Multiple sequence alignment - TraesCS2D01G496300

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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 TraesCS2D01G496300 chr2D 100.000 5131 0 0 1 5131 592639950 592634820 0.000000e+00 9476.0
1 TraesCS2D01G496300 chr2D 74.246 1293 302 26 2405 3685 644170765 644169492 9.850000e-142 514.0
2 TraesCS2D01G496300 chr2D 91.558 154 13 0 87 240 592647134 592646981 4.020000e-51 213.0
3 TraesCS2D01G496300 chr2D 98.214 56 1 0 30 85 592639864 592639809 1.180000e-16 99.0
4 TraesCS2D01G496300 chr2D 98.214 56 1 0 87 142 592639921 592639866 1.180000e-16 99.0
5 TraesCS2D01G496300 chr2B 96.538 3957 114 14 384 4333 718608425 718604485 0.000000e+00 6527.0
6 TraesCS2D01G496300 chr2B 92.496 613 6 6 4352 4952 718604506 718603922 0.000000e+00 841.0
7 TraesCS2D01G496300 chr2B 73.525 729 159 25 2603 3322 792954739 792955442 3.970000e-61 246.0
8 TraesCS2D01G496300 chr2B 89.268 205 4 2 4867 5057 718603962 718603762 1.850000e-59 241.0
9 TraesCS2D01G496300 chr2B 95.556 45 1 1 5088 5131 718603785 718603741 2.560000e-08 71.3
10 TraesCS2D01G496300 chr2B 91.111 45 0 1 4908 4952 718604003 718603963 2.000000e-04 58.4
11 TraesCS2D01G496300 chr2A 94.002 4185 182 34 92 4255 727196742 727192606 0.000000e+00 6274.0
12 TraesCS2D01G496300 chr2A 90.977 266 21 3 4644 4907 727192300 727192036 6.320000e-94 355.0
13 TraesCS2D01G496300 chr2A 93.000 100 6 1 4959 5057 727192015 727191916 1.490000e-30 145.0
14 TraesCS2D01G496300 chr2A 95.556 45 1 1 5088 5131 727191939 727191895 2.560000e-08 71.3
15 TraesCS2D01G496300 chr4D 73.469 1813 434 44 1895 3685 85261950 85260163 1.560000e-179 640.0
16 TraesCS2D01G496300 chr4A 73.388 1815 435 46 1895 3685 498987888 498986098 2.610000e-177 632.0
17 TraesCS2D01G496300 chr3A 72.979 1732 426 39 1929 3639 36301123 36302833 7.460000e-158 568.0
18 TraesCS2D01G496300 chr3A 73.838 1269 294 32 2439 3689 36290475 36291723 2.160000e-128 470.0
19 TraesCS2D01G496300 chr3A 77.483 755 153 14 2938 3685 36480684 36479940 2.190000e-118 436.0
20 TraesCS2D01G496300 chr3D 72.532 1722 430 36 1929 3627 26301727 26303428 2.120000e-143 520.0
21 TraesCS2D01G496300 chr3D 76.045 981 210 20 2713 3682 26282920 26283886 2.150000e-133 486.0
22 TraesCS2D01G496300 chr3D 71.491 1824 470 46 1881 3682 26221675 26219880 4.720000e-120 442.0
23 TraesCS2D01G496300 chr5A 72.315 1788 432 51 1925 3682 650280454 650282208 7.670000e-138 501.0


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 TraesCS2D01G496300 chr2D 592634820 592639950 5130 True 3224.666667 9476 98.809333 1 5131 3 chr2D.!!$R3 5130
1 TraesCS2D01G496300 chr2D 644169492 644170765 1273 True 514.000000 514 74.246000 2405 3685 1 chr2D.!!$R2 1280
2 TraesCS2D01G496300 chr2B 718603741 718608425 4684 True 1547.740000 6527 92.993800 384 5131 5 chr2B.!!$R1 4747
3 TraesCS2D01G496300 chr2B 792954739 792955442 703 False 246.000000 246 73.525000 2603 3322 1 chr2B.!!$F1 719
4 TraesCS2D01G496300 chr2A 727191895 727196742 4847 True 1711.325000 6274 93.383750 92 5131 4 chr2A.!!$R1 5039
5 TraesCS2D01G496300 chr4D 85260163 85261950 1787 True 640.000000 640 73.469000 1895 3685 1 chr4D.!!$R1 1790
6 TraesCS2D01G496300 chr4A 498986098 498987888 1790 True 632.000000 632 73.388000 1895 3685 1 chr4A.!!$R1 1790
7 TraesCS2D01G496300 chr3A 36301123 36302833 1710 False 568.000000 568 72.979000 1929 3639 1 chr3A.!!$F2 1710
8 TraesCS2D01G496300 chr3A 36290475 36291723 1248 False 470.000000 470 73.838000 2439 3689 1 chr3A.!!$F1 1250
9 TraesCS2D01G496300 chr3A 36479940 36480684 744 True 436.000000 436 77.483000 2938 3685 1 chr3A.!!$R1 747
10 TraesCS2D01G496300 chr3D 26301727 26303428 1701 False 520.000000 520 72.532000 1929 3627 1 chr3D.!!$F2 1698
11 TraesCS2D01G496300 chr3D 26282920 26283886 966 False 486.000000 486 76.045000 2713 3682 1 chr3D.!!$F1 969
12 TraesCS2D01G496300 chr3D 26219880 26221675 1795 True 442.000000 442 71.491000 1881 3682 1 chr3D.!!$R1 1801
13 TraesCS2D01G496300 chr5A 650280454 650282208 1754 False 501.000000 501 72.315000 1925 3682 1 chr5A.!!$F1 1757

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
51 52 0.250295 TGGGAAGCCGTCTTTGACTG 60.250 55.000 0.00 0.00 31.48 3.51 F
53 54 0.250338 GGAAGCCGTCTTTGACTGGT 60.250 55.000 9.13 0.82 32.13 4.00 F
113 114 0.250338 AGCCGTCTTTGACTGGTTCC 60.250 55.000 9.13 0.00 32.13 3.62 F
1149 1164 0.254178 TTGATCCCCAGCAAGCTCTC 59.746 55.000 0.00 0.00 0.00 3.20 F
