Multiple sequence alignment - TraesCS6B01G289300

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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 TraesCS6B01G289300 chr6B 100.000 2459 0 0 1 2459 520547733 520545275 0.000000e+00 4542.0
1 TraesCS6B01G289300 chr6A 86.903 1886 118 62 632 2431 485157982 485156140 0.000000e+00 1995.0
2 TraesCS6B01G289300 chr6A 90.000 210 15 5 129 334 485160172 485159965 1.450000e-67 267.0
3 TraesCS6B01G289300 chr6D 90.273 1501 82 30 527 2007 344703195 344701739 0.000000e+00 1905.0
4 TraesCS6B01G289300 chr6D 87.281 228 22 5 129 351 344703413 344703188 1.130000e-63 254.0
5 TraesCS6B01G289300 chr6D 75.365 479 52 37 1987 2422 344701663 344701208 1.170000e-38 171.0
6 TraesCS6B01G289300 chr6D 93.651 63 4 0 1 63 344703469 344703407 7.240000e-16 95.3
7 TraesCS6B01G289300 chr1B 95.429 175 8 0 352 526 15747037 15747211 1.860000e-71 279.0
8 TraesCS6B01G289300 chr1B 93.785 177 10 1 350 526 355814520 355814345 5.210000e-67 265.0
9 TraesCS6B01G289300 chr7B 94.318 176 10 0 351 526 667475904 667475729 1.120000e-68 270.0
10 TraesCS6B01G289300 chr7B 92.262 168 12 1 358 525 332258956 332258790 1.140000e-58 237.0
11 TraesCS6B01G289300 chr7B 95.238 42 1 1 88 128 113482088 113482047 5.680000e-07 65.8
12 TraesCS6B01G289300 chr4B 93.714 175 11 0 352 526 543329471 543329297 1.880000e-66 263.0
13 TraesCS6B01G289300 chr3B 93.750 176 10 1 352 527 65199641 65199815 1.880000e-66 263.0
14 TraesCS6B01G289300 chr1A 94.186 172 9 1 353 524 536636671 536636841 6.740000e-66 261.0
15 TraesCS6B01G289300 chr1A 100.000 28 0 0 85 112 65900337 65900310 4.000000e-03 52.8
16 TraesCS6B01G289300 chr2B 85.876 177 23 2 352 526 121646300 121646124 1.160000e-43 187.0
17 TraesCS6B01G289300 chr2B 85.311 177 21 5 352 526 2513129 2513302 6.990000e-41 178.0


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 TraesCS6B01G289300 chr6B 520545275 520547733 2458 True 4542.000 4542 100.0000 1 2459 1 chr6B.!!$R1 2458
1 TraesCS6B01G289300 chr6A 485156140 485160172 4032 True 1131.000 1995 88.4515 129 2431 2 chr6A.!!$R1 2302
2 TraesCS6B01G289300 chr6D 344701208 344703469 2261 True 606.325 1905 86.6425 1 2422 4 chr6D.!!$R1 2421

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
98 99 0.035439 CCCTGTGGCCGTAGAACAAT 60.035 55.0 7.58 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 3846 0.882927 TTTCGGCCTGTTCGTTGAGG 60.883 55.0 0.0 0.0 0.0 3.86 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
22 23 0.611200 TACCATGTGAGGAACCCACG 59.389 55.000 0.00 0.00 41.11 4.94
26 27 1.768684 ATGTGAGGAACCCACGCTGT 61.769 55.000 0.00 0.00 41.11 4.40
27 28 1.227853 GTGAGGAACCCACGCTGTT 60.228 57.895 0.00 0.00 0.00 3.16
60 61 3.687572 GCAGTTAGCCATCATCACAAG 57.312 47.619 0.00 0.00 37.23 3.16
61 62 3.012518 GCAGTTAGCCATCATCACAAGT 58.987 45.455 0.00 0.00 37.23 3.16
62 63 3.181503 GCAGTTAGCCATCATCACAAGTG 60.182 47.826 0.00 0.00 37.23 3.16
63 64 3.012518 AGTTAGCCATCATCACAAGTGC 58.987 45.455 0.00 0.00 0.00 4.40
64 65 2.749076 GTTAGCCATCATCACAAGTGCA 59.251 45.455 0.00 0.00 0.00 4.57
65 66 1.913778 AGCCATCATCACAAGTGCAA 58.086 45.000 0.00 0.00 0.00 4.08
66 67 1.816835 AGCCATCATCACAAGTGCAAG 59.183 47.619 0.00 0.00 0.00 4.01
67 68 1.814394 GCCATCATCACAAGTGCAAGA 59.186 47.619 0.00 0.00 0.00 3.02
68 69 2.415090 GCCATCATCACAAGTGCAAGAC 60.415 50.000 0.00 0.00 0.00 3.01
69 70 3.079578 CCATCATCACAAGTGCAAGACT 58.920 45.455 0.00 0.00 35.94 3.24
70 71 3.504906 CCATCATCACAAGTGCAAGACTT 59.495 43.478 0.00 0.00 46.52 3.01
71 72 4.022589 CCATCATCACAAGTGCAAGACTTT 60.023 41.667 0.00 0.00 42.70 2.66
72 73 5.508489 CCATCATCACAAGTGCAAGACTTTT 60.508 40.000 0.00 0.00 42.70 2.27
73 74 5.581126 TCATCACAAGTGCAAGACTTTTT 57.419 34.783 0.00 0.00 42.70 1.94
74 75 5.581605 TCATCACAAGTGCAAGACTTTTTC 58.418 37.500 0.00 0.00 42.70 2.29
75 76 5.357878 TCATCACAAGTGCAAGACTTTTTCT 59.642 36.000 0.00 0.00 42.70 2.52
76 77 5.643379 TCACAAGTGCAAGACTTTTTCTT 57.357 34.783 0.00 0.00 42.70 2.52
77 78 6.024552 TCACAAGTGCAAGACTTTTTCTTT 57.975 33.333 0.00 0.00 42.70 2.52
78 79 7.151999 TCACAAGTGCAAGACTTTTTCTTTA 57.848 32.000 0.00 0.00 42.70 1.85
79 80 7.027161 TCACAAGTGCAAGACTTTTTCTTTAC 58.973 34.615 0.00 0.00 42.70 2.01
80 81 6.253512 CACAAGTGCAAGACTTTTTCTTTACC 59.746 38.462 0.00 0.00 42.70 2.85
81 82 5.515797 AGTGCAAGACTTTTTCTTTACCC 57.484 39.130 0.00 0.00 42.37 3.69
82 83 5.201243 AGTGCAAGACTTTTTCTTTACCCT 58.799 37.500 0.00 0.00 42.37 4.34
83 84 5.067805 AGTGCAAGACTTTTTCTTTACCCTG 59.932 40.000 0.00 0.00 42.37 4.45
84 85 4.953579 TGCAAGACTTTTTCTTTACCCTGT 59.046 37.500 0.00 0.00 42.37 4.00
85 86 5.163561 TGCAAGACTTTTTCTTTACCCTGTG 60.164 40.000 0.00 0.00 42.37 3.66
86 87 5.736207 GCAAGACTTTTTCTTTACCCTGTGG 60.736 44.000 0.00 0.00 42.37 4.17
87 88 3.889538 AGACTTTTTCTTTACCCTGTGGC 59.110 43.478 0.00 0.00 33.59 5.01
88 89 2.963101 ACTTTTTCTTTACCCTGTGGCC 59.037 45.455 0.00 0.00 33.59 5.36
89 90 1.611519 TTTTCTTTACCCTGTGGCCG 58.388 50.000 0.00 0.00 33.59 6.13
90 91 0.475044 TTTCTTTACCCTGTGGCCGT 59.525 50.000 0.00 0.00 33.59 5.68
