Multiple sequence alignment - TraesCS7D01G087300

Loading Multiple Alignment...

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 TraesCS7D01G087300 chr7D 100.000 4901 0 0 1 4901 53506444 53501544 0.000000e+00 9051.0
1 TraesCS7D01G087300 chr7D 91.852 135 8 3 226 359 501098109 501097977 8.380000e-43 185.0
2 TraesCS7D01G087300 chr7D 85.714 119 17 0 4438 4556 458363928 458363810 5.150000e-25 126.0
3 TraesCS7D01G087300 chr7D 86.517 89 5 3 3870 3951 53502428 53502340 1.880000e-14 91.6
4 TraesCS7D01G087300 chr7D 86.517 89 5 3 4017 4105 53502575 53502494 1.880000e-14 91.6
5 TraesCS7D01G087300 chr7A 94.416 2883 141 5 401 3270 55891636 55888761 0.000000e+00 4414.0
6 TraesCS7D01G087300 chr7A 95.528 246 10 1 1 246 55892006 55891762 4.600000e-105 392.0
7 TraesCS7D01G087300 chr7A 85.670 321 36 7 4553 4871 55888452 55888140 3.660000e-86 329.0
8 TraesCS7D01G087300 chr7A 95.041 121 5 1 4437 4556 496091414 496091534 6.480000e-44 189.0
9 TraesCS7D01G087300 chr7A 92.373 118 8 1 4208 4325 55888762 55888646 3.030000e-37 167.0
10 TraesCS7D01G087300 chr7A 100.000 33 0 0 356 388 55891766 55891734 1.470000e-05 62.1
11 TraesCS7D01G087300 chr4A 96.270 2681 93 4 1769 4442 668154894 668152214 0.000000e+00 4390.0
12 TraesCS7D01G087300 chr4A 90.428 397 26 3 401 786 668155819 668155424 3.380000e-141 512.0
13 TraesCS7D01G087300 chr4A 94.444 144 8 0 4758 4901 668152159 668152016 6.390000e-54 222.0
14 TraesCS7D01G087300 chr4A 86.517 89 5 3 4017 4105 668152788 668152707 1.880000e-14 91.6
15 TraesCS7D01G087300 chr4A 85.393 89 6 3 3870 3951 668152641 668152553 8.740000e-13 86.1
16 TraesCS7D01G087300 chr4A 97.436 39 1 0 359 397 668155947 668155909 3.170000e-07 67.6
17 TraesCS7D01G087300 chr5B 79.734 2704 510 29 1118 3802 511605947 511608631 0.000000e+00 1923.0
18 TraesCS7D01G087300 chr5B 93.701 127 7 1 233 359 659171473 659171598 6.480000e-44 189.0
19 TraesCS7D01G087300 chr5B 87.395 119 15 0 4439 4557 660683176 660683058 2.380000e-28 137.0
20 TraesCS7D01G087300 chr5B 86.066 122 15 2 4436 4556 594746991 594747111 3.980000e-26 130.0
21 TraesCS7D01G087300 chr5D 79.237 2803 536 31 1024 3802 423833718 423836498 0.000000e+00 1910.0
22 TraesCS7D01G087300 chr5D 100.000 118 0 0 4440 4557 334273728 334273611 8.260000e-53 219.0
23 TraesCS7D01G087300 chr5D 96.581 117 4 0 244 360 270254028 270254144 1.390000e-45 195.0
24 TraesCS7D01G087300 chr5D 92.593 135 7 3 227 359 138565538 138565671 1.800000e-44 191.0
25 TraesCS7D01G087300 chr5D 91.791 134 8 3 229 360 312934216 312934348 3.010000e-42 183.0
26 TraesCS7D01G087300 chr5D 85.593 118 15 2 4440 4556 47538620 47538504 6.660000e-24 122.0
27 TraesCS7D01G087300 chr5D 85.593 118 14 1 4440 4557 382258533 382258647 2.400000e-23 121.0
28 TraesCS7D01G087300 chr2D 87.671 219 24 2 445 660 647763146 647763364 8.140000e-63 252.0
29 TraesCS7D01G087300 chr2D 90.756 119 11 0 4439 4557 155730888 155731006 5.080000e-35 159.0
30 TraesCS7D01G087300 chrUn 87.037 216 25 2 445 657 24269917 24270132 1.760000e-59 241.0
31 TraesCS7D01G087300 chrUn 85.333 225 29 3 445 665 92971085 92970861 3.820000e-56 230.0
32 TraesCS7D01G087300 chrUn 91.892 74 6 0 4484 4557 338020872 338020799 2.410000e-18 104.0
33 TraesCS7D01G087300 chrUn 83.761 117 9 3 4440 4556 84602928 84603034 8.680000e-18 102.0
34 TraesCS7D01G087300 chrUn 82.906 117 16 3 4440 4556 156524331 156524219 8.680000e-18 102.0
35 TraesCS7D01G087300 chrUn 83.761 117 9 3 4440 4556 320050139 320050245 8.680000e-18 102.0
36 TraesCS7D01G087300 chrUn 88.312 77 9 0 4484 4560 318992628 318992704 5.220000e-15 93.5
37 TraesCS7D01G087300 chrUn 87.671 73 9 0 4484 4556 306051214 306051286 8.740000e-13 86.1
38 TraesCS7D01G087300 chrUn 87.671 73 9 0 4484 4556 306068230 306068302 8.740000e-13 86.1
39 TraesCS7D01G087300 chrUn 86.301 73 10 0 4484 4556 329663272 329663344 4.070000e-11 80.5
40 TraesCS7D01G087300 chrUn 86.301 73 10 0 4484 4556 331481946 331482018 4.070000e-11 80.5
41 TraesCS7D01G087300 chrUn 80.000 120 14 3 4439 4558 454753335 454753226 4.070000e-11 80.5
42 TraesCS7D01G087300 chrUn 83.333 84 13 1 4437 4519 462080108 462080025 5.260000e-10 76.8
43 TraesCS7D01G087300 chrUn 81.928 83 15 0 4437 4519 466639543 466639461 2.450000e-08 71.3
44 TraesCS7D01G087300 chr3B 87.619 210 22 4 450 656 519860864 519860656 1.760000e-59 241.0
45 TraesCS7D01G087300 chr1D 85.590 229 27 4 445 669 442997923 442998149 8.200000e-58 235.0
46 TraesCS7D01G087300 chr1D 86.441 118 16 0 4440 4557 222028426 222028543 3.980000e-26 130.0
47 TraesCS7D01G087300 chr1D 86.441 118 16 0 4440 4557 418011658 418011541 3.980000e-26 130.0
48 TraesCS7D01G087300 chr1D 83.846 130 21 0 4426 4555 490939122 490939251 1.850000e-24 124.0
49 TraesCS7D01G087300 chr1D 82.927 123 20 1 4438 4560 94084273 94084394 5.190000e-20 110.0
50 TraesCS7D01G087300 chr3A 85.973 221 27 2 445 662 388358501 388358282 2.950000e-57 233.0
51 TraesCS7D01G087300 chr3A 95.868 121 5 0 244 364 22891591 22891711 3.870000e-46 196.0
52 TraesCS7D01G087300 chr6D 85.973 221 26 4 445 661 141141542 141141761 1.060000e-56 231.0
53 TraesCS7D01G087300 chr6D 84.762 105 14 2 4453 4556 214540237 214540134 2.410000e-18 104.0
54 TraesCS7D01G087300 chr6D 81.600 125 20 3 4439 4562 363881250 363881372 3.120000e-17 100.0
