Multiple sequence alignment - TraesCS5A01G112500

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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 TraesCS5A01G112500 chr5A 100.000 9235 0 0 1 9235 219681314 219690548 0.000000e+00 17054.0
1 TraesCS5A01G112500 chr5A 98.586 4880 51 2 1194 6057 676383830 676378953 0.000000e+00 8613.0
2 TraesCS5A01G112500 chr5A 89.327 787 79 4 1 786 524341269 524342051 0.000000e+00 983.0
3 TraesCS5A01G112500 chr5A 86.294 197 20 6 8800 8992 596040448 596040255 3.380000e-49 207.0
4 TraesCS5A01G112500 chr5A 94.845 97 4 1 8144 8240 157237927 157237832 5.780000e-32 150.0
5 TraesCS5A01G112500 chr4B 98.689 4881 47 2 1194 6057 545463607 545458727 0.000000e+00 8643.0
6 TraesCS5A01G112500 chr1B 98.586 4881 53 2 1193 6057 670955608 670950728 0.000000e+00 8617.0
7 TraesCS5A01G112500 chr1B 98.506 4886 51 3 1194 6057 457063206 457058321 0.000000e+00 8599.0
8 TraesCS5A01G112500 chr1B 94.898 98 4 1 8143 8240 671967467 671967563 1.610000e-32 152.0
9 TraesCS5A01G112500 chr5B 98.586 4880 50 2 1194 6057 337169055 337173931 0.000000e+00 8612.0
10 TraesCS5A01G112500 chr5B 98.095 4882 66 4 1194 6057 137990660 137985788 0.000000e+00 8475.0
11 TraesCS5A01G112500 chr5B 98.502 4539 52 1 1535 6057 545082803 545078265 0.000000e+00 7991.0
12 TraesCS5A01G112500 chr5B 95.771 2081 68 10 6071 8143 208709710 208707642 0.000000e+00 3338.0
13 TraesCS5A01G112500 chr5B 90.511 411 16 6 801 1195 208710163 208709760 1.060000e-143 521.0
14 TraesCS5A01G112500 chr5B 99.187 123 1 0 8229 8351 208707654 208707532 1.210000e-53 222.0
15 TraesCS5A01G112500 chr5B 92.929 99 5 2 8143 8240 706981476 706981379 9.670000e-30 143.0
16 TraesCS5A01G112500 chr5B 89.362 94 10 0 7728 7821 100836921 100837014 1.630000e-22 119.0
17 TraesCS5A01G112500 chr4A 98.525 4880 53 2 1194 6057 714276497 714271621 0.000000e+00 8595.0
18 TraesCS5A01G112500 chr4A 90.991 111 10 0 7752 7862 257295306 257295196 5.780000e-32 150.0
19 TraesCS5A01G112500 chr7A 98.443 4881 60 1 1193 6057 148165048 148169928 0.000000e+00 8578.0
20 TraesCS5A01G112500 chr7A 84.235 647 85 15 1 642 119481160 119480526 1.700000e-171 614.0
21 TraesCS5A01G112500 chr7A 78.993 457 59 21 8800 9235 250692635 250692195 2.540000e-70 278.0
22 TraesCS5A01G112500 chr6B 98.443 4880 56 3 1194 6057 87528422 87533297 0.000000e+00 8573.0
23 TraesCS5A01G112500 chr6B 98.404 4887 55 3 1194 6057 361591321 361586435 0.000000e+00 8571.0
24 TraesCS5A01G112500 chr6B 98.362 4884 60 4 1192 6057 498854954 498859835 0.000000e+00 8558.0
25 TraesCS5A01G112500 chr6B 98.021 4902 59 8 1194 6057 17104643 17099742 0.000000e+00 8480.0
26 TraesCS5A01G112500 chr6B 98.481 4675 55 1 1399 6057 604695419 604690745 0.000000e+00 8226.0
27 TraesCS5A01G112500 chr6B 97.879 1886 24 1 4188 6057 80972564 80970679 0.000000e+00 3247.0
28 TraesCS5A01G112500 chr6B 97.158 1689 31 2 4385 6057 537320950 537322637 0.000000e+00 2837.0
29 TraesCS5A01G112500 chr2B 98.266 3980 50 3 2095 6058 123116070 123120046 0.000000e+00 6950.0
30 TraesCS5A01G112500 chr2B 85.390 794 98 10 2 781 134381914 134381125 0.000000e+00 808.0
31 TraesCS5A01G112500 chr2B 85.714 91 13 0 8352 8442 212937899 212937989 7.630000e-16 97.1
32 TraesCS5A01G112500 chr5D 95.677 1920 54 12 6229 8143 202906025 202907920 0.000000e+00 3059.0
33 TraesCS5A01G112500 chr5D 86.493 422 19 17 801 1193 202905314 202905726 6.630000e-116 429.0
34 TraesCS5A01G112500 chr5D 79.254 617 82 33 8641 9235 368822598 368822006 1.120000e-103 388.0
35 TraesCS5A01G112500 chr5D 99.167 120 1 0 6071 6190 202905778 202905897 5.620000e-52 217.0
36 TraesCS5A01G112500 chr5D 95.935 123 2 1 8229 8351 202907908 202908027 7.320000e-46 196.0
37 TraesCS5A01G112500 chr5D 90.226 133 13 0 7728 7860 436547032 436546900 3.430000e-39 174.0
38 TraesCS5A01G112500 chr5D 92.727 110 6 2 8132 8240 330892279 330892387 3.450000e-34 158.0
39 TraesCS5A01G112500 chr2D 93.281 893 31 15 8345 9235 539257314 539258179 0.000000e+00 1290.0
40 TraesCS5A01G112500 chr2D 84.197 791 70 23 1 786 165005079 165004339 0.000000e+00 717.0
41 TraesCS5A01G112500 chr2D 93.000 100 6 1 8141 8240 643739849 643739947 2.690000e-30 145.0
42 TraesCS5A01G112500 chr3A 88.005 792 70 11 1 782 99566015 99565239 0.000000e+00 913.0
43 TraesCS5A01G112500 chr3A 96.491 342 9 3 8895 9235 547411933 547411594 6.260000e-156 562.0
44 TraesCS5A01G112500 chr3A 93.562 233 9 6 8612 8842 547412152 547411924 8.880000e-90 342.0
45 TraesCS5A01G112500 chr3A 92.523 107 7 1 8341 8446 33141654 33141760 1.610000e-32 152.0
46 TraesCS5A01G112500 chr3A 88.172 93 11 0 8350 8442 102104995 102104903 2.730000e-20 111.0
47 TraesCS5A01G112500 chr3D 87.595 790 90 5 1 786 475301769 475302554 0.000000e+00 909.0
48 TraesCS5A01G112500 chr2A 87.084 782 85 8 1 781 739177356 739178122 0.000000e+00 870.0
49 TraesCS5A01G112500 chr2A 86.772 635 70 8 154 777 116455570 116454939 0.000000e+00 695.0
50 TraesCS5A01G112500 chr2A 86.268 619 73 10 169 786 459835525 459834918 0.000000e+00 662.0
