Multiple sequence alignment - TraesCS2D01G029800

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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 TraesCS2D01G029800 chr2D 100.000 3692 0 0 1 3692 12297630 12293939 0.000000e+00 6818.0
1 TraesCS2D01G029800 chr2D 92.572 552 40 1 3130 3680 32976636 32977187 0.000000e+00 791.0
2 TraesCS2D01G029800 chrUn 94.778 2432 104 8 721 3137 12467311 12469734 0.000000e+00 3766.0
3 TraesCS2D01G029800 chrUn 80.218 1466 257 24 1071 2519 241688425 241689874 0.000000e+00 1070.0
4 TraesCS2D01G029800 chrUn 90.799 663 38 14 228 888 12466735 12467376 0.000000e+00 865.0
5 TraesCS2D01G029800 chrUn 81.250 176 27 5 3 175 430915997 430915825 1.790000e-28 137.0
6 TraesCS2D01G029800 chrUn 84.000 150 14 5 746 888 12467283 12467429 6.430000e-28 135.0
7 TraesCS2D01G029800 chr2A 86.273 1814 184 29 953 2757 12913349 12911592 0.000000e+00 1910.0
8 TraesCS2D01G029800 chr2A 90.068 292 27 1 422 711 12914155 12913864 9.680000e-101 377.0
9 TraesCS2D01G029800 chr2A 85.922 206 26 3 172 376 12915122 12914919 2.230000e-52 217.0
10 TraesCS2D01G029800 chr2B 84.772 1865 205 37 938 2757 18321067 18319237 0.000000e+00 1797.0
11 TraesCS2D01G029800 chr2B 86.386 1594 172 20 938 2519 18387445 18385885 0.000000e+00 1700.0
12 TraesCS2D01G029800 chr2B 87.310 197 22 3 204 399 18321524 18321330 4.800000e-54 222.0
13 TraesCS2D01G029800 chr2B 87.402 127 13 3 275 400 18387830 18387706 3.840000e-30 143.0
14 TraesCS2D01G029800 chr2B 75.564 266 54 10 2798 3058 649713109 649712850 1.800000e-23 121.0
15 TraesCS2D01G029800 chr2B 87.671 73 4 1 422 489 18321329 18321257 3.060000e-11 80.5
16 TraesCS2D01G029800 chr2B 89.831 59 1 1 430 483 18387697 18387639 1.840000e-08 71.3
17 TraesCS2D01G029800 chr4A 80.791 1442 239 22 1094 2519 714293718 714295137 0.000000e+00 1094.0
18 TraesCS2D01G029800 chr6D 80.218 1466 257 24 1071 2519 470067881 470069330 0.000000e+00 1070.0
19 TraesCS2D01G029800 chr6D 91.803 549 44 1 3133 3680 351928359 351928907 0.000000e+00 763.0
20 TraesCS2D01G029800 chr6D 91.758 546 44 1 3136 3680 115189528 115190073 0.000000e+00 758.0
21 TraesCS2D01G029800 chr6D 82.000 200 25 6 2846 3041 114793798 114793606 3.820000e-35 159.0
22 TraesCS2D01G029800 chr7D 92.870 547 38 1 3134 3680 538991677 538991132 0.000000e+00 793.0
23 TraesCS2D01G029800 chr7D 92.096 544 43 0 3137 3680 59870653 59871196 0.000000e+00 767.0
24 TraesCS2D01G029800 chr7D 91.941 546 39 4 3138 3680 422575318 422574775 0.000000e+00 760.0
25 TraesCS2D01G029800 chr7D 100.000 32 0 0 801 832 6947261 6947230 3.980000e-05 60.2
26 TraesCS2D01G029800 chr7D 100.000 32 0 0 801 832 44738185 44738154 3.980000e-05 60.2
27 TraesCS2D01G029800 chr7D 100.000 32 0 0 801 832 381934751 381934720 3.980000e-05 60.2
28 TraesCS2D01G029800 chr5D 92.210 552 42 1 3130 3680 444885884 444886435 0.000000e+00 780.0
29 TraesCS2D01G029800 chr5D 91.336 554 46 2 3128 3680 564121712 564121160 0.000000e+00 756.0
30 TraesCS2D01G029800 chr5D 75.862 261 56 6 2799 3055 550559122 550559379 3.870000e-25 126.0
31 TraesCS2D01G029800 chr5D 77.326 172 23 8 1 172 118453081 118452926 1.830000e-13 87.9
32 TraesCS2D01G029800 chr5D 84.127 63 7 3 2151 2212 366743855 366743915 1.430000e-04 58.4
33 TraesCS2D01G029800 chr3D 93.143 525 34 1 3136 3660 136771471 136770949 0.000000e+00 769.0
34 TraesCS2D01G029800 chr3D 76.226 265 53 9 2799 3057 353418120 353417860 8.320000e-27 132.0
35 TraesCS2D01G029800 chr5B 74.383 1499 293 62 1089 2531 571480054 571481517 1.160000e-154 556.0
36 TraesCS2D01G029800 chr5B 80.682 176 28 5 3 175 266347146 266347318 8.320000e-27 132.0
37 TraesCS2D01G029800 chr5B 76.744 172 24 5 1 172 130509931 130509776 8.500000e-12 82.4
38 TraesCS2D01G029800 chr5B 90.698 43 4 0 2144 2186 433894303 433894345 1.430000e-04 58.4
39 TraesCS2D01G029800 chr5A 76.208 269 53 9 2796 3057 691037843 691038107 8.320000e-27 132.0
40 TraesCS2D01G029800 chr5A 77.841 176 35 4 3 176 315963131 315963304 5.040000e-19 106.0
41 TraesCS2D01G029800 chr5A 100.000 32 0 0 801 832 420153268 420153237 3.980000e-05 60.2
42 TraesCS2D01G029800 chr5A 100.000 32 0 0 801 832 467758300 467758331 3.980000e-05 60.2
43 TraesCS2D01G029800 chr5A 100.000 32 0 0 801 832 485169671 485169640 3.980000e-05 60.2
44 TraesCS2D01G029800 chr1D 76.494 251 54 4 2799 3046 247873996 247874244 8.320000e-27 132.0
45 TraesCS2D01G029800 chr1D 75.849 265 53 8 2799 3058 475514777 475515035 1.390000e-24 124.0
46 TraesCS2D01G029800 chr1D 100.000 29 0 0 1725 1753 413319109 413319081 2.000000e-03 54.7
47 TraesCS2D01G029800 chr7A 75.092 273 59 7 2793 3060 158339540 158339808 6.480000e-23 119.0
48 TraesCS2D01G029800 chr1B 100.000 34 0 0 801 834 588844034 588844001 3.080000e-06 63.9
49 TraesCS2D01G029800 chr6A 100.000 32 0 0 801 832 435978811 435978780 3.980000e-05 60.2
50 TraesCS2D01G029800 chr1A 100.000 32 0 0 801 832 334063737 334063768 3.980000e-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 TraesCS2D01G029800 chr2D 12293939 12297630 3691 True 6818.000000 6818 100.000000 1 3692 1 chr2D.!!$R1 3691
