Multiple sequence alignment - TraesCS7A01G308100

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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 TraesCS7A01G308100 chr7A 100.000 2631 0 0 1 2631 435876756 435874126 0.000000e+00 4859.0
1 TraesCS7A01G308100 chr7A 92.000 125 9 1 1860 1984 662139566 662139443 9.680000e-40 174.0
2 TraesCS7A01G308100 chr7A 90.991 111 8 2 224 333 435934147 435934256 5.870000e-32 148.0
3 TraesCS7A01G308100 chr7A 94.444 90 4 1 224 312 26590710 26590799 1.270000e-28 137.0
4 TraesCS7A01G308100 chr7A 84.615 130 17 3 1855 1984 508567201 508567075 2.750000e-25 126.0
5 TraesCS7A01G308100 chr7B 92.954 1547 75 16 315 1847 380889044 380887518 0.000000e+00 2222.0
6 TraesCS7A01G308100 chr7B 81.579 342 37 3 6 323 11301173 11301512 2.600000e-65 259.0
7 TraesCS7A01G308100 chr7B 84.416 231 26 5 1 230 687332506 687332285 4.410000e-53 219.0
8 TraesCS7A01G308100 chr3A 93.112 784 38 6 1860 2631 53291621 53292400 0.000000e+00 1134.0
9 TraesCS7A01G308100 chr3A 92.949 780 44 8 1860 2631 689513035 689512259 0.000000e+00 1125.0
10 TraesCS7A01G308100 chr3A 88.060 335 16 2 5 315 349737763 349737429 2.470000e-100 375.0
11 TraesCS7A01G308100 chr2A 92.711 782 45 8 1860 2631 716222252 716223031 0.000000e+00 1118.0
12 TraesCS7A01G308100 chr2A 93.608 704 29 7 1940 2631 394262826 394263525 0.000000e+00 1037.0
13 TraesCS7A01G308100 chr2A 92.011 701 41 11 1939 2629 63370523 63371218 0.000000e+00 970.0
14 TraesCS7A01G308100 chr2A 84.906 318 40 5 1 316 23926726 23926415 5.470000e-82 315.0
15 TraesCS7A01G308100 chr7D 91.523 814 49 9 384 1185 386595612 386594807 0.000000e+00 1103.0
16 TraesCS7A01G308100 chr7D 94.690 565 21 5 1285 1847 386594773 386594216 0.000000e+00 869.0
17 TraesCS7A01G308100 chr7D 83.983 231 33 4 1 230 538596795 538596568 4.410000e-53 219.0
18 TraesCS7A01G308100 chr7D 94.681 94 4 1 224 316 366659162 366659255 7.590000e-31 145.0
19 TraesCS7A01G308100 chr7D 90.805 87 8 0 230 316 366639496 366639410 1.650000e-22 117.0
20 TraesCS7A01G308100 chr7D 87.059 85 10 1 230 313 538596544 538596460 7.750000e-16 95.3
21 TraesCS7A01G308100 chr5A 90.875 789 39 16 1873 2631 382330739 382331524 0.000000e+00 1027.0
22 TraesCS7A01G308100 chr5A 93.305 702 35 9 1939 2631 703675543 703676241 0.000000e+00 1026.0
23 TraesCS7A01G308100 chr5A 93.010 701 37 9 1941 2631 460470550 460471248 0.000000e+00 1013.0
24 TraesCS7A01G308100 chr5A 86.901 313 34 3 1 312 681378772 681379078 6.970000e-91 344.0
25 TraesCS7A01G308100 chr5A 93.043 230 15 1 1 230 391986804 391987032 4.200000e-88 335.0
26 TraesCS7A01G308100 chr5A 92.913 127 8 1 1858 1984 502280189 502280314 1.610000e-42 183.0
27 TraesCS7A01G308100 chr5A 94.505 91 4 1 224 313 391982615 391982525 3.530000e-29 139.0
28 TraesCS7A01G308100 chr5A 85.827 127 16 2 1858 1984 331953610 331953734 1.640000e-27 134.0
29 TraesCS7A01G308100 chr6A 92.472 704 37 7 1939 2631 581809660 581810358 0.000000e+00 992.0
30 TraesCS7A01G308100 chr6A 87.611 339 17 2 1 314 104124366 104124028 1.150000e-98 370.0
31 TraesCS7A01G308100 chr1A 85.503 338 24 4 1 313 281368416 281368079 1.950000e-86 329.0
32 TraesCS7A01G308100 chr1B 85.260 346 19 12 1 314 654536471 654536816 7.020000e-86 327.0
33 TraesCS7A01G308100 chr1B 89.224 232 24 1 1 231 687690740 687690509 3.310000e-74 289.0
34 TraesCS7A01G308100 chr1B 80.428 327 44 14 1 314 581186135 581186454 5.660000e-57 231.0
35 TraesCS7A01G308100 chr1B 94.505 91 4 1 224 313 581170514 581170424 3.530000e-29 139.0
36 TraesCS7A01G308100 chr1B 93.478 92 5 1 224 314 599204247 599204156 4.570000e-28 135.0
37 TraesCS7A01G308100 chr1B 93.407 91 5 1 224 313 654531842 654531752 1.640000e-27 134.0
38 TraesCS7A01G308100 chr3B 84.457 341 28 2 2 317 750920795 750921135 1.970000e-81 313.0
39 TraesCS7A01G308100 chr3B 90.789 228 20 1 4 230 485695234 485695007 1.180000e-78 303.0
40 TraesCS7A01G308100 chr1D 84.524 336 28 1 1 312 468701183 468701518 7.070000e-81 311.0
41 TraesCS7A01G308100 chr1D 93.478 92 5 1 224 314 45808069 45808160 4.570000e-28 135.0
42 TraesCS7A01G308100 chr6B 90.476 231 21 1 1 230 24939668 24939438 1.180000e-78 303.0
43 TraesCS7A01G308100 chr6B 88.696 230 23 2 1 230 624410823 624410597 7.170000e-71 278.0
44 TraesCS7A01G308100 chr6B 92.308 91 6 1 224 313 24984902 24984992 7.640000e-26 128.0
