Multiple sequence alignment - TraesCS1D01G316800

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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 TraesCS1D01G316800 chr1D 100.000 2765 0 0 1 2765 411748704 411751468 0.000000e+00 5107.0
1 TraesCS1D01G316800 chr1D 91.391 1812 117 21 976 2765 411583191 411584985 0.000000e+00 2446.0
2 TraesCS1D01G316800 chr1D 91.539 1241 92 9 641 1880 411697429 411698657 0.000000e+00 1698.0
3 TraesCS1D01G316800 chr1D 92.044 729 41 9 2051 2765 411705603 411706328 0.000000e+00 1009.0
4 TraesCS1D01G316800 chr1D 92.411 224 15 1 422 645 442835683 442835904 4.440000e-83 318.0
5 TraesCS1D01G316800 chr1D 92.342 222 15 1 424 645 50897818 50898037 5.750000e-82 315.0
6 TraesCS1D01G316800 chr1D 92.857 196 13 1 205 399 97740342 97740147 1.620000e-72 283.0
7 TraesCS1D01G316800 chr1D 94.118 153 9 0 1 153 411582713 411582865 1.660000e-57 233.0
8 TraesCS1D01G316800 chr1D 94.118 153 9 0 1 153 411703635 411703787 1.660000e-57 233.0
9 TraesCS1D01G316800 chr1A 91.357 2152 138 28 641 2765 508285886 508288016 0.000000e+00 2900.0
10 TraesCS1D01G316800 chr1A 91.264 2152 139 29 641 2765 508318008 508320137 0.000000e+00 2887.0
11 TraesCS1D01G316800 chr1A 94.771 153 8 0 1 153 508285708 508285860 3.560000e-59 239.0
12 TraesCS1D01G316800 chr1B 90.269 2158 143 34 641 2765 555122133 555124256 0.000000e+00 2760.0
13 TraesCS1D01G316800 chr1B 89.602 1558 131 19 641 2186 555068363 555069901 0.000000e+00 1951.0
14 TraesCS1D01G316800 chr1B 89.538 1558 132 19 641 2186 555073706 555075244 0.000000e+00 1945.0
15 TraesCS1D01G316800 chr1B 89.024 1558 140 19 641 2186 555009729 555011267 0.000000e+00 1901.0
16 TraesCS1D01G316800 chr1B 88.632 1557 147 20 641 2186 555015083 555016620 0.000000e+00 1868.0
17 TraesCS1D01G316800 chr1B 88.575 1558 146 21 641 2186 555063011 555064548 0.000000e+00 1862.0
18 TraesCS1D01G316800 chr1B 87.896 1545 135 21 653 2186 555087748 555089251 0.000000e+00 1770.0
19 TraesCS1D01G316800 chr1B 85.185 270 19 4 145 395 323620263 323620530 9.830000e-65 257.0
20 TraesCS1D01G316800 chr1B 95.425 153 7 0 1 153 555009551 555009703 7.650000e-61 244.0
21 TraesCS1D01G316800 chr1B 95.425 153 7 0 1 153 555062833 555062985 7.650000e-61 244.0
22 TraesCS1D01G316800 chr1B 94.771 153 8 0 1 153 555068185 555068337 3.560000e-59 239.0
23 TraesCS1D01G316800 chr1B 94.771 153 8 0 1 153 555073528 555073680 3.560000e-59 239.0
24 TraesCS1D01G316800 chr1B 94.771 153 7 1 1 153 555014906 555015057 1.280000e-58 237.0
25 TraesCS1D01G316800 chrUn 92.082 1023 55 10 1759 2765 385318805 385319817 0.000000e+00 1417.0
26 TraesCS1D01G316800 chrUn 91.887 1023 56 11 1759 2765 298504752 298505763 0.000000e+00 1404.0
27 TraesCS1D01G316800 chrUn 91.825 526 31 5 2252 2765 413506873 413507398 0.000000e+00 723.0
28 TraesCS1D01G316800 chrUn 94.771 153 8 0 1 153 11272373 11272221 3.560000e-59 239.0
29 TraesCS1D01G316800 chr5D 92.889 225 13 2 422 645 421982589 421982367 9.550000e-85 324.0
30 TraesCS1D01G316800 chr5D 85.502 269 19 5 146 395 371848300 371848567 2.110000e-66 263.0
31 TraesCS1D01G316800 chr6B 90.612 245 20 2 151 395 610062857 610063098 3.440000e-84 322.0
32 TraesCS1D01G316800 chr2D 92.793 222 14 1 424 645 284560176 284559957 1.240000e-83 320.0
33 TraesCS1D01G316800 chr2D 91.556 225 17 1 422 646 357651002 357650780 2.670000e-80 309.0
34 TraesCS1D01G316800 chr4A 92.035 226 16 1 420 645 640236069 640235846 1.600000e-82 316.0
35 TraesCS1D01G316800 chr7D 92.342 222 15 1 425 646 326052763 326052544 5.750000e-82 315.0
36 TraesCS1D01G316800 chr7D 92.857 196 13 1 205 399 239882450 239882255 1.620000e-72 283.0
37 TraesCS1D01G316800 chr3D 92.342 222 15 1 424 645 108291062 108290843 5.750000e-82 315.0
38 TraesCS1D01G316800 chr3D 92.000 225 14 3 421 645 2720102 2719882 2.070000e-81 313.0
39 TraesCS1D01G316800 chr5A 90.456 241 17 2 154 394 679842236 679842470 2.070000e-81 313.0
40 TraesCS1D01G316800 chr5A 88.664 247 22 3 154 395 216994927 216994682 2.080000e-76 296.0
41 TraesCS1D01G316800 chr7A 95.288 191 9 0 205 395 202997048 202997238 1.240000e-78 303.0
42 TraesCS1D01G316800 chr7B 94.764 191 9 1 205 395 514515429 514515240 2.080000e-76 296.0
43 TraesCS1D01G316800 chr2B 94.241 191 11 0 205 395 357919628 357919818 2.690000e-75 292.0
44 TraesCS1D01G316800 chr2B 84.328 268 20 9 147 394 399328214 399328479 2.750000e-60 243.0
45 TraesCS1D01G316800 chr6D 87.705 244 23 3 156 395 37460930 37460690 7.540000e-71 278.0
46 TraesCS1D01G316800 chr4B 83.654 208 14 7 147 334 215669203 215669410 7.870000e-41 178.0
47 TraesCS1D01G316800 chr4D 93.846 65 3 1 147 210 332377516 332377452 2.270000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G316800 chr1D 411748704 411751468 2764 False 5107.0 5107 100.000000 1 2765 1 chr1D.!!$F3 2764
1 TraesCS1D01G316800 chr1D 411697429 411698657 1228 False 1698.0 1698 91.539000 641 1880 1 chr1D.!!$F2 1239
2 TraesCS1D01G316800 chr1D 411582713 411584985 2272 False 1339.5 2446 92.754500 1 2765 2 chr1D.!!$F5 2764
3 TraesCS1D01G316800 chr1D 411703635 411706328 2693 False 621.0 1009 93.081000 1 2765 2 chr1D.!!$F6 2764
4 TraesCS1D01G316800 chr1A 508318008 508320137 2129 False 2887.0 2887 91.264000 641 2765 1 chr1A.!!$F1 2124
