Multiple sequence alignment - TraesCS2A01G220900

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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 TraesCS2A01G220900 chr2A 100.000 9619 0 0 1 9619 209386105 209395723 0.000000e+00 17764.0
1 TraesCS2A01G220900 chr2D 96.065 7523 164 41 290 7756 194754261 194761707 0.000000e+00 12131.0
2 TraesCS2A01G220900 chr2D 92.440 1680 62 26 7966 9619 194761719 194763359 0.000000e+00 2338.0
3 TraesCS2A01G220900 chr2D 87.288 118 3 8 211 325 194754157 194754265 3.650000e-24 124.0
4 TraesCS2A01G220900 chr2B 96.997 6960 140 22 834 7750 250735166 250742099 0.000000e+00 11631.0
5 TraesCS2A01G220900 chr2B 95.000 1680 51 14 7966 9619 250742105 250743777 0.000000e+00 2606.0
6 TraesCS2A01G220900 chr2B 87.894 603 34 15 234 825 250730471 250731045 0.000000e+00 673.0
7 TraesCS2A01G220900 chr2B 92.737 179 9 2 1 179 250730203 250730377 1.240000e-63 255.0
8 TraesCS2A01G220900 chrUn 100.000 414 0 0 6346 6759 477336710 477336297 0.000000e+00 765.0
9 TraesCS2A01G220900 chr7A 88.796 357 33 5 5948 6299 145457161 145456807 1.920000e-116 431.0
10 TraesCS2A01G220900 chr6B 88.136 354 35 5 5948 6296 538998818 538999169 1.930000e-111 414.0
11 TraesCS2A01G220900 chr6B 98.454 194 3 0 7775 7968 583189041 583189234 9.250000e-90 342.0
12 TraesCS2A01G220900 chr4A 87.853 354 36 5 5948 6296 514233431 514233782 8.990000e-110 409.0
13 TraesCS2A01G220900 chr4A 89.130 138 14 1 6118 6255 436458686 436458822 4.620000e-38 171.0
14 TraesCS2A01G220900 chr4A 88.406 138 14 2 6118 6255 384242637 384242772 2.150000e-36 165.0
15 TraesCS2A01G220900 chr5A 87.395 357 38 5 5948 6299 452465619 452465265 4.180000e-108 403.0
16 TraesCS2A01G220900 chr7B 96.602 206 6 1 7775 7980 464539884 464539680 3.330000e-89 340.0
17 TraesCS2A01G220900 chr7B 97.015 201 3 3 7775 7975 713286379 713286182 1.550000e-87 335.0
18 TraesCS2A01G220900 chr7B 85.714 91 11 2 1218 1308 458530685 458530773 2.860000e-15 95.3
19 TraesCS2A01G220900 chr3B 97.938 194 4 0 7775 7968 464610405 464610212 4.300000e-88 337.0
20 TraesCS2A01G220900 chr3B 96.552 203 6 1 7775 7976 576453829 576453627 1.550000e-87 335.0
21 TraesCS2A01G220900 chr3B 96.907 194 6 0 7775 7968 744727740 744727547 9.320000e-85 326.0
22 TraesCS2A01G220900 chr1D 97.938 194 4 0 7775 7968 153918793 153918986 4.300000e-88 337.0
23 TraesCS2A01G220900 chr1D 90.741 54 5 0 1218 1271 364473096 364473149 1.340000e-08 73.1
24 TraesCS2A01G220900 chr4B 97.449 196 5 0 7775 7970 418510914 418510719 1.550000e-87 335.0
25 TraesCS2A01G220900 chr7D 97.409 193 5 0 7775 7967 209183735 209183927 7.200000e-86 329.0
26 TraesCS2A01G220900 chr1A 88.406 138 13 2 6118 6255 530277335 530277469 7.730000e-36 163.0
27 TraesCS2A01G220900 chr1A 90.361 83 7 1 1226 1308 34933778 34933859 3.670000e-19 108.0
28 TraesCS2A01G220900 chr3D 94.231 52 3 0 1223 1274 560151668 560151719 8.010000e-11 80.5


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 TraesCS2A01G220900 chr2A 209386105 209395723 9618 False 17764.000000 17764 100.0000 1 9619 1 chr2A.!!$F1 9618
1 TraesCS2A01G220900 chr2D 194754157 194763359 9202 False 4864.333333 12131 91.9310 211 9619 3 chr2D.!!$F1 9408
2 TraesCS2A01G220900 chr2B 250735166 250743777 8611 False 7118.500000 11631 95.9985 834 9619 2 chr2B.!!$F2 8785
3 TraesCS2A01G220900 chr2B 250730203 250731045 842 False 464.000000 673 90.3155 1 825 2 chr2B.!!$F1 824

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
336 407 0.036010 AACGAGGATCACAAGCAGGG 60.036 55.000 0.00 0.00 33.17 4.45 F
501 576 0.036671 CTTCCCTTCCGTACCGCTTT 60.037 55.000 0.00 0.00 0.00 3.51 F
1704 1812 0.316204 GCTGTGTTTGGATGCTTGCT 59.684 50.000 0.00 0.00 0.00 3.91 F
1708 1816 0.599558 TGTTTGGATGCTTGCTCTGC 59.400 50.000 0.00 0.00 0.00 4.26 F
1710 1818 0.885879 TTTGGATGCTTGCTCTGCAG 59.114 50.000 7.63 7.63 44.04 4.41 F
3376 3516 0.514691 GCCTTGCTCTTTCGTCACTG 59.485 55.000 0.00 0.00 0.00 3.66 F
4502 4651 1.135489 CAGCACAGCGCAGATCAATTT 60.135 47.619 11.47 0.00 46.13 1.82 F
4918 5067 2.948315 GGAATGGCAGAAAGTCCATCTC 59.052 50.000 0.00 0.00 41.92 2.75 F
5433 5586 3.896648 ATGTGCAACCAGTTCTTTACG 57.103 42.857 0.00 0.00 34.36 3.18 F
6162 6317 0.905357 AGGCTGCAACCGAAGAGTAT 59.095 50.000 0.50 0.00 33.69 2.12 F
7594 7749 0.319469 CGAAACATTGGTGGTTGGCC 60.319 55.000 0.00 0.00 34.78 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 2349 0.318955 CCTTGCAGCCGACAAAAAGG 60.319 55.000 0.00 0.00 0.00 3.11 R
2418 2558 5.008019 ACAGAAACTAGCATGTTGTTGTCAG 59.992 40.000 0.00 0.00 0.00 3.51 R
3222 3362 0.449388 GAGTAGGTACCACGTGACGG 59.551 60.000 19.30 2.28 0.00 4.79 R
3376 3516 3.133691 TGCTGATGAAATATCTGACGCC 58.866 45.455 0.00 0.00 0.00 5.68 R
3550 3690 4.346129 CACAAAGTGCTTTCAGTGACTTC 58.654 43.478 8.54 0.00 31.85 3.01 R
4875 5024 0.466124 GTGATACCTCCAGAGTGCCC 59.534 60.000 0.00 0.00 0.00 5.36 R
5623 5776 1.761784 CTGGAAGAGGGAGATCTGTGG 59.238 57.143 0.00 0.00 34.07 4.17 R
5979 6134 3.401033 TGGCTATGTTGATATGGGTCG 57.599 47.619 0.00 0.00 0.00 4.79 R
