Multiple sequence alignment - TraesCS2A01G285800

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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 TraesCS2A01G285800 chr2A 100.000 2397 0 0 1 2397 485219429 485221825 0.000000e+00 4427
1 TraesCS2A01G285800 chr2A 95.749 1670 62 2 736 2397 485199593 485201261 0.000000e+00 2682
2 TraesCS2A01G285800 chr2A 94.703 1548 75 5 852 2397 687889853 687891395 0.000000e+00 2398
3 TraesCS2A01G285800 chr2A 89.454 531 44 6 877 1399 724520812 724520286 0.000000e+00 660
4 TraesCS2A01G285800 chr2A 93.917 411 23 2 313 721 485198888 485199298 9.410000e-174 619
5 TraesCS2A01G285800 chr2A 90.306 392 19 8 1397 1770 724520234 724519844 1.660000e-136 496
6 TraesCS2A01G285800 chr2A 95.035 282 13 1 1898 2178 724518957 724518676 2.190000e-120 442
7 TraesCS2A01G285800 chr2A 91.489 141 11 1 1763 1902 724519176 724519036 2.430000e-45 193
8 TraesCS2A01G285800 chr2A 86.441 177 10 4 2222 2397 724518683 724518520 5.260000e-42 182
9 TraesCS2A01G285800 chr2B 94.958 1547 69 6 852 2397 263832338 263833876 0.000000e+00 2416
10 TraesCS2A01G285800 chr2B 94.378 1512 75 4 887 2397 772923888 772922386 0.000000e+00 2313
11 TraesCS2A01G285800 chr2B 90.625 480 40 3 921 1399 714782684 714782209 1.210000e-177 632
12 TraesCS2A01G285800 chr2B 94.817 328 13 4 1 325 774677148 774677474 2.130000e-140 508
13 TraesCS2A01G285800 chr6B 94.904 1511 77 0 887 2397 95969845 95971355 0.000000e+00 2364
14 TraesCS2A01G285800 chr2D 90.110 637 43 7 1766 2397 590151578 590150957 0.000000e+00 809
15 TraesCS2A01G285800 chr2D 96.543 376 12 1 1395 1770 590152632 590152258 2.620000e-174 621
16 TraesCS2A01G285800 chr2D 89.348 460 37 9 941 1399 590153130 590152682 3.460000e-158 568
17 TraesCS2A01G285800 chr7B 89.899 594 28 9 319 880 27767690 27767097 0.000000e+00 736
18 TraesCS2A01G285800 chr7B 88.022 551 33 7 357 874 707971622 707972172 2.620000e-174 621
19 TraesCS2A01G285800 chr7B 94.512 328 13 4 1 325 526030239 526030564 3.560000e-138 501
20 TraesCS2A01G285800 chr5B 90.121 496 26 10 313 785 667473421 667472926 7.280000e-175 623
21 TraesCS2A01G285800 chr5B 86.509 593 42 16 313 874 73526088 73526673 3.390000e-173 617
22 TraesCS2A01G285800 chr5B 93.902 328 15 4 1 325 544200836 544200511 7.700000e-135 490
23 TraesCS2A01G285800 chr5A 86.172 593 44 15 313 874 498505868 498506453 7.330000e-170 606
24 TraesCS2A01G285800 chr6A 85.667 600 40 18 313 874 149570101 149570692 7.380000e-165 590
25 TraesCS2A01G285800 chr7A 94.207 328 15 3 1 325 17537292 17537618 4.600000e-137 497
26 TraesCS2A01G285800 chr7A 87.213 305 21 7 578 874 717344333 717344627 4.940000e-87 331
27 TraesCS2A01G285800 chr7A 88.776 98 3 3 785 874 717344438 717344535 1.950000e-21 113
28 TraesCS2A01G285800 chr1B 94.207 328 14 4 1 325 34501129 34501454 1.660000e-136 496
29 TraesCS2A01G285800 chr1B 93.902 328 14 5 1 325 490120775 490121099 7.700000e-135 490
30 TraesCS2A01G285800 chr1B 92.308 299 13 2 576 866 545450520 545450816 1.330000e-112 416
31 TraesCS2A01G285800 chr1A 94.207 328 14 4 1 325 532156156 532156481 1.660000e-136 496
32 TraesCS2A01G285800 chr1A 94.190 327 14 4 1 325 532117074 532117397 5.950000e-136 494
33 TraesCS2A01G285800 chrUn 93.902 328 15 4 1 325 360156177 360155852 7.700000e-135 490
34 TraesCS2A01G285800 chr5D 88.564 411 20 14 320 704 445143952 445143543 7.750000e-130 473
35 TraesCS2A01G285800 chr5D 85.956 413 34 15 319 707 6684127 6683715 1.020000e-113 420
36 TraesCS2A01G285800 chr5D 89.198 324 18 4 566 881 532475792 532475478 2.890000e-104 388
37 TraesCS2A01G285800 chr5D 92.251 271 17 2 313 579 12359794 12360064 4.840000e-102 381
38 TraesCS2A01G285800 chr4D 82.278 553 44 34 313 822 505943979 505944520 1.700000e-116 429
39 TraesCS2A01G285800 chr4B 93.040 273 16 2 313 582 41176733 41177005 1.730000e-106 396


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 TraesCS2A01G285800 chr2A 485219429 485221825 2396 False 4427.0 4427 100.000000 1 2397 1 chr2A.!!$F1 2396
1 TraesCS2A01G285800 chr2A 687889853 687891395 1542 False 2398.0 2398 94.703000 852 2397 1 chr2A.!!$F2 1545
