Multiple sequence alignment - TraesCS7B01G193300

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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 TraesCS7B01G193300 chr7B 100.000 2898 0 0 1 2898 332173775 332170878 0.000000e+00 5352.0
1 TraesCS7B01G193300 chr7B 93.092 912 38 1 1169 2080 332242763 332241877 0.000000e+00 1312.0
2 TraesCS7B01G193300 chr7B 87.928 613 58 5 2298 2898 332241871 332241263 0.000000e+00 708.0
3 TraesCS7B01G193300 chr7B 93.280 372 23 1 802 1171 332243257 332242886 5.460000e-152 547.0
4 TraesCS7B01G193300 chr7B 83.554 377 43 6 804 1166 332256280 332255909 4.630000e-88 335.0
5 TraesCS7B01G193300 chr7A 91.518 1285 81 10 801 2080 195567754 195569015 0.000000e+00 1744.0
6 TraesCS7B01G193300 chr7A 94.433 503 15 7 765 1266 195733661 195734151 0.000000e+00 761.0
7 TraesCS7B01G193300 chr7A 87.884 619 58 5 2294 2898 195569017 195569632 0.000000e+00 712.0
8 TraesCS7B01G193300 chr7A 87.603 605 36 17 1476 2077 195734795 195735363 0.000000e+00 665.0
9 TraesCS7B01G193300 chr7A 86.334 622 67 8 2294 2898 195735368 195735988 0.000000e+00 662.0
10 TraesCS7B01G193300 chr7A 91.235 251 19 1 1257 1507 195734615 195734862 3.580000e-89 339.0
11 TraesCS7B01G193300 chr7A 88.933 253 27 1 1 252 195733178 195733430 7.800000e-81 311.0
12 TraesCS7B01G193300 chr7A 82.228 377 47 6 805 1166 195549946 195550317 1.010000e-79 307.0
13 TraesCS7B01G193300 chr7A 76.923 520 83 18 1 518 195567164 195567648 7.970000e-66 261.0
14 TraesCS7B01G193300 chr7A 95.588 136 5 1 581 716 195733525 195733659 1.750000e-52 217.0
15 TraesCS7B01G193300 chr7A 88.489 139 15 1 2080 2218 670949081 670948944 1.790000e-37 167.0
16 TraesCS7B01G193300 chr7A 85.714 70 10 0 2222 2291 671706057 671705988 1.110000e-09 75.0
17 TraesCS7B01G193300 chr7A 92.683 41 3 0 2173 2213 59803845 59803805 3.120000e-05 60.2
18 TraesCS7B01G193300 chr7A 91.892 37 3 0 2177 2213 209621655 209621691 5.000000e-03 52.8
19 TraesCS7B01G193300 chr7D 91.944 1142 78 8 940 2080 188319259 188318131 0.000000e+00 1587.0
20 TraesCS7B01G193300 chr7D 84.286 350 33 10 2566 2898 188309112 188308768 3.600000e-84 322.0
21 TraesCS7B01G193300 chr7D 87.234 282 35 1 2294 2574 188318129 188317848 1.300000e-83 320.0
22 TraesCS7B01G193300 chr7D 83.198 369 43 7 809 1166 188361633 188361273 1.300000e-83 320.0
23 TraesCS7B01G193300 chr7D 93.671 158 9 1 801 957 188319439 188319282 4.830000e-58 235.0
24 TraesCS7B01G193300 chr4D 90.411 146 13 1 616 760 51007075 51006930 1.060000e-44 191.0
25 TraesCS7B01G193300 chr5D 88.489 139 16 0 2080 2218 275421365 275421503 4.970000e-38 169.0
26 TraesCS7B01G193300 chr2D 86.111 144 19 1 2076 2218 379728065 379727922 1.390000e-33 154.0
27 TraesCS7B01G193300 chr2D 91.525 59 1 1 516 570 568125823 568125881 8.610000e-11 78.7
28 TraesCS7B01G193300 chr2D 95.238 42 1 1 542 582 603503653 603503612 6.700000e-07 65.8
29 TraesCS7B01G193300 chr2D 97.059 34 1 0 508 541 131313099 131313132 1.120000e-04 58.4
30 TraesCS7B01G193300 chr2D 96.970 33 1 0 509 541 631792664 631792696 4.030000e-04 56.5
31 TraesCS7B01G193300 chr2D 90.244 41 4 0 2173 2213 25754362 25754402 1.000000e-03 54.7
32 TraesCS7B01G193300 chr3A 86.029 136 19 0 2080 2215 497664545 497664680 2.330000e-31 147.0
33 TraesCS7B01G193300 chr6D 84.615 143 16 6 2078 2218 436324733 436324595 1.400000e-28 137.0
34 TraesCS7B01G193300 chr6D 89.706 68 7 0 2151 2218 291383354 291383287 1.430000e-13 87.9
35 TraesCS7B01G193300 chr4B 87.097 93 11 1 616 708 75124139 75124048 1.420000e-18 104.0
36 TraesCS7B01G193300 chr3B 90.141 71 3 2 515 581 284425143 284425213 3.980000e-14 89.8
37 TraesCS7B01G193300 chr3B 100.000 37 0 0 888 924 322659709 322659745 5.180000e-08 69.4
38 TraesCS7B01G193300 chr3B 93.478 46 1 2 542 585 828522937 828522982 1.860000e-07 67.6
39 TraesCS7B01G193300 chr3B 91.304 46 3 1 537 581 56067374 56067419 8.670000e-06 62.1
40 TraesCS7B01G193300 chr3B 92.683 41 3 0 2173 2213 803760899 803760859 3.120000e-05 60.2
41 TraesCS7B01G193300 chr5A 94.737 57 1 1 514 570 474578150 474578204 1.430000e-13 87.9
42 TraesCS7B01G193300 chr5A 84.127 63 6 4 2226 2286 676374116 676374176 1.120000e-04 58.4
43 TraesCS7B01G193300 chr1A 89.552 67 7 0 2225 2291 497588032 497587966 5.150000e-13 86.1
44 TraesCS7B01G193300 chr1A 87.273 55 2 3 516 570 549055237 549055188 1.120000e-04 58.4
45 TraesCS7B01G193300 chr5B 87.324 71 4 2 515 580 321417175 321417105 3.100000e-10 76.8
46 TraesCS7B01G193300 chr6B 91.667 48 1 3 542 587 69962938 69962984 2.410000e-06 63.9
47 TraesCS7B01G193300 chr6B 100.000 31 0 0 511 541 55822621 55822651 1.120000e-04 58.4
48 TraesCS7B01G193300 chr2A 92.683 41 3 0 2173 2213 48665299 48665339 3.120000e-05 60.2
49 TraesCS7B01G193300 chr2A 100.000 29 0 0 516 544 185123778 185123750 1.000000e-03 54.7
50 TraesCS7B01G193300 chr1D 92.683 41 3 0 2173 2213 238457115 238457155 3.120000e-05 60.2
51 TraesCS7B01G193300 chr2B 97.059 34 0 1 508 541 332407767 332407735 4.030000e-04 56.5


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 TraesCS7B01G193300 chr7B 332170878 332173775 2897 True 5352.000000 5352 100.000000 1 2898 1 chr7B.!!$R1 2897
1 TraesCS7B01G193300 chr7B 332241263 332243257 1994 True 855.666667 1312 91.433333 802 2898 3 chr7B.!!$R3 2096
2 TraesCS7B01G193300 chr7A 195567164 195569632 2468 False 905.666667 1744 85.441667 1 2898 3 chr7A.!!$F3 2897