51 TraesCS5A01G112500 chr7D 86.658 787 89 12 1 786 608484367 608485138 0.000000e+00 857.0
52 TraesCS5A01G112500 chr6D 85.347 778 92 9 2 778 384205781 384205025 0.000000e+00 785.0
53 TraesCS5A01G112500 chr6D 93.814 97 5 1 8144 8240 135554919 135555014 2.690000e-30 145.0
54 TraesCS5A01G112500 chr1A 83.777 789 114 10 1 782 419024147 419023366 0.000000e+00 736.0
55 TraesCS5A01G112500 chr3B 92.143 140 8 1 7724 7860 273250204 273250343 2.630000e-45 195.0
56 TraesCS5A01G112500 chr3B 93.878 98 4 2 8143 8240 449313172 449313077 7.470000e-31 147.0
57 TraesCS5A01G112500 chr1D 91.429 140 9 1 7724 7860 241967655 241967516 1.220000e-43 189.0
58 TraesCS5A01G112500 chr1D 96.907 97 2 1 8138 8234 442700764 442700669 2.670000e-35 161.0
59 TraesCS5A01G112500 chr1D 94.681 94 4 1 8141 8234 4629650 4629558 2.690000e-30 145.0
60 TraesCS5A01G112500 chr7B 94.059 101 4 2 8892 8991 557434058 557434157 1.610000e-32 152.0


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 TraesCS5A01G112500 chr5A 219681314 219690548 9234 False 17054.000000 17054 100.000000 1 9235 1 chr5A.!!$F1 9234
1 TraesCS5A01G112500 chr5A 676378953 676383830 4877 True 8613.000000 8613 98.586000 1194 6057 1 chr5A.!!$R3 4863
2 TraesCS5A01G112500 chr5A 524341269 524342051 782 False 983.000000 983 89.327000 1 786 1 chr5A.!!$F2 785
3 TraesCS5A01G112500 chr4B 545458727 545463607 4880 True 8643.000000 8643 98.689000 1194 6057 1 chr4B.!!$R1 4863
4 TraesCS5A01G112500 chr1B 670950728 670955608 4880 True 8617.000000 8617 98.586000 1193 6057 1 chr1B.!!$R2 4864
5 TraesCS5A01G112500 chr1B 457058321 457063206 4885 True 8599.000000 8599 98.506000 1194 6057 1 chr1B.!!$R1 4863
6 TraesCS5A01G112500 chr5B 337169055 337173931 4876 False 8612.000000 8612 98.586000 1194 6057 1 chr5B.!!$F2 4863
7 TraesCS5A01G112500 chr5B 137985788 137990660 4872 True 8475.000000 8475 98.095000 1194 6057 1 chr5B.!!$R1 4863
8 TraesCS5A01G112500 chr5B 545078265 545082803 4538 True 7991.000000 7991 98.502000 1535 6057 1 chr5B.!!$R2 4522
9 TraesCS5A01G112500 chr5B 208707532 208710163 2631 True 1360.333333 3338 95.156333 801 8351 3 chr5B.!!$R4 7550
10 TraesCS5A01G112500 chr4A 714271621 714276497 4876 True 8595.000000 8595 98.525000 1194 6057 1 chr4A.!!$R2 4863
11 TraesCS5A01G112500 chr7A 148165048 148169928 4880 False 8578.000000 8578 98.443000 1193 6057 1 chr7A.!!$F1 4864
12 TraesCS5A01G112500 chr7A 119480526 119481160 634 True 614.000000 614 84.235000 1 642 1 chr7A.!!$R1 641
13 TraesCS5A01G112500 chr6B 87528422 87533297 4875 False 8573.000000 8573 98.443000 1194 6057 1 chr6B.!!$F1 4863
14 TraesCS5A01G112500 chr6B 361586435 361591321 4886 True 8571.000000 8571 98.404000 1194 6057 1 chr6B.!!$R3 4863
15 TraesCS5A01G112500 chr6B 498854954 498859835 4881 False 8558.000000 8558 98.362000 1192 6057 1 chr6B.!!$F2 4865
16 TraesCS5A01G112500 chr6B 17099742 17104643 4901 True 8480.000000 8480 98.021000 1194 6057 1 chr6B.!!$R1 4863
17 TraesCS5A01G112500 chr6B 604690745 604695419 4674 True 8226.000000 8226 98.481000 1399 6057 1 chr6B.!!$R4 4658
18 TraesCS5A01G112500 chr6B 80970679 80972564 1885 True 3247.000000 3247 97.879000 4188 6057 1 chr6B.!!$R2 1869
19 TraesCS5A01G112500 chr6B 537320950 537322637 1687 False 2837.000000 2837 97.158000 4385 6057 1 chr6B.!!$F3 1672
20 TraesCS5A01G112500 chr2B 123116070 123120046 3976 False 6950.000000 6950 98.266000 2095 6058 1 chr2B.!!$F1 3963
21 TraesCS5A01G112500 chr2B 134381125 134381914 789 True 808.000000 808 85.390000 2 781 1 chr2B.!!$R1 779
22 TraesCS5A01G112500 chr5D 202905314 202908027 2713 False 975.250000 3059 94.318000 801 8351 4 chr5D.!!$F2 7550
23 TraesCS5A01G112500 chr5D 368822006 368822598 592 True 388.000000 388 79.254000 8641 9235 1 chr5D.!!$R1 594
24 TraesCS5A01G112500 chr2D 539257314 539258179 865 False 1290.000000 1290 93.281000 8345 9235 1 chr2D.!!$F1 890
25 TraesCS5A01G112500 chr2D 165004339 165005079 740 True 717.000000 717 84.197000 1 786 1 chr2D.!!$R1 785
26 TraesCS5A01G112500 chr3A 99565239 99566015 776 True 913.000000 913 88.005000 1 782 1 chr3A.!!$R1 781
27 TraesCS5A01G112500 chr3A 547411594 547412152 558 True 452.000000 562 95.026500 8612 9235 2 chr3A.!!$R3 623
28 TraesCS5A01G112500 chr3D 475301769 475302554 785 False 909.000000 909 87.595000 1 786 1 chr3D.!!$F1 785
29 TraesCS5A01G112500 chr2A 739177356 739178122 766 False 870.000000 870 87.084000 1 781 1 chr2A.!!$F1 780
30 TraesCS5A01G112500 chr2A 116454939 116455570 631 True 695.000000 695 86.772000 154 777 1 chr2A.!!$R1 623
31 TraesCS5A01G112500 chr2A 459834918 459835525 607 True 662.000000 662 86.268000 169 786 1 chr2A.!!$R2 617
32 TraesCS5A01G112500 chr7D 608484367 608485138 771 False 857.000000 857 86.658000 1 786 1 chr7D.!!$F1 785
33 TraesCS5A01G112500 chr6D 384205025 384205781 756 True 785.000000 785 85.347000 2 778 1 chr6D.!!$R1 776
34 TraesCS5A01G112500 chr1A 419023366 419024147 781 True 736.000000 736 83.777000 1 782 1 chr1A.!!$R1 781

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
