Multiple sequence alignment - TraesCS7A01G359600

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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 TraesCS7A01G359600 chr7A 100.000 2441 0 0 1 2441 533507783 533505343 0.000000e+00 4508.0
1 TraesCS7A01G359600 chr7A 90.107 839 57 11 1607 2441 44435415 44434599 0.000000e+00 1066.0
2 TraesCS7A01G359600 chr7A 85.047 963 91 27 620 1570 44436331 44435410 0.000000e+00 931.0
3 TraesCS7A01G359600 chr7A 86.025 322 27 6 214 517 44436918 44436597 1.810000e-86 329.0
4 TraesCS7A01G359600 chr7A 98.305 59 1 0 1 59 12553288 12553230 1.190000e-18 104.0
5 TraesCS7A01G359600 chr3B 84.693 1594 147 39 895 2441 739846714 739845171 0.000000e+00 1502.0
6 TraesCS7A01G359600 chr3B 84.548 1262 122 24 895 2143 753927374 753928575 0.000000e+00 1182.0
7 TraesCS7A01G359600 chr3B 95.161 62 3 0 1 62 729001680 729001619 5.550000e-17 99.0
8 TraesCS7A01G359600 chr4B 83.761 1675 159 55 810 2441 652268233 652266629 0.000000e+00 1482.0
9 TraesCS7A01G359600 chr4B 96.226 53 1 1 213 264 652270094 652270042 4.320000e-13 86.1
10 TraesCS7A01G359600 chr3A 85.228 1293 116 33 1192 2441 94115911 94114651 0.000000e+00 1260.0
11 TraesCS7A01G359600 chr3A 84.528 1144 118 27 1192 2310 720322523 720323632 0.000000e+00 1077.0
12 TraesCS7A01G359600 chr3A 83.760 1133 105 37 1354 2441 393190820 393191918 0.000000e+00 1000.0
13 TraesCS7A01G359600 chr3A 89.552 67 5 2 212 277 720321275 720321340 1.560000e-12 84.2
14 TraesCS7A01G359600 chr3A 93.182 44 2 1 206 249 548048035 548048077 2.030000e-06 63.9
15 TraesCS7A01G359600 chr2A 87.683 1023 84 16 565 1570 385327361 385328358 0.000000e+00 1153.0
16 TraesCS7A01G359600 chr2A 89.141 838 62 13 1607 2441 385328353 385329164 0.000000e+00 1016.0
17 TraesCS7A01G359600 chr2A 85.280 1019 109 17 894 1890 153032500 153033499 0.000000e+00 1013.0
18 TraesCS7A01G359600 chr2A 85.047 321 35 6 215 523 385326956 385327275 5.070000e-82 315.0
19 TraesCS7A01G359600 chr7D 89.988 839 57 12 1607 2441 87752984 87753799 0.000000e+00 1059.0
20 TraesCS7A01G359600 chr7D 89.750 839 59 15 1607 2441 2016488 2017303 0.000000e+00 1048.0
21 TraesCS7A01G359600 chr7D 86.735 980 83 22 565 1528 87751887 87752835 0.000000e+00 1046.0
22 TraesCS7A01G359600 chr7D 85.513 994 85 22 565 1528 2015373 2016337 0.000000e+00 983.0
23 TraesCS7A01G359600 chr7D 86.378 323 26 8 213 517 87751473 87751795 1.080000e-88 337.0
24 TraesCS7A01G359600 chr7D 82.026 306 31 9 224 517 2014988 2015281 3.140000e-59 239.0
25 TraesCS7A01G359600 chr3D 89.988 839 56 13 1607 2441 289811236 289812050 0.000000e+00 1059.0
26 TraesCS7A01G359600 chr3D 86.415 979 86 23 565 1528 289810139 289811085 0.000000e+00 1027.0
27 TraesCS7A01G359600 chr3D 86.728 324 25 8 212 517 289809724 289810047 6.460000e-91 344.0
28 TraesCS7A01G359600 chr1D 89.893 841 56 13 1607 2441 12309019 12308202 0.000000e+00 1055.0
29 TraesCS7A01G359600 chr1D 86.810 978 83 20 568 1528 12310118 12309170 0.000000e+00 1050.0
30 TraesCS7A01G359600 chr1D 86.111 324 27 7 212 517 12310535 12310212 1.400000e-87 333.0
31 TraesCS7A01G359600 chr1D 95.312 64 3 0 1 64 77334733 77334670 4.290000e-18 102.0
32 TraesCS7A01G359600 chr6A 85.563 1039 89 26 569 1570 437496880 437497894 0.000000e+00 1031.0
33 TraesCS7A01G359600 chr6A 87.933 779 68 10 1665 2441 437497916 437498670 0.000000e+00 894.0
34 TraesCS7A01G359600 chr6A 98.438 64 1 0 1 64 134593615 134593678 1.980000e-21 113.0
35 TraesCS7A01G359600 chr6A 95.312 64 3 0 1 64 607454469 607454406 4.290000e-18 102.0
36 TraesCS7A01G359600 chr6A 91.549 71 5 1 1 71 595895077 595895146 2.000000e-16 97.1
37 TraesCS7A01G359600 chr6A 91.304 46 4 0 201 246 457041279 457041324 2.030000e-06 63.9
38 TraesCS7A01G359600 chrUn 88.769 837 67 12 1607 2441 71654701 71653890 0.000000e+00 1000.0
39 TraesCS7A01G359600 chrUn 88.632 475 35 8 1462 1923 8773349 8773817 5.890000e-156 560.0
40 TraesCS7A01G359600 chr7B 85.624 633 70 10 811 1433 568793343 568792722 0.000000e+00 645.0
41 TraesCS7A01G359600 chr7B 87.640 445 47 5 2001 2441 568782958 568782518 6.020000e-141 510.0
42 TraesCS7A01G359600 chr7B 87.565 386 32 6 1498 1871 568784026 568783645 1.340000e-117 433.0
43 TraesCS7A01G359600 chr7B 100.000 31 0 0 676 706 14910867 14910897 9.430000e-05 58.4
44 TraesCS7A01G359600 chr1A 96.875 64 2 0 1 64 460549069 460549006 9.230000e-20 108.0
45 TraesCS7A01G359600 chr4D 95.312 64 3 0 1 64 96794916 96794853 4.290000e-18 102.0
46 TraesCS7A01G359600 chr6D 93.750 64 4 0 1 64 95868736 95868799 2.000000e-16 97.1
47 TraesCS7A01G359600 chr6D 93.478 46 1 2 213 256 120662818 120662773 1.570000e-07 67.6
48 TraesCS7A01G359600 chr4A 86.486 74 5 3 560 632 640972938 640972869 2.600000e-10 76.8
49 TraesCS7A01G359600 chr5A 87.302 63 7 1 568 629 566047996 566048058 1.210000e-08 71.3
50 TraesCS7A01G359600 chr6B 95.000 40 2 0 205 244 632826071 632826110 2.030000e-06 63.9


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 TraesCS7A01G359600 chr7A 533505343 533507783 2440 True 4508.000000 4508 100.000000 1 2441 1 chr7A.!!$R2 2440
1 TraesCS7A01G359600 chr7A 44434599 44436918 2319 True 775.333333 1066 87.059667 214 2441 3 chr7A.!!$R3 2227
