Multiple sequence alignment - TraesCS2D01G427900

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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 TraesCS2D01G427900 chr2D 100.000 8834 0 0 1 8834 539889354 539880521 0.000000e+00 16314.0
1 TraesCS2D01G427900 chr2D 96.875 64 1 1 7016 7078 592583139 592583076 1.210000e-18 106.0
2 TraesCS2D01G427900 chr2D 95.122 41 2 0 2563 2603 3013689 3013729 2.060000e-06 65.8
3 TraesCS2D01G427900 chr2B 95.922 3801 92 22 2250 6005 644157120 644153338 0.000000e+00 6102.0
4 TraesCS2D01G427900 chr2B 98.518 1012 15 0 6004 7015 644153224 644152213 0.000000e+00 1786.0
5 TraesCS2D01G427900 chr2B 94.513 1057 45 4 871 1915 644158645 644157590 0.000000e+00 1618.0
6 TraesCS2D01G427900 chr2B 90.887 1218 60 20 7077 8272 644152220 644151032 0.000000e+00 1587.0
7 TraesCS2D01G427900 chr2B 87.663 843 74 18 4 833 644159477 644158652 0.000000e+00 953.0
8 TraesCS2D01G427900 chr2B 93.558 326 6 6 1912 2235 644157507 644157195 1.040000e-128 472.0
9 TraesCS2D01G427900 chr2A 95.194 3142 84 26 1914 5010 683522688 683519569 0.000000e+00 4903.0
10 TraesCS2D01G427900 chr2A 96.560 2006 63 5 5012 7015 683519453 683517452 0.000000e+00 3317.0
11 TraesCS2D01G427900 chr2A 89.993 1529 109 20 7077 8589 683517459 683515959 0.000000e+00 1936.0
12 TraesCS2D01G427900 chr2A 94.487 1179 42 13 757 1916 683523904 683522730 0.000000e+00 1796.0
13 TraesCS2D01G427900 chr2A 85.690 594 62 16 4 587 683524937 683524357 9.810000e-169 604.0
14 TraesCS2D01G427900 chr2A 93.243 148 10 0 8685 8832 683515956 683515809 1.490000e-52 219.0
15 TraesCS2D01G427900 chr2A 82.883 222 25 8 2385 2603 2699504 2699293 4.210000e-43 187.0
16 TraesCS2D01G427900 chr2A 100.000 44 0 0 3257 3300 683521385 683521342 2.040000e-11 82.4
17 TraesCS2D01G427900 chr3D 79.710 345 50 11 2277 2603 9618016 9618358 1.920000e-56 231.0
18 TraesCS2D01G427900 chr3D 84.821 112 15 2 2500 2610 2261532 2261422 2.610000e-20 111.0
19 TraesCS2D01G427900 chr3D 96.875 64 1 1 7016 7078 390098439 390098502 1.210000e-18 106.0
20 TraesCS2D01G427900 chr5D 96.875 64 1 1 7016 7078 398804776 398804713 1.210000e-18 106.0
21 TraesCS2D01G427900 chr5D 89.024 82 9 0 2526 2607 141446312 141446393 1.570000e-17 102.0
22 TraesCS2D01G427900 chr5D 100.000 32 0 0 8743 8774 462023844 462023875 9.580000e-05 60.2
23 TraesCS2D01G427900 chr4D 96.875 64 1 1 7016 7078 216324117 216324054 1.210000e-18 106.0
24 TraesCS2D01G427900 chr1D 96.875 64 1 1 7016 7078 116458953 116459016 1.210000e-18 106.0
25 TraesCS2D01G427900 chr1B 96.875 64 1 1 7016 7078 57684789 57684852 1.210000e-18 106.0
26 TraesCS2D01G427900 chr5B 94.203 69 2 2 7016 7082 593472635 593472567 4.360000e-18 104.0
27 TraesCS2D01G427900 chr5B 94.203 69 2 2 7016 7082 593556645 593556577 4.360000e-18 104.0
28 TraesCS2D01G427900 chr5B 100.000 32 0 0 8743 8774 568176651 568176682 9.580000e-05 60.2
29 TraesCS2D01G427900 chr1A 95.161 62 2 1 7018 7078 39151552 39151613 7.300000e-16 97.1
30 TraesCS2D01G427900 chr7A 95.000 40 2 0 2565 2604 79811525 79811564 7.400000e-06 63.9
31 TraesCS2D01G427900 chr5A 100.000 32 0 0 8743 8774 582100234 582100265 9.580000e-05 60.2


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 TraesCS2D01G427900 chr2D 539880521 539889354 8833 True 16314.000000 16314 100.000000 1 8834 1 chr2D.!!$R1 8833
1 TraesCS2D01G427900 chr2B 644151032 644159477 8445 True 2086.333333 6102 93.510167 4 8272 6 chr2B.!!$R1 8268
2 TraesCS2D01G427900 chr2A 683515809 683524937 9128 True 1836.771429 4903 93.595286 4 8832 7 chr2A.!!$R2 8828

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
849 1203 0.179000 CACATAGCCGCTCCCTTCTT 59.821 55.000 0.00 0.00 0.00 2.52 F
850 1204 0.466124 ACATAGCCGCTCCCTTCTTC 59.534 55.000 0.00 0.00 0.00 2.87 F
1446 1805 0.536460 TTCTCCCCGTGGTTGCTTTC 60.536 55.000 0.00 0.00 0.00 2.62 F
2273 2794 2.377628 TAGCCCGCTATTTCCCGCTG 62.378 60.000 0.00 0.00 0.00 5.18 F
2906 3447 0.807667 AATCGATGTCGCTCCTGTGC 60.808 55.000 0.00 0.00 39.60 4.57 F
3940 4487 2.306805 ACCTGGAAGATGTCAGAATGCA 59.693 45.455 0.00 0.00 34.07 3.96 F
5495 6193 1.808343 GATTGCACAGTCATGTCTGCA 59.192 47.619 18.24 10.66 37.65 4.41 F
6261 7078 3.370209 GGGTTCCTACTCGCCTTAATGTT 60.370 47.826 0.00 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 2882 2.105006 AGCTTCACACTATGCACCAG 57.895 50.000 0.00 0.0 0.00 4.00 R
2787 3328 3.814842 CACCTCACAAGCAATGAGTACAA 59.185 43.478 10.03 0.0 41.78 2.41 R
2906 3447 1.012086 CGGCATCAACATCTGGACAG 58.988 55.000 0.00 0.0 0.00 3.51 R
3940 4487 1.812571 GCCACTGGACAAATTGACGAT 59.187 47.619 0.00 0.0 0.00 3.73 R
4344 4898 1.752498 ACGGTGTAGACTTCACACACA 59.248 47.619 13.45 0.0 46.53 3.72 R
5638 6338 0.804364 CAAAGCGTGCTGGCTATCAA 59.196 50.000 0.00 0.0 43.93 2.57 R
6591 7408 0.246360 TGGTGAGTACAGGATGCACG 59.754 55.000 0.00 0.0 42.53 5.34 R
8077 8899 0.034767 TCGGACGTCATACCAGGAGT 60.035 55.000 18.91 0.0 0.00 3.85 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
26 27 6.926630 ATTTTCAGCCCTTATACAAACCAA 57.073 33.333 0.00 0.00 0.00 3.67
