Multiple sequence alignment - TraesCS6B01G398400

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 TraesCS6B01G398400 chr6B 100.000 4790 0 0 1 4790 673762525 673767314 0.000000e+00 8846.0
1 TraesCS6B01G398400 chr6B 89.261 2300 203 18 1002 3270 672500179 672497893 0.000000e+00 2839.0
2 TraesCS6B01G398400 chr6B 83.012 1713 260 24 1668 3363 618670276 618668578 0.000000e+00 1522.0
3 TraesCS6B01G398400 chr6B 88.527 706 69 6 1094 1791 22118623 22117922 0.000000e+00 845.0
4 TraesCS6B01G398400 chr6B 88.244 706 72 7 1094 1791 9132281 9131579 0.000000e+00 833.0
5 TraesCS6B01G398400 chr6B 88.102 706 70 10 1094 1791 9112701 9112002 0.000000e+00 826.0
6 TraesCS6B01G398400 chr6B 84.344 709 80 14 3952 4645 673337161 673336469 0.000000e+00 665.0
7 TraesCS6B01G398400 chr6B 86.871 457 49 7 4169 4619 673344957 673344506 7.160000e-138 501.0
8 TraesCS6B01G398400 chr6B 88.424 406 37 8 4 406 672501001 672500603 9.320000e-132 481.0
9 TraesCS6B01G398400 chr6B 84.475 438 46 17 529 963 672500605 672500187 3.450000e-111 412.0
10 TraesCS6B01G398400 chr6B 83.224 304 49 2 4389 4692 672164863 672164562 1.310000e-70 278.0
11 TraesCS6B01G398400 chr6B 96.454 141 4 1 404 544 612317132 612317271 1.040000e-56 231.0
12 TraesCS6B01G398400 chr6B 94.326 141 8 0 404 544 207511027 207510887 2.900000e-52 217.0
13 TraesCS6B01G398400 chr6B 76.962 395 55 22 3846 4215 672461048 672460665 4.890000e-45 193.0
14 TraesCS6B01G398400 chr6A 94.779 2777 101 20 1575 4333 592599372 592602122 0.000000e+00 4285.0
15 TraesCS6B01G398400 chr6A 89.328 2305 195 24 1002 3270 592469850 592467561 0.000000e+00 2846.0
16 TraesCS6B01G398400 chr6A 84.828 1628 223 17 1671 3284 592458965 592457348 0.000000e+00 1616.0
17 TraesCS6B01G398400 chr6A 85.384 1512 212 7 1764 3270 556038385 556036878 0.000000e+00 1559.0
18 TraesCS6B01G398400 chr6A 89.213 445 30 7 4329 4758 592602150 592602591 1.520000e-149 540.0
19 TraesCS6B01G398400 chr6A 87.297 370 42 4 11 379 592470945 592470580 7.410000e-113 418.0
20 TraesCS6B01G398400 chr6A 84.825 257 18 9 529 768 592470533 592470281 6.200000e-59 239.0
21 TraesCS6B01G398400 chr6A 96.324 136 5 0 395 530 189553707 189553572 1.730000e-54 224.0
22 TraesCS6B01G398400 chr6A 90.476 168 16 0 796 963 592470024 592469857 6.240000e-54 222.0
23 TraesCS6B01G398400 chr6A 100.000 32 0 0 376 407 592470561 592470530 5.180000e-05 60.2
24 TraesCS6B01G398400 chr6D 90.230 1955 176 11 1326 3270 445794208 445792259 0.000000e+00 2538.0
25 TraesCS6B01G398400 chr6D 82.234 1925 282 46 1668 3554 411470976 411469074 0.000000e+00 1605.0
26 TraesCS6B01G398400 chr6D 84.319 1607 232 15 1678 3270 445788959 445787359 0.000000e+00 1554.0
27 TraesCS6B01G398400 chr6D 83.636 440 49 13 529 964 445794910 445794490 4.490000e-105 392.0
28 TraesCS6B01G398400 chr6D 82.848 309 51 2 4384 4692 445731208 445730902 4.720000e-70 276.0
29 TraesCS6B01G398400 chr6D 82.313 147 25 1 4379 4525 445758271 445758416 5.030000e-25 126.0
30 TraesCS6B01G398400 chr6D 98.462 65 1 0 315 379 445795021 445794957 1.090000e-21 115.0
31 TraesCS6B01G398400 chr1A 88.810 706 69 5 1094 1791 69141737 69142440 0.000000e+00 857.0
32 TraesCS6B01G398400 chr5B 88.210 704 72 7 1094 1789 667208821 667209521 0.000000e+00 830.0
33 TraesCS6B01G398400 chr5B 94.521 146 6 2 399 543 13357088 13356944 1.730000e-54 224.0
34 TraesCS6B01G398400 chr1B 87.960 706 73 8 1094 1791 614436627 614437328 0.000000e+00 822.0
35 TraesCS6B01G398400 chr1B 94.406 143 5 2 403 545 56893363 56893224 2.900000e-52 217.0
36 TraesCS6B01G398400 chr1B 88.776 98 9 2 3756 3852 61526010 61525914 8.420000e-23 119.0
37 TraesCS6B01G398400 chr4A 87.767 703 76 5 1097 1791 635617654 635618354 0.000000e+00 813.0
38 TraesCS6B01G398400 chr2B 99.242 132 1 0 403 534 646951414 646951283 6.200000e-59 239.0
39 TraesCS6B01G398400 chr4B 97.163 141 3 1 404 544 149160533 149160394 2.230000e-58 237.0
40 TraesCS6B01G398400 chr4B 91.026 156 12 2 404 558 576982442 576982596 4.860000e-50 209.0
41 TraesCS6B01G398400 chr2D 95.652 138 5 1 400 537 622315787 622315651 2.240000e-53 220.0
42 TraesCS6B01G398400 chr2D 91.304 92 6 2 3763 3853 53145814 53145724 1.810000e-24 124.0
43 TraesCS6B01G398400 chr2D 88.298 94 9 2 3757 3849 54674333 54674241 1.410000e-20 111.0
44 TraesCS6B01G398400 chr5A 93.103 87 5 1 3766 3852 367595300 367595215 5.030000e-25 126.0
45 TraesCS6B01G398400 chr3D 92.222 90 6 1 3763 3851 180394995 180394906 5.030000e-25 126.0
46 TraesCS6B01G398400 chr3D 90.526 95 8 1 3757 3850 121985633 121985539 1.810000e-24 124.0
47 TraesCS6B01G398400 chr7D 89.796 98 8 2 3754 3850 519264535 519264631 1.810000e-24 124.0
48 TraesCS6B01G398400 chr5D 92.135 89 6 1 3762 3849 66745390 66745478 1.810000e-24 124.0


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 TraesCS6B01G398400 chr6B 673762525 673767314 4789 False 8846.00 8846 100.000000 1 4790 1 chr6B.!!$F2 4789
1 TraesCS6B01G398400 chr6B 618668578 618670276 1698 True 1522.00 1522 83.012000 1668 3363 1 chr6B.!!$R5 1695
