Multiple sequence alignment - TraesCS7B01G335600

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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 TraesCS7B01G335600 chr7B 100.000 2750 0 0 1 2750 590502146 590499397 0.000000e+00 5079.0
1 TraesCS7B01G335600 chr7B 98.889 90 1 0 2661 2750 132398957 132398868 7.880000e-36 161.0
2 TraesCS7B01G335600 chr7B 98.876 89 1 0 2662 2750 724996827 724996739 2.830000e-35 159.0
3 TraesCS7B01G335600 chr7D 91.746 1890 74 36 500 2337 547458744 547456885 0.000000e+00 2551.0
4 TraesCS7B01G335600 chr7D 85.127 316 17 8 213 516 547459067 547458770 2.070000e-76 296.0
5 TraesCS7B01G335600 chr7D 84.524 84 3 1 2591 2664 547456693 547456610 1.060000e-09 75.0
6 TraesCS7B01G335600 chr7A 88.404 1880 105 45 500 2326 631364548 631366367 0.000000e+00 2159.0
7 TraesCS7B01G335600 chr7A 87.834 337 26 10 2341 2664 631366355 631366689 5.560000e-102 381.0
8 TraesCS7B01G335600 chr7A 88.750 320 22 4 202 516 631364220 631364530 2.000000e-101 379.0
9 TraesCS7B01G335600 chrUn 98.876 89 1 0 2662 2750 56170826 56170738 2.830000e-35 159.0
10 TraesCS7B01G335600 chr6B 98.876 89 1 0 2662 2750 111879894 111879806 2.830000e-35 159.0
11 TraesCS7B01G335600 chr5B 98.876 89 1 0 2662 2750 428544891 428544979 2.830000e-35 159.0
12 TraesCS7B01G335600 chr5B 80.909 110 18 3 1302 1411 656926020 656926126 1.750000e-12 84.2
13 TraesCS7B01G335600 chr4D 98.876 89 1 0 2662 2750 509132929 509132841 2.830000e-35 159.0
14 TraesCS7B01G335600 chr4D 78.199 211 34 11 1208 1412 121970959 121971163 1.030000e-24 124.0
15 TraesCS7B01G335600 chr3D 98.876 89 1 0 2662 2750 269662102 269662190 2.830000e-35 159.0
16 TraesCS7B01G335600 chr2D 98.876 89 1 0 2662 2750 550637232 550637144 2.830000e-35 159.0
17 TraesCS7B01G335600 chr3B 97.778 90 2 0 2661 2750 315404846 315404757 3.670000e-34 156.0
18 TraesCS7B01G335600 chr5D 72.232 551 110 32 1208 1746 424033439 424033958 2.220000e-26 130.0
19 TraesCS7B01G335600 chr5D 72.451 461 94 28 1302 1738 520910224 520910675 1.730000e-22 117.0
20 TraesCS7B01G335600 chr4B 78.673 211 33 12 1208 1412 184865091 184865295 2.220000e-26 130.0
21 TraesCS7B01G335600 chr4B 72.581 496 93 32 1271 1737 494692158 494691677 3.720000e-24 122.0
22 TraesCS7B01G335600 chr4A 77.885 208 34 11 1211 1412 449117542 449117341 4.810000e-23 119.0
23 TraesCS7B01G335600 chr5A 80.000 110 19 3 1302 1411 649441684 649441790 8.170000e-11 78.7


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 TraesCS7B01G335600 chr7B 590499397 590502146 2749 True 5079 5079 100.000000 1 2750 1 chr7B.!!$R2 2749
1 TraesCS7B01G335600 chr7D 547456610 547459067 2457 True 974 2551 87.132333 213 2664 3 chr7D.!!$R1 2451
2 TraesCS7B01G335600 chr7A 631364220 631366689 2469 False 973 2159 88.329333 202 2664 3 chr7A.!!$F1 2462

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
362 366 0.031917 TGCTATTCACCCCCTCCGTA 60.032 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2495 1.202698 GGAGTGCAAACTGGAGTGTCT 60.203 52.381 0.0 0.0 0.0 3.41 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
32 33 6.817765 TTTAAAACACAGCTCCTATTCTGG 57.182 37.500 0.00 0.00 34.76 3.86
33 34 2.409948 AACACAGCTCCTATTCTGGC 57.590 50.000 0.00 0.00 34.76 4.85
34 35 0.543749 ACACAGCTCCTATTCTGGCC 59.456 55.000 0.00 0.00 34.76 5.36
35 36 0.531532 CACAGCTCCTATTCTGGCCG 60.532 60.000 0.00 0.00 34.76 6.13
36 37 0.978146 ACAGCTCCTATTCTGGCCGT 60.978 55.000 0.00 0.00 34.76 5.68
37 38 0.531532 CAGCTCCTATTCTGGCCGTG 60.532 60.000 0.00 0.00 0.00 4.94
38 39 0.978146 AGCTCCTATTCTGGCCGTGT 60.978 55.000 0.00 0.00 0.00 4.49
39 40 0.750850 GCTCCTATTCTGGCCGTGTA 59.249 55.000 0.00 0.00 0.00 2.90
40 41 1.269831 GCTCCTATTCTGGCCGTGTAG 60.270 57.143 0.00 0.00 0.00 2.74
41 42 2.032620 CTCCTATTCTGGCCGTGTAGT 58.967 52.381 0.00 0.00 0.00 2.73
42 43 3.220110 CTCCTATTCTGGCCGTGTAGTA 58.780 50.000 0.00 0.00 0.00 1.82
43 44 3.220110 TCCTATTCTGGCCGTGTAGTAG 58.780 50.000 0.00 0.00 0.00 2.57
44 45 2.957006 CCTATTCTGGCCGTGTAGTAGT 59.043 50.000 0.00 0.00 0.00 2.73
45 46 4.139786 CCTATTCTGGCCGTGTAGTAGTA 58.860 47.826 0.00 0.00 0.00 1.82
46 47 4.215827 CCTATTCTGGCCGTGTAGTAGTAG 59.784 50.000 0.00 0.00 0.00 2.57
47 48 2.795231 TCTGGCCGTGTAGTAGTAGT 57.205 50.000 0.00 0.00 0.00 2.73
48 49 3.912496 TCTGGCCGTGTAGTAGTAGTA 57.088 47.619 0.00 0.00 0.00 1.82
49 50 3.535561 TCTGGCCGTGTAGTAGTAGTAC 58.464 50.000 8.04 8.04 0.00 2.73
50 51 3.055167 TCTGGCCGTGTAGTAGTAGTACA 60.055 47.826 12.90 12.90 32.00 2.90
51 52 3.881688 CTGGCCGTGTAGTAGTAGTACAT 59.118 47.826 18.56 0.00 36.51 2.29
52 53 3.879295 TGGCCGTGTAGTAGTAGTACATC 59.121 47.826 18.56 12.14 36.51 3.06
53 54 3.879295 GGCCGTGTAGTAGTAGTACATCA 59.121 47.826 18.56 5.78 36.51 3.07
54 55 4.024218 GGCCGTGTAGTAGTAGTACATCAG 60.024 50.000 18.56 13.34 36.51 2.90
55 56 4.574013 GCCGTGTAGTAGTAGTACATCAGT 59.426 45.833 18.56 0.00 36.51 3.41
56 57 5.277250 GCCGTGTAGTAGTAGTACATCAGTC 60.277 48.000 18.56 6.82 36.51 3.51
57 58 6.047870 CCGTGTAGTAGTAGTACATCAGTCT 58.952 44.000 18.56 0.00 36.51 3.24
58 59 7.205992 CCGTGTAGTAGTAGTACATCAGTCTA 58.794 42.308 18.56 0.00 36.51 2.59
59 60 7.871973 CCGTGTAGTAGTAGTACATCAGTCTAT 59.128 40.741 18.56 0.00 36.51 1.98
60 61 9.258826 CGTGTAGTAGTAGTACATCAGTCTATT 57.741 37.037 18.56 0.00 36.51 1.73