3 TraesCS7B01G193300 chr7A 195733178 195735988 2810 False 492.500000 761 90.687667 1 2898 6 chr7A.!!$F4 2897
4 TraesCS7B01G193300 chr7D 188317848 188319439 1591 True 714.000000 1587 90.949667 801 2574 3 chr7D.!!$R3 1773

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
724 727 0.026803 GGCTTGATGCGTTGATCGTC 59.973 55.0 0.0 0.0 44.05 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 2829 0.532115 ATCTCCAAAAACATGGGCGC 59.468 50.0 0.0 0.0 41.05 6.53 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
30 31 0.531532 CATCGCTCCAGTCATGTCCC 60.532 60.000 0.00 0.00 0.00 4.46
42 43 0.740868 CATGTCCCGTCACGCATCTT 60.741 55.000 0.00 0.00 0.00 2.40
44 45 0.604073 TGTCCCGTCACGCATCTTTA 59.396 50.000 0.00 0.00 0.00 1.85
45 46 1.206132 TGTCCCGTCACGCATCTTTAT 59.794 47.619 0.00 0.00 0.00 1.40
102 103 2.026590 GCATGCCGCTACAATGCC 59.973 61.111 6.36 0.00 37.77 4.40
114 115 1.675310 CAATGCCGGCTCCAGTGAA 60.675 57.895 29.70 4.25 30.46 3.18
153 154 2.679837 AGCCGACATTAATGTGAAGCTG 59.320 45.455 25.42 8.63 41.95 4.24
157 158 3.065786 CGACATTAATGTGAAGCTGGCAT 59.934 43.478 25.42 0.00 41.95 4.40
164 166 1.072806 TGTGAAGCTGGCATTCTGAGT 59.927 47.619 2.81 0.00 0.00 3.41
195 197 1.346365 GCATGAATGTGCAGCAACTG 58.654 50.000 0.00 0.00 44.43 3.16
202 204 0.179070 TGTGCAGCAACTGGTTCGTA 60.179 50.000 0.00 0.00 31.21 3.43
211 213 0.251077 ACTGGTTCGTACGGGAGAGT 60.251 55.000 16.52 9.92 0.00 3.24
266 268 1.683790 GGTGTCAGACGCGTATGTGC 61.684 60.000 30.52 23.83 0.00 4.57
269 271 0.806102 GTCAGACGCGTATGTGCCAT 60.806 55.000 30.52 0.00 0.00 4.40
270 272 0.527600 TCAGACGCGTATGTGCCATC 60.528 55.000 30.52 7.23 0.00 3.51
272 274 1.587876 GACGCGTATGTGCCATCGA 60.588 57.895 13.97 0.00 0.00 3.59
274 276 0.529773 ACGCGTATGTGCCATCGATT 60.530 50.000 11.67 0.00 0.00 3.34
279 281 2.032894 CGTATGTGCCATCGATTTGGAC 60.033 50.000 9.29 9.02 39.25 4.02
283 285 0.249120 TGCCATCGATTTGGACGTCT 59.751 50.000 16.46 0.00 39.25 4.18
284 286 1.338674 TGCCATCGATTTGGACGTCTT 60.339 47.619 16.46 0.00 39.25 3.01
290 292 2.478894 TCGATTTGGACGTCTTCAAAGC 59.521 45.455 19.27 19.27 36.49 3.51
294 297 1.375326 GGACGTCTTCAAAGCCCCT 59.625 57.895 16.46 0.00 0.00 4.79
300 303 2.039418 GTCTTCAAAGCCCCTTGGTTT 58.961 47.619 0.00 0.00 45.20 3.27
303 306 4.390341 AAAGCCCCTTGGTTTGCA 57.610 50.000 0.00 0.00 42.81 4.08
306 309 0.178924 AAGCCCCTTGGTTTGCATCT 60.179 50.000 0.00 0.00 33.24 2.90
307 310 0.901580 AGCCCCTTGGTTTGCATCTG 60.902 55.000 0.00 0.00 0.00 2.90
309 312 1.593265 CCCTTGGTTTGCATCTGGC 59.407 57.895 0.00 0.00 45.13 4.85
321 324 6.091305 GGTTTGCATCTGGCTTTTAGAATTTC 59.909 38.462 0.00 0.00 45.15 2.17
322 325 5.329035 TGCATCTGGCTTTTAGAATTTCC 57.671 39.130 0.00 0.00 45.15 3.13
323 326 4.771577 TGCATCTGGCTTTTAGAATTTCCA 59.228 37.500 0.00 0.00 45.15 3.53
330 333 8.061304 TCTGGCTTTTAGAATTTCCAATATCCT 58.939 33.333 0.00 0.00 0.00 3.24
331 334 8.010733 TGGCTTTTAGAATTTCCAATATCCTG 57.989 34.615 0.00 0.00 0.00 3.86
332 335 7.838696 TGGCTTTTAGAATTTCCAATATCCTGA 59.161 33.333 0.00 0.00 0.00 3.86
333 336 8.138074 GGCTTTTAGAATTTCCAATATCCTGAC 58.862 37.037 0.00 0.00 0.00 3.51
334 337 8.907885 GCTTTTAGAATTTCCAATATCCTGACT 58.092 33.333 0.00 0.00 0.00 3.41
336 339 9.973661 TTTTAGAATTTCCAATATCCTGACTGA 57.026 29.630 0.00 0.00 0.00 3.41
338 341 9.784531 TTAGAATTTCCAATATCCTGACTGATC 57.215 33.333 0.00 0.00 0.00 2.92
339 342 8.043429 AGAATTTCCAATATCCTGACTGATCT 57.957 34.615 0.00 0.00 0.00 2.75
340 343 9.163894 AGAATTTCCAATATCCTGACTGATCTA 57.836 33.333 0.00 0.00 0.00 1.98
341 344 9.213799 GAATTTCCAATATCCTGACTGATCTAC 57.786 37.037 0.00 0.00 0.00 2.59
342 345 7.675161 TTTCCAATATCCTGACTGATCTACA 57.325 36.000 0.00 0.00 0.00 2.74
359 362 8.865420 TGATCTACAGACTAATAGGATACCAC 57.135 38.462 0.00 0.00 37.17 4.16
363 366 6.786967 ACAGACTAATAGGATACCACGTTT 57.213 37.500 0.00 0.00 37.17 3.60
364 367 7.886629 ACAGACTAATAGGATACCACGTTTA 57.113 36.000 0.00 0.00 37.17 2.01
376 379 2.289547 ACCACGTTTAATGACACACTGC 59.710 45.455 0.00 0.00 0.00 4.40
381 384 1.803334 TTAATGACACACTGCGTCCC 58.197 50.000 0.00 0.00 32.15 4.46
387 390 3.224324 ACACTGCGTCCCGACAGT 61.224 61.111 7.54 7.54 41.74 3.55
390 393 0.108804 CACTGCGTCCCGACAGTTAT 60.109 55.000 9.74 0.00 40.19 1.89
423 426 0.794473 CGAGTGTTTTAAGGGTCCGC 59.206 55.000 0.00 0.00 0.00 5.54
424 427 1.874739 CGAGTGTTTTAAGGGTCCGCA 60.875 52.381 0.00 0.00 0.00 5.69
425 428 2.223745 GAGTGTTTTAAGGGTCCGCAA 58.776 47.619 0.00 0.00 0.00 4.85
428 431 2.295070 GTGTTTTAAGGGTCCGCAATGT 59.705 45.455 0.00 0.00 0.00 2.71
430 433 3.754323 TGTTTTAAGGGTCCGCAATGTAG 59.246 43.478 0.00 0.00 0.00 2.74
431 434 2.702592 TTAAGGGTCCGCAATGTAGG 57.297 50.000 0.00 0.00 0.00 3.18
434 437 2.112815 GGGTCCGCAATGTAGGTGC 61.113 63.158 0.00 0.00 38.68 5.01
440 443 1.400494 CCGCAATGTAGGTGCCTTTAC 59.600 52.381 0.00 0.00 38.86 2.01
447 450 5.693769 ATGTAGGTGCCTTTACACTGTAT 57.306 39.130 0.00 0.00 40.52 2.29
455 458 5.354234 GTGCCTTTACACTGTATGTTAGCAT 59.646 40.000 0.00 0.00 43.19 3.79
457 460 5.584649 GCCTTTACACTGTATGTTAGCATGA 59.415 40.000 1.80 0.00 43.19 3.07
458 461 6.260936 GCCTTTACACTGTATGTTAGCATGAT 59.739 38.462 1.80 0.00 43.19 2.45
459 462 7.633621 CCTTTACACTGTATGTTAGCATGATG 58.366 38.462 1.80 0.00 43.19 3.07
536 539 9.813826 ATTAATACTCCCTCCATTCCAAAATAG 57.186 33.333 0.00 0.00 0.00 1.73
