Multiple sequence alignment - TraesCS5A01G172600

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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 TraesCS5A01G172600 chr5A 100.000 7527 0 0 1 7527 365674243 365666717 0.000000e+00 13900
1 TraesCS5A01G172600 chr5A 89.147 129 12 2 592 719 307708544 307708671 7.820000e-35 159
2 TraesCS5A01G172600 chr5D 95.799 5832 133 30 1 5770 276942426 276936645 0.000000e+00 9310
3 TraesCS5A01G172600 chr5D 91.692 1312 55 23 5792 7065 276936663 276935368 0.000000e+00 1770
4 TraesCS5A01G172600 chr5D 91.429 350 25 1 7171 7515 276935342 276934993 6.830000e-130 475
5 TraesCS5A01G172600 chr5D 95.699 93 3 1 7062 7153 276935416 276935324 1.690000e-31 148
6 TraesCS5A01G172600 chr5B 96.124 2580 40 10 2192 4738 314303654 314301102 0.000000e+00 4156
7 TraesCS5A01G172600 chr5B 95.352 2216 73 8 1 2198 314306441 314304238 0.000000e+00 3494
8 TraesCS5A01G172600 chr5B 95.468 993 20 5 4764 5756 314301107 314300140 0.000000e+00 1561
9 TraesCS5A01G172600 chr5B 91.304 483 27 9 5792 6265 314300136 314299660 0.000000e+00 645
10 TraesCS5A01G172600 chr5B 91.089 303 17 4 6271 6563 314299525 314299223 1.180000e-107 401
11 TraesCS5A01G172600 chr5B 98.658 149 2 0 6596 6744 314299226 314299078 1.610000e-66 265
12 TraesCS5A01G172600 chr5B 91.057 123 5 3 7325 7446 314298233 314298350 2.170000e-35 161
13 TraesCS5A01G172600 chr5B 94.382 89 5 0 7238 7326 314297818 314297906 3.660000e-28 137
14 TraesCS5A01G172600 chr5B 94.186 86 4 1 6771 6856 314299078 314298994 6.130000e-26 130
15 TraesCS5A01G172600 chr1B 89.930 715 49 10 1 707 54872603 54871904 0.000000e+00 900
16 TraesCS5A01G172600 chr1B 88.128 716 59 12 1 707 597262259 597261561 0.000000e+00 828
17 TraesCS5A01G172600 chr1B 87.138 311 21 11 176 480 54859835 54860132 1.210000e-87 335
18 TraesCS5A01G172600 chr1B 90.323 124 8 3 466 589 54860518 54860637 7.820000e-35 159
19 TraesCS5A01G172600 chr4A 88.156 743 57 14 1 717 635962605 635961868 0.000000e+00 856
20 TraesCS5A01G172600 chr2A 88.640 625 46 11 91 707 43682876 43683483 0.000000e+00 737
21 TraesCS5A01G172600 chr7B 84.615 338 29 13 218 552 152792619 152792936 1.580000e-81 315
22 TraesCS5A01G172600 chr7B 82.328 232 34 5 964 1190 436083174 436083403 2.140000e-45 195
23 TraesCS5A01G172600 chr3A 84.861 251 25 8 305 552 552627261 552627501 2.710000e-59 241
24 TraesCS5A01G172600 chr7D 83.190 232 32 5 964 1190 420087313 420087542 9.900000e-49 206
25 TraesCS5A01G172600 chr7A 82.128 235 35 5 964 1193 512764208 512763976 2.140000e-45 195
26 TraesCS5A01G172600 chr6D 89.922 129 11 2 592 719 24254368 24254495 1.680000e-36 165
27 TraesCS5A01G172600 chrUn 89.062 128 12 2 592 718 11032599 11032473 2.810000e-34 158
28 TraesCS5A01G172600 chr2D 88.462 130 13 2 592 720 633460934 633461062 1.010000e-33 156


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 TraesCS5A01G172600 chr5A 365666717 365674243 7526 True 13900.000000 13900 100.000000 1 7527 1 chr5A.!!$R1 7526
1 TraesCS5A01G172600 chr5D 276934993 276942426 7433 True 2925.750000 9310 93.654750 1 7515 4 chr5D.!!$R1 7514
2 TraesCS5A01G172600 chr5B 314298994 314306441 7447 True 1521.714286 4156 94.597286 1 6856 7 chr5B.!!$R1 6855
3 TraesCS5A01G172600 chr1B 54871904 54872603 699 True 900.000000 900 89.930000 1 707 1 chr1B.!!$R1 706
4 TraesCS5A01G172600 chr1B 597261561 597262259 698 True 828.000000 828 88.128000 1 707 1 chr1B.!!$R2 706
5 TraesCS5A01G172600 chr1B 54859835 54860637 802 False 247.000000 335 88.730500 176 589 2 chr1B.!!$F1 413
6 TraesCS5A01G172600 chr4A 635961868 635962605 737 True 856.000000 856 88.156000 1 717 1 chr4A.!!$R1 716
7 TraesCS5A01G172600 chr2A 43682876 43683483 607 False 737.000000 737 88.640000 91 707 1 chr2A.!!$F1 616

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
382 391 0.108585 GTGGTGCAGGGAGAAGTGAA 59.891 55.000 0.00 0.00 0.00 3.18 F
468 889 0.178068 AAGTGCATAGGTAGTGGCCG 59.822 55.000 0.00 0.00 0.00 6.13 F
1630 2074 0.811616 GCCCGGCTCAGTATTGACAG 60.812 60.000 0.71 0.00 0.00 3.51 F
2144 2603 2.724977 TGTCTCTGGCACTAGTTTCG 57.275 50.000 0.00 0.00 0.00 3.46 F
3505 4562 1.552792 GCTAGAGCTTTGAGACCTGGT 59.447 52.381 0.00 0.00 38.21 4.00 F
4066 5151 1.153706 GCCAAGCCACATGATGTGC 60.154 57.895 19.69 14.56 46.51 4.57 F
5462 6564 1.202746 GCAGGGAGGGACATCAGATTC 60.203 57.143 0.00 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 2603 2.036862 ACACGTTAAGGAGGTCAGGAAC 59.963 50.000 1.43 0.00 0.00 3.62 R
2176 2635 3.904800 ACCAATACACACATGATCCGA 57.095 42.857 0.00 0.00 0.00 4.55 R
