Multiple sequence alignment - TraesCS6D01G219600

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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 TraesCS6D01G219600 chr6D 100.000 3962 0 0 1 3962 309948120 309952081 0.000000e+00 7317.0
1 TraesCS6D01G219600 chr6D 83.654 208 31 3 663 868 304688727 304688521 4.040000e-45 193.0
2 TraesCS6D01G219600 chr6D 88.525 61 0 6 855 909 78083181 78083122 2.560000e-07 67.6
3 TraesCS6D01G219600 chr6B 91.471 1747 106 21 2029 3740 477786997 477788735 0.000000e+00 2361.0
4 TraesCS6D01G219600 chr6B 92.891 1069 41 9 911 1956 477785942 477786998 0.000000e+00 1520.0
5 TraesCS6D01G219600 chr6B 90.015 671 53 6 1 664 477785158 477785821 0.000000e+00 856.0
6 TraesCS6D01G219600 chr6B 95.023 221 11 0 3741 3961 477788770 477788990 8.150000e-92 348.0
7 TraesCS6D01G219600 chr6B 84.058 207 31 2 663 868 518677114 518677319 8.680000e-47 198.0
8 TraesCS6D01G219600 chr6B 90.566 53 1 4 859 909 296405368 296405318 2.560000e-07 67.6
9 TraesCS6D01G219600 chr6A 91.007 1757 92 23 2031 3740 446725289 446727026 0.000000e+00 2309.0
10 TraesCS6D01G219600 chr6A 91.935 992 46 12 915 1885 446724129 446725107 0.000000e+00 1358.0
11 TraesCS6D01G219600 chr6A 95.495 222 10 0 3741 3962 446727067 446727288 4.870000e-94 355.0
12 TraesCS6D01G219600 chr6A 94.737 57 3 0 1955 2011 604890750 604890694 5.450000e-14 89.8
13 TraesCS6D01G219600 chr4D 94.019 535 29 3 1702 2235 226630820 226631352 0.000000e+00 808.0
14 TraesCS6D01G219600 chr4D 93.220 59 4 0 1955 2013 503813685 503813743 1.960000e-13 87.9
15 TraesCS6D01G219600 chr4D 92.453 53 0 3 861 910 359199887 359199836 5.490000e-09 73.1
16 TraesCS6D01G219600 chr4D 90.566 53 1 4 860 908 224838511 224838563 2.560000e-07 67.6
17 TraesCS6D01G219600 chr4A 76.190 420 88 8 253 664 125375875 125376290 1.120000e-50 211.0
18 TraesCS6D01G219600 chr4A 77.454 377 57 17 308 664 87241207 87240839 2.410000e-47 200.0
19 TraesCS6D01G219600 chr4A 84.772 197 29 1 663 858 686242242 686242046 3.120000e-46 196.0
20 TraesCS6D01G219600 chr2A 84.762 210 29 3 663 870 692242275 692242483 1.440000e-49 207.0
21 TraesCS6D01G219600 chr2A 84.024 169 25 2 497 664 765591660 765591827 1.140000e-35 161.0
22 TraesCS6D01G219600 chr2A 75.478 314 73 4 287 598 770379151 770379462 2.470000e-32 150.0
23 TraesCS6D01G219600 chr1D 87.027 185 23 1 663 846 110975982 110976166 1.440000e-49 207.0
24 TraesCS6D01G219600 chr1D 87.931 58 4 1 855 909 114366405 114366348 9.190000e-07 65.8
25 TraesCS6D01G219600 chr1D 87.500 56 5 2 854 908 106843194 106843248 3.310000e-06 63.9
26 TraesCS6D01G219600 chr3B 85.279 197 28 1 663 858 741435244 741435048 6.710000e-48 202.0
27 TraesCS6D01G219600 chr2D 84.466 206 29 3 663 868 559399064 559398862 2.410000e-47 200.0
28 TraesCS6D01G219600 chr2D 91.667 60 5 0 1952 2011 61023706 61023765 2.540000e-12 84.2
29 TraesCS6D01G219600 chr2D 92.157 51 1 2 864 911 647796708 647796658 7.100000e-08 69.4
30 TraesCS6D01G219600 chr5D 78.808 302 57 7 366 664 385924937 385924640 3.120000e-46 196.0
31 TraesCS6D01G219600 chr5D 81.443 194 30 5 474 664 385696258 385696068 1.910000e-33 154.0
32 TraesCS6D01G219600 chr5D 74.279 416 84 14 253 664 519704035 519704431 1.910000e-33 154.0
33 TraesCS6D01G219600 chr5B 83.886 211 29 3 663 872 270321465 270321671 3.120000e-46 196.0
34 TraesCS6D01G219600 chr5B 80.952 189 32 3 477 664 113689039 113689224 3.190000e-31 147.0
35 TraesCS6D01G219600 chr5B 93.103 58 4 0 1954 2011 391148495 391148438 7.050000e-13 86.1
36 TraesCS6D01G219600 chr5B 87.719 57 3 4 855 909 669446964 669447018 3.310000e-06 63.9
37 TraesCS6D01G219600 chr7B 83.099 213 34 2 663 873 104298538 104298326 4.040000e-45 193.0
38 TraesCS6D01G219600 chr7B 80.952 189 30 5 477 664 535496605 535496422 1.150000e-30 145.0
39 TraesCS6D01G219600 chr7B 90.476 63 5 1 1949 2011 534047700 534047761 9.130000e-12 82.4
40 TraesCS6D01G219600 chr4B 76.751 357 60 11 281 618 664765739 664765387 1.130000e-40 178.0
41 TraesCS6D01G219600 chr4B 90.741 54 1 3 864 913 484771826 484771773 7.100000e-08 69.4
42 TraesCS6D01G219600 chr1A 79.679 187 35 3 474 658 108105838 108105653 8.930000e-27 132.0
43 TraesCS6D01G219600 chr1A 77.326 172 31 6 253 420 358807175 358807342 1.170000e-15 95.3
44 TraesCS6D01G219600 chr1A 91.803 61 4 1 1951 2011 568391290 568391231 2.540000e-12 84.2
45 TraesCS6D01G219600 chr7A 91.935 62 4 1 1950 2011 195397795 195397855 7.050000e-13 86.1
46 TraesCS6D01G219600 chr2B 83.908 87 14 0 375 461 586563 586477 2.540000e-12 84.2
47 TraesCS6D01G219600 chr1B 91.667 60 5 0 1952 2011 88754783 88754724 2.540000e-12 84.2


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 TraesCS6D01G219600 chr6D 309948120 309952081 3961 False 7317.000000 7317 100.000000 1 3962 1 chr6D.!!$F1 3961
1 TraesCS6D01G219600 chr6B 477785158 477788990 3832 False 1271.250000 2361 92.350000 1 3961 4 chr6B.!!$F2 3960
2 TraesCS6D01G219600 chr6A 446724129 446727288 3159 False 1340.666667 2309 92.812333 915 3962 3 chr6A.!!$F1 3047
3 TraesCS6D01G219600 chr4D 226630820 226631352 532 False 808.000000 808 94.019000 1702 2235 1 chr4D.!!$F2 533

