Multiple sequence alignment - TraesCS2D01G330000

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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 TraesCS2D01G330000 chr2D 100.000 2525 0 0 1 2525 423174211 423171687 0.000000e+00 4663.0
1 TraesCS2D01G330000 chr2D 83.926 591 68 13 933 1517 423209562 423208993 7.950000e-150 540.0
2 TraesCS2D01G330000 chr2D 76.768 297 25 15 463 751 423210080 423209820 2.640000e-25 126.0
3 TraesCS2D01G330000 chr2A 88.032 1972 133 40 627 2517 565372700 565374649 0.000000e+00 2239.0
4 TraesCS2D01G330000 chr2A 81.167 600 78 15 933 1517 565368325 565368904 1.380000e-122 449.0
5 TraesCS2D01G330000 chr2A 88.670 203 21 1 437 639 565371893 565372093 1.940000e-61 246.0
6 TraesCS2D01G330000 chr2A 86.096 187 14 3 570 751 565367933 565368112 9.220000e-45 191.0
7 TraesCS2D01G330000 chr2B 88.870 1770 122 33 583 2312 495896385 495894651 0.000000e+00 2108.0
8 TraesCS2D01G330000 chr2B 82.968 593 73 15 933 1517 495901704 495901132 6.230000e-141 510.0
9 TraesCS2D01G330000 chr2B 95.714 140 5 1 1 139 425456797 425456936 9.090000e-55 224.0
10 TraesCS2D01G330000 chr2B 81.818 286 23 8 307 564 495896659 495896375 1.970000e-51 213.0
11 TraesCS2D01G330000 chr2B 93.103 116 7 1 175 290 495896844 495896730 4.320000e-38 169.0
12 TraesCS2D01G330000 chr2B 87.075 147 19 0 2379 2525 495893900 495893754 1.550000e-37 167.0
13 TraesCS2D01G330000 chr2B 83.060 183 16 3 567 743 495902609 495902436 4.350000e-33 152.0
14 TraesCS2D01G330000 chr4A 79.249 559 98 12 1975 2525 678136390 678135842 8.530000e-100 374.0
15 TraesCS2D01G330000 chr1D 97.810 137 2 1 1 136 203064800 203064664 4.200000e-58 235.0
16 TraesCS2D01G330000 chr6B 97.778 135 2 1 1 134 551764048 551764182 5.430000e-57 231.0
17 TraesCS2D01G330000 chr6B 97.059 136 3 1 1 135 23327793 23327658 7.030000e-56 228.0
18 TraesCS2D01G330000 chr5D 97.778 135 2 1 1 134 92155669 92155535 5.430000e-57 231.0
19 TraesCS2D01G330000 chr5D 97.059 136 3 1 1 135 92160649 92160514 7.030000e-56 228.0
20 TraesCS2D01G330000 chr5D 97.037 135 3 1 1 134 398791987 398792121 2.530000e-55 226.0
21 TraesCS2D01G330000 chr7D 97.059 136 3 1 1 135 520323701 520323566 7.030000e-56 228.0
22 TraesCS2D01G330000 chr3D 97.059 136 3 1 1 135 126229111 126228976 7.030000e-56 228.0
23 TraesCS2D01G330000 chr3D 88.889 45 5 0 2433 2477 556257115 556257071 3.510000e-04 56.5
24 TraesCS2D01G330000 chr4D 76.744 172 33 6 1977 2145 14559821 14559654 3.460000e-14 89.8
25 TraesCS2D01G330000 chr4D 88.679 53 5 1 2098 2150 361886280 361886331 2.100000e-06 63.9
26 TraesCS2D01G330000 chr5B 91.304 46 4 0 2433 2478 136429786 136429741 2.100000e-06 63.9
27 TraesCS2D01G330000 chr1B 89.130 46 5 0 2433 2478 633622793 633622748 9.760000e-05 58.4
28 TraesCS2D01G330000 chr1A 96.774 31 1 0 2430 2460 550223129 550223159 5.000000e-03 52.8


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 TraesCS2D01G330000 chr2D 423171687 423174211 2524 True 4663.00 4663 100.00000 1 2525 1 chr2D.!!$R1 2524
1 TraesCS2D01G330000 chr2D 423208993 423210080 1087 True 333.00 540 80.34700 463 1517 2 chr2D.!!$R2 1054
2 TraesCS2D01G330000 chr2A 565367933 565374649 6716 False 781.25 2239 85.99125 437 2517 4 chr2A.!!$F1 2080
3 TraesCS2D01G330000 chr2B 495893754 495896844 3090 True 664.25 2108 87.71650 175 2525 4 chr2B.!!$R1 2350
4 TraesCS2D01G330000 chr2B 495901132 495902609 1477 True 331.00 510 83.01400 567 1517 2 chr2B.!!$R2 950
5 TraesCS2D01G330000 chr4A 678135842 678136390 548 True 374.00 374 79.24900 1975 2525 1 chr4A.!!$R1 550

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
380 436 0.104304 ACCGCAGAACTAATAGGGCG 59.896 55.0 9.67 9.67 43.68 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 7733 0.256752 TGATCTTGGAGGCCATGTGG 59.743 55.0 5.01 0.0 31.53 4.17 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
30 31 4.236755 CGATGTATTGATCGTGCATAGC 57.763 45.455 0.00 0.00 40.32 2.97
31 32 3.241458 CGATGTATTGATCGTGCATAGCG 60.241 47.826 0.00 0.00 40.32 4.26
32 33 1.792367 TGTATTGATCGTGCATAGCGC 59.208 47.619 0.00 0.00 42.89 5.92
45 46 3.702330 GCATAGCGCACGTATATATGGA 58.298 45.455 11.47 0.00 41.79 3.41
46 47 3.731216 GCATAGCGCACGTATATATGGAG 59.269 47.826 11.47 0.43 41.79 3.86
47 48 4.733815 GCATAGCGCACGTATATATGGAGT 60.734 45.833 11.47 0.00 41.79 3.85
48 49 5.505159 GCATAGCGCACGTATATATGGAGTA 60.505 44.000 11.47 0.00 41.79 2.59
