Multiple sequence alignment - TraesCS3A01G418100

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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 TraesCS3A01G418100 chr3A 100.000 2927 0 0 1 2927 660194842 660197768 0.000000e+00 5406.0
1 TraesCS3A01G418100 chr3A 87.111 225 23 3 86 310 457686792 457686574 1.740000e-62 250.0
2 TraesCS3A01G418100 chr3A 79.787 188 36 2 1223 1409 746634161 746633975 5.090000e-28 135.0
3 TraesCS3A01G418100 chr3A 90.741 54 4 1 378 431 672807261 672807313 1.460000e-08 71.3
4 TraesCS3A01G418100 chr3B 88.980 1833 101 36 476 2279 694262876 694264636 0.000000e+00 2172.0
5 TraesCS3A01G418100 chr3B 98.671 301 4 0 45 345 672772066 672772366 4.290000e-148 534.0
6 TraesCS3A01G418100 chr3B 87.805 246 28 2 101 345 293098884 293099128 1.330000e-73 287.0
7 TraesCS3A01G418100 chr3B 79.787 188 36 2 1223 1409 829542112 829541926 5.090000e-28 135.0
8 TraesCS3A01G418100 chr3B 88.136 59 4 3 29 86 144219101 144219045 1.880000e-07 67.6
9 TraesCS3A01G418100 chr3B 97.368 38 0 1 39 75 641261251 641261288 2.440000e-06 63.9
10 TraesCS3A01G418100 chr3D 91.851 1129 56 15 456 1567 525918435 525917326 0.000000e+00 1543.0
11 TraesCS3A01G418100 chr3D 88.806 804 47 17 1609 2390 525917329 525916547 0.000000e+00 946.0
12 TraesCS3A01G418100 chr3D 96.000 525 18 2 2406 2927 584701382 584700858 0.000000e+00 850.0
13 TraesCS3A01G418100 chr3D 96.000 525 18 2 2406 2927 613711280 613711804 0.000000e+00 850.0
14 TraesCS3A01G418100 chr3D 95.167 538 24 1 2392 2927 56276246 56275709 0.000000e+00 848.0
15 TraesCS3A01G418100 chr3D 83.766 308 50 0 1208 1515 5147383 5147690 2.850000e-75 292.0
16 TraesCS3A01G418100 chr3D 79.787 188 36 2 1223 1409 611919005 611918819 5.090000e-28 135.0
17 TraesCS3A01G418100 chr3D 90.164 61 4 2 1343 1402 48071107 48071166 8.700000e-11 78.7
18 TraesCS3A01G418100 chr1D 96.381 525 15 3 2406 2927 60171805 60171282 0.000000e+00 861.0
19 TraesCS3A01G418100 chr1D 96.000 525 18 2 2406 2927 205134687 205134163 0.000000e+00 850.0
20 TraesCS3A01G418100 chr1D 96.000 525 18 2 2406 2927 247505748 247505224 0.000000e+00 850.0
21 TraesCS3A01G418100 chr1D 86.667 75 10 0 1229 1303 449983277 449983203 1.870000e-12 84.2
22 TraesCS3A01G418100 chr1D 90.566 53 3 2 1351 1402 364624908 364624857 5.230000e-08 69.4
23 TraesCS3A01G418100 chr1D 96.875 32 1 0 2197 2228 203534914 203534883 1.000000e-03 54.7
24 TraesCS3A01G418100 chr2D 96.000 525 18 2 2406 2927 73126862 73126338 0.000000e+00 850.0
25 TraesCS3A01G418100 chr5A 95.825 527 19 2 2404 2927 547123898 547124424 0.000000e+00 848.0
26 TraesCS3A01G418100 chr7D 95.802 524 19 2 2406 2927 497560917 497561439 0.000000e+00 843.0
27 TraesCS3A01G418100 chr6A 96.743 307 4 2 43 344 601202891 601203196 9.360000e-140 507.0
28 TraesCS3A01G418100 chr1B 98.566 279 4 0 65 343 550935803 550936081 7.290000e-136 494.0
29 TraesCS3A01G418100 chr1B 88.000 75 9 0 1229 1303 616136505 616136431 4.020000e-14 89.8
30 TraesCS3A01G418100 chr1B 97.674 43 1 0 1226 1268 616566503 616566545 1.130000e-09 75.0
31 TraesCS3A01G418100 chr7A 98.566 279 3 1 64 341 43514226 43513948 2.620000e-135 492.0
32 TraesCS3A01G418100 chr7A 98.214 280 5 0 64 343 657713265 657713544 9.430000e-135 490.0
33 TraesCS3A01G418100 chr2B 98.221 281 5 0 64 344 198358301 198358021 2.620000e-135 492.0
34 TraesCS3A01G418100 chr2B 97.857 280 6 0 64 343 97402015 97401736 4.390000e-133 484.0
35 TraesCS3A01G418100 chr2B 84.711 242 18 10 1869 2092 158889790 158889550 1.060000e-54 224.0
36 TraesCS3A01G418100 chr2B 87.879 66 8 0 1343 1408 550213833 550213768 8.700000e-11 78.7
37 TraesCS3A01G418100 chr4B 97.872 282 6 0 64 345 99342496 99342215 3.390000e-134 488.0
38 TraesCS3A01G418100 chr4B 88.274 307 36 0 1211 1517 393406270 393406576 4.610000e-98 368.0
39 TraesCS3A01G418100 chr7B 95.681 301 12 1 43 343 729026746 729027045 1.580000e-132 483.0
40 TraesCS3A01G418100 chr7B 84.519 239 18 10 1869 2089 637621014 637621251 4.910000e-53 219.0
41 TraesCS3A01G418100 chr4A 88.438 320 36 1 1214 1532 159294850 159294531 4.580000e-103 385.0
42 TraesCS3A01G418100 chr4A 83.784 185 28 2 1343 1526 437483394 437483211 1.080000e-39 174.0
43 TraesCS3A01G418100 chr4D 87.616 323 39 1 1211 1532 315597323 315597645 9.910000e-100 374.0
44 TraesCS3A01G418100 chr4D 82.011 189 32 2 1343 1530 129777071 129777258 3.020000e-35 159.0
45 TraesCS3A01G418100 chr4D 90.741 54 5 0 1351 1404 497126496 497126549 4.050000e-09 73.1
46 TraesCS3A01G418100 chr4D 97.368 38 1 0 1365 1402 506606738 506606701 6.770000e-07 65.8
47 TraesCS3A01G418100 chrUn 82.759 203 31 3 1343 1544 58870305 58870106 8.340000e-41 178.0
48 TraesCS3A01G418100 chr2A 81.522 184 22 4 127 310 161949429 161949600 1.090000e-29 141.0
49 TraesCS3A01G418100 chr2A 76.339 224 37 12 90 310 19451599 19451809 3.990000e-19 106.0
50 TraesCS3A01G418100 chr5B 90.164 61 4 2 1343 1402 514279237 514279178 8.700000e-11 78.7
51 TraesCS3A01G418100 chr1A 81.250 96 18 0 1229 1324 545025095 545025000 8.700000e-11 78.7
52 TraesCS3A01G418100 chr1A 96.875 32 1 0 2197 2228 258179430 258179399 1.000000e-03 54.7
53 TraesCS3A01G418100 chr5D 92.453 53 2 2 1351 1402 200501552 200501603 1.130000e-09 75.0