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
728 736 0.181350 AATGAAGGAGGGGCGATGAC 59.819 55.0 0.00 0.00 0.00 3.06 F
731 739 0.250081 GAAGGAGGGGCGATGACATC 60.250 60.0 5.28 5.28 0.00 3.06 F
1720 1754 0.395312 TTGGTCCGAGGAGTGGAAAC 59.605 55.0 0.00 0.00 37.23 2.78 F
2608 2771 0.413037 TTCCAACATGGCCCATCCTT 59.587 50.0 0.00 0.00 37.47 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2595 2758 1.822990 GCATGATAAGGATGGGCCATG 59.177 52.381 26.77 8.85 40.02 3.66 R
2600 2763 3.087031 GGACATGCATGATAAGGATGGG 58.913 50.000 32.75 1.99 38.89 4.00 R
2786 2949 0.391661 AGTGCTCCATACACTTGCGG 60.392 55.000 0.00 0.00 46.01 5.69 R
3881 4114 1.080025 GTCACGTACCAGTGCTCCC 60.080 63.158 0.00 0.00 41.61 4.30 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
91 92 3.385433 TGGAGAAGTCACCGTTTTCTACA 59.615 43.478 0.00 0.00 38.98 2.74
92 93 4.141892 TGGAGAAGTCACCGTTTTCTACAA 60.142 41.667 0.00 0.00 38.49 2.41
128 129 2.152016 GCCCTAAAACTTGCTTCGACT 58.848 47.619 0.00 0.00 0.00 4.18
129 130 3.244284 TGCCCTAAAACTTGCTTCGACTA 60.244 43.478 0.00 0.00 0.00 2.59
134 135 3.879932 AAACTTGCTTCGACTACTTGC 57.120 42.857 0.00 0.00 0.00 4.01
139 140 2.833794 TGCTTCGACTACTTGCTGTTT 58.166 42.857 0.00 0.00 0.00 2.83
179 186 5.050644 TGCTCTTATTGCAGTGAATGTTG 57.949 39.130 0.00 0.00 35.31 3.33
182 189 5.163723 GCTCTTATTGCAGTGAATGTTGCTA 60.164 40.000 0.00 0.00 40.87 3.49
183 190 6.182039 TCTTATTGCAGTGAATGTTGCTAC 57.818 37.500 0.00 0.00 40.87 3.58
184 191 5.939883 TCTTATTGCAGTGAATGTTGCTACT 59.060 36.000 0.00 0.00 40.87 2.57
185 192 4.691860 ATTGCAGTGAATGTTGCTACTC 57.308 40.909 0.00 0.00 40.87 2.59
186 193 2.068519 TGCAGTGAATGTTGCTACTCG 58.931 47.619 0.00 0.00 40.87 4.18
204 211 8.141268 TGCTACTCGAATTTTGGAAAGAAAAAT 58.859 29.630 0.00 0.00 38.54 1.82
208 215 7.169813 ACTCGAATTTTGGAAAGAAAAATCAGC 59.830 33.333 0.00 0.00 36.46 4.26
220 227 0.970640 AAATCAGCTTGCATGCCACA 59.029 45.000 19.99 5.66 0.00 4.17
240 247 5.932303 CCACAAAAAGTCGAGAAGAGGATAA 59.068 40.000 0.00 0.00 0.00 1.75
245 252 6.445357 AAAGTCGAGAAGAGGATAAGAGAC 57.555 41.667 0.00 0.00 0.00 3.36
256 263 3.709141 AGGATAAGAGACAGAAGAAGGGC 59.291 47.826 0.00 0.00 0.00 5.19
266 273 4.758688 ACAGAAGAAGGGCTTTGTTTTTG 58.241 39.130 0.00 0.00 36.83 2.44
271 278 3.966665 AGAAGGGCTTTGTTTTTGGATGA 59.033 39.130 0.00 0.00 0.00 2.92
272 279 4.594491 AGAAGGGCTTTGTTTTTGGATGAT 59.406 37.500 0.00 0.00 0.00 2.45
273 280 4.980339 AGGGCTTTGTTTTTGGATGATT 57.020 36.364 0.00 0.00 0.00 2.57
278 285 6.934083 GGGCTTTGTTTTTGGATGATTTTCTA 59.066 34.615 0.00 0.00 0.00 2.10
279 286 7.607607 GGGCTTTGTTTTTGGATGATTTTCTAT 59.392 33.333 0.00 0.00 0.00 1.98
291 299 9.200817 TGGATGATTTTCTATTTTTCTTAGGGG 57.799 33.333 0.00 0.00 0.00 4.79
296 304 9.856488 GATTTTCTATTTTTCTTAGGGGTTGTC 57.144 33.333 0.00 0.00 0.00 3.18
299 307 6.403878 TCTATTTTTCTTAGGGGTTGTCTCG 58.596 40.000 0.00 0.00 0.00 4.04
313 321 0.448593 GTCTCGTGTTCGGAGAGAGG 59.551 60.000 0.00 0.00 41.12 3.69
325 333 4.200283 GAGAGGAGGCGGCGACAG 62.200 72.222 18.30 0.00 0.00 3.51
338 346 2.290916 CGGCGACAGCTCTCTAAAGATA 59.709 50.000 0.00 0.00 44.37 1.98
361 369 6.248569 AGAATAAATTTCTTCCCGCCTAGA 57.751 37.500 11.51 0.00 0.00 2.43
370 378 1.753463 CCCGCCTAGACCTCGTTCT 60.753 63.158 0.00 0.00 0.00 3.01
378 386 0.247736 AGACCTCGTTCTGATGGTGC 59.752 55.000 0.00 0.00 31.03 5.01
381 389 1.338200 ACCTCGTTCTGATGGTGCTTC 60.338 52.381 0.00 0.00 30.11 3.86
408 416 3.314331 CAGAGGGTGTGCGGAGGT 61.314 66.667 0.00 0.00 0.00 3.85
411 419 0.834687 AGAGGGTGTGCGGAGGTTTA 60.835 55.000 0.00 0.00 0.00 2.01
412 420 0.252197 GAGGGTGTGCGGAGGTTTAT 59.748 55.000 0.00 0.00 0.00 1.40
441 449 2.208431 GATCTTGCAGGATTCAGTCGG 58.792 52.381 13.14 0.00 0.00 4.79
449 457 0.872388 GGATTCAGTCGGCGTTTGTT 59.128 50.000 6.85 0.00 0.00 2.83
479 487 1.065491 TCCATGTGGATCCGGTCTTTG 60.065 52.381 7.39 0.00 39.78 2.77
515 523 4.041740 TGTTGGATCCTTTCGATCTACG 57.958 45.455 14.23 0.00 45.90 3.51
521 529 4.500035 GGATCCTTTCGATCTACGCTTCTT 60.500 45.833 3.84 0.00 45.90 2.52
532 540 2.422276 ACGCTTCTTTTCAATGGCAC 57.578 45.000 0.00 0.00 0.00 5.01
542 550 1.774110 TCAATGGCACTGGTTGTTGT 58.226 45.000 0.00 0.00 0.00 3.32
564 572 0.969149 TGATGCGCTGGTCCTATAGG 59.031 55.000 13.07 13.07 0.00 2.57
574 582 1.650528 GTCCTATAGGGCCTCAGCAT 58.349 55.000 18.97 0.00 42.56 3.79
592 600 2.922758 GCATGACGACTTCTCGACTGTT 60.923 50.000 0.00 0.00 43.06 3.16
598 606 5.028428 ACGACTTCTCGACTGTTTACTAC 57.972 43.478 0.00 0.00 43.06 2.73
601 609 5.339085 CGACTTCTCGACTGTTTACTACAAC 59.661 44.000 0.00 0.00 43.06 3.32
620 628 2.944129 ACAAGTTTTGCCCAGCTCTAA 58.056 42.857 0.00 0.00 0.00 2.10
636 644 1.694150 TCTAATGAAGGAGGGGCGATG 59.306 52.381 0.00 0.00 0.00 3.84
664 672 2.861006 GCCTTCGGTTCGCTTCAC 59.139 61.111 0.00 0.00 0.00 3.18
665 673 3.011760 GCCTTCGGTTCGCTTCACG 62.012 63.158 0.00 0.00 45.62 4.35
677 685 2.264109 GCTTCACGATGACTTCTCGA 57.736 50.000 0.00 0.00 39.38 4.04
678 686 1.914700 GCTTCACGATGACTTCTCGAC 59.085 52.381 0.00 0.00 39.38 4.20
679 687 2.414824 GCTTCACGATGACTTCTCGACT 60.415 50.000 0.00 0.00 39.38 4.18
680 688 2.902065 TCACGATGACTTCTCGACTG 57.098 50.000 0.00 0.00 39.38 3.51
