Multiple sequence alignment - TraesCS2D01G508000

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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 TraesCS2D01G508000 chr2D 100.000 3114 0 0 1 3114 601256084 601252971 0.000000e+00 5751.0
1 TraesCS2D01G508000 chr2D 81.373 2040 291 41 1078 3092 601263527 601261552 0.000000e+00 1580.0
2 TraesCS2D01G508000 chr2D 79.318 469 87 8 553 1018 601263974 601263513 1.390000e-83 320.0
3 TraesCS2D01G508000 chr2B 94.638 1007 53 1 1080 2086 731481994 731480989 0.000000e+00 1559.0
4 TraesCS2D01G508000 chr2B 94.604 834 38 5 189 1021 731482806 731481979 0.000000e+00 1284.0
5 TraesCS2D01G508000 chr2B 86.175 651 72 7 2465 3112 731476722 731476087 0.000000e+00 688.0
6 TraesCS2D01G508000 chr2B 80.899 712 120 13 1343 2048 731526317 731525616 5.870000e-152 547.0
7 TraesCS2D01G508000 chr2B 97.059 68 2 0 1021 1088 799274345 799274412 7.060000e-22 115.0
8 TraesCS2D01G508000 chr2A 81.354 1802 252 34 1078 2818 734653819 734652041 0.000000e+00 1389.0
9 TraesCS2D01G508000 chr2A 80.128 468 85 7 553 1018 734654266 734653805 2.970000e-90 342.0
10 TraesCS2D01G508000 chr2A 95.890 73 0 3 1012 1083 762700431 762700501 7.060000e-22 115.0
11 TraesCS2D01G508000 chr2A 93.421 76 2 3 1009 1083 771713768 771713841 3.280000e-20 110.0
12 TraesCS2D01G508000 chr2A 93.333 75 4 1 1009 1083 776582293 776582366 3.280000e-20 110.0
13 TraesCS2D01G508000 chr7D 83.128 972 153 10 1078 2044 61228399 61227434 0.000000e+00 876.0
14 TraesCS2D01G508000 chr7D 83.351 931 148 7 1117 2044 60705013 60704087 0.000000e+00 854.0
15 TraesCS2D01G508000 chr7D 79.611 976 195 4 1078 2051 62280555 62281528 0.000000e+00 697.0
16 TraesCS2D01G508000 chr7B 82.777 958 160 5 1078 2033 3342025 3341071 0.000000e+00 850.0
17 TraesCS2D01G508000 chr7A 82.613 972 158 10 1078 2044 65154311 65153346 0.000000e+00 848.0
18 TraesCS2D01G508000 chr7A 84.158 101 9 6 2497 2594 33378155 33378059 1.190000e-14 91.6
19 TraesCS2D01G508000 chr6D 97.183 71 0 2 1013 1083 207398600 207398668 5.460000e-23 119.0
20 TraesCS2D01G508000 chr6D 92.500 80 2 4 1007 1083 353103991 353103913 9.130000e-21 111.0
21 TraesCS2D01G508000 chr1A 95.833 72 2 1 1012 1083 52516867 52516937 7.060000e-22 115.0
22 TraesCS2D01G508000 chr1A 92.308 78 6 0 1009 1086 515857782 515857705 9.130000e-21 111.0
23 TraesCS2D01G508000 chr3B 95.775 71 2 1 1013 1083 737348090 737348021 2.540000e-21 113.0


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 TraesCS2D01G508000 chr2D 601252971 601256084 3113 True 5751.0 5751 100.0000 1 3114 1 chr2D.!!$R1 3113
1 TraesCS2D01G508000 chr2D 601261552 601263974 2422 True 950.0 1580 80.3455 553 3092 2 chr2D.!!$R2 2539
2 TraesCS2D01G508000 chr2B 731480989 731482806 1817 True 1421.5 1559 94.6210 189 2086 2 chr2B.!!$R3 1897
3 TraesCS2D01G508000 chr2B 731476087 731476722 635 True 688.0 688 86.1750 2465 3112 1 chr2B.!!$R1 647
4 TraesCS2D01G508000 chr2B 731525616 731526317 701 True 547.0 547 80.8990 1343 2048 1 chr2B.!!$R2 705
5 TraesCS2D01G508000 chr2A 734652041 734654266 2225 True 865.5 1389 80.7410 553 2818 2 chr2A.!!$R1 2265
6 TraesCS2D01G508000 chr7D 61227434 61228399 965 True 876.0 876 83.1280 1078 2044 1 chr7D.!!$R2 966
7 TraesCS2D01G508000 chr7D 60704087 60705013 926 True 854.0 854 83.3510 1117 2044 1 chr7D.!!$R1 927
8 TraesCS2D01G508000 chr7D 62280555 62281528 973 False 697.0 697 79.6110 1078 2051 1 chr7D.!!$F1 973
9 TraesCS2D01G508000 chr7B 3341071 3342025 954 True 850.0 850 82.7770 1078 2033 1 chr7B.!!$R1 955
10 TraesCS2D01G508000 chr7A 65153346 65154311 965 True 848.0 848 82.6130 1078 2044 1 chr7A.!!$R2 966

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
51 52 0.099968 CACAAAGCTGCCATCCATCG 59.900 55.0 0.0 0.0 0.00 3.84 F
1047 1049 0.107165 GAAAAGGAGGATGACCCCCG 60.107 60.0 0.0 0.0 36.73 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1427 0.036306 AACCGAAATCGAGCCTTGGT 59.964 50.0 4.04 0.0 43.02 3.67 R
2824 2892 0.179073 ATCTGCTTGGATTCGGTCGG 60.179 55.0 0.00 0.0 0.00 4.79 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
27 28 5.862678 ATTTCCTTTCGTTCTTTTTCCCA 57.137 34.783 0.00 0.00 0.00 4.37
28 29 4.642445 TTCCTTTCGTTCTTTTTCCCAC 57.358 40.909 0.00 0.00 0.00 4.61
29 30 3.622630 TCCTTTCGTTCTTTTTCCCACA 58.377 40.909 0.00 0.00 0.00 4.17
30 31 4.017808 TCCTTTCGTTCTTTTTCCCACAA 58.982 39.130 0.00 0.00 0.00 3.33
31 32 4.097286 TCCTTTCGTTCTTTTTCCCACAAG 59.903 41.667 0.00 0.00 0.00 3.16
32 33 3.430333 TTCGTTCTTTTTCCCACAAGC 57.570 42.857 0.00 0.00 0.00 4.01
33 34 2.370349 TCGTTCTTTTTCCCACAAGCA 58.630 42.857 0.00 0.00 0.00 3.91
34 35 2.098443 TCGTTCTTTTTCCCACAAGCAC 59.902 45.455 0.00 0.00 0.00 4.40
35 36 2.159310 CGTTCTTTTTCCCACAAGCACA 60.159 45.455 0.00 0.00 0.00 4.57
36 37 3.674682 CGTTCTTTTTCCCACAAGCACAA 60.675 43.478 0.00 0.00 0.00 3.33
37 38 4.249661 GTTCTTTTTCCCACAAGCACAAA 58.750 39.130 0.00 0.00 0.00 2.83
38 39 4.122143 TCTTTTTCCCACAAGCACAAAG 57.878 40.909 0.00 0.00 0.00 2.77
39 40 2.307934 TTTTCCCACAAGCACAAAGC 57.692 45.000 0.00 0.00 46.19 3.51
48 49 3.368822 GCACAAAGCTGCCATCCA 58.631 55.556 0.00 0.00 41.15 3.41
49 50 1.895238 GCACAAAGCTGCCATCCAT 59.105 52.632 0.00 0.00 41.15 3.41
50 51 0.179119 GCACAAAGCTGCCATCCATC 60.179 55.000 0.00 0.00 41.15 3.51
51 52 0.099968 CACAAAGCTGCCATCCATCG 59.900 55.000 0.00 0.00 0.00 3.84
