Multiple sequence alignment - TraesCS5D01G080500

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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 TraesCS5D01G080500 chr5D 100.000 4233 0 0 1 4233 80369809 80374041 0.000000e+00 7817
1 TraesCS5D01G080500 chr5D 83.129 652 73 10 222 838 520768747 520768098 1.030000e-155 560
2 TraesCS5D01G080500 chr5B 96.553 2988 84 10 857 3840 89231846 89234818 0.000000e+00 4929
3 TraesCS5D01G080500 chr5B 96.010 401 12 3 3835 4233 89234843 89235241 0.000000e+00 649
4 TraesCS5D01G080500 chr5B 82.173 589 70 7 201 759 568941269 568940686 1.380000e-129 473
5 TraesCS5D01G080500 chr5A 95.918 2989 91 14 833 3806 76907553 76910525 0.000000e+00 4815
6 TraesCS5D01G080500 chr5A 96.857 350 9 2 3884 4233 76910568 76910915 6.100000e-163 584
7 TraesCS5D01G080500 chr5A 81.361 676 78 17 201 838 482627940 482628605 1.360000e-139 507
8 TraesCS5D01G080500 chr5A 93.277 119 7 1 1 118 626074303 626074421 1.560000e-39 174
9 TraesCS5D01G080500 chr5A 93.277 119 7 1 1 118 688864643 688864525 1.560000e-39 174
10 TraesCS5D01G080500 chrUn 84.509 652 63 16 201 820 223002360 223001715 1.010000e-170 610
11 TraesCS5D01G080500 chrUn 83.691 233 29 4 596 821 69441578 69441808 1.190000e-50 211
12 TraesCS5D01G080500 chr3D 84.202 652 65 16 201 820 29494013 29493368 2.180000e-167 599
13 TraesCS5D01G080500 chr3D 83.896 652 67 17 201 820 29565882 29565237 4.710000e-164 588
14 TraesCS5D01G080500 chr3D 83.742 652 68 17 201 820 29528942 29528297 2.190000e-162 582
15 TraesCS5D01G080500 chr3D 82.159 667 84 14 200 838 599270128 599269469 1.340000e-149 540
16 TraesCS5D01G080500 chr3D 80.828 652 70 14 203 822 591098168 591097540 1.070000e-125 460
17 TraesCS5D01G080500 chr1D 83.438 634 70 11 202 805 439108948 439108320 1.330000e-154 556
18 TraesCS5D01G080500 chr7D 84.247 584 57 13 201 754 602080621 602081199 1.730000e-148 536
19 TraesCS5D01G080500 chr7D 85.316 538 52 12 201 715 602082340 602082873 8.060000e-147 531
20 TraesCS5D01G080500 chr7D 81.481 675 88 18 201 846 104369140 104368474 1.740000e-143 520
21 TraesCS5D01G080500 chr7D 87.745 408 44 3 203 607 465920717 465920313 4.950000e-129 472
22 TraesCS5D01G080500 chr7D 98.305 118 2 0 1 118 19248063 19248180 1.540000e-49 207
23 TraesCS5D01G080500 chr4D 84.962 532 57 4 205 715 505503005 505502476 6.270000e-143 518
24 TraesCS5D01G080500 chr7B 78.025 628 97 18 201 804 332292426 332293036 1.450000e-94 357
25 TraesCS5D01G080500 chr2D 84.706 255 27 3 596 838 63372082 63372336 1.180000e-60 244
26 TraesCS5D01G080500 chr3A 79.853 273 39 12 451 712 14162424 14162691 7.230000e-43 185
27 TraesCS5D01G080500 chr3A 93.277 119 7 1 1 118 419475291 419475173 1.560000e-39 174
28 TraesCS5D01G080500 chr2A 93.333 120 6 2 1 119 100884957 100884839 4.350000e-40 176
29 TraesCS5D01G080500 chr7A 93.277 119 7 1 1 118 498487079 498487197 1.560000e-39 174
30 TraesCS5D01G080500 chr7A 93.277 119 7 1 1 118 700429285 700429167 1.560000e-39 174
31 TraesCS5D01G080500 chr4A 93.277 119 7 1 1 118 479325852 479325734 1.560000e-39 174
32 TraesCS5D01G080500 chr6A 93.220 118 7 1 1 118 423316028 423316144 5.630000e-39 172


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 TraesCS5D01G080500 chr5D 80369809 80374041 4232 False 7817.0 7817 100.0000 1 4233 1 chr5D.!!$F1 4232
1 TraesCS5D01G080500 chr5D 520768098 520768747 649 True 560.0 560 83.1290 222 838 1 chr5D.!!$R1 616
2 TraesCS5D01G080500 chr5B 89231846 89235241 3395 False 2789.0 4929 96.2815 857 4233 2 chr5B.!!$F1 3376
3 TraesCS5D01G080500 chr5B 568940686 568941269 583 True 473.0 473 82.1730 201 759 1 chr5B.!!$R1 558
4 TraesCS5D01G080500 chr5A 76907553 76910915 3362 False 2699.5 4815 96.3875 833 4233 2 chr5A.!!$F3 3400
5 TraesCS5D01G080500 chr5A 482627940 482628605 665 False 507.0 507 81.3610 201 838 1 chr5A.!!$F1 637
6 TraesCS5D01G080500 chrUn 223001715 223002360 645 True 610.0 610 84.5090 201 820 1 chrUn.!!$R1 619
