Multiple sequence alignment - TraesCS1A01G180500

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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 TraesCS1A01G180500 chr1A 100.000 3960 0 0 3704 7663 326210826 326214785 0.000000e+00 7313.0
1 TraesCS1A01G180500 chr1A 100.000 3469 0 0 1 3469 326207123 326210591 0.000000e+00 6407.0
2 TraesCS1A01G180500 chr1A 98.052 462 8 1 308 769 5071356 5071816 0.000000e+00 802.0
3 TraesCS1A01G180500 chr1A 98.446 386 6 0 383 768 5066161 5066546 0.000000e+00 680.0
4 TraesCS1A01G180500 chr1A 98.494 332 5 0 437 768 326202182 326202513 3.080000e-163 586.0
5 TraesCS1A01G180500 chr1A 94.805 154 4 2 187 336 5071196 5071349 3.570000e-58 237.0
6 TraesCS1A01G180500 chr1B 93.892 3520 138 25 3997 7487 358024945 358021474 0.000000e+00 5238.0
7 TraesCS1A01G180500 chr1B 97.801 1410 30 1 773 2181 358028276 358026867 0.000000e+00 2431.0
8 TraesCS1A01G180500 chr1B 94.867 526 17 3 2945 3469 358026356 358025840 0.000000e+00 813.0
9 TraesCS1A01G180500 chr1B 91.214 387 27 4 2208 2593 358026869 358026489 3.170000e-143 520.0
10 TraesCS1A01G180500 chr1B 94.333 300 13 2 3705 4001 358025364 358025066 2.520000e-124 457.0
11 TraesCS1A01G180500 chr1D 97.494 2753 55 7 4541 7291 254608549 254611289 0.000000e+00 4689.0
12 TraesCS1A01G180500 chr1D 97.439 2148 48 4 796 2936 254604431 254606578 0.000000e+00 3655.0
13 TraesCS1A01G180500 chr1D 96.292 836 14 7 3704 4523 254607724 254608558 0.000000e+00 1356.0
14 TraesCS1A01G180500 chr1D 98.299 529 9 0 2941 3469 254606724 254607252 0.000000e+00 928.0
15 TraesCS1A01G180500 chr7A 93.064 793 6 2 1 768 119793492 119792724 0.000000e+00 1114.0
16 TraesCS1A01G180500 chr7A 99.741 386 1 0 383 768 119798471 119798086 0.000000e+00 708.0
17 TraesCS1A01G180500 chr7A 90.805 348 20 10 308 653 119802878 119802541 9.060000e-124 455.0
18 TraesCS1A01G180500 chr7A 85.119 336 26 9 1 336 574118425 574118114 9.590000e-84 322.0
19 TraesCS1A01G180500 chr7A 93.985 133 8 0 204 336 119803017 119802885 1.300000e-47 202.0
20 TraesCS1A01G180500 chr5A 89.578 806 35 15 1 769 552271090 552270297 0.000000e+00 977.0
21 TraesCS1A01G180500 chr5A 94.690 339 15 1 1 336 52219604 52219266 2.450000e-144 523.0
22 TraesCS1A01G180500 chr5A 90.415 386 11 1 383 768 552276084 552275725 1.160000e-132 484.0
23 TraesCS1A01G180500 chr5A 100.000 32 0 0 2190 2221 397251830 397251799 8.300000e-05 60.2
24 TraesCS1A01G180500 chr3A 98.052 462 8 1 308 769 203992005 203992465 0.000000e+00 802.0
25 TraesCS1A01G180500 chr3A 99.223 386 3 0 383 768 203986448 203986833 0.000000e+00 697.0
26 TraesCS1A01G180500 chr3A 83.631 336 31 2 1 336 35429887 35429576 2.090000e-75 294.0
27 TraesCS1A01G180500 chr3A 99.375 160 1 0 177 336 203991839 203991998 2.710000e-74 291.0
28 TraesCS1A01G180500 chr3A 98.319 119 2 0 1 119 203991425 203991543 7.790000e-50 209.0
29 TraesCS1A01G180500 chr6A 94.985 339 13 2 1 336 352156241 352155904 5.270000e-146 529.0
30 TraesCS1A01G180500 chr6A 85.417 336 25 9 1 336 440242223 440242534 2.060000e-85 327.0
31 TraesCS1A01G180500 chr2A 99.375 160 1 0 7504 7663 535702554 535702713 2.710000e-74 291.0
32 TraesCS1A01G180500 chr2A 100.000 28 0 0 2199 2226 680522031 680522058 1.400000e-02 52.8
33 TraesCS1A01G180500 chr3D 94.268 157 7 2 7506 7662 359522350 359522196 9.940000e-59 239.0
34 TraesCS1A01G180500 chr5D 93.711 159 8 2 7506 7663 389527573 389527416 3.570000e-58 237.0
35 TraesCS1A01G180500 chr5D 93.038 158 10 1 7506 7663 541528056 541527900 5.980000e-56 230.0
36 TraesCS1A01G180500 chr5D 92.500 160 10 2 7505 7663 59940716 59940558 2.150000e-55 228.0
37 TraesCS1A01G180500 chr5D 91.975 162 12 1 7502 7663 544818477 544818637 7.740000e-55 226.0
38 TraesCS1A01G180500 chr7D 93.082 159 9 2 7506 7663 126484104 126483947 1.660000e-56 231.0
39 TraesCS1A01G180500 chr7D 91.515 165 12 2 7499 7663 11017921 11018083 7.740000e-55 226.0
40 TraesCS1A01G180500 chrUn 80.236 339 37 14 1 336 384234746 384235057 2.150000e-55 228.0
41 TraesCS1A01G180500 chr6D 91.124 169 11 4 7496 7663 435350575 435350410 7.740000e-55 226.0
42 TraesCS1A01G180500 chr6B 95.349 43 2 0 2180 2222 464921819 464921861 1.380000e-07 69.4
