Multiple sequence alignment - TraesCS1D01G167800

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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 TraesCS1D01G167800 chr1D 100.000 3894 0 0 396 4289 239801828 239805721 0.000000e+00 7191.0
1 TraesCS1D01G167800 chr1D 100.000 52 0 0 1 52 239801433 239801484 3.530000e-16 97.1
2 TraesCS1D01G167800 chr1D 97.561 41 1 0 2768 2808 239804156 239804196 2.140000e-08 71.3
3 TraesCS1D01G167800 chr1D 97.561 41 1 0 2724 2764 239804200 239804240 2.140000e-08 71.3
4 TraesCS1D01G167800 chr1A 94.849 1262 49 10 649 1896 303849257 303850516 0.000000e+00 1956.0
5 TraesCS1D01G167800 chr1A 97.638 889 19 2 2722 3610 303851471 303852357 0.000000e+00 1524.0
6 TraesCS1D01G167800 chr1A 95.689 835 18 7 1894 2722 303850582 303851404 0.000000e+00 1327.0
7 TraesCS1D01G167800 chr1A 91.052 637 31 12 3674 4285 303852461 303853096 0.000000e+00 837.0
8 TraesCS1D01G167800 chr1A 89.855 138 10 2 527 660 303849102 303849239 1.590000e-39 174.0
9 TraesCS1D01G167800 chr1A 89.630 135 13 1 397 530 303815148 303815282 2.050000e-38 171.0
10 TraesCS1D01G167800 chr1A 94.340 53 1 1 2758 2808 303851461 303851513 3.560000e-11 80.5
11 TraesCS1D01G167800 chr1A 97.674 43 1 0 2722 2764 303851515 303851557 1.650000e-09 75.0
12 TraesCS1D01G167800 chr1B 90.331 724 51 11 759 1472 334237584 334238298 0.000000e+00 931.0
13 TraesCS1D01G167800 chr1B 94.934 454 23 0 2270 2723 334239628 334240081 0.000000e+00 712.0
14 TraesCS1D01G167800 chr1B 97.094 413 12 0 2828 3240 334240242 334240654 0.000000e+00 697.0
15 TraesCS1D01G167800 chr1B 94.091 220 8 2 4010 4228 334241154 334241369 3.200000e-86 329.0
16 TraesCS1D01G167800 chr1B 91.549 213 6 2 3324 3536 334240687 334240887 2.520000e-72 283.0
17 TraesCS1D01G167800 chr1B 93.122 189 12 1 1588 1775 334238939 334239127 4.220000e-70 276.0
18 TraesCS1D01G167800 chr1B 92.814 167 8 4 528 691 334237405 334237570 5.540000e-59 239.0
19 TraesCS1D01G167800 chr1B 93.443 122 6 2 3780 3899 334241023 334241144 3.410000e-41 180.0
20 TraesCS1D01G167800 chr1B 92.857 70 4 1 1535 1604 334238613 334238681 2.730000e-17 100.0
21 TraesCS1D01G167800 chr4D 87.456 287 35 1 4001 4286 46621871 46622157 3.200000e-86 329.0
22 TraesCS1D01G167800 chr4B 87.153 288 36 1 4001 4287 68119090 68119377 4.140000e-85 326.0
23 TraesCS1D01G167800 chr4A 87.108 287 36 1 4001 4286 533461318 533461604 1.490000e-84 324.0
24 TraesCS1D01G167800 chr4A 86.411 287 38 1 4001 4286 552256657 552256371 3.220000e-81 313.0
25 TraesCS1D01G167800 chr4A 97.059 34 1 0 3626 3659 724801712 724801679 1.670000e-04 58.4
26 TraesCS1D01G167800 chr2B 97.297 37 1 0 3626 3662 637770473 637770509 3.580000e-06 63.9
27 TraesCS1D01G167800 chr2B 94.444 36 1 1 3627 3662 704720953 704720919 2.000000e-03 54.7
28 TraesCS1D01G167800 chr6D 97.059 34 1 0 3626 3659 456321043 456321010 1.670000e-04 58.4
29 TraesCS1D01G167800 chr5B 97.059 34 1 0 3626 3659 403701187 403701220 1.670000e-04 58.4
30 TraesCS1D01G167800 chr5D 96.970 33 1 0 3627 3659 317879844 317879812 5.990000e-04 56.5
31 TraesCS1D01G167800 chr5D 90.698 43 3 1 3627 3669 497301302 497301343 5.990000e-04 56.5
32 TraesCS1D01G167800 chr5D 96.970 33 1 0 3627 3659 547431573 547431541 5.990000e-04 56.5
33 TraesCS1D01G167800 chr3A 94.444 36 1 1 3627 3662 214839898 214839864 2.000000e-03 54.7


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 TraesCS1D01G167800 chr1D 239801433 239805721 4288 False 1857.675000 7191 98.780500 1 4289 4 chr1D.!!$F1 4288
1 TraesCS1D01G167800 chr1A 303849102 303853096 3994 False 853.357143 1956 94.442429 527 4285 7 chr1A.!!$F2 3758
2 TraesCS1D01G167800 chr1B 334237405 334241369 3964 False 416.333333 931 93.359444 528 4228 9 chr1B.!!$F1 3700

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
43 44 0.027979 CAACGCTGGAGTTGTGTGTG 59.972 55.0 8.62 0.0 44.58 3.82 F
484 485 0.039074 CGACCGATCTGGCATCTACC 60.039 60.0 3.85 0.0 43.94 3.18 F
713 747 0.040425 CGGTTGCACCACTGCTAAAC 60.040 55.0 6.21 0.0 44.57 2.01 F
1521 1590 0.106469 GCTCCCATTTCTTCTCCCCC 60.106 60.0 0.00 0.0 0.00 5.40 F
2766 3702 0.249489 ACAGCAGGTGTCTGAACGTC 60.249 55.0 0.00 0.0 43.49 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 2482 0.249699 TCACGCGGTTCTGACAACAT 60.250 50.000 12.47 0.00 0.00 2.71 R
2478 3271 1.283029 ACCTGTGCATCATAAGCTGGT 59.717 47.619 0.00 0.00 0.00 4.00 R
2766 3702 8.479313 TTGTACTCTACAAGCATGATGTTTAG 57.521 34.615 9.48 9.61 43.23 1.85 R
3233 4169 1.061546 ACCCACAAGTCATAACCGGT 58.938 50.000 0.00 0.00 0.00 5.28 R
3609 4545 0.246635 CAATCGTGAACGGAGGGAGT 59.753 55.000 2.59 0.00 40.29 3.85 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
17 18 4.942900 ATGGTGGGAAGCTAGGGT 57.057 55.556 0.00 0.00 0.00 4.34
18 19 2.311287 ATGGTGGGAAGCTAGGGTG 58.689 57.895 0.00 0.00 0.00 4.61
