Multiple sequence alignment - TraesCS6A01G396900

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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 TraesCS6A01G396900 chr6A 100.000 4347 0 0 1 4347 608794824 608790478 0.000000e+00 8028.0
1 TraesCS6A01G396900 chr6A 97.084 2023 35 6 1328 3347 608680142 608678141 0.000000e+00 3387.0
2 TraesCS6A01G396900 chr6A 85.856 1711 209 23 1440 3141 554834433 554832747 0.000000e+00 1788.0
3 TraesCS6A01G396900 chr6A 84.468 1777 233 23 1440 3199 135224403 135226153 0.000000e+00 1712.0
4 TraesCS6A01G396900 chr6A 83.442 1848 253 31 1461 3280 613092215 613090393 0.000000e+00 1668.0
5 TraesCS6A01G396900 chr6A 84.362 1669 226 26 1453 3098 574222153 574220497 0.000000e+00 1604.0
6 TraesCS6A01G396900 chr6A 98.677 378 5 0 951 1328 608680765 608680388 0.000000e+00 671.0
7 TraesCS6A01G396900 chr6A 89.474 361 30 5 3989 4347 608677616 608677262 2.380000e-122 449.0
8 TraesCS6A01G396900 chr6A 89.884 346 15 6 3541 3886 608677938 608677613 1.120000e-115 427.0
9 TraesCS6A01G396900 chr6A 92.500 120 6 2 3360 3477 608678061 608677943 7.480000e-38 169.0
10 TraesCS6A01G396900 chr6D 96.150 1922 64 6 1328 3248 461820279 461818367 0.000000e+00 3131.0
11 TraesCS6A01G396900 chr6D 88.851 2359 177 40 1400 3728 462026531 462024229 0.000000e+00 2820.0
12 TraesCS6A01G396900 chr6D 84.944 1780 210 33 1440 3197 110868540 110870283 0.000000e+00 1749.0
13 TraesCS6A01G396900 chr6D 78.655 937 137 39 2444 3347 466524960 466525866 8.160000e-157 564.0
14 TraesCS6A01G396900 chr6D 90.347 404 22 3 3946 4347 461816875 461816487 8.340000e-142 514.0
15 TraesCS6A01G396900 chr6D 98.712 233 3 0 1097 1329 461820760 461820528 8.700000e-112 414.0
16 TraesCS6A01G396900 chr6D 87.273 330 37 2 3360 3689 461817992 461817668 5.310000e-99 372.0
17 TraesCS6A01G396900 chr6D 91.515 165 13 1 3730 3893 462024176 462024012 4.370000e-55 226.0
18 TraesCS6A01G396900 chr6D 94.505 91 5 0 1008 1098 461821211 461821121 1.630000e-29 141.0
19 TraesCS6A01G396900 chr6D 92.857 70 2 3 1 68 461823230 461823162 9.950000e-17 99.0
20 TraesCS6A01G396900 chr6B 91.505 1907 131 12 1400 3295 704155679 704153793 0.000000e+00 2595.0
21 TraesCS6A01G396900 chr6B 85.759 1910 224 27 1440 3342 615087849 615085981 0.000000e+00 1977.0
22 TraesCS6A01G396900 chr6B 84.286 1871 249 30 1439 3280 711739400 711737546 0.000000e+00 1784.0
23 TraesCS6A01G396900 chr6B 84.227 1883 228 32 1440 3296 199741455 199743294 0.000000e+00 1768.0
24 TraesCS6A01G396900 chr6B 84.726 1676 208 25 1453 3098 645653581 645655238 0.000000e+00 1633.0
25 TraesCS6A01G396900 chr6B 87.912 546 50 9 3360 3893 1183119 1182578 2.850000e-176 628.0
26 TraesCS6A01G396900 chr6B 94.515 237 13 0 4111 4347 704151160 704150924 2.470000e-97 366.0
27 TraesCS6A01G396900 chr6B 91.071 168 12 3 623 788 604223193 604223027 1.570000e-54 224.0
28 TraesCS6A01G396900 chr6B 95.620 137 6 0 3377 3513 704153796 704153660 2.040000e-53 220.0
29 TraesCS6A01G396900 chr6B 93.243 148 10 0 951 1098 717247579 717247726 7.320000e-53 219.0
30 TraesCS6A01G396900 chr6B 90.000 160 12 2 3949 4104 704153018 704152859 2.050000e-48 204.0
31 TraesCS6A01G396900 chr6B 82.482 137 21 3 1097 1231 708254308 708254443 2.750000e-22 117.0
32 TraesCS6A01G396900 chr5B 89.011 546 43 10 3360 3893 517432044 517432584 0.000000e+00 660.0
33 TraesCS6A01G396900 chr5B 93.243 148 10 0 951 1098 530186058 530185911 7.320000e-53 219.0
34 TraesCS6A01G396900 chr5A 89.031 547 39 12 3360 3893 450326938 450327476 0.000000e+00 658.0
35 TraesCS6A01G396900 chr4B 88.462 546 46 9 3360 3893 215239969 215240509 1.020000e-180 643.0
36 TraesCS6A01G396900 chr4B 93.243 148 10 0 951 1098 260582609 260582462 7.320000e-53 219.0
37 TraesCS6A01G396900 chr4B 93.243 148 10 0 951 1098 261074004 261073857 7.320000e-53 219.0
38 TraesCS6A01G396900 chr4B 92.568 148 11 0 951 1098 260904033 260903886 3.410000e-51 213.0
39 TraesCS6A01G396900 chr4B 90.541 148 14 0 951 1098 260747016 260746869 3.430000e-46 196.0
40 TraesCS6A01G396900 chr7A 88.764 534 43 8 3360 3882 287665996 287666523 4.740000e-179 638.0
41 TraesCS6A01G396900 chr3B 87.912 546 41 14 3360 3893 785215604 785216136 1.720000e-173 619.0
42 TraesCS6A01G396900 chr3B 84.200 500 64 7 303 788 739226224 739225726 5.090000e-129 472.0
43 TraesCS6A01G396900 chr2B 84.318 491 63 11 303 783 754935357 754935843 6.580000e-128 468.0
44 TraesCS6A01G396900 chr2B 83.077 130 14 7 1097 1223 184113339 184113463 1.280000e-20 111.0
45 TraesCS6A01G396900 chr7B 84.872 390 50 5 303 685 694193033 694193420 6.820000e-103 385.0
46 TraesCS6A01G396900 chr7B 80.576 139 23 3 1097 1232 710982922 710983059 2.140000e-18 104.0
47 TraesCS6A01G396900 chr7B 80.986 142 16 7 1097 1232 632942666 632942530 7.690000e-18 102.0
48 TraesCS6A01G396900 chr7B 79.562 137 25 2 1097 1231 380355264 380355129 1.290000e-15 95.3
49 TraesCS6A01G396900 chr3D 90.254 236 19 3 557 788 445641516 445641281 5.460000e-79 305.0
50 TraesCS6A01G396900 chr3D 81.119 143 21 3 1097 1234 382318948 382319089 4.600000e-20 110.0
51 TraesCS6A01G396900 chr1B 92.308 143 11 0 956 1098 57977291 57977433 2.050000e-48 204.0
52 TraesCS6A01G396900 chr7D 85.926 135 14 5 1097 1230 618502100 618501970 5.860000e-29 139.0