1272 1287 0.461548 TACAAGGGCGCATCTCTCTG 59.538 55.000 10.83 4.25 0.00 3.35 F
1889 1904 3.299503 AGCTGTCCTTGGTTGATTTGTT 58.700 40.909 0.00 0.00 0.00 2.83 F
2910 2928 0.179073 CCTGCCCTGTCATACCTTCG 60.179 60.000 0.00 0.00 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 1323 1.438651 TGAACAGATTGCGTGGTAGC 58.561 50.000 0.00 0.00 37.71 3.58 R
1727 1742 1.555075 TGGAGGCAAGGCTTAGTACAG 59.445 52.381 0.00 0.00 0.00 2.74 R
1872 1887 4.918810 ACTCAACAAATCAACCAAGGAC 57.081 40.909 0.00 0.00 0.00 3.85 R
2579 2597 1.377725 CCCAGTGTGTCAGGGATGC 60.378 63.158 0.00 0.00 44.52 3.91 R
2789 2807 2.483889 CCTATTTCTGGGACTTCGCCTC 60.484 54.545 0.00 0.00 0.00 4.70 R
3785 3803 1.603326 TCTGTAACAGCACGTACGACA 59.397 47.619 24.41 12.67 0.00 4.35 R
4367 4396 0.457443 CTGCAGGACTACGAGCATCA 59.543 55.000 5.57 0.00 35.14 3.07 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
25 26 8.334263 TGAAATTGTGTCAATAATGCTACTGA 57.666 30.769 0.00 0.00 0.00 3.41
26 27 8.959548 TGAAATTGTGTCAATAATGCTACTGAT 58.040 29.630 0.00 0.00 0.00 2.90
27 28 9.443283 GAAATTGTGTCAATAATGCTACTGATC 57.557 33.333 0.00 0.00 0.00 2.92
28 29 8.510243 AATTGTGTCAATAATGCTACTGATCA 57.490 30.769 0.00 0.00 0.00 2.92
29 30 6.908870 TGTGTCAATAATGCTACTGATCAC 57.091 37.500 0.00 0.00 0.00 3.06
30 31 5.817296 TGTGTCAATAATGCTACTGATCACC 59.183 40.000 0.00 0.00 0.00 4.02
31 32 5.817296 GTGTCAATAATGCTACTGATCACCA 59.183 40.000 0.00 0.00 0.00 4.17
32 33 6.484643 GTGTCAATAATGCTACTGATCACCAT 59.515 38.462 0.00 0.00 0.00 3.55
33 34 6.484308 TGTCAATAATGCTACTGATCACCATG 59.516 38.462 0.00 0.00 0.00 3.66
34 35 5.999600 TCAATAATGCTACTGATCACCATGG 59.000 40.000 11.19 11.19 0.00 3.66
35 36 2.945080 ATGCTACTGATCACCATGGG 57.055 50.000 18.09 5.22 0.00 4.00
36 37 1.878211 TGCTACTGATCACCATGGGA 58.122 50.000 18.09 11.04 0.00 4.37
37 38 2.195727 TGCTACTGATCACCATGGGAA 58.804 47.619 18.09 3.39 0.00 3.97
38 39 2.171237 TGCTACTGATCACCATGGGAAG 59.829 50.000 18.09 5.69 0.00 3.46
39 40 2.843701 CTACTGATCACCATGGGAAGC 58.156 52.381 18.09 6.82 0.00 3.86
40 41 0.257039 ACTGATCACCATGGGAAGCC 59.743 55.000 18.09 1.57 0.00 4.35
41 42 0.816825 CTGATCACCATGGGAAGCCG 60.817 60.000 18.09 0.00 0.00 5.52
42 43 1.224592 GATCACCATGGGAAGCCGT 59.775 57.895 18.09 0.00 0.00 5.68
43 44 0.815615 GATCACCATGGGAAGCCGTC 60.816 60.000 18.09 1.30 0.00 4.79
44 45 1.274703 ATCACCATGGGAAGCCGTCT 61.275 55.000 18.09 0.00 0.00 4.18
45 46 1.002134 CACCATGGGAAGCCGTCTT 60.002 57.895 18.09 0.00 34.68 3.01
46 47 0.609131 CACCATGGGAAGCCGTCTTT 60.609 55.000 18.09 0.00 31.48 2.52
47 48 0.609131 ACCATGGGAAGCCGTCTTTG 60.609 55.000 18.09 0.00 31.48 2.77
48 49 0.322456 CCATGGGAAGCCGTCTTTGA 60.322 55.000 2.85 0.00 31.48 2.69
49 50 0.804989 CATGGGAAGCCGTCTTTGAC 59.195 55.000 0.00 0.00 31.48 3.18
50 51 0.693049 ATGGGAAGCCGTCTTTGACT 59.307 50.000 0.00 0.00 31.48 3.41
51 52 0.250295 TGGGAAGCCGTCTTTGACTG 60.250 55.000 0.00 0.00 31.48 3.51
52 53 0.955919 GGGAAGCCGTCTTTGACTGG 60.956 60.000 0.00 0.00 31.48 4.00
53 54 0.250338 GGAAGCCGTCTTTGACTGGT 60.250 55.000 9.13 0.82 32.13 4.00
54 55 1.594331 GAAGCCGTCTTTGACTGGTT 58.406 50.000 6.34 6.34 39.40 3.67
55 56 1.947456 GAAGCCGTCTTTGACTGGTTT 59.053 47.619 7.69 8.43 37.54 3.27
56 57 1.594331 AGCCGTCTTTGACTGGTTTC 58.406 50.000 9.13 0.00 32.13 2.78
57 58 1.134220 AGCCGTCTTTGACTGGTTTCA 60.134 47.619 9.13 0.00 32.13 2.69
58 59 1.880027 GCCGTCTTTGACTGGTTTCAT 59.120 47.619 9.13 0.00 32.13 2.57
59 60 2.350772 GCCGTCTTTGACTGGTTTCATG 60.351 50.000 9.13 0.00 32.13 3.07
60 61 2.226437 CCGTCTTTGACTGGTTTCATGG 59.774 50.000 0.00 0.00 0.00 3.66
61 62 3.138304 CGTCTTTGACTGGTTTCATGGA 58.862 45.455 0.00 0.00 0.00 3.41
62 63 3.753272 CGTCTTTGACTGGTTTCATGGAT 59.247 43.478 0.00 0.00 0.00 3.41
63 64 4.935205 CGTCTTTGACTGGTTTCATGGATA 59.065 41.667 0.00 0.00 0.00 2.59
64 65 5.063944 CGTCTTTGACTGGTTTCATGGATAG 59.936 44.000 0.00 0.00 0.00 2.08
65 66 5.355350 GTCTTTGACTGGTTTCATGGATAGG 59.645 44.000 0.00 0.00 0.00 2.57
66 67 3.931907 TGACTGGTTTCATGGATAGGG 57.068 47.619 0.00 0.00 0.00 3.53
67 68 3.459828 TGACTGGTTTCATGGATAGGGA 58.540 45.455 0.00 0.00 0.00 4.20
68 69 3.199946 TGACTGGTTTCATGGATAGGGAC 59.800 47.826 0.00 0.00 0.00 4.46
69 70 3.456277 GACTGGTTTCATGGATAGGGACT 59.544 47.826 0.00 0.00 46.37 3.85
70 71 3.200825 ACTGGTTTCATGGATAGGGACTG 59.799 47.826 0.00 0.00 41.52 3.51
71 72 2.509548 TGGTTTCATGGATAGGGACTGG 59.490 50.000 0.00 0.00 41.52 4.00