537 540 7.465900 AATACTCCCTCCATTCCAAAATAGA 57.534 36.000 0.00 0.00 0.00 1.98
538 541 7.654287 ATACTCCCTCCATTCCAAAATAGAT 57.346 36.000 0.00 0.00 0.00 1.98
539 542 5.699143 ACTCCCTCCATTCCAAAATAGATG 58.301 41.667 0.00 0.00 0.00 2.90
540 543 5.433051 ACTCCCTCCATTCCAAAATAGATGA 59.567 40.000 0.00 0.00 0.00 2.92
541 544 6.068853 ACTCCCTCCATTCCAAAATAGATGAA 60.069 38.462 0.00 0.00 0.00 2.57
542 545 6.367983 TCCCTCCATTCCAAAATAGATGAAG 58.632 40.000 0.00 0.00 0.00 3.02
543 546 6.068853 TCCCTCCATTCCAAAATAGATGAAGT 60.069 38.462 0.00 0.00 0.00 3.01
544 547 7.128728 TCCCTCCATTCCAAAATAGATGAAGTA 59.871 37.037 0.00 0.00 0.00 2.24
545 548 7.229506 CCCTCCATTCCAAAATAGATGAAGTAC 59.770 40.741 0.00 0.00 0.00 2.73
546 549 7.775093 CCTCCATTCCAAAATAGATGAAGTACA 59.225 37.037 0.00 0.00 0.00 2.90
547 550 9.177608 CTCCATTCCAAAATAGATGAAGTACAA 57.822 33.333 0.00 0.00 0.00 2.41
548 551 9.527157 TCCATTCCAAAATAGATGAAGTACAAA 57.473 29.630 0.00 0.00 0.00 2.83
549 552 9.793252 CCATTCCAAAATAGATGAAGTACAAAG 57.207 33.333 0.00 0.00 0.00 2.77
553 556 8.792633 TCCAAAATAGATGAAGTACAAAGTTGG 58.207 33.333 0.00 0.00 0.00 3.77
554 557 8.028938 CCAAAATAGATGAAGTACAAAGTTGGG 58.971 37.037 0.00 0.00 0.00 4.12
555 558 8.576442 CAAAATAGATGAAGTACAAAGTTGGGT 58.424 33.333 0.00 0.00 0.00 4.51
556 559 7.923414 AATAGATGAAGTACAAAGTTGGGTC 57.077 36.000 0.00 0.00 0.00 4.46
557 560 5.304686 AGATGAAGTACAAAGTTGGGTCA 57.695 39.130 0.00 0.00 0.00 4.02
558 561 5.880901 AGATGAAGTACAAAGTTGGGTCAT 58.119 37.500 0.00 0.00 0.00 3.06
559 562 5.940470 AGATGAAGTACAAAGTTGGGTCATC 59.060 40.000 14.35 14.35 0.00 2.92
560 563 5.304686 TGAAGTACAAAGTTGGGTCATCT 57.695 39.130 0.00 0.00 0.00 2.90
561 564 6.428083 TGAAGTACAAAGTTGGGTCATCTA 57.572 37.500 0.00 0.00 0.00 1.98
562 565 7.016153 TGAAGTACAAAGTTGGGTCATCTAT 57.984 36.000 0.00 0.00 0.00 1.98
563 566 7.458397 TGAAGTACAAAGTTGGGTCATCTATT 58.542 34.615 0.00 0.00 0.00 1.73
564 567 7.942341 TGAAGTACAAAGTTGGGTCATCTATTT 59.058 33.333 0.00 0.00 0.00 1.40
565 568 8.706322 AAGTACAAAGTTGGGTCATCTATTTT 57.294 30.769 0.00 0.00 0.00 1.82
566 569 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
567 570 7.942341 AGTACAAAGTTGGGTCATCTATTTTGA 59.058 33.333 0.00 0.00 0.00 2.69
568 571 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
569 572 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
570 573 8.650490 ACAAAGTTGGGTCATCTATTTTGAAAT 58.350 29.630 0.00 0.00 0.00 2.17
571 574 8.928733 CAAAGTTGGGTCATCTATTTTGAAATG 58.071 33.333 0.00 0.00 0.00 2.32
572 575 7.174107 AGTTGGGTCATCTATTTTGAAATGG 57.826 36.000 0.00 0.00 0.00 3.16
573 576 6.155049 AGTTGGGTCATCTATTTTGAAATGGG 59.845 38.462 0.00 0.00 0.00 4.00
574 577 4.961730 TGGGTCATCTATTTTGAAATGGGG 59.038 41.667 0.00 0.00 0.00 4.96
575 578 4.344968 GGGTCATCTATTTTGAAATGGGGG 59.655 45.833 0.00 0.00 0.00 5.40
595 598 2.514803 GGGTAGTGCACAAAAGTGGAT 58.485 47.619 21.04 0.00 0.00 3.41
599 602 5.393027 GGGTAGTGCACAAAAGTGGATAATG 60.393 44.000 21.04 0.00 0.00 1.90
685 688 1.928503 GGATCGAACGGCGTTATTCAA 59.071 47.619 26.87 9.69 41.80 2.69
698 701 5.337554 GCGTTATTCAATTTTGGTCTACCC 58.662 41.667 0.00 0.00 34.29 3.69
716 719 1.105167 CCATGGATGGCTTGATGCGT 61.105 55.000 5.56 0.00 41.75 5.24
717 720 0.742505 CATGGATGGCTTGATGCGTT 59.257 50.000 0.00 0.00 44.05 4.84
718 721 0.742505 ATGGATGGCTTGATGCGTTG 59.257 50.000 0.00 0.00 44.05 4.10
719 722 0.322366 TGGATGGCTTGATGCGTTGA 60.322 50.000 0.00 0.00 44.05 3.18
720 723 1.027357 GGATGGCTTGATGCGTTGAT 58.973 50.000 0.00 0.00 44.05 2.57
721 724 1.002033 GGATGGCTTGATGCGTTGATC 60.002 52.381 0.00 0.00 44.05 2.92
722 725 0.659427 ATGGCTTGATGCGTTGATCG 59.341 50.000 0.00 0.00 44.05 3.69
723 726 0.673333 TGGCTTGATGCGTTGATCGT 60.673 50.000 0.00 0.00 44.05 3.73
724 727 0.026803 GGCTTGATGCGTTGATCGTC 59.973 55.000 0.00 0.00 44.05 4.20
725 728 1.002366 GCTTGATGCGTTGATCGTCT 58.998 50.000 0.00 0.00 42.13 4.18
726 729 1.267235 GCTTGATGCGTTGATCGTCTG 60.267 52.381 0.00 0.00 42.13 3.51
727 730 2.262211 CTTGATGCGTTGATCGTCTGA 58.738 47.619 0.00 0.00 42.13 3.27
728 731 2.362169 TGATGCGTTGATCGTCTGAA 57.638 45.000 0.00 0.00 42.13 3.02
729 732 2.682836 TGATGCGTTGATCGTCTGAAA 58.317 42.857 0.00 0.00 42.13 2.69
730 733 3.063485 TGATGCGTTGATCGTCTGAAAA 58.937 40.909 0.00 0.00 42.13 2.29
731 734 3.684305 TGATGCGTTGATCGTCTGAAAAT 59.316 39.130 0.00 0.00 42.13 1.82
732 735 3.722555 TGCGTTGATCGTCTGAAAATC 57.277 42.857 0.00 0.00 42.13 2.17
733 736 2.092055 TGCGTTGATCGTCTGAAAATCG 59.908 45.455 0.00 0.00 42.13 3.34
734 737 2.092211 GCGTTGATCGTCTGAAAATCGT 59.908 45.455 0.00 0.00 42.13 3.73
735 738 3.778070 GCGTTGATCGTCTGAAAATCGTC 60.778 47.826 0.00 0.00 42.13 4.20
736 739 3.241678 CGTTGATCGTCTGAAAATCGTCC 60.242 47.826 0.00 0.00 34.52 4.79
737 740 3.586100 TGATCGTCTGAAAATCGTCCA 57.414 42.857 0.00 0.00 0.00 4.02
738 741 3.250744 TGATCGTCTGAAAATCGTCCAC 58.749 45.455 0.00 0.00 0.00 4.02
739 742 2.804697 TCGTCTGAAAATCGTCCACA 57.195 45.000 0.00 0.00 0.00 4.17
740 743 3.100658 TCGTCTGAAAATCGTCCACAA 57.899 42.857 0.00 0.00 0.00 3.33
741 744 3.459145 TCGTCTGAAAATCGTCCACAAA 58.541 40.909 0.00 0.00 0.00 2.83
742 745 3.493129 TCGTCTGAAAATCGTCCACAAAG 59.507 43.478 0.00 0.00 0.00 2.77
743 746 3.555518 GTCTGAAAATCGTCCACAAAGC 58.444 45.455 0.00 0.00 0.00 3.51
744 747 3.251004 GTCTGAAAATCGTCCACAAAGCT 59.749 43.478 0.00 0.00 0.00 3.74