52 53 0.322816 ACAAAGCTGCCATCCATCGT 60.323 50.000 0.00 0.00 0.00 3.73
53 54 0.813184 CAAAGCTGCCATCCATCGTT 59.187 50.000 0.00 0.00 0.00 3.85
54 55 2.016318 CAAAGCTGCCATCCATCGTTA 58.984 47.619 0.00 0.00 0.00 3.18
55 56 2.418368 AAGCTGCCATCCATCGTTAA 57.582 45.000 0.00 0.00 0.00 2.01
56 57 2.418368 AGCTGCCATCCATCGTTAAA 57.582 45.000 0.00 0.00 0.00 1.52
57 58 2.722094 AGCTGCCATCCATCGTTAAAA 58.278 42.857 0.00 0.00 0.00 1.52
58 59 3.088532 AGCTGCCATCCATCGTTAAAAA 58.911 40.909 0.00 0.00 0.00 1.94
89 90 9.702726 GTTTTATGAAAAAGAAAAACAGAAGCC 57.297 29.630 0.00 0.00 40.09 4.35
90 91 9.442047 TTTTATGAAAAAGAAAAACAGAAGCCA 57.558 25.926 0.00 0.00 31.04 4.75
91 92 9.442047 TTTATGAAAAAGAAAAACAGAAGCCAA 57.558 25.926 0.00 0.00 0.00 4.52
92 93 7.920160 ATGAAAAAGAAAAACAGAAGCCAAA 57.080 28.000 0.00 0.00 0.00 3.28
93 94 7.363205 TGAAAAAGAAAAACAGAAGCCAAAG 57.637 32.000 0.00 0.00 0.00 2.77
94 95 6.934083 TGAAAAAGAAAAACAGAAGCCAAAGT 59.066 30.769 0.00 0.00 0.00 2.66
95 96 8.091449 TGAAAAAGAAAAACAGAAGCCAAAGTA 58.909 29.630 0.00 0.00 0.00 2.24
96 97 7.827819 AAAAGAAAAACAGAAGCCAAAGTAC 57.172 32.000 0.00 0.00 0.00 2.73
97 98 6.524101 AAGAAAAACAGAAGCCAAAGTACA 57.476 33.333 0.00 0.00 0.00 2.90
98 99 6.136541 AGAAAAACAGAAGCCAAAGTACAG 57.863 37.500 0.00 0.00 0.00 2.74
99 100 5.885912 AGAAAAACAGAAGCCAAAGTACAGA 59.114 36.000 0.00 0.00 0.00 3.41
100 101 6.377146 AGAAAAACAGAAGCCAAAGTACAGAA 59.623 34.615 0.00 0.00 0.00 3.02
101 102 6.524101 AAAACAGAAGCCAAAGTACAGAAA 57.476 33.333 0.00 0.00 0.00 2.52
102 103 5.757850 AACAGAAGCCAAAGTACAGAAAG 57.242 39.130 0.00 0.00 0.00 2.62
103 104 4.781934 ACAGAAGCCAAAGTACAGAAAGT 58.218 39.130 0.00 0.00 0.00 2.66
104 105 4.576463 ACAGAAGCCAAAGTACAGAAAGTG 59.424 41.667 0.00 0.00 0.00 3.16
105 106 3.565902 AGAAGCCAAAGTACAGAAAGTGC 59.434 43.478 0.00 0.00 0.00 4.40
106 107 2.930950 AGCCAAAGTACAGAAAGTGCA 58.069 42.857 0.00 0.00 35.00 4.57
107 108 3.287222 AGCCAAAGTACAGAAAGTGCAA 58.713 40.909 0.00 0.00 35.00 4.08
108 109 3.316308 AGCCAAAGTACAGAAAGTGCAAG 59.684 43.478 0.00 0.00 35.00 4.01
109 110 3.315191 GCCAAAGTACAGAAAGTGCAAGA 59.685 43.478 0.00 0.00 35.00 3.02
110 111 4.202010 GCCAAAGTACAGAAAGTGCAAGAA 60.202 41.667 0.00 0.00 35.00 2.52
111 112 5.678616 GCCAAAGTACAGAAAGTGCAAGAAA 60.679 40.000 0.00 0.00 35.00 2.52
112 113 6.329496 CCAAAGTACAGAAAGTGCAAGAAAA 58.671 36.000 0.00 0.00 35.00 2.29
113 114 6.811170 CCAAAGTACAGAAAGTGCAAGAAAAA 59.189 34.615 0.00 0.00 35.00 1.94
114 115 7.492344 CCAAAGTACAGAAAGTGCAAGAAAAAT 59.508 33.333 0.00 0.00 35.00 1.82
115 116 9.515020 CAAAGTACAGAAAGTGCAAGAAAAATA 57.485 29.630 0.00 0.00 35.00 1.40
116 117 9.736023 AAAGTACAGAAAGTGCAAGAAAAATAG 57.264 29.630 0.00 0.00 35.00 1.73
117 118 8.677148 AGTACAGAAAGTGCAAGAAAAATAGA 57.323 30.769 0.00 0.00 35.00 1.98
118 119 9.289782 AGTACAGAAAGTGCAAGAAAAATAGAT 57.710 29.630 0.00 0.00 35.00 1.98
122 123 9.727627 CAGAAAGTGCAAGAAAAATAGATATCC 57.272 33.333 0.00 0.00 0.00 2.59
123 124 8.907885 AGAAAGTGCAAGAAAAATAGATATCCC 58.092 33.333 0.00 0.00 0.00 3.85
124 125 8.593945 AAAGTGCAAGAAAAATAGATATCCCA 57.406 30.769 0.00 0.00 0.00 4.37
125 126 8.593945 AAGTGCAAGAAAAATAGATATCCCAA 57.406 30.769 0.00 0.00 0.00 4.12
126 127 8.593945 AGTGCAAGAAAAATAGATATCCCAAA 57.406 30.769 0.00 0.00 0.00 3.28
127 128 9.205513 AGTGCAAGAAAAATAGATATCCCAAAT 57.794 29.630 0.00 0.00 0.00 2.32
128 129 9.822185 GTGCAAGAAAAATAGATATCCCAAATT 57.178 29.630 0.00 0.00 0.00 1.82
147 148 7.581011 CAAATTAGTTGGCTGGTTCATTTAC 57.419 36.000 0.00 0.00 33.18 2.01
148 149 6.909550 AATTAGTTGGCTGGTTCATTTACA 57.090 33.333 0.00 0.00 0.00 2.41
149 150 6.909550 ATTAGTTGGCTGGTTCATTTACAA 57.090 33.333 0.00 0.00 0.00 2.41
150 151 6.909550 TTAGTTGGCTGGTTCATTTACAAT 57.090 33.333 0.00 0.00 0.00 2.71
151 152 5.391312 AGTTGGCTGGTTCATTTACAATC 57.609 39.130 0.00 0.00 0.00 2.67
152 153 4.220602 AGTTGGCTGGTTCATTTACAATCC 59.779 41.667 0.00 0.00 0.00 3.01
153 154 4.046286 TGGCTGGTTCATTTACAATCCT 57.954 40.909 0.00 0.00 0.00 3.24
154 155 4.415596 TGGCTGGTTCATTTACAATCCTT 58.584 39.130 0.00 0.00 0.00 3.36
155 156 4.837860 TGGCTGGTTCATTTACAATCCTTT 59.162 37.500 0.00 0.00 0.00 3.11
156 157 5.306678 TGGCTGGTTCATTTACAATCCTTTT 59.693 36.000 0.00 0.00 0.00 2.27
157 158 5.869344 GGCTGGTTCATTTACAATCCTTTTC 59.131 40.000 0.00 0.00 0.00 2.29
158 159 6.454795 GCTGGTTCATTTACAATCCTTTTCA 58.545 36.000 0.00 0.00 0.00 2.69
159 160 6.928492 GCTGGTTCATTTACAATCCTTTTCAA 59.072 34.615 0.00 0.00 0.00 2.69
160 161 7.603784 GCTGGTTCATTTACAATCCTTTTCAAT 59.396 33.333 0.00 0.00 0.00 2.57
222 223 0.248621 GTGTTCCTGTTGTGCAGTGC 60.249 55.000 8.58 8.58 43.55 4.40
243 244 3.489398 GCGAAAAACATGGGTTACACACA 60.489 43.478 0.00 0.00 35.08 3.72
245 246 4.501198 CGAAAAACATGGGTTACACACAAC 59.499 41.667 0.00 0.00 33.78 3.32
272 273 5.163571 TGCACCATGAAAAATATGCACGTAT 60.164 36.000 0.00 0.00 38.11 3.06
301 303 2.973406 GGTTAAGAGTAGGGATGGAGGG 59.027 54.545 0.00 0.00 0.00 4.30
308 310 2.158234 AGTAGGGATGGAGGGTCTCATC 60.158 54.545 0.00 0.00 31.08 2.92
350 352 9.346725 CAAGGACTGCTAGAAATTTATTTGAAC 57.653 33.333 0.00 0.00 0.00 3.18
351 353 8.870075 AGGACTGCTAGAAATTTATTTGAACT 57.130 30.769 0.00 0.00 0.00 3.01
352 354 9.959721 AGGACTGCTAGAAATTTATTTGAACTA 57.040 29.630 0.00 0.00 0.00 2.24
447 449 8.520351 GCCCTTGTATAAATATCCCATTGTTAC 58.480 37.037 0.00 0.00 0.00 2.50