7126 7281 1.944709 GTTCCTACTTGTGTTTGGCGT 59.055 47.619 0.00 0.00 0.00 5.68 R
8000 8155 1.134098 CAGGTTATGCTACCAGGGTGG 60.134 57.143 0.06 0.00 45.02 4.61 R
9437 9620 0.663153 AACGACTGACCTTGCTTTGC 59.337 50.000 0.00 0.00 0.00 3.68 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
30 31 3.813166 TCCTTCTCGATCCACACAAAAAC 59.187 43.478 0.00 0.00 0.00 2.43
31 32 3.058224 CCTTCTCGATCCACACAAAAACC 60.058 47.826 0.00 0.00 0.00 3.27
32 33 2.500229 TCTCGATCCACACAAAAACCC 58.500 47.619 0.00 0.00 0.00 4.11
33 34 2.158740 TCTCGATCCACACAAAAACCCA 60.159 45.455 0.00 0.00 0.00 4.51
34 35 1.950909 TCGATCCACACAAAAACCCAC 59.049 47.619 0.00 0.00 0.00 4.61
61 62 4.922206 TGAACAAGCAGAATCCTTATGGT 58.078 39.130 0.00 0.00 33.51 3.55
67 68 3.142174 GCAGAATCCTTATGGTGCTACC 58.858 50.000 1.89 0.00 39.22 3.18
106 107 0.348370 AGGGGGAGAGGGAATCATGT 59.652 55.000 0.00 0.00 0.00 3.21
120 121 2.685850 TCATGTGCAGATCTGTCCAG 57.314 50.000 23.38 10.54 0.00 3.86
140 141 0.790993 ACCTGTAAGTGGAGGGAGGA 59.209 55.000 0.00 0.00 33.16 3.71
145 146 2.873557 TAAGTGGAGGGAGGAGCGGG 62.874 65.000 0.00 0.00 0.00 6.13
159 160 4.431131 CGGGGGCAAGTGGATGCT 62.431 66.667 0.00 0.00 45.68 3.79
182 183 4.286320 GGATCGGCGCCGTCTGAT 62.286 66.667 44.16 31.96 40.74 2.90
183 184 3.032609 GATCGGCGCCGTCTGATG 61.033 66.667 44.16 18.80 40.74 3.07
184 185 3.484742 GATCGGCGCCGTCTGATGA 62.485 63.158 44.16 26.72 40.74 2.92
187 188 4.148825 GGCGCCGTCTGATGAGGT 62.149 66.667 12.58 0.00 0.00 3.85
188 189 2.583593 GCGCCGTCTGATGAGGTC 60.584 66.667 0.00 0.00 0.00 3.85
189 190 2.885113 CGCCGTCTGATGAGGTCA 59.115 61.111 0.00 0.00 35.05 4.02
196 197 3.298958 TGATGAGGTCAGGACGGC 58.701 61.111 0.00 0.00 31.80 5.68
259 299 0.895530 AGGAGAAGGTTGATTCGCGA 59.104 50.000 3.71 3.71 34.27 5.87
269 309 0.318441 TGATTCGCGAGATGGGGATC 59.682 55.000 9.59 8.36 44.04 3.36
272 312 4.363990 CGCGAGATGGGGATCGGG 62.364 72.222 0.00 0.00 0.00 5.14
273 313 4.008933 GCGAGATGGGGATCGGGG 62.009 72.222 0.00 0.00 0.00 5.73
274 314 2.203640 CGAGATGGGGATCGGGGA 60.204 66.667 0.00 0.00 0.00 4.81
275 315 2.279069 CGAGATGGGGATCGGGGAG 61.279 68.421 0.00 0.00 0.00 4.30
276 316 1.156330 GAGATGGGGATCGGGGAGA 59.844 63.158 0.00 0.00 0.00 3.71
277 317 0.902516 GAGATGGGGATCGGGGAGAG 60.903 65.000 0.00 0.00 0.00 3.20
278 318 1.156330 GATGGGGATCGGGGAGAGA 59.844 63.158 0.00 0.00 0.00 3.10
279 319 0.902516 GATGGGGATCGGGGAGAGAG 60.903 65.000 0.00 0.00 0.00 3.20
280 320 2.920384 GGGGATCGGGGAGAGAGC 60.920 72.222 0.00 0.00 0.00 4.09
336 407 0.036010 AACGAGGATCACAAGCAGGG 60.036 55.000 0.00 0.00 33.17 4.45
342 413 0.747283 GATCACAAGCAGGGAGGCAG 60.747 60.000 0.00 0.00 35.83 4.85
366 437 7.653311 CAGAAGAAACCAATAAAAACAAGGGAG 59.347 37.037 0.00 0.00 0.00 4.30
381 452 0.182299 GGGAGGCAGAGAATGGAAGG 59.818 60.000 0.00 0.00 0.00 3.46
385 456 0.106967 GGCAGAGAATGGAAGGTCCC 60.107 60.000 0.00 0.00 35.03 4.46
501 576 0.036671 CTTCCCTTCCGTACCGCTTT 60.037 55.000 0.00 0.00 0.00 3.51
502 577 0.320946 TTCCCTTCCGTACCGCTTTG 60.321 55.000 0.00 0.00 0.00 2.77
503 578 1.743995 CCCTTCCGTACCGCTTTGG 60.744 63.158 0.00 0.00 46.41 3.28
513 588 1.203313 CCGCTTTGGTTCGACGAAC 59.797 57.895 28.38 28.38 41.32 3.95
542 622 3.169099 CACGATGGGGAGGAGATAGATT 58.831 50.000 0.00 0.00 0.00 2.40
580 660 2.365293 ACAAAGTGAAGACAATTGGGCC 59.635 45.455 10.83 0.00 34.54 5.80
641 721 3.073735 CCTCGCCTCTCCAGCTGT 61.074 66.667 13.81 0.00 0.00 4.40
652 732 2.957402 TCCAGCTGTTTGGAGTTGAT 57.043 45.000 13.81 0.00 42.24 2.57
688 775 0.696501 TTTGGAGTTGGGTAGCCTCC 59.303 55.000 13.11 11.43 44.16 4.30
689 776 1.205460 TTGGAGTTGGGTAGCCTCCC 61.205 60.000 13.11 8.31 43.42 4.30
690 777 2.376165 GGAGTTGGGTAGCCTCCCC 61.376 68.421 13.11 4.65 46.48 4.81
691 778 1.307084 GAGTTGGGTAGCCTCCCCT 60.307 63.158 13.11 2.37 46.48 4.79
692 779 1.307084 AGTTGGGTAGCCTCCCCTC 60.307 63.158 13.11 4.79 46.48 4.30
694 781 1.306997 TTGGGTAGCCTCCCCTCAG 60.307 63.158 13.11 0.00 46.48 3.35
695 782 1.821966 TTGGGTAGCCTCCCCTCAGA 61.822 60.000 13.11 0.00 46.48 3.27
696 783 1.003051 GGGTAGCCTCCCCTCAGAA 59.997 63.158 2.95 0.00 41.54 3.02
751 838 4.892433 TCGTTAATTTCGGGTAGGAAACA 58.108 39.130 3.61 0.00 38.61 2.83
774 861 0.540133 TGCTGTGGACCCGTACAGTA 60.540 55.000 11.08 5.03 44.66 2.74
827 914 6.042777 CCAAACAGAAAGAAAGAAAAGGGAC 58.957 40.000 0.00 0.00 0.00 4.46
828 915 5.500645 AACAGAAAGAAAGAAAAGGGACG 57.499 39.130 0.00 0.00 0.00 4.79
829 916 3.315470 ACAGAAAGAAAGAAAAGGGACGC 59.685 43.478 0.00 0.00 0.00 5.19
830 917 3.315191 CAGAAAGAAAGAAAAGGGACGCA 59.685 43.478 0.00 0.00 0.00 5.24
832 919 4.401202 AGAAAGAAAGAAAAGGGACGCAAA 59.599 37.500 0.00 0.00 0.00 3.68
858 948 2.028925 CGCAGGGCCAAACCAAAC 59.971 61.111 6.18 0.00 42.05 2.93
903 997 2.804167 CGCTCCTCTGATCTGCGT 59.196 61.111 9.16 0.00 41.45 5.24
914 1008 1.272490 TGATCTGCGTTCGTCTTCCTT 59.728 47.619 0.00 0.00 0.00 3.36
935 1029 1.142870 CTCACACCACTTCCTCCCAAA 59.857 52.381 0.00 0.00 0.00 3.28
936 1030 1.780309 TCACACCACTTCCTCCCAAAT 59.220 47.619 0.00 0.00 0.00 2.32