2 TraesCS2A01G285800 chr2A 485198888 485201261 2373 False 1650.5 2682 94.833000 313 2397 2 chr2A.!!$F3 2084
3 TraesCS2A01G285800 chr2A 724518520 724520812 2292 True 394.6 660 90.545000 877 2397 5 chr2A.!!$R1 1520
4 TraesCS2A01G285800 chr2B 263832338 263833876 1538 False 2416.0 2416 94.958000 852 2397 1 chr2B.!!$F1 1545
5 TraesCS2A01G285800 chr2B 772922386 772923888 1502 True 2313.0 2313 94.378000 887 2397 1 chr2B.!!$R2 1510
6 TraesCS2A01G285800 chr6B 95969845 95971355 1510 False 2364.0 2364 94.904000 887 2397 1 chr6B.!!$F1 1510
7 TraesCS2A01G285800 chr2D 590150957 590153130 2173 True 666.0 809 92.000333 941 2397 3 chr2D.!!$R1 1456
8 TraesCS2A01G285800 chr7B 27767097 27767690 593 True 736.0 736 89.899000 319 880 1 chr7B.!!$R1 561
9 TraesCS2A01G285800 chr7B 707971622 707972172 550 False 621.0 621 88.022000 357 874 1 chr7B.!!$F2 517
10 TraesCS2A01G285800 chr5B 73526088 73526673 585 False 617.0 617 86.509000 313 874 1 chr5B.!!$F1 561
11 TraesCS2A01G285800 chr5A 498505868 498506453 585 False 606.0 606 86.172000 313 874 1 chr5A.!!$F1 561
12 TraesCS2A01G285800 chr6A 149570101 149570692 591 False 590.0 590 85.667000 313 874 1 chr6A.!!$F1 561
13 TraesCS2A01G285800 chr4D 505943979 505944520 541 False 429.0 429 82.278000 313 822 1 chr4D.!!$F1 509

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
249 250 0.104855 CTTCCATCTGAATCGGCGGA 59.895 55.0 7.21 0.00 31.06 5.54 F
250 251 0.539518 TTCCATCTGAATCGGCGGAA 59.460 50.0 7.21 8.22 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1659 1.202302 ACACCGCGACATCTGTATCAG 60.202 52.381 8.23 0.00 0.00 2.90 R
1492 1877 1.474077 GGCAGCATTTCGAAGGATGTT 59.526 47.619 15.47 6.27 30.27 2.71 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
25 26 7.988737 CACATATAATGACACAATGTGAAGGT 58.011 34.615 21.34 5.13 46.57 3.50
26 27 8.461222 CACATATAATGACACAATGTGAAGGTT 58.539 33.333 21.34 10.95 46.57 3.50
27 28 9.023962 ACATATAATGACACAATGTGAAGGTTT 57.976 29.630 21.34 8.36 36.96 3.27
28 29 9.859427 CATATAATGACACAATGTGAAGGTTTT 57.141 29.630 21.34 7.09 36.96 2.43
30 31 4.647424 TGACACAATGTGAAGGTTTTCC 57.353 40.909 21.34 0.00 36.96 3.13
31 32 4.019858 TGACACAATGTGAAGGTTTTCCA 58.980 39.130 21.34 1.17 38.58 3.53
32 33 4.464244 TGACACAATGTGAAGGTTTTCCAA 59.536 37.500 21.34 0.00 38.58 3.53
33 34 5.128499 TGACACAATGTGAAGGTTTTCCAAT 59.872 36.000 21.34 0.00 38.58 3.16
34 35 5.988287 ACACAATGTGAAGGTTTTCCAATT 58.012 33.333 21.34 0.00 38.58 2.32
35 36 6.413892 ACACAATGTGAAGGTTTTCCAATTT 58.586 32.000 21.34 0.00 38.58 1.82
36 37 6.883756 ACACAATGTGAAGGTTTTCCAATTTT 59.116 30.769 21.34 0.00 38.58 1.82
37 38 7.392953 ACACAATGTGAAGGTTTTCCAATTTTT 59.607 29.630 21.34 0.00 38.58 1.94
76 77 4.999751 TTTTATGCCCGTTTGAAAATGC 57.000 36.364 0.00 0.00 0.00 3.56
77 78 2.270275 TATGCCCGTTTGAAAATGCG 57.730 45.000 0.00 0.00 0.00 4.73
78 79 0.389687 ATGCCCGTTTGAAAATGCGG 60.390 50.000 0.00 0.00 42.03 5.69
79 80 1.006688 GCCCGTTTGAAAATGCGGT 60.007 52.632 5.02 0.00 41.20 5.68
80 81 1.006825 GCCCGTTTGAAAATGCGGTC 61.007 55.000 5.02 0.00 41.20 4.79
81 82 0.312416 CCCGTTTGAAAATGCGGTCA 59.688 50.000 5.02 0.00 41.20 4.02
82 83 1.269309 CCCGTTTGAAAATGCGGTCAA 60.269 47.619 5.02 0.00 41.20 3.18
83 84 2.464865 CCGTTTGAAAATGCGGTCAAA 58.535 42.857 0.00 0.00 40.52 2.69
84 85 2.860735 CCGTTTGAAAATGCGGTCAAAA 59.139 40.909 0.71 0.00 43.40 2.44
85 86 3.302156 CCGTTTGAAAATGCGGTCAAAAC 60.302 43.478 0.71 0.00 43.40 2.43
86 87 3.598225 CGTTTGAAAATGCGGTCAAAACG 60.598 43.478 0.00 0.00 43.40 3.60
87 88 2.126914 TGAAAATGCGGTCAAAACGG 57.873 45.000 0.00 0.00 0.00 4.44
94 95 3.292159 GGTCAAAACGGCGGGCTT 61.292 61.111 13.24 0.00 0.00 4.35
95 96 2.050442 GTCAAAACGGCGGGCTTG 60.050 61.111 13.24 11.50 0.00 4.01
96 97 2.203224 TCAAAACGGCGGGCTTGA 60.203 55.556 13.24 13.73 0.00 3.02
97 98 2.050442 CAAAACGGCGGGCTTGAC 60.050 61.111 13.24 0.00 0.00 3.18
98 99 3.292159 AAAACGGCGGGCTTGACC 61.292 61.111 13.24 0.00 37.93 4.02
106 107 4.934989 GGGCTTGACCGTTCCTAG 57.065 61.111 0.00 0.00 40.62 3.02
107 108 1.449778 GGGCTTGACCGTTCCTAGC 60.450 63.158 0.00 0.00 40.62 3.42
