Multiple sequence alignment - TraesCS6A01G148600

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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 TraesCS6A01G148600 chr6A 100.000 3299 0 0 1 3299 129932049 129935347 0.000000e+00 6093.0
1 TraesCS6A01G148600 chr6A 85.542 83 7 4 342 422 428672711 428672790 7.590000e-12 82.4
2 TraesCS6A01G148600 chr6B 90.087 3208 166 65 139 3299 193890646 193893748 0.000000e+00 4023.0
3 TraesCS6A01G148600 chr6D 94.618 1505 48 20 1808 3299 106697951 106699435 0.000000e+00 2300.0
4 TraesCS6A01G148600 chr6D 93.313 987 41 13 841 1810 106696948 106697926 0.000000e+00 1434.0
5 TraesCS6A01G148600 chr6D 89.669 242 11 7 549 788 106696703 106696932 2.490000e-76 296.0
6 TraesCS6A01G148600 chr6D 97.674 86 2 0 1 86 28943026 28943111 7.380000e-32 148.0
7 TraesCS6A01G148600 chr6D 95.402 87 4 0 1 87 393926395 393926481 4.440000e-29 139.0
8 TraesCS6A01G148600 chr2A 96.552 87 3 0 1 87 482310624 482310710 9.540000e-31 145.0
9 TraesCS6A01G148600 chr2A 96.471 85 3 0 1 85 133674346 133674430 1.230000e-29 141.0
10 TraesCS6A01G148600 chr7A 96.512 86 3 0 1 86 529439689 529439604 3.430000e-30 143.0
11 TraesCS6A01G148600 chr7A 91.489 47 4 0 1968 2014 692054979 692054933 7.640000e-07 65.8
12 TraesCS6A01G148600 chr4B 96.512 86 3 0 1 86 426774421 426774336 3.430000e-30 143.0
13 TraesCS6A01G148600 chr4A 95.455 88 4 0 1 88 295336917 295336830 1.230000e-29 141.0
14 TraesCS6A01G148600 chr4A 90.385 52 4 1 1399 1450 639965840 639965890 2.120000e-07 67.6
15 TraesCS6A01G148600 chr2B 96.471 85 3 0 1 85 64186848 64186764 1.230000e-29 141.0
16 TraesCS6A01G148600 chr5D 94.118 85 5 0 1 85 437350742 437350826 2.670000e-26 130.0
17 TraesCS6A01G148600 chrUn 90.385 52 4 1 1399 1450 262578062 262578112 2.120000e-07 67.6
18 TraesCS6A01G148600 chrUn 90.385 52 4 1 1399 1450 262587678 262587728 2.120000e-07 67.6
19 TraesCS6A01G148600 chrUn 90.385 52 4 1 1399 1450 271996380 271996430 2.120000e-07 67.6
20 TraesCS6A01G148600 chr5A 86.885 61 7 1 1390 1450 42630236 42630295 2.120000e-07 67.6
21 TraesCS6A01G148600 chr7B 97.143 35 1 0 1968 2002 679682700 679682666 3.560000e-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 TraesCS6A01G148600 chr6A 129932049 129935347 3298 False 6093.000000 6093 100.000000 1 3299 1 chr6A.!!$F1 3298
1 TraesCS6A01G148600 chr6B 193890646 193893748 3102 False 4023.000000 4023 90.087000 139 3299 1 chr6B.!!$F1 3160
2 TraesCS6A01G148600 chr6D 106696703 106699435 2732 False 1343.333333 2300 92.533333 549 3299 3 chr6D.!!$F3 2750

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
932 965 0.106519 AAAGGGAATCATCTGCCGGG 60.107 55.0 2.18 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2703 2788 0.031857 TGTTGCAAGGCACCATTTCG 59.968 50.0 0.0 0.0 38.71 3.46 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
44 45 8.521170 AGTAACTTAGACTAGTGTCATATGCA 57.479 34.615 0.00 0.00 45.20 3.96
45 46 9.137459 AGTAACTTAGACTAGTGTCATATGCAT 57.863 33.333 3.79 3.79 45.20 3.96
46 47 9.186323 GTAACTTAGACTAGTGTCATATGCATG 57.814 37.037 10.16 0.00 45.20 4.06
47 48 7.588497 ACTTAGACTAGTGTCATATGCATGA 57.412 36.000 10.16 0.00 45.20 3.07
61 62 8.962884 TCATATGCATGACATTAGTGTAAGTT 57.037 30.769 10.16 0.00 40.38 2.66
65 66 7.827819 TGCATGACATTAGTGTAAGTTACTC 57.172 36.000 14.00 10.39 39.09 2.59
66 67 6.816640 TGCATGACATTAGTGTAAGTTACTCC 59.183 38.462 14.00 5.11 39.09 3.85
67 68 6.258068 GCATGACATTAGTGTAAGTTACTCCC 59.742 42.308 14.00 2.83 39.09 4.30
68 69 6.290294 TGACATTAGTGTAAGTTACTCCCC 57.710 41.667 14.00 0.58 39.09 4.81
69 70 5.781306 TGACATTAGTGTAAGTTACTCCCCA 59.219 40.000 14.00 0.00 39.09 4.96
70 71 6.046290 ACATTAGTGTAAGTTACTCCCCAC 57.954 41.667 14.00 3.86 36.63 4.61
71 72 5.783875 ACATTAGTGTAAGTTACTCCCCACT 59.216 40.000 14.00 10.58 36.63 4.00
72 73 6.955851 ACATTAGTGTAAGTTACTCCCCACTA 59.044 38.462 14.00 9.69 36.63 2.74
73 74 7.622479 ACATTAGTGTAAGTTACTCCCCACTAT 59.378 37.037 14.00 7.06 36.63 2.12
74 75 5.934402 AGTGTAAGTTACTCCCCACTATG 57.066 43.478 14.00 0.00 31.80 2.23
75 76 5.586877 AGTGTAAGTTACTCCCCACTATGA 58.413 41.667 14.00 0.00 31.80 2.15
76 77 5.421374 AGTGTAAGTTACTCCCCACTATGAC 59.579 44.000 14.00 0.00 31.80 3.06
77 78 4.713321 TGTAAGTTACTCCCCACTATGACC 59.287 45.833 14.00 0.00 0.00 4.02
78 79 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
79 80 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
80 81 3.105283 GTTACTCCCCACTATGACCAGT 58.895 50.000 0.00 0.00 0.00 4.00
81 82 1.867363 ACTCCCCACTATGACCAGTC 58.133 55.000 0.00 0.00 0.00 3.51
82 83 1.362932 ACTCCCCACTATGACCAGTCT 59.637 52.381 0.00 0.00 0.00 3.24