803 858 0.453793 CCGAACGACTGAGATGCTCT 59.546 55.000 0.00 0.0 0.00 4.09 F
1045 1104 0.838229 GCTGTCGTTATCGCTACACG 59.162 55.000 0.00 0.0 45.62 4.49 F
2330 2455 2.309755 TCATCAATGAGAGGGGCAACTT 59.690 45.455 0.00 0.0 32.11 2.66 F
2576 2701 1.526575 CTTTGTGGTTGCGATGGGCT 61.527 55.000 0.00 0.0 44.05 5.19 F
4147 4277 4.437682 TGTTTGGAGATTCTGGAAGTGT 57.562 40.909 0.00 0.0 33.76 3.55 F
4687 4817 2.092291 CGTCCACATACGCGCAGTT 61.092 57.895 5.73 0.0 35.87 3.16 F
6196 6342 2.482333 CCGATTCGGTCCGCTCTCT 61.482 63.158 17.08 0.0 42.73 3.10 F
6218 6365 0.109086 CGCCTCTCTTTCGCTTCTCA 60.109 55.000 0.00 0.0 0.00 3.27 F
7659 7901 0.744057 TATGTGGACATGCTGTGCCG 60.744 55.000 2.38 0.0 37.97 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2283 0.246635 GCGGTGGAGTCAAGCTTCTA 59.753 55.000 0.00 0.0 0.00 2.10 R
2576 2701 1.533033 TGACACTTCGAGGCCCAGA 60.533 57.895 0.00 0.0 0.00 3.86 R
4147 4277 0.456221 GGCGACGAAGAGGAAGATGA 59.544 55.000 0.00 0.0 0.00 2.92 R
4542 4672 4.162690 GGCGAAGACTGGCCCGAT 62.163 66.667 0.00 0.0 43.64 4.18 R
6063 6209 0.462789 TTTCGTATCTTCCTCCGCCC 59.537 55.000 0.00 0.0 0.00 6.13 R
6205 6352 0.243907 CCGAGGTGAGAAGCGAAAGA 59.756 55.000 0.00 0.0 0.00 2.52 R
7169 7410 1.072331 AGCACAGTTCGATTTCAGGGT 59.928 47.619 0.00 0.0 0.00 4.34 R
8209 8458 0.035056 ATGCAGAGGCCAGGTGTTAC 60.035 55.000 5.01 0.0 40.13 2.50 R
8509 8759 0.531657 GTTGGCATGCCATGTAAGCA 59.468 50.000 38.78 20.4 46.64 3.91 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
115 116 1.296715 GGTGCCCTCGTCATCAACT 59.703 57.895 0.00 0.00 0.00 3.16
248 249 3.530910 CTGCCCCCAACGACGAGTT 62.531 63.158 0.00 0.00 45.45 3.01
264 265 1.301716 GTTCGCTCTCAAGTGGGCA 60.302 57.895 0.00 0.00 33.64 5.36
316 317 4.071875 AATGCCGGGCGTACACGA 62.072 61.111 15.33 0.00 43.02 4.35
443 447 2.803155 CTTCGCCAGGGCTACAGCAA 62.803 60.000 8.91 0.00 44.36 3.91
479 483 2.661537 CCAGCTGCGTGACGACAA 60.662 61.111 10.10 0.00 0.00 3.18
553 605 4.034258 GACGACGGCGGACAGTGA 62.034 66.667 18.49 0.00 43.17 3.41
566 618 1.226603 CAGTGACGGCTAGGCGTAC 60.227 63.158 39.68 32.50 0.00 3.67
712 766 2.098831 GGAGCTACCGTTGAACCGC 61.099 63.158 0.00 0.00 0.00 5.68
732 786 1.353804 GACTGAGAGCTAGGTCGCG 59.646 63.158 18.77 15.53 34.40 5.87
749 803 4.195308 GCCCACGCGTCAATCTAA 57.805 55.556 9.86 0.00 0.00 2.10
786 841 2.561373 GGCTCTTTTTCGGTGCCG 59.439 61.111 3.94 3.94 41.35 5.69
795 850 3.289062 TCGGTGCCGAACGACTGA 61.289 61.111 11.22 0.00 46.01 3.41
796 851 2.805353 CGGTGCCGAACGACTGAG 60.805 66.667 4.35 0.00 42.83 3.35
797 852 2.649034 GGTGCCGAACGACTGAGA 59.351 61.111 0.00 0.00 0.00 3.27
798 853 1.215647 GGTGCCGAACGACTGAGAT 59.784 57.895 0.00 0.00 0.00 2.75
799 854 1.078759 GGTGCCGAACGACTGAGATG 61.079 60.000 0.00 0.00 0.00 2.90
800 855 1.446099 TGCCGAACGACTGAGATGC 60.446 57.895 0.00 0.00 0.00 3.91
801 856 1.153745 GCCGAACGACTGAGATGCT 60.154 57.895 0.00 0.00 0.00 3.79
802 857 1.142778 GCCGAACGACTGAGATGCTC 61.143 60.000 0.00 0.00 0.00 4.26
803 858 0.453793 CCGAACGACTGAGATGCTCT 59.546 55.000 0.00 0.00 0.00 4.09
804 859 1.671328 CCGAACGACTGAGATGCTCTA 59.329 52.381 0.00 0.00 0.00 2.43
835 892 8.625651 TCAAAGAATCGTCAAAAAGGTAAATGA 58.374 29.630 0.00 0.00 0.00 2.57
851 909 3.806625 AATGAGAAATTGGAATGCCCG 57.193 42.857 0.00 0.00 37.93 6.13
911 969 2.675056 GCCAGCAGCACAACGAGAG 61.675 63.158 0.00 0.00 42.97 3.20
943 1002 1.369321 TGTGCACGTGCTCACCATA 59.631 52.632 37.59 17.50 39.29 2.74
1045 1104 0.838229 GCTGTCGTTATCGCTACACG 59.162 55.000 0.00 0.00 45.62 4.49
2158 2283 4.599036 GCCAACTTGGGGAGTGTT 57.401 55.556 9.95 0.00 39.00 3.32
2330 2455 2.309755 TCATCAATGAGAGGGGCAACTT 59.690 45.455 0.00 0.00 32.11 2.66
2576 2701 1.526575 CTTTGTGGTTGCGATGGGCT 61.527 55.000 0.00 0.00 44.05 5.19
2938 3065 4.870426 GCAATGTTCTTCGAGTTCCATCTA 59.130 41.667 0.00 0.00 0.00 1.98
3458 3587 6.471841 TCTGATGTGTTTGACATTTTTGTTCG 59.528 34.615 0.00 0.00 45.90 3.95
3790 3919 5.223449 AGTTCTCCTTAATGAACAACCGA 57.777 39.130 14.35 0.00 43.38 4.69
4126 4256 4.643387 GCACTGGTCGTGGGGCTT 62.643 66.667 0.00 0.00 43.97 4.35
4147 4277 4.437682 TGTTTGGAGATTCTGGAAGTGT 57.562 40.909 0.00 0.00 33.76 3.55
4270 4400 4.514577 CGATCGACGCCCTGGCTT 62.515 66.667 10.26 0.00 39.32 4.35
4542 4672 3.005539 GCCTCTGAGCCCCTGTCA 61.006 66.667 0.00 0.00 0.00 3.58
4687 4817 2.092291 CGTCCACATACGCGCAGTT 61.092 57.895 5.73 0.00 35.87 3.16
4895 5025 3.136443 ACTCTTGTTCCTCCACAATCACA 59.864 43.478 0.00 0.00 36.08 3.58
4912 5042 8.676401 CACAATCACAGGTAAATGTCATTGATA 58.324 33.333 9.90 0.00 42.33 2.15
5806 5936 3.110358 CGCTATATTCGTTTCACGGTGA 58.890 45.455 6.76 6.76 42.81 4.02
6053 6199 5.605488 TCAGGAGTTAAGTATACCCCAATCC 59.395 44.000 0.00 2.00 0.00 3.01
6196 6342 2.482333 CCGATTCGGTCCGCTCTCT 61.482 63.158 17.08 0.00 42.73 3.10
6218 6365 0.109086 CGCCTCTCTTTCGCTTCTCA 60.109 55.000 0.00 0.00 0.00 3.27
6221 6368 1.548269 CCTCTCTTTCGCTTCTCACCT 59.452 52.381 0.00 0.00 0.00 4.00
6349 6590 9.077885 TCTAACTGTTCCTTCATTATTTTTGCT 57.922 29.630 0.00 0.00 0.00 3.91
