Multiple sequence alignment - TraesCS4B01G096000

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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 TraesCS4B01G096000 chr4B 100.000 2564 0 0 1 2564 99593118 99595681 0.000000e+00 4735.0
1 TraesCS4B01G096000 chr4A 90.573 1973 149 21 588 2543 516582874 516584826 0.000000e+00 2579.0
2 TraesCS4B01G096000 chr4A 79.975 804 121 26 807 1588 641443083 641442298 8.010000e-155 556.0
3 TraesCS4B01G096000 chr4A 86.441 177 13 4 145 319 516581262 516581429 1.570000e-42 183.0
4 TraesCS4B01G096000 chr4D 88.279 2005 160 32 588 2562 67326601 67324642 0.000000e+00 2331.0
5 TraesCS4B01G096000 chr4D 89.394 198 12 2 153 350 67327389 67327201 9.170000e-60 241.0
6 TraesCS4B01G096000 chr5D 77.735 777 118 30 817 1573 530834514 530835255 2.360000e-115 425.0
7 TraesCS4B01G096000 chr6D 92.683 41 3 0 506 546 317479743 317479783 2.760000e-05 60.2
8 TraesCS4B01G096000 chr6B 92.500 40 3 0 513 552 506720237 506720198 9.910000e-05 58.4


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 TraesCS4B01G096000 chr4B 99593118 99595681 2563 False 4735 4735 100.0000 1 2564 1 chr4B.!!$F1 2563
1 TraesCS4B01G096000 chr4A 516581262 516584826 3564 False 1381 2579 88.5070 145 2543 2 chr4A.!!$F1 2398
2 TraesCS4B01G096000 chr4A 641442298 641443083 785 True 556 556 79.9750 807 1588 1 chr4A.!!$R1 781
3 TraesCS4B01G096000 chr4D 67324642 67327389 2747 True 1286 2331 88.8365 153 2562 2 chr4D.!!$R1 2409
4 TraesCS4B01G096000 chr5D 530834514 530835255 741 False 425 425 77.7350 817 1573 1 chr5D.!!$F1 756

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
514 551 0.109532 TTTGCCGGAACACCAGATGA 59.89 50.0 5.05 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 3314 0.035439 CACATTTCACCTAGGCCCGT 60.035 55.0 9.3 0.0 0.0 5.28 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
20 21 2.542766 TTTTGCTGCGAATCGGATTC 57.457 45.000 18.61 18.61 35.94 2.52
32 33 2.039818 TCGGATTCGAGACACTAGCT 57.960 50.000 0.00 0.00 40.88 3.32
33 34 3.189618 TCGGATTCGAGACACTAGCTA 57.810 47.619 0.00 0.00 40.88 3.32
34 35 3.132160 TCGGATTCGAGACACTAGCTAG 58.868 50.000 19.44 19.44 40.88 3.42
35 36 2.873472 CGGATTCGAGACACTAGCTAGT 59.127 50.000 20.95 20.95 39.00 2.57
36 37 4.056740 CGGATTCGAGACACTAGCTAGTA 58.943 47.826 25.63 9.33 39.00 1.82
37 38 4.084433 CGGATTCGAGACACTAGCTAGTAC 60.084 50.000 25.63 20.71 39.00 2.73
38 39 5.058490 GGATTCGAGACACTAGCTAGTACT 58.942 45.833 25.63 24.48 34.13 2.73
39 40 5.528320 GGATTCGAGACACTAGCTAGTACTT 59.472 44.000 25.63 13.17 34.13 2.24
40 41 6.293027 GGATTCGAGACACTAGCTAGTACTTC 60.293 46.154 25.63 20.14 34.13 3.01
41 42 4.440880 TCGAGACACTAGCTAGTACTTCC 58.559 47.826 25.63 14.64 34.13 3.46
42 43 3.560896 CGAGACACTAGCTAGTACTTCCC 59.439 52.174 25.63 12.23 34.13 3.97
43 44 4.683942 CGAGACACTAGCTAGTACTTCCCT 60.684 50.000 25.63 15.08 34.13 4.20
44 45 4.784177 AGACACTAGCTAGTACTTCCCTC 58.216 47.826 25.63 11.19 34.13 4.30
45 46 3.543665 ACACTAGCTAGTACTTCCCTCG 58.456 50.000 25.63 12.53 34.13 4.63
46 47 3.054508 ACACTAGCTAGTACTTCCCTCGT 60.055 47.826 25.63 13.16 34.13 4.18
47 48 3.560896 CACTAGCTAGTACTTCCCTCGTC 59.439 52.174 25.63 0.00 34.13 4.20
48 49 3.455543 ACTAGCTAGTACTTCCCTCGTCT 59.544 47.826 24.97 0.00 34.13 4.18
49 50 3.369242 AGCTAGTACTTCCCTCGTCTT 57.631 47.619 0.00 0.00 0.00 3.01
50 51 4.500499 AGCTAGTACTTCCCTCGTCTTA 57.500 45.455 0.00 0.00 0.00 2.10
51 52 5.051409 AGCTAGTACTTCCCTCGTCTTAT 57.949 43.478 0.00 0.00 0.00 1.73
52 53 6.185114 AGCTAGTACTTCCCTCGTCTTATA 57.815 41.667 0.00 0.00 0.00 0.98
53 54 6.599445 AGCTAGTACTTCCCTCGTCTTATAA 58.401 40.000 0.00 0.00 0.00 0.98
54 55 7.232910 AGCTAGTACTTCCCTCGTCTTATAAT 58.767 38.462 0.00 0.00 0.00 1.28
55 56 7.175293 AGCTAGTACTTCCCTCGTCTTATAATG 59.825 40.741 0.00 0.00 0.00 1.90
56 57 7.040548 GCTAGTACTTCCCTCGTCTTATAATGT 60.041 40.741 0.00 0.00 0.00 2.71
57 58 9.499479 CTAGTACTTCCCTCGTCTTATAATGTA 57.501 37.037 0.00 0.00 0.00 2.29
58 59 8.757982 AGTACTTCCCTCGTCTTATAATGTAA 57.242 34.615 0.00 0.00 0.00 2.41
59 60 8.848182 AGTACTTCCCTCGTCTTATAATGTAAG 58.152 37.037 0.00 0.00 0.00 2.34
60 61 7.893124 ACTTCCCTCGTCTTATAATGTAAGA 57.107 36.000 0.00 0.00 0.00 2.10
61 62 8.480133 ACTTCCCTCGTCTTATAATGTAAGAT 57.520 34.615 2.87 0.00 36.16 2.40
62 63 8.925338 ACTTCCCTCGTCTTATAATGTAAGATT 58.075 33.333 2.87 0.00 36.16 2.40
84 85 9.933723 AGATTATTTTGCAAGCTAAAAACATCT 57.066 25.926 0.00 13.56 31.62 2.90