45 TraesCS7A01G308100 chr5B 84.132 334 28 2 5 313 38469085 38469418 1.530000e-77 300.0
46 TraesCS7A01G308100 chr5B 78.779 344 38 18 1 317 479887580 479887245 5.740000e-47 198.0
47 TraesCS7A01G308100 chr2D 83.432 338 31 2 1 314 118132021 118131685 9.210000e-75 291.0
48 TraesCS7A01G308100 chr6D 81.525 341 32 7 5 319 451331027 451330692 4.350000e-63 252.0
49 TraesCS7A01G308100 chr6D 93.976 83 5 0 230 312 451335843 451335925 2.750000e-25 126.0
50 TraesCS7A01G308100 chr6D 89.011 91 9 1 224 313 437675817 437675907 7.700000e-21 111.0
51 TraesCS7A01G308100 chr4D 95.652 92 3 1 224 314 467594559 467594650 2.110000e-31 147.0
52 TraesCS7A01G308100 chr4D 93.976 83 3 2 232 313 467587120 467587039 9.890000e-25 124.0
53 TraesCS7A01G308100 chr2B 93.548 93 4 2 224 314 161509039 161508947 1.270000e-28 137.0
54 TraesCS7A01G308100 chr4B 92.222 90 6 1 224 312 13907345 13907256 2.750000e-25 126.0


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 TraesCS7A01G308100 chr7A 435874126 435876756 2630 True 4859 4859 100.0000 1 2631 1 chr7A.!!$R1 2630
1 TraesCS7A01G308100 chr7B 380887518 380889044 1526 True 2222 2222 92.9540 315 1847 1 chr7B.!!$R1 1532
2 TraesCS7A01G308100 chr3A 53291621 53292400 779 False 1134 1134 93.1120 1860 2631 1 chr3A.!!$F1 771
3 TraesCS7A01G308100 chr3A 689512259 689513035 776 True 1125 1125 92.9490 1860 2631 1 chr3A.!!$R2 771
4 TraesCS7A01G308100 chr2A 716222252 716223031 779 False 1118 1118 92.7110 1860 2631 1 chr2A.!!$F3 771
5 TraesCS7A01G308100 chr2A 394262826 394263525 699 False 1037 1037 93.6080 1940 2631 1 chr2A.!!$F2 691
6 TraesCS7A01G308100 chr2A 63370523 63371218 695 False 970 970 92.0110 1939 2629 1 chr2A.!!$F1 690
7 TraesCS7A01G308100 chr7D 386594216 386595612 1396 True 986 1103 93.1065 384 1847 2 chr7D.!!$R2 1463
8 TraesCS7A01G308100 chr5A 382330739 382331524 785 False 1027 1027 90.8750 1873 2631 1 chr5A.!!$F2 758
9 TraesCS7A01G308100 chr5A 703675543 703676241 698 False 1026 1026 93.3050 1939 2631 1 chr5A.!!$F7 692
10 TraesCS7A01G308100 chr5A 460470550 460471248 698 False 1013 1013 93.0100 1941 2631 1 chr5A.!!$F4 690
11 TraesCS7A01G308100 chr6A 581809660 581810358 698 False 992 992 92.4720 1939 2631 1 chr6A.!!$F1 692

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
23 24 0.114168 CCATGGGTGGGGAAAGAACA 59.886 55.0 2.85 0.0 42.11 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1698 1.06861 GCAGCGATACCAAAAGCACAA 60.069 47.619 0.0 0.0 0.0 3.33 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
22 23 2.976099 CCATGGGTGGGGAAAGAAC 58.024 57.895 2.85 0.00 42.11 3.01
23 24 0.114168 CCATGGGTGGGGAAAGAACA 59.886 55.000 2.85 0.00 42.11 3.18
24 25 1.549203 CATGGGTGGGGAAAGAACAG 58.451 55.000 0.00 0.00 0.00 3.16
25 26 1.075374 CATGGGTGGGGAAAGAACAGA 59.925 52.381 0.00 0.00 0.00 3.41
26 27 1.227249 TGGGTGGGGAAAGAACAGAA 58.773 50.000 0.00 0.00 0.00 3.02
27 28 1.571457 TGGGTGGGGAAAGAACAGAAA 59.429 47.619 0.00 0.00 0.00 2.52
28 29 2.239400 GGGTGGGGAAAGAACAGAAAG 58.761 52.381 0.00 0.00 0.00 2.62
29 30 2.158519 GGGTGGGGAAAGAACAGAAAGA 60.159 50.000 0.00 0.00 0.00 2.52
30 31 3.149981 GGTGGGGAAAGAACAGAAAGAG 58.850 50.000 0.00 0.00 0.00 2.85
31 32 3.149981 GTGGGGAAAGAACAGAAAGAGG 58.850 50.000 0.00 0.00 0.00 3.69
32 33 3.053077 TGGGGAAAGAACAGAAAGAGGA 58.947 45.455 0.00 0.00 0.00 3.71
33 34 3.073062 TGGGGAAAGAACAGAAAGAGGAG 59.927 47.826 0.00 0.00 0.00 3.69
34 35 3.328050 GGGGAAAGAACAGAAAGAGGAGA 59.672 47.826 0.00 0.00 0.00 3.71
35 36 4.564613 GGGGAAAGAACAGAAAGAGGAGAG 60.565 50.000 0.00 0.00 0.00 3.20
36 37 4.284746 GGGAAAGAACAGAAAGAGGAGAGA 59.715 45.833 0.00 0.00 0.00 3.10
37 38 5.221742 GGGAAAGAACAGAAAGAGGAGAGAA 60.222 44.000 0.00 0.00 0.00 2.87
38 39 6.292150 GGAAAGAACAGAAAGAGGAGAGAAA 58.708 40.000 0.00 0.00 0.00 2.52
39 40 6.426633 GGAAAGAACAGAAAGAGGAGAGAAAG 59.573 42.308 0.00 0.00 0.00 2.62
40 41 6.739331 AAGAACAGAAAGAGGAGAGAAAGA 57.261 37.500 0.00 0.00 0.00 2.52
41 42 6.739331 AGAACAGAAAGAGGAGAGAAAGAA 57.261 37.500 0.00 0.00 0.00 2.52
42 43 7.130681 AGAACAGAAAGAGGAGAGAAAGAAA 57.869 36.000 0.00 0.00 0.00 2.52
43 44 7.569240 AGAACAGAAAGAGGAGAGAAAGAAAA 58.431 34.615 0.00 0.00 0.00 2.29
44 45 8.049721 AGAACAGAAAGAGGAGAGAAAGAAAAA 58.950 33.333 0.00 0.00 0.00 1.94
60 61 1.986882 AAAAACACAGAGCAGAGGGG 58.013 50.000 0.00 0.00 0.00 4.79
61 62 0.538287 AAAACACAGAGCAGAGGGGC 60.538 55.000 0.00 0.00 0.00 5.80