6350 6591 9.696917 CTAACTGTTCCTTCATTATTTTTGCTT 57.303 29.630 0.00 0.00 0.00 3.91
6387 6628 4.503741 AATGACGTGGAAATGTTTCTGG 57.496 40.909 0.00 0.00 37.35 3.86
6544 6785 7.816995 CCTTAAAAACTTGCATGTTATTGGCTA 59.183 33.333 17.36 2.42 0.00 3.93
6624 6865 5.810095 AGGCTTATAGCTTTCCATACCATC 58.190 41.667 0.00 0.00 41.99 3.51
6658 6899 2.621998 CCTGATGCTCATTTTAGCCCAG 59.378 50.000 0.00 0.00 42.05 4.45
6703 6944 4.954202 ACATATACTCGACCAGGTCTTTCA 59.046 41.667 17.95 0.85 0.00 2.69
6717 6958 9.308000 ACCAGGTCTTTCATTATTTACAAATGA 57.692 29.630 0.00 0.00 40.63 2.57
6732 6973 5.824904 ACAAATGATGCTACTGGAATCAC 57.175 39.130 0.00 0.00 42.33 3.06
6733 6974 5.255687 ACAAATGATGCTACTGGAATCACA 58.744 37.500 0.00 0.00 42.33 3.58
7056 7297 6.205464 TGATCAAGATCAACTGTTGACCTTTC 59.795 38.462 24.16 20.17 40.66 2.62
7057 7298 5.436175 TCAAGATCAACTGTTGACCTTTCA 58.564 37.500 24.16 13.11 40.66 2.69
7105 7346 2.306219 AGAAACAGTAGGGAAAGCCTCC 59.694 50.000 0.00 0.00 44.54 4.30
7169 7410 6.110033 ACGGTTATGTACAATGTCAATGCTA 58.890 36.000 0.00 0.00 0.00 3.49
7179 7420 5.126061 ACAATGTCAATGCTACCCTGAAATC 59.874 40.000 0.00 0.00 0.00 2.17
7383 7624 9.987272 TGATCCAGTTTGTATACAGATCTAATG 57.013 33.333 22.55 11.26 34.11 1.90
7498 7739 7.750229 TCTCAAAATATTTGTCAGCACTTCT 57.250 32.000 0.39 0.00 0.00 2.85
7537 7778 3.393278 TGTGGCTAACTGGACCTAACTTT 59.607 43.478 0.00 0.00 0.00 2.66
7582 7823 5.992217 GGTTGAGATACTGGTGGATATTGTC 59.008 44.000 0.00 0.00 0.00 3.18
7659 7901 0.744057 TATGTGGACATGCTGTGCCG 60.744 55.000 2.38 0.00 37.97 5.69
7704 7946 7.803724 ACAATTGGTGATTCGTTAGTTTCTAC 58.196 34.615 10.83 0.00 0.00 2.59
7705 7947 6.980051 ATTGGTGATTCGTTAGTTTCTACC 57.020 37.500 0.00 0.00 0.00 3.18
7706 7948 4.824289 TGGTGATTCGTTAGTTTCTACCC 58.176 43.478 0.00 0.00 0.00 3.69
7726 7968 4.529377 ACCCGAAAGATTGAGTAGTAACCA 59.471 41.667 0.00 0.00 0.00 3.67
7736 7978 7.839705 AGATTGAGTAGTAACCAATCCAGTAGA 59.160 37.037 16.22 0.00 40.48 2.59
7745 7987 9.668497 AGTAACCAATCCAGTAGAATTAACTTC 57.332 33.333 0.00 0.00 0.00 3.01
7747 7989 7.027874 ACCAATCCAGTAGAATTAACTTCCA 57.972 36.000 0.00 0.00 34.11 3.53
7932 8174 5.457140 TCGCTTGGTAAAGTTGCAAATAAG 58.543 37.500 0.00 0.92 35.69 1.73
8004 8249 5.562506 GGGAAAAACTATCTCCCGAAAAG 57.437 43.478 0.00 0.00 39.59 2.27
8121 8370 2.036475 ACAGCTCAGCGAAGAAGAAGAA 59.964 45.455 0.00 0.00 0.00 2.52
8123 8372 2.560542 AGCTCAGCGAAGAAGAAGAAGA 59.439 45.455 0.00 0.00 0.00 2.87
8124 8373 2.923020 GCTCAGCGAAGAAGAAGAAGAG 59.077 50.000 0.00 0.00 0.00 2.85
8127 8376 1.066502 AGCGAAGAAGAAGAAGAGGGC 60.067 52.381 0.00 0.00 0.00 5.19
8128 8377 1.634702 CGAAGAAGAAGAAGAGGGCG 58.365 55.000 0.00 0.00 0.00 6.13
8129 8378 1.737363 CGAAGAAGAAGAAGAGGGCGG 60.737 57.143 0.00 0.00 0.00 6.13
8130 8379 1.276705 GAAGAAGAAGAAGAGGGCGGT 59.723 52.381 0.00 0.00 0.00 5.68
8131 8380 2.233305 AGAAGAAGAAGAGGGCGGTA 57.767 50.000 0.00 0.00 0.00 4.02
8132 8381 2.537143 AGAAGAAGAAGAGGGCGGTAA 58.463 47.619 0.00 0.00 0.00 2.85
8133 8382 2.234168 AGAAGAAGAAGAGGGCGGTAAC 59.766 50.000 0.00 0.00 0.00 2.50
8134 8383 1.939980 AGAAGAAGAGGGCGGTAACT 58.060 50.000 0.00 0.00 0.00 2.24
8135 8384 3.097342 AGAAGAAGAGGGCGGTAACTA 57.903 47.619 0.00 0.00 0.00 2.24
8136 8385 2.759535 AGAAGAAGAGGGCGGTAACTAC 59.240 50.000 0.00 0.00 0.00 2.73
8137 8386 1.101331 AGAAGAGGGCGGTAACTACG 58.899 55.000 0.00 0.00 0.00 3.51
8138 8387 0.813821 GAAGAGGGCGGTAACTACGT 59.186 55.000 0.00 0.00 0.00 3.57
8139 8388 2.017049 GAAGAGGGCGGTAACTACGTA 58.983 52.381 0.00 0.00 0.00 3.57
8140 8389 2.355010 AGAGGGCGGTAACTACGTAT 57.645 50.000 0.00 0.00 0.00 3.06
8141 8390 1.952296 AGAGGGCGGTAACTACGTATG 59.048 52.381 0.00 0.00 0.00 2.39
8142 8391 1.678101 GAGGGCGGTAACTACGTATGT 59.322 52.381 0.00 0.00 0.00 2.29
8143 8392 2.099756 GAGGGCGGTAACTACGTATGTT 59.900 50.000 12.76 12.76 0.00 2.71
8144 8393 2.497273 AGGGCGGTAACTACGTATGTTT 59.503 45.455 13.21 3.46 0.00 2.83
8145 8394 3.055891 AGGGCGGTAACTACGTATGTTTT 60.056 43.478 13.21 1.40 0.00 2.43
8146 8395 3.684305 GGGCGGTAACTACGTATGTTTTT 59.316 43.478 13.21 0.00 0.00 1.94
8174 8423 9.567776 TTGATAAAGGGCGATTTTATTATCTCA 57.432 29.630 0.00 0.00 32.42 3.27
8175 8424 9.567776 TGATAAAGGGCGATTTTATTATCTCAA 57.432 29.630 0.00 0.00 32.42 3.02
8179 8428 9.533253 AAAGGGCGATTTTATTATCTCAAAATG 57.467 29.630 0.00 0.00 35.14 2.32
8180 8429 8.237811 AGGGCGATTTTATTATCTCAAAATGT 57.762 30.769 0.00 0.00 35.14 2.71
8181 8430 9.349713 AGGGCGATTTTATTATCTCAAAATGTA 57.650 29.630 0.00 0.00 35.14 2.29
8182 8431 9.612620 GGGCGATTTTATTATCTCAAAATGTAG 57.387 33.333 0.00 0.00 35.14 2.74
8183 8432 9.118236 GGCGATTTTATTATCTCAAAATGTAGC 57.882 33.333 0.00 0.00 35.14 3.58
8184 8433 9.663904 GCGATTTTATTATCTCAAAATGTAGCA 57.336 29.630 0.00 0.00 35.14 3.49
8192 8441 6.939132 ATCTCAAAATGTAGCATCAAGAGG 57.061 37.500 0.00 0.00 0.00 3.69
8193 8442 6.053632 TCTCAAAATGTAGCATCAAGAGGA 57.946 37.500 0.00 0.00 0.00 3.71
8194 8443 6.656902 TCTCAAAATGTAGCATCAAGAGGAT 58.343 36.000 0.00 0.00 36.39 3.24
