Multiple sequence alignment - TraesCS3D01G435900

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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 TraesCS3D01G435900 chr3D 100.000 5279 0 0 1 5279 548019210 548013932 0.000000e+00 9749.0
1 TraesCS3D01G435900 chr3D 94.624 93 3 2 2948 3038 168584865 168584773 5.510000e-30 143.0
2 TraesCS3D01G435900 chr3A 97.434 3469 71 8 1815 5279 684886729 684883275 0.000000e+00 5897.0
3 TraesCS3D01G435900 chr3A 94.256 1271 59 13 506 1766 684888012 684886746 0.000000e+00 1930.0
4 TraesCS3D01G435900 chr3A 92.336 274 17 3 155 425 684888282 684888010 2.310000e-103 387.0
5 TraesCS3D01G435900 chr3A 89.375 160 14 3 1 159 685012815 685012658 1.160000e-46 198.0
6 TraesCS3D01G435900 chr3A 92.857 98 5 2 2944 3039 12778805 12778902 1.980000e-29 141.0
7 TraesCS3D01G435900 chr3A 91.346 104 7 1 2938 3039 470095675 470095778 1.980000e-29 141.0
8 TraesCS3D01G435900 chr3B 95.460 2357 92 11 585 2931 725581607 725579256 0.000000e+00 3746.0
9 TraesCS3D01G435900 chr3B 96.133 2250 67 11 3046 5279 725579201 725576956 0.000000e+00 3655.0
10 TraesCS3D01G435900 chr5B 92.381 105 6 1 2937 3039 166379078 166379182 1.180000e-31 148.0
11 TraesCS3D01G435900 chr7B 93.617 94 4 2 2948 3039 162120905 162120812 7.130000e-29 139.0
12 TraesCS3D01G435900 chr7B 95.349 43 2 0 422 464 721442004 721442046 9.490000e-08 69.4
13 TraesCS3D01G435900 chrUn 91.919 99 6 2 2944 3040 15904018 15903920 2.560000e-28 137.0
14 TraesCS3D01G435900 chrUn 95.349 43 2 0 422 464 343014673 343014715 9.490000e-08 69.4
15 TraesCS3D01G435900 chrUn 95.349 43 2 0 422 464 343024974 343024932 9.490000e-08 69.4
16 TraesCS3D01G435900 chrUn 95.349 43 2 0 422 464 374493589 374493547 9.490000e-08 69.4
17 TraesCS3D01G435900 chrUn 95.349 43 2 0 422 464 387474637 387474679 9.490000e-08 69.4
18 TraesCS3D01G435900 chr5D 89.815 108 6 4 2937 3039 139441023 139440916 3.320000e-27 134.0
19 TraesCS3D01G435900 chr7A 85.950 121 12 5 2921 3039 671454922 671454805 2.000000e-24 124.0
20 TraesCS3D01G435900 chr2A 81.818 99 17 1 417 515 408811646 408811743 1.220000e-11 82.4
21 TraesCS3D01G435900 chr2A 85.714 56 8 0 440 495 779659817 779659762 5.710000e-05 60.2
22 TraesCS3D01G435900 chr2B 80.583 103 13 4 414 511 439690917 439691017 7.330000e-09 73.1
23 TraesCS3D01G435900 chr4A 93.333 45 3 0 420 464 598240116 598240160 3.410000e-07 67.6


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 TraesCS3D01G435900 chr3D 548013932 548019210 5278 True 9749.0 9749 100.000000 1 5279 1 chr3D.!!$R2 5278
1 TraesCS3D01G435900 chr3A 684883275 684888282 5007 True 2738.0 5897 94.675333 155 5279 3 chr3A.!!$R2 5124
2 TraesCS3D01G435900 chr3B 725576956 725581607 4651 True 3700.5 3746 95.796500 585 5279 2 chr3B.!!$R1 4694

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
24 25 0.107557 TTCCCGCGGAATAAACCCTC 60.108 55.000 30.73 0.00 36.71 4.30 F
36 37 0.250989 AAACCCTCGCAATTCCGGAA 60.251 50.000 21.37 21.37 0.00 4.30 F
37 38 0.676782 AACCCTCGCAATTCCGGAAG 60.677 55.000 23.47 11.11 0.00 3.46 F
246 247 1.000896 CGGTGCCTCCCCAAAGAAT 60.001 57.895 0.00 0.00 0.00 2.40 F
2245 2270 1.035139 CCATGCCATAGTTTGCCTCC 58.965 55.000 0.00 0.00 0.00 4.30 F
3044 3070 0.386113 GATCGGAGGGAGTACTGCAC 59.614 60.000 16.81 9.21 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1838 0.036732 TGTCATTCCTGAGGGTGCAC 59.963 55.000 8.80 8.80 30.18 4.57 R
1814 1839 0.994247 ATGTCATTCCTGAGGGTGCA 59.006 50.000 0.00 2.07 30.18 4.57 R
1975 2000 2.705658 AGGTGTGGAGTCAAATGTGAGA 59.294 45.455 0.00 0.00 33.27 3.27 R
2262 2287 7.298507 TCAATTAGCGTTAGTTTCACCATAC 57.701 36.000 0.00 0.00 0.00 2.39 R
3939 3983 2.035321 CCTAGCTCTGGCAAGTAGTAGC 59.965 54.545 0.00 0.00 41.70 3.58 R
4997 5045 2.288457 GCAAAAGGCCAAGTTCCTCTTC 60.288 50.000 5.01 0.00 36.11 2.87 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
22 23 4.641784 TTCCCGCGGAATAAACCC 57.358 55.556 30.73 0.00 36.71 4.11
23 24 1.992844 TTCCCGCGGAATAAACCCT 59.007 52.632 30.73 0.00 36.71 4.34
24 25 0.107557 TTCCCGCGGAATAAACCCTC 60.108 55.000 30.73 0.00 36.71 4.30
25 26 1.885850 CCCGCGGAATAAACCCTCG 60.886 63.158 30.73 0.00 0.00 4.63