70 71 4.803426 CAGAGGGGCTCGTGCGAC 62.803 72.222 3.02 0.00 40.82 5.19
79 80 4.757554 TCGTGCGACGATGTAGTG 57.242 55.556 0.00 0.00 46.73 2.74
80 81 2.164491 TCGTGCGACGATGTAGTGA 58.836 52.632 0.00 0.00 46.73 3.41
81 82 0.518195 TCGTGCGACGATGTAGTGAA 59.482 50.000 0.00 0.00 46.73 3.18
82 83 0.907837 CGTGCGACGATGTAGTGAAG 59.092 55.000 0.00 0.00 46.05 3.02
83 84 1.269166 GTGCGACGATGTAGTGAAGG 58.731 55.000 0.00 0.00 0.00 3.46
84 85 0.172578 TGCGACGATGTAGTGAAGGG 59.827 55.000 0.00 0.00 0.00 3.95
85 86 0.527817 GCGACGATGTAGTGAAGGGG 60.528 60.000 0.00 0.00 0.00 4.79
86 87 0.815734 CGACGATGTAGTGAAGGGGT 59.184 55.000 0.00 0.00 0.00 4.95
87 88 2.019249 CGACGATGTAGTGAAGGGGTA 58.981 52.381 0.00 0.00 0.00 3.69
88 89 2.621998 CGACGATGTAGTGAAGGGGTAT 59.378 50.000 0.00 0.00 0.00 2.73
89 90 3.550233 CGACGATGTAGTGAAGGGGTATG 60.550 52.174 0.00 0.00 0.00 2.39
90 91 2.698797 ACGATGTAGTGAAGGGGTATGG 59.301 50.000 0.00 0.00 0.00 2.74
91 92 2.548067 CGATGTAGTGAAGGGGTATGGC 60.548 54.545 0.00 0.00 0.00 4.40
92 93 0.828022 TGTAGTGAAGGGGTATGGCG 59.172 55.000 0.00 0.00 0.00 5.69
93 94 0.532196 GTAGTGAAGGGGTATGGCGC 60.532 60.000 0.00 0.00 0.00 6.53
118 119 4.789075 CGGGGCGTCGTGGTACAG 62.789 72.222 0.00 0.00 41.80 2.74
122 123 4.367023 GCGTCGTGGTACAGCCCA 62.367 66.667 0.00 0.00 41.80 5.36
123 124 2.577059 CGTCGTGGTACAGCCCAT 59.423 61.111 0.00 0.00 41.80 4.00
124 125 1.811195 CGTCGTGGTACAGCCCATA 59.189 57.895 0.00 0.00 41.80 2.74
125 126 0.248907 CGTCGTGGTACAGCCCATAG 60.249 60.000 0.00 0.00 41.80 2.23
126 127 0.529992 GTCGTGGTACAGCCCATAGC 60.530 60.000 0.00 0.00 41.80 2.97
207 208 3.411351 CGACGCCGTTGACCAAGG 61.411 66.667 0.00 0.00 0.00 3.61
208 209 3.723348 GACGCCGTTGACCAAGGC 61.723 66.667 0.00 10.92 46.88 4.35
211 212 3.284449 GCCGTTGACCAAGGCGTT 61.284 61.111 7.21 0.00 41.53 4.84
212 213 1.962306 GCCGTTGACCAAGGCGTTA 60.962 57.895 0.00 0.00 41.53 3.18
213 214 1.303091 GCCGTTGACCAAGGCGTTAT 61.303 55.000 0.00 0.00 41.53 1.89
214 215 0.446222 CCGTTGACCAAGGCGTTATG 59.554 55.000 0.00 0.00 0.00 1.90
215 216 1.153353 CGTTGACCAAGGCGTTATGT 58.847 50.000 0.00 0.00 0.00 2.29
216 217 1.533731 CGTTGACCAAGGCGTTATGTT 59.466 47.619 0.00 0.00 0.00 2.71
217 218 2.737783 CGTTGACCAAGGCGTTATGTTA 59.262 45.455 0.00 0.00 0.00 2.41
218 219 3.372822 CGTTGACCAAGGCGTTATGTTAT 59.627 43.478 0.00 0.00 0.00 1.89
219 220 4.493545 CGTTGACCAAGGCGTTATGTTATC 60.494 45.833 0.00 0.00 0.00 1.75
220 221 4.481368 TGACCAAGGCGTTATGTTATCT 57.519 40.909 0.00 0.00 0.00 1.98
221 222 5.601583 TGACCAAGGCGTTATGTTATCTA 57.398 39.130 0.00 0.00 0.00 1.98
222 223 5.597806 TGACCAAGGCGTTATGTTATCTAG 58.402 41.667 0.00 0.00 0.00 2.43
223 224 4.377897 ACCAAGGCGTTATGTTATCTAGC 58.622 43.478 0.00 0.00 0.00 3.42
224 225 4.141801 ACCAAGGCGTTATGTTATCTAGCA 60.142 41.667 0.00 0.00 0.00 3.49
225 226 4.997395 CCAAGGCGTTATGTTATCTAGCAT 59.003 41.667 0.00 0.00 0.00 3.79
226 227 5.106948 CCAAGGCGTTATGTTATCTAGCATG 60.107 44.000 0.00 0.00 0.00 4.06
227 228 4.569943 AGGCGTTATGTTATCTAGCATGG 58.430 43.478 0.00 0.00 0.00 3.66
228 229 3.125316 GGCGTTATGTTATCTAGCATGGC 59.875 47.826 0.00 0.00 0.00 4.40
229 230 3.181530 GCGTTATGTTATCTAGCATGGCG 60.182 47.826 0.00 3.41 32.94 5.69
230 231 3.987868 CGTTATGTTATCTAGCATGGCGT 59.012 43.478 0.00 0.00 0.00 5.68
231 232 5.158494 CGTTATGTTATCTAGCATGGCGTA 58.842 41.667 0.00 0.00 0.00 4.42
232 233 5.286320 CGTTATGTTATCTAGCATGGCGTAG 59.714 44.000 0.00 0.00 0.00 3.51
233 234 3.660501 TGTTATCTAGCATGGCGTAGG 57.339 47.619 0.00 0.00 0.00 3.18
234 235 2.299013 TGTTATCTAGCATGGCGTAGGG 59.701 50.000 0.00 0.00 0.00 3.53
235 236 0.895530 TATCTAGCATGGCGTAGGGC 59.104 55.000 1.39 1.39 42.51 5.19
248 249 4.584327 GCGTAGGGCCATTTTATGAAAT 57.416 40.909 6.18 0.00 35.90 2.17
249 250 5.699097 GCGTAGGGCCATTTTATGAAATA 57.301 39.130 6.18 0.00 34.18 1.40
250 251 6.267496 GCGTAGGGCCATTTTATGAAATAT 57.733 37.500 6.18 0.00 34.18 1.28
251 252 6.687604 GCGTAGGGCCATTTTATGAAATATT 58.312 36.000 6.18 0.00 34.18 1.28
252 253 7.151976 GCGTAGGGCCATTTTATGAAATATTT 58.848 34.615 6.18 0.00 34.18 1.40
253 254 7.655732 GCGTAGGGCCATTTTATGAAATATTTT 59.344 33.333 6.18 0.00 34.18 1.82
254 255 9.541143 CGTAGGGCCATTTTATGAAATATTTTT 57.459 29.630 6.18 0.00 33.78 1.94
274 275 6.809630 TTTTAAAATAGGGCCATTTTGTGC 57.190 33.333 24.48 0.00 38.31 4.57
275 276 5.753721 TTAAAATAGGGCCATTTTGTGCT 57.246 34.783 24.48 2.14 38.31 4.40