43 TraesCS1A01G180500 chr5B 100.000 32 0 0 2198 2229 296251589 296251620 8.300000e-05 60.2
44 TraesCS1A01G180500 chr2D 100.000 28 0 0 2199 2226 475092976 475092949 1.400000e-02 52.8


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 TraesCS1A01G180500 chr1A 326207123 326214785 7662 False 6860.0 7313 100.0000 1 7663 2 chr1A.!!$F4 7662
1 TraesCS1A01G180500 chr1A 5071196 5071816 620 False 519.5 802 96.4285 187 769 2 chr1A.!!$F3 582
2 TraesCS1A01G180500 chr1B 358021474 358028276 6802 True 1891.8 5238 94.4214 773 7487 5 chr1B.!!$R1 6714
3 TraesCS1A01G180500 chr1D 254604431 254611289 6858 False 2657.0 4689 97.3810 796 7291 4 chr1D.!!$F1 6495
4 TraesCS1A01G180500 chr7A 119792724 119793492 768 True 1114.0 1114 93.0640 1 768 1 chr7A.!!$R1 767
5 TraesCS1A01G180500 chr5A 552270297 552271090 793 True 977.0 977 89.5780 1 769 1 chr5A.!!$R3 768
6 TraesCS1A01G180500 chr3A 203991425 203992465 1040 False 434.0 802 98.5820 1 769 3 chr3A.!!$F2 768

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
218 487 0.822532 GATGGCTGGATGGGAAGCTG 60.823 60.000 0.0 0.00 39.46 4.24 F
442 745 0.863220 TAGGGGAAGGAGGGGGAAGA 60.863 60.000 0.0 0.00 0.00 2.87 F
769 1072 1.153168 CCTGGCCGGTCATAACAGG 60.153 63.158 10.4 10.88 43.00 4.00 F
2747 3062 1.259609 ACATTCGGACCACGGTTCTA 58.740 50.000 0.0 0.00 44.45 2.10 F
3427 3885 1.181741 TTTGCCAACCGCCATAGCAA 61.182 50.000 0.0 0.00 41.39 3.91 F
4763 5609 2.611292 ACGTGACTATAGCGTGTCCTAC 59.389 50.000 0.0 0.00 37.47 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1076 1379 0.461961 AGTTGGAGATCGCCTGCTAC 59.538 55.000 17.00 9.25 38.73 3.58 R
1713 2016 1.259840 GCTTGATGCCATGGGGTGTT 61.260 55.000 15.13 0.00 36.17 3.32 R
2757 3072 0.249615 AGCCGACATGACATGGATCG 60.250 55.000 19.39 18.16 33.60 3.69 R
4682 5527 1.026718 GCAGTGACATACAGGCCCAC 61.027 60.000 0.00 0.00 0.00 4.61 R
4802 5648 3.195825 GGTCGCTACCTGCCTCATATAAT 59.804 47.826 0.00 0.00 43.08 1.28 R
6715 7563 0.383949 TCAAGAAAGTTGCCGGTTGC 59.616 50.000 1.90 0.00 41.77 4.17 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
200 469 4.838152 GATGGGAAGCTGCGGCGA 62.838 66.667 12.98 0.00 44.37 5.54
201 470 4.181010 ATGGGAAGCTGCGGCGAT 62.181 61.111 12.98 5.04 44.37 4.58
209 478 4.923942 CTGCGGCGATGGCTGGAT 62.924 66.667 12.98 0.00 45.41 3.41
213 482 3.877450 GGCGATGGCTGGATGGGA 61.877 66.667 0.00 0.00 39.81 4.37
214 483 2.192979 GCGATGGCTGGATGGGAA 59.807 61.111 0.00 0.00 35.83 3.97
215 484 1.895707 GCGATGGCTGGATGGGAAG 60.896 63.158 0.00 0.00 35.83 3.46
216 485 1.895707 CGATGGCTGGATGGGAAGC 60.896 63.158 0.00 0.00 38.76 3.86
217 486 1.535685 GATGGCTGGATGGGAAGCT 59.464 57.895 0.00 0.00 39.46 3.74
218 487 0.822532 GATGGCTGGATGGGAAGCTG 60.823 60.000 0.00 0.00 39.46 4.24
219 488 2.832201 GGCTGGATGGGAAGCTGC 60.832 66.667 0.00 0.00 39.46 5.25
220 489 3.207669 GCTGGATGGGAAGCTGCG 61.208 66.667 0.00 0.00 36.47 5.18
221 490 2.515523 CTGGATGGGAAGCTGCGG 60.516 66.667 0.00 0.00 0.00 5.69
222 491 4.802051 TGGATGGGAAGCTGCGGC 62.802 66.667 10.33 10.33 39.06 6.53
442 745 0.863220 TAGGGGAAGGAGGGGGAAGA 60.863 60.000 0.00 0.00 0.00 2.87
769 1072 1.153168 CCTGGCCGGTCATAACAGG 60.153 63.158 10.40 10.88 43.00 4.00
770 1073 1.153168 CTGGCCGGTCATAACAGGG 60.153 63.158 10.40 0.00 40.72 4.45
771 1074 1.613928 TGGCCGGTCATAACAGGGA 60.614 57.895 3.51 0.00 40.72 4.20
776 1079 2.093341 GCCGGTCATAACAGGGAGTTTA 60.093 50.000 1.90 0.00 40.72 2.01
839 1142 5.560724 ACATACTAAGGCACACATCTGTTT 58.439 37.500 0.00 0.00 0.00 2.83
1076 1379 4.201589 CCATAAAGTGCTTCGTCGTACAAG 60.202 45.833 0.00 0.00 0.00 3.16
1143 1446 7.309133 CCTGTATTTCCAGAAACAAGCAATACA 60.309 37.037 0.00 0.00 35.42 2.29
1286 1589 8.325787 TGGGAAGCTTACATTAGATAACAAAGA 58.674 33.333 11.69 0.00 0.00 2.52
1575 1878 2.579207 CATGCATGCCCTCTTGAAAG 57.421 50.000 14.93 0.00 0.00 2.62
1713 2016 7.552330 TCAGCAATGCTATGTAAATCTGTTACA 59.448 33.333 7.70 1.70 36.40 2.41
1864 2167 6.721318 TGGTAGATCTAGCAAAGTTTTCCAT 58.279 36.000 27.93 0.00 40.17 3.41
2254 2558 6.313519 ACACTGTCATACCATTGATTACCT 57.686 37.500 0.00 0.00 0.00 3.08
2257 2561 6.823182 CACTGTCATACCATTGATTACCTTCA 59.177 38.462 0.00 0.00 0.00 3.02