54 TraesCS3A01G418100 chr5D 95.556 45 1 1 1359 1402 425077076 425077032 1.460000e-08 71.3
55 TraesCS3A01G418100 chr6D 88.333 60 7 0 1343 1402 309719552 309719611 4.050000e-09 73.1
56 TraesCS3A01G418100 chr6D 100.000 30 0 0 1373 1402 292737717 292737688 4.080000e-04 56.5


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 TraesCS3A01G418100 chr3A 660194842 660197768 2926 False 5406.0 5406 100.0000 1 2927 1 chr3A.!!$F1 2926
1 TraesCS3A01G418100 chr3B 694262876 694264636 1760 False 2172.0 2172 88.9800 476 2279 1 chr3B.!!$F4 1803
2 TraesCS3A01G418100 chr3D 525916547 525918435 1888 True 1244.5 1543 90.3285 456 2390 2 chr3D.!!$R4 1934
3 TraesCS3A01G418100 chr3D 584700858 584701382 524 True 850.0 850 96.0000 2406 2927 1 chr3D.!!$R2 521
4 TraesCS3A01G418100 chr3D 613711280 613711804 524 False 850.0 850 96.0000 2406 2927 1 chr3D.!!$F3 521
5 TraesCS3A01G418100 chr3D 56275709 56276246 537 True 848.0 848 95.1670 2392 2927 1 chr3D.!!$R1 535
6 TraesCS3A01G418100 chr1D 60171282 60171805 523 True 861.0 861 96.3810 2406 2927 1 chr1D.!!$R1 521
7 TraesCS3A01G418100 chr1D 205134163 205134687 524 True 850.0 850 96.0000 2406 2927 1 chr1D.!!$R3 521
8 TraesCS3A01G418100 chr1D 247505224 247505748 524 True 850.0 850 96.0000 2406 2927 1 chr1D.!!$R4 521
9 TraesCS3A01G418100 chr2D 73126338 73126862 524 True 850.0 850 96.0000 2406 2927 1 chr2D.!!$R1 521
10 TraesCS3A01G418100 chr5A 547123898 547124424 526 False 848.0 848 95.8250 2404 2927 1 chr5A.!!$F1 523
11 TraesCS3A01G418100 chr7D 497560917 497561439 522 False 843.0 843 95.8020 2406 2927 1 chr7D.!!$F1 521

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
376 377 0.105658 ATTAGCCTAGCTCCGTCCCA 60.106 55.0 0.00 0.00 40.44 4.37 F
381 382 0.183014 CCTAGCTCCGTCCCAGAGTA 59.817 60.0 0.00 0.00 33.69 2.59 F
389 390 0.316772 CGTCCCAGAGTATACGCGTG 60.317 60.0 24.59 2.24 0.00 5.34 F
418 419 0.366871 GCGTCTGCGTCTGTATTGTG 59.633 55.0 0.00 0.00 40.81 3.33 F
997 1019 0.462225 TAGCTCACTCTCGAGTCCGG 60.462 60.0 13.13 0.00 40.20 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1595 0.872021 GGCGCGACACTAAGAGGATG 60.872 60.000 12.10 0.0 0.00 3.51 R
1720 1748 2.143594 GAGCCTGACCAGTTCGTCGT 62.144 60.000 0.00 0.0 35.40 4.34 R
1871 1899 2.158959 CACTTGTCGTCGCCGGATC 61.159 63.158 5.05 0.0 33.95 3.36 R
1876 1904 3.112709 GCTCCACTTGTCGTCGCC 61.113 66.667 0.00 0.0 0.00 5.54 R
2534 2582 0.396695 TCAAGGGGTAGGAGTAGCGG 60.397 60.000 0.00 0.0 0.00 5.52 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
55 56 2.689658 AGTGCATACTATACCTGGCCA 58.310 47.619 4.71 4.71 34.74 5.36
56 57 3.251484 AGTGCATACTATACCTGGCCAT 58.749 45.455 5.51 0.00 34.74 4.40
57 58 3.008375 AGTGCATACTATACCTGGCCATG 59.992 47.826 5.51 6.06 34.74 3.66
58 59 2.305635 TGCATACTATACCTGGCCATGG 59.694 50.000 5.51 13.05 0.00 3.66
59 60 2.356125 GCATACTATACCTGGCCATGGG 60.356 54.545 20.97 16.10 0.00 4.00
60 61 3.181329 CATACTATACCTGGCCATGGGA 58.819 50.000 17.65 12.89 0.00 4.37
61 62 2.206322 ACTATACCTGGCCATGGGAA 57.794 50.000 17.65 9.02 0.00 3.97
62 63 2.057922 ACTATACCTGGCCATGGGAAG 58.942 52.381 17.65 14.95 0.00 3.46
63 64 0.771127 TATACCTGGCCATGGGAAGC 59.229 55.000 17.65 0.00 0.00 3.86
116 117 2.570135 CTCAGGCCTAGATTTTGAGCC 58.430 52.381 3.98 0.00 44.20 4.70
117 118 1.212935 TCAGGCCTAGATTTTGAGCCC 59.787 52.381 3.98 0.00 45.00 5.19
118 119 0.181350 AGGCCTAGATTTTGAGCCCG 59.819 55.000 1.29 0.00 45.00 6.13
119 120 0.180406 GGCCTAGATTTTGAGCCCGA 59.820 55.000 0.00 0.00 37.66 5.14
120 121 1.408266 GGCCTAGATTTTGAGCCCGAA 60.408 52.381 0.00 0.00 37.66 4.30
121 122 1.943340 GCCTAGATTTTGAGCCCGAAG 59.057 52.381 0.00 0.00 0.00 3.79
155 156 2.678580 CCCGGGCCCGTCATTTTT 60.679 61.111 40.52 0.00 37.81 1.94
156 157 2.571231 CCGGGCCCGTCATTTTTG 59.429 61.111 40.52 20.46 37.81 2.44
157 158 2.126110 CGGGCCCGTCATTTTTGC 60.126 61.111 36.64 0.00 34.35 3.68
158 159 2.126110 GGGCCCGTCATTTTTGCG 60.126 61.111 5.69 0.00 0.00 4.85
159 160 2.809174 GGCCCGTCATTTTTGCGC 60.809 61.111 0.00 0.00 0.00 6.09
160 161 2.258286 GCCCGTCATTTTTGCGCT 59.742 55.556 9.73 0.00 0.00 5.92
161 162 1.372872 GCCCGTCATTTTTGCGCTT 60.373 52.632 9.73 0.00 0.00 4.68
162 163 0.943835 GCCCGTCATTTTTGCGCTTT 60.944 50.000 9.73 0.00 0.00 3.51
163 164 1.059942 CCCGTCATTTTTGCGCTTTC 58.940 50.000 9.73 0.00 0.00 2.62
164 165 1.059942 CCGTCATTTTTGCGCTTTCC 58.940 50.000 9.73 0.00 0.00 3.13
165 166 1.335872 CCGTCATTTTTGCGCTTTCCT 60.336 47.619 9.73 0.00 0.00 3.36
166 167 1.715519 CGTCATTTTTGCGCTTTCCTG 59.284 47.619 9.73 0.91 0.00 3.86
167 168 2.604373 CGTCATTTTTGCGCTTTCCTGA 60.604 45.455 9.73 3.60 0.00 3.86
168 169 3.380142 GTCATTTTTGCGCTTTCCTGAA 58.620 40.909 9.73 0.00 0.00 3.02
169 170 3.426525 GTCATTTTTGCGCTTTCCTGAAG 59.573 43.478 9.73 0.00 38.45 3.02
170 171 2.507339 TTTTTGCGCTTTCCTGAAGG 57.493 45.000 9.73 0.00 35.82 3.46
171 172 1.398692 TTTTGCGCTTTCCTGAAGGT 58.601 45.000 9.73 0.00 35.82 3.50
172 173 0.951558 TTTGCGCTTTCCTGAAGGTC 59.048 50.000 9.73 0.00 35.82 3.85
173 174 1.227999 TTGCGCTTTCCTGAAGGTCG 61.228 55.000 9.73 0.00 35.82 4.79
174 175 2.391389 GCGCTTTCCTGAAGGTCGG 61.391 63.158 0.00 0.00 35.82 4.79
175 176 1.741770 CGCTTTCCTGAAGGTCGGG 60.742 63.158 0.00 0.00 44.41 5.14