276 277 3.615224 AAATAGGGCCATTTTGTGCTG 57.385 42.857 6.18 0.00 0.00 4.41
277 278 2.530460 ATAGGGCCATTTTGTGCTGA 57.470 45.000 6.18 0.00 0.00 4.26
278 279 2.300956 TAGGGCCATTTTGTGCTGAA 57.699 45.000 6.18 0.00 0.00 3.02
279 280 0.681175 AGGGCCATTTTGTGCTGAAC 59.319 50.000 6.18 0.00 0.00 3.18
280 281 0.681175 GGGCCATTTTGTGCTGAACT 59.319 50.000 4.39 0.00 0.00 3.01
281 282 1.070601 GGGCCATTTTGTGCTGAACTT 59.929 47.619 4.39 0.00 0.00 2.66
282 283 2.485302 GGGCCATTTTGTGCTGAACTTT 60.485 45.455 4.39 0.00 0.00 2.66
283 284 2.545106 GGCCATTTTGTGCTGAACTTTG 59.455 45.455 0.00 0.00 0.00 2.77
284 285 2.545106 GCCATTTTGTGCTGAACTTTGG 59.455 45.455 0.00 0.00 0.00 3.28
285 286 2.545106 CCATTTTGTGCTGAACTTTGGC 59.455 45.455 0.00 0.00 0.00 4.52
286 287 2.307934 TTTTGTGCTGAACTTTGGCC 57.692 45.000 0.00 0.00 0.00 5.36
287 288 1.189752 TTTGTGCTGAACTTTGGCCA 58.810 45.000 0.00 0.00 0.00 5.36
288 289 1.189752 TTGTGCTGAACTTTGGCCAA 58.810 45.000 16.05 16.05 0.00 4.52
289 290 1.189752 TGTGCTGAACTTTGGCCAAA 58.810 45.000 28.65 28.65 0.00 3.28
304 305 2.926778 CCAAAGGGCCAATTTTGTGA 57.073 45.000 19.14 0.00 33.52 3.58
305 306 3.421919 CCAAAGGGCCAATTTTGTGAT 57.578 42.857 19.14 0.00 33.52 3.06
306 307 3.753815 CCAAAGGGCCAATTTTGTGATT 58.246 40.909 19.14 0.00 33.52 2.57
307 308 4.143543 CCAAAGGGCCAATTTTGTGATTT 58.856 39.130 19.14 0.00 33.52 2.17
308 309 4.583907 CCAAAGGGCCAATTTTGTGATTTT 59.416 37.500 19.14 0.00 33.52 1.82
309 310 5.068855 CCAAAGGGCCAATTTTGTGATTTTT 59.931 36.000 19.14 0.00 33.52 1.94
310 311 6.207928 CAAAGGGCCAATTTTGTGATTTTTC 58.792 36.000 6.18 0.00 31.36 2.29
311 312 5.046288 AGGGCCAATTTTGTGATTTTTCA 57.954 34.783 6.18 0.00 0.00 2.69
312 313 4.821260 AGGGCCAATTTTGTGATTTTTCAC 59.179 37.500 6.18 0.00 40.78 3.18
313 314 4.023279 GGGCCAATTTTGTGATTTTTCACC 60.023 41.667 4.39 0.00 39.72 4.02
318 319 7.354257 CCAATTTTGTGATTTTTCACCATGTC 58.646 34.615 3.84 0.00 39.72 3.06
329 330 1.136891 TCACCATGTCGAGGTAGCATG 59.863 52.381 6.09 6.09 37.23 4.06
471 474 2.099592 TGCCAGTTGTGAAAAGCAGAAG 59.900 45.455 0.00 0.00 29.42 2.85
623 626 2.885266 CTGATTTGATGCTCATCCCAGG 59.115 50.000 7.34 0.00 37.02 4.45
643 655 4.214971 CAGGGCATTAGATTTCTTCATCGG 59.785 45.833 0.00 0.00 0.00 4.18
650 662 1.327764 GATTTCTTCATCGGACGGCAC 59.672 52.381 0.00 0.00 0.00 5.01
686 698 5.209818 TGGATAGCCCACTTAGTTAATCG 57.790 43.478 0.00 0.00 40.82 3.34
758 770 6.606796 ACTGTCCATGGATAGCTAGATATGAG 59.393 42.308 32.01 10.63 36.94 2.90
838 850 3.759086 TCGCTCGATCTAGCTAATCCAAT 59.241 43.478 16.34 0.00 40.49 3.16
864 876 7.922837 TGATTGCATGGATTTATATATCAGCG 58.077 34.615 5.66 0.00 0.00 5.18
865 877 5.739752 TGCATGGATTTATATATCAGCGC 57.260 39.130 0.00 0.00 0.00 5.92
866 878 5.430886 TGCATGGATTTATATATCAGCGCT 58.569 37.500 2.64 2.64 0.00 5.92
867 879 6.581712 TGCATGGATTTATATATCAGCGCTA 58.418 36.000 10.99 0.00 0.00 4.26
868 880 7.047271 TGCATGGATTTATATATCAGCGCTAA 58.953 34.615 10.99 0.00 0.00 3.09
869 881 7.225341 TGCATGGATTTATATATCAGCGCTAAG 59.775 37.037 10.99 0.00 0.00 2.18
911 923 4.669318 CATTGCATGCTAACTCCTTTCTG 58.331 43.478 20.33 0.00 0.00 3.02
924 938 1.066787 CCTTTCTGTCTCTCCCCGTTC 60.067 57.143 0.00 0.00 0.00 3.95
926 940 1.257743 TTCTGTCTCTCCCCGTTCTG 58.742 55.000 0.00 0.00 0.00 3.02
936 950 0.250295 CCCCGTTCTGTTCTGCTTGA 60.250 55.000 0.00 0.00 0.00 3.02
956 970 1.535444 TCTTCCAGGTTCCAGCCGA 60.535 57.895 0.00 0.00 0.00 5.54
957 971 0.909610 TCTTCCAGGTTCCAGCCGAT 60.910 55.000 0.00 0.00 0.00 4.18
963 977 1.043116 AGGTTCCAGCCGATCGATCA 61.043 55.000 24.40 1.36 0.00 2.92
1040 1054 3.767230 CGCCGTGACTGTTGCTCG 61.767 66.667 0.00 0.00 0.00 5.03
1185 1199 2.094338 AGCCGCACTAACTAACAGTACC 60.094 50.000 0.00 0.00 0.00 3.34
1193 1207 7.221452 CGCACTAACTAACAGTACCGATTAATT 59.779 37.037 0.00 0.00 0.00 1.40
1194 1208 9.520204 GCACTAACTAACAGTACCGATTAATTA 57.480 33.333 0.00 0.00 0.00 1.40
1293 1307 7.394641 AGCCTTTTTATTTAACCTCTTCTCCTG 59.605 37.037 0.00 0.00 0.00 3.86
1294 1308 7.539436 CCTTTTTATTTAACCTCTTCTCCTGC 58.461 38.462 0.00 0.00 0.00 4.85
1327 1341 1.464687 GCAGCGTTTACGTACTCGAGA 60.465 52.381 21.68 0.00 42.22 4.04
1609 1623 1.078848 GGTGACGCATGCTCTCCTT 60.079 57.895 17.13 0.00 0.00 3.36
1611 1625 1.742880 TGACGCATGCTCTCCTTGC 60.743 57.895 17.13 0.00 40.24 4.01
1659 1673 2.030946 ACGTACGTCCGTAGTATGCTTC 59.969 50.000 16.72 0.00 39.73 3.86