2363 2673 9.883142 TCATTGTTTTACCAGATTTTTGAAGTT 57.117 25.926 0.00 0.00 0.00 2.66
2435 2745 4.692228 ACTGCAAAGTTGTATTTGGGTTG 58.308 39.130 1.80 0.00 39.94 3.77
2438 2748 5.112686 TGCAAAGTTGTATTTGGGTTGTTC 58.887 37.500 1.80 0.00 39.94 3.18
2674 2989 9.688091 TTGTATGCTGTATAGTTTAAAATCCCA 57.312 29.630 0.00 0.00 0.00 4.37
2675 2990 9.688091 TGTATGCTGTATAGTTTAAAATCCCAA 57.312 29.630 0.00 0.00 0.00 4.12
2711 3026 5.960202 AGCCTGATTTTACCTTTGATTCCAT 59.040 36.000 0.00 0.00 0.00 3.41
2747 3062 1.259609 ACATTCGGACCACGGTTCTA 58.740 50.000 0.00 0.00 44.45 2.10
2748 3063 1.829222 ACATTCGGACCACGGTTCTAT 59.171 47.619 0.00 0.00 44.45 1.98
2757 3072 5.220529 CGGACCACGGTTCTATAAACATTTC 60.221 44.000 0.00 0.00 39.42 2.17
2827 3142 8.085296 ACTTCTTATGTCAGTTACTCAGTTCTG 58.915 37.037 4.01 4.01 0.00 3.02
2841 3156 5.178096 TCAGTTCTGGGATGCTGAATTTA 57.822 39.130 0.00 0.00 35.36 1.40
2845 3160 7.500227 TCAGTTCTGGGATGCTGAATTTATTAG 59.500 37.037 0.00 0.00 35.36 1.73
2924 3240 2.283298 AGGTGATGCTCGTTTATGCAG 58.717 47.619 0.00 0.00 42.74 4.41
3427 3885 1.181741 TTTGCCAACCGCCATAGCAA 61.182 50.000 0.00 0.00 41.39 3.91
4020 4848 6.625532 AATCTTTAACATTTGAGGGCCATT 57.374 33.333 6.18 0.00 0.00 3.16
4522 5366 9.921637 GTTCCCTGATGTAAAACAATTTAATCA 57.078 29.630 0.00 0.00 32.98 2.57
4590 5435 4.513442 TGTACACTGAAATGCCAGTATCC 58.487 43.478 0.00 0.00 44.87 2.59
4603 5448 5.063204 TGCCAGTATCCCAAATATCTTTCG 58.937 41.667 0.00 0.00 0.00 3.46
4608 5453 7.068226 CCAGTATCCCAAATATCTTTCGGTTTT 59.932 37.037 0.00 0.00 0.00 2.43
4682 5527 3.290710 CCTCCCTATGGTTCCATTTGTG 58.709 50.000 9.70 1.25 0.00 3.33
4763 5609 2.611292 ACGTGACTATAGCGTGTCCTAC 59.389 50.000 0.00 0.00 37.47 3.18
4909 5755 0.417437 TTCCCTGAGATCCCTCCACA 59.583 55.000 0.00 0.00 38.66 4.17
5072 5920 7.358023 CGCCAACAAAGTGAAAATATGTTGTAC 60.358 37.037 13.81 6.65 45.74 2.90
5073 5921 7.436673 GCCAACAAAGTGAAAATATGTTGTACA 59.563 33.333 13.81 0.00 45.74 2.90
5074 5922 8.967218 CCAACAAAGTGAAAATATGTTGTACAG 58.033 33.333 13.81 0.00 45.74 2.74
5075 5923 9.515020 CAACAAAGTGAAAATATGTTGTACAGT 57.485 29.630 8.38 0.00 43.49 3.55
5187 6035 6.528014 TCAATTATTGTGCTTGCAACTTTG 57.472 33.333 4.77 0.00 0.00 2.77
5190 6038 7.708322 TCAATTATTGTGCTTGCAACTTTGTTA 59.292 29.630 4.77 0.00 0.00 2.41
5792 6640 1.197721 GAACCATCTGAACTTGTGCGG 59.802 52.381 0.00 0.00 0.00 5.69
6447 7295 4.033358 CGAGCATCCAGTTTTACTCATCAC 59.967 45.833 0.00 0.00 0.00 3.06
6635 7483 1.135972 CAGCAAAGTCGTTTGATCGGG 60.136 52.381 2.90 0.00 45.22 5.14
6705 7553 3.265479 AGCCCTATATCTGCCTGGAAATC 59.735 47.826 0.00 0.00 0.00 2.17
6707 7555 3.369892 CCCTATATCTGCCTGGAAATCCG 60.370 52.174 0.00 0.00 39.43 4.18
6715 7563 1.308069 CCTGGAAATCCGCACCTGTG 61.308 60.000 0.00 0.00 39.43 3.66
6765 7613 0.035725 CTGCATCCAGAACAGCCTCA 60.036 55.000 0.00 0.00 41.77 3.86
6795 7643 0.868406 GGCACATATAACTCCAGCGC 59.132 55.000 0.00 0.00 0.00 5.92
6804 7652 1.442769 AACTCCAGCGCTGTACATTG 58.557 50.000 33.75 18.57 0.00 2.82
6830 7678 1.278985 TGATGACCGAAAGTGCCAGAT 59.721 47.619 0.00 0.00 0.00 2.90
6928 7776 1.337260 GGCTGGTATCGGATGTGCTAG 60.337 57.143 0.00 0.17 0.00 3.42
6931 7779 1.613925 TGGTATCGGATGTGCTAGAGC 59.386 52.381 0.00 0.00 42.50 4.09
6993 7842 0.692476 AGAACAGCATGGTGCCTACA 59.308 50.000 24.31 0.00 46.52 2.74
7107 7956 0.321919 TGTCCCTGATCAGCTTGTGC 60.322 55.000 17.76 4.42 40.05 4.57
7108 7957 1.028868 GTCCCTGATCAGCTTGTGCC 61.029 60.000 17.76 0.00 40.80 5.01
7172 8021 5.954150 TCCCGGTATAGTATAGGATTTGGAC 59.046 44.000 0.00 0.00 0.00 4.02
7244 8093 8.188139 CACCTATAGTTCTTTTTGTGTTTGTGT 58.812 33.333 0.00 0.00 0.00 3.72
7245 8094 8.745590 ACCTATAGTTCTTTTTGTGTTTGTGTT 58.254 29.630 0.00 0.00 0.00 3.32
7246 8095 9.581099 CCTATAGTTCTTTTTGTGTTTGTGTTT 57.419 29.630 0.00 0.00 0.00 2.83
7248 8097 8.825667 ATAGTTCTTTTTGTGTTTGTGTTTGT 57.174 26.923 0.00 0.00 0.00 2.83
7249 8098 6.942891 AGTTCTTTTTGTGTTTGTGTTTGTG 58.057 32.000 0.00 0.00 0.00 3.33
7259 8108 0.734253 TGTGTTTGTGTTTGTGCGCC 60.734 50.000 4.18 0.00 0.00 6.53
7300 8149 1.251251 AATTTGTCCCAGCTGTCTGC 58.749 50.000 13.81 0.44 39.00 4.26
7304 8153 0.909133 TGTCCCAGCTGTCTGCCATA 60.909 55.000 13.81 0.00 44.23 2.74
7310 8159 1.806542 CAGCTGTCTGCCATAAACGTT 59.193 47.619 5.25 0.00 44.23 3.99
