Multiple sequence alignment - TraesCS6D01G190500

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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 TraesCS6D01G190500 chr6D 100.000 6166 0 0 1 6166 263050748 263044583 0.000000e+00 11387.0
1 TraesCS6D01G190500 chr6D 93.590 78 5 0 1106 1183 425004341 425004264 3.910000e-22 117.0
2 TraesCS6D01G190500 chr6D 77.070 157 26 5 5507 5661 381344021 381344169 1.420000e-11 82.4
3 TraesCS6D01G190500 chr6D 89.831 59 5 1 1439 1496 425004262 425004204 2.380000e-09 75.0
4 TraesCS6D01G190500 chr6B 94.148 2683 92 21 793 3446 346313522 346316168 0.000000e+00 4024.0
5 TraesCS6D01G190500 chr6B 94.451 901 39 6 4565 5455 346319222 346320121 0.000000e+00 1376.0
6 TraesCS6D01G190500 chr6B 94.253 783 36 2 1 774 132110878 132111660 0.000000e+00 1188.0
7 TraesCS6D01G190500 chr6B 89.035 912 50 14 3504 4383 346318332 346319225 0.000000e+00 1085.0
8 TraesCS6D01G190500 chr6B 89.602 779 72 3 5 774 48171411 48172189 0.000000e+00 981.0
9 TraesCS6D01G190500 chr6B 89.269 438 29 5 5744 6166 346409696 346410130 3.270000e-147 532.0
10 TraesCS6D01G190500 chr6B 92.520 254 14 3 1440 1691 63922293 63922043 5.880000e-95 359.0
11 TraesCS6D01G190500 chr6B 83.986 281 38 5 5441 5718 346350470 346350746 4.740000e-66 263.0
12 TraesCS6D01G190500 chr6B 77.206 136 27 4 5529 5661 101727640 101727506 6.630000e-10 76.8
13 TraesCS6D01G190500 chr6A 95.552 2181 63 16 791 2966 358606024 358603873 0.000000e+00 3459.0
14 TraesCS6D01G190500 chr6A 92.824 2397 114 23 3310 5690 358595713 358593359 0.000000e+00 3421.0
15 TraesCS6D01G190500 chr6A 98.898 363 4 0 2962 3324 358599091 358598729 0.000000e+00 649.0
16 TraesCS6D01G190500 chr6A 89.172 471 10 10 5720 6166 358593362 358592909 3.250000e-152 549.0
17 TraesCS6D01G190500 chr6A 94.318 88 2 1 1604 1691 53686972 53686888 1.390000e-26 132.0
18 TraesCS6D01G190500 chr6A 93.182 88 3 2 1604 1691 245229059 245228975 6.490000e-25 126.0
19 TraesCS6D01G190500 chr6A 84.946 93 12 2 5486 5578 176992628 176992718 6.580000e-15 93.5
20 TraesCS6D01G190500 chr2D 93.916 789 36 4 1 777 610245966 610245178 0.000000e+00 1181.0
21 TraesCS6D01G190500 chr2D 91.826 783 52 3 1 774 380691577 380692356 0.000000e+00 1081.0
22 TraesCS6D01G190500 chr2D 79.433 141 27 2 5526 5664 628612499 628612359 1.410000e-16 99.0
23 TraesCS6D01G190500 chr4B 93.384 786 42 3 1 777 510842800 510842016 0.000000e+00 1155.0
24 TraesCS6D01G190500 chr4B 93.239 710 39 2 77 777 13967346 13966637 0.000000e+00 1037.0
25 TraesCS6D01G190500 chr2B 93.257 786 44 2 1 777 25740904 25740119 0.000000e+00 1149.0
26 TraesCS6D01G190500 chr2B 94.510 255 9 3 1439 1691 502651600 502651851 7.500000e-104 388.0
27 TraesCS6D01G190500 chr1B 93.257 786 44 2 1 777 566122209 566121424 0.000000e+00 1149.0
28 TraesCS6D01G190500 chr1B 94.390 713 31 2 74 777 185229040 185228328 0.000000e+00 1086.0
29 TraesCS6D01G190500 chr1B 89.413 784 70 8 2 774 559341003 559341784 0.000000e+00 976.0
30 TraesCS6D01G190500 chr1B 81.188 101 16 3 5485 5584 322955349 322955251 1.840000e-10 78.7
31 TraesCS6D01G190500 chr3D 93.231 783 42 3 1 774 80601808 80602588 0.000000e+00 1142.0
32 TraesCS6D01G190500 chr3D 90.196 255 20 3 1439 1691 234201394 234201143 1.660000e-85 327.0
33 TraesCS6D01G190500 chr3B 91.603 786 56 5 1 777 182376931 182376147 0.000000e+00 1077.0
34 TraesCS6D01G190500 chr3B 96.591 88 0 1 1604 1691 791024652 791024736 6.440000e-30 143.0
35 TraesCS6D01G190500 chr7B 90.776 683 50 7 5 674 732596807 732597489 0.000000e+00 900.0
36 TraesCS6D01G190500 chr7B 95.455 88 1 1 1604 1691 612597577 612597661 3.000000e-28 137.0
37 TraesCS6D01G190500 chr1D 91.496 341 28 1 4624 4963 203367914 203367574 9.360000e-128 468.0
38 TraesCS6D01G190500 chr1D 82.022 89 14 2 5497 5584 223533014 223532927 2.380000e-09 75.0
39 TraesCS6D01G190500 chr1D 74.713 174 41 3 5495 5665 438318973 438319146 2.380000e-09 75.0
40 TraesCS6D01G190500 chr5B 85.817 416 48 7 372 777 419727064 419726650 1.230000e-116 431.0
41 TraesCS6D01G190500 chr5B 90.980 255 18 5 1439 1691 688629999 688629748 7.660000e-89 339.0
42 TraesCS6D01G190500 chr5B 92.045 88 4 2 1604 1691 23307384 23307300 3.020000e-23 121.0
43 TraesCS6D01G190500 chr5B 80.714 140 24 3 5526 5663 241402272 241402410 8.450000e-19 106.0
44 TraesCS6D01G190500 chr7D 80.000 250 46 4 5448 5694 116468362 116468610 1.370000e-41 182.0
45 TraesCS6D01G190500 chr7D 78.873 142 28 2 5506 5646 182992706 182992846 1.830000e-15 95.3