2 TraesCS7A01G359600 chr3B 739845171 739846714 1543 True 1502.000000 1502 84.693000 895 2441 1 chr3B.!!$R2 1546
3 TraesCS7A01G359600 chr3B 753927374 753928575 1201 False 1182.000000 1182 84.548000 895 2143 1 chr3B.!!$F1 1248
4 TraesCS7A01G359600 chr4B 652266629 652270094 3465 True 784.050000 1482 89.993500 213 2441 2 chr4B.!!$R1 2228
5 TraesCS7A01G359600 chr3A 94114651 94115911 1260 True 1260.000000 1260 85.228000 1192 2441 1 chr3A.!!$R1 1249
6 TraesCS7A01G359600 chr3A 393190820 393191918 1098 False 1000.000000 1000 83.760000 1354 2441 1 chr3A.!!$F1 1087
7 TraesCS7A01G359600 chr3A 720321275 720323632 2357 False 580.600000 1077 87.040000 212 2310 2 chr3A.!!$F3 2098
8 TraesCS7A01G359600 chr2A 153032500 153033499 999 False 1013.000000 1013 85.280000 894 1890 1 chr2A.!!$F1 996
9 TraesCS7A01G359600 chr2A 385326956 385329164 2208 False 828.000000 1153 87.290333 215 2441 3 chr2A.!!$F2 2226
10 TraesCS7A01G359600 chr7D 87751473 87753799 2326 False 814.000000 1059 87.700333 213 2441 3 chr7D.!!$F2 2228
11 TraesCS7A01G359600 chr7D 2014988 2017303 2315 False 756.666667 1048 85.763000 224 2441 3 chr7D.!!$F1 2217
12 TraesCS7A01G359600 chr3D 289809724 289812050 2326 False 810.000000 1059 87.710333 212 2441 3 chr3D.!!$F1 2229
13 TraesCS7A01G359600 chr1D 12308202 12310535 2333 True 812.666667 1055 87.604667 212 2441 3 chr1D.!!$R2 2229
14 TraesCS7A01G359600 chr6A 437496880 437498670 1790 False 962.500000 1031 86.748000 569 2441 2 chr6A.!!$F4 1872
15 TraesCS7A01G359600 chrUn 71653890 71654701 811 True 1000.000000 1000 88.769000 1607 2441 1 chrUn.!!$R1 834
16 TraesCS7A01G359600 chr7B 568792722 568793343 621 True 645.000000 645 85.624000 811 1433 1 chr7B.!!$R1 622
17 TraesCS7A01G359600 chr7B 568782518 568784026 1508 True 471.500000 510 87.602500 1498 2441 2 chr7B.!!$R2 943

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
84 85 0.033504 GGCTGGTCTTCTTGTGTCGA 59.966 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 3833 0.257039 AGCGGGATCAAGCCAAATCT 59.743 50.0 7.86 0.0 0.0 2.4 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
24 25 6.435430 TGCCATGCTTACTGTTTACTTATG 57.565 37.500 0.00 0.00 0.00 1.90
25 26 5.356751 TGCCATGCTTACTGTTTACTTATGG 59.643 40.000 0.00 0.00 36.51 2.74
26 27 5.588648 GCCATGCTTACTGTTTACTTATGGA 59.411 40.000 0.00 0.00 35.69 3.41
27 28 6.263168 GCCATGCTTACTGTTTACTTATGGAT 59.737 38.462 0.00 0.00 35.69 3.41
28 29 7.201821 GCCATGCTTACTGTTTACTTATGGATT 60.202 37.037 0.00 0.00 35.69 3.01
29 30 9.337396 CCATGCTTACTGTTTACTTATGGATTA 57.663 33.333 0.00 0.00 35.69 1.75
47 48 7.303634 TGGATTAGATTAGTCGAAAAAGTGC 57.696 36.000 0.00 0.00 0.00 4.40
48 49 7.103641 TGGATTAGATTAGTCGAAAAAGTGCT 58.896 34.615 0.00 0.00 0.00 4.40
49 50 8.255206 TGGATTAGATTAGTCGAAAAAGTGCTA 58.745 33.333 0.00 0.00 0.00 3.49
50 51 9.095065 GGATTAGATTAGTCGAAAAAGTGCTAA 57.905 33.333 0.00 0.00 0.00 3.09
58 59 7.681939 AGTCGAAAAAGTGCTAATATTTCCA 57.318 32.000 0.00 0.00 0.00 3.53
59 60 8.106247 AGTCGAAAAAGTGCTAATATTTCCAA 57.894 30.769 0.00 0.00 0.00 3.53
60 61 8.021396 AGTCGAAAAAGTGCTAATATTTCCAAC 58.979 33.333 0.00 0.00 0.00 3.77
61 62 7.806014 GTCGAAAAAGTGCTAATATTTCCAACA 59.194 33.333 0.00 0.00 0.00 3.33
62 63 8.353684 TCGAAAAAGTGCTAATATTTCCAACAA 58.646 29.630 0.00 0.00 0.00 2.83
63 64 9.139174 CGAAAAAGTGCTAATATTTCCAACAAT 57.861 29.630 0.00 0.00 0.00 2.71
67 68 7.277174 AGTGCTAATATTTCCAACAATAGGC 57.723 36.000 0.00 0.00 0.00 3.93
68 69 7.062957 AGTGCTAATATTTCCAACAATAGGCT 58.937 34.615 0.00 0.00 0.00 4.58
69 70 7.013655 AGTGCTAATATTTCCAACAATAGGCTG 59.986 37.037 0.00 0.00 0.00 4.85
70 71 6.265196 TGCTAATATTTCCAACAATAGGCTGG 59.735 38.462 0.00 0.00 0.00 4.85
71 72 6.265422 GCTAATATTTCCAACAATAGGCTGGT 59.735 38.462 0.00 0.00 0.00 4.00
72 73 6.715347 AATATTTCCAACAATAGGCTGGTC 57.285 37.500 0.00 0.00 0.00 4.02
73 74 3.806949 TTTCCAACAATAGGCTGGTCT 57.193 42.857 0.00 0.00 0.00 3.85
74 75 3.806949 TTCCAACAATAGGCTGGTCTT 57.193 42.857 0.00 0.00 0.00 3.01
75 76 3.350219 TCCAACAATAGGCTGGTCTTC 57.650 47.619 0.00 0.00 0.00 2.87
76 77 2.912956 TCCAACAATAGGCTGGTCTTCT 59.087 45.455 0.00 0.00 0.00 2.85
77 78 3.330701 TCCAACAATAGGCTGGTCTTCTT 59.669 43.478 0.00 0.00 0.00 2.52
78 79 3.441572 CCAACAATAGGCTGGTCTTCTTG 59.558 47.826 0.00 0.00 0.00 3.02
79 80 4.074970 CAACAATAGGCTGGTCTTCTTGT 58.925 43.478 0.00 0.00 0.00 3.16
80 81 3.679389 ACAATAGGCTGGTCTTCTTGTG 58.321 45.455 0.00 0.00 0.00 3.33
81 82 3.073062 ACAATAGGCTGGTCTTCTTGTGT 59.927 43.478 0.00 0.00 0.00 3.72
82 83 3.618690 ATAGGCTGGTCTTCTTGTGTC 57.381 47.619 0.00 0.00 0.00 3.67
83 84 0.034059 AGGCTGGTCTTCTTGTGTCG 59.966 55.000 0.00 0.00 0.00 4.35
84 85 0.033504 GGCTGGTCTTCTTGTGTCGA 59.966 55.000 0.00 0.00 0.00 4.20
85 86 1.423395 GCTGGTCTTCTTGTGTCGAG 58.577 55.000 0.00 0.00 0.00 4.04
86 87 1.937108 GCTGGTCTTCTTGTGTCGAGG 60.937 57.143 0.00 0.00 0.00 4.63
87 88 1.613925 CTGGTCTTCTTGTGTCGAGGA 59.386 52.381 0.00 0.00 0.00 3.71
88 89 2.232452 CTGGTCTTCTTGTGTCGAGGAT 59.768 50.000 0.00 0.00 0.00 3.24
89 90 2.231478 TGGTCTTCTTGTGTCGAGGATC 59.769 50.000 0.00 0.00 0.00 3.36