55 TraesCS7D01G087300 chr6D 78.992 119 15 4 4439 4557 334284325 334284217 6.800000e-09 73.1
56 TraesCS7D01G087300 chr6D 82.927 82 13 1 4438 4519 459191784 459191704 6.800000e-09 73.1
57 TraesCS7D01G087300 chr2A 95.798 119 5 0 243 361 451004778 451004896 5.010000e-45 193.0
58 TraesCS7D01G087300 chr2A 95.082 122 6 0 242 363 502330482 502330361 5.010000e-45 193.0
59 TraesCS7D01G087300 chr2A 87.395 119 15 0 4438 4556 37267644 37267526 2.380000e-28 137.0
60 TraesCS7D01G087300 chr6A 93.023 129 8 1 233 360 447643718 447643846 2.330000e-43 187.0
61 TraesCS7D01G087300 chr2B 89.256 121 11 2 4437 4556 606045484 606045365 3.060000e-32 150.0
62 TraesCS7D01G087300 chr3D 90.000 110 11 0 4447 4556 432026491 432026382 5.110000e-30 143.0
63 TraesCS7D01G087300 chr1B 87.097 124 16 0 4437 4560 573577809 573577686 1.840000e-29 141.0
64 TraesCS7D01G087300 chr1B 88.034 117 14 0 4440 4556 10078773 10078657 6.620000e-29 139.0
65 TraesCS7D01G087300 chr1B 85.484 124 18 0 4433 4556 674620621 674620744 3.980000e-26 130.0
66 TraesCS7D01G087300 chr1B 85.593 118 17 0 4439 4556 58710559 58710676 1.850000e-24 124.0
67 TraesCS7D01G087300 chr1B 85.124 121 18 0 4436 4556 462971527 462971647 1.850000e-24 124.0
68 TraesCS7D01G087300 chr1B 85.000 120 18 0 4437 4556 521691648 521691767 6.660000e-24 122.0
69 TraesCS7D01G087300 chr4B 86.441 118 16 0 4440 4557 360788503 360788386 3.980000e-26 130.0
70 TraesCS7D01G087300 chr6B 85.950 121 16 1 4440 4560 245428325 245428444 1.430000e-25 128.0
71 TraesCS7D01G087300 chr6B 86.441 118 14 2 4442 4557 435837503 435837386 1.430000e-25 128.0
72 TraesCS7D01G087300 chr6B 86.325 117 16 0 4440 4556 704015381 704015497 1.430000e-25 128.0


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 TraesCS7D01G087300 chr7D 53501544 53506444 4900 True 9051.000000 9051 100.0000 1 4901 1 chr7D.!!$R1 4900
1 TraesCS7D01G087300 chr7A 55888140 55892006 3866 True 1072.820000 4414 93.5974 1 4871 5 chr7A.!!$R1 4870
2 TraesCS7D01G087300 chr4A 668152016 668155947 3931 True 894.883333 4390 91.7480 359 4901 6 chr4A.!!$R1 4542
3 TraesCS7D01G087300 chr5B 511605947 511608631 2684 False 1923.000000 1923 79.7340 1118 3802 1 chr5B.!!$F1 2684
4 TraesCS7D01G087300 chr5D 423833718 423836498 2780 False 1910.000000 1910 79.2370 1024 3802 1 chr5D.!!$F5 2778

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
974 1074 0.034059 ACGTCCTCAGAGCACCAAAG 59.966 55.0 0.00 0.00 0.00 2.77 F
1859 2040 0.335705 TGGGATGTTGGCACCATCAT 59.664 50.0 23.84 12.06 40.38 2.45 F
3492 3678 0.322636 TGGAGTCTCTCGACCTGTCC 60.323 60.0 0.00 0.00 41.16 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2941 3124 1.055040 ACCAACTCTGAGCAGCTCTT 58.945 50.0 23.15 6.39 0.00 2.85 R
3522 3708 1.025041 TCATGATGTCCGAGAGACCG 58.975 55.0 0.00 0.00 45.68 4.79 R
4838 5110 0.933097 CGTTGCTCATCTCGGAATGG 59.067 55.0 0.00 0.00 0.00 3.16 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
91 92 5.042593 CAGTTTAGCTGCAAATCAACACAA 58.957 37.500 1.02 0.00 38.52 3.33
101 102 4.739716 GCAAATCAACACAAGTAACCTGTG 59.260 41.667 4.90 4.90 39.26 3.66
129 130 1.354040 CCGTCATGACTTCAGACAGC 58.646 55.000 22.95 0.00 32.68 4.40
162 163 5.332106 TCTCTATCTGATAGGTGCCTTCT 57.668 43.478 21.28 0.00 33.64 2.85
169 170 4.287067 TCTGATAGGTGCCTTCTTTGACTT 59.713 41.667 0.00 0.00 0.00 3.01
175 176 3.119137 GGTGCCTTCTTTGACTTGTTTGT 60.119 43.478 0.00 0.00 0.00 2.83
185 186 0.248621 ACTTGTTTGTCAGCTTGCGC 60.249 50.000 0.00 0.00 0.00 6.09
253 254 5.786264 ATTGTTATACAGTACTCCCTCCG 57.214 43.478 0.00 0.00 0.00 4.63
254 255 4.240881 TGTTATACAGTACTCCCTCCGT 57.759 45.455 0.00 0.00 0.00 4.69
255 256 4.202441 TGTTATACAGTACTCCCTCCGTC 58.798 47.826 0.00 0.00 0.00 4.79
256 257 2.361643 ATACAGTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
257 258 0.107508 TACAGTACTCCCTCCGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
258 259 2.439883 AGTACTCCCTCCGTCCGC 60.440 66.667 0.00 0.00 0.00 5.54
259 260 2.753043 GTACTCCCTCCGTCCGCA 60.753 66.667 0.00 0.00 0.00 5.69
260 261 2.036098 TACTCCCTCCGTCCGCAA 59.964 61.111 0.00 0.00 0.00 4.85
261 262 1.607178 TACTCCCTCCGTCCGCAAA 60.607 57.895 0.00 0.00 0.00 3.68
262 263 0.974010 TACTCCCTCCGTCCGCAAAT 60.974 55.000 0.00 0.00 0.00 2.32
263 264 0.974010 ACTCCCTCCGTCCGCAAATA 60.974 55.000 0.00 0.00 0.00 1.40
264 265 0.529992 CTCCCTCCGTCCGCAAATAC 60.530 60.000 0.00 0.00 0.00 1.89
265 266 0.974010 TCCCTCCGTCCGCAAATACT 60.974 55.000 0.00 0.00 0.00 2.12
266 267 0.107848 CCCTCCGTCCGCAAATACTT 60.108 55.000 0.00 0.00 0.00 2.24
267 268 1.006832 CCTCCGTCCGCAAATACTTG 58.993 55.000 0.00 0.00 35.49 3.16
268 269 1.674817 CCTCCGTCCGCAAATACTTGT 60.675 52.381 0.00 0.00 34.79 3.16
269 270 1.659098 CTCCGTCCGCAAATACTTGTC 59.341 52.381 0.00 0.00 34.79 3.18
270 271 0.725117 CCGTCCGCAAATACTTGTCC 59.275 55.000 0.00 0.00 34.79 4.02
271 272 1.674817 CCGTCCGCAAATACTTGTCCT 60.675 52.381 0.00 0.00 34.79 3.85
272 273 1.659098 CGTCCGCAAATACTTGTCCTC 59.341 52.381 0.00 0.00 34.79 3.71
273 274 1.659098 GTCCGCAAATACTTGTCCTCG 59.341 52.381 0.00 0.00 34.79 4.63
274 275 1.546923 TCCGCAAATACTTGTCCTCGA 59.453 47.619 0.00 0.00 34.79 4.04
275 276 2.028839 TCCGCAAATACTTGTCCTCGAA 60.029 45.455 0.00 0.00 34.79 3.71
276 277 2.739913 CCGCAAATACTTGTCCTCGAAA 59.260 45.455 0.00 0.00 34.79 3.46