49 50 4.352600 AGCGCACGTATATATGGAGTAC 57.647 45.455 11.47 0.00 0.00 2.73
50 51 3.754850 AGCGCACGTATATATGGAGTACA 59.245 43.478 11.47 0.00 0.00 2.90
51 52 4.216902 AGCGCACGTATATATGGAGTACAA 59.783 41.667 11.47 0.00 0.00 2.41
52 53 4.557690 GCGCACGTATATATGGAGTACAAG 59.442 45.833 0.30 0.00 0.00 3.16
53 54 5.093457 CGCACGTATATATGGAGTACAAGG 58.907 45.833 6.89 0.00 0.00 3.61
54 55 5.335426 CGCACGTATATATGGAGTACAAGGT 60.335 44.000 6.89 0.00 0.00 3.50
55 56 5.862323 GCACGTATATATGGAGTACAAGGTG 59.138 44.000 6.89 0.00 0.00 4.00
56 57 6.387465 CACGTATATATGGAGTACAAGGTGG 58.613 44.000 6.89 0.00 0.00 4.61
57 58 5.479375 ACGTATATATGGAGTACAAGGTGGG 59.521 44.000 6.89 0.00 0.00 4.61
58 59 4.910458 ATATATGGAGTACAAGGTGGGC 57.090 45.455 0.00 0.00 0.00 5.36
59 60 1.209621 TATGGAGTACAAGGTGGGCC 58.790 55.000 0.00 0.00 0.00 5.80
60 61 0.844661 ATGGAGTACAAGGTGGGCCA 60.845 55.000 0.00 0.00 37.19 5.36
61 62 1.002502 GGAGTACAAGGTGGGCCAC 60.003 63.158 28.69 28.69 37.19 5.01
62 63 1.758592 GAGTACAAGGTGGGCCACA 59.241 57.895 35.69 14.37 35.86 4.17
63 64 0.109723 GAGTACAAGGTGGGCCACAA 59.890 55.000 35.69 14.04 35.86 3.33
64 65 0.179001 AGTACAAGGTGGGCCACAAC 60.179 55.000 35.69 23.35 35.86 3.32
65 66 1.151908 TACAAGGTGGGCCACAACC 59.848 57.895 35.69 20.64 37.57 3.77
66 67 1.357272 TACAAGGTGGGCCACAACCT 61.357 55.000 35.69 22.62 37.57 3.50
67 68 1.903404 CAAGGTGGGCCACAACCTC 60.903 63.158 35.69 19.26 37.57 3.85
68 69 2.391130 AAGGTGGGCCACAACCTCA 61.391 57.895 35.69 0.00 37.57 3.86
69 70 1.943730 AAGGTGGGCCACAACCTCAA 61.944 55.000 35.69 0.00 37.57 3.02
70 71 2.200337 GGTGGGCCACAACCTCAAC 61.200 63.158 35.69 13.88 35.86 3.18
71 72 1.152756 GTGGGCCACAACCTCAACT 60.153 57.895 31.26 0.00 34.08 3.16
72 73 0.109723 GTGGGCCACAACCTCAACTA 59.890 55.000 31.26 0.00 34.08 2.24
73 74 1.072266 TGGGCCACAACCTCAACTAT 58.928 50.000 0.00 0.00 0.00 2.12
74 75 2.026636 GTGGGCCACAACCTCAACTATA 60.027 50.000 31.26 0.00 34.08 1.31
75 76 2.026636 TGGGCCACAACCTCAACTATAC 60.027 50.000 0.00 0.00 0.00 1.47
76 77 2.026636 GGGCCACAACCTCAACTATACA 60.027 50.000 4.39 0.00 0.00 2.29
77 78 3.560453 GGGCCACAACCTCAACTATACAA 60.560 47.826 4.39 0.00 0.00 2.41
78 79 4.076394 GGCCACAACCTCAACTATACAAA 58.924 43.478 0.00 0.00 0.00 2.83
79 80 4.156008 GGCCACAACCTCAACTATACAAAG 59.844 45.833 0.00 0.00 0.00 2.77
80 81 5.001232 GCCACAACCTCAACTATACAAAGA 58.999 41.667 0.00 0.00 0.00 2.52
81 82 5.106673 GCCACAACCTCAACTATACAAAGAC 60.107 44.000 0.00 0.00 0.00 3.01
82 83 6.231211 CCACAACCTCAACTATACAAAGACT 58.769 40.000 0.00 0.00 0.00 3.24
83 84 7.383687 CCACAACCTCAACTATACAAAGACTA 58.616 38.462 0.00 0.00 0.00 2.59
84 85 7.545965 CCACAACCTCAACTATACAAAGACTAG 59.454 40.741 0.00 0.00 0.00 2.57
85 86 7.545965 CACAACCTCAACTATACAAAGACTAGG 59.454 40.741 0.00 0.00 0.00 3.02
86 87 7.453752 ACAACCTCAACTATACAAAGACTAGGA 59.546 37.037 0.00 0.00 0.00 2.94
87 88 7.648039 ACCTCAACTATACAAAGACTAGGAG 57.352 40.000 0.00 0.00 0.00 3.69
88 89 6.608002 ACCTCAACTATACAAAGACTAGGAGG 59.392 42.308 0.00 0.00 42.02 4.30
89 90 6.608002 CCTCAACTATACAAAGACTAGGAGGT 59.392 42.308 0.00 0.00 33.95 3.85
90 91 7.406031 TCAACTATACAAAGACTAGGAGGTG 57.594 40.000 0.00 0.00 0.00 4.00
91 92 6.380274 TCAACTATACAAAGACTAGGAGGTGG 59.620 42.308 0.00 0.00 0.00 4.61
92 93 6.088541 ACTATACAAAGACTAGGAGGTGGA 57.911 41.667 0.00 0.00 0.00 4.02
93 94 5.892686 ACTATACAAAGACTAGGAGGTGGAC 59.107 44.000 0.00 0.00 0.00 4.02
94 95 2.258109 ACAAAGACTAGGAGGTGGACC 58.742 52.381 0.00 0.00 0.00 4.46
95 96 2.257207 CAAAGACTAGGAGGTGGACCA 58.743 52.381 0.00 0.00 38.89 4.02
96 97 2.234908 CAAAGACTAGGAGGTGGACCAG 59.765 54.545 0.00 0.00 38.89 4.00
97 98 0.336737 AGACTAGGAGGTGGACCAGG 59.663 60.000 0.00 0.00 38.89 4.45
98 99 1.306226 ACTAGGAGGTGGACCAGGC 60.306 63.158 0.00 0.00 38.89 4.85
99 100 1.002274 CTAGGAGGTGGACCAGGCT 59.998 63.158 0.00 0.00 38.89 4.58
100 101 0.261991 CTAGGAGGTGGACCAGGCTA 59.738 60.000 0.00 0.00 38.89 3.93
101 102 0.941963 TAGGAGGTGGACCAGGCTAT 59.058 55.000 0.00 0.00 38.89 2.97
102 103 0.941963 AGGAGGTGGACCAGGCTATA 59.058 55.000 0.00 0.00 38.89 1.31
103 104 1.049402 GGAGGTGGACCAGGCTATAC 58.951 60.000 0.00 0.00 38.89 1.47
104 105 1.691482 GGAGGTGGACCAGGCTATACA 60.691 57.143 0.00 0.00 38.89 2.29
105 106 2.116238 GAGGTGGACCAGGCTATACAA 58.884 52.381 0.00 0.00 38.89 2.41
106 107 2.706190 GAGGTGGACCAGGCTATACAAT 59.294 50.000 0.00 0.00 38.89 2.71
107 108 3.901844 GAGGTGGACCAGGCTATACAATA 59.098 47.826 0.00 0.00 38.89 1.90