19 20 1.926426 ATGGTGGGAAGCTAGGGTGC 61.926 60.000 0.00 0.00 0.00 5.01
20 21 2.125106 GTGGGAAGCTAGGGTGCG 60.125 66.667 0.00 0.00 38.13 5.34
21 22 4.096003 TGGGAAGCTAGGGTGCGC 62.096 66.667 0.00 0.00 38.13 6.09
22 23 3.787001 GGGAAGCTAGGGTGCGCT 61.787 66.667 9.73 0.00 38.30 5.92
23 24 2.432300 GGGAAGCTAGGGTGCGCTA 61.432 63.158 9.73 0.00 34.96 4.26
24 25 1.227292 GGAAGCTAGGGTGCGCTAC 60.227 63.158 9.73 5.08 34.96 3.58
25 26 1.515954 GAAGCTAGGGTGCGCTACA 59.484 57.895 9.73 0.00 34.96 2.74
26 27 0.108329 GAAGCTAGGGTGCGCTACAA 60.108 55.000 9.73 0.00 34.96 2.41
27 28 0.391263 AAGCTAGGGTGCGCTACAAC 60.391 55.000 9.73 0.00 34.96 3.32
28 29 2.165301 GCTAGGGTGCGCTACAACG 61.165 63.158 9.73 0.00 36.55 4.10
36 37 4.261888 CGCTACAACGCTGGAGTT 57.738 55.556 0.00 0.00 35.69 3.01
42 43 2.393557 CAACGCTGGAGTTGTGTGT 58.606 52.632 8.62 0.00 44.58 3.72
43 44 0.027979 CAACGCTGGAGTTGTGTGTG 59.972 55.000 8.62 0.00 44.58 3.82
44 45 0.392461 AACGCTGGAGTTGTGTGTGT 60.392 50.000 0.00 0.00 32.39 3.72
45 46 1.089481 ACGCTGGAGTTGTGTGTGTG 61.089 55.000 0.00 0.00 0.00 3.82
46 47 1.089481 CGCTGGAGTTGTGTGTGTGT 61.089 55.000 0.00 0.00 0.00 3.72
47 48 0.378257 GCTGGAGTTGTGTGTGTGTG 59.622 55.000 0.00 0.00 0.00 3.82
48 49 1.737838 CTGGAGTTGTGTGTGTGTGT 58.262 50.000 0.00 0.00 0.00 3.72
49 50 1.398041 CTGGAGTTGTGTGTGTGTGTG 59.602 52.381 0.00 0.00 0.00 3.82
50 51 0.732571 GGAGTTGTGTGTGTGTGTGG 59.267 55.000 0.00 0.00 0.00 4.17
51 52 0.732571 GAGTTGTGTGTGTGTGTGGG 59.267 55.000 0.00 0.00 0.00 4.61
413 414 3.365536 AGCGTGAGGAAGGAGAAGA 57.634 52.632 0.00 0.00 0.00 2.87
414 415 1.633774 AGCGTGAGGAAGGAGAAGAA 58.366 50.000 0.00 0.00 0.00 2.52
415 416 2.183679 AGCGTGAGGAAGGAGAAGAAT 58.816 47.619 0.00 0.00 0.00 2.40
416 417 2.167487 AGCGTGAGGAAGGAGAAGAATC 59.833 50.000 0.00 0.00 0.00 2.52
417 418 2.803451 CGTGAGGAAGGAGAAGAATCG 58.197 52.381 0.00 0.00 0.00 3.34
418 419 2.480416 CGTGAGGAAGGAGAAGAATCGG 60.480 54.545 0.00 0.00 0.00 4.18
419 420 2.761208 GTGAGGAAGGAGAAGAATCGGA 59.239 50.000 0.00 0.00 0.00 4.55
420 421 3.027412 TGAGGAAGGAGAAGAATCGGAG 58.973 50.000 0.00 0.00 0.00 4.63
421 422 2.364002 GAGGAAGGAGAAGAATCGGAGG 59.636 54.545 0.00 0.00 0.00 4.30
422 423 1.202592 GGAAGGAGAAGAATCGGAGGC 60.203 57.143 0.00 0.00 0.00 4.70
423 424 1.482593 GAAGGAGAAGAATCGGAGGCA 59.517 52.381 0.00 0.00 0.00 4.75
424 425 1.573108 AGGAGAAGAATCGGAGGCAA 58.427 50.000 0.00 0.00 0.00 4.52
425 426 2.122768 AGGAGAAGAATCGGAGGCAAT 58.877 47.619 0.00 0.00 0.00 3.56
426 427 2.103941 AGGAGAAGAATCGGAGGCAATC 59.896 50.000 0.00 0.00 0.00 2.67
427 428 2.103941 GGAGAAGAATCGGAGGCAATCT 59.896 50.000 0.00 0.00 0.00 2.40
428 429 3.322254 GGAGAAGAATCGGAGGCAATCTA 59.678 47.826 0.00 0.00 0.00 1.98
429 430 4.202264 GGAGAAGAATCGGAGGCAATCTAA 60.202 45.833 0.00 0.00 0.00 2.10
430 431 4.698575 AGAAGAATCGGAGGCAATCTAAC 58.301 43.478 0.00 0.00 0.00 2.34
431 432 4.162320 AGAAGAATCGGAGGCAATCTAACA 59.838 41.667 0.00 0.00 0.00 2.41
432 433 4.696479 AGAATCGGAGGCAATCTAACAT 57.304 40.909 0.00 0.00 0.00 2.71
433 434 5.041191 AGAATCGGAGGCAATCTAACATT 57.959 39.130 0.00 0.00 0.00 2.71
434 435 4.818546 AGAATCGGAGGCAATCTAACATTG 59.181 41.667 0.00 0.00 0.00 2.82
441 442 3.004024 GCAATCTAACATTGCGGGATG 57.996 47.619 3.67 0.00 43.80 3.51
442 443 2.358898 GCAATCTAACATTGCGGGATGT 59.641 45.455 3.67 0.00 43.80 3.06
444 445 4.677779 GCAATCTAACATTGCGGGATGTTT 60.678 41.667 15.20 0.00 45.38 2.83
445 446 4.900635 ATCTAACATTGCGGGATGTTTC 57.099 40.909 15.20 0.00 45.38 2.78
446 447 3.680490 TCTAACATTGCGGGATGTTTCA 58.320 40.909 15.20 3.72 45.38 2.69
447 448 4.075682 TCTAACATTGCGGGATGTTTCAA 58.924 39.130 15.20 1.51 45.38 2.69
448 449 3.959535 AACATTGCGGGATGTTTCAAT 57.040 38.095 6.99 0.00 45.38 2.57
449 450 3.508744 ACATTGCGGGATGTTTCAATC 57.491 42.857 0.00 0.00 36.92 2.67
450 451 3.091545 ACATTGCGGGATGTTTCAATCT 58.908 40.909 0.00 0.00 36.92 2.40
451 452 3.119388 ACATTGCGGGATGTTTCAATCTG 60.119 43.478 0.00 0.00 36.92 2.90
452 453 2.488204 TGCGGGATGTTTCAATCTGA 57.512 45.000 0.00 0.00 0.00 3.27
453 454 2.083774 TGCGGGATGTTTCAATCTGAC 58.916 47.619 0.00 0.00 0.00 3.51
454 455 1.062587 GCGGGATGTTTCAATCTGACG 59.937 52.381 0.00 0.00 0.00 4.35
455 456 1.665679 CGGGATGTTTCAATCTGACGG 59.334 52.381 0.00 0.00 0.00 4.79
456 457 2.711542 GGGATGTTTCAATCTGACGGT 58.288 47.619 0.00 0.00 0.00 4.83
457 458 2.420022 GGGATGTTTCAATCTGACGGTG 59.580 50.000 0.00 0.00 0.00 4.94
458 459 2.420022 GGATGTTTCAATCTGACGGTGG 59.580 50.000 0.00 0.00 0.00 4.61
459 460 2.920724 TGTTTCAATCTGACGGTGGA 57.079 45.000 0.00 0.00 0.00 4.02
460 461 2.489971 TGTTTCAATCTGACGGTGGAC 58.510 47.619 0.00 0.00 0.00 4.02
461 462 2.158885 TGTTTCAATCTGACGGTGGACA 60.159 45.455 0.00 0.00 0.00 4.02
462 463 2.163818 TTCAATCTGACGGTGGACAC 57.836 50.000 0.00 0.00 0.00 3.67
