Multiple sequence alignment - TraesCS5A01G042900

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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 TraesCS5A01G042900 chr5A 100.000 3922 0 0 1 3922 38789138 38793059 0.000000e+00 7243.0
1 TraesCS5A01G042900 chr5A 84.183 1353 193 18 1532 2876 573601879 573603218 0.000000e+00 1293.0
2 TraesCS5A01G042900 chr5A 95.455 242 11 0 356 597 542313005 542313246 1.710000e-103 387.0
3 TraesCS5A01G042900 chr5A 79.429 350 61 11 1065 1407 472110734 472111079 1.820000e-58 237.0
4 TraesCS5A01G042900 chr5A 98.551 69 0 1 646 714 38789432 38789499 1.910000e-23 121.0
5 TraesCS5A01G042900 chr5A 98.551 69 0 1 295 362 38789783 38789851 1.910000e-23 121.0
6 TraesCS5A01G042900 chr5A 71.543 499 106 23 3426 3898 604946545 604947033 6.930000e-18 102.0
7 TraesCS5A01G042900 chr5D 95.917 2400 82 8 1530 3922 49294861 49297251 0.000000e+00 3875.0
8 TraesCS5A01G042900 chr5D 84.804 1349 183 19 1536 2876 454204056 454205390 0.000000e+00 1336.0
9 TraesCS5A01G042900 chr5D 92.127 851 27 14 650 1500 49293732 49294542 0.000000e+00 1164.0
10 TraesCS5A01G042900 chr5D 78.779 344 62 9 1065 1401 369578104 369578443 1.830000e-53 220.0
11 TraesCS5A01G042900 chr5D 96.774 62 2 0 298 359 49293732 49293793 1.930000e-18 104.0
12 TraesCS5A01G042900 chr5B 94.562 1839 64 18 1530 3362 51969253 51971061 0.000000e+00 2809.0
13 TraesCS5A01G042900 chr5B 87.484 799 30 20 712 1510 51968293 51969021 0.000000e+00 857.0
14 TraesCS5A01G042900 chr5B 85.941 505 60 9 3374 3872 51971492 51971991 2.680000e-146 529.0
15 TraesCS5A01G042900 chr5B 78.613 346 59 12 1065 1401 438795397 438795736 8.540000e-52 215.0
16 TraesCS5A01G042900 chr5B 86.705 173 21 2 1 173 51968031 51968201 1.440000e-44 191.0
17 TraesCS5A01G042900 chr5B 77.451 204 37 9 3412 3611 572457720 572457522 3.200000e-21 113.0
18 TraesCS5A01G042900 chr5B 86.420 81 9 2 602 680 51968210 51968290 1.940000e-13 87.9
19 TraesCS5A01G042900 chr1A 95.455 242 11 0 356 597 185148324 185148083 1.710000e-103 387.0
20 TraesCS5A01G042900 chr1A 93.902 246 15 0 356 601 586266851 586267096 4.790000e-99 372.0
21 TraesCS5A01G042900 chr6A 94.715 246 12 1 356 601 571138564 571138808 7.950000e-102 381.0
22 TraesCS5A01G042900 chr6A 94.628 242 13 0 356 597 591389664 591389423 3.700000e-100 375.0
23 TraesCS5A01G042900 chr2A 94.355 248 14 0 358 605 623151340 623151093 7.950000e-102 381.0
24 TraesCS5A01G042900 chr2A 94.606 241 13 0 356 596 620302186 620301946 1.330000e-99 374.0
25 TraesCS5A01G042900 chr3A 94.650 243 13 0 356 598 698277473 698277715 1.030000e-100 377.0
26 TraesCS5A01G042900 chr3A 92.885 253 16 2 356 606 186706025 186705773 2.230000e-97 366.0
27 TraesCS5A01G042900 chr3A 100.000 28 0 0 3201 3228 371324304 371324331 7.000000e-03 52.8
28 TraesCS5A01G042900 chr3D 80.636 346 61 5 1065 1407 114204853 114205195 3.010000e-66 263.0
29 TraesCS5A01G042900 chr1D 78.607 201 36 5 3657 3853 486191521 486191718 4.110000e-25 126.0
30 TraesCS5A01G042900 chr7B 74.694 245 57 3 3657 3898 79074723 79074965 1.930000e-18 104.0
31 TraesCS5A01G042900 chr7B 96.774 31 1 0 3085 3115 716999168 716999138 7.000000e-03 52.8
32 TraesCS5A01G042900 chr4A 75.610 246 41 14 1065 1299 92299529 92299766 1.930000e-18 104.0
33 TraesCS5A01G042900 chr3B 88.732 71 8 0 3160 3230 446748002 446747932 1.940000e-13 87.9
34 TraesCS5A01G042900 chr7D 78.632 117 22 3 3783 3898 458592164 458592050 1.510000e-09 75.0
35 TraesCS5A01G042900 chr7A 95.122 41 2 0 3190 3230 621504387 621504427 9.100000e-07 65.8


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 TraesCS5A01G042900 chr5A 38789138 38793059 3921 False 2495.000000 7243 99.034000 1 3922 3 chr5A.!!$F5 3921
1 TraesCS5A01G042900 chr5A 573601879 573603218 1339 False 1293.000000 1293 84.183000 1532 2876 1 chr5A.!!$F3 1344
2 TraesCS5A01G042900 chr5D 49293732 49297251 3519 False 1714.333333 3875 94.939333 298 3922 3 chr5D.!!$F3 3624
3 TraesCS5A01G042900 chr5D 454204056 454205390 1334 False 1336.000000 1336 84.804000 1536 2876 1 chr5D.!!$F2 1340
4 TraesCS5A01G042900 chr5B 51968031 51971991 3960 False 894.780000 2809 88.222400 1 3872 5 chr5B.!!$F2 3871

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
702 705 0.036875 CGGCCTTTCAACTCCTTCCT 59.963 55.0 0.00 0.0 0.00 3.36 F
883 889 0.040157 TACATATACGCACGCCCGAC 60.040 55.0 2.15 0.0 0.00 4.79 F
1419 1425 0.529833 CAGTCGCAGGTGACTCTCAT 59.470 55.0 12.27 0.0 45.97 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 1536 1.067060 CCTGCATGCATGGAGTCAATG 59.933 52.381 36.46 22.39 43.71 2.82 R
2076 2380 2.202623 GAGCGTGACGGCGAGAAT 60.203 61.111 16.62 0.00 38.18 2.40 R
3414 4146 4.536765 CCTAAGGCCACAAAATATGAGGT 58.463 43.478 5.01 0.00 41.44 3.85 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
34 35 2.366266 AGCACCATCTTGCACAACAATT 59.634 40.909 0.00 0.00 45.62 2.32
35 36 3.132925 GCACCATCTTGCACAACAATTT 58.867 40.909 0.00 0.00 42.49 1.82
36 37 3.184986 GCACCATCTTGCACAACAATTTC 59.815 43.478 0.00 0.00 42.49 2.17
37 38 3.742369 CACCATCTTGCACAACAATTTCC 59.258 43.478 0.00 0.00 37.72 3.13
42 43 6.423862 CATCTTGCACAACAATTTCCTTTTG 58.576 36.000 0.00 0.00 37.72 2.44
70 71 8.616076 GGATGACCTGTAACTTTATTCAATCTG 58.384 37.037 0.00 0.00 0.00 2.90
