Multiple sequence alignment - TraesCS2D01G317700

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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 TraesCS2D01G317700 chr2D 100.000 7017 0 0 1 7017 407215053 407222069 0.000000e+00 12959.0
1 TraesCS2D01G317700 chr2D 94.651 673 35 1 24 695 582023253 582023925 0.000000e+00 1042.0
2 TraesCS2D01G317700 chr2D 85.405 692 96 4 4 694 638337018 638336331 0.000000e+00 713.0
3 TraesCS2D01G317700 chr2D 99.563 229 1 0 4889 5117 407219712 407219940 1.090000e-112 418.0
4 TraesCS2D01G317700 chr2D 99.563 229 1 0 4660 4888 407219941 407220169 1.090000e-112 418.0
5 TraesCS2D01G317700 chr4D 99.451 2367 9 2 1946 4312 329008793 329006431 0.000000e+00 4296.0
6 TraesCS2D01G317700 chr4D 96.912 2170 22 11 4889 7017 329006144 329003979 0.000000e+00 3594.0
7 TraesCS2D01G317700 chr4D 99.115 1243 3 1 706 1948 329010211 329008977 0.000000e+00 2228.0
8 TraesCS2D01G317700 chr4D 99.421 518 2 1 4372 4888 329006432 329005915 0.000000e+00 939.0
9 TraesCS2D01G317700 chr4D 84.483 116 17 1 6288 6402 374095934 374095819 5.750000e-21 113.0
10 TraesCS2D01G317700 chr4B 97.618 2393 47 5 1946 4337 408957700 408955317 0.000000e+00 4095.0
11 TraesCS2D01G317700 chr4B 96.473 1219 35 2 5063 6277 408954868 408953654 0.000000e+00 2006.0
12 TraesCS2D01G317700 chr4B 95.582 1245 40 8 706 1948 408959115 408957884 0.000000e+00 1980.0
13 TraesCS2D01G317700 chr4B 95.987 299 7 3 4362 4660 408955326 408955033 1.370000e-131 481.0
14 TraesCS2D01G317700 chr4A 97.395 2380 53 4 1943 4321 141119735 141122106 0.000000e+00 4043.0
15 TraesCS2D01G317700 chr4A 94.498 1236 38 8 718 1948 141118342 141119552 0.000000e+00 1879.0
16 TraesCS2D01G317700 chr4A 91.993 587 28 7 5087 5670 141122829 141123399 0.000000e+00 806.0
17 TraesCS2D01G317700 chr4A 90.662 589 43 4 5686 6272 141123496 141124074 0.000000e+00 773.0
18 TraesCS2D01G317700 chr4A 90.274 329 15 8 4360 4684 141122104 141122419 1.410000e-111 414.0
19 TraesCS2D01G317700 chr4A 95.652 46 2 0 4815 4860 141122623 141122668 2.710000e-09 75.0
20 TraesCS2D01G317700 chr4A 95.652 46 2 0 5044 5089 141122623 141122668 2.710000e-09 75.0
21 TraesCS2D01G317700 chr4A 100.000 31 0 0 4858 4888 141122829 141122859 2.730000e-04 58.4
22 TraesCS2D01G317700 chr1B 98.404 1942 27 3 2371 4312 135942032 135943969 0.000000e+00 3411.0
23 TraesCS2D01G317700 chr1B 97.932 1257 23 2 5023 6277 135957900 135959155 0.000000e+00 2174.0
24 TraesCS2D01G317700 chr1B 94.925 1202 42 10 758 1948 135940035 135941228 0.000000e+00 1864.0
25 TraesCS2D01G317700 chr1B 97.623 631 8 2 1943 2571 135941409 135942034 0.000000e+00 1075.0
26 TraesCS2D01G317700 chr1B 97.394 307 7 1 4356 4662 135957583 135957888 8.070000e-144 521.0
27 TraesCS2D01G317700 chr1B 98.947 95 1 0 4794 4888 135957900 135957994 3.370000e-38 171.0
28 TraesCS2D01G317700 chrUn 97.932 1257 23 2 5023 6277 326354636 326355891 0.000000e+00 2174.0
29 TraesCS2D01G317700 chrUn 85.174 688 102 0 8 695 412439473 412440160 0.000000e+00 706.0
30 TraesCS2D01G317700 chrUn 97.720 307 6 1 4356 4662 326354319 326354624 1.730000e-145 527.0
31 TraesCS2D01G317700 chrUn 93.750 144 6 3 4658 4798 17025400 17025257 5.510000e-51 213.0
32 TraesCS2D01G317700 chrUn 93.750 144 6 3 4658 4798 17027633 17027490 5.510000e-51 213.0
33 TraesCS2D01G317700 chrUn 93.750 144 6 3 4658 4798 292131046 292131189 5.510000e-51 213.0
34 TraesCS2D01G317700 chrUn 93.750 144 6 3 4658 4798 302852116 302852259 5.510000e-51 213.0
35 TraesCS2D01G317700 chrUn 93.750 144 6 3 4658 4798 302859439 302859296 5.510000e-51 213.0
36 TraesCS2D01G317700 chrUn 92.517 147 7 4 4884 5027 17025402 17025257 2.570000e-49 207.0
37 TraesCS2D01G317700 chrUn 92.517 147 7 4 4884 5027 17027635 17027490 2.570000e-49 207.0
38 TraesCS2D01G317700 chrUn 92.517 147 7 4 4884 5027 292131044 292131189 2.570000e-49 207.0
39 TraesCS2D01G317700 chrUn 92.517 147 7 4 4884 5027 302852114 302852259 2.570000e-49 207.0
40 TraesCS2D01G317700 chrUn 92.517 147 7 4 4884 5027 302859441 302859296 2.570000e-49 207.0
41 TraesCS2D01G317700 chrUn 98.947 95 1 0 4794 4888 326354636 326354730 3.370000e-38 171.0
42 TraesCS2D01G317700 chr6D 96.970 693 20 1 1 693 162273006 162273697 0.000000e+00 1162.0
43 TraesCS2D01G317700 chr6D 83.951 162 16 5 6291 6442 116568224 116568063 5.670000e-31 147.0
44 TraesCS2D01G317700 chr6D 87.778 90 10 1 6290 6379 193209048 193208960 3.460000e-18 104.0
45 TraesCS2D01G317700 chr1D 96.542 694 24 0 1 694 81458134 81458827 0.000000e+00 1149.0
46 TraesCS2D01G317700 chr1D 88.136 59 7 0 6304 6362 53230661 53230603 3.510000e-08 71.3
47 TraesCS2D01G317700 chr6A 93.931 692 42 0 1 692 12398522 12399213 0.000000e+00 1046.0
48 TraesCS2D01G317700 chr6A 83.073 384 53 10 6291 6665 600275296 600274916 8.720000e-89 339.0
49 TraesCS2D01G317700 chr6A 84.821 112 17 0 6291 6402 592706023 592706134 5.750000e-21 113.0