1722 1736 4.731961 CGCTGCTTGTGATTGATATTTCAC 59.268 41.667 0.00 7.20 42.05 3.18
1773 1788 8.876275 TCGGATTAAAGCATACGTTTATAACT 57.124 30.769 0.00 0.00 31.84 2.24
1830 1845 2.413371 GGCTTGACTTCTGCATTCGAAC 60.413 50.000 0.00 0.00 0.00 3.95
1847 1862 4.066490 TCGAACGGACACAACCAAATTAT 58.934 39.130 0.00 0.00 0.00 1.28
1848 1863 4.515944 TCGAACGGACACAACCAAATTATT 59.484 37.500 0.00 0.00 0.00 1.40
1849 1864 5.699915 TCGAACGGACACAACCAAATTATTA 59.300 36.000 0.00 0.00 0.00 0.98
1850 1865 6.204301 TCGAACGGACACAACCAAATTATTAA 59.796 34.615 0.00 0.00 0.00 1.40
1851 1866 6.856938 CGAACGGACACAACCAAATTATTAAA 59.143 34.615 0.00 0.00 0.00 1.52
1852 1867 7.149096 CGAACGGACACAACCAAATTATTAAAC 60.149 37.037 0.00 0.00 0.00 2.01
1853 1868 6.448852 ACGGACACAACCAAATTATTAAACC 58.551 36.000 0.00 0.00 0.00 3.27
1854 1869 5.865013 CGGACACAACCAAATTATTAAACCC 59.135 40.000 0.00 0.00 0.00 4.11
1855 1870 6.516860 CGGACACAACCAAATTATTAAACCCA 60.517 38.462 0.00 0.00 0.00 4.51
1856 1871 7.390823 GGACACAACCAAATTATTAAACCCAT 58.609 34.615 0.00 0.00 0.00 4.00
1857 1872 7.880713 GGACACAACCAAATTATTAAACCCATT 59.119 33.333 0.00 0.00 0.00 3.16
1858 1873 9.930693 GACACAACCAAATTATTAAACCCATTA 57.069 29.630 0.00 0.00 0.00 1.90
2204 2249 1.066143 AGATGTCCAACCACCGATCAC 60.066 52.381 0.00 0.00 0.00 3.06
2205 2250 0.984230 ATGTCCAACCACCGATCACT 59.016 50.000 0.00 0.00 0.00 3.41
2262 2307 4.415332 ATCGGACTGCGCGTTCGT 62.415 61.111 24.78 14.11 45.05 3.85
2530 2583 0.250684 TGAAAGTTCATCTGGCCGCA 60.251 50.000 0.00 0.00 31.01 5.69
2533 2586 2.434185 GTTCATCTGGCCGCACGA 60.434 61.111 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.114364 GTTCTTTCCCCACCCATGGT 59.886 55.000 11.73 0.00 45.66 3.55
4 5 0.114168 TGTTCTTTCCCCACCCATGG 59.886 55.000 4.14 4.14 46.81 3.66
6 7 1.455822 TCTGTTCTTTCCCCACCCAT 58.544 50.000 0.00 0.00 0.00 4.00
7 8 1.227249 TTCTGTTCTTTCCCCACCCA 58.773 50.000 0.00 0.00 0.00 4.51
8 9 2.158519 TCTTTCTGTTCTTTCCCCACCC 60.159 50.000 0.00 0.00 0.00 4.61
9 10 3.149981 CTCTTTCTGTTCTTTCCCCACC 58.850 50.000 0.00 0.00 0.00 4.61
10 11 3.149981 CCTCTTTCTGTTCTTTCCCCAC 58.850 50.000 0.00 0.00 0.00 4.61
11 12 3.053077 TCCTCTTTCTGTTCTTTCCCCA 58.947 45.455 0.00 0.00 0.00 4.96
12 13 3.328050 TCTCCTCTTTCTGTTCTTTCCCC 59.672 47.826 0.00 0.00 0.00 4.81
13 14 4.284746 TCTCTCCTCTTTCTGTTCTTTCCC 59.715 45.833 0.00 0.00 0.00 3.97
14 15 5.476091 TCTCTCCTCTTTCTGTTCTTTCC 57.524 43.478 0.00 0.00 0.00 3.13
15 16 7.213678 TCTTTCTCTCCTCTTTCTGTTCTTTC 58.786 38.462 0.00 0.00 0.00 2.62
16 17 7.130681 TCTTTCTCTCCTCTTTCTGTTCTTT 57.869 36.000 0.00 0.00 0.00 2.52
17 18 6.739331 TCTTTCTCTCCTCTTTCTGTTCTT 57.261 37.500 0.00 0.00 0.00 2.52
18 19 6.739331 TTCTTTCTCTCCTCTTTCTGTTCT 57.261 37.500 0.00 0.00 0.00 3.01
19 20 7.793927 TTTTCTTTCTCTCCTCTTTCTGTTC 57.206 36.000 0.00 0.00 0.00 3.18
41 42 1.986882 CCCCTCTGCTCTGTGTTTTT 58.013 50.000 0.00 0.00 0.00 1.94
42 43 0.538287 GCCCCTCTGCTCTGTGTTTT 60.538 55.000 0.00 0.00 0.00 2.43
43 44 1.073897 GCCCCTCTGCTCTGTGTTT 59.926 57.895 0.00 0.00 0.00 2.83
44 45 1.845205 AGCCCCTCTGCTCTGTGTT 60.845 57.895 0.00 0.00 36.75 3.32
45 46 2.203907 AGCCCCTCTGCTCTGTGT 60.204 61.111 0.00 0.00 36.75 3.72
53 54 4.803426 GTCGCACGAGCCCCTCTG 62.803 72.222 0.00 0.00 37.52 3.35
63 64 0.907837 CTTCACTACATCGTCGCACG 59.092 55.000 2.79 2.79 44.19 5.34
64 65 1.269166 CCTTCACTACATCGTCGCAC 58.731 55.000 0.00 0.00 0.00 5.34
65 66 0.172578 CCCTTCACTACATCGTCGCA 59.827 55.000 0.00 0.00 0.00 5.10
66 67 0.527817 CCCCTTCACTACATCGTCGC 60.528 60.000 0.00 0.00 0.00 5.19
67 68 0.815734 ACCCCTTCACTACATCGTCG 59.184 55.000 0.00 0.00 0.00 5.12
68 69 3.243771 CCATACCCCTTCACTACATCGTC 60.244 52.174 0.00 0.00 0.00 4.20
69 70 2.698797 CCATACCCCTTCACTACATCGT 59.301 50.000 0.00 0.00 0.00 3.73
70 71 2.548067 GCCATACCCCTTCACTACATCG 60.548 54.545 0.00 0.00 0.00 3.84
71 72 2.548067 CGCCATACCCCTTCACTACATC 60.548 54.545 0.00 0.00 0.00 3.06
72 73 1.416401 CGCCATACCCCTTCACTACAT 59.584 52.381 0.00 0.00 0.00 2.29
73 74 0.828022 CGCCATACCCCTTCACTACA 59.172 55.000 0.00 0.00 0.00 2.74
74 75 0.532196 GCGCCATACCCCTTCACTAC 60.532 60.000 0.00 0.00 0.00 2.73
75 76 1.692173 GGCGCCATACCCCTTCACTA 61.692 60.000 24.80 0.00 0.00 2.74
76 77 2.590092 GCGCCATACCCCTTCACT 59.410 61.111 0.00 0.00 0.00 3.41
77 78 2.516225 GGCGCCATACCCCTTCAC 60.516 66.667 24.80 0.00 0.00 3.18
78 79 3.804329 GGGCGCCATACCCCTTCA 61.804 66.667 30.85 0.00 42.01 3.02