3505 4562 5.129634 TCAGCTTGATTACAAAGAACACCA 58.870 37.500 0.00 0.00 35.49 4.17 R
4043 5128 1.135199 CATCATGTGGCTTGGCTGTTC 60.135 52.381 0.00 0.00 0.00 3.18 R
5370 6472 0.471211 ACTGGTCGACCCTCTTTGGA 60.471 55.000 31.19 9.47 38.35 3.53 R
5838 6948 1.065551 GTTGGAAGAACAAACGCTGCT 59.934 47.619 0.00 0.00 31.17 4.24 R
7236 8529 0.033228 CGGGCCAAATTCTTGTGCAA 59.967 50.000 4.39 0.00 33.10 4.08 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
229 230 0.112412 TTCTGTTCCTTCCCTTGCCC 59.888 55.000 0.00 0.00 0.00 5.36
242 243 0.749649 CTTGCCCGATCTACTCTGCT 59.250 55.000 0.00 0.00 0.00 4.24
273 274 0.179078 GATGCTGCAGTGAGGGAGAG 60.179 60.000 16.64 0.00 0.00 3.20
382 391 0.108585 GTGGTGCAGGGAGAAGTGAA 59.891 55.000 0.00 0.00 0.00 3.18
468 889 0.178068 AAGTGCATAGGTAGTGGCCG 59.822 55.000 0.00 0.00 0.00 6.13
484 905 3.096852 TGGCCGAATCTCTCAGTCTTTA 58.903 45.455 0.00 0.00 0.00 1.85
529 950 2.095853 CGGTACATGCTAAACTGCTTGG 59.904 50.000 0.00 0.00 40.83 3.61
676 1111 7.055378 ACTAGACTAGTCACGATTGGTCTATT 58.945 38.462 24.44 7.74 39.22 1.73
695 1130 1.263356 TAGTCTCAACCCTGGAACGG 58.737 55.000 0.00 0.00 0.00 4.44
775 1210 7.984050 AGTTTCTCATCCACTTATATGTCTGTG 59.016 37.037 0.00 0.00 0.00 3.66
800 1235 3.552684 GGTGCATGCTTGTTATGTGTGTT 60.553 43.478 20.33 0.00 0.00 3.32
925 1360 5.634896 CAGAAATTGTGTATTCTCCTGTGC 58.365 41.667 0.00 0.00 33.73 4.57
1228 1665 4.951715 TCAATTGCATCATCCTTGCTACTT 59.048 37.500 0.00 0.00 40.77 2.24
1358 1797 2.311542 TCCAATGTGGCCAGGTATTTCT 59.688 45.455 5.11 0.00 37.47 2.52
1402 1842 5.997746 TCTATTGCTTGATGGTTATACCTGC 59.002 40.000 0.00 0.00 39.58 4.85
1422 1862 6.655003 ACCTGCCATTAGAATAATAATCCACG 59.345 38.462 0.00 0.00 0.00 4.94
1464 1904 5.295292 AGTTTTCTACATCCATTCATGCGAG 59.705 40.000 0.00 0.00 0.00 5.03
1561 2001 6.618287 TTAGTGCTGAATCGATAAAATGGG 57.382 37.500 0.00 0.00 0.00 4.00
1630 2074 0.811616 GCCCGGCTCAGTATTGACAG 60.812 60.000 0.71 0.00 0.00 3.51
1752 2196 2.958355 CTCAACACACCCCTTTTGACAT 59.042 45.455 0.00 0.00 0.00 3.06
2144 2603 2.724977 TGTCTCTGGCACTAGTTTCG 57.275 50.000 0.00 0.00 0.00 3.46
2176 2635 6.713450 ACCTCCTTAACGTGTTTATGTTTCAT 59.287 34.615 0.00 0.00 37.27 2.57
2252 3301 8.891671 AAGTATGTTCAATTGTTTCTGCAAAT 57.108 26.923 5.13 0.00 31.63 2.32
2325 3374 6.071728 CCAATTGCTCTTTACCATCTCACTTT 60.072 38.462 0.00 0.00 0.00 2.66
2473 3522 4.003648 GGAAGTCACCATACCAAGAAGTG 58.996 47.826 0.00 0.00 0.00 3.16
3083 4139 7.826744 AAAGATTTCTTCCCAGACTTATCTGTC 59.173 37.037 3.76 0.00 42.12 3.51
3405 4462 7.994425 TGAGTATTTATCTTTGTTCTTGCCA 57.006 32.000 0.00 0.00 0.00 4.92
3505 4562 1.552792 GCTAGAGCTTTGAGACCTGGT 59.447 52.381 0.00 0.00 38.21 4.00
3713 4770 8.225777 GTGGTCTTTACTTAGGTTAATGTTTCG 58.774 37.037 0.00 0.00 0.00 3.46
3781 4838 5.909477 TCCTTTCGAACAACTTCTGAGTTA 58.091 37.500 0.00 0.00 44.14 2.24
3782 4839 6.342906 TCCTTTCGAACAACTTCTGAGTTAA 58.657 36.000 0.00 0.00 44.14 2.01
3783 4840 6.819649 TCCTTTCGAACAACTTCTGAGTTAAA 59.180 34.615 0.00 0.00 44.14 1.52
3784 4841 7.334921 TCCTTTCGAACAACTTCTGAGTTAAAA 59.665 33.333 0.00 0.00 44.14 1.52
3785 4842 7.966204 CCTTTCGAACAACTTCTGAGTTAAAAA 59.034 33.333 0.00 0.00 44.14 1.94
4043 5128 8.043113 TGGCAGTTTGCTATTATATCTCATAGG 58.957 37.037 0.67 0.00 44.28 2.57
4066 5151 1.153706 GCCAAGCCACATGATGTGC 60.154 57.895 19.69 14.56 46.51 4.57
4072 5157 4.357142 CAAGCCACATGATGTGCTAAATC 58.643 43.478 19.69 4.49 46.51 2.17
4092 5177 9.360093 CTAAATCTAGCATGCACCTATTAGTAC 57.640 37.037 21.98 0.00 0.00 2.73
4341 5433 6.069905 TGCACATACTAGGGACTTGGAATAAA 60.070 38.462 0.00 0.00 41.75 1.40
4628 5729 5.766174 ACATTTTACCTGGTTTATGTCGTGT 59.234 36.000 3.84 0.00 0.00 4.49
5201 6303 2.203394 CAACCCACTGCTGGCTGT 60.203 61.111 0.00 0.00 36.00 4.40
5370 6472 4.514816 GTGCAATTGGGTTTTTGCTATGTT 59.485 37.500 7.72 0.00 46.50 2.71
5462 6564 1.202746 GCAGGGAGGGACATCAGATTC 60.203 57.143 0.00 0.00 0.00 2.52
5506 6608 9.720769 TTCTGTTTAGAAAGTTACCTATCTTGG 57.279 33.333 0.00 0.00 39.89 3.61
5507 6609 8.877195 TCTGTTTAGAAAGTTACCTATCTTGGT 58.123 33.333 0.00 0.00 43.66 3.67
5508 6610 9.503399 CTGTTTAGAAAGTTACCTATCTTGGTT 57.497 33.333 0.00 0.00 41.22 3.67
5509 6611 9.856162 TGTTTAGAAAGTTACCTATCTTGGTTT 57.144 29.630 0.00 0.00 41.22 3.27
5520 6622 9.948964 TTACCTATCTTGGTTTAGAAAGTTACC 57.051 33.333 0.00 0.00 41.22 2.85
5521 6623 8.215954 ACCTATCTTGGTTTAGAAAGTTACCT 57.784 34.615 0.00 0.00 36.89 3.08
5522 6624 9.330220 ACCTATCTTGGTTTAGAAAGTTACCTA 57.670 33.333 0.00 0.00 36.89 3.08
5582 6684 9.363401 TGTCTTGGTATATGCTGTAGTATACTT 57.637 33.333 11.40 0.00 43.54 2.24