1 TraesCS2D01G029800 chr2D 32976636 32977187 551 False 791.000000 791 92.572000 3130 3680 1 chr2D.!!$F1 550
2 TraesCS2D01G029800 chrUn 12466735 12469734 2999 False 1588.666667 3766 89.859000 228 3137 3 chrUn.!!$F2 2909
3 TraesCS2D01G029800 chrUn 241688425 241689874 1449 False 1070.000000 1070 80.218000 1071 2519 1 chrUn.!!$F1 1448
4 TraesCS2D01G029800 chr2A 12911592 12915122 3530 True 834.666667 1910 87.421000 172 2757 3 chr2A.!!$R1 2585
5 TraesCS2D01G029800 chr2B 18319237 18321524 2287 True 699.833333 1797 86.584333 204 2757 3 chr2B.!!$R2 2553
6 TraesCS2D01G029800 chr2B 18385885 18387830 1945 True 638.100000 1700 87.873000 275 2519 3 chr2B.!!$R3 2244
7 TraesCS2D01G029800 chr4A 714293718 714295137 1419 False 1094.000000 1094 80.791000 1094 2519 1 chr4A.!!$F1 1425
8 TraesCS2D01G029800 chr6D 470067881 470069330 1449 False 1070.000000 1070 80.218000 1071 2519 1 chr6D.!!$F3 1448
9 TraesCS2D01G029800 chr6D 351928359 351928907 548 False 763.000000 763 91.803000 3133 3680 1 chr6D.!!$F2 547
10 TraesCS2D01G029800 chr6D 115189528 115190073 545 False 758.000000 758 91.758000 3136 3680 1 chr6D.!!$F1 544
11 TraesCS2D01G029800 chr7D 538991132 538991677 545 True 793.000000 793 92.870000 3134 3680 1 chr7D.!!$R5 546
12 TraesCS2D01G029800 chr7D 59870653 59871196 543 False 767.000000 767 92.096000 3137 3680 1 chr7D.!!$F1 543
13 TraesCS2D01G029800 chr7D 422574775 422575318 543 True 760.000000 760 91.941000 3138 3680 1 chr7D.!!$R4 542
14 TraesCS2D01G029800 chr5D 444885884 444886435 551 False 780.000000 780 92.210000 3130 3680 1 chr5D.!!$F2 550
15 TraesCS2D01G029800 chr5D 564121160 564121712 552 True 756.000000 756 91.336000 3128 3680 1 chr5D.!!$R2 552
16 TraesCS2D01G029800 chr3D 136770949 136771471 522 True 769.000000 769 93.143000 3136 3660 1 chr3D.!!$R1 524
17 TraesCS2D01G029800 chr5B 571480054 571481517 1463 False 556.000000 556 74.383000 1089 2531 1 chr5B.!!$F3 1442

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
812 2019 0.107410 TTGCAATAGGGGCCACGTAG 60.107 55.000 4.39 0.0 0.00 3.51 F
814 2021 0.532196 GCAATAGGGGCCACGTAGAC 60.532 60.000 4.39 0.0 0.00 2.59 F
820 2027 1.063114 AGGGGCCACGTAGACTATTCT 60.063 52.381 4.39 0.0 35.66 2.40 F
2419 3753 0.178861 AGGTGATGAGGACCAGGGTT 60.179 55.000 0.00 0.0 35.76 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 3433 1.026718 GTTTGTGGAGCCCAGGATCG 61.027 60.000 0.00 0.0 32.34 3.69 R
2419 3753 1.480954 GACTTTGAGGCGAGGTCCATA 59.519 52.381 0.00 0.0 0.00 2.74 R
2607 3964 2.754946 AACATACGTCGTGGATTGGT 57.245 45.000 8.47 0.0 0.00 3.67 R
3657 5033 1.963855 TTGCGCATACGTGGCAACT 60.964 52.632 12.75 0.0 42.83 3.16 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
20 21 3.797348 GAGAGAAAGAAAGTTGTCCGC 57.203 47.619 0.00 0.00 0.00 5.54
21 22 3.131396 GAGAGAAAGAAAGTTGTCCGCA 58.869 45.455 0.00 0.00 0.00 5.69
22 23 3.541632 AGAGAAAGAAAGTTGTCCGCAA 58.458 40.909 0.00 0.00 0.00 4.85
32 33 1.243902 TTGTCCGCAACAATCCTTCC 58.756 50.000 0.00 0.00 42.95 3.46
33 34 0.400213 TGTCCGCAACAATCCTTCCT 59.600 50.000 0.00 0.00 34.03 3.36
34 35 1.626321 TGTCCGCAACAATCCTTCCTA 59.374 47.619 0.00 0.00 34.03 2.94
35 36 2.280628 GTCCGCAACAATCCTTCCTAG 58.719 52.381 0.00 0.00 0.00 3.02
36 37 1.209504 TCCGCAACAATCCTTCCTAGG 59.790 52.381 0.82 0.82 43.46 3.02
37 38 1.065418 CCGCAACAATCCTTCCTAGGT 60.065 52.381 9.08 0.00 42.60 3.08
38 39 2.618045 CCGCAACAATCCTTCCTAGGTT 60.618 50.000 9.08 0.00 42.60 3.50
39 40 3.081804 CGCAACAATCCTTCCTAGGTTT 58.918 45.455 9.08 0.00 42.60 3.27
45 46 4.936685 AATCCTTCCTAGGTTTGAAGCT 57.063 40.909 9.08 0.80 42.60 3.74
46 47 3.703001 TCCTTCCTAGGTTTGAAGCTG 57.297 47.619 9.08 0.00 42.60 4.24
47 48 2.305927 TCCTTCCTAGGTTTGAAGCTGG 59.694 50.000 9.08 2.81 42.60 4.85
48 49 2.087646 CTTCCTAGGTTTGAAGCTGGC 58.912 52.381 9.08 0.00 37.33 4.85
49 50 1.064003 TCCTAGGTTTGAAGCTGGCA 58.936 50.000 9.08 0.00 37.33 4.92
50 51 1.635487 TCCTAGGTTTGAAGCTGGCAT 59.365 47.619 9.08 0.00 37.33 4.40
51 52 2.019984 CCTAGGTTTGAAGCTGGCATC 58.980 52.381 0.00 0.00 37.33 3.91
52 53 2.356535 CCTAGGTTTGAAGCTGGCATCT 60.357 50.000 0.00 0.00 37.33 2.90
53 54 3.118261 CCTAGGTTTGAAGCTGGCATCTA 60.118 47.826 0.00 0.00 37.33 1.98
54 55 2.716217 AGGTTTGAAGCTGGCATCTAC 58.284 47.619 0.00 0.00 35.05 2.59
55 56 1.745653 GGTTTGAAGCTGGCATCTACC 59.254 52.381 0.00 0.00 0.00 3.18
56 57 2.619074 GGTTTGAAGCTGGCATCTACCT 60.619 50.000 11.99 0.00 0.00 3.08
57 58 3.084786 GTTTGAAGCTGGCATCTACCTT 58.915 45.455 0.00 0.00 0.00 3.50
58 59 2.698855 TGAAGCTGGCATCTACCTTC 57.301 50.000 0.00 0.00 34.12 3.46
59 60 2.191400 TGAAGCTGGCATCTACCTTCT 58.809 47.619 0.00 0.00 34.51 2.85
60 61 2.169352 TGAAGCTGGCATCTACCTTCTC 59.831 50.000 0.00 0.00 34.51 2.87
61 62 1.127343 AGCTGGCATCTACCTTCTCC 58.873 55.000 0.00 0.00 0.00 3.71
62 63 0.833287 GCTGGCATCTACCTTCTCCA 59.167 55.000 0.00 0.00 0.00 3.86
63 64 1.474143 GCTGGCATCTACCTTCTCCAC 60.474 57.143 0.00 0.00 0.00 4.02
64 65 0.824109 TGGCATCTACCTTCTCCACG 59.176 55.000 0.00 0.00 0.00 4.94
