Multiple sequence alignment - TraesCS3B01G137600

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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 TraesCS3B01G137600 chr3B 100.000 3440 0 0 1 3440 123032316 123035755 0.000000e+00 6353.0
1 TraesCS3B01G137600 chr3B 91.154 1413 113 4 1030 2433 122826287 122827696 0.000000e+00 1906.0
2 TraesCS3B01G137600 chr3B 86.513 608 69 8 2755 3353 551512341 551511738 0.000000e+00 656.0
3 TraesCS3B01G137600 chr3B 100.000 46 0 0 3222 3267 123035586 123035631 6.120000e-13 86.1
4 TraesCS3B01G137600 chr3D 93.333 2085 92 25 655 2705 75961751 75963822 0.000000e+00 3037.0
5 TraesCS3B01G137600 chr3D 92.449 1417 92 9 1030 2434 75946814 75948227 0.000000e+00 2010.0
6 TraesCS3B01G137600 chr3D 88.000 225 24 2 424 646 75961338 75961561 2.630000e-66 263.0
7 TraesCS3B01G137600 chr3D 87.324 142 11 4 15 150 75960967 75961107 4.600000e-34 156.0
8 TraesCS3B01G137600 chr3A 91.643 2082 106 32 657 2705 90363739 90365785 0.000000e+00 2819.0
9 TraesCS3B01G137600 chr3A 92.406 1409 100 4 1029 2433 90293326 90294731 0.000000e+00 2002.0
10 TraesCS3B01G137600 chr3A 88.312 231 16 9 2 223 90305704 90305932 2.040000e-67 267.0
11 TraesCS3B01G137600 chr3A 97.727 44 1 0 3224 3267 110131640 110131683 3.680000e-10 76.8
12 TraesCS3B01G137600 chr6B 85.130 1419 169 24 1042 2433 6213365 6211962 0.000000e+00 1413.0
13 TraesCS3B01G137600 chr6B 88.218 696 68 11 2755 3440 184631056 184630365 0.000000e+00 819.0
14 TraesCS3B01G137600 chr6D 84.262 915 108 18 1601 2481 3038419 3037507 0.000000e+00 859.0
15 TraesCS3B01G137600 chr6D 86.182 702 77 16 2752 3439 23078143 23078838 0.000000e+00 741.0
16 TraesCS3B01G137600 chr6D 84.211 570 61 13 1042 1609 3040178 3039636 8.460000e-146 527.0
17 TraesCS3B01G137600 chr6D 95.455 44 2 0 3224 3267 445155059 445155102 1.710000e-08 71.3
18 TraesCS3B01G137600 chr1B 89.240 697 62 10 2753 3440 301818060 301817368 0.000000e+00 859.0
19 TraesCS3B01G137600 chr1B 87.216 704 70 14 2750 3440 577676183 577676879 0.000000e+00 784.0
20 TraesCS3B01G137600 chr1B 86.913 703 72 14 2753 3440 61022782 61023479 0.000000e+00 771.0
21 TraesCS3B01G137600 chr1B 78.342 374 73 7 2028 2398 180406912 180407280 5.740000e-58 235.0
22 TraesCS3B01G137600 chr5B 88.698 699 65 9 2752 3440 382570606 382571300 0.000000e+00 841.0
23 TraesCS3B01G137600 chr5B 87.925 588 59 11 2860 3440 398343674 398344256 0.000000e+00 682.0
24 TraesCS3B01G137600 chr7B 87.500 696 73 11 2753 3439 203857781 203858471 0.000000e+00 791.0
25 TraesCS3B01G137600 chr4B 87.626 695 67 13 2758 3440 671847521 671846834 0.000000e+00 789.0
26 TraesCS3B01G137600 chr2D 87.356 696 73 14 2755 3440 364968814 364969504 0.000000e+00 784.0
27 TraesCS3B01G137600 chr2D 85.980 699 79 13 2755 3440 641011982 641012674 0.000000e+00 730.0
28 TraesCS3B01G137600 chr5D 86.390 698 79 11 2755 3440 503735853 503735160 0.000000e+00 749.0
29 TraesCS3B01G137600 chr5D 86.815 584 63 9 2866 3440 225855566 225854988 1.040000e-179 640.0
30 TraesCS3B01G137600 chr5D 95.455 44 2 0 3224 3267 45674783 45674826 1.710000e-08 71.3
31 TraesCS3B01G137600 chr5D 95.455 44 2 0 3224 3267 216061971 216062014 1.710000e-08 71.3
32 TraesCS3B01G137600 chr5D 97.222 36 1 0 2126 2161 542107239 542107274 1.030000e-05 62.1
33 TraesCS3B01G137600 chr7D 86.305 701 73 14 2755 3439 536607134 536607827 0.000000e+00 741.0
34 TraesCS3B01G137600 chr7D 83.103 651 83 20 2805 3440 434164659 434164021 4.980000e-158 568.0
35 TraesCS3B01G137600 chr7D 83.721 172 28 0 2065 2236 454379292 454379463 2.750000e-36 163.0
36 TraesCS3B01G137600 chr7A 85.429 700 85 15 2751 3440 681395231 681394539 0.000000e+00 712.0
37 TraesCS3B01G137600 chr7A 97.727 44 1 0 3224 3267 663765352 663765309 3.680000e-10 76.8
38 TraesCS3B01G137600 chr4D 85.349 703 81 18 2753 3440 72716146 72715451 0.000000e+00 708.0
39 TraesCS3B01G137600 chr1A 80.175 343 64 4 2058 2398 130150325 130150665 1.580000e-63 254.0
40 TraesCS3B01G137600 chr1D 77.778 378 79 5 2059 2433 118511595 118511970 9.600000e-56 228.0
41 TraesCS3B01G137600 chr1D 95.455 44 2 0 3224 3267 59103671 59103714 1.710000e-08 71.3
42 TraesCS3B01G137600 chr1D 95.455 44 2 0 3224 3267 409809867 409809910 1.710000e-08 71.3
43 TraesCS3B01G137600 chr2A 77.333 150 30 4 1376 1523 719204958 719205105 6.120000e-13 86.1
44 TraesCS3B01G137600 chr2B 76.623 154 31 5 1376 1527 705327789 705327639 2.850000e-11 80.5
45 TraesCS3B01G137600 chrUn 97.727 44 1 0 3224 3267 319323815 319323858 3.680000e-10 76.8


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 TraesCS3B01G137600 chr3B 123032316 123035755 3439 False 3219.55 6353 100.000000 1 3440 2 chr3B.!!$F2 3439
1 TraesCS3B01G137600 chr3B 122826287 122827696 1409 False 1906.00 1906 91.154000 1030 2433 1 chr3B.!!$F1 1403