73 74 7.606456 TGACCTGTAACTTTATTCAATCTGGAC 59.394 37.037 0.00 0.00 0.00 4.02
74 75 6.884836 ACCTGTAACTTTATTCAATCTGGACC 59.115 38.462 0.00 0.00 0.00 4.46
93 94 5.067153 TGGACCAAATTATAACCATGCTTCG 59.933 40.000 0.00 0.00 0.00 3.79
96 97 6.560711 ACCAAATTATAACCATGCTTCGAAC 58.439 36.000 0.00 0.00 0.00 3.95
109 110 6.455646 CCATGCTTCGAACTGTATTGTAGTTC 60.456 42.308 0.00 7.60 46.57 3.01
119 120 9.612620 GAACTGTATTGTAGTTCCAAGAAATTG 57.387 33.333 6.61 0.00 45.14 2.32
132 133 6.690530 TCCAAGAAATTGCAAAATACTCCAG 58.309 36.000 1.71 0.00 0.00 3.86
137 138 7.597386 AGAAATTGCAAAATACTCCAGAACTC 58.403 34.615 1.71 0.00 0.00 3.01
138 139 5.904362 ATTGCAAAATACTCCAGAACTCC 57.096 39.130 1.71 0.00 0.00 3.85
139 140 4.640771 TGCAAAATACTCCAGAACTCCT 57.359 40.909 0.00 0.00 0.00 3.69
140 141 4.326826 TGCAAAATACTCCAGAACTCCTG 58.673 43.478 0.00 0.00 42.55 3.86
160 161 7.345914 ACTCCTGGAGTAGCTTTTATGACTAAT 59.654 37.037 27.37 0.00 41.51 1.73
192 193 9.766277 CAGTGAATTCTCTATTACTTTTTCTGC 57.234 33.333 9.59 0.00 0.00 4.26
193 194 9.507329 AGTGAATTCTCTATTACTTTTTCTGCA 57.493 29.630 8.25 0.00 0.00 4.41
194 195 9.766277 GTGAATTCTCTATTACTTTTTCTGCAG 57.234 33.333 7.63 7.63 0.00 4.41
195 196 9.507329 TGAATTCTCTATTACTTTTTCTGCAGT 57.493 29.630 14.67 0.00 0.00 4.40
206 207 7.208225 ACTTTTTCTGCAGTTAGATTTCTCC 57.792 36.000 14.67 0.00 0.00 3.71
207 208 6.207614 ACTTTTTCTGCAGTTAGATTTCTCCC 59.792 38.462 14.67 0.00 0.00 4.30
208 209 3.914426 TCTGCAGTTAGATTTCTCCCC 57.086 47.619 14.67 0.00 0.00 4.81
209 210 2.505819 TCTGCAGTTAGATTTCTCCCCC 59.494 50.000 14.67 0.00 0.00 5.40
210 211 2.507471 CTGCAGTTAGATTTCTCCCCCT 59.493 50.000 5.25 0.00 0.00 4.79
211 212 2.919602 TGCAGTTAGATTTCTCCCCCTT 59.080 45.455 0.00 0.00 0.00 3.95
212 213 3.333680 TGCAGTTAGATTTCTCCCCCTTT 59.666 43.478 0.00 0.00 0.00 3.11
213 214 4.202673 TGCAGTTAGATTTCTCCCCCTTTT 60.203 41.667 0.00 0.00 0.00 2.27
214 215 4.772624 GCAGTTAGATTTCTCCCCCTTTTT 59.227 41.667 0.00 0.00 0.00 1.94
257 258 3.945981 TTTTTGCGGGGGAAATTCTAC 57.054 42.857 0.00 0.00 0.00 2.59
258 259 2.588464 TTTGCGGGGGAAATTCTACA 57.412 45.000 0.00 0.00 0.00 2.74
259 260 2.122783 TTGCGGGGGAAATTCTACAG 57.877 50.000 0.00 0.00 0.00 2.74
260 261 0.988832 TGCGGGGGAAATTCTACAGT 59.011 50.000 0.00 0.00 0.00 3.55
261 262 1.353022 TGCGGGGGAAATTCTACAGTT 59.647 47.619 0.00 0.00 0.00 3.16
262 263 2.572556 TGCGGGGGAAATTCTACAGTTA 59.427 45.455 0.00 0.00 0.00 2.24
263 264 3.203716 GCGGGGGAAATTCTACAGTTAG 58.796 50.000 0.00 0.00 0.00 2.34
264 265 3.370209 GCGGGGGAAATTCTACAGTTAGT 60.370 47.826 0.00 0.00 0.00 2.24
265 266 4.840271 CGGGGGAAATTCTACAGTTAGTT 58.160 43.478 0.00 0.00 0.00 2.24
266 267 5.250982 CGGGGGAAATTCTACAGTTAGTTT 58.749 41.667 0.00 0.00 0.00 2.66
267 268 5.353400 CGGGGGAAATTCTACAGTTAGTTTC 59.647 44.000 0.00 0.00 0.00 2.78
268 269 6.482524 GGGGGAAATTCTACAGTTAGTTTCT 58.517 40.000 0.00 0.00 0.00 2.52
269 270 6.598457 GGGGGAAATTCTACAGTTAGTTTCTC 59.402 42.308 0.00 0.00 0.00 2.87
270 271 7.166167 GGGGAAATTCTACAGTTAGTTTCTCA 58.834 38.462 0.00 0.00 28.64 3.27
271 272 7.664318 GGGGAAATTCTACAGTTAGTTTCTCAA 59.336 37.037 0.00 0.00 28.64 3.02
272 273 9.063615 GGGAAATTCTACAGTTAGTTTCTCAAA 57.936 33.333 0.00 0.00 28.06 2.69
276 277 9.931210 AATTCTACAGTTAGTTTCTCAAAAACG 57.069 29.630 0.00 0.00 35.42 3.60
277 278 8.483307 TTCTACAGTTAGTTTCTCAAAAACGT 57.517 30.769 0.00 0.00 35.42 3.99
278 279 8.483307 TCTACAGTTAGTTTCTCAAAAACGTT 57.517 30.769 0.00 0.00 35.42 3.99
279 280 8.938906 TCTACAGTTAGTTTCTCAAAAACGTTT 58.061 29.630 7.96 7.96 35.42 3.60
280 281 7.790861 ACAGTTAGTTTCTCAAAAACGTTTG 57.209 32.000 15.46 3.70 44.71 2.93
281 282 7.364970 ACAGTTAGTTTCTCAAAAACGTTTGT 58.635 30.769 15.46 5.99 43.90 2.83
282 283 7.536281 ACAGTTAGTTTCTCAAAAACGTTTGTC 59.464 33.333 15.46 0.00 43.90 3.18
283 284 7.535940 CAGTTAGTTTCTCAAAAACGTTTGTCA 59.464 33.333 15.46 0.00 43.90 3.58
284 285 8.077386 AGTTAGTTTCTCAAAAACGTTTGTCAA 58.923 29.630 15.46 0.00 43.90 3.18
285 286 6.927933 AGTTTCTCAAAAACGTTTGTCAAG 57.072 33.333 15.46 8.87 43.90 3.02
286 287 5.344933 AGTTTCTCAAAAACGTTTGTCAAGC 59.655 36.000 15.46 3.87 43.90 4.01
287 288 3.421741 TCTCAAAAACGTTTGTCAAGCG 58.578 40.909 15.46 18.74 43.90 4.68
288 289 1.914700 TCAAAAACGTTTGTCAAGCGC 59.085 42.857 20.02 0.00 43.90 5.92
289 290 1.651138 CAAAAACGTTTGTCAAGCGCA 59.349 42.857 20.02 0.00 39.49 6.09
290 291 1.544686 AAAACGTTTGTCAAGCGCAG 58.455 45.000 20.02 0.72 0.00 5.18
291 292 0.248458 AAACGTTTGTCAAGCGCAGG 60.248 50.000 20.02 0.00 0.00 4.85
292 293 2.427410 CGTTTGTCAAGCGCAGGC 60.427 61.111 11.47 3.29 40.37 4.85
352 353 2.290071 CGGCCTTTCAACTCCTTCCTTA 60.290 50.000 0.00 0.00 0.00 2.69
359 360 3.861840 TCAACTCCTTCCTTATCGCAAG 58.138 45.455 0.00 0.00 0.00 4.01
360 361 2.317530 ACTCCTTCCTTATCGCAAGC 57.682 50.000 0.00 0.00 37.18 4.01
361 362 1.555075 ACTCCTTCCTTATCGCAAGCA 59.445 47.619 0.00 0.00 37.18 3.91
362 363 2.171448 ACTCCTTCCTTATCGCAAGCAT 59.829 45.455 0.00 0.00 37.18 3.79
363 364 2.547211 CTCCTTCCTTATCGCAAGCATG 59.453 50.000 0.00 0.00 37.18 4.06
377 378 4.485024 CAAGCATGCTACCTCATCATTC 57.515 45.455 23.00 0.00 0.00 2.67
378 379 3.851458 AGCATGCTACCTCATCATTCA 57.149 42.857 21.21 0.00 0.00 2.57
379 380 4.160642 AGCATGCTACCTCATCATTCAA 57.839 40.909 21.21 0.00 0.00 2.69
