Multiple sequence alignment - TraesCS1B01G274300

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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 TraesCS1B01G274300 chr1B 100.000 3488 0 0 1 3488 481543400 481539913 0.000000e+00 6442.0
1 TraesCS1B01G274300 chr1D 93.829 3014 117 29 489 3488 359666612 359663654 0.000000e+00 4471.0
2 TraesCS1B01G274300 chr1D 85.621 153 9 2 311 463 359666731 359666592 7.800000e-32 148.0
3 TraesCS1B01G274300 chr1A 90.218 1789 84 35 142 1885 459189311 459187569 0.000000e+00 2250.0
4 TraesCS1B01G274300 chr1A 90.241 953 51 12 1963 2901 459187536 459186612 0.000000e+00 1206.0
5 TraesCS1B01G274300 chr1A 87.339 466 45 5 3004 3464 459183836 459183380 3.990000e-144 521.0
6 TraesCS1B01G274300 chr3D 84.843 541 56 15 1045 1575 515776438 515776962 3.990000e-144 521.0
7 TraesCS1B01G274300 chr3D 81.882 287 31 12 2209 2486 515777675 515777949 4.530000e-54 222.0
8 TraesCS1B01G274300 chr3A 84.843 541 56 18 1045 1580 650056186 650056705 3.990000e-144 521.0
9 TraesCS1B01G274300 chr3A 98.601 143 2 0 1 143 459586508 459586366 1.610000e-63 254.0
10 TraesCS1B01G274300 chr3A 81.229 293 31 14 2204 2486 650057432 650057710 7.580000e-52 215.0
11 TraesCS1B01G274300 chr3B 83.978 543 67 17 1046 1579 678548296 678548827 1.450000e-138 503.0
12 TraesCS1B01G274300 chr3B 98.601 143 2 0 1 143 468949828 468949970 1.610000e-63 254.0
13 TraesCS1B01G274300 chr3B 97.945 146 3 0 1 146 609780879 609781024 1.610000e-63 254.0
14 TraesCS1B01G274300 chr3B 80.836 287 34 12 2209 2486 678549540 678549814 4.560000e-49 206.0
15 TraesCS1B01G274300 chr4A 91.915 235 17 2 1318 1551 521919706 521919473 9.330000e-86 327.0
16 TraesCS1B01G274300 chr4A 96.689 151 4 1 1 151 166039561 166039710 2.080000e-62 250.0
17 TraesCS1B01G274300 chr4D 91.064 235 19 2 1318 1551 69679958 69679725 2.020000e-82 316.0
18 TraesCS1B01G274300 chr4B 90.638 235 20 2 1318 1551 103056204 103055971 9.400000e-81 311.0
19 TraesCS1B01G274300 chr4B 97.931 145 3 0 1 145 509372478 509372334 5.780000e-63 252.0
20 TraesCS1B01G274300 chr5B 96.711 152 3 2 1 150 515303402 515303553 5.780000e-63 252.0
21 TraesCS1B01G274300 chr5B 97.931 145 3 0 1 145 649009534 649009390 5.780000e-63 252.0
22 TraesCS1B01G274300 chr7B 95.484 155 6 1 1 154 613419208 613419054 2.690000e-61 246.0
23 TraesCS1B01G274300 chr6A 93.865 163 7 3 1 161 475869153 475869314 3.480000e-60 243.0
24 TraesCS1B01G274300 chr6A 80.567 247 44 3 1302 1545 30191055 30190810 1.650000e-43 187.0
25 TraesCS1B01G274300 chr5D 80.851 141 25 2 1058 1197 519277283 519277422 3.680000e-20 110.0
26 TraesCS1B01G274300 chr2B 97.619 42 1 0 2052 2093 85176826 85176785 4.830000e-09 73.1


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 TraesCS1B01G274300 chr1B 481539913 481543400 3487 True 6442.000000 6442 100.0000 1 3488 1 chr1B.!!$R1 3487
1 TraesCS1B01G274300 chr1D 359663654 359666731 3077 True 2309.500000 4471 89.7250 311 3488 2 chr1D.!!$R1 3177
2 TraesCS1B01G274300 chr1A 459183380 459189311 5931 True 1325.666667 2250 89.2660 142 3464 3 chr1A.!!$R1 3322
3 TraesCS1B01G274300 chr3D 515776438 515777949 1511 False 371.500000 521 83.3625 1045 2486 2 chr3D.!!$F1 1441
4 TraesCS1B01G274300 chr3A 650056186 650057710 1524 False 368.000000 521 83.0360 1045 2486 2 chr3A.!!$F1 1441
5 TraesCS1B01G274300 chr3B 678548296 678549814 1518 False 354.500000 503 82.4070 1046 2486 2 chr3B.!!$F3 1440

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
78 79 0.172578 TGAGAATACCGTGCGTGAGG 59.827 55.0 0.00 0.00 0.00 3.86 F
1583 1637 0.249489 GCCTCAGGGTACGCACTATG 60.249 60.0 12.95 1.68 34.45 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2531 0.518636 CCAGTCATCCAACTGCAACG 59.481 55.0 0.00 0.0 44.34 4.10 R
2924 6125 0.034337 GGCAACGTCCTGGACTACAA 59.966 55.0 23.49 0.0 0.00 2.41 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
23 24 6.712241 CTATCATATACGTGAGCCAAAAGG 57.288 41.667 0.00 0.00 0.00 3.11
24 25 3.202906 TCATATACGTGAGCCAAAAGGC 58.797 45.455 0.00 0.00 0.00 4.35
25 26 1.647346 TATACGTGAGCCAAAAGGCG 58.353 50.000 0.00 0.00 40.23 5.52
26 27 1.644786 ATACGTGAGCCAAAAGGCGC 61.645 55.000 0.00 0.00 40.23 6.53
27 28 2.997952 TACGTGAGCCAAAAGGCGCA 62.998 55.000 10.83 8.86 41.90 6.09
28 29 2.727544 GTGAGCCAAAAGGCGCAA 59.272 55.556 14.31 0.00 45.17 4.85
29 30 1.067250 GTGAGCCAAAAGGCGCAAA 59.933 52.632 14.31 0.00 45.17 3.68
30 31 1.067250 TGAGCCAAAAGGCGCAAAC 59.933 52.632 10.83 0.00 41.28 2.93