745 748 3.882888 TCTGAAAATCGTCCACAAAGCTT 59.117 39.130 0.00 0.00 0.00 3.74
746 749 4.024048 TCTGAAAATCGTCCACAAAGCTTC 60.024 41.667 0.00 0.00 0.00 3.86
747 750 2.969443 AAATCGTCCACAAAGCTTCG 57.031 45.000 0.00 0.00 0.00 3.79
748 751 1.156736 AATCGTCCACAAAGCTTCGG 58.843 50.000 0.00 0.78 0.00 4.30
749 752 1.298859 ATCGTCCACAAAGCTTCGGC 61.299 55.000 0.00 0.00 42.17 5.54
840 892 4.270325 GTGACAACGAGATATACCAAAGCC 59.730 45.833 0.00 0.00 0.00 4.35
926 979 8.731275 AAGGTTGAAACTTTTAAAATTGGAGG 57.269 30.769 0.09 0.00 0.00 4.30
976 1069 5.067544 GTCTTGCCTCTTCTATAAGTACGGT 59.932 44.000 0.00 0.00 34.13 4.83
1007 1100 4.572909 CAGCGATATCATCTCATCCCAAA 58.427 43.478 3.12 0.00 0.00 3.28
1022 1115 8.594550 TCTCATCCCAAACTAGCTATTATAACC 58.405 37.037 0.00 0.00 0.00 2.85
1023 1116 7.383687 TCATCCCAAACTAGCTATTATAACCG 58.616 38.462 0.00 0.00 0.00 4.44
1117 1210 2.136196 CTCTCCGAGGATGTAGCGGC 62.136 65.000 0.00 0.00 44.45 6.53
1121 1214 2.280457 GAGGATGTAGCGGCTGCC 60.280 66.667 15.55 9.11 44.31 4.85
1138 1231 2.168106 CTGCCAGAGAGCTTACAGATGT 59.832 50.000 0.00 0.00 29.82 3.06
1280 1974 3.019564 GCCTACCTCAAGCAATGTTCAT 58.980 45.455 0.00 0.00 0.00 2.57
1378 2072 3.173151 GAAATGGGGAGGTGGAAACAAT 58.827 45.455 0.00 0.00 46.06 2.71
1416 2131 0.909623 AACGGTGGAGGGTATGGAAG 59.090 55.000 0.00 0.00 0.00 3.46
1449 2164 1.134228 GGTAACGGTGGGGGATATGT 58.866 55.000 0.00 0.00 0.00 2.29
1542 2257 3.829601 GGAAACAATGTTGGTGGGTATGA 59.170 43.478 0.00 0.00 0.00 2.15
1569 2284 2.457743 TACGGCAATTCTGGGCACGT 62.458 55.000 0.00 0.00 39.21 4.49
1583 2298 1.673009 CACGTTGGCGGTTATGGGT 60.673 57.895 0.00 0.00 43.45 4.51
1592 2307 1.611148 GCGGTTATGGGTGTGGTTACA 60.611 52.381 0.00 0.00 0.00 2.41
1594 2309 2.289819 CGGTTATGGGTGTGGTTACAGT 60.290 50.000 0.00 0.00 37.52 3.55
1652 2367 1.468985 CAATGGCGGTGGAAATGGTA 58.531 50.000 0.00 0.00 0.00 3.25
1674 2389 4.577677 TGGCAGCGGCTTTGGTGA 62.578 61.111 9.17 0.00 39.68 4.02
1730 2445 2.666207 GATACGGTGGTGGTGGCA 59.334 61.111 0.00 0.00 0.00 4.92
1753 2468 2.046604 GGTGGAGGTTACGGTGGC 60.047 66.667 0.00 0.00 0.00 5.01
1795 2510 5.988865 ATCCCTGATATGGATATGTGCAT 57.011 39.130 1.45 1.45 40.85 3.96
1951 2668 3.256136 AGGTCTGTAAGGTTGAGAAGTCG 59.744 47.826 0.00 0.00 0.00 4.18
1955 2672 1.001633 GTAAGGTTGAGAAGTCGGGCA 59.998 52.381 0.00 0.00 0.00 5.36
1957 2674 0.472471 AGGTTGAGAAGTCGGGCAAA 59.528 50.000 0.00 0.00 0.00 3.68
1993 2717 9.689075 CTTGTGTTGTTTCTTATCGTATGTATG 57.311 33.333 0.00 0.00 0.00 2.39
2088 2813 8.728596 ATGTGCCTATATATTATACTCCCTCC 57.271 38.462 0.00 0.00 0.00 4.30
2089 2814 7.658260 TGTGCCTATATATTATACTCCCTCCA 58.342 38.462 0.00 0.00 0.00 3.86
2090 2815 8.296906 TGTGCCTATATATTATACTCCCTCCAT 58.703 37.037 0.00 0.00 0.00 3.41
2091 2816 9.160412 GTGCCTATATATTATACTCCCTCCATT 57.840 37.037 0.00 0.00 0.00 3.16
2092 2817 9.744125 TGCCTATATATTATACTCCCTCCATTT 57.256 33.333 0.00 0.00 0.00 2.32
2100 2825 8.814038 ATTATACTCCCTCCATTTCATAATGC 57.186 34.615 0.00 0.00 39.87 3.56
2101 2826 4.524802 ACTCCCTCCATTTCATAATGCA 57.475 40.909 0.00 0.00 39.87 3.96
2102 2827 4.467769 ACTCCCTCCATTTCATAATGCAG 58.532 43.478 0.00 0.00 39.87 4.41
2103 2828 4.079558 ACTCCCTCCATTTCATAATGCAGT 60.080 41.667 0.00 0.00 39.87 4.40
2104 2829 4.209538 TCCCTCCATTTCATAATGCAGTG 58.790 43.478 0.00 0.00 39.87 3.66
2105 2830 3.243636 CCCTCCATTTCATAATGCAGTGC 60.244 47.826 8.58 8.58 39.87 4.40
2106 2831 3.549423 CCTCCATTTCATAATGCAGTGCG 60.549 47.826 11.20 0.00 39.87 5.34
2107 2832 2.121786 CCATTTCATAATGCAGTGCGC 58.878 47.619 11.20 0.00 39.87 6.09
2108 2833 2.121786 CATTTCATAATGCAGTGCGCC 58.878 47.619 11.20 0.00 41.33 6.53
2109 2834 0.455410 TTTCATAATGCAGTGCGCCC 59.545 50.000 11.20 0.00 41.33 6.13
2110 2835 0.679321 TTCATAATGCAGTGCGCCCA 60.679 50.000 11.20 0.00 41.33 5.36
2111 2836 0.466007 TCATAATGCAGTGCGCCCAT 60.466 50.000 11.20 0.00 41.33 4.00
2112 2837 0.318360 CATAATGCAGTGCGCCCATG 60.318 55.000 11.20 7.44 41.33 3.66
2113 2838 0.752743 ATAATGCAGTGCGCCCATGT 60.753 50.000 11.20 0.00 41.33 3.21
2114 2839 0.964860 TAATGCAGTGCGCCCATGTT 60.965 50.000 11.20 0.00 41.33 2.71
2115 2840 1.818959 AATGCAGTGCGCCCATGTTT 61.819 50.000 11.20 0.00 41.33 2.83
2116 2841 1.818959 ATGCAGTGCGCCCATGTTTT 61.819 50.000 11.20 0.00 41.33 2.43
2117 2842 1.300853 GCAGTGCGCCCATGTTTTT 60.301 52.632 4.18 0.00 32.94 1.94
2118 2843 1.559149 GCAGTGCGCCCATGTTTTTG 61.559 55.000 4.18 0.00 32.94 2.44
2119 2844 0.945265 CAGTGCGCCCATGTTTTTGG 60.945 55.000 4.18 0.00 36.46 3.28
2120 2845 1.112315 AGTGCGCCCATGTTTTTGGA 61.112 50.000 4.18 0.00 39.25 3.53
2121 2846 0.667184 GTGCGCCCATGTTTTTGGAG 60.667 55.000 4.18 0.00 39.25 3.86
2122 2847 0.825425 TGCGCCCATGTTTTTGGAGA 60.825 50.000 4.18 0.00 39.25 3.71
2123 2848 0.532115 GCGCCCATGTTTTTGGAGAT 59.468 50.000 0.00 0.00 39.25 2.75
2124 2849 1.066929 GCGCCCATGTTTTTGGAGATT 60.067 47.619 0.00 0.00 39.25 2.40
2125 2850 2.879826 CGCCCATGTTTTTGGAGATTC 58.120 47.619 0.00 0.00 39.25 2.52
2126 2851 2.230992 CGCCCATGTTTTTGGAGATTCA 59.769 45.455 0.00 0.00 39.25 2.57
2127 2852 3.305950 CGCCCATGTTTTTGGAGATTCAA 60.306 43.478 0.00 0.00 39.25 2.69
2128 2853 3.996363 GCCCATGTTTTTGGAGATTCAAC 59.004 43.478 0.00 0.00 39.25 3.18
2129 2854 4.262592 GCCCATGTTTTTGGAGATTCAACT 60.263 41.667 0.00 0.00 39.25 3.16
2130 2855 5.742838 GCCCATGTTTTTGGAGATTCAACTT 60.743 40.000 0.00 0.00 39.25 2.66