108 109 4.503398 AGGTGGACCAGGCTATACAATAT 58.497 43.478 0.00 0.00 38.89 1.28
109 110 5.661565 AGGTGGACCAGGCTATACAATATA 58.338 41.667 0.00 0.00 38.89 0.86
110 111 5.484290 AGGTGGACCAGGCTATACAATATAC 59.516 44.000 0.00 0.00 38.89 1.47
111 112 5.247564 GGTGGACCAGGCTATACAATATACA 59.752 44.000 0.00 0.00 35.64 2.29
112 113 6.070194 GGTGGACCAGGCTATACAATATACAT 60.070 42.308 0.00 0.00 35.64 2.29
113 114 6.818644 GTGGACCAGGCTATACAATATACATG 59.181 42.308 0.00 0.00 0.00 3.21
114 115 5.817816 GGACCAGGCTATACAATATACATGC 59.182 44.000 0.00 0.00 0.00 4.06
115 116 6.373005 ACCAGGCTATACAATATACATGCA 57.627 37.500 0.00 0.00 0.00 3.96
116 117 6.173339 ACCAGGCTATACAATATACATGCAC 58.827 40.000 0.00 0.00 0.00 4.57
117 118 6.172630 CCAGGCTATACAATATACATGCACA 58.827 40.000 0.00 0.00 0.00 4.57
118 119 6.654582 CCAGGCTATACAATATACATGCACAA 59.345 38.462 0.00 0.00 0.00 3.33
119 120 7.174772 CCAGGCTATACAATATACATGCACAAA 59.825 37.037 0.00 0.00 0.00 2.83
120 121 8.733458 CAGGCTATACAATATACATGCACAAAT 58.267 33.333 0.00 0.00 0.00 2.32
121 122 8.950210 AGGCTATACAATATACATGCACAAATC 58.050 33.333 0.00 0.00 0.00 2.17
122 123 8.729756 GGCTATACAATATACATGCACAAATCA 58.270 33.333 0.00 0.00 0.00 2.57
134 135 8.861033 ACATGCACAAATCATATATTCAACAC 57.139 30.769 0.00 0.00 0.00 3.32
135 136 8.468399 ACATGCACAAATCATATATTCAACACA 58.532 29.630 0.00 0.00 0.00 3.72
136 137 9.471084 CATGCACAAATCATATATTCAACACAT 57.529 29.630 0.00 0.00 0.00 3.21
147 148 9.269415 CATATATTCAACACATATCATGCAACG 57.731 33.333 0.00 0.00 0.00 4.10
148 149 5.565592 ATTCAACACATATCATGCAACGT 57.434 34.783 0.00 0.00 0.00 3.99
149 150 4.339439 TCAACACATATCATGCAACGTG 57.661 40.909 0.00 0.00 0.00 4.49
150 151 3.750652 TCAACACATATCATGCAACGTGT 59.249 39.130 0.00 5.35 39.15 4.49
151 152 3.745332 ACACATATCATGCAACGTGTG 57.255 42.857 15.12 15.12 41.84 3.82
152 153 2.419673 ACACATATCATGCAACGTGTGG 59.580 45.455 18.65 7.16 40.76 4.17
153 154 1.401552 ACATATCATGCAACGTGTGGC 59.598 47.619 0.00 0.00 0.00 5.01
154 155 1.401199 CATATCATGCAACGTGTGGCA 59.599 47.619 4.24 4.24 45.23 4.92
155 156 1.528129 TATCATGCAACGTGTGGCAA 58.472 45.000 6.09 0.00 44.20 4.52
156 157 0.672889 ATCATGCAACGTGTGGCAAA 59.327 45.000 6.09 0.00 44.20 3.68
157 158 0.457443 TCATGCAACGTGTGGCAAAA 59.543 45.000 6.09 0.00 44.20 2.44
158 159 1.134995 TCATGCAACGTGTGGCAAAAA 60.135 42.857 6.09 0.00 44.20 1.94
198 199 5.338219 AAGTGATCAGAGCACTAAGCAAGAT 60.338 40.000 21.53 0.57 45.27 2.40
214 215 5.469763 AGCAAGATTTCAGTGCTTTCCACA 61.470 41.667 3.66 0.00 46.25 4.17
278 279 0.794473 GGCGTCTCAAAAGGTAACCG 59.206 55.000 0.00 0.00 37.17 4.44
280 281 1.869132 GCGTCTCAAAAGGTAACCGTT 59.131 47.619 0.00 0.00 37.17 4.44
285 286 5.332808 CGTCTCAAAAGGTAACCGTTAGTTG 60.333 44.000 0.00 0.00 39.67 3.16
287 297 4.197750 TCAAAAGGTAACCGTTAGTTGCA 58.802 39.130 0.00 0.00 42.38 4.08
290 300 6.655848 TCAAAAGGTAACCGTTAGTTGCATAT 59.344 34.615 0.00 0.00 42.38 1.78
294 304 8.822652 AAGGTAACCGTTAGTTGCATATATAC 57.177 34.615 0.00 0.00 42.38 1.47
307 317 9.537192 AGTTGCATATATACTTTGCGTTAGTTA 57.463 29.630 0.00 0.00 39.23 2.24
345 401 8.593492 TCATACTCATACATAATCAGTGTTGC 57.407 34.615 0.00 0.00 0.00 4.17
349 405 5.049828 TCATACATAATCAGTGTTGCTCGG 58.950 41.667 0.00 0.00 0.00 4.63
351 407 1.331756 CATAATCAGTGTTGCTCGGGC 59.668 52.381 0.00 0.00 39.26 6.13
361 417 0.901827 TTGCTCGGGCTTCACATCTA 59.098 50.000 9.62 0.00 39.59 1.98
371 427 2.675317 GCTTCACATCTACCGCAGAACT 60.675 50.000 0.00 0.00 36.67 3.01
374 430 5.339008 TTCACATCTACCGCAGAACTAAT 57.661 39.130 0.00 0.00 36.67 1.73
377 433 5.009710 TCACATCTACCGCAGAACTAATAGG 59.990 44.000 0.00 0.00 36.67 2.57
380 436 0.104304 ACCGCAGAACTAATAGGGCG 59.896 55.000 9.67 9.67 43.68 6.13
383 439 1.867166 GCAGAACTAATAGGGCGTCC 58.133 55.000 0.00 0.00 0.00 4.79
384 440 1.868519 GCAGAACTAATAGGGCGTCCG 60.869 57.143 0.00 0.00 38.33 4.79
396 452 1.445871 GGCGTCCGGACAAATTAACT 58.554 50.000 32.80 0.00 0.00 2.24
422 478 6.366877 GTCAAAAATGTCTGTCCAAATCCATG 59.633 38.462 0.00 0.00 0.00 3.66
425 481 6.764308 AAATGTCTGTCCAAATCCATGTAG 57.236 37.500 0.00 0.00 0.00 2.74
427 483 5.241403 TGTCTGTCCAAATCCATGTAGTT 57.759 39.130 0.00 0.00 0.00 2.24
429 485 5.705441 TGTCTGTCCAAATCCATGTAGTTTC 59.295 40.000 0.00 0.00 0.00 2.78
430 486 5.705441 GTCTGTCCAAATCCATGTAGTTTCA 59.295 40.000 0.00 0.00 0.00 2.69
431 487 6.375455 GTCTGTCCAAATCCATGTAGTTTCAT 59.625 38.462 0.00 0.00 0.00 2.57