463 464 1.044611 TCAATCTGACGGTGGACACA 58.955 50.000 4.69 0.00 0.00 3.72
464 465 1.000843 TCAATCTGACGGTGGACACAG 59.999 52.381 4.69 2.82 0.00 3.66
465 466 0.320771 AATCTGACGGTGGACACAGC 60.321 55.000 4.69 0.00 41.58 4.40
471 472 3.986006 GGTGGACACAGCGACCGA 61.986 66.667 4.69 0.00 35.13 4.69
472 473 2.261671 GTGGACACAGCGACCGAT 59.738 61.111 0.00 0.00 31.20 4.18
473 474 1.805945 GTGGACACAGCGACCGATC 60.806 63.158 0.00 0.00 31.20 3.69
474 475 1.977009 TGGACACAGCGACCGATCT 60.977 57.895 0.00 0.00 31.20 2.75
475 476 1.517257 GGACACAGCGACCGATCTG 60.517 63.158 0.00 0.00 36.45 2.90
476 477 1.517257 GACACAGCGACCGATCTGG 60.517 63.158 2.55 2.55 46.41 3.86
477 478 2.887568 CACAGCGACCGATCTGGC 60.888 66.667 3.85 0.00 43.94 4.85
478 479 3.381983 ACAGCGACCGATCTGGCA 61.382 61.111 3.85 0.00 43.94 4.92
479 480 2.107750 CAGCGACCGATCTGGCAT 59.892 61.111 3.85 0.00 43.94 4.40
480 481 1.953138 CAGCGACCGATCTGGCATC 60.953 63.158 3.85 0.00 43.94 3.91
481 482 2.130426 AGCGACCGATCTGGCATCT 61.130 57.895 3.85 0.00 43.94 2.90
482 483 0.823769 AGCGACCGATCTGGCATCTA 60.824 55.000 3.85 0.00 43.94 1.98
483 484 0.664767 GCGACCGATCTGGCATCTAC 60.665 60.000 3.85 0.00 43.94 2.59
484 485 0.039074 CGACCGATCTGGCATCTACC 60.039 60.000 3.85 0.00 43.94 3.18
485 486 0.318762 GACCGATCTGGCATCTACCC 59.681 60.000 3.85 0.00 43.94 3.69
486 487 1.290324 CCGATCTGGCATCTACCCG 59.710 63.158 0.00 0.00 0.00 5.28
487 488 1.290324 CGATCTGGCATCTACCCGG 59.710 63.158 0.00 0.00 0.00 5.73
488 489 1.464376 CGATCTGGCATCTACCCGGT 61.464 60.000 0.00 0.00 0.00 5.28
489 490 0.318762 GATCTGGCATCTACCCGGTC 59.681 60.000 0.00 0.00 0.00 4.79
490 491 1.464376 ATCTGGCATCTACCCGGTCG 61.464 60.000 0.00 0.00 0.00 4.79
491 492 2.043752 TGGCATCTACCCGGTCGA 60.044 61.111 0.00 0.00 0.00 4.20
492 493 2.351336 CTGGCATCTACCCGGTCGAC 62.351 65.000 7.13 7.13 0.00 4.20
493 494 2.416260 GCATCTACCCGGTCGACC 59.584 66.667 25.28 25.28 0.00 4.79
512 513 2.043953 GCATCGGCCTTCCCCTTT 60.044 61.111 0.00 0.00 0.00 3.11
513 514 1.682344 GCATCGGCCTTCCCCTTTT 60.682 57.895 0.00 0.00 0.00 2.27
514 515 1.257750 GCATCGGCCTTCCCCTTTTT 61.258 55.000 0.00 0.00 0.00 1.94
515 516 0.532115 CATCGGCCTTCCCCTTTTTG 59.468 55.000 0.00 0.00 0.00 2.44
516 517 0.614697 ATCGGCCTTCCCCTTTTTGG 60.615 55.000 0.00 0.00 0.00 3.28
517 518 1.533033 CGGCCTTCCCCTTTTTGGT 60.533 57.895 0.00 0.00 0.00 3.67
518 519 1.815817 CGGCCTTCCCCTTTTTGGTG 61.816 60.000 0.00 0.00 0.00 4.17
519 520 0.471022 GGCCTTCCCCTTTTTGGTGA 60.471 55.000 0.00 0.00 0.00 4.02
520 521 0.969149 GCCTTCCCCTTTTTGGTGAG 59.031 55.000 0.00 0.00 0.00 3.51
521 522 1.757764 GCCTTCCCCTTTTTGGTGAGT 60.758 52.381 0.00 0.00 0.00 3.41
522 523 1.963515 CCTTCCCCTTTTTGGTGAGTG 59.036 52.381 0.00 0.00 0.00 3.51
523 524 2.424234 CCTTCCCCTTTTTGGTGAGTGA 60.424 50.000 0.00 0.00 0.00 3.41
524 525 3.500343 CTTCCCCTTTTTGGTGAGTGAT 58.500 45.455 0.00 0.00 0.00 3.06
525 526 2.875296 TCCCCTTTTTGGTGAGTGATG 58.125 47.619 0.00 0.00 0.00 3.07
532 533 6.208644 CCTTTTTGGTGAGTGATGTAAGTTG 58.791 40.000 0.00 0.00 0.00 3.16
566 568 1.141019 ATGACCACCCGTTCGATCG 59.859 57.895 9.36 9.36 0.00 3.69
567 569 1.317431 ATGACCACCCGTTCGATCGA 61.317 55.000 15.15 15.15 0.00 3.59
707 741 4.012895 GCGACGGTTGCACCACTG 62.013 66.667 15.42 1.40 38.47 3.66
713 747 0.040425 CGGTTGCACCACTGCTAAAC 60.040 55.000 6.21 0.00 44.57 2.01
730 764 5.245075 TGCTAAACCCCAAAATTCGAAATCT 59.755 36.000 0.00 0.00 0.00 2.40
746 780 0.250553 ATCTCCCAACCGTGCGAAAA 60.251 50.000 0.00 0.00 0.00 2.29
763 797 1.568504 AAATACGAGACAGCCCCTGA 58.431 50.000 0.00 0.00 35.18 3.86
792 826 4.754667 GCTCCCAACGGTCGGACC 62.755 72.222 17.38 17.38 34.05 4.46
807 841 4.096003 ACCAATCCGGCCGTCCAG 62.096 66.667 26.12 8.83 39.03 3.86
842 877 3.196613 GGCATACCCGTCGAGATTC 57.803 57.895 0.00 0.00 0.00 2.52
855 891 1.723288 GAGATTCGAATCCCCTCCCT 58.277 55.000 29.82 13.17 36.04 4.20
900 936 4.047059 GGCAGAACCGTCCGACGA 62.047 66.667 22.40 0.00 46.05 4.20
902 938 2.087009 GCAGAACCGTCCGACGAAG 61.087 63.158 22.40 8.95 46.05 3.79
925 961 9.131791 GAAGAAGTCTCTCTCACCTTATATCTT 57.868 37.037 0.00 0.00 0.00 2.40
970 1011 1.600485 GAAAACCTTCCTCGCGAAACA 59.400 47.619 11.33 0.00 0.00 2.83
1111 1159 2.578981 GACGGCGCCTACTTCGTC 60.579 66.667 26.68 20.84 43.62 4.20
1232 1280 1.611673 CGTCTTCCAATGGCCTGTTCT 60.612 52.381 3.32 0.00 0.00 3.01
1283 1351 1.561717 CGGGTGCGATTTGTGTTCGA 61.562 55.000 0.00 0.00 38.88 3.71
1485 1553 2.813754 GCAGGATGTGTTCAACAAGCTA 59.186 45.455 0.00 0.00 43.61 3.32
1521 1590 0.106469 GCTCCCATTTCTTCTCCCCC 60.106 60.000 0.00 0.00 0.00 5.40
1754 2348 4.870426 TCGAGACATCACATTTTTAGGCTC 59.130 41.667 0.00 0.00 0.00 4.70
1822 2479 4.734398 TTTTGTTGTGTGGAGAATTGCT 57.266 36.364 0.00 0.00 0.00 3.91
1825 2482 7.517614 TTTTGTTGTGTGGAGAATTGCTATA 57.482 32.000 0.00 0.00 0.00 1.31
1899 2625 5.316167 ACACATGAGCAGTCTGGATTAAAA 58.684 37.500 0.00 0.00 0.00 1.52