83 84 5.621197 TTTTTGCGCATAAGTACATCAGT 57.379 34.783 12.75 0.00 0.00 3.41
84 85 4.857871 TTTGCGCATAAGTACATCAGTC 57.142 40.909 12.75 0.00 0.00 3.51
85 86 3.518634 TGCGCATAAGTACATCAGTCA 57.481 42.857 5.66 0.00 0.00 3.41
86 87 3.855858 TGCGCATAAGTACATCAGTCAA 58.144 40.909 5.66 0.00 0.00 3.18
87 88 4.441792 TGCGCATAAGTACATCAGTCAAT 58.558 39.130 5.66 0.00 0.00 2.57
88 89 4.875536 TGCGCATAAGTACATCAGTCAATT 59.124 37.500 5.66 0.00 0.00 2.32
89 90 6.045955 TGCGCATAAGTACATCAGTCAATTA 58.954 36.000 5.66 0.00 0.00 1.40
90 91 6.019075 TGCGCATAAGTACATCAGTCAATTAC 60.019 38.462 5.66 0.00 0.00 1.89
91 92 6.201044 GCGCATAAGTACATCAGTCAATTACT 59.799 38.462 0.30 0.00 39.81 2.24
104 105 5.330295 AGTCAATTACTGTAGCGTAACTCG 58.670 41.667 0.00 0.00 36.93 4.18
105 106 5.091431 GTCAATTACTGTAGCGTAACTCGT 58.909 41.667 0.00 0.00 42.13 4.18
106 107 5.570589 GTCAATTACTGTAGCGTAACTCGTT 59.429 40.000 0.00 0.00 42.13 3.85
107 108 6.088616 GTCAATTACTGTAGCGTAACTCGTTT 59.911 38.462 0.00 0.00 42.13 3.60
108 109 6.088483 TCAATTACTGTAGCGTAACTCGTTTG 59.912 38.462 0.00 0.00 42.13 2.93
109 110 3.360249 ACTGTAGCGTAACTCGTTTGT 57.640 42.857 0.00 0.00 42.13 2.83
110 111 3.709987 ACTGTAGCGTAACTCGTTTGTT 58.290 40.909 0.00 0.00 42.13 2.83
111 112 3.732721 ACTGTAGCGTAACTCGTTTGTTC 59.267 43.478 0.00 0.00 42.13 3.18
112 113 3.968649 TGTAGCGTAACTCGTTTGTTCT 58.031 40.909 0.00 0.00 42.13 3.01
113 114 4.362279 TGTAGCGTAACTCGTTTGTTCTT 58.638 39.130 0.00 0.00 42.13 2.52
114 115 4.805192 TGTAGCGTAACTCGTTTGTTCTTT 59.195 37.500 0.00 0.00 42.13 2.52
115 116 4.448363 AGCGTAACTCGTTTGTTCTTTC 57.552 40.909 0.00 0.00 42.13 2.62
116 117 3.060740 AGCGTAACTCGTTTGTTCTTTCG 60.061 43.478 0.00 0.00 42.13 3.46
117 118 3.302028 GCGTAACTCGTTTGTTCTTTCGT 60.302 43.478 0.00 0.00 42.13 3.85
118 119 4.085619 GCGTAACTCGTTTGTTCTTTCGTA 60.086 41.667 0.00 0.00 42.13 3.43
119 120 5.554324 GCGTAACTCGTTTGTTCTTTCGTAA 60.554 40.000 0.00 0.00 42.13 3.18
120 121 6.402017 CGTAACTCGTTTGTTCTTTCGTAAA 58.598 36.000 0.00 0.00 34.52 2.01
121 122 7.059212 CGTAACTCGTTTGTTCTTTCGTAAAT 58.941 34.615 0.00 0.00 34.52 1.40
122 123 8.207252 CGTAACTCGTTTGTTCTTTCGTAAATA 58.793 33.333 0.00 0.00 34.52 1.40
123 124 9.508495 GTAACTCGTTTGTTCTTTCGTAAATAG 57.492 33.333 0.00 0.00 0.00 1.73
124 125 7.935338 ACTCGTTTGTTCTTTCGTAAATAGA 57.065 32.000 0.00 0.00 0.00 1.98
125 126 8.356533 ACTCGTTTGTTCTTTCGTAAATAGAA 57.643 30.769 0.00 0.00 0.00 2.10
126 127 8.819974 ACTCGTTTGTTCTTTCGTAAATAGAAA 58.180 29.630 0.00 0.00 36.34 2.52
127 128 9.640974 CTCGTTTGTTCTTTCGTAAATAGAAAA 57.359 29.630 0.00 0.00 37.18 2.29
128 129 9.985318 TCGTTTGTTCTTTCGTAAATAGAAAAA 57.015 25.926 0.00 0.00 37.18 1.94
150 151 2.303163 AAACAAGGGCGTTTTGTTCC 57.697 45.000 11.90 0.00 45.28 3.62
151 152 1.480789 AACAAGGGCGTTTTGTTCCT 58.519 45.000 7.34 0.00 43.26 3.36
152 153 0.744281 ACAAGGGCGTTTTGTTCCTG 59.256 50.000 0.00 0.00 35.32 3.86
153 154 0.744281 CAAGGGCGTTTTGTTCCTGT 59.256 50.000 0.00 0.00 0.00 4.00
154 155 1.136110 CAAGGGCGTTTTGTTCCTGTT 59.864 47.619 0.00 0.00 0.00 3.16
155 156 1.480789 AGGGCGTTTTGTTCCTGTTT 58.519 45.000 0.00 0.00 0.00 2.83
156 157 1.136110 AGGGCGTTTTGTTCCTGTTTG 59.864 47.619 0.00 0.00 0.00 2.93
157 158 1.135333 GGGCGTTTTGTTCCTGTTTGA 59.865 47.619 0.00 0.00 0.00 2.69
158 159 2.190161 GGCGTTTTGTTCCTGTTTGAC 58.810 47.619 0.00 0.00 0.00 3.18
159 160 1.843753 GCGTTTTGTTCCTGTTTGACG 59.156 47.619 0.00 0.00 0.00 4.35
160 161 2.729778 GCGTTTTGTTCCTGTTTGACGT 60.730 45.455 0.00 0.00 0.00 4.34
161 162 3.494232 CGTTTTGTTCCTGTTTGACGTT 58.506 40.909 0.00 0.00 0.00 3.99
162 163 3.299542 CGTTTTGTTCCTGTTTGACGTTG 59.700 43.478 0.00 0.00 0.00 4.10
163 164 3.495670 TTTGTTCCTGTTTGACGTTGG 57.504 42.857 0.00 0.00 0.00 3.77
164 165 2.116827 TGTTCCTGTTTGACGTTGGT 57.883 45.000 0.00 0.00 0.00 3.67
165 166 2.011222 TGTTCCTGTTTGACGTTGGTC 58.989 47.619 0.00 0.00 43.71 4.02
166 167 1.332686 GTTCCTGTTTGACGTTGGTCC 59.667 52.381 0.00 0.00 42.73 4.46
167 168 0.179040 TCCTGTTTGACGTTGGTCCC 60.179 55.000 0.00 0.00 42.73 4.46
168 169 0.464735 CCTGTTTGACGTTGGTCCCA 60.465 55.000 0.00 0.00 42.73 4.37
169 170 0.944386 CTGTTTGACGTTGGTCCCAG 59.056 55.000 0.00 0.00 42.73 4.45
170 171 0.253610 TGTTTGACGTTGGTCCCAGT 59.746 50.000 0.00 0.00 42.73 4.00
171 172 0.942252 GTTTGACGTTGGTCCCAGTC 59.058 55.000 0.00 0.07 42.73 3.51
172 173 0.531090 TTTGACGTTGGTCCCAGTCG 60.531 55.000 10.06 10.06 42.73 4.18
173 174 2.048503 GACGTTGGTCCCAGTCGG 60.049 66.667 14.17 0.00 37.19 4.79
174 175 2.522436 ACGTTGGTCCCAGTCGGA 60.522 61.111 14.17 0.00 38.83 4.55
175 176 2.261671 CGTTGGTCCCAGTCGGAG 59.738 66.667 5.49 0.00 43.19 4.63
176 177 2.571216 CGTTGGTCCCAGTCGGAGT 61.571 63.158 5.49 0.00 43.19 3.85
177 178 1.246056 CGTTGGTCCCAGTCGGAGTA 61.246 60.000 5.49 0.00 43.19 2.59
178 179 0.531200 GTTGGTCCCAGTCGGAGTAG 59.469 60.000 0.00 0.00 43.19 2.57
179 180 0.613853 TTGGTCCCAGTCGGAGTAGG 60.614 60.000 0.00 0.00 43.19 3.18
180 181 1.000107 GGTCCCAGTCGGAGTAGGT 60.000 63.158 0.00 0.00 43.19 3.08
181 182 0.614134 GGTCCCAGTCGGAGTAGGTT 60.614 60.000 0.00 0.00 43.19 3.50
182 183 0.531200 GTCCCAGTCGGAGTAGGTTG 59.469 60.000 0.00 0.00 43.19 3.77
183 184 0.406750 TCCCAGTCGGAGTAGGTTGA 59.593 55.000 0.00 0.00 34.86 3.18
184 185 0.818296 CCCAGTCGGAGTAGGTTGAG 59.182 60.000 0.00 0.00 0.00 3.02