41 42 4.069304 CAAACCAATCAACCTTCGGACTA 58.931 43.478 0.00 0.00 0.00 2.59
65 66 1.951130 CATCTGCGTCGCGGCTATT 60.951 57.895 21.37 3.18 34.49 1.73
76 77 1.739929 CGGCTATTGTGGTGTCGCA 60.740 57.895 0.00 0.00 0.00 5.10
99 100 6.512741 GCAGTTTCCAATTTCTTCTGTACGAA 60.513 38.462 0.00 0.00 0.00 3.85
133 135 2.753055 TTCGACCATGGAATCAACGA 57.247 45.000 21.47 15.15 0.00 3.85
252 262 5.875359 GTCTCGTTCAAAGTCCATAGGAAAT 59.125 40.000 0.00 0.00 31.38 2.17
260 270 5.982890 AAGTCCATAGGAAATTGTTGTGG 57.017 39.130 0.00 0.00 31.38 4.17
323 333 1.807814 ATAGGAATCTCCAACGGGCT 58.192 50.000 0.00 0.00 39.61 5.19
338 348 1.482954 GGGCTACGACTAGAGGGTTT 58.517 55.000 0.00 0.00 0.00 3.27
499 509 2.403561 TCCCCTTTGTTTTCCTTTGGG 58.596 47.619 0.00 0.00 0.00 4.12
503 513 4.568804 CCCCTTTGTTTTCCTTTGGGTTTT 60.569 41.667 0.00 0.00 0.00 2.43
541 551 5.163673 TGCTTTCATTTTTGTTTCTTTGGCC 60.164 36.000 0.00 0.00 0.00 5.36
631 644 6.535274 ACACGTGAAACTTTTACCTGATAC 57.465 37.500 25.01 0.00 31.75 2.24
633 646 6.708949 ACACGTGAAACTTTTACCTGATACAT 59.291 34.615 25.01 0.00 31.75 2.29
636 649 7.227910 ACGTGAAACTTTTACCTGATACATGTT 59.772 33.333 2.30 0.00 31.75 2.71
641 654 7.435068 ACTTTTACCTGATACATGTTGACAC 57.565 36.000 2.30 0.00 0.00 3.67
663 676 7.976826 ACACTTTTCAAATACAAGTTGTACGA 58.023 30.769 17.79 11.73 35.42 3.43
664 677 7.906527 ACACTTTTCAAATACAAGTTGTACGAC 59.093 33.333 17.79 4.97 35.42 4.34
669 682 7.124347 TCAAATACAAGTTGTACGACCATTC 57.876 36.000 17.79 0.00 35.42 2.67
778 1118 8.832458 TCCATAAATAAAGTAAAAAGGAGGGG 57.168 34.615 0.00 0.00 0.00 4.79
810 1150 3.059099 TCAGCATGACGAGCCACA 58.941 55.556 0.00 0.00 42.56 4.17
848 1202 1.690219 CCACATAGCCGCTCCCTTCT 61.690 60.000 0.00 0.00 0.00 2.85
849 1203 0.179000 CACATAGCCGCTCCCTTCTT 59.821 55.000 0.00 0.00 0.00 2.52
850 1204 0.466124 ACATAGCCGCTCCCTTCTTC 59.534 55.000 0.00 0.00 0.00 2.87
851 1205 0.598680 CATAGCCGCTCCCTTCTTCG 60.599 60.000 0.00 0.00 0.00 3.79
852 1206 1.749334 ATAGCCGCTCCCTTCTTCGG 61.749 60.000 0.00 0.00 44.29 4.30
853 1207 2.849096 TAGCCGCTCCCTTCTTCGGA 62.849 60.000 0.00 0.00 44.23 4.55
861 1215 1.550976 TCCCTTCTTCGGAGAAAGAGC 59.449 52.381 7.73 0.00 45.90 4.09
862 1216 1.406205 CCCTTCTTCGGAGAAAGAGCC 60.406 57.143 7.73 0.00 45.90 4.70
863 1217 1.276421 CCTTCTTCGGAGAAAGAGCCA 59.724 52.381 7.73 0.00 45.90 4.75
864 1218 2.093235 CCTTCTTCGGAGAAAGAGCCAT 60.093 50.000 7.73 0.00 45.90 4.40
865 1219 3.604582 CTTCTTCGGAGAAAGAGCCATT 58.395 45.455 7.73 0.00 45.90 3.16
866 1220 2.977914 TCTTCGGAGAAAGAGCCATTG 58.022 47.619 0.00 0.00 45.90 2.82
867 1221 1.399791 CTTCGGAGAAAGAGCCATTGC 59.600 52.381 0.00 0.00 45.90 3.56
868 1222 0.740868 TCGGAGAAAGAGCCATTGCG 60.741 55.000 0.00 0.00 44.33 4.85
869 1223 1.431036 GGAGAAAGAGCCATTGCGC 59.569 57.895 0.00 0.00 44.33 6.09
1390 1748 4.077180 GGGACGGGGAGGAGGTCT 62.077 72.222 0.00 0.00 0.00 3.85
1446 1805 0.536460 TTCTCCCCGTGGTTGCTTTC 60.536 55.000 0.00 0.00 0.00 2.62
1505 1872 2.669240 GGTTCTCCCCGTTCCCTG 59.331 66.667 0.00 0.00 0.00 4.45
1526 1893 3.235200 GGTCACTAGGTCAGAGCCATAT 58.765 50.000 0.00 0.00 0.00 1.78
1548 1915 8.896744 CATATGTTTGAGAATCTACATTGGTGT 58.103 33.333 2.87 0.00 40.07 4.16
1855 2225 4.020485 CCTTCCCCTATATTTGTACGGAGG 60.020 50.000 0.00 0.00 0.00 4.30
1858 2228 5.714863 TCCCCTATATTTGTACGGAGGTTA 58.285 41.667 0.00 0.00 0.00 2.85
1879 2250 4.374843 AGGTTTTAAACGGTTCCACAAC 57.625 40.909 0.00 0.00 0.00 3.32
2008 2467 3.806625 GCATGAAAATGCACCACCTAT 57.193 42.857 5.83 0.00 46.25 2.57
2173 2632 8.780249 TCAAAGTTTTAAATATCCGGCTATAGC 58.220 33.333 16.78 16.78 41.14 2.97
2174 2633 8.784043 CAAAGTTTTAAATATCCGGCTATAGCT 58.216 33.333 23.53 7.05 41.70 3.32
2175 2634 8.919777 AAGTTTTAAATATCCGGCTATAGCTT 57.080 30.769 23.53 10.94 41.70 3.74
2176 2635 8.549338 AGTTTTAAATATCCGGCTATAGCTTC 57.451 34.615 23.53 7.74 41.70 3.86
2177 2636 7.331193 AGTTTTAAATATCCGGCTATAGCTTCG 59.669 37.037 23.53 18.50 41.70 3.79
2178 2637 2.873133 ATATCCGGCTATAGCTTCGC 57.127 50.000 23.53 6.66 41.70 4.70
2273 2794 2.377628 TAGCCCGCTATTTCCCGCTG 62.378 60.000 0.00 0.00 0.00 5.18
2300 2821 6.773976 CTAAATTTGGAGTCATTTAGCCCA 57.226 37.500 0.00 0.00 36.59 5.36
2459 2988 8.974408 TGTGTTTATGTCAAGTATATGCGATAC 58.026 33.333 0.00 1.25 0.00 2.24
2565 3102 3.906720 TTTAATAGCTTCTGGCCGAGT 57.093 42.857 0.00 0.00 43.05 4.18
2786 3327 9.822185 AGTTGAATTGAGAAAACTTTTATGCTT 57.178 25.926 0.00 0.00 28.57 3.91
2807 3348 5.437289 TTTTGTACTCATTGCTTGTGAGG 57.563 39.130 14.85 2.05 45.72 3.86
2906 3447 0.807667 AATCGATGTCGCTCCTGTGC 60.808 55.000 0.00 0.00 39.60 4.57
3705 4252 5.435041 TCCATTCCCATATCAAGTACCCTTT 59.565 40.000 0.00 0.00 0.00 3.11
3940 4487 2.306805 ACCTGGAAGATGTCAGAATGCA 59.693 45.455 0.00 0.00 34.07 3.96
4076 4630 6.575162 ACTTGCCCAGAATAGTTTACAAAG 57.425 37.500 0.00 0.00 0.00 2.77
4203 4757 9.836076 GAATTTATCGTTTTGCTAGTTTAAGGT 57.164 29.630 0.00 0.00 0.00 3.50
4324 4878 8.840833 TGCTTATTTACTGTTTCTGTATGACA 57.159 30.769 0.00 0.00 0.00 3.58
4325 4879 8.717821 TGCTTATTTACTGTTTCTGTATGACAC 58.282 33.333 0.00 0.00 0.00 3.67
4514 5085 4.202461 TGAGTAGTCAATCCCTGTGCTTTT 60.202 41.667 0.00 0.00 0.00 2.27