83 84 2.585900 ACTCCCCACTATGACCAGTCTA 59.414 50.000 0.00 0.00 0.00 2.59
84 85 3.012502 ACTCCCCACTATGACCAGTCTAA 59.987 47.826 0.00 0.00 0.00 2.10
85 86 3.639094 CTCCCCACTATGACCAGTCTAAG 59.361 52.174 0.00 0.00 0.00 2.18
86 87 3.271225 TCCCCACTATGACCAGTCTAAGA 59.729 47.826 0.00 0.00 0.00 2.10
87 88 3.385111 CCCCACTATGACCAGTCTAAGAC 59.615 52.174 0.00 0.00 0.00 3.01
88 89 4.023980 CCCACTATGACCAGTCTAAGACA 58.976 47.826 0.00 0.00 34.60 3.41
89 90 4.466370 CCCACTATGACCAGTCTAAGACAA 59.534 45.833 0.00 0.00 34.60 3.18
90 91 5.129485 CCCACTATGACCAGTCTAAGACAAT 59.871 44.000 0.00 0.00 34.60 2.71
91 92 6.045318 CCACTATGACCAGTCTAAGACAATG 58.955 44.000 0.00 0.00 34.60 2.82
92 93 5.521735 CACTATGACCAGTCTAAGACAATGC 59.478 44.000 0.00 0.00 34.60 3.56
93 94 4.558226 ATGACCAGTCTAAGACAATGCA 57.442 40.909 0.00 0.00 34.60 3.96
94 95 4.350368 TGACCAGTCTAAGACAATGCAA 57.650 40.909 0.00 0.00 34.60 4.08
95 96 4.910195 TGACCAGTCTAAGACAATGCAAT 58.090 39.130 0.00 0.00 34.60 3.56
96 97 4.696877 TGACCAGTCTAAGACAATGCAATG 59.303 41.667 0.00 0.00 34.60 2.82
97 98 4.910195 ACCAGTCTAAGACAATGCAATGA 58.090 39.130 9.20 0.00 34.60 2.57
98 99 5.316167 ACCAGTCTAAGACAATGCAATGAA 58.684 37.500 9.20 0.00 34.60 2.57
99 100 5.769662 ACCAGTCTAAGACAATGCAATGAAA 59.230 36.000 9.20 0.00 34.60 2.69
100 101 6.088824 CCAGTCTAAGACAATGCAATGAAAC 58.911 40.000 9.20 0.00 34.60 2.78
101 102 6.294120 CCAGTCTAAGACAATGCAATGAAACA 60.294 38.462 9.20 0.00 34.60 2.83
102 103 7.140705 CAGTCTAAGACAATGCAATGAAACAA 58.859 34.615 9.20 0.00 34.60 2.83
103 104 7.811236 CAGTCTAAGACAATGCAATGAAACAAT 59.189 33.333 9.20 0.00 34.60 2.71
104 105 7.811236 AGTCTAAGACAATGCAATGAAACAATG 59.189 33.333 9.20 0.00 34.60 2.82
105 106 7.062605 GTCTAAGACAATGCAATGAAACAATGG 59.937 37.037 9.20 0.00 32.09 3.16
106 107 5.471556 AGACAATGCAATGAAACAATGGA 57.528 34.783 9.20 0.00 0.00 3.41
107 108 5.856156 AGACAATGCAATGAAACAATGGAA 58.144 33.333 9.20 0.00 0.00 3.53
108 109 6.289834 AGACAATGCAATGAAACAATGGAAA 58.710 32.000 9.20 0.00 0.00 3.13
109 110 6.938030 AGACAATGCAATGAAACAATGGAAAT 59.062 30.769 9.20 0.00 0.00 2.17
110 111 7.118680 AGACAATGCAATGAAACAATGGAAATC 59.881 33.333 9.20 0.00 0.00 2.17
111 112 6.938030 ACAATGCAATGAAACAATGGAAATCT 59.062 30.769 9.20 0.00 0.00 2.40
112 113 6.978343 ATGCAATGAAACAATGGAAATCTG 57.022 33.333 0.00 0.00 0.00 2.90
113 114 4.691685 TGCAATGAAACAATGGAAATCTGC 59.308 37.500 0.00 0.00 0.00 4.26
114 115 4.933400 GCAATGAAACAATGGAAATCTGCT 59.067 37.500 0.00 0.00 0.00 4.24
115 116 5.410439 GCAATGAAACAATGGAAATCTGCTT 59.590 36.000 0.00 0.00 0.00 3.91
116 117 6.591062 GCAATGAAACAATGGAAATCTGCTTA 59.409 34.615 0.00 0.00 0.00 3.09
117 118 7.118101 GCAATGAAACAATGGAAATCTGCTTAA 59.882 33.333 0.00 0.00 0.00 1.85
118 119 8.653338 CAATGAAACAATGGAAATCTGCTTAAG 58.347 33.333 0.00 0.00 0.00 1.85
119 120 7.523293 TGAAACAATGGAAATCTGCTTAAGA 57.477 32.000 6.67 0.00 39.94 2.10
120 121 7.370383 TGAAACAATGGAAATCTGCTTAAGAC 58.630 34.615 6.67 0.00 37.88 3.01
121 122 6.899393 AACAATGGAAATCTGCTTAAGACA 57.101 33.333 6.67 3.07 37.88 3.41
122 123 6.899393 ACAATGGAAATCTGCTTAAGACAA 57.101 33.333 6.67 0.00 37.88 3.18
123 124 7.288810 ACAATGGAAATCTGCTTAAGACAAA 57.711 32.000 6.67 0.00 37.88 2.83
124 125 7.373493 ACAATGGAAATCTGCTTAAGACAAAG 58.627 34.615 6.67 0.00 37.88 2.77
125 126 5.964958 TGGAAATCTGCTTAAGACAAAGG 57.035 39.130 6.67 0.00 37.88 3.11
126 127 5.630121 TGGAAATCTGCTTAAGACAAAGGA 58.370 37.500 6.67 0.00 37.88 3.36
127 128 6.068010 TGGAAATCTGCTTAAGACAAAGGAA 58.932 36.000 6.67 0.00 37.88 3.36
128 129 6.549364 TGGAAATCTGCTTAAGACAAAGGAAA 59.451 34.615 6.67 0.00 37.88 3.13
129 130 7.087007 GGAAATCTGCTTAAGACAAAGGAAAG 58.913 38.462 6.67 0.00 37.88 2.62
130 131 6.581171 AATCTGCTTAAGACAAAGGAAAGG 57.419 37.500 6.67 0.00 37.88 3.11
131 132 5.304686 TCTGCTTAAGACAAAGGAAAGGA 57.695 39.130 6.67 0.00 0.00 3.36
132 133 5.690865 TCTGCTTAAGACAAAGGAAAGGAA 58.309 37.500 6.67 0.00 0.00 3.36
133 134 6.126409 TCTGCTTAAGACAAAGGAAAGGAAA 58.874 36.000 6.67 0.00 0.00 3.13
134 135 6.777580 TCTGCTTAAGACAAAGGAAAGGAAAT 59.222 34.615 6.67 0.00 0.00 2.17
135 136 6.981722 TGCTTAAGACAAAGGAAAGGAAATC 58.018 36.000 6.67 0.00 0.00 2.17
136 137 6.777580 TGCTTAAGACAAAGGAAAGGAAATCT 59.222 34.615 6.67 0.00 0.00 2.40
137 138 7.087007 GCTTAAGACAAAGGAAAGGAAATCTG 58.913 38.462 6.67 0.00 0.00 2.90
142 143 2.907458 AGGAAAGGAAATCTGTGGGG 57.093 50.000 0.00 0.00 0.00 4.96
157 158 0.913934 TGGGGTCATGCTTAGCTGGA 60.914 55.000 5.60 0.00 0.00 3.86
159 160 0.811616 GGGTCATGCTTAGCTGGACG 60.812 60.000 17.46 0.00 34.80 4.79
171 172 2.851195 AGCTGGACGCCCATAAATTAG 58.149 47.619 0.00 0.00 42.59 1.73