380 381 3.881688 AGCATGCTACCTCATCATTCAAC 59.118 43.478 21.21 0.00 0.00 3.18
381 382 3.628942 GCATGCTACCTCATCATTCAACA 59.371 43.478 11.37 0.00 0.00 3.33
382 383 4.277672 GCATGCTACCTCATCATTCAACAT 59.722 41.667 11.37 0.00 0.00 2.71
383 384 5.758924 CATGCTACCTCATCATTCAACATG 58.241 41.667 0.00 0.00 0.00 3.21
384 385 3.628942 TGCTACCTCATCATTCAACATGC 59.371 43.478 0.00 0.00 0.00 4.06
385 386 3.628942 GCTACCTCATCATTCAACATGCA 59.371 43.478 0.00 0.00 0.00 3.96
386 387 4.277672 GCTACCTCATCATTCAACATGCAT 59.722 41.667 0.00 0.00 0.00 3.96
387 388 5.471116 GCTACCTCATCATTCAACATGCATA 59.529 40.000 0.00 0.00 0.00 3.14
388 389 6.016860 GCTACCTCATCATTCAACATGCATAA 60.017 38.462 0.00 0.00 0.00 1.90
389 390 6.387041 ACCTCATCATTCAACATGCATAAG 57.613 37.500 0.00 0.00 0.00 1.73
390 391 5.301045 ACCTCATCATTCAACATGCATAAGG 59.699 40.000 0.00 0.00 0.00 2.69
391 392 5.533528 CCTCATCATTCAACATGCATAAGGA 59.466 40.000 0.00 0.00 0.00 3.36
392 393 6.040054 CCTCATCATTCAACATGCATAAGGAA 59.960 38.462 0.00 3.66 0.00 3.36
393 394 7.407393 TCATCATTCAACATGCATAAGGAAA 57.593 32.000 0.00 0.00 0.00 3.13
394 395 7.485810 TCATCATTCAACATGCATAAGGAAAG 58.514 34.615 0.00 0.80 0.00 2.62
395 396 6.211587 TCATTCAACATGCATAAGGAAAGG 57.788 37.500 0.00 1.28 0.00 3.11
396 397 4.454728 TTCAACATGCATAAGGAAAGGC 57.545 40.909 0.00 0.00 0.00 4.35
397 398 2.760092 TCAACATGCATAAGGAAAGGCC 59.240 45.455 0.00 0.00 0.00 5.19
398 399 1.780503 ACATGCATAAGGAAAGGCCC 58.219 50.000 0.00 0.00 37.37 5.80
399 400 1.006998 ACATGCATAAGGAAAGGCCCA 59.993 47.619 0.00 0.00 37.37 5.36
400 401 1.410153 CATGCATAAGGAAAGGCCCAC 59.590 52.381 0.00 0.00 37.37 4.61
401 402 0.324275 TGCATAAGGAAAGGCCCACC 60.324 55.000 0.00 0.00 37.37 4.61
414 415 2.666317 GGCCCACCTTAATATGCAACT 58.334 47.619 0.00 0.00 0.00 3.16
415 416 3.827722 GGCCCACCTTAATATGCAACTA 58.172 45.455 0.00 0.00 0.00 2.24
416 417 4.407365 GGCCCACCTTAATATGCAACTAT 58.593 43.478 0.00 0.00 0.00 2.12
417 418 4.832823 GGCCCACCTTAATATGCAACTATT 59.167 41.667 0.00 0.00 0.00 1.73
418 419 5.048013 GGCCCACCTTAATATGCAACTATTC 60.048 44.000 0.00 0.00 0.00 1.75
419 420 5.534654 GCCCACCTTAATATGCAACTATTCA 59.465 40.000 0.00 0.00 0.00 2.57
420 421 6.209391 GCCCACCTTAATATGCAACTATTCAT 59.791 38.462 0.00 0.00 0.00 2.57
421 422 7.393234 GCCCACCTTAATATGCAACTATTCATA 59.607 37.037 0.00 0.00 0.00 2.15
422 423 9.466497 CCCACCTTAATATGCAACTATTCATAT 57.534 33.333 0.00 0.00 37.45 1.78
444 445 9.800433 CATATTAAAAATCCACTACAACATGCA 57.200 29.630 0.00 0.00 0.00 3.96
446 447 8.706492 ATTAAAAATCCACTACAACATGCATG 57.294 30.769 25.09 25.09 0.00 4.06
447 448 3.788333 AATCCACTACAACATGCATGC 57.212 42.857 26.53 11.82 0.00 4.06
448 449 2.197283 TCCACTACAACATGCATGCA 57.803 45.000 26.53 25.04 0.00 3.96
449 450 2.725637 TCCACTACAACATGCATGCAT 58.274 42.857 27.46 27.46 37.08 3.96
464 465 8.903570 CATGCATGCATGTAAAATTTCATTTT 57.096 26.923 40.30 12.04 46.20 1.82
465 466 9.989869 CATGCATGCATGTAAAATTTCATTTTA 57.010 25.926 40.30 7.89 46.20 1.52
577 578 9.834628 AATATTATAAATATTCCCGCAACAACG 57.165 29.630 0.00 0.00 0.00 4.10
578 579 6.680874 TTATAAATATTCCCGCAACAACGT 57.319 33.333 0.00 0.00 0.00 3.99
579 580 2.911819 AATATTCCCGCAACAACGTG 57.088 45.000 0.00 0.00 0.00 4.49
580 581 0.450184 ATATTCCCGCAACAACGTGC 59.550 50.000 0.00 0.00 41.32 5.34
587 588 4.681643 CAACAACGTGCGGCGCAT 62.682 61.111 38.43 21.08 46.11 4.73
588 589 4.383602 AACAACGTGCGGCGCATC 62.384 61.111 38.43 27.49 46.11 3.91
590 591 4.164664 CAACGTGCGGCGCATCAT 62.165 61.111 38.43 22.80 46.11 2.45
591 592 3.864686 AACGTGCGGCGCATCATC 61.865 61.111 38.43 23.35 46.11 2.92
592 593 4.819761 ACGTGCGGCGCATCATCT 62.820 61.111 38.43 15.34 46.11 2.90
593 594 2.658268 CGTGCGGCGCATCATCTA 60.658 61.111 38.43 10.27 41.91 1.98
594 595 2.652079 CGTGCGGCGCATCATCTAG 61.652 63.158 38.43 18.09 41.91 2.43
595 596 1.592669 GTGCGGCGCATCATCTAGT 60.593 57.895 38.43 0.00 41.91 2.57
596 597 1.143838 TGCGGCGCATCATCTAGTT 59.856 52.632 33.07 0.00 31.71 2.24
597 598 0.461870 TGCGGCGCATCATCTAGTTT 60.462 50.000 33.07 0.00 31.71 2.66
598 599 0.233332 GCGGCGCATCATCTAGTTTC 59.767 55.000 29.21 0.00 0.00 2.78
599 600 1.570813 CGGCGCATCATCTAGTTTCA 58.429 50.000 10.83 0.00 0.00 2.69
600 601 2.138320 CGGCGCATCATCTAGTTTCAT 58.862 47.619 10.83 0.00 0.00 2.57
640 641 2.581354 CCCAGTTCCCTGCGAGAG 59.419 66.667 0.00 0.00 37.38 3.20
641 642 2.581354 CCAGTTCCCTGCGAGAGG 59.419 66.667 0.00 0.00 42.38 3.69
642 643 2.125350 CAGTTCCCTGCGAGAGGC 60.125 66.667 0.00 0.00 41.19 4.70
655 658 2.896443 GAGGCAGGAACCCTCTCG 59.104 66.667 0.33 0.00 44.40 4.04
667 670 2.575993 CTCTCGACAGGCCCAGTG 59.424 66.667 0.00 0.00 0.00 3.66
695 698 2.282462 CCAGGCGGCCTTTCAACT 60.282 61.111 21.26 0.00 0.00 3.16
696 699 2.335712 CCAGGCGGCCTTTCAACTC 61.336 63.158 21.26 0.00 0.00 3.01
697 700 2.034221 AGGCGGCCTTTCAACTCC 59.966 61.111 17.69 0.00 0.00 3.85
698 701 2.034221 GGCGGCCTTTCAACTCCT 59.966 61.111 12.87 0.00 0.00 3.69
699 702 1.603739 GGCGGCCTTTCAACTCCTT 60.604 57.895 12.87 0.00 0.00 3.36
700 703 1.587043 GGCGGCCTTTCAACTCCTTC 61.587 60.000 12.87 0.00 0.00 3.46
701 704 1.587043 GCGGCCTTTCAACTCCTTCC 61.587 60.000 0.00 0.00 0.00 3.46
702 705 0.036875 CGGCCTTTCAACTCCTTCCT 59.963 55.000 0.00 0.00 0.00 3.36