5 TraesCS1D01G316800 chr1A 508285708 508288016 2308 False 1569.5 2900 93.064000 1 2765 2 chr1A.!!$F2 2764
6 TraesCS1D01G316800 chr1B 555122133 555124256 2123 False 2760.0 2760 90.269000 641 2765 1 chr1B.!!$F3 2124
7 TraesCS1D01G316800 chr1B 555087748 555089251 1503 False 1770.0 1770 87.896000 653 2186 1 chr1B.!!$F2 1533
8 TraesCS1D01G316800 chr1B 555062833 555075244 12411 False 1080.0 1951 92.113667 1 2186 6 chr1B.!!$F5 2185
9 TraesCS1D01G316800 chr1B 555009551 555016620 7069 False 1062.5 1901 91.963000 1 2186 4 chr1B.!!$F4 2185
10 TraesCS1D01G316800 chrUn 385318805 385319817 1012 False 1417.0 1417 92.082000 1759 2765 1 chrUn.!!$F2 1006
11 TraesCS1D01G316800 chrUn 298504752 298505763 1011 False 1404.0 1404 91.887000 1759 2765 1 chrUn.!!$F1 1006
12 TraesCS1D01G316800 chrUn 413506873 413507398 525 False 723.0 723 91.825000 2252 2765 1 chrUn.!!$F3 513

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
455 5808 0.095245 CTCAGTTTACATGGTGCGCG 59.905 55.0 0.00 0.0 0.0 6.86 F
623 5976 0.102481 AGGTATACGCGCAGGACTTG 59.898 55.0 5.73 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 6877 0.186386 ACTCGCTATGGGGCTAGAGT 59.814 55.0 0.0 0.0 34.54 3.24 R
2453 13620 0.324460 CTTAGGACGAGACCAGGGGT 60.324 60.0 0.0 0.0 39.44 4.95 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
43 5396 6.568869 AGTGAATTTCCGTGAATTTTGACAA 58.431 32.000 0.00 0.00 29.75 3.18
121 5474 4.426416 TGACGTACCAATGTAGTACATGC 58.574 43.478 16.46 0.00 37.97 4.06
138 5491 3.931130 CGCGCACCAACACGTTCA 61.931 61.111 8.75 0.00 0.00 3.18
150 5503 5.355910 ACCAACACGTTCAGATTGTTTAACT 59.644 36.000 0.00 0.00 30.98 2.24
151 5504 6.539464 ACCAACACGTTCAGATTGTTTAACTA 59.461 34.615 0.00 0.00 30.98 2.24
152 5505 7.069569 CCAACACGTTCAGATTGTTTAACTAG 58.930 38.462 0.00 0.00 30.98 2.57
153 5506 7.254658 CCAACACGTTCAGATTGTTTAACTAGT 60.255 37.037 0.00 0.00 30.98 2.57
154 5507 8.757789 CAACACGTTCAGATTGTTTAACTAGTA 58.242 33.333 0.00 0.00 30.98 1.82
155 5508 8.290663 ACACGTTCAGATTGTTTAACTAGTAC 57.709 34.615 0.00 0.00 0.00 2.73
156 5509 8.139989 ACACGTTCAGATTGTTTAACTAGTACT 58.860 33.333 0.00 0.00 0.00 2.73
157 5510 8.636843 CACGTTCAGATTGTTTAACTAGTACTC 58.363 37.037 0.00 0.00 0.00 2.59
158 5511 8.574737 ACGTTCAGATTGTTTAACTAGTACTCT 58.425 33.333 0.00 0.00 0.00 3.24
159 5512 9.063739 CGTTCAGATTGTTTAACTAGTACTCTC 57.936 37.037 0.00 0.00 0.00 3.20
162 5515 8.958506 TCAGATTGTTTAACTAGTACTCTCTCC 58.041 37.037 0.00 0.00 0.00 3.71
163 5516 7.911205 CAGATTGTTTAACTAGTACTCTCTCCG 59.089 40.741 0.00 0.00 0.00 4.63
164 5517 7.611079 AGATTGTTTAACTAGTACTCTCTCCGT 59.389 37.037 0.00 0.00 0.00 4.69
165 5518 7.516198 TTGTTTAACTAGTACTCTCTCCGTT 57.484 36.000 0.00 0.00 0.00 4.44
166 5519 7.516198 TGTTTAACTAGTACTCTCTCCGTTT 57.484 36.000 0.00 0.00 0.00 3.60
167 5520 7.588512 TGTTTAACTAGTACTCTCTCCGTTTC 58.411 38.462 0.00 0.00 0.00 2.78
168 5521 7.446625 TGTTTAACTAGTACTCTCTCCGTTTCT 59.553 37.037 0.00 0.00 0.00 2.52
169 5522 7.992754 TTAACTAGTACTCTCTCCGTTTCTT 57.007 36.000 0.00 0.00 0.00 2.52
170 5523 6.897706 AACTAGTACTCTCTCCGTTTCTTT 57.102 37.500 0.00 0.00 0.00 2.52
171 5524 6.897706 ACTAGTACTCTCTCCGTTTCTTTT 57.102 37.500 0.00 0.00 0.00 2.27
172 5525 7.287512 ACTAGTACTCTCTCCGTTTCTTTTT 57.712 36.000 0.00 0.00 0.00 1.94
173 5526 8.401490 ACTAGTACTCTCTCCGTTTCTTTTTA 57.599 34.615 0.00 0.00 0.00 1.52
174 5527 8.513774 ACTAGTACTCTCTCCGTTTCTTTTTAG 58.486 37.037 0.00 0.00 0.00 1.85
175 5528 7.287512 AGTACTCTCTCCGTTTCTTTTTAGT 57.712 36.000 0.00 0.00 0.00 2.24
176 5529 7.724287 AGTACTCTCTCCGTTTCTTTTTAGTT 58.276 34.615 0.00 0.00 0.00 2.24
177 5530 8.202811 AGTACTCTCTCCGTTTCTTTTTAGTTT 58.797 33.333 0.00 0.00 0.00 2.66
178 5531 7.247929 ACTCTCTCCGTTTCTTTTTAGTTTG 57.752 36.000 0.00 0.00 0.00 2.93
179 5532 6.056428 TCTCTCCGTTTCTTTTTAGTTTGC 57.944 37.500 0.00 0.00 0.00 3.68
180 5533 5.587043 TCTCTCCGTTTCTTTTTAGTTTGCA 59.413 36.000 0.00 0.00 0.00 4.08
181 5534 6.262273 TCTCTCCGTTTCTTTTTAGTTTGCAT 59.738 34.615 0.00 0.00 0.00 3.96
182 5535 7.442969 TCTCTCCGTTTCTTTTTAGTTTGCATA 59.557 33.333 0.00 0.00 0.00 3.14
183 5536 8.106247 TCTCCGTTTCTTTTTAGTTTGCATAT 57.894 30.769 0.00 0.00 0.00 1.78
184 5537 9.221933 TCTCCGTTTCTTTTTAGTTTGCATATA 57.778 29.630 0.00 0.00 0.00 0.86
185 5538 9.834628 CTCCGTTTCTTTTTAGTTTGCATATAA 57.165 29.630 0.00 0.00 0.00 0.98
186 5539 9.834628 TCCGTTTCTTTTTAGTTTGCATATAAG 57.165 29.630 0.00 0.00 0.00 1.73
187 5540 9.834628 CCGTTTCTTTTTAGTTTGCATATAAGA 57.165 29.630 0.00 0.00 0.00 2.10
199 5552 8.971073 AGTTTGCATATAAGATTTAGCCAAAGT 58.029 29.630 0.00 0.00 0.00 2.66
200 5553 9.237846 GTTTGCATATAAGATTTAGCCAAAGTC 57.762 33.333 0.00 0.00 0.00 3.01
201 5554 8.518430 TTGCATATAAGATTTAGCCAAAGTCA 57.482 30.769 0.00 0.00 0.00 3.41
202 5555 8.518430 TGCATATAAGATTTAGCCAAAGTCAA 57.482 30.769 0.00 0.00 0.00 3.18
203 5556 8.965819 TGCATATAAGATTTAGCCAAAGTCAAA 58.034 29.630 0.00 0.00 0.00 2.69
204 5557 9.237846 GCATATAAGATTTAGCCAAAGTCAAAC 57.762 33.333 0.00 0.00 0.00 2.93
223 5576 9.793259 AGTCAAACTTTGTAGGAAAAGATATCA 57.207 29.630 5.32 0.00 39.12 2.15
232 5585 9.513906 TTGTAGGAAAAGATATCAACATTCACA 57.486 29.630 5.32 0.00 0.00 3.58
233 5586 8.946085 TGTAGGAAAAGATATCAACATTCACAC 58.054 33.333 5.32 6.01 0.00 3.82