277 278 3.374058 CCGCAAATACTTGTCCTCGAAAT 59.626 43.478 0.00 0.00 34.79 2.17
278 279 4.334443 CGCAAATACTTGTCCTCGAAATG 58.666 43.478 0.00 0.00 34.79 2.32
279 280 4.662145 GCAAATACTTGTCCTCGAAATGG 58.338 43.478 0.00 0.00 34.79 3.16
280 281 4.156008 GCAAATACTTGTCCTCGAAATGGT 59.844 41.667 0.00 0.00 34.79 3.55
281 282 5.335661 GCAAATACTTGTCCTCGAAATGGTT 60.336 40.000 0.00 0.00 34.79 3.67
282 283 5.880054 AATACTTGTCCTCGAAATGGTTG 57.120 39.130 0.00 0.00 0.00 3.77
283 284 3.208747 ACTTGTCCTCGAAATGGTTGT 57.791 42.857 0.00 0.00 0.00 3.32
284 285 4.345859 ACTTGTCCTCGAAATGGTTGTA 57.654 40.909 0.00 0.00 0.00 2.41
285 286 4.906618 ACTTGTCCTCGAAATGGTTGTAT 58.093 39.130 0.00 0.00 0.00 2.29
286 287 4.935808 ACTTGTCCTCGAAATGGTTGTATC 59.064 41.667 0.00 0.00 0.00 2.24
287 288 4.819105 TGTCCTCGAAATGGTTGTATCT 57.181 40.909 0.00 0.00 0.00 1.98
288 289 5.925506 TGTCCTCGAAATGGTTGTATCTA 57.074 39.130 0.00 0.00 0.00 1.98
289 290 5.902681 TGTCCTCGAAATGGTTGTATCTAG 58.097 41.667 0.00 0.00 0.00 2.43
290 291 5.655090 TGTCCTCGAAATGGTTGTATCTAGA 59.345 40.000 0.00 0.00 0.00 2.43
291 292 5.978322 GTCCTCGAAATGGTTGTATCTAGAC 59.022 44.000 0.00 0.00 0.00 2.59
292 293 5.892119 TCCTCGAAATGGTTGTATCTAGACT 59.108 40.000 0.00 0.00 0.00 3.24
293 294 6.380274 TCCTCGAAATGGTTGTATCTAGACTT 59.620 38.462 0.00 0.00 0.00 3.01
294 295 7.558807 TCCTCGAAATGGTTGTATCTAGACTTA 59.441 37.037 0.00 0.00 0.00 2.24
295 296 8.361139 CCTCGAAATGGTTGTATCTAGACTTAT 58.639 37.037 0.00 0.00 0.00 1.73
296 297 9.751542 CTCGAAATGGTTGTATCTAGACTTATT 57.248 33.333 0.00 0.00 0.00 1.40
333 334 7.392766 ACATCCATTGTATCCATTTCTAGGA 57.607 36.000 0.00 0.00 36.57 2.94
334 335 7.227156 ACATCCATTGTATCCATTTCTAGGAC 58.773 38.462 0.00 0.00 38.13 3.85
335 336 6.823286 TCCATTGTATCCATTTCTAGGACA 57.177 37.500 0.00 0.00 38.13 4.02
336 337 7.206789 TCCATTGTATCCATTTCTAGGACAA 57.793 36.000 0.00 0.00 38.13 3.18
337 338 7.282585 TCCATTGTATCCATTTCTAGGACAAG 58.717 38.462 0.00 0.00 38.13 3.16
338 339 7.056635 CCATTGTATCCATTTCTAGGACAAGT 58.943 38.462 0.00 0.00 38.13 3.16
339 340 8.210946 CCATTGTATCCATTTCTAGGACAAGTA 58.789 37.037 0.00 0.00 38.13 2.24
340 341 9.784531 CATTGTATCCATTTCTAGGACAAGTAT 57.215 33.333 0.00 0.00 38.13 2.12
343 344 9.832445 TGTATCCATTTCTAGGACAAGTATTTC 57.168 33.333 0.00 0.00 38.13 2.17
344 345 9.274206 GTATCCATTTCTAGGACAAGTATTTCC 57.726 37.037 0.00 0.00 38.13 3.13
345 346 6.346096 TCCATTTCTAGGACAAGTATTTCCG 58.654 40.000 0.00 0.00 36.95 4.30
346 347 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
347 348 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
348 349 4.996788 TCTAGGACAAGTATTTCCGGAC 57.003 45.455 1.83 0.00 36.95 4.79
349 350 2.667473 AGGACAAGTATTTCCGGACG 57.333 50.000 1.83 0.00 36.95 4.79
350 351 2.173519 AGGACAAGTATTTCCGGACGA 58.826 47.619 1.83 0.00 36.95 4.20
351 352 2.564062 AGGACAAGTATTTCCGGACGAA 59.436 45.455 1.83 0.00 36.95 3.85
352 353 2.928116 GGACAAGTATTTCCGGACGAAG 59.072 50.000 1.83 0.00 0.00 3.79
353 354 2.928116 GACAAGTATTTCCGGACGAAGG 59.072 50.000 1.83 0.00 0.00 3.46
354 355 2.277084 CAAGTATTTCCGGACGAAGGG 58.723 52.381 1.83 0.00 0.00 3.95
390 391 9.644993 GTTGACTTGGTAAAACAAAAATAATGC 57.355 29.630 0.00 0.00 0.00 3.56
397 398 8.358148 TGGTAAAACAAAAATAATGCCGAGTTA 58.642 29.630 0.00 0.00 0.00 2.24
426 513 4.351127 AGTAGTACTCCCTCCGTTCAAAT 58.649 43.478 0.00 0.00 0.00 2.32
484 571 9.145865 CTTTGACCAAGTTTATAGAGAGAACTC 57.854 37.037 0.00 0.00 42.90 3.01
592 679 8.307483 TGTAAATGTTTTTCTCCACAAACTTGA 58.693 29.630 0.00 0.00 34.52 3.02
595 682 5.577835 TGTTTTTCTCCACAAACTTGATCG 58.422 37.500 0.00 0.00 34.52 3.69
774 872 4.351938 CGGTCGTTGCCTCGTGGA 62.352 66.667 7.92 0.00 34.57 4.02
786 884 1.339055 CCTCGTGGAGCCTTCATTCAA 60.339 52.381 0.00 0.00 34.57 2.69
791 889 2.227388 GTGGAGCCTTCATTCAACACAG 59.773 50.000 0.00 0.00 0.00 3.66
900 1000 2.518112 TTTGTCAGCTTGCGGCCA 60.518 55.556 2.24 0.00 43.05 5.36
946 1046 1.811778 TATCAGGGCCAGAGCTTCAT 58.188 50.000 6.18 0.00 39.73 2.57
952 1052 0.957362 GGCCAGAGCTTCATATTGCC 59.043 55.000 0.00 0.00 39.73 4.52
967 1067 0.175760 TTGCCATACGTCCTCAGAGC 59.824 55.000 0.00 0.00 0.00 4.09
974 1074 0.034059 ACGTCCTCAGAGCACCAAAG 59.966 55.000 0.00 0.00 0.00 2.77
1116 1257 1.425267 GGCAACAAACCAACAACGGC 61.425 55.000 0.00 0.00 0.00 5.68
1129 1270 4.634703 ACGGCGGGTGCATCACAA 62.635 61.111 13.24 0.00 45.35 3.33
1131 1272 2.568090 GGCGGGTGCATCACAAAG 59.432 61.111 0.00 0.00 45.35 2.77
1135 1276 1.308069 CGGGTGCATCACAAAGGAGG 61.308 60.000 0.00 0.00 35.86 4.30
1140 1281 0.681243 GCATCACAAAGGAGGGGGAC 60.681 60.000 0.00 0.00 0.00 4.46
1411 1583 5.136068 AGATCTGAGTGGGAACTATCTCA 57.864 43.478 0.00 0.00 35.92 3.27
1435 1607 1.525995 GTGGATGTGCCCATACCCG 60.526 63.158 0.00 0.00 38.66 5.28
1621 1802 1.690283 CTCATGGTTGCTGCGTCTCG 61.690 60.000 0.00 0.00 0.00 4.04
1642 1823 3.067833 GCTTTGCTAAGGTTTCTCGACT 58.932 45.455 9.94 0.00 31.76 4.18
1757 1938 4.638865 ACTTGTTTTTCCACAGACACCTAC 59.361 41.667 0.00 0.00 0.00 3.18
1859 2040 0.335705 TGGGATGTTGGCACCATCAT 59.664 50.000 23.84 12.06 40.38 2.45
1887 2068 9.869844 CATCTTGACCTTACGAATAATGAAATC 57.130 33.333 0.00 0.00 0.00 2.17
1962 2143 2.842496 TCTTGGAGGCAATCATCTCACT 59.158 45.455 0.00 0.00 0.00 3.41
2094 2275 4.469586 TGTGCATGGAGTAAGATGGAGTTA 59.530 41.667 0.00 0.00 0.00 2.24