101 102 4.789075 CTGTACCACGACGCCCCG 62.789 72.222 0.00 0.00 0.00 5.73
105 106 2.287457 TATGGGCTGTACCACGACGC 62.287 60.000 0.00 0.00 44.72 5.19
106 107 0.248907 CTATGGGCTGTACCACGACG 60.249 60.000 0.00 0.00 44.72 5.12
107 108 0.529992 GCTATGGGCTGTACCACGAC 60.530 60.000 0.00 0.00 44.72 4.34
108 109 1.820581 GCTATGGGCTGTACCACGA 59.179 57.895 0.00 0.00 44.72 4.35
109 110 1.591594 CGCTATGGGCTGTACCACG 60.592 63.158 0.00 0.00 44.72 4.94
110 111 1.887707 GCGCTATGGGCTGTACCAC 60.888 63.158 0.00 0.00 44.72 4.16
111 112 2.504032 GCGCTATGGGCTGTACCA 59.496 61.111 0.00 0.00 46.24 3.25
112 113 2.280865 GGCGCTATGGGCTGTACC 60.281 66.667 7.64 0.00 41.33 3.34
113 114 2.280865 GGGCGCTATGGGCTGTAC 60.281 66.667 7.64 0.00 41.33 2.90
114 115 2.445845 AGGGCGCTATGGGCTGTA 60.446 61.111 7.64 0.00 41.33 2.74
115 116 4.181010 CAGGGCGCTATGGGCTGT 62.181 66.667 7.64 0.00 41.33 4.40
116 117 4.943252 CCAGGGCGCTATGGGCTG 62.943 72.222 19.75 0.00 41.33 4.85
137 138 4.424711 TTGGGCCCATGACGCCTC 62.425 66.667 29.23 12.17 46.24 4.70
138 139 4.431131 CTTGGGCCCATGACGCCT 62.431 66.667 29.65 0.00 46.24 5.52
190 191 3.411351 CCTTGGTCAACGGCGTCG 61.411 66.667 15.17 8.42 43.02 5.12
191 192 3.723348 GCCTTGGTCAACGGCGTC 61.723 66.667 15.17 0.09 33.64 5.19
194 195 1.303091 ATAACGCCTTGGTCAACGGC 61.303 55.000 11.49 11.49 40.40 5.68
195 196 0.446222 CATAACGCCTTGGTCAACGG 59.554 55.000 0.00 0.00 0.00 4.44
196 197 1.153353 ACATAACGCCTTGGTCAACG 58.847 50.000 0.00 0.00 0.00 4.10
197 198 4.634443 AGATAACATAACGCCTTGGTCAAC 59.366 41.667 0.00 0.00 0.00 3.18
198 199 4.839121 AGATAACATAACGCCTTGGTCAA 58.161 39.130 0.00 0.00 0.00 3.18
199 200 4.481368 AGATAACATAACGCCTTGGTCA 57.519 40.909 0.00 0.00 0.00 4.02
200 201 4.448060 GCTAGATAACATAACGCCTTGGTC 59.552 45.833 0.00 0.00 0.00 4.02
201 202 4.141801 TGCTAGATAACATAACGCCTTGGT 60.142 41.667 0.00 0.00 0.00 3.67
202 203 4.377021 TGCTAGATAACATAACGCCTTGG 58.623 43.478 0.00 0.00 0.00 3.61
203 204 5.106948 CCATGCTAGATAACATAACGCCTTG 60.107 44.000 0.00 0.00 0.00 3.61
204 205 4.997395 CCATGCTAGATAACATAACGCCTT 59.003 41.667 0.00 0.00 0.00 4.35
205 206 4.569943 CCATGCTAGATAACATAACGCCT 58.430 43.478 0.00 0.00 0.00 5.52
206 207 3.125316 GCCATGCTAGATAACATAACGCC 59.875 47.826 0.00 0.00 0.00 5.68
207 208 3.181530 CGCCATGCTAGATAACATAACGC 60.182 47.826 0.00 0.00 0.00 4.84
208 209 3.987868 ACGCCATGCTAGATAACATAACG 59.012 43.478 0.00 0.00 32.87 3.18
209 210 5.577164 CCTACGCCATGCTAGATAACATAAC 59.423 44.000 0.00 0.00 0.00 1.89
210 211 5.337250 CCCTACGCCATGCTAGATAACATAA 60.337 44.000 0.00 0.00 0.00 1.90
211 212 4.159693 CCCTACGCCATGCTAGATAACATA 59.840 45.833 0.00 0.00 0.00 2.29
212 213 3.055819 CCCTACGCCATGCTAGATAACAT 60.056 47.826 0.00 0.00 0.00 2.71
213 214 2.299013 CCCTACGCCATGCTAGATAACA 59.701 50.000 0.00 0.00 0.00 2.41
214 215 2.931320 GCCCTACGCCATGCTAGATAAC 60.931 54.545 0.00 0.00 0.00 1.89
215 216 1.275291 GCCCTACGCCATGCTAGATAA 59.725 52.381 0.00 0.00 0.00 1.75
216 217 0.895530 GCCCTACGCCATGCTAGATA 59.104 55.000 0.00 0.00 0.00 1.98
217 218 1.674057 GCCCTACGCCATGCTAGAT 59.326 57.895 0.00 0.00 0.00 1.98
218 219 3.138625 GCCCTACGCCATGCTAGA 58.861 61.111 0.00 0.00 0.00 2.43
227 228 4.584327 ATTTCATAAAATGGCCCTACGC 57.416 40.909 0.00 0.00 33.78 4.42
228 229 9.541143 AAAAATATTTCATAAAATGGCCCTACG 57.459 29.630 0.00 0.00 35.84 3.51
248 249 8.951243 GCACAAAATGGCCCTATTTTAAAAATA 58.049 29.630 12.16 0.00 37.97 1.40
249 250 7.669304 AGCACAAAATGGCCCTATTTTAAAAAT 59.331 29.630 12.16 0.00 37.97 1.82
250 251 7.001073 AGCACAAAATGGCCCTATTTTAAAAA 58.999 30.769 12.16 0.00 37.97 1.94
251 252 6.429385 CAGCACAAAATGGCCCTATTTTAAAA 59.571 34.615 12.16 2.51 37.97 1.52
252 253 5.936956 CAGCACAAAATGGCCCTATTTTAAA 59.063 36.000 12.16 0.00 37.97 1.52
253 254 5.247110 TCAGCACAAAATGGCCCTATTTTAA 59.753 36.000 12.16 0.00 37.97 1.52
254 255 4.774726 TCAGCACAAAATGGCCCTATTTTA 59.225 37.500 12.16 0.00 37.97 1.52
255 256 3.582208 TCAGCACAAAATGGCCCTATTTT 59.418 39.130 0.00 3.88 40.00 1.82
256 257 3.172339 TCAGCACAAAATGGCCCTATTT 58.828 40.909 0.00 0.00 31.87 1.40
257 258 2.818921 TCAGCACAAAATGGCCCTATT 58.181 42.857 0.00 0.00 0.00 1.73
258 259 2.497273 GTTCAGCACAAAATGGCCCTAT 59.503 45.455 0.00 0.00 0.00 2.57
259 260 1.892474 GTTCAGCACAAAATGGCCCTA 59.108 47.619 0.00 0.00 0.00 3.53
260 261 0.681175 GTTCAGCACAAAATGGCCCT 59.319 50.000 0.00 0.00 0.00 5.19