703 706 1.545651 CGGCCTTTCAACTCCTTCCTT 60.546 52.381 0.00 0.00 0.00 3.36
704 707 2.290071 CGGCCTTTCAACTCCTTCCTTA 60.290 50.000 0.00 0.00 0.00 2.69
705 708 3.622455 CGGCCTTTCAACTCCTTCCTTAT 60.622 47.826 0.00 0.00 0.00 1.73
706 709 3.948473 GGCCTTTCAACTCCTTCCTTATC 59.052 47.826 0.00 0.00 0.00 1.75
707 710 3.623510 GCCTTTCAACTCCTTCCTTATCG 59.376 47.826 0.00 0.00 0.00 2.92
708 711 3.623510 CCTTTCAACTCCTTCCTTATCGC 59.376 47.826 0.00 0.00 0.00 4.58
709 712 3.973206 TTCAACTCCTTCCTTATCGCA 57.027 42.857 0.00 0.00 0.00 5.10
710 713 3.973206 TCAACTCCTTCCTTATCGCAA 57.027 42.857 0.00 0.00 0.00 4.85
711 714 3.861840 TCAACTCCTTCCTTATCGCAAG 58.138 45.455 0.00 0.00 0.00 4.01
712 715 2.317530 ACTCCTTCCTTATCGCAAGC 57.682 50.000 0.00 0.00 37.18 4.01
713 716 1.555075 ACTCCTTCCTTATCGCAAGCA 59.445 47.619 0.00 0.00 37.18 3.91
760 763 2.531927 TTCCACAGCCGCGTACGTAG 62.532 60.000 17.90 11.26 37.70 3.51
762 765 2.150218 CACAGCCGCGTACGTAGTG 61.150 63.158 17.90 13.75 45.73 2.74
763 766 3.245315 CAGCCGCGTACGTAGTGC 61.245 66.667 17.90 13.75 45.73 4.40
764 767 3.740397 AGCCGCGTACGTAGTGCA 61.740 61.111 17.90 0.00 45.55 4.57
787 793 1.079543 CTCCGGTGAGGCTGTTGAG 60.080 63.158 0.00 0.00 40.77 3.02
788 794 1.821061 CTCCGGTGAGGCTGTTGAGT 61.821 60.000 0.00 0.00 40.77 3.41
789 795 1.669115 CCGGTGAGGCTGTTGAGTG 60.669 63.158 0.00 0.00 0.00 3.51
790 796 1.069765 CGGTGAGGCTGTTGAGTGT 59.930 57.895 0.00 0.00 0.00 3.55
791 797 0.532862 CGGTGAGGCTGTTGAGTGTT 60.533 55.000 0.00 0.00 0.00 3.32
792 798 0.947244 GGTGAGGCTGTTGAGTGTTG 59.053 55.000 0.00 0.00 0.00 3.33
793 799 1.475034 GGTGAGGCTGTTGAGTGTTGA 60.475 52.381 0.00 0.00 0.00 3.18
820 826 1.391485 CAACTCGCTTGATTCCACTCG 59.609 52.381 0.00 0.00 30.42 4.18
825 831 1.991430 CTTGATTCCACTCGACGCG 59.009 57.895 3.53 3.53 0.00 6.01
879 885 1.538512 TCTCCTACATATACGCACGCC 59.461 52.381 0.00 0.00 0.00 5.68
883 889 0.040157 TACATATACGCACGCCCGAC 60.040 55.000 2.15 0.00 0.00 4.79
909 915 2.938451 TGCATCGGTCACAGATTCATTC 59.062 45.455 0.00 0.00 0.00 2.67
1290 1296 2.125512 ATCTTCGTGCTCACCGGC 60.126 61.111 0.00 0.00 0.00 6.13
1413 1419 1.153549 GATCCCAGTCGCAGGTGAC 60.154 63.158 4.86 4.86 39.21 3.67
1415 1421 1.608717 ATCCCAGTCGCAGGTGACTC 61.609 60.000 12.27 0.00 45.97 3.36
1416 1422 2.279069 CCCAGTCGCAGGTGACTCT 61.279 63.158 12.27 0.00 45.97 3.24
1417 1423 1.214062 CCAGTCGCAGGTGACTCTC 59.786 63.158 12.27 0.00 45.97 3.20
1418 1424 1.527433 CCAGTCGCAGGTGACTCTCA 61.527 60.000 12.27 0.00 45.97 3.27
1419 1425 0.529833 CAGTCGCAGGTGACTCTCAT 59.470 55.000 12.27 0.00 45.97 2.90
1420 1426 0.814457 AGTCGCAGGTGACTCTCATC 59.186 55.000 9.58 0.00 45.97 2.92
1421 1427 0.814457 GTCGCAGGTGACTCTCATCT 59.186 55.000 5.76 0.00 38.64 2.90
1422 1428 1.098869 TCGCAGGTGACTCTCATCTC 58.901 55.000 0.00 0.00 35.21 2.75
1433 1439 4.583907 TGACTCTCATCTCATCTCATGTCC 59.416 45.833 0.00 0.00 0.00 4.02
1455 1461 4.799419 GATCTACGGCTAGATCGTATCC 57.201 50.000 15.65 7.50 43.52 2.59
1456 1462 3.977134 TCTACGGCTAGATCGTATCCT 57.023 47.619 15.65 0.00 41.39 3.24
1457 1463 5.599732 GATCTACGGCTAGATCGTATCCTA 58.400 45.833 15.65 6.30 43.52 2.94
1514 1530 5.010922 GCATGAGATGGATGAGTAGAACTCT 59.989 44.000 8.42 0.00 45.27 3.24
1515 1531 6.680810 CATGAGATGGATGAGTAGAACTCTC 58.319 44.000 8.42 4.02 45.27 3.20
1516 1532 5.760131 TGAGATGGATGAGTAGAACTCTCA 58.240 41.667 8.42 1.43 45.27 3.27
1525 1541 7.894753 ATGAGTAGAACTCTCATCTCATTGA 57.105 36.000 8.42 0.00 45.78 2.57
1526 1542 7.094508 TGAGTAGAACTCTCATCTCATTGAC 57.905 40.000 8.42 0.00 45.27 3.18
1527 1543 6.889177 TGAGTAGAACTCTCATCTCATTGACT 59.111 38.462 8.42 0.00 45.27 3.41
1528 1544 7.066887 TGAGTAGAACTCTCATCTCATTGACTC 59.933 40.741 8.42 0.00 45.27 3.36
2076 2380 1.900016 ACCACCGTCGTCTACTGCA 60.900 57.895 0.00 0.00 0.00 4.41
2078 2382 0.108804 CCACCGTCGTCTACTGCATT 60.109 55.000 0.00 0.00 0.00 3.56
2477 2781 3.207669 CGCTACTACGCCTCCGGT 61.208 66.667 0.00 0.00 39.22 5.28
2917 3221 0.659957 GAAATTGCCGGAGCTAGCAG 59.340 55.000 18.83 7.69 40.73 4.24
2918 3222 1.379642 AAATTGCCGGAGCTAGCAGC 61.380 55.000 18.83 14.17 40.73 5.25
2977 3281 7.237871 TGTACGTCCATTATTTTTCACAATCG 58.762 34.615 0.00 0.00 0.00 3.34
2982 3286 7.358765 CGTCCATTATTTTTCACAATCGCAAAA 60.359 33.333 0.00 0.00 0.00 2.44
3104 3417 9.521503 TCTCAATTAATTAAGTCTCAGTCGATG 57.478 33.333 0.00 0.00 0.00 3.84
3186 3499 9.577110 TTTTTATTTTCTCTCTTGCATGCTATG 57.423 29.630 20.33 8.92 0.00 2.23
3199 3512 4.764308 TGCATGCTATGTAACTTGACCAAA 59.236 37.500 20.33 0.00 0.00 3.28
3221 3534 7.435192 CCAAAACTTGGTTAAATCTCAGTCAAC 59.565 37.037 0.00 0.00 45.93 3.18
3222 3535 7.881775 AAACTTGGTTAAATCTCAGTCAACT 57.118 32.000 0.00 0.00 0.00 3.16
3235 3548 4.533919 CAGTCAACTGAGATCTCAACCT 57.466 45.455 25.09 13.42 46.59 3.50
3236 3549 4.892433 CAGTCAACTGAGATCTCAACCTT 58.108 43.478 25.09 13.94 46.59 3.50
3237 3550 4.928615 CAGTCAACTGAGATCTCAACCTTC 59.071 45.833 25.09 15.33 46.59 3.46
3238 3551 4.590647 AGTCAACTGAGATCTCAACCTTCA 59.409 41.667 25.09 5.87 39.39 3.02
3239 3552 5.070981 AGTCAACTGAGATCTCAACCTTCAA 59.929 40.000 25.09 5.90 39.39 2.69
3281 3594 8.311836 CAATCTAAATCTTATACCTCGGCCTAA 58.688 37.037 0.00 0.00 0.00 2.69
3414 4146 1.592400 GAGGTGGTGTCGTCGATCCA 61.592 60.000 15.03 15.03 0.00 3.41