176 177 2.041115 GCTTTCCTGAAGGTCGGGC 61.041 63.158 0.00 0.00 42.73 6.13
177 178 1.377333 CTTTCCTGAAGGTCGGGCC 60.377 63.158 0.00 0.00 42.73 5.80
178 179 3.248446 TTTCCTGAAGGTCGGGCCG 62.248 63.158 22.51 22.51 42.73 6.13
209 210 2.666812 CCCGACGGGCTTTTAGGT 59.333 61.111 22.37 0.00 35.35 3.08
210 211 1.743995 CCCGACGGGCTTTTAGGTG 60.744 63.158 22.37 0.00 35.35 4.00
211 212 1.004200 CCGACGGGCTTTTAGGTGT 60.004 57.895 5.81 0.00 0.00 4.16
212 213 0.604511 CCGACGGGCTTTTAGGTGTT 60.605 55.000 5.81 0.00 0.00 3.32
213 214 0.794473 CGACGGGCTTTTAGGTGTTC 59.206 55.000 0.00 0.00 0.00 3.18
214 215 0.794473 GACGGGCTTTTAGGTGTTCG 59.206 55.000 0.00 0.00 0.00 3.95
215 216 0.604511 ACGGGCTTTTAGGTGTTCGG 60.605 55.000 0.00 0.00 0.00 4.30
216 217 1.303091 CGGGCTTTTAGGTGTTCGGG 61.303 60.000 0.00 0.00 0.00 5.14
217 218 1.592400 GGGCTTTTAGGTGTTCGGGC 61.592 60.000 0.00 0.00 0.00 6.13
218 219 1.592400 GGCTTTTAGGTGTTCGGGCC 61.592 60.000 0.00 0.00 0.00 5.80
219 220 1.918868 GCTTTTAGGTGTTCGGGCCG 61.919 60.000 22.51 22.51 0.00 6.13
220 221 1.302671 TTTTAGGTGTTCGGGCCGG 60.303 57.895 27.98 7.65 0.00 6.13
221 222 2.751357 TTTTAGGTGTTCGGGCCGGG 62.751 60.000 27.98 0.00 0.00 5.73
249 250 4.366159 AAAAACAGGCCCGTTGGT 57.634 50.000 4.78 0.00 0.00 3.67
250 251 2.120765 AAAAACAGGCCCGTTGGTC 58.879 52.632 4.78 0.00 36.05 4.02
251 252 1.730451 AAAAACAGGCCCGTTGGTCG 61.730 55.000 4.78 0.00 42.85 4.79
280 281 2.526624 GCCTGGGCCTGGGTTTTT 60.527 61.111 28.34 0.00 34.56 1.94
294 295 2.725008 TTTTTGCGTCGGGCTTGG 59.275 55.556 0.00 0.00 44.05 3.61
295 296 3.492311 TTTTTGCGTCGGGCTTGGC 62.492 57.895 0.00 0.00 44.05 4.52
296 297 4.947147 TTTGCGTCGGGCTTGGCT 62.947 61.111 0.00 0.00 44.05 4.75
297 298 3.538785 TTTGCGTCGGGCTTGGCTA 62.539 57.895 0.00 0.00 44.05 3.93
298 299 3.950794 TTGCGTCGGGCTTGGCTAG 62.951 63.158 0.00 0.00 44.05 3.42
338 339 4.256180 GCCCGAGGTATGGCCAGG 62.256 72.222 13.05 6.01 41.97 4.45
339 340 2.768344 CCCGAGGTATGGCCAGGT 60.768 66.667 13.05 0.00 40.61 4.00
340 341 1.458777 CCCGAGGTATGGCCAGGTA 60.459 63.158 13.05 0.00 40.61 3.08
341 342 0.836400 CCCGAGGTATGGCCAGGTAT 60.836 60.000 13.05 0.00 40.61 2.73
342 343 1.551560 CCCGAGGTATGGCCAGGTATA 60.552 57.143 13.05 0.00 40.61 1.47
343 344 1.825474 CCGAGGTATGGCCAGGTATAG 59.175 57.143 13.05 0.92 40.61 1.31
344 345 2.526432 CGAGGTATGGCCAGGTATAGT 58.474 52.381 13.05 0.00 40.61 2.12
345 346 2.231478 CGAGGTATGGCCAGGTATAGTG 59.769 54.545 13.05 0.00 40.61 2.74
346 347 1.978580 AGGTATGGCCAGGTATAGTGC 59.021 52.381 13.05 0.00 40.61 4.40
347 348 1.697432 GGTATGGCCAGGTATAGTGCA 59.303 52.381 13.05 0.00 37.17 4.57
348 349 2.305927 GGTATGGCCAGGTATAGTGCAT 59.694 50.000 13.05 0.00 37.17 3.96
349 350 3.517901 GGTATGGCCAGGTATAGTGCATA 59.482 47.826 13.05 0.00 37.17 3.14
350 351 3.703001 ATGGCCAGGTATAGTGCATAC 57.297 47.619 13.05 0.00 39.11 2.39
363 364 6.824305 ATAGTGCATACCATTGAATTAGCC 57.176 37.500 0.00 0.00 0.00 3.93
364 365 4.796606 AGTGCATACCATTGAATTAGCCT 58.203 39.130 0.00 0.00 0.00 4.58
365 366 5.940617 AGTGCATACCATTGAATTAGCCTA 58.059 37.500 0.00 0.00 0.00 3.93
366 367 6.000219 AGTGCATACCATTGAATTAGCCTAG 59.000 40.000 0.00 0.00 0.00 3.02
367 368 4.761739 TGCATACCATTGAATTAGCCTAGC 59.238 41.667 0.00 0.00 0.00 3.42
368 369 5.006386 GCATACCATTGAATTAGCCTAGCT 58.994 41.667 0.00 0.00 43.41 3.32
369 370 5.123027 GCATACCATTGAATTAGCCTAGCTC 59.877 44.000 0.00 0.00 40.44 4.09
370 371 4.092116 ACCATTGAATTAGCCTAGCTCC 57.908 45.455 0.00 0.00 40.44 4.70
371 372 3.070018 CCATTGAATTAGCCTAGCTCCG 58.930 50.000 0.00 0.00 40.44 4.63
372 373 3.495100 CCATTGAATTAGCCTAGCTCCGT 60.495 47.826 0.00 0.00 40.44 4.69
373 374 3.454371 TTGAATTAGCCTAGCTCCGTC 57.546 47.619 0.00 0.00 40.44 4.79
374 375 1.687123 TGAATTAGCCTAGCTCCGTCC 59.313 52.381 0.00 0.00 40.44 4.79
375 376 1.001068 GAATTAGCCTAGCTCCGTCCC 59.999 57.143 0.00 0.00 40.44 4.46
376 377 0.105658 ATTAGCCTAGCTCCGTCCCA 60.106 55.000 0.00 0.00 40.44 4.37
377 378 0.755698 TTAGCCTAGCTCCGTCCCAG 60.756 60.000 0.00 0.00 40.44 4.45
378 379 1.642513 TAGCCTAGCTCCGTCCCAGA 61.643 60.000 0.00 0.00 40.44 3.86
379 380 2.494530 GCCTAGCTCCGTCCCAGAG 61.495 68.421 0.00 0.00 0.00 3.35
380 381 1.076632 CCTAGCTCCGTCCCAGAGT 60.077 63.158 0.00 0.00 33.69 3.24
381 382 0.183014 CCTAGCTCCGTCCCAGAGTA 59.817 60.000 0.00 0.00 33.69 2.59
382 383 1.202952 CCTAGCTCCGTCCCAGAGTAT 60.203 57.143 0.00 0.00 33.69 2.12
383 384 2.040012 CCTAGCTCCGTCCCAGAGTATA 59.960 54.545 0.00 0.00 33.69 1.47
384 385 1.984066 AGCTCCGTCCCAGAGTATAC 58.016 55.000 0.00 0.00 33.69 1.47
385 386 0.592148 GCTCCGTCCCAGAGTATACG 59.408 60.000 0.00 0.00 33.69 3.06
386 387 0.592148 CTCCGTCCCAGAGTATACGC 59.408 60.000 0.00 0.00 34.13 4.42
387 388 1.162181 TCCGTCCCAGAGTATACGCG 61.162 60.000 3.53 3.53 34.13 6.01
388 389 1.442526 CCGTCCCAGAGTATACGCGT 61.443 60.000 19.17 19.17 34.13 6.01
389 390 0.316772 CGTCCCAGAGTATACGCGTG 60.317 60.000 24.59 2.24 0.00 5.34
390 391 0.737219 GTCCCAGAGTATACGCGTGT 59.263 55.000 24.59 19.31 0.00 4.49
391 392 1.942657 GTCCCAGAGTATACGCGTGTA 59.057 52.381 24.59 18.01 34.45 2.90
392 393 2.551459 GTCCCAGAGTATACGCGTGTAT 59.449 50.000 24.59 23.84 43.62 2.29
393 394 3.748048 GTCCCAGAGTATACGCGTGTATA 59.252 47.826 24.59 21.82 41.50 1.47