172 173 2.172717 AGCTGGACGCCCATAAATTAGT 59.827 45.455 0.00 0.00 42.59 2.24
180 181 3.003689 CGCCCATAAATTAGTCAAGCAGG 59.996 47.826 0.00 0.00 0.00 4.85
183 184 5.239525 GCCCATAAATTAGTCAAGCAGGTAG 59.760 44.000 0.00 0.00 0.00 3.18
287 289 8.376942 CAAACCATAATTTACCGTTTTACATGC 58.623 33.333 0.00 0.00 0.00 4.06
289 291 7.030768 ACCATAATTTACCGTTTTACATGCAC 58.969 34.615 0.00 0.00 0.00 4.57
298 300 4.201910 CCGTTTTACATGCACCCTGAATAG 60.202 45.833 0.00 0.00 0.00 1.73
328 330 4.434520 TCAACGTTGTCACAACATAGTCA 58.565 39.130 26.47 0.26 34.73 3.41
330 332 4.054780 ACGTTGTCACAACATAGTCAGT 57.945 40.909 20.58 5.46 34.73 3.41
331 333 3.802139 ACGTTGTCACAACATAGTCAGTG 59.198 43.478 20.58 3.41 34.73 3.66
332 334 3.362986 CGTTGTCACAACATAGTCAGTGC 60.363 47.826 20.58 0.00 34.73 4.40
337 339 1.078709 CAACATAGTCAGTGCCACCG 58.921 55.000 0.00 0.00 0.00 4.94
339 341 1.079197 CATAGTCAGTGCCACCGCA 60.079 57.895 0.00 0.00 44.78 5.69
351 353 3.706373 ACCGCAGCCGAGGACAAT 61.706 61.111 0.00 0.00 35.72 2.71
375 377 1.069978 TCACACGCCATCACTCTTCAA 59.930 47.619 0.00 0.00 0.00 2.69
382 384 4.943705 ACGCCATCACTCTTCAAATGTTAT 59.056 37.500 0.00 0.00 0.00 1.89
403 405 7.707464 TGTTATTTTCATTCCATAGCAATGCAG 59.293 33.333 8.35 0.00 32.17 4.41
415 420 1.193323 CAATGCAGGGGTATTTGGCA 58.807 50.000 0.00 0.00 39.03 4.92
423 428 4.398319 CAGGGGTATTTGGCATAGTTAGG 58.602 47.826 0.00 0.00 0.00 2.69
424 429 4.104102 CAGGGGTATTTGGCATAGTTAGGA 59.896 45.833 0.00 0.00 0.00 2.94
431 436 8.745590 GGTATTTGGCATAGTTAGGAAAAAGAA 58.254 33.333 0.00 0.00 0.00 2.52
433 438 8.650143 ATTTGGCATAGTTAGGAAAAAGAAGA 57.350 30.769 0.00 0.00 0.00 2.87
434 439 7.687941 TTGGCATAGTTAGGAAAAAGAAGAG 57.312 36.000 0.00 0.00 0.00 2.85
435 440 6.180472 TGGCATAGTTAGGAAAAAGAAGAGG 58.820 40.000 0.00 0.00 0.00 3.69
436 441 5.066634 GGCATAGTTAGGAAAAAGAAGAGGC 59.933 44.000 0.00 0.00 0.00 4.70
437 442 5.648092 GCATAGTTAGGAAAAAGAAGAGGCA 59.352 40.000 0.00 0.00 0.00 4.75
438 443 6.403746 GCATAGTTAGGAAAAAGAAGAGGCAC 60.404 42.308 0.00 0.00 0.00 5.01
451 456 3.787001 GGCACTCTCCCCCTTCCG 61.787 72.222 0.00 0.00 0.00 4.30
452 457 4.475135 GCACTCTCCCCCTTCCGC 62.475 72.222 0.00 0.00 0.00 5.54
453 458 3.003173 CACTCTCCCCCTTCCGCA 61.003 66.667 0.00 0.00 0.00 5.69
454 459 2.685380 ACTCTCCCCCTTCCGCAG 60.685 66.667 0.00 0.00 0.00 5.18
458 463 1.131303 TCTCCCCCTTCCGCAGAAAA 61.131 55.000 0.00 0.00 0.00 2.29
485 490 4.507710 TGGCATGAATAGTGAACTGTCTC 58.492 43.478 0.00 0.00 0.00 3.36
486 491 3.553511 GGCATGAATAGTGAACTGTCTCG 59.446 47.826 0.00 0.00 0.00 4.04
487 492 4.424626 GCATGAATAGTGAACTGTCTCGA 58.575 43.478 0.00 0.00 0.00 4.04
488 493 4.864806 GCATGAATAGTGAACTGTCTCGAA 59.135 41.667 0.00 0.00 0.00 3.71
489 494 5.348724 GCATGAATAGTGAACTGTCTCGAAA 59.651 40.000 0.00 0.00 0.00 3.46
490 495 6.128553 GCATGAATAGTGAACTGTCTCGAAAA 60.129 38.462 0.00 0.00 0.00 2.29
491 496 6.764877 TGAATAGTGAACTGTCTCGAAAAC 57.235 37.500 0.00 0.00 0.00 2.43
492 497 6.277605 TGAATAGTGAACTGTCTCGAAAACA 58.722 36.000 0.87 0.87 0.00 2.83
493 498 6.929049 TGAATAGTGAACTGTCTCGAAAACAT 59.071 34.615 1.15 0.00 0.00 2.71
494 499 7.441157 TGAATAGTGAACTGTCTCGAAAACATT 59.559 33.333 1.15 0.00 0.00 2.71
495 500 8.827177 AATAGTGAACTGTCTCGAAAACATTA 57.173 30.769 1.15 0.00 0.00 1.90
496 501 6.526566 AGTGAACTGTCTCGAAAACATTAC 57.473 37.500 1.15 0.00 0.00 1.89
497 502 6.281405 AGTGAACTGTCTCGAAAACATTACT 58.719 36.000 1.15 0.00 0.00 2.24
498 503 6.421202 AGTGAACTGTCTCGAAAACATTACTC 59.579 38.462 1.15 0.00 0.00 2.59
499 504 5.401376 TGAACTGTCTCGAAAACATTACTCG 59.599 40.000 1.15 0.00 0.00 4.18
500 505 3.673809 ACTGTCTCGAAAACATTACTCGC 59.326 43.478 1.15 0.00 32.66 5.03
501 506 3.644823 TGTCTCGAAAACATTACTCGCA 58.355 40.909 0.00 0.00 32.66 5.10
502 507 4.052608 TGTCTCGAAAACATTACTCGCAA 58.947 39.130 0.00 0.00 32.66 4.85
503 508 4.508492 TGTCTCGAAAACATTACTCGCAAA 59.492 37.500 0.00 0.00 32.66 3.68
504 509 5.006844 TGTCTCGAAAACATTACTCGCAAAA 59.993 36.000 0.00 0.00 32.66 2.44
505 510 5.905181 GTCTCGAAAACATTACTCGCAAAAA 59.095 36.000 0.00 0.00 32.66 1.94
532 537 8.527567 AAAACTGTCTCGAAAACAATGAAAAA 57.472 26.923 2.34 0.00 0.00 1.94
565 582 2.342648 GAGGTCCACGGTGTCCAC 59.657 66.667 17.49 10.34 0.00 4.02
566 583 3.569049 GAGGTCCACGGTGTCCACG 62.569 68.421 17.49 0.00 37.36 4.94
644 661 1.004440 GGCTATGGATCAGACCGGC 60.004 63.158 0.00 0.00 0.00 6.13
645 662 1.476007 GGCTATGGATCAGACCGGCT 61.476 60.000 0.00 0.00 0.00 5.52
757 775 3.882888 TGAATTGATTCGATTGTAGGGGC 59.117 43.478 3.79 0.00 39.62 5.80
785 803 3.645687 CCTGATAAAGAGGAGGAGAAGGG 59.354 52.174 0.00 0.00 31.48 3.95
819 843 2.363018 GGCCAGCTCTTTTCCCCC 60.363 66.667 0.00 0.00 0.00 5.40