90 91 2.231478 GGTCTTCTTGTGTCGAGGATCA 59.769 50.000 0.00 0.00 33.17 2.92
91 92 3.306088 GGTCTTCTTGTGTCGAGGATCAA 60.306 47.826 0.00 0.00 33.17 2.57
92 93 4.307432 GTCTTCTTGTGTCGAGGATCAAA 58.693 43.478 0.00 0.00 33.17 2.69
93 94 4.932200 GTCTTCTTGTGTCGAGGATCAAAT 59.068 41.667 0.00 0.00 33.17 2.32
94 95 4.931601 TCTTCTTGTGTCGAGGATCAAATG 59.068 41.667 0.00 0.00 33.17 2.32
95 96 3.599343 TCTTGTGTCGAGGATCAAATGG 58.401 45.455 0.00 0.00 33.17 3.16
96 97 3.007940 TCTTGTGTCGAGGATCAAATGGT 59.992 43.478 0.00 0.00 33.17 3.55
97 98 3.417069 TGTGTCGAGGATCAAATGGTT 57.583 42.857 0.00 0.00 33.17 3.67
98 99 3.334691 TGTGTCGAGGATCAAATGGTTC 58.665 45.455 0.00 0.00 33.17 3.62
99 100 3.244387 TGTGTCGAGGATCAAATGGTTCA 60.244 43.478 0.00 0.00 33.17 3.18
100 101 3.372206 GTGTCGAGGATCAAATGGTTCAG 59.628 47.826 0.00 0.00 33.17 3.02
101 102 3.007940 TGTCGAGGATCAAATGGTTCAGT 59.992 43.478 0.00 0.00 33.17 3.41
102 103 3.372206 GTCGAGGATCAAATGGTTCAGTG 59.628 47.826 0.00 0.00 33.17 3.66
103 104 2.096496 CGAGGATCAAATGGTTCAGTGC 59.904 50.000 0.00 0.00 33.17 4.40
104 105 3.084039 GAGGATCAAATGGTTCAGTGCA 58.916 45.455 0.00 0.00 33.17 4.57
105 106 3.087031 AGGATCAAATGGTTCAGTGCAG 58.913 45.455 0.00 0.00 0.00 4.41
106 107 2.165030 GGATCAAATGGTTCAGTGCAGG 59.835 50.000 0.00 0.00 0.00 4.85
107 108 2.655090 TCAAATGGTTCAGTGCAGGA 57.345 45.000 0.00 0.00 0.00 3.86
108 109 2.942804 TCAAATGGTTCAGTGCAGGAA 58.057 42.857 0.00 0.00 0.00 3.36
109 110 2.622942 TCAAATGGTTCAGTGCAGGAAC 59.377 45.455 18.42 18.42 42.99 3.62
110 111 2.624838 CAAATGGTTCAGTGCAGGAACT 59.375 45.455 23.13 8.46 43.20 3.01
111 112 3.788227 AATGGTTCAGTGCAGGAACTA 57.212 42.857 23.13 19.84 43.20 2.24
112 113 4.307032 AATGGTTCAGTGCAGGAACTAT 57.693 40.909 23.13 20.86 44.90 2.12
113 114 3.334583 TGGTTCAGTGCAGGAACTATC 57.665 47.619 23.13 12.32 43.20 2.08
114 115 2.906389 TGGTTCAGTGCAGGAACTATCT 59.094 45.455 23.13 0.00 43.20 1.98
115 116 3.265791 GGTTCAGTGCAGGAACTATCTG 58.734 50.000 23.13 9.93 43.20 2.90
116 117 3.265791 GTTCAGTGCAGGAACTATCTGG 58.734 50.000 19.05 0.00 41.05 3.86
117 118 1.208052 TCAGTGCAGGAACTATCTGGC 59.792 52.381 0.00 0.00 36.02 4.85
118 119 1.065926 CAGTGCAGGAACTATCTGGCA 60.066 52.381 0.00 0.00 36.02 4.92
119 120 1.209019 AGTGCAGGAACTATCTGGCAG 59.791 52.381 8.58 8.58 36.02 4.85
120 121 0.107508 TGCAGGAACTATCTGGCAGC 60.108 55.000 10.34 0.00 36.02 5.25
121 122 0.179936 GCAGGAACTATCTGGCAGCT 59.820 55.000 10.34 2.00 36.02 4.24
122 123 1.809651 GCAGGAACTATCTGGCAGCTC 60.810 57.143 10.34 1.00 36.02 4.09
123 124 1.483827 CAGGAACTATCTGGCAGCTCA 59.516 52.381 10.34 0.00 36.02 4.26
124 125 2.104451 CAGGAACTATCTGGCAGCTCAT 59.896 50.000 10.34 0.49 36.02 2.90
125 126 3.323115 CAGGAACTATCTGGCAGCTCATA 59.677 47.826 10.34 1.81 36.02 2.15
126 127 4.020396 CAGGAACTATCTGGCAGCTCATAT 60.020 45.833 10.34 0.00 36.02 1.78
127 128 4.222588 AGGAACTATCTGGCAGCTCATATC 59.777 45.833 10.34 3.73 36.02 1.63
128 129 4.222588 GGAACTATCTGGCAGCTCATATCT 59.777 45.833 10.34 0.00 0.00 1.98
129 130 5.279910 GGAACTATCTGGCAGCTCATATCTT 60.280 44.000 10.34 0.00 0.00 2.40
130 131 5.149973 ACTATCTGGCAGCTCATATCTTG 57.850 43.478 10.34 0.00 0.00 3.02
131 132 2.924757 TCTGGCAGCTCATATCTTGG 57.075 50.000 10.34 0.00 0.00 3.61
132 133 1.202734 TCTGGCAGCTCATATCTTGGC 60.203 52.381 10.34 0.00 0.00 4.52
133 134 0.547553 TGGCAGCTCATATCTTGGCA 59.452 50.000 0.00 0.00 0.00 4.92
134 135 1.064537 TGGCAGCTCATATCTTGGCAA 60.065 47.619 0.00 0.00 0.00 4.52
135 136 2.236766 GGCAGCTCATATCTTGGCAAT 58.763 47.619 0.00 0.00 0.00 3.56
136 137 2.626743 GGCAGCTCATATCTTGGCAATT 59.373 45.455 0.00 0.00 0.00 2.32
137 138 3.069158 GGCAGCTCATATCTTGGCAATTT 59.931 43.478 0.00 0.00 0.00 1.82
138 139 4.279169 GGCAGCTCATATCTTGGCAATTTA 59.721 41.667 0.00 0.00 0.00 1.40
139 140 5.218139 GCAGCTCATATCTTGGCAATTTAC 58.782 41.667 0.00 0.00 0.00 2.01
140 141 5.009410 GCAGCTCATATCTTGGCAATTTACT 59.991 40.000 0.00 0.00 0.00 2.24
141 142 6.666417 CAGCTCATATCTTGGCAATTTACTC 58.334 40.000 0.00 0.00 0.00 2.59
142 143 6.485984 CAGCTCATATCTTGGCAATTTACTCT 59.514 38.462 0.00 0.00 0.00 3.24
143 144 6.485984 AGCTCATATCTTGGCAATTTACTCTG 59.514 38.462 0.00 0.00 0.00 3.35
144 145 6.261826 GCTCATATCTTGGCAATTTACTCTGT 59.738 38.462 0.00 0.00 0.00 3.41
145 146 7.201767 GCTCATATCTTGGCAATTTACTCTGTT 60.202 37.037 0.00 0.00 0.00 3.16
146 147 9.330063 CTCATATCTTGGCAATTTACTCTGTTA 57.670 33.333 0.00 0.00 0.00 2.41
147 148 9.851686 TCATATCTTGGCAATTTACTCTGTTAT 57.148 29.630 0.00 0.00 0.00 1.89
148 149 9.888878 CATATCTTGGCAATTTACTCTGTTATG 57.111 33.333 0.00 0.00 0.00 1.90
149 150 9.851686 ATATCTTGGCAATTTACTCTGTTATGA 57.148 29.630 0.00 0.00 0.00 2.15
150 151 8.757982 ATCTTGGCAATTTACTCTGTTATGAT 57.242 30.769 0.00 0.00 0.00 2.45
151 152 8.579850 TCTTGGCAATTTACTCTGTTATGATT 57.420 30.769 0.00 0.00 0.00 2.57
152 153 8.461222 TCTTGGCAATTTACTCTGTTATGATTG 58.539 33.333 0.00 0.00 0.00 2.67
153 154 7.099266 TGGCAATTTACTCTGTTATGATTGG 57.901 36.000 0.00 0.00 0.00 3.16
154 155 6.663093 TGGCAATTTACTCTGTTATGATTGGT 59.337 34.615 0.00 0.00 0.00 3.67
155 156 7.178274 TGGCAATTTACTCTGTTATGATTGGTT 59.822 33.333 0.00 0.00 0.00 3.67