87 88 6.984740 TTTTGCAAGCTAAAAACATCTACG 57.015 33.333 0.00 0.00 0.00 3.51
88 89 5.682943 TTGCAAGCTAAAAACATCTACGT 57.317 34.783 0.00 0.00 0.00 3.57
89 90 6.788684 TTGCAAGCTAAAAACATCTACGTA 57.211 33.333 0.00 0.00 0.00 3.57
90 91 6.788684 TGCAAGCTAAAAACATCTACGTAA 57.211 33.333 0.00 0.00 0.00 3.18
91 92 6.595794 TGCAAGCTAAAAACATCTACGTAAC 58.404 36.000 0.00 0.00 0.00 2.50
92 93 6.425721 TGCAAGCTAAAAACATCTACGTAACT 59.574 34.615 0.00 0.00 0.00 2.24
93 94 6.736853 GCAAGCTAAAAACATCTACGTAACTG 59.263 38.462 0.00 0.00 0.00 3.16
94 95 7.570691 GCAAGCTAAAAACATCTACGTAACTGT 60.571 37.037 0.00 0.11 0.00 3.55
95 96 7.347508 AGCTAAAAACATCTACGTAACTGTG 57.652 36.000 9.68 3.39 0.00 3.66
96 97 6.013689 GCTAAAAACATCTACGTAACTGTGC 58.986 40.000 9.68 5.86 0.00 4.57
97 98 5.994887 AAAAACATCTACGTAACTGTGCA 57.005 34.783 9.68 0.00 0.00 4.57
98 99 5.994887 AAAACATCTACGTAACTGTGCAA 57.005 34.783 9.68 0.00 0.00 4.08
99 100 5.591643 AAACATCTACGTAACTGTGCAAG 57.408 39.130 9.68 0.00 0.00 4.01
100 101 2.993899 ACATCTACGTAACTGTGCAAGC 59.006 45.455 8.46 0.00 0.00 4.01
101 102 2.804697 TCTACGTAACTGTGCAAGCA 57.195 45.000 0.00 0.00 0.00 3.91
102 103 2.400399 TCTACGTAACTGTGCAAGCAC 58.600 47.619 17.76 17.76 46.33 4.40
114 115 2.919229 GTGCAAGCACAACATATCAAGC 59.081 45.455 19.47 0.00 45.53 4.01
115 116 2.094597 TGCAAGCACAACATATCAAGCC 60.095 45.455 0.00 0.00 0.00 4.35
116 117 2.736400 GCAAGCACAACATATCAAGCCC 60.736 50.000 0.00 0.00 0.00 5.19
117 118 2.756760 CAAGCACAACATATCAAGCCCT 59.243 45.455 0.00 0.00 0.00 5.19
118 119 2.372264 AGCACAACATATCAAGCCCTG 58.628 47.619 0.00 0.00 0.00 4.45
119 120 1.202336 GCACAACATATCAAGCCCTGC 60.202 52.381 0.00 0.00 0.00 4.85
120 121 2.372264 CACAACATATCAAGCCCTGCT 58.628 47.619 0.00 0.00 42.56 4.24
131 132 2.947127 AGCCCTGCTTTCATCCTATC 57.053 50.000 0.00 0.00 33.89 2.08
132 133 1.071385 AGCCCTGCTTTCATCCTATCG 59.929 52.381 0.00 0.00 33.89 2.92
133 134 1.517242 CCCTGCTTTCATCCTATCGC 58.483 55.000 0.00 0.00 0.00 4.58
134 135 1.202687 CCCTGCTTTCATCCTATCGCA 60.203 52.381 0.00 0.00 0.00 5.10
135 136 2.564771 CCTGCTTTCATCCTATCGCAA 58.435 47.619 0.00 0.00 0.00 4.85
136 137 2.945008 CCTGCTTTCATCCTATCGCAAA 59.055 45.455 0.00 0.00 0.00 3.68
137 138 3.378112 CCTGCTTTCATCCTATCGCAAAA 59.622 43.478 0.00 0.00 0.00 2.44
138 139 4.142403 CCTGCTTTCATCCTATCGCAAAAA 60.142 41.667 0.00 0.00 0.00 1.94
159 160 2.021355 AAGAGCTCTGCTTTCATCCG 57.979 50.000 19.06 0.00 39.88 4.18
168 169 2.547211 CTGCTTTCATCCGTGATCCATC 59.453 50.000 0.00 0.00 33.56 3.51
169 170 1.876156 GCTTTCATCCGTGATCCATCC 59.124 52.381 0.00 0.00 33.56 3.51
191 192 3.476646 CGACTCGCACTGCTGCTG 61.477 66.667 4.89 4.89 41.77 4.41
192 193 3.117171 GACTCGCACTGCTGCTGG 61.117 66.667 11.29 1.84 41.77 4.85
250 251 2.435586 CTCAGCTCTGGTTGCCCG 60.436 66.667 0.00 0.00 0.00 6.13
297 298 1.866853 GCCCACTACACAAAGGCTGC 61.867 60.000 0.00 0.00 40.57 5.25
299 300 0.602638 CCACTACACAAAGGCTGCGA 60.603 55.000 0.00 0.00 0.00 5.10
300 301 1.442769 CACTACACAAAGGCTGCGAT 58.557 50.000 0.00 0.00 0.00 4.58
301 302 1.129251 CACTACACAAAGGCTGCGATG 59.871 52.381 0.00 0.00 0.00 3.84
302 303 1.001974 ACTACACAAAGGCTGCGATGA 59.998 47.619 0.00 0.00 0.00 2.92
338 340 4.042934 ACCCTAGCTTGTCTACCAACAAAT 59.957 41.667 0.00 0.00 38.60 2.32
339 341 5.249852 ACCCTAGCTTGTCTACCAACAAATA 59.750 40.000 0.00 0.00 38.60 1.40
340 342 5.585047 CCCTAGCTTGTCTACCAACAAATAC 59.415 44.000 0.00 0.00 38.60 1.89
341 343 6.170506 CCTAGCTTGTCTACCAACAAATACA 58.829 40.000 0.00 0.00 38.60 2.29
342 344 6.823689 CCTAGCTTGTCTACCAACAAATACAT 59.176 38.462 0.00 0.00 38.60 2.29
343 345 7.985184 CCTAGCTTGTCTACCAACAAATACATA 59.015 37.037 0.00 0.00 38.60 2.29
344 346 9.378551 CTAGCTTGTCTACCAACAAATACATAA 57.621 33.333 0.00 0.00 38.60 1.90
345 347 8.807948 AGCTTGTCTACCAACAAATACATAAT 57.192 30.769 0.00 0.00 38.60 1.28
346 348 9.243105 AGCTTGTCTACCAACAAATACATAATT 57.757 29.630 0.00 0.00 38.60 1.40
347 349 9.855021 GCTTGTCTACCAACAAATACATAATTT 57.145 29.630 0.00 0.00 38.60 1.82
392 394 6.969828 ACAGAATTTTCGTTCTATCCAGTC 57.030 37.500 0.00 0.00 36.33 3.51
397 434 1.067582 CGTTCTATCCAGTCGGGGC 59.932 63.158 0.00 0.00 37.22 5.80
409 446 2.415825 TCGGGGCTCGATAACTCAG 58.584 57.895 4.77 0.00 43.74 3.35
418 455 3.791455 GCTCGATAACTCAGGTACCGTTC 60.791 52.174 6.18 0.00 0.00 3.95
419 456 3.614092 TCGATAACTCAGGTACCGTTCT 58.386 45.455 6.18 0.00 0.00 3.01
431 468 5.929992 CAGGTACCGTTCTTTTACATCTCAA 59.070 40.000 6.18 0.00 0.00 3.02