46 TraesCS6D01G190500 chr4A 94.318 88 2 1 1604 1691 39721799 39721883 1.390000e-26 132.0
47 TraesCS6D01G190500 chr4A 94.937 79 4 0 1106 1184 292707826 292707904 2.330000e-24 124.0
48 TraesCS6D01G190500 chr1A 96.154 78 3 0 1106 1183 558756803 558756880 1.800000e-25 128.0
49 TraesCS6D01G190500 chr1A 80.597 134 23 3 5485 5616 591095998 591095866 3.930000e-17 100.0
50 TraesCS6D01G190500 chr1A 82.243 107 15 4 5507 5611 496646162 496646266 8.510000e-14 89.8
51 TraesCS6D01G190500 chr1A 91.525 59 4 1 1439 1496 558756882 558756940 5.120000e-11 80.5
52 TraesCS6D01G190500 chr5D 94.872 78 4 0 1106 1183 68973314 68973237 8.390000e-24 122.0
53 TraesCS6D01G190500 chr5D 91.525 59 4 1 1439 1496 68973235 68973177 5.120000e-11 80.5
54 TraesCS6D01G190500 chr2A 79.739 153 28 3 5510 5660 82363374 82363223 2.350000e-19 108.0
55 TraesCS6D01G190500 chr5A 78.313 166 31 5 5495 5657 291792513 291792676 1.090000e-17 102.0
56 TraesCS6D01G190500 chr3A 78.986 138 25 4 5527 5661 696236073 696235937 2.370000e-14 91.6
57 TraesCS6D01G190500 chrUn 100.000 34 0 0 5525 5558 262510109 262510142 5.160000e-06 63.9


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 TraesCS6D01G190500 chr6D 263044583 263050748 6165 True 11387.000000 11387 100.000000 1 6166 1 chr6D.!!$R1 6165
1 TraesCS6D01G190500 chr6B 346313522 346320121 6599 False 2161.666667 4024 92.544667 793 5455 3 chr6B.!!$F5 4662
2 TraesCS6D01G190500 chr6B 132110878 132111660 782 False 1188.000000 1188 94.253000 1 774 1 chr6B.!!$F2 773
3 TraesCS6D01G190500 chr6B 48171411 48172189 778 False 981.000000 981 89.602000 5 774 1 chr6B.!!$F1 769
4 TraesCS6D01G190500 chr6A 358603873 358606024 2151 True 3459.000000 3459 95.552000 791 2966 1 chr6A.!!$R3 2175
5 TraesCS6D01G190500 chr6A 358592909 358599091 6182 True 1539.666667 3421 93.631333 2962 6166 3 chr6A.!!$R4 3204
6 TraesCS6D01G190500 chr2D 610245178 610245966 788 True 1181.000000 1181 93.916000 1 777 1 chr2D.!!$R1 776
7 TraesCS6D01G190500 chr2D 380691577 380692356 779 False 1081.000000 1081 91.826000 1 774 1 chr2D.!!$F1 773
8 TraesCS6D01G190500 chr4B 510842016 510842800 784 True 1155.000000 1155 93.384000 1 777 1 chr4B.!!$R2 776
9 TraesCS6D01G190500 chr4B 13966637 13967346 709 True 1037.000000 1037 93.239000 77 777 1 chr4B.!!$R1 700
10 TraesCS6D01G190500 chr2B 25740119 25740904 785 True 1149.000000 1149 93.257000 1 777 1 chr2B.!!$R1 776
11 TraesCS6D01G190500 chr1B 566121424 566122209 785 True 1149.000000 1149 93.257000 1 777 1 chr1B.!!$R3 776
12 TraesCS6D01G190500 chr1B 185228328 185229040 712 True 1086.000000 1086 94.390000 74 777 1 chr1B.!!$R1 703
13 TraesCS6D01G190500 chr1B 559341003 559341784 781 False 976.000000 976 89.413000 2 774 1 chr1B.!!$F1 772
14 TraesCS6D01G190500 chr3D 80601808 80602588 780 False 1142.000000 1142 93.231000 1 774 1 chr3D.!!$F1 773
15 TraesCS6D01G190500 chr3B 182376147 182376931 784 True 1077.000000 1077 91.603000 1 777 1 chr3B.!!$R1 776
16 TraesCS6D01G190500 chr7B 732596807 732597489 682 False 900.000000 900 90.776000 5 674 1 chr7B.!!$F2 669

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
889 907 0.802222 CACACGTAGCACCAGGATCG 60.802 60.000 0.00 0.00 0.00 3.69 F
996 1015 2.581953 CTCTCAAGCTCGCTCGCC 60.582 66.667 0.00 0.00 0.00 5.54 F
1900 1923 1.036707 GCAGTAGGCCACCACAAAAA 58.963 50.000 5.01 0.00 36.11 1.94 F
1982 2005 1.372582 TGAGCACATGAAGATTCGCC 58.627 50.000 0.00 0.00 0.00 5.54 F
2269 2292 1.468520 CGGTCACTGCCTTGTAAATGG 59.531 52.381 0.00 0.00 0.00 3.16 F
2617 2641 1.537202 GATTCTTCCAGTGTGCACCAC 59.463 52.381 15.69 12.49 44.89 4.16 F
3758 8972 1.542915 CCAATCTTTCTGCCACCACTG 59.457 52.381 0.00 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 1889 0.883814 ACTGCTCACTGCTCAGTTGC 60.884 55.000 14.06 14.06 40.20 4.17 R
1932 1955 1.600023 AACTGTCCCGATTCGCAAAA 58.400 45.000 0.00 0.00 0.00 2.44 R
2790 2816 3.360249 AAGACAAGCACAAATCAGCAC 57.640 42.857 0.00 0.00 0.00 4.40 R
3758 8972 4.254492 GACTCCACATAGAACAAAGGTCC 58.746 47.826 0.00 0.00 0.00 4.46 R
4185 9402 1.013596 CACCACAGTCAAAACGAGCA 58.986 50.000 0.00 0.00 0.00 4.26 R
4486 9703 1.602377 AGCAACCGAAAAGAACCTTCG 59.398 47.619 0.00 0.00 44.11 3.79 R
5493 10725 0.168788 CTGCCATGCAAATCGTTCGT 59.831 50.000 0.00 0.00 38.41 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 220 0.954452 CAGGCGAGGCTTTTGTCTTT 59.046 50.000 0.00 0.00 32.51 2.52
271 276 2.111669 TCGAGGTCGCGGGCTATA 59.888 61.111 6.13 0.00 39.60 1.31
274 279 1.793134 CGAGGTCGCGGGCTATAGTT 61.793 60.000 6.13 0.00 0.00 2.24