234 5587 9.167311 GTAGGAAAAGATATCAACATTCACACT 57.833 33.333 5.32 0.63 0.00 3.55
236 5589 9.911788 AGGAAAAGATATCAACATTCACACTAT 57.088 29.630 5.32 0.00 0.00 2.12
237 5590 9.941664 GGAAAAGATATCAACATTCACACTATG 57.058 33.333 5.32 0.00 0.00 2.23
359 5712 9.984190 ACTTTACAAAGTTTGACTTTAACCAAA 57.016 25.926 22.23 6.72 45.84 3.28
386 5739 9.834628 TCTTATATGCAAACTAAAAAGAAACGG 57.165 29.630 0.00 0.00 0.00 4.44
387 5740 9.834628 CTTATATGCAAACTAAAAAGAAACGGA 57.165 29.630 0.00 0.00 0.00 4.69
388 5741 9.834628 TTATATGCAAACTAAAAAGAAACGGAG 57.165 29.630 0.00 0.00 0.00 4.63
389 5742 4.927422 TGCAAACTAAAAAGAAACGGAGG 58.073 39.130 0.00 0.00 0.00 4.30
390 5743 4.202070 TGCAAACTAAAAAGAAACGGAGGG 60.202 41.667 0.00 0.00 0.00 4.30
391 5744 4.037089 GCAAACTAAAAAGAAACGGAGGGA 59.963 41.667 0.00 0.00 0.00 4.20
392 5745 5.758924 CAAACTAAAAAGAAACGGAGGGAG 58.241 41.667 0.00 0.00 0.00 4.30
412 5765 8.429237 AGGGAGTAGAGAATATGTTGGATTAG 57.571 38.462 0.00 0.00 0.00 1.73
430 5783 9.895138 TTGGATTAGTTTATGTTTAGTACTCCC 57.105 33.333 0.00 0.00 0.00 4.30
431 5784 9.275572 TGGATTAGTTTATGTTTAGTACTCCCT 57.724 33.333 0.00 0.00 0.00 4.20
432 5785 9.761504 GGATTAGTTTATGTTTAGTACTCCCTC 57.238 37.037 0.00 0.00 0.00 4.30
435 5788 9.765295 TTAGTTTATGTTTAGTACTCCCTCTCT 57.235 33.333 0.00 0.00 0.00 3.10
436 5789 8.296211 AGTTTATGTTTAGTACTCCCTCTCTC 57.704 38.462 0.00 0.00 0.00 3.20
437 5790 8.117312 AGTTTATGTTTAGTACTCCCTCTCTCT 58.883 37.037 0.00 0.00 0.00 3.10
438 5791 8.407832 GTTTATGTTTAGTACTCCCTCTCTCTC 58.592 40.741 0.00 0.00 0.00 3.20
439 5792 5.516059 TGTTTAGTACTCCCTCTCTCTCA 57.484 43.478 0.00 0.00 0.00 3.27
440 5793 5.502079 TGTTTAGTACTCCCTCTCTCTCAG 58.498 45.833 0.00 0.00 0.00 3.35
441 5794 5.014333 TGTTTAGTACTCCCTCTCTCTCAGT 59.986 44.000 0.00 0.00 0.00 3.41
442 5795 5.782677 TTAGTACTCCCTCTCTCTCAGTT 57.217 43.478 0.00 0.00 0.00 3.16
443 5796 4.668138 AGTACTCCCTCTCTCTCAGTTT 57.332 45.455 0.00 0.00 0.00 2.66
444 5797 5.782677 AGTACTCCCTCTCTCTCAGTTTA 57.217 43.478 0.00 0.00 0.00 2.01
445 5798 5.503002 AGTACTCCCTCTCTCTCAGTTTAC 58.497 45.833 0.00 0.00 0.00 2.01
446 5799 4.390129 ACTCCCTCTCTCTCAGTTTACA 57.610 45.455 0.00 0.00 0.00 2.41
447 5800 4.941713 ACTCCCTCTCTCTCAGTTTACAT 58.058 43.478 0.00 0.00 0.00 2.29
448 5801 4.709397 ACTCCCTCTCTCTCAGTTTACATG 59.291 45.833 0.00 0.00 0.00 3.21
449 5802 4.026744 TCCCTCTCTCTCAGTTTACATGG 58.973 47.826 0.00 0.00 0.00 3.66
450 5803 3.772025 CCCTCTCTCTCAGTTTACATGGT 59.228 47.826 0.00 0.00 0.00 3.55
451 5804 4.382470 CCCTCTCTCTCAGTTTACATGGTG 60.382 50.000 0.00 0.00 0.00 4.17
452 5805 4.180057 CTCTCTCTCAGTTTACATGGTGC 58.820 47.826 0.00 0.00 0.00 5.01
453 5806 2.926200 CTCTCTCAGTTTACATGGTGCG 59.074 50.000 0.00 0.00 0.00 5.34
454 5807 1.394917 CTCTCAGTTTACATGGTGCGC 59.605 52.381 0.00 0.00 0.00 6.09
455 5808 0.095245 CTCAGTTTACATGGTGCGCG 59.905 55.000 0.00 0.00 0.00 6.86
456 5809 1.511887 CAGTTTACATGGTGCGCGC 60.512 57.895 27.26 27.26 0.00 6.86
457 5810 2.202427 GTTTACATGGTGCGCGCC 60.202 61.111 32.83 32.83 0.00 6.53
458 5811 2.359354 TTTACATGGTGCGCGCCT 60.359 55.556 37.39 22.19 0.00 5.52
459 5812 1.079057 TTTACATGGTGCGCGCCTA 60.079 52.632 37.39 24.95 0.00 3.93
460 5813 1.363145 TTTACATGGTGCGCGCCTAC 61.363 55.000 37.39 21.13 0.00 3.18
461 5814 3.726595 TACATGGTGCGCGCCTACC 62.727 63.158 37.39 28.33 37.48 3.18
465 5818 4.151582 GGTGCGCGCCTACCCTTA 62.152 66.667 32.27 3.44 0.00 2.69
466 5819 2.125431 GTGCGCGCCTACCCTTAA 60.125 61.111 30.77 2.53 0.00 1.85
467 5820 2.171725 GTGCGCGCCTACCCTTAAG 61.172 63.158 30.77 0.00 0.00 1.85
468 5821 2.186125 GCGCGCCTACCCTTAAGT 59.814 61.111 23.24 0.00 0.00 2.24
469 5822 1.881709 GCGCGCCTACCCTTAAGTC 60.882 63.158 23.24 0.00 0.00 3.01
470 5823 1.588139 CGCGCCTACCCTTAAGTCG 60.588 63.158 0.00 0.00 0.00 4.18
471 5824 1.514553 GCGCCTACCCTTAAGTCGT 59.485 57.895 0.00 0.00 0.00 4.34
472 5825 0.527169 GCGCCTACCCTTAAGTCGTC 60.527 60.000 0.00 0.00 0.00 4.20
473 5826 0.813184 CGCCTACCCTTAAGTCGTCA 59.187 55.000 0.97 0.00 0.00 4.35
474 5827 1.203052 CGCCTACCCTTAAGTCGTCAA 59.797 52.381 0.97 0.00 0.00 3.18
475 5828 2.159142 CGCCTACCCTTAAGTCGTCAAT 60.159 50.000 0.97 0.00 0.00 2.57
476 5829 3.677976 CGCCTACCCTTAAGTCGTCAATT 60.678 47.826 0.97 0.00 0.00 2.32
477 5830 4.259356 GCCTACCCTTAAGTCGTCAATTT 58.741 43.478 0.97 0.00 0.00 1.82
478 5831 4.698780 GCCTACCCTTAAGTCGTCAATTTT 59.301 41.667 0.97 0.00 0.00 1.82
479 5832 5.876460 GCCTACCCTTAAGTCGTCAATTTTA 59.124 40.000 0.97 0.00 0.00 1.52
480 5833 6.183360 GCCTACCCTTAAGTCGTCAATTTTAC 60.183 42.308 0.97 0.00 0.00 2.01
481 5834 6.314648 CCTACCCTTAAGTCGTCAATTTTACC 59.685 42.308 0.97 0.00 0.00 2.85
482 5835 5.623169 ACCCTTAAGTCGTCAATTTTACCA 58.377 37.500 0.97 0.00 0.00 3.25
483 5836 6.063404 ACCCTTAAGTCGTCAATTTTACCAA 58.937 36.000 0.97 0.00 0.00 3.67
484 5837 6.016860 ACCCTTAAGTCGTCAATTTTACCAAC 60.017 38.462 0.97 0.00 0.00 3.77
485 5838 6.376177 CCTTAAGTCGTCAATTTTACCAACC 58.624 40.000 0.97 0.00 0.00 3.77
486 5839 6.206048 CCTTAAGTCGTCAATTTTACCAACCT 59.794 38.462 0.97 0.00 0.00 3.50
487 5840 7.388500 CCTTAAGTCGTCAATTTTACCAACCTA 59.612 37.037 0.97 0.00 0.00 3.08
488 5841 8.674263 TTAAGTCGTCAATTTTACCAACCTAA 57.326 30.769 0.00 0.00 0.00 2.69
489 5842 7.754851 AAGTCGTCAATTTTACCAACCTAAT 57.245 32.000 0.00 0.00 0.00 1.73