1310 1406 0.587737 GTCGTCTGCGTCGATCTCAG 60.588 60.000 0.00 0.00 39.45 3.35
1704 1812 0.316204 GCTGTGTTTGGATGCTTGCT 59.684 50.000 0.00 0.00 0.00 3.91
1705 1813 1.668047 GCTGTGTTTGGATGCTTGCTC 60.668 52.381 0.00 0.00 0.00 4.26
1706 1814 1.884579 CTGTGTTTGGATGCTTGCTCT 59.115 47.619 0.00 0.00 0.00 4.09
1707 1815 1.610038 TGTGTTTGGATGCTTGCTCTG 59.390 47.619 0.00 0.00 0.00 3.35
1708 1816 0.599558 TGTTTGGATGCTTGCTCTGC 59.400 50.000 0.00 0.00 0.00 4.26
1709 1817 0.599558 GTTTGGATGCTTGCTCTGCA 59.400 50.000 1.83 1.83 44.95 4.41
1710 1818 0.885879 TTTGGATGCTTGCTCTGCAG 59.114 50.000 7.63 7.63 44.04 4.41
1798 1914 4.332637 GCGCTGTGCCTTGTGGTG 62.333 66.667 0.00 0.00 37.76 4.17
1902 2019 3.857665 CAGTGTGAAATTCAGCATCATGC 59.142 43.478 0.00 0.00 45.46 4.06
1968 2091 4.912214 TGTTTGATGCTTAATGCTGATCG 58.088 39.130 0.00 0.00 43.37 3.69
2004 2127 2.160417 GCCTGTTCTGTGCATTCAGTAC 59.840 50.000 7.02 7.02 36.65 2.73
2044 2167 4.020218 ACATTTGCAGTAGGACAGCTTCTA 60.020 41.667 0.00 0.00 31.40 2.10
2162 2302 9.602568 TTATTAACAGTTTCACTAGTGTTGTCA 57.397 29.630 21.99 12.35 40.79 3.58
2188 2328 3.182572 GTGACTTGTTACGTGCTTCTCAG 59.817 47.826 0.00 0.00 0.00 3.35
2203 2343 7.689812 CGTGCTTCTCAGTTTTGAAATACTATG 59.310 37.037 0.00 0.00 31.69 2.23
2418 2558 4.820284 AGAACTTGAAAGTGCTTACAGC 57.180 40.909 0.00 0.00 42.36 4.40
2655 2795 1.400494 GAACACAACAAGCTTGTCCGT 59.600 47.619 31.20 26.20 41.31 4.69
2733 2873 8.201554 TCTGTAGCTTCTATTAATTTGTGCTG 57.798 34.615 0.00 1.84 0.00 4.41
2740 2880 8.435430 GCTTCTATTAATTTGTGCTGTTTTTCC 58.565 33.333 0.00 0.00 0.00 3.13
2741 2881 9.696917 CTTCTATTAATTTGTGCTGTTTTTCCT 57.303 29.630 0.00 0.00 0.00 3.36
2742 2882 9.691362 TTCTATTAATTTGTGCTGTTTTTCCTC 57.309 29.630 0.00 0.00 0.00 3.71
2743 2883 8.855110 TCTATTAATTTGTGCTGTTTTTCCTCA 58.145 29.630 0.00 0.00 0.00 3.86
2744 2884 7.713764 ATTAATTTGTGCTGTTTTTCCTCAC 57.286 32.000 0.00 0.00 0.00 3.51
2783 2923 1.023513 GCAGGTCAGTGCCTAAGCTG 61.024 60.000 5.89 5.31 40.56 4.24
3245 3385 2.294233 GTCACGTGGTACCTACTCAACA 59.706 50.000 17.00 0.00 0.00 3.33
3376 3516 0.514691 GCCTTGCTCTTTCGTCACTG 59.485 55.000 0.00 0.00 0.00 3.66
3496 3636 3.314913 CAGTATTGCAAGTTGTGGTCACA 59.685 43.478 4.94 0.00 39.98 3.58
3550 3690 5.624344 AGATGTTGAGAAAAGATGTGCTG 57.376 39.130 0.00 0.00 0.00 4.41
3850 3991 2.734079 GCTCTCGCAATTCTAGGTATGC 59.266 50.000 4.96 4.96 35.78 3.14
4414 4563 5.423704 TGGGTCGAAGGTATAAATGAACA 57.576 39.130 0.00 0.00 0.00 3.18
4502 4651 1.135489 CAGCACAGCGCAGATCAATTT 60.135 47.619 11.47 0.00 46.13 1.82
4653 4802 4.467198 TTCCGGAACTATCAGGTTCTTC 57.533 45.455 14.35 0.00 43.43 2.87
4687 4836 9.520204 CCATTATTGCTCTATCGTTTTCAATTT 57.480 29.630 0.00 0.00 0.00 1.82
4696 4845 9.530129 CTCTATCGTTTTCAATTTCAACTGTAC 57.470 33.333 0.00 0.00 0.00 2.90
4736 4885 8.506168 TGCTGGGACTATTTAGTTATCAAAAG 57.494 34.615 0.00 0.00 36.50 2.27
4875 5024 6.697395 TGATAATGTATTCCAGTATCCACCG 58.303 40.000 7.16 0.00 45.94 4.94
4918 5067 2.948315 GGAATGGCAGAAAGTCCATCTC 59.052 50.000 0.00 0.00 41.92 2.75
5113 5262 8.464770 TTCAATTTGTGCAAGAATTAGTATGC 57.535 30.769 7.88 0.00 39.22 3.14
5180 5329 8.209917 TGTTTACTGTTTTCTTCCTCTCTTTC 57.790 34.615 0.00 0.00 0.00 2.62
5185 5334 8.354711 ACTGTTTTCTTCCTCTCTTTCTTTTT 57.645 30.769 0.00 0.00 0.00 1.94
5186 5335 9.462606 ACTGTTTTCTTCCTCTCTTTCTTTTTA 57.537 29.630 0.00 0.00 0.00 1.52
5373 5522 4.389890 TGAATTTGCTGCTTCAACAACT 57.610 36.364 0.00 0.00 0.00 3.16
5374 5523 4.757594 TGAATTTGCTGCTTCAACAACTT 58.242 34.783 0.00 0.00 0.00 2.66
5375 5524 4.805192 TGAATTTGCTGCTTCAACAACTTC 59.195 37.500 0.00 6.27 33.12 3.01
5413 5565 3.897141 TGTTGTGCGATAGGTATCCAA 57.103 42.857 0.00 0.00 0.00 3.53
5433 5586 3.896648 ATGTGCAACCAGTTCTTTACG 57.103 42.857 0.00 0.00 34.36 3.18
5482 5635 9.225682 TGTGGGAAATTACTTCTCCTATTCTAT 57.774 33.333 0.00 0.00 32.99 1.98
5578 5731 4.454728 TGCAGGATTTTCCATTAAGTGC 57.545 40.909 0.00 0.00 39.61 4.40
5623 5776 6.869388 GTCTAACCTGCTCTATATTTAGTGGC 59.131 42.308 0.00 4.86 0.00 5.01
5976 6131 6.169557 TCTAACTTTCAAGGAAGCTGTACA 57.830 37.500 0.00 0.00 0.00 2.90
5979 6134 5.948992 ACTTTCAAGGAAGCTGTACATTC 57.051 39.130 0.00 0.00 0.00 2.67
5996 6151 7.151976 TGTACATTCGACCCATATCAACATAG 58.848 38.462 0.00 0.00 0.00 2.23
6162 6317 0.905357 AGGCTGCAACCGAAGAGTAT 59.095 50.000 0.50 0.00 33.69 2.12
6885 7040 3.923017 AACAAGCATTTCTGTACCTGC 57.077 42.857 0.00 0.00 34.85 4.85
7060 7215 9.362539 GCATATTCTGTTTCAAAGATTTCATGT 57.637 29.630 0.00 0.00 0.00 3.21
7126 7281 5.138276 GGGATACATCACCGCTATATAGGA 58.862 45.833 11.72 0.80 39.74 2.94
7328 7483 4.520492 CCATTATGGGTAGATTGCACTTCC 59.480 45.833 2.72 0.00 32.67 3.46
7355 7510 7.559335 TGAACTAGCCTTCATATGTCCATAT 57.441 36.000 1.90 0.00 34.50 1.78
7594 7749 0.319469 CGAAACATTGGTGGTTGGCC 60.319 55.000 0.00 0.00 34.78 5.36
7634 7789 4.672542 GCACCGTTCACGTATAAGACAGTA 60.673 45.833 0.00 0.00 37.74 2.74
7710 7865 0.454600 ACCCAGTATCACAGTACGCG 59.545 55.000 3.53 3.53 0.00 6.01