432 488 7.552687 GTCTGTCCAAATCCATGTAGTTTCATA 59.447 37.037 0.00 0.00 0.00 2.15
434 490 8.050778 TGTCCAAATCCATGTAGTTTCATAAC 57.949 34.615 0.00 0.00 34.36 1.89
436 492 7.122055 GTCCAAATCCATGTAGTTTCATAACCA 59.878 37.037 0.00 0.00 34.71 3.67
437 493 7.838696 TCCAAATCCATGTAGTTTCATAACCAT 59.161 33.333 0.00 0.00 34.71 3.55
439 495 9.304731 CAAATCCATGTAGTTTCATAACCATTG 57.695 33.333 0.00 0.00 34.71 2.82
441 497 9.693739 AATCCATGTAGTTTCATAACCATTGTA 57.306 29.630 0.00 0.00 34.71 2.41
442 498 9.693739 ATCCATGTAGTTTCATAACCATTGTAA 57.306 29.630 0.00 0.00 34.71 2.41
443 499 8.952278 TCCATGTAGTTTCATAACCATTGTAAC 58.048 33.333 0.00 0.00 34.71 2.50
444 500 8.956426 CCATGTAGTTTCATAACCATTGTAACT 58.044 33.333 0.00 0.00 38.04 2.24
491 574 5.957796 GCTAATTCACGTACTTTACACATGC 59.042 40.000 0.00 0.00 0.00 4.06
529 612 1.079543 CAGAGCAAGACTGTCGGGG 60.080 63.158 1.52 0.00 0.00 5.73
561 644 4.531659 ACGCTAGTCAGTCAAACAAAAC 57.468 40.909 0.00 0.00 0.00 2.43
563 646 4.393680 ACGCTAGTCAGTCAAACAAAACAA 59.606 37.500 0.00 0.00 0.00 2.83
564 647 5.106475 ACGCTAGTCAGTCAAACAAAACAAA 60.106 36.000 0.00 0.00 0.00 2.83
589 676 6.934048 AACCTTCAGAAAAGAGAAACAGAG 57.066 37.500 0.00 0.00 0.00 3.35
604 693 6.226787 AGAAACAGAGTAACATGTCAAGAGG 58.773 40.000 0.00 0.00 0.00 3.69
625 714 0.745845 ACACGGAGATGCAGCAATCC 60.746 55.000 16.77 16.77 0.00 3.01
639 732 1.822186 AATCCGGCGGTAACATGGC 60.822 57.895 27.32 0.00 0.00 4.40
682 776 1.823828 CCAAAGTATCGACGTCTCCG 58.176 55.000 14.70 0.70 40.83 4.63
764 1129 1.059692 CTTGATCTACGCGCTTGTGTG 59.940 52.381 5.73 0.00 36.86 3.82
773 1138 3.615709 GCTTGTGTGGGTTGGGGC 61.616 66.667 0.00 0.00 0.00 5.80
775 1377 1.458486 CTTGTGTGGGTTGGGGCTA 59.542 57.895 0.00 0.00 0.00 3.93
797 1399 4.475345 AGATTAAGCCGTCCATACTCTCT 58.525 43.478 0.00 0.00 0.00 3.10
798 1400 4.521256 AGATTAAGCCGTCCATACTCTCTC 59.479 45.833 0.00 0.00 0.00 3.20
912 1556 3.025262 ACTTACAGAGGCTACCTGCTAC 58.975 50.000 3.29 0.00 42.39 3.58
979 1631 2.028112 ACTGCATCAGTGTCACGGTATT 60.028 45.455 2.95 0.00 43.63 1.89
980 1632 2.345876 TGCATCAGTGTCACGGTATTG 58.654 47.619 2.95 2.05 0.00 1.90
1081 6435 6.778821 TCTCCTGATTGTTACTGAAAATGGA 58.221 36.000 0.00 0.00 0.00 3.41
1089 6443 6.500684 TGTTACTGAAAATGGAATGCTCTC 57.499 37.500 0.00 0.00 0.00 3.20
1092 6446 4.268359 ACTGAAAATGGAATGCTCTCCTC 58.732 43.478 6.27 0.00 36.35 3.71
1095 6449 3.294038 AAATGGAATGCTCTCCTCCTG 57.706 47.619 6.27 0.00 36.35 3.86
1126 6482 0.994247 AGATGGTGATCAGGGTGCAA 59.006 50.000 0.00 0.00 0.00 4.08
1168 6524 1.543944 CCAAGGCAATGGGGTTGGTC 61.544 60.000 1.64 0.00 38.29 4.02
1178 6534 2.125793 GGTTGGTCGCCTCGGTAC 60.126 66.667 0.00 0.00 0.00 3.34
1201 6558 2.805671 CGGTGAGTTGCAGTTCACATTA 59.194 45.455 24.90 0.00 44.23 1.90
1211 6568 1.913419 AGTTCACATTACCGGGGTCAT 59.087 47.619 6.32 0.00 0.00 3.06
1228 6585 6.515200 CGGGGTCATATCCTTGATATACGATC 60.515 46.154 0.00 0.00 33.98 3.69
1246 6603 3.684788 CGATCAGGTTTCCAACTAACTGG 59.315 47.826 0.00 0.00 37.87 4.00
1363 6724 2.665000 CCTGCCTGCGGAAGAAGA 59.335 61.111 4.33 0.00 40.08 2.87
1640 7046 9.722056 CCATTTGATGCTTATACAAAGTCTTAC 57.278 33.333 0.00 0.00 37.04 2.34
1689 7098 7.255491 TCAAGCATAAACATGAGCAGATAAG 57.745 36.000 0.00 0.00 0.00 1.73
1691 7100 7.718314 TCAAGCATAAACATGAGCAGATAAGAT 59.282 33.333 0.00 0.00 0.00 2.40
1692 7101 8.996271 CAAGCATAAACATGAGCAGATAAGATA 58.004 33.333 0.00 0.00 0.00 1.98
1693 7102 9.565090 AAGCATAAACATGAGCAGATAAGATAA 57.435 29.630 0.00 0.00 0.00 1.75
1694 7103 8.997323 AGCATAAACATGAGCAGATAAGATAAC 58.003 33.333 0.00 0.00 0.00 1.89
1695 7104 8.777413 GCATAAACATGAGCAGATAAGATAACA 58.223 33.333 0.00 0.00 0.00 2.41
1719 7131 4.735338 GCGAAGACAAAAACAGAAGGAAAG 59.265 41.667 0.00 0.00 0.00 2.62
1738 7150 1.177401 GGCTCCCATGTTTCCTTCAC 58.823 55.000 0.00 0.00 0.00 3.18
1757 7169 4.160329 TCACCTAATGTGTCTTCCTGTCT 58.840 43.478 0.00 0.00 45.61 3.41
1815 7227 1.414181 CACCTTGGATCCGTGCTAGAT 59.586 52.381 7.39 0.00 0.00 1.98
1851 7263 0.529378 CCTTCTGCAATTGAGCCCAC 59.471 55.000 10.34 0.00 0.00 4.61
1855 7267 2.262471 CTGCAATTGAGCCCACGAGC 62.262 60.000 10.34 0.00 0.00 5.03
1856 7268 3.056313 GCAATTGAGCCCACGAGCC 62.056 63.158 10.34 0.00 0.00 4.70
1892 7304 4.322650 GGGCAAAATGAATCAGTAAGGCAA 60.323 41.667 9.99 0.00 0.00 4.52
1901 7313 2.457598 TCAGTAAGGCAAGGATCGTCT 58.542 47.619 0.00 0.00 0.00 4.18
1970 7382 1.135402 CGAAACAATGGCAGCTAACCC 60.135 52.381 2.63 0.00 0.00 4.11