289 294 4.101741 GCTATAGTTGTTGGAGGTCCATCT 59.898 45.833 0.00 0.10 46.97 2.90
380 388 1.078709 TACGATTTGCTGCTGCTGTC 58.921 50.000 17.00 10.44 40.48 3.51
427 435 1.210204 TGGGAGATCCTGCTTTGCCT 61.210 55.000 0.00 0.00 36.20 4.75
481 490 2.680841 CGGATGACTCGAGTTCTCTTCT 59.319 50.000 21.08 0.00 0.00 2.85
549 558 1.666209 GCTGTTGCAGGTGTGTTGGT 61.666 55.000 0.00 0.00 39.41 3.67
575 592 1.003580 GTCCATGCCCTCTCAGTCAAA 59.996 52.381 0.00 0.00 0.00 2.69
597 614 1.048601 AAGAGGAAACAGAGTGGCGA 58.951 50.000 0.00 0.00 0.00 5.54
689 706 7.015098 GTCTTCTCTCAAGATTCAGGGATGATA 59.985 40.741 0.00 0.00 28.87 2.15
692 709 6.042552 TCTCTCAAGATTCAGGGATGATAACC 59.957 42.308 0.00 0.00 0.00 2.85
774 792 4.387559 GTCCTTTGTTTTTGCGTTTCAGTT 59.612 37.500 0.00 0.00 0.00 3.16
777 795 4.653806 TTGTTTTTGCGTTTCAGTTTGG 57.346 36.364 0.00 0.00 0.00 3.28
778 796 3.914312 TGTTTTTGCGTTTCAGTTTGGA 58.086 36.364 0.00 0.00 0.00 3.53
779 797 4.499183 TGTTTTTGCGTTTCAGTTTGGAT 58.501 34.783 0.00 0.00 0.00 3.41
780 798 4.932200 TGTTTTTGCGTTTCAGTTTGGATT 59.068 33.333 0.00 0.00 0.00 3.01
781 799 5.409826 TGTTTTTGCGTTTCAGTTTGGATTT 59.590 32.000 0.00 0.00 0.00 2.17
782 800 6.073003 TGTTTTTGCGTTTCAGTTTGGATTTT 60.073 30.769 0.00 0.00 0.00 1.82
783 801 5.710613 TTTGCGTTTCAGTTTGGATTTTC 57.289 34.783 0.00 0.00 0.00 2.29
784 802 4.647424 TGCGTTTCAGTTTGGATTTTCT 57.353 36.364 0.00 0.00 0.00 2.52
785 803 5.004922 TGCGTTTCAGTTTGGATTTTCTT 57.995 34.783 0.00 0.00 0.00 2.52
786 804 6.137794 TGCGTTTCAGTTTGGATTTTCTTA 57.862 33.333 0.00 0.00 0.00 2.10
787 805 6.565234 TGCGTTTCAGTTTGGATTTTCTTAA 58.435 32.000 0.00 0.00 0.00 1.85
788 806 7.036220 TGCGTTTCAGTTTGGATTTTCTTAAA 58.964 30.769 0.00 0.00 0.00 1.52
789 807 7.545965 TGCGTTTCAGTTTGGATTTTCTTAAAA 59.454 29.630 0.00 0.00 34.41 1.52
818 836 7.602517 AAGAGAAGAACAATAAACAGGATCG 57.397 36.000 0.00 0.00 0.00 3.69
819 837 6.702329 AGAGAAGAACAATAAACAGGATCGT 58.298 36.000 0.00 0.00 0.00 3.73
820 838 6.814146 AGAGAAGAACAATAAACAGGATCGTC 59.186 38.462 0.00 0.00 0.00 4.20
821 839 6.464222 AGAAGAACAATAAACAGGATCGTCA 58.536 36.000 0.00 0.00 0.00 4.35
830 848 2.146342 ACAGGATCGTCAAAGCTGTTG 58.854 47.619 0.00 0.00 0.00 3.33
842 860 2.253758 GCTGTTGCTTGCCTCGTCA 61.254 57.895 0.00 0.00 36.03 4.35
878 896 3.567530 TCGTTTACCACATCACACGTAG 58.432 45.455 0.00 0.00 0.00 3.51
889 907 0.802222 CACACGTAGCACCAGGATCG 60.802 60.000 0.00 0.00 0.00 3.69
996 1015 2.581953 CTCTCAAGCTCGCTCGCC 60.582 66.667 0.00 0.00 0.00 5.54
1042 1061 4.222336 TCATCTCTTCCTTCTCATCCTCC 58.778 47.826 0.00 0.00 0.00 4.30
1319 1338 3.723348 GGACAACAAGCGCCCGTC 61.723 66.667 2.29 3.60 0.00 4.79
1703 1723 3.554934 TCTGTGTCTGCAAGTCCAAAAT 58.445 40.909 0.00 0.00 33.76 1.82
1855 1878 8.719648 GGAGTCAATTTCATGCTATCTAGAATG 58.280 37.037 0.00 0.00 40.14 2.67
1891 1914 2.665000 GCAGTGAGCAGTAGGCCA 59.335 61.111 5.01 0.00 46.50 5.36
1900 1923 1.036707 GCAGTAGGCCACCACAAAAA 58.963 50.000 5.01 0.00 36.11 1.94
1932 1955 7.829725 TGTTCATTTTATTGCTCAGTGCTATT 58.170 30.769 0.00 0.00 43.37 1.73
1981 2004 2.778659 GTTGAGCACATGAAGATTCGC 58.221 47.619 0.00 0.00 0.00 4.70
1982 2005 1.372582 TGAGCACATGAAGATTCGCC 58.627 50.000 0.00 0.00 0.00 5.54
2119 2142 1.688772 ATGGAGTGAATGATGCAGGC 58.311 50.000 0.00 0.00 0.00 4.85
2269 2292 1.468520 CGGTCACTGCCTTGTAAATGG 59.531 52.381 0.00 0.00 0.00 3.16
2290 2313 4.262617 GGTGGTACTCCAGAATTCCTTTC 58.737 47.826 0.65 0.00 45.24 2.62
2518 2541 9.975218 AGTCTATAATACCATGTCCAACTTTTT 57.025 29.630 0.00 0.00 0.00 1.94
2617 2641 1.537202 GATTCTTCCAGTGTGCACCAC 59.463 52.381 15.69 12.49 44.89 4.16
2635 2659 2.365582 CACGTTCCCCCTTTATCCTTG 58.634 52.381 0.00 0.00 0.00 3.61
2790 2816 2.930826 ACAACCTGGTACCTTGTGAG 57.069 50.000 15.22 10.06 0.00 3.51
2813 2839 5.067674 AGTGCTGATTTGTGCTTGTCTTTTA 59.932 36.000 0.00 0.00 0.00 1.52
2943 2969 3.008813 CCCTGGCAGATATAATGAGCACT 59.991 47.826 17.94 0.00 0.00 4.40
3397 6476 4.339872 AAGCATTGGAACATGCAGAAAA 57.660 36.364 8.31 0.00 42.35 2.29
3405 6484 7.517614 TTGGAACATGCAGAAAATTAGTGTA 57.482 32.000 0.00 0.00 39.30 2.90
3460 6968 5.149273 CCTTCAGTTCGTCATCACAATTTG 58.851 41.667 0.00 0.00 0.00 2.32
3655 8869 8.093927 CCTTTCTTTTGGCACTTCCATTATTAA 58.906 33.333 0.00 0.00 46.04 1.40
3758 8972 1.542915 CCAATCTTTCTGCCACCACTG 59.457 52.381 0.00 0.00 0.00 3.66
3854 9068 6.600246 GCAGTAAGGTTGCTTACTATTACC 57.400 41.667 0.00 0.00 45.25 2.85
4075 9292 9.471702 AAGATTCCACAGATGTCATCTAAAATT 57.528 29.630 15.05 3.49 37.58 1.82
4185 9402 6.930722 GTGGTGATGTTCATTTTGGAGAAATT 59.069 34.615 0.00 0.00 0.00 1.82