448 450 9.807921 CCCTTGTATAAATATCCCATTGTTACT 57.192 33.333 0.00 0.00 0.00 2.24
468 470 0.255890 GGCCTTGGTTGCTATCCTCA 59.744 55.000 0.00 0.00 0.00 3.86
471 473 2.487934 CCTTGGTTGCTATCCTCATCG 58.512 52.381 0.00 0.00 0.00 3.84
482 484 4.619160 GCTATCCTCATCGACATATGCACA 60.619 45.833 1.58 0.00 0.00 4.57
488 490 1.137459 TCGACATATGCACACGACGC 61.137 55.000 1.58 0.00 0.00 5.19
524 526 5.939883 CCCAACAACATGAGTTCTCATCTTA 59.060 40.000 11.75 0.00 35.28 2.10
579 581 0.911769 ACCCTCATCCTGCGAATTGA 59.088 50.000 0.00 0.00 0.00 2.57
617 619 0.468226 AGGTGCCGTTCTCACAAAGA 59.532 50.000 0.00 0.00 36.22 2.52
630 632 3.153919 TCACAAAGATTACACAAGGGGC 58.846 45.455 0.00 0.00 0.00 5.80
640 642 2.435586 CAAGGGGCTGTCTCTGCG 60.436 66.667 0.00 0.00 0.00 5.18
753 755 2.159407 GCACTCCGTCCTAGAACTGTAC 60.159 54.545 0.00 0.00 0.00 2.90
759 761 3.079578 CGTCCTAGAACTGTACACCTCA 58.920 50.000 0.00 0.00 0.00 3.86
782 784 0.523072 ACTATGCTTGCTTTGTGGCG 59.477 50.000 0.00 0.00 34.52 5.69
859 861 8.484214 TCACCTTTGCTAGATGATTCTACTAT 57.516 34.615 0.00 0.00 33.17 2.12
971 973 1.291184 TTGATGAAGCACACGCGGAG 61.291 55.000 12.47 4.93 45.49 4.63
980 982 2.273179 ACACGCGGAGGCAGAGTTA 61.273 57.895 12.47 0.00 39.92 2.24
1003 1005 2.301583 TCGTGTTCCCAGTGATTGATGA 59.698 45.455 0.00 0.00 0.00 2.92
1004 1006 3.073678 CGTGTTCCCAGTGATTGATGAA 58.926 45.455 0.00 0.00 0.00 2.57
1005 1007 3.120199 CGTGTTCCCAGTGATTGATGAAC 60.120 47.826 0.00 0.00 38.13 3.18
1006 1008 4.074970 GTGTTCCCAGTGATTGATGAACT 58.925 43.478 10.05 0.00 38.30 3.01
1007 1009 4.520492 GTGTTCCCAGTGATTGATGAACTT 59.480 41.667 10.05 0.00 38.30 2.66
1008 1010 5.010012 GTGTTCCCAGTGATTGATGAACTTT 59.990 40.000 10.05 0.00 38.30 2.66
1009 1011 5.598005 TGTTCCCAGTGATTGATGAACTTTT 59.402 36.000 10.05 0.00 38.30 2.27
1010 1012 6.098124 TGTTCCCAGTGATTGATGAACTTTTT 59.902 34.615 10.05 0.00 38.30 1.94
1011 1013 6.088016 TCCCAGTGATTGATGAACTTTTTG 57.912 37.500 0.00 0.00 0.00 2.44
1012 1014 4.687483 CCCAGTGATTGATGAACTTTTTGC 59.313 41.667 0.00 0.00 0.00 3.68
1013 1015 4.687483 CCAGTGATTGATGAACTTTTTGCC 59.313 41.667 0.00 0.00 0.00 4.52
1014 1016 5.291178 CAGTGATTGATGAACTTTTTGCCA 58.709 37.500 0.00 0.00 0.00 4.92
1015 1017 5.754406 CAGTGATTGATGAACTTTTTGCCAA 59.246 36.000 0.00 0.00 0.00 4.52
1016 1018 5.987347 AGTGATTGATGAACTTTTTGCCAAG 59.013 36.000 0.00 0.00 0.00 3.61
1017 1019 5.984926 GTGATTGATGAACTTTTTGCCAAGA 59.015 36.000 0.00 0.00 0.00 3.02
1018 1020 6.647895 GTGATTGATGAACTTTTTGCCAAGAT 59.352 34.615 0.00 0.00 0.00 2.40
1019 1021 7.814107 GTGATTGATGAACTTTTTGCCAAGATA 59.186 33.333 0.00 0.00 0.00 1.98
1020 1022 8.533657 TGATTGATGAACTTTTTGCCAAGATAT 58.466 29.630 0.00 0.00 0.00 1.63
1021 1023 9.374838 GATTGATGAACTTTTTGCCAAGATATT 57.625 29.630 0.00 0.00 0.00 1.28
1022 1024 9.729281 ATTGATGAACTTTTTGCCAAGATATTT 57.271 25.926 0.00 0.00 0.00 1.40
1023 1025 9.558396 TTGATGAACTTTTTGCCAAGATATTTT 57.442 25.926 0.00 0.00 0.00 1.82
1024 1026 9.558396 TGATGAACTTTTTGCCAAGATATTTTT 57.442 25.926 0.00 0.00 0.00 1.94
1045 1047 4.586306 TTTAGAAAAGGAGGATGACCCC 57.414 45.455 0.00 0.00 36.73 4.95
1046 1048 1.299939 AGAAAAGGAGGATGACCCCC 58.700 55.000 0.00 0.00 36.73 5.40
1047 1049 0.107165 GAAAAGGAGGATGACCCCCG 60.107 60.000 0.00 0.00 36.73 5.73
1048 1050 1.571773 AAAAGGAGGATGACCCCCGG 61.572 60.000 0.00 0.00 36.73 5.73
1054 1056 3.866582 GATGACCCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
1060 1062 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
1061 1063 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
1062 1064 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
1065 1067 4.166888 GCCTCTGCATCTGGGCGA 62.167 66.667 0.00 0.00 37.47 5.54
1066 1068 2.827423 CCTCTGCATCTGGGCGAT 59.173 61.111 0.00 0.00 36.28 4.58
1073 1075 2.156542 CATCTGGGCGATGCATACG 58.843 57.895 0.00 6.68 42.75 3.06
1074 1076 1.004560 ATCTGGGCGATGCATACGG 60.005 57.895 16.56 6.65 0.00 4.02
1100 1102 2.747396 TTTTGCCAAGACATGCATCC 57.253 45.000 0.00 0.00 37.33 3.51
1144 1146 3.719268 ATCACCAACTGCAGTGGATTA 57.281 42.857 30.11 19.16 34.67 1.75
1164 1166 2.512974 CCCGGTACCATCCAACGC 60.513 66.667 13.54 0.00 0.00 4.84
1419 1421 1.621301 CGCCAAGCTCTTGTCGACTG 61.621 60.000 17.92 9.81 43.57 3.51
1425 1427 0.811915 GCTCTTGTCGACTGCTAGGA 59.188 55.000 17.92 1.07 0.00 2.94
1443 1445 0.391263 GACCAAGGCTCGATTTCGGT 60.391 55.000 0.00 0.00 40.29 4.69
1459 1461 1.814772 CGGTTTGAGCATTTGGCCCA 61.815 55.000 0.00 0.00 46.50 5.36
1463 1465 0.178967 TTGAGCATTTGGCCCAGACA 60.179 50.000 0.00 0.00 46.50 3.41
1499 1501 1.261938 ATGCTGCCTACCGGTGTGTA 61.262 55.000 19.93 6.57 0.00 2.90
1539 1541 1.217942 AGGGAAACTTTGGGACTGCTT 59.782 47.619 0.00 0.00 0.00 3.91
1541 1543 2.434336 GGGAAACTTTGGGACTGCTTTT 59.566 45.455 0.00 0.00 0.00 2.27
1556 1558 7.827729 GGGACTGCTTTTTCTAAAGACCTTATA 59.172 37.037 2.02 0.00 42.78 0.98
1644 1646 2.741517 GAGCTTCTCAGAGTTTTGCTCC 59.258 50.000 17.63 7.37 45.21 4.70
1668 1670 0.597568 CATGGCGAAAAAGGTGCTCA 59.402 50.000 0.00 0.00 0.00 4.26
1699 1701 1.541233 GGCGAGACAATACATCCCCAG 60.541 57.143 0.00 0.00 0.00 4.45
2025 2027 2.193127 TCCATCGTTACCCAGTGGATT 58.807 47.619 11.95 0.00 34.23 3.01
2078 2088 9.557061 TTAATCACATCGACATCTACTACTACT 57.443 33.333 0.00 0.00 0.00 2.57
2079 2089 6.846325 TCACATCGACATCTACTACTACTG 57.154 41.667 0.00 0.00 0.00 2.74
2080 2090 6.346896 TCACATCGACATCTACTACTACTGT 58.653 40.000 0.00 0.00 0.00 3.55