108 109 1.597461 GGCTTGACCGTTCCTAGCT 59.403 57.895 0.00 0.00 31.95 3.32
109 110 0.822164 GGCTTGACCGTTCCTAGCTA 59.178 55.000 0.00 0.00 31.95 3.32
110 111 1.202428 GGCTTGACCGTTCCTAGCTAG 60.202 57.143 14.20 14.20 31.95 3.42
111 112 1.477295 GCTTGACCGTTCCTAGCTAGT 59.523 52.381 19.31 0.06 0.00 2.57
112 113 2.735762 GCTTGACCGTTCCTAGCTAGTG 60.736 54.545 19.31 10.88 0.00 2.74
113 114 1.471119 TGACCGTTCCTAGCTAGTGG 58.529 55.000 19.31 16.16 0.00 4.00
114 115 1.272313 TGACCGTTCCTAGCTAGTGGT 60.272 52.381 19.31 18.90 0.00 4.16
115 116 1.823610 GACCGTTCCTAGCTAGTGGTT 59.176 52.381 19.31 6.67 0.00 3.67
116 117 1.549170 ACCGTTCCTAGCTAGTGGTTG 59.451 52.381 19.31 7.50 0.00 3.77
117 118 1.822990 CCGTTCCTAGCTAGTGGTTGA 59.177 52.381 19.31 6.30 0.00 3.18
118 119 2.232941 CCGTTCCTAGCTAGTGGTTGAA 59.767 50.000 19.31 11.82 0.00 2.69
119 120 3.118738 CCGTTCCTAGCTAGTGGTTGAAT 60.119 47.826 19.31 0.00 0.00 2.57
120 121 4.113354 CGTTCCTAGCTAGTGGTTGAATC 58.887 47.826 19.31 8.76 0.00 2.52
121 122 4.142138 CGTTCCTAGCTAGTGGTTGAATCT 60.142 45.833 19.31 0.00 0.00 2.40
122 123 5.624738 CGTTCCTAGCTAGTGGTTGAATCTT 60.625 44.000 19.31 0.00 0.00 2.40
123 124 6.405508 CGTTCCTAGCTAGTGGTTGAATCTTA 60.406 42.308 19.31 0.00 0.00 2.10
124 125 6.716934 TCCTAGCTAGTGGTTGAATCTTAG 57.283 41.667 19.31 0.00 0.00 2.18
125 126 6.432581 TCCTAGCTAGTGGTTGAATCTTAGA 58.567 40.000 19.31 1.64 0.00 2.10
126 127 6.895756 TCCTAGCTAGTGGTTGAATCTTAGAA 59.104 38.462 19.31 0.00 0.00 2.10
127 128 7.565398 TCCTAGCTAGTGGTTGAATCTTAGAAT 59.435 37.037 19.31 0.00 0.00 2.40
128 129 8.207545 CCTAGCTAGTGGTTGAATCTTAGAATT 58.792 37.037 19.31 0.00 0.00 2.17
129 130 9.606631 CTAGCTAGTGGTTGAATCTTAGAATTT 57.393 33.333 12.92 0.00 0.00 1.82
130 131 8.870075 AGCTAGTGGTTGAATCTTAGAATTTT 57.130 30.769 0.00 0.00 0.00 1.82
131 132 9.301897 AGCTAGTGGTTGAATCTTAGAATTTTT 57.698 29.630 0.00 0.00 0.00 1.94
210 211 6.840780 AAAATAGCAAACTATGAGGCAACT 57.159 33.333 0.00 0.00 44.77 3.16
211 212 5.824904 AATAGCAAACTATGAGGCAACTG 57.175 39.130 0.00 0.00 42.90 3.16
212 213 3.629398 ATAGCAAACTATGAGGCAACTGC 59.371 43.478 0.00 0.00 41.28 4.40
213 214 4.867927 ATAGCAAACTATGAGGCAACTGCA 60.868 41.667 3.76 0.00 41.28 4.41
214 215 6.659317 ATAGCAAACTATGAGGCAACTGCAG 61.659 44.000 13.48 13.48 41.28 4.41
215 216 8.981659 ATAGCAAACTATGAGGCAACTGCAGT 62.982 42.308 15.25 15.25 41.28 4.40
224 225 3.865224 GGCAACTGCAGTTCAAATTTG 57.135 42.857 28.97 17.64 44.36 2.32
225 226 3.456280 GGCAACTGCAGTTCAAATTTGA 58.544 40.909 28.97 16.91 44.36 2.69
226 227 3.245990 GGCAACTGCAGTTCAAATTTGAC 59.754 43.478 28.97 15.64 44.36 3.18
227 228 4.114794 GCAACTGCAGTTCAAATTTGACT 58.885 39.130 28.97 16.55 41.59 3.41
228 229 4.207841 GCAACTGCAGTTCAAATTTGACTC 59.792 41.667 28.97 15.51 41.59 3.36
229 230 4.214980 ACTGCAGTTCAAATTTGACTCG 57.785 40.909 20.35 12.00 36.83 4.18
230 231 2.975851 CTGCAGTTCAAATTTGACTCGC 59.024 45.455 20.35 20.28 36.83 5.03
231 232 2.618241 TGCAGTTCAAATTTGACTCGCT 59.382 40.909 20.35 12.74 36.83 4.93
232 233 3.066621 TGCAGTTCAAATTTGACTCGCTT 59.933 39.130 20.35 0.65 36.83 4.68
233 234 3.665871 GCAGTTCAAATTTGACTCGCTTC 59.334 43.478 20.35 7.54 36.83 3.86
234 235 4.222114 CAGTTCAAATTTGACTCGCTTCC 58.778 43.478 20.35 2.19 36.83 3.46
235 236 3.882888 AGTTCAAATTTGACTCGCTTCCA 59.117 39.130 20.35 0.00 36.83 3.53
236 237 4.520492 AGTTCAAATTTGACTCGCTTCCAT 59.480 37.500 20.35 0.00 36.83 3.41
237 238 4.685169 TCAAATTTGACTCGCTTCCATC 57.315 40.909 16.91 0.00 31.01 3.51
238 239 4.326826 TCAAATTTGACTCGCTTCCATCT 58.673 39.130 16.91 0.00 31.01 2.90
239 240 4.154737 TCAAATTTGACTCGCTTCCATCTG 59.845 41.667 16.91 0.00 31.01 2.90
240 241 3.616956 ATTTGACTCGCTTCCATCTGA 57.383 42.857 0.00 0.00 0.00 3.27
241 242 3.401033 TTTGACTCGCTTCCATCTGAA 57.599 42.857 0.00 0.00 0.00 3.02
242 243 3.616956 TTGACTCGCTTCCATCTGAAT 57.383 42.857 0.00 0.00 31.06 2.57
243 244 3.170791 TGACTCGCTTCCATCTGAATC 57.829 47.619 0.00 0.00 31.06 2.52
244 245 2.123342 GACTCGCTTCCATCTGAATCG 58.877 52.381 0.00 0.00 42.43 3.34
245 246 1.202463 ACTCGCTTCCATCTGAATCGG 60.202 52.381 0.00 0.00 41.62 4.18
246 247 0.530650 TCGCTTCCATCTGAATCGGC 60.531 55.000 0.00 0.00 41.62 5.54