490 5843 7.754851 AGTCGTCAATTTTACCAACCTAATT 57.245 32.000 0.00 0.00 0.00 1.40
491 5844 7.813645 AGTCGTCAATTTTACCAACCTAATTC 58.186 34.615 0.00 0.00 0.00 2.17
492 5845 7.446013 AGTCGTCAATTTTACCAACCTAATTCA 59.554 33.333 0.00 0.00 0.00 2.57
493 5846 8.077386 GTCGTCAATTTTACCAACCTAATTCAA 58.923 33.333 0.00 0.00 0.00 2.69
494 5847 8.293867 TCGTCAATTTTACCAACCTAATTCAAG 58.706 33.333 0.00 0.00 0.00 3.02
495 5848 8.079809 CGTCAATTTTACCAACCTAATTCAAGT 58.920 33.333 0.00 0.00 0.00 3.16
496 5849 9.406828 GTCAATTTTACCAACCTAATTCAAGTC 57.593 33.333 0.00 0.00 0.00 3.01
497 5850 9.137459 TCAATTTTACCAACCTAATTCAAGTCA 57.863 29.630 0.00 0.00 0.00 3.41
498 5851 9.927668 CAATTTTACCAACCTAATTCAAGTCAT 57.072 29.630 0.00 0.00 0.00 3.06
551 5904 7.301054 AGCTTCAGATGTTCTATTTTCAAACG 58.699 34.615 0.00 0.00 0.00 3.60
552 5905 6.524586 GCTTCAGATGTTCTATTTTCAAACGG 59.475 38.462 0.00 0.00 0.00 4.44
553 5906 7.504924 TTCAGATGTTCTATTTTCAAACGGT 57.495 32.000 0.00 0.00 0.00 4.83
554 5907 8.610248 TTCAGATGTTCTATTTTCAAACGGTA 57.390 30.769 0.00 0.00 0.00 4.02
555 5908 8.786826 TCAGATGTTCTATTTTCAAACGGTAT 57.213 30.769 0.00 0.00 0.00 2.73
556 5909 9.878667 TCAGATGTTCTATTTTCAAACGGTATA 57.121 29.630 0.00 0.00 0.00 1.47
614 5967 6.833342 AAATTAACAACCTAGGTATACGCG 57.167 37.500 16.67 3.53 0.00 6.01
615 5968 2.214387 AACAACCTAGGTATACGCGC 57.786 50.000 16.67 0.00 0.00 6.86
616 5969 1.105457 ACAACCTAGGTATACGCGCA 58.895 50.000 16.67 0.00 0.00 6.09
617 5970 1.066605 ACAACCTAGGTATACGCGCAG 59.933 52.381 16.67 2.42 0.00 5.18
618 5971 0.672342 AACCTAGGTATACGCGCAGG 59.328 55.000 16.67 6.39 0.00 4.85
619 5972 0.179009 ACCTAGGTATACGCGCAGGA 60.179 55.000 14.41 0.00 0.00 3.86
620 5973 0.240411 CCTAGGTATACGCGCAGGAC 59.760 60.000 5.73 0.00 0.00 3.85
621 5974 1.236628 CTAGGTATACGCGCAGGACT 58.763 55.000 5.73 1.68 0.00 3.85
622 5975 1.607628 CTAGGTATACGCGCAGGACTT 59.392 52.381 5.73 0.00 0.00 3.01
623 5976 0.102481 AGGTATACGCGCAGGACTTG 59.898 55.000 5.73 0.00 0.00 3.16
624 5977 0.179119 GGTATACGCGCAGGACTTGT 60.179 55.000 5.73 0.00 0.00 3.16
625 5978 1.066002 GGTATACGCGCAGGACTTGTA 59.934 52.381 5.73 0.00 0.00 2.41
626 5979 2.480073 GGTATACGCGCAGGACTTGTAA 60.480 50.000 5.73 0.00 0.00 2.41
627 5980 2.373540 ATACGCGCAGGACTTGTAAA 57.626 45.000 5.73 0.00 0.00 2.01
628 5981 1.421382 TACGCGCAGGACTTGTAAAC 58.579 50.000 5.73 0.00 0.00 2.01
629 5982 0.249741 ACGCGCAGGACTTGTAAACT 60.250 50.000 5.73 0.00 0.00 2.66
630 5983 0.163788 CGCGCAGGACTTGTAAACTG 59.836 55.000 8.75 0.00 0.00 3.16
631 5984 1.508632 GCGCAGGACTTGTAAACTGA 58.491 50.000 0.30 0.00 32.86 3.41
632 5985 1.871039 GCGCAGGACTTGTAAACTGAA 59.129 47.619 0.30 0.00 32.86 3.02
633 5986 2.289547 GCGCAGGACTTGTAAACTGAAA 59.710 45.455 0.30 0.00 32.86 2.69
634 5987 3.848554 GCGCAGGACTTGTAAACTGAAAC 60.849 47.826 0.30 0.00 32.86 2.78
635 5988 3.603857 CGCAGGACTTGTAAACTGAAACG 60.604 47.826 0.00 0.00 32.86 3.60
636 5989 3.303791 GCAGGACTTGTAAACTGAAACGG 60.304 47.826 0.00 0.00 32.86 4.44
637 5990 4.124238 CAGGACTTGTAAACTGAAACGGA 58.876 43.478 0.00 0.00 32.86 4.69
638 5991 4.211374 CAGGACTTGTAAACTGAAACGGAG 59.789 45.833 0.00 0.00 32.86 4.63
639 5992 3.497262 GGACTTGTAAACTGAAACGGAGG 59.503 47.826 0.00 0.00 0.00 4.30
645 5998 6.594788 TGTAAACTGAAACGGAGGTAGTAT 57.405 37.500 0.00 0.00 0.00 2.12
655 6008 0.661552 GAGGTAGTATGCTCGTGCGA 59.338 55.000 4.84 0.00 43.34 5.10
672 6025 0.805614 CGAGCATCCGGATCTATCGT 59.194 55.000 24.28 5.64 0.00 3.73
717 6070 7.330700 GCTACTGATGATCTCCTAACTAATTGC 59.669 40.741 0.00 0.00 0.00 3.56
746 6099 5.241506 ACATGGTCTACTGACAATTTGGTTG 59.758 40.000 0.00 0.00 44.61 3.77
751 6108 6.371389 GTCTACTGACAATTTGGTTGCTAAC 58.629 40.000 0.78 0.00 41.69 2.34
769 6126 0.767060 ACCGTTTTCTCCCCAGACCT 60.767 55.000 0.00 0.00 0.00 3.85
896 6269 6.139013 CGTGTACGATGTTATTTTCATGCATG 59.861 38.462 21.07 21.07 43.02 4.06
938 6311 1.279527 CCTCGTCAACGCGCTTACAA 61.280 55.000 5.73 0.00 39.60 2.41
939 6312 0.713883 CTCGTCAACGCGCTTACAAT 59.286 50.000 5.73 0.00 39.60 2.71
951 6324 3.363378 GCGCTTACAATCGATGATCCTTG 60.363 47.826 0.00 0.00 0.00 3.61
1004 6377 7.978414 ACACACTAGTATCAATGATCTCACAAG 59.022 37.037 0.00 0.00 0.00 3.16
1057 6430 2.005451 CTTCCTTGGAGCTTGTGATCG 58.995 52.381 0.00 0.00 0.00 3.69
1109 6484 0.527817 CTAGCGCTAACTTCCACCCG 60.528 60.000 19.37 0.00 0.00 5.28
1120 6495 2.708861 ACTTCCACCCGCCATCATATTA 59.291 45.455 0.00 0.00 0.00 0.98
1126 6594 5.885352 TCCACCCGCCATCATATTATTATTG 59.115 40.000 0.00 0.00 0.00 1.90
1169 6642 9.796120 CAGCTAGCTAGTAGATCCATATTTAAC 57.204 37.037 18.86 0.00 0.00 2.01
1206 6679 3.430929 GCTCTTATTCTCATCACCGTGGT 60.431 47.826 0.00 0.00 0.00 4.16
1210 6683 2.672961 TTCTCATCACCGTGGTCATC 57.327 50.000 0.00 0.00 0.00 2.92
1278 6751 2.431942 CGGTTCGTGGGACCTTCG 60.432 66.667 0.00 0.00 34.95 3.79
1320 6793 4.082125 GTTTCCAGAATCAGGTTCACCAT 58.918 43.478 0.00 0.00 39.39 3.55
1404 6877 1.899814 AGGGTATGACTCTTGCAACGA 59.100 47.619 0.00 0.00 0.00 3.85
1408 6881 3.367498 GGTATGACTCTTGCAACGACTCT 60.367 47.826 0.00 0.00 0.00 3.24
1422 6895 0.885196 GACTCTAGCCCCATAGCGAG 59.115 60.000 0.00 0.00 36.89 5.03
1429 6902 1.912220 CCCCATAGCGAGTTTCCCA 59.088 57.895 0.00 0.00 0.00 4.37
1537 7010 1.001597 GTCGAGGTCAACGTCAAGTCT 60.002 52.381 0.00 0.00 0.00 3.24
