Multiple sequence alignment - TraesCS3D01G149800

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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 TraesCS3D01G149800 chr3D 100.000 4619 0 0 1 4619 114491301 114495919 0.000000e+00 8530.0
1 TraesCS3D01G149800 chr3D 79.868 760 110 24 1285 2017 114226702 114225959 2.460000e-142 516.0
2 TraesCS3D01G149800 chr3D 85.526 304 30 7 972 1275 114229085 114228796 5.810000e-79 305.0
3 TraesCS3D01G149800 chr3B 93.793 3738 153 22 298 3974 166286084 166282365 0.000000e+00 5544.0
4 TraesCS3D01G149800 chr3A 95.198 1062 48 1 972 2033 110470986 110472044 0.000000e+00 1676.0
5 TraesCS3D01G149800 chr3A 87.558 643 72 2 1866 2500 110073400 110072758 0.000000e+00 737.0
6 TraesCS3D01G149800 chr3A 96.543 376 9 2 3349 3724 110472044 110472415 1.830000e-173 619.0
7 TraesCS3D01G149800 chr3A 81.948 698 95 20 1059 1736 110131104 110130418 3.120000e-156 562.0
8 TraesCS3D01G149800 chr3A 88.603 272 6 3 3724 3974 110472685 110472952 1.610000e-79 307.0
9 TraesCS3D01G149800 chr7D 94.590 647 32 3 3974 4619 264044317 264043673 0.000000e+00 998.0
10 TraesCS3D01G149800 chr7D 93.189 646 43 1 3975 4619 53291478 53292123 0.000000e+00 948.0
11 TraesCS3D01G149800 chr7D 81.065 169 29 3 1069 1236 511530340 511530506 1.040000e-26 132.0
12 TraesCS3D01G149800 chr7D 85.149 101 11 2 1141 1237 511534893 511534993 2.940000e-17 100.0
13 TraesCS3D01G149800 chr5D 94.118 646 34 4 3976 4619 29148141 29147498 0.000000e+00 979.0
14 TraesCS3D01G149800 chr5D 83.456 272 41 4 496 763 543670718 543670989 2.760000e-62 250.0
15 TraesCS3D01G149800 chr5D 83.273 275 41 5 496 765 536022335 536022061 9.920000e-62 248.0
16 TraesCS3D01G149800 chr5D 89.474 57 6 0 436 492 539958400 539958344 6.410000e-09 73.1
17 TraesCS3D01G149800 chr6B 93.653 646 39 2 3975 4619 574468279 574468923 0.000000e+00 965.0
18 TraesCS3D01G149800 chr2D 93.519 648 39 3 3973 4619 640517042 640517687 0.000000e+00 961.0
19 TraesCS3D01G149800 chr2D 93.199 647 41 2 3976 4619 298459386 298460032 0.000000e+00 948.0
20 TraesCS3D01G149800 chr4B 93.333 645 41 2 3975 4619 460747257 460747899 0.000000e+00 952.0
21 TraesCS3D01G149800 chr4B 93.323 644 41 2 3976 4618 585011219 585010577 0.000000e+00 950.0
22 TraesCS3D01G149800 chr4B 83.486 109 10 5 1 105 481690822 481690926 1.370000e-15 95.3
23 TraesCS3D01G149800 chr4B 90.164 61 6 0 433 493 145521366 145521306 3.830000e-11 80.5
24 TraesCS3D01G149800 chr1A 93.168 644 42 2 3976 4619 439691464 439692105 0.000000e+00 944.0
25 TraesCS3D01G149800 chr1A 85.507 69 9 1 1949 2016 279825889 279825957 2.310000e-08 71.3
26 TraesCS3D01G149800 chr7A 81.699 306 56 0 1822 2127 584038901 584039206 5.930000e-64 255.0
27 TraesCS3D01G149800 chr7A 81.985 272 45 4 496 763 190014026 190014297 1.290000e-55 228.0
28 TraesCS3D01G149800 chr7A 82.353 170 28 2 1069 1237 584038079 584038247 3.720000e-31 147.0
29 TraesCS3D01G149800 chr5B 82.609 276 42 5 496 765 482295337 482295612 5.970000e-59 239.0
30 TraesCS3D01G149800 chr5B 84.884 86 9 1 57 138 571845768 571845853 2.960000e-12 84.2
31 TraesCS3D01G149800 chr2A 82.482 274 44 4 494 763 78553956 78553683 2.150000e-58 237.0
32 TraesCS3D01G149800 chr2A 81.884 276 44 5 496 765 434579961 434580236 1.290000e-55 228.0
33 TraesCS3D01G149800 chr2A 75.140 358 53 18 64 394 197325386 197325038 8.060000e-28 135.0
34 TraesCS3D01G149800 chr1B 82.051 273 44 5 496 763 58567898 58568170 1.290000e-55 228.0
35 TraesCS3D01G149800 chr1B 81.985 272 45 4 496 763 601378806 601378535 1.290000e-55 228.0
36 TraesCS3D01G149800 chr1B 82.759 87 11 2 57 139 610025760 610025846 1.780000e-09 75.0
37 TraesCS3D01G149800 chr2B 75.493 355 54 19 64 393 624619166 624618820 4.820000e-30 143.0
38 TraesCS3D01G149800 chr4A 80.892 157 16 10 1 148 527518139 527517988 1.360000e-20 111.0
39 TraesCS3D01G149800 chr4A 93.878 49 3 0 57 105 647547924 647547876 1.780000e-09 75.0
40 TraesCS3D01G149800 chr1D 81.046 153 17 9 1 145 459026341 459026489 1.360000e-20 111.0
41 TraesCS3D01G149800 chr6A 75.966 233 39 12 1 224 239304319 239304543 2.270000e-18 104.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G149800 chr3D 114491301 114495919 4618 False 8530.000000 8530 100.000 1 4619 1 chr3D.!!$F1 4618
1 TraesCS3D01G149800 chr3D 114225959 114229085 3126 True 410.500000 516 82.697 972 2017 2 chr3D.!!$R1 1045
2 TraesCS3D01G149800 chr3B 166282365 166286084 3719 True 5544.000000 5544 93.793 298 3974 1 chr3B.!!$R1 3676
3 TraesCS3D01G149800 chr3A 110470986 110472952 1966 False 867.333333 1676 93.448 972 3974 3 chr3A.!!$F1 3002
4 TraesCS3D01G149800 chr3A 110072758 110073400 642 True 737.000000 737 87.558 1866 2500 1 chr3A.!!$R1 634
5 TraesCS3D01G149800 chr3A 110130418 110131104 686 True 562.000000 562 81.948 1059 1736 1 chr3A.!!$R2 677
6 TraesCS3D01G149800 chr7D 264043673 264044317 644 True 998.000000 998 94.590 3974 4619 1 chr7D.!!$R1 645
7 TraesCS3D01G149800 chr7D 53291478 53292123 645 False 948.000000 948 93.189 3975 4619 1 chr7D.!!$F1 644
8 TraesCS3D01G149800 chr5D 29147498 29148141 643 True 979.000000 979 94.118 3976 4619 1 chr5D.!!$R1 643
9 TraesCS3D01G149800 chr6B 574468279 574468923 644 False 965.000000 965 93.653 3975 4619 1 chr6B.!!$F1 644
10 TraesCS3D01G149800 chr2D 640517042 640517687 645 False 961.000000 961 93.519 3973 4619 1 chr2D.!!$F2 646
11 TraesCS3D01G149800 chr2D 298459386 298460032 646 False 948.000000 948 93.199 3976 4619 1 chr2D.!!$F1 643
