Multiple sequence alignment - TraesCS4D01G111800

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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 TraesCS4D01G111800 chr4D 100.000 9066 0 0 1 9066 92649718 92658783 0.000000e+00 16742.0
1 TraesCS4D01G111800 chr4A 98.042 3575 53 7 1023 4591 489890391 489886828 0.000000e+00 6198.0
2 TraesCS4D01G111800 chr4A 97.629 2404 27 10 4628 7023 489886264 489883883 0.000000e+00 4096.0
3 TraesCS4D01G111800 chr4A 98.267 923 15 1 7144 8066 489883885 489882964 0.000000e+00 1615.0
4 TraesCS4D01G111800 chr4A 93.397 939 35 11 8152 9066 489882653 489881718 0.000000e+00 1365.0
5 TraesCS4D01G111800 chr4A 89.695 951 78 10 1 942 489891661 489890722 0.000000e+00 1195.0
6 TraesCS4D01G111800 chr4A 100.000 40 0 0 4572 4611 489886830 489886791 3.510000e-09 75.0
7 TraesCS4D01G111800 chr4A 100.000 35 0 0 8069 8103 489882933 489882899 2.110000e-06 65.8
8 TraesCS4D01G111800 chr4A 88.000 50 4 2 4288 4336 227091245 227091197 3.540000e-04 58.4
9 TraesCS4D01G111800 chr4A 94.595 37 2 0 4288 4324 662287254 662287218 3.540000e-04 58.4
10 TraesCS4D01G111800 chr4A 94.595 37 2 0 4288 4324 662287720 662287684 3.540000e-04 58.4
11 TraesCS4D01G111800 chr4B 98.501 3336 46 4 1278 4611 130223647 130226980 0.000000e+00 5880.0
12 TraesCS4D01G111800 chr4B 98.170 2405 29 9 4628 7023 130227795 130230193 0.000000e+00 4183.0
13 TraesCS4D01G111800 chr4B 94.926 1084 12 7 7144 8188 130230191 130231270 0.000000e+00 1657.0
14 TraesCS4D01G111800 chr4B 92.393 907 31 11 8185 9066 130231804 130232697 0.000000e+00 1258.0
15 TraesCS4D01G111800 chr4B 95.952 420 11 5 471 888 130222444 130222859 0.000000e+00 676.0
16 TraesCS4D01G111800 chr4B 98.824 170 2 0 999 1168 130223473 130223642 4.110000e-78 303.0
17 TraesCS4D01G111800 chr4B 92.361 144 5 4 7009 7150 399945299 399945438 5.550000e-47 200.0
18 TraesCS4D01G111800 chr4B 94.444 36 2 0 4288 4323 246316519 246316484 1.000000e-03 56.5
19 TraesCS4D01G111800 chr5B 78.723 470 92 7 4 468 597195638 597196104 3.180000e-79 307.0
20 TraesCS4D01G111800 chr5B 96.875 128 2 1 7021 7146 125229816 125229943 7.130000e-51 213.0
21 TraesCS4D01G111800 chr5B 97.059 34 0 1 4288 4321 564512014 564512046 1.000000e-03 56.5
22 TraesCS4D01G111800 chr5D 87.111 225 24 5 6721 6943 540293171 540293392 5.430000e-62 250.0
23 TraesCS4D01G111800 chr5D 96.850 127 2 1 7022 7146 231736906 231736780 2.560000e-50 211.0
24 TraesCS4D01G111800 chr5D 100.000 30 0 0 4289 4318 554506286 554506315 1.000000e-03 56.5
25 TraesCS4D01G111800 chr3D 77.500 400 77 10 80 469 481936498 481936894 2.550000e-55 228.0
26 TraesCS4D01G111800 chr1A 95.455 132 4 1 7017 7146 486045904 486045773 9.220000e-50 209.0
27 TraesCS4D01G111800 chr1A 97.561 41 1 0 4275 4315 582414235 582414275 4.540000e-08 71.3
28 TraesCS4D01G111800 chr7B 94.815 135 4 2 7014 7146 108491021 108491154 3.320000e-49 207.0
29 TraesCS4D01G111800 chr7B 90.323 155 8 6 7021 7171 281384159 281384008 7.180000e-46 196.0
30 TraesCS4D01G111800 chr3A 94.161 137 5 2 7022 7156 644809129 644809264 1.190000e-48 206.0
31 TraesCS4D01G111800 chr7A 92.857 140 8 1 7022 7159 78506137 78506276 1.540000e-47 202.0
32 TraesCS4D01G111800 chr2D 90.604 149 10 3 7022 7168 546779663 546779517 2.580000e-45 195.0
33 TraesCS4D01G111800 chr2B 86.517 89 11 1 6855 6943 37340111 37340024 7.490000e-16 97.1


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 TraesCS4D01G111800 chr4D 92649718 92658783 9065 False 16742.000000 16742 100.000000 1 9066 1 chr4D.!!$F1 9065
1 TraesCS4D01G111800 chr4A 489881718 489891661 9943 True 2087.114286 6198 96.718571 1 9066 7 chr4A.!!$R2 9065
2 TraesCS4D01G111800 chr4B 130222444 130232697 10253 False 2326.166667 5880 96.461000 471 9066 6 chr4B.!!$F2 8595

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
358 361 0.179048 TAGGGTGGCGCATGAGATTG 60.179 55.000 10.83 0.00 0.00 2.67 F
738 741 0.537188 CCGCTCCCACTGACATACTT 59.463 55.000 0.00 0.00 0.00 2.24 F
1205 1711 1.281867 TGCGGGATTGGATTTCTCTGT 59.718 47.619 0.00 0.00 0.00 3.41 F
2813 3320 1.878102 GCACAGAGTCCATTGGTTCGT 60.878 52.381 1.86 3.04 0.00 3.85 F
3605 4117 1.332195 AAAGGAAAAGGTGCTGGAGC 58.668 50.000 0.00 0.00 42.50 4.70 F
4621 5152 0.800012 GATAAAAAGCACGCCGACCA 59.200 50.000 0.00 0.00 0.00 4.02 F
4623 5154 0.800012 TAAAAAGCACGCCGACCATC 59.200 50.000 0.00 0.00 0.00 3.51 F