2 TraesCS6B01G398400 chr6B 672497893 672501001 3108 True 1244.00 2839 87.386667 4 3270 3 chr6B.!!$R10 3266
3 TraesCS6B01G398400 chr6B 22117922 22118623 701 True 845.00 845 88.527000 1094 1791 1 chr6B.!!$R3 697
4 TraesCS6B01G398400 chr6B 9131579 9132281 702 True 833.00 833 88.244000 1094 1791 1 chr6B.!!$R2 697
5 TraesCS6B01G398400 chr6B 9112002 9112701 699 True 826.00 826 88.102000 1094 1791 1 chr6B.!!$R1 697
6 TraesCS6B01G398400 chr6B 673336469 673337161 692 True 665.00 665 84.344000 3952 4645 1 chr6B.!!$R8 693
7 TraesCS6B01G398400 chr6A 592599372 592602591 3219 False 2412.50 4285 91.996000 1575 4758 2 chr6A.!!$F1 3183
8 TraesCS6B01G398400 chr6A 592457348 592458965 1617 True 1616.00 1616 84.828000 1671 3284 1 chr6A.!!$R3 1613
9 TraesCS6B01G398400 chr6A 556036878 556038385 1507 True 1559.00 1559 85.384000 1764 3270 1 chr6A.!!$R2 1506
10 TraesCS6B01G398400 chr6A 592467561 592470945 3384 True 757.04 2846 90.385200 11 3270 5 chr6A.!!$R4 3259
11 TraesCS6B01G398400 chr6D 411469074 411470976 1902 True 1605.00 1605 82.234000 1668 3554 1 chr6D.!!$R1 1886
12 TraesCS6B01G398400 chr6D 445787359 445795021 7662 True 1149.75 2538 89.161750 315 3270 4 chr6D.!!$R3 2955
13 TraesCS6B01G398400 chr1A 69141737 69142440 703 False 857.00 857 88.810000 1094 1791 1 chr1A.!!$F1 697
14 TraesCS6B01G398400 chr5B 667208821 667209521 700 False 830.00 830 88.210000 1094 1789 1 chr5B.!!$F1 695
15 TraesCS6B01G398400 chr1B 614436627 614437328 701 False 822.00 822 87.960000 1094 1791 1 chr1B.!!$F1 697
16 TraesCS6B01G398400 chr4A 635617654 635618354 700 False 813.00 813 87.767000 1097 1791 1 chr4A.!!$F1 694

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
417 466 0.245539 TTTGCTACTCCCTCCGTTCG 59.754 55.0 0.0 0.0 0.00 3.95 F
1084 1419 0.035915 GTTTCCTCACAGCTCTCCCC 60.036 60.0 0.0 0.0 0.00 4.81 F
1153 1489 0.616891 AGGTACGGATTTGGGTCCAC 59.383 55.0 0.0 0.0 38.21 4.02 F
2149 2533 0.174845 CATCATTGCCCCTTGCTGTG 59.825 55.0 0.0 0.0 42.00 3.66 F
3224 3609 0.610232 AGGGTGCTGCCAAATCAGTC 60.610 55.0 0.0 0.0 39.65 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2355 0.391661 CAGCCAACACGGATAGCACT 60.392 55.0 0.00 0.0 36.56 4.40 R
2021 2405 0.680061 AGAACCGGGAGAACAGTGAC 59.320 55.0 6.32 0.0 0.00 3.67 R
2543 2927 2.926200 CAAACTATCACAGCAGAGGTCG 59.074 50.0 0.00 0.0 0.00 4.79 R
3587 4040 1.508632 TCCGAAAAAGCAAGACCTCG 58.491 50.0 0.00 0.0 0.00 4.63 R
4237 4742 0.255890 AACGCCTGATGCCCTTGTAT 59.744 50.0 0.00 0.0 36.24 2.29 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
26 27 1.204146 TGGTAGCTCCTTCACCATCC 58.796 55.000 0.95 0.00 37.42 3.51
51 52 5.486526 GAAGGATCATACCTAATCCAGCAG 58.513 45.833 4.36 0.00 43.33 4.24
63 64 0.622136 TCCAGCAGAGCCATCAACAT 59.378 50.000 0.00 0.00 0.00 2.71
77 78 6.038356 GCCATCAACATCAAAAGAACCATAG 58.962 40.000 0.00 0.00 0.00 2.23
131 132 1.817099 CCATGCCGTCTGAAGCTCC 60.817 63.158 0.00 0.00 0.00 4.70
132 133 2.169789 CATGCCGTCTGAAGCTCCG 61.170 63.158 0.00 0.00 0.00 4.63
143 144 2.932614 CTGAAGCTCCGAAATCGTCATT 59.067 45.455 1.79 0.00 37.74 2.57
144 145 2.672874 TGAAGCTCCGAAATCGTCATTG 59.327 45.455 1.79 0.00 37.74 2.82
160 163 4.325204 CGTCATTGCATGTGAAGATTTTGG 59.675 41.667 9.03 0.00 0.00 3.28
190 194 5.348997 GCTCATAACTGACTACACACCTTTC 59.651 44.000 0.00 0.00 0.00 2.62
198 203 2.092103 ACTACACACCTTTCCCTTTGCA 60.092 45.455 0.00 0.00 0.00 4.08
199 204 2.086610 ACACACCTTTCCCTTTGCAT 57.913 45.000 0.00 0.00 0.00 3.96
206 211 1.969923 CTTTCCCTTTGCATGGGTCAA 59.030 47.619 20.55 14.77 44.84 3.18
214 219 3.448093 TTGCATGGGTCAACAATAGGA 57.552 42.857 0.00 0.00 0.00 2.94
225 230 5.647658 GGTCAACAATAGGATCATGTGACAA 59.352 40.000 0.00 0.00 32.11 3.18
241 246 7.283807 TCATGTGACAATTCCTAAGATGGATTG 59.716 37.037 0.00 0.00 35.83 2.67
254 259 9.021807 CCTAAGATGGATTGAAGATAATTGCAT 57.978 33.333 0.00 0.00 0.00 3.96
269 274 9.857656 AGATAATTGCATAGGAAATCTTCTTGA 57.142 29.630 0.00 0.00 0.00 3.02
275 280 8.613060 TGCATAGGAAATCTTCTTGATACATC 57.387 34.615 0.00 0.00 34.45 3.06
288 293 3.023119 TGATACATCCATTTGTGGTGGC 58.977 45.455 0.00 0.00 36.66 5.01
403 452 0.457035 CATGGTGCGGCTAATTTGCT 59.543 50.000 11.61 0.00 0.00 3.91
404 453 1.675483 CATGGTGCGGCTAATTTGCTA 59.325 47.619 11.61 0.00 0.00 3.49
405 454 1.091537 TGGTGCGGCTAATTTGCTAC 58.908 50.000 11.61 8.41 0.00 3.58
406 455 1.339631 TGGTGCGGCTAATTTGCTACT 60.340 47.619 11.61 0.00 0.00 2.57
407 456 1.330829 GGTGCGGCTAATTTGCTACTC 59.669 52.381 11.61 5.33 0.00 2.59
408 457 1.330829 GTGCGGCTAATTTGCTACTCC 59.669 52.381 11.61 0.00 0.00 3.85
409 458 0.945099 GCGGCTAATTTGCTACTCCC 59.055 55.000 11.61 0.00 0.00 4.30
410 459 1.475213 GCGGCTAATTTGCTACTCCCT 60.475 52.381 11.61 0.00 0.00 4.20
411 460 2.484889 CGGCTAATTTGCTACTCCCTC 58.515 52.381 11.61 0.00 0.00 4.30
412 461 2.807108 CGGCTAATTTGCTACTCCCTCC 60.807 54.545 11.61 0.00 0.00 4.30
413 462 2.484889 GCTAATTTGCTACTCCCTCCG 58.515 52.381 4.53 0.00 0.00 4.63
414 463 2.158943 GCTAATTTGCTACTCCCTCCGT 60.159 50.000 4.53 0.00 0.00 4.69