156 157 7.489113 GGCAATTTACTCTGTTATGATTGGTTG 59.511 37.037 0.00 0.00 0.00 3.77
157 158 8.028938 GCAATTTACTCTGTTATGATTGGTTGT 58.971 33.333 0.00 0.00 0.00 3.32
158 159 9.912634 CAATTTACTCTGTTATGATTGGTTGTT 57.087 29.630 0.00 0.00 0.00 2.83
159 160 9.912634 AATTTACTCTGTTATGATTGGTTGTTG 57.087 29.630 0.00 0.00 0.00 3.33
160 161 5.376854 ACTCTGTTATGATTGGTTGTTGC 57.623 39.130 0.00 0.00 0.00 4.17
161 162 4.826733 ACTCTGTTATGATTGGTTGTTGCA 59.173 37.500 0.00 0.00 0.00 4.08
162 163 5.477984 ACTCTGTTATGATTGGTTGTTGCAT 59.522 36.000 0.00 0.00 0.00 3.96
163 164 5.953183 TCTGTTATGATTGGTTGTTGCATC 58.047 37.500 0.00 0.00 0.00 3.91
164 165 5.476254 TCTGTTATGATTGGTTGTTGCATCA 59.524 36.000 0.00 0.00 0.00 3.07
165 166 6.153170 TCTGTTATGATTGGTTGTTGCATCAT 59.847 34.615 0.00 0.00 39.28 2.45
166 167 6.699366 TGTTATGATTGGTTGTTGCATCATT 58.301 32.000 0.00 0.00 37.51 2.57
167 168 6.590677 TGTTATGATTGGTTGTTGCATCATTG 59.409 34.615 0.00 0.00 37.51 2.82
168 169 4.603989 TGATTGGTTGTTGCATCATTGT 57.396 36.364 0.00 0.00 0.00 2.71
169 170 4.308265 TGATTGGTTGTTGCATCATTGTG 58.692 39.130 0.00 0.00 0.00 3.33
170 171 4.038883 TGATTGGTTGTTGCATCATTGTGA 59.961 37.500 0.00 0.00 0.00 3.58
171 172 3.646611 TGGTTGTTGCATCATTGTGAG 57.353 42.857 0.00 0.00 0.00 3.51
172 173 2.957680 TGGTTGTTGCATCATTGTGAGT 59.042 40.909 0.00 0.00 0.00 3.41
173 174 4.140536 TGGTTGTTGCATCATTGTGAGTA 58.859 39.130 0.00 0.00 0.00 2.59
174 175 4.766373 TGGTTGTTGCATCATTGTGAGTAT 59.234 37.500 0.00 0.00 0.00 2.12
175 176 5.106197 TGGTTGTTGCATCATTGTGAGTATC 60.106 40.000 0.00 0.00 0.00 2.24
176 177 5.124457 GGTTGTTGCATCATTGTGAGTATCT 59.876 40.000 0.00 0.00 34.92 1.98
177 178 6.316140 GGTTGTTGCATCATTGTGAGTATCTA 59.684 38.462 0.00 0.00 34.92 1.98
178 179 7.404985 GTTGTTGCATCATTGTGAGTATCTAG 58.595 38.462 0.00 0.00 34.92 2.43
179 180 6.643388 TGTTGCATCATTGTGAGTATCTAGT 58.357 36.000 0.00 0.00 34.92 2.57
180 181 7.105588 TGTTGCATCATTGTGAGTATCTAGTT 58.894 34.615 0.00 0.00 34.92 2.24
181 182 7.278646 TGTTGCATCATTGTGAGTATCTAGTTC 59.721 37.037 0.00 0.00 34.92 3.01
182 183 5.979517 TGCATCATTGTGAGTATCTAGTTCG 59.020 40.000 0.00 0.00 34.92 3.95
183 184 5.980116 GCATCATTGTGAGTATCTAGTTCGT 59.020 40.000 0.00 0.00 34.92 3.85
184 185 6.143118 GCATCATTGTGAGTATCTAGTTCGTC 59.857 42.308 0.00 0.00 34.92 4.20
185 186 6.753107 TCATTGTGAGTATCTAGTTCGTCA 57.247 37.500 0.00 0.00 34.92 4.35
186 187 7.153217 TCATTGTGAGTATCTAGTTCGTCAA 57.847 36.000 0.00 0.00 34.92 3.18
187 188 7.599171 TCATTGTGAGTATCTAGTTCGTCAAA 58.401 34.615 0.00 0.00 34.92 2.69
188 189 8.251026 TCATTGTGAGTATCTAGTTCGTCAAAT 58.749 33.333 0.00 0.00 34.92 2.32
189 190 9.516314 CATTGTGAGTATCTAGTTCGTCAAATA 57.484 33.333 0.00 0.00 34.92 1.40
203 204 9.817809 AGTTCGTCAAATATATAGTTCACACAT 57.182 29.630 0.00 0.00 0.00 3.21
257 258 6.170506 ACACACGTCTCCATTAACACATAAT 58.829 36.000 0.00 0.00 34.45 1.28
298 1063 5.624281 GCAACAAGGCCATACACACATAAAT 60.624 40.000 5.01 0.00 0.00 1.40
403 1635 2.773993 TACGATCCCTTGTTCAACCC 57.226 50.000 0.00 0.00 0.00 4.11
439 2012 0.912486 CTCCGACAATTCCTTCCCCT 59.088 55.000 0.00 0.00 0.00 4.79
442 2015 1.838077 CCGACAATTCCTTCCCCTAGT 59.162 52.381 0.00 0.00 0.00 2.57
448 2021 0.410663 TTCCTTCCCCTAGTCGTCCA 59.589 55.000 0.00 0.00 0.00 4.02
472 2057 4.457496 CGCCAGCCACCATCGTCT 62.457 66.667 0.00 0.00 0.00 4.18
544 2150 2.152016 CTCCTGTTTTTCTCCGGGAAC 58.848 52.381 0.00 0.15 33.13 3.62
563 2169 3.931907 ACCTTCACCATTGCTATGCTA 57.068 42.857 2.27 0.00 0.00 3.49
566 2196 4.202441 CCTTCACCATTGCTATGCTACTT 58.798 43.478 2.27 0.00 0.00 2.24
629 2380 0.178861 AAGCTTCTTCCTCCCCTCCA 60.179 55.000 0.00 0.00 0.00 3.86
681 2432 4.285003 TCTCCCTTCAACCAAAATCGACTA 59.715 41.667 0.00 0.00 0.00 2.59
691 2442 4.763279 ACCAAAATCGACTAACCCGAATTT 59.237 37.500 0.00 0.00 39.00 1.82
758 2511 7.719778 TCTCATGCACATCAGACAATATTAC 57.280 36.000 0.00 0.00 0.00 1.89
759 2512 6.707608 TCTCATGCACATCAGACAATATTACC 59.292 38.462 0.00 0.00 0.00 2.85
760 2513 6.594744 TCATGCACATCAGACAATATTACCT 58.405 36.000 0.00 0.00 0.00 3.08
761 2514 7.734942 TCATGCACATCAGACAATATTACCTA 58.265 34.615 0.00 0.00 0.00 3.08
846 2677 1.134068 TGAATTGGACAACACCGGACA 60.134 47.619 9.46 0.00 0.00 4.02
853 2684 3.118920 TGGACAACACCGGACACTATATG 60.119 47.826 9.46 0.00 0.00 1.78
931 2797 0.912006 GCCCCCTCTCAGTTCTCCTT 60.912 60.000 0.00 0.00 0.00 3.36
932 2798 0.908198 CCCCCTCTCAGTTCTCCTTG 59.092 60.000 0.00 0.00 0.00 3.61
933 2799 0.908198 CCCCTCTCAGTTCTCCTTGG 59.092 60.000 0.00 0.00 0.00 3.61
934 2800 1.650528 CCCTCTCAGTTCTCCTTGGT 58.349 55.000 0.00 0.00 0.00 3.67
935 2801 1.552792 CCCTCTCAGTTCTCCTTGGTC 59.447 57.143 0.00 0.00 0.00 4.02
936 2802 1.552792 CCTCTCAGTTCTCCTTGGTCC 59.447 57.143 0.00 0.00 0.00 4.46
937 2803 2.534990 CTCTCAGTTCTCCTTGGTCCT 58.465 52.381 0.00 0.00 0.00 3.85
959 2827 1.664321 CCTCGTCACCTACCTTCCCG 61.664 65.000 0.00 0.00 0.00 5.14
969 2842 2.425975 CCTACCTTCCCGACCCTTATCT 60.426 54.545 0.00 0.00 0.00 1.98
987 2860 0.610687 CTCTTCACTGTCTCCCCACC 59.389 60.000 0.00 0.00 0.00 4.61
1039 2968 2.171237 CAGCTCTCTCTCTCTCCTCAGA 59.829 54.545 0.00 0.00 0.00 3.27
1054 2983 2.529389 AGACCGCCCCTCCTGTTT 60.529 61.111 0.00 0.00 0.00 2.83