7 TraesCS5D01G080500 chr3D 29493368 29494013 645 True 599.0 599 84.2020 201 820 1 chr3D.!!$R1 619
8 TraesCS5D01G080500 chr3D 29565237 29565882 645 True 588.0 588 83.8960 201 820 1 chr3D.!!$R3 619
9 TraesCS5D01G080500 chr3D 29528297 29528942 645 True 582.0 582 83.7420 201 820 1 chr3D.!!$R2 619
10 TraesCS5D01G080500 chr3D 599269469 599270128 659 True 540.0 540 82.1590 200 838 1 chr3D.!!$R5 638
11 TraesCS5D01G080500 chr3D 591097540 591098168 628 True 460.0 460 80.8280 203 822 1 chr3D.!!$R4 619
12 TraesCS5D01G080500 chr1D 439108320 439108948 628 True 556.0 556 83.4380 202 805 1 chr1D.!!$R1 603
13 TraesCS5D01G080500 chr7D 602080621 602082873 2252 False 533.5 536 84.7815 201 754 2 chr7D.!!$F2 553
14 TraesCS5D01G080500 chr7D 104368474 104369140 666 True 520.0 520 81.4810 201 846 1 chr7D.!!$R1 645
15 TraesCS5D01G080500 chr4D 505502476 505503005 529 True 518.0 518 84.9620 205 715 1 chr4D.!!$R1 510
16 TraesCS5D01G080500 chr7B 332292426 332293036 610 False 357.0 357 78.0250 201 804 1 chr7B.!!$F1 603

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
169 170 0.035439 TTGAGCGAACCCTCCAATCC 60.035 55.0 0.0 0.0 0.0 3.01 F
171 172 0.035439 GAGCGAACCCTCCAATCCAA 60.035 55.0 0.0 0.0 0.0 3.53 F
1376 1461 0.234625 TCAGCGTTGCTTACTTTGCG 59.765 50.0 0.0 0.0 36.4 4.85 F
1683 1768 1.153353 GTCGGAATCAAAAGACGGCA 58.847 50.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1809 1.127343 GAAGATCCTCCCTCCCAGTG 58.873 60.000 0.00 0.00 0.00 3.66 R
1790 1884 3.119637 TGAAGCATGCACAATCACAGATG 60.120 43.478 21.98 0.00 0.00 2.90 R
2692 3103 0.536260 CAGGCAGAGAACCTCAGAGG 59.464 60.000 15.72 15.72 42.49 3.69 R
3466 3883 2.187958 ACCAGTGCCTTACTAGATGCA 58.812 47.619 0.00 0.00 37.60 3.96 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
56 57 8.928733 ACTTCAAATATTCATGTTTCATGCAAC 58.071 29.630 0.84 0.84 0.00 4.17
57 58 7.509050 TCAAATATTCATGTTTCATGCAACG 57.491 32.000 3.78 0.00 0.00 4.10
58 59 7.311408 TCAAATATTCATGTTTCATGCAACGA 58.689 30.769 3.78 0.00 0.00 3.85
59 60 7.811713 TCAAATATTCATGTTTCATGCAACGAA 59.188 29.630 3.78 2.93 0.00 3.85
60 61 8.597227 CAAATATTCATGTTTCATGCAACGAAT 58.403 29.630 12.97 12.97 0.00 3.34
61 62 7.919313 ATATTCATGTTTCATGCAACGAATC 57.081 32.000 12.16 0.00 0.00 2.52
62 63 4.762956 TCATGTTTCATGCAACGAATCA 57.237 36.364 12.67 12.67 0.00 2.57
63 64 4.475028 TCATGTTTCATGCAACGAATCAC 58.525 39.130 12.59 6.26 0.00 3.06
64 65 3.978718 TGTTTCATGCAACGAATCACA 57.021 38.095 3.78 0.00 0.00 3.58
65 66 3.626977 TGTTTCATGCAACGAATCACAC 58.373 40.909 3.78 0.00 0.00 3.82
66 67 3.314913 TGTTTCATGCAACGAATCACACT 59.685 39.130 3.78 0.00 0.00 3.55
67 68 3.541071 TTCATGCAACGAATCACACTG 57.459 42.857 0.00 0.00 0.00 3.66
68 69 2.765122 TCATGCAACGAATCACACTGA 58.235 42.857 0.00 0.00 0.00 3.41
69 70 3.137533 TCATGCAACGAATCACACTGAA 58.862 40.909 0.00 0.00 0.00 3.02
70 71 3.563390 TCATGCAACGAATCACACTGAAA 59.437 39.130 0.00 0.00 0.00 2.69
71 72 4.216042 TCATGCAACGAATCACACTGAAAT 59.784 37.500 0.00 0.00 0.00 2.17
72 73 5.411053 TCATGCAACGAATCACACTGAAATA 59.589 36.000 0.00 0.00 0.00 1.40
73 74 5.878332 TGCAACGAATCACACTGAAATAT 57.122 34.783 0.00 0.00 0.00 1.28
74 75 5.630061 TGCAACGAATCACACTGAAATATG 58.370 37.500 0.00 0.00 0.00 1.78
75 76 5.181056 TGCAACGAATCACACTGAAATATGT 59.819 36.000 0.00 0.00 0.00 2.29
76 77 6.086222 GCAACGAATCACACTGAAATATGTT 58.914 36.000 0.00 0.00 0.00 2.71
77 78 6.032775 GCAACGAATCACACTGAAATATGTTG 59.967 38.462 0.00 0.00 35.99 3.33
78 79 5.631026 ACGAATCACACTGAAATATGTTGC 58.369 37.500 0.00 0.00 0.00 4.17
79 80 5.181056 ACGAATCACACTGAAATATGTTGCA 59.819 36.000 0.00 0.00 0.00 4.08
80 81 6.085573 CGAATCACACTGAAATATGTTGCAA 58.914 36.000 0.00 0.00 0.00 4.08
81 82 6.581919 CGAATCACACTGAAATATGTTGCAAA 59.418 34.615 0.00 0.00 0.00 3.68
82 83 7.114670 CGAATCACACTGAAATATGTTGCAAAA 59.885 33.333 0.00 0.00 0.00 2.44
83 84 8.836268 AATCACACTGAAATATGTTGCAAAAT 57.164 26.923 7.40 7.40 0.00 1.82
84 85 9.926158 AATCACACTGAAATATGTTGCAAAATA 57.074 25.926 11.74 11.74 0.00 1.40