7714 7869 2.414957 CCAGTATCACAGTACGCGTCAA 60.415 50.000 18.63 0.00 0.00 3.18
7810 7965 9.710818 AGAAAAGTAGGTACATCTAGAATACCA 57.289 33.333 26.72 15.98 40.81 3.25
7815 7970 8.368668 AGTAGGTACATCTAGAATACCAAATGC 58.631 37.037 26.72 15.90 40.81 3.56
7816 7971 7.136822 AGGTACATCTAGAATACCAAATGCA 57.863 36.000 26.72 0.00 40.81 3.96
7817 7972 6.992715 AGGTACATCTAGAATACCAAATGCAC 59.007 38.462 26.72 9.05 40.81 4.57
7818 7973 6.765989 GGTACATCTAGAATACCAAATGCACA 59.234 38.462 22.87 0.00 38.61 4.57
7819 7974 7.445402 GGTACATCTAGAATACCAAATGCACAT 59.555 37.037 22.87 0.00 38.61 3.21
7820 7975 7.502120 ACATCTAGAATACCAAATGCACATC 57.498 36.000 0.00 0.00 0.00 3.06
7821 7976 7.056006 ACATCTAGAATACCAAATGCACATCA 58.944 34.615 0.00 0.00 0.00 3.07
7822 7977 7.722728 ACATCTAGAATACCAAATGCACATCAT 59.277 33.333 0.00 0.00 36.87 2.45
7823 7978 8.573885 CATCTAGAATACCAAATGCACATCATT 58.426 33.333 0.00 0.00 46.82 2.57
7824 7979 7.933396 TCTAGAATACCAAATGCACATCATTG 58.067 34.615 0.00 0.00 44.23 2.82
7825 7980 5.909477 AGAATACCAAATGCACATCATTGG 58.091 37.500 11.02 11.02 44.23 3.16
7826 7981 5.657745 AGAATACCAAATGCACATCATTGGA 59.342 36.000 17.12 5.42 44.23 3.53
7827 7982 6.325545 AGAATACCAAATGCACATCATTGGAT 59.674 34.615 17.12 6.97 44.23 3.41
7828 7983 7.506599 AGAATACCAAATGCACATCATTGGATA 59.493 33.333 17.12 8.79 44.23 2.59
7829 7984 5.266733 ACCAAATGCACATCATTGGATAC 57.733 39.130 17.12 0.00 44.23 2.24
7869 8024 9.689976 TTTTCAGAATGTACATGTTTGGTATTG 57.310 29.630 9.63 0.00 37.40 1.90
7870 8025 7.994425 TCAGAATGTACATGTTTGGTATTGT 57.006 32.000 9.63 0.00 37.40 2.71
7871 8026 9.508642 TTCAGAATGTACATGTTTGGTATTGTA 57.491 29.630 9.63 0.00 37.40 2.41
7872 8027 9.161629 TCAGAATGTACATGTTTGGTATTGTAG 57.838 33.333 9.63 0.00 37.40 2.74
7873 8028 9.161629 CAGAATGTACATGTTTGGTATTGTAGA 57.838 33.333 9.63 0.00 0.00 2.59
7874 8029 9.905713 AGAATGTACATGTTTGGTATTGTAGAT 57.094 29.630 9.63 0.00 31.99 1.98
7875 8030 9.935682 GAATGTACATGTTTGGTATTGTAGATG 57.064 33.333 9.63 0.00 31.34 2.90
7876 8031 9.461312 AATGTACATGTTTGGTATTGTAGATGT 57.539 29.630 9.63 0.00 31.34 3.06
7878 8033 9.594478 TGTACATGTTTGGTATTGTAGATGTAG 57.406 33.333 2.30 0.00 0.00 2.74
7879 8034 9.811995 GTACATGTTTGGTATTGTAGATGTAGA 57.188 33.333 2.30 0.00 0.00 2.59
7880 8035 8.718102 ACATGTTTGGTATTGTAGATGTAGAC 57.282 34.615 0.00 0.00 0.00 2.59
7881 8036 8.318412 ACATGTTTGGTATTGTAGATGTAGACA 58.682 33.333 0.00 0.00 0.00 3.41
7882 8037 8.820933 CATGTTTGGTATTGTAGATGTAGACAG 58.179 37.037 0.00 0.00 0.00 3.51
7883 8038 7.903145 TGTTTGGTATTGTAGATGTAGACAGT 58.097 34.615 0.00 0.00 0.00 3.55
7884 8039 8.372459 TGTTTGGTATTGTAGATGTAGACAGTT 58.628 33.333 0.00 0.00 0.00 3.16
7885 8040 9.216117 GTTTGGTATTGTAGATGTAGACAGTTT 57.784 33.333 0.00 0.00 0.00 2.66
7886 8041 9.787435 TTTGGTATTGTAGATGTAGACAGTTTT 57.213 29.630 0.00 0.00 0.00 2.43
7887 8042 8.997621 TGGTATTGTAGATGTAGACAGTTTTC 57.002 34.615 0.00 0.00 0.00 2.29
7888 8043 8.812972 TGGTATTGTAGATGTAGACAGTTTTCT 58.187 33.333 0.00 0.00 0.00 2.52
7889 8044 9.303537 GGTATTGTAGATGTAGACAGTTTTCTC 57.696 37.037 0.00 0.00 0.00 2.87
7897 8052 9.469097 AGATGTAGACAGTTTTCTCTATACACT 57.531 33.333 0.00 0.00 0.00 3.55
7899 8054 9.862371 ATGTAGACAGTTTTCTCTATACACTTG 57.138 33.333 0.00 0.00 0.00 3.16
7900 8055 8.304596 TGTAGACAGTTTTCTCTATACACTTGG 58.695 37.037 0.00 0.00 0.00 3.61
7901 8056 7.304497 AGACAGTTTTCTCTATACACTTGGT 57.696 36.000 0.00 0.00 0.00 3.67
7902 8057 7.379750 AGACAGTTTTCTCTATACACTTGGTC 58.620 38.462 0.00 0.00 0.00 4.02
7903 8058 7.015292 AGACAGTTTTCTCTATACACTTGGTCA 59.985 37.037 0.00 0.00 0.00 4.02
7904 8059 7.506114 ACAGTTTTCTCTATACACTTGGTCAA 58.494 34.615 0.00 0.00 0.00 3.18
7905 8060 7.990886 ACAGTTTTCTCTATACACTTGGTCAAA 59.009 33.333 0.00 0.00 0.00 2.69
7906 8061 8.499162 CAGTTTTCTCTATACACTTGGTCAAAG 58.501 37.037 0.00 0.00 42.07 2.77
7916 8071 3.525268 CTTGGTCAAAGTTGGCAAAGT 57.475 42.857 0.00 0.00 38.66 2.66
7917 8072 3.860641 CTTGGTCAAAGTTGGCAAAGTT 58.139 40.909 0.00 0.00 38.66 2.66
7918 8073 3.971245 TGGTCAAAGTTGGCAAAGTTT 57.029 38.095 0.00 0.42 39.10 2.66
7924 8079 5.861222 CAAAGTTGGCAAAGTTTGTCTTT 57.139 34.783 21.47 17.87 45.59 2.52
7925 8080 5.857394 CAAAGTTGGCAAAGTTTGTCTTTC 58.143 37.500 21.47 10.71 45.59 2.62
7926 8081 4.799564 AGTTGGCAAAGTTTGTCTTTCA 57.200 36.364 20.24 7.47 43.57 2.69
7927 8082 4.494484 AGTTGGCAAAGTTTGTCTTTCAC 58.506 39.130 20.24 11.64 43.57 3.18
7928 8083 4.021544 AGTTGGCAAAGTTTGTCTTTCACA 60.022 37.500 20.24 0.00 43.57 3.58
7929 8084 4.527509 TGGCAAAGTTTGTCTTTCACAA 57.472 36.364 20.24 0.00 43.57 3.33
7942 8097 7.994425 TGTCTTTCACAAAAATCTATAGGCA 57.006 32.000 0.00 0.00 29.30 4.75
7943 8098 7.816640 TGTCTTTCACAAAAATCTATAGGCAC 58.183 34.615 0.00 0.00 29.30 5.01
7944 8099 7.665559 TGTCTTTCACAAAAATCTATAGGCACT 59.334 33.333 0.00 0.00 35.11 4.40
7960 8115 4.978099 AGGCACTATATTGTGGAATGGAG 58.022 43.478 17.22 0.00 36.02 3.86
7961 8116 4.074970 GGCACTATATTGTGGAATGGAGG 58.925 47.826 17.22 0.00 38.31 4.30
7962 8117 4.074970 GCACTATATTGTGGAATGGAGGG 58.925 47.826 17.22 0.00 38.31 4.30
