Multiple sequence alignment - TraesCS4A01G492700

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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 TraesCS4A01G492700 chr4A 100.000 2675 0 0 1 2675 741587190 741589864 0.000000e+00 4940.0
1 TraesCS4A01G492700 chr4A 97.310 1041 22 3 506 1540 741491745 741490705 0.000000e+00 1762.0
2 TraesCS4A01G492700 chr4A 96.860 860 27 0 1816 2675 741795950 741795091 0.000000e+00 1439.0
3 TraesCS4A01G492700 chr4A 96.512 860 30 0 1816 2675 740022150 740021291 0.000000e+00 1423.0
4 TraesCS4A01G492700 chr4A 95.524 849 35 3 1829 2675 741485613 741484766 0.000000e+00 1354.0
5 TraesCS4A01G492700 chr4A 96.437 814 26 1 1861 2674 740456805 740455995 0.000000e+00 1339.0
6 TraesCS4A01G492700 chr4A 94.700 849 42 3 1829 2675 739650643 739651490 0.000000e+00 1315.0
7 TraesCS4A01G492700 chr4A 94.229 849 46 3 1829 2675 742055922 742056769 0.000000e+00 1293.0
8 TraesCS4A01G492700 chr4A 92.632 855 60 2 1820 2674 740303692 740304543 0.000000e+00 1227.0
9 TraesCS4A01G492700 chr4A 92.632 855 60 2 1820 2674 740346946 740347797 0.000000e+00 1227.0
10 TraesCS4A01G492700 chr4A 89.111 799 58 15 759 1539 739860482 739861269 0.000000e+00 966.0
11 TraesCS4A01G492700 chr4A 90.069 725 58 8 824 1539 740022946 740022227 0.000000e+00 928.0
12 TraesCS4A01G492700 chr4A 87.735 799 59 16 759 1539 740566277 740567054 0.000000e+00 896.0
13 TraesCS4A01G492700 chr4A 92.446 556 35 4 998 1550 740926794 740927345 0.000000e+00 787.0
14 TraesCS4A01G492700 chr4A 85.443 790 64 21 759 1540 739642631 739643377 0.000000e+00 774.0
15 TraesCS4A01G492700 chr4A 85.050 796 70 21 759 1540 742047755 742048515 0.000000e+00 765.0
16 TraesCS4A01G492700 chr4A 91.320 553 44 2 998 1550 740268862 740269410 0.000000e+00 752.0
17 TraesCS4A01G492700 chr4A 91.320 553 41 5 998 1550 740303015 740303560 0.000000e+00 749.0
18 TraesCS4A01G492700 chr4A 90.958 553 46 2 998 1550 740346267 740346815 0.000000e+00 741.0
19 TraesCS4A01G492700 chr4A 89.636 357 18 4 414 763 742047460 742047804 1.140000e-118 436.0
20 TraesCS4A01G492700 chr4A 89.045 356 21 4 414 763 739642337 739642680 2.460000e-115 425.0
21 TraesCS4A01G492700 chr4A 91.469 211 9 5 1 202 741494470 741494260 5.640000e-72 281.0
22 TraesCS4A01G492700 chr4A 89.655 203 19 2 2 202 739642045 739642247 9.500000e-65 257.0
23 TraesCS4A01G492700 chr4A 89.163 203 21 1 1 202 740024494 740024292 4.420000e-63 252.0
24 TraesCS4A01G492700 chr4A 88.670 203 21 2 2 202 742047168 742047370 2.060000e-61 246.0
25 TraesCS4A01G492700 chr4A 93.827 162 9 1 603 763 740566165 740566326 2.660000e-60 243.0
26 TraesCS4A01G492700 chr4A 93.210 162 10 1 603 763 739860370 739860531 1.240000e-58 237.0
27 TraesCS4A01G492700 chr4A 94.444 126 5 2 585 708 740023753 740023628 2.720000e-45 193.0
28 TraesCS4A01G492700 chr4A 83.425 181 20 10 1541 1720 661959761 661959590 2.760000e-35 159.0
29 TraesCS4A01G492700 chr4A 95.833 96 4 0 414 509 741494172 741494077 3.570000e-34 156.0
30 TraesCS4A01G492700 chr4A 96.970 66 2 0 517 582 740024141 740024076 7.830000e-21 111.0
31 TraesCS4A01G492700 chr4A 100.000 48 0 0 1717 1764 740269400 740269447 3.670000e-14 89.8
32 TraesCS4A01G492700 chr4A 100.000 48 0 0 1717 1764 740346805 740346852 3.670000e-14 89.8
33 TraesCS4A01G492700 chr4A 97.959 49 0 1 1717 1764 740303550 740303598 1.710000e-12 84.2
34 TraesCS4A01G492700 chr4A 85.897 78 8 2 1745 1819 739920261 739920184 2.210000e-11 80.5
35 TraesCS4A01G492700 chr4A 93.333 45 1 1 1765 1809 739861503 739861545 6.180000e-07 65.8
36 TraesCS4A01G492700 chr4A 93.333 45 1 1 1765 1809 740567493 740567535 6.180000e-07 65.8
37 TraesCS4A01G492700 chr7D 96.984 862 24 1 1816 2675 2611298 2610437 0.000000e+00 1447.0
38 TraesCS4A01G492700 chr7D 89.962 528 47 2 1003 1527 2359819 2359295 0.000000e+00 676.0
39 TraesCS4A01G492700 chr7D 88.785 107 6 2 1713 1819 2611434 2611334 2.800000e-25 126.0
40 TraesCS4A01G492700 chr7A 87.702 805 67 14 759 1549 3285039 3285825 0.000000e+00 909.0
41 TraesCS4A01G492700 chr7A 90.676 547 45 4 987 1531 2002643 2002101 0.000000e+00 723.0
42 TraesCS4A01G492700 chr7A 92.857 350 21 3 414 763 3284743 3285088 3.070000e-139 505.0
43 TraesCS4A01G492700 chr7A 85.057 174 16 8 1542 1714 32283710 32283874 4.580000e-38 169.0
44 TraesCS4A01G492700 chr7A 85.143 175 15 10 1541 1714 113023302 113023466 4.580000e-38 169.0
45 TraesCS4A01G492700 chr2D 86.207 174 15 8 1541 1714 634497690 634497854 2.120000e-41 180.0
46 TraesCS4A01G492700 chr2D 84.393 173 18 9 1542 1714 286464876 286465039 7.660000e-36 161.0
47 TraesCS4A01G492700 chr2B 96.190 105 4 0 195 299 584129502 584129398 3.540000e-39 172.0
48 TraesCS4A01G492700 chr2B 93.043 115 6 2 190 303 418953673 418953560 1.650000e-37 167.0
49 TraesCS4A01G492700 chr7B 95.370 108 4 1 192 299 188953746 188953640 1.270000e-38 171.0