8195 8444 7.795047 TCTCAAAATGTAGCATCAAGAGGATA 58.205 34.615 0.00 0.00 33.95 2.59
8196 8445 7.712639 TCTCAAAATGTAGCATCAAGAGGATAC 59.287 37.037 3.48 3.48 34.94 2.24
8197 8446 7.337938 TCAAAATGTAGCATCAAGAGGATACA 58.662 34.615 13.99 13.99 45.77 2.29
8198 8447 7.496920 TCAAAATGTAGCATCAAGAGGATACAG 59.503 37.037 16.21 5.27 45.09 2.74
8199 8448 6.737720 AATGTAGCATCAAGAGGATACAGA 57.262 37.500 16.21 0.00 45.09 3.41
8200 8449 6.737720 ATGTAGCATCAAGAGGATACAGAA 57.262 37.500 16.21 0.00 45.09 3.02
8201 8450 5.907207 TGTAGCATCAAGAGGATACAGAAC 58.093 41.667 8.52 0.00 38.75 3.01
8202 8451 5.422012 TGTAGCATCAAGAGGATACAGAACA 59.578 40.000 8.52 0.00 38.75 3.18
8203 8452 5.627182 AGCATCAAGAGGATACAGAACAT 57.373 39.130 0.00 0.00 41.41 2.71
8204 8453 5.999044 AGCATCAAGAGGATACAGAACATT 58.001 37.500 0.00 0.00 41.41 2.71
8205 8454 7.129457 AGCATCAAGAGGATACAGAACATTA 57.871 36.000 0.00 0.00 41.41 1.90
8206 8455 7.743749 AGCATCAAGAGGATACAGAACATTAT 58.256 34.615 0.00 0.00 41.41 1.28
8207 8456 7.660617 AGCATCAAGAGGATACAGAACATTATG 59.339 37.037 0.00 0.00 41.41 1.90
8208 8457 7.658982 GCATCAAGAGGATACAGAACATTATGA 59.341 37.037 0.00 0.00 41.41 2.15
8209 8458 9.205719 CATCAAGAGGATACAGAACATTATGAG 57.794 37.037 0.00 0.00 41.41 2.90
8210 8459 8.311395 TCAAGAGGATACAGAACATTATGAGT 57.689 34.615 0.00 0.00 41.41 3.41
8211 8460 9.421399 TCAAGAGGATACAGAACATTATGAGTA 57.579 33.333 0.00 0.00 41.41 2.59
8214 8463 9.201989 AGAGGATACAGAACATTATGAGTAACA 57.798 33.333 0.00 0.00 41.41 2.41
8215 8464 9.250624 GAGGATACAGAACATTATGAGTAACAC 57.749 37.037 0.00 0.00 41.41 3.32
8216 8465 8.204836 AGGATACAGAACATTATGAGTAACACC 58.795 37.037 0.00 0.00 41.41 4.16
8217 8466 8.204836 GGATACAGAACATTATGAGTAACACCT 58.795 37.037 0.00 0.00 0.00 4.00
8218 8467 8.948631 ATACAGAACATTATGAGTAACACCTG 57.051 34.615 0.00 0.00 0.00 4.00
8219 8468 6.173339 ACAGAACATTATGAGTAACACCTGG 58.827 40.000 0.00 0.00 0.00 4.45
8220 8469 5.065218 CAGAACATTATGAGTAACACCTGGC 59.935 44.000 0.00 0.00 0.00 4.85
8221 8470 3.886123 ACATTATGAGTAACACCTGGCC 58.114 45.455 0.00 0.00 0.00 5.36
8222 8471 3.523564 ACATTATGAGTAACACCTGGCCT 59.476 43.478 3.32 0.00 0.00 5.19
8223 8472 3.906720 TTATGAGTAACACCTGGCCTC 57.093 47.619 3.32 0.00 0.00 4.70
8224 8473 1.958288 ATGAGTAACACCTGGCCTCT 58.042 50.000 3.32 0.00 0.00 3.69
8225 8474 0.976641 TGAGTAACACCTGGCCTCTG 59.023 55.000 3.32 0.00 0.00 3.35
8226 8475 0.391793 GAGTAACACCTGGCCTCTGC 60.392 60.000 3.32 0.00 0.00 4.26
8227 8476 1.127567 AGTAACACCTGGCCTCTGCA 61.128 55.000 3.32 0.00 40.13 4.41
8361 8611 9.989869 GACTTGTTTACAAAAGAGCTAATATCC 57.010 33.333 0.00 0.00 35.15 2.59
8381 8631 3.581332 TCCCCGAAAGTCATAGAACTTGT 59.419 43.478 0.00 0.00 39.40 3.16
8389 8639 6.492007 AAGTCATAGAACTTGTGCTTGATG 57.508 37.500 0.00 0.00 38.06 3.07
8394 8644 4.825546 AGAACTTGTGCTTGATGTTCAG 57.174 40.909 0.00 0.00 39.33 3.02
8410 8660 7.861630 TGATGTTCAGTTTAGTGCTAAAACTC 58.138 34.615 6.02 0.00 36.86 3.01
8412 8662 9.204570 GATGTTCAGTTTAGTGCTAAAACTCTA 57.795 33.333 6.02 0.20 36.86 2.43
8451 8701 4.009675 GTCATTCAACTTGTCCCTGCATA 58.990 43.478 0.00 0.00 0.00 3.14
8454 8704 3.719268 TCAACTTGTCCCTGCATACAT 57.281 42.857 0.00 0.00 0.00 2.29
8461 8711 2.028476 TGTCCCTGCATACATATACGGC 60.028 50.000 0.00 0.00 0.00 5.68
8464 8714 2.346803 CCTGCATACATATACGGCCAC 58.653 52.381 2.24 0.00 0.00 5.01
8465 8715 2.028112 CCTGCATACATATACGGCCACT 60.028 50.000 2.24 0.00 0.00 4.00
8466 8716 3.557054 CCTGCATACATATACGGCCACTT 60.557 47.826 2.24 0.00 0.00 3.16
8467 8717 3.659786 TGCATACATATACGGCCACTTC 58.340 45.455 2.24 0.00 0.00 3.01
8468 8718 3.323691 TGCATACATATACGGCCACTTCT 59.676 43.478 2.24 0.00 0.00 2.85
8469 8719 4.525100 TGCATACATATACGGCCACTTCTA 59.475 41.667 2.24 0.00 0.00 2.10
8470 8720 5.103000 GCATACATATACGGCCACTTCTAG 58.897 45.833 2.24 0.00 0.00 2.43
8471 8721 5.105877 GCATACATATACGGCCACTTCTAGA 60.106 44.000 2.24 0.00 0.00 2.43
8472 8722 4.850347 ACATATACGGCCACTTCTAGAC 57.150 45.455 2.24 0.00 0.00 2.59
8473 8723 4.212716 ACATATACGGCCACTTCTAGACA 58.787 43.478 2.24 0.00 0.00 3.41
8474 8724 4.833380 ACATATACGGCCACTTCTAGACAT 59.167 41.667 2.24 0.00 0.00 3.06
8475 8725 6.008331 ACATATACGGCCACTTCTAGACATA 58.992 40.000 2.24 0.00 0.00 2.29
8476 8726 6.663953 ACATATACGGCCACTTCTAGACATAT 59.336 38.462 2.24 0.00 0.00 1.78
8477 8727 3.735237 ACGGCCACTTCTAGACATATG 57.265 47.619 2.24 0.00 0.00 1.78
8478 8728 3.031736 ACGGCCACTTCTAGACATATGT 58.968 45.455 8.43 8.43 0.00 2.29
8479 8729 3.451178 ACGGCCACTTCTAGACATATGTT 59.549 43.478 10.30 3.01 0.00 2.71
8480 8730 3.804325 CGGCCACTTCTAGACATATGTTG 59.196 47.826 10.30 2.15 0.00 3.33
8481 8731 4.680708 CGGCCACTTCTAGACATATGTTGT 60.681 45.833 10.30 3.39 42.79 3.32
8482 8732 4.572389 GGCCACTTCTAGACATATGTTGTG 59.428 45.833 10.30 11.46 39.18 3.33
8490 8740 3.262420 AGACATATGTTGTGCTTCGTCC 58.738 45.455 10.30 0.00 39.18 4.79
8491 8741 3.000041 GACATATGTTGTGCTTCGTCCA 59.000 45.455 10.30 0.00 39.18 4.02
8509 8759 7.761038 TCGTCCATATCTAGACATATGTTGT 57.239 36.000 10.30 3.39 42.79 3.32