2 TraesCS3B01G137600 chr3B 551511738 551512341 603 True 656.00 656 86.513000 2755 3353 1 chr3B.!!$R1 598
3 TraesCS3B01G137600 chr3D 75946814 75948227 1413 False 2010.00 2010 92.449000 1030 2434 1 chr3D.!!$F1 1404
4 TraesCS3B01G137600 chr3D 75960967 75963822 2855 False 1152.00 3037 89.552333 15 2705 3 chr3D.!!$F2 2690
5 TraesCS3B01G137600 chr3A 90363739 90365785 2046 False 2819.00 2819 91.643000 657 2705 1 chr3A.!!$F3 2048
6 TraesCS3B01G137600 chr3A 90293326 90294731 1405 False 2002.00 2002 92.406000 1029 2433 1 chr3A.!!$F1 1404
7 TraesCS3B01G137600 chr6B 6211962 6213365 1403 True 1413.00 1413 85.130000 1042 2433 1 chr6B.!!$R1 1391
8 TraesCS3B01G137600 chr6B 184630365 184631056 691 True 819.00 819 88.218000 2755 3440 1 chr6B.!!$R2 685
9 TraesCS3B01G137600 chr6D 23078143 23078838 695 False 741.00 741 86.182000 2752 3439 1 chr6D.!!$F1 687
10 TraesCS3B01G137600 chr6D 3037507 3040178 2671 True 693.00 859 84.236500 1042 2481 2 chr6D.!!$R1 1439
11 TraesCS3B01G137600 chr1B 301817368 301818060 692 True 859.00 859 89.240000 2753 3440 1 chr1B.!!$R1 687
12 TraesCS3B01G137600 chr1B 577676183 577676879 696 False 784.00 784 87.216000 2750 3440 1 chr1B.!!$F3 690
13 TraesCS3B01G137600 chr1B 61022782 61023479 697 False 771.00 771 86.913000 2753 3440 1 chr1B.!!$F1 687
14 TraesCS3B01G137600 chr5B 382570606 382571300 694 False 841.00 841 88.698000 2752 3440 1 chr5B.!!$F1 688
15 TraesCS3B01G137600 chr5B 398343674 398344256 582 False 682.00 682 87.925000 2860 3440 1 chr5B.!!$F2 580
16 TraesCS3B01G137600 chr7B 203857781 203858471 690 False 791.00 791 87.500000 2753 3439 1 chr7B.!!$F1 686
17 TraesCS3B01G137600 chr4B 671846834 671847521 687 True 789.00 789 87.626000 2758 3440 1 chr4B.!!$R1 682
18 TraesCS3B01G137600 chr2D 364968814 364969504 690 False 784.00 784 87.356000 2755 3440 1 chr2D.!!$F1 685
19 TraesCS3B01G137600 chr2D 641011982 641012674 692 False 730.00 730 85.980000 2755 3440 1 chr2D.!!$F2 685
20 TraesCS3B01G137600 chr5D 503735160 503735853 693 True 749.00 749 86.390000 2755 3440 1 chr5D.!!$R2 685
21 TraesCS3B01G137600 chr5D 225854988 225855566 578 True 640.00 640 86.815000 2866 3440 1 chr5D.!!$R1 574
22 TraesCS3B01G137600 chr7D 536607134 536607827 693 False 741.00 741 86.305000 2755 3439 1 chr7D.!!$F2 684
23 TraesCS3B01G137600 chr7D 434164021 434164659 638 True 568.00 568 83.103000 2805 3440 1 chr7D.!!$R1 635
24 TraesCS3B01G137600 chr7A 681394539 681395231 692 True 712.00 712 85.429000 2751 3440 1 chr7A.!!$R2 689
25 TraesCS3B01G137600 chr4D 72715451 72716146 695 True 708.00 708 85.349000 2753 3440 1 chr4D.!!$R1 687

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
266 359 0.036164 TTGCCAGTACTGCCAATCGT 59.964 50.0 14.88 0.0 0.00 3.73 F
418 511 0.108138 GTTGGTGACAGATCGGGAGG 60.108 60.0 0.00 0.0 44.54 4.30 F
558 651 0.601558 AGCACTGCATCTTTGGCTTG 59.398 50.0 3.30 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 3246 1.890979 CCATCGCATCAGGCTCCAC 60.891 63.158 0.00 0.00 41.67 4.02 R
1863 3395 1.923395 CTCCAGGTACCCCTTGCCA 60.923 63.158 8.74 0.00 39.89 4.92 R
2520 4099 0.882474 GGACACAGTACTGCTCGAGT 59.118 55.000 22.90 13.04 38.88 4.18 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
58 62 8.669946 AAAACAAAGAAAACAGAAAAAGGTGA 57.330 26.923 0.00 0.00 0.00 4.02
59 63 8.669946 AAACAAAGAAAACAGAAAAAGGTGAA 57.330 26.923 0.00 0.00 0.00 3.18
60 64 7.889589 ACAAAGAAAACAGAAAAAGGTGAAG 57.110 32.000 0.00 0.00 0.00 3.02
62 66 8.147704 ACAAAGAAAACAGAAAAAGGTGAAGAA 58.852 29.630 0.00 0.00 0.00 2.52
66 70 9.725019 AGAAAACAGAAAAAGGTGAAGAAAAAT 57.275 25.926 0.00 0.00 0.00 1.82
69 73 8.846943 AACAGAAAAAGGTGAAGAAAAATTGT 57.153 26.923 0.00 0.00 0.00 2.71
70 74 8.846943 ACAGAAAAAGGTGAAGAAAAATTGTT 57.153 26.923 0.00 0.00 0.00 2.83
92 97 7.799784 TGTTTCTTTTACCTTAAGTATGTCGC 58.200 34.615 0.97 0.00 0.00 5.19
125 130 4.188462 TCATCACGAACTCAACACAAAGT 58.812 39.130 0.00 0.00 0.00 2.66
135 140 1.745087 CAACACAAAGTGCAGTGGACT 59.255 47.619 12.08 12.08 39.99 3.85
150 155 1.475280 TGGACTGCGTCGCTATAAACT 59.525 47.619 19.50 0.00 32.65 2.66
152 157 3.317149 TGGACTGCGTCGCTATAAACTAT 59.683 43.478 19.50 0.00 32.65 2.12
167 260 4.929146 AAACTATCTAGCAAACCCAGGT 57.071 40.909 0.00 0.00 0.00 4.00
169 262 4.489306 ACTATCTAGCAAACCCAGGTTC 57.511 45.455 1.78 0.00 37.35 3.62
170 263 3.844211 ACTATCTAGCAAACCCAGGTTCA 59.156 43.478 1.78 0.00 37.35 3.18
171 264 3.806949 ATCTAGCAAACCCAGGTTCAA 57.193 42.857 1.78 0.00 37.35 2.69
197 290 1.464997 GGCTTCGAGACACAACAATCC 59.535 52.381 0.00 0.00 0.00 3.01
234 327 1.138883 GAGACATAGTCGCCGTGCA 59.861 57.895 0.00 0.00 37.67 4.57
235 328 1.140407 GAGACATAGTCGCCGTGCAC 61.140 60.000 6.82 6.82 37.67 4.57
236 329 2.125673 ACATAGTCGCCGTGCACC 60.126 61.111 12.15 0.00 0.00 5.01
237 330 2.125713 CATAGTCGCCGTGCACCA 60.126 61.111 12.15 0.00 0.00 4.17