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 TraesCS6A01G396900 chr6A 608790478 608794824 4346 True 8028.00 8028 100.000000 1 4347 1 chr6A.!!$R3 4346
1 TraesCS6A01G396900 chr6A 554832747 554834433 1686 True 1788.00 1788 85.856000 1440 3141 1 chr6A.!!$R1 1701
2 TraesCS6A01G396900 chr6A 135224403 135226153 1750 False 1712.00 1712 84.468000 1440 3199 1 chr6A.!!$F1 1759
3 TraesCS6A01G396900 chr6A 613090393 613092215 1822 True 1668.00 1668 83.442000 1461 3280 1 chr6A.!!$R4 1819
4 TraesCS6A01G396900 chr6A 574220497 574222153 1656 True 1604.00 1604 84.362000 1453 3098 1 chr6A.!!$R2 1645
5 TraesCS6A01G396900 chr6A 608677262 608680765 3503 True 1020.60 3387 93.523800 951 4347 5 chr6A.!!$R5 3396
6 TraesCS6A01G396900 chr6D 110868540 110870283 1743 False 1749.00 1749 84.944000 1440 3197 1 chr6D.!!$F1 1757
7 TraesCS6A01G396900 chr6D 462024012 462026531 2519 True 1523.00 2820 90.183000 1400 3893 2 chr6D.!!$R2 2493
8 TraesCS6A01G396900 chr6D 461816487 461823230 6743 True 778.50 3131 93.307333 1 4347 6 chr6D.!!$R1 4346
9 TraesCS6A01G396900 chr6D 466524960 466525866 906 False 564.00 564 78.655000 2444 3347 1 chr6D.!!$F2 903
10 TraesCS6A01G396900 chr6B 615085981 615087849 1868 True 1977.00 1977 85.759000 1440 3342 1 chr6B.!!$R3 1902
11 TraesCS6A01G396900 chr6B 711737546 711739400 1854 True 1784.00 1784 84.286000 1439 3280 1 chr6B.!!$R4 1841
12 TraesCS6A01G396900 chr6B 199741455 199743294 1839 False 1768.00 1768 84.227000 1440 3296 1 chr6B.!!$F1 1856
13 TraesCS6A01G396900 chr6B 645653581 645655238 1657 False 1633.00 1633 84.726000 1453 3098 1 chr6B.!!$F2 1645
14 TraesCS6A01G396900 chr6B 704150924 704155679 4755 True 846.25 2595 92.910000 1400 4347 4 chr6B.!!$R5 2947
15 TraesCS6A01G396900 chr6B 1182578 1183119 541 True 628.00 628 87.912000 3360 3893 1 chr6B.!!$R1 533
16 TraesCS6A01G396900 chr5B 517432044 517432584 540 False 660.00 660 89.011000 3360 3893 1 chr5B.!!$F1 533
17 TraesCS6A01G396900 chr5A 450326938 450327476 538 False 658.00 658 89.031000 3360 3893 1 chr5A.!!$F1 533
18 TraesCS6A01G396900 chr4B 215239969 215240509 540 False 643.00 643 88.462000 3360 3893 1 chr4B.!!$F1 533
19 TraesCS6A01G396900 chr7A 287665996 287666523 527 False 638.00 638 88.764000 3360 3882 1 chr7A.!!$F1 522
20 TraesCS6A01G396900 chr3B 785215604 785216136 532 False 619.00 619 87.912000 3360 3893 1 chr3B.!!$F1 533

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
621 623 0.039256 CACGGGGCACAAGTGAAATG 60.039 55.000 7.94 0.0 39.04 2.32 F
739 743 1.883926 CCGGTTTTAGACTTTGGGTGG 59.116 52.381 0.00 0.0 0.00 4.61 F
832 1115 2.097142 GCTCACATGCTCCTTGATGAAC 59.903 50.000 0.00 0.0 0.00 3.18 F
1437 3249 2.739609 CGTGCTTCACAGGCATCTATGA 60.740 50.000 0.00 0.0 41.86 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2517 4350 4.202336 TGGAACACCGGTAACAATTGTCTA 60.202 41.667 12.39 4.14 0.00 2.59 R
3156 5046 8.777413 AGTGACAATTAATCCATGAATCATACG 58.223 33.333 0.00 0.00 0.00 3.06 R
3301 5388 5.649782 AACCAGGTTCAAGCATTTATCAG 57.350 39.130 0.00 0.00 0.00 2.90 R
3699 6062 0.674895 AGGTTTAGCTCGCAGGCTTG 60.675 55.000 5.74 0.00 42.97 4.01 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
63 64 8.614469 TTTTTGGAATTTCAAAGACTGTTTGT 57.386 26.923 11.67 0.00 37.82 2.83
68 69 8.502387 TGGAATTTCAAAGACTGTTTGTTTTTG 58.498 29.630 0.00 5.73 46.10 2.44
69 70 8.503196 GGAATTTCAAAGACTGTTTGTTTTTGT 58.497 29.630 10.20 0.00 45.41 2.83
74 75 9.482627 TTCAAAGACTGTTTGTTTTTGTAATGT 57.517 25.926 10.20 0.00 45.41 2.71
75 76 9.482627 TCAAAGACTGTTTGTTTTTGTAATGTT 57.517 25.926 10.20 0.00 45.41 2.71
76 77 9.739786 CAAAGACTGTTTGTTTTTGTAATGTTC 57.260 29.630 0.00 0.00 42.37 3.18
77 78 9.482627 AAAGACTGTTTGTTTTTGTAATGTTCA 57.517 25.926 0.00 0.00 32.65 3.18
79 80 9.086336 AGACTGTTTGTTTTTGTAATGTTCATG 57.914 29.630 0.00 0.00 0.00 3.07
80 81 8.770438 ACTGTTTGTTTTTGTAATGTTCATGT 57.230 26.923 0.00 0.00 0.00 3.21
81 82 9.213799 ACTGTTTGTTTTTGTAATGTTCATGTT 57.786 25.926 0.00 0.00 0.00 2.71
82 83 9.687717 CTGTTTGTTTTTGTAATGTTCATGTTC 57.312 29.630 0.00 0.00 0.00 3.18
83 84 9.429359 TGTTTGTTTTTGTAATGTTCATGTTCT 57.571 25.926 0.00 0.00 0.00 3.01
120 121 8.614469 TTTTTGGAATTCAAAGACTGTTTGTT 57.386 26.923 7.93 0.00 45.00 2.83
121 122 8.614469 TTTTGGAATTCAAAGACTGTTTGTTT 57.386 26.923 7.93 0.00 45.00 2.83
122 123 8.614469 TTTGGAATTCAAAGACTGTTTGTTTT 57.386 26.923 7.93 0.00 40.14 2.43
123 124 8.614469 TTGGAATTCAAAGACTGTTTGTTTTT 57.386 26.923 7.93 0.00 33.91 1.94
221 222 8.871686 AAGTTCACGCTTTAATTTCTTTTCAT 57.128 26.923 0.00 0.00 0.00 2.57
301 303 9.943163 TCAAGTTTTTAAAAATTAAATGCTGCC 57.057 25.926 16.02 0.00 0.00 4.85
302 304 9.949174 CAAGTTTTTAAAAATTAAATGCTGCCT 57.051 25.926 16.02 2.11 0.00 4.75
304 306 8.495148 AGTTTTTAAAAATTAAATGCTGCCTCG 58.505 29.630 16.02 0.00 0.00 4.63
305 307 6.401955 TTTAAAAATTAAATGCTGCCTCGC 57.598 33.333 0.00 0.00 0.00 5.03
306 308 2.584492 AAATTAAATGCTGCCTCGCC 57.416 45.000 0.00 0.00 0.00 5.54
308 310 1.447317 ATTAAATGCTGCCTCGCCGG 61.447 55.000 0.00 0.00 0.00 6.13
324 326 4.891566 GGCGATGTCGACTTCTGT 57.108 55.556 24.01 4.21 45.57 3.41
325 327 3.123674 GGCGATGTCGACTTCTGTT 57.876 52.632 24.01 1.53 45.57 3.16
326 328 1.429463 GGCGATGTCGACTTCTGTTT 58.571 50.000 24.01 0.00 45.57 2.83