1542 7015 4.618965 GAGGTCAACGTCAAGTCTAAAGT 58.381 43.478 0.00 0.00 0.00 2.66
1549 7022 3.251729 ACGTCAAGTCTAAAGTAGTGCGA 59.748 43.478 0.00 0.00 0.00 5.10
1553 7026 6.376978 GTCAAGTCTAAAGTAGTGCGAACTA 58.623 40.000 0.00 0.00 0.00 2.24
1616 7089 4.890581 AGTCCGAGACAGTATTAAGCTCAT 59.109 41.667 6.78 0.00 34.60 2.90
1835 7310 5.397360 AGACATCTTCTTGGAAAAACCCAT 58.603 37.500 0.00 0.00 35.87 4.00
1836 7311 5.244626 AGACATCTTCTTGGAAAAACCCATG 59.755 40.000 0.00 0.00 35.87 3.66
1898 7373 1.687660 TGTGTTGGCTGCAATGACATT 59.312 42.857 0.50 0.00 0.00 2.71
1899 7374 2.889678 TGTGTTGGCTGCAATGACATTA 59.110 40.909 0.50 0.00 0.00 1.90
1900 7375 3.244976 GTGTTGGCTGCAATGACATTAC 58.755 45.455 0.50 0.00 0.00 1.89
1901 7376 2.889678 TGTTGGCTGCAATGACATTACA 59.110 40.909 0.50 0.25 0.00 2.41
1902 7377 3.510753 TGTTGGCTGCAATGACATTACAT 59.489 39.130 0.50 0.00 0.00 2.29
1903 7378 3.786516 TGGCTGCAATGACATTACATG 57.213 42.857 0.50 0.00 0.00 3.21
1904 7379 3.354467 TGGCTGCAATGACATTACATGA 58.646 40.909 0.00 0.00 0.00 3.07
1905 7380 3.955551 TGGCTGCAATGACATTACATGAT 59.044 39.130 0.00 0.00 0.00 2.45
2092 7898 8.103935 TGAAAAGGAAAACAAACCCTAACAAAT 58.896 29.630 0.00 0.00 0.00 2.32
2171 13338 7.801547 AAGCATTGTCATATTTCGTTTTCAG 57.198 32.000 0.00 0.00 0.00 3.02
2221 13388 2.325761 CTGAAAACCGTCAGTAGTCCG 58.674 52.381 0.00 0.00 40.22 4.79
2222 13389 1.955778 TGAAAACCGTCAGTAGTCCGA 59.044 47.619 0.00 0.00 0.00 4.55
2237 13404 0.750249 TCCGAAGAGGATAATGCGCA 59.250 50.000 14.96 14.96 45.98 6.09
2238 13405 1.138069 TCCGAAGAGGATAATGCGCAA 59.862 47.619 17.11 0.00 45.98 4.85
2287 13454 0.249699 TGGTGAGTGTACGCAGGTTG 60.250 55.000 9.48 0.00 0.00 3.77
2304 13471 1.936767 TTGGGGCCCTCATCATGGAC 61.937 60.000 25.93 0.18 0.00 4.02
2404 13571 5.888691 ATCGAGACGATGATGCTATAGTT 57.111 39.130 5.86 0.00 45.24 2.24
2414 13581 6.405176 CGATGATGCTATAGTTAGATGCCTCA 60.405 42.308 0.84 0.00 34.11 3.86
2450 13617 6.088824 GTCTCGTCTTATAAAGGTGTTCGAA 58.911 40.000 0.00 0.00 0.00 3.71
2451 13618 6.033302 GTCTCGTCTTATAAAGGTGTTCGAAC 59.967 42.308 21.42 21.42 0.00 3.95
2452 13619 6.017400 TCGTCTTATAAAGGTGTTCGAACT 57.983 37.500 27.32 10.73 0.00 3.01
2453 13620 7.119699 TCTCGTCTTATAAAGGTGTTCGAACTA 59.880 37.037 27.32 12.57 0.00 2.24
2455 13622 6.252228 CGTCTTATAAAGGTGTTCGAACTACC 59.748 42.308 28.07 28.07 33.27 3.18
2456 13623 6.533012 GTCTTATAAAGGTGTTCGAACTACCC 59.467 42.308 29.91 24.65 33.43 3.69
2457 13624 2.556144 AAAGGTGTTCGAACTACCCC 57.444 50.000 29.91 22.87 33.43 4.95
2458 13625 1.725803 AAGGTGTTCGAACTACCCCT 58.274 50.000 29.91 24.15 33.43 4.79
2459 13626 0.974383 AGGTGTTCGAACTACCCCTG 59.026 55.000 29.91 0.00 33.43 4.45
2460 13627 0.036671 GGTGTTCGAACTACCCCTGG 60.037 60.000 27.32 0.00 0.00 4.45
2461 13628 0.683412 GTGTTCGAACTACCCCTGGT 59.317 55.000 27.32 0.00 40.16 4.00
2462 13629 0.971386 TGTTCGAACTACCCCTGGTC 59.029 55.000 27.32 0.00 37.09 4.02
2463 13630 1.264295 GTTCGAACTACCCCTGGTCT 58.736 55.000 20.97 0.00 37.09 3.85
2466 13645 0.964358 CGAACTACCCCTGGTCTCGT 60.964 60.000 0.00 0.00 37.09 4.18
2471 13650 1.002069 TACCCCTGGTCTCGTCCTAA 58.998 55.000 0.00 0.00 37.09 2.69
2503 13682 1.000955 GACGAGGGCTTCTTGACTTGA 59.999 52.381 0.00 0.00 0.00 3.02
2612 13795 1.412710 CCATTGACCGCTTCCTAGCTA 59.587 52.381 0.00 0.00 45.51 3.32
2673 13856 5.072741 TCAAGCTTGTCTAGAATTTTGGCT 58.927 37.500 25.19 0.00 0.00 4.75
2744 13927 4.462834 TGTGTCAAATAAACCACACCAACA 59.537 37.500 0.00 0.00 38.73 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 5461 0.650512 GTGCGCGCATGTACTACATT 59.349 50.000 38.62 0.00 36.53 2.71
121 5474 3.838229 CTGAACGTGTTGGTGCGCG 62.838 63.158 0.00 0.00 46.38 6.86
138 5491 7.611079 ACGGAGAGAGTACTAGTTAAACAATCT 59.389 37.037 0.00 0.00 0.00 2.40
150 5503 8.401490 ACTAAAAAGAAACGGAGAGAGTACTA 57.599 34.615 0.00 0.00 0.00 1.82
151 5504 7.287512 ACTAAAAAGAAACGGAGAGAGTACT 57.712 36.000 0.00 0.00 0.00 2.73
152 5505 7.943413 AACTAAAAAGAAACGGAGAGAGTAC 57.057 36.000 0.00 0.00 0.00 2.73
153 5506 7.042254 GCAAACTAAAAAGAAACGGAGAGAGTA 60.042 37.037 0.00 0.00 0.00 2.59
154 5507 6.238402 GCAAACTAAAAAGAAACGGAGAGAGT 60.238 38.462 0.00 0.00 0.00 3.24
155 5508 6.136743 GCAAACTAAAAAGAAACGGAGAGAG 58.863 40.000 0.00 0.00 0.00 3.20
156 5509 5.587043 TGCAAACTAAAAAGAAACGGAGAGA 59.413 36.000 0.00 0.00 0.00 3.10
157 5510 5.816919 TGCAAACTAAAAAGAAACGGAGAG 58.183 37.500 0.00 0.00 0.00 3.20
158 5511 5.821516 TGCAAACTAAAAAGAAACGGAGA 57.178 34.783 0.00 0.00 0.00 3.71
159 5512 9.834628 TTATATGCAAACTAAAAAGAAACGGAG 57.165 29.630 0.00 0.00 0.00 4.63
160 5513 9.834628 CTTATATGCAAACTAAAAAGAAACGGA 57.165 29.630 0.00 0.00 0.00 4.69
161 5514 9.834628 TCTTATATGCAAACTAAAAAGAAACGG 57.165 29.630 0.00 0.00 0.00 4.44
173 5526 8.971073 ACTTTGGCTAAATCTTATATGCAAACT 58.029 29.630 0.00 0.00 0.00 2.66
174 5527 9.237846 GACTTTGGCTAAATCTTATATGCAAAC 57.762 33.333 0.00 0.00 0.00 2.93
175 5528 8.965819 TGACTTTGGCTAAATCTTATATGCAAA 58.034 29.630 0.00 0.00 0.00 3.68
176 5529 8.518430 TGACTTTGGCTAAATCTTATATGCAA 57.482 30.769 0.00 0.00 0.00 4.08
177 5530 8.518430 TTGACTTTGGCTAAATCTTATATGCA 57.482 30.769 0.00 0.00 0.00 3.96
178 5531 9.237846 GTTTGACTTTGGCTAAATCTTATATGC 57.762 33.333 0.00 0.00 0.00 3.14