247 248 1.825285 CGCTTCCATCTGAATCGGCG 61.825 60.000 0.00 0.00 38.57 6.46
248 249 1.502163 GCTTCCATCTGAATCGGCGG 61.502 60.000 7.21 0.00 31.06 6.13
249 250 0.104855 CTTCCATCTGAATCGGCGGA 59.895 55.000 7.21 0.00 31.06 5.54
250 251 0.539518 TTCCATCTGAATCGGCGGAA 59.460 50.000 7.21 8.22 0.00 4.30
251 252 0.539518 TCCATCTGAATCGGCGGAAA 59.460 50.000 7.21 0.00 0.00 3.13
252 253 1.140852 TCCATCTGAATCGGCGGAAAT 59.859 47.619 7.21 0.00 0.00 2.17
253 254 1.949525 CCATCTGAATCGGCGGAAATT 59.050 47.619 7.21 0.00 0.00 1.82
254 255 2.358898 CCATCTGAATCGGCGGAAATTT 59.641 45.455 7.21 0.00 0.00 1.82
255 256 3.365832 CATCTGAATCGGCGGAAATTTG 58.634 45.455 7.21 0.00 0.00 2.32
256 257 2.432444 TCTGAATCGGCGGAAATTTGT 58.568 42.857 7.21 0.00 0.00 2.83
257 258 2.418628 TCTGAATCGGCGGAAATTTGTC 59.581 45.455 7.21 0.00 0.00 3.18
258 259 2.420022 CTGAATCGGCGGAAATTTGTCT 59.580 45.455 7.21 0.00 0.00 3.41
259 260 2.817258 TGAATCGGCGGAAATTTGTCTT 59.183 40.909 7.21 0.00 0.00 3.01
260 261 3.254657 TGAATCGGCGGAAATTTGTCTTT 59.745 39.130 7.21 0.00 0.00 2.52
261 262 2.981400 TCGGCGGAAATTTGTCTTTC 57.019 45.000 7.21 0.00 34.95 2.62
262 263 2.500229 TCGGCGGAAATTTGTCTTTCT 58.500 42.857 7.21 0.00 35.81 2.52
263 264 2.482721 TCGGCGGAAATTTGTCTTTCTC 59.517 45.455 7.21 0.00 35.81 2.87
264 265 2.225491 CGGCGGAAATTTGTCTTTCTCA 59.775 45.455 0.00 0.00 35.81 3.27
265 266 3.565516 GGCGGAAATTTGTCTTTCTCAC 58.434 45.455 0.00 0.00 35.81 3.51
266 267 3.565516 GCGGAAATTTGTCTTTCTCACC 58.434 45.455 0.00 0.00 35.81 4.02
267 268 3.004315 GCGGAAATTTGTCTTTCTCACCA 59.996 43.478 0.00 0.00 35.81 4.17
268 269 4.787598 CGGAAATTTGTCTTTCTCACCAG 58.212 43.478 0.00 0.00 35.81 4.00
269 270 4.515191 CGGAAATTTGTCTTTCTCACCAGA 59.485 41.667 0.00 0.00 35.81 3.86
270 271 5.334414 CGGAAATTTGTCTTTCTCACCAGAG 60.334 44.000 0.00 0.00 43.48 3.35
271 272 5.048434 GGAAATTTGTCTTTCTCACCAGAGG 60.048 44.000 0.00 0.00 42.34 3.69
272 273 4.713792 ATTTGTCTTTCTCACCAGAGGT 57.286 40.909 0.00 0.00 42.34 3.85
273 274 9.333750 GGAAATTTGTCTTTCTCACCAGAGGTG 62.334 44.444 9.87 9.87 41.44 4.00
284 285 2.364972 CCAGAGGTGGGTCAAAACTT 57.635 50.000 0.00 0.00 40.67 2.66
285 286 2.666317 CCAGAGGTGGGTCAAAACTTT 58.334 47.619 0.00 0.00 40.67 2.66
286 287 3.031013 CCAGAGGTGGGTCAAAACTTTT 58.969 45.455 0.00 0.00 40.67 2.27
287 288 3.450817 CCAGAGGTGGGTCAAAACTTTTT 59.549 43.478 0.00 0.00 40.67 1.94
288 289 4.647399 CCAGAGGTGGGTCAAAACTTTTTA 59.353 41.667 0.00 0.00 40.67 1.52
289 290 5.451381 CCAGAGGTGGGTCAAAACTTTTTAC 60.451 44.000 0.00 0.00 40.67 2.01
290 291 5.126384 CAGAGGTGGGTCAAAACTTTTTACA 59.874 40.000 1.93 0.00 0.00 2.41
291 292 5.126545 AGAGGTGGGTCAAAACTTTTTACAC 59.873 40.000 1.93 0.00 0.00 2.90
292 293 4.160814 AGGTGGGTCAAAACTTTTTACACC 59.839 41.667 15.15 15.15 38.59 4.16
293 294 4.435425 GTGGGTCAAAACTTTTTACACCC 58.565 43.478 18.88 18.88 44.84 4.61
294 295 4.739587 GGGTCAAAACTTTTTACACCCA 57.260 40.909 19.95 0.00 44.43 4.51
295 296 5.087391 GGGTCAAAACTTTTTACACCCAA 57.913 39.130 19.95 0.00 44.43 4.12
296 297 4.871557 GGGTCAAAACTTTTTACACCCAAC 59.128 41.667 19.95 3.22 44.43 3.77
297 298 4.871557 GGTCAAAACTTTTTACACCCAACC 59.128 41.667 1.93 0.00 31.07 3.77
298 299 5.480205 GTCAAAACTTTTTACACCCAACCA 58.520 37.500 0.00 0.00 0.00 3.67
299 300 6.110033 GTCAAAACTTTTTACACCCAACCAT 58.890 36.000 0.00 0.00 0.00 3.55
300 301 6.596106 GTCAAAACTTTTTACACCCAACCATT 59.404 34.615 0.00 0.00 0.00 3.16
301 302 7.119992 GTCAAAACTTTTTACACCCAACCATTT 59.880 33.333 0.00 0.00 0.00 2.32
302 303 7.665974 TCAAAACTTTTTACACCCAACCATTTT 59.334 29.630 0.00 0.00 0.00 1.82
303 304 6.993786 AACTTTTTACACCCAACCATTTTG 57.006 33.333 0.00 0.00 0.00 2.44
304 305 6.056090 ACTTTTTACACCCAACCATTTTGT 57.944 33.333 0.00 0.00 0.00 2.83
305 306 6.110033 ACTTTTTACACCCAACCATTTTGTC 58.890 36.000 0.00 0.00 0.00 3.18
306 307 5.677319 TTTTACACCCAACCATTTTGTCA 57.323 34.783 0.00 0.00 0.00 3.58
307 308 5.677319 TTTACACCCAACCATTTTGTCAA 57.323 34.783 0.00 0.00 0.00 3.18
308 309 5.878406 TTACACCCAACCATTTTGTCAAT 57.122 34.783 0.00 0.00 0.00 2.57
309 310 4.769345 ACACCCAACCATTTTGTCAATT 57.231 36.364 0.00 0.00 0.00 2.32