86 87 9.926158 TCACACTGAAATATGTTGCAAAATATT 57.074 25.926 23.65 23.65 31.74 1.28
88 89 9.369904 ACACTGAAATATGTTGCAAAATATTCC 57.630 29.630 27.48 19.68 30.44 3.01
89 90 8.819974 CACTGAAATATGTTGCAAAATATTCCC 58.180 33.333 27.48 22.47 30.44 3.97
90 91 7.706179 ACTGAAATATGTTGCAAAATATTCCCG 59.294 33.333 27.48 17.91 30.44 5.14
91 92 6.478344 TGAAATATGTTGCAAAATATTCCCGC 59.522 34.615 27.48 19.15 30.44 6.13
92 93 3.883830 ATGTTGCAAAATATTCCCGCA 57.116 38.095 0.00 3.09 0.00 5.69
93 94 3.667497 TGTTGCAAAATATTCCCGCAA 57.333 38.095 0.00 12.54 40.08 4.85
95 96 3.667497 TTGCAAAATATTCCCGCAACA 57.333 38.095 12.54 0.00 37.64 3.33
96 97 3.667497 TGCAAAATATTCCCGCAACAA 57.333 38.095 4.44 0.00 0.00 2.83
97 98 3.321497 TGCAAAATATTCCCGCAACAAC 58.679 40.909 4.44 0.00 0.00 3.32
98 99 2.344142 GCAAAATATTCCCGCAACAACG 59.656 45.455 0.00 0.00 0.00 4.10
99 100 3.570559 CAAAATATTCCCGCAACAACGT 58.429 40.909 0.00 0.00 0.00 3.99
100 101 3.926821 AAATATTCCCGCAACAACGTT 57.073 38.095 0.00 0.00 0.00 3.99
101 102 3.481112 AATATTCCCGCAACAACGTTC 57.519 42.857 0.00 0.00 0.00 3.95
102 103 0.791422 TATTCCCGCAACAACGTTCG 59.209 50.000 0.00 0.00 0.00 3.95
103 104 1.847890 ATTCCCGCAACAACGTTCGG 61.848 55.000 16.77 16.77 41.41 4.30
105 106 4.020378 CCGCAACAACGTTCGGGG 62.020 66.667 16.12 12.78 38.35 5.73
106 107 3.273834 CGCAACAACGTTCGGGGT 61.274 61.111 0.00 0.00 0.00 4.95
107 108 1.955157 CGCAACAACGTTCGGGGTA 60.955 57.895 0.00 0.00 0.00 3.69
108 109 1.293267 CGCAACAACGTTCGGGGTAT 61.293 55.000 0.00 0.00 0.00 2.73
109 110 0.445043 GCAACAACGTTCGGGGTATC 59.555 55.000 0.00 0.00 0.00 2.24
110 111 1.798283 CAACAACGTTCGGGGTATCA 58.202 50.000 0.00 0.00 0.00 2.15
111 112 2.352388 CAACAACGTTCGGGGTATCAT 58.648 47.619 0.00 0.00 0.00 2.45
112 113 2.304751 ACAACGTTCGGGGTATCATC 57.695 50.000 0.00 0.00 0.00 2.92
113 114 1.829222 ACAACGTTCGGGGTATCATCT 59.171 47.619 0.00 0.00 0.00 2.90
114 115 3.025978 ACAACGTTCGGGGTATCATCTA 58.974 45.455 0.00 0.00 0.00 1.98
115 116 3.067742 ACAACGTTCGGGGTATCATCTAG 59.932 47.826 0.00 0.00 0.00 2.43
116 117 2.941480 ACGTTCGGGGTATCATCTAGT 58.059 47.619 0.00 0.00 0.00 2.57
117 118 3.294214 ACGTTCGGGGTATCATCTAGTT 58.706 45.455 0.00 0.00 0.00 2.24
118 119 3.067742 ACGTTCGGGGTATCATCTAGTTG 59.932 47.826 0.00 0.00 0.00 3.16
119 120 3.552273 CGTTCGGGGTATCATCTAGTTGG 60.552 52.174 1.00 0.00 0.00 3.77
120 121 3.323774 TCGGGGTATCATCTAGTTGGT 57.676 47.619 1.00 0.00 0.00 3.67
121 122 2.963101 TCGGGGTATCATCTAGTTGGTG 59.037 50.000 1.00 0.00 0.00 4.17
122 123 2.963101 CGGGGTATCATCTAGTTGGTGA 59.037 50.000 1.00 0.00 0.00 4.02
123 124 3.386726 CGGGGTATCATCTAGTTGGTGAA 59.613 47.826 1.00 0.00 0.00 3.18
124 125 4.141801 CGGGGTATCATCTAGTTGGTGAAA 60.142 45.833 1.00 0.00 0.00 2.69
125 126 5.628200 CGGGGTATCATCTAGTTGGTGAAAA 60.628 44.000 1.00 0.00 0.00 2.29
126 127 6.365520 GGGGTATCATCTAGTTGGTGAAAAT 58.634 40.000 1.00 0.00 0.00 1.82
127 128 6.833933 GGGGTATCATCTAGTTGGTGAAAATT 59.166 38.462 1.00 0.00 0.00 1.82
128 129 7.996644 GGGGTATCATCTAGTTGGTGAAAATTA 59.003 37.037 1.00 0.00 0.00 1.40
129 130 8.837389 GGGTATCATCTAGTTGGTGAAAATTAC 58.163 37.037 1.00 0.00 0.00 1.89
130 131 9.614792 GGTATCATCTAGTTGGTGAAAATTACT 57.385 33.333 1.00 0.00 0.00 2.24
134 135 9.871238 TCATCTAGTTGGTGAAAATTACTACTC 57.129 33.333 1.00 0.00 0.00 2.59
135 136 9.099454 CATCTAGTTGGTGAAAATTACTACTCC 57.901 37.037 0.00 0.00 0.00 3.85
136 137 7.618137 TCTAGTTGGTGAAAATTACTACTCCC 58.382 38.462 0.00 0.00 0.00 4.30
137 138 6.449830 AGTTGGTGAAAATTACTACTCCCT 57.550 37.500 0.00 0.00 0.00 4.20
138 139 6.473758 AGTTGGTGAAAATTACTACTCCCTC 58.526 40.000 0.00 0.00 0.00 4.30
139 140 5.431179 TGGTGAAAATTACTACTCCCTCC 57.569 43.478 0.00 0.00 0.00 4.30
140 141 4.081309 TGGTGAAAATTACTACTCCCTCCG 60.081 45.833 0.00 0.00 0.00 4.63
141 142 4.161001 GGTGAAAATTACTACTCCCTCCGA 59.839 45.833 0.00 0.00 0.00 4.55
142 143 5.163332 GGTGAAAATTACTACTCCCTCCGAT 60.163 44.000 0.00 0.00 0.00 4.18
143 144 5.984323 GTGAAAATTACTACTCCCTCCGATC 59.016 44.000 0.00 0.00 0.00 3.69