820 844 2.766660 GCCAGCTCTTTTCCCCCT 59.233 61.111 0.00 0.00 0.00 4.79
821 845 1.680314 GCCAGCTCTTTTCCCCCTG 60.680 63.158 0.00 0.00 0.00 4.45
822 846 1.000396 CCAGCTCTTTTCCCCCTGG 60.000 63.158 0.00 0.00 37.35 4.45
823 847 1.770324 CAGCTCTTTTCCCCCTGGT 59.230 57.895 0.00 0.00 0.00 4.00
824 848 0.610232 CAGCTCTTTTCCCCCTGGTG 60.610 60.000 0.00 0.00 0.00 4.17
825 849 1.304464 GCTCTTTTCCCCCTGGTGG 60.304 63.158 0.00 0.00 0.00 4.61
826 850 2.081585 GCTCTTTTCCCCCTGGTGGT 62.082 60.000 0.00 0.00 0.00 4.16
827 851 0.251341 CTCTTTTCCCCCTGGTGGTG 60.251 60.000 0.00 0.00 0.00 4.17
828 852 1.228862 CTTTTCCCCCTGGTGGTGG 60.229 63.158 0.00 0.00 0.00 4.61
829 853 1.701757 TTTTCCCCCTGGTGGTGGA 60.702 57.895 0.00 0.00 33.20 4.02
830 854 1.725169 TTTTCCCCCTGGTGGTGGAG 61.725 60.000 0.00 0.00 35.61 3.86
853 877 3.123620 CGAGCTGCTGTTCCTGCC 61.124 66.667 7.01 0.00 0.00 4.85
932 965 0.106519 AAAGGGAATCATCTGCCGGG 60.107 55.000 2.18 0.00 0.00 5.73
1056 1089 2.202810 GACCTCTGCTGCTACGGC 60.203 66.667 0.00 0.00 39.26 5.68
1108 1141 2.906389 TCCCTTTGCTCTGCTTCTTAGA 59.094 45.455 0.00 0.00 0.00 2.10
1109 1142 3.006247 CCCTTTGCTCTGCTTCTTAGAC 58.994 50.000 0.00 0.00 0.00 2.59
1145 1178 1.886542 GAAGACGGCCAGATTTGGTTT 59.113 47.619 2.24 0.00 46.80 3.27
1168 1201 1.009389 CAGTTCTTGACCGCCGTCTC 61.009 60.000 6.74 0.00 39.94 3.36
1267 1305 7.753309 TTCAACCCGATTTCATTTCTTCTTA 57.247 32.000 0.00 0.00 0.00 2.10
1273 1311 5.520288 CCGATTTCATTTCTTCTTAGCTCGA 59.480 40.000 0.00 0.00 0.00 4.04
1292 1337 1.303799 ACTCGAATTGCTGCTGCTGG 61.304 55.000 17.00 0.00 40.48 4.85
1302 1347 2.017623 GCTGCTGCTGGTGATCTGATT 61.018 52.381 8.53 0.00 36.03 2.57
1324 1369 1.067749 CTCTGCTGATCTCAGGCCG 59.932 63.158 9.15 0.00 43.94 6.13
1390 1435 1.399714 CCACGCCCTACATCTACTCA 58.600 55.000 0.00 0.00 0.00 3.41
1537 1582 2.314647 CGCCGACGCCAAGAAAAGA 61.315 57.895 0.00 0.00 0.00 2.52
1543 1588 0.182775 ACGCCAAGAAAAGAGTGGGT 59.817 50.000 0.00 0.00 32.71 4.51
1544 1589 0.593128 CGCCAAGAAAAGAGTGGGTG 59.407 55.000 0.00 0.00 32.71 4.61
1562 1607 2.662070 GCCCTACCCACCGCTTGTA 61.662 63.158 0.00 0.00 0.00 2.41
1585 1630 2.772691 GCTGCCTTGCCTGCATCTC 61.773 63.158 0.00 0.00 38.22 2.75
1598 1643 3.937706 CCTGCATCTCTAAGTTTGACTGG 59.062 47.826 0.00 0.00 0.00 4.00
1661 1710 2.604174 GGTGTTCTGCGTGTTCGGG 61.604 63.158 0.00 0.00 37.56 5.14
1791 1840 6.037610 GTCCATCATTGTGAGTCCTGAAATAC 59.962 42.308 0.00 0.00 0.00 1.89
1877 1954 1.557832 TCCTTCGTAGGTTTGATGGGG 59.442 52.381 8.06 0.00 42.60 4.96
1915 1992 7.615582 TCTCATCTGACCATGTTTGTTATTC 57.384 36.000 0.00 0.00 0.00 1.75
1916 1993 7.167535 TCTCATCTGACCATGTTTGTTATTCA 58.832 34.615 0.00 0.00 0.00 2.57
2125 2202 1.549203 TCAGGGATTTTGCTTGGAGC 58.451 50.000 0.00 0.00 42.82 4.70
2127 2204 0.038166 AGGGATTTTGCTTGGAGCGA 59.962 50.000 0.00 0.00 46.26 4.93
2203 2280 2.349672 CCCAATGGCATCGGCACAA 61.350 57.895 0.00 0.00 41.84 3.33
2224 2301 3.887621 TCCTAGGTGTCATACAGTTGC 57.112 47.619 9.08 0.00 0.00 4.17
2356 2433 7.228706 AGCTATTTACTGTTATATGCGGCTTTT 59.771 33.333 0.00 0.00 0.00 2.27
2419 2497 2.792116 CACACGTTTAAAGCGCCATTTT 59.208 40.909 2.29 0.06 0.00 1.82
2424 2502 5.343593 CACGTTTAAAGCGCCATTTTAATGA 59.656 36.000 15.59 2.01 38.70 2.57
2426 2504 6.252655 ACGTTTAAAGCGCCATTTTAATGATC 59.747 34.615 15.59 7.27 38.70 2.92
2451 2529 3.105937 GCAAACTTTGGTGTCTCGTTTC 58.894 45.455 3.69 0.00 0.00 2.78
2526 2610 1.378250 GCTCCAGCTCTGTTGCCAT 60.378 57.895 0.00 0.00 38.21 4.40
2529 2613 0.694771 TCCAGCTCTGTTGCCATCTT 59.305 50.000 0.00 0.00 0.00 2.40
2647 2731 5.802956 CGAGTGAAGATCTCTACCAAGTTTC 59.197 44.000 0.00 0.00 0.00 2.78
2821 2907 8.815565 TTTAGCATGAATTATAACTTGGACCA 57.184 30.769 0.00 0.00 0.00 4.02
2822 2908 8.815565 TTAGCATGAATTATAACTTGGACCAA 57.184 30.769 6.76 6.76 0.00 3.67
2823 2909 7.338800 AGCATGAATTATAACTTGGACCAAG 57.661 36.000 29.13 29.13 45.85 3.61
3098 3199 0.539051 CTGTAAGCCTACAGCCTGCT 59.461 55.000 9.50 0.00 46.46 4.24
3099 3200 1.741732 CTGTAAGCCTACAGCCTGCTG 60.742 57.143 17.21 17.21 46.46 4.41
3192 3297 8.879759 TCCTCGAGTCATTTGTTTATATTGTTC 58.120 33.333 12.31 0.00 0.00 3.18
3215 3320 3.916359 TCCGGTGAGCCATTATTTGTA 57.084 42.857 0.00 0.00 34.09 2.41
3254 3359 3.664107 GGCGAGCATTAATGGATCACTA 58.336 45.455 17.02 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.623000 TGCATATGACACTAGTCTAAGTTACTA 57.377 33.333 6.97 0.00 45.20 1.82
19 20 8.521170 TGCATATGACACTAGTCTAAGTTACT 57.479 34.615 6.97 0.00 45.20 2.24
20 21 9.186323 CATGCATATGACACTAGTCTAAGTTAC 57.814 37.037 6.97 0.00 45.20 2.50
21 22 9.131791 TCATGCATATGACACTAGTCTAAGTTA 57.868 33.333 6.97 0.00 45.20 2.24