310 311 4.450053 ACACCCAACCATTTTGTCAATTG 58.550 39.130 0.00 0.00 0.00 2.32
311 312 4.080638 ACACCCAACCATTTTGTCAATTGT 60.081 37.500 5.13 0.00 0.00 2.71
312 313 4.272991 CACCCAACCATTTTGTCAATTGTG 59.727 41.667 5.13 0.00 0.00 3.33
313 314 3.250521 CCCAACCATTTTGTCAATTGTGC 59.749 43.478 5.13 0.74 0.00 4.57
314 315 3.875727 CCAACCATTTTGTCAATTGTGCA 59.124 39.130 5.13 3.47 0.00 4.57
315 316 4.515944 CCAACCATTTTGTCAATTGTGCAT 59.484 37.500 5.13 0.00 0.00 3.96
316 317 5.008811 CCAACCATTTTGTCAATTGTGCATT 59.991 36.000 5.13 0.00 0.00 3.56
317 318 5.927954 ACCATTTTGTCAATTGTGCATTC 57.072 34.783 5.13 0.00 0.00 2.67
325 326 7.549615 TTGTCAATTGTGCATTCAAAAATGA 57.450 28.000 5.13 0.00 44.25 2.57
549 550 0.789687 ACATTTTCCATCCACCCCCA 59.210 50.000 0.00 0.00 0.00 4.96
556 561 1.231018 CCATCCACCCCCATCCTTTA 58.769 55.000 0.00 0.00 0.00 1.85
564 598 3.205282 CACCCCCATCCTTTATTTCTCCT 59.795 47.826 0.00 0.00 0.00 3.69
596 630 1.234529 CTCCTCTCCCCCGATCCTT 59.765 63.158 0.00 0.00 0.00 3.36
724 759 1.342474 TGTCTCCTCCTCCCATCAGAC 60.342 57.143 0.00 0.00 0.00 3.51
778 1093 1.123077 CTTCAGATCCATCCACCCGA 58.877 55.000 0.00 0.00 0.00 5.14
936 1266 4.704833 ACCGCTGCCGCTGTTGAT 62.705 61.111 0.00 0.00 28.52 2.57
944 1274 2.434884 CGCTGTTGATCACCCGCT 60.435 61.111 5.21 0.00 0.00 5.52
969 1299 4.241555 GGGTCCGCGATGCATCCT 62.242 66.667 20.87 0.00 0.00 3.24
1041 1371 2.765807 CCCGATGAGGAGGTGGCT 60.766 66.667 0.00 0.00 45.00 4.75
1044 1374 2.191641 GATGAGGAGGTGGCTGCC 59.808 66.667 12.87 12.87 0.00 4.85
1087 1417 2.513204 CGAGGCTGCAGTCCATGG 60.513 66.667 23.46 4.97 0.00 3.66
1123 1453 1.446366 GACCCCATTCTAGCCGACC 59.554 63.158 0.00 0.00 0.00 4.79
1127 1457 0.760945 CCCATTCTAGCCGACCTCCT 60.761 60.000 0.00 0.00 0.00 3.69
1181 1511 2.564553 ATCAACCTCGAGCTCGGCAC 62.565 60.000 33.98 0.00 40.29 5.01
1254 1584 4.814294 CCCTCTTCGAACCCCGCG 62.814 72.222 0.00 0.00 38.37 6.46
1323 1653 0.859232 CGTGTTCCTCTTGTCGTTGG 59.141 55.000 0.00 0.00 0.00 3.77
1329 1659 0.602905 CCTCTTGTCGTTGGGGTGAC 60.603 60.000 0.00 0.00 35.67 3.67
1393 1723 3.719268 TTGAAGCTGGCTATCAGGAAA 57.281 42.857 0.00 0.00 43.54 3.13
1492 1877 9.098355 GCTGACATGTGTTGATCTAATTAGTTA 57.902 33.333 1.15 0.00 0.00 2.24
1561 1949 1.578897 TGATGGGCACTAAGGCACTA 58.421 50.000 0.00 0.00 46.44 2.74
1624 2019 4.386867 TCTAAATAAGCTGAGGGTCACG 57.613 45.455 0.00 0.00 0.00 4.35
1713 2116 6.364976 GTGTTTTAGTTTGACTTTGCACTGTT 59.635 34.615 0.00 0.00 0.00 3.16
1775 2863 4.641989 GCCTGCTTGAATTAGATTCCAAGA 59.358 41.667 0.00 0.00 38.50 3.02
1794 2882 8.455903 TCCAAGATGGAGCTTATTCTAATTTG 57.544 34.615 0.00 0.00 42.67 2.32
2057 3229 0.108615 ACTCCATGAAGCTTCGGTCG 60.109 55.000 21.11 13.92 0.00 4.79
2070 3242 2.282701 TCGGTCGTGTGGTTATAAGC 57.717 50.000 7.74 7.74 0.00 3.09
2158 3330 4.142708 TGGCATCAGTATTTGTTAACGCTG 60.143 41.667 0.26 4.71 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.988737 ACCTTCACATTGTGTCATTATATGTG 58.011 34.615 16.06 0.00 44.52 3.21
1 2 8.579850 AACCTTCACATTGTGTCATTATATGT 57.420 30.769 16.06 0.00 34.79 2.29
2 3 9.859427 AAAACCTTCACATTGTGTCATTATATG 57.141 29.630 16.06 0.00 34.79 1.78
5 6 7.015098 TGGAAAACCTTCACATTGTGTCATTAT 59.985 33.333 16.06 0.00 34.79 1.28
6 7 6.322456 TGGAAAACCTTCACATTGTGTCATTA 59.678 34.615 16.06 0.00 34.79 1.90
7 8 5.128499 TGGAAAACCTTCACATTGTGTCATT 59.872 36.000 16.06 4.95 34.79 2.57
8 9 4.648762 TGGAAAACCTTCACATTGTGTCAT 59.351 37.500 16.06 0.00 34.79 3.06
9 10 4.019858 TGGAAAACCTTCACATTGTGTCA 58.980 39.130 16.06 4.29 34.79 3.58
10 11 4.647424 TGGAAAACCTTCACATTGTGTC 57.353 40.909 16.06 4.95 34.79 3.67
11 12 5.612725 ATTGGAAAACCTTCACATTGTGT 57.387 34.783 16.06 0.00 34.79 3.72
12 13 6.923928 AAATTGGAAAACCTTCACATTGTG 57.076 33.333 10.64 10.64 32.75 3.33
13 14 7.936496 AAAAATTGGAAAACCTTCACATTGT 57.064 28.000 0.00 0.00 32.75 2.71
54 55 4.084328 CGCATTTTCAAACGGGCATAAAAA 60.084 37.500 0.00 0.00 0.00 1.94
55 56 3.430218 CGCATTTTCAAACGGGCATAAAA 59.570 39.130 0.00 0.00 0.00 1.52
56 57 2.989840 CGCATTTTCAAACGGGCATAAA 59.010 40.909 0.00 0.00 0.00 1.40
57 58 2.600731 CGCATTTTCAAACGGGCATAA 58.399 42.857 0.00 0.00 0.00 1.90