2081 2091 6.822170 TCACATCGACATCTACTACTACTGTT 59.178 38.462 0.00 0.00 0.00 3.16
2082 2092 6.907748 CACATCGACATCTACTACTACTGTTG 59.092 42.308 0.00 0.00 0.00 3.33
2083 2093 5.481200 TCGACATCTACTACTACTGTTGC 57.519 43.478 0.00 0.00 0.00 4.17
2084 2094 5.183969 TCGACATCTACTACTACTGTTGCT 58.816 41.667 0.00 0.00 0.00 3.91
2085 2095 5.064834 TCGACATCTACTACTACTGTTGCTG 59.935 44.000 0.00 0.00 0.00 4.41
2086 2096 5.583495 GACATCTACTACTACTGTTGCTGG 58.417 45.833 0.00 0.00 0.00 4.85
2102 2148 5.582269 TGTTGCTGGTACTACTACTACTACG 59.418 44.000 0.00 0.00 0.00 3.51
2105 2151 4.442733 GCTGGTACTACTACTACTACGTCG 59.557 50.000 0.00 0.00 0.00 5.12
2121 2167 2.096174 ACGTCGACATCTAGAAGAGCAC 59.904 50.000 17.16 0.00 0.00 4.40
2154 2200 9.226606 TGATAATCCAATAAAAAGACACGACTT 57.773 29.630 0.00 0.00 0.00 3.01
2158 2204 6.285224 TCCAATAAAAAGACACGACTTCTCA 58.715 36.000 0.00 0.00 0.00 3.27
2178 2224 0.471591 ACTCCATTGCCCAAAAGCCA 60.472 50.000 0.00 0.00 0.00 4.75
2210 2256 5.483937 TGTTTAGAGAGGGCAGAATAGTCAA 59.516 40.000 0.00 0.00 0.00 3.18
2237 2283 5.912149 TGGGCACTTTAGAGATTATCCAT 57.088 39.130 0.00 0.00 0.00 3.41
2256 2304 4.278170 TCCATGCGAATGTTTTTCTCAGTT 59.722 37.500 1.88 0.00 0.00 3.16
2278 2326 7.223971 CAGTTATTGTATCGGCTTTGCTAGTTA 59.776 37.037 0.00 0.00 0.00 2.24
2282 2330 7.473027 TTGTATCGGCTTTGCTAGTTATAAC 57.527 36.000 7.57 7.57 0.00 1.89
2296 2347 7.764443 TGCTAGTTATAACTAAGTTGCTTGAGG 59.236 37.037 22.47 10.10 40.70 3.86
2300 2351 8.376270 AGTTATAACTAAGTTGCTTGAGGACTT 58.624 33.333 16.60 0.00 37.52 3.01
2302 2353 4.689612 ACTAAGTTGCTTGAGGACTTCA 57.310 40.909 0.00 0.00 35.43 3.02
2306 2357 3.144506 AGTTGCTTGAGGACTTCATGTG 58.855 45.455 0.00 0.00 35.27 3.21
2319 2370 6.758886 AGGACTTCATGTGTCTAATTCGATTC 59.241 38.462 16.60 2.39 35.04 2.52
2322 2373 5.351948 TCATGTGTCTAATTCGATTCCCA 57.648 39.130 0.00 0.00 0.00 4.37
2324 2375 5.817296 TCATGTGTCTAATTCGATTCCCAAG 59.183 40.000 0.00 0.00 0.00 3.61
2334 2385 3.420893 TCGATTCCCAAGAAAGTGCAAT 58.579 40.909 0.00 0.00 35.09 3.56
2340 2391 7.170658 CGATTCCCAAGAAAGTGCAATTTTAAA 59.829 33.333 14.04 3.27 35.09 1.52
2399 2459 1.139498 TTTGGATGGAGGGAGTGGCA 61.139 55.000 0.00 0.00 0.00 4.92
2402 2462 0.691078 GGATGGAGGGAGTGGCACTA 60.691 60.000 22.11 3.71 0.00 2.74
2411 2471 0.452585 GAGTGGCACTACGAGAGGAC 59.547 60.000 22.11 0.21 0.00 3.85
2413 2473 2.102553 GGCACTACGAGAGGACGC 59.897 66.667 0.00 0.00 36.70 5.19
2419 2479 1.018148 CTACGAGAGGACGCTGATGT 58.982 55.000 0.00 0.00 36.70 3.06
2420 2480 1.003331 CTACGAGAGGACGCTGATGTC 60.003 57.143 0.00 0.00 38.17 3.06
2421 2481 0.678366 ACGAGAGGACGCTGATGTCT 60.678 55.000 0.00 0.00 38.91 3.41
2422 2482 1.300481 CGAGAGGACGCTGATGTCTA 58.700 55.000 1.44 0.00 38.91 2.59
2427 2488 0.104855 GGACGCTGATGTCTATGGCA 59.895 55.000 0.00 0.00 38.91 4.92
2436 2497 3.135167 TGATGTCTATGGCAAGCATGAGA 59.865 43.478 0.00 0.00 0.00 3.27
2450 2511 2.650608 CATGAGAACGCATGCATGATG 58.349 47.619 30.64 22.14 40.29 3.07
2451 2512 1.741528 TGAGAACGCATGCATGATGT 58.258 45.000 30.64 22.80 34.14 3.06
2461 2522 3.127376 GCATGCATGATGTTGTGTAGACA 59.873 43.478 30.64 0.00 34.14 3.41
2487 2552 3.125316 CAACTGGCTGTTTTTCATGTGG 58.875 45.455 7.06 0.00 36.63 4.17
2490 2555 3.642848 ACTGGCTGTTTTTCATGTGGAAT 59.357 39.130 0.00 0.00 34.91 3.01
2499 2564 0.617935 TCATGTGGAATGGCCGAAGA 59.382 50.000 0.00 0.00 40.66 2.87
2517 2583 8.204836 GGCCGAAGACCATATATTAAGTATCAT 58.795 37.037 0.00 0.00 0.00 2.45
2534 2601 6.223852 AGTATCATAGGTCCTTGCAAATACG 58.776 40.000 0.00 0.00 0.00 3.06
2578 2646 5.806654 ACAATGTAATTTTTGGGAGTGCT 57.193 34.783 0.00 0.00 31.22 4.40
2598 2666 2.992543 CTGAAGTCTTCTTCCTCTTGCG 59.007 50.000 13.67 0.00 46.66 4.85
2603 2671 0.038159 CTTCTTCCTCTTGCGTCCGT 60.038 55.000 0.00 0.00 0.00 4.69
2608 2676 2.049156 CTCTTGCGTCCGTCAGCA 60.049 61.111 0.00 0.00 42.15 4.41
2620 2688 2.202946 TCAGCAACACGCCGTGAA 60.203 55.556 25.94 0.00 44.04 3.18
2628 2696 0.528924 ACACGCCGTGAACATAGCTA 59.471 50.000 25.94 0.00 36.96 3.32
2666 2734 3.190874 CTCCGCCTTGACTGAGTAAATC 58.809 50.000 0.00 0.00 0.00 2.17
2671 2739 5.063564 CCGCCTTGACTGAGTAAATCTTAAC 59.936 44.000 0.00 0.00 0.00 2.01
2675 2743 7.803659 GCCTTGACTGAGTAAATCTTAACAAAC 59.196 37.037 0.00 0.00 0.00 2.93
2689 2757 9.515226 AATCTTAACAAACCTATGAGCTTGTAA 57.485 29.630 0.00 0.00 31.90 2.41
2707 2775 3.558099 AAAGCAGCGGCCGAAAAGC 62.558 57.895 33.48 24.89 42.56 3.51
2722 2790 0.811616 AAAGCCGTCGATGCAGATCC 60.812 55.000 11.76 0.00 0.00 3.36
2773 2841 2.931246 CAAACCAAATTGCTGCCCC 58.069 52.632 0.00 0.00 0.00 5.80
2813 2881 4.937201 AAAGGCCTGTAAAAACTCCAAG 57.063 40.909 5.69 0.00 0.00 3.61
2814 2882 3.876309 AGGCCTGTAAAAACTCCAAGA 57.124 42.857 3.11 0.00 0.00 3.02
2815 2883 3.487372 AGGCCTGTAAAAACTCCAAGAC 58.513 45.455 3.11 0.00 0.00 3.01
2816 2884 2.557056 GGCCTGTAAAAACTCCAAGACC 59.443 50.000 0.00 0.00 0.00 3.85
2817 2885 3.219281 GCCTGTAAAAACTCCAAGACCA 58.781 45.455 0.00 0.00 0.00 4.02
2818 2886 3.004419 GCCTGTAAAAACTCCAAGACCAC 59.996 47.826 0.00 0.00 0.00 4.16
2819 2887 3.250040 CCTGTAAAAACTCCAAGACCACG 59.750 47.826 0.00 0.00 0.00 4.94
2820 2888 4.124238 CTGTAAAAACTCCAAGACCACGA 58.876 43.478 0.00 0.00 0.00 4.35
2821 2889 4.515361 TGTAAAAACTCCAAGACCACGAA 58.485 39.130 0.00 0.00 0.00 3.85
2822 2890 4.942483 TGTAAAAACTCCAAGACCACGAAA 59.058 37.500 0.00 0.00 0.00 3.46