12 TraesCS3D01G149800 chr4B 460747257 460747899 642 False 952.000000 952 93.333 3975 4619 1 chr4B.!!$F1 644
13 TraesCS3D01G149800 chr4B 585010577 585011219 642 True 950.000000 950 93.323 3976 4618 1 chr4B.!!$R2 642
14 TraesCS3D01G149800 chr1A 439691464 439692105 641 False 944.000000 944 93.168 3976 4619 1 chr1A.!!$F2 643
15 TraesCS3D01G149800 chr7A 584038079 584039206 1127 False 201.000000 255 82.026 1069 2127 2 chr7A.!!$F2 1058

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
281 282 0.034477 ACCCGGCTTACTCAAATGGG 60.034 55.000 0.00 0.0 41.06 4.00 F
851 884 0.323629 TCCTTCCGGCCAAGTTACTG 59.676 55.000 2.24 0.0 0.00 2.74 F
1506 3641 0.167470 TCGTCGAGCAAGACCGTAAG 59.833 55.000 6.08 0.0 37.85 2.34 F
1742 3883 0.461870 TCGATTGATCTTGGTGCCGG 60.462 55.000 0.00 0.0 0.00 6.13 F
2159 4362 1.747924 CAGTTCTCTCTCGGAGCATGA 59.252 52.381 0.00 0.0 41.60 3.07 F
2735 4941 2.561569 CGGTGTGAATCCCAAGGTATC 58.438 52.381 0.00 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 1294 0.108329 TCCTCAATTTCGTCCTCGGC 60.108 55.000 0.00 0.00 37.69 5.54 R
2664 4870 0.178953 AGGGCAGCAGAAATGGTTGT 60.179 50.000 0.00 0.00 0.00 3.32 R
3242 5449 0.322277 CCATCACAGCTGCACTTCCT 60.322 55.000 15.27 0.00 0.00 3.36 R
3404 5611 1.701545 GAAATCATCGCGGCGTCCAA 61.702 55.000 22.90 2.64 0.00 3.53 R
3472 5679 1.984297 GACTTGAAACTCGTAGCGACC 59.016 52.381 0.00 0.00 0.00 4.79 R
4176 6680 0.534877 TCGGATGGCGCTTGCATAAT 60.535 50.000 7.64 0.00 41.71 1.28 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
69 70 9.796120 AACAAAATTAAAGAAATCACGAGTTCA 57.204 25.926 9.61 0.00 37.82 3.18
70 71 9.233232 ACAAAATTAAAGAAATCACGAGTTCAC 57.767 29.630 9.61 0.00 37.82 3.18
71 72 9.232082 CAAAATTAAAGAAATCACGAGTTCACA 57.768 29.630 9.61 0.00 37.82 3.58
72 73 9.796120 AAAATTAAAGAAATCACGAGTTCACAA 57.204 25.926 9.61 1.57 37.82 3.33
73 74 9.796120 AAATTAAAGAAATCACGAGTTCACAAA 57.204 25.926 9.61 1.58 37.82 2.83
74 75 9.796120 AATTAAAGAAATCACGAGTTCACAAAA 57.204 25.926 9.61 0.08 37.82 2.44
75 76 8.609478 TTAAAGAAATCACGAGTTCACAAAAC 57.391 30.769 9.61 0.00 37.82 2.43
76 77 5.811399 AGAAATCACGAGTTCACAAAACA 57.189 34.783 9.61 0.00 37.82 2.83
77 78 6.189677 AGAAATCACGAGTTCACAAAACAA 57.810 33.333 9.61 0.00 37.82 2.83
78 79 6.258160 AGAAATCACGAGTTCACAAAACAAG 58.742 36.000 9.61 0.00 37.82 3.16
79 80 5.811399 AATCACGAGTTCACAAAACAAGA 57.189 34.783 0.00 0.00 0.00 3.02
80 81 6.377327 AATCACGAGTTCACAAAACAAGAT 57.623 33.333 0.00 0.00 0.00 2.40
81 82 5.403897 TCACGAGTTCACAAAACAAGATC 57.596 39.130 0.00 0.00 0.00 2.75
82 83 4.873259 TCACGAGTTCACAAAACAAGATCA 59.127 37.500 0.00 0.00 0.00 2.92
83 84 5.352846 TCACGAGTTCACAAAACAAGATCAA 59.647 36.000 0.00 0.00 0.00 2.57
84 85 5.452302 CACGAGTTCACAAAACAAGATCAAC 59.548 40.000 0.00 0.00 0.00 3.18
85 86 4.666176 CGAGTTCACAAAACAAGATCAACG 59.334 41.667 0.00 0.00 0.00 4.10
86 87 4.351192 AGTTCACAAAACAAGATCAACGC 58.649 39.130 0.00 0.00 0.00 4.84
87 88 4.101942 GTTCACAAAACAAGATCAACGCA 58.898 39.130 0.00 0.00 0.00 5.24
88 89 4.566545 TCACAAAACAAGATCAACGCAT 57.433 36.364 0.00 0.00 0.00 4.73
89 90 4.930963 TCACAAAACAAGATCAACGCATT 58.069 34.783 0.00 0.00 0.00 3.56
90 91 5.347342 TCACAAAACAAGATCAACGCATTT 58.653 33.333 0.00 0.00 0.00 2.32
91 92 6.499172 TCACAAAACAAGATCAACGCATTTA 58.501 32.000 0.00 0.00 0.00 1.40
92 93 6.975197 TCACAAAACAAGATCAACGCATTTAA 59.025 30.769 0.00 0.00 0.00 1.52
93 94 7.489435 TCACAAAACAAGATCAACGCATTTAAA 59.511 29.630 0.00 0.00 0.00 1.52
94 95 7.578736 CACAAAACAAGATCAACGCATTTAAAC 59.421 33.333 0.00 0.00 0.00 2.01
95 96 7.276658 ACAAAACAAGATCAACGCATTTAAACA 59.723 29.630 0.00 0.00 0.00 2.83
96 97 7.763172 AAACAAGATCAACGCATTTAAACAA 57.237 28.000 0.00 0.00 0.00 2.83
97 98 6.991485 ACAAGATCAACGCATTTAAACAAG 57.009 33.333 0.00 0.00 0.00 3.16
98 99 6.734137 ACAAGATCAACGCATTTAAACAAGA 58.266 32.000 0.00 0.00 0.00 3.02
99 100 7.370383 ACAAGATCAACGCATTTAAACAAGAT 58.630 30.769 0.00 0.00 0.00 2.40
100 101 7.538678 ACAAGATCAACGCATTTAAACAAGATC 59.461 33.333 0.00 0.00 0.00 2.75
101 102 6.250819 AGATCAACGCATTTAAACAAGATCG 58.749 36.000 0.00 0.00 35.69 3.69
102 103 5.351233 TCAACGCATTTAAACAAGATCGT 57.649 34.783 0.00 0.00 0.00 3.73
103 104 5.143660 TCAACGCATTTAAACAAGATCGTG 58.856 37.500 7.13 7.13 0.00 4.35
104 105 3.488489 ACGCATTTAAACAAGATCGTGC 58.512 40.909 8.68 0.00 0.00 5.34
105 106 2.521933 CGCATTTAAACAAGATCGTGCG 59.478 45.455 8.68 12.42 46.15 5.34
106 107 2.845967 GCATTTAAACAAGATCGTGCGG 59.154 45.455 8.68 0.00 0.00 5.69
107 108 3.425404 CATTTAAACAAGATCGTGCGGG 58.575 45.455 8.68 0.00 0.00 6.13
108 109 2.172851 TTAAACAAGATCGTGCGGGT 57.827 45.000 8.68 0.00 0.00 5.28
109 110 3.316071 TTAAACAAGATCGTGCGGGTA 57.684 42.857 8.68 0.00 0.00 3.69
110 111 2.172851 AAACAAGATCGTGCGGGTAA 57.827 45.000 8.68 0.00 0.00 2.85
111 112 1.722011 AACAAGATCGTGCGGGTAAG 58.278 50.000 8.68 0.00 0.00 2.34
112 113 0.606604 ACAAGATCGTGCGGGTAAGT 59.393 50.000 8.68 0.00 0.00 2.24
113 114 1.278238 CAAGATCGTGCGGGTAAGTC 58.722 55.000 0.00 0.00 0.00 3.01
114 115 0.892755 AAGATCGTGCGGGTAAGTCA 59.107 50.000 0.00 0.00 0.00 3.41
115 116 0.892755 AGATCGTGCGGGTAAGTCAA 59.107 50.000 0.00 0.00 0.00 3.18
116 117 1.135083 AGATCGTGCGGGTAAGTCAAG 60.135 52.381 0.00 0.00 0.00 3.02
117 118 0.892755 ATCGTGCGGGTAAGTCAAGA 59.107 50.000 0.00 0.00 0.00 3.02
118 119 0.242825 TCGTGCGGGTAAGTCAAGAG 59.757 55.000 0.00 0.00 0.00 2.85