5617 6719 9.803507 AATGATGCAGAATTCTAATATTCCTCA 57.196 29.630 7.86 3.85 35.56 3.86
5710 6812 8.846211 TCTTTAAAAATACTCCACTCCAACTTG 58.154 33.333 0.00 0.00 0.00 3.16
5722 6824 3.202906 CTCCAACTTGGACGTGAGAAAA 58.797 45.455 6.39 0.00 42.67 2.29
5733 6835 3.740115 ACGTGAGAAAACTGGCATTACT 58.260 40.909 0.00 0.00 0.00 2.24
5750 6852 6.694447 GCATTACTATTCATTGCCATCCATT 58.306 36.000 0.00 0.00 0.00 3.16
5751 6853 7.829725 GCATTACTATTCATTGCCATCCATTA 58.170 34.615 0.00 0.00 0.00 1.90
5752 6854 8.306038 GCATTACTATTCATTGCCATCCATTAA 58.694 33.333 0.00 0.00 0.00 1.40
5753 6855 9.850628 CATTACTATTCATTGCCATCCATTAAG 57.149 33.333 0.00 0.00 0.00 1.85
5754 6856 6.336842 ACTATTCATTGCCATCCATTAAGC 57.663 37.500 0.00 0.00 0.00 3.09
5755 6857 5.834742 ACTATTCATTGCCATCCATTAAGCA 59.165 36.000 0.00 0.00 0.00 3.91
5756 6858 4.389890 TTCATTGCCATCCATTAAGCAC 57.610 40.909 0.00 0.00 34.37 4.40
5757 6859 3.363627 TCATTGCCATCCATTAAGCACA 58.636 40.909 0.00 0.00 34.37 4.57
5758 6860 3.130869 TCATTGCCATCCATTAAGCACAC 59.869 43.478 0.00 0.00 34.37 3.82
5759 6861 2.512692 TGCCATCCATTAAGCACACT 57.487 45.000 0.00 0.00 0.00 3.55
5760 6862 2.093890 TGCCATCCATTAAGCACACTG 58.906 47.619 0.00 0.00 0.00 3.66
5761 6863 2.290832 TGCCATCCATTAAGCACACTGA 60.291 45.455 0.00 0.00 0.00 3.41
5762 6864 2.954318 GCCATCCATTAAGCACACTGAT 59.046 45.455 0.00 0.00 0.00 2.90
5763 6865 3.382546 GCCATCCATTAAGCACACTGATT 59.617 43.478 0.00 0.00 0.00 2.57
5764 6866 4.142093 GCCATCCATTAAGCACACTGATTT 60.142 41.667 0.00 0.00 0.00 2.17
5765 6867 5.345702 CCATCCATTAAGCACACTGATTTG 58.654 41.667 0.00 0.00 0.00 2.32
5766 6868 5.105635 CCATCCATTAAGCACACTGATTTGT 60.106 40.000 0.00 0.00 0.00 2.83
5767 6869 6.392354 CATCCATTAAGCACACTGATTTGTT 58.608 36.000 0.00 0.00 0.00 2.83
5768 6870 6.403866 TCCATTAAGCACACTGATTTGTTT 57.596 33.333 0.00 0.00 0.00 2.83
5769 6871 6.815089 TCCATTAAGCACACTGATTTGTTTT 58.185 32.000 0.00 0.00 0.00 2.43
5770 6872 6.922957 TCCATTAAGCACACTGATTTGTTTTC 59.077 34.615 0.00 0.00 0.00 2.29
5771 6873 6.925165 CCATTAAGCACACTGATTTGTTTTCT 59.075 34.615 0.00 0.00 0.00 2.52
5772 6874 7.095940 CCATTAAGCACACTGATTTGTTTTCTG 60.096 37.037 0.00 0.00 0.00 3.02
5773 6875 5.581126 AAGCACACTGATTTGTTTTCTGA 57.419 34.783 0.00 0.00 0.00 3.27
5774 6876 5.581126 AGCACACTGATTTGTTTTCTGAA 57.419 34.783 0.00 0.00 0.00 3.02
5775 6877 6.152932 AGCACACTGATTTGTTTTCTGAAT 57.847 33.333 0.00 0.00 0.00 2.57
5776 6878 6.211515 AGCACACTGATTTGTTTTCTGAATC 58.788 36.000 0.00 0.00 0.00 2.52
5777 6879 5.116074 GCACACTGATTTGTTTTCTGAATCG 59.884 40.000 0.00 0.00 33.55 3.34
5778 6880 6.201517 CACACTGATTTGTTTTCTGAATCGT 58.798 36.000 0.00 0.00 33.55 3.73
5779 6881 7.351981 CACACTGATTTGTTTTCTGAATCGTA 58.648 34.615 0.00 0.00 33.55 3.43
5780 6882 8.017373 CACACTGATTTGTTTTCTGAATCGTAT 58.983 33.333 0.00 0.00 33.55 3.06
5781 6883 8.017373 ACACTGATTTGTTTTCTGAATCGTATG 58.983 33.333 0.00 0.00 33.55 2.39
5782 6884 7.482743 CACTGATTTGTTTTCTGAATCGTATGG 59.517 37.037 0.00 0.00 33.55 2.74
5783 6885 6.851609 TGATTTGTTTTCTGAATCGTATGGG 58.148 36.000 0.00 0.00 33.55 4.00
5784 6886 6.657117 TGATTTGTTTTCTGAATCGTATGGGA 59.343 34.615 0.00 0.00 33.55 4.37
5785 6887 6.885952 TTTGTTTTCTGAATCGTATGGGAA 57.114 33.333 0.00 0.00 0.00 3.97
5786 6888 6.885952 TTGTTTTCTGAATCGTATGGGAAA 57.114 33.333 0.00 0.00 0.00 3.13
5787 6889 6.885952 TGTTTTCTGAATCGTATGGGAAAA 57.114 33.333 0.00 0.00 32.62 2.29
5788 6890 7.278461 TGTTTTCTGAATCGTATGGGAAAAA 57.722 32.000 0.00 0.00 35.46 1.94
5835 6945 2.404995 GGCTGCTGACCAGATGCAC 61.405 63.158 0.00 0.00 44.64 4.57
5838 6948 0.036671 CTGCTGACCAGATGCACAGA 60.037 55.000 4.08 0.00 44.64 3.41
5958 7070 7.661536 ATCTGCCTGTGTATTCTCTTTACTA 57.338 36.000 0.00 0.00 0.00 1.82
5959 7071 7.661536 TCTGCCTGTGTATTCTCTTTACTAT 57.338 36.000 0.00 0.00 0.00 2.12
5967 7079 7.601130 TGTGTATTCTCTTTACTATGCGTGTTT 59.399 33.333 0.00 0.00 0.00 2.83
6128 7243 6.038356 AGAGTTTTCTTGACTGCAACATTTG 58.962 36.000 0.00 0.00 0.00 2.32
6180 7297 2.884639 GACTTGTTGGCTGGTTGTACAT 59.115 45.455 0.00 0.00 0.00 2.29
6268 7386 2.592102 TGCTTTCAGGCCTTTGAGAT 57.408 45.000 0.00 0.00 0.00 2.75
6498 7763 2.034879 CAGCGAAGGTTGCCATCGT 61.035 57.895 13.12 0.00 44.99 3.73
6520 7785 4.275936 GTGCCACACAGTGAAATTCTTACT 59.724 41.667 7.81 0.00 35.23 2.24
6528 7793 7.880195 ACACAGTGAAATTCTTACTGCTTAGAT 59.120 33.333 7.81 0.00 44.22 1.98
6539 7804 0.687757 TGCTTAGATGAGGGCTCCGT 60.688 55.000 0.00 0.00 0.00 4.69
6564 7829 1.269883 TGTTCAACCGTCGTGTGCTAT 60.270 47.619 0.00 0.00 0.00 2.97