50 TraesCS2D01G317700 chr5A 90.897 769 28 9 6291 7017 615324610 615323842 0.000000e+00 994.0
51 TraesCS2D01G317700 chr5A 84.879 701 104 2 1 699 629280190 629280890 0.000000e+00 706.0
52 TraesCS2D01G317700 chr5A 89.091 110 12 0 6293 6402 635383680 635383789 3.410000e-28 137.0
53 TraesCS2D01G317700 chr5A 87.179 117 14 1 6287 6402 40268106 40267990 1.590000e-26 132.0
54 TraesCS2D01G317700 chr3B 89.610 693 72 0 1 693 679519193 679519885 0.000000e+00 881.0
55 TraesCS2D01G317700 chr3B 87.898 157 15 3 4670 4824 807600444 807600598 1.550000e-41 182.0
56 TraesCS2D01G317700 chr2B 87.821 624 72 4 73 694 5789052 5788431 0.000000e+00 728.0
57 TraesCS2D01G317700 chr2B 87.864 412 31 10 6302 6697 11339018 11338610 3.830000e-127 466.0
58 TraesCS2D01G317700 chr2B 93.443 122 6 2 6826 6945 11338592 11338471 5.590000e-41 180.0
59 TraesCS2D01G317700 chr3A 80.105 764 104 26 6291 7016 163099820 163100573 6.240000e-145 525.0
60 TraesCS2D01G317700 chr7A 83.047 407 49 11 6291 6678 80533519 80533114 1.120000e-92 351.0
61 TraesCS2D01G317700 chr7A 88.393 112 13 0 6291 6402 658928211 658928100 1.230000e-27 135.0
62 TraesCS2D01G317700 chr6B 93.793 145 7 2 4899 5041 703667465 703667609 4.260000e-52 217.0
63 TraesCS2D01G317700 chr6B 93.103 145 8 2 4670 4812 703667465 703667609 1.980000e-50 211.0
64 TraesCS2D01G317700 chr3D 95.588 136 5 1 4670 4804 412099941 412099806 4.260000e-52 217.0
65 TraesCS2D01G317700 chr3D 94.853 136 6 1 4899 5033 412099941 412099806 1.980000e-50 211.0
66 TraesCS2D01G317700 chr2A 89.286 112 12 0 6291 6402 753678567 753678456 2.640000e-29 141.0
67 TraesCS2D01G317700 chr5B 86.047 129 17 1 6286 6413 39774996 39775124 3.410000e-28 137.0
68 TraesCS2D01G317700 chr7B 88.393 112 13 0 6291 6402 19532349 19532238 1.230000e-27 135.0
69 TraesCS2D01G317700 chr7D 86.607 112 15 0 6291 6402 568909056 568909167 2.660000e-24 124.0
70 TraesCS2D01G317700 chr7D 85.714 112 16 0 6291 6402 555670830 555670719 1.240000e-22 119.0
71 TraesCS2D01G317700 chr5D 87.640 89 11 0 6292 6380 430725048 430724960 3.460000e-18 104.0
72 TraesCS2D01G317700 chr1A 82.906 117 19 1 6287 6402 6920863 6920747 3.460000e-18 104.0


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 TraesCS2D01G317700 chr2D 407215053 407222069 7016 False 4598.333333 12959 99.708667 1 7017 3 chr2D.!!$F2 7016
1 TraesCS2D01G317700 chr2D 582023253 582023925 672 False 1042.000000 1042 94.651000 24 695 1 chr2D.!!$F1 671
2 TraesCS2D01G317700 chr2D 638336331 638337018 687 True 713.000000 713 85.405000 4 694 1 chr2D.!!$R1 690
3 TraesCS2D01G317700 chr4D 329003979 329010211 6232 True 2764.250000 4296 98.724750 706 7017 4 chr4D.!!$R2 6311
4 TraesCS2D01G317700 chr4B 408953654 408959115 5461 True 2140.500000 4095 96.415000 706 6277 4 chr4B.!!$R1 5571
5 TraesCS2D01G317700 chr4A 141118342 141124074 5732 False 1015.425000 4043 94.515750 718 6272 8 chr4A.!!$F1 5554
6 TraesCS2D01G317700 chr1B 135940035 135943969 3934 False 2116.666667 3411 96.984000 758 4312 3 chr1B.!!$F1 3554
7 TraesCS2D01G317700 chr1B 135957583 135959155 1572 False 955.333333 2174 98.091000 4356 6277 3 chr1B.!!$F2 1921
8 TraesCS2D01G317700 chrUn 326354319 326355891 1572 False 957.333333 2174 98.199667 4356 6277 3 chrUn.!!$F4 1921
9 TraesCS2D01G317700 chrUn 412439473 412440160 687 False 706.000000 706 85.174000 8 695 1 chrUn.!!$F1 687
10 TraesCS2D01G317700 chrUn 17025257 17027635 2378 True 210.000000 213 93.133500 4658 5027 4 chrUn.!!$R1 369
11 TraesCS2D01G317700 chr6D 162273006 162273697 691 False 1162.000000 1162 96.970000 1 693 1 chr6D.!!$F1 692
12 TraesCS2D01G317700 chr1D 81458134 81458827 693 False 1149.000000 1149 96.542000 1 694 1 chr1D.!!$F1 693
13 TraesCS2D01G317700 chr6A 12398522 12399213 691 False 1046.000000 1046 93.931000 1 692 1 chr6A.!!$F1 691
14 TraesCS2D01G317700 chr5A 615323842 615324610 768 True 994.000000 994 90.897000 6291 7017 1 chr5A.!!$R2 726
15 TraesCS2D01G317700 chr5A 629280190 629280890 700 False 706.000000 706 84.879000 1 699 1 chr5A.!!$F1 698
16 TraesCS2D01G317700 chr3B 679519193 679519885 692 False 881.000000 881 89.610000 1 693 1 chr3B.!!$F1 692
17 TraesCS2D01G317700 chr2B 5788431 5789052 621 True 728.000000 728 87.821000 73 694 1 chr2B.!!$R1 621
18 TraesCS2D01G317700 chr2B 11338471 11339018 547 True 323.000000 466 90.653500 6302 6945 2 chr2B.!!$R2 643
19 TraesCS2D01G317700 chr3A 163099820 163100573 753 False 525.000000 525 80.105000 6291 7016 1 chr3A.!!$F1 725

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
616 618 1.142314 GCCGCCGTGTATGGTTAGA 59.858 57.895 0.0 0.00 0.00 2.10 F
652 654 2.356553 TTTCGTCCCGGCTCAACG 60.357 61.111 0.0 3.00 37.74 4.10 F
1653 1675 0.036388 CATGGGCGGAGTGTGTAACT 60.036 55.000 0.0 0.00 43.85 2.24 F
1654 1676 0.036388 ATGGGCGGAGTGTGTAACTG 60.036 55.000 0.0 0.00 40.07 3.16 F
1657 1679 0.249741 GGCGGAGTGTGTAACTGTGT 60.250 55.000 0.0 0.00 40.07 3.72 F