8615 8865 8.858003 ACATATACACTCTCGTTGTCAATTAG 57.142 34.615 0.00 0.00 0.00 1.73
8639 8889 3.901797 AACAGCTTTCGGGGCTCGG 62.902 63.158 7.05 0.00 38.03 4.63
8852 9108 5.957771 ACTGTCCAAGATATTAGCAGGAA 57.042 39.130 0.00 0.00 0.00 3.36
9036 9319 8.259411 TCCAATGGTCTCCATCAATAATTTTTG 58.741 33.333 0.00 2.51 44.40 2.44
9126 9409 3.552132 TGGAATCGTGCATAGGCTTTA 57.448 42.857 0.00 0.00 41.91 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 249 0.603707 CTTTGCCCACTTGAGAGCGA 60.604 55.000 0.00 0.00 0.00 4.93
264 265 2.228343 CTCACGAACGTAGTCCTCCTTT 59.772 50.000 0.00 0.00 45.00 3.11
301 302 4.728102 CTTCGTGTACGCCCGGCA 62.728 66.667 10.77 0.00 39.60 5.69
467 471 3.020105 CGTCGTTGTCGTCACGCA 61.020 61.111 0.00 0.00 38.33 5.24
471 475 0.723459 CATCGTCGTCGTTGTCGTCA 60.723 55.000 1.33 0.00 38.33 4.35
472 476 0.451628 TCATCGTCGTCGTTGTCGTC 60.452 55.000 11.74 0.00 37.80 4.20
473 477 0.723790 GTCATCGTCGTCGTTGTCGT 60.724 55.000 11.74 0.00 37.80 4.34
474 478 1.708375 CGTCATCGTCGTCGTTGTCG 61.708 60.000 14.84 14.84 39.85 4.35
475 479 0.451628 TCGTCATCGTCGTCGTTGTC 60.452 55.000 11.74 6.65 37.80 3.18
476 480 0.723790 GTCGTCATCGTCGTCGTTGT 60.724 55.000 11.74 0.00 37.80 3.32
477 481 1.708375 CGTCGTCATCGTCGTCGTTG 61.708 60.000 6.76 6.76 41.73 4.10
478 482 1.508539 CGTCGTCATCGTCGTCGTT 60.509 57.895 1.33 0.00 41.73 3.85
479 483 2.095282 CGTCGTCATCGTCGTCGT 59.905 61.111 1.33 0.00 41.73 4.34
553 605 0.743097 CCTAAAGTACGCCTAGCCGT 59.257 55.000 3.53 3.53 44.62 5.68
566 618 3.213249 ACGACTGAACTACGCCTAAAG 57.787 47.619 0.00 0.00 0.00 1.85
696 750 2.047560 GGCGGTTCAACGGTAGCT 60.048 61.111 0.00 0.00 0.00 3.32
699 753 2.049248 GTCGGCGGTTCAACGGTA 60.049 61.111 7.21 0.00 0.00 4.02
712 766 2.018544 CGACCTAGCTCTCAGTCGG 58.981 63.158 15.85 0.08 46.24 4.79
732 786 1.713830 GTTAGATTGACGCGTGGGC 59.286 57.895 20.70 1.97 0.00 5.36
799 854 4.568359 TGACGATTCTTTGATGCTTAGAGC 59.432 41.667 0.00 0.00 42.82 4.09
800 855 6.653273 TTGACGATTCTTTGATGCTTAGAG 57.347 37.500 0.00 0.00 0.00 2.43
801 856 7.433708 TTTTGACGATTCTTTGATGCTTAGA 57.566 32.000 0.00 0.00 0.00 2.10
802 857 7.272084 CCTTTTTGACGATTCTTTGATGCTTAG 59.728 37.037 0.00 0.00 0.00 2.18
803 858 7.083858 CCTTTTTGACGATTCTTTGATGCTTA 58.916 34.615 0.00 0.00 0.00 3.09
804 859 5.922544 CCTTTTTGACGATTCTTTGATGCTT 59.077 36.000 0.00 0.00 0.00 3.91
819 874 9.541143 TTCCAATTTCTCATTTACCTTTTTGAC 57.459 29.630 0.00 0.00 0.00 3.18
835 892 1.094785 CGTCGGGCATTCCAATTTCT 58.905 50.000 0.00 0.00 34.36 2.52
851 909 1.390463 GAAACAGATGAACGAGCCGTC 59.610 52.381 0.69 0.00 39.99 4.79
911 969 3.022287 CACACGTGCACTTGGGAC 58.978 61.111 25.13 0.00 33.95 4.46
943 1002 1.705337 GAGCGTGTGTGTGCTTGTGT 61.705 55.000 0.00 0.00 42.60 3.72
972 1031 4.742201 CCCGCCACTCGTGACTGG 62.742 72.222 0.00 0.00 36.19 4.00
973 1032 3.633094 CTCCCGCCACTCGTGACTG 62.633 68.421 0.00 0.00 36.19 3.51
974 1033 3.374402 CTCCCGCCACTCGTGACT 61.374 66.667 0.00 0.00 36.19 3.41
1028 1087 1.527591 CGACGTGTAGCGATAACGACA 60.528 52.381 17.68 0.00 44.77 4.35
1115 1198 1.955663 TCGAACGAGGACGACGACA 60.956 57.895 0.00 0.00 42.08 4.35
2158 2283 0.246635 GCGGTGGAGTCAAGCTTCTA 59.753 55.000 0.00 0.00 0.00 2.10
2349 2474 2.842320 GAGGCGTGAAAAGACCTCC 58.158 57.895 0.00 0.00 42.44 4.30
2576 2701 1.533033 TGACACTTCGAGGCCCAGA 60.533 57.895 0.00 0.00 0.00 3.86
2938 3065 8.105829 AGGAACTGAAAGAAGATTACATGTCAT 58.894 33.333 0.00 0.00 37.18 3.06
3458 3587 3.000825 GCGTTCAACATGTTTTTGGAACC 59.999 43.478 23.33 16.33 0.00 3.62
4126 4256 4.141505 TGACACTTCCAGAATCTCCAAACA 60.142 41.667 0.00 0.00 0.00 2.83
4147 4277 0.456221 GGCGACGAAGAGGAAGATGA 59.544 55.000 0.00 0.00 0.00 2.92
4542 4672 4.162690 GGCGAAGACTGGCCCGAT 62.163 66.667 0.00 0.00 43.64 4.18
4895 5025 7.069826 CCCATTTGGTATCAATGACATTTACCT 59.930 37.037 21.60 6.91 34.65 3.08
4912 5042 5.188751 TCTTCACTTTGAAAACCCATTTGGT 59.811 36.000 0.00 0.00 39.71 3.67
5806 5936 4.088634 ACAACCATATGCAAACCATGAGT 58.911 39.130 0.00 0.00 35.34 3.41
5967 6113 2.171448 CCACAGCCTTATACTCAGCCTT 59.829 50.000 0.00 0.00 0.00 4.35
6060 6206 3.602677 TATCTTCCTCCGCCCGCG 61.603 66.667 0.00 0.00 39.44 6.46
6061 6207 2.029221 GTATCTTCCTCCGCCCGC 59.971 66.667 0.00 0.00 0.00 6.13
6062 6208 1.731433 TTCGTATCTTCCTCCGCCCG 61.731 60.000 0.00 0.00 0.00 6.13
6063 6209 0.462789 TTTCGTATCTTCCTCCGCCC 59.537 55.000 0.00 0.00 0.00 6.13
6064 6210 1.854227 CTTTCGTATCTTCCTCCGCC 58.146 55.000 0.00 0.00 0.00 6.13
6065 6211 1.209998 GCTTTCGTATCTTCCTCCGC 58.790 55.000 0.00 0.00 0.00 5.54
6066 6212 1.478137 CGCTTTCGTATCTTCCTCCG 58.522 55.000 0.00 0.00 0.00 4.63
6067 6213 1.538419 CCCGCTTTCGTATCTTCCTCC 60.538 57.143 0.00 0.00 0.00 4.30
6068 6214 1.136500 ACCCGCTTTCGTATCTTCCTC 59.864 52.381 0.00 0.00 0.00 3.71
6069 6215 1.134788 CACCCGCTTTCGTATCTTCCT 60.135 52.381 0.00 0.00 0.00 3.36
6196 6342 2.227089 GAAGCGAAAGAGAGGCGGGA 62.227 60.000 0.00 0.00 0.00 5.14
6205 6352 0.243907 CCGAGGTGAGAAGCGAAAGA 59.756 55.000 0.00 0.00 0.00 2.52
6238 6473 2.135933 ACAGAACAGCGTGCTAGTTTC 58.864 47.619 9.79 6.55 0.00 2.78