6572 7837 2.540515 CGTCGTGTGCTATCAGGAAAT 58.459 47.619 0.00 0.00 34.73 2.17
6589 7854 4.828072 GAAATGGTTCCTCTCCACTAGT 57.172 45.455 0.00 0.00 37.81 2.57
6744 8010 2.706190 AGAGAAAGTTGTGTGGCTACCT 59.294 45.455 0.00 0.00 0.00 3.08
6745 8011 3.901844 AGAGAAAGTTGTGTGGCTACCTA 59.098 43.478 0.00 0.00 0.00 3.08
6746 8012 3.995048 GAGAAAGTTGTGTGGCTACCTAC 59.005 47.826 0.00 0.00 0.00 3.18
6747 8013 2.853235 AAGTTGTGTGGCTACCTACC 57.147 50.000 0.00 0.00 0.00 3.18
6787 8053 1.713830 GCGTAGTCATTTCGGGTGC 59.286 57.895 0.00 0.00 0.00 5.01
6870 8153 2.919229 CGCTGTAAGTAGTAACCGTTGG 59.081 50.000 0.00 0.00 35.30 3.77
6872 8155 4.559153 GCTGTAAGTAGTAACCGTTGGAA 58.441 43.478 0.00 0.00 35.30 3.53
6873 8156 4.990426 GCTGTAAGTAGTAACCGTTGGAAA 59.010 41.667 0.00 0.00 35.30 3.13
6874 8157 5.466393 GCTGTAAGTAGTAACCGTTGGAAAA 59.534 40.000 0.00 0.00 35.30 2.29
6875 8158 6.148315 GCTGTAAGTAGTAACCGTTGGAAAAT 59.852 38.462 0.00 0.00 35.30 1.82
6876 8159 7.622880 GCTGTAAGTAGTAACCGTTGGAAAATC 60.623 40.741 0.00 0.00 35.30 2.17
6878 8161 4.582869 AGTAGTAACCGTTGGAAAATCCC 58.417 43.478 0.00 0.00 35.03 3.85
6879 8162 2.799017 AGTAACCGTTGGAAAATCCCC 58.201 47.619 0.00 0.00 35.03 4.81
6880 8163 2.108601 AGTAACCGTTGGAAAATCCCCA 59.891 45.455 0.00 0.00 35.03 4.96
6882 8165 0.891904 ACCGTTGGAAAATCCCCACG 60.892 55.000 9.94 9.94 40.16 4.94
6883 8166 1.211709 CGTTGGAAAATCCCCACGC 59.788 57.895 5.58 0.00 36.05 5.34
6884 8167 1.211709 GTTGGAAAATCCCCACGCG 59.788 57.895 3.53 3.53 35.03 6.01
6963 8255 0.251742 CCCAGCAAATCTTCACCCCA 60.252 55.000 0.00 0.00 0.00 4.96
6976 8268 2.348998 CCCCAGTCGCAGCTTTCT 59.651 61.111 0.00 0.00 0.00 2.52
6983 8275 2.670934 CGCAGCTTTCTGGTGGCT 60.671 61.111 0.00 0.00 43.78 4.75
6998 8290 4.547859 GCTGATGCCGATTCCAGT 57.452 55.556 0.00 0.00 0.00 4.00
7001 8293 2.013563 GCTGATGCCGATTCCAGTTCA 61.014 52.381 0.00 0.00 0.00 3.18
7015 8307 2.360801 CCAGTTCATTGAAACCACGGTT 59.639 45.455 0.00 0.00 40.45 4.44
7025 8317 2.507339 AACCACGGTTGCATCTTTTG 57.493 45.000 0.00 0.00 36.91 2.44
7026 8318 1.686355 ACCACGGTTGCATCTTTTGA 58.314 45.000 0.00 0.00 0.00 2.69
7027 8319 2.238521 ACCACGGTTGCATCTTTTGAT 58.761 42.857 0.00 0.00 40.34 2.57
7028 8320 2.627699 ACCACGGTTGCATCTTTTGATT 59.372 40.909 0.00 0.00 36.97 2.57
7029 8321 2.988493 CCACGGTTGCATCTTTTGATTG 59.012 45.455 0.00 0.00 36.97 2.67
7030 8322 2.409378 CACGGTTGCATCTTTTGATTGC 59.591 45.455 0.00 0.00 36.97 3.56
7031 8323 1.994779 CGGTTGCATCTTTTGATTGCC 59.005 47.619 0.00 0.00 36.97 4.52
7032 8324 1.994779 GGTTGCATCTTTTGATTGCCG 59.005 47.619 0.00 0.00 36.97 5.69
7033 8325 2.352617 GGTTGCATCTTTTGATTGCCGA 60.353 45.455 0.00 0.00 36.97 5.54
7034 8326 3.514645 GTTGCATCTTTTGATTGCCGAT 58.485 40.909 0.00 0.00 36.97 4.18
7035 8327 3.872511 TGCATCTTTTGATTGCCGATT 57.127 38.095 0.00 0.00 36.97 3.34
7036 8328 3.513662 TGCATCTTTTGATTGCCGATTG 58.486 40.909 0.00 0.00 36.97 2.67
7037 8329 2.283351 GCATCTTTTGATTGCCGATTGC 59.717 45.455 0.00 0.00 36.97 3.56
7046 8338 2.202570 GCCGATTGCAGCAGCTTG 60.203 61.111 1.76 0.00 42.74 4.01
7047 8339 2.986306 GCCGATTGCAGCAGCTTGT 61.986 57.895 1.76 0.00 42.74 3.16
7048 8340 1.154093 CCGATTGCAGCAGCTTGTG 60.154 57.895 1.76 0.00 42.74 3.33
7049 8341 1.154093 CGATTGCAGCAGCTTGTGG 60.154 57.895 1.76 0.00 42.74 4.17
7050 8342 1.445582 GATTGCAGCAGCTTGTGGC 60.446 57.895 1.76 0.00 42.74 5.01
7051 8343 2.830704 GATTGCAGCAGCTTGTGGCC 62.831 60.000 1.76 0.00 43.05 5.36
7054 8346 3.730761 CAGCAGCTTGTGGCCGTC 61.731 66.667 0.00 0.00 43.05 4.79
7057 8349 3.414700 CAGCTTGTGGCCGTCGTC 61.415 66.667 0.00 0.00 43.05 4.20
7058 8350 4.681978 AGCTTGTGGCCGTCGTCC 62.682 66.667 0.00 0.00 43.05 4.79
7060 8352 4.308458 CTTGTGGCCGTCGTCCCA 62.308 66.667 0.00 0.00 0.00 4.37
7061 8353 4.308458 TTGTGGCCGTCGTCCCAG 62.308 66.667 0.00 0.00 0.00 4.45
7066 8358 4.148825 GCCGTCGTCCCAGCATCT 62.149 66.667 0.00 0.00 0.00 2.90
7067 8359 2.579201 CCGTCGTCCCAGCATCTT 59.421 61.111 0.00 0.00 0.00 2.40
7068 8360 1.079127 CCGTCGTCCCAGCATCTTT 60.079 57.895 0.00 0.00 0.00 2.52
7069 8361 0.673644 CCGTCGTCCCAGCATCTTTT 60.674 55.000 0.00 0.00 0.00 2.27
7120 8413 2.803155 TTCCAGCATCGACAGGTGCC 62.803 60.000 12.07 0.00 42.20 5.01
7127 8420 1.537814 ATCGACAGGTGCCGGTTGTA 61.538 55.000 1.90 0.00 0.00 2.41
7151 8444 1.070786 ACGGTGTTTGGATGCGTCT 59.929 52.632 5.77 0.00 0.00 4.18
7152 8445 0.534203 ACGGTGTTTGGATGCGTCTT 60.534 50.000 5.77 0.00 0.00 3.01
7153 8446 0.165944 CGGTGTTTGGATGCGTCTTC 59.834 55.000 5.77 0.00 0.00 2.87
7154 8447 1.523758 GGTGTTTGGATGCGTCTTCT 58.476 50.000 5.77 0.00 0.00 2.85