1055 2984 2.154074 AGACCGCCCCTCCTGTTTT 61.154 57.895 0.00 0.00 0.00 2.43
1258 3195 3.966543 CAACCTCCGCCCCTGGTT 61.967 66.667 0.00 0.00 43.98 3.67
1269 3206 0.252927 CCCCTGGTTCCTTCCTCTCT 60.253 60.000 0.00 0.00 0.00 3.10
1272 3209 3.116707 CCCCTGGTTCCTTCCTCTCTATA 60.117 52.174 0.00 0.00 0.00 1.31
1303 3241 3.570212 GCTCCCACCACCCTGTGT 61.570 66.667 0.00 0.00 34.35 3.72
1348 3286 2.656646 CCAGGCACGACAGCAGTA 59.343 61.111 0.00 0.00 35.83 2.74
1351 3289 2.434359 GGCACGACAGCAGTACCC 60.434 66.667 0.00 0.00 35.83 3.69
1357 3295 2.525877 ACAGCAGTACCCCGGTGT 60.526 61.111 0.00 0.00 38.94 4.16
1465 3411 1.916181 CTCCCCATTACCCACTTCTGT 59.084 52.381 0.00 0.00 0.00 3.41
1589 3653 6.916440 AGTTGGGGTGATTTTATTTTCGTAC 58.084 36.000 0.00 0.00 0.00 3.67
1636 3700 4.790140 TCGATTAGACGTTCTTAACTTCGC 59.210 41.667 0.00 0.00 35.09 4.70
1641 3705 2.206750 ACGTTCTTAACTTCGCTGCAA 58.793 42.857 0.00 0.00 0.00 4.08
1725 3789 5.410355 AGTTGATTGATTGGTGGATTTGG 57.590 39.130 0.00 0.00 0.00 3.28
1769 3833 1.481871 GGACCAAGACGGATGAGGTA 58.518 55.000 0.00 0.00 38.63 3.08
1788 3853 0.257039 AGATTTGGCTTGATCCCGCT 59.743 50.000 3.73 0.00 0.00 5.52
1805 3871 6.737254 TCCCGCTAAAGAAATTTACTTCTG 57.263 37.500 0.00 0.00 35.79 3.02
1858 3938 7.145932 AGTTTTCAAATGCGAGCTTTATAGT 57.854 32.000 0.00 0.00 0.00 2.12
1891 4196 5.463154 AGGATCAAGAGAAGCATAGTAGGT 58.537 41.667 0.00 0.00 0.00 3.08
1894 4199 7.014808 AGGATCAAGAGAAGCATAGTAGGTTAC 59.985 40.741 0.00 0.00 0.00 2.50
1895 4200 7.014808 GGATCAAGAGAAGCATAGTAGGTTACT 59.985 40.741 0.00 0.00 42.68 2.24
1896 4201 8.998277 ATCAAGAGAAGCATAGTAGGTTACTA 57.002 34.615 0.00 0.00 44.64 1.82
1947 4316 7.584122 TGACTCTAGGATAATACAGGTTGAC 57.416 40.000 0.00 0.00 0.00 3.18
2014 4712 3.520317 TCATATAAAGGACGGTGGTTGGT 59.480 43.478 0.00 0.00 0.00 3.67
2065 4764 5.509670 GCCTTTCTGTGAATAACTTGCCTTT 60.510 40.000 0.00 0.00 0.00 3.11
2147 4846 7.547019 AGTGATATTCATGATATAGCACAACCG 59.453 37.037 28.08 0.00 43.68 4.44
2195 4895 4.141413 GGACCCCCGGTTATAACATAAGTT 60.141 45.833 17.16 0.00 37.67 2.66
2196 4896 5.071653 GGACCCCCGGTTATAACATAAGTTA 59.928 44.000 17.16 0.00 39.29 2.24
2212 4912 7.762382 ACATAAGTTATTTTGCAGGCTTAGAC 58.238 34.615 0.00 0.00 0.00 2.59
2225 4925 5.932303 GCAGGCTTAGACGAAATGGATATTA 59.068 40.000 0.00 0.00 0.00 0.98
2332 5079 2.442878 TGCCTGCCATATACATCAACCT 59.557 45.455 0.00 0.00 0.00 3.50
2341 5088 6.514048 GCCATATACATCAACCTGAAGCTTTC 60.514 42.308 0.00 0.00 0.00 2.62
2342 5089 6.543465 CCATATACATCAACCTGAAGCTTTCA 59.457 38.462 0.00 0.00 38.17 2.69
2436 5190 9.256228 TGATCAGGTACTTACTCACTTAATTCT 57.744 33.333 0.00 0.00 34.60 2.40
2437 5191 9.522804 GATCAGGTACTTACTCACTTAATTCTG 57.477 37.037 0.00 0.00 34.60 3.02
2438 5192 8.645814 TCAGGTACTTACTCACTTAATTCTGA 57.354 34.615 0.00 0.00 34.60 3.27
2440 5194 9.877178 CAGGTACTTACTCACTTAATTCTGAAT 57.123 33.333 0.00 0.00 34.60 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.127758 CCATAAGTAAACAGTAAGCATGGCAA 60.128 38.462 0.00 0.00 0.00 4.52
1 2 5.356751 CCATAAGTAAACAGTAAGCATGGCA 59.643 40.000 0.00 0.00 0.00 4.92
2 3 5.588648 TCCATAAGTAAACAGTAAGCATGGC 59.411 40.000 0.00 0.00 32.29 4.40
3 4 7.807977 ATCCATAAGTAAACAGTAAGCATGG 57.192 36.000 0.00 0.00 33.28 3.66
21 22 9.042008 GCACTTTTTCGACTAATCTAATCCATA 57.958 33.333 0.00 0.00 0.00 2.74
22 23 7.770897 AGCACTTTTTCGACTAATCTAATCCAT 59.229 33.333 0.00 0.00 0.00 3.41
23 24 7.103641 AGCACTTTTTCGACTAATCTAATCCA 58.896 34.615 0.00 0.00 0.00 3.41
24 25 7.541122 AGCACTTTTTCGACTAATCTAATCC 57.459 36.000 0.00 0.00 0.00 3.01
32 33 9.221933 TGGAAATATTAGCACTTTTTCGACTAA 57.778 29.630 0.00 0.00 0.00 2.24
33 34 8.780846 TGGAAATATTAGCACTTTTTCGACTA 57.219 30.769 0.00 0.00 0.00 2.59
34 35 7.681939 TGGAAATATTAGCACTTTTTCGACT 57.318 32.000 0.00 0.00 0.00 4.18
35 36 7.806014 TGTTGGAAATATTAGCACTTTTTCGAC 59.194 33.333 0.00 0.00 0.00 4.20
36 37 7.877003 TGTTGGAAATATTAGCACTTTTTCGA 58.123 30.769 0.00 0.00 0.00 3.71
37 38 8.514136 TTGTTGGAAATATTAGCACTTTTTCG 57.486 30.769 0.00 0.00 0.00 3.46
41 42 8.197439 GCCTATTGTTGGAAATATTAGCACTTT 58.803 33.333 0.00 0.00 0.00 2.66
42 43 7.561356 AGCCTATTGTTGGAAATATTAGCACTT 59.439 33.333 0.00 0.00 0.00 3.16
43 44 7.013655 CAGCCTATTGTTGGAAATATTAGCACT 59.986 37.037 0.00 0.00 0.00 4.40
44 45 7.141363 CAGCCTATTGTTGGAAATATTAGCAC 58.859 38.462 0.00 0.00 0.00 4.40
45 46 6.265196 CCAGCCTATTGTTGGAAATATTAGCA 59.735 38.462 0.00 0.00 33.76 3.49
46 47 6.265422 ACCAGCCTATTGTTGGAAATATTAGC 59.735 38.462 1.91 0.00 35.89 3.09
47 48 7.721399 AGACCAGCCTATTGTTGGAAATATTAG 59.279 37.037 1.91 0.00 35.89 1.73
48 49 7.582719 AGACCAGCCTATTGTTGGAAATATTA 58.417 34.615 1.91 0.00 35.89 0.98
49 50 6.435164 AGACCAGCCTATTGTTGGAAATATT 58.565 36.000 1.91 0.00 35.89 1.28
50 51 6.018433 AGACCAGCCTATTGTTGGAAATAT 57.982 37.500 1.91 0.00 35.89 1.28
51 52 5.450818 AGACCAGCCTATTGTTGGAAATA 57.549 39.130 1.91 0.00 35.89 1.40
52 53 4.322057 AGACCAGCCTATTGTTGGAAAT 57.678 40.909 1.91 0.00 35.89 2.17
53 54 3.806949 AGACCAGCCTATTGTTGGAAA 57.193 42.857 1.91 0.00 35.89 3.13
54 55 3.330701 AGAAGACCAGCCTATTGTTGGAA 59.669 43.478 1.91 0.00 35.89 3.53
55 56 2.912956 AGAAGACCAGCCTATTGTTGGA 59.087 45.455 1.91 0.00 35.89 3.53