328 330 2.411547 GGCGATGTCGACTTCTGTTTTG 60.412 50.000 24.01 11.88 45.57 2.44
329 331 2.827555 CGATGTCGACTTCTGTTTTGC 58.172 47.619 24.01 2.08 43.02 3.68
330 332 2.718789 CGATGTCGACTTCTGTTTTGCG 60.719 50.000 24.01 9.43 43.02 4.85
333 335 0.850217 TCGACTTCTGTTTTGCGTCG 59.150 50.000 0.00 0.00 46.17 5.12
334 336 0.575390 CGACTTCTGTTTTGCGTCGT 59.425 50.000 0.00 0.00 41.60 4.34
336 338 0.655733 ACTTCTGTTTTGCGTCGTGG 59.344 50.000 0.00 0.00 0.00 4.94
338 340 0.653636 TTCTGTTTTGCGTCGTGGTC 59.346 50.000 0.00 0.00 0.00 4.02
339 341 1.155424 TCTGTTTTGCGTCGTGGTCC 61.155 55.000 0.00 0.00 0.00 4.46
340 342 1.153329 TGTTTTGCGTCGTGGTCCT 60.153 52.632 0.00 0.00 0.00 3.85
341 343 1.278637 GTTTTGCGTCGTGGTCCTG 59.721 57.895 0.00 0.00 0.00 3.86
342 344 1.144276 TTTTGCGTCGTGGTCCTGA 59.856 52.632 0.00 0.00 0.00 3.86
343 345 0.878523 TTTTGCGTCGTGGTCCTGAG 60.879 55.000 0.00 0.00 0.00 3.35
344 346 3.858868 TTGCGTCGTGGTCCTGAGC 62.859 63.158 0.00 0.00 0.00 4.26
346 348 4.778415 CGTCGTGGTCCTGAGCCG 62.778 72.222 0.00 0.00 0.00 5.52
364 366 2.280389 CCCTCATGGCCATCGTCG 60.280 66.667 17.61 4.60 0.00 5.12
373 375 4.570663 CCATCGTCGCCGTCCTCC 62.571 72.222 0.00 0.00 35.01 4.30
375 377 3.518998 ATCGTCGCCGTCCTCCTG 61.519 66.667 0.00 0.00 35.01 3.86
381 383 4.803426 GCCGTCCTCCTGCTGTCG 62.803 72.222 0.00 0.00 0.00 4.35
383 385 2.126307 CGTCCTCCTGCTGTCGTG 60.126 66.667 0.00 0.00 0.00 4.35
384 386 2.433318 GTCCTCCTGCTGTCGTGC 60.433 66.667 0.00 0.00 0.00 5.34
386 388 2.267006 CCTCCTGCTGTCGTGCAT 59.733 61.111 0.00 0.00 42.48 3.96
387 389 2.104859 CCTCCTGCTGTCGTGCATG 61.105 63.158 0.00 0.00 42.48 4.06
388 390 2.046988 TCCTGCTGTCGTGCATGG 60.047 61.111 5.98 0.00 42.48 3.66
389 391 3.807538 CCTGCTGTCGTGCATGGC 61.808 66.667 2.79 2.79 42.48 4.40
393 395 3.490759 CTGTCGTGCATGGCGGAC 61.491 66.667 14.41 5.76 35.94 4.79
432 434 4.504916 CTCGTCGGAGCTGGGCAG 62.505 72.222 0.00 0.00 32.61 4.85
439 441 4.828925 GAGCTGGGCAGGAGCGAC 62.829 72.222 0.00 0.00 43.41 5.19
442 444 4.767255 CTGGGCAGGAGCGACACC 62.767 72.222 0.00 0.00 43.41 4.16
445 447 2.512515 GGCAGGAGCGACACCATC 60.513 66.667 0.00 0.00 43.41 3.51
446 448 2.265739 GCAGGAGCGACACCATCA 59.734 61.111 0.00 0.00 0.00 3.07
447 449 1.153289 GCAGGAGCGACACCATCAT 60.153 57.895 0.00 0.00 0.00 2.45
448 450 1.156645 GCAGGAGCGACACCATCATC 61.157 60.000 0.00 0.00 0.00 2.92
449 451 0.176449 CAGGAGCGACACCATCATCA 59.824 55.000 0.00 0.00 0.00 3.07
450 452 0.176680 AGGAGCGACACCATCATCAC 59.823 55.000 0.00 0.00 0.00 3.06
451 453 0.811616 GGAGCGACACCATCATCACC 60.812 60.000 0.00 0.00 0.00 4.02
452 454 1.148157 GAGCGACACCATCATCACCG 61.148 60.000 0.00 0.00 0.00 4.94
453 455 1.447838 GCGACACCATCATCACCGT 60.448 57.895 0.00 0.00 0.00 4.83
455 457 0.108851 CGACACCATCATCACCGTGA 60.109 55.000 3.10 3.10 0.00 4.35
456 458 1.645034 GACACCATCATCACCGTGAG 58.355 55.000 7.41 0.03 0.00 3.51
485 487 4.106925 GGCACCTCCTGAGCCCTG 62.107 72.222 0.00 0.00 42.58 4.45
486 488 4.106925 GCACCTCCTGAGCCCTGG 62.107 72.222 0.00 0.00 0.00 4.45
487 489 2.608988 CACCTCCTGAGCCCTGGT 60.609 66.667 0.00 0.00 33.58 4.00
488 490 2.608988 ACCTCCTGAGCCCTGGTG 60.609 66.667 0.00 0.00 33.58 4.17
489 491 2.284921 CCTCCTGAGCCCTGGTGA 60.285 66.667 0.00 0.00 33.58 4.02
490 492 2.664081 CCTCCTGAGCCCTGGTGAC 61.664 68.421 0.00 0.00 33.58 3.67
491 493 2.607750 TCCTGAGCCCTGGTGACC 60.608 66.667 0.00 0.00 33.58 4.02
492 494 2.930019 CCTGAGCCCTGGTGACCA 60.930 66.667 3.40 3.40 0.00 4.02
493 495 2.348998 CTGAGCCCTGGTGACCAC 59.651 66.667 0.00 0.00 0.00 4.16
494 496 3.596066 CTGAGCCCTGGTGACCACG 62.596 68.421 0.00 0.00 0.00 4.94
498 500 3.941188 CCCTGGTGACCACGCACT 61.941 66.667 0.00 0.00 38.78 4.40
499 501 2.357517 CCTGGTGACCACGCACTC 60.358 66.667 0.00 0.00 38.78 3.51
500 502 2.734723 CTGGTGACCACGCACTCG 60.735 66.667 0.00 0.00 38.78 4.18
501 503 4.293648 TGGTGACCACGCACTCGG 62.294 66.667 0.00 0.00 40.69 4.63
503 505 4.295119 GTGACCACGCACTCGGGT 62.295 66.667 0.00 0.00 40.34 5.28
504 506 2.598099 TGACCACGCACTCGGGTA 60.598 61.111 0.00 0.00 38.67 3.69
505 507 2.126189 GACCACGCACTCGGGTAC 60.126 66.667 0.00 0.00 38.67 3.34
506 508 2.913578 ACCACGCACTCGGGTACA 60.914 61.111 0.00 0.00 37.42 2.90
507 509 2.340809 CCACGCACTCGGGTACAA 59.659 61.111 0.00 0.00 37.42 2.41
508 510 1.079405 CCACGCACTCGGGTACAAT 60.079 57.895 0.00 0.00 37.42 2.71
509 511 1.082117 CCACGCACTCGGGTACAATC 61.082 60.000 0.00 0.00 37.42 2.67
510 512 1.082117 CACGCACTCGGGTACAATCC 61.082 60.000 0.00 0.00 40.69 3.01
511 513 1.520787 CGCACTCGGGTACAATCCC 60.521 63.158 0.00 0.00 43.78 3.85
512 514 1.153229 GCACTCGGGTACAATCCCC 60.153 63.158 0.00 0.00 44.32 4.81
518 520 4.476752 GGTACAATCCCCGCGGCA 62.477 66.667 22.85 8.89 0.00 5.69
519 521 3.199891 GTACAATCCCCGCGGCAC 61.200 66.667 22.85 4.17 0.00 5.01
520 522 3.395702 TACAATCCCCGCGGCACT 61.396 61.111 22.85 2.01 0.00 4.40
521 523 2.059190 TACAATCCCCGCGGCACTA 61.059 57.895 22.85 4.27 0.00 2.74
522 524 2.023414 TACAATCCCCGCGGCACTAG 62.023 60.000 22.85 11.70 0.00 2.57
523 525 4.547367 AATCCCCGCGGCACTAGC 62.547 66.667 22.85 0.00 41.10 3.42
533 535 2.561373 GCACTAGCGCCAACAACC 59.439 61.111 2.29 0.00 0.00 3.77
534 536 1.966451 GCACTAGCGCCAACAACCT 60.966 57.895 2.29 0.00 0.00 3.50
535 537 1.912371 GCACTAGCGCCAACAACCTC 61.912 60.000 2.29 0.00 0.00 3.85