197 5550 9.793259 TGATATCTTTTCCTACAAAGTTTGACT 57.207 29.630 22.23 3.29 35.56 3.41
206 5559 9.513906 TGTGAATGTTGATATCTTTTCCTACAA 57.486 29.630 3.98 0.00 0.00 2.41
207 5560 8.946085 GTGTGAATGTTGATATCTTTTCCTACA 58.054 33.333 3.98 0.30 0.00 2.74
208 5561 9.167311 AGTGTGAATGTTGATATCTTTTCCTAC 57.833 33.333 3.98 4.53 0.00 3.18
210 5563 9.911788 ATAGTGTGAATGTTGATATCTTTTCCT 57.088 29.630 3.98 0.00 0.00 3.36
211 5564 9.941664 CATAGTGTGAATGTTGATATCTTTTCC 57.058 33.333 3.98 0.00 0.00 3.13
360 5713 9.834628 CCGTTTCTTTTTAGTTTGCATATAAGA 57.165 29.630 0.00 0.00 0.00 2.10
361 5714 9.834628 TCCGTTTCTTTTTAGTTTGCATATAAG 57.165 29.630 0.00 0.00 0.00 1.73
362 5715 9.834628 CTCCGTTTCTTTTTAGTTTGCATATAA 57.165 29.630 0.00 0.00 0.00 0.98
363 5716 8.455682 CCTCCGTTTCTTTTTAGTTTGCATATA 58.544 33.333 0.00 0.00 0.00 0.86
364 5717 7.312899 CCTCCGTTTCTTTTTAGTTTGCATAT 58.687 34.615 0.00 0.00 0.00 1.78
365 5718 6.294286 CCCTCCGTTTCTTTTTAGTTTGCATA 60.294 38.462 0.00 0.00 0.00 3.14
366 5719 5.508994 CCCTCCGTTTCTTTTTAGTTTGCAT 60.509 40.000 0.00 0.00 0.00 3.96
367 5720 4.202070 CCCTCCGTTTCTTTTTAGTTTGCA 60.202 41.667 0.00 0.00 0.00 4.08
368 5721 4.037089 TCCCTCCGTTTCTTTTTAGTTTGC 59.963 41.667 0.00 0.00 0.00 3.68
369 5722 5.298527 ACTCCCTCCGTTTCTTTTTAGTTTG 59.701 40.000 0.00 0.00 0.00 2.93
370 5723 5.443283 ACTCCCTCCGTTTCTTTTTAGTTT 58.557 37.500 0.00 0.00 0.00 2.66
371 5724 5.045012 ACTCCCTCCGTTTCTTTTTAGTT 57.955 39.130 0.00 0.00 0.00 2.24
372 5725 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
373 5726 6.034161 TCTACTCCCTCCGTTTCTTTTTAG 57.966 41.667 0.00 0.00 0.00 1.85
374 5727 5.776716 TCTCTACTCCCTCCGTTTCTTTTTA 59.223 40.000 0.00 0.00 0.00 1.52
375 5728 4.591924 TCTCTACTCCCTCCGTTTCTTTTT 59.408 41.667 0.00 0.00 0.00 1.94
376 5729 4.158015 TCTCTACTCCCTCCGTTTCTTTT 58.842 43.478 0.00 0.00 0.00 2.27
377 5730 3.775910 TCTCTACTCCCTCCGTTTCTTT 58.224 45.455 0.00 0.00 0.00 2.52
378 5731 3.453059 TCTCTACTCCCTCCGTTTCTT 57.547 47.619 0.00 0.00 0.00 2.52
379 5732 3.453059 TTCTCTACTCCCTCCGTTTCT 57.547 47.619 0.00 0.00 0.00 2.52
380 5733 5.302313 ACATATTCTCTACTCCCTCCGTTTC 59.698 44.000 0.00 0.00 0.00 2.78
381 5734 5.209659 ACATATTCTCTACTCCCTCCGTTT 58.790 41.667 0.00 0.00 0.00 3.60
382 5735 4.805744 ACATATTCTCTACTCCCTCCGTT 58.194 43.478 0.00 0.00 0.00 4.44
383 5736 4.456662 ACATATTCTCTACTCCCTCCGT 57.543 45.455 0.00 0.00 0.00 4.69
384 5737 4.021894 CCAACATATTCTCTACTCCCTCCG 60.022 50.000 0.00 0.00 0.00 4.63
385 5738 5.148502 TCCAACATATTCTCTACTCCCTCC 58.851 45.833 0.00 0.00 0.00 4.30
386 5739 6.926630 ATCCAACATATTCTCTACTCCCTC 57.073 41.667 0.00 0.00 0.00 4.30
387 5740 8.013667 ACTAATCCAACATATTCTCTACTCCCT 58.986 37.037 0.00 0.00 0.00 4.20
388 5741 8.196378 ACTAATCCAACATATTCTCTACTCCC 57.804 38.462 0.00 0.00 0.00 4.30
412 5765 8.296211 AGAGAGAGGGAGTACTAAACATAAAC 57.704 38.462 0.00 0.00 0.00 2.01
421 5774 5.782677 AAACTGAGAGAGAGGGAGTACTA 57.217 43.478 0.00 0.00 0.00 1.82
422 5775 4.668138 AAACTGAGAGAGAGGGAGTACT 57.332 45.455 0.00 0.00 0.00 2.73
423 5776 5.254901 TGTAAACTGAGAGAGAGGGAGTAC 58.745 45.833 0.00 0.00 0.00 2.73
424 5777 5.516059 TGTAAACTGAGAGAGAGGGAGTA 57.484 43.478 0.00 0.00 0.00 2.59
425 5778 4.390129 TGTAAACTGAGAGAGAGGGAGT 57.610 45.455 0.00 0.00 0.00 3.85
426 5779 4.099266 CCATGTAAACTGAGAGAGAGGGAG 59.901 50.000 0.00 0.00 0.00 4.30
427 5780 4.026744 CCATGTAAACTGAGAGAGAGGGA 58.973 47.826 0.00 0.00 0.00 4.20
428 5781 3.772025 ACCATGTAAACTGAGAGAGAGGG 59.228 47.826 0.00 0.00 0.00 4.30
429 5782 4.753233 CACCATGTAAACTGAGAGAGAGG 58.247 47.826 0.00 0.00 0.00 3.69
430 5783 4.180057 GCACCATGTAAACTGAGAGAGAG 58.820 47.826 0.00 0.00 0.00 3.20
431 5784 3.367395 CGCACCATGTAAACTGAGAGAGA 60.367 47.826 0.00 0.00 0.00 3.10
432 5785 2.926200 CGCACCATGTAAACTGAGAGAG 59.074 50.000 0.00 0.00 0.00 3.20
433 5786 2.930887 GCGCACCATGTAAACTGAGAGA 60.931 50.000 0.30 0.00 0.00 3.10
434 5787 1.394917 GCGCACCATGTAAACTGAGAG 59.605 52.381 0.30 0.00 0.00 3.20
435 5788 1.438651 GCGCACCATGTAAACTGAGA 58.561 50.000 0.30 0.00 0.00 3.27
436 5789 0.095245 CGCGCACCATGTAAACTGAG 59.905 55.000 8.75 0.00 0.00 3.35
437 5790 1.906994 GCGCGCACCATGTAAACTGA 61.907 55.000 29.10 0.00 0.00 3.41
438 5791 1.511887 GCGCGCACCATGTAAACTG 60.512 57.895 29.10 0.00 0.00 3.16
439 5792 2.686816 GGCGCGCACCATGTAAACT 61.687 57.895 34.42 0.00 0.00 2.66
440 5793 1.363145 TAGGCGCGCACCATGTAAAC 61.363 55.000 34.42 11.21 0.00 2.01
441 5794 1.079057 TAGGCGCGCACCATGTAAA 60.079 52.632 34.42 3.38 0.00 2.01
442 5795 1.812093 GTAGGCGCGCACCATGTAA 60.812 57.895 34.42 5.10 0.00 2.41
443 5796 2.202824 GTAGGCGCGCACCATGTA 60.203 61.111 34.42 10.73 0.00 2.29
448 5801 3.668980 TTAAGGGTAGGCGCGCACC 62.669 63.158 34.42 30.53 0.00 5.01
449 5802 2.125431 TTAAGGGTAGGCGCGCAC 60.125 61.111 34.42 23.13 0.00 5.34
450 5803 2.185867 CTTAAGGGTAGGCGCGCA 59.814 61.111 34.42 10.96 0.00 6.09
451 5804 1.881709 GACTTAAGGGTAGGCGCGC 60.882 63.158 25.94 25.94 0.00 6.86
452 5805 1.588139 CGACTTAAGGGTAGGCGCG 60.588 63.158 0.00 0.00 37.33 6.86
453 5806 4.414732 CGACTTAAGGGTAGGCGC 57.585 61.111 7.53 0.00 37.33 6.53
455 5808 3.538634 ATTGACGACTTAAGGGTAGGC 57.461 47.619 7.53 0.00 0.00 3.93
456 5809 6.314648 GGTAAAATTGACGACTTAAGGGTAGG 59.685 42.308 7.53 0.00 0.00 3.18