144 145 5.070047 TGAAAATTACTACTCCCTCCGATCC 59.930 44.000 0.00 0.00 0.00 3.36
145 146 3.897657 ATTACTACTCCCTCCGATCCA 57.102 47.619 0.00 0.00 0.00 3.41
146 147 3.897657 TTACTACTCCCTCCGATCCAT 57.102 47.619 0.00 0.00 0.00 3.41
147 148 2.777459 ACTACTCCCTCCGATCCATT 57.223 50.000 0.00 0.00 0.00 3.16
148 149 3.047695 ACTACTCCCTCCGATCCATTT 57.952 47.619 0.00 0.00 0.00 2.32
149 150 3.385115 ACTACTCCCTCCGATCCATTTT 58.615 45.455 0.00 0.00 0.00 1.82
150 151 3.780850 ACTACTCCCTCCGATCCATTTTT 59.219 43.478 0.00 0.00 0.00 1.94
165 166 3.811031 TTTTTGAGCGAACCCTCCA 57.189 47.368 0.00 0.00 0.00 3.86
166 167 2.060050 TTTTTGAGCGAACCCTCCAA 57.940 45.000 0.00 0.00 0.00 3.53
167 168 2.286365 TTTTGAGCGAACCCTCCAAT 57.714 45.000 0.00 0.00 0.00 3.16
168 169 1.821216 TTTGAGCGAACCCTCCAATC 58.179 50.000 0.00 0.00 0.00 2.67
169 170 0.035439 TTGAGCGAACCCTCCAATCC 60.035 55.000 0.00 0.00 0.00 3.01
170 171 1.198094 TGAGCGAACCCTCCAATCCA 61.198 55.000 0.00 0.00 0.00 3.41
171 172 0.035439 GAGCGAACCCTCCAATCCAA 60.035 55.000 0.00 0.00 0.00 3.53
172 173 0.625849 AGCGAACCCTCCAATCCAAT 59.374 50.000 0.00 0.00 0.00 3.16
173 174 1.843851 AGCGAACCCTCCAATCCAATA 59.156 47.619 0.00 0.00 0.00 1.90
174 175 2.443255 AGCGAACCCTCCAATCCAATAT 59.557 45.455 0.00 0.00 0.00 1.28
175 176 3.117512 AGCGAACCCTCCAATCCAATATT 60.118 43.478 0.00 0.00 0.00 1.28
176 177 3.636764 GCGAACCCTCCAATCCAATATTT 59.363 43.478 0.00 0.00 0.00 1.40
177 178 4.099419 GCGAACCCTCCAATCCAATATTTT 59.901 41.667 0.00 0.00 0.00 1.82
178 179 5.395214 GCGAACCCTCCAATCCAATATTTTT 60.395 40.000 0.00 0.00 0.00 1.94
271 277 9.952188 GACCTAAGATCCAATAAAATACAAAGC 57.048 33.333 0.00 0.00 0.00 3.51
316 322 7.581213 ACAATGAAATCTCTTGTAAACACCA 57.419 32.000 0.00 0.00 31.62 4.17
328 334 3.749088 TGTAAACACCATCTTTGCGGTAG 59.251 43.478 0.00 0.00 32.98 3.18
379 385 4.816925 AGACTTCAGTAAAGAGGTTGCAAC 59.183 41.667 21.59 21.59 38.44 4.17
457 480 3.186909 GTTTTTGAAAGCGCCTTGAGTT 58.813 40.909 2.29 0.00 0.00 3.01
523 550 2.854253 GGATGATCCCCTGCAGGTA 58.146 57.895 30.63 18.99 0.00 3.08
526 553 1.701847 GATGATCCCCTGCAGGTACAT 59.298 52.381 30.63 25.53 0.00 2.29
544 571 4.521130 ACATGCCGTCGAATCACTATAT 57.479 40.909 0.00 0.00 0.00 0.86
545 572 5.638596 ACATGCCGTCGAATCACTATATA 57.361 39.130 0.00 0.00 0.00 0.86
597 624 3.891366 ACCTCCACAAAGAATCAAACCAG 59.109 43.478 0.00 0.00 0.00 4.00
715 764 5.825507 TCTCACAGAACTATGATGATCACG 58.174 41.667 0.00 0.00 0.00 4.35
731 788 4.634443 TGATCACGACGAAGAACATAGAGA 59.366 41.667 0.00 0.00 0.00 3.10
749 807 5.428184 AGAGATCTTGAAAATCCGAGGTT 57.572 39.130 0.00 0.00 0.00 3.50
764 823 4.724262 GTTCCCCAACCTCTCAGC 57.276 61.111 0.00 0.00 0.00 4.26
840 918 2.747686 GGCACGAGAAACCCTCCA 59.252 61.111 0.00 0.00 38.71 3.86
852 930 6.605471 AGAAACCCTCCAATCCAAAATAAC 57.395 37.500 0.00 0.00 0.00 1.89
940 1020 1.185315 GCCCACATAATGCACCAACT 58.815 50.000 0.00 0.00 0.00 3.16
981 1066 0.613777 GATCCGAAACCCTGACCTGT 59.386 55.000 0.00 0.00 0.00 4.00
1110 1195 2.190578 GGGATTCTGGGCCGTCTG 59.809 66.667 0.00 0.00 0.00 3.51
1376 1461 0.234625 TCAGCGTTGCTTACTTTGCG 59.765 50.000 0.00 0.00 36.40 4.85
1382 1467 2.459934 GTTGCTTACTTTGCGCACTTT 58.540 42.857 11.12 0.00 32.71 2.66
1390 1475 3.839293 ACTTTGCGCACTTTTTGTTACA 58.161 36.364 11.12 0.00 0.00 2.41
1395 1480 2.403698 GCGCACTTTTTGTTACAATCCG 59.596 45.455 0.30 0.00 0.00 4.18
1505 1590 2.004808 GCAATTCGCAAGCCCTACCC 62.005 60.000 0.00 0.00 41.79 3.69
1522 1607 2.106683 CCGTCTTCAATGTCGGGGC 61.107 63.158 0.00 0.00 39.41 5.80
1653 1738 2.799017 TGCACATTGCCTCTCTTGATT 58.201 42.857 0.00 0.00 44.23 2.57
1664 1749 4.505922 GCCTCTCTTGATTATGTGTTCTCG 59.494 45.833 0.00 0.00 0.00 4.04
1682 1767 3.969795 GTCGGAATCAAAAGACGGC 57.030 52.632 0.00 0.00 0.00 5.68
1683 1768 1.153353 GTCGGAATCAAAAGACGGCA 58.847 50.000 0.00 0.00 0.00 5.69
1724 1809 5.049818 GCTAGTTGGCATGATTACTGATGAC 60.050 44.000 0.00 0.00 0.00 3.06
1812 1906 2.506444 TCTGTGATTGTGCATGCTTCA 58.494 42.857 20.33 14.97 0.00 3.02