4984 5562 7.511268 AGACGATTCTCTAACTCTACAGGTAT 58.489 38.462 0.00 0.00 0.00 2.73
5078 5770 3.394674 TCAGCTTGTGGTGTTCGAATA 57.605 42.857 0.00 0.00 41.91 1.75
5126 5818 6.039382 GGGATGGCTAGACGTATGAAATTTTT 59.961 38.462 0.00 0.00 0.00 1.94
5180 5872 9.444600 ACGTGAATATCAAGTAAACACCTTTAT 57.555 29.630 0.00 0.00 37.33 1.40
5255 5947 9.565213 GTCAGAAATATTTTGAGGTGAGATTTG 57.435 33.333 1.43 0.00 0.00 2.32
5475 6173 2.472816 GTGACCAAACATTTGCCACAG 58.527 47.619 16.46 1.57 38.68 3.66
5495 6193 1.808343 GATTGCACAGTCATGTCTGCA 59.192 47.619 18.24 10.66 37.65 4.41
5638 6338 5.069251 TGGACGGACAATTGGTTAAATGTTT 59.931 36.000 10.83 0.00 0.00 2.83
5676 6378 7.021790 CGCTTTGGAGGAAGAAAATAGTAAAC 58.978 38.462 0.00 0.00 0.00 2.01
5744 6446 7.775053 AATCACTGTTGTGGTTATATTTGGT 57.225 32.000 0.00 0.00 44.83 3.67
5839 6541 7.117956 GGAAACAAGACCAATCTGTAGTCTAAC 59.882 40.741 0.00 0.00 39.92 2.34
6101 6918 3.476552 ACAATGAACTCGAAGGCAAGAA 58.523 40.909 0.00 0.00 0.00 2.52
6150 6967 3.552132 TTTGTGTACAGCTCTGTTGGA 57.448 42.857 7.92 0.00 41.83 3.53
6261 7078 3.370209 GGGTTCCTACTCGCCTTAATGTT 60.370 47.826 0.00 0.00 0.00 2.71
6591 7408 2.034221 GCTTCCACACCACCCTCC 59.966 66.667 0.00 0.00 0.00 4.30
6732 7549 2.622942 GTGCTTTGTGGTGGAGATGAAA 59.377 45.455 0.00 0.00 0.00 2.69
6849 7666 0.842030 TTGCTGGTCCAGATCCACCT 60.842 55.000 23.77 0.00 32.44 4.00
6981 7798 4.061596 GGCACAAGGTAAGAGCTATCATC 58.938 47.826 0.00 0.00 0.00 2.92
7010 7827 8.082242 GGTATTTTGTGCATATCCCTTATCAAC 58.918 37.037 0.00 0.00 0.00 3.18
7011 7828 7.902920 ATTTTGTGCATATCCCTTATCAACT 57.097 32.000 0.00 0.00 0.00 3.16
7012 7829 7.716799 TTTTGTGCATATCCCTTATCAACTT 57.283 32.000 0.00 0.00 0.00 2.66
7013 7830 8.815565 TTTTGTGCATATCCCTTATCAACTTA 57.184 30.769 0.00 0.00 0.00 2.24
7014 7831 8.450578 TTTGTGCATATCCCTTATCAACTTAG 57.549 34.615 0.00 0.00 0.00 2.18
7015 7832 7.136822 TGTGCATATCCCTTATCAACTTAGT 57.863 36.000 0.00 0.00 0.00 2.24
7016 7833 7.217200 TGTGCATATCCCTTATCAACTTAGTC 58.783 38.462 0.00 0.00 0.00 2.59
7017 7834 7.071196 TGTGCATATCCCTTATCAACTTAGTCT 59.929 37.037 0.00 0.00 0.00 3.24
7018 7835 7.600752 GTGCATATCCCTTATCAACTTAGTCTC 59.399 40.741 0.00 0.00 0.00 3.36
7019 7836 6.809196 GCATATCCCTTATCAACTTAGTCTCG 59.191 42.308 0.00 0.00 0.00 4.04
7020 7837 7.309255 GCATATCCCTTATCAACTTAGTCTCGA 60.309 40.741 0.00 0.00 0.00 4.04
7021 7838 8.577296 CATATCCCTTATCAACTTAGTCTCGAA 58.423 37.037 0.00 0.00 0.00 3.71
7022 7839 7.604657 ATCCCTTATCAACTTAGTCTCGAAT 57.395 36.000 0.00 0.00 0.00 3.34
7023 7840 8.707796 ATCCCTTATCAACTTAGTCTCGAATA 57.292 34.615 0.00 0.00 0.00 1.75
7024 7841 8.707796 TCCCTTATCAACTTAGTCTCGAATAT 57.292 34.615 0.00 0.00 0.00 1.28
7025 7842 8.577296 TCCCTTATCAACTTAGTCTCGAATATG 58.423 37.037 0.00 0.00 0.00 1.78
7026 7843 7.329717 CCCTTATCAACTTAGTCTCGAATATGC 59.670 40.741 0.00 0.00 0.00 3.14
7027 7844 7.867909 CCTTATCAACTTAGTCTCGAATATGCA 59.132 37.037 0.00 0.00 0.00 3.96
7028 7845 9.416794 CTTATCAACTTAGTCTCGAATATGCAT 57.583 33.333 3.79 3.79 0.00 3.96
7029 7846 7.649370 ATCAACTTAGTCTCGAATATGCATG 57.351 36.000 10.16 0.00 0.00 4.06
7030 7847 6.805713 TCAACTTAGTCTCGAATATGCATGA 58.194 36.000 10.16 0.00 0.00 3.07
7031 7848 6.920210 TCAACTTAGTCTCGAATATGCATGAG 59.080 38.462 10.16 7.46 0.00 2.90
7032 7849 6.398234 ACTTAGTCTCGAATATGCATGAGT 57.602 37.500 10.16 2.19 0.00 3.41
7033 7850 6.212235 ACTTAGTCTCGAATATGCATGAGTG 58.788 40.000 10.16 0.00 0.00 3.51
7034 7851 4.662468 AGTCTCGAATATGCATGAGTGT 57.338 40.909 10.16 0.00 0.00 3.55
7035 7852 4.366586 AGTCTCGAATATGCATGAGTGTG 58.633 43.478 10.16 0.00 0.00 3.82
7036 7853 3.060003 GTCTCGAATATGCATGAGTGTGC 60.060 47.826 10.16 0.00 45.25 4.57
7051 7868 9.338291 GCATGAGTGTGCATATCATTATTAAAG 57.662 33.333 0.00 0.00 44.43 1.85
7078 7895 3.419793 CAAAGAGTGCCTCCACCAA 57.580 52.632 0.00 0.00 43.09 3.67
7343 8160 4.000988 GCCAAAGACGAGGAGATAAACAA 58.999 43.478 0.00 0.00 0.00 2.83
7350 8167 2.677037 CGAGGAGATAAACAAGCGGGTT 60.677 50.000 0.00 0.00 0.00 4.11
7368 8185 0.619255 TTGATCGGGCCTCCAAGGTA 60.619 55.000 0.84 0.00 37.80 3.08
7371 8188 1.275573 GATCGGGCCTCCAAGGTATAC 59.724 57.143 0.84 0.00 37.80 1.47
7374 8191 0.391966 GGGCCTCCAAGGTATACGAC 59.608 60.000 0.84 0.00 37.80 4.34
7431 8248 0.934436 CTGCCGCAAACAAGAAACCG 60.934 55.000 0.00 0.00 0.00 4.44
7440 8257 4.230657 CAAACAAGAAACCGTTGTCACAA 58.769 39.130 0.00 0.00 37.13 3.33
7443 8260 0.655733 AGAAACCGTTGTCACAAGCG 59.344 50.000 0.00 0.00 0.00 4.68
7476 8293 0.603569 AGTCACAGCTTGGTCCGTAG 59.396 55.000 0.00 0.00 0.00 3.51
7491 8308 1.135460 CCGTAGTCGAGAAACCTGACC 60.135 57.143 0.00 0.00 39.71 4.02
7493 8310 2.159544 CGTAGTCGAGAAACCTGACCTC 60.160 54.545 0.00 0.00 39.71 3.85
7494 8311 1.996798 AGTCGAGAAACCTGACCTCA 58.003 50.000 0.00 0.00 33.09 3.86
7503 8320 6.380079 AGAAACCTGACCTCACATATTCTT 57.620 37.500 0.00 0.00 0.00 2.52
7506 8323 3.456277 ACCTGACCTCACATATTCTTCCC 59.544 47.826 0.00 0.00 0.00 3.97
7507 8324 3.493350 CCTGACCTCACATATTCTTCCCG 60.493 52.174 0.00 0.00 0.00 5.14