681 689 2.152016 TCACGATGACTTCTCGACTGT 58.848 47.619 0.00 0.00 39.38 3.55
682 690 2.159824 TCACGATGACTTCTCGACTGTC 59.840 50.000 0.00 0.00 39.38 3.51
683 691 2.160615 CACGATGACTTCTCGACTGTCT 59.839 50.000 6.21 0.00 39.38 3.41
684 692 3.371285 CACGATGACTTCTCGACTGTCTA 59.629 47.826 6.21 0.00 39.38 2.59
685 693 3.371591 ACGATGACTTCTCGACTGTCTAC 59.628 47.826 6.21 3.58 39.38 2.59
686 694 3.619483 CGATGACTTCTCGACTGTCTACT 59.381 47.826 6.21 0.00 38.38 2.57
687 695 4.804665 CGATGACTTCTCGACTGTCTACTA 59.195 45.833 6.21 0.00 38.38 1.82
688 696 5.276489 CGATGACTTCTCGACTGTCTACTAC 60.276 48.000 6.21 0.00 38.38 2.73
689 697 4.891260 TGACTTCTCGACTGTCTACTACA 58.109 43.478 6.21 0.00 36.42 2.74
690 698 5.303165 TGACTTCTCGACTGTCTACTACAA 58.697 41.667 6.21 0.00 37.74 2.41
691 699 5.178996 TGACTTCTCGACTGTCTACTACAAC 59.821 44.000 6.21 0.00 37.74 3.32
692 700 5.061853 ACTTCTCGACTGTCTACTACAACA 58.938 41.667 6.21 0.00 37.74 3.33
693 701 5.530171 ACTTCTCGACTGTCTACTACAACAA 59.470 40.000 6.21 0.00 37.74 2.83
694 702 5.608676 TCTCGACTGTCTACTACAACAAG 57.391 43.478 6.21 0.00 37.74 3.16
695 703 5.061853 TCTCGACTGTCTACTACAACAAGT 58.938 41.667 6.21 0.00 37.74 3.16
696 704 5.530171 TCTCGACTGTCTACTACAACAAGTT 59.470 40.000 6.21 0.00 37.74 2.66
697 705 6.039047 TCTCGACTGTCTACTACAACAAGTTT 59.961 38.462 6.21 0.00 37.74 2.66
698 706 6.567050 TCGACTGTCTACTACAACAAGTTTT 58.433 36.000 6.21 0.00 37.74 2.43
699 707 6.474427 TCGACTGTCTACTACAACAAGTTTTG 59.526 38.462 6.21 0.00 37.74 2.44
700 708 6.359480 ACTGTCTACTACAACAAGTTTTGC 57.641 37.500 0.00 0.00 37.74 3.68
701 709 5.296035 ACTGTCTACTACAACAAGTTTTGCC 59.704 40.000 0.00 0.00 37.74 4.52
702 710 4.577283 TGTCTACTACAACAAGTTTTGCCC 59.423 41.667 0.00 0.00 34.29 5.36
703 711 4.577283 GTCTACTACAACAAGTTTTGCCCA 59.423 41.667 0.00 0.00 0.00 5.36
704 712 4.819630 TCTACTACAACAAGTTTTGCCCAG 59.180 41.667 0.00 0.00 0.00 4.45
705 713 2.100749 ACTACAACAAGTTTTGCCCAGC 59.899 45.455 0.00 0.00 0.00 4.85
706 714 1.194218 ACAACAAGTTTTGCCCAGCT 58.806 45.000 0.00 0.00 0.00 4.24
707 715 1.136891 ACAACAAGTTTTGCCCAGCTC 59.863 47.619 0.00 0.00 0.00 4.09
708 716 1.410153 CAACAAGTTTTGCCCAGCTCT 59.590 47.619 0.00 0.00 0.00 4.09
709 717 2.622942 CAACAAGTTTTGCCCAGCTCTA 59.377 45.455 0.00 0.00 0.00 2.43
710 718 2.944129 ACAAGTTTTGCCCAGCTCTAA 58.056 42.857 0.00 0.00 0.00 2.10
711 719 3.500343 ACAAGTTTTGCCCAGCTCTAAT 58.500 40.909 0.00 0.00 0.00 1.73
712 720 3.256631 ACAAGTTTTGCCCAGCTCTAATG 59.743 43.478 0.00 0.00 0.00 1.90
713 721 3.439857 AGTTTTGCCCAGCTCTAATGA 57.560 42.857 0.00 0.00 0.00 2.57
714 722 3.766545 AGTTTTGCCCAGCTCTAATGAA 58.233 40.909 0.00 0.00 0.00 2.57
715 723 3.760684 AGTTTTGCCCAGCTCTAATGAAG 59.239 43.478 0.00 0.00 0.00 3.02
716 724 2.425143 TTGCCCAGCTCTAATGAAGG 57.575 50.000 0.00 0.00 0.00 3.46
717 725 1.583556 TGCCCAGCTCTAATGAAGGA 58.416 50.000 0.00 0.00 0.00 3.36
718 726 1.487976 TGCCCAGCTCTAATGAAGGAG 59.512 52.381 0.00 0.00 0.00 3.69
719 727 1.202746 GCCCAGCTCTAATGAAGGAGG 60.203 57.143 0.00 0.00 0.00 4.30
720 728 1.419387 CCCAGCTCTAATGAAGGAGGG 59.581 57.143 0.00 0.00 0.00 4.30
721 729 1.419387 CCAGCTCTAATGAAGGAGGGG 59.581 57.143 0.00 0.00 0.00 4.79
722 730 1.135960 AGCTCTAATGAAGGAGGGGC 58.864 55.000 0.00 0.00 0.00 5.80
723 731 0.250081 GCTCTAATGAAGGAGGGGCG 60.250 60.000 0.00 0.00 0.00 6.13
724 732 1.414158 CTCTAATGAAGGAGGGGCGA 58.586 55.000 0.00 0.00 0.00 5.54
725 733 1.974236 CTCTAATGAAGGAGGGGCGAT 59.026 52.381 0.00 0.00 0.00 4.58
726 734 1.694150 TCTAATGAAGGAGGGGCGATG 59.306 52.381 0.00 0.00 0.00 3.84
727 735 1.694150 CTAATGAAGGAGGGGCGATGA 59.306 52.381 0.00 0.00 0.00 2.92
728 736 0.181350 AATGAAGGAGGGGCGATGAC 59.819 55.000 0.00 0.00 0.00 3.06
729 737 0.982852 ATGAAGGAGGGGCGATGACA 60.983 55.000 0.00 0.00 0.00 3.58
730 738 0.982852 TGAAGGAGGGGCGATGACAT 60.983 55.000 0.00 0.00 0.00 3.06
731 739 0.250081 GAAGGAGGGGCGATGACATC 60.250 60.000 5.28 5.28 0.00 3.06
740 748 2.202932 GATGACATCGGTGCGCCT 60.203 61.111 15.69 0.00 0.00 5.52
741 749 1.815421 GATGACATCGGTGCGCCTT 60.815 57.895 15.69 0.00 0.00 4.35
742 750 1.766143 GATGACATCGGTGCGCCTTC 61.766 60.000 15.69 5.97 0.00 3.46
743 751 3.554692 GACATCGGTGCGCCTTCG 61.555 66.667 15.69 6.35 39.07 3.79
746 754 4.388499 ATCGGTGCGCCTTCGGTT 62.388 61.111 15.69 0.00 35.95 4.44
747 755 3.894547 ATCGGTGCGCCTTCGGTTT 62.895 57.895 15.69 0.00 35.95 3.27
748 756 4.383602 CGGTGCGCCTTCGGTTTG 62.384 66.667 15.69 0.00 35.95 2.93
749 757 4.700365 GGTGCGCCTTCGGTTTGC 62.700 66.667 9.68 0.00 35.95 3.68
750 758 3.660111 GTGCGCCTTCGGTTTGCT 61.660 61.111 4.18 0.00 35.95 3.91
751 759 2.904866 TGCGCCTTCGGTTTGCTT 60.905 55.556 4.18 0.00 35.95 3.91
752 760 2.126850 GCGCCTTCGGTTTGCTTC 60.127 61.111 0.00 0.00 35.95 3.86
753 761 2.903547 GCGCCTTCGGTTTGCTTCA 61.904 57.895 0.00 0.00 35.95 3.02
754 762 1.652012 CGCCTTCGGTTTGCTTCAA 59.348 52.632 0.00 0.00 0.00 2.69
757 765 1.701704 CCTTCGGTTTGCTTCAATGC 58.298 50.000 0.00 0.00 0.00 3.56
760 768 3.057596 CCTTCGGTTTGCTTCAATGCTTA 60.058 43.478 0.00 0.00 0.00 3.09
773 781 4.534168 TCAATGCTTATAGTCGTCGCTAC 58.466 43.478 0.00 0.00 0.00 3.58