91 92 1.350071 TTCTTTACCCTGTGGCCGTA 58.650 50.000 0.00 0.00 33.59 4.02
92 93 0.899720 TCTTTACCCTGTGGCCGTAG 59.100 55.000 0.00 0.00 33.59 3.51
93 94 0.899720 CTTTACCCTGTGGCCGTAGA 59.100 55.000 7.58 0.00 33.59 2.59
94 95 1.276989 CTTTACCCTGTGGCCGTAGAA 59.723 52.381 7.58 0.00 33.59 2.10
95 96 0.609662 TTACCCTGTGGCCGTAGAAC 59.390 55.000 7.58 0.00 33.59 3.01
96 97 0.542467 TACCCTGTGGCCGTAGAACA 60.542 55.000 7.58 0.13 33.59 3.18
97 98 1.373435 CCCTGTGGCCGTAGAACAA 59.627 57.895 7.58 0.00 0.00 2.83
98 99 0.035439 CCCTGTGGCCGTAGAACAAT 60.035 55.000 7.58 0.00 0.00 2.71
99 100 1.613255 CCCTGTGGCCGTAGAACAATT 60.613 52.381 7.58 0.00 0.00 2.32
100 101 1.468520 CCTGTGGCCGTAGAACAATTG 59.531 52.381 3.24 3.24 0.00 2.32
101 102 2.151202 CTGTGGCCGTAGAACAATTGT 58.849 47.619 4.92 4.92 0.00 2.71
102 103 2.552315 CTGTGGCCGTAGAACAATTGTT 59.448 45.455 23.49 23.49 41.64 2.83
195 196 8.360390 GTTTCTTGGTAGATTTTGGAATGAAGT 58.640 33.333 0.00 0.00 0.00 3.01
212 213 2.359850 TGCGATGCTCGGCCTTTT 60.360 55.556 0.00 0.00 40.84 2.27
232 233 1.746615 CACCATCTCCACCTTGCCG 60.747 63.158 0.00 0.00 0.00 5.69
240 241 4.028490 CACCTTGCCGGGGTGCTA 62.028 66.667 14.43 0.00 45.97 3.49
243 244 1.823899 CCTTGCCGGGGTGCTATTC 60.824 63.158 2.18 0.00 0.00 1.75
254 258 4.025145 CGGGGTGCTATTCGAAATTAAGAC 60.025 45.833 0.00 0.00 0.00 3.01
255 259 5.123936 GGGGTGCTATTCGAAATTAAGACT 58.876 41.667 0.00 0.00 0.00 3.24
259 263 6.018669 GGTGCTATTCGAAATTAAGACTGAGG 60.019 42.308 0.00 0.00 0.00 3.86
279 283 5.163733 TGAGGTGGTTCTTTGAACGTTAAAC 60.164 40.000 0.00 0.00 0.00 2.01
295 299 5.740099 ACGTTAAACAGAAAATCAAACCACG 59.260 36.000 0.00 0.00 0.00 4.94
302 307 0.525761 AAATCAAACCACGATGCCCG 59.474 50.000 0.00 0.00 45.44 6.13
325 331 6.456988 CCGTACTCAAAATGATGGTTTAGCTC 60.457 42.308 0.00 0.00 0.00 4.09
333 339 8.352942 CAAAATGATGGTTTAGCTCCTTATACC 58.647 37.037 0.00 0.00 0.00 2.73
343 349 9.726438 GTTTAGCTCCTTATACCATTCACATAT 57.274 33.333 0.00 0.00 0.00 1.78
344 350 9.725019 TTTAGCTCCTTATACCATTCACATATG 57.275 33.333 0.00 0.00 0.00 1.78
345 351 7.321717 AGCTCCTTATACCATTCACATATGT 57.678 36.000 1.41 1.41 0.00 2.29
346 352 7.749666 AGCTCCTTATACCATTCACATATGTT 58.250 34.615 5.37 0.00 0.00 2.71
347 353 8.220559 AGCTCCTTATACCATTCACATATGTTT 58.779 33.333 5.37 0.00 0.00 2.83
348 354 9.502091 GCTCCTTATACCATTCACATATGTTTA 57.498 33.333 5.37 0.00 0.00 2.01
354 360 8.752005 ATACCATTCACATATGTTTAAGCAGT 57.248 30.769 5.37 5.69 0.00 4.40
355 361 6.855836 ACCATTCACATATGTTTAAGCAGTG 58.144 36.000 5.37 1.42 0.00 3.66
356 362 6.127647 ACCATTCACATATGTTTAAGCAGTGG 60.128 38.462 5.37 10.19 0.00 4.00
357 363 4.963276 TCACATATGTTTAAGCAGTGGC 57.037 40.909 5.37 0.00 41.61 5.01
375 381 4.448537 TGGCGGACCAAGAAATAAAATG 57.551 40.909 0.00 0.00 45.37 2.32
376 382 3.186909 GGCGGACCAAGAAATAAAATGC 58.813 45.455 0.00 0.00 35.26 3.56
377 383 3.367910 GGCGGACCAAGAAATAAAATGCA 60.368 43.478 0.00 0.00 35.26 3.96
378 384 3.859386 GCGGACCAAGAAATAAAATGCAG 59.141 43.478 0.00 0.00 0.00 4.41
379 385 4.423732 CGGACCAAGAAATAAAATGCAGG 58.576 43.478 0.00 0.00 0.00 4.85
380 386 4.677779 CGGACCAAGAAATAAAATGCAGGG 60.678 45.833 0.00 0.00 0.00 4.45
381 387 4.222810 GGACCAAGAAATAAAATGCAGGGT 59.777 41.667 0.00 0.00 0.00 4.34
382 388 5.151297 ACCAAGAAATAAAATGCAGGGTG 57.849 39.130 0.00 0.00 0.00 4.61
383 389 4.592778 ACCAAGAAATAAAATGCAGGGTGT 59.407 37.500 0.00 0.00 0.00 4.16
384 390 4.931002 CCAAGAAATAAAATGCAGGGTGTG 59.069 41.667 0.00 0.00 0.00 3.82
393 399 4.557554 CAGGGTGTGCACACTTCA 57.442 55.556 40.20 9.98 43.83 3.02
394 400 2.792500 CAGGGTGTGCACACTTCAA 58.208 52.632 40.20 9.13 43.83 2.69
395 401 1.102154 CAGGGTGTGCACACTTCAAA 58.898 50.000 40.20 8.35 43.83 2.69
396 402 1.476085 CAGGGTGTGCACACTTCAAAA 59.524 47.619 40.20 7.56 43.83 2.44
397 403 2.094286 CAGGGTGTGCACACTTCAAAAA 60.094 45.455 40.20 6.78 43.83 1.94
427 433 9.550406 AATGTATATTTTCATTGGCTTGAATGG 57.450 29.630 4.66 0.00 35.64 3.16
428 434 7.499292 TGTATATTTTCATTGGCTTGAATGGG 58.501 34.615 4.66 0.00 35.64 4.00
429 435 2.766345 TTTCATTGGCTTGAATGGGC 57.234 45.000 4.66 0.00 35.64 5.36
437 443 3.694043 GGCTTGAATGGGCCTTAAAAA 57.306 42.857 4.53 0.00 44.48 1.94
438 444 4.220693 GGCTTGAATGGGCCTTAAAAAT 57.779 40.909 4.53 0.00 44.48 1.82
439 445 4.191544 GGCTTGAATGGGCCTTAAAAATC 58.808 43.478 4.53 0.00 44.48 2.17
440 446 4.323409 GGCTTGAATGGGCCTTAAAAATCA 60.323 41.667 4.53 0.00 44.48 2.57
441 447 5.244755 GCTTGAATGGGCCTTAAAAATCAA 58.755 37.500 4.53 4.28 0.00 2.57
442 448 5.122239 GCTTGAATGGGCCTTAAAAATCAAC 59.878 40.000 4.53 0.00 0.00 3.18
443 449 6.432403 TTGAATGGGCCTTAAAAATCAACT 57.568 33.333 4.53 0.00 0.00 3.16
444 450 7.546250 TTGAATGGGCCTTAAAAATCAACTA 57.454 32.000 4.53 0.00 0.00 2.24
445 451 7.546250 TGAATGGGCCTTAAAAATCAACTAA 57.454 32.000 4.53 0.00 0.00 2.24
446 452 8.144862 TGAATGGGCCTTAAAAATCAACTAAT 57.855 30.769 4.53 0.00 0.00 1.73
447 453 8.601546 TGAATGGGCCTTAAAAATCAACTAATT 58.398 29.630 4.53 0.00 0.00 1.40
480 486 9.898152 TGGTAAAAGAACATTTTCCAAAATTCT 57.102 25.926 0.00 0.00 36.97 2.40
483 489 7.806409 AAAGAACATTTTCCAAAATTCTGGG 57.194 32.000 0.00 0.00 36.52 4.45