7362 8211 4.587262 CCTGCAGGTACATATGTGGTACTA 59.413 45.833 25.53 0.00 40.67 1.82
7390 8239 4.591321 TGTTCTCTGCTGGGGAATAAAT 57.409 40.909 0.00 0.00 0.00 1.40
7407 8256 9.515226 GGGAATAAATAGCATGGTTTGATAGTA 57.485 33.333 1.12 0.00 27.90 1.82
7421 8270 7.450014 TGGTTTGATAGTATGACATTGTTGGTT 59.550 33.333 0.00 0.00 0.00 3.67
7422 8271 8.952278 GGTTTGATAGTATGACATTGTTGGTTA 58.048 33.333 0.00 0.00 0.00 2.85
7425 8274 9.679661 TTGATAGTATGACATTGTTGGTTACAT 57.320 29.630 0.00 0.00 36.44 2.29
7429 8278 7.930217 AGTATGACATTGTTGGTTACATATGC 58.070 34.615 1.58 0.00 36.44 3.14
7434 8283 5.893255 ACATTGTTGGTTACATATGCCTGAT 59.107 36.000 1.58 0.00 36.44 2.90
7448 8307 8.292448 ACATATGCCTGATTTTATCATTTCGTC 58.708 33.333 1.58 0.00 38.85 4.20
7451 8310 5.593909 TGCCTGATTTTATCATTTCGTCCAT 59.406 36.000 0.00 0.00 38.85 3.41
7457 8316 7.012327 TGATTTTATCATTTCGTCCATGAGGAC 59.988 37.037 4.59 4.59 46.46 3.85
7473 8333 0.394352 GGACCATACAACCCCTGCAG 60.394 60.000 6.78 6.78 0.00 4.41
7487 8347 2.450476 CCTGCAGGGCTGAAACTTATT 58.550 47.619 26.14 0.00 0.00 1.40
7488 8348 3.620488 CCTGCAGGGCTGAAACTTATTA 58.380 45.455 26.14 0.00 0.00 0.98
7489 8349 4.016444 CCTGCAGGGCTGAAACTTATTAA 58.984 43.478 26.14 0.00 0.00 1.40
7490 8350 4.646492 CCTGCAGGGCTGAAACTTATTAAT 59.354 41.667 26.14 0.00 0.00 1.40
7491 8351 5.221126 CCTGCAGGGCTGAAACTTATTAATC 60.221 44.000 26.14 0.00 0.00 1.75
7492 8352 5.260424 TGCAGGGCTGAAACTTATTAATCA 58.740 37.500 0.00 0.00 0.00 2.57
7493 8353 5.714333 TGCAGGGCTGAAACTTATTAATCAA 59.286 36.000 0.00 0.00 0.00 2.57
7494 8354 6.036470 GCAGGGCTGAAACTTATTAATCAAC 58.964 40.000 0.00 0.00 0.00 3.18
7495 8355 6.350110 GCAGGGCTGAAACTTATTAATCAACA 60.350 38.462 0.00 0.00 0.00 3.33
7496 8356 7.601856 CAGGGCTGAAACTTATTAATCAACAA 58.398 34.615 0.00 0.00 0.00 2.83
7497 8357 8.087750 CAGGGCTGAAACTTATTAATCAACAAA 58.912 33.333 0.00 0.00 0.00 2.83
7498 8358 8.646900 AGGGCTGAAACTTATTAATCAACAAAA 58.353 29.630 0.00 0.00 0.00 2.44
7499 8359 9.267084 GGGCTGAAACTTATTAATCAACAAAAA 57.733 29.630 0.00 0.00 0.00 1.94
7520 8380 7.929941 AAAAAGGCAAAAATACAAAGGTGAA 57.070 28.000 0.00 0.00 0.00 3.18
7521 8381 6.918892 AAAGGCAAAAATACAAAGGTGAAC 57.081 33.333 0.00 0.00 0.00 3.18
7522 8382 5.606348 AGGCAAAAATACAAAGGTGAACA 57.394 34.783 0.00 0.00 0.00 3.18
7523 8383 6.173427 AGGCAAAAATACAAAGGTGAACAT 57.827 33.333 0.00 0.00 0.00 2.71
7524 8384 5.990996 AGGCAAAAATACAAAGGTGAACATG 59.009 36.000 0.00 0.00 0.00 3.21
7525 8385 5.179182 GGCAAAAATACAAAGGTGAACATGG 59.821 40.000 0.00 0.00 0.00 3.66
7526 8386 5.179182 GCAAAAATACAAAGGTGAACATGGG 59.821 40.000 0.00 0.00 0.00 4.00
7527 8387 6.287525 CAAAAATACAAAGGTGAACATGGGT 58.712 36.000 0.00 0.00 0.00 4.51
7528 8388 5.467035 AAATACAAAGGTGAACATGGGTG 57.533 39.130 0.00 0.00 0.00 4.61
7529 8389 2.452600 ACAAAGGTGAACATGGGTGT 57.547 45.000 0.00 0.00 41.28 4.16
7530 8390 2.031120 ACAAAGGTGAACATGGGTGTG 58.969 47.619 0.00 0.00 38.92 3.82
7531 8391 1.039856 AAAGGTGAACATGGGTGTGC 58.960 50.000 0.00 0.00 38.92 4.57
7532 8392 1.172180 AAGGTGAACATGGGTGTGCG 61.172 55.000 0.00 0.00 36.61 5.34
7533 8393 2.255252 GTGAACATGGGTGTGCGC 59.745 61.111 0.00 0.00 36.61 6.09
7534 8394 3.353029 TGAACATGGGTGTGCGCG 61.353 61.111 0.00 0.00 36.61 6.86
7535 8395 4.759096 GAACATGGGTGTGCGCGC 62.759 66.667 27.26 27.26 38.92 6.86
7548 8408 2.811747 CGCGCACCCACGTGAATA 60.812 61.111 19.30 0.00 46.13 1.75
7549 8409 2.798501 CGCGCACCCACGTGAATAG 61.799 63.158 19.30 5.19 46.13 1.73
7550 8410 1.740296 GCGCACCCACGTGAATAGT 60.740 57.895 19.30 5.88 43.14 2.12
7551 8411 0.458889 GCGCACCCACGTGAATAGTA 60.459 55.000 19.30 0.00 43.14 1.82
7552 8412 1.999048 CGCACCCACGTGAATAGTAA 58.001 50.000 19.30 0.00 43.14 2.24
7553 8413 2.339418 CGCACCCACGTGAATAGTAAA 58.661 47.619 19.30 0.00 43.14 2.01
7554 8414 2.933906 CGCACCCACGTGAATAGTAAAT 59.066 45.455 19.30 0.00 43.14 1.40
7555 8415 3.372822 CGCACCCACGTGAATAGTAAATT 59.627 43.478 19.30 0.00 43.14 1.82
7556 8416 4.493545 CGCACCCACGTGAATAGTAAATTC 60.494 45.833 19.30 0.00 43.14 2.17
7557 8417 4.393680 GCACCCACGTGAATAGTAAATTCA 59.606 41.667 19.30 0.00 43.14 2.57
7558 8418 5.065988 GCACCCACGTGAATAGTAAATTCAT 59.934 40.000 19.30 0.00 43.14 2.57