2131 2856 6.290605 CCCATGTTTTTGGAGATTCAACTTT 58.709 36.000 0.00 0.00 39.25 2.66
2132 2857 6.203338 CCCATGTTTTTGGAGATTCAACTTTG 59.797 38.462 0.00 0.00 39.25 2.77
2133 2858 6.985645 CCATGTTTTTGGAGATTCAACTTTGA 59.014 34.615 0.00 0.00 39.25 2.69
2134 2859 7.658575 CCATGTTTTTGGAGATTCAACTTTGAT 59.341 33.333 0.00 0.00 39.25 2.57
2135 2860 8.706035 CATGTTTTTGGAGATTCAACTTTGATC 58.294 33.333 0.00 0.00 37.00 2.92
2136 2861 7.780064 TGTTTTTGGAGATTCAACTTTGATCA 58.220 30.769 0.00 0.00 37.00 2.92
2137 2862 8.423349 TGTTTTTGGAGATTCAACTTTGATCAT 58.577 29.630 0.00 0.00 37.00 2.45
2138 2863 9.912634 GTTTTTGGAGATTCAACTTTGATCATA 57.087 29.630 0.00 0.00 37.00 2.15
2222 2947 6.339587 TGAATACAAATTCAAAGGTCACCC 57.660 37.500 0.00 0.00 46.64 4.61
2223 2948 5.835819 TGAATACAAATTCAAAGGTCACCCA 59.164 36.000 0.00 0.00 46.64 4.51
2224 2949 6.496565 TGAATACAAATTCAAAGGTCACCCAT 59.503 34.615 0.00 0.00 46.64 4.00
2225 2950 4.605640 ACAAATTCAAAGGTCACCCATG 57.394 40.909 0.00 0.00 0.00 3.66
2226 2951 3.966665 ACAAATTCAAAGGTCACCCATGT 59.033 39.130 0.00 0.00 0.00 3.21
2227 2952 4.408596 ACAAATTCAAAGGTCACCCATGTT 59.591 37.500 0.00 0.00 0.00 2.71
2228 2953 4.605640 AATTCAAAGGTCACCCATGTTG 57.394 40.909 0.00 0.00 0.00 3.33
2229 2954 1.993956 TCAAAGGTCACCCATGTTGG 58.006 50.000 0.00 0.00 37.25 3.77
2230 2955 1.216678 TCAAAGGTCACCCATGTTGGT 59.783 47.619 0.00 0.00 39.96 3.67
2231 2956 2.038659 CAAAGGTCACCCATGTTGGTT 58.961 47.619 0.00 0.00 36.12 3.67
2232 2957 3.117474 TCAAAGGTCACCCATGTTGGTTA 60.117 43.478 0.00 0.00 36.12 2.85
2233 2958 3.603965 AAGGTCACCCATGTTGGTTAA 57.396 42.857 0.00 0.00 36.12 2.01
2234 2959 3.603965 AGGTCACCCATGTTGGTTAAA 57.396 42.857 0.00 0.00 36.12 1.52
2235 2960 4.126520 AGGTCACCCATGTTGGTTAAAT 57.873 40.909 0.00 0.00 36.12 1.40
2236 2961 4.488770 AGGTCACCCATGTTGGTTAAATT 58.511 39.130 0.00 0.00 36.12 1.82
2237 2962 4.904853 AGGTCACCCATGTTGGTTAAATTT 59.095 37.500 0.00 0.00 36.12 1.82
2238 2963 6.078664 AGGTCACCCATGTTGGTTAAATTTA 58.921 36.000 0.00 0.00 36.12 1.40
2239 2964 6.728632 AGGTCACCCATGTTGGTTAAATTTAT 59.271 34.615 0.00 0.00 36.12 1.40
2240 2965 7.896496 AGGTCACCCATGTTGGTTAAATTTATA 59.104 33.333 0.00 0.00 36.12 0.98
2241 2966 8.194769 GGTCACCCATGTTGGTTAAATTTATAG 58.805 37.037 0.00 0.00 36.12 1.31
2242 2967 8.745590 GTCACCCATGTTGGTTAAATTTATAGT 58.254 33.333 0.00 0.00 36.12 2.12
2243 2968 8.962679 TCACCCATGTTGGTTAAATTTATAGTC 58.037 33.333 0.00 0.00 36.12 2.59
2244 2969 8.744652 CACCCATGTTGGTTAAATTTATAGTCA 58.255 33.333 0.00 0.00 36.12 3.41
2245 2970 9.315363 ACCCATGTTGGTTAAATTTATAGTCAA 57.685 29.630 0.00 0.00 33.91 3.18
2264 2989 7.914537 AGTCAAAGTTAAATCTCAAAAAGCG 57.085 32.000 0.00 0.00 0.00 4.68
2265 2990 7.480810 AGTCAAAGTTAAATCTCAAAAAGCGT 58.519 30.769 0.00 0.00 0.00 5.07
2266 2991 7.432252 AGTCAAAGTTAAATCTCAAAAAGCGTG 59.568 33.333 0.00 0.00 0.00 5.34
2267 2992 7.431084 GTCAAAGTTAAATCTCAAAAAGCGTGA 59.569 33.333 0.00 0.00 0.00 4.35
2268 2993 7.971168 TCAAAGTTAAATCTCAAAAAGCGTGAA 59.029 29.630 0.00 0.00 0.00 3.18
2269 2994 7.679659 AAGTTAAATCTCAAAAAGCGTGAAC 57.320 32.000 0.00 0.00 0.00 3.18
2270 2995 5.907391 AGTTAAATCTCAAAAAGCGTGAACG 59.093 36.000 0.00 0.00 43.27 3.95
2287 3012 7.937387 CGTGAACGCATTATATTATGGAATG 57.063 36.000 4.02 0.00 34.37 2.67
2288 3013 6.960992 CGTGAACGCATTATATTATGGAATGG 59.039 38.462 4.02 0.00 32.33 3.16
2289 3014 7.148490 CGTGAACGCATTATATTATGGAATGGA 60.148 37.037 4.02 0.00 32.33 3.41
2290 3015 8.177663 GTGAACGCATTATATTATGGAATGGAG 58.822 37.037 4.02 0.00 32.33 3.86
2291 3016 7.882791 TGAACGCATTATATTATGGAATGGAGT 59.117 33.333 4.02 0.00 32.33 3.85
2292 3017 9.378551 GAACGCATTATATTATGGAATGGAGTA 57.621 33.333 4.02 0.00 32.33 2.59
2330 3055 4.021104 CGATTTAGATGAGTAGCCCCATGA 60.021 45.833 0.00 0.00 0.00 3.07
2367 3092 1.515954 CCCGAGCGGTCTACAACAT 59.484 57.895 13.48 0.00 0.00 2.71
2410 3135 9.720769 CTCTTCTTAAACTATTGTTTCCTACCA 57.279 33.333 8.57 0.00 44.35 3.25
2537 3262 2.614481 GCAAGGAAATCACCACCGAGTA 60.614 50.000 0.00 0.00 0.00 2.59
2648 3374 0.970937 AGAGCCCGAGAACGATCCAA 60.971 55.000 0.00 0.00 42.66 3.53
2649 3375 0.528684 GAGCCCGAGAACGATCCAAG 60.529 60.000 0.00 0.00 42.66 3.61
2659 3385 3.576982 AGAACGATCCAAGGAAGTACACA 59.423 43.478 0.00 0.00 0.00 3.72
2678 3405 9.915629 AGTACACAATTTGACAAGTAAAAACAA 57.084 25.926 2.79 0.00 0.00 2.83
2689 3417 9.809096 TGACAAGTAAAAACAATGAAAGCATAA 57.191 25.926 0.00 0.00 33.44 1.90
2699 3427 6.732154 ACAATGAAAGCATAATCATCTTCGG 58.268 36.000 0.00 0.00 35.29 4.30
2759 3504 6.153067 TGTTTCAAACGTGTTGACTTGAAAT 58.847 32.000 20.39 0.00 0.00 2.17
2852 3597 9.494055 CCACTAGGATTTAGGAATGATATAGGA 57.506 37.037 0.00 0.00 36.89 2.94
2877 3622 7.584987 AGTTGACATAAAGAAAAGGAATGACG 58.415 34.615 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.156645 GGACATGACTGGAGCGATGC 61.157 60.000 0.00 0.00 0.00 3.91
30 31 5.458779 TGTTCTGATATAAAGATGCGTGACG 59.541 40.000 0.00 0.00 0.00 4.35
42 43 5.289595 GTCTCCGTGCATGTTCTGATATAA 58.710 41.667 4.96 0.00 0.00 0.98
44 45 3.493350 GGTCTCCGTGCATGTTCTGATAT 60.493 47.826 4.96 0.00 0.00 1.63
45 46 2.159099 GGTCTCCGTGCATGTTCTGATA 60.159 50.000 4.96 0.00 0.00 2.15
102 103 1.738099 CGACCTTTCACTGGAGCCG 60.738 63.158 0.00 0.00 0.00 5.52
114 115 4.052229 CGGAGCGGACACGACCTT 62.052 66.667 0.00 0.00 44.60 3.50