2041 2767 6.998673 CCTTACTTCTTGTTATTCCATAGGGG 59.001 42.308 0.00 0.00 38.37 4.79
2042 2768 5.388599 ACTTCTTGTTATTCCATAGGGGG 57.611 43.478 0.00 0.00 37.22 5.40
2093 2823 2.932614 ACTGTCGCAGCATATTGAAGTC 59.067 45.455 6.74 0.00 34.37 3.01
2213 2943 3.161866 GCCAACCCCATTCTTTCTGTAA 58.838 45.455 0.00 0.00 0.00 2.41
2376 3169 1.378250 GCCTGCCAAGTCTGCATCT 60.378 57.895 0.00 0.00 38.22 2.90
2406 3199 4.521062 GCTCAGCCTCCGTCGCAT 62.521 66.667 0.00 0.00 0.00 4.73
2725 3661 5.005779 CGGTAAGTAGCAGAAATGCTTGTAG 59.994 44.000 8.20 0.00 43.52 2.74
2766 3702 0.249489 ACAGCAGGTGTCTGAACGTC 60.249 55.000 0.00 0.00 43.49 4.34
3138 4074 2.040330 CTCCAGGATGAGGCTCTCG 58.960 63.158 16.72 0.00 39.69 4.04
3233 4169 2.375174 AGGGGCTGAGTTGTTGTCATTA 59.625 45.455 0.00 0.00 0.00 1.90
3273 4209 5.684184 GGGTTTATCTTGTGTTGTTTCGTTC 59.316 40.000 0.00 0.00 0.00 3.95
3339 4275 2.664402 ACCTGCCTTTGACTGTGATT 57.336 45.000 0.00 0.00 0.00 2.57
3455 4391 1.137513 CAGGACGGTCTGTTTTCGAC 58.862 55.000 8.23 0.00 0.00 4.20
3476 4412 1.216941 CCAAAAAGGTTGCTGCGCTG 61.217 55.000 9.73 10.04 0.00 5.18
3480 4416 2.063541 AAAGGTTGCTGCGCTGTGAC 62.064 55.000 16.05 13.50 0.00 3.67
3546 4482 3.559242 CGCCTGAATCCTCTTCATCTTTC 59.441 47.826 0.00 0.00 0.00 2.62
3606 4542 1.675641 GCTCGACCAACCTGCCATT 60.676 57.895 0.00 0.00 0.00 3.16
3607 4543 0.392461 GCTCGACCAACCTGCCATTA 60.392 55.000 0.00 0.00 0.00 1.90
3608 4544 1.747206 GCTCGACCAACCTGCCATTAT 60.747 52.381 0.00 0.00 0.00 1.28
3609 4545 2.484770 GCTCGACCAACCTGCCATTATA 60.485 50.000 0.00 0.00 0.00 0.98
3610 4546 3.131396 CTCGACCAACCTGCCATTATAC 58.869 50.000 0.00 0.00 0.00 1.47
3611 4547 2.769663 TCGACCAACCTGCCATTATACT 59.230 45.455 0.00 0.00 0.00 2.12
3612 4548 3.131396 CGACCAACCTGCCATTATACTC 58.869 50.000 0.00 0.00 0.00 2.59
3613 4549 3.477530 GACCAACCTGCCATTATACTCC 58.522 50.000 0.00 0.00 0.00 3.85
3614 4550 2.174854 ACCAACCTGCCATTATACTCCC 59.825 50.000 0.00 0.00 0.00 4.30
3615 4551 2.443255 CCAACCTGCCATTATACTCCCT 59.557 50.000 0.00 0.00 0.00 4.20
3616 4552 3.496870 CCAACCTGCCATTATACTCCCTC 60.497 52.174 0.00 0.00 0.00 4.30
3617 4553 2.339769 ACCTGCCATTATACTCCCTCC 58.660 52.381 0.00 0.00 0.00 4.30
3618 4554 1.276421 CCTGCCATTATACTCCCTCCG 59.724 57.143 0.00 0.00 0.00 4.63
3619 4555 1.971357 CTGCCATTATACTCCCTCCGT 59.029 52.381 0.00 0.00 0.00 4.69
3620 4556 2.368875 CTGCCATTATACTCCCTCCGTT 59.631 50.000 0.00 0.00 0.00 4.44
3621 4557 2.367567 TGCCATTATACTCCCTCCGTTC 59.632 50.000 0.00 0.00 0.00 3.95
3622 4558 2.367567 GCCATTATACTCCCTCCGTTCA 59.632 50.000 0.00 0.00 0.00 3.18
3623 4559 3.802675 GCCATTATACTCCCTCCGTTCAC 60.803 52.174 0.00 0.00 0.00 3.18
3624 4560 3.552273 CCATTATACTCCCTCCGTTCACG 60.552 52.174 0.00 0.00 39.44 4.35
3625 4561 2.715749 TATACTCCCTCCGTTCACGA 57.284 50.000 0.00 0.00 43.02 4.35
3626 4562 2.068834 ATACTCCCTCCGTTCACGAT 57.931 50.000 0.00 0.00 43.02 3.73
3627 4563 1.843368 TACTCCCTCCGTTCACGATT 58.157 50.000 0.00 0.00 43.02 3.34
3628 4564 0.246635 ACTCCCTCCGTTCACGATTG 59.753 55.000 0.00 0.00 43.02 2.67
3629 4565 0.530744 CTCCCTCCGTTCACGATTGA 59.469 55.000 0.00 0.00 43.02 2.57
3630 4566 0.530744 TCCCTCCGTTCACGATTGAG 59.469 55.000 0.00 0.00 43.02 3.02
3631 4567 0.246635 CCCTCCGTTCACGATTGAGT 59.753 55.000 0.00 0.00 43.02 3.41
3632 4568 1.630148 CCTCCGTTCACGATTGAGTC 58.370 55.000 0.00 0.00 43.02 3.36
3633 4569 1.067846 CCTCCGTTCACGATTGAGTCA 60.068 52.381 0.00 0.00 43.02 3.41
3634 4570 2.417379 CCTCCGTTCACGATTGAGTCAT 60.417 50.000 0.00 0.00 43.02 3.06
3635 4571 2.854777 CTCCGTTCACGATTGAGTCATC 59.145 50.000 0.00 0.00 43.02 2.92
3636 4572 2.492088 TCCGTTCACGATTGAGTCATCT 59.508 45.455 0.00 0.00 43.02 2.90
3637 4573 3.692593 TCCGTTCACGATTGAGTCATCTA 59.307 43.478 0.00 0.00 43.02 1.98
3638 4574 4.338400 TCCGTTCACGATTGAGTCATCTAT 59.662 41.667 0.00 0.00 43.02 1.98
3639 4575 5.043903 CCGTTCACGATTGAGTCATCTATT 58.956 41.667 0.00 0.00 43.02 1.73
3640 4576 5.520288 CCGTTCACGATTGAGTCATCTATTT 59.480 40.000 0.00 0.00 43.02 1.40
3641 4577 6.036083 CCGTTCACGATTGAGTCATCTATTTT 59.964 38.462 0.00 0.00 43.02 1.82
3642 4578 6.896613 CGTTCACGATTGAGTCATCTATTTTG 59.103 38.462 0.00 0.00 43.02 2.44
3643 4579 6.908870 TCACGATTGAGTCATCTATTTTGG 57.091 37.500 0.00 0.00 0.00 3.28
3644 4580 6.639563 TCACGATTGAGTCATCTATTTTGGA 58.360 36.000 0.00 0.00 0.00 3.53
3645 4581 7.102993 TCACGATTGAGTCATCTATTTTGGAA 58.897 34.615 0.00 0.00 0.00 3.53
3646 4582 7.064609 TCACGATTGAGTCATCTATTTTGGAAC 59.935 37.037 0.00 0.00 0.00 3.62
3647 4583 6.036083 ACGATTGAGTCATCTATTTTGGAACG 59.964 38.462 0.00 0.00 0.00 3.95
3648 4584 6.510157 CGATTGAGTCATCTATTTTGGAACGG 60.510 42.308 0.00 0.00 0.00 4.44
3649 4585 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
3650 4586 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
