Multiple sequence alignment - TraesCS6D01G144600

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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 TraesCS6D01G144600 chr6D 100.000 3488 0 0 1 3488 115052660 115049173 0.000000e+00 6442.0
1 TraesCS6D01G144600 chr6D 81.467 518 73 14 2189 2704 7275548 7276044 1.510000e-108 403.0
2 TraesCS6D01G144600 chr6D 79.174 533 89 14 2189 2720 55142310 55142821 1.990000e-92 350.0
3 TraesCS6D01G144600 chr6D 89.720 107 2 6 692 792 196357892 196357995 1.020000e-25 128.0
4 TraesCS6D01G144600 chr6B 94.277 1293 56 8 1877 3165 204476809 204475531 0.000000e+00 1962.0
5 TraesCS6D01G144600 chr6B 95.658 760 30 2 992 1750 204477563 204476806 0.000000e+00 1218.0
6 TraesCS6D01G144600 chr6B 96.694 242 6 1 3168 3409 204475388 204475149 5.420000e-108 401.0
7 TraesCS6D01G144600 chr6B 97.059 136 4 0 1747 1882 143751346 143751481 2.710000e-56 230.0
8 TraesCS6D01G144600 chr6B 95.652 92 4 0 3397 3488 204467706 204467615 7.800000e-32 148.0
9 TraesCS6D01G144600 chr6B 94.382 89 2 3 703 790 135505590 135505676 2.180000e-27 134.0
10 TraesCS6D01G144600 chr6B 92.593 81 4 2 3 83 204479526 204479448 7.910000e-22 115.0
11 TraesCS6D01G144600 chr6A 92.852 1301 55 12 1877 3165 143452303 143451029 0.000000e+00 1853.0
12 TraesCS6D01G144600 chr6A 96.126 955 29 4 801 1750 143453251 143452300 0.000000e+00 1552.0
13 TraesCS6D01G144600 chr6A 92.476 412 22 8 1 407 143454040 143453633 6.490000e-162 580.0
14 TraesCS6D01G144600 chr6A 95.724 304 13 0 3185 3488 143450883 143450580 1.130000e-134 490.0
15 TraesCS6D01G144600 chr6A 78.669 511 80 16 2192 2699 583877005 583876521 2.610000e-81 313.0
16 TraesCS6D01G144600 chr6A 87.850 107 5 5 692 792 508000844 508000948 6.120000e-23 119.0
17 TraesCS6D01G144600 chr7D 79.811 530 85 14 2192 2720 578174983 578174475 1.980000e-97 366.0
18 TraesCS6D01G144600 chrUn 79.174 533 87 14 2189 2720 260710741 260711250 7.170000e-92 348.0
19 TraesCS6D01G144600 chr4A 79.245 530 85 15 2189 2717 598468011 598468516 2.580000e-91 346.0
20 TraesCS6D01G144600 chr4A 89.381 113 12 0 423 535 298356503 298356391 3.630000e-30 143.0
21 TraesCS6D01G144600 chr4A 86.842 114 10 3 419 532 377054438 377054546 4.730000e-24 122.0
22 TraesCS6D01G144600 chr5A 79.065 535 84 16 2189 2720 647910470 647910979 3.330000e-90 342.0
23 TraesCS6D01G144600 chr5A 97.059 136 4 0 1748 1883 590920459 590920324 2.710000e-56 230.0
24 TraesCS6D01G144600 chr5A 87.850 107 5 5 692 792 560883495 560883391 6.120000e-23 119.0
25 TraesCS6D01G144600 chr3D 79.231 520 86 15 2202 2720 603819712 603819214 3.330000e-90 342.0
26 TraesCS6D01G144600 chr1B 79.057 530 87 14 2192 2720 3506950 3506444 3.330000e-90 342.0
27 TraesCS6D01G144600 chr1B 78.682 516 83 12 2192 2704 16063275 16062784 5.620000e-83 318.0
28 TraesCS6D01G144600 chr1B 95.714 140 6 0 1747 1886 50990079 50990218 3.500000e-55 226.0
29 TraesCS6D01G144600 chr1A 79.223 515 80 13 2192 2704 79272196 79271707 2.010000e-87 333.0
30 TraesCS6D01G144600 chr1A 90.789 152 10 3 1731 1879 285990996 285990846 2.120000e-47 200.0
31 TraesCS6D01G144600 chr1A 90.278 144 13 1 1735 1878 240318244 240318386 1.650000e-43 187.0
32 TraesCS6D01G144600 chr1A 87.850 107 4 6 692 792 527084032 527083929 2.200000e-22 117.0
33 TraesCS6D01G144600 chr7A 78.736 522 82 18 2189 2707 729968135 729968630 4.340000e-84 322.0
34 TraesCS6D01G144600 chr2D 81.132 371 56 9 2189 2555 647308172 647308532 5.700000e-73 285.0
35 TraesCS6D01G144600 chr2D 87.500 128 15 1 423 550 607233472 607233598 2.810000e-31 147.0
36 TraesCS6D01G144600 chr3B 96.000 150 4 2 1747 1896 809457971 809457824 3.480000e-60 243.0
37 TraesCS6D01G144600 chr3B 95.804 143 4 2 1743 1883 153653571 153653429 2.710000e-56 230.0
38 TraesCS6D01G144600 chr3B 90.123 81 7 1 1743 1823 226079733 226079654 1.710000e-18 104.0
39 TraesCS6D01G144600 chr1D 98.529 136 1 1 1743 1878 179435091 179435225 4.500000e-59 239.0
40 TraesCS6D01G144600 chr1D 95.035 141 7 0 1744 1884 407699532 407699392 4.530000e-54 222.0
41 TraesCS6D01G144600 chr2B 98.450 129 2 0 1750 1878 653915258 653915386 9.740000e-56 228.0
42 TraesCS6D01G144600 chr2B 88.750 80 7 2 1734 1813 748596886 748596963 2.870000e-16 97.1
43 TraesCS6D01G144600 chr4B 96.296 135 5 0 1746 1880 536695245 536695111 4.530000e-54 222.0
44 TraesCS6D01G144600 chr5D 89.655 116 11 1 422 536 457550509 457550624 2.810000e-31 147.0
45 TraesCS6D01G144600 chr5D 92.391 92 2 4 710 796 520110184 520110275 3.650000e-25 126.0
46 TraesCS6D01G144600 chr5D 86.066 122 6 8 685 796 513975032 513975152 1.700000e-23 121.0
47 TraesCS6D01G144600 chr2A 88.525 122 13 1 420 540 674085199 674085320 2.810000e-31 147.0
48 TraesCS6D01G144600 chr2A 88.525 122 13 1 420 540 674167677 674167798 2.810000e-31 147.0
49 TraesCS6D01G144600 chr2A 88.785 107 4 5 692 792 65084798 65084902 1.310000e-24 124.0
50 TraesCS6D01G144600 chr3A 91.509 106 8 1 422 526 272996910 272996805 1.010000e-30 145.0
51 TraesCS6D01G144600 chr5B 86.441 118 5 10 700 810 45538262 45538375 6.120000e-23 119.0
52 TraesCS6D01G144600 chr4D 91.566 83 7 0 423 505 172769050 172768968 7.910000e-22 115.0


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 TraesCS6D01G144600 chr6D 115049173 115052660 3487 True 6442.00 6442 100.0000 1 3488 1 chr6D.!!$R1 3487
1 TraesCS6D01G144600 chr6D 55142310 55142821 511 False 350.00 350 79.1740 2189 2720 1 chr6D.!!$F2 531