50 TraesCS4A01G492700 chr7B 84.971 173 17 9 1542 1714 562382321 562382158 1.650000e-37 167.0
51 TraesCS4A01G492700 chr7B 90.400 125 11 1 175 298 40404438 40404562 2.130000e-36 163.0
52 TraesCS4A01G492700 chr6B 95.327 107 4 1 190 295 654640755 654640649 4.580000e-38 169.0
53 TraesCS4A01G492700 chr6B 94.444 108 6 0 191 298 534500612 534500505 1.650000e-37 167.0
54 TraesCS4A01G492700 chr5B 94.495 109 6 0 190 298 502504014 502503906 4.580000e-38 169.0
55 TraesCS4A01G492700 chr3B 93.860 114 4 3 198 311 5705927 5706037 4.580000e-38 169.0
56 TraesCS4A01G492700 chr6A 96.970 99 3 0 197 295 315625264 315625362 1.650000e-37 167.0
57 TraesCS4A01G492700 chr3A 83.708 178 24 5 1540 1714 644664104 644663929 2.130000e-36 163.0
58 TraesCS4A01G492700 chr3D 84.615 169 16 9 1538 1705 130950046 130950205 2.760000e-35 159.0
59 TraesCS4A01G492700 chr4D 82.967 182 21 8 1533 1714 122699498 122699669 3.570000e-34 156.0


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 TraesCS4A01G492700 chr4A 741587190 741589864 2674 False 4940.000000 4940 100.000000 1 2675 1 chr4A.!!$F3 2674
1 TraesCS4A01G492700 chr4A 741795091 741795950 859 True 1439.000000 1439 96.860000 1816 2675 1 chr4A.!!$R5 859
2 TraesCS4A01G492700 chr4A 741484766 741485613 847 True 1354.000000 1354 95.524000 1829 2675 1 chr4A.!!$R4 846
3 TraesCS4A01G492700 chr4A 740455995 740456805 810 True 1339.000000 1339 96.437000 1861 2674 1 chr4A.!!$R3 813
4 TraesCS4A01G492700 chr4A 739650643 739651490 847 False 1315.000000 1315 94.700000 1829 2675 1 chr4A.!!$F1 846
5 TraesCS4A01G492700 chr4A 742055922 742056769 847 False 1293.000000 1293 94.229000 1829 2675 1 chr4A.!!$F4 846
6 TraesCS4A01G492700 chr4A 740926794 740927345 551 False 787.000000 787 92.446000 998 1550 1 chr4A.!!$F2 552
7 TraesCS4A01G492700 chr4A 741490705 741494470 3765 True 733.000000 1762 94.870667 1 1540 3 chr4A.!!$R7 1539
8 TraesCS4A01G492700 chr4A 740303015 740304543 1528 False 686.733333 1227 93.970333 998 2674 3 chr4A.!!$F8 1676
9 TraesCS4A01G492700 chr4A 740346267 740347797 1530 False 685.933333 1227 94.530000 998 2674 3 chr4A.!!$F9 1676
10 TraesCS4A01G492700 chr4A 740021291 740024494 3203 True 581.400000 1423 93.431600 1 2675 5 chr4A.!!$R6 2674
11 TraesCS4A01G492700 chr4A 739642045 739643377 1332 False 485.333333 774 88.047667 2 1540 3 chr4A.!!$F5 1538
12 TraesCS4A01G492700 chr4A 742047168 742048515 1347 False 482.333333 765 87.785333 2 1540 3 chr4A.!!$F11 1538
13 TraesCS4A01G492700 chr4A 739860370 739861545 1175 False 422.933333 966 91.884667 603 1809 3 chr4A.!!$F6 1206
14 TraesCS4A01G492700 chr4A 740268862 740269447 585 False 420.900000 752 95.660000 998 1764 2 chr4A.!!$F7 766
15 TraesCS4A01G492700 chr4A 740566165 740567535 1370 False 401.600000 896 91.631667 603 1809 3 chr4A.!!$F10 1206
16 TraesCS4A01G492700 chr7D 2610437 2611434 997 True 786.500000 1447 92.884500 1713 2675 2 chr7D.!!$R2 962
17 TraesCS4A01G492700 chr7D 2359295 2359819 524 True 676.000000 676 89.962000 1003 1527 1 chr7D.!!$R1 524
18 TraesCS4A01G492700 chr7A 2002101 2002643 542 True 723.000000 723 90.676000 987 1531 1 chr7A.!!$R1 544
19 TraesCS4A01G492700 chr7A 3284743 3285825 1082 False 707.000000 909 90.279500 414 1549 2 chr7A.!!$F3 1135

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
296 307 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 5482 0.108281 GGAGTTACTCCCTGCGTTCC 60.108 60.0 20.11 0.0 44.36 3.62 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
27 29 9.650371 TCTTCGCATTCGATAAAATAAAATCAG 57.350 29.630 0.00 0.00 45.04 2.90
30 32 6.857964 CGCATTCGATAAAATAAAATCAGGCT 59.142 34.615 0.00 0.00 38.10 4.58
36 38 9.567776 TCGATAAAATAAAATCAGGCTCCAATA 57.432 29.630 0.00 0.00 0.00 1.90
61 63 5.908562 ATGAATGATGGAGGATGAGAACT 57.091 39.130 0.00 0.00 0.00 3.01
120 123 1.482593 CAGACACTTCCGAGGGCTTAT 59.517 52.381 0.00 0.00 0.00 1.73
131 134 0.183731 AGGGCTTATAGGTGCTTGCC 59.816 55.000 0.00 0.00 39.61 4.52
202 213 8.080417 TGAGGTGTGAACGCTTATATTATACTC 58.920 37.037 0.00 0.00 0.00 2.59
203 214 7.376615 AGGTGTGAACGCTTATATTATACTCC 58.623 38.462 0.00 0.00 0.00 3.85
204 215 6.589139 GGTGTGAACGCTTATATTATACTCCC 59.411 42.308 0.00 0.00 0.00 4.30
205 216 7.376615 GTGTGAACGCTTATATTATACTCCCT 58.623 38.462 0.00 0.00 0.00 4.20
206 217 7.541437 GTGTGAACGCTTATATTATACTCCCTC 59.459 40.741 0.00 0.00 0.00 4.30
207 218 7.034397 GTGAACGCTTATATTATACTCCCTCC 58.966 42.308 0.00 0.00 0.00 4.30
208 219 6.722590 TGAACGCTTATATTATACTCCCTCCA 59.277 38.462 0.00 0.00 0.00 3.86
209 220 7.399191 TGAACGCTTATATTATACTCCCTCCAT 59.601 37.037 0.00 0.00 0.00 3.41
210 221 7.349412 ACGCTTATATTATACTCCCTCCATC 57.651 40.000 0.00 0.00 0.00 3.51
211 222 7.126733 ACGCTTATATTATACTCCCTCCATCT 58.873 38.462 0.00 0.00 0.00 2.90
212 223 7.620094 ACGCTTATATTATACTCCCTCCATCTT 59.380 37.037 0.00 0.00 0.00 2.40