4416 9633 5.023514 TGACAGCATATATCCCCCTAAGA 57.976 43.478 0.00 0.00 0.00 2.10
4424 9641 8.900802 AGCATATATCCCCCTAAGAAACAATTA 58.099 33.333 0.00 0.00 0.00 1.40
4427 9644 7.723109 ATATCCCCCTAAGAAACAATTACCT 57.277 36.000 0.00 0.00 0.00 3.08
4486 9703 9.219603 TGCCTTGCTTCTATCATATTACAATAC 57.780 33.333 0.00 0.00 0.00 1.89
4527 9744 4.392138 GCTGGTGTAGTTGTAATCTGTTCC 59.608 45.833 0.00 0.00 0.00 3.62
4528 9745 5.794894 CTGGTGTAGTTGTAATCTGTTCCT 58.205 41.667 0.00 0.00 0.00 3.36
4529 9746 6.182507 TGGTGTAGTTGTAATCTGTTCCTT 57.817 37.500 0.00 0.00 0.00 3.36
4530 9747 6.597562 TGGTGTAGTTGTAATCTGTTCCTTT 58.402 36.000 0.00 0.00 0.00 3.11
4531 9748 6.485313 TGGTGTAGTTGTAATCTGTTCCTTTG 59.515 38.462 0.00 0.00 0.00 2.77
4532 9749 6.485648 GGTGTAGTTGTAATCTGTTCCTTTGT 59.514 38.462 0.00 0.00 0.00 2.83
4533 9750 7.012989 GGTGTAGTTGTAATCTGTTCCTTTGTT 59.987 37.037 0.00 0.00 0.00 2.83
4534 9751 8.403236 GTGTAGTTGTAATCTGTTCCTTTGTTT 58.597 33.333 0.00 0.00 0.00 2.83
4535 9752 9.616156 TGTAGTTGTAATCTGTTCCTTTGTTTA 57.384 29.630 0.00 0.00 0.00 2.01
4540 9757 3.955524 TCTGTTCCTTTGTTTACCCCA 57.044 42.857 0.00 0.00 0.00 4.96
4570 9787 8.328864 GCATATTTAGTACTTGTAGCTTCACAC 58.671 37.037 0.00 0.00 0.00 3.82
4576 9793 4.531659 ACTTGTAGCTTCACACGTTTTC 57.468 40.909 0.00 0.00 27.29 2.29
4609 9827 5.440610 AGCTGCAGTTTAATGCTATTACCT 58.559 37.500 16.64 0.00 46.63 3.08
4622 9840 7.944729 ATGCTATTACCTTGAAACTGTGAAT 57.055 32.000 0.00 0.00 0.00 2.57
4623 9841 7.377766 TGCTATTACCTTGAAACTGTGAATC 57.622 36.000 0.00 0.00 0.00 2.52
4624 9842 6.939730 TGCTATTACCTTGAAACTGTGAATCA 59.060 34.615 0.00 0.00 0.00 2.57
4625 9843 7.094805 TGCTATTACCTTGAAACTGTGAATCAC 60.095 37.037 6.41 6.41 34.56 3.06
4636 9858 8.402472 TGAAACTGTGAATCACTACGAATTTTT 58.598 29.630 14.97 2.72 35.11 1.94
4684 9906 5.554822 TGTGGTTTGAGTTGTTCTTGTAC 57.445 39.130 0.00 0.00 0.00 2.90
4687 9909 4.569162 TGGTTTGAGTTGTTCTTGTACTCG 59.431 41.667 0.00 0.00 40.86 4.18
4694 9916 5.597806 AGTTGTTCTTGTACTCGTTCATCA 58.402 37.500 0.00 0.00 0.00 3.07
4705 9927 2.996621 CTCGTTCATCAGTTGGTCCTTC 59.003 50.000 0.00 0.00 0.00 3.46
4768 9990 6.844696 TCGAAATAGATTGGAATGCAGTAC 57.155 37.500 0.00 0.00 0.00 2.73
4985 10207 3.072476 ACCATTGCCGGTATGCTACTAAT 59.928 43.478 1.90 0.00 37.57 1.73
5018 10240 7.499292 TCAACATTTCAAACCATGATTTGTCT 58.501 30.769 12.34 0.00 39.97 3.41
5101 10323 2.540931 CAGTTTTTGTCATTGCTGTGGC 59.459 45.455 0.00 0.00 39.26 5.01
5220 10442 5.977489 TTCGATCTGACTAGAGTTGGAAA 57.023 39.130 0.00 0.00 36.14 3.13
5264 10486 1.634973 TGAGCAGGGATGTTGATTGGA 59.365 47.619 0.00 0.00 0.00 3.53
5280 10502 2.920724 TGGACAAGGATCAACACGAA 57.079 45.000 0.00 0.00 0.00 3.85
5298 10523 7.899178 ACACGAACACTTGATTGTGAATATA 57.101 32.000 12.48 0.00 40.12 0.86
5325 10551 3.402110 CTGTGAGCACATACTGGACAAA 58.598 45.455 3.49 0.00 41.01 2.83
5371 10597 3.997021 CCGTATAGCATGGTGGAGAAATC 59.003 47.826 7.89 0.00 0.00 2.17
5404 10630 4.871933 ATCCCTTTGGTTGACAATGAAC 57.128 40.909 0.00 0.00 39.21 3.18
5438 10670 6.526674 GGGTTTATCTGTTTGTTTTCTATGCG 59.473 38.462 0.00 0.00 0.00 4.73
5451 10683 6.913673 TGTTTTCTATGCGTTTTTGTTAGGAC 59.086 34.615 0.00 0.00 0.00 3.85
5470 10702 0.739813 CCCTCTTAACCAGCGAACGG 60.740 60.000 0.00 0.00 0.00 4.44
5477 10709 1.812686 AACCAGCGAACGGTCAGCTA 61.813 55.000 17.16 0.00 39.48 3.32
5491 10723 3.526534 GTCAGCTAGGAAGGATGACAAC 58.473 50.000 7.13 0.00 45.70 3.32
5493 10725 4.402793 GTCAGCTAGGAAGGATGACAACTA 59.597 45.833 7.13 0.00 45.70 2.24
5495 10727 3.381908 AGCTAGGAAGGATGACAACTACG 59.618 47.826 0.00 0.00 0.00 3.51
5506 10738 3.124560 TGACAACTACGAACGATTTGCA 58.875 40.909 0.14 0.00 0.00 4.08
5516 10748 2.068837 ACGATTTGCATGGCAGTTTG 57.931 45.000 0.00 0.00 40.61 2.93
5524 10756 0.390124 CATGGCAGTTTGTGTTGGCT 59.610 50.000 0.00 0.00 40.23 4.75
5550 10782 3.708563 TGACAAGTTTAGTTGGCAAGC 57.291 42.857 0.00 0.00 42.70 4.01
5562 10794 1.630223 TGGCAAGCATGACAAATCCA 58.370 45.000 0.00 0.00 43.21 3.41
5566 10798 1.894466 CAAGCATGACAAATCCACCCA 59.106 47.619 0.00 0.00 0.00 4.51
5568 10800 2.173519 AGCATGACAAATCCACCCAAG 58.826 47.619 0.00 0.00 0.00 3.61
5609 10841 8.024865 GGATTTACCGTGCTTACAAACTAAAAT 58.975 33.333 0.00 0.00 0.00 1.82
5612 10844 6.380095 ACCGTGCTTACAAACTAAAATTGA 57.620 33.333 0.00 0.00 0.00 2.57
5619 10851 8.081633 TGCTTACAAACTAAAATTGACATCCTG 58.918 33.333 0.00 0.00 0.00 3.86
5620 10852 8.296713 GCTTACAAACTAAAATTGACATCCTGA 58.703 33.333 0.00 0.00 0.00 3.86
5686 10920 2.231215 ATGAACATCAGCCGAGTAGC 57.769 50.000 0.00 0.00 0.00 3.58