2823 2891 4.632538 AAAAACTCCAAGACCACGAAAG 57.367 40.909 0.00 0.00 0.00 2.62
2824 2892 1.594331 AACTCCAAGACCACGAAAGC 58.406 50.000 0.00 0.00 0.00 3.51
2825 2893 0.250338 ACTCCAAGACCACGAAAGCC 60.250 55.000 0.00 0.00 0.00 4.35
2826 2894 1.291877 CTCCAAGACCACGAAAGCCG 61.292 60.000 0.00 0.00 45.44 5.52
2827 2895 1.301401 CCAAGACCACGAAAGCCGA 60.301 57.895 0.00 0.00 41.76 5.54
2828 2896 1.566018 CCAAGACCACGAAAGCCGAC 61.566 60.000 0.00 0.00 41.76 4.79
2829 2897 1.301479 AAGACCACGAAAGCCGACC 60.301 57.895 0.00 0.00 41.76 4.79
2830 2898 3.110178 GACCACGAAAGCCGACCG 61.110 66.667 0.00 0.00 41.76 4.79
2831 2899 3.562779 GACCACGAAAGCCGACCGA 62.563 63.158 0.00 0.00 41.76 4.69
2832 2900 2.356553 CCACGAAAGCCGACCGAA 60.357 61.111 0.00 0.00 41.76 4.30
2833 2901 1.740296 CCACGAAAGCCGACCGAAT 60.740 57.895 0.00 0.00 41.76 3.34
2834 2902 1.693083 CCACGAAAGCCGACCGAATC 61.693 60.000 0.00 0.00 41.76 2.52
2835 2903 1.447314 ACGAAAGCCGACCGAATCC 60.447 57.895 0.00 0.00 41.76 3.01
2836 2904 1.447140 CGAAAGCCGACCGAATCCA 60.447 57.895 0.00 0.00 41.76 3.41
2837 2905 1.017177 CGAAAGCCGACCGAATCCAA 61.017 55.000 0.00 0.00 41.76 3.53
2838 2906 0.727398 GAAAGCCGACCGAATCCAAG 59.273 55.000 0.00 0.00 0.00 3.61
2839 2907 1.305930 AAAGCCGACCGAATCCAAGC 61.306 55.000 0.00 0.00 0.00 4.01
2843 2911 0.179073 CCGACCGAATCCAAGCAGAT 60.179 55.000 0.00 0.00 0.00 2.90
2870 2966 6.600882 TCAGAAACCTAAACCGACTAGATT 57.399 37.500 0.00 0.00 0.00 2.40
2968 3064 3.591527 TGGGGAGAACATTGTTCCTACAT 59.408 43.478 22.70 6.89 33.44 2.29
2988 3084 2.568090 GGACAATGTTGCCGCCTG 59.432 61.111 0.00 0.00 0.00 4.85
3028 3124 7.609532 CAGACATGAAGACTCCCTAAAGAAAAT 59.390 37.037 0.00 0.00 0.00 1.82
3089 3187 5.068329 TCTGAGTATGATGTTGAAGATCGCT 59.932 40.000 0.00 0.00 0.00 4.93
3094 3192 1.063174 GATGTTGAAGATCGCTGCACC 59.937 52.381 0.00 0.00 26.09 5.01
3112 3210 3.967335 GGATCTCTCCGACCGCCG 61.967 72.222 0.00 0.00 38.18 6.46
3113 3211 4.632458 GATCTCTCCGACCGCCGC 62.632 72.222 0.00 0.00 36.84 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.250246 TGGGAAAAAGAACGAAAGGAAATATAT 57.750 29.630 0.00 0.00 0.00 0.86
2 3 8.517056 GTGGGAAAAAGAACGAAAGGAAATATA 58.483 33.333 0.00 0.00 0.00 0.86
3 4 7.014808 TGTGGGAAAAAGAACGAAAGGAAATAT 59.985 33.333 0.00 0.00 0.00 1.28
4 5 6.321690 TGTGGGAAAAAGAACGAAAGGAAATA 59.678 34.615 0.00 0.00 0.00 1.40
5 6 5.128008 TGTGGGAAAAAGAACGAAAGGAAAT 59.872 36.000 0.00 0.00 0.00 2.17
6 7 4.463186 TGTGGGAAAAAGAACGAAAGGAAA 59.537 37.500 0.00 0.00 0.00 3.13
7 8 4.017808 TGTGGGAAAAAGAACGAAAGGAA 58.982 39.130 0.00 0.00 0.00 3.36
8 9 3.622630 TGTGGGAAAAAGAACGAAAGGA 58.377 40.909 0.00 0.00 0.00 3.36
9 10 4.359706 CTTGTGGGAAAAAGAACGAAAGG 58.640 43.478 0.00 0.00 0.00 3.11
10 11 3.796717 GCTTGTGGGAAAAAGAACGAAAG 59.203 43.478 0.00 0.00 0.00 2.62
11 12 3.193691 TGCTTGTGGGAAAAAGAACGAAA 59.806 39.130 0.00 0.00 0.00 3.46
12 13 2.755655 TGCTTGTGGGAAAAAGAACGAA 59.244 40.909 0.00 0.00 0.00 3.85
13 14 2.098443 GTGCTTGTGGGAAAAAGAACGA 59.902 45.455 0.00 0.00 0.00 3.85
14 15 2.159310 TGTGCTTGTGGGAAAAAGAACG 60.159 45.455 0.00 0.00 35.06 3.95
15 16 3.518634 TGTGCTTGTGGGAAAAAGAAC 57.481 42.857 0.00 0.00 33.22 3.01
16 17 4.502962 CTTTGTGCTTGTGGGAAAAAGAA 58.497 39.130 0.00 0.00 41.33 2.52
17 18 3.678529 GCTTTGTGCTTGTGGGAAAAAGA 60.679 43.478 4.42 0.00 41.33 2.52
18 19 2.609002 GCTTTGTGCTTGTGGGAAAAAG 59.391 45.455 0.00 0.00 41.61 2.27
19 20 2.626840 GCTTTGTGCTTGTGGGAAAAA 58.373 42.857 0.00 0.00 38.95 1.94
20 21 2.307934 GCTTTGTGCTTGTGGGAAAA 57.692 45.000 0.00 0.00 38.95 2.29
31 32 0.179119 GATGGATGGCAGCTTTGTGC 60.179 55.000 1.50 0.00 43.19 4.57
32 33 0.099968 CGATGGATGGCAGCTTTGTG 59.900 55.000 1.50 0.00 0.00 3.33
33 34 0.322816 ACGATGGATGGCAGCTTTGT 60.323 50.000 1.50 0.00 0.00 2.83
34 35 0.813184 AACGATGGATGGCAGCTTTG 59.187 50.000 1.50 0.00 0.00 2.77
35 36 2.418368 TAACGATGGATGGCAGCTTT 57.582 45.000 1.50 0.00 0.00 3.51
36 37 2.418368 TTAACGATGGATGGCAGCTT 57.582 45.000 1.50 0.00 0.00 3.74
37 38 2.418368 TTTAACGATGGATGGCAGCT 57.582 45.000 1.50 0.00 0.00 4.24
38 39 3.502191 TTTTTAACGATGGATGGCAGC 57.498 42.857 0.00 0.00 0.00 5.25
63 64 9.702726 GGCTTCTGTTTTTCTTTTTCATAAAAC 57.297 29.630 0.00 0.00 39.62 2.43
64 65 9.442047 TGGCTTCTGTTTTTCTTTTTCATAAAA 57.558 25.926 0.00 0.00 0.00 1.52
65 66 9.442047 TTGGCTTCTGTTTTTCTTTTTCATAAA 57.558 25.926 0.00 0.00 0.00 1.40
66 67 9.442047 TTTGGCTTCTGTTTTTCTTTTTCATAA 57.558 25.926 0.00 0.00 0.00 1.90
67 68 9.097257 CTTTGGCTTCTGTTTTTCTTTTTCATA 57.903 29.630 0.00 0.00 0.00 2.15
68 69 7.607607 ACTTTGGCTTCTGTTTTTCTTTTTCAT 59.392 29.630 0.00 0.00 0.00 2.57
69 70 6.934083 ACTTTGGCTTCTGTTTTTCTTTTTCA 59.066 30.769 0.00 0.00 0.00 2.69
70 71 7.364522 ACTTTGGCTTCTGTTTTTCTTTTTC 57.635 32.000 0.00 0.00 0.00 2.29
71 72 7.875554 TGTACTTTGGCTTCTGTTTTTCTTTTT 59.124 29.630 0.00 0.00 0.00 1.94
72 73 7.382898 TGTACTTTGGCTTCTGTTTTTCTTTT 58.617 30.769 0.00 0.00 0.00 2.27
73 74 6.930731 TGTACTTTGGCTTCTGTTTTTCTTT 58.069 32.000 0.00 0.00 0.00 2.52
74 75 6.377146 TCTGTACTTTGGCTTCTGTTTTTCTT 59.623 34.615 0.00 0.00 0.00 2.52
75 76 5.885912 TCTGTACTTTGGCTTCTGTTTTTCT 59.114 36.000 0.00 0.00 0.00 2.52
76 77 6.131544 TCTGTACTTTGGCTTCTGTTTTTC 57.868 37.500 0.00 0.00 0.00 2.29
77 78 6.524101 TTCTGTACTTTGGCTTCTGTTTTT 57.476 33.333 0.00 0.00 0.00 1.94
78 79 6.152831 ACTTTCTGTACTTTGGCTTCTGTTTT 59.847 34.615 0.00 0.00 0.00 2.43