238 331 2.125673 ATAGTCGCCGTGCACCAC 60.126 61.111 12.15 2.08 0.00 4.16
239 332 3.659089 ATAGTCGCCGTGCACCACC 62.659 63.158 12.15 0.00 0.00 4.61
246 339 4.467084 CGTGCACCACCGCCCTAT 62.467 66.667 12.15 0.00 0.00 2.57
247 340 2.045340 GTGCACCACCGCCCTATT 60.045 61.111 5.22 0.00 0.00 1.73
248 341 1.677633 GTGCACCACCGCCCTATTT 60.678 57.895 5.22 0.00 0.00 1.40
249 342 1.677300 TGCACCACCGCCCTATTTG 60.677 57.895 0.00 0.00 0.00 2.32
251 344 2.044352 ACCACCGCCCTATTTGCC 60.044 61.111 0.00 0.00 0.00 4.52
254 347 1.378514 CACCGCCCTATTTGCCAGT 60.379 57.895 0.00 0.00 0.00 4.00
255 348 0.107410 CACCGCCCTATTTGCCAGTA 60.107 55.000 0.00 0.00 0.00 2.74
256 349 0.107361 ACCGCCCTATTTGCCAGTAC 60.107 55.000 0.00 0.00 0.00 2.73
258 351 1.299541 CGCCCTATTTGCCAGTACTG 58.700 55.000 16.34 16.34 0.00 2.74
259 352 1.025041 GCCCTATTTGCCAGTACTGC 58.975 55.000 17.86 13.07 0.00 4.40
260 353 1.680338 CCCTATTTGCCAGTACTGCC 58.320 55.000 17.86 7.19 0.00 4.85
261 354 1.064758 CCCTATTTGCCAGTACTGCCA 60.065 52.381 17.86 10.27 0.00 4.92
262 355 2.620367 CCCTATTTGCCAGTACTGCCAA 60.620 50.000 14.88 14.88 0.00 4.52
263 356 3.290710 CCTATTTGCCAGTACTGCCAAT 58.709 45.455 18.98 16.94 27.70 3.16
264 357 3.316308 CCTATTTGCCAGTACTGCCAATC 59.684 47.826 18.98 5.47 27.70 2.67
265 358 1.164411 TTTGCCAGTACTGCCAATCG 58.836 50.000 18.98 5.26 27.70 3.34
266 359 0.036164 TTGCCAGTACTGCCAATCGT 59.964 50.000 14.88 0.00 0.00 3.73
268 361 1.421410 GCCAGTACTGCCAATCGTCG 61.421 60.000 17.86 1.58 0.00 5.12
270 363 0.735978 CAGTACTGCCAATCGTCGCA 60.736 55.000 10.54 0.00 0.00 5.10
271 364 0.736325 AGTACTGCCAATCGTCGCAC 60.736 55.000 0.00 0.00 0.00 5.34
273 366 2.845752 TACTGCCAATCGTCGCACCC 62.846 60.000 0.00 0.00 0.00 4.61
276 369 2.124736 CCAATCGTCGCACCCCAT 60.125 61.111 0.00 0.00 0.00 4.00
277 370 2.180204 CCAATCGTCGCACCCCATC 61.180 63.158 0.00 0.00 0.00 3.51
278 371 2.202878 AATCGTCGCACCCCATCG 60.203 61.111 0.00 0.00 0.00 3.84
279 372 4.891727 ATCGTCGCACCCCATCGC 62.892 66.667 0.00 0.00 0.00 4.58
284 377 4.552365 CGCACCCCATCGCTCCAT 62.552 66.667 0.00 0.00 0.00 3.41
285 378 2.592861 GCACCCCATCGCTCCATC 60.593 66.667 0.00 0.00 0.00 3.51
286 379 2.280389 CACCCCATCGCTCCATCG 60.280 66.667 0.00 0.00 0.00 3.84
287 380 4.241555 ACCCCATCGCTCCATCGC 62.242 66.667 0.00 0.00 0.00 4.58
290 383 3.344215 CCATCGCTCCATCGCAGC 61.344 66.667 0.00 0.00 0.00 5.25
291 384 2.586914 CATCGCTCCATCGCAGCA 60.587 61.111 0.00 0.00 36.61 4.41
292 385 2.279985 ATCGCTCCATCGCAGCAG 60.280 61.111 0.00 0.00 36.61 4.24
293 386 2.789715 ATCGCTCCATCGCAGCAGA 61.790 57.895 0.00 0.00 36.61 4.26
295 388 2.894387 GCTCCATCGCAGCAGACC 60.894 66.667 0.00 0.00 36.82 3.85
297 390 1.145598 CTCCATCGCAGCAGACCAT 59.854 57.895 0.00 0.00 0.00 3.55
298 391 0.390492 CTCCATCGCAGCAGACCATA 59.610 55.000 0.00 0.00 0.00 2.74
299 392 1.001746 CTCCATCGCAGCAGACCATAT 59.998 52.381 0.00 0.00 0.00 1.78
300 393 1.001293 TCCATCGCAGCAGACCATATC 59.999 52.381 0.00 0.00 0.00 1.63
301 394 1.001746 CCATCGCAGCAGACCATATCT 59.998 52.381 0.00 0.00 38.66 1.98
302 395 2.335752 CATCGCAGCAGACCATATCTC 58.664 52.381 0.00 0.00 34.41 2.75
303 396 1.697284 TCGCAGCAGACCATATCTCT 58.303 50.000 0.00 0.00 34.41 3.10
304 397 1.611006 TCGCAGCAGACCATATCTCTC 59.389 52.381 0.00 0.00 34.41 3.20
305 398 1.612950 CGCAGCAGACCATATCTCTCT 59.387 52.381 0.00 0.00 34.41 3.10
306 399 2.035704 CGCAGCAGACCATATCTCTCTT 59.964 50.000 0.00 0.00 34.41 2.85
307 400 3.492309 CGCAGCAGACCATATCTCTCTTT 60.492 47.826 0.00 0.00 34.41 2.52
308 401 3.808726 GCAGCAGACCATATCTCTCTTTG 59.191 47.826 0.00 0.00 34.41 2.77
309 402 3.808726 CAGCAGACCATATCTCTCTTTGC 59.191 47.826 0.00 0.00 34.41 3.68
310 403 3.453717 AGCAGACCATATCTCTCTTTGCA 59.546 43.478 0.00 0.00 34.41 4.08
311 404 3.808726 GCAGACCATATCTCTCTTTGCAG 59.191 47.826 0.00 0.00 34.41 4.41
312 405 3.808726 CAGACCATATCTCTCTTTGCAGC 59.191 47.826 0.00 0.00 34.41 5.25
313 406 3.453717 AGACCATATCTCTCTTTGCAGCA 59.546 43.478 0.00 0.00 28.16 4.41
314 407 4.102838 AGACCATATCTCTCTTTGCAGCAT 59.897 41.667 0.00 0.00 28.16 3.79
315 408 4.387598 ACCATATCTCTCTTTGCAGCATC 58.612 43.478 0.00 0.00 0.00 3.91
316 409 3.432592 CCATATCTCTCTTTGCAGCATCG 59.567 47.826 0.00 0.00 0.00 3.84
317 410 1.297664 ATCTCTCTTTGCAGCATCGC 58.702 50.000 0.00 0.00 0.00 4.58
318 411 0.742281 TCTCTCTTTGCAGCATCGCC 60.742 55.000 0.00 0.00 0.00 5.54
319 412 0.743701 CTCTCTTTGCAGCATCGCCT 60.744 55.000 0.00 0.00 0.00 5.52
320 413 1.022982 TCTCTTTGCAGCATCGCCTG 61.023 55.000 0.00 0.00 35.93 4.85
329 422 4.824166 CATCGCCTGCTGCAACGC 62.824 66.667 17.04 13.82 41.33 4.84
333 426 3.663176 GCCTGCTGCAACGCTGAA 61.663 61.111 3.02 0.00 40.77 3.02
334 427 3.033184 CCTGCTGCAACGCTGAAA 58.967 55.556 3.02 0.00 0.00 2.69
335 428 1.081641 CCTGCTGCAACGCTGAAAG 60.082 57.895 3.02 0.00 0.00 2.62