3651 4587 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
3652 4588 4.469945 AGTCATCTATTTTGGAACGGAGGA 59.530 41.667 0.00 0.00 0.00 3.71
3653 4589 5.045869 AGTCATCTATTTTGGAACGGAGGAA 60.046 40.000 0.00 0.00 0.00 3.36
3654 4590 5.823045 GTCATCTATTTTGGAACGGAGGAAT 59.177 40.000 0.00 0.00 0.00 3.01
3657 4593 7.497909 TCATCTATTTTGGAACGGAGGAATTAC 59.502 37.037 0.00 0.00 0.00 1.89
3672 4723 5.203528 AGGAATTACTGTGCTGGCAATAAT 58.796 37.500 0.00 0.34 0.00 1.28
3703 4754 1.033574 TTTAGTGTTTTGGTGGCCCG 58.966 50.000 0.00 0.00 0.00 6.13
3818 4874 1.613437 CGGATGCAAAGGGAACAAGTT 59.387 47.619 0.00 0.00 0.00 2.66
3899 4956 3.628032 CACTGGCGTCTCTCAGTTATCTA 59.372 47.826 0.00 0.00 41.71 1.98
3900 4957 3.628487 ACTGGCGTCTCTCAGTTATCTAC 59.372 47.826 0.00 0.00 40.91 2.59
3905 4962 6.205076 TGGCGTCTCTCAGTTATCTACTTATC 59.795 42.308 0.00 0.00 33.85 1.75
3907 4964 7.295201 GCGTCTCTCAGTTATCTACTTATCTG 58.705 42.308 0.00 0.00 33.85 2.90
3908 4965 7.041644 GCGTCTCTCAGTTATCTACTTATCTGT 60.042 40.741 0.00 0.00 33.85 3.41
3909 4966 8.832521 CGTCTCTCAGTTATCTACTTATCTGTT 58.167 37.037 0.00 0.00 33.85 3.16
3937 5001 7.972832 ATTACTGTCGTTTTCACCATTAAGA 57.027 32.000 0.00 0.00 0.00 2.10
3938 5002 5.668558 ACTGTCGTTTTCACCATTAAGAC 57.331 39.130 0.00 0.00 0.00 3.01
4056 5131 5.530171 AGCCTGCAAATACAGACATAGAATG 59.470 40.000 0.00 0.00 40.25 2.67
4148 5223 8.695284 GTGTTCGCAATACATTCTCTATTAGAG 58.305 37.037 13.60 13.60 43.64 2.43
4254 5330 6.607600 TGAGCTAGATAATAGTCACACACCTT 59.392 38.462 0.00 0.00 0.00 3.50
4257 5333 7.124298 AGCTAGATAATAGTCACACACCTTCAA 59.876 37.037 0.00 0.00 0.00 2.69
4261 5337 0.179018 AGTCACACACCTTCAAGGCC 60.179 55.000 2.20 0.00 39.63 5.19
4263 5339 0.108585 TCACACACCTTCAAGGCCTC 59.891 55.000 5.23 0.00 39.63 4.70
4275 5351 6.126361 ACCTTCAAGGCCTCATTATGTCTTAT 60.126 38.462 5.23 0.00 39.63 1.73
4285 5361 7.768120 GCCTCATTATGTCTTATATCAGGGAAG 59.232 40.741 0.00 0.00 0.00 3.46
4286 5362 8.820831 CCTCATTATGTCTTATATCAGGGAAGT 58.179 37.037 0.00 0.00 0.00 3.01
4287 5363 9.650539 CTCATTATGTCTTATATCAGGGAAGTG 57.349 37.037 0.00 0.00 0.00 3.16
4288 5364 8.097038 TCATTATGTCTTATATCAGGGAAGTGC 58.903 37.037 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.926426 GCACCCTAGCTTCCCACCAT 61.926 60.000 0.00 0.00 0.00 3.55
1 2 2.602676 GCACCCTAGCTTCCCACCA 61.603 63.158 0.00 0.00 0.00 4.17
2 3 2.272471 GCACCCTAGCTTCCCACC 59.728 66.667 0.00 0.00 0.00 4.61
3 4 2.125106 CGCACCCTAGCTTCCCAC 60.125 66.667 0.00 0.00 0.00 4.61
4 5 4.096003 GCGCACCCTAGCTTCCCA 62.096 66.667 0.30 0.00 0.00 4.37
5 6 2.432300 TAGCGCACCCTAGCTTCCC 61.432 63.158 11.47 0.00 44.15 3.97
6 7 1.227292 GTAGCGCACCCTAGCTTCC 60.227 63.158 11.47 0.00 44.15 3.46
7 8 0.108329 TTGTAGCGCACCCTAGCTTC 60.108 55.000 11.47 0.00 44.15 3.86
8 9 0.391263 GTTGTAGCGCACCCTAGCTT 60.391 55.000 11.47 0.00 44.15 3.74
9 10 1.218316 GTTGTAGCGCACCCTAGCT 59.782 57.895 11.47 0.00 46.53 3.32
10 11 2.165301 CGTTGTAGCGCACCCTAGC 61.165 63.158 11.47 0.00 0.00 3.42
11 12 4.088421 CGTTGTAGCGCACCCTAG 57.912 61.111 11.47 0.00 0.00 3.02
19 20 1.781555 CAACTCCAGCGTTGTAGCG 59.218 57.895 0.00 0.00 43.00 4.26
25 26 0.392461 ACACACACAACTCCAGCGTT 60.392 50.000 0.00 0.00 0.00 4.84
26 27 1.089481 CACACACACAACTCCAGCGT 61.089 55.000 0.00 0.00 0.00 5.07
27 28 1.089481 ACACACACACAACTCCAGCG 61.089 55.000 0.00 0.00 0.00 5.18
28 29 0.378257 CACACACACACAACTCCAGC 59.622 55.000 0.00 0.00 0.00 4.85
29 30 1.398041 CACACACACACACAACTCCAG 59.602 52.381 0.00 0.00 0.00 3.86
30 31 1.447945 CACACACACACACAACTCCA 58.552 50.000 0.00 0.00 0.00 3.86
31 32 0.732571 CCACACACACACACAACTCC 59.267 55.000 0.00 0.00 0.00 3.85
32 33 0.732571 CCCACACACACACACAACTC 59.267 55.000 0.00 0.00 0.00 3.01
33 34 2.866872 CCCACACACACACACAACT 58.133 52.632 0.00 0.00 0.00 3.16
395 396 1.633774 TTCTTCTCCTTCCTCACGCT 58.366 50.000 0.00 0.00 0.00 5.07
396 397 2.545731 GATTCTTCTCCTTCCTCACGC 58.454 52.381 0.00 0.00 0.00 5.34
397 398 2.480416 CCGATTCTTCTCCTTCCTCACG 60.480 54.545 0.00 0.00 0.00 4.35
398 399 2.761208 TCCGATTCTTCTCCTTCCTCAC 59.239 50.000 0.00 0.00 0.00 3.51
399 400 3.027412 CTCCGATTCTTCTCCTTCCTCA 58.973 50.000 0.00 0.00 0.00 3.86
400 401 2.364002 CCTCCGATTCTTCTCCTTCCTC 59.636 54.545 0.00 0.00 0.00 3.71
401 402 2.393646 CCTCCGATTCTTCTCCTTCCT 58.606 52.381 0.00 0.00 0.00 3.36
402 403 1.202592 GCCTCCGATTCTTCTCCTTCC 60.203 57.143 0.00 0.00 0.00 3.46
403 404 1.482593 TGCCTCCGATTCTTCTCCTTC 59.517 52.381 0.00 0.00 0.00 3.46
404 405 1.573108 TGCCTCCGATTCTTCTCCTT 58.427 50.000 0.00 0.00 0.00 3.36
405 406 1.573108 TTGCCTCCGATTCTTCTCCT 58.427 50.000 0.00 0.00 0.00 3.69
406 407 2.103941 AGATTGCCTCCGATTCTTCTCC 59.896 50.000 0.00 0.00 0.00 3.71
407 408 3.467374 AGATTGCCTCCGATTCTTCTC 57.533 47.619 0.00 0.00 0.00 2.87
408 409 4.162320 TGTTAGATTGCCTCCGATTCTTCT 59.838 41.667 0.00 0.00 0.00 2.85