79 80 5.652452 ACTTTCTGTACTTTGGCTTCTGTTT 59.348 36.000 0.00 0.00 0.00 2.83
80 81 5.066505 CACTTTCTGTACTTTGGCTTCTGTT 59.933 40.000 0.00 0.00 0.00 3.16
81 82 4.576463 CACTTTCTGTACTTTGGCTTCTGT 59.424 41.667 0.00 0.00 0.00 3.41
82 83 4.555511 GCACTTTCTGTACTTTGGCTTCTG 60.556 45.833 0.00 0.00 0.00 3.02
83 84 3.565902 GCACTTTCTGTACTTTGGCTTCT 59.434 43.478 0.00 0.00 0.00 2.85
84 85 3.315191 TGCACTTTCTGTACTTTGGCTTC 59.685 43.478 0.00 0.00 0.00 3.86
85 86 3.287222 TGCACTTTCTGTACTTTGGCTT 58.713 40.909 0.00 0.00 0.00 4.35
86 87 2.930950 TGCACTTTCTGTACTTTGGCT 58.069 42.857 0.00 0.00 0.00 4.75
87 88 3.315191 TCTTGCACTTTCTGTACTTTGGC 59.685 43.478 0.00 0.00 0.00 4.52
88 89 5.499139 TTCTTGCACTTTCTGTACTTTGG 57.501 39.130 0.00 0.00 0.00 3.28
89 90 7.810766 TTTTTCTTGCACTTTCTGTACTTTG 57.189 32.000 0.00 0.00 0.00 2.77
90 91 9.736023 CTATTTTTCTTGCACTTTCTGTACTTT 57.264 29.630 0.00 0.00 0.00 2.66
91 92 9.120538 TCTATTTTTCTTGCACTTTCTGTACTT 57.879 29.630 0.00 0.00 0.00 2.24
92 93 8.677148 TCTATTTTTCTTGCACTTTCTGTACT 57.323 30.769 0.00 0.00 0.00 2.73
96 97 9.727627 GGATATCTATTTTTCTTGCACTTTCTG 57.272 33.333 2.05 0.00 0.00 3.02
97 98 8.907885 GGGATATCTATTTTTCTTGCACTTTCT 58.092 33.333 2.05 0.00 0.00 2.52
98 99 8.686334 TGGGATATCTATTTTTCTTGCACTTTC 58.314 33.333 2.05 0.00 0.00 2.62
99 100 8.593945 TGGGATATCTATTTTTCTTGCACTTT 57.406 30.769 2.05 0.00 0.00 2.66
100 101 8.593945 TTGGGATATCTATTTTTCTTGCACTT 57.406 30.769 2.05 0.00 0.00 3.16
101 102 8.593945 TTTGGGATATCTATTTTTCTTGCACT 57.406 30.769 2.05 0.00 0.00 4.40
102 103 9.822185 AATTTGGGATATCTATTTTTCTTGCAC 57.178 29.630 2.05 0.00 0.00 4.57
123 124 7.151308 TGTAAATGAACCAGCCAACTAATTTG 58.849 34.615 0.00 0.00 34.63 2.32
124 125 7.296628 TGTAAATGAACCAGCCAACTAATTT 57.703 32.000 0.00 0.00 0.00 1.82
125 126 6.909550 TGTAAATGAACCAGCCAACTAATT 57.090 33.333 0.00 0.00 0.00 1.40
126 127 6.909550 TTGTAAATGAACCAGCCAACTAAT 57.090 33.333 0.00 0.00 0.00 1.73
127 128 6.071616 GGATTGTAAATGAACCAGCCAACTAA 60.072 38.462 0.00 0.00 0.00 2.24
128 129 5.417580 GGATTGTAAATGAACCAGCCAACTA 59.582 40.000 0.00 0.00 0.00 2.24
129 130 4.220602 GGATTGTAAATGAACCAGCCAACT 59.779 41.667 0.00 0.00 0.00 3.16
130 131 4.220602 AGGATTGTAAATGAACCAGCCAAC 59.779 41.667 0.00 0.00 0.00 3.77
131 132 4.415596 AGGATTGTAAATGAACCAGCCAA 58.584 39.130 0.00 0.00 0.00 4.52
132 133 4.046286 AGGATTGTAAATGAACCAGCCA 57.954 40.909 0.00 0.00 0.00 4.75
133 134 5.405935 AAAGGATTGTAAATGAACCAGCC 57.594 39.130 0.00 0.00 0.00 4.85
134 135 6.454795 TGAAAAGGATTGTAAATGAACCAGC 58.545 36.000 0.00 0.00 0.00 4.85
222 223 4.294416 TGTGTGTAACCCATGTTTTTCG 57.706 40.909 0.00 0.00 35.87 3.46
243 244 4.931002 GCATATTTTTCATGGTGCACAGTT 59.069 37.500 20.43 0.00 33.09 3.16
245 246 4.496360 TGCATATTTTTCATGGTGCACAG 58.504 39.130 20.43 8.03 37.63 3.66
251 252 6.691754 TCATACGTGCATATTTTTCATGGT 57.308 33.333 0.00 0.00 0.00 3.55
252 253 7.984002 TTTCATACGTGCATATTTTTCATGG 57.016 32.000 0.00 0.00 0.00 3.66
268 269 8.582437 TCCCTACTCTTAACCATATTTCATACG 58.418 37.037 0.00 0.00 0.00 3.06
272 273 7.570982 TCCATCCCTACTCTTAACCATATTTCA 59.429 37.037 0.00 0.00 0.00 2.69
284 285 1.940957 AGACCCTCCATCCCTACTCTT 59.059 52.381 0.00 0.00 0.00 2.85
301 303 4.615949 AGCAATGATCGTACAGATGAGAC 58.384 43.478 5.18 0.00 40.26 3.36
308 310 3.553511 GTCCTTGAGCAATGATCGTACAG 59.446 47.826 0.00 0.00 0.00 2.74
352 354 8.136165 GGAGAAATACGTAACATCACATCTACT 58.864 37.037 0.00 0.00 0.00 2.57
353 355 7.381678 GGGAGAAATACGTAACATCACATCTAC 59.618 40.741 0.00 0.00 0.00 2.59
447 449 0.257039 AGGATAGCAACCAAGGCCAG 59.743 55.000 5.01 0.00 0.00 4.85
448 450 0.255890 GAGGATAGCAACCAAGGCCA 59.744 55.000 5.01 0.00 0.00 5.36
468 470 1.477105 CGTCGTGTGCATATGTCGAT 58.523 50.000 15.08 0.00 33.35 3.59
471 473 0.025001 GTGCGTCGTGTGCATATGTC 59.975 55.000 4.29 0.00 45.34 3.06
482 484 0.947180 GGTAATGTGGTGTGCGTCGT 60.947 55.000 0.00 0.00 0.00 4.34
488 490 2.690497 TGTTGTTGGGTAATGTGGTGTG 59.310 45.455 0.00 0.00 0.00 3.82
524 526 9.686683 AAGATGGTATAGCAATCTTAAGTGTTT 57.313 29.630 19.25 0.00 44.04 2.83
549 551 0.895100 GATGAGGGTGTTGGCAGCAA 60.895 55.000 5.34 0.00 44.31 3.91
579 581 1.800586 CTGCGAGTGTAGTTGCAATGT 59.199 47.619 0.59 0.00 36.36 2.71
617 619 2.026822 CAGAGACAGCCCCTTGTGTAAT 60.027 50.000 0.00 0.00 0.00 1.89
630 632 0.390866 AATCTGGTGCGCAGAGACAG 60.391 55.000 12.22 17.14 31.61 3.51
699 701 3.878086 TGCTGTGACGATGAAAAGAAC 57.122 42.857 0.00 0.00 0.00 3.01
753 755 3.276857 AGCAAGCATAGTCAATGAGGTG 58.723 45.455 0.00 0.00 37.86 4.00
759 761 3.367703 GCCACAAAGCAAGCATAGTCAAT 60.368 43.478 0.00 0.00 0.00 2.57
782 784 4.755266 TGGGTATCTAAACTTGGAGCTC 57.245 45.455 4.71 4.71 0.00 4.09
817 819 2.562635 GTGAGAGATGTGCATGCTCAT 58.437 47.619 29.85 29.85 37.84 2.90
859 861 7.470702 GCTCCAGAATAGTAGCTATGAAGTTGA 60.471 40.741 0.00 0.00 32.18 3.18
964 966 1.935327 GACTAACTCTGCCTCCGCGT 61.935 60.000 4.92 0.00 38.08 6.01
971 973 1.672145 GGGAACACGACTAACTCTGCC 60.672 57.143 0.00 0.00 0.00 4.85
980 982 1.691976 TCAATCACTGGGAACACGACT 59.308 47.619 0.00 0.00 35.60 4.18
1022 1024 5.330233 GGGGTCATCCTCCTTTTCTAAAAA 58.670 41.667 0.00 0.00 35.33 1.94
1023 1025 4.930696 GGGGTCATCCTCCTTTTCTAAAA 58.069 43.478 0.00 0.00 35.33 1.52
1024 1026 4.586306 GGGGTCATCCTCCTTTTCTAAA 57.414 45.455 0.00 0.00 35.33 1.85