804 813 9.830975 TCTACGAATCTGGATGAATTTTTATCA 57.169 29.630 0.00 0.00 0.00 2.15
811 820 9.760077 ATCTGGATGAATTTTTATCATTTCTGC 57.240 29.630 0.00 0.00 37.64 4.26
814 823 8.487848 TGGATGAATTTTTATCATTTCTGCCAT 58.512 29.630 0.00 0.00 37.64 4.40
820 829 7.579589 TTTTTATCATTTCTGCCATTCGTTG 57.420 32.000 0.00 0.00 0.00 4.10
823 832 4.944962 TCATTTCTGCCATTCGTTGTAG 57.055 40.909 0.00 0.00 0.00 2.74
825 834 4.154015 TCATTTCTGCCATTCGTTGTAGTG 59.846 41.667 0.00 0.00 0.00 2.74
845 854 9.485206 TGTAGTGTCATGATTGATGATGAATAG 57.515 33.333 0.00 0.00 43.20 1.73
848 857 7.388224 AGTGTCATGATTGATGATGAATAGCTC 59.612 37.037 0.00 0.00 43.20 4.09
880 889 6.806388 TTTTAGAAAAACATACTCCCGTCC 57.194 37.500 0.00 0.00 0.00 4.79
881 890 3.345508 AGAAAAACATACTCCCGTCCC 57.654 47.619 0.00 0.00 0.00 4.46
882 891 2.640826 AGAAAAACATACTCCCGTCCCA 59.359 45.455 0.00 0.00 0.00 4.37
883 892 3.265995 AGAAAAACATACTCCCGTCCCAT 59.734 43.478 0.00 0.00 0.00 4.00
884 893 4.472108 AGAAAAACATACTCCCGTCCCATA 59.528 41.667 0.00 0.00 0.00 2.74
885 894 4.847990 AAAACATACTCCCGTCCCATAA 57.152 40.909 0.00 0.00 0.00 1.90
886 895 5.382664 AAAACATACTCCCGTCCCATAAT 57.617 39.130 0.00 0.00 0.00 1.28
887 896 6.503560 AAAACATACTCCCGTCCCATAATA 57.496 37.500 0.00 0.00 0.00 0.98
888 897 6.697641 AAACATACTCCCGTCCCATAATAT 57.302 37.500 0.00 0.00 0.00 1.28
889 898 7.801893 AAACATACTCCCGTCCCATAATATA 57.198 36.000 0.00 0.00 0.00 0.86
890 899 7.801893 AACATACTCCCGTCCCATAATATAA 57.198 36.000 0.00 0.00 0.00 0.98
891 900 7.419711 ACATACTCCCGTCCCATAATATAAG 57.580 40.000 0.00 0.00 0.00 1.73
892 901 7.186972 ACATACTCCCGTCCCATAATATAAGA 58.813 38.462 0.00 0.00 0.00 2.10
893 902 7.342284 ACATACTCCCGTCCCATAATATAAGAG 59.658 40.741 0.00 0.00 0.00 2.85
894 903 4.466726 ACTCCCGTCCCATAATATAAGAGC 59.533 45.833 0.00 0.00 0.00 4.09
895 904 3.446161 TCCCGTCCCATAATATAAGAGCG 59.554 47.826 0.00 0.00 0.00 5.03
896 905 3.194968 CCCGTCCCATAATATAAGAGCGT 59.805 47.826 0.00 0.00 0.00 5.07
897 906 4.322499 CCCGTCCCATAATATAAGAGCGTT 60.322 45.833 0.00 0.00 0.00 4.84
898 907 5.235516 CCGTCCCATAATATAAGAGCGTTT 58.764 41.667 0.00 0.00 0.00 3.60
899 908 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
900 909 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
901 910 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
902 911 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
903 912 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
904 913 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
905 914 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
906 915 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
909 918 8.773404 AATATAAGAGCGTTTTTGACACTACT 57.227 30.769 0.00 0.00 0.00 2.57
917 926 7.927048 AGCGTTTTTGACACTACTTAGAAAAT 58.073 30.769 0.00 0.00 0.00 1.82
1167 1179 1.450312 GGCTGCCGCAGAACATAGT 60.450 57.895 24.80 0.00 38.10 2.12
1265 1277 1.819632 GATTGCTGGGTGGTAGGCG 60.820 63.158 0.00 0.00 0.00 5.52
1398 1410 4.649267 TTCCACCCATGTTCATCAGTTA 57.351 40.909 0.00 0.00 0.00 2.24
1422 1434 3.245016 TGGAGTCATGATGCTTCTTGGTT 60.245 43.478 13.43 4.70 0.00 3.67
1431 1443 4.402155 TGATGCTTCTTGGTTGTGTTCTTT 59.598 37.500 0.88 0.00 0.00 2.52
1478 1493 2.892425 CCGTGGAGAAGCGCATCC 60.892 66.667 11.47 14.83 36.05 3.51
1510 1525 5.888161 GGAGGATTACATCAAGGTTTGTCAT 59.112 40.000 0.00 0.00 0.00 3.06
1572 1588 4.339247 AGACTTAAAATGATTGGGCGGATG 59.661 41.667 0.00 0.00 0.00 3.51
1653 1670 2.877097 TGTGTGGTCCTGTATGCAAT 57.123 45.000 0.00 0.00 0.00 3.56
1720 1754 0.395312 TTGGTCCGAGGAGTGGAAAC 59.605 55.000 0.00 0.00 37.23 2.78
1722 1756 1.203087 TGGTCCGAGGAGTGGAAACTA 60.203 52.381 0.00 0.00 37.23 2.24
1759 1793 6.978080 TGAGAATTTAGTTTCTGGCAAACAAC 59.022 34.615 4.98 0.65 36.10 3.32
1887 2031 1.536766 TGTGCATGCTGTTCTACTTGC 59.463 47.619 20.33 0.00 37.44 4.01
1963 2107 5.209659 TCTTCCTTGTTATCTACTCCCTCC 58.790 45.833 0.00 0.00 0.00 4.30
1964 2108 4.620086 TCCTTGTTATCTACTCCCTCCA 57.380 45.455 0.00 0.00 0.00 3.86
1980 2124 6.381133 ACTCCCTCCAATCCAAATTAATTGTC 59.619 38.462 0.39 0.00 37.32 3.18
1982 2126 5.127031 CCCTCCAATCCAAATTAATTGTCGT 59.873 40.000 0.39 0.00 37.32 4.34
2034 2178 4.417426 TTGGATCGGAGGGAGTATTTTC 57.583 45.455 0.00 0.00 0.00 2.29
2100 2244 4.406003 AGATGAAATTAGCCTGTACTCCGT 59.594 41.667 0.00 0.00 0.00 4.69
2112 2256 5.661458 CCTGTACTCCGTTTTCAGATACAT 58.339 41.667 0.00 0.00 0.00 2.29
2237 2400 5.696270 AGCTACCAAAAAGTAAAAATGCTGC 59.304 36.000 0.00 0.00 0.00 5.25
2370 2533 5.954150 GGCCCATCCATTATTGATGATAAGT 59.046 40.000 7.71 0.00 41.72 2.24
2373 2536 7.318141 CCCATCCATTATTGATGATAAGTTGC 58.682 38.462 7.71 0.00 41.72 4.17
2378 2541 7.014422 TCCATTATTGATGATAAGTTGCATGCA 59.986 33.333 18.46 18.46 38.03 3.96
2504 2667 6.174049 AGCTAAAAGTCATCCTTCCACTAAC 58.826 40.000 0.00 0.00 31.27 2.34
2511 2674 5.071788 AGTCATCCTTCCACTAACTTCAACA 59.928 40.000 0.00 0.00 0.00 3.33
2595 2758 6.206634 TGGACTTGAAAGTATGATGTTCCAAC 59.793 38.462 0.00 0.00 39.88 3.77
2608 2771 0.413037 TTCCAACATGGCCCATCCTT 59.587 50.000 0.00 0.00 37.47 3.36
2655 2818 1.203994 GCTTTGCTTGATGTGCCTCAT 59.796 47.619 0.00 0.00 39.77 2.90