261 262 0.681175 AGTTCAGCACAAAATGGCCC 59.319 50.000 0.00 0.00 0.00 5.80
262 263 2.531522 AAGTTCAGCACAAAATGGCC 57.468 45.000 0.00 0.00 0.00 5.36
263 264 2.545106 CCAAAGTTCAGCACAAAATGGC 59.455 45.455 0.00 0.00 0.00 4.40
264 265 2.545106 GCCAAAGTTCAGCACAAAATGG 59.455 45.455 0.00 0.00 0.00 3.16
265 266 2.545106 GGCCAAAGTTCAGCACAAAATG 59.455 45.455 0.00 0.00 0.00 2.32
266 267 2.170187 TGGCCAAAGTTCAGCACAAAAT 59.830 40.909 0.61 0.00 0.00 1.82
267 268 1.552337 TGGCCAAAGTTCAGCACAAAA 59.448 42.857 0.61 0.00 0.00 2.44
268 269 1.189752 TGGCCAAAGTTCAGCACAAA 58.810 45.000 0.61 0.00 0.00 2.83
269 270 1.189752 TTGGCCAAAGTTCAGCACAA 58.810 45.000 17.98 0.00 0.00 3.33
270 271 1.136695 CTTTGGCCAAAGTTCAGCACA 59.863 47.619 39.09 13.67 42.02 4.57
271 272 1.538849 CCTTTGGCCAAAGTTCAGCAC 60.539 52.381 41.82 0.00 44.66 4.40
272 273 0.752054 CCTTTGGCCAAAGTTCAGCA 59.248 50.000 41.82 17.85 44.66 4.41
273 274 0.033920 CCCTTTGGCCAAAGTTCAGC 59.966 55.000 41.82 0.00 44.66 4.26
285 286 2.926778 TCACAAAATTGGCCCTTTGG 57.073 45.000 20.16 12.03 36.94 3.28
286 287 5.771153 AAAATCACAAAATTGGCCCTTTG 57.229 34.783 16.47 16.47 38.29 2.77
287 288 5.890419 TGAAAAATCACAAAATTGGCCCTTT 59.110 32.000 0.00 0.00 0.00 3.11
288 289 5.299028 GTGAAAAATCACAAAATTGGCCCTT 59.701 36.000 0.00 0.00 40.16 3.95
289 290 4.821260 GTGAAAAATCACAAAATTGGCCCT 59.179 37.500 0.00 0.00 40.16 5.19
290 291 4.023279 GGTGAAAAATCACAAAATTGGCCC 60.023 41.667 0.00 0.00 42.07 5.80
291 292 4.578105 TGGTGAAAAATCACAAAATTGGCC 59.422 37.500 10.75 0.00 42.07 5.36
292 293 5.747951 TGGTGAAAAATCACAAAATTGGC 57.252 34.783 10.75 0.00 42.07 4.52
293 294 7.261829 ACATGGTGAAAAATCACAAAATTGG 57.738 32.000 10.75 0.00 42.07 3.16
294 295 7.042858 TCGACATGGTGAAAAATCACAAAATTG 60.043 33.333 10.75 0.00 42.07 2.32
295 296 6.983307 TCGACATGGTGAAAAATCACAAAATT 59.017 30.769 10.75 0.00 42.07 1.82
296 297 6.511416 TCGACATGGTGAAAAATCACAAAAT 58.489 32.000 10.75 0.00 42.07 1.82
297 298 5.895928 TCGACATGGTGAAAAATCACAAAA 58.104 33.333 10.75 0.00 42.07 2.44
298 299 5.506686 TCGACATGGTGAAAAATCACAAA 57.493 34.783 10.75 0.00 42.07 2.83
299 300 4.023279 CCTCGACATGGTGAAAAATCACAA 60.023 41.667 10.75 0.00 42.07 3.33
300 301 3.501828 CCTCGACATGGTGAAAAATCACA 59.498 43.478 10.75 0.00 42.07 3.58
301 302 3.502211 ACCTCGACATGGTGAAAAATCAC 59.498 43.478 0.00 0.36 36.30 3.06
302 303 3.750371 ACCTCGACATGGTGAAAAATCA 58.250 40.909 0.00 0.00 36.30 2.57
303 304 4.201822 GCTACCTCGACATGGTGAAAAATC 60.202 45.833 5.14 0.00 38.42 2.17
304 305 3.689649 GCTACCTCGACATGGTGAAAAAT 59.310 43.478 5.14 0.00 38.42 1.82
305 306 3.071479 GCTACCTCGACATGGTGAAAAA 58.929 45.455 5.14 0.00 38.42 1.94
306 307 2.037902 TGCTACCTCGACATGGTGAAAA 59.962 45.455 5.14 0.00 38.42 2.29
307 308 1.621317 TGCTACCTCGACATGGTGAAA 59.379 47.619 5.14 0.00 38.42 2.69
308 309 1.262417 TGCTACCTCGACATGGTGAA 58.738 50.000 5.14 0.00 38.42 3.18
309 310 1.136891 CATGCTACCTCGACATGGTGA 59.863 52.381 5.14 0.00 37.99 4.02
310 311 1.575244 CATGCTACCTCGACATGGTG 58.425 55.000 5.14 0.00 37.99 4.17
311 312 0.179073 GCATGCTACCTCGACATGGT 60.179 55.000 11.37 7.44 41.17 3.55
312 313 0.105593 AGCATGCTACCTCGACATGG 59.894 55.000 21.21 1.74 41.17 3.66
313 314 1.596260 CAAGCATGCTACCTCGACATG 59.404 52.381 23.00 8.31 43.21 3.21
357 358 8.938883 TCTTCTATGTCCAAATATCTAGCCTTT 58.061 33.333 0.00 0.00 0.00 3.11
471 474 1.063469 GTTGGTATGTACGGCATGCAC 59.937 52.381 21.36 9.98 41.19 4.57
623 626 4.084328 CGTCCGATGAAGAAATCTAATGCC 60.084 45.833 0.00 0.00 0.00 4.40
651 663 2.397413 CTATCCATGGACGGTGGCCC 62.397 65.000 18.99 0.00 36.66 5.80
652 664 1.071471 CTATCCATGGACGGTGGCC 59.929 63.158 18.99 0.00 36.66 5.36
653 665 1.598130 GCTATCCATGGACGGTGGC 60.598 63.158 18.99 11.73 36.66 5.01
654 666 1.071471 GGCTATCCATGGACGGTGG 59.929 63.158 18.99 4.52 38.11 4.61
655 667 1.071471 GGGCTATCCATGGACGGTG 59.929 63.158 18.99 8.60 35.00 4.94
657 669 3.562250 TGGGCTATCCATGGACGG 58.438 61.111 18.99 13.82 41.46 4.79
664 676 4.502604 GCGATTAACTAAGTGGGCTATCCA 60.503 45.833 0.00 0.00 44.79 3.41
665 677 3.995048 GCGATTAACTAAGTGGGCTATCC 59.005 47.826 0.00 0.00 0.00 2.59
666 678 3.995048 GGCGATTAACTAAGTGGGCTATC 59.005 47.826 0.00 0.00 0.00 2.08
667 679 3.244457 GGGCGATTAACTAAGTGGGCTAT 60.244 47.826 0.00 0.00 0.00 2.97
679 691 3.134458 CAAGAGGATCAGGGCGATTAAC 58.866 50.000 0.00 0.00 37.82 2.01
686 698 1.941325 CGTAACAAGAGGATCAGGGC 58.059 55.000 0.00 0.00 37.82 5.19