457 5810 6.875195 TGGTAAAATTGACGACTTAAGGGTAG 59.125 38.462 7.53 0.00 0.00 3.18
458 5811 6.767456 TGGTAAAATTGACGACTTAAGGGTA 58.233 36.000 7.53 0.00 0.00 3.69
459 5812 5.623169 TGGTAAAATTGACGACTTAAGGGT 58.377 37.500 7.53 4.25 0.00 4.34
460 5813 6.376177 GTTGGTAAAATTGACGACTTAAGGG 58.624 40.000 7.53 0.72 0.00 3.95
461 5814 6.206048 AGGTTGGTAAAATTGACGACTTAAGG 59.794 38.462 7.53 0.00 0.00 2.69
462 5815 7.198306 AGGTTGGTAAAATTGACGACTTAAG 57.802 36.000 0.00 0.00 0.00 1.85
463 5816 8.674263 TTAGGTTGGTAAAATTGACGACTTAA 57.326 30.769 0.00 0.00 0.00 1.85
464 5817 8.851541 ATTAGGTTGGTAAAATTGACGACTTA 57.148 30.769 0.00 0.00 0.00 2.24
465 5818 7.754851 ATTAGGTTGGTAAAATTGACGACTT 57.245 32.000 0.00 0.00 0.00 3.01
466 5819 7.446013 TGAATTAGGTTGGTAAAATTGACGACT 59.554 33.333 0.00 0.00 0.00 4.18
467 5820 7.586747 TGAATTAGGTTGGTAAAATTGACGAC 58.413 34.615 0.00 0.00 0.00 4.34
468 5821 7.747155 TGAATTAGGTTGGTAAAATTGACGA 57.253 32.000 0.00 0.00 0.00 4.20
469 5822 8.079809 ACTTGAATTAGGTTGGTAAAATTGACG 58.920 33.333 0.00 0.00 0.00 4.35
470 5823 9.406828 GACTTGAATTAGGTTGGTAAAATTGAC 57.593 33.333 0.00 0.00 0.00 3.18
471 5824 9.137459 TGACTTGAATTAGGTTGGTAAAATTGA 57.863 29.630 0.00 0.00 0.00 2.57
472 5825 9.927668 ATGACTTGAATTAGGTTGGTAAAATTG 57.072 29.630 0.00 0.00 0.00 2.32
525 5878 7.805071 CGTTTGAAAATAGAACATCTGAAGCTT 59.195 33.333 0.00 0.00 0.00 3.74
526 5879 7.301054 CGTTTGAAAATAGAACATCTGAAGCT 58.699 34.615 0.00 0.00 0.00 3.74
527 5880 6.524586 CCGTTTGAAAATAGAACATCTGAAGC 59.475 38.462 0.00 0.00 0.00 3.86
528 5881 7.584987 ACCGTTTGAAAATAGAACATCTGAAG 58.415 34.615 0.00 0.00 0.00 3.02
529 5882 7.504924 ACCGTTTGAAAATAGAACATCTGAA 57.495 32.000 0.00 0.00 0.00 3.02
530 5883 8.786826 ATACCGTTTGAAAATAGAACATCTGA 57.213 30.769 0.00 0.00 0.00 3.27
588 5941 8.981647 CGCGTATACCTAGGTTGTTAATTTTAT 58.018 33.333 22.11 5.71 0.00 1.40
589 5942 7.042791 GCGCGTATACCTAGGTTGTTAATTTTA 60.043 37.037 22.11 0.00 0.00 1.52
590 5943 6.238184 GCGCGTATACCTAGGTTGTTAATTTT 60.238 38.462 22.11 0.00 0.00 1.82
591 5944 5.234972 GCGCGTATACCTAGGTTGTTAATTT 59.765 40.000 22.11 0.00 0.00 1.82
592 5945 4.746611 GCGCGTATACCTAGGTTGTTAATT 59.253 41.667 22.11 0.00 0.00 1.40
593 5946 4.202141 TGCGCGTATACCTAGGTTGTTAAT 60.202 41.667 22.11 9.64 0.00 1.40
594 5947 3.130164 TGCGCGTATACCTAGGTTGTTAA 59.870 43.478 22.11 0.75 0.00 2.01
595 5948 2.687425 TGCGCGTATACCTAGGTTGTTA 59.313 45.455 22.11 1.21 0.00 2.41
596 5949 1.477700 TGCGCGTATACCTAGGTTGTT 59.522 47.619 22.11 8.31 0.00 2.83
597 5950 1.066605 CTGCGCGTATACCTAGGTTGT 59.933 52.381 22.11 12.13 0.00 3.32
598 5951 1.602165 CCTGCGCGTATACCTAGGTTG 60.602 57.143 22.11 9.15 0.00 3.77
599 5952 0.672342 CCTGCGCGTATACCTAGGTT 59.328 55.000 22.11 10.62 0.00 3.50
600 5953 0.179009 TCCTGCGCGTATACCTAGGT 60.179 55.000 20.57 20.57 0.00 3.08
601 5954 0.240411 GTCCTGCGCGTATACCTAGG 59.760 60.000 7.41 7.41 0.00 3.02
602 5955 1.236628 AGTCCTGCGCGTATACCTAG 58.763 55.000 8.43 0.00 0.00 3.02
603 5956 1.335810 CAAGTCCTGCGCGTATACCTA 59.664 52.381 8.43 0.00 0.00 3.08
604 5957 0.102481 CAAGTCCTGCGCGTATACCT 59.898 55.000 8.43 0.00 0.00 3.08
605 5958 0.179119 ACAAGTCCTGCGCGTATACC 60.179 55.000 8.43 0.00 0.00 2.73
606 5959 2.480224 TACAAGTCCTGCGCGTATAC 57.520 50.000 8.43 4.74 0.00 1.47
607 5960 3.119388 AGTTTACAAGTCCTGCGCGTATA 60.119 43.478 8.43 0.00 0.00 1.47
608 5961 1.997606 GTTTACAAGTCCTGCGCGTAT 59.002 47.619 8.43 0.00 0.00 3.06
609 5962 1.000060 AGTTTACAAGTCCTGCGCGTA 60.000 47.619 8.43 0.71 0.00 4.42
610 5963 0.249741 AGTTTACAAGTCCTGCGCGT 60.250 50.000 8.43 0.00 0.00 6.01
611 5964 0.163788 CAGTTTACAAGTCCTGCGCG 59.836 55.000 0.00 0.00 0.00 6.86
612 5965 1.508632 TCAGTTTACAAGTCCTGCGC 58.491 50.000 0.00 0.00 0.00 6.09
613 5966 3.603857 CGTTTCAGTTTACAAGTCCTGCG 60.604 47.826 0.00 0.00 0.00 5.18
614 5967 3.303791 CCGTTTCAGTTTACAAGTCCTGC 60.304 47.826 0.00 0.00 0.00 4.85
615 5968 4.124238 TCCGTTTCAGTTTACAAGTCCTG 58.876 43.478 0.00 0.00 0.00 3.86
616 5969 4.377897 CTCCGTTTCAGTTTACAAGTCCT 58.622 43.478 0.00 0.00 0.00 3.85
617 5970 3.497262 CCTCCGTTTCAGTTTACAAGTCC 59.503 47.826 0.00 0.00 0.00 3.85
618 5971 4.124970 ACCTCCGTTTCAGTTTACAAGTC 58.875 43.478 0.00 0.00 0.00 3.01
619 5972 4.146745 ACCTCCGTTTCAGTTTACAAGT 57.853 40.909 0.00 0.00 0.00 3.16
620 5973 5.295152 ACTACCTCCGTTTCAGTTTACAAG 58.705 41.667 0.00 0.00 0.00 3.16
621 5974 5.280654 ACTACCTCCGTTTCAGTTTACAA 57.719 39.130 0.00 0.00 0.00 2.41
622 5975 4.942761 ACTACCTCCGTTTCAGTTTACA 57.057 40.909 0.00 0.00 0.00 2.41
623 5976 5.290400 GCATACTACCTCCGTTTCAGTTTAC 59.710 44.000 0.00 0.00 0.00 2.01
624 5977 5.186409 AGCATACTACCTCCGTTTCAGTTTA 59.814 40.000 0.00 0.00 0.00 2.01
625 5978 4.020485 AGCATACTACCTCCGTTTCAGTTT 60.020 41.667 0.00 0.00 0.00 2.66
626 5979 3.514309 AGCATACTACCTCCGTTTCAGTT 59.486 43.478 0.00 0.00 0.00 3.16
627 5980 3.097614 AGCATACTACCTCCGTTTCAGT 58.902 45.455 0.00 0.00 0.00 3.41
628 5981 3.707793 GAGCATACTACCTCCGTTTCAG 58.292 50.000 0.00 0.00 0.00 3.02
629 5982 2.098607 CGAGCATACTACCTCCGTTTCA 59.901 50.000 0.00 0.00 0.00 2.69
630 5983 2.098770 ACGAGCATACTACCTCCGTTTC 59.901 50.000 0.00 0.00 0.00 2.78
631 5984 2.097825 ACGAGCATACTACCTCCGTTT 58.902 47.619 0.00 0.00 0.00 3.60
632 5985 1.404391 CACGAGCATACTACCTCCGTT 59.596 52.381 0.00 0.00 0.00 4.44