31 32 2.016165 GAGCCAAAAGGCGCAAACG 61.016 57.895 10.83 0.00 44.07 3.60
32 33 3.035503 GCCAAAAGGCGCAAACGG 61.036 61.111 10.83 3.45 40.57 4.44
33 34 2.415426 CCAAAAGGCGCAAACGGT 59.585 55.556 10.83 0.00 40.57 4.83
34 35 1.660264 CCAAAAGGCGCAAACGGTC 60.660 57.895 10.83 0.00 40.57 4.79
35 36 1.660264 CAAAAGGCGCAAACGGTCC 60.660 57.895 10.83 0.00 40.57 4.46
36 37 2.852180 AAAAGGCGCAAACGGTCCC 61.852 57.895 10.83 0.00 40.57 4.46
37 38 4.572571 AAGGCGCAAACGGTCCCA 62.573 61.111 10.83 0.00 40.57 4.37
42 43 4.966787 GCAAACGGTCCCAGGCCA 62.967 66.667 5.01 0.00 0.00 5.36
43 44 2.672996 CAAACGGTCCCAGGCCAG 60.673 66.667 5.01 0.00 0.00 4.85
44 45 3.966543 AAACGGTCCCAGGCCAGG 61.967 66.667 7.34 7.34 0.00 4.45
46 47 3.857521 AACGGTCCCAGGCCAGGTA 62.858 63.158 13.97 0.00 0.00 3.08
47 48 3.006728 CGGTCCCAGGCCAGGTAA 61.007 66.667 13.97 0.00 0.00 2.85
48 49 2.998949 GGTCCCAGGCCAGGTAAG 59.001 66.667 13.97 0.00 0.00 2.34
49 50 2.680370 GGTCCCAGGCCAGGTAAGG 61.680 68.421 13.97 0.00 0.00 2.69
50 51 1.923909 GTCCCAGGCCAGGTAAGGT 60.924 63.158 13.97 0.00 0.00 3.50
51 52 1.923395 TCCCAGGCCAGGTAAGGTG 60.923 63.158 13.97 0.00 0.00 4.00
52 53 2.677228 CCAGGCCAGGTAAGGTGG 59.323 66.667 5.01 0.00 38.21 4.61
57 58 2.355115 CCAGGTAAGGTGGCACCC 59.645 66.667 32.30 17.45 39.75 4.61
58 59 2.046314 CAGGTAAGGTGGCACCCG 60.046 66.667 32.30 10.84 39.75 5.28
59 60 2.528378 AGGTAAGGTGGCACCCGT 60.528 61.111 32.30 22.68 39.75 5.28
60 61 2.359478 GGTAAGGTGGCACCCGTG 60.359 66.667 32.30 0.00 39.75 4.94
61 62 2.745037 GTAAGGTGGCACCCGTGA 59.255 61.111 32.30 12.91 39.75 4.35
62 63 1.375523 GTAAGGTGGCACCCGTGAG 60.376 63.158 32.30 0.00 39.75 3.51
63 64 1.534476 TAAGGTGGCACCCGTGAGA 60.534 57.895 32.30 9.21 39.75 3.27
64 65 1.122632 TAAGGTGGCACCCGTGAGAA 61.123 55.000 32.30 7.96 39.75 2.87
65 66 1.779061 AAGGTGGCACCCGTGAGAAT 61.779 55.000 32.30 9.13 39.75 2.40
66 67 0.907704 AGGTGGCACCCGTGAGAATA 60.908 55.000 32.30 0.00 39.75 1.75
67 68 0.743345 GGTGGCACCCGTGAGAATAC 60.743 60.000 26.51 0.00 30.04 1.89
68 69 0.743345 GTGGCACCCGTGAGAATACC 60.743 60.000 6.29 0.00 0.00 2.73
69 70 1.520787 GGCACCCGTGAGAATACCG 60.521 63.158 0.00 0.00 0.00 4.02
70 71 1.217244 GCACCCGTGAGAATACCGT 59.783 57.895 0.00 0.00 0.00 4.83
71 72 1.082117 GCACCCGTGAGAATACCGTG 61.082 60.000 0.00 0.00 0.00 4.94
72 73 1.082117 CACCCGTGAGAATACCGTGC 61.082 60.000 0.00 0.00 0.00 5.34
73 74 1.876714 CCCGTGAGAATACCGTGCG 60.877 63.158 0.00 0.00 0.00 5.34
74 75 1.153901 CCGTGAGAATACCGTGCGT 60.154 57.895 0.00 0.00 0.00 5.24
75 76 1.410737 CCGTGAGAATACCGTGCGTG 61.411 60.000 0.00 0.00 0.00 5.34
76 77 0.455464 CGTGAGAATACCGTGCGTGA 60.455 55.000 0.00 0.00 0.00 4.35
77 78 1.269166 GTGAGAATACCGTGCGTGAG 58.731 55.000 0.00 0.00 0.00 3.51
78 79 0.172578 TGAGAATACCGTGCGTGAGG 59.827 55.000 0.00 0.00 0.00 3.86
79 80 1.146358 GAGAATACCGTGCGTGAGGC 61.146 60.000 0.00 0.00 43.96 4.70
80 81 2.125269 AATACCGTGCGTGAGGCC 60.125 61.111 0.00 0.00 42.61 5.19
81 82 4.508128 ATACCGTGCGTGAGGCCG 62.508 66.667 0.00 0.00 42.61 6.13
89 90 2.664851 CGTGAGGCCGCAAAGTGA 60.665 61.111 12.05 0.00 0.00 3.41
90 91 2.034879 CGTGAGGCCGCAAAGTGAT 61.035 57.895 12.05 0.00 0.00 3.06
91 92 0.739462 CGTGAGGCCGCAAAGTGATA 60.739 55.000 12.05 0.00 0.00 2.15
92 93 1.668419 GTGAGGCCGCAAAGTGATAT 58.332 50.000 12.05 0.00 0.00 1.63
93 94 1.331756 GTGAGGCCGCAAAGTGATATG 59.668 52.381 12.05 0.00 0.00 1.78
94 95 1.209261 TGAGGCCGCAAAGTGATATGA 59.791 47.619 6.75 0.00 0.00 2.15
95 96 2.158769 TGAGGCCGCAAAGTGATATGAT 60.159 45.455 6.75 0.00 0.00 2.45
96 97 2.224606 AGGCCGCAAAGTGATATGATG 58.775 47.619 0.00 0.00 0.00 3.07
97 98 1.949525 GGCCGCAAAGTGATATGATGT 59.050 47.619 0.00 0.00 0.00 3.06
98 99 2.287188 GGCCGCAAAGTGATATGATGTG 60.287 50.000 0.00 0.00 0.00 3.21
99 100 2.355756 GCCGCAAAGTGATATGATGTGT 59.644 45.455 0.00 0.00 0.00 3.72
100 101 3.181497 GCCGCAAAGTGATATGATGTGTT 60.181 43.478 0.00 0.00 0.00 3.32
101 102 4.035091 GCCGCAAAGTGATATGATGTGTTA 59.965 41.667 0.00 0.00 0.00 2.41
102 103 5.501715 CCGCAAAGTGATATGATGTGTTAC 58.498 41.667 0.00 0.00 0.00 2.50
103 104 5.064579 CCGCAAAGTGATATGATGTGTTACA 59.935 40.000 0.00 0.00 0.00 2.41
104 105 6.238456 CCGCAAAGTGATATGATGTGTTACAT 60.238 38.462 0.00 0.00 42.43 2.29
105 106 6.630045 CGCAAAGTGATATGATGTGTTACATG 59.370 38.462 0.00 0.00 39.27 3.21
106 107 6.415867 GCAAAGTGATATGATGTGTTACATGC 59.584 38.462 0.00 0.00 39.27 4.06