5021 6355 2.368221 GTCCTCTAGCATTCATCCAGCT 59.632 50.000 0.00 0.00 42.14 4.24 F
7040 8384 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 2435 1.156645 GCGCAAGATGGGAGCTACAG 61.157 60.000 0.30 0.00 43.02 2.74 R
2813 3320 2.057922 AGAAGTTCCCTGGAGAAGCAA 58.942 47.619 0.00 0.00 0.00 3.91 R
2975 3482 6.019559 GGAAGAACTTGAGAAACAAAATGCAC 60.020 38.462 0.00 0.00 38.08 4.57 R
4622 5153 1.764134 ACCACAACTTGAGTAACCCGA 59.236 47.619 0.00 0.00 0.00 5.14 R
4623 5154 2.249844 ACCACAACTTGAGTAACCCG 57.750 50.000 0.00 0.00 0.00 5.28 R
5998 7334 0.108041 TTATCCAACCCCGTCGCTTC 60.108 55.000 0.00 0.00 0.00 3.86 R
6764 8102 0.517316 CACTCAACTAAACCTGCCGC 59.483 55.000 0.00 0.00 0.00 6.53 R
7024 8368 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 R
8910 11055 0.742990 TCATCAACAACGGATCCGCC 60.743 55.000 33.62 0.00 44.19 6.13 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
43 45 3.708403 TGTGGAAGCATGAGATCTGTT 57.292 42.857 0.00 0.00 0.00 3.16
47 49 4.569966 GTGGAAGCATGAGATCTGTTAGTG 59.430 45.833 0.00 0.00 0.00 2.74
56 58 4.841813 TGAGATCTGTTAGTGTTGGGGTTA 59.158 41.667 0.00 0.00 0.00 2.85
83 85 4.682021 AGAAATCATCTGGGGGAAGTTT 57.318 40.909 0.00 0.00 36.88 2.66
85 87 4.774200 AGAAATCATCTGGGGGAAGTTTTG 59.226 41.667 0.00 0.00 36.88 2.44
94 96 4.097418 TGGGGGAAGTTTTGTTTTCTTCA 58.903 39.130 0.00 0.00 39.19 3.02
97 99 5.396324 GGGGGAAGTTTTGTTTTCTTCATGT 60.396 40.000 0.00 0.00 39.19 3.21
108 110 6.380995 TGTTTTCTTCATGTGATTTCATCCG 58.619 36.000 0.00 0.00 0.00 4.18
110 112 5.801350 TTCTTCATGTGATTTCATCCGTC 57.199 39.130 0.00 0.00 0.00 4.79
111 113 4.191544 TCTTCATGTGATTTCATCCGTCC 58.808 43.478 0.00 0.00 0.00 4.79
117 119 2.601763 GTGATTTCATCCGTCCGTGTAC 59.398 50.000 0.00 0.00 0.00 2.90
118 120 2.199236 GATTTCATCCGTCCGTGTACC 58.801 52.381 0.00 0.00 0.00 3.34
121 123 1.518572 CATCCGTCCGTGTACCTGC 60.519 63.158 0.00 0.00 0.00 4.85
122 124 1.980232 ATCCGTCCGTGTACCTGCA 60.980 57.895 0.00 0.00 0.00 4.41
123 125 1.327690 ATCCGTCCGTGTACCTGCAT 61.328 55.000 0.00 0.00 0.00 3.96
134 136 0.829990 TACCTGCATGGATGAAGCGA 59.170 50.000 8.91 0.00 39.71 4.93
137 139 1.679680 CCTGCATGGATGAAGCGAAAT 59.320 47.619 0.00 0.00 38.35 2.17
163 165 2.795175 CGTGTCTCGCCAGGTTATAT 57.205 50.000 0.00 0.00 0.00 0.86
216 218 4.370364 TGGAAACTGACTGTTCTTTTGC 57.630 40.909 0.00 0.00 38.03 3.68
222 224 4.199310 ACTGACTGTTCTTTTGCTGCTTA 58.801 39.130 0.00 0.00 0.00 3.09
229 231 6.698766 ACTGTTCTTTTGCTGCTTATTTTCTG 59.301 34.615 0.00 0.00 0.00 3.02
239 241 4.881920 TGCTTATTTTCTGGCAAAGGAAC 58.118 39.130 0.00 0.00 0.00 3.62
240 242 4.245660 GCTTATTTTCTGGCAAAGGAACC 58.754 43.478 0.00 0.00 0.00 3.62
260 262 4.235372 ACCCATTAATAGGTCTCCTCTGG 58.765 47.826 0.00 0.00 34.61 3.86
278 280 3.009473 TCTGGTGGATCTGAAAAAGGAGG 59.991 47.826 0.00 0.00 0.00 4.30
283 285 1.812571 GATCTGAAAAAGGAGGCGCAA 59.187 47.619 10.83 0.00 0.00 4.85
285 287 2.238521 TCTGAAAAAGGAGGCGCAAAT 58.761 42.857 10.83 0.00 0.00 2.32
286 288 2.228822 TCTGAAAAAGGAGGCGCAAATC 59.771 45.455 10.83 3.51 0.00 2.17
297 300 1.062148 GGCGCAAATCGTCCTAAGTTC 59.938 52.381 10.83 0.00 41.07 3.01
301 304 3.301835 CGCAAATCGTCCTAAGTTCATCG 60.302 47.826 0.00 0.00 0.00 3.84
305 308 2.022195 TCGTCCTAAGTTCATCGAGGG 58.978 52.381 0.00 0.00 0.00 4.30
307 310 2.165845 CGTCCTAAGTTCATCGAGGGTT 59.834 50.000 0.00 0.00 0.00 4.11
316 319 5.070001 AGTTCATCGAGGGTTTCAAAATCA 58.930 37.500 0.00 0.00 0.00 2.57
333 336 8.936070 TCAAAATCATGAAAATTGATAGGCAG 57.064 30.769 13.88 0.00 33.52 4.85
358 361 0.179048 TAGGGTGGCGCATGAGATTG 60.179 55.000 10.83 0.00 0.00 2.67
377 380 9.515020 TGAGATTGTGAAATTTAGTTTTGACAC 57.485 29.630 0.00 0.00 0.00 3.67
380 383 8.647143 ATTGTGAAATTTAGTTTTGACACCAG 57.353 30.769 0.00 0.00 0.00 4.00
384 387 9.313118 GTGAAATTTAGTTTTGACACCAGATTT 57.687 29.630 0.00 0.00 0.00 2.17
409 412 8.208718 TGATGGTGCTTATTGTAATAGTGTTC 57.791 34.615 0.00 0.00 0.00 3.18
410 413 8.046708 TGATGGTGCTTATTGTAATAGTGTTCT 58.953 33.333 0.00 0.00 0.00 3.01
412 415 6.093495 TGGTGCTTATTGTAATAGTGTTCTGC 59.907 38.462 0.00 0.00 0.00 4.26
430 433 2.644992 CCTGCGTGGCAAACCTTC 59.355 61.111 0.00 0.00 38.41 3.46
435 438 1.539388 TGCGTGGCAAACCTTCTAATG 59.461 47.619 0.00 0.00 34.76 1.90
439 442 2.819608 GTGGCAAACCTTCTAATGCTCA 59.180 45.455 0.00 0.00 38.79 4.26
449 452 8.635765 AACCTTCTAATGCTCAATTGTAAGAA 57.364 30.769 5.13 6.15 0.00 2.52
450 453 8.814038 ACCTTCTAATGCTCAATTGTAAGAAT 57.186 30.769 5.13 0.00 0.00 2.40