1850 1944 9.447157 TCATTTAATCTACATGATGTTGTGTGA 57.553 29.630 2.29 0.23 35.21 3.58
1853 1947 8.791327 TTAATCTACATGATGTTGTGTGATGT 57.209 30.769 2.29 0.00 35.21 3.06
2011 2105 7.897864 ACAGTAAAGGTATATAGCAGATGTCC 58.102 38.462 14.11 0.00 0.00 4.02
2012 2106 7.730784 ACAGTAAAGGTATATAGCAGATGTCCT 59.269 37.037 14.11 0.00 0.00 3.85
2017 2111 6.326970 AGGTATATAGCAGATGTCCTTTCCT 58.673 40.000 14.11 0.00 0.00 3.36
2044 2139 5.483811 TGATTTGTTCGCCTGTTGATAGTA 58.516 37.500 0.00 0.00 0.00 1.82
2045 2140 5.935206 TGATTTGTTCGCCTGTTGATAGTAA 59.065 36.000 0.00 0.00 0.00 2.24
2301 2451 6.877611 ATGTGGTTAGTTTAAAGACACAGG 57.122 37.500 12.65 0.00 40.20 4.00
2426 2576 9.383519 ACTTACATATAATGTTGAGTTCACTGG 57.616 33.333 0.00 0.00 41.63 4.00
2519 2669 3.303495 CGCAAGTCGTAATCTTACAGGTG 59.697 47.826 1.41 0.00 33.28 4.00
2692 3103 3.361794 TGATAGCGATGAGTCTGCTTC 57.638 47.619 9.75 8.28 36.29 3.86
2874 3285 7.942341 ACCTGTATGACCATTTCTTTTCACTAA 59.058 33.333 0.00 0.00 0.00 2.24
2899 3310 1.555967 AGGTTCTGGACTGAGAGAGC 58.444 55.000 0.00 0.00 0.00 4.09
2984 3395 6.481644 AGCTGCTTCATTGTCTTTATAGCTAC 59.518 38.462 0.00 0.00 36.16 3.58
3087 3504 3.030291 TGAATGTGCCCACTTGTTTCTT 58.970 40.909 0.00 0.00 0.00 2.52
3251 3668 4.813161 ACTGACACTTGTTCATTGAGTGAG 59.187 41.667 9.45 0.04 42.54 3.51
3396 3813 2.370519 TGTTTGTAGTGCCAGAAGCCTA 59.629 45.455 0.00 0.00 42.71 3.93
3466 3883 4.215109 ACTTGCTTGGGATAACAGTGTTT 58.785 39.130 14.90 2.06 0.00 2.83
3489 3906 4.010349 GCATCTAGTAAGGCACTGGTTTT 58.990 43.478 0.00 0.00 40.86 2.43
3523 3940 7.453393 TCTGCCATATTCTTAGAATTACCCTG 58.547 38.462 13.00 4.11 0.00 4.45
3526 3943 6.072452 GCCATATTCTTAGAATTACCCTGCAC 60.072 42.308 13.00 0.00 0.00 4.57
3600 4017 9.391006 AGTTAAAACATGTCTGAAACTTGTAGA 57.609 29.630 0.00 0.00 43.38 2.59
3601 4018 9.651718 GTTAAAACATGTCTGAAACTTGTAGAG 57.348 33.333 0.00 0.00 43.38 2.43
3806 4224 8.943002 ACTATGTGCTGTATAAACTTTTGTACC 58.057 33.333 6.26 0.00 34.91 3.34
3809 4227 7.221450 TGTGCTGTATAAACTTTTGTACCTCT 58.779 34.615 6.26 0.00 34.91 3.69
3947 4438 6.521133 CAGAGTCTGTTACGAATTGAAAATGC 59.479 38.462 12.28 0.00 0.00 3.56
4106 4730 5.571784 ATCATGTTACTCCTGCACATTTG 57.428 39.130 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.928733 GTTGCATGAAACATGAATATTTGAAGT 58.071 29.630 11.98 0.00 0.00 3.01
31 32 8.105742 CGTTGCATGAAACATGAATATTTGAAG 58.894 33.333 16.90 0.00 0.00 3.02
32 33 7.811713 TCGTTGCATGAAACATGAATATTTGAA 59.188 29.630 16.90 0.00 0.00 2.69
33 34 7.311408 TCGTTGCATGAAACATGAATATTTGA 58.689 30.769 16.90 0.00 0.00 2.69
34 35 7.509050 TCGTTGCATGAAACATGAATATTTG 57.491 32.000 16.90 0.00 0.00 2.32
35 36 8.706492 ATTCGTTGCATGAAACATGAATATTT 57.294 26.923 16.90 0.00 0.00 1.40
36 37 7.975058 TGATTCGTTGCATGAAACATGAATATT 59.025 29.630 16.90 0.00 0.00 1.28
37 38 7.433131 GTGATTCGTTGCATGAAACATGAATAT 59.567 33.333 16.90 0.00 30.43 1.28
38 39 6.746822 GTGATTCGTTGCATGAAACATGAATA 59.253 34.615 16.90 5.30 30.43 1.75
39 40 5.574055 GTGATTCGTTGCATGAAACATGAAT 59.426 36.000 16.90 16.19 30.43 2.57
40 41 4.916831 GTGATTCGTTGCATGAAACATGAA 59.083 37.500 16.90 12.41 30.43 2.57
41 42 4.023365 TGTGATTCGTTGCATGAAACATGA 60.023 37.500 16.90 3.82 30.43 3.07
42 43 4.088923 GTGTGATTCGTTGCATGAAACATG 59.911 41.667 16.90 7.29 30.43 3.21
43 44 4.022935 AGTGTGATTCGTTGCATGAAACAT 60.023 37.500 16.90 3.25 30.43 2.71
44 45 3.314913 AGTGTGATTCGTTGCATGAAACA 59.685 39.130 16.90 6.95 0.00 2.83
45 46 3.665409 CAGTGTGATTCGTTGCATGAAAC 59.335 43.478 6.48 6.48 0.00 2.78
46 47 3.563390 TCAGTGTGATTCGTTGCATGAAA 59.437 39.130 0.00 0.00 0.00 2.69
47 48 3.137533 TCAGTGTGATTCGTTGCATGAA 58.862 40.909 0.00 4.58 0.00 2.57
48 49 2.765122 TCAGTGTGATTCGTTGCATGA 58.235 42.857 0.00 0.00 0.00 3.07
49 50 3.541071 TTCAGTGTGATTCGTTGCATG 57.459 42.857 0.00 0.00 0.00 4.06
50 51 4.771590 ATTTCAGTGTGATTCGTTGCAT 57.228 36.364 0.00 0.00 0.00 3.96
51 52 5.181056 ACATATTTCAGTGTGATTCGTTGCA 59.819 36.000 0.00 0.00 0.00 4.08