7155 8448 1.464997 GGTGTTTGGATGCGTCTTCTC 59.535 52.381 5.77 0.00 0.00 2.87
7156 8449 1.464997 GTGTTTGGATGCGTCTTCTCC 59.535 52.381 5.77 0.00 0.00 3.71
7157 8450 1.071542 TGTTTGGATGCGTCTTCTCCA 59.928 47.619 5.77 0.00 37.29 3.86
7158 8451 1.734465 GTTTGGATGCGTCTTCTCCAG 59.266 52.381 5.77 0.00 40.06 3.86
7159 8452 0.391661 TTGGATGCGTCTTCTCCAGC 60.392 55.000 5.77 0.00 40.06 4.85
7160 8453 1.219124 GGATGCGTCTTCTCCAGCA 59.781 57.895 5.77 0.00 44.13 4.41
7162 8455 3.376218 ATGCGTCTTCTCCAGCATC 57.624 52.632 0.00 0.00 45.97 3.91
7163 8456 0.529337 ATGCGTCTTCTCCAGCATCG 60.529 55.000 0.00 0.00 45.97 3.84
7164 8457 1.139734 GCGTCTTCTCCAGCATCGA 59.860 57.895 0.00 0.00 0.00 3.59
7165 8458 0.249238 GCGTCTTCTCCAGCATCGAT 60.249 55.000 0.00 0.00 0.00 3.59
7166 8459 1.485397 CGTCTTCTCCAGCATCGATG 58.515 55.000 21.27 21.27 0.00 3.84
7167 8460 1.863267 GTCTTCTCCAGCATCGATGG 58.137 55.000 26.00 12.35 40.92 3.51
7168 8461 0.105593 TCTTCTCCAGCATCGATGGC 59.894 55.000 26.00 17.68 39.19 4.40
7169 8462 0.106335 CTTCTCCAGCATCGATGGCT 59.894 55.000 26.00 19.51 39.19 4.75
7170 8463 0.105593 TTCTCCAGCATCGATGGCTC 59.894 55.000 26.00 10.25 39.19 4.70
7171 8464 1.664017 CTCCAGCATCGATGGCTCG 60.664 63.158 26.00 15.69 46.41 5.03
7172 8465 2.664185 CCAGCATCGATGGCTCGG 60.664 66.667 26.00 19.65 45.10 4.63
7173 8466 3.344215 CAGCATCGATGGCTCGGC 61.344 66.667 26.00 11.09 45.10 5.54
7174 8467 4.957684 AGCATCGATGGCTCGGCG 62.958 66.667 26.00 0.00 45.10 6.46
7176 8469 2.586079 CATCGATGGCTCGGCGTT 60.586 61.111 17.96 0.00 45.10 4.84
7177 8470 2.173669 CATCGATGGCTCGGCGTTT 61.174 57.895 17.96 0.00 45.10 3.60
7178 8471 2.173669 ATCGATGGCTCGGCGTTTG 61.174 57.895 6.85 0.00 45.10 2.93
7179 8472 3.864686 CGATGGCTCGGCGTTTGG 61.865 66.667 6.85 0.00 41.27 3.28
7180 8473 2.435938 GATGGCTCGGCGTTTGGA 60.436 61.111 6.85 0.00 0.00 3.53
7181 8474 1.819632 GATGGCTCGGCGTTTGGAT 60.820 57.895 6.85 0.00 0.00 3.41
7182 8475 2.051804 GATGGCTCGGCGTTTGGATG 62.052 60.000 6.85 0.00 0.00 3.51
7183 8476 4.179579 GGCTCGGCGTTTGGATGC 62.180 66.667 6.85 1.40 37.06 3.91
7184 8477 4.520846 GCTCGGCGTTTGGATGCG 62.521 66.667 6.85 0.00 38.73 4.73
7185 8478 3.118454 CTCGGCGTTTGGATGCGT 61.118 61.111 6.85 0.00 38.73 5.24
7186 8479 3.083600 CTCGGCGTTTGGATGCGTC 62.084 63.158 6.85 0.00 38.73 5.19
7213 8506 9.862149 TTTTTCCTATTTAGTTCTTCTCCAAGT 57.138 29.630 0.00 0.00 0.00 3.16
7227 8520 5.179045 TCTCCAAGTTAATCGTACCGATC 57.821 43.478 0.00 0.00 46.30 3.69
7234 8527 4.161001 AGTTAATCGTACCGATCTTTGGGT 59.839 41.667 0.00 0.00 46.30 4.51
7235 8528 2.596904 ATCGTACCGATCTTTGGGTG 57.403 50.000 0.66 0.00 43.45 4.61
7236 8529 1.259609 TCGTACCGATCTTTGGGTGT 58.740 50.000 0.66 0.00 35.33 4.16
7253 8546 1.866601 GTGTTGCACAAGAATTTGGCC 59.133 47.619 0.00 0.00 38.66 5.36
7265 8558 3.829601 AGAATTTGGCCCGTGTTTGAATA 59.170 39.130 0.00 0.00 0.00 1.75
7266 8559 4.282195 AGAATTTGGCCCGTGTTTGAATAA 59.718 37.500 0.00 0.00 0.00 1.40
7273 8566 3.862642 GCCCGTGTTTGAATAATTGCCAA 60.863 43.478 0.00 0.00 0.00 4.52
7277 8570 5.107530 CCGTGTTTGAATAATTGCCAAACTG 60.108 40.000 21.55 16.71 45.71 3.16
7292 8585 1.484038 AACTGTTGTGCCATTGTGGT 58.516 45.000 0.00 0.00 40.46 4.16
7293 8586 1.484038 ACTGTTGTGCCATTGTGGTT 58.516 45.000 0.00 0.00 40.46 3.67
7318 8611 1.139256 GCCTACTTTCTGGCTACTCCC 59.861 57.143 0.00 0.00 45.26 4.30
7329 8622 5.525484 TCTGGCTACTCCCTAGTCAAAATA 58.475 41.667 0.00 0.00 36.61 1.40
7341 8634 7.121168 TCCCTAGTCAAAATATGAGCAACAAAG 59.879 37.037 0.00 0.00 39.19 2.77
7350 8643 0.102844 GAGCAACAAAGCCTTGCACA 59.897 50.000 5.96 0.00 45.48 4.57
7383 8676 8.650143 TTGGTAGGCTTTTATCAGATTTTCTT 57.350 30.769 0.00 0.00 0.00 2.52
7457 8750 1.257743 TGGAAGCTCTGCTACGACTT 58.742 50.000 0.00 0.00 38.25 3.01
7458 8751 1.618837 TGGAAGCTCTGCTACGACTTT 59.381 47.619 0.00 0.00 38.25 2.66
7461 8759 3.119424 GGAAGCTCTGCTACGACTTTACT 60.119 47.826 0.00 0.00 38.25 2.24
7474 8772 6.328641 ACGACTTTACTAGCTCTTTTCTCA 57.671 37.500 0.00 0.00 0.00 3.27
7487 8785 5.626955 GCTCTTTTCTCATACAAACACAAGC 59.373 40.000 0.00 0.00 0.00 4.01
7515 8813 3.762407 ATATGCATGCCGGTACACTAA 57.238 42.857 16.68 0.00 0.00 2.24
7516 8814 1.953559 ATGCATGCCGGTACACTAAG 58.046 50.000 16.68 0.00 0.00 2.18
7517 8815 0.107897 TGCATGCCGGTACACTAAGG 60.108 55.000 16.68 0.00 0.00 2.69
7518 8816 0.814010 GCATGCCGGTACACTAAGGG 60.814 60.000 6.36 0.00 0.00 3.95
7519 8817 0.814010 CATGCCGGTACACTAAGGGC 60.814 60.000 1.90 0.00 44.00 5.19
7520 8818 2.983791 GCCGGTACACTAAGGGCA 59.016 61.111 1.90 0.00 43.23 5.36
7521 8819 1.525442 GCCGGTACACTAAGGGCAT 59.475 57.895 1.90 0.00 43.23 4.40