65 66 1.112113 GGCATCTACCTTCTCCACGA 58.888 55.000 0.00 0.00 0.00 4.35
66 67 1.689273 GGCATCTACCTTCTCCACGAT 59.311 52.381 0.00 0.00 0.00 3.73
67 68 2.103263 GGCATCTACCTTCTCCACGATT 59.897 50.000 0.00 0.00 0.00 3.34
68 69 3.126831 GCATCTACCTTCTCCACGATTG 58.873 50.000 0.00 0.00 0.00 2.67
69 70 3.430929 GCATCTACCTTCTCCACGATTGT 60.431 47.826 0.00 0.00 0.00 2.71
70 71 4.363999 CATCTACCTTCTCCACGATTGTC 58.636 47.826 0.00 0.00 0.00 3.18
71 72 3.427573 TCTACCTTCTCCACGATTGTCA 58.572 45.455 0.00 0.00 0.00 3.58
72 73 2.457366 ACCTTCTCCACGATTGTCAC 57.543 50.000 0.00 0.00 0.00 3.67
73 74 1.971357 ACCTTCTCCACGATTGTCACT 59.029 47.619 0.00 0.00 0.00 3.41
74 75 3.162666 ACCTTCTCCACGATTGTCACTA 58.837 45.455 0.00 0.00 0.00 2.74
75 76 3.769844 ACCTTCTCCACGATTGTCACTAT 59.230 43.478 0.00 0.00 0.00 2.12
76 77 4.954202 ACCTTCTCCACGATTGTCACTATA 59.046 41.667 0.00 0.00 0.00 1.31
77 78 5.598830 ACCTTCTCCACGATTGTCACTATAT 59.401 40.000 0.00 0.00 0.00 0.86
78 79 5.923114 CCTTCTCCACGATTGTCACTATATG 59.077 44.000 0.00 0.00 0.00 1.78
79 80 4.871513 TCTCCACGATTGTCACTATATGC 58.128 43.478 0.00 0.00 0.00 3.14
80 81 4.340950 TCTCCACGATTGTCACTATATGCA 59.659 41.667 0.00 0.00 0.00 3.96
81 82 4.620982 TCCACGATTGTCACTATATGCAG 58.379 43.478 0.00 0.00 0.00 4.41
82 83 3.742882 CCACGATTGTCACTATATGCAGG 59.257 47.826 0.00 0.00 0.00 4.85
83 84 4.501400 CCACGATTGTCACTATATGCAGGA 60.501 45.833 0.00 0.00 0.00 3.86
84 85 5.049828 CACGATTGTCACTATATGCAGGAA 58.950 41.667 0.00 0.00 0.00 3.36
85 86 5.050490 ACGATTGTCACTATATGCAGGAAC 58.950 41.667 0.00 0.00 0.00 3.62
86 87 5.049828 CGATTGTCACTATATGCAGGAACA 58.950 41.667 0.00 0.00 0.00 3.18
87 88 5.523552 CGATTGTCACTATATGCAGGAACAA 59.476 40.000 0.00 0.00 32.29 2.83
88 89 6.037062 CGATTGTCACTATATGCAGGAACAAA 59.963 38.462 0.00 0.00 31.84 2.83
89 90 7.413988 CGATTGTCACTATATGCAGGAACAAAA 60.414 37.037 0.00 0.00 31.84 2.44
90 91 7.701539 TTGTCACTATATGCAGGAACAAAAT 57.298 32.000 0.00 0.00 0.00 1.82
91 92 7.701539 TGTCACTATATGCAGGAACAAAATT 57.298 32.000 0.00 0.00 0.00 1.82
92 93 7.537715 TGTCACTATATGCAGGAACAAAATTG 58.462 34.615 0.00 0.00 0.00 2.32
93 94 7.176515 TGTCACTATATGCAGGAACAAAATTGT 59.823 33.333 0.00 0.00 44.72 2.71
94 95 7.485913 GTCACTATATGCAGGAACAAAATTGTG 59.514 37.037 0.00 0.00 41.31 3.33
95 96 6.254157 CACTATATGCAGGAACAAAATTGTGC 59.746 38.462 0.00 0.00 41.31 4.57
96 97 3.756933 ATGCAGGAACAAAATTGTGCT 57.243 38.095 4.35 0.00 41.31 4.40
97 98 3.096489 TGCAGGAACAAAATTGTGCTC 57.904 42.857 4.35 0.00 41.31 4.26
98 99 2.429971 TGCAGGAACAAAATTGTGCTCA 59.570 40.909 4.35 0.00 41.31 4.26
99 100 3.069872 TGCAGGAACAAAATTGTGCTCAT 59.930 39.130 4.35 0.00 41.31 2.90
100 101 4.060205 GCAGGAACAAAATTGTGCTCATT 58.940 39.130 4.35 0.00 41.31 2.57
101 102 4.151157 GCAGGAACAAAATTGTGCTCATTC 59.849 41.667 4.35 0.00 41.31 2.67
102 103 5.291178 CAGGAACAAAATTGTGCTCATTCA 58.709 37.500 4.35 0.00 41.31 2.57
103 104 5.404366 CAGGAACAAAATTGTGCTCATTCAG 59.596 40.000 4.35 0.00 41.31 3.02
104 105 5.069516 AGGAACAAAATTGTGCTCATTCAGT 59.930 36.000 4.35 0.00 41.31 3.41
105 106 6.265196 AGGAACAAAATTGTGCTCATTCAGTA 59.735 34.615 4.35 0.00 41.31 2.74
106 107 6.583806 GGAACAAAATTGTGCTCATTCAGTAG 59.416 38.462 4.35 0.00 41.31 2.57
107 108 5.464168 ACAAAATTGTGCTCATTCAGTAGC 58.536 37.500 0.00 0.00 40.49 3.58
108 109 4.346734 AAATTGTGCTCATTCAGTAGCG 57.653 40.909 0.00 0.00 41.77 4.26
109 110 2.741759 TTGTGCTCATTCAGTAGCGA 57.258 45.000 0.00 0.00 41.77 4.93
110 111 1.996292 TGTGCTCATTCAGTAGCGAC 58.004 50.000 0.00 0.00 41.77 5.19
111 112 0.917259 GTGCTCATTCAGTAGCGACG 59.083 55.000 0.00 0.00 41.77 5.12
112 113 0.526211 TGCTCATTCAGTAGCGACGT 59.474 50.000 0.00 0.00 41.77 4.34
113 114 1.192793 GCTCATTCAGTAGCGACGTC 58.807 55.000 5.18 5.18 0.00 4.34
114 115 1.457738 CTCATTCAGTAGCGACGTCG 58.542 55.000 32.57 32.57 43.27 5.12
115 116 1.062148 CTCATTCAGTAGCGACGTCGA 59.938 52.381 39.74 18.94 43.02 4.20
116 117 1.465777 TCATTCAGTAGCGACGTCGAA 59.534 47.619 39.74 24.01 43.02 3.71
117 118 2.095617 TCATTCAGTAGCGACGTCGAAA 60.096 45.455 39.74 23.76 43.02 3.46
118 119 1.959747 TTCAGTAGCGACGTCGAAAG 58.040 50.000 39.74 22.66 43.02 2.62
119 120 1.150827 TCAGTAGCGACGTCGAAAGA 58.849 50.000 39.74 24.39 43.02 2.52
120 121 1.532437 TCAGTAGCGACGTCGAAAGAA 59.468 47.619 39.74 17.41 45.01 2.52
121 122 2.161012 TCAGTAGCGACGTCGAAAGAAT 59.839 45.455 39.74 17.64 45.01 2.40
122 123 2.526688 CAGTAGCGACGTCGAAAGAATC 59.473 50.000 39.74 20.48 45.01 2.52
123 124 2.419324 AGTAGCGACGTCGAAAGAATCT 59.581 45.455 39.74 25.89 45.01 2.40
124 125 2.349297 AGCGACGTCGAAAGAATCTT 57.651 45.000 39.74 10.71 45.01 2.40
125 126 2.673833 AGCGACGTCGAAAGAATCTTT 58.326 42.857 39.74 8.12 45.01 2.52
126 127 2.662156 AGCGACGTCGAAAGAATCTTTC 59.338 45.455 39.74 22.16 45.01 2.62
127 128 2.407361 GCGACGTCGAAAGAATCTTTCA 59.593 45.455 39.74 16.51 45.01 2.69
128 129 3.480505 GCGACGTCGAAAGAATCTTTCAG 60.481 47.826 39.74 21.84 45.01 3.02
129 130 3.059570 CGACGTCGAAAGAATCTTTCAGG 59.940 47.826 33.35 22.34 45.01 3.86