213 224 9.132923 CGCTTATATTATACTCCCTCCATCTTA 57.867 37.037 0.00 0.00 0.00 2.10
223 234 7.272144 ACTCCCTCCATCTTAAAATAAGTGT 57.728 36.000 0.00 0.00 0.00 3.55
224 235 7.339482 ACTCCCTCCATCTTAAAATAAGTGTC 58.661 38.462 0.00 0.00 0.00 3.67
225 236 7.182930 ACTCCCTCCATCTTAAAATAAGTGTCT 59.817 37.037 0.00 0.00 0.00 3.41
226 237 7.565680 TCCCTCCATCTTAAAATAAGTGTCTC 58.434 38.462 0.00 0.00 0.00 3.36
227 238 7.182026 TCCCTCCATCTTAAAATAAGTGTCTCA 59.818 37.037 0.00 0.00 0.00 3.27
228 239 7.829211 CCCTCCATCTTAAAATAAGTGTCTCAA 59.171 37.037 0.00 0.00 0.00 3.02
229 240 8.669243 CCTCCATCTTAAAATAAGTGTCTCAAC 58.331 37.037 0.00 0.00 0.00 3.18
230 241 9.442047 CTCCATCTTAAAATAAGTGTCTCAACT 57.558 33.333 0.00 0.00 0.00 3.16
231 242 9.793259 TCCATCTTAAAATAAGTGTCTCAACTT 57.207 29.630 0.00 0.00 42.89 2.66
242 253 9.694137 ATAAGTGTCTCAACTTTGTACTAGTTC 57.306 33.333 0.00 0.00 40.77 3.01
243 254 7.349412 AGTGTCTCAACTTTGTACTAGTTCT 57.651 36.000 0.00 3.09 33.73 3.01
244 255 8.461249 AGTGTCTCAACTTTGTACTAGTTCTA 57.539 34.615 0.00 0.00 33.73 2.10
245 256 8.569641 AGTGTCTCAACTTTGTACTAGTTCTAG 58.430 37.037 0.00 5.43 33.73 2.43
246 257 8.351461 GTGTCTCAACTTTGTACTAGTTCTAGT 58.649 37.037 15.38 15.38 33.73 2.57
247 258 9.565090 TGTCTCAACTTTGTACTAGTTCTAGTA 57.435 33.333 13.61 13.61 33.73 1.82
271 282 7.801716 ACAAATTTGTACTAAGCTCAAGACA 57.198 32.000 22.10 0.00 40.16 3.41
272 283 7.639945 ACAAATTTGTACTAAGCTCAAGACAC 58.360 34.615 22.10 2.09 40.16 3.67
273 284 7.499232 ACAAATTTGTACTAAGCTCAAGACACT 59.501 33.333 22.10 0.00 40.16 3.55
274 285 8.345565 CAAATTTGTACTAAGCTCAAGACACTT 58.654 33.333 10.15 0.00 0.00 3.16
275 286 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
276 287 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
277 288 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
278 289 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
279 290 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
280 291 8.988934 TGTACTAAGCTCAAGACACTTATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
281 292 7.440523 ACTAAGCTCAAGACACTTATTTTGG 57.559 36.000 3.19 0.00 0.00 3.28
282 293 5.712152 AAGCTCAAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
283 294 4.985538 AGCTCAAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
284 295 4.762251 AGCTCAAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
285 296 4.378459 GCTCAAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
286 297 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
287 298 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
288 299 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
289 300 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
290 301 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
291 302 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
292 303 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
293 304 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
294 305 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
295 306 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
296 307 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
297 308 0.115745 TTGGGACGGAGGGAGTACTT 59.884 55.000 0.00 0.00 0.00 2.24
298 309 1.002069 TGGGACGGAGGGAGTACTTA 58.998 55.000 0.00 0.00 0.00 2.24
310 321 4.347000 AGGGAGTACTTAGTGTCTTGCAAA 59.653 41.667 0.00 0.00 0.00 3.68
315 330 8.135529 GGAGTACTTAGTGTCTTGCAAAATTTT 58.864 33.333 0.00 0.00 0.00 1.82
364 380 7.249858 ACAATGTAAAAACCTAAAACGAACGT 58.750 30.769 0.00 0.00 0.00 3.99
384 400 7.097329 CGAACGTTTGAAAGTAACAAATGGTAC 60.097 37.037 10.16 0.24 41.98 3.34
392 408 5.733620 AGTAACAAATGGTACTCCTTCGA 57.266 39.130 5.31 0.00 44.72 3.71
393 409 5.476614 AGTAACAAATGGTACTCCTTCGAC 58.523 41.667 5.31 0.00 44.72 4.20
394 410 4.345859 AACAAATGGTACTCCTTCGACA 57.654 40.909 0.00 0.00 34.23 4.35
395 411 4.345859 ACAAATGGTACTCCTTCGACAA 57.654 40.909 0.00 0.00 34.23 3.18
396 412 4.906618 ACAAATGGTACTCCTTCGACAAT 58.093 39.130 0.00 0.00 34.23 2.71
397 413 5.313712 ACAAATGGTACTCCTTCGACAATT 58.686 37.500 0.00 0.00 34.23 2.32
398 414 6.469410 ACAAATGGTACTCCTTCGACAATTA 58.531 36.000 0.00 0.00 34.23 1.40
399 415 6.938030 ACAAATGGTACTCCTTCGACAATTAA 59.062 34.615 0.00 0.00 34.23 1.40
400 416 7.610305 ACAAATGGTACTCCTTCGACAATTAAT 59.390 33.333 0.00 0.00 34.23 1.40
401 417 8.458843 CAAATGGTACTCCTTCGACAATTAATT 58.541 33.333 0.00 0.00 34.23 1.40
402 418 6.978343 TGGTACTCCTTCGACAATTAATTG 57.022 37.500 23.60 23.60 37.93 2.32
403 419 5.878116 TGGTACTCCTTCGACAATTAATTGG 59.122 40.000 27.43 13.86 37.06 3.16
404 420 6.110707 GGTACTCCTTCGACAATTAATTGGA 58.889 40.000 27.43 15.69 41.96 3.53
405 421 6.766467 GGTACTCCTTCGACAATTAATTGGAT 59.234 38.462 27.43 11.38 41.96 3.41
406 422 6.683974 ACTCCTTCGACAATTAATTGGATG 57.316 37.500 27.43 17.79 41.96 3.51