153 154 1.198637 GTCAGCACAACTCAGAATGCC 59.801 52.381 0.00 0.00 38.92 4.40
157 158 0.249868 CCGGTCAGCACAACTCAGAA 60.250 55.000 0.00 0.00 0.00 3.02
195 197 0.450983 CTCACTCTCCCGTACGAACC 59.549 60.000 18.76 0.00 0.00 3.62
242 244 4.742201 CGCGTCTGACACCCCAGG 62.742 72.222 8.73 0.00 34.99 4.45
266 268 2.616960 TGAAGACGTCCAAATCGATGG 58.383 47.619 13.01 0.00 42.12 3.51
269 271 2.478894 GCTTTGAAGACGTCCAAATCGA 59.521 45.455 13.01 3.12 32.60 3.59
270 272 2.412847 GGCTTTGAAGACGTCCAAATCG 60.413 50.000 13.01 6.99 32.60 3.34
272 274 1.886542 GGGCTTTGAAGACGTCCAAAT 59.113 47.619 13.01 0.00 33.77 2.32
274 276 0.536460 GGGGCTTTGAAGACGTCCAA 60.536 55.000 13.01 7.57 33.77 3.53
279 281 0.537371 ACCAAGGGGCTTTGAAGACG 60.537 55.000 4.27 0.00 37.90 4.18
283 285 0.467804 GCAAACCAAGGGGCTTTGAA 59.532 50.000 5.22 0.00 37.36 2.69
284 286 0.689080 TGCAAACCAAGGGGCTTTGA 60.689 50.000 5.22 0.00 37.36 2.69
290 292 1.891722 GCCAGATGCAAACCAAGGGG 61.892 60.000 0.00 0.00 40.77 4.79
294 297 3.894427 TCTAAAAGCCAGATGCAAACCAA 59.106 39.130 0.00 0.00 44.83 3.67
300 303 4.771577 TGGAAATTCTAAAAGCCAGATGCA 59.228 37.500 0.00 0.00 44.83 3.96
303 306 8.864087 GGATATTGGAAATTCTAAAAGCCAGAT 58.136 33.333 0.00 0.00 0.00 2.90
306 309 7.838696 TCAGGATATTGGAAATTCTAAAAGCCA 59.161 33.333 0.00 0.00 0.00 4.75
307 310 8.138074 GTCAGGATATTGGAAATTCTAAAAGCC 58.862 37.037 0.00 0.00 0.00 4.35
321 324 6.493115 AGTCTGTAGATCAGTCAGGATATTGG 59.507 42.308 0.00 0.00 43.97 3.16
322 325 7.523293 AGTCTGTAGATCAGTCAGGATATTG 57.477 40.000 0.00 0.00 43.97 1.90
323 326 9.821240 ATTAGTCTGTAGATCAGTCAGGATATT 57.179 33.333 0.00 0.00 43.97 1.28
330 333 9.727859 GTATCCTATTAGTCTGTAGATCAGTCA 57.272 37.037 0.00 0.00 43.97 3.41
331 334 9.169592 GGTATCCTATTAGTCTGTAGATCAGTC 57.830 40.741 0.00 0.00 43.97 3.51
332 335 8.670490 TGGTATCCTATTAGTCTGTAGATCAGT 58.330 37.037 0.00 0.00 43.97 3.41
333 336 8.952278 GTGGTATCCTATTAGTCTGTAGATCAG 58.048 40.741 0.00 0.00 44.85 2.90
334 337 7.606839 CGTGGTATCCTATTAGTCTGTAGATCA 59.393 40.741 0.00 0.00 0.00 2.92
335 338 7.607223 ACGTGGTATCCTATTAGTCTGTAGATC 59.393 40.741 0.00 0.00 0.00 2.75
336 339 7.460071 ACGTGGTATCCTATTAGTCTGTAGAT 58.540 38.462 0.00 0.00 0.00 1.98
337 340 6.835174 ACGTGGTATCCTATTAGTCTGTAGA 58.165 40.000 0.00 0.00 0.00 2.59
338 341 7.507733 AACGTGGTATCCTATTAGTCTGTAG 57.492 40.000 0.00 0.00 0.00 2.74
339 342 7.886629 AAACGTGGTATCCTATTAGTCTGTA 57.113 36.000 0.00 0.00 0.00 2.74
340 343 6.786967 AAACGTGGTATCCTATTAGTCTGT 57.213 37.500 0.00 0.00 0.00 3.41
341 344 9.193133 CATTAAACGTGGTATCCTATTAGTCTG 57.807 37.037 0.00 0.00 0.00 3.51
342 345 9.139734 TCATTAAACGTGGTATCCTATTAGTCT 57.860 33.333 0.00 0.00 0.00 3.24
343 346 9.189723 GTCATTAAACGTGGTATCCTATTAGTC 57.810 37.037 0.00 0.00 0.00 2.59
344 347 8.698210 TGTCATTAAACGTGGTATCCTATTAGT 58.302 33.333 0.00 0.00 0.00 2.24
345 348 8.975439 GTGTCATTAAACGTGGTATCCTATTAG 58.025 37.037 0.00 0.00 0.00 1.73
346 349 8.476447 TGTGTCATTAAACGTGGTATCCTATTA 58.524 33.333 0.00 0.00 0.00 0.98
347 350 7.279313 GTGTGTCATTAAACGTGGTATCCTATT 59.721 37.037 0.00 0.00 0.00 1.73
348 351 6.759827 GTGTGTCATTAAACGTGGTATCCTAT 59.240 38.462 0.00 0.00 0.00 2.57
349 352 6.071221 AGTGTGTCATTAAACGTGGTATCCTA 60.071 38.462 0.00 0.00 0.00 2.94
350 353 4.933400 GTGTGTCATTAAACGTGGTATCCT 59.067 41.667 0.00 0.00 0.00 3.24
351 354 4.933400 AGTGTGTCATTAAACGTGGTATCC 59.067 41.667 0.00 0.00 0.00 2.59
352 355 5.670341 GCAGTGTGTCATTAAACGTGGTATC 60.670 44.000 0.00 0.00 0.00 2.24
353 356 4.153475 GCAGTGTGTCATTAAACGTGGTAT 59.847 41.667 0.00 0.00 0.00 2.73
354 357 3.495377 GCAGTGTGTCATTAAACGTGGTA 59.505 43.478 0.00 0.00 0.00 3.25
355 358 2.289547 GCAGTGTGTCATTAAACGTGGT 59.710 45.455 0.00 0.00 0.00 4.16
356 359 2.661709 CGCAGTGTGTCATTAAACGTGG 60.662 50.000 0.00 0.00 0.00 4.94
359 362 2.941891 ACGCAGTGTGTCATTAAACG 57.058 45.000 2.75 0.00 42.51 3.60
390 393 0.102300 CACTCGCATATGTCCGGACA 59.898 55.000 37.79 37.79 46.44 4.02
395 398 4.035208 CCCTTAAAACACTCGCATATGTCC 59.965 45.833 4.29 0.00 0.00 4.02
399 402 4.196971 GGACCCTTAAAACACTCGCATAT 58.803 43.478 0.00 0.00 0.00 1.78
402 405 1.874739 CGGACCCTTAAAACACTCGCA 60.875 52.381 0.00 0.00 0.00 5.10
405 408 1.886886 TGCGGACCCTTAAAACACTC 58.113 50.000 0.00 0.00 0.00 3.51
423 426 4.072131 ACAGTGTAAAGGCACCTACATTG 58.928 43.478 11.50 11.50 39.25 2.82
424 427 4.367039 ACAGTGTAAAGGCACCTACATT 57.633 40.909 0.00 0.00 40.04 2.71
425 428 5.045869 ACATACAGTGTAAAGGCACCTACAT 60.046 40.000 7.16 0.00 39.91 2.29
428 431 5.492855 AACATACAGTGTAAAGGCACCTA 57.507 39.130 7.16 0.00 41.14 3.08
430 433 4.094442 GCTAACATACAGTGTAAAGGCACC 59.906 45.833 7.16 0.00 41.14 5.01
431 434 4.693566 TGCTAACATACAGTGTAAAGGCAC 59.306 41.667 7.16 0.00 41.14 5.01
434 437 7.495606 TCATCATGCTAACATACAGTGTAAAGG 59.504 37.037 7.16 2.95 41.14 3.11
440 443 6.044682 TGACTCATCATGCTAACATACAGTG 58.955 40.000 0.00 0.00 33.67 3.66
473 476 6.935240 TTCCTTGATCGATTATATCCTGGT 57.065 37.500 0.00 0.00 0.00 4.00
518 521 5.992564 TCATCTATTTTGGAATGGAGGGA 57.007 39.130 0.00 0.00 36.39 4.20
520 523 7.775093 TGTACTTCATCTATTTTGGAATGGAGG 59.225 37.037 0.00 0.00 36.39 4.30
521 524 8.737168 TGTACTTCATCTATTTTGGAATGGAG 57.263 34.615 0.00 0.00 36.39 3.86
522 525 9.527157 TTTGTACTTCATCTATTTTGGAATGGA 57.473 29.630 0.00 0.00 37.20 3.41
523 526 9.793252 CTTTGTACTTCATCTATTTTGGAATGG 57.207 33.333 0.00 0.00 0.00 3.16