432 469 6.090898 CAGGTACCGTTCTTTTACATCTCAAG 59.909 42.308 6.18 0.00 0.00 3.02
433 470 6.014840 AGGTACCGTTCTTTTACATCTCAAGA 60.015 38.462 6.18 0.00 0.00 3.02
434 471 6.310711 GGTACCGTTCTTTTACATCTCAAGAG 59.689 42.308 0.00 0.00 0.00 2.85
435 472 4.691216 ACCGTTCTTTTACATCTCAAGAGC 59.309 41.667 0.00 0.00 0.00 4.09
437 474 5.179368 CCGTTCTTTTACATCTCAAGAGCAA 59.821 40.000 0.00 0.00 30.44 3.91
438 475 6.293407 CCGTTCTTTTACATCTCAAGAGCAAA 60.293 38.462 0.00 0.00 30.44 3.68
439 476 6.575201 CGTTCTTTTACATCTCAAGAGCAAAC 59.425 38.462 0.00 0.00 30.44 2.93
440 477 6.560253 TCTTTTACATCTCAAGAGCAAACC 57.440 37.500 0.00 0.00 0.00 3.27
441 478 6.061441 TCTTTTACATCTCAAGAGCAAACCA 58.939 36.000 0.00 0.00 0.00 3.67
442 479 5.689383 TTTACATCTCAAGAGCAAACCAC 57.311 39.130 0.00 0.00 0.00 4.16
443 480 2.508526 ACATCTCAAGAGCAAACCACC 58.491 47.619 0.00 0.00 0.00 4.61
444 481 2.158623 ACATCTCAAGAGCAAACCACCA 60.159 45.455 0.00 0.00 0.00 4.17
445 482 1.967319 TCTCAAGAGCAAACCACCAC 58.033 50.000 0.00 0.00 0.00 4.16
446 483 1.211703 TCTCAAGAGCAAACCACCACA 59.788 47.619 0.00 0.00 0.00 4.17
447 484 2.158623 TCTCAAGAGCAAACCACCACAT 60.159 45.455 0.00 0.00 0.00 3.21
448 485 1.955778 TCAAGAGCAAACCACCACATG 59.044 47.619 0.00 0.00 0.00 3.21
459 496 3.405823 CCACCACATGGCATTTTTCTT 57.594 42.857 0.00 0.00 43.24 2.52
460 497 3.742385 CCACCACATGGCATTTTTCTTT 58.258 40.909 0.00 0.00 43.24 2.52
461 498 4.136051 CCACCACATGGCATTTTTCTTTT 58.864 39.130 0.00 0.00 43.24 2.27
462 499 4.579753 CCACCACATGGCATTTTTCTTTTT 59.420 37.500 0.00 0.00 43.24 1.94
479 516 2.579878 TTTTTGCGGGAACACCACA 58.420 47.368 0.00 0.00 40.22 4.17
480 517 1.115467 TTTTTGCGGGAACACCACAT 58.885 45.000 0.00 0.00 40.22 3.21
481 518 0.387202 TTTTGCGGGAACACCACATG 59.613 50.000 0.00 0.00 40.22 3.21
482 519 0.466372 TTTGCGGGAACACCACATGA 60.466 50.000 0.00 0.00 40.22 3.07
483 520 1.169661 TTGCGGGAACACCACATGAC 61.170 55.000 0.00 0.00 40.22 3.06
484 521 1.599518 GCGGGAACACCACATGACA 60.600 57.895 0.00 0.00 40.22 3.58
485 522 1.169661 GCGGGAACACCACATGACAA 61.170 55.000 0.00 0.00 40.22 3.18
486 523 1.533625 CGGGAACACCACATGACAAT 58.466 50.000 0.00 0.00 40.22 2.71
487 524 1.885887 CGGGAACACCACATGACAATT 59.114 47.619 0.00 0.00 40.22 2.32
488 525 2.295909 CGGGAACACCACATGACAATTT 59.704 45.455 0.00 0.00 40.22 1.82
489 526 3.243704 CGGGAACACCACATGACAATTTT 60.244 43.478 0.00 0.00 40.22 1.82
490 527 4.306600 GGGAACACCACATGACAATTTTC 58.693 43.478 0.00 0.00 39.85 2.29
491 528 4.306600 GGAACACCACATGACAATTTTCC 58.693 43.478 0.00 0.43 0.00 3.13
492 529 4.039124 GGAACACCACATGACAATTTTCCT 59.961 41.667 0.00 0.00 0.00 3.36
493 530 5.453198 GGAACACCACATGACAATTTTCCTT 60.453 40.000 0.00 0.00 0.00 3.36
494 531 5.612725 ACACCACATGACAATTTTCCTTT 57.387 34.783 0.00 0.00 0.00 3.11
495 532 5.988287 ACACCACATGACAATTTTCCTTTT 58.012 33.333 0.00 0.00 0.00 2.27
496 533 6.413892 ACACCACATGACAATTTTCCTTTTT 58.586 32.000 0.00 0.00 0.00 1.94
511 548 3.192799 TTTTTGCCGGAACACCAGA 57.807 47.368 5.05 0.00 0.00 3.86
512 549 1.698506 TTTTTGCCGGAACACCAGAT 58.301 45.000 5.05 0.00 0.00 2.90
513 550 0.958091 TTTTGCCGGAACACCAGATG 59.042 50.000 5.05 0.00 0.00 2.90
514 551 0.109532 TTTGCCGGAACACCAGATGA 59.890 50.000 5.05 0.00 0.00 2.92
515 552 0.605319 TTGCCGGAACACCAGATGAC 60.605 55.000 5.05 0.00 0.00 3.06
516 553 1.003839 GCCGGAACACCAGATGACA 60.004 57.895 5.05 0.00 0.00 3.58
517 554 0.605319 GCCGGAACACCAGATGACAA 60.605 55.000 5.05 0.00 0.00 3.18
518 555 1.890876 CCGGAACACCAGATGACAAA 58.109 50.000 0.00 0.00 0.00 2.83
519 556 2.436417 CCGGAACACCAGATGACAAAT 58.564 47.619 0.00 0.00 0.00 2.32
520 557 2.162208 CCGGAACACCAGATGACAAATG 59.838 50.000 0.00 0.00 0.00 2.32
521 558 2.813754 CGGAACACCAGATGACAAATGT 59.186 45.455 0.00 0.00 0.00 2.71
522 559 3.365264 CGGAACACCAGATGACAAATGTG 60.365 47.826 0.00 0.00 0.00 3.21
523 560 3.057315 GGAACACCAGATGACAAATGTGG 60.057 47.826 0.27 0.27 38.32 4.17
524 561 3.228188 ACACCAGATGACAAATGTGGT 57.772 42.857 1.53 1.53 45.20 4.16
525 562 4.365514 ACACCAGATGACAAATGTGGTA 57.634 40.909 6.82 0.00 42.86 3.25
526 563 4.724399 ACACCAGATGACAAATGTGGTAA 58.276 39.130 6.82 0.00 42.86 2.85
527 564 4.761739 ACACCAGATGACAAATGTGGTAAG 59.238 41.667 6.82 0.00 42.86 2.34
528 565 3.758554 ACCAGATGACAAATGTGGTAAGC 59.241 43.478 5.42 0.00 42.91 3.09
529 566 3.758023 CCAGATGACAAATGTGGTAAGCA 59.242 43.478 0.00 0.00 0.00 3.91
530 567 4.218200 CCAGATGACAAATGTGGTAAGCAA 59.782 41.667 0.00 0.00 0.00 3.91