7514 8331 3.704566 TCACATATTCTTCCCGTACAGCT 59.295 43.478 0.00 0.00 0.00 4.24
7537 8354 2.057137 TCATGCCCTAACATGCTTCC 57.943 50.000 0.00 0.00 45.75 3.46
7539 8356 2.777114 TCATGCCCTAACATGCTTCCTA 59.223 45.455 0.00 0.00 45.75 2.94
7540 8357 2.710096 TGCCCTAACATGCTTCCTAC 57.290 50.000 0.00 0.00 0.00 3.18
7552 8369 4.367039 TGCTTCCTACCTGCTAAAACTT 57.633 40.909 0.00 0.00 0.00 2.66
7553 8370 4.072131 TGCTTCCTACCTGCTAAAACTTG 58.928 43.478 0.00 0.00 0.00 3.16
7683 8500 1.892338 CACAGGAATGGCGCCATTT 59.108 52.632 45.38 32.62 45.50 2.32
7934 8752 2.017049 CAAAAACTATGGAGGGCTCGG 58.983 52.381 0.00 0.00 0.00 4.63
7956 8774 2.543687 CTTCCGGATCGTGTCGTGCT 62.544 60.000 4.15 0.00 0.00 4.40
7972 8790 0.034337 TGCTCGTAGGTTGTTGGGAC 59.966 55.000 0.00 0.00 0.00 4.46
7973 8791 0.672711 GCTCGTAGGTTGTTGGGACC 60.673 60.000 0.00 0.00 37.44 4.46
7974 8792 0.389426 CTCGTAGGTTGTTGGGACCG 60.389 60.000 0.00 0.00 42.11 4.79
7975 8793 0.827089 TCGTAGGTTGTTGGGACCGA 60.827 55.000 0.00 0.00 42.11 4.69
7991 8809 1.280710 ACCGAGTGTGAATTATGCCCA 59.719 47.619 0.00 0.00 0.00 5.36
7993 8811 2.097466 CCGAGTGTGAATTATGCCCAAC 59.903 50.000 0.00 0.00 0.00 3.77
7996 8814 0.449786 TGTGAATTATGCCCAACGCG 59.550 50.000 3.53 3.53 42.08 6.01
8008 8826 1.509787 CAACGCGGCGAAGATTGTG 60.510 57.895 30.94 10.47 0.00 3.33
8043 8865 5.466820 CGACGCTACGTTTAAATCAGTTAC 58.533 41.667 0.00 0.00 41.37 2.50
8077 8899 7.771826 ACAACTGCTTAAGAGGTTTGTTACTAA 59.228 33.333 6.67 0.00 0.00 2.24
8098 8920 0.750546 TCCTGGTATGACGTCCGAGG 60.751 60.000 14.12 13.40 0.00 4.63
8160 9004 4.284490 AGAAGATGTGAAGCCTGACAGTAA 59.716 41.667 0.93 0.00 0.00 2.24
8237 9081 6.265196 CCTGCTGCCTTATTTGGTTCATTATA 59.735 38.462 0.00 0.00 0.00 0.98
8238 9082 7.039504 CCTGCTGCCTTATTTGGTTCATTATAT 60.040 37.037 0.00 0.00 0.00 0.86
8239 9083 8.248904 TGCTGCCTTATTTGGTTCATTATATT 57.751 30.769 0.00 0.00 0.00 1.28
8240 9084 8.143193 TGCTGCCTTATTTGGTTCATTATATTG 58.857 33.333 0.00 0.00 0.00 1.90
8241 9085 8.359642 GCTGCCTTATTTGGTTCATTATATTGA 58.640 33.333 0.00 0.00 0.00 2.57
8257 9101 8.886719 CATTATATTGATTGACGTATCCATGCT 58.113 33.333 0.00 0.00 0.00 3.79
8258 9102 8.846943 TTATATTGATTGACGTATCCATGCTT 57.153 30.769 0.00 0.00 0.00 3.91
8275 9119 2.092968 TGCTTGACTATTTCCGGCTGAT 60.093 45.455 0.00 0.00 0.00 2.90
8317 9161 4.342987 TCGCTGCTCGCTTGACGT 62.343 61.111 0.00 0.00 44.19 4.34
8318 9162 3.832171 CGCTGCTCGCTTGACGTC 61.832 66.667 9.11 9.11 44.19 4.34
8319 9163 3.832171 GCTGCTCGCTTGACGTCG 61.832 66.667 11.62 0.00 44.19 5.12
8419 9264 5.854010 AACATGTACATGGACGATCTAGT 57.146 39.130 33.32 10.92 42.91 2.57
8430 9275 4.113354 GGACGATCTAGTTTGGCTGTTAG 58.887 47.826 0.00 0.00 0.00 2.34
8431 9276 4.142227 GGACGATCTAGTTTGGCTGTTAGA 60.142 45.833 0.00 0.00 0.00 2.10
8432 9277 5.000012 ACGATCTAGTTTGGCTGTTAGAG 58.000 43.478 0.00 0.00 0.00 2.43
8433 9278 4.705507 ACGATCTAGTTTGGCTGTTAGAGA 59.294 41.667 0.00 0.00 0.00 3.10
8434 9279 5.361285 ACGATCTAGTTTGGCTGTTAGAGAT 59.639 40.000 0.00 0.00 0.00 2.75
8435 9280 6.127310 ACGATCTAGTTTGGCTGTTAGAGATT 60.127 38.462 0.00 0.00 0.00 2.40
8436 9281 6.758886 CGATCTAGTTTGGCTGTTAGAGATTT 59.241 38.462 0.00 0.00 0.00 2.17
8437 9282 7.278868 CGATCTAGTTTGGCTGTTAGAGATTTT 59.721 37.037 0.00 0.00 0.00 1.82
8485 9335 2.359107 AGATATGCATGCCCGCCG 60.359 61.111 16.68 0.00 0.00 6.46
8499 9349 1.662608 CGCCGGAGATATCTGCAGT 59.337 57.895 22.29 3.75 33.58 4.40
8511 9361 9.717942 GGAGATATCTGCAGTATCTGTTTAAAT 57.282 33.333 28.38 10.91 38.63 1.40
8523 9373 8.462016 AGTATCTGTTTAAATGGAGATTTGCAC 58.538 33.333 10.75 5.59 33.63 4.57
8526 9376 4.173256 GTTTAAATGGAGATTTGCACGGG 58.827 43.478 0.00 0.00 33.63 5.28
8527 9377 2.214376 AAATGGAGATTTGCACGGGA 57.786 45.000 0.00 0.00 30.17 5.14
8528 9378 1.755179 AATGGAGATTTGCACGGGAG 58.245 50.000 0.00 0.00 0.00 4.30
8601 9451 3.833645 CGACGGGCGGATTCCTCA 61.834 66.667 0.00 0.00 36.03 3.86
8602 9452 2.107141 GACGGGCGGATTCCTCAG 59.893 66.667 0.30 0.00 0.00 3.35
8603 9453 4.162690 ACGGGCGGATTCCTCAGC 62.163 66.667 0.30 0.00 41.28 4.26
8629 9479 3.064987 GCGACAAGCCGGAGAGCTA 62.065 63.158 5.05 0.00 44.11 3.32
8630 9480 1.226717 CGACAAGCCGGAGAGCTAC 60.227 63.158 5.05 0.00 44.11 3.58
8631 9481 1.142097 GACAAGCCGGAGAGCTACC 59.858 63.158 5.05 0.00 44.11 3.18
8632 9482 1.305381 ACAAGCCGGAGAGCTACCT 60.305 57.895 5.05 0.00 44.11 3.08
8633 9483 1.142748 CAAGCCGGAGAGCTACCTG 59.857 63.158 5.05 2.89 44.11 4.00
8634 9484 2.726351 AAGCCGGAGAGCTACCTGC 61.726 63.158 5.05 14.75 44.11 4.85
8659 9509 3.612251 CCGTTTCGGCCTAGAGGA 58.388 61.111 0.00 0.00 41.17 3.71
8660 9510 1.141234 CCGTTTCGGCCTAGAGGAC 59.859 63.158 0.00 0.00 41.17 3.85
8661 9511 1.141234 CGTTTCGGCCTAGAGGACC 59.859 63.158 0.00 0.00 41.34 4.46
8662 9512 1.321074 CGTTTCGGCCTAGAGGACCT 61.321 60.000 0.00 0.00 41.34 3.85
8663 9513 0.175989 GTTTCGGCCTAGAGGACCTG 59.824 60.000 0.00 0.00 41.34 4.00
8664 9514 0.976073 TTTCGGCCTAGAGGACCTGG 60.976 60.000 0.00 0.00 41.34 4.45
8665 9515 1.870941 TTCGGCCTAGAGGACCTGGA 61.871 60.000 0.00 0.00 41.34 3.86
8666 9516 2.128507 CGGCCTAGAGGACCTGGAC 61.129 68.421 0.00 0.00 41.34 4.02