394 395 4.394300 GTCCCAGAGTATACGCGTGTATAT 59.606 45.833 26.67 17.34 43.52 0.86
395 396 5.582269 GTCCCAGAGTATACGCGTGTATATA 59.418 44.000 26.67 8.85 43.52 0.86
396 397 6.259608 GTCCCAGAGTATACGCGTGTATATAT 59.740 42.308 26.67 19.69 43.52 0.86
397 398 6.259387 TCCCAGAGTATACGCGTGTATATATG 59.741 42.308 26.67 22.88 43.52 1.78
398 399 6.259387 CCCAGAGTATACGCGTGTATATATGA 59.741 42.308 26.67 8.09 43.52 2.15
399 400 7.345943 CCAGAGTATACGCGTGTATATATGAG 58.654 42.308 26.67 16.95 43.52 2.90
400 401 6.846786 CAGAGTATACGCGTGTATATATGAGC 59.153 42.308 26.67 15.28 43.52 4.26
404 405 3.118807 CGCGTGTATATATGAGCGTCT 57.881 47.619 15.69 0.00 42.26 4.18
405 406 2.840752 CGCGTGTATATATGAGCGTCTG 59.159 50.000 15.69 1.40 42.26 3.51
406 407 2.594654 GCGTGTATATATGAGCGTCTGC 59.405 50.000 0.00 0.00 43.24 4.26
417 418 2.738147 GCGTCTGCGTCTGTATTGT 58.262 52.632 0.00 0.00 40.81 2.71
418 419 0.366871 GCGTCTGCGTCTGTATTGTG 59.633 55.000 0.00 0.00 40.81 3.33
419 420 1.698165 CGTCTGCGTCTGTATTGTGT 58.302 50.000 0.00 0.00 0.00 3.72
420 421 2.058798 CGTCTGCGTCTGTATTGTGTT 58.941 47.619 0.00 0.00 0.00 3.32
421 422 2.475111 CGTCTGCGTCTGTATTGTGTTT 59.525 45.455 0.00 0.00 0.00 2.83
422 423 3.059868 CGTCTGCGTCTGTATTGTGTTTT 60.060 43.478 0.00 0.00 0.00 2.43
423 424 4.149221 CGTCTGCGTCTGTATTGTGTTTTA 59.851 41.667 0.00 0.00 0.00 1.52
424 425 5.371629 GTCTGCGTCTGTATTGTGTTTTAC 58.628 41.667 0.00 0.00 0.00 2.01
425 426 5.050634 GTCTGCGTCTGTATTGTGTTTTACA 60.051 40.000 0.00 0.00 37.56 2.41
447 448 4.341366 AAAAACTTGCCCCTGAGAAATG 57.659 40.909 0.00 0.00 0.00 2.32
448 449 2.978156 AACTTGCCCCTGAGAAATGA 57.022 45.000 0.00 0.00 0.00 2.57
449 450 2.978156 ACTTGCCCCTGAGAAATGAA 57.022 45.000 0.00 0.00 0.00 2.57
450 451 2.519013 ACTTGCCCCTGAGAAATGAAC 58.481 47.619 0.00 0.00 0.00 3.18
451 452 2.158475 ACTTGCCCCTGAGAAATGAACA 60.158 45.455 0.00 0.00 0.00 3.18
452 453 1.909700 TGCCCCTGAGAAATGAACAC 58.090 50.000 0.00 0.00 0.00 3.32
453 454 1.177401 GCCCCTGAGAAATGAACACC 58.823 55.000 0.00 0.00 0.00 4.16
454 455 1.839424 CCCCTGAGAAATGAACACCC 58.161 55.000 0.00 0.00 0.00 4.61
465 466 7.118496 AGAAATGAACACCCAAACATGTTTA 57.882 32.000 22.87 6.08 39.13 2.01
468 469 4.023980 TGAACACCCAAACATGTTTACCA 58.976 39.130 22.87 10.34 39.13 3.25
469 470 4.098654 TGAACACCCAAACATGTTTACCAG 59.901 41.667 22.87 15.28 39.13 4.00
470 471 3.904717 ACACCCAAACATGTTTACCAGA 58.095 40.909 22.87 0.00 0.00 3.86
471 472 4.282496 ACACCCAAACATGTTTACCAGAA 58.718 39.130 22.87 0.00 0.00 3.02
551 555 1.079543 CGAGAGCCACCCTCAGTTG 60.080 63.158 0.00 0.00 43.31 3.16
554 558 1.003233 GAGCCACCCTCAGTTGGTC 60.003 63.158 0.00 0.00 40.45 4.02
652 668 3.242772 ACGCATCAGTAGTACATCAGTCG 60.243 47.826 2.52 1.79 0.00 4.18
755 771 3.633094 AACACGAGAGCGCGCATCT 62.633 57.895 35.10 29.69 42.48 2.90
758 774 2.161486 ACGAGAGCGCGCATCTTTC 61.161 57.895 35.10 21.49 42.48 2.62
785 804 9.524106 TTCTCATTTAAAATCAGCATTAGCATG 57.476 29.630 0.00 0.00 45.49 4.06
928 950 1.230635 CGAACTTCCACCTGCACCAG 61.231 60.000 0.00 0.00 0.00 4.00
946 968 1.577134 CAGCAAACGACAACAACAACG 59.423 47.619 0.00 0.00 0.00 4.10
995 1017 2.210116 CTCTAGCTCACTCTCGAGTCC 58.790 57.143 13.13 0.00 40.20 3.85
996 1018 0.934496 CTAGCTCACTCTCGAGTCCG 59.066 60.000 13.13 5.02 40.20 4.79
997 1019 0.462225 TAGCTCACTCTCGAGTCCGG 60.462 60.000 13.13 0.00 40.20 5.14
998 1020 2.795297 CTCACTCTCGAGTCCGGC 59.205 66.667 13.13 0.00 40.20 6.13
999 1021 2.750637 TCACTCTCGAGTCCGGCC 60.751 66.667 13.13 0.00 40.20 6.13
1014 1036 1.154205 CGGCCATGGATCACTTCGAC 61.154 60.000 18.40 0.00 0.00 4.20
1029 1051 2.883621 GACTCCTTCGGGTCGACC 59.116 66.667 27.04 27.04 34.89 4.79
1049 1071 2.509336 CATGGACGCCGTCTGGAC 60.509 66.667 17.76 0.40 37.49 4.02
1202 1227 2.435059 GTGGAACGAGCTGGCCTC 60.435 66.667 3.32 0.00 37.22 4.70
1338 1363 2.203422 CACTTCCGGTGGGGCAAA 60.203 61.111 0.00 0.00 41.90 3.68
1404 1429 2.197577 GAGATCAAGAACTACTGGCGC 58.802 52.381 0.00 0.00 0.00 6.53
1408 1433 1.003718 AAGAACTACTGGCGCACCC 60.004 57.895 10.83 0.00 33.59 4.61
1626 1654 1.077930 CATGTGCCACTCCCCTGAG 60.078 63.158 0.00 0.00 44.62 3.35
1720 1748 2.992689 TCTTGACGGCCGGCAGTA 60.993 61.111 35.65 23.63 33.06 2.74
1786 1814 2.593134 GCGAGGAGCGATGACATGC 61.593 63.158 0.00 0.00 44.57 4.06
1855 1883 1.375326 GACTCTGTGGTGTTCCCCC 59.625 63.158 0.00 0.00 0.00 5.40
1869 1897 3.096852 GTTCCCCCACTTTGAATTAGGG 58.903 50.000 0.00 0.00 39.29 3.53
1876 1904 3.214328 CACTTTGAATTAGGGGGATCCG 58.786 50.000 5.45 0.00 41.52 4.18
1878 1906 0.476771 TTGAATTAGGGGGATCCGGC 59.523 55.000 5.45 0.00 41.52 6.13
1920 1948 0.036732 ACATCTGGTCGCAACACCAT 59.963 50.000 0.00 0.00 45.76 3.55
1927 1955 2.147958 GGTCGCAACACCATTACTGAA 58.852 47.619 0.00 0.00 36.32 3.02
1928 1956 2.550606 GGTCGCAACACCATTACTGAAA 59.449 45.455 0.00 0.00 36.32 2.69
1929 1957 3.551551 GTCGCAACACCATTACTGAAAC 58.448 45.455 0.00 0.00 0.00 2.78
1930 1958 3.250040 GTCGCAACACCATTACTGAAACT 59.750 43.478 0.00 0.00 0.00 2.66
1931 1959 3.880490 TCGCAACACCATTACTGAAACTT 59.120 39.130 0.00 0.00 0.00 2.66
1932 1960 3.974401 CGCAACACCATTACTGAAACTTG 59.026 43.478 0.00 0.00 0.00 3.16
2000 2028 9.845305 CTCGATTTTATTAACGACCAGATTTAC 57.155 33.333 0.00 0.00 0.00 2.01
2007 2041 9.577110 TTATTAACGACCAGATTTACTGTAGTG 57.423 33.333 0.00 0.00 44.40 2.74