536 538 0.602638 CACTAGCGCCAACAACCTCA 60.603 55.000 2.29 0.00 0.00 3.86
537 539 0.602905 ACTAGCGCCAACAACCTCAC 60.603 55.000 2.29 0.00 0.00 3.51
538 540 1.298859 CTAGCGCCAACAACCTCACC 61.299 60.000 2.29 0.00 0.00 4.02
539 541 2.741486 TAGCGCCAACAACCTCACCC 62.741 60.000 2.29 0.00 0.00 4.61
540 542 2.113139 CGCCAACAACCTCACCCT 59.887 61.111 0.00 0.00 0.00 4.34
541 543 2.260869 CGCCAACAACCTCACCCTG 61.261 63.158 0.00 0.00 0.00 4.45
542 544 1.903404 GCCAACAACCTCACCCTGG 60.903 63.158 0.00 0.00 0.00 4.45
543 545 1.843421 CCAACAACCTCACCCTGGA 59.157 57.895 0.00 0.00 0.00 3.86
544 546 0.405585 CCAACAACCTCACCCTGGAT 59.594 55.000 0.00 0.00 0.00 3.41
545 547 1.538047 CAACAACCTCACCCTGGATG 58.462 55.000 0.00 0.00 34.17 3.51
546 548 0.405585 AACAACCTCACCCTGGATGG 59.594 55.000 0.00 0.00 32.55 3.51
547 549 0.475632 ACAACCTCACCCTGGATGGA 60.476 55.000 0.00 0.00 38.35 3.41
548 550 0.921896 CAACCTCACCCTGGATGGAT 59.078 55.000 0.00 0.00 38.35 3.41
549 551 0.921896 AACCTCACCCTGGATGGATG 59.078 55.000 0.00 0.00 38.35 3.51
550 552 0.990282 ACCTCACCCTGGATGGATGG 60.990 60.000 0.00 0.00 38.35 3.51
551 553 0.990282 CCTCACCCTGGATGGATGGT 60.990 60.000 0.00 0.00 38.35 3.55
552 554 0.471617 CTCACCCTGGATGGATGGTC 59.528 60.000 0.00 0.00 38.35 4.02
553 555 0.253113 TCACCCTGGATGGATGGTCA 60.253 55.000 0.00 0.00 38.35 4.02
554 556 0.182061 CACCCTGGATGGATGGTCAG 59.818 60.000 0.00 0.00 38.35 3.51
555 557 0.044702 ACCCTGGATGGATGGTCAGA 59.955 55.000 0.00 0.00 38.35 3.27
556 558 0.763652 CCCTGGATGGATGGTCAGAG 59.236 60.000 0.00 0.00 38.35 3.35
557 559 0.108207 CCTGGATGGATGGTCAGAGC 59.892 60.000 0.00 0.00 38.35 4.09
558 560 0.108207 CTGGATGGATGGTCAGAGCC 59.892 60.000 0.00 0.00 0.00 4.70
559 561 0.621280 TGGATGGATGGTCAGAGCCA 60.621 55.000 0.00 0.00 43.48 4.75
567 569 2.113860 TGGTCAGAGCCATTACTTGC 57.886 50.000 0.00 0.00 32.81 4.01
568 570 1.340017 TGGTCAGAGCCATTACTTGCC 60.340 52.381 0.00 0.00 32.81 4.52
569 571 1.383523 GTCAGAGCCATTACTTGCCC 58.616 55.000 0.00 0.00 0.00 5.36
570 572 0.107703 TCAGAGCCATTACTTGCCCG 60.108 55.000 0.00 0.00 0.00 6.13
571 573 1.097547 CAGAGCCATTACTTGCCCGG 61.098 60.000 0.00 0.00 0.00 5.73
572 574 2.440247 AGCCATTACTTGCCCGGC 60.440 61.111 1.04 1.04 43.31 6.13
573 575 3.887868 GCCATTACTTGCCCGGCG 61.888 66.667 4.58 0.00 32.14 6.46
574 576 2.124901 CCATTACTTGCCCGGCGA 60.125 61.111 9.30 1.12 0.00 5.54
575 577 2.180204 CCATTACTTGCCCGGCGAG 61.180 63.158 23.34 23.34 44.94 5.03
576 578 1.153449 CATTACTTGCCCGGCGAGA 60.153 57.895 30.36 11.75 42.27 4.04
577 579 0.532862 CATTACTTGCCCGGCGAGAT 60.533 55.000 30.36 17.51 42.27 2.75
578 580 0.532862 ATTACTTGCCCGGCGAGATG 60.533 55.000 30.36 8.18 42.27 2.90
579 581 3.733344 TACTTGCCCGGCGAGATGC 62.733 63.158 30.36 6.07 42.27 3.91
580 582 4.845580 CTTGCCCGGCGAGATGCT 62.846 66.667 20.90 0.00 42.27 3.79
581 583 4.838152 TTGCCCGGCGAGATGCTC 62.838 66.667 9.30 0.00 45.43 4.26
596 598 2.768253 TGCTCGGTCATCAAGAACAT 57.232 45.000 0.00 0.00 31.63 2.71
597 599 2.349590 TGCTCGGTCATCAAGAACATG 58.650 47.619 0.00 0.00 31.63 3.21
600 602 0.374758 CGGTCATCAAGAACATGGCG 59.625 55.000 0.00 0.00 31.63 5.69
603 605 2.076100 GTCATCAAGAACATGGCGTCA 58.924 47.619 0.00 0.00 0.00 4.35
616 618 3.345808 CGTCACGGGGCACAAGTG 61.346 66.667 7.41 7.41 38.31 3.16
617 619 2.110213 GTCACGGGGCACAAGTGA 59.890 61.111 11.77 11.77 42.13 3.41
618 620 1.525077 GTCACGGGGCACAAGTGAA 60.525 57.895 16.48 1.06 44.76 3.18
619 621 1.098712 GTCACGGGGCACAAGTGAAA 61.099 55.000 16.48 0.00 44.76 2.69
620 622 0.179004 TCACGGGGCACAAGTGAAAT 60.179 50.000 13.16 0.00 41.63 2.17
621 623 0.039256 CACGGGGCACAAGTGAAATG 60.039 55.000 7.94 0.00 39.04 2.32
650 653 4.040706 TCAACAACCTATAGTCAAACCGGT 59.959 41.667 0.00 0.00 0.00 5.28
651 654 4.628963 ACAACCTATAGTCAAACCGGTT 57.371 40.909 15.86 15.86 35.28 4.44
673 676 4.810345 TGTAATCCTTCCCAAAACCACTT 58.190 39.130 0.00 0.00 0.00 3.16
677 680 2.512056 TCCTTCCCAAAACCACTTGAGA 59.488 45.455 0.00 0.00 0.00 3.27
685 688 4.082571 CCAAAACCACTTGAGAGGCTTATG 60.083 45.833 0.00 0.00 0.00 1.90
689 692 3.135530 ACCACTTGAGAGGCTTATGGATC 59.864 47.826 0.00 0.00 0.00 3.36
700 703 2.744202 GCTTATGGATCCGGTATTGCAG 59.256 50.000 7.39 0.00 0.00 4.41
701 704 3.557054 GCTTATGGATCCGGTATTGCAGA 60.557 47.826 7.39 0.00 0.00 4.26
720 724 3.509967 CAGAGTTTGGGGGTGATTTAACC 59.490 47.826 0.00 0.00 39.71 2.85
730 734 4.156556 GGGGTGATTTAACCGGTTTTAGAC 59.843 45.833 27.64 15.21 41.52 2.59
732 736 5.474532 GGGTGATTTAACCGGTTTTAGACTT 59.525 40.000 27.64 0.00 41.52 3.01
733 737 6.016024 GGGTGATTTAACCGGTTTTAGACTTT 60.016 38.462 27.64 0.00 41.52 2.66
734 738 6.859508 GGTGATTTAACCGGTTTTAGACTTTG 59.140 38.462 27.64 0.00 0.00 2.77
735 739 6.859508 GTGATTTAACCGGTTTTAGACTTTGG 59.140 38.462 27.64 0.00 0.00 3.28
736 740 5.771153 TTTAACCGGTTTTAGACTTTGGG 57.229 39.130 27.64 0.00 0.00 4.12
737 741 3.301794 AACCGGTTTTAGACTTTGGGT 57.698 42.857 15.86 0.00 0.00 4.51
738 742 2.578786 ACCGGTTTTAGACTTTGGGTG 58.421 47.619 0.00 0.00 0.00 4.61
739 743 1.883926 CCGGTTTTAGACTTTGGGTGG 59.116 52.381 0.00 0.00 0.00 4.61
740 744 2.578786 CGGTTTTAGACTTTGGGTGGT 58.421 47.619 0.00 0.00 0.00 4.16
741 745 3.496515 CCGGTTTTAGACTTTGGGTGGTA 60.497 47.826 0.00 0.00 0.00 3.25
742 746 4.329392 CGGTTTTAGACTTTGGGTGGTAT 58.671 43.478 0.00 0.00 0.00 2.73