7559 8419 6.259167 GCACCCACGTGAATAGTAAATTCATA 59.741 38.462 19.30 0.00 43.14 2.15
7560 8420 7.201661 GCACCCACGTGAATAGTAAATTCATAA 60.202 37.037 19.30 0.00 43.14 1.90
7561 8421 8.670135 CACCCACGTGAATAGTAAATTCATAAA 58.330 33.333 19.30 0.00 43.14 1.40
7562 8422 9.233649 ACCCACGTGAATAGTAAATTCATAAAA 57.766 29.630 19.30 0.00 39.80 1.52
7607 8467 8.600449 AAATTCTGAAATTTTTGCGGTATGAA 57.400 26.923 0.00 0.00 41.27 2.57
7608 8468 7.581011 ATTCTGAAATTTTTGCGGTATGAAC 57.419 32.000 0.00 0.00 0.00 3.18
7609 8469 5.465935 TCTGAAATTTTTGCGGTATGAACC 58.534 37.500 0.00 0.00 42.95 3.62
7610 8470 5.242838 TCTGAAATTTTTGCGGTATGAACCT 59.757 36.000 0.00 0.00 44.35 3.50
7611 8471 5.848406 TGAAATTTTTGCGGTATGAACCTT 58.152 33.333 0.00 0.00 44.35 3.50
7612 8472 6.982852 TGAAATTTTTGCGGTATGAACCTTA 58.017 32.000 0.00 0.00 44.35 2.69
7613 8473 7.087639 TGAAATTTTTGCGGTATGAACCTTAG 58.912 34.615 0.00 0.00 44.35 2.18
7614 8474 6.584185 AATTTTTGCGGTATGAACCTTAGT 57.416 33.333 0.00 0.00 44.35 2.24
7615 8475 5.616488 TTTTTGCGGTATGAACCTTAGTC 57.384 39.130 0.00 0.00 44.35 2.59
7616 8476 2.572191 TGCGGTATGAACCTTAGTCG 57.428 50.000 0.00 0.00 44.35 4.18
7617 8477 2.093890 TGCGGTATGAACCTTAGTCGA 58.906 47.619 0.00 0.00 44.35 4.20
7618 8478 2.691526 TGCGGTATGAACCTTAGTCGAT 59.308 45.455 0.00 0.00 44.35 3.59
7619 8479 3.243301 TGCGGTATGAACCTTAGTCGATC 60.243 47.826 0.00 0.00 44.35 3.69
7620 8480 3.243301 GCGGTATGAACCTTAGTCGATCA 60.243 47.826 0.00 0.00 44.35 2.92
7621 8481 4.558898 GCGGTATGAACCTTAGTCGATCAT 60.559 45.833 0.00 0.00 44.35 2.45
7622 8482 5.529791 CGGTATGAACCTTAGTCGATCATT 58.470 41.667 1.13 0.00 44.35 2.57
7623 8483 5.629849 CGGTATGAACCTTAGTCGATCATTC 59.370 44.000 1.13 0.00 44.35 2.67
7624 8484 6.515200 CGGTATGAACCTTAGTCGATCATTCT 60.515 42.308 1.13 0.00 44.35 2.40
7625 8485 7.308408 CGGTATGAACCTTAGTCGATCATTCTA 60.308 40.741 1.13 0.00 44.35 2.10
7626 8486 7.808856 GGTATGAACCTTAGTCGATCATTCTAC 59.191 40.741 1.13 0.00 43.08 2.59
7627 8487 7.589958 ATGAACCTTAGTCGATCATTCTACT 57.410 36.000 0.00 0.00 32.98 2.57
7628 8488 7.028926 TGAACCTTAGTCGATCATTCTACTC 57.971 40.000 0.00 0.00 31.03 2.59
7629 8489 6.602009 TGAACCTTAGTCGATCATTCTACTCA 59.398 38.462 0.00 0.00 31.03 3.41
7630 8490 6.380095 ACCTTAGTCGATCATTCTACTCAC 57.620 41.667 0.00 0.00 31.03 3.51
7631 8491 5.007823 ACCTTAGTCGATCATTCTACTCACG 59.992 44.000 0.00 0.00 31.03 4.35
7632 8492 5.007823 CCTTAGTCGATCATTCTACTCACGT 59.992 44.000 0.00 0.00 31.03 4.49
7633 8493 4.280101 AGTCGATCATTCTACTCACGTG 57.720 45.455 9.94 9.94 0.00 4.49
7634 8494 3.690139 AGTCGATCATTCTACTCACGTGT 59.310 43.478 16.51 0.00 0.00 4.49
7635 8495 3.786576 GTCGATCATTCTACTCACGTGTG 59.213 47.826 16.51 16.06 0.00 3.82
7636 8496 3.687698 TCGATCATTCTACTCACGTGTGA 59.312 43.478 23.32 14.13 38.06 3.58
7637 8497 4.155280 TCGATCATTCTACTCACGTGTGAA 59.845 41.667 23.32 18.02 39.39 3.18
7638 8498 4.497251 CGATCATTCTACTCACGTGTGAAG 59.503 45.833 23.32 12.53 39.39 3.02
7639 8499 4.848562 TCATTCTACTCACGTGTGAAGT 57.151 40.909 23.32 17.54 39.39 3.01
7640 8500 5.952526 TCATTCTACTCACGTGTGAAGTA 57.047 39.130 23.32 17.72 39.39 2.24
7641 8501 6.510879 TCATTCTACTCACGTGTGAAGTAT 57.489 37.500 23.32 11.17 39.39 2.12
7642 8502 6.552629 TCATTCTACTCACGTGTGAAGTATC 58.447 40.000 23.32 0.00 39.39 2.24
7643 8503 5.952526 TTCTACTCACGTGTGAAGTATCA 57.047 39.130 23.32 7.42 39.39 2.15
7644 8504 6.510879 TTCTACTCACGTGTGAAGTATCAT 57.489 37.500 23.32 1.82 39.39 2.45
7645 8505 6.120378 TCTACTCACGTGTGAAGTATCATC 57.880 41.667 23.32 0.00 39.39 2.92
7646 8506 4.783764 ACTCACGTGTGAAGTATCATCA 57.216 40.909 23.32 0.00 39.39 3.07
7647 8507 5.330455 ACTCACGTGTGAAGTATCATCAT 57.670 39.130 23.32 0.00 39.39 2.45
7648 8508 5.105063 ACTCACGTGTGAAGTATCATCATG 58.895 41.667 23.32 0.00 39.39 3.07
7649 8509 5.072040 TCACGTGTGAAGTATCATCATGT 57.928 39.130 16.51 0.00 38.01 3.21
7650 8510 6.127730 ACTCACGTGTGAAGTATCATCATGTA 60.128 38.462 23.32 0.00 39.39 2.29
7651 8511 6.805713 TCACGTGTGAAGTATCATCATGTAT 58.194 36.000 16.51 0.00 38.01 2.29
7652 8512 7.264947 TCACGTGTGAAGTATCATCATGTATT 58.735 34.615 16.51 0.00 38.01 1.89
7653 8513 7.222611 TCACGTGTGAAGTATCATCATGTATTG 59.777 37.037 16.51 0.00 38.01 1.90