1037 1039 3.866582 CAGAGGCCGGGGGTCATC 61.867 72.222 2.18 0.00 0.00 2.92
1043 1045 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
1044 1046 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
1045 1047 4.559063 CCCAGATGCAGAGGCCGG 62.559 72.222 0.00 0.00 40.13 6.13
1048 1050 3.472943 ATCGCCCAGATGCAGAGGC 62.473 63.158 8.59 8.59 42.18 4.70
1049 1051 2.827423 ATCGCCCAGATGCAGAGG 59.173 61.111 0.00 0.00 38.36 3.69
1056 1058 1.004560 CCGTATGCATCGCCCAGAT 60.005 57.895 0.19 0.00 41.01 2.90
1057 1059 2.421314 CCGTATGCATCGCCCAGA 59.579 61.111 0.19 0.00 0.00 3.86
1058 1060 3.349006 GCCGTATGCATCGCCCAG 61.349 66.667 0.19 0.00 40.77 4.45
1059 1061 4.927782 GGCCGTATGCATCGCCCA 62.928 66.667 17.54 0.00 43.89 5.36
1060 1062 4.927782 TGGCCGTATGCATCGCCC 62.928 66.667 22.75 16.75 43.89 6.13
1061 1063 3.649986 GTGGCCGTATGCATCGCC 61.650 66.667 20.23 20.23 43.89 5.54
1062 1064 3.649986 GGTGGCCGTATGCATCGC 61.650 66.667 0.19 3.34 43.89 4.58
1063 1065 1.095228 AAAGGTGGCCGTATGCATCG 61.095 55.000 0.19 7.03 43.89 3.84
1064 1066 1.102978 AAAAGGTGGCCGTATGCATC 58.897 50.000 0.19 0.00 43.89 3.91
1065 1067 1.204467 CAAAAAGGTGGCCGTATGCAT 59.796 47.619 3.79 3.79 43.89 3.96
1066 1068 0.600557 CAAAAAGGTGGCCGTATGCA 59.399 50.000 0.00 0.00 43.89 3.96
1067 1069 0.735978 GCAAAAAGGTGGCCGTATGC 60.736 55.000 0.00 0.00 40.16 3.14
1068 1070 0.108851 GGCAAAAAGGTGGCCGTATG 60.109 55.000 0.00 0.00 38.04 2.39
1069 1071 2.272923 GGCAAAAAGGTGGCCGTAT 58.727 52.632 0.00 0.00 38.04 3.06
1070 1072 3.766432 GGCAAAAAGGTGGCCGTA 58.234 55.556 0.00 0.00 38.04 4.02
1074 1076 0.463620 TGTCTTGGCAAAAAGGTGGC 59.536 50.000 0.00 0.00 44.09 5.01
1075 1077 2.758009 CATGTCTTGGCAAAAAGGTGG 58.242 47.619 0.00 0.00 0.00 4.61
1076 1078 2.137523 GCATGTCTTGGCAAAAAGGTG 58.862 47.619 0.00 0.00 0.00 4.00
1100 1102 2.202743 ACGGATCGCATCACGGTG 60.203 61.111 0.56 0.56 43.89 4.94
1144 1146 1.226262 GTTGGATGGTACCGGGCAT 59.774 57.895 6.32 0.00 0.00 4.40
1164 1166 5.876460 TGTATCTGTTCACAATCATGTCAGG 59.124 40.000 0.00 0.00 37.82 3.86
1419 1421 0.466124 AATCGAGCCTTGGTCCTAGC 59.534 55.000 0.00 0.00 0.00 3.42
1425 1427 0.036306 AACCGAAATCGAGCCTTGGT 59.964 50.000 4.04 0.00 43.02 3.67
1459 1461 3.151554 TCATTTGCTGCAGTGATTGTCT 58.848 40.909 16.64 0.00 0.00 3.41
1499 1501 6.388814 TCCCTTCTCATCTTCCTCTTGATAT 58.611 40.000 0.00 0.00 0.00 1.63
1556 1558 4.606071 GCATCTCTTGCGACACCT 57.394 55.556 0.00 0.00 42.54 4.00
1565 1567 7.066766 GTGATATTTTCCTTCAGTGCATCTCTT 59.933 37.037 0.00 0.00 0.00 2.85
1668 1670 2.038007 TCTCGCCCTCCTTGAGCT 59.962 61.111 0.00 0.00 0.00 4.09
1699 1701 3.125316 TGCTCAAATGCAAGACAAAAGC 58.875 40.909 0.00 0.00 40.29 3.51
1892 1894 0.754957 TCCACACCCTGTTGCCTTTG 60.755 55.000 0.00 0.00 0.00 2.77
2025 2027 8.846211 CCTCTTAGTTTAAACATTGTTGGAGAA 58.154 33.333 20.06 0.00 0.00 2.87
2078 2088 5.582269 CGTAGTAGTAGTAGTACCAGCAACA 59.418 44.000 14.39 0.00 33.10 3.33
2079 2089 5.582665 ACGTAGTAGTAGTAGTACCAGCAAC 59.417 44.000 14.39 3.06 41.94 4.17
2080 2090 5.734720 ACGTAGTAGTAGTAGTACCAGCAA 58.265 41.667 14.39 0.00 41.94 3.91
2081 2091 5.344743 ACGTAGTAGTAGTAGTACCAGCA 57.655 43.478 14.39 0.00 41.94 4.41
2102 2148 3.766676 TGTGCTCTTCTAGATGTCGAC 57.233 47.619 9.11 9.11 0.00 4.20
2105 2151 8.105097 TCATACTATGTGCTCTTCTAGATGTC 57.895 38.462 5.60 0.95 0.00 3.06
2136 2182 7.630924 AGTTGAGAAGTCGTGTCTTTTTATTG 58.369 34.615 0.00 0.00 0.00 1.90
2144 2190 2.307768 TGGAGTTGAGAAGTCGTGTCT 58.692 47.619 0.00 0.00 0.00 3.41
2150 2196 2.087646 GGGCAATGGAGTTGAGAAGTC 58.912 52.381 0.00 0.00 40.37 3.01
2154 2200 2.673775 TTTGGGCAATGGAGTTGAGA 57.326 45.000 0.00 0.00 40.37 3.27
2158 2204 0.686789 GGCTTTTGGGCAATGGAGTT 59.313 50.000 0.00 0.00 40.53 3.01
2178 2224 3.330701 TGCCCTCTCTAAACAAGACCATT 59.669 43.478 0.00 0.00 0.00 3.16
2210 2256 6.547510 GGATAATCTCTAAAGTGCCCAACATT 59.452 38.462 0.00 0.00 0.00 2.71
2237 2283 6.734137 ACAATAACTGAGAAAAACATTCGCA 58.266 32.000 0.00 0.00 0.00 5.10
2256 2304 9.199982 GTTATAACTAGCAAAGCCGATACAATA 57.800 33.333 8.41 0.00 0.00 1.90
2278 2326 6.769512 TGAAGTCCTCAAGCAACTTAGTTAT 58.230 36.000 0.00 0.00 33.54 1.89
2282 2330 4.999950 ACATGAAGTCCTCAAGCAACTTAG 59.000 41.667 0.00 0.00 37.67 2.18
2296 2347 6.018669 GGGAATCGAATTAGACACATGAAGTC 60.019 42.308 0.00 7.34 36.26 3.01
2300 2351 5.351948 TGGGAATCGAATTAGACACATGA 57.648 39.130 0.00 0.00 0.00 3.07
2302 2353 5.989477 TCTTGGGAATCGAATTAGACACAT 58.011 37.500 0.00 0.00 0.00 3.21
2306 2357 6.675728 GCACTTTCTTGGGAATCGAATTAGAC 60.676 42.308 0.00 0.00 0.00 2.59
2340 2391 8.622948 TGTGTTTTCCACCAATTAAAACTTTT 57.377 26.923 12.40 0.00 43.85 2.27
2346 2397 8.145122 GGAGTAATGTGTTTTCCACCAATTAAA 58.855 33.333 0.00 0.00 43.85 1.52
2350 2401 4.217550 CGGAGTAATGTGTTTTCCACCAAT 59.782 41.667 0.00 0.00 43.85 3.16
2357 2408 9.485591 CAAATATACACGGAGTAATGTGTTTTC 57.514 33.333 3.12 0.00 46.61 2.29
2365 2416 7.311092 TCCATCCAAATATACACGGAGTAAT 57.689 36.000 0.00 0.00 41.61 1.89
2366 2417 6.239487 CCTCCATCCAAATATACACGGAGTAA 60.239 42.308 0.00 0.00 41.61 2.24
2370 2422 3.326588 CCCTCCATCCAAATATACACGGA 59.673 47.826 0.00 0.00 0.00 4.69
2373 2425 5.308825 CACTCCCTCCATCCAAATATACAC 58.691 45.833 0.00 0.00 0.00 2.90
2399 2459 1.018148 CATCAGCGTCCTCTCGTAGT 58.982 55.000 0.00 0.00 0.00 2.73
2402 2462 0.678366 AGACATCAGCGTCCTCTCGT 60.678 55.000 0.00 0.00 36.52 4.18
2411 2471 0.585357 GCTTGCCATAGACATCAGCG 59.415 55.000 0.00 0.00 0.00 5.18