2082 2116 5.942236 TGAATTCTGATATATGCCTCCTTGC 59.058 40.000 7.05 0.00 0.00 4.01
2095 2143 1.659098 CTCCTTGCACGGTCGAATTAC 59.341 52.381 9.36 0.00 0.00 1.89
2115 2163 9.574516 GAATTACCATAGGACCATTAGTTTCAT 57.425 33.333 0.00 0.00 0.00 2.57
2175 2223 5.117355 TGTTTCGGTCAGTCAAGTAGTAG 57.883 43.478 0.00 0.00 0.00 2.57
2176 2224 4.581824 TGTTTCGGTCAGTCAAGTAGTAGT 59.418 41.667 0.00 0.00 0.00 2.73
2177 2225 5.764686 TGTTTCGGTCAGTCAAGTAGTAGTA 59.235 40.000 0.00 0.00 0.00 1.82
2218 2266 6.343703 ACCTATTGGTCTACGGTATTTTCAC 58.656 40.000 0.00 0.00 44.78 3.18
2268 2316 7.095695 TGTACACAAAAGAAGAAGGAAAAGG 57.904 36.000 0.00 0.00 0.00 3.11
2313 2361 8.270744 AGAGCTTATTATCCAATGTCAGTTCTT 58.729 33.333 0.00 0.00 0.00 2.52
2314 2362 8.814038 AGCTTATTATCCAATGTCAGTTCTTT 57.186 30.769 0.00 0.00 0.00 2.52
2315 2363 8.680903 AGCTTATTATCCAATGTCAGTTCTTTG 58.319 33.333 0.00 0.00 0.00 2.77
2333 2381 6.801539 TCTTTGTGACTATCATGGTCAAAC 57.198 37.500 5.24 0.00 43.90 2.93
2351 2399 5.928264 GTCAAACTCCAATTGCTATTTTGCT 59.072 36.000 0.00 0.00 0.00 3.91
2376 2424 4.334759 GTGCAGTTCATTCTAGATGTGCAT 59.665 41.667 15.30 0.00 38.25 3.96
2390 2438 3.513680 TGTGCATCAATCCATTCTTGC 57.486 42.857 0.00 0.00 0.00 4.01
2391 2439 3.093814 TGTGCATCAATCCATTCTTGCT 58.906 40.909 0.00 0.00 0.00 3.91
2392 2440 3.129813 TGTGCATCAATCCATTCTTGCTC 59.870 43.478 0.00 0.00 0.00 4.26
2393 2441 3.380637 GTGCATCAATCCATTCTTGCTCT 59.619 43.478 0.00 0.00 0.00 4.09
2394 2442 4.021229 TGCATCAATCCATTCTTGCTCTT 58.979 39.130 0.00 0.00 0.00 2.85
2395 2443 4.097437 TGCATCAATCCATTCTTGCTCTTC 59.903 41.667 0.00 0.00 0.00 2.87
2396 2444 4.338682 GCATCAATCCATTCTTGCTCTTCT 59.661 41.667 0.00 0.00 0.00 2.85
2397 2445 5.163540 GCATCAATCCATTCTTGCTCTTCTT 60.164 40.000 0.00 0.00 0.00 2.52
2398 2446 6.627508 GCATCAATCCATTCTTGCTCTTCTTT 60.628 38.462 0.00 0.00 0.00 2.52
2399 2447 6.906157 TCAATCCATTCTTGCTCTTCTTTT 57.094 33.333 0.00 0.00 0.00 2.27
2400 2448 8.464404 CATCAATCCATTCTTGCTCTTCTTTTA 58.536 33.333 0.00 0.00 0.00 1.52
2401 2449 8.408043 TCAATCCATTCTTGCTCTTCTTTTAA 57.592 30.769 0.00 0.00 0.00 1.52
2402 2450 8.859090 TCAATCCATTCTTGCTCTTCTTTTAAA 58.141 29.630 0.00 0.00 0.00 1.52
2444 2492 0.676184 GCCTCTGCATCTGGACGATA 59.324 55.000 0.00 0.00 37.47 2.92
2452 2500 3.506067 TGCATCTGGACGATACATACGAT 59.494 43.478 0.00 0.00 34.70 3.73
2455 2503 5.677344 GCATCTGGACGATACATACGATCAT 60.677 44.000 0.00 0.00 34.70 2.45
2614 2663 4.016444 ACATCGCACCAAATCCTAACATT 58.984 39.130 0.00 0.00 0.00 2.71
2793 2844 2.524394 ACAGCTCGACCACCCTGT 60.524 61.111 0.00 0.00 33.96 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.661954 AGGTATAGTATGCACTATATAGCCATT 57.338 33.333 16.96 7.28 46.77 3.16
25 26 9.083422 CAGGTATAGTATGCACTATATAGCCAT 57.917 37.037 9.78 13.82 46.77 4.40
26 27 7.505923 CCAGGTATAGTATGCACTATATAGCCA 59.494 40.741 9.78 7.77 46.77 4.75
27 28 7.524038 GCCAGGTATAGTATGCACTATATAGCC 60.524 44.444 9.78 2.19 46.77 3.93
28 29 7.371936 GCCAGGTATAGTATGCACTATATAGC 58.628 42.308 9.78 9.85 46.77 2.97
29 30 7.505923 TGGCCAGGTATAGTATGCACTATATAG 59.494 40.741 0.00 8.27 46.77 1.31
30 31 7.359056 TGGCCAGGTATAGTATGCACTATATA 58.641 38.462 0.00 0.00 46.77 0.86
31 32 6.202331 TGGCCAGGTATAGTATGCACTATAT 58.798 40.000 0.00 0.74 46.77 0.86
32 33 5.585894 TGGCCAGGTATAGTATGCACTATA 58.414 41.667 0.00 0.00 44.53 1.31
34 35 3.851979 TGGCCAGGTATAGTATGCACTA 58.148 45.455 0.00 0.00 41.47 2.74
35 36 2.689658 TGGCCAGGTATAGTATGCACT 58.310 47.619 0.00 0.00 38.91 4.40
36 37 3.338249 CATGGCCAGGTATAGTATGCAC 58.662 50.000 13.05 0.00 0.00 4.57
37 38 2.305635 CCATGGCCAGGTATAGTATGCA 59.694 50.000 17.55 0.00 0.00 3.96
38 39 2.356125 CCCATGGCCAGGTATAGTATGC 60.356 54.545 17.55 0.00 0.00 3.14
39 40 3.181329 TCCCATGGCCAGGTATAGTATG 58.819 50.000 17.55 3.23 0.00 2.39
40 41 3.577968 TCCCATGGCCAGGTATAGTAT 57.422 47.619 17.55 0.00 0.00 2.12
41 42 3.248024 CTTCCCATGGCCAGGTATAGTA 58.752 50.000 17.55 0.00 0.00 1.82
42 43 2.057922 CTTCCCATGGCCAGGTATAGT 58.942 52.381 17.55 0.00 0.00 2.12
43 44 1.271597 GCTTCCCATGGCCAGGTATAG 60.272 57.143 17.55 10.70 0.00 1.31
44 45 0.771127 GCTTCCCATGGCCAGGTATA 59.229 55.000 17.55 0.00 0.00 1.47
45 46 1.538666 GCTTCCCATGGCCAGGTAT 59.461 57.895 17.55 0.00 0.00 2.73
46 47 2.689691 GGCTTCCCATGGCCAGGTA 61.690 63.158 17.55 3.27 46.84 3.08
47 48 4.066139 GGCTTCCCATGGCCAGGT 62.066 66.667 17.55 0.00 46.84 4.00
96 97 2.570135 GGCTCAAAATCTAGGCCTGAG 58.430 52.381 17.99 13.59 39.68 3.35
97 98 2.717639 GGCTCAAAATCTAGGCCTGA 57.282 50.000 17.99 11.61 39.68 3.86
101 102 1.943340 CTTCGGGCTCAAAATCTAGGC 59.057 52.381 0.00 0.00 37.55 3.93
102 103 2.092914 ACCTTCGGGCTCAAAATCTAGG 60.093 50.000 0.00 0.00 39.10 3.02
103 104 3.198872 GACCTTCGGGCTCAAAATCTAG 58.801 50.000 0.00 0.00 39.10 2.43
104 105 2.418197 CGACCTTCGGGCTCAAAATCTA 60.418 50.000 0.00 0.00 39.10 1.98
105 106 1.676014 CGACCTTCGGGCTCAAAATCT 60.676 52.381 0.00 0.00 39.10 2.40
106 107 0.727398 CGACCTTCGGGCTCAAAATC 59.273 55.000 0.00 0.00 39.10 2.17
107 108 2.854522 CGACCTTCGGGCTCAAAAT 58.145 52.632 0.00 0.00 39.10 1.82
108 109 4.371975 CGACCTTCGGGCTCAAAA 57.628 55.556 0.00 0.00 39.10 2.44
138 139 2.678580 AAAAATGACGGGCCCGGG 60.679 61.111 44.99 22.37 44.69 5.73