2112 2293 5.874810 GGAGTTATTAGACATGTCTTGCACA 59.125 40.000 32.14 12.37 40.93 4.57
2262 2443 7.277981 CAGTTGTATCTAGACGGCAACTATTTT 59.722 37.037 25.11 10.86 45.17 1.82
2427 2610 3.941704 ATGGGACCTCATTTTCCTCTC 57.058 47.619 0.00 0.00 31.90 3.20
2436 2619 5.044550 ACCTCATTTTCCTCTCTGGCTAAAT 60.045 40.000 0.00 0.00 33.25 1.40
2437 2620 5.890419 CCTCATTTTCCTCTCTGGCTAAATT 59.110 40.000 0.00 0.00 31.79 1.82
2532 2715 6.640907 GGAGTGTGGTTTCAAATGTTCAATAC 59.359 38.462 0.00 0.00 0.00 1.89
2767 2950 6.709846 GCTTTCTGAGAATAGTATCAATGGCT 59.290 38.462 0.00 0.00 0.00 4.75
2865 3048 2.224305 CCCCGTCTGTTCAGAAGAAACT 60.224 50.000 15.11 0.00 35.08 2.66
2941 3124 5.837979 TCTGGTGAATTCCCTTCATTTTTGA 59.162 36.000 2.27 0.00 45.36 2.69
2990 3173 1.201181 TCTTGCGCACAACAACTTTGT 59.799 42.857 11.12 0.00 44.72 2.83
3018 3201 1.153842 GCCGGCATGGTTAGCAAAC 60.154 57.895 24.80 0.00 41.21 2.93
3090 3273 2.102252 CTCTATTCCAGGTCAGCTCACC 59.898 54.545 0.00 0.00 36.58 4.02
3196 3379 4.927267 ATGATACAGGAGGACCAAACAA 57.073 40.909 0.00 0.00 38.94 2.83
3288 3474 4.286297 TGACAGCTTAGCAGTGGTAATT 57.714 40.909 14.80 4.61 0.00 1.40
3317 3503 3.059352 AGACCTTGATTACACCAGCAC 57.941 47.619 0.00 0.00 0.00 4.40
3492 3678 0.322636 TGGAGTCTCTCGACCTGTCC 60.323 60.000 0.00 0.00 41.16 4.02
3513 3699 2.370281 TCAATGAACTCTCTGGCGAC 57.630 50.000 0.00 0.00 0.00 5.19
3516 3702 2.593346 ATGAACTCTCTGGCGACATC 57.407 50.000 0.00 0.00 41.51 3.06
3522 3708 1.144936 CTCTGGCGACATCCCTTCC 59.855 63.158 0.00 0.00 41.51 3.46
3559 3745 5.005740 TCATGATGTTAAGCAAGCTGAACT 58.994 37.500 20.01 8.39 38.06 3.01
3600 3786 8.221058 TTTCAGGAAGAATACCCTCAGGGAAC 62.221 46.154 20.10 4.36 39.83 3.62
3661 3847 2.027192 GGCAACAACTATCTCTGTGGGA 60.027 50.000 0.00 0.00 0.00 4.37
3846 4035 1.007734 CGGAGCAATGCCATCATGC 60.008 57.895 0.00 0.00 32.23 4.06
3963 4152 1.394917 GGAACTAGCGTTGATGCAGTG 59.605 52.381 0.00 0.00 37.31 3.66
4002 4191 3.829044 GCCATGCCATTGCGCTCA 61.829 61.111 9.73 0.00 41.78 4.26
4028 4217 0.112995 TTGCCTGAAGGATTGGTGCT 59.887 50.000 0.00 0.00 37.39 4.40
4159 4348 9.260002 GATGTTGTGATTTGGACAGTTTAAAAT 57.740 29.630 0.00 0.00 0.00 1.82
4168 4358 8.423906 TTTGGACAGTTTAAAATATAAGGGCA 57.576 30.769 0.00 0.00 0.00 5.36
4353 4623 6.849305 CGGTGTTGTTGTCTAAATAGTTTCAC 59.151 38.462 0.00 0.00 0.00 3.18
4355 4625 9.048446 GGTGTTGTTGTCTAAATAGTTTCACTA 57.952 33.333 0.00 0.00 34.82 2.74
4413 4684 9.464248 CGCTTTTATTGATTATTTTCAAGTTGC 57.536 29.630 0.00 0.00 38.90 4.17
4441 4712 8.718102 ATGTTATAGATGGTGTTGTCAAGTAC 57.282 34.615 0.00 0.00 0.00 2.73
4442 4713 7.903145 TGTTATAGATGGTGTTGTCAAGTACT 58.097 34.615 0.00 0.00 0.00 2.73
4443 4714 8.033038 TGTTATAGATGGTGTTGTCAAGTACTC 58.967 37.037 0.00 0.00 0.00 2.59
4444 4715 4.273148 AGATGGTGTTGTCAAGTACTCC 57.727 45.455 0.00 0.00 0.00 3.85
4445 4716 2.922740 TGGTGTTGTCAAGTACTCCC 57.077 50.000 0.00 0.00 0.00 4.30
4446 4717 2.404559 TGGTGTTGTCAAGTACTCCCT 58.595 47.619 0.00 0.00 0.00 4.20
4447 4718 2.367567 TGGTGTTGTCAAGTACTCCCTC 59.632 50.000 0.00 0.00 0.00 4.30
4448 4719 2.289506 GGTGTTGTCAAGTACTCCCTCC 60.290 54.545 0.00 0.00 0.00 4.30
4449 4720 1.616865 TGTTGTCAAGTACTCCCTCCG 59.383 52.381 0.00 0.00 0.00 4.63
4450 4721 1.617357 GTTGTCAAGTACTCCCTCCGT 59.383 52.381 0.00 0.00 0.00 4.69
4451 4722 2.005370 TGTCAAGTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
4452 4723 1.891150 TGTCAAGTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
4453 4724 1.135460 GTCAAGTACTCCCTCCGTTCG 60.135 57.143 0.00 0.00 0.00 3.95
4454 4725 0.172803 CAAGTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
4455 4726 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
4456 4727 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
4457 4728 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
4458 4729 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
4459 4730 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
4460 4731 1.755380 ACTCCCTCCGTTCGGAATTAG 59.245 52.381 14.79 13.09 33.41 1.73
4461 4732 1.755380 CTCCCTCCGTTCGGAATTAGT 59.245 52.381 14.79 0.00 33.41 2.24
4462 4733 2.167900 CTCCCTCCGTTCGGAATTAGTT 59.832 50.000 14.79 0.00 33.41 2.24
4463 4734 2.093869 TCCCTCCGTTCGGAATTAGTTG 60.094 50.000 14.79 1.97 33.41 3.16
4464 4735 2.354403 CCCTCCGTTCGGAATTAGTTGT 60.354 50.000 14.79 0.00 33.41 3.32
4465 4736 2.928116 CCTCCGTTCGGAATTAGTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
4466 4737 2.597305 CTCCGTTCGGAATTAGTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
4467 4738 1.060122 CCGTTCGGAATTAGTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
4468 4739 1.722464 CGTTCGGAATTAGTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
4469 4740 2.156117 CGTTCGGAATTAGTTGTCGCAA 59.844 45.455 0.00 0.00 0.00 4.85
4470 4741 3.363182 CGTTCGGAATTAGTTGTCGCAAA 60.363 43.478 0.00 0.00 0.00 3.68
4471 4742 4.529446 GTTCGGAATTAGTTGTCGCAAAA 58.471 39.130 0.00 0.00 0.00 2.44
4472 4743 4.815040 TCGGAATTAGTTGTCGCAAAAA 57.185 36.364 0.00 0.00 0.00 1.94
4473 4744 5.365403 TCGGAATTAGTTGTCGCAAAAAT 57.635 34.783 0.00 0.00 0.00 1.82
4474 4745 5.150683 TCGGAATTAGTTGTCGCAAAAATG 58.849 37.500 0.00 0.00 0.00 2.32
4475 4746 4.323336 CGGAATTAGTTGTCGCAAAAATGG 59.677 41.667 0.00 0.00 0.00 3.16
4476 4747 5.465935 GGAATTAGTTGTCGCAAAAATGGA 58.534 37.500 0.00 0.00 0.00 3.41