2 TraesCS6D01G144600 chr6B 204475149 204479526 4377 True 924.00 1962 94.8055 3 3409 4 chr6B.!!$R2 3406
3 TraesCS6D01G144600 chr6A 143450580 143454040 3460 True 1118.75 1853 94.2945 1 3488 4 chr6A.!!$R2 3487
4 TraesCS6D01G144600 chr7D 578174475 578174983 508 True 366.00 366 79.8110 2192 2720 1 chr7D.!!$R1 528
5 TraesCS6D01G144600 chrUn 260710741 260711250 509 False 348.00 348 79.1740 2189 2720 1 chrUn.!!$F1 531
6 TraesCS6D01G144600 chr4A 598468011 598468516 505 False 346.00 346 79.2450 2189 2717 1 chr4A.!!$F2 528
7 TraesCS6D01G144600 chr5A 647910470 647910979 509 False 342.00 342 79.0650 2189 2720 1 chr5A.!!$F1 531
8 TraesCS6D01G144600 chr1B 3506444 3506950 506 True 342.00 342 79.0570 2192 2720 1 chr1B.!!$R1 528

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
501 514 0.038166 TGGGTGGAAAGACATCAGCC 59.962 55.0 0.0 0.0 45.99 4.85 F
518 531 0.107643 GCCCCTTCTCATCACTAGGC 59.892 60.0 0.0 0.0 0.00 3.93 F
1843 3364 0.106469 AGATGCTCCAGCTCCTCGTA 60.106 55.0 0.0 0.0 42.66 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 3345 0.106469 TACGAGGAGCTGGAGCATCT 60.106 55.0 0.0 0.0 45.16 2.90 R
1859 3380 0.178990 AAGGCCCTGTTTGGAGTCAC 60.179 55.0 0.0 0.0 38.35 3.67 R
2673 4205 0.450583 ATGCAATCACGCTCAAGCAG 59.549 50.0 2.5 0.0 42.21 4.24 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
148 153 5.640357 AGAACTAATTGCATTCCGTAAACGA 59.360 36.000 3.65 0.00 43.02 3.85
161 166 0.249953 TAAACGAGCAGCCGGACAAA 60.250 50.000 5.05 0.00 0.00 2.83
217 222 1.956477 GGTTTGCTCAACATGGACAGT 59.044 47.619 0.00 0.00 37.07 3.55
224 229 1.831106 TCAACATGGACAGTCGGCTAT 59.169 47.619 0.00 0.00 0.00 2.97
226 231 3.641436 TCAACATGGACAGTCGGCTATAT 59.359 43.478 0.00 0.00 0.00 0.86
255 260 6.642540 GCAAAAAGCTGAATAAACAAGCTACT 59.357 34.615 0.00 0.00 41.15 2.57
380 388 2.753452 CAAGCACTTGATTCTCATGCCT 59.247 45.455 4.31 0.00 42.93 4.75
381 389 2.366533 AGCACTTGATTCTCATGCCTG 58.633 47.619 0.00 0.00 33.99 4.85
383 391 1.404391 CACTTGATTCTCATGCCTGGC 59.596 52.381 12.87 12.87 0.00 4.85
397 410 5.660417 TCATGCCTGGCCTTGATTTTATTTA 59.340 36.000 17.53 0.00 0.00 1.40
398 411 6.327104 TCATGCCTGGCCTTGATTTTATTTAT 59.673 34.615 17.53 0.00 0.00 1.40
401 414 7.047271 TGCCTGGCCTTGATTTTATTTATTTC 58.953 34.615 17.53 0.00 0.00 2.17
439 452 8.491958 ACTAAAAGACCCCTACAGTATAATTGG 58.508 37.037 0.00 0.00 0.00 3.16
440 453 6.903340 AAAGACCCCTACAGTATAATTGGT 57.097 37.500 0.00 0.00 0.00 3.67
441 454 8.396619 AAAAGACCCCTACAGTATAATTGGTA 57.603 34.615 0.00 0.00 0.00 3.25
442 455 6.990908 AGACCCCTACAGTATAATTGGTAC 57.009 41.667 0.00 0.00 0.00 3.34
443 456 6.446451 AGACCCCTACAGTATAATTGGTACA 58.554 40.000 0.00 0.00 0.00 2.90
460 473 6.540438 TGGTACAACAAACCCAAATTGTAA 57.460 33.333 0.00 0.00 39.98 2.41
462 475 6.154706 TGGTACAACAAACCCAAATTGTAAGT 59.845 34.615 0.00 0.00 39.98 2.24
463 476 7.341256 TGGTACAACAAACCCAAATTGTAAGTA 59.659 33.333 0.00 0.00 39.98 2.24
465 478 6.575267 ACAACAAACCCAAATTGTAAGTACC 58.425 36.000 0.00 0.00 39.98 3.34
466 479 6.154706 ACAACAAACCCAAATTGTAAGTACCA 59.845 34.615 0.00 0.00 39.98 3.25
468 481 8.361139 CAACAAACCCAAATTGTAAGTACCATA 58.639 33.333 0.00 0.00 39.98 2.74
469 482 7.888424 ACAAACCCAAATTGTAAGTACCATAC 58.112 34.615 0.00 0.00 39.14 2.39
470 483 7.039574 ACAAACCCAAATTGTAAGTACCATACC 60.040 37.037 4.49 0.00 39.14 2.73
475 488 9.245481 CCCAAATTGTAAGTACCATACCTTAAA 57.755 33.333 4.49 0.00 0.00 1.52
479 492 9.457436 AATTGTAAGTACCATACCTTAAACCTG 57.543 33.333 4.49 0.00 0.00 4.00
480 493 7.795534 TGTAAGTACCATACCTTAAACCTGA 57.204 36.000 4.49 0.00 0.00 3.86
481 494 7.844009 TGTAAGTACCATACCTTAAACCTGAG 58.156 38.462 4.49 0.00 0.00 3.35
482 495 6.947376 AAGTACCATACCTTAAACCTGAGT 57.053 37.500 0.00 0.00 0.00 3.41
484 497 4.569719 ACCATACCTTAAACCTGAGTGG 57.430 45.455 0.00 0.00 42.93 4.00
485 498 3.265995 ACCATACCTTAAACCTGAGTGGG 59.734 47.826 0.00 0.00 41.11 4.61
486 499 3.265995 CCATACCTTAAACCTGAGTGGGT 59.734 47.826 0.00 0.00 42.05 4.51
487 500 2.951229 ACCTTAAACCTGAGTGGGTG 57.049 50.000 0.00 0.00 39.85 4.61
488 501 1.423921 ACCTTAAACCTGAGTGGGTGG 59.576 52.381 0.00 0.00 39.85 4.61
489 502 1.702957 CCTTAAACCTGAGTGGGTGGA 59.297 52.381 0.00 0.00 39.85 4.02
491 504 3.435890 CCTTAAACCTGAGTGGGTGGAAA 60.436 47.826 0.00 0.00 39.85 3.13
492 505 2.364972 AAACCTGAGTGGGTGGAAAG 57.635 50.000 0.00 0.00 39.85 2.62
493 506 1.518367 AACCTGAGTGGGTGGAAAGA 58.482 50.000 0.00 0.00 39.85 2.52
494 507 0.765510 ACCTGAGTGGGTGGAAAGAC 59.234 55.000 0.00 0.00 41.11 3.01
496 509 1.352352 CCTGAGTGGGTGGAAAGACAT 59.648 52.381 0.00 0.00 0.00 3.06
497 510 2.616510 CCTGAGTGGGTGGAAAGACATC 60.617 54.545 0.00 0.00 0.00 3.06
498 511 2.038952 CTGAGTGGGTGGAAAGACATCA 59.961 50.000 0.00 0.00 0.00 3.07
499 512 2.038952 TGAGTGGGTGGAAAGACATCAG 59.961 50.000 0.00 0.00 0.00 2.90
500 513 1.168714 GTGGGTGGAAAGACATCAGC 58.831 55.000 0.00 0.00 0.00 4.26
501 514 0.038166 TGGGTGGAAAGACATCAGCC 59.962 55.000 0.00 0.00 45.99 4.85
502 515 0.681243 GGGTGGAAAGACATCAGCCC 60.681 60.000 0.00 0.00 41.62 5.19
504 517 0.329596 GTGGAAAGACATCAGCCCCT 59.670 55.000 0.00 0.00 0.00 4.79
505 518 1.075601 TGGAAAGACATCAGCCCCTT 58.924 50.000 0.00 0.00 0.00 3.95
507 520 1.283321 GGAAAGACATCAGCCCCTTCT 59.717 52.381 0.00 0.00 0.00 2.85
508 521 2.637947 GAAAGACATCAGCCCCTTCTC 58.362 52.381 0.00 0.00 0.00 2.87