415 464 3.681874 GCTAATTTGCTACTCCCTCCGTT 60.682 47.826 4.53 0.00 0.00 4.44
416 465 2.693267 ATTTGCTACTCCCTCCGTTC 57.307 50.000 0.00 0.00 0.00 3.95
417 466 0.245539 TTTGCTACTCCCTCCGTTCG 59.754 55.000 0.00 0.00 0.00 3.95
418 467 1.601419 TTGCTACTCCCTCCGTTCGG 61.601 60.000 4.74 4.74 0.00 4.30
419 468 1.751927 GCTACTCCCTCCGTTCGGA 60.752 63.158 13.34 13.34 0.00 4.55
420 469 1.318158 GCTACTCCCTCCGTTCGGAA 61.318 60.000 14.79 0.04 33.41 4.30
421 470 1.180029 CTACTCCCTCCGTTCGGAAA 58.820 55.000 14.79 3.49 33.41 3.13
422 471 1.755380 CTACTCCCTCCGTTCGGAAAT 59.245 52.381 14.79 2.39 33.41 2.17
423 472 1.856629 ACTCCCTCCGTTCGGAAATA 58.143 50.000 14.79 2.82 33.41 1.40
424 473 1.479730 ACTCCCTCCGTTCGGAAATAC 59.520 52.381 14.79 0.00 33.41 1.89
425 474 1.755380 CTCCCTCCGTTCGGAAATACT 59.245 52.381 14.79 0.00 33.41 2.12
426 475 2.167900 CTCCCTCCGTTCGGAAATACTT 59.832 50.000 14.79 0.00 33.41 2.24
427 476 2.093869 TCCCTCCGTTCGGAAATACTTG 60.094 50.000 14.79 1.97 33.41 3.16
428 477 2.354403 CCCTCCGTTCGGAAATACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
429 478 2.928116 CCTCCGTTCGGAAATACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
430 479 3.581755 CTCCGTTCGGAAATACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
431 480 4.181578 CTCCGTTCGGAAATACTTGTCAT 58.818 43.478 14.79 0.00 33.41 3.06
432 481 4.178540 TCCGTTCGGAAATACTTGTCATC 58.821 43.478 11.66 0.00 0.00 2.92
433 482 3.930229 CCGTTCGGAAATACTTGTCATCA 59.070 43.478 5.19 0.00 0.00 3.07
434 483 4.390603 CCGTTCGGAAATACTTGTCATCAA 59.609 41.667 5.19 0.00 0.00 2.57
435 484 5.106869 CCGTTCGGAAATACTTGTCATCAAA 60.107 40.000 5.19 0.00 32.87 2.69
436 485 6.367421 CGTTCGGAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
437 486 7.021196 CGTTCGGAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
438 487 7.007367 CGTTCGGAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
439 488 6.851609 TCGGAAATACTTGTCATCAAAATGG 58.148 36.000 0.00 0.00 33.42 3.16
440 489 6.657117 TCGGAAATACTTGTCATCAAAATGGA 59.343 34.615 0.00 0.00 33.42 3.41
441 490 7.339212 TCGGAAATACTTGTCATCAAAATGGAT 59.661 33.333 0.00 0.00 33.42 3.41
442 491 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
448 497 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
449 498 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
450 499 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
451 500 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
452 501 7.147689 TGTCATCAAAATGGATAAAAGGGGATG 60.148 37.037 0.00 0.00 33.42 3.51
453 502 6.902416 TCATCAAAATGGATAAAAGGGGATGT 59.098 34.615 0.00 0.00 33.42 3.06
454 503 8.064389 TCATCAAAATGGATAAAAGGGGATGTA 58.936 33.333 0.00 0.00 33.42 2.29
455 504 8.873144 CATCAAAATGGATAAAAGGGGATGTAT 58.127 33.333 0.00 0.00 0.00 2.29
456 505 8.477419 TCAAAATGGATAAAAGGGGATGTATC 57.523 34.615 0.00 0.00 0.00 2.24
457 506 8.288812 TCAAAATGGATAAAAGGGGATGTATCT 58.711 33.333 0.00 0.00 0.00 1.98
458 507 9.586732 CAAAATGGATAAAAGGGGATGTATCTA 57.413 33.333 0.00 0.00 0.00 1.98
459 508 9.813826 AAAATGGATAAAAGGGGATGTATCTAG 57.186 33.333 0.00 0.00 0.00 2.43
460 509 8.757307 AATGGATAAAAGGGGATGTATCTAGA 57.243 34.615 0.00 0.00 0.00 2.43
461 510 8.940012 ATGGATAAAAGGGGATGTATCTAGAT 57.060 34.615 10.73 10.73 0.00 1.98
462 511 8.150827 TGGATAAAAGGGGATGTATCTAGATG 57.849 38.462 15.79 0.00 0.00 2.90
463 512 7.739444 TGGATAAAAGGGGATGTATCTAGATGT 59.261 37.037 15.79 1.25 0.00 3.06
464 513 9.268282 GGATAAAAGGGGATGTATCTAGATGTA 57.732 37.037 15.79 4.44 0.00 2.29
471 520 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
501 550 9.300681 AGATACATCTCTTTTTGTCCATTTTGA 57.699 29.630 0.00 0.00 29.30 2.69
503 552 9.865321 ATACATCTCTTTTTGTCCATTTTGATG 57.135 29.630 0.00 0.00 35.23 3.07
504 553 7.954835 ACATCTCTTTTTGTCCATTTTGATGA 58.045 30.769 0.00 0.00 33.85 2.92
505 554 7.869429 ACATCTCTTTTTGTCCATTTTGATGAC 59.131 33.333 0.00 0.00 33.85 3.06
506 555 7.345422 TCTCTTTTTGTCCATTTTGATGACA 57.655 32.000 0.00 0.00 0.00 3.58
507 556 7.780064 TCTCTTTTTGTCCATTTTGATGACAA 58.220 30.769 0.00 0.00 34.47 3.18
508 557 7.922278 TCTCTTTTTGTCCATTTTGATGACAAG 59.078 33.333 0.00 0.00 37.13 3.16
509 558 7.555087 TCTTTTTGTCCATTTTGATGACAAGT 58.445 30.769 0.00 0.00 37.13 3.16
510 559 8.690884 TCTTTTTGTCCATTTTGATGACAAGTA 58.309 29.630 0.00 0.00 37.13 2.24
511 560 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
512 561 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
513 562 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
514 563 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
515 564 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
516 565 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
517 566 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
518 567 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
519 568 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
520 569 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