185 186 1.546961 CCAGTCGGAGTAGGTTGAGT 58.453 55.000 0.00 0.00 0.00 3.41
186 187 1.893801 CCAGTCGGAGTAGGTTGAGTT 59.106 52.381 0.00 0.00 0.00 3.01
187 188 2.352814 CCAGTCGGAGTAGGTTGAGTTG 60.353 54.545 0.00 0.00 0.00 3.16
188 189 2.557056 CAGTCGGAGTAGGTTGAGTTGA 59.443 50.000 0.00 0.00 0.00 3.18
189 190 2.820787 AGTCGGAGTAGGTTGAGTTGAG 59.179 50.000 0.00 0.00 0.00 3.02
190 191 2.557490 GTCGGAGTAGGTTGAGTTGAGT 59.443 50.000 0.00 0.00 0.00 3.41
191 192 3.005578 GTCGGAGTAGGTTGAGTTGAGTT 59.994 47.826 0.00 0.00 0.00 3.01
192 193 3.640029 TCGGAGTAGGTTGAGTTGAGTTT 59.360 43.478 0.00 0.00 0.00 2.66
193 194 4.100498 TCGGAGTAGGTTGAGTTGAGTTTT 59.900 41.667 0.00 0.00 0.00 2.43
194 195 4.814771 CGGAGTAGGTTGAGTTGAGTTTTT 59.185 41.667 0.00 0.00 0.00 1.94
226 227 4.487714 AGGTTGAGTTGAGTTGACTTGA 57.512 40.909 0.00 0.00 0.00 3.02
291 295 2.740055 GCAGTGGAGTGGTGCGAG 60.740 66.667 0.00 0.00 0.00 5.03
334 338 4.444024 CATCACGTGGCCGCAACG 62.444 66.667 18.84 18.84 46.32 4.10
348 352 0.108138 GCAACGGACCAGAGTGCTAT 60.108 55.000 0.00 0.00 30.87 2.97
353 357 1.471676 CGGACCAGAGTGCTATTCACC 60.472 57.143 0.00 0.00 46.81 4.02
358 362 1.139853 CAGAGTGCTATTCACCCCCTC 59.860 57.143 0.00 0.00 46.81 4.30
360 364 1.146263 GTGCTATTCACCCCCTCCG 59.854 63.158 0.00 0.00 39.79 4.63
361 365 1.306654 TGCTATTCACCCCCTCCGT 60.307 57.895 0.00 0.00 0.00 4.69
362 366 0.031917 TGCTATTCACCCCCTCCGTA 60.032 55.000 0.00 0.00 0.00 4.02
363 367 0.680061 GCTATTCACCCCCTCCGTAG 59.320 60.000 0.00 0.00 0.00 3.51
364 368 2.033208 GCTATTCACCCCCTCCGTAGT 61.033 57.143 0.00 0.00 0.00 2.73
365 369 2.754186 GCTATTCACCCCCTCCGTAGTA 60.754 54.545 0.00 0.00 0.00 1.82
366 370 2.083628 ATTCACCCCCTCCGTAGTAG 57.916 55.000 0.00 0.00 0.00 2.57
367 371 0.032813 TTCACCCCCTCCGTAGTAGG 60.033 60.000 0.00 0.00 31.22 3.18
368 372 0.920763 TCACCCCCTCCGTAGTAGGA 60.921 60.000 0.00 0.00 34.53 2.94
498 516 3.301379 GCATGCATTCAATACAACGTGTG 59.699 43.478 14.21 0.00 0.00 3.82
516 534 5.096169 CGTGTGTAAACATGGTTTTTGTCA 58.904 37.500 0.00 0.00 0.00 3.58
535 599 2.434884 CAAGCCACAGCCGATCGT 60.435 61.111 15.09 0.00 41.25 3.73
545 615 3.179265 CCGATCGTGTCACCGCAC 61.179 66.667 15.09 0.00 36.12 5.34
548 618 1.447838 GATCGTGTCACCGCACCAT 60.448 57.895 0.00 0.00 36.08 3.55
549 619 1.421410 GATCGTGTCACCGCACCATC 61.421 60.000 0.00 0.00 36.08 3.51
550 620 2.166130 ATCGTGTCACCGCACCATCA 62.166 55.000 0.00 0.00 36.08 3.07
551 621 1.741401 CGTGTCACCGCACCATCAT 60.741 57.895 0.00 0.00 36.08 2.45
562 632 2.033801 CGCACCATCATCTTCCCATTTC 59.966 50.000 0.00 0.00 0.00 2.17
570 640 0.960364 TCTTCCCATTTCTGCGTGCC 60.960 55.000 0.00 0.00 0.00 5.01
657 744 2.096860 GGCGAAAGTTTCTCTCGTTCAC 60.097 50.000 13.56 0.00 35.06 3.18
658 745 2.538449 GCGAAAGTTTCTCTCGTTCACA 59.462 45.455 13.56 0.00 35.06 3.58
659 746 3.000925 GCGAAAGTTTCTCTCGTTCACAA 59.999 43.478 13.56 0.00 35.06 3.33
661 750 4.267928 CGAAAGTTTCTCTCGTTCACAAGT 59.732 41.667 13.56 0.00 0.00 3.16
673 762 3.728718 CGTTCACAAGTTTTTCCATTCGG 59.271 43.478 0.00 0.00 0.00 4.30
675 764 4.561735 TCACAAGTTTTTCCATTCGGAC 57.438 40.909 0.00 0.00 42.67 4.79
681 770 7.333423 CACAAGTTTTTCCATTCGGACTAGATA 59.667 37.037 0.00 0.00 42.67 1.98
710 816 5.115923 CGTTTTTACGGGCAGTACATTTTTC 59.884 40.000 0.00 0.00 34.56 2.29
715 821 2.030457 CGGGCAGTACATTTTTCTAGCG 59.970 50.000 0.00 0.00 0.00 4.26
724 830 3.873952 ACATTTTTCTAGCGCTCCATCTC 59.126 43.478 16.34 0.00 0.00 2.75
725 831 2.209838 TTTTCTAGCGCTCCATCTCG 57.790 50.000 16.34 0.00 0.00 4.04
740 846 2.045242 TCGCTCCGCTCTGTACCT 60.045 61.111 0.00 0.00 0.00 3.08
759 865 1.815003 CTCCTCACATGGCAAAAGGTC 59.185 52.381 0.00 0.00 0.00 3.85
761 867 1.548582 CCTCACATGGCAAAAGGTCCT 60.549 52.381 0.00 0.00 0.00 3.85
766 872 1.538687 ATGGCAAAAGGTCCTGCTGC 61.539 55.000 14.54 14.54 38.65 5.25
816 923 2.887152 CAGACTTTACAGCCAGCCTTTT 59.113 45.455 0.00 0.00 0.00 2.27
846 953 0.409484 AAAACCCACCCTCCATCCAG 59.591 55.000 0.00 0.00 0.00 3.86
884 991 3.570912 ACCCTCATTAAATACACCCCG 57.429 47.619 0.00 0.00 0.00 5.73
989 1097 3.045142 GCAAGCAGCCAAGAAGCA 58.955 55.556 0.00 0.00 37.23 3.91
1007 1115 1.830279 CACACACAGGAGATGGCAAT 58.170 50.000 0.00 0.00 0.00 3.56
1206 1314 4.414956 TCCATCCGCCTCCCCACT 62.415 66.667 0.00 0.00 0.00 4.00
1794 1902 3.390967 TGATCCAAACCTGAAGACAGTGA 59.609 43.478 0.00 0.00 42.05 3.41
1889 2017 2.735134 GTGCCGGGATCGATAATAACAC 59.265 50.000 2.18 1.11 39.00 3.32
1890 2018 2.289195 TGCCGGGATCGATAATAACACC 60.289 50.000 2.18 0.00 39.00 4.16
1895 2023 4.315803 GGGATCGATAATAACACCAGTGG 58.684 47.826 7.91 7.91 34.19 4.00
1896 2024 4.202326 GGGATCGATAATAACACCAGTGGT 60.202 45.833 9.70 9.70 35.62 4.16
1897 2025 5.011329 GGGATCGATAATAACACCAGTGGTA 59.989 44.000 16.22 0.00 37.15 3.25
1898 2026 6.295688 GGGATCGATAATAACACCAGTGGTAT 60.296 42.308 16.22 9.79 44.74 2.73
1905 2033 5.927281 ATAACACCAGTGGTATTCGTAGT 57.073 39.130 16.22 3.69 40.32 2.73
1906 2034 3.863142 ACACCAGTGGTATTCGTAGTC 57.137 47.619 16.22 0.00 32.11 2.59
1907 2035 2.163010 ACACCAGTGGTATTCGTAGTCG 59.837 50.000 16.22 0.51 32.11 4.18
1908 2036 2.163010 CACCAGTGGTATTCGTAGTCGT 59.837 50.000 16.22 0.00 34.43 4.34
1909 2037 3.374988 CACCAGTGGTATTCGTAGTCGTA 59.625 47.826 16.22 0.00 34.43 3.43