3460 4192 2.386100 GGGGGCATGGTGGATCTCA 61.386 63.158 0.00 0.00 0.00 3.27
3468 4201 1.203441 TGGTGGATCTCAGCCTTGCT 61.203 55.000 9.83 0.00 42.81 3.91
3543 4276 4.148825 CCCGGGAAGGCGAGACAG 62.149 72.222 18.48 0.00 39.21 3.51
3549 4282 1.372997 GAAGGCGAGACAGCGACAA 60.373 57.895 0.00 0.00 43.13 3.18
3556 4289 1.423395 GAGACAGCGACAACTTCCTG 58.577 55.000 0.00 0.00 0.00 3.86
3645 4379 4.943705 GTGTGGAGGTATGTCACATGATTT 59.056 41.667 0.00 0.00 42.34 2.17
3699 4433 5.293814 CGGATCTAGTCTTCGTTCTTCTACA 59.706 44.000 0.00 0.00 0.00 2.74
3718 4452 4.536364 ACATTCGTGTGTCTTCAAGTTG 57.464 40.909 0.00 0.00 0.00 3.16
3750 4487 5.886474 TCGACCTATACTCTTCATTGACAGT 59.114 40.000 3.54 3.54 0.00 3.55
3779 4516 5.183140 GCTGTGTTTGGTACATTGTTCCTAT 59.817 40.000 12.92 0.00 39.39 2.57
3894 4631 2.224066 ACTCGCTTCAGTGCTTGTAGTT 60.224 45.455 0.00 0.00 0.00 2.24
3897 4634 2.096713 CGCTTCAGTGCTTGTAGTTGTC 60.097 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.911390 AGTTACAGGTCATCCTCAAAAGG 58.089 43.478 0.00 0.00 43.07 3.11
37 38 6.884280 AAAGTTACAGGTCATCCTCAAAAG 57.116 37.500 0.00 0.00 43.07 2.27
42 43 8.738645 ATTGAATAAAGTTACAGGTCATCCTC 57.261 34.615 0.00 0.00 43.07 3.71
67 68 5.765510 AGCATGGTTATAATTTGGTCCAGA 58.234 37.500 0.00 0.00 0.00 3.86
70 71 5.298276 TCGAAGCATGGTTATAATTTGGTCC 59.702 40.000 10.70 0.00 0.00 4.46
73 74 6.692681 CAGTTCGAAGCATGGTTATAATTTGG 59.307 38.462 10.70 0.00 0.00 3.28
74 75 7.250569 ACAGTTCGAAGCATGGTTATAATTTG 58.749 34.615 10.70 11.84 0.00 2.32
85 86 6.408858 AACTACAATACAGTTCGAAGCATG 57.591 37.500 0.00 0.30 30.36 4.06
96 97 7.592938 TGCAATTTCTTGGAACTACAATACAG 58.407 34.615 0.00 0.00 32.72 2.74
109 110 6.690530 TCTGGAGTATTTTGCAATTTCTTGG 58.309 36.000 0.00 0.00 32.72 3.61
119 120 4.954092 CAGGAGTTCTGGAGTATTTTGC 57.046 45.455 0.00 0.00 39.76 3.68
132 133 5.813157 GTCATAAAAGCTACTCCAGGAGTTC 59.187 44.000 27.73 18.51 40.28 3.01
180 181 8.784043 GGAGAAATCTAACTGCAGAAAAAGTAA 58.216 33.333 23.35 0.00 0.00 2.24
181 182 7.390718 GGGAGAAATCTAACTGCAGAAAAAGTA 59.609 37.037 23.35 0.00 0.00 2.24
182 183 6.207614 GGGAGAAATCTAACTGCAGAAAAAGT 59.792 38.462 23.35 0.00 0.00 2.66
183 184 6.349694 GGGGAGAAATCTAACTGCAGAAAAAG 60.350 42.308 23.35 11.46 0.00 2.27
184 185 5.476945 GGGGAGAAATCTAACTGCAGAAAAA 59.523 40.000 23.35 3.23 0.00 1.94
185 186 5.010282 GGGGAGAAATCTAACTGCAGAAAA 58.990 41.667 23.35 3.88 0.00 2.29
186 187 4.567747 GGGGGAGAAATCTAACTGCAGAAA 60.568 45.833 23.35 6.66 0.00 2.52
187 188 3.054361 GGGGGAGAAATCTAACTGCAGAA 60.054 47.826 23.35 7.06 0.00 3.02
188 189 2.505819 GGGGGAGAAATCTAACTGCAGA 59.494 50.000 23.35 0.00 0.00 4.26
189 190 2.507471 AGGGGGAGAAATCTAACTGCAG 59.493 50.000 13.48 13.48 0.00 4.41
190 191 2.562296 AGGGGGAGAAATCTAACTGCA 58.438 47.619 0.00 0.00 0.00 4.41
191 192 3.653835 AAGGGGGAGAAATCTAACTGC 57.346 47.619 0.00 0.00 0.00 4.40
237 238 3.231818 TGTAGAATTTCCCCCGCAAAAA 58.768 40.909 0.00 0.00 0.00 1.94
238 239 2.823154 CTGTAGAATTTCCCCCGCAAAA 59.177 45.455 0.00 0.00 0.00 2.44
239 240 2.224917 ACTGTAGAATTTCCCCCGCAAA 60.225 45.455 0.00 0.00 0.00 3.68
240 241 1.353022 ACTGTAGAATTTCCCCCGCAA 59.647 47.619 0.00 0.00 0.00 4.85
241 242 0.988832 ACTGTAGAATTTCCCCCGCA 59.011 50.000 0.00 0.00 0.00 5.69
242 243 2.124277 AACTGTAGAATTTCCCCCGC 57.876 50.000 0.00 0.00 0.00 6.13
243 244 4.482952 ACTAACTGTAGAATTTCCCCCG 57.517 45.455 0.00 0.00 0.00 5.73
244 245 6.482524 AGAAACTAACTGTAGAATTTCCCCC 58.517 40.000 0.00 0.00 0.00 5.40
245 246 7.166167 TGAGAAACTAACTGTAGAATTTCCCC 58.834 38.462 0.00 0.00 0.00 4.81
246 247 8.617290 TTGAGAAACTAACTGTAGAATTTCCC 57.383 34.615 0.00 0.00 0.00 3.97
250 251 9.931210 CGTTTTTGAGAAACTAACTGTAGAATT 57.069 29.630 0.00 0.00 0.00 2.17
251 252 9.106070 ACGTTTTTGAGAAACTAACTGTAGAAT 57.894 29.630 0.00 0.00 0.00 2.40
252 253 8.483307 ACGTTTTTGAGAAACTAACTGTAGAA 57.517 30.769 0.00 0.00 0.00 2.10
253 254 8.483307 AACGTTTTTGAGAAACTAACTGTAGA 57.517 30.769 0.00 0.00 0.00 2.59
254 255 8.995906 CAAACGTTTTTGAGAAACTAACTGTAG 58.004 33.333 11.66 0.00 44.38 2.74
255 256 8.505625 ACAAACGTTTTTGAGAAACTAACTGTA 58.494 29.630 11.66 0.00 44.38 2.74
256 257 7.364970 ACAAACGTTTTTGAGAAACTAACTGT 58.635 30.769 11.66 0.00 44.38 3.55
257 258 7.535940 TGACAAACGTTTTTGAGAAACTAACTG 59.464 33.333 11.66 0.00 44.38 3.16
258 259 7.586747 TGACAAACGTTTTTGAGAAACTAACT 58.413 30.769 11.66 0.00 44.38 2.24
259 260 7.784790 TGACAAACGTTTTTGAGAAACTAAC 57.215 32.000 11.66 0.00 44.38 2.34
260 261 7.061326 GCTTGACAAACGTTTTTGAGAAACTAA 59.939 33.333 11.66 0.00 44.38 2.24
261 262 6.525280 GCTTGACAAACGTTTTTGAGAAACTA 59.475 34.615 11.66 0.00 44.38 2.24
262 263 5.344933 GCTTGACAAACGTTTTTGAGAAACT 59.655 36.000 11.66 0.00 44.38 2.66
263 264 5.538308 GCTTGACAAACGTTTTTGAGAAAC 58.462 37.500 11.66 0.00 44.38 2.78
264 265 4.322274 CGCTTGACAAACGTTTTTGAGAAA 59.678 37.500 11.66 0.06 44.38 2.52
265 266 3.849145 CGCTTGACAAACGTTTTTGAGAA 59.151 39.130 11.66 0.00 44.38 2.87
266 267 3.421741 CGCTTGACAAACGTTTTTGAGA 58.578 40.909 11.66 0.00 44.38 3.27
267 268 2.035756 GCGCTTGACAAACGTTTTTGAG 60.036 45.455 11.66 8.25 44.38 3.02
268 269 1.914700 GCGCTTGACAAACGTTTTTGA 59.085 42.857 11.66 0.00 44.38 2.69
269 270 1.651138 TGCGCTTGACAAACGTTTTTG 59.349 42.857 11.66 4.42 46.61 2.44