409 410 4.442706 TGTTAGATTGCCTCCGATTCTTC 58.557 43.478 0.00 0.00 0.00 2.87
410 411 4.487714 TGTTAGATTGCCTCCGATTCTT 57.512 40.909 0.00 0.00 0.00 2.52
411 412 4.696479 ATGTTAGATTGCCTCCGATTCT 57.304 40.909 0.00 0.00 0.00 2.40
412 413 4.555511 GCAATGTTAGATTGCCTCCGATTC 60.556 45.833 15.02 0.00 46.21 2.52
413 414 3.316308 GCAATGTTAGATTGCCTCCGATT 59.684 43.478 15.02 0.00 46.21 3.34
414 415 2.880890 GCAATGTTAGATTGCCTCCGAT 59.119 45.455 15.02 0.00 46.21 4.18
415 416 2.288666 GCAATGTTAGATTGCCTCCGA 58.711 47.619 15.02 0.00 46.21 4.55
416 417 2.763249 GCAATGTTAGATTGCCTCCG 57.237 50.000 15.02 0.00 46.21 4.63
420 421 7.630525 AAACATCCCGCAATGTTAGATTGCC 62.631 44.000 19.06 4.44 46.49 4.52
421 422 3.181487 AACATCCCGCAATGTTAGATTGC 60.181 43.478 15.79 15.79 45.61 3.56
422 423 4.637483 AACATCCCGCAATGTTAGATTG 57.363 40.909 10.76 0.00 45.61 2.67
423 424 4.704540 TGAAACATCCCGCAATGTTAGATT 59.295 37.500 12.30 0.19 46.49 2.40
424 425 4.269183 TGAAACATCCCGCAATGTTAGAT 58.731 39.130 12.30 0.48 46.49 1.98
425 426 3.680490 TGAAACATCCCGCAATGTTAGA 58.320 40.909 12.30 2.51 46.49 2.10
426 427 4.433186 TTGAAACATCCCGCAATGTTAG 57.567 40.909 12.30 0.00 46.49 2.34
427 428 4.704540 AGATTGAAACATCCCGCAATGTTA 59.295 37.500 12.30 0.99 46.49 2.41
429 430 3.091545 AGATTGAAACATCCCGCAATGT 58.908 40.909 0.00 0.00 41.60 2.71
430 431 3.129113 TCAGATTGAAACATCCCGCAATG 59.871 43.478 0.00 0.00 31.65 2.82
431 432 3.129287 GTCAGATTGAAACATCCCGCAAT 59.871 43.478 0.00 0.00 33.97 3.56
432 433 2.487762 GTCAGATTGAAACATCCCGCAA 59.512 45.455 0.00 0.00 0.00 4.85
433 434 2.083774 GTCAGATTGAAACATCCCGCA 58.916 47.619 0.00 0.00 0.00 5.69
434 435 1.062587 CGTCAGATTGAAACATCCCGC 59.937 52.381 0.00 0.00 0.00 6.13
435 436 1.665679 CCGTCAGATTGAAACATCCCG 59.334 52.381 0.00 0.00 0.00 5.14
436 437 2.420022 CACCGTCAGATTGAAACATCCC 59.580 50.000 0.00 0.00 0.00 3.85
437 438 2.420022 CCACCGTCAGATTGAAACATCC 59.580 50.000 0.00 0.00 0.00 3.51
438 439 3.125316 GTCCACCGTCAGATTGAAACATC 59.875 47.826 0.00 0.00 0.00 3.06
439 440 3.074412 GTCCACCGTCAGATTGAAACAT 58.926 45.455 0.00 0.00 0.00 2.71
440 441 2.158885 TGTCCACCGTCAGATTGAAACA 60.159 45.455 0.00 0.00 0.00 2.83
441 442 2.223377 GTGTCCACCGTCAGATTGAAAC 59.777 50.000 0.00 0.00 0.00 2.78
442 443 2.158885 TGTGTCCACCGTCAGATTGAAA 60.159 45.455 0.00 0.00 0.00 2.69
443 444 1.414550 TGTGTCCACCGTCAGATTGAA 59.585 47.619 0.00 0.00 0.00 2.69
444 445 1.000843 CTGTGTCCACCGTCAGATTGA 59.999 52.381 0.00 0.00 0.00 2.57
445 446 1.432514 CTGTGTCCACCGTCAGATTG 58.567 55.000 0.00 0.00 0.00 2.67
446 447 0.320771 GCTGTGTCCACCGTCAGATT 60.321 55.000 0.00 0.00 0.00 2.40
447 448 1.293498 GCTGTGTCCACCGTCAGAT 59.707 57.895 0.00 0.00 0.00 2.90
448 449 2.734591 GCTGTGTCCACCGTCAGA 59.265 61.111 0.00 0.00 0.00 3.27
449 450 2.734723 CGCTGTGTCCACCGTCAG 60.735 66.667 0.00 0.00 0.00 3.51
450 451 3.220658 TCGCTGTGTCCACCGTCA 61.221 61.111 0.00 0.00 0.00 4.35
451 452 2.733593 GTCGCTGTGTCCACCGTC 60.734 66.667 0.00 0.00 0.00 4.79
452 453 4.295119 GGTCGCTGTGTCCACCGT 62.295 66.667 0.00 0.00 0.00 4.83
454 455 3.296709 ATCGGTCGCTGTGTCCACC 62.297 63.158 5.41 0.00 0.00 4.61
455 456 1.805945 GATCGGTCGCTGTGTCCAC 60.806 63.158 5.41 0.00 0.00 4.02
456 457 1.977009 AGATCGGTCGCTGTGTCCA 60.977 57.895 5.41 0.00 0.00 4.02
457 458 1.517257 CAGATCGGTCGCTGTGTCC 60.517 63.158 0.00 0.00 0.00 4.02
458 459 1.517257 CCAGATCGGTCGCTGTGTC 60.517 63.158 0.00 0.00 0.00 3.67
459 460 2.573869 CCAGATCGGTCGCTGTGT 59.426 61.111 0.00 0.00 0.00 3.72
460 461 2.887568 GCCAGATCGGTCGCTGTG 60.888 66.667 5.66 0.00 36.97 3.66
461 462 2.635229 GATGCCAGATCGGTCGCTGT 62.635 60.000 5.66 0.00 36.97 4.40
462 463 1.953138 GATGCCAGATCGGTCGCTG 60.953 63.158 5.66 0.00 36.97 5.18
463 464 0.823769 TAGATGCCAGATCGGTCGCT 60.824 55.000 5.66 3.69 36.97 4.93
464 465 0.664767 GTAGATGCCAGATCGGTCGC 60.665 60.000 5.66 0.00 36.97 5.19
465 466 0.039074 GGTAGATGCCAGATCGGTCG 60.039 60.000 5.66 0.00 36.97 4.79
466 467 0.318762 GGGTAGATGCCAGATCGGTC 59.681 60.000 0.00 0.00 36.97 4.79
467 468 1.464376 CGGGTAGATGCCAGATCGGT 61.464 60.000 5.66 0.00 36.97 4.69
468 469 1.290324 CGGGTAGATGCCAGATCGG 59.710 63.158 0.00 0.00 38.11 4.18
469 470 1.290324 CCGGGTAGATGCCAGATCG 59.710 63.158 0.00 0.00 0.00 3.69
470 471 0.318762 GACCGGGTAGATGCCAGATC 59.681 60.000 6.32 0.00 0.00 2.75
471 472 1.464376 CGACCGGGTAGATGCCAGAT 61.464 60.000 6.32 0.00 0.00 2.90
472 473 2.125326 CGACCGGGTAGATGCCAGA 61.125 63.158 6.32 0.00 0.00 3.86
473 474 2.125326 TCGACCGGGTAGATGCCAG 61.125 63.158 6.32 0.00 0.00 4.85
474 475 2.043752 TCGACCGGGTAGATGCCA 60.044 61.111 6.32 0.00 0.00 4.92
475 476 2.416260 GTCGACCGGGTAGATGCC 59.584 66.667 13.22 0.00 0.00 4.40
476 477 2.416260 GGTCGACCGGGTAGATGC 59.584 66.667 20.85 1.58 0.00 3.91