1915 2043 6.697455 CAGTGGTATTCGTAGTCGTAGTAGTA 59.303 42.308 0.00 0.00 38.33 1.82
1924 2052 4.943142 AGTCGTAGTAGTAGCAGTGAAC 57.057 45.455 0.00 0.00 0.00 3.18
1974 2106 6.069615 GCCTGGATGGGTATAATAGTATGGTT 60.070 42.308 0.00 0.00 36.00 3.67
2052 2185 1.608025 GGTTGATTCTGTCCTCGTGCA 60.608 52.381 0.00 0.00 0.00 4.57
2090 2234 5.220529 GCATTCATTTTTCCTGCATTGCTAC 60.221 40.000 10.49 0.00 33.13 3.58
2091 2235 4.095410 TCATTTTTCCTGCATTGCTACG 57.905 40.909 10.49 0.00 0.00 3.51
2092 2236 3.505680 TCATTTTTCCTGCATTGCTACGT 59.494 39.130 10.49 0.00 0.00 3.57
2093 2237 4.697828 TCATTTTTCCTGCATTGCTACGTA 59.302 37.500 10.49 0.00 0.00 3.57
2096 2240 2.579207 TCCTGCATTGCTACGTACTC 57.421 50.000 10.49 0.00 0.00 2.59
2108 2259 5.779922 TGCTACGTACTCTTGATTTCTTGT 58.220 37.500 0.00 0.00 0.00 3.16
2182 2333 2.665165 TGAACATTTTCAGCAGTGGGT 58.335 42.857 0.00 0.00 36.79 4.51
2252 2403 3.197790 AGTGCGCCGCATTAGCTG 61.198 61.111 17.54 0.00 41.91 4.24
2290 2441 5.163764 GCTTTTGTCACGGAACATCATCATA 60.164 40.000 0.00 0.00 0.00 2.15
2359 2510 2.262423 AGGAAGACACTCCAGTTTGC 57.738 50.000 0.00 0.00 38.02 3.68
2369 2524 1.525995 CCAGTTTGCACTCCGGTGT 60.526 57.895 2.61 2.61 44.65 4.16
2418 2573 1.597663 CGTTGGATACTTGGATTCCGC 59.402 52.381 0.00 0.00 37.61 5.54
2419 2574 1.597663 GTTGGATACTTGGATTCCGCG 59.402 52.381 0.00 0.00 37.61 6.46
2420 2575 1.116308 TGGATACTTGGATTCCGCGA 58.884 50.000 8.23 0.00 37.61 5.87
2436 2592 0.519999 GCGAAATGCAGCGACTCTTG 60.520 55.000 10.12 0.00 45.45 3.02
2451 2607 1.217244 CTTGTACCGTCTTCCCCCG 59.783 63.158 0.00 0.00 0.00 5.73
2452 2608 2.847435 CTTGTACCGTCTTCCCCCGC 62.847 65.000 0.00 0.00 0.00 6.13
2455 2611 2.215625 TACCGTCTTCCCCCGCAAA 61.216 57.895 0.00 0.00 0.00 3.68
2457 2613 2.332654 CCGTCTTCCCCCGCAAAAG 61.333 63.158 0.00 0.00 0.00 2.27
2472 2630 4.336101 CGCAAAAGCGTATAAATTTCCGA 58.664 39.130 0.00 0.00 0.00 4.55
2473 2631 4.789119 CGCAAAAGCGTATAAATTTCCGAA 59.211 37.500 0.00 0.00 0.00 4.30
2504 2662 9.222916 CGCTGAAGAAATACCAGTATATATACG 57.777 37.037 15.57 11.05 38.28 3.06
2527 2685 8.316640 ACGCATCTTTATTTGGAGATAATCTC 57.683 34.615 0.00 0.00 42.66 2.75
2529 2687 7.239972 GCATCTTTATTTGGAGATAATCTCGC 58.760 38.462 0.00 0.00 44.28 5.03
2531 2689 8.944029 CATCTTTATTTGGAGATAATCTCGCAT 58.056 33.333 0.00 0.00 44.28 4.73
2578 2737 4.674623 GCAGAAAAGCTCACCTCATTCATG 60.675 45.833 0.00 0.00 0.00 3.07
2583 2742 3.806380 AGCTCACCTCATTCATGTCATC 58.194 45.455 0.00 0.00 0.00 2.92
2589 2759 4.939439 CACCTCATTCATGTCATCTTCACA 59.061 41.667 0.00 0.00 0.00 3.58
2647 2830 2.041891 AGCCAGTAGAGTGTACTCCAGT 59.958 50.000 8.34 0.00 43.88 4.00
2664 2847 2.852413 CCAGTATTCACGTCGCAGTTAG 59.148 50.000 0.00 0.00 0.00 2.34
2665 2848 3.427098 CCAGTATTCACGTCGCAGTTAGA 60.427 47.826 0.00 0.00 0.00 2.10
2666 2849 3.786576 CAGTATTCACGTCGCAGTTAGAG 59.213 47.826 0.00 0.00 0.00 2.43
2667 2850 1.630148 ATTCACGTCGCAGTTAGAGC 58.370 50.000 0.00 0.00 0.00 4.09
2668 2851 0.312729 TTCACGTCGCAGTTAGAGCA 59.687 50.000 0.00 0.00 0.00 4.26
2669 2852 0.312729 TCACGTCGCAGTTAGAGCAA 59.687 50.000 0.00 0.00 0.00 3.91
2670 2853 0.710567 CACGTCGCAGTTAGAGCAAG 59.289 55.000 0.00 0.00 0.00 4.01
2671 2854 0.314302 ACGTCGCAGTTAGAGCAAGT 59.686 50.000 0.00 0.00 0.00 3.16
2672 2855 1.538512 ACGTCGCAGTTAGAGCAAGTA 59.461 47.619 0.00 0.00 0.00 2.24
2673 2856 2.163815 ACGTCGCAGTTAGAGCAAGTAT 59.836 45.455 0.00 0.00 0.00 2.12
2674 2857 3.376234 ACGTCGCAGTTAGAGCAAGTATA 59.624 43.478 0.00 0.00 0.00 1.47
2675 2858 4.142534 ACGTCGCAGTTAGAGCAAGTATAA 60.143 41.667 0.00 0.00 0.00 0.98
2676 2859 4.976731 CGTCGCAGTTAGAGCAAGTATAAT 59.023 41.667 0.00 0.00 0.00 1.28
2677 2860 6.140786 CGTCGCAGTTAGAGCAAGTATAATA 58.859 40.000 0.00 0.00 0.00 0.98
2678 2861 6.303496 CGTCGCAGTTAGAGCAAGTATAATAG 59.697 42.308 0.00 0.00 0.00 1.73
2679 2862 7.361127 GTCGCAGTTAGAGCAAGTATAATAGA 58.639 38.462 0.00 0.00 0.00 1.98
2680 2863 7.535940 GTCGCAGTTAGAGCAAGTATAATAGAG 59.464 40.741 0.00 0.00 0.00 2.43
2681 2864 6.306837 CGCAGTTAGAGCAAGTATAATAGAGC 59.693 42.308 0.00 0.00 0.00 4.09
2682 2865 7.375053 GCAGTTAGAGCAAGTATAATAGAGCT 58.625 38.462 0.00 0.00 34.61 4.09
2683 2866 7.328249 GCAGTTAGAGCAAGTATAATAGAGCTG 59.672 40.741 0.00 0.00 31.61 4.24
2684 2867 8.572185 CAGTTAGAGCAAGTATAATAGAGCTGA 58.428 37.037 0.00 0.00 31.61 4.26
2685 2868 8.792633 AGTTAGAGCAAGTATAATAGAGCTGAG 58.207 37.037 0.00 0.00 31.61 3.35
2686 2869 8.573035 GTTAGAGCAAGTATAATAGAGCTGAGT 58.427 37.037 0.00 0.00 31.61 3.41
2687 2870 7.214467 AGAGCAAGTATAATAGAGCTGAGTC 57.786 40.000 0.00 0.00 31.61 3.36
2688 2871 6.775142 AGAGCAAGTATAATAGAGCTGAGTCA 59.225 38.462 0.00 0.00 31.61 3.41
2689 2872 6.980593 AGCAAGTATAATAGAGCTGAGTCAG 58.019 40.000 16.21 16.21 34.12 3.51
2700 2883 2.430546 CTGAGTCAGCGGGCTATAAG 57.569 55.000 7.33 0.00 0.00 1.73
2701 2884 1.000283 CTGAGTCAGCGGGCTATAAGG 60.000 57.143 7.33 0.00 0.00 2.69
2702 2885 1.329256 GAGTCAGCGGGCTATAAGGA 58.671 55.000 0.00 0.00 0.00 3.36
2703 2886 1.687123 GAGTCAGCGGGCTATAAGGAA 59.313 52.381 0.00 0.00 0.00 3.36
2704 2887 2.300437 GAGTCAGCGGGCTATAAGGAAT 59.700 50.000 0.00 0.00 0.00 3.01
2705 2888 3.507411 AGTCAGCGGGCTATAAGGAATA 58.493 45.455 0.00 0.00 0.00 1.75
2706 2889 3.901844 AGTCAGCGGGCTATAAGGAATAA 59.098 43.478 0.00 0.00 0.00 1.40
2707 2890 4.347000 AGTCAGCGGGCTATAAGGAATAAA 59.653 41.667 0.00 0.00 0.00 1.40