484 490 6.499106 AGAACATTTTCCAAAATTCTGGGT 57.501 33.333 0.00 0.00 36.52 4.51
485 491 6.290605 AGAACATTTTCCAAAATTCTGGGTG 58.709 36.000 0.00 0.00 36.52 4.61
486 492 5.628797 ACATTTTCCAAAATTCTGGGTGT 57.371 34.783 0.00 0.00 36.52 4.16
487 493 5.367302 ACATTTTCCAAAATTCTGGGTGTG 58.633 37.500 0.00 0.00 36.52 3.82
488 494 3.467374 TTTCCAAAATTCTGGGTGTGC 57.533 42.857 0.00 0.00 37.06 4.57
489 495 1.337118 TCCAAAATTCTGGGTGTGCC 58.663 50.000 0.00 0.00 37.06 5.01
490 496 1.047002 CCAAAATTCTGGGTGTGCCA 58.953 50.000 0.00 0.00 36.17 4.92
491 497 1.624813 CCAAAATTCTGGGTGTGCCAT 59.375 47.619 0.00 0.00 36.17 4.40
492 498 2.613474 CCAAAATTCTGGGTGTGCCATG 60.613 50.000 0.00 0.00 36.17 3.66
493 499 1.269012 AAATTCTGGGTGTGCCATGG 58.731 50.000 7.63 7.63 36.17 3.66
494 500 1.259840 AATTCTGGGTGTGCCATGGC 61.260 55.000 30.54 30.54 42.35 4.40
518 524 3.990492 TGGCACACCCCCTAGATAT 57.010 52.632 0.00 0.00 33.59 1.63
519 525 1.434188 TGGCACACCCCCTAGATATG 58.566 55.000 0.00 0.00 33.59 1.78
520 526 0.036875 GGCACACCCCCTAGATATGC 59.963 60.000 0.00 0.00 0.00 3.14
521 527 0.036875 GCACACCCCCTAGATATGCC 59.963 60.000 0.00 0.00 0.00 4.40
522 528 1.434188 CACACCCCCTAGATATGCCA 58.566 55.000 0.00 0.00 0.00 4.92
523 529 1.072331 CACACCCCCTAGATATGCCAC 59.928 57.143 0.00 0.00 0.00 5.01
524 530 1.061346 ACACCCCCTAGATATGCCACT 60.061 52.381 0.00 0.00 0.00 4.00
525 531 1.349026 CACCCCCTAGATATGCCACTG 59.651 57.143 0.00 0.00 0.00 3.66
544 550 5.382303 CACTGTGTTTAAGAAAGGCATACG 58.618 41.667 0.00 0.00 0.00 3.06
555 726 7.535489 AAGAAAGGCATACGTAGAATGTTAC 57.465 36.000 0.08 0.00 0.00 2.50
556 727 6.047231 AGAAAGGCATACGTAGAATGTTACC 58.953 40.000 0.08 0.00 0.00 2.85
562 733 1.205657 CGTAGAATGTTACCGCGCAT 58.794 50.000 8.75 0.00 0.00 4.73
563 734 1.071502 CGTAGAATGTTACCGCGCATG 60.072 52.381 8.75 0.00 0.00 4.06
564 735 2.198406 GTAGAATGTTACCGCGCATGA 58.802 47.619 8.75 0.00 0.00 3.07
565 736 1.953559 AGAATGTTACCGCGCATGAT 58.046 45.000 8.75 0.00 0.00 2.45
566 737 2.288666 AGAATGTTACCGCGCATGATT 58.711 42.857 8.75 0.00 0.00 2.57
715 2608 1.267121 AATGTAGTGTCTCCGCCACT 58.733 50.000 0.00 0.00 44.90 4.00
753 2646 5.221441 TGCATCTAGGTGTTTGATATACGCT 60.221 40.000 4.60 0.00 0.00 5.07
754 2647 6.015772 TGCATCTAGGTGTTTGATATACGCTA 60.016 38.462 4.60 0.00 0.00 4.26
755 2648 6.308282 GCATCTAGGTGTTTGATATACGCTAC 59.692 42.308 4.60 0.00 0.00 3.58
756 2649 6.947644 TCTAGGTGTTTGATATACGCTACA 57.052 37.500 0.00 0.00 0.00 2.74
757 2650 6.732154 TCTAGGTGTTTGATATACGCTACAC 58.268 40.000 0.00 0.00 36.15 2.90
773 2666 6.487103 ACGCTACACAAAGAAAGAAAGAAAG 58.513 36.000 0.00 0.00 0.00 2.62
774 2667 6.315393 ACGCTACACAAAGAAAGAAAGAAAGA 59.685 34.615 0.00 0.00 0.00 2.52
775 2668 7.148306 ACGCTACACAAAGAAAGAAAGAAAGAA 60.148 33.333 0.00 0.00 0.00 2.52
776 2669 7.696453 CGCTACACAAAGAAAGAAAGAAAGAAA 59.304 33.333 0.00 0.00 0.00 2.52
777 2670 9.014533 GCTACACAAAGAAAGAAAGAAAGAAAG 57.985 33.333 0.00 0.00 0.00 2.62
780 2673 9.981114 ACACAAAGAAAGAAAGAAAGAAAGAAA 57.019 25.926 0.00 0.00 0.00 2.52
801 2694 8.890124 AGAAAGAAAAGAACTACTCCAACTAC 57.110 34.615 0.00 0.00 0.00 2.73
822 2715 1.613925 GCAGCCGTACAGGATATCAGA 59.386 52.381 4.83 0.00 45.00 3.27
829 2722 4.476862 CGTACAGGATATCAGAATCACGG 58.523 47.826 4.83 0.00 0.00 4.94
848 2741 2.983791 GGGATCCCGGACGAAACA 59.016 61.111 17.02 0.00 0.00 2.83
930 2823 4.631740 TCCCCGGCAGACTCCACA 62.632 66.667 0.00 0.00 0.00 4.17
964 2864 1.741525 CCAACCAACCCAGCAACAG 59.258 57.895 0.00 0.00 0.00 3.16
976 2876 1.003580 CAGCAACAGGGAAGGAGCTAA 59.996 52.381 0.00 0.00 0.00 3.09
981 2881 0.744771 CAGGGAAGGAGCTAAACGGC 60.745 60.000 0.00 0.00 0.00 5.68
982 2882 1.198759 AGGGAAGGAGCTAAACGGCA 61.199 55.000 0.00 0.00 34.17 5.69
1038 2938 1.614824 CCCCAGCTCCTTGGAGACT 60.615 63.158 19.85 12.92 40.87 3.24
1141 3041 4.651008 GGTTCCGTGACGACGCCA 62.651 66.667 6.54 0.00 44.68 5.69
1167 3067 2.423898 CGGCCACCACTACCTCGAT 61.424 63.158 2.24 0.00 0.00 3.59
1233 3133 7.624549 ACATCTTCATGTACAGGTAAACATCT 58.375 34.615 7.49 0.00 41.81 2.90
1383 3284 2.545731 GCGGAGAAGAGATCCAAGAAC 58.454 52.381 0.00 0.00 36.57 3.01
1492 3393 5.185056 TCGATCGATCTATCAAATGGCCTAA 59.815 40.000 22.43 0.00 0.00 2.69
1510 3411 4.142271 GCCTAATATGCTCGATGCTACTCT 60.142 45.833 8.07 0.00 43.37 3.24
1511 3412 5.577835 CCTAATATGCTCGATGCTACTCTC 58.422 45.833 8.07 0.00 43.37 3.20
1520 3421 3.759086 TCGATGCTACTCTCCATCCATAC 59.241 47.826 0.00 0.00 35.55 2.39
1540 3441 6.828273 CCATACAAACTTCAGGATTGTGGATA 59.172 38.462 9.37 0.00 37.78 2.59
1572 3473 3.190079 GACGTGATATGAGCAGCTTGAA 58.810 45.455 0.00 0.00 0.00 2.69
1685 3587 2.030805 GCTTTCTTCCTTGTGTGCGATT 60.031 45.455 0.00 0.00 0.00 3.34
1737 3639 2.088104 ATAAGATCACCGAGGCTCCA 57.912 50.000 9.32 0.00 0.00 3.86
1760 3662 1.002624 ATGGCGATTGTGTCCGGTT 60.003 52.632 0.00 0.00 0.00 4.44
1762 3664 1.231958 TGGCGATTGTGTCCGGTTTC 61.232 55.000 0.00 0.00 0.00 2.78
1773 3675 3.980775 GTGTCCGGTTTCATGTTGAAATG 59.019 43.478 0.00 3.03 46.55 2.32
1816 3722 0.723414 GTCCGTGTCACATGCATGAG 59.277 55.000 32.75 24.74 0.00 2.90