5687 10921 0.894835 TGAACATCAGCCGAGTAGCA 59.105 50.000 0.00 0.00 34.23 3.49
5688 10922 1.482182 TGAACATCAGCCGAGTAGCAT 59.518 47.619 0.00 0.00 34.23 3.79
5689 10923 2.093500 TGAACATCAGCCGAGTAGCATT 60.093 45.455 0.00 0.00 34.23 3.56
5690 10924 3.132111 TGAACATCAGCCGAGTAGCATTA 59.868 43.478 0.00 0.00 34.23 1.90
5691 10925 3.099267 ACATCAGCCGAGTAGCATTAC 57.901 47.619 0.00 0.00 34.23 1.89
5692 10926 2.224066 ACATCAGCCGAGTAGCATTACC 60.224 50.000 0.00 0.00 34.23 2.85
5693 10927 0.384309 TCAGCCGAGTAGCATTACCG 59.616 55.000 0.00 0.00 34.23 4.02
5694 10928 0.102481 CAGCCGAGTAGCATTACCGT 59.898 55.000 0.00 0.00 34.23 4.83
5695 10929 0.384669 AGCCGAGTAGCATTACCGTC 59.615 55.000 0.00 0.00 34.23 4.79
5696 10930 0.384669 GCCGAGTAGCATTACCGTCT 59.615 55.000 0.00 0.00 0.00 4.18
5697 10931 1.202382 GCCGAGTAGCATTACCGTCTT 60.202 52.381 0.00 0.00 0.00 3.01
5698 10932 2.460918 CCGAGTAGCATTACCGTCTTG 58.539 52.381 0.00 0.00 0.00 3.02
5699 10933 2.159282 CCGAGTAGCATTACCGTCTTGT 60.159 50.000 0.00 0.00 0.00 3.16
5700 10934 3.106672 CGAGTAGCATTACCGTCTTGTC 58.893 50.000 0.00 0.00 0.00 3.18
5701 10935 3.427098 CGAGTAGCATTACCGTCTTGTCA 60.427 47.826 0.00 0.00 0.00 3.58
5702 10936 4.683832 GAGTAGCATTACCGTCTTGTCAT 58.316 43.478 0.00 0.00 0.00 3.06
5703 10937 4.433615 AGTAGCATTACCGTCTTGTCATG 58.566 43.478 0.00 0.00 0.00 3.07
5704 10938 2.632377 AGCATTACCGTCTTGTCATGG 58.368 47.619 0.00 0.00 0.00 3.66
5705 10939 2.027192 AGCATTACCGTCTTGTCATGGT 60.027 45.455 0.00 0.00 39.21 3.55
5706 10940 2.747446 GCATTACCGTCTTGTCATGGTT 59.253 45.455 0.00 0.00 36.94 3.67
5707 10941 3.426159 GCATTACCGTCTTGTCATGGTTG 60.426 47.826 0.00 0.00 36.94 3.77
5708 10942 3.755112 TTACCGTCTTGTCATGGTTGA 57.245 42.857 0.00 0.00 36.94 3.18
5709 10943 2.859165 ACCGTCTTGTCATGGTTGAT 57.141 45.000 0.00 0.00 30.84 2.57
5710 10944 3.140325 ACCGTCTTGTCATGGTTGATT 57.860 42.857 0.00 0.00 30.84 2.57
5711 10945 3.074412 ACCGTCTTGTCATGGTTGATTC 58.926 45.455 0.00 0.00 30.84 2.52
5712 10946 3.244561 ACCGTCTTGTCATGGTTGATTCT 60.245 43.478 0.00 0.00 30.84 2.40
5713 10947 3.125829 CCGTCTTGTCATGGTTGATTCTG 59.874 47.826 0.00 0.00 33.56 3.02
5714 10948 3.125829 CGTCTTGTCATGGTTGATTCTGG 59.874 47.826 0.00 0.00 33.56 3.86
5715 10949 4.074970 GTCTTGTCATGGTTGATTCTGGT 58.925 43.478 0.00 0.00 33.56 4.00
5716 10950 4.074259 TCTTGTCATGGTTGATTCTGGTG 58.926 43.478 0.00 0.00 33.56 4.17
5717 10951 3.786368 TGTCATGGTTGATTCTGGTGA 57.214 42.857 0.00 0.00 33.56 4.02
5718 10952 3.411446 TGTCATGGTTGATTCTGGTGAC 58.589 45.455 0.00 0.00 36.09 3.67
5719 10953 2.416547 GTCATGGTTGATTCTGGTGACG 59.583 50.000 0.00 0.00 33.56 4.35
5737 10971 2.481952 GACGATTTGATGGATAGGCTGC 59.518 50.000 0.00 0.00 0.00 5.25
5755 10989 3.952628 CTGCCGTCTTCCCCGTTCC 62.953 68.421 0.00 0.00 0.00 3.62
5778 11012 2.650322 TGGAAAGAAGTTGTGTGTCCC 58.350 47.619 0.00 0.00 0.00 4.46
5825 11059 2.822561 TCTTGTGTTGGTCTGTTTGCAA 59.177 40.909 0.00 0.00 0.00 4.08
5826 11060 2.937469 TGTGTTGGTCTGTTTGCAAG 57.063 45.000 0.00 0.00 0.00 4.01
6039 11297 4.176752 GTCCCACTCCCCGCCATC 62.177 72.222 0.00 0.00 0.00 3.51
6044 11302 4.468769 ACTCCCCGCCATCCCGTA 62.469 66.667 0.00 0.00 0.00 4.02
6045 11303 3.925090 CTCCCCGCCATCCCGTAC 61.925 72.222 0.00 0.00 0.00 3.67
6046 11304 4.781616 TCCCCGCCATCCCGTACA 62.782 66.667 0.00 0.00 0.00 2.90
6047 11305 3.788145 CCCCGCCATCCCGTACAA 61.788 66.667 0.00 0.00 0.00 2.41
6048 11306 2.269562 CCCGCCATCCCGTACAAA 59.730 61.111 0.00 0.00 0.00 2.83
6049 11307 1.377463 CCCGCCATCCCGTACAAAA 60.377 57.895 0.00 0.00 0.00 2.44
6050 11308 0.961358 CCCGCCATCCCGTACAAAAA 60.961 55.000 0.00 0.00 0.00 1.94
6051 11309 0.169451 CCGCCATCCCGTACAAAAAC 59.831 55.000 0.00 0.00 0.00 2.43
6052 11310 0.875728 CGCCATCCCGTACAAAAACA 59.124 50.000 0.00 0.00 0.00 2.83
6053 11311 1.267261 CGCCATCCCGTACAAAAACAA 59.733 47.619 0.00 0.00 0.00 2.83
6057 11315 4.321675 GCCATCCCGTACAAAAACAAATCT 60.322 41.667 0.00 0.00 0.00 2.40
6070 11328 6.763303 AAAACAAATCTCGTGCATAAAACC 57.237 33.333 0.00 0.00 0.00 3.27
6071 11329 5.446143 AACAAATCTCGTGCATAAAACCA 57.554 34.783 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 3.087031 CACCTAGTAAACAGACCCGAGA 58.913 50.000 0.00 0.00 0.00 4.04
215 220 2.037367 ACCGCTGGCTCCTAGACA 59.963 61.111 0.00 0.00 0.00 3.41
245 250 3.023950 CGACCTCGACGAGATCCC 58.976 66.667 26.11 10.37 43.02 3.85
289 294 1.971167 GATCCAAACGGCCAGTGCA 60.971 57.895 2.24 0.00 40.13 4.57
380 388 1.731160 CAGCGCAGAGAAAGAAGAAGG 59.269 52.381 11.47 0.00 0.00 3.46