2708 2891 4.451435 GTCAGCGGGCTATAAGGAATAAAC 59.549 45.833 0.00 0.00 0.00 2.01
2709 2892 4.347000 TCAGCGGGCTATAAGGAATAAACT 59.653 41.667 0.00 0.00 0.00 2.66
2710 2893 5.541101 TCAGCGGGCTATAAGGAATAAACTA 59.459 40.000 0.00 0.00 0.00 2.24
2711 2894 5.869888 CAGCGGGCTATAAGGAATAAACTAG 59.130 44.000 0.00 0.00 0.00 2.57
2712 2895 5.543020 AGCGGGCTATAAGGAATAAACTAGT 59.457 40.000 0.00 0.00 0.00 2.57
2713 2896 6.723052 AGCGGGCTATAAGGAATAAACTAGTA 59.277 38.462 0.00 0.00 0.00 1.82
2714 2897 7.399478 AGCGGGCTATAAGGAATAAACTAGTAT 59.601 37.037 0.00 0.00 0.00 2.12
2715 2898 8.689972 GCGGGCTATAAGGAATAAACTAGTATA 58.310 37.037 0.00 0.00 0.00 1.47
2736 2919 9.959721 AGTATATTTCTGCTTAGTTGGAAGAAA 57.040 29.630 0.00 0.00 41.06 2.52
2739 2922 6.867662 TTTCTGCTTAGTTGGAAGAAAGAG 57.132 37.500 0.00 0.00 34.49 2.85
2740 2923 5.808366 TCTGCTTAGTTGGAAGAAAGAGA 57.192 39.130 0.00 0.00 0.00 3.10
2741 2924 6.174720 TCTGCTTAGTTGGAAGAAAGAGAA 57.825 37.500 0.00 0.00 0.00 2.87
2742 2925 6.226787 TCTGCTTAGTTGGAAGAAAGAGAAG 58.773 40.000 0.00 0.00 0.00 2.85
2743 2926 6.042093 TCTGCTTAGTTGGAAGAAAGAGAAGA 59.958 38.462 0.00 0.00 0.00 2.87
2744 2927 6.226787 TGCTTAGTTGGAAGAAAGAGAAGAG 58.773 40.000 0.00 0.00 0.00 2.85
2745 2928 5.641636 GCTTAGTTGGAAGAAAGAGAAGAGG 59.358 44.000 0.00 0.00 0.00 3.69
2746 2929 6.519213 GCTTAGTTGGAAGAAAGAGAAGAGGA 60.519 42.308 0.00 0.00 0.00 3.71
2747 2930 5.482163 AGTTGGAAGAAAGAGAAGAGGAG 57.518 43.478 0.00 0.00 0.00 3.69
2748 2931 5.151454 AGTTGGAAGAAAGAGAAGAGGAGA 58.849 41.667 0.00 0.00 0.00 3.71
2749 2932 5.245977 AGTTGGAAGAAAGAGAAGAGGAGAG 59.754 44.000 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.657336 CCAGAATAGGAGCTGTGTTTTAAAAA 58.343 34.615 1.31 0.00 0.00 1.94
8 9 6.294508 GCCAGAATAGGAGCTGTGTTTTAAAA 60.295 38.462 0.00 0.00 0.00 1.52
9 10 5.183140 GCCAGAATAGGAGCTGTGTTTTAAA 59.817 40.000 0.00 0.00 0.00 1.52
10 11 4.700213 GCCAGAATAGGAGCTGTGTTTTAA 59.300 41.667 0.00 0.00 0.00 1.52
11 12 4.261801 GCCAGAATAGGAGCTGTGTTTTA 58.738 43.478 0.00 0.00 0.00 1.52
12 13 3.084786 GCCAGAATAGGAGCTGTGTTTT 58.915 45.455 0.00 0.00 0.00 2.43
13 14 2.619074 GGCCAGAATAGGAGCTGTGTTT 60.619 50.000 0.00 0.00 0.00 2.83
14 15 1.065126 GGCCAGAATAGGAGCTGTGTT 60.065 52.381 0.00 0.00 0.00 3.32
15 16 0.543749 GGCCAGAATAGGAGCTGTGT 59.456 55.000 0.00 0.00 0.00 3.72
16 17 0.531532 CGGCCAGAATAGGAGCTGTG 60.532 60.000 2.24 0.00 0.00 3.66
17 18 0.978146 ACGGCCAGAATAGGAGCTGT 60.978 55.000 2.24 0.00 39.96 4.40
18 19 0.531532 CACGGCCAGAATAGGAGCTG 60.532 60.000 2.24 0.00 37.63 4.24
19 20 0.978146 ACACGGCCAGAATAGGAGCT 60.978 55.000 2.24 0.00 0.00 4.09
20 21 0.750850 TACACGGCCAGAATAGGAGC 59.249 55.000 2.24 0.00 0.00 4.70
21 22 2.032620 ACTACACGGCCAGAATAGGAG 58.967 52.381 2.24 0.00 0.00 3.69
22 23 2.154567 ACTACACGGCCAGAATAGGA 57.845 50.000 2.24 0.00 0.00 2.94
23 24 2.957006 ACTACTACACGGCCAGAATAGG 59.043 50.000 2.24 0.00 0.00 2.57
24 25 4.820716 ACTACTACTACACGGCCAGAATAG 59.179 45.833 2.24 0.86 0.00 1.73
25 26 4.785301 ACTACTACTACACGGCCAGAATA 58.215 43.478 2.24 0.00 0.00 1.75
26 27 3.629087 ACTACTACTACACGGCCAGAAT 58.371 45.455 2.24 0.00 0.00 2.40
27 28 3.077484 ACTACTACTACACGGCCAGAA 57.923 47.619 2.24 0.00 0.00 3.02
28 29 2.795231 ACTACTACTACACGGCCAGA 57.205 50.000 2.24 0.00 0.00 3.86
29 30 3.273434 TGTACTACTACTACACGGCCAG 58.727 50.000 2.24 0.00 0.00 4.85
30 31 3.348647 TGTACTACTACTACACGGCCA 57.651 47.619 2.24 0.00 0.00 5.36
31 32 3.879295 TGATGTACTACTACTACACGGCC 59.121 47.826 0.00 0.00 0.00 6.13
32 33 4.574013 ACTGATGTACTACTACTACACGGC 59.426 45.833 0.00 0.00 0.00 5.68
33 34 6.047870 AGACTGATGTACTACTACTACACGG 58.952 44.000 0.00 0.00 0.00 4.94
34 35 8.815141 ATAGACTGATGTACTACTACTACACG 57.185 38.462 0.00 0.00 0.00 4.49
61 62 5.180304 TGACTGATGTACTTATGCGCAAAAA 59.820 36.000 17.11 11.54 0.00 1.94
62 63 4.693095 TGACTGATGTACTTATGCGCAAAA 59.307 37.500 17.11 2.00 0.00 2.44
63 64 4.249661 TGACTGATGTACTTATGCGCAAA 58.750 39.130 17.11 9.55 0.00 3.68
64 65 3.855858 TGACTGATGTACTTATGCGCAA 58.144 40.909 17.11 0.00 0.00 4.85
65 66 3.518634 TGACTGATGTACTTATGCGCA 57.481 42.857 14.96 14.96 0.00 6.09
66 67 5.409643 AATTGACTGATGTACTTATGCGC 57.590 39.130 0.00 0.00 0.00 6.09
67 68 7.700322 AGTAATTGACTGATGTACTTATGCG 57.300 36.000 0.00 0.00 36.87 4.73
78 79 8.149363 CGAGTTACGCTACAGTAATTGACTGAT 61.149 40.741 8.23 0.00 46.08 2.90
79 80 6.891536 CGAGTTACGCTACAGTAATTGACTGA 60.892 42.308 8.23 0.00 46.08 3.41
81 82 5.106396 ACGAGTTACGCTACAGTAATTGACT 60.106 40.000 0.00 0.00 46.94 3.41
82 83 5.091431 ACGAGTTACGCTACAGTAATTGAC 58.909 41.667 0.00 0.00 46.94 3.18
83 84 5.300969 ACGAGTTACGCTACAGTAATTGA 57.699 39.130 0.00 0.00 46.94 2.57
84 85 6.129009 ACAAACGAGTTACGCTACAGTAATTG 60.129 38.462 0.00 0.00 46.94 2.32
85 86 5.922544 ACAAACGAGTTACGCTACAGTAATT 59.077 36.000 0.00 0.00 46.94 1.40
86 87 5.464168 ACAAACGAGTTACGCTACAGTAAT 58.536 37.500 0.00 0.00 46.94 1.89
87 88 4.858935 ACAAACGAGTTACGCTACAGTAA 58.141 39.130 0.00 0.00 46.94 2.24
88 89 4.488126 ACAAACGAGTTACGCTACAGTA 57.512 40.909 0.00 0.00 46.94 2.74
89 90 3.360249 ACAAACGAGTTACGCTACAGT 57.640 42.857 0.00 0.00 46.94 3.55
90 91 3.979495 AGAACAAACGAGTTACGCTACAG 59.021 43.478 0.00 0.00 46.94 2.74
91 92 3.968649 AGAACAAACGAGTTACGCTACA 58.031 40.909 0.00 0.00 46.94 2.74