7654 8514 7.222611 CACGTGTGAAGTATCATCATGTATTGA 59.777 37.037 7.58 0.00 38.01 2.57
7655 8515 7.222805 ACGTGTGAAGTATCATCATGTATTGAC 59.777 37.037 0.00 0.00 38.01 3.18
7656 8516 7.222611 CGTGTGAAGTATCATCATGTATTGACA 59.777 37.037 0.00 0.00 38.01 3.58
7657 8517 9.049523 GTGTGAAGTATCATCATGTATTGACAT 57.950 33.333 0.00 0.00 41.55 3.06
7658 8518 9.264719 TGTGAAGTATCATCATGTATTGACATC 57.735 33.333 0.00 0.00 40.07 3.06
7659 8519 8.715998 GTGAAGTATCATCATGTATTGACATCC 58.284 37.037 0.00 0.00 40.07 3.51
7660 8520 8.431222 TGAAGTATCATCATGTATTGACATCCA 58.569 33.333 0.00 0.00 44.82 3.41
7661 8521 9.445878 GAAGTATCATCATGTATTGACATCCAT 57.554 33.333 0.00 0.00 44.82 3.41
7662 8522 8.788325 AGTATCATCATGTATTGACATCCATG 57.212 34.615 0.00 0.00 44.82 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 468 0.822532 CAGCTTCCCATCCAGCCATC 60.823 60.000 0.00 0.00 36.62 3.51
200 469 1.229359 CAGCTTCCCATCCAGCCAT 59.771 57.895 0.00 0.00 36.62 4.40
201 470 2.679092 CAGCTTCCCATCCAGCCA 59.321 61.111 0.00 0.00 36.62 4.75
202 471 2.832201 GCAGCTTCCCATCCAGCC 60.832 66.667 0.00 0.00 36.62 4.85
203 472 3.207669 CGCAGCTTCCCATCCAGC 61.208 66.667 0.00 0.00 36.16 4.85
204 473 2.515523 CCGCAGCTTCCCATCCAG 60.516 66.667 0.00 0.00 0.00 3.86
205 474 4.802051 GCCGCAGCTTCCCATCCA 62.802 66.667 0.00 0.00 35.50 3.41
769 1072 6.259550 ACTGATCAAAGTGCAATAAACTCC 57.740 37.500 0.00 0.00 0.00 3.85
770 1073 7.141363 ACAACTGATCAAAGTGCAATAAACTC 58.859 34.615 0.00 0.00 0.00 3.01
771 1074 7.042797 ACAACTGATCAAAGTGCAATAAACT 57.957 32.000 0.00 0.00 0.00 2.66
776 1079 4.053295 GCAACAACTGATCAAAGTGCAAT 58.947 39.130 0.00 0.00 0.00 3.56
1076 1379 0.461961 AGTTGGAGATCGCCTGCTAC 59.538 55.000 17.00 9.25 38.73 3.58
1172 1475 3.648339 TTTCTGGATCTTTGCTTGCAC 57.352 42.857 0.00 0.00 0.00 4.57
1286 1589 1.940613 GTTCACCTGAAACGCTTCTGT 59.059 47.619 0.00 0.00 35.58 3.41
1575 1878 4.102367 AGCAGGAAAGTCCATTAGATCTCC 59.898 45.833 0.00 0.00 39.61 3.71
1713 2016 1.259840 GCTTGATGCCATGGGGTGTT 61.260 55.000 15.13 0.00 36.17 3.32
1801 2104 4.517285 TCAGGATGACAAGTATCTTTGGC 58.483 43.478 0.00 0.00 42.56 4.52
2254 2558 6.867816 GTGATCCTAACAACATTGCATTTGAA 59.132 34.615 9.52 0.00 0.00 2.69
2257 2561 5.182950 TCGTGATCCTAACAACATTGCATTT 59.817 36.000 0.00 0.00 0.00 2.32
2435 2745 6.627243 AGTGTTCCCAGTTTACAAAAAGAAC 58.373 36.000 0.00 0.00 31.57 3.01
2438 2748 7.320399 AGAAAGTGTTCCCAGTTTACAAAAAG 58.680 34.615 0.00 0.00 42.82 2.27
2641 2952 9.803315 TTAAACTATACAGCATACAAGACTCAG 57.197 33.333 0.00 0.00 0.00 3.35
2668 2983 4.414846 AGGCTAGTGATTGAGATTGGGATT 59.585 41.667 0.00 0.00 0.00 3.01
2674 2989 7.500559 GGTAAAATCAGGCTAGTGATTGAGATT 59.499 37.037 8.82 3.74 44.72 2.40
2675 2990 6.995091 GGTAAAATCAGGCTAGTGATTGAGAT 59.005 38.462 8.82 1.44 44.72 2.75
2711 3026 1.590591 TGTAGGGCCAGGCTAATGAA 58.409 50.000 12.43 0.00 0.00 2.57
2747 3062 7.518848 CGACATGACATGGATCGAAATGTTTAT 60.519 37.037 19.39 7.97 37.15 1.40
2748 3063 6.238076 CGACATGACATGGATCGAAATGTTTA 60.238 38.462 19.39 6.47 37.15 2.01
2757 3072 0.249615 AGCCGACATGACATGGATCG 60.250 55.000 19.39 18.16 33.60 3.69
2827 3142 6.393171 GCATTCCTAATAAATTCAGCATCCC 58.607 40.000 0.00 0.00 0.00 3.85
2841 3156 6.904626 AGAGTACAGAAATGGCATTCCTAAT 58.095 36.000 14.04 0.29 0.00 1.73
2845 3160 5.415701 TCAAAGAGTACAGAAATGGCATTCC 59.584 40.000 14.04 0.00 0.00 3.01
2939 3255 4.772886 ACCAGACAAAAGTACTTGAGGT 57.227 40.909 9.34 7.78 0.00 3.85
3258 3715 5.104360 TCGTTACTATACCACACTAGACCCT 60.104 44.000 0.00 0.00 0.00 4.34
3755 4453 6.624423 CAGAATTTCTTTCAGGGTATTGTGG 58.376 40.000 0.00 0.00 36.75 4.17
4127 4963 2.176889 TCAGGACCTGTAGTTAGCACC 58.823 52.381 21.06 0.00 32.61 5.01
4339 5177 6.764560 ACATAGAAAACCGTCAGTAAAACTGT 59.235 34.615 6.93 0.00 46.03 3.55
4522 5366 9.282569 GATGAGATTTAGCTGAACCTAATTCAT 57.717 33.333 0.00 0.00 46.37 2.57
4590 5435 8.587952 AGAAACAAAAACCGAAAGATATTTGG 57.412 30.769 0.00 0.00 33.31 3.28
4682 5527 1.026718 GCAGTGACATACAGGCCCAC 61.027 60.000 0.00 0.00 0.00 4.61
4763 5609 7.714377 AGATGTATGATAAGAAAGGCTCAACAG 59.286 37.037 0.00 0.00 0.00 3.16
4802 5648 3.195825 GGTCGCTACCTGCCTCATATAAT 59.804 47.826 0.00 0.00 43.08 1.28