119 120 0.038526 CGTGCGGGTAAGTCAAGAGT 60.039 55.000 0.00 0.00 0.00 3.24
120 121 1.200716 CGTGCGGGTAAGTCAAGAGTA 59.799 52.381 0.00 0.00 0.00 2.59
121 122 2.159282 CGTGCGGGTAAGTCAAGAGTAT 60.159 50.000 0.00 0.00 0.00 2.12
122 123 3.675228 CGTGCGGGTAAGTCAAGAGTATT 60.675 47.826 0.00 0.00 0.00 1.89
123 124 4.251268 GTGCGGGTAAGTCAAGAGTATTT 58.749 43.478 0.00 0.00 0.00 1.40
124 125 4.694037 GTGCGGGTAAGTCAAGAGTATTTT 59.306 41.667 0.00 0.00 0.00 1.82
125 126 4.693566 TGCGGGTAAGTCAAGAGTATTTTG 59.306 41.667 0.00 0.00 0.00 2.44
126 127 4.094442 GCGGGTAAGTCAAGAGTATTTTGG 59.906 45.833 0.00 0.00 0.00 3.28
127 128 4.634443 CGGGTAAGTCAAGAGTATTTTGGG 59.366 45.833 0.00 0.00 0.00 4.12
128 129 5.567430 GGGTAAGTCAAGAGTATTTTGGGT 58.433 41.667 0.00 0.00 0.00 4.51
129 130 5.646793 GGGTAAGTCAAGAGTATTTTGGGTC 59.353 44.000 0.00 0.00 0.00 4.46
130 131 5.350640 GGTAAGTCAAGAGTATTTTGGGTCG 59.649 44.000 0.00 0.00 0.00 4.79
131 132 4.884668 AGTCAAGAGTATTTTGGGTCGA 57.115 40.909 0.00 0.00 0.00 4.20
132 133 5.223449 AGTCAAGAGTATTTTGGGTCGAA 57.777 39.130 0.00 0.00 0.00 3.71
133 134 5.238583 AGTCAAGAGTATTTTGGGTCGAAG 58.761 41.667 0.00 0.00 0.00 3.79
134 135 4.000988 TCAAGAGTATTTTGGGTCGAAGC 58.999 43.478 0.00 0.00 0.00 3.86
135 136 3.983044 AGAGTATTTTGGGTCGAAGCT 57.017 42.857 0.00 0.00 0.00 3.74
136 137 5.046878 TCAAGAGTATTTTGGGTCGAAGCTA 60.047 40.000 0.00 0.00 0.00 3.32
137 138 5.012328 AGAGTATTTTGGGTCGAAGCTAG 57.988 43.478 0.00 0.00 0.00 3.42
138 139 3.532542 AGTATTTTGGGTCGAAGCTAGC 58.467 45.455 6.62 6.62 0.00 3.42
139 140 1.369625 ATTTTGGGTCGAAGCTAGCG 58.630 50.000 9.55 2.74 0.00 4.26
140 141 0.672401 TTTTGGGTCGAAGCTAGCGG 60.672 55.000 9.55 2.98 0.00 5.52
141 142 3.659089 TTGGGTCGAAGCTAGCGGC 62.659 63.158 9.55 6.97 42.19 6.53
160 161 2.973694 CTGCGTTAGCCTAGGGTAAA 57.026 50.000 30.13 16.85 44.33 2.01
161 162 2.822764 CTGCGTTAGCCTAGGGTAAAG 58.177 52.381 30.66 30.66 44.33 1.85
162 163 2.167900 CTGCGTTAGCCTAGGGTAAAGT 59.832 50.000 32.89 0.00 44.33 2.66
163 164 3.364549 TGCGTTAGCCTAGGGTAAAGTA 58.635 45.455 32.89 29.30 44.33 2.24
164 165 3.382546 TGCGTTAGCCTAGGGTAAAGTAG 59.617 47.826 32.89 24.37 44.33 2.57
165 166 3.382865 GCGTTAGCCTAGGGTAAAGTAGT 59.617 47.826 32.89 0.00 39.36 2.73
166 167 4.142071 GCGTTAGCCTAGGGTAAAGTAGTT 60.142 45.833 32.89 1.04 39.36 2.24
167 168 5.067805 GCGTTAGCCTAGGGTAAAGTAGTTA 59.932 44.000 32.89 12.83 39.36 2.24
168 169 6.405842 GCGTTAGCCTAGGGTAAAGTAGTTAA 60.406 42.308 32.89 13.68 39.36 2.01
169 170 7.685398 GCGTTAGCCTAGGGTAAAGTAGTTAAT 60.685 40.741 32.89 0.00 39.36 1.40
170 171 8.200120 CGTTAGCCTAGGGTAAAGTAGTTAATT 58.800 37.037 30.13 0.00 39.36 1.40
171 172 9.539825 GTTAGCCTAGGGTAAAGTAGTTAATTC 57.460 37.037 30.13 12.84 39.36 2.17
172 173 7.991647 AGCCTAGGGTAAAGTAGTTAATTCT 57.008 36.000 12.99 0.00 0.00 2.40
173 174 8.389979 AGCCTAGGGTAAAGTAGTTAATTCTT 57.610 34.615 12.99 0.00 0.00 2.52
174 175 8.833734 AGCCTAGGGTAAAGTAGTTAATTCTTT 58.166 33.333 12.99 0.00 35.86 2.52
175 176 9.458727 GCCTAGGGTAAAGTAGTTAATTCTTTT 57.541 33.333 11.72 0.00 34.09 2.27
234 235 9.542462 TTAGAAGGAATTAGTACACATGTATGC 57.458 33.333 0.00 0.00 32.54 3.14
235 236 7.796054 AGAAGGAATTAGTACACATGTATGCT 58.204 34.615 0.00 0.00 32.54 3.79
236 237 8.924303 AGAAGGAATTAGTACACATGTATGCTA 58.076 33.333 0.00 0.00 32.54 3.49
237 238 9.712305 GAAGGAATTAGTACACATGTATGCTAT 57.288 33.333 2.63 0.00 32.54 2.97
240 241 9.923143 GGAATTAGTACACATGTATGCTATACA 57.077 33.333 2.63 10.18 32.54 2.29
242 243 8.965986 ATTAGTACACATGTATGCTATACACG 57.034 34.615 2.63 6.14 32.54 4.49
243 244 5.769367 AGTACACATGTATGCTATACACGG 58.231 41.667 0.00 8.64 32.54 4.94
244 245 3.990092 ACACATGTATGCTATACACGGG 58.010 45.455 0.00 6.98 0.00 5.28
245 246 3.386726 ACACATGTATGCTATACACGGGT 59.613 43.478 0.00 0.00 0.00 5.28
246 247 4.585581 ACACATGTATGCTATACACGGGTA 59.414 41.667 0.00 0.00 24.39 3.69
247 248 5.245301 ACACATGTATGCTATACACGGGTAT 59.755 40.000 15.89 15.89 42.71 2.73
248 249 5.576774 CACATGTATGCTATACACGGGTATG 59.423 44.000 20.65 11.12 40.40 2.39
249 250 5.479027 ACATGTATGCTATACACGGGTATGA 59.521 40.000 20.65 4.61 40.40 2.15
250 251 5.638596 TGTATGCTATACACGGGTATGAG 57.361 43.478 20.65 13.68 40.40 2.90
251 252 5.074804 TGTATGCTATACACGGGTATGAGT 58.925 41.667 20.65 6.35 40.40 3.41
252 253 6.240145 TGTATGCTATACACGGGTATGAGTA 58.760 40.000 20.65 12.67 40.40 2.59
253 254 6.888088 TGTATGCTATACACGGGTATGAGTAT 59.112 38.462 20.65 17.73 40.40 2.12
254 255 6.852420 ATGCTATACACGGGTATGAGTATT 57.148 37.500 20.65 0.00 40.40 1.89
255 256 6.020971 TGCTATACACGGGTATGAGTATTG 57.979 41.667 20.65 0.00 40.40 1.90
256 257 4.863131 GCTATACACGGGTATGAGTATTGC 59.137 45.833 20.65 3.64 40.40 3.56
257 258 4.948341 ATACACGGGTATGAGTATTGCA 57.052 40.909 10.14 0.00 38.76 4.08
258 259 3.838244 ACACGGGTATGAGTATTGCAT 57.162 42.857 0.00 0.00 0.00 3.96
259 260 4.150897 ACACGGGTATGAGTATTGCATT 57.849 40.909 0.00 0.00 0.00 3.56
260 261 3.876914 ACACGGGTATGAGTATTGCATTG 59.123 43.478 0.00 0.00 0.00 2.82
261 262 3.876914 CACGGGTATGAGTATTGCATTGT 59.123 43.478 0.00 0.00 0.00 2.71
262 263 5.053811 CACGGGTATGAGTATTGCATTGTA 58.946 41.667 0.00 0.00 0.00 2.41
263 264 5.050363 CACGGGTATGAGTATTGCATTGTAC 60.050 44.000 0.00 0.00 0.00 2.90
264 265 4.451096 CGGGTATGAGTATTGCATTGTACC 59.549 45.833 0.00 0.00 0.00 3.34
265 266 4.760204 GGGTATGAGTATTGCATTGTACCC 59.240 45.833 10.31 10.31 35.83 3.69