4477 4748 6.099341 GGAATTAGTTGTCGCAAAAATGGAT 58.901 36.000 0.00 0.00 0.00 3.41
4478 4749 7.254852 GGAATTAGTTGTCGCAAAAATGGATA 58.745 34.615 0.00 0.00 0.00 2.59
4479 4750 7.757624 GGAATTAGTTGTCGCAAAAATGGATAA 59.242 33.333 0.00 0.00 0.00 1.75
4480 4751 9.134734 GAATTAGTTGTCGCAAAAATGGATAAA 57.865 29.630 0.00 0.00 0.00 1.40
4481 4752 8.687824 ATTAGTTGTCGCAAAAATGGATAAAG 57.312 30.769 0.00 0.00 0.00 1.85
4482 4753 6.084326 AGTTGTCGCAAAAATGGATAAAGT 57.916 33.333 0.00 0.00 0.00 2.66
4483 4754 6.512297 AGTTGTCGCAAAAATGGATAAAGTT 58.488 32.000 0.00 0.00 0.00 2.66
4484 4755 6.420604 AGTTGTCGCAAAAATGGATAAAGTTG 59.579 34.615 0.00 0.00 0.00 3.16
4485 4756 5.226396 TGTCGCAAAAATGGATAAAGTTGG 58.774 37.500 0.00 0.00 0.00 3.77
4486 4757 5.010112 TGTCGCAAAAATGGATAAAGTTGGA 59.990 36.000 0.00 0.00 0.00 3.53
4487 4758 6.099341 GTCGCAAAAATGGATAAAGTTGGAT 58.901 36.000 0.00 0.00 0.00 3.41
4488 4759 6.034898 GTCGCAAAAATGGATAAAGTTGGATG 59.965 38.462 0.00 0.00 0.00 3.51
4489 4760 5.868801 CGCAAAAATGGATAAAGTTGGATGT 59.131 36.000 0.00 0.00 0.00 3.06
4490 4761 7.032580 CGCAAAAATGGATAAAGTTGGATGTA 58.967 34.615 0.00 0.00 0.00 2.29
4491 4762 7.706179 CGCAAAAATGGATAAAGTTGGATGTAT 59.294 33.333 0.00 0.00 0.00 2.29
4492 4763 9.034544 GCAAAAATGGATAAAGTTGGATGTATC 57.965 33.333 0.00 0.00 0.00 2.24
4531 4802 9.915629 ACATCTAGATACATTAATTCCTTCGAC 57.084 33.333 4.54 0.00 0.00 4.20
4532 4803 9.914131 CATCTAGATACATTAATTCCTTCGACA 57.086 33.333 4.54 0.00 0.00 4.35
4534 4805 9.967346 TCTAGATACATTAATTCCTTCGACAAG 57.033 33.333 0.00 0.00 0.00 3.16
4535 4806 9.751542 CTAGATACATTAATTCCTTCGACAAGT 57.248 33.333 0.00 0.00 0.00 3.16
4546 4817 6.939551 TCCTTCGACAAGTAATTTAGAACG 57.060 37.500 0.00 0.00 0.00 3.95
4547 4818 5.865552 TCCTTCGACAAGTAATTTAGAACGG 59.134 40.000 0.00 0.00 0.00 4.44
4548 4819 5.865552 CCTTCGACAAGTAATTTAGAACGGA 59.134 40.000 0.00 0.00 0.00 4.69
4549 4820 6.034683 CCTTCGACAAGTAATTTAGAACGGAG 59.965 42.308 0.00 0.00 0.00 4.63
4550 4821 5.404946 TCGACAAGTAATTTAGAACGGAGG 58.595 41.667 0.00 0.00 0.00 4.30
4551 4822 4.565564 CGACAAGTAATTTAGAACGGAGGG 59.434 45.833 0.00 0.00 0.00 4.30
4552 4823 5.622914 CGACAAGTAATTTAGAACGGAGGGA 60.623 44.000 0.00 0.00 0.00 4.20
4553 4824 5.731591 ACAAGTAATTTAGAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
4554 4825 5.247792 ACAAGTAATTTAGAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
4567 4839 2.094130 GGAGGGAGTACGAAGAAACCAG 60.094 54.545 0.00 0.00 0.00 4.00
4635 4907 8.655651 TGAACAAATACCTTCATTTTTGGAAC 57.344 30.769 0.00 0.00 34.23 3.62
4636 4908 8.260818 TGAACAAATACCTTCATTTTTGGAACA 58.739 29.630 0.00 0.00 34.23 3.18
4638 4910 8.606040 ACAAATACCTTCATTTTTGGAACATG 57.394 30.769 0.00 0.00 39.30 3.21
4642 4914 9.874205 AATACCTTCATTTTTGGAACATGTATG 57.126 29.630 0.00 0.00 39.30 2.39
4653 4925 9.559732 TTTTGGAACATGTATGTATCCTAGATG 57.440 33.333 13.37 0.00 40.80 2.90
4655 4927 6.498303 TGGAACATGTATGTATCCTAGATGCT 59.502 38.462 13.37 0.00 40.80 3.79
4662 4934 3.092301 TGTATCCTAGATGCTGGATCCG 58.908 50.000 7.39 3.14 41.67 4.18
4663 4935 2.317371 ATCCTAGATGCTGGATCCGT 57.683 50.000 7.39 0.00 38.60 4.69
4680 4952 7.120051 TGGATCCGTCTAAATAATTTGGGAAA 58.880 34.615 7.39 0.00 0.00 3.13
4717 4989 8.570068 TTTTCTAGTTTTTGTCCTAGTTGTGT 57.430 30.769 0.00 0.00 33.81 3.72
4718 4990 7.781548 TTCTAGTTTTTGTCCTAGTTGTGTC 57.218 36.000 0.00 0.00 33.81 3.67
4730 5002 6.146347 GTCCTAGTTGTGTCATGAAGAAACTC 59.854 42.308 16.99 4.73 35.36 3.01
4733 5005 4.274459 AGTTGTGTCATGAAGAAACTCAGC 59.726 41.667 0.00 0.00 35.36 4.26
4736 5008 3.812053 GTGTCATGAAGAAACTCAGCACT 59.188 43.478 0.00 0.00 31.33 4.40
4753 5025 1.550524 CACTTGTCCTAGCTAGCCACA 59.449 52.381 15.74 15.96 0.00 4.17
4876 5148 5.164158 GCAACGACTTTGAATTAGTGCATTG 60.164 40.000 0.00 0.00 37.39 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 0.889186 AGTCATGACGGCAACAACCC 60.889 55.000 19.85 0.00 36.20 4.11
104 105 1.872952 CTGAAGTCATGACGGCAACAA 59.127 47.619 19.85 2.77 36.20 2.83
129 130 7.923344 ACCTATCAGATAGAGAAAAATGTGTCG 59.077 37.037 17.91 0.10 34.77 4.35
162 163 3.510719 GCAAGCTGACAAACAAGTCAAA 58.489 40.909 0.00 0.00 46.90 2.69
238 239 0.107508 CGGACGGAGGGAGTACTGTA 60.108 60.000 0.00 0.00 0.00 2.74
241 242 2.439883 GCGGACGGAGGGAGTACT 60.440 66.667 0.00 0.00 0.00 2.73
242 243 1.880819 TTTGCGGACGGAGGGAGTAC 61.881 60.000 0.00 0.00 0.00 2.73
243 244 0.974010 ATTTGCGGACGGAGGGAGTA 60.974 55.000 0.00 0.00 0.00 2.59
244 245 0.974010 TATTTGCGGACGGAGGGAGT 60.974 55.000 0.00 0.00 0.00 3.85
245 246 0.529992 GTATTTGCGGACGGAGGGAG 60.530 60.000 0.00 0.00 0.00 4.30
246 247 0.974010 AGTATTTGCGGACGGAGGGA 60.974 55.000 0.00 0.00 0.00 4.20
247 248 0.107848 AAGTATTTGCGGACGGAGGG 60.108 55.000 0.00 0.00 0.00 4.30
248 249 1.006832 CAAGTATTTGCGGACGGAGG 58.993 55.000 0.00 0.00 0.00 4.30
249 250 1.659098 GACAAGTATTTGCGGACGGAG 59.341 52.381 0.00 0.00 37.85 4.63
250 251 1.673626 GGACAAGTATTTGCGGACGGA 60.674 52.381 0.00 0.00 37.85 4.69
251 252 0.725117 GGACAAGTATTTGCGGACGG 59.275 55.000 0.00 0.00 37.85 4.79
252 253 1.659098 GAGGACAAGTATTTGCGGACG 59.341 52.381 0.00 0.00 37.85 4.79
253 254 1.659098 CGAGGACAAGTATTTGCGGAC 59.341 52.381 0.00 0.00 37.85 4.79
254 255 1.546923 TCGAGGACAAGTATTTGCGGA 59.453 47.619 0.00 0.00 37.85 5.54
255 256 2.004583 TCGAGGACAAGTATTTGCGG 57.995 50.000 0.00 0.00 37.85 5.69