4909 5755 5.129485 TGTTGTATTTTTGTGTGGGTCCATT 59.871 36.000 0.00 0.00 0.00 3.16
5073 5921 5.165961 AGCAAACATGACATACAGGTACT 57.834 39.130 0.00 0.00 42.83 2.73
5074 5922 7.279981 TCAATAGCAAACATGACATACAGGTAC 59.720 37.037 0.00 0.00 42.83 3.34
5075 5923 7.279981 GTCAATAGCAAACATGACATACAGGTA 59.720 37.037 0.00 0.00 42.83 3.08
5076 5924 6.094048 GTCAATAGCAAACATGACATACAGGT 59.906 38.462 0.00 0.00 45.64 4.00
5792 6640 3.848272 TTTGATTTCGGATCAAGTGCC 57.152 42.857 12.62 0.00 38.98 5.01
6447 7295 8.883731 ACTAGAATTGGATAATTGTTTCTGTCG 58.116 33.333 0.00 0.00 36.66 4.35
6635 7483 1.533994 AGGGTTTTTGGCTGGCCTC 60.534 57.895 13.05 0.00 36.94 4.70
6715 7563 0.383949 TCAAGAAAGTTGCCGGTTGC 59.616 50.000 1.90 0.00 41.77 4.17
6765 7613 4.467795 AGTTATATGTGCCTGTCTGTCAGT 59.532 41.667 0.00 0.00 42.19 3.41
6795 7643 3.127548 GGTCATCAAGCACCAATGTACAG 59.872 47.826 0.33 0.00 32.33 2.74
6804 7652 1.197721 CACTTTCGGTCATCAAGCACC 59.802 52.381 0.00 0.00 0.00 5.01
6928 7776 2.878580 CTGATCAGATAGATGGCGCTC 58.121 52.381 18.34 0.00 37.00 5.03
6931 7779 1.626747 CGCTGATCAGATAGATGGCG 58.373 55.000 27.04 16.36 43.66 5.69
6993 7842 2.515991 CAACCGCACACACCAGGT 60.516 61.111 0.00 0.00 38.88 4.00
7107 7956 0.509499 TTCGCGCTTTCTGTAAACGG 59.491 50.000 5.56 0.00 0.00 4.44
7108 7957 1.071107 TGTTCGCGCTTTCTGTAAACG 60.071 47.619 5.56 0.00 0.00 3.60
7244 8093 0.244994 ACTTGGCGCACAAACACAAA 59.755 45.000 10.83 0.00 38.91 2.83
7245 8094 0.457509 CACTTGGCGCACAAACACAA 60.458 50.000 10.83 0.68 38.91 3.33
7246 8095 1.138459 CACTTGGCGCACAAACACA 59.862 52.632 10.83 0.00 38.91 3.72
7247 8096 1.138671 ACACTTGGCGCACAAACAC 59.861 52.632 10.83 0.00 38.91 3.32
7248 8097 1.138459 CACACTTGGCGCACAAACA 59.862 52.632 10.83 0.00 38.91 2.83
7249 8098 0.030638 ATCACACTTGGCGCACAAAC 59.969 50.000 10.83 0.00 38.91 2.93
7259 8108 9.897744 AAATTACAACTCAATACATCACACTTG 57.102 29.630 0.00 0.00 0.00 3.16
7300 8149 9.801873 AAGATTTATGATCCAAAACGTTTATGG 57.198 29.630 24.41 24.41 35.49 2.74
7304 8153 9.191995 GACAAAGATTTATGATCCAAAACGTTT 57.808 29.630 7.96 7.96 0.00 3.60
7362 8211 2.233271 CCCAGCAGAGAACAACACATT 58.767 47.619 0.00 0.00 0.00 2.71
7390 8239 7.992608 ACAATGTCATACTATCAAACCATGCTA 59.007 33.333 0.00 0.00 0.00 3.49
7407 8256 5.893255 AGGCATATGTAACCAACAATGTCAT 59.107 36.000 4.29 0.00 42.70 3.06
7421 8270 9.283768 ACGAAATGATAAAATCAGGCATATGTA 57.716 29.630 4.29 0.00 43.53 2.29
7422 8271 8.169977 ACGAAATGATAAAATCAGGCATATGT 57.830 30.769 4.29 0.00 43.53 2.29
7425 8274 6.770303 TGGACGAAATGATAAAATCAGGCATA 59.230 34.615 0.00 0.00 43.53 3.14
7427 8276 4.946772 TGGACGAAATGATAAAATCAGGCA 59.053 37.500 0.00 0.00 43.53 4.75
7428 8277 5.499139 TGGACGAAATGATAAAATCAGGC 57.501 39.130 0.00 0.00 43.53 4.85
7429 8278 7.263100 TCATGGACGAAATGATAAAATCAGG 57.737 36.000 0.00 0.00 43.53 3.86
7448 8307 1.133792 GGGGTTGTATGGTCCTCATGG 60.134 57.143 0.00 0.00 37.30 3.66
7451 8310 1.285280 CAGGGGTTGTATGGTCCTCA 58.715 55.000 0.00 0.00 0.00 3.86
7457 8316 4.664062 CCTGCAGGGGTTGTATGG 57.336 61.111 26.14 0.00 0.00 2.74
7473 8333 8.825667 TTTTGTTGATTAATAAGTTTCAGCCC 57.174 30.769 0.00 0.00 0.00 5.19
7496 8356 7.391833 TGTTCACCTTTGTATTTTTGCCTTTTT 59.608 29.630 0.00 0.00 0.00 1.94
7497 8357 6.881602 TGTTCACCTTTGTATTTTTGCCTTTT 59.118 30.769 0.00 0.00 0.00 2.27
7498 8358 6.410540 TGTTCACCTTTGTATTTTTGCCTTT 58.589 32.000 0.00 0.00 0.00 3.11
7499 8359 5.983540 TGTTCACCTTTGTATTTTTGCCTT 58.016 33.333 0.00 0.00 0.00 4.35
7500 8360 5.606348 TGTTCACCTTTGTATTTTTGCCT 57.394 34.783 0.00 0.00 0.00 4.75
7501 8361 5.179182 CCATGTTCACCTTTGTATTTTTGCC 59.821 40.000 0.00 0.00 0.00 4.52
7502 8362 5.179182 CCCATGTTCACCTTTGTATTTTTGC 59.821 40.000 0.00 0.00 0.00 3.68
7503 8363 6.202570 CACCCATGTTCACCTTTGTATTTTTG 59.797 38.462 0.00 0.00 0.00 2.44
7504 8364 6.126911 ACACCCATGTTCACCTTTGTATTTTT 60.127 34.615 0.00 0.00 34.46 1.94
7505 8365 5.365314 ACACCCATGTTCACCTTTGTATTTT 59.635 36.000 0.00 0.00 34.46 1.82
7506 8366 4.898861 ACACCCATGTTCACCTTTGTATTT 59.101 37.500 0.00 0.00 34.46 1.40
7507 8367 4.280677 CACACCCATGTTCACCTTTGTATT 59.719 41.667 0.00 0.00 36.72 1.89
7508 8368 3.826157 CACACCCATGTTCACCTTTGTAT 59.174 43.478 0.00 0.00 36.72 2.29