26 27 2.531376 CCGCGGAATAAACCCTCGC 61.531 63.158 24.07 0.00 42.51 5.03
27 28 1.812093 CGCGGAATAAACCCTCGCA 60.812 57.895 0.00 0.00 45.66 5.10
28 29 1.363145 CGCGGAATAAACCCTCGCAA 61.363 55.000 0.00 0.00 45.66 4.85
29 30 1.021968 GCGGAATAAACCCTCGCAAT 58.978 50.000 0.00 0.00 44.87 3.56
30 31 1.404035 GCGGAATAAACCCTCGCAATT 59.596 47.619 0.00 0.00 44.87 2.32
31 32 2.540973 GCGGAATAAACCCTCGCAATTC 60.541 50.000 0.00 0.00 44.87 2.17
32 33 2.032924 CGGAATAAACCCTCGCAATTCC 59.967 50.000 0.00 0.00 41.36 3.01
33 34 2.032924 GGAATAAACCCTCGCAATTCCG 59.967 50.000 0.00 0.00 37.08 4.30
34 35 1.675552 ATAAACCCTCGCAATTCCGG 58.324 50.000 0.00 0.00 0.00 5.14
35 36 0.614294 TAAACCCTCGCAATTCCGGA 59.386 50.000 0.00 0.00 0.00 5.14
36 37 0.250989 AAACCCTCGCAATTCCGGAA 60.251 50.000 21.37 21.37 0.00 4.30
37 38 0.676782 AACCCTCGCAATTCCGGAAG 60.677 55.000 23.47 11.11 0.00 3.46
38 39 2.472909 CCCTCGCAATTCCGGAAGC 61.473 63.158 23.47 19.59 0.00 3.86
39 40 2.472909 CCTCGCAATTCCGGAAGCC 61.473 63.158 23.47 11.74 0.00 4.35
40 41 1.450312 CTCGCAATTCCGGAAGCCT 60.450 57.895 23.47 6.72 0.00 4.58
41 42 1.432270 CTCGCAATTCCGGAAGCCTC 61.432 60.000 23.47 10.31 0.00 4.70
42 43 1.450312 CGCAATTCCGGAAGCCTCT 60.450 57.895 23.47 1.61 0.00 3.69
43 44 1.026718 CGCAATTCCGGAAGCCTCTT 61.027 55.000 23.47 8.65 0.00 2.85
44 45 1.742411 CGCAATTCCGGAAGCCTCTTA 60.742 52.381 23.47 0.00 0.00 2.10
45 46 2.365582 GCAATTCCGGAAGCCTCTTAA 58.634 47.619 23.47 0.00 0.00 1.85
46 47 2.952310 GCAATTCCGGAAGCCTCTTAAT 59.048 45.455 23.47 0.00 0.00 1.40
47 48 3.381590 GCAATTCCGGAAGCCTCTTAATT 59.618 43.478 23.47 5.53 0.00 1.40
48 49 4.142160 GCAATTCCGGAAGCCTCTTAATTT 60.142 41.667 23.47 4.76 0.00 1.82
49 50 5.582550 CAATTCCGGAAGCCTCTTAATTTC 58.417 41.667 23.47 0.00 0.00 2.17
50 51 3.277142 TCCGGAAGCCTCTTAATTTCC 57.723 47.619 0.00 0.00 36.56 3.13
51 52 2.574369 TCCGGAAGCCTCTTAATTTCCA 59.426 45.455 0.00 0.00 39.20 3.53
52 53 2.945668 CCGGAAGCCTCTTAATTTCCAG 59.054 50.000 0.00 0.00 39.20 3.86
53 54 2.356069 CGGAAGCCTCTTAATTTCCAGC 59.644 50.000 3.36 0.00 39.20 4.85
54 55 3.356290 GGAAGCCTCTTAATTTCCAGCA 58.644 45.455 0.00 0.00 39.09 4.41
55 56 3.956848 GGAAGCCTCTTAATTTCCAGCAT 59.043 43.478 0.00 0.00 39.09 3.79
56 57 4.202090 GGAAGCCTCTTAATTTCCAGCATG 60.202 45.833 0.00 0.00 39.09 4.06
57 58 4.240881 AGCCTCTTAATTTCCAGCATGA 57.759 40.909 0.00 0.00 39.69 3.07
58 59 4.205587 AGCCTCTTAATTTCCAGCATGAG 58.794 43.478 0.00 0.00 39.69 2.90
59 60 4.080129 AGCCTCTTAATTTCCAGCATGAGA 60.080 41.667 0.00 0.00 39.69 3.27
60 61 4.826183 GCCTCTTAATTTCCAGCATGAGAT 59.174 41.667 0.00 0.00 39.69 2.75
61 62 5.278364 GCCTCTTAATTTCCAGCATGAGATG 60.278 44.000 0.00 0.00 39.69 2.90
62 63 5.826737 CCTCTTAATTTCCAGCATGAGATGT 59.173 40.000 0.00 0.00 39.69 3.06
63 64 6.017275 CCTCTTAATTTCCAGCATGAGATGTC 60.017 42.308 0.00 0.00 39.69 3.06
64 65 5.824624 TCTTAATTTCCAGCATGAGATGTCC 59.175 40.000 0.00 0.00 39.69 4.02
65 66 3.657398 ATTTCCAGCATGAGATGTCCA 57.343 42.857 0.00 0.00 39.69 4.02
66 67 3.657398 TTTCCAGCATGAGATGTCCAT 57.343 42.857 0.00 0.00 39.69 3.41
67 68 2.632987 TCCAGCATGAGATGTCCATG 57.367 50.000 0.00 0.00 43.06 3.66
68 69 2.121129 TCCAGCATGAGATGTCCATGA 58.879 47.619 0.00 0.00 42.89 3.07
69 70 2.709397 TCCAGCATGAGATGTCCATGAT 59.291 45.455 0.00 0.00 42.89 2.45
70 71 3.075148 CCAGCATGAGATGTCCATGATC 58.925 50.000 0.00 0.00 42.89 2.92
71 72 3.496160 CCAGCATGAGATGTCCATGATCA 60.496 47.826 0.00 0.00 42.89 2.92
72 73 3.748568 CAGCATGAGATGTCCATGATCAG 59.251 47.826 0.09 0.00 42.89 2.90
73 74 3.646637 AGCATGAGATGTCCATGATCAGA 59.353 43.478 0.09 0.00 42.89 3.27
74 75 4.287326 AGCATGAGATGTCCATGATCAGAT 59.713 41.667 0.09 0.00 42.89 2.90
75 76 5.004448 GCATGAGATGTCCATGATCAGATT 58.996 41.667 0.09 0.00 42.89 2.40
76 77 5.473846 GCATGAGATGTCCATGATCAGATTT 59.526 40.000 0.09 0.00 42.89 2.17
77 78 6.568653 GCATGAGATGTCCATGATCAGATTTG 60.569 42.308 0.09 0.00 42.89 2.32
78 79 5.997843 TGAGATGTCCATGATCAGATTTGT 58.002 37.500 0.09 0.00 0.00 2.83
79 80 6.053650 TGAGATGTCCATGATCAGATTTGTC 58.946 40.000 0.09 0.00 0.00 3.18
80 81 5.055144 AGATGTCCATGATCAGATTTGTCG 58.945 41.667 0.09 0.00 0.00 4.35