743 747 4.763279 CGGTTTTAGACTTTGGGTGGTATT 59.237 41.667 0.00 0.00 0.00 1.89
744 748 5.242171 CGGTTTTAGACTTTGGGTGGTATTT 59.758 40.000 0.00 0.00 0.00 1.40
745 749 6.452242 GGTTTTAGACTTTGGGTGGTATTTG 58.548 40.000 0.00 0.00 0.00 2.32
746 750 6.265876 GGTTTTAGACTTTGGGTGGTATTTGA 59.734 38.462 0.00 0.00 0.00 2.69
747 751 7.039293 GGTTTTAGACTTTGGGTGGTATTTGAT 60.039 37.037 0.00 0.00 0.00 2.57
748 752 7.696992 TTTAGACTTTGGGTGGTATTTGATC 57.303 36.000 0.00 0.00 0.00 2.92
749 753 4.600062 AGACTTTGGGTGGTATTTGATCC 58.400 43.478 0.00 0.00 0.00 3.36
750 754 4.044065 AGACTTTGGGTGGTATTTGATCCA 59.956 41.667 0.00 0.00 0.00 3.41
751 755 4.946646 ACTTTGGGTGGTATTTGATCCAT 58.053 39.130 0.00 0.00 36.09 3.41
752 756 4.956075 ACTTTGGGTGGTATTTGATCCATC 59.044 41.667 0.00 0.00 36.09 3.51
753 757 4.879295 TTGGGTGGTATTTGATCCATCT 57.121 40.909 0.00 0.00 35.40 2.90
754 758 5.985175 TTGGGTGGTATTTGATCCATCTA 57.015 39.130 0.00 0.00 35.40 1.98
755 759 6.529084 TTGGGTGGTATTTGATCCATCTAT 57.471 37.500 0.00 0.00 35.40 1.98
756 760 7.640577 TTGGGTGGTATTTGATCCATCTATA 57.359 36.000 0.00 0.00 35.40 1.31
757 761 7.829224 TGGGTGGTATTTGATCCATCTATAT 57.171 36.000 0.00 0.00 35.40 0.86
758 762 7.632861 TGGGTGGTATTTGATCCATCTATATG 58.367 38.462 0.00 0.00 35.40 1.78
832 1115 2.097142 GCTCACATGCTCCTTGATGAAC 59.903 50.000 0.00 0.00 0.00 3.18
833 1116 3.340928 CTCACATGCTCCTTGATGAACA 58.659 45.455 0.00 0.00 0.00 3.18
842 1125 6.866480 TGCTCCTTGATGAACAATAAAATCC 58.134 36.000 0.00 0.00 37.88 3.01
843 1126 6.436847 TGCTCCTTGATGAACAATAAAATCCA 59.563 34.615 0.00 0.00 37.88 3.41
844 1127 7.039152 TGCTCCTTGATGAACAATAAAATCCAA 60.039 33.333 0.00 0.00 37.88 3.53
907 1191 4.753233 TGAAAGTTTTAGCTTGCTGCAAA 58.247 34.783 16.74 0.00 45.94 3.68
920 1204 5.406767 TTGCTGCAAATTTTTGTGATGAC 57.593 34.783 13.51 0.00 40.24 3.06
1437 3249 2.739609 CGTGCTTCACAGGCATCTATGA 60.740 50.000 0.00 0.00 41.86 2.15
1840 3655 4.102113 GGCCAGACTGTTGCCAAT 57.898 55.556 15.57 0.00 44.70 3.16
2026 3841 6.216456 AGAATTTGAGGTTAGGAGAATCAGGT 59.784 38.462 0.00 0.00 36.25 4.00
3241 5136 3.292460 CTGAGTCGAGGAGGATAAGGTT 58.708 50.000 0.00 0.00 0.00 3.50
3248 5160 6.060788 GTCGAGGAGGATAAGGTTTACTCTA 58.939 44.000 0.00 0.00 0.00 2.43
3301 5388 9.838339 ATGGATATCGTGGATATTTCTTATTCC 57.162 33.333 0.00 0.00 35.64 3.01
3339 5426 5.846203 ACCTGGTTTTCATTGTGAAATGAG 58.154 37.500 6.01 3.49 44.75 2.90
3342 5429 6.762661 CCTGGTTTTCATTGTGAAATGAGTTT 59.237 34.615 6.01 0.00 44.75 2.66
3343 5430 7.280652 CCTGGTTTTCATTGTGAAATGAGTTTT 59.719 33.333 6.01 0.00 44.75 2.43
3352 5439 9.173939 CATTGTGAAATGAGTTTTACTTCTCAC 57.826 33.333 0.00 0.00 42.30 3.51
3371 5560 6.759272 TCTCACTGTACTAAGAATGCAAACT 58.241 36.000 0.00 0.00 0.00 2.66
3388 5682 1.704641 ACTTTGCTTTCCAGGGGAAC 58.295 50.000 0.00 0.00 41.87 3.62
3538 5834 0.749091 CGGGCTCAGGATGCATTTCA 60.749 55.000 0.00 0.00 34.76 2.69
3555 5860 6.985645 TGCATTTCAGTTTCATAGCAAAAGTT 59.014 30.769 0.00 0.00 0.00 2.66
3578 5883 4.701171 TCGAGAGGTAGAAGAAGAGGTTTC 59.299 45.833 0.00 0.00 0.00 2.78
3657 5969 3.825908 ACAGAAAAGGAAATGGGGCTA 57.174 42.857 0.00 0.00 0.00 3.93
3674 5986 2.349969 CTAGTGGCCGCGACTATGCA 62.350 60.000 14.75 0.00 34.15 3.96
3699 6062 1.065854 CCTCATCCACTCCAGGTTGTC 60.066 57.143 0.00 0.00 31.67 3.18
3872 6294 3.708563 TCACAGGTTTAAACTGCTTGC 57.291 42.857 17.50 0.45 39.55 4.01
3886 6308 3.620374 ACTGCTTGCTGAATGATACGAAG 59.380 43.478 6.50 0.00 0.00 3.79
3903 6361 3.825014 ACGAAGTAGCACTGGAAGTCTTA 59.175 43.478 0.00 0.00 43.45 2.10
3905 6363 7.562917 ACGAAGTAGCACTGGAAGTCTTAGC 62.563 48.000 0.00 0.00 43.45 3.09
3921 6379 7.778470 AGTCTTAGCTTAAGATTTTCATCCG 57.222 36.000 6.67 0.00 45.63 4.18
3929 6387 4.301072 AAGATTTTCATCCGGAACCTGA 57.699 40.909 9.01 4.89 34.56 3.86
3937 6395 7.547697 TTTCATCCGGAACCTGACATATATA 57.452 36.000 9.01 0.00 34.56 0.86
3938 6396 7.733773 TTCATCCGGAACCTGACATATATAT 57.266 36.000 9.01 0.00 0.00 0.86
3939 6397 7.112452 TCATCCGGAACCTGACATATATATG 57.888 40.000 19.21 19.21 39.55 1.78
3941 6399 6.280855 TCCGGAACCTGACATATATATGTG 57.719 41.667 28.82 18.26 46.20 3.21
3942 6400 5.186992 TCCGGAACCTGACATATATATGTGG 59.813 44.000 28.82 25.03 46.20 4.17
3943 6401 5.419542 CGGAACCTGACATATATATGTGGG 58.580 45.833 28.82 27.53 46.20 4.61
3944 6402 5.186198 GGAACCTGACATATATATGTGGGC 58.814 45.833 28.82 19.57 46.20 5.36
3959 6878 4.459390 TGTGGGCATCTTCATGAATTTG 57.541 40.909 8.96 10.55 30.57 2.32
4050 6973 6.363473 CGATCCTGAAGTGTAAACAAAACTC 58.637 40.000 0.00 0.00 0.00 3.01
4128 8743 7.801547 AAAATGCACGATGAACATTTTCTAG 57.198 32.000 7.02 0.00 45.92 2.43
4134 8749 7.010460 TGCACGATGAACATTTTCTAGATACAG 59.990 37.037 0.00 0.00 32.36 2.74
4162 8777 6.867816 TCAACAATTTTGATGCATGGTACTTC 59.132 34.615 2.46 0.00 31.83 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 8.614469 AACAAACAGTCTTTGAATTCCAAAAA 57.386 26.923 2.27 0.00 43.50 1.94
96 97 8.614469 AAACAAACAGTCTTTGAATTCCAAAA 57.386 26.923 2.27 0.00 43.50 2.44
97 98 8.614469 AAAACAAACAGTCTTTGAATTCCAAA 57.386 26.923 2.27 3.32 42.07 3.28
98 99 8.614469 AAAAACAAACAGTCTTTGAATTCCAA 57.386 26.923 2.27 0.00 33.83 3.53
203 204 9.913451 TTTGAAACATGAAAAGAAATTAAAGCG 57.087 25.926 0.00 0.00 0.00 4.68
284 286 4.429108 GGCGAGGCAGCATTTAATTTTTA 58.571 39.130 7.25 0.00 39.27 1.52