6387 6628 4.342665 CCAACCTCCCTAACTAGTGAGATC 59.657 50.000 9.03 0.00 30.60 2.75
6568 6809 2.626743 GCTCTGGCTTGCATGGATAATT 59.373 45.455 1.34 0.00 35.22 1.40
6624 6865 1.180029 CATCAGGTTCAAAGGGGCAG 58.820 55.000 0.00 0.00 0.00 4.85
6682 6923 6.732896 AATGAAAGACCTGGTCGAGTATAT 57.267 37.500 20.49 9.29 37.67 0.86
6683 6924 7.834881 ATAATGAAAGACCTGGTCGAGTATA 57.165 36.000 20.49 11.36 37.67 1.47
6717 6958 2.681976 GCCTGTGTGATTCCAGTAGCAT 60.682 50.000 0.00 0.00 0.00 3.79
6732 6973 4.092091 GTCAGAAGTTTCTTATCGCCTGTG 59.908 45.833 0.00 0.00 34.74 3.66
6733 6974 4.246458 GTCAGAAGTTTCTTATCGCCTGT 58.754 43.478 0.00 0.00 34.74 4.00
7056 7297 3.570926 AGAAGCAGCATTGACATTGTG 57.429 42.857 0.00 0.00 0.00 3.33
7057 7298 4.595762 AAAGAAGCAGCATTGACATTGT 57.404 36.364 0.00 0.00 0.00 2.71
7105 7346 2.153366 AAAAGGAAAATGGCGCAGTG 57.847 45.000 10.83 0.00 0.00 3.66
7169 7410 1.072331 AGCACAGTTCGATTTCAGGGT 59.928 47.619 0.00 0.00 0.00 4.34
7179 7420 2.479837 TGGTAGACAAAGCACAGTTCG 58.520 47.619 0.00 0.00 0.00 3.95
7383 7624 7.179076 TCCTAGTTCCTACATTACCAAACTC 57.821 40.000 0.00 0.00 0.00 3.01
7384 7625 7.750947 ATCCTAGTTCCTACATTACCAAACT 57.249 36.000 0.00 0.00 0.00 2.66
7416 7657 6.962311 AGAATGAGAAGATGCCCACCTATATA 59.038 38.462 0.00 0.00 0.00 0.86
7537 7778 6.216801 ACCATTTCTAGCGTCACAACTATA 57.783 37.500 0.00 0.00 0.00 1.31
7659 7901 5.248870 TGTTTCCACTTCAGAAAAGAAGC 57.751 39.130 3.78 0.00 46.97 3.86
7704 7946 5.080969 TGGTTACTACTCAATCTTTCGGG 57.919 43.478 0.00 0.00 0.00 5.14
7705 7947 6.258068 GGATTGGTTACTACTCAATCTTTCGG 59.742 42.308 12.87 0.00 43.52 4.30
7706 7948 6.816640 TGGATTGGTTACTACTCAATCTTTCG 59.183 38.462 12.87 0.00 43.52 3.46
7736 7978 7.231925 ACCCGTAGACAAAATTGGAAGTTAATT 59.768 33.333 0.00 0.00 0.00 1.40
7745 7987 4.320870 ACTGTACCCGTAGACAAAATTGG 58.679 43.478 0.00 0.00 0.00 3.16
7747 7989 6.100404 TGTACTGTACCCGTAGACAAAATT 57.900 37.500 14.91 0.00 0.00 1.82
7932 8174 3.253432 GTCAAAATCTGGTGGTGGAAGAC 59.747 47.826 0.00 0.00 0.00 3.01
8004 8249 3.592898 AGAATTCGAATTTGGCCCAAC 57.407 42.857 23.49 9.01 0.00 3.77
8121 8370 1.952296 CATACGTAGTTACCGCCCTCT 59.048 52.381 0.08 0.00 37.78 3.69
8123 8372 1.767759 ACATACGTAGTTACCGCCCT 58.232 50.000 0.08 0.00 37.78 5.19
8124 8373 2.584492 AACATACGTAGTTACCGCCC 57.416 50.000 0.08 0.00 37.78 6.13
8148 8397 9.567776 TGAGATAATAAAATCGCCCTTTATCAA 57.432 29.630 0.00 0.00 31.56 2.57
8149 8398 9.567776 TTGAGATAATAAAATCGCCCTTTATCA 57.432 29.630 0.00 0.00 31.56 2.15
8153 8402 9.533253 CATTTTGAGATAATAAAATCGCCCTTT 57.467 29.630 0.00 0.00 35.07 3.11
8154 8403 8.695456 ACATTTTGAGATAATAAAATCGCCCTT 58.305 29.630 0.00 0.00 35.07 3.95
8155 8404 8.237811 ACATTTTGAGATAATAAAATCGCCCT 57.762 30.769 0.00 0.00 35.07 5.19
8156 8405 9.612620 CTACATTTTGAGATAATAAAATCGCCC 57.387 33.333 0.00 0.00 35.07 6.13
8157 8406 9.118236 GCTACATTTTGAGATAATAAAATCGCC 57.882 33.333 0.00 0.00 35.07 5.54
8158 8407 9.663904 TGCTACATTTTGAGATAATAAAATCGC 57.336 29.630 0.00 0.00 35.07 4.58
8166 8415 9.064706 CCTCTTGATGCTACATTTTGAGATAAT 57.935 33.333 0.00 0.00 0.00 1.28
8167 8416 8.267183 TCCTCTTGATGCTACATTTTGAGATAA 58.733 33.333 0.00 0.00 0.00 1.75
8168 8417 7.795047 TCCTCTTGATGCTACATTTTGAGATA 58.205 34.615 0.00 0.00 0.00 1.98
8169 8418 6.656902 TCCTCTTGATGCTACATTTTGAGAT 58.343 36.000 0.00 0.00 0.00 2.75
8170 8419 6.053632 TCCTCTTGATGCTACATTTTGAGA 57.946 37.500 0.00 0.00 0.00 3.27
8171 8420 6.939132 ATCCTCTTGATGCTACATTTTGAG 57.061 37.500 0.00 0.00 30.54 3.02
8172 8421 7.337938 TGTATCCTCTTGATGCTACATTTTGA 58.662 34.615 0.00 0.00 37.04 2.69
8173 8422 7.496920 TCTGTATCCTCTTGATGCTACATTTTG 59.503 37.037 0.00 0.00 37.04 2.44
8174 8423 7.568349 TCTGTATCCTCTTGATGCTACATTTT 58.432 34.615 0.00 0.00 37.04 1.82
8175 8424 7.129457 TCTGTATCCTCTTGATGCTACATTT 57.871 36.000 0.00 0.00 37.04 2.32
8176 8425 6.737720 TCTGTATCCTCTTGATGCTACATT 57.262 37.500 0.00 0.00 37.04 2.71
8177 8426 6.098838 TGTTCTGTATCCTCTTGATGCTACAT 59.901 38.462 0.00 0.00 37.04 2.29
8178 8427 5.422012 TGTTCTGTATCCTCTTGATGCTACA 59.578 40.000 0.00 0.00 37.04 2.74
8179 8428 5.907207 TGTTCTGTATCCTCTTGATGCTAC 58.093 41.667 0.00 0.00 37.04 3.58
8180 8429 6.737720 ATGTTCTGTATCCTCTTGATGCTA 57.262 37.500 0.00 0.00 37.04 3.49
8181 8430 5.627182 ATGTTCTGTATCCTCTTGATGCT 57.373 39.130 0.00 0.00 37.04 3.79
8182 8431 7.658982 TCATAATGTTCTGTATCCTCTTGATGC 59.341 37.037 0.00 0.00 36.68 3.91
8183 8432 9.205719 CTCATAATGTTCTGTATCCTCTTGATG 57.794 37.037 0.00 0.00 34.76 3.07
8184 8433 8.932610 ACTCATAATGTTCTGTATCCTCTTGAT 58.067 33.333 0.00 0.00 37.49 2.57
8185 8434 8.311395 ACTCATAATGTTCTGTATCCTCTTGA 57.689 34.615 0.00 0.00 0.00 3.02
8188 8437 9.201989 TGTTACTCATAATGTTCTGTATCCTCT 57.798 33.333 0.00 0.00 0.00 3.69
8189 8438 9.250624 GTGTTACTCATAATGTTCTGTATCCTC 57.749 37.037 0.00 0.00 0.00 3.71
8190 8439 8.204836 GGTGTTACTCATAATGTTCTGTATCCT 58.795 37.037 0.00 0.00 0.00 3.24
8191 8440 8.204836 AGGTGTTACTCATAATGTTCTGTATCC 58.795 37.037 0.00 0.00 0.00 2.59