8667 9517 2.128507 GGCCTAGAGGACCTGGACG 61.129 68.421 0.00 0.00 37.19 4.79
8668 9518 1.380112 GCCTAGAGGACCTGGACGT 60.380 63.158 0.00 0.00 37.39 4.34
8669 9519 1.668101 GCCTAGAGGACCTGGACGTG 61.668 65.000 0.00 0.00 37.39 4.49
8670 9520 1.038130 CCTAGAGGACCTGGACGTGG 61.038 65.000 0.00 0.00 37.39 4.94
8671 9521 0.323542 CTAGAGGACCTGGACGTGGT 60.324 60.000 0.00 0.00 41.07 4.16
8672 9522 0.611062 TAGAGGACCTGGACGTGGTG 60.611 60.000 0.00 0.00 38.03 4.17
8673 9523 2.923035 AGGACCTGGACGTGGTGG 60.923 66.667 0.00 0.00 38.03 4.61
8674 9524 3.239253 GGACCTGGACGTGGTGGT 61.239 66.667 0.00 1.68 38.03 4.16
8675 9525 2.030562 GACCTGGACGTGGTGGTG 59.969 66.667 0.00 0.00 38.03 4.17
8676 9526 2.766651 ACCTGGACGTGGTGGTGT 60.767 61.111 0.00 0.00 36.30 4.16
8677 9527 2.280797 CCTGGACGTGGTGGTGTG 60.281 66.667 0.00 0.00 0.00 3.82
8678 9528 2.280797 CTGGACGTGGTGGTGTGG 60.281 66.667 0.00 0.00 0.00 4.17
8679 9529 2.764547 TGGACGTGGTGGTGTGGA 60.765 61.111 0.00 0.00 0.00 4.02
8680 9530 2.318519 CTGGACGTGGTGGTGTGGAA 62.319 60.000 0.00 0.00 0.00 3.53
8681 9531 1.597027 GGACGTGGTGGTGTGGAAG 60.597 63.158 0.00 0.00 0.00 3.46
8682 9532 1.444250 GACGTGGTGGTGTGGAAGA 59.556 57.895 0.00 0.00 0.00 2.87
8683 9533 0.179067 GACGTGGTGGTGTGGAAGAA 60.179 55.000 0.00 0.00 0.00 2.52
8690 9540 1.056660 TGGTGTGGAAGAAGACCCTC 58.943 55.000 0.00 0.00 32.49 4.30
8698 9548 0.909610 AAGAAGACCCTCGCCATGGA 60.910 55.000 18.40 0.00 0.00 3.41
8704 9554 2.586245 CCTCGCCATGGAGAAGCA 59.414 61.111 19.39 0.00 36.08 3.91
8728 9578 4.778143 CAAGGGGGAAGGCGACCG 62.778 72.222 0.00 0.00 0.00 4.79
8784 9634 1.376812 GACATCCACCACCGGGAAC 60.377 63.158 6.32 0.00 38.09 3.62
8822 9672 1.153289 CTTCTGCAGCGCCACCTAT 60.153 57.895 9.47 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.158021 TGGTTTGTATAAGGGCTGAAAATTTG 58.842 34.615 0.00 0.00 0.00 2.32
1 2 7.309770 TGGTTTGTATAAGGGCTGAAAATTT 57.690 32.000 0.00 0.00 0.00 1.82
2 3 6.926630 TGGTTTGTATAAGGGCTGAAAATT 57.073 33.333 0.00 0.00 0.00 1.82
10 11 4.709886 AGGTTGATTGGTTTGTATAAGGGC 59.290 41.667 0.00 0.00 0.00 5.19
41 42 2.278857 GCGACGCAGATGGACGAT 60.279 61.111 16.42 0.00 0.00 3.73
65 66 0.393132 TTGGAAACTGCGACACCACA 60.393 50.000 0.00 0.00 0.00 4.17
113 114 3.046968 TCGTTGATTCCATGGTCGAAA 57.953 42.857 12.58 0.00 0.00 3.46
133 135 6.512297 AGGTTATCTGATTTTTGTTTGCGTT 58.488 32.000 0.00 0.00 0.00 4.84
171 176 4.853468 TCCTGCTGGTTTGAATATACCA 57.147 40.909 9.73 0.00 41.97 3.25
182 188 2.897326 GGTTTTGGTAATCCTGCTGGTT 59.103 45.455 9.73 6.17 34.23 3.67
215 225 4.675510 TGAACGAGACTAACAACGTCTTT 58.324 39.130 0.00 0.00 41.53 2.52
227 237 4.087182 TCCTATGGACTTTGAACGAGACT 58.913 43.478 0.00 0.00 0.00 3.24
252 262 2.413453 GCGCTTTTTGAAACCACAACAA 59.587 40.909 0.00 0.00 0.00 2.83
260 270 0.512518 GCCATGGCGCTTTTTGAAAC 59.487 50.000 23.48 0.00 0.00 2.78
338 348 1.091537 GCAAACTACGCTAATGGGCA 58.908 50.000 0.00 0.00 0.00 5.36
370 380 2.180276 ACCGAAGCAGAGTGAACCTAT 58.820 47.619 0.00 0.00 0.00 2.57
418 428 8.893727 CCAAAGAGAAACCGATGAAAAGTATAT 58.106 33.333 0.00 0.00 0.00 0.86
422 432 4.278419 CCCAAAGAGAAACCGATGAAAAGT 59.722 41.667 0.00 0.00 0.00 2.66
423 433 4.278419 ACCCAAAGAGAAACCGATGAAAAG 59.722 41.667 0.00 0.00 0.00 2.27
426 436 3.502123 ACCCAAAGAGAAACCGATGAA 57.498 42.857 0.00 0.00 0.00 2.57
473 483 6.176896 CAAAGGAAAACAAAGGGGAAAAAGA 58.823 36.000 0.00 0.00 0.00 2.52
480 490 2.123589 ACCCAAAGGAAAACAAAGGGG 58.876 47.619 0.00 0.00 39.15 4.79
605 618 5.871539 TCAGGTAAAAGTTTCACGTGTTTC 58.128 37.500 16.51 6.95 31.70 2.78
624 637 6.558771 TGAAAAGTGTCAACATGTATCAGG 57.441 37.500 0.00 0.00 0.00 3.86
631 644 8.633075 ACTTGTATTTGAAAAGTGTCAACATG 57.367 30.769 0.00 0.00 37.24 3.21
633 646 8.085296 ACAACTTGTATTTGAAAAGTGTCAACA 58.915 29.630 0.00 0.00 37.24 3.33
636 649 7.906010 CGTACAACTTGTATTTGAAAAGTGTCA 59.094 33.333 4.93 0.00 35.05 3.58
641 654 7.411274 TGGTCGTACAACTTGTATTTGAAAAG 58.589 34.615 4.93 0.00 35.05 2.27
654 667 6.817765 ATGAAAATGAATGGTCGTACAACT 57.182 33.333 0.00 0.00 0.00 3.16
751 1091 9.475620 CCCTCCTTTTTACTTTATTTATGGAGT 57.524 33.333 0.00 0.00 36.55 3.85
778 1118 6.132056 GTCATGCTGACGTCATATCAATTTC 58.868 40.000 20.40 6.68 37.67 2.17
848 1202 1.453155 GCAATGGCTCTTTCTCCGAA 58.547 50.000 0.00 0.00 36.96 4.30
849 1203 0.740868 CGCAATGGCTCTTTCTCCGA 60.741 55.000 0.00 0.00 38.10 4.55
850 1204 1.717937 CGCAATGGCTCTTTCTCCG 59.282 57.895 0.00 0.00 38.10 4.63
851 1205 1.431036 GCGCAATGGCTCTTTCTCC 59.569 57.895 0.30 0.00 38.10 3.71
852 1206 1.061570 CGCGCAATGGCTCTTTCTC 59.938 57.895 8.75 0.00 38.10 2.87
853 1207 3.044059 GCGCGCAATGGCTCTTTCT 62.044 57.895 29.10 0.00 38.10 2.52
854 1208 2.577911 GCGCGCAATGGCTCTTTC 60.578 61.111 29.10 0.00 38.10 2.62
855 1209 4.120331 GGCGCGCAATGGCTCTTT 62.120 61.111 34.42 0.00 38.10 2.52
862 1216 4.228097 CTTCGAGGGCGCGCAATG 62.228 66.667 34.42 18.94 37.46 2.82
863 1217 4.760047 ACTTCGAGGGCGCGCAAT 62.760 61.111 34.42 21.03 37.46 3.56
866 1220 2.126417 TATAGACTTCGAGGGCGCGC 62.126 60.000 25.94 25.94 37.46 6.86
867 1221 0.385723 GTATAGACTTCGAGGGCGCG 60.386 60.000 0.00 0.00 37.46 6.86