52 53 5.631026 ACATATTTCAGTGTGATTCGTTGC 58.369 37.500 0.00 0.00 0.00 4.17
53 54 6.032775 GCAACATATTTCAGTGTGATTCGTTG 59.967 38.462 0.00 0.00 33.71 4.10
54 55 6.086222 GCAACATATTTCAGTGTGATTCGTT 58.914 36.000 0.00 0.00 0.00 3.85
55 56 5.181056 TGCAACATATTTCAGTGTGATTCGT 59.819 36.000 0.00 0.00 0.00 3.85
56 57 5.630061 TGCAACATATTTCAGTGTGATTCG 58.370 37.500 0.00 0.00 0.00 3.34
57 58 7.872163 TTTGCAACATATTTCAGTGTGATTC 57.128 32.000 0.00 0.00 0.00 2.52
58 59 8.836268 ATTTTGCAACATATTTCAGTGTGATT 57.164 26.923 0.00 0.00 0.00 2.57
60 61 9.926158 AATATTTTGCAACATATTTCAGTGTGA 57.074 25.926 20.22 0.00 0.00 3.58
62 63 9.369904 GGAATATTTTGCAACATATTTCAGTGT 57.630 29.630 24.51 7.56 0.00 3.55
63 64 8.819974 GGGAATATTTTGCAACATATTTCAGTG 58.180 33.333 26.76 0.00 0.00 3.66
64 65 7.706179 CGGGAATATTTTGCAACATATTTCAGT 59.294 33.333 26.76 11.02 0.00 3.41
65 66 7.306749 GCGGGAATATTTTGCAACATATTTCAG 60.307 37.037 26.76 24.59 0.00 3.02
66 67 6.478344 GCGGGAATATTTTGCAACATATTTCA 59.522 34.615 26.76 3.82 0.00 2.69
67 68 6.478344 TGCGGGAATATTTTGCAACATATTTC 59.522 34.615 24.51 22.86 31.69 2.17
68 69 6.344500 TGCGGGAATATTTTGCAACATATTT 58.656 32.000 24.51 13.16 31.69 1.40
69 70 5.911752 TGCGGGAATATTTTGCAACATATT 58.088 33.333 24.14 24.14 31.69 1.28
70 71 5.528043 TGCGGGAATATTTTGCAACATAT 57.472 34.783 11.50 11.50 31.69 1.78
71 72 4.991153 TGCGGGAATATTTTGCAACATA 57.009 36.364 7.71 7.71 31.69 2.29
72 73 3.883830 TGCGGGAATATTTTGCAACAT 57.116 38.095 0.00 0.00 31.69 2.71
73 74 3.667497 TTGCGGGAATATTTTGCAACA 57.333 38.095 14.93 0.00 40.31 3.33
75 76 3.667497 TGTTGCGGGAATATTTTGCAA 57.333 38.095 14.93 14.93 42.68 4.08
76 77 3.321497 GTTGTTGCGGGAATATTTTGCA 58.679 40.909 6.21 6.21 0.00 4.08
77 78 2.344142 CGTTGTTGCGGGAATATTTTGC 59.656 45.455 0.00 0.00 0.00 3.68
78 79 3.570559 ACGTTGTTGCGGGAATATTTTG 58.429 40.909 0.00 0.00 35.98 2.44
79 80 3.926821 ACGTTGTTGCGGGAATATTTT 57.073 38.095 0.00 0.00 35.98 1.82
80 81 3.668491 CGAACGTTGTTGCGGGAATATTT 60.668 43.478 5.00 0.00 35.98 1.40
81 82 2.159626 CGAACGTTGTTGCGGGAATATT 60.160 45.455 5.00 0.00 35.98 1.28
82 83 1.395608 CGAACGTTGTTGCGGGAATAT 59.604 47.619 5.00 0.00 35.98 1.28
83 84 0.791422 CGAACGTTGTTGCGGGAATA 59.209 50.000 5.00 0.00 35.98 1.75
84 85 1.572447 CGAACGTTGTTGCGGGAAT 59.428 52.632 5.00 0.00 35.98 3.01
85 86 2.535788 CCGAACGTTGTTGCGGGAA 61.536 57.895 16.12 0.00 40.08 3.97
86 87 2.968156 CCGAACGTTGTTGCGGGA 60.968 61.111 16.12 0.00 40.08 5.14
88 89 4.020378 CCCCGAACGTTGTTGCGG 62.020 66.667 16.77 16.77 43.20 5.69
89 90 1.293267 ATACCCCGAACGTTGTTGCG 61.293 55.000 5.00 2.25 37.94 4.85
90 91 0.445043 GATACCCCGAACGTTGTTGC 59.555 55.000 5.00 0.00 0.00 4.17
91 92 1.798283 TGATACCCCGAACGTTGTTG 58.202 50.000 5.00 0.00 0.00 3.33
92 93 2.235402 AGATGATACCCCGAACGTTGTT 59.765 45.455 5.00 0.00 0.00 2.83
93 94 1.829222 AGATGATACCCCGAACGTTGT 59.171 47.619 5.00 0.00 0.00 3.32
94 95 2.596904 AGATGATACCCCGAACGTTG 57.403 50.000 5.00 0.00 0.00 4.10
95 96 3.294214 ACTAGATGATACCCCGAACGTT 58.706 45.455 0.00 0.00 0.00 3.99
96 97 2.941480 ACTAGATGATACCCCGAACGT 58.059 47.619 0.00 0.00 0.00 3.99
97 98 3.552273 CCAACTAGATGATACCCCGAACG 60.552 52.174 0.79 0.00 0.00 3.95
98 99 3.387050 ACCAACTAGATGATACCCCGAAC 59.613 47.826 0.79 0.00 0.00 3.95
99 100 3.386726 CACCAACTAGATGATACCCCGAA 59.613 47.826 0.79 0.00 0.00 4.30
100 101 2.963101 CACCAACTAGATGATACCCCGA 59.037 50.000 0.79 0.00 0.00 5.14
101 102 2.963101 TCACCAACTAGATGATACCCCG 59.037 50.000 0.79 0.00 0.00 5.73
102 103 5.367945 TTTCACCAACTAGATGATACCCC 57.632 43.478 0.79 0.00 0.00 4.95
103 104 7.881775 AATTTTCACCAACTAGATGATACCC 57.118 36.000 0.79 0.00 0.00 3.69
104 105 9.614792 AGTAATTTTCACCAACTAGATGATACC 57.385 33.333 0.79 0.00 0.00 2.73
108 109 9.871238 GAGTAGTAATTTTCACCAACTAGATGA 57.129 33.333 0.79 0.00 0.00 2.92
109 110 9.099454 GGAGTAGTAATTTTCACCAACTAGATG 57.901 37.037 0.00 0.00 0.00 2.90
110 111 8.265764 GGGAGTAGTAATTTTCACCAACTAGAT 58.734 37.037 0.00 0.00 0.00 1.98
111 112 7.456902 AGGGAGTAGTAATTTTCACCAACTAGA 59.543 37.037 0.00 0.00 0.00 2.43