107 108 7.680350 GCAAAGTGATATGATGTGTTACATGCT 60.680 37.037 0.00 0.00 39.27 3.79
108 109 8.829612 CAAAGTGATATGATGTGTTACATGCTA 58.170 33.333 0.00 0.00 39.27 3.49
109 110 8.599055 AAGTGATATGATGTGTTACATGCTAG 57.401 34.615 0.00 0.00 39.27 3.42
110 111 7.955918 AGTGATATGATGTGTTACATGCTAGA 58.044 34.615 0.00 0.00 39.27 2.43
111 112 8.591940 AGTGATATGATGTGTTACATGCTAGAT 58.408 33.333 0.00 0.00 39.27 1.98
112 113 8.867935 GTGATATGATGTGTTACATGCTAGATC 58.132 37.037 0.00 0.00 39.27 2.75
113 114 7.756722 TGATATGATGTGTTACATGCTAGATCG 59.243 37.037 0.00 0.00 39.27 3.69
114 115 4.620982 TGATGTGTTACATGCTAGATCGG 58.379 43.478 0.00 0.00 39.27 4.18
115 116 4.099419 TGATGTGTTACATGCTAGATCGGT 59.901 41.667 0.00 0.00 39.27 4.69
116 117 3.780902 TGTGTTACATGCTAGATCGGTG 58.219 45.455 0.00 0.00 0.00 4.94
117 118 3.194755 TGTGTTACATGCTAGATCGGTGT 59.805 43.478 0.00 0.00 0.00 4.16
118 119 3.551890 GTGTTACATGCTAGATCGGTGTG 59.448 47.826 0.00 0.00 0.00 3.82
119 120 3.445805 TGTTACATGCTAGATCGGTGTGA 59.554 43.478 0.00 0.00 0.00 3.58
120 121 2.586258 ACATGCTAGATCGGTGTGAC 57.414 50.000 0.00 0.00 0.00 3.67
121 122 2.103373 ACATGCTAGATCGGTGTGACT 58.897 47.619 0.00 0.00 0.00 3.41
122 123 2.099921 ACATGCTAGATCGGTGTGACTC 59.900 50.000 0.00 0.00 0.00 3.36
123 124 1.834188 TGCTAGATCGGTGTGACTCA 58.166 50.000 0.00 0.00 0.00 3.41
124 125 1.745653 TGCTAGATCGGTGTGACTCAG 59.254 52.381 0.00 0.00 0.00 3.35
125 126 1.066303 GCTAGATCGGTGTGACTCAGG 59.934 57.143 0.00 0.00 0.00 3.86
126 127 2.644676 CTAGATCGGTGTGACTCAGGA 58.355 52.381 0.00 0.00 0.00 3.86
127 128 2.151502 AGATCGGTGTGACTCAGGAT 57.848 50.000 0.00 0.00 0.00 3.24
128 129 2.028130 AGATCGGTGTGACTCAGGATC 58.972 52.381 8.80 8.80 37.41 3.36
129 130 0.741326 ATCGGTGTGACTCAGGATCG 59.259 55.000 0.00 0.00 0.00 3.69
130 131 1.139734 CGGTGTGACTCAGGATCGG 59.860 63.158 0.00 0.00 0.00 4.18
131 132 1.517832 GGTGTGACTCAGGATCGGG 59.482 63.158 0.00 0.00 0.00 5.14
132 133 1.517832 GTGTGACTCAGGATCGGGG 59.482 63.158 0.00 0.00 0.00 5.73
133 134 1.078528 TGTGACTCAGGATCGGGGT 59.921 57.895 0.00 0.00 0.00 4.95
134 135 0.970937 TGTGACTCAGGATCGGGGTC 60.971 60.000 8.64 8.64 0.00 4.46
135 136 1.381327 TGACTCAGGATCGGGGTCC 60.381 63.158 12.05 0.00 38.62 4.46
140 141 2.777853 AGGATCGGGGTCCTGACA 59.222 61.111 0.00 0.00 46.76 3.58
158 159 3.244770 TGACAAATAGGGCCGAGTCTTTT 60.245 43.478 14.49 0.00 0.00 2.27
210 211 1.392589 AGAAGTGTTGTGGTGGCAAG 58.607 50.000 0.00 0.00 0.00 4.01
271 272 2.082231 CACTCTTTGCTCCATGGAGTG 58.918 52.381 36.32 24.09 44.66 3.51
370 371 6.197096 CGACCTATACAACCGTATACAACAAC 59.803 42.308 3.32 0.00 39.17 3.32
463 469 2.185004 CCATGGGGATCCGTACATTC 57.815 55.000 2.85 0.00 35.59 2.67
464 470 1.699634 CCATGGGGATCCGTACATTCT 59.300 52.381 2.85 0.00 35.59 2.40
465 471 2.550855 CCATGGGGATCCGTACATTCTG 60.551 54.545 2.85 0.88 35.59 3.02
466 472 2.168458 TGGGGATCCGTACATTCTGA 57.832 50.000 5.45 0.00 35.24 3.27
468 474 1.270358 GGGGATCCGTACATTCTGAGC 60.270 57.143 5.45 0.00 0.00 4.26
471 477 3.126831 GGATCCGTACATTCTGAGCTTG 58.873 50.000 0.00 0.00 0.00 4.01
472 478 2.672961 TCCGTACATTCTGAGCTTGG 57.327 50.000 0.00 0.00 0.00 3.61
474 480 2.094182 TCCGTACATTCTGAGCTTGGTC 60.094 50.000 0.00 0.00 0.00 4.02
475 481 2.271800 CGTACATTCTGAGCTTGGTCC 58.728 52.381 0.00 0.00 0.00 4.46
476 482 2.271800 GTACATTCTGAGCTTGGTCCG 58.728 52.381 0.00 0.00 0.00 4.79
477 483 0.674895 ACATTCTGAGCTTGGTCCGC 60.675 55.000 0.00 0.00 0.00 5.54
478 484 1.078143 ATTCTGAGCTTGGTCCGCC 60.078 57.895 0.00 0.00 0.00 6.13
479 485 2.543067 ATTCTGAGCTTGGTCCGCCC 62.543 60.000 0.00 0.00 0.00 6.13
609 615 3.041940 CGGAACACCTGTCCACGC 61.042 66.667 0.00 0.00 0.00 5.34
899 906 1.158484 TCGATCGTCCGGTCTAGCTG 61.158 60.000 15.94 0.00 0.00 4.24
912 942 3.799420 GGTCTAGCTGTTTCTGCTTATCG 59.201 47.826 0.00 0.00 39.30 2.92
913 943 4.440250 GGTCTAGCTGTTTCTGCTTATCGA 60.440 45.833 0.00 0.00 39.30 3.59
923 953 7.047891 TGTTTCTGCTTATCGATATCTGGTTT 58.952 34.615 5.84 0.00 0.00 3.27
1080 1115 1.227383 GCCGGGGTTCAGATTCCAT 59.773 57.895 2.18 0.00 0.00 3.41
1263 1303 1.290203 CTCGCGTGGCAGTATGATTT 58.710 50.000 5.77 0.00 39.69 2.17
1264 1304 2.469826 CTCGCGTGGCAGTATGATTTA 58.530 47.619 5.77 0.00 39.69 1.40
1265 1305 2.198406 TCGCGTGGCAGTATGATTTAC 58.802 47.619 5.77 0.00 39.69 2.01
1307 1361 3.869272 CGTGCAGGAATGGCGCTC 61.869 66.667 7.64 0.00 39.53 5.03
1580 1634 2.283966 AGCCTCAGGGTACGCACT 60.284 61.111 12.95 0.00 34.45 4.40
1583 1637 0.249489 GCCTCAGGGTACGCACTATG 60.249 60.000 12.95 1.68 34.45 2.23