7963 8118 4.202461 GCACTATATTGTGGAATGGAGGGA 60.202 45.833 17.22 0.00 38.31 4.20
7964 8119 5.555017 CACTATATTGTGGAATGGAGGGAG 58.445 45.833 9.17 0.00 34.56 4.30
8000 8155 1.609208 TTTGACCTGCTTTCCTCTGC 58.391 50.000 0.00 0.00 0.00 4.26
8075 8230 4.253685 TGTACTCTTTCAATAGCTGCCAC 58.746 43.478 0.00 0.00 0.00 5.01
8113 8268 6.463995 TTTCTGTTTGCCATGTTTTCTACT 57.536 33.333 0.00 0.00 0.00 2.57
8151 8306 2.095853 CACGGCGCTCTTGATTTGTTAT 59.904 45.455 6.90 0.00 0.00 1.89
8152 8307 3.308595 CACGGCGCTCTTGATTTGTTATA 59.691 43.478 6.90 0.00 0.00 0.98
8241 8396 1.817099 GGTCTTGCTCATGGCCTCG 60.817 63.158 3.32 0.00 40.92 4.63
8648 8804 9.730420 GTGATATTCACAACCCATACAAAATAC 57.270 33.333 2.85 0.00 46.22 1.89
8775 8932 1.980052 CAGGCGGAGGTAGGTGAAA 59.020 57.895 0.00 0.00 0.00 2.69
8776 8933 0.541863 CAGGCGGAGGTAGGTGAAAT 59.458 55.000 0.00 0.00 0.00 2.17
8777 8934 0.831307 AGGCGGAGGTAGGTGAAATC 59.169 55.000 0.00 0.00 0.00 2.17
8779 8936 1.209747 GGCGGAGGTAGGTGAAATCTT 59.790 52.381 0.00 0.00 0.00 2.40
8782 8939 2.481449 CGGAGGTAGGTGAAATCTTCCG 60.481 54.545 0.00 0.00 0.00 4.30
8783 8940 2.552031 GAGGTAGGTGAAATCTTCCGC 58.448 52.381 0.00 0.00 0.00 5.54
8894 9074 6.826231 TGGTAGTGTTTCTGTTGAGATTCAAA 59.174 34.615 0.00 0.00 38.22 2.69
8920 9100 4.621034 CCTGCGGTGTTATTGTTGAATTTC 59.379 41.667 0.00 0.00 0.00 2.17
8958 9138 4.906437 GTGATTTCTTCGTTCTCAGCAAAC 59.094 41.667 0.00 0.00 0.00 2.93
8965 9145 0.040958 GTTCTCAGCAAACGTGGCAG 60.041 55.000 14.05 6.85 0.00 4.85
9115 9298 1.566018 GGAAGAACTGTTGACCGGCG 61.566 60.000 0.00 0.00 0.00 6.46
9118 9301 2.954753 GAACTGTTGACCGGCGCAG 61.955 63.158 10.83 4.65 35.31 5.18
9144 9327 1.021968 GTAAGCCACTAAATGCCGGG 58.978 55.000 2.18 0.00 0.00 5.73
9302 9485 4.495184 GCCGGTTACATAGTTGCATAACAC 60.495 45.833 1.90 0.00 39.30 3.32
9437 9620 1.069823 CCATGGAGATCAGGTCCTTCG 59.930 57.143 5.56 0.00 34.86 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.152777 TGCTTGTTCAGTGGGTGGG 60.153 57.895 0.00 0.00 0.00 4.61
31 32 0.179020 TCTGCTTGTTCAGTGGGTGG 60.179 55.000 0.00 0.00 35.63 4.61
32 33 1.679139 TTCTGCTTGTTCAGTGGGTG 58.321 50.000 0.00 0.00 35.63 4.61
33 34 2.508526 GATTCTGCTTGTTCAGTGGGT 58.491 47.619 0.00 0.00 35.63 4.51
34 35 1.815003 GGATTCTGCTTGTTCAGTGGG 59.185 52.381 0.00 0.00 35.63 4.61
61 62 3.961225 TTAGGGCCGTCCGGTAGCA 62.961 63.158 0.00 0.00 41.52 3.49
67 68 0.177141 TTCAGAATTAGGGCCGTCCG 59.823 55.000 0.00 0.00 41.52 4.79
93 94 3.047115 AGATCTGCACATGATTCCCTCT 58.953 45.455 0.00 0.00 0.00 3.69
106 107 3.388497 AGGTCTGGACAGATCTGCA 57.612 52.632 22.83 12.28 46.52 4.41
120 121 1.196012 CCTCCCTCCACTTACAGGTC 58.804 60.000 0.00 0.00 0.00 3.85
140 141 4.431131 CATCCACTTGCCCCCGCT 62.431 66.667 0.00 0.00 35.36 5.52
145 146 2.401766 CGTCAGCATCCACTTGCCC 61.402 63.158 0.00 0.00 43.83 5.36
148 149 0.320683 TCCACGTCAGCATCCACTTG 60.321 55.000 0.00 0.00 0.00 3.16
179 180 2.710902 CGCCGTCCTGACCTCATCA 61.711 63.158 0.00 0.00 35.45 3.07
180 181 2.105128 CGCCGTCCTGACCTCATC 59.895 66.667 0.00 0.00 0.00 2.92
181 182 3.461773 CCGCCGTCCTGACCTCAT 61.462 66.667 0.00 0.00 0.00 2.90
196 197 3.636313 TAGGGTTCGTTGCTCGCCG 62.636 63.158 0.00 0.00 39.67 6.46
199 200 1.683790 CGCTTAGGGTTCGTTGCTCG 61.684 60.000 0.00 0.00 41.41 5.03
200 201 1.359459 CCGCTTAGGGTTCGTTGCTC 61.359 60.000 0.00 0.00 35.97 4.26
203 204 2.396157 GGCCGCTTAGGGTTCGTTG 61.396 63.158 0.00 0.00 41.48 4.10
204 205 2.046604 GGCCGCTTAGGGTTCGTT 60.047 61.111 0.00 0.00 41.48 3.85
236 276 2.933260 GCGAATCAACCTTCTCCTTCTC 59.067 50.000 0.00 0.00 0.00 2.87
259 299 1.157276 CTCTCCCCGATCCCCATCT 59.843 63.158 0.00 0.00 0.00 2.90
269 309 1.739338 ATAGCGTTGCTCTCTCCCCG 61.739 60.000 0.00 0.00 40.44 5.73
272 312 2.099921 TCTTCATAGCGTTGCTCTCTCC 59.900 50.000 0.00 0.00 40.44 3.71
273 313 3.428746 TCTTCATAGCGTTGCTCTCTC 57.571 47.619 0.00 0.00 40.44 3.20
274 314 3.445450 TCTTCTTCATAGCGTTGCTCTCT 59.555 43.478 0.00 0.00 40.44 3.10
275 315 3.775202 TCTTCTTCATAGCGTTGCTCTC 58.225 45.455 0.00 0.00 40.44 3.20
276 316 3.876274 TCTTCTTCATAGCGTTGCTCT 57.124 42.857 0.00 0.00 40.44 4.09
277 317 4.928661 TTTCTTCTTCATAGCGTTGCTC 57.071 40.909 0.00 0.00 40.44 4.26
278 318 4.333926 GGATTTCTTCTTCATAGCGTTGCT 59.666 41.667 0.00 0.00 43.41 3.91
279 319 4.094887 TGGATTTCTTCTTCATAGCGTTGC 59.905 41.667 0.00 0.00 0.00 4.17
280 320 5.563842 GTGGATTTCTTCTTCATAGCGTTG 58.436 41.667 0.00 0.00 0.00 4.10
315 355 2.154462 CCTGCTTGTGATCCTCGTTTT 58.846 47.619 0.00 0.00 0.00 2.43
336 407 6.512297 TGTTTTTATTGGTTTCTTCTGCCTC 58.488 36.000 0.00 0.00 0.00 4.70
342 413 6.929049 CCTCCCTTGTTTTTATTGGTTTCTTC 59.071 38.462 0.00 0.00 0.00 2.87
366 437 0.106967 GGGACCTTCCATTCTCTGCC 60.107 60.000 0.00 0.00 38.64 4.85
381 452 2.783288 CGCGGAGGAAGGTAGGGAC 61.783 68.421 0.00 0.00 0.00 4.46
385 456 1.810030 GCAACGCGGAGGAAGGTAG 60.810 63.158 12.47 0.00 0.00 3.18
478 549 1.221021 GGTACGGAAGGGAAGCAGG 59.779 63.158 0.00 0.00 0.00 4.85
506 581 1.063412 TCGTGCATCTTCGTTCGTCG 61.063 55.000 0.00 0.00 41.41 5.12