531 568 5.105635 CCAGATGACAAATGTGGTAAGCAAT 60.106 40.000 0.00 0.00 0.00 3.56
532 569 6.032094 CAGATGACAAATGTGGTAAGCAATC 58.968 40.000 0.00 0.00 0.00 2.67
533 570 5.948162 AGATGACAAATGTGGTAAGCAATCT 59.052 36.000 0.00 0.00 0.00 2.40
534 571 7.066163 CAGATGACAAATGTGGTAAGCAATCTA 59.934 37.037 0.00 0.00 0.00 1.98
535 572 7.611467 AGATGACAAATGTGGTAAGCAATCTAA 59.389 33.333 0.00 0.00 0.00 2.10
536 573 7.517614 TGACAAATGTGGTAAGCAATCTAAA 57.482 32.000 0.00 0.00 0.00 1.85
537 574 7.367285 TGACAAATGTGGTAAGCAATCTAAAC 58.633 34.615 0.00 0.00 0.00 2.01
538 575 7.230510 TGACAAATGTGGTAAGCAATCTAAACT 59.769 33.333 0.00 0.00 0.00 2.66
539 576 8.630054 ACAAATGTGGTAAGCAATCTAAACTA 57.370 30.769 0.00 0.00 0.00 2.24
540 577 9.243105 ACAAATGTGGTAAGCAATCTAAACTAT 57.757 29.630 0.00 0.00 0.00 2.12
578 615 0.249953 TCTAGCTAGCTCCGACCGAG 60.250 60.000 23.26 11.42 42.04 4.63
618 2168 4.079558 AGTTGCCAAGTATTCATCCTCCAT 60.080 41.667 0.00 0.00 0.00 3.41
622 2179 5.369404 TGCCAAGTATTCATCCTCCATAGAA 59.631 40.000 0.00 0.00 0.00 2.10
631 2188 1.759445 TCCTCCATAGAAGCTGTGAGC 59.241 52.381 0.00 0.00 42.84 4.26
633 2190 1.483827 CTCCATAGAAGCTGTGAGCCA 59.516 52.381 0.00 0.00 43.77 4.75
636 2193 2.617308 CCATAGAAGCTGTGAGCCATTG 59.383 50.000 0.00 0.00 43.77 2.82
637 2194 2.408271 TAGAAGCTGTGAGCCATTGG 57.592 50.000 0.00 0.00 43.77 3.16
658 2215 1.271379 CGATTTGAGTTCCACCCCAGT 60.271 52.381 0.00 0.00 0.00 4.00
674 2231 4.484270 ACCCCAGTGATTAATATTTCCCCA 59.516 41.667 0.00 0.00 0.00 4.96
692 2252 0.806102 CATAGTTGACTCGCCACCGG 60.806 60.000 0.00 0.00 34.56 5.28
706 2266 0.957395 CACCGGCAGCTGAAATCTGT 60.957 55.000 20.43 1.78 34.21 3.41
743 2303 6.480763 ACCACAATCCACAAGTAACATCATA 58.519 36.000 0.00 0.00 0.00 2.15
751 2311 7.171653 TCCACAAGTAACATCATAACCATTGA 58.828 34.615 0.00 0.00 0.00 2.57
756 2316 8.562892 CAAGTAACATCATAACCATTGATCCTC 58.437 37.037 0.00 0.00 31.50 3.71
762 2322 5.311265 TCATAACCATTGATCCTCTGCATC 58.689 41.667 0.00 0.00 0.00 3.91
790 2350 2.653726 CCAGCTGCATACCACCATTAA 58.346 47.619 8.66 0.00 0.00 1.40
793 2353 3.633525 CAGCTGCATACCACCATTAACAT 59.366 43.478 0.00 0.00 0.00 2.71
794 2354 3.885297 AGCTGCATACCACCATTAACATC 59.115 43.478 1.02 0.00 0.00 3.06
812 2372 0.322997 TCGGTGCCCATTTTACCCTG 60.323 55.000 0.00 0.00 0.00 4.45
823 2385 1.282382 TTTACCCTGCTACCACTCCC 58.718 55.000 0.00 0.00 0.00 4.30
859 2422 1.097232 TCTGAATCCCAATTGCTGCG 58.903 50.000 0.00 0.00 0.00 5.18
956 2523 3.183754 CACAAGTCACAGACACACGTAA 58.816 45.455 0.00 0.00 34.60 3.18
1137 2713 1.150536 ATTGGCACCGACACACCTT 59.849 52.632 0.00 0.00 0.00 3.50
1163 2739 0.520404 TACTTCCACGACAGCTCGAC 59.480 55.000 1.98 0.00 43.06 4.20
1227 2803 1.040339 TGCCGTTGCAGACCCTTTTT 61.040 50.000 0.00 0.00 44.23 1.94
1276 2852 4.506255 CGGTTGGGCCAGATCCCC 62.506 72.222 6.23 2.26 45.97 4.81
1320 2896 2.848678 AGGGACTGTACATAGGAGCA 57.151 50.000 0.00 0.00 37.18 4.26
1323 2899 3.116939 AGGGACTGTACATAGGAGCAGAT 60.117 47.826 0.00 0.00 37.18 2.90
1330 2906 2.660572 ACATAGGAGCAGATCAGACGT 58.339 47.619 0.00 0.00 0.00 4.34
1334 2910 1.203523 AGGAGCAGATCAGACGTCAAC 59.796 52.381 19.50 5.80 0.00 3.18
1362 2938 2.109126 GCAGGCCATGAACCTCGTC 61.109 63.158 5.01 0.00 34.42 4.20
1425 3001 2.038269 CCGCAACAACCCGTATGCT 61.038 57.895 0.00 0.00 36.67 3.79
1515 3091 1.033574 GGACCTACTCGATGGACCTG 58.966 60.000 11.35 0.00 35.74 4.00
1603 3180 5.220931 GGGCTTACTGATTGTAATGCTTCAG 60.221 44.000 0.00 0.00 40.02 3.02
1606 3183 6.128172 GCTTACTGATTGTAATGCTTCAGTGT 60.128 38.462 13.18 0.00 46.11 3.55
1621 3205 6.817641 TGCTTCAGTGTGTTTTCATTTCATTT 59.182 30.769 0.00 0.00 0.00 2.32
1684 3268 8.311109 TGGACTTTTCCTTTTCCTAAATATTGC 58.689 33.333 0.00 0.00 43.31 3.56
1708 3292 1.735700 GCCTTTGCTTGGGTTAATCGC 60.736 52.381 0.00 0.00 33.53 4.58
1733 3317 2.986479 GCAAGTGGCAAGAAATAAACGG 59.014 45.455 0.00 0.00 43.97 4.44
1734 3318 3.574614 CAAGTGGCAAGAAATAAACGGG 58.425 45.455 0.00 0.00 0.00 5.28
1764 3348 4.869297 TGAAATGTGGTGTGCTTTTTCTTG 59.131 37.500 0.00 0.00 0.00 3.02
1812 3396 7.042119 CGCATTTAAATTTGTGTTCCCTTCTTT 60.042 33.333 0.00 0.00 0.00 2.52
1860 3444 2.310052 ACTTTATCCTTGCTGCTCCCTT 59.690 45.455 0.00 0.00 0.00 3.95
1866 3450 1.610624 CCTTGCTGCTCCCTTCGTTTA 60.611 52.381 0.00 0.00 0.00 2.01
1985 3569 5.290158 TCACCGATGTAGATTTTTAAGTCGC 59.710 40.000 0.00 0.00 0.00 5.19
1995 3580 6.086871 AGATTTTTAAGTCGCTTTAAGCTGC 58.913 36.000 15.29 7.37 39.60 5.25
2033 3618 7.278646 TGCTATTTTTCACTCAGTGTGCTATAG 59.721 37.037 4.28 9.36 45.81 1.31