483 486 8.323567 AGTTAATTAATACGTATATGGGTGGGG 58.676 37.037 8.83 0.00 0.00 4.96
489 492 4.858965 ACGTATATGGGTGGGGTTAAAA 57.141 40.909 0.00 0.00 0.00 1.52
515 518 8.553459 AATATATATTCAGAAACCCTTGCTCG 57.447 34.615 1.91 0.00 0.00 5.03
635 638 7.065324 CCAACCGCCACAATTATATCGTTATAT 59.935 37.037 0.00 0.00 32.87 0.86
636 639 9.089601 CAACCGCCACAATTATATCGTTATATA 57.910 33.333 0.00 0.00 30.72 0.86
738 741 0.537188 CCGCTCCCACTGACATACTT 59.463 55.000 0.00 0.00 0.00 2.24
756 759 2.753043 GGTCCACATGCCAGCCAG 60.753 66.667 0.00 0.00 0.00 4.85
930 936 4.864334 GCCCCTGCGTGATCCCAG 62.864 72.222 0.00 0.00 0.00 4.45
942 948 3.208884 ATCCCAGCGTACGCCGATC 62.209 63.158 34.88 9.25 43.17 3.69
943 949 4.944372 CCCAGCGTACGCCGATCC 62.944 72.222 34.88 8.46 43.17 3.36
944 950 4.944372 CCAGCGTACGCCGATCCC 62.944 72.222 34.88 7.68 43.17 3.85
945 951 4.944372 CAGCGTACGCCGATCCCC 62.944 72.222 34.88 6.89 43.17 4.81
1119 1625 2.408022 CGTAAGCTACGCTCCGCT 59.592 61.111 0.00 0.00 45.81 5.52
1169 1675 1.673700 GCAAAGTACGCGGCAATTGC 61.674 55.000 22.47 22.47 36.73 3.56
1199 1705 1.597742 CTCGATGCGGGATTGGATTT 58.402 50.000 0.00 0.00 0.00 2.17
1205 1711 1.281867 TGCGGGATTGGATTTCTCTGT 59.718 47.619 0.00 0.00 0.00 3.41
1394 1900 5.680594 TTTTGCTACCCGGATAACTAGAA 57.319 39.130 0.73 0.00 0.00 2.10
1537 2043 6.978080 GGTAGAGTTGAGAACTTGAGATCATC 59.022 42.308 0.00 0.00 43.03 2.92
1666 2173 3.039743 TGGAAGTAGTGGTTGGTGTACA 58.960 45.455 0.00 0.00 0.00 2.90
1701 2208 9.483062 CTTCTTTGCTGATCTTCTAATTTTACG 57.517 33.333 0.00 0.00 0.00 3.18
1806 2313 7.470702 GCTTCTAGCATTTCCTATGAGTAGACA 60.471 40.741 0.00 0.00 41.89 3.41
1928 2435 7.234187 TGCAACTATTGATTTCTACATCGTC 57.766 36.000 0.00 0.00 0.00 4.20
2813 3320 1.878102 GCACAGAGTCCATTGGTTCGT 60.878 52.381 1.86 3.04 0.00 3.85
2893 3400 7.652105 CGCAAGTCCTATGTAAGCTCTTAATTA 59.348 37.037 0.00 0.00 0.00 1.40
2975 3482 7.749570 GTCATGACATGTTCAGAAGAAAATCAG 59.250 37.037 21.07 0.00 37.77 2.90
3600 4112 3.321968 GTCCATCAAAAGGAAAAGGTGCT 59.678 43.478 0.00 0.00 36.80 4.40
3605 4117 1.332195 AAAGGAAAAGGTGCTGGAGC 58.668 50.000 0.00 0.00 42.50 4.70
3957 4469 2.808543 CAAAGGTTCTGTTCCTTCCTCG 59.191 50.000 0.00 0.00 43.50 4.63
4614 5145 9.393249 TCTAATTTTTGTGAGATAAAAAGCACG 57.607 29.630 0.00 0.00 39.51 5.34
4616 5147 3.552604 TTGTGAGATAAAAAGCACGCC 57.447 42.857 0.00 0.00 34.12 5.68
4617 5148 1.463056 TGTGAGATAAAAAGCACGCCG 59.537 47.619 0.00 0.00 34.12 6.46
4621 5152 0.800012 GATAAAAAGCACGCCGACCA 59.200 50.000 0.00 0.00 0.00 4.02
4622 5153 1.400494 GATAAAAAGCACGCCGACCAT 59.600 47.619 0.00 0.00 0.00 3.55
4623 5154 0.800012 TAAAAAGCACGCCGACCATC 59.200 50.000 0.00 0.00 0.00 3.51
4768 6099 3.450457 TGGTTTGTGAAAAGAAGGCATGT 59.550 39.130 0.00 0.00 0.00 3.21
4805 6139 7.708752 AGCTTTGAAATAGCTCAGTATCACTAC 59.291 37.037 0.00 0.00 45.52 2.73
4806 6140 7.708752 GCTTTGAAATAGCTCAGTATCACTACT 59.291 37.037 0.00 0.00 35.86 2.57
4807 6141 9.593134 CTTTGAAATAGCTCAGTATCACTACTT 57.407 33.333 0.00 0.00 35.99 2.24
5019 6353 4.412796 TTGTCCTCTAGCATTCATCCAG 57.587 45.455 0.00 0.00 0.00 3.86
5021 6355 2.368221 GTCCTCTAGCATTCATCCAGCT 59.632 50.000 0.00 0.00 42.14 4.24
5089 6423 5.968848 GGATCTCTTGTCGATCGCTAATATC 59.031 44.000 11.09 10.23 38.49 1.63
5095 6429 3.058501 TGTCGATCGCTAATATCGCAGAA 60.059 43.478 11.09 0.00 44.53 3.02
5180 6514 2.949177 TTGTGCCTTCTCCTTAGCAA 57.051 45.000 0.00 0.00 36.91 3.91
5568 6903 7.153985 CAGGAAGAGACAGATAATCAGAATCC 58.846 42.308 0.00 0.00 0.00 3.01
5998 7334 5.584649 TCTTGTAGACAAAGTGTTCCAACTG 59.415 40.000 0.00 0.00 35.15 3.16
6405 7743 6.207928 TGCAGAACATTATGTTTGACTTGTG 58.792 36.000 12.13 0.00 41.28 3.33
6406 7744 6.183360 TGCAGAACATTATGTTTGACTTGTGT 60.183 34.615 12.13 0.00 41.28 3.72
6764 8102 6.236941 GCGTATTAGTTTCAGCACGAAAATTG 60.237 38.462 6.85 0.00 45.11 2.32
6766 8104 2.384382 AGTTTCAGCACGAAAATTGCG 58.616 42.857 3.19 0.00 45.11 4.85
6776 8114 2.250188 CGAAAATTGCGGCAGGTTTAG 58.750 47.619 13.42 9.77 0.00 1.85
6782 8120 0.107831 TGCGGCAGGTTTAGTTGAGT 59.892 50.000 0.00 0.00 0.00 3.41
6876 8214 7.280205 TCCTTTCCAGAAAAATAGCGATAGTTC 59.720 37.037 0.00 0.00 39.35 3.01
6908 8246 4.597507 TGTAAGTGAATGGGAGAAGAAGGT 59.402 41.667 0.00 0.00 0.00 3.50
6943 8281 5.991861 AGATTATGGGATTGCATGCAAAAA 58.008 33.333 34.84 20.75 39.55 1.94
6989 8333 7.712797 AGTACTTGGTACCAAATCACTTTTTG 58.287 34.615 26.90 13.99 39.58 2.44