4095 4507 2.026542 TGCTCTGCATCCATGTCTTTCT 60.027 45.455 0.0 0.00 31.71 2.52 F
4898 5435 0.240945 GGCAACCTCGACATGTTTGG 59.759 55.000 0.0 5.49 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1675 4.513519 GCGCCTGCTGTATACACA 57.486 55.556 0.08 4.88 38.39 3.72 R
3293 3705 4.398358 TCGGTTTTGTTACACCATGTTTCA 59.602 37.500 0.00 0.00 31.84 2.69 R
4095 4507 1.680735 GTGGTGAAAATGTGCAGTGGA 59.319 47.619 0.00 0.00 0.00 4.02 R
4369 4781 5.139727 TCATGGGAGAAACAAACAGACATT 58.860 37.500 0.00 0.00 0.00 2.71 R
4411 4823 2.986050 TCCTATTGGAGGGGGTATGTC 58.014 52.381 0.00 0.00 46.70 3.06 R
4899 5436 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59 R
6665 7481 1.139058 CAGGCGTGCCTCTTTATAGGT 59.861 52.381 11.22 0.00 46.28 3.08 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
45 46 1.576356 GGCGATCTGGAGTGCTAAAG 58.424 55.000 0.00 0.00 0.00 1.85
247 248 3.601277 CAGCAGTTGCAGAGAGACA 57.399 52.632 6.90 0.00 45.16 3.41
483 485 1.426041 GGAATACGGCGCGATTGTGT 61.426 55.000 12.10 0.00 0.00 3.72
616 618 1.142314 GCCGCCGTGTATGGTTAGA 59.858 57.895 0.00 0.00 0.00 2.10
625 627 3.383505 CGTGTATGGTTAGATCACCCTGA 59.616 47.826 0.00 0.00 35.73 3.86
652 654 2.356553 TTTCGTCCCGGCTCAACG 60.357 61.111 0.00 3.00 37.74 4.10
1652 1674 0.321298 ACATGGGCGGAGTGTGTAAC 60.321 55.000 0.00 0.00 37.35 2.50
1653 1675 0.036388 CATGGGCGGAGTGTGTAACT 60.036 55.000 0.00 0.00 43.85 2.24
1654 1676 0.036388 ATGGGCGGAGTGTGTAACTG 60.036 55.000 0.00 0.00 40.07 3.16
1656 1678 0.949105 GGGCGGAGTGTGTAACTGTG 60.949 60.000 0.00 0.00 40.07 3.66
1657 1679 0.249741 GGCGGAGTGTGTAACTGTGT 60.250 55.000 0.00 0.00 40.07 3.72
2255 2473 6.831727 CAGTTCAAAGAAATGAAATGCACA 57.168 33.333 4.81 0.00 44.94 4.57
3293 3705 9.468532 GAAGCTTCATACACAAGAAAAGAAAAT 57.531 29.630 21.67 0.00 0.00 1.82
3426 3838 3.933955 CTCCTCTTCTGCAAGTGATGAAG 59.066 47.826 5.08 5.08 35.80 3.02
3901 4313 9.424319 CAGTTTCAGCTTAAAGTTCTATCACTA 57.576 33.333 0.00 0.00 0.00 2.74
4095 4507 2.026542 TGCTCTGCATCCATGTCTTTCT 60.027 45.455 0.00 0.00 31.71 2.52
4523 4938 8.703604 TTGATATAAGACTTCTTGAGTTTCCG 57.296 34.615 1.52 0.00 39.19 4.30
4853 5390 2.226437 GCACCATGTTCAGAATGTTCGT 59.774 45.455 0.00 0.00 37.40 3.85
4854 5391 3.813800 CACCATGTTCAGAATGTTCGTG 58.186 45.455 0.00 0.00 37.40 4.35
4855 5392 3.498018 CACCATGTTCAGAATGTTCGTGA 59.502 43.478 0.00 0.00 37.40 4.35
4856 5393 4.154737 CACCATGTTCAGAATGTTCGTGAT 59.845 41.667 0.00 0.00 37.40 3.06
4857 5394 4.154737 ACCATGTTCAGAATGTTCGTGATG 59.845 41.667 0.00 0.00 37.40 3.07
4858 5395 4.154737 CCATGTTCAGAATGTTCGTGATGT 59.845 41.667 0.00 0.00 37.40 3.06
4859 5396 5.351189 CCATGTTCAGAATGTTCGTGATGTA 59.649 40.000 0.00 0.00 37.40 2.29
4860 5397 6.128309 CCATGTTCAGAATGTTCGTGATGTAA 60.128 38.462 0.00 0.00 37.40 2.41
4861 5398 6.223138 TGTTCAGAATGTTCGTGATGTAAC 57.777 37.500 0.00 0.00 37.40 2.50
4862 5399 5.989168 TGTTCAGAATGTTCGTGATGTAACT 59.011 36.000 0.00 0.00 37.40 2.24
4863 5400 6.073819 TGTTCAGAATGTTCGTGATGTAACTG 60.074 38.462 0.00 0.00 37.40 3.16
4864 5401 5.538118 TCAGAATGTTCGTGATGTAACTGT 58.462 37.500 0.00 0.00 37.40 3.55
4865 5402 5.989168 TCAGAATGTTCGTGATGTAACTGTT 59.011 36.000 0.00 0.00 37.40 3.16
4866 5403 7.149307 TCAGAATGTTCGTGATGTAACTGTTA 58.851 34.615 0.00 0.00 37.40 2.41
4867 5404 7.817478 TCAGAATGTTCGTGATGTAACTGTTAT 59.183 33.333 3.23 0.00 37.40 1.89
4868 5405 8.443160 CAGAATGTTCGTGATGTAACTGTTATT 58.557 33.333 3.23 0.00 0.00 1.40
4869 5406 8.443160 AGAATGTTCGTGATGTAACTGTTATTG 58.557 33.333 3.23 0.00 0.00 1.90
4870 5407 7.667043 ATGTTCGTGATGTAACTGTTATTGT 57.333 32.000 3.23 0.00 0.00 2.71
4871 5408 8.766000 ATGTTCGTGATGTAACTGTTATTGTA 57.234 30.769 3.23 0.00 0.00 2.41
4872 5409 8.234887 TGTTCGTGATGTAACTGTTATTGTAG 57.765 34.615 3.23 0.00 0.00 2.74
4873 5410 7.868922 TGTTCGTGATGTAACTGTTATTGTAGT 59.131 33.333 3.23 0.00 0.00 2.73
4874 5411 8.706035 GTTCGTGATGTAACTGTTATTGTAGTT 58.294 33.333 3.23 0.00 40.09 2.24
4875 5412 8.821147 TCGTGATGTAACTGTTATTGTAGTTT 57.179 30.769 3.23 0.00 38.11 2.66
4876 5413 8.918658 TCGTGATGTAACTGTTATTGTAGTTTC 58.081 33.333 3.23 0.00 38.11 2.78
4877 5414 8.166706 CGTGATGTAACTGTTATTGTAGTTTCC 58.833 37.037 3.23 0.00 38.11 3.13
4878 5415 9.216117 GTGATGTAACTGTTATTGTAGTTTCCT 57.784 33.333 3.23 0.00 38.11 3.36
4879 5416 9.214957 TGATGTAACTGTTATTGTAGTTTCCTG 57.785 33.333 3.23 0.00 38.11 3.86
4880 5417 7.972832 TGTAACTGTTATTGTAGTTTCCTGG 57.027 36.000 3.23 0.00 38.11 4.45
4881 5418 5.959618 AACTGTTATTGTAGTTTCCTGGC 57.040 39.130 0.00 0.00 33.59 4.85
4882 5419 4.980573 ACTGTTATTGTAGTTTCCTGGCA 58.019 39.130 0.00 0.00 0.00 4.92
4883 5420 5.381757 ACTGTTATTGTAGTTTCCTGGCAA 58.618 37.500 0.00 0.00 0.00 4.52
4884 5421 5.240844 ACTGTTATTGTAGTTTCCTGGCAAC 59.759 40.000 0.60 0.60 0.00 4.17
4885 5422 4.521256 TGTTATTGTAGTTTCCTGGCAACC 59.479 41.667 5.57 0.00 0.00 3.77
4886 5423 3.525800 ATTGTAGTTTCCTGGCAACCT 57.474 42.857 5.57 0.00 0.00 3.50
4887 5424 2.561478 TGTAGTTTCCTGGCAACCTC 57.439 50.000 5.57 0.72 0.00 3.85