2023 7440 3.947196 TCATCGAAATTGAGAATGTGGGG 59.053 43.478 0.00 0.00 0.00 4.96
2025 7442 3.081061 TCGAAATTGAGAATGTGGGGTG 58.919 45.455 0.00 0.00 0.00 4.61
2031 7448 1.133513 TGAGAATGTGGGGTGCAGTTT 60.134 47.619 0.00 0.00 0.00 2.66
2119 7536 8.334263 TGAACTATGTGCTTCAACATTGATAA 57.666 30.769 5.91 0.00 41.09 1.75
2130 7547 5.547465 TCAACATTGATAACACGACCTTCT 58.453 37.500 0.00 0.00 31.01 2.85
2161 7580 3.831715 ACAACTAAAAAGCGATGCCTC 57.168 42.857 0.00 0.00 0.00 4.70
2183 7603 9.006839 GCCTCACATTAATCTCAATGATAATGA 57.993 33.333 17.17 0.00 38.01 2.57
2206 7626 4.957954 ACTCCATTACTACCACGGTTATCA 59.042 41.667 0.00 0.00 0.00 2.15
2210 7630 5.049680 CCATTACTACCACGGTTATCATTGC 60.050 44.000 0.00 0.00 0.00 3.56
2211 7631 3.620427 ACTACCACGGTTATCATTGCA 57.380 42.857 0.00 0.00 0.00 4.08
2279 7700 5.338381 GGTGAAGGTTGTGATCCTCTGATAA 60.338 44.000 0.00 0.00 33.76 1.75
2312 7733 1.378911 TGCATGTGATGGCCTCCAC 60.379 57.895 17.51 17.51 35.80 4.02
2313 7734 2.123428 GCATGTGATGGCCTCCACC 61.123 63.158 20.24 6.42 35.80 4.61
2331 8355 0.256752 CCACATGGCCTCCAAGATCA 59.743 55.000 3.32 0.00 36.95 2.92
2357 8444 5.201243 GGATCATACCTTTAACCAAAGCCT 58.799 41.667 0.00 0.00 39.95 4.58
2390 8495 3.760580 AGGTTTTGTCTCTGTCTCTGG 57.239 47.619 0.00 0.00 0.00 3.86
2399 8504 2.523168 TGTCTCTGGACACGGCCA 60.523 61.111 2.24 0.00 46.19 5.36
2478 8583 1.411977 CAATGGTGGTGCTTTTGGTCA 59.588 47.619 0.00 0.00 0.00 4.02
2486 8591 3.957497 TGGTGCTTTTGGTCACTAATGTT 59.043 39.130 0.00 0.00 33.91 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.334435 CGATCAATACATCGTGAAGCATT 57.666 39.130 0.00 0.00 40.72 3.56
1 2 4.979564 CGATCAATACATCGTGAAGCAT 57.020 40.909 0.00 0.00 40.72 3.79
10 11 3.482598 GCGCTATGCACGATCAATACATC 60.483 47.826 0.00 0.00 45.45 3.06
11 12 2.413112 GCGCTATGCACGATCAATACAT 59.587 45.455 0.00 0.00 45.45 2.29
12 13 1.792367 GCGCTATGCACGATCAATACA 59.208 47.619 0.00 0.00 45.45 2.29
13 14 2.493997 GCGCTATGCACGATCAATAC 57.506 50.000 0.00 0.00 45.45 1.89
24 25 3.702330 TCCATATATACGTGCGCTATGC 58.298 45.455 9.73 0.00 46.70 3.14
25 26 4.921547 ACTCCATATATACGTGCGCTATG 58.078 43.478 9.73 6.27 0.00 2.23
26 27 5.587443 TGTACTCCATATATACGTGCGCTAT 59.413 40.000 9.73 0.17 0.00 2.97
27 28 4.937015 TGTACTCCATATATACGTGCGCTA 59.063 41.667 9.73 0.00 0.00 4.26
28 29 3.754850 TGTACTCCATATATACGTGCGCT 59.245 43.478 9.73 0.00 0.00 5.92
29 30 4.087510 TGTACTCCATATATACGTGCGC 57.912 45.455 0.00 0.00 0.00 6.09
30 31 5.093457 CCTTGTACTCCATATATACGTGCG 58.907 45.833 0.00 0.00 0.00 5.34
31 32 5.862323 CACCTTGTACTCCATATATACGTGC 59.138 44.000 0.00 0.00 0.00 5.34
32 33 6.387465 CCACCTTGTACTCCATATATACGTG 58.613 44.000 0.00 0.00 0.00 4.49
33 34 5.479375 CCCACCTTGTACTCCATATATACGT 59.521 44.000 0.00 0.00 0.00 3.57
34 35 5.623824 GCCCACCTTGTACTCCATATATACG 60.624 48.000 0.00 0.00 0.00 3.06
35 36 5.338137 GGCCCACCTTGTACTCCATATATAC 60.338 48.000 0.00 0.00 0.00 1.47
36 37 4.781087 GGCCCACCTTGTACTCCATATATA 59.219 45.833 0.00 0.00 0.00 0.86
37 38 3.587506 GGCCCACCTTGTACTCCATATAT 59.412 47.826 0.00 0.00 0.00 0.86
38 39 2.976882 GGCCCACCTTGTACTCCATATA 59.023 50.000 0.00 0.00 0.00 0.86
39 40 1.774856 GGCCCACCTTGTACTCCATAT 59.225 52.381 0.00 0.00 0.00 1.78
40 41 1.209621 GGCCCACCTTGTACTCCATA 58.790 55.000 0.00 0.00 0.00 2.74
41 42 0.844661 TGGCCCACCTTGTACTCCAT 60.845 55.000 0.00 0.00 36.63 3.41
42 43 1.462432 TGGCCCACCTTGTACTCCA 60.462 57.895 0.00 0.00 36.63 3.86
43 44 1.002502 GTGGCCCACCTTGTACTCC 60.003 63.158 1.17 0.00 36.63 3.85
44 45 0.109723 TTGTGGCCCACCTTGTACTC 59.890 55.000 12.25 0.00 36.63 2.59
45 46 0.179001 GTTGTGGCCCACCTTGTACT 60.179 55.000 12.25 0.00 36.63 2.73
46 47 1.176619 GGTTGTGGCCCACCTTGTAC 61.177 60.000 12.25 1.80 36.63 2.90
47 48 1.151908 GGTTGTGGCCCACCTTGTA 59.848 57.895 12.25 0.00 36.63 2.41
48 49 2.123468 GGTTGTGGCCCACCTTGT 60.123 61.111 12.25 0.00 36.63 3.16
49 50 1.903404 GAGGTTGTGGCCCACCTTG 60.903 63.158 17.32 0.00 36.63 3.61
50 51 1.943730 TTGAGGTTGTGGCCCACCTT 61.944 55.000 17.32 0.00 36.63 3.50
51 52 2.391130 TTGAGGTTGTGGCCCACCT 61.391 57.895 16.46 16.46 36.63 4.00
52 53 2.197324 TTGAGGTTGTGGCCCACC 59.803 61.111 12.25 3.64 32.73 4.61
53 54 0.109723 TAGTTGAGGTTGTGGCCCAC 59.890 55.000 7.01 7.01 34.56 4.61
54 55 1.072266 ATAGTTGAGGTTGTGGCCCA 58.928 50.000 0.00 0.00 0.00 5.36
55 56 2.026636 TGTATAGTTGAGGTTGTGGCCC 60.027 50.000 0.00 0.00 0.00 5.80
56 57 3.343941 TGTATAGTTGAGGTTGTGGCC 57.656 47.619 0.00 0.00 0.00 5.36