72 73 2.777692 GGTTTCATGGATAGGGACTGGA 59.222 50.000 0.00 0.00 41.52 3.86
73 74 3.433740 GGTTTCATGGATAGGGACTGGAC 60.434 52.174 0.00 0.00 41.52 4.02
74 75 3.421394 TTCATGGATAGGGACTGGACT 57.579 47.619 0.00 0.00 41.52 3.85
75 76 2.682594 TCATGGATAGGGACTGGACTG 58.317 52.381 0.00 0.00 41.52 3.51
76 77 2.023015 TCATGGATAGGGACTGGACTGT 60.023 50.000 0.00 0.00 41.52 3.55
77 78 3.206639 TCATGGATAGGGACTGGACTGTA 59.793 47.826 0.00 0.00 41.52 2.74
78 79 3.314307 TGGATAGGGACTGGACTGTAG 57.686 52.381 0.00 0.00 41.52 2.74
79 80 2.856864 TGGATAGGGACTGGACTGTAGA 59.143 50.000 0.00 0.00 41.52 2.59
80 81 3.271225 TGGATAGGGACTGGACTGTAGAA 59.729 47.826 0.00 0.00 41.52 2.10
81 82 4.264668 TGGATAGGGACTGGACTGTAGAAA 60.265 45.833 0.00 0.00 41.52 2.52
82 83 4.342665 GGATAGGGACTGGACTGTAGAAAG 59.657 50.000 0.00 0.00 41.52 2.62
83 84 3.544698 AGGGACTGGACTGTAGAAAGA 57.455 47.619 0.00 0.00 37.18 2.52
84 85 3.858135 AGGGACTGGACTGTAGAAAGAA 58.142 45.455 0.00 0.00 37.18 2.52
85 86 4.430441 AGGGACTGGACTGTAGAAAGAAT 58.570 43.478 0.00 0.00 37.18 2.40
86 87 4.468153 AGGGACTGGACTGTAGAAAGAATC 59.532 45.833 0.00 0.00 37.18 2.52
87 88 4.383226 GGGACTGGACTGTAGAAAGAATCC 60.383 50.000 0.00 0.00 0.00 3.01
88 89 4.223032 GGACTGGACTGTAGAAAGAATCCA 59.777 45.833 0.00 0.00 35.04 3.41
89 90 5.104735 GGACTGGACTGTAGAAAGAATCCAT 60.105 44.000 0.00 0.00 35.73 3.41
90 91 5.738909 ACTGGACTGTAGAAAGAATCCATG 58.261 41.667 0.00 0.00 35.73 3.66
99 100 0.625849 AAGAATCCATGGGAAGCCGT 59.374 50.000 13.02 0.00 34.34 5.68
105 106 0.322456 CCATGGGAAGCCGTCTTTGA 60.322 55.000 2.85 0.00 31.48 2.69
113 114 0.250338 AGCCGTCTTTGACTGGTTCC 60.250 55.000 9.13 0.00 32.13 3.62
115 116 1.882352 GCCGTCTTTGACTGGTTCCAT 60.882 52.381 0.00 0.00 32.13 3.41
121 122 4.878397 GTCTTTGACTGGTTCCATGGATAG 59.122 45.833 17.06 16.23 0.00 2.08
125 126 2.104963 GACTGGTTCCATGGATAGGGAC 59.895 54.545 17.06 10.25 36.30 4.46
133 134 2.402564 CATGGATAGGGACTGGACTGT 58.597 52.381 0.00 0.00 41.52 3.55
142 143 3.835395 AGGGACTGGACTGTAGAAAGAAG 59.165 47.826 0.00 0.00 37.18 2.85
145 146 5.046231 GGGACTGGACTGTAGAAAGAAGAAT 60.046 44.000 0.00 0.00 0.00 2.40
146 147 6.154706 GGGACTGGACTGTAGAAAGAAGAATA 59.845 42.308 0.00 0.00 0.00 1.75
147 148 7.036829 GGACTGGACTGTAGAAAGAAGAATAC 58.963 42.308 0.00 0.00 0.00 1.89
149 150 8.140112 ACTGGACTGTAGAAAGAAGAATACAT 57.860 34.615 0.00 0.00 0.00 2.29
151 152 9.092876 CTGGACTGTAGAAAGAAGAATACATTC 57.907 37.037 0.00 0.00 37.06 2.67
203 206 6.379988 TGACATTATAGCTTGTCAGTGGTAGA 59.620 38.462 13.67 0.00 45.35 2.59
222 225 6.324512 TGGTAGATACTTGGTTCGCCTATAAA 59.675 38.462 0.00 0.00 38.36 1.40
235 238 4.921515 TCGCCTATAAATGAAGCGTGTATC 59.078 41.667 2.45 0.00 46.49 2.24
295 298 2.222953 GCCGCTATCCAACAAAAGTACG 60.223 50.000 0.00 0.00 0.00 3.67
296 299 2.222953 CCGCTATCCAACAAAAGTACGC 60.223 50.000 0.00 0.00 0.00 4.42
297 300 2.413796 CGCTATCCAACAAAAGTACGCA 59.586 45.455 0.00 0.00 0.00 5.24
298 301 3.063452 CGCTATCCAACAAAAGTACGCAT 59.937 43.478 0.00 0.00 0.00 4.73
329 332 1.214175 TCTGAAGGAGGTGGTGCAAAA 59.786 47.619 0.00 0.00 0.00 2.44
337 340 0.600782 GGTGGTGCAAAAGCATGGTG 60.601 55.000 0.00 0.00 38.84 4.17
468 471 0.606096 GGTGGGTAATGGCCAACAAC 59.394 55.000 10.96 8.36 34.10 3.32
537 540 5.228945 ACCTCTTTTCCAGATCGAGAAAA 57.771 39.130 18.78 18.78 39.12 2.29
582 585 2.776330 CGCAATTTTATACGCGTTGGT 58.224 42.857 20.78 6.92 42.66 3.67
651 655 9.941664 GATACAAACATGTTTTCCTGATAGATG 57.058 33.333 21.10 8.79 0.00 2.90
652 656 7.765695 ACAAACATGTTTTCCTGATAGATGT 57.234 32.000 21.10 9.42 0.00 3.06
654 658 8.730680 ACAAACATGTTTTCCTGATAGATGTAC 58.269 33.333 21.10 0.00 0.00 2.90
656 660 9.466497 AAACATGTTTTCCTGATAGATGTACAT 57.534 29.630 18.13 8.43 0.00 2.29
669 676 9.542462 TGATAGATGTACATAAAAGCTTACCAC 57.458 33.333 8.71 0.00 0.00 4.16
671 678 9.899661 ATAGATGTACATAAAAGCTTACCACAA 57.100 29.630 8.71 0.00 0.00 3.33
713 720 5.049336 GGTCAACTCTTGCTAGGAAAGTTTC 60.049 44.000 16.21 7.09 0.00 2.78
717 724 5.059833 ACTCTTGCTAGGAAAGTTTCTGTG 58.940 41.667 15.05 6.72 0.00 3.66
718 725 5.036117 TCTTGCTAGGAAAGTTTCTGTGT 57.964 39.130 15.05 1.42 0.00 3.72
719 726 5.057149 TCTTGCTAGGAAAGTTTCTGTGTC 58.943 41.667 15.05 0.00 0.00 3.67
720 727 3.740115 TGCTAGGAAAGTTTCTGTGTCC 58.260 45.455 15.05 0.00 0.00 4.02
721 728 3.391296 TGCTAGGAAAGTTTCTGTGTCCT 59.609 43.478 15.05 6.20 41.60 3.85
722 729 4.591498 TGCTAGGAAAGTTTCTGTGTCCTA 59.409 41.667 15.05 7.01 39.46 2.94