521 570 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
522 571 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
523 572 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
524 573 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
525 574 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
526 575 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
527 576 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
549 598 6.715718 GGAGTACCTAGCAGACACATCTAATA 59.284 42.308 0.00 0.00 32.25 0.98
675 726 6.092955 AGTGATCATGCTTGACACAAAAAT 57.907 33.333 23.82 10.43 36.85 1.82
823 1150 3.589988 TCTCGAGAAGAGGCAATTTGTC 58.410 45.455 14.01 0.00 46.82 3.18
860 1187 8.719596 TCTAATTATTTACATTAGGCCTGGTCA 58.280 33.333 17.99 0.00 35.64 4.02
915 1242 2.037620 GCATCATCGAGTCAGGCCCT 62.038 60.000 0.00 0.00 0.00 5.19
917 1244 1.271934 CATCATCGAGTCAGGCCCTAG 59.728 57.143 0.00 0.00 0.00 3.02
928 1255 2.689813 GCCCTAGGCCCAAACCAT 59.310 61.111 2.05 0.00 44.06 3.55
950 1277 0.737367 TTGCTGCTGCTGCGTACTAG 60.737 55.000 23.38 3.43 43.34 2.57
970 1297 4.889427 CGAAGCCACGATGTCTCA 57.111 55.556 0.00 0.00 35.09 3.27
971 1298 3.122150 CGAAGCCACGATGTCTCAA 57.878 52.632 0.00 0.00 35.09 3.02
972 1299 1.428448 CGAAGCCACGATGTCTCAAA 58.572 50.000 0.00 0.00 35.09 2.69
973 1300 1.798223 CGAAGCCACGATGTCTCAAAA 59.202 47.619 0.00 0.00 35.09 2.44
974 1301 2.223144 CGAAGCCACGATGTCTCAAAAA 59.777 45.455 0.00 0.00 35.09 1.94
1073 1408 0.953471 CAATCACCGCCGTTTCCTCA 60.953 55.000 0.00 0.00 0.00 3.86
1084 1419 0.035915 GTTTCCTCACAGCTCTCCCC 60.036 60.000 0.00 0.00 0.00 4.81
1153 1489 0.616891 AGGTACGGATTTGGGTCCAC 59.383 55.000 0.00 0.00 38.21 4.02
1393 1738 3.199880 TGCTAGAGGAAATAGCTTGGC 57.800 47.619 0.00 0.00 44.83 4.52
1396 1741 3.563390 GCTAGAGGAAATAGCTTGGCTTG 59.437 47.826 0.00 0.00 41.96 4.01
1450 1795 8.391106 AGAAATTGTTATACTCGTCTGATTTGC 58.609 33.333 0.00 0.00 0.00 3.68
1500 1846 3.606595 TCAGCAGAGGAATGTTCAGAG 57.393 47.619 0.00 0.00 0.00 3.35
1568 1922 3.891366 CCCCACCCAGCAGAAATTTATAG 59.109 47.826 0.00 0.00 0.00 1.31
1569 1923 3.891366 CCCACCCAGCAGAAATTTATAGG 59.109 47.826 0.00 0.00 0.00 2.57
1664 2024 4.625311 GCTGCTGCATTAATTTACCGTTTT 59.375 37.500 11.11 0.00 39.41 2.43
1665 2025 5.802956 GCTGCTGCATTAATTTACCGTTTTA 59.197 36.000 11.11 0.00 39.41 1.52
1666 2026 6.309251 GCTGCTGCATTAATTTACCGTTTTAA 59.691 34.615 11.11 0.00 39.41 1.52
1705 2075 9.749490 CACATAAAACTTTCGACACGTATAAAT 57.251 29.630 0.00 0.00 0.00 1.40
1943 2327 2.387125 TTTGCCTCGTGTCAAAGCGC 62.387 55.000 0.00 0.00 0.00 5.92
2021 2405 1.068474 CTACAACGGAAGCCTTGACG 58.932 55.000 0.00 0.00 0.00 4.35
2149 2533 0.174845 CATCATTGCCCCTTGCTGTG 59.825 55.000 0.00 0.00 42.00 3.66
2543 2927 2.028020 GTCTGGCTACCCATATGGCTAC 60.028 54.545 16.97 5.09 41.21 3.58
3224 3609 0.610232 AGGGTGCTGCCAAATCAGTC 60.610 55.000 0.00 0.00 39.65 3.51
3338 3723 5.750067 TGTAGTCTTTGGTCGTTACTTTGAC 59.250 40.000 0.00 0.00 0.00 3.18
3370 3806 5.045012 TGCAGCTATCATTTTCCTCTGAT 57.955 39.130 0.00 0.00 36.19 2.90
3372 3808 4.152045 GCAGCTATCATTTTCCTCTGATCG 59.848 45.833 0.00 0.00 34.14 3.69
3426 3862 2.851263 ATGAACAGCCACCGTTCTTA 57.149 45.000 0.00 0.00 42.63 2.10
3433 3869 4.839121 ACAGCCACCGTTCTTATTTATGA 58.161 39.130 0.00 0.00 0.00 2.15
3435 3871 5.296780 ACAGCCACCGTTCTTATTTATGATG 59.703 40.000 0.00 0.00 0.00 3.07
3436 3872 5.296780 CAGCCACCGTTCTTATTTATGATGT 59.703 40.000 0.00 0.00 0.00 3.06
3587 4040 2.484889 GTTCTGTATCCCGATTCAGGC 58.515 52.381 10.35 2.78 37.00 4.85
3653 4106 1.337447 CGTAATCGGGGACTTGTGTGT 60.337 52.381 0.00 0.00 0.00 3.72
3803 4256 7.061789 CCCATAATTTAAGAGCGTTTTTGACAC 59.938 37.037 0.00 0.00 0.00 3.67
3824 4277 5.044428 ACTAGTGTAGTGTTAAGACGCTG 57.956 43.478 0.00 0.00 45.74 5.18
3825 4278 4.518211 ACTAGTGTAGTGTTAAGACGCTGT 59.482 41.667 0.00 0.00 45.74 4.40
3838 4291 5.562298 AAGACGCTGTTATATTATGGGGT 57.438 39.130 0.00 0.00 0.00 4.95
3858 4311 2.032620 TGGAGGGAGTAGCTTCGATTC 58.967 52.381 0.00 0.00 0.00 2.52
3867 4320 6.349033 GGGAGTAGCTTCGATTCTATCTCTTC 60.349 46.154 0.00 4.02 0.00 2.87
3870 4323 2.654528 GCTTCGATTCTATCTCTTCGCG 59.345 50.000 0.00 0.00 0.00 5.87
3920 4377 8.054572 TCCTTTGATTGAGATATCCAAACATGA 58.945 33.333 0.00 9.98 0.00 3.07
3978 4438 7.500559 ACATTTTAGAAGCATATCAGGTTCCTC 59.499 37.037 0.00 0.00 44.76 3.71
4084 4544 0.102481 ACAGCGGTATCTGCGTTAGG 59.898 55.000 0.00 0.00 37.59 2.69
4113 4573 7.044966 GGAATTTTCATAACTTATCAACACGCG 60.045 37.037 3.53 3.53 0.00 6.01
4149 4618 4.706962 AGCAAAGGGATTATGAACAAGGAC 59.293 41.667 0.00 0.00 0.00 3.85
4180 4649 5.687285 CCTTTTTCTTACACTGAACATGCAC 59.313 40.000 0.00 0.00 0.00 4.57
4187 4656 2.483877 ACACTGAACATGCACGGTAATG 59.516 45.455 0.00 2.40 0.00 1.90
4228 4733 4.581824 AGAGAAAACAGTGTTCATGCATGT 59.418 37.500 25.43 3.61 0.00 3.21
4229 4734 5.764686 AGAGAAAACAGTGTTCATGCATGTA 59.235 36.000 25.43 14.44 0.00 2.29
4230 4735 6.262944 AGAGAAAACAGTGTTCATGCATGTAA 59.737 34.615 25.43 15.45 0.00 2.41