2079 3664 8.380099 TGTTTAATACTCACATGGGTCTTAGTT 58.620 33.333 0.00 0.00 0.00 2.24
2081 3666 9.802039 TTTAATACTCACATGGGTCTTAGTTTT 57.198 29.630 0.00 0.00 0.00 2.43
2137 3722 4.561500 TTAACCCCTCGAATCATGTCAA 57.438 40.909 0.00 0.00 0.00 3.18
2244 3831 4.846168 AAGACCCTTCCTTACAATCCTC 57.154 45.455 0.00 0.00 0.00 3.71
2280 3868 7.820044 TTAATGCTATTTTTGGGCTTAAACG 57.180 32.000 0.00 0.00 0.00 3.60
2297 3885 0.030638 ACGCCATGTCTTTGCAACAC 59.969 50.000 0.00 0.00 0.00 3.32
2298 3886 0.030504 CGCCATGTCTTTGCAACACA 59.969 50.000 11.82 11.82 0.00 3.72
2371 3959 7.771826 ACAATAATGTAGTAGGCCAAATTACGT 59.228 33.333 5.01 2.50 38.24 3.57
2373 3961 3.264104 TGTAGTAGGCCAAATTACGTGC 58.736 45.455 5.01 0.00 0.00 5.34
2376 3965 1.370587 TAGGCCAAATTACGTGCGCC 61.371 55.000 5.01 0.00 34.42 6.53
2390 3979 2.723719 GCGCCGACGTTTGGTCTAC 61.724 63.158 0.00 0.00 43.79 2.59
2397 3986 0.032540 ACGTTTGGTCTACGGGTGTC 59.967 55.000 0.00 0.00 42.99 3.67
2491 4080 4.287766 ACTTGACCTTCCATTGTACTCC 57.712 45.455 0.00 0.00 0.00 3.85
2535 4124 0.250338 AACCCGTTGACTTCAGAGCC 60.250 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.542766 GAATCCGATTCGCAGCAAAA 57.457 45.000 5.36 0.00 0.00 2.44
10 11 3.003897 AGCTAGTGTCTCGAATCCGATTC 59.996 47.826 10.64 10.64 44.62 2.52
11 12 2.952978 AGCTAGTGTCTCGAATCCGATT 59.047 45.455 0.00 0.00 44.62 3.34
12 13 2.577700 AGCTAGTGTCTCGAATCCGAT 58.422 47.619 0.00 0.00 44.62 4.18
13 14 2.039818 AGCTAGTGTCTCGAATCCGA 57.960 50.000 0.00 0.00 43.35 4.55
14 15 2.873472 ACTAGCTAGTGTCTCGAATCCG 59.127 50.000 25.52 0.00 34.72 4.18
15 16 5.058490 AGTACTAGCTAGTGTCTCGAATCC 58.942 45.833 32.21 9.72 37.10 3.01
16 17 6.293027 GGAAGTACTAGCTAGTGTCTCGAATC 60.293 46.154 32.21 21.58 37.10 2.52
17 18 5.528320 GGAAGTACTAGCTAGTGTCTCGAAT 59.472 44.000 32.21 16.26 37.10 3.34
18 19 4.874966 GGAAGTACTAGCTAGTGTCTCGAA 59.125 45.833 32.21 11.10 37.10 3.71
19 20 4.440880 GGAAGTACTAGCTAGTGTCTCGA 58.559 47.826 32.21 11.83 37.10 4.04
20 21 3.560896 GGGAAGTACTAGCTAGTGTCTCG 59.439 52.174 32.21 4.53 37.10 4.04
21 22 4.784177 AGGGAAGTACTAGCTAGTGTCTC 58.216 47.826 32.21 24.74 37.10 3.36
22 23 4.683942 CGAGGGAAGTACTAGCTAGTGTCT 60.684 50.000 32.21 25.51 37.10 3.41
23 24 3.560896 CGAGGGAAGTACTAGCTAGTGTC 59.439 52.174 32.21 24.48 37.10 3.67
24 25 3.054508 ACGAGGGAAGTACTAGCTAGTGT 60.055 47.826 32.21 18.58 37.10 3.55
25 26 3.543665 ACGAGGGAAGTACTAGCTAGTG 58.456 50.000 32.21 16.55 37.10 2.74
26 27 3.455543 AGACGAGGGAAGTACTAGCTAGT 59.544 47.826 28.50 28.50 40.24 2.57
27 28 4.075963 AGACGAGGGAAGTACTAGCTAG 57.924 50.000 19.44 19.44 0.00 3.42
28 29 4.500499 AAGACGAGGGAAGTACTAGCTA 57.500 45.455 0.00 0.00 0.00 3.32
29 30 3.369242 AAGACGAGGGAAGTACTAGCT 57.631 47.619 0.00 0.00 0.00 3.32
30 31 6.874288 TTATAAGACGAGGGAAGTACTAGC 57.126 41.667 0.00 0.00 0.00 3.42
31 32 8.393671 ACATTATAAGACGAGGGAAGTACTAG 57.606 38.462 0.00 0.00 0.00 2.57
32 33 9.851686 TTACATTATAAGACGAGGGAAGTACTA 57.148 33.333 0.00 0.00 0.00 1.82
33 34 8.757982 TTACATTATAAGACGAGGGAAGTACT 57.242 34.615 0.00 0.00 0.00 2.73
34 35 8.844244 TCTTACATTATAAGACGAGGGAAGTAC 58.156 37.037 0.00 0.00 0.00 2.73
35 36 8.985315 TCTTACATTATAAGACGAGGGAAGTA 57.015 34.615 0.00 0.00 0.00 2.24
36 37 7.893124 TCTTACATTATAAGACGAGGGAAGT 57.107 36.000 0.00 0.00 0.00 3.01
58 59 9.933723 AGATGTTTTTAGCTTGCAAAATAATCT 57.066 25.926 0.00 6.25 30.70 2.40
61 62 9.123709 CGTAGATGTTTTTAGCTTGCAAAATAA 57.876 29.630 0.00 0.00 0.00 1.40
62 63 8.293867 ACGTAGATGTTTTTAGCTTGCAAAATA 58.706 29.630 0.00 0.00 0.00 1.40
63 64 7.145323 ACGTAGATGTTTTTAGCTTGCAAAAT 58.855 30.769 0.00 0.00 0.00 1.82
64 65 6.500041 ACGTAGATGTTTTTAGCTTGCAAAA 58.500 32.000 0.00 0.00 0.00 2.44
65 66 6.067263 ACGTAGATGTTTTTAGCTTGCAAA 57.933 33.333 0.00 0.00 0.00 3.68
66 67 5.682943 ACGTAGATGTTTTTAGCTTGCAA 57.317 34.783 0.00 0.00 0.00 4.08
67 68 6.425721 AGTTACGTAGATGTTTTTAGCTTGCA 59.574 34.615 0.00 0.00 0.00 4.08
68 69 6.736853 CAGTTACGTAGATGTTTTTAGCTTGC 59.263 38.462 0.00 0.00 0.00 4.01
69 70 7.740346 CACAGTTACGTAGATGTTTTTAGCTTG 59.260 37.037 10.93 0.00 0.00 4.01
70 71 7.570691 GCACAGTTACGTAGATGTTTTTAGCTT 60.571 37.037 10.93 0.00 0.00 3.74
71 72 6.128634 GCACAGTTACGTAGATGTTTTTAGCT 60.129 38.462 10.93 0.00 0.00 3.32
72 73 6.013689 GCACAGTTACGTAGATGTTTTTAGC 58.986 40.000 10.93 8.23 0.00 3.09
73 74 7.112528 TGCACAGTTACGTAGATGTTTTTAG 57.887 36.000 10.93 3.26 0.00 1.85