7023 8367 7.811117 TGGCATAACATAAATACCAAGGTAC 57.189 36.000 0.14 0.00 33.01 3.34
7025 8369 7.717875 TGGCATAACATAAATACCAAGGTACTC 59.282 37.037 0.14 0.00 38.49 2.59
7026 8370 7.174426 GGCATAACATAAATACCAAGGTACTCC 59.826 40.741 0.14 0.00 38.49 3.85
7027 8371 7.174426 GCATAACATAAATACCAAGGTACTCCC 59.826 40.741 0.14 0.00 38.49 4.30
7029 8373 6.496144 ACATAAATACCAAGGTACTCCCTC 57.504 41.667 0.14 0.00 45.47 4.30
7030 8374 5.368816 ACATAAATACCAAGGTACTCCCTCC 59.631 44.000 0.14 0.00 45.47 4.30
7031 8375 2.083628 ATACCAAGGTACTCCCTCCG 57.916 55.000 0.14 0.00 45.47 4.63
7032 8376 0.706433 TACCAAGGTACTCCCTCCGT 59.294 55.000 0.00 0.00 45.47 4.69
7033 8377 0.614134 ACCAAGGTACTCCCTCCGTC 60.614 60.000 0.00 0.00 45.47 4.79
7034 8378 1.328430 CCAAGGTACTCCCTCCGTCC 61.328 65.000 0.00 0.00 45.47 4.79
7035 8379 1.379576 AAGGTACTCCCTCCGTCCG 60.380 63.158 0.00 0.00 45.47 4.79
7036 8380 2.832201 GGTACTCCCTCCGTCCGG 60.832 72.222 0.00 0.00 0.00 5.14
7037 8381 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
7038 8382 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
7039 8383 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
7040 8384 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
7041 8385 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
7042 8386 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
7043 8387 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
7044 8388 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
7045 8389 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
7046 8390 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
7047 8391 2.354403 CCTCCGTCCGGAAATACTTGTT 60.354 50.000 5.23 0.00 44.66 2.83
7048 8392 2.928116 CTCCGTCCGGAAATACTTGTTC 59.072 50.000 5.23 0.00 44.66 3.18
7049 8393 2.299582 TCCGTCCGGAAATACTTGTTCA 59.700 45.455 5.23 0.00 42.05 3.18
7050 8394 3.068560 CCGTCCGGAAATACTTGTTCAA 58.931 45.455 5.23 0.00 37.50 2.69
7051 8395 3.499157 CCGTCCGGAAATACTTGTTCAAA 59.501 43.478 5.23 0.00 37.50 2.69
7052 8396 4.023878 CCGTCCGGAAATACTTGTTCAAAA 60.024 41.667 5.23 0.00 37.50 2.44
7053 8397 5.335348 CCGTCCGGAAATACTTGTTCAAAAT 60.335 40.000 5.23 0.00 37.50 1.82
7054 8398 5.567534 CGTCCGGAAATACTTGTTCAAAATG 59.432 40.000 5.23 0.00 0.00 2.32
7055 8399 5.861787 GTCCGGAAATACTTGTTCAAAATGG 59.138 40.000 5.23 0.00 0.00 3.16
7056 8400 5.770663 TCCGGAAATACTTGTTCAAAATGGA 59.229 36.000 0.00 0.00 0.00 3.41
7057 8401 6.435904 TCCGGAAATACTTGTTCAAAATGGAT 59.564 34.615 0.00 0.00 0.00 3.41
7058 8402 7.612244 TCCGGAAATACTTGTTCAAAATGGATA 59.388 33.333 0.00 0.00 0.00 2.59
7059 8403 7.915397 CCGGAAATACTTGTTCAAAATGGATAG 59.085 37.037 0.00 0.00 0.00 2.08
7060 8404 8.673711 CGGAAATACTTGTTCAAAATGGATAGA 58.326 33.333 0.00 0.00 0.00 1.98
7066 8410 8.924511 ACTTGTTCAAAATGGATAGAAAGAGA 57.075 30.769 0.00 0.00 0.00 3.10
7067 8411 9.525826 ACTTGTTCAAAATGGATAGAAAGAGAT 57.474 29.630 0.00 0.00 0.00 2.75
7068 8412 9.784680 CTTGTTCAAAATGGATAGAAAGAGATG 57.215 33.333 0.00 0.00 0.00 2.90
7069 8413 8.868522 TGTTCAAAATGGATAGAAAGAGATGT 57.131 30.769 0.00 0.00 0.00 3.06
7070 8414 9.958180 TGTTCAAAATGGATAGAAAGAGATGTA 57.042 29.630 0.00 0.00 0.00 2.29
7102 8446 9.551734 AACTAAAATACGTCTAAATACATCCCC 57.448 33.333 0.00 0.00 0.00 4.81
7103 8447 8.931568 ACTAAAATACGTCTAAATACATCCCCT 58.068 33.333 0.00 0.00 0.00 4.79
7104 8448 9.774413 CTAAAATACGTCTAAATACATCCCCTT 57.226 33.333 0.00 0.00 0.00 3.95
7106 8450 9.470399 AAAATACGTCTAAATACATCCCCTTTT 57.530 29.630 0.00 0.00 0.00 2.27
7109 8453 9.939802 ATACGTCTAAATACATCCCCTTTTATC 57.060 33.333 0.00 0.00 0.00 1.75
7110 8454 7.222161 ACGTCTAAATACATCCCCTTTTATCC 58.778 38.462 0.00 0.00 0.00 2.59
7111 8455 7.147444 ACGTCTAAATACATCCCCTTTTATCCA 60.147 37.037 0.00 0.00 0.00 3.41
7112 8456 7.883311 CGTCTAAATACATCCCCTTTTATCCAT 59.117 37.037 0.00 0.00 0.00 3.41
7113 8457 9.588096 GTCTAAATACATCCCCTTTTATCCATT 57.412 33.333 0.00 0.00 0.00 3.16
7117 8461 8.852671 AATACATCCCCTTTTATCCATTTTGA 57.147 30.769 0.00 0.00 0.00 2.69
7118 8462 9.451206 AATACATCCCCTTTTATCCATTTTGAT 57.549 29.630 0.00 0.00 0.00 2.57
7119 8463 7.128234 ACATCCCCTTTTATCCATTTTGATG 57.872 36.000 0.00 0.00 33.80 3.07
7120 8464 6.902416 ACATCCCCTTTTATCCATTTTGATGA 59.098 34.615 0.00 0.00 32.39 2.92
7121 8465 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
7122 8466 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