1831 3737 3.266772 TGCATGAGGAATTTACAGGGAGT 59.733 43.478 0.00 0.00 0.00 3.85
1832 3738 3.629398 GCATGAGGAATTTACAGGGAGTG 59.371 47.826 0.00 0.00 0.00 3.51
1833 3739 4.202441 CATGAGGAATTTACAGGGAGTGG 58.798 47.826 0.00 0.00 0.00 4.00
1837 3743 2.290960 GGAATTTACAGGGAGTGGCAGT 60.291 50.000 0.00 0.00 0.00 4.40
1904 3811 5.482163 TTATTCACTCTCATGTGTCACCA 57.518 39.130 0.00 0.00 38.90 4.17
1905 3812 3.391506 TTCACTCTCATGTGTCACCAG 57.608 47.619 0.00 0.00 38.90 4.00
1983 3894 1.287425 GTTGTATACGCACAGGAGGC 58.713 55.000 0.00 0.00 0.00 4.70
1985 3896 1.299926 GTATACGCACAGGAGGCCG 60.300 63.158 0.00 0.00 0.00 6.13
1986 3897 1.755395 TATACGCACAGGAGGCCGT 60.755 57.895 0.00 0.00 0.00 5.68
1987 3898 0.466007 TATACGCACAGGAGGCCGTA 60.466 55.000 0.00 0.00 0.00 4.02
1988 3899 1.113517 ATACGCACAGGAGGCCGTAT 61.114 55.000 0.00 0.00 0.00 3.06
1989 3900 1.731433 TACGCACAGGAGGCCGTATC 61.731 60.000 0.00 0.00 0.00 2.24
1992 3999 0.601311 GCACAGGAGGCCGTATCATC 60.601 60.000 0.00 0.00 0.00 2.92
1996 4003 3.259374 CACAGGAGGCCGTATCATCTAAT 59.741 47.826 0.00 0.00 0.00 1.73
2017 4024 8.638873 TCTAATCGTATTATTCATGTCCACTGT 58.361 33.333 0.00 0.00 0.00 3.55
2019 4026 8.589335 AATCGTATTATTCATGTCCACTGTAC 57.411 34.615 0.00 0.00 0.00 2.90
2021 4028 8.454570 TCGTATTATTCATGTCCACTGTACTA 57.545 34.615 0.00 0.00 0.00 1.82
2022 4029 8.565416 TCGTATTATTCATGTCCACTGTACTAG 58.435 37.037 0.00 0.00 0.00 2.57
2063 4071 7.842525 ATCTTATTTTATTGCGATCTTTGCG 57.157 32.000 0.00 0.00 34.24 4.85
2064 4072 7.010697 TCTTATTTTATTGCGATCTTTGCGA 57.989 32.000 0.00 0.00 34.24 5.10
2078 4086 5.933187 TCTTTGCGATGTTGTTAAGCTAA 57.067 34.783 0.00 0.00 0.00 3.09
2129 4141 5.705441 TGTGGATTTTCTGCGAAAGAATACT 59.295 36.000 2.28 0.00 44.46 2.12
2130 4142 6.024049 GTGGATTTTCTGCGAAAGAATACTG 58.976 40.000 2.28 0.00 44.46 2.74
2131 4143 5.937540 TGGATTTTCTGCGAAAGAATACTGA 59.062 36.000 2.28 0.00 44.46 3.41
2132 4144 6.429692 TGGATTTTCTGCGAAAGAATACTGAA 59.570 34.615 2.28 0.00 44.46 3.02
2133 4145 7.121168 TGGATTTTCTGCGAAAGAATACTGAAT 59.879 33.333 2.28 0.06 44.46 2.57
2134 4146 8.612619 GGATTTTCTGCGAAAGAATACTGAATA 58.387 33.333 2.28 0.00 44.46 1.75
2135 4147 9.427127 GATTTTCTGCGAAAGAATACTGAATAC 57.573 33.333 2.28 0.00 44.46 1.89
2155 4167 0.999406 ATACATGTCACTTCACGCGC 59.001 50.000 5.73 0.00 0.00 6.86
2177 4189 5.938322 GCTCCACGAGTTCAATTGAAAATA 58.062 37.500 22.07 0.00 35.58 1.40
2178 4190 6.555315 GCTCCACGAGTTCAATTGAAAATAT 58.445 36.000 22.07 9.01 35.58 1.28
2179 4191 7.693952 GCTCCACGAGTTCAATTGAAAATATA 58.306 34.615 22.07 0.00 35.58 0.86
2180 4192 8.345565 GCTCCACGAGTTCAATTGAAAATATAT 58.654 33.333 22.07 4.95 35.58 0.86
2203 4215 5.759506 ACACTTCGTATCAGGATACAGAG 57.240 43.478 17.06 14.97 42.82 3.35
2204 4216 5.437946 ACACTTCGTATCAGGATACAGAGA 58.562 41.667 17.06 6.01 42.82 3.10
2205 4217 5.529430 ACACTTCGTATCAGGATACAGAGAG 59.471 44.000 17.06 13.79 42.82 3.20
2206 4218 5.529430 CACTTCGTATCAGGATACAGAGAGT 59.471 44.000 17.06 15.20 42.82 3.24
2207 4219 5.761234 ACTTCGTATCAGGATACAGAGAGTC 59.239 44.000 17.06 0.00 42.82 3.36
2208 4220 5.291905 TCGTATCAGGATACAGAGAGTCA 57.708 43.478 17.06 0.00 42.82 3.41
2209 4221 5.301555 TCGTATCAGGATACAGAGAGTCAG 58.698 45.833 17.06 1.13 42.82 3.51
2210 4222 5.070580 TCGTATCAGGATACAGAGAGTCAGA 59.929 44.000 17.06 3.11 42.82 3.27
2231 4246 8.025445 GTCAGAAGCACATAATTTCTCAACAAT 58.975 33.333 0.00 0.00 0.00 2.71
2232 4247 8.579006 TCAGAAGCACATAATTTCTCAACAATT 58.421 29.630 0.00 0.00 0.00 2.32
2233 4248 8.644619 CAGAAGCACATAATTTCTCAACAATTG 58.355 33.333 3.24 3.24 0.00 2.32
2234 4249 8.579006 AGAAGCACATAATTTCTCAACAATTGA 58.421 29.630 13.59 0.00 38.17 2.57
2252 4279 8.919777 ACAATTGAGCTAAAAAGTAAGTACCT 57.080 30.769 13.59 0.00 0.00 3.08
2264 4291 8.488651 AAAAGTAAGTACCTTATGATTGGACG 57.511 34.615 0.00 0.00 0.00 4.79
2266 4293 5.659971 AGTAAGTACCTTATGATTGGACGGT 59.340 40.000 0.00 0.00 0.00 4.83
2267 4294 5.431179 AAGTACCTTATGATTGGACGGTT 57.569 39.130 0.00 0.00 0.00 4.44
2269 4296 3.992943 ACCTTATGATTGGACGGTTCA 57.007 42.857 0.00 0.00 0.00 3.18
2272 4299 4.122776 CCTTATGATTGGACGGTTCAGAG 58.877 47.826 0.00 0.00 0.00 3.35
2273 4300 2.698855 ATGATTGGACGGTTCAGAGG 57.301 50.000 0.00 0.00 0.00 3.69
2274 4301 0.036388 TGATTGGACGGTTCAGAGGC 60.036 55.000 0.00 0.00 0.00 4.70
2275 4302 0.036388 GATTGGACGGTTCAGAGGCA 60.036 55.000 0.00 0.00 0.00 4.75
2276 4303 0.321653 ATTGGACGGTTCAGAGGCAC 60.322 55.000 0.00 0.00 0.00 5.01
2277 4304 2.432628 GGACGGTTCAGAGGCACG 60.433 66.667 0.00 0.00 0.00 5.34
2278 4305 2.649034 GACGGTTCAGAGGCACGA 59.351 61.111 0.00 0.00 0.00 4.35
2280 4307 2.805353 CGGTTCAGAGGCACGACG 60.805 66.667 0.00 0.00 0.00 5.12
2282 4309 1.006571 GGTTCAGAGGCACGACGAA 60.007 57.895 0.00 0.00 0.00 3.85
2284 4311 0.784778 GTTCAGAGGCACGACGAAAG 59.215 55.000 0.00 0.00 0.00 2.62
2285 4312 0.671796 TTCAGAGGCACGACGAAAGA 59.328 50.000 0.00 0.00 0.00 2.52
2287 4314 0.241213 CAGAGGCACGACGAAAGAGA 59.759 55.000 0.00 0.00 0.00 3.10
2288 4315 0.241481 AGAGGCACGACGAAAGAGAC 59.759 55.000 0.00 0.00 0.00 3.36
2289 4316 0.733223 GAGGCACGACGAAAGAGACC 60.733 60.000 0.00 0.00 0.00 3.85