513 588 0.877649 CTCCCCATCGTGCATCTTCG 60.878 60.000 0.00 0.00 0.00 3.79
542 622 0.468958 TGTTTTAAGCCCAGCCAGCA 60.469 50.000 0.00 0.00 0.00 4.41
665 752 1.534729 GCTACCCAACTCCAAACAGG 58.465 55.000 0.00 0.00 39.47 4.00
751 838 1.835267 TACGGGTCCACAGCACAGT 60.835 57.895 0.00 0.00 0.00 3.55
774 861 0.899720 TTCCAAACTCCGCTACCGAT 59.100 50.000 0.00 0.00 36.29 4.18
827 914 1.339711 CCTGCGGAATTTTCTTTGCG 58.660 50.000 0.00 0.00 42.46 4.85
828 915 1.713597 CCCTGCGGAATTTTCTTTGC 58.286 50.000 0.00 0.00 0.00 3.68
829 916 1.672737 GGCCCTGCGGAATTTTCTTTG 60.673 52.381 0.00 0.00 0.00 2.77
830 917 0.608130 GGCCCTGCGGAATTTTCTTT 59.392 50.000 0.00 0.00 0.00 2.52
832 919 0.541764 TTGGCCCTGCGGAATTTTCT 60.542 50.000 0.00 0.00 0.00 2.52
858 948 4.117372 GTTGCGCGTCTCGGTTCG 62.117 66.667 8.43 0.00 38.94 3.95
903 997 2.036387 TGGTGTGAGAAGGAAGACGAA 58.964 47.619 0.00 0.00 0.00 3.85
914 1008 0.105194 TGGGAGGAAGTGGTGTGAGA 60.105 55.000 0.00 0.00 0.00 3.27
1332 1428 4.489771 CGCATCTCCACCCCCACC 62.490 72.222 0.00 0.00 0.00 4.61
1537 1633 4.385405 GCAGAGGCTGAGCACCGT 62.385 66.667 6.82 0.00 36.96 4.83
1709 1817 0.471617 AAAGCAGACCAGTGCAGACT 59.528 50.000 0.00 0.00 46.60 3.24
1710 1818 1.002033 CAAAAGCAGACCAGTGCAGAC 60.002 52.381 0.00 0.00 46.60 3.51
1902 2019 0.742990 ACACCACCAGTCACACAACG 60.743 55.000 0.00 0.00 0.00 4.10
1968 2091 4.762251 AGAACAGGCATCTTCCTACAAAAC 59.238 41.667 0.00 0.00 33.95 2.43
2004 2127 6.700960 TGCAAATGTTAGGTTTCATTGTTCAG 59.299 34.615 0.00 0.00 34.98 3.02
2013 2136 5.472137 TGTCCTACTGCAAATGTTAGGTTTC 59.528 40.000 0.00 0.00 0.00 2.78
2162 2302 2.901249 AGCACGTAACAAGTCACAGTT 58.099 42.857 0.00 0.00 0.00 3.16
2203 2343 2.857104 GCAGCCGACAAAAAGGTAACAC 60.857 50.000 0.00 0.00 41.41 3.32
2209 2349 0.318955 CCTTGCAGCCGACAAAAAGG 60.319 55.000 0.00 0.00 0.00 3.11
2418 2558 5.008019 ACAGAAACTAGCATGTTGTTGTCAG 59.992 40.000 0.00 0.00 0.00 3.51
2744 2884 3.108144 GCGGGAAATCGACAATGAATTG 58.892 45.455 1.45 1.45 43.26 2.32
3222 3362 0.449388 GAGTAGGTACCACGTGACGG 59.551 60.000 19.30 2.28 0.00 4.79
3376 3516 3.133691 TGCTGATGAAATATCTGACGCC 58.866 45.455 0.00 0.00 0.00 5.68
3487 3627 7.032580 CAGAAACAAAAGTTAATGTGACCACA 58.967 34.615 5.22 5.22 46.44 4.17
3496 3636 8.981647 GCAACATGATCAGAAACAAAAGTTAAT 58.018 29.630 0.00 0.00 0.00 1.40
3550 3690 4.346129 CACAAAGTGCTTTCAGTGACTTC 58.654 43.478 8.54 0.00 31.85 3.01
3850 3991 7.596494 ACAAGTCAATCAGAACCAACAATATG 58.404 34.615 0.00 0.00 0.00 1.78
4248 4389 7.031372 CAGCAGTTTAATTGACAGCACATTAT 58.969 34.615 11.69 0.00 32.65 1.28
4414 4563 4.385358 AACGCCACAAAGAAGTTCAATT 57.615 36.364 5.50 0.00 0.00 2.32
4502 4651 6.934645 CACACATTTCCTTTAGTAACCTCTCA 59.065 38.462 0.00 0.00 0.00 3.27
4653 4802 7.551585 ACGATAGAGCAATAATGGAGGATAAG 58.448 38.462 0.00 0.00 41.38 1.73
4800 4949 2.029470 AGAAGACAGAGAACGGAAGCAG 60.029 50.000 0.00 0.00 0.00 4.24
4875 5024 0.466124 GTGATACCTCCAGAGTGCCC 59.534 60.000 0.00 0.00 0.00 5.36
4918 5067 3.726517 CGTTCCAACTGCGCCAGG 61.727 66.667 4.18 0.88 35.51 4.45
5113 5262 6.212388 AGGTACATGCTCCAAGATAATAGAGG 59.788 42.308 9.03 0.00 0.00 3.69
5185 5334 6.934083 TGCCAGCGATTTACATCTGATAATTA 59.066 34.615 0.00 0.00 0.00 1.40
5186 5335 5.764686 TGCCAGCGATTTACATCTGATAATT 59.235 36.000 0.00 0.00 0.00 1.40
5187 5336 5.308014 TGCCAGCGATTTACATCTGATAAT 58.692 37.500 0.00 0.00 0.00 1.28
5375 5524 9.838163 CGCACAACATTGAATATTTTAATGATG 57.162 29.630 22.70 22.10 39.21 3.07
5413 5565 3.472652 TCGTAAAGAACTGGTTGCACAT 58.527 40.909 0.00 0.00 0.00 3.21
5433 5586 6.490381 ACAGGAAAAAGGAAAGTACCAATCTC 59.510 38.462 0.00 0.00 0.00 2.75
5623 5776 1.761784 CTGGAAGAGGGAGATCTGTGG 59.238 57.143 0.00 0.00 34.07 4.17
5976 6131 4.041567 TGGCTATGTTGATATGGGTCGAAT 59.958 41.667 0.00 0.00 0.00 3.34
5979 6134 3.401033 TGGCTATGTTGATATGGGTCG 57.599 47.619 0.00 0.00 0.00 4.79
6885 7040 5.375417 TTTGCATCACATAACCAGAACTG 57.625 39.130 0.00 0.00 0.00 3.16
7018 7173 7.836183 ACAGAATATGCACCCTTTCTTTTAGAT 59.164 33.333 0.00 0.00 0.00 1.98
7060 7215 3.462483 TCCGCAACTAACTCAGACAAA 57.538 42.857 0.00 0.00 0.00 2.83
7126 7281 1.944709 GTTCCTACTTGTGTTTGGCGT 59.055 47.619 0.00 0.00 0.00 5.68
7328 7483 6.115446 TGGACATATGAAGGCTAGTTCAAAG 58.885 40.000 10.38 0.00 39.84 2.77
7355 7510 8.630054 AAGCATTTTGTACAACAGTTCCTATA 57.370 30.769 8.07 0.00 0.00 1.31
7594 7749 2.287788 GGTGCCTCTTTGTCACAACATG 60.288 50.000 0.00 0.00 34.73 3.21
7603 7758 1.157870 CGTGAACGGTGCCTCTTTGT 61.158 55.000 0.00 0.00 35.37 2.83
7634 7789 4.051478 TGTGAATATACCCATTCCCCTGT 58.949 43.478 0.00 0.00 34.59 4.00
7710 7865 3.992427 CCCTACTTTAGGTGACGTTTGAC 59.008 47.826 0.00 0.00 44.73 3.18
7714 7869 2.613129 ACCCCTACTTTAGGTGACGTT 58.387 47.619 0.00 0.00 44.73 3.99
7784 7939 9.710818 TGGTATTCTAGATGTACCTACTTTTCT 57.289 33.333 24.31 0.00 38.89 2.52
7789 7944 8.368668 GCATTTGGTATTCTAGATGTACCTACT 58.631 37.037 24.31 14.71 38.89 2.57
7790 7945 8.148351 TGCATTTGGTATTCTAGATGTACCTAC 58.852 37.037 24.31 14.77 38.89 3.18
7791 7946 8.148351 GTGCATTTGGTATTCTAGATGTACCTA 58.852 37.037 24.31 18.45 38.89 3.08