723 730 4.930405 GCTAGGAAAGTTTCTGTGTCCTAC 59.070 45.833 15.05 0.80 39.46 3.18
724 731 5.510861 GCTAGGAAAGTTTCTGTGTCCTACA 60.511 44.000 15.05 0.00 39.46 2.74
738 745 3.257375 TGTCCTACACACACACAGTATCC 59.743 47.826 0.00 0.00 0.00 2.59
847 860 2.635427 GGAACAGAGAGGAAGAGTTGGT 59.365 50.000 0.00 0.00 0.00 3.67
857 870 4.143986 GGAAGAGTTGGTTCCTGATAGG 57.856 50.000 0.00 0.00 40.46 2.57
903 917 7.554118 ACTTCACTCACCAACAATTCCATATAG 59.446 37.037 0.00 0.00 0.00 1.31
904 918 6.957631 TCACTCACCAACAATTCCATATAGT 58.042 36.000 0.00 0.00 0.00 2.12
905 919 8.084985 TCACTCACCAACAATTCCATATAGTA 57.915 34.615 0.00 0.00 0.00 1.82
982 997 8.786898 GCATATAATGAAGCTCTAAATTGGACA 58.213 33.333 0.00 0.00 0.00 4.02
1149 1164 0.254178 TTGATCCCCAGCAAGCTCTC 59.746 55.000 0.00 0.00 0.00 3.20
1168 1183 1.911357 TCATGTCCTGGAATGACAGCT 59.089 47.619 13.86 0.00 44.55 4.24
1173 1188 0.467384 CCTGGAATGACAGCTCGGAT 59.533 55.000 0.00 0.00 37.16 4.18
1272 1287 0.461548 TACAAGGGCGCATCTCTCTG 59.538 55.000 10.83 4.25 0.00 3.35
1315 1330 8.704234 CATTTCTAAGAAATCTATCGCTACCAC 58.296 37.037 0.00 0.00 0.00 4.16
1474 1489 3.531538 GATCGCAATCACCTAGTTGGAA 58.468 45.455 0.00 0.00 39.71 3.53
1581 1596 6.964741 TCACTTTTTAACGTCACAACACTA 57.035 33.333 0.00 0.00 0.00 2.74
1594 1609 4.982295 TCACAACACTAACTCGACTTGATG 59.018 41.667 0.00 0.00 0.00 3.07
1727 1742 3.668447 TCCTCAATGTGTCTTCTCTTGC 58.332 45.455 0.00 0.00 0.00 4.01
1889 1904 3.299503 AGCTGTCCTTGGTTGATTTGTT 58.700 40.909 0.00 0.00 0.00 2.83
2579 2597 5.614324 TCATCTAATAACCTGTCCAGTGG 57.386 43.478 1.40 1.40 0.00 4.00
2910 2928 0.179073 CCTGCCCTGTCATACCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
3281 3299 4.467084 GCGGCACCGGAATCTGGA 62.467 66.667 16.23 0.00 40.19 3.86
3501 3519 0.850100 TCCACCATGACAACCAAGGT 59.150 50.000 0.00 0.00 46.90 3.50
3564 3582 7.734924 TTTGGATGATAATATGACAGCTCAC 57.265 36.000 0.00 0.00 0.00 3.51
3701 3719 4.398044 AGGTGATGTCTGTTGTTCGTTTTT 59.602 37.500 0.00 0.00 0.00 1.94
3796 3814 4.853196 TGACTAAACTATTGTCGTACGTGC 59.147 41.667 16.05 10.15 33.81 5.34
3836 3854 1.067060 GGTGGTGAAGTTTCAGTTGCC 59.933 52.381 0.00 0.00 37.98 4.52
3843 3861 1.527380 GTTTCAGTTGCCGGGGACA 60.527 57.895 2.18 0.00 0.00 4.02
4010 4028 0.824759 AAGATCGTCCAGTAGCCACC 59.175 55.000 0.00 0.00 0.00 4.61
4128 4146 0.465460 TGCAAGCCTTCACGGAGTTT 60.465 50.000 0.00 0.00 41.61 2.66
4282 4308 2.049228 GTCACTGTCGTAACCGTTCAG 58.951 52.381 0.00 0.00 40.21 3.02
4337 4366 8.465273 AAATATAACTAACTTGATGCTTCCCC 57.535 34.615 0.00 0.00 0.00 4.81
4338 4367 2.403252 ACTAACTTGATGCTTCCCCG 57.597 50.000 0.00 0.00 0.00 5.73
4339 4368 1.017387 CTAACTTGATGCTTCCCCGC 58.983 55.000 0.00 0.00 0.00 6.13
4340 4369 0.326595 TAACTTGATGCTTCCCCGCA 59.673 50.000 0.00 0.00 45.10 5.69
4341 4370 0.539438 AACTTGATGCTTCCCCGCAA 60.539 50.000 0.00 0.00 44.06 4.85
4342 4371 0.539438 ACTTGATGCTTCCCCGCAAA 60.539 50.000 0.00 0.00 44.06 3.68
4343 4372 0.602562 CTTGATGCTTCCCCGCAAAA 59.397 50.000 0.00 0.00 44.06 2.44
4344 4373 1.000731 CTTGATGCTTCCCCGCAAAAA 59.999 47.619 0.00 0.00 44.06 1.94
4458 4498 1.668151 GCGTGGTCAGGGTGTTCTC 60.668 63.158 0.00 0.00 0.00 2.87
4680 4770 3.181458 TGGTCTGGACTCTTTTGGTGTAC 60.181 47.826 0.67 0.00 0.00 2.90
4920 5053 4.102113 GCAGGTTGATGCAAGGGT 57.898 55.556 0.00 0.00 45.77 4.34
4921 5054 2.354902 GCAGGTTGATGCAAGGGTT 58.645 52.632 0.00 0.00 45.77 4.11
4922 5055 0.681175 GCAGGTTGATGCAAGGGTTT 59.319 50.000 0.00 0.00 45.77 3.27
4923 5056 1.892474 GCAGGTTGATGCAAGGGTTTA 59.108 47.619 0.00 0.00 45.77 2.01
5041 5189 3.829226 CAGGGCTGGGGATGGCAT 61.829 66.667 0.00 0.00 0.00 4.40
5042 5190 2.038438 AGGGCTGGGGATGGCATA 60.038 61.111 0.00 0.00 0.00 3.14
5043 5191 2.158810 AGGGCTGGGGATGGCATAG 61.159 63.158 0.00 0.00 0.00 2.23
5044 5192 2.282745 GGCTGGGGATGGCATAGC 60.283 66.667 10.78 10.78 0.00 2.97
5045 5193 2.517414 GCTGGGGATGGCATAGCA 59.483 61.111 13.67 0.00 34.64 3.49
5046 5194 1.152694 GCTGGGGATGGCATAGCAA 60.153 57.895 13.67 0.00 34.64 3.91
5047 5195 0.756442 GCTGGGGATGGCATAGCAAA 60.756 55.000 13.67 0.00 34.64 3.68
5048 5196 1.035139 CTGGGGATGGCATAGCAAAC 58.965 55.000 0.00 0.00 0.00 2.93
5049 5197 0.630673 TGGGGATGGCATAGCAAACT 59.369 50.000 0.00 0.00 0.00 2.66
5050 5198 1.322442 GGGGATGGCATAGCAAACTC 58.678 55.000 0.00 0.00 0.00 3.01
5051 5199 1.133668 GGGGATGGCATAGCAAACTCT 60.134 52.381 0.00 0.00 0.00 3.24
5052 5200 2.106511 GGGGATGGCATAGCAAACTCTA 59.893 50.000 0.00 0.00 0.00 2.43