346 439 2.253452 CTGAAAGCACGGCACTGC 59.747 61.111 0.00 0.00 37.44 4.40
360 453 2.060326 CACTGCTTGCAACATTGAGG 57.940 50.000 0.00 0.00 0.00 3.86
361 454 0.316204 ACTGCTTGCAACATTGAGGC 59.684 50.000 0.00 0.00 0.00 4.70
362 455 0.731514 CTGCTTGCAACATTGAGGCG 60.732 55.000 0.00 0.00 0.00 5.52
363 456 1.286880 GCTTGCAACATTGAGGCGT 59.713 52.632 0.00 0.00 0.00 5.68
364 457 0.521291 GCTTGCAACATTGAGGCGTA 59.479 50.000 0.00 0.00 0.00 4.42
365 458 1.466360 GCTTGCAACATTGAGGCGTAG 60.466 52.381 0.00 0.00 0.00 3.51
380 473 4.998400 TAGCAGCAACGCCGGCAA 62.998 61.111 28.98 0.00 32.91 4.52
383 476 4.980903 CAGCAACGCCGGCAACAC 62.981 66.667 28.98 13.03 0.00 3.32
386 479 4.659874 CAACGCCGGCAACACGTC 62.660 66.667 28.98 0.00 46.92 4.34
393 486 3.712881 GGCAACACGTCACCGCTC 61.713 66.667 0.00 0.00 37.70 5.03
394 487 2.964925 GCAACACGTCACCGCTCA 60.965 61.111 0.00 0.00 37.70 4.26
395 488 2.928361 CAACACGTCACCGCTCAC 59.072 61.111 0.00 0.00 37.70 3.51
396 489 1.880796 CAACACGTCACCGCTCACA 60.881 57.895 0.00 0.00 37.70 3.58
397 490 1.153529 AACACGTCACCGCTCACAA 60.154 52.632 0.00 0.00 37.70 3.33
398 491 1.426041 AACACGTCACCGCTCACAAC 61.426 55.000 0.00 0.00 37.70 3.32
399 492 2.657296 ACGTCACCGCTCACAACG 60.657 61.111 0.00 0.00 37.70 4.10
400 493 2.657296 CGTCACCGCTCACAACGT 60.657 61.111 0.00 0.00 0.00 3.99
401 494 2.235016 CGTCACCGCTCACAACGTT 61.235 57.895 0.00 0.00 0.00 3.99
402 495 1.275657 GTCACCGCTCACAACGTTG 59.724 57.895 26.20 26.20 0.00 4.10
403 496 1.885388 TCACCGCTCACAACGTTGG 60.885 57.895 30.34 19.40 0.00 3.77
404 497 2.177580 CACCGCTCACAACGTTGGT 61.178 57.895 30.34 15.83 0.00 3.67
405 498 2.177580 ACCGCTCACAACGTTGGTG 61.178 57.895 30.34 23.74 37.60 4.17
406 499 1.885388 CCGCTCACAACGTTGGTGA 60.885 57.895 30.34 26.01 42.62 4.02
407 500 1.275657 CGCTCACAACGTTGGTGAC 59.724 57.895 30.34 20.58 40.16 3.67
408 501 1.425267 CGCTCACAACGTTGGTGACA 61.425 55.000 30.34 11.29 40.16 3.58
409 502 0.304705 GCTCACAACGTTGGTGACAG 59.695 55.000 30.34 19.18 44.54 3.51
410 503 1.934589 CTCACAACGTTGGTGACAGA 58.065 50.000 30.34 16.44 44.54 3.41
411 504 2.483876 CTCACAACGTTGGTGACAGAT 58.516 47.619 30.34 5.60 44.54 2.90
412 505 2.476619 CTCACAACGTTGGTGACAGATC 59.523 50.000 30.34 0.00 44.54 2.75
413 506 1.192312 CACAACGTTGGTGACAGATCG 59.808 52.381 30.34 2.81 44.54 3.69
414 507 0.790207 CAACGTTGGTGACAGATCGG 59.210 55.000 20.71 0.00 44.54 4.18
415 508 0.320421 AACGTTGGTGACAGATCGGG 60.320 55.000 0.00 0.00 44.54 5.14
416 509 1.183030 ACGTTGGTGACAGATCGGGA 61.183 55.000 0.00 0.00 44.54 5.14
417 510 0.458543 CGTTGGTGACAGATCGGGAG 60.459 60.000 0.00 0.00 44.54 4.30
418 511 0.108138 GTTGGTGACAGATCGGGAGG 60.108 60.000 0.00 0.00 44.54 4.30
419 512 1.899437 TTGGTGACAGATCGGGAGGC 61.899 60.000 0.00 0.00 44.54 4.70
420 513 2.060980 GGTGACAGATCGGGAGGCT 61.061 63.158 0.00 0.00 0.00 4.58
421 514 1.142748 GTGACAGATCGGGAGGCTG 59.857 63.158 0.00 0.00 38.20 4.85
422 515 2.060383 TGACAGATCGGGAGGCTGG 61.060 63.158 0.00 0.00 37.11 4.85
448 541 3.717775 CTGCAACAACAGCACACAA 57.282 47.368 0.00 0.00 37.02 3.33
454 547 1.533625 ACAACAGCACACAACACTGT 58.466 45.000 0.00 0.00 46.27 3.55
465 558 3.986072 AACACTGTGTGCACCGCCA 62.986 57.895 15.11 7.57 36.98 5.69
466 559 2.979676 CACTGTGTGCACCGCCAT 60.980 61.111 15.69 0.00 0.00 4.40
475 568 3.027170 GCACCGCCATTGAGACGTG 62.027 63.158 0.00 0.00 0.00 4.49
558 651 0.601558 AGCACTGCATCTTTGGCTTG 59.398 50.000 3.30 0.00 0.00 4.01
561 654 1.814394 CACTGCATCTTTGGCTTGCTA 59.186 47.619 0.00 0.00 37.28 3.49
562 655 1.815003 ACTGCATCTTTGGCTTGCTAC 59.185 47.619 0.00 0.00 37.28 3.58
578 673 2.032924 TGCTACGTGATGAGACATACGG 59.967 50.000 0.00 0.00 40.56 4.02
630 725 4.678743 GGCACCCCGAGCCCTTTT 62.679 66.667 0.00 0.00 46.50 2.27
639 734 1.021390 CGAGCCCTTTTCAGCGTGAT 61.021 55.000 0.00 0.00 0.00 3.06
646 741 1.531739 TTTTCAGCGTGATTGCCCCC 61.532 55.000 0.00 0.00 34.65 5.40
647 742 2.424842 TTTCAGCGTGATTGCCCCCT 62.425 55.000 0.00 0.00 34.65 4.79
652 747 4.506255 GTGATTGCCCCCTCCCCG 62.506 72.222 0.00 0.00 0.00 5.73
653 748 4.750695 TGATTGCCCCCTCCCCGA 62.751 66.667 0.00 0.00 0.00 5.14
693 969 1.269778 GCCAGTGTATCGCTCTATGCA 60.270 52.381 0.00 0.00 43.06 3.96
699 975 4.112634 GTGTATCGCTCTATGCAACTGAA 58.887 43.478 0.00 0.00 43.06 3.02
707 983 4.730657 CTCTATGCAACTGAAGCCAAAAG 58.269 43.478 0.00 0.00 0.00 2.27
860 1141 1.550524 CAGCCTTACTACACCTCAGCA 59.449 52.381 0.00 0.00 0.00 4.41
875 1156 1.005037 AGCACTTTCGTCATCGCCA 60.005 52.632 0.00 0.00 36.96 5.69
886 1167 3.120095 TCGTCATCGCCACCGTATATAAG 60.120 47.826 0.00 0.00 36.96 1.73
887 1168 3.120095 CGTCATCGCCACCGTATATAAGA 60.120 47.826 0.00 0.00 35.54 2.10
888 1169 4.614306 CGTCATCGCCACCGTATATAAGAA 60.614 45.833 0.00 0.00 35.54 2.52
889 1170 4.857588 GTCATCGCCACCGTATATAAGAAG 59.142 45.833 0.00 0.00 35.54 2.85