4233 4738 6.579666 AAACAGTGTTCATGCATGTAAGAT 57.420 33.333 25.43 8.41 0.00 2.40
4234 4739 6.579666 AACAGTGTTCATGCATGTAAGATT 57.420 33.333 25.43 11.27 0.00 2.40
4235 4740 5.946298 ACAGTGTTCATGCATGTAAGATTG 58.054 37.500 25.43 21.64 0.00 2.67
4236 4741 5.474532 ACAGTGTTCATGCATGTAAGATTGT 59.525 36.000 25.43 22.16 0.00 2.71
4237 4742 6.654582 ACAGTGTTCATGCATGTAAGATTGTA 59.345 34.615 25.43 0.46 0.00 2.41
4238 4743 7.337689 ACAGTGTTCATGCATGTAAGATTGTAT 59.662 33.333 25.43 7.41 0.00 2.29
4239 4744 8.829612 CAGTGTTCATGCATGTAAGATTGTATA 58.170 33.333 25.43 0.00 0.00 1.47
4296 5093 1.356624 GCGGGCTACATGTGAATGC 59.643 57.895 9.11 7.45 0.00 3.56
4336 5378 4.451096 TGAGTTTAAACTTGATGCGAGGAC 59.549 41.667 21.40 5.47 39.88 3.85
4349 5391 0.994995 CGAGGACTTCATTCACAGCG 59.005 55.000 0.00 0.00 0.00 5.18
4432 5481 4.181578 ACATTTCTAACACTCGGGAATCG 58.818 43.478 0.00 0.00 40.90 3.34
4433 5482 2.953466 TTCTAACACTCGGGAATCGG 57.047 50.000 0.00 0.00 39.77 4.18
4459 5516 3.892581 GCGCCCATAGCCTGCAAC 61.893 66.667 0.00 0.00 38.78 4.17
4481 5538 9.608617 GCAACCAGTAGAAAAGTAAATTTAGAC 57.391 33.333 0.00 0.00 0.00 2.59
4510 5567 2.498644 TCAGACCACACACACCAAAA 57.501 45.000 0.00 0.00 0.00 2.44
4533 5590 1.186200 GGGCCATGTTTTCTTCCTCC 58.814 55.000 4.39 0.00 0.00 4.30
4538 5595 4.526970 GCCATGTTTTCTTCCTCCTCATA 58.473 43.478 0.00 0.00 0.00 2.15
4595 5652 8.583765 GTTGCGATTATTAGCTTTTGGTTAAAG 58.416 33.333 0.00 0.00 44.99 1.85
4631 5733 0.544357 CGGGGATATCCTGTAGGGCA 60.544 60.000 21.18 0.00 37.13 5.36
4667 5769 1.134367 CATCAAGCAAGCACATCCAGG 59.866 52.381 0.00 0.00 0.00 4.45
4698 5800 3.982576 AGAAACAAACACATCCCGAAC 57.017 42.857 0.00 0.00 0.00 3.95
4712 5814 6.149474 CACATCCCGAACTAGAGAAAAACAAT 59.851 38.462 0.00 0.00 0.00 2.71
4739 5841 2.747446 ACATGCCGCGGGATAATAAATC 59.253 45.455 32.53 8.57 0.00 2.17
4741 5843 0.725117 GCCGCGGGATAATAAATCCG 59.275 55.000 29.38 0.00 44.70 4.18
4749 5851 5.299148 CGGGATAATAAATCCGTTGTGGTA 58.701 41.667 0.00 0.00 39.07 3.25
4758 5860 1.411977 TCCGTTGTGGTAACGAGGAAA 59.588 47.619 13.10 0.00 45.64 3.13
4759 5861 1.528161 CCGTTGTGGTAACGAGGAAAC 59.472 52.381 13.10 0.00 45.64 2.78
4761 5863 2.867975 CGTTGTGGTAACGAGGAAACTT 59.132 45.455 6.34 0.00 45.64 2.66
4762 5864 3.060070 CGTTGTGGTAACGAGGAAACTTC 60.060 47.826 6.34 0.00 45.64 3.01
4763 5865 3.823281 TGTGGTAACGAGGAAACTTCA 57.177 42.857 0.00 0.00 44.43 3.02
4764 5866 3.460103 TGTGGTAACGAGGAAACTTCAC 58.540 45.455 0.00 0.00 44.43 3.18
4765 5867 2.473984 GTGGTAACGAGGAAACTTCACG 59.526 50.000 0.00 0.00 44.43 4.35
4766 5868 2.361757 TGGTAACGAGGAAACTTCACGA 59.638 45.455 12.64 0.00 44.43 4.35
4767 5869 2.728318 GGTAACGAGGAAACTTCACGAC 59.272 50.000 12.64 4.50 44.43 4.34
4768 5870 2.884894 AACGAGGAAACTTCACGACT 57.115 45.000 12.64 0.00 44.43 4.18
4769 5871 2.135664 ACGAGGAAACTTCACGACTG 57.864 50.000 12.64 0.00 44.43 3.51
4770 5872 1.679680 ACGAGGAAACTTCACGACTGA 59.320 47.619 12.64 0.00 44.43 3.41
4771 5873 2.100252 ACGAGGAAACTTCACGACTGAA 59.900 45.455 12.64 0.00 44.43 3.02
4772 5874 3.120792 CGAGGAAACTTCACGACTGAAA 58.879 45.455 0.00 0.00 44.43 2.69
4773 5875 3.741344 CGAGGAAACTTCACGACTGAAAT 59.259 43.478 0.00 0.00 44.43 2.17
4775 5877 5.404366 CGAGGAAACTTCACGACTGAAATAA 59.596 40.000 0.00 0.00 44.43 1.40
4776 5878 6.400091 CGAGGAAACTTCACGACTGAAATAAG 60.400 42.308 0.00 0.00 44.43 1.73
4778 5880 6.647067 AGGAAACTTCACGACTGAAATAAGAG 59.353 38.462 0.00 0.00 37.44 2.85
4779 5881 5.847670 AACTTCACGACTGAAATAAGAGC 57.152 39.130 0.00 0.00 35.92 4.09
4781 5883 5.164954 ACTTCACGACTGAAATAAGAGCTC 58.835 41.667 5.27 5.27 35.92 4.09
4782 5884 4.111375 TCACGACTGAAATAAGAGCTCC 57.889 45.455 10.93 0.00 0.00 4.70
4783 5885 2.854777 CACGACTGAAATAAGAGCTCCG 59.145 50.000 10.93 5.10 0.00 4.63
4786 5888 3.927142 CGACTGAAATAAGAGCTCCGTTT 59.073 43.478 10.93 9.11 0.00 3.60
4787 5889 4.031878 CGACTGAAATAAGAGCTCCGTTTC 59.968 45.833 20.57 20.57 0.00 2.78
4788 5890 3.927142 ACTGAAATAAGAGCTCCGTTTCG 59.073 43.478 21.30 18.75 32.85 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.181470 GGTGAAGGAGCTACCATCTTCTC 60.181 52.174 0.00 0.36 42.04 2.87
1 2 2.769095 GGTGAAGGAGCTACCATCTTCT 59.231 50.000 0.00 0.00 42.04 2.85
2 3 2.501723 TGGTGAAGGAGCTACCATCTTC 59.498 50.000 0.95 4.27 39.43 2.87
9 10 0.105039 CGGGATGGTGAAGGAGCTAC 59.895 60.000 0.00 0.00 0.00 3.58
26 27 4.621747 GCTGGATTAGGTATGATCCTTCGG 60.622 50.000 4.24 0.00 41.22 4.30
42 43 1.005097 TGTTGATGGCTCTGCTGGATT 59.995 47.619 0.00 0.00 0.00 3.01
43 44 0.622136 TGTTGATGGCTCTGCTGGAT 59.378 50.000 0.00 0.00 0.00 3.41
51 52 4.022068 TGGTTCTTTTGATGTTGATGGCTC 60.022 41.667 0.00 0.00 0.00 4.70
63 64 6.248433 AGCTCAATTCCTATGGTTCTTTTGA 58.752 36.000 0.00 0.00 0.00 2.69
77 78 2.027385 GGATGGGTGAAGCTCAATTCC 58.973 52.381 0.00 0.00 0.00 3.01
109 110 2.434185 TTCAGACGGCATGGTCGC 60.434 61.111 0.00 0.00 41.81 5.19
115 116 1.888436 TTCGGAGCTTCAGACGGCAT 61.888 55.000 0.00 0.00 0.00 4.40
121 122 1.544246 TGACGATTTCGGAGCTTCAGA 59.456 47.619 4.84 0.00 44.95 3.27