868 1222 0.666913 TGTATAGACTTCGAGGGCGC 59.333 55.000 0.00 0.00 37.46 6.53
869 1223 2.219458 TCTGTATAGACTTCGAGGGCG 58.781 52.381 0.00 0.00 39.35 6.13
1372 1730 4.393778 GACCTCCTCCCCGTCCCA 62.394 72.222 0.00 0.00 0.00 4.37
1413 1771 2.305927 GGGGAGAAATCACTTCACCTCA 59.694 50.000 0.00 0.00 43.06 3.86
1446 1805 5.244785 TCACAGTGCCTTTATACTACGAG 57.755 43.478 0.00 0.00 0.00 4.18
1505 1872 1.490574 ATGGCTCTGACCTAGTGACC 58.509 55.000 0.00 0.00 0.00 4.02
1526 1893 6.427853 CAGACACCAATGTAGATTCTCAAACA 59.572 38.462 0.00 0.00 39.95 2.83
1548 1915 1.976404 TGAATTGCAAATTGCCCCAGA 59.024 42.857 15.98 0.00 44.23 3.86
1855 2225 5.497635 TGTGGAACCGTTTAAAACCTAAC 57.502 39.130 0.00 0.00 34.36 2.34
1858 2228 3.762823 TGTTGTGGAACCGTTTAAAACCT 59.237 39.130 0.00 0.00 34.36 3.50
1879 2250 9.688592 AAAAATGAGCTCAGAGAAACTTTAATG 57.311 29.630 22.96 0.00 0.00 1.90
2008 2467 3.369147 CCAAAACGTGAAAATGCACAACA 59.631 39.130 0.00 0.00 38.69 3.33
2187 2646 2.366916 GGAGAGCTCAAAGGCTATAGCA 59.633 50.000 25.53 4.32 43.20 3.49
2241 2702 3.490348 AGCGGGCTATTAGCATCATTTT 58.510 40.909 17.11 0.00 44.75 1.82
2248 2769 2.290071 GGGAAATAGCGGGCTATTAGCA 60.290 50.000 22.29 0.00 45.37 3.49
2273 2794 3.782889 AATGACTCCAAATTTAGCGCC 57.217 42.857 2.29 0.00 0.00 6.53
2300 2821 4.682778 TGGTTTCATATAGCGCCTTAGT 57.317 40.909 2.29 0.00 0.00 2.24
2361 2882 2.105006 AGCTTCACACTATGCACCAG 57.895 50.000 0.00 0.00 0.00 4.00
2786 3327 4.275689 CACCTCACAAGCAATGAGTACAAA 59.724 41.667 10.03 0.00 41.78 2.83
2787 3328 3.814842 CACCTCACAAGCAATGAGTACAA 59.185 43.478 10.03 0.00 41.78 2.41
2906 3447 1.012086 CGGCATCAACATCTGGACAG 58.988 55.000 0.00 0.00 0.00 3.51
3201 3742 8.579850 ACTAATGACATGCAGGAGAAATAAAA 57.420 30.769 4.84 0.00 0.00 1.52
3202 3743 7.828717 TGACTAATGACATGCAGGAGAAATAAA 59.171 33.333 4.84 0.00 0.00 1.40
3738 4285 3.320541 AGAGATGAAGAATGGGCGTAGAG 59.679 47.826 0.00 0.00 0.00 2.43
3843 4390 5.709164 AGATCAAATAACCTGCATAGATGGC 59.291 40.000 0.00 0.00 0.00 4.40
3940 4487 1.812571 GCCACTGGACAAATTGACGAT 59.187 47.619 0.00 0.00 0.00 3.73
4158 4712 5.954153 ATTCCCATATGCAAAATTCACCA 57.046 34.783 0.00 0.00 0.00 4.17
4344 4898 1.752498 ACGGTGTAGACTTCACACACA 59.248 47.619 13.45 0.00 46.53 3.72
4385 4939 9.938670 CTTGAAAGAAAAATTGAAATGCATGAA 57.061 25.926 0.00 0.00 0.00 2.57
4514 5085 6.155827 GCATAAACAGGCTTACATGTGAAAA 58.844 36.000 9.11 0.00 0.00 2.29
4822 5400 8.597662 ACAACATTTGGATTTGAAGATTTCAG 57.402 30.769 0.00 0.00 36.54 3.02
5078 5770 5.537674 CCAAGATAATAAAAGCATCAGCCCT 59.462 40.000 0.00 0.00 43.56 5.19
5255 5947 2.953466 TGCTACTTGTATCCACGGTC 57.047 50.000 0.00 0.00 0.00 4.79
5275 5967 2.171448 ACAGCAAGGAATAGAGGCGATT 59.829 45.455 0.00 0.00 0.00 3.34
5379 6077 3.785486 TCGGATTGACTATGAGCACTTG 58.215 45.455 0.00 0.00 0.00 3.16
5475 6173 1.808343 TGCAGACATGACTGTGCAATC 59.192 47.619 22.99 8.67 39.73 2.67
5540 6238 5.356882 TTTGCTGACACAATTACAGTAGC 57.643 39.130 0.00 0.00 34.60 3.58
5572 6272 9.051027 GTACAATATTTGTTGACACATTTCTCG 57.949 33.333 0.00 0.00 42.22 4.04
5638 6338 0.804364 CAAAGCGTGCTGGCTATCAA 59.196 50.000 0.00 0.00 43.93 2.57
5676 6378 8.939929 ACAGTAGAATCAATGTTCAACATAGTG 58.060 33.333 2.67 0.00 37.97 2.74
6101 6918 3.142174 GCTTTACCTTCACAAGAGCTGT 58.858 45.455 0.00 0.00 39.56 4.40
6261 7078 4.512484 TCTTTATGCGTCCATGTGAATCA 58.488 39.130 0.00 0.00 32.85 2.57
6357 7174 6.486253 TCTGTATTGCTCTTCACATTTGAC 57.514 37.500 0.00 0.00 0.00 3.18
6591 7408 0.246360 TGGTGAGTACAGGATGCACG 59.754 55.000 0.00 0.00 42.53 5.34
6669 7486 3.582998 ACTAACTGCACATGGCCATAT 57.417 42.857 20.30 3.35 43.89 1.78
6849 7666 6.070251 TCAGGCTTGTTGAAGATGGAAGTATA 60.070 38.462 0.00 0.00 0.00 1.47
6981 7798 6.409524 AAGGGATATGCACAAAATACCATG 57.590 37.500 0.00 0.00 0.00 3.66
7010 7827 6.143598 CACACTCATGCATATTCGAGACTAAG 59.856 42.308 16.34 5.55 0.00 2.18
7011 7828 5.979517 CACACTCATGCATATTCGAGACTAA 59.020 40.000 16.34 0.00 0.00 2.24
7012 7829 5.523369 CACACTCATGCATATTCGAGACTA 58.477 41.667 16.34 0.00 0.00 2.59
7013 7830 4.366586 CACACTCATGCATATTCGAGACT 58.633 43.478 16.34 1.02 0.00 3.24
7014 7831 3.060003 GCACACTCATGCATATTCGAGAC 60.060 47.826 16.34 2.42 45.39 3.36
7015 7832 3.126073 GCACACTCATGCATATTCGAGA 58.874 45.455 16.34 0.93 45.39 4.04
7016 7833 3.516681 GCACACTCATGCATATTCGAG 57.483 47.619 0.00 4.40 45.39 4.04
7025 7842 9.338291 CTTTAATAATGATATGCACACTCATGC 57.662 33.333 7.92 0.00 46.32 4.06
7043 7860 8.082242 GCACTCTTTGCCTTTCTTCTTTAATAA 58.918 33.333 0.00 0.00 46.63 1.40
7044 7861 7.593825 GCACTCTTTGCCTTTCTTCTTTAATA 58.406 34.615 0.00 0.00 46.63 0.98
7045 7862 6.450545 GCACTCTTTGCCTTTCTTCTTTAAT 58.549 36.000 0.00 0.00 46.63 1.40
7046 7863 5.831997 GCACTCTTTGCCTTTCTTCTTTAA 58.168 37.500 0.00 0.00 46.63 1.52
7047 7864 5.438761 GCACTCTTTGCCTTTCTTCTTTA 57.561 39.130 0.00 0.00 46.63 1.85
7048 7865 4.313277 GCACTCTTTGCCTTTCTTCTTT 57.687 40.909 0.00 0.00 46.63 2.52
7049 7866 3.998099 GCACTCTTTGCCTTTCTTCTT 57.002 42.857 0.00 0.00 46.63 2.52
7066 7883 2.561478 TTCTAAGTTGGTGGAGGCAC 57.439 50.000 0.00 0.00 0.00 5.01