7123 8467 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
7124 8468 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
7125 8469 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
7126 8470 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
7132 8476 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
7133 8477 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
7134 8478 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
7135 8479 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
7136 8480 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
7137 8481 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
7138 8482 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
7139 8483 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
7140 8484 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
7141 8485 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
7142 8486 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
7143 8487 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
7144 8488 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
7145 8489 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
7176 8527 9.231297 GCAAATTATTCTTATATGCTAGGGTCA 57.769 33.333 0.00 0.00 0.00 4.02
7605 8956 2.169937 ATTGGGCGGTGTTTGCATGG 62.170 55.000 0.00 0.00 0.00 3.66
7978 9329 0.539051 ATGAGAAGGGTCGCAAGGAG 59.461 55.000 0.00 0.00 37.11 3.69
8107 9486 2.068821 GCAGAGCTGGATCCAGGGA 61.069 63.158 36.92 6.61 43.77 4.20
8118 9497 3.698765 CCAGGGATTGGTTGGTGC 58.301 61.111 0.00 0.00 42.41 5.01
8119 9498 1.984026 CCAGGGATTGGTTGGTGCC 60.984 63.158 0.00 0.00 42.41 5.01
8120 9499 1.984026 CAGGGATTGGTTGGTGCCC 60.984 63.158 0.00 0.00 39.12 5.36
8122 9501 2.119391 GGATTGGTTGGTGCCCCA 59.881 61.111 0.00 0.00 39.65 4.96
8124 9503 1.228862 GATTGGTTGGTGCCCCACT 60.229 57.895 0.00 0.00 41.67 4.00
8125 9504 0.831711 GATTGGTTGGTGCCCCACTT 60.832 55.000 0.00 0.00 41.67 3.16
8126 9505 0.485099 ATTGGTTGGTGCCCCACTTA 59.515 50.000 0.00 0.00 41.67 2.24
8188 9764 2.627515 GCACCCTGATGCAATCTAGA 57.372 50.000 0.00 0.00 45.81 2.43
8189 9765 2.492012 GCACCCTGATGCAATCTAGAG 58.508 52.381 0.00 0.00 45.81 2.43
8190 9766 2.492012 CACCCTGATGCAATCTAGAGC 58.508 52.381 0.00 0.00 45.81 4.09
8192 9768 1.342496 CCCTGATGCAATCTAGAGCGA 59.658 52.381 0.00 0.00 45.81 4.93
8194 9770 2.609984 CCTGATGCAATCTAGAGCGAGG 60.610 54.545 0.00 0.99 45.81 4.63
8195 9771 2.295629 CTGATGCAATCTAGAGCGAGGA 59.704 50.000 0.00 0.00 45.81 3.71
8196 9772 2.295629 TGATGCAATCTAGAGCGAGGAG 59.704 50.000 0.00 0.00 45.81 3.69
8197 9773 1.769026 TGCAATCTAGAGCGAGGAGT 58.231 50.000 0.00 0.00 0.00 3.85
8362 10475 0.743688 TGCCGCATGTTGTGTTCTTT 59.256 45.000 0.00 0.00 0.00 2.52
8400 10513 2.755686 TCTCTGGAGATGAGCATCCAA 58.244 47.619 6.84 0.00 44.82 3.53
8449 10563 4.381398 CCTTGGTGTATCTCTGTGACTGAG 60.381 50.000 12.62 12.62 0.00 3.35
8527 10645 2.611292 CGCAGGAAATGGAGATCTGTTC 59.389 50.000 0.00 0.00 0.00 3.18
8566 10684 4.935205 GTCTGGTATGTATGTGCAGTTGAA 59.065 41.667 0.00 0.00 0.00 2.69
8714 10852 5.261040 TCCATGAACTTTCTTTCCATCCT 57.739 39.130 0.00 0.00 0.00 3.24
8739 10878 5.422970 TGGTTAACTAACTCGACCCATGTAT 59.577 40.000 5.42 0.00 36.47 2.29
8779 10919 3.462021 CTGGAGATAAGCTACCAGTTGC 58.538 50.000 0.00 0.00 43.16 4.17
8823 10965 5.779529 AGACTGCACATGAAACAAAGATT 57.220 34.783 0.00 0.00 0.00 2.40
8941 11086 6.309494 TCCGTTGTTGATGAGACGTTTATTAG 59.691 38.462 0.00 0.00 33.95 1.73
8960 11105 9.493206 TTTATTAGCACCGAAAAATTACGATTC 57.507 29.630 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.646930 TCCACAAAGCTAGCATCCATG 58.353 47.619 18.83 10.21 0.00 3.66
9 10 3.285484 CTTCCACAAAGCTAGCATCCAT 58.715 45.455 18.83 0.00 0.00 3.41
43 45 1.208535 CTGGCGATAACCCCAACACTA 59.791 52.381 0.00 0.00 0.00 2.74
47 49 1.828979 TTTCTGGCGATAACCCCAAC 58.171 50.000 0.00 0.00 0.00 3.77
63 65 4.528206 ACAAAACTTCCCCCAGATGATTTC 59.472 41.667 0.00 0.00 0.00 2.17
64 66 4.492646 ACAAAACTTCCCCCAGATGATTT 58.507 39.130 0.00 0.00 0.00 2.17
73 75 4.746535 TGAAGAAAACAAAACTTCCCCC 57.253 40.909 0.00 0.00 39.14 5.40
78 80 9.434420 TGAAATCACATGAAGAAAACAAAACTT 57.566 25.926 0.00 0.00 0.00 2.66
108 110 0.178068 ATCCATGCAGGTACACGGAC 59.822 55.000 0.00 0.00 39.02 4.79
110 112 0.177836 TCATCCATGCAGGTACACGG 59.822 55.000 0.00 0.00 39.02 4.94
111 113 1.935873 CTTCATCCATGCAGGTACACG 59.064 52.381 0.00 0.00 39.02 4.49