22 23 8.011844 TCATGCATATGACACTAGTCTAAGTT 57.988 34.615 6.97 0.00 45.20 2.66
23 24 7.588497 TCATGCATATGACACTAGTCTAAGT 57.412 36.000 6.97 0.00 45.20 2.24
36 37 8.962884 AACTTACACTAATGTCATGCATATGA 57.037 30.769 6.97 0.00 40.48 2.15
39 40 9.529325 GAGTAACTTACACTAATGTCATGCATA 57.471 33.333 0.00 0.00 40.48 3.14
40 41 7.495934 GGAGTAACTTACACTAATGTCATGCAT 59.504 37.037 0.00 0.00 40.48 3.96
41 42 6.816640 GGAGTAACTTACACTAATGTCATGCA 59.183 38.462 1.79 0.00 40.48 3.96
42 43 6.258068 GGGAGTAACTTACACTAATGTCATGC 59.742 42.308 1.79 0.00 40.48 4.06
43 44 6.761714 GGGGAGTAACTTACACTAATGTCATG 59.238 42.308 1.79 0.00 40.48 3.07
44 45 6.442564 TGGGGAGTAACTTACACTAATGTCAT 59.557 38.462 1.79 0.00 40.48 3.06
45 46 5.781306 TGGGGAGTAACTTACACTAATGTCA 59.219 40.000 1.79 0.00 40.48 3.58
46 47 6.070938 AGTGGGGAGTAACTTACACTAATGTC 60.071 42.308 1.79 0.00 40.48 3.06
47 48 5.783875 AGTGGGGAGTAACTTACACTAATGT 59.216 40.000 1.79 0.00 43.30 2.71
48 49 6.295719 AGTGGGGAGTAACTTACACTAATG 57.704 41.667 1.79 0.00 37.41 1.90
49 50 7.842743 TCATAGTGGGGAGTAACTTACACTAAT 59.157 37.037 11.50 2.29 42.51 1.73
50 51 7.123247 GTCATAGTGGGGAGTAACTTACACTAA 59.877 40.741 11.50 0.00 42.51 2.24
51 52 6.604795 GTCATAGTGGGGAGTAACTTACACTA 59.395 42.308 0.00 0.00 43.13 2.74
52 53 5.421374 GTCATAGTGGGGAGTAACTTACACT 59.579 44.000 0.00 0.00 41.52 3.55
53 54 5.394993 GGTCATAGTGGGGAGTAACTTACAC 60.395 48.000 1.79 0.00 0.00 2.90
54 55 4.713321 GGTCATAGTGGGGAGTAACTTACA 59.287 45.833 1.79 0.00 0.00 2.41
55 56 4.713321 TGGTCATAGTGGGGAGTAACTTAC 59.287 45.833 0.00 0.00 0.00 2.34
56 57 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
57 58 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
58 59 3.246021 ACTGGTCATAGTGGGGAGTAACT 60.246 47.826 0.00 0.00 0.00 2.24
59 60 3.105283 ACTGGTCATAGTGGGGAGTAAC 58.895 50.000 0.00 0.00 0.00 2.50
60 61 3.012502 AGACTGGTCATAGTGGGGAGTAA 59.987 47.826 3.51 0.00 0.00 2.24
61 62 2.585900 AGACTGGTCATAGTGGGGAGTA 59.414 50.000 3.51 0.00 0.00 2.59
62 63 1.362932 AGACTGGTCATAGTGGGGAGT 59.637 52.381 3.51 0.00 0.00 3.85
63 64 2.166907 AGACTGGTCATAGTGGGGAG 57.833 55.000 3.51 0.00 0.00 4.30
64 65 3.271225 TCTTAGACTGGTCATAGTGGGGA 59.729 47.826 3.51 0.00 0.00 4.81
65 66 3.385111 GTCTTAGACTGGTCATAGTGGGG 59.615 52.174 4.94 0.00 0.00 4.96
66 67 4.023980 TGTCTTAGACTGGTCATAGTGGG 58.976 47.826 13.86 0.00 33.15 4.61
67 68 5.661056 TTGTCTTAGACTGGTCATAGTGG 57.339 43.478 13.86 0.00 33.15 4.00
68 69 5.521735 GCATTGTCTTAGACTGGTCATAGTG 59.478 44.000 13.86 0.03 33.15 2.74
69 70 5.187772 TGCATTGTCTTAGACTGGTCATAGT 59.812 40.000 13.86 0.00 33.15 2.12
70 71 5.664457 TGCATTGTCTTAGACTGGTCATAG 58.336 41.667 13.86 0.62 33.15 2.23
71 72 5.675684 TGCATTGTCTTAGACTGGTCATA 57.324 39.130 13.86 0.00 33.15 2.15
72 73 4.558226 TGCATTGTCTTAGACTGGTCAT 57.442 40.909 13.86 0.00 33.15 3.06
73 74 4.350368 TTGCATTGTCTTAGACTGGTCA 57.650 40.909 13.86 4.26 33.15 4.02
74 75 4.937620 TCATTGCATTGTCTTAGACTGGTC 59.062 41.667 13.86 1.81 33.15 4.02
75 76 4.910195 TCATTGCATTGTCTTAGACTGGT 58.090 39.130 13.86 0.00 33.15 4.00
76 77 5.885230 TTCATTGCATTGTCTTAGACTGG 57.115 39.130 13.86 4.31 33.15 4.00
77 78 6.671190 TGTTTCATTGCATTGTCTTAGACTG 58.329 36.000 13.86 5.65 33.15 3.51
78 79 6.882610 TGTTTCATTGCATTGTCTTAGACT 57.117 33.333 13.86 0.00 33.15 3.24
79 80 7.062605 CCATTGTTTCATTGCATTGTCTTAGAC 59.937 37.037 5.27 5.27 0.00 2.59
80 81 7.039853 TCCATTGTTTCATTGCATTGTCTTAGA 60.040 33.333 8.36 0.00 0.00 2.10
81 82 7.092079 TCCATTGTTTCATTGCATTGTCTTAG 58.908 34.615 8.36 0.00 0.00 2.18
82 83 6.990798 TCCATTGTTTCATTGCATTGTCTTA 58.009 32.000 8.36 0.00 0.00 2.10
83 84 5.856156 TCCATTGTTTCATTGCATTGTCTT 58.144 33.333 8.36 0.00 0.00 3.01
84 85 5.471556 TCCATTGTTTCATTGCATTGTCT 57.528 34.783 8.36 0.00 0.00 3.41
85 86 6.542574 TTTCCATTGTTTCATTGCATTGTC 57.457 33.333 8.36 2.47 0.00 3.18
86 87 6.938030 AGATTTCCATTGTTTCATTGCATTGT 59.062 30.769 8.36 0.00 0.00 2.71
87 88 7.240674 CAGATTTCCATTGTTTCATTGCATTG 58.759 34.615 2.08 2.08 0.00 2.82
88 89 6.128117 GCAGATTTCCATTGTTTCATTGCATT 60.128 34.615 0.00 0.00 0.00 3.56
89 90 5.353123 GCAGATTTCCATTGTTTCATTGCAT 59.647 36.000 0.00 0.00 0.00 3.96
90 91 4.691685 GCAGATTTCCATTGTTTCATTGCA 59.308 37.500 0.00 0.00 0.00 4.08
91 92 4.933400 AGCAGATTTCCATTGTTTCATTGC 59.067 37.500 0.00 0.00 0.00 3.56
92 93 8.537049 TTAAGCAGATTTCCATTGTTTCATTG 57.463 30.769 0.00 0.00 0.00 2.82
93 94 8.587608 TCTTAAGCAGATTTCCATTGTTTCATT 58.412 29.630 0.00 0.00 0.00 2.57
94 95 8.031277 GTCTTAAGCAGATTTCCATTGTTTCAT 58.969 33.333 0.00 0.00 32.60 2.57
95 96 7.014134 TGTCTTAAGCAGATTTCCATTGTTTCA 59.986 33.333 0.00 0.00 32.60 2.69