256 257 4.334443 CATTTCGAGGACAAGTATTTGCG 58.666 43.478 0.00 0.00 37.85 4.85
257 258 4.156008 ACCATTTCGAGGACAAGTATTTGC 59.844 41.667 0.00 0.00 37.85 3.68
258 259 5.880054 ACCATTTCGAGGACAAGTATTTG 57.120 39.130 0.00 0.00 40.24 2.32
259 260 5.768164 ACAACCATTTCGAGGACAAGTATTT 59.232 36.000 0.00 0.00 0.00 1.40
260 261 5.313712 ACAACCATTTCGAGGACAAGTATT 58.686 37.500 0.00 0.00 0.00 1.89
261 262 4.906618 ACAACCATTTCGAGGACAAGTAT 58.093 39.130 0.00 0.00 0.00 2.12
262 263 4.345859 ACAACCATTTCGAGGACAAGTA 57.654 40.909 0.00 0.00 0.00 2.24
263 264 3.208747 ACAACCATTTCGAGGACAAGT 57.791 42.857 0.00 0.00 0.00 3.16
264 265 5.178797 AGATACAACCATTTCGAGGACAAG 58.821 41.667 0.00 0.00 0.00 3.16
265 266 5.160607 AGATACAACCATTTCGAGGACAA 57.839 39.130 0.00 0.00 0.00 3.18
266 267 4.819105 AGATACAACCATTTCGAGGACA 57.181 40.909 0.00 0.00 0.00 4.02
267 268 5.978322 GTCTAGATACAACCATTTCGAGGAC 59.022 44.000 0.00 0.00 0.00 3.85
268 269 5.892119 AGTCTAGATACAACCATTTCGAGGA 59.108 40.000 0.00 0.00 0.00 3.71
269 270 6.150396 AGTCTAGATACAACCATTTCGAGG 57.850 41.667 0.00 0.00 0.00 4.63
270 271 9.751542 AATAAGTCTAGATACAACCATTTCGAG 57.248 33.333 0.00 0.00 0.00 4.04
318 319 9.274206 GGAAATACTTGTCCTAGAAATGGATAC 57.726 37.037 0.00 0.00 35.87 2.24
319 320 8.148351 CGGAAATACTTGTCCTAGAAATGGATA 58.852 37.037 0.00 0.00 35.87 2.59
320 321 6.992715 CGGAAATACTTGTCCTAGAAATGGAT 59.007 38.462 0.00 0.00 35.87 3.41
321 322 6.346096 CGGAAATACTTGTCCTAGAAATGGA 58.654 40.000 0.00 0.00 0.00 3.41
322 323 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
323 324 6.258068 GTCCGGAAATACTTGTCCTAGAAATG 59.742 42.308 5.23 0.00 0.00 2.32
324 325 6.346896 GTCCGGAAATACTTGTCCTAGAAAT 58.653 40.000 5.23 0.00 0.00 2.17
325 326 5.622914 CGTCCGGAAATACTTGTCCTAGAAA 60.623 44.000 5.23 0.00 0.00 2.52
326 327 4.142315 CGTCCGGAAATACTTGTCCTAGAA 60.142 45.833 5.23 0.00 0.00 2.10
327 328 3.379372 CGTCCGGAAATACTTGTCCTAGA 59.621 47.826 5.23 0.00 0.00 2.43
328 329 3.379372 TCGTCCGGAAATACTTGTCCTAG 59.621 47.826 5.23 0.00 0.00 3.02
329 330 3.355378 TCGTCCGGAAATACTTGTCCTA 58.645 45.455 5.23 0.00 0.00 2.94
330 331 2.173519 TCGTCCGGAAATACTTGTCCT 58.826 47.619 5.23 0.00 0.00 3.85
331 332 2.660189 TCGTCCGGAAATACTTGTCC 57.340 50.000 5.23 0.00 0.00 4.02
332 333 2.928116 CCTTCGTCCGGAAATACTTGTC 59.072 50.000 5.23 0.00 33.34 3.18
333 334 2.354403 CCCTTCGTCCGGAAATACTTGT 60.354 50.000 5.23 0.00 33.34 3.16
334 335 2.093869 TCCCTTCGTCCGGAAATACTTG 60.094 50.000 5.23 0.00 33.34 3.16
335 336 2.167900 CTCCCTTCGTCCGGAAATACTT 59.832 50.000 5.23 0.00 33.34 2.24
336 337 1.755380 CTCCCTTCGTCCGGAAATACT 59.245 52.381 5.23 0.00 33.34 2.12
337 338 1.479730 ACTCCCTTCGTCCGGAAATAC 59.520 52.381 5.23 0.00 33.34 1.89
338 339 1.856629 ACTCCCTTCGTCCGGAAATA 58.143 50.000 5.23 0.00 33.34 1.40
339 340 1.479730 GTACTCCCTTCGTCCGGAAAT 59.520 52.381 5.23 0.00 33.34 2.17
340 341 0.890683 GTACTCCCTTCGTCCGGAAA 59.109 55.000 5.23 0.00 33.34 3.13
341 342 0.967380 GGTACTCCCTTCGTCCGGAA 60.967 60.000 5.23 0.00 0.00 4.30
342 343 1.379044 GGTACTCCCTTCGTCCGGA 60.379 63.158 0.00 0.00 0.00 5.14
343 344 1.252904 TTGGTACTCCCTTCGTCCGG 61.253 60.000 0.00 0.00 0.00 5.14
344 345 0.604578 TTTGGTACTCCCTTCGTCCG 59.395 55.000 0.00 0.00 0.00 4.79
345 346 1.622312 ACTTTGGTACTCCCTTCGTCC 59.378 52.381 0.00 0.00 0.00 4.79
346 347 3.064931 CAACTTTGGTACTCCCTTCGTC 58.935 50.000 0.00 0.00 0.00 4.20
347 348 2.701951 TCAACTTTGGTACTCCCTTCGT 59.298 45.455 0.00 0.00 0.00 3.85
348 349 3.064931 GTCAACTTTGGTACTCCCTTCG 58.935 50.000 0.00 0.00 0.00 3.79
349 350 4.353383 AGTCAACTTTGGTACTCCCTTC 57.647 45.455 0.00 0.00 0.00 3.46
350 351 4.461198 CAAGTCAACTTTGGTACTCCCTT 58.539 43.478 0.00 0.00 33.11 3.95
351 352 3.181443 CCAAGTCAACTTTGGTACTCCCT 60.181 47.826 0.00 0.00 33.11 4.20
352 353 3.146847 CCAAGTCAACTTTGGTACTCCC 58.853 50.000 0.00 0.00 33.11 4.30
353 354 3.816994 ACCAAGTCAACTTTGGTACTCC 58.183 45.455 7.82 0.00 36.39 3.85
354 355 6.930667 TTTACCAAGTCAACTTTGGTACTC 57.069 37.500 14.54 0.00 38.30 2.59
397 398 3.564264 GGAGGGAGTACTACTTTCCGAT 58.436 50.000 4.77 0.00 30.55 4.18
399 400 1.674962 CGGAGGGAGTACTACTTTCCG 59.325 57.143 26.22 26.22 39.10 4.30
426 513 5.710099 AGTCTGAACAGAAACTTGGTCAAAA 59.290 36.000 6.08 0.00 43.71 2.44
592 679 9.810545 TTTGAAAAGTCAAACCTTAATTTCGAT 57.189 25.926 0.00 0.00 46.48 3.59
629 719 3.832490 CCCTCCGTTCCATCATATAGTGA 59.168 47.826 0.00 0.00 42.06 3.41
638 728 3.764218 TCTATACTCCCTCCGTTCCATC 58.236 50.000 0.00 0.00 0.00 3.51
731 829 5.593095 AGACTAGTGCGACAGATTACCAATA 59.407 40.000 0.00 0.00 0.00 1.90
774 872 3.498774 AGACTGTGTTGAATGAAGGCT 57.501 42.857 0.00 0.00 0.00 4.58
791 889 2.483876 TGTGTTGACTTGCAGCTAGAC 58.516 47.619 11.12 5.11 0.00 2.59
923 1023 2.711895 AGCTCTGGCCCTGATATAGT 57.288 50.000 0.00 0.00 39.73 2.12
924 1024 2.902486 TGAAGCTCTGGCCCTGATATAG 59.098 50.000 0.00 0.00 39.73 1.31
925 1025 2.976440 TGAAGCTCTGGCCCTGATATA 58.024 47.619 0.00 0.00 39.73 0.86
926 1026 1.811778 TGAAGCTCTGGCCCTGATAT 58.188 50.000 0.00 0.00 39.73 1.63
927 1027 1.811778 ATGAAGCTCTGGCCCTGATA 58.188 50.000 0.00 0.00 39.73 2.15
929 1029 1.811778 ATATGAAGCTCTGGCCCTGA 58.188 50.000 0.00 0.00 39.73 3.86
930 1030 2.228059 CAATATGAAGCTCTGGCCCTG 58.772 52.381 0.00 0.00 39.73 4.45