5053 5201 3.245052 GGGGATGGCATAGCAAACTCTAT 60.245 47.826 0.00 0.00 0.00 1.98
5054 5202 4.006319 GGGATGGCATAGCAAACTCTATC 58.994 47.826 0.00 0.00 0.00 2.08
5055 5203 4.006319 GGATGGCATAGCAAACTCTATCC 58.994 47.826 0.00 0.00 0.00 2.59
5056 5204 4.263243 GGATGGCATAGCAAACTCTATCCT 60.263 45.833 0.00 0.00 0.00 3.24
5057 5205 4.342862 TGGCATAGCAAACTCTATCCTC 57.657 45.455 0.00 0.00 0.00 3.71
5058 5206 3.969976 TGGCATAGCAAACTCTATCCTCT 59.030 43.478 0.00 0.00 0.00 3.69
5059 5207 4.039730 TGGCATAGCAAACTCTATCCTCTC 59.960 45.833 0.00 0.00 0.00 3.20
5060 5208 4.283212 GGCATAGCAAACTCTATCCTCTCT 59.717 45.833 0.00 0.00 0.00 3.10
5061 5209 5.478679 GGCATAGCAAACTCTATCCTCTCTA 59.521 44.000 0.00 0.00 0.00 2.43
5062 5210 6.154363 GGCATAGCAAACTCTATCCTCTCTAT 59.846 42.308 0.00 0.00 0.00 1.98
5063 5211 7.257722 GCATAGCAAACTCTATCCTCTCTATC 58.742 42.308 0.00 0.00 0.00 2.08
5064 5212 7.630513 GCATAGCAAACTCTATCCTCTCTATCC 60.631 44.444 0.00 0.00 0.00 2.59
5065 5213 5.964288 AGCAAACTCTATCCTCTCTATCCT 58.036 41.667 0.00 0.00 0.00 3.24
5066 5214 6.381250 AGCAAACTCTATCCTCTCTATCCTT 58.619 40.000 0.00 0.00 0.00 3.36
5067 5215 6.843861 AGCAAACTCTATCCTCTCTATCCTTT 59.156 38.462 0.00 0.00 0.00 3.11
5068 5216 7.346960 AGCAAACTCTATCCTCTCTATCCTTTT 59.653 37.037 0.00 0.00 0.00 2.27
5069 5217 7.990314 GCAAACTCTATCCTCTCTATCCTTTTT 59.010 37.037 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.334263 TCAGTAGCATTATTGACACAATTTCA 57.666 30.769 2.40 0.00 0.00 2.69
1 2 9.443283 GATCAGTAGCATTATTGACACAATTTC 57.557 33.333 2.40 0.00 29.61 2.17
2 3 8.959548 TGATCAGTAGCATTATTGACACAATTT 58.040 29.630 0.00 0.00 29.61 1.82
3 4 8.400947 GTGATCAGTAGCATTATTGACACAATT 58.599 33.333 0.00 0.00 33.31 2.32
4 5 7.012704 GGTGATCAGTAGCATTATTGACACAAT 59.987 37.037 0.00 0.00 33.92 2.71
5 6 6.316140 GGTGATCAGTAGCATTATTGACACAA 59.684 38.462 0.00 0.00 33.92 3.33
6 7 5.817296 GGTGATCAGTAGCATTATTGACACA 59.183 40.000 0.00 0.00 33.92 3.72
7 8 5.817296 TGGTGATCAGTAGCATTATTGACAC 59.183 40.000 0.00 0.00 32.89 3.67
8 9 5.988287 TGGTGATCAGTAGCATTATTGACA 58.012 37.500 0.00 0.00 29.61 3.58
9 10 6.072838 CCATGGTGATCAGTAGCATTATTGAC 60.073 42.308 2.57 0.00 34.32 3.18
10 11 5.999600 CCATGGTGATCAGTAGCATTATTGA 59.000 40.000 2.57 0.00 34.32 2.57
11 12 5.182570 CCCATGGTGATCAGTAGCATTATTG 59.817 44.000 11.73 0.00 34.32 1.90
12 13 5.073554 TCCCATGGTGATCAGTAGCATTATT 59.926 40.000 11.73 0.00 34.32 1.40
13 14 4.598807 TCCCATGGTGATCAGTAGCATTAT 59.401 41.667 11.73 0.00 34.32 1.28
14 15 3.973305 TCCCATGGTGATCAGTAGCATTA 59.027 43.478 11.73 0.00 34.32 1.90
15 16 2.779430 TCCCATGGTGATCAGTAGCATT 59.221 45.455 11.73 0.00 34.32 3.56
16 17 2.411583 TCCCATGGTGATCAGTAGCAT 58.588 47.619 11.73 0.00 36.76 3.79
17 18 1.878211 TCCCATGGTGATCAGTAGCA 58.122 50.000 11.73 0.00 0.00 3.49
18 19 2.843701 CTTCCCATGGTGATCAGTAGC 58.156 52.381 11.73 0.00 0.00 3.58
19 20 2.486191 GGCTTCCCATGGTGATCAGTAG 60.486 54.545 11.73 3.18 0.00 2.57
20 21 1.490490 GGCTTCCCATGGTGATCAGTA 59.510 52.381 11.73 0.00 0.00 2.74
21 22 0.257039 GGCTTCCCATGGTGATCAGT 59.743 55.000 11.73 0.00 0.00 3.41
22 23 0.816825 CGGCTTCCCATGGTGATCAG 60.817 60.000 11.73 4.53 0.00 2.90
23 24 1.224315 CGGCTTCCCATGGTGATCA 59.776 57.895 11.73 0.00 0.00 2.92
24 25 0.815615 GACGGCTTCCCATGGTGATC 60.816 60.000 11.73 3.28 0.00 2.92
25 26 1.224592 GACGGCTTCCCATGGTGAT 59.775 57.895 11.73 0.00 0.00 3.06
26 27 1.488705 AAGACGGCTTCCCATGGTGA 61.489 55.000 11.73 4.83 0.00 4.02
27 28 0.609131 AAAGACGGCTTCCCATGGTG 60.609 55.000 2.63 2.15 31.82 4.17
28 29 0.609131 CAAAGACGGCTTCCCATGGT 60.609 55.000 2.63 0.00 31.82 3.55
29 30 0.322456 TCAAAGACGGCTTCCCATGG 60.322 55.000 2.63 4.14 31.82 3.66
30 31 0.804989 GTCAAAGACGGCTTCCCATG 59.195 55.000 2.63 0.00 31.82 3.66
31 32 0.693049 AGTCAAAGACGGCTTCCCAT 59.307 50.000 2.63 0.00 37.67 4.00
32 33 0.250295 CAGTCAAAGACGGCTTCCCA 60.250 55.000 2.63 0.00 37.67 4.37
33 34 0.955919 CCAGTCAAAGACGGCTTCCC 60.956 60.000 2.63 0.00 37.67 3.97
34 35 0.250338 ACCAGTCAAAGACGGCTTCC 60.250 55.000 2.63 0.00 37.67 3.46
35 36 1.594331 AACCAGTCAAAGACGGCTTC 58.406 50.000 2.63 0.00 37.67 3.86
36 37 1.947456 GAAACCAGTCAAAGACGGCTT 59.053 47.619 0.00 0.00 37.67 4.35
37 38 1.134220 TGAAACCAGTCAAAGACGGCT 60.134 47.619 0.00 0.00 37.67 5.52
38 39 1.305201 TGAAACCAGTCAAAGACGGC 58.695 50.000 7.57 0.00 37.67 5.68
39 40 2.226437 CCATGAAACCAGTCAAAGACGG 59.774 50.000 0.00 0.00 37.67 4.79