7792 7947 6.992715 GTGCATTTGGTATTCTAGATGTACCT 59.007 38.462 24.31 10.63 38.89 3.08
7793 7948 6.765989 TGTGCATTTGGTATTCTAGATGTACC 59.234 38.462 20.29 20.29 38.65 3.34
7794 7949 7.786178 TGTGCATTTGGTATTCTAGATGTAC 57.214 36.000 0.00 0.27 32.91 2.90
7795 7950 8.210265 TGATGTGCATTTGGTATTCTAGATGTA 58.790 33.333 0.00 0.00 0.00 2.29
7796 7951 7.056006 TGATGTGCATTTGGTATTCTAGATGT 58.944 34.615 0.00 0.00 0.00 3.06
7797 7952 7.500720 TGATGTGCATTTGGTATTCTAGATG 57.499 36.000 0.00 0.00 0.00 2.90
7798 7953 8.573885 CAATGATGTGCATTTGGTATTCTAGAT 58.426 33.333 0.00 0.00 44.68 1.98
7799 7954 7.013559 CCAATGATGTGCATTTGGTATTCTAGA 59.986 37.037 0.00 0.00 44.68 2.43
7800 7955 7.013559 TCCAATGATGTGCATTTGGTATTCTAG 59.986 37.037 12.63 0.00 44.68 2.43
7801 7956 6.832900 TCCAATGATGTGCATTTGGTATTCTA 59.167 34.615 12.63 0.00 44.68 2.10
7802 7957 5.657745 TCCAATGATGTGCATTTGGTATTCT 59.342 36.000 12.63 0.00 44.68 2.40
7803 7958 5.904941 TCCAATGATGTGCATTTGGTATTC 58.095 37.500 12.63 0.00 44.68 1.75
7804 7959 5.936187 TCCAATGATGTGCATTTGGTATT 57.064 34.783 12.63 0.00 44.68 1.89
7805 7960 6.550481 TGTATCCAATGATGTGCATTTGGTAT 59.450 34.615 12.63 9.03 44.68 2.73
7806 7961 5.890419 TGTATCCAATGATGTGCATTTGGTA 59.110 36.000 12.63 5.40 44.68 3.25
7807 7962 4.710865 TGTATCCAATGATGTGCATTTGGT 59.289 37.500 12.63 6.06 44.68 3.67
7808 7963 5.265350 TGTATCCAATGATGTGCATTTGG 57.735 39.130 8.57 8.57 44.68 3.28
7809 7964 6.759356 ACAATGTATCCAATGATGTGCATTTG 59.241 34.615 0.00 0.00 44.68 2.32
7810 7965 6.759356 CACAATGTATCCAATGATGTGCATTT 59.241 34.615 0.00 0.00 44.68 2.32
7812 7967 5.595133 TCACAATGTATCCAATGATGTGCAT 59.405 36.000 0.00 0.00 39.43 3.96
7813 7968 4.948621 TCACAATGTATCCAATGATGTGCA 59.051 37.500 0.00 0.00 32.18 4.57
7814 7969 5.066893 ACTCACAATGTATCCAATGATGTGC 59.933 40.000 0.00 0.00 32.18 4.57
7815 7970 6.688637 ACTCACAATGTATCCAATGATGTG 57.311 37.500 0.00 0.00 32.18 3.21
7816 7971 8.985315 ATAACTCACAATGTATCCAATGATGT 57.015 30.769 0.00 0.00 32.18 3.06
7843 7998 9.689976 CAATACCAAACATGTACATTCTGAAAA 57.310 29.630 5.37 0.00 0.00 2.29
7844 7999 8.855110 ACAATACCAAACATGTACATTCTGAAA 58.145 29.630 5.37 0.00 0.00 2.69
7845 8000 8.402798 ACAATACCAAACATGTACATTCTGAA 57.597 30.769 5.37 0.00 0.00 3.02
7846 8001 7.994425 ACAATACCAAACATGTACATTCTGA 57.006 32.000 5.37 0.00 0.00 3.27
7847 8002 9.161629 TCTACAATACCAAACATGTACATTCTG 57.838 33.333 5.37 0.00 0.00 3.02
7848 8003 9.905713 ATCTACAATACCAAACATGTACATTCT 57.094 29.630 5.37 0.00 0.00 2.40
7849 8004 9.935682 CATCTACAATACCAAACATGTACATTC 57.064 33.333 5.37 0.00 0.00 2.67
7850 8005 9.461312 ACATCTACAATACCAAACATGTACATT 57.539 29.630 5.37 0.00 0.00 2.71
7852 8007 9.594478 CTACATCTACAATACCAAACATGTACA 57.406 33.333 0.00 0.00 0.00 2.90
7853 8008 9.811995 TCTACATCTACAATACCAAACATGTAC 57.188 33.333 0.00 0.00 0.00 2.90
7854 8009 9.811995 GTCTACATCTACAATACCAAACATGTA 57.188 33.333 0.00 0.00 0.00 2.29
7855 8010 8.318412 TGTCTACATCTACAATACCAAACATGT 58.682 33.333 0.00 0.00 0.00 3.21
7856 8011 8.716646 TGTCTACATCTACAATACCAAACATG 57.283 34.615 0.00 0.00 0.00 3.21
7857 8012 8.540388 ACTGTCTACATCTACAATACCAAACAT 58.460 33.333 0.00 0.00 0.00 2.71
7858 8013 7.903145 ACTGTCTACATCTACAATACCAAACA 58.097 34.615 0.00 0.00 0.00 2.83
7859 8014 8.773404 AACTGTCTACATCTACAATACCAAAC 57.227 34.615 0.00 0.00 0.00 2.93
7860 8015 9.787435 AAAACTGTCTACATCTACAATACCAAA 57.213 29.630 0.00 0.00 0.00 3.28
7861 8016 9.431887 GAAAACTGTCTACATCTACAATACCAA 57.568 33.333 0.00 0.00 0.00 3.67
7862 8017 8.812972 AGAAAACTGTCTACATCTACAATACCA 58.187 33.333 0.00 0.00 0.00 3.25
7863 8018 9.303537 GAGAAAACTGTCTACATCTACAATACC 57.696 37.037 0.00 0.00 0.00 2.73
7871 8026 9.469097 AGTGTATAGAGAAAACTGTCTACATCT 57.531 33.333 0.00 0.00 0.00 2.90
7873 8028 9.862371 CAAGTGTATAGAGAAAACTGTCTACAT 57.138 33.333 0.00 0.00 0.00 2.29
7874 8029 8.304596 CCAAGTGTATAGAGAAAACTGTCTACA 58.695 37.037 0.00 0.00 0.00 2.74
7875 8030 8.305317 ACCAAGTGTATAGAGAAAACTGTCTAC 58.695 37.037 0.00 0.00 0.00 2.59
7876 8031 8.418597 ACCAAGTGTATAGAGAAAACTGTCTA 57.581 34.615 0.00 0.00 0.00 2.59
7877 8032 7.015292 TGACCAAGTGTATAGAGAAAACTGTCT 59.985 37.037 0.00 0.00 0.00 3.41
7878 8033 7.152645 TGACCAAGTGTATAGAGAAAACTGTC 58.847 38.462 0.00 0.00 0.00 3.51
7879 8034 7.062749 TGACCAAGTGTATAGAGAAAACTGT 57.937 36.000 0.00 0.00 0.00 3.55
7880 8035 7.962964 TTGACCAAGTGTATAGAGAAAACTG 57.037 36.000 0.00 0.00 0.00 3.16
7881 8036 8.211629 ACTTTGACCAAGTGTATAGAGAAAACT 58.788 33.333 0.00 0.00 44.70 2.66
7882 8037 8.379457 ACTTTGACCAAGTGTATAGAGAAAAC 57.621 34.615 0.00 0.00 44.70 2.43
7883 8038 8.836413 CAACTTTGACCAAGTGTATAGAGAAAA 58.164 33.333 0.00 0.00 45.77 2.29
7884 8039 7.444183 CCAACTTTGACCAAGTGTATAGAGAAA 59.556 37.037 0.00 0.00 45.77 2.52
7885 8040 6.934645 CCAACTTTGACCAAGTGTATAGAGAA 59.065 38.462 0.00 0.00 45.77 2.87
7886 8041 6.464222 CCAACTTTGACCAAGTGTATAGAGA 58.536 40.000 0.00 0.00 45.77 3.10
7887 8042 5.122396 GCCAACTTTGACCAAGTGTATAGAG 59.878 44.000 0.00 0.00 45.77 2.43