130 131 4.235360 GACGTCGAAAGAATCTTTCAGGA 58.765 43.478 28.54 18.63 45.01 3.86
131 132 4.628074 ACGTCGAAAGAATCTTTCAGGAA 58.372 39.130 28.54 12.71 45.01 3.36
132 133 5.054477 ACGTCGAAAGAATCTTTCAGGAAA 58.946 37.500 28.54 10.68 45.01 3.13
133 134 5.701290 ACGTCGAAAGAATCTTTCAGGAAAT 59.299 36.000 28.54 11.95 45.01 2.17
134 135 6.017933 CGTCGAAAGAATCTTTCAGGAAATG 58.982 40.000 28.54 14.62 45.01 2.32
135 136 6.347725 CGTCGAAAGAATCTTTCAGGAAATGT 60.348 38.462 28.54 0.00 45.01 2.71
136 137 7.363431 GTCGAAAGAATCTTTCAGGAAATGTT 58.637 34.615 28.54 0.00 45.01 2.71
137 138 7.324616 GTCGAAAGAATCTTTCAGGAAATGTTG 59.675 37.037 28.54 12.87 45.01 3.33
138 139 6.583806 CGAAAGAATCTTTCAGGAAATGTTGG 59.416 38.462 28.54 9.58 0.00 3.77
139 140 5.990120 AGAATCTTTCAGGAAATGTTGGG 57.010 39.130 0.00 0.00 0.00 4.12
140 141 5.397360 AGAATCTTTCAGGAAATGTTGGGT 58.603 37.500 0.00 0.00 0.00 4.51
141 142 5.478332 AGAATCTTTCAGGAAATGTTGGGTC 59.522 40.000 0.00 0.00 0.00 4.46
142 143 4.453480 TCTTTCAGGAAATGTTGGGTCT 57.547 40.909 0.00 0.00 0.00 3.85
143 144 5.576563 TCTTTCAGGAAATGTTGGGTCTA 57.423 39.130 0.00 0.00 0.00 2.59
144 145 6.139679 TCTTTCAGGAAATGTTGGGTCTAT 57.860 37.500 0.00 0.00 0.00 1.98
145 146 6.180472 TCTTTCAGGAAATGTTGGGTCTATC 58.820 40.000 0.00 0.00 0.00 2.08
146 147 5.512942 TTCAGGAAATGTTGGGTCTATCA 57.487 39.130 0.00 0.00 0.00 2.15
147 148 5.715439 TCAGGAAATGTTGGGTCTATCAT 57.285 39.130 0.00 0.00 0.00 2.45
148 149 5.439721 TCAGGAAATGTTGGGTCTATCATG 58.560 41.667 0.00 0.00 0.00 3.07
149 150 4.581824 CAGGAAATGTTGGGTCTATCATGG 59.418 45.833 0.00 0.00 0.00 3.66
150 151 4.230502 AGGAAATGTTGGGTCTATCATGGT 59.769 41.667 0.00 0.00 0.00 3.55
151 152 4.339247 GGAAATGTTGGGTCTATCATGGTG 59.661 45.833 0.00 0.00 0.00 4.17
152 153 4.591321 AATGTTGGGTCTATCATGGTGT 57.409 40.909 0.00 0.00 0.00 4.16
153 154 5.708736 AATGTTGGGTCTATCATGGTGTA 57.291 39.130 0.00 0.00 0.00 2.90
154 155 4.753516 TGTTGGGTCTATCATGGTGTAG 57.246 45.455 0.00 0.00 0.00 2.74
155 156 4.101114 TGTTGGGTCTATCATGGTGTAGT 58.899 43.478 0.00 0.00 0.00 2.73
156 157 4.161565 TGTTGGGTCTATCATGGTGTAGTC 59.838 45.833 0.00 0.00 0.00 2.59
157 158 3.305720 TGGGTCTATCATGGTGTAGTCC 58.694 50.000 0.00 1.28 0.00 3.85
158 159 2.296471 GGGTCTATCATGGTGTAGTCCG 59.704 54.545 0.00 0.00 30.11 4.79
159 160 2.957006 GGTCTATCATGGTGTAGTCCGT 59.043 50.000 0.00 0.00 0.00 4.69
160 161 3.243434 GGTCTATCATGGTGTAGTCCGTG 60.243 52.174 0.00 0.00 43.59 4.94
161 162 3.380637 GTCTATCATGGTGTAGTCCGTGT 59.619 47.826 0.00 0.00 42.98 4.49
162 163 4.577693 GTCTATCATGGTGTAGTCCGTGTA 59.422 45.833 0.00 0.00 42.98 2.90
163 164 3.795623 ATCATGGTGTAGTCCGTGTAC 57.204 47.619 0.00 0.00 42.98 2.90
164 165 2.516906 TCATGGTGTAGTCCGTGTACA 58.483 47.619 0.00 0.00 42.98 2.90
165 166 2.490509 TCATGGTGTAGTCCGTGTACAG 59.509 50.000 0.00 0.00 42.98 2.74
166 167 2.275134 TGGTGTAGTCCGTGTACAGA 57.725 50.000 0.00 0.00 31.00 3.41
167 168 2.585330 TGGTGTAGTCCGTGTACAGAA 58.415 47.619 0.00 0.00 31.00 3.02
168 169 2.555325 TGGTGTAGTCCGTGTACAGAAG 59.445 50.000 0.00 0.00 31.00 2.85
169 170 2.593257 GTGTAGTCCGTGTACAGAAGC 58.407 52.381 0.00 0.00 31.00 3.86
170 171 1.542915 TGTAGTCCGTGTACAGAAGCC 59.457 52.381 0.00 0.00 0.00 4.35
179 180 3.667960 CGTGTACAGAAGCCTTGCATTTC 60.668 47.826 0.00 0.00 0.00 2.17
183 184 2.942710 CAGAAGCCTTGCATTTCTGTG 58.057 47.619 16.43 2.29 41.66 3.66
184 185 1.271656 AGAAGCCTTGCATTTCTGTGC 59.728 47.619 0.00 0.00 45.25 4.57
188 189 0.387622 CCTTGCATTTCTGTGCCACG 60.388 55.000 0.00 0.00 44.43 4.94
189 190 1.005294 CTTGCATTTCTGTGCCACGC 61.005 55.000 0.00 0.00 44.43 5.34
196 197 0.666274 TTCTGTGCCACGCGAACTAG 60.666 55.000 15.93 3.19 0.00 2.57
225 226 6.902224 TGATCCACGTAATATGTTCAACAG 57.098 37.500 0.00 0.00 0.00 3.16
284 285 8.939929 TGAGAATATTTGTGAAGAAGTCATGAC 58.060 33.333 18.47 18.47 38.90 3.06
357 358 9.797642 TGATTTTAGCTCCATATGATTGTACAT 57.202 29.630 3.65 0.00 0.00 2.29
428 1169 9.806448 AAGTAATTAATGGCATATGGTGTATGA 57.194 29.630 0.00 0.00 0.00 2.15
537 1283 5.364446 TGTCACTTGTGTAGGAGGTAAGAAA 59.636 40.000 0.46 0.00 0.00 2.52
676 1422 2.159099 TCATGTGTGGAAGATAGTCCGC 60.159 50.000 0.00 0.00 46.58 5.54
775 1982 4.127171 GCGGAATTTTCTGAGCTATACCA 58.873 43.478 3.30 0.00 35.56 3.25
806 2013 3.384816 GCAATTTGCAATAGGGGCC 57.615 52.632 16.35 0.00 44.26 5.80
807 2014 0.540923 GCAATTTGCAATAGGGGCCA 59.459 50.000 16.35 0.00 44.26 5.36
808 2015 1.743431 GCAATTTGCAATAGGGGCCAC 60.743 52.381 16.35 0.00 44.26 5.01
810 2017 0.324275 ATTTGCAATAGGGGCCACGT 60.324 50.000 4.39 0.00 0.00 4.49
812 2019 0.107410 TTGCAATAGGGGCCACGTAG 60.107 55.000 4.39 0.00 0.00 3.51
813 2020 0.978667 TGCAATAGGGGCCACGTAGA 60.979 55.000 4.39 0.00 0.00 2.59
814 2021 0.532196 GCAATAGGGGCCACGTAGAC 60.532 60.000 4.39 0.00 0.00 2.59
816 2023 2.313317 CAATAGGGGCCACGTAGACTA 58.687 52.381 4.39 0.00 0.00 2.59
818 2025 2.761786 TAGGGGCCACGTAGACTATT 57.238 50.000 4.39 0.00 0.00 1.73
819 2026 1.411041 AGGGGCCACGTAGACTATTC 58.589 55.000 4.39 0.00 0.00 1.75
820 2027 1.063114 AGGGGCCACGTAGACTATTCT 60.063 52.381 4.39 0.00 35.66 2.40