139 140 2.571231 CAAAAATGACGGGCCCGG 59.429 61.111 44.99 28.13 44.69 5.73
140 141 2.126110 GCAAAAATGACGGGCCCG 60.126 61.111 42.17 42.17 46.03 6.13
141 142 2.126110 CGCAAAAATGACGGGCCC 60.126 61.111 13.57 13.57 0.00 5.80
142 143 2.763627 AAGCGCAAAAATGACGGGCC 62.764 55.000 11.47 0.00 39.23 5.80
143 144 0.943835 AAAGCGCAAAAATGACGGGC 60.944 50.000 11.47 0.00 38.75 6.13
144 145 1.059942 GAAAGCGCAAAAATGACGGG 58.940 50.000 11.47 0.00 0.00 5.28
145 146 1.059942 GGAAAGCGCAAAAATGACGG 58.940 50.000 11.47 0.00 0.00 4.79
146 147 1.715519 CAGGAAAGCGCAAAAATGACG 59.284 47.619 11.47 0.00 0.00 4.35
147 148 3.011949 TCAGGAAAGCGCAAAAATGAC 57.988 42.857 11.47 0.00 0.00 3.06
148 149 3.552684 CCTTCAGGAAAGCGCAAAAATGA 60.553 43.478 11.47 5.25 37.39 2.57
149 150 2.733026 CCTTCAGGAAAGCGCAAAAATG 59.267 45.455 11.47 2.50 37.39 2.32
150 151 2.365293 ACCTTCAGGAAAGCGCAAAAAT 59.635 40.909 11.47 0.00 38.94 1.82
151 152 1.754226 ACCTTCAGGAAAGCGCAAAAA 59.246 42.857 11.47 0.00 38.94 1.94
152 153 1.336755 GACCTTCAGGAAAGCGCAAAA 59.663 47.619 11.47 0.00 38.94 2.44
153 154 0.951558 GACCTTCAGGAAAGCGCAAA 59.048 50.000 11.47 0.00 38.94 3.68
154 155 1.227999 CGACCTTCAGGAAAGCGCAA 61.228 55.000 11.47 0.00 38.94 4.85
155 156 1.667830 CGACCTTCAGGAAAGCGCA 60.668 57.895 11.47 0.00 38.94 6.09
156 157 2.391389 CCGACCTTCAGGAAAGCGC 61.391 63.158 0.00 0.00 38.94 5.92
157 158 1.741770 CCCGACCTTCAGGAAAGCG 60.742 63.158 0.00 0.00 38.94 4.68
158 159 2.041115 GCCCGACCTTCAGGAAAGC 61.041 63.158 0.00 0.00 38.94 3.51
159 160 1.377333 GGCCCGACCTTCAGGAAAG 60.377 63.158 0.00 0.00 38.94 2.62
160 161 2.754375 GGCCCGACCTTCAGGAAA 59.246 61.111 0.00 0.00 38.94 3.13
161 162 3.702048 CGGCCCGACCTTCAGGAA 61.702 66.667 0.00 0.00 38.94 3.36
193 194 0.604511 AACACCTAAAAGCCCGTCGG 60.605 55.000 3.60 3.60 0.00 4.79
194 195 0.794473 GAACACCTAAAAGCCCGTCG 59.206 55.000 0.00 0.00 0.00 5.12
195 196 0.794473 CGAACACCTAAAAGCCCGTC 59.206 55.000 0.00 0.00 0.00 4.79
196 197 0.604511 CCGAACACCTAAAAGCCCGT 60.605 55.000 0.00 0.00 0.00 5.28
197 198 1.303091 CCCGAACACCTAAAAGCCCG 61.303 60.000 0.00 0.00 0.00 6.13
198 199 1.592400 GCCCGAACACCTAAAAGCCC 61.592 60.000 0.00 0.00 0.00 5.19
199 200 1.592400 GGCCCGAACACCTAAAAGCC 61.592 60.000 0.00 0.00 0.00 4.35
200 201 1.880894 GGCCCGAACACCTAAAAGC 59.119 57.895 0.00 0.00 0.00 3.51
201 202 1.303091 CCGGCCCGAACACCTAAAAG 61.303 60.000 3.71 0.00 0.00 2.27
202 203 1.302671 CCGGCCCGAACACCTAAAA 60.303 57.895 3.71 0.00 0.00 1.52
203 204 2.348243 CCGGCCCGAACACCTAAA 59.652 61.111 3.71 0.00 0.00 1.85
204 205 3.708544 CCCGGCCCGAACACCTAA 61.709 66.667 3.71 0.00 0.00 2.69
232 233 1.730451 CGACCAACGGGCCTGTTTTT 61.730 55.000 27.83 16.86 37.90 1.94
233 234 2.190841 CGACCAACGGGCCTGTTTT 61.191 57.895 27.83 17.24 37.90 2.43
234 235 2.593436 CGACCAACGGGCCTGTTT 60.593 61.111 27.83 14.63 37.90 2.83
263 264 2.526624 AAAAACCCAGGCCCAGGC 60.527 61.111 8.60 0.00 41.06 4.85
277 278 2.725008 CCAAGCCCGACGCAAAAA 59.275 55.556 0.00 0.00 41.38 1.94
278 279 3.972276 GCCAAGCCCGACGCAAAA 61.972 61.111 0.00 0.00 41.38 2.44
279 280 3.538785 TAGCCAAGCCCGACGCAAA 62.539 57.895 0.00 0.00 41.38 3.68
280 281 3.950794 CTAGCCAAGCCCGACGCAA 62.951 63.158 0.00 0.00 41.38 4.85
281 282 4.451150 CTAGCCAAGCCCGACGCA 62.451 66.667 0.00 0.00 41.38 5.24
322 323 0.836400 ATACCTGGCCATACCTCGGG 60.836 60.000 5.51 4.26 40.22 5.14
323 324 1.825474 CTATACCTGGCCATACCTCGG 59.175 57.143 5.51 5.16 40.22 4.63
324 325 2.231478 CACTATACCTGGCCATACCTCG 59.769 54.545 5.51 0.00 40.22 4.63
325 326 2.028020 GCACTATACCTGGCCATACCTC 60.028 54.545 5.51 0.00 40.22 3.85
326 327 1.978580 GCACTATACCTGGCCATACCT 59.021 52.381 5.51 0.00 40.22 3.08
327 328 1.697432 TGCACTATACCTGGCCATACC 59.303 52.381 5.51 0.00 39.84 2.73
328 329 3.703001 ATGCACTATACCTGGCCATAC 57.297 47.619 5.51 0.00 0.00 2.39
329 330 4.819105 GTATGCACTATACCTGGCCATA 57.181 45.455 5.51 0.00 36.45 2.74
330 331 3.703001 GTATGCACTATACCTGGCCAT 57.297 47.619 5.51 0.00 36.45 4.40
338 339 7.607991 AGGCTAATTCAATGGTATGCACTATAC 59.392 37.037 0.00 0.00 40.79 1.47
339 340 7.689299 AGGCTAATTCAATGGTATGCACTATA 58.311 34.615 0.00 0.00 0.00 1.31
340 341 6.546484 AGGCTAATTCAATGGTATGCACTAT 58.454 36.000 0.00 0.00 0.00 2.12
341 342 5.940617 AGGCTAATTCAATGGTATGCACTA 58.059 37.500 0.00 0.00 0.00 2.74
342 343 4.796606 AGGCTAATTCAATGGTATGCACT 58.203 39.130 0.00 0.00 0.00 4.40
343 344 5.335191 GCTAGGCTAATTCAATGGTATGCAC 60.335 44.000 0.00 0.00 0.00 4.57
344 345 4.761739 GCTAGGCTAATTCAATGGTATGCA 59.238 41.667 0.00 0.00 0.00 3.96
345 346 5.006386 AGCTAGGCTAATTCAATGGTATGC 58.994 41.667 0.00 0.00 36.99 3.14
346 347 5.645497 GGAGCTAGGCTAATTCAATGGTATG 59.355 44.000 0.00 0.00 39.88 2.39
347 348 5.569630 CGGAGCTAGGCTAATTCAATGGTAT 60.570 44.000 0.00 0.00 39.88 2.73
348 349 4.262463 CGGAGCTAGGCTAATTCAATGGTA 60.262 45.833 0.00 0.00 39.88 3.25
349 350 3.495100 CGGAGCTAGGCTAATTCAATGGT 60.495 47.826 0.00 0.00 39.88 3.55
350 351 3.070018 CGGAGCTAGGCTAATTCAATGG 58.930 50.000 0.00 0.00 39.88 3.16
351 352 3.733337 ACGGAGCTAGGCTAATTCAATG 58.267 45.455 0.00 0.00 39.88 2.82
352 353 3.244249 GGACGGAGCTAGGCTAATTCAAT 60.244 47.826 0.00 0.00 39.88 2.57
353 354 2.102588 GGACGGAGCTAGGCTAATTCAA 59.897 50.000 0.00 0.00 39.88 2.69