931 1031 1.478288 GCAATATGAAGCTCTGGCCCT 60.478 52.381 0.00 0.00 39.73 5.19
932 1032 0.957362 GCAATATGAAGCTCTGGCCC 59.043 55.000 0.00 0.00 39.73 5.80
946 1046 2.035961 GCTCTGAGGACGTATGGCAATA 59.964 50.000 6.83 0.00 0.00 1.90
952 1052 0.817654 TGGTGCTCTGAGGACGTATG 59.182 55.000 20.74 0.00 37.44 2.39
982 1082 8.789762 ACTCGCCATTATTTTTGTTTTACTACT 58.210 29.630 0.00 0.00 0.00 2.57
983 1083 8.959734 ACTCGCCATTATTTTTGTTTTACTAC 57.040 30.769 0.00 0.00 0.00 2.73
1007 1107 1.152383 GGATACCGGAGCTGCGAAAC 61.152 60.000 30.34 14.62 0.00 2.78
1116 1257 1.308069 CCTCCTTTGTGATGCACCCG 61.308 60.000 0.00 0.00 32.73 5.28
1129 1270 3.322466 CAGTGCGTCCCCCTCCTT 61.322 66.667 0.00 0.00 0.00 3.36
1135 1276 3.537206 AAGACAGCAGTGCGTCCCC 62.537 63.158 25.84 10.74 34.52 4.81
1140 1281 0.788995 CTCTGAAAGACAGCAGTGCG 59.211 55.000 10.00 7.44 45.38 5.34
1208 1380 1.375098 GCTCCACTGGCAGCAATCTC 61.375 60.000 15.89 0.00 35.56 2.75
1310 1482 3.674997 TGAGGATTTTCACTGTACCAGC 58.325 45.455 0.00 0.00 34.37 4.85
1327 1499 0.394216 TTCCCACGCATTCCATGAGG 60.394 55.000 0.00 0.00 34.14 3.86
1411 1583 1.210204 ATGGGCACATCCACTCCACT 61.210 55.000 0.00 0.00 39.97 4.00
1435 1607 1.281925 TGGAGGGAGCCCAAGAATCC 61.282 60.000 8.53 6.11 38.92 3.01
1621 1802 3.067833 AGTCGAGAAACCTTAGCAAAGC 58.932 45.455 0.00 0.00 0.00 3.51
1642 1823 5.011635 TGGCACTAAGATTCACACTAGTCAA 59.988 40.000 0.00 0.00 0.00 3.18
1694 1875 6.081049 CGAAGGACTCTTAGATTGTATAGCG 58.919 44.000 0.00 0.00 32.52 4.26
1701 1882 4.927422 GGAGACGAAGGACTCTTAGATTG 58.073 47.826 0.00 0.00 35.94 2.67
1757 1938 4.093998 GTGATGTGAGGTTAGAATGCACAG 59.906 45.833 0.00 0.00 42.02 3.66
1859 2040 6.345298 TCATTATTCGTAAGGTCAAGATGCA 58.655 36.000 0.00 0.00 38.47 3.96
1887 2068 1.533338 GCATCTGGAAATGCTTCAGCG 60.533 52.381 1.74 0.00 46.81 5.18
1962 2143 4.586001 CCCAGTACTTCCGGCTTTATACTA 59.414 45.833 0.00 0.00 0.00 1.82
2094 2275 6.207221 TGACATTTGTGCAAGACATGTCTAAT 59.793 34.615 28.10 18.87 41.93 1.73
2112 2293 2.176045 GGAATTTCCCCGGTGACATTT 58.824 47.619 3.89 0.00 0.00 2.32
2262 2443 9.607333 AGATGTTCCTCTGATATAGAACCATTA 57.393 33.333 0.00 0.00 38.24 1.90
2304 2485 4.026356 AGACAAGTCCAATTCCTCCAAG 57.974 45.455 0.00 0.00 0.00 3.61
2427 2610 1.753073 CCCTTCTGCCAATTTAGCCAG 59.247 52.381 0.00 0.00 0.00 4.85
2436 2619 1.859302 AAACAACACCCTTCTGCCAA 58.141 45.000 0.00 0.00 0.00 4.52
2437 2620 2.738587 TAAACAACACCCTTCTGCCA 57.261 45.000 0.00 0.00 0.00 4.92
2532 2715 9.403110 CTGATTTGGTTAAAAGAGATGTTCAAG 57.597 33.333 0.00 0.00 0.00 3.02
2767 2950 6.992123 AGCTGACAAATATATGTTGGAATCGA 59.008 34.615 0.00 0.00 32.57 3.59
2941 3124 1.055040 ACCAACTCTGAGCAGCTCTT 58.945 50.000 23.15 6.39 0.00 2.85
3090 3273 2.550830 ACTGTAGGTGTTCAAGCTGG 57.449 50.000 0.00 0.00 37.17 4.85
3196 3379 2.719705 TCCACACTAAGGGGTTCCAAAT 59.280 45.455 0.00 0.00 43.37 2.32
3288 3474 5.007682 GTGTAATCAAGGTCTTGGCCTTTA 58.992 41.667 3.32 0.00 45.91 1.85
3492 3678 2.670414 GTCGCCAGAGAGTTCATTGAAG 59.330 50.000 0.00 0.00 0.00 3.02
3522 3708 1.025041 TCATGATGTCCGAGAGACCG 58.975 55.000 0.00 0.00 45.68 4.79
3539 3725 5.112220 CAAGTTCAGCTTGCTTAACATCA 57.888 39.130 18.12 0.00 46.68 3.07
3600 3786 1.082679 CGATGAGTGACTGCAGCTGG 61.083 60.000 17.12 1.57 0.00 4.85
3963 4152 1.135315 GCATCACACCATCACGCAC 59.865 57.895 0.00 0.00 0.00 5.34
4002 4191 0.110486 ATCCTTCAGGCAACCGTGTT 59.890 50.000 0.00 0.00 34.44 3.32
4028 4217 3.923864 ACCCACGACGAAGCTGCA 61.924 61.111 0.00 0.00 0.00 4.41
4129 4318 4.171005 CTGTCCAAATCACAACATCATGC 58.829 43.478 0.00 0.00 0.00 4.06
4168 4358 7.906327 AGGTGTGGCTTACAATCATTTTAATT 58.094 30.769 0.00 0.00 41.89 1.40
4299 4569 7.769272 AAACAGTTTAAACAACATCATGTGG 57.231 32.000 20.06 0.00 32.81 4.17
4413 4684 7.987458 ACTTGACAACACCATCTATAACATAGG 59.013 37.037 0.00 0.00 0.00 2.57
4421 4692 5.104900 GGGAGTACTTGACAACACCATCTAT 60.105 44.000 0.00 0.00 0.00 1.98
4440 4711 1.755380 CTAATTCCGAACGGAGGGAGT 59.245 52.381 15.34 4.12 46.06 3.85
4441 4712 1.755380 ACTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 14.71 46.06 4.30
4442 4713 1.856629 ACTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
4443 4714 2.277084 CAACTAATTCCGAACGGAGGG 58.723 52.381 15.34 9.70 46.06 4.30
4444 4715 2.928116 GACAACTAATTCCGAACGGAGG 59.072 50.000 15.34 10.00 46.06 4.30
4445 4716 2.597305 CGACAACTAATTCCGAACGGAG 59.403 50.000 15.34 7.27 46.06 4.63
4446 4717 2.598589 CGACAACTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
4447 4718 1.060122 GCGACAACTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
4448 4719 1.722464 TGCGACAACTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
4449 4720 3.799137 TTGCGACAACTAATTCCGAAC 57.201 42.857 0.00 0.00 0.00 3.95
4450 4721 4.815040 TTTTGCGACAACTAATTCCGAA 57.185 36.364 0.00 0.00 0.00 4.30
4451 4722 4.815040 TTTTTGCGACAACTAATTCCGA 57.185 36.364 0.00 0.00 0.00 4.55
4452 4723 4.323336 CCATTTTTGCGACAACTAATTCCG 59.677 41.667 0.00 0.00 0.00 4.30
4453 4724 5.465935 TCCATTTTTGCGACAACTAATTCC 58.534 37.500 0.00 0.00 0.00 3.01
4454 4725 8.682128 TTATCCATTTTTGCGACAACTAATTC 57.318 30.769 0.00 0.00 0.00 2.17
4455 4726 9.139174 CTTTATCCATTTTTGCGACAACTAATT 57.861 29.630 0.00 0.00 0.00 1.40
4456 4727 8.303876 ACTTTATCCATTTTTGCGACAACTAAT 58.696 29.630 0.00 0.00 0.00 1.73
4457 4728 7.653647 ACTTTATCCATTTTTGCGACAACTAA 58.346 30.769 0.00 0.00 0.00 2.24