287 289 1.202290 CGGCGAGGCAGCATTTAATTT 60.202 47.619 0.00 0.00 39.27 1.82
304 306 3.255379 GAAGTCGACATCGCCGGC 61.255 66.667 19.07 19.07 39.60 6.13
305 307 1.874019 CAGAAGTCGACATCGCCGG 60.874 63.158 19.50 0.00 39.60 6.13
306 308 0.732880 AACAGAAGTCGACATCGCCG 60.733 55.000 19.50 11.68 39.60 6.46
308 310 2.827555 CAAAACAGAAGTCGACATCGC 58.172 47.619 19.50 3.61 39.60 4.58
309 311 2.718789 CGCAAAACAGAAGTCGACATCG 60.719 50.000 19.50 13.64 41.45 3.84
310 312 2.221055 ACGCAAAACAGAAGTCGACATC 59.779 45.455 19.50 15.98 0.00 3.06
312 314 1.591158 GACGCAAAACAGAAGTCGACA 59.409 47.619 19.50 0.00 0.00 4.35
313 315 2.280764 GACGCAAAACAGAAGTCGAC 57.719 50.000 7.70 7.70 0.00 4.20
315 317 3.328939 CGACGCAAAACAGAAGTCG 57.671 52.632 1.99 1.99 46.32 4.18
316 318 1.332904 CCACGACGCAAAACAGAAGTC 60.333 52.381 0.00 0.00 0.00 3.01
317 319 0.655733 CCACGACGCAAAACAGAAGT 59.344 50.000 0.00 0.00 0.00 3.01
319 321 0.653636 GACCACGACGCAAAACAGAA 59.346 50.000 0.00 0.00 0.00 3.02
320 322 1.155424 GGACCACGACGCAAAACAGA 61.155 55.000 0.00 0.00 0.00 3.41
323 325 1.155424 TCAGGACCACGACGCAAAAC 61.155 55.000 0.00 0.00 0.00 2.43
324 326 0.878523 CTCAGGACCACGACGCAAAA 60.879 55.000 0.00 0.00 0.00 2.44
325 327 1.300620 CTCAGGACCACGACGCAAA 60.301 57.895 0.00 0.00 0.00 3.68
326 328 2.338620 CTCAGGACCACGACGCAA 59.661 61.111 0.00 0.00 0.00 4.85
329 331 4.778415 CGGCTCAGGACCACGACG 62.778 72.222 0.00 0.00 0.00 5.12
336 338 3.474570 ATGAGGGCGGCTCAGGAC 61.475 66.667 9.56 0.00 34.04 3.85
338 340 4.559063 CCATGAGGGCGGCTCAGG 62.559 72.222 9.56 12.00 34.04 3.86
347 349 2.280389 CGACGATGGCCATGAGGG 60.280 66.667 26.56 11.94 40.85 4.30
361 363 4.803426 CAGCAGGAGGACGGCGAC 62.803 72.222 16.62 7.58 45.49 5.19
363 365 4.803426 GACAGCAGGAGGACGGCG 62.803 72.222 4.80 4.80 45.49 6.46
364 366 4.803426 CGACAGCAGGAGGACGGC 62.803 72.222 0.00 0.00 40.88 5.68
367 369 2.433318 GCACGACAGCAGGAGGAC 60.433 66.667 0.00 0.00 0.00 3.85
368 370 2.917227 TGCACGACAGCAGGAGGA 60.917 61.111 0.00 0.00 40.11 3.71
376 378 3.490759 GTCCGCCATGCACGACAG 61.491 66.667 7.82 0.00 0.00 3.51
415 417 4.504916 CTGCCCAGCTCCGACGAG 62.505 72.222 0.00 0.00 39.33 4.18
418 420 4.154347 CTCCTGCCCAGCTCCGAC 62.154 72.222 0.00 0.00 0.00 4.79
422 424 4.828925 GTCGCTCCTGCCCAGCTC 62.829 72.222 0.00 0.00 34.45 4.09
425 427 4.767255 GGTGTCGCTCCTGCCCAG 62.767 72.222 0.00 0.00 35.36 4.45
428 430 2.512515 GATGGTGTCGCTCCTGCC 60.513 66.667 0.00 0.00 35.36 4.85
429 431 1.153289 ATGATGGTGTCGCTCCTGC 60.153 57.895 0.90 0.00 0.00 4.85
430 432 0.176449 TGATGATGGTGTCGCTCCTG 59.824 55.000 0.90 0.00 0.00 3.86
431 433 0.176680 GTGATGATGGTGTCGCTCCT 59.823 55.000 0.90 0.00 0.00 3.69
432 434 0.811616 GGTGATGATGGTGTCGCTCC 60.812 60.000 0.00 0.00 0.00 4.70
433 435 1.148157 CGGTGATGATGGTGTCGCTC 61.148 60.000 0.00 0.00 0.00 5.03
434 436 1.153568 CGGTGATGATGGTGTCGCT 60.154 57.895 0.00 0.00 0.00 4.93
437 439 1.645034 CTCACGGTGATGATGGTGTC 58.355 55.000 11.86 0.00 0.00 3.67
438 440 0.250234 CCTCACGGTGATGATGGTGT 59.750 55.000 11.86 0.00 0.00 4.16
439 441 0.462581 CCCTCACGGTGATGATGGTG 60.463 60.000 11.86 0.00 31.61 4.17
440 442 1.907739 CCCTCACGGTGATGATGGT 59.092 57.895 11.86 0.00 31.61 3.55
441 443 1.524621 GCCCTCACGGTGATGATGG 60.525 63.158 11.86 9.10 37.42 3.51
442 444 1.884464 CGCCCTCACGGTGATGATG 60.884 63.158 11.86 0.00 45.94 3.07
443 445 2.501128 CGCCCTCACGGTGATGAT 59.499 61.111 11.86 0.00 45.94 2.45
445 447 4.758251 TGCGCCCTCACGGTGATG 62.758 66.667 11.86 8.87 45.94 3.07
446 448 4.760047 GTGCGCCCTCACGGTGAT 62.760 66.667 11.86 0.00 45.94 3.06
460 462 3.971702 AGGAGGTGCCCAAGGTGC 61.972 66.667 0.00 0.00 37.37 5.01
461 463 2.034687 CAGGAGGTGCCCAAGGTG 59.965 66.667 0.00 0.00 37.37 4.00
462 464 2.121963 TCAGGAGGTGCCCAAGGT 60.122 61.111 0.00 0.00 37.37 3.50
463 465 2.673523 CTCAGGAGGTGCCCAAGG 59.326 66.667 0.00 0.00 37.37 3.61
464 466 2.045536 GCTCAGGAGGTGCCCAAG 60.046 66.667 0.00 0.00 37.37 3.61
469 471 4.106925 CCAGGGCTCAGGAGGTGC 62.107 72.222 0.00 0.00 35.29 5.01
470 472 2.608988 ACCAGGGCTCAGGAGGTG 60.609 66.667 0.04 0.00 0.00 4.00
471 473 2.608988 CACCAGGGCTCAGGAGGT 60.609 66.667 0.04 0.00 0.00 3.85
472 474 2.284921 TCACCAGGGCTCAGGAGG 60.285 66.667 0.04 0.00 0.00 4.30
473 475 2.664081 GGTCACCAGGGCTCAGGAG 61.664 68.421 0.04 0.00 0.00 3.69
474 476 2.607750 GGTCACCAGGGCTCAGGA 60.608 66.667 0.04 0.00 0.00 3.86
475 477 2.930019 TGGTCACCAGGGCTCAGG 60.930 66.667 0.00 0.00 0.00 3.86
476 478 2.348998 GTGGTCACCAGGGCTCAG 59.651 66.667 0.00 0.00 32.34 3.35
477 479 3.625897 CGTGGTCACCAGGGCTCA 61.626 66.667 8.81 0.00 35.96 4.26
481 483 3.883744 GAGTGCGTGGTCACCAGGG 62.884 68.421 18.22 4.52 39.49 4.45
482 484 2.357517 GAGTGCGTGGTCACCAGG 60.358 66.667 12.50 12.50 41.71 4.45
483 485 2.734723 CGAGTGCGTGGTCACCAG 60.735 66.667 0.00 0.00 37.68 4.00
484 486 4.293648 CCGAGTGCGTGGTCACCA 62.294 66.667 0.00 0.00 37.68 4.17
486 488 2.922950 TACCCGAGTGCGTGGTCAC 61.923 63.158 0.00 0.00 40.17 3.67
487 489 2.598099 TACCCGAGTGCGTGGTCA 60.598 61.111 0.00 0.00 40.17 4.02
488 490 2.126189 GTACCCGAGTGCGTGGTC 60.126 66.667 0.00 0.00 40.17 4.02
489 491 1.823169 ATTGTACCCGAGTGCGTGGT 61.823 55.000 0.00 0.00 41.66 4.16
490 492 1.079405 ATTGTACCCGAGTGCGTGG 60.079 57.895 0.00 0.00 35.23 4.94