7067 7884 4.227300 ACATATTCTAAGTTGGTGGAGGCA 59.773 41.667 0.00 0.00 0.00 4.75
7068 7885 4.781934 ACATATTCTAAGTTGGTGGAGGC 58.218 43.478 0.00 0.00 0.00 4.70
7069 7886 5.989477 TGACATATTCTAAGTTGGTGGAGG 58.011 41.667 0.00 0.00 0.00 4.30
7070 7887 9.212641 CATATGACATATTCTAAGTTGGTGGAG 57.787 37.037 5.15 0.00 0.00 3.86
7071 7888 7.661437 GCATATGACATATTCTAAGTTGGTGGA 59.339 37.037 6.97 0.00 0.00 4.02
7072 7889 7.094634 GGCATATGACATATTCTAAGTTGGTGG 60.095 40.741 6.97 0.00 0.00 4.61
7073 7890 7.445096 TGGCATATGACATATTCTAAGTTGGTG 59.555 37.037 7.32 0.00 0.00 4.17
7074 7891 7.517320 TGGCATATGACATATTCTAAGTTGGT 58.483 34.615 7.32 0.00 0.00 3.67
7075 7892 7.984422 TGGCATATGACATATTCTAAGTTGG 57.016 36.000 7.32 0.00 0.00 3.77
7076 7893 9.836076 CAATGGCATATGACATATTCTAAGTTG 57.164 33.333 24.38 12.26 44.48 3.16
7077 7894 9.578576 ACAATGGCATATGACATATTCTAAGTT 57.421 29.630 24.38 3.41 44.48 2.66
7078 7895 9.578576 AACAATGGCATATGACATATTCTAAGT 57.421 29.630 24.38 11.16 44.48 2.24
7311 8128 3.190874 CTCGTCTTTGGCTTCTATGGAC 58.809 50.000 0.00 0.00 0.00 4.02
7350 8167 0.399949 ATACCTTGGAGGCCCGATCA 60.400 55.000 0.00 0.00 39.63 2.92
7368 8185 2.073816 CGCTTTTCCAACAGGTCGTAT 58.926 47.619 0.00 0.00 0.00 3.06
7371 8188 1.082104 GCGCTTTTCCAACAGGTCG 60.082 57.895 0.00 0.00 0.00 4.79
7374 8191 2.083774 TCTATGCGCTTTTCCAACAGG 58.916 47.619 9.73 0.00 0.00 4.00
7383 8200 3.753272 TCTTGAAGCTTTCTATGCGCTTT 59.247 39.130 9.73 0.00 43.42 3.51
7431 8248 1.571460 CAGCTCCGCTTGTGACAAC 59.429 57.895 0.00 0.00 36.40 3.32
7440 8257 1.294780 CTTGAACTCCAGCTCCGCT 59.705 57.895 0.00 0.00 40.77 5.52
7443 8260 1.070758 TGTGACTTGAACTCCAGCTCC 59.929 52.381 0.00 0.00 0.00 4.70
7476 8293 1.340248 TGTGAGGTCAGGTTTCTCGAC 59.660 52.381 0.00 0.00 0.00 4.20
7491 8308 4.051922 GCTGTACGGGAAGAATATGTGAG 58.948 47.826 3.34 0.00 0.00 3.51
7493 8310 4.060038 AGCTGTACGGGAAGAATATGTG 57.940 45.455 3.34 0.00 0.00 3.21
7494 8311 4.161565 TGAAGCTGTACGGGAAGAATATGT 59.838 41.667 3.34 0.00 0.00 2.29
7503 8320 1.473257 GCATGATGAAGCTGTACGGGA 60.473 52.381 3.34 0.00 0.00 5.14
7506 8323 0.940126 GGGCATGATGAAGCTGTACG 59.060 55.000 0.00 0.00 0.00 3.67
7507 8324 2.338577 AGGGCATGATGAAGCTGTAC 57.661 50.000 0.00 0.00 0.00 2.90
7514 8331 3.301794 AGCATGTTAGGGCATGATGAA 57.698 42.857 9.87 0.00 46.65 2.57
7532 8349 4.072839 ACAAGTTTTAGCAGGTAGGAAGC 58.927 43.478 0.00 0.00 0.00 3.86
7552 8369 0.323302 TCCGCAAACCTATCTGCACA 59.677 50.000 0.00 0.00 38.52 4.57
7553 8370 0.727398 GTCCGCAAACCTATCTGCAC 59.273 55.000 0.00 0.00 38.52 4.57
7888 8706 1.108776 CATCTGCCACCAATTCCCTG 58.891 55.000 0.00 0.00 0.00 4.45
7956 8774 0.827089 TCGGTCCCAACAACCTACGA 60.827 55.000 0.00 0.00 34.45 3.43
7972 8790 2.036958 TGGGCATAATTCACACTCGG 57.963 50.000 0.00 0.00 0.00 4.63
7973 8791 2.223021 CGTTGGGCATAATTCACACTCG 60.223 50.000 0.00 0.00 0.00 4.18
7974 8792 2.477863 GCGTTGGGCATAATTCACACTC 60.478 50.000 0.00 0.00 42.87 3.51
7975 8793 1.472480 GCGTTGGGCATAATTCACACT 59.528 47.619 0.00 0.00 42.87 3.55
7991 8809 2.677003 CCACAATCTTCGCCGCGTT 61.677 57.895 13.39 0.00 0.00 4.84
7993 8811 2.802667 CTCCACAATCTTCGCCGCG 61.803 63.158 6.39 6.39 0.00 6.46
7996 8814 2.427506 ACTTTCTCCACAATCTTCGCC 58.572 47.619 0.00 0.00 0.00 5.54
8008 8826 4.089983 GCGTCGGCTACTTTCTCC 57.910 61.111 0.00 0.00 35.83 3.71
8033 8851 7.068226 AGCAGTTGTACCAAAAGTAACTGATTT 59.932 33.333 18.84 5.67 43.40 2.17
8043 8865 5.531287 ACCTCTTAAGCAGTTGTACCAAAAG 59.469 40.000 0.00 0.00 0.00 2.27
8077 8899 0.034767 TCGGACGTCATACCAGGAGT 60.035 55.000 18.91 0.00 0.00 3.85
8098 8920 5.563085 CGACCATACTGAAGGCTACATAGAC 60.563 48.000 0.00 0.00 0.00 2.59
8237 9081 5.008019 GTCAAGCATGGATACGTCAATCAAT 59.992 40.000 0.00 0.00 42.51 2.57
8238 9082 4.332543 GTCAAGCATGGATACGTCAATCAA 59.667 41.667 0.00 0.00 42.51 2.57
8239 9083 3.871006 GTCAAGCATGGATACGTCAATCA 59.129 43.478 0.00 0.00 42.51 2.57
8240 9084 4.122776 AGTCAAGCATGGATACGTCAATC 58.877 43.478 0.00 0.00 42.51 2.67
8241 9085 4.142609 AGTCAAGCATGGATACGTCAAT 57.857 40.909 0.00 0.00 42.51 2.57
8242 9086 3.610040 AGTCAAGCATGGATACGTCAA 57.390 42.857 0.00 0.00 42.51 3.18
8257 9101 2.503765 TCCATCAGCCGGAAATAGTCAA 59.496 45.455 5.05 0.00 0.00 3.18
8258 9102 2.115427 TCCATCAGCCGGAAATAGTCA 58.885 47.619 5.05 0.00 0.00 3.41
8329 9174 2.174349 GCAAAGCCGACGAAGCAG 59.826 61.111 0.00 0.00 0.00 4.24
8336 9181 4.875544 TTTGTATATCAGCAAAGCCGAC 57.124 40.909 0.00 0.00 31.82 4.79
8444 9289 3.767673 GTCTCTGGAGTACATACCAACCA 59.232 47.826 0.00 0.00 35.67 3.67
8446 9291 3.693085 TCGTCTCTGGAGTACATACCAAC 59.307 47.826 0.00 0.00 35.67 3.77
8448 9293 3.199289 TCTCGTCTCTGGAGTACATACCA 59.801 47.826 0.00 0.91 33.26 3.25
8450 9295 6.402766 GCATATCTCGTCTCTGGAGTACATAC 60.403 46.154 0.00 0.00 33.26 2.39
8451 9296 5.644206 GCATATCTCGTCTCTGGAGTACATA 59.356 44.000 0.00 0.00 33.26 2.29
8452 9297 4.457603 GCATATCTCGTCTCTGGAGTACAT 59.542 45.833 0.00 0.00 33.26 2.29
8453 9298 3.815962 GCATATCTCGTCTCTGGAGTACA 59.184 47.826 0.00 0.00 33.26 2.90
8454 9299 3.815962 TGCATATCTCGTCTCTGGAGTAC 59.184 47.826 0.00 0.00 33.26 2.73