633 5986 1.022735 CACGAGCATACTACCTCCGT 58.977 55.000 0.00 0.00 0.00 4.69
634 5987 0.317938 GCACGAGCATACTACCTCCG 60.318 60.000 0.00 0.00 41.58 4.63
635 5988 0.317938 CGCACGAGCATACTACCTCC 60.318 60.000 5.50 0.00 42.27 4.30
636 5989 0.661552 TCGCACGAGCATACTACCTC 59.338 55.000 5.50 0.00 42.27 3.85
637 5990 0.663688 CTCGCACGAGCATACTACCT 59.336 55.000 7.18 0.00 42.27 3.08
638 5991 3.165559 CTCGCACGAGCATACTACC 57.834 57.895 7.18 0.00 42.27 3.18
655 6008 0.891373 CCACGATAGATCCGGATGCT 59.109 55.000 24.82 19.89 41.38 3.79
717 6070 3.961480 TGTCAGTAGACCATGTCCAAG 57.039 47.619 0.00 0.00 44.33 3.61
746 6099 1.002773 TCTGGGGAGAAAACGGTTAGC 59.997 52.381 0.00 0.00 0.00 3.09
751 6108 0.321653 CAGGTCTGGGGAGAAAACGG 60.322 60.000 0.00 0.00 0.00 4.44
769 6126 1.028330 CGGTAGCCGTCAGTAGACCA 61.028 60.000 0.00 0.00 42.73 4.02
790 6147 7.609532 AGAAAACTAACAATGGAGAAGATGAGG 59.390 37.037 0.00 0.00 0.00 3.86
868 6241 6.521821 GCATGAAAATAACATCGTACACGTTT 59.478 34.615 0.00 0.00 40.80 3.60
896 6269 5.007528 GGTGACATAGAGTAGGTCGTCTAAC 59.992 48.000 0.00 0.00 42.01 2.34
938 6311 4.141642 TGGATGTGTTCAAGGATCATCGAT 60.142 41.667 0.00 0.00 36.68 3.59
939 6312 3.197549 TGGATGTGTTCAAGGATCATCGA 59.802 43.478 0.00 0.00 36.68 3.59
951 6324 6.341316 ACATATATAGGCGATGGATGTGTTC 58.659 40.000 7.90 0.00 0.00 3.18
1004 6377 1.527844 GGCTGCAGGATGGATGGTC 60.528 63.158 17.12 0.00 34.26 4.02
1057 6430 7.667043 TTGGTTATGTTGTCTGATCACTAAC 57.333 36.000 0.00 0.00 0.00 2.34
1109 6484 9.224267 AGTGACTCACAATAATAATATGATGGC 57.776 33.333 11.80 0.00 36.74 4.40
1120 6495 7.976734 GCTGACTTAGTAGTGACTCACAATAAT 59.023 37.037 11.80 0.00 36.74 1.28
1126 6594 5.448089 GCTAGCTGACTTAGTAGTGACTCAC 60.448 48.000 7.70 0.38 37.10 3.51
1169 6642 1.380380 GAGCTTTGGTCCCCATGGG 60.380 63.158 25.30 25.30 46.11 4.00
1195 6668 2.173669 GGCGATGACCACGGTGATG 61.174 63.158 10.28 0.00 0.00 3.07
1206 6679 0.820482 CATCCCAAGCATGGCGATGA 60.820 55.000 23.80 9.55 46.09 2.92
1278 6751 2.474410 CCACTGGGAGTAGTTGGTTC 57.526 55.000 0.00 0.00 35.59 3.62
1320 6793 0.458543 GAACTTGAGCTCATCGCCGA 60.459 55.000 19.04 0.00 40.39 5.54
1404 6877 0.186386 ACTCGCTATGGGGCTAGAGT 59.814 55.000 0.00 0.00 34.54 3.24
1408 6881 0.756903 GGAAACTCGCTATGGGGCTA 59.243 55.000 0.00 0.00 0.00 3.93
1422 6895 3.143728 ACATCGTTACCAGTTGGGAAAC 58.856 45.455 0.00 3.37 40.32 2.78
1429 6902 2.803956 CGGAACAACATCGTTACCAGTT 59.196 45.455 0.00 0.00 0.00 3.16
1537 7010 3.863424 GCTGCATAGTTCGCACTACTTTA 59.137 43.478 0.00 0.00 38.38 1.85
1542 7015 0.527600 CCGCTGCATAGTTCGCACTA 60.528 55.000 0.00 0.00 39.94 2.74
1549 7022 2.819595 CGGCACCGCTGCATAGTT 60.820 61.111 4.88 0.00 46.28 2.24
1825 7299 5.575218 CGCTTGGTTATTACATGGGTTTTTC 59.425 40.000 0.00 0.00 0.00 2.29
1835 7310 7.273712 TCATGGTTATACGCTTGGTTATTACA 58.726 34.615 0.00 0.00 0.00 2.41
1836 7311 7.718272 TCATGGTTATACGCTTGGTTATTAC 57.282 36.000 0.00 0.00 0.00 1.89
1982 7458 2.906897 AGTGGTGTTTGCCCGCTG 60.907 61.111 0.00 0.00 41.20 5.18
2068 7873 8.735315 CAATTTGTTAGGGTTTGTTTTCCTTTT 58.265 29.630 0.00 0.00 32.46 2.27
2069 7874 8.103935 TCAATTTGTTAGGGTTTGTTTTCCTTT 58.896 29.630 0.00 0.00 32.46 3.11
2114 8011 5.767665 TGGCAAGCTGAACTCTTGTAATTTA 59.232 36.000 0.00 0.00 42.06 1.40
2171 13338 5.009610 TCACTAATTCTTTTGGGACACAAGC 59.990 40.000 0.00 0.00 44.89 4.01
2221 13388 3.122613 CGATCTTGCGCATTATCCTCTTC 59.877 47.826 12.75 0.00 0.00 2.87
2222 13389 3.062763 CGATCTTGCGCATTATCCTCTT 58.937 45.455 12.75 0.00 0.00 2.85
2230 13397 1.933853 GTACTTCCGATCTTGCGCATT 59.066 47.619 12.75 0.00 0.00 3.56
2266 13433 1.733041 CCTGCGTACACTCACCACG 60.733 63.158 0.00 0.00 38.66 4.94
2280 13447 4.066139 ATGAGGGCCCCAACCTGC 62.066 66.667 21.43 0.00 38.79 4.85
2287 13454 2.517919 GTCCATGATGAGGGCCCC 59.482 66.667 21.43 11.17 0.00 5.80
2404 13571 2.771943 CAGGGGTAGTTTGAGGCATCTA 59.228 50.000 0.00 0.00 0.00 1.98
2414 13581 1.203149 AGACGAGACCAGGGGTAGTTT 60.203 52.381 0.00 0.00 35.25 2.66
2450 13617 1.000107 GGACGAGACCAGGGGTAGT 60.000 63.158 0.00 0.00 35.25 2.73
2451 13618 0.549950 TAGGACGAGACCAGGGGTAG 59.450 60.000 0.00 0.00 35.25 3.18
2452 13619 1.002069 TTAGGACGAGACCAGGGGTA 58.998 55.000 0.00 0.00 35.25 3.69
2453 13620 0.324460 CTTAGGACGAGACCAGGGGT 60.324 60.000 0.00 0.00 39.44 4.95
2455 13622 0.324460 ACCTTAGGACGAGACCAGGG 60.324 60.000 4.77 0.00 30.30 4.45
2456 13623 1.104630 GACCTTAGGACGAGACCAGG 58.895 60.000 4.77 0.00 31.77 4.45
2457 13624 1.104630 GGACCTTAGGACGAGACCAG 58.895 60.000 4.77 0.00 0.00 4.00
2458 13625 0.679002 CGGACCTTAGGACGAGACCA 60.679 60.000 4.77 0.00 0.00 4.02
2459 13626 1.382692 CCGGACCTTAGGACGAGACC 61.383 65.000 18.08 5.78 0.00 3.85
2460 13627 0.393537 TCCGGACCTTAGGACGAGAC 60.394 60.000 18.08 0.00 0.00 3.36
2461 13628 0.549950 ATCCGGACCTTAGGACGAGA 59.450 55.000 6.12 14.09 39.66 4.04
2462 13629 0.953003 GATCCGGACCTTAGGACGAG 59.047 60.000 6.12 10.36 39.66 4.18
2463 13630 0.816825 CGATCCGGACCTTAGGACGA 60.817 60.000 6.12 1.99 39.66 4.20
2503 13682 1.139853 GGAGGATCTCATCTTGGCGTT 59.860 52.381 0.00 0.00 33.73 4.84
2673 13856 2.894126 GGGAGATTCCGAGAGAAGCATA 59.106 50.000 0.00 0.00 43.58 3.14
2697 13880 2.238646 AGGAGCCCAACACGATTTCATA 59.761 45.455 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.