890 1171 3.293311 TCGCCACCGTATATAAGAAGC 57.707 47.619 0.00 0.00 35.54 3.86
891 1172 1.983605 CGCCACCGTATATAAGAAGCG 59.016 52.381 10.54 10.54 34.70 4.68
892 1173 2.351060 CGCCACCGTATATAAGAAGCGA 60.351 50.000 15.99 0.00 43.43 4.93
909 1190 4.736896 AAGCCGAAGCCCGTCGAC 62.737 66.667 5.18 5.18 43.86 4.20
921 1207 2.098680 GTCGACGACTCGCCTCAG 59.901 66.667 20.52 0.00 39.96 3.35
942 1228 3.645975 AACCCAAGCAACGACGCG 61.646 61.111 3.53 3.53 36.85 6.01
996 1282 3.184683 CTCGCTCTTGCACTCGCC 61.185 66.667 0.00 0.00 39.64 5.54
1015 1301 4.517815 CAATGCCGGCCATGGTGC 62.518 66.667 26.77 14.24 33.49 5.01
1692 3203 2.962569 CTCCTCGACGTGCTGGAA 59.037 61.111 0.00 0.00 0.00 3.53
1821 3332 2.683933 TCCTTCCTGGACGCCTCC 60.684 66.667 0.00 0.00 40.56 4.30
1893 3425 4.007644 CTGGAGTGGCTGGACGCA 62.008 66.667 0.00 0.00 41.67 5.24
2304 3858 2.829003 CTGGAGGCCGACGAGCTA 60.829 66.667 0.00 0.00 0.00 3.32
2318 3872 2.962253 GCTACGGAGGTGCATCGC 60.962 66.667 0.00 0.00 0.00 4.58
2520 4099 1.342796 CGAGACGAGTGACGAGACGA 61.343 60.000 0.00 0.00 45.77 4.20
2637 4229 2.701587 CACGTGTTCCATGTGGTGT 58.298 52.632 7.58 0.00 44.71 4.16
2663 4262 1.971357 ACTGTTGGTAGTGCTGCTACT 59.029 47.619 15.15 5.63 46.99 2.57
2673 4274 0.898320 TGCTGCTACTTGGGAGAGAC 59.102 55.000 0.00 0.00 0.00 3.36
2687 4289 2.586079 AGACCGAATGCCATCGCG 60.586 61.111 0.00 0.00 41.40 5.87
2693 4295 0.858583 CGAATGCCATCGCGTATTGA 59.141 50.000 5.77 0.00 38.08 2.57
2715 4317 4.483243 ATTTCCGGTGCCGCGGAT 62.483 61.111 33.48 7.77 38.24 4.18
2720 4322 3.732892 CGGTGCCGCGGATGTTTT 61.733 61.111 33.48 0.00 0.00 2.43
2721 4323 2.648454 GGTGCCGCGGATGTTTTT 59.352 55.556 33.48 0.00 0.00 1.94
2747 4349 2.727777 CGATGAACATATCGGACGTGT 58.272 47.619 0.00 0.00 44.56 4.49
2748 4350 3.113322 CGATGAACATATCGGACGTGTT 58.887 45.455 0.00 8.93 44.56 3.32
2787 4389 3.861263 GCGATCCCAAACGGACGC 61.861 66.667 0.00 0.00 46.09 5.19
2821 4424 4.383118 CGGATTCTGTCTGTTTGGATAGGT 60.383 45.833 0.00 0.00 0.00 3.08
3081 4702 4.425772 TGAGTTGGATTAGGGTCTTCTCA 58.574 43.478 0.00 0.00 0.00 3.27
3172 4802 1.344438 TCGATGTTGCTTCCTCACACT 59.656 47.619 0.00 0.00 0.00 3.55
3189 4819 3.188667 CACACTTAGTCTCGTGTCTAGCA 59.811 47.826 5.19 0.00 42.05 3.49
3222 4852 0.590195 CAAGTGCACTTGTCTCCAGC 59.410 55.000 39.48 2.92 46.11 4.85
3225 4855 0.801251 GTGCACTTGTCTCCAGCATC 59.199 55.000 10.32 0.00 37.56 3.91
3227 4857 1.202794 TGCACTTGTCTCCAGCATCAA 60.203 47.619 0.00 0.00 0.00 2.57
3228 4858 2.089980 GCACTTGTCTCCAGCATCAAT 58.910 47.619 0.00 0.00 0.00 2.57
3229 4859 3.273434 GCACTTGTCTCCAGCATCAATA 58.727 45.455 0.00 0.00 0.00 1.90
3230 4860 3.881688 GCACTTGTCTCCAGCATCAATAT 59.118 43.478 0.00 0.00 0.00 1.28
3231 4861 5.059161 GCACTTGTCTCCAGCATCAATATA 58.941 41.667 0.00 0.00 0.00 0.86
3232 4862 5.704515 GCACTTGTCTCCAGCATCAATATAT 59.295 40.000 0.00 0.00 0.00 0.86
3233 4863 6.128336 GCACTTGTCTCCAGCATCAATATATC 60.128 42.308 0.00 0.00 0.00 1.63
3234 4864 6.932960 CACTTGTCTCCAGCATCAATATATCA 59.067 38.462 0.00 0.00 0.00 2.15
3235 4865 7.443272 CACTTGTCTCCAGCATCAATATATCAA 59.557 37.037 0.00 0.00 0.00 2.57
3236 4866 8.162085 ACTTGTCTCCAGCATCAATATATCAAT 58.838 33.333 0.00 0.00 0.00 2.57
3237 4867 9.662947 CTTGTCTCCAGCATCAATATATCAATA 57.337 33.333 0.00 0.00 0.00 1.90
3269 4899 2.952978 TCCAATACCAAAACTTGCACGT 59.047 40.909 0.00 0.00 0.00 4.49
3270 4900 3.049206 CCAATACCAAAACTTGCACGTG 58.951 45.455 12.28 12.28 0.00 4.49
3414 5064 3.706600 ACCCCATCGTTTAAGCACTTA 57.293 42.857 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 58 9.378551 AGGTAAAAGAAACAATTTTTCTTCACC 57.621 29.630 25.41 25.41 45.07 4.02
66 70 8.284693 GCGACATACTTAAGGTAAAAGAAACAA 58.715 33.333 7.53 0.00 33.74 2.83
68 72 6.952083 CGCGACATACTTAAGGTAAAAGAAAC 59.048 38.462 0.00 0.00 33.74 2.78
69 73 6.646240 ACGCGACATACTTAAGGTAAAAGAAA 59.354 34.615 15.93 0.00 33.74 2.52
70 74 6.158598 ACGCGACATACTTAAGGTAAAAGAA 58.841 36.000 15.93 0.00 33.74 2.52
87 92 0.885879 ATGAACTGTAGGACGCGACA 59.114 50.000 15.93 5.48 0.00 4.35
90 95 1.269166 GTGATGAACTGTAGGACGCG 58.731 55.000 3.53 3.53 0.00 6.01
92 97 2.913777 TCGTGATGAACTGTAGGACG 57.086 50.000 0.00 0.00 0.00 4.79
135 140 4.214758 TGCTAGATAGTTTATAGCGACGCA 59.785 41.667 23.70 8.56 43.88 5.24
140 145 6.220930 TGGGTTTGCTAGATAGTTTATAGCG 58.779 40.000 0.00 0.00 43.88 4.26
150 155 4.919774 TTGAACCTGGGTTTGCTAGATA 57.080 40.909 6.46 0.00 38.60 1.98
152 157 3.219281 GTTTGAACCTGGGTTTGCTAGA 58.781 45.455 6.46 0.00 38.60 2.43
167 260 0.762418 TCTCGAAGCCAGGGTTTGAA 59.238 50.000 19.99 10.06 33.78 2.69
169 262 0.250295 TGTCTCGAAGCCAGGGTTTG 60.250 55.000 12.04 12.04 0.00 2.93
170 263 0.250338 GTGTCTCGAAGCCAGGGTTT 60.250 55.000 5.08 0.00 0.00 3.27
171 264 1.371558 GTGTCTCGAAGCCAGGGTT 59.628 57.895 2.64 2.64 0.00 4.11