92 93 4.961433 AAGAACAAACGAGTTACGCTAC 57.039 40.909 0.00 0.00 46.94 3.58
93 94 4.146961 CGAAAGAACAAACGAGTTACGCTA 59.853 41.667 0.00 0.00 46.94 4.26
94 95 3.060740 CGAAAGAACAAACGAGTTACGCT 60.061 43.478 0.00 0.00 46.94 5.07
95 96 3.205089 CGAAAGAACAAACGAGTTACGC 58.795 45.455 0.00 0.00 46.94 4.42
97 98 9.508495 CTATTTACGAAAGAACAAACGAGTTAC 57.492 33.333 0.00 0.00 0.00 2.50
98 99 9.462174 TCTATTTACGAAAGAACAAACGAGTTA 57.538 29.630 0.00 0.00 0.00 2.24
99 100 8.356533 TCTATTTACGAAAGAACAAACGAGTT 57.643 30.769 0.00 0.00 0.00 3.01
100 101 7.935338 TCTATTTACGAAAGAACAAACGAGT 57.065 32.000 0.00 0.00 0.00 4.18
101 102 9.640974 TTTTCTATTTACGAAAGAACAAACGAG 57.359 29.630 0.00 0.00 32.55 4.18
102 103 9.985318 TTTTTCTATTTACGAAAGAACAAACGA 57.015 25.926 0.00 0.00 32.55 3.85
129 130 3.004171 GGAACAAAACGCCCTTGTTTTT 58.996 40.909 10.36 0.00 46.84 1.94
131 132 1.828595 AGGAACAAAACGCCCTTGTTT 59.171 42.857 10.36 0.00 44.85 2.83
132 133 1.136110 CAGGAACAAAACGCCCTTGTT 59.864 47.619 9.17 9.17 46.89 2.83
133 134 0.744281 CAGGAACAAAACGCCCTTGT 59.256 50.000 0.00 0.00 38.65 3.16
134 135 0.744281 ACAGGAACAAAACGCCCTTG 59.256 50.000 0.00 0.00 0.00 3.61
135 136 1.480789 AACAGGAACAAAACGCCCTT 58.519 45.000 0.00 0.00 0.00 3.95
136 137 1.136110 CAAACAGGAACAAAACGCCCT 59.864 47.619 0.00 0.00 0.00 5.19
137 138 1.135333 TCAAACAGGAACAAAACGCCC 59.865 47.619 0.00 0.00 0.00 6.13
138 139 2.190161 GTCAAACAGGAACAAAACGCC 58.810 47.619 0.00 0.00 0.00 5.68
139 140 1.843753 CGTCAAACAGGAACAAAACGC 59.156 47.619 0.00 0.00 0.00 4.84
140 141 3.125698 ACGTCAAACAGGAACAAAACG 57.874 42.857 0.00 0.00 35.20 3.60
141 142 3.610677 CCAACGTCAAACAGGAACAAAAC 59.389 43.478 0.00 0.00 0.00 2.43
142 143 3.256136 ACCAACGTCAAACAGGAACAAAA 59.744 39.130 0.00 0.00 0.00 2.44
143 144 2.820787 ACCAACGTCAAACAGGAACAAA 59.179 40.909 0.00 0.00 0.00 2.83
144 145 2.420722 GACCAACGTCAAACAGGAACAA 59.579 45.455 0.00 0.00 38.99 2.83
145 146 2.011222 GACCAACGTCAAACAGGAACA 58.989 47.619 0.00 0.00 38.99 3.18
146 147 1.332686 GGACCAACGTCAAACAGGAAC 59.667 52.381 0.00 0.00 41.13 3.62
147 148 1.670791 GGACCAACGTCAAACAGGAA 58.329 50.000 0.00 0.00 41.13 3.36
148 149 0.179040 GGGACCAACGTCAAACAGGA 60.179 55.000 0.00 0.00 41.13 3.86
149 150 0.464735 TGGGACCAACGTCAAACAGG 60.465 55.000 0.00 0.00 41.13 4.00
150 151 0.944386 CTGGGACCAACGTCAAACAG 59.056 55.000 0.00 0.00 41.13 3.16
151 152 0.253610 ACTGGGACCAACGTCAAACA 59.746 50.000 0.00 0.00 41.13 2.83
152 153 0.942252 GACTGGGACCAACGTCAAAC 59.058 55.000 6.01 0.00 41.13 2.93
153 154 0.531090 CGACTGGGACCAACGTCAAA 60.531 55.000 10.25 0.00 41.13 2.69
154 155 1.068417 CGACTGGGACCAACGTCAA 59.932 57.895 10.25 0.00 41.13 3.18
155 156 2.732016 CGACTGGGACCAACGTCA 59.268 61.111 10.25 0.00 41.13 4.35
156 157 2.048503 CCGACTGGGACCAACGTC 60.049 66.667 13.54 8.21 38.47 4.34
157 158 2.522436 TCCGACTGGGACCAACGT 60.522 61.111 13.54 0.91 40.94 3.99
158 159 1.246056 TACTCCGACTGGGACCAACG 61.246 60.000 9.55 9.55 40.94 4.10
159 160 0.531200 CTACTCCGACTGGGACCAAC 59.469 60.000 0.00 0.00 40.94 3.77
160 161 0.613853 CCTACTCCGACTGGGACCAA 60.614 60.000 0.00 0.00 40.94 3.67
161 162 1.000019 CCTACTCCGACTGGGACCA 60.000 63.158 0.00 0.00 40.94 4.02
162 163 0.614134 AACCTACTCCGACTGGGACC 60.614 60.000 0.00 0.00 40.94 4.46
163 164 0.531200 CAACCTACTCCGACTGGGAC 59.469 60.000 0.00 0.00 40.94 4.46
164 165 0.406750 TCAACCTACTCCGACTGGGA 59.593 55.000 0.00 0.00 44.68 4.37
165 166 0.818296 CTCAACCTACTCCGACTGGG 59.182 60.000 0.00 0.00 35.24 4.45
166 167 1.546961 ACTCAACCTACTCCGACTGG 58.453 55.000 0.00 0.00 0.00 4.00
167 168 2.557056 TCAACTCAACCTACTCCGACTG 59.443 50.000 0.00 0.00 0.00 3.51
168 169 2.820787 CTCAACTCAACCTACTCCGACT 59.179 50.000 0.00 0.00 0.00 4.18
169 170 2.557490 ACTCAACTCAACCTACTCCGAC 59.443 50.000 0.00 0.00 0.00 4.79
170 171 2.872732 ACTCAACTCAACCTACTCCGA 58.127 47.619 0.00 0.00 0.00 4.55
171 172 3.662247 AACTCAACTCAACCTACTCCG 57.338 47.619 0.00 0.00 0.00 4.63
194 195 5.298276 ACTCAACTCAACCTATTCGCAAAAA 59.702 36.000 0.00 0.00 0.00 1.94
195 196 4.819630 ACTCAACTCAACCTATTCGCAAAA 59.180 37.500 0.00 0.00 0.00 2.44
196 197 4.385825 ACTCAACTCAACCTATTCGCAAA 58.614 39.130 0.00 0.00 0.00 3.68
197 198 4.002906 ACTCAACTCAACCTATTCGCAA 57.997 40.909 0.00 0.00 0.00 4.85
198 199 3.678056 ACTCAACTCAACCTATTCGCA 57.322 42.857 0.00 0.00 0.00 5.10
199 200 3.994392 TCAACTCAACTCAACCTATTCGC 59.006 43.478 0.00 0.00 0.00 4.70
200 201 5.230942 AGTCAACTCAACTCAACCTATTCG 58.769 41.667 0.00 0.00 0.00 3.34
201 202 6.706270 TCAAGTCAACTCAACTCAACCTATTC 59.294 38.462 0.00 0.00 0.00 1.75
202 203 6.483640 GTCAAGTCAACTCAACTCAACCTATT 59.516 38.462 0.00 0.00 0.00 1.73
203 204 5.992217 GTCAAGTCAACTCAACTCAACCTAT 59.008 40.000 0.00 0.00 0.00 2.57
204 205 5.105106 TGTCAAGTCAACTCAACTCAACCTA 60.105 40.000 0.00 0.00 0.00 3.08
205 206 4.192317 GTCAAGTCAACTCAACTCAACCT 58.808 43.478 0.00 0.00 0.00 3.50
206 207 3.938963 TGTCAAGTCAACTCAACTCAACC 59.061 43.478 0.00 0.00 0.00 3.77
207 208 4.494855 GCTGTCAAGTCAACTCAACTCAAC 60.495 45.833 0.00 0.00 0.00 3.18
208 209 3.623060 GCTGTCAAGTCAACTCAACTCAA 59.377 43.478 0.00 0.00 0.00 3.02
247 248 3.060602 CAAACTCTTCTCCTTCACGGAC 58.939 50.000 0.00 0.00 36.69 4.79
261 262 0.109342 CCACTGCTCCCACAAACTCT 59.891 55.000 0.00 0.00 0.00 3.24