266 267 4.451096 GGTATGAGTATTGCATTGTACCCG 59.549 45.833 0.00 0.00 0.00 5.28
267 268 2.912771 TGAGTATTGCATTGTACCCGG 58.087 47.619 0.00 0.00 0.00 5.73
268 269 1.602377 GAGTATTGCATTGTACCCGGC 59.398 52.381 0.00 0.00 0.00 6.13
269 270 1.211949 AGTATTGCATTGTACCCGGCT 59.788 47.619 0.00 0.00 0.00 5.52
270 271 2.021457 GTATTGCATTGTACCCGGCTT 58.979 47.619 0.00 0.00 0.00 4.35
271 272 2.428544 ATTGCATTGTACCCGGCTTA 57.571 45.000 0.00 0.00 0.00 3.09
272 273 1.455248 TTGCATTGTACCCGGCTTAC 58.545 50.000 0.00 0.00 0.00 2.34
273 274 0.616371 TGCATTGTACCCGGCTTACT 59.384 50.000 11.53 0.00 0.00 2.24
274 275 1.296727 GCATTGTACCCGGCTTACTC 58.703 55.000 11.53 0.00 0.00 2.59
275 276 1.406341 GCATTGTACCCGGCTTACTCA 60.406 52.381 11.53 1.33 0.00 3.41
276 277 2.937873 GCATTGTACCCGGCTTACTCAA 60.938 50.000 11.53 4.68 0.00 3.02
277 278 3.340034 CATTGTACCCGGCTTACTCAAA 58.660 45.455 11.53 0.80 0.00 2.69
278 279 3.706600 TTGTACCCGGCTTACTCAAAT 57.293 42.857 11.53 0.00 0.00 2.32
279 280 2.980568 TGTACCCGGCTTACTCAAATG 58.019 47.619 11.53 0.00 0.00 2.32
280 281 2.285977 GTACCCGGCTTACTCAAATGG 58.714 52.381 0.00 0.00 0.00 3.16
281 282 0.034477 ACCCGGCTTACTCAAATGGG 60.034 55.000 0.00 0.00 41.06 4.00
282 283 1.384222 CCCGGCTTACTCAAATGGGC 61.384 60.000 0.00 0.00 0.00 5.36
283 284 0.679640 CCGGCTTACTCAAATGGGCA 60.680 55.000 0.00 0.00 0.00 5.36
284 285 0.451783 CGGCTTACTCAAATGGGCAC 59.548 55.000 0.00 0.00 0.00 5.01
285 286 1.544724 GGCTTACTCAAATGGGCACA 58.455 50.000 0.00 0.00 0.00 4.57
286 287 2.102578 GGCTTACTCAAATGGGCACAT 58.897 47.619 0.00 0.00 39.54 3.21
355 356 6.544931 ACTTTCCTAATAGGATTTTTACCCGC 59.455 38.462 10.21 0.00 45.34 6.13
357 358 3.749609 CCTAATAGGATTTTTACCCGCCG 59.250 47.826 0.00 0.00 37.67 6.46
359 360 7.719761 CCTAATAGGATTTTTACCCGCCGGT 62.720 48.000 1.90 1.41 41.52 5.28
364 365 1.177895 TTTTTACCCGCCGGTTTCCC 61.178 55.000 1.90 0.00 40.58 3.97
374 375 2.516909 GGTTTCCCGGGTTGTGGA 59.483 61.111 22.86 0.00 0.00 4.02
377 378 1.456296 GTTTCCCGGGTTGTGGATAC 58.544 55.000 22.86 0.96 0.00 2.24
402 403 1.105759 GCCATGTTGAGGGGAGATGC 61.106 60.000 0.00 0.00 0.00 3.91
407 408 0.615331 GTTGAGGGGAGATGCTCACA 59.385 55.000 0.00 0.00 35.24 3.58
462 463 6.656693 CGCCCTCCATCTCAAAATATAAGATT 59.343 38.462 0.00 0.00 0.00 2.40
533 562 8.561212 AGTACAAACACAAACGCTCATATTTAA 58.439 29.630 0.00 0.00 0.00 1.52
534 563 7.851822 ACAAACACAAACGCTCATATTTAAG 57.148 32.000 0.00 0.00 0.00 1.85
547 576 6.102006 TCATATTTAAGCGCACACACTTAC 57.898 37.500 11.47 0.00 0.00 2.34
548 577 3.824414 ATTTAAGCGCACACACTTACC 57.176 42.857 11.47 0.00 0.00 2.85
549 578 2.536761 TTAAGCGCACACACTTACCT 57.463 45.000 11.47 0.00 0.00 3.08
554 583 3.021695 AGCGCACACACTTACCTCTATA 58.978 45.455 11.47 0.00 0.00 1.31
559 588 5.166398 GCACACACTTACCTCTATAAACGT 58.834 41.667 0.00 0.00 0.00 3.99
565 594 7.972277 CACACTTACCTCTATAAACGTACACAT 59.028 37.037 0.00 0.00 0.00 3.21
575 604 9.341078 TCTATAAACGTACACATATACACCTCA 57.659 33.333 0.00 0.00 0.00 3.86
583 612 5.972698 ACACATATACACCTCACCCCTATA 58.027 41.667 0.00 0.00 0.00 1.31
585 614 7.023120 ACACATATACACCTCACCCCTATAAT 58.977 38.462 0.00 0.00 0.00 1.28
604 633 2.949451 TCACCTTCGAGAGATTGAGC 57.051 50.000 0.00 0.00 41.60 4.26
606 635 0.457851 ACCTTCGAGAGATTGAGCCG 59.542 55.000 0.00 0.00 41.60 5.52
608 637 0.457851 CTTCGAGAGATTGAGCCGGT 59.542 55.000 1.90 0.00 41.60 5.28
613 642 4.079970 TCGAGAGATTGAGCCGGTATATT 58.920 43.478 1.90 0.00 33.31 1.28
616 645 7.052248 TCGAGAGATTGAGCCGGTATATTATA 58.948 38.462 1.90 0.00 33.31 0.98
619 648 9.469807 GAGAGATTGAGCCGGTATATTATATTG 57.530 37.037 1.90 0.00 0.00 1.90
648 677 4.700700 ACAAAGTTACCATAGGCGTATCC 58.299 43.478 0.00 0.00 0.00 2.59
659 688 3.290776 GCGTATCCTAGCCAACAGG 57.709 57.895 0.00 0.00 34.20 4.00
668 697 2.420687 CCTAGCCAACAGGAATGTCTCC 60.421 54.545 0.00 0.00 45.81 3.71
681 710 1.079750 GTCTCCTCCCACTGAACGC 60.080 63.158 0.00 0.00 0.00 4.84
708 737 5.816919 TCGCCGAAAATCCTGAAATAAATC 58.183 37.500 0.00 0.00 0.00 2.17
709 738 5.355630 TCGCCGAAAATCCTGAAATAAATCA 59.644 36.000 0.00 0.00 0.00 2.57
737 766 5.835113 ATGCGAGCACCATAATTTAAACT 57.165 34.783 0.00 0.00 0.00 2.66
741 770 5.064707 GCGAGCACCATAATTTAAACTCTGA 59.935 40.000 0.00 0.00 0.00 3.27
823 856 6.459066 CAAGGGAATAGATATCGTGTCATGT 58.541 40.000 0.00 0.00 0.00 3.21
838 871 3.244770 TGTCATGTGTAGGGTTTCCTTCC 60.245 47.826 0.00 0.00 41.56 3.46
851 884 0.323629 TCCTTCCGGCCAAGTTACTG 59.676 55.000 2.24 0.00 0.00 2.74
1054 1090 1.600511 TTGTCCTGATGGCGCTACGA 61.601 55.000 7.64 0.00 0.00 3.43
1055 1091 1.299468 GTCCTGATGGCGCTACGAG 60.299 63.158 7.64 0.00 0.00 4.18
1119 1155 1.515736 CGGTTTCTACGAGTCGGCC 60.516 63.158 18.30 7.79 0.00 6.13
1276 1327 4.041691 ACGAAATTGAGGAGGAAGAGGAAA 59.958 41.667 0.00 0.00 0.00 3.13
1277 1328 5.189180 CGAAATTGAGGAGGAAGAGGAAAT 58.811 41.667 0.00 0.00 0.00 2.17
1278 1329 5.295540 CGAAATTGAGGAGGAAGAGGAAATC 59.704 44.000 0.00 0.00 0.00 2.17
1486 3621 4.753662 TCCTCGGCGCTGTAGGGT 62.754 66.667 25.11 0.00 0.00 4.34
1489 3624 4.124351 TCGGCGCTGTAGGGTTCG 62.124 66.667 17.37 3.06 0.00 3.95
1506 3641 0.167470 TCGTCGAGCAAGACCGTAAG 59.833 55.000 6.08 0.00 37.85 2.34
1533 3668 3.723348 GGCGAGCCCGTGTTCAAC 61.723 66.667 1.97 0.00 38.24 3.18
1553 3688 3.942829 ACATCATGTCACCTACAACCAG 58.057 45.455 0.00 0.00 42.70 4.00
1604 3739 1.304381 GGCATCCCAAACCAGCAGA 60.304 57.895 0.00 0.00 0.00 4.26