1586 1640 0.744874 TCAGGGTACGCACTATGCTC 59.255 55.000 12.95 0.00 42.25 4.26
1607 1665 3.007920 CCTGCCCTCTGACCTGCT 61.008 66.667 0.00 0.00 0.00 4.24
1955 2029 7.837202 ATGGATTAAAATTCGTTCGTGACTA 57.163 32.000 0.00 0.00 0.00 2.59
2021 2504 7.429374 AGAGGTATGATTTCTGTTCTGATCA 57.571 36.000 0.00 0.00 33.50 2.92
2022 2505 8.032045 AGAGGTATGATTTCTGTTCTGATCAT 57.968 34.615 0.00 0.00 40.98 2.45
2023 2506 7.932491 AGAGGTATGATTTCTGTTCTGATCATG 59.068 37.037 0.00 0.00 39.05 3.07
2024 2507 7.571919 AGGTATGATTTCTGTTCTGATCATGT 58.428 34.615 0.00 0.00 39.05 3.21
2048 2531 3.241678 CGTCGATCGATCTTTTTGTGGTC 60.242 47.826 22.50 2.21 42.86 4.02
2073 2556 0.773644 AGTTGGATGACTGGGTGCTT 59.226 50.000 0.00 0.00 0.00 3.91
2195 2693 3.741476 GAAACTGGCCCTGCTGCG 61.741 66.667 0.00 0.00 0.00 5.18
2521 3076 1.281656 GCTGTACGTGTGGTTTGGC 59.718 57.895 0.00 0.00 0.00 4.52
2522 3077 1.567537 CTGTACGTGTGGTTTGGCG 59.432 57.895 0.00 0.00 0.00 5.69
2523 3078 2.250190 GTACGTGTGGTTTGGCGC 59.750 61.111 0.00 0.00 0.00 6.53
2524 3079 2.109387 TACGTGTGGTTTGGCGCT 59.891 55.556 7.64 0.00 0.00 5.92
2527 3082 3.977244 GTGTGGTTTGGCGCTGGG 61.977 66.667 7.64 0.00 0.00 4.45
2528 3083 4.196778 TGTGGTTTGGCGCTGGGA 62.197 61.111 7.64 0.00 0.00 4.37
2531 3086 2.361104 GGTTTGGCGCTGGGATGA 60.361 61.111 7.64 0.00 0.00 2.92
2545 3105 1.621814 GGGATGAAATCGATCGGGGTA 59.378 52.381 16.41 0.00 46.86 3.69
2546 3106 2.353803 GGGATGAAATCGATCGGGGTAG 60.354 54.545 16.41 0.00 46.86 3.18
2590 3150 3.790089 TCTATCGGCAGGAGATACTCA 57.210 47.619 0.00 0.00 31.08 3.41
2614 3174 3.070018 GCCGTTGGATGGAAGATATCAG 58.930 50.000 5.32 0.00 0.00 2.90
2630 3190 3.601443 ATCAGTAGTGCACAAGGAGTC 57.399 47.619 21.04 1.02 0.00 3.36
2746 3315 8.412456 TGTGTATATGCGATTGATTTGGAAATT 58.588 29.630 0.00 0.00 0.00 1.82
2749 3318 3.859443 TGCGATTGATTTGGAAATTGGG 58.141 40.909 0.00 0.00 0.00 4.12
2869 3438 0.958382 CCCCGTGCGATCTTTTTCCA 60.958 55.000 0.00 0.00 0.00 3.53
2881 3450 5.788531 CGATCTTTTTCCACGAATACACAAC 59.211 40.000 0.00 0.00 0.00 3.32
2886 3455 5.605564 TTTCCACGAATACACAACAGATG 57.394 39.130 0.00 0.00 0.00 2.90
2949 6150 2.432628 CAGGACGTTGCCTCGGTC 60.433 66.667 0.00 0.00 35.66 4.79
2950 6151 2.915659 AGGACGTTGCCTCGGTCA 60.916 61.111 0.00 0.00 30.76 4.02
2963 6164 2.663196 GGTCAGCGCCCACTAACT 59.337 61.111 2.29 0.00 0.00 2.24
2976 6177 2.029290 CCACTAACTAGTCTTGCCACGT 60.029 50.000 0.00 0.00 33.46 4.49
2977 6178 2.987149 CACTAACTAGTCTTGCCACGTG 59.013 50.000 9.08 9.08 33.46 4.49
2985 6242 0.319555 TCTTGCCACGTGTAGTCTGC 60.320 55.000 15.65 9.99 0.00 4.26
3004 6261 2.523168 TCACACGAGGGGCAGACA 60.523 61.111 0.00 0.00 0.00 3.41
3005 6262 2.357517 CACACGAGGGGCAGACAC 60.358 66.667 0.00 0.00 0.00 3.67
3006 6263 2.842462 ACACGAGGGGCAGACACA 60.842 61.111 0.00 0.00 0.00 3.72
3007 6264 2.357517 CACGAGGGGCAGACACAC 60.358 66.667 0.00 0.00 0.00 3.82
3008 6265 3.991051 ACGAGGGGCAGACACACG 61.991 66.667 0.00 0.00 0.00 4.49
3009 6266 3.680786 CGAGGGGCAGACACACGA 61.681 66.667 0.00 0.00 0.00 4.35
3010 6267 2.262915 GAGGGGCAGACACACGAG 59.737 66.667 0.00 0.00 0.00 4.18
3011 6268 3.302347 GAGGGGCAGACACACGAGG 62.302 68.421 0.00 0.00 0.00 4.63
3012 6269 4.394712 GGGGCAGACACACGAGGG 62.395 72.222 0.00 0.00 0.00 4.30
3013 6270 4.394712 GGGCAGACACACGAGGGG 62.395 72.222 0.00 0.00 0.00 4.79
3015 6272 4.314440 GCAGACACACGAGGGGCA 62.314 66.667 0.00 0.00 0.00 5.36
3016 6273 2.047844 CAGACACACGAGGGGCAG 60.048 66.667 0.00 0.00 0.00 4.85
3017 6274 2.203640 AGACACACGAGGGGCAGA 60.204 61.111 0.00 0.00 0.00 4.26
3018 6275 2.048127 GACACACGAGGGGCAGAC 60.048 66.667 0.00 0.00 0.00 3.51
3019 6276 3.916392 GACACACGAGGGGCAGACG 62.916 68.421 0.00 0.00 0.00 4.18
3020 6277 3.680786 CACACGAGGGGCAGACGA 61.681 66.667 0.00 0.00 0.00 4.20
3021 6278 3.681835 ACACGAGGGGCAGACGAC 61.682 66.667 0.00 0.00 0.00 4.34
3022 6279 3.680786 CACGAGGGGCAGACGACA 61.681 66.667 0.00 0.00 0.00 4.35
3023 6280 2.915659 ACGAGGGGCAGACGACAA 60.916 61.111 0.00 0.00 0.00 3.18
3024 6281 2.432628 CGAGGGGCAGACGACAAC 60.433 66.667 0.00 0.00 0.00 3.32
3043 6300 2.044555 AGGTGAAGACGCGGATCGA 61.045 57.895 12.47 0.00 41.67 3.59
3049 6306 2.098607 TGAAGACGCGGATCGAATAGTT 59.901 45.455 12.47 0.00 41.67 2.24
3052 6309 2.098607 AGACGCGGATCGAATAGTTTGA 59.901 45.455 12.47 0.00 41.67 2.69
3058 6315 4.421058 CGGATCGAATAGTTTGAGTCACA 58.579 43.478 0.00 0.00 0.00 3.58
3059 6316 4.500837 CGGATCGAATAGTTTGAGTCACAG 59.499 45.833 0.00 0.00 0.00 3.66