509 522 1.661463 AAGACATCAGCCCCTTCTCA 58.339 50.000 0.00 0.00 0.00 3.27
510 523 1.890552 AGACATCAGCCCCTTCTCAT 58.109 50.000 0.00 0.00 0.00 2.90
511 524 1.767681 AGACATCAGCCCCTTCTCATC 59.232 52.381 0.00 0.00 0.00 2.92
512 525 1.487976 GACATCAGCCCCTTCTCATCA 59.512 52.381 0.00 0.00 0.00 3.07
513 526 1.211457 ACATCAGCCCCTTCTCATCAC 59.789 52.381 0.00 0.00 0.00 3.06
514 527 1.489649 CATCAGCCCCTTCTCATCACT 59.510 52.381 0.00 0.00 0.00 3.41
515 528 2.550277 TCAGCCCCTTCTCATCACTA 57.450 50.000 0.00 0.00 0.00 2.74
517 530 1.415659 CAGCCCCTTCTCATCACTAGG 59.584 57.143 0.00 0.00 0.00 3.02
518 531 0.107643 GCCCCTTCTCATCACTAGGC 59.892 60.000 0.00 0.00 0.00 3.93
520 533 2.964209 CCCCTTCTCATCACTAGGCTA 58.036 52.381 0.00 0.00 0.00 3.93
521 534 3.515562 CCCCTTCTCATCACTAGGCTAT 58.484 50.000 0.00 0.00 0.00 2.97
522 535 3.260380 CCCCTTCTCATCACTAGGCTATG 59.740 52.174 0.00 0.00 0.00 2.23
695 2209 5.580998 TGTGCAACCCCCACTAATTATTAA 58.419 37.500 0.00 0.00 34.36 1.40
736 2250 7.927092 ACTTCCTCCGTAAAGAAATATAAGAGC 59.073 37.037 0.00 0.00 0.00 4.09
737 2251 6.444633 TCCTCCGTAAAGAAATATAAGAGCG 58.555 40.000 0.00 0.00 0.00 5.03
738 2252 6.040166 TCCTCCGTAAAGAAATATAAGAGCGT 59.960 38.462 0.00 0.00 0.00 5.07
739 2253 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
740 2254 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
741 2255 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
742 2256 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
743 2257 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
755 2269 9.988815 ATAAGAGCGTTTAGATTCATTAGTGAT 57.011 29.630 0.00 0.00 33.56 3.06
756 2270 7.938563 AGAGCGTTTAGATTCATTAGTGATC 57.061 36.000 0.00 0.00 33.56 2.92
757 2271 7.721402 AGAGCGTTTAGATTCATTAGTGATCT 58.279 34.615 0.00 0.00 33.56 2.75
758 2272 8.851145 AGAGCGTTTAGATTCATTAGTGATCTA 58.149 33.333 0.00 0.00 33.56 1.98
759 2273 9.464714 GAGCGTTTAGATTCATTAGTGATCTAA 57.535 33.333 12.10 12.10 39.95 2.10
760 2274 9.817809 AGCGTTTAGATTCATTAGTGATCTAAA 57.182 29.630 18.21 18.21 39.21 1.85
761 2275 9.851043 GCGTTTAGATTCATTAGTGATCTAAAC 57.149 33.333 27.19 27.19 45.37 2.01
765 2279 9.745880 TTAGATTCATTAGTGATCTAAACGGTC 57.254 33.333 13.01 0.00 39.23 4.79
766 2280 8.012957 AGATTCATTAGTGATCTAAACGGTCT 57.987 34.615 0.00 0.00 39.23 3.85
767 2281 8.478877 AGATTCATTAGTGATCTAAACGGTCTT 58.521 33.333 0.00 0.00 39.23 3.01
768 2282 9.745880 GATTCATTAGTGATCTAAACGGTCTTA 57.254 33.333 0.00 0.00 39.23 2.10
784 2298 8.943909 AACGGTCTTATATTTCTTTACAGAGG 57.056 34.615 0.00 0.00 0.00 3.69
785 2299 7.498443 ACGGTCTTATATTTCTTTACAGAGGG 58.502 38.462 0.00 0.00 0.00 4.30
786 2300 7.343833 ACGGTCTTATATTTCTTTACAGAGGGA 59.656 37.037 0.00 0.00 0.00 4.20
787 2301 7.868415 CGGTCTTATATTTCTTTACAGAGGGAG 59.132 40.741 0.00 0.00 0.00 4.30
788 2302 8.706521 GGTCTTATATTTCTTTACAGAGGGAGT 58.293 37.037 0.00 0.00 0.00 3.85
796 2310 8.804912 TTTCTTTACAGAGGGAGTACTAGTAG 57.195 38.462 1.87 0.00 0.00 2.57
878 2392 0.568192 CCTCCCTTCCCTCCTCCATA 59.432 60.000 0.00 0.00 0.00 2.74
879 2393 1.484065 CCTCCCTTCCCTCCTCCATAG 60.484 61.905 0.00 0.00 0.00 2.23
880 2394 1.221781 CTCCCTTCCCTCCTCCATAGT 59.778 57.143 0.00 0.00 0.00 2.12
881 2395 2.451273 CTCCCTTCCCTCCTCCATAGTA 59.549 54.545 0.00 0.00 0.00 1.82
882 2396 3.078305 CTCCCTTCCCTCCTCCATAGTAT 59.922 52.174 0.00 0.00 0.00 2.12
884 2398 3.841255 CCCTTCCCTCCTCCATAGTATTC 59.159 52.174 0.00 0.00 0.00 1.75
885 2399 4.451460 CCCTTCCCTCCTCCATAGTATTCT 60.451 50.000 0.00 0.00 0.00 2.40
886 2400 4.775253 CCTTCCCTCCTCCATAGTATTCTC 59.225 50.000 0.00 0.00 0.00 2.87
926 2441 1.398799 AGGAGGGAAGAGAAGAGGGA 58.601 55.000 0.00 0.00 0.00 4.20
927 2442 1.007842 AGGAGGGAAGAGAAGAGGGAC 59.992 57.143 0.00 0.00 0.00 4.46
981 2498 1.005450 ACACCTCTCTCTCTCCCACTC 59.995 57.143 0.00 0.00 0.00 3.51
982 2499 1.284785 CACCTCTCTCTCTCCCACTCT 59.715 57.143 0.00 0.00 0.00 3.24
983 2500 1.564348 ACCTCTCTCTCTCCCACTCTC 59.436 57.143 0.00 0.00 0.00 3.20
1013 2530 4.116238 GAGAAAATGATGACGAGGTCTCC 58.884 47.826 0.00 0.00 33.15 3.71
1093 2610 2.750637 GGGTCAGCTCGTCCGAGA 60.751 66.667 20.07 0.00 44.53 4.04
1398 2915 1.585006 GGACGACTTCTTGAGCCGA 59.415 57.895 0.00 0.00 0.00 5.54
1480 2997 0.307760 CCAACCAACAACTGACGAGC 59.692 55.000 0.00 0.00 0.00 5.03
1497 3017 2.976509 CGAGCAGTACTTCATATCGCAG 59.023 50.000 0.00 0.00 0.00 5.18
1645 3166 6.502136 AGTTTGTGAGAATTTTAGCTAGCC 57.498 37.500 12.13 0.00 0.00 3.93
1659 3180 1.202818 GCTAGCCACCATCCTTTAGGG 60.203 57.143 2.29 0.00 35.41 3.53
1756 3277 5.598416 TGTACATCACATCTTAGGTCCTG 57.402 43.478 0.00 0.00 30.04 3.86
1757 3278 5.023452 TGTACATCACATCTTAGGTCCTGT 58.977 41.667 0.00 0.00 30.04 4.00
1758 3279 5.483937 TGTACATCACATCTTAGGTCCTGTT 59.516 40.000 0.00 0.00 30.04 3.16
1759 3280 5.091261 ACATCACATCTTAGGTCCTGTTC 57.909 43.478 0.00 0.00 0.00 3.18
1760 3281 3.868757 TCACATCTTAGGTCCTGTTCG 57.131 47.619 0.00 0.00 0.00 3.95
1761 3282 2.496070 TCACATCTTAGGTCCTGTTCGG 59.504 50.000 0.00 0.00 0.00 4.30
1762 3283 2.496070 CACATCTTAGGTCCTGTTCGGA 59.504 50.000 0.00 0.00 40.30 4.55
1763 3284 2.761208 ACATCTTAGGTCCTGTTCGGAG 59.239 50.000 0.00 0.00 44.20 4.63
1764 3285 2.893215 TCTTAGGTCCTGTTCGGAGA 57.107 50.000 0.00 0.00 44.20 3.71
1765 3286 2.444421 TCTTAGGTCCTGTTCGGAGAC 58.556 52.381 0.00 0.00 44.20 3.36
1767 3288 2.979649 GGTCCTGTTCGGAGACCC 59.020 66.667 3.41 0.00 44.20 4.46