527 530 8.792633 CCAACTTTGTACTTCATCTATTTTGGA 58.207 33.333 0.00 0.00 30.87 3.53
528 531 8.028938 CCCAACTTTGTACTTCATCTATTTTGG 58.971 37.037 0.00 0.00 0.00 3.28
529 532 8.576442 ACCCAACTTTGTACTTCATCTATTTTG 58.424 33.333 0.00 0.00 0.00 2.44
530 533 8.706322 ACCCAACTTTGTACTTCATCTATTTT 57.294 30.769 0.00 0.00 0.00 1.82
531 534 7.942341 TGACCCAACTTTGTACTTCATCTATTT 59.058 33.333 0.00 0.00 0.00 1.40
532 535 7.458397 TGACCCAACTTTGTACTTCATCTATT 58.542 34.615 0.00 0.00 0.00 1.73
533 536 7.016153 TGACCCAACTTTGTACTTCATCTAT 57.984 36.000 0.00 0.00 0.00 1.98
534 537 6.428083 TGACCCAACTTTGTACTTCATCTA 57.572 37.500 0.00 0.00 0.00 1.98
535 538 5.304686 TGACCCAACTTTGTACTTCATCT 57.695 39.130 0.00 0.00 0.00 2.90
536 539 5.940470 AGATGACCCAACTTTGTACTTCATC 59.060 40.000 0.00 0.00 0.00 2.92
537 540 5.880901 AGATGACCCAACTTTGTACTTCAT 58.119 37.500 0.00 0.00 0.00 2.57
538 541 5.304686 AGATGACCCAACTTTGTACTTCA 57.695 39.130 0.00 0.00 0.00 3.02
539 542 7.923414 AATAGATGACCCAACTTTGTACTTC 57.077 36.000 0.00 0.00 0.00 3.01
540 543 8.576442 CAAAATAGATGACCCAACTTTGTACTT 58.424 33.333 0.00 0.00 0.00 2.24
541 544 7.942341 TCAAAATAGATGACCCAACTTTGTACT 59.058 33.333 0.00 0.00 0.00 2.73
542 545 8.106247 TCAAAATAGATGACCCAACTTTGTAC 57.894 34.615 0.00 0.00 0.00 2.90
543 546 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
544 547 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
545 548 8.928733 CATTTCAAAATAGATGACCCAACTTTG 58.071 33.333 0.00 0.00 0.00 2.77
546 549 8.096414 CCATTTCAAAATAGATGACCCAACTTT 58.904 33.333 0.00 0.00 0.00 2.66
547 550 7.310609 CCCATTTCAAAATAGATGACCCAACTT 60.311 37.037 0.00 0.00 0.00 2.66
548 551 6.155049 CCCATTTCAAAATAGATGACCCAACT 59.845 38.462 0.00 0.00 0.00 3.16
549 552 6.340522 CCCATTTCAAAATAGATGACCCAAC 58.659 40.000 0.00 0.00 0.00 3.77
550 553 5.424895 CCCCATTTCAAAATAGATGACCCAA 59.575 40.000 0.00 0.00 0.00 4.12
551 554 4.961730 CCCCATTTCAAAATAGATGACCCA 59.038 41.667 0.00 0.00 0.00 4.51
552 555 4.344968 CCCCCATTTCAAAATAGATGACCC 59.655 45.833 0.00 0.00 0.00 4.46
553 556 5.535753 CCCCCATTTCAAAATAGATGACC 57.464 43.478 0.00 0.00 0.00 4.02
573 576 0.958822 CACTTTTGTGCACTACCCCC 59.041 55.000 19.41 0.00 44.07 5.40
595 598 7.949903 TTTCGTGCTAACAAAGTAGACATTA 57.050 32.000 0.00 0.00 0.00 1.90
599 602 5.564127 GCAATTTCGTGCTAACAAAGTAGAC 59.436 40.000 0.00 0.00 41.51 2.59
613 616 1.201877 CGTCCTTACCGCAATTTCGTG 60.202 52.381 0.00 0.00 0.00 4.35
656 659 0.459585 CCGTTCGATCCACCAATCGT 60.460 55.000 6.22 0.00 46.64 3.73
698 701 0.742505 AACGCATCAAGCCATCCATG 59.257 50.000 0.00 0.00 41.38 3.66
716 719 3.678072 GTGGACGATTTTCAGACGATCAA 59.322 43.478 0.00 0.00 0.00 2.57
717 720 3.250744 GTGGACGATTTTCAGACGATCA 58.749 45.455 0.00 0.00 0.00 2.92
718 721 3.250744 TGTGGACGATTTTCAGACGATC 58.749 45.455 0.00 0.00 0.00 3.69
719 722 3.313012 TGTGGACGATTTTCAGACGAT 57.687 42.857 0.00 0.00 0.00 3.73
720 723 2.804697 TGTGGACGATTTTCAGACGA 57.195 45.000 0.00 0.00 0.00 4.20
721 724 3.799035 CTTTGTGGACGATTTTCAGACG 58.201 45.455 0.00 0.00 0.00 4.18
722 725 3.251004 AGCTTTGTGGACGATTTTCAGAC 59.749 43.478 0.00 0.00 0.00 3.51
723 726 3.476552 AGCTTTGTGGACGATTTTCAGA 58.523 40.909 0.00 0.00 0.00 3.27
724 727 3.904136 AGCTTTGTGGACGATTTTCAG 57.096 42.857 0.00 0.00 0.00 3.02
725 728 3.303725 CGAAGCTTTGTGGACGATTTTCA 60.304 43.478 0.00 0.00 0.00 2.69
726 729 3.226347 CGAAGCTTTGTGGACGATTTTC 58.774 45.455 0.00 0.00 0.00 2.29
727 730 2.031157 CCGAAGCTTTGTGGACGATTTT 60.031 45.455 12.77 0.00 0.00 1.82
728 731 1.535462 CCGAAGCTTTGTGGACGATTT 59.465 47.619 12.77 0.00 0.00 2.17
729 732 1.156736 CCGAAGCTTTGTGGACGATT 58.843 50.000 12.77 0.00 0.00 3.34
730 733 1.298859 GCCGAAGCTTTGTGGACGAT 61.299 55.000 12.77 0.00 35.50 3.73
731 734 1.959226 GCCGAAGCTTTGTGGACGA 60.959 57.895 12.77 0.00 35.50 4.20
732 735 2.556287 GCCGAAGCTTTGTGGACG 59.444 61.111 12.77 4.55 35.50 4.79
752 755 4.878439 AGAACGATGTGTAAACTGCTACA 58.122 39.130 0.00 0.00 0.00 2.74
753 756 5.176958 ACAAGAACGATGTGTAAACTGCTAC 59.823 40.000 0.00 0.00 0.00 3.58
754 757 5.294356 ACAAGAACGATGTGTAAACTGCTA 58.706 37.500 0.00 0.00 0.00 3.49
755 758 4.127171 ACAAGAACGATGTGTAAACTGCT 58.873 39.130 0.00 0.00 0.00 4.24
756 759 4.468095 ACAAGAACGATGTGTAAACTGC 57.532 40.909 0.00 0.00 0.00 4.40
757 760 6.071463 GCTAACAAGAACGATGTGTAAACTG 58.929 40.000 0.00 0.00 0.00 3.16
758 761 5.756347 TGCTAACAAGAACGATGTGTAAACT 59.244 36.000 0.00 0.00 0.00 2.66
759 762 5.981174 TGCTAACAAGAACGATGTGTAAAC 58.019 37.500 0.00 0.00 0.00 2.01
760 763 6.606234 TTGCTAACAAGAACGATGTGTAAA 57.394 33.333 0.00 0.00 0.00 2.01
926 979 1.845809 GCATGCACGCCTATGCCTAC 61.846 60.000 14.21 0.00 45.50 3.18
976 1069 7.396540 TGAGATGATATCGCTGCTAGAATTA 57.603 36.000 0.00 0.00 0.00 1.40
1007 1100 8.088981 CAGTTTGATCCGGTTATAATAGCTAGT 58.911 37.037 0.00 0.00 0.00 2.57
1117 1210 2.168106 ACATCTGTAAGCTCTCTGGCAG 59.832 50.000 8.58 8.58 34.17 4.85
1121 1214 6.402222 ACCTTTAACATCTGTAAGCTCTCTG 58.598 40.000 0.00 0.00 0.00 3.35
1280 1974 7.288810 ACTCTGCATGAACAAAATTCCTTAA 57.711 32.000 0.00 0.00 0.00 1.85
1378 2072 3.243737 CGTTTCCGTATCCTCCATCATGA 60.244 47.826 0.00 0.00 0.00 3.07
1416 2131 0.807275 GTTACCGTATCCACCACCGC 60.807 60.000 0.00 0.00 0.00 5.68
1449 2164 7.334921 CGTTTCCATAACCTTCACCACTATTTA 59.665 37.037 0.00 0.00 0.00 1.40