4888 5425 1.270625 TGTAGTTTCCTGGCAACCTCG 60.271 52.381 5.57 0.00 0.00 4.63
4889 5426 1.001633 GTAGTTTCCTGGCAACCTCGA 59.998 52.381 5.57 0.00 0.00 4.04
4890 5427 0.250338 AGTTTCCTGGCAACCTCGAC 60.250 55.000 5.57 0.00 0.00 4.20
4891 5428 0.534203 GTTTCCTGGCAACCTCGACA 60.534 55.000 0.00 0.00 0.00 4.35
4892 5429 0.400213 TTTCCTGGCAACCTCGACAT 59.600 50.000 0.00 0.00 0.00 3.06
4893 5430 0.321564 TTCCTGGCAACCTCGACATG 60.322 55.000 0.00 0.00 0.00 3.21
4894 5431 1.003355 CCTGGCAACCTCGACATGT 60.003 57.895 0.00 0.00 0.00 3.21
4895 5432 0.606401 CCTGGCAACCTCGACATGTT 60.606 55.000 0.00 0.00 0.00 2.71
4896 5433 1.238439 CTGGCAACCTCGACATGTTT 58.762 50.000 0.00 0.00 0.00 2.83
4897 5434 0.950836 TGGCAACCTCGACATGTTTG 59.049 50.000 0.00 0.84 0.00 2.93
4898 5435 0.240945 GGCAACCTCGACATGTTTGG 59.759 55.000 0.00 5.49 0.00 3.28
4899 5436 0.951558 GCAACCTCGACATGTTTGGT 59.048 50.000 0.00 6.17 0.00 3.67
4900 5437 2.147958 GCAACCTCGACATGTTTGGTA 58.852 47.619 15.47 0.00 0.00 3.25
4901 5438 2.095919 GCAACCTCGACATGTTTGGTAC 60.096 50.000 15.47 9.51 0.00 3.34
4902 5439 3.399330 CAACCTCGACATGTTTGGTACT 58.601 45.455 15.47 2.78 0.00 2.73
4903 5440 3.314541 ACCTCGACATGTTTGGTACTC 57.685 47.619 14.12 0.00 0.00 2.59
4904 5441 2.028385 ACCTCGACATGTTTGGTACTCC 60.028 50.000 14.12 0.00 0.00 3.85
4905 5442 2.618053 CTCGACATGTTTGGTACTCCC 58.382 52.381 0.00 0.00 0.00 4.30
4906 5443 2.233922 CTCGACATGTTTGGTACTCCCT 59.766 50.000 0.00 0.00 0.00 4.20
4907 5444 2.232941 TCGACATGTTTGGTACTCCCTC 59.767 50.000 0.00 0.00 0.00 4.30
4908 5445 2.677037 CGACATGTTTGGTACTCCCTCC 60.677 54.545 0.00 0.00 0.00 4.30
4909 5446 1.278127 ACATGTTTGGTACTCCCTCCG 59.722 52.381 0.00 0.00 0.00 4.63
4910 5447 1.278127 CATGTTTGGTACTCCCTCCGT 59.722 52.381 0.00 0.00 0.00 4.69
4911 5448 0.971386 TGTTTGGTACTCCCTCCGTC 59.029 55.000 0.00 0.00 0.00 4.79
4912 5449 0.248565 GTTTGGTACTCCCTCCGTCC 59.751 60.000 0.00 0.00 0.00 4.79
4913 5450 1.252904 TTTGGTACTCCCTCCGTCCG 61.253 60.000 0.00 0.00 0.00 4.79
4914 5451 2.832201 GGTACTCCCTCCGTCCGG 60.832 72.222 0.00 0.00 0.00 5.14
4915 5452 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
4916 5453 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
4917 5454 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
4918 5455 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4919 5456 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4920 5457 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4921 5458 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4922 5459 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4923 5460 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4924 5461 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4925 5462 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4926 5463 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4927 5464 1.997606 CCGTCCGGAAATACTTGTCAC 59.002 52.381 5.23 0.00 37.50 3.67
4928 5465 1.997606 CGTCCGGAAATACTTGTCACC 59.002 52.381 5.23 0.00 0.00 4.02
4929 5466 2.610976 CGTCCGGAAATACTTGTCACCA 60.611 50.000 5.23 0.00 0.00 4.17
4930 5467 3.404899 GTCCGGAAATACTTGTCACCAA 58.595 45.455 5.23 0.00 0.00 3.67
4931 5468 3.816523 GTCCGGAAATACTTGTCACCAAA 59.183 43.478 5.23 0.00 0.00 3.28
4932 5469 4.276431 GTCCGGAAATACTTGTCACCAAAA 59.724 41.667 5.23 0.00 0.00 2.44
4933 5470 5.048294 GTCCGGAAATACTTGTCACCAAAAT 60.048 40.000 5.23 0.00 0.00 1.82
4934 5471 5.048364 TCCGGAAATACTTGTCACCAAAATG 60.048 40.000 0.00 0.00 0.00 2.32
4935 5472 5.160641 CGGAAATACTTGTCACCAAAATGG 58.839 41.667 0.00 0.00 45.02 3.16
4936 5473 5.048364 CGGAAATACTTGTCACCAAAATGGA 60.048 40.000 2.85 0.00 40.96 3.41
4937 5474 6.350110 CGGAAATACTTGTCACCAAAATGGAT 60.350 38.462 2.85 0.00 40.96 3.41
4938 5475 7.148154 CGGAAATACTTGTCACCAAAATGGATA 60.148 37.037 2.85 0.00 40.96 2.59
4939 5476 8.527810 GGAAATACTTGTCACCAAAATGGATAA 58.472 33.333 2.85 0.00 40.96 1.75
4940 5477 9.921637 GAAATACTTGTCACCAAAATGGATAAA 57.078 29.630 2.85 0.00 40.96 1.40
4942 5479 9.927668 AATACTTGTCACCAAAATGGATAAAAG 57.072 29.630 2.85 4.20 40.96 2.27
4943 5480 6.758254 ACTTGTCACCAAAATGGATAAAAGG 58.242 36.000 2.85 0.00 40.96 3.11
4944 5481 5.146010 TGTCACCAAAATGGATAAAAGGC 57.854 39.130 2.85 0.00 40.96 4.35
4945 5482 4.173256 GTCACCAAAATGGATAAAAGGCG 58.827 43.478 2.85 0.00 40.96 5.52
4946 5483 4.082463 GTCACCAAAATGGATAAAAGGCGA 60.082 41.667 2.85 0.00 40.96 5.54
4947 5484 4.709397 TCACCAAAATGGATAAAAGGCGAT 59.291 37.500 2.85 0.00 40.96 4.58
4948 5485 4.805192 CACCAAAATGGATAAAAGGCGATG 59.195 41.667 2.85 0.00 40.96 3.84
4949 5486 4.466015 ACCAAAATGGATAAAAGGCGATGT 59.534 37.500 2.85 0.00 40.96 3.06
4950 5487 5.654650 ACCAAAATGGATAAAAGGCGATGTA 59.345 36.000 2.85 0.00 40.96 2.29
4951 5488 6.323739 ACCAAAATGGATAAAAGGCGATGTAT 59.676 34.615 2.85 0.00 40.96 2.29
4952 5489 6.863126 CCAAAATGGATAAAAGGCGATGTATC 59.137 38.462 0.00 0.00 40.96 2.24