332 336 1.204941 GTGAATAGCACTCTGGTCCGT 59.795 52.381 0.00 0.00 44.27 4.69
334 338 1.134371 GGGTGAATAGCACTCTGGTCC 60.134 57.143 0.00 0.00 44.89 4.46
348 352 0.032813 CCTACTACGGAGGGGGTGAA 60.033 60.000 0.00 0.00 0.00 3.18
358 362 0.942962 CCTGCGTACTCCTACTACGG 59.057 60.000 0.00 0.00 37.94 4.02
360 364 3.132925 CTCTCCTGCGTACTCCTACTAC 58.867 54.545 0.00 0.00 0.00 2.73
361 365 2.770802 ACTCTCCTGCGTACTCCTACTA 59.229 50.000 0.00 0.00 0.00 1.82
362 366 1.560611 ACTCTCCTGCGTACTCCTACT 59.439 52.381 0.00 0.00 0.00 2.57
363 367 1.671845 CACTCTCCTGCGTACTCCTAC 59.328 57.143 0.00 0.00 0.00 3.18
364 368 1.408405 CCACTCTCCTGCGTACTCCTA 60.408 57.143 0.00 0.00 0.00 2.94
365 369 0.681564 CCACTCTCCTGCGTACTCCT 60.682 60.000 0.00 0.00 0.00 3.69
366 370 0.680280 TCCACTCTCCTGCGTACTCC 60.680 60.000 0.00 0.00 0.00 3.85
367 371 0.736053 CTCCACTCTCCTGCGTACTC 59.264 60.000 0.00 0.00 0.00 2.59
368 372 0.038455 ACTCCACTCTCCTGCGTACT 59.962 55.000 0.00 0.00 0.00 2.73
474 489 2.161410 ACGTTGTATTGAATGCATGCGT 59.839 40.909 14.09 10.53 34.31 5.24
498 516 5.276820 GCTTGCTGACAAAAACCATGTTTAC 60.277 40.000 0.00 0.00 34.74 2.01
516 534 2.437359 GATCGGCTGTGGCTTGCT 60.437 61.111 0.00 0.00 38.73 3.91
535 599 0.324614 AAGATGATGGTGCGGTGACA 59.675 50.000 0.00 0.00 0.00 3.58
545 615 2.292569 CGCAGAAATGGGAAGATGATGG 59.707 50.000 0.00 0.00 0.00 3.51
548 618 2.358957 CACGCAGAAATGGGAAGATGA 58.641 47.619 0.00 0.00 0.00 2.92
549 619 1.202222 GCACGCAGAAATGGGAAGATG 60.202 52.381 0.00 0.00 0.00 2.90
550 620 1.098050 GCACGCAGAAATGGGAAGAT 58.902 50.000 0.00 0.00 0.00 2.40
551 621 0.960364 GGCACGCAGAAATGGGAAGA 60.960 55.000 0.00 0.00 0.00 2.87
589 659 2.289382 TGCGCACAAGTGGAAAGATAGA 60.289 45.455 5.66 0.00 0.00 1.98
673 762 6.143598 GCCCGTAAAAACGAGAATATCTAGTC 59.856 42.308 0.00 0.00 31.03 2.59
675 764 5.981315 TGCCCGTAAAAACGAGAATATCTAG 59.019 40.000 0.00 0.00 34.64 2.43
681 770 2.774687 ACTGCCCGTAAAAACGAGAAT 58.225 42.857 0.00 0.00 34.64 2.40
726 832 0.394488 TGAGGAGGTACAGAGCGGAG 60.394 60.000 0.00 0.00 0.00 4.63
727 833 0.680280 GTGAGGAGGTACAGAGCGGA 60.680 60.000 0.00 0.00 0.00 5.54
728 834 0.965866 TGTGAGGAGGTACAGAGCGG 60.966 60.000 0.00 0.00 0.00 5.52
740 846 1.547675 GGACCTTTTGCCATGTGAGGA 60.548 52.381 0.00 0.00 0.00 3.71
759 865 0.896940 AACCAACCATCAGCAGCAGG 60.897 55.000 0.00 0.00 0.00 4.85
761 867 0.178995 TCAACCAACCATCAGCAGCA 60.179 50.000 0.00 0.00 0.00 4.41
766 872 3.310774 GTCATCGATCAACCAACCATCAG 59.689 47.826 0.00 0.00 0.00 2.90
792 898 0.036875 GCTGGCTGTAAAGTCTGGGT 59.963 55.000 0.00 0.00 0.00 4.51
816 923 0.035739 GTGGGTTTTGGCTCCGAGTA 59.964 55.000 0.00 0.00 0.00 2.59
884 991 2.225727 GAGTGATTTTGTGGGGTTCGTC 59.774 50.000 0.00 0.00 0.00 4.20
989 1097 1.615116 CCATTGCCATCTCCTGTGTGT 60.615 52.381 0.00 0.00 0.00 3.72
1131 1239 3.854669 AGGATCTCCTTGCCGGCG 61.855 66.667 23.90 8.36 46.09 6.46
1516 1624 4.988598 CACGACCCTGTTGCCGCT 62.989 66.667 0.00 0.00 0.00 5.52
1563 1671 2.882777 CAGCAGTACTCGGCGCTG 60.883 66.667 15.94 15.94 45.17 5.18
1794 1902 6.653020 TGCCTCAACTGAATCAACATACTAT 58.347 36.000 0.00 0.00 0.00 2.12
1830 1958 3.430218 CGACAGCAAGAACCTAAGAACAG 59.570 47.826 0.00 0.00 0.00 3.16
1889 2017 3.624861 ACTACGACTACGAATACCACTGG 59.375 47.826 0.00 0.00 42.66 4.00
1890 2018 4.871993 ACTACGACTACGAATACCACTG 57.128 45.455 0.00 0.00 42.66 3.66
1895 2023 6.419413 ACTGCTACTACTACGACTACGAATAC 59.581 42.308 0.00 0.00 42.66 1.89
1896 2024 6.419116 CACTGCTACTACTACGACTACGAATA 59.581 42.308 0.00 0.00 42.66 1.75
1897 2025 5.233902 CACTGCTACTACTACGACTACGAAT 59.766 44.000 0.00 0.00 42.66 3.34
1898 2026 4.564372 CACTGCTACTACTACGACTACGAA 59.436 45.833 0.00 0.00 42.66 3.85
1899 2027 4.108336 CACTGCTACTACTACGACTACGA 58.892 47.826 0.00 0.00 42.66 3.43
1900 2028 4.108336 TCACTGCTACTACTACGACTACG 58.892 47.826 0.00 0.00 45.75 3.51
1901 2029 5.580297 AGTTCACTGCTACTACTACGACTAC 59.420 44.000 0.00 0.00 0.00 2.73
1902 2030 5.579904 CAGTTCACTGCTACTACTACGACTA 59.420 44.000 0.00 0.00 37.15 2.59
1903 2031 4.392445 CAGTTCACTGCTACTACTACGACT 59.608 45.833 0.00 0.00 37.15 4.18
1904 2032 4.391216 TCAGTTCACTGCTACTACTACGAC 59.609 45.833 1.74 0.00 43.46 4.34
1905 2033 4.572909 TCAGTTCACTGCTACTACTACGA 58.427 43.478 1.74 0.00 43.46 3.43
1906 2034 4.941325 TCAGTTCACTGCTACTACTACG 57.059 45.455 1.74 0.00 43.46 3.51
1907 2035 5.048224 TGGTTCAGTTCACTGCTACTACTAC 60.048 44.000 1.74 0.00 43.46 2.73
1908 2036 5.074804 TGGTTCAGTTCACTGCTACTACTA 58.925 41.667 1.74 0.00 43.46 1.82
1909 2037 3.895656 TGGTTCAGTTCACTGCTACTACT 59.104 43.478 1.74 0.00 43.46 2.57
1915 2043 1.486310 TCACTGGTTCAGTTCACTGCT 59.514 47.619 1.74 0.00 42.59 4.24
2052 2185 2.175184 GAATGCAAGCACGCACGACT 62.175 55.000 1.79 0.00 46.56 4.18
2060 2204 3.120442 GCAGGAAAAATGAATGCAAGCAC 60.120 43.478 0.00 0.00 36.88 4.40
2066 2210 3.687698 AGCAATGCAGGAAAAATGAATGC 59.312 39.130 8.35 0.00 37.40 3.56
2090 2234 5.824243 ACGAACAAGAAATCAAGAGTACG 57.176 39.130 0.00 0.00 0.00 3.67
2091 2235 7.169308 TCTGAACGAACAAGAAATCAAGAGTAC 59.831 37.037 0.00 0.00 0.00 2.73
2092 2236 7.207383 TCTGAACGAACAAGAAATCAAGAGTA 58.793 34.615 0.00 0.00 0.00 2.59
2093 2237 6.049149 TCTGAACGAACAAGAAATCAAGAGT 58.951 36.000 0.00 0.00 0.00 3.24
2096 2240 7.014115 CAGATCTGAACGAACAAGAAATCAAG 58.986 38.462 18.34 0.00 0.00 3.02