143 144 3.069872 ACTTGCCAAAATCTTCACATGCA 59.930 39.130 0.00 0.00 0.00 3.96
144 145 3.430895 CACTTGCCAAAATCTTCACATGC 59.569 43.478 0.00 0.00 0.00 4.06
160 163 4.092091 GTGTAGTCAGTTATGAGCACTTGC 59.908 45.833 0.00 0.00 35.66 4.01
198 203 5.103982 TCACATGATCCTATTGTTGACCCAT 60.104 40.000 0.00 0.00 0.00 4.00
199 204 4.227073 TCACATGATCCTATTGTTGACCCA 59.773 41.667 0.00 0.00 0.00 4.51
206 211 6.666678 AGGAATTGTCACATGATCCTATTGT 58.333 36.000 0.00 0.00 35.59 2.71
214 219 6.903516 TCCATCTTAGGAATTGTCACATGAT 58.096 36.000 0.00 0.00 33.93 2.45
255 260 8.910944 CAAATGGATGTATCAAGAAGATTTCCT 58.089 33.333 0.00 0.00 38.19 3.36
279 284 2.106338 TCATGAGAAGAAGCCACCACAA 59.894 45.455 0.00 0.00 0.00 3.33
288 293 8.495361 AGAATGAAATCACTCATGAGAAGAAG 57.505 34.615 29.27 12.48 38.57 2.85
403 452 1.856629 ATTTCCGAACGGAGGGAGTA 58.143 50.000 15.34 0.00 46.06 2.59
404 453 1.479730 GTATTTCCGAACGGAGGGAGT 59.520 52.381 15.34 1.96 46.06 3.85
405 454 1.755380 AGTATTTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
406 455 1.856629 AGTATTTCCGAACGGAGGGA 58.143 50.000 15.34 7.17 46.06 4.20
407 456 2.277084 CAAGTATTTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
408 457 2.928116 GACAAGTATTTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
409 458 3.581755 TGACAAGTATTTCCGAACGGAG 58.418 45.455 15.34 5.60 46.06 4.63
410 459 3.663995 TGACAAGTATTTCCGAACGGA 57.336 42.857 12.04 12.04 43.52 4.69
411 460 3.930229 TGATGACAAGTATTTCCGAACGG 59.070 43.478 6.94 6.94 0.00 4.44
412 461 5.524511 TTGATGACAAGTATTTCCGAACG 57.475 39.130 0.00 0.00 0.00 3.95
413 462 7.273381 CCATTTTGATGACAAGTATTTCCGAAC 59.727 37.037 0.00 0.00 37.32 3.95
414 463 7.175816 TCCATTTTGATGACAAGTATTTCCGAA 59.824 33.333 0.00 0.00 37.32 4.30
415 464 6.657117 TCCATTTTGATGACAAGTATTTCCGA 59.343 34.615 0.00 0.00 37.32 4.55
416 465 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
422 471 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
423 472 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
424 473 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
425 474 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
426 475 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
427 476 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
428 477 6.902416 ACATCCCCTTTTATCCATTTTGATGA 59.098 34.615 0.00 0.00 32.39 2.92
429 478 7.128234 ACATCCCCTTTTATCCATTTTGATG 57.872 36.000 0.00 0.00 33.80 3.07
430 479 9.093458 GATACATCCCCTTTTATCCATTTTGAT 57.907 33.333 0.00 0.00 0.00 2.57
431 480 8.288812 AGATACATCCCCTTTTATCCATTTTGA 58.711 33.333 0.00 0.00 0.00 2.69
432 481 8.482852 AGATACATCCCCTTTTATCCATTTTG 57.517 34.615 0.00 0.00 0.00 2.44
433 482 9.813826 CTAGATACATCCCCTTTTATCCATTTT 57.186 33.333 0.00 0.00 0.00 1.82
434 483 9.182642 TCTAGATACATCCCCTTTTATCCATTT 57.817 33.333 0.00 0.00 0.00 2.32
435 484 8.757307 TCTAGATACATCCCCTTTTATCCATT 57.243 34.615 0.00 0.00 0.00 3.16
436 485 8.776119 CATCTAGATACATCCCCTTTTATCCAT 58.224 37.037 4.54 0.00 0.00 3.41
437 486 7.739444 ACATCTAGATACATCCCCTTTTATCCA 59.261 37.037 4.54 0.00 0.00 3.41
438 487 8.152023 ACATCTAGATACATCCCCTTTTATCC 57.848 38.462 4.54 0.00 0.00 2.59
445 494 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
475 524 9.300681 TCAAAATGGACAAAAAGAGATGTATCT 57.699 29.630 0.00 0.00 40.50 1.98
477 526 9.865321 CATCAAAATGGACAAAAAGAGATGTAT 57.135 29.630 0.00 0.00 0.00 2.29
478 527 9.076781 TCATCAAAATGGACAAAAAGAGATGTA 57.923 29.630 0.00 0.00 33.42 2.29
479 528 7.869429 GTCATCAAAATGGACAAAAAGAGATGT 59.131 33.333 0.00 0.00 33.42 3.06
480 529 7.868922 TGTCATCAAAATGGACAAAAAGAGATG 59.131 33.333 0.00 0.00 33.42 2.90
481 530 7.954835 TGTCATCAAAATGGACAAAAAGAGAT 58.045 30.769 0.00 0.00 33.42 2.75
482 531 7.345422 TGTCATCAAAATGGACAAAAAGAGA 57.655 32.000 0.00 0.00 33.42 3.10
483 532 7.707893 ACTTGTCATCAAAATGGACAAAAAGAG 59.292 33.333 7.70 0.00 34.98 2.85
484 533 7.555087 ACTTGTCATCAAAATGGACAAAAAGA 58.445 30.769 7.70 0.00 34.98 2.52
485 534 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
486 535 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
487 536 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
488 537 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
489 538 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
490 539 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
491 540 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
492 541 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
493 542 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
494 543 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
495 544 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
496 545 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
497 546 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
498 547 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
499 548 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
500 549 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