3062 6319 5.462530 TCGAATAGTTTGAGTCACAGGAA 57.537 39.130 0.00 0.00 0.00 3.36
3065 6322 2.262423 AGTTTGAGTCACAGGAAGGC 57.738 50.000 0.00 0.00 0.00 4.35
3159 6416 0.042131 TGGGGAGGACCTTACGATGT 59.958 55.000 0.00 0.00 40.03 3.06
3213 6470 4.030216 ACCAATCCAGAAAACCAACAGTT 58.970 39.130 0.00 0.00 41.81 3.16
3382 6640 7.807907 CGAAAAAGTAAGCAGTCAACCATAAAT 59.192 33.333 0.00 0.00 0.00 1.40
3404 6662 1.710013 ACGATCTTGTAGTGCCAACG 58.290 50.000 0.00 0.00 0.00 4.10
3423 6681 4.703645 ACGAGATGAAGAACTTCGATCA 57.296 40.909 18.83 7.63 42.28 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.712241 CCTTTTGGCTCACGTATATGATAG 57.288 41.667 0.00 0.00 0.00 2.08
16 17 1.660264 GACCGTTTGCGCCTTTTGG 60.660 57.895 4.18 2.72 44.18 3.28
17 18 1.660264 GGACCGTTTGCGCCTTTTG 60.660 57.895 4.18 0.00 36.67 2.44
18 19 2.725641 GGACCGTTTGCGCCTTTT 59.274 55.556 4.18 0.00 36.67 2.27
19 20 3.292159 GGGACCGTTTGCGCCTTT 61.292 61.111 4.18 0.00 36.67 3.11
20 21 4.572571 TGGGACCGTTTGCGCCTT 62.573 61.111 4.18 0.00 36.67 4.35
25 26 4.966787 TGGCCTGGGACCGTTTGC 62.967 66.667 3.32 0.00 0.00 3.68
26 27 2.672996 CTGGCCTGGGACCGTTTG 60.673 66.667 3.32 0.00 0.00 2.93
27 28 3.966543 CCTGGCCTGGGACCGTTT 61.967 66.667 20.77 0.00 0.00 3.60
28 29 3.857521 TACCTGGCCTGGGACCGTT 62.858 63.158 30.19 12.44 0.00 4.44
29 30 3.857521 TTACCTGGCCTGGGACCGT 62.858 63.158 30.19 13.14 0.00 4.83
30 31 3.006728 TTACCTGGCCTGGGACCG 61.007 66.667 30.19 7.41 0.00 4.79
31 32 2.680370 CCTTACCTGGCCTGGGACC 61.680 68.421 30.19 0.00 0.00 4.46
32 33 1.923909 ACCTTACCTGGCCTGGGAC 60.924 63.158 30.19 0.00 0.00 4.46
33 34 1.923395 CACCTTACCTGGCCTGGGA 60.923 63.158 30.19 21.82 0.00 4.37
34 35 2.677228 CACCTTACCTGGCCTGGG 59.323 66.667 30.19 21.31 0.00 4.45
35 36 2.677228 CCACCTTACCTGGCCTGG 59.323 66.667 26.14 26.14 0.00 4.45
40 41 2.355115 GGGTGCCACCTTACCTGG 59.645 66.667 14.71 0.00 38.64 4.45
41 42 2.046314 CGGGTGCCACCTTACCTG 60.046 66.667 14.71 0.00 38.64 4.00
42 43 2.528378 ACGGGTGCCACCTTACCT 60.528 61.111 14.71 0.00 38.64 3.08
43 44 2.359478 CACGGGTGCCACCTTACC 60.359 66.667 14.71 0.00 38.64 2.85
44 45 1.375523 CTCACGGGTGCCACCTTAC 60.376 63.158 14.71 0.00 38.64 2.34
45 46 1.122632 TTCTCACGGGTGCCACCTTA 61.123 55.000 14.71 0.00 38.64 2.69
46 47 1.779061 ATTCTCACGGGTGCCACCTT 61.779 55.000 14.71 0.00 38.64 3.50
47 48 0.907704 TATTCTCACGGGTGCCACCT 60.908 55.000 14.71 0.00 38.64 4.00
48 49 0.743345 GTATTCTCACGGGTGCCACC 60.743 60.000 4.93 4.93 37.60 4.61
49 50 0.743345 GGTATTCTCACGGGTGCCAC 60.743 60.000 0.00 0.00 0.00 5.01
50 51 1.600107 GGTATTCTCACGGGTGCCA 59.400 57.895 0.00 0.00 0.00 4.92
51 52 1.520787 CGGTATTCTCACGGGTGCC 60.521 63.158 0.00 0.00 0.00 5.01
52 53 1.082117 CACGGTATTCTCACGGGTGC 61.082 60.000 0.00 0.00 0.00 5.01
53 54 1.082117 GCACGGTATTCTCACGGGTG 61.082 60.000 0.00 0.00 32.75 4.61
54 55 1.217244 GCACGGTATTCTCACGGGT 59.783 57.895 0.00 0.00 32.75 5.28
55 56 1.876714 CGCACGGTATTCTCACGGG 60.877 63.158 0.00 0.00 0.00 5.28
56 57 1.153901 ACGCACGGTATTCTCACGG 60.154 57.895 0.00 0.00 0.00 4.94
57 58 0.455464 TCACGCACGGTATTCTCACG 60.455 55.000 0.00 0.00 0.00 4.35
58 59 1.269166 CTCACGCACGGTATTCTCAC 58.731 55.000 0.00 0.00 0.00 3.51
59 60 0.172578 CCTCACGCACGGTATTCTCA 59.827 55.000 0.00 0.00 0.00 3.27
60 61 1.146358 GCCTCACGCACGGTATTCTC 61.146 60.000 0.00 0.00 37.47 2.87
61 62 1.153628 GCCTCACGCACGGTATTCT 60.154 57.895 0.00 0.00 37.47 2.40
62 63 2.171725 GGCCTCACGCACGGTATTC 61.172 63.158 0.00 0.00 40.31 1.75
63 64 2.125269 GGCCTCACGCACGGTATT 60.125 61.111 0.00 0.00 40.31 1.89
64 65 4.508128 CGGCCTCACGCACGGTAT 62.508 66.667 0.00 0.00 40.31 2.73
72 73 0.739462 TATCACTTTGCGGCCTCACG 60.739 55.000 0.00 0.00 0.00 4.35
73 74 1.331756 CATATCACTTTGCGGCCTCAC 59.668 52.381 0.00 0.00 0.00 3.51
74 75 1.209261 TCATATCACTTTGCGGCCTCA 59.791 47.619 0.00 0.00 0.00 3.86
75 76 1.953559 TCATATCACTTTGCGGCCTC 58.046 50.000 0.00 0.00 0.00 4.70
76 77 2.224606 CATCATATCACTTTGCGGCCT 58.775 47.619 0.00 0.00 0.00 5.19
77 78 1.949525 ACATCATATCACTTTGCGGCC 59.050 47.619 0.00 0.00 0.00 6.13
78 79 2.355756 ACACATCATATCACTTTGCGGC 59.644 45.455 0.00 0.00 0.00 6.53
79 80 4.621068 AACACATCATATCACTTTGCGG 57.379 40.909 0.00 0.00 0.00 5.69
80 81 6.105657 TGTAACACATCATATCACTTTGCG 57.894 37.500 0.00 0.00 0.00 4.85
81 82 6.415867 GCATGTAACACATCATATCACTTTGC 59.584 38.462 0.00 0.00 36.53 3.68
82 83 7.700505 AGCATGTAACACATCATATCACTTTG 58.299 34.615 0.00 0.00 36.53 2.77