821 2028 1.068741 GGGGCCACGTAGACTATTCTG 59.931 57.143 4.39 0.00 32.75 3.02
822 2029 2.029623 GGGCCACGTAGACTATTCTGA 58.970 52.381 4.39 0.00 32.75 3.27
823 2030 2.034812 GGGCCACGTAGACTATTCTGAG 59.965 54.545 4.39 0.00 32.75 3.35
824 2031 2.034812 GGCCACGTAGACTATTCTGAGG 59.965 54.545 0.00 0.00 32.75 3.86
825 2032 2.688958 GCCACGTAGACTATTCTGAGGT 59.311 50.000 0.00 0.00 32.75 3.85
826 2033 3.489398 GCCACGTAGACTATTCTGAGGTG 60.489 52.174 0.00 0.00 32.75 4.00
827 2034 3.066900 CCACGTAGACTATTCTGAGGTGG 59.933 52.174 11.74 11.74 36.36 4.61
828 2035 3.695060 CACGTAGACTATTCTGAGGTGGT 59.305 47.826 0.00 0.00 32.75 4.16
861 2072 3.666883 TTTGCAATACGTATGCGGAAG 57.333 42.857 9.24 0.00 46.76 3.46
933 2197 9.612066 ATGGCATAATTCCGTTAATTTGAAAAT 57.388 25.926 0.00 0.00 38.71 1.82
1023 2287 1.092921 AAATAGGCCGAAATGCGCGA 61.093 50.000 12.10 0.00 39.11 5.87
1078 2351 8.735315 TCGTTGAAAATAATAAAGATGGCTTCA 58.265 29.630 3.03 0.00 31.82 3.02
1706 3033 5.068234 TCGATACATCTTCGACAAGGTTT 57.932 39.130 0.00 0.00 40.44 3.27
1753 3084 1.660575 CGCCGTCAACACGTTCTCT 60.661 57.895 0.00 0.00 45.17 3.10
1975 3309 2.188994 GCATCGGAGGCTCAGCTT 59.811 61.111 17.69 0.00 0.00 3.74
2077 3411 2.358737 GGGTGGGAGAAGCGTGTG 60.359 66.667 0.00 0.00 0.00 3.82
2419 3753 0.178861 AGGTGATGAGGACCAGGGTT 60.179 55.000 0.00 0.00 35.76 4.11
2594 3946 3.498774 ATGTGGCTTTCAGTCTGTTCT 57.501 42.857 0.00 0.00 0.00 3.01
2607 3964 9.621629 TTTCAGTCTGTTCTATTTTTCCTTGTA 57.378 29.630 0.00 0.00 0.00 2.41
2651 4015 9.872757 TTTTCGTCTAGTATTTGTTTTGTCATC 57.127 29.630 0.00 0.00 0.00 2.92
2652 4016 8.827177 TTCGTCTAGTATTTGTTTTGTCATCT 57.173 30.769 0.00 0.00 0.00 2.90
2653 4017 8.239681 TCGTCTAGTATTTGTTTTGTCATCTG 57.760 34.615 0.00 0.00 0.00 2.90
2674 4038 6.751157 TCTGGTATTTTGAACTCGTCTGTTA 58.249 36.000 0.00 0.00 0.00 2.41
2768 4137 0.721718 GCAACTAGATGACACACCGC 59.278 55.000 3.85 0.00 0.00 5.68
2769 4138 1.939381 GCAACTAGATGACACACCGCA 60.939 52.381 3.85 0.00 0.00 5.69
2807 4176 9.000486 GCAAATTAGTTACAATATACTCCCTCC 58.000 37.037 0.00 0.00 0.00 4.30
2839 4208 7.636259 TTTTTACTTTGCATCCGAGATTTTG 57.364 32.000 0.00 0.00 0.00 2.44
2860 4229 5.250235 TGCCGATGTCAAACTTTGTAAAA 57.750 34.783 1.44 0.00 0.00 1.52
2959 4328 9.121517 CGATACATCTAATGAAATTGATTTGGC 57.878 33.333 0.00 0.00 36.99 4.52
2965 4334 9.675464 ATCTAATGAAATTGATTTGGCATTGTT 57.325 25.926 10.96 0.00 36.99 2.83
3042 4414 7.662669 AGGCAAAACTTATCTACGGAGTAAAAA 59.337 33.333 0.00 0.00 45.13 1.94
3071 4444 5.698545 GGAGGGAGTATTTCAATGAGATTCG 59.301 44.000 0.00 0.00 0.00 3.34
3072 4445 5.059833 AGGGAGTATTTCAATGAGATTCGC 58.940 41.667 0.00 0.00 0.00 4.70
3083 4456 5.007039 TCAATGAGATTCGCTTGTATTCAGC 59.993 40.000 0.00 0.00 0.00 4.26
3202 4576 3.636043 CACCGTGTGTGGCGTGAC 61.636 66.667 0.00 0.00 41.52 3.67
3249 4623 3.438781 GTGTGGGCGAACATTAGAATTGA 59.561 43.478 0.00 0.00 31.49 2.57
3376 4750 1.684983 GCTATGTTAGGTACCAGCGGA 59.315 52.381 15.94 0.00 0.00 5.54
3424 4798 3.181469 TGGCAGATGTAGTTATTCGGGAC 60.181 47.826 0.00 0.00 0.00 4.46
3506 4881 6.772716 CCATGTCTAATTTATGGTAGTTGCCT 59.227 38.462 0.00 0.00 37.24 4.75
3650 5025 6.128035 TGGTTAATCACAGTTATCATGTGTGC 60.128 38.462 8.19 0.00 46.49 4.57
3657 5033 7.781056 TCACAGTTATCATGTGTGCTTATCTA 58.219 34.615 8.19 0.00 46.49 1.98
3669 5045 4.142026 TGTGCTTATCTAGTTGCCACGTAT 60.142 41.667 0.00 0.00 0.00 3.06
3689 5065 3.966215 GCAACTGCGGCTAGACAA 58.034 55.556 0.00 0.00 0.00 3.18
3690 5066 1.790387 GCAACTGCGGCTAGACAAG 59.210 57.895 0.00 0.00 0.00 3.16
3691 5067 1.639298 GCAACTGCGGCTAGACAAGG 61.639 60.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.131396 TGCGGACAACTTTCTTTCTCTC 58.869 45.455 0.00 0.00 0.00 3.20
1 2 3.194005 TGCGGACAACTTTCTTTCTCT 57.806 42.857 0.00 0.00 0.00 3.10
2 3 3.963383 TTGCGGACAACTTTCTTTCTC 57.037 42.857 0.00 0.00 0.00 2.87
14 15 0.400213 AGGAAGGATTGTTGCGGACA 59.600 50.000 0.00 0.00 36.19 4.02
15 16 2.280628 CTAGGAAGGATTGTTGCGGAC 58.719 52.381 0.00 0.00 0.00 4.79
16 17 2.691409 CTAGGAAGGATTGTTGCGGA 57.309 50.000 0.00 0.00 0.00 5.54
17 18 6.161806 CAAACCTAGGAAGGATTGTTGCGG 62.162 50.000 17.98 0.00 45.83 5.69
18 19 3.119849 CAAACCTAGGAAGGATTGTTGCG 60.120 47.826 17.98 0.00 45.83 4.85
19 20 4.440839 CAAACCTAGGAAGGATTGTTGC 57.559 45.455 17.98 0.00 45.83 4.17
28 29 2.087646 GCCAGCTTCAAACCTAGGAAG 58.912 52.381 17.98 9.73 42.62 3.46
29 30 1.423541 TGCCAGCTTCAAACCTAGGAA 59.576 47.619 17.98 0.00 0.00 3.36
30 31 1.064003 TGCCAGCTTCAAACCTAGGA 58.936 50.000 17.98 0.00 0.00 2.94
31 32 2.019984 GATGCCAGCTTCAAACCTAGG 58.980 52.381 7.41 7.41 0.00 3.02
32 33 2.996631 AGATGCCAGCTTCAAACCTAG 58.003 47.619 8.09 0.00 0.00 3.02
33 34 3.370527 GGTAGATGCCAGCTTCAAACCTA 60.371 47.826 16.38 0.00 31.69 3.08
34 35 2.619074 GGTAGATGCCAGCTTCAAACCT 60.619 50.000 16.38 0.00 31.69 3.50
35 36 1.745653 GGTAGATGCCAGCTTCAAACC 59.254 52.381 8.09 10.12 0.00 3.27
36 37 2.716217 AGGTAGATGCCAGCTTCAAAC 58.284 47.619 8.09 5.67 0.00 2.93
37 38 3.347216 GAAGGTAGATGCCAGCTTCAAA 58.653 45.455 8.88 0.00 45.48 2.69