1778 3299 4.083862 GAGACCCGCCACTCCACC 62.084 72.222 0.00 0.00 0.00 4.61
1779 3300 4.954118 AGACCCGCCACTCCACCA 62.954 66.667 0.00 0.00 0.00 4.17
1780 3301 4.699522 GACCCGCCACTCCACCAC 62.700 72.222 0.00 0.00 0.00 4.16
1782 3303 4.394712 CCCGCCACTCCACCACTC 62.395 72.222 0.00 0.00 0.00 3.51
1783 3304 4.394712 CCGCCACTCCACCACTCC 62.395 72.222 0.00 0.00 0.00 3.85
1784 3305 4.742201 CGCCACTCCACCACTCCG 62.742 72.222 0.00 0.00 0.00 4.63
1786 3307 3.314331 CCACTCCACCACTCCGCT 61.314 66.667 0.00 0.00 0.00 5.52
1787 3308 2.262915 CACTCCACCACTCCGCTC 59.737 66.667 0.00 0.00 0.00 5.03
1788 3309 2.997897 ACTCCACCACTCCGCTCC 60.998 66.667 0.00 0.00 0.00 4.70
1789 3310 3.775654 CTCCACCACTCCGCTCCC 61.776 72.222 0.00 0.00 0.00 4.30
1802 3323 4.113617 CTCCCGGAGTTGGAGTCA 57.886 61.111 0.73 0.00 43.68 3.41
1803 3324 2.362242 CTCCCGGAGTTGGAGTCAA 58.638 57.895 0.73 0.00 43.68 3.18
1804 3325 0.685097 CTCCCGGAGTTGGAGTCAAA 59.315 55.000 0.73 0.00 43.68 2.69
1805 3326 1.071699 CTCCCGGAGTTGGAGTCAAAA 59.928 52.381 0.73 0.00 43.68 2.44
1806 3327 1.071699 TCCCGGAGTTGGAGTCAAAAG 59.928 52.381 0.73 0.00 34.28 2.27
1807 3328 1.523758 CCGGAGTTGGAGTCAAAAGG 58.476 55.000 0.00 0.00 34.28 3.11
1808 3329 0.875059 CGGAGTTGGAGTCAAAAGGC 59.125 55.000 0.00 0.00 34.28 4.35
1809 3330 1.813862 CGGAGTTGGAGTCAAAAGGCA 60.814 52.381 0.00 0.00 34.28 4.75
1810 3331 1.609072 GGAGTTGGAGTCAAAAGGCAC 59.391 52.381 0.00 0.00 34.28 5.01
1811 3332 1.264288 GAGTTGGAGTCAAAAGGCACG 59.736 52.381 0.00 0.00 34.28 5.34
1812 3333 0.310854 GTTGGAGTCAAAAGGCACGG 59.689 55.000 0.00 0.00 34.28 4.94
1813 3334 0.181587 TTGGAGTCAAAAGGCACGGA 59.818 50.000 0.00 0.00 0.00 4.69
1814 3335 0.250295 TGGAGTCAAAAGGCACGGAG 60.250 55.000 0.00 0.00 0.00 4.63
1815 3336 1.578206 GGAGTCAAAAGGCACGGAGC 61.578 60.000 0.00 0.00 44.65 4.70
1816 3337 0.603975 GAGTCAAAAGGCACGGAGCT 60.604 55.000 0.00 0.00 44.79 4.09
1817 3338 0.886490 AGTCAAAAGGCACGGAGCTG 60.886 55.000 0.00 0.00 44.79 4.24
1818 3339 1.600636 TCAAAAGGCACGGAGCTGG 60.601 57.895 0.00 0.00 44.79 4.85
1819 3340 2.282462 AAAAGGCACGGAGCTGGG 60.282 61.111 0.00 0.00 44.79 4.45
1820 3341 2.829384 AAAAGGCACGGAGCTGGGA 61.829 57.895 0.00 0.00 44.79 4.37
1821 3342 2.351924 AAAAGGCACGGAGCTGGGAA 62.352 55.000 0.00 0.00 44.79 3.97
1822 3343 2.351924 AAAGGCACGGAGCTGGGAAA 62.352 55.000 0.00 0.00 44.79 3.13
1823 3344 2.747855 GGCACGGAGCTGGGAAAG 60.748 66.667 0.00 0.00 44.79 2.62
1824 3345 2.347490 GCACGGAGCTGGGAAAGA 59.653 61.111 0.00 0.00 41.15 2.52
1825 3346 1.743252 GCACGGAGCTGGGAAAGAG 60.743 63.158 0.00 0.00 41.15 2.85
1826 3347 1.975327 CACGGAGCTGGGAAAGAGA 59.025 57.895 0.00 0.00 0.00 3.10
1827 3348 0.539051 CACGGAGCTGGGAAAGAGAT 59.461 55.000 0.00 0.00 0.00 2.75
1828 3349 0.539051 ACGGAGCTGGGAAAGAGATG 59.461 55.000 0.00 0.00 0.00 2.90
1829 3350 0.813210 CGGAGCTGGGAAAGAGATGC 60.813 60.000 0.00 0.00 0.00 3.91
1830 3351 0.545646 GGAGCTGGGAAAGAGATGCT 59.454 55.000 0.00 0.00 0.00 3.79
1831 3352 1.474855 GGAGCTGGGAAAGAGATGCTC 60.475 57.143 0.00 0.00 44.08 4.26
1832 3353 0.545646 AGCTGGGAAAGAGATGCTCC 59.454 55.000 0.00 0.00 0.00 4.70
1833 3354 0.254178 GCTGGGAAAGAGATGCTCCA 59.746 55.000 0.00 0.00 0.00 3.86
1834 3355 1.746516 GCTGGGAAAGAGATGCTCCAG 60.747 57.143 0.00 0.00 43.20 3.86
1835 3356 0.254178 TGGGAAAGAGATGCTCCAGC 59.746 55.000 0.00 0.00 42.50 4.85
1836 3357 0.545646 GGGAAAGAGATGCTCCAGCT 59.454 55.000 0.00 0.00 42.66 4.24
1837 3358 1.474855 GGGAAAGAGATGCTCCAGCTC 60.475 57.143 2.47 2.47 45.85 4.09
1838 3359 1.474855 GGAAAGAGATGCTCCAGCTCC 60.475 57.143 6.85 0.00 46.56 4.70
1839 3360 1.485895 GAAAGAGATGCTCCAGCTCCT 59.514 52.381 6.85 0.00 46.56 3.69
1840 3361 1.122227 AAGAGATGCTCCAGCTCCTC 58.878 55.000 6.85 10.76 46.56 3.71
1841 3362 1.108727 AGAGATGCTCCAGCTCCTCG 61.109 60.000 6.85 0.00 46.56 4.63
1842 3363 1.381056 AGATGCTCCAGCTCCTCGT 60.381 57.895 0.00 0.00 42.66 4.18
1843 3364 0.106469 AGATGCTCCAGCTCCTCGTA 60.106 55.000 0.00 0.00 42.66 3.43
1844 3365 0.965439 GATGCTCCAGCTCCTCGTAT 59.035 55.000 0.00 0.00 42.66 3.06
1845 3366 1.342819 GATGCTCCAGCTCCTCGTATT 59.657 52.381 0.00 0.00 42.66 1.89
1846 3367 1.195115 TGCTCCAGCTCCTCGTATTT 58.805 50.000 0.00 0.00 42.66 1.40
1847 3368 1.555075 TGCTCCAGCTCCTCGTATTTT 59.445 47.619 0.00 0.00 42.66 1.82
1848 3369 2.027192 TGCTCCAGCTCCTCGTATTTTT 60.027 45.455 0.00 0.00 42.66 1.94
1849 3370 3.196901 TGCTCCAGCTCCTCGTATTTTTA 59.803 43.478 0.00 0.00 42.66 1.52
1850 3371 3.804873 GCTCCAGCTCCTCGTATTTTTAG 59.195 47.826 0.00 0.00 38.21 1.85
1851 3372 4.372656 CTCCAGCTCCTCGTATTTTTAGG 58.627 47.826 0.00 0.00 0.00 2.69
1852 3373 4.028131 TCCAGCTCCTCGTATTTTTAGGA 58.972 43.478 0.00 0.00 37.07 2.94
1859 3380 5.974108 TCCTCGTATTTTTAGGAGTTGGAG 58.026 41.667 0.00 0.00 34.46 3.86
1860 3381 5.482878 TCCTCGTATTTTTAGGAGTTGGAGT 59.517 40.000 0.00 0.00 34.46 3.85
1861 3382 5.581085 CCTCGTATTTTTAGGAGTTGGAGTG 59.419 44.000 0.00 0.00 31.94 3.51
1862 3383 6.349243 TCGTATTTTTAGGAGTTGGAGTGA 57.651 37.500 0.00 0.00 0.00 3.41
1863 3384 6.161381 TCGTATTTTTAGGAGTTGGAGTGAC 58.839 40.000 0.00 0.00 0.00 3.67
1864 3385 6.014840 TCGTATTTTTAGGAGTTGGAGTGACT 60.015 38.462 0.00 0.00 0.00 3.41
1865 3386 6.310711 CGTATTTTTAGGAGTTGGAGTGACTC 59.689 42.308 3.47 3.47 42.16 3.36
1875 3396 2.934083 GAGTGACTCCAAACAGGGC 58.066 57.895 0.00 0.00 38.24 5.19