81 82 4.470334 TGTCCATGATCAGATTTGTCGA 57.530 40.909 0.09 0.00 0.00 4.20
82 83 4.831107 TGTCCATGATCAGATTTGTCGAA 58.169 39.130 0.09 0.00 0.00 3.71
83 84 4.631377 TGTCCATGATCAGATTTGTCGAAC 59.369 41.667 0.09 0.00 0.00 3.95
84 85 3.865164 TCCATGATCAGATTTGTCGAACG 59.135 43.478 0.09 0.00 0.00 3.95
85 86 3.865164 CCATGATCAGATTTGTCGAACGA 59.135 43.478 0.09 0.00 0.00 3.85
86 87 4.259970 CCATGATCAGATTTGTCGAACGAC 60.260 45.833 18.48 18.48 44.77 4.34
87 88 4.174411 TGATCAGATTTGTCGAACGACT 57.826 40.909 23.90 7.90 44.80 4.18
88 89 5.305139 TGATCAGATTTGTCGAACGACTA 57.695 39.130 23.90 16.12 44.80 2.59
89 90 5.705902 TGATCAGATTTGTCGAACGACTAA 58.294 37.500 23.90 22.38 44.80 2.24
90 91 6.330278 TGATCAGATTTGTCGAACGACTAAT 58.670 36.000 26.36 26.36 46.99 1.73
91 92 6.811665 TGATCAGATTTGTCGAACGACTAATT 59.188 34.615 26.60 16.76 45.39 1.40
92 93 6.627690 TCAGATTTGTCGAACGACTAATTC 57.372 37.500 26.60 21.00 45.39 2.17
104 105 3.522362 CGACTAATTCGTTAATGCAGCG 58.478 45.455 0.00 0.00 43.24 5.18
105 106 3.242016 CGACTAATTCGTTAATGCAGCGA 59.758 43.478 0.00 0.00 43.24 4.93
106 107 4.506217 GACTAATTCGTTAATGCAGCGAC 58.494 43.478 0.00 0.00 39.78 5.19
107 108 2.825086 AATTCGTTAATGCAGCGACC 57.175 45.000 0.00 0.00 39.78 4.79
108 109 1.732941 ATTCGTTAATGCAGCGACCA 58.267 45.000 0.00 0.00 39.78 4.02
109 110 1.514003 TTCGTTAATGCAGCGACCAA 58.486 45.000 0.00 0.00 39.78 3.67
110 111 1.732941 TCGTTAATGCAGCGACCAAT 58.267 45.000 0.00 0.00 34.70 3.16
111 112 2.894902 TCGTTAATGCAGCGACCAATA 58.105 42.857 0.00 0.00 34.70 1.90
112 113 3.263261 TCGTTAATGCAGCGACCAATAA 58.737 40.909 0.00 0.00 34.70 1.40
113 114 3.062909 TCGTTAATGCAGCGACCAATAAC 59.937 43.478 0.00 0.00 34.70 1.89
114 115 3.181515 CGTTAATGCAGCGACCAATAACA 60.182 43.478 0.00 0.00 31.32 2.41
115 116 4.342772 GTTAATGCAGCGACCAATAACAG 58.657 43.478 0.00 0.00 31.88 3.16
116 117 2.401583 ATGCAGCGACCAATAACAGA 57.598 45.000 0.00 0.00 0.00 3.41
117 118 2.177394 TGCAGCGACCAATAACAGAA 57.823 45.000 0.00 0.00 0.00 3.02
118 119 1.804151 TGCAGCGACCAATAACAGAAC 59.196 47.619 0.00 0.00 0.00 3.01
119 120 1.804151 GCAGCGACCAATAACAGAACA 59.196 47.619 0.00 0.00 0.00 3.18
120 121 2.159653 GCAGCGACCAATAACAGAACAG 60.160 50.000 0.00 0.00 0.00 3.16
121 122 3.067106 CAGCGACCAATAACAGAACAGT 58.933 45.455 0.00 0.00 0.00 3.55
122 123 3.498397 CAGCGACCAATAACAGAACAGTT 59.502 43.478 0.00 0.00 35.55 3.16
123 124 4.688879 CAGCGACCAATAACAGAACAGTTA 59.311 41.667 0.00 0.00 38.25 2.24
124 125 4.929808 AGCGACCAATAACAGAACAGTTAG 59.070 41.667 0.00 0.00 37.39 2.34
125 126 4.927425 GCGACCAATAACAGAACAGTTAGA 59.073 41.667 0.00 0.00 37.39 2.10
126 127 5.581085 GCGACCAATAACAGAACAGTTAGAT 59.419 40.000 0.00 0.00 37.39 1.98
127 128 6.092259 GCGACCAATAACAGAACAGTTAGATT 59.908 38.462 0.00 0.00 37.39 2.40
128 129 7.456253 CGACCAATAACAGAACAGTTAGATTG 58.544 38.462 0.00 0.00 37.39 2.67
129 130 7.330946 CGACCAATAACAGAACAGTTAGATTGA 59.669 37.037 0.00 0.00 37.39 2.57
130 131 8.918202 ACCAATAACAGAACAGTTAGATTGAA 57.082 30.769 0.00 0.00 37.39 2.69
131 132 9.520515 ACCAATAACAGAACAGTTAGATTGAAT 57.479 29.630 0.00 0.00 37.39 2.57
153 154 9.823647 TGAATTATAACTGAAAGATCTGACCTC 57.176 33.333 0.00 0.00 37.43 3.85
168 169 4.838423 TCTGACCTCTGTAACCAGAATGAA 59.162 41.667 0.00 0.00 46.79 2.57
187 188 5.850557 TGAAATGAAGTTGTGTCCATGTT 57.149 34.783 0.00 0.00 0.00 2.71
190 191 5.850557 AATGAAGTTGTGTCCATGTTTGA 57.149 34.783 0.00 0.00 0.00 2.69
214 215 2.859165 TCAAGGATGGACAAGGACAC 57.141 50.000 0.00 0.00 0.00 3.67
227 228 5.048991 GGACAAGGACACAATCAAAATACGT 60.049 40.000 0.00 0.00 0.00 3.57
234 235 2.160813 ACAATCAAAATACGTCGGTGCC 59.839 45.455 0.00 0.00 0.00 5.01
236 237 1.717194 TCAAAATACGTCGGTGCCTC 58.283 50.000 0.00 0.00 0.00 4.70
246 247 1.000896 CGGTGCCTCCCCAAAGAAT 60.001 57.895 0.00 0.00 0.00 2.40
270 271 1.885359 GCGATGATGGATGATGGCCTT 60.885 52.381 3.32 0.00 0.00 4.35
283 284 1.231958 TGGCCTTGACGTTTAAGCCG 61.232 55.000 3.32 2.28 0.00 5.52
350 351 4.743493 GGCAATGCCTTCGATTAAAGAAA 58.257 39.130 18.47 0.00 46.69 2.52
364 365 9.119418 TCGATTAAAGAAATTATGGATTGCTCA 57.881 29.630 0.00 0.00 32.04 4.26
372 373 8.323567 AGAAATTATGGATTGCTCAAAACCAAT 58.676 29.630 12.94 0.00 35.62 3.16