354 355 1.687123 GGACGGAGCTAGGCTAATTCA 59.313 52.381 0.00 0.00 39.88 2.57
355 356 1.001068 GGGACGGAGCTAGGCTAATTC 59.999 57.143 0.00 0.00 39.88 2.17
356 357 1.049402 GGGACGGAGCTAGGCTAATT 58.951 55.000 0.00 0.00 39.88 1.40
357 358 0.105658 TGGGACGGAGCTAGGCTAAT 60.106 55.000 0.00 0.00 39.88 1.73
358 359 0.755698 CTGGGACGGAGCTAGGCTAA 60.756 60.000 0.00 0.00 39.88 3.09
359 360 1.152735 CTGGGACGGAGCTAGGCTA 60.153 63.158 0.00 0.00 39.88 3.93
360 361 2.443016 CTGGGACGGAGCTAGGCT 60.443 66.667 0.00 0.00 43.88 4.58
361 362 2.442272 TCTGGGACGGAGCTAGGC 60.442 66.667 0.00 0.00 39.80 3.93
368 369 1.162181 CGCGTATACTCTGGGACGGA 61.162 60.000 0.00 0.00 44.24 4.69
369 370 1.281960 CGCGTATACTCTGGGACGG 59.718 63.158 0.00 0.00 35.87 4.79
370 371 0.316772 CACGCGTATACTCTGGGACG 60.317 60.000 13.44 0.00 38.32 4.79
371 372 0.737219 ACACGCGTATACTCTGGGAC 59.263 55.000 13.44 0.00 0.00 4.46
372 373 2.330440 TACACGCGTATACTCTGGGA 57.670 50.000 13.44 0.00 0.00 4.37
373 374 4.959596 ATATACACGCGTATACTCTGGG 57.040 45.455 13.44 0.00 42.10 4.45
374 375 7.242914 TCATATATACACGCGTATACTCTGG 57.757 40.000 13.44 0.00 42.10 3.86
375 376 6.846786 GCTCATATATACACGCGTATACTCTG 59.153 42.308 13.44 4.92 42.10 3.35
376 377 6.292221 CGCTCATATATACACGCGTATACTCT 60.292 42.308 13.44 0.00 42.10 3.24
377 378 5.839753 CGCTCATATATACACGCGTATACTC 59.160 44.000 13.44 0.00 42.10 2.59
378 379 5.735324 CGCTCATATATACACGCGTATACT 58.265 41.667 13.44 0.00 42.10 2.12
384 385 2.840752 CAGACGCTCATATATACACGCG 59.159 50.000 3.53 3.53 45.32 6.01
385 386 2.594654 GCAGACGCTCATATATACACGC 59.405 50.000 0.00 0.00 34.30 5.34
386 387 2.840752 CGCAGACGCTCATATATACACG 59.159 50.000 0.00 0.00 35.30 4.49
387 388 3.822996 ACGCAGACGCTCATATATACAC 58.177 45.455 0.00 0.00 45.53 2.90
388 389 3.751698 AGACGCAGACGCTCATATATACA 59.248 43.478 0.00 0.00 45.53 2.29
389 390 4.092120 CAGACGCAGACGCTCATATATAC 58.908 47.826 0.00 0.00 45.53 1.47
390 391 3.751698 ACAGACGCAGACGCTCATATATA 59.248 43.478 0.00 0.00 45.53 0.86
391 392 2.554462 ACAGACGCAGACGCTCATATAT 59.446 45.455 0.00 0.00 45.53 0.86
392 393 1.947456 ACAGACGCAGACGCTCATATA 59.053 47.619 0.00 0.00 45.53 0.86
393 394 0.741326 ACAGACGCAGACGCTCATAT 59.259 50.000 0.00 0.00 45.53 1.78
394 395 1.375551 TACAGACGCAGACGCTCATA 58.624 50.000 0.00 0.00 45.53 2.15
395 396 0.741326 ATACAGACGCAGACGCTCAT 59.259 50.000 0.00 0.00 45.53 2.90
396 397 0.526211 AATACAGACGCAGACGCTCA 59.474 50.000 0.00 0.00 45.53 4.26
397 398 0.917259 CAATACAGACGCAGACGCTC 59.083 55.000 0.00 0.00 45.53 5.03
398 399 0.243907 ACAATACAGACGCAGACGCT 59.756 50.000 0.00 0.00 45.53 5.07
399 400 0.366871 CACAATACAGACGCAGACGC 59.633 55.000 0.00 0.00 45.53 5.19
400 401 8.184225 TGTAAAACACAATACAGACGCAGACG 62.184 42.308 0.00 0.00 38.84 4.18
401 402 4.468095 AAAACACAATACAGACGCAGAC 57.532 40.909 0.00 0.00 0.00 3.51
402 403 5.051153 TGTAAAACACAATACAGACGCAGA 58.949 37.500 0.00 0.00 32.95 4.26
403 404 5.337219 TGTAAAACACAATACAGACGCAG 57.663 39.130 0.00 0.00 32.95 5.18
404 405 5.736486 TTGTAAAACACAATACAGACGCA 57.264 34.783 0.00 0.00 42.29 5.24
405 406 7.439204 TTTTTGTAAAACACAATACAGACGC 57.561 32.000 0.00 0.00 46.38 5.19
426 427 3.966665 TCATTTCTCAGGGGCAAGTTTTT 59.033 39.130 0.00 0.00 0.00 1.94
427 428 3.575805 TCATTTCTCAGGGGCAAGTTTT 58.424 40.909 0.00 0.00 0.00 2.43
428 429 3.243359 TCATTTCTCAGGGGCAAGTTT 57.757 42.857 0.00 0.00 0.00 2.66
429 430 2.893489 GTTCATTTCTCAGGGGCAAGTT 59.107 45.455 0.00 0.00 0.00 2.66
430 431 2.158475 TGTTCATTTCTCAGGGGCAAGT 60.158 45.455 0.00 0.00 0.00 3.16
431 432 2.229784 GTGTTCATTTCTCAGGGGCAAG 59.770 50.000 0.00 0.00 0.00 4.01
432 433 2.238521 GTGTTCATTTCTCAGGGGCAA 58.761 47.619 0.00 0.00 0.00 4.52
433 434 1.547675 GGTGTTCATTTCTCAGGGGCA 60.548 52.381 0.00 0.00 0.00 5.36
434 435 1.177401 GGTGTTCATTTCTCAGGGGC 58.823 55.000 0.00 0.00 0.00 5.80
435 436 1.075374 TGGGTGTTCATTTCTCAGGGG 59.925 52.381 0.00 0.00 0.00 4.79
436 437 2.584835 TGGGTGTTCATTTCTCAGGG 57.415 50.000 0.00 0.00 0.00 4.45
437 438 3.636300 TGTTTGGGTGTTCATTTCTCAGG 59.364 43.478 0.00 0.00 0.00 3.86
438 439 4.916983 TGTTTGGGTGTTCATTTCTCAG 57.083 40.909 0.00 0.00 0.00 3.35
439 440 4.648762 ACATGTTTGGGTGTTCATTTCTCA 59.351 37.500 0.00 0.00 0.00 3.27
440 441 5.200368 ACATGTTTGGGTGTTCATTTCTC 57.800 39.130 0.00 0.00 0.00 2.87
441 442 5.612725 AACATGTTTGGGTGTTCATTTCT 57.387 34.783 4.92 0.00 33.53 2.52
442 443 6.201997 GGTAAACATGTTTGGGTGTTCATTTC 59.798 38.462 29.72 0.98 37.56 2.17
443 444 6.052360 GGTAAACATGTTTGGGTGTTCATTT 58.948 36.000 29.72 5.07 37.56 2.32
444 445 5.129485 TGGTAAACATGTTTGGGTGTTCATT 59.871 36.000 29.72 5.27 37.56 2.57
445 446 4.651503 TGGTAAACATGTTTGGGTGTTCAT 59.348 37.500 29.72 5.77 37.56 2.57
446 447 4.023980 TGGTAAACATGTTTGGGTGTTCA 58.976 39.130 29.72 15.17 37.56 3.18
447 448 4.339814 TCTGGTAAACATGTTTGGGTGTTC 59.660 41.667 29.72 13.23 37.56 3.18
448 449 4.282496 TCTGGTAAACATGTTTGGGTGTT 58.718 39.130 29.72 7.91 40.06 3.32
449 450 3.904717 TCTGGTAAACATGTTTGGGTGT 58.095 40.909 29.72 8.62 34.23 4.16
450 451 4.927978 TTCTGGTAAACATGTTTGGGTG 57.072 40.909 29.72 18.00 34.23 4.61
451 452 7.310361 CCATATTTCTGGTAAACATGTTTGGGT 60.310 37.037 29.72 9.71 34.23 4.51