96 97 7.370383 TGTCTTAAGCAGATTTCCATTGTTTC 58.630 34.615 0.00 0.00 32.60 2.78
97 98 7.288810 TGTCTTAAGCAGATTTCCATTGTTT 57.711 32.000 0.00 0.00 32.60 2.83
98 99 6.899393 TGTCTTAAGCAGATTTCCATTGTT 57.101 33.333 0.00 0.00 32.60 2.83
99 100 6.899393 TTGTCTTAAGCAGATTTCCATTGT 57.101 33.333 0.00 0.00 32.60 2.71
100 101 6.810182 CCTTTGTCTTAAGCAGATTTCCATTG 59.190 38.462 0.00 0.00 32.60 2.82
101 102 6.721208 TCCTTTGTCTTAAGCAGATTTCCATT 59.279 34.615 0.00 0.00 32.60 3.16
102 103 6.248433 TCCTTTGTCTTAAGCAGATTTCCAT 58.752 36.000 0.00 0.00 32.60 3.41
103 104 5.630121 TCCTTTGTCTTAAGCAGATTTCCA 58.370 37.500 0.00 0.00 32.60 3.53
104 105 6.575162 TTCCTTTGTCTTAAGCAGATTTCC 57.425 37.500 0.00 0.00 32.60 3.13
105 106 7.040409 TCCTTTCCTTTGTCTTAAGCAGATTTC 60.040 37.037 0.00 0.00 32.60 2.17
106 107 6.777580 TCCTTTCCTTTGTCTTAAGCAGATTT 59.222 34.615 0.00 0.00 32.60 2.17
107 108 6.306987 TCCTTTCCTTTGTCTTAAGCAGATT 58.693 36.000 0.00 0.00 32.60 2.40
108 109 5.880901 TCCTTTCCTTTGTCTTAAGCAGAT 58.119 37.500 0.00 0.00 32.60 2.90
109 110 5.304686 TCCTTTCCTTTGTCTTAAGCAGA 57.695 39.130 0.00 0.00 0.00 4.26
110 111 6.391227 TTTCCTTTCCTTTGTCTTAAGCAG 57.609 37.500 0.00 0.00 0.00 4.24
111 112 6.777580 AGATTTCCTTTCCTTTGTCTTAAGCA 59.222 34.615 0.00 0.00 0.00 3.91
112 113 7.087007 CAGATTTCCTTTCCTTTGTCTTAAGC 58.913 38.462 0.00 0.00 0.00 3.09
113 114 8.078596 CACAGATTTCCTTTCCTTTGTCTTAAG 58.921 37.037 0.00 0.00 0.00 1.85
114 115 7.014230 CCACAGATTTCCTTTCCTTTGTCTTAA 59.986 37.037 0.00 0.00 0.00 1.85
115 116 6.490040 CCACAGATTTCCTTTCCTTTGTCTTA 59.510 38.462 0.00 0.00 0.00 2.10
116 117 5.302823 CCACAGATTTCCTTTCCTTTGTCTT 59.697 40.000 0.00 0.00 0.00 3.01
117 118 4.829492 CCACAGATTTCCTTTCCTTTGTCT 59.171 41.667 0.00 0.00 0.00 3.41
118 119 4.021981 CCCACAGATTTCCTTTCCTTTGTC 60.022 45.833 0.00 0.00 0.00 3.18
119 120 3.897505 CCCACAGATTTCCTTTCCTTTGT 59.102 43.478 0.00 0.00 0.00 2.83
120 121 3.259123 CCCCACAGATTTCCTTTCCTTTG 59.741 47.826 0.00 0.00 0.00 2.77
121 122 3.116746 ACCCCACAGATTTCCTTTCCTTT 60.117 43.478 0.00 0.00 0.00 3.11
122 123 2.450886 ACCCCACAGATTTCCTTTCCTT 59.549 45.455 0.00 0.00 0.00 3.36
123 124 2.041755 GACCCCACAGATTTCCTTTCCT 59.958 50.000 0.00 0.00 0.00 3.36
124 125 2.225017 TGACCCCACAGATTTCCTTTCC 60.225 50.000 0.00 0.00 0.00 3.13
125 126 3.154827 TGACCCCACAGATTTCCTTTC 57.845 47.619 0.00 0.00 0.00 2.62
126 127 3.434309 CATGACCCCACAGATTTCCTTT 58.566 45.455 0.00 0.00 0.00 3.11
127 128 2.885554 GCATGACCCCACAGATTTCCTT 60.886 50.000 0.00 0.00 0.00 3.36
128 129 1.341383 GCATGACCCCACAGATTTCCT 60.341 52.381 0.00 0.00 0.00 3.36
129 130 1.106285 GCATGACCCCACAGATTTCC 58.894 55.000 0.00 0.00 0.00 3.13
130 131 2.134789 AGCATGACCCCACAGATTTC 57.865 50.000 0.00 0.00 0.00 2.17
131 132 2.610438 AAGCATGACCCCACAGATTT 57.390 45.000 0.00 0.00 0.00 2.17
132 133 2.684927 GCTAAGCATGACCCCACAGATT 60.685 50.000 0.00 0.00 0.00 2.40
133 134 1.133976 GCTAAGCATGACCCCACAGAT 60.134 52.381 0.00 0.00 0.00 2.90
134 135 0.253044 GCTAAGCATGACCCCACAGA 59.747 55.000 0.00 0.00 0.00 3.41
135 136 0.254178 AGCTAAGCATGACCCCACAG 59.746 55.000 0.00 0.00 0.00 3.66
136 137 0.035152 CAGCTAAGCATGACCCCACA 60.035 55.000 0.00 0.00 0.00 4.17
137 138 0.749454 CCAGCTAAGCATGACCCCAC 60.749 60.000 0.00 0.00 0.00 4.61
142 143 2.009888 GCGTCCAGCTAAGCATGAC 58.990 57.895 0.00 0.00 44.04 3.06
157 158 3.616219 TGCTTGACTAATTTATGGGCGT 58.384 40.909 0.00 0.00 0.00 5.68
159 160 3.954258 ACCTGCTTGACTAATTTATGGGC 59.046 43.478 0.00 0.00 0.00 5.36
171 172 3.707102 AGAGGGATAACTACCTGCTTGAC 59.293 47.826 0.00 0.00 37.18 3.18
172 173 3.995636 AGAGGGATAACTACCTGCTTGA 58.004 45.455 0.00 0.00 37.18 3.02
188 189 9.310449 TCCTACTAGCAGTAATTATTTAGAGGG 57.690 37.037 0.00 0.00 29.00 4.30
251 253 9.639636 CGGTAAATTATGGTTTGTTTTGAAAAC 57.360 29.630 13.55 13.55 36.90 2.43
252 254 9.379791 ACGGTAAATTATGGTTTGTTTTGAAAA 57.620 25.926 0.00 0.00 0.00 2.29
253 255 8.943909 ACGGTAAATTATGGTTTGTTTTGAAA 57.056 26.923 0.00 0.00 0.00 2.69
271 273 3.253677 CAGGGTGCATGTAAAACGGTAAA 59.746 43.478 0.00 0.00 0.00 2.01
287 289 5.520288 CGTTGATGACTAACTATTCAGGGTG 59.480 44.000 0.00 0.00 0.00 4.61
289 291 5.661458 ACGTTGATGACTAACTATTCAGGG 58.339 41.667 0.00 0.00 0.00 4.45
298 300 5.195379 GTTGTGACAACGTTGATGACTAAC 58.805 41.667 33.66 22.59 0.00 2.34
343 345 1.352156 GCGTGTGACCGATTGTCCTC 61.352 60.000 0.00 0.00 43.78 3.71
351 353 2.048597 GTGATGGCGTGTGACCGA 60.049 61.111 0.00 0.00 0.00 4.69
357 359 2.254546 TTTGAAGAGTGATGGCGTGT 57.745 45.000 0.00 0.00 0.00 4.49
375 377 9.048446 GCATTGCTATGGAATGAAAATAACATT 57.952 29.630 14.33 0.00 35.37 2.71