74 75 7.479897 TTGCACAGTTACGTAGATGTTTTTA 57.520 32.000 10.93 0.00 0.00 1.52
75 76 5.994887 TGCACAGTTACGTAGATGTTTTT 57.005 34.783 10.93 0.00 0.00 1.94
76 77 5.560183 GCTTGCACAGTTACGTAGATGTTTT 60.560 40.000 10.93 0.00 0.00 2.43
77 78 4.084013 GCTTGCACAGTTACGTAGATGTTT 60.084 41.667 10.93 0.00 0.00 2.83
78 79 3.432252 GCTTGCACAGTTACGTAGATGTT 59.568 43.478 10.93 0.00 0.00 2.71
79 80 2.993899 GCTTGCACAGTTACGTAGATGT 59.006 45.455 8.48 8.48 0.00 3.06
80 81 2.993220 TGCTTGCACAGTTACGTAGATG 59.007 45.455 7.37 7.37 0.00 2.90
81 82 2.993899 GTGCTTGCACAGTTACGTAGAT 59.006 45.455 19.36 0.00 0.00 1.98
82 83 2.223852 TGTGCTTGCACAGTTACGTAGA 60.224 45.455 22.47 0.00 0.00 2.59
83 84 2.131972 TGTGCTTGCACAGTTACGTAG 58.868 47.619 22.47 0.00 0.00 3.51
84 85 2.226602 TGTGCTTGCACAGTTACGTA 57.773 45.000 22.47 0.00 0.00 3.57
85 86 1.063469 GTTGTGCTTGCACAGTTACGT 59.937 47.619 24.39 0.00 36.35 3.57
86 87 1.063321 TGTTGTGCTTGCACAGTTACG 59.937 47.619 24.39 0.00 36.35 3.18
87 88 2.842208 TGTTGTGCTTGCACAGTTAC 57.158 45.000 24.39 20.49 36.35 2.50
88 89 4.759183 TGATATGTTGTGCTTGCACAGTTA 59.241 37.500 24.39 17.87 36.35 2.24
89 90 3.569277 TGATATGTTGTGCTTGCACAGTT 59.431 39.130 24.39 16.60 36.35 3.16
90 91 3.148412 TGATATGTTGTGCTTGCACAGT 58.852 40.909 24.39 17.67 36.35 3.55
91 92 3.835378 TGATATGTTGTGCTTGCACAG 57.165 42.857 24.39 0.00 36.35 3.66
92 93 3.612241 GCTTGATATGTTGTGCTTGCACA 60.612 43.478 22.47 22.47 0.00 4.57
93 94 2.919229 GCTTGATATGTTGTGCTTGCAC 59.081 45.455 17.73 17.73 0.00 4.57
94 95 2.094597 GGCTTGATATGTTGTGCTTGCA 60.095 45.455 0.00 0.00 0.00 4.08
95 96 2.533266 GGCTTGATATGTTGTGCTTGC 58.467 47.619 0.00 0.00 0.00 4.01
96 97 2.756760 AGGGCTTGATATGTTGTGCTTG 59.243 45.455 0.00 0.00 0.00 4.01
97 98 2.756760 CAGGGCTTGATATGTTGTGCTT 59.243 45.455 0.00 0.00 0.00 3.91
98 99 2.372264 CAGGGCTTGATATGTTGTGCT 58.628 47.619 0.00 0.00 0.00 4.40
99 100 1.202336 GCAGGGCTTGATATGTTGTGC 60.202 52.381 0.00 0.00 0.00 4.57
100 101 2.372264 AGCAGGGCTTGATATGTTGTG 58.628 47.619 0.00 0.00 33.89 3.33
101 102 2.814805 AGCAGGGCTTGATATGTTGT 57.185 45.000 0.00 0.00 33.89 3.32
112 113 1.071385 CGATAGGATGAAAGCAGGGCT 59.929 52.381 0.00 0.00 42.56 5.19
113 114 1.517242 CGATAGGATGAAAGCAGGGC 58.483 55.000 0.00 0.00 0.00 5.19
114 115 1.202687 TGCGATAGGATGAAAGCAGGG 60.203 52.381 0.00 0.00 0.00 4.45
115 116 2.245159 TGCGATAGGATGAAAGCAGG 57.755 50.000 0.00 0.00 0.00 4.85
116 117 4.621068 TTTTGCGATAGGATGAAAGCAG 57.379 40.909 0.00 0.00 35.95 4.24
137 138 3.190118 CGGATGAAAGCAGAGCTCTTTTT 59.810 43.478 15.27 17.20 38.25 1.94
138 139 2.746362 CGGATGAAAGCAGAGCTCTTTT 59.254 45.455 15.27 13.47 38.25 2.27
139 140 2.289945 ACGGATGAAAGCAGAGCTCTTT 60.290 45.455 15.27 6.12 38.25 2.52
140 141 1.277557 ACGGATGAAAGCAGAGCTCTT 59.722 47.619 15.27 0.00 38.25 2.85
141 142 0.901124 ACGGATGAAAGCAGAGCTCT 59.099 50.000 11.45 11.45 38.25 4.09
142 143 1.005340 CACGGATGAAAGCAGAGCTC 58.995 55.000 5.27 5.27 38.25 4.09
143 144 0.610174 TCACGGATGAAAGCAGAGCT 59.390 50.000 0.00 0.00 42.56 4.09
144 145 1.596727 GATCACGGATGAAAGCAGAGC 59.403 52.381 0.00 0.00 38.69 4.09
145 146 2.208431 GGATCACGGATGAAAGCAGAG 58.792 52.381 0.00 0.00 38.69 3.35
146 147 1.554617 TGGATCACGGATGAAAGCAGA 59.445 47.619 0.00 0.00 38.69 4.26
147 148 2.028420 TGGATCACGGATGAAAGCAG 57.972 50.000 0.00 0.00 38.69 4.24
148 149 2.564771 GATGGATCACGGATGAAAGCA 58.435 47.619 0.00 0.00 38.69 3.91
149 150 1.876156 GGATGGATCACGGATGAAAGC 59.124 52.381 0.00 0.00 38.69 3.51
150 151 3.136763 CTGGATGGATCACGGATGAAAG 58.863 50.000 0.00 0.00 38.69 2.62
151 152 2.771372 TCTGGATGGATCACGGATGAAA 59.229 45.455 0.00 0.00 38.69 2.69
159 160 0.749649 AGTCGCTCTGGATGGATCAC 59.250 55.000 0.00 0.00 0.00 3.06
215 216 4.501921 GCTGAGAAAACTCAAAAAGCACTG 59.498 41.667 0.00 0.00 32.43 3.66
226 227 2.225255 GCAACCAGAGCTGAGAAAACTC 59.775 50.000 0.00 0.00 0.00 3.01
250 251 4.043200 GTGCTTGGCTTCCACGCC 62.043 66.667 11.09 0.00 46.33 5.68
297 298 1.131126 GGTGCAGAATGTTGGTCATCG 59.869 52.381 0.00 0.00 39.31 3.84
299 300 1.076024 AGGGTGCAGAATGTTGGTCAT 59.924 47.619 0.00 0.00 39.31 3.06
300 301 0.478072 AGGGTGCAGAATGTTGGTCA 59.522 50.000 0.00 0.00 39.31 4.02
301 302 2.359900 CTAGGGTGCAGAATGTTGGTC 58.640 52.381 0.00 0.00 39.31 4.02
302 303 1.614317 GCTAGGGTGCAGAATGTTGGT 60.614 52.381 0.00 0.00 39.31 3.67
368 370 6.750501 CGACTGGATAGAACGAAAATTCTGTA 59.249 38.462 0.00 0.00 39.33 2.74
380 382 0.389757 GAGCCCCGACTGGATAGAAC 59.610 60.000 0.00 0.00 37.49 3.01