373 374 8.496707 AAATTATGGATTGCTCAAAACCAATC 57.503 30.769 12.94 5.11 44.01 2.67
394 395 8.224720 CCAATCTTTTAGGGGATCCTATTACAA 58.775 37.037 12.58 1.16 44.51 2.41
405 406 9.862149 GGGGATCCTATTACAATTTTTCTAGAA 57.138 33.333 12.58 0.00 0.00 2.10
428 432 9.274206 AGAACTTTTTCTTGTATCTTGTACTCC 57.726 33.333 0.00 0.00 39.17 3.85
429 433 7.981102 ACTTTTTCTTGTATCTTGTACTCCC 57.019 36.000 0.00 0.00 0.00 4.30
430 434 7.746703 ACTTTTTCTTGTATCTTGTACTCCCT 58.253 34.615 0.00 0.00 0.00 4.20
431 435 7.878644 ACTTTTTCTTGTATCTTGTACTCCCTC 59.121 37.037 0.00 0.00 0.00 4.30
432 436 5.934402 TTCTTGTATCTTGTACTCCCTCC 57.066 43.478 0.00 0.00 0.00 4.30
433 437 3.952323 TCTTGTATCTTGTACTCCCTCCG 59.048 47.826 0.00 0.00 0.00 4.63
434 438 3.377253 TGTATCTTGTACTCCCTCCGT 57.623 47.619 0.00 0.00 0.00 4.69
435 439 3.285484 TGTATCTTGTACTCCCTCCGTC 58.715 50.000 0.00 0.00 0.00 4.79
436 440 2.830651 ATCTTGTACTCCCTCCGTCT 57.169 50.000 0.00 0.00 0.00 4.18
437 441 2.599408 TCTTGTACTCCCTCCGTCTT 57.401 50.000 0.00 0.00 0.00 3.01
438 442 3.726557 TCTTGTACTCCCTCCGTCTTA 57.273 47.619 0.00 0.00 0.00 2.10
439 443 4.246712 TCTTGTACTCCCTCCGTCTTAT 57.753 45.455 0.00 0.00 0.00 1.73
440 444 5.378230 TCTTGTACTCCCTCCGTCTTATA 57.622 43.478 0.00 0.00 0.00 0.98
441 445 5.759059 TCTTGTACTCCCTCCGTCTTATAA 58.241 41.667 0.00 0.00 0.00 0.98
442 446 6.371278 TCTTGTACTCCCTCCGTCTTATAAT 58.629 40.000 0.00 0.00 0.00 1.28
443 447 7.520798 TCTTGTACTCCCTCCGTCTTATAATA 58.479 38.462 0.00 0.00 0.00 0.98
444 448 8.168725 TCTTGTACTCCCTCCGTCTTATAATAT 58.831 37.037 0.00 0.00 0.00 1.28
445 449 9.458727 CTTGTACTCCCTCCGTCTTATAATATA 57.541 37.037 0.00 0.00 0.00 0.86
446 450 9.812347 TTGTACTCCCTCCGTCTTATAATATAA 57.188 33.333 0.00 0.00 0.00 0.98
447 451 9.458727 TGTACTCCCTCCGTCTTATAATATAAG 57.541 37.037 12.58 12.58 0.00 1.73
448 452 9.678260 GTACTCCCTCCGTCTTATAATATAAGA 57.322 37.037 16.39 16.39 0.00 2.10
450 454 9.597681 ACTCCCTCCGTCTTATAATATAAGAAA 57.402 33.333 20.58 10.84 35.58 2.52
475 479 6.922247 TTTTTGACACTATCGTGGTGTAAA 57.078 33.333 2.10 4.40 46.23 2.01
476 480 6.922247 TTTTGACACTATCGTGGTGTAAAA 57.078 33.333 10.79 10.79 46.23 1.52
477 481 6.922247 TTTGACACTATCGTGGTGTAAAAA 57.078 33.333 11.82 10.30 46.23 1.94
498 502 7.619964 AAAAACACTCTTATATTACGGGGTG 57.380 36.000 0.00 0.00 0.00 4.61
499 503 4.950205 ACACTCTTATATTACGGGGTGG 57.050 45.455 0.00 0.00 0.00 4.61
500 504 4.549668 ACACTCTTATATTACGGGGTGGA 58.450 43.478 0.00 0.00 0.00 4.02
501 505 4.587684 ACACTCTTATATTACGGGGTGGAG 59.412 45.833 0.00 0.00 0.00 3.86
502 506 4.021368 CACTCTTATATTACGGGGTGGAGG 60.021 50.000 0.00 0.00 0.00 4.30
503 507 3.513517 TCTTATATTACGGGGTGGAGGG 58.486 50.000 0.00 0.00 0.00 4.30
504 508 3.142597 TCTTATATTACGGGGTGGAGGGA 59.857 47.826 0.00 0.00 0.00 4.20
561 565 4.713321 AGCAGTTAATACTCCCTCCGTAAA 59.287 41.667 0.00 0.00 30.26 2.01
617 621 2.294074 CTCTCTGGAAGTAGGACTCGG 58.706 57.143 0.00 0.00 33.76 4.63
696 700 1.337823 CGAAATCAACGGAGGTGAGGT 60.338 52.381 0.00 0.00 0.00 3.85
1199 1220 3.274455 CTCGTGCTGCTGACTCCGT 62.274 63.158 0.00 0.00 0.00 4.69
1312 1333 6.887368 TGACGATTCACAGAATTACAACTTG 58.113 36.000 0.00 0.00 0.00 3.16
1547 1569 4.824479 AACCCCAATTTTTATGCCAGAG 57.176 40.909 0.00 0.00 0.00 3.35
1585 1607 6.601332 ACTGAAACTTTGGTCCATTCTTCTA 58.399 36.000 0.00 0.00 0.00 2.10
1653 1675 7.991084 TCTTGAATGTGTCATTCATTCTTCT 57.009 32.000 20.67 0.00 46.31 2.85
1803 1828 1.600957 GATGTGTGGGATGATGCTTCG 59.399 52.381 0.00 0.00 0.00 3.79
1813 1838 4.510711 GGGATGATGCTTCGCTATGATATG 59.489 45.833 0.00 0.00 0.00 1.78
1814 1839 5.114780 GGATGATGCTTCGCTATGATATGT 58.885 41.667 0.00 0.00 0.00 2.29
1823 1848 2.289010 CGCTATGATATGTGCACCCTCA 60.289 50.000 15.69 14.30 0.00 3.86
1837 1862 3.424703 CACCCTCAGGAATGACATGTTT 58.575 45.455 0.00 0.00 36.73 2.83
1845 1870 7.201679 CCTCAGGAATGACATGTTTATCACTTC 60.202 40.741 0.00 0.41 0.00 3.01
1963 1988 1.967319 ATGACGGCAACAAGACACTT 58.033 45.000 0.00 0.00 0.00 3.16
1975 2000 6.751888 GCAACAAGACACTTCAGTATGTTTTT 59.248 34.615 0.00 0.00 37.40 1.94
2245 2270 1.035139 CCATGCCATAGTTTGCCTCC 58.965 55.000 0.00 0.00 0.00 4.30
2262 2287 9.736023 GTTTGCCTCCATTTAATACTTCAATAG 57.264 33.333 0.00 0.00 0.00 1.73