56 57 3.356529 AGAAGACCAGCCTATTGTTGG 57.643 47.619 0.00 0.00 37.98 3.77
57 58 4.074970 ACAAGAAGACCAGCCTATTGTTG 58.925 43.478 0.00 0.00 33.51 3.33
58 59 4.074970 CACAAGAAGACCAGCCTATTGTT 58.925 43.478 0.00 0.00 29.29 2.83
59 60 3.073062 ACACAAGAAGACCAGCCTATTGT 59.927 43.478 0.00 0.00 30.83 2.71
60 61 3.679389 ACACAAGAAGACCAGCCTATTG 58.321 45.455 0.00 0.00 0.00 1.90
61 62 3.617531 CGACACAAGAAGACCAGCCTATT 60.618 47.826 0.00 0.00 0.00 1.73
62 63 2.093973 CGACACAAGAAGACCAGCCTAT 60.094 50.000 0.00 0.00 0.00 2.57
63 64 1.272490 CGACACAAGAAGACCAGCCTA 59.728 52.381 0.00 0.00 0.00 3.93
64 65 0.034059 CGACACAAGAAGACCAGCCT 59.966 55.000 0.00 0.00 0.00 4.58
65 66 0.033504 TCGACACAAGAAGACCAGCC 59.966 55.000 0.00 0.00 0.00 4.85
66 67 1.423395 CTCGACACAAGAAGACCAGC 58.577 55.000 0.00 0.00 0.00 4.85
67 68 1.613925 TCCTCGACACAAGAAGACCAG 59.386 52.381 0.00 0.00 0.00 4.00
68 69 1.699730 TCCTCGACACAAGAAGACCA 58.300 50.000 0.00 0.00 0.00 4.02
69 70 2.231478 TGATCCTCGACACAAGAAGACC 59.769 50.000 0.00 0.00 0.00 3.85
70 71 3.577649 TGATCCTCGACACAAGAAGAC 57.422 47.619 0.00 0.00 0.00 3.01
71 72 4.600692 TTTGATCCTCGACACAAGAAGA 57.399 40.909 0.00 0.00 0.00 2.87
72 73 4.093998 CCATTTGATCCTCGACACAAGAAG 59.906 45.833 0.00 0.00 0.00 2.85
73 74 4.002982 CCATTTGATCCTCGACACAAGAA 58.997 43.478 0.00 0.00 0.00 2.52
74 75 3.007940 ACCATTTGATCCTCGACACAAGA 59.992 43.478 0.00 0.00 0.00 3.02
75 76 3.338249 ACCATTTGATCCTCGACACAAG 58.662 45.455 0.00 0.00 0.00 3.16
76 77 3.417069 ACCATTTGATCCTCGACACAA 57.583 42.857 0.00 0.00 0.00 3.33
77 78 3.244387 TGAACCATTTGATCCTCGACACA 60.244 43.478 0.00 0.00 0.00 3.72
78 79 3.334691 TGAACCATTTGATCCTCGACAC 58.665 45.455 0.00 0.00 0.00 3.67
79 80 3.007940 ACTGAACCATTTGATCCTCGACA 59.992 43.478 0.00 0.00 0.00 4.35
80 81 3.372206 CACTGAACCATTTGATCCTCGAC 59.628 47.826 0.00 0.00 0.00 4.20
81 82 3.599343 CACTGAACCATTTGATCCTCGA 58.401 45.455 0.00 0.00 0.00 4.04
82 83 2.096496 GCACTGAACCATTTGATCCTCG 59.904 50.000 0.00 0.00 0.00 4.63
83 84 3.084039 TGCACTGAACCATTTGATCCTC 58.916 45.455 0.00 0.00 0.00 3.71
84 85 3.087031 CTGCACTGAACCATTTGATCCT 58.913 45.455 0.00 0.00 0.00 3.24
85 86 2.165030 CCTGCACTGAACCATTTGATCC 59.835 50.000 0.00 0.00 0.00 3.36
86 87 3.084039 TCCTGCACTGAACCATTTGATC 58.916 45.455 0.00 0.00 0.00 2.92
87 88 3.159213 TCCTGCACTGAACCATTTGAT 57.841 42.857 0.00 0.00 0.00 2.57
88 89 2.622942 GTTCCTGCACTGAACCATTTGA 59.377 45.455 11.60 0.00 36.87 2.69
89 90 2.624838 AGTTCCTGCACTGAACCATTTG 59.375 45.455 16.81 0.00 42.41 2.32
90 91 2.949447 AGTTCCTGCACTGAACCATTT 58.051 42.857 16.81 1.05 42.41 2.32
91 92 2.664402 AGTTCCTGCACTGAACCATT 57.336 45.000 16.81 1.33 42.41 3.16
92 93 3.521126 AGATAGTTCCTGCACTGAACCAT 59.479 43.478 16.81 11.25 42.41 3.55
93 94 2.906389 AGATAGTTCCTGCACTGAACCA 59.094 45.455 16.81 7.57 42.41 3.67
94 95 3.265791 CAGATAGTTCCTGCACTGAACC 58.734 50.000 16.81 6.08 42.41 3.62
95 96 3.265791 CCAGATAGTTCCTGCACTGAAC 58.734 50.000 13.90 13.90 41.89 3.18
96 97 2.355108 GCCAGATAGTTCCTGCACTGAA 60.355 50.000 0.00 0.00 0.00 3.02
97 98 1.208052 GCCAGATAGTTCCTGCACTGA 59.792 52.381 0.00 0.00 0.00 3.41
98 99 1.065926 TGCCAGATAGTTCCTGCACTG 60.066 52.381 0.00 0.00 0.00 3.66
99 100 1.209019 CTGCCAGATAGTTCCTGCACT 59.791 52.381 0.00 0.00 0.00 4.40
100 101 1.661341 CTGCCAGATAGTTCCTGCAC 58.339 55.000 0.00 0.00 0.00 4.57
101 102 0.107508 GCTGCCAGATAGTTCCTGCA 60.108 55.000 0.00 0.00 0.00 4.41
102 103 0.179936 AGCTGCCAGATAGTTCCTGC 59.820 55.000 0.00 0.00 0.00 4.85
103 104 1.483827 TGAGCTGCCAGATAGTTCCTG 59.516 52.381 0.00 0.00 0.00 3.86
104 105 1.871418 TGAGCTGCCAGATAGTTCCT 58.129 50.000 0.00 0.00 0.00 3.36
105 106 2.926778 ATGAGCTGCCAGATAGTTCC 57.073 50.000 0.00 0.00 0.00 3.62
106 107 5.404466 AGATATGAGCTGCCAGATAGTTC 57.596 43.478 0.00 0.00 0.00 3.01
107 108 5.512749 CCAAGATATGAGCTGCCAGATAGTT 60.513 44.000 0.00 0.00 0.00 2.24
108 109 4.020396 CCAAGATATGAGCTGCCAGATAGT 60.020 45.833 0.00 0.00 0.00 2.12
109 110 4.505808 CCAAGATATGAGCTGCCAGATAG 58.494 47.826 0.00 0.00 0.00 2.08
110 111 3.307269 GCCAAGATATGAGCTGCCAGATA 60.307 47.826 0.00 0.00 0.00 1.98
111 112 2.552591 GCCAAGATATGAGCTGCCAGAT 60.553 50.000 0.00 0.00 0.00 2.90
112 113 1.202734 GCCAAGATATGAGCTGCCAGA 60.203 52.381 0.00 0.00 0.00 3.86
113 114 1.236628 GCCAAGATATGAGCTGCCAG 58.763 55.000 0.00 0.00 0.00 4.85
114 115 0.547553 TGCCAAGATATGAGCTGCCA 59.452 50.000 0.00 0.00 0.00 4.92
115 116 1.683943 TTGCCAAGATATGAGCTGCC 58.316 50.000 0.00 0.00 0.00 4.85
116 117 4.317671 AAATTGCCAAGATATGAGCTGC 57.682 40.909 0.00 0.00 0.00 5.25
117 118 6.485984 AGAGTAAATTGCCAAGATATGAGCTG 59.514 38.462 0.00 0.00 0.00 4.24
118 119 6.485984 CAGAGTAAATTGCCAAGATATGAGCT 59.514 38.462 0.00 0.00 0.00 4.09
119 120 6.261826 ACAGAGTAAATTGCCAAGATATGAGC 59.738 38.462 0.00 0.00 0.00 4.26
120 121 7.798596 ACAGAGTAAATTGCCAAGATATGAG 57.201 36.000 0.00 0.00 0.00 2.90
121 122 9.851686 ATAACAGAGTAAATTGCCAAGATATGA 57.148 29.630 0.00 0.00 0.00 2.15
122 123 9.888878 CATAACAGAGTAAATTGCCAAGATATG 57.111 33.333 0.00 0.00 0.00 1.78
123 124 9.851686 TCATAACAGAGTAAATTGCCAAGATAT 57.148 29.630 0.00 0.00 0.00 1.63