1876 3397 0.606673 GAGTGACTCCAAACAGGGCC 60.607 60.000 0.00 0.00 38.24 5.80
1877 3398 1.062488 AGTGACTCCAAACAGGGCCT 61.062 55.000 0.00 0.00 38.24 5.19
1878 3399 0.178990 GTGACTCCAAACAGGGCCTT 60.179 55.000 1.32 0.00 38.24 4.35
1879 3400 1.073284 GTGACTCCAAACAGGGCCTTA 59.927 52.381 1.32 0.00 38.24 2.69
1957 3478 1.576272 AGGGGTAGGTCTACAGCTGAT 59.424 52.381 23.35 7.41 37.78 2.90
2074 3595 5.646793 CCATGATTATGTATTCCTGGAGCAG 59.353 44.000 0.00 0.00 31.47 4.24
2096 3618 5.048083 CAGAGCCTAGTTCAGCTATCCTTAG 60.048 48.000 0.00 0.00 40.11 2.18
2121 3643 6.128418 GGAAAGCAGAAGACAGATAAGTTGTC 60.128 42.308 0.00 0.00 44.09 3.18
2187 3712 1.134310 CACTCATCCCAGCATAGCACA 60.134 52.381 0.00 0.00 0.00 4.57
2248 3773 5.510520 GGCTCCTGGTGAATTCAGTCTATAG 60.511 48.000 8.80 4.07 0.00 1.31
2290 3816 4.162698 ACAAGGAACAGTACACTAACCACA 59.837 41.667 0.00 0.00 0.00 4.17
2293 3819 2.144482 ACAGTACACTAACCACACGC 57.856 50.000 0.00 0.00 0.00 5.34
2397 3923 0.878523 TGGACGACCACGCTGAAAAG 60.879 55.000 1.37 0.00 41.77 2.27
2469 3995 2.367202 GCCGATGTCCTTCTCCCCA 61.367 63.158 0.00 0.00 0.00 4.96
2518 4044 2.771435 CGTGATGCCATCAAGCTGA 58.229 52.632 9.36 0.00 41.69 4.26
2618 4148 4.736126 AAAAAGGTTTCTGAACTGTGGG 57.264 40.909 0.00 0.00 36.03 4.61
2673 4205 2.221169 TGTCCACTGCAAGATGTTCAC 58.779 47.619 0.00 0.00 37.43 3.18
2731 4263 4.966805 AGGGGTAACTATGCTAGCACTTAA 59.033 41.667 22.07 5.13 25.69 1.85
2811 4344 0.894835 AAACGCTTAATTGGCCTGGG 59.105 50.000 3.32 0.00 0.00 4.45
2848 4381 8.887717 CATTAACAAACTTCTTCTGAGGGATAG 58.112 37.037 0.00 0.00 0.00 2.08
2877 4414 8.766994 AATTTATAGGTGGCATTTCAGTACAT 57.233 30.769 0.00 0.00 0.00 2.29
3040 4579 1.815613 TGCACCCACATTATTGTTCCG 59.184 47.619 0.00 0.00 32.34 4.30
3086 4626 1.270625 TGTTCCCTTGTGGTCACGATC 60.271 52.381 0.00 0.00 34.77 3.69
3124 4664 8.084684 ACTGGAAGCTTAAAATTCAATCTTGAC 58.915 33.333 0.00 0.00 37.60 3.18
3165 4707 6.655003 CACTGGAAGCTTAAAACTCAATCCTA 59.345 38.462 0.00 0.00 37.60 2.94
3166 4708 6.655425 ACTGGAAGCTTAAAACTCAATCCTAC 59.345 38.462 0.00 0.00 37.60 3.18
3352 5094 2.154567 AAGTGCTCCCAGGATACGTA 57.845 50.000 0.00 0.00 46.39 3.57
3360 5102 4.142093 GCTCCCAGGATACGTACAAGTTAA 60.142 45.833 0.00 0.00 46.39 2.01
3423 5165 3.984732 GGCCACCTTTCAGGGGCT 61.985 66.667 17.05 0.00 45.41 5.19
3437 5179 0.109532 GGGGCTATGAAGGGAAGCTC 59.890 60.000 0.00 0.00 35.93 4.09
3438 5180 0.250081 GGGCTATGAAGGGAAGCTCG 60.250 60.000 0.00 0.00 36.48 5.03
3452 5194 0.033228 AGCTCGCCATCATAGCTGTC 59.967 55.000 0.00 0.00 44.67 3.51
3457 5199 0.940126 GCCATCATAGCTGTCCGTTG 59.060 55.000 0.00 0.00 0.00 4.10
3460 5202 1.854743 CATCATAGCTGTCCGTTGTCG 59.145 52.381 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.729868 CGGATTTGGGGAAAGATATCCTT 58.270 43.478 0.00 0.00 39.57 3.36
71 72 7.388500 ACATGCCTTTGTTTTCATTTATTCTGG 59.612 33.333 0.00 0.00 0.00 3.86
73 74 8.149647 TCACATGCCTTTGTTTTCATTTATTCT 58.850 29.630 0.00 0.00 0.00 2.40
148 153 2.985847 GGCTTTTGTCCGGCTGCT 60.986 61.111 0.00 0.00 0.00 4.24
203 208 0.036952 AGCCGACTGTCCATGTTGAG 60.037 55.000 1.55 0.00 0.00 3.02
217 222 4.455533 CAGCTTTTTGCCATATATAGCCGA 59.544 41.667 0.47 0.00 44.23 5.54
224 229 9.585099 CTTGTTTATTCAGCTTTTTGCCATATA 57.415 29.630 0.00 0.00 44.23 0.86
226 231 6.368516 GCTTGTTTATTCAGCTTTTTGCCATA 59.631 34.615 0.00 0.00 44.23 2.74
255 260 6.597562 AGTAGGAAAAGTTTCATGTGTACCA 58.402 36.000 6.15 0.00 38.92 3.25
319 325 4.467795 AGCACTTTAGCTTCCACTCTATGA 59.532 41.667 0.00 0.00 43.70 2.15
413 426 8.491958 CCAATTATACTGTAGGGGTCTTTTAGT 58.508 37.037 0.00 0.00 0.00 2.24
414 427 8.491958 ACCAATTATACTGTAGGGGTCTTTTAG 58.508 37.037 0.00 0.00 0.00 1.85
415 428 8.396619 ACCAATTATACTGTAGGGGTCTTTTA 57.603 34.615 0.00 0.00 0.00 1.52
416 429 7.280044 ACCAATTATACTGTAGGGGTCTTTT 57.720 36.000 0.00 0.00 0.00 2.27
420 433 6.736110 TGTACCAATTATACTGTAGGGGTC 57.264 41.667 0.00 0.00 0.00 4.46
421 434 6.444493 TGTTGTACCAATTATACTGTAGGGGT 59.556 38.462 0.00 0.00 0.00 4.95
422 435 6.891388 TGTTGTACCAATTATACTGTAGGGG 58.109 40.000 0.00 0.00 0.00 4.79
423 436 8.671028 GTTTGTTGTACCAATTATACTGTAGGG 58.329 37.037 0.00 0.00 0.00 3.53
424 437 8.671028 GGTTTGTTGTACCAATTATACTGTAGG 58.329 37.037 0.00 0.00 35.67 3.18
425 438 8.671028 GGGTTTGTTGTACCAATTATACTGTAG 58.329 37.037 0.00 0.00 37.40 2.74
426 439 8.162085 TGGGTTTGTTGTACCAATTATACTGTA 58.838 33.333 0.00 0.00 37.40 2.74
427 440 7.005296 TGGGTTTGTTGTACCAATTATACTGT 58.995 34.615 0.00 0.00 37.40 3.55
428 441 7.455641 TGGGTTTGTTGTACCAATTATACTG 57.544 36.000 0.00 0.00 37.40 2.74
430 443 9.713713 AATTTGGGTTTGTTGTACCAATTATAC 57.286 29.630 0.00 0.00 42.09 1.47
431 444 9.712305 CAATTTGGGTTTGTTGTACCAATTATA 57.288 29.630 0.00 0.00 42.09 0.98
432 445 8.214364 ACAATTTGGGTTTGTTGTACCAATTAT 58.786 29.630 0.78 0.00 42.09 1.28
433 446 7.565680 ACAATTTGGGTTTGTTGTACCAATTA 58.434 30.769 0.78 0.00 42.09 1.40
434 447 6.418946 ACAATTTGGGTTTGTTGTACCAATT 58.581 32.000 0.78 0.00 42.09 2.32
435 448 5.995446 ACAATTTGGGTTTGTTGTACCAAT 58.005 33.333 0.78 0.00 42.09 3.16
436 449 5.422214 ACAATTTGGGTTTGTTGTACCAA 57.578 34.783 0.78 0.00 40.94 3.67
437 450 6.154706 ACTTACAATTTGGGTTTGTTGTACCA 59.845 34.615 0.78 0.00 36.93 3.25
438 451 6.575267 ACTTACAATTTGGGTTTGTTGTACC 58.425 36.000 0.78 0.00 36.93 3.34
439 452 7.648908 GGTACTTACAATTTGGGTTTGTTGTAC 59.351 37.037 15.83 15.83 40.37 2.90