1605 3740 1.318158 GGCATCCCAAACCAGCAGAG 61.318 60.000 0.00 0.00 0.00 3.35
1619 3754 1.220206 CAGAGCTGATGGGCGTCTT 59.780 57.895 0.00 0.00 37.29 3.01
1742 3883 0.461870 TCGATTGATCTTGGTGCCGG 60.462 55.000 0.00 0.00 0.00 6.13
1969 4164 2.150051 GGCTACTGCTATGGCCCCT 61.150 63.158 0.00 0.00 40.26 4.79
2159 4362 1.747924 CAGTTCTCTCTCGGAGCATGA 59.252 52.381 0.00 0.00 41.60 3.07
2405 4608 2.613977 GCACAGTTGAGCACCTCACTAT 60.614 50.000 0.00 0.00 40.46 2.12
2562 4768 5.280215 CCAAGAGTTCTATGTCAGGAAGGTT 60.280 44.000 0.00 0.00 0.00 3.50
2567 4773 7.400339 AGAGTTCTATGTCAGGAAGGTTAATGA 59.600 37.037 0.00 0.00 0.00 2.57
2568 4774 8.095452 AGTTCTATGTCAGGAAGGTTAATGAT 57.905 34.615 0.00 0.00 0.00 2.45
2577 4783 6.436847 TCAGGAAGGTTAATGATGCATTGAAA 59.563 34.615 0.00 0.00 35.54 2.69
2664 4870 6.166279 GTGTATCAGGATTCAAAGTGACTCA 58.834 40.000 0.00 0.00 28.82 3.41
2735 4941 2.561569 CGGTGTGAATCCCAAGGTATC 58.438 52.381 0.00 0.00 0.00 2.24
2790 4996 8.738645 AGAGGTTCAAATATGAGTATTTCCAC 57.261 34.615 0.00 0.00 38.21 4.02
2877 5083 4.635765 GCTGAGTGTAGCAATGGTGATAAA 59.364 41.667 0.00 0.00 43.17 1.40
2888 5094 4.989875 ATGGTGATAAAGATGAGGAGGG 57.010 45.455 0.00 0.00 0.00 4.30
3234 5441 4.695455 TCTTATGGCAGTAAACTTCTGTGC 59.305 41.667 0.00 0.00 35.60 4.57
3236 5443 3.762407 TGGCAGTAAACTTCTGTGCTA 57.238 42.857 0.00 0.00 35.60 3.49
3242 5449 6.100004 GCAGTAAACTTCTGTGCTATCTGTA 58.900 40.000 0.00 0.00 35.60 2.74
3311 5518 4.000988 TCTCTTTTTATGTTGAGGCCGAC 58.999 43.478 0.00 0.00 0.00 4.79
3315 5522 2.684001 TTATGTTGAGGCCGACGATT 57.316 45.000 0.00 0.00 0.00 3.34
3331 5538 7.201376 GGCCGACGATTTAATTTAACCTTTTTC 60.201 37.037 0.00 0.00 0.00 2.29
3472 5679 8.824159 AGATGTCCTAATTCAAACTATCATCG 57.176 34.615 0.00 0.00 34.92 3.84
3661 5868 0.999406 CCAAGTACGAGAATGGTGCG 59.001 55.000 0.00 0.00 34.09 5.34
3668 5875 1.749063 ACGAGAATGGTGCGTGAGATA 59.251 47.619 0.00 0.00 36.83 1.98
3674 5881 3.758755 ATGGTGCGTGAGATATGTGAT 57.241 42.857 0.00 0.00 0.00 3.06
3675 5882 4.871933 ATGGTGCGTGAGATATGTGATA 57.128 40.909 0.00 0.00 0.00 2.15
3676 5883 3.977427 TGGTGCGTGAGATATGTGATAC 58.023 45.455 0.00 0.00 0.00 2.24
3768 6244 9.658799 TCAACCTTTCACTAGATTTGATAGAAG 57.341 33.333 0.00 0.00 0.00 2.85
3773 6249 7.749377 TTCACTAGATTTGATAGAAGGGGAA 57.251 36.000 0.00 0.00 0.00 3.97
3903 6401 1.238439 AACAATGTCGGACAAGCAGG 58.762 50.000 15.72 5.73 0.00 4.85
4043 6543 5.350633 TGCATGCAGCCATCTTATTAAAAC 58.649 37.500 18.46 0.00 44.83 2.43
4062 6563 5.356882 AAACACCACAAAGTATCGTCATG 57.643 39.130 0.00 0.00 0.00 3.07
4098 6599 1.758783 CAAACGGAGCAGAACAAAGC 58.241 50.000 0.00 0.00 0.00 3.51
4099 6600 0.307760 AAACGGAGCAGAACAAAGCG 59.692 50.000 0.00 0.00 35.48 4.68
4176 6680 3.889482 AGCTCCCTAGACTCCTATCCTA 58.111 50.000 0.00 0.00 0.00 2.94
4341 6846 4.097892 ACCTGCAAGAAAGTTAAAGTGTGG 59.902 41.667 0.00 0.00 34.07 4.17
4414 6919 7.844493 AGTGCACATATTCCAATCCAAATAT 57.156 32.000 21.04 0.00 0.00 1.28
4613 7118 4.263594 ACTTCCTACCCATCGCCTTTTAAA 60.264 41.667 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.796120 TGAACTCGTGATTTCTTTAATTTTGTT 57.204 25.926 0.00 0.00 0.00 2.83
44 45 9.233232 GTGAACTCGTGATTTCTTTAATTTTGT 57.767 29.630 0.00 0.00 0.00 2.83
45 46 9.232082 TGTGAACTCGTGATTTCTTTAATTTTG 57.768 29.630 0.00 0.00 0.00 2.44
46 47 9.796120 TTGTGAACTCGTGATTTCTTTAATTTT 57.204 25.926 0.00 0.00 0.00 1.82
47 48 9.796120 TTTGTGAACTCGTGATTTCTTTAATTT 57.204 25.926 0.00 0.00 0.00 1.82
48 49 9.796120 TTTTGTGAACTCGTGATTTCTTTAATT 57.204 25.926 0.00 0.00 0.00 1.40
49 50 9.233232 GTTTTGTGAACTCGTGATTTCTTTAAT 57.767 29.630 0.00 0.00 0.00 1.40
50 51 8.237949 TGTTTTGTGAACTCGTGATTTCTTTAA 58.762 29.630 0.00 0.00 0.00 1.52
51 52 7.753659 TGTTTTGTGAACTCGTGATTTCTTTA 58.246 30.769 0.00 0.00 0.00 1.85
52 53 6.616947 TGTTTTGTGAACTCGTGATTTCTTT 58.383 32.000 0.00 0.00 0.00 2.52
53 54 6.189677 TGTTTTGTGAACTCGTGATTTCTT 57.810 33.333 0.00 0.00 0.00 2.52
54 55 5.811399 TGTTTTGTGAACTCGTGATTTCT 57.189 34.783 0.00 0.00 0.00 2.52
55 56 6.255215 TCTTGTTTTGTGAACTCGTGATTTC 58.745 36.000 0.00 0.00 0.00 2.17
56 57 6.189677 TCTTGTTTTGTGAACTCGTGATTT 57.810 33.333 0.00 0.00 0.00 2.17
57 58 5.811399 TCTTGTTTTGTGAACTCGTGATT 57.189 34.783 0.00 0.00 0.00 2.57
58 59 5.527214 TGATCTTGTTTTGTGAACTCGTGAT 59.473 36.000 0.00 0.00 0.00 3.06
59 60 4.873259 TGATCTTGTTTTGTGAACTCGTGA 59.127 37.500 0.00 0.00 0.00 4.35
60 61 5.155509 TGATCTTGTTTTGTGAACTCGTG 57.844 39.130 0.00 0.00 0.00 4.35
61 62 5.569413 GTTGATCTTGTTTTGTGAACTCGT 58.431 37.500 0.00 0.00 0.00 4.18
62 63 4.666176 CGTTGATCTTGTTTTGTGAACTCG 59.334 41.667 0.00 0.00 0.00 4.18
63 64 4.437820 GCGTTGATCTTGTTTTGTGAACTC 59.562 41.667 0.00 0.00 0.00 3.01
64 65 4.142491 TGCGTTGATCTTGTTTTGTGAACT 60.142 37.500 0.00 0.00 0.00 3.01
65 66 4.101942 TGCGTTGATCTTGTTTTGTGAAC 58.898 39.130 0.00 0.00 0.00 3.18
66 67 4.362932 TGCGTTGATCTTGTTTTGTGAA 57.637 36.364 0.00 0.00 0.00 3.18
67 68 4.566545 ATGCGTTGATCTTGTTTTGTGA 57.433 36.364 0.00 0.00 0.00 3.58
68 69 5.640218 AAATGCGTTGATCTTGTTTTGTG 57.360 34.783 0.00 0.00 0.00 3.33
69 70 7.276658 TGTTTAAATGCGTTGATCTTGTTTTGT 59.723 29.630 0.00 0.00 0.00 2.83
70 71 7.616673 TGTTTAAATGCGTTGATCTTGTTTTG 58.383 30.769 0.00 0.00 0.00 2.44
71 72 7.763172 TGTTTAAATGCGTTGATCTTGTTTT 57.237 28.000 0.00 0.00 0.00 2.43
72 73 7.704472 TCTTGTTTAAATGCGTTGATCTTGTTT 59.296 29.630 0.00 0.00 0.00 2.83
73 74 7.199766 TCTTGTTTAAATGCGTTGATCTTGTT 58.800 30.769 0.00 0.00 0.00 2.83