7522 8820 0.814010 GCCGGTACACTAAGGGCATG 60.814 60.000 1.90 0.00 43.23 4.06
7523 8821 0.539986 CCGGTACACTAAGGGCATGT 59.460 55.000 0.00 0.00 0.00 3.21
7524 8822 1.065709 CCGGTACACTAAGGGCATGTT 60.066 52.381 0.00 0.00 0.00 2.71
7525 8823 2.617021 CCGGTACACTAAGGGCATGTTT 60.617 50.000 0.00 0.00 0.00 2.83
7526 8824 2.418628 CGGTACACTAAGGGCATGTTTG 59.581 50.000 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 165 4.954970 CTTGCCACCACTGCCGGT 62.955 66.667 1.90 0.00 41.07 5.28
172 173 2.277591 GCAATGCTCCTTGCCACCA 61.278 57.895 0.00 0.00 44.56 4.17
229 230 3.129462 TCCTTCAACAGCAGAGTAGATCG 59.871 47.826 0.00 0.00 0.00 3.69
242 243 0.322816 GCAGCATCCCTCCTTCAACA 60.323 55.000 0.00 0.00 0.00 3.33
273 274 4.274147 TCATGACCCTAGTCTTCTCTGAC 58.726 47.826 0.00 0.00 43.91 3.51
382 391 9.707957 CCTATGACCTAATTCTACTATCCTCAT 57.292 37.037 0.00 0.00 0.00 2.90
438 455 0.676466 TATGCACTTCCTTGTGGCCG 60.676 55.000 0.00 0.00 38.31 6.13
529 950 4.329528 CAGACATAGAAGAAACAGAGCAGC 59.670 45.833 0.00 0.00 0.00 5.25
626 1061 1.303799 GCTGGACTAGTCGACGTGGA 61.304 60.000 16.56 0.00 0.00 4.02
676 1111 1.263356 CCGTTCCAGGGTTGAGACTA 58.737 55.000 0.00 0.00 0.00 2.59
695 1130 0.167689 AGGTTTACGAGTCGACGAGC 59.832 55.000 21.50 12.88 37.03 5.03
775 1210 3.119388 ACACATAACAAGCATGCACCATC 60.119 43.478 21.98 0.00 0.00 3.51
800 1235 6.821160 TCGTAATGAATGCCAAAAGATCACTA 59.179 34.615 0.00 0.00 0.00 2.74
925 1360 9.877178 AGACTTGAAGGAACAATAAGTATACAG 57.123 33.333 5.50 0.00 32.23 2.74
983 1420 4.197750 CTCCATGGATCCTGTTCTTTGAG 58.802 47.826 16.63 6.04 0.00 3.02
1454 1894 6.436261 CAGAATAGCATTTTCTCGCATGAAT 58.564 36.000 0.00 0.00 31.11 2.57
1464 1904 7.334421 TCAAGTGTCTACCAGAATAGCATTTTC 59.666 37.037 0.00 0.00 0.00 2.29
1561 2001 8.291740 AGGCAAAAGCATTCATTCATTAAAAAC 58.708 29.630 0.00 0.00 0.00 2.43
1570 2014 4.992951 ACAGAAAGGCAAAAGCATTCATTC 59.007 37.500 0.00 0.00 0.00 2.67
1571 2015 4.964593 ACAGAAAGGCAAAAGCATTCATT 58.035 34.783 0.00 0.00 0.00 2.57
1572 2016 4.612264 ACAGAAAGGCAAAAGCATTCAT 57.388 36.364 0.00 0.00 0.00 2.57
1573 2017 4.405116 AACAGAAAGGCAAAAGCATTCA 57.595 36.364 0.00 0.00 0.00 2.57
1752 2196 5.221945 TGTCCACCATACTTCACAATAACCA 60.222 40.000 0.00 0.00 0.00 3.67
1949 2393 4.420168 ACACGAAAACCATTGACAACAAG 58.580 39.130 0.00 0.00 39.46 3.16
1950 2394 4.156922 AGACACGAAAACCATTGACAACAA 59.843 37.500 0.00 0.00 40.42 2.83
1952 2396 4.287238 AGACACGAAAACCATTGACAAC 57.713 40.909 0.00 0.00 0.00 3.32
2144 2603 2.036862 ACACGTTAAGGAGGTCAGGAAC 59.963 50.000 1.43 0.00 0.00 3.62
2176 2635 3.904800 ACCAATACACACATGATCCGA 57.095 42.857 0.00 0.00 0.00 4.55
2257 3306 7.780008 AGCGCATAGTACATGTAAACAAATA 57.220 32.000 11.47 0.00 0.00 1.40
2325 3374 5.975693 AGTAAATGCCCGAGAAAAATGAA 57.024 34.783 0.00 0.00 0.00 2.57
3377 4433 7.164826 GCAAGAACAAAGATAAATACTCATGCG 59.835 37.037 0.00 0.00 0.00 4.73
3405 4462 7.147915 ACAGTGCCGAATGGATAATGTAAAAAT 60.148 33.333 0.00 0.00 37.49 1.82
3505 4562 5.129634 TCAGCTTGATTACAAAGAACACCA 58.870 37.500 0.00 0.00 35.49 4.17
3677 4734 3.626930 AGTAAAGACCACAAAACAGGCA 58.373 40.909 0.00 0.00 0.00 4.75
4043 5128 1.135199 CATCATGTGGCTTGGCTGTTC 60.135 52.381 0.00 0.00 0.00 3.18
4066 5151 9.360093 GTACTAATAGGTGCATGCTAGATTTAG 57.640 37.037 20.33 19.76 0.00 1.85
4072 5157 6.015856 AGTCTGTACTAATAGGTGCATGCTAG 60.016 42.308 20.33 13.05 32.84 3.42
4092 5177 7.433680 ACAACCAAATAAAAAGGCTAAGTCTG 58.566 34.615 0.00 0.00 0.00 3.51
4341 5433 4.330250 AGAAGAATGTGTATGCAGCAAGT 58.670 39.130 0.00 0.00 0.00 3.16
4534 5634 1.818642 GCTCCTTGCATGAGTTGAGT 58.181 50.000 13.48 0.00 42.31 3.41
4628 5729 2.093500 ACATCTCGCATCAACCAGCTAA 60.093 45.455 0.00 0.00 0.00 3.09
4866 5968 6.515272 TCAGGATGGTTTCTTATTTGCTTC 57.485 37.500 0.00 0.00 36.16 3.86
5101 6203 5.106157 GCAGCTGACACCAACACTTAATAAT 60.106 40.000 20.43 0.00 0.00 1.28
5201 6303 8.635328 TCTTAATGCGTATACTAACAGGAATGA 58.365 33.333 0.56 0.00 0.00 2.57
5370 6472 0.471211 ACTGGTCGACCCTCTTTGGA 60.471 55.000 31.19 9.47 38.35 3.53
5617 6719 7.526608 CATGAAATCATTGCAGCAGAAAATTT 58.473 30.769 0.00 1.28 33.61 1.82
5710 6812 1.523758 ATGCCAGTTTTCTCACGTCC 58.476 50.000 0.00 0.00 0.00 4.79
5733 6835 5.597594 TGTGCTTAATGGATGGCAATGAATA 59.402 36.000 0.00 0.00 36.43 1.75
5750 6852 6.691754 TCAGAAAACAAATCAGTGTGCTTA 57.308 33.333 0.00 0.00 0.00 3.09
5751 6853 5.581126 TCAGAAAACAAATCAGTGTGCTT 57.419 34.783 0.00 0.00 0.00 3.91
5752 6854 5.581126 TTCAGAAAACAAATCAGTGTGCT 57.419 34.783 0.00 0.00 0.00 4.40