452 453 7.041107 CCATATTTCTGGTAAACATGTTTGGG 58.959 38.462 29.72 17.34 34.23 4.12
453 454 7.835822 TCCATATTTCTGGTAAACATGTTTGG 58.164 34.615 29.72 19.34 37.57 3.28
454 455 9.874205 ATTCCATATTTCTGGTAAACATGTTTG 57.126 29.630 29.72 15.45 37.57 2.93
500 501 7.491682 GTGCACCCTGATGAATAATAACAAAT 58.508 34.615 5.22 0.00 0.00 2.32
502 503 5.065859 CGTGCACCCTGATGAATAATAACAA 59.934 40.000 12.15 0.00 0.00 2.83
503 504 4.574421 CGTGCACCCTGATGAATAATAACA 59.426 41.667 12.15 0.00 0.00 2.41
504 505 4.574828 ACGTGCACCCTGATGAATAATAAC 59.425 41.667 12.15 0.00 0.00 1.89
505 506 4.574421 CACGTGCACCCTGATGAATAATAA 59.426 41.667 12.15 0.00 0.00 1.40
506 507 4.126437 CACGTGCACCCTGATGAATAATA 58.874 43.478 12.15 0.00 0.00 0.98
507 508 2.945008 CACGTGCACCCTGATGAATAAT 59.055 45.455 12.15 0.00 0.00 1.28
515 516 1.591703 GAGATCACGTGCACCCTGA 59.408 57.895 11.67 12.61 0.00 3.86
551 555 6.031471 GTCTCTATCTGACTTCTTTTCGACC 58.969 44.000 0.00 0.00 0.00 4.79
554 558 5.870444 TCGTCTCTATCTGACTTCTTTTCG 58.130 41.667 0.00 0.00 32.70 3.46
652 668 0.942252 GGGTTGAACGTTGACCTGAC 59.058 55.000 22.67 4.89 33.90 3.51
758 774 9.745880 ATGCTAATGCTGATTTTAAATGAGAAG 57.254 29.630 8.27 1.44 40.48 2.85
785 804 1.015607 CAGCCGCAAAATGGAAAGGC 61.016 55.000 0.00 0.00 44.45 4.35
793 812 3.603365 GCTACCCAGCCGCAAAAT 58.397 55.556 0.00 0.00 42.37 1.82
892 913 0.816018 TCGGATGAGACGAGGAGAGC 60.816 60.000 0.00 0.00 35.12 4.09
928 950 1.575803 GTCGTTGTTGTTGTCGTTTGC 59.424 47.619 0.00 0.00 0.00 3.68
946 968 6.633500 AGTGATCTAGAGCTTGAGTATGTC 57.367 41.667 9.79 0.00 0.00 3.06
995 1017 1.143838 TCGAAGTGATCCATGGCCG 59.856 57.895 6.96 1.92 0.00 6.13
996 1018 0.179000 AGTCGAAGTGATCCATGGCC 59.821 55.000 6.96 0.00 0.00 5.36
997 1019 1.576356 GAGTCGAAGTGATCCATGGC 58.424 55.000 6.96 0.00 0.00 4.40
998 1020 1.759445 AGGAGTCGAAGTGATCCATGG 59.241 52.381 4.97 4.97 34.08 3.66
999 1021 3.452474 GAAGGAGTCGAAGTGATCCATG 58.548 50.000 0.00 0.00 34.08 3.66
1338 1363 4.148825 GCGATCCTGGACCAGCGT 62.149 66.667 16.72 6.26 0.00 5.07
1371 1396 1.872679 GATCTCGTTGTCCGTCCGC 60.873 63.158 0.00 0.00 37.94 5.54
1404 1429 4.641645 TGCTTCTGCACCCGGGTG 62.642 66.667 43.50 43.50 45.31 4.61
1498 1523 2.560119 CGGCCTGGATCCTCTCGAG 61.560 68.421 14.23 5.93 0.00 4.04
1567 1595 0.872021 GGCGCGACACTAAGAGGATG 60.872 60.000 12.10 0.00 0.00 3.51
1569 1597 2.882876 GGCGCGACACTAAGAGGA 59.117 61.111 12.10 0.00 0.00 3.71
1617 1645 2.751913 CGTCGTCGTCTCAGGGGAG 61.752 68.421 0.00 0.00 42.80 4.30
1620 1648 3.054503 ACCGTCGTCGTCTCAGGG 61.055 66.667 0.71 0.00 35.01 4.45
1626 1654 2.428071 GTGGTCACCGTCGTCGTC 60.428 66.667 0.71 0.00 35.01 4.20
1720 1748 2.143594 GAGCCTGACCAGTTCGTCGT 62.144 60.000 0.00 0.00 35.40 4.34
1855 1883 3.214328 CGGATCCCCCTAATTCAAAGTG 58.786 50.000 6.06 0.00 0.00 3.16
1869 1897 4.137872 TTGTCGTCGCCGGATCCC 62.138 66.667 5.05 0.00 33.95 3.85
1871 1899 2.158959 CACTTGTCGTCGCCGGATC 61.159 63.158 5.05 0.00 33.95 3.36
1876 1904 3.112709 GCTCCACTTGTCGTCGCC 61.113 66.667 0.00 0.00 0.00 5.54
1878 1906 4.655527 AAGCTCCACTTGTCGTCG 57.344 55.556 0.00 0.00 37.17 5.12
1910 1938 3.896648 AGTTTCAGTAATGGTGTTGCG 57.103 42.857 0.00 0.00 0.00 4.85
1911 1939 4.976116 GTCAAGTTTCAGTAATGGTGTTGC 59.024 41.667 0.00 0.00 0.00 4.17
1920 1948 9.778741 AATTGATCAGTAGTCAAGTTTCAGTAA 57.221 29.630 0.00 0.00 38.81 2.24
2000 2028 4.201792 GCAATCAAGCAGATCACACTACAG 60.202 45.833 0.00 0.00 35.39 2.74
2007 2041 5.746307 TGATTAGCAATCAAGCAGATCAC 57.254 39.130 8.52 0.00 44.47 3.06
2082 2116 3.378339 GTCCTATGGTAATTCGACCGTG 58.622 50.000 2.81 0.00 42.99 4.94
2124 2172 7.710475 TCAAATTTGAGTGAATTCTCCCAAAAC 59.290 33.333 16.91 2.24 33.93 2.43
2125 2173 7.790027 TCAAATTTGAGTGAATTCTCCCAAAA 58.210 30.769 16.91 10.27 33.93 2.44
2126 2174 7.358770 TCAAATTTGAGTGAATTCTCCCAAA 57.641 32.000 16.91 16.30 33.93 3.28
2135 2183 7.710475 ACCGAAACATTTCAAATTTGAGTGAAT 59.290 29.630 28.11 19.97 38.61 2.57
2142 2190 6.475076 TGACTGACCGAAACATTTCAAATTTG 59.525 34.615 12.15 12.15 37.01 2.32
2238 2286 8.378172 TCCTTCTTCTTTTGTGTACATGTTAG 57.622 34.615 2.30 0.00 0.00 2.34
2242 2290 7.649306 CCTTTTCCTTCTTCTTTTGTGTACATG 59.351 37.037 0.00 0.00 0.00 3.21
2246 2294 7.948034 TTCCTTTTCCTTCTTCTTTTGTGTA 57.052 32.000 0.00 0.00 0.00 2.90
2247 2295 6.850752 TTCCTTTTCCTTCTTCTTTTGTGT 57.149 33.333 0.00 0.00 0.00 3.72
2305 2353 6.114187 ACCATGATAGTCACAAAGAACTGA 57.886 37.500 0.00 0.00 0.00 3.41
2313 2361 5.221823 TGGAGTTTGACCATGATAGTCACAA 60.222 40.000 3.12 0.51 43.70 3.33
2314 2362 4.285775 TGGAGTTTGACCATGATAGTCACA 59.714 41.667 3.12 0.00 43.70 3.58
2315 2363 4.832248 TGGAGTTTGACCATGATAGTCAC 58.168 43.478 3.12 0.00 43.70 3.67
2333 2381 5.039333 GCACTAGCAAAATAGCAATTGGAG 58.961 41.667 7.72 0.00 41.58 3.86
2351 2399 5.111989 GCACATCTAGAATGAACTGCACTA 58.888 41.667 10.74 0.00 0.00 2.74
2365 2413 6.669278 CAAGAATGGATTGATGCACATCTAG 58.331 40.000 11.66 0.00 38.60 2.43
2376 2424 6.906157 AAAAGAAGAGCAAGAATGGATTGA 57.094 33.333 0.00 0.00 0.00 2.57
2420 2468 3.473647 CAGATGCAGAGGCCGGGA 61.474 66.667 2.18 0.00 40.13 5.14
2506 2554 2.698855 GCCTAGATGTTGGCTTCAGA 57.301 50.000 8.09 0.00 45.26 3.27
2534 2582 0.396695 TCAAGGGGTAGGAGTAGCGG 60.397 60.000 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.