407 423 5.590259 ACTCCTTCGACAATTAATTGGATGG 59.410 40.000 27.43 23.77 41.96 3.51
408 424 5.750524 TCCTTCGACAATTAATTGGATGGA 58.249 37.500 27.43 25.12 41.96 3.41
409 425 5.822519 TCCTTCGACAATTAATTGGATGGAG 59.177 40.000 27.43 19.84 41.96 3.86
410 426 5.009010 CCTTCGACAATTAATTGGATGGAGG 59.991 44.000 27.43 23.51 41.96 4.30
411 427 4.460263 TCGACAATTAATTGGATGGAGGG 58.540 43.478 27.43 10.45 41.96 4.30
412 428 4.165180 TCGACAATTAATTGGATGGAGGGA 59.835 41.667 27.43 12.15 41.96 4.20
502 518 0.955428 TTGCGACTTTAGCAGGCCTG 60.955 55.000 29.34 29.34 46.01 4.85
509 2860 2.846827 ACTTTAGCAGGCCTGGTCTAAT 59.153 45.455 39.28 21.33 41.96 1.73
1532 5315 0.508641 CAAGGTGACACTTCGCTTCG 59.491 55.000 5.39 0.00 32.36 3.79
1540 5323 0.440371 CACTTCGCTTCGCTCCTTTC 59.560 55.000 0.00 0.00 0.00 2.62
1541 5324 0.318762 ACTTCGCTTCGCTCCTTTCT 59.681 50.000 0.00 0.00 0.00 2.52
1542 5325 1.544691 ACTTCGCTTCGCTCCTTTCTA 59.455 47.619 0.00 0.00 0.00 2.10
1543 5326 1.921230 CTTCGCTTCGCTCCTTTCTAC 59.079 52.381 0.00 0.00 0.00 2.59
1544 5327 1.174783 TCGCTTCGCTCCTTTCTACT 58.825 50.000 0.00 0.00 0.00 2.57
1547 5330 1.471851 GCTTCGCTCCTTTCTACTCCC 60.472 57.143 0.00 0.00 0.00 4.30
1549 5332 1.765230 TCGCTCCTTTCTACTCCCTC 58.235 55.000 0.00 0.00 0.00 4.30
1550 5333 0.747852 CGCTCCTTTCTACTCCCTCC 59.252 60.000 0.00 0.00 0.00 4.30
1551 5334 0.747852 GCTCCTTTCTACTCCCTCCG 59.252 60.000 0.00 0.00 0.00 4.63
1552 5335 1.960953 GCTCCTTTCTACTCCCTCCGT 60.961 57.143 0.00 0.00 0.00 4.69
1553 5336 2.458620 CTCCTTTCTACTCCCTCCGTT 58.541 52.381 0.00 0.00 0.00 4.44
1554 5337 2.427812 CTCCTTTCTACTCCCTCCGTTC 59.572 54.545 0.00 0.00 0.00 3.95
1555 5338 1.481363 CCTTTCTACTCCCTCCGTTCC 59.519 57.143 0.00 0.00 0.00 3.62
1556 5339 2.458620 CTTTCTACTCCCTCCGTTCCT 58.541 52.381 0.00 0.00 0.00 3.36
1557 5340 3.626729 CCTTTCTACTCCCTCCGTTCCTA 60.627 52.174 0.00 0.00 0.00 2.94
1558 5341 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
1559 5342 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
1560 5343 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
1561 5344 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
1562 5345 5.136105 TCTACTCCCTCCGTTCCTAAATAC 58.864 45.833 0.00 0.00 0.00 1.89
1563 5346 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
1564 5347 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
1565 5348 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
1566 5349 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
1567 5350 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
1568 5351 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
1569 5352 5.349809 CCTCCGTTCCTAAATACTTGTCTC 58.650 45.833 0.00 0.00 0.00 3.36
1570 5353 5.127356 CCTCCGTTCCTAAATACTTGTCTCT 59.873 44.000 0.00 0.00 0.00 3.10
1571 5354 6.205101 TCCGTTCCTAAATACTTGTCTCTC 57.795 41.667 0.00 0.00 0.00 3.20
1572 5355 5.950549 TCCGTTCCTAAATACTTGTCTCTCT 59.049 40.000 0.00 0.00 0.00 3.10
1573 5356 7.114754 TCCGTTCCTAAATACTTGTCTCTCTA 58.885 38.462 0.00 0.00 0.00 2.43
1574 5357 7.282675 TCCGTTCCTAAATACTTGTCTCTCTAG 59.717 40.741 0.00 0.00 0.00 2.43
1575 5358 7.282675 CCGTTCCTAAATACTTGTCTCTCTAGA 59.717 40.741 0.00 0.00 0.00 2.43
1576 5359 8.339714 CGTTCCTAAATACTTGTCTCTCTAGAG 58.660 40.741 13.98 13.98 43.36 2.43
1590 5373 7.724490 TCTCTCTAGAGATTTCAAATGGTCA 57.276 36.000 22.59 0.00 45.48 4.02
1591 5374 7.551585 TCTCTCTAGAGATTTCAAATGGTCAC 58.448 38.462 22.59 0.00 45.48 3.67
1592 5375 6.644347 TCTCTAGAGATTTCAAATGGTCACC 58.356 40.000 18.76 0.00 31.41 4.02
1593 5376 6.213397 TCTCTAGAGATTTCAAATGGTCACCA 59.787 38.462 18.76 0.00 32.83 4.17
1594 5377 6.173339 TCTAGAGATTTCAAATGGTCACCAC 58.827 40.000 0.00 0.00 35.80 4.16
1595 5378 4.728772 AGAGATTTCAAATGGTCACCACA 58.271 39.130 0.00 0.00 35.80 4.17
1596 5379 5.327732 AGAGATTTCAAATGGTCACCACAT 58.672 37.500 0.00 0.00 35.80 3.21
1597 5380 6.484288 AGAGATTTCAAATGGTCACCACATA 58.516 36.000 0.00 0.00 35.80 2.29
1598 5381 6.375455 AGAGATTTCAAATGGTCACCACATAC 59.625 38.462 0.00 0.00 35.80 2.39
1599 5382 4.757799 TTTCAAATGGTCACCACATACG 57.242 40.909 0.00 0.00 35.80 3.06
1600 5383 2.705730 TCAAATGGTCACCACATACGG 58.294 47.619 0.00 0.00 35.80 4.02
1601 5384 2.303311 TCAAATGGTCACCACATACGGA 59.697 45.455 0.00 0.00 35.80 4.69
1602 5385 3.054728 TCAAATGGTCACCACATACGGAT 60.055 43.478 0.00 0.00 35.80 4.18
1603 5386 2.620251 ATGGTCACCACATACGGATG 57.380 50.000 5.94 5.94 35.80 3.51
1605 5388 2.458620 TGGTCACCACATACGGATGTA 58.541 47.619 14.23 0.00 44.82 2.29
1606 5389 3.035363 TGGTCACCACATACGGATGTAT 58.965 45.455 14.23 1.38 44.82 2.29
1607 5390 4.216708 TGGTCACCACATACGGATGTATA 58.783 43.478 14.23 0.00 44.82 1.47
1608 5391 4.836175 TGGTCACCACATACGGATGTATAT 59.164 41.667 14.23 0.00 44.82 0.86
1609 5392 6.011481 TGGTCACCACATACGGATGTATATA 58.989 40.000 14.23 0.00 44.82 0.86
1610 5393 6.152154 TGGTCACCACATACGGATGTATATAG 59.848 42.308 14.23 0.00 44.82 1.31