40 41 3.138304 TCCATGAAACCAGTCAAAGACG 58.862 45.455 0.00 0.00 37.67 4.18
41 42 5.355350 CCTATCCATGAAACCAGTCAAAGAC 59.645 44.000 0.00 0.00 0.00 3.01
42 43 5.500234 CCTATCCATGAAACCAGTCAAAGA 58.500 41.667 0.00 0.00 0.00 2.52
43 44 4.641989 CCCTATCCATGAAACCAGTCAAAG 59.358 45.833 0.00 0.00 0.00 2.77
44 45 4.290985 TCCCTATCCATGAAACCAGTCAAA 59.709 41.667 0.00 0.00 0.00 2.69
45 46 3.849574 TCCCTATCCATGAAACCAGTCAA 59.150 43.478 0.00 0.00 0.00 3.18
46 47 3.199946 GTCCCTATCCATGAAACCAGTCA 59.800 47.826 0.00 0.00 0.00 3.41
47 48 3.456277 AGTCCCTATCCATGAAACCAGTC 59.544 47.826 0.00 0.00 0.00 3.51
48 49 3.200825 CAGTCCCTATCCATGAAACCAGT 59.799 47.826 0.00 0.00 0.00 4.00
49 50 3.434167 CCAGTCCCTATCCATGAAACCAG 60.434 52.174 0.00 0.00 0.00 4.00
50 51 2.509548 CCAGTCCCTATCCATGAAACCA 59.490 50.000 0.00 0.00 0.00 3.67
51 52 2.777692 TCCAGTCCCTATCCATGAAACC 59.222 50.000 0.00 0.00 0.00 3.27
52 53 3.456277 AGTCCAGTCCCTATCCATGAAAC 59.544 47.826 0.00 0.00 0.00 2.78
53 54 3.455910 CAGTCCAGTCCCTATCCATGAAA 59.544 47.826 0.00 0.00 0.00 2.69
54 55 3.041211 CAGTCCAGTCCCTATCCATGAA 58.959 50.000 0.00 0.00 0.00 2.57
55 56 2.023015 ACAGTCCAGTCCCTATCCATGA 60.023 50.000 0.00 0.00 0.00 3.07
56 57 2.402564 ACAGTCCAGTCCCTATCCATG 58.597 52.381 0.00 0.00 0.00 3.66
57 58 2.877154 ACAGTCCAGTCCCTATCCAT 57.123 50.000 0.00 0.00 0.00 3.41
58 59 2.856864 TCTACAGTCCAGTCCCTATCCA 59.143 50.000 0.00 0.00 0.00 3.41
59 60 3.596940 TCTACAGTCCAGTCCCTATCC 57.403 52.381 0.00 0.00 0.00 2.59
60 61 5.202004 TCTTTCTACAGTCCAGTCCCTATC 58.798 45.833 0.00 0.00 0.00 2.08
61 62 5.208294 TCTTTCTACAGTCCAGTCCCTAT 57.792 43.478 0.00 0.00 0.00 2.57
62 63 4.669866 TCTTTCTACAGTCCAGTCCCTA 57.330 45.455 0.00 0.00 0.00 3.53
63 64 3.544698 TCTTTCTACAGTCCAGTCCCT 57.455 47.619 0.00 0.00 0.00 4.20
64 65 4.383226 GGATTCTTTCTACAGTCCAGTCCC 60.383 50.000 0.00 0.00 0.00 4.46
65 66 4.223032 TGGATTCTTTCTACAGTCCAGTCC 59.777 45.833 0.00 0.00 32.38 3.85
66 67 5.407407 TGGATTCTTTCTACAGTCCAGTC 57.593 43.478 0.00 0.00 32.38 3.51
67 68 5.338708 CCATGGATTCTTTCTACAGTCCAGT 60.339 44.000 5.56 0.00 38.95 4.00
68 69 5.121811 CCATGGATTCTTTCTACAGTCCAG 58.878 45.833 5.56 0.00 38.95 3.86
69 70 4.080356 CCCATGGATTCTTTCTACAGTCCA 60.080 45.833 15.22 0.00 39.79 4.02
70 71 4.164221 TCCCATGGATTCTTTCTACAGTCC 59.836 45.833 15.22 0.00 0.00 3.85
71 72 5.359194 TCCCATGGATTCTTTCTACAGTC 57.641 43.478 15.22 0.00 0.00 3.51
72 73 5.749462 CTTCCCATGGATTCTTTCTACAGT 58.251 41.667 15.22 0.00 0.00 3.55
73 74 4.578105 GCTTCCCATGGATTCTTTCTACAG 59.422 45.833 15.22 0.00 0.00 2.74
74 75 4.526970 GCTTCCCATGGATTCTTTCTACA 58.473 43.478 15.22 0.00 0.00 2.74
75 76 3.885901 GGCTTCCCATGGATTCTTTCTAC 59.114 47.826 15.22 0.00 0.00 2.59
76 77 3.433598 CGGCTTCCCATGGATTCTTTCTA 60.434 47.826 15.22 0.00 0.00 2.10
77 78 2.684927 CGGCTTCCCATGGATTCTTTCT 60.685 50.000 15.22 0.00 0.00 2.52
78 79 1.678101 CGGCTTCCCATGGATTCTTTC 59.322 52.381 15.22 0.00 0.00 2.62
79 80 1.005924 ACGGCTTCCCATGGATTCTTT 59.994 47.619 15.22 0.00 0.00 2.52
80 81 0.625849 ACGGCTTCCCATGGATTCTT 59.374 50.000 15.22 0.00 0.00 2.52
81 82 0.181350 GACGGCTTCCCATGGATTCT 59.819 55.000 15.22 0.00 0.00 2.40
82 83 0.181350 AGACGGCTTCCCATGGATTC 59.819 55.000 15.22 0.00 0.00 2.52
83 84 0.625849 AAGACGGCTTCCCATGGATT 59.374 50.000 15.22 0.00 0.00 3.01
84 85 0.625849 AAAGACGGCTTCCCATGGAT 59.374 50.000 15.22 0.00 31.82 3.41
85 86 0.322456 CAAAGACGGCTTCCCATGGA 60.322 55.000 15.22 0.00 31.82 3.41
86 87 0.322456 TCAAAGACGGCTTCCCATGG 60.322 55.000 2.63 4.14 31.82 3.66
87 88 0.804989 GTCAAAGACGGCTTCCCATG 59.195 55.000 2.63 0.00 31.82 3.66
88 89 0.693049 AGTCAAAGACGGCTTCCCAT 59.307 50.000 2.63 0.00 37.67 4.00
89 90 0.250295 CAGTCAAAGACGGCTTCCCA 60.250 55.000 2.63 0.00 37.67 4.37
90 91 0.955919 CCAGTCAAAGACGGCTTCCC 60.956 60.000 2.63 0.00 37.67 3.97
99 100 4.080356 CCTATCCATGGAACCAGTCAAAGA 60.080 45.833 20.67 0.00 0.00 2.52
105 106 2.127708 GTCCCTATCCATGGAACCAGT 58.872 52.381 20.67 3.98 31.03 4.00
113 114 2.402564 ACAGTCCAGTCCCTATCCATG 58.597 52.381 0.00 0.00 0.00 3.66
115 116 2.856864 TCTACAGTCCAGTCCCTATCCA 59.143 50.000 0.00 0.00 0.00 3.41
121 122 3.833070 TCTTCTTTCTACAGTCCAGTCCC 59.167 47.826 0.00 0.00 0.00 4.46
125 126 9.092876 GAATGTATTCTTCTTTCTACAGTCCAG 57.907 37.037 0.00 0.00 34.71 3.86
168 169 7.422399 ACAAGCTATAATGTCAACGTGTTTTT 58.578 30.769 0.00 0.00 0.00 1.94
203 206 6.204882 GCTTCATTTATAGGCGAACCAAGTAT 59.795 38.462 0.00 0.00 39.06 2.12