83 84 7.870509 AGCATGTAACACATCATATCACTTT 57.129 32.000 0.00 0.00 36.53 2.66
84 85 8.424133 TCTAGCATGTAACACATCATATCACTT 58.576 33.333 0.00 0.00 36.53 3.16
85 86 7.955918 TCTAGCATGTAACACATCATATCACT 58.044 34.615 0.00 0.00 36.53 3.41
86 87 8.768957 ATCTAGCATGTAACACATCATATCAC 57.231 34.615 0.00 0.00 36.53 3.06
87 88 7.756722 CGATCTAGCATGTAACACATCATATCA 59.243 37.037 0.00 0.00 36.53 2.15
88 89 7.221645 CCGATCTAGCATGTAACACATCATATC 59.778 40.741 0.00 0.00 36.53 1.63
89 90 7.038048 CCGATCTAGCATGTAACACATCATAT 58.962 38.462 0.00 0.00 36.53 1.78
90 91 6.015434 ACCGATCTAGCATGTAACACATCATA 60.015 38.462 0.00 0.00 36.53 2.15
91 92 5.221521 ACCGATCTAGCATGTAACACATCAT 60.222 40.000 0.00 0.00 36.53 2.45
92 93 4.099419 ACCGATCTAGCATGTAACACATCA 59.901 41.667 0.00 0.00 36.53 3.07
93 94 4.445718 CACCGATCTAGCATGTAACACATC 59.554 45.833 0.00 0.00 36.53 3.06
94 95 4.141937 ACACCGATCTAGCATGTAACACAT 60.142 41.667 0.00 0.00 39.91 3.21
95 96 3.194755 ACACCGATCTAGCATGTAACACA 59.805 43.478 0.00 0.00 0.00 3.72
96 97 3.551890 CACACCGATCTAGCATGTAACAC 59.448 47.826 0.00 0.00 0.00 3.32
97 98 3.445805 TCACACCGATCTAGCATGTAACA 59.554 43.478 0.00 0.00 0.00 2.41
98 99 3.797256 GTCACACCGATCTAGCATGTAAC 59.203 47.826 0.00 0.00 0.00 2.50
99 100 3.699538 AGTCACACCGATCTAGCATGTAA 59.300 43.478 0.00 0.00 0.00 2.41
100 101 3.288092 AGTCACACCGATCTAGCATGTA 58.712 45.455 0.00 0.00 0.00 2.29
101 102 2.099921 GAGTCACACCGATCTAGCATGT 59.900 50.000 0.00 0.00 0.00 3.21
102 103 2.099756 TGAGTCACACCGATCTAGCATG 59.900 50.000 0.00 0.00 0.00 4.06
103 104 2.360483 CTGAGTCACACCGATCTAGCAT 59.640 50.000 0.00 0.00 0.00 3.79
104 105 1.745653 CTGAGTCACACCGATCTAGCA 59.254 52.381 0.00 0.00 0.00 3.49
105 106 1.066303 CCTGAGTCACACCGATCTAGC 59.934 57.143 0.00 0.00 0.00 3.42
106 107 2.644676 TCCTGAGTCACACCGATCTAG 58.355 52.381 0.00 0.00 0.00 2.43
107 108 2.801077 TCCTGAGTCACACCGATCTA 57.199 50.000 0.00 0.00 0.00 1.98
108 109 2.028130 GATCCTGAGTCACACCGATCT 58.972 52.381 0.00 0.00 31.64 2.75
109 110 1.268794 CGATCCTGAGTCACACCGATC 60.269 57.143 0.00 0.00 0.00 3.69
110 111 0.741326 CGATCCTGAGTCACACCGAT 59.259 55.000 0.00 0.00 0.00 4.18
111 112 1.313091 CCGATCCTGAGTCACACCGA 61.313 60.000 0.00 0.00 0.00 4.69
112 113 1.139734 CCGATCCTGAGTCACACCG 59.860 63.158 0.00 0.00 0.00 4.94
113 114 1.517832 CCCGATCCTGAGTCACACC 59.482 63.158 0.00 0.00 0.00 4.16
114 115 1.258445 ACCCCGATCCTGAGTCACAC 61.258 60.000 0.00 0.00 0.00 3.82
115 116 0.970937 GACCCCGATCCTGAGTCACA 60.971 60.000 0.00 0.00 0.00 3.58
116 117 1.677637 GGACCCCGATCCTGAGTCAC 61.678 65.000 0.00 0.00 35.68 3.67
117 118 1.381327 GGACCCCGATCCTGAGTCA 60.381 63.158 0.00 0.00 35.68 3.41
118 119 3.539842 GGACCCCGATCCTGAGTC 58.460 66.667 0.00 0.00 35.68 3.36
124 125 0.546598 ATTTGTCAGGACCCCGATCC 59.453 55.000 0.00 0.00 39.28 3.36
125 126 2.224305 CCTATTTGTCAGGACCCCGATC 60.224 54.545 0.00 0.00 34.91 3.69
126 127 1.768870 CCTATTTGTCAGGACCCCGAT 59.231 52.381 0.00 0.00 34.91 4.18
127 128 1.200519 CCTATTTGTCAGGACCCCGA 58.799 55.000 0.00 0.00 34.91 5.14
128 129 0.180406 CCCTATTTGTCAGGACCCCG 59.820 60.000 0.00 0.00 34.91 5.73
129 130 0.106669 GCCCTATTTGTCAGGACCCC 60.107 60.000 0.00 0.00 34.91 4.95
130 131 0.106669 GGCCCTATTTGTCAGGACCC 60.107 60.000 0.00 0.00 34.91 4.46
131 132 0.463833 CGGCCCTATTTGTCAGGACC 60.464 60.000 0.00 0.00 34.91 4.46
132 133 0.539986 TCGGCCCTATTTGTCAGGAC 59.460 55.000 0.00 0.00 34.91 3.85
133 134 0.830648 CTCGGCCCTATTTGTCAGGA 59.169 55.000 0.00 0.00 34.91 3.86
134 135 0.541863 ACTCGGCCCTATTTGTCAGG 59.458 55.000 0.00 0.00 0.00 3.86
135 136 1.482593 AGACTCGGCCCTATTTGTCAG 59.517 52.381 0.00 0.00 0.00 3.51
136 137 1.568504 AGACTCGGCCCTATTTGTCA 58.431 50.000 0.00 0.00 0.00 3.58
137 138 2.693267 AAGACTCGGCCCTATTTGTC 57.307 50.000 0.00 0.00 0.00 3.18
138 139 3.434940 AAAAGACTCGGCCCTATTTGT 57.565 42.857 0.00 0.00 0.00 2.83
158 159 9.279904 CACTTCATTGTTGTACTTTTTCGTAAA 57.720 29.630 0.00 0.00 0.00 2.01
160 161 6.908284 GCACTTCATTGTTGTACTTTTTCGTA 59.092 34.615 0.00 0.00 0.00 3.43
163 164 6.273071 AGGCACTTCATTGTTGTACTTTTTC 58.727 36.000 0.00 0.00 27.25 2.29
164 165 6.220726 AGGCACTTCATTGTTGTACTTTTT 57.779 33.333 0.00 0.00 27.25 1.94
175 176 4.999950 ACACTTCTTCTAGGCACTTCATTG 59.000 41.667 0.00 0.00 41.75 2.82
210 211 0.726452 TGCCGCGAACATAAAAACGC 60.726 50.000 8.23 0.00 46.08 4.84
268 269 2.365582 GTCCACGATTTAATGCCCACT 58.634 47.619 0.00 0.00 0.00 4.00