4953 5490 7.255590 CCAAAATGGATAAAAGGCGATGTATCT 60.256 37.037 0.00 0.00 40.96 1.98
4954 5491 8.783093 CAAAATGGATAAAAGGCGATGTATCTA 58.217 33.333 0.00 0.00 0.00 1.98
4955 5492 8.553459 AAATGGATAAAAGGCGATGTATCTAG 57.447 34.615 0.00 0.00 0.00 2.43
4956 5493 6.911250 TGGATAAAAGGCGATGTATCTAGA 57.089 37.500 0.00 0.00 0.00 2.43
4957 5494 6.688578 TGGATAAAAGGCGATGTATCTAGAC 58.311 40.000 0.00 0.00 0.00 2.59
4958 5495 5.800941 GGATAAAAGGCGATGTATCTAGACG 59.199 44.000 0.00 0.00 0.00 4.18
4959 5496 4.650754 AAAAGGCGATGTATCTAGACGT 57.349 40.909 0.00 0.00 0.00 4.34
4960 5497 5.762825 AAAAGGCGATGTATCTAGACGTA 57.237 39.130 0.00 0.00 0.00 3.57
4961 5498 5.961396 AAAGGCGATGTATCTAGACGTAT 57.039 39.130 0.00 0.00 0.00 3.06
4962 5499 5.961396 AAGGCGATGTATCTAGACGTATT 57.039 39.130 0.00 0.00 0.00 1.89
4963 5500 5.961396 AGGCGATGTATCTAGACGTATTT 57.039 39.130 0.00 0.00 0.00 1.40
4964 5501 6.328641 AGGCGATGTATCTAGACGTATTTT 57.671 37.500 0.00 0.00 0.00 1.82
4965 5502 7.444629 AGGCGATGTATCTAGACGTATTTTA 57.555 36.000 0.00 0.00 0.00 1.52
4966 5503 7.528307 AGGCGATGTATCTAGACGTATTTTAG 58.472 38.462 0.00 0.00 0.00 1.85
4967 5504 7.174599 AGGCGATGTATCTAGACGTATTTTAGT 59.825 37.037 0.00 0.00 0.00 2.24
4968 5505 7.806960 GGCGATGTATCTAGACGTATTTTAGTT 59.193 37.037 0.00 0.00 0.00 2.24
4969 5506 8.838961 GCGATGTATCTAGACGTATTTTAGTTC 58.161 37.037 0.00 0.00 0.00 3.01
5011 5548 8.726650 TGTTCATTTTGATGACAGTATTTTCG 57.273 30.769 0.00 0.00 0.00 3.46
5012 5549 7.807433 TGTTCATTTTGATGACAGTATTTTCGG 59.193 33.333 0.00 0.00 0.00 4.30
5013 5550 7.680442 TCATTTTGATGACAGTATTTTCGGA 57.320 32.000 0.00 0.00 0.00 4.55
5014 5551 8.279970 TCATTTTGATGACAGTATTTTCGGAT 57.720 30.769 0.00 0.00 0.00 4.18
5015 5552 8.183536 TCATTTTGATGACAGTATTTTCGGATG 58.816 33.333 0.00 0.00 0.00 3.51
5016 5553 6.435430 TTTGATGACAGTATTTTCGGATGG 57.565 37.500 0.00 0.00 0.00 3.51
5017 5554 5.351948 TGATGACAGTATTTTCGGATGGA 57.648 39.130 0.00 0.00 0.00 3.41
5018 5555 5.359756 TGATGACAGTATTTTCGGATGGAG 58.640 41.667 0.00 0.00 0.00 3.86
5019 5556 4.137116 TGACAGTATTTTCGGATGGAGG 57.863 45.455 0.00 0.00 0.00 4.30
5020 5557 3.118408 TGACAGTATTTTCGGATGGAGGG 60.118 47.826 0.00 0.00 0.00 4.30
5021 5558 3.112263 ACAGTATTTTCGGATGGAGGGA 58.888 45.455 0.00 0.00 0.00 4.20
5022 5559 3.134804 ACAGTATTTTCGGATGGAGGGAG 59.865 47.826 0.00 0.00 0.00 4.30
5023 5560 3.134804 CAGTATTTTCGGATGGAGGGAGT 59.865 47.826 0.00 0.00 0.00 3.85
5024 5561 4.344102 CAGTATTTTCGGATGGAGGGAGTA 59.656 45.833 0.00 0.00 0.00 2.59
5025 5562 5.012148 CAGTATTTTCGGATGGAGGGAGTAT 59.988 44.000 0.00 0.00 0.00 2.12
5026 5563 5.607171 AGTATTTTCGGATGGAGGGAGTATT 59.393 40.000 0.00 0.00 0.00 1.89
5027 5564 6.785963 AGTATTTTCGGATGGAGGGAGTATTA 59.214 38.462 0.00 0.00 0.00 0.98
5028 5565 5.546621 TTTTCGGATGGAGGGAGTATTAG 57.453 43.478 0.00 0.00 0.00 1.73
5029 5566 4.464652 TTCGGATGGAGGGAGTATTAGA 57.535 45.455 0.00 0.00 0.00 2.10
5030 5567 4.676799 TCGGATGGAGGGAGTATTAGAT 57.323 45.455 0.00 0.00 0.00 1.98
5031 5568 5.791303 TCGGATGGAGGGAGTATTAGATA 57.209 43.478 0.00 0.00 0.00 1.98
5032 5569 6.148735 TCGGATGGAGGGAGTATTAGATAA 57.851 41.667 0.00 0.00 0.00 1.75
5033 5570 6.742756 TCGGATGGAGGGAGTATTAGATAAT 58.257 40.000 0.00 0.00 0.00 1.28
5034 5571 6.607600 TCGGATGGAGGGAGTATTAGATAATG 59.392 42.308 0.00 0.00 0.00 1.90
5035 5572 6.587273 GGATGGAGGGAGTATTAGATAATGC 58.413 44.000 0.00 0.00 0.00 3.56
5036 5573 6.156949 GGATGGAGGGAGTATTAGATAATGCA 59.843 42.308 0.00 0.00 31.78 3.96
5037 5574 6.360370 TGGAGGGAGTATTAGATAATGCAC 57.640 41.667 0.00 0.00 31.78 4.57
5038 5575 5.843969 TGGAGGGAGTATTAGATAATGCACA 59.156 40.000 0.00 0.00 31.78 4.57
5039 5576 6.328934 TGGAGGGAGTATTAGATAATGCACAA 59.671 38.462 0.00 0.00 31.78 3.33
5040 5577 6.651225 GGAGGGAGTATTAGATAATGCACAAC 59.349 42.308 0.00 0.00 31.78 3.32
5041 5578 6.223852 AGGGAGTATTAGATAATGCACAACG 58.776 40.000 0.00 0.00 31.78 4.10
5042 5579 5.107065 GGGAGTATTAGATAATGCACAACGC 60.107 44.000 0.00 0.00 42.89 4.84
5060 5597 3.179925 CATGTATGCACTGGCCACT 57.820 52.632 0.00 0.00 40.13 4.00
5061 5598 0.736636 CATGTATGCACTGGCCACTG 59.263 55.000 0.00 4.27 40.13 3.66
5062 5599 1.033746 ATGTATGCACTGGCCACTGC 61.034 55.000 25.46 25.46 40.13 4.40
5064 5601 1.675310 TATGCACTGGCCACTGCAC 60.675 57.895 33.62 11.52 45.91 4.57
5067 5604 2.282674 CACTGGCCACTGCACCAT 60.283 61.111 0.00 0.00 40.13 3.55
5068 5605 2.282674 ACTGGCCACTGCACCATG 60.283 61.111 0.00 0.00 40.13 3.66
5069 5606 2.282674 CTGGCCACTGCACCATGT 60.283 61.111 0.00 0.00 40.13 3.21
5070 5607 1.904865 CTGGCCACTGCACCATGTT 60.905 57.895 0.00 0.00 40.13 2.71
5071 5608 1.870055 CTGGCCACTGCACCATGTTC 61.870 60.000 0.00 0.00 40.13 3.18
5072 5609 1.902918 GGCCACTGCACCATGTTCA 60.903 57.895 0.00 0.00 40.13 3.18
5073 5610 1.582968 GCCACTGCACCATGTTCAG 59.417 57.895 0.00 0.00 37.47 3.02
5074 5611 0.890542 GCCACTGCACCATGTTCAGA 60.891 55.000 11.50 0.00 37.47 3.27