440 453 7.341256 TGGTACTTACAATTTGGGTTTGTTGTA 59.659 33.333 0.78 0.00 38.26 2.41
441 454 6.154706 TGGTACTTACAATTTGGGTTTGTTGT 59.845 34.615 0.78 0.00 38.26 3.32
442 455 6.574350 TGGTACTTACAATTTGGGTTTGTTG 58.426 36.000 0.78 0.00 38.26 3.33
443 456 6.793505 TGGTACTTACAATTTGGGTTTGTT 57.206 33.333 0.78 0.00 38.26 2.83
445 458 7.177744 AGGTATGGTACTTACAATTTGGGTTTG 59.822 37.037 0.78 0.00 0.00 2.93
446 459 7.243091 AGGTATGGTACTTACAATTTGGGTTT 58.757 34.615 0.78 0.00 0.00 3.27
447 460 6.796648 AGGTATGGTACTTACAATTTGGGTT 58.203 36.000 0.78 0.00 0.00 4.11
448 461 6.397217 AGGTATGGTACTTACAATTTGGGT 57.603 37.500 0.78 0.07 0.00 4.51
449 462 8.810990 TTAAGGTATGGTACTTACAATTTGGG 57.189 34.615 0.78 0.00 0.00 4.12
454 467 8.828751 TCAGGTTTAAGGTATGGTACTTACAAT 58.171 33.333 0.00 0.00 0.00 2.71
455 468 8.204903 TCAGGTTTAAGGTATGGTACTTACAA 57.795 34.615 0.00 0.00 0.00 2.41
456 469 7.455638 ACTCAGGTTTAAGGTATGGTACTTACA 59.544 37.037 0.00 0.00 0.00 2.41
457 470 7.763071 CACTCAGGTTTAAGGTATGGTACTTAC 59.237 40.741 0.00 0.00 0.00 2.34
460 473 5.189145 CCACTCAGGTTTAAGGTATGGTACT 59.811 44.000 0.00 0.00 0.00 2.73
462 475 4.472108 CCCACTCAGGTTTAAGGTATGGTA 59.528 45.833 0.00 0.00 34.66 3.25
463 476 3.265995 CCCACTCAGGTTTAAGGTATGGT 59.734 47.826 0.00 0.00 34.66 3.55
465 478 4.261801 CACCCACTCAGGTTTAAGGTATG 58.738 47.826 0.00 0.00 38.39 2.39
466 479 3.265995 CCACCCACTCAGGTTTAAGGTAT 59.734 47.826 0.00 0.00 38.39 2.73
468 481 1.423921 CCACCCACTCAGGTTTAAGGT 59.576 52.381 0.00 0.00 38.39 3.50
469 482 1.702957 TCCACCCACTCAGGTTTAAGG 59.297 52.381 0.00 0.00 38.39 2.69
470 483 3.502123 TTCCACCCACTCAGGTTTAAG 57.498 47.619 0.00 0.00 38.39 1.85
475 488 0.765510 GTCTTTCCACCCACTCAGGT 59.234 55.000 0.00 0.00 42.40 4.00
476 489 0.764890 TGTCTTTCCACCCACTCAGG 59.235 55.000 0.00 0.00 37.03 3.86
477 490 2.038952 TGATGTCTTTCCACCCACTCAG 59.961 50.000 0.00 0.00 0.00 3.35
479 492 2.704572 CTGATGTCTTTCCACCCACTC 58.295 52.381 0.00 0.00 0.00 3.51
480 493 1.271597 GCTGATGTCTTTCCACCCACT 60.272 52.381 0.00 0.00 0.00 4.00
481 494 1.168714 GCTGATGTCTTTCCACCCAC 58.831 55.000 0.00 0.00 0.00 4.61
482 495 0.038166 GGCTGATGTCTTTCCACCCA 59.962 55.000 0.00 0.00 0.00 4.51
484 497 0.681243 GGGGCTGATGTCTTTCCACC 60.681 60.000 0.00 0.00 0.00 4.61
485 498 0.329596 AGGGGCTGATGTCTTTCCAC 59.670 55.000 0.00 0.00 0.00 4.02
486 499 1.004745 GAAGGGGCTGATGTCTTTCCA 59.995 52.381 0.00 0.00 0.00 3.53
487 500 1.283321 AGAAGGGGCTGATGTCTTTCC 59.717 52.381 0.00 0.00 0.00 3.13
488 501 2.026822 TGAGAAGGGGCTGATGTCTTTC 60.027 50.000 0.00 0.00 0.00 2.62
489 502 1.988107 TGAGAAGGGGCTGATGTCTTT 59.012 47.619 0.00 0.00 0.00 2.52
491 504 1.767681 GATGAGAAGGGGCTGATGTCT 59.232 52.381 0.00 0.00 0.00 3.41
492 505 1.487976 TGATGAGAAGGGGCTGATGTC 59.512 52.381 0.00 0.00 0.00 3.06
493 506 1.211457 GTGATGAGAAGGGGCTGATGT 59.789 52.381 0.00 0.00 0.00 3.06
494 507 1.489649 AGTGATGAGAAGGGGCTGATG 59.510 52.381 0.00 0.00 0.00 3.07
496 509 2.392662 CTAGTGATGAGAAGGGGCTGA 58.607 52.381 0.00 0.00 0.00 4.26
497 510 1.415659 CCTAGTGATGAGAAGGGGCTG 59.584 57.143 0.00 0.00 0.00 4.85
498 511 1.799933 CCTAGTGATGAGAAGGGGCT 58.200 55.000 0.00 0.00 0.00 5.19
499 512 0.107643 GCCTAGTGATGAGAAGGGGC 59.892 60.000 0.00 0.00 0.00 5.80
500 513 1.799933 AGCCTAGTGATGAGAAGGGG 58.200 55.000 0.00 0.00 0.00 4.79
501 514 3.306641 GCATAGCCTAGTGATGAGAAGGG 60.307 52.174 0.00 0.00 0.00 3.95
502 515 3.306641 GGCATAGCCTAGTGATGAGAAGG 60.307 52.174 0.00 0.00 46.69 3.46
710 2224 7.927092 GCTCTTATATTTCTTTACGGAGGAAGT 59.073 37.037 0.00 0.00 0.00 3.01
711 2225 7.115095 CGCTCTTATATTTCTTTACGGAGGAAG 59.885 40.741 0.00 0.00 0.00 3.46
712 2226 6.921857 CGCTCTTATATTTCTTTACGGAGGAA 59.078 38.462 0.00 0.00 0.00 3.36
713 2227 6.040166 ACGCTCTTATATTTCTTTACGGAGGA 59.960 38.462 0.00 0.00 0.00 3.71
714 2228 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
715 2229 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
716 2230 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
717 2231 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
729 2243 9.988815 ATCACTAATGAATCTAAACGCTCTTAT 57.011 29.630 0.00 0.00 38.69 1.73
730 2244 9.464714 GATCACTAATGAATCTAAACGCTCTTA 57.535 33.333 0.00 0.00 38.69 2.10
731 2245 8.200792 AGATCACTAATGAATCTAAACGCTCTT 58.799 33.333 0.00 0.00 38.69 2.85
732 2246 7.721402 AGATCACTAATGAATCTAAACGCTCT 58.279 34.615 0.00 0.00 38.69 4.09
733 2247 7.938563 AGATCACTAATGAATCTAAACGCTC 57.061 36.000 0.00 0.00 38.69 5.03
734 2248 9.817809 TTTAGATCACTAATGAATCTAAACGCT 57.182 29.630 10.98 0.00 38.42 5.07
735 2249 9.851043 GTTTAGATCACTAATGAATCTAAACGC 57.149 33.333 21.74 8.92 43.90 4.84
739 2253 9.745880 GACCGTTTAGATCACTAATGAATCTAA 57.254 33.333 0.00 0.00 38.69 2.10
740 2254 9.132923 AGACCGTTTAGATCACTAATGAATCTA 57.867 33.333 0.00 0.00 38.69 1.98
741 2255 8.012957 AGACCGTTTAGATCACTAATGAATCT 57.987 34.615 0.00 0.00 38.69 2.40
742 2256 8.649973 AAGACCGTTTAGATCACTAATGAATC 57.350 34.615 0.00 0.00 38.69 2.52
758 2272 9.379791 CCTCTGTAAAGAAATATAAGACCGTTT 57.620 33.333 0.00 0.00 0.00 3.60
759 2273 7.985752 CCCTCTGTAAAGAAATATAAGACCGTT 59.014 37.037 0.00 0.00 0.00 4.44
760 2274 7.343833 TCCCTCTGTAAAGAAATATAAGACCGT 59.656 37.037 0.00 0.00 0.00 4.83
761 2275 7.723324 TCCCTCTGTAAAGAAATATAAGACCG 58.277 38.462 0.00 0.00 0.00 4.79
762 2276 8.706521 ACTCCCTCTGTAAAGAAATATAAGACC 58.293 37.037 0.00 0.00 0.00 3.85