38 39 2.991250 GAAGGTAGATGCCAGCTTCAA 58.009 47.619 8.88 0.00 45.48 2.69
39 40 2.698855 GAAGGTAGATGCCAGCTTCA 57.301 50.000 8.88 0.00 45.48 3.02
40 41 2.484594 GGAGAAGGTAGATGCCAGCTTC 60.485 54.545 6.24 6.24 46.16 3.86
41 42 1.488393 GGAGAAGGTAGATGCCAGCTT 59.512 52.381 0.00 0.00 36.48 3.74
42 43 1.127343 GGAGAAGGTAGATGCCAGCT 58.873 55.000 0.00 0.00 0.00 4.24
43 44 0.833287 TGGAGAAGGTAGATGCCAGC 59.167 55.000 0.00 0.00 0.00 4.85
44 45 1.202463 CGTGGAGAAGGTAGATGCCAG 60.202 57.143 0.00 0.00 0.00 4.85
45 46 0.824109 CGTGGAGAAGGTAGATGCCA 59.176 55.000 0.00 0.00 0.00 4.92
46 47 1.112113 TCGTGGAGAAGGTAGATGCC 58.888 55.000 0.00 0.00 0.00 4.40
47 48 3.126831 CAATCGTGGAGAAGGTAGATGC 58.873 50.000 0.00 0.00 0.00 3.91
48 49 4.142160 TGACAATCGTGGAGAAGGTAGATG 60.142 45.833 0.00 0.00 0.00 2.90
49 50 4.023980 TGACAATCGTGGAGAAGGTAGAT 58.976 43.478 0.00 0.00 0.00 1.98
50 51 3.192844 GTGACAATCGTGGAGAAGGTAGA 59.807 47.826 0.00 0.00 0.00 2.59
51 52 3.193691 AGTGACAATCGTGGAGAAGGTAG 59.806 47.826 0.00 0.00 0.00 3.18
52 53 3.162666 AGTGACAATCGTGGAGAAGGTA 58.837 45.455 0.00 0.00 0.00 3.08
53 54 1.971357 AGTGACAATCGTGGAGAAGGT 59.029 47.619 0.00 0.00 0.00 3.50
54 55 2.751166 AGTGACAATCGTGGAGAAGG 57.249 50.000 0.00 0.00 0.00 3.46
55 56 5.403766 GCATATAGTGACAATCGTGGAGAAG 59.596 44.000 0.00 0.00 0.00 2.85
56 57 5.163457 TGCATATAGTGACAATCGTGGAGAA 60.163 40.000 0.00 0.00 0.00 2.87
57 58 4.340950 TGCATATAGTGACAATCGTGGAGA 59.659 41.667 0.00 0.00 0.00 3.71
58 59 4.620982 TGCATATAGTGACAATCGTGGAG 58.379 43.478 0.00 0.00 0.00 3.86
59 60 4.501400 CCTGCATATAGTGACAATCGTGGA 60.501 45.833 0.00 0.00 0.00 4.02
60 61 3.742882 CCTGCATATAGTGACAATCGTGG 59.257 47.826 0.00 0.00 0.00 4.94
61 62 4.620982 TCCTGCATATAGTGACAATCGTG 58.379 43.478 0.00 0.00 0.00 4.35
62 63 4.937201 TCCTGCATATAGTGACAATCGT 57.063 40.909 0.00 0.00 0.00 3.73
63 64 5.049828 TGTTCCTGCATATAGTGACAATCG 58.950 41.667 0.00 0.00 0.00 3.34
64 65 6.925610 TTGTTCCTGCATATAGTGACAATC 57.074 37.500 0.00 0.00 0.00 2.67
65 66 7.701539 TTTTGTTCCTGCATATAGTGACAAT 57.298 32.000 0.00 0.00 0.00 2.71
66 67 7.701539 ATTTTGTTCCTGCATATAGTGACAA 57.298 32.000 0.00 0.00 0.00 3.18
67 68 7.176515 ACAATTTTGTTCCTGCATATAGTGACA 59.823 33.333 0.00 0.00 38.47 3.58
68 69 7.485913 CACAATTTTGTTCCTGCATATAGTGAC 59.514 37.037 0.00 0.00 39.91 3.67
69 70 7.537715 CACAATTTTGTTCCTGCATATAGTGA 58.462 34.615 0.00 0.00 39.91 3.41
70 71 6.254157 GCACAATTTTGTTCCTGCATATAGTG 59.746 38.462 0.00 0.00 39.91 2.74
71 72 6.153340 AGCACAATTTTGTTCCTGCATATAGT 59.847 34.615 6.44 0.00 39.91 2.12
72 73 6.567050 AGCACAATTTTGTTCCTGCATATAG 58.433 36.000 6.44 0.00 39.91 1.31
73 74 6.152492 TGAGCACAATTTTGTTCCTGCATATA 59.848 34.615 6.06 0.00 39.91 0.86
74 75 5.047164 TGAGCACAATTTTGTTCCTGCATAT 60.047 36.000 6.06 0.00 39.91 1.78
75 76 4.280425 TGAGCACAATTTTGTTCCTGCATA 59.720 37.500 6.06 0.00 39.91 3.14
76 77 3.069872 TGAGCACAATTTTGTTCCTGCAT 59.930 39.130 6.06 0.00 39.91 3.96
77 78 2.429971 TGAGCACAATTTTGTTCCTGCA 59.570 40.909 6.06 0.00 39.91 4.41
78 79 3.096489 TGAGCACAATTTTGTTCCTGC 57.904 42.857 6.06 0.00 39.91 4.85
79 80 5.291178 TGAATGAGCACAATTTTGTTCCTG 58.709 37.500 6.06 0.00 39.91 3.86
80 81 5.069516 ACTGAATGAGCACAATTTTGTTCCT 59.930 36.000 6.06 0.00 39.91 3.36
81 82 5.291971 ACTGAATGAGCACAATTTTGTTCC 58.708 37.500 6.06 0.00 39.91 3.62
82 83 6.088616 GCTACTGAATGAGCACAATTTTGTTC 59.911 38.462 1.83 1.83 39.91 3.18
83 84 5.922544 GCTACTGAATGAGCACAATTTTGTT 59.077 36.000 0.00 0.00 39.91 2.83
84 85 5.464168 GCTACTGAATGAGCACAATTTTGT 58.536 37.500 0.00 0.00 43.36 2.83
85 86 4.556135 CGCTACTGAATGAGCACAATTTTG 59.444 41.667 0.00 0.00 38.69 2.44
86 87 4.455533 TCGCTACTGAATGAGCACAATTTT 59.544 37.500 0.00 0.00 38.69 1.82
87 88 4.002982 TCGCTACTGAATGAGCACAATTT 58.997 39.130 0.00 0.00 38.69 1.82
88 89 3.372206 GTCGCTACTGAATGAGCACAATT 59.628 43.478 0.00 0.00 38.69 2.32
89 90 2.932614 GTCGCTACTGAATGAGCACAAT 59.067 45.455 0.00 0.00 38.69 2.71
90 91 2.337583 GTCGCTACTGAATGAGCACAA 58.662 47.619 0.00 0.00 38.69 3.33
91 92 1.732405 CGTCGCTACTGAATGAGCACA 60.732 52.381 0.00 0.00 38.69 4.57
92 93 0.917259 CGTCGCTACTGAATGAGCAC 59.083 55.000 0.00 0.00 38.69 4.40
93 94 0.526211 ACGTCGCTACTGAATGAGCA 59.474 50.000 0.00 0.00 38.69 4.26
94 95 1.192793 GACGTCGCTACTGAATGAGC 58.807 55.000 0.00 0.00 35.24 4.26
95 96 1.062148 TCGACGTCGCTACTGAATGAG 59.938 52.381 32.19 2.37 39.60 2.90
96 97 1.081094 TCGACGTCGCTACTGAATGA 58.919 50.000 32.19 8.87 39.60 2.57
97 98 1.891178 TTCGACGTCGCTACTGAATG 58.109 50.000 32.19 3.14 39.60 2.67
98 99 2.161012 TCTTTCGACGTCGCTACTGAAT 59.839 45.455 32.19 0.00 39.60 2.57
99 100 1.532437 TCTTTCGACGTCGCTACTGAA 59.468 47.619 32.19 17.52 39.60 3.02
100 101 1.150827 TCTTTCGACGTCGCTACTGA 58.849 50.000 32.19 20.49 39.60 3.41
101 102 1.959747 TTCTTTCGACGTCGCTACTG 58.040 50.000 32.19 18.73 39.60 2.74
102 103 2.419324 AGATTCTTTCGACGTCGCTACT 59.581 45.455 32.19 18.99 39.60 2.57
103 104 2.783333 AGATTCTTTCGACGTCGCTAC 58.217 47.619 32.19 17.28 39.60 3.58
104 105 3.482722 AAGATTCTTTCGACGTCGCTA 57.517 42.857 32.19 19.57 39.60 4.26