2323 2348 3.262420 AGGAAATACTAAGCTGCACACG 58.738 45.455 1.02 0.00 0.00 4.49
2461 2486 9.162764 GGTGAGCAGAGTATTTTATTTGTCTTA 57.837 33.333 0.00 0.00 0.00 2.10
2866 2891 2.458592 GTGTGAGAATTGCGCATACC 57.541 50.000 12.75 2.71 33.47 2.73
2925 2951 0.798776 CCTTTGCACGCTAGAAGTGG 59.201 55.000 16.92 4.25 39.80 4.00
2965 2991 8.924303 CATAGTATTCCCTCCGATCCATAATAA 58.076 37.037 0.00 0.00 0.00 1.40
2966 2992 7.425224 AGTATTCCCTCCGATCCATAATAAG 57.575 40.000 0.00 0.00 0.00 1.73
3044 3070 0.386113 GATCGGAGGGAGTACTGCAC 59.614 60.000 16.81 9.21 0.00 4.57
3220 3254 2.706339 GAGTGGATCCAGCTGATGTT 57.294 50.000 16.81 0.00 32.41 2.71
3318 3352 4.254492 GTCCACCTACCAATTCTTGACTC 58.746 47.826 0.00 0.00 0.00 3.36
3587 3624 1.279558 TCGTTGCTGTAAATAGGGGCA 59.720 47.619 0.00 0.00 0.00 5.36
3770 3807 5.991328 ATGTGAGTTTTCATATGTAGCGG 57.009 39.130 1.90 0.00 34.32 5.52
3801 3838 2.350522 GATGCACGTCATCCTCTGTTT 58.649 47.619 13.70 0.00 44.54 2.83
3802 3839 3.521560 GATGCACGTCATCCTCTGTTTA 58.478 45.455 13.70 0.00 44.54 2.01
3803 3840 3.610040 TGCACGTCATCCTCTGTTTAT 57.390 42.857 0.00 0.00 0.00 1.40
3804 3841 3.937814 TGCACGTCATCCTCTGTTTATT 58.062 40.909 0.00 0.00 0.00 1.40
3805 3842 5.079689 TGCACGTCATCCTCTGTTTATTA 57.920 39.130 0.00 0.00 0.00 0.98
3806 3843 4.868171 TGCACGTCATCCTCTGTTTATTAC 59.132 41.667 0.00 0.00 0.00 1.89
3807 3844 4.868171 GCACGTCATCCTCTGTTTATTACA 59.132 41.667 0.00 0.00 34.95 2.41
4029 4073 6.285990 GTTGGAGGTAAAGTCAACACTCTTA 58.714 40.000 0.00 0.00 39.22 2.10
4072 4116 8.858003 TTTGTTGCGACATTTTCACTTTAATA 57.142 26.923 7.83 0.00 35.29 0.98
4107 4151 4.931661 ACAATTGATCTGAATCCATGGC 57.068 40.909 13.59 0.00 0.00 4.40
4587 4631 1.541588 GACTTCCTTTCAAGGCGCAAT 59.458 47.619 10.83 0.00 46.06 3.56
4712 4758 6.645415 AGTTTCATAAACCTAGTGTCAGAACG 59.355 38.462 0.00 0.00 42.34 3.95
4723 4769 3.374058 AGTGTCAGAACGGTTGAAACAAG 59.626 43.478 0.00 0.00 35.64 3.16
4839 4885 4.129380 TGAATTATCTCAACATGGCTCCG 58.871 43.478 0.00 0.00 0.00 4.63
4874 4920 4.127171 CTGTGTAGGTTTTACAGCTGTGT 58.873 43.478 29.57 6.74 41.06 3.72
4997 5045 2.744202 GTGAACTGGTATGGCAAGTCAG 59.256 50.000 11.13 11.13 29.22 3.51
5110 5159 0.394565 AGGACAGTCACTCAAGTGCC 59.605 55.000 2.17 1.02 45.25 5.01
5112 5161 1.221414 GACAGTCACTCAAGTGCCAC 58.779 55.000 5.25 0.08 45.25 5.01
5203 5252 1.869767 CAACTGGAGCAACACTGTCTC 59.130 52.381 0.00 0.00 0.00 3.36
5204 5253 0.394565 ACTGGAGCAACACTGTCTCC 59.605 55.000 9.18 9.18 42.03 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.107557 GAGGGTTTATTCCGCGGGAA 60.108 55.000 27.83 18.43 46.39 3.97
6 7 1.523524 GAGGGTTTATTCCGCGGGA 59.476 57.895 27.83 20.01 0.00 5.14
7 8 1.885850 CGAGGGTTTATTCCGCGGG 60.886 63.158 27.83 6.80 42.43 6.13
8 9 2.531376 GCGAGGGTTTATTCCGCGG 61.531 63.158 22.12 22.12 45.39 6.46
10 11 1.021968 ATTGCGAGGGTTTATTCCGC 58.978 50.000 0.00 0.00 45.28 5.54
11 12 2.032924 GGAATTGCGAGGGTTTATTCCG 59.967 50.000 0.00 0.00 36.12 4.30
12 13 2.032924 CGGAATTGCGAGGGTTTATTCC 59.967 50.000 14.84 0.00 40.40 3.01
13 14 2.032924 CCGGAATTGCGAGGGTTTATTC 59.967 50.000 21.76 0.00 0.00 1.75
14 15 2.021457 CCGGAATTGCGAGGGTTTATT 58.979 47.619 21.76 0.00 0.00 1.40
15 16 1.210967 TCCGGAATTGCGAGGGTTTAT 59.789 47.619 21.76 0.00 0.00 1.40
16 17 0.614294 TCCGGAATTGCGAGGGTTTA 59.386 50.000 21.76 0.00 0.00 2.01
17 18 0.250989 TTCCGGAATTGCGAGGGTTT 60.251 50.000 21.76 0.00 0.00 3.27
18 19 0.676782 CTTCCGGAATTGCGAGGGTT 60.677 55.000 21.76 0.00 0.00 4.11
19 20 1.078426 CTTCCGGAATTGCGAGGGT 60.078 57.895 21.76 0.00 0.00 4.34
20 21 2.472909 GCTTCCGGAATTGCGAGGG 61.473 63.158 21.76 10.47 0.00 4.30
21 22 2.472909 GGCTTCCGGAATTGCGAGG 61.473 63.158 21.76 10.81 0.00 4.63
22 23 1.432270 GAGGCTTCCGGAATTGCGAG 61.432 60.000 21.76 12.10 0.00 5.03
23 24 1.449601 GAGGCTTCCGGAATTGCGA 60.450 57.895 21.76 4.16 0.00 5.10
24 25 1.026718 AAGAGGCTTCCGGAATTGCG 61.027 55.000 19.21 12.93 0.00 4.85
25 26 2.038387 TAAGAGGCTTCCGGAATTGC 57.962 50.000 19.21 18.37 0.00 3.56
26 27 5.450550 GGAAATTAAGAGGCTTCCGGAATTG 60.451 44.000 19.21 8.34 0.00 2.32
27 28 4.645136 GGAAATTAAGAGGCTTCCGGAATT 59.355 41.667 19.21 11.30 0.00 2.17