117 119 1.097232 TTTCGCTTCATCCATGCAGG 58.903 50.000 0.00 0.00 39.47 4.85
118 120 3.431922 AATTTCGCTTCATCCATGCAG 57.568 42.857 0.00 0.00 0.00 4.41
134 136 2.159181 CGAGACACGCCCGAAATTT 58.841 52.632 0.00 0.00 34.51 1.82
188 190 9.936759 AAAAGAACAGTCAGTTTCCAAAATAAA 57.063 25.926 0.00 0.00 41.51 1.40
197 199 3.793492 GCAGCAAAAGAACAGTCAGTTTC 59.207 43.478 0.00 0.00 41.51 2.78
202 204 5.772825 AATAAGCAGCAAAAGAACAGTCA 57.227 34.783 0.00 0.00 0.00 3.41
210 212 4.309099 TGCCAGAAAATAAGCAGCAAAAG 58.691 39.130 0.00 0.00 0.00 2.27
216 218 4.789012 TCCTTTGCCAGAAAATAAGCAG 57.211 40.909 0.00 0.00 36.44 4.24
222 224 2.688477 TGGGTTCCTTTGCCAGAAAAT 58.312 42.857 0.00 0.00 0.00 1.82
229 231 4.286707 ACCTATTAATGGGTTCCTTTGCC 58.713 43.478 17.23 0.00 38.65 4.52
239 241 4.040952 CACCAGAGGAGACCTATTAATGGG 59.959 50.000 15.85 15.85 31.76 4.00
240 242 4.040952 CCACCAGAGGAGACCTATTAATGG 59.959 50.000 0.00 0.00 31.76 3.16
260 262 1.740025 CGCCTCCTTTTTCAGATCCAC 59.260 52.381 0.00 0.00 0.00 4.02
278 280 1.730064 TGAACTTAGGACGATTTGCGC 59.270 47.619 0.00 0.00 46.04 6.09
283 285 3.068307 CCCTCGATGAACTTAGGACGATT 59.932 47.826 0.00 0.00 0.00 3.34
285 287 2.022195 CCCTCGATGAACTTAGGACGA 58.978 52.381 0.00 0.00 0.00 4.20
286 288 1.749634 ACCCTCGATGAACTTAGGACG 59.250 52.381 0.00 0.00 0.00 4.79
297 300 5.565592 TCATGATTTTGAAACCCTCGATG 57.434 39.130 0.00 0.00 0.00 3.84
301 304 8.606040 TCAATTTTCATGATTTTGAAACCCTC 57.394 30.769 11.10 0.00 43.38 4.30
305 308 9.977762 GCCTATCAATTTTCATGATTTTGAAAC 57.022 29.630 15.30 6.09 43.38 2.78
307 310 9.373603 CTGCCTATCAATTTTCATGATTTTGAA 57.626 29.630 15.30 0.00 38.44 2.69
316 319 3.645434 TGGCCTGCCTATCAATTTTCAT 58.355 40.909 9.97 0.00 36.94 2.57
358 361 8.871686 AATCTGGTGTCAAAACTAAATTTCAC 57.128 30.769 0.00 0.00 0.00 3.18
377 380 5.587388 ACAATAAGCACCATCAAATCTGG 57.413 39.130 0.00 0.00 39.80 3.86
380 383 9.669353 CACTATTACAATAAGCACCATCAAATC 57.331 33.333 0.00 0.00 0.00 2.17
384 387 8.046708 AGAACACTATTACAATAAGCACCATCA 58.953 33.333 0.00 0.00 0.00 3.07
396 399 3.343617 GCAGGGCAGAACACTATTACAA 58.656 45.455 0.00 0.00 0.00 2.41
412 415 2.912025 AAGGTTTGCCACGCAGGG 60.912 61.111 0.00 0.00 40.61 4.45
489 492 9.003658 CGAGCAAGGGTTTCTGAATATATATTT 57.996 33.333 9.33 0.00 0.00 1.40
492 495 7.297936 TCGAGCAAGGGTTTCTGAATATATA 57.702 36.000 0.00 0.00 0.00 0.86
494 497 5.607939 TCGAGCAAGGGTTTCTGAATATA 57.392 39.130 0.00 0.00 0.00 0.86
495 498 4.487714 TCGAGCAAGGGTTTCTGAATAT 57.512 40.909 0.00 0.00 0.00 1.28
496 499 3.973206 TCGAGCAAGGGTTTCTGAATA 57.027 42.857 0.00 0.00 0.00 1.75
635 638 5.979993 TGGCTTAACGGTTGATATCTTGTA 58.020 37.500 3.07 0.00 0.00 2.41
636 639 4.839121 TGGCTTAACGGTTGATATCTTGT 58.161 39.130 3.07 0.00 0.00 3.16
697 700 2.546789 GGAGTGTGACGGTTTTAGTTGG 59.453 50.000 0.00 0.00 0.00 3.77
738 741 3.572447 CTGGCTGGCATGTGGACCA 62.572 63.158 3.74 0.00 0.00 4.02
816 819 0.245539 CTTCCTGTTTCGGAGGCGTA 59.754 55.000 0.00 0.00 33.89 4.42
990 996 4.838152 TTCCGCATCTCTGCCCGC 62.838 66.667 0.00 0.00 46.07 6.13
991 997 2.587194 CTTCCGCATCTCTGCCCG 60.587 66.667 0.00 0.00 46.07 6.13
992 998 2.203126 CCTTCCGCATCTCTGCCC 60.203 66.667 0.00 0.00 46.07 5.36
993 999 2.899339 GCCTTCCGCATCTCTGCC 60.899 66.667 0.00 0.00 46.07 4.85
994 1000 2.985512 ATCGCCTTCCGCATCTCTGC 62.986 60.000 0.00 0.00 45.31 4.26
995 1001 1.068753 ATCGCCTTCCGCATCTCTG 59.931 57.895 0.00 0.00 37.30 3.35
996 1002 1.068753 CATCGCCTTCCGCATCTCT 59.931 57.895 0.00 0.00 37.30 3.10
997 1003 1.958205 CCATCGCCTTCCGCATCTC 60.958 63.158 0.00 0.00 37.30 2.75
1119 1625 1.117150 GTAGCATACGTGGAAGGGGA 58.883 55.000 0.00 0.00 0.00 4.81
1128 1634 3.714391 GAAAATCGAGGGTAGCATACGT 58.286 45.455 0.00 0.00 44.28 3.57
1199 1705 3.099905 ACGATCCAATTCCAGACAGAGA 58.900 45.455 0.00 0.00 0.00 3.10
1205 1711 3.737972 CGACATGACGATCCAATTCCAGA 60.738 47.826 12.27 0.00 35.09 3.86
1394 1900 4.725556 CGTAGCAAATGTACACACAAGT 57.274 40.909 0.00 0.00 38.42 3.16
1610 2117 4.935885 AGAGATTCATCAAACGACTTGC 57.064 40.909 0.00 0.00 34.76 4.01
1666 2173 4.710375 AGATCAGCAAAGAAGGCATCATTT 59.290 37.500 0.00 0.00 0.00 2.32
1701 2208 6.206634 TCATCTACTGATCCAAAACAAACACC 59.793 38.462 0.00 0.00 0.00 4.16
1806 2313 9.656040 AAATATGTTGCACATAATTCACACATT 57.344 25.926 11.35 0.00 43.50 2.71
1928 2435 1.156645 GCGCAAGATGGGAGCTACAG 61.157 60.000 0.30 0.00 43.02 2.74
2813 3320 2.057922 AGAAGTTCCCTGGAGAAGCAA 58.942 47.619 0.00 0.00 0.00 3.91