1611 5394 6.376299 GGTCACCACATACGGATGTATATAGA 59.624 42.308 14.23 4.80 44.82 1.98
1612 5395 7.249147 GTCACCACATACGGATGTATATAGAC 58.751 42.308 14.23 12.97 44.82 2.59
1613 5396 6.943718 TCACCACATACGGATGTATATAGACA 59.056 38.462 14.23 2.07 44.82 3.41
1614 5397 7.614192 TCACCACATACGGATGTATATAGACAT 59.386 37.037 14.23 12.70 44.82 3.06
1615 5398 8.899771 CACCACATACGGATGTATATAGACATA 58.100 37.037 14.23 0.00 44.82 2.29
1616 5399 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
1664 5447 7.956328 ACATCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
1665 5448 7.772166 ACATCTATATACATCCGTATGTGGTG 58.228 38.462 3.56 0.00 45.99 4.17
1666 5449 7.614192 ACATCTATATACATCCGTATGTGGTGA 59.386 37.037 3.56 0.00 45.99 4.02
1667 5450 7.387119 TCTATATACATCCGTATGTGGTGAC 57.613 40.000 3.56 0.00 45.99 3.67
1668 5451 3.746045 ATACATCCGTATGTGGTGACC 57.254 47.619 3.56 0.00 45.99 4.02
1669 5452 1.271856 ACATCCGTATGTGGTGACCA 58.728 50.000 0.00 0.00 44.79 4.02
1670 5453 1.837439 ACATCCGTATGTGGTGACCAT 59.163 47.619 7.94 0.00 44.79 3.55
1671 5454 2.238646 ACATCCGTATGTGGTGACCATT 59.761 45.455 7.94 0.86 44.79 3.16
1672 5455 3.278574 CATCCGTATGTGGTGACCATTT 58.721 45.455 7.94 0.45 35.28 2.32
1673 5456 2.705730 TCCGTATGTGGTGACCATTTG 58.294 47.619 7.94 0.00 35.28 2.32
1674 5457 2.303311 TCCGTATGTGGTGACCATTTGA 59.697 45.455 7.94 0.00 35.28 2.69
1675 5458 3.078097 CCGTATGTGGTGACCATTTGAA 58.922 45.455 7.94 0.00 35.28 2.69
1676 5459 3.504134 CCGTATGTGGTGACCATTTGAAA 59.496 43.478 7.94 0.00 35.28 2.69
1677 5460 4.157656 CCGTATGTGGTGACCATTTGAAAT 59.842 41.667 7.94 0.00 35.28 2.17
1678 5461 5.331902 CGTATGTGGTGACCATTTGAAATC 58.668 41.667 7.94 0.00 35.28 2.17
1679 5462 5.123820 CGTATGTGGTGACCATTTGAAATCT 59.876 40.000 7.94 0.00 35.28 2.40
1680 5463 5.649782 ATGTGGTGACCATTTGAAATCTC 57.350 39.130 7.94 0.00 35.28 2.75
1681 5464 4.728772 TGTGGTGACCATTTGAAATCTCT 58.271 39.130 7.94 0.00 35.28 3.10
1682 5465 5.875224 TGTGGTGACCATTTGAAATCTCTA 58.125 37.500 7.94 0.00 35.28 2.43
1683 5466 5.939883 TGTGGTGACCATTTGAAATCTCTAG 59.060 40.000 7.94 0.00 35.28 2.43
1684 5467 6.173339 GTGGTGACCATTTGAAATCTCTAGA 58.827 40.000 7.94 0.00 35.28 2.43
1685 5468 6.655003 GTGGTGACCATTTGAAATCTCTAGAA 59.345 38.462 7.94 0.00 35.28 2.10
1686 5469 7.174946 GTGGTGACCATTTGAAATCTCTAGAAA 59.825 37.037 7.94 0.00 35.28 2.52
1687 5470 7.723616 TGGTGACCATTTGAAATCTCTAGAAAA 59.276 33.333 0.00 0.00 0.00 2.29
1688 5471 8.576442 GGTGACCATTTGAAATCTCTAGAAAAA 58.424 33.333 0.00 0.00 0.00 1.94
1689 5472 9.399403 GTGACCATTTGAAATCTCTAGAAAAAC 57.601 33.333 0.00 0.00 0.00 2.43
1690 5473 9.130661 TGACCATTTGAAATCTCTAGAAAAACA 57.869 29.630 0.00 0.00 0.00 2.83
1691 5474 9.965824 GACCATTTGAAATCTCTAGAAAAACAA 57.034 29.630 0.00 0.00 0.00 2.83
1692 5475 9.971922 ACCATTTGAAATCTCTAGAAAAACAAG 57.028 29.630 0.00 0.00 0.00 3.16
1693 5476 9.971922 CCATTTGAAATCTCTAGAAAAACAAGT 57.028 29.630 0.00 0.00 0.00 3.16
1705 5488 8.715088 TCTAGAAAAACAAGTATTTAGGAACGC 58.285 33.333 0.00 0.00 0.00 4.84
1706 5489 7.266922 AGAAAAACAAGTATTTAGGAACGCA 57.733 32.000 0.00 0.00 0.00 5.24
1707 5490 7.360361 AGAAAAACAAGTATTTAGGAACGCAG 58.640 34.615 0.00 0.00 0.00 5.18
1708 5491 5.622770 AAACAAGTATTTAGGAACGCAGG 57.377 39.130 0.00 0.00 0.00 4.85
1709 5492 3.606687 ACAAGTATTTAGGAACGCAGGG 58.393 45.455 0.00 0.00 0.00 4.45
1710 5493 3.262405 ACAAGTATTTAGGAACGCAGGGA 59.738 43.478 0.00 0.00 0.00 4.20
1711 5494 3.821421 AGTATTTAGGAACGCAGGGAG 57.179 47.619 0.00 0.00 0.00 4.30
1715 5498 3.323751 TTTAGGAACGCAGGGAGTAAC 57.676 47.619 0.00 0.00 0.00 2.50
1811 5642 4.614946 TGATGCTGACATAACTCGATCTG 58.385 43.478 0.00 0.00 36.35 2.90
1883 5755 9.334693 CTGCTTGTGTAAACTAAATCATTCTTC 57.665 33.333 0.00 0.00 0.00 2.87
1902 5774 9.971922 CATTCTTCCTTGTCTATGTTTCTTTTT 57.028 29.630 0.00 0.00 0.00 1.94
1943 5815 1.301558 GGCAGAGAGATGGATGCGG 60.302 63.158 0.00 0.00 39.58 5.69
2025 5897 1.134189 TCCTCATGGATGCAAGCTGAG 60.134 52.381 8.83 8.83 37.46 3.35
2325 6197 6.375455 GTGTCAGGACATGTAATCTCCAAAAT 59.625 38.462 5.29 0.00 43.97 1.82
2609 6481 3.397482 GCTAATGATGAGAATCGGCAGT 58.603 45.455 0.00 0.00 38.61 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 29 5.809001 TCCATCATTCATAGTATTGGAGCC 58.191 41.667 0.00 0.00 0.00 4.70
30 32 7.458806 TCATCCTCCATCATTCATAGTATTGGA 59.541 37.037 0.26 0.26 0.00 3.53
36 38 6.558014 AGTTCTCATCCTCCATCATTCATAGT 59.442 38.462 0.00 0.00 0.00 2.12
38 40 8.496534 TTAGTTCTCATCCTCCATCATTCATA 57.503 34.615 0.00 0.00 0.00 2.15
61 63 1.329256 GCCGCTCTCATCTACCCTTA 58.671 55.000 0.00 0.00 0.00 2.69
99 102 0.832135 AAGCCCTCGGAAGTGTCTGA 60.832 55.000 0.00 0.00 36.78 3.27
120 123 2.602676 GGAGTGGGGCAAGCACCTA 61.603 63.158 15.34 0.00 40.96 3.08
202 213 7.338710 TGAGACACTTATTTTAAGATGGAGGG 58.661 38.462 1.47 0.00 0.00 4.30