174 267 0.249868 TGTTGTGTCTCGAAGCCAGG 60.250 55.000 0.00 0.00 0.00 4.45
176 269 2.143122 GATTGTTGTGTCTCGAAGCCA 58.857 47.619 0.00 0.00 0.00 4.75
197 290 3.574396 TCTCGCATTAGGTATCCCTGAAG 59.426 47.826 0.00 0.00 42.67 3.02
206 299 4.744136 CGACTATGTCTCGCATTAGGTA 57.256 45.455 0.00 0.00 38.94 3.08
218 311 2.165301 GGTGCACGGCGACTATGTC 61.165 63.158 16.62 0.00 0.00 3.06
231 324 1.677300 CAAATAGGGCGGTGGTGCA 60.677 57.895 0.00 0.00 36.28 4.57
234 327 2.044352 GGCAAATAGGGCGGTGGT 60.044 61.111 0.00 0.00 0.00 4.16
235 328 2.044451 TGGCAAATAGGGCGGTGG 60.044 61.111 0.00 0.00 35.84 4.61
236 329 3.513225 CTGGCAAATAGGGCGGTG 58.487 61.111 0.00 0.00 35.17 4.94
237 330 3.087065 ACTGGCAAATAGGGCGGT 58.913 55.556 0.00 0.00 46.86 5.68
238 331 0.180406 AGTACTGGCAAATAGGGCGG 59.820 55.000 0.00 0.00 44.69 6.13
239 332 1.299541 CAGTACTGGCAAATAGGGCG 58.700 55.000 15.49 0.00 35.84 6.13
240 333 1.025041 GCAGTACTGGCAAATAGGGC 58.975 55.000 23.95 1.85 0.00 5.19
251 344 0.735978 TGCGACGATTGGCAGTACTG 60.736 55.000 18.93 18.93 33.52 2.74
254 347 1.447140 GGTGCGACGATTGGCAGTA 60.447 57.895 0.00 0.00 40.32 2.74
255 348 2.742372 GGTGCGACGATTGGCAGT 60.742 61.111 0.00 0.00 40.32 4.40
256 349 3.499737 GGGTGCGACGATTGGCAG 61.500 66.667 0.00 0.00 40.32 4.85
259 352 2.124736 ATGGGGTGCGACGATTGG 60.125 61.111 0.00 0.00 0.00 3.16
260 353 2.525248 CGATGGGGTGCGACGATTG 61.525 63.158 0.00 0.00 0.00 2.67
261 354 2.202878 CGATGGGGTGCGACGATT 60.203 61.111 0.00 0.00 0.00 3.34
262 355 4.891727 GCGATGGGGTGCGACGAT 62.892 66.667 0.00 0.00 0.00 3.73
268 361 2.592861 GATGGAGCGATGGGGTGC 60.593 66.667 0.00 0.00 34.73 5.01
270 363 4.241555 GCGATGGAGCGATGGGGT 62.242 66.667 0.00 0.00 0.00 4.95
271 364 4.240103 TGCGATGGAGCGATGGGG 62.240 66.667 0.00 0.00 40.67 4.96
273 366 3.344215 GCTGCGATGGAGCGATGG 61.344 66.667 0.00 0.00 40.67 3.51
274 367 2.586914 TGCTGCGATGGAGCGATG 60.587 61.111 5.84 0.00 39.47 3.84
276 369 3.451894 TCTGCTGCGATGGAGCGA 61.452 61.111 5.84 3.76 39.47 4.93
277 370 3.260483 GTCTGCTGCGATGGAGCG 61.260 66.667 5.84 1.54 39.47 5.03
278 371 2.894387 GGTCTGCTGCGATGGAGC 60.894 66.667 3.15 3.15 36.95 4.70
279 372 0.390492 TATGGTCTGCTGCGATGGAG 59.610 55.000 0.00 0.00 0.00 3.86
280 373 1.001293 GATATGGTCTGCTGCGATGGA 59.999 52.381 0.00 0.00 0.00 3.41
281 374 1.001746 AGATATGGTCTGCTGCGATGG 59.998 52.381 0.00 0.00 35.31 3.51
282 375 2.029200 AGAGATATGGTCTGCTGCGATG 60.029 50.000 0.00 0.00 37.29 3.84
284 377 1.611006 GAGAGATATGGTCTGCTGCGA 59.389 52.381 0.00 0.00 37.29 5.10
285 378 1.612950 AGAGAGATATGGTCTGCTGCG 59.387 52.381 0.00 0.00 37.29 5.18
286 379 3.749665 AAGAGAGATATGGTCTGCTGC 57.250 47.619 0.00 0.00 37.29 5.25
287 380 3.808726 GCAAAGAGAGATATGGTCTGCTG 59.191 47.826 0.00 0.00 37.29 4.41
290 383 3.808726 GCTGCAAAGAGAGATATGGTCTG 59.191 47.826 0.00 0.00 37.29 3.51
291 384 3.453717 TGCTGCAAAGAGAGATATGGTCT 59.546 43.478 0.00 0.00 40.81 3.85
292 385 3.801698 TGCTGCAAAGAGAGATATGGTC 58.198 45.455 0.00 0.00 0.00 4.02
293 386 3.920231 TGCTGCAAAGAGAGATATGGT 57.080 42.857 0.00 0.00 0.00 3.55
295 388 3.120615 GCGATGCTGCAAAGAGAGATATG 60.121 47.826 6.36 0.00 34.15 1.78
297 390 2.477825 GCGATGCTGCAAAGAGAGATA 58.522 47.619 6.36 0.00 34.15 1.98
298 391 1.297664 GCGATGCTGCAAAGAGAGAT 58.702 50.000 6.36 0.00 34.15 2.75
299 392 0.742281 GGCGATGCTGCAAAGAGAGA 60.742 55.000 6.36 0.00 36.28 3.10
300 393 0.743701 AGGCGATGCTGCAAAGAGAG 60.744 55.000 6.36 0.00 36.28 3.20
301 394 1.022982 CAGGCGATGCTGCAAAGAGA 61.023 55.000 6.36 0.00 36.28 3.10
302 395 1.428219 CAGGCGATGCTGCAAAGAG 59.572 57.895 6.36 0.00 36.28 2.85
303 396 3.582148 CAGGCGATGCTGCAAAGA 58.418 55.556 6.36 0.00 36.28 2.52
316 409 3.198236 TTTCAGCGTTGCAGCAGGC 62.198 57.895 11.53 11.53 45.13 4.85
317 410 1.081641 CTTTCAGCGTTGCAGCAGG 60.082 57.895 0.24 0.00 40.15 4.85
318 411 1.728426 GCTTTCAGCGTTGCAGCAG 60.728 57.895 15.29 0.00 40.15 4.24
319 412 2.332514 GCTTTCAGCGTTGCAGCA 59.667 55.556 15.29 0.00 40.15 4.41
320 413 2.012948 GTGCTTTCAGCGTTGCAGC 61.013 57.895 13.89 13.89 46.26 5.25
321 414 1.723542 CGTGCTTTCAGCGTTGCAG 60.724 57.895 0.00 0.00 46.26 4.41
322 415 2.327592 CGTGCTTTCAGCGTTGCA 59.672 55.556 0.00 0.00 46.26 4.08
323 416 2.427410 CCGTGCTTTCAGCGTTGC 60.427 61.111 0.00 0.00 46.26 4.17
324 417 2.427410 GCCGTGCTTTCAGCGTTG 60.427 61.111 0.00 0.00 46.26 4.10
325 418 2.899838 TGCCGTGCTTTCAGCGTT 60.900 55.556 0.00 0.00 46.26 4.84
326 419 3.649986 GTGCCGTGCTTTCAGCGT 61.650 61.111 0.00 0.00 46.26 5.07
327 420 3.349006 AGTGCCGTGCTTTCAGCG 61.349 61.111 0.00 0.00 46.26 5.18
328 421 2.253452 CAGTGCCGTGCTTTCAGC 59.747 61.111 0.00 0.00 42.82 4.26
329 422 2.253452 GCAGTGCCGTGCTTTCAG 59.747 61.111 2.85 0.00 40.54 3.02
341 434 1.933500 GCCTCAATGTTGCAAGCAGTG 60.934 52.381 17.53 17.53 33.80 3.66
342 435 0.316204 GCCTCAATGTTGCAAGCAGT 59.684 50.000 0.00 0.00 0.00 4.40