758 770 0.171903 GTTGCTGGGTCATGTCATGC 59.828 55.000 8.03 3.59 0.00 4.06
838 850 8.400186 CGCTGATATATAAATCCATGCAATCAA 58.600 33.333 0.00 0.00 0.00 2.57
898 910 3.449377 GGGGAGAGACAGAAAGGAGTTAG 59.551 52.174 0.00 0.00 0.00 2.34
901 913 1.893210 CGGGGAGAGACAGAAAGGAGT 60.893 57.143 0.00 0.00 0.00 3.85
902 914 0.820871 CGGGGAGAGACAGAAAGGAG 59.179 60.000 0.00 0.00 0.00 3.69
903 915 0.114560 ACGGGGAGAGACAGAAAGGA 59.885 55.000 0.00 0.00 0.00 3.36
904 916 0.977395 AACGGGGAGAGACAGAAAGG 59.023 55.000 0.00 0.00 0.00 3.11
905 917 1.896465 AGAACGGGGAGAGACAGAAAG 59.104 52.381 0.00 0.00 0.00 2.62
906 918 1.618837 CAGAACGGGGAGAGACAGAAA 59.381 52.381 0.00 0.00 0.00 2.52
909 921 0.969894 AACAGAACGGGGAGAGACAG 59.030 55.000 0.00 0.00 0.00 3.51
911 923 1.067495 CAGAACAGAACGGGGAGAGAC 60.067 57.143 0.00 0.00 0.00 3.36
924 938 3.065655 CTGGAAGAGTCAAGCAGAACAG 58.934 50.000 0.00 0.00 34.07 3.16
926 940 2.224402 ACCTGGAAGAGTCAAGCAGAAC 60.224 50.000 0.00 0.00 34.07 3.01
936 950 1.831652 CGGCTGGAACCTGGAAGAGT 61.832 60.000 0.00 0.00 34.07 3.24
956 970 2.874014 TCTCCATCTCTGCTGATCGAT 58.126 47.619 0.00 0.00 0.00 3.59
957 971 2.355010 TCTCCATCTCTGCTGATCGA 57.645 50.000 0.00 0.00 0.00 3.59
963 977 1.050204 GCCTGATCTCCATCTCTGCT 58.950 55.000 0.00 0.00 0.00 4.24
1026 1040 2.029073 ACCCGAGCAACAGTCACG 59.971 61.111 0.00 0.00 0.00 4.35
1030 1044 4.643387 GGCCACCCGAGCAACAGT 62.643 66.667 0.00 0.00 0.00 3.55
1059 1073 2.433004 GCCCCCACCGTGTAACTT 59.567 61.111 0.00 0.00 31.75 2.66
1083 1097 3.578286 TGCATGTCCCACAGCCCA 61.578 61.111 0.00 0.00 0.00 5.36
1185 1199 6.677781 ATGGGTGTGTGAGTTAATTAATCG 57.322 37.500 0.31 0.00 0.00 3.34
1193 1207 1.518325 CGCAATGGGTGTGTGAGTTA 58.482 50.000 0.00 0.00 32.74 2.24
1194 1208 1.795170 GCGCAATGGGTGTGTGAGTT 61.795 55.000 0.30 0.00 40.09 3.01
1196 1210 2.191354 CTGCGCAATGGGTGTGTGAG 62.191 60.000 13.05 0.00 40.09 3.51
1315 1329 1.288350 GCAGCTCTCTCGAGTACGTA 58.712 55.000 13.13 0.00 39.53 3.57
1327 1341 3.606662 ACCACGTCGTGCAGCTCT 61.607 61.111 20.01 0.00 31.34 4.09
1447 1461 1.323271 TGAGGCCGCAGAGGAAGTAG 61.323 60.000 4.49 0.00 45.00 2.57
1546 1560 3.697747 TTACCCCCGGCAGACGTG 61.698 66.667 0.00 0.00 42.24 4.49
1600 1614 1.077930 GATGCTGGCAAGGAGAGCA 60.078 57.895 0.00 0.00 46.32 4.26
1609 1623 2.435410 CAGACGCTGATGCTGGCA 60.435 61.111 0.00 0.00 36.97 4.92
1676 1690 5.465056 CGATACCAAAAGCACAAACCAAAAT 59.535 36.000 0.00 0.00 0.00 1.82
1679 1693 3.797184 GCGATACCAAAAGCACAAACCAA 60.797 43.478 0.00 0.00 0.00 3.67
1680 1694 2.287909 GCGATACCAAAAGCACAAACCA 60.288 45.455 0.00 0.00 0.00 3.67
1681 1695 2.030274 AGCGATACCAAAAGCACAAACC 60.030 45.455 0.00 0.00 0.00 3.27
1682 1696 2.979813 CAGCGATACCAAAAGCACAAAC 59.020 45.455 0.00 0.00 0.00 2.93
1683 1697 2.606795 GCAGCGATACCAAAAGCACAAA 60.607 45.455 0.00 0.00 0.00 2.83
1684 1698 1.068610 GCAGCGATACCAAAAGCACAA 60.069 47.619 0.00 0.00 0.00 3.33
1722 1736 2.414161 GCGATCCACCGGAAAGAAAAAG 60.414 50.000 9.46 0.00 34.34 2.27
1830 1845 5.865013 GGGTTTAATAATTTGGTTGTGTCCG 59.135 40.000 0.00 0.00 0.00 4.79
1847 1862 6.073447 TGGAGATGCTCTTAATGGGTTTAA 57.927 37.500 0.00 0.00 0.00 1.52
1848 1863 5.708736 TGGAGATGCTCTTAATGGGTTTA 57.291 39.130 0.00 0.00 0.00 2.01
1849 1864 4.591321 TGGAGATGCTCTTAATGGGTTT 57.409 40.909 0.00 0.00 0.00 3.27
1850 1865 4.263905 TGTTGGAGATGCTCTTAATGGGTT 60.264 41.667 0.00 0.00 0.00 4.11
1851 1866 3.266772 TGTTGGAGATGCTCTTAATGGGT 59.733 43.478 0.00 0.00 0.00 4.51
1852 1867 3.881688 CTGTTGGAGATGCTCTTAATGGG 59.118 47.826 0.00 0.00 0.00 4.00
1853 1868 4.574013 GTCTGTTGGAGATGCTCTTAATGG 59.426 45.833 0.00 0.00 31.63 3.16
1854 1869 4.269603 CGTCTGTTGGAGATGCTCTTAATG 59.730 45.833 0.00 0.00 30.78 1.90
1855 1870 4.437239 CGTCTGTTGGAGATGCTCTTAAT 58.563 43.478 0.00 0.00 30.78 1.40
1856 1871 3.849911 CGTCTGTTGGAGATGCTCTTAA 58.150 45.455 0.00 0.00 30.78 1.85
1857 1872 3.510388 CGTCTGTTGGAGATGCTCTTA 57.490 47.619 0.00 0.00 30.78 2.10
1858 1873 2.376808 CGTCTGTTGGAGATGCTCTT 57.623 50.000 0.00 0.00 30.78 2.85
2204 2249 1.487231 CGTTCTTCACGCCGAACAG 59.513 57.895 0.00 0.00 43.37 3.16
2205 2250 3.620286 CGTTCTTCACGCCGAACA 58.380 55.556 0.00 0.00 43.37 3.18
2390 2435 4.131088 GGAGGACGAGCGGGTCAC 62.131 72.222 8.06 0.78 38.70 3.67


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

AutoCloner maintained by Alex Coulton.