58 59 1.135257 CCGCATTTTCAAACGGGCATA 60.135 47.619 0.00 0.00 41.95 3.14
59 60 0.389687 CCGCATTTTCAAACGGGCAT 60.390 50.000 0.00 0.00 41.95 4.40
60 61 1.006805 CCGCATTTTCAAACGGGCA 60.007 52.632 0.00 0.00 41.95 5.36
61 62 3.855109 CCGCATTTTCAAACGGGC 58.145 55.556 0.00 0.00 41.95 6.13
64 65 3.598225 CGTTTTGACCGCATTTTCAAACG 60.598 43.478 0.00 0.00 40.56 3.60
65 66 3.302156 CCGTTTTGACCGCATTTTCAAAC 60.302 43.478 0.00 0.00 40.56 2.93
66 67 2.860735 CCGTTTTGACCGCATTTTCAAA 59.139 40.909 0.00 0.00 39.42 2.69
67 68 2.464865 CCGTTTTGACCGCATTTTCAA 58.535 42.857 0.00 0.00 0.00 2.69
68 69 1.866063 GCCGTTTTGACCGCATTTTCA 60.866 47.619 0.00 0.00 0.00 2.69
69 70 0.781787 GCCGTTTTGACCGCATTTTC 59.218 50.000 0.00 0.00 0.00 2.29
70 71 0.937231 CGCCGTTTTGACCGCATTTT 60.937 50.000 0.00 0.00 0.00 1.82
71 72 1.371145 CGCCGTTTTGACCGCATTT 60.371 52.632 0.00 0.00 0.00 2.32
72 73 2.254051 CGCCGTTTTGACCGCATT 59.746 55.556 0.00 0.00 0.00 3.56
73 74 3.732892 CCGCCGTTTTGACCGCAT 61.733 61.111 0.00 0.00 0.00 4.73
77 78 3.292159 AAGCCCGCCGTTTTGACC 61.292 61.111 0.00 0.00 0.00 4.02
78 79 2.050442 CAAGCCCGCCGTTTTGAC 60.050 61.111 0.00 0.00 0.00 3.18
79 80 2.203224 TCAAGCCCGCCGTTTTGA 60.203 55.556 0.00 0.00 0.00 2.69
80 81 2.050442 GTCAAGCCCGCCGTTTTG 60.050 61.111 0.00 0.00 0.00 2.44
81 82 3.292159 GGTCAAGCCCGCCGTTTT 61.292 61.111 0.00 0.00 0.00 2.43
89 90 1.449778 GCTAGGAACGGTCAAGCCC 60.450 63.158 14.37 0.00 31.36 5.19
90 91 0.822164 TAGCTAGGAACGGTCAAGCC 59.178 55.000 19.89 6.06 35.78 4.35
91 92 1.477295 ACTAGCTAGGAACGGTCAAGC 59.523 52.381 24.35 16.85 35.54 4.01
92 93 2.159226 CCACTAGCTAGGAACGGTCAAG 60.159 54.545 24.35 0.00 0.00 3.02
93 94 1.822990 CCACTAGCTAGGAACGGTCAA 59.177 52.381 24.35 0.00 0.00 3.18
94 95 1.272313 ACCACTAGCTAGGAACGGTCA 60.272 52.381 24.35 0.00 0.00 4.02
95 96 1.472188 ACCACTAGCTAGGAACGGTC 58.528 55.000 24.35 0.00 0.00 4.79
96 97 1.549170 CAACCACTAGCTAGGAACGGT 59.451 52.381 24.35 19.79 0.00 4.83
97 98 1.822990 TCAACCACTAGCTAGGAACGG 59.177 52.381 24.35 19.20 0.00 4.44
98 99 3.587797 TTCAACCACTAGCTAGGAACG 57.412 47.619 24.35 10.70 0.00 3.95
99 100 5.346181 AGATTCAACCACTAGCTAGGAAC 57.654 43.478 24.35 11.51 0.00 3.62
100 101 6.895756 TCTAAGATTCAACCACTAGCTAGGAA 59.104 38.462 24.35 16.74 0.00 3.36
101 102 6.432581 TCTAAGATTCAACCACTAGCTAGGA 58.567 40.000 24.35 8.96 0.00 2.94
102 103 6.716934 TCTAAGATTCAACCACTAGCTAGG 57.283 41.667 24.35 11.41 0.00 3.02
103 104 9.606631 AAATTCTAAGATTCAACCACTAGCTAG 57.393 33.333 19.44 19.44 0.00 3.42
104 105 9.959721 AAAATTCTAAGATTCAACCACTAGCTA 57.040 29.630 0.00 0.00 0.00 3.32
105 106 8.870075 AAAATTCTAAGATTCAACCACTAGCT 57.130 30.769 0.00 0.00 0.00 3.32
186 187 7.092716 CAGTTGCCTCATAGTTTGCTATTTTT 58.907 34.615 0.00 0.00 35.85 1.94
187 188 6.624423 CAGTTGCCTCATAGTTTGCTATTTT 58.376 36.000 0.00 0.00 35.85 1.82
188 189 5.393461 GCAGTTGCCTCATAGTTTGCTATTT 60.393 40.000 0.00 0.00 33.76 1.40
189 190 4.096984 GCAGTTGCCTCATAGTTTGCTATT 59.903 41.667 0.00 0.00 33.76 1.73
190 191 3.629398 GCAGTTGCCTCATAGTTTGCTAT 59.371 43.478 0.00 0.00 35.20 2.97
191 192 3.009723 GCAGTTGCCTCATAGTTTGCTA 58.990 45.455 0.00 0.00 34.31 3.49
192 193 1.815003 GCAGTTGCCTCATAGTTTGCT 59.185 47.619 0.00 0.00 34.31 3.91
193 194 1.541147 TGCAGTTGCCTCATAGTTTGC 59.459 47.619 1.06 0.00 41.18 3.68
194 195 2.816087 ACTGCAGTTGCCTCATAGTTTG 59.184 45.455 15.25 0.00 41.18 2.93
195 196 3.146104 ACTGCAGTTGCCTCATAGTTT 57.854 42.857 15.25 0.00 41.18 2.66
196 197 2.867109 ACTGCAGTTGCCTCATAGTT 57.133 45.000 15.25 0.00 41.18 2.24
197 198 2.038952 TGAACTGCAGTTGCCTCATAGT 59.961 45.455 35.67 8.58 38.56 2.12
198 199 2.703416 TGAACTGCAGTTGCCTCATAG 58.297 47.619 35.67 0.00 38.56 2.23
199 200 2.857186 TGAACTGCAGTTGCCTCATA 57.143 45.000 35.67 10.45 38.56 2.15
200 201 1.985473 TTGAACTGCAGTTGCCTCAT 58.015 45.000 35.67 11.09 38.56 2.90
201 202 1.761449 TTTGAACTGCAGTTGCCTCA 58.239 45.000 35.67 24.02 38.56 3.86
202 203 3.375782 AATTTGAACTGCAGTTGCCTC 57.624 42.857 35.67 21.66 38.56 4.70
203 204 3.132646 TCAAATTTGAACTGCAGTTGCCT 59.867 39.130 35.67 13.21 38.56 4.75