2290 4317 2.087009 GGCACGACGAAAGAGACCG 61.087 63.158 0.00 0.00 0.00 4.79
2291 4318 2.717809 GCACGACGAAAGAGACCGC 61.718 63.158 0.00 0.00 0.00 5.68
2297 4324 1.667830 CGAAAGAGACCGCAAGCCA 60.668 57.895 0.00 0.00 0.00 4.75
2316 4343 2.993899 CCAGTGTGATTTGTACGGAGTC 59.006 50.000 0.00 0.00 43.93 3.36
2317 4344 3.554129 CCAGTGTGATTTGTACGGAGTCA 60.554 47.826 0.00 0.00 43.93 3.41
2322 4353 2.631062 TGATTTGTACGGAGTCACACCT 59.369 45.455 0.00 0.00 43.93 4.00
2328 4359 1.213013 CGGAGTCACACCTTCGGAG 59.787 63.158 0.00 0.00 29.50 4.63
2342 4373 3.826637 CGGAGTCCGTAACATTGGT 57.173 52.632 23.83 0.00 42.73 3.67
2343 4374 1.355971 CGGAGTCCGTAACATTGGTG 58.644 55.000 23.83 0.00 42.73 4.17
2344 4375 1.067425 CGGAGTCCGTAACATTGGTGA 60.067 52.381 23.83 0.00 42.73 4.02
2412 4458 2.359848 GAGTTAACAAACCGGCCAAAGT 59.640 45.455 8.61 0.00 0.00 2.66
2413 4459 2.100087 AGTTAACAAACCGGCCAAAGTG 59.900 45.455 8.61 0.00 0.00 3.16
2431 4477 3.290710 AGTGCCAAACTTCACTCACAAT 58.709 40.909 0.00 0.00 39.11 2.71
2432 4478 4.460263 AGTGCCAAACTTCACTCACAATA 58.540 39.130 0.00 0.00 39.11 1.90
2433 4479 5.072741 AGTGCCAAACTTCACTCACAATAT 58.927 37.500 0.00 0.00 39.11 1.28
2434 4480 6.237901 AGTGCCAAACTTCACTCACAATATA 58.762 36.000 0.00 0.00 39.11 0.86
2435 4481 6.149474 AGTGCCAAACTTCACTCACAATATAC 59.851 38.462 0.00 0.00 39.11 1.47
2436 4482 6.149474 GTGCCAAACTTCACTCACAATATACT 59.851 38.462 0.00 0.00 0.00 2.12
2437 4483 7.333423 GTGCCAAACTTCACTCACAATATACTA 59.667 37.037 0.00 0.00 0.00 1.82
2438 4484 7.333423 TGCCAAACTTCACTCACAATATACTAC 59.667 37.037 0.00 0.00 0.00 2.73
2439 4485 7.549488 GCCAAACTTCACTCACAATATACTACT 59.451 37.037 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.054878 CTGCCAATTTTCTCACAACAGC 58.945 45.455 0.00 0.00 0.00 4.40
26 27 4.870363 GCTAACTGCCAATTTTCTCACAA 58.130 39.130 0.00 0.00 35.15 3.33
27 28 4.503741 GCTAACTGCCAATTTTCTCACA 57.496 40.909 0.00 0.00 35.15 3.58
56 57 6.330278 GGTAAAGAAAAAGTCTTGCACTTGT 58.670 36.000 0.00 0.00 46.36 3.16
57 58 5.748630 GGGTAAAGAAAAAGTCTTGCACTTG 59.251 40.000 0.00 0.00 46.36 3.16
58 59 5.656859 AGGGTAAAGAAAAAGTCTTGCACTT 59.343 36.000 0.00 0.00 46.36 3.16
59 60 5.067805 CAGGGTAAAGAAAAAGTCTTGCACT 59.932 40.000 0.00 0.00 46.36 4.40
60 61 5.163550 ACAGGGTAAAGAAAAAGTCTTGCAC 60.164 40.000 0.00 0.00 46.36 4.57
61 62 4.953579 ACAGGGTAAAGAAAAAGTCTTGCA 59.046 37.500 0.00 0.00 46.36 4.08
62 63 5.281727 CACAGGGTAAAGAAAAAGTCTTGC 58.718 41.667 0.00 0.00 46.36 4.01
63 64 5.736207 GCCACAGGGTAAAGAAAAAGTCTTG 60.736 44.000 0.00 0.00 40.28 3.02
64 65 4.341235 GCCACAGGGTAAAGAAAAAGTCTT 59.659 41.667 0.00 0.00 41.88 3.01
65 66 3.889538 GCCACAGGGTAAAGAAAAAGTCT 59.110 43.478 0.00 0.00 35.42 3.24
66 67 3.005472 GGCCACAGGGTAAAGAAAAAGTC 59.995 47.826 0.00 0.00 36.17 3.01
67 68 2.963101 GGCCACAGGGTAAAGAAAAAGT 59.037 45.455 0.00 0.00 36.17 2.66
68 69 2.030274 CGGCCACAGGGTAAAGAAAAAG 60.030 50.000 2.24 0.00 36.17 2.27
69 70 1.957877 CGGCCACAGGGTAAAGAAAAA 59.042 47.619 2.24 0.00 36.17 1.94
70 71 1.133730 ACGGCCACAGGGTAAAGAAAA 60.134 47.619 2.24 0.00 36.17 2.29
71 72 0.475044 ACGGCCACAGGGTAAAGAAA 59.525 50.000 2.24 0.00 36.17 2.52
72 73 1.276989 CTACGGCCACAGGGTAAAGAA 59.723 52.381 2.24 0.00 36.17 2.52
73 74 0.899720 CTACGGCCACAGGGTAAAGA 59.100 55.000 2.24 0.00 36.17 2.52
74 75 0.899720 TCTACGGCCACAGGGTAAAG 59.100 55.000 2.24 0.00 36.17 1.85
75 76 1.002315 GTTCTACGGCCACAGGGTAAA 59.998 52.381 2.24 0.00 36.17 2.01
76 77 0.609662 GTTCTACGGCCACAGGGTAA 59.390 55.000 2.24 0.00 36.17 2.85
77 78 0.542467 TGTTCTACGGCCACAGGGTA 60.542 55.000 2.24 0.00 36.17 3.69
78 79 1.412453 TTGTTCTACGGCCACAGGGT 61.412 55.000 2.24 0.00 36.17 4.34
79 80 0.035439 ATTGTTCTACGGCCACAGGG 60.035 55.000 2.24 0.00 37.18 4.45
80 81 1.468520 CAATTGTTCTACGGCCACAGG 59.531 52.381 2.24 0.00 0.00 4.00
81 82 2.151202 ACAATTGTTCTACGGCCACAG 58.849 47.619 4.92 0.00 0.00 3.66
82 83 2.264005 ACAATTGTTCTACGGCCACA 57.736 45.000 4.92 0.00 0.00 4.17
114 115 9.585099 GCCTCACATTTGTATTTAATTCATGAA 57.415 29.630 11.26 11.26 0.00 2.57
115 116 8.747471 TGCCTCACATTTGTATTTAATTCATGA 58.253 29.630 0.00 0.00 0.00 3.07
116 117 8.929827 TGCCTCACATTTGTATTTAATTCATG 57.070 30.769 0.00 0.00 0.00 3.07
212 213 1.303561 GCAAGGTGGAGATGGTGCA 60.304 57.895 0.00 0.00 32.29 4.57
232 233 5.007724 CAGTCTTAATTTCGAATAGCACCCC 59.992 44.000 0.00 0.00 0.00 4.95
240 241 5.805728 ACCACCTCAGTCTTAATTTCGAAT 58.194 37.500 0.00 0.00 0.00 3.34
243 244 5.238583 AGAACCACCTCAGTCTTAATTTCG 58.761 41.667 0.00 0.00 0.00 3.46
254 258 2.561569 ACGTTCAAAGAACCACCTCAG 58.438 47.619 4.47 0.00 0.00 3.35
255 259 2.702592 ACGTTCAAAGAACCACCTCA 57.297 45.000 4.47 0.00 0.00 3.86
259 263 5.871539 TCTGTTTAACGTTCAAAGAACCAC 58.128 37.500 2.82 0.00 0.00 4.16
279 283 3.244976 GGCATCGTGGTTTGATTTTCTG 58.755 45.455 0.00 0.00 0.00 3.02
295 299 3.003689 CCATCATTTTGAGTACGGGCATC 59.996 47.826 0.00 0.00 0.00 3.91
302 307 6.599638 AGGAGCTAAACCATCATTTTGAGTAC 59.400 38.462 0.00 0.00 0.00 2.73
308 314 8.058847 TGGTATAAGGAGCTAAACCATCATTTT 58.941 33.333 0.00 0.00 32.24 1.82