768 2282 9.939424 ACTAGTACTCCCTCTGTAAAGAAATAT 57.061 33.333 0.00 0.00 0.00 1.28
770 2284 9.411189 CTACTAGTACTCCCTCTGTAAAGAAAT 57.589 37.037 0.00 0.00 0.00 2.17
771 2285 8.389366 ACTACTAGTACTCCCTCTGTAAAGAAA 58.611 37.037 0.00 0.00 0.00 2.52
772 2286 7.926705 ACTACTAGTACTCCCTCTGTAAAGAA 58.073 38.462 0.00 0.00 0.00 2.52
773 2287 7.507797 ACTACTAGTACTCCCTCTGTAAAGA 57.492 40.000 0.00 0.00 0.00 2.52
774 2288 8.661352 GTACTACTAGTACTCCCTCTGTAAAG 57.339 42.308 16.30 0.00 45.70 1.85
792 2306 9.662947 GGATAAATGGTTTGTTGTAGTACTACT 57.337 33.333 28.56 10.48 37.00 2.57
793 2307 8.886719 GGGATAAATGGTTTGTTGTAGTACTAC 58.113 37.037 23.58 23.58 36.63 2.73
796 2310 7.933215 AGGGATAAATGGTTTGTTGTAGTAC 57.067 36.000 0.00 0.00 0.00 2.73
878 2392 3.632333 TGTCTCACCGATGGAGAATACT 58.368 45.455 0.00 0.00 42.63 2.12
879 2393 3.243569 CCTGTCTCACCGATGGAGAATAC 60.244 52.174 0.00 0.00 42.63 1.89
880 2394 2.959030 CCTGTCTCACCGATGGAGAATA 59.041 50.000 0.00 0.00 42.63 1.75
881 2395 1.759445 CCTGTCTCACCGATGGAGAAT 59.241 52.381 0.00 0.00 42.63 2.40
882 2396 1.186200 CCTGTCTCACCGATGGAGAA 58.814 55.000 0.00 0.00 42.63 2.87
884 2398 0.174389 CACCTGTCTCACCGATGGAG 59.826 60.000 0.00 0.00 0.00 3.86
885 2399 1.257750 CCACCTGTCTCACCGATGGA 61.258 60.000 0.00 0.00 0.00 3.41
886 2400 1.219124 CCACCTGTCTCACCGATGG 59.781 63.158 0.00 0.00 0.00 3.51
926 2441 2.203640 TGCTCTCCACACTCCCGT 60.204 61.111 0.00 0.00 0.00 5.28
927 2442 0.965866 TACTGCTCTCCACACTCCCG 60.966 60.000 0.00 0.00 0.00 5.14
959 2474 1.076438 TGGGAGAGAGAGAGGTGTGA 58.924 55.000 0.00 0.00 0.00 3.58
981 2498 2.010145 TCATTTTCTCGCGGGAAGAG 57.990 50.000 22.32 15.21 37.09 2.85
982 2499 2.093711 TCATCATTTTCTCGCGGGAAGA 60.094 45.455 22.32 18.62 0.00 2.87
983 2500 2.030946 GTCATCATTTTCTCGCGGGAAG 59.969 50.000 22.32 10.89 0.00 3.46
1480 2997 3.319405 ACTCCCTGCGATATGAAGTACTG 59.681 47.826 0.00 0.00 0.00 2.74
1497 3017 6.428159 CAGTATGGCATCAGTTATTAACTCCC 59.572 42.308 1.65 5.83 40.46 4.30
1659 3180 9.208022 CCAAAATAAAAACAAGGAAAGGAGATC 57.792 33.333 0.00 0.00 0.00 2.75
1750 3271 2.979649 GGGTCTCCGAACAGGACC 59.020 66.667 0.00 0.00 45.98 4.46
1761 3282 4.083862 GGTGGAGTGGCGGGTCTC 62.084 72.222 0.00 0.00 0.00 3.36
1762 3283 4.954118 TGGTGGAGTGGCGGGTCT 62.954 66.667 0.00 0.00 0.00 3.85
1763 3284 4.699522 GTGGTGGAGTGGCGGGTC 62.700 72.222 0.00 0.00 0.00 4.46
1765 3286 4.394712 GAGTGGTGGAGTGGCGGG 62.395 72.222 0.00 0.00 0.00 6.13
1766 3287 4.394712 GGAGTGGTGGAGTGGCGG 62.395 72.222 0.00 0.00 0.00 6.13
1767 3288 4.742201 CGGAGTGGTGGAGTGGCG 62.742 72.222 0.00 0.00 0.00 5.69
1769 3290 3.302347 GAGCGGAGTGGTGGAGTGG 62.302 68.421 0.00 0.00 0.00 4.00
1770 3291 2.262915 GAGCGGAGTGGTGGAGTG 59.737 66.667 0.00 0.00 0.00 3.51
1771 3292 2.997897 GGAGCGGAGTGGTGGAGT 60.998 66.667 0.00 0.00 0.00 3.85
1772 3293 3.775654 GGGAGCGGAGTGGTGGAG 61.776 72.222 0.00 0.00 0.00 3.86
1781 3302 4.689549 TCCAACTCCGGGAGCGGA 62.690 66.667 24.76 24.76 33.83 5.54
1782 3303 4.148825 CTCCAACTCCGGGAGCGG 62.149 72.222 23.84 22.59 44.95 5.52
1786 3307 1.071699 CTTTTGACTCCAACTCCGGGA 59.928 52.381 0.00 0.00 30.88 5.14
1787 3308 1.523758 CTTTTGACTCCAACTCCGGG 58.476 55.000 0.00 0.00 30.88 5.73
1788 3309 1.523758 CCTTTTGACTCCAACTCCGG 58.476 55.000 0.00 0.00 30.88 5.14
1789 3310 0.875059 GCCTTTTGACTCCAACTCCG 59.125 55.000 0.00 0.00 30.88 4.63
1790 3311 1.609072 GTGCCTTTTGACTCCAACTCC 59.391 52.381 0.00 0.00 30.88 3.85
1791 3312 1.264288 CGTGCCTTTTGACTCCAACTC 59.736 52.381 0.00 0.00 30.88 3.01
1792 3313 1.308998 CGTGCCTTTTGACTCCAACT 58.691 50.000 0.00 0.00 30.88 3.16
1793 3314 0.310854 CCGTGCCTTTTGACTCCAAC 59.689 55.000 0.00 0.00 30.88 3.77
1794 3315 0.181587 TCCGTGCCTTTTGACTCCAA 59.818 50.000 0.00 0.00 0.00 3.53
1795 3316 0.250295 CTCCGTGCCTTTTGACTCCA 60.250 55.000 0.00 0.00 0.00 3.86
1796 3317 1.578206 GCTCCGTGCCTTTTGACTCC 61.578 60.000 0.00 0.00 35.15 3.85
1797 3318 0.603975 AGCTCCGTGCCTTTTGACTC 60.604 55.000 0.00 0.00 44.23 3.36
1798 3319 0.886490 CAGCTCCGTGCCTTTTGACT 60.886 55.000 0.00 0.00 44.23 3.41
1799 3320 1.576421 CAGCTCCGTGCCTTTTGAC 59.424 57.895 0.00 0.00 44.23 3.18
1800 3321 1.600636 CCAGCTCCGTGCCTTTTGA 60.601 57.895 0.00 0.00 44.23 2.69
1801 3322 2.629656 CCCAGCTCCGTGCCTTTTG 61.630 63.158 0.00 0.00 44.23 2.44
1802 3323 2.282462 CCCAGCTCCGTGCCTTTT 60.282 61.111 0.00 0.00 44.23 2.27
1803 3324 2.351924 TTTCCCAGCTCCGTGCCTTT 62.352 55.000 0.00 0.00 44.23 3.11
1804 3325 2.754664 CTTTCCCAGCTCCGTGCCTT 62.755 60.000 0.00 0.00 44.23 4.35
1805 3326 3.249189 TTTCCCAGCTCCGTGCCT 61.249 61.111 0.00 0.00 44.23 4.75
1806 3327 2.747855 CTTTCCCAGCTCCGTGCC 60.748 66.667 0.00 0.00 44.23 5.01
1807 3328 1.743252 CTCTTTCCCAGCTCCGTGC 60.743 63.158 0.00 0.00 43.29 5.34
1808 3329 0.539051 ATCTCTTTCCCAGCTCCGTG 59.461 55.000 0.00 0.00 0.00 4.94
1809 3330 0.539051 CATCTCTTTCCCAGCTCCGT 59.461 55.000 0.00 0.00 0.00 4.69
1810 3331 0.813210 GCATCTCTTTCCCAGCTCCG 60.813 60.000 0.00 0.00 0.00 4.63
1811 3332 0.545646 AGCATCTCTTTCCCAGCTCC 59.454 55.000 0.00 0.00 0.00 4.70
1812 3333 1.474855 GGAGCATCTCTTTCCCAGCTC 60.475 57.143 0.00 0.00 45.65 4.09
1813 3334 0.545646 GGAGCATCTCTTTCCCAGCT 59.454 55.000 0.00 0.00 33.73 4.24
1814 3335 0.254178 TGGAGCATCTCTTTCCCAGC 59.746 55.000 0.00 0.00 33.73 4.85
1815 3336 1.746516 GCTGGAGCATCTCTTTCCCAG 60.747 57.143 0.00 0.00 42.88 4.45