28 29 4.207955 GGAAATTAAGAGGCTTCCGGAAT 58.792 43.478 19.21 2.10 0.00 3.01
29 30 3.009695 TGGAAATTAAGAGGCTTCCGGAA 59.990 43.478 17.73 17.73 40.26 4.30
30 31 2.574369 TGGAAATTAAGAGGCTTCCGGA 59.426 45.455 0.00 0.00 40.26 5.14
31 32 2.945668 CTGGAAATTAAGAGGCTTCCGG 59.054 50.000 0.00 0.00 40.26 5.14
32 33 2.356069 GCTGGAAATTAAGAGGCTTCCG 59.644 50.000 0.00 0.00 40.26 4.30
33 34 3.356290 TGCTGGAAATTAAGAGGCTTCC 58.644 45.455 0.00 0.00 38.26 3.46
34 35 4.641989 TCATGCTGGAAATTAAGAGGCTTC 59.358 41.667 0.00 0.00 0.00 3.86
35 36 4.603131 TCATGCTGGAAATTAAGAGGCTT 58.397 39.130 0.00 0.00 0.00 4.35
36 37 4.080129 TCTCATGCTGGAAATTAAGAGGCT 60.080 41.667 0.00 0.00 0.00 4.58
37 38 4.202441 TCTCATGCTGGAAATTAAGAGGC 58.798 43.478 0.00 0.00 0.00 4.70
38 39 5.826737 ACATCTCATGCTGGAAATTAAGAGG 59.173 40.000 0.00 0.00 0.00 3.69
39 40 6.017275 GGACATCTCATGCTGGAAATTAAGAG 60.017 42.308 0.00 0.00 0.00 2.85
40 41 5.824624 GGACATCTCATGCTGGAAATTAAGA 59.175 40.000 0.00 0.00 0.00 2.10
41 42 5.591472 TGGACATCTCATGCTGGAAATTAAG 59.409 40.000 0.00 0.00 0.00 1.85
42 43 5.508567 TGGACATCTCATGCTGGAAATTAA 58.491 37.500 0.00 0.00 0.00 1.40
43 44 5.114764 TGGACATCTCATGCTGGAAATTA 57.885 39.130 0.00 0.00 0.00 1.40
44 45 3.972133 TGGACATCTCATGCTGGAAATT 58.028 40.909 0.00 0.00 0.00 1.82
45 46 3.657398 TGGACATCTCATGCTGGAAAT 57.343 42.857 0.00 0.00 0.00 2.17
46 47 3.054213 TCATGGACATCTCATGCTGGAAA 60.054 43.478 0.00 0.00 41.11 3.13
47 48 2.506644 TCATGGACATCTCATGCTGGAA 59.493 45.455 0.00 0.00 41.11 3.53
48 49 2.121129 TCATGGACATCTCATGCTGGA 58.879 47.619 0.00 0.00 41.11 3.86
49 50 2.632987 TCATGGACATCTCATGCTGG 57.367 50.000 0.00 0.00 41.11 4.85
50 51 3.740115 TGATCATGGACATCTCATGCTG 58.260 45.455 0.00 0.00 41.11 4.41
51 52 3.646637 TCTGATCATGGACATCTCATGCT 59.353 43.478 0.00 0.00 41.11 3.79
52 53 4.004196 TCTGATCATGGACATCTCATGC 57.996 45.455 0.00 0.00 41.11 4.06
53 54 6.486993 ACAAATCTGATCATGGACATCTCATG 59.513 38.462 0.00 0.00 42.28 3.07
54 55 6.602278 ACAAATCTGATCATGGACATCTCAT 58.398 36.000 0.00 0.00 0.00 2.90
55 56 5.997843 ACAAATCTGATCATGGACATCTCA 58.002 37.500 0.00 0.00 0.00 3.27
56 57 5.177142 CGACAAATCTGATCATGGACATCTC 59.823 44.000 0.00 0.00 0.00 2.75
57 58 5.055144 CGACAAATCTGATCATGGACATCT 58.945 41.667 0.00 0.00 0.00 2.90
58 59 5.052481 TCGACAAATCTGATCATGGACATC 58.948 41.667 0.00 0.00 0.00 3.06
59 60 5.027293 TCGACAAATCTGATCATGGACAT 57.973 39.130 0.00 0.00 0.00 3.06
60 61 4.470334 TCGACAAATCTGATCATGGACA 57.530 40.909 0.00 0.00 0.00 4.02
61 62 4.259970 CGTTCGACAAATCTGATCATGGAC 60.260 45.833 0.00 0.00 0.00 4.02
62 63 3.865164 CGTTCGACAAATCTGATCATGGA 59.135 43.478 0.00 0.00 0.00 3.41
63 64 3.865164 TCGTTCGACAAATCTGATCATGG 59.135 43.478 0.00 0.00 0.00 3.66
64 65 4.564372 AGTCGTTCGACAAATCTGATCATG 59.436 41.667 23.70 0.00 37.59 3.07
65 66 4.748892 AGTCGTTCGACAAATCTGATCAT 58.251 39.130 23.70 0.00 37.59 2.45
66 67 4.174411 AGTCGTTCGACAAATCTGATCA 57.826 40.909 23.70 0.00 37.59 2.92
67 68 6.814076 ATTAGTCGTTCGACAAATCTGATC 57.186 37.500 23.70 0.00 37.59 2.92
68 69 7.223058 GAATTAGTCGTTCGACAAATCTGAT 57.777 36.000 23.70 5.77 37.59 2.90
69 70 6.627690 GAATTAGTCGTTCGACAAATCTGA 57.372 37.500 23.70 3.85 37.59 3.27
84 85 4.506217 GTCGCTGCATTAACGAATTAGTC 58.494 43.478 0.00 0.00 37.60 2.59
85 86 3.308866 GGTCGCTGCATTAACGAATTAGT 59.691 43.478 0.00 0.00 37.60 2.24
86 87 3.308595 TGGTCGCTGCATTAACGAATTAG 59.691 43.478 0.00 0.00 37.60 1.73
87 88 3.263261 TGGTCGCTGCATTAACGAATTA 58.737 40.909 0.00 0.00 37.60 1.40
88 89 2.080693 TGGTCGCTGCATTAACGAATT 58.919 42.857 0.00 0.00 37.60 2.17
89 90 1.732941 TGGTCGCTGCATTAACGAAT 58.267 45.000 0.00 0.00 37.60 3.34
90 91 1.514003 TTGGTCGCTGCATTAACGAA 58.486 45.000 0.00 0.00 37.60 3.85
91 92 1.732941 ATTGGTCGCTGCATTAACGA 58.267 45.000 0.00 0.00 0.00 3.85
92 93 3.181515 TGTTATTGGTCGCTGCATTAACG 60.182 43.478 0.00 0.00 0.00 3.18
93 94 4.094294 TCTGTTATTGGTCGCTGCATTAAC 59.906 41.667 0.00 0.00 0.00 2.01
94 95 4.257731 TCTGTTATTGGTCGCTGCATTAA 58.742 39.130 0.00 0.00 0.00 1.40
95 96 3.867857 TCTGTTATTGGTCGCTGCATTA 58.132 40.909 0.00 0.00 0.00 1.90
96 97 2.710377 TCTGTTATTGGTCGCTGCATT 58.290 42.857 0.00 0.00 0.00 3.56