343 436 0.731514 CGCCTCAATGTTGCAAGCAG 60.732 55.000 0.00 0.00 0.00 4.24
344 437 1.286570 CGCCTCAATGTTGCAAGCA 59.713 52.632 0.00 1.30 0.00 3.91
345 438 0.521291 TACGCCTCAATGTTGCAAGC 59.479 50.000 0.00 0.00 0.00 4.01
346 439 1.466360 GCTACGCCTCAATGTTGCAAG 60.466 52.381 0.00 0.00 36.93 4.01
347 440 0.521291 GCTACGCCTCAATGTTGCAA 59.479 50.000 0.00 0.00 36.93 4.08
348 441 0.605050 TGCTACGCCTCAATGTTGCA 60.605 50.000 0.00 0.00 42.82 4.08
349 442 0.097674 CTGCTACGCCTCAATGTTGC 59.902 55.000 0.00 0.00 37.36 4.17
350 443 0.097674 GCTGCTACGCCTCAATGTTG 59.902 55.000 0.00 0.00 0.00 3.33
351 444 0.321564 TGCTGCTACGCCTCAATGTT 60.322 50.000 0.00 0.00 0.00 2.71
352 445 0.321564 TTGCTGCTACGCCTCAATGT 60.322 50.000 0.00 0.00 0.00 2.71
353 446 0.097674 GTTGCTGCTACGCCTCAATG 59.902 55.000 0.00 0.00 0.00 2.82
354 447 1.361668 CGTTGCTGCTACGCCTCAAT 61.362 55.000 21.98 0.00 31.73 2.57
355 448 2.027073 CGTTGCTGCTACGCCTCAA 61.027 57.895 21.98 0.00 31.73 3.02
356 449 2.432456 CGTTGCTGCTACGCCTCA 60.432 61.111 21.98 0.00 31.73 3.86
363 456 4.998400 TTGCCGGCGTTGCTGCTA 62.998 61.111 23.90 0.00 32.89 3.49
366 459 4.980903 GTGTTGCCGGCGTTGCTG 62.981 66.667 23.90 0.00 34.23 4.41
369 462 4.659874 GACGTGTTGCCGGCGTTG 62.660 66.667 23.90 12.13 39.06 4.10
384 477 3.713963 AACGTTGTGAGCGGTGAC 58.286 55.556 0.00 0.00 0.00 3.67
386 479 2.177580 ACCAACGTTGTGAGCGGTG 61.178 57.895 25.63 10.94 45.52 4.94
387 480 2.177580 CACCAACGTTGTGAGCGGT 61.178 57.895 25.63 13.26 0.00 5.68
388 481 1.885388 TCACCAACGTTGTGAGCGG 60.885 57.895 25.63 12.60 0.00 5.52
389 482 1.275657 GTCACCAACGTTGTGAGCG 59.724 57.895 25.63 13.02 0.00 5.03
390 483 0.304705 CTGTCACCAACGTTGTGAGC 59.695 55.000 25.63 19.77 0.00 4.26
391 484 1.934589 TCTGTCACCAACGTTGTGAG 58.065 50.000 25.63 15.54 0.00 3.51
392 485 2.479837 GATCTGTCACCAACGTTGTGA 58.520 47.619 25.63 23.32 0.00 3.58
393 486 1.192312 CGATCTGTCACCAACGTTGTG 59.808 52.381 25.63 21.68 0.00 3.33
394 487 1.497991 CGATCTGTCACCAACGTTGT 58.502 50.000 25.63 11.94 0.00 3.32
395 488 0.790207 CCGATCTGTCACCAACGTTG 59.210 55.000 21.47 21.47 0.00 4.10
396 489 0.320421 CCCGATCTGTCACCAACGTT 60.320 55.000 0.00 0.00 0.00 3.99
397 490 1.183030 TCCCGATCTGTCACCAACGT 61.183 55.000 0.00 0.00 0.00 3.99
398 491 0.458543 CTCCCGATCTGTCACCAACG 60.459 60.000 0.00 0.00 0.00 4.10
399 492 0.108138 CCTCCCGATCTGTCACCAAC 60.108 60.000 0.00 0.00 0.00 3.77
400 493 1.899437 GCCTCCCGATCTGTCACCAA 61.899 60.000 0.00 0.00 0.00 3.67
401 494 2.359169 GCCTCCCGATCTGTCACCA 61.359 63.158 0.00 0.00 0.00 4.17
402 495 2.060980 AGCCTCCCGATCTGTCACC 61.061 63.158 0.00 0.00 0.00 4.02
403 496 1.142748 CAGCCTCCCGATCTGTCAC 59.857 63.158 0.00 0.00 0.00 3.67
404 497 2.060383 CCAGCCTCCCGATCTGTCA 61.060 63.158 0.00 0.00 0.00 3.58
405 498 2.818132 CCAGCCTCCCGATCTGTC 59.182 66.667 0.00 0.00 0.00 3.51
406 499 3.474570 GCCAGCCTCCCGATCTGT 61.475 66.667 0.00 0.00 0.00 3.41
407 500 2.937379 CTTGCCAGCCTCCCGATCTG 62.937 65.000 0.00 0.00 0.00 2.90
408 501 2.688666 TTGCCAGCCTCCCGATCT 60.689 61.111 0.00 0.00 0.00 2.75
409 502 2.203126 CTTGCCAGCCTCCCGATC 60.203 66.667 0.00 0.00 0.00 3.69
410 503 4.496336 GCTTGCCAGCCTCCCGAT 62.496 66.667 0.00 0.00 40.61 4.18
418 511 3.986006 TTGCAGCAGCTTGCCAGC 61.986 61.111 7.90 0.46 46.52 4.85
419 512 2.049433 GTTGCAGCAGCTTGCCAG 60.049 61.111 7.90 1.78 46.52 4.85
420 513 2.424733 TTGTTGCAGCAGCTTGCCA 61.425 52.632 10.92 0.00 46.52 4.92
421 514 1.952635 GTTGTTGCAGCAGCTTGCC 60.953 57.895 10.92 0.00 46.52 4.52
422 515 1.213094 CTGTTGTTGCAGCAGCTTGC 61.213 55.000 17.55 3.32 45.46 4.01
432 525 0.991344 GTGTTGTGTGCTGTTGTTGC 59.009 50.000 0.00 0.00 0.00 4.17
448 541 3.772853 ATGGCGGTGCACACAGTGT 62.773 57.895 20.43 0.00 35.75 3.55
454 547 1.965930 GTCTCAATGGCGGTGCACA 60.966 57.895 20.43 0.00 0.00 4.57
465 558 1.568612 CTGCAACCGCACGTCTCAAT 61.569 55.000 0.00 0.00 45.36 2.57
466 559 2.202946 TGCAACCGCACGTCTCAA 60.203 55.556 0.00 0.00 45.36 3.02
496 589 2.358247 CTAACCGGTGCCGCAAGT 60.358 61.111 8.52 0.00 38.24 3.16
525 618 4.431131 TGCTGCAAGGGCTAGGGC 62.431 66.667 0.00 0.00 41.91 5.19
552 645 0.894835 TCTCATCACGTAGCAAGCCA 59.105 50.000 0.00 0.00 0.00 4.75
558 651 2.033049 ACCGTATGTCTCATCACGTAGC 59.967 50.000 0.00 0.00 32.66 3.58
561 654 2.876091 CAACCGTATGTCTCATCACGT 58.124 47.619 0.00 0.00 32.66 4.49
562 655 1.588404 GCAACCGTATGTCTCATCACG 59.412 52.381 0.00 0.00 0.00 4.35
616 711 2.757077 CTGAAAAGGGCTCGGGGT 59.243 61.111 0.00 0.00 0.00 4.95
624 719 0.109132 GGCAATCACGCTGAAAAGGG 60.109 55.000 0.00 0.00 0.00 3.95
629 724 2.361104 GGGGGCAATCACGCTGAA 60.361 61.111 0.00 0.00 0.00 3.02
630 725 3.329542 GAGGGGGCAATCACGCTGA 62.330 63.158 0.00 0.00 0.00 4.26
652 747 2.730524 GGAGACAGGGAGGCTGCTC 61.731 68.421 5.84 0.00 41.26 4.26