5753 6855 5.116074 CGATTCAGAAAACAAATCAGTGTGC 59.884 40.000 0.00 0.00 31.25 4.57
5754 6856 6.201517 ACGATTCAGAAAACAAATCAGTGTG 58.798 36.000 0.00 0.00 31.25 3.82
5755 6857 6.377327 ACGATTCAGAAAACAAATCAGTGT 57.623 33.333 0.00 0.00 31.25 3.55
5756 6858 7.482743 CCATACGATTCAGAAAACAAATCAGTG 59.517 37.037 0.00 0.00 31.25 3.66
5757 6859 7.362056 CCCATACGATTCAGAAAACAAATCAGT 60.362 37.037 0.00 0.00 31.25 3.41
5758 6860 6.968904 CCCATACGATTCAGAAAACAAATCAG 59.031 38.462 0.00 0.00 31.25 2.90
5759 6861 6.657117 TCCCATACGATTCAGAAAACAAATCA 59.343 34.615 0.00 0.00 31.25 2.57
5760 6862 7.083875 TCCCATACGATTCAGAAAACAAATC 57.916 36.000 0.00 0.00 0.00 2.17
5761 6863 7.461182 TTCCCATACGATTCAGAAAACAAAT 57.539 32.000 0.00 0.00 0.00 2.32
5762 6864 6.885952 TTCCCATACGATTCAGAAAACAAA 57.114 33.333 0.00 0.00 0.00 2.83
5763 6865 6.885952 TTTCCCATACGATTCAGAAAACAA 57.114 33.333 0.00 0.00 0.00 2.83
5764 6866 6.885952 TTTTCCCATACGATTCAGAAAACA 57.114 33.333 0.00 0.00 30.55 2.83
5813 6923 1.250328 CATCTGGTCAGCAGCCAAAA 58.750 50.000 0.00 0.00 35.32 2.44
5814 6924 1.246056 GCATCTGGTCAGCAGCCAAA 61.246 55.000 0.00 0.00 35.32 3.28
5815 6925 1.676635 GCATCTGGTCAGCAGCCAA 60.677 57.895 0.00 0.00 35.32 4.52
5816 6926 2.045634 GCATCTGGTCAGCAGCCA 60.046 61.111 0.00 0.00 34.42 4.75
5835 6945 1.069636 GGAAGAACAAACGCTGCTCTG 60.070 52.381 0.00 0.00 30.65 3.35
5838 6948 1.065551 GTTGGAAGAACAAACGCTGCT 59.934 47.619 0.00 0.00 31.17 4.24
5958 7070 5.384063 TGTCCAAATTATGAAACACGCAT 57.616 34.783 0.00 0.00 0.00 4.73
5959 7071 4.837896 TGTCCAAATTATGAAACACGCA 57.162 36.364 0.00 0.00 0.00 5.24
5967 7079 8.825745 GCTTTCAAAAAGTTGTCCAAATTATGA 58.174 29.630 1.78 0.13 36.07 2.15
6180 7297 9.679661 TTTGATCTGATTGTATTAGCAGGTAAA 57.320 29.630 0.00 0.00 0.00 2.01
6494 7759 1.896220 ATTTCACTGTGTGGCACGAT 58.104 45.000 13.77 0.00 37.14 3.73
6498 7763 4.275689 CAGTAAGAATTTCACTGTGTGGCA 59.724 41.667 7.79 0.00 35.91 4.92
6520 7785 0.687757 ACGGAGCCCTCATCTAAGCA 60.688 55.000 0.00 0.00 0.00 3.91
6528 7793 1.407656 AACAAGTCACGGAGCCCTCA 61.408 55.000 0.00 0.00 0.00 3.86
6539 7804 1.282817 CACGACGGTTGAACAAGTCA 58.717 50.000 18.33 0.00 33.56 3.41
6572 7837 3.271225 TGGATACTAGTGGAGAGGAACCA 59.729 47.826 5.39 0.00 33.99 3.67
6744 8010 1.758280 CCCAGTGCCAATACTACGGTA 59.242 52.381 0.00 0.00 0.00 4.02
6745 8011 0.539986 CCCAGTGCCAATACTACGGT 59.460 55.000 0.00 0.00 0.00 4.83
6746 8012 0.179056 CCCCAGTGCCAATACTACGG 60.179 60.000 0.00 0.00 0.00 4.02
6747 8013 0.814010 GCCCCAGTGCCAATACTACG 60.814 60.000 0.00 0.00 0.00 3.51
6787 8053 2.684881 CCTAGCAGTGCCCAACTAAATG 59.315 50.000 12.58 0.00 36.83 2.32
6849 8115 2.919229 CCAACGGTTACTACTTACAGCG 59.081 50.000 0.00 0.00 36.25 5.18
6870 8153 2.782615 CGACGCGTGGGGATTTTC 59.217 61.111 20.70 0.00 0.00 2.29
6872 8155 3.894547 AAGCGACGCGTGGGGATTT 62.895 57.895 20.70 0.00 0.00 2.17
6873 8156 4.388499 AAGCGACGCGTGGGGATT 62.388 61.111 20.70 7.98 0.00 3.01
6878 8161 2.127758 GTTTCAAGCGACGCGTGG 60.128 61.111 30.37 18.91 38.48 4.94
6879 8162 0.587737 TTTGTTTCAAGCGACGCGTG 60.588 50.000 26.64 26.64 39.24 5.34
6880 8163 0.097325 TTTTGTTTCAAGCGACGCGT 59.903 45.000 13.85 13.85 0.00 6.01
6903 8195 4.899239 GAGCGATGAGGCGTGGGG 62.899 72.222 0.00 0.00 38.18 4.96
6963 8255 1.302033 CCACCAGAAAGCTGCGACT 60.302 57.895 0.00 0.00 40.91 4.18
6983 8275 2.684374 CAATGAACTGGAATCGGCATCA 59.316 45.455 0.00 0.00 0.00 3.07
6997 8289 2.124122 GCAACCGTGGTTTCAATGAAC 58.876 47.619 0.44 0.00 36.00 3.18
6998 8290 1.751351 TGCAACCGTGGTTTCAATGAA 59.249 42.857 0.44 0.00 36.00 2.57
7001 8293 2.238521 AGATGCAACCGTGGTTTCAAT 58.761 42.857 8.14 0.00 35.21 2.57
7015 8307 3.513662 CAATCGGCAATCAAAAGATGCA 58.486 40.909 0.00 0.00 41.80 3.96
7029 8321 2.202570 CAAGCTGCTGCAATCGGC 60.203 61.111 18.42 10.54 44.80 5.54
7030 8322 1.154093 CACAAGCTGCTGCAATCGG 60.154 57.895 18.42 4.62 42.74 4.18
7031 8323 1.154093 CCACAAGCTGCTGCAATCG 60.154 57.895 18.42 5.30 42.74 3.34
7032 8324 1.445582 GCCACAAGCTGCTGCAATC 60.446 57.895 18.42 0.00 42.74 2.67
7033 8325 2.654877 GCCACAAGCTGCTGCAAT 59.345 55.556 18.42 3.15 42.74 3.56
7034 8326 3.608662 GGCCACAAGCTGCTGCAA 61.609 61.111 18.42 0.00 43.05 4.08
7041 8333 4.681978 GGACGACGGCCACAAGCT 62.682 66.667 16.92 0.00 43.05 3.74
7043 8335 4.308458 TGGGACGACGGCCACAAG 62.308 66.667 23.92 0.00 0.00 3.16
7044 8336 4.308458 CTGGGACGACGGCCACAA 62.308 66.667 23.92 5.36 0.00 3.33
7049 8341 3.665675 AAGATGCTGGGACGACGGC 62.666 63.158 0.00 0.00 43.06 5.68
7050 8342 0.673644 AAAAGATGCTGGGACGACGG 60.674 55.000 0.00 0.00 0.00 4.79
7051 8343 0.443869 CAAAAGATGCTGGGACGACG 59.556 55.000 0.00 0.00 0.00 5.12