124 125 9.851686 ATCATAACAGAGTAAATTGCCAAGATA 57.148 29.630 0.00 0.00 0.00 1.98
125 126 8.757982 ATCATAACAGAGTAAATTGCCAAGAT 57.242 30.769 0.00 0.00 0.00 2.40
126 127 8.461222 CAATCATAACAGAGTAAATTGCCAAGA 58.539 33.333 0.00 0.00 0.00 3.02
127 128 7.703621 CCAATCATAACAGAGTAAATTGCCAAG 59.296 37.037 0.00 0.00 0.00 3.61
128 129 7.178274 ACCAATCATAACAGAGTAAATTGCCAA 59.822 33.333 0.00 0.00 0.00 4.52
129 130 6.663093 ACCAATCATAACAGAGTAAATTGCCA 59.337 34.615 0.00 0.00 0.00 4.92
130 131 7.100458 ACCAATCATAACAGAGTAAATTGCC 57.900 36.000 0.00 0.00 0.00 4.52
131 132 8.028938 ACAACCAATCATAACAGAGTAAATTGC 58.971 33.333 0.00 0.00 0.00 3.56
132 133 9.912634 AACAACCAATCATAACAGAGTAAATTG 57.087 29.630 0.00 0.00 0.00 2.32
133 134 9.912634 CAACAACCAATCATAACAGAGTAAATT 57.087 29.630 0.00 0.00 0.00 1.82
134 135 8.028938 GCAACAACCAATCATAACAGAGTAAAT 58.971 33.333 0.00 0.00 0.00 1.40
135 136 7.013750 TGCAACAACCAATCATAACAGAGTAAA 59.986 33.333 0.00 0.00 0.00 2.01
136 137 6.488344 TGCAACAACCAATCATAACAGAGTAA 59.512 34.615 0.00 0.00 0.00 2.24
137 138 6.000840 TGCAACAACCAATCATAACAGAGTA 58.999 36.000 0.00 0.00 0.00 2.59
138 139 4.826733 TGCAACAACCAATCATAACAGAGT 59.173 37.500 0.00 0.00 0.00 3.24
139 140 5.375417 TGCAACAACCAATCATAACAGAG 57.625 39.130 0.00 0.00 0.00 3.35
140 141 5.476254 TGATGCAACAACCAATCATAACAGA 59.524 36.000 0.00 0.00 0.00 3.41
141 142 5.712004 TGATGCAACAACCAATCATAACAG 58.288 37.500 0.00 0.00 0.00 3.16
142 143 5.718724 TGATGCAACAACCAATCATAACA 57.281 34.783 0.00 0.00 0.00 2.41
143 144 6.591062 ACAATGATGCAACAACCAATCATAAC 59.409 34.615 0.00 0.00 0.00 1.89
144 145 6.590677 CACAATGATGCAACAACCAATCATAA 59.409 34.615 0.00 0.00 0.00 1.90
145 146 6.071503 TCACAATGATGCAACAACCAATCATA 60.072 34.615 0.00 0.00 0.00 2.15
146 147 4.932799 CACAATGATGCAACAACCAATCAT 59.067 37.500 0.00 0.00 0.00 2.45
147 148 4.038883 TCACAATGATGCAACAACCAATCA 59.961 37.500 0.00 0.00 0.00 2.57
148 149 4.558178 TCACAATGATGCAACAACCAATC 58.442 39.130 0.00 0.00 0.00 2.67
149 150 4.039488 ACTCACAATGATGCAACAACCAAT 59.961 37.500 0.00 0.00 0.00 3.16
150 151 3.384146 ACTCACAATGATGCAACAACCAA 59.616 39.130 0.00 0.00 0.00 3.67
151 152 2.957680 ACTCACAATGATGCAACAACCA 59.042 40.909 0.00 0.00 0.00 3.67
152 153 3.648339 ACTCACAATGATGCAACAACC 57.352 42.857 0.00 0.00 0.00 3.77
153 154 6.187125 AGATACTCACAATGATGCAACAAC 57.813 37.500 0.00 0.00 0.00 3.32
154 155 7.105588 ACTAGATACTCACAATGATGCAACAA 58.894 34.615 0.00 0.00 0.00 2.83
155 156 6.643388 ACTAGATACTCACAATGATGCAACA 58.357 36.000 0.00 0.00 0.00 3.33
156 157 7.515841 CGAACTAGATACTCACAATGATGCAAC 60.516 40.741 0.00 0.00 0.00 4.17
157 158 6.476706 CGAACTAGATACTCACAATGATGCAA 59.523 38.462 0.00 0.00 0.00 4.08
158 159 5.979517 CGAACTAGATACTCACAATGATGCA 59.020 40.000 0.00 0.00 0.00 3.96
159 160 5.980116 ACGAACTAGATACTCACAATGATGC 59.020 40.000 0.00 0.00 0.00 3.91
160 161 7.196331 TGACGAACTAGATACTCACAATGATG 58.804 38.462 0.00 0.00 0.00 3.07
161 162 7.334844 TGACGAACTAGATACTCACAATGAT 57.665 36.000 0.00 0.00 0.00 2.45
162 163 6.753107 TGACGAACTAGATACTCACAATGA 57.247 37.500 0.00 0.00 0.00 2.57
163 164 7.812309 TTTGACGAACTAGATACTCACAATG 57.188 36.000 0.00 0.00 0.00 2.82
177 178 9.817809 ATGTGTGAACTATATATTTGACGAACT 57.182 29.630 0.00 0.00 0.00 3.01
196 197 8.343366 CGCTTACTAGTAGAGATAAATGTGTGA 58.657 37.037 3.59 0.00 0.00 3.58
197 198 8.129840 ACGCTTACTAGTAGAGATAAATGTGTG 58.870 37.037 3.59 0.00 0.00 3.82
198 199 8.129840 CACGCTTACTAGTAGAGATAAATGTGT 58.870 37.037 3.59 0.00 0.00 3.72
199 200 7.113684 GCACGCTTACTAGTAGAGATAAATGTG 59.886 40.741 3.59 5.40 0.00 3.21
200 201 7.140048 GCACGCTTACTAGTAGAGATAAATGT 58.860 38.462 3.59 0.00 0.00 2.71
201 202 7.113684 GTGCACGCTTACTAGTAGAGATAAATG 59.886 40.741 0.00 0.00 0.00 2.32
202 203 7.140048 GTGCACGCTTACTAGTAGAGATAAAT 58.860 38.462 0.00 0.00 0.00 1.40
203 204 6.493116 GTGCACGCTTACTAGTAGAGATAAA 58.507 40.000 0.00 0.00 0.00 1.40
204 205 5.277202 CGTGCACGCTTACTAGTAGAGATAA 60.277 44.000 28.16 0.00 0.00 1.75
205 206 4.210746 CGTGCACGCTTACTAGTAGAGATA 59.789 45.833 28.16 0.00 0.00 1.98
206 207 3.002451 CGTGCACGCTTACTAGTAGAGAT 59.998 47.826 28.16 0.00 0.00 2.75
207 208 2.350804 CGTGCACGCTTACTAGTAGAGA 59.649 50.000 28.16 0.00 0.00 3.10
208 209 2.095532 ACGTGCACGCTTACTAGTAGAG 59.904 50.000 37.35 8.10 44.43 2.43
209 210 2.079158 ACGTGCACGCTTACTAGTAGA 58.921 47.619 37.35 0.00 44.43 2.59
210 211 2.174764 CACGTGCACGCTTACTAGTAG 58.825 52.381 37.35 8.78 44.43 2.57
243 244 9.883142 AAATGGGTACAAATTATGTGTTAATGG 57.117 29.630 0.00 0.00 43.77 3.16
257 258 7.551585 CCTTGTTGCATATAAATGGGTACAAA 58.448 34.615 0.00 0.00 33.38 2.83
298 1063 7.524863 CGATTTACACTTGGCCACTCCTATATA 60.525 40.741 3.88 0.00 35.26 0.86
339 1232 1.408822 GGAAAGAATCGACTGGCCCAT 60.409 52.381 0.00 0.00 0.00 4.00
403 1635 1.481363 GGAGGTAGAAGAAAGTCCCGG 59.519 57.143 0.00 0.00 0.00 5.73
448 2021 4.740822 GGTGGCTGGCGGTCCATT 62.741 66.667 11.73 0.00 42.51 3.16
472 2057 4.285790 AGGTTCCAGGGAGGGCCA 62.286 66.667 6.18 0.00 38.24 5.36
517 2102 2.489073 GGAGAAAAACAGGAGAGGCCAA 60.489 50.000 5.01 0.00 40.02 4.52
519 2104 1.827681 GGAGAAAAACAGGAGAGGCC 58.172 55.000 0.00 0.00 0.00 5.19