105 106 2.349297 AAGATTCTTTCGACGTCGCT 57.651 45.000 32.19 18.51 39.60 4.93
106 107 2.407361 TGAAAGATTCTTTCGACGTCGC 59.593 45.455 32.19 16.50 39.60 5.19
107 108 3.059570 CCTGAAAGATTCTTTCGACGTCG 59.940 47.826 31.30 31.30 36.97 5.12
108 109 4.235360 TCCTGAAAGATTCTTTCGACGTC 58.765 43.478 26.16 5.18 34.07 4.34
109 110 4.252971 TCCTGAAAGATTCTTTCGACGT 57.747 40.909 26.16 0.00 34.07 4.34
110 111 5.591643 TTTCCTGAAAGATTCTTTCGACG 57.408 39.130 26.16 18.83 34.07 5.12
111 112 6.903419 ACATTTCCTGAAAGATTCTTTCGAC 58.097 36.000 26.16 10.74 34.07 4.20
112 113 7.362662 CAACATTTCCTGAAAGATTCTTTCGA 58.637 34.615 26.16 18.42 34.07 3.71
113 114 6.583806 CCAACATTTCCTGAAAGATTCTTTCG 59.416 38.462 26.16 21.19 34.07 3.46
114 115 6.870439 CCCAACATTTCCTGAAAGATTCTTTC 59.130 38.462 25.61 25.61 34.07 2.62
115 116 6.327365 ACCCAACATTTCCTGAAAGATTCTTT 59.673 34.615 11.40 11.40 34.07 2.52
116 117 5.840693 ACCCAACATTTCCTGAAAGATTCTT 59.159 36.000 0.00 0.00 34.07 2.52
117 118 5.397360 ACCCAACATTTCCTGAAAGATTCT 58.603 37.500 0.00 0.00 34.07 2.40
118 119 5.478332 AGACCCAACATTTCCTGAAAGATTC 59.522 40.000 0.00 0.00 34.07 2.52
119 120 5.397360 AGACCCAACATTTCCTGAAAGATT 58.603 37.500 0.00 0.00 34.07 2.40
120 121 5.003096 AGACCCAACATTTCCTGAAAGAT 57.997 39.130 0.00 0.00 34.07 2.40
121 122 4.453480 AGACCCAACATTTCCTGAAAGA 57.547 40.909 0.00 0.00 34.07 2.52
122 123 5.945784 TGATAGACCCAACATTTCCTGAAAG 59.054 40.000 0.00 0.00 33.32 2.62
123 124 5.886609 TGATAGACCCAACATTTCCTGAAA 58.113 37.500 0.00 0.00 34.46 2.69
124 125 5.512942 TGATAGACCCAACATTTCCTGAA 57.487 39.130 0.00 0.00 0.00 3.02
125 126 5.439721 CATGATAGACCCAACATTTCCTGA 58.560 41.667 0.00 0.00 0.00 3.86
126 127 4.581824 CCATGATAGACCCAACATTTCCTG 59.418 45.833 0.00 0.00 0.00 3.86
127 128 4.230502 ACCATGATAGACCCAACATTTCCT 59.769 41.667 0.00 0.00 0.00 3.36
128 129 4.339247 CACCATGATAGACCCAACATTTCC 59.661 45.833 0.00 0.00 0.00 3.13
129 130 4.949856 ACACCATGATAGACCCAACATTTC 59.050 41.667 0.00 0.00 0.00 2.17
130 131 4.934356 ACACCATGATAGACCCAACATTT 58.066 39.130 0.00 0.00 0.00 2.32
131 132 4.591321 ACACCATGATAGACCCAACATT 57.409 40.909 0.00 0.00 0.00 2.71
132 133 4.721776 ACTACACCATGATAGACCCAACAT 59.278 41.667 0.00 0.00 0.00 2.71
133 134 4.101114 ACTACACCATGATAGACCCAACA 58.899 43.478 0.00 0.00 0.00 3.33
134 135 4.443034 GGACTACACCATGATAGACCCAAC 60.443 50.000 0.00 0.00 29.98 3.77
135 136 3.709653 GGACTACACCATGATAGACCCAA 59.290 47.826 0.00 0.00 29.98 4.12
136 137 3.305720 GGACTACACCATGATAGACCCA 58.694 50.000 0.00 0.00 29.98 4.51
137 138 2.296471 CGGACTACACCATGATAGACCC 59.704 54.545 0.00 0.67 31.82 4.46
138 139 2.957006 ACGGACTACACCATGATAGACC 59.043 50.000 0.00 2.48 32.08 3.85
139 140 3.380637 ACACGGACTACACCATGATAGAC 59.619 47.826 0.00 0.00 0.00 2.59
140 141 3.628008 ACACGGACTACACCATGATAGA 58.372 45.455 0.00 0.00 0.00 1.98
141 142 4.337274 TGTACACGGACTACACCATGATAG 59.663 45.833 0.00 0.00 0.00 2.08
142 143 4.271661 TGTACACGGACTACACCATGATA 58.728 43.478 0.00 0.00 0.00 2.15
143 144 3.093814 TGTACACGGACTACACCATGAT 58.906 45.455 0.00 0.00 0.00 2.45
144 145 2.490509 CTGTACACGGACTACACCATGA 59.509 50.000 0.00 0.00 0.00 3.07
145 146 2.490509 TCTGTACACGGACTACACCATG 59.509 50.000 0.00 0.00 0.00 3.66
146 147 2.799017 TCTGTACACGGACTACACCAT 58.201 47.619 0.00 0.00 0.00 3.55
147 148 2.275134 TCTGTACACGGACTACACCA 57.725 50.000 0.00 0.00 0.00 4.17
148 149 2.670509 GCTTCTGTACACGGACTACACC 60.671 54.545 0.00 0.00 0.00 4.16
149 150 2.593257 GCTTCTGTACACGGACTACAC 58.407 52.381 0.00 0.00 0.00 2.90
150 151 1.542915 GGCTTCTGTACACGGACTACA 59.457 52.381 0.00 0.00 0.00 2.74
151 152 1.817447 AGGCTTCTGTACACGGACTAC 59.183 52.381 0.00 0.00 0.00 2.73
152 153 2.211250 AGGCTTCTGTACACGGACTA 57.789 50.000 0.00 0.00 0.00 2.59
153 154 1.000955 CAAGGCTTCTGTACACGGACT 59.999 52.381 0.00 0.00 0.00 3.85
154 155 1.429463 CAAGGCTTCTGTACACGGAC 58.571 55.000 0.00 0.00 0.00 4.79
155 156 0.320421 GCAAGGCTTCTGTACACGGA 60.320 55.000 0.00 0.00 0.00 4.69
156 157 0.602638 TGCAAGGCTTCTGTACACGG 60.603 55.000 0.00 0.00 0.00 4.94
157 158 1.442769 ATGCAAGGCTTCTGTACACG 58.557 50.000 0.00 0.00 0.00 4.49
158 159 3.503748 AGAAATGCAAGGCTTCTGTACAC 59.496 43.478 0.00 0.00 0.00 2.90
159 160 3.503363 CAGAAATGCAAGGCTTCTGTACA 59.497 43.478 16.87 0.00 40.67 2.90
160 161 4.088823 CAGAAATGCAAGGCTTCTGTAC 57.911 45.455 16.87 0.00 40.67 2.90
164 165 1.271656 GCACAGAAATGCAAGGCTTCT 59.728 47.619 0.00 0.00 45.39 2.85
165 166 1.706443 GCACAGAAATGCAAGGCTTC 58.294 50.000 0.00 0.00 45.39 3.86
166 167 3.900446 GCACAGAAATGCAAGGCTT 57.100 47.368 0.00 0.00 45.39 4.35
179 180 1.372997 ACTAGTTCGCGTGGCACAG 60.373 57.895 19.09 11.03 41.80 3.66
201 202 7.047891 ACTGTTGAACATATTACGTGGATCAT 58.952 34.615 0.00 0.00 0.00 2.45
266 267 8.771920 ATATTACGTCATGACTTCTTCACAAA 57.228 30.769 22.95 4.31 36.92 2.83
318 319 9.494271 TGGAGCTAAAATCATAATAGATGACAC 57.506 33.333 0.00 0.00 0.00 3.67
411 1152 6.270927 AGAAGTACTCATACACCATATGCCAT 59.729 38.462 0.00 0.00 33.30 4.40