1542 2257 2.224621 CCAGAATTGCCGTATCCTCCAT 60.225 50.000 0.00 0.00 0.00 3.41
1569 2284 1.303724 CCACACCCATAACCGCCAA 60.304 57.895 0.00 0.00 0.00 4.52
1583 2298 0.762418 CCTCCACCACTGTAACCACA 59.238 55.000 0.00 0.00 0.00 4.17
1592 2307 0.983378 GGTCCATAGCCTCCACCACT 60.983 60.000 0.00 0.00 0.00 4.00
1594 2309 0.982852 CAGGTCCATAGCCTCCACCA 60.983 60.000 0.00 0.00 33.31 4.17
1652 2367 1.588082 CAAAGCCGCTGCCAAATCT 59.412 52.632 0.00 0.00 38.69 2.40
1674 2389 2.452064 CCGCCACCACCATATCCCT 61.452 63.158 0.00 0.00 0.00 4.20
1730 2445 1.273438 ACCGTAACCTCCACCATACCT 60.273 52.381 0.00 0.00 0.00 3.08
1753 2468 4.838152 CCACCGCCACCAGATCCG 62.838 72.222 0.00 0.00 0.00 4.18
1795 2510 1.250328 CATTGCAACCTCTTGGCTCA 58.750 50.000 0.00 0.00 36.63 4.26
2080 2805 4.524802 TGCATTATGAAATGGAGGGAGT 57.475 40.909 0.00 0.00 42.39 3.85
2086 2811 2.223548 GCGCACTGCATTATGAAATGGA 60.224 45.455 0.30 0.00 45.45 3.41
2087 2812 2.121786 GCGCACTGCATTATGAAATGG 58.878 47.619 0.30 0.00 45.45 3.16
2099 2824 1.300853 AAAAACATGGGCGCACTGC 60.301 52.632 12.74 0.00 45.38 4.40
2100 2825 0.945265 CCAAAAACATGGGCGCACTG 60.945 55.000 12.74 9.54 36.79 3.66
2101 2826 1.112315 TCCAAAAACATGGGCGCACT 61.112 50.000 12.74 0.00 41.05 4.40
2102 2827 0.667184 CTCCAAAAACATGGGCGCAC 60.667 55.000 10.83 6.04 41.05 5.34
2103 2828 0.825425 TCTCCAAAAACATGGGCGCA 60.825 50.000 10.83 5.70 41.05 6.09
2104 2829 0.532115 ATCTCCAAAAACATGGGCGC 59.468 50.000 0.00 0.00 41.05 6.53
2105 2830 2.230992 TGAATCTCCAAAAACATGGGCG 59.769 45.455 0.00 0.00 41.05 6.13
2106 2831 3.959535 TGAATCTCCAAAAACATGGGC 57.040 42.857 0.00 0.00 41.05 5.36
2107 2832 5.473066 AGTTGAATCTCCAAAAACATGGG 57.527 39.130 0.00 0.00 41.05 4.00
2108 2833 6.985645 TCAAAGTTGAATCTCCAAAAACATGG 59.014 34.615 0.00 0.00 36.66 3.66
2109 2834 8.597662 ATCAAAGTTGAATCTCCAAAAACATG 57.402 30.769 0.00 0.00 41.13 3.21
2110 2835 8.423349 TGATCAAAGTTGAATCTCCAAAAACAT 58.577 29.630 0.00 0.00 41.13 2.71
2111 2836 7.780064 TGATCAAAGTTGAATCTCCAAAAACA 58.220 30.769 0.00 0.00 41.13 2.83
2112 2837 8.822652 ATGATCAAAGTTGAATCTCCAAAAAC 57.177 30.769 0.00 0.00 41.13 2.43
2216 2941 8.745590 ACTATAAATTTAACCAACATGGGTGAC 58.254 33.333 1.21 0.00 38.40 3.67
2217 2942 8.887264 ACTATAAATTTAACCAACATGGGTGA 57.113 30.769 1.21 0.00 38.40 4.02
2218 2943 8.744652 TGACTATAAATTTAACCAACATGGGTG 58.255 33.333 1.21 0.00 38.40 4.61
2219 2944 8.887264 TGACTATAAATTTAACCAACATGGGT 57.113 30.769 1.21 0.00 43.37 4.51
2238 2963 9.612620 CGCTTTTTGAGATTTAACTTTGACTAT 57.387 29.630 0.00 0.00 0.00 2.12
2239 2964 8.617809 ACGCTTTTTGAGATTTAACTTTGACTA 58.382 29.630 0.00 0.00 0.00 2.59
2240 2965 7.432252 CACGCTTTTTGAGATTTAACTTTGACT 59.568 33.333 0.00 0.00 0.00 3.41
2241 2966 7.431084 TCACGCTTTTTGAGATTTAACTTTGAC 59.569 33.333 0.00 0.00 0.00 3.18
2242 2967 7.476667 TCACGCTTTTTGAGATTTAACTTTGA 58.523 30.769 0.00 0.00 0.00 2.69
2243 2968 7.678194 TCACGCTTTTTGAGATTTAACTTTG 57.322 32.000 0.00 0.00 0.00 2.77
2244 2969 7.044314 CGTTCACGCTTTTTGAGATTTAACTTT 60.044 33.333 0.00 0.00 0.00 2.66
2245 2970 6.413818 CGTTCACGCTTTTTGAGATTTAACTT 59.586 34.615 0.00 0.00 0.00 2.66
2246 2971 5.907391 CGTTCACGCTTTTTGAGATTTAACT 59.093 36.000 0.00 0.00 0.00 2.24
2247 2972 6.111862 CGTTCACGCTTTTTGAGATTTAAC 57.888 37.500 0.00 0.00 0.00 2.01
2263 2988 6.960992 CCATTCCATAATATAATGCGTTCACG 59.039 38.462 0.00 0.00 43.27 4.35
2264 2989 8.039603 TCCATTCCATAATATAATGCGTTCAC 57.960 34.615 0.00 0.00 30.81 3.18
2265 2990 7.882791 ACTCCATTCCATAATATAATGCGTTCA 59.117 33.333 0.00 0.00 30.81 3.18
2266 2991 8.268850 ACTCCATTCCATAATATAATGCGTTC 57.731 34.615 0.00 0.00 30.81 3.95
2267 2992 9.733556 TTACTCCATTCCATAATATAATGCGTT 57.266 29.630 0.00 0.00 30.81 4.84
2268 2993 9.905713 ATTACTCCATTCCATAATATAATGCGT 57.094 29.630 0.00 0.00 30.81 5.24
2282 3007 9.233232 CGTAAATGCTTTTTATTACTCCATTCC 57.767 33.333 2.59 0.00 0.00 3.01
2283 3008 9.997482 TCGTAAATGCTTTTTATTACTCCATTC 57.003 29.630 2.59 0.00 0.00 2.67
2304 3029 4.897076 TGGGGCTACTCATCTAAATCGTAA 59.103 41.667 0.00 0.00 0.00 3.18
2307 3032 4.021104 TCATGGGGCTACTCATCTAAATCG 60.021 45.833 0.00 0.00 0.00 3.34
2367 3092 6.027025 AGAAGAGTAGTACCATATGTCCCA 57.973 41.667 1.24 0.00 0.00 4.37
2461 3186 0.823356 TTCAAGCACACCTCCTTGCC 60.823 55.000 0.00 0.00 39.75 4.52
2466 3191 1.808945 CATGTCTTCAAGCACACCTCC 59.191 52.381 0.00 0.00 0.00 4.30
2552 3278 0.691078 ACTGTCCATCCCGCCATAGT 60.691 55.000 0.00 0.00 0.00 2.12
2555 3281 1.077501 CAACTGTCCATCCCGCCAT 60.078 57.895 0.00 0.00 0.00 4.40
2648 3374 8.514330 TTTACTTGTCAAATTGTGTACTTCCT 57.486 30.769 0.00 0.00 0.00 3.36
2649 3375 9.575783 TTTTTACTTGTCAAATTGTGTACTTCC 57.424 29.630 0.00 0.00 0.00 3.46
2659 3385 9.986833 GCTTTCATTGTTTTTACTTGTCAAATT 57.013 25.926 0.00 0.00 0.00 1.82
2678 3405 6.057533 TGACCGAAGATGATTATGCTTTCAT 58.942 36.000 0.00 0.00 35.33 2.57
2684 3412 4.972440 GCTTTTGACCGAAGATGATTATGC 59.028 41.667 0.00 0.00 0.00 3.14
2689 3417 3.629398 GGATGCTTTTGACCGAAGATGAT 59.371 43.478 0.00 0.00 0.00 2.45
2699 3427 3.191371 AGACCGATTTGGATGCTTTTGAC 59.809 43.478 0.00 0.00 42.00 3.18
2801 3546 7.330454 GGTGTTGTCATATGTAGATATGCTGAG 59.670 40.741 13.71 0.00 40.92 3.35
2852 3597 7.444183 TCGTCATTCCTTTTCTTTATGTCAACT 59.556 33.333 0.00 0.00 0.00 3.16
2877 3622 2.279741 TGTATTCATGTTGCGCCTCTC 58.720 47.619 4.18 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.