7052 8344 1.808411 TCAAAAGATGCTGGGACGAC 58.192 50.000 0.00 0.00 0.00 4.34
7053 8345 2.749076 CAATCAAAAGATGCTGGGACGA 59.251 45.455 0.00 0.00 0.00 4.20
7054 8346 2.733227 GCAATCAAAAGATGCTGGGACG 60.733 50.000 0.00 0.00 37.12 4.79
7055 8347 2.417787 GGCAATCAAAAGATGCTGGGAC 60.418 50.000 0.00 0.00 39.94 4.46
7056 8348 1.826720 GGCAATCAAAAGATGCTGGGA 59.173 47.619 0.00 0.00 39.94 4.37
7057 8349 1.470285 CGGCAATCAAAAGATGCTGGG 60.470 52.381 0.00 0.00 41.62 4.45
7058 8350 1.917273 CGGCAATCAAAAGATGCTGG 58.083 50.000 0.00 0.00 41.62 4.85
7059 8351 1.203052 ACCGGCAATCAAAAGATGCTG 59.797 47.619 0.00 0.00 44.23 4.41
7060 8352 1.549203 ACCGGCAATCAAAAGATGCT 58.451 45.000 0.00 0.00 39.94 3.79
7061 8353 1.994779 CAACCGGCAATCAAAAGATGC 59.005 47.619 0.00 0.00 39.33 3.91
7062 8354 1.994779 GCAACCGGCAATCAAAAGATG 59.005 47.619 0.00 0.00 43.97 2.90
7063 8355 2.368655 GCAACCGGCAATCAAAAGAT 57.631 45.000 0.00 0.00 43.97 2.40
7064 8356 3.883997 GCAACCGGCAATCAAAAGA 57.116 47.368 0.00 0.00 43.97 2.52
7110 8402 1.736645 CTACAACCGGCACCTGTCG 60.737 63.158 0.00 0.00 43.72 4.35
7120 8413 0.669318 ACACCGTGATGCTACAACCG 60.669 55.000 5.28 0.00 0.00 4.44
7127 8420 1.167851 CATCCAAACACCGTGATGCT 58.832 50.000 5.28 0.00 0.00 3.79
7151 8444 0.105593 GAGCCATCGATGCTGGAGAA 59.894 55.000 20.25 0.00 39.69 2.87
7152 8445 1.744639 GAGCCATCGATGCTGGAGA 59.255 57.895 20.25 0.00 39.69 3.71
7153 8446 4.357699 GAGCCATCGATGCTGGAG 57.642 61.111 20.25 7.05 39.69 3.86
7163 8456 1.819632 ATCCAAACGCCGAGCCATC 60.820 57.895 0.00 0.00 0.00 3.51
7164 8457 2.114670 CATCCAAACGCCGAGCCAT 61.115 57.895 0.00 0.00 0.00 4.40
7165 8458 2.745884 CATCCAAACGCCGAGCCA 60.746 61.111 0.00 0.00 0.00 4.75
7166 8459 4.179579 GCATCCAAACGCCGAGCC 62.180 66.667 0.00 0.00 0.00 4.70
7167 8460 4.520846 CGCATCCAAACGCCGAGC 62.521 66.667 0.00 0.00 0.00 5.03
7168 8461 3.083600 GACGCATCCAAACGCCGAG 62.084 63.158 0.00 0.00 0.00 4.63
7169 8462 3.115892 GACGCATCCAAACGCCGA 61.116 61.111 0.00 0.00 0.00 5.54
7170 8463 2.182614 AAAGACGCATCCAAACGCCG 62.183 55.000 0.00 0.00 0.00 6.46
7171 8464 0.039527 AAAAGACGCATCCAAACGCC 60.040 50.000 0.00 0.00 0.00 5.68
7172 8465 1.713932 GAAAAAGACGCATCCAAACGC 59.286 47.619 0.00 0.00 0.00 4.84
7173 8466 2.031157 AGGAAAAAGACGCATCCAAACG 60.031 45.455 0.00 0.00 34.30 3.60
7174 8467 3.643159 AGGAAAAAGACGCATCCAAAC 57.357 42.857 0.00 0.00 34.30 2.93
7175 8468 5.975693 AATAGGAAAAAGACGCATCCAAA 57.024 34.783 0.00 0.00 34.30 3.28
7176 8469 5.975693 AAATAGGAAAAAGACGCATCCAA 57.024 34.783 0.00 0.00 34.30 3.53
7177 8470 6.177610 ACTAAATAGGAAAAAGACGCATCCA 58.822 36.000 0.00 0.00 34.30 3.41
7178 8471 6.679327 ACTAAATAGGAAAAAGACGCATCC 57.321 37.500 0.00 0.00 0.00 3.51
7179 8472 7.975750 AGAACTAAATAGGAAAAAGACGCATC 58.024 34.615 0.00 0.00 0.00 3.91
7180 8473 7.923414 AGAACTAAATAGGAAAAAGACGCAT 57.077 32.000 0.00 0.00 0.00 4.73
7181 8474 7.660208 AGAAGAACTAAATAGGAAAAAGACGCA 59.340 33.333 0.00 0.00 0.00 5.24
7182 8475 8.030744 AGAAGAACTAAATAGGAAAAAGACGC 57.969 34.615 0.00 0.00 0.00 5.19
7183 8476 8.657729 GGAGAAGAACTAAATAGGAAAAAGACG 58.342 37.037 0.00 0.00 0.00 4.18
7184 8477 9.503399 TGGAGAAGAACTAAATAGGAAAAAGAC 57.497 33.333 0.00 0.00 0.00 3.01
7235 8528 1.511850 GGGCCAAATTCTTGTGCAAC 58.488 50.000 4.39 0.00 33.10 4.17
7236 8529 0.033228 CGGGCCAAATTCTTGTGCAA 59.967 50.000 4.39 0.00 33.10 4.08
7253 8546 5.262714 GTTTGGCAATTATTCAAACACGG 57.737 39.130 17.85 0.00 45.41 4.94
7265 8558 1.209019 TGGCACAACAGTTTGGCAATT 59.791 42.857 16.85 0.00 44.57 2.32
7266 8559 0.829333 TGGCACAACAGTTTGGCAAT 59.171 45.000 16.85 0.00 44.57 3.56
7315 8608 6.061022 TGTTGCTCATATTTTGACTAGGGA 57.939 37.500 0.00 0.00 0.00 4.20
7318 8611 6.749118 GGCTTTGTTGCTCATATTTTGACTAG 59.251 38.462 0.00 0.00 0.00 2.57
7329 8622 3.900446 GCAAGGCTTTGTTGCTCAT 57.100 47.368 10.54 0.00 45.67 2.90
7341 8634 3.727726 ACCAAAATTAACTGTGCAAGGC 58.272 40.909 0.00 0.00 0.00 4.35
7350 8643 9.528489 TCTGATAAAAGCCTACCAAAATTAACT 57.472 29.630 0.00 0.00 0.00 2.24
7383 8676 1.830587 ATGTCTGACGGCAAGCCTCA 61.831 55.000 9.73 10.55 0.00 3.86
7457 8750 9.204570 GTGTTTGTATGAGAAAAGAGCTAGTAA 57.795 33.333 0.00 0.00 0.00 2.24
7458 8751 8.364894 TGTGTTTGTATGAGAAAAGAGCTAGTA 58.635 33.333 0.00 0.00 0.00 1.82
7461 8759 7.307989 GCTTGTGTTTGTATGAGAAAAGAGCTA 60.308 37.037 0.00 0.00 0.00 3.32
7474 8772 7.628366 GCATATAGGTTGTGCTTGTGTTTGTAT 60.628 37.037 0.00 0.00 36.02 2.29
7487 8785 1.536766 CCGGCATGCATATAGGTTGTG 59.463 52.381 21.36 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.