495 496 1.257750 AAAAAGGGGAAGGCCGATGC 61.258 55.000 0.00 0.00 33.83 3.91
496 497 0.532115 CAAAAAGGGGAAGGCCGATG 59.468 55.000 0.00 0.00 33.83 3.84
497 498 0.614697 CCAAAAAGGGGAAGGCCGAT 60.615 55.000 0.00 0.00 33.83 4.18
498 499 1.228737 CCAAAAAGGGGAAGGCCGA 60.229 57.895 0.00 0.00 33.83 5.54
499 500 1.533033 ACCAAAAAGGGGAAGGCCG 60.533 57.895 0.00 0.00 43.89 6.13
500 501 4.639726 ACCAAAAAGGGGAAGGCC 57.360 55.556 0.00 0.00 43.89 5.19
506 507 2.597455 ACATCACTCACCAAAAAGGGG 58.403 47.619 0.00 0.00 44.73 4.79
507 508 4.827284 ACTTACATCACTCACCAAAAAGGG 59.173 41.667 0.00 0.00 43.89 3.95
508 509 6.208644 CAACTTACATCACTCACCAAAAAGG 58.791 40.000 0.00 0.00 45.67 3.11
509 510 6.208644 CCAACTTACATCACTCACCAAAAAG 58.791 40.000 0.00 0.00 0.00 2.27
510 511 5.451242 GCCAACTTACATCACTCACCAAAAA 60.451 40.000 0.00 0.00 0.00 1.94
511 512 4.037446 GCCAACTTACATCACTCACCAAAA 59.963 41.667 0.00 0.00 0.00 2.44
512 513 3.568007 GCCAACTTACATCACTCACCAAA 59.432 43.478 0.00 0.00 0.00 3.28
513 514 3.146066 GCCAACTTACATCACTCACCAA 58.854 45.455 0.00 0.00 0.00 3.67
514 515 2.105649 TGCCAACTTACATCACTCACCA 59.894 45.455 0.00 0.00 0.00 4.17
515 516 2.744202 CTGCCAACTTACATCACTCACC 59.256 50.000 0.00 0.00 0.00 4.02
516 517 2.744202 CCTGCCAACTTACATCACTCAC 59.256 50.000 0.00 0.00 0.00 3.51
517 518 2.875672 GCCTGCCAACTTACATCACTCA 60.876 50.000 0.00 0.00 0.00 3.41
518 519 1.740025 GCCTGCCAACTTACATCACTC 59.260 52.381 0.00 0.00 0.00 3.51
519 520 1.352352 AGCCTGCCAACTTACATCACT 59.648 47.619 0.00 0.00 0.00 3.41
520 521 1.826385 AGCCTGCCAACTTACATCAC 58.174 50.000 0.00 0.00 0.00 3.06
521 522 2.161855 CAAGCCTGCCAACTTACATCA 58.838 47.619 0.00 0.00 0.00 3.07
522 523 1.474077 CCAAGCCTGCCAACTTACATC 59.526 52.381 0.00 0.00 0.00 3.06
523 524 1.549203 CCAAGCCTGCCAACTTACAT 58.451 50.000 0.00 0.00 0.00 2.29
524 525 0.539438 CCCAAGCCTGCCAACTTACA 60.539 55.000 0.00 0.00 0.00 2.41
525 526 1.250840 CCCCAAGCCTGCCAACTTAC 61.251 60.000 0.00 0.00 0.00 2.34
549 551 1.525718 TTCGATCGAACGGGTGGTCA 61.526 55.000 25.96 0.14 0.00 4.02
566 568 1.818850 TGCTACGAGTAATCGCGTTC 58.181 50.000 13.21 0.34 46.69 3.95
567 569 2.267188 TTGCTACGAGTAATCGCGTT 57.733 45.000 13.21 2.26 46.69 4.84
706 740 4.939052 TTTCGAATTTTGGGGTTTAGCA 57.061 36.364 0.00 0.00 0.00 3.49
707 741 5.720202 AGATTTCGAATTTTGGGGTTTAGC 58.280 37.500 0.00 0.00 0.00 3.09
713 747 3.096092 TGGGAGATTTCGAATTTTGGGG 58.904 45.455 0.00 0.00 0.00 4.96
730 764 1.158434 GTATTTTCGCACGGTTGGGA 58.842 50.000 0.00 0.00 42.66 4.37
746 780 1.043673 GGTCAGGGGCTGTCTCGTAT 61.044 60.000 0.00 0.00 32.61 3.06
838 873 0.250510 GCAGGGAGGGGATTCGAATC 60.251 60.000 26.64 26.64 34.66 2.52
841 876 2.768344 GGCAGGGAGGGGATTCGA 60.768 66.667 0.00 0.00 0.00 3.71
842 877 3.878667 GGGCAGGGAGGGGATTCG 61.879 72.222 0.00 0.00 0.00 3.34
900 936 8.912988 CAAGATATAAGGTGAGAGAGACTTCTT 58.087 37.037 0.00 0.00 32.53 2.52
902 938 7.657336 CCAAGATATAAGGTGAGAGAGACTTC 58.343 42.308 0.00 0.00 0.00 3.01
1111 1159 3.486252 GAGGATCTCGTTCCGCCCG 62.486 68.421 0.00 0.00 40.94 6.13
1208 1256 2.115291 GGCCATTGGAAGACGAGGC 61.115 63.158 6.95 0.00 41.29 4.70
1283 1351 0.446222 CATCCCGAAACGCAACGAAT 59.554 50.000 0.00 0.00 0.00 3.34
1485 1553 0.250901 AGCGCACCTTGGTGATCTTT 60.251 50.000 22.52 1.23 0.00 2.52
1526 1595 1.732941 ACGCCACATAAATTCGCTCA 58.267 45.000 0.00 0.00 0.00 4.26
1754 2348 8.768955 CCTTCTATTCAGATCCGTATTTTGAAG 58.231 37.037 0.00 0.00 32.00 3.02
1806 2463 6.658816 ACAACATATAGCAATTCTCCACACAA 59.341 34.615 0.00 0.00 0.00 3.33
1822 2479 3.119424 TCACGCGGTTCTGACAACATATA 60.119 43.478 12.47 0.00 0.00 0.86
1825 2482 0.249699 TCACGCGGTTCTGACAACAT 60.250 50.000 12.47 0.00 0.00 2.71
1872 2529 2.369860 TCCAGACTGCTCATGTGTTTCT 59.630 45.455 0.00 0.00 0.00 2.52
1876 2533 4.558226 TTAATCCAGACTGCTCATGTGT 57.442 40.909 0.00 0.00 0.00 3.72
1917 2643 8.020819 CCATTTATGTAGGTTGTACACAGTTTG 58.979 37.037 0.00 0.00 0.00 2.93
2093 2823 4.202090 GGCCTTCCTTTGATGAGCTTATTG 60.202 45.833 0.00 0.00 0.00 1.90
2213 2943 7.907841 TGGTAACACTACTGGTCATATATGT 57.092 36.000 12.42 0.00 46.17 2.29
2376 3169 1.529010 CTGAGCTTTGTGGGTGGCA 60.529 57.895 0.00 0.00 0.00 4.92
2477 3270 1.674441 CCTGTGCATCATAAGCTGGTG 59.326 52.381 0.00 0.00 39.14 4.17
2478 3271 1.283029 ACCTGTGCATCATAAGCTGGT 59.717 47.619 0.00 0.00 0.00 4.00
2766 3702 8.479313 TTGTACTCTACAAGCATGATGTTTAG 57.521 34.615 9.48 9.61 43.23 1.85
3233 4169 1.061546 ACCCACAAGTCATAACCGGT 58.938 50.000 0.00 0.00 0.00 5.28
3273 4209 6.141527 CACACACATTATAACACCAAACAACG 59.858 38.462 0.00 0.00 0.00 4.10
3438 4374 1.416373 GAGTCGAAAACAGACCGTCC 58.584 55.000 0.00 0.00 39.31 4.79
3455 4391 3.184094 CGCAGCAACCTTTTTGGAG 57.816 52.632 0.00 0.00 39.71 3.86
3606 4542 2.715749 TCGTGAACGGAGGGAGTATA 57.284 50.000 2.59 0.00 40.29 1.47
3607 4543 2.068834 ATCGTGAACGGAGGGAGTAT 57.931 50.000 2.59 0.00 40.29 2.12