2670 2833 3.192466 GCCTCATTTGATGTGGAAATGC 58.808 45.455 11.94 0.00 44.58 3.56
2671 2834 3.788937 CCTCATTTGATGTGGAAATGCC 58.211 45.455 3.54 0.00 44.58 4.40
2672 2835 3.441163 CTCATTTGATGTGGAAATGCCG 58.559 45.455 0.00 0.00 39.60 5.69
2696 2859 9.245962 CCGTTTATATTTAGTAAGGAGACACTG 57.754 37.037 0.00 0.00 0.00 3.66
2708 2871 0.674534 AGACACTGAACGGTGGACTC 59.325 55.000 16.49 6.72 41.09 3.36
2709 2872 0.674534 GACACTGAACGGTGGACTCT 59.325 55.000 16.49 0.00 41.09 3.24
2744 2907 1.002544 AGAGAAGGGAAAGAACTGCCG 59.997 52.381 0.00 0.00 0.00 5.69
2747 2910 1.266989 GAAGGGAAAGAACTGCCGTTG 59.733 52.381 0.00 0.00 32.39 4.10
2759 2922 1.358759 GCCGTTGTTGAAGGTGTGG 59.641 57.895 0.00 0.00 0.00 4.17
2818 2988 2.030185 TGGAGCACTTAGACGAACTGAC 60.030 50.000 0.00 0.00 0.00 3.51
2826 2996 0.110147 AGACGAACTGACGAGCTTCG 60.110 55.000 0.37 0.37 46.93 3.79
2862 3032 6.881602 AGGTTGTTGATCTTTTATCTGGAGAC 59.118 38.462 0.00 0.00 0.00 3.36
2963 3133 8.950208 ATAGCTAATCAGAAAGGTGTTTAGAC 57.050 34.615 0.00 0.00 33.96 2.59
2970 3140 6.601332 TCAGAAAGGTGTTTAGACAGGAAAT 58.399 36.000 0.00 0.00 36.20 2.17
2974 3144 9.892130 AGAAAGGTGTTTAGACAGGAAATATAG 57.108 33.333 0.00 0.00 36.20 1.31
2996 3166 3.064545 GTGGAATCTTGAGCTGCATACAC 59.935 47.826 1.02 0.00 0.00 2.90
3058 3228 7.926674 AAAGGAATTAGAAATGGCATTTTGG 57.073 32.000 25.02 0.00 31.47 3.28
3072 3242 4.261155 GGCATTTTGGCTTCCTTTTTGAAC 60.261 41.667 0.00 0.00 40.14 3.18
3099 3271 3.572584 GTCTTCAAACGTCGACCTATGT 58.427 45.455 10.58 0.00 0.00 2.29
3274 3446 6.670695 ACTAAATGAATTTGGTGCCTCTTT 57.329 33.333 4.22 0.00 39.53 2.52
3283 3455 0.307760 GGTGCCTCTTTTGTGACGTG 59.692 55.000 0.00 0.00 0.00 4.49
3300 3472 5.404366 GTGACGTGTTTATGTGATGTGTACT 59.596 40.000 0.00 0.00 0.00 2.73
3306 3478 8.652463 CGTGTTTATGTGATGTGTACTTCATAA 58.348 33.333 4.25 0.00 33.49 1.90
3307 3479 9.973246 GTGTTTATGTGATGTGTACTTCATAAG 57.027 33.333 4.25 0.00 33.49 1.73
3371 3543 3.947834 CACTGTTGTTCTTGGGTCTCTTT 59.052 43.478 0.00 0.00 0.00 2.52
3388 3560 4.074970 CTCTTTGCAGAAACCAGGTATGT 58.925 43.478 0.00 0.00 0.00 2.29
3432 3604 6.686130 ACGAGTTAACAAGAGTAATTGTCG 57.314 37.500 8.61 6.19 42.49 4.35
3446 3618 6.166279 AGTAATTGTCGTCATGAGTCATTGT 58.834 36.000 1.86 0.00 0.00 2.71
3459 3632 7.834681 TCATGAGTCATTGTAGTAAGAGGTACT 59.165 37.037 1.86 0.00 45.42 2.73
3486 3659 9.097257 CACTTGTAATTTAGGGCCATTAAATTG 57.903 33.333 29.29 21.02 39.65 2.32
3559 3733 6.074356 CCTTTGTATGCTGTTTTTGTTGTAGC 60.074 38.462 0.00 0.00 35.06 3.58
3707 3900 1.559682 ACCCCATGTCCACATCAGTAC 59.440 52.381 0.00 0.00 33.61 2.73
3721 3914 4.202253 ACATCAGTACAAGCAGAACAGACA 60.202 41.667 0.00 0.00 0.00 3.41
3764 3997 1.398041 CTCACACACCACACACACAAG 59.602 52.381 0.00 0.00 0.00 3.16
3822 4055 1.148498 GGCCTGAAGTTATCCCGGG 59.852 63.158 16.85 16.85 0.00 5.73
3835 4068 0.837272 TCCCGGGCTTAGAAATGAGG 59.163 55.000 18.49 0.00 0.00 3.86
3840 4073 2.644676 GGGCTTAGAAATGAGGTGACC 58.355 52.381 0.00 0.00 0.00 4.02
3846 4079 1.425066 AGAAATGAGGTGACCAAGGCA 59.575 47.619 3.63 0.00 0.00 4.75
3881 4114 1.961277 GGCCACCTCACAACTCACG 60.961 63.158 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 5.783111 AGCAAGTTTTAGGGCATACAAAAG 58.217 37.500 0.00 0.00 0.00 2.27
104 105 3.687698 TCGAAGCAAGTTTTAGGGCATAC 59.312 43.478 0.00 0.00 0.00 2.39
114 115 3.248602 CAGCAAGTAGTCGAAGCAAGTTT 59.751 43.478 0.00 0.00 0.00 2.66
128 129 7.447238 ACCTGCTCTATTTTAAAACAGCAAGTA 59.553 33.333 20.65 7.67 36.48 2.24
129 130 6.265422 ACCTGCTCTATTTTAAAACAGCAAGT 59.735 34.615 22.12 20.21 36.48 3.16
179 186 7.924103 TTTTTCTTTCCAAAATTCGAGTAGC 57.076 32.000 0.00 0.00 0.00 3.58
182 189 7.169813 GCTGATTTTTCTTTCCAAAATTCGAGT 59.830 33.333 0.00 0.00 34.61 4.18
183 190 7.383300 AGCTGATTTTTCTTTCCAAAATTCGAG 59.617 33.333 0.00 0.00 34.61 4.04
184 191 7.209475 AGCTGATTTTTCTTTCCAAAATTCGA 58.791 30.769 0.00 0.00 34.61 3.71
185 192 7.412137 AGCTGATTTTTCTTTCCAAAATTCG 57.588 32.000 0.00 0.00 34.61 3.34
186 193 7.588854 GCAAGCTGATTTTTCTTTCCAAAATTC 59.411 33.333 0.00 0.00 34.61 2.17
204 211 0.751452 TTTTGTGGCATGCAAGCTGA 59.249 45.000 21.36 0.00 34.17 4.26
208 215 1.788308 CGACTTTTTGTGGCATGCAAG 59.212 47.619 21.36 15.19 0.00 4.01
220 227 7.039644 TGTCTCTTATCCTCTTCTCGACTTTTT 60.040 37.037 0.00 0.00 0.00 1.94
240 247 2.708325 ACAAAGCCCTTCTTCTGTCTCT 59.292 45.455 0.00 0.00 32.88 3.10
245 252 4.122046 CCAAAAACAAAGCCCTTCTTCTG 58.878 43.478 0.00 0.00 32.88 3.02
266 273 9.201989 ACCCCTAAGAAAAATAGAAAATCATCC 57.798 33.333 0.00 0.00 0.00 3.51
271 278 9.601810 AGACAACCCCTAAGAAAAATAGAAAAT 57.398 29.630 0.00 0.00 0.00 1.82
272 279 9.074576 GAGACAACCCCTAAGAAAAATAGAAAA 57.925 33.333 0.00 0.00 0.00 2.29
273 280 7.389607 CGAGACAACCCCTAAGAAAAATAGAAA 59.610 37.037 0.00 0.00 0.00 2.52
278 285 4.760204 CACGAGACAACCCCTAAGAAAAAT 59.240 41.667 0.00 0.00 0.00 1.82
279 286 4.131596 CACGAGACAACCCCTAAGAAAAA 58.868 43.478 0.00 0.00 0.00 1.94
291 299 1.266175 TCTCTCCGAACACGAGACAAC 59.734 52.381 0.00 0.00 0.00 3.32
296 304 0.730265 CTCCTCTCTCCGAACACGAG 59.270 60.000 0.00 0.00 0.00 4.18
299 307 1.513622 GCCTCCTCTCTCCGAACAC 59.486 63.158 0.00 0.00 0.00 3.32