5075 5612 1.608055 CCACTGCACCATGTTCAGAA 58.392 50.000 11.50 0.00 31.69 3.02
5076 5613 2.165167 CCACTGCACCATGTTCAGAAT 58.835 47.619 11.50 0.00 31.69 2.40
5077 5614 2.094906 CCACTGCACCATGTTCAGAATG 60.095 50.000 11.50 2.91 31.69 2.67
5078 5615 2.555325 CACTGCACCATGTTCAGAATGT 59.445 45.455 11.50 0.00 37.40 2.71
5079 5616 3.005050 CACTGCACCATGTTCAGAATGTT 59.995 43.478 11.50 0.00 37.40 2.71
5080 5617 3.254166 ACTGCACCATGTTCAGAATGTTC 59.746 43.478 11.50 0.00 37.40 3.18
5081 5618 2.226200 TGCACCATGTTCAGAATGTTCG 59.774 45.455 0.00 0.00 37.40 3.95
5524 6227 3.243704 TGCCATGTGTTTTTGCTTCCTAC 60.244 43.478 0.00 0.00 0.00 3.18
5948 6736 7.932491 TCCAATCTGATGAAGATGAAGAAGATC 59.068 37.037 0.00 0.00 45.37 2.75
6379 7171 3.573967 GGATTTGTGGTCATCCAACTTGT 59.426 43.478 0.00 0.00 46.15 3.16
6389 7181 5.057149 GTCATCCAACTTGTGTTCTAGTGT 58.943 41.667 0.00 0.00 33.52 3.55
6665 7481 4.037565 CACTGCACCGACTACATATTCCTA 59.962 45.833 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.777459 TCCTCATAGACCTCCTTCCC 57.223 55.000 0.00 0.00 0.00 3.97
247 248 0.753479 TGCAATTGTTCCCACACCGT 60.753 50.000 7.40 0.00 30.32 4.83
483 485 7.671819 ACTGCTAGAGTAGGCTATGATTTCATA 59.328 37.037 0.00 0.65 33.65 2.15
616 618 4.657013 GAAAGAGAGGTTTTCAGGGTGAT 58.343 43.478 0.00 0.00 35.22 3.06
652 654 2.884827 AGCTTTATTACGTCGTCACCC 58.115 47.619 0.00 0.00 0.00 4.61
695 697 1.147376 TGGTCGGAGGTGTGTTTGG 59.853 57.895 0.00 0.00 0.00 3.28
697 699 0.106149 GAGTGGTCGGAGGTGTGTTT 59.894 55.000 0.00 0.00 0.00 2.83
698 700 1.746517 GAGTGGTCGGAGGTGTGTT 59.253 57.895 0.00 0.00 0.00 3.32
699 701 2.561956 CGAGTGGTCGGAGGTGTGT 61.562 63.158 0.00 0.00 42.87 3.72
700 702 2.258591 CGAGTGGTCGGAGGTGTG 59.741 66.667 0.00 0.00 42.87 3.82
701 703 3.681835 GCGAGTGGTCGGAGGTGT 61.682 66.667 0.00 0.00 46.91 4.16
702 704 3.343788 GAGCGAGTGGTCGGAGGTG 62.344 68.421 0.00 0.00 46.91 4.00
703 705 3.063084 GAGCGAGTGGTCGGAGGT 61.063 66.667 0.00 0.00 46.91 3.85
704 706 3.827898 GGAGCGAGTGGTCGGAGG 61.828 72.222 0.00 0.00 46.91 4.30
1653 1675 4.513519 GCGCCTGCTGTATACACA 57.486 55.556 0.08 4.88 38.39 3.72
3293 3705 4.398358 TCGGTTTTGTTACACCATGTTTCA 59.602 37.500 0.00 0.00 31.84 2.69
3901 4313 7.843490 ACACGTACATAGTAAAGATGCAAAT 57.157 32.000 0.00 0.00 0.00 2.32
4095 4507 1.680735 GTGGTGAAAATGTGCAGTGGA 59.319 47.619 0.00 0.00 0.00 4.02
4369 4781 5.139727 TCATGGGAGAAACAAACAGACATT 58.860 37.500 0.00 0.00 0.00 2.71
4411 4823 2.986050 TCCTATTGGAGGGGGTATGTC 58.014 52.381 0.00 0.00 46.70 3.06
4853 5390 9.214957 CAGGAAACTACAATAACAGTTACATCA 57.785 33.333 0.00 0.00 40.21 3.07
4854 5391 8.665685 CCAGGAAACTACAATAACAGTTACATC 58.334 37.037 0.00 0.00 40.21 3.06
4855 5392 7.120726 GCCAGGAAACTACAATAACAGTTACAT 59.879 37.037 0.00 0.00 40.21 2.29
4856 5393 6.428771 GCCAGGAAACTACAATAACAGTTACA 59.571 38.462 0.00 0.00 40.21 2.41
4857 5394 6.428771 TGCCAGGAAACTACAATAACAGTTAC 59.571 38.462 0.00 0.00 40.21 2.50
4858 5395 6.535540 TGCCAGGAAACTACAATAACAGTTA 58.464 36.000 0.00 0.00 40.21 2.24
4859 5396 5.381757 TGCCAGGAAACTACAATAACAGTT 58.618 37.500 0.00 0.00 40.21 3.16
4860 5397 4.980573 TGCCAGGAAACTACAATAACAGT 58.019 39.130 0.00 0.00 40.21 3.55
4861 5398 5.335661 GGTTGCCAGGAAACTACAATAACAG 60.336 44.000 10.46 0.00 40.21 3.16
4862 5399 4.521256 GGTTGCCAGGAAACTACAATAACA 59.479 41.667 10.46 0.00 40.21 2.41
4863 5400 4.765339 AGGTTGCCAGGAAACTACAATAAC 59.235 41.667 10.46 0.00 40.21 1.89
4864 5401 4.993028 AGGTTGCCAGGAAACTACAATAA 58.007 39.130 10.46 0.00 40.21 1.40
4865 5402 4.585879 GAGGTTGCCAGGAAACTACAATA 58.414 43.478 10.46 0.00 40.21 1.90
4866 5403 3.421844 GAGGTTGCCAGGAAACTACAAT 58.578 45.455 10.46 0.00 40.21 2.71
4867 5404 2.808933 CGAGGTTGCCAGGAAACTACAA 60.809 50.000 10.46 0.00 40.21 2.41
4868 5405 1.270625 CGAGGTTGCCAGGAAACTACA 60.271 52.381 10.46 0.00 40.21 2.74
4869 5406 1.001633 TCGAGGTTGCCAGGAAACTAC 59.998 52.381 10.46 4.04 40.21 2.73
4870 5407 1.001633 GTCGAGGTTGCCAGGAAACTA 59.998 52.381 10.46 0.00 40.21 2.24
4871 5408 0.250338 GTCGAGGTTGCCAGGAAACT 60.250 55.000 10.46 0.00 46.44 2.66
4872 5409 0.534203 TGTCGAGGTTGCCAGGAAAC 60.534 55.000 0.72 0.72 0.00 2.78
4873 5410 0.400213 ATGTCGAGGTTGCCAGGAAA 59.600 50.000 0.00 0.00 0.00 3.13
4874 5411 0.321564 CATGTCGAGGTTGCCAGGAA 60.322 55.000 0.00 0.00 0.00 3.36
4875 5412 1.296392 CATGTCGAGGTTGCCAGGA 59.704 57.895 0.00 0.00 0.00 3.86
4876 5413 0.606401 AACATGTCGAGGTTGCCAGG 60.606 55.000 0.00 0.00 0.00 4.45
4877 5414 1.069022 CAAACATGTCGAGGTTGCCAG 60.069 52.381 0.00 0.00 0.00 4.85
4878 5415 0.950836 CAAACATGTCGAGGTTGCCA 59.049 50.000 0.00 0.00 0.00 4.92
4879 5416 0.240945 CCAAACATGTCGAGGTTGCC 59.759 55.000 0.00 0.00 0.00 4.52
4880 5417 0.951558 ACCAAACATGTCGAGGTTGC 59.048 50.000 0.00 0.00 0.00 4.17
4881 5418 3.399330 AGTACCAAACATGTCGAGGTTG 58.601 45.455 18.32 10.32 33.91 3.77
4882 5419 3.556423 GGAGTACCAAACATGTCGAGGTT 60.556 47.826 18.32 5.48 33.91 3.50
4883 5420 2.028385 GGAGTACCAAACATGTCGAGGT 60.028 50.000 17.53 17.53 36.40 3.85