74 75 6.734137 TCTTGTTTAAATGCGTTGATCTTGT 58.266 32.000 0.00 0.00 0.00 3.16
75 76 7.253092 CGATCTTGTTTAAATGCGTTGATCTTG 60.253 37.037 9.77 0.00 0.00 3.02
76 77 6.742718 CGATCTTGTTTAAATGCGTTGATCTT 59.257 34.615 9.77 0.00 0.00 2.40
77 78 6.128282 ACGATCTTGTTTAAATGCGTTGATCT 60.128 34.615 9.77 0.00 0.00 2.75
78 79 6.021596 ACGATCTTGTTTAAATGCGTTGATC 58.978 36.000 0.00 0.00 0.00 2.92
79 80 5.794945 CACGATCTTGTTTAAATGCGTTGAT 59.205 36.000 0.00 0.00 0.00 2.57
80 81 5.143660 CACGATCTTGTTTAAATGCGTTGA 58.856 37.500 0.00 0.00 0.00 3.18
81 82 4.201391 GCACGATCTTGTTTAAATGCGTTG 60.201 41.667 0.73 0.00 0.00 4.10
82 83 3.911964 GCACGATCTTGTTTAAATGCGTT 59.088 39.130 0.73 0.00 0.00 4.84
83 84 3.488489 GCACGATCTTGTTTAAATGCGT 58.512 40.909 0.73 0.00 0.00 5.24
85 86 2.845967 CCGCACGATCTTGTTTAAATGC 59.154 45.455 0.73 0.00 0.00 3.56
86 87 3.119990 ACCCGCACGATCTTGTTTAAATG 60.120 43.478 0.73 0.00 0.00 2.32
87 88 3.078837 ACCCGCACGATCTTGTTTAAAT 58.921 40.909 0.73 0.00 0.00 1.40
88 89 2.496111 ACCCGCACGATCTTGTTTAAA 58.504 42.857 0.73 0.00 0.00 1.52
89 90 2.172851 ACCCGCACGATCTTGTTTAA 57.827 45.000 0.73 0.00 0.00 1.52
90 91 3.255725 CTTACCCGCACGATCTTGTTTA 58.744 45.455 0.73 0.00 0.00 2.01
91 92 2.073816 CTTACCCGCACGATCTTGTTT 58.926 47.619 0.73 0.00 0.00 2.83
92 93 1.001633 ACTTACCCGCACGATCTTGTT 59.998 47.619 0.73 0.00 0.00 2.83
93 94 0.606604 ACTTACCCGCACGATCTTGT 59.393 50.000 0.73 0.00 0.00 3.16
94 95 1.278238 GACTTACCCGCACGATCTTG 58.722 55.000 0.00 0.00 0.00 3.02
95 96 0.892755 TGACTTACCCGCACGATCTT 59.107 50.000 0.00 0.00 0.00 2.40
96 97 0.892755 TTGACTTACCCGCACGATCT 59.107 50.000 0.00 0.00 0.00 2.75
97 98 1.135199 TCTTGACTTACCCGCACGATC 60.135 52.381 0.00 0.00 0.00 3.69
98 99 0.892755 TCTTGACTTACCCGCACGAT 59.107 50.000 0.00 0.00 0.00 3.73
99 100 0.242825 CTCTTGACTTACCCGCACGA 59.757 55.000 0.00 0.00 0.00 4.35
100 101 0.038526 ACTCTTGACTTACCCGCACG 60.039 55.000 0.00 0.00 0.00 5.34
101 102 3.521947 ATACTCTTGACTTACCCGCAC 57.478 47.619 0.00 0.00 0.00 5.34
102 103 4.546829 AAATACTCTTGACTTACCCGCA 57.453 40.909 0.00 0.00 0.00 5.69
103 104 4.094442 CCAAAATACTCTTGACTTACCCGC 59.906 45.833 0.00 0.00 0.00 6.13
104 105 4.634443 CCCAAAATACTCTTGACTTACCCG 59.366 45.833 0.00 0.00 0.00 5.28
105 106 5.567430 ACCCAAAATACTCTTGACTTACCC 58.433 41.667 0.00 0.00 0.00 3.69
106 107 5.350640 CGACCCAAAATACTCTTGACTTACC 59.649 44.000 0.00 0.00 0.00 2.85
107 108 6.161381 TCGACCCAAAATACTCTTGACTTAC 58.839 40.000 0.00 0.00 0.00 2.34
108 109 6.349243 TCGACCCAAAATACTCTTGACTTA 57.651 37.500 0.00 0.00 0.00 2.24
109 110 5.223449 TCGACCCAAAATACTCTTGACTT 57.777 39.130 0.00 0.00 0.00 3.01
110 111 4.884668 TCGACCCAAAATACTCTTGACT 57.115 40.909 0.00 0.00 0.00 3.41
111 112 4.142881 GCTTCGACCCAAAATACTCTTGAC 60.143 45.833 0.00 0.00 0.00 3.18
112 113 4.000988 GCTTCGACCCAAAATACTCTTGA 58.999 43.478 0.00 0.00 0.00 3.02
113 114 4.003648 AGCTTCGACCCAAAATACTCTTG 58.996 43.478 0.00 0.00 0.00 3.02
114 115 4.287766 AGCTTCGACCCAAAATACTCTT 57.712 40.909 0.00 0.00 0.00 2.85
115 116 3.983044 AGCTTCGACCCAAAATACTCT 57.017 42.857 0.00 0.00 0.00 3.24
116 117 3.556365 GCTAGCTTCGACCCAAAATACTC 59.444 47.826 7.70 0.00 0.00 2.59
117 118 3.532542 GCTAGCTTCGACCCAAAATACT 58.467 45.455 7.70 0.00 0.00 2.12
118 119 2.284417 CGCTAGCTTCGACCCAAAATAC 59.716 50.000 13.93 0.00 0.00 1.89
119 120 2.546778 CGCTAGCTTCGACCCAAAATA 58.453 47.619 13.93 0.00 0.00 1.40
120 121 1.369625 CGCTAGCTTCGACCCAAAAT 58.630 50.000 13.93 0.00 0.00 1.82
121 122 0.672401 CCGCTAGCTTCGACCCAAAA 60.672 55.000 13.93 0.00 0.00 2.44
122 123 1.079405 CCGCTAGCTTCGACCCAAA 60.079 57.895 13.93 0.00 0.00 3.28
123 124 2.577059 CCGCTAGCTTCGACCCAA 59.423 61.111 13.93 0.00 0.00 4.12
124 125 4.143333 GCCGCTAGCTTCGACCCA 62.143 66.667 13.93 0.00 38.99 4.51
141 142 2.167900 ACTTTACCCTAGGCTAACGCAG 59.832 50.000 2.05 0.00 38.10 5.18
142 143 2.181975 ACTTTACCCTAGGCTAACGCA 58.818 47.619 2.05 0.00 38.10 5.24
143 144 2.975732 ACTTTACCCTAGGCTAACGC 57.024 50.000 2.05 0.00 0.00 4.84
144 145 5.588958 AACTACTTTACCCTAGGCTAACG 57.411 43.478 2.05 0.77 0.00 3.18
145 146 9.539825 GAATTAACTACTTTACCCTAGGCTAAC 57.460 37.037 2.05 0.00 0.00 2.34
146 147 9.498039 AGAATTAACTACTTTACCCTAGGCTAA 57.502 33.333 2.05 0.00 0.00 3.09
147 148 9.498039 AAGAATTAACTACTTTACCCTAGGCTA 57.502 33.333 2.05 0.00 0.00 3.93
148 149 7.991647 AGAATTAACTACTTTACCCTAGGCT 57.008 36.000 2.05 0.00 0.00 4.58
149 150 9.458727 AAAAGAATTAACTACTTTACCCTAGGC 57.541 33.333 2.05 0.00 34.18 3.93
175 176 9.817809 GGTCTTATCTGTCATTCAGTAAATGTA 57.182 33.333 0.00 0.00 44.36 2.29
176 177 8.543774 AGGTCTTATCTGTCATTCAGTAAATGT 58.456 33.333 0.00 0.00 44.36 2.71
177 178 8.954950 AGGTCTTATCTGTCATTCAGTAAATG 57.045 34.615 0.00 0.00 45.22 2.32
179 180 9.871238 GTTAGGTCTTATCTGTCATTCAGTAAA 57.129 33.333 0.00 0.00 43.97 2.01
180 181 9.256228 AGTTAGGTCTTATCTGTCATTCAGTAA 57.744 33.333 0.00 0.00 43.97 2.24
181 182 8.824756 AGTTAGGTCTTATCTGTCATTCAGTA 57.175 34.615 0.00 0.00 43.97 2.74
182 183 7.726033 AGTTAGGTCTTATCTGTCATTCAGT 57.274 36.000 0.00 0.00 43.97 3.41
208 209 9.542462 GCATACATGTGTACTAATTCCTTCTAA 57.458 33.333 9.11 0.00 32.72 2.10
209 210 8.924303 AGCATACATGTGTACTAATTCCTTCTA 58.076 33.333 9.11 0.00 32.72 2.10
210 211 7.796054 AGCATACATGTGTACTAATTCCTTCT 58.204 34.615 9.11 0.00 32.72 2.85
211 212 9.712305 ATAGCATACATGTGTACTAATTCCTTC 57.288 33.333 9.11 0.00 32.72 3.46