501 550 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
502 551 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
503 552 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
504 553 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
505 554 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
506 555 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
507 556 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
508 557 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
509 558 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
510 559 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
511 560 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
512 561 0.967380 GGTACTCCCTCCGTCCGAAA 60.967 60.000 0.00 0.00 0.00 3.46
513 562 1.379044 GGTACTCCCTCCGTCCGAA 60.379 63.158 0.00 0.00 0.00 4.30
514 563 0.982852 TAGGTACTCCCTCCGTCCGA 60.983 60.000 0.00 0.00 44.81 4.55
515 564 0.534652 CTAGGTACTCCCTCCGTCCG 60.535 65.000 0.00 0.00 44.81 4.79
516 565 0.822944 GCTAGGTACTCCCTCCGTCC 60.823 65.000 0.00 0.00 44.81 4.79
517 566 0.106819 TGCTAGGTACTCCCTCCGTC 60.107 60.000 0.00 0.00 44.81 4.79
518 567 0.106619 CTGCTAGGTACTCCCTCCGT 60.107 60.000 0.00 0.00 44.81 4.69
519 568 0.183014 TCTGCTAGGTACTCCCTCCG 59.817 60.000 0.00 0.00 44.81 4.63
520 569 1.063867 TGTCTGCTAGGTACTCCCTCC 60.064 57.143 0.00 0.00 44.81 4.30
521 570 2.025898 GTGTCTGCTAGGTACTCCCTC 58.974 57.143 0.00 0.00 44.81 4.30
522 571 6.175536 AGATGTGTCTGCTAGGTACTCCCT 62.176 50.000 0.00 0.00 39.34 4.20
523 572 1.848652 TGTGTCTGCTAGGTACTCCC 58.151 55.000 0.00 0.00 41.75 4.30
524 573 3.292460 AGATGTGTCTGCTAGGTACTCC 58.708 50.000 0.00 0.00 34.34 3.85
525 574 6.642707 ATTAGATGTGTCTGCTAGGTACTC 57.357 41.667 0.00 0.00 36.39 2.59
526 575 9.983024 ATATATTAGATGTGTCTGCTAGGTACT 57.017 33.333 0.00 0.00 38.05 2.73
549 598 4.592942 AGCACCACATGTTGAGTTCATAT 58.407 39.130 3.55 0.00 0.00 1.78
780 850 9.116067 CGAGAAAAATATATGAACACCCCTAAA 57.884 33.333 0.00 0.00 0.00 1.85
781 851 8.487848 TCGAGAAAAATATATGAACACCCCTAA 58.512 33.333 0.00 0.00 0.00 2.69
782 852 8.025270 TCGAGAAAAATATATGAACACCCCTA 57.975 34.615 0.00 0.00 0.00 3.53
783 853 6.895782 TCGAGAAAAATATATGAACACCCCT 58.104 36.000 0.00 0.00 0.00 4.79
784 854 6.990349 TCTCGAGAAAAATATATGAACACCCC 59.010 38.462 14.01 0.00 0.00 4.95
785 855 8.433421 TTCTCGAGAAAAATATATGAACACCC 57.567 34.615 25.19 0.00 0.00 4.61
786 856 9.314321 TCTTCTCGAGAAAAATATATGAACACC 57.686 33.333 26.87 0.00 33.07 4.16
788 858 9.534565 CCTCTTCTCGAGAAAAATATATGAACA 57.465 33.333 26.87 1.55 42.62 3.18
789 859 8.491950 GCCTCTTCTCGAGAAAAATATATGAAC 58.508 37.037 26.87 10.35 42.62 3.18
790 860 8.204160 TGCCTCTTCTCGAGAAAAATATATGAA 58.796 33.333 26.87 2.20 42.62 2.57
791 861 7.726216 TGCCTCTTCTCGAGAAAAATATATGA 58.274 34.615 26.87 16.85 42.62 2.15
792 862 7.953158 TGCCTCTTCTCGAGAAAAATATATG 57.047 36.000 26.87 13.72 42.62 1.78
793 863 9.566432 AATTGCCTCTTCTCGAGAAAAATATAT 57.434 29.630 26.87 14.32 42.62 0.86
884 1211 1.825090 GATGATGCGGCCCATATTCA 58.175 50.000 6.69 3.27 33.29 2.57
915 1242 1.077005 AGCAAAGATGGTTTGGGCCTA 59.923 47.619 4.53 0.00 32.07 3.93
917 1244 0.037046 CAGCAAAGATGGTTTGGGCC 60.037 55.000 0.00 0.00 34.35 5.80
928 1255 1.301637 TACGCAGCAGCAGCAAAGA 60.302 52.632 10.77 0.00 45.49 2.52
950 1277 1.687494 GAGACATCGTGGCTTCGCAC 61.687 60.000 0.00 0.00 34.53 5.34
981 1308 1.263217 CGTGGCTTCGCACTAGTTTTT 59.737 47.619 0.00 0.00 0.00 1.94
982 1309 0.865769 CGTGGCTTCGCACTAGTTTT 59.134 50.000 0.00 0.00 0.00 2.43
983 1310 0.949105 CCGTGGCTTCGCACTAGTTT 60.949 55.000 0.00 0.00 0.00 2.66
984 1311 1.374252 CCGTGGCTTCGCACTAGTT 60.374 57.895 0.00 0.00 0.00 2.24
985 1312 2.214181 CTCCGTGGCTTCGCACTAGT 62.214 60.000 0.00 0.00 0.00 2.57
986 1313 1.517257 CTCCGTGGCTTCGCACTAG 60.517 63.158 0.00 0.00 0.00 2.57
987 1314 2.571757 CTCCGTGGCTTCGCACTA 59.428 61.111 0.00 0.00 0.00 2.74
988 1315 4.379243 CCTCCGTGGCTTCGCACT 62.379 66.667 0.00 0.00 0.00 4.40
997 1324 3.952628 GAAACCCTCGCCTCCGTGG 62.953 68.421 0.00 0.00 45.21 4.94
998 1325 2.434359 GAAACCCTCGCCTCCGTG 60.434 66.667 0.00 0.00 35.54 4.94
999 1326 4.065281 CGAAACCCTCGCCTCCGT 62.065 66.667 0.00 0.00 41.49 4.69
1073 1408 4.787280 CGGGGAGGGGAGAGCTGT 62.787 72.222 0.00 0.00 0.00 4.40
1153 1489 0.898320 TGCTCGAGAGGGAAAAGGAG 59.102 55.000 18.75 0.00 0.00 3.69
1199 1536 0.246635 AGTTCAGGTGGACGAATCGG 59.753 55.000 7.80 0.00 0.00 4.18
1206 1543 0.391597 TCGACCAAGTTCAGGTGGAC 59.608 55.000 0.00 0.00 38.69 4.02
1393 1738 5.997746 TCCAGAACAGATTTTACTGACCAAG 59.002 40.000 0.00 0.00 40.63 3.61
1396 1741 5.409826 CACTCCAGAACAGATTTTACTGACC 59.590 44.000 0.00 0.00 40.63 4.02
1500 1846 4.278170 TCTGAACAACAAACCCACATGATC 59.722 41.667 0.00 0.00 0.00 2.92
1568 1922 9.999660 TTTCAAATTAAAATAACACCCTAACCC 57.000 29.630 0.00 0.00 0.00 4.11
1601 1961 8.122952 CCATTCCGTAGAACAAAGAATTGATAC 58.877 37.037 0.00 0.00 39.91 2.24
1607 1967 5.066505 GCATCCATTCCGTAGAACAAAGAAT 59.933 40.000 0.00 0.00 33.97 2.40