4884 5421 2.618053 GGAGTACCAAACATGTCGAGG 58.382 52.381 0.00 4.11 35.97 4.63
4885 5422 2.233922 AGGGAGTACCAAACATGTCGAG 59.766 50.000 0.00 0.00 43.89 4.04
4886 5423 2.232941 GAGGGAGTACCAAACATGTCGA 59.767 50.000 0.00 0.00 43.89 4.20
4887 5424 2.618053 GAGGGAGTACCAAACATGTCG 58.382 52.381 0.00 0.00 43.89 4.35
4888 5425 2.677037 CGGAGGGAGTACCAAACATGTC 60.677 54.545 0.00 0.00 43.89 3.06
4889 5426 1.278127 CGGAGGGAGTACCAAACATGT 59.722 52.381 0.00 0.00 43.89 3.21
4890 5427 1.278127 ACGGAGGGAGTACCAAACATG 59.722 52.381 0.00 0.00 43.89 3.21
4891 5428 1.553704 GACGGAGGGAGTACCAAACAT 59.446 52.381 0.00 0.00 43.89 2.71
4892 5429 0.971386 GACGGAGGGAGTACCAAACA 59.029 55.000 0.00 0.00 43.89 2.83
4893 5430 0.248565 GGACGGAGGGAGTACCAAAC 59.751 60.000 0.00 0.00 43.89 2.93
4894 5431 1.252904 CGGACGGAGGGAGTACCAAA 61.253 60.000 0.00 0.00 43.89 3.28
4895 5432 1.679977 CGGACGGAGGGAGTACCAA 60.680 63.158 0.00 0.00 43.89 3.67
4896 5433 2.044650 CGGACGGAGGGAGTACCA 60.045 66.667 0.00 0.00 43.89 3.25
4897 5434 2.832201 CCGGACGGAGGGAGTACC 60.832 72.222 4.40 0.00 37.50 3.34
4898 5435 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
4899 5436 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4900 5437 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
4901 5438 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4902 5439 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4903 5440 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4904 5441 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4905 5442 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4906 5443 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4907 5444 1.997606 GTGACAAGTATTTCCGGACGG 59.002 52.381 1.83 3.96 0.00 4.79
4908 5445 1.997606 GGTGACAAGTATTTCCGGACG 59.002 52.381 1.83 0.00 0.00 4.79
4909 5446 3.048337 TGGTGACAAGTATTTCCGGAC 57.952 47.619 1.83 0.00 37.44 4.79
4922 5459 4.321601 CGCCTTTTATCCATTTTGGTGACA 60.322 41.667 0.00 0.00 39.03 3.58
4923 5460 4.082463 TCGCCTTTTATCCATTTTGGTGAC 60.082 41.667 0.00 0.00 39.03 3.67
4924 5461 4.082845 TCGCCTTTTATCCATTTTGGTGA 58.917 39.130 0.00 0.00 39.03 4.02
4925 5462 4.448537 TCGCCTTTTATCCATTTTGGTG 57.551 40.909 0.00 0.00 39.03 4.17
4926 5463 4.466015 ACATCGCCTTTTATCCATTTTGGT 59.534 37.500 0.00 0.00 39.03 3.67
4927 5464 5.009854 ACATCGCCTTTTATCCATTTTGG 57.990 39.130 0.00 0.00 39.43 3.28
4928 5465 7.651808 AGATACATCGCCTTTTATCCATTTTG 58.348 34.615 0.00 0.00 0.00 2.44
4929 5466 7.823745 AGATACATCGCCTTTTATCCATTTT 57.176 32.000 0.00 0.00 0.00 1.82
4930 5467 8.375506 TCTAGATACATCGCCTTTTATCCATTT 58.624 33.333 0.00 0.00 0.00 2.32
4931 5468 7.819900 GTCTAGATACATCGCCTTTTATCCATT 59.180 37.037 0.00 0.00 0.00 3.16
4932 5469 7.324178 GTCTAGATACATCGCCTTTTATCCAT 58.676 38.462 0.00 0.00 0.00 3.41
4933 5470 6.569801 CGTCTAGATACATCGCCTTTTATCCA 60.570 42.308 0.00 0.00 0.00 3.41
4934 5471 5.800941 CGTCTAGATACATCGCCTTTTATCC 59.199 44.000 0.00 0.00 0.00 2.59
4935 5472 6.380190 ACGTCTAGATACATCGCCTTTTATC 58.620 40.000 0.00 0.00 0.00 1.75
4936 5473 6.328641 ACGTCTAGATACATCGCCTTTTAT 57.671 37.500 0.00 0.00 0.00 1.40
4937 5474 5.762825 ACGTCTAGATACATCGCCTTTTA 57.237 39.130 0.00 0.00 0.00 1.52
4938 5475 4.650754 ACGTCTAGATACATCGCCTTTT 57.349 40.909 0.00 0.00 0.00 2.27
4939 5476 5.961396 ATACGTCTAGATACATCGCCTTT 57.039 39.130 0.00 0.00 0.00 3.11
4940 5477 5.961396 AATACGTCTAGATACATCGCCTT 57.039 39.130 0.00 0.00 0.00 4.35
4941 5478 5.961396 AAATACGTCTAGATACATCGCCT 57.039 39.130 0.00 0.00 0.00 5.52
4942 5479 7.303998 ACTAAAATACGTCTAGATACATCGCC 58.696 38.462 0.00 0.00 0.00 5.54
4943 5480 8.725212 AACTAAAATACGTCTAGATACATCGC 57.275 34.615 0.00 0.00 0.00 4.58
4985 5522 9.179552 CGAAAATACTGTCATCAAAATGAACAA 57.820 29.630 0.00 0.00 43.42 2.83
4986 5523 7.807433 CCGAAAATACTGTCATCAAAATGAACA 59.193 33.333 0.00 0.00 43.42 3.18
4987 5524 8.020819 TCCGAAAATACTGTCATCAAAATGAAC 58.979 33.333 0.00 0.00 43.42 3.18
4988 5525 8.105097 TCCGAAAATACTGTCATCAAAATGAA 57.895 30.769 0.00 0.00 43.42 2.57
4989 5526 7.680442 TCCGAAAATACTGTCATCAAAATGA 57.320 32.000 0.00 0.00 39.63 2.57
4990 5527 7.433131 CCATCCGAAAATACTGTCATCAAAATG 59.567 37.037 0.00 0.00 0.00 2.32
4991 5528 7.339212 TCCATCCGAAAATACTGTCATCAAAAT 59.661 33.333 0.00 0.00 0.00 1.82
4992 5529 6.657117 TCCATCCGAAAATACTGTCATCAAAA 59.343 34.615 0.00 0.00 0.00 2.44
4993 5530 6.176896 TCCATCCGAAAATACTGTCATCAAA 58.823 36.000 0.00 0.00 0.00 2.69
4994 5531 5.739959 TCCATCCGAAAATACTGTCATCAA 58.260 37.500 0.00 0.00 0.00 2.57
4995 5532 5.351948 TCCATCCGAAAATACTGTCATCA 57.648 39.130 0.00 0.00 0.00 3.07
4996 5533 4.752101 CCTCCATCCGAAAATACTGTCATC 59.248 45.833 0.00 0.00 0.00 2.92
4997 5534 4.444876 CCCTCCATCCGAAAATACTGTCAT 60.445 45.833 0.00 0.00 0.00 3.06
4998 5535 3.118408 CCCTCCATCCGAAAATACTGTCA 60.118 47.826 0.00 0.00 0.00 3.58
4999 5536 3.134081 TCCCTCCATCCGAAAATACTGTC 59.866 47.826 0.00 0.00 0.00 3.51