491 493 1.082117 GGATTGTACCCGAGTGCGTG 61.082 60.000 0.00 0.00 35.23 5.34
492 494 1.217244 GGATTGTACCCGAGTGCGT 59.783 57.895 0.00 0.00 35.23 5.24
493 495 1.520787 GGGATTGTACCCGAGTGCG 60.521 63.158 0.00 0.00 40.49 5.34
494 496 4.534401 GGGATTGTACCCGAGTGC 57.466 61.111 0.00 0.00 40.49 4.40
501 503 4.476752 TGCCGCGGGGATTGTACC 62.477 66.667 29.38 7.00 34.06 3.34
502 504 2.300850 TAGTGCCGCGGGGATTGTAC 62.301 60.000 29.38 9.18 34.06 2.90
503 505 2.023414 CTAGTGCCGCGGGGATTGTA 62.023 60.000 29.38 6.43 34.06 2.41
504 506 3.385749 CTAGTGCCGCGGGGATTGT 62.386 63.158 29.38 5.51 34.06 2.71
505 507 2.588877 CTAGTGCCGCGGGGATTG 60.589 66.667 29.38 0.00 34.06 2.67
506 508 4.547367 GCTAGTGCCGCGGGGATT 62.547 66.667 29.38 8.31 34.06 3.01
516 518 1.912371 GAGGTTGTTGGCGCTAGTGC 61.912 60.000 20.17 20.17 0.00 4.40
517 519 0.602638 TGAGGTTGTTGGCGCTAGTG 60.603 55.000 7.64 0.00 0.00 2.74
518 520 0.602905 GTGAGGTTGTTGGCGCTAGT 60.603 55.000 7.64 0.00 0.00 2.57
519 521 1.298859 GGTGAGGTTGTTGGCGCTAG 61.299 60.000 7.64 0.00 0.00 3.42
520 522 1.302192 GGTGAGGTTGTTGGCGCTA 60.302 57.895 7.64 0.00 0.00 4.26
521 523 2.594592 GGTGAGGTTGTTGGCGCT 60.595 61.111 7.64 0.00 0.00 5.92
522 524 3.670377 GGGTGAGGTTGTTGGCGC 61.670 66.667 0.00 0.00 0.00 6.53
523 525 2.113139 AGGGTGAGGTTGTTGGCG 59.887 61.111 0.00 0.00 0.00 5.69
524 526 1.903404 CCAGGGTGAGGTTGTTGGC 60.903 63.158 0.00 0.00 0.00 4.52
525 527 0.405585 ATCCAGGGTGAGGTTGTTGG 59.594 55.000 0.00 0.00 0.00 3.77
526 528 1.538047 CATCCAGGGTGAGGTTGTTG 58.462 55.000 0.00 0.00 0.00 3.33
527 529 0.405585 CCATCCAGGGTGAGGTTGTT 59.594 55.000 0.00 0.00 0.00 2.83
528 530 0.475632 TCCATCCAGGGTGAGGTTGT 60.476 55.000 0.00 0.00 38.24 3.32
529 531 0.921896 ATCCATCCAGGGTGAGGTTG 59.078 55.000 0.00 0.00 38.24 3.77
530 532 3.443095 ATCCATCCAGGGTGAGGTT 57.557 52.632 0.00 0.00 38.24 3.50
536 538 0.044702 TCTGACCATCCATCCAGGGT 59.955 55.000 0.00 0.00 38.24 4.34
537 539 0.763652 CTCTGACCATCCATCCAGGG 59.236 60.000 0.00 0.00 38.24 4.45
538 540 0.108207 GCTCTGACCATCCATCCAGG 59.892 60.000 0.00 0.00 39.47 4.45
539 541 0.108207 GGCTCTGACCATCCATCCAG 59.892 60.000 0.00 0.00 0.00 3.86
540 542 0.621280 TGGCTCTGACCATCCATCCA 60.621 55.000 0.00 0.00 33.75 3.41
541 543 2.224821 TGGCTCTGACCATCCATCC 58.775 57.895 0.00 0.00 33.75 3.51
548 550 2.113860 GCAAGTAATGGCTCTGACCA 57.886 50.000 2.26 2.26 45.82 4.02
557 559 2.124901 TCGCCGGGCAAGTAATGG 60.125 61.111 20.71 0.00 0.00 3.16
558 560 0.532862 ATCTCGCCGGGCAAGTAATG 60.533 55.000 20.71 0.11 0.00 1.90
559 561 0.532862 CATCTCGCCGGGCAAGTAAT 60.533 55.000 20.71 0.00 0.00 1.89
560 562 1.153449 CATCTCGCCGGGCAAGTAA 60.153 57.895 20.71 0.00 0.00 2.24
561 563 2.499205 CATCTCGCCGGGCAAGTA 59.501 61.111 20.71 0.48 0.00 2.24
563 565 4.845580 AGCATCTCGCCGGGCAAG 62.846 66.667 20.71 10.84 44.04 4.01
564 566 4.838152 GAGCATCTCGCCGGGCAA 62.838 66.667 20.71 0.00 44.04 4.52
573 575 2.863137 GTTCTTGATGACCGAGCATCTC 59.137 50.000 15.32 0.00 43.89 2.75
574 576 2.234661 TGTTCTTGATGACCGAGCATCT 59.765 45.455 15.32 0.00 43.89 2.90
575 577 2.621338 TGTTCTTGATGACCGAGCATC 58.379 47.619 9.62 9.62 43.84 3.91
576 578 2.768253 TGTTCTTGATGACCGAGCAT 57.232 45.000 0.00 0.00 0.00 3.79
577 579 2.349590 CATGTTCTTGATGACCGAGCA 58.650 47.619 0.00 0.00 0.00 4.26
578 580 1.667724 CCATGTTCTTGATGACCGAGC 59.332 52.381 0.00 0.00 0.00 5.03
579 581 1.667724 GCCATGTTCTTGATGACCGAG 59.332 52.381 0.00 0.00 0.00 4.63
580 582 1.737838 GCCATGTTCTTGATGACCGA 58.262 50.000 0.00 0.00 0.00 4.69
581 583 0.374758 CGCCATGTTCTTGATGACCG 59.625 55.000 0.00 0.00 0.00 4.79
582 584 1.398390 GACGCCATGTTCTTGATGACC 59.602 52.381 0.00 0.00 0.00 4.02
583 585 2.076100 TGACGCCATGTTCTTGATGAC 58.924 47.619 0.00 0.00 0.00 3.06
584 586 2.076100 GTGACGCCATGTTCTTGATGA 58.924 47.619 0.00 0.00 0.00 2.92
585 587 1.201954 CGTGACGCCATGTTCTTGATG 60.202 52.381 0.00 0.00 0.00 3.07
586 588 1.078709 CGTGACGCCATGTTCTTGAT 58.921 50.000 0.00 0.00 0.00 2.57
587 589 0.948623 CCGTGACGCCATGTTCTTGA 60.949 55.000 0.00 0.00 0.00 3.02
588 590 1.497278 CCGTGACGCCATGTTCTTG 59.503 57.895 0.00 0.00 0.00 3.02
589 591 1.671054 CCCGTGACGCCATGTTCTT 60.671 57.895 0.00 0.00 0.00 2.52
590 592 2.047274 CCCGTGACGCCATGTTCT 60.047 61.111 0.00 0.00 0.00 3.01
600 602 1.098712 TTTCACTTGTGCCCCGTGAC 61.099 55.000 0.00 0.00 37.40 3.67
603 605 0.179004 TCATTTCACTTGTGCCCCGT 60.179 50.000 0.00 0.00 0.00 5.28
610 612 5.895636 TGTTGACTTGTCATTTCACTTGT 57.104 34.783 4.18 0.00 0.00 3.16
611 613 5.516339 GGTTGTTGACTTGTCATTTCACTTG 59.484 40.000 4.18 0.00 0.00 3.16
612 614 5.418840 AGGTTGTTGACTTGTCATTTCACTT 59.581 36.000 4.18 0.00 0.00 3.16
613 615 4.949856 AGGTTGTTGACTTGTCATTTCACT 59.050 37.500 4.18 0.00 0.00 3.41
614 616 5.248870 AGGTTGTTGACTTGTCATTTCAC 57.751 39.130 4.18 0.91 0.00 3.18
615 617 7.936847 ACTATAGGTTGTTGACTTGTCATTTCA 59.063 33.333 4.43 2.78 0.00 2.69
616 618 8.324163 ACTATAGGTTGTTGACTTGTCATTTC 57.676 34.615 4.43 0.43 0.00 2.17
617 619 7.936847 TGACTATAGGTTGTTGACTTGTCATTT 59.063 33.333 4.43 0.00 0.00 2.32
618 620 7.450074 TGACTATAGGTTGTTGACTTGTCATT 58.550 34.615 4.43 0.00 0.00 2.57
619 621 7.004555 TGACTATAGGTTGTTGACTTGTCAT 57.995 36.000 4.43 0.00 0.00 3.06
620 622 6.413783 TGACTATAGGTTGTTGACTTGTCA 57.586 37.500 4.43 0.00 0.00 3.58