1673 2039 7.116662 ACGTGTCGAAAGTTTTATGTGCTTATA 59.883 33.333 0.00 0.00 0.00 0.98
1971 2355 0.391661 CAGCCAACACGGATAGCACT 60.392 55.000 0.00 0.00 36.56 4.40
2021 2405 0.680061 AGAACCGGGAGAACAGTGAC 59.320 55.000 6.32 0.00 0.00 3.67
2149 2533 4.153117 CACAGAAGCTTAAGGTGACATCAC 59.847 45.833 8.16 3.27 45.72 3.06
2543 2927 2.926200 CAAACTATCACAGCAGAGGTCG 59.074 50.000 0.00 0.00 0.00 4.79
3370 3806 2.301870 ACACCTAGAGCATTTGAACCGA 59.698 45.455 0.00 0.00 0.00 4.69
3372 3808 5.705905 AGTTAACACCTAGAGCATTTGAACC 59.294 40.000 8.61 0.00 0.00 3.62
3587 4040 1.508632 TCCGAAAAAGCAAGACCTCG 58.491 50.000 0.00 0.00 0.00 4.63
3653 4106 9.868277 CATTAAGCATAAATTACAAACAAGGGA 57.132 29.630 0.00 0.00 0.00 4.20
3757 4210 2.037772 GGACGGAGGGAGTACTATCGTA 59.962 54.545 0.00 0.00 32.98 3.43
3803 4256 5.044428 ACAGCGTCTTAACACTACACTAG 57.956 43.478 0.00 0.00 0.00 2.57
3824 4277 4.850386 ACTCCCTCCACCCCATAATATAAC 59.150 45.833 0.00 0.00 0.00 1.89
3825 4278 5.114743 ACTCCCTCCACCCCATAATATAA 57.885 43.478 0.00 0.00 0.00 0.98
3838 4291 2.032620 GAATCGAAGCTACTCCCTCCA 58.967 52.381 0.00 0.00 0.00 3.86
3858 4311 2.356382 ACAGGAGAACGCGAAGAGATAG 59.644 50.000 15.93 0.00 0.00 2.08
3867 4320 1.618861 CTTACAGACAGGAGAACGCG 58.381 55.000 3.53 3.53 0.00 6.01
3870 4323 5.011586 AGTAGACCTTACAGACAGGAGAAC 58.988 45.833 0.00 0.00 35.14 3.01
3920 4377 8.823220 ACATGCTATTAAGAATAAAAGGGTGT 57.177 30.769 0.00 0.00 0.00 4.16
3958 4417 4.590647 CCAGAGGAACCTGATATGCTTCTA 59.409 45.833 0.00 0.00 36.29 2.10
3960 4419 3.737850 CCAGAGGAACCTGATATGCTTC 58.262 50.000 0.00 0.00 36.29 3.86
4084 4544 9.076596 GTGTTGATAAGTTATGAAAATTCCTGC 57.923 33.333 0.00 0.00 0.00 4.85
4113 4573 2.751806 CCCTTTGCTCTGTTTCAGATCC 59.248 50.000 0.00 0.00 39.92 3.36
4149 4618 4.041723 CAGTGTAAGAAAAAGGCGTTTGG 58.958 43.478 4.95 0.00 0.00 3.28
4180 4649 3.363426 CGTTTTGCAATGAACCATTACCG 59.637 43.478 0.00 0.00 32.35 4.02
4187 4656 1.139163 CTGCCGTTTTGCAATGAACC 58.861 50.000 0.00 0.00 41.51 3.62
4228 4733 6.533730 CCTGATGCCCTTGTATACAATCTTA 58.466 40.000 18.35 6.93 35.02 2.10
4229 4734 5.380043 CCTGATGCCCTTGTATACAATCTT 58.620 41.667 18.35 9.08 35.02 2.40
4230 4735 4.747931 GCCTGATGCCCTTGTATACAATCT 60.748 45.833 18.35 2.58 35.02 2.40
4233 4738 2.744823 CGCCTGATGCCCTTGTATACAA 60.745 50.000 17.16 17.16 36.24 2.41
4234 4739 1.202639 CGCCTGATGCCCTTGTATACA 60.203 52.381 0.08 0.08 36.24 2.29
4235 4740 1.202651 ACGCCTGATGCCCTTGTATAC 60.203 52.381 0.00 0.00 36.24 1.47
4236 4741 1.128200 ACGCCTGATGCCCTTGTATA 58.872 50.000 0.00 0.00 36.24 1.47
4237 4742 0.255890 AACGCCTGATGCCCTTGTAT 59.744 50.000 0.00 0.00 36.24 2.29
4238 4743 0.906066 TAACGCCTGATGCCCTTGTA 59.094 50.000 0.00 0.00 36.24 2.41
4239 4744 0.676782 GTAACGCCTGATGCCCTTGT 60.677 55.000 0.00 0.00 36.24 3.16
4336 5378 2.158449 GTGTTCTCCGCTGTGAATGAAG 59.842 50.000 0.00 0.00 0.00 3.02
4349 5391 4.283722 TCTTCTCTACCCAAAGTGTTCTCC 59.716 45.833 0.00 0.00 0.00 3.71
4387 5436 2.476619 GTGCATCAGCGTGTATATGTCC 59.523 50.000 0.00 0.00 46.23 4.02
4398 5447 2.624316 AGAAATGTTGTGCATCAGCG 57.376 45.000 0.00 0.00 46.23 5.18
4432 5481 3.338275 TATGGGCGCTGGGTTGACC 62.338 63.158 7.64 0.00 40.81 4.02
4433 5482 1.819632 CTATGGGCGCTGGGTTGAC 60.820 63.158 7.64 0.00 0.00 3.18
4447 5496 2.988010 TCTACTGGTTGCAGGCTATG 57.012 50.000 0.00 0.00 0.00 2.23
4481 5538 3.066380 TGTGTGGTCTGAAACATCATCG 58.934 45.455 0.00 0.00 0.00 3.84
4510 5567 1.534729 GAAGAAAACATGGCCCTCGT 58.465 50.000 0.00 0.00 0.00 4.18
4538 5595 9.507329 AAACACAATAGTCTGTCAATCTTACAT 57.493 29.630 0.00 0.00 0.00 2.29
4595 5652 1.342082 CCGACGACGACATGGAACAC 61.342 60.000 9.28 0.00 41.92 3.32
4631 5733 4.082026 GCTTGATGGTGGCTTTCTGTATTT 60.082 41.667 0.00 0.00 0.00 1.40
4667 5769 8.447053 GGATGTGTTTGTTTCTTCTCTCTAATC 58.553 37.037 0.00 0.00 0.00 1.75
4698 5800 7.115378 GGCATGTGTTTGATTGTTTTTCTCTAG 59.885 37.037 0.00 0.00 0.00 2.43
4712 5814 3.361158 CCCGCGGCATGTGTTTGA 61.361 61.111 22.85 0.00 0.00 2.69
4739 5841 1.528161 GTTTCCTCGTTACCACAACGG 59.472 52.381 9.39 1.45 43.24 4.44
4741 5843 3.872771 TGAAGTTTCCTCGTTACCACAAC 59.127 43.478 0.00 0.00 0.00 3.32
4749 5851 2.100252 TCAGTCGTGAAGTTTCCTCGTT 59.900 45.455 6.50 0.00 0.00 3.85
4758 5860 5.140747 AGCTCTTATTTCAGTCGTGAAGT 57.859 39.130 0.00 0.00 43.66 3.01
4759 5861 4.564769 GGAGCTCTTATTTCAGTCGTGAAG 59.435 45.833 14.64 0.00 43.66 3.02
4761 5863 3.427638 CGGAGCTCTTATTTCAGTCGTGA 60.428 47.826 14.64 0.00 0.00 4.35
4762 5864 2.854777 CGGAGCTCTTATTTCAGTCGTG 59.145 50.000 14.64 0.00 0.00 4.35
4763 5865 2.492484 ACGGAGCTCTTATTTCAGTCGT 59.508 45.455 14.64 7.58 0.00 4.34
4764 5866 3.152261 ACGGAGCTCTTATTTCAGTCG 57.848 47.619 14.64 6.90 0.00 4.18
4765 5867 4.031878 CGAAACGGAGCTCTTATTTCAGTC 59.968 45.833 24.47 9.69 31.11 3.51
4766 5868 3.927142 CGAAACGGAGCTCTTATTTCAGT 59.073 43.478 24.47 9.30 31.11 3.41
4767 5869 4.506838 CGAAACGGAGCTCTTATTTCAG 57.493 45.455 24.47 17.65 31.11 3.02


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

AutoCloner maintained by Alex Coulton.