383 385 1.528542 TCGAGCCCCGACTGGATAG 60.529 63.158 0.00 0.00 43.23 2.08
384 386 2.599032 TCGAGCCCCGACTGGATA 59.401 61.111 0.00 0.00 43.23 2.59
392 394 1.364171 CCTGAGTTATCGAGCCCCG 59.636 63.158 0.00 0.00 40.25 5.73
397 434 3.626670 AGAACGGTACCTGAGTTATCGAG 59.373 47.826 10.90 0.00 0.00 4.04
409 446 6.161381 TCTTGAGATGTAAAAGAACGGTACC 58.839 40.000 0.16 0.16 0.00 3.34
418 455 6.145535 GTGGTTTGCTCTTGAGATGTAAAAG 58.854 40.000 1.30 0.00 0.00 2.27
419 456 5.009610 GGTGGTTTGCTCTTGAGATGTAAAA 59.990 40.000 1.30 0.00 0.00 1.52
431 468 3.040965 CCATGTGGTGGTTTGCTCT 57.959 52.632 0.00 0.00 43.44 4.09
440 477 5.754543 AAAAAGAAAAATGCCATGTGGTG 57.245 34.783 0.35 0.00 37.57 4.17
466 503 1.169661 TTGTCATGTGGTGTTCCCGC 61.170 55.000 0.00 0.00 44.53 6.13
467 504 1.533625 ATTGTCATGTGGTGTTCCCG 58.466 50.000 0.00 0.00 35.15 5.14
468 505 4.306600 GAAAATTGTCATGTGGTGTTCCC 58.693 43.478 0.00 0.00 0.00 3.97
469 506 4.039124 AGGAAAATTGTCATGTGGTGTTCC 59.961 41.667 0.00 1.07 33.66 3.62
470 507 5.200368 AGGAAAATTGTCATGTGGTGTTC 57.800 39.130 0.00 0.00 0.00 3.18
471 508 5.612725 AAGGAAAATTGTCATGTGGTGTT 57.387 34.783 0.00 0.00 0.00 3.32
472 509 5.612725 AAAGGAAAATTGTCATGTGGTGT 57.387 34.783 0.00 0.00 0.00 4.16
473 510 6.923928 AAAAAGGAAAATTGTCATGTGGTG 57.076 33.333 0.00 0.00 0.00 4.17
493 530 1.339610 CATCTGGTGTTCCGGCAAAAA 59.660 47.619 0.00 0.00 39.81 1.94
494 531 0.958091 CATCTGGTGTTCCGGCAAAA 59.042 50.000 0.00 0.00 39.81 2.44
495 532 0.109532 TCATCTGGTGTTCCGGCAAA 59.890 50.000 0.00 0.00 39.81 3.68
496 533 0.605319 GTCATCTGGTGTTCCGGCAA 60.605 55.000 0.00 0.00 39.81 4.52
497 534 1.003839 GTCATCTGGTGTTCCGGCA 60.004 57.895 0.00 0.00 39.81 5.69
498 535 0.605319 TTGTCATCTGGTGTTCCGGC 60.605 55.000 0.00 0.00 39.81 6.13
499 536 1.890876 TTTGTCATCTGGTGTTCCGG 58.109 50.000 0.00 0.00 41.27 5.14
500 537 2.813754 ACATTTGTCATCTGGTGTTCCG 59.186 45.455 0.00 0.00 36.30 4.30
501 538 3.057315 CCACATTTGTCATCTGGTGTTCC 60.057 47.826 0.00 0.00 0.00 3.62
502 539 3.569701 ACCACATTTGTCATCTGGTGTTC 59.430 43.478 0.00 0.00 0.00 3.18
503 540 3.565307 ACCACATTTGTCATCTGGTGTT 58.435 40.909 0.00 0.00 0.00 3.32
504 541 3.228188 ACCACATTTGTCATCTGGTGT 57.772 42.857 0.00 0.00 0.00 4.16
505 542 4.379813 GCTTACCACATTTGTCATCTGGTG 60.380 45.833 0.00 0.00 0.00 4.17
506 543 3.758554 GCTTACCACATTTGTCATCTGGT 59.241 43.478 0.00 0.00 0.00 4.00
507 544 3.758023 TGCTTACCACATTTGTCATCTGG 59.242 43.478 0.00 0.00 0.00 3.86
508 545 5.375417 TTGCTTACCACATTTGTCATCTG 57.625 39.130 0.00 0.00 0.00 2.90
509 546 5.948162 AGATTGCTTACCACATTTGTCATCT 59.052 36.000 0.00 0.00 0.00 2.90
510 547 6.199937 AGATTGCTTACCACATTTGTCATC 57.800 37.500 0.00 0.00 0.00 2.92
511 548 7.701539 TTAGATTGCTTACCACATTTGTCAT 57.298 32.000 0.00 0.00 0.00 3.06
512 549 7.230510 AGTTTAGATTGCTTACCACATTTGTCA 59.769 33.333 0.00 0.00 0.00 3.58
513 550 7.593825 AGTTTAGATTGCTTACCACATTTGTC 58.406 34.615 0.00 0.00 0.00 3.18
514 551 7.524717 AGTTTAGATTGCTTACCACATTTGT 57.475 32.000 0.00 0.00 0.00 2.83
542 579 9.794685 GCTAGCTAGAATTGCTCTTTTTATTTT 57.205 29.630 25.15 0.00 41.46 1.82
543 580 9.183368 AGCTAGCTAGAATTGCTCTTTTTATTT 57.817 29.630 25.15 0.00 41.46 1.40
544 581 8.744568 AGCTAGCTAGAATTGCTCTTTTTATT 57.255 30.769 25.15 0.00 41.46 1.40
545 582 7.443879 GGAGCTAGCTAGAATTGCTCTTTTTAT 59.556 37.037 25.15 0.00 46.39 1.40
546 583 6.763610 GGAGCTAGCTAGAATTGCTCTTTTTA 59.236 38.462 25.15 0.00 46.39 1.52
547 584 5.588246 GGAGCTAGCTAGAATTGCTCTTTTT 59.412 40.000 25.15 0.00 46.39 1.94
548 585 5.122519 GGAGCTAGCTAGAATTGCTCTTTT 58.877 41.667 25.15 0.00 46.39 2.27
549 586 4.702831 GGAGCTAGCTAGAATTGCTCTTT 58.297 43.478 25.15 0.00 46.39 2.52
550 587 3.243704 CGGAGCTAGCTAGAATTGCTCTT 60.244 47.826 25.15 0.00 46.39 2.85
551 588 2.295909 CGGAGCTAGCTAGAATTGCTCT 59.704 50.000 25.15 9.61 46.39 4.09
552 589 2.294791 TCGGAGCTAGCTAGAATTGCTC 59.705 50.000 25.15 21.48 46.43 4.26
553 590 2.035321 GTCGGAGCTAGCTAGAATTGCT 59.965 50.000 25.15 14.42 43.79 3.91
554 591 2.399448 GTCGGAGCTAGCTAGAATTGC 58.601 52.381 25.15 9.41 0.00 3.56
555 592 2.605823 CGGTCGGAGCTAGCTAGAATTG 60.606 54.545 25.15 10.60 0.00 2.32
556 593 1.609555 CGGTCGGAGCTAGCTAGAATT 59.390 52.381 25.15 8.68 0.00 2.17
557 594 1.202782 TCGGTCGGAGCTAGCTAGAAT 60.203 52.381 25.15 11.71 0.00 2.40
558 595 0.179702 TCGGTCGGAGCTAGCTAGAA 59.820 55.000 25.15 2.45 0.00 2.10
559 596 0.249953 CTCGGTCGGAGCTAGCTAGA 60.250 60.000 25.15 17.28 35.63 2.43