1816 3337 0.254178 GCTGGAGCATCTCTTTCCCA 59.746 55.000 0.00 0.00 41.59 4.37
1817 3338 0.545646 AGCTGGAGCATCTCTTTCCC 59.454 55.000 0.65 0.00 45.16 3.97
1818 3339 1.474855 GGAGCTGGAGCATCTCTTTCC 60.475 57.143 0.00 0.00 45.16 3.13
1819 3340 1.485895 AGGAGCTGGAGCATCTCTTTC 59.514 52.381 0.00 0.00 45.16 2.62
1820 3341 1.485895 GAGGAGCTGGAGCATCTCTTT 59.514 52.381 0.00 0.00 45.16 2.52
1821 3342 1.122227 GAGGAGCTGGAGCATCTCTT 58.878 55.000 0.00 0.00 45.16 2.85
1822 3343 1.108727 CGAGGAGCTGGAGCATCTCT 61.109 60.000 14.87 2.67 45.16 3.10
1823 3344 1.363443 CGAGGAGCTGGAGCATCTC 59.637 63.158 0.00 6.34 45.16 2.75
1824 3345 0.106469 TACGAGGAGCTGGAGCATCT 60.106 55.000 0.00 0.00 45.16 2.90
1825 3346 0.965439 ATACGAGGAGCTGGAGCATC 59.035 55.000 0.00 0.00 45.16 3.91
1826 3347 1.418334 AATACGAGGAGCTGGAGCAT 58.582 50.000 0.00 0.00 45.16 3.79
1827 3348 1.195115 AAATACGAGGAGCTGGAGCA 58.805 50.000 0.00 0.00 45.16 4.26
1828 3349 2.317530 AAAATACGAGGAGCTGGAGC 57.682 50.000 0.00 0.00 42.49 4.70
1829 3350 4.099573 TCCTAAAAATACGAGGAGCTGGAG 59.900 45.833 0.00 0.00 34.36 3.86
1830 3351 4.028131 TCCTAAAAATACGAGGAGCTGGA 58.972 43.478 0.00 0.00 34.36 3.86
1831 3352 4.402056 TCCTAAAAATACGAGGAGCTGG 57.598 45.455 0.00 0.00 34.36 4.85
1836 3357 5.482878 ACTCCAACTCCTAAAAATACGAGGA 59.517 40.000 0.00 0.00 37.02 3.71
1837 3358 5.581085 CACTCCAACTCCTAAAAATACGAGG 59.419 44.000 0.00 0.00 0.00 4.63
1838 3359 6.310711 GTCACTCCAACTCCTAAAAATACGAG 59.689 42.308 0.00 0.00 0.00 4.18
1839 3360 6.014840 AGTCACTCCAACTCCTAAAAATACGA 60.015 38.462 0.00 0.00 0.00 3.43
1840 3361 6.164176 AGTCACTCCAACTCCTAAAAATACG 58.836 40.000 0.00 0.00 0.00 3.06
1841 3362 7.598189 GAGTCACTCCAACTCCTAAAAATAC 57.402 40.000 0.00 0.00 37.72 1.89
1857 3378 0.606673 GGCCCTGTTTGGAGTCACTC 60.607 60.000 0.00 0.00 38.35 3.51
1858 3379 1.062488 AGGCCCTGTTTGGAGTCACT 61.062 55.000 0.00 0.00 38.35 3.41
1859 3380 0.178990 AAGGCCCTGTTTGGAGTCAC 60.179 55.000 0.00 0.00 38.35 3.67
1860 3381 1.440618 TAAGGCCCTGTTTGGAGTCA 58.559 50.000 0.00 0.00 38.35 3.41
1861 3382 2.579410 TTAAGGCCCTGTTTGGAGTC 57.421 50.000 0.00 0.00 38.35 3.36
1862 3383 3.542969 AATTAAGGCCCTGTTTGGAGT 57.457 42.857 0.00 0.00 38.35 3.85
1863 3384 4.089361 AGAAATTAAGGCCCTGTTTGGAG 58.911 43.478 0.00 0.00 38.35 3.86
1864 3385 4.126520 AGAAATTAAGGCCCTGTTTGGA 57.873 40.909 0.00 0.00 38.35 3.53
1865 3386 4.040339 ACAAGAAATTAAGGCCCTGTTTGG 59.960 41.667 0.00 0.00 0.00 3.28
1866 3387 5.213891 ACAAGAAATTAAGGCCCTGTTTG 57.786 39.130 0.00 0.00 0.00 2.93
1867 3388 5.887214 AACAAGAAATTAAGGCCCTGTTT 57.113 34.783 0.00 0.00 0.00 2.83
1868 3389 5.887214 AAACAAGAAATTAAGGCCCTGTT 57.113 34.783 0.00 0.00 0.00 3.16
1869 3390 5.887214 AAAACAAGAAATTAAGGCCCTGT 57.113 34.783 0.00 0.00 0.00 4.00
1870 3391 8.846943 AAATAAAACAAGAAATTAAGGCCCTG 57.153 30.769 0.00 0.00 0.00 4.45
1872 3393 9.378551 CCTAAATAAAACAAGAAATTAAGGCCC 57.621 33.333 0.00 0.00 0.00 5.80
1873 3394 9.938280 ACCTAAATAAAACAAGAAATTAAGGCC 57.062 29.630 0.00 0.00 0.00 5.19
2074 3595 4.219725 CCTAAGGATAGCTGAACTAGGCTC 59.780 50.000 0.00 0.00 39.65 4.70
2096 3618 5.703130 ACAACTTATCTGTCTTCTGCTTTCC 59.297 40.000 0.00 0.00 0.00 3.13
2187 3712 7.763528 TGCCATTTAAAAAGATGTTTATGCGAT 59.236 29.630 0.00 0.00 0.00 4.58
2248 3773 7.208080 TCCTTGTCACTAAACTCTGAAAGTAC 58.792 38.462 0.00 0.00 37.17 2.73
2290 3816 1.474879 GAGCAGAAGAGAGGTAAGCGT 59.525 52.381 0.00 0.00 0.00 5.07
2293 3819 4.381505 GGTCAAGAGCAGAAGAGAGGTAAG 60.382 50.000 0.00 0.00 0.00 2.34
2391 3917 1.806542 GCTTCTGATCCGCACTTTTCA 59.193 47.619 0.00 0.00 0.00 2.69
2397 3923 1.522580 GAGGGCTTCTGATCCGCAC 60.523 63.158 0.00 0.00 0.00 5.34
2518 4044 5.265191 TCTCTGCTACTACAAACTGAGGAT 58.735 41.667 0.00 0.00 0.00 3.24
2601 4129 1.202651 CGACCCACAGTTCAGAAACCT 60.203 52.381 0.00 0.00 35.92 3.50
2618 4148 6.399743 ACTTTCTCCCTCTCTTTTATTCGAC 58.600 40.000 0.00 0.00 0.00 4.20
2673 4205 0.450583 ATGCAATCACGCTCAAGCAG 59.549 50.000 2.50 0.00 42.21 4.24
2731 4263 3.684788 ACGCGACATCAAATTTCTTAGCT 59.315 39.130 15.93 0.00 0.00 3.32
2734 4266 4.250464 AGGACGCGACATCAAATTTCTTA 58.750 39.130 15.93 0.00 0.00 2.10
2848 4381 6.147864 TGAAATGCCACCTATAAATTCTGC 57.852 37.500 0.00 0.00 0.00 4.26
2893 4430 5.047802 CCATGTTTCTGCTGTGATTTACCTT 60.048 40.000 0.00 0.00 0.00 3.50
3124 4664 3.056393 TCCAGTGTGTCCTAATAACACCG 60.056 47.826 4.14 0.00 45.10 4.94
3165 4707 3.192466 GAGCGATATGTTAACGTTGGGT 58.808 45.455 11.99 1.61 0.00 4.51
3166 4708 2.542595 GGAGCGATATGTTAACGTTGGG 59.457 50.000 11.99 0.00 0.00 4.12
3271 5013 1.888436 TACAGCTGAAGCAGGTCCGG 61.888 60.000 23.35 0.00 40.40 5.14
3352 5094 2.306847 CACCAGGCACCTTTAACTTGT 58.693 47.619 0.00 0.00 0.00 3.16
3360 5102 1.767692 CCTTACCACCAGGCACCTT 59.232 57.895 0.00 0.00 39.06 3.50
3423 5165 1.070758 GATGGCGAGCTTCCCTTCATA 59.929 52.381 12.01 0.00 0.00 2.15
3437 5179 0.530650 AACGGACAGCTATGATGGCG 60.531 55.000 0.00 0.00 34.52 5.69
3438 5180 0.940126 CAACGGACAGCTATGATGGC 59.060 55.000 0.00 0.00 0.00 4.40
3449 5191 1.210545 GAAGAACGCGACAACGGACA 61.211 55.000 15.93 0.00 40.15 4.02
3452 5194 1.487231 CTGAAGAACGCGACAACGG 59.513 57.895 15.93 6.09 40.15 4.44
3457 5199 3.016474 GCCTGCTGAAGAACGCGAC 62.016 63.158 15.93 6.52 0.00 5.19
3460 5202 2.866028 CAGCCTGCTGAAGAACGC 59.134 61.111 13.85 0.00 46.30 4.84


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

AutoCloner maintained by Alex Coulton.