653 748 2.686835 GGAGACAGGGAGGCTGCT 60.687 66.667 5.84 0.00 41.26 4.24
693 969 4.953579 TGGTTTCTACTTTTGGCTTCAGTT 59.046 37.500 0.00 0.00 0.00 3.16
699 975 3.487372 GGTCTGGTTTCTACTTTTGGCT 58.513 45.455 0.00 0.00 0.00 4.75
875 1156 3.611057 CGGCTTCGCTTCTTATATACGGT 60.611 47.826 0.00 0.00 0.00 4.83
886 1167 3.500642 GGGCTTCGGCTTCGCTTC 61.501 66.667 0.00 0.00 41.44 3.86
891 1172 4.430765 TCGACGGGCTTCGGCTTC 62.431 66.667 8.77 0.00 46.68 3.86
892 1173 4.736896 GTCGACGGGCTTCGGCTT 62.737 66.667 0.00 0.00 46.68 4.35
909 1190 4.069232 TTGGGCTGAGGCGAGTCG 62.069 66.667 8.54 8.54 39.81 4.18
921 1207 2.909965 TCGTTGCTTGGGTTGGGC 60.910 61.111 0.00 0.00 0.00 5.36
930 1216 4.293626 GTGTGCGCGTCGTTGCTT 62.294 61.111 8.43 0.00 0.00 3.91
942 1228 1.136611 GTCTTTGTCGTCGATGTGTGC 60.137 52.381 4.21 0.00 0.00 4.57
1144 1430 4.097361 GACGGGGGTGGAGAAGGC 62.097 72.222 0.00 0.00 0.00 4.35
1735 3246 1.890979 CCATCGCATCAGGCTCCAC 60.891 63.158 0.00 0.00 41.67 4.02
1863 3395 1.923395 CTCCAGGTACCCCTTGCCA 60.923 63.158 8.74 0.00 39.89 4.92
2223 3774 3.329889 TTCCGCTCCACCAGCCAT 61.330 61.111 0.00 0.00 46.74 4.40
2304 3858 3.665675 GAAGGCGATGCACCTCCGT 62.666 63.158 0.00 0.00 36.14 4.69
2318 3872 2.885644 CATCCGACGTGGCGAAGG 60.886 66.667 0.00 0.00 37.80 3.46
2496 4075 1.013005 TCGTCACTCGTCTCGTCCTC 61.013 60.000 0.00 0.00 40.80 3.71
2520 4099 0.882474 GGACACAGTACTGCTCGAGT 59.118 55.000 22.90 13.04 38.88 4.18
2595 4186 9.271828 GTGGTTTCAATCCAAACTTGATTAAAT 57.728 29.630 0.00 0.00 36.62 1.40
2637 4229 3.466836 CAGCACTACCAACAGTCTTTGA 58.533 45.455 0.00 0.00 0.00 2.69
2663 4262 1.198094 TGGCATTCGGTCTCTCCCAA 61.198 55.000 0.00 0.00 0.00 4.12
2673 4274 0.110688 CAATACGCGATGGCATTCGG 60.111 55.000 15.93 13.36 39.49 4.30
2727 4329 2.727777 ACACGTCCGATATGTTCATCG 58.272 47.619 0.00 0.00 45.81 3.84
2728 4330 4.260212 CCAAACACGTCCGATATGTTCATC 60.260 45.833 0.00 0.00 35.54 2.92
2729 4331 3.621268 CCAAACACGTCCGATATGTTCAT 59.379 43.478 0.00 0.00 35.54 2.57
2730 4332 2.997303 CCAAACACGTCCGATATGTTCA 59.003 45.455 0.00 0.00 35.54 3.18
2731 4333 2.997986 ACCAAACACGTCCGATATGTTC 59.002 45.455 0.00 0.00 35.54 3.18
2732 4334 3.048337 ACCAAACACGTCCGATATGTT 57.952 42.857 0.00 0.00 38.18 2.71
2733 4335 2.754946 ACCAAACACGTCCGATATGT 57.245 45.000 0.00 0.00 0.00 2.29
2734 4336 3.554324 CCTAACCAAACACGTCCGATATG 59.446 47.826 0.00 0.00 0.00 1.78
2735 4337 3.788937 CCTAACCAAACACGTCCGATAT 58.211 45.455 0.00 0.00 0.00 1.63
2736 4338 2.674747 GCCTAACCAAACACGTCCGATA 60.675 50.000 0.00 0.00 0.00 2.92
2737 4339 1.942586 GCCTAACCAAACACGTCCGAT 60.943 52.381 0.00 0.00 0.00 4.18
2738 4340 0.600782 GCCTAACCAAACACGTCCGA 60.601 55.000 0.00 0.00 0.00 4.55
2739 4341 1.571215 GGCCTAACCAAACACGTCCG 61.571 60.000 0.00 0.00 38.86 4.79
2740 4342 2.250646 GGCCTAACCAAACACGTCC 58.749 57.895 0.00 0.00 38.86 4.79
2787 4389 3.007635 GACAGAATCCGGGTAAAACAGG 58.992 50.000 0.00 0.00 0.00 4.00
2821 4424 1.589630 CCGGACACGACTCCATTGA 59.410 57.895 0.00 0.00 44.60 2.57
3081 4702 4.552355 CACACATCAACAATGAGTGCATT 58.448 39.130 0.00 0.00 45.67 3.56
3099 4720 1.040339 AGATCGAGCCTCCTCCACAC 61.040 60.000 0.00 0.00 34.49 3.82
3172 4802 6.993308 AGATTAGATGCTAGACACGAGACTAA 59.007 38.462 0.00 0.00 0.00 2.24
3237 4867 9.588096 AAGTTTTGGTATTGGAAAGAAGAGTAT 57.412 29.630 0.00 0.00 0.00 2.12
3238 4868 8.846211 CAAGTTTTGGTATTGGAAAGAAGAGTA 58.154 33.333 0.00 0.00 0.00 2.59
3239 4869 7.684428 GCAAGTTTTGGTATTGGAAAGAAGAGT 60.684 37.037 0.00 0.00 0.00 3.24
3240 4870 6.642540 GCAAGTTTTGGTATTGGAAAGAAGAG 59.357 38.462 0.00 0.00 0.00 2.85
3241 4871 6.097554 TGCAAGTTTTGGTATTGGAAAGAAGA 59.902 34.615 0.00 0.00 0.00 2.87
3242 4872 6.200854 GTGCAAGTTTTGGTATTGGAAAGAAG 59.799 38.462 0.00 0.00 0.00 2.85
3243 4873 6.045955 GTGCAAGTTTTGGTATTGGAAAGAA 58.954 36.000 0.00 0.00 0.00 2.52
3244 4874 5.596845 GTGCAAGTTTTGGTATTGGAAAGA 58.403 37.500 0.00 0.00 0.00 2.52
3245 4875 4.444056 CGTGCAAGTTTTGGTATTGGAAAG 59.556 41.667 0.00 0.00 0.00 2.62
3246 4876 4.142138 ACGTGCAAGTTTTGGTATTGGAAA 60.142 37.500 0.00 0.00 0.00 3.13
3247 4877 3.381908 ACGTGCAAGTTTTGGTATTGGAA 59.618 39.130 0.00 0.00 0.00 3.53
3248 4878 2.952978 ACGTGCAAGTTTTGGTATTGGA 59.047 40.909 0.00 0.00 0.00 3.53
3249 4879 3.049206 CACGTGCAAGTTTTGGTATTGG 58.951 45.455 0.82 0.00 0.00 3.16
3250 4880 2.470999 GCACGTGCAAGTTTTGGTATTG 59.529 45.455 34.52 0.00 41.59 1.90
3251 4881 2.738135 GCACGTGCAAGTTTTGGTATT 58.262 42.857 34.52 0.00 41.59 1.89
3286 4935 9.588096 AAGTTTTGGTATTGGAAAGAAGAGTAT 57.412 29.630 0.00 0.00 0.00 2.12
3341 4991 7.226325 GCTCTAGATTTGATGAGTTGTGCTAAT 59.774 37.037 0.00 0.00 0.00 1.73
3353 5003 4.631377 TCGGTTTGTGCTCTAGATTTGATG 59.369 41.667 0.00 0.00 0.00 3.07
3354 5004 4.832248 TCGGTTTGTGCTCTAGATTTGAT 58.168 39.130 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.