2913 3420 8.260818 AGAAGCATGTAGTAGAGCTCAATAAAA 58.739 33.333 17.77 0.00 36.07 1.52
2975 3482 6.019559 GGAAGAACTTGAGAAACAAAATGCAC 60.020 38.462 0.00 0.00 38.08 4.57
3405 3914 5.630121 TGGTCATCCACTAACACTTTTGAT 58.370 37.500 0.00 0.00 39.03 2.57
3600 4112 0.666913 GAACGCTATCTACCGCTCCA 59.333 55.000 0.00 0.00 0.00 3.86
3605 4117 2.153247 GCATTTCGAACGCTATCTACCG 59.847 50.000 10.72 0.00 0.00 4.02
3957 4469 4.452455 GCATACATTAGTACCTCACCATGC 59.548 45.833 0.00 0.00 31.96 4.06
4621 5152 2.370849 ACCACAACTTGAGTAACCCGAT 59.629 45.455 0.00 0.00 0.00 4.18
4622 5153 1.764134 ACCACAACTTGAGTAACCCGA 59.236 47.619 0.00 0.00 0.00 5.14
4623 5154 2.249844 ACCACAACTTGAGTAACCCG 57.750 50.000 0.00 0.00 0.00 5.28
4768 6099 6.208644 GCTATTTCAAAGCTGTTCAGAAACA 58.791 36.000 3.84 0.00 43.06 2.83
5089 6423 2.313234 CAAACTTCATGCTGTTCTGCG 58.687 47.619 4.15 0.00 35.36 5.18
5095 6429 4.590222 AGAAAATCCCAAACTTCATGCTGT 59.410 37.500 0.00 0.00 0.00 4.40
5180 6514 9.903682 CACAAAATTATGTGTTCATCTTTCTCT 57.096 29.630 0.00 0.00 44.46 3.10
5568 6903 5.567138 ACTTCCCAAATTTCTATTCTGCG 57.433 39.130 0.00 0.00 0.00 5.18
5998 7334 0.108041 TTATCCAACCCCGTCGCTTC 60.108 55.000 0.00 0.00 0.00 3.86
6764 8102 0.517316 CACTCAACTAAACCTGCCGC 59.483 55.000 0.00 0.00 0.00 6.53
6766 8104 3.010420 GGATCACTCAACTAAACCTGCC 58.990 50.000 0.00 0.00 0.00 4.85
6776 8114 7.014711 TCCTAGTATGAGATTGGATCACTCAAC 59.985 40.741 12.51 11.67 42.55 3.18
6782 8120 5.247110 GCCTTCCTAGTATGAGATTGGATCA 59.753 44.000 0.00 0.00 0.00 2.92
6876 8214 3.312421 CCCATTCACTTACAGCCATAACG 59.688 47.826 0.00 0.00 0.00 3.18
6908 8246 3.962063 TCCCATAATCTAAGGTGCACGTA 59.038 43.478 13.22 5.60 0.00 3.57
6989 8333 5.682943 TTATGTTATGCCATCGTTTAGCC 57.317 39.130 0.00 0.00 0.00 3.93
7023 8367 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
7024 8368 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
7025 8369 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
7026 8370 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
7027 8371 2.667473 ACAAGTATTTCCGGACGGAG 57.333 50.000 13.64 3.15 46.06 4.63
7028 8372 2.299582 TGAACAAGTATTTCCGGACGGA 59.700 45.455 1.83 9.76 43.52 4.69
7029 8373 2.690786 TGAACAAGTATTTCCGGACGG 58.309 47.619 1.83 3.96 0.00 4.79
7030 8374 4.735662 TTTGAACAAGTATTTCCGGACG 57.264 40.909 1.83 0.00 0.00 4.79
7031 8375 5.861787 CCATTTTGAACAAGTATTTCCGGAC 59.138 40.000 1.83 0.00 0.00 4.79
7032 8376 5.770663 TCCATTTTGAACAAGTATTTCCGGA 59.229 36.000 0.00 0.00 0.00 5.14
7033 8377 6.019779 TCCATTTTGAACAAGTATTTCCGG 57.980 37.500 0.00 0.00 0.00 5.14
7034 8378 8.673711 TCTATCCATTTTGAACAAGTATTTCCG 58.326 33.333 0.00 0.00 0.00 4.30
7041 8385 8.924511 TCTCTTTCTATCCATTTTGAACAAGT 57.075 30.769 0.00 0.00 0.00 3.16
7042 8386 9.784680 CATCTCTTTCTATCCATTTTGAACAAG 57.215 33.333 0.00 0.00 0.00 3.16
7043 8387 9.300681 ACATCTCTTTCTATCCATTTTGAACAA 57.699 29.630 0.00 0.00 0.00 2.83
7044 8388 8.868522 ACATCTCTTTCTATCCATTTTGAACA 57.131 30.769 0.00 0.00 0.00 3.18
7076 8420 9.551734 GGGGATGTATTTAGACGTATTTTAGTT 57.448 33.333 0.00 0.00 0.00 2.24
7077 8421 8.931568 AGGGGATGTATTTAGACGTATTTTAGT 58.068 33.333 0.00 0.00 0.00 2.24
7078 8422 9.774413 AAGGGGATGTATTTAGACGTATTTTAG 57.226 33.333 0.00 0.00 0.00 1.85
7080 8424 9.470399 AAAAGGGGATGTATTTAGACGTATTTT 57.530 29.630 0.00 0.00 0.00 1.82
7083 8427 9.939802 GATAAAAGGGGATGTATTTAGACGTAT 57.060 33.333 0.00 0.00 0.00 3.06
7084 8428 8.370182 GGATAAAAGGGGATGTATTTAGACGTA 58.630 37.037 0.00 0.00 0.00 3.57
7085 8429 7.147444 TGGATAAAAGGGGATGTATTTAGACGT 60.147 37.037 0.00 0.00 0.00 4.34
7086 8430 7.221450 TGGATAAAAGGGGATGTATTTAGACG 58.779 38.462 0.00 0.00 0.00 4.18
7087 8431 9.588096 AATGGATAAAAGGGGATGTATTTAGAC 57.412 33.333 0.00 0.00 0.00 2.59
7091 8435 9.278011 TCAAAATGGATAAAAGGGGATGTATTT 57.722 29.630 0.00 0.00 0.00 1.40
7092 8436 8.852671 TCAAAATGGATAAAAGGGGATGTATT 57.147 30.769 0.00 0.00 0.00 1.89
7093 8437 8.873144 CATCAAAATGGATAAAAGGGGATGTAT 58.127 33.333 0.00 0.00 0.00 2.29
7094 8438 8.064389 TCATCAAAATGGATAAAAGGGGATGTA 58.936 33.333 0.00 0.00 33.42 2.29
7095 8439 6.902416 TCATCAAAATGGATAAAAGGGGATGT 59.098 34.615 0.00 0.00 33.42 3.06
7096 8440 7.147689 TGTCATCAAAATGGATAAAAGGGGATG 60.148 37.037 0.00 0.00 33.42 3.51
7097 8441 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
7098 8442 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