271 272 1.658994 TCGTCCACGATTTAATGCCC 58.341 50.000 0.00 0.00 44.22 5.36
293 294 2.509336 GGCGCGTACATGCTCTGT 60.509 61.111 8.43 0.00 42.13 3.41
294 295 2.202797 AGGCGCGTACATGCTCTG 60.203 61.111 8.43 0.00 0.00 3.35
370 371 4.184629 GGGACTCTAATGTAACTGCAGTG 58.815 47.826 22.49 5.89 0.00 3.66
406 412 6.406737 GCGTAGGACTAGATTAGGGTTTTTCT 60.407 42.308 0.00 0.00 0.00 2.52
407 413 5.752472 GCGTAGGACTAGATTAGGGTTTTTC 59.248 44.000 0.00 0.00 0.00 2.29
419 425 2.026542 TCAGTTGGAGCGTAGGACTAGA 60.027 50.000 0.00 0.00 0.00 2.43
426 432 0.389948 GGGTGTCAGTTGGAGCGTAG 60.390 60.000 0.00 0.00 0.00 3.51
460 466 1.078143 GGCGGACCAAGCTCAGAAT 60.078 57.895 0.00 0.00 35.26 2.40
463 469 4.785453 GGGGCGGACCAAGCTCAG 62.785 72.222 0.36 0.00 42.91 3.35
489 495 3.892581 GTACGTACTCCCGCCGGG 61.893 72.222 18.41 18.41 46.11 5.73
490 496 3.892581 GGTACGTACTCCCGCCGG 61.893 72.222 24.07 0.00 0.00 6.13
491 497 1.937546 AAAGGTACGTACTCCCGCCG 61.938 60.000 24.07 0.00 0.00 6.46
492 498 0.179127 GAAAGGTACGTACTCCCGCC 60.179 60.000 24.07 7.57 0.00 6.13
493 499 0.179127 GGAAAGGTACGTACTCCCGC 60.179 60.000 24.07 8.13 0.00 6.13
494 500 0.099436 CGGAAAGGTACGTACTCCCG 59.901 60.000 24.07 23.33 0.00 5.14
495 501 0.179127 GCGGAAAGGTACGTACTCCC 60.179 60.000 24.07 17.38 0.00 4.30
496 502 0.813821 AGCGGAAAGGTACGTACTCC 59.186 55.000 24.07 20.76 0.00 3.85
497 503 2.643933 AAGCGGAAAGGTACGTACTC 57.356 50.000 24.07 14.22 0.00 2.59
498 504 2.611224 CCAAAGCGGAAAGGTACGTACT 60.611 50.000 24.07 5.64 36.56 2.73
499 505 1.728425 CCAAAGCGGAAAGGTACGTAC 59.272 52.381 17.56 17.56 36.56 3.67
500 506 1.940752 GCCAAAGCGGAAAGGTACGTA 60.941 52.381 0.00 0.00 36.56 3.57
501 507 1.232621 GCCAAAGCGGAAAGGTACGT 61.233 55.000 0.00 0.00 36.56 3.57
502 508 1.231958 TGCCAAAGCGGAAAGGTACG 61.232 55.000 0.00 0.00 44.31 3.67
899 906 7.484035 AAACCAGATATCGATAAGCAGAAAC 57.516 36.000 9.61 0.00 0.00 2.78
912 942 4.310769 ACTGCTGCGATAAACCAGATATC 58.689 43.478 0.00 0.00 0.00 1.63
913 943 4.342862 ACTGCTGCGATAAACCAGATAT 57.657 40.909 0.00 0.00 0.00 1.63
923 953 0.250234 AGCTCCAAACTGCTGCGATA 59.750 50.000 0.00 0.00 38.21 2.92
968 1003 3.065510 CCTTCTTCTCGCTCGATTGTAGA 59.934 47.826 0.00 0.00 0.00 2.59
969 1004 3.065510 TCCTTCTTCTCGCTCGATTGTAG 59.934 47.826 0.00 0.00 0.00 2.74
970 1005 3.014623 TCCTTCTTCTCGCTCGATTGTA 58.985 45.455 0.00 0.00 0.00 2.41
971 1006 1.819288 TCCTTCTTCTCGCTCGATTGT 59.181 47.619 0.00 0.00 0.00 2.71
972 1007 2.568696 TCCTTCTTCTCGCTCGATTG 57.431 50.000 0.00 0.00 0.00 2.67
973 1008 2.287308 CGATCCTTCTTCTCGCTCGATT 60.287 50.000 0.00 0.00 0.00 3.34
1072 1107 0.750546 TCGTCCGTCGGATGGAATCT 60.751 55.000 28.81 0.00 44.71 2.40
1074 1109 1.734137 CTCGTCCGTCGGATGGAAT 59.266 57.895 28.81 0.00 39.09 3.01
1080 1115 4.405671 AGCTCCTCGTCCGTCGGA 62.406 66.667 10.71 10.71 40.32 4.55
1263 1303 4.390603 ACGCAGATGCAAAAACGATTAGTA 59.609 37.500 5.55 0.00 42.21 1.82
1264 1304 3.188460 ACGCAGATGCAAAAACGATTAGT 59.812 39.130 5.55 0.00 42.21 2.24
1265 1305 3.539563 CACGCAGATGCAAAAACGATTAG 59.460 43.478 5.55 0.00 42.21 1.73
1307 1361 1.313812 ACCACTCCTTCTCGCCGTAG 61.314 60.000 0.00 0.00 0.00 3.51
1607 1665 2.230508 CAGTTCGAGCCACCTACTGTTA 59.769 50.000 0.00 0.00 33.34 2.41
1763 1822 1.296392 CTGCCCGTGACAAGGATCA 59.704 57.895 9.22 5.70 0.00 2.92
1955 2029 9.363401 ACATGAATCCATCATCATAAACTGATT 57.637 29.630 0.00 0.00 45.91 2.57
2002 2327 8.197439 ACGTACATGATCAGAACAGAAATCATA 58.803 33.333 0.00 0.00 36.87 2.15
2021 2504 5.004440 CACAAAAAGATCGATCGACGTACAT 59.996 40.000 22.06 2.53 43.13 2.29
2022 2505 4.322539 CACAAAAAGATCGATCGACGTACA 59.677 41.667 22.06 0.00 43.13 2.90
2023 2506 4.259292 CCACAAAAAGATCGATCGACGTAC 60.259 45.833 22.06 12.09 43.13 3.67
2024 2507 3.855379 CCACAAAAAGATCGATCGACGTA 59.145 43.478 22.06 0.00 43.13 3.57
2048 2531 0.518636 CCAGTCATCCAACTGCAACG 59.481 55.000 0.00 0.00 44.34 4.10
2073 2556 3.410631 TTCTTGTTGTAGATCCGGCAA 57.589 42.857 0.00 0.00 0.00 4.52
2402 2915 2.892425 CCGGGTCGAGCATCAAGC 60.892 66.667 17.59 0.00 46.19 4.01
2403 2916 2.892425 GCCGGGTCGAGCATCAAG 60.892 66.667 17.59 0.75 33.17 3.02
2404 2917 4.812476 CGCCGGGTCGAGCATCAA 62.812 66.667 17.59 0.00 33.17 2.57
2521 3076 0.786581 CGATCGATTTCATCCCAGCG 59.213 55.000 10.26 0.00 0.00 5.18
2522 3077 1.151668 CCGATCGATTTCATCCCAGC 58.848 55.000 18.66 0.00 0.00 4.85
2523 3078 1.609061 CCCCGATCGATTTCATCCCAG 60.609 57.143 18.66 0.00 0.00 4.45
2524 3079 0.396435 CCCCGATCGATTTCATCCCA 59.604 55.000 18.66 0.00 0.00 4.37