214 215 9.923143 TGTATAGCATACATGTGTACTAATTCC 57.077 33.333 9.11 0.00 32.72 3.01
216 217 9.406828 CGTGTATAGCATACATGTGTACTAATT 57.593 33.333 9.11 0.00 32.72 1.40
217 218 8.027189 CCGTGTATAGCATACATGTGTACTAAT 58.973 37.037 9.11 0.24 33.76 1.73
218 219 7.364970 CCGTGTATAGCATACATGTGTACTAA 58.635 38.462 9.11 0.00 33.76 2.24
219 220 6.072342 CCCGTGTATAGCATACATGTGTACTA 60.072 42.308 9.11 6.82 33.76 1.82
220 221 5.278808 CCCGTGTATAGCATACATGTGTACT 60.279 44.000 9.11 4.38 33.76 2.73
221 222 4.921515 CCCGTGTATAGCATACATGTGTAC 59.078 45.833 9.11 0.00 33.76 2.90
222 223 4.585581 ACCCGTGTATAGCATACATGTGTA 59.414 41.667 9.11 0.00 33.76 2.90
223 224 3.386726 ACCCGTGTATAGCATACATGTGT 59.613 43.478 9.11 14.22 33.76 3.72
224 225 3.990092 ACCCGTGTATAGCATACATGTG 58.010 45.455 9.11 13.79 33.76 3.21
225 226 5.479027 TCATACCCGTGTATAGCATACATGT 59.521 40.000 18.75 2.69 35.89 3.21
226 227 5.961272 TCATACCCGTGTATAGCATACATG 58.039 41.667 15.76 15.76 35.89 3.21
227 228 5.715279 ACTCATACCCGTGTATAGCATACAT 59.285 40.000 10.74 1.05 35.89 2.29
228 229 5.074804 ACTCATACCCGTGTATAGCATACA 58.925 41.667 5.28 5.28 35.89 2.29
229 230 5.640189 ACTCATACCCGTGTATAGCATAC 57.360 43.478 0.00 0.00 35.89 2.39
230 231 7.629866 GCAATACTCATACCCGTGTATAGCATA 60.630 40.741 0.00 0.00 35.89 3.14
231 232 6.631016 CAATACTCATACCCGTGTATAGCAT 58.369 40.000 0.00 0.00 35.89 3.79
232 233 5.566032 GCAATACTCATACCCGTGTATAGCA 60.566 44.000 0.00 0.00 35.89 3.49
233 234 4.863131 GCAATACTCATACCCGTGTATAGC 59.137 45.833 0.00 0.00 35.89 2.97
234 235 6.020971 TGCAATACTCATACCCGTGTATAG 57.979 41.667 0.00 0.00 35.89 1.31
235 236 6.599356 ATGCAATACTCATACCCGTGTATA 57.401 37.500 0.00 0.00 35.89 1.47
236 237 4.948341 TGCAATACTCATACCCGTGTAT 57.052 40.909 0.00 0.00 38.21 2.29
237 238 4.948341 ATGCAATACTCATACCCGTGTA 57.052 40.909 0.00 0.00 0.00 2.90
238 239 3.838244 ATGCAATACTCATACCCGTGT 57.162 42.857 0.00 0.00 0.00 4.49
239 240 3.876914 ACAATGCAATACTCATACCCGTG 59.123 43.478 0.00 0.00 0.00 4.94
240 241 4.150897 ACAATGCAATACTCATACCCGT 57.849 40.909 0.00 0.00 0.00 5.28
241 242 4.451096 GGTACAATGCAATACTCATACCCG 59.549 45.833 0.00 0.00 0.00 5.28
242 243 4.760204 GGGTACAATGCAATACTCATACCC 59.240 45.833 11.56 11.56 34.76 3.69
243 244 4.451096 CGGGTACAATGCAATACTCATACC 59.549 45.833 0.00 0.00 0.00 2.73
244 245 4.451096 CCGGGTACAATGCAATACTCATAC 59.549 45.833 0.00 0.00 0.00 2.39
245 246 4.637276 CCGGGTACAATGCAATACTCATA 58.363 43.478 0.00 0.00 0.00 2.15
246 247 3.476552 CCGGGTACAATGCAATACTCAT 58.523 45.455 0.00 0.00 0.00 2.90
247 248 2.912771 CCGGGTACAATGCAATACTCA 58.087 47.619 0.00 0.00 0.00 3.41
248 249 1.602377 GCCGGGTACAATGCAATACTC 59.398 52.381 2.18 0.00 0.00 2.59
249 250 1.211949 AGCCGGGTACAATGCAATACT 59.788 47.619 3.10 0.00 0.00 2.12
250 251 1.675552 AGCCGGGTACAATGCAATAC 58.324 50.000 3.10 0.00 0.00 1.89
251 252 2.428544 AAGCCGGGTACAATGCAATA 57.571 45.000 6.57 0.00 0.00 1.90
252 253 2.021457 GTAAGCCGGGTACAATGCAAT 58.979 47.619 6.57 0.00 0.00 3.56
253 254 1.003812 AGTAAGCCGGGTACAATGCAA 59.996 47.619 6.57 0.00 0.00 4.08
254 255 0.616371 AGTAAGCCGGGTACAATGCA 59.384 50.000 6.57 0.00 0.00 3.96
255 256 1.296727 GAGTAAGCCGGGTACAATGC 58.703 55.000 6.57 0.00 0.00 3.56
256 257 2.684001 TGAGTAAGCCGGGTACAATG 57.316 50.000 6.57 0.00 0.00 2.82
257 258 3.706600 TTTGAGTAAGCCGGGTACAAT 57.293 42.857 6.57 0.00 0.00 2.71
258 259 3.340034 CATTTGAGTAAGCCGGGTACAA 58.660 45.455 6.57 8.88 0.00 2.41
259 260 2.355310 CCATTTGAGTAAGCCGGGTACA 60.355 50.000 6.57 2.40 0.00 2.90
260 261 2.285977 CCATTTGAGTAAGCCGGGTAC 58.714 52.381 6.57 5.84 0.00 3.34
261 262 1.210967 CCCATTTGAGTAAGCCGGGTA 59.789 52.381 6.57 0.00 0.00 3.69
262 263 0.034477 CCCATTTGAGTAAGCCGGGT 60.034 55.000 0.00 0.00 0.00 5.28
263 264 1.384222 GCCCATTTGAGTAAGCCGGG 61.384 60.000 2.18 0.00 35.18 5.73
264 265 0.679640 TGCCCATTTGAGTAAGCCGG 60.680 55.000 0.00 0.00 0.00 6.13
265 266 0.451783 GTGCCCATTTGAGTAAGCCG 59.548 55.000 0.00 0.00 0.00 5.52
266 267 1.544724 TGTGCCCATTTGAGTAAGCC 58.455 50.000 0.00 0.00 0.00 4.35
267 268 3.874392 AATGTGCCCATTTGAGTAAGC 57.126 42.857 0.00 0.00 38.10 3.09
357 358 5.775222 ATGTATCCACAACCCGGGAAACC 62.775 52.174 32.02 5.07 42.75 3.27
359 360 1.065647 TGTATCCACAACCCGGGAAA 58.934 50.000 32.02 5.53 36.62 3.13
364 365 2.552315 GGCAATATGTATCCACAACCCG 59.448 50.000 0.00 0.00 38.42 5.28
365 366 3.561143 TGGCAATATGTATCCACAACCC 58.439 45.455 0.00 0.00 38.42 4.11
374 375 4.106179 TCCCCTCAACATGGCAATATGTAT 59.894 41.667 0.00 0.00 40.24 2.29
377 378 2.889045 CTCCCCTCAACATGGCAATATG 59.111 50.000 0.00 0.00 0.00 1.78
379 380 2.204463 TCTCCCCTCAACATGGCAATA 58.796 47.619 0.00 0.00 0.00 1.90
402 403 1.654220 CAGGCCGGTGTTTTGTGAG 59.346 57.895 1.90 0.00 0.00 3.51
426 427 3.821033 AGATGGAGGGCGTATTATTTTGC 59.179 43.478 0.00 0.00 0.00 3.68
510 539 6.362283 GCTTAAATATGAGCGTTTGTGTTTGT 59.638 34.615 0.00 0.00 0.00 2.83
533 562 1.254026 TAGAGGTAAGTGTGTGCGCT 58.746 50.000 9.73 0.00 36.97 5.92
534 563 2.295253 ATAGAGGTAAGTGTGTGCGC 57.705 50.000 0.00 0.00 0.00 6.09
547 576 8.790718 AGGTGTATATGTGTACGTTTATAGAGG 58.209 37.037 0.00 0.00 0.00 3.69
548 577 9.823098 GAGGTGTATATGTGTACGTTTATAGAG 57.177 37.037 0.00 0.00 0.00 2.43
549 578 9.341078 TGAGGTGTATATGTGTACGTTTATAGA 57.659 33.333 0.00 0.00 0.00 1.98
554 583 5.413499 GGTGAGGTGTATATGTGTACGTTT 58.587 41.667 0.00 0.00 0.00 3.60
559 588 4.274794 AGGGGTGAGGTGTATATGTGTA 57.725 45.455 0.00 0.00 0.00 2.90