427 1168 7.721402 ACAATCATCCATCTACAGAAGTACTC 58.279 38.462 0.00 0.00 0.00 2.59
428 1169 7.667575 ACAATCATCCATCTACAGAAGTACT 57.332 36.000 0.00 0.00 0.00 2.73
537 1283 6.283694 ACGACAAGATATATGCACATGACTT 58.716 36.000 0.00 0.00 0.00 3.01
676 1422 4.996758 TGCATATGACCATTCAACGATAGG 59.003 41.667 6.97 0.00 34.61 2.57
775 1982 2.677613 GCAAATTGCCGGACCATTCAAT 60.678 45.455 5.05 0.34 37.42 2.57
786 1993 0.530431 GCCCCTATTGCAAATTGCCG 60.530 55.000 15.98 1.41 44.23 5.69
798 2005 2.994957 ATAGTCTACGTGGCCCCTAT 57.005 50.000 0.00 0.00 0.00 2.57
800 2007 1.063114 AGAATAGTCTACGTGGCCCCT 60.063 52.381 0.00 0.00 29.93 4.79
801 2008 1.068741 CAGAATAGTCTACGTGGCCCC 59.931 57.143 0.00 0.00 30.85 5.80
803 2010 2.034812 CCTCAGAATAGTCTACGTGGCC 59.965 54.545 0.00 0.00 30.85 5.36
804 2011 2.688958 ACCTCAGAATAGTCTACGTGGC 59.311 50.000 0.00 0.00 30.85 5.01
805 2012 3.066900 CCACCTCAGAATAGTCTACGTGG 59.933 52.174 14.40 14.40 37.24 4.94
806 2013 3.695060 ACCACCTCAGAATAGTCTACGTG 59.305 47.826 0.00 0.00 30.85 4.49
807 2014 3.965694 ACCACCTCAGAATAGTCTACGT 58.034 45.455 0.00 0.00 30.85 3.57
808 2015 5.048643 CCATACCACCTCAGAATAGTCTACG 60.049 48.000 0.00 0.00 30.85 3.51
810 2017 6.027025 ACCATACCACCTCAGAATAGTCTA 57.973 41.667 0.00 0.00 30.85 2.59
812 2019 4.896482 AGACCATACCACCTCAGAATAGTC 59.104 45.833 0.00 0.00 0.00 2.59
813 2020 4.651503 CAGACCATACCACCTCAGAATAGT 59.348 45.833 0.00 0.00 0.00 2.12
814 2021 4.039730 CCAGACCATACCACCTCAGAATAG 59.960 50.000 0.00 0.00 0.00 1.73
816 2023 2.774234 CCAGACCATACCACCTCAGAAT 59.226 50.000 0.00 0.00 0.00 2.40
818 2025 1.866015 CCAGACCATACCACCTCAGA 58.134 55.000 0.00 0.00 0.00 3.27
819 2026 0.179000 GCCAGACCATACCACCTCAG 59.821 60.000 0.00 0.00 0.00 3.35
820 2027 0.546507 TGCCAGACCATACCACCTCA 60.547 55.000 0.00 0.00 0.00 3.86
821 2028 0.618458 TTGCCAGACCATACCACCTC 59.382 55.000 0.00 0.00 0.00 3.85
822 2029 1.298953 ATTGCCAGACCATACCACCT 58.701 50.000 0.00 0.00 0.00 4.00
823 2030 2.143876 AATTGCCAGACCATACCACC 57.856 50.000 0.00 0.00 0.00 4.61
824 2031 2.417243 GCAAATTGCCAGACCATACCAC 60.417 50.000 6.72 0.00 37.42 4.16
825 2032 1.824230 GCAAATTGCCAGACCATACCA 59.176 47.619 6.72 0.00 37.42 3.25
826 2033 1.824230 TGCAAATTGCCAGACCATACC 59.176 47.619 15.98 0.00 44.23 2.73
827 2034 3.591196 TTGCAAATTGCCAGACCATAC 57.409 42.857 15.98 0.00 44.23 2.39
828 2035 4.202000 CGTATTGCAAATTGCCAGACCATA 60.202 41.667 15.98 0.13 44.23 2.74
856 2067 3.181489 ACGGTATAGCTCAGAAACTTCCG 60.181 47.826 0.00 0.00 40.00 4.30
861 2072 5.006746 CCATTCAACGGTATAGCTCAGAAAC 59.993 44.000 0.00 0.00 0.00 2.78
933 2197 9.574516 TGTAGAGTGATAAGCTCTATACATGAA 57.425 33.333 0.00 0.00 44.38 2.57
1023 2287 3.965258 TGGGTGGCTTCGGCATGT 61.965 61.111 0.00 0.00 43.96 3.21
1042 2306 6.980051 ATTATTTTCAACGACCACTAGGAC 57.020 37.500 0.00 0.00 38.69 3.85
1691 3012 5.066505 GCATGGAATAAACCTTGTCGAAGAT 59.933 40.000 0.00 0.00 40.67 2.40
1753 3084 2.607442 TACTGCTGCTCCAGGCCA 60.607 61.111 5.01 0.00 40.92 5.36
1784 3115 2.751688 GACGTACCCTTGGCCCAA 59.248 61.111 0.00 0.00 0.00 4.12
1975 3309 2.364970 CAACCCAAGAGCAATTTGGTCA 59.635 45.455 25.63 0.00 46.52 4.02
2093 3427 1.369321 GAGCCCAGGATCGGATGAC 59.631 63.158 0.00 0.00 0.00 3.06
2099 3433 1.026718 GTTTGTGGAGCCCAGGATCG 61.027 60.000 0.00 0.00 32.34 3.69
2146 3480 2.476051 CACTGCGTCACGAATGCC 59.524 61.111 0.00 0.00 39.30 4.40
2255 3589 2.033065 CGATTCCTAGTACGTCCGTGAG 60.033 54.545 1.98 0.00 0.00 3.51
2419 3753 1.480954 GACTTTGAGGCGAGGTCCATA 59.519 52.381 0.00 0.00 0.00 2.74
2607 3964 2.754946 AACATACGTCGTGGATTGGT 57.245 45.000 8.47 0.00 0.00 3.67
2651 4015 5.924475 AACAGACGAGTTCAAAATACCAG 57.076 39.130 0.00 0.00 0.00 4.00
2652 4016 9.309516 GATATAACAGACGAGTTCAAAATACCA 57.690 33.333 0.00 0.00 33.07 3.25
2653 4017 9.530633 AGATATAACAGACGAGTTCAAAATACC 57.469 33.333 0.00 0.00 33.07 2.73
2839 4208 6.763303 AATTTTACAAAGTTTGACATCGGC 57.237 33.333 22.23 0.00 0.00 5.54
2933 4302 9.121517 GCCAAATCAATTTCATTAGATGTATCG 57.878 33.333 0.00 0.00 0.00 2.92
3028 4400 5.105064 CCCTCCATTCTTTTTACTCCGTAGA 60.105 44.000 0.00 0.00 0.00 2.59
3029 4401 5.105064 TCCCTCCATTCTTTTTACTCCGTAG 60.105 44.000 0.00 0.00 0.00 3.51
3031 4403 3.585732 TCCCTCCATTCTTTTTACTCCGT 59.414 43.478 0.00 0.00 0.00 4.69
3042 4414 6.388100 TCTCATTGAAATACTCCCTCCATTCT 59.612 38.462 0.00 0.00 0.00 2.40
3160 4534 3.006859 TGGACGGATGTCTAATATGCCAG 59.993 47.826 0.00 0.00 44.83 4.85
3202 4576 2.990479 GTGTGGGCTACCTCCTGG 59.010 66.667 0.00 0.00 37.76 4.45
3376 4750 3.312421 CGGATGGCAACTAAATCGTCATT 59.688 43.478 0.00 0.00 37.61 2.57
3424 4798 2.968655 GCTTTTACAACTACGTTTGCCG 59.031 45.455 0.00 0.00 44.03 5.69
3506 4881 4.393680 GGCAACTATGGTTTGATTACACGA 59.606 41.667 0.00 0.00 32.73 4.35
3640 5015 4.818546 GGCAACTAGATAAGCACACATGAT 59.181 41.667 0.00 0.00 0.00 2.45
3650 5025 3.425525 CGCATACGTGGCAACTAGATAAG 59.574 47.826 13.38 0.00 37.61 1.73
3657 5033 1.963855 TTGCGCATACGTGGCAACT 60.964 52.632 12.75 0.00 42.83 3.16


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

AutoCloner maintained by Alex Coulton.