203 214 8.669243 GTTGAGACACTTATTTTAAGATGGAGG 58.331 37.037 1.47 0.00 0.00 4.30
204 215 9.442047 AGTTGAGACACTTATTTTAAGATGGAG 57.558 33.333 1.47 0.00 0.00 3.86
205 216 9.793259 AAGTTGAGACACTTATTTTAAGATGGA 57.207 29.630 1.47 0.00 35.10 3.41
216 227 9.694137 GAACTAGTACAAAGTTGAGACACTTAT 57.306 33.333 15.86 0.00 37.31 1.73
217 228 8.910944 AGAACTAGTACAAAGTTGAGACACTTA 58.089 33.333 15.86 0.00 37.31 2.24
218 229 7.783042 AGAACTAGTACAAAGTTGAGACACTT 58.217 34.615 15.86 0.00 37.31 3.16
219 230 7.349412 AGAACTAGTACAAAGTTGAGACACT 57.651 36.000 15.86 5.54 37.31 3.55
220 231 8.351461 ACTAGAACTAGTACAAAGTTGAGACAC 58.649 37.037 15.86 3.73 43.98 3.67
221 232 8.461249 ACTAGAACTAGTACAAAGTTGAGACA 57.539 34.615 15.86 0.15 43.98 3.41
246 257 8.770828 GTGTCTTGAGCTTAGTACAAATTTGTA 58.229 33.333 23.91 23.91 42.35 2.41
247 258 7.499232 AGTGTCTTGAGCTTAGTACAAATTTGT 59.501 33.333 25.99 25.99 44.86 2.83
248 259 7.865707 AGTGTCTTGAGCTTAGTACAAATTTG 58.134 34.615 16.67 16.67 0.00 2.32
249 260 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
250 261 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
251 262 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
252 263 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
253 264 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
254 265 8.988934 CAAAATAAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
255 266 8.443937 CCAAAATAAGTGTCTTGAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
256 267 7.606456 CCCAAAATAAGTGTCTTGAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
257 268 6.431234 CCCAAAATAAGTGTCTTGAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
258 269 6.655003 TCCCAAAATAAGTGTCTTGAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
259 270 6.430000 GTCCCAAAATAAGTGTCTTGAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
260 271 5.241728 GTCCCAAAATAAGTGTCTTGAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
261 272 4.762251 GTCCCAAAATAAGTGTCTTGAGCT 59.238 41.667 0.00 0.00 0.00 4.09
262 273 4.378459 CGTCCCAAAATAAGTGTCTTGAGC 60.378 45.833 0.00 0.00 0.00 4.26
263 274 4.154195 CCGTCCCAAAATAAGTGTCTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
264 275 4.069304 CCGTCCCAAAATAAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
265 276 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
266 277 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
267 278 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
268 279 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
269 280 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
270 281 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
271 282 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
272 283 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
273 284 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
274 285 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
275 286 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
276 287 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
277 288 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
278 289 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
279 290 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
280 291 1.064091 ACTAAGTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
281 292 2.022934 CACTAAGTACTCCCTCCGTCC 58.977 57.143 0.00 0.00 0.00 4.79
282 293 2.682352 GACACTAAGTACTCCCTCCGTC 59.318 54.545 0.00 0.00 0.00 4.79
283 294 2.308275 AGACACTAAGTACTCCCTCCGT 59.692 50.000 0.00 0.00 0.00 4.69
284 295 3.002038 AGACACTAAGTACTCCCTCCG 57.998 52.381 0.00 0.00 0.00 4.63
285 296 3.119065 GCAAGACACTAAGTACTCCCTCC 60.119 52.174 0.00 0.00 0.00 4.30
286 297 3.510360 TGCAAGACACTAAGTACTCCCTC 59.490 47.826 0.00 0.00 0.00 4.30
287 298 3.507411 TGCAAGACACTAAGTACTCCCT 58.493 45.455 0.00 0.00 0.00 4.20
288 299 3.955650 TGCAAGACACTAAGTACTCCC 57.044 47.619 0.00 0.00 0.00 4.30
289 300 6.803154 ATTTTGCAAGACACTAAGTACTCC 57.197 37.500 0.00 0.00 0.00 3.85
290 301 9.516314 AAAAATTTTGCAAGACACTAAGTACTC 57.484 29.630 3.73 0.00 0.00 2.59
354 370 7.620397 TTTGTTACTTTCAAACGTTCGTTTT 57.380 28.000 18.46 8.44 36.35 2.43
364 380 8.528044 AAGGAGTACCATTTGTTACTTTCAAA 57.472 30.769 0.00 0.00 38.77 2.69
384 400 5.822519 TCCATCCAATTAATTGTCGAAGGAG 59.177 40.000 23.24 8.49 36.06 3.69
385 401 5.750524 TCCATCCAATTAATTGTCGAAGGA 58.249 37.500 23.24 20.92 36.06 3.36
386 402 5.009010 CCTCCATCCAATTAATTGTCGAAGG 59.991 44.000 23.24 19.41 36.06 3.46
387 403 5.009010 CCCTCCATCCAATTAATTGTCGAAG 59.991 44.000 23.24 12.88 36.06 3.79
388 404 4.887071 CCCTCCATCCAATTAATTGTCGAA 59.113 41.667 23.24 9.15 36.06 3.71
389 405 4.165180 TCCCTCCATCCAATTAATTGTCGA 59.835 41.667 23.24 15.87 36.06 4.20
390 406 4.460263 TCCCTCCATCCAATTAATTGTCG 58.540 43.478 23.24 11.61 36.06 4.35
391 407 5.449553 ACTCCCTCCATCCAATTAATTGTC 58.550 41.667 23.24 0.00 36.06 3.18