57 58 5.001232 TCTTTGTATAGTTGAGGTTGTGGC 58.999 41.667 0.00 0.00 0.00 5.01
58 59 6.231211 AGTCTTTGTATAGTTGAGGTTGTGG 58.769 40.000 0.00 0.00 0.00 4.17
59 60 7.545965 CCTAGTCTTTGTATAGTTGAGGTTGTG 59.454 40.741 0.00 0.00 0.00 3.33
60 61 7.453752 TCCTAGTCTTTGTATAGTTGAGGTTGT 59.546 37.037 0.00 0.00 0.00 3.32
61 62 7.837863 TCCTAGTCTTTGTATAGTTGAGGTTG 58.162 38.462 0.00 0.00 0.00 3.77
62 63 7.124448 CCTCCTAGTCTTTGTATAGTTGAGGTT 59.876 40.741 0.00 0.00 31.94 3.50
63 64 6.608002 CCTCCTAGTCTTTGTATAGTTGAGGT 59.392 42.308 0.00 0.00 31.94 3.85
64 65 6.608002 ACCTCCTAGTCTTTGTATAGTTGAGG 59.392 42.308 0.00 0.00 40.19 3.86
65 66 7.416890 CCACCTCCTAGTCTTTGTATAGTTGAG 60.417 44.444 0.00 0.00 0.00 3.02
66 67 6.380274 CCACCTCCTAGTCTTTGTATAGTTGA 59.620 42.308 0.00 0.00 0.00 3.18
67 68 6.380274 TCCACCTCCTAGTCTTTGTATAGTTG 59.620 42.308 0.00 0.00 0.00 3.16
68 69 6.380560 GTCCACCTCCTAGTCTTTGTATAGTT 59.619 42.308 0.00 0.00 0.00 2.24
69 70 5.892686 GTCCACCTCCTAGTCTTTGTATAGT 59.107 44.000 0.00 0.00 0.00 2.12
70 71 5.302313 GGTCCACCTCCTAGTCTTTGTATAG 59.698 48.000 0.00 0.00 0.00 1.31
71 72 5.206587 GGTCCACCTCCTAGTCTTTGTATA 58.793 45.833 0.00 0.00 0.00 1.47
72 73 4.031611 GGTCCACCTCCTAGTCTTTGTAT 58.968 47.826 0.00 0.00 0.00 2.29
73 74 3.181415 TGGTCCACCTCCTAGTCTTTGTA 60.181 47.826 0.00 0.00 36.82 2.41
74 75 2.258109 GGTCCACCTCCTAGTCTTTGT 58.742 52.381 0.00 0.00 0.00 2.83
75 76 2.234908 CTGGTCCACCTCCTAGTCTTTG 59.765 54.545 0.00 0.00 36.82 2.77
76 77 2.541466 CTGGTCCACCTCCTAGTCTTT 58.459 52.381 0.00 0.00 36.82 2.52
77 78 1.273324 CCTGGTCCACCTCCTAGTCTT 60.273 57.143 0.00 0.00 36.82 3.01
78 79 0.336737 CCTGGTCCACCTCCTAGTCT 59.663 60.000 0.00 0.00 36.82 3.24
79 80 1.331399 GCCTGGTCCACCTCCTAGTC 61.331 65.000 0.00 0.00 36.82 2.59
80 81 1.306226 GCCTGGTCCACCTCCTAGT 60.306 63.158 0.00 0.00 36.82 2.57
81 82 0.261991 TAGCCTGGTCCACCTCCTAG 59.738 60.000 0.00 0.00 36.82 3.02
82 83 0.941963 ATAGCCTGGTCCACCTCCTA 59.058 55.000 0.00 0.00 36.82 2.94
83 84 0.941963 TATAGCCTGGTCCACCTCCT 59.058 55.000 0.00 0.00 36.82 3.69
84 85 1.049402 GTATAGCCTGGTCCACCTCC 58.951 60.000 0.00 0.00 36.82 4.30
85 86 1.789523 TGTATAGCCTGGTCCACCTC 58.210 55.000 0.00 0.00 36.82 3.85
86 87 2.263895 TTGTATAGCCTGGTCCACCT 57.736 50.000 0.00 0.00 36.82 4.00
87 88 4.910458 ATATTGTATAGCCTGGTCCACC 57.090 45.455 0.00 0.00 0.00 4.61
88 89 6.354794 TGTATATTGTATAGCCTGGTCCAC 57.645 41.667 0.00 0.00 0.00 4.02
89 90 6.576244 GCATGTATATTGTATAGCCTGGTCCA 60.576 42.308 0.00 0.00 0.00 4.02
90 91 5.817816 GCATGTATATTGTATAGCCTGGTCC 59.182 44.000 0.00 0.00 0.00 4.46
91 92 6.313905 GTGCATGTATATTGTATAGCCTGGTC 59.686 42.308 0.00 0.00 0.00 4.02
92 93 6.173339 GTGCATGTATATTGTATAGCCTGGT 58.827 40.000 0.00 0.00 0.00 4.00
93 94 6.172630 TGTGCATGTATATTGTATAGCCTGG 58.827 40.000 0.00 0.00 0.00 4.45
94 95 7.671495 TTGTGCATGTATATTGTATAGCCTG 57.329 36.000 0.00 0.00 0.00 4.85
95 96 8.868522 ATTTGTGCATGTATATTGTATAGCCT 57.131 30.769 0.00 0.00 0.00 4.58
96 97 8.729756 TGATTTGTGCATGTATATTGTATAGCC 58.270 33.333 0.00 0.00 0.00 3.93
108 109 9.949174 GTGTTGAATATATGATTTGTGCATGTA 57.051 29.630 0.00 0.00 0.00 2.29
109 110 8.468399 TGTGTTGAATATATGATTTGTGCATGT 58.532 29.630 0.00 0.00 0.00 3.21
110 111 8.859517 TGTGTTGAATATATGATTTGTGCATG 57.140 30.769 0.00 0.00 0.00 4.06
121 122 9.269415 CGTTGCATGATATGTGTTGAATATATG 57.731 33.333 0.00 0.00 0.00 1.78
122 123 9.002600 ACGTTGCATGATATGTGTTGAATATAT 57.997 29.630 0.00 0.00 0.00 0.86
123 124 8.281893 CACGTTGCATGATATGTGTTGAATATA 58.718 33.333 0.00 0.00 0.00 0.86
124 125 7.134163 CACGTTGCATGATATGTGTTGAATAT 58.866 34.615 0.00 0.00 0.00 1.28
125 126 6.093357 ACACGTTGCATGATATGTGTTGAATA 59.907 34.615 15.65 0.00 40.58 1.75
126 127 5.106197 ACACGTTGCATGATATGTGTTGAAT 60.106 36.000 15.65 0.00 40.58 2.57
127 128 4.215185 ACACGTTGCATGATATGTGTTGAA 59.785 37.500 15.65 0.00 40.58 2.69
128 129 3.750652 ACACGTTGCATGATATGTGTTGA 59.249 39.130 15.65 0.00 40.58 3.18
129 130 3.847457 CACACGTTGCATGATATGTGTTG 59.153 43.478 17.71 11.99 41.29 3.33
130 131 3.119884 CCACACGTTGCATGATATGTGTT 60.120 43.478 17.71 6.16 41.29 3.32
131 132 2.419673 CCACACGTTGCATGATATGTGT 59.580 45.455 15.65 15.65 43.34 3.72
132 133 2.792196 GCCACACGTTGCATGATATGTG 60.792 50.000 14.66 14.66 37.72 3.21
133 134 1.401552 GCCACACGTTGCATGATATGT 59.598 47.619 0.00 0.00 0.00 2.29
134 135 1.401199 TGCCACACGTTGCATGATATG 59.599 47.619 0.00 0.00 31.31 1.78