333 339 5.745294 GCCACTGCTTAAACATATGTGAATG 59.255 40.000 9.63 4.42 33.53 2.67
343 349 0.887387 GGTCCGCCACTGCTTAAACA 60.887 55.000 0.00 0.00 34.43 2.83
344 350 0.887387 TGGTCCGCCACTGCTTAAAC 60.887 55.000 0.00 0.00 40.46 2.01
345 351 0.179015 TTGGTCCGCCACTGCTTAAA 60.179 50.000 0.00 0.00 46.01 1.52
346 352 0.605319 CTTGGTCCGCCACTGCTTAA 60.605 55.000 0.00 0.00 46.01 1.85
347 353 1.003839 CTTGGTCCGCCACTGCTTA 60.004 57.895 0.00 0.00 46.01 3.09
348 354 2.281761 CTTGGTCCGCCACTGCTT 60.282 61.111 0.00 0.00 46.01 3.91
349 355 2.337879 TTTCTTGGTCCGCCACTGCT 62.338 55.000 0.00 0.00 46.01 4.24
350 356 1.244019 ATTTCTTGGTCCGCCACTGC 61.244 55.000 0.00 0.00 46.01 4.40
351 357 2.107950 TATTTCTTGGTCCGCCACTG 57.892 50.000 0.00 0.00 46.01 3.66
352 358 2.871096 TTATTTCTTGGTCCGCCACT 57.129 45.000 0.00 0.00 46.01 4.00
353 359 3.926821 TTTTATTTCTTGGTCCGCCAC 57.073 42.857 0.00 0.00 46.01 5.01
354 360 3.367910 GCATTTTATTTCTTGGTCCGCCA 60.368 43.478 0.00 0.00 44.38 5.69
355 361 3.186909 GCATTTTATTTCTTGGTCCGCC 58.813 45.455 0.00 0.00 0.00 6.13
356 362 3.843999 TGCATTTTATTTCTTGGTCCGC 58.156 40.909 0.00 0.00 0.00 5.54
357 363 4.423732 CCTGCATTTTATTTCTTGGTCCG 58.576 43.478 0.00 0.00 0.00 4.79
358 364 4.222810 ACCCTGCATTTTATTTCTTGGTCC 59.777 41.667 0.00 0.00 0.00 4.46
359 365 5.170748 CACCCTGCATTTTATTTCTTGGTC 58.829 41.667 0.00 0.00 0.00 4.02
360 366 4.592778 ACACCCTGCATTTTATTTCTTGGT 59.407 37.500 0.00 0.00 0.00 3.67
361 367 4.931002 CACACCCTGCATTTTATTTCTTGG 59.069 41.667 0.00 0.00 0.00 3.61
362 368 4.389687 GCACACCCTGCATTTTATTTCTTG 59.610 41.667 0.00 0.00 46.29 3.02
363 369 4.568956 GCACACCCTGCATTTTATTTCTT 58.431 39.130 0.00 0.00 46.29 2.52
364 370 4.192429 GCACACCCTGCATTTTATTTCT 57.808 40.909 0.00 0.00 46.29 2.52
401 407 9.550406 CCATTCAAGCCAATGAAAATATACATT 57.450 29.630 1.86 0.00 42.22 2.71
402 408 8.152246 CCCATTCAAGCCAATGAAAATATACAT 58.848 33.333 1.86 0.00 42.22 2.29
403 409 7.499292 CCCATTCAAGCCAATGAAAATATACA 58.501 34.615 1.86 0.00 42.22 2.29
404 410 6.424812 GCCCATTCAAGCCAATGAAAATATAC 59.575 38.462 1.86 0.00 42.22 1.47
405 411 6.523840 GCCCATTCAAGCCAATGAAAATATA 58.476 36.000 1.86 0.00 42.22 0.86
406 412 5.370679 GCCCATTCAAGCCAATGAAAATAT 58.629 37.500 1.86 0.00 42.22 1.28
407 413 4.768583 GCCCATTCAAGCCAATGAAAATA 58.231 39.130 1.86 0.00 42.22 1.40
408 414 3.613030 GCCCATTCAAGCCAATGAAAAT 58.387 40.909 1.86 0.00 42.22 1.82
409 415 3.056588 GCCCATTCAAGCCAATGAAAA 57.943 42.857 1.86 0.00 42.22 2.29
410 416 2.766345 GCCCATTCAAGCCAATGAAA 57.234 45.000 1.86 0.00 42.22 2.69
418 424 4.831107 TGATTTTTAAGGCCCATTCAAGC 58.169 39.130 0.00 0.00 0.00 4.01
419 425 6.466812 AGTTGATTTTTAAGGCCCATTCAAG 58.533 36.000 0.00 0.00 0.00 3.02
420 426 6.432403 AGTTGATTTTTAAGGCCCATTCAA 57.568 33.333 0.00 0.00 0.00 2.69
421 427 7.546250 TTAGTTGATTTTTAAGGCCCATTCA 57.454 32.000 0.00 0.00 0.00 2.57
454 460 9.898152 AGAATTTTGGAAAATGTTCTTTTACCA 57.102 25.926 0.00 0.00 38.53 3.25
457 463 9.336171 CCCAGAATTTTGGAAAATGTTCTTTTA 57.664 29.630 16.44 0.00 40.87 1.52
458 464 7.833682 ACCCAGAATTTTGGAAAATGTTCTTTT 59.166 29.630 16.44 0.00 40.87 2.27
459 465 7.282901 CACCCAGAATTTTGGAAAATGTTCTTT 59.717 33.333 16.44 0.00 40.87 2.52
460 466 6.767423 CACCCAGAATTTTGGAAAATGTTCTT 59.233 34.615 16.44 0.00 40.87 2.52
461 467 6.126796 ACACCCAGAATTTTGGAAAATGTTCT 60.127 34.615 16.44 0.00 40.87 3.01
462 468 6.018016 CACACCCAGAATTTTGGAAAATGTTC 60.018 38.462 16.44 0.00 40.87 3.18
463 469 5.821995 CACACCCAGAATTTTGGAAAATGTT 59.178 36.000 16.44 0.00 40.87 2.71
464 470 5.367302 CACACCCAGAATTTTGGAAAATGT 58.633 37.500 16.44 11.27 40.87 2.71
465 471 4.213906 GCACACCCAGAATTTTGGAAAATG 59.786 41.667 16.44 10.72 40.87 2.32
466 472 4.388485 GCACACCCAGAATTTTGGAAAAT 58.612 39.130 16.44 0.00 40.87 1.82
467 473 3.432890 GGCACACCCAGAATTTTGGAAAA 60.433 43.478 16.44 0.00 40.87 2.29
468 474 2.103941 GGCACACCCAGAATTTTGGAAA 59.896 45.455 16.44 0.00 40.87 3.13
469 475 1.691434 GGCACACCCAGAATTTTGGAA 59.309 47.619 16.44 0.00 40.87 3.53
470 476 1.337118 GGCACACCCAGAATTTTGGA 58.663 50.000 16.44 0.00 40.87 3.53
471 477 1.047002 TGGCACACCCAGAATTTTGG 58.953 50.000 8.06 8.06 39.18 3.28
490 496 2.277591 GGTGTGCCATGTGTGCCAT 61.278 57.895 0.00 0.00 34.09 4.40
491 497 2.911509 GGTGTGCCATGTGTGCCA 60.912 61.111 0.00 0.00 34.09 4.92
492 498 3.683937 GGGTGTGCCATGTGTGCC 61.684 66.667 0.00 0.00 36.17 5.01
493 499 3.683937 GGGGTGTGCCATGTGTGC 61.684 66.667 0.00 0.00 36.17 4.57
494 500 2.135903 TAGGGGGTGTGCCATGTGTG 62.136 60.000 0.00 0.00 36.17 3.82
495 501 1.850289 TAGGGGGTGTGCCATGTGT 60.850 57.895 0.00 0.00 36.17 3.72
496 502 1.077501 CTAGGGGGTGTGCCATGTG 60.078 63.158 0.00 0.00 36.17 3.21
497 503 0.624500 ATCTAGGGGGTGTGCCATGT 60.625 55.000 0.00 0.00 36.17 3.21
498 504 1.434188 TATCTAGGGGGTGTGCCATG 58.566 55.000 0.00 0.00 36.17 3.66
499 505 1.988107 CATATCTAGGGGGTGTGCCAT 59.012 52.381 0.00 0.00 36.17 4.40
500 506 1.434188 CATATCTAGGGGGTGTGCCA 58.566 55.000 0.00 0.00 36.17 4.92
501 507 0.036875 GCATATCTAGGGGGTGTGCC 59.963 60.000 0.00 0.00 0.00 5.01
502 508 0.036875 GGCATATCTAGGGGGTGTGC 59.963 60.000 0.00 0.00 0.00 4.57