4458 4729 7.209471 ACTTTATCCATTTTTGCGACAACTA 57.791 32.000 0.00 0.00 0.00 2.24
4459 4730 6.084326 ACTTTATCCATTTTTGCGACAACT 57.916 33.333 0.00 0.00 0.00 3.16
4460 4731 6.346518 CCAACTTTATCCATTTTTGCGACAAC 60.347 38.462 0.00 0.00 0.00 3.32
4461 4732 5.694006 CCAACTTTATCCATTTTTGCGACAA 59.306 36.000 0.00 0.00 0.00 3.18
4462 4733 5.010112 TCCAACTTTATCCATTTTTGCGACA 59.990 36.000 0.00 0.00 0.00 4.35
4463 4734 5.465935 TCCAACTTTATCCATTTTTGCGAC 58.534 37.500 0.00 0.00 0.00 5.19
4464 4735 5.713792 TCCAACTTTATCCATTTTTGCGA 57.286 34.783 0.00 0.00 0.00 5.10
4465 4736 5.868801 ACATCCAACTTTATCCATTTTTGCG 59.131 36.000 0.00 0.00 0.00 4.85
4466 4737 8.947055 ATACATCCAACTTTATCCATTTTTGC 57.053 30.769 0.00 0.00 0.00 3.68
4505 4776 9.915629 GTCGAAGGAATTAATGTATCTAGATGT 57.084 33.333 15.79 0.00 0.00 3.06
4506 4777 9.914131 TGTCGAAGGAATTAATGTATCTAGATG 57.086 33.333 15.79 0.00 0.00 2.90
4508 4779 9.967346 CTTGTCGAAGGAATTAATGTATCTAGA 57.033 33.333 0.00 0.00 0.00 2.43
4509 4780 9.751542 ACTTGTCGAAGGAATTAATGTATCTAG 57.248 33.333 0.00 0.00 32.95 2.43
4521 4792 7.064253 CCGTTCTAAATTACTTGTCGAAGGAAT 59.936 37.037 0.00 0.00 43.61 3.01
4522 4793 6.366877 CCGTTCTAAATTACTTGTCGAAGGAA 59.633 38.462 0.00 0.00 36.40 3.36
4523 4794 5.865552 CCGTTCTAAATTACTTGTCGAAGGA 59.134 40.000 0.00 0.00 32.95 3.36
4524 4795 5.865552 TCCGTTCTAAATTACTTGTCGAAGG 59.134 40.000 0.00 0.00 32.95 3.46
4525 4796 6.034683 CCTCCGTTCTAAATTACTTGTCGAAG 59.965 42.308 0.00 0.00 35.07 3.79
4526 4797 5.865552 CCTCCGTTCTAAATTACTTGTCGAA 59.134 40.000 0.00 0.00 0.00 3.71
4527 4798 5.404946 CCTCCGTTCTAAATTACTTGTCGA 58.595 41.667 0.00 0.00 0.00 4.20
4528 4799 4.565564 CCCTCCGTTCTAAATTACTTGTCG 59.434 45.833 0.00 0.00 0.00 4.35
4529 4800 5.727434 TCCCTCCGTTCTAAATTACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
4530 4801 5.247792 ACTCCCTCCGTTCTAAATTACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
4531 4802 5.731591 ACTCCCTCCGTTCTAAATTACTTG 58.268 41.667 0.00 0.00 0.00 3.16
4532 4803 6.405176 CGTACTCCCTCCGTTCTAAATTACTT 60.405 42.308 0.00 0.00 0.00 2.24
4533 4804 5.067023 CGTACTCCCTCCGTTCTAAATTACT 59.933 44.000 0.00 0.00 0.00 2.24
4534 4805 5.066505 TCGTACTCCCTCCGTTCTAAATTAC 59.933 44.000 0.00 0.00 0.00 1.89
4535 4806 5.192927 TCGTACTCCCTCCGTTCTAAATTA 58.807 41.667 0.00 0.00 0.00 1.40
4536 4807 4.019174 TCGTACTCCCTCCGTTCTAAATT 58.981 43.478 0.00 0.00 0.00 1.82
4537 4808 3.624777 TCGTACTCCCTCCGTTCTAAAT 58.375 45.455 0.00 0.00 0.00 1.40
4538 4809 3.071874 TCGTACTCCCTCCGTTCTAAA 57.928 47.619 0.00 0.00 0.00 1.85
4539 4810 2.787473 TCGTACTCCCTCCGTTCTAA 57.213 50.000 0.00 0.00 0.00 2.10
4540 4811 2.237143 TCTTCGTACTCCCTCCGTTCTA 59.763 50.000 0.00 0.00 0.00 2.10
4541 4812 1.004044 TCTTCGTACTCCCTCCGTTCT 59.996 52.381 0.00 0.00 0.00 3.01
4542 4813 1.457346 TCTTCGTACTCCCTCCGTTC 58.543 55.000 0.00 0.00 0.00 3.95
4543 4814 1.915141 TTCTTCGTACTCCCTCCGTT 58.085 50.000 0.00 0.00 0.00 4.44
4544 4815 1.543358 GTTTCTTCGTACTCCCTCCGT 59.457 52.381 0.00 0.00 0.00 4.69
4545 4816 1.135170 GGTTTCTTCGTACTCCCTCCG 60.135 57.143 0.00 0.00 0.00 4.63
4546 4817 1.897802 TGGTTTCTTCGTACTCCCTCC 59.102 52.381 0.00 0.00 0.00 4.30
4547 4818 2.561858 ACTGGTTTCTTCGTACTCCCTC 59.438 50.000 0.00 0.00 0.00 4.30
4548 4819 2.606378 ACTGGTTTCTTCGTACTCCCT 58.394 47.619 0.00 0.00 0.00 4.20
4549 4820 3.397849 AACTGGTTTCTTCGTACTCCC 57.602 47.619 0.00 0.00 0.00 4.30
4550 4821 5.746307 AAAAACTGGTTTCTTCGTACTCC 57.254 39.130 0.00 0.00 31.45 3.85
4573 4845 5.261216 AGATCCGAAATAGCAAAAGGGAAA 58.739 37.500 0.00 0.00 0.00 3.13
4576 4848 4.455606 AGAGATCCGAAATAGCAAAAGGG 58.544 43.478 0.00 0.00 0.00 3.95
4590 4862 6.756542 TGTTCAATGTAACACATAGAGATCCG 59.243 38.462 0.00 0.00 37.97 4.18
4618 4890 8.415950 ACATACATGTTCCAAAAATGAAGGTA 57.584 30.769 2.30 0.00 37.90 3.08
4635 4907 6.535963 TCCAGCATCTAGGATACATACATG 57.464 41.667 0.00 0.00 41.41 3.21
4636 4908 6.326064 GGATCCAGCATCTAGGATACATACAT 59.674 42.308 6.95 0.00 44.44 2.29
4638 4910 5.221145 CGGATCCAGCATCTAGGATACATAC 60.221 48.000 13.41 0.00 44.11 2.39
4642 4914 3.093057 ACGGATCCAGCATCTAGGATAC 58.907 50.000 13.41 0.00 44.44 2.24
4652 4924 5.530915 CCAAATTATTTAGACGGATCCAGCA 59.469 40.000 13.41 0.00 0.00 4.41
4653 4925 5.048713 CCCAAATTATTTAGACGGATCCAGC 60.049 44.000 13.41 2.31 0.00 4.85
4655 4927 6.255294 TCCCAAATTATTTAGACGGATCCA 57.745 37.500 13.41 0.00 0.00 3.41
4662 4934 7.062956 CGCCTTTGTTTCCCAAATTATTTAGAC 59.937 37.037 0.00 0.00 42.02 2.59
4663 4935 7.093992 CGCCTTTGTTTCCCAAATTATTTAGA 58.906 34.615 0.00 0.00 42.02 2.10
4680 4952 2.514803 ACTAGAAAATGGCGCCTTTGT 58.485 42.857 29.70 23.13 0.00 2.83
4686 4958 3.673338 GGACAAAAACTAGAAAATGGCGC 59.327 43.478 0.00 0.00 0.00 6.53
4717 4989 4.454678 ACAAGTGCTGAGTTTCTTCATGA 58.545 39.130 0.00 0.00 0.00 3.07
4718 4990 4.320057 GGACAAGTGCTGAGTTTCTTCATG 60.320 45.833 0.00 0.00 0.00 3.07
4730 5002 1.472376 GGCTAGCTAGGACAAGTGCTG 60.472 57.143 22.10 0.00 37.02 4.41
4733 5005 1.550524 TGTGGCTAGCTAGGACAAGTG 59.449 52.381 22.10 0.00 0.00 3.16
4736 5008 1.486310 CCATGTGGCTAGCTAGGACAA 59.514 52.381 22.10 0.00 0.00 3.18
4768 5040 5.086104 TGGATGAAGCTAGAACAAGTACC 57.914 43.478 0.00 0.00 0.00 3.34
4838 5110 0.933097 CGTTGCTCATCTCGGAATGG 59.067 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.