382 384 4.141892 CCCTGCATTGCTATGGAATGAAAA 60.142 41.667 14.33 0.77 33.36 2.29
403 405 4.717279 TCCTAACTATGCCAAATACCCC 57.283 45.455 0.00 0.00 0.00 4.95
415 420 7.021998 AGTGCCTCTTCTTTTTCCTAACTAT 57.978 36.000 0.00 0.00 0.00 2.12
423 428 3.078097 GGGAGAGTGCCTCTTCTTTTTC 58.922 50.000 9.55 0.00 41.35 2.29
424 429 2.224892 GGGGAGAGTGCCTCTTCTTTTT 60.225 50.000 9.55 0.00 41.35 1.94
431 436 1.306568 GAAGGGGGAGAGTGCCTCT 60.307 63.158 4.59 4.59 42.24 3.69
433 438 2.285743 GGAAGGGGGAGAGTGCCT 60.286 66.667 0.00 0.00 0.00 4.75
434 439 3.787001 CGGAAGGGGGAGAGTGCC 61.787 72.222 0.00 0.00 0.00 5.01
435 440 4.475135 GCGGAAGGGGGAGAGTGC 62.475 72.222 0.00 0.00 0.00 4.40
436 441 3.003173 TGCGGAAGGGGGAGAGTG 61.003 66.667 0.00 0.00 0.00 3.51
437 442 2.685380 CTGCGGAAGGGGGAGAGT 60.685 66.667 0.00 0.00 0.00 3.24
438 443 1.553690 TTTCTGCGGAAGGGGGAGAG 61.554 60.000 8.23 0.00 33.28 3.20
441 446 1.847686 TTTTTCTGCGGAAGGGGGA 59.152 52.632 8.23 0.00 32.61 4.81
442 447 4.511838 TTTTTCTGCGGAAGGGGG 57.488 55.556 8.23 0.00 32.61 5.40
458 463 6.996509 ACAGTTCACTATTCATGCCATTTTT 58.003 32.000 0.00 0.00 0.00 1.94
461 466 5.503927 AGACAGTTCACTATTCATGCCATT 58.496 37.500 0.00 0.00 0.00 3.16
462 467 5.108187 AGACAGTTCACTATTCATGCCAT 57.892 39.130 0.00 0.00 0.00 4.40
468 473 6.277605 TGTTTTCGAGACAGTTCACTATTCA 58.722 36.000 0.14 0.00 0.00 2.57
471 476 8.088981 AGTAATGTTTTCGAGACAGTTCACTAT 58.911 33.333 8.82 0.00 0.00 2.12
473 478 6.281405 AGTAATGTTTTCGAGACAGTTCACT 58.719 36.000 8.82 5.54 0.00 3.41
478 483 3.673809 GCGAGTAATGTTTTCGAGACAGT 59.326 43.478 9.19 8.89 36.49 3.55
481 486 4.640805 TTGCGAGTAATGTTTTCGAGAC 57.359 40.909 0.00 0.00 36.49 3.36
506 511 8.527567 TTTTCATTGTTTTCGAGACAGTTTTT 57.472 26.923 4.27 0.00 0.00 1.94
507 512 8.527567 TTTTTCATTGTTTTCGAGACAGTTTT 57.472 26.923 4.27 0.00 0.00 2.43
508 513 8.702163 ATTTTTCATTGTTTTCGAGACAGTTT 57.298 26.923 4.27 0.00 0.00 2.66
509 514 9.450807 CTATTTTTCATTGTTTTCGAGACAGTT 57.549 29.630 4.27 0.00 0.00 3.16
510 515 7.591426 GCTATTTTTCATTGTTTTCGAGACAGT 59.409 33.333 4.27 0.00 0.00 3.55
511 516 7.805071 AGCTATTTTTCATTGTTTTCGAGACAG 59.195 33.333 4.27 0.00 0.00 3.51
512 517 7.591057 CAGCTATTTTTCATTGTTTTCGAGACA 59.409 33.333 0.14 0.14 0.00 3.41
513 518 7.591426 ACAGCTATTTTTCATTGTTTTCGAGAC 59.409 33.333 0.00 0.00 0.00 3.36
514 519 7.591057 CACAGCTATTTTTCATTGTTTTCGAGA 59.409 33.333 0.00 0.00 0.00 4.04
515 520 7.617935 GCACAGCTATTTTTCATTGTTTTCGAG 60.618 37.037 0.00 0.00 0.00 4.04
516 521 6.143758 GCACAGCTATTTTTCATTGTTTTCGA 59.856 34.615 0.00 0.00 0.00 3.71
517 522 6.144402 AGCACAGCTATTTTTCATTGTTTTCG 59.856 34.615 0.00 0.00 36.99 3.46
518 523 7.285788 CAGCACAGCTATTTTTCATTGTTTTC 58.714 34.615 0.00 0.00 36.40 2.29
527 532 2.509870 GACGCAGCACAGCTATTTTTC 58.490 47.619 0.00 0.00 36.40 2.29
530 535 0.389817 TCGACGCAGCACAGCTATTT 60.390 50.000 0.00 0.00 36.40 1.40
532 537 1.226802 CTCGACGCAGCACAGCTAT 60.227 57.895 0.00 0.00 36.40 2.97
629 646 1.179174 CCGAGCCGGTCTGATCCATA 61.179 60.000 1.90 0.00 42.73 2.74
644 661 1.526917 GGGGATGTTGATGGCCGAG 60.527 63.158 0.00 0.00 0.00 4.63
645 662 2.595095 GGGGATGTTGATGGCCGA 59.405 61.111 0.00 0.00 0.00 5.54
727 745 9.992910 CTACAATCGAATCAATTCATCAAAAGA 57.007 29.630 0.00 0.00 36.61 2.52
728 746 9.229784 CCTACAATCGAATCAATTCATCAAAAG 57.770 33.333 0.00 0.00 36.61 2.27
729 747 8.190122 CCCTACAATCGAATCAATTCATCAAAA 58.810 33.333 0.00 0.00 36.61 2.44
730 748 7.201812 CCCCTACAATCGAATCAATTCATCAAA 60.202 37.037 0.00 0.00 36.61 2.69
731 749 6.262944 CCCCTACAATCGAATCAATTCATCAA 59.737 38.462 0.00 0.00 36.61 2.57
732 750 5.764686 CCCCTACAATCGAATCAATTCATCA 59.235 40.000 0.00 0.00 36.61 3.07
733 751 5.335191 GCCCCTACAATCGAATCAATTCATC 60.335 44.000 0.00 0.00 36.61 2.92
734 752 4.520492 GCCCCTACAATCGAATCAATTCAT 59.480 41.667 0.00 0.00 36.61 2.57
735 753 3.882888 GCCCCTACAATCGAATCAATTCA 59.117 43.478 0.00 0.00 36.61 2.57
736 754 3.058914 CGCCCCTACAATCGAATCAATTC 60.059 47.826 0.00 0.00 0.00 2.17
737 755 2.878406 CGCCCCTACAATCGAATCAATT 59.122 45.455 0.00 0.00 0.00 2.32
738 756 2.494059 CGCCCCTACAATCGAATCAAT 58.506 47.619 0.00 0.00 0.00 2.57
745 763 2.280186 GCTCCGCCCCTACAATCG 60.280 66.667 0.00 0.00 0.00 3.34
757 775 1.342819 CTCCTCTTTATCAGGGCTCCG 59.657 57.143 0.00 0.00 0.00 4.63
764 782 3.645687 CCCCTTCTCCTCCTCTTTATCAG 59.354 52.174 0.00 0.00 0.00 2.90
771 789 1.598856 CCTCCCCCTTCTCCTCCTCT 61.599 65.000 0.00 0.00 0.00 3.69
785 803 3.157949 CCGCTTCCTCCTCCTCCC 61.158 72.222 0.00 0.00 0.00 4.30
822 846 4.767255 CTCGCCTGGCTCCACCAC 62.767 72.222 17.92 0.00 46.36 4.16
831 855 3.123620 GAACAGCAGCTCGCCTGG 61.124 66.667 0.00 0.00 44.04 4.45