313 321 4.863925 GAGAGCTGTCGCCGCCTC 62.864 72.222 0.00 0.00 36.60 4.70
338 346 6.056236 GTCTAGGCGGGAAGAAATTTATTCT 58.944 40.000 21.37 7.32 0.00 2.40
351 359 1.751927 GAACGAGGTCTAGGCGGGA 60.752 63.158 0.00 0.00 0.00 5.14
361 369 0.687354 AAGCACCATCAGAACGAGGT 59.313 50.000 0.00 0.00 33.91 3.85
370 378 0.179137 CGACGCTAGAAGCACCATCA 60.179 55.000 0.00 0.00 42.58 3.07
378 386 0.378962 CCCTCTGACGACGCTAGAAG 59.621 60.000 0.00 0.00 0.00 2.85
381 389 1.306642 ACACCCTCTGACGACGCTAG 61.307 60.000 0.00 0.00 0.00 3.42
408 416 1.540363 GCAAGATCCGCCGGAGATAAA 60.540 52.381 13.12 0.00 34.05 1.40
411 419 2.374830 CTGCAAGATCCGCCGGAGAT 62.375 60.000 13.12 6.33 34.05 2.75
412 420 3.074369 TGCAAGATCCGCCGGAGA 61.074 61.111 13.12 0.00 34.05 3.71
416 424 1.502163 GAATCCTGCAAGATCCGCCG 61.502 60.000 0.00 0.00 34.07 6.46
441 449 2.131972 GGATCCACCAAAAACAAACGC 58.868 47.619 6.95 0.00 38.79 4.84
470 478 0.580104 GACACACGAACAAAGACCGG 59.420 55.000 0.00 0.00 0.00 5.28
515 523 2.036346 ACCAGTGCCATTGAAAAGAAGC 59.964 45.455 0.00 0.00 0.00 3.86
521 529 2.499289 ACAACAACCAGTGCCATTGAAA 59.501 40.909 6.92 0.00 0.00 2.69
532 540 1.664016 GCGCATCAGAACAACAACCAG 60.664 52.381 0.30 0.00 0.00 4.00
542 550 1.123077 ATAGGACCAGCGCATCAGAA 58.877 50.000 11.47 0.00 0.00 3.02
564 572 1.078848 AAGTCGTCATGCTGAGGCC 60.079 57.895 0.00 0.00 37.74 5.19
574 582 3.562973 AGTAAACAGTCGAGAAGTCGTCA 59.437 43.478 0.00 0.00 46.85 4.35
592 600 4.202070 GCTGGGCAAAACTTGTTGTAGTAA 60.202 41.667 0.00 0.00 0.00 2.24
598 606 1.410153 AGAGCTGGGCAAAACTTGTTG 59.590 47.619 0.00 0.00 0.00 3.33
601 609 3.507233 TCATTAGAGCTGGGCAAAACTTG 59.493 43.478 0.00 0.00 0.00 3.16
620 628 0.982852 TGTCATCGCCCCTCCTTCAT 60.983 55.000 0.00 0.00 0.00 2.57
664 672 3.619483 AGTAGACAGTCGAGAAGTCATCG 59.381 47.826 12.59 0.00 41.50 3.84
665 673 5.581479 TGTAGTAGACAGTCGAGAAGTCATC 59.419 44.000 12.59 6.45 34.80 2.92
666 674 5.489249 TGTAGTAGACAGTCGAGAAGTCAT 58.511 41.667 12.59 3.35 34.80 3.06
667 675 4.891260 TGTAGTAGACAGTCGAGAAGTCA 58.109 43.478 12.59 0.00 34.80 3.41
668 676 5.178996 TGTTGTAGTAGACAGTCGAGAAGTC 59.821 44.000 0.00 4.19 39.88 3.01
669 677 5.061853 TGTTGTAGTAGACAGTCGAGAAGT 58.938 41.667 0.00 0.00 39.88 3.01
670 678 5.608676 TGTTGTAGTAGACAGTCGAGAAG 57.391 43.478 0.00 0.00 39.88 2.85
671 679 5.530171 ACTTGTTGTAGTAGACAGTCGAGAA 59.470 40.000 0.00 0.00 39.88 2.87
672 680 5.061853 ACTTGTTGTAGTAGACAGTCGAGA 58.938 41.667 0.00 0.00 39.88 4.04
673 681 5.359716 ACTTGTTGTAGTAGACAGTCGAG 57.640 43.478 0.00 0.00 39.88 4.04
674 682 5.762825 AACTTGTTGTAGTAGACAGTCGA 57.237 39.130 0.00 0.00 39.88 4.20
675 683 6.637365 CAAAACTTGTTGTAGTAGACAGTCG 58.363 40.000 0.00 0.00 39.88 4.18
676 684 6.419771 GCAAAACTTGTTGTAGTAGACAGTC 58.580 40.000 0.00 0.00 39.88 3.51
677 685 5.296035 GGCAAAACTTGTTGTAGTAGACAGT 59.704 40.000 0.00 0.00 39.88 3.55
678 686 5.277828 GGGCAAAACTTGTTGTAGTAGACAG 60.278 44.000 0.00 0.00 39.88 3.51
679 687 4.577283 GGGCAAAACTTGTTGTAGTAGACA 59.423 41.667 0.00 0.00 35.78 3.41
680 688 4.577283 TGGGCAAAACTTGTTGTAGTAGAC 59.423 41.667 0.00 0.00 0.00 2.59
681 689 4.783055 TGGGCAAAACTTGTTGTAGTAGA 58.217 39.130 0.00 0.00 0.00 2.59
682 690 4.556699 GCTGGGCAAAACTTGTTGTAGTAG 60.557 45.833 0.00 0.00 0.00 2.57
683 691 3.316868 GCTGGGCAAAACTTGTTGTAGTA 59.683 43.478 0.00 0.00 0.00 1.82
684 692 2.100749 GCTGGGCAAAACTTGTTGTAGT 59.899 45.455 0.00 0.00 0.00 2.73
685 693 2.362077 AGCTGGGCAAAACTTGTTGTAG 59.638 45.455 0.00 0.00 0.00 2.74
686 694 2.360801 GAGCTGGGCAAAACTTGTTGTA 59.639 45.455 0.00 0.00 0.00 2.41
687 695 1.136891 GAGCTGGGCAAAACTTGTTGT 59.863 47.619 0.00 0.00 0.00 3.32
688 696 1.410153 AGAGCTGGGCAAAACTTGTTG 59.590 47.619 0.00 0.00 0.00 3.33
689 697 1.780503 AGAGCTGGGCAAAACTTGTT 58.219 45.000 0.00 0.00 0.00 2.83
690 698 2.656947 TAGAGCTGGGCAAAACTTGT 57.343 45.000 0.00 0.00 0.00 3.16
691 699 3.507233 TCATTAGAGCTGGGCAAAACTTG 59.493 43.478 0.00 0.00 0.00 3.16
692 700 3.766545 TCATTAGAGCTGGGCAAAACTT 58.233 40.909 0.00 0.00 0.00 2.66
693 701 3.439857 TCATTAGAGCTGGGCAAAACT 57.560 42.857 0.00 0.00 0.00 2.66
694 702 3.119352 CCTTCATTAGAGCTGGGCAAAAC 60.119 47.826 0.00 0.00 0.00 2.43
695 703 3.091545 CCTTCATTAGAGCTGGGCAAAA 58.908 45.455 0.00 0.00 0.00 2.44
696 704 2.308570 TCCTTCATTAGAGCTGGGCAAA 59.691 45.455 0.00 0.00 0.00 3.68
697 705 1.915489 TCCTTCATTAGAGCTGGGCAA 59.085 47.619 0.00 0.00 0.00 4.52
698 706 1.487976 CTCCTTCATTAGAGCTGGGCA 59.512 52.381 0.00 0.00 0.00 5.36
699 707 1.202746 CCTCCTTCATTAGAGCTGGGC 60.203 57.143 0.00 0.00 0.00 5.36
700 708 1.419387 CCCTCCTTCATTAGAGCTGGG 59.581 57.143 0.00 0.00 0.00 4.45
701 709 1.419387 CCCCTCCTTCATTAGAGCTGG 59.581 57.143 0.00 0.00 0.00 4.85
702 710 1.202746 GCCCCTCCTTCATTAGAGCTG 60.203 57.143 0.00 0.00 0.00 4.24
703 711 1.135960 GCCCCTCCTTCATTAGAGCT 58.864 55.000 0.00 0.00 0.00 4.09
704 712 0.250081 CGCCCCTCCTTCATTAGAGC 60.250 60.000 0.00 0.00 0.00 4.09
705 713 1.414158 TCGCCCCTCCTTCATTAGAG 58.586 55.000 0.00 0.00 0.00 2.43
706 714 1.694150 CATCGCCCCTCCTTCATTAGA 59.306 52.381 0.00 0.00 0.00 2.10
707 715 1.694150 TCATCGCCCCTCCTTCATTAG 59.306 52.381 0.00 0.00 0.00 1.73
708 716 1.416401 GTCATCGCCCCTCCTTCATTA 59.584 52.381 0.00 0.00 0.00 1.90