7509 8369 3.218453 CACACCCATGTTCACCTTTGTA 58.782 45.455 0.00 0.00 36.72 2.41
7510 8370 2.031120 CACACCCATGTTCACCTTTGT 58.969 47.619 0.00 0.00 36.72 2.83
7511 8371 1.269726 GCACACCCATGTTCACCTTTG 60.270 52.381 0.00 0.00 36.72 2.77
7512 8372 1.039856 GCACACCCATGTTCACCTTT 58.960 50.000 0.00 0.00 36.72 3.11
7513 8373 1.172180 CGCACACCCATGTTCACCTT 61.172 55.000 0.00 0.00 36.72 3.50
7514 8374 1.600636 CGCACACCCATGTTCACCT 60.601 57.895 0.00 0.00 36.72 4.00
7515 8375 2.953821 CGCACACCCATGTTCACC 59.046 61.111 0.00 0.00 36.72 4.02
7516 8376 2.255252 GCGCACACCCATGTTCAC 59.745 61.111 0.30 0.00 36.72 3.18
7517 8377 3.353029 CGCGCACACCCATGTTCA 61.353 61.111 8.75 0.00 36.72 3.18
7518 8378 4.759096 GCGCGCACACCCATGTTC 62.759 66.667 29.10 0.00 36.72 3.18
7531 8391 2.798501 CTATTCACGTGGGTGCGCG 61.799 63.158 17.00 0.00 44.03 6.86
7532 8392 0.458889 TACTATTCACGTGGGTGCGC 60.459 55.000 17.00 0.00 44.03 6.09
7533 8393 1.999048 TTACTATTCACGTGGGTGCG 58.001 50.000 17.00 3.60 44.03 5.34
7534 8394 4.393680 TGAATTTACTATTCACGTGGGTGC 59.606 41.667 17.00 1.35 44.03 5.01
7535 8395 6.677781 ATGAATTTACTATTCACGTGGGTG 57.322 37.500 17.00 6.47 45.78 4.61
7536 8396 8.795842 TTTATGAATTTACTATTCACGTGGGT 57.204 30.769 17.00 11.87 40.37 4.51
7582 8442 8.495148 GTTCATACCGCAAAAATTTCAGAATTT 58.505 29.630 0.00 0.00 45.06 1.82
7583 8443 7.117667 GGTTCATACCGCAAAAATTTCAGAATT 59.882 33.333 0.00 0.00 34.24 2.17
7584 8444 6.589907 GGTTCATACCGCAAAAATTTCAGAAT 59.410 34.615 0.00 0.00 34.01 2.40
7585 8445 5.923684 GGTTCATACCGCAAAAATTTCAGAA 59.076 36.000 0.00 0.00 34.01 3.02
7586 8446 5.465935 GGTTCATACCGCAAAAATTTCAGA 58.534 37.500 0.00 0.00 34.01 3.27
7587 8447 5.761818 GGTTCATACCGCAAAAATTTCAG 57.238 39.130 0.00 0.00 34.01 3.02
7600 8460 6.750148 AGAATGATCGACTAAGGTTCATACC 58.250 40.000 0.00 0.00 45.39 2.73
7601 8461 8.569641 AGTAGAATGATCGACTAAGGTTCATAC 58.430 37.037 0.00 0.00 39.41 2.39
7602 8462 8.693120 AGTAGAATGATCGACTAAGGTTCATA 57.307 34.615 0.00 0.00 39.41 2.15
7603 8463 7.285629 TGAGTAGAATGATCGACTAAGGTTCAT 59.714 37.037 0.00 0.00 40.99 2.57
7604 8464 6.602009 TGAGTAGAATGATCGACTAAGGTTCA 59.398 38.462 0.00 0.00 40.99 3.18
7605 8465 6.913673 GTGAGTAGAATGATCGACTAAGGTTC 59.086 42.308 0.00 0.00 40.99 3.62
7606 8466 6.458478 CGTGAGTAGAATGATCGACTAAGGTT 60.458 42.308 0.00 0.00 40.99 3.50
7607 8467 5.007823 CGTGAGTAGAATGATCGACTAAGGT 59.992 44.000 0.00 0.00 40.99 3.50
7608 8468 5.007823 ACGTGAGTAGAATGATCGACTAAGG 59.992 44.000 0.00 0.00 46.88 2.69
7609 8469 6.050454 ACGTGAGTAGAATGATCGACTAAG 57.950 41.667 0.00 0.00 46.88 2.18
7618 8478 7.148069 ATGATACTTCACACGTGAGTAGAATGA 60.148 37.037 25.01 10.74 41.13 2.57
7619 8479 6.975197 ATGATACTTCACACGTGAGTAGAATG 59.025 38.462 25.01 8.23 41.13 2.67
7620 8480 7.101652 ATGATACTTCACACGTGAGTAGAAT 57.898 36.000 25.01 13.32 41.13 2.40
7621 8481 6.150474 TGATGATACTTCACACGTGAGTAGAA 59.850 38.462 25.01 17.65 41.13 2.10
7622 8482 5.646360 TGATGATACTTCACACGTGAGTAGA 59.354 40.000 25.01 11.34 41.13 2.59
7623 8483 5.880341 TGATGATACTTCACACGTGAGTAG 58.120 41.667 25.01 19.68 41.13 2.57
7624 8484 5.890424 TGATGATACTTCACACGTGAGTA 57.110 39.130 25.01 19.30 41.13 2.59
7625 8485 4.783764 TGATGATACTTCACACGTGAGT 57.216 40.909 25.01 17.66 41.13 3.41
7626 8486 5.105063 ACATGATGATACTTCACACGTGAG 58.895 41.667 25.01 15.63 41.13 3.51
7627 8487 5.072040 ACATGATGATACTTCACACGTGA 57.928 39.130 25.01 0.00 34.93 4.35
7628 8488 7.222611 TCAATACATGATGATACTTCACACGTG 59.777 37.037 15.48 15.48 35.97 4.49
7629 8489 7.222805 GTCAATACATGATGATACTTCACACGT 59.777 37.037 0.00 0.00 40.97 4.49
7630 8490 7.222611 TGTCAATACATGATGATACTTCACACG 59.777 37.037 0.00 0.00 40.97 4.49
7631 8491 8.424274 TGTCAATACATGATGATACTTCACAC 57.576 34.615 0.00 0.00 40.97 3.82
7632 8492 9.264719 GATGTCAATACATGATGATACTTCACA 57.735 33.333 0.00 0.00 46.49 3.58
7633 8493 8.715998 GGATGTCAATACATGATGATACTTCAC 58.284 37.037 0.00 0.00 46.49 3.18
7634 8494 8.431222 TGGATGTCAATACATGATGATACTTCA 58.569 33.333 0.00 0.00 46.49 3.02
7635 8495 8.837788 TGGATGTCAATACATGATGATACTTC 57.162 34.615 0.00 0.30 46.49 3.01


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

AutoCloner maintained by Alex Coulton.