 3.66
1307 1394 2.639286 CACGTGTTGGCCAGCTTC 59.361 61.111 21.11 12.39 0.00 3.86
1308 1395 3.595758 GCACGTGTTGGCCAGCTT 61.596 61.111 21.11 2.08 0.00 3.74
1309 1396 4.873810 TGCACGTGTTGGCCAGCT 62.874 61.111 21.11 0.00 0.00 4.24
1310 1397 3.898509 TTGCACGTGTTGGCCAGC 61.899 61.111 18.38 13.50 0.00 4.85
1311 1398 2.026014 GTTGCACGTGTTGGCCAG 59.974 61.111 18.38 0.00 0.00 4.85
1312 1399 3.882013 CGTTGCACGTGTTGGCCA 61.882 61.111 18.38 0.00 36.74 5.36
1320 1407 4.000557 CAGCTTCGCGTTGCACGT 62.001 61.111 22.70 5.08 44.73 4.49
1321 1408 4.724697 CCAGCTTCGCGTTGCACG 62.725 66.667 22.70 14.98 45.88 5.34
1325 1412 3.659092 TTGGCCAGCTTCGCGTTG 61.659 61.111 5.11 0.75 0.00 4.10
1326 1413 3.660111 GTTGGCCAGCTTCGCGTT 61.660 61.111 13.08 0.00 0.00 4.84
1327 1414 4.927782 TGTTGGCCAGCTTCGCGT 62.928 61.111 21.11 0.00 0.00 6.01
1328 1415 4.389576 GTGTTGGCCAGCTTCGCG 62.390 66.667 21.11 0.00 0.00 5.87
1329 1416 4.389576 CGTGTTGGCCAGCTTCGC 62.390 66.667 21.11 11.15 0.00 4.70
1330 1417 2.972505 ACGTGTTGGCCAGCTTCG 60.973 61.111 25.54 25.54 0.00 3.79
1427 1514 1.153429 GGATCACGTGGGGTAGTGC 60.153 63.158 17.00 0.00 38.19 4.40
1534 1628 5.902613 TGGTCTATGAAAAATTGCCTCTG 57.097 39.130 0.00 0.00 0.00 3.35
1541 1636 7.775053 TGCTTACCTTGGTCTATGAAAAATT 57.225 32.000 0.00 0.00 0.00 1.82
1553 1648 2.578021 AGACATGGATGCTTACCTTGGT 59.422 45.455 0.00 0.00 37.04 3.67
1574 1669 3.008157 ACCAGCCAAAATTTGCATCATCA 59.992 39.130 0.00 0.00 0.00 3.07
1579 1674 2.106166 TGGAACCAGCCAAAATTTGCAT 59.894 40.909 0.00 0.00 34.31 3.96
1611 1706 0.039618 AAGATTGCACGGTGGGGAAT 59.960 50.000 10.60 0.00 0.00 3.01
1650 1745 7.689812 CAGATTGAATTAGCTAAACAGACAACG 59.310 37.037 10.85 2.94 0.00 4.10
1726 1823 8.604640 TGTTCACGTTGTTTCCAATATAACTA 57.395 30.769 0.00 0.00 32.11 2.24
1752 1849 1.895131 TGATTGGAAAAAGGAGCAGCC 59.105 47.619 0.00 0.00 0.00 4.85
1802 1900 4.666253 GCTTCCCCACAGCTGCCA 62.666 66.667 15.27 0.00 34.15 4.92
1818 1916 0.239347 AGTCGCAAATCAGCTTGTGC 59.761 50.000 0.00 0.00 36.86 4.57
1958 2056 6.070538 GCTATTTCTAGCCAAGATAGATGGGA 60.071 42.308 0.00 0.00 43.90 4.37
2027 2125 3.126831 GGTGAATCCTATGTGCGAGAAG 58.873 50.000 0.00 0.00 0.00 2.85
2069 2167 6.934056 TGCTTTCCACTTTATGCAACATAAT 58.066 32.000 0.00 0.00 0.00 1.28
2150 2252 3.002965 TGCATGCTGAAGAGAATTATGCG 59.997 43.478 20.33 0.00 41.55 4.73
2203 2305 3.971894 CCCGACTGGCTTCCCTAT 58.028 61.111 0.00 0.00 0.00 2.57
2279 2383 5.129815 TCTTGGTGTAAACAAGTACTCCTGT 59.870 40.000 0.00 0.00 44.29 4.00
2394 2664 6.012508 ACCTGAATTCCTTATTCTGTCCAAGA 60.013 38.462 2.27 0.00 42.63 3.02


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

AutoCloner maintained by Alex Coulton.