709 717 0.181350 GTCATCGCCCCTCCTTCATT 59.819 55.000 0.00 0.00 0.00 2.57
710 718 0.982852 TGTCATCGCCCCTCCTTCAT 60.983 55.000 0.00 0.00 0.00 2.57
711 719 0.982852 ATGTCATCGCCCCTCCTTCA 60.983 55.000 0.00 0.00 0.00 3.02
712 720 0.250081 GATGTCATCGCCCCTCCTTC 60.250 60.000 0.00 0.00 0.00 3.46
713 721 1.832912 GATGTCATCGCCCCTCCTT 59.167 57.895 0.00 0.00 0.00 3.36
714 722 2.502492 CGATGTCATCGCCCCTCCT 61.502 63.158 21.42 0.00 46.55 3.69
715 723 2.029666 CGATGTCATCGCCCCTCC 59.970 66.667 21.42 0.00 46.55 4.30
723 731 1.766143 GAAGGCGCACCGATGTCATC 61.766 60.000 10.83 2.43 42.76 2.92
724 732 1.815421 GAAGGCGCACCGATGTCAT 60.815 57.895 10.83 0.00 42.76 3.06
725 733 2.434185 GAAGGCGCACCGATGTCA 60.434 61.111 10.83 0.00 42.76 3.58
726 734 3.554692 CGAAGGCGCACCGATGTC 61.555 66.667 10.83 0.00 42.76 3.06
737 745 4.538736 AGCATTGAAGCAAACCGAAGGC 62.539 50.000 0.00 0.00 46.15 4.35
739 747 2.712057 AGCATTGAAGCAAACCGAAG 57.288 45.000 0.00 0.00 36.85 3.79
740 748 4.782019 ATAAGCATTGAAGCAAACCGAA 57.218 36.364 0.00 0.00 36.85 4.30
741 749 4.941263 ACTATAAGCATTGAAGCAAACCGA 59.059 37.500 0.00 0.00 36.85 4.69
742 750 5.235305 ACTATAAGCATTGAAGCAAACCG 57.765 39.130 0.00 0.00 36.85 4.44
743 751 5.163754 ACGACTATAAGCATTGAAGCAAACC 60.164 40.000 0.00 0.00 36.85 3.27
744 752 5.869350 ACGACTATAAGCATTGAAGCAAAC 58.131 37.500 0.00 0.00 36.85 2.93
745 753 5.220397 CGACGACTATAAGCATTGAAGCAAA 60.220 40.000 0.00 0.00 36.85 3.68
746 754 4.267690 CGACGACTATAAGCATTGAAGCAA 59.732 41.667 0.00 0.00 36.85 3.91
747 755 3.796717 CGACGACTATAAGCATTGAAGCA 59.203 43.478 0.00 0.00 36.85 3.91
748 756 3.362110 GCGACGACTATAAGCATTGAAGC 60.362 47.826 0.00 0.00 0.00 3.86
749 757 4.045104 AGCGACGACTATAAGCATTGAAG 58.955 43.478 0.00 0.00 0.00 3.02
750 758 4.041740 AGCGACGACTATAAGCATTGAA 57.958 40.909 0.00 0.00 0.00 2.69
751 759 3.710326 AGCGACGACTATAAGCATTGA 57.290 42.857 0.00 0.00 0.00 2.57
752 760 4.870315 GTAGCGACGACTATAAGCATTG 57.130 45.455 0.00 0.00 0.00 2.82
786 794 8.199449 GGCAGAAATGATAAAAATTCATCCAGA 58.801 33.333 0.00 0.00 32.72 3.86
796 805 7.151308 ACAACGAATGGCAGAAATGATAAAAA 58.849 30.769 0.00 0.00 0.00 1.94
804 813 4.072131 ACACTACAACGAATGGCAGAAAT 58.928 39.130 0.00 0.00 0.00 2.17
811 820 5.351189 TCAATCATGACACTACAACGAATGG 59.649 40.000 0.00 0.00 0.00 3.16
814 823 6.162777 TCATCAATCATGACACTACAACGAA 58.837 36.000 0.00 0.00 38.69 3.85
820 829 8.441608 GCTATTCATCATCAATCATGACACTAC 58.558 37.037 0.00 0.00 44.70 2.73
823 832 7.388224 AGAGCTATTCATCATCAATCATGACAC 59.612 37.037 0.00 0.00 44.70 3.67
825 834 7.908827 AGAGCTATTCATCATCAATCATGAC 57.091 36.000 0.00 0.00 44.70 3.06
872 881 4.440250 CGCTCTTATATTATGGGACGGGAG 60.440 50.000 0.00 0.00 0.00 4.30
873 882 3.446161 CGCTCTTATATTATGGGACGGGA 59.554 47.826 0.00 0.00 0.00 5.14
874 883 3.194968 ACGCTCTTATATTATGGGACGGG 59.805 47.826 0.00 0.00 0.00 5.28
875 884 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
876 885 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
877 886 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
878 887 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
879 888 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
880 889 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
883 892 9.865321 AGTAGTGTCAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 45.69 0.98
884 893 8.773404 AGTAGTGTCAAAAACGCTCTTATATT 57.227 30.769 0.00 0.00 45.69 1.28
885 894 8.773404 AAGTAGTGTCAAAAACGCTCTTATAT 57.227 30.769 0.00 0.00 45.69 0.86
886 895 9.350357 CTAAGTAGTGTCAAAAACGCTCTTATA 57.650 33.333 0.00 0.00 45.69 0.98
887 896 8.086522 TCTAAGTAGTGTCAAAAACGCTCTTAT 58.913 33.333 0.00 0.00 45.69 1.73
888 897 7.428020 TCTAAGTAGTGTCAAAAACGCTCTTA 58.572 34.615 0.00 3.56 45.69 2.10
889 898 6.278363 TCTAAGTAGTGTCAAAAACGCTCTT 58.722 36.000 0.00 2.70 45.69 2.85
890 899 5.839621 TCTAAGTAGTGTCAAAAACGCTCT 58.160 37.500 0.00 0.00 45.69 4.09
891 900 6.520792 TTCTAAGTAGTGTCAAAAACGCTC 57.479 37.500 0.00 0.00 45.69 5.03
893 902 9.821662 ATATTTTCTAAGTAGTGTCAAAAACGC 57.178 29.630 0.00 0.00 38.74 4.84
902 911 9.938280 TGTGCTTACATATTTTCTAAGTAGTGT 57.062 29.630 0.00 0.00 0.00 3.55
917 926 7.657354 GGATTGACTCATACATGTGCTTACATA 59.343 37.037 9.11 0.00 0.00 2.29
920 929 5.050769 CGGATTGACTCATACATGTGCTTAC 60.051 44.000 9.11 0.00 0.00 2.34
1265 1277 2.464459 CCTCGCCAAATCTGCCGAC 61.464 63.158 0.00 0.00 0.00 4.79
1398 1410 3.607741 CAAGAAGCATCATGACTCCAGT 58.392 45.455 0.00 0.00 0.00 4.00
1422 1434 7.062956 CAGCGTACTACATATGAAAAGAACACA 59.937 37.037 10.38 0.00 0.00 3.72
1431 1443 5.515797 AAGCTCAGCGTACTACATATGAA 57.484 39.130 10.38 0.00 0.00 2.57
1478 1493 0.469917 ATGTAATCCTCCACGGCCTG 59.530 55.000 0.00 0.00 0.00 4.85
1510 1525 3.381272 CAGAAAACAAGGAGGCAAGACAA 59.619 43.478 0.00 0.00 0.00 3.18
1572 1588 3.126831 CAAATCGACCTCATCACTAGCC 58.873 50.000 0.00 0.00 0.00 3.93
1653 1670 4.858850 ACCAAATCATATCCACAGCTTCA 58.141 39.130 0.00 0.00 0.00 3.02
1685 1719 7.363443 CCTCGGACCAAAACAACCAATAATTAT 60.363 37.037 0.00 0.00 0.00 1.28
1720 1754 8.206325 ACTAAATTCTCAACATGACTGCATAG 57.794 34.615 0.00 0.00 32.27 2.23