270 271 1.917303 CTGCGCTTGACAAACGTTTTT 59.083 42.857 11.66 4.79 0.00 1.94
271 272 1.544686 CTGCGCTTGACAAACGTTTT 58.455 45.000 11.66 3.05 0.00 2.43
272 273 0.248458 CCTGCGCTTGACAAACGTTT 60.248 50.000 7.96 7.96 0.00 3.60
273 274 1.355210 CCTGCGCTTGACAAACGTT 59.645 52.632 9.73 0.00 0.00 3.99
274 275 3.022287 CCTGCGCTTGACAAACGT 58.978 55.556 9.73 0.00 0.00 3.99
275 276 2.427410 GCCTGCGCTTGACAAACG 60.427 61.111 9.73 6.62 0.00 3.60
276 277 1.370900 CAGCCTGCGCTTGACAAAC 60.371 57.895 9.73 0.00 45.55 2.93
277 278 1.100463 TTCAGCCTGCGCTTGACAAA 61.100 50.000 9.73 0.00 45.55 2.83
278 279 1.525765 TTCAGCCTGCGCTTGACAA 60.526 52.632 9.73 0.00 45.55 3.18
279 280 2.110835 TTCAGCCTGCGCTTGACA 59.889 55.556 9.73 0.00 45.55 3.58
280 281 2.558313 GTTCAGCCTGCGCTTGAC 59.442 61.111 9.73 0.00 45.55 3.18
281 282 2.669569 GGTTCAGCCTGCGCTTGA 60.670 61.111 9.73 4.62 45.55 3.02
282 283 2.670934 AGGTTCAGCCTGCGCTTG 60.671 61.111 9.73 0.00 45.55 4.01
290 291 1.216710 CCTGTCGAGAGGTTCAGCC 59.783 63.158 20.26 0.00 37.58 4.85
291 292 1.446966 GCCTGTCGAGAGGTTCAGC 60.447 63.158 27.69 10.88 35.29 4.26
292 293 1.216710 GGCCTGTCGAGAGGTTCAG 59.783 63.158 27.69 10.67 35.29 3.02
293 294 2.283529 GGGCCTGTCGAGAGGTTCA 61.284 63.158 27.69 0.46 35.29 3.18
294 295 2.232298 CTGGGCCTGTCGAGAGGTTC 62.232 65.000 27.69 19.92 35.29 3.62
295 296 2.203788 TGGGCCTGTCGAGAGGTT 60.204 61.111 27.69 0.00 35.29 3.50
296 297 2.681778 CTGGGCCTGTCGAGAGGT 60.682 66.667 27.69 0.00 35.29 3.85
329 330 1.587043 GAAGGAGTTGAAAGGCCGCC 61.587 60.000 0.00 0.00 0.00 6.13
359 360 3.628942 TGTTGAATGATGAGGTAGCATGC 59.371 43.478 10.51 10.51 35.16 4.06
360 361 5.758924 CATGTTGAATGATGAGGTAGCATG 58.241 41.667 0.00 0.00 35.16 4.06
361 362 4.277672 GCATGTTGAATGATGAGGTAGCAT 59.722 41.667 0.00 0.00 36.88 3.79
362 363 3.628942 GCATGTTGAATGATGAGGTAGCA 59.371 43.478 0.00 0.00 0.00 3.49
363 364 3.628942 TGCATGTTGAATGATGAGGTAGC 59.371 43.478 0.00 0.00 0.00 3.58
364 365 7.308408 CCTTATGCATGTTGAATGATGAGGTAG 60.308 40.741 10.16 0.00 0.00 3.18
365 366 6.487668 CCTTATGCATGTTGAATGATGAGGTA 59.512 38.462 10.16 0.00 0.00 3.08
366 367 5.301045 CCTTATGCATGTTGAATGATGAGGT 59.699 40.000 10.16 0.00 0.00 3.85
367 368 5.533528 TCCTTATGCATGTTGAATGATGAGG 59.466 40.000 10.16 0.00 0.00 3.86
368 369 6.628919 TCCTTATGCATGTTGAATGATGAG 57.371 37.500 10.16 0.00 0.00 2.90
369 370 7.407393 TTTCCTTATGCATGTTGAATGATGA 57.593 32.000 10.16 0.00 0.00 2.92
370 371 6.700081 CCTTTCCTTATGCATGTTGAATGATG 59.300 38.462 10.16 1.17 0.00 3.07
371 372 6.684613 GCCTTTCCTTATGCATGTTGAATGAT 60.685 38.462 10.16 0.00 0.00 2.45
372 373 5.394443 GCCTTTCCTTATGCATGTTGAATGA 60.394 40.000 10.16 0.00 0.00 2.57
373 374 4.807304 GCCTTTCCTTATGCATGTTGAATG 59.193 41.667 10.16 10.28 0.00 2.67
374 375 4.141869 GGCCTTTCCTTATGCATGTTGAAT 60.142 41.667 10.16 0.00 0.00 2.57
375 376 3.195396 GGCCTTTCCTTATGCATGTTGAA 59.805 43.478 10.16 6.00 0.00 2.69
376 377 2.760092 GGCCTTTCCTTATGCATGTTGA 59.240 45.455 10.16 0.00 0.00 3.18
377 378 2.159057 GGGCCTTTCCTTATGCATGTTG 60.159 50.000 10.16 0.00 34.39 3.33
378 379 2.110578 GGGCCTTTCCTTATGCATGTT 58.889 47.619 10.16 0.00 34.39 2.71
379 380 1.006998 TGGGCCTTTCCTTATGCATGT 59.993 47.619 10.16 0.00 34.39 3.21
380 381 1.410153 GTGGGCCTTTCCTTATGCATG 59.590 52.381 10.16 0.00 34.39 4.06
381 382 1.689258 GGTGGGCCTTTCCTTATGCAT 60.689 52.381 4.53 3.79 34.39 3.96
382 383 0.324275 GGTGGGCCTTTCCTTATGCA 60.324 55.000 4.53 0.00 34.39 3.96
383 384 0.033109 AGGTGGGCCTTTCCTTATGC 60.033 55.000 4.53 0.00 44.18 3.14
394 395 2.666317 AGTTGCATATTAAGGTGGGCC 58.334 47.619 0.00 0.00 0.00 5.80
395 396 5.534654 TGAATAGTTGCATATTAAGGTGGGC 59.465 40.000 0.00 0.00 0.00 5.36
396 397 7.765695 ATGAATAGTTGCATATTAAGGTGGG 57.234 36.000 0.00 0.00 0.00 4.61
418 419 9.800433 TGCATGTTGTAGTGGATTTTTAATATG 57.200 29.630 0.00 0.00 0.00 1.78
420 421 9.800433 CATGCATGTTGTAGTGGATTTTTAATA 57.200 29.630 18.91 0.00 0.00 0.98
421 422 7.278424 GCATGCATGTTGTAGTGGATTTTTAAT 59.722 33.333 26.79 0.00 0.00 1.40
422 423 6.589523 GCATGCATGTTGTAGTGGATTTTTAA 59.410 34.615 26.79 0.00 0.00 1.52
423 424 6.098679 GCATGCATGTTGTAGTGGATTTTTA 58.901 36.000 26.79 0.00 0.00 1.52
424 425 4.931002 GCATGCATGTTGTAGTGGATTTTT 59.069 37.500 26.79 0.00 0.00 1.94
425 426 4.021280 TGCATGCATGTTGTAGTGGATTTT 60.021 37.500 26.79 0.00 0.00 1.82
426 427 3.510753 TGCATGCATGTTGTAGTGGATTT 59.489 39.130 26.79 0.00 0.00 2.17
427 428 3.090790 TGCATGCATGTTGTAGTGGATT 58.909 40.909 26.79 0.00 0.00 3.01
428 429 2.725637 TGCATGCATGTTGTAGTGGAT 58.274 42.857 26.79 0.00 0.00 3.41
429 430 2.197283 TGCATGCATGTTGTAGTGGA 57.803 45.000 26.79 0.00 0.00 4.02
430 431 2.804647 CATGCATGCATGTTGTAGTGG 58.195 47.619 40.30 20.25 46.20 4.00
551 552 9.834628 CGTTGTTGCGGGAATATTTATAATATT 57.165 29.630 4.74 4.74 0.00 1.28
552 553 9.005777 ACGTTGTTGCGGGAATATTTATAATAT 57.994 29.630 0.00 0.00 35.98 1.28
553 554 8.283992 CACGTTGTTGCGGGAATATTTATAATA 58.716 33.333 0.00 0.00 37.48 0.98
554 555 7.136119 CACGTTGTTGCGGGAATATTTATAAT 58.864 34.615 0.00 0.00 37.48 1.28
555 556 6.487960 CACGTTGTTGCGGGAATATTTATAA 58.512 36.000 0.00 0.00 37.48 0.98
556 557 5.504337 GCACGTTGTTGCGGGAATATTTATA 60.504 40.000 0.00 0.00 37.48 0.98
557 558 4.732355 GCACGTTGTTGCGGGAATATTTAT 60.732 41.667 0.00 0.00 37.48 1.40