2413 2473 3.473625 TCATGCTTGCCATAGACATCAG 58.526 45.455 0.00 0.00 31.47 2.90
2419 2479 2.554142 CGTTCTCATGCTTGCCATAGA 58.446 47.619 0.00 0.00 31.47 1.98
2420 2480 1.003116 GCGTTCTCATGCTTGCCATAG 60.003 52.381 0.00 0.00 31.47 2.23
2421 2481 1.016627 GCGTTCTCATGCTTGCCATA 58.983 50.000 0.00 0.00 31.47 2.74
2422 2482 0.961857 TGCGTTCTCATGCTTGCCAT 60.962 50.000 0.00 0.00 35.72 4.40
2436 2497 1.270274 ACACAACATCATGCATGCGTT 59.730 42.857 22.25 21.90 35.65 4.84
2448 2509 3.391296 AGTTGACCCTGTCTACACAACAT 59.609 43.478 13.49 1.48 39.86 2.71
2449 2510 2.769663 AGTTGACCCTGTCTACACAACA 59.230 45.455 13.49 0.00 39.86 3.33
2450 2511 3.131396 CAGTTGACCCTGTCTACACAAC 58.869 50.000 10.53 0.00 39.86 3.32
2451 2512 2.104111 CCAGTTGACCCTGTCTACACAA 59.896 50.000 10.53 0.00 39.86 3.33
2461 2522 2.031870 GAAAAACAGCCAGTTGACCCT 58.968 47.619 0.00 0.00 41.19 4.34
2487 2552 6.879458 ACTTAATATATGGTCTTCGGCCATTC 59.121 38.462 5.20 0.00 43.65 2.67
2490 2555 5.818678 ACTTAATATATGGTCTTCGGCCA 57.181 39.130 2.24 0.00 40.68 5.36
2517 2583 2.235155 TGAGCGTATTTGCAAGGACCTA 59.765 45.455 0.00 0.00 37.31 3.08
2562 2630 5.385198 AGACTTCAGCACTCCCAAAAATTA 58.615 37.500 0.00 0.00 0.00 1.40
2578 2646 2.365617 ACGCAAGAGGAAGAAGACTTCA 59.634 45.455 17.34 0.00 46.83 3.02
2598 2666 3.712881 GGCGTGTTGCTGACGGAC 61.713 66.667 0.00 0.00 45.43 4.79
2608 2676 0.320421 AGCTATGTTCACGGCGTGTT 60.320 50.000 35.65 21.94 34.79 3.32
2620 2688 3.270877 CAAAAGCGGGACTTAGCTATGT 58.729 45.455 11.80 11.80 43.78 2.29
2657 2725 9.162764 GCTCATAGGTTTGTTAAGATTTACTCA 57.837 33.333 0.00 0.00 0.00 3.41
2666 2734 9.612620 CTTTTACAAGCTCATAGGTTTGTTAAG 57.387 33.333 2.52 4.21 40.21 1.85
2689 2757 2.644992 CTTTTCGGCCGCTGCTTT 59.355 55.556 23.51 0.00 37.74 3.51
2707 2775 2.349969 TTCCGGATCTGCATCGACGG 62.350 60.000 4.15 12.19 35.97 4.79
2741 2809 1.212751 GTTTGCAGAATCACGCCCC 59.787 57.895 0.00 0.00 0.00 5.80
2744 2812 2.132740 TTTGGTTTGCAGAATCACGC 57.867 45.000 0.00 0.00 0.00 5.34
2756 2824 1.370810 CGGGGCAGCAATTTGGTTT 59.629 52.632 0.00 0.00 0.00 3.27
2773 2841 0.948678 TTTTGGCGTTTCCTTCTCCG 59.051 50.000 0.00 0.00 35.26 4.63
2798 2866 4.124238 TCGTGGTCTTGGAGTTTTTACAG 58.876 43.478 0.00 0.00 0.00 2.74
2811 2879 1.301479 GGTCGGCTTTCGTGGTCTT 60.301 57.895 0.00 0.00 40.32 3.01
2813 2881 3.110178 CGGTCGGCTTTCGTGGTC 61.110 66.667 0.00 0.00 40.32 4.02
2814 2882 2.444700 ATTCGGTCGGCTTTCGTGGT 62.445 55.000 0.00 0.00 40.32 4.16
2815 2883 1.693083 GATTCGGTCGGCTTTCGTGG 61.693 60.000 0.00 0.00 40.32 4.94
2816 2884 1.693083 GGATTCGGTCGGCTTTCGTG 61.693 60.000 0.00 0.00 40.32 4.35
2817 2885 1.447314 GGATTCGGTCGGCTTTCGT 60.447 57.895 0.00 0.00 40.32 3.85
2818 2886 1.017177 TTGGATTCGGTCGGCTTTCG 61.017 55.000 0.00 0.00 40.90 3.46
2819 2887 0.727398 CTTGGATTCGGTCGGCTTTC 59.273 55.000 0.00 0.00 0.00 2.62
2820 2888 1.305930 GCTTGGATTCGGTCGGCTTT 61.306 55.000 0.00 0.00 0.00 3.51
2821 2889 1.745489 GCTTGGATTCGGTCGGCTT 60.745 57.895 0.00 0.00 0.00 4.35
2822 2890 2.125106 GCTTGGATTCGGTCGGCT 60.125 61.111 0.00 0.00 0.00 5.52
2823 2891 2.435938 TGCTTGGATTCGGTCGGC 60.436 61.111 0.00 0.00 0.00 5.54
2824 2892 0.179073 ATCTGCTTGGATTCGGTCGG 60.179 55.000 0.00 0.00 0.00 4.79
2825 2893 1.212616 GATCTGCTTGGATTCGGTCG 58.787 55.000 0.00 0.00 0.00 4.79
2826 2894 1.134401 TGGATCTGCTTGGATTCGGTC 60.134 52.381 0.00 0.00 0.00 4.79
2827 2895 0.911769 TGGATCTGCTTGGATTCGGT 59.088 50.000 0.00 0.00 0.00 4.69
2828 2896 2.149578 GATGGATCTGCTTGGATTCGG 58.850 52.381 0.00 0.00 0.00 4.30
2829 2897 2.806818 CTGATGGATCTGCTTGGATTCG 59.193 50.000 0.00 0.00 0.00 3.34
2830 2898 4.082665 TCTGATGGATCTGCTTGGATTC 57.917 45.455 0.00 0.00 0.00 2.52
2831 2899 4.515028 TTCTGATGGATCTGCTTGGATT 57.485 40.909 0.00 0.00 0.00 3.01
2832 2900 4.205587 GTTTCTGATGGATCTGCTTGGAT 58.794 43.478 0.00 0.00 0.00 3.41
2833 2901 3.614092 GTTTCTGATGGATCTGCTTGGA 58.386 45.455 0.00 0.00 0.00 3.53
2834 2902 2.686915 GGTTTCTGATGGATCTGCTTGG 59.313 50.000 0.00 0.00 0.00 3.61
2835 2903 3.618351 AGGTTTCTGATGGATCTGCTTG 58.382 45.455 0.00 0.00 0.00 4.01
2836 2904 5.441718 TTAGGTTTCTGATGGATCTGCTT 57.558 39.130 0.00 0.00 0.00 3.91
2837 2905 5.189180 GTTTAGGTTTCTGATGGATCTGCT 58.811 41.667 0.00 0.00 0.00 4.24
2838 2906 4.336713 GGTTTAGGTTTCTGATGGATCTGC 59.663 45.833 0.00 0.00 0.00 4.26
2839 2907 4.572389 CGGTTTAGGTTTCTGATGGATCTG 59.428 45.833 0.00 0.00 0.00 2.90
2843 2911 3.581332 AGTCGGTTTAGGTTTCTGATGGA 59.419 43.478 0.00 0.00 0.00 3.41
2870 2966 0.417437 TCTCCCATGGGTCTTCTGGA 59.583 55.000 30.28 14.19 36.47 3.86
2907 3003 1.603678 GGTGTGCTTACGACCGAAGAA 60.604 52.381 0.00 0.00 0.00 2.52
2910 3006 4.659480 GGTGTGCTTACGACCGAA 57.341 55.556 0.00 0.00 0.00 4.30
2916 3012 4.728102 TCCGCCGGTGTGCTTACG 62.728 66.667 15.14 0.00 0.00 3.18
2959 3055 4.618227 GCAACATTGTCCCAATGTAGGAAC 60.618 45.833 19.58 7.24 39.73 3.62
2968 3064 2.569354 GGCGGCAACATTGTCCCAA 61.569 57.895 3.07 0.00 0.00 4.12
2988 3084 4.344865 TCTGGTTTGGAGGCGGCC 62.345 66.667 12.11 12.11 0.00 6.13
2992 3088 1.815003 CTTCATGTCTGGTTTGGAGGC 59.185 52.381 0.00 0.00 0.00 4.70
2995 3091 3.244561 GGAGTCTTCATGTCTGGTTTGGA 60.245 47.826 0.00 0.00 0.00 3.53
3040 3138 0.968901 CCTGCAGCAACATGGGTGAT 60.969 55.000 8.66 0.00 38.52 3.06


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

AutoCloner maintained by Alex Coulton.