503 509 1.072331 GTGGCATATCTAGGGGGTGTG 59.928 57.143 0.00 0.00 0.00 3.82
504 510 1.061346 AGTGGCATATCTAGGGGGTGT 60.061 52.381 0.00 0.00 0.00 4.16
505 511 1.349026 CAGTGGCATATCTAGGGGGTG 59.651 57.143 0.00 0.00 0.00 4.61
506 512 1.061346 ACAGTGGCATATCTAGGGGGT 60.061 52.381 0.00 0.00 0.00 4.95
507 513 1.349026 CACAGTGGCATATCTAGGGGG 59.651 57.143 0.00 0.00 0.00 5.40
508 514 2.050144 ACACAGTGGCATATCTAGGGG 58.950 52.381 5.31 0.00 0.00 4.79
509 515 3.845781 AACACAGTGGCATATCTAGGG 57.154 47.619 5.31 0.00 0.00 3.53
510 516 6.582636 TCTTAAACACAGTGGCATATCTAGG 58.417 40.000 5.31 0.00 0.00 3.02
511 517 8.492673 TTTCTTAAACACAGTGGCATATCTAG 57.507 34.615 5.31 0.00 0.00 2.43
512 518 7.552687 CCTTTCTTAAACACAGTGGCATATCTA 59.447 37.037 5.31 0.00 0.00 1.98
513 519 6.375455 CCTTTCTTAAACACAGTGGCATATCT 59.625 38.462 5.31 0.00 0.00 1.98
514 520 6.555315 CCTTTCTTAAACACAGTGGCATATC 58.445 40.000 5.31 0.00 0.00 1.63
515 521 5.105756 GCCTTTCTTAAACACAGTGGCATAT 60.106 40.000 5.31 0.00 37.91 1.78
516 522 4.217550 GCCTTTCTTAAACACAGTGGCATA 59.782 41.667 5.31 0.00 37.91 3.14
517 523 3.005791 GCCTTTCTTAAACACAGTGGCAT 59.994 43.478 5.31 0.00 37.91 4.40
518 524 2.360801 GCCTTTCTTAAACACAGTGGCA 59.639 45.455 5.31 0.00 37.91 4.92
519 525 2.360801 TGCCTTTCTTAAACACAGTGGC 59.639 45.455 5.31 0.00 38.42 5.01
520 526 4.853924 ATGCCTTTCTTAAACACAGTGG 57.146 40.909 5.31 0.00 0.00 4.00
521 527 5.049680 ACGTATGCCTTTCTTAAACACAGTG 60.050 40.000 0.00 0.00 0.00 3.66
522 528 5.061179 ACGTATGCCTTTCTTAAACACAGT 58.939 37.500 0.00 0.00 0.00 3.55
523 529 5.607119 ACGTATGCCTTTCTTAAACACAG 57.393 39.130 0.00 0.00 0.00 3.66
524 530 6.457355 TCTACGTATGCCTTTCTTAAACACA 58.543 36.000 0.00 0.00 0.00 3.72
525 531 6.956299 TCTACGTATGCCTTTCTTAAACAC 57.044 37.500 0.00 0.00 0.00 3.32
544 550 2.198406 TCATGCGCGGTAACATTCTAC 58.802 47.619 8.83 0.00 0.00 2.59
715 2608 0.031585 GATGCACGTACGCCTATCCA 59.968 55.000 16.72 3.97 0.00 3.41
754 2647 9.981114 TTTCTTTCTTTCTTTCTTTCTTTGTGT 57.019 25.926 0.00 0.00 0.00 3.72
773 2666 8.894731 AGTTGGAGTAGTTCTTTTCTTTCTTTC 58.105 33.333 0.00 0.00 0.00 2.62
774 2667 8.809468 AGTTGGAGTAGTTCTTTTCTTTCTTT 57.191 30.769 0.00 0.00 0.00 2.52
775 2668 9.327628 GTAGTTGGAGTAGTTCTTTTCTTTCTT 57.672 33.333 0.00 0.00 0.00 2.52
776 2669 7.652507 CGTAGTTGGAGTAGTTCTTTTCTTTCT 59.347 37.037 0.00 0.00 0.00 2.52
777 2670 7.569043 GCGTAGTTGGAGTAGTTCTTTTCTTTC 60.569 40.741 0.00 0.00 0.00 2.62
778 2671 6.202379 GCGTAGTTGGAGTAGTTCTTTTCTTT 59.798 38.462 0.00 0.00 0.00 2.52
779 2672 5.695363 GCGTAGTTGGAGTAGTTCTTTTCTT 59.305 40.000 0.00 0.00 0.00 2.52
780 2673 5.221382 TGCGTAGTTGGAGTAGTTCTTTTCT 60.221 40.000 0.00 0.00 0.00 2.52
781 2674 4.986659 TGCGTAGTTGGAGTAGTTCTTTTC 59.013 41.667 0.00 0.00 0.00 2.29
801 2694 0.313987 TGATATCCTGTACGGCTGCG 59.686 55.000 0.00 0.00 0.00 5.18
817 2710 0.034059 GATCCCGCCGTGATTCTGAT 59.966 55.000 0.00 0.00 0.00 2.90
840 2733 2.249844 TTTGGACCCTCTGTTTCGTC 57.750 50.000 0.00 0.00 0.00 4.20
848 2741 1.954382 GCTTTTCGTTTTGGACCCTCT 59.046 47.619 0.00 0.00 0.00 3.69
919 2812 0.036858 GAGGAGGTTGTGGAGTCTGC 60.037 60.000 0.00 0.00 0.00 4.26
922 2815 1.276705 GAAGGAGGAGGTTGTGGAGTC 59.723 57.143 0.00 0.00 0.00 3.36
930 2823 0.196118 TTGGGAGGAAGGAGGAGGTT 59.804 55.000 0.00 0.00 0.00 3.50
964 2864 0.322187 TTGCCGTTTAGCTCCTTCCC 60.322 55.000 0.00 0.00 0.00 3.97
968 2868 0.109723 TTGGTTGCCGTTTAGCTCCT 59.890 50.000 0.00 0.00 0.00 3.69
981 2881 0.821711 TTTCCTGGCTCGGTTGGTTG 60.822 55.000 0.00 0.00 0.00 3.77
982 2882 0.112412 ATTTCCTGGCTCGGTTGGTT 59.888 50.000 0.00 0.00 0.00 3.67
1038 2938 3.138283 ACCCTCTGTGGACAATTTCAGAA 59.862 43.478 0.00 0.00 36.67 3.02
1192 3092 1.734465 GATGTCCTTGTTTCCAGCGAG 59.266 52.381 0.00 0.00 0.00 5.03
1510 3411 5.715439 ATCCTGAAGTTTGTATGGATGGA 57.285 39.130 0.00 0.00 33.59 3.41
1511 3412 5.653769 ACAATCCTGAAGTTTGTATGGATGG 59.346 40.000 0.00 0.00 34.89 3.51
1520 3421 7.365741 GCATATATCCACAATCCTGAAGTTTG 58.634 38.462 0.00 0.00 0.00 2.93
1540 3441 1.241165 TATCACGTCGGTCCGCATAT 58.759 50.000 6.34 0.00 0.00 1.78
1572 3473 7.205515 CCAATAGGGAATATAATCAGCTCCT 57.794 40.000 0.00 0.00 40.01 3.69
1597 3498 5.003804 TCTTTTGCCTCCAAGAACTGTATC 58.996 41.667 0.00 0.00 31.52 2.24
1737 3639 1.392589 GGACACAATCGCCATGGATT 58.607 50.000 18.40 4.10 37.11 3.01
1785 3690 4.023450 TGTGACACGGACTAGTAAGTGAAG 60.023 45.833 27.06 9.64 35.56 3.02
1816 3722 2.290960 ACTGCCACTCCCTGTAAATTCC 60.291 50.000 0.00 0.00 0.00 3.01
1831 3737 1.601903 CTACTCGTTGCAAAACTGCCA 59.398 47.619 0.00 0.00 0.00 4.92
1832 3738 1.663161 GCTACTCGTTGCAAAACTGCC 60.663 52.381 0.00 0.00 0.00 4.85
1833 3739 1.264288 AGCTACTCGTTGCAAAACTGC 59.736 47.619 0.00 1.41 33.84 4.40
1837 3743 2.803956 GGTACAGCTACTCGTTGCAAAA 59.196 45.455 0.00 0.00 33.84 2.44
1888 3795 1.620819 GACCTGGTGACACATGAGAGT 59.379 52.381 2.82 0.00 35.60 3.24
1935 3846 0.882927 TTTCGGCCTGTTCGTTGAGG 60.883 55.000 0.00 0.00 0.00 3.86
1947 3858 0.953960 AACGACCATGAGTTTCGGCC 60.954 55.000 0.00 0.00 37.07 6.13
1988 3899 9.639601 GTGGACATGAATAATACGATTAGATGA 57.360 33.333 0.00 0.00 0.00 2.92