3608 4544 1.475280 CAATCGTGAACGGAGGGAGTA 59.525 52.381 2.59 0.00 40.29 2.59
3609 4545 0.246635 CAATCGTGAACGGAGGGAGT 59.753 55.000 2.59 0.00 40.29 3.85
3610 4546 0.530744 TCAATCGTGAACGGAGGGAG 59.469 55.000 2.59 0.00 40.29 4.30
3611 4547 0.530744 CTCAATCGTGAACGGAGGGA 59.469 55.000 2.59 0.00 40.29 4.20
3612 4548 0.246635 ACTCAATCGTGAACGGAGGG 59.753 55.000 2.59 0.00 40.29 4.30
3613 4549 1.067846 TGACTCAATCGTGAACGGAGG 60.068 52.381 2.59 0.00 40.29 4.30
3614 4550 2.347697 TGACTCAATCGTGAACGGAG 57.652 50.000 2.59 4.74 40.29 4.63
3615 4551 2.492088 AGATGACTCAATCGTGAACGGA 59.508 45.455 2.59 0.00 40.29 4.69
3616 4552 2.881074 AGATGACTCAATCGTGAACGG 58.119 47.619 2.59 0.00 40.29 4.44
3617 4553 6.575083 AAATAGATGACTCAATCGTGAACG 57.425 37.500 0.00 0.00 41.45 3.95
3618 4554 7.064609 TCCAAAATAGATGACTCAATCGTGAAC 59.935 37.037 0.00 0.00 31.88 3.18
3619 4555 7.102993 TCCAAAATAGATGACTCAATCGTGAA 58.897 34.615 0.00 0.00 31.88 3.18
3620 4556 6.639563 TCCAAAATAGATGACTCAATCGTGA 58.360 36.000 0.00 0.00 0.00 4.35
3621 4557 6.908870 TCCAAAATAGATGACTCAATCGTG 57.091 37.500 0.00 0.00 0.00 4.35
3622 4558 6.036083 CGTTCCAAAATAGATGACTCAATCGT 59.964 38.462 0.00 0.00 0.00 3.73
3623 4559 6.414079 CGTTCCAAAATAGATGACTCAATCG 58.586 40.000 0.00 0.00 0.00 3.34
3624 4560 6.538742 TCCGTTCCAAAATAGATGACTCAATC 59.461 38.462 0.00 0.00 0.00 2.67
3625 4561 6.414732 TCCGTTCCAAAATAGATGACTCAAT 58.585 36.000 0.00 0.00 0.00 2.57
3626 4562 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
3627 4563 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
3628 4564 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
3629 4565 4.469945 TCCTCCGTTCCAAAATAGATGACT 59.530 41.667 0.00 0.00 0.00 3.41
3630 4566 4.766375 TCCTCCGTTCCAAAATAGATGAC 58.234 43.478 0.00 0.00 0.00 3.06
3631 4567 5.429681 TTCCTCCGTTCCAAAATAGATGA 57.570 39.130 0.00 0.00 0.00 2.92
3632 4568 6.699575 AATTCCTCCGTTCCAAAATAGATG 57.300 37.500 0.00 0.00 0.00 2.90
3633 4569 7.499232 CAGTAATTCCTCCGTTCCAAAATAGAT 59.501 37.037 0.00 0.00 0.00 1.98
3634 4570 6.821665 CAGTAATTCCTCCGTTCCAAAATAGA 59.178 38.462 0.00 0.00 0.00 1.98
3635 4571 6.598064 ACAGTAATTCCTCCGTTCCAAAATAG 59.402 38.462 0.00 0.00 0.00 1.73
3636 4572 6.373216 CACAGTAATTCCTCCGTTCCAAAATA 59.627 38.462 0.00 0.00 0.00 1.40
3637 4573 5.183140 CACAGTAATTCCTCCGTTCCAAAAT 59.817 40.000 0.00 0.00 0.00 1.82
3638 4574 4.517453 CACAGTAATTCCTCCGTTCCAAAA 59.483 41.667 0.00 0.00 0.00 2.44
3639 4575 4.069304 CACAGTAATTCCTCCGTTCCAAA 58.931 43.478 0.00 0.00 0.00 3.28
3640 4576 3.670625 CACAGTAATTCCTCCGTTCCAA 58.329 45.455 0.00 0.00 0.00 3.53
3641 4577 2.614481 GCACAGTAATTCCTCCGTTCCA 60.614 50.000 0.00 0.00 0.00 3.53
3642 4578 2.007608 GCACAGTAATTCCTCCGTTCC 58.992 52.381 0.00 0.00 0.00 3.62
3643 4579 2.673368 CAGCACAGTAATTCCTCCGTTC 59.327 50.000 0.00 0.00 0.00 3.95
3644 4580 2.615493 CCAGCACAGTAATTCCTCCGTT 60.615 50.000 0.00 0.00 0.00 4.44
3645 4581 1.066143 CCAGCACAGTAATTCCTCCGT 60.066 52.381 0.00 0.00 0.00 4.69
3646 4582 1.656652 CCAGCACAGTAATTCCTCCG 58.343 55.000 0.00 0.00 0.00 4.63
3647 4583 1.340017 TGCCAGCACAGTAATTCCTCC 60.340 52.381 0.00 0.00 0.00 4.30
3648 4584 2.113860 TGCCAGCACAGTAATTCCTC 57.886 50.000 0.00 0.00 0.00 3.71
3649 4585 2.584835 TTGCCAGCACAGTAATTCCT 57.415 45.000 0.00 0.00 0.00 3.36
3650 4586 4.981806 TTATTGCCAGCACAGTAATTCC 57.018 40.909 0.00 0.00 0.00 3.01
3651 4587 7.832503 AAAATTATTGCCAGCACAGTAATTC 57.167 32.000 12.17 0.00 39.87 2.17
3652 4588 8.096414 AGAAAAATTATTGCCAGCACAGTAATT 58.904 29.630 0.00 8.24 41.46 1.40
3653 4589 7.614494 AGAAAAATTATTGCCAGCACAGTAAT 58.386 30.769 0.00 0.00 34.89 1.89
3654 4590 6.991938 AGAAAAATTATTGCCAGCACAGTAA 58.008 32.000 0.00 0.00 0.00 2.24
3657 4593 6.424509 TCAAAGAAAAATTATTGCCAGCACAG 59.575 34.615 0.00 0.00 0.00 3.66
3694 4745 1.152440 AAAAATCACCGGGCCACCA 60.152 52.632 6.32 0.00 36.13 4.17
3810 4866 5.763204 TCCCAGATACTTCAACAACTTGTTC 59.237 40.000 4.06 0.00 38.77 3.18
3813 4869 5.997746 TCTTCCCAGATACTTCAACAACTTG 59.002 40.000 0.00 0.00 0.00 3.16
3818 4874 7.037586 AGGTAAATCTTCCCAGATACTTCAACA 60.038 37.037 0.00 0.00 39.00 3.33
3905 4962 8.714179 TGGTGAAAACGACAGTAATATAAACAG 58.286 33.333 0.00 0.00 0.00 3.16
3913 4970 7.660208 AGTCTTAATGGTGAAAACGACAGTAAT 59.340 33.333 0.00 0.00 0.00 1.89
4056 5131 2.038295 CCTGAATCCCTAGATGTGGAGC 59.962 54.545 0.00 0.00 33.27 4.70
4239 5315 3.412386 GCCTTGAAGGTGTGTGACTATT 58.588 45.455 13.58 0.00 37.80 1.73
4254 5330 8.206126 TGATATAAGACATAATGAGGCCTTGA 57.794 34.615 6.77 0.00 0.00 3.02
4257 5333 6.157645 CCCTGATATAAGACATAATGAGGCCT 59.842 42.308 3.86 3.86 0.00 5.19
4261 5337 9.650539 CACTTCCCTGATATAAGACATAATGAG 57.349 37.037 0.00 0.00 0.00 2.90
4263 5339 8.261492 GCACTTCCCTGATATAAGACATAATG 57.739 38.462 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.