112 113 7.621796 AGGGAGTAGTAATTTTCACCAACTAG 58.378 38.462 0.00 0.00 0.00 2.57
113 114 7.310858 GGAGGGAGTAGTAATTTTCACCAACTA 60.311 40.741 0.00 0.00 0.00 2.24
114 115 6.449830 AGGGAGTAGTAATTTTCACCAACT 57.550 37.500 0.00 0.00 0.00 3.16
115 116 5.646793 GGAGGGAGTAGTAATTTTCACCAAC 59.353 44.000 0.00 0.00 0.00 3.77
116 117 5.570034 CGGAGGGAGTAGTAATTTTCACCAA 60.570 44.000 0.00 0.00 0.00 3.67
117 118 4.081309 CGGAGGGAGTAGTAATTTTCACCA 60.081 45.833 0.00 0.00 0.00 4.17
118 119 4.161001 TCGGAGGGAGTAGTAATTTTCACC 59.839 45.833 0.00 0.00 0.00 4.02
119 120 5.334724 TCGGAGGGAGTAGTAATTTTCAC 57.665 43.478 0.00 0.00 0.00 3.18
120 121 5.070047 GGATCGGAGGGAGTAGTAATTTTCA 59.930 44.000 0.00 0.00 0.00 2.69
121 122 5.070047 TGGATCGGAGGGAGTAGTAATTTTC 59.930 44.000 0.00 0.00 0.00 2.29
122 123 4.966805 TGGATCGGAGGGAGTAGTAATTTT 59.033 41.667 0.00 0.00 0.00 1.82
123 124 4.553678 TGGATCGGAGGGAGTAGTAATTT 58.446 43.478 0.00 0.00 0.00 1.82
124 125 4.194678 TGGATCGGAGGGAGTAGTAATT 57.805 45.455 0.00 0.00 0.00 1.40
125 126 3.897657 TGGATCGGAGGGAGTAGTAAT 57.102 47.619 0.00 0.00 0.00 1.89
126 127 3.897657 ATGGATCGGAGGGAGTAGTAA 57.102 47.619 0.00 0.00 0.00 2.24
127 128 3.897657 AATGGATCGGAGGGAGTAGTA 57.102 47.619 0.00 0.00 0.00 1.82
128 129 2.777459 AATGGATCGGAGGGAGTAGT 57.223 50.000 0.00 0.00 0.00 2.73
129 130 4.423625 AAAAATGGATCGGAGGGAGTAG 57.576 45.455 0.00 0.00 0.00 2.57
147 148 2.060050 TTGGAGGGTTCGCTCAAAAA 57.940 45.000 16.40 6.90 0.00 1.94
148 149 2.159382 GATTGGAGGGTTCGCTCAAAA 58.841 47.619 16.40 11.19 0.00 2.44
149 150 1.613255 GGATTGGAGGGTTCGCTCAAA 60.613 52.381 16.40 12.66 0.00 2.69
150 151 0.035439 GGATTGGAGGGTTCGCTCAA 60.035 55.000 16.40 4.77 0.00 3.02
151 152 1.198094 TGGATTGGAGGGTTCGCTCA 61.198 55.000 16.40 0.45 0.00 4.26
152 153 0.035439 TTGGATTGGAGGGTTCGCTC 60.035 55.000 8.11 8.11 0.00 5.03
153 154 0.625849 ATTGGATTGGAGGGTTCGCT 59.374 50.000 0.00 0.00 0.00 4.93
154 155 2.341846 TATTGGATTGGAGGGTTCGC 57.658 50.000 0.00 0.00 0.00 4.70
155 156 5.852282 AAAATATTGGATTGGAGGGTTCG 57.148 39.130 0.00 0.00 0.00 3.95
176 177 6.361768 AAAGTTACAGGTGTTTCCCAAAAA 57.638 33.333 0.00 0.00 36.75 1.94
177 178 6.166982 CAAAAGTTACAGGTGTTTCCCAAAA 58.833 36.000 0.00 0.00 36.75 2.44
178 179 5.246429 ACAAAAGTTACAGGTGTTTCCCAAA 59.754 36.000 0.00 0.00 36.75 3.28
179 180 4.773149 ACAAAAGTTACAGGTGTTTCCCAA 59.227 37.500 0.00 0.00 36.75 4.12
180 181 4.345854 ACAAAAGTTACAGGTGTTTCCCA 58.654 39.130 0.00 0.00 36.75 4.37
181 182 4.994907 ACAAAAGTTACAGGTGTTTCCC 57.005 40.909 0.00 0.00 36.75 3.97
182 183 7.092137 AGTTACAAAAGTTACAGGTGTTTCC 57.908 36.000 0.00 0.00 0.00 3.13
183 184 8.975410 AAAGTTACAAAAGTTACAGGTGTTTC 57.025 30.769 0.00 0.00 0.00 2.78
289 295 9.394477 GGTGTTTACAAGAGATTTCATTGTAAC 57.606 33.333 15.14 12.33 44.65 2.50
379 385 6.475076 GTGACAACATCATTGCTCTAGTCTAG 59.525 42.308 0.00 0.00 40.28 2.43
517 544 0.810031 ATTCGACGGCATGTACCTGC 60.810 55.000 14.10 14.10 41.53 4.85
518 545 1.209128 GATTCGACGGCATGTACCTG 58.791 55.000 0.00 0.00 0.00 4.00
520 547 0.928229 GTGATTCGACGGCATGTACC 59.072 55.000 0.00 0.00 0.00 3.34
523 550 2.890808 ATAGTGATTCGACGGCATGT 57.109 45.000 0.00 0.00 0.00 3.21
526 553 6.150474 TGAAGATATATAGTGATTCGACGGCA 59.850 38.462 0.00 0.00 0.00 5.69
597 624 6.785488 TCGGATATGATGAGTTTATGTTGC 57.215 37.500 0.00 0.00 0.00 4.17
643 692 3.686726 GTGCCATGAGGTTAGAGAGTTTG 59.313 47.826 0.00 0.00 37.19 2.93
715 764 8.467402 TTTTCAAGATCTCTATGTTCTTCGTC 57.533 34.615 0.00 0.00 33.73 4.20
749 807 2.610859 GGGCTGAGAGGTTGGGGA 60.611 66.667 0.00 0.00 0.00 4.81
760 819 2.380365 AGCTGTCATCTTGGGCTGA 58.620 52.632 0.00 0.00 31.68 4.26
761 820 2.478989 CAGCTGTCATCTTGGGCTG 58.521 57.895 5.25 0.00 43.03 4.85
762 821 0.694771 TTCAGCTGTCATCTTGGGCT 59.305 50.000 14.67 0.00 0.00 5.19
763 822 1.404391 CATTCAGCTGTCATCTTGGGC 59.596 52.381 14.67 0.00 0.00 5.36
764 823 1.404391 GCATTCAGCTGTCATCTTGGG 59.596 52.381 14.67 0.00 41.15 4.12