97 98 2.401583 TCTGTTATTGGTCGCTGCAT 57.598 45.000 0.00 0.00 0.00 3.96
98 99 1.804151 GTTCTGTTATTGGTCGCTGCA 59.196 47.619 0.00 0.00 0.00 4.41
99 100 1.804151 TGTTCTGTTATTGGTCGCTGC 59.196 47.619 0.00 0.00 0.00 5.25
100 101 3.067106 ACTGTTCTGTTATTGGTCGCTG 58.933 45.455 0.00 0.00 0.00 5.18
101 102 3.402628 ACTGTTCTGTTATTGGTCGCT 57.597 42.857 0.00 0.00 0.00 4.93
102 103 4.927425 TCTAACTGTTCTGTTATTGGTCGC 59.073 41.667 0.00 0.00 32.76 5.19
103 104 7.330946 TCAATCTAACTGTTCTGTTATTGGTCG 59.669 37.037 0.00 0.00 31.75 4.79
104 105 8.547967 TCAATCTAACTGTTCTGTTATTGGTC 57.452 34.615 0.00 0.00 31.75 4.02
105 106 8.918202 TTCAATCTAACTGTTCTGTTATTGGT 57.082 30.769 0.00 0.00 31.75 3.67
127 128 9.823647 GAGGTCAGATCTTTCAGTTATAATTCA 57.176 33.333 0.00 0.00 0.00 2.57
129 130 9.829507 CAGAGGTCAGATCTTTCAGTTATAATT 57.170 33.333 0.00 0.00 0.00 1.40
130 131 8.986991 ACAGAGGTCAGATCTTTCAGTTATAAT 58.013 33.333 0.00 0.00 0.00 1.28
131 132 8.367660 ACAGAGGTCAGATCTTTCAGTTATAA 57.632 34.615 0.00 0.00 0.00 0.98
132 133 7.962995 ACAGAGGTCAGATCTTTCAGTTATA 57.037 36.000 0.00 0.00 0.00 0.98
133 134 6.865834 ACAGAGGTCAGATCTTTCAGTTAT 57.134 37.500 0.00 0.00 0.00 1.89
134 135 7.309867 GGTTACAGAGGTCAGATCTTTCAGTTA 60.310 40.741 0.00 0.00 0.00 2.24
135 136 6.459923 GTTACAGAGGTCAGATCTTTCAGTT 58.540 40.000 0.00 0.00 0.00 3.16
136 137 5.046950 GGTTACAGAGGTCAGATCTTTCAGT 60.047 44.000 0.00 0.00 0.00 3.41
137 138 5.047021 TGGTTACAGAGGTCAGATCTTTCAG 60.047 44.000 0.00 0.00 0.00 3.02
138 139 4.838423 TGGTTACAGAGGTCAGATCTTTCA 59.162 41.667 0.00 0.00 0.00 2.69
139 140 5.407407 TGGTTACAGAGGTCAGATCTTTC 57.593 43.478 0.00 0.00 0.00 2.62
153 154 7.592533 CACAACTTCATTTCATTCTGGTTACAG 59.407 37.037 0.00 0.00 46.30 2.74
168 169 5.451798 GGTCAAACATGGACACAACTTCATT 60.452 40.000 0.00 0.00 37.00 2.57
187 188 3.805066 TGTCCATCCTTGATTGGTCAA 57.195 42.857 0.00 0.00 41.89 3.18
190 191 2.649312 TCCTTGTCCATCCTTGATTGGT 59.351 45.455 0.00 0.00 0.00 3.67
214 215 2.418628 AGGCACCGACGTATTTTGATTG 59.581 45.455 0.00 0.00 0.00 2.67
227 228 1.497309 ATTCTTTGGGGAGGCACCGA 61.497 55.000 0.00 0.00 40.11 4.69
234 235 1.533625 TCGCAACATTCTTTGGGGAG 58.466 50.000 0.74 0.00 39.33 4.30
236 237 1.818060 TCATCGCAACATTCTTTGGGG 59.182 47.619 0.74 0.00 39.33 4.96
246 247 2.223745 CCATCATCCATCATCGCAACA 58.776 47.619 0.00 0.00 0.00 3.33
270 271 0.305313 GTGTTGCGGCTTAAACGTCA 59.695 50.000 0.00 0.00 0.00 4.35
350 351 7.427989 AGATTGGTTTTGAGCAATCCATAAT 57.572 32.000 21.06 6.13 35.35 1.28
364 365 5.915628 AGGATCCCCTAAAAGATTGGTTTT 58.084 37.500 8.55 0.00 42.15 2.43
402 403 9.274206 GGAGTACAAGATACAAGAAAAAGTTCT 57.726 33.333 0.00 0.00 46.47 3.01
403 404 8.504815 GGGAGTACAAGATACAAGAAAAAGTTC 58.495 37.037 0.00 0.00 0.00 3.01
405 406 7.746703 AGGGAGTACAAGATACAAGAAAAAGT 58.253 34.615 0.00 0.00 0.00 2.66
406 407 7.334671 GGAGGGAGTACAAGATACAAGAAAAAG 59.665 40.741 0.00 0.00 0.00 2.27
422 426 9.678260 TCTTATATTATAAGACGGAGGGAGTAC 57.322 37.037 18.17 0.00 0.00 2.73
424 428 9.597681 TTTCTTATATTATAAGACGGAGGGAGT 57.402 33.333 20.71 0.00 33.73 3.85
474 478 6.600427 CCACCCCGTAATATAAGAGTGTTTTT 59.400 38.462 0.00 0.00 0.00 1.94
475 479 6.070078 TCCACCCCGTAATATAAGAGTGTTTT 60.070 38.462 0.00 0.00 0.00 2.43
476 480 5.426185 TCCACCCCGTAATATAAGAGTGTTT 59.574 40.000 0.00 0.00 0.00 2.83
477 481 4.964262 TCCACCCCGTAATATAAGAGTGTT 59.036 41.667 0.00 0.00 0.00 3.32
478 482 4.549668 TCCACCCCGTAATATAAGAGTGT 58.450 43.478 0.00 0.00 0.00 3.55
479 483 4.021368 CCTCCACCCCGTAATATAAGAGTG 60.021 50.000 0.00 0.00 0.00 3.51
480 484 4.158015 CCTCCACCCCGTAATATAAGAGT 58.842 47.826 0.00 0.00 0.00 3.24
481 485 3.514309 CCCTCCACCCCGTAATATAAGAG 59.486 52.174 0.00 0.00 0.00 2.85
482 486 3.142597 TCCCTCCACCCCGTAATATAAGA 59.857 47.826 0.00 0.00 0.00 2.10
483 487 3.513517 TCCCTCCACCCCGTAATATAAG 58.486 50.000 0.00 0.00 0.00 1.73
484 488 3.116629 ACTCCCTCCACCCCGTAATATAA 60.117 47.826 0.00 0.00 0.00 0.98
485 489 2.452047 ACTCCCTCCACCCCGTAATATA 59.548 50.000 0.00 0.00 0.00 0.86
486 490 1.222298 ACTCCCTCCACCCCGTAATAT 59.778 52.381 0.00 0.00 0.00 1.28
487 491 0.638292 ACTCCCTCCACCCCGTAATA 59.362 55.000 0.00 0.00 0.00 0.98