392 408 5.472301 ACTCCCTCCATCCAATTAATTGT 57.528 39.130 23.24 6.48 36.06 2.71
393 409 7.062957 ACTTACTCCCTCCATCCAATTAATTG 58.937 38.462 19.40 19.40 37.52 2.32
394 410 7.226059 ACTTACTCCCTCCATCCAATTAATT 57.774 36.000 0.00 0.00 0.00 1.40
395 411 6.848562 ACTTACTCCCTCCATCCAATTAAT 57.151 37.500 0.00 0.00 0.00 1.40
396 412 6.631766 CGAACTTACTCCCTCCATCCAATTAA 60.632 42.308 0.00 0.00 0.00 1.40
397 413 5.163343 CGAACTTACTCCCTCCATCCAATTA 60.163 44.000 0.00 0.00 0.00 1.40
398 414 4.384208 CGAACTTACTCCCTCCATCCAATT 60.384 45.833 0.00 0.00 0.00 2.32
399 415 3.134804 CGAACTTACTCCCTCCATCCAAT 59.865 47.826 0.00 0.00 0.00 3.16
400 416 2.500098 CGAACTTACTCCCTCCATCCAA 59.500 50.000 0.00 0.00 0.00 3.53
401 417 2.108168 CGAACTTACTCCCTCCATCCA 58.892 52.381 0.00 0.00 0.00 3.41
402 418 2.108970 ACGAACTTACTCCCTCCATCC 58.891 52.381 0.00 0.00 0.00 3.51
403 419 4.441217 GGTTACGAACTTACTCCCTCCATC 60.441 50.000 0.00 0.00 0.00 3.51
404 420 3.450096 GGTTACGAACTTACTCCCTCCAT 59.550 47.826 0.00 0.00 0.00 3.41
405 421 2.827921 GGTTACGAACTTACTCCCTCCA 59.172 50.000 0.00 0.00 0.00 3.86
406 422 2.827921 TGGTTACGAACTTACTCCCTCC 59.172 50.000 0.00 0.00 0.00 4.30
407 423 4.441217 GGATGGTTACGAACTTACTCCCTC 60.441 50.000 0.00 0.00 0.00 4.30
408 424 3.450096 GGATGGTTACGAACTTACTCCCT 59.550 47.826 0.00 0.00 0.00 4.20
409 425 3.196254 TGGATGGTTACGAACTTACTCCC 59.804 47.826 0.00 0.00 0.00 4.30
410 426 4.179298 GTGGATGGTTACGAACTTACTCC 58.821 47.826 0.00 0.00 0.00 3.85
411 427 4.624452 GTGTGGATGGTTACGAACTTACTC 59.376 45.833 0.00 0.00 0.00 2.59
412 428 4.039488 TGTGTGGATGGTTACGAACTTACT 59.961 41.667 0.00 0.00 0.00 2.24
502 518 4.040584 CCTCCTAAGGTTGCCTATTAGACC 59.959 50.000 0.00 0.00 37.94 3.85
509 2860 0.420272 ACCCCTCCTAAGGTTGCCTA 59.580 55.000 0.00 0.00 41.59 3.93
1532 5315 0.747852 CGGAGGGAGTAGAAAGGAGC 59.252 60.000 0.00 0.00 0.00 4.70
1540 5323 5.139001 AGTATTTAGGAACGGAGGGAGTAG 58.861 45.833 0.00 0.00 0.00 2.57
1541 5324 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
1542 5325 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
1543 5326 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
1544 5327 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1547 5330 6.095720 AGAGAGACAAGTATTTAGGAACGGAG 59.904 42.308 0.00 0.00 0.00 4.63
1549 5332 6.210287 AGAGAGACAAGTATTTAGGAACGG 57.790 41.667 0.00 0.00 0.00 4.44
1550 5333 8.211116 TCTAGAGAGACAAGTATTTAGGAACG 57.789 38.462 0.00 0.00 0.00 3.95
1551 5334 9.398538 TCTCTAGAGAGACAAGTATTTAGGAAC 57.601 37.037 18.76 0.00 45.48 3.62
1567 5350 6.760770 GGTGACCATTTGAAATCTCTAGAGAG 59.239 42.308 25.86 12.38 41.33 3.20
1568 5351 6.213397 TGGTGACCATTTGAAATCTCTAGAGA 59.787 38.462 24.36 24.36 42.37 3.10
1569 5352 6.314896 GTGGTGACCATTTGAAATCTCTAGAG 59.685 42.308 13.98 13.98 35.28 2.43
1570 5353 6.173339 GTGGTGACCATTTGAAATCTCTAGA 58.827 40.000 7.94 0.00 35.28 2.43
1571 5354 5.939883 TGTGGTGACCATTTGAAATCTCTAG 59.060 40.000 7.94 0.00 35.28 2.43
1572 5355 5.875224 TGTGGTGACCATTTGAAATCTCTA 58.125 37.500 7.94 0.00 35.28 2.43
1573 5356 4.728772 TGTGGTGACCATTTGAAATCTCT 58.271 39.130 7.94 0.00 35.28 3.10
1574 5357 5.649782 ATGTGGTGACCATTTGAAATCTC 57.350 39.130 7.94 0.00 35.28 2.75
1575 5358 5.123820 CGTATGTGGTGACCATTTGAAATCT 59.876 40.000 7.94 0.00 35.28 2.40
1576 5359 5.331902 CGTATGTGGTGACCATTTGAAATC 58.668 41.667 7.94 0.00 35.28 2.17
1577 5360 4.157656 CCGTATGTGGTGACCATTTGAAAT 59.842 41.667 7.94 0.00 35.28 2.17
1578 5361 3.504134 CCGTATGTGGTGACCATTTGAAA 59.496 43.478 7.94 0.00 35.28 2.69
1579 5362 3.078097 CCGTATGTGGTGACCATTTGAA 58.922 45.455 7.94 0.00 35.28 2.69
1580 5363 2.303311 TCCGTATGTGGTGACCATTTGA 59.697 45.455 7.94 0.00 35.28 2.69
1581 5364 2.705730 TCCGTATGTGGTGACCATTTG 58.294 47.619 7.94 0.00 35.28 2.32
1582 5365 3.278574 CATCCGTATGTGGTGACCATTT 58.721 45.455 7.94 0.45 35.28 2.32
1583 5366 2.238646 ACATCCGTATGTGGTGACCATT 59.761 45.455 7.94 0.86 44.79 3.16
1584 5367 1.837439 ACATCCGTATGTGGTGACCAT 59.163 47.619 7.94 0.00 44.79 3.55
1585 5368 1.271856 ACATCCGTATGTGGTGACCA 58.728 50.000 0.00 0.00 44.79 4.02
1586 5369 3.746045 ATACATCCGTATGTGGTGACC 57.254 47.619 3.56 0.00 45.99 4.02
1587 5370 7.094506 TGTCTATATACATCCGTATGTGGTGAC 60.095 40.741 3.56 5.93 45.99 3.67
1588 5371 6.943718 TGTCTATATACATCCGTATGTGGTGA 59.056 38.462 3.56 0.00 45.99 4.02
1589 5372 7.153217 TGTCTATATACATCCGTATGTGGTG 57.847 40.000 3.56 0.00 45.99 4.17
1590 5373 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
1638 5421 9.642343 ACCACATACGGATGTATATAGATGTAT 57.358 33.333 14.23 0.00 44.82 2.29
1639 5422 8.899771 CACCACATACGGATGTATATAGATGTA 58.100 37.037 14.23 0.00 44.82 2.29
1640 5423 7.614192 TCACCACATACGGATGTATATAGATGT 59.386 37.037 14.23 0.00 44.82 3.06
1641 5424 7.915923 GTCACCACATACGGATGTATATAGATG 59.084 40.741 14.23 0.00 44.82 2.90