1989 3900 9.645059 AGTGGACATGAATAATACGATTAGATG 57.355 33.333 0.00 0.00 0.00 2.90
1992 3999 8.818141 ACAGTGGACATGAATAATACGATTAG 57.182 34.615 0.00 0.00 0.00 1.73
1996 4003 7.342769 AGTACAGTGGACATGAATAATACGA 57.657 36.000 8.55 0.00 0.00 3.43
2037 4044 9.546909 CGCAAAGATCGCAATAAAATAAGATAT 57.453 29.630 0.00 0.00 0.00 1.63
2040 4047 7.010697 TCGCAAAGATCGCAATAAAATAAGA 57.989 32.000 0.00 0.00 0.00 2.10
2041 4048 7.376866 ACATCGCAAAGATCGCAATAAAATAAG 59.623 33.333 0.00 0.00 37.52 1.73
2049 4056 2.162208 ACAACATCGCAAAGATCGCAAT 59.838 40.909 0.00 0.00 37.52 3.56
2058 4066 5.425577 TGTTAGCTTAACAACATCGCAAA 57.574 34.783 0.00 0.00 44.95 3.68
2063 4071 5.220681 GCTAGGCTGTTAGCTTAACAACATC 60.221 44.000 0.00 0.00 46.90 3.06
2064 4072 4.636206 GCTAGGCTGTTAGCTTAACAACAT 59.364 41.667 0.00 0.00 46.90 2.71
2085 4093 5.233083 ACATATATGTGTGTATGCCAGCT 57.767 39.130 17.60 0.00 40.03 4.24
2108 4120 6.422776 TCAGTATTCTTTCGCAGAAAATCC 57.577 37.500 1.52 0.00 45.06 3.01
2129 4141 5.290885 GCGTGAAGTGACATGTATGTATTCA 59.709 40.000 0.00 12.18 41.95 2.57
2130 4142 5.554510 CGCGTGAAGTGACATGTATGTATTC 60.555 44.000 0.00 0.23 41.95 1.75
2131 4143 4.267690 CGCGTGAAGTGACATGTATGTATT 59.732 41.667 0.00 0.00 41.95 1.89
2132 4144 3.796717 CGCGTGAAGTGACATGTATGTAT 59.203 43.478 0.00 0.00 41.95 2.29
2133 4145 3.175929 CGCGTGAAGTGACATGTATGTA 58.824 45.455 0.00 0.00 41.95 2.29
2134 4146 1.992667 CGCGTGAAGTGACATGTATGT 59.007 47.619 0.00 0.00 45.16 2.29
2135 4147 1.267038 GCGCGTGAAGTGACATGTATG 60.267 52.381 8.43 0.00 0.00 2.39
2177 4189 9.168451 CTCTGTATCCTGATACGAAGTGTATAT 57.832 37.037 11.55 0.00 43.87 0.86
2178 4190 8.373220 TCTCTGTATCCTGATACGAAGTGTATA 58.627 37.037 11.55 0.00 43.87 1.47
2179 4191 7.225011 TCTCTGTATCCTGATACGAAGTGTAT 58.775 38.462 11.55 0.00 46.51 2.29
2180 4192 6.589135 TCTCTGTATCCTGATACGAAGTGTA 58.411 40.000 11.55 0.00 45.73 2.90
2181 4193 5.437946 TCTCTGTATCCTGATACGAAGTGT 58.562 41.667 11.55 0.00 45.73 3.55
2182 4194 5.529430 ACTCTCTGTATCCTGATACGAAGTG 59.471 44.000 11.55 12.72 45.73 3.16
2203 4215 6.974932 TGAGAAATTATGTGCTTCTGACTC 57.025 37.500 0.00 0.00 29.59 3.36
2204 4216 6.712095 TGTTGAGAAATTATGTGCTTCTGACT 59.288 34.615 0.00 0.00 29.59 3.41
2205 4217 6.902341 TGTTGAGAAATTATGTGCTTCTGAC 58.098 36.000 0.00 0.00 29.59 3.51
2206 4218 7.509141 TTGTTGAGAAATTATGTGCTTCTGA 57.491 32.000 0.00 0.00 29.59 3.27
2207 4219 8.644619 CAATTGTTGAGAAATTATGTGCTTCTG 58.355 33.333 0.00 0.00 29.59 3.02
2208 4220 8.579006 TCAATTGTTGAGAAATTATGTGCTTCT 58.421 29.630 5.13 0.00 34.08 2.85
2209 4221 8.746922 TCAATTGTTGAGAAATTATGTGCTTC 57.253 30.769 5.13 0.00 34.08 3.86
2252 4279 3.681594 GCCTCTGAACCGTCCAATCATAA 60.682 47.826 0.00 0.00 0.00 1.90
2254 4281 1.407437 GCCTCTGAACCGTCCAATCAT 60.407 52.381 0.00 0.00 0.00 2.45
2264 4291 0.599204 TTTCGTCGTGCCTCTGAACC 60.599 55.000 0.00 0.00 0.00 3.62
2266 4293 0.671796 TCTTTCGTCGTGCCTCTGAA 59.328 50.000 0.00 0.00 0.00 3.02
2267 4294 0.241213 CTCTTTCGTCGTGCCTCTGA 59.759 55.000 0.00 0.00 0.00 3.27
2269 4296 0.241481 GTCTCTTTCGTCGTGCCTCT 59.759 55.000 0.00 0.00 0.00 3.69
2272 4299 2.087009 CGGTCTCTTTCGTCGTGCC 61.087 63.158 0.00 0.00 0.00 5.01
2273 4300 2.717809 GCGGTCTCTTTCGTCGTGC 61.718 63.158 0.00 0.00 0.00 5.34
2274 4301 0.937699 TTGCGGTCTCTTTCGTCGTG 60.938 55.000 0.00 0.00 0.00 4.35
2275 4302 0.663568 CTTGCGGTCTCTTTCGTCGT 60.664 55.000 0.00 0.00 0.00 4.34
2276 4303 1.945776 GCTTGCGGTCTCTTTCGTCG 61.946 60.000 0.00 0.00 0.00 5.12
2277 4304 1.627550 GGCTTGCGGTCTCTTTCGTC 61.628 60.000 0.00 0.00 0.00 4.20
2278 4305 1.668151 GGCTTGCGGTCTCTTTCGT 60.668 57.895 0.00 0.00 0.00 3.85
2280 4307 0.603975 ACTGGCTTGCGGTCTCTTTC 60.604 55.000 0.00 0.00 0.00 2.62
2282 4309 1.302033 CACTGGCTTGCGGTCTCTT 60.302 57.895 0.00 0.00 0.00 2.85
2284 4311 2.031163 ACACTGGCTTGCGGTCTC 59.969 61.111 0.00 0.00 0.00 3.36
2285 4312 2.116983 ATCACACTGGCTTGCGGTCT 62.117 55.000 0.00 0.00 0.00 3.85
2287 4314 0.823356 AAATCACACTGGCTTGCGGT 60.823 50.000 0.00 0.00 0.00 5.68
2288 4315 0.387622 CAAATCACACTGGCTTGCGG 60.388 55.000 0.00 0.00 0.00 5.69
2289 4316 0.311790 ACAAATCACACTGGCTTGCG 59.688 50.000 0.00 0.00 0.00 4.85
2290 4317 2.665519 CGTACAAATCACACTGGCTTGC 60.666 50.000 0.00 0.00 0.00 4.01
2291 4318 2.095768 CCGTACAAATCACACTGGCTTG 60.096 50.000 0.00 0.00 0.00 4.01
2297 4324 3.069016 TGTGACTCCGTACAAATCACACT 59.931 43.478 12.64 0.00 43.48 3.55
2328 4359 4.151157 GTGTAGTTCACCAATGTTACGGAC 59.849 45.833 0.00 0.00 40.84 4.79
2341 4372 1.125566 GCGCGGTAAAGTGTAGTTCAC 59.874 52.381 8.83 0.00 46.46 3.18
2342 4373 1.421382 GCGCGGTAAAGTGTAGTTCA 58.579 50.000 8.83 0.00 0.00 3.18
2343 4374 0.717784 GGCGCGGTAAAGTGTAGTTC 59.282 55.000 8.83 0.00 0.00 3.01
2344 4375 0.033781 TGGCGCGGTAAAGTGTAGTT 59.966 50.000 8.83 0.00 0.00 2.24
2357 4388 0.039437 ATAAGTACTCCGATGGCGCG 60.039 55.000 0.00 0.00 35.83 6.86
2412 4458 6.237901 AGTATATTGTGAGTGAAGTTTGGCA 58.762 36.000 0.00 0.00 0.00 4.92
2413 4459 6.743575 AGTATATTGTGAGTGAAGTTTGGC 57.256 37.500 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.