204 205 3.245990 GTCAAATTTGAACTGCAGTTGCC 59.754 43.478 35.67 22.23 39.21 4.52
205 206 4.114794 AGTCAAATTTGAACTGCAGTTGC 58.885 39.130 35.67 24.79 39.21 4.17
206 207 4.438797 CGAGTCAAATTTGAACTGCAGTTG 59.561 41.667 35.67 20.24 39.21 3.16
207 208 4.601019 CGAGTCAAATTTGAACTGCAGTT 58.399 39.130 31.57 31.57 39.21 3.16
208 209 3.548818 GCGAGTCAAATTTGAACTGCAGT 60.549 43.478 22.07 15.25 39.21 4.40
209 210 2.975851 GCGAGTCAAATTTGAACTGCAG 59.024 45.455 22.07 13.48 39.21 4.41
210 211 2.618241 AGCGAGTCAAATTTGAACTGCA 59.382 40.909 27.48 6.70 39.21 4.41
211 212 3.273919 AGCGAGTCAAATTTGAACTGC 57.726 42.857 22.07 22.30 39.21 4.40
212 213 4.222114 GGAAGCGAGTCAAATTTGAACTG 58.778 43.478 22.07 14.71 39.21 3.16
213 214 3.882888 TGGAAGCGAGTCAAATTTGAACT 59.117 39.130 22.07 19.43 39.21 3.01
214 215 4.223320 TGGAAGCGAGTCAAATTTGAAC 57.777 40.909 22.07 16.93 39.21 3.18
215 216 4.761739 AGATGGAAGCGAGTCAAATTTGAA 59.238 37.500 22.07 4.26 39.21 2.69
216 217 4.154737 CAGATGGAAGCGAGTCAAATTTGA 59.845 41.667 16.91 16.91 34.20 2.69
217 218 4.154737 TCAGATGGAAGCGAGTCAAATTTG 59.845 41.667 12.15 12.15 0.00 2.32
218 219 4.326826 TCAGATGGAAGCGAGTCAAATTT 58.673 39.130 0.00 0.00 0.00 1.82
219 220 3.942829 TCAGATGGAAGCGAGTCAAATT 58.057 40.909 0.00 0.00 0.00 1.82
220 221 3.616956 TCAGATGGAAGCGAGTCAAAT 57.383 42.857 0.00 0.00 0.00 2.32
221 222 3.401033 TTCAGATGGAAGCGAGTCAAA 57.599 42.857 0.00 0.00 0.00 2.69
222 223 3.525537 GATTCAGATGGAAGCGAGTCAA 58.474 45.455 0.00 0.00 39.30 3.18
223 224 3.170791 GATTCAGATGGAAGCGAGTCA 57.829 47.619 0.00 0.00 39.30 3.41
229 230 1.502163 CCGCCGATTCAGATGGAAGC 61.502 60.000 0.00 0.00 39.30 3.86
230 231 0.104855 TCCGCCGATTCAGATGGAAG 59.895 55.000 0.00 0.00 39.30 3.46
231 232 0.539518 TTCCGCCGATTCAGATGGAA 59.460 50.000 0.00 0.00 40.46 3.53
232 233 0.539518 TTTCCGCCGATTCAGATGGA 59.460 50.000 0.00 0.00 0.00 3.41
233 234 1.597742 ATTTCCGCCGATTCAGATGG 58.402 50.000 0.00 0.00 0.00 3.51
234 235 3.181497 ACAAATTTCCGCCGATTCAGATG 60.181 43.478 0.00 0.00 0.00 2.90
235 236 3.016736 ACAAATTTCCGCCGATTCAGAT 58.983 40.909 0.00 0.00 0.00 2.90
236 237 2.418628 GACAAATTTCCGCCGATTCAGA 59.581 45.455 0.00 0.00 0.00 3.27
237 238 2.420022 AGACAAATTTCCGCCGATTCAG 59.580 45.455 0.00 0.00 0.00 3.02
238 239 2.432444 AGACAAATTTCCGCCGATTCA 58.568 42.857 0.00 0.00 0.00 2.57
239 240 3.487563 AAGACAAATTTCCGCCGATTC 57.512 42.857 0.00 0.00 0.00 2.52
240 241 3.506067 AGAAAGACAAATTTCCGCCGATT 59.494 39.130 0.00 0.00 39.53 3.34
241 242 3.081804 AGAAAGACAAATTTCCGCCGAT 58.918 40.909 0.00 0.00 39.53 4.18
242 243 2.482721 GAGAAAGACAAATTTCCGCCGA 59.517 45.455 0.00 0.00 39.53 5.54
243 244 2.225491 TGAGAAAGACAAATTTCCGCCG 59.775 45.455 0.00 0.00 39.53 6.46
244 245 3.565516 GTGAGAAAGACAAATTTCCGCC 58.434 45.455 0.00 0.00 39.53 6.13
245 246 3.004315 TGGTGAGAAAGACAAATTTCCGC 59.996 43.478 0.00 0.00 39.53 5.54
246 247 4.515191 TCTGGTGAGAAAGACAAATTTCCG 59.485 41.667 0.00 0.00 39.53 4.30
247 248 5.048434 CCTCTGGTGAGAAAGACAAATTTCC 60.048 44.000 0.00 0.00 42.73 3.13
248 249 5.532779 ACCTCTGGTGAGAAAGACAAATTTC 59.467 40.000 0.00 0.00 42.73 2.17
249 250 5.449553 ACCTCTGGTGAGAAAGACAAATTT 58.550 37.500 0.00 0.00 42.73 1.82
250 251 5.053978 ACCTCTGGTGAGAAAGACAAATT 57.946 39.130 0.00 0.00 42.73 1.82
251 252 4.713792 ACCTCTGGTGAGAAAGACAAAT 57.286 40.909 0.00 0.00 42.73 2.32
264 265 1.222567 AGTTTTGACCCACCTCTGGT 58.777 50.000 0.00 0.00 39.32 4.00
265 266 2.364972 AAGTTTTGACCCACCTCTGG 57.635 50.000 0.00 0.00 37.29 3.86
266 267 4.736126 AAAAAGTTTTGACCCACCTCTG 57.264 40.909 0.61 0.00 0.00 3.35
267 268 5.126545 GTGTAAAAAGTTTTGACCCACCTCT 59.873 40.000 12.48 0.00 0.00 3.69
268 269 5.345702 GTGTAAAAAGTTTTGACCCACCTC 58.654 41.667 12.48 0.00 0.00 3.85
269 270 4.160814 GGTGTAAAAAGTTTTGACCCACCT 59.839 41.667 20.61 2.47 35.50 4.00
270 271 4.435425 GGTGTAAAAAGTTTTGACCCACC 58.565 43.478 12.48 14.90 33.38 4.61
271 272 4.435425 GGGTGTAAAAAGTTTTGACCCAC 58.565 43.478 25.24 17.75 44.97 4.61
272 273 4.739587 GGGTGTAAAAAGTTTTGACCCA 57.260 40.909 25.24 10.26 44.97 4.51
273 274 4.739587 TGGGTGTAAAAAGTTTTGACCC 57.260 40.909 24.26 24.26 45.37 4.46