521 2106 1.339151 CCCGGAGAAAAACAGGAGAGG 60.339 57.143 0.73 0.00 0.00 3.69
523 2108 1.724545 TCCCGGAGAAAAACAGGAGA 58.275 50.000 0.73 0.00 0.00 3.71
524 2109 2.152016 GTTCCCGGAGAAAAACAGGAG 58.848 52.381 0.73 0.00 35.85 3.69
528 2113 2.092321 TGAAGGTTCCCGGAGAAAAACA 60.092 45.455 0.73 1.65 35.85 2.83
529 2114 2.292569 GTGAAGGTTCCCGGAGAAAAAC 59.707 50.000 0.73 0.00 35.85 2.43
544 2150 3.813443 AGTAGCATAGCAATGGTGAAGG 58.187 45.455 0.00 0.00 43.52 3.46
550 2156 2.158623 TGGGGAAGTAGCATAGCAATGG 60.159 50.000 0.00 0.00 33.38 3.16
557 2163 0.345502 AGGGGTGGGGAAGTAGCATA 59.654 55.000 0.00 0.00 0.00 3.14
558 2164 0.345502 TAGGGGTGGGGAAGTAGCAT 59.654 55.000 0.00 0.00 0.00 3.79
563 2169 1.164288 TAGGGTAGGGGTGGGGAAGT 61.164 60.000 0.00 0.00 0.00 3.01
566 2196 0.861364 TCTTAGGGTAGGGGTGGGGA 60.861 60.000 0.00 0.00 0.00 4.81
629 2380 2.621556 AGAGGAGGAAGAAGCTCACT 57.378 50.000 0.00 0.00 0.00 3.41
681 2432 3.550030 CGCTTGACTTTCAAATTCGGGTT 60.550 43.478 0.00 0.00 35.73 4.11
825 2656 1.950909 GTCCGGTGTTGTCCAATTCAA 59.049 47.619 0.00 0.00 0.00 2.69
846 2677 4.949856 CCTTTTGGCCAAGTCACATATAGT 59.050 41.667 19.48 0.00 0.00 2.12
931 2797 2.741092 GTGACGAGGCAAGGACCA 59.259 61.111 0.00 0.00 0.00 4.02
932 2798 1.255667 TAGGTGACGAGGCAAGGACC 61.256 60.000 0.00 0.00 0.00 4.46
933 2799 0.108756 GTAGGTGACGAGGCAAGGAC 60.109 60.000 0.00 0.00 0.00 3.85
934 2800 1.255667 GGTAGGTGACGAGGCAAGGA 61.256 60.000 0.00 0.00 0.00 3.36
935 2801 1.218316 GGTAGGTGACGAGGCAAGG 59.782 63.158 0.00 0.00 0.00 3.61
936 2802 0.608640 AAGGTAGGTGACGAGGCAAG 59.391 55.000 0.00 0.00 0.00 4.01
937 2803 0.606604 GAAGGTAGGTGACGAGGCAA 59.393 55.000 0.00 0.00 0.00 4.52
959 2827 4.098807 GGAGACAGTGAAGAGATAAGGGTC 59.901 50.000 0.00 0.00 0.00 4.46
969 2842 0.105194 TGGTGGGGAGACAGTGAAGA 60.105 55.000 0.00 0.00 0.00 2.87
987 2860 1.477558 GCCACCATGGAATAGGGAGTG 60.478 57.143 21.47 2.08 40.96 3.51
1039 2968 1.228459 GAAAAACAGGAGGGGCGGT 60.228 57.895 0.00 0.00 0.00 5.68
1078 3015 0.390472 GAAGAGTGGGAAGAGTGCGG 60.390 60.000 0.00 0.00 0.00 5.69
1229 3166 2.027073 GAGGTTGCGACGCATGACA 61.027 57.895 25.09 5.45 38.76 3.58
1230 3167 2.740714 GGAGGTTGCGACGCATGAC 61.741 63.158 25.09 19.28 38.76 3.06
1251 3188 2.552093 TAGAGAGGAAGGAACCAGGG 57.448 55.000 0.00 0.00 0.00 4.45
1258 3195 3.008157 ACGAGCGATATAGAGAGGAAGGA 59.992 47.826 0.00 0.00 0.00 3.36
1336 3274 2.126071 CGGGGTACTGCTGTCGTG 60.126 66.667 0.00 0.00 0.00 4.35
1406 3352 8.621532 AAATAAGCATATATGAAAGCCGAAGA 57.378 30.769 17.10 0.00 0.00 2.87
1442 3388 3.113043 AGAAGTGGGTAATGGGGAGTAC 58.887 50.000 0.00 0.00 0.00 2.73
1465 3411 7.890127 CAGGAATGGATAGCAATTAGGGATTAA 59.110 37.037 0.00 0.00 0.00 1.40
1560 3624 8.466798 CGAAAATAAAATCACCCCAACTTCTAT 58.533 33.333 0.00 0.00 0.00 1.98
1577 3641 9.932207 TCCAAGATTAGACAGTACGAAAATAAA 57.068 29.630 0.00 0.00 0.00 1.40
1578 3642 9.582431 CTCCAAGATTAGACAGTACGAAAATAA 57.418 33.333 0.00 0.00 0.00 1.40
1609 3673 7.008086 CGAAGTTAAGAACGTCTAATCGAACAT 59.992 37.037 0.00 0.00 37.68 2.71
1636 3700 3.058016 CCCACTCATAACAGTTGTTGCAG 60.058 47.826 7.73 3.65 38.90 4.41
1641 3705 4.289672 AGAATCCCCACTCATAACAGTTGT 59.710 41.667 0.00 0.00 0.00 3.32
1725 3789 1.839894 CCCCTAGCCACCCAGAATC 59.160 63.158 0.00 0.00 0.00 2.52
1769 3833 0.257039 AGCGGGATCAAGCCAAATCT 59.743 50.000 7.86 0.00 0.00 2.40
1816 3882 9.651913 TTGAAAACTTCTAAAAACATGCTTTCT 57.348 25.926 0.00 0.00 0.00 2.52
1839 3917 8.432110 TGATTTACTATAAAGCTCGCATTTGA 57.568 30.769 0.00 0.00 0.00 2.69
1858 3938 7.397221 TGCTTCTCTTGATCCTCTTTGATTTA 58.603 34.615 0.00 0.00 0.00 1.40
1896 4201 8.998277 ACACTCATACATACTTATCCTACTGT 57.002 34.615 0.00 0.00 0.00 3.55
1901 4206 9.815306 AGTCATACACTCATACATACTTATCCT 57.185 33.333 0.00 0.00 0.00 3.24
1917 4222 8.449625 ACCTGTATTATCCTAGAGTCATACACT 58.550 37.037 0.00 0.00 38.45 3.55
1918 4223 8.638629 ACCTGTATTATCCTAGAGTCATACAC 57.361 38.462 0.00 0.00 0.00 2.90
2039 4738 4.082026 GGCAAGTTATTCACAGAAAGGCAT 60.082 41.667 0.00 0.00 0.00 4.40
2041 4740 3.507622 AGGCAAGTTATTCACAGAAAGGC 59.492 43.478 0.00 0.00 0.00 4.35
2049 4748 7.808381 GGACTTCTAAAAAGGCAAGTTATTCAC 59.192 37.037 0.00 0.00 0.00 3.18
2050 4749 7.504238 TGGACTTCTAAAAAGGCAAGTTATTCA 59.496 33.333 0.00 0.00 0.00 2.57
2065 4764 8.593679 TGTCAGAGATGTTTATGGACTTCTAAA 58.406 33.333 0.00 0.00 35.08 1.85
2089 4788 7.039644 AGCTGTTGTAAGTAGTACTGAAGATGT 60.040 37.037 5.39 0.00 33.46 3.06
2109 4808 4.074259 TGAATATCACTTGTGCAGCTGTT 58.926 39.130 16.64 0.00 0.00 3.16
2147 4846 8.557029 CCGGGACAACAAGAAATATATCTAAAC 58.443 37.037 0.00 0.00 0.00 2.01
2195 4895 5.163663 CCATTTCGTCTAAGCCTGCAAAATA 60.164 40.000 0.00 0.00 0.00 1.40
2196 4896 4.380867 CCATTTCGTCTAAGCCTGCAAAAT 60.381 41.667 0.00 0.00 0.00 1.82
2210 4910 8.608844 AGATGGTCTTTAATATCCATTTCGTC 57.391 34.615 0.00 0.00 40.24 4.20
2225 4925 4.689062 TCCCTCACTCTTAGATGGTCTTT 58.311 43.478 0.00 0.00 0.00 2.52
2341 5088 3.944422 ACTTGTTCTGTACAACGCTTG 57.056 42.857 0.00 0.00 41.73 4.01
2342 5089 6.259167 TCAATTACTTGTTCTGTACAACGCTT 59.741 34.615 0.00 0.00 41.73 4.68


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

AutoCloner maintained by Alex Coulton.