8192 8441 9.035607 CAGGTGTTACTCATAATGTTCTGTATC 57.964 37.037 0.00 0.00 0.00 2.24
8193 8442 7.987458 CCAGGTGTTACTCATAATGTTCTGTAT 59.013 37.037 0.00 0.00 0.00 2.29
8194 8443 7.327975 CCAGGTGTTACTCATAATGTTCTGTA 58.672 38.462 0.00 0.00 0.00 2.74
8195 8444 6.173339 CCAGGTGTTACTCATAATGTTCTGT 58.827 40.000 0.00 0.00 0.00 3.41
8196 8445 5.065218 GCCAGGTGTTACTCATAATGTTCTG 59.935 44.000 0.00 0.00 0.00 3.02
8197 8446 5.186198 GCCAGGTGTTACTCATAATGTTCT 58.814 41.667 0.00 0.00 0.00 3.01
8198 8447 4.335594 GGCCAGGTGTTACTCATAATGTTC 59.664 45.833 0.00 0.00 0.00 3.18
8199 8448 4.018415 AGGCCAGGTGTTACTCATAATGTT 60.018 41.667 5.01 0.00 0.00 2.71
8200 8449 3.523564 AGGCCAGGTGTTACTCATAATGT 59.476 43.478 5.01 0.00 0.00 2.71
8201 8450 4.130118 GAGGCCAGGTGTTACTCATAATG 58.870 47.826 5.01 0.00 0.00 1.90
8202 8451 4.040755 AGAGGCCAGGTGTTACTCATAAT 58.959 43.478 5.01 0.00 0.00 1.28
8203 8452 3.197766 CAGAGGCCAGGTGTTACTCATAA 59.802 47.826 5.01 0.00 0.00 1.90
8204 8453 2.766263 CAGAGGCCAGGTGTTACTCATA 59.234 50.000 5.01 0.00 0.00 2.15
8205 8454 1.556911 CAGAGGCCAGGTGTTACTCAT 59.443 52.381 5.01 0.00 0.00 2.90
8206 8455 0.976641 CAGAGGCCAGGTGTTACTCA 59.023 55.000 5.01 0.00 0.00 3.41
8207 8456 0.391793 GCAGAGGCCAGGTGTTACTC 60.392 60.000 5.01 0.00 0.00 2.59
8208 8457 1.127567 TGCAGAGGCCAGGTGTTACT 61.128 55.000 5.01 0.00 40.13 2.24
8209 8458 0.035056 ATGCAGAGGCCAGGTGTTAC 60.035 55.000 5.01 0.00 40.13 2.50
8210 8459 1.578897 TATGCAGAGGCCAGGTGTTA 58.421 50.000 5.01 0.00 40.13 2.41
8211 8460 0.698238 TTATGCAGAGGCCAGGTGTT 59.302 50.000 5.01 0.00 40.13 3.32
8212 8461 0.035056 GTTATGCAGAGGCCAGGTGT 60.035 55.000 5.01 0.00 40.13 4.16
8213 8462 0.254178 AGTTATGCAGAGGCCAGGTG 59.746 55.000 5.01 0.00 40.13 4.00
8214 8463 1.879575 TAGTTATGCAGAGGCCAGGT 58.120 50.000 5.01 0.00 40.13 4.00
8215 8464 2.171448 ACTTAGTTATGCAGAGGCCAGG 59.829 50.000 5.01 0.00 40.13 4.45
8216 8465 3.550437 ACTTAGTTATGCAGAGGCCAG 57.450 47.619 5.01 0.00 40.13 4.85
8217 8466 4.408921 ACATACTTAGTTATGCAGAGGCCA 59.591 41.667 5.01 0.00 40.13 5.36
8218 8467 4.752101 CACATACTTAGTTATGCAGAGGCC 59.248 45.833 0.00 0.00 40.13 5.19
8219 8468 5.360591 ACACATACTTAGTTATGCAGAGGC 58.639 41.667 0.00 0.00 41.68 4.70
8220 8469 8.360390 TGATACACATACTTAGTTATGCAGAGG 58.640 37.037 0.00 0.00 0.00 3.69
8221 8470 9.920133 ATGATACACATACTTAGTTATGCAGAG 57.080 33.333 0.00 0.00 37.46 3.35
8361 8611 3.125316 GCACAAGTTCTATGACTTTCGGG 59.875 47.826 0.00 0.00 37.76 5.14
8381 8631 4.136796 AGCACTAAACTGAACATCAAGCA 58.863 39.130 0.00 0.00 0.00 3.91
8451 8701 4.212716 TGTCTAGAAGTGGCCGTATATGT 58.787 43.478 0.00 0.00 0.00 2.29
8454 8704 6.008331 ACATATGTCTAGAAGTGGCCGTATA 58.992 40.000 1.41 0.00 0.00 1.47
8461 8711 5.423015 AGCACAACATATGTCTAGAAGTGG 58.577 41.667 9.23 0.00 41.46 4.00
8464 8714 5.807520 ACGAAGCACAACATATGTCTAGAAG 59.192 40.000 9.23 0.32 41.46 2.85
8465 8715 5.720202 ACGAAGCACAACATATGTCTAGAA 58.280 37.500 9.23 0.00 41.46 2.10
8466 8716 5.324784 ACGAAGCACAACATATGTCTAGA 57.675 39.130 9.23 0.00 41.46 2.43
8467 8717 4.504461 GGACGAAGCACAACATATGTCTAG 59.496 45.833 9.23 5.16 41.46 2.43
8468 8718 4.081917 TGGACGAAGCACAACATATGTCTA 60.082 41.667 9.23 0.00 41.46 2.59
8469 8719 3.262420 GGACGAAGCACAACATATGTCT 58.738 45.455 9.23 0.00 41.46 3.41
8470 8720 3.000041 TGGACGAAGCACAACATATGTC 59.000 45.455 9.23 0.00 41.46 3.06
8471 8721 3.052455 TGGACGAAGCACAACATATGT 57.948 42.857 1.41 1.41 45.34 2.29
8472 8722 5.698089 AGATATGGACGAAGCACAACATATG 59.302 40.000 0.00 0.00 33.19 1.78
8473 8723 5.858381 AGATATGGACGAAGCACAACATAT 58.142 37.500 0.00 0.00 35.06 1.78
8474 8724 5.276461 AGATATGGACGAAGCACAACATA 57.724 39.130 0.00 0.00 0.00 2.29
8475 8725 4.142609 AGATATGGACGAAGCACAACAT 57.857 40.909 0.00 0.00 0.00 2.71
8476 8726 3.610040 AGATATGGACGAAGCACAACA 57.390 42.857 0.00 0.00 0.00 3.33
8477 8727 4.740695 GTCTAGATATGGACGAAGCACAAC 59.259 45.833 0.00 0.00 0.00 3.32
8478 8728 4.401202 TGTCTAGATATGGACGAAGCACAA 59.599 41.667 0.00 0.00 35.45 3.33
8479 8729 3.951680 TGTCTAGATATGGACGAAGCACA 59.048 43.478 0.00 0.00 35.45 4.57
8480 8730 4.569761 TGTCTAGATATGGACGAAGCAC 57.430 45.455 0.00 0.00 35.45 4.40
8481 8731 6.434340 ACATATGTCTAGATATGGACGAAGCA 59.566 38.462 11.93 0.00 39.64 3.91
8482 8732 6.857956 ACATATGTCTAGATATGGACGAAGC 58.142 40.000 11.93 0.00 39.64 3.86
8490 8740 9.696917 TGTAAGCACAACATATGTCTAGATATG 57.303 33.333 9.23 11.16 41.46 1.78
8509 8759 0.531657 GTTGGCATGCCATGTAAGCA 59.468 50.000 38.78 20.40 46.64 3.91
8556 8806 2.201732 CACACGTAGCACTCTGTTGTT 58.798 47.619 0.00 0.00 0.00 2.83
8639 8889 4.203950 CTCGTACATGAGCTAGTGAGTC 57.796 50.000 0.00 0.00 0.00 3.36
8764 9020 1.007964 CGGCATTTTTGGTCGCACA 60.008 52.632 0.00 0.00 0.00 4.57
8830 9086 5.957771 TTCCTGCTAATATCTTGGACAGT 57.042 39.130 0.00 0.00 0.00 3.55
8831 9087 7.814264 AAATTCCTGCTAATATCTTGGACAG 57.186 36.000 0.00 0.00 0.00 3.51
8852 9108 6.379417 GGGATTTCTCAGACCAGAATGAAAAT 59.621 38.462 0.00 0.00 39.69 1.82


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

AutoCloner maintained by Alex Coulton.