481 490 2.578786 GAAAAGTGTCCCTTCCGGAAA 58.421 47.619 19.39 0.00 44.47 3.13
549 558 1.634973 TGAGAGGGCATGGACATCAAA 59.365 47.619 0.00 0.00 0.00 2.69
575 592 2.618709 CGCCACTCTGTTTCCTCTTTTT 59.381 45.455 0.00 0.00 0.00 1.94
579 596 0.318762 GTCGCCACTCTGTTTCCTCT 59.681 55.000 0.00 0.00 0.00 3.69
590 607 0.034337 ACGGTACAATTGTCGCCACT 59.966 50.000 23.48 11.03 0.00 4.00
597 614 2.036217 TCTTCGACCACGGTACAATTGT 59.964 45.455 16.68 16.68 40.21 2.71
798 816 6.721571 TGACGATCCTGTTTATTGTTCTTC 57.278 37.500 0.00 0.00 0.00 2.87
804 822 5.106555 ACAGCTTTGACGATCCTGTTTATTG 60.107 40.000 0.00 0.00 33.29 1.90
806 824 4.579869 ACAGCTTTGACGATCCTGTTTAT 58.420 39.130 0.00 0.00 33.29 1.40
807 825 4.002906 ACAGCTTTGACGATCCTGTTTA 57.997 40.909 0.00 0.00 33.29 2.01
808 826 2.851195 ACAGCTTTGACGATCCTGTTT 58.149 42.857 0.00 0.00 33.29 2.83
809 827 2.549754 CAACAGCTTTGACGATCCTGTT 59.450 45.455 5.70 5.70 44.81 3.16
810 828 2.146342 CAACAGCTTTGACGATCCTGT 58.854 47.619 0.00 0.00 38.30 4.00
811 829 1.135859 GCAACAGCTTTGACGATCCTG 60.136 52.381 11.34 0.00 0.00 3.86
812 830 1.160137 GCAACAGCTTTGACGATCCT 58.840 50.000 11.34 0.00 0.00 3.24
813 831 1.160137 AGCAACAGCTTTGACGATCC 58.840 50.000 11.34 0.00 34.18 3.36
814 832 2.578495 CAAGCAACAGCTTTGACGATC 58.422 47.619 11.34 0.00 45.93 3.69
815 833 1.335324 GCAAGCAACAGCTTTGACGAT 60.335 47.619 11.34 0.00 45.93 3.73
816 834 0.029300 GCAAGCAACAGCTTTGACGA 59.971 50.000 11.34 0.00 45.93 4.20
817 835 0.936297 GGCAAGCAACAGCTTTGACG 60.936 55.000 11.34 0.00 45.93 4.35
818 836 0.386838 AGGCAAGCAACAGCTTTGAC 59.613 50.000 11.34 3.20 45.93 3.18
819 837 0.670162 GAGGCAAGCAACAGCTTTGA 59.330 50.000 11.34 0.00 45.93 2.69
820 838 0.662374 CGAGGCAAGCAACAGCTTTG 60.662 55.000 0.00 0.00 45.93 2.77
821 839 1.103398 ACGAGGCAAGCAACAGCTTT 61.103 50.000 0.00 0.00 45.93 3.51
842 860 4.335647 CGAAGCAGGTGGGTGGCT 62.336 66.667 0.00 0.00 40.14 4.75
878 896 1.287730 GCATCGATCGATCCTGGTGC 61.288 60.000 27.20 22.99 31.62 5.01
941 959 2.434359 GGTTCCGCGGAGAAGTGG 60.434 66.667 29.20 0.00 42.87 4.00
942 960 2.434359 GGGTTCCGCGGAGAAGTG 60.434 66.667 29.20 0.00 0.00 3.16
1020 1039 4.078688 AGGAGGATGAGAAGGAAGAGATGA 60.079 45.833 0.00 0.00 0.00 2.92
1474 1493 1.467035 GCAATTCAAGAGAGCAAGCGG 60.467 52.381 0.00 0.00 0.00 5.52
1477 1496 3.940221 AGCTAGCAATTCAAGAGAGCAAG 59.060 43.478 18.83 0.00 0.00 4.01
1647 1667 8.575649 AAACAATGGACTATTTAACCCTGTAG 57.424 34.615 0.00 0.00 0.00 2.74
1703 1723 1.427368 ACCCAGCTCCAACAAACCATA 59.573 47.619 0.00 0.00 0.00 2.74
1866 1889 0.883814 ACTGCTCACTGCTCAGTTGC 60.884 55.000 14.06 14.06 40.20 4.17
1932 1955 1.600023 AACTGTCCCGATTCGCAAAA 58.400 45.000 0.00 0.00 0.00 2.44
1981 2004 9.124807 GAAATAAGAAACGATAACAAAGTTGGG 57.875 33.333 0.00 0.00 0.00 4.12
1982 2005 9.672086 TGAAATAAGAAACGATAACAAAGTTGG 57.328 29.630 0.00 0.00 0.00 3.77
2119 2142 8.567285 AGAACACTTTTCCACTATATTCCTTG 57.433 34.615 0.00 0.00 0.00 3.61
2269 2292 5.167303 AGAAAGGAATTCTGGAGTACCAC 57.833 43.478 5.23 0.00 46.71 4.16
2290 2313 7.853524 TGCAAGAAACATCATAAAGCAAAAAG 58.146 30.769 0.00 0.00 0.00 2.27
2540 2564 7.930217 TCCTATTTGAACAAGAGTTTGACAAG 58.070 34.615 0.00 0.00 38.30 3.16
2617 2641 2.801077 ACAAGGATAAAGGGGGAACG 57.199 50.000 0.00 0.00 0.00 3.95
2635 2659 6.753107 ATGGTACTTGGTTGCAAGTTATAC 57.247 37.500 0.00 0.00 42.16 1.47
2790 2816 3.360249 AAGACAAGCACAAATCAGCAC 57.640 42.857 0.00 0.00 0.00 4.40
2813 2839 9.740239 CTATATATGCAAAAGCAACATCAACTT 57.260 29.630 0.00 0.00 0.00 2.66
2943 2969 7.384439 TGTCAACAACTCAAAACTTATGACA 57.616 32.000 0.00 0.00 41.44 3.58
3405 6484 7.016170 ACCCAAACTTTGCAAATTCCTTATACT 59.984 33.333 13.23 0.00 0.00 2.12
3460 6968 4.757149 GGTTCAATACTATCATCTGCCACC 59.243 45.833 0.00 0.00 0.00 4.61
3758 8972 4.254492 GACTCCACATAGAACAAAGGTCC 58.746 47.826 0.00 0.00 0.00 4.46
3876 9091 7.332926 AGCTACTTCATAATGAATATGCCGAAG 59.667 37.037 0.00 0.00 41.08 3.79
3877 9092 7.118245 CAGCTACTTCATAATGAATATGCCGAA 59.882 37.037 0.00 0.00 41.08 4.30
3878 9093 6.591448 CAGCTACTTCATAATGAATATGCCGA 59.409 38.462 0.00 0.00 41.08 5.54
4185 9402 1.013596 CACCACAGTCAAAACGAGCA 58.986 50.000 0.00 0.00 0.00 4.26
4406 9623 5.871324 AAGGTAATTGTTTCTTAGGGGGA 57.129 39.130 0.00 0.00 0.00 4.81
4416 9633 7.987649 TCAAACACGTTCTAAGGTAATTGTTT 58.012 30.769 0.00 0.00 0.00 2.83
4424 9641 6.319399 CAAAACTTCAAACACGTTCTAAGGT 58.681 36.000 0.00 1.02 0.00 3.50
4427 9644 5.096849 GCCAAAACTTCAAACACGTTCTAA 58.903 37.500 0.00 0.00 0.00 2.10
4486 9703 1.602377 AGCAACCGAAAAGAACCTTCG 59.398 47.619 0.00 0.00 44.11 3.79