235 238 4.294416 TCTTTACTAGCTGCTTAGAGCG 57.706 45.455 7.79 0.00 46.26 5.03
278 281 4.142708 TGCATGCGTACTTTTGTTGGATAG 60.143 41.667 14.09 0.00 0.00 2.08
280 283 2.556189 TGCATGCGTACTTTTGTTGGAT 59.444 40.909 14.09 0.00 0.00 3.41
295 298 0.107800 TTCAGAGAGAGCCTGCATGC 60.108 55.000 11.82 11.82 0.00 4.06
296 299 1.473610 CCTTCAGAGAGAGCCTGCATG 60.474 57.143 0.00 0.00 0.00 4.06
297 300 0.831966 CCTTCAGAGAGAGCCTGCAT 59.168 55.000 0.00 0.00 0.00 3.96
298 301 0.251967 TCCTTCAGAGAGAGCCTGCA 60.252 55.000 0.00 0.00 0.00 4.41
401 404 6.019779 AGAGAGTGATCTGAAGTTGTACAC 57.980 41.667 0.00 0.00 0.00 2.90
406 409 7.670009 AAATGAAGAGAGTGATCTGAAGTTG 57.330 36.000 0.00 0.00 0.00 3.16
455 458 4.202202 CCTTCAAGTTGTTGTTGGCCATTA 60.202 41.667 6.09 0.00 34.98 1.90
468 471 3.068590 AGACATTTGTGCCCTTCAAGTTG 59.931 43.478 0.00 0.00 0.00 3.16
517 520 5.388890 CGTGTTTTCTCGATCTGGAAAAGAG 60.389 44.000 17.17 4.64 40.55 2.85
525 528 4.681942 AGAAACTCGTGTTTTCTCGATCTG 59.318 41.667 15.98 0.00 45.36 2.90
537 540 4.820897 TCATGCTGATTAGAAACTCGTGT 58.179 39.130 0.00 0.00 0.00 4.49
563 566 3.783943 CAGACCAACGCGTATAAAATTGC 59.216 43.478 14.46 0.00 0.00 3.56
573 576 0.098025 CAAAACACAGACCAACGCGT 59.902 50.000 5.58 5.58 0.00 6.01
577 580 3.380004 TCATCACCAAAACACAGACCAAC 59.620 43.478 0.00 0.00 0.00 3.77
580 583 4.853924 AATCATCACCAAAACACAGACC 57.146 40.909 0.00 0.00 0.00 3.85
608 612 3.193903 TGTATCAACTAGCAAGCACCGTA 59.806 43.478 0.00 0.00 0.00 4.02
651 655 9.821662 CTACTTTTGTGGTAAGCTTTTATGTAC 57.178 33.333 3.20 0.00 0.00 2.90
652 656 9.563748 ACTACTTTTGTGGTAAGCTTTTATGTA 57.436 29.630 3.20 0.00 42.46 2.29
694 701 5.059833 CACAGAAACTTTCCTAGCAAGAGT 58.940 41.667 6.86 0.00 0.00 3.24
700 707 4.009370 AGGACACAGAAACTTTCCTAGC 57.991 45.455 0.00 0.00 34.80 3.42
701 708 6.097915 TGTAGGACACAGAAACTTTCCTAG 57.902 41.667 0.00 0.00 39.18 3.02
717 724 3.672511 CGGATACTGTGTGTGTGTAGGAC 60.673 52.174 0.00 0.00 0.00 3.85
718 725 2.490509 CGGATACTGTGTGTGTGTAGGA 59.509 50.000 0.00 0.00 0.00 2.94
719 726 2.490509 TCGGATACTGTGTGTGTGTAGG 59.509 50.000 0.00 0.00 0.00 3.18
720 727 3.842732 TCGGATACTGTGTGTGTGTAG 57.157 47.619 0.00 0.00 0.00 2.74
721 728 4.490743 CATTCGGATACTGTGTGTGTGTA 58.509 43.478 0.00 0.00 0.00 2.90
722 729 3.325870 CATTCGGATACTGTGTGTGTGT 58.674 45.455 0.00 0.00 0.00 3.72
723 730 2.672874 CCATTCGGATACTGTGTGTGTG 59.327 50.000 0.00 0.00 0.00 3.82
724 731 2.935238 GCCATTCGGATACTGTGTGTGT 60.935 50.000 0.00 0.00 0.00 3.72
725 732 1.665679 GCCATTCGGATACTGTGTGTG 59.334 52.381 0.00 0.00 0.00 3.82
726 733 1.277842 TGCCATTCGGATACTGTGTGT 59.722 47.619 0.00 0.00 0.00 3.72
727 734 2.022764 TGCCATTCGGATACTGTGTG 57.977 50.000 0.00 0.00 0.00 3.82
792 805 7.934120 AGATTAAGCACAAGTCAAAAGTAGAGT 59.066 33.333 0.00 0.00 0.00 3.24
798 811 6.143438 CAGCAAGATTAAGCACAAGTCAAAAG 59.857 38.462 0.00 0.00 0.00 2.27
836 849 3.118223 CCCTATCAGGAACCAACTCTTCC 60.118 52.174 0.00 0.00 37.67 3.46
837 850 3.682999 GCCCTATCAGGAACCAACTCTTC 60.683 52.174 0.00 0.00 37.67 2.87
841 854 1.561542 CTGCCCTATCAGGAACCAACT 59.438 52.381 0.00 0.00 37.67 3.16
857 870 0.984995 ACCTGAAAGACTACCCTGCC 59.015 55.000 0.00 0.00 34.07 4.85
864 877 5.243283 GGTGAGTGAAGTACCTGAAAGACTA 59.757 44.000 0.00 0.00 34.07 2.59
978 993 3.573967 TGGCTGGATTTCTTTCTTTGTCC 59.426 43.478 0.00 0.00 0.00 4.02
982 997 5.105064 CCATCATGGCTGGATTTCTTTCTTT 60.105 40.000 9.01 0.00 35.70 2.52
983 998 4.404715 CCATCATGGCTGGATTTCTTTCTT 59.595 41.667 9.01 0.00 35.70 2.52
984 999 3.958798 CCATCATGGCTGGATTTCTTTCT 59.041 43.478 9.01 0.00 35.70 2.52
985 1000 3.703052 ACCATCATGGCTGGATTTCTTTC 59.297 43.478 18.59 0.00 42.67 2.62
1149 1164 2.286872 GAGCTGTCATTCCAGGACATG 58.713 52.381 0.00 0.00 43.72 3.21
1168 1183 3.055385 CCTTCCCAGTTACAGAAATCCGA 60.055 47.826 0.00 0.00 0.00 4.55
1173 1188 3.714798 AGACACCTTCCCAGTTACAGAAA 59.285 43.478 0.00 0.00 0.00 2.52
1272 1287 6.969828 AGAAATGTAAGATTTCCGAGTGAC 57.030 37.500 5.83 0.00 38.44 3.67
1308 1323 1.438651 TGAACAGATTGCGTGGTAGC 58.561 50.000 0.00 0.00 37.71 3.58
1315 1330 3.557577 TTGTCCAATGAACAGATTGCG 57.442 42.857 0.00 0.00 32.77 4.85
1474 1489 5.760484 AAATTGGCATGTGTAGGGATTTT 57.240 34.783 0.00 0.00 0.00 1.82
1594 1609 2.854777 CACTGATCCGATTTGACGAGAC 59.145 50.000 0.00 0.00 35.09 3.36
1727 1742 1.555075 TGGAGGCAAGGCTTAGTACAG 59.445 52.381 0.00 0.00 0.00 2.74
1872 1887 4.918810 ACTCAACAAATCAACCAAGGAC 57.081 40.909 0.00 0.00 0.00 3.85