8455 9300 4.086706 TGCATATCTCGTCTCTGGAGTA 57.913 45.455 0.00 0.00 33.26 2.59
8456 9301 2.937519 TGCATATCTCGTCTCTGGAGT 58.062 47.619 0.00 0.00 33.26 3.85
8457 9302 3.835779 CATGCATATCTCGTCTCTGGAG 58.164 50.000 0.00 0.00 0.00 3.86
8458 9303 2.029560 GCATGCATATCTCGTCTCTGGA 60.030 50.000 14.21 0.00 0.00 3.86
8460 9305 2.335752 GGCATGCATATCTCGTCTCTG 58.664 52.381 21.36 0.00 0.00 3.35
8485 9335 9.717942 ATTTAAACAGATACTGCAGATATCTCC 57.282 33.333 23.35 0.00 37.30 3.71
8499 9349 7.415095 CCGTGCAAATCTCCATTTAAACAGATA 60.415 37.037 0.00 0.00 30.51 1.98
8511 9361 0.250234 CTCTCCCGTGCAAATCTCCA 59.750 55.000 0.00 0.00 0.00 3.86
8512 9362 0.250513 ACTCTCCCGTGCAAATCTCC 59.749 55.000 0.00 0.00 0.00 3.71
8526 9376 1.828979 CTAGCCGGGATCCTACTCTC 58.171 60.000 12.58 0.00 0.00 3.20
8527 9377 0.251430 GCTAGCCGGGATCCTACTCT 60.251 60.000 12.58 6.64 0.00 3.24
8528 9378 1.252215 GGCTAGCCGGGATCCTACTC 61.252 65.000 20.16 0.00 0.00 2.59
8551 9401 0.179205 GCGCTCTCAGATTGTGTTGC 60.179 55.000 0.00 0.00 0.00 4.17
8586 9436 4.162690 GCTGAGGAATCCGCCCGT 62.163 66.667 0.00 0.00 0.00 5.28
8611 9461 3.064987 TAGCTCTCCGGCTTGTCGC 62.065 63.158 0.00 0.00 42.97 5.19
8612 9462 1.226717 GTAGCTCTCCGGCTTGTCG 60.227 63.158 0.00 0.00 42.97 4.35
8613 9463 1.142097 GGTAGCTCTCCGGCTTGTC 59.858 63.158 0.00 0.00 42.97 3.18
8614 9464 1.305381 AGGTAGCTCTCCGGCTTGT 60.305 57.895 0.00 0.00 42.97 3.16
8615 9465 1.142748 CAGGTAGCTCTCCGGCTTG 59.857 63.158 0.00 0.00 42.97 4.01
8616 9466 2.726351 GCAGGTAGCTCTCCGGCTT 61.726 63.158 19.78 0.00 42.97 4.35
8617 9467 3.151022 GCAGGTAGCTCTCCGGCT 61.151 66.667 19.78 0.00 45.29 5.52
8618 9468 4.577246 CGCAGGTAGCTCTCCGGC 62.577 72.222 18.05 18.05 42.61 6.13
8643 9493 1.141234 GGTCCTCTAGGCCGAAACG 59.859 63.158 0.00 0.00 34.44 3.60
8644 9494 0.175989 CAGGTCCTCTAGGCCGAAAC 59.824 60.000 0.00 0.00 36.77 2.78
8645 9495 0.976073 CCAGGTCCTCTAGGCCGAAA 60.976 60.000 0.00 0.00 36.77 3.46
8646 9496 1.381327 CCAGGTCCTCTAGGCCGAA 60.381 63.158 0.00 0.00 36.77 4.30
8647 9497 2.279073 CCAGGTCCTCTAGGCCGA 59.721 66.667 0.00 0.00 36.77 5.54
8648 9498 2.128507 GTCCAGGTCCTCTAGGCCG 61.129 68.421 0.00 0.00 36.77 6.13
8649 9499 2.128507 CGTCCAGGTCCTCTAGGCC 61.129 68.421 0.00 0.00 34.44 5.19
8650 9500 1.380112 ACGTCCAGGTCCTCTAGGC 60.380 63.158 0.00 0.00 34.44 3.93
8651 9501 1.038130 CCACGTCCAGGTCCTCTAGG 61.038 65.000 0.00 0.00 0.00 3.02
8652 9502 0.323542 ACCACGTCCAGGTCCTCTAG 60.324 60.000 0.00 0.00 32.90 2.43
8653 9503 0.611062 CACCACGTCCAGGTCCTCTA 60.611 60.000 0.00 0.00 37.23 2.43
8654 9504 1.908793 CACCACGTCCAGGTCCTCT 60.909 63.158 0.00 0.00 37.23 3.69
8655 9505 2.657237 CACCACGTCCAGGTCCTC 59.343 66.667 0.00 0.00 37.23 3.71
8656 9506 2.923035 CCACCACGTCCAGGTCCT 60.923 66.667 0.00 0.00 37.23 3.85
8657 9507 3.239253 ACCACCACGTCCAGGTCC 61.239 66.667 0.00 0.00 37.23 4.46
8658 9508 2.030562 CACCACCACGTCCAGGTC 59.969 66.667 0.00 0.00 37.23 3.85
8659 9509 2.766651 ACACCACCACGTCCAGGT 60.767 61.111 0.00 0.00 40.85 4.00
8660 9510 2.280797 CACACCACCACGTCCAGG 60.281 66.667 0.00 0.00 0.00 4.45
8661 9511 2.280797 CCACACCACCACGTCCAG 60.281 66.667 0.00 0.00 0.00 3.86
8662 9512 2.318519 CTTCCACACCACCACGTCCA 62.319 60.000 0.00 0.00 0.00 4.02
8663 9513 1.597027 CTTCCACACCACCACGTCC 60.597 63.158 0.00 0.00 0.00 4.79
8664 9514 0.179067 TTCTTCCACACCACCACGTC 60.179 55.000 0.00 0.00 0.00 4.34
8665 9515 0.179056 CTTCTTCCACACCACCACGT 60.179 55.000 0.00 0.00 0.00 4.49
8666 9516 0.105964 TCTTCTTCCACACCACCACG 59.894 55.000 0.00 0.00 0.00 4.94
8667 9517 1.594331 GTCTTCTTCCACACCACCAC 58.406 55.000 0.00 0.00 0.00 4.16
8668 9518 0.472471 GGTCTTCTTCCACACCACCA 59.528 55.000 0.00 0.00 0.00 4.17
8669 9519 0.250770 GGGTCTTCTTCCACACCACC 60.251 60.000 0.00 0.00 0.00 4.61
8670 9520 0.765510 AGGGTCTTCTTCCACACCAC 59.234 55.000 0.00 0.00 0.00 4.16
8671 9521 1.056660 GAGGGTCTTCTTCCACACCA 58.943 55.000 0.00 0.00 0.00 4.17
8672 9522 0.037232 CGAGGGTCTTCTTCCACACC 60.037 60.000 0.00 0.00 0.00 4.16
8673 9523 0.670854 GCGAGGGTCTTCTTCCACAC 60.671 60.000 0.00 0.00 0.00 3.82
8674 9524 1.671742 GCGAGGGTCTTCTTCCACA 59.328 57.895 0.00 0.00 0.00 4.17
8675 9525 1.079057 GGCGAGGGTCTTCTTCCAC 60.079 63.158 0.00 0.00 0.00 4.02
8676 9526 0.909610 ATGGCGAGGGTCTTCTTCCA 60.910 55.000 0.00 0.00 0.00 3.53
8677 9527 0.462759 CATGGCGAGGGTCTTCTTCC 60.463 60.000 0.00 0.00 0.00 3.46
8678 9528 0.462759 CCATGGCGAGGGTCTTCTTC 60.463 60.000 0.00 0.00 0.00 2.87
8679 9529 0.909610 TCCATGGCGAGGGTCTTCTT 60.910 55.000 6.96 0.00 0.00 2.52
8680 9530 1.306141 TCCATGGCGAGGGTCTTCT 60.306 57.895 6.96 0.00 0.00 2.85
8681 9531 1.144936 CTCCATGGCGAGGGTCTTC 59.855 63.158 6.96 0.00 0.00 2.87
8682 9532 0.909610 TTCTCCATGGCGAGGGTCTT 60.910 55.000 6.96 0.00 0.00 3.01
8683 9533 1.306141 TTCTCCATGGCGAGGGTCT 60.306 57.895 6.96 0.00 0.00 3.85
8690 9540 2.124819 AGCTGCTTCTCCATGGCG 60.125 61.111 6.96 0.00 0.00 5.69
8742 9592 2.833582 GGCGAGGTCGATCTCCCA 60.834 66.667 19.87 0.00 43.02 4.37


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

AutoCloner maintained by Alex Coulton.