2527 3082 2.028930 AGCTACCCCGATCGATTTCATC 60.029 50.000 18.66 0.00 0.00 2.92
2528 3083 1.971357 AGCTACCCCGATCGATTTCAT 59.029 47.619 18.66 0.00 0.00 2.57
2531 3086 0.314302 CGAGCTACCCCGATCGATTT 59.686 55.000 18.66 1.88 44.81 2.17
2590 3150 4.532126 TGATATCTTCCATCCAACGGCTAT 59.468 41.667 3.98 0.00 0.00 2.97
2614 3174 1.419374 CGTGACTCCTTGTGCACTAC 58.581 55.000 19.41 0.00 0.00 2.73
2842 3411 1.971357 AGATCGCACGGGGAGAATAAT 59.029 47.619 0.00 0.00 0.00 1.28
2850 3419 0.958382 TGGAAAAAGATCGCACGGGG 60.958 55.000 0.00 0.00 0.00 5.73
2886 3455 8.213518 TCTCCTATCAATAAAAAGATGCACAC 57.786 34.615 0.00 0.00 0.00 3.82
2916 6117 5.014858 ACGTCCTGGACTACAATCTTCTTA 58.985 41.667 23.49 0.00 0.00 2.10
2920 6121 3.864921 GCAACGTCCTGGACTACAATCTT 60.865 47.826 23.49 2.09 0.00 2.40
2923 6124 1.338769 GGCAACGTCCTGGACTACAAT 60.339 52.381 23.49 3.45 0.00 2.71
2924 6125 0.034337 GGCAACGTCCTGGACTACAA 59.966 55.000 23.49 0.00 0.00 2.41
2927 6128 1.592400 CGAGGCAACGTCCTGGACTA 61.592 60.000 23.49 0.00 46.39 2.59
2949 6150 0.818296 AGACTAGTTAGTGGGCGCTG 59.182 55.000 7.64 0.00 36.50 5.18
2950 6151 1.204941 CAAGACTAGTTAGTGGGCGCT 59.795 52.381 7.64 0.00 36.50 5.92
2963 6164 2.228103 CAGACTACACGTGGCAAGACTA 59.772 50.000 21.57 0.00 0.00 2.59
2976 6177 0.237498 CTCGTGTGACGCAGACTACA 59.763 55.000 0.00 0.00 42.21 2.74
2977 6178 0.454620 CCTCGTGTGACGCAGACTAC 60.455 60.000 0.00 0.00 42.21 2.73
2985 6242 3.680786 TCTGCCCCTCGTGTGACG 61.681 66.667 0.00 0.00 44.19 4.35
2999 6256 2.047844 CTGCCCCTCGTGTGTCTG 60.048 66.667 0.00 0.00 0.00 3.51
3004 6261 3.681835 GTCGTCTGCCCCTCGTGT 61.682 66.667 0.00 0.00 0.00 4.49
3005 6262 3.220999 TTGTCGTCTGCCCCTCGTG 62.221 63.158 0.00 0.00 0.00 4.35
3006 6263 2.915659 TTGTCGTCTGCCCCTCGT 60.916 61.111 0.00 0.00 0.00 4.18
3007 6264 2.432628 GTTGTCGTCTGCCCCTCG 60.433 66.667 0.00 0.00 0.00 4.63
3008 6265 1.374758 CTGTTGTCGTCTGCCCCTC 60.375 63.158 0.00 0.00 0.00 4.30
3009 6266 2.743718 CTGTTGTCGTCTGCCCCT 59.256 61.111 0.00 0.00 0.00 4.79
3010 6267 2.358737 CCTGTTGTCGTCTGCCCC 60.359 66.667 0.00 0.00 0.00 5.80
3011 6268 1.961277 CACCTGTTGTCGTCTGCCC 60.961 63.158 0.00 0.00 0.00 5.36
3012 6269 0.531974 TTCACCTGTTGTCGTCTGCC 60.532 55.000 0.00 0.00 0.00 4.85
3013 6270 0.861837 CTTCACCTGTTGTCGTCTGC 59.138 55.000 0.00 0.00 0.00 4.26
3014 6271 2.128035 GTCTTCACCTGTTGTCGTCTG 58.872 52.381 0.00 0.00 0.00 3.51
3015 6272 1.269102 CGTCTTCACCTGTTGTCGTCT 60.269 52.381 0.00 0.00 0.00 4.18
3016 6273 1.129326 CGTCTTCACCTGTTGTCGTC 58.871 55.000 0.00 0.00 0.00 4.20
3017 6274 0.874607 GCGTCTTCACCTGTTGTCGT 60.875 55.000 0.00 0.00 0.00 4.34
3018 6275 1.853319 GCGTCTTCACCTGTTGTCG 59.147 57.895 0.00 0.00 0.00 4.35
3019 6276 1.557443 CCGCGTCTTCACCTGTTGTC 61.557 60.000 4.92 0.00 0.00 3.18
3020 6277 1.594293 CCGCGTCTTCACCTGTTGT 60.594 57.895 4.92 0.00 0.00 3.32
3021 6278 0.670546 ATCCGCGTCTTCACCTGTTG 60.671 55.000 4.92 0.00 0.00 3.33
3022 6279 0.389948 GATCCGCGTCTTCACCTGTT 60.390 55.000 4.92 0.00 0.00 3.16
3023 6280 1.215647 GATCCGCGTCTTCACCTGT 59.784 57.895 4.92 0.00 0.00 4.00
3024 6281 1.874019 CGATCCGCGTCTTCACCTG 60.874 63.158 4.92 0.00 34.64 4.00
3043 6300 4.327680 GCCTTCCTGTGACTCAAACTATT 58.672 43.478 0.00 0.00 0.00 1.73
3049 6306 0.397941 CTGGCCTTCCTGTGACTCAA 59.602 55.000 3.32 0.00 0.00 3.02
3052 6309 1.821061 CGTCTGGCCTTCCTGTGACT 61.821 60.000 3.32 0.00 33.50 3.41
3058 6315 1.757699 GAGTTATCGTCTGGCCTTCCT 59.242 52.381 3.32 0.00 0.00 3.36
3059 6316 1.480954 TGAGTTATCGTCTGGCCTTCC 59.519 52.381 3.32 0.00 0.00 3.46
3062 6319 2.093447 CCTTTGAGTTATCGTCTGGCCT 60.093 50.000 3.32 0.00 0.00 5.19
3065 6322 4.188247 TCACCTTTGAGTTATCGTCTGG 57.812 45.455 0.00 0.00 0.00 3.86
3111 6368 5.363562 TCATACTCTCTGCATGGTGAATT 57.636 39.130 0.00 0.00 0.00 2.17
3159 6416 3.233231 AACGTTTCCCCGTCCGGA 61.233 61.111 0.00 0.00 40.85 5.14
3213 6470 2.881539 ATCTCTCACCGCCCGACGTA 62.882 60.000 0.00 0.00 41.42 3.57
3267 6524 1.359168 GGACTACCCCTTCACCTGTT 58.641 55.000 0.00 0.00 0.00 3.16
3359 6617 8.177119 TGATTTATGGTTGACTGCTTACTTTT 57.823 30.769 0.00 0.00 0.00 2.27
3382 6640 3.064207 GTTGGCACTACAAGATCGTTGA 58.936 45.455 10.61 0.00 0.00 3.18
3404 6662 4.803088 CCTGTGATCGAAGTTCTTCATCTC 59.197 45.833 12.15 12.92 0.00 2.75
3423 6681 1.003355 CGCACTTGGGATGTCCTGT 60.003 57.895 0.00 0.00 36.20 4.00


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

AutoCloner maintained by Alex Coulton.