565 594 6.021030 GGTGATTATAGGGGTGAGGTGTATA 58.979 44.000 0.00 0.00 0.00 1.47
575 604 4.140994 TCTCTCGAAGGTGATTATAGGGGT 60.141 45.833 0.00 0.00 0.00 4.95
583 612 3.431486 GGCTCAATCTCTCGAAGGTGATT 60.431 47.826 0.00 0.00 0.00 2.57
585 614 1.478510 GGCTCAATCTCTCGAAGGTGA 59.521 52.381 0.00 0.00 0.00 4.02
616 645 8.903820 GCCTATGGTAACTTTGTAAATCTCAAT 58.096 33.333 0.00 0.00 37.61 2.57
619 648 6.537660 ACGCCTATGGTAACTTTGTAAATCTC 59.462 38.462 0.00 0.00 37.61 2.75
648 677 2.911484 GGAGACATTCCTGTTGGCTAG 58.089 52.381 0.00 0.00 43.16 3.42
659 688 2.675317 CGTTCAGTGGGAGGAGACATTC 60.675 54.545 0.00 0.00 0.00 2.67
668 697 2.434884 ATGCGCGTTCAGTGGGAG 60.435 61.111 8.43 0.00 0.00 4.30
669 698 2.434185 GATGCGCGTTCAGTGGGA 60.434 61.111 8.43 0.00 0.00 4.37
670 699 3.853330 CGATGCGCGTTCAGTGGG 61.853 66.667 8.43 0.00 34.64 4.61
671 700 4.505217 GCGATGCGCGTTCAGTGG 62.505 66.667 8.43 0.00 44.55 4.00
681 710 1.010797 CAGGATTTTCGGCGATGCG 60.011 57.895 11.76 0.00 0.00 4.73
724 753 6.547141 TCAGCCCATCAGAGTTTAAATTATGG 59.453 38.462 5.62 5.11 33.67 2.74
728 757 5.819991 TCTCAGCCCATCAGAGTTTAAATT 58.180 37.500 0.00 0.00 31.08 1.82
733 762 3.135530 GGTATCTCAGCCCATCAGAGTTT 59.864 47.826 0.00 0.00 31.08 2.66
734 763 2.703007 GGTATCTCAGCCCATCAGAGTT 59.297 50.000 0.00 0.00 31.08 3.01
737 766 2.042464 GTGGTATCTCAGCCCATCAGA 58.958 52.381 0.00 0.00 0.00 3.27
741 770 1.765314 GACAGTGGTATCTCAGCCCAT 59.235 52.381 0.00 0.00 0.00 4.00
791 824 2.691409 TCTATTCCCTTGGTCGCAAG 57.309 50.000 0.00 0.00 0.00 4.01
838 871 5.379732 TTTATTTTCCAGTAACTTGGCCG 57.620 39.130 0.00 0.00 38.16 6.13
870 903 1.268692 TGGCCGCGATTACTAACTACG 60.269 52.381 8.23 0.00 0.00 3.51
871 904 2.122564 GTGGCCGCGATTACTAACTAC 58.877 52.381 8.23 0.00 0.00 2.73
966 1002 1.194781 TTGCTCTTTCTCTCCGGCCT 61.195 55.000 0.00 0.00 0.00 5.19
969 1005 1.719600 CACTTGCTCTTTCTCTCCGG 58.280 55.000 0.00 0.00 0.00 5.14
1054 1090 1.477295 GTCCTGCCTAACGCTCTTACT 59.523 52.381 0.00 0.00 38.78 2.24
1055 1091 1.203994 TGTCCTGCCTAACGCTCTTAC 59.796 52.381 0.00 0.00 38.78 2.34
1246 1294 0.108329 TCCTCAATTTCGTCCTCGGC 60.108 55.000 0.00 0.00 37.69 5.54
1276 1327 4.837860 GGTCCTCACCTTAGAGATGATGAT 59.162 45.833 0.00 0.00 40.00 2.45
1277 1328 4.219115 GGTCCTCACCTTAGAGATGATGA 58.781 47.826 0.00 0.00 40.00 2.92
1278 1329 3.963374 TGGTCCTCACCTTAGAGATGATG 59.037 47.826 0.00 0.00 44.17 3.07
1486 3621 0.592637 TTACGGTCTTGCTCGACGAA 59.407 50.000 0.00 0.00 34.75 3.85
1489 3624 1.467713 CCTCTTACGGTCTTGCTCGAC 60.468 57.143 0.00 0.00 0.00 4.20
1533 3668 4.206477 TCTGGTTGTAGGTGACATGATG 57.794 45.455 0.00 0.00 38.07 3.07
1553 3688 0.543749 AGCACACTCCAGGGCTATTC 59.456 55.000 0.00 0.00 34.25 1.75
1604 3739 2.437359 GCAAGACGCCCATCAGCT 60.437 61.111 0.00 0.00 32.94 4.24
1605 3740 2.437359 AGCAAGACGCCCATCAGC 60.437 61.111 0.00 0.00 44.04 4.26
1609 3744 0.322816 AATGACAGCAAGACGCCCAT 60.323 50.000 0.00 0.00 44.04 4.00
1619 3754 1.550072 TCCGAGACATCAATGACAGCA 59.450 47.619 0.00 0.00 0.00 4.41
1742 3883 6.014070 ACCCCTCTTTCTCTTCTTCTTTCTAC 60.014 42.308 0.00 0.00 0.00 2.59
1782 3968 2.483106 CCACTCAGCAGATTCTGTGTTG 59.517 50.000 14.90 10.91 38.34 3.33
1969 4164 2.831526 TGATGTTCGAGACAGGATCCAA 59.168 45.455 15.82 0.00 42.62 3.53
2159 4362 0.990374 AAGAAGGTGCCAGAGAGCAT 59.010 50.000 0.00 0.00 46.24 3.79
2405 4608 3.953612 AGGTGAAGATTTTGACACAAGCA 59.046 39.130 0.00 0.00 35.33 3.91
2580 4786 2.962859 ACCCCTGTTTGCTGAGATTTT 58.037 42.857 0.00 0.00 0.00 1.82
2581 4787 2.629617 CAACCCCTGTTTGCTGAGATTT 59.370 45.455 0.00 0.00 30.42 2.17
2582 4788 2.242043 CAACCCCTGTTTGCTGAGATT 58.758 47.619 0.00 0.00 30.42 2.40
2583 4789 1.548582 CCAACCCCTGTTTGCTGAGAT 60.549 52.381 0.00 0.00 30.42 2.75
2664 4870 0.178953 AGGGCAGCAGAAATGGTTGT 60.179 50.000 0.00 0.00 0.00 3.32
2735 4941 8.304596 TGTACAGATAAGTAGTTGAACCTTCAG 58.695 37.037 0.00 0.00 38.61 3.02
2790 4996 2.361757 TGGTGTTGCCAAGAAGTTGATG 59.638 45.455 0.00 0.00 45.94 3.07
2877 5083 2.688477 GATGGTCTTCCCTCCTCATCT 58.312 52.381 0.00 0.00 0.00 2.90
2888 5094 1.400242 GCAAGCACAACGATGGTCTTC 60.400 52.381 0.00 0.00 0.00 2.87
3089 5295 3.257375 ACAACCTACATACAGCAGAACGA 59.743 43.478 0.00 0.00 0.00 3.85
3234 5441 3.131933 ACAGCTGCACTTCCTACAGATAG 59.868 47.826 15.27 0.00 33.10 2.08
3236 5443 1.905215 ACAGCTGCACTTCCTACAGAT 59.095 47.619 15.27 0.00 33.10 2.90
3242 5449 0.322277 CCATCACAGCTGCACTTCCT 60.322 55.000 15.27 0.00 0.00 3.36
3315 5522 9.267084 GCTGTCATTGGAAAAAGGTTAAATTAA 57.733 29.630 0.00 0.00 0.00 1.40
3331 5538 2.789917 GCAGCGAGCTGTCATTGG 59.210 61.111 23.79 0.00 45.24 3.16
3404 5611 1.701545 GAAATCATCGCGGCGTCCAA 61.702 55.000 22.90 2.64 0.00 3.53
3472 5679 1.984297 GACTTGAAACTCGTAGCGACC 59.016 52.381 0.00 0.00 0.00 4.79
3661 5868 9.803315 TGAAACTGTTAGTATCACATATCTCAC 57.197 33.333 0.00 0.00 0.00 3.51
3697 5904 5.612351 ACAAGAACAGGGAAAGAGTACTTC 58.388 41.667 0.00 0.00 35.05 3.01
3915 6413 8.860088 AGATTCCAAGTAAAGCAAATTTGTAGT 58.140 29.630 19.03 4.68 32.01 2.73
4043 6543 4.093408 CCTTCATGACGATACTTTGTGGTG 59.907 45.833 0.00 0.00 0.00 4.17
4062 6563 2.080286 TTGCGAGCTGTAAGACCTTC 57.920 50.000 0.00 0.00 34.07 3.46
4176 6680 0.534877 TCGGATGGCGCTTGCATAAT 60.535 50.000 7.64 0.00 41.71 1.28
4414 6919 1.621317 TGAACAGATTACTGCGACCCA 59.379 47.619 0.00 0.00 46.95 4.51


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

AutoCloner maintained by Alex Coulton.