274 275 4.871557 GGTTGGGTGTAAAAAGTTTTGACC 59.128 41.667 12.48 12.67 35.17 4.02
275 276 5.480205 TGGTTGGGTGTAAAAAGTTTTGAC 58.520 37.500 8.70 8.70 0.00 3.18
276 277 5.740290 TGGTTGGGTGTAAAAAGTTTTGA 57.260 34.783 0.61 0.00 0.00 2.69
277 278 6.993786 AATGGTTGGGTGTAAAAAGTTTTG 57.006 33.333 0.61 0.00 0.00 2.44
278 279 7.448777 ACAAAATGGTTGGGTGTAAAAAGTTTT 59.551 29.630 0.00 0.00 0.00 2.43
279 280 6.943146 ACAAAATGGTTGGGTGTAAAAAGTTT 59.057 30.769 0.00 0.00 0.00 2.66
280 281 6.477253 ACAAAATGGTTGGGTGTAAAAAGTT 58.523 32.000 0.00 0.00 0.00 2.66
281 282 6.056090 ACAAAATGGTTGGGTGTAAAAAGT 57.944 33.333 0.00 0.00 0.00 2.66
282 283 6.109359 TGACAAAATGGTTGGGTGTAAAAAG 58.891 36.000 0.00 0.00 0.00 2.27
283 284 6.049955 TGACAAAATGGTTGGGTGTAAAAA 57.950 33.333 0.00 0.00 0.00 1.94
284 285 5.677319 TGACAAAATGGTTGGGTGTAAAA 57.323 34.783 0.00 0.00 0.00 1.52
285 286 5.677319 TTGACAAAATGGTTGGGTGTAAA 57.323 34.783 0.00 0.00 0.00 2.01
286 287 5.878406 ATTGACAAAATGGTTGGGTGTAA 57.122 34.783 0.00 0.00 0.00 2.41
287 288 5.129485 ACAATTGACAAAATGGTTGGGTGTA 59.871 36.000 13.59 0.00 0.00 2.90
288 289 4.080638 ACAATTGACAAAATGGTTGGGTGT 60.081 37.500 13.59 0.00 0.00 4.16
289 290 4.272991 CACAATTGACAAAATGGTTGGGTG 59.727 41.667 13.59 0.00 0.00 4.61
290 291 4.450053 CACAATTGACAAAATGGTTGGGT 58.550 39.130 13.59 0.00 0.00 4.51
291 292 3.250521 GCACAATTGACAAAATGGTTGGG 59.749 43.478 13.59 3.54 0.00 4.12
292 293 3.875727 TGCACAATTGACAAAATGGTTGG 59.124 39.130 13.59 0.00 0.00 3.77
293 294 5.676532 ATGCACAATTGACAAAATGGTTG 57.323 34.783 13.59 0.00 0.00 3.77
294 295 5.821470 TGAATGCACAATTGACAAAATGGTT 59.179 32.000 13.59 0.38 0.00 3.67
295 296 5.366460 TGAATGCACAATTGACAAAATGGT 58.634 33.333 13.59 0.00 0.00 3.55
296 297 5.926214 TGAATGCACAATTGACAAAATGG 57.074 34.783 13.59 0.00 0.00 3.16
297 298 8.616377 TTTTTGAATGCACAATTGACAAAATG 57.384 26.923 13.59 0.00 36.28 2.32
298 299 9.239002 CATTTTTGAATGCACAATTGACAAAAT 57.761 25.926 13.59 9.07 36.28 1.82
299 300 8.456471 TCATTTTTGAATGCACAATTGACAAAA 58.544 25.926 13.59 15.11 35.17 2.44
300 301 7.982224 TCATTTTTGAATGCACAATTGACAAA 58.018 26.923 13.59 10.81 0.00 2.83
301 302 7.549615 TCATTTTTGAATGCACAATTGACAA 57.450 28.000 13.59 5.80 0.00 3.18
302 303 7.549615 TTCATTTTTGAATGCACAATTGACA 57.450 28.000 13.59 10.32 29.11 3.58
303 304 8.838452 TTTTCATTTTTGAATGCACAATTGAC 57.162 26.923 13.59 4.32 29.11 3.18
392 393 0.892063 TGCAGCACACCAGTACGATA 59.108 50.000 0.00 0.00 0.00 2.92
400 401 2.548280 CCAATCAAAATGCAGCACACCA 60.548 45.455 0.00 0.00 0.00 4.17
401 402 2.070783 CCAATCAAAATGCAGCACACC 58.929 47.619 0.00 0.00 0.00 4.16
549 550 4.417183 GGGAGGGAAGGAGAAATAAAGGAT 59.583 45.833 0.00 0.00 0.00 3.24
556 561 1.915983 GCGGGAGGGAAGGAGAAAT 59.084 57.895 0.00 0.00 0.00 2.17
738 1053 1.480498 GGAGGAGGAGATGAGGAGGTC 60.480 61.905 0.00 0.00 0.00 3.85
924 1254 2.359850 GGGTGATCAACAGCGGCA 60.360 61.111 13.90 0.00 46.51 5.69
965 1295 1.910722 AGCGTGATTGGCTCAGGAT 59.089 52.632 1.17 0.00 41.32 3.24
1041 1371 2.679996 TCGCTGCTCTGGTAGGCA 60.680 61.111 0.00 0.00 36.94 4.75
1044 1374 2.105930 GCCTCGCTGCTCTGGTAG 59.894 66.667 0.00 0.00 0.00 3.18
1123 1453 3.474570 CGGGGGCTTCCTCAGGAG 61.475 72.222 0.00 0.00 31.21 3.69
1206 1536 1.474320 CCAAACGAGGTGTTGTCCAGA 60.474 52.381 0.00 0.00 40.84 3.86
1254 1584 5.989551 AAGTGATTTGGACAAAAATGTGC 57.010 34.783 1.17 0.00 33.56 4.57
1283 1613 5.586243 CACGAATTGAGATGTGGGATAAACT 59.414 40.000 0.00 0.00 0.00 2.66
1323 1653 2.799917 GCGACATCTGTATCAGTCACCC 60.800 54.545 0.00 0.00 32.61 4.61
1329 1659 1.202302 ACACCGCGACATCTGTATCAG 60.202 52.381 8.23 0.00 0.00 2.90
1492 1877 1.474077 GGCAGCATTTCGAAGGATGTT 59.526 47.619 15.47 6.27 30.27 2.71
1794 2882 6.972328 TCAAGTTCAGTGCAAAATCAAACTAC 59.028 34.615 0.00 0.00 0.00 2.73
2057 3229 7.652507 GTGTCCTAGATAAGCTTATAACCACAC 59.347 40.741 18.87 20.14 0.00 3.82
2070 3242 7.011482 GGCAAACAATGTAGTGTCCTAGATAAG 59.989 40.741 0.00 0.00 0.00 1.73
2176 3348 5.685728 AGCCTTTCTTGGATGAATAGGTAC 58.314 41.667 0.00 0.00 32.26 3.34


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

AutoCloner maintained by Alex Coulton.