135 136 1.748950 TGCCACACGTTGCATGATAT 58.251 45.000 0.00 0.00 31.31 1.63
136 137 1.528129 TTGCCACACGTTGCATGATA 58.472 45.000 0.00 0.00 37.33 2.15
137 138 0.672889 TTTGCCACACGTTGCATGAT 59.327 45.000 0.00 0.00 37.33 2.45
138 139 0.457443 TTTTGCCACACGTTGCATGA 59.543 45.000 0.00 0.00 37.33 3.07
139 140 1.284657 TTTTTGCCACACGTTGCATG 58.715 45.000 5.14 0.00 37.33 4.06
140 141 3.748863 TTTTTGCCACACGTTGCAT 57.251 42.105 5.14 0.00 37.33 3.96
155 156 9.378551 GATCACTTCCTTTTTACCTTTGTTTTT 57.621 29.630 0.00 0.00 0.00 1.94
156 157 8.536175 TGATCACTTCCTTTTTACCTTTGTTTT 58.464 29.630 0.00 0.00 0.00 2.43
157 158 8.073467 TGATCACTTCCTTTTTACCTTTGTTT 57.927 30.769 0.00 0.00 0.00 2.83
158 159 7.559897 TCTGATCACTTCCTTTTTACCTTTGTT 59.440 33.333 0.00 0.00 0.00 2.83
159 160 7.060421 TCTGATCACTTCCTTTTTACCTTTGT 58.940 34.615 0.00 0.00 0.00 2.83
160 161 7.510549 TCTGATCACTTCCTTTTTACCTTTG 57.489 36.000 0.00 0.00 0.00 2.77
161 162 6.207614 GCTCTGATCACTTCCTTTTTACCTTT 59.792 38.462 0.00 0.00 0.00 3.11
162 163 5.707764 GCTCTGATCACTTCCTTTTTACCTT 59.292 40.000 0.00 0.00 0.00 3.50
163 164 5.221925 TGCTCTGATCACTTCCTTTTTACCT 60.222 40.000 0.00 0.00 0.00 3.08
164 165 5.003804 TGCTCTGATCACTTCCTTTTTACC 58.996 41.667 0.00 0.00 0.00 2.85
165 166 5.703130 AGTGCTCTGATCACTTCCTTTTTAC 59.297 40.000 8.27 0.00 41.61 2.01
166 167 5.869579 AGTGCTCTGATCACTTCCTTTTTA 58.130 37.500 8.27 0.00 41.61 1.52
167 168 4.723309 AGTGCTCTGATCACTTCCTTTTT 58.277 39.130 8.27 0.00 41.61 1.94
168 169 4.363991 AGTGCTCTGATCACTTCCTTTT 57.636 40.909 8.27 0.00 41.61 2.27
169 170 5.486526 CTTAGTGCTCTGATCACTTCCTTT 58.513 41.667 18.09 0.00 41.61 3.11
170 171 4.622695 GCTTAGTGCTCTGATCACTTCCTT 60.623 45.833 18.09 0.00 41.61 3.36
171 172 3.118811 GCTTAGTGCTCTGATCACTTCCT 60.119 47.826 18.09 0.00 41.61 3.36
172 173 3.194062 GCTTAGTGCTCTGATCACTTCC 58.806 50.000 18.09 5.17 41.61 3.46
173 174 3.854666 TGCTTAGTGCTCTGATCACTTC 58.145 45.455 18.09 9.47 41.61 3.01
198 199 4.442753 GGGAAATTGTGGAAAGCACTGAAA 60.443 41.667 0.00 0.00 0.00 2.69
208 209 2.614134 ATTCCCGGGAAATTGTGGAA 57.386 45.000 38.52 14.53 39.28 3.53
209 210 2.614134 AATTCCCGGGAAATTGTGGA 57.386 45.000 38.52 15.36 37.69 4.02
244 245 2.052157 GACGCCATAAGACGCACTATC 58.948 52.381 0.00 0.00 0.00 2.08
278 279 9.793245 CTAACGCAAAGTATATATGCAACTAAC 57.207 33.333 3.52 0.00 40.04 2.34
280 281 9.537192 AACTAACGCAAAGTATATATGCAACTA 57.463 29.630 3.52 0.00 40.04 2.24
294 304 9.559958 AGATTTCAATGATTAACTAACGCAAAG 57.440 29.630 0.00 0.00 0.00 2.77
328 384 4.380531 CCCGAGCAACACTGATTATGTAT 58.619 43.478 0.00 0.00 0.00 2.29
345 401 0.249073 CGGTAGATGTGAAGCCCGAG 60.249 60.000 0.00 0.00 37.66 4.63
349 405 0.175760 TCTGCGGTAGATGTGAAGCC 59.824 55.000 0.00 0.00 0.00 4.35
351 407 3.238108 AGTTCTGCGGTAGATGTGAAG 57.762 47.619 0.00 0.00 34.80 3.02
361 417 0.104304 CGCCCTATTAGTTCTGCGGT 59.896 55.000 0.00 0.00 38.46 5.68
371 427 1.193323 TTTGTCCGGACGCCCTATTA 58.807 50.000 28.70 6.50 0.00 0.98
374 430 1.193323 TAATTTGTCCGGACGCCCTA 58.807 50.000 28.70 14.91 0.00 3.53
377 433 1.129811 CAGTTAATTTGTCCGGACGCC 59.870 52.381 28.70 6.87 0.00 5.68
380 436 5.427036 TTTGACAGTTAATTTGTCCGGAC 57.573 39.130 28.17 28.17 43.32 4.79
383 439 7.647715 AGACATTTTTGACAGTTAATTTGTCCG 59.352 33.333 16.04 5.23 43.32 4.79
384 440 8.755018 CAGACATTTTTGACAGTTAATTTGTCC 58.245 33.333 16.04 3.59 43.32 4.02
396 452 5.362143 TGGATTTGGACAGACATTTTTGACA 59.638 36.000 0.00 0.00 0.00 3.58
442 498 8.463607 GCAAGACAGACTATAGACTAGAAAAGT 58.536 37.037 6.78 0.00 42.80 2.66
443 499 8.682710 AGCAAGACAGACTATAGACTAGAAAAG 58.317 37.037 6.78 0.00 0.00 2.27
444 500 8.582657 AGCAAGACAGACTATAGACTAGAAAA 57.417 34.615 6.78 0.00 0.00 2.29
455 534 5.967088 ACGTGAATTAGCAAGACAGACTAT 58.033 37.500 0.00 0.00 0.00 2.12
563 646 8.122472 TCTGTTTCTCTTTTCTGAAGGTTTTT 57.878 30.769 0.00 0.00 0.00 1.94
564 647 7.394641 ACTCTGTTTCTCTTTTCTGAAGGTTTT 59.605 33.333 0.00 0.00 0.00 2.43
589 676 3.432252 CCGTGTTCCTCTTGACATGTTAC 59.568 47.826 0.00 0.00 32.26 2.50
604 693 1.063174 GATTGCTGCATCTCCGTGTTC 59.937 52.381 1.84 0.00 0.00 3.18
639 732 5.263185 CGTCTGTTATTTATTCCTTTGGCG 58.737 41.667 0.00 0.00 0.00 5.69
682 776 2.517450 CCGCGTTTCATCTCTCGCC 61.517 63.158 4.92 0.00 44.73 5.54
764 1129 1.982660 GCTTAATCTAGCCCCAACCC 58.017 55.000 0.00 0.00 35.06 4.11
773 1138 5.708230 AGAGAGTATGGACGGCTTAATCTAG 59.292 44.000 2.50 0.00 0.00 2.43
775 1377 4.475345 AGAGAGTATGGACGGCTTAATCT 58.525 43.478 2.16 2.16 0.00 2.40