7888 8043 5.001232 GCCAACTTTGACCAAGTGTATAGA 58.999 41.667 0.00 0.00 45.77 1.98
7889 8044 4.759693 TGCCAACTTTGACCAAGTGTATAG 59.240 41.667 0.00 0.00 45.77 1.31
7890 8045 4.720046 TGCCAACTTTGACCAAGTGTATA 58.280 39.130 0.00 0.00 45.77 1.47
7891 8046 3.561143 TGCCAACTTTGACCAAGTGTAT 58.439 40.909 0.00 0.00 45.77 2.29
7892 8047 3.006112 TGCCAACTTTGACCAAGTGTA 57.994 42.857 0.00 0.00 45.77 2.90
7893 8048 1.846007 TGCCAACTTTGACCAAGTGT 58.154 45.000 0.00 0.00 45.77 3.55
7894 8049 2.957491 TTGCCAACTTTGACCAAGTG 57.043 45.000 0.00 0.00 45.77 3.16
7896 8051 3.525268 ACTTTGCCAACTTTGACCAAG 57.475 42.857 0.00 0.00 38.64 3.61
7897 8052 3.971245 AACTTTGCCAACTTTGACCAA 57.029 38.095 0.00 0.00 0.00 3.67
7898 8053 3.007398 ACAAACTTTGCCAACTTTGACCA 59.993 39.130 11.80 0.00 0.00 4.02
7899 8054 3.595173 ACAAACTTTGCCAACTTTGACC 58.405 40.909 11.80 0.00 0.00 4.02
7900 8055 4.494484 AGACAAACTTTGCCAACTTTGAC 58.506 39.130 11.80 7.20 0.00 3.18
7901 8056 4.799564 AGACAAACTTTGCCAACTTTGA 57.200 36.364 11.80 0.00 0.00 2.69
7902 8057 5.861222 AAAGACAAACTTTGCCAACTTTG 57.139 34.783 1.14 5.58 45.66 2.77
7917 8072 8.296713 GTGCCTATAGATTTTTGTGAAAGACAA 58.703 33.333 0.00 0.00 43.11 3.18
7918 8073 7.665559 AGTGCCTATAGATTTTTGTGAAAGACA 59.334 33.333 0.00 0.00 0.00 3.41
7919 8074 8.045176 AGTGCCTATAGATTTTTGTGAAAGAC 57.955 34.615 0.00 0.00 0.00 3.01
7920 8075 9.905713 ATAGTGCCTATAGATTTTTGTGAAAGA 57.094 29.630 0.00 0.00 0.00 2.52
7931 8086 9.896645 CATTCCACAATATAGTGCCTATAGATT 57.103 33.333 0.00 0.00 38.18 2.40
7932 8087 8.489489 CCATTCCACAATATAGTGCCTATAGAT 58.511 37.037 0.00 0.00 38.18 1.98
7933 8088 7.678171 TCCATTCCACAATATAGTGCCTATAGA 59.322 37.037 0.00 0.00 38.18 1.98
7934 8089 7.851228 TCCATTCCACAATATAGTGCCTATAG 58.149 38.462 0.00 0.00 38.18 1.31
7935 8090 7.092891 CCTCCATTCCACAATATAGTGCCTATA 60.093 40.741 0.00 4.91 38.18 1.31
7936 8091 6.296662 CCTCCATTCCACAATATAGTGCCTAT 60.297 42.308 0.00 1.18 38.18 2.57
7937 8092 5.013079 CCTCCATTCCACAATATAGTGCCTA 59.987 44.000 0.00 0.00 38.18 3.93
7938 8093 4.202503 CCTCCATTCCACAATATAGTGCCT 60.203 45.833 0.00 0.00 38.18 4.75
7939 8094 4.074970 CCTCCATTCCACAATATAGTGCC 58.925 47.826 0.00 0.00 38.18 5.01
7940 8095 4.074970 CCCTCCATTCCACAATATAGTGC 58.925 47.826 0.00 0.00 38.18 4.40
7941 8096 5.072329 ACTCCCTCCATTCCACAATATAGTG 59.928 44.000 0.00 0.00 39.21 2.74
7942 8097 5.227593 ACTCCCTCCATTCCACAATATAGT 58.772 41.667 0.00 0.00 0.00 2.12
7943 8098 5.832539 ACTCCCTCCATTCCACAATATAG 57.167 43.478 0.00 0.00 0.00 1.31
7944 8099 7.022496 TGATACTCCCTCCATTCCACAATATA 58.978 38.462 0.00 0.00 0.00 0.86
7945 8100 5.851693 TGATACTCCCTCCATTCCACAATAT 59.148 40.000 0.00 0.00 0.00 1.28
7946 8101 5.223655 TGATACTCCCTCCATTCCACAATA 58.776 41.667 0.00 0.00 0.00 1.90
7947 8102 4.047166 TGATACTCCCTCCATTCCACAAT 58.953 43.478 0.00 0.00 0.00 2.71
7948 8103 3.459828 TGATACTCCCTCCATTCCACAA 58.540 45.455 0.00 0.00 0.00 3.33
7949 8104 3.129262 TGATACTCCCTCCATTCCACA 57.871 47.619 0.00 0.00 0.00 4.17
7950 8105 3.711704 TCTTGATACTCCCTCCATTCCAC 59.288 47.826 0.00 0.00 0.00 4.02
7951 8106 4.007581 TCTTGATACTCCCTCCATTCCA 57.992 45.455 0.00 0.00 0.00 3.53
7952 8107 5.373812 TTTCTTGATACTCCCTCCATTCC 57.626 43.478 0.00 0.00 0.00 3.01
7953 8108 7.286313 AGATTTTCTTGATACTCCCTCCATTC 58.714 38.462 0.00 0.00 0.00 2.67
7954 8109 7.218314 AGATTTTCTTGATACTCCCTCCATT 57.782 36.000 0.00 0.00 0.00 3.16
7955 8110 6.838401 AGATTTTCTTGATACTCCCTCCAT 57.162 37.500 0.00 0.00 0.00 3.41
7956 8111 7.937700 ATAGATTTTCTTGATACTCCCTCCA 57.062 36.000 0.00 0.00 0.00 3.86
7957 8112 9.634021 AAAATAGATTTTCTTGATACTCCCTCC 57.366 33.333 0.00 0.00 35.18 4.30
7964 8119 9.508567 GCAGGTCAAAATAGATTTTCTTGATAC 57.491 33.333 0.00 0.00 37.86 2.24
8000 8155 1.134098 CAGGTTATGCTACCAGGGTGG 60.134 57.143 0.06 0.00 45.02 4.61
8113 8268 3.554960 GCCGTGAACTCTGGATATGCATA 60.555 47.826 9.27 9.27 0.00 3.14
8151 8306 8.871629 TGAGCCAAAAATATGAGTTTAAGGTA 57.128 30.769 0.00 0.00 0.00 3.08
8152 8307 7.093771 CCTGAGCCAAAAATATGAGTTTAAGGT 60.094 37.037 0.00 0.00 0.00 3.50
8226 8381 0.674581 TTGACGAGGCCATGAGCAAG 60.675 55.000 5.01 0.00 46.50 4.01
8230 8385 4.528674 CCTTGACGAGGCCATGAG 57.471 61.111 5.01 0.00 39.09 2.90
8241 8396 2.096496 CAGAATCCACGAATGCCTTGAC 59.904 50.000 0.00 0.00 0.00 3.18
8752 8909 2.185350 CTACCTCCGCCTGCACAG 59.815 66.667 0.00 0.00 0.00 3.66
8920 9100 7.305763 CGAAGAAATCACAAAAACTAAAACCCG 60.306 37.037 0.00 0.00 0.00 5.28
8958 9138 3.120199 CCAGACAGTATTTTTCTGCCACG 60.120 47.826 0.00 0.00 36.26 4.94
9135 9318 5.136828 TCATGTATATTTGACCCGGCATTT 58.863 37.500 0.00 0.00 0.00 2.32
9302 9485 1.818642 ACCTTGCTTCAGCTTGCTAG 58.181 50.000 0.00 7.31 42.66 3.42
9352 9535 2.485814 GTCATCCTTGAACTGAGGCAAC 59.514 50.000 0.00 0.00 34.17 4.17
9360 9543 1.148310 CGTTGCGTCATCCTTGAACT 58.852 50.000 0.00 0.00 32.48 3.01
9437 9620 0.663153 AACGACTGACCTTGCTTTGC 59.337 50.000 0.00 0.00 0.00 3.68
9527 9710 3.344515 GTTTGGGGTGTGTAGATTCTCC 58.655 50.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.