7099 8443 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
7100 8444 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
7106 8450 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
7107 8451 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
7108 8452 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
7109 8453 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
7110 8454 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
7111 8455 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
7112 8456 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
7113 8457 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
7114 8458 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
7115 8459 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
7116 8460 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
7117 8461 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
7118 8462 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
7119 8463 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
7120 8464 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
7121 8465 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
7122 8466 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
7123 8467 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
7124 8468 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
7125 8469 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
7126 8470 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
7127 8471 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
7128 8472 0.032813 ATTACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
7129 8473 0.032813 AATTACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
7130 8474 1.612463 CTAATTACTCCCTCCGTCCGG 59.388 57.143 0.00 0.00 0.00 5.14
7131 8475 1.000496 GCTAATTACTCCCTCCGTCCG 60.000 57.143 0.00 0.00 0.00 4.79
7132 8476 2.037144 TGCTAATTACTCCCTCCGTCC 58.963 52.381 0.00 0.00 0.00 4.79
7133 8477 3.814005 TTGCTAATTACTCCCTCCGTC 57.186 47.619 0.00 0.00 0.00 4.79
7134 8478 4.772886 ATTTGCTAATTACTCCCTCCGT 57.227 40.909 0.00 0.00 0.00 4.69
7135 8479 7.661847 AGAATAATTTGCTAATTACTCCCTCCG 59.338 37.037 15.26 0.00 38.63 4.63
7136 8480 8.926092 AGAATAATTTGCTAATTACTCCCTCC 57.074 34.615 15.26 0.00 38.63 4.30
7605 8956 9.875675 GTTGCTTCTATCACATATCTGAATTTC 57.124 33.333 0.00 0.00 0.00 2.17
7978 9329 1.810151 TGGTAAATGAACGAGGCTTGC 59.190 47.619 0.37 0.00 0.00 4.01
8118 9497 5.885912 ACAGCTGTACATATTTTAAGTGGGG 59.114 40.000 20.16 0.00 0.00 4.96
8119 9498 8.677148 ATACAGCTGTACATATTTTAAGTGGG 57.323 34.615 28.28 0.00 32.72 4.61
8126 9505 9.935241 CTCCTGATATACAGCTGTACATATTTT 57.065 33.333 28.28 13.36 44.52 1.82
8148 9533 5.071923 GTGCCTAATTTACATACCTCCTCCT 59.928 44.000 0.00 0.00 0.00 3.69
8149 9534 5.306394 GTGCCTAATTTACATACCTCCTCC 58.694 45.833 0.00 0.00 0.00 4.30
8150 9535 5.306394 GGTGCCTAATTTACATACCTCCTC 58.694 45.833 0.00 0.00 0.00 3.71
8188 9764 2.365617 TCTGAACTCAAAACTCCTCGCT 59.634 45.455 0.00 0.00 0.00 4.93
8189 9765 2.734079 CTCTGAACTCAAAACTCCTCGC 59.266 50.000 0.00 0.00 0.00 5.03
8190 9766 3.983741 ACTCTGAACTCAAAACTCCTCG 58.016 45.455 0.00 0.00 0.00 4.63
8192 9768 5.104259 ACAACTCTGAACTCAAAACTCCT 57.896 39.130 0.00 0.00 0.00 3.69
8194 9770 7.921745 AGTAGTACAACTCTGAACTCAAAACTC 59.078 37.037 2.52 0.00 0.00 3.01
8195 9771 7.783042 AGTAGTACAACTCTGAACTCAAAACT 58.217 34.615 2.52 0.00 0.00 2.66
8196 9772 9.182933 CTAGTAGTACAACTCTGAACTCAAAAC 57.817 37.037 2.52 0.00 0.00 2.43
8197 9773 8.358148 CCTAGTAGTACAACTCTGAACTCAAAA 58.642 37.037 2.52 0.00 0.00 2.44
8362 10475 5.494724 CAGAGAATGGTCTGATTTCCTCAA 58.505 41.667 0.00 0.00 46.02 3.02
8400 10513 2.684881 GTTCACGATGCTCCATTGGATT 59.315 45.455 5.70 0.00 30.00 3.01
8449 10563 1.211709 CCAAACGGGCCGAACATTC 59.788 57.895 35.78 0.00 0.00 2.67
8527 10645 1.663702 GACACGTCCGGAACACAGG 60.664 63.158 5.23 0.00 0.00 4.00
8566 10684 5.543405 TCAATTTTCCAACCCAAGTCATCAT 59.457 36.000 0.00 0.00 0.00 2.45
8714 10852 4.040706 ACATGGGTCGAGTTAGTTAACCAA 59.959 41.667 0.88 0.00 36.88 3.67
8779 10919 1.071605 CCTCGTTCGCTTTCAAGGAG 58.928 55.000 0.00 0.00 36.12 3.69
8823 10965 2.104111 AGACATCCGTGGACAAAACTCA 59.896 45.455 0.00 0.00 0.00 3.41
8910 11055 0.742990 TCATCAACAACGGATCCGCC 60.743 55.000 33.62 0.00 44.19 6.13
8941 11086 4.351131 AGGAATCGTAATTTTTCGGTGC 57.649 40.909 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.