2126 2277 5.968848 CACTTTTTAAAGTACAGCGCTCAAA 59.031 36.000 7.13 0.00 46.89 2.69
2131 2282 3.885358 AGCACTTTTTAAAGTACAGCGC 58.115 40.909 0.00 0.00 46.89 5.92
2182 2333 1.351017 CACCCAAGGAAAGGAGCAGTA 59.649 52.381 0.00 0.00 0.00 2.74
2246 2397 2.372688 CCTCCCCTCCCCAGCTAA 59.627 66.667 0.00 0.00 0.00 3.09
2252 2403 3.972328 AAAGCTCCCTCCCCTCCCC 62.972 68.421 0.00 0.00 0.00 4.81
2290 2441 3.522553 GAATCCTTCACGTCCTCGATTT 58.477 45.455 0.00 0.00 40.62 2.17
2334 2485 5.568620 AACTGGAGTGTCTTCCTTATTGT 57.431 39.130 0.00 0.00 38.12 2.71
2336 2487 4.762251 GCAAACTGGAGTGTCTTCCTTATT 59.238 41.667 0.00 0.00 38.12 1.40
2337 2488 4.202461 TGCAAACTGGAGTGTCTTCCTTAT 60.202 41.667 0.00 0.00 38.12 1.73
2338 2489 3.135712 TGCAAACTGGAGTGTCTTCCTTA 59.864 43.478 0.00 0.00 38.12 2.69
2339 2490 2.092429 TGCAAACTGGAGTGTCTTCCTT 60.092 45.455 0.00 0.00 38.12 3.36
2340 2491 1.490490 TGCAAACTGGAGTGTCTTCCT 59.510 47.619 0.00 0.00 38.12 3.36
2341 2492 1.604278 GTGCAAACTGGAGTGTCTTCC 59.396 52.381 0.00 0.00 37.77 3.46
2342 2493 2.545946 GAGTGCAAACTGGAGTGTCTTC 59.454 50.000 0.00 0.00 0.00 2.87
2343 2494 2.565841 GAGTGCAAACTGGAGTGTCTT 58.434 47.619 0.00 0.00 0.00 3.01
2344 2495 1.202698 GGAGTGCAAACTGGAGTGTCT 60.203 52.381 0.00 0.00 0.00 3.41
2345 2496 1.230324 GGAGTGCAAACTGGAGTGTC 58.770 55.000 0.00 0.00 0.00 3.67
2369 2524 4.124351 CGTCCAGCGCCTCGGTTA 62.124 66.667 2.29 0.00 34.62 2.85
2418 2573 0.792640 ACAAGAGTCGCTGCATTTCG 59.207 50.000 0.00 0.00 0.00 3.46
2419 2574 2.094417 GGTACAAGAGTCGCTGCATTTC 59.906 50.000 0.00 0.00 0.00 2.17
2420 2575 2.076863 GGTACAAGAGTCGCTGCATTT 58.923 47.619 0.00 0.00 0.00 2.32
2436 2592 2.453379 TTTGCGGGGGAAGACGGTAC 62.453 60.000 0.00 0.00 0.00 3.34
2451 2607 6.025280 TCTTCGGAAATTTATACGCTTTTGC 58.975 36.000 0.00 0.00 43.23 3.68
2452 2608 8.363029 GTTTCTTCGGAAATTTATACGCTTTTG 58.637 33.333 0.00 0.00 44.43 2.44
2455 2611 6.245724 CGTTTCTTCGGAAATTTATACGCTT 58.754 36.000 0.00 0.00 44.43 4.68
2457 2613 4.432345 GCGTTTCTTCGGAAATTTATACGC 59.568 41.667 0.00 0.00 43.90 4.42
2472 2630 5.063880 ACTGGTATTTCTTCAGCGTTTCTT 58.936 37.500 0.00 0.00 32.19 2.52
2473 2631 4.642429 ACTGGTATTTCTTCAGCGTTTCT 58.358 39.130 0.00 0.00 32.19 2.52
2504 2662 7.095060 TGCGAGATTATCTCCAAATAAAGATGC 60.095 37.037 15.68 9.32 40.34 3.91
2512 2670 6.106648 TCAGATGCGAGATTATCTCCAAAT 57.893 37.500 15.68 7.47 40.34 2.32
2517 2675 4.808558 AGCTTCAGATGCGAGATTATCTC 58.191 43.478 11.92 11.92 40.06 2.75
2523 2681 1.028130 TCGAGCTTCAGATGCGAGAT 58.972 50.000 2.74 0.00 35.28 2.75
2527 2685 1.587490 CTCTTTCGAGCTTCAGATGCG 59.413 52.381 2.74 0.00 35.28 4.73
2529 2687 5.220117 CGTAAACTCTTTCGAGCTTCAGATG 60.220 44.000 0.00 0.00 41.09 2.90
2531 2689 4.023450 TCGTAAACTCTTTCGAGCTTCAGA 60.023 41.667 0.00 0.00 41.09 3.27
2578 2737 1.446907 CAGGCAGGTGTGAAGATGAC 58.553 55.000 0.00 0.00 0.00 3.06
2583 2742 2.674380 GGGCAGGCAGGTGTGAAG 60.674 66.667 0.00 0.00 0.00 3.02
2589 2759 2.689034 GGTAGAGGGCAGGCAGGT 60.689 66.667 0.00 0.00 0.00 4.00
2647 2830 2.162809 TGCTCTAACTGCGACGTGAATA 59.837 45.455 0.00 0.00 0.00 1.75
2664 2847 6.976088 TGACTCAGCTCTATTATACTTGCTC 58.024 40.000 0.00 0.00 0.00 4.26
2665 2848 6.968263 TGACTCAGCTCTATTATACTTGCT 57.032 37.500 0.00 0.00 0.00 3.91
2681 2864 1.000283 CCTTATAGCCCGCTGACTCAG 60.000 57.143 1.21 1.21 34.12 3.35
2682 2865 1.040646 CCTTATAGCCCGCTGACTCA 58.959 55.000 0.00 0.00 0.00 3.41
2683 2866 1.329256 TCCTTATAGCCCGCTGACTC 58.671 55.000 0.00 0.00 0.00 3.36
2684 2867 1.789523 TTCCTTATAGCCCGCTGACT 58.210 50.000 0.00 0.00 0.00 3.41
2685 2868 2.841442 ATTCCTTATAGCCCGCTGAC 57.159 50.000 0.00 0.00 0.00 3.51
2686 2869 4.347000 AGTTTATTCCTTATAGCCCGCTGA 59.653 41.667 0.00 0.00 0.00 4.26
2687 2870 4.642429 AGTTTATTCCTTATAGCCCGCTG 58.358 43.478 0.00 0.00 0.00 5.18
2688 2871 4.976540 AGTTTATTCCTTATAGCCCGCT 57.023 40.909 0.00 0.00 0.00 5.52
2689 2872 5.791666 ACTAGTTTATTCCTTATAGCCCGC 58.208 41.667 0.00 0.00 0.00 6.13
2710 2893 9.959721 TTTCTTCCAACTAAGCAGAAATATACT 57.040 29.630 0.00 0.00 30.30 2.12
2713 2896 9.171877 CTCTTTCTTCCAACTAAGCAGAAATAT 57.828 33.333 0.00 0.00 33.95 1.28
2714 2897 8.375506 TCTCTTTCTTCCAACTAAGCAGAAATA 58.624 33.333 0.00 0.00 33.95 1.40
2715 2898 7.227156 TCTCTTTCTTCCAACTAAGCAGAAAT 58.773 34.615 0.00 0.00 33.95 2.17
2716 2899 6.591935 TCTCTTTCTTCCAACTAAGCAGAAA 58.408 36.000 0.00 0.00 33.48 2.52
2717 2900 6.174720 TCTCTTTCTTCCAACTAAGCAGAA 57.825 37.500 0.00 0.00 0.00 3.02
2718 2901 5.808366 TCTCTTTCTTCCAACTAAGCAGA 57.192 39.130 0.00 0.00 0.00 4.26
2719 2902 6.226787 TCTTCTCTTTCTTCCAACTAAGCAG 58.773 40.000 0.00 0.00 0.00 4.24
2720 2903 6.174720 TCTTCTCTTTCTTCCAACTAAGCA 57.825 37.500 0.00 0.00 0.00 3.91
2721 2904 5.641636 CCTCTTCTCTTTCTTCCAACTAAGC 59.358 44.000 0.00 0.00 0.00 3.09
2722 2905 6.998802 TCCTCTTCTCTTTCTTCCAACTAAG 58.001 40.000 0.00 0.00 0.00 2.18
2723 2906 6.782988 TCTCCTCTTCTCTTTCTTCCAACTAA 59.217 38.462 0.00 0.00 0.00 2.24
2724 2907 6.315714 TCTCCTCTTCTCTTTCTTCCAACTA 58.684 40.000 0.00 0.00 0.00 2.24
2725 2908 5.151454 TCTCCTCTTCTCTTTCTTCCAACT 58.849 41.667 0.00 0.00 0.00 3.16
2726 2909 5.476091 TCTCCTCTTCTCTTTCTTCCAAC 57.524 43.478 0.00 0.00 0.00 3.77
2727 2910 5.736951 CTCTCCTCTTCTCTTTCTTCCAA 57.263 43.478 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.