1722 1756 7.458409 AACTAAATTCTCAACATGACTGCAT 57.542 32.000 0.00 0.00 34.29 3.96
1759 1793 7.736031 CATCAAGATGCACAAGAACAAATAG 57.264 36.000 0.00 0.00 31.39 1.73
1887 2031 7.591057 TGAAGCATAAAAACAAGAGAACATTCG 59.409 33.333 0.00 0.00 0.00 3.34
1937 2081 4.202274 GGGAGTAGATAACAAGGAAGAGCC 60.202 50.000 0.00 0.00 0.00 4.70
2034 2178 4.806640 ACCATTGCAATACCAAAGGAAG 57.193 40.909 12.53 0.00 37.11 3.46
2141 2285 6.876257 AGCACTTAAAAGTTCAGAGTCCATAG 59.124 38.462 0.00 0.00 37.08 2.23
2237 2400 8.846943 TGCAATATGTTATAATGGTCACTAGG 57.153 34.615 0.00 0.00 0.00 3.02
2269 2432 5.219633 GCGATTTACAACAAACCAGTCATT 58.780 37.500 0.00 0.00 0.00 2.57
2370 2533 4.804868 ACCTGACAATAATTGCATGCAA 57.195 36.364 33.57 33.57 40.47 4.08
2373 2536 7.929159 TGTACATACCTGACAATAATTGCATG 58.071 34.615 0.00 0.00 0.00 4.06
2378 2541 8.965819 TGCAAATGTACATACCTGACAATAATT 58.034 29.630 9.21 0.00 0.00 1.40
2460 2623 3.429085 CTTTTGGTAAGATCGCATGCAC 58.571 45.455 19.57 6.78 0.00 4.57
2504 2667 7.976175 TCAGATGCTTATAGTACAGTGTTGAAG 59.024 37.037 0.00 0.00 0.00 3.02
2544 2707 5.794687 TGGAACTGTAATATGCAAGTTCG 57.205 39.130 16.53 0.84 37.21 3.95
2595 2758 1.822990 GCATGATAAGGATGGGCCATG 59.177 52.381 26.77 8.85 40.02 3.66
2600 2763 3.087031 GGACATGCATGATAAGGATGGG 58.913 50.000 32.75 1.99 38.89 4.00
2608 2771 7.701539 AAAGTAAACAAGGACATGCATGATA 57.298 32.000 32.75 9.27 0.00 2.15
2645 2808 3.090210 TCCACATCAAATGAGGCACAT 57.910 42.857 0.00 0.00 40.33 3.21
2655 2818 3.742433 AAACGGCATTTCCACATCAAA 57.258 38.095 0.00 0.00 34.01 2.69
2670 2833 9.245962 CAGTGTCTCCTTACTAAATATAAACGG 57.754 37.037 0.00 0.00 0.00 4.44
2696 2859 3.655276 TTTACAGAGAGTCCACCGTTC 57.345 47.619 0.00 0.00 0.00 3.95
2698 2861 3.162666 TGATTTACAGAGAGTCCACCGT 58.837 45.455 0.00 0.00 0.00 4.83
2699 2862 3.868757 TGATTTACAGAGAGTCCACCG 57.131 47.619 0.00 0.00 0.00 4.94
2744 2907 2.687935 ACATGACCACACCTTCAACAAC 59.312 45.455 0.00 0.00 0.00 3.32
2747 2910 5.003804 AGAATACATGACCACACCTTCAAC 58.996 41.667 0.00 0.00 0.00 3.18
2785 2948 1.078497 TGCTCCATACACTTGCGGG 60.078 57.895 0.00 0.00 0.00 6.13
2786 2949 0.391661 AGTGCTCCATACACTTGCGG 60.392 55.000 0.00 0.00 46.01 5.69
2787 2950 3.143675 AGTGCTCCATACACTTGCG 57.856 52.632 0.00 0.00 46.01 4.85
2805 2975 2.412455 CGAAGCTCGTCAGTTCGTCTAA 60.412 50.000 0.00 0.00 38.57 2.10
2809 2979 4.535425 CGAAGCTCGTCAGTTCGT 57.465 55.556 0.00 0.00 38.57 3.85
2818 2988 1.205064 CAACCTGCAACGAAGCTCG 59.795 57.895 0.00 4.36 46.93 5.03
2826 2996 1.748493 TCAACAACCTCAACCTGCAAC 59.252 47.619 0.00 0.00 0.00 4.17
2862 3032 3.412386 ACTCAATTTTTCTCCCTCGGTG 58.588 45.455 0.00 0.00 0.00 4.94
2912 3082 1.335810 CTTTCTGCTGTTCAGCTTGCA 59.664 47.619 22.44 5.51 42.56 4.08
2913 3083 1.929482 GCTTTCTGCTGTTCAGCTTGC 60.929 52.381 22.44 15.37 42.56 4.01
2920 3090 3.916776 GCTATTGTTGCTTTCTGCTGTTC 59.083 43.478 0.00 0.00 43.37 3.18
2925 3095 5.883661 TGATTAGCTATTGTTGCTTTCTGC 58.116 37.500 0.00 0.00 41.46 4.26
2937 3107 9.384764 GTCTAAACACCTTTCTGATTAGCTATT 57.615 33.333 0.00 0.00 30.39 1.73
2963 3133 7.172875 CAGCTCAAGATTCCACTATATTTCCTG 59.827 40.741 0.00 0.00 0.00 3.86
2970 3140 5.557576 ATGCAGCTCAAGATTCCACTATA 57.442 39.130 0.00 0.00 0.00 1.31
2974 3144 3.064545 GTGTATGCAGCTCAAGATTCCAC 59.935 47.826 0.00 0.00 0.00 4.02
2996 3166 1.466167 CAGCGGACCACTTCAGATTTG 59.534 52.381 0.00 0.00 0.00 2.32
3038 3208 6.037500 GGAAGCCAAAATGCCATTTCTAATTC 59.962 38.462 2.61 6.40 0.00 2.17
3058 3228 3.977427 ACCATTCGTTCAAAAAGGAAGC 58.023 40.909 0.00 0.00 41.20 3.86
3072 3242 2.055838 TCGACGTTTGAAGACCATTCG 58.944 47.619 0.00 0.00 0.00 3.34
3099 3271 7.067421 AGTAGAGCAATATAGTGTTACAGGGA 58.933 38.462 1.67 0.00 0.00 4.20
3274 3446 4.572795 ACACATCACATAAACACGTCACAA 59.427 37.500 0.00 0.00 0.00 3.33
3306 3478 7.275183 TGCTACAGTTATATTGCATGACTTCT 58.725 34.615 0.00 0.00 0.00 2.85
3307 3479 7.482654 TGCTACAGTTATATTGCATGACTTC 57.517 36.000 0.00 0.00 0.00 3.01
3343 3515 2.549992 CCCAAGAACAACAGTGGATCGA 60.550 50.000 0.00 0.00 32.54 3.59
3371 3543 2.563620 TCGTACATACCTGGTTTCTGCA 59.436 45.455 3.84 0.00 0.00 4.41
3388 3560 7.814107 ACTCGTAATCAACCAAAGTAAATCGTA 59.186 33.333 0.00 0.00 0.00 3.43
3432 3604 6.868622 ACCTCTTACTACAATGACTCATGAC 58.131 40.000 0.00 0.00 0.00 3.06
3459 3632 8.602472 ATTTAATGGCCCTAAATTACAAGTGA 57.398 30.769 12.14 0.00 0.00 3.41
3486 3659 7.534723 AATTACTGGTCCTTTCCCTAAAAAC 57.465 36.000 0.00 0.00 0.00 2.43
3619 3797 9.146984 CTTGCCATTTATTTGCTGGATATATTG 57.853 33.333 0.00 0.00 31.38 1.90
3673 3865 2.435372 TGGGGTTGTGAATCTATGGC 57.565 50.000 0.00 0.00 0.00 4.40
3679 3871 1.818674 GTGGACATGGGGTTGTGAATC 59.181 52.381 0.00 0.00 0.00 2.52
3822 4055 3.691609 CCTTGGTCACCTCATTTCTAAGC 59.308 47.826 0.00 0.00 0.00 3.09
3835 4068 2.427095 ACAAGTTCTTTGCCTTGGTCAC 59.573 45.455 0.00 0.00 41.84 3.67
3840 4073 2.951642 TGGAGACAAGTTCTTTGCCTTG 59.048 45.455 0.00 0.00 42.91 3.61
3881 4114 1.080025 GTCACGTACCAGTGCTCCC 60.080 63.158 0.00 0.00 41.61 4.30
3912 4145 6.301169 AGTTCTTCCATAGACTTGTAAGGG 57.699 41.667 0.00 0.00 30.90 3.95


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

AutoCloner maintained by Alex Coulton.