5000 5537 3.112263 TCCCTCCATCCGAAAATACTGT 58.888 45.455 0.00 0.00 0.00 3.55
5001 5538 3.134804 ACTCCCTCCATCCGAAAATACTG 59.865 47.826 0.00 0.00 0.00 2.74
5002 5539 3.385115 ACTCCCTCCATCCGAAAATACT 58.615 45.455 0.00 0.00 0.00 2.12
5003 5540 3.840124 ACTCCCTCCATCCGAAAATAC 57.160 47.619 0.00 0.00 0.00 1.89
5004 5541 7.014449 TCTAATACTCCCTCCATCCGAAAATA 58.986 38.462 0.00 0.00 0.00 1.40
5005 5542 5.844516 TCTAATACTCCCTCCATCCGAAAAT 59.155 40.000 0.00 0.00 0.00 1.82
5006 5543 5.213519 TCTAATACTCCCTCCATCCGAAAA 58.786 41.667 0.00 0.00 0.00 2.29
5007 5544 4.811498 TCTAATACTCCCTCCATCCGAAA 58.189 43.478 0.00 0.00 0.00 3.46
5008 5545 4.464652 TCTAATACTCCCTCCATCCGAA 57.535 45.455 0.00 0.00 0.00 4.30
5009 5546 4.676799 ATCTAATACTCCCTCCATCCGA 57.323 45.455 0.00 0.00 0.00 4.55
5010 5547 6.684111 GCATTATCTAATACTCCCTCCATCCG 60.684 46.154 0.00 0.00 0.00 4.18
5011 5548 6.156949 TGCATTATCTAATACTCCCTCCATCC 59.843 42.308 0.00 0.00 0.00 3.51
5012 5549 7.044798 GTGCATTATCTAATACTCCCTCCATC 58.955 42.308 0.00 0.00 0.00 3.51
5013 5550 6.501805 TGTGCATTATCTAATACTCCCTCCAT 59.498 38.462 0.00 0.00 0.00 3.41
5014 5551 5.843969 TGTGCATTATCTAATACTCCCTCCA 59.156 40.000 0.00 0.00 0.00 3.86
5015 5552 6.360370 TGTGCATTATCTAATACTCCCTCC 57.640 41.667 0.00 0.00 0.00 4.30
5016 5553 6.366332 CGTTGTGCATTATCTAATACTCCCTC 59.634 42.308 0.00 0.00 0.00 4.30
5017 5554 6.223852 CGTTGTGCATTATCTAATACTCCCT 58.776 40.000 0.00 0.00 0.00 4.20
5018 5555 5.107065 GCGTTGTGCATTATCTAATACTCCC 60.107 44.000 0.00 0.00 45.45 4.30
5019 5556 5.916969 GCGTTGTGCATTATCTAATACTCC 58.083 41.667 0.00 0.00 45.45 3.85
5042 5579 0.736636 CAGTGGCCAGTGCATACATG 59.263 55.000 27.20 1.50 40.13 3.21
5043 5580 3.179925 CAGTGGCCAGTGCATACAT 57.820 52.632 27.20 0.00 40.13 2.29
5044 5581 4.720127 CAGTGGCCAGTGCATACA 57.280 55.556 27.20 0.00 40.13 2.29
5050 5587 2.282674 ATGGTGCAGTGGCCAGTG 60.283 61.111 32.59 32.59 38.27 3.66
5051 5588 2.282674 CATGGTGCAGTGGCCAGT 60.283 61.111 5.11 6.41 38.27 4.00
5052 5589 1.870055 GAACATGGTGCAGTGGCCAG 61.870 60.000 5.11 0.00 38.27 4.85
5053 5590 1.902918 GAACATGGTGCAGTGGCCA 60.903 57.895 0.00 0.00 40.13 5.36
5054 5591 1.870055 CTGAACATGGTGCAGTGGCC 61.870 60.000 0.00 0.00 34.66 5.36
5055 5592 0.890542 TCTGAACATGGTGCAGTGGC 60.891 55.000 4.37 0.00 40.00 5.01
5056 5593 1.608055 TTCTGAACATGGTGCAGTGG 58.392 50.000 4.37 0.00 40.00 4.00
5057 5594 2.555325 ACATTCTGAACATGGTGCAGTG 59.445 45.455 4.37 0.00 40.00 3.66
5058 5595 2.867624 ACATTCTGAACATGGTGCAGT 58.132 42.857 4.37 0.00 40.00 4.40
5059 5596 3.668757 CGAACATTCTGAACATGGTGCAG 60.669 47.826 0.00 0.59 40.40 4.41
5060 5597 2.226200 CGAACATTCTGAACATGGTGCA 59.774 45.455 0.00 0.00 0.00 4.57
5061 5598 2.226437 ACGAACATTCTGAACATGGTGC 59.774 45.455 0.00 0.00 0.00 5.01
5062 5599 3.498018 TCACGAACATTCTGAACATGGTG 59.502 43.478 0.00 0.55 0.00 4.17
5063 5600 3.738982 TCACGAACATTCTGAACATGGT 58.261 40.909 0.00 0.00 0.00 3.55
5064 5601 4.154737 ACATCACGAACATTCTGAACATGG 59.845 41.667 0.00 0.00 0.00 3.66
5065 5602 5.287170 ACATCACGAACATTCTGAACATG 57.713 39.130 0.00 0.00 0.00 3.21
5066 5603 6.650807 AGTTACATCACGAACATTCTGAACAT 59.349 34.615 0.00 0.00 0.00 2.71
5067 5604 5.989168 AGTTACATCACGAACATTCTGAACA 59.011 36.000 0.00 0.00 0.00 3.18
5068 5605 6.073765 ACAGTTACATCACGAACATTCTGAAC 60.074 38.462 0.00 0.00 0.00 3.18
5069 5606 5.989168 ACAGTTACATCACGAACATTCTGAA 59.011 36.000 0.00 0.00 0.00 3.02
5070 5607 5.538118 ACAGTTACATCACGAACATTCTGA 58.462 37.500 0.00 0.00 0.00 3.27
5071 5608 5.845985 ACAGTTACATCACGAACATTCTG 57.154 39.130 0.00 0.00 0.00 3.02
5072 5609 8.443160 CAATAACAGTTACATCACGAACATTCT 58.557 33.333 0.00 0.00 0.00 2.40
5073 5610 8.227791 ACAATAACAGTTACATCACGAACATTC 58.772 33.333 0.00 0.00 0.00 2.67
5074 5611 8.094798 ACAATAACAGTTACATCACGAACATT 57.905 30.769 0.00 0.00 0.00 2.71
5075 5612 7.667043 ACAATAACAGTTACATCACGAACAT 57.333 32.000 0.00 0.00 0.00 2.71
5076 5613 7.868922 ACTACAATAACAGTTACATCACGAACA 59.131 33.333 0.00 0.00 0.00 3.18
5077 5614 8.236084 ACTACAATAACAGTTACATCACGAAC 57.764 34.615 0.00 0.00 0.00 3.95
5078 5615 8.821147 AACTACAATAACAGTTACATCACGAA 57.179 30.769 0.00 0.00 33.29 3.85
5079 5616 8.821147 AAACTACAATAACAGTTACATCACGA 57.179 30.769 0.00 0.00 33.92 4.35
5080 5617 8.166706 GGAAACTACAATAACAGTTACATCACG 58.833 37.037 0.00 0.00 33.92 4.35
5081 5618 9.216117 AGGAAACTACAATAACAGTTACATCAC 57.784 33.333 0.00 0.00 40.61 3.06
5524 6227 5.649395 TGTTGCATTTCTCTCCCAAATAGAG 59.351 40.000 0.00 0.00 41.59 2.43
5948 6736 7.321908 TCACCATACACCATTTCATCAATTTG 58.678 34.615 0.00 0.00 0.00 2.32
6054 6842 3.804786 TCTTGACCGTACACAAAGTCA 57.195 42.857 0.00 0.00 37.46 3.41
6379 7171 5.393124 CGTGACCGTATTTACACTAGAACA 58.607 41.667 0.00 0.00 0.00 3.18
6665 7481 1.139058 CAGGCGTGCCTCTTTATAGGT 59.861 52.381 11.22 0.00 46.28 3.08


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

AutoCloner maintained by Alex Coulton.