4527 9744 6.469782 AATATGCAGATGGGGTAAACAAAG 57.530 37.500 0.00 0.00 0.00 2.77
4528 9745 6.865834 AAATATGCAGATGGGGTAAACAAA 57.134 33.333 0.00 0.00 0.00 2.83
4529 9746 7.122715 ACTAAATATGCAGATGGGGTAAACAA 58.877 34.615 0.00 0.00 0.00 2.83
4530 9747 6.668645 ACTAAATATGCAGATGGGGTAAACA 58.331 36.000 0.00 0.00 0.00 2.83
4531 9748 7.937394 AGTACTAAATATGCAGATGGGGTAAAC 59.063 37.037 0.00 0.00 0.00 2.01
4532 9749 8.041143 AGTACTAAATATGCAGATGGGGTAAA 57.959 34.615 0.00 0.00 0.00 2.01
4533 9750 7.626999 AGTACTAAATATGCAGATGGGGTAA 57.373 36.000 0.00 0.00 0.00 2.85
4534 9751 7.071950 ACAAGTACTAAATATGCAGATGGGGTA 59.928 37.037 0.00 0.00 0.00 3.69
4535 9752 6.126478 ACAAGTACTAAATATGCAGATGGGGT 60.126 38.462 0.00 0.00 0.00 4.95
4540 9757 9.482627 GAAGCTACAAGTACTAAATATGCAGAT 57.517 33.333 0.00 0.00 0.00 2.90
4570 9787 5.095691 TGCAGCTTTTAGAAGAGAAAACG 57.904 39.130 0.00 0.00 34.71 3.60
4576 9793 6.525976 GCATTAAACTGCAGCTTTTAGAAGAG 59.474 38.462 15.27 3.47 41.87 2.85
4609 9827 7.490962 AATTCGTAGTGATTCACAGTTTCAA 57.509 32.000 18.57 4.41 36.74 2.69
4622 9840 3.929094 ACGGGCTAAAAATTCGTAGTGA 58.071 40.909 0.00 0.00 32.03 3.41
4623 9841 5.978934 ATACGGGCTAAAAATTCGTAGTG 57.021 39.130 0.00 0.00 39.21 2.74
4624 9842 6.990341 AAATACGGGCTAAAAATTCGTAGT 57.010 33.333 0.00 0.00 39.21 2.73
4625 9843 9.940166 AATTAAATACGGGCTAAAAATTCGTAG 57.060 29.630 0.00 0.00 39.21 3.51
4636 9858 9.127277 AGCAGAAAATAAATTAAATACGGGCTA 57.873 29.630 0.00 0.00 0.00 3.93
4684 9906 2.751166 AGGACCAACTGATGAACGAG 57.249 50.000 0.00 0.00 0.00 4.18
4687 9909 3.744660 ACAGAAGGACCAACTGATGAAC 58.255 45.455 19.87 0.00 35.85 3.18
4694 9916 3.366052 ACAACAACAGAAGGACCAACT 57.634 42.857 0.00 0.00 0.00 3.16
4705 9927 5.063944 GCTGACCTGATACATACAACAACAG 59.936 44.000 0.00 0.00 0.00 3.16
4743 9965 6.309712 ACTGCATTCCAATCTATTTCGATG 57.690 37.500 0.00 0.00 0.00 3.84
4768 9990 3.824443 AGTTCAATTTTAACCCGTGGAGG 59.176 43.478 0.00 0.00 40.63 4.30
4803 10025 2.296752 CACACCATCAACAGAATTGCCA 59.703 45.455 0.00 0.00 0.00 4.92
4985 10207 7.552330 TCATGGTTTGAAATGTTGAGATCGATA 59.448 33.333 0.00 0.00 0.00 2.92
5018 10240 1.881973 GTGCTGCAATGTGAGGAAAGA 59.118 47.619 2.77 0.00 0.00 2.52
5220 10442 3.885297 CTGGTCAGTGTCCAATTCAGTTT 59.115 43.478 10.41 0.00 34.35 2.66
5264 10486 3.194005 AGTGTTCGTGTTGATCCTTGT 57.806 42.857 0.00 0.00 0.00 3.16
5280 10502 5.220662 GCGTGCTATATTCACAATCAAGTGT 60.221 40.000 8.06 0.00 40.37 3.55
5298 10523 1.016130 GTATGTGCTCACAGCGTGCT 61.016 55.000 8.74 0.00 46.26 4.40
5325 10551 4.081972 AGACTCATCACAGCTTCGTTACAT 60.082 41.667 0.00 0.00 0.00 2.29
5371 10597 3.770933 ACCAAAGGGATTTCCATGACATG 59.229 43.478 8.56 8.56 38.24 3.21
5404 10630 5.987347 ACAAACAGATAAACCCGTATATCCG 59.013 40.000 0.00 0.00 30.41 4.18
5438 10670 5.829391 TGGTTAAGAGGGTCCTAACAAAAAC 59.171 40.000 4.23 0.00 0.00 2.43
5451 10683 0.739813 CCGTTCGCTGGTTAAGAGGG 60.740 60.000 0.00 0.00 0.00 4.30
5470 10702 3.196685 AGTTGTCATCCTTCCTAGCTGAC 59.803 47.826 0.00 0.00 35.11 3.51
5477 10709 3.367087 CGTTCGTAGTTGTCATCCTTCCT 60.367 47.826 0.00 0.00 0.00 3.36
5491 10723 1.396648 TGCCATGCAAATCGTTCGTAG 59.603 47.619 0.00 0.00 34.76 3.51
5493 10725 0.168788 CTGCCATGCAAATCGTTCGT 59.831 50.000 0.00 0.00 38.41 3.85
5495 10727 2.352503 AACTGCCATGCAAATCGTTC 57.647 45.000 0.00 0.00 38.41 3.95
5506 10738 0.390124 CAGCCAACACAAACTGCCAT 59.610 50.000 0.00 0.00 0.00 4.40
5516 10748 1.808945 CTTGTCATCCTCAGCCAACAC 59.191 52.381 0.00 0.00 0.00 3.32
5524 10756 4.072131 GCCAACTAAACTTGTCATCCTCA 58.928 43.478 0.00 0.00 0.00 3.86
5550 10782 3.573538 TGAACTTGGGTGGATTTGTCATG 59.426 43.478 0.00 0.00 0.00 3.07
5580 10812 3.965379 TGTAAGCACGGTAAATCCTGA 57.035 42.857 0.00 0.00 0.00 3.86
5589 10821 6.183360 TGTCAATTTTAGTTTGTAAGCACGGT 60.183 34.615 0.00 0.00 0.00 4.83
5609 10841 8.611757 CAATTTATATTGTCGTCAGGATGTCAA 58.388 33.333 4.18 4.18 37.06 3.18
5665 10897 2.541762 GCTACTCGGCTGATGTTCATTC 59.458 50.000 0.00 0.00 0.00 2.67
5666 10898 2.093500 TGCTACTCGGCTGATGTTCATT 60.093 45.455 0.00 0.00 0.00 2.57
5667 10899 1.482182 TGCTACTCGGCTGATGTTCAT 59.518 47.619 0.00 0.00 0.00 2.57
5668 10900 0.894835 TGCTACTCGGCTGATGTTCA 59.105 50.000 0.00 0.00 0.00 3.18
5686 10920 4.000325 TCAACCATGACAAGACGGTAATG 59.000 43.478 0.00 0.00 30.60 1.90
5687 10921 4.280436 TCAACCATGACAAGACGGTAAT 57.720 40.909 0.00 0.00 0.00 1.89
5688 10922 3.755112 TCAACCATGACAAGACGGTAA 57.245 42.857 0.00 0.00 0.00 2.85
5689 10923 3.973206 ATCAACCATGACAAGACGGTA 57.027 42.857 0.00 0.00 38.69 4.02