2579 2597 1.377725 CCCAGTGTGTCAGGGATGC 60.378 63.158 0.00 0.00 44.52 3.91
2598 2616 7.334171 TCAATGTATTCCATACTGTCACAGTTG 59.666 37.037 17.55 13.56 44.77 3.16
2789 2807 2.483889 CCTATTTCTGGGACTTCGCCTC 60.484 54.545 0.00 0.00 0.00 4.70
2910 2928 4.725556 TGTCACGTGCTTAGTTGAATTC 57.274 40.909 11.67 0.00 0.00 2.17
3281 3299 3.006323 CGAGCAAGCAGTTAGGATAGGAT 59.994 47.826 0.00 0.00 0.00 3.24
3501 3519 6.587226 GCTTCAAATCACAATGAACAATAGCA 59.413 34.615 0.00 0.00 32.46 3.49
3564 3582 1.669795 GCAAGGCCAAAATCTCCAACG 60.670 52.381 5.01 0.00 0.00 4.10
3785 3803 1.603326 TCTGTAACAGCACGTACGACA 59.397 47.619 24.41 12.67 0.00 4.35
3796 3814 2.146342 CAGTTGCCCACTCTGTAACAG 58.854 52.381 0.00 0.00 30.92 3.16
3836 3854 3.517901 TCCCATAGCTATAAATGTCCCCG 59.482 47.826 5.77 0.00 0.00 5.73
3869 3887 5.562890 CGGTCTCTTCCTCAAAAATGTTTCC 60.563 44.000 0.00 0.00 0.00 3.13
3938 3956 2.692041 CCCAGCAGGAAAATTCATCTCC 59.308 50.000 0.00 0.00 38.24 3.71
4010 4028 8.197439 ACTAAACAGTCCAAATCTTTTTCCTTG 58.803 33.333 0.00 0.00 0.00 3.61
4128 4146 2.454772 TCCCTCCAAGATATGCCTCCTA 59.545 50.000 0.00 0.00 0.00 2.94
4282 4308 4.644103 TGTATCAGGTTAGTTCGCCTAC 57.356 45.455 0.00 0.00 33.07 3.18
4352 4381 7.492352 ACGAGCATCAAGTTAGTTAGTTTTT 57.508 32.000 0.00 0.00 33.17 1.94
4353 4382 7.871463 ACTACGAGCATCAAGTTAGTTAGTTTT 59.129 33.333 0.00 0.00 27.54 2.43
4354 4383 7.376615 ACTACGAGCATCAAGTTAGTTAGTTT 58.623 34.615 0.00 0.00 27.54 2.66
4355 4384 6.921914 ACTACGAGCATCAAGTTAGTTAGTT 58.078 36.000 0.00 0.00 27.54 2.24
4356 4385 6.404513 GGACTACGAGCATCAAGTTAGTTAGT 60.405 42.308 0.00 0.00 31.85 2.24
4357 4386 5.972382 GGACTACGAGCATCAAGTTAGTTAG 59.028 44.000 0.00 0.00 31.85 2.34
4358 4387 5.651139 AGGACTACGAGCATCAAGTTAGTTA 59.349 40.000 0.00 0.00 31.85 2.24
4359 4388 4.463186 AGGACTACGAGCATCAAGTTAGTT 59.537 41.667 0.00 0.00 31.85 2.24
4360 4389 4.017808 AGGACTACGAGCATCAAGTTAGT 58.982 43.478 0.00 0.00 31.85 2.24
4361 4390 4.355437 CAGGACTACGAGCATCAAGTTAG 58.645 47.826 0.00 0.00 31.85 2.34
4362 4391 3.428999 GCAGGACTACGAGCATCAAGTTA 60.429 47.826 0.00 0.00 31.85 2.24
4363 4392 2.675317 GCAGGACTACGAGCATCAAGTT 60.675 50.000 0.00 0.00 31.85 2.66
4364 4393 1.134965 GCAGGACTACGAGCATCAAGT 60.135 52.381 0.00 0.00 34.10 3.16
4365 4394 1.134995 TGCAGGACTACGAGCATCAAG 60.135 52.381 0.00 0.00 33.17 3.02
4366 4395 0.894835 TGCAGGACTACGAGCATCAA 59.105 50.000 0.00 0.00 33.17 2.57
4367 4396 0.457443 CTGCAGGACTACGAGCATCA 59.543 55.000 5.57 0.00 35.14 3.07
4368 4397 0.741326 TCTGCAGGACTACGAGCATC 59.259 55.000 15.13 0.00 35.14 3.91
4369 4398 1.407936 ATCTGCAGGACTACGAGCAT 58.592 50.000 15.13 0.00 35.14 3.79
4370 4399 1.186200 AATCTGCAGGACTACGAGCA 58.814 50.000 15.13 0.00 34.61 4.26
4371 4400 2.544069 GGTAATCTGCAGGACTACGAGC 60.544 54.545 15.13 0.00 28.43 5.03
4372 4401 2.952978 AGGTAATCTGCAGGACTACGAG 59.047 50.000 15.13 0.00 28.43 4.18
4373 4402 2.950309 GAGGTAATCTGCAGGACTACGA 59.050 50.000 15.13 0.00 28.43 3.43
4458 4498 5.531287 AGCAAAAACAACTTGTAGTAGGAGG 59.469 40.000 0.00 0.00 0.00 4.30
4680 4770 5.182001 AGCTGTAAGAAATAGTTGCCACTTG 59.818 40.000 0.00 0.00 34.07 3.16
4758 4850 3.985279 TCAACTTACATGTACAGACGCAC 59.015 43.478 4.68 0.00 0.00 5.34
4887 4979 3.502875 GCCCCTCTTCCCCATCCC 61.503 72.222 0.00 0.00 0.00 3.85
4920 5053 2.918266 TCCCCATCCGTTTAACCCTAAA 59.082 45.455 0.00 0.00 0.00 1.85
4921 5054 2.560080 TCCCCATCCGTTTAACCCTAA 58.440 47.619 0.00 0.00 0.00 2.69
4922 5055 2.267160 TCCCCATCCGTTTAACCCTA 57.733 50.000 0.00 0.00 0.00 3.53
4923 5056 1.283905 CTTCCCCATCCGTTTAACCCT 59.716 52.381 0.00 0.00 0.00 4.34
5022 5170 4.512914 GCCATCCCCAGCCCTGTC 62.513 72.222 0.00 0.00 0.00 3.51
5040 5188 7.708624 AGGATAGAGAGGATAGAGTTTGCTAT 58.291 38.462 0.00 0.00 33.91 2.97
5041 5189 7.097623 AGGATAGAGAGGATAGAGTTTGCTA 57.902 40.000 0.00 0.00 0.00 3.49
5042 5190 5.964288 AGGATAGAGAGGATAGAGTTTGCT 58.036 41.667 0.00 0.00 0.00 3.91
5043 5191 6.664428 AAGGATAGAGAGGATAGAGTTTGC 57.336 41.667 0.00 0.00 0.00 3.68
5089 5237 9.250246 GGACTTAGGATAGAGTTTGCTATCTAT 57.750 37.037 10.24 0.00 43.93 1.98
5090 5238 8.449625 AGGACTTAGGATAGAGTTTGCTATCTA 58.550 37.037 10.24 0.00 43.93 1.98
5091 5239 7.302184 AGGACTTAGGATAGAGTTTGCTATCT 58.698 38.462 10.24 0.00 43.93 1.98
5092 5240 7.533289 AGGACTTAGGATAGAGTTTGCTATC 57.467 40.000 0.00 0.00 43.80 2.08


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

AutoCloner maintained by Alex Coulton.