558 559 3.426426 GCACGTTGTTGCGGGAATATTTA 60.426 43.478 0.00 0.00 37.48 1.40
559 560 2.669950 GCACGTTGTTGCGGGAATATTT 60.670 45.455 0.00 0.00 37.48 1.40
560 561 1.135517 GCACGTTGTTGCGGGAATATT 60.136 47.619 0.00 0.00 37.48 1.28
561 562 0.450184 GCACGTTGTTGCGGGAATAT 59.550 50.000 0.00 0.00 37.48 1.28
562 563 1.870383 GCACGTTGTTGCGGGAATA 59.130 52.632 0.00 0.00 37.48 1.75
563 564 2.642700 GCACGTTGTTGCGGGAAT 59.357 55.556 0.00 0.00 37.48 3.01
570 571 4.681643 ATGCGCCGCACGTTGTTG 62.682 61.111 16.70 0.00 43.04 3.33
571 572 4.383602 GATGCGCCGCACGTTGTT 62.384 61.111 16.70 0.00 43.04 2.83
573 574 4.164664 ATGATGCGCCGCACGTTG 62.165 61.111 16.70 0.00 43.04 4.10
574 575 2.899345 TAGATGATGCGCCGCACGTT 62.899 55.000 16.70 0.00 43.04 3.99
575 576 3.424639 TAGATGATGCGCCGCACGT 62.425 57.895 16.70 10.17 43.04 4.49
576 577 2.652079 CTAGATGATGCGCCGCACG 61.652 63.158 16.70 0.00 43.04 5.34
577 578 1.154205 AACTAGATGATGCGCCGCAC 61.154 55.000 16.70 9.47 43.04 5.34
578 579 0.461870 AAACTAGATGATGCGCCGCA 60.462 50.000 16.69 16.69 44.86 5.69
579 580 0.233332 GAAACTAGATGATGCGCCGC 59.767 55.000 4.18 0.00 0.00 6.53
580 581 1.570813 TGAAACTAGATGATGCGCCG 58.429 50.000 4.18 0.00 0.00 6.46
581 582 5.673337 TTTATGAAACTAGATGATGCGCC 57.327 39.130 4.18 0.00 0.00 6.53
582 583 6.139169 CGTTTTTATGAAACTAGATGATGCGC 59.861 38.462 0.00 0.00 0.00 6.09
583 584 7.180079 ACGTTTTTATGAAACTAGATGATGCG 58.820 34.615 0.00 0.00 0.00 4.73
584 585 8.391106 AGACGTTTTTATGAAACTAGATGATGC 58.609 33.333 0.00 0.00 0.00 3.91
585 586 9.694520 CAGACGTTTTTATGAAACTAGATGATG 57.305 33.333 0.00 0.00 0.00 3.07
586 587 9.436957 ACAGACGTTTTTATGAAACTAGATGAT 57.563 29.630 0.00 0.00 0.00 2.45
587 588 8.827177 ACAGACGTTTTTATGAAACTAGATGA 57.173 30.769 0.00 0.00 0.00 2.92
588 589 8.708742 TGACAGACGTTTTTATGAAACTAGATG 58.291 33.333 0.00 0.00 0.00 2.90
589 590 8.827177 TGACAGACGTTTTTATGAAACTAGAT 57.173 30.769 0.00 0.00 0.00 1.98
590 591 8.651391 TTGACAGACGTTTTTATGAAACTAGA 57.349 30.769 0.00 0.00 0.00 2.43
591 592 7.530861 GCTTGACAGACGTTTTTATGAAACTAG 59.469 37.037 0.00 0.00 0.00 2.57
592 593 7.349711 GCTTGACAGACGTTTTTATGAAACTA 58.650 34.615 0.00 0.00 0.00 2.24
593 594 6.199393 GCTTGACAGACGTTTTTATGAAACT 58.801 36.000 0.00 0.00 0.00 2.66
594 595 5.113529 CGCTTGACAGACGTTTTTATGAAAC 59.886 40.000 0.00 0.00 0.00 2.78
595 596 5.201910 CGCTTGACAGACGTTTTTATGAAA 58.798 37.500 0.00 0.00 0.00 2.69
596 597 4.768145 CGCTTGACAGACGTTTTTATGAA 58.232 39.130 0.00 0.00 0.00 2.57
597 598 3.363575 GCGCTTGACAGACGTTTTTATGA 60.364 43.478 0.00 0.00 0.00 2.15
598 599 2.902484 GCGCTTGACAGACGTTTTTATG 59.098 45.455 0.00 0.00 0.00 1.90
599 600 2.546368 TGCGCTTGACAGACGTTTTTAT 59.454 40.909 9.73 0.00 0.00 1.40
600 601 1.934525 TGCGCTTGACAGACGTTTTTA 59.065 42.857 9.73 0.00 0.00 1.52
634 635 3.378399 GAGGGTTCCTGCCTCTCGC 62.378 68.421 0.00 0.00 31.76 5.03
640 641 2.232298 CTGTCGAGAGGGTTCCTGCC 62.232 65.000 0.62 0.00 31.76 4.85
641 642 1.216710 CTGTCGAGAGGGTTCCTGC 59.783 63.158 0.62 0.00 31.76 4.85
642 643 1.893786 CCTGTCGAGAGGGTTCCTG 59.106 63.158 20.75 0.00 31.76 3.86
643 644 1.985116 GCCTGTCGAGAGGGTTCCT 60.985 63.158 28.23 0.00 36.03 3.36
644 645 2.579738 GCCTGTCGAGAGGGTTCC 59.420 66.667 28.23 9.32 33.17 3.62
648 651 3.465403 CTGGGCCTGTCGAGAGGG 61.465 72.222 28.23 9.32 33.17 4.30
655 658 1.588082 CATTTGCACTGGGCCTGTC 59.412 57.895 13.73 9.20 43.89 3.51
667 670 4.807039 CGCCTGGCTGCCATTTGC 62.807 66.667 23.64 22.17 41.77 3.68
680 683 2.034221 GGAGTTGAAAGGCCGCCT 59.966 61.111 5.94 5.94 33.87 5.52
681 684 1.587043 GAAGGAGTTGAAAGGCCGCC 61.587 60.000 0.00 0.00 0.00 6.13
685 688 3.623510 CGATAAGGAAGGAGTTGAAAGGC 59.376 47.826 0.00 0.00 0.00 4.35
686 689 3.623510 GCGATAAGGAAGGAGTTGAAAGG 59.376 47.826 0.00 0.00 0.00 3.11
687 690 4.253685 TGCGATAAGGAAGGAGTTGAAAG 58.746 43.478 0.00 0.00 0.00 2.62
688 691 4.280436 TGCGATAAGGAAGGAGTTGAAA 57.720 40.909 0.00 0.00 0.00 2.69
689 692 3.973206 TGCGATAAGGAAGGAGTTGAA 57.027 42.857 0.00 0.00 0.00 2.69
690 693 3.861840 CTTGCGATAAGGAAGGAGTTGA 58.138 45.455 0.00 0.00 43.52 3.18
691 694 2.352960 GCTTGCGATAAGGAAGGAGTTG 59.647 50.000 1.89 0.00 46.73 3.16
692 695 2.027192 TGCTTGCGATAAGGAAGGAGTT 60.027 45.455 1.89 0.00 46.73 3.01
693 696 1.555075 TGCTTGCGATAAGGAAGGAGT 59.445 47.619 1.89 0.00 46.73 3.85
694 697 2.315925 TGCTTGCGATAAGGAAGGAG 57.684 50.000 1.89 0.00 46.73 3.69
695 698 1.134401 CCTGCTTGCGATAAGGAAGGA 60.134 52.381 1.89 0.00 46.73 3.36
696 699 1.303309 CCTGCTTGCGATAAGGAAGG 58.697 55.000 1.89 0.00 46.73 3.46
698 701 0.748005 GGCCTGCTTGCGATAAGGAA 60.748 55.000 0.00 0.00 30.92 3.36
699 702 1.153168 GGCCTGCTTGCGATAAGGA 60.153 57.895 0.00 0.00 30.92 3.36
700 703 2.189499 GGGCCTGCTTGCGATAAGG 61.189 63.158 0.84 0.00 0.00 2.69
701 704 2.537560 CGGGCCTGCTTGCGATAAG 61.538 63.158 0.84 0.00 0.00 1.73
702 705 2.513666 CGGGCCTGCTTGCGATAA 60.514 61.111 0.84 0.00 0.00 1.75
703 706 4.545706 CCGGGCCTGCTTGCGATA 62.546 66.667 5.85 0.00 0.00 2.92
724 727 0.297820 GAAATGTCGTCGATCGTGCC 59.702 55.000 15.94 3.66 40.80 5.01
760 763 1.812922 CTCACCGGAGATGCTGCAC 60.813 63.158 9.46 0.00 44.26 4.57
762 765 2.202987 CCTCACCGGAGATGCTGC 60.203 66.667 9.46 0.00 44.26 5.25