790 1392 4.205587 GGGGAATGTACTTCGAGAGAGTA 58.794 47.826 0.00 0.00 43.69 2.59
797 1399 1.518774 GCCGGGGAATGTACTTCGA 59.481 57.895 2.18 0.00 34.45 3.71
798 1400 1.881252 CGCCGGGGAATGTACTTCG 60.881 63.158 14.46 0.00 34.45 3.79
969 1621 3.119602 TCTGCTACAGACAATACCGTGAC 60.120 47.826 0.00 0.00 35.39 3.67
972 1624 2.427453 CCTCTGCTACAGACAATACCGT 59.573 50.000 0.00 0.00 35.39 4.83
979 1631 1.273606 GTTGCTCCTCTGCTACAGACA 59.726 52.381 0.00 0.00 35.39 3.41
980 1632 1.273606 TGTTGCTCCTCTGCTACAGAC 59.726 52.381 0.00 0.00 41.93 3.51
1046 6396 2.235650 CAATCAGGAGAGGAGAGCAACA 59.764 50.000 0.00 0.00 0.00 3.33
1081 6435 1.632409 TGAAAGCAGGAGGAGAGCATT 59.368 47.619 0.00 0.00 0.00 3.56
1126 6482 0.109781 GGCATTTGTCGCACGTCATT 60.110 50.000 0.00 0.00 0.00 2.57
1168 6524 3.678717 CTCACCGTGTACCGAGGCG 62.679 68.421 0.00 0.00 39.56 5.52
1178 6534 0.304705 GTGAACTGCAACTCACCGTG 59.695 55.000 14.25 0.00 36.72 4.94
1201 6558 2.118403 ATCAAGGATATGACCCCGGT 57.882 50.000 0.00 0.00 30.82 5.28
1211 6568 7.453439 TGGAAACCTGATCGTATATCAAGGATA 59.547 37.037 0.00 0.00 0.00 2.59
1246 6603 4.894784 TCCACTCCTACACAATCAAGTTC 58.105 43.478 0.00 0.00 0.00 3.01
1363 6724 3.834799 GAGGTCCGCGTTCCCGAT 61.835 66.667 4.92 0.00 35.63 4.18
1448 6809 2.897350 GATACCACTGCTGCGGGC 60.897 66.667 13.87 0.00 42.22 6.13
1449 6810 2.203070 GGATACCACTGCTGCGGG 60.203 66.667 13.87 8.29 0.00 6.13
1492 6859 1.497161 GGGTAGCAGTGGGAGTATGT 58.503 55.000 0.00 0.00 0.00 2.29
1689 7098 5.985781 TCTGTTTTTGTCTTCGCTGTTATC 58.014 37.500 0.00 0.00 0.00 1.75
1691 7100 5.220777 CCTTCTGTTTTTGTCTTCGCTGTTA 60.221 40.000 0.00 0.00 0.00 2.41
1692 7101 4.438744 CCTTCTGTTTTTGTCTTCGCTGTT 60.439 41.667 0.00 0.00 0.00 3.16
1693 7102 3.065371 CCTTCTGTTTTTGTCTTCGCTGT 59.935 43.478 0.00 0.00 0.00 4.40
1694 7103 3.312421 TCCTTCTGTTTTTGTCTTCGCTG 59.688 43.478 0.00 0.00 0.00 5.18
1695 7104 3.541632 TCCTTCTGTTTTTGTCTTCGCT 58.458 40.909 0.00 0.00 0.00 4.93
1719 7131 1.177401 GTGAAGGAAACATGGGAGCC 58.823 55.000 0.00 0.00 0.00 4.70
1738 7150 6.227298 ACATAGACAGGAAGACACATTAGG 57.773 41.667 0.00 0.00 0.00 2.69
1757 7169 3.306294 CGCAGAGCTAATGGATGGACATA 60.306 47.826 0.00 0.00 0.00 2.29
1815 7227 6.605594 TGCAGAAGGAAAAGGAAAAGAAGTTA 59.394 34.615 0.00 0.00 0.00 2.24
1909 7321 2.582202 AATTGCGTGCTTCCGATGCG 62.582 55.000 2.15 0.00 0.00 4.73
1933 7345 2.710096 TCGACAATCTGGAAATCCCC 57.290 50.000 0.00 0.00 34.29 4.81
1937 7349 5.713025 CCATTGTTTCGACAATCTGGAAAT 58.287 37.500 6.19 0.00 38.16 2.17
1982 7397 5.357032 CGATGAATAAAGCTTGGTTTACCCT 59.643 40.000 0.00 0.00 34.29 4.34
2023 7440 1.098712 TCCCACGACCAAAACTGCAC 61.099 55.000 0.00 0.00 0.00 4.57
2025 7442 0.958822 AATCCCACGACCAAAACTGC 59.041 50.000 0.00 0.00 0.00 4.40
2031 7448 0.474614 TTGTCCAATCCCACGACCAA 59.525 50.000 0.00 0.00 0.00 3.67
2091 7508 3.743521 TGTTGAAGCACATAGTTCAGCT 58.256 40.909 0.00 0.00 35.56 4.24
2095 7512 8.236586 TGTTATCAATGTTGAAGCACATAGTTC 58.763 33.333 0.00 0.00 41.13 3.01
2183 7603 4.957954 TGATAACCGTGGTAGTAATGGAGT 59.042 41.667 0.00 0.00 0.00 3.85
2206 7626 4.458397 CAGGTCATAGGTGAATCTGCAAT 58.542 43.478 0.00 0.00 35.80 3.56
2210 7630 3.834489 AGCAGGTCATAGGTGAATCTG 57.166 47.619 0.00 0.00 39.19 2.90
2211 7631 3.118112 CCAAGCAGGTCATAGGTGAATCT 60.118 47.826 0.00 0.00 35.80 2.40
2266 7687 3.784178 CCCTAGCCTTATCAGAGGATCA 58.216 50.000 0.00 0.00 39.25 2.92
2291 7712 1.225426 GAGGCCATCACATGCAGGA 59.775 57.895 4.84 0.00 0.00 3.86
2312 7733 0.256752 TGATCTTGGAGGCCATGTGG 59.743 55.000 5.01 0.00 31.53 4.17
2313 7734 2.133281 TTGATCTTGGAGGCCATGTG 57.867 50.000 5.01 0.00 31.53 3.21
2315 7736 1.961394 CCATTGATCTTGGAGGCCATG 59.039 52.381 5.01 0.00 36.26 3.66
2331 8355 6.098266 GGCTTTGGTTAAAGGTATGATCCATT 59.902 38.462 0.00 0.00 42.81 3.16
2362 8449 2.106511 CAGAGACAAAACCTTCCAGGGA 59.893 50.000 0.00 0.00 40.58 4.20
2366 8453 3.711704 AGAGACAGAGACAAAACCTTCCA 59.288 43.478 0.00 0.00 0.00 3.53
2390 8495 1.221414 GATTCAGCTATGGCCGTGTC 58.779 55.000 8.05 0.00 39.73 3.67
2399 8504 3.153919 GAGGAGTCGAGGATTCAGCTAT 58.846 50.000 0.00 0.00 0.00 2.97
2408 8513 1.749638 GCCGAAGAGGAGTCGAGGA 60.750 63.158 0.00 0.00 45.00 3.71
2478 8583 7.670605 TCTATACTAGTGGGCAAACATTAGT 57.329 36.000 5.39 12.58 43.49 2.24
2486 8591 3.324846 CAGCCATCTATACTAGTGGGCAA 59.675 47.826 5.39 0.00 43.50 4.52


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

AutoCloner maintained by Alex Coulton.