621 623 7.307811 GGTTTGACTATAGGTTGTTGACTTGTC 60.308 40.741 4.43 0.00 0.00 3.18
650 653 4.810345 AGTGGTTTTGGGAAGGATTACAA 58.190 39.130 0.00 0.00 0.00 2.41
651 654 4.463050 AGTGGTTTTGGGAAGGATTACA 57.537 40.909 0.00 0.00 0.00 2.41
673 676 1.342074 CCGGATCCATAAGCCTCTCA 58.658 55.000 13.41 0.00 0.00 3.27
677 680 2.290323 GCAATACCGGATCCATAAGCCT 60.290 50.000 9.46 0.00 0.00 4.58
685 688 2.614057 CAAACTCTGCAATACCGGATCC 59.386 50.000 9.46 0.00 0.00 3.36
689 692 1.094785 CCCAAACTCTGCAATACCGG 58.905 55.000 0.00 0.00 0.00 5.28
700 703 2.490509 CGGTTAAATCACCCCCAAACTC 59.509 50.000 0.00 0.00 32.48 3.01
701 704 2.521126 CGGTTAAATCACCCCCAAACT 58.479 47.619 0.00 0.00 32.48 2.66
720 724 2.578786 ACCACCCAAAGTCTAAAACCG 58.421 47.619 0.00 0.00 0.00 4.44
730 734 5.203528 AGATGGATCAAATACCACCCAAAG 58.796 41.667 0.00 0.00 39.06 2.77
732 736 4.879295 AGATGGATCAAATACCACCCAA 57.121 40.909 0.00 0.00 39.06 4.12
733 737 7.632861 CATATAGATGGATCAAATACCACCCA 58.367 38.462 0.00 0.00 39.06 4.51
749 753 6.392911 TTCCCCCTCAAATCCATATAGATG 57.607 41.667 0.00 0.00 0.00 2.90
750 754 7.075526 ACTTTTCCCCCTCAAATCCATATAGAT 59.924 37.037 0.00 0.00 0.00 1.98
751 755 6.392842 ACTTTTCCCCCTCAAATCCATATAGA 59.607 38.462 0.00 0.00 0.00 1.98
752 756 6.614657 ACTTTTCCCCCTCAAATCCATATAG 58.385 40.000 0.00 0.00 0.00 1.31
753 757 6.606241 ACTTTTCCCCCTCAAATCCATATA 57.394 37.500 0.00 0.00 0.00 0.86
754 758 5.487861 ACTTTTCCCCCTCAAATCCATAT 57.512 39.130 0.00 0.00 0.00 1.78
755 759 4.965283 ACTTTTCCCCCTCAAATCCATA 57.035 40.909 0.00 0.00 0.00 2.74
756 760 3.852858 ACTTTTCCCCCTCAAATCCAT 57.147 42.857 0.00 0.00 0.00 3.41
757 761 4.965283 ATACTTTTCCCCCTCAAATCCA 57.035 40.909 0.00 0.00 0.00 3.41
758 762 6.014771 AGTATACTTTTCCCCCTCAAATCC 57.985 41.667 0.00 0.00 0.00 3.01
759 763 7.956328 AAAGTATACTTTTCCCCCTCAAATC 57.044 36.000 22.49 0.00 43.07 2.17
789 1072 1.257936 CGGATTCAAATACTCCGCGTG 59.742 52.381 4.92 0.00 44.65 5.34
884 1168 4.589216 TGCAGCAAGCTAAAACTTTCAT 57.411 36.364 0.00 0.00 45.94 2.57
886 1170 5.912360 ATTTGCAGCAAGCTAAAACTTTC 57.088 34.783 8.12 0.00 45.94 2.62
896 1180 3.948196 TCACAAAAATTTGCAGCAAGC 57.052 38.095 8.12 0.00 41.79 4.01
907 1191 8.474006 CATGAATGTCATGTCATCACAAAAAT 57.526 30.769 5.90 0.00 46.80 1.82
1437 3249 8.746530 AGTTGATTTCTTGTTAGCATCATCATT 58.253 29.630 0.00 0.00 0.00 2.57
1840 3655 5.711468 TCAACCTTTTGTGTTGCTATGGCA 61.711 41.667 0.00 0.00 42.17 4.92
2026 3841 6.894654 TGCATATACTGAAAATCTTGGGGAAA 59.105 34.615 0.00 0.00 0.00 3.13
2470 4302 8.668510 ATCTGCAAAAGATGTAGTAATGTAGG 57.331 34.615 0.00 0.00 44.36 3.18
2517 4350 4.202336 TGGAACACCGGTAACAATTGTCTA 60.202 41.667 12.39 4.14 0.00 2.59
3156 5046 8.777413 AGTGACAATTAATCCATGAATCATACG 58.223 33.333 0.00 0.00 0.00 3.06
3301 5388 5.649782 AACCAGGTTCAAGCATTTATCAG 57.350 39.130 0.00 0.00 0.00 2.90
3342 5429 7.892609 TGCATTCTTAGTACAGTGAGAAGTAA 58.107 34.615 0.00 0.00 32.25 2.24
3343 5430 7.462571 TGCATTCTTAGTACAGTGAGAAGTA 57.537 36.000 0.00 0.00 32.25 2.24
3371 5560 1.703411 CAGTTCCCCTGGAAAGCAAA 58.297 50.000 0.00 0.00 43.86 3.68
3388 5682 1.602311 AGCCACTGAAACTGAAGCAG 58.398 50.000 0.00 0.00 37.52 4.24
3538 5834 5.409826 CCTCTCGAACTTTTGCTATGAAACT 59.590 40.000 0.00 0.00 0.00 2.66
3555 5860 4.304048 AACCTCTTCTTCTACCTCTCGA 57.696 45.455 0.00 0.00 0.00 4.04
3578 5883 1.871772 CAGAAGTTTGAGCAGCCCG 59.128 57.895 0.00 0.00 0.00 6.13
3657 5969 3.770040 TGCATAGTCGCGGCCACT 61.770 61.111 7.31 5.48 33.35 4.00
3674 5986 1.504912 CTGGAGTGGATGAGGATGGT 58.495 55.000 0.00 0.00 0.00 3.55
3699 6062 0.674895 AGGTTTAGCTCGCAGGCTTG 60.675 55.000 5.74 0.00 42.97 4.01
3818 6239 3.863142 AAAGAAGCCACTGATCAATGC 57.137 42.857 0.00 0.61 0.00 3.56
3872 6294 4.742167 CCAGTGCTACTTCGTATCATTCAG 59.258 45.833 0.00 0.00 0.00 3.02
3886 6308 3.878160 AGCTAAGACTTCCAGTGCTAC 57.122 47.619 0.00 0.00 0.00 3.58
3887 6309 5.715279 TCTTAAGCTAAGACTTCCAGTGCTA 59.285 40.000 0.00 0.00 39.73 3.49
3895 6353 8.331742 CGGATGAAAATCTTAAGCTAAGACTTC 58.668 37.037 0.00 11.81 46.58 3.01
3903 6361 4.640647 GGTTCCGGATGAAAATCTTAAGCT 59.359 41.667 4.15 0.00 33.94 3.74
3905 6363 5.880332 TCAGGTTCCGGATGAAAATCTTAAG 59.120 40.000 4.15 0.00 33.94 1.85
3907 6365 5.183228 GTCAGGTTCCGGATGAAAATCTTA 58.817 41.667 4.15 0.00 33.94 2.10
3912 6370 2.940994 TGTCAGGTTCCGGATGAAAA 57.059 45.000 4.15 0.00 33.94 2.29
3921 6379 5.186198 GCCCACATATATATGTCAGGTTCC 58.814 45.833 27.30 15.97 44.57 3.62
3937 6395 4.712829 TCAAATTCATGAAGATGCCCACAT 59.287 37.500 14.54 0.00 39.98 3.21
3938 6396 4.087907 TCAAATTCATGAAGATGCCCACA 58.912 39.130 14.54 0.00 0.00 4.17
3939 6397 4.724074 TCAAATTCATGAAGATGCCCAC 57.276 40.909 14.54 0.00 0.00 4.61
3941 6399 7.619964 ATTTTTCAAATTCATGAAGATGCCC 57.380 32.000 14.54 0.00 40.21 5.36
3942 6400 8.508875 ACAATTTTTCAAATTCATGAAGATGCC 58.491 29.630 14.54 0.00 40.21 4.40
3943 6401 9.887406 AACAATTTTTCAAATTCATGAAGATGC 57.113 25.926 14.54 0.00 40.21 3.91
3959 6878 7.420184 AATCCATGGAAACGAACAATTTTTC 57.580 32.000 20.67 0.00 0.00 2.29
4050 6973 4.039032 ACAAACAAGCACGAAAAATACGG 58.961 39.130 0.00 0.00 34.93 4.02
4212 8828 4.992319 CGTGTCTTACAAATGTCCCTTGTA 59.008 41.667 0.00 0.00 38.05 2.41
4293 8909 3.882888 TCGCCATGTCTTCAAACTTTTCT 59.117 39.130 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.