5690 10924 2.859165 ATCAACCATGACAAGACGGT 57.141 45.000 0.00 0.00 38.69 4.83
5691 10925 3.125829 CAGAATCAACCATGACAAGACGG 59.874 47.826 0.00 0.00 38.69 4.79
5692 10926 3.125829 CCAGAATCAACCATGACAAGACG 59.874 47.826 0.00 0.00 38.69 4.18
5693 10927 4.074970 ACCAGAATCAACCATGACAAGAC 58.925 43.478 0.00 0.00 38.69 3.01
5694 10928 4.074259 CACCAGAATCAACCATGACAAGA 58.926 43.478 0.00 0.00 38.69 3.02
5695 10929 4.074259 TCACCAGAATCAACCATGACAAG 58.926 43.478 0.00 0.00 38.69 3.16
5696 10930 3.820467 GTCACCAGAATCAACCATGACAA 59.180 43.478 0.00 0.00 38.69 3.18
5697 10931 3.411446 GTCACCAGAATCAACCATGACA 58.589 45.455 0.00 0.00 38.69 3.58
5698 10932 2.416547 CGTCACCAGAATCAACCATGAC 59.583 50.000 0.00 0.00 38.69 3.06
5699 10933 2.301583 TCGTCACCAGAATCAACCATGA 59.698 45.455 0.00 0.00 40.57 3.07
5700 10934 2.698803 TCGTCACCAGAATCAACCATG 58.301 47.619 0.00 0.00 0.00 3.66
5701 10935 3.634397 ATCGTCACCAGAATCAACCAT 57.366 42.857 0.00 0.00 0.00 3.55
5702 10936 3.417069 AATCGTCACCAGAATCAACCA 57.583 42.857 0.00 0.00 0.00 3.67
5703 10937 3.751175 TCAAATCGTCACCAGAATCAACC 59.249 43.478 0.00 0.00 0.00 3.77
5704 10938 5.327091 CATCAAATCGTCACCAGAATCAAC 58.673 41.667 0.00 0.00 0.00 3.18
5705 10939 4.395854 CCATCAAATCGTCACCAGAATCAA 59.604 41.667 0.00 0.00 0.00 2.57
5706 10940 3.940852 CCATCAAATCGTCACCAGAATCA 59.059 43.478 0.00 0.00 0.00 2.57
5707 10941 4.191544 TCCATCAAATCGTCACCAGAATC 58.808 43.478 0.00 0.00 0.00 2.52
5708 10942 4.220693 TCCATCAAATCGTCACCAGAAT 57.779 40.909 0.00 0.00 0.00 2.40
5709 10943 3.694043 TCCATCAAATCGTCACCAGAA 57.306 42.857 0.00 0.00 0.00 3.02
5710 10944 3.912496 ATCCATCAAATCGTCACCAGA 57.088 42.857 0.00 0.00 0.00 3.86
5711 10945 4.060900 CCTATCCATCAAATCGTCACCAG 58.939 47.826 0.00 0.00 0.00 4.00
5712 10946 3.744214 GCCTATCCATCAAATCGTCACCA 60.744 47.826 0.00 0.00 0.00 4.17
5713 10947 2.808543 GCCTATCCATCAAATCGTCACC 59.191 50.000 0.00 0.00 0.00 4.02
5714 10948 3.496130 CAGCCTATCCATCAAATCGTCAC 59.504 47.826 0.00 0.00 0.00 3.67
5715 10949 3.732212 CAGCCTATCCATCAAATCGTCA 58.268 45.455 0.00 0.00 0.00 4.35
5716 10950 2.481952 GCAGCCTATCCATCAAATCGTC 59.518 50.000 0.00 0.00 0.00 4.20
5717 10951 2.105477 AGCAGCCTATCCATCAAATCGT 59.895 45.455 0.00 0.00 0.00 3.73
5718 10952 2.483106 CAGCAGCCTATCCATCAAATCG 59.517 50.000 0.00 0.00 0.00 3.34
5719 10953 2.228343 GCAGCAGCCTATCCATCAAATC 59.772 50.000 0.00 0.00 33.58 2.17
5737 10971 2.434359 GAACGGGGAAGACGGCAG 60.434 66.667 0.00 0.00 35.23 4.85
5749 10983 2.200373 ACTTCTTTCCATGGGAACGG 57.800 50.000 13.02 0.00 41.87 4.44
5751 10985 3.636764 ACACAACTTCTTTCCATGGGAAC 59.363 43.478 13.02 0.00 41.87 3.62
5755 10989 3.004734 GGACACACAACTTCTTTCCATGG 59.995 47.826 4.97 4.97 0.00 3.66
5825 11059 3.048602 CGGAGACACCACGGAACT 58.951 61.111 0.00 0.00 38.90 3.01
5826 11060 1.870055 TAGCGGAGACACCACGGAAC 61.870 60.000 0.00 0.00 38.90 3.62
6037 11295 4.758165 ACGAGATTTGTTTTTGTACGGGAT 59.242 37.500 0.00 0.00 0.00 3.85
6038 11296 4.024725 CACGAGATTTGTTTTTGTACGGGA 60.025 41.667 0.00 0.00 0.00 5.14
6039 11297 4.215965 CACGAGATTTGTTTTTGTACGGG 58.784 43.478 0.00 0.00 0.00 5.28
6040 11298 3.662186 GCACGAGATTTGTTTTTGTACGG 59.338 43.478 0.00 0.00 0.00 4.02
6041 11299 4.275662 TGCACGAGATTTGTTTTTGTACG 58.724 39.130 0.00 0.00 0.00 3.67
6042 11300 7.845617 TTATGCACGAGATTTGTTTTTGTAC 57.154 32.000 0.00 0.00 0.00 2.90
6043 11301 8.747666 GTTTTATGCACGAGATTTGTTTTTGTA 58.252 29.630 0.00 0.00 0.00 2.41
6044 11302 7.254286 GGTTTTATGCACGAGATTTGTTTTTGT 60.254 33.333 0.00 0.00 0.00 2.83
6045 11303 7.062848 GGTTTTATGCACGAGATTTGTTTTTG 58.937 34.615 0.00 0.00 0.00 2.44
6046 11304 6.758886 TGGTTTTATGCACGAGATTTGTTTTT 59.241 30.769 0.00 0.00 0.00 1.94
6047 11305 6.200097 GTGGTTTTATGCACGAGATTTGTTTT 59.800 34.615 0.00 0.00 0.00 2.43
6048 11306 5.689961 GTGGTTTTATGCACGAGATTTGTTT 59.310 36.000 0.00 0.00 0.00 2.83
6049 11307 5.219633 GTGGTTTTATGCACGAGATTTGTT 58.780 37.500 0.00 0.00 0.00 2.83
6050 11308 4.320935 GGTGGTTTTATGCACGAGATTTGT 60.321 41.667 0.00 0.00 0.00 2.83
6051 11309 4.165779 GGTGGTTTTATGCACGAGATTTG 58.834 43.478 0.00 0.00 0.00 2.32
6052 11310 3.823873 TGGTGGTTTTATGCACGAGATTT 59.176 39.130 0.00 0.00 0.00 2.17
6053 11311 3.190535 GTGGTGGTTTTATGCACGAGATT 59.809 43.478 0.00 0.00 0.00 2.40
6057 11315 0.869068 CGTGGTGGTTTTATGCACGA 59.131 50.000 0.00 0.00 36.81 4.35
6070 11328 2.393768 GCTGCCTGATGTCGTGGTG 61.394 63.158 0.00 0.00 0.00 4.17
6071 11329 2.046892 GCTGCCTGATGTCGTGGT 60.047 61.111 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.