962 1045 0.613777 ACAGGTCAGGGTTTCGGATC 59.386 55.000 0.00 0.00 0.00 3.36
963 1046 0.324943 CACAGGTCAGGGTTTCGGAT 59.675 55.000 0.00 0.00 0.00 4.18
964 1047 1.752198 CACAGGTCAGGGTTTCGGA 59.248 57.895 0.00 0.00 0.00 4.55
965 1048 1.966451 GCACAGGTCAGGGTTTCGG 60.966 63.158 0.00 0.00 0.00 4.30
967 1050 2.617274 GCGCACAGGTCAGGGTTTC 61.617 63.158 0.30 0.00 0.00 2.78
981 1066 4.100084 CTGGGATGGACAGGCGCA 62.100 66.667 10.83 0.00 32.38 6.09
1045 1130 2.284995 GGAGGAGGAGCAGTGGGT 60.285 66.667 0.00 0.00 0.00 4.51
1110 1195 2.665185 GCGGCACCGGATATGGAC 60.665 66.667 9.46 0.00 40.19 4.02
1376 1461 5.038033 TCAACGGATTGTAACAAAAAGTGC 58.962 37.500 0.00 0.00 37.11 4.40
1382 1467 8.759641 CAATTCATTTCAACGGATTGTAACAAA 58.240 29.630 0.00 0.00 37.11 2.83
1390 1475 6.091169 GCATCAACAATTCATTTCAACGGATT 59.909 34.615 0.00 0.00 0.00 3.01
1395 1480 5.175491 ACACGCATCAACAATTCATTTCAAC 59.825 36.000 0.00 0.00 0.00 3.18
1505 1590 2.452813 CGCCCCGACATTGAAGACG 61.453 63.158 0.00 0.00 0.00 4.18
1599 1684 1.594518 CGGCAACAAACTCGACACAAG 60.595 52.381 0.00 0.00 0.00 3.16
1653 1738 4.443913 TTGATTCCGACGAGAACACATA 57.556 40.909 0.00 0.00 0.00 2.29
1664 1749 1.153353 TGCCGTCTTTTGATTCCGAC 58.847 50.000 0.00 0.00 0.00 4.79
1682 1767 1.378250 CTCCCTCAGCCTGCCTTTG 60.378 63.158 0.00 0.00 0.00 2.77
1683 1768 3.085223 CTCCCTCAGCCTGCCTTT 58.915 61.111 0.00 0.00 0.00 3.11
1724 1809 1.127343 GAAGATCCTCCCTCCCAGTG 58.873 60.000 0.00 0.00 0.00 3.66
1790 1884 3.119637 TGAAGCATGCACAATCACAGATG 60.120 43.478 21.98 0.00 0.00 2.90
1794 1888 3.945981 ATTGAAGCATGCACAATCACA 57.054 38.095 26.15 14.08 29.89 3.58
1846 1940 3.481453 TCACCGAATGGAAAACATCACA 58.519 40.909 0.00 0.00 39.40 3.58
1850 1944 7.040062 TGACTTTAATCACCGAATGGAAAACAT 60.040 33.333 0.00 0.00 43.07 2.71
1853 1947 6.712998 TCTGACTTTAATCACCGAATGGAAAA 59.287 34.615 0.00 0.00 39.21 2.29
2011 2105 5.801947 CAGGCGAACAAATCATAAAGGAAAG 59.198 40.000 0.00 0.00 0.00 2.62
2012 2106 5.242838 ACAGGCGAACAAATCATAAAGGAAA 59.757 36.000 0.00 0.00 0.00 3.13
2017 2111 5.697473 TCAACAGGCGAACAAATCATAAA 57.303 34.783 0.00 0.00 0.00 1.40
2044 2139 8.432805 TCCTCTAAGTTTCTCATGTTCTCTTTT 58.567 33.333 0.00 0.00 0.00 2.27
2045 2140 7.967908 TCCTCTAAGTTTCTCATGTTCTCTTT 58.032 34.615 0.00 0.00 0.00 2.52
2301 2451 3.347216 TGCAAGGCCTATCAAGAAGTTC 58.653 45.455 5.16 0.00 0.00 3.01
2426 2576 1.597742 TCTTCAGCTCAGTTTGGTGC 58.402 50.000 0.00 0.00 33.48 5.01
2519 2669 7.056635 TCTCCTCCTGTCAATGGAAATTAATC 58.943 38.462 0.00 0.00 32.61 1.75
2692 3103 0.536260 CAGGCAGAGAACCTCAGAGG 59.464 60.000 15.72 15.72 42.49 3.69
2767 3178 7.022384 CAGATCAATTTTCTTCTGAGACTTGC 58.978 38.462 0.00 0.00 38.25 4.01
2874 3285 3.772025 CTCTCAGTCCAGAACCTTGGTAT 59.228 47.826 0.00 0.00 39.35 2.73
2984 3395 6.313658 TGCTTAACTACTGATAACATGCACTG 59.686 38.462 0.00 0.00 0.00 3.66
3087 3504 7.362834 CCAAATCAATGGAGTAACTGCACATAA 60.363 37.037 0.00 0.00 43.54 1.90
3251 3668 7.797038 TTCTTTCTTACAGTAAGTTTGGGAC 57.203 36.000 18.16 0.00 37.10 4.46
3310 3727 7.399523 CGGATGTTAAAGTATGCAGAGTAAAC 58.600 38.462 0.00 0.00 0.00 2.01
3396 3813 3.777522 CCCAACTAGGAAGGAATCTCTGT 59.222 47.826 0.00 0.00 41.22 3.41
3466 3883 2.187958 ACCAGTGCCTTACTAGATGCA 58.812 47.619 0.00 0.00 37.60 3.96
3489 3906 7.851228 TCTAAGAATATGGCAGAAGTCTGAAA 58.149 34.615 12.54 0.00 46.59 2.69
3601 4018 5.402398 GCAAGTGATGGTTTCCTTTATCAC 58.598 41.667 0.00 0.00 45.98 3.06
3831 4249 6.479990 TCTGAAAGTATCCTATCAATGCAACG 59.520 38.462 0.00 0.00 33.76 4.10
3864 4314 7.956943 GCCAATATGCAACATTTTTCTGTAAAC 59.043 33.333 0.00 0.00 0.00 2.01
3901 4392 9.367444 ACTCTGTATTCCTTCAATTTTACTACG 57.633 33.333 0.00 0.00 0.00 3.51
3924 4415 5.795441 GGCATTTTCAATTCGTAACAGACTC 59.205 40.000 0.00 0.00 0.00 3.36
3947 4438 2.032054 GGTGATGTGTATGCATGTTCGG 59.968 50.000 10.16 0.00 0.00 4.30
4106 4730 2.994578 GGACTTAACTGTCTCGGAAAGC 59.005 50.000 0.00 0.00 37.16 3.51


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

AutoCloner maintained by Alex Coulton.