560 597 2.240230 CTCGGTCGGAGCTAGCTAG 58.760 63.158 19.38 16.84 35.63 3.42
561 598 4.458666 CTCGGTCGGAGCTAGCTA 57.541 61.111 19.38 0.00 35.63 3.32
578 615 1.117150 ACTGGCAAATCCATGGATGC 58.883 50.000 27.97 26.81 45.50 3.91
618 2168 1.679944 GCCAATGGCTCACAGCTTCTA 60.680 52.381 18.47 0.00 46.69 2.10
631 2188 1.818060 TGGAACTCAAATCGCCAATGG 59.182 47.619 0.00 0.00 0.00 3.16
633 2190 1.818674 GGTGGAACTCAAATCGCCAAT 59.181 47.619 0.00 0.00 36.74 3.16
636 2193 1.313091 GGGGTGGAACTCAAATCGCC 61.313 60.000 0.00 0.00 41.20 5.54
637 2194 0.608035 TGGGGTGGAACTCAAATCGC 60.608 55.000 0.00 0.00 41.20 4.58
646 2203 6.040504 GGAAATATTAATCACTGGGGTGGAAC 59.959 42.308 0.00 0.00 43.17 3.62
658 2215 9.793259 GAGTCAACTATGGGGAAATATTAATCA 57.207 33.333 0.00 0.00 0.00 2.57
674 2231 1.515954 CCGGTGGCGAGTCAACTAT 59.484 57.895 0.00 0.00 0.00 2.12
692 2252 2.751259 TGGATCAACAGATTTCAGCTGC 59.249 45.455 9.47 0.00 36.86 5.25
706 2266 3.323403 GGATTGTGGTTTTGGTGGATCAA 59.677 43.478 0.00 0.00 0.00 2.57
743 2303 2.092753 ACGATGCAGAGGATCAATGGTT 60.093 45.455 0.00 0.00 37.82 3.67
762 2322 3.390183 TATGCAGCTGGGGAGCACG 62.390 63.158 17.12 0.00 41.60 5.34
799 2359 2.025321 AGTGGTAGCAGGGTAAAATGGG 60.025 50.000 0.00 0.00 0.00 4.00
812 2372 1.483415 TCCATAAACGGGAGTGGTAGC 59.517 52.381 0.00 0.00 46.69 3.58
823 2385 1.667724 CAGAAGGCTGCTCCATAAACG 59.332 52.381 0.00 0.00 34.95 3.60
859 2422 3.269347 ACAAGTGACACGTGGCGC 61.269 61.111 27.48 27.48 31.79 6.53
871 2434 2.876550 GGAGCGTAAAAGGAACACAAGT 59.123 45.455 0.00 0.00 0.00 3.16
956 2523 3.253677 GTGTGCTACTCCGTAGATGCTAT 59.746 47.826 5.28 0.00 38.29 2.97
1120 2696 1.525077 GAAGGTGTGTCGGTGCCAA 60.525 57.895 0.00 0.00 0.00 4.52
1137 2713 2.030185 GCTGTCGTGGAAGTAGAAGTGA 60.030 50.000 0.00 0.00 0.00 3.41
1227 2803 2.998480 ATCACGTACACCGCCCCA 60.998 61.111 0.00 0.00 41.42 4.96
1305 2881 4.582656 GTCTGATCTGCTCCTATGTACAGT 59.417 45.833 0.33 0.00 0.00 3.55
1317 2893 0.109086 CCGTTGACGTCTGATCTGCT 60.109 55.000 17.92 0.00 37.74 4.24
1320 2896 1.215647 GCCCGTTGACGTCTGATCT 59.784 57.895 17.92 0.00 37.74 2.75
1323 2899 1.006571 GAAGCCCGTTGACGTCTGA 60.007 57.895 17.92 2.36 37.74 3.27
1330 2906 2.032528 CTGCAGGAAGCCCGTTGA 59.967 61.111 5.57 0.00 44.83 3.18
1420 2996 1.444917 ATCTCGCGGACGTCAGCATA 61.445 55.000 33.98 22.53 41.18 3.14
1421 2997 2.775856 ATCTCGCGGACGTCAGCAT 61.776 57.895 33.98 20.61 41.18 3.79
1425 3001 4.492160 GGCATCTCGCGGACGTCA 62.492 66.667 18.91 0.00 43.84 4.35
1488 3064 2.363925 GAGTAGGTCCGGGCCTGT 60.364 66.667 38.16 24.66 39.60 4.00
1603 3180 9.934190 AGCAATAAAAATGAAATGAAAACACAC 57.066 25.926 0.00 0.00 0.00 3.82
1621 3205 4.219725 GGCCAACCTGAAGTAAGCAATAAA 59.780 41.667 0.00 0.00 0.00 1.40
1684 3268 1.327303 TAACCCAAGCAAAGGCACAG 58.673 50.000 0.00 0.00 44.61 3.66
1708 3292 5.402398 GTTTATTTCTTGCCACTTGCTAGG 58.598 41.667 0.00 0.00 42.26 3.02
1730 3314 0.035439 CACATTTCACCTAGGCCCGT 60.035 55.000 9.30 0.00 0.00 5.28
1731 3315 0.748005 CCACATTTCACCTAGGCCCG 60.748 60.000 9.30 0.00 0.00 6.13
1733 3317 1.271926 ACACCACATTTCACCTAGGCC 60.272 52.381 9.30 0.00 0.00 5.19
1734 3318 1.812571 CACACCACATTTCACCTAGGC 59.187 52.381 9.30 0.00 0.00 3.93
1764 3348 9.683069 ATGCGATAAATAAGTTTCCATTGATTC 57.317 29.630 0.00 0.00 0.00 2.52
1812 3396 2.229543 AGCAATCAAATTCAGAAGCGCA 59.770 40.909 11.47 0.00 0.00 6.09
1860 3444 6.528014 TCAGCGACACTTAATTTTAAACGA 57.472 33.333 0.00 0.00 0.00 3.85
1940 3524 3.777106 TGGCAAGATGTCAGTCTCTTT 57.223 42.857 0.00 0.00 29.34 2.52
1947 3531 1.012086 CGGTGATGGCAAGATGTCAG 58.988 55.000 0.00 0.00 34.38 3.51
1952 3536 2.700371 TCTACATCGGTGATGGCAAGAT 59.300 45.455 0.65 0.00 43.60 2.40
1995 3580 5.621228 GTGAAAAATAGCACTGACTGAAACG 59.379 40.000 0.00 0.00 32.44 3.60
2033 3618 4.392940 ACATTGGAGGAATGCTAGTATGC 58.607 43.478 0.00 0.00 44.85 3.14
2163 3750 9.703892 GTCATAGTGCTAAGATCAAGTCATAAT 57.296 33.333 0.00 0.00 0.00 1.28
2244 3831 6.436843 AAATAGCATTAAAACCTGTCCTCG 57.563 37.500 0.00 0.00 0.00 4.63
2250 3837 6.172630 AGCCCAAAAATAGCATTAAAACCTG 58.827 36.000 0.00 0.00 0.00 4.00
2280 3868 3.963676 TGTGTTGCAAAGACATGGC 57.036 47.368 0.00 0.00 45.90 4.40
2371 3959 3.210223 TAGACCAAACGTCGGCGCA 62.210 57.895 10.50 0.00 46.92 6.09
2373 3961 2.430942 CGTAGACCAAACGTCGGCG 61.431 63.158 8.42 8.42 46.92 6.46
2376 3965 1.005294 CACCCGTAGACCAAACGTCG 61.005 60.000 0.00 0.00 46.92 5.12


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

AutoCloner maintained by Alex Coulton.