488 492 0.638292 TACTCCCTCCACCCCGTAAT 59.362 55.000 0.00 0.00 0.00 1.89
489 493 0.413037 TTACTCCCTCCACCCCGTAA 59.587 55.000 0.00 0.00 0.00 3.18
490 494 0.638292 ATTACTCCCTCCACCCCGTA 59.362 55.000 0.00 0.00 0.00 4.02
491 495 0.638292 TATTACTCCCTCCACCCCGT 59.362 55.000 0.00 0.00 0.00 5.28
492 496 2.025636 ATATTACTCCCTCCACCCCG 57.974 55.000 0.00 0.00 0.00 5.73
493 497 7.578458 TTTTATATATTACTCCCTCCACCCC 57.422 40.000 0.00 0.00 0.00 4.95
494 498 7.037514 AGCTTTTATATATTACTCCCTCCACCC 60.038 40.741 0.00 0.00 0.00 4.61
495 499 7.824779 CAGCTTTTATATATTACTCCCTCCACC 59.175 40.741 0.00 0.00 0.00 4.61
496 500 8.594550 TCAGCTTTTATATATTACTCCCTCCAC 58.405 37.037 0.00 0.00 0.00 4.02
497 501 8.736097 TCAGCTTTTATATATTACTCCCTCCA 57.264 34.615 0.00 0.00 0.00 3.86
578 582 7.308109 CCAGAGAGGCGATTAGTAGTACTAAAG 60.308 44.444 23.19 20.03 43.16 1.85
617 621 7.581011 ATTGCAAAATATTTTTCAGGACGAC 57.419 32.000 10.77 0.00 0.00 4.34
1184 1205 1.153745 CCTACGGAGTCAGCAGCAC 60.154 63.158 0.00 0.00 43.93 4.40
1519 1541 8.095452 TGGCATAAAAATTGGGGTTTATGTAT 57.905 30.769 16.26 0.00 44.28 2.29
1547 1569 4.260170 AGTTTCAGTTGAGATCTCATGGC 58.740 43.478 25.64 17.72 39.64 4.40
1585 1607 8.096414 CCCTTTCACTTCATTCAACCATTAATT 58.904 33.333 0.00 0.00 0.00 1.40
1592 1614 4.620982 CAACCCTTTCACTTCATTCAACC 58.379 43.478 0.00 0.00 0.00 3.77
1653 1675 4.523943 AGTGGAATAGCACAGAAAAATGCA 59.476 37.500 0.00 0.00 44.59 3.96
1719 1742 5.289595 GTTTCACACACATCTACTCAGACA 58.710 41.667 0.00 0.00 32.25 3.41
1803 1828 3.332919 CTGAGGGTGCACATATCATAGC 58.667 50.000 20.43 0.00 0.00 2.97
1813 1838 0.036732 TGTCATTCCTGAGGGTGCAC 59.963 55.000 8.80 8.80 30.18 4.57
1814 1839 0.994247 ATGTCATTCCTGAGGGTGCA 59.006 50.000 0.00 2.07 30.18 4.57
1823 1848 8.641498 AAAGAAGTGATAAACATGTCATTCCT 57.359 30.769 0.00 0.00 0.00 3.36
1837 1862 8.990163 AGGAAAGGTAAACAAAAGAAGTGATA 57.010 30.769 0.00 0.00 0.00 2.15
1845 1870 5.815222 CCCAACAAGGAAAGGTAAACAAAAG 59.185 40.000 0.00 0.00 41.22 2.27
1963 1988 8.450578 AGTCAAATGTGAGAAAAACATACTGA 57.549 30.769 0.00 0.00 37.27 3.41
1975 2000 2.705658 AGGTGTGGAGTCAAATGTGAGA 59.294 45.455 0.00 0.00 33.27 3.27
2262 2287 7.298507 TCAATTAGCGTTAGTTTCACCATAC 57.701 36.000 0.00 0.00 0.00 2.39
2323 2348 1.470112 GCAACTAGTTCCTCGAGCTCC 60.470 57.143 6.99 0.00 0.00 4.70
2512 2537 6.480320 GGTTCAATGAATCGCTAACTATGAGT 59.520 38.462 0.00 0.00 0.00 3.41
2515 2540 6.603237 TGGTTCAATGAATCGCTAACTATG 57.397 37.500 0.00 0.00 0.00 2.23
2866 2891 4.810790 ACTGATAACAGAACAAGGAGTCG 58.189 43.478 7.05 0.00 46.03 4.18
2965 2991 3.560068 CCTTAGTTCAAAACTGCGACACT 59.440 43.478 2.65 0.00 42.84 3.55
2966 2992 3.311596 ACCTTAGTTCAAAACTGCGACAC 59.688 43.478 2.65 0.00 42.84 3.67
3001 3027 7.831753 TCCAAAATAAGTGTCAACTTTGAACA 58.168 30.769 0.00 0.00 44.47 3.18
3044 3070 7.293402 TGAAATTTTTGAACAGCTTGTGAAG 57.707 32.000 0.00 0.00 0.00 3.02
3220 3254 6.186234 TGTAAATGTTCCCATCATGATGTCA 58.814 36.000 29.23 22.01 37.11 3.58
3587 3624 3.503748 CCCGAATCTGAGCAAGTTTCTTT 59.496 43.478 7.99 0.00 33.93 2.52
3791 3828 8.523915 TCATGCAAATGTAATAAACAGAGGAT 57.476 30.769 0.00 0.00 42.70 3.24
3939 3983 2.035321 CCTAGCTCTGGCAAGTAGTAGC 59.965 54.545 0.00 0.00 41.70 3.58
4029 4073 2.696707 CAAAGCATGTAGGGGCATTGAT 59.303 45.455 0.00 0.00 40.14 2.57
4072 4116 8.321353 TCAGATCAATTGTACTCTGTATTTGGT 58.679 33.333 22.65 0.00 37.12 3.67
4107 4151 7.149031 CGCATAATCTACAAATGCATTCACATG 60.149 37.037 13.38 9.80 44.95 3.21
4587 4631 3.554960 GGACATGGTCGATGCAGCTAATA 60.555 47.826 0.00 0.00 35.15 0.98
4723 4769 7.682981 GCACTTGGGAGATTTTAAGATCCAATC 60.683 40.741 2.48 0.00 33.15 2.67
4771 4817 5.816682 TCCTACACACTGATCACTAGAAGA 58.183 41.667 0.00 0.00 0.00 2.87
4965 5013 6.372659 GCCATACCAGTTCACCATAATATCTG 59.627 42.308 0.00 0.00 0.00 2.90
4997 5045 2.288457 GCAAAAGGCCAAGTTCCTCTTC 60.288 50.000 5.01 0.00 36.11 2.87
5110 5159 0.179026 CCTGCCTCCTGATGATGGTG 60.179 60.000 0.00 0.00 0.00 4.17
5112 5161 1.427809 TACCTGCCTCCTGATGATGG 58.572 55.000 0.00 0.00 0.00 3.51
5203 5252 1.379044 GAGGCACATTGGACCAGGG 60.379 63.158 0.00 0.00 0.00 4.45
5204 5253 0.679002 CAGAGGCACATTGGACCAGG 60.679 60.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.