832 856 3.123620 GGAACAGCAGCTCGCCTG 61.124 66.667 0.00 4.62 44.04 4.85
833 857 3.317571 AGGAACAGCAGCTCGCCT 61.318 61.111 0.00 0.00 44.04 5.52
834 858 3.123620 CAGGAACAGCAGCTCGCC 61.124 66.667 0.00 0.00 44.04 5.54
835 859 3.797546 GCAGGAACAGCAGCTCGC 61.798 66.667 0.00 0.47 41.82 5.03
836 860 3.123620 GGCAGGAACAGCAGCTCG 61.124 66.667 0.00 0.00 44.97 5.03
837 861 2.749441 GGGCAGGAACAGCAGCTC 60.749 66.667 0.00 0.00 44.97 4.09
838 862 2.838467 AAGGGCAGGAACAGCAGCT 61.838 57.895 0.00 0.00 44.97 4.24
839 863 2.282745 AAGGGCAGGAACAGCAGC 60.283 61.111 0.00 0.00 44.97 5.25
853 877 4.261783 GGGTTCTTTCTTTTCAGAGCAAGG 60.262 45.833 0.00 0.00 0.00 3.61
917 950 2.113986 CCCCCGGCAGATGATTCC 59.886 66.667 0.00 0.00 0.00 3.01
1056 1089 2.125552 TGACCTGCGATTCCTGCG 60.126 61.111 0.00 0.00 34.24 5.18
1082 1115 0.407139 AGCAGAGCAAAGGGAATGGT 59.593 50.000 0.00 0.00 0.00 3.55
1108 1141 3.374402 CTCCACGACGGCAGAGGT 61.374 66.667 0.00 0.00 33.14 3.85
1109 1142 2.549611 CTTCTCCACGACGGCAGAGG 62.550 65.000 0.00 0.00 33.14 3.69
1168 1201 3.133721 AGATGTTCCCTGGAAGAAGATCG 59.866 47.826 13.38 0.00 44.52 3.69
1267 1305 1.080995 GCAGCAATTCGAGTCGAGCT 61.081 55.000 18.84 18.84 35.81 4.09
1273 1311 1.303799 CCAGCAGCAGCAATTCGAGT 61.304 55.000 3.17 0.00 45.49 4.18
1302 1347 1.687660 GCCTGAGATCAGCAGAGATCA 59.312 52.381 14.94 6.31 45.39 2.92
1312 1357 1.137675 CTGAATGTCGGCCTGAGATCA 59.862 52.381 0.00 0.00 28.69 2.92
1324 1369 1.269309 CGGACGATCCTCCTGAATGTC 60.269 57.143 8.83 0.00 33.30 3.06
1390 1435 0.540830 AGACGAGGCAGTTGAGGAGT 60.541 55.000 0.00 0.00 0.00 3.85
1495 1540 0.248907 CGATGAAGACGGCGGTGTAT 60.249 55.000 13.24 0.00 0.00 2.29
1543 1588 4.028490 CAAGCGGTGGGTAGGGCA 62.028 66.667 0.00 0.00 0.00 5.36
1544 1589 2.662070 TACAAGCGGTGGGTAGGGC 61.662 63.158 0.00 0.00 0.00 5.19
1562 1607 2.864471 GCAGGCAAGGCAGCAAAGT 61.864 57.895 6.15 0.00 35.83 2.66
1585 1630 4.881850 AGAAACCACACCAGTCAAACTTAG 59.118 41.667 0.00 0.00 0.00 2.18
1598 1643 0.595825 GCTGCAGCAAGAAACCACAC 60.596 55.000 33.36 0.00 41.59 3.82
1661 1710 4.024556 GCCATACTGACATACACAATCAGC 60.025 45.833 0.47 0.00 43.04 4.26
1877 1954 2.744202 AGATGAGATCAACAACGCCAAC 59.256 45.455 0.00 0.00 0.00 3.77
2044 2121 3.781307 AGAAGCGCCCCGTATGCA 61.781 61.111 2.29 0.00 0.00 3.96
2127 2204 3.334583 AACAGACGTGATGTTAGGCAT 57.665 42.857 12.73 0.00 39.06 4.40
2140 2217 1.266989 GAAAGAAGGGCCAAACAGACG 59.733 52.381 6.18 0.00 0.00 4.18
2203 2280 4.033709 AGCAACTGTATGACACCTAGGAT 58.966 43.478 17.98 2.27 0.00 3.24
2356 2433 6.340962 TCAGGAAACTCAACGAGAAATAGA 57.659 37.500 0.00 0.00 40.21 1.98
2419 2497 5.301551 ACACCAAAGTTTGCACAGATCATTA 59.698 36.000 10.25 0.00 0.00 1.90
2424 2502 3.290710 AGACACCAAAGTTTGCACAGAT 58.709 40.909 10.25 0.00 0.00 2.90
2426 2504 2.539547 CGAGACACCAAAGTTTGCACAG 60.540 50.000 10.25 0.00 0.00 3.66
2529 2613 9.392506 TCAGATAAAGGGAACAGATATTATGGA 57.607 33.333 0.00 0.00 0.00 3.41
2584 2668 3.650139 ACAAGTCTTGCTTACCTGTACG 58.350 45.455 12.66 0.00 35.27 3.67
2703 2788 0.031857 TGTTGCAAGGCACCATTTCG 59.968 50.000 0.00 0.00 38.71 3.46
2820 2906 3.888930 ACCATTGACCACCAAGTAACTTG 59.111 43.478 0.00 0.00 40.75 3.16
2821 2907 3.888930 CACCATTGACCACCAAGTAACTT 59.111 43.478 0.00 0.00 38.31 2.66
2822 2908 3.486383 CACCATTGACCACCAAGTAACT 58.514 45.455 0.00 0.00 38.31 2.24
2823 2909 2.556622 CCACCATTGACCACCAAGTAAC 59.443 50.000 0.00 0.00 38.31 2.50
2824 2910 2.175931 ACCACCATTGACCACCAAGTAA 59.824 45.455 0.00 0.00 38.31 2.24
2825 2911 1.777878 ACCACCATTGACCACCAAGTA 59.222 47.619 0.00 0.00 38.31 2.24
2826 2912 0.555769 ACCACCATTGACCACCAAGT 59.444 50.000 0.00 0.00 38.31 3.16
2827 2913 0.961019 CACCACCATTGACCACCAAG 59.039 55.000 0.00 0.00 38.31 3.61
2886 2987 3.085443 TCAATTTTCCGCGCAAAAGAA 57.915 38.095 14.02 2.27 0.00 2.52
2887 2988 2.783828 TCAATTTTCCGCGCAAAAGA 57.216 40.000 14.02 3.69 0.00 2.52
2888 2989 2.730928 ACATCAATTTTCCGCGCAAAAG 59.269 40.909 14.02 1.18 0.00 2.27
2889 2990 2.748605 ACATCAATTTTCCGCGCAAAA 58.251 38.095 10.83 10.83 0.00 2.44
2935 3036 7.246171 TCTGTCTGTAGCCTTCTAGAAAAAT 57.754 36.000 6.63 0.00 0.00 1.82
3098 3199 2.104792 CAGAGAACCTCAACCCTGAACA 59.895 50.000 0.00 0.00 32.06 3.18
3099 3200 2.772287 CAGAGAACCTCAACCCTGAAC 58.228 52.381 0.00 0.00 32.06 3.18
3100 3201 1.072331 GCAGAGAACCTCAACCCTGAA 59.928 52.381 0.00 0.00 32.06 3.02
3192 3297 3.443681 ACAAATAATGGCTCACCGGAAAG 59.556 43.478 9.46 5.89 39.70 2.62
3215 3320 4.816392 TCGCCGTACATAGCATCAAATAT 58.184 39.130 0.00 0.00 0.00 1.28
3254 3359 3.693807 ACATCCATCAAGTCTGCACATT 58.306 40.909 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.