763 766 2.202987 GCCTCACCGGAGATGCTG 60.203 66.667 19.11 1.59 44.26 4.41
764 767 2.364842 AGCCTCACCGGAGATGCT 60.365 61.111 22.36 22.36 44.26 3.79
787 793 1.396815 GCGAGTTGCTTACGTCAACAC 60.397 52.381 17.68 11.90 44.50 3.32
788 794 0.856641 GCGAGTTGCTTACGTCAACA 59.143 50.000 17.68 1.34 44.50 3.33
789 795 3.633774 GCGAGTTGCTTACGTCAAC 57.366 52.632 9.86 9.86 42.92 3.18
799 805 1.129437 GAGTGGAATCAAGCGAGTTGC 59.871 52.381 0.00 0.00 46.98 4.17
808 814 0.038983 TTCGCGTCGAGTGGAATCAA 60.039 50.000 5.77 0.00 37.14 2.57
820 826 2.704193 CGGTGAGTTCGTTCGCGTC 61.704 63.158 5.77 0.00 42.11 5.19
825 831 1.356938 GGAATCCGGTGAGTTCGTTC 58.643 55.000 0.00 0.00 0.00 3.95
883 889 1.820906 CTGTGACCGATGCATGGGG 60.821 63.158 28.73 19.86 0.00 4.96
886 892 2.282407 TGAATCTGTGACCGATGCATG 58.718 47.619 2.46 0.00 0.00 4.06
887 893 2.696989 TGAATCTGTGACCGATGCAT 57.303 45.000 0.00 0.00 0.00 3.96
888 894 2.696989 ATGAATCTGTGACCGATGCA 57.303 45.000 0.00 0.00 31.27 3.96
889 895 3.201290 AGAATGAATCTGTGACCGATGC 58.799 45.455 0.00 0.00 36.88 3.91
909 915 3.303928 GGGTATCTCGGGGCGGAG 61.304 72.222 0.00 0.00 35.32 4.63
1164 1170 4.702081 GCGTGCACCTCGACGTCT 62.702 66.667 14.70 0.00 37.89 4.18
1413 1419 3.819902 TCGGACATGAGATGAGATGAGAG 59.180 47.826 0.00 0.00 0.00 3.20
1414 1420 3.825328 TCGGACATGAGATGAGATGAGA 58.175 45.455 0.00 0.00 0.00 3.27
1415 1421 4.460034 AGATCGGACATGAGATGAGATGAG 59.540 45.833 0.00 0.00 0.00 2.90
1416 1422 4.405548 AGATCGGACATGAGATGAGATGA 58.594 43.478 0.00 0.00 0.00 2.92
1417 1423 4.787260 AGATCGGACATGAGATGAGATG 57.213 45.455 0.00 0.00 0.00 2.90
1418 1424 4.394610 CGTAGATCGGACATGAGATGAGAT 59.605 45.833 0.00 0.00 35.71 2.75
1419 1425 3.748568 CGTAGATCGGACATGAGATGAGA 59.251 47.826 0.00 0.00 35.71 3.27
1420 1426 4.077063 CGTAGATCGGACATGAGATGAG 57.923 50.000 0.00 0.00 35.71 2.90
1454 1460 3.624777 TGGAAGTAGGAACGTAGGTAGG 58.375 50.000 0.00 0.00 0.00 3.18
1455 1461 5.359009 TCAATGGAAGTAGGAACGTAGGTAG 59.641 44.000 0.00 0.00 0.00 3.18
1456 1462 5.126061 GTCAATGGAAGTAGGAACGTAGGTA 59.874 44.000 0.00 0.00 0.00 3.08
1457 1463 4.081807 GTCAATGGAAGTAGGAACGTAGGT 60.082 45.833 0.00 0.00 0.00 3.08
1514 1530 3.918294 TGCATGGAGTCAATGAGATGA 57.082 42.857 11.98 0.00 0.00 2.92
1515 1531 3.304726 GCATGCATGGAGTCAATGAGATG 60.305 47.826 27.34 12.34 0.00 2.90
1516 1532 2.885266 GCATGCATGGAGTCAATGAGAT 59.115 45.455 27.34 0.00 0.00 2.75
1517 1533 2.294979 GCATGCATGGAGTCAATGAGA 58.705 47.619 27.34 0.00 0.00 3.27
1519 1535 2.021457 CTGCATGCATGGAGTCAATGA 58.979 47.619 33.11 0.00 40.79 2.57
1520 1536 1.067060 CCTGCATGCATGGAGTCAATG 59.933 52.381 36.46 22.39 43.71 2.82
1521 1537 1.399714 CCTGCATGCATGGAGTCAAT 58.600 50.000 36.46 0.00 43.71 2.57
1522 1538 1.317431 GCCTGCATGCATGGAGTCAA 61.317 55.000 36.46 9.69 43.71 3.18
1523 1539 1.751544 GCCTGCATGCATGGAGTCA 60.752 57.895 36.46 21.71 43.71 3.41
1524 1540 2.831366 CGCCTGCATGCATGGAGTC 61.831 63.158 36.46 28.28 43.71 3.36
1525 1541 2.827190 CGCCTGCATGCATGGAGT 60.827 61.111 36.46 0.00 43.71 3.85
1526 1542 3.592814 CCGCCTGCATGCATGGAG 61.593 66.667 34.14 34.14 44.66 3.86
1527 1543 3.942377 AACCGCCTGCATGCATGGA 62.942 57.895 29.73 23.99 0.00 3.41
1528 1544 3.420214 GAACCGCCTGCATGCATGG 62.420 63.158 27.34 23.82 0.00 3.66
1712 2016 3.200593 TAGTCCTCGGCGAGCGAC 61.201 66.667 32.61 32.61 33.36 5.19
2076 2380 2.202623 GAGCGTGACGGCGAGAAT 60.203 61.111 16.62 0.00 38.18 2.40
2078 2382 4.103103 CAGAGCGTGACGGCGAGA 62.103 66.667 16.62 0.00 38.18 4.04
2477 2781 4.877619 TTGGCGGCGGTGGTTTCA 62.878 61.111 9.78 0.00 0.00 2.69
2918 3222 9.553064 AGTCTAATGAATTCCTGTGCTAATTAG 57.447 33.333 8.20 8.20 0.00 1.73
2977 3281 8.649973 AGTAGCTAGTACATCAACTATTTTGC 57.350 34.615 0.00 0.00 33.55 3.68
3136 3449 8.594418 AAAATTGAAAACAAAATGTTACGCAC 57.406 26.923 0.00 0.00 40.14 5.34
3199 3512 7.264373 CAGTTGACTGAGATTTAACCAAGTT 57.736 36.000 5.19 0.00 46.59 2.66
3216 3529 4.887748 TGAAGGTTGAGATCTCAGTTGAC 58.112 43.478 23.92 18.74 41.13 3.18
3257 3570 8.611051 ATTAGGCCGAGGTATAAGATTTAGAT 57.389 34.615 0.00 0.00 0.00 1.98
3281 3594 7.764901 GGTCCTTCGAGACTTCAGTATTTTAAT 59.235 37.037 4.97 0.00 36.95 1.40
3414 4146 4.536765 CCTAAGGCCACAAAATATGAGGT 58.463 43.478 5.01 0.00 41.44 3.85
3439 4171 0.403304 AGATCCACCATGCCCCCATA 60.403 55.000 0.00 0.00 0.00 2.74
3460 4192 2.348998 CCTTCCGTCAGCAAGGCT 59.651 61.111 0.00 0.00 40.77 4.58
3468 4201 3.713826 AATAAAAGAGCCCTTCCGTCA 57.286 42.857 0.00 0.00 0.00 4.35
3508 4241 0.831711 GGCAGGACACAAACCCCAAT 60.832 55.000 0.00 0.00 0.00 3.16
3556 4289 3.380320 CGGGGGAACATTATTCCAACTTC 59.620 47.826 7.93 0.00 40.32 3.01
3611 4345 1.745890 CTCCACACGTTCCCTGACA 59.254 57.895 0.00 0.00 0.00 3.58
3645 4379 5.389520 TCCATTAAAGACAACCACCAATCA 58.610 37.500 0.00 0.00 0.00 2.57
3699 4433 5.751680 CATTCAACTTGAAGACACACGAAT 58.248 37.500 9.97 0.00 40.05 3.34
3718 4452 6.273825 TGAAGAGTATAGGTCGAAAGCATTC 58.726 40.000 0.00 0.00 0.00 2.67
3750 4487 1.756430 TGTACCAAACACAGCAAGCA 58.244 45.000 0.00 0.00 31.43 3.91
3779 4516 0.606604 GTTGTCGGACTAAGGCCTCA 59.393 55.000 5.23 0.00 0.00 3.86
3853 4590 2.202703 AAGGCGCGTCGGTATCAC 60.203 61.111 8.43 0.00 0.00 3.06
3894 4631 9.482627 ACACTGAAAACAAAATTTACAAAGACA 57.517 25.926 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.