1642 5425 7.068348 GGTCACCACATACGGATGTATATAGAT 59.932 40.741 14.23 0.00 44.82 1.98
1643 5426 6.376299 GGTCACCACATACGGATGTATATAGA 59.624 42.308 14.23 4.80 44.82 1.98
1644 5427 6.152154 TGGTCACCACATACGGATGTATATAG 59.848 42.308 14.23 0.00 44.82 1.31
1645 5428 6.011481 TGGTCACCACATACGGATGTATATA 58.989 40.000 14.23 0.00 44.82 0.86
1646 5429 4.836175 TGGTCACCACATACGGATGTATAT 59.164 41.667 14.23 0.00 44.82 0.86
1647 5430 4.216708 TGGTCACCACATACGGATGTATA 58.783 43.478 14.23 0.00 44.82 1.47
1648 5431 3.035363 TGGTCACCACATACGGATGTAT 58.965 45.455 14.23 1.38 44.82 2.29
1649 5432 2.458620 TGGTCACCACATACGGATGTA 58.541 47.619 14.23 0.00 44.82 2.29
1651 5434 2.620251 ATGGTCACCACATACGGATG 57.380 50.000 5.94 5.94 35.80 3.51
1652 5435 3.054728 TCAAATGGTCACCACATACGGAT 60.055 43.478 0.00 0.00 35.80 4.18
1653 5436 2.303311 TCAAATGGTCACCACATACGGA 59.697 45.455 0.00 0.00 35.80 4.69
1654 5437 2.705730 TCAAATGGTCACCACATACGG 58.294 47.619 0.00 0.00 35.80 4.02
1655 5438 4.757799 TTTCAAATGGTCACCACATACG 57.242 40.909 0.00 0.00 35.80 3.06
1656 5439 6.375455 AGAGATTTCAAATGGTCACCACATAC 59.625 38.462 0.00 0.00 35.80 2.39
1657 5440 6.484288 AGAGATTTCAAATGGTCACCACATA 58.516 36.000 0.00 0.00 35.80 2.29
1658 5441 5.327732 AGAGATTTCAAATGGTCACCACAT 58.672 37.500 0.00 0.00 35.80 3.21
1659 5442 4.728772 AGAGATTTCAAATGGTCACCACA 58.271 39.130 0.00 0.00 35.80 4.17
1660 5443 6.173339 TCTAGAGATTTCAAATGGTCACCAC 58.827 40.000 0.00 0.00 35.80 4.16
1661 5444 6.373005 TCTAGAGATTTCAAATGGTCACCA 57.627 37.500 0.00 0.00 38.19 4.17
1662 5445 7.687941 TTTCTAGAGATTTCAAATGGTCACC 57.312 36.000 0.00 0.00 0.00 4.02
1663 5446 9.399403 GTTTTTCTAGAGATTTCAAATGGTCAC 57.601 33.333 0.00 0.00 0.00 3.67
1664 5447 9.130661 TGTTTTTCTAGAGATTTCAAATGGTCA 57.869 29.630 0.00 0.00 0.00 4.02
1665 5448 9.965824 TTGTTTTTCTAGAGATTTCAAATGGTC 57.034 29.630 0.00 0.00 0.00 4.02
1666 5449 9.971922 CTTGTTTTTCTAGAGATTTCAAATGGT 57.028 29.630 0.00 0.00 0.00 3.55
1667 5450 9.971922 ACTTGTTTTTCTAGAGATTTCAAATGG 57.028 29.630 0.00 0.00 0.00 3.16
1679 5462 8.715088 GCGTTCCTAAATACTTGTTTTTCTAGA 58.285 33.333 0.00 0.00 0.00 2.43
1680 5463 8.500773 TGCGTTCCTAAATACTTGTTTTTCTAG 58.499 33.333 0.00 0.00 0.00 2.43
1681 5464 8.380743 TGCGTTCCTAAATACTTGTTTTTCTA 57.619 30.769 0.00 0.00 0.00 2.10
1682 5465 7.266922 TGCGTTCCTAAATACTTGTTTTTCT 57.733 32.000 0.00 0.00 0.00 2.52
1683 5466 6.581166 CCTGCGTTCCTAAATACTTGTTTTTC 59.419 38.462 0.00 0.00 0.00 2.29
1684 5467 6.443792 CCTGCGTTCCTAAATACTTGTTTTT 58.556 36.000 0.00 0.00 0.00 1.94
1685 5468 5.048294 CCCTGCGTTCCTAAATACTTGTTTT 60.048 40.000 0.00 0.00 0.00 2.43
1686 5469 4.457949 CCCTGCGTTCCTAAATACTTGTTT 59.542 41.667 0.00 0.00 0.00 2.83
1687 5470 4.007659 CCCTGCGTTCCTAAATACTTGTT 58.992 43.478 0.00 0.00 0.00 2.83
1688 5471 3.262405 TCCCTGCGTTCCTAAATACTTGT 59.738 43.478 0.00 0.00 0.00 3.16
1689 5472 3.869065 TCCCTGCGTTCCTAAATACTTG 58.131 45.455 0.00 0.00 0.00 3.16
1690 5473 3.518303 ACTCCCTGCGTTCCTAAATACTT 59.482 43.478 0.00 0.00 0.00 2.24
1691 5474 3.105283 ACTCCCTGCGTTCCTAAATACT 58.895 45.455 0.00 0.00 0.00 2.12
1692 5475 3.538634 ACTCCCTGCGTTCCTAAATAC 57.461 47.619 0.00 0.00 0.00 1.89
1693 5476 4.713321 AGTTACTCCCTGCGTTCCTAAATA 59.287 41.667 0.00 0.00 0.00 1.40
1694 5477 3.518303 AGTTACTCCCTGCGTTCCTAAAT 59.482 43.478 0.00 0.00 0.00 1.40
1695 5478 2.901839 AGTTACTCCCTGCGTTCCTAAA 59.098 45.455 0.00 0.00 0.00 1.85
1696 5479 2.494870 GAGTTACTCCCTGCGTTCCTAA 59.505 50.000 0.00 0.00 0.00 2.69
1697 5480 2.097825 GAGTTACTCCCTGCGTTCCTA 58.902 52.381 0.00 0.00 0.00 2.94
1698 5481 0.896226 GAGTTACTCCCTGCGTTCCT 59.104 55.000 0.00 0.00 0.00 3.36
1699 5482 0.108281 GGAGTTACTCCCTGCGTTCC 60.108 60.000 20.11 0.00 44.36 3.62
1700 5483 3.437746 GGAGTTACTCCCTGCGTTC 57.562 57.895 20.11 0.00 44.36 3.95
1709 5492 7.077050 TGTAGTAGAGGGATAGGAGTTACTC 57.923 44.000 3.36 3.36 0.00 2.59
1710 5493 7.463054 TTGTAGTAGAGGGATAGGAGTTACT 57.537 40.000 0.00 0.00 0.00 2.24
1711 5494 8.530804 TTTTGTAGTAGAGGGATAGGAGTTAC 57.469 38.462 0.00 0.00 0.00 2.50
1715 5498 7.899648 TCTTTTTGTAGTAGAGGGATAGGAG 57.100 40.000 0.00 0.00 0.00 3.69
1811 5642 0.242017 AAGAAATGAGCTGCGCAACC 59.758 50.000 13.05 5.46 0.00 3.77
1902 5774 1.568504 ACCTCCCGCTGAAACATCTA 58.431 50.000 0.00 0.00 0.00 1.98
1914 5786 0.821711 CTCTCTGCCTCTACCTCCCG 60.822 65.000 0.00 0.00 0.00 5.14
1943 5815 1.609072 GCCCAGAGAAACACTGAAACC 59.391 52.381 0.00 0.00 37.54 3.27
2025 5897 1.215423 ACCTATCATTGACCCCCTTGC 59.785 52.381 0.00 0.00 0.00 4.01
2144 6016 6.051074 TGTCATAAGATAACTCATGTGCCTG 58.949 40.000 0.00 0.00 0.00 4.85
2325 6197 5.618863 GCACAAATTACATCAACACGGATGA 60.619 40.000 9.90 0.00 46.00 2.92
2609 6481 2.028476 CGTGAATAGACACCACCCTGAA 60.028 50.000 0.00 0.00 37.48 3.02


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

AutoCloner maintained by Alex Coulton.